[python-xrayutilities] 01/03: Imported Upstream version 1.2.0
Eugen Wintersberger
eugenwintersberger-guest at moszumanska.debian.org
Sun Aug 16 14:55:12 UTC 2015
This is an automated email from the git hooks/post-receive script.
eugenwintersberger-guest pushed a commit to branch master
in repository python-xrayutilities.
commit a6a78543327c683bda62802445a37132d18af730
Author: Eugen Wintersberger <eugen.wintersberger at gmail.com>
Date: Sun Aug 16 16:38:42 2015 +0200
Imported Upstream version 1.2.0
---
CHANGES.txt | 12 +
PKG-INFO | 9 +-
README.txt | 5 +-
doc/source/conf.py | 5 +-
doc/source/examples.rst | 17 +-
doc/source/{examples.rst => examples.rst~} | 15 +-
doc/source/index.rst | 13 +-
doc/source/index.rst~ | 248 -
doc/source/xrayutilities.io.rst | 8 -
doc/source/xrayutilities.materials.rst | 8 +
examples/xrayutilities_math_fitting.py | 5 +-
setup.py | 4 +-
xrayutilities.pdf | 12932 +++++++++----------
xrayutilities/analysis/sample_align.py | 291 +-
xrayutilities/gridder2d.py | 2 +-
xrayutilities/io/__init__.py | 6 -
xrayutilities/io/cbf.py | 171 +-
xrayutilities/io/desy_tty08.py | 26 +-
xrayutilities/io/edf.py | 79 +-
xrayutilities/io/fastscan.py | 15 +-
xrayutilities/io/helper.py | 16 +-
xrayutilities/io/imagereader.py | 63 +-
xrayutilities/io/panalytical_xml.py | 5 +-
xrayutilities/io/pdcif.py | 65 +-
xrayutilities/io/radicon.py | 298 -
xrayutilities/io/rotanode_alignment.py | 16 +-
xrayutilities/io/seifert.py | 129 +-
xrayutilities/io/spec.py | 167 +-
xrayutilities/io/spectra.py | 902 +-
xrayutilities/materials/__init__.py | 2 +-
xrayutilities/materials/_create_database.py | 45 +-
xrayutilities/materials/atom.py | 102 +
xrayutilities/materials/data/elements.db | Bin 5223396 -> 4514920 bytes
xrayutilities/materials/database.py | 481 +-
xrayutilities/materials/elements.py | 330 +-
xrayutilities/materials/lattice.py | 108 +-
xrayutilities/materials/material.py | 10 +-
xrayutilities/materials/predefined_materials.py | 4 +-
xrayutilities/math/__init__.py | 1 +
xrayutilities/math/fit.py | 88 +-
xrayutilities/normalize.py | 2 +-
xrayutilities/tests/test_HXRD.py | 15 +-
xrayutilities/tests/test_NonCOP.py | 15 +-
xrayutilities/tests/test_blockaverage.py | 3 +-
xrayutilities/tests/test_database.py | 52 +
xrayutilities/tests/test_functions.py | 17 +-
xrayutilities/tests/test_getang.py | 51 +
xrayutilities/tests/test_gridder1d.py | 21 +-
xrayutilities/tests/test_gridder2d.py | 25 +-
.../{test_gridder2d.py => test_gridder2dlist.py} | 51 +-
xrayutilities/tests/test_gridder3d.py | 29 +-
xrayutilities/tests/test_io_cbf.py | 79 +
xrayutilities/tests/test_io_edf.py | 79 +
xrayutilities/tests/test_io_esg.py | 59 +
xrayutilities/tests/test_io_fio.py | 91 +
xrayutilities/tests/test_io_nja.py | 64 +
xrayutilities/tests/test_io_nja_map.py | 58 +
xrayutilities/tests/test_io_nja_tsk.py | 60 +
xrayutilities/tests/test_io_pdcif.py | 61 +
xrayutilities/tests/test_io_perkinelmer.py | 54 +
xrayutilities/tests/test_io_roperccd.py | 54 +
xrayutilities/tests/test_io_spec.py | 84 +
xrayutilities/tests/test_io_specalignmentlog.py | 48 +
.../tests/{test_NonCOP.py => test_io_speclog.py} | 41 +-
xrayutilities/tests/test_io_tty.py | 65 +
xrayutilities/tests/test_io_xrdml.py | 63 +
xrayutilities/tests/test_maplog.py | 66 +
xrayutilities/tests/test_npygridder1d.py | 21 +-
.../tests/{test_NonCOP.py => test_q2angfit.py} | 35 +-
xrayutilities/tests/test_qconversion.py | 15 +-
xrayutilities/tests/test_qconversion_area.py | 25 +-
xrayutilities/tests/test_qconversion_linear.py | 21 +-
xrayutilities/tests/test_qconversion_trans.py | 36 +-
xrayutilities/tests/test_structure_factor.py | 53 +
xrayutilities/tests/test_transforms.py | 81 +
xrayutilities/utilities.py | 1 -
xrayutilities/utilities_noconf.py | 8 +-
77 files changed, 9033 insertions(+), 9273 deletions(-)
diff --git a/CHANGES.txt b/CHANGES.txt
index 3a75c72..8c2bf49 100644
--- a/CHANGES.txt
+++ b/CHANGES.txt
@@ -1,3 +1,15 @@
+v1.2.0, 2015-08-03
+
+* Radicon file support was removed (no test scripts available!)
+* replace pytables by faster and more convenient h5py
+* bug fixes/improvements in the file parsers (discovered by the unit tests!)
+* new unittests for file parsers (spec, edf, xrdml, esg, nja, fio, cbf, tif)
+* added different oxidation states of the chemical elements to the database
+* huge speed improvements for the database access, especially when querying
+ multiple values at the same time
+* add PseudoVoigtAsym option in xu.math.peakfit
+* memory usage optimization in FastScanCCD
+
v1.1.2, 2015-04-22
* new webpage theme to allow for easier reading (esp. mobile devices)
diff --git a/PKG-INFO b/PKG-INFO
index e2c4645..7b1e94f 100644
--- a/PKG-INFO
+++ b/PKG-INFO
@@ -1,6 +1,6 @@
Metadata-Version: 1.1
Name: xrayutilities
-Version: 1.1.2
+Version: 1.2.0
Summary: package for x-ray diffraction data evaluation
Home-page: http://xrayutilities.sourceforge.net
Author: Dominik Kriegner
@@ -27,7 +27,7 @@ Description:
--------
* examples: directory with example scripts and configurations
- * python: directory with the sources for the Python package
+ * xrayutilities: directory with the sources for the Python package
* setup.py: distutils install script used for the package installation
* xrayutilities.pdf: pdf-file with documentation of the package
@@ -55,8 +55,7 @@ Description:
- Python
- C-compiler (preferential with OpenMP support)
- - HDF5
- - pytables
+ - h5py
- scipy
- numpy
- matplotlib (optionally)
@@ -194,4 +193,4 @@ Classifier: License :: OSI Approved :: GNU General Public License v2 or later (G
Requires: numpy
Requires: scipy
Requires: matplotlib
-Requires: tables
+Requires: h5py
diff --git a/README.txt b/README.txt
index 10a1ba0..d143c13 100644
--- a/README.txt
+++ b/README.txt
@@ -19,7 +19,7 @@ Contents
--------
* examples: directory with example scripts and configurations
-* python: directory with the sources for the Python package
+* xrayutilities: directory with the sources for the Python package
* setup.py: distutils install script used for the package installation
* xrayutilities.pdf: pdf-file with documentation of the package
@@ -47,8 +47,7 @@ system
- Python
- C-compiler (preferential with OpenMP support)
-- HDF5
-- pytables
+- h5py
- scipy
- numpy
- matplotlib (optionally)
diff --git a/doc/source/conf.py b/doc/source/conf.py
index f71467c..8271825 100644
--- a/doc/source/conf.py
+++ b/doc/source/conf.py
@@ -35,7 +35,6 @@ extensions = [
'sphinx.ext.todo',
'sphinx.ext.coverage',
'sphinx.ext.pngmath',
- 'sphinx.ext.mathjax',
'sphinx.ext.viewcode',
'rst2pdf.pdfbuilder']
@@ -60,9 +59,9 @@ copyright = u'2015, Dominik Kriegner, Eugen Wintersberger'
# built documents.
#
# The short X.Y version.
-version = '1.1'
+version = '1.2'
# The full version, including alpha/beta/rc tags.
-release = '1.1.2'
+release = '1.2.0'
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
diff --git a/doc/source/examples.rst b/doc/source/examples.rst
index ac7d080..360bf4d 100644
--- a/doc/source/examples.rst
+++ b/doc/source/examples.rst
@@ -28,7 +28,6 @@ Both methods work incremental, so they do not start at the beginning of the file
An working example for both methods is given in the following.::
- import tables
import xrayutilities as xu
import os
@@ -76,26 +75,22 @@ Reading EDF files
EDF files are mostly used to store CCD frames at ESRF recorded from various different detectors. This format is therefore used in combination with SPEC files. In an example the EDFFile class is used to parse the data from EDF files and store them to an HDF5 file. HDF5 if perfectly suited because it can handle large amount of data and compression.::
- import tables
import xrayutilities as xu
import numpy
specfile = "specfile.spec"
h5file = "h5file.h5"
- h5 = tables.openFile(h5file, mode='a')
- s = xu.io.SPECFile(specfile, path=specdir)
- s.Save2HDF5(h5) # save to hdf5 file
+ s = xu.io.SPECFile(specfile)
+ s.Save2HDF5(h5file) # save to hdf5 file
# read ccd frames from EDF files
- for i in range(1, 1000, 1):
- efile = "edfdir/sample_%04d.edf" %i
- e = xu.io.edf.EDFFile(efile, path=specdir)
+ for i in range(1, 1001, 1):
+ efile = "edfdir/sample_%04d.edf" % i
+ e = xu.io.edf.EDFFile(efile)
e.ReadData()
- g5 = h5.createGroup(h5.root, "frelon_%04d" %i)
- e.Save2HDF5(h5, group=g5)
+ e.Save2HDF5(h5file, group="/frelon_%04d" % i)
- h5.close()
.. seealso::
the fully working example provided in the ``examples`` directory perfectly suited for reading data from beamline ID01
diff --git a/doc/source/examples.rst b/doc/source/examples.rst~
similarity index 98%
copy from doc/source/examples.rst
copy to doc/source/examples.rst~
index ac7d080..644749c 100644
--- a/doc/source/examples.rst
+++ b/doc/source/examples.rst~
@@ -28,7 +28,6 @@ Both methods work incremental, so they do not start at the beginning of the file
An working example for both methods is given in the following.::
- import tables
import xrayutilities as xu
import os
@@ -76,26 +75,22 @@ Reading EDF files
EDF files are mostly used to store CCD frames at ESRF recorded from various different detectors. This format is therefore used in combination with SPEC files. In an example the EDFFile class is used to parse the data from EDF files and store them to an HDF5 file. HDF5 if perfectly suited because it can handle large amount of data and compression.::
- import tables
import xrayutilities as xu
import numpy
specfile = "specfile.spec"
h5file = "h5file.h5"
- h5 = tables.openFile(h5file, mode='a')
- s = xu.io.SPECFile(specfile, path=specdir)
- s.Save2HDF5(h5) # save to hdf5 file
+ s = xu.io.SPECFile(specfile)
+ s.Save2HDF5(h5file) # save to hdf5 file
# read ccd frames from EDF files
for i in range(1, 1000, 1):
- efile = "edfdir/sample_%04d.edf" %i
- e = xu.io.edf.EDFFile(efile, path=specdir)
+ efile = "edfdir/sample_%04d.edf" % i
+ e = xu.io.edf.EDFFile(efile)
e.ReadData()
- g5 = h5.createGroup(h5.root, "frelon_%04d" %i)
- e.Save2HDF5(h5, group=g5)
+ e.Save2HDF5(h5file, group="/frelon_%04d" % i)
- h5.close()
.. seealso::
the fully working example provided in the ``examples`` directory perfectly suited for reading data from beamline ID01
diff --git a/doc/source/index.rst b/doc/source/index.rst
index 0b0d0f9..1ae1e25 100644
--- a/doc/source/index.rst
+++ b/doc/source/index.rst
@@ -131,7 +131,7 @@ large number of third party libraries and Python modules.
The needed dependencies are:
* **GCC** Gnu Compiler Collection or any compatible C compiler. On windows you most probably should use MinGW or CygWin. Others might work but are untested.
* **HDF5** a versatile binary data format (library is implemented in C).
- Although the library is not called directly, it is needed by the pytables Python
+ Although the library is not called directly, it is needed by the h5py Python
module (see below).
* **Python** the scripting language in which most of *xrayutilities* code is written in.
* **git** a version control system used to keep track on the *xrayutilities* development. (only needed for development)
@@ -139,7 +139,7 @@ The needed dependencies are:
Additionally, the following Python modules are needed in order to make *xrayutilities* work as intended:
* **Numpy** a Python module providing numerical array objects
* **Scipy** a Python module providing standard numerical routines, which is heavily using numpy arrays
- * **Python-Tables** a powerful Python interface to HDF5.
+ * **h5py** a powerful Python interface to HDF5.
* **Matplotlib** a Python module for high quality 1D and 2D plotting (optionally)
* **IPython** although not a dependency of *xrayutilities* the IPython shell is perfectly suited for the interactive use of the *xrayutilities* python package.
@@ -212,15 +212,6 @@ Using Python(x,y) you want to specify 'mingw32' as compiler name. With the WinPy
is recommended to use the MS Visual Studio Express 2008 (which is freely available for download)
and can also build the code for 64bit Windows. In this case us 'msvc' as compiler name.
-In case you want to do it the hard way install all of the following (versions in brackets indicate the tested set of versions by the author (2.3.2012)):
- * MinGW (0.4alpha)
- * Python (2.7.2)
- * numpy (1.6.1)
- * scipy (0.10.1)
- * numexpr (1.4.2) needed for pytables
- * pytables (2.3.1)
- * matplotlib (1.1.0)
-
It is suggested to add the MinGW binary directory, as well as the Python and Python-scripts directory
to the Path environment variable as described above! Installation is done as described above.
diff --git a/doc/source/index.rst~ b/doc/source/index.rst~
deleted file mode 100644
index b013516..0000000
--- a/doc/source/index.rst~
+++ /dev/null
@@ -1,248 +0,0 @@
-.. xrayutilities documentation master file, created by
- sphinx-quickstart on Sat Mar 2 11:39:01 2013.
- You can adapt this file completely to your liking, but it should at least
- contain the root `toctree` directive.
-
-Welcome to xrayutilities's documentation!
-=========================================
-
-If you look for downloading the package go to `Sourceforge <https://sourceforge.net/projects/xrayutilities>`_ (source distribution) or the `Python package index <https://pypi.python.org/pypi/xrayutilities>`_ (MS Windows binary).
-Installation instructions you find further down `Installation`_.
-
-Read more about *xrayutilities* below or in `Journal of Applied Crystallography 2013, Volume 46, 1162-1170 <http://dx.doi.org/10.1107/S0021889813017214>`_
-
-
-Introduction
-============
-
-*xrayutilities* is a collection of scripts used to analyze x-ray diffraction data. It consists of a python package and several routines coded in C.
-It especially useful for the reciprocal space conversion of diffraction data taken with linear and area detectors.
-
-In the following two concepts of usage for the *xrayutilities* package will be described.
-First one should get a brief idea of how to analyze x-ray diffraction data with *xrayutilities*.
-After that the concept of how angular coordinates of Bragg reflections are calculated is presented.
-
-Concept of usage
-----------------
-
-.. image:: pics/xu_usage.png
- :width: 400px
- :align: right
- :alt: Flow diagram showing how to analyze x-ray diffraction data using xrayutilities
-
-*xrayutilities* provides a set of functions to read experimental data from various data file formats.
-All of them are gathered in the :mod:`io`-subpackage.
-After reading data with a function from the io-submodule the data might be corrected for monitor counts and/or absorption factor of a beam attenuator.
-A special set of functions is provided to perform this for point, linear and area detectors.
-
-Since the amount of data taken with modern detectors often is too large to be able to work with them properly, a functions for reducing the data from linear and area detectors are provided.
-They use block-averaging to reduce the amount of data.
-Use those carefully not to loose the features you are interested in in your measurements.
-
-After the pre-treatment of the data, the core part of the package is the transformation of the angular data to reciprocal space.
-This is done as described in more detail below using the :mod:`experiment`-module`.
-The classes provided within the experiment module provide routines to help performing X-ray diffraction experiments.
-This includes methods to calculate the diffraction angles (described below) needed to align crystalline samples and to convert data between angular and reciprocal space.
-The conversion from angular to reciprocal space is implemented very general for various goniometer geometries.
-It is especially useful in combination with linear and area detectors as described in this `article <http://dx.doi.org/10.1107/S0021889813017214>`_.
-In standard cases, Users will only need the initialized routines, which predefine a certain goniometer geometry like the popular four-cirlce and six-circle geometries.
-
-After the conversion to reciprocal space, it is convenient to transform the data to a regular grid for visualization.
-For this purpose the :mod:`gridder`-module has been included into *xrayutilities*.
-For the visualization of the data in reciprocal space the usage of `matplotlib <http://matplotlib.org>`_ is recommended.
-
-A practical example showing the usage is given below.
-
-Angle calculation using the material classes
---------------------------------------------
-
-.. image:: pics/xu_usage_planning.png
- :width: 400px
- :align: right
- :alt: Flow diagram showing how to calculate angular positions of Bragg reflection using xrayutilities
-
-Calculation of angles needed to align Bragg reflections in various diffraction geometries is done using the Materials defined in the :mod:`materials`-package.
-This package provides a set of classes to describe crystal lattices and materials.
-Once such a material is properly defined one can calculate its properties, which includes the reciprocal lattice points, lattice plane distances, optical properties like
-the refractive index, the structure factor (including the atomic scattering factor) and the complex polarizability.
-These atomic properties are extracted from a database included in *xrayutilities*.
-
-Using such a material and an experimental class from the :mod:`experiment`-module, describing the experimental setup, the needed diffraction angles can be calculated for certain coplanar diffraction (high, low incidence), grazing incidence diffraction and also special non-coplanar diffraction geometries.
-In the predefined experimental classes fixed geometries are used. For angle calculation of custom geometries using arbitrary geometries (max. of three free angles) the :mod:`q2ang_fit`-module can be used as described in one of the included example files.
-
-.. _helloworld:
-
-hello world
------------
-
-A first example with step by step explanation is shown in the following.
-It showcases the use of *xrayutilities* to calculate angles and read a scan recorded with a linear detector from `spec <http://www.certif.com>`_-file and plots
-the result as reciprocal space map using matplotlib.
-
-.. literalinclude:: example_xu_read_spec_easy.py
- :linenos:
- :language: python
-
-
-More such examples can be found on the :ref:`examplespage` page.
-
-xrayutilities Python package
-============================
-
-.. automodule:: xrayutilities
- :members:
- :undoc-members:
- :show-inheritance:
-
-for more details see the full API documentation of :mod:`xrayutilities` found here: :ref:`expapi`.
-
-Installation
-============
-
-Express instructions
---------------------
-
- * install the dependencies (Windows: `pythonxy <http://www.pythonxy.com>`_; Linux/Unix: see below for dependencies).
- * download *xrayutilities* from `here <https://sourceforge.net/projects/xrayutilities>`_ or use git to check out the `latest <https://sourceforge.net/p/xrayutilities/code/>`_ version.
- * open a command line and navigate to the downloaded sources and execute:
-
-.. code-block:: bash
- > python setup.py install
-
-which will install *xrayutilities* to the default directory. It should be possible to use it (*import xrayutilities*) from now on in python scripts.
-
-.. note:: The python package of *xrayutilities* was formerly called ''xrutils''
-
-Detailed instructions
----------------------
-
-Installing *xrayutilities* is done using Python's distutils
-
-The package can be installed on Linux, Mac OS X and Microsoft Windows, however, it is mostly tested on Linux/Unix platforms.
-Please inform one of the authors in case the installation fails!
-
-Required third party software
------------------------------
-
-To keep the coding effort as small as possible *xrayutilities* depends on a
-large number of third party libraries and Python modules.
-
-The needed dependencies are:
- * **GCC** Gnu Compiler Collection or any compatible C compiler. On windows you most probably should use MinGW or CygWin. Others might work but are untested.
- * **HDF5** a versatile binary data format (library is implemented in C).
- Although the library is not called directly, it is needed by the pytables Python
- module (see below).
- * **Python** the scripting language in which most of *xrayutilities* code is written in.
- * **git** a version control system used to keep track on the *xrayutilities* development. (only needed for development)
-
-Additionally, the following Python modules are needed in order to make *xrayutilities* work as intended:
- * **Numpy** a Python module providing numerical array objects
- * **Scipy** a Python module providing standard numerical routines, which is heavily using numpy arrays
- * **Python-Tables** a powerful Python interface to HDF5.
- * **Matplotlib** a Python module for high quality 1D and 2D plotting (optionally)
- * **IPython** although not a dependency of *xrayutilities* the IPython shell is perfectly suited for the interactive use of the *xrayutilities* python package.
-
-After installing all required packages you can continue with installing and
-building the C library.
-
-Building and installing the library and python package
-------------------------------------------------------
-
-*xrayutilities* uses the distutils packaging system to build and install all of its components. You can perform the installation by executing
-
-.. code-block:: bash
- >python setup.py install
-
-or
-
-.. code-block:: bash
-
- >python setup.py install --prefix=INSTALLPATH
-
-in the root directory of the source distribution.
-
-The *--prefix* option sets the root directory for the installation. If it is omitted
-the libary is installed under /usr/lib/ on Unix systems or in the Python installation directory on Windows.
-
-Setup of the Python package
----------------------------
-
-You need to make your Python installation aware of where to look for the module.
-This is usually only needed when installing in non-standard *<install path>* locations.
-For this case append the installation directory to your *PYTHONPATH* environment variable by
-
-.. code-block:: bash
-
- >export PYTHONPATH=$PYTHONPATH:<local install path>/lib64/python2.7/site-packages
-
-on a Unix/Linux terminal. Or, to make this configuration persistent append this line to
-your local *.bashrc* file in your home directory.
-On MS Windows you would like to create a environment variable in the
-system preferences under system in the advanced tab (Using Python(x,y) this is done automatically).
-Be sure to use the correct directory which might be similar to
-
-.. code-block:: bash
-
- <local install path>/Lib/site-packages
-
-on Windows systems.
-
-Notes for installing on Windows
--------------------------------
-
-Since there is no packages manager on Windows the packages need to be installed manual
-(including all the dependecies) or a pre-packed solution needs two be used. We strongly suggest to
-use the `Python(x,y) <https://code.google.com/p/pythonxy/>`_ or
-`WinPython <https://winpython.github.io/>`_ Python distributions,
-which include already all of the needed dependencies for installing *xrayutilities*.
-
-The setup of the environment variables is also done by the Python distributions.
-One can proceed with the installation of *xrayutilities* directly!
-The easiest way to do this on windows is to use the binaries distributed on the `Python package index <https://pypi.python.org/pypi/xrayutilities>`_, otherwise one can follow the general installation instructions.
-Depending on your compiler on Microsoft Windows it might be necessary to perform the building of the Python extension separately and specify the compiler manually.
-This is done by
-
-.. code-block:: bash
-
- python setup.py build -c <compiler_name>
-
-Using Python(x,y) you want to specify 'mingw32' as compiler name. With the WinPython it
-is recommended to use the MS Visual Studio Express 2008 (which is freely available for download)
-and can also build the code for 64bit Windows. In this case us 'msvc' as compiler name.
-
-In case you want to do it the hard way install all of the following (versions in brackets indicate the tested set of versions by the author (2.3.2012)):
- * MinGW (0.4alpha)
- * Python (2.7.2)
- * numpy (1.6.1)
- * scipy (0.10.1)
- * numexpr (1.4.2) needed for pytables
- * pytables (2.3.1)
- * matplotlib (1.1.0)
-
-It is suggested to add the MinGW binary directory, as well as the Python and Python-scripts directory
-to the Path environment variable as described above! Installation is done as described above.
-
-.. _expapi:
-
-Examples and API-documentation
-==============================
-
-.. toctree::
- :maxdepth: 2
-
- examples
- xrayutilities
- xrayutilities.analysis
- xrayutilities.io
- xrayutilities.materials
- xrayutilities.math
- modules
-
-
-Indices and tables
-==================
-
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
-
diff --git a/doc/source/xrayutilities.io.rst b/doc/source/xrayutilities.io.rst
index d893f4a..f8d0c66 100644
--- a/doc/source/xrayutilities.io.rst
+++ b/doc/source/xrayutilities.io.rst
@@ -68,14 +68,6 @@ xrayutilities.io.pdcif module
:undoc-members:
:show-inheritance:
-xrayutilities.io.radicon module
--------------------------------
-
-.. automodule:: xrayutilities.io.radicon
- :members:
- :undoc-members:
- :show-inheritance:
-
xrayutilities.io.rotanode_alignment module
------------------------------------------
diff --git a/doc/source/xrayutilities.materials.rst b/doc/source/xrayutilities.materials.rst
index b18f20b..3578d2a 100644
--- a/doc/source/xrayutilities.materials.rst
+++ b/doc/source/xrayutilities.materials.rst
@@ -4,6 +4,14 @@ xrayutilities.materials package
Submodules
----------
+xrayutilities.materials.atom module
+-----------------------------------
+
+.. automodule:: xrayutilities.materials.atom
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
xrayutilities.materials.cif module
----------------------------------
diff --git a/examples/xrayutilities_math_fitting.py b/examples/xrayutilities_math_fitting.py
index cfe2562..1f17dd6 100644
--- a/examples/xrayutilities_math_fitting.py
+++ b/examples/xrayutilities_math_fitting.py
@@ -20,11 +20,12 @@ import numpy
xu.config.VERBOSITY = 3
x = numpy.linspace(10, 20, 250)
-y = xu.math.PseudoVoigt1d(x, 12, 0.2, 0.1, 10, numpy.random.rand()) + 0.01 * (numpy.random.rand(len(x))-0.5)
+y = (xu.math.PseudoVoigt1d(x, 12, 0.2, 0.1, 10, numpy.random.rand()) +
+ 0.01 * (numpy.random.rand(len(x))-0.5))
# peaktype can be 'PseudoVoigt', 'Lorentz' or 'Gauss'
# furthermore a constant background (optional also linear with the option
# background='linear') can be added
-xu.math.peak_fit(x,y, peaktype='PseudoVoigt', plot=True)
+xu.math.peak_fit(x, y, peaktype='PseudoVoigt', plot=True)
# for fitting multiple peaks simultansously see xu.math.multPeakFit
diff --git a/setup.py b/setup.py
index 831aa07..2dd2230 100644
--- a/setup.py
+++ b/setup.py
@@ -120,7 +120,7 @@ except ImportError:
setup(
name="xrayutilities",
- version="1.1.2",
+ version="1.2.0",
author="Eugen Wintersberger, Dominik Kriegner",
description="package for x-ray diffraction data evaluation",
classifiers=[
@@ -150,7 +150,7 @@ setup(
os.path.join("data", "*.cif")
]
},
- requires=['numpy', 'scipy', 'matplotlib', 'tables'],
+ requires=['numpy', 'scipy', 'matplotlib', 'h5py'],
include_dirs=[numpy.get_include()],
ext_modules=[extmodul],
cmdclass=cmdclass,
diff --git a/xrayutilities.pdf b/xrayutilities.pdf
index 035b0c9..90b6b16 100644
--- a/xrayutilities.pdf
+++ b/xrayutilities.pdf
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<<
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<<
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<<
/Filter [/ASCII85Decode /FlateDecode]
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/Filter [/ASCII85Decode /FlateDecode]
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/Filter [/ASCII85Decode /FlateDecode]
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<<
/Filter [/ASCII85Decode /FlateDecode]
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<<
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<<
/Filter [/ASCII85Decode /FlateDecode]
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<<
/Filter [/ASCII85Decode /FlateDecode]
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<<
/Filter [/ASCII85Decode /FlateDecode]
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>>
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<<
/Filter [/ASCII85Decode /FlateDecode]
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>>
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<<
/Filter [/ASCII85Decode /FlateDecode]
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<<
/Filter [/ASCII85Decode /FlateDecode]
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<<
/Filter [/ASCII85Decode /FlateDecode]
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<<
/Filter [/ASCII85Decode /FlateDecode]
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<<
/Filter [/ASCII85Decode /FlateDecode]
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/Filter [/ASCII85Decode /FlateDecode]
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/Filter [/ASCII85Decode /FlateDecode]
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endstream
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<<
/Filter [/ASCII85Decode /FlateDecode]
-/Length 1946
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>>
stream
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<<
/Filter [/ASCII85Decode /FlateDecode]
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>>
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<<
/Filter [/ASCII85Decode /FlateDecode]
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>>
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<<
/Filter [/ASCII85Decode /FlateDecode]
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>>
stream
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<<
/Filter [/ASCII85Decode /FlateDecode]
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>>
stream
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<<
/Filter [/ASCII85Decode /FlateDecode]
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>>
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<<
/Filter [/ASCII85Decode /FlateDecode]
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>>
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<<
/Filter [/ASCII85Decode /FlateDecode]
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>>
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<<
/Filter [/ASCII85Decode /FlateDecode]
-/Length 2349
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<<
/Filter [/ASCII85Decode /FlateDecode]
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>>
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<<
/Filter [/ASCII85Decode /FlateDecode]
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/Filter [/ASCII85Decode /FlateDecode]
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<<
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/Filter [/ASCII85Decode /FlateDecode]
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<<
/Filter [/ASCII85Decode /FlateDecode]
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/Filter [/ASCII85Decode /FlateDecode]
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/Filter [/ASCII85Decode /FlateDecode]
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endstream
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<<
/Filter [/ASCII85Decode /FlateDecode]
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>>
stream
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<<
/Filter [/ASCII85Decode /FlateDecode]
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>>
stream
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<<
/Filter [/ASCII85Decode /FlateDecode]
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>>
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<<
/Filter [/ASCII85Decode /FlateDecode]
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>>
stream
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<<
/Filter [/ASCII85Decode /FlateDecode]
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>>
stream
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<<
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<<
/Filter [/ASCII85Decode /FlateDecode]
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<<
/Filter [/ASCII85Decode /FlateDecode]
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>>
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<<
/Filter [/ASCII85Decode /FlateDecode]
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>>
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<<
/Filter [/ASCII85Decode /FlateDecode]
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>>
stream
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<<
/Filter [/ASCII85Decode /FlateDecode]
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>>
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<<
/Filter [/ASCII85Decode /FlateDecode]
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<<
/Filter [/ASCII85Decode /FlateDecode]
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<<
/Filter [/ASCII85Decode /FlateDecode]
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>>
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<<
/Filter [/ASCII85Decode /FlateDecode]
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/Filter [/ASCII85Decode /FlateDecode]
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/Filter [/ASCII85Decode /FlateDecode]
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stream
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endstream
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<<
/Filter [/ASCII85Decode /FlateDecode]
-/Length 2814
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>>
stream
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endstream
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<<
/Filter [/ASCII85Decode /FlateDecode]
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>>
stream
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endstream
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<<
/Filter [/ASCII85Decode /FlateDecode]
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>>
stream
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endstream
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<<
/Filter [/ASCII85Decode /FlateDecode]
-/Length 2401
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>>
stream
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<<
/Filter [/ASCII85Decode /FlateDecode]
-/Length 2792
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>>
stream
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<<
/Filter [/ASCII85Decode /FlateDecode]
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>>
stream
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<<
/Filter [/ASCII85Decode /FlateDecode]
-/Length 2572
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>>
stream
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<<
/Filter [/ASCII85Decode /FlateDecode]
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>>
stream
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<<
/Filter [/ASCII85Decode /FlateDecode]
-/Length 1985
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<<
/Filter [/ASCII85Decode /FlateDecode]
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>>
stream
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<<
/Filter [/ASCII85Decode /FlateDecode]
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>>
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<<
/Filter [/ASCII85Decode /FlateDecode]
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>>
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<<
/Filter [/ASCII85Decode /FlateDecode]
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>>
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<<
/Filter [/ASCII85Decode /FlateDecode]
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>>
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<<
/Filter [/ASCII85Decode /FlateDecode]
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>>
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<<
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<<
/Filter [/ASCII85Decode /FlateDecode]
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>>
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<<
/Filter [/ASCII85Decode /FlateDecode]
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<<
/Filter [/ASCII85Decode /FlateDecode]
-/Length 2191
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>>
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<<
/Filter [/ASCII85Decode /FlateDecode]
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<<
/Filter [/ASCII85Decode /FlateDecode]
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>>
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<<
/Filter [/ASCII85Decode /FlateDecode]
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>>
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<<
/Filter [/ASCII85Decode /FlateDecode]
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>>
stream
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<<
/Filter [/ASCII85Decode /FlateDecode]
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-/Filter [/ASCII85Decode /FlateDecode]
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<<
/Filter [/ASCII85Decode /FlateDecode]
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/Filter [/ASCII85Decode /FlateDecode]
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<<
/Filter [/ASCII85Decode /FlateDecode]
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>>
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<<
/Filter [/ASCII85Decode /FlateDecode]
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>>
stream
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<<
/Filter [/ASCII85Decode /FlateDecode]
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>>
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/Filter [/ASCII85Decode /FlateDecode]
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<<
/Filter [/ASCII85Decode /FlateDecode]
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>>
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<<
/Filter [/ASCII85Decode /FlateDecode]
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>>
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/Filter [/ASCII85Decode /FlateDecode]
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<<
/Filter [/ASCII85Decode /FlateDecode]
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>>
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<<
/Filter [/ASCII85Decode /FlateDecode]
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<<
/Filter [/ASCII85Decode /FlateDecode]
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<<
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<<
/Filter [/ASCII85Decode /FlateDecode]
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/Filter [/ASCII85Decode /FlateDecode]
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<<
/Filter [/ASCII85Decode /FlateDecode]
/Length 2320
>>
stream
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-<<
-/Filter [/ASCII85Decode /FlateDecode]
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<<
/Filter [/ASCII85Decode /FlateDecode]
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>>
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<<
/Filter [/ASCII85Decode /FlateDecode]
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>>
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<<
/Filter [/ASCII85Decode /FlateDecode]
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>>
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/Filter [/ASCII85Decode /FlateDecode]
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>>
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<<
/Filter [/ASCII85Decode /FlateDecode]
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>>
stream
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<<
/Filter [/ASCII85Decode /FlateDecode]
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>>
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/Filter [/ASCII85Decode /FlateDecode]
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stream
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<<
/Filter [/ASCII85Decode /FlateDecode]
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<<
/Filter [/ASCII85Decode /FlateDecode]
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>>
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<<
/Filter [/ASCII85Decode /FlateDecode]
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<<
/Filter [/ASCII85Decode /FlateDecode]
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<<
/Filter [/ASCII85Decode /FlateDecode]
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/Filter [/ASCII85Decode /FlateDecode]
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/Filter [/ASCII85Decode /FlateDecode]
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/Filter [/ASCII85Decode /FlateDecode]
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<<
/Filter [/ASCII85Decode /FlateDecode]
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<<
/Filter [/ASCII85Decode /FlateDecode]
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<<
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/Filter [/ASCII85Decode /FlateDecode]
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/Filter [/ASCII85Decode /FlateDecode]
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/Filter [/ASCII85Decode /FlateDecode]
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<<
/Filter [/ASCII85Decode /FlateDecode]
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>>
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<<
/Filter [/ASCII85Decode /FlateDecode]
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<<
/Filter [/ASCII85Decode /FlateDecode]
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<<
/Filter [/ASCII85Decode /FlateDecode]
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>>
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<<
/Filter [/ASCII85Decode /FlateDecode]
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/Filter [/ASCII85Decode /FlateDecode]
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<<
/Filter [/ASCII85Decode /FlateDecode]
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/Filter [/ASCII85Decode /FlateDecode]
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/Filter [/ASCII85Decode /FlateDecode]
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stream
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endstream
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<<
/Filter [/ASCII85Decode /FlateDecode]
-/Length 2684
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>>
stream
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<<
/Filter [/ASCII85Decode /FlateDecode]
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>>
stream
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<<
/Filter [/ASCII85Decode /FlateDecode]
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>>
stream
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<<
/Filter [/ASCII85Decode /FlateDecode]
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>>
stream
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<<
/Filter [/ASCII85Decode /FlateDecode]
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>>
stream
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<<
/Filter [/ASCII85Decode /FlateDecode]
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>>
stream
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<<
/Filter [/ASCII85Decode /FlateDecode]
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>>
stream
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<<
/Filter [/ASCII85Decode /FlateDecode]
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>>
stream
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<<
/Filter [/ASCII85Decode /FlateDecode]
-/Length 1979
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/Filter [/ASCII85Decode /FlateDecode]
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<<
/Filter [/ASCII85Decode /FlateDecode]
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/Filter [/ASCII85Decode /FlateDecode]
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/Filter [/ASCII85Decode /FlateDecode]
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/Filter [/ASCII85Decode /FlateDecode]
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/Filter [/ASCII85Decode /FlateDecode]
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/Filter [/ASCII85Decode /FlateDecode]
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/Filter [/ASCII85Decode /FlateDecode]
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/Filter [/ASCII85Decode /FlateDecode]
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/Filter [/ASCII85Decode /FlateDecode]
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diff --git a/xrayutilities/analysis/sample_align.py b/xrayutilities/analysis/sample_align.py
index 7d9e112..80b2cbd 100644
--- a/xrayutilities/analysis/sample_align.py
+++ b/xrayutilities/analysis/sample_align.py
@@ -13,7 +13,7 @@
# You should have received a copy of the GNU General Public License
# along with this program; if not, see <http://www.gnu.org/licenses/>.
#
-# Copyright (C) 2011,2013 Dominik Kriegner <dominik.kriegner at gmail.com>
+# Copyright (C) 2011-2015 Dominik Kriegner <dominik.kriegner at gmail.com>
"""
functions to help with experimental alignment during experiments, especially
@@ -21,12 +21,12 @@ for experiments with linear and area detectors
"""
import re
-import numpy
import numbers
+import time
+
+import numpy
import scipy
-import scipy.stats
import scipy.optimize as optimize
-import time
from scipy.odr import odrpack as odr
from scipy.odr import models
from scipy.ndimage.measurements import center_of_mass
@@ -38,13 +38,6 @@ from .line_cuts import fwhm_exp
from ..exception import InputError
from .. import cxrayutilities
-try:
- from matplotlib import pyplot as plt
-except ImportError:
- if config.VERBOSITY >= config.INFO_ALL:
- print("XU.analysis.sample_align: warning; plotting functionality "
- "not available")
-
# regular expression to check goniometer circle syntax
circleSyntax = re.compile("[xyz][+-]")
@@ -178,12 +171,14 @@ def psd_chdeg(angles, channels, stdev=None, usetilt=True, plot=True,
my_odr.set_job(fit_type=2)
fittilt = my_odr.run()
- try:
- plt.__name__
- except NameError:
- print("XU.analyis.psd_chdeg: Warning: plot functionality not "
- "available")
- plot = False
+ if plot:
+ try:
+ from matplotlib import pyplot as plt
+ except ImportError:
+ if config.VERBOSITY >= config.INFO_ALL:
+ print("XU.analysis.psd_chdeg: warning; plotting "
+ "functionality not available")
+ plot = False
if plot:
markersize = 6.0
@@ -430,17 +425,16 @@ def linear_detector_calib(angle, mca_spectra, **keyargs):
return detparam
+
######################################################
# detector parameter calculation from scan with
# area detector (determine maximum by center of mass)
######################################################
-
-
def area_detector_calib(angle1, angle2, ccdimages, detaxis, r_i, plot=True,
cut_off=0.7, start=(0, 0, 0, 0),
fix=(False, False, False, False),
- fig=None, wl=None, plotlog=False, debug=False,
- nwindow=50):
+ fig=None, wl=None, plotlog=False, nwindow=50,
+ debug=False):
"""
function to calibrate the detector parameters of an area detector
it determines the detector tilt possible rotations and offsets in the
@@ -484,10 +478,11 @@ def area_detector_calib(angle1, angle2, ccdimages, detaxis, r_i, plot=True,
if plot:
try:
- plt.__name__
- except NameError:
- print("XU.analyis.area_detector_calib: Warning: plot functionality"
- " not available")
+ from matplotlib import pyplot as plt
+ except ImportError:
+ if config.VERBOSITY >= config.INFO_ALL:
+ print("XU.analysis.area_detector_calib: warning; plotting "
+ "functionality not available")
plot = False
if wl is None:
@@ -517,26 +512,10 @@ def area_detector_calib(angle1, angle2, ccdimages, detaxis, r_i, plot=True,
if debug:
print("average intensity per image: %.1f" % avg)
- nw = nwindow // 2
for i in range(Npoints):
img = ccdimages[i]
if numpy.sum(img) > cut_off * avg:
- [cen1r, cen2r] = center_of_mass(img)
- [cen1, cen2] = center_of_mass(
- img[max(int(cen1r) - nw, 0):
- min(int(cen1r) + nw, img.shape[0]),
- max(int(cen2r) - nw, 0):
- min(int(cen2r) + nw, img.shape[1])])
- cen1 += max(int(cen1r) - nw, 0)
- cen2 += max(int(cen2r) - nw, 0)
- if debug:
- plt.figure("_ccd")
- plt.imshow(utilities.maplog(img), origin='low')
- plt.plot(cen2, cen1, "wo", mfc='none')
- plt.axis([cen2 - nw, cen2 + nw, cen1 - nw, cen1 + nw])
- plt.savefig("xu_calib_ccd_img%d.png" % i)
- plt.close("_ccd")
-
+ cen1, cen2 = _peak_position(img, nwindow, plot=debug and plot)
n1 = numpy.append(n1, cen1)
n2 = numpy.append(n2, cen2)
ang1 = numpy.append(ang1, angle1[i])
@@ -688,32 +667,57 @@ def area_detector_calib(angle1, angle2, ccdimages, detaxis, r_i, plot=True,
tilt, detrot, outerangle_offset), eps
+def _peak_position(img, nwindow, plot=False):
+ """
+ function to determine the peak position on the detector using the center of
+ mass (COM)
+
+ Parameters
+ ----------
+ img: detector image data as 2D array
+ nwindow: to avoid influence of hot pixels far away from the peak
+ position the center of mass approach is repeated with a window
+ around the COM of the full image.
+ COM of the size (nwindow, nwindow)
+ plot: (optional) the result of the of the determination can be saved
+ as a plot
+ """
+ nw = nwindow // 2
+ [cen1r, cen2r] = center_of_mass(img)
+ [cen1, cen2] = center_of_mass(
+ img[max(int(cen1r) - nw, 0):
+ min(int(cen1r) + nw, img.shape[0]),
+ max(int(cen2r) - nw, 0):
+ min(int(cen2r) + nw, img.shape[1])])
+ cen1 += max(int(cen1r) - nw, 0)
+ cen2 += max(int(cen2r) - nw, 0)
+ if plot:
+ try:
+ from matplotlib import pyplot as plt
+ except ImportError:
+ if config.VERBOSITY >= config.INFO_ALL:
+ print("XU.analysis._peak_position: warning; plotting "
+ "functionality not available")
+
+ plt.figure("_ccd")
+ plt.imshow(utilities.maplog(img), origin='low')
+ plt.plot(cen2, cen1, "wo", mfc='none')
+ plt.axis([cen2 - nw, cen2 + nw, cen1 - nw, cen1 + nw])
+ plt.savefig("xu_calib_ccd_img%d.png" % i)
+ plt.close("_ccd")
+ return cen1, cen2
+
+
def _determine_detdir(ang1, ang2, n1, n2, detaxis, r_i):
"""
determines detector pixel direction from correlation analysis of linear
fits to the observed pixel numbers of the primary beam.
"""
- debug = False
# center channel and detector pixel direction and pixel size
- (s1, i1, r1, dummy, dummy) = scipy.stats.linregress(ang1, n1)
- (s2, i2, r2, dummy, dummy) = scipy.stats.linregress(ang1, n2)
- (s3, i3, r3, dummy, dummy) = scipy.stats.linregress(ang2, n1)
- (s4, i4, r4, dummy, dummy) = scipy.stats.linregress(ang2, n2)
- if debug:
- print("%.2f %.2f %.2f %.2f" % (s1, s2, s3, s4))
- print("%.2f %.2f %.2f %.2f" % (r1, r2, r3, r4))
- if plot:
- plt.figure()
- plt.subplot(211)
- plt.plot(ang1, n1, 'bx', label='channel 1')
- plt.plot(ang1, n2, 'rx', label='channel 2')
- plt.legend()
- plt.xlabel('angle 1')
- plt.subplot(212)
- plt.plot(ang2, n1, 'bx', label='channel 1')
- plt.plot(ang2, n2, 'rx', label='channel 2')
- plt.legend()
- plt.xlabel('angle 2')
+ (s1, i1), r1 = math.linregress(ang1, n1)
+ (s2, i2), r2 = math.linregress(ang1, n2)
+ (s3, i3), r3 = math.linregress(ang2, n1)
+ (s4, i4), r4 = math.linregress(ang2, n2)
# determine detector directions
s = ord('x') + ord('y') + ord('z')
@@ -1071,10 +1075,10 @@ def _area_detector_calib_fit(ang1, ang2, n1, n2, detaxis, r_i, detdir1,
# guess initial parameters
# center channel and detector pixel direction and pixel size
- (s1, i1, r1, dummy, dummy) = scipy.stats.linregress(ang1 - start[3], n1)
- (s2, i2, r2, dummy, dummy) = scipy.stats.linregress(ang1 - start[3], n2)
- (s3, i3, r3, dummy, dummy) = scipy.stats.linregress(ang2, n1)
- (s4, i4, r4, dummy, dummy) = scipy.stats.linregress(ang2, n2)
+ (s1, i1), r1 = math.linregress(ang1 - start[3], n1)
+ (s2, i2), r2 = math.linregress(ang1 - start[3], n2)
+ (s3, i3), r3 = math.linregress(ang2, n1)
+ (s4, i4), r4 = math.linregress(ang2, n2)
if r1 ** 2 > r2 ** 2:
cch1 = i1
@@ -1142,24 +1146,6 @@ def _area_detector_calib_fit(ang1, ang2, n1, n2, detaxis, r_i, detdir1,
detaxis, wl)
final_error = numpy.mean(final_q)
- if False: # inactive code path
- if fig:
- plt.figure(fig.number)
- else:
- plt.figure("CCD Calib fit")
- plt.grid(True)
- plt.xlabel("Image number")
- plt.ylabel(r"|$\Delta$Q|")
- errp1, = plt.semilogy(afunc(my_odr.beta0, x, detdir1, detdir2, r_i,
- detaxis, wl),
- 'x-', label='initial param')
- errp2, = plt.semilogy(afunc(fit.beta, x, detdir1, detdir2, r_i,
- detaxis, wl),
- 'x-', label='param: %.1f %.1f %5.2g %5.2g %.1f '
- '%.2f %.3f %.3f'
- % (cch1, cch2, pwidth1, pwidth2, tiltazimuth,
- tilt, detrot, outerangle_offset))
-
if debug:
print("fitted parameters: (%d,%s) " % (fit.info, repr(fit.stopreason)))
print("primary beam / detector pixel directions / distance: "
@@ -1186,7 +1172,7 @@ def area_detector_calib_hkl(sampleang, angle1, angle2, ccdimages, hkls,
cut_off=0.1, start=(0, 0, 0, 0, 0, 0, 'config'),
fix=(False, False, False, False, False, False,
False),
- fig=None, plotlog=False, debug=False):
+ fig=None, plotlog=False, nwindow=50, debug=False):
"""
function to calibrate the detector parameters of an area detector
it determines the detector tilt possible rotations and offsets in the
@@ -1220,7 +1206,7 @@ def area_detector_calib_hkl(sampleang, angle1, angle2, ccdimages, hkls,
plot .... flag to determine if results and intermediate results should
be plotted. default: True
cut_off . cut off intensity to decide if image is used for the
- determination or not. default: 0.7 = 70%
+ determination or not. default: 0.1 = 10%
start ... sequence of start values of the fit for parameters,
which can not be estimated automatically. these are:
tiltazimuth, tilt, detector_rotation, outerangle_offset,
@@ -1232,16 +1218,20 @@ def area_detector_calib_hkl(sampleang, angle1, angle2, ccdimages, hkls,
default: None (creates own figure)
plotlog . flag to specify if the created error plot should be on
log-scale
+ nwindow . window size for determination of the center of mass position
+ after the center of mass of every full image is determined,
+ the center of mass is determined again using a window of
+ size nwindow in order to reduce the effect of hot pixels.
debug ... flag to tell if you want to see debug output of the script
(switch this to true only if you can handle it :))
"""
-
if plot:
try:
- plt.__name__
- except NameError:
- print("XU.analyis.area_detector_calib_hkl: Warning: plot "
- "functionality not available")
+ from matplotlib import pyplot as plt
+ except ImportError:
+ if config.VERBOSITY >= config.INFO_ALL:
+ print("XU.analyis.area_detector_calib_hkl: Warning: plot "
+ "functionality not available")
plot = False
if start[-1] == 'config':
@@ -1286,23 +1276,18 @@ def area_detector_calib_hkl(sampleang, angle1, angle2, ccdimages, hkls,
img = ccdimages[i]
if ((numpy.sum(img) > cut_off * avg) or
(numpy.all(hkls[i] != (0, 0, 0)))):
- [cen1, cen2] = center_of_mass(img)
- if debug:
- plt.figure("_ccd")
- plt.imshow(utilities.maplog(img), origin='low')
- plt.plot(cen2, cen1, "wo", mfc='none')
- plt.axis([cen2 - 25, cen2 + 25, cen1 - 25, cen1 + 25])
- plt.savefig("xu_calib_hkl_ccd_img%d.png" % i)
- plt.close("_ccd")
+ cen1, cen2 = _peak_position(img, nwindow, plot=debug and plot)
+
n1 = numpy.append(n1, cen1)
n2 = numpy.append(n2, cen2)
ang1 = numpy.append(ang1, angle1[i])
ang2 = numpy.append(ang2, angle2[i])
sang = numpy.append(sang, sampleang[i])
usedhkls.append(hkls[i])
- # if debug:
- # print("%8.3f %8.3f \t%.2f %.2f" % (angle1[i], angle2[i],
- # cen1, cen2))
+ if debug:
+ print("%8.3f %8.3f \t%.2f %.2f" % (angle1[i], angle2[i],
+ cen1, cen2))
+
Nused = len(ang1)
usedhkls = numpy.array(usedhkls)
@@ -1397,7 +1382,11 @@ def area_detector_calib_hkl(sampleang, angle1, angle2, ccdimages, hkls,
if fig:
plt.figure(fig.number)
else:
- plt.figure("CCD Calib fit")
+ figlabel = "CCD Calib fit %d"
+ i = 1
+ while figlabel % i in plt.get_figlabels():
+ i += 1
+ plt.figure(figlabel % i)
nparams = numpy.array(paramlist)
neps = numpy.array(epslist)
labels = (
@@ -1464,7 +1453,7 @@ def area_detector_calib_hkl(sampleang, angle1, angle2, ccdimages, hkls,
"OUTER DETECTOR ANGLE!" % (outerangle_offset))
return (cch1, cch2, pwidth1, pwidth2, tiltazimuth,
- tilt, detrot, outerangle_offset), eps
+ tilt, detrot, outerangle_offset, stilt, stazimuth, wavelength), eps
def _area_detector_calib_fit2(sang, ang1, ang2, n1, n2, hkls, experiment,
@@ -1769,19 +1758,6 @@ def _area_detector_calib_fit2(sang, ang1, ang2, n1, n2, hkls, experiment,
sang, angle1, angle2, n1, n2, delta=[0, param[7], 0.],
distance=1., UB=ubmat, wl=wl)
-# f= plt.figure("afunc")
-# plt.ion()
-# f.clear()
-# plt.plot(qx-h,'k-',label='x')
-# plt.plot(qy-k,'r-',label='y')
-# plt.plot(qz-l,'g-',label='z')
-# print("param: (cch1, cch2, pwidth1, pwidth2, tiltazimuth, tilt, "
-# "detrot, outerangle_offset)")
-# print(param)
-# plt.legend()
-# plt.draw()
-# plt.waitforbuttonpress()
-
return (qx - h) ** 2 + (qy - k) ** 2 + (qz - l) ** 2
Npoints = len(ang1)
@@ -1811,10 +1787,10 @@ def _area_detector_calib_fit2(sang, ang1, ang2, n1, n2, hkls, experiment,
sangs = numpy.append(sangs, sang[i])
# center channel and detector pixel direction and pixel size
- (s1, i1, r1, dummy, dummy) = scipy.stats.linregress(ang10 - start[3], n10)
- (s2, i2, r2, dummy, dummy) = scipy.stats.linregress(ang10 - start[3], n20)
- (s3, i3, r3, dummy, dummy) = scipy.stats.linregress(ang20, n10)
- (s4, i4, r4, dummy, dummy) = scipy.stats.linregress(ang20, n20)
+ (s1, i1), r1 = math.linregress(ang10 - start[3], n10)
+ (s2, i2), r2 = math.linregress(ang10 - start[3], n20)
+ (s3, i3), r3 = math.linregress(ang20, n10)
+ (s4, i4), r4 = math.linregress(ang20, n20)
if r1 ** 2 > r2 ** 2:
cch1 = i1
@@ -1913,24 +1889,6 @@ def _area_detector_calib_fit2(sang, ang1, ang2, n1, n2, hkls, experiment,
x, detdir1, detdir2, r_i, detaxis)
final_error = numpy.mean(final_q)
- if False: # inactive code path
- f = plt.figure("CCD Calib fit")
- f.clear()
- plt.grid(True)
- plt.xlabel("Image number")
- plt.ylabel(r"|$\Delta$Q|")
- errp1, = plt.semilogy(afunc(my_odr.beta0, x, detdir1, detdir2, r_i,
- detaxis), 'x-', label='initial param')
- errp2, = plt.semilogy(afunc(fit.beta, x, detdir1, detdir2, r_i,
- detaxis),
- 'x-', label='param: %.1f %.1f %5.2g %5.2g %.1f '
- '%.2f %.3f %.3f %.3f %.2f %.4f'
- % (cch1, cch2, pwidth1, pwidth2,
- tiltazimuth, tilt, detrot,
- outerangle_offset, sampletilt,
- stazimuth, wavelength))
- plt.waitforbuttonpress()
-
if debug:
print("fitted parameters: (%d,%s) " % (fit.info, repr(fit.stopreason)))
print("primary beam / detector pixel directions / distance: %s / %s "
@@ -1975,17 +1933,17 @@ def psd_refl_align(primarybeam, angles, channels, plot=True):
-------
>>> psd_refl_align(500,[0,0.1,0.2,0.3],[550,600,640,700])
"""
+ if plot:
+ try:
+ from matplotlib import pyplot as plt
+ except ImportError:
+ if config.VERBOSITY >= config.INFO_ALL:
+ print("XU.analyis.psd_refl_align: Warning: plot "
+ "functionality not available")
+ plot = False
- (a_s, b_s, r, tt, stderr) = scipy.stats.linregress(channels, angles)
-
- zeropos = scipy.polyval(numpy.array([a_s, b_s]), primarybeam)
-
- try:
- plt.__name__
- except NameError:
- print("XU.analyis.psd_refl_align: Warning: plot functionality not "
- "available")
- plot = False
+ p, rsq = math.linregress(channels, angles)
+ zeropos = numpy.polyval(p, primarybeam)
if plot:
xmin = min(min(channels), primarybeam)
@@ -1996,7 +1954,7 @@ def psd_refl_align(primarybeam, angles, channels, plot=True):
plt.figure()
plt.plot(channels, angles, 'kx', ms=8., mew=2.)
plt.plot([xmin - (xmax - xmin) * 0.1, xmax + (xmax - xmin) * 0.1],
- scipy.polyval(numpy.array([a_s, b_s]),
+ numpy.polyval(p,
[xmin - (xmax - xmin) * 0.1,
xmax + (xmax - xmin) * 0.1]),
'g-',
@@ -2014,15 +1972,14 @@ def psd_refl_align(primarybeam, angles, channels, plot=True):
if config.VERBOSITY >= config.INFO_LOW:
print("XU.analysis.psd_refl_align: sample is parallel to beam at "
- "goniometer angle %8.4f (R=%6.4f)" % (zeropos, r))
+ "goniometer angle %8.4f (R^2=%6.4f)" % (zeropos, rsq))
return zeropos
+
#################################################
# miscut calculation from alignment in 2 and
# more azimuths
#################################################
-
-
def miscut_calc(phi, aomega, zeros=None, omega0=None, plot=True):
"""
function to calculate the miscut direction and miscut angle of a sample
@@ -2055,6 +2012,14 @@ def miscut_calc(phi, aomega, zeros=None, omega0=None, plot=True):
phi0: the azimuth in which the primary beam looks upstairs
miscut: amplitude of the sinusoidal variation == miscut angle
"""
+ if plot:
+ try:
+ from matplotlib import pyplot as plt
+ except ImportError:
+ if config.VERBOSITY >= config.INFO_ALL:
+ print("XU.analyis.miscut_calc: Warning: plot "
+ "functionality not available")
+ plot = False
if zeros is not None:
om = (numpy.array(aomega) - numpy.array(zeros))
@@ -2088,14 +2053,6 @@ def miscut_calc(phi, aomega, zeros=None, omega0=None, plot=True):
"%d" % success)
if plot:
- try:
- plt.__name__
- except NameError:
- print("XU.analyis.misfit_calc: Warning: plot functionality not "
- "available")
- plot = False
-
- if plot:
plt.figure()
plt.plot(a, om, 'kx', mew=2, ms=8)
linx = numpy.linspace(a.min() - 45, a.min() + 360 - 45, num=1000)
@@ -2117,12 +2074,11 @@ def miscut_calc(phi, aomega, zeros=None, omega0=None, plot=True):
return ret
+
#################################################
# correct substrate Bragg peak position in
# reciprocal space maps
#################################################
-
-
def fit_bragg_peak(om, tt, psd, omalign, ttalign, exphxrd, frange=(0.03, 0.03),
peaktype='Gauss', plot=True):
"""
@@ -2157,6 +2113,15 @@ def fit_bragg_peak(om, tt, psd, omalign, ttalign, exphxrd, frange=(0.03, 0.03),
omfit,ttfit,params,covariance: fitted angular values, and the fit
parameters (of the Gaussian/Lorentzian) as well as their errors
"""
+ if plot:
+ try:
+ from matplotlib import pyplot as plt
+ except ImportError:
+ if config.VERBOSITY >= config.INFO_ALL:
+ print("XU.analyis.fit_bragg_peak: Warning: plot "
+ "functionality not available")
+ plot = False
+
if peaktype == 'Gauss':
func = math.Gauss2d
elif peaktype == 'Lorentz':
diff --git a/xrayutilities/gridder2d.py b/xrayutilities/gridder2d.py
index 08626dd..d68276b 100644
--- a/xrayutilities/gridder2d.py
+++ b/xrayutilities/gridder2d.py
@@ -246,7 +246,7 @@ class Gridder2DList(Gridder2D):
# perform gridding this should be moved to native code if possible
def gindex(x, min, delt):
- return numpy.round((x - min) / delt)
+ return numpy.round((x - min) / delt).astype(numpy.int)
xdelta = delta(self.xmin, self.xmax, self.nx)
ydelta = delta(self.ymin, self.ymax, self.ny)
diff --git a/xrayutilities/io/__init__.py b/xrayutilities/io/__init__.py
index 91055cc..fd6fb40 100644
--- a/xrayutilities/io/__init__.py
+++ b/xrayutilities/io/__init__.py
@@ -19,10 +19,6 @@
from .helper import xu_open
from .helper import xu_h5open
-from .radicon import rad2hdf5
-from .radicon import hst2hdf5
-from .radicon import selecthst
-
from .seifert import SeifertScan
from .seifert import SeifertMultiScan
from .seifert import getSeifert_map
@@ -51,8 +47,6 @@ from .fastscan import FastScan
from .fastscan import FastScanCCD
from .fastscan import FastScanSeries
-from .spectra import Spectra
-
from .panalytical_xml import XRDMLFile
from .panalytical_xml import getxrdml_map
from .panalytical_xml import getxrdml_scan
diff --git a/xrayutilities/io/cbf.py b/xrayutilities/io/cbf.py
index 820c002..5af6795 100644
--- a/xrayutilities/io/cbf.py
+++ b/xrayutilities/io/cbf.py
@@ -13,22 +13,31 @@
# You should have received a copy of the GNU General Public License
# along with this program; if not, see <http://www.gnu.org/licenses/>.
#
-# Copyright (C) 2013 Dominik Kriegner <dominik.kriegner at gmail.com>
+# Copyright (C) 2013, 2015 Dominik Kriegner <dominik.kriegner at gmail.com>
# module for handling files stored in the CBF data format
-import numpy
-import os
import os.path
-import gzip
import re
+import glob
+
+import numpy
+import h5py
+from .helper import xu_open, xu_h5open
from .. import cxrayutilities
from .. import config
cbf_name_start_num = re.compile(r"^\d")
+def makeNaturalName(name):
+ ret = name.replace(" ", "_")
+ ret = ret.replace("-", "_")
+ ret = ret.replace(".", "_")
+ return ret
+
+
class CBFFile(object):
def __init__(self, fname, nxkey="X-Binary-Size-Fastest-Dimension",
@@ -63,46 +72,26 @@ class CBFFile(object):
# create attributes for holding data
self.data = None
- self._open()
self.ReadData()
- self.fid.close()
-
- def _open(self):
- """
- open data file for reading
- """
- try:
- if os.path.splitext(self.full_filename)[-1] == '.gz':
- self.fid = gzip.open(self.full_filename, "rb")
- else:
- self.fid = open(self.full_filename, "rb")
- except:
- raise IOError("cannot open file %s" % (self.full_filename))
def ReadData(self):
"""
Read the CCD data into the .data object
this function is called by the initialization
"""
- wasclosed = False
- if self.fid.closed:
- wasclosed = True
- self._open()
-
- tmp = numpy.fromfile(file=self.fid, dtype="u1").tostring()
- tmp2 = tmp.decode('ascii', 'ignore')
- # read header information
- pos = tmp2.index(self.nxkey + ':') + len(self.nxkey + ':')
- self.xdim = int(tmp2[pos:pos + 6].strip())
- pos = tmp2.index(self.nykey + ':') + len(self.nykey + ':')
- self.ydim = int(tmp2[pos:pos + 6].strip())
-
- self.data = cxrayutilities.cbfread(tmp, self.xdim, self.ydim)
- self.data.shape = (self.ydim, self.xdim)
- if wasclosed:
- self.fid.close()
-
- def Save2HDF5(self, h5, group="/", comp=True):
+ with xu_open(self.full_filename, 'rb') as fid:
+ tmp = numpy.fromfile(file=fid, dtype="u1").tostring()
+ tmp2 = tmp.decode('ascii', 'ignore')
+ # read header information
+ pos = tmp2.index(self.nxkey + ':') + len(self.nxkey + ':')
+ self.xdim = int(tmp2[pos:pos + 6].strip())
+ pos = tmp2.index(self.nykey + ':') + len(self.nykey + ':')
+ self.ydim = int(tmp2[pos:pos + 6].strip())
+
+ self.data = cxrayutilities.cbfread(tmp, self.xdim, self.ydim)
+ self.data.shape = (self.ydim, self.xdim)
+
+ def Save2HDF5(self, h5f, group="/", comp=True):
"""
Saves the data stored in the EDF file in a HDF5 file as a HDF5 array.
By default the data is stored in the root group of the HDF5 file - this
@@ -111,54 +100,45 @@ class CBFFile(object):
Parameters
----------
- h5 ........ a HDF5 file object
+ h5f ....... a HDF5 file object or name
optional keyword arguments:
group ..... group where to store the data (default to the root of the
file)
comp ...... activate compression - true by default
"""
+ with xu_h5open(h5f, 'a') as h5:
+ if isinstance(group, str):
+ g = h5.get(group)
+ else:
+ g = group
+
+ # create the array name
+ name = os.path.split(self.filename)[-1]
+ name = os.path.splitext(name)[0]
+ # perform a second time for case of .cbf.gz files
+ name = os.path.splitext(name)[0]
+ name = makeNaturalName(name)
+ if cbf_name_start_num.match(name):
+ name = "ccd_" + name
+ if config.VERBOSITY >= config.INFO_ALL:
+ print("xu.io.CBFFile: HDF5 group name: %s" % name)
+
+ # create the array description
+ desc = "CBF CCD data from file %s " % (self.filename)
+
+ # create the dataset for the array
+ kwds = {'fletcher32': True}
+ if comp:
+ kwds['compression'] = 'gzip'
- if isinstance(group, str):
- g = h5.getNode(group)
- else:
- g = group
-
- # create the array name
- ca_name = os.path.split(self.filename)[-1]
- ca_name = os.path.splitext(ca_name)[0]
- # perform a second time for case of .cbf.gz files
- ca_name = os.path.splitext(ca_name)[0]
- ca_name = ca_name.replace("-", "_")
- if cbf_name_start_num.match(ca_name):
- ca_name = "ccd_" + ca_name
- if config.VERBOSITY >= config.INFO_ALL:
- print(ca_name)
- ca_name = ca_name.replace(" ", "_")
-
- # create the array description
- ca_desc = "CBF CCD data from file %s " % (self.filename)
-
- # create the Atom for the array
- a = tables.Atom.from_dtype(self.data.dtype)
- f = tables.Filters(complevel=7, complib="zlib", fletcher32=True)
- if comp:
- try:
- ca = h5.createCArray(g, ca_name, a, self.data.shape,
- ca_desc, filters=f)
- except:
- h5.removeNode(g, ca_name, recursive=True)
- ca = h5.createCArray(g, ca_name, a, self.data.shape,
- ca_desc, filters=f)
- else:
try:
- ca = h5.createCArray(g, ca_name, a, self.data.shape, ca_desc)
- except:
- h5.removeNode(g, ca_name, recursive=True)
- ca = h5.createCArray(g, ca_name, a, self.data.shape, ca_desc)
+ ca = g.create_dataset(name, data=self.data, **kwds)
+ except ValueError:
+ del g[name]
+ ca = g.create_dataset(name, data=self.data, **kwds)
- # write the data
- ca[...] = self.data[...]
+ ca.attrs['TITLE'] = desc
class CBFDirectory(object):
@@ -197,7 +177,7 @@ class CBFDirectory(object):
self.init_keyargs = keyargs
- def Save2HDF5(self, h5, group="", comp=True):
+ def Save2HDF5(self, h5f, group="", comp=True):
"""
Saves the data stored in the CBF files in the specified directory in a
HDF5 file as a HDF5 arrays in a subgroup. By default the data is
@@ -207,32 +187,25 @@ class CBFDirectory(object):
Parameters
----------
- h5 ........ a HDF5 file object
+ h5f ....... a HDF5 file object or name
optional keyword arguments:
group ..... group where to store the data (defaults to
pathname if group is empty string)
comp ...... activate compression - true by default
"""
+ with xu_h5open(h5f, 'a') as h5:
+ if isinstance(group, str):
+ if group == "":
+ group = os.path.split(self.datapath)[1]
+ g = h5.get(group)
+ if not g:
+ g = h5.create_group(group)
+ else:
+ g = group
- if isinstance(group, str):
- if group == "":
- group = os.path.split(self.datapath)[1]
- try:
- g = h5.getNode(h5.root, group)
- except:
- g = h5.createGroup(h5.root, group)
- else:
- g = group
-
- if "comp" in keyargs:
- compflag = keyargs["comp"]
- else:
- compflag = True
-
- for infile in self.files:
- # read EDFFile and save to hdf5
- filename = os.path.split(infile)[1]
- e = CBFFile(filename, path=self.datapath, **self.init_keyargs)
- # e.ReadData()
- e.Save2HDF5(h5, group=g)
+ for infile in self.files:
+ # read CBFFile and save to hdf5
+ filename = os.path.split(infile)[1]
+ e = CBFFile(filename, path=self.datapath, **self.init_keyargs)
+ e.Save2HDF5(h5, group=g, comp=comp)
diff --git a/xrayutilities/io/desy_tty08.py b/xrayutilities/io/desy_tty08.py
index 237e91a..fee4524 100644
--- a/xrayutilities/io/desy_tty08.py
+++ b/xrayutilities/io/desy_tty08.py
@@ -17,18 +17,19 @@
"""
-class for reading data+header information from tty08 data files
+class for reading data + header information from tty08 data files
-tty08 is system used at beamline P08 at Hasylab Hamburg and creates simple
+tty08 is a system used at beamline P08 at Hasylab Hamburg and creates simple
ASCII files to save the data. Information is easily read from the multicolumn
-data file. the functions below enable also to parse the information of the
+data file. the functions below enable also to parse the information of the
header
"""
import re
+import os.path
+
import numpy
-import os
-import matplotlib
+import numpy.lib.recfunctions
# relative imports from xrayutilities
from .helper import xu_open
@@ -78,7 +79,6 @@ class tty08File(object):
self.ReadMCA()
def ReadMCA(self):
-
mca = numpy.empty((len(raws), numpy.loadtxt(raws[0]).shape[0]),
dtype=numpy.float)
for i in range(len(raws)):
@@ -99,9 +99,9 @@ class tty08File(object):
dlist.append(data.tolist())
self.mca = mca
- self.data = matplotlib.mlab.rec_append_fields(
- self.data, 'MCA', self.mca,
- dtypes=[(numpy.double, self.mca.shape[1])])
+ mcatemp = mca.view([('MCA', (mca.dtype, mca.shape[1]))])
+ self.data = numpy.lib.recfunctions.merge_arrays([self.data, mcatemp],
+ flatten=True)
def Read(self):
"""
@@ -143,7 +143,7 @@ class tty08File(object):
self.data = numpy.rec.fromrecords(self.data, names=self.columns)
-def gettty08_scan(scanname, scannumbers, *args):
+def gettty08_scan(scanname, scannumbers, *args, **keyargs):
"""
function to obtain the angular cooridinates as well as intensity values
saved in TTY08 datafiles. Especially usefull for reciprocal space map
@@ -164,6 +164,8 @@ def gettty08_scan(scanname, scannumbers, *args):
omname: e.g. name of the omega motor (or its equivalent)
ttname: e.g. name of the two theta motor (or its equivalent)
+ **keyargs: keyword arguments are passed on to tty08File
+
Returns
-------
MAP
@@ -195,7 +197,7 @@ def gettty08_scan(scanname, scannumbers, *args):
MAP = numpy.zeros(0)
for nr in scanlist:
- scan = tty08File(scanname % nr)
+ scan = tty08File(scanname % nr, **keyargs)
sdata = scan.data
if MAP.dtype == numpy.float64:
MAP.dtype = sdata.dtype
@@ -218,5 +220,7 @@ def gettty08_scan(scanname, scannumbers, *args):
if len(args) == 0:
return MAP
+ elif len(args) == 1:
+ return retval[0], MAP
else:
return retval, MAP
diff --git a/xrayutilities/io/edf.py b/xrayutilities/io/edf.py
index b3d2429..a1d3791 100644
--- a/xrayutilities/io/edf.py
+++ b/xrayutilities/io/edf.py
@@ -20,16 +20,14 @@
# module for handling files stored in the EDF data format developed by the ESRF
-import numpy
import re
import struct
-import tables
-import os
import os.path
import glob
-import gzip
-from .helper import xu_open
+import numpy
+import h5py
+
from .helper import xu_open, xu_h5open
from .. import config
@@ -52,13 +50,19 @@ DataTypeDict = {"SignedByte": "b",
"UnsignedShort": "H",
"UnsignedInt": "I",
"UnsignedLong": "L"}
-
# SignedLong is only 4byte, on my 64bit machine using SignedLong:"l" caused
# troubles
# UnsignedLong is only 4byte, on my 64bit machine using UnsignedLong:"L"
# caused troubles ("I" works)
+def makeNaturalName(name):
+ ret = name.replace(" ", "_")
+ ret = ret.replace("-", "_")
+ ret = ret.replace(".", "_")
+ return ret
+
+
class EDFFile(object):
def __init__(self, fname, nxkey="Dim_1", nykey="Dim_2",
@@ -341,7 +345,12 @@ class EDFFile(object):
"""
with xu_h5open(h5f, 'a') as h5:
if isinstance(group, str):
- g = h5.getNode(group)
+ if group == '/':
+ g = h5
+ else:
+ if group in h5:
+ del h5[group]
+ g = h5.create_group(group)
else:
g = group
@@ -350,8 +359,7 @@ class EDFFile(object):
ca_name = os.path.splitext(ca_name)[0]
# perform a second time for case of .edf.gz files
ca_name = os.path.splitext(ca_name)[0]
- ca_name = ca_name.replace("-", "_")
- ca_name = ca_name.replace(" ", "_")
+ ca_name = makeNaturalName(ca_name)
if edf_name_start_num.match(ca_name):
ca_name = "ccd_" + ca_name
if config.VERBOSITY >= config.INFO_ALL:
@@ -359,9 +367,10 @@ class EDFFile(object):
# create the array description
ca_desc = "EDF CCD data from file %s " % (self.filename)
+ kwds = {'fletcher32': True}
+ if comp:
+ kwds['compression'] = 'gzip'
- # create the Atom for the array
- f = tables.Filters(complevel=7, complib="zlib", fletcher32=True)
if self.nimages != 1:
ca_name += '_{n:04d}'
@@ -369,31 +378,18 @@ class EDFFile(object):
for n in range(self.nimages):
if self.nimages != 1:
d = self.data[n]
- s = d.shape
- a = tables.Atom.from_dtype(d.dtype)
name = ca_name.format(n=n)
- if comp:
- try:
- ca = h5.createCArray(g, name, a, s, ca_desc,
- filters=f)
- except:
- h5.removeNode(g, name, recursive=True)
- ca = h5.createCArray(g, name, a, s, ca_desc,
- filters=f)
- else:
- try:
- ca = h5.createCArray(g, name, a, s, ca_desc)
- except:
- h5.removeNode(g, name, recursive=True)
- ca = h5.createCArray(g, name, a, s, ca_desc)
- # write the data
- ca[...] = d[...]
+ try:
+ ca = g.create_dataset(name, data=d, **kwds)
+ except ValueError:
+ del g[name]
+ ca = g.create_dataset(name, data=d, **kwds)
- # finally we have to append the attributes
- for k in self.header.keys():
- aname = k.replace(".", "_")
- aname = aname.replace(" ", "_")
- ca.attrs.__setattr__(aname, self.header[k])
+ ca.attrs['TITLE'] = ca_desc
+
+ # finally we have to append the attributes
+ for k in self.header.keys():
+ ca.attrs[makeNaturalName(k)] = self.header[k]
class EDFDirectory(object):
@@ -454,21 +450,14 @@ class EDFDirectory(object):
if isinstance(group, str):
if group == "":
group = os.path.split(self.datapath)[1]
- try:
- g = h5.getNode(h5.root, group)
- except:
- g = h5.createGroup(h5.root, group)
+ g = h5.get(group)
+ if not g:
+ g = h5.create_group(group)
else:
g = group
- if "comp" in keyargs:
- compflag = keyargs["comp"]
- else:
- compflag = True
-
for infile in self.files:
# read EDFFile and save to hdf5
filename = os.path.split(infile)[1]
e = EDFFile(filename, path=self.datapath, **self.init_keyargs)
- # e.ReadData()
- e.Save2HDF5(h5, group=g)
+ e.Save2HDF5(h5, group=g, comp=comp)
diff --git a/xrayutilities/io/fastscan.py b/xrayutilities/io/fastscan.py
index ffb73b7..1301e38 100644
--- a/xrayutilities/io/fastscan.py
+++ b/xrayutilities/io/fastscan.py
@@ -14,7 +14,7 @@
# along with this program; if not, see <http://www.gnu.org/licenses/>.
#
# Copyright (C) 2014 Raphael Grifone <raphael.grifone at esrf.fr>
-# Copyright (C) 2014 Dominik Kriegner <dominik.kriegner at gmail.com>
+# Copyright (C) 2014-2015 Dominik Kriegner <dominik.kriegner at gmail.com>
"""
modules to help with the analysis of FastScan data acquired at the ESRF.
@@ -37,10 +37,11 @@ see examples/xrayutilities_kmap_ESRF.py for an example script
"""
import os.path
-import numpy
import re
import glob
+import numpy
+
# relative imports
from . import SPECFile
from . import EDFFile
@@ -374,7 +375,7 @@ class FastScanCCD(FastScan):
print('XU.io.FastScanCCD: open file %s' % filename)
e = EDFFile(filename, keep_open=True)
ccdshape = blockAverage2D(e.ReadData(), nav[0], nav[1], roi=roi).shape
- self.ccddata = numpy.zeros((nx, ny, ccdshape[0], ccdshape[1]))
+ ccddata = numpy.zeros((nx, ny, ccdshape[0], ccdshape[1]))
nimage = e.nimages
# go through the gridded data and average the ccdframes
@@ -400,12 +401,12 @@ class FastScanCCD(FastScan):
ccdfilt = e.ReadData(imgindex)
ccdframe = blockAverage2D(ccdfilt, nav[0], nav[1],
roi=roi)
- self.ccddata[i, j, :, :] += ccdframe
+ ccddata[i, j, :, :] += ccdframe
framecount += 1
- self.ccddata[i, j, :, :] = self.ccddata[i, j, :, :] / \
- float(framecount)
+ ccddata[i, j, :, :] = ccddata[i, j, :, :] / \
+ float(framecount)
- return g2l.xmatrix, g2l.ymatrix, self.ccddata
+ return g2l.xmatrix, g2l.ymatrix, ccddata
class FastScanSeries(object):
diff --git a/xrayutilities/io/helper.py b/xrayutilities/io/helper.py
index 61c1cd3..262b4ae 100644
--- a/xrayutilities/io/helper.py
+++ b/xrayutilities/io/helper.py
@@ -23,11 +23,11 @@ these functions should be used in new parsers since they transparently allow to
open gzipped and bzipped files
"""
-import os
+import os.path
import gzip
import bz2
import sys
-import tables
+import h5py
from .. import config
from ..exception import InputError
@@ -80,21 +80,21 @@ def xu_open(filename, mode='rb'):
class xu_h5open(object):
"""
- helper object to decide if a HDF5 file has to opened/closed when
+ helper object to decide if a HDF5 file has to be opened/closed when
using with a 'with' statement.
"""
def __init__(self, f, mode='r'):
"""
Parameters
----------
- f: filename or tables.file.File instance
+ f: filename or h5py.File instance
mode: mode in which the file should be opened. ignored in case a
file handle is passed as f
"""
self.closeFile = True
self.fid = None
self.mode = mode
- if isinstance(f, tables.file.File):
+ if isinstance(f, h5py.File):
self.fid = f
self.closeFile = False
self.filename = f.filename
@@ -106,10 +106,10 @@ class xu_h5open(object):
def __enter__(self):
if self.fid:
- if not self.fid.isopen:
- self.fid = tables.openFile(self.filename, mode=self.mode)
+ if not self.fid.fid.valid:
+ self.fid = h5py.File(self.filename, self.mode)
else:
- self.fid = tables.openFile(self.filename, mode=self.mode)
+ self.fid = h5py.File(self.filename, self.mode)
return self.fid
def __exit__(self, type, value, traceback):
diff --git a/xrayutilities/io/imagereader.py b/xrayutilities/io/imagereader.py
index ab9d3c0..c0c16e1 100644
--- a/xrayutilities/io/imagereader.py
+++ b/xrayutilities/io/imagereader.py
@@ -17,7 +17,7 @@
import numpy
import time
-import os
+import os.path
import subprocess
# relative imports from xrayutilities
@@ -118,7 +118,7 @@ class ImageReader(object):
else:
self.darkc = False
- def readImage(self, filename):
+ def readImage(self, filename, path=None):
"""
read image file
and correct for dark- and flatfield in case the necessary data are
@@ -130,49 +130,34 @@ class ImageReader(object):
---------
filename: filename of the image to be read. so far only single
filenames are supported. The data might be compressed.
- supported extensions: .tiff, .bin and .bin.xz
+ supported extensions: .tif, .bin and .bin.xz
"""
+ if path:
+ full_filename = os.path.join(path, filename)
+ else:
+ full_filename = filename
if config.VERBOSITY >= config.INFO_ALL:
- print("XU.io.ImageReader.readImage: file %s" % (filename))
+ print("XU.io.ImageReader.readImage: file %s" % (full_filename))
t1 = time.time()
- if filename[-2:] == 'xz':
- if config.VERBOSITY >= config.INFO_ALL:
- print("XU.io.ImageReader.readImage: uncompressing file %s"
- % (filename))
-
- subprocess.call("xz --decompress --verbose --keep %s"
- % (filename), shell=True)
- fh = open(filename[:-3], 'rb')
- else:
- fh = xu_open(filename)
-
- # jump over header
- fh.seek(self.hdrlen)
- # read image
- if filename[-2:] == 'gz':
+ with xu_open(full_filename) as fh:
+ # jump over header
+ fh.seek(self.hdrlen)
+ # read image
img = numpy.fromstring(fh.read(), dtype=self.dtype,
count=self.nop1 * self.nop2)
- else:
- img = numpy.fromfile(fh, dtype=self.dtype,
- count=self.nop1 * self.nop2)
- if self.byteswap:
- img = img.byteswap()
- img.shape = (self.nop1, self.nop2) # reshape the data
- # darkfield correction
- if self.darkc:
- imgf = (img - self.darkfield).astype(numpy.float32)
- else:
- imgf = img.astype(numpy.float32)
- # kill negativ pixels
- # numpy.clip(imgf,1e-6,numpy.Inf,out=imgf)
- # flatfield correction
- if self.flatc:
- imgf = imgf / self.flatfield
- fh.close()
- if os.path.splitext(filename)[1] == '.xz':
- subprocess.call(["rm", "%s" % (filename[:-3])])
+ if self.byteswap:
+ img = img.byteswap()
+ img.shape = (self.nop1, self.nop2) # reshape the data
+ # darkfield correction
+ if self.darkc:
+ imgf = (img - self.darkfield).astype(numpy.float32)
+ else:
+ imgf = img.astype(numpy.float32)
+ # flatfield correction
+ if self.flatc:
+ imgf = imgf / self.flatfield
if config.VERBOSITY >= config.INFO_ALL:
t2 = time.time()
@@ -185,7 +170,7 @@ class ImageReader(object):
class PerkinElmer(ImageReader):
"""
- parse PerkinElmer CCD frames (*.bin) to numpy arrays
+ parse PerkinElmer CCD frames (*.tif) to numpy arrays
Ignore the header since it seems to contain no useful data
The routine was tested only for files with 2048x2048 pixel images
diff --git a/xrayutilities/io/panalytical_xml.py b/xrayutilities/io/panalytical_xml.py
index e52c3d6..53d7631 100644
--- a/xrayutilities/io/panalytical_xml.py
+++ b/xrayutilities/io/panalytical_xml.py
@@ -24,7 +24,7 @@ want to keep the number of dependancies as small as possible
from xml.etree import cElementTree as ElementTree
import numpy
-import os
+import os.path
import warnings
from .helper import xu_open
@@ -179,7 +179,8 @@ class XRDMLFile(object):
"""
self.filename = fname
- d = ElementTree.parse(xu_open(fname))
+ with xu_open(fname) as fid:
+ d = ElementTree.parse(fid)
root = d.getroot()
try:
namespace = root.tag[:root.tag.index('}')+1]
diff --git a/xrayutilities/io/pdcif.py b/xrayutilities/io/pdcif.py
index 8a044e1..5be9d44 100644
--- a/xrayutilities/io/pdcif.py
+++ b/xrayutilities/io/pdcif.py
@@ -15,12 +15,14 @@
#
# Copyright (C) 2014 Dominik Kriegner <dominik.kriegner at gmail.com>
-import numpy
import re
import copy
import shlex
+import numpy
+
from . import xu_open
+from .. import config
re_label = re.compile(r'^\s*_')
re_default = re.compile(r'^\s*_('
@@ -35,6 +37,12 @@ re_nop = re.compile(r'^\s*_(pd_meas_number_of_points|pd_meas_detector_id)')
re_multiline = re.compile(r';')
+def remove_comments(line, sep='#'):
+ for s in sep:
+ line = line.split(s)[0]
+ return line
+
+
class pdCIF(object):
"""
@@ -76,20 +84,22 @@ class pdCIF(object):
parser of the pdCIF file. the method reads the data from the file and
fills the data and header attributes with content
"""
-
with xu_open(self.filename) as fh:
self._parse_single(fh)
- def _parse_single(self, fh):
+ def _parse_single(self, fh, breakAfterData=False):
"""
internal routine to parse a single loop of the pdCIF file
Parameters
----------
fh: file handle
+ breakAfterData: (optional) allowing to stop the parsing after
+ data loop was found (default:False)
"""
loopStart = False
dataLoop = False
+ dataDone = False
loopheader = []
numOfEntries = -1
multiline = None
@@ -99,8 +109,15 @@ class pdCIF(object):
if not line:
break
+ line = remove_comments(line)
if re_loop.match(line):
loopStart = True
+ remainingline = re.sub('loop_', '', line).strip()
+ if re_label.match(remainingline):
+ if ((self.datacolumn is None and re_default.match(line)) or
+ line.strip() == self.datacolumn):
+ dataLoop = True
+ loopheader.append(remainingline)
continue
if multiline:
@@ -130,10 +147,8 @@ class pdCIF(object):
line2 = fh.readline().decode('ascii')
if re_multiline.match(line2):
multiline = line2
- else:
- fh.seek(fh.tell() - len(line2))
- raise ValueError('a value is missing for label %s'
- % label)
+ else: # single value must be in second line
+ self.header[label] = line2
elif re_label.match(line) and loopStart:
# read loop entries
@@ -144,23 +159,33 @@ class pdCIF(object):
elif loopStart:
fh.seek(fh.tell() - len(line))
- if numOfEntries != -1 and dataLoop:
+ if numOfEntries != -1 and dataLoop and not dataDone:
self.data = self._parse_loop_numpy(fh, loopheader,
numOfEntries)
- break
- elif dataLoop:
+ dataDone = True
+ if breakAfterData:
+ break
+ elif dataLoop and not dataDone:
self._parse_loop(fh, loopheader)
length = len(self.header[loopheader[0]])
- dtypes = [(entry, type(self.header[entry][0]))
+ dtypes = [(str(entry), type(self.header[entry][0]))
for entry in loopheader]
for i in range(len(dtypes)):
- if dtypes[i][1] == str:
- dtypes[i] = (dtypes[i][0], numpy.str_, 64)
+ if dtypes[i][1] is str:
+ dtypes[i] = (str(dtypes[i][0]), numpy.str_, 64)
self.data = numpy.zeros(length, dtype=dtypes)
for entry in loopheader:
self.data[entry] = self.header.pop(entry)
+ dataDone = True
+ if breakAfterData:
+ break
else:
- self._parse_loop(fh, loopheader)
+ try:
+ self._parse_loop(fh, loopheader)
+ except ValueError:
+ if config.VERBOSITY >= config.INFO_LOW:
+ print('XU.io.pdCIF: unable to handle loop at %d'
+ % fh.tell())
dataLoop = False
loopStart = False
loopheader = []
@@ -211,7 +236,7 @@ class pdCIF(object):
if re_label.match(line) or line.strip() == '':
fh.seek(fh.tell() - len(line))
break
- row = shlex.split(line)
+ row = shlex.split(line, comments=True)
for i in range(len(fields)):
try:
self.header[fields[i]].append(float(row[i]))
@@ -219,13 +244,16 @@ class pdCIF(object):
self.header[fields[i]].append(row[i])
except IndexError: # maybe multiline field
line2 = fh.readline().decode('ascii')
+ line2 = remove_comments(line2)
if re_multiline.match(line2):
multiline = line2
while True:
line = fh.readline().decode('ascii')
+ line = remove_comments(line)
if not line:
+ fh.seek(fh.tell() - len(line))
break
- if not re_multiline.match(line):
+ if re_multiline.match(line) and line.strip()[1:]:
multiline += line
else:
self.header[fields[i]].append(multiline)
@@ -261,10 +289,9 @@ class pdESG(pdCIF):
parser of the pdCIF file. the method reads the data from the file and
fills the data and header attributes with content
"""
-
with xu_open(self.filename) as fh:
# parse first header and loop
- self._parse_single(fh)
+ self._parse_single(fh, breakAfterData=True)
self.fileheader = copy.deepcopy(self.header)
self.header = {}
fdata = self.data
@@ -274,7 +301,7 @@ class pdESG(pdCIF):
while True: # try to parse all scans
tell = fh.tell()
try:
- self._parse_single(fh)
+ self._parse_single(fh, breakAfterData=True)
except:
break
if tell == fh.tell():
diff --git a/xrayutilities/io/radicon.py b/xrayutilities/io/radicon.py
deleted file mode 100644
index 822f2b9..0000000
--- a/xrayutilities/io/radicon.py
+++ /dev/null
@@ -1,298 +0,0 @@
-# This file is part of xrayutilities.
-#
-# xrayutilities is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation; either version 2 of the License, or
-# (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program; if not, see <http://www.gnu.org/licenses/>.
-#
-# Copyright (C) 2009 Eugen Wintersberger <eugen.wintersberger at desy.de>
-# Copyright (C) 2010 Dominik Kriegner <dominik.kriegner at gmail.com>
-
-"""
-python module for converting radicon data to
-HDF5
-"""
-
-import re
-import tables
-import struct
-import numpy
-import os.path
-
-from .. import config
-
-rdc_start = re.compile(r"^START")
-rdc_end = re.compile(r"^END")
-
-rdc_mopo = re.compile(r"^[A-Z]+=.*")
-rdc_param = re.compile(r"^.*:.+")
-
-rdc_colname = re.compile(r"^-+")
-rdc_data_line = re.compile(r"(\s*[0-9\.]\s*)+")
-
-rem_blank = re.compile(r"\s+") # remove all multiple blanks in a line
-# extract all columns seperated by single blanks
-blank_extract = re.compile(r"\S+")
-
-
-def rad2hdf5(h5, rdcfile, h5path="/", rdcpath="."):
- """
- Converts a RDC file to an HDF5 file.
-
- Required input arguments:
- h5 .................. HDF5 object where to store the data
- rdcfile ............. name of the RDC file
-
- optional input arguments:
- h5path .............. Path in the HDF5 file where to store the data
- (default to root)
- rdcpath ............. path where the RDC file is located (default
- is the current working directory)
- """
-
- rdcfilename = os.path.join(rdcpath, rdcfile)
-
- try:
- rdcfid = open(rdcfilename, mode="r")
- if config.VERBOSITY >= config.INFO_LOW:
- print("XU.io.rad2hdf5: successfully opened RDC file %s for reading"
- % rdcfilename)
- except:
- raise IOError("error opening RDC file %s !" % rdcfilename)
-
- line_buffer = " "
- while True:
-
- # read a line from the file
- line_buffer = rdcfid.readline().decode('ascii')
-
- if line_buffer == "":
- if config.VERBOSITY >= config.DEBUG:
- print("XU.io.rad2hdf5: reached end of RDC file")
- break
-
- line_buffer = line_buffer.strip()
-
- if rdc_start.match(line_buffer):
- # reaching the start of a new scan - reinit all variables
- motor_list = []
- # list with the names of the motors in the motor pos
- # table
- motor_pos_list = []
- # list of the initial motor positions
- param_name_list = []
- # parameter names
- param_value_list = []
- # parameter values
-
- col_name_list = []
- # list with column names
- tab_dict = {}
- # dictionary for the table
-
- if rdc_param.match(line_buffer):
- data_buffer = re.compile(r":\s+").split(line_buffer)
- data_buffer[0] = data_buffer[0].replace("/", "_")
- param_name_list.append(data_buffer[0])
- param_value_list.append(data_buffer[1])
- if data_buffer[0] == "Scan":
- param_name_list.append("scantype")
- line_buffer = rdcfid.readline().decode('ascii')
- line_buffer = line_buffer.strip()
- param_value_list.append(line_buffer)
-
- if rdc_mopo.match(line_buffer):
- data_buffer = re.compile(r"=\s+").split(line_buffer)
- motor_list.append(data_buffer[0])
- motor_pos_list.append(data_buffer[1])
-
- if rdc_colname.match(line_buffer):
- line_buffer = rdcfid.readline().decode('ascii')
- line_buffer = line_buffer.strip()
- col_name_list = re.compile(r"\s+").split(line_buffer)
- # perform an extra read cycle
- line_buffer = rdcfid.readline().decode('ascii')
-
- # after the column names have been read - build the table and
- # add the header attributes
- tab_name = param_value_list[0] + '_' + param_value_list[1]
- tab_title = ("Scan %s of type %s on sample %s"
- % (param_value_list[0],
- param_value_list[1],
- param_value_list[2]))
- # build the table dictionary
- for name in col_name_list:
- tab_dict[name] = tables.FloatCol()
-
- # create the new table object
- table = h5.createTable(h5path, tab_name, tab_dict, tab_title)
-
- # add the attributes (parameters and initial motor positions)
- for i in range(len(param_name_list)):
- param_name = param_name_list[i]
- param_value = param_value_list[i]
- param_name = param_name.replace(" ", "_")
- param_name = param_name.replace(".", "")
- param_name = param_name.replace("-", "_")
- param_name = param_name.replace("(", "")
- param_name = param_name.replace(")", "")
- table.attrs.__setattr__(param_name, param_value)
-
- for i in range(len(motor_list)):
- table.attrs.__setattr__(motor_list[i], motor_pos_list[i])
-
- # set finally the scan status to aborted (will be corrected if the
- # scan has finished properly
- table.attrs.scan_status = "ABORTED"
-
- if rdc_data_line.match(line_buffer):
- data_buffer = re.compile("\s+").split(line_buffer)
-
- # store the data in the table
- for i in range(len(data_buffer)):
- table.row[col_name_list[i]] = float(data_buffer[i])
-
- table.row.append()
-
- if rdc_end.match(line_buffer):
- table.attrs.scan_status = "SUCCEEDED"
- table.flush()
- if config.VERBOSITY >= config.INFO_ALL:
- print("XU.io.rad2hdf5: scan finished")
-
- # flush the last table (for sure)
- table.flush()
- rdcfid.close()
-
-
-def hst2hdf5(h5, hstfile, nofchannels, h5path="/", hstpath="."):
- """
- Converts a HST file to an HDF5 file.
-
- Required input arguments:
- h5 .................. HDF5 object where to store the data
- hstfile ............. name of the HST file
- nofchannels ......... number of channels
-
- optional input arguments:
- h5path .............. Path in the HDF5 file where to store the data
- hstpath ............. path where the HST file is located (default
- is the current working directory)
- """
-
- hstfilename = os.path.join(hstpath, hstfile)
-
- try:
- hstfid = open(hstfilename, mode="r")
- except:
- raise IOError("XU.io.hst2hdf5: error opening HST file %s !"
- % hstfilename)
-
- filters = tables.Filters(complevel=5, complib="zlib",
- shuffle=True, fletcher32=True)
-
- # jump the first header entry - it is nof of interest
- hstfid.seek(12, 0)
-
- nofhists = 0
-
- # some format strings used to read the file
- fmt_hist = 'ii128c128c8HiId' + nofchannels * "i"
- fmt_hist_size = struct.calcsize(fmt_hist)
-
- # read the top header and determine the number of histograms
- # and the size of the histograms
- data_buffer = struct.unpack("i", hstfid.read(struct.calcsize("i")))
- nofhists = data_buffer[0]
-
- if config.VERBOSITY >= config.INFO_ALL:
- print("XU.io.hst2hdf5: number of histograms found: %d" % nofhists)
-
- # now the table and the EArray
- table_dict = {}
- table_dict["index"] = tables.IntCol()
- table_dict["channels"] = tables.IntCol()
- table_dict["type"] = tables.IntCol()
- table_dict["name"] = tables.StringCol(itemsize=128)
- table_dict["ExpTime"] = tables.FloatCol()
- table = h5.createTable(h5path, "MCA_info", table_dict, "MCA info table")
-
- atype = tables.IntAtom()
- array = h5.createEArray(h5path, "MCAarray", atype, (0, nofchannels),
- "MCA data of file %s" % (hstfilename),
- filters=filters)
-
- # setup the buffer array for storing a single spectrum
- data = numpy.zeros((nofchannels), numpy.int)
-
- # loop over all histograms
- for i in range(nofhists):
- # read the header structure
- data_buffer = struct.unpack(fmt_hist, hstfid.read(fmt_hist_size))
- table.row["index"] = i
- table.row["type"] = data_buffer[1]
- table.row["name"] = (
- ("".join(data_buffer[2:(2 + 128)])).replace(" ", "")).strip()
- table.row["channels"] = data_buffer[0]
- table.row["ExpTime"] = data_buffer[268]
-
- table.row.append()
-
- # copy the data to the storage array
- for j in range(nofchannels):
- data[j] = data_buffer[269 + j]
-
- # append the array to the EArray
- array.append([data])
-
- table.flush()
-
- hstfid.close()
-
-
-def selecthst(et_limit, mca_info, mca_array):
- """
- Select historgrams form the complete set of recorded MCA data
- and stores it into a new numpy array. The selection is done due to a
- exposure time limit. Spectra below this limit are ignored.
-
- required input arguments:
- et_limit .............. exposure time limit
- mca_info .............. pytables table with the exposure data
- mca_array ............. array with all the MCA spectra
-
- return value:
- a numpy array with the selected mca spectra of shape (hstnr,channels).
- """
-
- # read the exposure time
- et = mca_info.cols.ExpTime[:]
- sel = numpy.zeros(et.shape, dtype=numpy.int)
-
- for i in range(et.shape[0]):
- if et[i] > et_limit:
- sel[i] = 1
-
- if config.VERBOSITY >= config.DEBUG:
- print("XU.io.selecthst: found %i valid arrays" % sel.sum())
-
- # load the data
- mca = mca_array.read()
-
- # create data array
- data = numpy.zeros((sel.sum(), mca.shape[1]), dtype=numpy.float)
- cnt = 0
- for i in range(sel.shape[0]):
- if sel[i]:
- data[cnt, :] = mca[i, :]
- cnt += 1
-
- return data
diff --git a/xrayutilities/io/rotanode_alignment.py b/xrayutilities/io/rotanode_alignment.py
index 927f45c..d6aeedd 100644
--- a/xrayutilities/io/rotanode_alignment.py
+++ b/xrayutilities/io/rotanode_alignment.py
@@ -25,13 +25,6 @@ import re
from .. import config
from .helper import xu_open
-try:
- from matplotlib import pylab as plt
-except ImportError:
- if config.VERBOSITY >= config.INFO_ALL:
- print("rotanode_alignment: warning; plotting functionality "
- "not available")
-
LOG_comment = re.compile(r"^#C")
LOG_peakname = re.compile(r"^#P")
LOG_motorname = re.compile(r"^#M")
@@ -209,11 +202,12 @@ class RA_Alignment(object):
----------
pname: peakname for which the alignment should be plotted
"""
-
try:
- plt.__version__
- except NameError:
- print("RA_Alignment.plot: error: plot functionality not available")
+ from matplotlib import pyplot as plt
+ except ImportError:
+ if config.VERBOSITY >= config.INFO_ALL:
+ print("XU.io.RA_Alignment: Warning: plot "
+ "functionality not available")
return
if pname not in self.peaks:
diff --git a/xrayutilities/io/seifert.py b/xrayutilities/io/seifert.py
index 8f1f0c5..1587b04 100644
--- a/xrayutilities/io/seifert.py
+++ b/xrayutilities/io/seifert.py
@@ -28,11 +28,11 @@ In the first case the data ist stored
"""
import re
-import tables
-import numpy
-import os
+import os.path
import itertools
+import numpy
+
from .helper import xu_open
from .. import config
@@ -78,7 +78,9 @@ def repair_key(key):
class SeifertHeader(object):
-
+ """
+ helper class to represent a Seifert (NJA) scan file header
+ """
def __init__(self):
pass
@@ -93,14 +95,11 @@ class SeifertHeader(object):
return ostr
- def save_h5_attribs(self, obj):
- for a in self.__dict__.keys():
- value = self.__getattribute__(a)
- obj._v_attrs.__setattr__(a, value)
-
class SeifertMultiScan(object):
-
+ """
+ Class to parse a Seifert (NJA) multiscan file
+ """
def __init__(self, filename, m_scan, m2, path=None):
"""
Parse data from a multiscan Seifert file.
@@ -155,7 +154,7 @@ class SeifertMultiScan(object):
lb = list(itertools.islice(self.fid, 1))
if not lb:
break
- lb = lb[0].strip()
+ lb = lb[0].decode('ascii').strip()
# the first thing needed is the number of scans in the file (in
# file header)
@@ -195,50 +194,11 @@ class SeifertMultiScan(object):
self.m2_pos.shape = (self.nscans, self.n_sm_pos)
self.sm_pos.shape = (self.nscans, self.n_sm_pos)
- def dump2hdf5(self, h5, iname="INT", group="/"):
- """
- Saves the content of a multi-scan file to a HDF5 file. By default the
- data is stored in the root group of the file. To save data somewhere
- else the keyword argument "group" must be used.
-
- required arguments:
- h5 .............. a HDF5 file object
-
- optional keyword arguments:
- iname ........... name for the intensity matrix
- group ........... path to the HDF5 group where to store the data
- """
-
- iname = args[0]
- smname = self.scan_motor_name
- m2name = self.sec_motor_name
-
- g = group
-
- a = tables.Float32Atom()
- f = tables.Filters(complevel=9, complib="zlib", fletcher32=True)
-
- c = h5.createCArray(g, iname, a, self.int.shape, filters=f)
- c[...] = self.int[...]
- h5.flush()
-
- c = h5.createCArray(g, smname, a, self.sm_pos.shape, filters=f)
- c[...] = self.sm_pos[...]
- h5.flush()
-
- c = h5.createCArray(g, m2name, a, self.m2_pos.shape, filters=f)
- c[...] = self.m2_pos[...]
- h5.flush()
-
- def dump2mlab(self, fname, *args):
- """
- Store the data in a matlab file.
- """
- pass
-
class SeifertScan(object):
-
+ """
+ Class to parse a single Seifert (NJA) scan file
+ """
def __init__(self, filename, path=None):
"""
Constructor for a SeifertScan object.
@@ -334,69 +294,6 @@ class SeifertScan(object):
for key in self.axispos:
self.axispos[key] = numpy.array(self.axispos[key])
- def dump2h5(self, h5, *args, **keyargs):
- """
- Save the data stored in the Seifert ASCII file to a HDF5 file.
-
- required input arguments:
- h5 ............. HDF5 file object
-
- optional arguments:
-
- names to use to store the motors. The first must be the name for the
- intensity array. The number of names must be equal to the second
- element of the shape of the data object.
-
- optional keyword arguments:
- group .......... HDF5 group object where to store the data.
- """
-
- # handle optional arguments:
- motor_names = []
- if len(args) != 0:
- for name in args:
- motor_names.append(name)
- else:
- for i in range(self.data.shape[1] - 1):
- motor_names.append("motor_%i" % i)
- motor_names.append("Int")
-
- # evaluate optional keyword arguments:
- if "group" in keyargs:
- g = keyargs["group"]
- else:
- g = h5.root
-
- a = tables.FloatAtom()
- s = [self.data.shape[0]]
- if config.VERBOSITY >= config.INFO_ALL:
- print("XU.io.SeifertScan.dump2h5: shape of data %d" % s)
-
- for i in range(self.data.shape[1]):
- title = "SEIFERT data from %s" % self.Filename
- c = h5.createCArray(g, motor_names[i], a, s, title)
- c[...] = self.data[:, i][...]
-
- # dump the header data
- self.hdr.save_h5_attribs(g)
-
- h5.flush()
-
- def dump2mlab(self, fname, *args):
- """
- Save the data from a Seifert scan to a matlab file.
-
- required input arugments:
- fname .................. name of the matlab file
-
- optional position arguments:
-
- names to use to store the motors. The first must be the name for the
- intensity array. The number of names must be equal to the second
- element of the shape of the data object.
- """
- pass
-
def getSeifert_map(filetemplate, scannrs=None, path=".", scantype="map",
Nchannels=1280):
diff --git a/xrayutilities/io/spec.py b/xrayutilities/io/spec.py
index ed26837..10cc9cc 100644
--- a/xrayutilities/io/spec.py
+++ b/xrayutilities/io/spec.py
@@ -28,25 +28,17 @@ a reread of the file starting from a stored offset (last known scan position)
"""
import re
-import numpy
-import os
+import os.path
import time
-import tables
-import gzip
import warnings
+import numpy
+
# relative imports from xrayutilities
from .helper import xu_open, xu_h5open
from .. import config
from ..exception import InputError
-try:
- from matplotlib import pylab
-except ImportError:
- if config.VERBOSITY >= config.INFO_ALL:
- print("XU.io.spec: warning; spec class plotting "
- "functionality not available")
-
# define some uesfull regular expressions
SPEC_time_format = re.compile(r"\d\d:\d\d:\d\d")
SPEC_multi_blank = re.compile(r"\s+")
@@ -81,7 +73,6 @@ def makeNaturalName(name):
class SPECScan(object):
-
"""
Represents a single SPEC scan. This class is usually not called by the
user directly but used via the SPECFile class.
@@ -391,12 +382,12 @@ class SPECScan(object):
existing one will be used
logy: if True a semilogy plot will be done
"""
-
try:
- pylab.__version__
- except NameError:
- print("XU.io.SPECScan.plot: ERROR: plot functionality not "
- "available")
+ from matplotlib import pyplot as plt
+ except ImportError:
+ if config.VERBOSITY >= config.INFO_ALL:
+ print("XU.io.SPECScan: Warning: plot "
+ "functionality not available")
return
if "newfig" in keyargs:
@@ -422,8 +413,8 @@ class SPECScan(object):
raise InputError("wrong number of yname/style arguments!")
if newfig:
- pylab.figure()
- pylab.subplots_adjust(left=0.08, right=0.95)
+ plt.figure()
+ plt.subplots_adjust(left=0.08, right=0.95)
for i in range(0, len(alist), 2):
yname = alist[i]
@@ -434,22 +425,21 @@ class SPECScan(object):
raise InputError("no column with name %s exists!" % yname)
continue
if logy:
- pylab.semilogy(xdata, ydata, ystyle)
+ plt.semilogy(xdata, ydata, ystyle)
else:
- pylab.plot(xdata, ydata, ystyle)
+ plt.plot(xdata, ydata, ystyle)
leglist.append(yname)
- pylab.xlabel("%s" % xname)
- pylab.legend(leglist)
- pylab.title("scan %i %s\n%s %s"
- % (self.nr, self.command, self.date, self.time))
+ plt.xlabel("%s" % xname)
+ plt.legend(leglist)
+ plt.title("scan %i %s\n%s %s"
+ % (self.nr, self.command, self.date, self.time))
# need to adjust axis limits properly
- lim = pylab.axis()
- pylab.axis([xdata.min(), xdata.max(), lim[2], lim[3]])
+ lim = plt.axis()
+ plt.axis([xdata.min(), xdata.max(), lim[2], lim[3]])
- def Save2HDF5(self, h5f, group="/", title="", desc="",
- optattrs={}, comp=True):
+ def Save2HDF5(self, h5f, group="/", title="", optattrs={}, comp=True):
"""
Save a SPEC scan to an HDF5 file. The method creates a group with the
name of the scan and stores the data there as a table object with name
@@ -467,8 +457,6 @@ class SPECScan(object):
data
title ...... a string with the title for the data, defaults to the
name of scan if empty
- desc ....... a string with the description of the data, defaults to
- the scan command if empty
optattrs ... a dictionary with optional attributes to store for the
data
comp ....... activate compression - true by default
@@ -484,7 +472,7 @@ class SPECScan(object):
# parse keyword arguments:
if isinstance(group, str):
- rootgroup = h5.getNode(group)
+ rootgroup = h5.get(group)
else:
rootgroup = group
@@ -494,76 +482,46 @@ class SPECScan(object):
group_title = self.name
group_title = group_title.replace(".", "_")
- if desc != "":
- group_desc = desc
- else:
- group_desc = self.command
-
- # create the dictionary describing the table
- tab_desc_dict = {}
- col_name_list = []
- for d in self.data.dtype.descr:
- cname = d[0].encode('ascii', 'ignore')
- col_name_list.append(cname)
- if len(d[1:]) == 1:
- ctype = numpy.dtype((d[1]))
- else:
- ctype = numpy.dtype((d[1], d[2]))
- tab_desc_dict[cname] = tables.Col.from_dtype(ctype)
-
- # create the table object and fill it
- f = tables.Filters(complevel=7, complib="zlib", fletcher32=True)
+ # create the dataset and fill it
copy_count = 0
while True:
try:
# if everything goes well the group will be created and the
# loop stopped
- g = h5.createGroup(rootgroup, group_title, group_desc)
+ g = rootgroup.create_group(group_title)
break
except:
# if the group already exists the name must be changed and
# another will be made to create the group.
if self.ischanged:
- g = h5.removeNode(rootgroup, group_title,
- recursive=True)
+ del rootgroup[group_title]
else:
group_title = group_title + "_%i" % (copy_count)
copy_count = copy_count + 1
- with warnings.catch_warnings():
- warnings.simplefilter('ignore', tables.NaturalNameWarning)
- if comp:
- tab = h5.createTable(g, "data", tab_desc_dict, "scan data",
- filters=f)
- else:
- tab = h5.createTable(g, "data", tab_desc_dict, "scan data")
-
- for rec in self.data:
- for cname in rec.dtype.names:
- tab.row[cname] = rec[cname]
- tab.row.append()
+ kwds = {'fletcher32': True}
+ if comp:
+ kwds['compression'] = 'gzip'
- # finally after the table has been written to the table - commit
- # the table to the file
- tab.flush()
+ dset = g.create_dataset("data", data=self.data, **kwds)
# write attribute data for the scan
- g._v_attrs.ScanNumber = numpy.uint(self.nr)
- g._v_attrs.Command = self.command
- g._v_attrs.Date = self.date
- g._v_attrs.Time = self.time
+ g.attrs['ScanNumber'] = numpy.uint(self.nr)
+ g.attrs['Command'] = self.command
+ g.attrs['Date'] = self.date
+ g.attrs['Time'] = self.time
# write the initial motor positions as attributes
for k in self.init_motor_pos.keys():
- g._v_attrs.__setattr__(k, numpy.float(self.init_motor_pos[k]))
+ g.attrs[k] = numpy.float(self.init_motor_pos[k])
# if scan contains MCA data write also MCA parameters
- g._v_attrs.mca_start_channel = numpy.uint(self.mca_start_channel)
- g._v_attrs.mca_stop_channel = numpy.uint(self.mca_stop_channel)
- g._v_attrs.mca_nof_channels = numpy.uint(self.mca_channels)
+ g.attrs['mca_start_channel'] = numpy.uint(self.mca_start_channel)
+ g.attrs['mca_stop_channel'] = numpy.uint(self.mca_stop_channel)
+ g.attrs['mca_nof_channels'] = numpy.uint(self.mca_channels)
for k in optattrs.keys():
- g._v_attrs.__setattr__(k, opattrs[k])
+ g.attrs[k] = optattrs[k]
h5.flush()
@@ -667,16 +625,15 @@ class SPECFile(object):
comp .................. activate compression - true by default
"""
with xu_h5open(h5f, 'a') as h5:
+ groupname = os.path.splitext(os.path.splitext(self.filename)[0])[0]
try:
- g = h5.createGroup("/", os.path.splitext(
- os.path.splitext(self.filename)[0])[0],
- "Data of SPEC - File %s" % (self.filename))
- except:
- g = h5.getNode("/" + os.path.splitext(
- os.path.splitext(self.filename)[0])[0])
+ g = h5.create_group(groupname)
+ except ValueError:
+ g = h5.get(groupname)
+ g.attrs['TITLE'] = "Data of SPEC - File %s" % (self.filename)
for s in self.scan_list:
- if (((not g.__contains__(s.name)) or s.ischanged) and
+ if (((s.name not in g) or s.ischanged) and
s.scan_status != "NODATA"):
s.ReadData()
if s.data is not None:
@@ -941,10 +898,18 @@ class SPECCmdLine(object):
class SPECLog(object):
-
+ """
+ class to parse a SPEC log file to find the command history
+ """
def __init__(self, filename, prompt, path=""):
"""
init routine for a class to read a SPEC log file
+
+ Parameters
+ ----------
+ filename: SPEC log file name
+ prompt: SPEC command prompt (e.g. 'PSIC' or 'SPEC')
+ path: (optional) directory where the SPEC log can be found
"""
self.filename = filename
self.full_filename = os.path.join(path, self.filename)
@@ -970,6 +935,12 @@ class SPECLog(object):
self.cmdl_list.append(SPECCmdLine(int(float(line)),
self.prompt, cmd))
+ def __getitem__(self, index):
+ """
+ function to return the n-th cmd in the spec-log.
+ """
+ return self.cmdl_list[index]
+
def __str__(self):
ostr = "%s with %d lines\n" % (self.filename, self.line_counter)
@@ -983,14 +954,14 @@ def geth5_scan(h5f, scans, *args, **kwargs):
"""
function to obtain the angular cooridinates as well as intensity values
saved in an HDF5 file, which was created from a spec file by the Save2HDF5
- method. Especially usefull for reciprocal space map measurements.
+ method. Especially useful for reciprocal space map measurements.
further more it is possible to obtain even more positions from
the data file if more than two string arguments with its names are given
Parameters
----------
- h5f: file object of a HDF5 file opened using pytables or its filename
+ h5f: file object of a HDF5 file opened using h5py or its filename
scans: number of the scans of the reciprocal space map (int,tuple or
list)
@@ -1022,9 +993,9 @@ def geth5_scan(h5f, scans, *args, **kwargs):
with xu_h5open(h5f) as h5:
if "samplename" in kwargs:
- h5g = h5.getNode(h5.root, kwargs["samplename"])
+ h5g = h5.get(kwargs["samplename"])
else:
- h5g = h5.listNodes(h5.root)[0]
+ h5g = h5.get(list(h5.keys())[0])
if numpy.iterable(scans):
scanlist = scans
@@ -1041,9 +1012,8 @@ def geth5_scan(h5f, scans, *args, **kwargs):
MAP = numpy.zeros(0)
for nr in scanlist:
- h5scan = h5.getNode(h5g, "scan_%d" % nr)
- command = h5.getNodeAttr(h5scan, 'Command')
- sdata = h5scan.data.read()
+ h5scan = h5g.get("scan_%d" % nr)
+ sdata = numpy.asarray(h5scan.get('data'))
if MAP.dtype == numpy.float64:
MAP.dtype = sdata.dtype
# append scan data to MAP, where all data are stored
@@ -1062,9 +1032,8 @@ def geth5_scan(h5f, scans, *args, **kwargs):
scanshape = len(sdata)
for i in notscanmotors:
motname = args[i]
- buf = numpy.ones(
- scanshape) * h5.getNodeAttr(h5scan,
- "INIT_MOPO_%s" % motname)
+ buf = numpy.ones(scanshape) * \
+ h5scan.attrs["INIT_MOPO_%s" % motname]
angles[motname] = numpy.concatenate((angles[motname], buf))
retval = []
@@ -1102,7 +1071,8 @@ def getspec_scan(specf, scans, *args):
Example
-------
- >>> [om, tt] = xu.io.getspec_scan(s, 36, 'omega', 'gamma', 'Counter2')
+ >>> [om, tt, cnt2] = xu.io.getspec_scan(s, 36, 'omega', 'gamma',
+ 'Counter2')
"""
if len(args) == 0:
return
@@ -1122,7 +1092,6 @@ def getspec_scan(specf, scans, *args):
for nr in scanlist:
sscan = specf.__getattr__("scan%d" % nr)
- command = sscan.command
sscan.ReadData()
sdata = sscan.data
# check type of scan
@@ -1141,7 +1110,7 @@ def getspec_scan(specf, scans, *args):
motname = args[i]
buf = (numpy.ones(scanshape) *
sscan.init_motor_pos["INIT_MOPO_%s" % motname])
- angles[motname] = numpy.concatenate((angles[motname], buf))
+ angles[motname] = numpy.concatenate((angles[motname], buf))
retval = []
for motname in args:
diff --git a/xrayutilities/io/spectra.py b/xrayutilities/io/spectra.py
index 795bd7a..875b118 100644
--- a/xrayutilities/io/spectra.py
+++ b/xrayutilities/io/spectra.py
@@ -14,28 +14,23 @@
# along with this program; if not, see <http://www.gnu.org/licenses/>.
#
# Copyright (C) 2009-2010 Eugen Wintersberger <eugen.wintersberger at desy.de>
-# Copyright (C) 2009-2012 Dominik Kriegner <dominik.kriegner at gmail.com>
+# Copyright (C) 2009-2015 Dominik Kriegner <dominik.kriegner at gmail.com>
"""
module to handle spectra data
"""
-import numpy
-import os
import re
-import tables
-import os.path
-from numpy import rec
+import os
import glob
-from .. import config
+import numpy
+import numpy.lib.recfunctions
+from numpy import rec
+import h5py
-try:
- import matplotlib
-except ImportError:
- if config.VERBOSITY >= config.INFO_ALL:
- print("XU.io.spectra: warning; spectra class plotting "
- "functionality not available")
+from .helper import xu_h5open
+from .. import config
re_wspaces = re.compile(r"\s+")
re_colname = re.compile(r"^Col")
@@ -54,12 +49,8 @@ re_col_index = re.compile(r"\d+\s+")
re_col_type = re.compile(r"\[.+\]")
re_num = re.compile(r"[0-9]")
-re_mca_int_tmp = re.compile(r"%.*i")
-
dtype_map = {"FLOAT": "f4"}
-_absorber_factors = None
-
class SPECTRAFileComments(dict):
@@ -239,7 +230,6 @@ class SPECTRAFile(object):
self.mca_stop_index = mcastop
else:
# try to determine the number of MCA spectra automatically
- # spat = re_mca_int_tmp.sub("*",self.mca_file_template)
spat = self.mca_file_template.replace("%i", "*")
l = glob.glob(spat)
self.mca_start_index = 1
@@ -250,8 +240,7 @@ class SPECTRAFile(object):
if self.mca_stop_index != 0:
self.ReadMCA()
- def Save2HDF5(self, h5file, name, group="/", description="SPECTRA scan",
- mcaname="MCA"):
+ def Save2HDF5(self, h5file, name, group="/", mcaname="MCA"):
"""
Saves the scan to an HDF5 file. The scan is saved to a
seperate group of name "name". h5file is either a string
@@ -265,101 +254,61 @@ class SPECTRAFile(object):
optional keyword arguments:
group ............... root group where to store the data
- description ......... string with a description of the scan
+ mcaname ............. Name of the MCA in the HDF5 file
Return value:
The method returns None in the case of everything went fine, True
otherwise.
"""
- if isinstance(h5file, str):
+ with xu_h5open(h5file, 'w') as h5:
+ # create the group where to store the data
try:
- h5 = tables.openFile(h5file, mode="a")
- except:
- print("XU.io.spectra.Save2HDF5: cannot open file %s for "
- "writing!" % h5file)
+ g = h5.create_group(group + '/' + name)
+ except ValueError:
+ print("XU.io.spectra.Save2HDF5: cannot create group %s for "
+ "writing data!" % name)
return True
- else:
- h5 = h5file
-
- # create the group where to store the data
- try:
- g = h5.createGroup(group, name, title=description,
- createparents=True)
- except:
- print("XU.io.spectra.Save2HDF5: cannot create group %s for "
- "writing data!" % name)
- if isinstance(h5file, str):
- h5.close()
- return True
-
- # start with saving scan comments
- for k in self.comments.keys():
- try:
- h5.setNodeAttr(g, k, self.comments[k])
- except:
- print("XU.io.spectra.Save2HDF5: cannot save file comment "
- "%s = %s to group %s!" % (k, self.comments[k], name))
+ # start with saving scan comments
+ for k in self.comments.keys():
+ try:
+ g.attrs[k] = self.comments[k]
+ except:
+ print("XU.io.spectra.Save2HDF5: cannot save file comment "
+ "%s = %s to group %s!" % (k, self.comments[k], name))
- # save scan parameters
- for k in self.params.keys():
- try:
- h5.setNodeAttr(g, k, self.params[k])
- except:
- print("XU.io.spectra.Save2HDF5: cannot save file parametes "
- "%s to group %s!" % (k, name))
-
- # ----------finally we need to save the data -------------------
-
- # first save the data stored in the FIO file
- tab_desc_dict = {}
- if self.data.data is not None:
- for t in self.data.data.dtype.descr:
- cname = t[0]
- if len(t[1:]) == 1:
- ctype = numpy.dtype((t[1]))
- else:
- ctype = numpy.dtype((t[1], t[2]))
+ # save scan parameters
+ for k in self.params.keys():
+ try:
+ g.attrs[k] = self.params[k]
+ except:
+ print("XU.io.spectra.Save2HDF5: cannot save file parametes"
+ " %s to group %s!" % (k, name))
- tab_desc_dict[cname] = tables.Col.from_dtype(ctype)
+ # ----------finally we need to save the data -------------------
+ kwds = {'fletcher32': True, 'compression': 'gzip'}
- # create the table object
try:
- tab = h5.createTable(g, "data", tab_desc_dict, "scan data")
+ dset = g.create_dataset("data", data=self.data.data, **kwds)
except:
print("XU.io.spectra.Save2HDF5: cannot create table for "
"storing scan data!")
return True
- # now write the data to the tables
- for rec in self.data.data:
- for cname in rec.dtype.names:
- tab.row[cname] = rec[cname]
- tab.row.append()
-
- tab.flush()
-
- # if there is MCA data - store this
- if self.mca is not None:
- a = tables.Float32Atom()
- f = tables.Filters(complib="zlib", complevel=9, fletcher32=True)
- try:
- c = h5.createCArray(g, mcaname, a, self.mca.shape)
- except:
- print("XU.io.spectra.Save2HDF5: cannot create carray %s for "
- "MCA data!" % mcaname)
- return True
-
- c[...] = self.mca[...]
-
- # set MCA specific attributes
- h5.setNodeAttr(c, "channels", self.mca_channels)
- h5.setNodeAttr(c, "nchannels", self.mca_channels.shape[0])
+ # if there is MCA data - store this
+ if self.mca is not None:
+ try:
+ c = g.create_dataset(mcaname, data=self.mca, **kwds)
+ except:
+ print("XU.io.spectra.Save2HDF5: cannot create carray %s "
+ "for MCA data!" % mcaname)
+ return True
- h5.flush()
+ # set MCA specific attributes
+ c.attrs["channels"] = self.mca_channels
+ c.attrs["nchannels"] = self.mca_channels.shape[0]
- if isinstance(h5file, str):
- h5.close()
+ h5.flush()
return None
@@ -392,163 +341,158 @@ class SPECTRAFile(object):
"""
Read the data from the file.
"""
- try:
- fid = open(self.filename, "r")
- except:
- print("XU.io.SPECTRAFile.Read: cannot open data file %s for "
- "reading!" % (self.filename))
- return None
-
- col_names = ""
+ col_names = []
col_units = []
- col_types = ""
+ col_types = []
rec_list = []
+ with open(self.filename, 'rb') as fid:
+ while True:
+ lbuffer = fid.readline().decode('utf8', 'ignore')
+ if lbuffer == "":
+ break
+ lbuffer = lbuffer.strip()
+
+ # read the next line if the line starts with a "!"
+ if re_end_section.match(lbuffer):
+ continue
- while True:
- lbuffer = fid.readline()
- if lbuffer == "":
- break
- lbuffer = lbuffer.strip()
-
- # read the next line if the line starts with a "!"
- if re_end_section.match(lbuffer):
- continue
-
- # select the which section to read
- if re_comment_section.match(lbuffer):
- read_mode = 1
- continue
-
- if re_parameter_section.match(lbuffer):
- read_mode = 2
- continue
-
- if re_data_section.match(lbuffer):
- read_mode = 3
- continue
-
- # here we decide how to proceed with the data
- if read_mode == 1:
- # read the file comments
- try:
- (key, value) = lbuffer.split("=")
- except:
- # avoid annoying output
- if config.VERBOSITY >= config.INFO_ALL:
- print("XU.io.SPECTRAFile.Read: cannot interpret the "
- "comment string: %s" % (lbuffer))
+ # select the which section to read
+ if re_comment_section.match(lbuffer):
+ read_mode = 1
continue
- key = key.strip()
- # remove whitespaces to be conform with natural naming
- key = key.replace(' ', '')
- # remove possible number at first position
- if re_num.findall(key[0]) != []:
- key = "_" + key
- value = value.strip()
- if config.VERBOSITY >= config.DEBUG:
- print("XU.io.SPECTRAFile.Read: comment: k,v: %s, %s"
- % (key, value))
+ if re_parameter_section.match(lbuffer):
+ read_mode = 2
+ continue
- try:
- value = float(value)
- except:
- pass
+ if re_data_section.match(lbuffer):
+ read_mode = 3
+ continue
- # need to handle the case, that a key may appear several times
- # in the list
- kcnt = 0
- while True:
+ # here we decide how to proceed with the data
+ if read_mode == 1:
+ # read the file comments
try:
- self.comments[key] = value
- # if adding the key/value pair to the dictionary
- # was successful - leave the loop
- break
+ (key, value) = lbuffer.split("=")
except:
- key += "_%i" % (kcnt + 2)
-
- kcnt += 1
-
- elif read_mode == 2:
- # read scan parameters
- try:
- (key, value) = lbuffer.split("=")
- except:
- print("XU.io.SPECTRAFile.Read: cannot interpret the "
- "parameter string: %s" % (lbuffer))
-
- key = key.strip()
- # remove whitespaces to be conform with natural naming
- key = key.replace(' ', '')
- # remove possible number at first position
- if re_num.findall(key[0]) != []:
- key = "_" + key
- value = value.strip()
- if config.VERBOSITY >= config.DEBUG:
- print("XU.io.SPECTRAFile.Read: parameter: k,v: %s, %s"
- % (key, value))
+ # avoid annoying output
+ if config.VERBOSITY >= config.INFO_ALL:
+ print("XU.io.SPECTRAFile.Read: cannot interpret "
+ "the comment string: %s" % (lbuffer))
+ continue
+
+ key = key.strip()
+ # remove whitespaces to be conform with natural naming
+ key = key.replace(' ', '')
+ key = key.replace(':', '_')
+ # remove possible number at first position
+ if re_num.findall(key[0]) != []:
+ key = "_" + key
+ value = value.strip()
+ if config.VERBOSITY >= config.DEBUG:
+ print("XU.io.SPECTRAFile.Read: comment: k,v: %s, %s"
+ % (key, value))
- try:
- value = float(value)
- except:
- # if the conversion of the parameter to float
- # fails it will be saved as a string
- pass
-
- # need to handle the case, that a key may appear several times
- # in the list
- kcnt = 0
- while True:
try:
- self.params[key] = value
- # if adding the key/value pair to the dictionary
- # was successful - leave the loop
- break
+ value = float(value)
except:
- key += "_%i" % (kcnt + 2)
-
- kcnt += 1
-
- elif read_mode == 3:
- if re_column.match(lbuffer):
+ pass
+
+ # need to handle the case, that a key may appear several
+ # times in the list
+ kcnt = 0
+ while True:
+ try:
+ self.comments[key] = value
+ # if adding the key/value pair to the dictionary
+ # was successful - leave the loop
+ break
+ except:
+ key += "_%i" % (kcnt + 2)
+
+ kcnt += 1
+
+ elif read_mode == 2:
+ # read scan parameters
try:
- unit = re_unit.findall(lbuffer)[0]
- except IndexError:
- unit = "NONE"
+ (key, value) = lbuffer.split("=")
+ except:
+ print("XU.io.SPECTRAFile.Read: cannot interpret the "
+ "parameter string: %s" % (lbuffer))
+
+ key = key.strip()
+ # remove whitespaces to be conform with natural naming
+ key = key.replace(' ', '')
+ key = key.replace(':', '_')
+ # remove possible number at first position
+ if re_num.findall(key[0]) != []:
+ key = "_" + key
+ value = value.strip()
+ if config.VERBOSITY >= config.DEBUG:
+ print("XU.io.SPECTRAFile.Read: parameter: k,v: %s, %s"
+ % (key, value))
try:
- lval = re_obracket.split(lbuffer)[0]
- rval = re_cbracket.split(lbuffer)[-1]
- dtype = rval.strip()
- l = re_wspaces.split(lval)
- index = int(l[1])
- name = "".join(l[2:])
- except IndexError:
- l = re_wspaces.split(lbuffer)
- index = int(l[1])
- dtype = l[-1]
- name = "".join(l[2:-1])
-
- # store column definition
- self.data.append(
- SPECTRAFileDataColumn(index, name, unit, dtype))
-
- if name in col_names.split(","):
- name += "%s_1" % name
-
- col_names += "%s," % name
- col_types += "%s," % (dtype_map[dtype])
-
- else:
- # read data
- dlist = re_wspaces.split(lbuffer)
- for i in range(len(dlist)):
- dlist[i] = float(dlist[i])
-
- rec_list.append(dlist)
+ value = float(value)
+ except:
+ # if the conversion of the parameter to float
+ # fails it will be saved as a string
+ pass
+
+ # need to handle the case, that a key may appear several
+ # times in the list
+ kcnt = 0
+ while True:
+ try:
+ self.params[key] = value
+ # if adding the key/value pair to the dictionary
+ # was successful - leave the loop
+ break
+ except:
+ key += "_%i" % (kcnt + 2)
+
+ kcnt += 1
+
+ elif read_mode == 3:
+ if re_column.match(lbuffer):
+ try:
+ unit = re_unit.findall(lbuffer)[0]
+ except IndexError:
+ unit = "NONE"
+
+ try:
+ lval = re_obracket.split(lbuffer)[0]
+ rval = re_cbracket.split(lbuffer)[-1]
+ dtype = rval.strip()
+ l = re_wspaces.split(lval)
+ index = int(l[1])
+ name = "".join(l[2:])
+ name = name.replace(':', '_')
+ except IndexError:
+ l = re_wspaces.split(lbuffer)
+ index = int(l[1])
+ dtype = l[-1]
+ name = "".join(l[2:-1])
+ name = name.replace(':', '_')
+
+ # store column definition
+ self.data.append(
+ SPECTRAFileDataColumn(index, name, unit, dtype))
+
+ if name in col_names:
+ name += "%s_1" % name
+
+ col_names.append("%s" % name)
+ col_types.append("%s" % (dtype_map[dtype]))
+
+ else:
+ # read data
+ dlist = re_wspaces.split(lbuffer)
+ for i in range(len(dlist)):
+ dlist[i] = float(dlist[i])
+
+ rec_list.append(dlist)
- col_names = col_names[:-1]
- col_types = col_types[:-1]
if config.VERBOSITY >= config.DEBUG:
print("XU.io.SPECTRAFile.Read: data columns: name,type: %s, %s"
% (col_names, col_types))
@@ -559,357 +503,6 @@ class SPECTRAFile(object):
self.data.data = None
-class Spectra(object):
-
- def __init__(self, data_dir):
- self.data_dir = data_dir
- self.h5_file = None
- self.h5_group = None
- self.abs_factors = None
-
- def set_abs_factors(self, ff):
- """
- Set the global absorber factors in the module.
- """
- if isinstance(ff, list):
- self.abs_factors = numpy.array(ff, dtype=numpy.double)
- elif isinstance(ff, numpy.ndarray):
- self.abs_factors = ff
-
- def recarray2hdf5(self, h5g, rec, name, desc):
- """
- Save a record array in an HDF5 file. A pytables table
- object is used to store the data.
-
- required input arguments:
- h5g ................. HDF5 group object or path
- rec ................ record array
- name ............... name of the table in the file
- desc ............... description of the table in the file
-
- return value:
- tab ................. a HDF5 table object
- """
-
- # to build the table data types and names must be extracted
- descr = rec.dtype.descr
- tab_desc = {}
- cname_list = []
-
- for d in descr:
- tab_desc[d[0]] = tables.Col.from_dtype(numpy.dtype(d[1]))
- cname_list.append(d[0])
-
- # create the table object
- try:
- tab = self.h5_file.createTable(h5g, name, tab_desc, desc)
- except:
- print("XU.io.spectra.Spectra: Error creating table object %s!")
- return None
-
- # fill in data values
- for i in range(rec.shape[0]):
- for k in cname_list:
- tab.row[k] = rec[k][i]
-
- tab.row.append()
-
- tab.flush()
- self.h5_file.flush()
-
- def spectra2hdf5(self, dir, fname, mcatemp, name="", desc="SPECTRA data"):
- """
- Convert SPECTRA scan data to a HDF5 format.
-
- required input arguments:
- dir ............... directory where the scan is stored
- fname ............. name of the SPECTRA data file
- mcatemp ........... template for the MCA file names
-
- optional keyword arguments:
- name .............. optional name under which to save the data
- if empty the basename of the filename will be used
- desc .............. optional description of the scan
- """
-
- (basename, ext) = os.path.splitext(fname)
- mcadir = os.path.join(dir, name)
-
- # evaluate keyword arguments
- if name == "":
- sg_name = basename
- else:
- sg_name = name
-
- sg_desc = desc
-
- # check wether an MCA directory exists or not
- if os.path.exists(mcadir):
- has_mca = True
- else:
- has_mca = False
-
- fullfname = os.path.join(dir, fname)
- if not os.path.exists(fullfname):
- print("XU.io.spectra.Spectra.spectra2hdf5: data file does not "
- "exist!")
- return None
-
- # read data file
- (data, hdr) = read_data(fullfname)
-
- # create a new group to save the scan data in
- # this group is created below the default group determined by
- # self.h5_group
- try:
- sg = self.h5_file.createGroup(self.h5_group, sg_name, sg_desc)
- except:
- print("XU.io.spectra.Spectra.spectra2hdf5: cannot create scan "
- "group!")
- return None
-
- self.recarray2hdf5(sg, data, "data", "SPECTRA tabular data")
-
- # write attribute data
- for k in hdr.keys():
- self.h5_file.setNodeAttr(sg, "MOPOS_" + k, hdr[k])
-
- if has_mca:
- mca = read_mca_dir(mcadir, mcatemp)
- a = tables.Float64Atom()
- filter = tables.Filters(complib="zlib", complevel=4,
- fletcher32=True)
- c = self.h5_file.createCArray(sg, "MCA", a, mca.shape, "MCA data",
- filters=filter)
- c[...] = mca[...]
-
- self.h5_file.flush()
-
- return sg
-
- def abs_corr(self, data, f, **keyargs):
- """
- Perform absorber correction. Data can be either a 1 dimensional data
- (point detector) or a 2D MCA array. In the case of an array the data
- array should be of shape (N,NChannels) where N is the number of points
- in the scan an NChannels the number of channels of the MCA. The
- absorber values are passed to the function as a 1D array of N elements.
-
- By default the absorber values are taken form a global variable stored
- in the module called _absorver_factors. Despite this, costume values
- can be passed via optional keyword arguments.
-
- required input arguments:
- mca ............... matrix with the MCA data
- f ................. filter values along the scan
-
- optional keyword arguments:
- ff ................ custome filter factors
-
- return value:
- Array with the same shape as mca with the corrected MCA data.
- """
-
- mcan = numpy.zeros(data.shape, dtype=numpy.double)
-
- if "ff" in keyargs:
- ff = keyargs["ff"]
- else:
- ff = _absorber_factors
-
- if len(data.shape) == 2:
- # MCA and matrix data
- data = data * ff[f][:, numpy.newaxis]
- elif len(data.shape) == 1:
- data = data * ff[f]
-
- return data
-
-
-def get_spectra_files(dirname):
- """
- Return a list of spectra files within a directory.
-
- required input arguments:
- dirname .............. name of the directory to search
-
- return values:
- list with filenames
- """
-
- fnlist = os.listdir(dirname)
- onlist = []
-
- for fname in fnlist:
- (name, ext) = os.path.splitext(fname)
- if ext == ".fio":
- onlist.append(fname)
-
- onlist.sort()
- return onlist
-
-
-def read_mca_dir(dirname, filetemp, sort=True):
- """
- Read all MCA files within a directory
- """
-
- flist = get_spectra_files(dirname)
-
- # create a list with the numbers of the files
- nlist = []
- for fname in flist:
- (name, ext) = os.path.splitext(fname)
- name = name.replace(filetemp, "")
- nlist.append(int(name))
-
- if sort:
- nlist.sort()
-
- dlist = []
-
- for i in nlist:
- fname = os.path.join(dirname, filetemp + "%i.fio")
- fname = fname % (i)
- d = read_mca(fname)
- dlist.append(d.tolist())
-
- return numpy.array(dlist)
-
-
-def read_mca(fname):
- """
- Read a single SPECTRA MCA file.
-
- required input arguments:
- fname ............... name of the file to read
-
- return value:
- data ................ a numpy array witht the MCA data
- """
-
- try:
- fid = open(fname)
- except:
- print("XU.io.spectra.read_mca: cannot open file %s!" % fname)
- return None
-
- dlist = []
- hdr_flag = True
-
- while True:
- lbuffer = fid.readline()
-
- if lbuffer == "":
- break
- lbuffer = lbuffer.strip()
- if lbuffer == "%d":
- hdr_flag = False
- lbuffer = fid.readline()
- continue
-
- if not hdr_flag:
- dlist.append(float(lbuffer))
-
- return numpy.array(dlist, dtype=numpy.double)
-
-
-def read_mcas(ftemp, cntstart, cntstop):
- """
- Read MCA data from a SPECTRA MCA directory. The filename is passed as a
- generic
- """
-
- fnums = range(cntstart, cntstop + 1)
- mcalist = []
-
- for i in fnums:
- fname = ftemp % i
- print("XU.io.spectra.read_mcas: processing file %s ..." % fname)
- mcalist.append(read_mca(fname))
-
- return numpy.array(mcalist, dtype=numpy.double)
-
-
-def read_data(fname):
- """
- Read a spectra data file (a file with now MCA data).
-
- required input arguments:
- fname .................... name of the file to read
-
- return values: (data,hdr)
- data .......... numpy record array where the keys are the column names
- hdr ........... a dictionary with header information
- """
-
- try:
- fid = open(fname, "r")
- except:
- print("XU.io.spectra.read_data: cannot open file %s!" % fname)
- return None
-
- hdr_dict = {}
- hdr_flag = False
- data_flag = False
- col_cnt = 0 # column counter
- col_names = [] # list with column names
- data = []
-
- fname = os.path.basename(fname)
- fname, ext = os.path.splitext(fname)
- print(fname)
-
- while True:
- lbuffer = fid.readline()
- if lbuffer == "":
- break
-
- lbuffer = lbuffer.strip()
- # check for common break conditions
- # if the line is a comment skip it
- if lbuffer[0] == "!":
- continue
-
- # remove leading and trailing whitespace symbols
- lbuffer = lbuffer.strip()
-
- if lbuffer == "%p":
- hdr_flag = True
- continue
-
- if lbuffer == "%d":
- hdr_flag = False
- data_flag = True
- continue
-
- if hdr_flag:
- # read header data (initial motor positions)
- key, value = lbuffer.split("=")
- key = key.strip()
- value = value.strip()
- hdr_dict[key] = float(value)
-
- if data_flag:
- # have to read the column names first
- if re_colname.match(lbuffer):
- l = re_wspaces.split(lbuffer)
- col_names.append(l[2].replace(fname.upper() + "_", ""))
- else:
- # read data values
- dlist = re_wspaces.split(lbuffer)
- # convert strings to float values
- for i in range(len(dlist)):
- dlist[i] = float(dlist[i])
-
- data.append(dlist)
-
- # create a record array to hold data
- data = numpy.rec.fromrecords(data, names=col_names)
-
- return (data, hdr_dict)
-
-
def geth5_spectra_map(h5file, scans, *args, **kwargs):
"""
function to obtain the omega and twotheta as well as intensity values
@@ -921,7 +514,7 @@ def geth5_spectra_map(h5file, scans, *args, **kwargs):
Parameters
----------
- h5f: file object of a HDF5 file opened using pytables
+ h5f: file object of a HDF5 file opened using h5py
scans: number of the scans of the reciprocal space map (int,tuple or
list)
@@ -945,88 +538,67 @@ def geth5_spectra_map(h5file, scans, *args, **kwargs):
intensities e.g. MAP['MCA']).
"""
- try:
- matplotlib.__version__
- except NameError:
- print("XU.io.spectra.geth5_spectra_map: ERROR: matplotlib "
- "functionality not available")
- return
+ with xu_h5open(h5file) as h5:
+ if "mca" in kwargs:
+ mca = kwargs["mca"]
+ else:
+ mca = "MCA"
- if isinstance(h5file, str):
- try:
- h5 = tables.openFile(h5file, mode="r")
- except:
- print("XU.io.spectra.geth5_spectra_map: cannot open file %s "
- "for reading!" % h5file)
- return True
-
- else:
- h5 = h5file
-
- if "mca" in kwargs:
- mca = kwargs["mca"]
- else:
- mca = "MCA"
-
- if "samplename" in kwargs:
- basename = kwargs["samplename"]
- else:
- nodename = h5.listNodes(h5.root)[0]._v_name
- basenlist = re_underscore.split(nodename)
- basename = "_".join(basenlist[:-1])
- if config.VERBOSITY >= config.DEBUG:
- print("XU.io.spectra.geth5_spectra_map: using \'%s\' as basename"
- % (basename))
-
- if isinstance(scans, (list, tuple)):
- scanlist = scans
- else:
- scanlist = list([scans])
-
- angles = dict.fromkeys(args)
- for key in angles.keys():
- angles[key] = numpy.zeros(0)
- buf = numpy.zeros(0)
- MAP = numpy.zeros(0)
-
- for nr in scanlist:
- h5scan = h5.getNode(h5.root, basename + "_%05d" % nr)
- sdata = h5scan.data.read()
- if mca:
- mcanode = h5.getNode(h5.root, basename + "_%05d/%s" % (nr, mca))
- mcadata = mcanode.read()
-
- # append scan data to MAP, where all data are stored
- sdtmp = matplotlib.mlab.rec_append_fields(
- sdata,
- [mca, ], [mcadata, ],
- dtypes=[(numpy.double, mcadata.shape[1])])
- if MAP.dtype == numpy.float64:
- MAP.dtype = sdtmp.dtype
- MAP = numpy.append(MAP, sdtmp)
-
- # check type of scan
- notscanmotors = []
- for i in range(len(args)):
- motname = args[i]
- try:
- buf = sdata[motname]
- scanshape = buf.shape
+ if "samplename" in kwargs:
+ basename = kwargs["samplename"]
+ else:
+ nodename = list(h5.keys())[0]
+ basenlist = re_underscore.split(nodename)
+ basename = "_".join(basenlist[:-1])
+ if config.VERBOSITY >= config.DEBUG:
+ print("XU.io.spectra.geth5_spectra_map: using \'%s\' as "
+ "basename" % (basename))
+
+ if isinstance(scans, (list, tuple)):
+ scanlist = scans
+ else:
+ scanlist = list([scans])
+
+ angles = dict.fromkeys(args)
+ for key in angles.keys():
+ angles[key] = numpy.zeros(0)
+ buf = numpy.zeros(0)
+ MAP = numpy.zeros(0)
+
+ for nr in scanlist:
+ h5scan = h5.get(basename + "_%05d" % nr)
+ sdata = h5scan.get('data')
+ if mca:
+ mcanode = h5.get(basename + "_%05d/%s" % (nr, mca))
+ mcadata = numpy.asarray(mcanode)
+
+ # append scan data to MAP, where all data are stored
+ mcatemp = mcadata.view([(mca, (mcadata.dtype, mcadata.shape[1]))])
+ sdtmp = numpy.lib.recfunctions.merge_arrays([sdata, mcatemp],
+ flatten=True)
+ if MAP.dtype == numpy.float64:
+ MAP.dtype = sdtmp.dtype
+ MAP = numpy.append(MAP, sdtmp)
+
+ # check type of scan
+ notscanmotors = []
+ for i in range(len(args)):
+ motname = args[i]
+ try:
+ buf = sdata[motname]
+ scanshape = buf.shape
+ angles[motname] = numpy.concatenate((angles[motname], buf))
+ except:
+ notscanmotors.append(i)
+ for i in notscanmotors:
+ motname = args[i]
+ buf = numpy.ones(scanshape) * \
+ h5.getNodeAttr(h5scan, "%s" % motname)
angles[motname] = numpy.concatenate((angles[motname], buf))
- except:
- notscanmotors.append(i)
- for i in notscanmotors:
- motname = args[i]
- buf = numpy.ones(scanshape) * \
- h5.getNodeAttr(h5scan, "%s" % motname)
- angles[motname] = numpy.concatenate((angles[motname], buf))
retval = []
for motname in args:
# create return values in correct order
retval.append(angles[motname])
- if isinstance(h5file, str):
- h5.close()
-
return retval, MAP
diff --git a/xrayutilities/materials/__init__.py b/xrayutilities/materials/__init__.py
index 03e932c..3dc75f0 100644
--- a/xrayutilities/materials/__init__.py
+++ b/xrayutilities/materials/__init__.py
@@ -18,7 +18,7 @@
# import module objects
-from .lattice import Atom
+from .atom import Atom
from .lattice import LatticeBase
from .lattice import Lattice
from .lattice import CubicLattice
diff --git a/xrayutilities/materials/_create_database.py b/xrayutilities/materials/_create_database.py
index 043b45a..fecf35b 100644
--- a/xrayutilities/materials/_create_database.py
+++ b/xrayutilities/materials/_create_database.py
@@ -13,38 +13,49 @@
# You should have received a copy of the GNU General Public License
# along with this program; if not, see <http://www.gnu.org/licenses/>.
#
-# Copyright (C) 2012-2014 Dominik Kriegner <dominik.kriegner at gmail.com>
+# Copyright (C) 2012-2015 Dominik Kriegner <dominik.kriegner at gmail.com>
"""
script to create the HDF5 database from the raw data of XOP
this file is only needed for administration
"""
-import os
-
-# if __name__ == "__main__" and __package__ is None:
-# __package__ = "xrayutilities"
-# from . import database as db
-execfile('database.py')
-
-filename = os.path.join("data", "elements.db")
+import os.path
+import lzma
+exec(open('database.py', 'rb').read())
+filename = os.path.join('data', 'elements.db')
dbf = DataBase(filename)
-dbf.Create(filename,
- "Database with elemental data from XOP and Kissel databases")
+dbf.Create('elementdata',
+ 'Database with elemental data from XOP and Kissel databases')
init_material_db(dbf)
-add_mass_from_NIST(dbf, os.path.join("data", "nist_atom.dat"))
-add_f0_from_xop(dbf, os.path.join("data", "f0_xop.dat"))
-add_f1f2_from_kissel(dbf, os.path.join("data", "f1f2_asf_Kissel.dat"))
-# alternative use the Henke database
-# add_f1f2_from_henkedb(dbf,os.path.join("data","f1f2_Henke.dat"))
+# add a dummy element, this is useful not only for testing and should be
+# kept in future! It can be used for structure factor calculation tests, and
+# shows how the a database entry can be generated manually
+dbf.SetMaterial('dummy')
+dbf.SetF0([1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]) # atomic structure factors
+dbf.SetF1F2((0, 1e5), (0, 0), (0, 0)) # zero dispersion correction
+
+add_mass_from_NIST(dbf, os.path.join('data', 'nist_atom.dat'))
+
+# add F0(Q) for every element
+# with lzma.open(os.path.join('data', 'f0_xop.dat.xz'), 'r') as xop:
+# add_f0_from_xop(dbf, xop)
+with lzma.open(os.path.join('data', 'f0_InterTables.dat.xz'), 'r') as itf:
+ add_f0_from_intertab(dbf, itf)
+
+# add F1 and F2 from database
+with lzma.open(os.path.join('data', 'f1f2_asf_Kissel.dat.xz'), 'r') as kf:
+ add_f1f2_from_kissel(dbf, kf)
+# with lzma.open(os.path.join('data','f1f2_Henke.dat'), 'r') as hf:
+# add_f1f2_from_henkedb(dbf, hf)
# Also its possible to add costum data from different databases; e.g.
# created by Hepaestus (http://bruceravel.github.io/demeter/). This is also
# possible for specific elements only, therefore extract the data from
# Hephaestus or any other source producing ASCII files with three columns
# (energy (eV), f1, f2). To import such data use:
-# add_f1f2_from_ascii_file(dbf,os.path.join("data","Ga.f1f2"),'Ga')
+# add_f1f2_from_ascii_file(dbf, os.path.join('data','Ga.f1f2'), 'Ga')
dbf.Close()
diff --git a/xrayutilities/materials/atom.py b/xrayutilities/materials/atom.py
new file mode 100644
index 0000000..d6a9ce9
--- /dev/null
+++ b/xrayutilities/materials/atom.py
@@ -0,0 +1,102 @@
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, see <http://www.gnu.org/licenses/>.
+#
+# Copyright (C) 2009-2015 Dominik Kriegner <dominik.kriegner at gmail.com>
+
+"""
+module containing the Atom class which handles the database access for atomic
+scattering factors and the atomic mass.
+"""
+import atexit
+import os.path
+import re
+
+from . import __path__
+from . import database
+from .. import config
+from .. import utilities
+
+_db = database.DataBase(os.path.join(__path__[0], "data", config.DBNAME))
+_db.Open()
+
+
+def _db_cleanup():
+ _db.Close()
+
+atexit.register(_db_cleanup)
+
+
+class Atom(object):
+
+ def __init__(self, name, num):
+ self.name = name
+ self.ostate = re.sub('[A-Za-z]', '', name)
+ for r, o in zip(('dot', 'p', 'm'), ('.', '+', '-')):
+ self.ostate = self.ostate.replace(o, r)
+
+ self.basename = re.sub('[^A-Za-z]', '', name)
+ self.num = num
+
+ def __key__(self):
+ """ key function to return the elements number """
+ return self.num
+
+ def __lt__(self, other_el):
+ """ make elements sortable by their key """
+ return self.__key__() < other_el.__key__()
+
+ @property
+ def weight(self):
+ _db.SetMaterial(self.basename)
+ return _db.weight
+
+ def f0(self, q):
+ _db.SetMaterial(self.basename)
+ return _db.GetF0(q, self.ostate)
+
+ def f1(self, en="config"):
+ if en == "config":
+ en = utilities.energy(config.ENERGY)
+
+ _db.SetMaterial(self.basename)
+ return _db.GetF1(utilities.energy(en))
+
+ def f2(self, en="config"):
+ if en == "config":
+ en = utilities.energy(config.ENERGY)
+
+ _db.SetMaterial(self.basename)
+ return _db.GetF2(utilities.energy(en))
+
+ def f(self, q, en="config"):
+ """
+ function to calculate the atomic structure factor F
+
+ Parameter
+ ---------
+ q: momentum transfer
+ en: energy for which F should be calculated, if omitted the value
+ from the xrayutilities configuration is used
+
+ Returns
+ -------
+ f (float)
+ """
+ f = self.f0(q) + self.f1(en) + 1.j * self.f2(en)
+ return f
+
+ def __str__(self):
+ ostr = self.name
+ ostr += " (%2d)" % self.num
+ return ostr
+
+ def __repr__(self):
+ return self.__str__()
diff --git a/xrayutilities/materials/data/elements.db b/xrayutilities/materials/data/elements.db
index 59328a8..d31b3b2 100644
Binary files a/xrayutilities/materials/data/elements.db and b/xrayutilities/materials/data/elements.db differ
diff --git a/xrayutilities/materials/database.py b/xrayutilities/materials/database.py
index 3be855e..9fba19d 100644
--- a/xrayutilities/materials/database.py
+++ b/xrayutilities/materials/database.py
@@ -14,15 +14,14 @@
# along with this program; if not, see <http://www.gnu.org/licenses/>.
#
# Copyright (C) 2009 Eugen Wintersberger <eugen.wintersberger at desy.de>
-# Copyright (C) 2009-2010,2012 Dominik Kriegner <dominik.kriegner at gmail.com>
+# Copyright (C) 2009-2015 Dominik Kriegner <dominik.kriegner at gmail.com>
"""
-module to handle access to the optical parameters database
+module to handle the access to the optical parameters database
"""
-import tables
+import h5py
import numpy
-import scipy.interpolate
import scipy.constants
import re
@@ -38,6 +37,7 @@ class DataBase(object):
self.f1 = None
self.f2_en = None
self.f2 = None
+ self.weight = None
def Create(self, dbname, dbdesc):
"""
@@ -55,30 +55,29 @@ class DataBase(object):
# tryp to open the database file
try:
- self.h5file = tables.openFile(self.fname, mode="w")
+ self.h5file = h5py.File(self.fname, 'w')
except:
- print("cannot create database file %s!" % (self.fname))
+ print('cannot create database file %s!' % (self.fname))
return None
# set attributes to the root group with database name and
# description
- self.h5file.setNodeAttr("/", "DBName", dbname)
- self.h5file.setNodeAttr("/", "DBDesc", dbdesc)
+ self.h5file.attrs['DBName'] = dbname
+ self.h5file.attrs['DBDesc'] = dbdesc
- def Open(self, mode="r"):
+ def Open(self, mode='r'):
"""
Open an existing database file.
"""
if self.h5file is not None:
- print("database already opened - "
- "close first to open new database!")
- return None
+ print('database already opened - '
+ 'close first to open new database!')
+ return
try:
- self.h5file = tables.openFile(self.fname, mode=mode)
+ self.h5file = h5py.File(self.fname, mode)
except:
print("cannot open database file %s!" % (self.fname))
- return None
def Close(self):
"""
@@ -86,7 +85,7 @@ class DataBase(object):
"""
if self.h5file is None:
print("no database file opened!")
- return None
+ return
self.h5file.close()
self.h5file = None
@@ -102,18 +101,14 @@ class DataBase(object):
"""
if self.h5file is None:
print("no database file opened!")
- return None
+ return
- try:
- g = self.getNode("/", name)
- # if this operation succeeds the material node already exists and
- # a warning message is printed
+ if name in self.h5file:
+ # if the material node already exists a warning message is printed
print("material node already exists")
- return None
- except:
- pass
-
- g = self.h5file.createGroup("/", name, title=description)
+ else:
+ g = self.h5file.create_group(name)
+ g.attrs['name'] = description
def SetWeight(self, weight):
"""
@@ -125,10 +120,10 @@ class DataBase(object):
if not isinstance(weight, float):
raise TypeError("weight parameter must be a float!")
- self.h5group._v_attrs.atomic_standard_weight = weight
+ self.h5group.attrs['atomic_standard_weight'] = weight
self.h5file.flush()
- def SetF0(self, parameters):
+ def SetF0(self, parameters, subset='default'):
"""
Save f0 fit parameters for the set material. The fit parameters
are stored in the following order:
@@ -136,6 +131,8 @@ class DataBase(object):
required input argument:
parameters ........ list or numpy array with the fit parameters
+ subset ............ specifies under which name the f0 values should
+ be saved
"""
if isinstance(parameters, list):
p = numpy.array(parameters, dtype=numpy.float32)
@@ -145,94 +142,65 @@ class DataBase(object):
raise TypeError("f0 fit parameters must be a "
"list or a numpy array!")
+ if not subset:
+ subset = 'default'
+
try:
- self.h5file.removeNode(self.h5group, "f0")
+ del self.h5group['f0/%s' % subset]
except:
pass
- c = self.h5file.createArray(self.h5group, "f0", p, "f0 fit parameters")
+ self.h5group.create_dataset('f0/%s' % subset, data=p)
self.h5file.flush()
- def SetF1(self, en, f1):
+ def SetF1F2(self, en, f1, f2):
"""
- Set f1 tabels values for the active material.
+ Set f1, f2 values for the active material.
required input arguments:
en ................ list or numpy array with energy in (eV)
f1 ................ list or numpy array with f1 values
+ f2 ................ list or numpy array with f2 values
"""
- if isinstance(en, list):
+ if isinstance(en, (list, tuple)):
end = numpy.array(en, dtype=numpy.float32)
elif isinstance(en, numpy.ndarray):
end = en.astype(numpy.float32)
else:
raise TypeError("energy values must be a list or a numpy array!")
- if isinstance(f1, list):
+ if isinstance(f1, (list, tuple)):
f1d = numpy.array(f1, dtype=numpy.float32)
elif isinstance(f1, numpy.ndarray):
f1d = f1.astype(numpy.float32)
else:
raise TypeError("f1 values must be a list or a numpy array!")
- a = tables.Float32Atom()
-
- try:
- self.h5file.removeNode(self.h5group, "en_f1")
- except:
- pass
-
- try:
- self.h5file.removeNode(self.h5group, "f1")
- except:
- pass
-
- c = self.h5file.createArray(self.h5group, "en_f1",
- end, "f1 energy scale in (eV)")
- self.h5file.flush()
-
- c = self.h5file.createArray(self.h5group, "f1", f1d, "f1 data")
- self.h5file.flush()
-
- def SetF2(self, en, f2):
- """
- Set f2 tabels values for the active material.
-
- required input arguments:
- en ................ list or numpy array with energy in (eV)
- f2 ................ list or numpy array with f2 values
- """
- if isinstance(en, list):
- end = numpy.array(en, dtype=numpy.float32)
- elif isinstance(en, numpy.ndarray):
- end = en.astype(numpy.float32)
- else:
- raise TypeError("energy values must be a list or a numpy array!")
-
- if isinstance(f2, list):
+ if isinstance(f2, (list, tuple)):
f2d = numpy.array(f2, dtype=numpy.float32)
elif isinstance(f2, numpy.ndarray):
f2d = f2.astype(numpy.float32)
else:
raise TypeError("f2 values must be a list or a numpy array!")
- a = tables.Float32Atom()
-
try:
- self.h5file.removeNode(self.h5group, "en_f2")
+ del self.h5group['en_f12']
except:
pass
try:
- self.h5file.removeNode(self.h5group, "f2")
+ del self.h5group['f1']
except:
pass
- c = self.h5file.createArray(self.h5group, "en_f2",
- end, "f2 energy scale in (eV)")
- self.h5file.flush()
+ try:
+ del self.h5group['f2']
+ except:
+ pass
- c = self.h5file.createArray(self.h5group, "f2", f2d, "f2 data")
+ self.h5group.create_dataset('en_f12', data=end)
+ self.h5group.create_dataset('f1', data=f1d)
+ self.h5group.create_dataset('f2', data=f2d)
self.h5file.flush()
def SetMaterial(self, name):
@@ -241,50 +209,64 @@ class DataBase(object):
operations like setting and getting optical constants are done for this
particular material.
- requiered input arguments:
+ required input arguments:
name ............... string with the name of the material
"""
try:
- self.h5group = self.h5file.getNode("/", name)
+ self.h5group = self.h5file[name]
except:
- print("XU.materials.database: material does not exist!")
+ print("XU.materials.database: material '%s' not existing!" % name)
try:
- self.f0_params = self.h5group.f0
- self.f1_en = self.h5group.en_f1
- self.f1 = self.h5group.f1
- self.f2_en = self.h5group.en_f2
- self.f2 = self.h5group.f2
- self.weight = self.h5group._v_attrs.atomic_standard_weight
+ self.f0_params = self.h5group['f0']
except:
- print("XU.materials.database: some (optical|other) "
- "constants are missing!")
- # self.f0_params = None
- # self.f1_en = None
- # self.f1 = None
- # self.f2_en = None
- # self.f2 = None
-
- def GetF0(self, q):
+ self.f0_params = None
+ try:
+ self.f1_en = self.h5group['en_f12']
+ self.f1 = self.h5group['f1']
+ except:
+ self.f1_en = None
+ self.f1 = None
+ try:
+ self.f2_en = self.h5group['en_f12']
+ self.f2 = self.h5group['f2']
+ except:
+ self.f2_en = None
+ self.f2 = None
+ try:
+ self.weight = self.h5group.attrs['atomic_standard_weight']
+ except:
+ self.weight = None
+
+ def GetF0(self, q, dset='default'):
"""
Obtain the f0 scattering factor component for a particular
momentum transfer q.
required input argument:
q ......... single float value or numpy array
+ dset ...... specifies which dataset (different oxidation states)
+ should be used
"""
- # get parameters
- f0_params = self.f0_params.read()
- c = f0_params[0]
- k = q / (4. * numpy.pi)
- f0 = 0.
+ # get parameters from file
+ if not dset:
+ dset = 'default'
+ f0_params = self.f0_params[dset]
+ # calculate f0
+ if isinstance(q, (numpy.ndarray, list, tuple)):
+ ql = numpy.asarray(q)
+ f0 = f0_params[0] * numpy.ones(ql.shape)
+ else:
+ ql = q
+ f0 = f0_params[0]
+ k = ql / (4. * numpy.pi)
for i in range(1, len(f0_params) - 1, 2):
a = f0_params[i]
b = f0_params[i + 1]
f0 += a * numpy.exp(-b * k ** 2)
- return f0 + c
+ return f0
def GetF1(self, en):
"""
@@ -294,14 +276,10 @@ class DataBase(object):
required input arguments:
en ............. float or numpy array with the energy
"""
- # check if energy is covered by database data
- endb = self.f1_en.read()
- f1db = self.f1.read()
+ if1 = numpy.interp(en, self.f1_en, self.f1,
+ left=numpy.nan, right=numpy.nan)
- if1 = scipy.interpolate.interp1d(endb, f1db, kind=1)
- f1 = if1(en)
-
- return f1
+ return if1
def GetF2(self, en):
"""
@@ -311,18 +289,17 @@ class DataBase(object):
required input arguments:
en ............. float or numpy array with the energy
"""
- # check if energy is covered by database data
- endb = self.f2_en.read()
- f2db = self.f2.read()
-
- if2 = scipy.interpolate.interp1d(endb, f2db, kind=1)
- f2 = if2(en)
+ if2 = numpy.interp(en, self.f2_en, self.f2,
+ left=numpy.nan, right=numpy.nan)
- return f2
+ return if2
def init_material_db(db):
+ db.CreateMaterial("dummy", "Dummy atom")
db.CreateMaterial("H", "Hydrogen")
+ db.CreateMaterial("D", "Deuterium")
+ db.CreateMaterial("T", "Tritium")
db.CreateMaterial("He", "Helium")
db.CreateMaterial("Li", "Lithium")
db.CreateMaterial("Be", "Berylium")
@@ -414,29 +391,45 @@ def init_material_db(db):
db.CreateMaterial("Th", "Thorium")
db.CreateMaterial("Pa", "Protactinium")
db.CreateMaterial("U", "Urianium")
+ db.CreateMaterial("Np", "Neptunium")
+ db.CreateMaterial("Pu", "Plutonium")
+ db.CreateMaterial("Am", "Americium")
+ db.CreateMaterial("Cm", "Curium")
+ db.CreateMaterial("Bk", "Berkelium")
+ db.CreateMaterial("Cf", "Californium")
+ db.CreateMaterial("Es", "Einsteinium")
+ db.CreateMaterial("Fm", "Fermium")
+ db.CreateMaterial("Md", "Mendelevium")
+ db.CreateMaterial("No", "Nobelium")
+ db.CreateMaterial("Lr", "Lawrencium")
+ db.CreateMaterial("Rf", "Rutherfordium")
+ db.CreateMaterial("Db", "Dubnium")
+ db.CreateMaterial("Sg", "Seaborgium")
+ db.CreateMaterial("Bh", "Bohrium")
+ db.CreateMaterial("Hs", "Hassium")
+ db.CreateMaterial("Mt", "Meitnerium")
+ db.CreateMaterial("Ds", "Darmstadtium")
+ db.CreateMaterial("Rg", "Roentgenium")
+ db.CreateMaterial("Cn", "Copernicium")
+ db.CreateMaterial("Uut", "Ununtrium")
+ db.CreateMaterial("Uuq", "Flerovium")
+ db.CreateMaterial("Uup", "Ununpentium")
+ db.CreateMaterial("Uuh", "Livermorium")
+ db.CreateMaterial("Uus", "Ununseptium")
+ db.CreateMaterial("Uuo", "Ununoctium")
# functions to read database files
-def add_f0_from_intertab(db, itabfile):
+def add_f0_from_intertab(db, itf):
"""
- Read f0 data from international tables of crystallography and add
+ Read f0 data from International Tables of Crystallography and add
it to the database.
"""
-
- # parse the inter. tab. file
- try:
- itf = open(itabfile, "r")
- except:
- print("cannot open f0 database file")
- return None
-
# some regular expressions
elementstr = re.compile(r"^#S")
multiblank = re.compile(r"\s+")
- invalidelem = re.compile(r"[^A-Za-z]")
-
while True:
- lb = itf.readline()
+ lb = itf.readline().decode("utf-8")
if lb == "":
break
lb = lb.strip()
@@ -444,53 +437,49 @@ def add_f0_from_intertab(db, itabfile):
if elementstr.match(lb):
# found new element
lb = multiblank.split(lb)
- ename = lb[2]
- # check if this is not some funny isotope
-
- if invalidelem.findall(ename) == []:
- print("set element %s" % ename)
- db.SetMaterial(ename)
- # make one dummy read
- itf.readline()
- itf.readline()
- # read fit parameters
- lb = itf.readline()
- lb = lb.strip()
- lb = multiblank.split(lb)
- a1 = float(lb[0])
- a2 = float(lb[1])
- a3 = float(lb[2])
- a4 = float(lb[3])
- c = float(lb[4])
- b1 = float(lb[5])
- b2 = float(lb[6])
- b3 = float(lb[7])
- b4 = float(lb[8])
- db.SetF0([c, a1, b1, a2, b2, a3, b3, a4, b4])
- itf.close()
+ # determine oxidation state and element name
+ elemstate = re.sub('[A-Za-z]', '', lb[2])
+ for r, o in zip(('dot', 'p', 'm'), ('.', '+', '-')):
+ elemstate = elemstate.replace(o, r)
+ if elemstate == 'p2': # fix wrong name in the source file
+ elemstate = '2p'
+ ename = re.sub('[^A-Za-z]', '', lb[2])
-
-def add_f0_from_xop(db, xopfile):
+ print("{pyname} = Atom('{name}', {num})".format(
+ pyname=ename+elemstate, name=lb[2], num=lb[1]))
+ db.SetMaterial(ename)
+ # make two dummy reads
+ for i in range(2):
+ itf.readline()
+ # read fit parameters
+ lb = itf.readline().decode("utf-8")
+ lb = lb.strip()
+ lb = multiblank.split(lb)
+ a1 = float(lb[0])
+ a2 = float(lb[1])
+ a3 = float(lb[2])
+ a4 = float(lb[3])
+ c = float(lb[4])
+ b1 = float(lb[5])
+ b2 = float(lb[6])
+ b3 = float(lb[7])
+ b4 = float(lb[8])
+ db.SetF0([c, a1, b1, a2, b2, a3, b3, a4, b4], subset=elemstate)
+
+
+def add_f0_from_xop(db, xop):
"""
Read f0 data from f0_xop.dat and add
it to the database.
"""
-
- # parse the xop file
- try:
- xop = open(xopfile, "r")
- except:
- print("cannot open f0 database file")
- return None
-
# some regular expressions
elementstr = re.compile(r"^#S")
multiblank = re.compile(r"\s+")
invalidelem = re.compile(r"[^A-Za-z]")
while True:
- lb = xop.readline()
+ lb = xop.readline().decode("utf-8")
if lb == "":
break
lb = lb.strip()
@@ -498,62 +487,49 @@ def add_f0_from_xop(db, xopfile):
if elementstr.match(lb):
# found new element
lb = multiblank.split(lb)
- ename = lb[2]
- # check if this is not some funny isotope
+ # determine oxidation state and element name
+ elemstate = re.sub('[A-Za-z]', '', lb[2])
+ for r, o in zip(('dot', 'p', 'm'), ('.', '+', '-')):
+ elemstate = elemstate.replace(o, r)
+ ename = re.sub('[^A-Za-z]', '', lb[2])
+
+ print("{pyname} = Atom('{name}', {num})".format(
+ pyname=ename+elemstate, name=lb[2], num=lb[1]))
+ db.SetMaterial(ename)
- if invalidelem.findall(ename) == []:
- print("set element %s" % ename)
- db.SetMaterial(ename)
- # make nine dummy reads
- xop.readline()
- xop.readline()
- xop.readline()
- xop.readline()
- xop.readline()
+ # make nine dummy reads
+ for i in range(9):
xop.readline()
- xop.readline()
- xop.readline()
- xop.readline()
- # read fit parameters
- lb = xop.readline()
- lb = lb.strip()
- lb = multiblank.split(lb)
- a1 = float(lb[0])
- a2 = float(lb[1])
- a3 = float(lb[2])
- a4 = float(lb[3])
- a5 = float(lb[4])
- c = float(lb[5])
- b1 = float(lb[6])
- b2 = float(lb[7])
- b3 = float(lb[8])
- b4 = float(lb[9])
- b5 = float(lb[10])
- db.SetF0([c, a1, b1, a2, b2, a3, b3, a4, b4, a5, b5])
-
- xop.close()
-
-
-def add_f1f2_from_henkedb(db, henkefile):
+ # read fit parameters
+ lb = xop.readline().decode("utf-8")
+ lb = lb.strip()
+ lb = multiblank.split(lb)
+ a1 = float(lb[0])
+ a2 = float(lb[1])
+ a3 = float(lb[2])
+ a4 = float(lb[3])
+ a5 = float(lb[4])
+ c = float(lb[5])
+ b1 = float(lb[6])
+ b2 = float(lb[7])
+ b3 = float(lb[8])
+ b4 = float(lb[9])
+ b5 = float(lb[10])
+ db.SetF0([c, a1, b1, a2, b2, a3, b3, a4, b4, a5, b5])
+
+
+def add_f1f2_from_henkedb(db, hf):
"""
Read f1 and f2 data from Henke database and add
it to the database.
"""
-
- # parse the inter. tab. file
- try:
- hf = open(henkefile, "r")
- except:
- print("cannot open f1f2 database file")
- return None
-
# some regular expressions
elementstr = re.compile(r"^#S")
multiblank = re.compile(r"\s+")
invalidelem = re.compile(r"[^A-Za-z]")
while True:
- lb = hf.readline()
+ lb = hf.readline().decode("utf-8")
if lb == "":
break
lb = lb.strip()
@@ -577,7 +553,7 @@ def add_f1f2_from_henkedb(db, henkefile):
f1_list = []
f2_list = []
while True:
- lb = hf.readline()
+ lb = hf.readline().decode("utf-8")
lb = lb.strip()
lb = multiblank.split(lb)
en = float(lb[0])
@@ -588,33 +564,22 @@ def add_f1f2_from_henkedb(db, henkefile):
f1_list.append(f1)
f2_list.append(f2)
if en == 30000.:
- db.SetF1(en_list, f1_list)
- db.SetF2(en_list, f2_list)
+ db.SetF1F2(en_list, f1_list, f2_list)
break
- hf.close()
-
-def add_f1f2_from_kissel(db, kisselfile):
+def add_f1f2_from_kissel(db, kf):
"""
Read f1 and f2 data from Henke database and add
it to the database.
"""
-
- # parse the f1f2 file
- try:
- kf = open(kisselfile, "r")
- except:
- print("cannot open f1f2 database file")
- return None
-
# some regular expressions
elementstr = re.compile(r"^#S")
multiblank = re.compile(r"\s+")
invalidelem = re.compile(r"[^A-Za-z]")
while True:
- lb = kf.readline()
+ lb = kf.readline().decode("utf-8")
if lb == "":
break
lb = lb.strip()
@@ -638,7 +603,7 @@ def add_f1f2_from_kissel(db, kisselfile):
f1_list = []
f2_list = []
while True:
- lb = kf.readline()
+ lb = kf.readline().decode("utf-8")
lb = lb.strip()
lb = multiblank.split(lb)
try:
@@ -650,15 +615,12 @@ def add_f1f2_from_kissel(db, kisselfile):
f1_list.append(f1)
f2_list.append(f2)
if en == 10000000.:
- db.SetF1(en_list, f1_list)
- db.SetF2(en_list, f2_list)
+ db.SetF1F2(en_list, f1_list, f2_list)
break
except:
print(lb)
break
- kf.close()
-
def add_f1f2_from_ascii_file(db, asciifile, element):
"""
@@ -677,22 +639,14 @@ def add_f1f2_from_ascii_file(db, asciifile, element):
en = af[:, 0]
f1 = af[:, 1]
f2 = af[:, 2]
- db.SetF1(en, f1)
- db.SetF2(en, f2)
+ db.SetF1F2(en, f1, f2)
def add_mass_from_NIST(db, nistfile):
"""
Read atoms standard mass and save it to the database.
+ The mass of the natural isotope mixture is taken from the NIST data!
"""
-
- # parse the nist file
- try:
- nf = open(nistfile, "r")
- except:
- print("cannot open NIST data file")
- return None
-
# some regular expressions
commentline = re.compile(r"^#")
isotope = re.compile(r"^Atomic Number =")
@@ -700,36 +654,37 @@ def add_mass_from_NIST(db, nistfile):
number = re.compile(r"[0-9.]+")
multiblank = re.compile(r"\s+")
- while True:
- lb = nf.readline()
- if lb == "":
- break
- lb = lb.strip()
-
- if isotope.match(lb):
- # found new element
- lb = multiblank.split(lb)
- enum = int(lb[-1])
+ # parse the nist file
+ with open(nistfile, "r") as nf:
+ while True:
lb = nf.readline()
+ if lb == "":
+ break
lb = lb.strip()
- lb = multiblank.split(lb)
- ename = lb[-1]
- print("set element %s" % ename)
- db.SetMaterial(ename)
-
- # read data
- while True:
+ if isotope.match(lb):
+ # found new element
+ lb = multiblank.split(lb)
+ enum = int(lb[-1])
lb = nf.readline()
lb = lb.strip()
- if standardw.match(lb):
- lb = multiblank.split(lb)
- try:
- w = float(number.findall(lb[-1])[0]) # extract weight
- db.SetWeight(w * scipy.constants.atomic_mass)
- break
- except:
- print(lb)
- break
+ lb = multiblank.split(lb)
+ ename = lb[-1]
- nf.close()
+ print("set element %s" % ename)
+ db.SetMaterial(ename)
+
+ # read data
+ while True:
+ lb = nf.readline()
+ lb = lb.strip()
+ if standardw.match(lb):
+ lb = multiblank.split(lb)
+ try:
+ # extract weight
+ w = float(number.findall(lb[-1])[0])
+ db.SetWeight(w * scipy.constants.atomic_mass)
+ break
+ except:
+ print(lb)
+ break
diff --git a/xrayutilities/materials/elements.py b/xrayutilities/materials/elements.py
index cc73305..b8a76ba 100644
--- a/xrayutilities/materials/elements.py
+++ b/xrayutilities/materials/elements.py
@@ -14,99 +14,243 @@
# along with this program; if not, see <http://www.gnu.org/licenses/>.
#
# Copyright (C) 2009 Eugen Wintersberger <eugen.wintersberger at desy.de>
-# Copyright (C) 2010 Dominik Kriegner <dominik.kriegner at gmail.com>
+# Copyright (C) 2010-2015 Dominik Kriegner <dominik.kriegner at gmail.com>
from .lattice import Atom
-Ac = Atom("Ac", 89)
-Ag = Atom("Ag", 47)
-Al = Atom("Al", 13)
-Ar = Atom("Ar", 18)
-As = Atom("As", 33)
-At = Atom("At", 85)
-Au = Atom("Au", 79)
-B = Atom("B", 5)
-Ba = Atom("Ba", 56)
-Be = Atom("Be", 4)
-Bi = Atom("Bi", 83)
-Br = Atom("Br", 35)
-C = Atom("C", 6)
-Ca = Atom("Ca", 20)
-Cd = Atom("Cd", 48)
-Ce = Atom("Ce", 58)
-Cl = Atom("Cl", 17)
-Co = Atom("Co", 27)
-Cr = Atom("Cr", 24)
-Cs = Atom("Cs", 55)
-Cu = Atom("Cu", 29)
-Dy = Atom("Dy", 66)
-Er = Atom("Er", 68)
-Eu = Atom("Eu", 63)
-F = Atom("F", 9)
-Fe = Atom("Fe", 26)
-Fr = Atom("Fr", 87)
-Ga = Atom("Ga", 31)
-Gd = Atom("Gd", 64)
-Ge = Atom("Ge", 32)
-H = Atom("H", 1)
-He = Atom("He", 2)
-Hf = Atom("Hf", 72)
-Hg = Atom("Hg", 80)
-Ho = Atom("Ho", 67)
-I = Atom("I", 53)
-In = Atom("In", 49)
-Ir = Atom("Ir", 77)
-K = Atom("K", 19)
-Kr = Atom("Kr", 36)
-La = Atom("La", 57)
-Li = Atom("Li", 3)
-Lu = Atom("Lu", 71)
-Mg = Atom("Mg", 12)
-Mn = Atom("Mn", 25)
-Mo = Atom("Mo", 42)
-N = Atom("N", 7)
-Na = Atom("Na", 11)
-Nb = Atom("Nb", 41)
-Nd = Atom("Nd", 60)
-Ne = Atom("Ne", 10)
-Ni = Atom("Ni", 28)
-O = Atom("O", 8)
-Os = Atom("Os", 76)
-P = Atom("P", 15)
-Pa = Atom("Pa", 91)
-Pb = Atom("Pb", 82)
-Pd = Atom("Pd", 46)
-Pm = Atom("Pm", 61)
-Po = Atom("Po", 84)
-Pr = Atom("Pr", 59)
-Pt = Atom("Pt", 78)
-Ra = Atom("Ra", 88)
-Rb = Atom("Rb", 37)
-Re = Atom("Re", 75)
-Rh = Atom("Rh", 45)
-Rn = Atom("Rn", 86)
-Ru = Atom("Ru", 44)
-S = Atom("S", 16)
-Sb = Atom("Sb", 51)
-Sc = Atom("Sc", 21)
-Se = Atom("Se", 34)
-Si = Atom("Si", 14)
-Sm = Atom("Sm", 62)
-Sn = Atom("Sn", 50)
-Sr = Atom("Sr", 38)
-Ta = Atom("Ta", 73)
-Tb = Atom("Tb", 65)
-Tc = Atom("Tc", 43)
-Te = Atom("Te", 52)
-Th = Atom("Th", 90)
-Ti = Atom("Ti", 22)
-Tl = Atom("Tl", 81)
-Tm = Atom("Tm", 69)
-U = Atom("U", 92)
-V = Atom("V", 23)
-W = Atom("W", 74)
-Xe = Atom("Xe", 54)
-Y = Atom("Y", 39)
-Yb = Atom("Yb", 70)
-Zn = Atom("Zn", 30)
-Zr = Atom("Zr", 40)
+dummy = Atom('dummy', 0)
+H = Atom('H', 1)
+Hdot = Atom('H.', 1)
+H1m = Atom('H1-', 1)
+D = Atom('D', 1)
+T = Atom('T', 1)
+He = Atom('He', 2)
+Li = Atom('Li', 3)
+Li1p = Atom('Li1+', 3)
+Be = Atom('Be', 4)
+Be2p = Atom('Be2+', 4)
+B = Atom('B', 5)
+C = Atom('C', 6)
+Cdot = Atom('C.', 6)
+N = Atom('N', 7)
+O = Atom('O', 8)
+O1m = Atom('O1-', 8)
+O2mdot = Atom('O2-.', 8)
+F = Atom('F', 9)
+F1m = Atom('F1-', 9)
+Ne = Atom('Ne', 10)
+Na = Atom('Na', 11)
+Na1p = Atom('Na1+', 11)
+Mg = Atom('Mg', 12)
+Mg2p = Atom('Mg2+', 12)
+Al = Atom('Al', 13)
+Al3p = Atom('Al3+', 13)
+Si = Atom('Si', 14)
+Sidot = Atom('Si.', 14)
+Si4p = Atom('Si4+', 14)
+P = Atom('P', 15)
+S = Atom('S', 16)
+Cl = Atom('Cl', 17)
+Cl1m = Atom('Cl1-', 17)
+Ar = Atom('Ar', 18)
+K = Atom('K', 19)
+K1p = Atom('K1+', 19)
+Ca = Atom('Ca', 20)
+Ca2p = Atom('Ca2+', 20)
+Sc = Atom('Sc', 21)
+Sc3p = Atom('Sc3+', 21)
+Ti = Atom('Ti', 22)
+Ti2p = Atom('Ti2+', 22)
+Ti3p = Atom('Ti3+', 22)
+Ti4p = Atom('Ti4+', 22)
+V = Atom('V', 23)
+V2p = Atom('V2+', 23)
+V3p = Atom('V3+', 23)
+V5p = Atom('V5+', 23)
+Cr = Atom('Cr', 24)
+Cr2p = Atom('Cr2+', 24)
+Cr3p = Atom('Cr3+', 24)
+Mn = Atom('Mn', 25)
+Mn2p = Atom('Mn2+', 25)
+Mn3p = Atom('Mn3+', 25)
+Mn4p = Atom('Mn4+', 25)
+Fe = Atom('Fe', 26)
+Fe2p = Atom('Fe2+', 26)
+Fe3p = Atom('Fe3+', 26)
+Co = Atom('Co', 27)
+Co2p = Atom('Co2+', 27)
+Co3p = Atom('Co3+', 27)
+Ni = Atom('Ni', 28)
+Ni2p = Atom('Ni2+', 28)
+Ni3p = Atom('Ni3+', 28)
+Cu = Atom('Cu', 29)
+Cu1p = Atom('Cu1+', 29)
+Cu2p = Atom('Cu2+', 29)
+Zn = Atom('Zn', 30)
+Zn2p = Atom('Zn2+', 30)
+Ga = Atom('Ga', 31)
+Ga3p = Atom('Ga3+', 31)
+Ge = Atom('Ge', 32)
+Ge4p = Atom('Ge4+', 32)
+As = Atom('As', 33)
+Se = Atom('Se', 34)
+Br = Atom('Br', 35)
+Br1m = Atom('Br1-', 35)
+Kr = Atom('Kr', 36)
+Rb = Atom('Rb', 37)
+Rb1p = Atom('Rb1+', 37)
+Sr = Atom('Sr', 38)
+Sr2p = Atom('Sr2+', 38)
+Y = Atom('Y', 39)
+Y3p = Atom('Y3+', 39)
+Zr = Atom('Zr', 40)
+Zr4p = Atom('Zr4+', 40)
+Nb = Atom('Nb', 41)
+Nb3p = Atom('Nb3+', 41)
+Nb5p = Atom('Nb5+', 41)
+Mo = Atom('Mo', 42)
+Mo3p = Atom('Mo3+', 42)
+Mo5p = Atom('Mo5+', 42)
+Mo6p = Atom('Mo6+', 42)
+Tc = Atom('Tc', 43)
+Ru = Atom('Ru', 44)
+Ru3p = Atom('Ru3+', 44)
+Rup4 = Atom('Ru+4', 44)
+Rh = Atom('Rh', 45)
+Rh3p = Atom('Rh3+', 45)
+Rh4p = Atom('Rh4+', 45)
+Pd = Atom('Pd', 46)
+Pd2p = Atom('Pd2+', 46)
+Pd4p = Atom('Pd4+', 46)
+Ag = Atom('Ag', 47)
+Ag1p = Atom('Ag1+', 47)
+Ag2p = Atom('Ag2+', 47)
+Cd = Atom('Cd', 48)
+Cd2p = Atom('Cd2+', 48)
+In = Atom('In', 49)
+In3p = Atom('In3+', 49)
+Sn = Atom('Sn', 50)
+Sn2p = Atom('Sn2+', 50)
+Sn4p = Atom('Sn4+', 50)
+Sb = Atom('Sb', 51)
+Sb3p = Atom('Sb3+', 51)
+Sb5p = Atom('Sb5+', 51)
+Te = Atom('Te', 52)
+I = Atom('I', 53)
+I1m = Atom('I1-', 53)
+Xe = Atom('Xe', 54)
+Cs = Atom('Cs', 55)
+Cs1p = Atom('Cs1+', 55)
+Ba = Atom('Ba', 56)
+Ba2p = Atom('Ba2+', 56)
+La = Atom('La', 57)
+La3p = Atom('La3+', 57)
+Ce = Atom('Ce', 58)
+Ce3p = Atom('Ce3+', 58)
+Ce4p = Atom('Ce4+', 58)
+Pr = Atom('Pr', 59)
+Pr3p = Atom('Pr3+', 59)
+Pr4p = Atom('Pr4+', 59)
+Nd = Atom('Nd', 60)
+Nd3p = Atom('Nd3+', 60)
+Pm = Atom('Pm', 61)
+Pm3p = Atom('Pm3+', 61)
+Sm = Atom('Sm', 62)
+Sm3p = Atom('Sm3+', 62)
+Eu = Atom('Eu', 63)
+Eu2p = Atom('Eu2+', 63)
+Eu3p = Atom('Eu3+', 63)
+Gd = Atom('Gd', 64)
+Gd3p = Atom('Gd3+', 64)
+Tb = Atom('Tb', 65)
+Tb3p = Atom('Tb3+', 65)
+Dy = Atom('Dy', 66)
+Dy3p = Atom('Dy3+', 66)
+Ho = Atom('Ho', 67)
+Ho3p = Atom('Ho3+', 67)
+Er = Atom('Er', 68)
+Er3p = Atom('Er3+', 68)
+Tm = Atom('Tm', 69)
+Tm3p = Atom('Tm3+', 69)
+Yb = Atom('Yb', 70)
+Yb2p = Atom('Yb2+', 70)
+Yb3p = Atom('Yb3+', 70)
+Lu = Atom('Lu', 71)
+Lu3p = Atom('Lu3+', 71)
+Hf = Atom('Hf', 72)
+Hf4p = Atom('Hf4+', 72)
+Ta = Atom('Ta', 73)
+Ta5p = Atom('Ta5+', 73)
+W = Atom('W', 74)
+W6p = Atom('W6+', 74)
+Re = Atom('Re', 75)
+Os = Atom('Os', 76)
+Os4p = Atom('Os4+', 76)
+Ir = Atom('Ir', 77)
+Ir3p = Atom('Ir3+', 77)
+Ir4p = Atom('Ir4+', 77)
+Pt = Atom('Pt', 78)
+Pt2p = Atom('Pt2+', 78)
+Pt4p = Atom('Pt4+', 78)
+Au = Atom('Au', 79)
+Au1p = Atom('Au1+', 79)
+Au3p = Atom('Au3+', 79)
+Hg = Atom('Hg', 80)
+Hg1p = Atom('Hg1+', 80)
+Hg2p = Atom('Hg2+', 80)
+Tl = Atom('Tl', 81)
+Tl1p = Atom('Tl1+', 81)
+Tl3p = Atom('Tl3+', 81)
+Pb = Atom('Pb', 82)
+Pb2p = Atom('Pb2+', 82)
+Pb4p = Atom('Pb4+', 82)
+Bi = Atom('Bi', 83)
+Bi3p = Atom('Bi3+', 83)
+Bi5p = Atom('Bi5+', 83)
+Po = Atom('Po', 84)
+At = Atom('At', 85)
+Rn = Atom('Rn', 86)
+Fr = Atom('Fr', 87)
+Ra = Atom('Ra', 88)
+Ra2p = Atom('Ra2+', 88)
+Ac = Atom('Ac', 89)
+Ac3p = Atom('Ac3+', 89)
+Th = Atom('Th', 90)
+Th4p = Atom('Th4+', 90)
+Pa = Atom('Pa', 91)
+U = Atom('U', 92)
+U3p = Atom('U3+', 92)
+U4p = Atom('U4+', 92)
+U6p = Atom('U6+', 92)
+Np = Atom('Np', 93)
+Np3p = Atom('Np3+', 93)
+Np4p = Atom('Np4+', 93)
+Np6p = Atom('Np6+', 93)
+Pu = Atom('Pu', 94)
+Pu3p = Atom('Pu3+', 94)
+Pu4p = Atom('Pu4+', 94)
+Pu6p = Atom('Pu6+', 94)
+Am = Atom('Am', 95)
+Cm = Atom('Cm', 96)
+Bk = Atom('Bk', 97)
+Cf = Atom('Cf', 98)
+Es = Atom("Es", 99)
+Fm = Atom("Fm", 100)
+Md = Atom("Md", 101)
+No = Atom("No", 102)
+Lr = Atom("Lr", 103)
+Rf = Atom("Rf", 104)
+Db = Atom("Db", 105)
+Sg = Atom("Sg", 106)
+Bh = Atom("Bh", 107)
+Hs = Atom("Hs", 108)
+Mt = Atom("Mt", 109)
+Ds = Atom("Ds", 110)
+Rg = Atom("Rg", 111)
+Cn = Atom("Cn", 112)
+Uut = Atom("Uut", 113)
+Uuq = Atom("Uuq", 114)
+Uup = Atom("Uup", 115)
+Uuh = Atom("Uuh", 116)
+Uus = Atom("Uus", 117)
+Uuo = Atom("Uuo", 118)
diff --git a/xrayutilities/materials/lattice.py b/xrayutilities/materials/lattice.py
index b745b76..c17fec5 100644
--- a/xrayutilities/materials/lattice.py
+++ b/xrayutilities/materials/lattice.py
@@ -17,115 +17,19 @@
# Copyright (C) 2009-2010 Dominik Kriegner <dominik.kriegner at gmail.com>
"""
-module handling crystal lattice structures
+module handling crystal lattice structures. A Lattice consists of unit cell
+parameters and a LatticeBase. It offers methods to calculate the reciprocal
+space position of Bragg peaks and their structure factor.
"""
import numpy
-from numpy.linalg import norm
import numbers
-import atexit
-import os.path
-from . import __path__
-from . import database
+from .atom import Atom
from .. import math
from .. import config
-from .. import utilities
from ..exception import InputError
-_db = database.DataBase(os.path.join(__path__[0], "data", config.DBNAME))
-_db.Open()
-
-
-def _db_cleanup():
- _db.Close()
-
-atexit.register(_db_cleanup)
-
-
-class Atom(object):
-
- def __init__(self, name, num):
- self.name = name
- self.num = num
- _db.SetMaterial(self.name)
- self.weight = _db.weight
-
- def __key__(self):
- """ key function to return the elements number """
- return self.num
-
- def __lt__(self, other_el):
- """ make elements sortable by their key """
- return self.__key__() < other_el.__key__()
-
- def f0(self, q):
- _db.SetMaterial(self.name)
-
- if isinstance(q, numpy.ndarray) or isinstance(q, list):
- d = numpy.zeros((len(q)), dtype=numpy.double)
- for i in range(len(q)):
- d[i] = _db.GetF0(q[i])
-
- return d
- else:
- return _db.GetF0(q)
-
- def f1(self, en="config"):
- if en == "config":
- en = utilities.energy(config.ENERGY)
-
- _db.SetMaterial(self.name)
-
- if isinstance(en, numpy.ndarray) or isinstance(en, list):
- d = numpy.zeros((len(en)), dtype=numpy.double)
- for i in range(len(en)):
- d[i] = _db.GetF1(utilities.energy(en[i]))
-
- return d
- else:
- return _db.GetF1(utilities.energy(en))
-
- def f2(self, en="config"):
- if en == "config":
- en = utilities.energy(config.ENERGY)
-
- _db.SetMaterial(self.name)
-
- if isinstance(en, numpy.ndarray) or isinstance(en, list):
- d = numpy.zeros((len(en)), dtype=numpy.double)
- for i in range(len(en)):
- d[i] = _db.GetF2(utilities.energy(en[i]))
-
- return d
- else:
- return _db.GetF2(utilities.energy(en))
-
- def f(self, q, en="config"):
- """
- function to calculate the atomic structure factor F
-
- Parameter
- ---------
- q: momentum transfer
- en: energy for which F should be calculated, if omitted the value
- from the xrayutilities configuration is used
-
- Returns
- -------
- f (float)
- """
- f = self.f0(norm(q)) + self.f1(en) + 1.j * self.f2(en)
- return f
-
- def __str__(self):
- ostr = self.name
- ostr += " (%2d)" % self.num
- return ostr
-
- def __repr__(self):
- return self.__str__()
-
class LatticeBase(list):
@@ -155,7 +59,7 @@ class LatticeBase(list):
raise TypeError("atom must be an instance of class "
"xrayutilities.materials.Atom")
- if isinstance(pos, list):
+ if isinstance(pos, (list, tuple)):
pos = numpy.array(pos, dtype=numpy.double)
elif isinstance(pos, numpy.ndarray):
pos = pos
@@ -170,7 +74,7 @@ class LatticeBase(list):
raise TypeError("atom must be an instance of class "
"xrayutilities.materials.Atom!")
- if isinstance(pos, list):
+ if isinstance(pos, (list, tuple)):
p = numpy.array(pos, dtype=numpy.double)
elif isinstance(pos, numpy.ndarray):
p = pos
diff --git a/xrayutilities/materials/material.py b/xrayutilities/materials/material.py
index 89bacb0..3e8cff8 100644
--- a/xrayutilities/materials/material.py
+++ b/xrayutilities/materials/material.py
@@ -465,7 +465,7 @@ class Material(object):
exponentf = 3 / 2. * hbar ** 2 * 1.0e20 / \
(m * kb * self.thetaDebye) * (math.Debye1(x) / x + 0.25)
if config.VERBOSITY >= config.DEBUG:
- print("XU.materials.StructureFactor: DWF = exp(-W*q**2) W= %g"
+ print("XU.materials.chih: DWF = exp(-W*q**2) W= %g"
% exponentf)
dwf = numpy.exp(-exponentf * math.VecNorm(q) ** 2)
else:
@@ -636,12 +636,13 @@ class Material(object):
s = 0. + 0.j
# a: atom, p: position, o: occupancy, b: temperatur-factor
+ qnorm = math.VecNorm(q)
for a, p, o, b in self.lattice.base:
r = self.lattice.GetPoint(p)
if temp == 0:
- dwf = numpy.exp(-b * math.VecNorm(q) ** 2 /
+ dwf = numpy.exp(-b * qnorm ** 2 /
(4 * numpy.pi) ** 2)
- f = a.f(q, en) * o
+ f = a.f(qnorm, en) * o
s += f * numpy.exp(-1.j * math.VecDot(q, r)) * dwf
return s
@@ -795,8 +796,7 @@ class Material(object):
except ValueError:
# add atom type to list and calculate the scattering factor
types.append(len(atoms))
- f_q = at[0].f0(qnorm)
- f.append((f_q + at[0].f1(en0) + 1.j * at[0].f2(en0)))
+ f.append(at[0].f(qnorm, en0))
atoms.append(at[0])
s = 0. + 0.j
diff --git a/xrayutilities/materials/predefined_materials.py b/xrayutilities/materials/predefined_materials.py
index cdd4ec6..720ad5a 100644
--- a/xrayutilities/materials/predefined_materials.py
+++ b/xrayutilities/materials/predefined_materials.py
@@ -15,7 +15,7 @@
#
# Copyright (C) 2013,2015 Dominik Kriegner <dominik.kriegner at gmail.com>
-import os
+import os.path
import numpy
from . import __path__
@@ -134,6 +134,8 @@ GeTe = Material(
lattice.GeTeRhombohedral(elements.Ge, elements.Te, 5.996, 88.18, 0.237))
Al = Material("Al", lattice.FCCLattice(elements.Al, 4.04958))
Au = Material("Au", lattice.FCCLattice(elements.Au, 4.0782))
+Fe = Material("Fe", lattice.BCCLattice(elements.Fe, 2.8665))
+Rh = Material("Rh", lattice.FCCLattice(elements.Rh, 3.8034))
V = Material("V", lattice.BCCLattice(elements.V, 3.024))
Ta = Material("Ta", lattice.BCCLattice(elements.Ta, 3.306))
Ag2Se = Material(
diff --git a/xrayutilities/math/__init__.py b/xrayutilities/math/__init__.py
index fbf0de4..6424b9b 100644
--- a/xrayutilities/math/__init__.py
+++ b/xrayutilities/math/__init__.py
@@ -57,6 +57,7 @@ from .functions import PseudoVoigt1dArea
from .functions import multPeak1d
from .functions import multPeak2d
+from .fit import linregress
from .fit import fit_peak2d
from .fit import gauss_fit
from .fit import peak_fit
diff --git a/xrayutilities/math/fit.py b/xrayutilities/math/fit.py
index 12d0b5e..a19db4e 100644
--- a/xrayutilities/math/fit.py
+++ b/xrayutilities/math/fit.py
@@ -13,7 +13,7 @@
# You should have received a copy of the GNU General Public License
# along with this program; if not, see <http://www.gnu.org/licenses/>.
#
-# Copyright (C) 2012, 2014 Dominik Kriegner <dominik.kriegner at gmail.com>
+# Copyright (C) 2012-2015 Dominik Kriegner <dominik.kriegner at gmail.com>
"""
module with a function wrapper to scipy.optimize.leastsq
for fitting of a 2D function to a peak or a 1D Gauss fit with
@@ -31,14 +31,35 @@ from .. import config
from .. exception import InputError
from .functions import Gauss1d, Gauss1d_der_x, Gauss1d_der_p
from .functions import Lorentz1d, Lorentz1d_der_x, Lorentz1d_der_p
-from .functions import PseudoVoigt1d
+from .functions import PseudoVoigt1d, PseudoVoigt1dasym
-try:
- from matplotlib import pyplot as plt
-except ImportError:
- if config.VERBOSITY >= config.INFO_ALL:
- print("XU.analysis.sample_align: warning; plotting functionality not"
- "available")
+
+def linregress(x, y):
+ """
+ fast linregress to avoid usage of scipy.stats which is slow!
+
+ Parameters
+ ----------
+ x,y: data coordinates and values
+
+ Returns
+ -------
+ p, rsq: parameters of the linear fit (slope, offest) and the R^2 value
+
+ Example
+ -------
+ >>> (k, d), R2 = xu.math.linregress(x, y)
+ """
+ p = numpy.polyfit(x, y, 1)
+
+ # calculation of r-squared
+ f = numpy.polyval(p, x)
+ fbar = numpy.sum(y) / len(y)
+ ssreg = numpy.sum((f-fbar)**2)
+ sstot = numpy.sum((y - fbar)**2)
+ rsq = ssreg / sstot
+
+ return p, rsq
def peak_fit(xdata, ydata, iparams=[], peaktype='Gauss', maxit=300,
@@ -56,7 +77,8 @@ def peak_fit(xdata, ydata, iparams=[], peaktype='Gauss', maxit=300,
keyword parameters:
iparams: initial paramters for the fit,
determined automatically if not specified
- peaktype: type of peak to fit ('Gauss','Lorentz','PseudoVoigt')
+ peaktype: type of peak to fit: 'Gauss', 'Lorentz', 'PseudoVoigt',
+ 'PseudoVoigtAsym'
maxit: maximal iteration number of the fit
background: type of background, either 'constant' or 'linear'
plot: flag to ask for a plot to visually judge the fit
@@ -67,13 +89,21 @@ def peak_fit(xdata, ydata, iparams=[], peaktype='Gauss', maxit=300,
-------
params,sd_params,itlim[,fitfunc]
- the parameters as defined in function Gauss1d/Lorentz1d or
- PseudoVoigt1d(x, *param). In the case of linear background one more
+ the parameters as defined in function Gauss1d/Lorentz1d/PseudoVoigt1d/
+ PseudoVoigt1dasym(x, *param). In the case of linear background one more
parameter is included! For every parameter the corresponding errors of the
fit 'sd_params' are returned. A boolean flag 'itlim', which is False in
the case of a successful fit is added by default. Further the function
used in the fit can be returned (see func_out).
"""
+ if plot:
+ try:
+ from matplotlib import pyplot as plt
+ except ImportError:
+ if config.VERBOSITY >= config.INFO_ALL:
+ print("XU.math.peak_fit: Warning: plot "
+ "functionality not available")
+ plot = False
gfunc_dx = None
gfunc_dp = None
@@ -101,6 +131,12 @@ def peak_fit(xdata, ydata, iparams=[], peaktype='Gauss', maxit=300,
return PseudoVoigt1d(x, *param) + x * param[-1]
else:
def gfunc(param, x): return PseudoVoigt1d(x, *param)
+ elif peaktype == 'PseudoVoigtAsym':
+ if background == 'linear':
+ def gfunc(param, x):
+ return PseudoVoigt1dasym(x, *param) + x * param[-1]
+ else:
+ def gfunc(param, x): return PseudoVoigt1dasym(x, *param)
else:
raise InputError("keyword rgument peaktype takes invalid value!")
@@ -119,7 +155,9 @@ def peak_fit(xdata, ydata, iparams=[], peaktype='Gauss', maxit=300,
numpy.median(ydata)]
if peaktype in ['Lorentz', 'PseudoVoigt']:
iparams[1] *= 1/(2 * numpy.sqrt(2 * numpy.log(2)))
- if peaktype == 'PseudoVoigt':
+ if peaktype == 'PseudoVoigtAsym':
+ iparams.insert(1, iparams[1])
+ if peaktype in ['PseudoVoigt', 'PseudoVoigtAsym']:
# set ETA parameter to be between Gauss and Lorentz shape
iparams.append(0.5)
if background == 'linear':
@@ -153,17 +191,11 @@ def peak_fit(xdata, ydata, iparams=[], peaktype='Gauss', maxit=300,
"do not trust the result!")
if plot:
- try:
- plt.__name__
- except NameError:
- print("XU.math.peak_fit: Warning: plot functionality not "
- "available")
- else:
- plt.figure('XU:peak_fit')
- plt.plot(xdata, ydata, 'ko', label='data', mew=2)
- plt.plot(xdata, gfunc(fit.beta, xdata), 'r-',
- label='%s-fit' % peaktype)
- plt.legend()
+ plt.figure('XU:peak_fit')
+ plt.plot(xdata, ydata, 'ko', label='data', mew=2)
+ plt.plot(xdata, gfunc(fit.beta, xdata), 'r-',
+ label='%s-fit' % peaktype)
+ plt.legend()
if func_out:
return fit.beta, fit.sd_beta, itlim, lambda x: gfunc(fit.beta, x)
@@ -480,12 +512,12 @@ def multPeakPlot(x, fpos, fwidth, famp, background, dranges=None,
fig: matplotlib figure number or name
fact: factor to use as multiplicator in the plot
"""
-
try:
- plt.__name__
- except NameError:
- print("XU.math.multPeakPlot: Warning: plot functionality not "
- "available")
+ from matplotlib import pyplot as plt
+ except ImportError:
+ if config.VERBOSITY >= config.INFO_ALL:
+ print("XU.math.multPeakPlot: Warning: plot "
+ "functionality not available")
return
plt.figure(fig)
diff --git a/xrayutilities/normalize.py b/xrayutilities/normalize.py
index 2c2addb..73b30a7 100644
--- a/xrayutilities/normalize.py
+++ b/xrayutilities/normalize.py
@@ -166,7 +166,7 @@ class IntensityNormalizer(object):
single CCD frames) for count time and absorber factors
the class must be supplied with a absorber correction function
and works with data structures provided by xrayutilities.io classes or the
- corresponding objects from hdf5 files read by pytables
+ corresponding objects from hdf5 files
"""
def __init__(self, det, **keyargs):
diff --git a/xrayutilities/tests/test_HXRD.py b/xrayutilities/tests/test_HXRD.py
index e8798d0..35f1e15 100644
--- a/xrayutilities/tests/test_HXRD.py
+++ b/xrayutilities/tests/test_HXRD.py
@@ -15,19 +15,20 @@
#
# Copyright (C) 2014 Dominik Kriegner <dominik.kriegner at gmail.com>
+import unittest
+
import xrayutilities as xu
import numpy
-import unittest
class TestQ2Ang_HXRD(unittest.TestCase):
-
- def setUp(self):
- self.mat = xu.materials.GeTe
+ @classmethod
+ def setUpClass(cls):
+ cls.mat = xu.materials.GeTe
qconv = xu.QConversion(['x+', 'y+', 'z-'], 'x+', [0, 1, 0])
- inp = numpy.cross(self.mat.Q(1, -1, 0), self.mat.Q(1, 1, 1))
- self.hxrd = xu.HXRD(inp, self.mat.Q(1, 1, 1), qconv=qconv)
- self.hkltest = (1, 3, 2)
+ inp = numpy.cross(cls.mat.Q(1, -1, 0), cls.mat.Q(1, 1, 1))
+ cls.hxrd = xu.HXRD(inp, cls.mat.Q(1, 1, 1), qconv=qconv)
+ cls.hkltest = (1, 3, 2)
def test_Q2Ang_hxrd_point(self):
ang = self.hxrd.Q2Ang(self.mat.Q(self.hkltest))
diff --git a/xrayutilities/tests/test_NonCOP.py b/xrayutilities/tests/test_NonCOP.py
index 9f9f73c..3622939 100644
--- a/xrayutilities/tests/test_NonCOP.py
+++ b/xrayutilities/tests/test_NonCOP.py
@@ -15,18 +15,19 @@
#
# Copyright (C) 2014 Dominik Kriegner <dominik.kriegner at gmail.com>
+import unittest
+
import xrayutilities as xu
import numpy
-import unittest
class TestQ2Ang_nonCOP(unittest.TestCase):
-
- def setUp(self):
- self.mat = xu.materials.Al2O3
- self.hxrd = xu.NonCOP(self.mat.Q(1, 1, 0), self.mat.Q(0, 0, 1))
- self.hkltest = (1, 2, 3)
- self.hkltest2 = (-1.5, 3.1, 3)
+ @classmethod
+ def setUpClass(cls):
+ cls.mat = xu.materials.Al2O3
+ cls.hxrd = xu.NonCOP(cls.mat.Q(1, 1, 0), cls.mat.Q(0, 0, 1))
+ cls.hkltest = (1, 2, 3)
+ cls.hkltest2 = (-1.5, 3.1, 3)
def test_Q2Ang_nonCOP_point(self):
ang = self.hxrd.Q2Ang(self.mat.Q(self.hkltest))
diff --git a/xrayutilities/tests/test_blockaverage.py b/xrayutilities/tests/test_blockaverage.py
index 25547bc..5c9bd02 100644
--- a/xrayutilities/tests/test_blockaverage.py
+++ b/xrayutilities/tests/test_blockaverage.py
@@ -15,9 +15,10 @@
#
# Copyright (C) 2014 Dominik Kriegner <dominik.kriegner at gmail.com>
+import unittest
+
import xrayutilities as xu
import numpy
-import unittest
class TestBlockAverageFunctions(unittest.TestCase):
diff --git a/xrayutilities/tests/test_database.py b/xrayutilities/tests/test_database.py
new file mode 100644
index 0000000..d9aacdb
--- /dev/null
+++ b/xrayutilities/tests/test_database.py
@@ -0,0 +1,52 @@
+# This file is part of xrayutilities.
+#
+# xrayutilities is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, see <http://www.gnu.org/licenses/>.
+#
+# Copyright (C) 2015 Dominik Kriegner <dominik.kriegner at gmail.com>
+
+import unittest
+import math
+
+import xrayutilities as xu
+import numpy
+
+
+class TestDatabase(unittest.TestCase):
+ @classmethod
+ def setUpClass(cls):
+ cls.el = xu.materials.elements.dummy
+
+ def test_db_f0(self):
+ f0 = self.el.f0(0)
+ self.assertAlmostEqual(f0, 1.0, places=10)
+
+ def test_db_f1_neg(self):
+ f1 = self.el.f1(-1)
+ self.assertTrue(math.isnan(f1))
+
+ def test_db_f1(self):
+ f1 = self.el.f1(1000)
+ self.assertAlmostEqual(f1, 0.0, places=10)
+
+ def test_db_f2_neg(self):
+ f2 = self.el.f2(-1)
+ self.assertTrue(math.isnan(f2))
+
+ def test_db_f2(self):
+ f2 = self.el.f2(1000)
+ self.assertAlmostEqual(f2, 0.0, places=10)
+
+
+if __name__ == '__main__':
+ unittest.main()
diff --git a/xrayutilities/tests/test_functions.py b/xrayutilities/tests/test_functions.py
index b3c3ebe..513f73b 100644
--- a/xrayutilities/tests/test_functions.py
+++ b/xrayutilities/tests/test_functions.py
@@ -15,22 +15,23 @@
#
# Copyright (C) 2014 Dominik Kriegner <dominik.kriegner at gmail.com>
+import unittest
+
import xrayutilities as xu
import numpy
-import unittest
from scipy.integrate import quad, dblquad
class TestMathFunctions(unittest.TestCase):
-
- def setUp(self):
+ @classmethod
+ def setUpClass(cls):
amp = numpy.random.rand(1)[0]
fwhm = numpy.random.rand(1)[0] * 1.5 + 0.1
- self.x = numpy.arange(-3, 3, 0.0003)
- self.p = [0., fwhm, amp, 0.]
- self.p2d = [0., 0., fwhm, fwhm, amp, 0.,
- 2 * numpy.pi * numpy.random.rand(1)]
- self.sigma = fwhm / (2 * numpy.sqrt(2 * numpy.log(2)))
+ cls.x = numpy.arange(-3, 3, 0.0003)
+ cls.p = [0., fwhm, amp, 0.]
+ cls.p2d = [0., 0., fwhm, fwhm, amp, 0.,
+ 2 * numpy.pi * numpy.random.rand(1)]
+ cls.sigma = fwhm / (2 * numpy.sqrt(2 * numpy.log(2)))
def test_gauss1dwidth(self):
p = numpy.copy(self.p)
diff --git a/xrayutilities/tests/test_getang.py b/xrayutilities/tests/test_getang.py
new file mode 100644
index 0000000..8ab9ad3
--- /dev/null
+++ b/xrayutilities/tests/test_getang.py
@@ -0,0 +1,51 @@
+# This file is part of xrayutilities.
+#
+# xrayutilities is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, see <http://www.gnu.org/licenses/>.
+#
+# Copyright (C) 2014 Dominik Kriegner <dominik.kriegner at gmail.com>
+
+import unittest
+
+import xrayutilities as xu
+import numpy
+
+
+class TestGetAngles(unittest.TestCase):
+ chi111 = 70.528779365509308
+
+ @classmethod
+ def setUpClass(cls):
+ amp = numpy.random.rand(1)[0]
+ fwhm = numpy.random.rand(1)[0] * 1.5 + 0.1
+ cls.x = numpy.arange(-3, 3, 0.0003)
+ cls.p = [0., fwhm, amp, 0.]
+ cls.p2d = [0., 0., fwhm, fwhm, amp, 0.,
+ 2 * numpy.pi * numpy.random.rand(1)]
+ cls.sigma = fwhm / (2 * numpy.sqrt(2 * numpy.log(2)))
+
+ def test_getang111(self):
+ chi, phi = xu.analysis.getangles([1, 1, -1], [1, 1, 1], [2, 2, -4])
+ self.assertAlmostEqual(chi, self.chi111, places=10)
+ self.assertAlmostEqual(phi, 0, places=10)
+
+ def test_getang001(self):
+ chi, phi = xu.analysis.getangles([1, 1, 0], [0, 1, 0], [1, 0, 0])
+ self.assertAlmostEqual(chi, 45, places=10)
+ self.assertAlmostEqual(phi, 0, places=10)
+ chi, phi = xu.analysis.getangles([1, 0, 1], [0, 1, 0], [1, 0, 0])
+ self.assertAlmostEqual(chi, 90, places=10)
+ self.assertAlmostEqual(phi, -45, places=10)
+
+if __name__ == '__main__':
+ unittest.main()
diff --git a/xrayutilities/tests/test_gridder1d.py b/xrayutilities/tests/test_gridder1d.py
index aaaf84e..c247adb 100644
--- a/xrayutilities/tests/test_gridder1d.py
+++ b/xrayutilities/tests/test_gridder1d.py
@@ -15,21 +15,22 @@
#
# Copyright (C) 2014 Dominik Kriegner <dominik.kriegner at gmail.com>
+import unittest
+
import xrayutilities as xu
import numpy
-import unittest
class TestGridder1D(unittest.TestCase):
-
- def setUp(self):
- self.num = numpy.random.randint(10, 99)
- self.xmin = 1
- self.xmax = self.num
- self.x = numpy.linspace(self.xmin, self.xmax, num=self.num)
- self.data = numpy.random.rand(self.num)
- self.gridder = xu.Gridder1D(self.num)
- self.gridder(self.x, self.data)
+ @classmethod
+ def setUpClass(cls):
+ cls.num = numpy.random.randint(10, 99)
+ cls.xmin = 1
+ cls.xmax = cls.num
+ cls.x = numpy.linspace(cls.xmin, cls.xmax, num=cls.num)
+ cls.data = numpy.random.rand(cls.num)
+ cls.gridder = xu.Gridder1D(cls.num)
+ cls.gridder(cls.x, cls.data)
def test_gridder1d_axis(self):
# test length of xaxis
diff --git a/xrayutilities/tests/test_gridder2d.py b/xrayutilities/tests/test_gridder2d.py
index 6f10f2b..d670900 100644
--- a/xrayutilities/tests/test_gridder2d.py
+++ b/xrayutilities/tests/test_gridder2d.py
@@ -15,24 +15,25 @@
#
# Copyright (C) 2014 Dominik Kriegner <dominik.kriegner at gmail.com>
+import unittest
+
import xrayutilities as xu
import numpy
-import unittest
class TestGridder2D(unittest.TestCase):
-
- def setUp(self):
- self.nx = 10
+ @classmethod
+ def setUpClass(cls):
+ cls.nx = 10
# do not change this here unless you fix also the tests cases
- self.ny = 19
- self.xmin = 1
- self.xmax = 10
- self.x = numpy.linspace(self.xmin, self.xmax, num=self.nx)
- self.y = self.x.copy()
- self.data = numpy.random.rand(self.nx)
- self.gridder = xu.Gridder2D(self.nx, self.ny)
- self.gridder(self.x, self.y, self.data)
+ cls.ny = 19
+ cls.xmin = 1
+ cls.xmax = 10
+ cls.x = numpy.linspace(cls.xmin, cls.xmax, num=cls.nx)
+ cls.y = cls.x.copy()
+ cls.data = numpy.random.rand(cls.nx)
+ cls.gridder = xu.Gridder2D(cls.nx, cls.ny)
+ cls.gridder(cls.x, cls.y, cls.data)
def test_gridder2d_xaxis(self):
# test length of xaxis
diff --git a/xrayutilities/tests/test_gridder2d.py b/xrayutilities/tests/test_gridder2dlist.py
similarity index 51%
copy from xrayutilities/tests/test_gridder2d.py
copy to xrayutilities/tests/test_gridder2dlist.py
index 6f10f2b..561e71b 100644
--- a/xrayutilities/tests/test_gridder2d.py
+++ b/xrayutilities/tests/test_gridder2dlist.py
@@ -13,44 +13,27 @@
# You should have received a copy of the GNU General Public License
# along with this program; if not, see <http://www.gnu.org/licenses/>.
#
-# Copyright (C) 2014 Dominik Kriegner <dominik.kriegner at gmail.com>
+# Copyright (C) 2015 Dominik Kriegner <dominik.kriegner at gmail.com>
-import xrayutilities as xu
-import numpy
import unittest
+import xrayutilities as xu
+import numpy
-class TestGridder2D(unittest.TestCase):
- def setUp(self):
- self.nx = 10
+class TestGridder2DList(unittest.TestCase):
+ @classmethod
+ def setUpClass(cls):
+ cls.nx = 10
# do not change this here unless you fix also the tests cases
- self.ny = 19
- self.xmin = 1
- self.xmax = 10
- self.x = numpy.linspace(self.xmin, self.xmax, num=self.nx)
- self.y = self.x.copy()
- self.data = numpy.random.rand(self.nx)
- self.gridder = xu.Gridder2D(self.nx, self.ny)
- self.gridder(self.x, self.y, self.data)
-
- def test_gridder2d_xaxis(self):
- # test length of xaxis
- self.assertEqual(len(self.gridder.xaxis), self.nx)
- # test values of xaxis
- for i in range(self.nx):
- self.assertAlmostEqual(self.gridder.xaxis[i], self.x[i], places=12)
-
- def test_gridder2d_yaxis(self):
- # test length of yaxis
- self.assertEqual(len(self.gridder.yaxis), self.ny)
- # test end values of yaxis
- self.assertAlmostEqual(self.gridder.yaxis[0], self.y[0], places=12)
- self.assertAlmostEqual(self.gridder.yaxis[-1], self.y[-1], places=12)
- self.assertAlmostEqual(
- self.gridder.yaxis[1] - self.gridder.yaxis[0],
- (self.xmax - self.xmin) / float(self.ny - 1),
- places=12)
+ cls.ny = 19
+ cls.xmin = 1
+ cls.xmax = 10
+ cls.x = numpy.linspace(cls.xmin, cls.xmax, num=cls.nx)
+ cls.y = cls.x.copy()
+ cls.data = numpy.random.rand(cls.nx)
+ cls.gridder = xu.Gridder2DList(cls.nx, cls.ny)
+ cls.gridder(cls.x, cls.y, cls.data)
def test_gridder2d_data(self):
# test shape of data
@@ -64,10 +47,10 @@ class TestGridder2D(unittest.TestCase):
if k == 2 * j:
self.assertAlmostEqual(
self.gridder.data[j, 2 * j],
- self.data[j],
+ [self.data[j], ],
places=12)
else:
- self.assertEqual(self.gridder.data[j, k], 0.)
+ self.assertEqual(self.gridder.data[j, k], [])
if __name__ == '__main__':
unittest.main()
diff --git a/xrayutilities/tests/test_gridder3d.py b/xrayutilities/tests/test_gridder3d.py
index 22cea9b..36617a6 100644
--- a/xrayutilities/tests/test_gridder3d.py
+++ b/xrayutilities/tests/test_gridder3d.py
@@ -15,26 +15,27 @@
#
# Copyright (C) 2014 Dominik Kriegner <dominik.kriegner at gmail.com>
+import unittest
+
import xrayutilities as xu
import numpy
-import unittest
class TestGridder3D(unittest.TestCase):
-
- def setUp(self):
- self.nx = 10
+ @classmethod
+ def setUpClass(cls):
+ cls.nx = 10
# do not change this here unless you fix also the tests cases
- self.ny = 19
- self.nz = 10
- self.xmin = 1
- self.xmax = 10
- self.x = numpy.linspace(self.xmin, self.xmax, num=self.nx)
- self.y = self.x.copy()
- self.z = self.x.copy()
- self.data = numpy.random.rand(self.nx)
- self.gridder = xu.Gridder3D(self.nx, self.ny, self.nz)
- self.gridder(self.x, self.y, self.z, self.data)
+ cls.ny = 19
+ cls.nz = 10
+ cls.xmin = 1
+ cls.xmax = 10
+ cls.x = numpy.linspace(cls.xmin, cls.xmax, num=cls.nx)
+ cls.y = cls.x.copy()
+ cls.z = cls.x.copy()
+ cls.data = numpy.random.rand(cls.nx)
+ cls.gridder = xu.Gridder3D(cls.nx, cls.ny, cls.nz)
+ cls.gridder(cls.x, cls.y, cls.z, cls.data)
def test_gridder3d_xaxis(self):
# test length of xaxis
diff --git a/xrayutilities/tests/test_io_cbf.py b/xrayutilities/tests/test_io_cbf.py
new file mode 100644
index 0000000..a0d0000
--- /dev/null
+++ b/xrayutilities/tests/test_io_cbf.py
@@ -0,0 +1,79 @@
+# This file is part of xrayutilities.
+#
+# xrayutilities is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, see <http://www.gnu.org/licenses/>.
+#
+# Copyright (C) 2015 Dominik Kriegner <dominik.kriegner at gmail.com>
+
+import os.path
+import unittest
+
+import xrayutilities as xu
+import numpy
+import h5py
+
+testfile = 'eiger.cbf'
+datadir = 'data'
+fullfilename = os.path.join(datadir, testfile)
+
+
+ at unittest.skipIf(not os.path.isfile(fullfilename),
+ "additional test data needed (http://xrayutilities.sf.net)")
+class TestIO_CBF(unittest.TestCase):
+ dshape = (1065, 1030)
+ dmax = 1576.0
+ dmin = 0.0
+ tpos = (500, 500)
+ dtpos = 2.0
+ h5file = '_test_cbf.h5'
+
+ @classmethod
+ def setUpClass(cls):
+ cls.cbffile = xu.io.CBFFile(testfile, path=datadir)
+ cls.data = cls.cbffile.data
+
+ def tearDown(self):
+ try:
+ os.remove(self.h5file)
+ except:
+ pass
+
+ def test_datashape(self):
+ self.assertEqual(self.dshape, self.data.shape)
+
+ def test_datavalues(self):
+ self.assertAlmostEqual(self.dmax, self.data.max(), places=10)
+ self.assertAlmostEqual(self.dmin, self.data.min(), places=10)
+ self.assertAlmostEqual(self.dtpos,
+ self.data[self.tpos[0], self.tpos[1]],
+ places=10)
+
+ def test_savehdf5(self):
+ self.cbffile.Save2HDF5(self.h5file)
+ with h5py.File(self.h5file) as h5f:
+ h5d = h5f[list(h5f.keys())[0]]
+ h5d = numpy.asarray(h5d)
+ self.assertTrue(numpy.all(h5d == self.data))
+
+ def test_CBFDirectory(self):
+ ed = xu.io.CBFDirectory(datadir, 'cbf')
+ ed.Save2HDF5(self.h5file)
+ with h5py.File(self.h5file) as h5f:
+ h5g = h5f[datadir]
+ h5d = h5g[list(h5g.keys())[0]]
+ h5d = numpy.asarray(h5d)
+ self.assertTrue(numpy.all(h5d == self.data))
+
+
+if __name__ == '__main__':
+ unittest.main()
diff --git a/xrayutilities/tests/test_io_edf.py b/xrayutilities/tests/test_io_edf.py
new file mode 100644
index 0000000..c8cf88a
--- /dev/null
+++ b/xrayutilities/tests/test_io_edf.py
@@ -0,0 +1,79 @@
+# This file is part of xrayutilities.
+#
+# xrayutilities is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, see <http://www.gnu.org/licenses/>.
+#
+# Copyright (C) 2015 Dominik Kriegner <dominik.kriegner at gmail.com>
+
+import os.path
+import unittest
+
+import xrayutilities as xu
+import numpy
+import h5py
+
+testfile = 'esrf.edf.gz'
+datadir = 'data'
+fullfilename = os.path.join(datadir, testfile)
+
+
+ at unittest.skipIf(not os.path.isfile(fullfilename),
+ "additional test data needed (http://xrayutilities.sf.net)")
+class TestIO_EDF(unittest.TestCase):
+ dshape = (2048, 2048)
+ dmax = 60134
+ dmin = 72
+ tpos = (500, 500)
+ dtpos = 2349
+ h5file = '_test_edf.h5'
+
+ @classmethod
+ def setUpClass(cls):
+ cls.edffile = xu.io.EDFFile(testfile, path=datadir)
+ cls.data = cls.edffile.data
+
+ def tearDown(self):
+ try:
+ os.remove(self.h5file)
+ except:
+ pass
+
+ def test_datashape(self):
+ self.assertEqual(self.dshape, self.data.shape)
+
+ def test_datavalues(self):
+ self.assertAlmostEqual(self.dmax, self.data.max(), places=10)
+ self.assertAlmostEqual(self.dmin, self.data.min(), places=10)
+ self.assertAlmostEqual(self.dtpos,
+ self.data[self.tpos[0], self.tpos[1]],
+ places=10)
+
+ def test_savehdf5(self):
+ self.edffile.Save2HDF5(self.h5file)
+ with h5py.File(self.h5file) as h5f:
+ h5d = h5f[list(h5f.keys())[0]]
+ h5d = numpy.asarray(h5d)
+ self.assertTrue(numpy.all(h5d == self.data))
+
+ def test_EDFDirectory(self):
+ ed = xu.io.EDFDirectory(datadir, 'edf.gz')
+ ed.Save2HDF5(self.h5file)
+ with h5py.File(self.h5file) as h5f:
+ h5g = h5f[datadir]
+ h5d = h5g[list(h5g.keys())[0]]
+ h5d = numpy.asarray(h5d)
+ self.assertTrue(numpy.all(h5d == self.data))
+
+
+if __name__ == '__main__':
+ unittest.main()
diff --git a/xrayutilities/tests/test_io_esg.py b/xrayutilities/tests/test_io_esg.py
new file mode 100644
index 0000000..18d27f5
--- /dev/null
+++ b/xrayutilities/tests/test_io_esg.py
@@ -0,0 +1,59 @@
+# This file is part of xrayutilities.
+#
+# xrayutilities is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, see <http://www.gnu.org/licenses/>.
+#
+# Copyright (C) 2015 Dominik Kriegner <dominik.kriegner at gmail.com>
+
+import os.path
+import unittest
+
+import xrayutilities as xu
+import numpy
+
+testfile = 'sc.esg'
+datadir = 'data'
+fullfilename = os.path.join(datadir, testfile)
+
+
+ at unittest.skipIf(not os.path.isfile(fullfilename),
+ "additional test data needed (http://xrayutilities.sf.net)")
+class TestIO_ESG(unittest.TestCase):
+ dshape = (602, 4096)
+ dmax = 69282.0
+ dmin = 0.0
+ motorname = '_pd_meas_angle_omega'
+ motmin = 2.0
+ motmax = 20.0
+ dtpos = 9.0
+ tpos = (200, 600)
+
+ @classmethod
+ def setUpClass(cls):
+ cls.esgfile = xu.io.pdESG(fullfilename)
+
+ def test_datashape(self):
+ self.assertEqual(self.dshape, self.esgfile.data.shape)
+
+ def test_datavalues(self):
+ motor = self.esgfile.fileheader[self.motorname]
+ counter = self.esgfile.data
+ self.assertAlmostEqual(self.motmax, motor.max(), places=6)
+ self.assertAlmostEqual(self.motmin, motor.min(), places=6)
+ self.assertAlmostEqual(self.dmax, counter.max(), places=6)
+ self.assertAlmostEqual(self.dmin, counter.min(), places=6)
+ self.assertAlmostEqual(counter[self.tpos[0], self.tpos[1]], self.dtpos)
+
+
+if __name__ == '__main__':
+ unittest.main()
diff --git a/xrayutilities/tests/test_io_fio.py b/xrayutilities/tests/test_io_fio.py
new file mode 100644
index 0000000..3a43851
--- /dev/null
+++ b/xrayutilities/tests/test_io_fio.py
@@ -0,0 +1,91 @@
+# This file is part of xrayutilities.
+#
+# xrayutilities is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, see <http://www.gnu.org/licenses/>.
+#
+# Copyright (C) 2015 Dominik Kriegner <dominik.kriegner at gmail.com>
+
+import os.path
+import unittest
+
+import xrayutilities as xu
+import numpy
+
+testfile = 'p08_00019.FIO'
+datadir = 'data'
+fullfilename = os.path.join(datadir, testfile)
+
+
+ at unittest.skipIf(not os.path.isfile(fullfilename),
+ "additional test data needed (http://xrayutilities.sf.net)")
+class TestIO_FIO(unittest.TestCase):
+ dshape = (601,)
+ dmax = 2272108.0
+ dmin = 66133.0
+ dmaxcorr = 216583893672.0
+ dmincorr = 0.0
+ motmax = 8.000001
+ motmin = 0.0
+ tpos = 300
+ dtpos = 1278952.0
+ motorname = 'Motor_TT'
+ countername = 'MythenIntegral'
+ h5file = '_test_fio.h5'
+ P08_normalizer = xu.IntensityNormalizer(
+ "MCA",
+ time='CountingTime',
+ mon='MonitorEnergyWindow',
+ absfun=lambda d: d['AttenuationFactor'])
+
+ @classmethod
+ def setUpClass(cls):
+ scanname = os.path.splitext(testfile)[0]
+ mcatmp = os.path.join(datadir, scanname, scanname+"_mythen_%i.raw")
+ cls.fiofile = xu.io.SPECTRAFile(fullfilename, mcatmp=mcatmp)
+ cls.sdata = cls.fiofile.data
+ cls.motor = cls.sdata[cls.motorname]
+ cls.inte = cls.sdata[cls.countername]
+ cls.fiofile.Save2HDF5(cls.h5file, scanname)
+ [cls.h5tt, cls.h5int], cls.h5data = xu.io.geth5_spectra_map(
+ cls.h5file, [19], cls.motorname, cls.countername)
+
+ @classmethod
+ def tearDownClass(cls):
+ try:
+ os.remove(cls.h5file)
+ except:
+ pass
+
+ def test_datashape(self):
+ self.assertEqual(self.dshape, self.sdata[self.motorname].shape)
+ self.assertEqual(self.dshape, self.sdata[self.countername].shape)
+
+ def test_datavalues(self):
+ self.assertAlmostEqual(self.motmax, self.motor.max(), places=6)
+ self.assertAlmostEqual(self.motmin, self.motor.min(), places=6)
+ self.assertAlmostEqual(self.dmax, self.inte.max(), places=6)
+ self.assertAlmostEqual(self.dmin, self.inte.min(), places=6)
+ self.assertAlmostEqual(self.dtpos, self.inte[self.tpos], places=6)
+
+ def test_hdf5file(self):
+ self.assertTrue(numpy.all(self.inte == self.h5int))
+ self.assertTrue(numpy.all(self.motor == self.h5tt))
+
+ def test_normalizer(self):
+ mcac = self.P08_normalizer(self.h5data)
+ self.assertAlmostEqual(self.dmaxcorr, mcac.max(), places=6)
+ self.assertAlmostEqual(self.dmincorr, mcac.min(), places=6)
+
+
+if __name__ == '__main__':
+ unittest.main()
diff --git a/xrayutilities/tests/test_io_nja.py b/xrayutilities/tests/test_io_nja.py
new file mode 100644
index 0000000..183ff61
--- /dev/null
+++ b/xrayutilities/tests/test_io_nja.py
@@ -0,0 +1,64 @@
+# This file is part of xrayutilities.
+#
+# xrayutilities is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, see <http://www.gnu.org/licenses/>.
+#
+# Copyright (C) 2015 Dominik Kriegner <dominik.kriegner at gmail.com>
+
+import os.path
+import unittest
+
+import xrayutilities as xu
+import numpy
+
+xu.config.VERBOSITY = 0 # make no output during test
+testfile = 'seifert.nja.bz2'
+datadir = 'data'
+fullfilename = os.path.join(datadir, testfile)
+
+
+ at unittest.skipIf(not os.path.isfile(fullfilename),
+ "additional test data needed (http://xrayutilities.sf.net)")
+class TestIO_NJA(unittest.TestCase):
+ dshape = (501, 2)
+ dmax = 1344706.25
+ dmin = 90.0
+ motmin = -0.05
+ motmax = 0.15
+ axisT = 1.5
+ dtpos = [5.00000000e-02, 5.64250000e+03]
+ tpos = 250
+
+ @classmethod
+ def setUpClass(cls):
+ cls.njafile = xu.io.SeifertScan(testfile, path=datadir)
+
+ def test_datashape(self):
+ self.assertEqual(self.dshape, self.njafile.data.shape)
+
+ def test_headervalue(self):
+ self.assertAlmostEqual(self.axisT,
+ self.njafile.axispos['T'][0], places=6)
+
+ def test_datavalues(self):
+ motor = self.njafile.data[:, 0]
+ counter = self.njafile.data[:, 1]
+ self.assertAlmostEqual(self.motmax, motor.max(), places=6)
+ self.assertAlmostEqual(self.motmin, motor.min(), places=6)
+ self.assertAlmostEqual(self.dmax, counter.max(), places=6)
+ self.assertAlmostEqual(self.dmin, counter.min(), places=6)
+ self.assertTrue(numpy.all(self.dtpos == self.njafile.data[self.tpos]))
+
+
+if __name__ == '__main__':
+ unittest.main()
diff --git a/xrayutilities/tests/test_io_nja_map.py b/xrayutilities/tests/test_io_nja_map.py
new file mode 100644
index 0000000..f32524b
--- /dev/null
+++ b/xrayutilities/tests/test_io_nja_map.py
@@ -0,0 +1,58 @@
+# This file is part of xrayutilities.
+#
+# xrayutilities is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, see <http://www.gnu.org/licenses/>.
+#
+# Copyright (C) 2015 Dominik Kriegner <dominik.kriegner at gmail.com>
+
+import os.path
+import unittest
+
+import xrayutilities as xu
+import numpy
+
+xu.config.VERBOSITY = 0 # make no output during test
+testfile = 'seifert_map.nja.bz2'
+datadir = 'data'
+fullfilename = os.path.join(datadir, testfile)
+
+
+ at unittest.skipIf(not os.path.isfile(fullfilename),
+ "additional test data needed (http://xrayutilities.sf.net)")
+class TestIO_map_NJA(unittest.TestCase):
+ dshape = (601601,)
+ dmax = 12.8161590
+ dmin = 0.0
+ motmin = 77.0
+ motmax = 80.0
+ dtpos = 1.8286480
+ tpos = 294840
+
+ @classmethod
+ def setUpClass(cls):
+ cls.mot, cls.mot2, cls.data = xu.io.getSeifert_map(testfile,
+ path=datadir)
+
+ def test_datashape(self):
+ self.assertEqual(self.dshape, self.data.shape)
+
+ def test_datavalues(self):
+ self.assertAlmostEqual(self.motmax, self.mot.max(), places=6)
+ self.assertAlmostEqual(self.motmin, self.mot.min(), places=6)
+ self.assertAlmostEqual(self.dmax, self.data.max(), places=6)
+ self.assertAlmostEqual(self.dmin, self.data.min(), places=6)
+ self.assertAlmostEqual(self.dtpos, self.data[self.tpos], places=6)
+
+
+if __name__ == '__main__':
+ unittest.main()
diff --git a/xrayutilities/tests/test_io_nja_tsk.py b/xrayutilities/tests/test_io_nja_tsk.py
new file mode 100644
index 0000000..d34eaaf
--- /dev/null
+++ b/xrayutilities/tests/test_io_nja_tsk.py
@@ -0,0 +1,60 @@
+# This file is part of xrayutilities.
+#
+# xrayutilities is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, see <http://www.gnu.org/licenses/>.
+#
+# Copyright (C) 2015 Dominik Kriegner <dominik.kriegner at gmail.com>
+
+import os.path
+import unittest
+
+import xrayutilities as xu
+import numpy
+
+xu.config.VERBOSITY = 0 # make no output during test
+testfile = 'seifert_tsk.nja.gz'
+datadir = 'data'
+fullfilename = os.path.join(datadir, testfile)
+
+
+ at unittest.skipIf(not os.path.isfile(fullfilename),
+ "additional test data needed (http://xrayutilities.sf.net)")
+class TestIO_task_NJA(unittest.TestCase):
+ dshape = (4001, 1280)
+ dmax = 143563.531
+ dmin = 0.0
+ motmin = 7.5
+ motmax = 57.5
+ dtpos = 1.026
+ tpos = (1515, 640)
+
+ @classmethod
+ def setUpClass(cls):
+ cls.mot, cls.mot2, cls.data = xu.io.getSeifert_map(testfile,
+ path=datadir,
+ scantype='tsk')
+
+ def test_datashape(self):
+ self.assertEqual(self.dshape, self.data.shape)
+
+ def test_datavalues(self):
+ self.assertAlmostEqual(self.motmax, self.mot.max(), places=6)
+ self.assertAlmostEqual(self.motmin, self.mot.min(), places=6)
+ self.assertAlmostEqual(self.dmax, self.data.max(), places=6)
+ self.assertAlmostEqual(self.dmin, self.data.min(), places=6)
+ self.assertTrue(numpy.all(self.dtpos == self.data[self.tpos[0],
+ self.tpos[1]]))
+
+
+if __name__ == '__main__':
+ unittest.main()
diff --git a/xrayutilities/tests/test_io_pdcif.py b/xrayutilities/tests/test_io_pdcif.py
new file mode 100644
index 0000000..0f819c4
--- /dev/null
+++ b/xrayutilities/tests/test_io_pdcif.py
@@ -0,0 +1,61 @@
+# This file is part of xrayutilities.
+#
+# xrayutilities is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, see <http://www.gnu.org/licenses/>.
+#
+# Copyright (C) 2015 Dominik Kriegner <dominik.kriegner at gmail.com>
+
+import os.path
+import unittest
+
+import xrayutilities as xu
+import numpy
+
+xu.config.VERBOSITY = 0
+testfile = 'NISI.cif'
+datadir = 'data'
+fullfilename = os.path.join(datadir, testfile)
+
+
+ at unittest.skipIf(not os.path.isfile(fullfilename),
+ "additional test data needed (http://xrayutilities.sf.net)")
+class TestIO_pdCIF(unittest.TestCase):
+ dshape = (4495, )
+ # dmax = # needs update of pdCIF to handle value + error bar
+ # dmin =
+ motorname = '_pd_meas_time_of_flight'
+ motmin = 1000.0
+ motmax = 8190.4
+ # dtpos =
+ # tpos =
+
+ @classmethod
+ def setUpClass(cls):
+ cls.dfile = xu.io.pdCIF(fullfilename)
+
+ def test_datashape(self):
+ self.assertEqual(self.dshape, self.dfile.data.shape)
+
+ def test_datavalues(self):
+ motor = self.dfile.data[self.motorname]
+ # counter = self.dfile.data
+ self.assertAlmostEqual(self.motmax, motor.max(), places=6)
+ self.assertAlmostEqual(self.motmin, motor.min(), places=6)
+ # self.assertAlmostEqual(self.dmax, counter.max(), places=6)
+ # self.assertAlmostEqual(self.dmin, counter.min(), places=6)
+ # self.assertAlmostEqual(counter[self.tpos[0], self.tpos[1]],
+ # self.dtpos)
+
+
+if __name__ == '__main__':
+ unittest.main()
diff --git a/xrayutilities/tests/test_io_perkinelmer.py b/xrayutilities/tests/test_io_perkinelmer.py
new file mode 100644
index 0000000..dcde538
--- /dev/null
+++ b/xrayutilities/tests/test_io_perkinelmer.py
@@ -0,0 +1,54 @@
+# This file is part of xrayutilities.
+#
+# xrayutilities is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, see <http://www.gnu.org/licenses/>.
+#
+# Copyright (C) 2015 Dominik Kriegner <dominik.kriegner at gmail.com>
+
+import unittest
+import os.path
+
+import xrayutilities as xu
+
+testfile = 'perkinelmer.tif.bz2'
+datadir = 'data'
+fullfilename = os.path.join(datadir, testfile)
+
+
+ at unittest.skipIf(not os.path.isfile(fullfilename),
+ "additional test data needed (http://xrayutilities.sf.net)")
+class TestIO_PerkinElmer(unittest.TestCase):
+ dshape = (2048, 2048)
+ dmax = 173359.0
+ dmin = -113.0
+ tpos = (500, 500)
+ dtpos = 2929.0
+
+ @classmethod
+ def setUpClass(cls):
+ imgreader = xu.io.PerkinElmer()
+ cls.data = imgreader.readImage(testfile, path=datadir)
+
+ def test_datashape(self):
+ self.assertEqual(self.dshape, self.data.shape)
+
+ def test_datavalues(self):
+ self.assertAlmostEqual(self.dmax, self.data.max(), places=10)
+ self.assertAlmostEqual(self.dmin, self.data.min(), places=10)
+ self.assertAlmostEqual(self.dtpos,
+ self.data[self.tpos[0], self.tpos[1]],
+ places=10)
+
+
+if __name__ == '__main__':
+ unittest.main()
diff --git a/xrayutilities/tests/test_io_roperccd.py b/xrayutilities/tests/test_io_roperccd.py
new file mode 100644
index 0000000..198fec6
--- /dev/null
+++ b/xrayutilities/tests/test_io_roperccd.py
@@ -0,0 +1,54 @@
+# This file is part of xrayutilities.
+#
+# xrayutilities is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, see <http://www.gnu.org/licenses/>.
+#
+# Copyright (C) 2015 Dominik Kriegner <dominik.kriegner at gmail.com>
+
+import unittest
+import os.path
+
+import xrayutilities as xu
+
+testfile = 'roperccd.bin.gz'
+datadir = 'data'
+fullfilename = os.path.join(datadir, testfile)
+
+
+ at unittest.skipIf(not os.path.isfile(fullfilename),
+ "additional test data needed (http://xrayutilities.sf.net)")
+class TestIO_RoperCCD(unittest.TestCase):
+ dshape = (4096, 4096)
+ dmax = 2285.0
+ dmin = 273.0
+ tpos = (500, 500)
+ dtpos = 304.0
+
+ @classmethod
+ def setUpClass(cls):
+ imgreader = xu.io.RoperCCD()
+ cls.data = imgreader.readImage(testfile, path=datadir)
+
+ def test_datashape(self):
+ self.assertEqual(self.dshape, self.data.shape)
+
+ def test_datavalues(self):
+ self.assertAlmostEqual(self.dmax, self.data.max(), places=10)
+ self.assertAlmostEqual(self.dmin, self.data.min(), places=10)
+ self.assertAlmostEqual(self.dtpos,
+ self.data[self.tpos[0], self.tpos[1]],
+ places=10)
+
+
+if __name__ == '__main__':
+ unittest.main()
diff --git a/xrayutilities/tests/test_io_spec.py b/xrayutilities/tests/test_io_spec.py
new file mode 100644
index 0000000..d5a7702
--- /dev/null
+++ b/xrayutilities/tests/test_io_spec.py
@@ -0,0 +1,84 @@
+# This file is part of xrayutilities.
+#
+# xrayutilities is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, see <http://www.gnu.org/licenses/>.
+#
+# Copyright (C) 2015 Dominik Kriegner <dominik.kriegner at gmail.com>
+
+import os.path
+import unittest
+
+import xrayutilities as xu
+import numpy
+
+xu.config.VERBOSITY = 0 # make no output during test
+testfile = 'specmca.spec.gz'
+datadir = 'data'
+fullfilename = os.path.join(datadir, testfile)
+
+
+ at unittest.skipIf(not os.path.isfile(fullfilename),
+ "additional test data needed (http://xrayutilities.sf.net)")
+class TestIO_SPEC(unittest.TestCase):
+ dshape = (4001,)
+ dmax = 2567926.75
+ dmin = 1.0
+ motmax = 95.407753
+ motmin = 15.40775
+ tpos = 2400
+ dtpos = 6.0
+ scannr = 43
+ motorname = 'Nu'
+ countername = 'PSDCORR'
+ h5file = '_test_spec.h5'
+
+ @classmethod
+ def setUpClass(cls):
+ cls.specfile = xu.io.SPECFile(testfile, path=datadir)
+ cls.specfile.Update() # this should be a noop
+ cls.specfile.scan43.ReadData()
+ cls.sdata = cls.specfile.scan43.data
+ cls.motor, cls.inte = xu.io.getspec_scan(cls.specfile, cls.scannr,
+ cls.motorname,
+ cls.countername)
+
+ @classmethod
+ def tearDownClass(cls):
+ try:
+ os.remove(cls.h5file)
+ except:
+ pass
+
+ def test_datashape(self):
+ self.assertEqual(self.dshape, self.sdata.shape)
+ self.assertEqual(self.dshape, self.inte.shape)
+ self.assertEqual(self.dshape, self.motor.shape)
+
+ def test_datavalues(self):
+ self.assertAlmostEqual(self.motmax, self.motor.max(), places=6)
+ self.assertAlmostEqual(self.motmin, self.motor.min(), places=6)
+ self.assertAlmostEqual(self.dmax, self.inte.max(), places=6)
+ self.assertAlmostEqual(self.dmin, self.inte.min(), places=6)
+ self.assertAlmostEqual(self.dtpos, self.inte[self.tpos], places=6)
+
+ def test_datamethods(self):
+ self.assertTrue(numpy.all(self.sdata[self.countername] == self.inte))
+
+ def test_hdf5file(self):
+ self.specfile.Save2HDF5(self.h5file)
+ h5d = xu.io.geth5_scan(self.h5file, self.scannr)
+ self.assertTrue(numpy.all(self.inte == h5d[self.countername]))
+
+
+if __name__ == '__main__':
+ unittest.main()
diff --git a/xrayutilities/tests/test_io_specalignmentlog.py b/xrayutilities/tests/test_io_specalignmentlog.py
new file mode 100644
index 0000000..d98c6e9
--- /dev/null
+++ b/xrayutilities/tests/test_io_specalignmentlog.py
@@ -0,0 +1,48 @@
+# This file is part of xrayutilities.
+#
+# xrayutilities is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, see <http://www.gnu.org/licenses/>.
+#
+# Copyright (C) 2015 Dominik Kriegner <dominik.kriegner at gmail.com>
+
+import os.path
+import unittest
+
+import xrayutilities as xu
+import numpy
+
+xu.config.VERBOSITY = 0 # make no output during test
+testfile = 'alignment.log.gz'
+datadir = 'data'
+fullfilename = os.path.join(datadir, testfile)
+
+
+ at unittest.skipIf(not os.path.isfile(fullfilename),
+ "additional test data needed (http://xrayutilities.sf.net)")
+class TestIO_SPEC_RA_Log(unittest.TestCase):
+ peaks = [u'asymaz1', u'symaz1']
+ niterations = 639
+
+ @classmethod
+ def setUpClass(cls):
+ cls.logfile = xu.io.RA_Alignment(fullfilename)
+
+ def test_peaknames(self):
+ self.assertEqual(self.peaks, self.logfile.peaks)
+
+ def test_iterations(self):
+ self.assertEqual(self.niterations,
+ numpy.sum(numpy.sum(self.logfile.iterations)))
+
+if __name__ == '__main__':
+ unittest.main()
diff --git a/xrayutilities/tests/test_NonCOP.py b/xrayutilities/tests/test_io_speclog.py
similarity index 50%
copy from xrayutilities/tests/test_NonCOP.py
copy to xrayutilities/tests/test_io_speclog.py
index 9f9f73c..8495fc9 100644
--- a/xrayutilities/tests/test_NonCOP.py
+++ b/xrayutilities/tests/test_io_speclog.py
@@ -13,32 +13,35 @@
# You should have received a copy of the GNU General Public License
# along with this program; if not, see <http://www.gnu.org/licenses/>.
#
-# Copyright (C) 2014 Dominik Kriegner <dominik.kriegner at gmail.com>
+# Copyright (C) 2015 Dominik Kriegner <dominik.kriegner at gmail.com>
+
+import os.path
+import unittest
import xrayutilities as xu
import numpy
-import unittest
+xu.config.VERBOSITY = 0 # make no output during test
+testfile = 'speclog.log.gz'
+datadir = 'data'
+fullfilename = os.path.join(datadir, testfile)
-class TestQ2Ang_nonCOP(unittest.TestCase):
+
+ at unittest.skipIf(not os.path.isfile(fullfilename),
+ "additional test data needed (http://xrayutilities.sf.net)")
+class TestIO_SPECLog(unittest.TestCase):
+ prompt = 'PSIC'
+ line_cnt = 2046542
+ testcmd = '84.PSIC> mvr mu -.075; ct'
+ testcmdline = 25
def setUp(self):
- self.mat = xu.materials.Al2O3
- self.hxrd = xu.NonCOP(self.mat.Q(1, 1, 0), self.mat.Q(0, 0, 1))
- self.hkltest = (1, 2, 3)
- self.hkltest2 = (-1.5, 3.1, 3)
-
- def test_Q2Ang_nonCOP_point(self):
- ang = self.hxrd.Q2Ang(self.mat.Q(self.hkltest))
- qout = self.hxrd.Ang2HKL(*ang, mat=self.mat)
- for i in range(3):
- self.assertAlmostEqual(qout[i], self.hkltest[i], places=10)
-
- def test_Q2Ang_nonCOP_point2(self):
- ang = self.hxrd.Q2Ang(self.mat.Q(self.hkltest2))
- qout = self.hxrd.Ang2HKL(*ang, mat=self.mat)
- for i in range(3):
- self.assertAlmostEqual(qout[i], self.hkltest2[i], places=10)
+ self.logfile = xu.io.SPECLog(testfile, self.prompt, path=datadir)
+
+ def test_linenumber(self):
+ self.assertEqual(self.line_cnt, self.logfile.line_counter)
+ self.assertEqual(self.testcmd, str(self.logfile[self.testcmdline]))
+
if __name__ == '__main__':
unittest.main()
diff --git a/xrayutilities/tests/test_io_tty.py b/xrayutilities/tests/test_io_tty.py
new file mode 100644
index 0000000..abee16d
--- /dev/null
+++ b/xrayutilities/tests/test_io_tty.py
@@ -0,0 +1,65 @@
+# This file is part of xrayutilities.
+#
+# xrayutilities is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, see <http://www.gnu.org/licenses/>.
+#
+# Copyright (C) 2015 Dominik Kriegner <dominik.kriegner at gmail.com>
+
+import os.path
+import unittest
+
+import xrayutilities as xu
+import numpy
+
+testfiletmp = 'p08tty_%05d.dat'
+testfile = testfiletmp % 29
+datadir = 'data'
+fullfilename = os.path.join(datadir, testfile)
+
+
+ at unittest.skipIf(not os.path.isfile(fullfilename),
+ "additional test data needed (http://xrayutilities.sf.net)")
+class TestIO_FIO(unittest.TestCase):
+ dshape = (102,)
+ dmax = 1444999.0
+ dmin = 314133.0
+ motmax = 26.15
+ motmin = 13.0
+ tpos = 53
+ dtpos = 342586.0
+ motorname = 'om'
+ countername = 'EigerInt'
+
+ @classmethod
+ def setUpClass(cls):
+ cls.motor, cls.data = xu.io.gettty08_scan(testfiletmp, (29, 30),
+ cls.motorname, path=datadir)
+ cls.inte = cls.data[cls.countername]
+
+ def test_datashape(self):
+ self.assertEqual(self.dshape, self.data.shape)
+ self.assertEqual(self.dshape, self.motor.shape)
+
+ def test_datavalues(self):
+ self.assertAlmostEqual(self.motmax, self.motor.max(), places=6)
+ self.assertAlmostEqual(self.motmin, self.motor.min(), places=6)
+ self.assertAlmostEqual(self.dmax, self.inte.max(), places=6)
+ self.assertAlmostEqual(self.dmin, self.inte.min(), places=6)
+ self.assertAlmostEqual(self.dtpos, self.inte[self.tpos], places=6)
+
+ def test_equaldata(self):
+ self.assertTrue(numpy.all(self.motor == self.data[self.motorname]))
+
+
+if __name__ == '__main__':
+ unittest.main()
diff --git a/xrayutilities/tests/test_io_xrdml.py b/xrayutilities/tests/test_io_xrdml.py
new file mode 100644
index 0000000..ed4d860
--- /dev/null
+++ b/xrayutilities/tests/test_io_xrdml.py
@@ -0,0 +1,63 @@
+# This file is part of xrayutilities.
+#
+# xrayutilities is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, see <http://www.gnu.org/licenses/>.
+#
+# Copyright (C) 2015 Dominik Kriegner <dominik.kriegner at gmail.com>
+
+import os.path
+import unittest
+
+import xrayutilities as xu
+import numpy
+
+testfile = 'omega_mm.xrdml'
+datadir = 'data'
+fullfilename = os.path.join(datadir, testfile)
+
+
+ at unittest.skipIf(not os.path.isfile(fullfilename),
+ "additional test data needed (http://xrayutilities.sf.net)")
+class TestIO_XRDML(unittest.TestCase):
+ dshape = (499,)
+ dmax = 75052800.0
+ dmin = 54.0
+ motmax = 16.7872
+ motmin = 11.8072
+ tpos = 240
+ dtpos = 1502.0
+
+ @classmethod
+ def setUpClass(cls):
+ cls.xrdmlfile = xu.io.XRDMLFile(fullfilename)
+ cls.data1 = cls.xrdmlfile.scan['detector']
+ cls.motor, cls.data2 = xu.io.getxrdml_scan(fullfilename)
+
+ def test_datashape(self):
+ self.assertEqual(self.dshape, self.data1.shape)
+ self.assertEqual(self.dshape, self.data2.shape)
+ self.assertEqual(self.dshape, self.motor.shape)
+
+ def test_datavalues(self):
+ self.assertAlmostEqual(self.motmax, self.motor.max(), places=10)
+ self.assertAlmostEqual(self.motmin, self.motor.min(), places=10)
+ self.assertAlmostEqual(self.dmax, self.data1.max(), places=10)
+ self.assertAlmostEqual(self.dmin, self.data1.min(), places=10)
+ self.assertAlmostEqual(self.dtpos, self.data1[self.tpos], places=10)
+
+ def test_datamethods(self):
+ self.assertTrue(numpy.all(self.data1 == self.data2))
+
+
+if __name__ == '__main__':
+ unittest.main()
diff --git a/xrayutilities/tests/test_maplog.py b/xrayutilities/tests/test_maplog.py
new file mode 100644
index 0000000..5a4c6af
--- /dev/null
+++ b/xrayutilities/tests/test_maplog.py
@@ -0,0 +1,66 @@
+# This file is part of xrayutilities.
+#
+# xrayutilities is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, see <http://www.gnu.org/licenses/>.
+#
+# Copyright (C) 2015 Dominik Kriegner <dominik.kriegner at gmail.com>
+
+import unittest
+
+import xrayutilities as xu
+import numpy
+
+
+class Test_maplog(unittest.TestCase):
+ @classmethod
+ def setUpClass(cls):
+ cls.dmin = xu.config.DYNLOW
+ cls.dmax = xu.config.DYNHIGH
+
+ def test_maplog(self):
+ d = numpy.logspace(1, 6, 100)
+ # make noop
+ dm = xu.maplog(d, numpy.inf, -numpy.inf)
+ self.assertTrue(numpy.all(numpy.log10(d) == dm))
+ # cut bottom
+ dl = 3
+ dm = xu.maplog(d, dl, -numpy.inf)
+ dl = min(dl, self.dmin)
+ self.assertAlmostEqual(d.max(), 10.0**dm.max(), places=10)
+ self.assertAlmostEqual(d.max()/10.0**dl, 10**dm.min(), places=10)
+ # cut top
+ dt = 2
+ dm = xu.maplog(d, numpy.inf, dt)
+ dt = max(dt, self.dmax)
+ self.assertAlmostEqual(d.min(), 10.0**dm.min(), places=10)
+ self.assertAlmostEqual(d.max()/10.0**dt, 10.0**dm.max(), places=10)
+
+ def test_maplogzero(self):
+ d = numpy.array((0, 1))
+ # make function call with a zero and negative number
+ dm = xu.maplog(d)
+ self.assertAlmostEqual(d.max()/10.0**self.dmax,
+ 10.0**dm.max(), places=10)
+ self.assertAlmostEqual(d.max()/10.0**self.dmin,
+ 10**dm.min(), places=10)
+ # call with negative number
+ d[0] = -1
+ dm = xu.maplog(d)
+ self.assertAlmostEqual(d.max()/10.0**self.dmax,
+ 10.0**dm.max(), places=10)
+ self.assertAlmostEqual(d.max()/10.0**self.dmin,
+ 10**dm.min(), places=10)
+
+
+if __name__ == '__main__':
+ unittest.main()
diff --git a/xrayutilities/tests/test_npygridder1d.py b/xrayutilities/tests/test_npygridder1d.py
index 17ec7ca..24f3b49 100644
--- a/xrayutilities/tests/test_npygridder1d.py
+++ b/xrayutilities/tests/test_npygridder1d.py
@@ -15,21 +15,22 @@
#
# Copyright (C) 2014 Dominik Kriegner <dominik.kriegner at gmail.com>
+import unittest
+
import xrayutilities as xu
import numpy
-import unittest
class TestNpyGridder1D(unittest.TestCase):
-
- def setUp(self):
- self.num = numpy.random.randint(10, 99)
- self.xmin = 1
- self.xmax = self.num
- self.x = numpy.linspace(self.xmin, self.xmax, num=self.num)
- self.data = numpy.random.rand(self.num)
- self.gridder = xu.npyGridder1D(self.num)
- self.gridder(self.x, self.data)
+ @classmethod
+ def setUpClass(cls):
+ cls.num = numpy.random.randint(10, 99)
+ cls.xmin = 1
+ cls.xmax = cls.num
+ cls.x = numpy.linspace(cls.xmin, cls.xmax, num=cls.num)
+ cls.data = numpy.random.rand(cls.num)
+ cls.gridder = xu.npyGridder1D(cls.num)
+ cls.gridder(cls.x, cls.data)
def test_npygridder1d_axis(self):
hist, bins = numpy.histogram(self.x, bins=self.num)
diff --git a/xrayutilities/tests/test_NonCOP.py b/xrayutilities/tests/test_q2angfit.py
similarity index 50%
copy from xrayutilities/tests/test_NonCOP.py
copy to xrayutilities/tests/test_q2angfit.py
index 9f9f73c..162f197 100644
--- a/xrayutilities/tests/test_NonCOP.py
+++ b/xrayutilities/tests/test_q2angfit.py
@@ -13,32 +13,33 @@
# You should have received a copy of the GNU General Public License
# along with this program; if not, see <http://www.gnu.org/licenses/>.
#
-# Copyright (C) 2014 Dominik Kriegner <dominik.kriegner at gmail.com>
+# Copyright (C) 2015 Dominik Kriegner <dominik.kriegner at gmail.com>
+
+import unittest
import xrayutilities as xu
import numpy
-import unittest
-class TestQ2Ang_nonCOP(unittest.TestCase):
+class TestQ2AngFit(unittest.TestCase):
+ energy = 15000
- def setUp(self):
- self.mat = xu.materials.Al2O3
- self.hxrd = xu.NonCOP(self.mat.Q(1, 1, 0), self.mat.Q(0, 0, 1))
- self.hkltest = (1, 2, 3)
- self.hkltest2 = (-1.5, 3.1, 3)
+ @classmethod
+ def setUpClass(cls):
+ cls.qconv = xu.experiment.QConversion(['z+', 'y-', 'z-'],
+ ['z+', 'y-'],
+ [1, 0, 0])
+ cls.hxrd = xu.HXRD((1, 0, 0), (0, 0, 1), en=cls.energy,
+ qconv=cls.qconv)
+ cls.bounds = (0, (0, 90), 0, (-1, 90), (0, 90))
+ cls.qvec = numpy.array((0, 0, numpy.random.rand(1)[0]))
- def test_Q2Ang_nonCOP_point(self):
- ang = self.hxrd.Q2Ang(self.mat.Q(self.hkltest))
- qout = self.hxrd.Ang2HKL(*ang, mat=self.mat)
+ def test_q2angfit(self):
+ ang, qerror, errcode = xu.Q2AngFit(self.qvec, self.hxrd, self.bounds)
+ qout = self.hxrd.Ang2Q(*ang)
for i in range(3):
- self.assertAlmostEqual(qout[i], self.hkltest[i], places=10)
+ self.assertAlmostEqual(qout[i], self.qvec[i], places=6)
- def test_Q2Ang_nonCOP_point2(self):
- ang = self.hxrd.Q2Ang(self.mat.Q(self.hkltest2))
- qout = self.hxrd.Ang2HKL(*ang, mat=self.mat)
- for i in range(3):
- self.assertAlmostEqual(qout[i], self.hkltest2[i], places=10)
if __name__ == '__main__':
unittest.main()
diff --git a/xrayutilities/tests/test_qconversion.py b/xrayutilities/tests/test_qconversion.py
index 5fdf154..99873ef 100644
--- a/xrayutilities/tests/test_qconversion.py
+++ b/xrayutilities/tests/test_qconversion.py
@@ -15,18 +15,19 @@
#
# Copyright (C) 2014 Dominik Kriegner <dominik.kriegner at gmail.com>
+import unittest
+
import xrayutilities as xu
import numpy
-import unittest
class TestQConversion(unittest.TestCase):
-
- def setUp(self):
- self.mat = xu.materials.Si
- self.hxrd = xu.HXRD(self.mat.Q(1, 1, 0), self.mat.Q(0, 0, 1))
- self.hklsym = (0, 0, 4)
- self.hklasym = (2, 2, 4)
+ @classmethod
+ def setUpClass(cls):
+ cls.mat = xu.materials.Si
+ cls.hxrd = xu.HXRD(cls.mat.Q(1, 1, 0), cls.mat.Q(0, 0, 1))
+ cls.hklsym = (0, 0, 4)
+ cls.hklasym = (2, 2, 4)
def test_qconversion_point(self):
ang = self.hxrd.Q2Ang(self.mat.Q(self.hklsym))
diff --git a/xrayutilities/tests/test_qconversion_area.py b/xrayutilities/tests/test_qconversion_area.py
index 5a37238..6161dbf 100644
--- a/xrayutilities/tests/test_qconversion_area.py
+++ b/xrayutilities/tests/test_qconversion_area.py
@@ -15,23 +15,24 @@
#
# Copyright (C) 2014 Dominik Kriegner <dominik.kriegner at gmail.com>
+import unittest
+
import xrayutilities as xu
import numpy
-import unittest
class TestQConversion(unittest.TestCase):
-
- def setUp(self):
- self.mat = xu.materials.Si
- self.hxrd = xu.HXRD(self.mat.Q(1, 1, 0), self.mat.Q(0, 0, 1))
- self.nch = (9, 13)
- self.ncch1 = 4
- self.ncch2 = 6
- self.hxrd.Ang2Q.init_area('z+', 'x+', self.ncch1, self.ncch2,
- self.nch[0], self.nch[1], 1.0, 50e-6, 50e-6)
- self.hklsym = (0, 0, 4)
- self.hklasym = (2, 2, 4)
+ @classmethod
+ def setUpClass(cls):
+ cls.mat = xu.materials.Si
+ cls.hxrd = xu.HXRD(cls.mat.Q(1, 1, 0), cls.mat.Q(0, 0, 1))
+ cls.nch = (9, 13)
+ cls.ncch1 = 4
+ cls.ncch2 = 6
+ cls.hxrd.Ang2Q.init_area('z+', 'x+', cls.ncch1, cls.ncch2,
+ cls.nch[0], cls.nch[1], 1.0, 50e-6, 50e-6)
+ cls.hklsym = (0, 0, 4)
+ cls.hklasym = (2, 2, 4)
def test_qconversion_area(self):
ang = self.hxrd.Q2Ang(self.mat.Q(self.hklsym))
diff --git a/xrayutilities/tests/test_qconversion_linear.py b/xrayutilities/tests/test_qconversion_linear.py
index 28aaf10..8b32404 100644
--- a/xrayutilities/tests/test_qconversion_linear.py
+++ b/xrayutilities/tests/test_qconversion_linear.py
@@ -15,21 +15,22 @@
#
# Copyright (C) 2014 Dominik Kriegner <dominik.kriegner at gmail.com>
+import unittest
+
import xrayutilities as xu
import numpy
-import unittest
class TestQConversion(unittest.TestCase):
-
- def setUp(self):
- self.mat = xu.materials.Si
- self.hxrd = xu.HXRD(self.mat.Q(1, 1, 0), self.mat.Q(0, 0, 1))
- self.nch = 9
- self.ncch = 4
- self.hxrd.Ang2Q.init_linear('z+', self.ncch, self.nch, 1.0, 50e-6, 0.)
- self.hklsym = (0, 0, 4)
- self.hklasym = (2, 2, 4)
+ @classmethod
+ def setUpClass(cls):
+ cls.mat = xu.materials.Si
+ cls.hxrd = xu.HXRD(cls.mat.Q(1, 1, 0), cls.mat.Q(0, 0, 1))
+ cls.nch = 9
+ cls.ncch = 4
+ cls.hxrd.Ang2Q.init_linear('z+', cls.ncch, cls.nch, 1.0, 50e-6, 0.)
+ cls.hklsym = (0, 0, 4)
+ cls.hklasym = (2, 2, 4)
def test_qconversion_linear(self):
ang = self.hxrd.Q2Ang(self.mat.Q(self.hklsym))
diff --git a/xrayutilities/tests/test_qconversion_trans.py b/xrayutilities/tests/test_qconversion_trans.py
index 92d6b68..ba151e7 100644
--- a/xrayutilities/tests/test_qconversion_trans.py
+++ b/xrayutilities/tests/test_qconversion_trans.py
@@ -15,33 +15,33 @@
#
# Copyright (C) 2014 Dominik Kriegner <dominik.kriegner at gmail.com>
+import unittest
+
import xrayutilities as xu
import numpy
-import unittest
class TestQConversionTrans(unittest.TestCase):
-
- def setUp(self):
- self.nch = 9
- self.ncch = 4
- self.nch2d = (9, 13)
- self.ncch1 = 4
- self.ncch2 = 6
+ @classmethod
+ def setUpClass(cls):
+ cls.nch = 9
+ cls.ncch = 4
+ cls.nch2d = (9, 13)
+ cls.ncch1 = 4
+ cls.ncch2 = 6
# standard 1S+1D goniometer
qconv = xu.QConversion('x+', 'x+', (0, 1, 0))
- self.hxrd = xu.HXRD((1., 1., 0.), (0., 0., 1.), qconv=qconv)
+ cls.hxrd = xu.HXRD((1., 1., 0.), (0., 0., 1.), qconv=qconv)
# comparable goniometer with translations
qconv = xu.QConversion('x+', ['ty', 'tz'], (0, 1e-15, 0))
- self.hxrdtrans = xu.HXRD((1., 1., 0.), (0., 0., 1.), qconv=qconv,
- sampleor='z+')
- self.hxrdtrans.Ang2Q.init_linear('z+', self.ncch, self.nch,
- 1e-15, 50e-6)
- self.hxrdtrans.Ang2Q.init_area('z+', 'x+', self.ncch1, self.ncch2,
- self.nch2d[0], self.nch2d[1],
- 1e-15, 50e-6, 50e-6)
-
- self.angle = numpy.random.rand() * 45
+ cls.hxrdtrans = xu.HXRD((1., 1., 0.), (0., 0., 1.), qconv=qconv,
+ sampleor='z+')
+ cls.hxrdtrans.Ang2Q.init_linear('z+', cls.ncch, cls.nch, 1e-15, 50e-6)
+ cls.hxrdtrans.Ang2Q.init_area('z+', 'x+', cls.ncch1, cls.ncch2,
+ cls.nch2d[0], cls.nch2d[1],
+ 1e-15, 50e-6, 50e-6)
+
+ cls.angle = numpy.random.rand() * 45
def test_qtrans0(self):
qvec1 = self.hxrd.Ang2Q(self.angle, 0)
diff --git a/xrayutilities/tests/test_structure_factor.py b/xrayutilities/tests/test_structure_factor.py
new file mode 100644
index 0000000..04609b1
--- /dev/null
+++ b/xrayutilities/tests/test_structure_factor.py
@@ -0,0 +1,53 @@
+# This file is part of xrayutilities.
+#
+# xrayutilities is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, see <http://www.gnu.org/licenses/>.
+#
+# Copyright (C) 2015 Dominik Kriegner <dominik.kriegner at gmail.com>
+
+import unittest
+
+import xrayutilities as xu
+import numpy
+
+
+class TestStructureFactor(unittest.TestCase):
+ @classmethod
+ def setUpClass(cls):
+ cls.at = xu.materials.elements.dummy
+ cls.mat = xu.materials.Material('test',
+ xu.materials.DiamondLattice(cls.at, 4))
+
+ def test_StructureFactor(self):
+ f = self.mat.StructureFactor(self.mat.Q(1, 3, 1))
+ self.assertAlmostEqual(f, 4 - 4j, places=10)
+ f = self.mat.StructureFactor(self.mat.Q(0, 4, 0))
+ self.assertAlmostEqual(f, 8, places=10)
+ f = self.mat.StructureFactor(self.mat.Q(1, 2, 1))
+ self.assertAlmostEqual(f, 0, places=10)
+
+ def test_StructureFactorQ(self):
+ q = (self.mat.Q(1, 1, 1), self.mat.Q(0, 4, 0), self.mat.Q(1, 2, 1))
+ f = self.mat.StructureFactorForQ(q)
+ for i in range(3):
+ self.assertAlmostEqual(f[i], (4 + 4j, 8, 0)[i], places=10)
+
+ def test_StructureFactorE(self):
+ q = self.mat.Q(1, 1, 1)
+ f = self.mat.StructureFactorForEnergy(q, (1000, 2000, 3000))
+ for i in range(3):
+ self.assertAlmostEqual(f[i], 4 + 4j, places=10)
+
+
+if __name__ == '__main__':
+ unittest.main()
diff --git a/xrayutilities/tests/test_transforms.py b/xrayutilities/tests/test_transforms.py
new file mode 100644
index 0000000..7d70e5b
--- /dev/null
+++ b/xrayutilities/tests/test_transforms.py
@@ -0,0 +1,81 @@
+# This file is part of xrayutilities.
+#
+# xrayutilities is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, see <http://www.gnu.org/licenses/>.
+#
+# Copyright (C) 2015 Dominik Kriegner <dominik.kriegner at gmail.com>
+
+import unittest
+
+import xrayutilities as xu
+import numpy
+
+
+class TestTransforms(unittest.TestCase):
+ @classmethod
+ def setUpClass(cls):
+ cls.x = (1.0, 0.0, 0.0)
+ cls.y = (0.0, 1.0, 0.0)
+ cls.z = (0.0, 0.0, 1.0)
+
+ def test_Xrot(self):
+ xr = xu.math.XRotation(90)
+ for i in range(3):
+ self.assertAlmostEqual(xr(self.y)[i], self.z[i], places=10)
+ for i in range(3):
+ self.assertAlmostEqual(xr(self.z)[i], -self.y[i], places=10)
+
+ def test_Yrot(self):
+ yr = xu.math.YRotation(90)
+ for i in range(3):
+ self.assertAlmostEqual(yr(self.z)[i], self.x[i], places=10)
+ for i in range(3):
+ self.assertAlmostEqual(yr(self.x)[i], -self.z[i], places=10)
+
+ def test_Zrot(self):
+ zr = xu.math.ZRotation(90)
+ for i in range(3):
+ self.assertAlmostEqual(zr(self.x)[i], self.y[i], places=10)
+ for i in range(3):
+ self.assertAlmostEqual(zr(self.y)[i], -self.x[i], places=10)
+
+ def test_arbrot(self):
+ r = xu.math.rotarb
+ a = (1, 1, 1)
+ for i in range(3):
+ self.assertAlmostEqual(r(self.x, a, 120)[i], self.y[i], places=10)
+ for i in range(3):
+ self.assertAlmostEqual(r(self.z, a, 120)[i], self.x[i], places=10)
+
+ def test_Axis2Z(self):
+ a = numpy.random.rand(3)
+ a[2] = 2 # ensure non-zero vector
+ r = xu.math.AxisToZ(a)
+ for i in range(3):
+ self.assertAlmostEqual(r(a)[i],
+ self.z[i] * numpy.linalg.norm(a),
+ places=10)
+ r = xu.math.AxisToZ_keepXY(a)
+ for i in range(3):
+ self.assertAlmostEqual(r(a)[i],
+ self.z[i] * numpy.linalg.norm(a),
+ places=10)
+ # test inverse
+ for i in range(3):
+ self.assertAlmostEqual(r.inverse(self.z)[i],
+ a[i] / numpy.linalg.norm(a),
+ places=10)
+
+
+if __name__ == '__main__':
+ unittest.main()
diff --git a/xrayutilities/utilities.py b/xrayutilities/utilities.py
index 3cd2a11..defa761 100644
--- a/xrayutilities/utilities.py
+++ b/xrayutilities/utilities.py
@@ -52,7 +52,6 @@ def maplog(inte, dynlow="config", dynhigh="config", **keyargs):
-------
>>> lint = maplog(int,5,2)
"""
-
if dynlow == "config":
dynlow = config.DYNLOW
if dynhigh == "config":
diff --git a/xrayutilities/utilities_noconf.py b/xrayutilities/utilities_noconf.py
index 21cc09a..f828291 100644
--- a/xrayutilities/utilities_noconf.py
+++ b/xrayutilities/utilities_noconf.py
@@ -23,7 +23,7 @@ this part of utilities does not need the config class
import numbers
import numpy
import scipy.constants
-import os
+import os.path
from .exception import InputError
@@ -38,7 +38,9 @@ energies = {
'CuKa2': 8027.9117,
'CuKa12': 8041.18,
'CuKb': 8905.337,
- 'MoKa1': 17479.374}
+ 'MoKa1': 17479.374,
+ 'CoKa1': 6930.32,
+ 'CoKa2': 6915.30}
# wavelength values from International Tables of Crystallography:
# Vol C, 2nd Ed. page 203
# CuKa1: 1.54059292(45) the value in bracket is the uncertainty
@@ -46,6 +48,8 @@ energies = {
# CuKa12: mixture 2:1 a1 and a2
# CuKb: 1.392246(14)
# MoKa1: 0.70931713(41)
+# Xray data booklet:
+# CoKa1,2 energies
def lam2en(inp):
--
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