[ismrmrd] annotated tag v0.5.0 created (now d5a332c)
Ghislain Vaillant
ghisvail-guest at moszumanska.debian.org
Wed Jan 14 20:01:30 UTC 2015
This is an automated email from the git hooks/post-receive script.
ghisvail-guest pushed a change to annotated tag v0.5.0
in repository ismrmrd.
at d5a332c (tag)
tagging 1e307c1f42d6ad11155b5c3b306a531f9e6f95c2 (commit)
tagged by Michael S. Hansen
on Mon Jan 27 19:25:30 2014 -0500
- Log -----------------------------------------------------------------
Version 0.5.0
Hui Xue (1):
fix a warning on 1<<mask_bit
IDEA User (1):
inlined the quaternion to direction functions.
Joseph Naegele (47):
Added optional DICOM parameters to schema.
moved non-DICOM specific elements to the general header.
Added initialSeriesNumber to measurementInfo in the schema.
Erased all traces of quaternions. Replaced with 3 direction cosines.
rename *_cosines to *_dir and add quaternion helper functions
Merge branch 'master' into dir_cosines
semantics
fixed ismrmrd.h to compile with a C compiler.
t_cquaternions needs to be link with libm.
improving classes in Matlab ISMRMRD package
added base64 string userParameter to ISMRMRD schema.
added initial version of SWIG Python bindings
working on Python bindings
more work on Python and Java bindings
more progress on Java bindings. working getData()
added example code for java and python bindings
Merge branch 'base64param' into development
Merge branch 'development' of vatican.nhlbi.nih.gov:/home/gitrepos/ismrmrd into development
added custom command to make jar for java bindings
Merge branch 'development' of github.com:nih-fmrif/ismrmrd into development
added install target for java jar and library.
adding JNILibLoader and Java XML header marshaller.
added JAXB marshalling function to java bindings.
Merge remote-tracking branch 'vatican/development' into development
changing bindings to build conditionally
copied Gadgetron FindIsmrmrd.cmake to Ismrmrd.
finishing up Python bindings.
Added ismrmrd.py to install list for python bindings.
added additional include directory for java bindings
making java bindings build standalone class files
Merge branch 'development' of vatican.nhlbi.nih.gov:/home/gitrepos/ismrmrd into development
giving all complex types global names in schema
Merge branch 'development' of github.com:nih-fmrif/ismrmrd into development
using FindJNI for Java bindings.
heavily cleansing Python binding/API
adding FindNumPy.cmake for Python bindings.
forcing Fortran-style order in NumPy array (bindings)
updating FindXSD to respect find_package args.
changing binding install directories to language name
updating Java XML bindings for newest schema version.
working on Matlab + ISMRMRD + HDF5 interface
adding working example for Matlab API
moving Java XML API to the matlab package
Fixed python bindings to compile cleanly with NumPy 1.7 API
adding Java XML header API docs to matlab install destination
fixing build dependencies for Java API/docs
revert to Java .jar depending on native Java library.
Michael Hansen (12):
Small fixes for compilation on Mac
Added mac installation instructions
Made some build script changes to make build more robust on all platforms
Fixes to enable compile and linking on Windows
Merge branch 'master' of ssh://helix.nih.gov/home/hansenms/gitrepos/ismrmrd
Added some help for findHDF5.cmake on Windows, which does not work well
Started work on test applications
Complete first example of creating a dataset from scratch
Small changes to build on Windows
Added Powershell Script for installing dependencies on Windows
Merge branch 'master' of ssh://helix.nih.gov/home/hansenms/gitrepos/ismrmrd
Merge branch 'master' of ssh://137.187.134.61/home/gitrepos/ismrmrd
Michael S. Hansen (62):
Initial Commit
removed build directory
Added build/ to gitignore
Started work on HDF5 interface
Started implementation of HDF5 tools
More work on HDF5 interface
More work on HDF5 interface
Improved HDF5 saving support
Added examples 2D/3D and spiral with Matlab code
First version of README file with basic documentation
Spell check on README
Mods
Changing packing to 2 bytes for ismrmrd.h
Changes to documentation
Small typo correction
Added images to dataset and set up doxygen
Now supporting ISMRMRD Image format too
Removed Boost version requirement
Updated README.html
Fixed bug which caused problems when trying to write images to a non-existing file from multiple threads
Bug fix to data creation example
Added example reconstruction of test dataset
Small change to help cmake on Windows
Updated documentation and removed main.cpp, which wasn't doing much
MAJOR LAYOUT CHANGE: Acquisition data now stored as variable length array of FLOAT and not as a compound type. This change was made to improve interoperability with Matlab, etc.
Fixed bug introduced in FindXSD.cmake on Linux/Mac
Correct Matlab examples to reflect new storage convention
Split into two libraries, one for HDF5 RW and one for the XML XSD stuff.
Merge branch 'master' of ssh://137.187.134.61/home/gitrepos/ismrmrd
Small fix to Windows Exports
Added first draft for a parallel imaging section in the schema defintion
Updates to documentation
Merge branch 'master' of ssh://137.187.134.61/home/gitrepos/ismrmrd
Inlined all get data type functions to make it easier to include in multiple C++ files
Mod to gitignore
Merge branch 'master' of ssh://137.187.134.61/home/gitrepos/ismrmrd
Merge branch 'master' of ssh://git.code.sf.net/p/ismrmrd/code
Merge branch 'master' of ssh://git.code.sf.net/p/ismrmrd/code
Removed std::valarray assignments. They seem to be causing problems for GCC/G++ VERSION < 4.6
Merge branch 'master' of vatican.nhlbi.nih.gov:/home/gitrepos/ismrmrd
Updated documentation and moved matlab examples (temporarily) back to the original folder while new examples are being made
Encapsulation of Acquisition and Image
Fixed a bug that prevented trajectrory data arrays from getting resized when setting number of trajectory dimensions
Added some names and emails to header
Removed a comment
More work on comments
Small change
Some formatting
Some formatting
Corrected some indentations
Formatting
Formatting
Added first parts of utility functions for generating shepp-logan phantom datasets
Further improvements to shepp-logan phantom generator
Merge branch 'development' of vatican.nhlbi.nih.gov:/home/gitrepos/ismrmrd into development
Changed the build procedure for the shepp logan phantom generator to link statically to the XSD files to avoid clashes with boost program options on Windows
Added C++ multi slice recon
Merge branch 'development' of ssh://git.code.sf.net/p/ismrmrd/code into development
Added License
Merge branch 'master' of ssh://git.code.sf.net/p/ismrmrd/code
Updated readme file
Made changes to Java interface to expose getTraj and setTraj appropriately
Souheil Inati (47):
Initial work on the matlab wrappers.
Merge branch 'master' of ssh://137.187.134.61/home/gitrepos/ismrmrd
Most of the data structures are complete. Starting to make progress on the HDF5 low level read/write routines.
Merge branch 'master' of ssh://137.187.134.61/home/gitrepos/ismrmrd
Matlab code that would have worked (maybe) if only we could have used variable length arrays of compound types.
Starting conversion from hdf5 struct to Acquisition object
continuing to work on matlab implementation
Merge branch 'master' of ssh://137.187.134.61/home/gitrepos/ismrmrd
Working Java xml handling for Matlab. Examples in progress.
Working on the matlab
Merge branch 'master' of ssh://137.187.134.61/home/gitrepos/ismrmrd
Added functions to bind xml
working on test example.
Merge branch 'master' of ssh://137.187.134.61/home/gitrepos/ismrmrd
Moved old examples into deprecated. Will slowly pull back the relevant bits.
Moved c++ example and create standalone build cmake.
working on matlab example
working on matlab interface, xmlheader class
Merge branch 'master' of ssh://137.187.134.61/home/gitrepos/ismrmrd
Bringing back xml2struct.m for the simple matlab read examples.
Working version of SWIG Java bindings. Still missing append functions, but a pretty complete working copy so far.
Merged swig java wrappers into development branch.
Improvments to the java bindings. Now builds the jaxb stuff for the xmlheader. Creates a javadoc.
Put in the append functions stubs. Not working quite right, but the interface is correct.
Created a VERY simple example java program.
Fixed error in javadoc building.
Changed interface to the writeHeader function to make the input string a const.
Removed all of the HDF5 stuff from the matlab interface. The interface is now just contains
Reorganizing matlab interface. Got rid of native hdf5 stuff in preparation
Changes to schema and python bindings to fix xml header and readArray.
Fixed size of physio time stamps.
Reverted size of physiology_time_stamps change for now. Deferred to a mojore version change.
Continuing to work on matlab interace.
Install a copy of the jar file inside the matlab class. Matlab api fix so that an error isreturned if the data does not exist yet.
Merge branch 'development' of vatican.nhlbi.nih.gov:/home/gitrepos/ismrmrd into development
Fixed bug is matlab api, acquisition flagbit.
Changed matlab api so that readAcquisition sets the data shape to match what is given in the corresponding header.
Prepping for new matlab API.
New matlab API. Acquisitions are working. Lots more to do.
Slowly migrating back to a (faster) matlab class.
New matlab class style interface working for acquisitions.
Can now properly append acquisitions.
Started to migrage ImageHeader to new style matlab api.
Starting to fix bugs in ImageHeader in matlab api.
Merge branch 'development' of vatican.nhlbi.nih.gov:/home/gitrepos/ismrmrd into development
A simple matlab reconstruction example.
Fixed a few bugs in the matlab interface and add a recon example.
Thomas Sangild Sorensen (2):
Do no create the ismrmrd_xsd library. On Windows it would export symbols from std:: which caused duplicate defined symbols when linking different libraries together. Instead we now autogenerate ismrmrd.hxx and ismrmrd.cxx in the schema folder.
Resolved merge conflicts for Windows adaptions
hxue (7):
use the precompiled hdf5 for windows
Merge branch 'master' of vatican.nhlbi.nih.gov:/home/gitrepos/ismrmrd
fix hdf5 cmake in windows
make the new ismrmrd compiled in windows
first checkin on local branch
Merge remote-tracking branch 'origin/development' into hx_development
add more data types
inatisj (1):
Modified cmake file to put matlab m files in the right place.
kvahed (13):
'const' safties in NDArrayContainer methods and non-singleton dimensions
Replaced vector with valarray on NDArrayContainer
Replaced vector with valarray on NDArrayContainer
Replaced vector with valarray on NDArrayContainer
Replaced vector with valarray on NDArrayContainer
valarray / ndarraycontainer inheritance ... seems to work. consistency checks missing.
kv_storage initial push to integrate more inheritance and checks
Missing read speed test from Michael
Missing read speed test from Michael
Missing read speed test from Michael
Image test
More CODFile
Removed files replaced
xueh2 (2):
Merge branch 'development' into development_merge_hx
Merge branch 'development_merge_hx' of vatican.nhlbi.nih.gov:/home/gitrepos/ismrmrd into development
-----------------------------------------------------------------------
This annotated tag includes the following new commits:
new 875d4b5 Initial Commit
new 2438c2a removed build directory
new 2512b37 Added build/ to gitignore
new 7b53618 Started work on HDF5 interface
new 3f78d47 Started implementation of HDF5 tools
new e5f3134 More work on HDF5 interface
new 51ab520 More work on HDF5 interface
new 8e37561 Improved HDF5 saving support
new 3fbc194 Added examples 2D/3D and spiral with Matlab code
new 8b4f677 First version of README file with basic documentation
new 6c86c88 Spell check on README
new 8cd0ccd Mods
new 6cc3a34 Changing packing to 2 bytes for ismrmrd.h
new 8cc3642 Changes to documentation
new 410d9ec Small typo correction
new 4c7dbb9 Added images to dataset and set up doxygen
new dec2ac5 Now supporting ISMRMRD Image format too
new a8ec56f Small fixes for compilation on Mac
new 006c7ce Added mac installation instructions
new 54c1697 Removed Boost version requirement
new 8451b59 Updated README.html
new 98bf0c2 Made some build script changes to make build more robust on all platforms
new 599d8f9 Fixed bug which caused problems when trying to write images to a non-existing file from multiple threads
new ebde178 Fixes to enable compile and linking on Windows
new 0f05e6f Merge branch 'master' of ssh://helix.nih.gov/home/hansenms/gitrepos/ismrmrd
new 29bbabd Added some help for findHDF5.cmake on Windows, which does not work well
new b8433d5 Started work on test applications
new 977a936 Complete first example of creating a dataset from scratch
new e22d7e1 Bug fix to data creation example
new b0af0af Small changes to build on Windows
new 8387b1f Added example reconstruction of test dataset
new 5fff7ee Small change to help cmake on Windows
new 00a0b99 Added Powershell Script for installing dependencies on Windows
new 74f34c4 Merge branch 'master' of ssh://helix.nih.gov/home/hansenms/gitrepos/ismrmrd
new 6a608c9 Initial work on the matlab wrappers.
new ff558d5 Merge branch 'master' of ssh://137.187.134.61/home/gitrepos/ismrmrd
new 3cc712d Updated documentation and removed main.cpp, which wasn't doing much
new 1149c06 Merge branch 'master' of ssh://137.187.134.61/home/gitrepos/ismrmrd
new b2de938 Most of the data structures are complete. Starting to make progress on the HDF5 low level read/write routines.
new 8056299 Merge branch 'master' of ssh://137.187.134.61/home/gitrepos/ismrmrd
new 39bb838 Matlab code that would have worked (maybe) if only we could have used variable length arrays of compound types.
new e96c3d5 MAJOR LAYOUT CHANGE: Acquisition data now stored as variable length array of FLOAT and not as a compound type. This change was made to improve interoperability with Matlab, etc.
new 03d0770 Fixed bug introduced in FindXSD.cmake on Linux/Mac
new f36b114 Starting conversion from hdf5 struct to Acquisition object
new 9b382c2 Correct Matlab examples to reflect new storage convention
new d72c928 continuing to work on matlab implementation
new 150ae27 Merge branch 'master' of ssh://137.187.134.61/home/gitrepos/ismrmrd
new c5f569d Split into two libraries, one for HDF5 RW and one for the XML XSD stuff.
new 1a40aa0 Merge branch 'master' of ssh://137.187.134.61/home/gitrepos/ismrmrd
new 42b208c Small fix to Windows Exports
new 6980aba Added first draft for a parallel imaging section in the schema defintion
new 478467e Updates to documentation
new ef7e6a2 Working Java xml handling for Matlab. Examples in progress.
new 5d425b8 Working on the matlab
new fd4bd73 Merge branch 'master' of ssh://137.187.134.61/home/gitrepos/ismrmrd
new 000739f Modified cmake file to put matlab m files in the right place.
new 6202157 Added functions to bind xml
new 04f0fc2 Merge branch 'master' of ssh://137.187.134.61/home/gitrepos/ismrmrd
new 0736eb8 Inlined all get data type functions to make it easier to include in multiple C++ files
new 9461b76 Added optional DICOM parameters to schema.
new fa62f54 'const' safties in NDArrayContainer methods and non-singleton dimensions
new a3742bb Mod to gitignore
new 7570cac Merge branch 'master' of ssh://137.187.134.61/home/gitrepos/ismrmrd
new a78fb88 Merge branch 'master' of ssh://git.code.sf.net/p/ismrmrd/code
new 223a6d1 moved non-DICOM specific elements to the general header.
new 2f13721 working on test example.
new 4d97da4 Merge branch 'master' of ssh://137.187.134.61/home/gitrepos/ismrmrd
new c19cecc Moved old examples into deprecated. Will slowly pull back the relevant bits.
new d4bc435 Moved c++ example and create standalone build cmake.
new d108000 working on matlab example
new 555be4b use the precompiled hdf5 for windows
new f2145da Merge branch 'master' of vatican.nhlbi.nih.gov:/home/gitrepos/ismrmrd
new c85a564 working on matlab interface, xmlheader class
new 5c42062 Merge branch 'master' of ssh://137.187.134.61/home/gitrepos/ismrmrd
new f95a997 Replaced vector with valarray on NDArrayContainer
new 9017825 Replaced vector with valarray on NDArrayContainer
new 182c53a Replaced vector with valarray on NDArrayContainer
new 899569e Replaced vector with valarray on NDArrayContainer
new a5434b6 Merge branch 'master' of ssh://git.code.sf.net/p/ismrmrd/code
new 5d4f482 Removed std::valarray assignments. They seem to be causing problems for GCC/G++ VERSION < 4.6
new 59bf2be Merge branch 'master' of vatican.nhlbi.nih.gov:/home/gitrepos/ismrmrd
new d623407 Bringing back xml2struct.m for the simple matlab read examples. Added some documentation about generating the javadoc for the xml header api.
new 97ce954 Updated documentation and moved matlab examples (temporarily) back to the original folder while new examples are being made
new 18b089f valarray / ndarraycontainer inheritance ... seems to work. consistency checks missing.
new 1d3da9c kv_storage initial push to integrate more inheritance and checks
new d8b3f80 Missing read speed test from Michael
new 779bbae Missing read speed test from Michael
new d812d5d Missing read speed test from Michael
new e9a9c9a Image test
new 276f103 Added initialSeriesNumber to measurementInfo in the schema.
new 1a2e67b fix hdf5 cmake in windows
new e3d9db2 Encapsulation of Acquisition and Image
new 0c660f8 Erased all traces of quaternions. Replaced with 3 direction cosines.
new d406bdc rename *_cosines to *_dir and add quaternion helper functions
new 6bbcd34 Merge branch 'master' into dir_cosines
new 69b0f7b semantics
new 10b4ce2 inlined the quaternion to direction functions. `
new cbb1b25 fixed ismrmrd.h to compile with a C compiler.
new b0179ed t_cquaternions needs to be link with libm.
new e85c48a make the new ismrmrd compiled in windows
new 12afcff Fixed a bug that prevented trajectrory data arrays from getting resized when setting number of trajectory dimensions
new 3aa9c83 fix a warning on 1<<mask_bit
new 2748af4 Added some names and emails to header
new a999126 Removed a comment
new e427338 More work on comments
new 6aad946 Small change
new b4d0b3d Some formatting
new 3c7ae14 Some formatting
new 5fd0853 Corrected some indentations
new e588f87 improving classes in Matlab ISMRMRD package
new 613f6ce added base64 string userParameter to ISMRMRD schema.
new 0064539 Formatting
new 391179b Formatting
new 87417bb added initial version of SWIG Python bindings
new fa9bc6c working on Python bindings
new 838e295 more work on Python and Java bindings
new 173708f more progress on Java bindings. working getData()
new cb74efa added example code for java and python bindings
new 5567943 Merge branch 'base64param' into development
new 58ea6e0 Merge branch 'development' of vatican.nhlbi.nih.gov:/home/gitrepos/ismrmrd into development
new 1e49962 Added first parts of utility functions for generating shepp-logan phantom datasets
new 643bf27 Further improvements to shepp-logan phantom generator
new 3633b34 Merge branch 'development' of vatican.nhlbi.nih.gov:/home/gitrepos/ismrmrd into development
new cbea17a Working version of SWIG Java bindings. Still missing append functions, but a pretty complete working copy so far.
new e03d11b Merged swig java wrappers into development branch. i.e. Merge remote-tracking branch 'origin/development' into development
new 2ce8aee added custom command to make jar for java bindings
new e417bab Merge branch 'development' of github.com:nih-fmrif/ismrmrd into development
new 40d3039 added install target for java jar and library.
new 5e1fe48 Improvments to the java bindings. Now builds the jaxb stuff for the xmlheader. Creates a javadoc. Still working on the automatic loader for simplified matlab use. Still no Append methods.
new df16c08 adding JNILibLoader and Java XML header marshaller.
new ae30556 Put in the append functions stubs. Not working quite right, but the interface is correct.
new 52adfaf Created a VERY simple example java program.
new e3f5817 Fixed error in javadoc building.
new 4d5b6b0 added JAXB marshalling function to java bindings.
new 9ba431c Changed interface to the writeHeader function to make the input string a const.
new 79ef28a Changed the build procedure for the shepp logan phantom generator to link statically to the XSD files to avoid clashes with boost program options on Windows
new 6824922 Removed all of the HDF5 stuff from the matlab interface. The interface is now just contains what is need for hanling AcquisitionHeader and ImageHeader. The Java bindings are much better.
new 6859af4 Reorganizing matlab interface. Got rid of native hdf5 stuff in preparation for migrating to a thin wrapper around the java stuff.
new aebe640 Merge remote-tracking branch 'vatican/development' into development
new 0f8a011 changing bindings to build conditionally
new 50b8487 Do no create the ismrmrd_xsd library. On Windows it would export symbols from std:: which caused duplicate defined symbols when linking different libraries together. Instead we now autogenerate ismrmrd.hxx and ismrmrd.cxx in the schema folder.
new 55e061b Resolved merge conflicts for Windows adaptions
new 5b64f36 copied Gadgetron FindIsmrmrd.cmake to Ismrmrd.
new 5ce28a3 finishing up Python bindings.
new c2986c9 Added ismrmrd.py to install list for python bindings.
new 3c3eec7 added additional include directory for java bindings
new 8c92681 More CODFile
new ac872de Added C++ multi slice recon
new af48279 Merge branch 'development' of ssh://git.code.sf.net/p/ismrmrd/code into development
new d07ab1c Removed files replaced
new bae7652 Added License
new e1ea9a6 Merge branch 'master' of ssh://git.code.sf.net/p/ismrmrd/code
new 821a460 Updated readme file
new 2ce0b89 making java bindings build standalone class files
new 32e5d8b Merge branch 'development' of vatican.nhlbi.nih.gov:/home/gitrepos/ismrmrd into development
new 05ae22a Made changes to Java interface to expose getTraj and setTraj appropriately
new 4e6c6b9 giving all complex types global names in schema
new 31f0c7b Merge branch 'development' of github.com:nih-fmrif/ismrmrd into development
new 118018b Changes to schema and python bindings to fix xml header and readArray.
new 6cd599a using FindJNI for Java bindings.
new 7c73447 heavily cleansing Python binding/API
new c3fe968 first checkin on local branch
new bf7a472 adding FindNumPy.cmake for Python bindings.
new 96742ee forcing Fortran-style order in NumPy array (bindings)
new 57f173c updating FindXSD to respect find_package args.
new 36a6247 Merge remote-tracking branch 'origin/development' into hx_development
new 1c1dd3e add more data types
new f7b316d changing binding install directories to language name
new 0f7dd64 updating Java XML bindings for newest schema version.
new 91e52e7 working on Matlab + ISMRMRD + HDF5 interface
new 7e5011b Fixed size of physio time stamps.
new caf66d1 Reverted size of physiology_time_stamps change for now. Deferred to a mojore version change.
new 401fa57 adding working example for Matlab API
new 29434c9 moving Java XML API to the matlab package
new 4daeaf6 Continuing to work on matlab interace.
new 1454f25 Install a copy of the jar file inside the matlab class. Matlab api fix so that an error isreturned if the data does not exist yet.
new fb8e97f Merge branch 'development' of vatican.nhlbi.nih.gov:/home/gitrepos/ismrmrd into development
new 3e3bf48 Fixed bug is matlab api, acquisition flagbit.
new 933ab5d Changed matlab api so that readAcquisition sets the data shape to match what is given in the corresponding header.
new 0bb6439 Prepping for new matlab API.
new 54f99e1 New matlab API. Acquisitions are working. Lots more to do.
new d883988 Slowly migrating back to a (faster) matlab class.
new f49e7e4 New matlab class style interface working for acquisitions.
new c8a9671 Can now properly append acquisitions.
new 52aa30e Started to migrage ImageHeader to new style matlab api.
new dc8e0e3 Starting to fix bugs in ImageHeader in matlab api.
new bb0348c Merge branch 'development' into development_merge_hx
new f8d3082 Fixed python bindings to compile cleanly with NumPy 1.7 API
new 9c5fbca Merge branch 'development' of vatican.nhlbi.nih.gov:/home/gitrepos/ismrmrd into development
new a203d7d A simple matlab reconstruction example.
new 4fc2cd1 Fixed a few bugs in the matlab interface and add a recon example.
new 4bc1b14 adding Java XML header API docs to matlab install destination
new 3e9b42b fixing build dependencies for Java API/docs
new a082f58 Merge branch 'development_merge_hx' of vatican.nhlbi.nih.gov:/home/gitrepos/ismrmrd into development
new 1e307c1 revert to Java .jar depending on native Java library.
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