<commit_before>Change log history
==================

pymicro version 0.4.4
---------------------

* updated version number to 0.4.4, last in Python2 (Henry Proudhon)
* added some docstrings (Henry Proudhon)
* added extended sample geometry (Henry Proudhon)
* add binning support for RegArrayDetector2d (Henry Proudhon)
* fix no diffraction if no energy range is present (Henry Proudhon)
* renamed parameter fs_type into sim_type (Henry Proudhon)
* initial code for Forward Simulation of a complete X-ray experiment (Henry Proudhon)
* corrected typo (Henry Proudhon)
* added clear_data method and call it when creating a new detector (Henry Proudhon)
* added to_string method for Symmetry (Henry Proudhon)
* a Scene3d can now be automaticcaly created from an Experiment instance (Henry Proudhon)
* added sample and geometry to an Experiment (Henry Proudhon)
* modified the box_3d function to use an origin (Henry Proudhon)
* new Experiment class, with some tests (Henry Proudhon)
* start developing code to handle a complete experiment (Henry Proudhon)
* modified the way the detector tilts are handled (Henry Proudhon)
* Merge branch 'master' of https://github.com/heprom/pymicro (Henry Proudhon)
* added Co and Mn to xray data (Henry Proudhon)
* added fzDihedral function and load label grain volume when importing from dct (Henry Proudhon)
* fixed get_family calculations for hexagonal symmetry and added tests (Henry Proudhon)
* Solved version of detector (Alexiane Arnaud)
* Merge remote-tracking branch 'origin/master' (<NAME>)
* Update verbose (Alexiane Arnaud)<commit_msg>updated change log for version 0.4.5<commit_after>Change log history
==================

pymicro version 0.4.5
---------------------

* updated version number to 0.4.5 (Henry Proudhon)
* view_slice now allow to set the colormap (Henry Proudhon)
* new method to crop a microstructure (Henry Proudhon)
* factorized dilation code to create a static method just working on a numpy array (Henry Proudhon)
* updated copyright year (Henry Proudhon)
* new method to discretize a non punctual source (Henry Proudhon)
* added missing file containing the parameters for the atomic form factor calculations (Henry Proudhon)
* fix path issue when running from outside pymicro (Henry Proudhon)
* factorized code into fsim_laue method (Henry Proudhon)
* new f_atom function to compute the atomic for factor for Z<=30 (Henry Proudhon)
* added a new view_slice method (Henry Proudhon)
* fall back on matlab format when loading mask from hdf5 fails (Henry Proudhon)
* added data for Silicium material (Henry Proudhon)
* cleanup __init__.py (Henry Proudhon)
* removed old deprecated wx apps (Henry Proudhon)
* added check boxes to handle image flips (Henry Proudhon)
* updated for PyQt5 (Henry Proudhon)
* added cases to numpy_to_esrf_datatype to behave properly in Python3 (Henry Proudhon)
* add show_intersection args to add_hkl_plane_to_grain method and some cleanup (Henry Proudhon)
* added new method delete_orphan_nodes (Henry Proudhon)
* new methods get_bounds and save_to_geof (Henry Proudhon)
* added a parameter in tt_stack to control the number of projections to sum (Henry Proudhon)
* new test for find_neighbors function in Microstructure class (Henry Proudhon)
* new function find_neighbors (Henry Proudhon)
* fixed typo in docstring (Henry Proudhon)
* added method compute_elset_center_of_mass (Henry Proudhon)
* new methods get_grain_positions and from_grain_file in the Microstructure class (Henry Proudhon)
* added coverage.xml (Henry Proudhon)
* cleaning up plotting examples (Henry Proudhon)
* fixed legend when using grain_id field (Henry Proudhon)
* changed to scatter plot mode and fully moved to a kwargs mode (Henry Proudhon)
* add new get_grain_volume_fractions method to te grain class (Henry Proudhon)
* fixed missing data array (Henry Proudhon)
* fixed issue with data_type in edf_write (Henry Proudhon)
* add a new tt_stack method (Henry Proudhon)
* fix problem with mask (Henry Proudhon)
* new methode dilate_grain (Henry Proudhon)
* added new option to dilate only selected grains in a microstructure (Henry Proudhon)
* new function to create a random orientation (Henry Proudhon)
* changed package name in setup.py (Henry Proudhon)
* small fixes in from_dct method (Henry Proudhon)
* fixed probleme with grain ids being stored as none (Henry Proudhon)
* added verbose mode in grain_3d method (Henry Proudhon)
* new method get_frame_as_array (Henry Proudhon)
* added __pycache__ (Henry Proudhon)
* single sourced version number (Henry Proudhon)
* new indexed DCT file for examples (Henry Proudhon)
* remove all the deleted element ids from other elset (Henry Proudhon)
* update with voxel_size being an attribute of Microstructure (Henry Proudhon)
* polishing the new voxel_size attribute (Henry Proudhon)
* fine tuning packaging (Henry Proudhon)
* fixed bug in vtkRotateActorAroundAxis, closes #4 (Henry Proudhon)
* added an exception when a grain from the microstructure is not present in the grain map (Henry Proudhon)
* new methods compute_grain_center and recompute_grain_centers (Henry Proudhon)
* Forward simulation now support point, array and CAD geometry. (Henry Proudhon)
* Sample Geometry now supports point, array and cad properly (Henry Proudhon)
* new method is_in_array (Henry Proudhon)
* updated for new attribute voxel_size (Henry Proudhon)
* renamed grain attribute position into center (Henry Proudhon)
* added new voxel_size attribute to the Microstructure class (Henry Proudhon)
* quick fixes after renamning grain attribute position into center (Henry Proudhon)
* new test microstructure (slice from a DCT volume) (Henry Proudhon)
* use the new config file to determine the path to the data folder (Henry Proudhon)
* added test for Microstructure.from_h5 function (Henry Proudhon)
* renamed grain attribute position into center (Henry Proudhon)
* add a new config file at the project root (Henry Proudhon)
* new method to delete an elset from a FE_Mesh instance. (Henry Proudhon)
* new dilate_grains function for the microstructure module (Henry Proudhon)
* updated code with the new function from_dct to build the two microstructures (Henry Proudhon)
* quick bug fix to load the mask from a DCT reconstruction (Henry Proudhon)
* updated from_dct function in the Microstructure module (now uses the index.mat file) and new from_dct function in the Grain module (Henry Proudhon)
* added docstrings to has_grain (Henry Proudhon)
* new function merge_dct_scans (Henry Proudhon)
* added docstrings for merge_microstructures (Henry Proudhon)
* docstring fix (Henry Proudhon)
* new to_h5 and from_h5 functions (Henry Proudhon)
* new functions to create a Lattice instance from its symmetry and the list of lattice parameters (Henry Proudhon)
* replaced function names from_h5 / to_h5 by from_dream3d / to_dream3d (Henry Proudhon)
* added a crystal lattice attribute to the Microstructure class (Henry Proudhon)
* few tweaks to the new match_grains function (Henry Proudhon)
* added new match_grain function in class Microstructure (Henry Proudhon)
* replaced ''' by """ throughout the file (Henry Proudhon)
* removed unnecessary AxShowPixelValue class (Henry Proudhon)
* refactored forward simulation classes (Henry Proudhon)
* added circle=False parameter by default when computing radiographs with the radon transform (Henry Proudhon)
* made h, k and l properties in HklObject (Henry Proudhon)
* removed unused color_by_grain_id attribute (Henry Proudhon)
* removed print statement (Henry Proudhon)
* made a new class DctForwardSimulation, and updated Experiment code (Henry Proudhon)
* added circle=False parameter by default when computing radiographs with the radon transform (Henry Proudhon)
* fixed the show_array method that was broken for VTK > 6.2 (Henry Proudhon)
* resolved merge confict (Henry Proudhon)
* replaced has_key by in for python3 (Henry Proudhon)
* Add 'hkl_planes' in experiment file (Alexiane)
* Merge branch 'master' of https://github.com/heprom/pymicro (Henry Proudhon)
* add verbose mode to edf_read and edf_info (Henry Proudhon)
* Merge branch 'master' of https://github.com/heprom/pymicro (Alexiane)
* Remove unecessary print (Alexiane)
* comment out deprecated code (Alexiane)
* update save_vtk_repr method for VTK version > 5 (Henry Proudhon)
* update get_frame method for Python3 (Henry Proudhon)
* add edf file for tests (Henry Proudhon)
* also fixed edf_read and added corresponding test (Henry Proudhon)
* improved edf_info and unpack_header functions for both Python 2 and 3, added test (Henry Proudhon)
* Merge branch 'master' of https://github.com/heprom/pymicro (Henry Proudhon)
* new function to compute the diffractometer configuration and new test case (Henry Proudhon)
* now account for specific configuration of the instrument in topotomo_tilts function (Henry Proudhon)
* New Quaternion functions (Alexiane)
* normalize quaternion in __init__ (Henry Proudhon)
* increased tolerance on misorientation_from_delta for extremely low misorientation that may lead to a traceslightly larger than 3.O (Henry Proudhon)
* Merge branch 'master' of https://github.com/heprom/pymicro (Alexiane)
* New fonction for nomalization (Alexiane)
* add uv_exp field to Grain in experiment (Henry Proudhon)
* Merge branch 'master' of https://github.com/heprom/pymicro (Alexiane)
* Merge branch 'master' of https://github.com/heprom/pymicro (Henry Proudhon)
* First implementation of quaternions (Henry Proudhon)
* New functions for quaternions (Alexiane)
* Merge pull request #2 from tobyfrancis/master (Henry Proudhon)
* New functions with quaternions (Alexiane)
* New class for slits geometry (Alexiane)
* Merge remote-tracking branch 'origin/master' (Alexiane)
* fixed issue with 4x4 symmetry operators for hexagonal lattices (Henry Proudhon)
* added support to read EBSD scan from Oim (Henry Proudhon)
* new class for Slits description (Alexiane)
* new class for Slits description (Alexiane)
* python3 support (toby)
* added .coverage to .gitignore and removed from repository (Henry Proudhon)
* fixing source error in .coveragerc (Henry Proudhon)
* added coveralls to the build install requirements (Henry Proudhon)
* added code coverage for the tests (Henry Proudhon)
* added setup.py to package pymicro (Henry Proudhon)
* updated docsting for multiplicity method (Henry Proudhon)
* modified index.rst to include the README file (Henry Proudhon)
* updated .gitignore to ignore distribution files (Henry Proudhon)
* Merge branch 'master' of https://github.com/heprom/pymicro (Henry Proudhon)
* new method to create a detector from a poni file (Henry Proudhon)
* removed python 2.7 build for now (Henry Proudhon)
* added MIT license badge (Henry Proudhon)
* added testing with nosetests to travis (Henry Proudhon)
* changed dependency from skimage to scikit-image (Henry Proudhon)
* fixed travis badge path (Henry Proudhon)
* added pip instruction to travis build (Henry Proudhon)
* adding required libraries file (Henry Proudhon)
* fixing badge paths (Henry Proudhon)
* added travis file (Henry Proudhon)
* added README file (Henry Proudhon)
* reran cubic example (Henry Proudhon)
* fixed doc build (Henry Proudhon)
* added h5py as a dependency (Henry Proudhon)
* finally updated the installation section (Henry Proudhon)
* added Rodrigues2Axis method (Henry Proudhon)
* simplified a bit the View module and corrected a fex typos (Henry Proudhon)
* completed docstring of HST_read function (Henry Proudhon)
* New expression of the major axis factor (see article) (<NAME>)
* fixed old import statement (Henry Proudhon)
* allow uppercase data type from HST_info (Henry Proudhon)
* fixed Binning key in dictionnary (Henry Proudhon)
* now save binning and source energy range (Henry Proudhon)
* enforce default plane color to grey (Henry Proudhon)
* Merge branch 'master' of https://github.com/heprom/pymicro (<NAME>)
* fixed pixel size in forward simulation (<NAME>)
* added __pycache__ to .gitignore (Henry Proudhon)
* added support for python3 (Henry Proudhon)
* updated change log for version 0.4.4 (Henry Proudhon)
* Merge branch 'master' of https://github.com/heprom/pymicro (<NAME>)
* Merge branch 'master' of https://github.com/heprom/pymicro (<NAME>)
* solve version conflit (<NAME>)

pymicro version 0.4.4
---------------------

* updated version number to 0.4.4, last in Python2 (Henry Proudhon)
* added some docstrings (Henry Proudhon)
* added extended sample geometry (Henry Proudhon)
* add binning support for RegArrayDetector2d (Henry Proudhon)
* fix no diffraction if no energy range is present (Henry Proudhon)
* renamed parameter fs_type into sim_type (Henry Proudhon)
* initial code for Forward Simulation of a complete X-ray experiment (Henry Proudhon)
* corrected typo (Henry Proudhon)
* added clear_data method and call it when creating a new detector (Henry Proudhon)
* added to_string method for Symmetry (Henry Proudhon)
* a Scene3d can now be automaticcaly created from an Experiment instance (Henry Proudhon)
* added sample and geometry to an Experiment (Henry Proudhon)
* modified the box_3d function to use an origin (Henry Proudhon)
* new Experiment class, with some tests (Henry Proudhon)
* start developing code to handle a complete experiment (Henry Proudhon)
* modified the way the detector tilts are handled (Henry Proudhon)
* Merge branch 'master' of https://github.com/heprom/pymicro (Henry Proudhon)
* added Co and Mn to xray data (Henry Proudhon)
* added fzDihedral function and load label grain volume when importing from dct (Henry Proudhon)
* fixed get_family calculations for hexagonal symmetry and added tests (Henry Proudhon)
* Solved version of detector (<NAME>)
* Merge remote-tracking branch 'origin/master' (<NAME>)
* Update verbose (<NAME>)
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