Change log history¶
pymicro version 0.5.3¶
formatting according to PEP8 (Henry Proudhon)
Merge branch ‘master’ into devel (Henry Proudhon)
handle the case where the formula in empty when reading ang files (Henry Proudhon)
new test for the ebsd.py module (Henry Proudhon)
make sure we have at least one phase for grain segmentation (Henry Proudhon)
fix the name of the testing class (Henry Proudhon)
simplify try/except blocks (Henry Proudhon)
added new function to import EBSD data from CTF files (Henry Proudhon)
new batch eu2ro method, added non empty grain_map check in remove_small_grains (Henry Proudhon)
new function compute_mean_orientation (Henry Proudhon)
equation for the m factor includes abs (Henry Proudhon)
new test for the compute_m_factor function (Henry Proudhon)
new fonction to compute the m factor (Henry Proudhon)
improved docstrings (Henry Proudhon)
speed up function find_neighbors by using the grain bounding box (Henry Proudhon)
allow to pass a list of HklPlanes to this function (Henry Proudhon)
improve docstrings (Henry Proudhon)
Merge pull request #18 from heprom/basile (Basile Marchand)
Example update (bmarchand)
debugged get xdmf field for time collection grids (Aldo Marano)
Debug tests, updated documentation for new Microstructure class after_file_open method (Aldo Marano)
SampleData object constructor has a new dictionary argument aimed at containing arugments for the after_file_open method (Aldo Marano)
new Euler_rad2Rodrigues method (Henry Proudhon)
Removed automatic building of SampleData User Guide. Notebook are stored with output cells filled again (Aldo Marano)
solved kernel issue (Aldo Marano)
attempt to solve documentation autobuild with absolute pathes to import Pymicro module in Notebooks (Aldo Marano)
new kernel change for doc notebooks (Aldo Marano)
removed kernel changed in Notebook documentation building (Aldo Marano)
new attempt to solve readthedocs/nbsphinx autobuild of Notebooks (Aldo Marano)
Solved some documentation building warnings (Aldo Marano)
Changed SampleData User Guide Notebooks kernel to allow online building (Aldo Marano)
Documentation modified to have automatic execution of Notebooks when building the SampleData User Guide (Aldo Marano)
Microstructure class and SampleData derived classes documentation (Aldo Marano)
fix a bug with symmetry to compute the disorientation (Henry Proudhon)
minor update of test_derived_class in pymicro.core.tests (Aldo Marano)
light additions to SampleData unit test “test_derived_class” (Aldo Marano)
Improved data model handling for derived classes (Aldo Marano)
new example to load EBSD dat from .osc file (Henry Proudhon)
add a test for the Quaternion class (Henry Proudhon)
Documentation update, new example file for tests and doc (Aldo Marano)
new method read_osc (Henry Proudhon)
Remove __main__ test in examples and fix some py2/py3 print syntax error (bmarchand)
First draft for gitlab-ci pipeline (bmarchand)
Update python version to 3.6 in setup.py (bmarchand)
Add docstring (bmarchand)
make sure the scalar part of a Quaternion created from Euler angles is positive (Henry Proudhon)
Test example with data, use pymicro.example.PYMICRO_EXAMPLES_DATA_DIR variable (bmarchand)
Update setup.py to include examples in distribution as pymicro.examples module (bmarchand)
Add conda environment file (bmarchand)
expose more parameters for ebsd grain segmentation (Henry Proudhon)
update path for libUmatAmitex.so for grips and exterior too (Henry Proudhon)
update Ti_ebsd_demo_data.h5 (Henry Proudhon)
small update on printing out progress evolution (Henry Proudhon)
new parameter elasaniso_path for method to_amitex_fftp (Henry Proudhon)
make all unit tests pass (Aldo Marano)
General code improvement (Aldo Marano)
added 5 tutorials of the SampleData User Guide uploaded + update of documentation building files (Aldo Marano)
Added new reference files for tutorials/docs and tests (Aldo Marano)
minor adjustments for the requirements (Henry Proudhon)
updated documentation (Henry Proudhon)
new example with EBSD microstructure (Henry Proudhon)
add a new display argument in view_slice method (Henry Proudhon)
fix radian to degree conversion in change_orientation_reference_frame (Henry Proudhon)
small formatting changes (Henry Proudhon)
added slip traces vizualisation to the view_slice method (Henry Proudhon)
new method to change the orientation reference frame (Henry Proudhon)
improved doctrings (Henry Proudhon)
First attempt to introduce nbsphinx in pymicro’s autobuild, to make pymicro’s documentation from jupyter Notebooks.
Debugued auto mesh scaling in automatic meshers (Aldo Marano)
New initialization method _after_file_open, called when a hdf5 file is opened by the SampleData class (or inherited class) (Aldo Marano)
Minor debug (Aldo Marano)
Cleaned a few # TODO already done (Aldo Marano)
New module SDGridUtils: classes to interact and apply operations on Grids (Images and Meshes) (Aldo Marano)
Debugued elset and nodeset compression and added Skip phase ID 0 to Image mesher (Aldo Marano)
debuged ‘add_grid_time’ –> Now OK – Microstructure method ‘from_amitex_fftp’ now loads Amitex output fields as temporal series (Aldo Marano)
Implemented handling of time series attributes for XDMF grids (fields with values through time) (Aldo Marano)
Implementation of dictionary and attribute like access for SampleData datasets items (Aldo Marano)
Improved SampleData print methods (Aldo Marano)
Creation of a autorepack flag that controls activation of hdf5 file repacking in SampleData class destructor (Aldo Marano)
Added data normalization option for data compression (Aldo Marano)
Pass compression settings for all SampleData methods (Aldo Marano)
Debuged XDMF spacing and origin ordering (Aldo Marano)
Adapted Microstructure.from_amitex_fftp to new methods in SDAmitexUtils (Aldo Marano)
Added loading of finite strain stress/strain and internal variables fields to load_amitex_output_fields method (Aldo Marano)
Implemented loading of .std amitex output files for finite strain simulations (Aldo Marano)
implemented new definitive ordering convention of 2nd order tensors in vector notation (Aldo Marano)
Moved Amitex input/ouput utility methods from pymicro.crystal.microstructure to new module pymicro.core.utils.SDAmitexUtils (Aldo Marano)
Added .ut file argument for SDZset load_output methods (Aldo Marano)
adjust __repr__ method for the Lattice class (Henry Proudhon)
convert lattice constants to nm when importing an EBSD scan (Henry Proudhon)
improved the speed of the create_IPF_map method by using the grain bounding boxes (Henry Proudhon)
improved __repr__methods (Henry Proudhon)
Modified examples SampleData files to adapt tests to new data model (Aldo Marano)
Minor corrections (Aldo Marano)
Merge branch ‘AM_Zset_utils’ into master_test (Aldo Marano)
Orientation repr correction (Aldo Marano)
Added method to compute orthotropic elastic moduli (the 3 Young, 3 Poisson and 3 Shear moduli) from stiffness matrix in Lattice class (Aldo Marano)
fix typos in add_IPF_maps (Henry Proudhon)
new method add_IPF_maps to create and store all 3 IPF maps at once (Henry Proudhon)
data files modified after introducing phaes in Microstructure (Henry Proudhon)
add a new method to compute ipf coloring (Henry Proudhon)
add pyramidal1 <a> slip systems (Henry Proudhon)
fix miller indices in the test_4indices_representation (Henry Proudhon)
new option to use a mask for the tt_rock function (Henry Proudhon)
fixed a small issue in unit_arrow_3d (Henry Proudhon)
now create a default hexagonal lattice when using the 4 indices notation (Henry Proudhon)
add method move_vector_to_FZ to the Symmetry class (Henry Proudhon)
add more cases to test the Miller-Bravais conversion for the hexagonal lattice (Henry Proudhon)
Moved storaged of mesh element/node tags and grid field indexes to String arrays (Aldo Marano)
Added a new data structure for SampleData objects (Aldo Marano)
Adapted to_amitex_fftp to produce Amitex vtk input files from Microstructure ‘mask’ (Aldo Marano)
added generic methods in Microstructure class to read Amitex_fftp output files (Aldo Marano)
Small corrections in lattice and Microstructure class, introduced new method -from_amitex_fftp’ (Aldo Marano)
Bug correction in SampleData method ‘get_description’ (Aldo Marano)
corrected typo after refactoring (Henry Proudhon)
added method compute_ipf_maps (Henry Proudhon)
new method to read EBSD scan from .ang files (Henry Proudhon)
Fixed bug with empty node tags names where stored in node_tag_list (Aldo Marano)
new method get_slip_systems for the Lattice class (Henry Proudhon)
added new option show_grain_ids in the view_slice method (Henry Proudhon)
Merge branch ‘master’ into AM_utils_tmp (Aldo Marano)
Added some control options to Microstructure crop and mesh_grain_map (Aldo Marano)
Added output control for SDMeshers and auto-mesh resize from Image dimensions (Aldo Marano)
Small debugs for pathes in SampleData (Aldo Marano)
improve how phases are handled in Microstructure (Henry Proudhon)
add method set_lattice to CrystallinePhase (Henry Proudhon)
transpose volume data in from_labdct (Henry Proudhon)
added method to remove small grains with a volume threshold (Aldo Marano)
Correction of Microstructure.crop method to crop all fields in CellData group (Aldo Marano)
new from_labdct method (Henry Proudhon)
new test to add phases (Henry Proudhon)
the Microstructure class now has material phases (Henry Proudhon)
OimPhase now extends CrystallinePhase (Henry Proudhon)
new method add_slip_system_to_grain (Henry Proudhon)
new tt_rock method (Henry Proudhon)
add CrystallinePhase tests (Henry Proudhon)
continues implementing the CrystallinePhase class (Henry Proudhon)
Added clean grain map method to Microstructure class (Aldo Marano)
Adapted Microstructure ‘from_ebsd’ to latest changes in SampleData and Microstructure classes (Aldo Marano)
Add print of std output for morphological image cleaner (Aldo Marano)
minor SampleData print method debug (Aldo Marano)
Correct matlab ‘addpath’ command generation for automatic meshing tools (Aldo Marano)
light modifications for F. Nguyen meshing tools integration (Aldo Marano)
logo adjustment (Henry Proudhon)
removed blank spaces at endlines, solved a bug when having a None name entering SampleData._name_or_node_to_path (Aldo Marano)
Complete Integration of F. Nguyen Matlab/Zset image meshing tools in SDMeshers class (Aldo Marano)
new pymicro logo (Henry Proudhon)
start to add support for multi-phase materials (Henry Proudhon)
removed non ascii character in compute_grain_volume (Henry Proudhon)
remove non ascii character in create_orientation_map (Henry Proudhon)
Add automatic transposition of tensor fields components in hdf5 arrays to match Paraview/XDMF ordering convention (Aldo Marano)
Correction of field component names when writing Zset output from SampleData (Aldo Marano)
Bug solving: mesh field padding ignored when using add_field on Image groups (Aldo Marano)
Add methods to write SampleData Image groups as Zset outputs of fields defined on a regular hexaedral mesh (Aldo Marano)
Bug solving: mesh field padding ignored when using add_field on Image groups (Aldo Marano)
updated change log for version 0.5.2 (Henry Proudhon)
Bug corrections (print_index) (Aldo Marano)
SDZset : * method to read Zset output fields with automatic construction of vector and tensor fields (Aldo Marano)
Bug corrections (print_index) (Aldo Marano)
Minor debugs (Aldo Marano)
Added method to write Zset output from SampleData mesh groups and fields datasets (Aldo Marano)
Handling of nodes and elements IDs for returning basictools mesh objects (Aldo Marano)
Add computation of nodal normal fields from element wise normal fields for SampleData mesh groups (Aldo Marano)
New methods for mesh elements and elements tag manipulation (Aldo Marano)
Added a new class to handle Zset post_processing .inp blocks, based on SDZset (parent class) (Aldo Marano)
deform_mesh Zset mesher command interface implemented in SDZsetMesher (Aldo Marano)
Zset command options passing modification
New class SDZsetFieldTransfer to serve as interface between SampleData and Zset transfer_fields scripts (Aldo Marano)
Improved string templates handling in SDZsetUtils
New organization of core.utils.Zsetutils (Aldo Marano)
a few minor changes (Henry Proudhon)
SampleData class update with mesh field padding implementation (Aldo Marano)
Add method to reinitialize mesher commands (SDZsetMesher) (Aldo Marano)
added squeeze for the ids_to_blank array and improved docstrings (Henry Proudhon)
Handling of element wise fields who are defined only on bulk
Creation of multiple SDZsetMesher class methods to use Zset mesher commands (Aldo Marano)
SDZsetMesher class : Add safety check to ensure all mesher template arguments are set before runing mesher script (Aldo Marano)
Add mesh script and files cleaning methods in SDZsetMesher class
First minimal implementation of a working automatic Zset mesher
Debuged Sdmeshers and ScriptTemplate (Aldo Marano)
Creation of a dedicated class to handle script templates ScriptTemplate (Aldo Marano)
Addition of core subpackage utils to implement interfaces between SampleData objects and external tools (Aldo Marano)
pymicro version 0.5.2¶
updated version number to 0.5.2 (Henry Proudhon)
add methods to compute grain aspect ratios and sphericities (Henry Proudhon)
removed unnecessary print statement (Henry Proudhon)
new test for get_grain properties (Henry Proudhon)
fix all the get_grain properties methods, added docstrings (Henry Proudhon)
new method to build a condition to filter the grain data table based on a list of grain ids (Henry Proudhon)
Handling of nodes and elements IDs for returning basictools mesh objects (Aldo Marano)
Travis build bug solving (Aldo Marano)
Change one AssertEqual to AssertAlmostEqual to solve Travis build issues in test_Lattice.py (Aldo Marano)
Debuged test BasicTools_binding in core.tests package (Aldo Marano)
Merge pull request #12 from basileMarchand/master (Aldo Marano)
Disable system_site_packages in travis (because of the previous python version update) (Basile MARCHAND)
Update travis to use python 3.6 instead of python 3.5 neadeed for basic tools dependency (Basile MARCHAND)
Update setup.py and requirements.txt in order to install all required dependency. (Basile MARCHAND)
axes label modification allowed (Alexiane Arnaud)
change the way grain dilation is made replacing min by the most frequent value within the neighbors (Henry Proudhon)
debug print_dataset_content method, add new method to change indexnames in the dataset (set_new_indexname), new field index naming convention: if no indexname is provided indexname for fields is ‘grid_indexname_fieldname’ (Aldo Marano)
updated example for recent changes, fixes #10 (Henry Proudhon)
replaced is not by != to test the length of the elastic_constants list (Henry Proudhon)
SampleData class update -> Mesh field padding implementation to allow field shape compliance with mesh elements number (Aldo Marano)
Merge branch ‘AM_SD_grids’ (Aldo Marano) - Handling of element wise fields who are defined only on bulk (same dimensionality than the mesh) or boundary elements (dimensionality lower than the mesh), bulk and boundary elements count and element wise fields padding (Aldo Marano) - Solved issue with Mesh Geometry groups removal when removing recursively a Mesh Group with SampleData class (Aldo Marano)
Element and Node tags loading is now optional in get_mesh (Aldo Marano)
merged changes from last commit (Henry Proudhon)
fine tune to_amitex method (Henry Proudhon)
new method to create a VTK colormap from pyplot (Henry Proudhon)
more default values to init CrystallinePhase (Henry Proudhon)
added option overwrite_hdf5=True (Henry Proudhon)
corrections to remove documentation build warnings (Aldo Marano)
Merge branch ‘AM_SD_grids’ (Aldo Marano)
solved bug for get_element method
add_mesh and add_image now return mesh and image BasicTools objects (Aldo Marano)
Debuged connectivity shape and nature (numpy table option required to write .geof file) in get_mesh (Aldo Marano)
Add compression of elset indicator fields as defaut setting (1s and 0s => very strong compression ratios and no issue with Paraview visualization) (Aldo Marano)
Add option to dilate_grains, to automatically dilate until ID 0 is removed from grain map (Aldo Marano)
Debug to get passed nosetests –> OK (Aldo Marano)
Changed sample data nosetests reference file due to non retrocompatibility of recent developments (Aldo Marano)
Documentation update (docstrings), Microstructure Class update: renumbering grains consistant with grain map -> methods to recompute grain data table from grain map -> methods to synchronize grain data table with grain map (Aldo Marano)
Solved xdmf node removal bug (Aldo Marano)
Splitting of morphological cleaning and meshing methods (Aldo Marano)
updated example to python3 (Henry Proudhon)
updated change log for version 0.5.1 (Henry Proudhon)
Merge branch ‘master’ into AM_SD_grids (Aldo Marano)
Documentation build correction for Read the Docs online doc (Aldo Marano)
Debug to get passed the nosetests (Aldo Marano)
minor correction (Aldo Marano)
Multi_phase_mesher –> include storage of surface mesh and cleaned multi phase image (Aldo Marano)
Implementation of XDMF Sets format for elements and node sets (Aldo Marano)
SampleData automatic multiphase mesher V0 implementation (Aldo Marano)
Add method to create a grainID or orientation FEM field (resp. scalar/vector). Add ‘is_mesh’ SampleData private method (Aldo Marano)
Utility methods implemented to add a data array or a mesh from a file, create an orientation map in the Microstucture class from grain map and orientation data in GrainDataTable (Aldo Marano)
Add image automatic transposition whith add_field, and get_node, to get (X, Y, Z, Dim) indexing consistent with Paraview rendering (Aldo Marano)
Increased functionalities of print methods for conveniance (Aldo Marano)
New methods to convert an image group into a mesh group, with nodal Field transfer at least (Aldo Marano)
SampleData dev: integration with BasicTools mesh objects -> corrected bugs in nodesID and element tag indexing to allow from geof to geof (Aldo Marano)
SampleData dev: BasicTools mesh object integration (Aldo Marano)
Changed mesh data model and mesh_object support (Aldo Marano)
Debuged add_table_col consequences on table update at SD file opening (Aldo Marano)
Implemented possibility to add new columns to tables in dataset already existing structured storage tables (Aldo Marano)
SampleData dev: Solved initialization bugs with new method add_XXX methods implementation (Aldo Marano)
Moved to BasicTools ConstantRectilinearMesh object as Image based data object (Aldo Marano)
Solved a documentation construction bug, method pause_for_visualization options to open dataset with Paraview and / or Vitables (Aldo Marano)
pymicro version 0.5.1¶
updated version number to 0.5.1 (Henry Proudhon)
use Euler2Rodrigues directly in add_grains method (Henry Proudhon)
corrected examples according to recent changes in the Microstructure class (Henry Proudhon)
Add bibliography file to sphinxcontrib bibtex configuration (Aldo Marano)
Debug documentation to remove warnings and allow Read the Docs automatic doc building (Aldo Marano)
Add bibliography file to sphinxcontrib bibtex configuration (Aldo Marano)
Attempt to solve Travis building problems n2 (Aldo Marano)
Debug for travis build (Aldo Marano)
change the id used to pad arrays when preparing for amitex (Henry Proudhon)
updated test files after changes in the microstructure geometry calculations (Henry Proudhon)
updated the calculation of grain center to place the first voxel at (0.5, 0.5, 0.5) (Henry Proudhon)
Merge pull request #7 from basileMarchand/master (Henry Proudhon)
new method stiffness_matrix for the Symmetry class and new CrystallinePhase class (Henry Proudhon)
Update .travis.yml (Basile Marchand)
Update .travis.yml (Basile Marchand)
Update .travis.yml (Basile Marchand)
Update travis config for hdf5 (Basile MARCHAND)
updated change log for version 0.5.0 (Henry Proudhon)
pymicro version 0.5.0¶
updated version number to 0.5.0 (Henry Proudhon)
add element type c3d8r (Henry Proudhon)
new methods to transform vector/matrix to and from crystal/sample frames (Henry Proudhon)
bug fix in compute_grain_center method (Henry Proudhon)
new test for the renumber_grains function (Henry Proudhon)
new function to renumber the grains consecutively (Henry Proudhon)
try fixing hdf5 build error in travis CI (Henry Proudhon)
mark compute_grains_geometry as needing work (Henry Proudhon)
change how we recompute the grain geometries (Henry Proudhon)
fixed issue in example data file (Henry Proudhon)
improve performances while calculating grain geometry by using bounding boxes (Henry Proudhon)
fixed a performance issue with recompute_grain_bounding_boxes (Henry Proudhon)
fix the id of renumbered grains in merge_mirostructures (Henry Proudhon)
add test for merge_microstructures method (Henry Proudhon)
added test for the crop method (Henry Proudhon)
added a crop_name parameter to the crop method (Henry Proudhon)
a few tweaks to the merge_mirostructures method (Henry Proudhon)
add a few print statements to merge_microstructures (Henry Proudhon)
updated the from_grain_file method with the new SampleData organisation (Henry Proudhon)
fix access to old name attribute (Henry Proudhon)
recompute the geometry of the grains after the merge (Henry Proudhon)
follow up on merge_microstructures (Henry Proudhon)
fixing method merge_microstructures for the new sampleData organisation (Henry Proudhon)
fix the crop method in the Microstructure class (Henry Proudhon)
missing spaces (Henry Proudhon)
fix unit in compute_grain_volume (Henry Proudhon)
new IPF example to plot crystal rotation (Henry Proudhon)
additional fixes in set_map_field and plot (Henry Proudhon)
updated pole figure examples for the texture module changes (Henry Proudhon)
updated docstring (Henry Proudhon)
fixed set_map_field with the new Microstructure organization (Henry Proudhon)
new test for add_grains method (Henry Proudhon)
updated code to the new Mirostructure organisation inherited from SampleData (Henry Proudhon)
new function to add a list of grains to the microstructure (Henry Proudhon)
improved function to_amitex_fftp (Henry Proudhon)
Solve non-regression test error (Aldo Marano)
Bug introduced in the last commit solved –> non regression test OK (Aldo Marano)
improved from_indices method in the SlipSystem class (Henry Proudhon)
new parameters in to_amitex_fftp to add a buffer layer (Henry Proudhon)
(SampleData dev) Externalization of global variables of the core package in a specific module (Aldo Marano)
fixed grain map test in recompute_grain_bounding_boxes (Henry Proudhon)
added slip systems for hexagonal lattice (Henry Proudhon)
new method from_ebsd (Henry Proudhon)
reshape grain_map and mask to 3D if only 2D (Henry Proudhon)
new segment_grains method, transposed results to match pymicro’s convention, various improvements (Henry Proudhon)
Revert “Revert “new files for new test in Microstructure class”” (Alexiane Arnaud)
added overwrite_hdf5=True when creating microstructures from existing data (Henry Proudhon)
Revert “new files for new test in Microstructure class” (Alexiane Arnaud)
allow zero padding when loading the mask (Henry Proudhon)
Bug fixes in non regression tests. All OK now (Aldo Marano)
Bug fix –> Initialization bug with SampleData attribute Filters and with some methods argument name changes (Aldo Marano)
SampleData documentation corrections (Aldo Marano)
Revert “Test to solve read the doc compilation errors” (Aldo Marano)
New test to solve doc building issues on ReadThedocs (Aldo Marano)
Test to solve read the doc compilation errors (Aldo Marano)
Splitted crystal documentation into three pages, one for each module (lattice, microstructure, texture) (Aldo Marano)
Resolved most of documentation building Warnings and Errors (Aldo Marano)
Updated documentation of the samples modules and the core package (Aldo Marano)
Introduction of pymicro.core package into documentation and core.samples module (Aldo Marano)
end of code style modifications (Henry Proudhon)
removed extra parentheses (Henry Proudhon)
simpler Microstructure constructor by removing file_path (Henry Proudhon)
fix for Python3 (Henry Proudhon)
Correction of some bugs in documentation buildings, in progress. (Aldo Marano)
continuing to improve code style (Henry Proudhon)
improved docstring in __contains__ method (Henry Proudhon)
fixed typos and lines longer than 80 characters, improved documentation (Henry Proudhon)
fix pb with comparing two sequences as boolean (Henry Proudhon)
updates to account that Microstructure does not have a name attribute anymore (Henry Proudhon)
get rid of the grain_ids alias for now (Henry Proudhon)
cosmetic adjustments (Henry Proudhon)
fixed relace=True in set_mask, added a from_legacy_h5 method (Henry Proudhon)
improved getter and setter methods for sample_name and description (Henry Proudhon)
merged the name attribute with the sample_name of class SampleData (Henry Proudhon)
Correction of variable type for spacing attribute of SampleData image nodes (Aldo Marano)
moved code block outside except statement, improved code style (Henry Proudhon)
Merge branch ‘SampleData’ Merge dependency specification for SampleData integration (Aldo Marano)
Merge pull request #5 from Aldo Marano/SampleData (Henry Proudhon)
Added new requirements for SampleData integration (Aldo Marano)
SampleData/Pymicro integration: non-regression tests for core.samples and new methods to get specific data nodes disk size (Aldo Marano)
SampleData/Pymicro integration: new methods to set structured table data and specifics counterparts (Aldo Marano)
SampleData/Pymicro integration: new method copy_sample (Aldo Marano)
Externalization of Image and Mesh handling classes (Aldo Marano)
SampleData integration dev: finalization of the generic data model development (Aldo Marano)
Merge branch ‘master’ into SampleData_merge_master (Aldo Marano)
MAJOR DEVELOPMENT: SampleData and Pymicro merged, SampleData becomes the core package of Pymicro (Aldo Marano)
new files for new test in Microstructure class (Henry Proudhon)
new test to cover from_neper method (Henry Proudhon)
fix axes of the grain_map read from neper, improved slice_view (Henry Proudhon)
new method to_amitex_fftp (Henry Proudhon)
fixed typos in docstring (Henry Proudhon)
SampleData dev: small corrections (Aldo Marano)
added new method to import microstructure from a neper raster tesselation (Henry Proudhon)
added rotate_mesh and translate_mesh functions (Henry Proudhon)
changed the way the region ids are tested in show_boundaries (Henry Proudhon)
SampleData Development: alias name mechanism implementation (Aldo Marano)
SampleData Class Development: Last corrections for add_data_array (Aldo Marano)
SampleData Development: Finalization of add_data_array : xdmf field type detection developed (Aldo Marano)
SampleData Class development (Aldo Marano)
update dilate_labels fro 2D arrays (Henry Proudhon)
updated test for SampleData integration within the Microstructure class (Henry Proudhon)
continuing integration with the Microstructure class (Henry Proudhon)
continuing integration with SampleData class, fixed the set_grain_map and voxel_size issues (Henry Proudhon)
SampleData developments: changed information messages implementation (Aldo Marano)
add docstring to dct_projection method (Henry Proudhon)
change the way the get_grain_ids works (Henry Proudhon)
improve how the depth of the elset_id field is determined (Henry Proudhon)
factorized some code in new grain_projections method, improved docstrings (Henry Proudhon)
forward simulation now account for detector flips, also added an option to limit the grains used in the simulation (Henry Proudhon)
merge last SampleData modifs with Microstructure modifs (Aldo Marano)
(Debug) SampleData: remove errors when adding a node already existing (Aldo Marano)
moving to SampleData for storing image fields in the Microstructure class (Henry Proudhon)
Path update in imports for SampleData code in package core (Aldo Marano)
Introduction of SampleData source code for integration with Pymicro (Aldo Marano)
new class to handle chemical elements and their densities (Henry Proudhon)
added new example to plot atomic structure factors (Henry Proudhon)
corrected print statements for Python 3 (Henry Proudhon)
updated change log for version 0.4.5 (Henry Proudhon)
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) (Alexiane Arnaud)
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 (Alexiane Arnaud)
fixed pixel size in forward simulation (Alexiane Arnaud)
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 (Alexiane Arnaud)
Merge branch ‘master’ of https://github.com/heprom/pymicro (Alexiane Arnaud)
solve version conflit (Alexiane Arnaud)
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’ (Alexiane Arnaud)
Update verbose (Alexiane Arnaud)
New detector definition (Alexiane Arnaud)
added simple region growing algorithm (Henry Proudhon)
fixed bug after HST_info update (Henry Proudhon)
Merge branch ‘master’ of https://github.com/heprom/pymicro (Henry Proudhon)
added support to load a microstructure from a DCT reconstruction (Henry Proudhon)
Update LICENSE.md (Henry Proudhon)
new grain_3d_planes example (Henry Proudhon)
added sst_symmetry function so that ipf plotting now supports both cubic and hexagonal symmetries (Henry Proudhon)
cosmetic change from B to g (Henry Proudhon)
removed labels from ipf plot (Henry Proudhon)
added a plot_ipf_symmetry method (Henry Proudhon)
get_family now supports 4 indices for hexagonal symmetry (Henry Proudhon)
added a new test for the scattering_vector method (Henry Proudhon)
quick fix for new symmetry code (Henry Proudhon)
New folder organisation (Alexiane Arnaud)
Merge branch ‘master’ of https://github.com/heprom/pymicro (Alexiane Arnaud)
Test on detector tilt (Alexiane Arnaud)
add the colorbar (Henry Proudhon)
make use of the Symmetry class (Henry Proudhon)
updated examples with changes in the code (Henry Proudhon)
add new example using a color field within a IPF plot (Henry Proudhon)
fix an issue when using a color field (Henry Proudhon)
update to use the new Symmetry class (Henry Proudhon)
new Class Symmetry to handle lattice symmetries (Henry Proudhon)
added multiplicity method (Henry Proudhon)
remove unecessary for loops (Henry Proudhon)
generalized get_family method with any hkl triplet and any symmetry (Henry Proudhon)
fix a problem with the size of the arguments in pixel_to_lab (Henry Proudhon)
Get family new item (Alexiane Arnaud)
Build list new item (Alexiane Arnaud)
fixed typo in last commit (Henry Proudhon)
update how negative energy is handled (Henry Proudhon)
changed the way the friedel pairs are handled for diffraction (Henry Proudhon)
added new lattice plane families (Henry Proudhon)
more complete test for project_along_direction (Henry Proudhon)
get_family now accept any hkl combination (Henry Proudhon)
added 133 family to the get_family method (Henry Proudhon)
New Laue functions (Alexiane Arnaud)
New Laue functions (Alexiane Arnaud)
New function to get ellipsis easily (Alexiane Arnaud)
Merge branch ‘master’ of https://github.com/heprom/pymicro (Alexiane Arnaud)
now use a floating point precsion when testing if points are on the detector (Henry Proudhon)
the gnomonic projection of detecot image now uses the generalized code (Henry Proudhon)
added test for the gnomonic projection (Henry Proudhon)
test data for the gnomonic projection (Henry Proudhon)
small cleanup in lab_to_pixel (Henry Proudhon)
new test_detectors module (Henry Proudhon)
lab_to_pixel can now be used with arrays of points (Henry Proudhon)
FIXME message (Henry Proudhon)
explicitely use the centering parameter when creating a lattice instance (Henry Proudhon)
fixed print bug in print_camera_settings (Henry Proudhon)
fixed missing abs in lab_to_pixel (Henry Proudhon)
pixel_to_lab can now use arrays (Henry Proudhon)
removed unnecessary staticmethod decorator, new test (Henry Proudhon)
updated import after refactoring (Henry Proudhon)
updated import after refactoring (Henry Proudhon)
generalized the gnomonic projection (Henry Proudhon)
test the gnomonic projection with normal and non normal incidence (Henry Proudhon)
Merge branch ‘master’ of https://github.com/heprom/pymicro (Alexiane Arnaud)
cleanup and new function point_cloud_3d (Henry Proudhon)
renamed gethkl_from_two_directions to indices_from_two_directions plus some cleanup (Henry Proudhon)
added head docstrings (Henry Proudhon)
some cleanup in the laue module (Henry Proudhon)
added a new test with select_lambda (Henry Proudhon)
updated change log for version 0.4.3 (Henry Proudhon)
Merge branch ‘master’ of https://github.com/heprom/pymicro (Alexiane Arnaud)
Merge branch ‘master’ of https://github.com/heprom/pymicro (Alexiane Arnaud)
Practical modification of transmission plot (Alexiane Arnaud)
pymicro version 0.4.3¶
updated version number to 0.4.3 (Henry Proudhon)
much faster version of recad (Henry Proudhon)
small fix in gnomonic_projection_point2 (Henry Proudhon)
force direction to be a numpy array in case a list is given (Henry Proudhon)
updated compute_ellipsis and added gnomonic_projection_point2 for non normal X-ray incidence (Henry Proudhon)
refactoring after renaming four_to_three_indices method (Henry Proudhon)
some cleanup in names (Henry Proudhon)
updated the use of project_along_direction to its new signature (Henry Proudhon)
make the width variable being an integer (Henry Proudhon)
changed the pole list from a vector list to a list of HklPlane instances (Henry Proudhon)
change in from_h5 signature to be more versatile (Henry Proudhon)
added the possibility to directly pass a list of HklPlane instances to define the poles in a PoleFigure (Henry Proudhon)
quick fix on removing test files (Henry Proudhon)
new method to create a slip system from miller indices (Henry Proudhon)
added append to file mode to function HST_write (Henry Proudhon)
gethkl_fromtwo_directions new function (Alexiane Arnaud)
new tests for the vol_utils module (Henry Proudhon)
added new method min_max_cumsum and refactored auto_min_max code (Henry Proudhon)
the X-ray beam is no longer restricted to the X-axis (Henry Proudhon)
new apply_rotation_to_actor method and factorized code to use it (Henry Proudhon)
re-do the poll system update (Alexiane Arnaud)
Global commit (Alexiane Arnaud)
Add extinctions to the build_list function (Alexiane Arnaud)
convert bool arrays to uint8 in HST_write when not using pack_binary option (Henry Proudhon)
added try block to import modules (Henry Proudhon)
added symmetry operators for hexagonal lattice (Henry Proudhon)
added verbose option in poll_system (Henry Proudhon)
changed orthorhombic calls in tests according last commit (Henry Proudhon)
Orthorhombic modification (Alexiane Arnaud)
use the numpy array tye to create the right vtk array type in numpy_array_to_vtk_grid (Henry Proudhon)
fixed issue with Lattice transformation matrix in non cubic case (Henry Proudhon)
added new regression case for topotomo_tilts (Henry Proudhon)
updated slip traces example (Henry Proudhon)
fixed issue with calling slip_trace from plot_slip_traces method (Henry Proudhon)
exposed solve_trig_equation method and added regression tests (Henry Proudhon)
additional test for dct_omega_angles (Henry Proudhon)
added plane_origins option in grain_3d (Henry Proudhon)
added test for HklDirection 4 indices representation (Henry Proudhon)
fixed three_to_four_indices and the like for HklPlane and HklDirection classes (Henry Proudhon)
fixed docstring for hexagonal_lattice_grid (Henry Proudhon)
corrected example description (Henry Proudhon)
added non regression test for .info files without DATA_TYPE entry (Henry Proudhon)
fix data type issue in HST_info (Henry Proudhon)
Merge remote-tracking branch ‘origin/master’ (Alexiane Arnaud)
factorized code for slip plane traces (Henry Proudhon)
added initialisation of U field (Henry Proudhon)
removed print statement in misorientation_angle_from_delta (Henry Proudhon)
added symmetry operators for orthorhombic and an option to keep friedel pairs in skip_higher_order (Henry Proudhon)
update gnomonic projection code with a new gnomonic_projection_point method (Henry Proudhon)
added new test for gnomonic_projection_point method (Henry Proudhon)
fix import of tifffile (Henry Proudhon)
update Image Processing folder (Alexiane Arnaud)
updated cookbook to better explain the orientation matrix (Henry Proudhon)
from_euler now support the Roe convention to compute the orientation matrix (Henry Proudhon)
pymicro version 0.4.2¶
updated version number (Henry Proudhon)
new method pole_figure_3d and updated example (Henry Proudhon)
added new get method to retreive the orientation list (Henry Proudhon)
small code style improvements (Henry Proudhon)
corrected indentation in pointset_registration.rst (Henry Proudhon)
updated examples (Henry Proudhon)
updated .gitignore after changing source path (Henry Proudhon)
added point set registration entry in cookbook (Henry Proudhon)
updated paths to reflect source move to pymicro folder (Henry Proudhon)
removed files from tree corresponding to the previous move (Henry Proudhon)
moved source to a pymicro folder so the docs build properly on rtfd (Henry Proudhon)
try to fix path to build autodoc (Henry Proudhon)
added requirements file to build the documentation (Henry Proudhon)
removed old EBSDMicrostructure class (Henry Proudhon)
changed single quote to double quotes in docstrings (Henry Proudhon)
fixed issue with the no more needed col parameter (Henry Proudhon)
plot_sst now displays the 3 main crystal axes, refactored some code to use get_color_from_field, docstring improvements (Henry Proudhon)
changed a bit how the elset names are handled in compute_elset_id_field, plus docstrings and vtk version specific code (Henry Proudhon)
added new method to select cells in vtkUnstructuredGrid (Henry Proudhon)
corrected type in set_rank (Henry Proudhon)
updated make_vtu to supprt .mesh files and added docstring (Henry Proudhon)
new method load_from_mesh to create FE_Mesh object from .mesh files (Henry Proudhon)
new boundary parameter in extract_poly_data (Henry Proudhon)
factorized code with vtkExtractGeometry in new method extract_poly_data (Henry Proudhon)
Merge branch ‘master’ of https://github.com/heprom/pymicro (Henry Proudhon)
added nodal field support (Henry Proudhon)
Merge remote-tracking branch ‘origin/master’ (Alexiane Arnaud)
Update poll system function to see every solutions (Alexiane Arnaud)
fixed rounding float error in misorientation_angle_from_delta (Henry Proudhon)
added reference in misorientation_MacKenzie docstring (Henry Proudhon)
added sphinx-bibtex extension to handle references and started using it (Henry Proudhon)
added new function poll_system and confidence_index from the work of Wijdene (Henry Proudhon)
cosmetic changes (Henry Proudhon)
added todo to improve FZ computation (Henry Proudhon)
new tests for Rodrigues fundamental zone. (Henry Proudhon)
new methods to move rotations to the fundamental zone of the Rodrigues space. (Henry Proudhon)
updated OrientationMatrix2Euler method and strated FZ code (Henry Proudhon)
fixed plane normal not showing issue and cleaned the code by removing method add_plane_to_grid_with_normal (Henry Proudhon)
remove outdated read_dif method (Henry Proudhon)
change type of energy_lim param to list (support assignment) (Henry Proudhon)
change energy bound to 200 keV (Henry Proudhon)
added docstring for the read_image_sequence method. (Henry Proudhon)
added missing parameter in docstring and fixed print statements (Henry Proudhon)
fixed a small issue with working with a uint8 data array, now the array is only converted at the end of the function to uint8 (Henry Proudhon)
new recipe showing how to perform point set registration (Henry Proudhon)
new line_actor method to factorize some code (Henry Proudhon)
more detailed doctsring for compute_affine_transform (Henry Proudhon)
made line_3d and circle_line_3d use the new build_line_mesh function (Henry Proudhon)
new function build_line_mesh (Henry Proudhon)
new method to compute affine transform by point set registration (Henry Proudhon)
changes teh notation from B to g for the orientation matrix to avoid confusion. (Henry Proudhon)
added more Orientation tests (Henry Proudhon)
removed unnecessary eps parameter and fix docstrings (Henry Proudhon)
make sure origin is set properly in lattice_3d_with_planes (Henry Proudhon)
make sure origin is an array (Henry Proudhon)
Merge branch ‘master’ of https://github.com/heprom/pymicro (Henry Proudhon)
new gnomonic projection function (Henry Proudhon)
set default for origin in project_along_direction and docstring update (Henry Proudhon)
Correction : from compute_ellpisis to compute_ellipsis (Alexiane Arnaud)
cleaning up the new stitch method (Henry Proudhon)
new method to stitch image series (Henry Proudhon)
new method read_image_sequence (Henry Proudhon)
more docstring fixes (Henry Proudhon)
auto_min_max docstring improvements plus minor tweaks (Henry Proudhon)
updated change log for version 0.4.1 (Henry Proudhon)
pymicro version 0.4.1¶
updated version number (Henry Proudhon)
make sure motion components are interpreted as float in vtkMove animation (Henry Proudhon)
corrected typo in print statement (Henry Proudhon)
Merge remote-tracking branch ‘origin/master’ (Henry Proudhon)
updated compute_Laue_pattern method with new parameters such as spectrum and color_spots_by_energy (Henry Proudhon)
update imports to match the refactoring of the fitting module into the xray package (Henry Proudhon)
improved compute_Laue_pattern with new available methods from the Detector2d class (Henry Proudhon)
improved compute_Laue_pattern with new available methods from the Detector2d class (Henry Proudhon)
deleted excluded files in docs/_build directory (Henry Proudhon)
fixed a visibility issue when using an assembly instead of single actor (Henry Proudhon)
added the possibility to use a 4D array (multi-component 3D array) when converting from numpy to vtk (Henry Proudhon)
moved the fitting module to the xray package. This should fix import confict with the math module of python as well as simplify the tree structure. (Henry Proudhon)
new method def get_edges (Henry Proudhon)
temporarily changed from Microstructure object to a set of orientations in dct_projection, added include_direct_beam option. (Henry Proudhon)
added pixel_to_lab and get_origin methods (Henry Proudhon)
added dictionary to the read_orientations method. (Henry Proudhon)
renamed read_euler_txt to read_orientations and added a method for backward compatibility. (Henry Proudhon)
fixed the dct_omega_angle method which assumed a cubic lattice. (Henry Proudhon)
detector now handle a reference position, regular detectors have a better support with u and v directions (Henry Proudhon)
new method lattice_3d_with_plane_series (Henry Proudhon)
add new color parameter to axes_actor function (Henry Proudhon)
untrack files in docs/_build (Henry Proudhon)
completed euler_angle cookbook example with orientation matrix definition (Henry Proudhon)
fixed mathjax_path and updated some docstrings in the microstructure module to have math working. (Henry Proudhon)
add mathjax_path pointing to the cloudflare CDN (Henry Proudhon)
enable the mathjax extension (Henry Proudhon)
added docstring for class View (Henry Proudhon)
now handle instance of vtkActor as an argument (Henry Proudhon)
changes to use the readthedocs html theme (Henry Proudhon)
updated version of the Euler angles animation (Henry Proudhon)
fix issue with gif path in generated rst (Henry Proudhon)
Merge remote-tracking branch ‘origin/master’ (Henry Proudhon)
added missing files for new example (Henry Proudhon)
added missing files for new example (Henry Proudhon)
changed the sign of omega to conform with the passive convention for rotations (Henry Proudhon)
new animation example with cookbook entry (Henry Proudhon)
more mock definitions for skimage (Henry Proudhon)
fix auto generation with animation examples (Henry Proudhon)
removed hot method and some docstring changes (Henry Proudhon)
new method vtkUpdateText (Henry Proudhon)
added new methds Axis2OrientationMatrix and Euler2Axis to use the (axis, angle) representation of rotations. (Henry Proudhon)
added a new method to render animation at a given time. (Henry Proudhon)
added support for viewing 3D numpy arrays. (Henry Proudhon)
make sur we work with an array of angles in the radiographs method (Henry Proudhon)
new methods to compute radiographs of 3D objects. (Henry Proudhon)
new module dct with code to help process, analyse and simulate dct data (Henry Proudhon)
added automated method to find all hkl planes in a given family (plus some testing) (Henry Proudhon)
added module docstring and commented matplotlib rcparams stuff (Henry Proudhon)
docstring fixes (Henry Proudhon)
added verbose mode to diffracted_vector method (Henry Proudhon)
double checked (corrected notations) the orientation matrix in dct_omega_angles (Henry Proudhon)
added lattice parameter to the get_family method (Henry Proudhon)
add (113) hkl plane family (Henry Proudhon)
correct for wrong indentation causing problems to the literalinclude directive (Henry Proudhon)
docstring fixes/tests in the module header (Henry Proudhon)
updated documentation so it work better on readthedocs (Henry Proudhon)
more indentation fixes (Henry Proudhon)
pymicro version 0.4.0¶
updated version number to 0.4.0 (Henry Proudhon)
added license file (Henry Proudhon)
prefer the use of is instead of == testing for None (Henry Proudhon)
adjust assertion after updating Al cif file (Henry Proudhon)
new fil_utils tests (Henry Proudhon)
added memory mapping option to HST_read function (Henry Proudhon)
use the proper fcc Ni cif file (Henry Proudhon)
added Ga and Mn cif files (Henry Proudhon)
cleaening up cif files and minor tweaks (Henry Proudhon)
added lattice arg to angle_between_directions to prevent forcing it to cubic (Henry Proudhon)
added new test for angle between two hkl directions (Henry Proudhon)
reformated all code with a consisten style (Henry Proudhon)
doc changes to reflect new file organisation (Henry Proudhon)
moving a bunch of file for a better organisation, created external folder (Henry Proudhon)
cleaning old stuff, moving tifffile out (Henry Proudhon)
new edge_actor method and updated show_boundaries (Henry Proudhon)
hist now plot in a new figure (Henry Proudhon)
updated xray_trans function, added table for densities (Henry Proudhon)
moved all mass attenuation coefficients to the data folder (Henry Proudhon)
fixed all docstrings (Henry Proudhon)
fixed bug in compute_ellipsis method (Henry Proudhon)
fixed dupplicate link for packages and added xray package (Henry Proudhon)
added a4 paper option (Henry Proudhon)
new example laue_ellipse (Henry Proudhon)
more fixes to the compute_ellpisis method (Henry Proudhon)
new test for select_lambda method (Henry Proudhon)
added docstring + bugfix in compute_ellpisis (Henry Proudhon)
fix small typo with the data_type variable (Henry Proudhon)
make full use of the detector variable in compute_ellpisis (Henry Proudhon)
modified detector classes, added new class PerkinElmer1620 (Henry Proudhon)
added initial code for Laue diffraction calculation and one first unit test (Henry Proudhon)
added a vtkCleanPolyData step for the show_boundaries method (Henry Proudhon)
added docstring for function show_boundaries (Henry Proudhon)
updated changelog (Henry Proudhon)
pymicro version 0.3.3¶
updated version number (Henry Proudhon)
added new example for misorientation (Henry Proudhon)
corrested a few typos (Henry Proudhon)
corrected a few small bugs (Henry Proudhon)
new orientations types and misorientation code (Henry Proudhon)
added symmetry operator for cubic structure (Henry Proudhon)
new tests for misorientation caculations (Henry Proudhon)
make scene3d more simple to use with better defaults (Henry Proudhon)
initial support for volume rendering (Henry Proudhon)
working on ImageViewer (Henry Proudhon)
new xray absorption data (Henry Proudhon)
updated import_modules.py with new functions (Henry Proudhon)
new legend format option in plot_xray_trans (Henry Proudhon)
new absorption data (Henry Proudhon)
added color option for atoms and bond in lattice_3d (Henry Proudhon)
fixed version pb with np.savetxt (Henry Proudhon)
small fix with psi_values (Henry Proudhon)
modified ImageViewer to work with Qt (Henry Proudhon)
improved detector code, both for Mar and Xpad (Henry Proudhon)
fixed fwhm for Voigt function (Henry Proudhon)
removed broken method get_octaedral_slip_systems (Henry Proudhon)
added new sagital_regroup method (Henry Proudhon)
fix data folder (Henry Proudhon)
a first example for finite elements (Henry Proudhon)
__init__ file for fe package and texture rst file (Henry Proudhon)
initial commit of the finite element part of pymicro (Henry Proudhon)
fix typo, remove print output (Henry Proudhon)
small fix in xray_utils (Henry Proudhon)
new method angle_with_direction (Henry Proudhon)
add check for nbParams in init (Henry Proudhon)
added lambda to keV conversion functions (Henry Proudhon)
added installation section (Henry Proudhon)
new example with skimage and radon (Henry Proudhon)
docstrings for contourFilter (Henry Proudhon)
fix orientation_tensor stuff for Taylor calculation (Henry Proudhon)
fix orientation_tensor stuff for Taylor calculation (Henry Proudhon)
added contour plot for pole figures and a demonstrating example (Henry Proudhon)
added more slip planes families and slip systems families, updated testing (Henry Proudhon)
fixed typo in dct_omega_angles (Henry Proudhon)
moved dc_omega_angles to the Orientation class (Henry Proudhon)
fixed colors when plotting ipf (Henry Proudhon)
new options to dsplay mesh edges in show_mesh (Henry Proudhon)
cleanup: moved the testing code of TaylorModel to external files (Henry Proudhon)
fixed a missing Update which caused the actor not to be displayed (Henry Proudhon)
new Taylor model class (experimental) (Henry Proudhon)
updated xray data files for Cu and Al (Henry Proudhon)
new method to compute a slip system orientation strain and rotation tensors (Henry Proudhon)
added change log history to the documentation (Henry Proudhon)
pymicro version 0.3.2¶
updated version number (Henry Proudhon)
docstring changes (Henry Proudhon)
a few tweaks in dct_projection (Henry Proudhon)
changed numpy in np and added a new method circle_line_3d (Henry Proudhon)
update flat field code for xpad (Henry Proudhon)
improved xpad code to hangle multiple images in raw or nxs, added flat field correction (Henry Proudhon)
fixed minus sign in dct_omega_angles (Henry Proudhon)
one more fix to the elevationFilter (Henry Proudhon)
changed the way the elevation axis is handled (Henry Proudhon)
fixed broken docstring in elevationFilter (Henry Proudhon)
added the possibility to use any axis in the elevationFilter (Henry Proudhon)
added new example with segmented crack (Henry Proudhon)
add grain objects to View (Henry Proudhon)
new find_planes_in_zone method (Henry Proudhon)
fixed bug in lambda_nm_to_keV and lambda_angstrom_to_keV (Henry Proudhon)
updated documentation (Henry Proudhon)
recompiled some figures (Henry Proudhon)
new test apply_orientation_to_actor (Henry Proudhon)
added skimage dependency (Henry Proudhon)
fixed vtk version problem for function volren (Henry Proudhon)
fixed vtk version problem for function volren (Henry Proudhon)
small fix with f.tell() (Henry Proudhon)
fix int conversion for numpy version (Henry Proudhon)
imporved View app and added it to the list of imported modules (Henry Proudhon)
modified dct_projection to use radon from skimage (Henry Proudhon)
new methods for rotating crystals and topotomography alignment with tests (Henry Proudhon)
new method to compute the scattering vector (Henry Proudhon)
corrected type in docstring (Henry Proudhon)
changed copyright year (Henry Proudhon)
missing file from previous commit (Henry Proudhon)
increased a bit the resolution for 2 examples (Henry Proudhon)
added example for volume rendering (Henry Proudhon)
added change log history to the documentation (Henry Proudhon)
pymicro version 0.3.1¶
updated version number (Henry Proudhon)
added new example for misorientation (Henry Proudhon)
corrested a few typos (Henry Proudhon)
corrected a few small bugs (Henry Proudhon)
new orientations types and misorientation code (Henry Proudhon)
added symmetry operator for cubic structure (Henry Proudhon)
new tests for misorientation caculations (Henry Proudhon)
make scene3d more simple to use with better defaults (Henry Proudhon)
initial support for volume rendering (Henry Proudhon)
working on ImageViewer (Henry Proudhon)
new xray absorption data (Henry Proudhon)
updated import_modules.py with new functions (Henry Proudhon)
new legend format option in plot_xray_trans (Henry Proudhon)
new absorption data (Henry Proudhon)
added color option for atoms and bond in lattice_3d (Henry Proudhon)
fixed version pb with np.savetxt (Henry Proudhon)
small fix with psi_values (Henry Proudhon)
modified ImageViewer to work with Qt (Henry Proudhon)
improved detector code, both for Mar and Xpad (Henry Proudhon)
fixed fwhm for Voigt function (Henry Proudhon)
removed broken method get_octaedral_slip_systems (Henry Proudhon)
added new sagital_regroup method (Henry Proudhon)
fix data folder (Henry Proudhon)
a first example for finite elements (Henry Proudhon)
__init__ file for fe package and texture rst file (Henry Proudhon)
initial commit of the finite element part of pymicro (Henry Proudhon)
fix typo, remove print output (Henry Proudhon)
small fix in xray_utils (Henry Proudhon)
new method angle_with_direction (Henry Proudhon)
add check for nbParams in init (Henry Proudhon)
added lambda to keV conversion functions (Henry Proudhon)
added installation section (Henry Proudhon)
new example with skimage and radon (Henry Proudhon)
docstrings for contourFilter (Henry Proudhon)
fix orientation_tensor stuff for Taylor calculation (Henry Proudhon)
fix orientation_tensor stuff for Taylor calculation (Henry Proudhon)
added contour plot for pole figures and a demonstrating example (Henry Proudhon)
added more slip planes families and slip systems families, updated testing (Henry Proudhon)
fixed typo in dct_omega_angles (Henry Proudhon)
moved dc_omega_angles to the Orientation class (Henry Proudhon)
fixed colors when plotting ipf (Henry Proudhon)
new options to dsplay mesh edges in show_mesh (Henry Proudhon)
cleanup: moved the testing code of TaylorModel to external files (Henry Proudhon)
fixed a missing Update which caused the actor not to be displayed (Henry Proudhon)
new Taylor model class (experimental) (Henry Proudhon)
updated xray data files for Cu and Al (Henry Proudhon)
new method to compute a slip system orientation strain and rotation tensors (Henry Proudhon)
added change log history to the documentation (Henry Proudhon)
pymicro version 0.3.0¶
32120a1 changed version number to 0.3.0 (Henry Proudhon)
debfbb8 updated pole figure example (Henry Proudhon)
0cdd294 fixed colormap issue when using map_field option (Henry Proudhon)
7323228 changes in examples to account for previous commits (Henry Proudhon)
4a51061 small bounding box fix in the map_data_with_clip method (Henry Proudhon)
3b72591 significant changes to handle field map with pole figures (Henry Proudhon)
267ca37 new OrientationTests class (Henry Proudhon)
667fcaf new test_from_symbol test method (Henry Proudhon)
f94eb22 very small docstring changes (Henry Proudhon)
61e311e show_data has been split in show_array and show_mesh (Henry Proudhon)
b46f7e4 corrected typo (Henry Proudhon)
9a43e04 final docstring changes to the texture module (Henry Proudhon)
cbbe2ae new example to demonstrate field coloring in pole figures (Henry Proudhon)
5d090fe a little more explanations (Henry Proudhon)
2a4e4d2 more docstring fixes in texture.py (Henry Proudhon)
acdaa6e change part of the title for inverse pole figure from family to axis (Henry Proudhon)
64cca29 more docstring formatting (Henry Proudhon)
5c13e80 updated some docs with Info field lists (Henry Proudhon)
667b8f2 Merge branch ‘master’ of vcs:pymicro (Nicolas Gueninchault)
3f705d9 new methods Calculate_Omega_dct, calc_poles_id11, Sam2Lab, Lab2sam, Sam2Sam (Nicolas Gueninchault)
a161f58 new methods plot_ipf_density, Eul2Mat, Write_inp_crystals (Nicolas Gueninchault)
cdba718 improved docstrings in apply_orientation_to_actor (Henry Proudhon)
fc530aa changed the way the rotation is applied in apply_orientation_to_actor (Henry Proudhon)
5c15dda cleaned grain_hkl_anim_3d.py (Henry Proudhon)
6d8f9e0 added options in unit_arrow_3d to display text in 3d aside the arrow (Henry Proudhon)
e119dfe more file for X-ray attenuation coefficients (Henry Proudhon)
24f2700 new code for X-ray detectors with two examples (Henry Proudhon)
cc88b87 added extension option in load_STL_actor function (Henry Proudhon)
8dd35e4 add opacity in alpha_cmap (Henry Proudhon)
6edfd6e small fix with iren.AddObserver (Henry Proudhon)
8f5b9e5 improved handling of Voigt function (Henry Proudhon)
ffdaa04 updated example to use the new animation framework (Henry Proudhon)
9fd27d4 add new plot_pf_hot function (Henry Proudhon)
96bacb8 added x1x2x3 rotation type when importing orientations from z-set (Henry Proudhon)
a141131 small fix to read image with HST_read (Henry Proudhon)
99f276c updated version (Henry Proudhon)
692f89a new dct_projection function and various small fixes (Henry Proudhon)
a987c56 improved anim framework (Henry Proudhon)
31106b5 added new hkl families (Henry Proudhon)
b1623aa new set_opacity for assembly and more parameters in unit_arrow_3d (Henry Proudhon)
dcf3810 improved plot_xray_trans function (Henry Proudhon)
pymicro version 0.2.3¶
c5d5ebb small typo (Henry Proudhon)
eb77e84 new color_bar function and new colormaps (Henry Proudhon)
7c61f57 added class for the Voigt fitting function (Henry Proudhon)
c0f082d new recipe to explein how 3d images are structured and should be read (Henry Proudhon)
22b710d new class to allow pyplot showing the pixel value and associated example (Henry Proudhon)
a3ffd0e small fix to the Gold pole figure example (Henry Proudhon)
4a6984c testing the Orientation class, merged Schmid factor utilities from Nfun into the Orientation class (Henry Proudhon)
6e0e2e1 fidling with no longer supported matplotlib wx backend (Henry Proudhon)
271bbd8 new recipe to explain plotting, reading, writting 2d images with pyplot (Henry Proudhon)
46591a3 fix always plot sst in plot_pole_figures (Henry Proudhon)
31e27a6 added missing files to the tree (Henry Proudhon)
424d22b added a picture for fitting functions (Henry Proudhon)
fdde04a changed doc accordingly to build the new math module (Henry Proudhon)
pymicro version 0.2.2¶
cec8566 changed version number to 0.2.2 (Henry Proudhon)
34f0601 allow to use a custom fit function in the fitting module (Henry Proudhon)
02c1cf9 added a general use fit method (Henry Proudhon)
28fd8d3 added a new example to demonstrate fitting (Henry Proudhon)
af6c1ad new math package with fitting functions (Henry Proudhon)
7b442f7 added a Makefile to run all example at once (Henry Proudhon)
944cb9f modified all examples to use the new scene3d stuff (Henry Proudhon)
c40a540 new file to configure ipython and updated documentation (Henry Proudhon)
a4fc7f5 docstrings updates (Henry Proudhon)
b48f7c5 changed from angstrom to nanometer when loading from CIF (Henry Proudhon)
dc7eacd added a new way to create crystal lattice via CIF files (Henry Proudhon)
28709df further improvements with Scene3d (Henry Proudhon)
5cc5bbc minor changes after last commit (Henry Proudhon)
8e8a353 adapted cubic_crystal example to new scene3d code (Henry Proudhon)
05cd497 new code to simplify building a 3d scene (Henry Proudhon)
3af0c66 improved axes_actor (Henry Proudhon)
1771ee7 corrected small bug in HST_read parameters (Henry Proudhon)
caf7955 new method to generate a microstructure with a random texture (Henry Proudhon)
b9be508 added new elevationFilter (Henry Proudhon)
04a4aa9 added num_color parameter to show_grains (Henry Proudhon)
df2b20d new xray package with a first example (Henry Proudhon)
215f1bf corrected small bug with cut option in auto_min_max (Henry Proudhon)
b5b0c7d new method for inverting a vtk lookup table (Henry Proudhon)
d6d4bce added new vtk stuff for displaying a pin hole and a Fresnel zone plate (Henry Proudhon)
71b7d4d method to show xray arrow and fix to the slits (Henry Proudhon)
4fa08d4 new method read_euler_txt (Henry Proudhon)
f3402b2 new method to display X-ray slits (Henry Proudhon)
a757cda new method to import a list of orientation from a text file and 2 new pole figure examples with 10000 orientations (Henry Proudhon)
cbe74e9 changed default ipf color to black, removed unecessary output (Henry Proudhon)
7b420f4 small docstring fixes (Henry Proudhon)
fb5ae80 Worked on adding the possibility of plot direct and inverse PF not in reference to Z (Nicolas GUENINCHAULT)
836f143 updated my_fun.py, adding a function to plot crystal rotations into ipf, sst ,… (Nicolas GUENINCHAULT)
8e10d45 adding my_fun file containing simple functions using pymicro. For now my_fun contain one class ‘Nfun’ with two functions dedicated to compute Schmid factors (Nicolas GUENINCHAULT)
34d6516 some bugs get fixed … (Nicolas GUENINCHAULT)
1d40e45 test (Nicolas GUENINCHAULT)
cfa3dde Corrected x1, x2, x3 instead of x1, x1, x1 (Erembert Nizery)
076c91f Merge branch ‘master’ of vcs:pymicro (Erembert Nizery)
5da5d5e added normalized vectors to compute B. (thank you Erembert ;-) ) (Nicolas GUENINCHAULT)
861aef1 Merge branch ‘master’ of vcs:pymicro (Erembert Nizery)
2d09cd9 Merge branch ‘master’ of vcs:pymicro (Erembert Nizery)
9d117f3 Merge branch ‘master’ of vcs:pymicro (Nicolas GUENINCHAULT)
83209f3 added the possibility of computiong the orientation matric from rotation like in a .inp file from Zebulon : Zrot2OrientationMatrix (Nicolas GUENINCHAULT)
0004dc5 updated pole figure doc example (Henry Proudhon)
fb8b165 pole figures can now be plotted with respect to X, Y or Z direction (Henry Proudhon)
1d2679a Merge branch ‘master’ of vcs:pymicro (Henry Proudhon)
9574b8d lots of update to handle upgrade to centos7 with backward compatibility with centos5 (Henry Proudhon)
de17c9d added new example with map_data_with_clip (Henry Proudhon)
96b5538 added new test for vtk numpy array (Henry Proudhon)
329321f conf.py now gets the version number in the main __init__.py file (Henry Proudhon)
505ebd6 adding modified symetry function in plot_sst (ss_syletry to sst_symetry_cubic) (Nicolas GUENINCHAULT)
f48dc7a Merge branch ‘master’ of vcs:pymicro (Henry Proudhon)
7b94c4d updated docstrings for dct_omega_angles (Henry Proudhon)
dd5dd78 added reciprocal lattice calcultion (Henry Proudhon)
e9b1daa Bug corrected (function sst_symmetry_cubic called instead of sst_symmetry) (Erembert Nizery)
2ddb457 Merge branch ‘master’ of vcs:pymicro (Henry Proudhon)
58cc9ee new example to display a polycrystal in 3d (Henry Proudhon)
72404c9 new load_STL_actor and show_data methods (Henry Proudhon)
7bce0fb removed .pyc test files from tree (Henry Proudhon)
067e52b moved tests for HklPlane in single file (Henry Proudhon)
adc3ccd First version of fastcrystal.py (Erembert Nizery)
be2673a Plotting two points for directions lying in plane. (Erembert Nizery)
c1be990 Reduced IPF set as default in plot_pole_figures. (Erembert Nizery)
607bd2c sst_symmetry_cubic corrected (used for IPF plot) (Erembert Nizery)
24563a0 No change - only test. (Erembert Nizery)
af9999e Merge branch ‘master’ of vcs:pymicro (Nicolas GUENINCHAULT)
8754ac0 just a test (Nicolas GUENINCHAULT)
e0ed245 fix HST_read while using autoparse_filename option (Henry Proudhon)
acc05b2 added non single atom basis for unit cells (Henry Proudhon)
f1743ca new hcp crystal example (Henry Proudhon)
dca3079 fix show_grains not showing grain 1 (Henry Proudhon)
db72a68 fix print statement in edf_read (Henry Proudhon)
131cc1d fix version number for tagging (Henry Proudhon)
ef62d20 fix version number for tagging (Henry Proudhon)
17cf50e added all the possible lattice centering and subsequent fixes in docs and examples (Henry Proudhon)
0a9ba28 moved wxPlotPanel.py to apps sub-package (Henry Proudhon)
f710e6c added new static method to easily plot a pole figure for a single orientation, docstring fixes (Henry Proudhon)
92a2002 added new method map_data, new options to map_data_with_clip, fixed many docstrings (Henry Proudhon)
937993c added math to Orientation docstring (Henry Proudhon)
19dc758 moved wxPlotPanel.py to apps package (Henry Proudhon)
042faf4 fixed note directives in doctrings (Henry Proudhon)
b427466 fixed vtk.util mock (Henry Proudhon)
5c13de4 small doctring fixes and variable renaming (Henry Proudhon)
272498d fixed import * for vtk colors (Henry Proudhon)
15b8466 several fixes to edf_write, now handle SignedInteger encoding (Henry Proudhon)
94bb046 new method to compute euler angle as in MandelCrystal (Henry Proudhon)
819bf56 added more matplotlib mocks (Henry Proudhon)
76c1543 added more mocks (Henry Proudhon)
ba09f84 removed unecessary toctree maxdepth option (Henry Proudhon)
9264ef0 many docstrings fixes and new function plot_sst (Henry Proudhon)
825052f many docstrings fixes (Henry Proudhon)
ab42227 modified __init__ files (Henry Proudhon)
71cc94d new figure AlLi_sam8_pole_figure for documentation (Henry Proudhon)
3a902f8 small fix in new option autoparse_filename (Henry Proudhon)
8807aa4 added cookbook with first recipe (Henry Proudhon)
d9de338 mock tifffile to build doc (Henry Proudhon)
c428b7b subsequent modifications in edf_read and edf_write (Henry Proudhon)
84f1687 fixed Size field in edf header (Henry Proudhon)
4dc6d2e now using mock module to help build documentation (Henry Proudhon)
f4bf3e9 trying to fix sphinx path on remote server (Henry Proudhon)
36a4eb8 trying to fix sphinx path on remote server (Henry Proudhon)
83d081b removed unused jsMath and MathJax from tree (Henry Proudhon)
05eed8f trying to fix sphinx path on remote server (Henry Proudhon)
3ea96dd trying to fix sphinx path on remote server (Henry Proudhon)
0e25b9a modified files not to depend on matplotlib (Henry Proudhon)
293f4c6 added thumb images files for example gallery (Henry Proudhon)
8d022c8 added schmid factor calculations (for octaedral slip) (Henry Proudhon)
e080880 change number of bytes to 512 to peek in header in edf_info (Henry Proudhon)
18e7bd5 do not include auto_example in the tree (Henry Proudhon)
fd4f935 file changes for the automated gallery of example (Henry Proudhon)
38ea32b added an automated gallery of example (Henry Proudhon)
0c0b002 added max_opacity option in vtkSetVisibility animation (Henry Proudhon)
dc540a9 new function show_grains (Henry Proudhon)
e756429 fixes path to example files (Henry Proudhon)
84b9f42 small fixes to cubic_crystal_3d example (Henry Proudhon)
94259eb very small fix to lattice_3d_with_planes function for opacity (Henry Proudhon)
2802f36 make current image name readonly (StaticText) (Henry Proudhon)
fd7e133 added docstrings for edf_info and unpack_header (Henry Proudhon)
c1a6757 new functions edf_info and esrf_to_numpy_datatype (Henry Proudhon)
bd7cbd7 fixed doctstring for alpha_cmap (Henry Proudhon)
d79ebd4 moved example files (Henry Proudhon)
125f6bf updated documentation with examples (Henry Proudhon)
6e79251 added flat field correction function (Henry Proudhon)
7dbd525 more __init__ stuff (Henry Proudhon)
c1c1557 now load tif files as well (Henry Proudhon)
ff80f6e added recad util functions (Henry Proudhon)
9afc721 documented some functions likre vtk_write (Henry Proudhon)
8a0c100 small fix to the raw_mar_read function (Henry Proudhon)
057911c added/fixed docstrings (Henry Proudhon)
3e592b2 moved all examples to different subfolders (Henry Proudhon)
a4d68a1 new application to view image files in a folder (Henry Proudhon)
dbfa470 small change on how to get the image dim from the header in edf_read (Henry Proudhon)
8f161ae added mousse_3d example (Henry Proudhon)
7b23d95 bug fix in bragg calculation and minor docstring changes (Henry Proudhon)
6b9ead1 added more families in HklPlane get_family method (Henry Proudhon)
dba603f fixed docstrings in the microstructure module (Henry Proudhon)
6910930 added bragg_angle method with unit testing (Henry Proudhon)
85d07ca added image for hist function (Henry Proudhon)
9469a33 small docstrings changes (Henry Proudhon)
8f5499c added new method dct_omega_angles to the Grain class (Henry Proudhon)
80ab017 small docstrings changes (Henry Proudhon)
7f30e18 changed origin to lower in show_and_save function (Henry Proudhon)
0e2d8f1 added save option in render function and fixed the documentation (Henry Proudhon)
7706ffa a few more documentation fixes (Henry Proudhon)
5fa810f fixed the documentation of the hist function (Henry Proudhon)
b9696d9 added examples folder and some documentation of these examples (Henry Proudhon)
2204068 added new method show_and_save for a 2d image (Henry Proudhon)
fd873c9 improve documentation in vtk_utils (Henry Proudhon)
2bf1e91 added new vtk function map_data_with_clip (Henry Proudhon)
64f3871 improved documentation for color maps (Henry Proudhon)
a2b90e2 added test for tif file (Henry Proudhon)
c4d6dce added tifffile module (Henry Proudhon)
945257e improved documentation for vtk_utils (Henry Proudhon)
63465a0 improved the documentation with sphinx (Henry Proudhon)
9e8a10e added pymicro logo (Henry Proudhon)
2dd3e8b added Dependencies section to the documentation (Henry Proudhon)
5f437ac switched to shpinx theme proBlue (Henry Proudhon)
46d3ceb updated documentation (Henry Proudhon)
2d9cb0b remove old rst files from the crystal package (Henry Proudhon)
b9c398b updated documentation (Henry Proudhon)
7b9ddef new method grain_3d with subsequent changes (Henry Proudhon)
bbedd5e added verbose mode to hkl plane normal method (Henry Proudhon)
2fa7585 added modules in sphinx, updated documentation (Henry Proudhon)
5fd4612 deleted old unmaintained stuff (Henry Proudhon)
0a54b50 changed numpy import (Henry Proudhon)
1396e7a added new classes to handle animations through a 3d scene (Henry Proudhon)
3caf836 added support for hkl planes in hexagonal lattices (Henry Proudhon)
fec27d8 fixed a small issue with dot product for python2.6 at esrf (Henry Proudhon)
4c48986 added opacity control in add_plane_to_grid function (Henry Proudhon)
69fb39c bug correction in HklPlane normal (Henry Proudhon)
b66f374 removed printed output (Henry Proudhon)
8f3cbb8 several corrections + added hexagonal 3d lattice handling (Henry Proudhon)
3899715 remove old diffract.py file (Henry Proudhon)
af2c658 remove old grains.py file (Henry Proudhon)
7747c77 remove old grain_conn.py file (Henry Proudhon)
e474f65 remove old chg_label.py file (Henry Proudhon)
78e094b remove old grain_53.py file (Henry Proudhon)
539c61b remove old animp.py file (Henry Proudhon)
8ec9806 added a grain_ids filter to load a microstructure from an XML file (Henry Proudhon)
fd20143 added .gitignore file (Henry Proudhon)
cc51795 new file to handle animation (rotation around Z axis for now) (Henry Proudhon)
1ac249b added new add_grain_to_3d_scene method (Henry Proudhon)
fcab593 added new method: lattice_3d_with_planes (Henry Proudhon)
56858bc bug correction in slip plane rotation (Henry Proudhon)
370a5cd added a way to control which planes are used in add_HklPlanes_with_orientation_in_grain (Henry Proudhon)
5798f2d added a box_3d method (Henry Proudhon)
9a98c38 improve consistency in file names when saving microstructure in xml format (Henry Proudhon)
54c0693 added verbose mode to add_vtk_mesh in class Grain (Henry Proudhon)
c9c5758 small corrections like phi1 in phi1() (Henry Proudhon)
4d995ed added scaling possibility to unit_arrow_3d (Henry Proudhon)
622e39d removed shpinx doc build from tree (Henry Proudhon)
50d2923 removed .pyc files rom tree (Henry Proudhon)
5cfdc17 started to remove .pyc files (Henry Proudhon)
25629f0 small changes in pole figure legend handling (Henry Proudhon)
d683db9 small update of slip_traces doc (Henry Proudhon)
2f6ae4e added slip_traces methods for HklPlane class (Henry Proudhon)
b905bed added interplanar_spacing calculation for HklPlane class (Henry Proudhon)
15f28fc remove attribute normal from the HklPlane class (a method exists) (Henry Proudhon)
f90f19c added lattice attribute to the HklPlane class (Henry Proudhon)
5c64e60 corrected a small bug in get_family (Henry Proudhon)
245211d added doc to the get_family method (Henry Proudhon)
0fe48e5 added a static get_family method to the HklPlane class (Henry Proudhon)
4da82b5 changed default clipping range in setup_camera (Henry Proudhon)
6bfc2b5 added verbose option to read_image_data, changed setupCamera name to setup_camera (Henry Proudhon)
0ed75d4 fix header in edf_write according to data type (Henry Proudhon)
e5f61e8 added alpha_cmap method (Henry Proudhon)
666ed65 added a method to automatically setup the vtk camera (Henry Proudhon)
9cc44b5 fixed issue with .info file in HST_write (Henry Proudhon)
5732820 added VTK_UNSIGNED_INT to uint32 equivalence (Henry Proudhon)
b6aa3e6 added density option in grey level histogram plotting (Henry Proudhon)
ed6ad97 corrected prefix variable in grey level histogram plotting (Henry Proudhon)
d4e321d added new grey level histogram plotting (Henry Proudhon)
6fc4d64 add variable header in read_image_data (Henry Proudhon)
a5c51f7 fixed orientation issue in add_hklplane_to_grain (Henry Proudhon)
d873f01 added float and double conversion from numpy to vtk (Henry Proudhon)
b266ec4 merged contourByDiscreteMarchingCubes intour contour filter (Henry Proudhon)
d6c6735 removed crystal/microstructure.pyc (Henry Proudhon)
9b985d3 added contour filter method (Henry Proudhon)
fdbb00b corrected bug in OrientationMatrix2Euler when Phi=0 (Henry Proudhon)
230f395 changed from PyMicro to pymicro (Henry Proudhon)
3a7e3bf Show only one point per grain in legend in direct pole figures (Henry Proudhon)
a733719 added custom legend for direct pole figure (Henry Proudhon)
d42c915 updated apply_orientation_to_actor for new Orientation class syntax, added custom color for unit_arrow_3d (Henry Proudhon)
364d72b added euler angle corrections from orientation matrix (Henry Proudhon)
d2e754d improved pole figures (Henry Proudhon)
e23c32b added project documentation through sphinx (Henry Proudhon)
pymicro version 0.1.0¶
ce0ce0b changed from white color to (1,1,1) (Henry Proudhon)
008a44c cleaned up crystal_lattice_3d (Henry Proudhon)
a12ee2f documentation small correction (Henry Proudhon)
0cadf68 documentation small corrections (Henry Proudhon)
d86433a added several helper vtk functions (read, outline, render, contour) (Henry Proudhon)
b028bd2 added add_outline method in vtk_utils (Henry Proudhon)
9dac6e3 update happy new year (Henry Proudhon)
d8eb5f3 initial project version (Henry Proudhon)