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appveyor.yml\r\n\r\n* Update appveyor.yml\r\n\r\n* Update appveyor.yml\r\n\r\n* Update appveyor.yml\r\n\r\n* Add build wheels and tarball\r\n\r\n* Update README.md\r\n\r\n* Update __init__.py\r\n\r\n* Create eps_sig_solver_NEW.py\r\n\r\nCreate a new solver to compute strain and stress from ImageD11 ubis\r\n\r\n* Bugfix assemble_label.py\r\n\r\nset rather than list randomly permuted the order of scans. Oups.\r\n\r\n* compatible for python2.7\r\n\r\n* fix file path\r\n\r\n* corrected mistakes in eps_sig_solve_NEW.py + updated invariant properties function\r\n\r\n- corrected a few mistakes and typos in function description\r\n- corrected a mistake in convert_tensors_to_vect\r\n- changed invariant_prop function to return von Mises stress / strain instead of octahedral shear stress / strain\r\n\r\n* Update eps_sig_solver_NEW.py\r\n\r\n* corrected typo in form_stiffness_tensor\r\n\r\n* updated Cij_symmetry\r\n\r\n* Update eps_sig_solver_NEW.py\r\n\r\n* Rename eps_sig_solver_NEW.py to stress.py\r\n\r\n* Rename ImageD11/eps_sig_solver.py to ImageD11/depreciated/eps_sig_solver.py\r\n\r\n* Update stress.py\r\n\r\n* Update stress.py\r\n\r\n* Update stress.py\r\n\r\n* Update stress.py\r\n\r\n* Update stress.py\r\n\r\n* Add scanning 3DXRD example notebooks\r\n\r\n* Remove f-string for 2.7 compat.\r\n\r\n* Exclude Python 3.12 in setup.py\r\n\r\nUntil Numba updates to Python 3.12\r\nThis should fix the CI for Python 3.x\r\n\r\n* Exclude 3.12 from GitHub Actions CI\r\n\r\n* Fix GitHub actions yml typo\r\n\r\n* Third time lucky\r\n\r\n* Use GitHub Actions badges in README.md\r\n\r\n* Correct typo\r\n\r\n* Update README.md\r\n\r\n* fix the log strain - needs testing better\r\n\r\n* helper function from several notebooks\r\n\r\n* mlem and centers code\r\n\r\n* function from notebooks\r\n\r\n* function from notebooks\r\n\r\n* Change int32 and float32 to 64\r\n\r\n* remove broken test\r\n\r\n* put stress on hold while updating it\r\n\r\n* Update __init__.py v2.0.2\r\n\r\n* Update README.md v2.0.2\r\n\r\n* Update release.yml : no 3.12 version\r\n\r\n* Allow a fuller mask, to mask powder rings for example\r\n\r\n* fix mask for powder removal and reformat (black)\r\n\r\n* Resurrect tests for columnfile.py, correct np.int\r\n\r\nIn the Github Actions CI, the command \"python -m pytest\" is run to test ImageD11.\r\nBy default, this only runs test files with the naming convention `test_*.py`\r\nRenamed `testcolumnfile.py` to `test_columnfile.py` to fix this.\r\nAlso, replaced `np.int` references `int` to fix numpy depreciation errors.\r\n\r\n* Fix np.int64\r\n\r\n* Add colfile tests to run_tests.py\r\n\r\n* Significant notebook layout changes\r\n\r\n* Parallelised iradon\r\n\r\n* Ensure 0 fill value for np.interp\r\n\r\n* Add mask to MLEM\r\n\r\n* First attempt at enforcing file paths\r\n\r\n* A few bugfixes\r\n\r\n* update cibuildwheel and upload|download-artifacts\r\n\r\n* eps_sig_solver was deprecated\r\n\r\n* eps_sig_solver was deprecated + black formatted\r\n\r\n* Python 3.12 support\r\n\r\n* Add col3d file to dataset paths\r\n\r\n* Try to get rid of the fork problem\r\n\r\n* point by point - needs some more docs to expain pars\r\n\r\n* fixup 2.7\r\n\r\n* Add outsize support to MLEM\r\n\r\n* Clean up comment\r\n\r\n* convert nnz to ip function\r\n\r\n* error on typo in group names\r\n\r\n* fix forking problem/error\r\n\r\n* get the warnings to print, but only when needed\r\n\r\n* for CI only having 1 thread?\r\n\r\n* CI fails. Not sure why.\r\n\r\n* fixup\r\n\r\n* set forkserver here, todo: windows?\r\n\r\n* and for windows that does not fork anyway\r\n\r\n* and for windows that does not fork anyway\r\n\r\n* and for windows that does not fork anyway\r\n\r\n* percent, not fraction\r\n\r\n* tested on SS316\r\n\r\n* was not tested yet. pythonpath\r\n\r\n* tested once: should not be forking\r\n\r\n* seen to run once\r\n\r\n* with a threshold image option\r\n\r\n* Notebook for par file building from poni\r\n\r\n* A few small sinogram bugfixes\r\n\r\n* self.shape is undefined\r\n\r\n* Significant scanning notebook changes\r\n\r\nGeneral changes:\r\n- Moved quite a few common functions into utils.py. These need properly incorporating into ImageD11 in the future\r\n- All notebooks updated to obey DataSet filestructures for peaks and grains files\r\n\r\n0_S3DXRD_segment:\r\n- Added widget written by Pierre-Olivier for adjusting segmenter parameters\r\n- Added slurm bash \"listener\" that waits for slurm job to complete before next cell completes\r\n- Moves individual sparse files to their own subfolder after assembling\r\n\r\n1_S3DXRD_index:\r\n- More sensible indexer that prioritises low-multiplicity rings\r\n- Grains now saved in HDF5 format\r\n- Added another example notebook for indexing a minor phase\r\n\r\n2_S3DXRD_sinograms:\r\n- Added whole-sample sinogram reconstruction to use as a mask for individual grain reconstructions.\r\n- Added MLEM refinement stage (uses SLURM) to grain reconstructions using run_mlem_recon.py\r\n- Added another example notebook for mapping a minor phase (uses grain recons for centre-of-mass)\r\n\r\n3_S3DXRD_strain_maps_pbp:\r\n- Performs a point-by-point refinement of the grain-averaged UBI using 2D peak selection\r\n- Uses grain labels array from sinograms for grain shapes\r\n- Should give \"relative\" Type-III strains\r\n\r\n4_S3DXRD_plot_both_phases:\r\n- Small example notebook for plotting both phases in the same map\r\n- Some initial work on orientation relationship identification using Orix (not finished yet)\r\n\r\n* Add box-beam example notebooks\r\n\r\n- Similar to scanning notebooks but for box-beam 3DXRD\r\n- Currently only working for Frelon data\r\n- Uses Frelon segmenter from ma4750 (in sandbox) for peaksearching\r\n- Global parameter refinement notebook\r\n- Uses makemap.py to refine grain positions\r\n- Some extra notebooks for importing multiple slices in a z series and looking at peak shapes (still under development)\r\n\r\n* Build parameter file from CIF and pyFAI PONI\r\n\r\n* Clear notebook outputs\r\n\r\n* Correct pyplot typo\r\n\r\n* Allow flake 2.7 linting to pass\r\n\r\n* Python 2 compat\r\n\r\n* Remove duplicate segmentation notebook\r\n\r\n* Common utils between scanning and box-beam notebooks\r\n\r\n- Moved a few more functions out of notebooks into utils\r\n- This significantly simplifies the notebooks\r\n- MLEM recon: y0 now gets written to/read from the grain HDF5 file rather than command-line option\r\n\r\n* Replace FileNotFoundError with IOError for py2.7\r\n\r\n* Minor phase scanning notebooks now use nb_utils, needs testing\r\n\r\n* Correct ImageD11_gui bugs - broken log buttons and tth_histogram\r\n\r\n* Rename and add batch scripting\r\n\r\n* Add batch cells to scanning notebooks\r\n\r\n* All notebooks now use nb_utils.py\r\n\r\n* Remove WIP notebook from commit\r\n\r\n* Add RGB colour output to sinogram notebooks\r\n\r\n* Add widget with sliders for Frelon peaksearch data\r\n\r\n* Add RGB IPF X,Y,Z outputs to HDF, allows viewing with H5Web\r\n\r\n* py2 compat\r\n\r\n* Small bugfixes and tidying up\r\n\r\n* Small changes and bugfixes\r\n\r\n* Clear output\r\n\r\n* secret spacegroup number hidden option\r\n\r\n* secret spacegroup number hidden option\r\n\r\n* secret spacegroup number hidden option\r\n\r\n* secret spacegroup number hidden option\r\n\r\n* Correct very dodgy default cosine tolerance\r\n\r\n* Correct grain translation sign problems\r\n\r\n* Correct dodgy do_index scan\r\n\r\n* Handle missing samples in skips_dict, dset lists are now sorted too\r\n\r\n* More accurately find user home directory path\r\n\r\n* Just use default arguments for assemble_label and properties\r\n\r\n* Force only 2 threads for indexer (confirmed faster)\r\n\r\n* Improve comments about peak filtration\r\n\r\n* Correct origin for recon plots\r\n\r\n* Much faster spatial correction using lut\r\n\r\n* Lima segmenter now used in interactive notebook\r\n\r\n* Add howmany to Eiger interactive segmenter\r\n\r\n* Segment everything in parallel on SLURM\r\n\r\n* Cleaned-up local PBP indexer\r\n\r\n* Correct PBP results filename\r\n\r\n* Fix dodgy pbp name\r\n\r\n* Fix PBP output name for real this time\r\n\r\n* fixes #236\r\n\r\n* fixes #236\r\n\r\n* Correct home directory searching\r\n\r\n* added options to score_all_pairs for ring selection\r\n\r\n* added options to score_all_pairs for ring selection\r\n\r\n* Optionally scale sinogram rows by ring current\r\n\r\n* Forgot to also add to batch cells\r\n\r\n* Correct dodgy minor phase grain positioning\r\n\r\n* nb_utils function for ring current correction per scan\r\n\r\n* H5py in nb_utils\r\n\r\n* Make ring current correction optional and separate\r\n\r\n* More sensible default dstol\r\n\r\n* tag maintenance release\r\n\r\n---------\r\n\r\nCo-authored-by: Jean-Baptiste Jacob <137695414+jbjacob94@users.noreply.github.com>\r\nCo-authored-by: jadball <jadball@gmail.com>\r\nCo-authored-by: Thomas VINCENT <thomas.vincent@esrf.fr>\r\nCo-authored-by: James Ball <42615415+jadball@users.noreply.github.com>\r\nCo-authored-by: Jerome Kieffer <github@terre-adelie.org>\r\nCo-authored-by: Jonathan Wright 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