Multipeak updates to cohere-ui #14
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Make sure the results get saved in the right place, etc.
…ferent voxel size.
…have detectable signal in reciprocal space, but were beyond the scan range in one or more dimensions.
Conflicts: cohere-scripts/beamlines/aps_34idc/beam_stuff.py cohere-scripts/multipeak.py
Multipeak
… size, rs and ds voxel size.
# Conflicts: # cohere-scripts/multipeak.py
# Conflicts: # cohere-scripts/beamline_visualization.py # cohere-scripts/multipeak.py # cohere-scripts/prep_helper.py # cohere-scripts/standard_preprocess.py
…rectory. It was trying to save to exp_dir/results_phasing/results_viz, when it should have been saving to exp_dir/results_viz
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* changed for mpi support * added code to support mpi * fixed crop issue * changes for autodata option (#12) Co-authored-by: bfrosik <bfrosik@anl.gov> * added debug option * moved utilities from cohere-ui to cohere and cleaned * fix and removing prints * moved centering to reconstruction, removed cohere-ui util * bug fixes * support for auto data for separate scan ranges * removed prints added check for 0 * added check for zero auto_batches * added dm scripts for testing * fixed typo * fixed typo * fixed typo * fixed parameters * corrected function parameter * creating sub-directory in hpc_data directory * added save_dir in config_disp defaults * added save_dir to visualization * added save_dir to config_disp in dm * moved check for zero batches * removed trailing separators * removed trailing slash * added hpc script * added for work flows * copied write_config function into create_experiment to decouple from cohere, removed preprocess script as redundant * change arguments defs * added cluster capability * removed print statements * cleaned up, added description * added description * used common routines in scripts * replaced concatanate of path with function * cleaned up, fixed suport for multipeak, formatted text * added field in mp tab, and defaults, blocked binning when mp, and added auto preprocessing to mp * added report with correlation error * simplified pool * corrected verification of device in GUI * fixed bugs, added to description * Multipeak updates to cohere-ui (#14) * Updated multipeak phasing to work with direct phase/strain coupling * A few bugfixes Make sure the results get saved in the right place, etc. * Fixed an oversight that allowed each rotated Bragg peak to have a different voxel size. * Calculates correct voxel size for visualization * Creates a mask which indicates post-interpolation pixels that likely have detectable signal in reciprocal space, but were beyond the scan range in one or more dimensions. * Removed .idea directory from version control. * Fixed broken path name (trying to load wrong config file) * Refactored to record the B_recip matrix rather than applying the actual transform * Add some additional useful information to the saved geometry: lattice size, rs and ds voxel size. * Add some additional useful information to the saved geometry: final_size * fixed crop issue * Compatibility updates * Fixed compatibility with Cohere's Dev branch * Fixed bug that caused multipeak visualization to save in the wrong directory. It was trying to save to exp_dir/results_phasing/results_viz, when it should have been saving to exp_dir/results_viz --------- Co-authored-by: bfrosik <bfrosik@anl.gov> * modified defaults in GUI * added "loaded" switch to suspend warnings during experiment switch * removed print * removed incorrect print * added pid to hostfile and removed it after rec * fixed bug setting host file name to a value * modified description of rec parameters * renamed phase modulus to phase constrain * moved info msg to correct place * modified hpc scripts, added setup * added description * cleaned up cohere-defaults, restored create_experiment, and moved new version to hpc * added jupyter python example --------- Co-authored-by: pfrosik <pfrosik@outlook.com> Co-authored-by: cxduser <jacioneportier@gmail.com> Co-authored-by: Nick Porter <34489968+jacione@users.noreply.github.com>
bfrosik
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May 2, 2024
* changed for mpi support * added code to support mpi * fixed crop issue * changes for autodata option (#12) Co-authored-by: bfrosik <bfrosik@anl.gov> * added debug option * moved utilities from cohere-ui to cohere and cleaned * fix and removing prints * moved centering to reconstruction, removed cohere-ui util * bug fixes * support for auto data for separate scan ranges * removed prints added check for 0 * added check for zero auto_batches * added dm scripts for testing * fixed typo * fixed typo * fixed typo * fixed parameters * corrected function parameter * creating sub-directory in hpc_data directory * added save_dir in config_disp defaults * added save_dir to visualization * added save_dir to config_disp in dm * moved check for zero batches * removed trailing separators * removed trailing slash * added hpc script * added for work flows * copied write_config function into create_experiment to decouple from cohere, removed preprocess script as redundant * change arguments defs * added cluster capability * removed print statements * cleaned up, added description * added description * used common routines in scripts * replaced concatanate of path with function * cleaned up, fixed suport for multipeak, formatted text * added field in mp tab, and defaults, blocked binning when mp, and added auto preprocessing to mp * added report with correlation error * simplified pool * corrected verification of device in GUI * fixed bugs, added to description * Multipeak updates to cohere-ui (#14) * Updated multipeak phasing to work with direct phase/strain coupling * A few bugfixes Make sure the results get saved in the right place, etc. * Fixed an oversight that allowed each rotated Bragg peak to have a different voxel size. * Calculates correct voxel size for visualization * Creates a mask which indicates post-interpolation pixels that likely have detectable signal in reciprocal space, but were beyond the scan range in one or more dimensions. * Removed .idea directory from version control. * Fixed broken path name (trying to load wrong config file) * Refactored to record the B_recip matrix rather than applying the actual transform * Add some additional useful information to the saved geometry: lattice size, rs and ds voxel size. * Add some additional useful information to the saved geometry: final_size * fixed crop issue * Compatibility updates * Fixed compatibility with Cohere's Dev branch * Fixed bug that caused multipeak visualization to save in the wrong directory. It was trying to save to exp_dir/results_phasing/results_viz, when it should have been saving to exp_dir/results_viz --------- Co-authored-by: bfrosik <bfrosik@anl.gov> * modified defaults in GUI * added "loaded" switch to suspend warnings during experiment switch * removed print * removed incorrect print * added pid to hostfile and removed it after rec * fixed bug setting host file name to a value * modified description of rec parameters * renamed phase modulus to phase constrain * moved info msg to correct place * modified hpc scripts, added setup * added description * cleaned up cohere-defaults, restored create_experiment, and moved new version to hpc * added jupyter python example * fixed library issue for mac * modified loading modules on Windows --------- Co-authored-by: pfrosik <pfrosik@outlook.com> Co-authored-by: cxduser <jacioneportier@gmail.com> Co-authored-by: Nick Porter <34489968+jacione@users.noreply.github.com>
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This contains updates to the UI that match the updates in the cohere:Dev pull request: AdvancedPhotonSource/cohere#22
There was one little bug, which I also fixed: 4da655d