XY and Z drift stabilization #108
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…on and the optimizer to output the input zyx shape to yaml
… in the parent directory. adding slurmkit demo
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Replaced by #128 |
ieivanov
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Jul 2, 2024
* initial commit adding tools for cropping and registering with ants * adding lir crop * starting cleanup for registration * converting nan to zero * ants estimate affine * adding config file for estimate_transform * cleaning up some redundancies * fix edge case of input not being float32 * channel is an int * typo in napari add image for vs ants optimzer * adding utils yaml * separated the manual estimation from the optimizer * added ants to numpy and viceversa * adding input at the end to prevent from closing * replacing the reading of .mat to matrix from yaml * added changes to ants to numpy from Jordaos input * cannot have recOrder as dependency given different pycromanager versions * format * add test for optimize_affine and update readme * adding docstring * removed the config dependency * removing the focus_finding svg * removing the estimate_affine.yml and making flags to choose channels and verbose * added comment and code to use scipy. * -ls and -lf to -s and -t * document FOCUS_SLICE_ROI_WIDTH * `estimate-source-to-target-affine` -> `estimate-affine` * standardize `optimize-affine` arguments * cleaner docs * update RegistrationSettings * fix tests * remove duplicate * write indices to output config * read channels from file * test fix * echo improvments * black * stabilization draft * slurm z drift correction * pystackreg * functions for estimating the z_drift and xy translation over time * style * remove duplicate cli call * more intuitive manual registration * stabilization cli * patch for deskewing * fixing CLI calls and docstrings * addine more comments to doctring * stabilize_timalapse cli typo * stabilize_timalapse cli typo * removing some args in doctring. * testing slurmkit * fix apply affine example * matrix multiplication bugfix * updating the lir_crop using new registration * adding lir crop to the apply affine and modifying the manual estimation and the optimizer to output the input zyx shape to yaml * convert nans to zeros * updating the output saving scheme taking zarrs and saving the verbose in the parent directory. adding slurmkit demo * add affine test * fixing z-shift error * remove saving intermediate z-shifts * save to yml * prototype to change to v2 * fixing the xy drift calculation. refactoring placed xy order instead of yx * adding option to fill the zeroes with previous value. * adding tests * adding one more test * adding test for affine * removed main * fix `apply_affine` docstring * fixing formatting * remove crop-output from cli args * estimate affine cli docstrings * reverting changes to AnalysisSettings model. * optimize_affine cli docstrings * Revert "reverting changes to AnalysisSettings model." This reverts commit 0e2f8c4. * fix points layer grid mode bug * fix tests * add slurmkit * combining the croping and merging to the apply-affine * removing unnecessary prints() * add registration and stabilization modules * style * flake8 * Registration refator (#118) * refactor apply_affine * clean up Co-authored-by: Eduardo Hirata-Miyasaki <eduardo.hirata@czbiohub.org> * debug and add comments * updating estimate_affine to match new yml * don't start parallel pool for 1 iterable * patch previous commit * make sure the source_channel_used is first in the list for the optimizer * make optimize_affine accept the new config parameters * fix bug calling iohub info on paths with white spaces; rename target_channel_str * better white space cli bug fix * cleaner print statements * don't use itertools.starmap * clean up apply_affine print statements * clean up optimize_affine --------- Co-authored-by: Eduardo Hirata-Miyasaki <eduardo.hirata@czbiohub.org> Co-authored-by: Eduardo Hirata-Miyasaki <edhiratam@gmail.com> * removing the source n target shape zyx and testing keep overhang * updating estimate affine with previous commit changes * style * Update example_apply_affine_settings.yml * refactor registration and stabilization functions * fixing pytests * more intuitive function names * minor refactor of estimane_affine * bugfix * fixing the slurmkit files. * typo * cleaner processing of additioanal source channels * refactor apply_affine job submission * remove position batch processing * temporarily reorder functions * revert temp reorder functions * refactor functions * refactor combined matrix calculation * refactor z_drift multiprocessing * small refactor + messaging * renaming * this eliminates stabilization_ove_time_ants by reusing processing_single_position_v2. Also fixes a bug in the processing_single_position_v2. * modified the function to process channel indeces and copy over the other channels similar to affine transform. by default all channels are processed with the same transform. * remove `analysis/stabilize.py` * renaming * more renaming * update docstring * estimate_xy_stabilization uses the z indices calculated by estimate_z_stabilization * style * rename fields in position_focus.csv * update z_drift figure save path * add axis labels * fixing tests * fix method='ffill' deprecation issue * clean up slurmkit examples * update slurmkit_stabilize example * fix tests * minor fixes * fix ffill * add back `t_idx` param * more ffill fix * update apply_transform_to_zyx_and_save_v2 documentation --------- Co-authored-by: Eduardo Hirata-Miyasaki <edhiratam@gmail.com> Co-authored-by: Talon Chandler <talonchandler@gmail.com> Co-authored-by: Eduardo Hirata-Miyasaki <eduardo.hirata@czbiohub.org>
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TODO (01/19/24):
registration_v2/mantis/cli/stabilizationto/mantis/analysis/stablizeThis PR has the code for:
estimate_stabilization_affine()stabilize_timalpse()For the XY stabilization, you can use:
/hpc/projects/comp.micro/mantis/2023_09_22_A549_0.52NA_illum/3-registration/A549_MitoViewGreen_LysoTracker_W3_FOV5_1_phase.zarrFor Z drift, any of the timelapses:
/hpc/projects/comp.micro/mantis/2023_11_01_OpenCell_infection/4-registration/timelapse_7/timelapse_7_phase_registered.zarr