Code

MBL 2024#112

Code

Merged

gschlafly merged 57 commits intomainPolarizedLightFieldMicroscopy/BirTomo:mainfrom mbl_2024PolarizedLightFieldMicroscopy/BirTomo:mbl_2024Copy head branch name to clipboardOct 2, 2024

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Commits

Commits on Sep 21, 2024

• Add spicula reconstruction module and configuration

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• Replace epoch with iteration

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• Write command line output into log file

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• Exclude pycache files from view

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Commits on Sep 22, 2024

• Spicula to spicule

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• Refactor spicule module

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• Keep axial component of optic axis positive in the volume creation

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• Shift the shell position

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• Create pytest for optic axis

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• Modify initial volume creation optic axis

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• Disable gradients for simluation tests

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• Update images of shell for unit test

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• Hide verbose rays messages during reconstruction

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• adjust elipse hight for shells

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• remove roll and clip of volume for shell creation.

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• Shift elipse centering. account for shape = max_index+1

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• Adjust elipsoid shifting and removal amount

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• Allow for shell tallness and highness to be indepedanly adjusted

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• Save memory by removing gt initialization

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• remove floor from elipse centering

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• Add option to not scale plotly plot to microns

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• fix index shifts for shell. shell_tallness is like a size and so gets a -1 when doing index math

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• adjust limits of inclusion in the elipse

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• Detach loss terms from computational graph

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• Fix deletion method of voxel_parameters

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• Place verbose rays command in reconstruction function

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• Add fancy shift to ensure the tip of the elipse hits a grid point

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Commits on Sep 23, 2024

• added flipping option

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• Make the shell mode read in shell specific args

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• added shell args to shell_small_args

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• Plot scaled MIP with axial voxel size differs

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• Test axial voxels on spicule

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• Remove commented out shell methods

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• Add docstring to shell creation function

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• switch to geometric mean of radius in hopes of seeing the tip

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• Update shell and sphere test data

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• Merge pull request #109 from PolarizedLightFieldMicroscopy/axial_voxel

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• add shell_big_args

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• Lower minimum learning rate for optimizer scheduler

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• Merge branch 'mbl_2024' into shell

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• Merge pull request #110 from PolarizedLightFieldMicroscopy/shell

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• Uncomment basic simulation lines

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• Remove extra reconstructor attribute

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Commits on Sep 24, 2024

• Add use_microns flag as input to volume plots

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• Use volume generation module instead of static methods

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• Reduce redundant plotly setup

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• Rename epoch to iteration

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• Functionality to scale volume by retardance image

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• Remove extra config files and xylem images

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Commits on Sep 25, 2024

• Remove superfluous print of array shape

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• Adjust initial volume from retardance from spicule

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Commits on Sep 27, 2024

• Move voxel indices to gpu

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Commits on Oct 1, 2024

• Seperate optimizer schedulers and specify in config json

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• Specify scheduler with nerf mode

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Commits on Oct 2, 2024

• Create user-friendly reconstruction script

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• Always output reconstruction details to a log file

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• Remove spicule-specific files

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