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MBL 2024 #112

Merged
merged 57 commits into from
Oct 2, 2024
Merged

MBL 2024 #112

merged 57 commits into from
Oct 2, 2024

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gschlafly
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gschlafly and others added 30 commits September 21, 2024 10:27
@gschlafly
Add spicula reconstruction module and configuration
b0ea4eb
@gschlafly
Replace epoch with iteration
ac50e03
@gschlafly
Write command line output into log file
edcb5bf
@gschlafly
Exclude pycache files from view
20ecc67
@gschlafly
Spicula to spicule
6cf767d
@gschlafly
Refactor spicule module
4f6e536
@gschlafly
Keep axial component of optic axis positive in the volume creation
68ea960
@gschlafly
Shift the shell position
4e7d877
@gschlafly
Create pytest for optic axis
c1eabf7 
Verify all axial components of the optic axis are positive after the volume has been created.
@gschlafly
Modify initial volume creation optic axis
481cf5a 
Make all axial components positive
@gschlafly
Disable gradients for simluation tests
2d3d6fc
@gschlafly
Update images of shell for unit test
019b113
@gschlafly
Hide verbose rays messages during reconstruction
f1272a3
@Trevor-Anderberg
adjust elipse hight for shells
df4cf57
@Trevor-Anderberg
remove roll and clip of volume for shell creation.
3921a9f 
adjust removal_amount for our offset
@Trevor-Anderberg
Shift elipse centering. account for shape = max_index+1
b98652a
@Trevor-Anderberg
Adjust elipsoid shifting and removal amount
cad9361 
Use max_index instead of vol_shape
@Trevor-Anderberg
Allow for shell tallness and highness to be indepedanly adjusted
1bc6d42
@gschlafly
Save memory by removing gt initialization
d7bad0e
@Trevor-Anderberg
remove floor from elipse centering
ac8470d
@Trevor-Anderberg
Add option to not scale plotly plot to microns
64468a4
@Trevor-Anderberg
fix index shifts for shell. shell_tallness is like a size and so gets…
4aafc3d 
… a -1 when doing index math
@Trevor-Anderberg
adjust limits of inclusion in the elipse
2b5f4e3
@gschlafly
Detach loss terms from computational graph
b4de84d
@gschlafly
Fix deletion method of voxel_parameters
b5839a2 
Other typical deletion method were causing errors, like attribute did not exists. It did exist. This saves memory.
@gschlafly
Place verbose rays command in reconstruction function
06b457f 
It was too early and was now longer showing the progress bar for computing the ray geometry
@Trevor-Anderberg
Add fancy shift to ensure the tip of the elipse hits a grid point
ed45a99
@Trevor-Anderberg
added flipping option
732d2a5
@Trevor-Anderberg
Make the shell mode read in shell specific args
ae590b3 
They are:
- tallness (int) how tall the shell should be
- highness (int) how high the shell should be above the bottom of the volume
- flip (bool) should we flip the shell over
@Trevor-Anderberg
added shell args to shell_small_args
f1b994f
gschlafly and others added 27 commits September 22, 2024 19:28
@gschlafly
Plot scaled MIP with axial voxel size differs
15b0506
@gschlafly
Test axial voxels on spicule
69d4889
@gschlafly
Remove commented out shell methods
536f340
@gschlafly
Add docstring to shell creation function
3e7a6df
@Trevor-Anderberg
switch to geometric mean of radius in hopes of seeing the tip
68a6142
@gschlafly
Update shell and sphere test data
b050dd8
@gschlafly
Merge pull request #109 from PolarizedLightFieldMicroscopy/axial_voxel
2518d00 
Axial dimension of voxels can be larger
@Trevor-Anderberg
add shell_big_args
4f963e9 
to be used with optical_config_shell.json
@gschlafly
Lower minimum learning rate for optimizer scheduler
cfda454
@gschlafly
Merge branch 'mbl_2024' into shell
206dcbe
@gschlafly
Merge pull request #110 from PolarizedLightFieldMicroscopy/shell
46e6cec 
Shell
@gschlafly
Uncomment basic simulation lines
23254a5
@gschlafly
Remove extra reconstructor attribute
8fbe799
@gschlafly
Add use_microns flag as input to volume plots
6626500
@gschlafly
Use volume generation module instead of static methods
0ad8afc 
Also replaced more plotly volume size units params
@gschlafly
Reduce redundant plotly setup
51f3389
@gschlafly
Rename epoch to iteration
f6d15d5 
Primarily affects the key word in the iteration config file
@gschlafly
Functionality to scale volume by retardance image
f935610
@gschlafly
Remove extra config files and xylem images
f08d6e6
@gschlafly
Remove superfluous print of array shape
dff0189
@gschlafly
Adjust initial volume from retardance from spicule
4327d45
@gschlafly
Move voxel indices to gpu
65bccde
@gschlafly
Seperate optimizer schedulers and specify in config json
8706442 
- moved placement of verbose flag in recon so that it is adjustable before starting recon
- nerf mode does not quite work
- use voxel recon as a test case

All tests pass
@gschlafly
Specify scheduler with nerf mode
e788fe5
@gschlafly
Create user-friendly reconstruction script
ae7d0bc
@gschlafly
Always output reconstruction details to a log file
97e4799
@gschlafly
Remove spicule-specific files
0a337c3
@gschlafly gschlafly merged commit 4db3910 into main Oct 2, 2024
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2 participants
@gschlafly @Trevor-Anderberg