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Transfer function visuals #178

Merged
merged 10 commits into from
Dec 18, 2024
Merged

Transfer function visuals #178

merged 10 commits into from
Dec 18, 2024

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talonchandler
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@talonchandler talonchandler commented Nov 8, 2024 •
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This PR adds visualization scripts for the Green's tensor spectrum and transfer functions.

Tagging @mattersoflight, @edyoshikun, @ieivanov who have requested these.

Running these scripts results in:

Screen.Recording.2024-11-08.at.1.33.04.PM.mov
Screen.Recording.2024-11-08.at.2.01.11.PM.mov

ziw-liu and others added 5 commits October 29, 2024 16:06
@ziw-liu
Bump torch to unpin numpy (#176)
a7ac036 
* bump torch to unpin numpy

* add SPEC-0 conformant numpy requirement
@ziw-liu @talonchandler
Bump torch to unpin numpy (#176)
6fa90a0 
* bump torch to unpin numpy

* add SPEC-0 conformant numpy requirement
@talonchandler
first-pass scripts
dca4769
@talonchandler
cleanup greens
885e05e
@talonchandler
clean transfer function support
ac56d26
@talonchandler talonchandler marked this pull request as ready for review November 8, 2024 22:06
@talonchandler
fix naming issue
f507a4b
@talonchandler
Wrap-safe transfer functions (#175)
cbda81d 
* helper functions

* fluorescence wrap safety

* 3d phase wrap safety

* fix axial nyquist bug

* 2d phase wrap safety

* fix interaction between padding and wrap safety
mattersoflight
mattersoflight approved these changes Nov 12, 2024
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Hi @talonchandler, these scripts work well! I tested on Mac.

Surface rendering of the support of the Green's tensor spectrum just like you surface render support of OTFs will lead to a more intuitive and compelling visualization.

Minor point: For visualization and slides, the dark theme looks better to me.

image

@talonchandler
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talonchandler commented Nov 12, 2024 •
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Surface rendering of the support of the Green's tensor spectrum just like you surface render support of OTFs will lead to a more intuitive and compelling visualization.

I agree, I will iterate here. The aliasing and colormapping are making the volume renders suboptimal. I'll need to get a "marching cubes" or similar algorithm connected to napari's surface layer, but I don't expect an enormous lift.

Minor point: For visualization and slides, the dark theme looks better to me.

Sounds good, I can return to that default after changing to a surface rendered Green's.

@talonchandler
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  • Dark mode is now default for these scripts

  • Green's tensor is now rendered as a surface (see screenshots below)
    Screenshot 2024-12-05 at 5 17 08 PM

  • The paper figure is now updated with the surface renders
    Screenshot 2024-12-05 at 5 36 10 PM

@talonchandler talonchandler merged commit 6021e97 into vector-prototype Dec 18, 2024
3 checks passed
@talonchandler talonchandler deleted the tf-visuals branch December 18, 2024 23:49
talonchandler added a commit that referenced this pull request Dec 22, 2024
@talonchandler @ieivanov
@ziw-liu @mattersoflight
Vector-optics birefringence reconstruction prototype (#170)
1451bf1 
* Phase reconstruction is invariant to voxel-size (#164)

* fix bug finding focus in stack with only one slice

* refactor for clarify

* formatting

* print -> warnings.warn

* test single-slice case

* fix test bugs

* z-scale-invariant test object

* no rescaling on output

* forward simulation takes a "brightness" - simulating real microscope

* fix example script

* add background parameter for fluorescence forward model

* test voxel-size invariance

* rename I_norm -> direct_intensity

* refactor to clarify discretization factor

* remove comment

* fix fluorescence example bug

* improved docsring

---------

Co-authored-by: Ivan Ivanov <ivan.ivanov@czbiohub.org>

* poster scripting

* may 14 poster draft

* last-minute poster changes

* quick clearning

* checkpoint before svd refactor

* SVD refactor

* pass singular system

* update visualization script

* fix visualization script scaling

* correct phase recon regression, legacy recon assumes axially even green's function

* helper functions

* fluorescence wrap safety

* 3d phase wrap safety

* fix axial nyquist bug

* 2d phase wrap safety

* fix interaction between padding and wrap safety

* clean defaults

* refactor singular system computation

* remove accidental duplicate

* refactor visuals

* fix warnings from tensoring a tensor

* match defaults

* readme type

* handle napari dependency

* Revert "fix warnings from tensoring a tensor"

This reverts commit ca4e7c5.

* Reapply "fix warnings from tensoring a tensor"

This reverts commit 790df57.

* revive old version of greens tensor for backwards compatibility

* fix tests that fail because of napari on github

* wrap-safe vector transfer function

* sampling tests

* fourier-space oversampling

* better visualizations for debugging

* complex-valued napari visuals

* complex utils

* fix colormaps

* debugging coherent tfs

* formatting

* fix rotation matrices

* fix dc term

* cleaning up

* first-pass visuals checkpoint

* matplotlib visuals

* temporarily turn off rotations

* debugging progress

* example script to generate matplotlib tf figures

* add rose asset

* add all assets

* plot all stokes

* brighter plot for greens

* visual improvements

* revised rotation-symmetric Green's tensor

* ignore

* fix green's tensor units

* modify circular anisotropy gellman matrices so that all transfer function are hermitian

* improved matplotlib visuals

* clean up plotting script

* fix bug with 3x3 hardcoded shape

* update tf components

* minor reconstruction updates

* refactor greens tensor spectrum

* clean test script

* clean models

* simple memory reduction

* clean debug statements

* reorder svd for clean i/o

* invert phase contrast

* formatting

* padding warning

* revise visuals

* visual cleanup

* manage large reconstructions

* Transfer function visuals (#178)

* Bump torch to unpin numpy (#176)

* bump torch to unpin numpy

* add SPEC-0 conformant numpy requirement

* Bump torch to unpin numpy (#176)

* bump torch to unpin numpy

* add SPEC-0 conformant numpy requirement

* first-pass scripts

* cleanup greens

* clean transfer function support

* fix naming issue

* Wrap-safe transfer functions (#175)

* helper functions

* fluorescence wrap safety

* 3d phase wrap safety

* fix axial nyquist bug

* 2d phase wrap safety

* fix interaction between padding and wrap safety

* green's tensor surfaces

* dark theme default

---------

Co-authored-by: Ziwen Liu <67518483+ziw-liu@users.noreply.github.com>

* matplotlib movie features

* cheaper default viz script

* move all visuals to /examples/visuals

* update examples/README to table

* typo

* update badges

* typo

* revise main README

* add 10-second slideshow

* Clean installation instructions

* cleanup vector model example

* minor cleanup

* remove matplotlib plot example

* edits to README

* clarify contrast mechanisms in README

* simplify example installation w/ `pip install waveorder[examples]`

* fix unintended diff

* clarify `examples/README.md`

* document 3d-to-2d transfer function

* test orthonormal bases

* fix accidental deletion

* add deprecation warnings

* remove plotting assets

* label transfer function and simulation axes

* guard type hint

* matplotlib visuals docs and type hints

* add type hints throughout models

* revert TYPE_CHECKING to strings

---------

Co-authored-by: Ivan Ivanov <ivan.ivanov@czbiohub.org>
Co-authored-by: Ziwen Liu <67518483+ziw-liu@users.noreply.github.com>
Co-authored-by: Shalin Mehta <shalin.mehta@czbiohub.org>
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@mattersoflight mattersoflight mattersoflight approved these changes

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@talonchandler @mattersoflight @ziw-liu