8000 demos for AQLM 2025 by mattersoflight · Pull Request #446 · mehta-lab/waveorder · GitHub
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demos for AQLM 2025 #446

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mattersoflight
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@mattersoflight mattersoflight commented May 2, 2025 •
edited by talonchandler
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I am adding two demos in the examples/demos/ folder. These are based on simulations on examples/maintanence folder. During AQLM, we will finetune these demos. It would make sense to turn the examples/maintenance into non-interactive tests after we merge this PR.

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I've given these notebooks a pass, and they now run end to end locally.

The QPI simulation notebook runs on Colab, but I'm still trying to figure out iohub installation issues in Colab for the QPI experiment notebook.

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Found a solution in !pip install iohub==0.2.0.

FYI @edyoshikun @ziw-liu, iohub==0.1.0 doesn't seem to be working with colab.

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ziw-liu commented May 5, 2025

Found a solution in !pip install iohub==0.2.0.

FYI @edyoshikun @ziw-liu, iohub==0.1.0 doesn't seem to be working with colab.

I think the kernel needs to be restarted for the old version. But we should really update waveorder's dependencies. (#197)

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mattersoflight commented May 5, 2025 •
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@talonchandler, the demos via google colab worked well. I updated the phase from defocus demo to illustrate 3D OTF's magnitude and phase, which sparked good discussion.

Few observations and questions (I am getting familiar again with codebase and will continue to do so as we wrap up the paper):

  • QLIPP reconstruction is done through waveorder_simulator.waveorder_microscopy_simulator, which appears to be the code path from earlier (PTI submission). Should we switch to using waveorder.models.inplane_oriented_thick_pol3d_vector?
  • Is the code for inverse filter shared across above demos?

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@talonchandler why do we pin iohub to 0.1.0?

This cell shows this error - but the notebook runs fine.

import sys
import subprocess

# Install latest waveorder from main branch
subprocess.check_call(
    [
        sys.executable,
        "-m",
        "pip",
        "install",
        "git+https://github.com/mehta-lab/waveorder.git@main",
    ]
)
!pip install iohub==0.2.0

ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
waveorder 2.2.2.dev1378+g8315e00 requires iohub==0.1.0, but you have iohub 0.2.0 which is incompatible.
waveorder 2.2.2.dev1378+g8315e00 requires pydantic==1.10.19, but you have pydantic 2.11.4 which is incompatible.
Successfully installed iohub-0.2.0 numcodecs-0.15.1 pydantic-2.11.4 pydantic_extra_types-2.10.4 tifffile-2025.3.30 zarr-2.18.7

mattersoflight
mattersoflight commented May 5, 2025
View reviewed changes
docs/examples/demos/QLIPP/QLIPP_simulation.py
retardance, azimuth = setup.Birefringence_recon_2D(
S1_stack, S2_stack, method="Tikhonov", reg_br=1e-2
)

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Add a block on phase reconstruction as well.

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Perhaps using waveorder.models.inplane_oriented_thick_pol3d_vector

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@mattersoflight @talonchandler @ziw-liu
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