Phase contribution

[hrobarts]

Changes

Add Paganin phase retrieval methods based on the description in https://onlinelibrary.wiley.com/doi/10.1046/j.1365-2818.2002.01010.x

The phase retrieval can be applied using

processor = PaganinProcessor(delta, beta, energy)
processor.set_input(data)
thickness = processor.get_output()

Runs the Paganin method, returning the sample thickness,
$ T = -\frac{1}{\mu}\ln(F^{-1}\frac{F(M^2 I_{norm}(x,y,z=\Delta))}{1+\frac{\Delta\lambda\delta}{4\pi\beta}(k_x^2+k_y^2)})$

Or with the filter_type argument ='generalised_paganin_method' uses the filter described in https://iopscience.iop.org/article/10.1088/2040-8986/abbab9
$ T = -\frac{1}{\mu}\ln(F^{-1}\frac{F(M^2 I_{norm}(x,y,z=\Delta))}{1-\frac{2\Delta\lambda\delta}{4\pi\beta W^2}(cos(Wk_x)+cos(Wk_y)-2)})$

Both methods require normalised transmission data, $I_{norm}$, physical parameters for delta, beta (the real and complex part of the material refractive index) and energy. The propagation distance, $\Delta$, magnification, $M$, and pixel size, $W$, are accessed from the data geometry. If these values are not found in the geometry, the processor prints a warning and uses default values. The geometry values can be over-ridden using

processor = PaganinProcessor(delta, beta, energy)
processor.set_input(data)
processor.get_output(override_geometry={'propagation_distance': 0.1, override_filter={'alpha':1})

We can return only the filtered image using,

processor = PaganinProcessor(delta, beta, energy, full_retrieval=False)
processor.set_input(data)
filtered_image = processor.get_output()

which returns

$ I_{filtered} = F^{-1}\frac{F( I(x,y,z=\Delta))}{1+\frac{\Delta\lambda\delta}{4\pi\beta}(k_x^2+k_y^2)}$

Testing you performed

I've made a pull request to add an example to CIL-Demos/misc using these methods
TomographicImaging/CIL-Demos#151
Below is an output from the notebook showing a comparison of the cross-section of a test image with different phase retrieval methods. The scaled phase retrieval in CIL matches the phase retrieval method in Tomopy when performed on transmission data then converted to absorption, and the filter in CIL matches the Tomopy method performed on absorption data

where the Tomopy regularisation parameter argument is tomopy_alpha = 1/(4*np.pi**2*(delta/beta))

Unit tests of the functionality are in test_DataProcessor.py TestPaganinPhaseRetriver() and TestFilter()

Related issues/links

Checklist

• I have performed a self-review of my code
• I have added docstrings in line with the guidance in the developer guide
• I have updated the relevant documentation
• I have implemented unit tests that cover any new or modified functionality
• CHANGELOG.md has been updated with any functionality change
• Request review from all relevant developers
• Change pull request label to 'Waiting for review'

Contribution Notes

Please read and adhere to the developer guide and local patterns and conventions.

• The content of this Pull Request (the Contribution) is intentionally submitted for inclusion in CIL (the Work) under the terms and conditions of the Apache-2.0 License
• I confirm that the contribution does not violate any intellectual property rights of third parties

[jakobsj]

We don't normally require dask do we? Can we avoid it?

…

On Mon, 4 Mar 2024 at 15:58, Casper da Costa-Luis ***@***.***> wrote: ***@***.**** commented on this pull request. ------------------------------ In Wrappers/Python/cil/processors/PaganinPhaseProcessor.py <#1737 (comment)> : > @@ -0,0 +1,387 @@ +# -*- coding: utf-8 -*- ⬇️ Suggested change -# -*- coding: utf-8 -*- ------------------------------ In Wrappers/Python/cil/processors/PaganinPhaseProcessor.py <#1737 (comment)> : > +import dask +from dask import delayed if dask is a new dependency you'll need to add it to: - recipe/meta.yaml - scripts/create_local_env_for_cil_development.sh - scripts/requirements-test.yml — Reply to this email directly, view it on GitHub <#1737 (review)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACMDSCBUL3QNPDBDJ625ERTYWSD2BAVCNFSM6AAAAABECCP67KVHI2DSMVQWIX3LMV43YUDVNRWFEZLROVSXG5CSMV3GSZLXHMYTSMJUGUZTMNBYGI> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[hrobarts]

Hi Jakob, yes we can avoid it. I thought it already was a dependency but I can remove it if not

[gfardell]

It's looking good. Now I've had a good look I think we need to update the units handling here as I've suggested in individual comments. We can discuss this more though.

Otherwise I see some memory issues with the padding, but that's an easy fix.

[jakobsj]

Hi @hrobarts thanks for the update, I am happy with the changes. I added a couple of minor points and also a couple of my previous conversations remain open, could you take a look and respond to each so we can see (and have a record of) what has been done and if can be resolved? Thanks!

[jakobsj]

Happy with it!

[gfardell]

It looks great! I'm happy once tests pass.