Basic functionality #14

IgorTatarnikov · 2023-10-12T16:37:29Z

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Description

What is this PR

Bug fix
Addition of a new feature
Other

Why is this PR needed?
Starting development on bg-elastix. Allow ideal 2D images to be registered to an atlas using elastix.

What does this PR do?

Load a brain globe atlas into napari to select a 2D slice to register to
Allow translating, rotating, and scaling of the sample image to roughly match the atlas in napari
Pass the translation, rotation, and scaling to elastix
Provide some default pre-processing for the sample image
Provide a widget to allow custom pre-processing - Will be handled by the user for now
Provide default parameter sets to pass to elastix
Provide a widget to customise parameters passed back to elastix
Have some way to judge the registration success

References

#12

How has this PR been tested?

No tests currently written, but all code should have unit tests at least

Is this a breaking change?

N/A

Does this PR require an update to the documentation?

Yes

If any features have changed, or have been added. Please explain how the documentation has been updated (and link to the associated PR). See here for details.

Checklist:

The code has been tested locally
Tests have been added to cover all new functionality (unit & integration)
The documentation has been updated to reflect any changes
The code has been formatted with pre-commit

…ister [IBL] or ARA)

…and perform selected transforms with either elastix defaults or provided ARA defaults

…functionality # Conflicts: # src/bg_elastix/_widget.py

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IgorTatarnikov · 2023-10-12T16:39:52Z

This is my plan for now, after I get all of this working I think we can move on to damaged slice, and registering sub-volumes

adamltyson · 2023-10-13T09:03:53Z

src/bg_elastix/elastix/register.py



 def run_registration(
-    fixed_image,
+    brain_atlas,


Would it be better to keep the original naming of these variables, so the registration function could potentially be used for other things? If nothing else, not all BrainGlobe atlases are of brains.

I can change that back, at some point I considered passing a BrainGlobeAtlas object back but decided against it without changing it back.

adamltyson · 2023-10-13T09:05:53Z

src/bg_elastix/elastix/register.py

    )
    elastix_object.SetParameterObject(parameter_object)
-    elastix_object.SetLogToConsole(log)
+    elastix_object.LogToFileOn()
+    elastix_object.SetOutputDirectory("./logs")


This fails for me because the directory doesn't exist by default. Also, should logging to file be optional (alongside saving the results? A typical napari plugin wouldn't log to file. If it needs to log, it should maybe go into ~.brainglobe.

I can remove that, it was mostly for my own early testing to see what I could glean from logs in terms of how well the registration went. I was hoping there would be a set of numbers in the logs that we could monitor to pick the "best" registration

adamltyson · 2023-10-13T09:06:28Z

src/bg_elastix/elastix/register.py

+            )
+            parameter_object.AddParameterMap(parameter_map_bspline)
+        else:
+            parameter_object.AddParameterFile(


I assume the plan is eventually for the user to be able to pick from a list of existing parameter files?

That was my thought. We could curate some parameter sets from the model zoo, or other tools to present in a dropdown list of sorts.

adamltyson · 2023-10-13T09:07:06Z

src/bg_elastix/_widget.py

+        ]
+
+    @register.get_atlas_button.changed.connect
+    def get_atlas_button_click():


It would be cool to use brainrender-napari for this in some way rather than duplicating functionality here.

I've thought about this as well. I wasn't sure if we want to have a direct dependency. If we do, then I could reuse a lot of the QT code that @alessandrofelder has already written (such as the NapariAtlasRepresentation class). I also added a header to the plugin that's similar to brainrender-napari (has the brainglobe logo and links to repo/documentation). Is it worth potentially creating a brainglobe napari utils repository that all brainglobe napari plugins can depend on?

Does it need to be a dependency? Is there a way of users just directly using the brainrender plugin to load the atlas?

Is it worth potentially creating a brainglobe napari utils repository that all brainglobe napari plugins can depend on?

Definitely. We'd previously agreed to do this, just haven't got round to it.

Actually based on e.g. brainglobe/brainglobe-utils#3 I think we must have decided to put all napari stuff into https://github.com/brainglobe/brainglobe-utils

adamltyson · 2023-10-13T09:07:26Z

src/bg_elastix/_widget.py

+            register.rotate.value = 0
+
+    @register.start_alignment_button.changed.connect
+    def start_alignment_button_on_clik():


Suggested change

def start_alignment_button_on_clik():

def start_alignment_button_on_click():

adamltyson · 2023-10-13T09:09:43Z

src/bg_elastix/_widget.py

+                register.translate_y.value,
+                register.translate_x.value,
+            )
+            register.image_to_adjust.value.rotate = register.rotate.value


This rotates at the origin, it may be more intuitive for the user to rotate at the center of the image? I don't think napari can handle this directly, but this plugin may be useful.

The plugin looks great, easy to switch in

adamltyson · 2023-10-13T09:11:47Z

Looking very nice @IgorTatarnikov. I've left some comments.

alessandrofelder

Think this is a great start too 🎉 As discussed,

maybe worth separating functionality from callbacks so same napari functionality usable from e.g IPython
move from magicgui to qtpy directly at some point

(This can/should probably happen in a future PR/future PRs?)

…_widget.py now uses qtpy directly to replicate the majority of _widget.py functionality.

…functionality

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IgorTatarnikov · 2023-10-13T16:11:59Z

I've added a new version in registration_widget.py that now uses qtpy directly. It's all in one file and unteste but the functionality is the same as the version in _widget.py. I'll work on writing unit tests/docs early next week and then switch to a more TDD approach now that I'm more familiar with qtpy and napari itself.

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…ual UI component into its own file

… default param settings

… of transforms with unique defaults

… the selection in the second column of the widget

…ameter maps can be run in one go

…just image button

…ed to allow comments in parameter file

…or brainglobe_registration/widgets/adjust_moving_image.py

…w.py

…g to utils

IgorTatarnikov · 2023-11-27T11:21:16Z

I think this is ready as an early version. It can handle registering a 2D image to the selected atlas slice.

adamltyson

Looks good to me. I haven't gone through everything line by line, because I don't think it's very useful at this stage. I've raised issues for some larger points I had.

For some reason the tests fail for me with:

src/tests/test_adjust_moving_image_view.py Fatal Python error: Aborted

I wondered if I'm missing some dev dependencies?

src/brainglobe_registration/utils/brainglobe_logo.py

src/brainglobe_registration/registration_widget.py

…rlaid on sample image after run

Co-authored-by: Adam Tyson <code@adamltyson.com>

IgorTatarnikov · 2023-11-28T13:51:35Z

Looks good to me. I haven't gone through everything line by line, because I don't think it's very useful at this stage. I've raised issues for some larger points I had.

For some reason the tests fail for me with:
src/tests/test_adjust_moving_image_view.py Fatal Python error: Aborted
I wondered if I'm missing some dev dependencies?

I think this has to do with #18. I've reformated the project in standardise-package-structure. I'll merge this PR and immediately open a fresh one to address the project restructuring, if that works for everyone.

adamltyson · 2023-11-28T14:04:48Z

I'll merge this PR and immediately open a fresh one to address the project restructuring, if that works for everyone.

Go for it

IgorTatarnikov added 7 commits October 10, 2023 12:49

Added default parameter sets to be used for transforms (from brainreg…

e098aad

…ister [IBL] or ARA)

Basic magicgui that can import an atlas, translate the atlas/sample, …

0adedfa

…and perform selected transforms with either elastix defaults or provided ARA defaults

Added a button to reset the image back to origin

8265262

Added the ability to rotate the image and reset back to original state

8f37fad

Added start alignment button

ab375f8

Added start alignment button

d0bf17c

Merge remote-tracking branch 'origin/basic-functionality' into basic-…

ce73b7b

…functionality # Conflicts: # src/bg_elastix/_widget.py

IgorTatarnikov requested review from alessandrofelder and adamltyson October 12, 2023 16:37

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adamltyson reviewed Oct 13, 2023

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alessandrofelder approved these changes Oct 13, 2023

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IgorTatarnikov and others added 3 commits October 13, 2023 17:05

Transitioning basic function to qpty directly. Widget in registration…

ed93f0c

…_widget.py now uses qtpy directly to replicate the majority of _widget.py functionality.

Merge remote-tracking branch 'origin/basic-functionality' into basic-…

65c04a6

…functionality

[pre-commit.ci] auto fixes from pre-commit.com hooks

d53696f

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IgorTatarnikov and others added 3 commits October 16, 2023 12:54

Napari image layer is now rotated around the center not at origin

7297aec

Tests for setup_parameter_object done

2125849

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IgorTatarnikov linked an issue Oct 18, 2023 that may be closed by this pull request

[BUG] Plugin crash when no brainglobe atlases available #15

Open

IgorTatarnikov added 3 commits October 24, 2023 10:31

Wrote basic tests for registration_widget and register

35d39f0

Re-factored the core registration_widget.py to split off each individ…

5ee9e99

…ual UI component into its own file

Added a run settings widget to allow selection of transform types and…

4a7de5f

… default param settings

IgorTatarnikov and others added 20 commits November 3, 2023 17:04

First version of transform selection widget allowing arbitrary number…

44c0d02

… of transforms with unique defaults

Each column now dynamically imports the correct default file based on…

eb635e8

… the selection in the second column of the widget

Parameters are now read as lists from files, arbitrary numbers of par…

b668c7e

…ameter maps can be run in one go

Moving image adjusts immediately after values are entered, removed ad…

89065b2

…just image button

When reading parameter files anything after a '\' will now be discard…

cc1ec57

…ed to allow comments in parameter file

Updated tests for braingblobe_registration/register.py, added tests f…

5e93b54

…or brainglobe_registration/widgets/adjust_moving_image.py

Added tests for brainglobe_registration/widgets/select_images_view.py

381e2b9

Started tests for brainglobe_registration/widgets/parameter_list_view.py

fb0dc0e

Finished tests for brainglobe/registration/widgets/parameter_list_vie…

6945993

…w.py

Started tests for transform_select_view.py

f9e1d90

Updating README.md

8b51abc

Update README.md

c3db983

Updated README.md

b6eadfc

Added tests, added dynamic fetching for sample selection

63de272

Update README.md

1cef635

Refactored test_registration_widget.py to account for funcitons movin…

beaa9ad

…g to utils

Fixed line lengths

b325d56

WIP transforming annotations after registration

a19a95c

WIP transform annotations after registration

1e7de58

Transformed annotation and boundaries images from atlas to sample space

b188101

IgorTatarnikov changed the base branch from dev to main November 27, 2023 11:12

IgorTatarnikov marked this pull request as ready for review November 27, 2023 11:17

adamltyson approved these changes Nov 27, 2023

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src/brainglobe_registration/utils/brainglobe_logo.py Outdated Show resolved Hide resolved

src/brainglobe_registration/utils/brainglobe_logo.py Outdated Show resolved Hide resolved

src/brainglobe_registration/registration_widget.py Outdated Show resolved Hide resolved

IgorTatarnikov and others added 3 commits November 28, 2023 10:24

Registered boundaries are now added as an image layer, boundaries ove…

9614ce8

…rlaid on sample image after run

Changed the source link in the widget header

cdd5f1d

Co-authored-by: Adam Tyson <code@adamltyson.com>

Removed tutorial section of the header

77c28c9

IgorTatarnikov merged commit 53394b4 into main Nov 28, 2023
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Basic functionality #14

Basic functionality #14

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adamltyson commented Nov 28, 2023

	def start_alignment_button_on_clik():
	def start_alignment_button_on_click():

Basic functionality #14

Basic functionality #14

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IgorTatarnikov commented Oct 12, 2023 • edited

Description

References

How has this PR been tested?

Is this a breaking change?

Does this PR require an update to the documentation?

Checklist:

IgorTatarnikov commented Oct 12, 2023

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adamltyson commented Oct 13, 2023

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IgorTatarnikov commented Oct 12, 2023 •

edited