Roi #703

bnmajor · 2023-12-06T14:03:38Z

Depends on Kitware/itk-vtk-viewer#724 and #702

itkwidgets/viewer.py

thewtex · 2023-12-07T20:49:32Z

itkwidgets/viewer.py

+        x0, x1 = idxs['x']
+        y0, y1 = idxs['y']
+        z0, z1 = idxs['z']
+        return np.index_exp[z0:z1, y0:y1, x0:x1]


very cool!!

thewtex · 2023-12-07T20:49:50Z

loving it!

review-notebook-app · 2023-12-08T16:19:37Z

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bnmajor · 2023-12-08T16:24:58Z

@thewtex @PaulHax A new example notebook has been added but if there is better data to use (maybe a large dataset that is typically stuck to a lower scale?) I'd be happy to update with a different example. This data was more or less selected at random.

thewtex · 2023-12-09T18:09:16Z

@bnmajor awesome job!

A few requests inline.

This is a good dataset, but another to consider is:

https://data.kitware.com/#item/63476e0911dab81428208e27

for more scales / variety.

thewtex · 2023-12-09T18:09:51Z

@bnmajor awesome job!

A few requests inline.

This is a good dataset, but another to consider is:

https://data.kitware.com/#item/63476e0911dab81428208e27

for more scales / variety.

thewtex · 2023-12-09T18:09:56Z

examples/integrations/itk/SelectROI.ipynb

@@ -0,0 +1,350 @@
+{


This gif is wicked cool to have embedded in the notebook!! How did you do that? :-D

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It's just an html image tag in a markdown cell! Updated to use the full URL instead of the relative path though so it may appear broken in the review notebook now until these changes are merged in.

thewtex · 2023-12-09T18:09:56Z

examples/integrations/itk/SelectROI.ipynb

@@ -0,0 +1,350 @@
+{


Line #1. loaded_scale
Let's make a note, provide a reminder on how the scales, are defined, i.e. "Zero is the highest resolution scale."

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Sounds good, updated 👍

thewtex · 2023-12-09T18:09:56Z

examples/integrations/itk/SelectROI.ipynb

@@ -0,0 +1,350 @@
+{


Line #1. roi_region
Let's make a note / provide a reminder that these are in physical, world coordinates.

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thewtex · 2023-12-09T18:09:57Z

examples/integrations/itk/SelectROI.ipynb

@@ -0,0 +1,350 @@
+{


Line #3. # Request the highest level explicitly in case that is not what is loaded.
To make the connection clearer, let's use loaded_scale here.

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Sounds good!

thewtex · 2023-12-09T18:09:57Z

examples/integrations/itk/SelectROI.ipynb

@@ -0,0 +1,350 @@
+{


Line #1. roi_slice
Let's add another cell for illustration that calls viewer.get_roi_slice() (no argument) that demonstrates we get the same result since that is the current scale.

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Add support for being able to programmatically retrieve information about the current region of interest.

thewtex · 2023-12-12T03:08:40Z

Awesome!

thewtex · 2023-12-12T03:08:48Z

examples/integrations/itk/SelectROI.ipynb

@@ -0,0 +1,365 @@
+{


Line #2. print(roi_slices, default_roi_slices)
We could make these two print statements so they are easier to compare.

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bnmajor · 2023-12-12T13:44:31Z

@thewtex Two last items:

I did try the other dataset that you suggested but I did not use it because it appears to be missing spacing information?
When we grab the ROI for lower scales it seems that we lose the metadata or something... The resulting image is skewed (this does not happen at scale 0):

thewtex · 2023-12-12T21:41:06Z

@bnmajor what is your ngff_zarr.__version__?

thewtex · 2023-12-12T21:46:16Z

Checking this branch out locally, I could not reproduce with ngff-Zarr 0.6.0.

bnmajor · 2023-12-12T21:47:37Z

Checking this branch out locally, I could not reproduce with ngff-Zarr 0.6.0.

I was on 0.4.7... Sorry about that!

EDIT: Actually, still seeing it with 0.6.0...

thewtex · 2023-12-12T21:53:44Z

I seem to recall an older version of itk-vtk-viewer causing this behavior -- is it possible that an old version is used locally?

thewtex · 2023-12-12T22:02:14Z

I tried again with a fresh conda environment and repository checkout, the spacing was correct and consistent across scales.

bnmajor · 2023-12-12T22:02:38Z

I'm not using a local instance of the itk-vtk-viewer and we're currently using the latest release...

thewtex · 2023-12-12T22:03:22Z

Oh, I was just looking and viewer1 -- I do see that with viewer2 :-)

thewtex · 2023-12-12T22:04:54Z

roi = multiscales.images[loaded_scale].data[roi_slices]

This is extracting only the array and discarding the metadata.

thewtex · 2023-12-12T22:16:51Z

with:

# Create a new viewer using only the data in the ROI determined above
loaded_image = multiscales.images[loaded_scale]
roi_data = loaded_image.data[roi_slices]

from ngff_zarr import to_ngff_image

roi_image = to_ngff_image(roi_data, dims=loaded_image.dims, scale=loaded_image.scale, translation={'x': roi_region[0][0], 'y': roi_region[0][1], 'z': roi_region[0][2]})

from ngff_zarr import to_ngff_image

update the notebook according to the above.
could you please update get_roi_region to output a list of dictionaries, 'x', 'y', etc.

?

If we just grab the array we'll drop the metadata and get a skewed result.

bnmajor · 2023-12-12T22:30:35Z

update the notebook according to the above.

could you please update get_roi_region to output a list of dictionaries, 'x', 'y', etc.

?

Updates have been pushed, thank you

And multiscale-spatial-image.

thewtex · 2023-12-13T02:42:43Z

Sorry, I was not too clear -- I will push a patch with a minor tweak.

bnmajor · 2023-12-13T13:22:25Z

Sorry, I was not too clear -- I will push a patch with a minor tweak.

I see, sorry about my misunderstanding! Thanks for the fix!

bnmajor · 2023-12-13T13:23:11Z

@thewtex This is good to go from my end if everything is looking good for you as well

bnmajor force-pushed the roi branch from af3386f to 7bc2d54 Compare December 6, 2023 14:17

thewtex reviewed Dec 7, 2023

View reviewed changes

bnmajor force-pushed the roi branch from 7bc2d54 to cda4d84 Compare December 8, 2023 16:15

thewtex reviewed Dec 9, 2023

View reviewed changes

bnmajor added 2 commits December 11, 2023 15:16

ENH: Add initial ROI support

41b8a60

Add support for being able to programmatically retrieve information about the current region of interest.

ENH: Add clipping planes getter/setter

c1ac8a8

bnmajor force-pushed the roi branch from 52a35c3 to 74f85a1 Compare December 11, 2023 20:16

bnmajor added 3 commits December 11, 2023 17:46

DOC: Add a select roi example notebook

11277b6

MAINT: Use full URL instead of relative path for embedded gif

5c697a6

DOC: Add better comments in the notebook

baaa34a

bnmajor force-pushed the roi branch from 9b6db98 to baaa34a Compare December 11, 2023 22:47

thewtex reviewed Dec 12, 2023

View reviewed changes

thewtex approved these changes Dec 12, 2023

View reviewed changes

DOC: Separate print statements

fd26eb4

bnmajor marked this pull request as ready for review December 12, 2023 13:45

bnmajor added 2 commits December 12, 2023 17:27

ENH: Return dict from get_roi_region

a0d4938

BUG: Produce image rather than array for sliced data

a0a5f75

If we just grab the array we'll drop the metadata and get a skewed result.

BUG: Format of get_roi_region directly works with to_ngff_zarr

007cfe4

And multiscale-spatial-image.

thewtex merged commit ec9b018 into InsightSoftwareConsortium:main Dec 13, 2023
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Roi #703

Roi #703

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Roi #703

Roi #703

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