ENH: Add 2D cropping support and origin/spacing processing to ITK image readers#1511
Merged
joeykleingers merged 14 commits intoBlueQuartzSoftware:developfrom Feb 6, 2026
Conversation
joeykleingers
force-pushed
the
topic/CropImageGeometryParameter2D
branch
2 times, most recently
from
72d8e3b to
dd59d60
Compare
imikejackson
force-pushed
the
topic/CropImageGeometryParameter2D
branch
from
dd59d60 to
9ee9d79
Compare
joeykleingers
force-pushed
the
topic/CropImageGeometryParameter2D
branch
3 times, most recently
from
102dae3 to
abf5474
Compare
imikejackson
force-pushed
the
topic/CropImageGeometryParameter2D
branch
2 times, most recently
from
a7649de to
52c888d
Compare
imikejackson
requested changes
Feb 5, 2026
Contributor
imikejackson
left a comment
imikejackson
left a comment
There was a problem hiding this comment.
Use the Read Zeiss TXM filter to have the preflight create the before and after for the input geometry.
Signed-off-by: Joey Kleingers <joey.kleingers@bluequartz.net>
…cks. Also passed in NoCropping cropping options to Fiji Montage reader because it uses the same ITK Image Reader execute API. Still need to expose the cropping options for Fiji Montage reader as a filter parameter. Signed-off-by: Joey Kleingers <joey.kleingers@bluequartz.net>
… stack reader. This parameter determines whether the origin & spacing set by the user is set before or after reading and cropping/processing the image(s). Signed-off-by: Joey Kleingers <joey.kleingers@bluequartz.net>
Signed-off-by: Joey Kleingers <joey.kleingers@bluequartz.net>
Signed-off-by: Joey Kleingers <joey.kleingers@bluequartz.net>
Signed-off-by: Joey Kleingers <joey.kleingers@bluequartz.net>
Signed-off-by: Joey Kleingers <joey.kleingers@bluequartz.net>
Signed-off-by: Joey Kleingers <joey.kleingers@bluequartz.net>
Signed-off-by: Joey Kleingers <joey.kleingers@bluequartz.net>
Signed-off-by: Joey Kleingers <joey.kleingers@bluequartz.net>
imikejackson
force-pushed
the
topic/CropImageGeometryParameter2D
branch
from
3de8b2b to
22eb43c
Compare
…geometry. Signed-off-by: Joey Kleingers <joey.kleingers@bluequartz.net>
Signed-off-by: Joey Kleingers <joey.kleingers@bluequartz.net>
imikejackson
approved these changes
Feb 6, 2026
imikejackson
pushed a commit
to joeykleingers/simplnx
that referenced
this pull request
Feb 7, 2026
…ge readers (BlueQuartzSoftware#1511) Enhances ITK image reading filters with 2D-aware cropping capabilities and configurable origin/spacing processing timing, providing more flexible image import workflows. CropGeometryParameter Enhancement - Added `is_2d` flag to `CropGeometryParameter` to support 2D image cropping - Enables proper cropping of 2D images without Z-axis constraints ITKImageReader & ITKImportImageStack Improvements - Added cropping options: Both filters now support voxel-based and physical subvolume cropping during image import - Origin & Spacing Processing parameter: New parameter controls whether user-specified origin/spacing values are applied before (preprocessed) or after (postprocessed) image reading and cropping - Preprocessed: Origin/spacing applied before cropping (affects crop bounds interpretation) - Postprocessed: Origin/spacing applied after cropping (simpler workflow) - Updated `ReadImageUtils` to handle cropping and origin/spacing processing timing Testing - Completely rewrote `ITKImageReaderTest` and `ITKImportImageStackTest` to comprehensively test all code paths and feature interactions - Tests now validate all combinations of cropping, origin/spacing override, data type conversion, and processing timing Testing Performed - All new test cases pass with exemplar validation - Tested 2D and 3D image cropping scenarios - Verified origin/spacing processing in both pre and post modes - Validated data type conversions with cropping
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Summary
Enhances ITK image reading filters with 2D-aware cropping capabilities and configurable origin/spacing processing timing, providing more flexible image import workflows.
Key Changes
CropGeometryParameter Enhancement
is_2dflag toCropGeometryParameterto support 2D image croppingITKImageReader & ITKImportImageStack Improvements
ReadImageUtilsto handle cropping and origin/spacing processing timingTesting
ITKImageReaderTestandITKImportImageStackTestto comprehensively test all code paths and feature interactionsTesting Performed
NOTE
This PR goes hand in hand with #1030 and should be approved and merged with it.