Fix file reading errors #64

MikeLippincott · 2025-09-29T17:24:23Z

This PR adds a way to format input images (ome-tiff or tiff) to be compatible with nviz functions. Changes such as retyping, and dimensionality squeezing.
This PR is somewhat related to PR #12 if this one is merged #12 will be closed.

What kind of change(s) are included?

Documentation (changes docs or other related content)
Bug fix (fixes an issue).
Enhancement (adds functionality).
Breaking change (these changes would cause existing functionality to not work as expected).

Checklist

I have read and followed the CONTRIBUTING.md guidelines.
I have searched for existing content to ensure this is not a duplicate.
I have performed a self-review of these additions (including spelling, grammar, and related).
These changes pass all pre-commit checks.
I have added comments to my code to help provide understanding
I have added a test which covers the code changes found within this PR
I have deleted all non-relevant text in this pull request template.

* update labels parameter to include default * [pre-commit.ci lite] apply automatic fixes * Enable Linux compatibility with dependency changes and improved dev tooling (WayScience#17) * run linux tests on dev branch * don't show if headless * install qt deps * try async setting * Update run-tests.yml * try additional qt libs * troubleshoot further with docker * linting * Update run-tests.yml * Update run-tests.yml * Update run-tests.yml * Update uv.lock * fallback to napari[all] and setup qt for ubuntu * move to macos-14 for tests * add python3-pyqt5 installation * attempt to install different qt deps * Update run-tests.yml * attempt another linux dep step * update for linting step * update docs * [pre-commit.ci lite] apply automatic fixes * fix conflict i hope * [pre-commit.ci lite] apply automatic fixes --------- Co-authored-by: pre-commit-ci-lite[bot] <117423508+pre-commit-ci-lite[bot]@users.noreply.github.com> Co-authored-by: Dave Bunten <dave.bunten@cuanschutz.edu>

* add synapse download enhancement to test real data * Update conftest.py * Update coverage-badge.svg * [pre-commit.ci lite] apply automatic fixes * assert that the files exist prior to tests * Update conftest.py * Update conftest.py * [pre-commit.ci lite] apply automatic fixes * track down missing files within gh actions env * [pre-commit.ci lite] apply automatic fixes * pathlib correction * check for the token * [pre-commit.ci lite] apply automatic fixes * retry * move to pull request target * readd pull request trigger * remove verbose pytest output * linting * [pre-commit.ci lite] apply automatic fixes * Apply suggestions from code review Co-authored-by: Gregory Way <gregory.way@gmail.com> * [pre-commit.ci lite] apply automatic fixes --------- Co-authored-by: pre-commit-ci-lite[bot] <117423508+pre-commit-ci-lite[bot]@users.noreply.github.com> Co-authored-by: Gregory Way <gregory.way@gmail.com>

…ce#35) * enable downstream branches to be checked out * Update .pre-commit-config.yaml * linting

* add nviz cli * [pre-commit.ci lite] apply automatic fixes * updates based on feedback Co-Authored-By: Mike Lippincott <58147848+MikeLippincott@users.noreply.github.com> * ignore testing utils * ignore conftest for coverage --------- Co-authored-by: pre-commit-ci-lite[bot] <117423508+pre-commit-ci-lite[bot]@users.noreply.github.com> Co-authored-by: Mike Lippincott <58147848+MikeLippincott@users.noreply.github.com>

…e#40) * move to macos for pre-commit checks * linting * add context

…enges (WayScience#42) * Create check.py * path report capabilities * linting * [pre-commit.ci lite] apply automatic fixes * remove pull_request set of testion actions * Update .pre-commit-config.yaml * Update .pre-commit-config.yaml * use pull request src instead of target for chkout * add debug for actions * remove debug * update to avoid coverage discrepancies * Update coverage-badge.svg * move to macos for pre-commit checks * linting * ignore tests for coverage * remove coverage reporting * remove shellcheck because of docker * add path reporter to cli * update for return code expectations * add complete test data * update for tests and readd coverage just in case * test locally * Update run-tests.yml * Update coverage-badge.svg * Update coverage-badge.svg * readd coverage Co-Authored-By: Jenna Tomkinson <107513215+jenna-tomkinson@users.noreply.github.com> * Update .pre-commit-config.yaml --------- Co-authored-by: pre-commit-ci-lite[bot] <117423508+pre-commit-ci-lite[bot]@users.noreply.github.com> Co-authored-by: Jenna Tomkinson <107513215+jenna-tomkinson@users.noreply.github.com>

* update dockerfile for uv * update deps and fix pre-commit config * update dockerfile and poe task

* fix docs builds with linux headless config * Update .pre-commit-config.yaml * apply changes for pre-commit * Update coverage-badge.svg

* add software doi for reference * Update .pre-commit-config.yaml

* update pre-commit-lite conditions * correction

* update gh actions macos runner * Update .pre-commit-config.yaml

* Add Almanack to pre-commit checks * Update .pre-commit-config.yaml * add the fork remote for upstream ref * debugging information for git * Update run-tests.yml * remove git block

d33bs · 2025-09-29T17:53:48Z

src/nviz/view.py

    if not headless:
        # Start the Napari event loop
-        napari.run()
+        napari.run(force=True)


Consider adding a special note here about why we use force=True (I'm guessing it's to see that Napari loads but might sometimes not have an image to display).

d33bs · 2025-09-29T17:56:27Z

tests/test_image.py

+        assert tif.shape > 3  # Ensure there are multiple dimensions
+        assert tif.shape == 4  # includes channel names :)


I found that tests were failing after resolving an issue with the uv.lock file. Consider reducing this to one line (the explicit check for a len of 4 in a tuple returned from shape).

Suggested change

assert tif.shape > 3 # Ensure there are multiple dimensions

assert tif.shape == 4 # includes channel names :)

# Ensure tif has multiple dimensions

# and includes channel names :)

assert len(tif.series[0].shape) == 4

d33bs · 2025-09-29T17:57:20Z

uv.lock

This file looks to be corrupted. Consider removing it and re-running uv lock to recreate it.

d33bs · 2025-09-29T17:59:43Z

src/nviz/image.py


 from .image_meta import extract_z_slice_number_from_filename, generate_ome_xml

+def read_zstack_image(tiff_file_path):


Consider adding tests for this new function which otherwise is only implicitly checked.

d33bs · 2025-09-29T18:07:03Z

src/nviz/image.py

+        img = np.squeeze(img)
+
+    if img.dtype != np.uint16:
+        if img.dtype in [np.float32, np.float64]:


Consider using the following to check for all floats.

Suggested change

if img.dtype in [np.float32, np.float64]:

if np.issubdtype(img.dtype, np.floating):

d33bs · 2025-09-29T18:08:45Z

src/nviz/image.py

+    if img.dtype != np.uint16:
+        if img.dtype in [np.float32, np.float64]:
+            # For float images, first rescale to 0-1 range, then convert
+            img = skimage.exposure.rescale_intensity(img, out_range=(0, 1))


Do you feel this is important enough to warn the user about? If so, consider adding a log message for this. It could be that we document this behavior upfront (perhaps in the docstring of this function) and leave as-is for now.

d33bs · 2025-09-29T18:13:57Z

Also, @MikeLippincott, note that within the PR description you can use keywords to close PR's or issues.

d33bs

Nice job fixing the lockfile! I noticed the new error from CI relates to PyQt. One workaround might be to change the napari[all] dependency to use napari[pyside2] or napari[pyside2, optional]. Another option might be to constrain PyQt versions (earlier versions appeared to work with MacOS arm-based archs).

MikeLippincott and others added 23 commits February 20, 2025 08:39

adding scripts

bacc0e2

Enable downstream GitHub Actions runs to check out properly (WayScien…

7501e0b

…ce#35) * enable downstream branches to be checked out * Update .pre-commit-config.yaml * linting

Bump astral-sh/setup-uv from 5 to 6 (WayScience#39)

df85609

Bump pyvista/setup-headless-display-action from 3 to 4 (WayScience#38)

1bde834

Move to macos-14 for pre-commit checks within GH Actions (WayScienc…

2920812

…e#40) * move to macos for pre-commit checks * linting * add context

Update numpy requirement from <2.3 to <2.4 (WayScience#46)

b2580dc

Fix Linux CI (WayScience#50)

0b22013

* update dockerfile for uv * update deps and fix pre-commit config * update dockerfile and poe task

Fix docs builds with linux headless config (WayScience#41)

55cb0d5

* fix docs builds with linux headless config * Update .pre-commit-config.yaml * apply changes for pre-commit * Update coverage-badge.svg

Add software DOI for reference (WayScience#48)

ad4a6a3

* add software doi for reference * Update .pre-commit-config.yaml

Bump pyvista/setup-headless-display-action from 3 to 4 (WayScience#52)

52e4623

Bump astral-sh/setup-uv from 5 to 6 (WayScience#53)

cc1c404

Update pre-commit-lite conditions (WayScience#44)

8aff886

* update pre-commit-lite conditions * correction

Update GH Actions ubuntu (WayScience#43)

5fe8b57

Bump actions/checkout from 4 to 5 (WayScience#54)

7cc044c

Update dependabot to group Python updates together (WayScience#25)

c1b7452

* update gh actions macos runner * Update .pre-commit-config.yaml

Add Almanack to pre-commit checks (WayScience#47)

1c10aab

* Add Almanack to pre-commit checks * Update .pre-commit-config.yaml * add the fork remote for upstream ref * debugging information for git * Update run-tests.yml * remove git block

remove git remote newline and avoid lint (WayScience#56)

2ebb137

Merge remote-tracking branch 'upstream/main'

14392cd

applying fix

7991f02

d33bs self-requested a review September 29, 2025 17:30

d33bs reviewed Sep 29, 2025

View reviewed changes

redo the uv lock

a2e7788

d33bs reviewed Oct 1, 2025

View reviewed changes

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Fix file reading errors #64

Fix file reading errors #64

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		assert tif.shape > 3 # Ensure there are multiple dimensions
		assert tif.shape == 4 # includes channel names :)

-        assert tif.shape > 3  # Ensure there are multiple dimensions
-        assert tif.shape == 4  # includes channel names :)
+        # Ensure tif has multiple dimensions
+        # and includes channel names :)
+        assert len(tif.series[0].shape) == 4


		from .image_meta import extract_z_slice_number_from_filename, generate_ome_xml

		def read_zstack_image(tiff_file_path):

	if img.dtype in [np.float32, np.float64]:
	if np.issubdtype(img.dtype, np.floating):

Fix file reading errors #64

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Fix file reading errors #64

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MikeLippincott commented Sep 29, 2025

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