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bugfix/missing-comma-was-creating-a-new-file-format #11

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bugfix/missing-comma-was-creating-a-new-file-format #11

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413b0ee
newline + comma png
evamaxfield Jul 21, 2024
26dbc98
Mirror base imageio version from aicsimageio
evamaxfield Jul 23, 2024
b7bfecb
Install ffmpeg on CI runners
evamaxfield Jul 23, 2024
15d9930
Also mirror the RGB change associated with the version bump
evamaxfield Jul 23, 2024
2dd4029
rerun tests
BrianWhitneyAI Dec 11, 2024
6331880
rerun tests
BrianWhitneyAI Dec 11, 2024
0266ca0
Merge branch 'main' into bugfix/missing-comma-was-creating-a-fake-fil…
BrianWhitneyAI Dec 11, 2024
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2 changes: 2 additions & 0 deletions .github/workflows/ci.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -60,6 +60,8 @@ jobs:
- uses: extractions/setup-just@v2
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
- name: Set up FFMPEG
uses: FedericoCarboni/setup-ffmpeg@v3
- name: Install Dependencies
run: |
python -m pip install --upgrade pip
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3 changes: 2 additions & 1 deletion bioio_imageio/reader_metadata.py
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Expand Up @@ -77,7 +77,8 @@ def get_supported_extensions() -> List[str]:
"mpo",
"msp",
"pdf",
"png" "ppm",
"png",
"ppm",
"ps",
"zif",
]
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4 changes: 2 additions & 2 deletions bioio_imageio/tests/test_reader.py
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Expand Up @@ -15,10 +15,10 @@
@pytest.mark.parametrize(
"filename, set_scene, expected_shape, expected_dims_order",
[
("example.bmp", "Image:0", (480, 640, 4), "YXS"),
("example.bmp", "Image:0", (480, 640, 3), "YXS"),
("example.png", "Image:0", (800, 537, 4), "YXS"),
("example.jpg", "Image:0", (452, 400, 3), "YXS"),
("example.gif", "Image:0", (72, 268, 268, 4), "TYXS"),
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why'd we lose a scene here?

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S is not scene, it's "Samples", as in 3 means RGB and 4 means RGBA

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oh gotcha my mistake. I think my question persists though. What happened to our 4th sample?

("example.gif", "Image:0", (72, 268, 268, 3), "TYXS"),
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for example.gif we have an issue with the reader here.

            elif image_length > 1:
                # Read and stack all frames
                frames = []
                for frame in reader:
                    frames.append(frame)

                image_data = np.stack(frames)

We have a first frame that is uneven
locals

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@evamaxfield @toloudis any thoughts here? np.stack expects same-size arrays, not sure why the first one is missing a dim.

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I found this as a result of me upgrading the various base imageio libs. I don't think we changed anything, I think the underlying imageio library changed. I changed the test as a part of just fiddling around with stuff to figure out what was happening. I think we may just want to rollback the imageio upgrade.

(
"example_invalid_frame_count.mp4",
"Image:0",
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2 changes: 1 addition & 1 deletion pyproject.toml
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Expand Up @@ -30,7 +30,7 @@ dependencies = [
"bioio-base>=0.3.0",
"dask[array]>=2021.4.1",
"fsspec>=2022.8.0",
"imageio[ffmpeg]>=2.11.0,<2.28.0",
"imageio[ffmpeg]>=2.31.0",
"numpy>=1.21.0",
"Pillow>=9.3.0",
"xarray>=2022.6.0",
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