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When loading data for train allow to read data that has channel on first position #94

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merged 11 commits into from
Sep 21, 2022
Merged

When loading data for train allow to read data that has channel on first position #94

merged 11 commits into from
Sep 21, 2022

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Czaki
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@Czaki Czaki commented Sep 20, 2022

Add heuristics to allow to channel ais into being the first axis.
For better compatibility with preview data in napari, for example.

@constantinpape constantinpape mentioned this pull request Sep 20, 2022
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Thanks for starting to work on this @Czaki. I should have time to have a look at this later in the evening or tomorrow.

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Czaki commented Sep 20, 2022

In this PR, currently, there is no metadata parsing. Only guessing based on the size of the array.

constantinpape
constantinpape reviewed Sep 21, 2022
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Thanks for working on this! This is good to go once the tests pass (currently just missing a tempfile import.)

test/data/test_image_collection_dataset.py Show resolved Hide resolved
torch_em/data/image_collection_dataset.py Outdated
@@ -102,17 +102,23 @@ def _get_sample(self, index):

shape = raw.shape
# we assume images are loaded with channel last!
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Let's update this comment since we now decide on channel last vs. channel first based on the image shape.

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could you check the current version?

torch_em/data/image_collection_dataset.py Show resolved Hide resolved
@Czaki Czaki changed the title When loading data for train allow to read data that has hannel on first position When loading data for train allow to read data that has channel on first position Sep 21, 2022
constantinpape
constantinpape approved these changes Sep 21, 2022
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Thanks for the contribution!

@constantinpape constantinpape merged commit b9db670 into constantinpape:main Sep 21, 2022
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@Czaki @constantinpape