Fix MultiDimImageDataset metadata handling #458
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| """Dataset converting a `.csv` file listing multi dimensional (timelapse or multi-scene) files | ||
| and some metadata into batches of single- scene, single-timepoint, single-channel images.""" | ||
| class MultiDimImageDataset(CacheDataset): | ||
| """Dataset converting a `.csv` file or dictionary listing multi dimensional (timelapse or |
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Can you explain how this is different from DataframeDatamodule?
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It would be really useful to have an example function call or config for each dataset/datamodule
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Agreed on the config. This is standardizing the creation of a dataframe from a multi-scene/multi-timepoint image
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so youre saying dataframedaramodule does not work for multi-scene/multi-timepoint?
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It does if you enumerate all the scenes and timepoints for each multidim image in their own rows. Here, each row is just the multidim image path and the scenes/channels/timepoints you want to use
| img = np.expand_dims(img, 0) | ||
| return img | ||
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| def create_metatensor(self, img, meta): |
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why are we not doing all this anymore?
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This part was just baking in some transforms in an easily-broken way. I think it's better to leave all of this to downstream transforms (for example, all of this is handled by the bioio image loader)
cyto_dl/image/io/bioio_loader.py
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| kwargs = {k: self.split_args(data[k]) for k in self.kwargs_keys if k in data} | ||
| if self.dask_load: | ||
| img = img.get_image_dask_data(**kwargs).compute() | ||
| else: | ||
| img = img.get_image_data(**kwargs) | ||
| img = img.astype(self.dtype) | ||
| data[self.out_key] = MetaTensor(img, meta={"filename_or_obj": path, "kwargs": kwargs}) | ||
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| kwargs.update({"filename_or_obj": self._get_filename(path, kwargs)}) |
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filename_or_obj us a monai thing right?
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yes - we also use it for image saving
benjijamorris
dismissed stale reviews from mfs4rd and ritvikvasan
via
f173948
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Sorry had to re-request review after adding an example config! No code changes |
| num_workers: 8 | ||
| dict_meta: | ||
| path: | ||
| - /path/to/your/multidim_image.zarr |
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this points to a single image path? you can choose any because youre interested in metadata?
What does this PR do?
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