[python] Add export for MultiscaleImage to SpatialData
#3355
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## main #3355 +/- ##
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+ Coverage 85.66% 85.89% +0.22%
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Files 57 56 -1
Lines 6210 6166 -44
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- Hits 5320 5296 -24
+ Misses 890 870 -20
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johnkerl
changed the title
MultiscaleImage to SpatialData
| try: | ||
| import xarray as xr | ||
| except ImportError as err: | ||
| warnings.warn("Experimental spatial exporter requires the spatialdatda package.") |
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| warnings.warn("Experimental spatial exporter requires the spatialdatda package.") | |
| warnings.warn("Experimental spatial exporter requires the spatialdata package.") |
| import spatialdata as sd | ||
| from spatialdata.models.models import DataTree | ||
| except ImportError as err: | ||
| warnings.warn("Experimental spatial exporter requires the spatialdatda package.") |
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| warnings.warn("Experimental spatial exporter requires the spatialdatda package.") | |
| warnings.warn("Experimental spatial exporter requires the spatialdata package.") |
| patch = _str_to_int(split_version[2]) | ||
| except ValueError as err: | ||
| raise ValueError(f"Unable to parse version {version}.") from err | ||
| print(f"Actual: {(major, minor, patch)} and Compare: {upper_bound}") |
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| print(f"Actual: {(major, minor, patch)} and Compare: {upper_bound}") |
| def _version_less_than(version: str, upper_bound: Tuple[int, int, int]) -> bool: | ||
| split_version = version.split(".") | ||
| try: | ||
| major = _str_to_int(split_version[0]) | ||
| minor = _str_to_int(split_version[1]) | ||
| patch = _str_to_int(split_version[2]) | ||
| except ValueError as err: | ||
| raise ValueError(f"Unable to parse version {version}.") from err | ||
| print(f"Actual: {(major, minor, patch)} and Compare: {upper_bound}") | ||
| return ( | ||
| major < upper_bound[0] | ||
| or (major == upper_bound[0] and minor < upper_bound[1]) | ||
| or ( | ||
| major == upper_bound[0] | ||
| and minor == upper_bound[1] | ||
| and patch < upper_bound[2] | ||
| ) | ||
| ) |
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Just as a heads up, tiledbsoma has packaging as a transient dependency. It comes with a robust version parser + even a version type: https://packaging.pypa.io/en/latest/version.html
It's mostly what we use for this kind of thing in scverse packages.
| # of the DataTree. | ||
| if _version_less_than(sd.__version__, (0, 2, 5)): | ||
| return DataTree.from_dict( | ||
| {f"scale{index}": image for index, image in enumerate(image_data_arrays)} |
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Why add the "scale" prefix?
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It's what SpatialData uses: see https://github.com/scverse/spatialdata/blob/main/src/spatialdata/models/models.py#L256
| try: | ||
| import geopandas as gpd | ||
| except ImportError as err: | ||
| warnings.warn("Experimental spatial outgestor requires the geopandas package.") |
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I think it might make sense to import spatial data first, since geopandas is a hard dep there.
Then there isn't the UX of import, hit missing dep error, install geopandas, import, hit missing spatialdata
Add function to export a full
MultiscaleImageto a SpatialDataImage2DModelorImage3DModel.Note: At the time of this PR, SpatialData is in the process of changing the multiscale image model to move from the legacy
xarray_datatree.datatree.DataTreeclass to the newxarray.DataTreemodel. This PR implements both versions and checks which to use based on the SpatialData version.