Create an all-purpose ImageStack factory #1348
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ttung
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shanaxel42
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May 21, 2019
| @@ -41,6 +40,8 @@ def verify_physical_coordinates(stack: ImageStack, | |||
| # If zplane provided, test expected_z_coordinates on specific plane. | |||
| # Else just test expected_z_coordinates on entire array | |||
| if zplane is not None: | |||
| assert np.isclose(stack.xarray[Coordinates.Z.value][zplane], expected_z_coordinates) | |||
| assert np.isclose( | |||
| stack.xarray.sel({Axes.ZPLANE.value: zplane})[Coordinates.Z.value], | |||
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I don't think you need to do the sel, stack.xarray[Coordinates.Z.value].values should give you the array
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I don't want the array. I want a singular value for the plane.
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1. Create a `LocationAwareFetchedTile` class, which is like `FetchedTile`, but is explicitly aware of its location in 5D space. 2. Create an all_purpose.imagestack_factory method that produces an ImageStack with the provided coordinate ranges. 3. Fix existing tests that did not deal with coordinates properly. 4. Fix `imagestack_test_utils.py::verify_physical_coordinates`, which used zplane as an index rather than a value. In the case of labeled images, this makes a difference. Test plan: `make -j all`
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LocationAwareFetchedTileclass, which is likeFetchedTile, but is explicitly aware of its location in 5D space.imagestack_test_utils.py::verify_physical_coordinates, which used zplane as an index rather than a value. In the case of labeled images, this makes a difference.Test plan:
make -j all