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Fix HDF5 cropped reader #462

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Fix HDF5 cropped reader #462

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66d12ba
Add brackets
DanicaSTFC Feb 26, 2025
215f69b
Merge branch 'master' into fix-cilHDF5CroppedReader
DanicaSTFC Feb 26, 2025
70a8d72
Delete print
DanicaSTFC Feb 26, 2025
736ad2c
Fix dimensions
DanicaSTFC Feb 26, 2025
02bc69c
Automated autoyapf fixes
invalid-email-address Feb 26, 2025
4b47cd9
edit changelog
DanicaSTFC Feb 26, 2025
ecd8706
Merge branch 'fix-cilHDF5CroppedReader' of github.com:TomographicImag…
DanicaSTFC Feb 27, 2025
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3 changes: 3 additions & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,9 @@

## v25.0.0

Bugfix:
- Fix `cilHDF5CroppedReader` #462

Enhancements:
- Have `hdf5_attrs` as attribute to `HDF5InputDialog` #452
- Add `SaveableRawInputDialog` #444
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1 change: 0 additions & 1 deletion Wrappers/Python/ccpi/viewer/CILViewer2D.py
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Expand Up @@ -309,7 +309,6 @@ def OnMouseWheelBackward(self, interactor, event):
def AutoWindowLevelOnVolumeRange(self, update_slice=True):
'''Auto-adjusts window-level for the slice, based on the 5 and 95th percentiles of the whole image volume.'''
cmin, cmax = self._viewer.getImageMapRange((5., 95.), method="scalar")
print("Auto range for volume: ", cmin, cmax)
window, level = self._viewer.getSliceWindowLevelFromRange(cmin, cmax)

self._viewer.imageSlice.GetProperty().SetColorLevel(level)
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7 changes: 6 additions & 1 deletion Wrappers/Python/ccpi/viewer/utils/conversion.py
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Expand Up @@ -1713,12 +1713,17 @@ def RequestData(self, request, inInfo, outInfo):
full_reader = HDF5Reader()
full_reader.SetFileName(self.GetFileName())
full_reader.SetDatasetName(self.GetDatasetName())
dimensions = full_reader.GetDimensions()
reader = HDF5SubsetReader()
reader.SetInputConnection(full_reader.GetOutputPort())
# Either the TargetExtent or TargetZExtent should have been set.
# We prioritise the TargetExtent
if self.GetTargetExtent() is None:
extent = [0, -1, 0, -1, self.GetTargetZExtent[0], self.GetTargetZExtent[1]]
extent = [
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I think this should actually use the extent rather than the dimensions, but it should be fine for the time being. Maybe we should later add an issue.

0, dimensions[0] - 1, 0, dimensions[1] - 1,
self.GetTargetZExtent()[0],
self.GetTargetZExtent()[1]
]
else:
extent = self.GetTargetExtent()
reader.SetUpdateExtent(extent)
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