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add BrukerTiffImagingExtractor #220

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merged 27 commits into from
Apr 24, 2023
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ec9328f
add extractor
weiglszonja Mar 31, 2023
a3a63b1
Update src/roiextractors/extractors/tiffimagingextractors/brukertiffi…
weiglszonja Apr 3, 2023
5ea6240
apply changes from review
weiglszonja Apr 3, 2023
713eb48
fix access single frame
weiglszonja Apr 3, 2023
3ab2605
update
weiglszonja Apr 3, 2023
3790f72
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Apr 3, 2023
d6b3e4d
fix dict typehint
weiglszonja Apr 3, 2023
bf885d4
adapt to multiple z-planes
weiglszonja Apr 5, 2023
3aedfac
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Apr 5, 2023
037dac2
Merge branch 'master' into add_BrukerTiffImagingExtractor
weiglszonja Apr 5, 2023
1779ed6
Revert "adapt to multiple z-planes"
weiglszonja Apr 5, 2023
f2dc54c
update
weiglszonja Apr 19, 2023
6c4cd42
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Apr 19, 2023
bbe4308
add tests for BrukerTiffExtractor
weiglszonja Apr 19, 2023
ed3ff2b
Merge remote-tracking branch 'origin/add_BrukerTiffImagingExtractor' …
weiglszonja Apr 19, 2023
f3f295f
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Apr 19, 2023
5d138b4
update cache
CodyCBakerPhD Apr 19, 2023
2fc5eed
update path name
CodyCBakerPhD Apr 20, 2023
12b0e1b
loosen up tifffile version requirements-full.txt
weiglszonja Apr 20, 2023
4d81694
Merge remote-tracking branch 'origin/add_BrukerTiffImagingExtractor' …
weiglszonja Apr 20, 2023
5c446c3
try fix python3.7 CI error
weiglszonja Apr 20, 2023
fc77811
add test for single frame
weiglszonja Apr 20, 2023
358af54
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Apr 20, 2023
24dd6c9
rollback accidental folder_path change
weiglszonja Apr 20, 2023
40ffaaf
Merge remote-tracking branch 'origin/add_BrukerTiffImagingExtractor' …
weiglszonja Apr 20, 2023
184eaae
finish unittest for temporary directory
weiglszonja Apr 21, 2023
4f1b3f5
remove tmp directory after test
weiglszonja Apr 21, 2023
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[pre-commit.ci] auto fixes from pre-commit.com hooks
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pre-commit-ci[bot] committed Apr 19, 2023
commit 6c4cd426dfb4419544579a3a979abc35a7378c33
Original file line number Diff line number Diff line change
Expand Up @@ -147,7 +147,9 @@ def _frames_iterator(
) -> Iterable[np.memmap]:
if start_frame is not None and end_frame is not None:
if end_frame == start_frame:
yield self._tifffile.memmap(self.folder_path / self._file_paths[start_frame], mode="r", _multifile=False)
yield self._tifffile.memmap(
self.folder_path / self._file_paths[start_frame], mode="r", _multifile=False
)

for file in self._file_paths[start_frame:end_frame]:
yield self._tifffile.memmap(self.folder_path / file, mode="r", _multifile=False)
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