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Multi-Plane and Multi-Channel Support for ScanImage #241

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Multi-Plane and Multi-Channel Support for ScanImage #241

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d3f25b8
added multi-plane support to scanimage (first draft)
pauladkisson Sep 14, 2023
a2e0caf
switched extract_extra_metadata to local implementation to avoid neur…
pauladkisson Sep 14, 2023
882cf4c
Refactored ScanImage to support multi-channel and multi-plane directl…
pauladkisson Sep 14, 2023
8dd316b
Removed informal multiplane scanimage test
pauladkisson Sep 14, 2023
53634a0
Check that ScanImageReader works in CI tests
pauladkisson Sep 15, 2023
ce69ecd
Check that ScanImageReader works in CI tests
pauladkisson Sep 15, 2023
5b8fe3c
fixed local tests and removed unnecessary io check
pauladkisson Sep 15, 2023
be21dd7
setup informal test for newer ScanImageData
pauladkisson Sep 15, 2023
4819be2
refactored init to manually accept args rather than automatically par…
pauladkisson Sep 15, 2023
e84b6ad
refactored to take plane and channel at __init__ rather than in get_v…
pauladkisson Sep 18, 2023
243c168
refactored to take plane and channel at __init__ rather than in get_v…
pauladkisson Sep 18, 2023
8e407e8
added multi-plane extractor
pauladkisson Sep 18, 2023
b04baab
refactored out generic MultiPlaneImagingExtractor into its own class
pauladkisson Sep 19, 2023
b1cb564
added extra info to docstrings
pauladkisson Sep 19, 2023
380dd63
fixed bugs with multi-imaging extractor
pauladkisson Sep 19, 2023
d921342
Added depth to get_image_size to allow compatibility with MultiImagin…
pauladkisson Sep 19, 2023
3b65bf8
Refactored new ScanImage --> ScanImageTiffSinglePlaneIE and keep lega…
pauladkisson Sep 19, 2023
84c1946
Added legacy message to old ScanImageTiff
pauladkisson Sep 19, 2023
c3fcfea
Added legacy metadata parsing function
pauladkisson Sep 19, 2023
80ec40c
Added deprecation warning to legacy scanimage extractor
pauladkisson Sep 19, 2023
bc4fafe
Added deprecation warning to legacy scanimage extractor
pauladkisson Sep 19, 2023
1965be8
removed redundant metadata/input validation in ScanImageTiffMultiPlan…
pauladkisson Sep 19, 2023
c160d05
changed multiple frames per slice to warning to allow use of existing…
pauladkisson Sep 19, 2023
d6fe0a5
inital test setup
pauladkisson Sep 19, 2023
76f8485
added tests for new ScanImage stuff
pauladkisson Sep 20, 2023
36f43f6
added note about version support for parse_metadata
pauladkisson Sep 20, 2023
67ab8cb
added note about version support for extract_extra_metadata
pauladkisson Sep 20, 2023
41bf93b
channel --> channel_name
pauladkisson Sep 20, 2023
370341b
remove Optional for int plane
pauladkisson Sep 20, 2023
9831e5d
plane --> plane_name
pauladkisson Sep 21, 2023
c410cac
remove temp test
pauladkisson Sep 21, 2023
ee4dc1a
Update tests/test_scanimagetiffimagingextractor.py
pauladkisson Sep 21, 2023
a36e753
added input validation tests to get_frames and get_video
pauladkisson Sep 21, 2023
bd1070d
removed redundant get_channel_names
pauladkisson Sep 22, 2023
cbb1e03
temp removed get_channel_names from consistency checks AND fixed bug …
pauladkisson Sep 22, 2023
3bc556d
updated parse_metadata docstring
pauladkisson Sep 22, 2023
36105b9
added support for multiple frames per slice
pauladkisson Sep 22, 2023
dc54a03
revamped tests with new data (get_video still has some problems)
pauladkisson Sep 23, 2023
72f21c4
fixed bug in get_video for multiple frames per slice
pauladkisson Sep 25, 2023
663b819
optimized indexing to only i/o the necessary slice
pauladkisson Sep 25, 2023
36f9394
clean up code for readability
pauladkisson Sep 25, 2023
ac6a7c0
fixed typo in get_video
pauladkisson Sep 25, 2023
3f7d0d3
updated test filename
pauladkisson Sep 26, 2023
849b20c
Merge branch 'main' into 3DScanImage
pauladkisson Sep 26, 2023
cabfa84
added _times to account for variable sampling rates (multiple frames …
pauladkisson Sep 26, 2023
e6f4496
Switched sampling_frequency to scanFrameRate instead of scanVolumeRate
pauladkisson Sep 26, 2023
22aa9ec
Refactored stand-alone functions to separate scanimage_utils module
pauladkisson Sep 26, 2023
5f3980e
Added tests for scanimage utils
pauladkisson Sep 26, 2023
1289b70
Merge branch 'main' into 3DScanImage
pauladkisson Sep 28, 2023
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4 changes: 4 additions & 0 deletions src/roiextractors/extractorlist.py
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Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,8 @@
from .extractors.tiffimagingextractors import (
TiffImagingExtractor,
ScanImageTiffImagingExtractor,
ScanImageTiffSinglePlaneImagingExtractor,
ScanImageTiffMultiPlaneImagingExtractor,
BrukerTiffMultiPlaneImagingExtractor,
BrukerTiffSinglePlaneImagingExtractor,
MicroManagerTiffImagingExtractor,
Expand All @@ -31,6 +33,8 @@
Hdf5ImagingExtractor,
TiffImagingExtractor,
ScanImageTiffImagingExtractor,
ScanImageTiffSinglePlaneImagingExtractor,
ScanImageTiffMultiPlaneImagingExtractor,
BrukerTiffMultiPlaneImagingExtractor,
BrukerTiffSinglePlaneImagingExtractor,
MicroManagerTiffImagingExtractor,
Expand Down
12 changes: 10 additions & 2 deletions src/roiextractors/extractors/tiffimagingextractors/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,11 @@
TiffImagingExtractor
A ImagingExtractor for TIFF files.
ScanImageTiffImagingExtractor
Specialized extractor for reading TIFF files produced via ScanImage.
Legacy extractor for reading TIFF files produced via ScanImage v3.8.
ScanImageTiffSinglePlaneImagingExtractor
Specialized extractor for reading single-plane TIFF files produced via ScanImage.
ScanImageTiffMultiPlaneImagingExtractor
Specialized extractor for reading multi-plane TIFF files produced via ScanImage.
BrukerTiffMultiPlaneImagingExtractor
Specialized extractor for reading TIFF files produced via Bruker.
BrukerTiffSinglePlaneImagingExtractor
Expand All @@ -25,6 +29,10 @@
Specialized extractor for reading TIFF files produced via Micro-Manager.
"""
from .tiffimagingextractor import TiffImagingExtractor
from .scanimagetiffimagingextractor import ScanImageTiffImagingExtractor
from .scanimagetiffimagingextractor import (
ScanImageTiffImagingExtractor,
ScanImageTiffMultiPlaneImagingExtractor,
ScanImageTiffSinglePlaneImagingExtractor,
)
from .brukertiffimagingextractor import BrukerTiffMultiPlaneImagingExtractor, BrukerTiffSinglePlaneImagingExtractor
from .micromanagertiffimagingextractor import MicroManagerTiffImagingExtractor
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