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Add function to extract ROIs metadata from ScanImage tiff (#272)
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* add function to extract ROIs metadata from ScanImage tiff

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* implement requested changes

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* update test_parse_metadata accordingly

* correct wrong value for expected_metadata

* update to work with versions v3.8.0

* minor fix

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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@alessandratrapani @pre-commit-ci
alessandratrapani and pre-commit-ci[bot] authored Jan 24, 2024
1 parent f407c4f commit 1a136a5
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Showing 2 changed files with 179 additions and 2 deletions.
14 changes: 12 additions & 2 deletions src/roiextractors/extractors/tiffimagingextractors/scanimagetiff_utils.py
View file
Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
"""Utility functions for ScanImage TIFF Extractors."""
import numpy as np
import json
from ...extraction_tools import PathType, get_package


Expand Down Expand Up @@ -33,12 +34,16 @@ def extract_extra_metadata(
io = ScanImageTiffReader(str(file_path))
extra_metadata = {}
for metadata_string in (io.description(iframe=0), io.metadata()):
metadata_dict = {
system_metadata_dict = {
x.split("=")[0].strip(): x.split("=")[1].strip()
for x in metadata_string.replace("\n", "\r").split("\r")
if "=" in x
}
extra_metadata = dict(**extra_metadata, **metadata_dict)
extra_metadata = dict(**extra_metadata, **system_metadata_dict)
if "\n\n" in io.metadata():
additional_metadata_string = io.metadata().split("\n\n")[1]
additional_metadata = json.loads(additional_metadata_string)
extra_metadata = dict(**extra_metadata, **additional_metadata)
return extra_metadata


Expand Down Expand Up @@ -115,12 +120,17 @@ def parse_metadata(metadata: dict) -> dict:
channel_names = np.array(metadata["SI.hChannels.channelName"].split("'")[1::2])
channel_names = channel_names[channel_indices].tolist()
num_channels = len(channel_names)
if "RoiGroups" in metadata.keys():
roi_metadata = metadata["RoiGroups"]
else:
roi_metadata = None
metadata_parsed = dict(
sampling_frequency=sampling_frequency,
num_channels=num_channels,
num_planes=num_planes,
frames_per_slice=frames_per_slice,
channel_names=channel_names,
roi_metadata=roi_metadata,
)
return metadata_parsed

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167 changes: 167 additions & 0 deletions tests/test_scanimage_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -63,6 +63,73 @@ def test_parse_matlab_vector_invalid():
"num_planes": 20,
"frames_per_slice": 24,
"channel_names": ["Channel 1"],
"roi_metadata": {
"imagingRoiGroup": {
"ver": 1,
"classname": "scanimage.mroi.RoiGroup",
"name": "Default Imaging ROI Group",
"UserData": None,
"roiUuid": "E9CD2A60E29A5EDE",
"roiUuiduint64": 1.684716838e19,
"rois": {
"ver": 1,
"classname": "scanimage.mroi.Roi",
"name": "Default Imaging Roi",
"UserData": {
"imagingSystem": "Imaging_RGG",
"fillFractionSpatial": 0.9,
"forceSquarePixelation": 1,
"forceSquarePixels": 1,
"scanZoomFactor": 1,
"scanAngleShiftFast": 0,
"scanAngleMultiplierSlow": 1,
"scanAngleShiftSlow": 0,
"scanRotation": 0,
"pixelsPerLine": 1024,
"linesPerFrame": 1024,
},
"roiUuid": "1B54BED0B8A25D87",
"roiUuiduint64": 1.969408741e18,
"zs": 0,
"scanfields": {
"ver": 1,
"classname": "scanimage.mroi.scanfield.fields.RotatedRectangle",
"name": "Default Imaging Scanfield",
"UserData": None,
"roiUuid": "4309FD6B19453539",
"roiUuiduint64": 4.830670712e18,
"centerXY": [0, 0],
"sizeXY": [18, 18],
"rotationDegrees": 0,
"enable": 1,
"pixelResolutionXY": [1024, 1024],
"pixelToRefTransform": [
[0.017578125, 0, -9.008789063],
[0, 0.017578125, -9.008789063],
[0, 0, 1],
],
"affine": [[18, 0, -9], [0, 18, -9], [0, 0, 1]],
},
"discretePlaneMode": 0,
"powers": None,
"pzAdjust": [],
"Lzs": None,
"interlaceDecimation": None,
"interlaceOffset": None,
"enable": 1,
},
},
"photostimRoiGroups": None,
"integrationRoiGroup": {
"ver": 1,
"classname": "scanimage.mroi.RoiGroup",
"name": "",
"UserData": None,
"roiUuid": "9FC266E57D28670D",
"roiUuiduint64": 1.151187673e19,
"rois": {"_ArrayType_": "double", "_ArraySize_": [1, 0], "_ArrayData_": None},
},
},
},
),
(
Expand All @@ -73,6 +140,106 @@ def test_parse_matlab_vector_invalid():
"num_planes": 2,
"frames_per_slice": 2,
"channel_names": ["Channel 1", "Channel 4"],
"roi_metadata": {
"imagingRoiGroup": {
"ver": 1,
"classname": "scanimage.mroi.RoiGroup",
"name": "MROI Imaging ROI Group",
"UserData": None,
"roiUuid": "4118A30BD7393EFF",
"roiUuiduint64": 4.690678283e18,
"rois": [
{
"ver": 1,
"classname": "scanimage.mroi.Roi",
"name": "ROI 1",
"UserData": None,
"roiUuid": "8C08C657736FBC6C",
"roiUuiduint64": 1.009053304e19,
"zs": -11178.45,
"scanfields": {
"ver": 1,
"classname": "scanimage.mroi.scanfield.fields.RotatedRectangle",
"name": "",
"UserData": None,
"roiUuid": "2B42EE3A0B039B9E",
"roiUuiduint64": 3.117315825e18,
"centerXY": [0.2141430948, -6.019800333],
"sizeXY": [3.616638935, 3.521464226],
"rotationDegrees": 0,
"enable": 1,
"pixelResolutionXY": [256, 256],
"pixelToRefTransform": [
[0.01412749584, 0, -1.601240121],
[0, 0.01375571963, -7.787410306],
[0, 0, 1],
],
"affine": [
[3.616638935, 0, -1.594176373],
[0, 3.521464226, -7.780532446],
[0, 0, 1],
],
},
"discretePlaneMode": 0,
"powers": None,
"pzAdjust": [],
"Lzs": None,
"interlaceDecimation": None,
"interlaceOffset": None,
"enable": 1,
},
{
"ver": 1,
"classname": "scanimage.mroi.Roi",
"name": "ROI 2",
"UserData": None,
"roiUuid": "7C9E605DC6951B29",
"roiUuiduint64": 8.979720663e18,
"zs": -11178.45,
"scanfields": {
"ver": 1,
"classname": "scanimage.mroi.scanfield.fields.RotatedRectangle",
"name": "",
"UserData": None,
"roiUuid": "A02889BA5E5501AB",
"roiUuiduint64": 1.154062548e19,
"centerXY": [2.664891847, 6.376705491],
"sizeXY": [3.616638935, 3.759400998],
"rotationDegrees": 0,
"enable": 1,
"pixelResolutionXY": [256, 256],
"pixelToRefTransform": [
[0.01412749584, 0, 0.8495086314],
[0, 0.01468516015, 4.489662412],
[0, 0, 1],
],
"affine": [
[3.616638935, 0, 0.8565723794],
[0, 3.759400998, 4.497004992],
[0, 0, 1],
],
},
"discretePlaneMode": 0,
"powers": None,
"pzAdjust": [],
"Lzs": None,
"interlaceDecimation": None,
"interlaceOffset": None,
"enable": 1,
},
],
},
"photostimRoiGroups": None,
"integrationRoiGroup": {
"ver": 1,
"classname": "scanimage.mroi.RoiGroup",
"name": "",
"UserData": None,
"roiUuid": "1B4D989071535CF3",
"roiUuiduint64": 1.967396358e18,
"rois": {"_ArrayType_": "double", "_ArraySize_": [1, 0], "_ArrayData_": None},
},
},
},
),
],
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