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Protect import in sima #351

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merged 6 commits into from
Aug 13, 2024
Merged

Protect import in sima #351

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ac23102
safe import for sima
h-mayorquin Aug 7, 2024
a946ad7
protect sima extractor
h-mayorquin Aug 7, 2024
872f17b
changelog
h-mayorquin Aug 7, 2024
a7eabed
Update src/roiextractors/extractors/simaextractor/simasegmentationext…
h-mayorquin Aug 7, 2024
fea18ec
Update CHANGELOG.md
h-mayorquin Aug 13, 2024
be0fa79
Merge branch 'main' into protect_import_in_sima
h-mayorquin Aug 13, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -26,6 +26,7 @@
* The `Suite2PSegmentationExtractor` now produces an error when a required sub-file is missin: [#330](https://github.com/catalystneuro/roiextractors/pull/330)
* Added `_image_mask` initialization in `BaseSegmentationExtractor`; combined `abstractmethod`s into top of file: [#327](https://github.com/catalystneuro/roiextractors/pull/327)
* Optimize parsing of xml with `lxml` library for Burker extractors: [#346](https://github.com/catalystneuro/roiextractors/pull/346)
* Protect sima and dill expoert [#346](https://github.com/catalystneuro/roiextractors/pull/346)
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### Testing

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21 changes: 12 additions & 9 deletions src/roiextractors/extractors/simaextractor/simasegmentationextractor.py
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Expand Up @@ -16,14 +16,6 @@
from ...extraction_tools import PathType
from ...segmentationextractor import SegmentationExtractor

try:
import sima
import dill

HAVE_SIMA = True
except ImportError:
HAVE_SIMA = False


class SimaSegmentationExtractor(SegmentationExtractor):
"""A segmentation extractor for Sima.
Expand All @@ -34,7 +26,6 @@ class SimaSegmentationExtractor(SegmentationExtractor):
"""

extractor_name = "SimaSegmentation"
installed = HAVE_SIMA # check at class level if installed or not
is_writable = False
mode = "file"
# error message when not installed
Expand All @@ -51,6 +42,14 @@ def __init__(self, file_path: PathType, sima_segmentation_label: str = "auto_ROI
sima_segmentation_label: str
name of the ROIs in the dataset from which to extract all ROI info
"""
try:
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import sima
import dill

HAVE_SIMA = True
except ImportError:
HAVE_SIMA = False
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assert HAVE_SIMA, self.installation_mesg
SegmentationExtractor.__init__(self)
self.file_path = file_path
Expand Down Expand Up @@ -79,6 +78,8 @@ def _convert_sima(old_pkl_loc):
old_pkl_loc: str
Path of the pickle file to be converted
"""
import dill

# Make a name for the new pickle
old_pkl_loc = old_pkl_loc + "/"
for dirpath, dirnames, filenames in os.walk(old_pkl_loc):
Expand Down Expand Up @@ -108,6 +109,8 @@ def _convert_sima(old_pkl_loc):

def _file_extractor_read(self):
"""Read the sima file and return the sima.ImagingDataset object."""
import sima

_img_dataset = sima.ImagingDataset.load(self.file_path)
_img_dataset._savedir = self.file_path
return _img_dataset
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