Cristallina/cristallina_analysis_package
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fixed roi cutoffs

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steppke_a
2024-03-13 16:28:36 +01:00
parent bdeb37b5e2
commit 45b71789c8
1 changed files with 2 additions and 2 deletions
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4
src/cristallina/analysis.py
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@@ -36,7 +36,7 @@ def setup_cachedirs(pgroup=None, cachedir=None):
parts = re.split(r"(\d.*)", pgroup) # ['p', '2343', '']
pgroup_no = parts[-2]
candidates = [f"/das/work/units/cristallina/p{pgroup_no}",
candidates = [f"/sf/cristallina/data/p{pgroup_no}/work",
f"/sf/cristallina/data/p{pgroup_no}/res",]
for cache_parent_dir in candidates:
@@ -310,7 +310,7 @@ def perform_image_roi_crop(
im_ROI = im[:, roi.rows, roi.cols]
if lower_cutoff is not None:
im_ROI = np.clip(im_ROI, lower_cutoff, upper_cutoff)
im_ROI = np.where((im_ROI < lower_cutoff) | (im_ROI > upper_cutoff), 0, im_ROI)
rois_within_batch.extend(im_ROI)