diff --git a/src/cristallina/analysis.py b/src/cristallina/analysis.py index 1d30b22..e270a86 100644 --- a/src/cristallina/analysis.py +++ b/src/cristallina/analysis.py @@ -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)