From e7c3b0576a4c91e7580752c46975885c820f8f32 Mon Sep 17 00:00:00 2001 From: Po-Yu Kao Date: Tue, 17 Apr 2018 18:20:15 -0700 Subject: [PATCH 1/2] Update dataset.py --- dataset.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/dataset.py b/dataset.py index 1ed5782..86f0b5c 100644 --- a/dataset.py +++ b/dataset.py @@ -49,7 +49,7 @@ def cut_off_values_upper_lower_percentile(image, mask=None, percentile_lower=0.2 res = np.copy(image) res[(res < cut_off_lower) & (mask !=0)] = cut_off_lower res[(res > cut_off_upper) & (mask !=0)] = cut_off_upper - return image + return res def run(folder, out_folder, id, name, return_if_no_seg=True): @@ -87,11 +87,11 @@ def run(folder, out_folder, id, name, return_if_no_seg=True): # time this code was initially written. In order to not break anything we will keep it like it was brain_voxels = np.where(brain_mask != 0) minZidx = int(np.min(brain_voxels[0])) - maxZidx = int(np.max(brain_voxels[0])) + maxZidx = int(np.max(brain_voxels[0]))+1 minXidx = int(np.min(brain_voxels[1])) - maxXidx = int(np.max(brain_voxels[1])) + maxXidx = int(np.max(brain_voxels[1]))+1 minYidx = int(np.min(brain_voxels[2])) - maxYidx = int(np.max(brain_voxels[2])) + maxYidx = int(np.max(brain_voxels[2]))+1 with open(os.path.join(out_folder, "%03.0d.pkl" % id), 'w') as f: dp = {} dp['orig_shp'] = original_shape From c6431527659a307e989a0c471c061181e0334949 Mon Sep 17 00:00:00 2001 From: Po-Yu Kao Date: Tue, 17 Apr 2018 18:22:38 -0700 Subject: [PATCH 2/2] Update dataset.py --- dataset.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/dataset.py b/dataset.py index 86f0b5c..6379a51 100644 --- a/dataset.py +++ b/dataset.py @@ -30,11 +30,11 @@ def extract_brain_region(image, segmentation, outside_value=0): brain_voxels = np.where(segmentation != outside_value) minZidx = int(np.min(brain_voxels[0])) - maxZidx = int(np.max(brain_voxels[0])) + maxZidx = int(np.max(brain_voxels[0]))+1 minXidx = int(np.min(brain_voxels[1])) - maxXidx = int(np.max(brain_voxels[1])) + maxXidx = int(np.max(brain_voxels[1]))+1 minYidx = int(np.min(brain_voxels[2])) - maxYidx = int(np.max(brain_voxels[2])) + maxYidx = int(np.max(brain_voxels[2]))+1 # resize images resizer = (slice(minZidx, maxZidx), slice(minXidx, maxXidx), slice(minYidx, maxYidx))