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Update dataset.py #5

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e7c3b05
Update dataset.py
pykao Apr 18, 2018
c643152
Update dataset.py
pykao Apr 18, 2018
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14 changes: 7 additions & 7 deletions dataset.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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))
Expand All @@ -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):
Expand Down Expand Up @@ -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
Expand Down