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Fix segmentation plots in reports for input files that are non RAS oriented #16

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Fix segmentation plots in reports for input files that are non RAS oriented #16

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df2eff3
Reorient images to RAS for report plots
Jan 21, 2026
41758e6
Use tempfile temporary plot files instead of tmp.png in workdir (may …
Jan 21, 2026
6ace7eb
Remove wrong axis flip and fix origin='lower' in plot_segmentations_s…
Jan 21, 2026
1086fa6
Apply fixes for handling of non-RAS inputs also to other plot_segment…
Jan 21, 2026
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14 changes: 10 additions & 4 deletions scripts/manage_results/create_prediction_report.py
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Original file line number Diff line number Diff line change
Expand Up @@ -335,8 +335,12 @@ def plot_segmentations_subject(subject, hippunfold_folder, output_file, hemis=['
file_hipo_seg = os.path.join(hippunfold_folder, f'sub-{subject}', 'anat', f'sub-{subject}_hemi-{hemi}_space-cropT1w_desc-subfields_atlas-bigbrain_dseg.nii.gz')

#load images
img_array = sitk.GetArrayFromImage(sitk.ReadImage(file_hipo, sitk.sitkFloat32)) # convert to sitk object
seg_array = sitk.GetArrayFromImage(sitk.ReadImage(file_hipo_seg, sitk.sitkInt64))
img = sitk.ReadImage(file_hipo, sitk.sitkFloat32)
seg = sitk.ReadImage(file_hipo_seg, sitk.sitkInt64)
img = sitk.DICOMOrient(img, 'RAS') # reorient to RAS to make sure plotting works as expected
seg = sitk.DICOMOrient(seg, 'RAS')
img_array = sitk.GetArrayFromImage(img)
seg_array = sitk.GetArrayFromImage(seg)

# get cmap
_ , cmap_labels = return_labels_cmap()
Expand All @@ -345,7 +349,7 @@ def plot_segmentations_subject(subject, hippunfold_folder, output_file, hemis=['
img_array = np.rot90(img_array, 2)
seg_array = np.rot90(seg_array, 2)
x,y,z = coords_seg_extract(seg_array)
axs[0,i].imshow(img_array[x,:,:], cmap='gray')
axs[0,i].imshow(img_array[x,:,:], origin='lower', cmap='gray')
axs[0,i].imshow(seg_array[x,:,:], origin='lower', cmap=cmap_labels, alpha=0.4)
axs[0,i].axis('off')
axs[0,i].text(1, 125, 'R', fontsize = 8, color='red')
Expand Down Expand Up @@ -380,9 +384,11 @@ def plot_segmentations_subject(subject, hippunfold_folder, output_file, hemis=['

fig.savefig(output_file, dpi=96, transparent =True)

def create_surf_plot(borders, faces, vertices, cmap=False, file='./tmp.png'):
def create_surf_plot(borders, faces, vertices, cmap=False, file=None):
"""plot and reload surface images"""
from hippunfold_toolbox import plotting
if file is None:
file = tempfile.NamedTemporaryFile(suffix='.png').name
fig, ax_temp = plt.subplots(nrows=1, ncols=1, figsize=(8,8), subplot_kw={'projection': "3d"})
plotting.surfplot_cdata(ax_temp,borders,faces,vertices, cmap=cmap)
ax_temp.view_init(elev=90, azim=-90)
Expand Down
14 changes: 10 additions & 4 deletions scripts/new_patient_pipeline/run_pipeline_prediction.py
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Original file line number Diff line number Diff line change
Expand Up @@ -406,15 +406,19 @@ def plot_segmentations_subject(subject, hippunfold_folder, output_file, hemis=['
file_hipo_seg = os.path.join(hippunfold_folder, 'hippunfold', subject_bids, 'anat', f'{subject_bids}_hemi-{hemi}_space-cropT1w_desc-subfields_atlas-bigbrain_dseg.nii.gz')

#load images
img_array = sitk.GetArrayFromImage(sitk.ReadImage(file_hipo, sitk.sitkFloat32)) # convert to sitk object
seg_array = sitk.GetArrayFromImage(sitk.ReadImage(file_hipo_seg, sitk.sitkInt64))
img = sitk.ReadImage(file_hipo, sitk.sitkFloat32)
seg = sitk.ReadImage(file_hipo_seg, sitk.sitkInt64)
img = sitk.DICOMOrient(img, 'RAS') # reorient to RAS to make sure plotting works as expected
seg = sitk.DICOMOrient(seg, 'RAS')
img_array = sitk.GetArrayFromImage(img)
seg_array = sitk.GetArrayFromImage(seg)

# get cmap
_ , cmap_labels = return_labels_cmap()

# plot on conventional coronal view
x,y,z = coords_seg_extract(seg_array)
axs[0,i].imshow(np.fliplr(img_array[:,y,:]), cmap='gray')
axs[0,i].imshow(np.fliplr(img_array[:,y,:]), origin='lower', cmap='gray')
axs[0,i].imshow(np.fliplr(seg_array[:,y,:]), origin='lower', cmap=cmap_labels, alpha=0.4)
axs[0,i].axis('off')
axs[0,i].text(1, 125, 'R', fontsize = 8, color='red')
Expand Down Expand Up @@ -443,8 +447,10 @@ def plot_segmentations_subject(subject, hippunfold_folder, output_file, hemis=['

fig.savefig(output_file, dpi=96, transparent =True)

def create_surf_plot(borders, faces, vertices, cmap=False, file='/tmp/tmp.png'):
def create_surf_plot(borders, faces, vertices, cmap=False, file=None):
"""plot and reload surface images"""
if file is None:
file = tempfile.NamedTemporaryFile(suffix='.png').name
fig, ax_temp = plt.subplots(nrows=1, ncols=1, figsize=(8,8), subplot_kw={'projection': "3d"})
plotting.surfplot_cdata(ax_temp,borders,faces,vertices, cmap=cmap)
ax_temp.view_init(elev=90, azim=-90)
Expand Down