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Do not skip subject if other contrast does not exist #65

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Do not skip subject if other contrast does not exist #65

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675a894
Add condition to check if other contrast exists
valosekj Sep 17, 2023
a583248
Docstring and comments clarification
valosekj Sep 17, 2023
02ffb36
Docstring clarification
valosekj Sep 17, 2023
362ee06
Refactor the correct_segmentation() function to make it shorter and e…
valosekj Sep 17, 2023
a69d30e
Introduce construct_other_contrast_filename to make code cleaner
valosekj Sep 17, 2023
5529bca
Formatting fix
valosekj Sep 17, 2023
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148 changes: 80 additions & 68 deletions manual_correction.py
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Original file line number Diff line number Diff line change
Expand Up @@ -264,11 +264,7 @@ def create_fsleyes_script():
Create a custom Python script to interact with the FSLeyes API.
Note: the second orthoview cannot be opened from the CLI, instead, FSLeyes API via a custom Python script must
be used. For details, see: https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;ab356891.2301
:param fname: path of the input image.
:param fname_seg_out: path to the derivative label file
:param fname_other_contrast: path of the other contrast to be loaded in FSLeyes.
:param param_fsleyes:
:return:
:return: fname_script: filename of the custom Python script.
"""
python_script = [
"ortho_left = frame.addViewPanel(OrthoPanel)",
Expand Down Expand Up @@ -324,81 +320,78 @@ def correct_segmentation(fname, fname_seg_out, fname_other_contrast, viewer, par
:param param_fsleyes: parameters for FSLeyes viewer.
:return:
"""
# launch ITK-SNAP
if viewer == 'itksnap':

def _itk_snap():
print("In ITK-SNAP, correct the segmentation, then save it with the same name (overwrite).")
# Note: command line differs for macOs/Linux and Windows
if shutil.which('itksnap') is not None: # Check if command 'itksnap' exists
# macOS and Linux
subprocess.check_call(['itksnap',
'-g', fname,
'-s', fname_seg_out])
elif shutil.which('ITK-SNAP') is not None: # Check if command 'ITK-SNAP' exists
# Windows
subprocess.check_call(['ITK-SNAP',
'-g', fname,
'-s', fname_seg_out])
viewer_command = None

# macOS and Linux
if shutil.which('itksnap'):
viewer_command = 'itksnap'
# Windows
elif shutil.which('ITK-SNAP'):
viewer_command = 'ITK-SNAP'

# Construct command
if viewer_command:
subprocess.check_call([viewer_command, '-g', fname, '-s', fname_seg_out])
else:
viewer_not_found(viewer)
# launch FSLeyes
elif viewer == 'fsleyes':
if shutil.which('fsleyes') is not None: # Check if command 'fsleyes' exists

def _fsleyes():
if shutil.which('fsleyes'):
# Get min and max intensity
min_intensity, max_intensity = utils.get_image_intensities(fname)
# Set min intensity
param_fsleyes.min_dr = str((max_intensity * int(param_fsleyes.dr.split(',')[0]))/100)
param_fsleyes.min_dr = str((max_intensity * int(param_fsleyes.dr.split(',')[0])) / 100)
# Decrease max intensity
param_fsleyes.max_dr = str((max_intensity * int(param_fsleyes.dr.split(',')[1]))/100)
param_fsleyes.max_dr = str((max_intensity * int(param_fsleyes.dr.split(',')[1])) / 100)

print("In FSLeyes, click on 'Edit mode', correct the segmentation, and then save it with the same name "
"(overwrite).")
# FSLeyes arguments explanation:
# -S, --skipfslcheck Skip $FSLDIR check/warning
# -dr, --displayRange Set display range (min max) for the specified overlay
# -cm, --cmap Set colour map for the specified overlay
# -r, --runscript Run custom FSLeyes script

# Construct command
cmd_args = ['fsleyes', '-S', fname, '-dr', param_fsleyes.min_dr, param_fsleyes.max_dr, fname_seg_out, '-cm',
param_fsleyes.cm]

# Load a second contrast/image if provided
if fname_other_contrast:
# Open a second orthoview (i.e., open two orthoviews next to each other)
if param_fsleyes.second_orthoview:
fname_script = create_fsleyes_script()
subprocess.check_call(['fsleyes',
'-S',
'-r', fname_script,
fname, '-dr', param_fsleyes.min_dr, param_fsleyes.max_dr,
fname_other_contrast,
fname_seg_out, '-cm', param_fsleyes.cm])
# No second orthoview
else:
subprocess.check_call(['fsleyes',
'-S',
fname, '-dr', param_fsleyes.min_dr, param_fsleyes.max_dr,
fname_other_contrast,
fname_seg_out, '-cm', param_fsleyes.cm])
# Open a second orthoview without second contrast
elif param_fsleyes.second_orthoview:
fname_script = create_fsleyes_script()
subprocess.check_call(['fsleyes',
'-S',
'-r', fname_script,
fname, '-dr', param_fsleyes.min_dr, param_fsleyes.max_dr,
fname_seg_out, '-cm', param_fsleyes.cm])
# No second contrast, no second orthoview
else:
subprocess.check_call(['fsleyes',
'-S',
fname,
'-dr', param_fsleyes.min_dr, param_fsleyes.max_dr,
fname_seg_out, '-cm', param_fsleyes.cm])
# Intert '-r', create_fsleyes_script() after '-S'
cmd_args.insert(2, '-r ' + create_fsleyes_script())
cmd_args.append(fname_other_contrast)

# Convert list to string
cmd_args = ' '.join(cmd_args)
print(cmd_args)
os.system(cmd_args)
else:
viewer_not_found(viewer)
# launch 3D Slicer
elif viewer == 'slicer':

def _slicer():
if shutil.which('slicer') is not None:
print("ERROR: 3D Slicer is not supported yet.")
# TODO: Add instructions for 3D Slicer
pass
else:
viewer_not_found(viewer)

# launch ITK-SNAP
if viewer == 'itksnap':
_itk_snap()
# launch FSLeyes
elif viewer == 'fsleyes':
_fsleyes()
# launch 3D Slicer
elif viewer == 'slicer':
_slicer()


def viewer_not_found(viewer):
"""
Expand Down Expand Up @@ -635,6 +628,35 @@ def generate_qc(fname, fname_label, task, fname_qc, subject, config_file, qc_les
print("Archive created:\n--> {}".format(fname_qc + '.zip'))


def construct_other_contrast_filename(args, path_img, file):
"""
Construct filename of the other contrast.
:param args:
:param path_img:
:param file:
:return:
"""

subject, ses, filename, contrast = utils.fetch_subject_and_session(file)

if args.load_other_contrast:
# Do not include session in the filename
if ses == '':
other_contrast_filename = subject + '_' + args.load_other_contrast + '.nii.gz'
# Include session in the filename
else:
other_contrast_filename = subject + '_' + ses + '_' + args.load_other_contrast + '.nii.gz'
fname_other_contrast = os.path.join(path_img, subject, ses, contrast, other_contrast_filename)
# Check if other contrast exists
if not os.path.isfile(fname_other_contrast):
print(f'WARNING: {fname_other_contrast} not found. Skipping...')
fname_other_contrast = None
else:
fname_other_contrast = None

return fname_other_contrast


def denoise_image(fname):
"""
Denoise image using non-local means adaptative denoising from P. Coupe et al. as implemented in dipy. For details,
Expand Down Expand Up @@ -751,8 +773,7 @@ def main():
if '*' in files[0] and len(files) == 1:
subject, ses, filename, contrast = utils.fetch_subject_and_session(files[0])
# Get list of files recursively
glob_files = sorted(glob.glob(os.path.join(path_img, '**', filename),
recursive=True))
glob_files = sorted(glob.glob(os.path.join(path_img, '**', filename), recursive=True))
# Get list of already corrected files
if task.replace('FILES', 'CORR') in dict_yml.keys():
corr_files = dict_yml[task.replace('FILES', 'CORR')]
Expand All @@ -774,17 +795,8 @@ def main():
# Construct absolute path to the input file
# For example: '/Users/user/dataset/data_processed/sub-001/anat/sub-001_T2w.nii.gz'
fname = os.path.join(path_img, subject, ses, contrast, filename)
# Construct absolute path to the other contrast file
if args.load_other_contrast:
# Do not include session in the filename
if ses == '':
other_contrast_filename = subject + '_' + args.load_other_contrast + '.nii.gz'
# Include session in the filename
else:
other_contrast_filename = subject + '_' + ses + '_' + args.load_other_contrast + '.nii.gz'
fname_other_contrast = os.path.join(path_img, subject, ses, contrast, other_contrast_filename)
else:
fname_other_contrast = None
# Construct absolute path to the other contrast file, if specified
fname_other_contrast = construct_other_contrast_filename(args, path_img, file)
# Construct absolute path to the input label (segmentation, labeling etc.) file
# For example: '/Users/user/dataset/data_processed/sub-001/anat/sub-001_T2w_seg.nii.gz'
fname_label = utils.add_suffix(os.path.join(path_label, subject, ses, contrast, filename), suffix_dict[task])
Expand Down