def compute_dvr_image(pet_file,
gtmpvc_dir,
frame_start_times,
time_window_start_end,
ref_roi,
weighted_merge,
output_image,
spm_path=None):
"""
Computes the DVR for each input PET's voxel, and saves the result as a nifti image.
"""
spm_path = get_spm_path(spm_path)
unzipped_output_image = output_image
if output_image.suffix == '.gz':
unzipped_output_image = output_image[:-3]
matlab_output = matlab.run(
f"addpath {spm_path}; addpath {MATLAB_SRC_DIR}; compute_dvr_image('{pet_file}', '{gtmpvc_dir}', '{frame_start_times}', '{time_window_start_end}', '{ref_roi}', '{weighted_merge}', '{unzipped_output_image}')"
)
if output_image.suffix == '.gz':
from plumbum.cmd import gzip
gzip(unzipped_output_image)
return matlab_output
def compute_roi_dvrs(gtmpvc_dir,
frame_start_times,
time_window_start_end,
ref_roi,
weighted_merge,
output_csv,
spm_path=None):
"""
Computes the DVR for each Freesurfer gtmpvc ROI as well for each left and right hemisphere
combined ROI, and saves the result to a csv file.
"""
spm_path = get_spm_path(spm_path)
return matlab.run(
f"addpath {spm_path}; addpath {MATLAB_SRC_DIR}; compute_roi_dvrs('{gtmpvc_dir}', '{frame_start_times}', '{time_window_start_end}', '{ref_roi}', '{weighted_merge}', '{output_csv}')"
)
def ecat2nifti(ecat_filepath, output_dir, spm_path=None):
spm_path = find_spm_path(spm_path)
ecat_filepath_full = os.path.realpath(ecat_filepath)
matlab_command = [
f"addpath('{spm_path}')", f"spm_ecat2nifti('{ecat_filepath_full}')"
]
with local.cwd(output_dir):
retcode, stdout, stderr = matlab.run(matlab_command)
if not output_dir // '*.nii':
print(stdout)
print(stderr)
raise Exception(f"No niftis generated from ecat {ecat_filepath}")
return retcode, stdout, stderr
def test_list_command():
(retcode, stderr, _) = matlab.run(["disp('hello')", "disp('world')"])
assert retcode == 0
assert stderr.split('\n')[-3:] == ['hello', 'world', '']
def test_str_command():
(retcode, _, _) = matlab.run('disp([1 2 3])')
assert retcode == 0