def make_pdf(self):
"""Method to make the PDF for the spider.
:return: None
"""
output_folder = os.path.join(self.jobdir, 'outputs')
pdfs_dir = XnatUtils.makedir(os.path.join(output_folder, 'pdfs'))
fpages = list()
# Run matlab function
for nb_acq in range(1, self.nb_acquisition + 1):
pdf_page = os.path.join(output_folder, str(nb_acq),
'VerdictMapAcq%d.pdf' % nb_acq)
mat_lines = DEFAULT_PDF_MAKER.format(
matlab_code=self.matlab_code,
maps_folder=os.path.join(output_folder, str(nb_acq),
'AMICO', self.model),
subject=self.xnat_subject,
output_folder=pdfs_dir,
acq=nb_acq)
matlab_script = os.path.join(output_folder,
'run_pdf_page_%d.m' % nb_acq)
with open(matlab_script, "w") as f:
f.writelines(mat_lines)
XnatUtils.run_matlab(matlab_script, verbose=True)
# Get all PDFs:
pdf_pages = XnatUtils.find_files(pdfs_dir, '.pdf')
# Merge all pdfs into one:
self.merge_pdf_pages(pdf_pages, pdf_page)
fpages.append(pdf_page)
if len(fpages) > 1:
self.merge_pdf_pages(fpages, self.pdf_final)
else:
shutil.move(fpages[0], self.pdf_final)
def run(self):
"""Method running the process for the spider on the inputs data."""
output_folder = XnatUtils.makedir(os.path.join(self.jobdir, 'outputs'))
dcm_folder = XnatUtils.makedir(os.path.join(output_folder, 'OsiriX'))
pdfs_dir = XnatUtils.makedir(os.path.join(output_folder, 'pdfs'))
fpages = list()
# Load dicom headers
if not os.path.isfile(self.inputs['dcm']):
err = "DICOM File %s not found."
raise Exception(err % self.inputs['dcm'])
for nb_acq in range(1, self.nb_acquisition+1):
folder = os.path.join(output_folder, str(nb_acq))
os.makedirs(folder)
mat_lines = DEFAULT_VERDICT_TEMPLATE.format(
matlab_code=self.matlab_code,
input_path=os.path.dirname(self.inputs[nb_acq]),
subject=self.xnat_subject,
filename=os.path.basename(self.inputs[nb_acq]),
output=folder,
project=self.xnat_project,
camino=self.camino,
spams=self.spams,
scheme_filename=self.scheme_filename,
model=self.model,
dicom_file=self.inputs['dcm'],
out_dcm=dcm_folder,
acq=str(nb_acq),
suffix=PSUFFIX,
)
matlab_script = os.path.join(output_folder,
'run_verdict_map%d.m' % nb_acq)
with open(matlab_script, "w") as f:
f.writelines(mat_lines)
self.run_matlab(matlab_script, verbose=True)
mat_lines = PDF_TEMPLATE.format(
matlab_code=self.matlab_code,
subject=self.xnat_subject,
output=folder,
model=self.model,
out_pdf=pdfs_dir,
acq=str(nb_acq),
)
matlab_script = os.path.join(output_folder,
'run_pdf_%d.m' % nb_acq)
with open(matlab_script, "w") as f:
f.writelines(mat_lines)
XnatUtils.run_matlab(matlab_script, verbose=True)
pdf_pages = XnatUtils.find_files(pdfs_dir, '.pdf')
# Merge all pdfs into one:
pdf_page = os.path.join(output_folder, str(nb_acq),
'VerdictMapAcq%d.pdf' % nb_acq)
self.merge_pdf_pages(pdf_pages, pdf_page)
fpages.append(pdf_page)
# Merge PDFs:
if len(fpages) > 1:
self.merge_pdf_pages(fpages, self.pdf_final)
else:
shutil.move(fpages[0], self.pdf_final)
# Zip the DICOMs output:
initdir = os.getcwd()
# Zip all the files in the directory
zip_name = os.path.join(self.jobdir, 'outputs', 'OsiriX', 'osirix.zip')
os.chdir(os.path.join(self.jobdir, 'outputs', 'OsiriX'))
os.system('zip -r %s * > /dev/null' % zip_name)
# return to the initial directory:
os.chdir(initdir)
# Gzip nii:
XnatUtils.gzip_nii(os.path.join(output_folder, '1', 'AMICO',
self.model))
if self.nb_acquisition == 2:
XnatUtils.gzip_nii(os.path.join(output_folder, '2', 'AMICO',
self.model))
