Commit a07ee75a authored by Christoph Arthofer's avatar Christoph Arthofer
Browse files

resolved bug in mean mask generation

parent 4f3593fc
...@@ -854,7 +854,7 @@ if __name__ == "__main__": ...@@ -854,7 +854,7 @@ if __name__ == "__main__":
job_ids = ['' for _ in range(100)] job_ids = ['' for _ in range(100)]
task_count = 0 task_count = 0
os.mkdir(base_dir, mode=0o770) if not os.path.exists(base_dir) else print(base_dir + ' exists') os.makedirs(base_dir, mode=0o770) if not os.path.exists(base_dir) else print(base_dir + ' exists')
os.chmod(base_dir, 0o770) os.chmod(base_dir, 0o770)
tree = FileTree.read(tree_path, top_level='') tree = FileTree.read(tree_path, top_level='')
...@@ -1240,7 +1240,7 @@ if __name__ == "__main__": ...@@ -1240,7 +1240,7 @@ if __name__ == "__main__":
img_paths.append(tree.get('T1_brain_mask_to_MNI_img')) img_paths.append(tree.get('T1_brain_mask_to_MNI_img'))
aff_template_path = tree.get('T1_brain_mask_affine_template') aff_template_path = tree.get('T1_brain_mask_affine_template')
jobcmd = func_to_cmd(averageImages, args=(img_paths, aff_template_path, 'average', False), tmp_dir=script_dir, jobcmd = func_to_cmd(averageImages, args=(img_paths, aff_template_path, 'mean', False), tmp_dir=script_dir,
kwargs=None, clean="never") kwargs=None, clean="never")
# job_ids[22] = submitJob(tag+'_'+task_name, log_dir, command=jobcmd, queue=cpuq, wait_for=[job_ids[16]]) # job_ids[22] = submitJob(tag+'_'+task_name, log_dir, command=jobcmd, queue=cpuq, wait_for=[job_ids[16]])
job_ids[22] = submitJob(jobcmd, tag + '_' + task_name, log_dir, queue=cpuq, wait_for=[job_ids[16]], array_task=False, jobram=jobram_low, jobtime=jobtime_low) job_ids[22] = submitJob(jobcmd, tag + '_' + task_name, log_dir, queue=cpuq, wait_for=[job_ids[16]], array_task=False, jobram=jobram_low, jobtime=jobtime_low)
...@@ -1457,7 +1457,7 @@ if __name__ == "__main__": ...@@ -1457,7 +1457,7 @@ if __name__ == "__main__":
warp_paths.append(tree.get('mmorf_warp')) warp_paths.append(tree.get('mmorf_warp'))
avg_warp_path = tree.get('avg_warp') avg_warp_path = tree.get('avg_warp')
jobcmd = func_to_cmd(averageImages, args=(warp_paths, avg_warp_path, 'average', False), tmp_dir=script_dir, jobcmd = func_to_cmd(averageImages, args=(warp_paths, avg_warp_path, 'mean', False), tmp_dir=script_dir,
kwargs=None, clean="never") kwargs=None, clean="never")
# job_ids[29] = submitJob(tag+'_'+task_name, log_dir, command=jobcmd, queue=cpuq, wait_for=[job_ids[28]]) # job_ids[29] = submitJob(tag+'_'+task_name, log_dir, command=jobcmd, queue=cpuq, wait_for=[job_ids[28]])
job_ids[29] = submitJob(jobcmd, tag + '_' + task_name, log_dir, queue=cpuq,wait_for=[job_ids[28]], array_task=False, jobram=jobram_low, jobtime=jobtime_low) job_ids[29] = submitJob(jobcmd, tag + '_' + task_name, log_dir, queue=cpuq,wait_for=[job_ids[28]], array_task=False, jobram=jobram_low, jobtime=jobtime_low)
...@@ -1795,7 +1795,7 @@ if __name__ == "__main__": ...@@ -1795,7 +1795,7 @@ if __name__ == "__main__":
img_paths.append(tree.get('warped_T1brain_mask')) img_paths.append(tree.get('warped_T1brain_mask'))
nln_template_path = tree.get('T1_brain_mask_nln_template') nln_template_path = tree.get('T1_brain_mask_nln_template')
jobcmd = func_to_cmd(averageImages, args=(img_paths, nln_template_path, 'average', False), tmp_dir=script_dir, jobcmd = func_to_cmd(averageImages, args=(img_paths, nln_template_path, 'mean', False), tmp_dir=script_dir,
kwargs=None, clean="never") kwargs=None, clean="never")
# job_ids[49] = submitJob(tag+'_'+task_name, log_dir, command=jobcmd, queue=cpuq, wait_for=[job_ids[38]]) # job_ids[49] = submitJob(tag+'_'+task_name, log_dir, command=jobcmd, queue=cpuq, wait_for=[job_ids[38]])
job_ids[49] = submitJob(jobcmd, tag + '_' + task_name, log_dir, queue=cpuq, wait_for=[job_ids[38]], array_task=False, jobram=jobram_low, jobtime=jobtime_low) job_ids[49] = submitJob(jobcmd, tag + '_' + task_name, log_dir, queue=cpuq, wait_for=[job_ids[38]], array_task=False, jobram=jobram_low, jobtime=jobtime_low)
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