# pylint: disable= invalid-name
if __name__ == "__main__": # if 'unity' in hostname or 'compute' in hostname:
HOSTNAME = os.uname()[1]
if 'unity' in HOSTNAME or 'compute' in HOSTNAME:
path = "/work/danieli/GBM_survival/"
else:
os.nice(19)
path = "GBM_" + "{:%m_%d_%Y}".format(datetime.datetime.now()) + "/"
util.setup(path)
#image_ids, survival_days = util.get_image_id_and_survival_days(study_id="GBM_survival_time", registration_date_upper_lim="2018-10-29")
#image_ids = [10]
#image_ids = [10, 19, 35, 371, 71, 83,98, 103, 106, 116, 231, 392, 458]
#image_ids = [10, 19, 71, 83, 98, 103, 106, 116, 231, 392, 458]
#image_ids = range(454,465)
#image_ids = [413, 386, 398, 406, 416, 420, 419, 392, 412, 408, 405, 407]
image_ids = [75, 465, 125, 126, 183, 377, 220]
#image_ids = [413]
util.LOGGER.info(str(image_ids) + " " + str(len(image_ids)))
image_registration.get_transforms(
image_ids,
#reg_type=image_registration.RIGID,
#save_to_db=True,
#reg_type_be=image_registration.SIMILARITY)
reg_type=image_registration.SYN,
reg_type_be=image_registration.SIMILARITY,
save_to_db=True)
def find_images():
""" Find images for registration """
conn = sqlite3.connect(util.DB_PATH)
conn.text_factory = str
cursor = conn.execute('''SELECT pid from Patient''')
ids = []
for row in cursor:
cursor2 = conn.execute('''SELECT id from Images where pid = ?''', (row[0], ))
for _id in cursor2:
ids.append(_id[0])
cursor2.close()
cursor.close()
conn.close()
print(ids)
return ids
# pylint: disable= invalid-name
if __name__ == "__main__":
os.nice(19)
util.setup("GBM/")
moving_datasets_ids = find_images()
data_transforms = image_registration.get_transforms(moving_datasets_ids, image_registration.SYN)
# image_registration.save_transform_to_database(data_transforms)
path = "MM_TEMP_" + "{:%m_%d_%Y}_BE2".format(
datetime.datetime.now()) + "/"
util.setup(path, "MolekylareMarkorer")
#
# util.prepare_template(datasets.fetch_icbm152_2009(data_dir="./").get("t2"), util.TEMPLATE_MASK, True)
# moving_datasets_ids = find_images_from_pid([164])
# print(moving_datasets_ids, len(moving_datasets_ids))
# data_transforms = image_registration.get_transforms(moving_datasets_ids,
# image_registration.AFFINE,
# save_to_db=True)
util.prepare_template(
datasets.fetch_icbm152_2009(data_dir="./").get("t2"),
util.TEMPLATE_MASK, True)
moving_datasets_ids = find_images_from_pid([125, 2101])
print(moving_datasets_ids, len(moving_datasets_ids))
data_transforms = image_registration.get_transforms(
moving_datasets_ids, image_registration.AFFINE, save_to_db=True)
# moving_datasets_ids = find_images_from_pid([172])
# print(moving_datasets_ids, len(moving_datasets_ids))
# data_transforms = image_registration.get_transforms(moving_datasets_ids,
# image_registration.RIGID,
# save_to_db=True)
# print(moving_datasets_ids_affine, len(moving_datasets_ids_affine))
# data_transforms = image_registration.get_transforms(moving_datasets_ids_affine,
# image_registration.RIGID,
# save_to_db=True, be_method=0)
post_img.fixed_image = pre_image_id
pre_img = image_registration.pre_process(pre_img, False)
post_img = image_registration.pre_process(post_img, False)
img = image_registration.registration(post_img,
pre_img.pre_processed_filepath,
image_registration.RIGID)
print("\n\n\n\n -- Total run time: ")
print(datetime.datetime.now() - start_time)
img.fixed_image = pre_image_id
if save_to_db:
image_registration.save_transform_to_database([img])
if __name__ == "__main__":
os.nice(19)
HOSTNAME = os.uname()[1]
if 'unity' in HOSTNAME or 'compute' in HOSTNAME:
path = "/work/danieli/LGG_POST/"
else:
path = "LGG_POST_" + "{:%m_%d_%Y}".format(
datetime.datetime.now()) + "/"
util.setup(path)
post_images = find_images()
image_registration.get_transforms(post_images,
process_dataset_func=process_dataset,
save_to_db=True)
if 'unity' in HOSTNAME or 'compute' in HOSTNAME:
path = "/work/danieli/GBM_survival/"
else:
os.nice(19)
path = "GBM_" + "{:%m_%d_%Y}".format(datetime.datetime.now()) + "/"
util.setup(path)
(image_ids, survival_days) = util.get_image_id_and_survival_days(exclude_pid=[186], glioma_grades=[4])
if len(sys.argv) > 2:
# from mpi4py import MPI
# comm = MPI.COMM_WORLD
# split = comm.Get_rank()
# num_of_splits = comm.Get_size()
num_of_splits = int(sys.argv[1])
split = int(sys.argv[2])
length = int(len(image_ids) / num_of_splits)
start_idx = length * (split - 1)
if split < num_of_splits:
image_ids = image_ids[start_idx:(start_idx+length)]
else:
image_ids = image_ids[start_idx:]
util.LOGGER.info(str(image_ids) + " " + str(len(image_ids)))
image_registration.get_transforms(image_ids,
image_registration.RIGID,
save_to_db=True)
registration_date = cursor3.fetchone()[0]
cursor3.close()
if registration_date:
continue
ids.append(_id)
cursor2.close()
cursor.close()
conn.close()
return ids
# pylint: disable= invalid-name
if __name__ == "__main__":
os.nice(17)
HOSTNAME = os.uname()[1]
if 'unity' in HOSTNAME or 'compute' in HOSTNAME:
path = "/work/danieli/tumor_reg/"
else:
path = "tumor_reg_" + "{:%m_%d_%Y}".format(datetime.datetime.now()) + "/"
util.setup(path)
moving_datasets_ids = find_images()
print(moving_datasets_ids, len(moving_datasets_ids))
image_registration.get_transforms(moving_datasets_ids,
image_registration.SYN,
save_to_db=True)
def find_images():
""" Find images for registration """
conn = sqlite3.connect(util.DB_PATH)
conn.text_factory = str
cursor = conn.execute('''SELECT pid from Patient''')
ids = []
for row in cursor:
cursor2 = conn.execute('''SELECT id from Images where pid = ? AND diag_pre_post = ?''',
(row[0], "pre"))
for _id in cursor2:
ids.append(_id[0])
cursor2.close()
cursor.close()
conn.close()
return ids
# pylint: disable= invalid-name
if __name__ == "__main__":
os.nice(19)
util.setup("LGG_PRE/")
pre_images = find_images()
data_transforms = image_registration.get_transforms(pre_images, image_registration.SYN)
# image_registration.save_transform_to_database(data_transforms)
conn.close()
import datetime
start_time = datetime.datetime.now()
pre_img = img_data(pre_image_id, util.DATA_FOLDER, util.TEMP_FOLDER_PATH)
post_img = img_data(moving_image_id, util.DATA_FOLDER, util.TEMP_FOLDER_PATH)
pre_img = image_registration.pre_process(pre_img, False)
post_img = image_registration.pre_process(post_img, False)
img = image_registration.registration(post_img, pre_img.pre_processed_filepath,
image_registration.RIGID)
print("\n\n\n\n -- Total run time: ")
print(datetime.datetime.now() - start_time)
img.fixed_image = pre_image_id
return img
# pylint: disable= invalid-name
if __name__ == "__main__":
os.nice(19)
util.setup("LGG_POST/")
post_images = find_images()
data_transforms = image_registration.get_transforms(post_images,
process_dataset_func=process_dataset,
save_to_db=True)
# image_registration.save_transform_to_database(data_transforms)
cursor = conn.execute('''SELECT pid from Patient''')
ids = []
for row in cursor:
pid = row[0]
if pid not in pids_with_qol:
continue
cursor2 = conn.execute('''SELECT id from Images where pid = ? AND diag_pre_post = ?''',
(pid, "pre"))
for _id in cursor2:
ids.append(_id[0])
cursor2.close()
cursor.close()
conn.close()
return ids
# pylint: disable= invalid-name
if __name__ == "__main__":
os.nice(17)
util.setup("GBM_LGG_TEMP_" + "{:%m_%d_%Y}_BE2".format(datetime.datetime.now()) + "/")
moving_datasets_ids = find_images()
print(moving_datasets_ids, len(moving_datasets_ids))
data_transforms = image_registration.get_transforms(moving_datasets_ids,
image_registration.RIGID,
save_to_db=True)
# image_registration.save_transform_to_database(data_transforms)
split = int(sys.argv[2])
length = int(len(moving_datasets_ids) / num_of_splits)
start_idx = length * (split - 1)
if split < num_of_splits:
moving_datasets_ids = moving_datasets_ids[start_idx:(start_idx +
length)]
else:
moving_datasets_ids = moving_datasets_ids[start_idx:]
util.LOGGER.info(
str(moving_datasets_ids) + " " + str(len(moving_datasets_ids)))
image_registration.BET_FRAC = 0.2
image_registration.get_transforms(
moving_datasets_ids,
reg_type=image_registration.COMPOSITEAFFINE,
reg_type_be=image_registration.COMPOSITEAFFINE,
save_to_db=True)
# moving_datasets_ids = find_images([1052, 1167, 1, 31, 35, 192, 201, 388, 397, 463, 508, 530, 563, 709, 866, 927, 941, 981, 1020])
# #excluded: 1061, 709
# print(moving_datasets_ids)
# image_registration.get_transforms(moving_datasets_ids,
# image_registration.AFFINE,
# reg_type_be=image_registration.COMPOSITEAFFINE,
# save_to_db=True)
# 192, 201, 35, 463. 709, 1020
# 1, 35, 105, 192, 201, 463, 508, 530, 563, 709, 866, 1020, 1061, image_registration.BET_FRAC = 0.1
# 1, 35, 192, 201, 463, 508, 530, 709, 866, 1020, 1061, image_registration.BET_FRAC = 0.3
# 508, 866,
def find_images():
""" Find images for registration """
conn = sqlite3.connect(util.DB_PATH)
conn.text_factory = str
cursor = conn.execute('''SELECT pid from Patient''')
ids = []
for row in cursor:
cursor2 = conn.execute(
'''SELECT id from Images where pid = ? AND diag_pre_post = ?''',
(row[0], "pre"))
for _id in cursor2:
ids.append(_id[0])
cursor2.close()
cursor.close()
conn.close()
return ids
# pylint: disable= invalid-name
if __name__ == "__main__":
os.nice(19)
util.setup("LGG_PRE/")
pre_images = find_images()
image_registration.get_transforms(pre_images,
image_registration.SYN,
save_to_db=True)