def process_dataset(args, num_tries=3):
""" pre process and registrate volume"""
# pylint: disable= unused-argument
moving_image_id = args[0]
print(moving_image_id)
conn = sqlite3.connect(util.DB_PATH)
conn.text_factory = str
cursor = conn.execute('''SELECT pid from Images where id = ?''', (moving_image_id,))
pid = cursor.fetchone()[0]
cursor = conn.execute('''SELECT id from Images where pid = ? AND diag_pre_post = ?''',
(pid, "pre"))
db_temp = cursor.fetchone()
pre_image_id = db_temp[0]
cursor.close()
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
def _test_be(moving_image_id, reg):
img = image_registration.img_data(moving_image_id, util.DATA_FOLDER,
util.TEMP_FOLDER_PATH)
img = image_registration.pre_process(img, False)
resampled_file = img.pre_processed_filepath
name = splitext(splitext(basename(resampled_file))[0])[0] + "_bet"
img.pre_processed_filepath = util.TEMP_FOLDER_PATH + "/res/" +\
splitext(basename(resampled_file))[0] +\
'_bet.nii.gz'
reg.inputs.fixed_image = resampled_file
reg.inputs.fixed_image_mask = img.label_inv_filepath
reg.inputs.output_transform_prefix = util.TEMP_FOLDER_PATH + name
reg.inputs.output_warped_image = util.TEMP_FOLDER_PATH + name + '_betReg.nii'
transform = util.TEMP_FOLDER_PATH + name + 'InverseComposite.h5'
reg.run()
img.init_transform = transform
reg_volume = util.transform_volume(resampled_file, transform)
mult = ants.MultiplyImages()
mult.inputs.dimension = 3
mult.inputs.first_input = reg_volume
mult.inputs.second_input = image_registration.TEMPLATE_MASK
mult.inputs.output_product_image = img.pre_processed_filepath
mult.run()
util.generate_image(img.pre_processed_filepath,
image_registration.TEMPLATE_VOLUME)
def _test_be(moving_image_id, reg):
img = image_registration.img_data(moving_image_id, util.DATA_FOLDER, util.TEMP_FOLDER_PATH)
img = image_registration.pre_process(img, False)
resampled_file = img.pre_processed_filepath
name = splitext(splitext(basename(resampled_file))[0])[0] + "_bet"
img.pre_processed_filepath = util.TEMP_FOLDER_PATH + "/res/" +\
splitext(basename(resampled_file))[0] +\
'_bet.nii.gz'
reg.inputs.fixed_image = resampled_file
reg.inputs.fixed_image_mask = img.label_inv_filepath
reg.inputs.output_transform_prefix = util.TEMP_FOLDER_PATH + name
reg.inputs.output_warped_image = util.TEMP_FOLDER_PATH + name + '_betReg.nii'
transform = util.TEMP_FOLDER_PATH + name + 'InverseComposite.h5'
reg.run()
img.init_transform = transform
reg_volume = util.transform_volume(resampled_file, transform)
mult = ants.MultiplyImages()
mult.inputs.dimension = 3
mult.inputs.first_input = reg_volume
mult.inputs.second_input = image_registration.TEMPLATE_MASK
mult.inputs.output_product_image = img.pre_processed_filepath
mult.run()
util.generate_image(img.pre_processed_filepath, image_registration.TEMPLATE_VOLUME)
def process_dataset(args, num_tries=3):
""" pre process and registrate volume"""
# pylint: disable= unused-argument
(moving_image_id, _, save_to_db, _) = args
print(moving_image_id)
conn = sqlite3.connect(util.DB_PATH)
conn.text_factory = str
cursor = conn.execute('''SELECT pid from Images where id = ?''',
(moving_image_id, ))
pid = cursor.fetchone()[0]
cursor = conn.execute(
'''SELECT id from Images where pid = ? AND diag_pre_post = ?''',
(pid, "pre"))
db_temp = cursor.fetchone()
pre_image_id = db_temp[0]
cursor.close()
conn.close()
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)
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])
