def save_transform_to_database(data_transforms):
""" Save data transforms to database"""
# pylint: disable= too-many-locals, bare-except
conn = sqlite3.connect(util.DB_PATH)
conn.text_factory = str
for img in data_transforms:
cursor = conn.execute('''SELECT pid from Images where id = ? ''', (img.image_id,))
pid = cursor.fetchone()[0]
folder = util.DATA_FOLDER + str(pid) + "/registration_transforms/"
util.mkdir_p(folder)
transform_paths = ""
print(img.get_transforms())
for _transform in img.get_transforms():
print(_transform)
dst_file = folder + util.get_basename(_transform) + '.h5.gz'
if os.path.exists(dst_file):
os.remove(dst_file)
with open(_transform, 'rb') as f_in, gzip.open(dst_file, 'wb') as f_out:
shutil.copyfileobj(f_in, f_out)
transform_paths += str(pid) + "/registration_transforms/" +\
basename(_transform) + '.h5.gz' + ", "
transform_paths = transform_paths[:-2]
cursor2 = conn.execute('''UPDATE Images SET transform = ? WHERE id = ?''',
(transform_paths, img.image_id))
cursor2 = conn.execute('''UPDATE Images SET fixed_image = ? WHERE id = ?''',
(img.fixed_image, img.image_id))
folder = util.DATA_FOLDER + str(pid) + "/reg_volumes_labels/"
util.mkdir_p(folder)
vol_path = util.compress_vol(img.processed_filepath)
shutil.copy(vol_path, folder)
volume_db = str(pid) + "/reg_volumes_labels/" + basename(vol_path)
cursor2 = conn.execute('''UPDATE Images SET filepath_reg = ? WHERE id = ?''',
(volume_db, img.image_id))
cursor = conn.execute('''SELECT filepath, id from Labels where image_id = ? ''',
(img.image_id,))
for (row, label_id) in cursor:
temp = util.compress_vol(move_vol(util.DATA_FOLDER + row,
img.get_transforms(), True))
shutil.copy(temp, folder)
label_db = str(pid) + "/reg_volumes_labels/" + basename(temp)
cursor2 = conn.execute('''UPDATE Labels SET filepath_reg = ? WHERE id = ?''',
(label_db, label_id))
conn.commit()
cursor.close()
cursor2.close()
# cursor = conn.execute('''VACUUM; ''')
conn.close()
def transform_labels_temp(imgs):
""" Save transformed labels to a temp folder in database"""
# pylint: disable= too-many-locals, bare-except
conn = sqlite3.connect(util.DB_PATH, timeout=900)
conn.text_factory = str
for img in imgs:
cursor = conn.execute('''SELECT pid from Images where id = ? ''',
(img.image_id, ))
pid = cursor.fetchone()[0]
folder = util.DATA_FOLDER + str(pid) + "/reg_volumes_labels/temp/"
if not os.path.exists(folder):
os.makedirs(folder)
cursor = conn.execute(
'''SELECT filepath, id from Labels where image_id = ? ''',
(img.image_id, ))
for (filepath, label_id) in cursor:
temp = util.compress_vol(
move_vol(util.DATA_FOLDER + filepath, img.get_transforms(),
True))
shutil.copy(temp, folder)
conn.commit()
cursor.close()
conn.close()
def save_transform_to_database(imgs):
""" Save data transforms to database"""
# pylint: disable= too-many-locals, bare-except
conn = sqlite3.connect(util.DB_PATH, timeout=900)
conn.text_factory = str
try:
conn.execute(
"alter table Images add column 'registration_date' 'TEXT'")
except sqlite3.OperationalError:
pass
for img in imgs:
cursor = conn.execute('''SELECT pid from Images where id = ? ''',
(img.image_id, ))
pid = cursor.fetchone()[0]
folder = util.DATA_FOLDER + str(pid) + "/registration_transforms/"
if os.path.exists(folder):
shutil.rmtree(folder)
os.makedirs(folder)
transform_paths = ""
util.LOGGER.info(img.get_transforms())
for _transform in img.get_transforms():
util.LOGGER.info(_transform)
dst_file = folder + util.get_basename(_transform) + '.h5.gz'
with open(_transform, 'rb') as f_in, gzip.open(dst_file,
'wb') as f_out:
shutil.copyfileobj(f_in, f_out)
transform_paths += str(pid) + "/registration_transforms/" +\
util.get_basename(_transform) + '.h5.gz' + ", "
transform_paths = transform_paths[:-2]
cursor2 = conn.execute(
'''UPDATE Images SET transform = ? WHERE id = ?''',
(transform_paths, img.image_id))
cursor2 = conn.execute(
'''UPDATE Images SET fixed_image = ? WHERE id = ?''',
(img.fixed_image, img.image_id))
cursor2 = conn.execute(
'''UPDATE Images SET registration_date = ? WHERE id = ?''',
(datetime.datetime.now().strftime("%Y-%m-%d"), img.image_id))
folder = util.DATA_FOLDER + str(pid) + "/reg_volumes_labels/"
if os.path.exists(folder):
shutil.rmtree(folder)
os.makedirs(folder)
vol_path = util.compress_vol(img.processed_filepath)
shutil.copy(vol_path, folder)
volume_db = str(pid) + "/reg_volumes_labels/" + basename(vol_path)
cursor2 = conn.execute(
'''UPDATE Images SET filepath_reg = ? WHERE id = ?''',
(volume_db, img.image_id))
cursor = conn.execute(
'''SELECT filepath, id from Labels where image_id = ? ''',
(img.image_id, ))
for (filepath, label_id) in cursor:
temp = util.compress_vol(
move_vol(util.DATA_FOLDER + filepath, img.get_transforms(),
True))
shutil.copy(temp, folder)
label_db = str(pid) + "/reg_volumes_labels/" + basename(temp)
cursor2 = conn.execute(
'''UPDATE Labels SET filepath_reg = ? WHERE id = ?''',
(label_db, label_id))
conn.commit()
cursor.close()
cursor2.close()
cursor = conn.cursor()
modified_patients = [
subfolder_name
for subfolder_name in os.listdir(new_segmentations_folder) if
os.path.isdir(os.path.join(new_segmentations_folder, subfolder_name))
]
for pid in modified_patients:
cursor.execute("SELECT id FROM Images WHERE pid = ?", (int(pid), ))
image_id = cursor.fetchone()[0]
img = img_data(image_id, util.DATA_FOLDER, util.TEMP_FOLDER_PATH)
img.load_db_transforms()
#cursor.execute("SELECT filepath, filepath_reg FROM Labels WHERE image_id IN "
# "(SELECT id FROM Images WHERE pid = ?)", (int(pid),))
#(label_path, label_reg_path) = cursor.fetchone()
#cursor.execute("SELECT transform FROM Images WHERE pid = ?", (int(pid),))
#transform = cursor.fetchone()[0]
new_segmentation_path = glob.glob(new_segmentations_folder + str(pid) +
'/*label.nii')[0]
print(new_segmentation_path)
temp = util.compress_vol(
move_vol(new_segmentation_path, img.get_transforms(), True))
shutil.copy(temp, img.reg_label_filepath)
shutil.copy(new_segmentation_path, img.label_filepath)
#path = '/Volumes/Neuro/Segmentations/oppdaterte_filer/**/*label.nii'
#glob.glob(path)
def update_segmentations(path):
"""Update existing patients with new segmentations from Even"""
# pylint: disable= too-many-locals, too-many-branches, too-many-statements
conn = sqlite3.connect(util.DB_PATH)
cursor = conn.cursor()
log = ""
included_cases = path + "Included cases - final.xlsx"
case_list = load_workbook(included_cases,data_only=True)['Included cases - final']
for case in range(2, 213):
cell_name = "{}{}".format("A", case)
pid = str(case_list[cell_name].value)
cell_name = "{}{}".format("B", case)
new_segmentation = str(case_list[cell_name].value)
data_path = path + "Segmenteringer/" + pid + "/"
if new_segmentation == "1" and os.path.exists(util.DATA_FOLDER + pid + "/" ):# and pid == "711":
print("Converting image " + pid)
log = log + "\n Converting image " + pid
label_file_endings = ('*label.nrrd',
'*label_1.nrrd',
'Segmentation/*label.nrrd',
'Segmentering/*label.nrrd',
'*hele-label.nii')
for file_ending in label_file_endings:
volume_label = glob.glob(data_path + file_ending)
if volume_label:
break
if len(volume_label) > 1:
log = log + "\n Warning!! More than one file with label found "
for volume_label_i in volume_label:
log = log + volume_label_i
continue
volume_label = volume_label[0]
if not os.path.exists(volume_label):
log = log + "\n Warning!! No label found " + data_path + volume_label
cursor.execute("SELECT id FROM Images WHERE pid = ?", (pid,))
image_id = cursor.fetchone()
image_id = str(image_id[0])
cursor.execute("SELECT transform FROM Images WHERE id = ?", (image_id,))
transforms_temp = cursor.fetchone()
if transforms_temp is None:
log = log + "\n Warning!! No transform found for image " + image_id
else:
transforms_temp = str(transforms_temp[0])
transforms = []
for _transform in transforms_temp.split(","):
transforms.append(util.DATA_FOLDER + _transform.strip())
cursor.execute("SELECT filepath, filepath_reg FROM Labels WHERE image_id = ?", (image_id,))
for row in cursor:
_filepath = row[0]
_filepath_reg = row[1]
try:
os.remove(util.DATA_FOLDER + _filepath)
os.remove(util.DATA_FOLDER + _filepath_reg)
except OSError:
pass
# Converting file to nii.gz if necessary
os.system(CONVERTER_PATH + " '" + volume_label + "' " + util.DATA_FOLDER + _filepath)
temp = util.compress_vol( image_registration.move_vol(util.DATA_FOLDER + _filepath, transforms, True) )
shutil.copy(temp, util.DATA_FOLDER + _filepath_reg)
with open("Log.txt", "w") as text_file:
text_file.write(log)
cursor.close()
conn.close()