def test_download_frames(self, mock_session):
mock_session.return_value.__enter__.return_value = self.session
# Create dest dir
self.tempdir.makedir('dest_dir')
dest_dir = os.path.join(self.temp_path, 'dest_dir')
# Download data
data_downloader.download_data(
dataset_serial=self.dataset_serial,
login=self.credentials_path,
dest=dest_dir,
storage_access=self.mount_point,
)
# Images are separated by slice first then channel
im_order = [0, 2, 4, 1, 3, 5]
it = itertools.product(range(self.nbr_channels),
range(self.nbr_slices))
for i, (c, z) in enumerate(it):
im_name = 'im_c00{}_z00{}_t000_p000.png'.format(c, z)
im_path = os.path.join(
dest_dir,
self.dataset_serial,
im_name,
)
im = cv2.imread(im_path, cv2.IMREAD_ANYDEPTH)
numpy.testing.assert_array_equal(im, self.im[im_order[i], ...])
# Read and validate frames meta
meta_path = os.path.join(
dest_dir,
self.dataset_serial,
'frames_meta.csv',
)
frames_meta = pd.read_csv(meta_path)
for i, row in frames_meta.iterrows():
c = i // self.nbr_slices
z = i % self.nbr_slices
self.assertEqual(row.channel_idx, c)
self.assertEqual(row.slice_idx, z)
self.assertEqual(row.time_idx, 0)
self.assertEqual(row.pos_idx, 0)
im_name = 'im_c00{}_z00{}_t000_p000.png'.format(c, z)
self.assertEqual(row.file_name, im_name)
sha256 = meta_utils.gen_sha256(self.im[im_order[i], ...])
self.assertEqual(row.sha256, sha256)
# Read and validate global meta
meta_path = os.path.join(
dest_dir,
self.dataset_serial,
'global_metadata.json',
)
meta_json = json_ops.read_json_file(meta_path)
self.assertEqual(meta_json['storage_dir'], self.frames_storage_dir)
self.assertEqual(meta_json['nbr_frames'], 6)
self.assertEqual(meta_json['im_width'], 15)
self.assertEqual(meta_json['im_height'], 10)
self.assertEqual(meta_json['nbr_slices'], self.nbr_slices)
self.assertEqual(meta_json['nbr_channels'], self.nbr_channels)
self.assertEqual(meta_json['im_colors'], 1)
self.assertEqual(meta_json['nbr_timepoints'], 1)
self.assertEqual(meta_json['nbr_positions'], 1)
self.assertEqual(meta_json['bit_depth'], 'uint16')
def test_read_not_a_json_file():
with TempDirectory() as tempdir:
invalid_json = {"drivername": "postgres", "username": "******"}
# Remove last bracket
invalid_json_str = json.dumps(invalid_json)[:-1]
tempdir.write('invalid_json_file.json', invalid_json_str.encode())
json_object = json_ops.read_json_file(
os.path.join(tempdir.path, "invalid_json_file.json"), )
def get_connection_str(credentials_filename):
"""
Bundles the JSON read of the login credentials file with
a conversion to a URI for connecting to the database
:param credentials_filename: JSON file containing DB credentials
:return str connection_str: URI for connecting to the DB
"""
# Read and validate json
credentials_json = json_ops.read_json_file(
json_filename=credentials_filename,
schema_name="CREDENTIALS_SCHEMA")
# Convert json to string compatible with engine
return json_to_uri(credentials_json)
def split_file(self, file_path, schema_filename):
"""
Splits file into frames and gets metadata for each frame.
set_frame_info must be called prior to this function call.
:param str file_path: Full path to file
:param str schema_filename: Full path to schema file name
:return dataframe frames_meta: Metadata for all frames
:return np.array im_stack: Image stack extracted from file
"""
frames = tifffile.TiffFile(file_path)
# Get global metadata
nbr_frames = len(frames.pages)
# Create image stack with image bit depth 16 or 8
im_stack = np.empty((self.frame_shape[0],
self.frame_shape[1],
self.im_colors,
nbr_frames),
dtype=self.bit_depth)
# Get metadata schema
meta_schema = json_ops.read_json_file(schema_filename)
# Convert frames to numpy stack and collect metadata
# Separate structured metadata (with known fields)
# from unstructured, the latter goes into frames_json
frames_meta = meta_utils.make_dataframe(nbr_frames=nbr_frames)
# Pandas doesn't really support inserting dicts into dataframes,
# so micromanager metadata goes into a separate list
for i in range(nbr_frames):
page = frames.pages[i]
im_stack[..., i] = np.atleast_3d(page.asarray())
# Get dict with metadata from json schema
json_i, meta_i = json_ops.get_metadata_from_tags(
page=page,
meta_schema=meta_schema,
validate=True,
)
self.frames_json.append(json_i)
# Add required metadata fields to data frame
meta_names = meta_utils.META_NAMES
df_names = meta_utils.DF_NAMES
for meta_name, df_name in zip(meta_names, df_names):
if meta_name in meta_i.keys():
frames_meta.loc[i, df_name] = meta_i[meta_name]
# Create a file name and add it
im_name = self._get_imname(frames_meta.loc[i])
frames_meta.loc[i, "file_name"] = im_name
return frames_meta, im_stack
def test_read_json_file():
with TempDirectory() as tempdir:
valid_json = {
"drivername": "postgres",
"username": "******",
"password": "******",
"host": "db_host",
"port": 666,
"dbname": "db_name"
}
tempdir.write('valid_json_file.json', json.dumps(valid_json).encode())
json_object = json_ops.read_json_file(os.path.join(
tempdir.path, "valid_json_file.json"),
schema_name="CREDENTIALS_SCHEMA")
nose.tools.assert_equal(json_object, valid_json)
def test_read_nonexisting_json_file():
json_ops.read_json_file("not_a_json_file.json")
def get_frames_and_metadata(self, filename_parser='parse_idx_from_name'):
"""
Frame metadata is extracted from each frame, and frames are uploaded
on a file by file basis.
Since metadata is separated from files, the file name must contain the
required indices channel_idx, slice_idx, time and pos_idx. By default,
it will assume that the file name contains 4 integers corresponding to
these 4 indices. If that's not the case, you can specify a custom parser
in filename_parsers.
A global metadata dict is assumed to be in the same directory in a file
named metadata.txt. If not, the global_json will be empty and frame
info will be determined from the first frame.
The metadata.txt file (if there) is assumed to contain a minimum of the
following (with example values):
'Summary': {
'PixelType': 'GRAY16',
'BitDepth': 16,
'Width': 15,
'Height': 10
}
:param str filename_parser: Function name in filename_parsers.py
"""
assert os.path.isdir(self.data_path), \
"Directory doesn't exist: {}".format(self.data_path)
try:
parse_func = getattr(file_parsers, filename_parser)
except AttributeError as e:
raise AttributeError(
"Must use filename_parsers function for file name. {}".format(
e))
frame_paths = natsort.natsorted(
glob.glob(os.path.join(self.data_path, "*.tif")), )
nbr_frames = len(frame_paths)
metadata_path = os.path.join(self.data_path, "metadata.txt")
if len(glob.glob(metadata_path)) == 1:
self.global_json = json_ops.read_json_file(
os.path.join(self.data_path, "metadata.txt"), )
self.set_frame_info(self.global_json["Summary"])
else:
# No metadata.txt file in dir, get frame info from first frame
self.set_frame_info_from_file(frame_paths[0])
self.global_json = {}
self.frames_meta = meta_utils.make_dataframe(nbr_frames=nbr_frames)
self.frames_json = []
# Loop over all the frames to get metadata
for i, frame_path in enumerate(frame_paths):
# Get structured frames metadata
self.frames_meta.loc[i] = self._set_frame_meta(
parse_func=parse_func,
file_name=frame_path,
)
# Use multiprocessing for more efficient file read and upload
file_names = self.frames_meta['file_name']
with concurrent.futures.ProcessPoolExecutor(self.nbr_workers) as ex:
res = ex.map(self.serialize_upload, zip(frame_paths, file_names))
# Collect metadata for each uploaded file
for i, (sha256, dict_i) in enumerate(res):
self.frames_json.append(json.loads(dict_i))
self.frames_meta.loc[i, 'sha256'] = sha256
# Set global metadata
self.set_global_meta(nbr_frames=nbr_frames)
import imaging_db.database.db_operations as db_ops
import imaging_db.metadata.json_operations as json_ops
import imaging_db.utils.db_utils as db_utils
# Edit this depending on where your database credential file is stored
# This assumes it's stored in dir above imagingDB
dir_name = os.path.abspath(os.path.join('..'))
DB_CREDENTIALS_PATH = os.path.join(dir_name, 'db_credentials.json')
# this is the Alembic Config object, which provides
# access to the values within the .ini file in use.
config = context.config
# Overwrite the ini-file sqlalchemy.url path
credentials_json = json_ops.read_json_file(json_filename=DB_CREDENTIALS_PATH,
schema_name="CREDENTIALS_SCHEMA")
config.set_main_option('sqlalchemy.url',
db_utils.json_to_uri(credentials_json=credentials_json))
print("Using url:", config.get_main_option('sqlalchemy.url'))
# Add model metadata object
target_metadata = db_ops.Base.metadata
# other values from the config, defined by the needs of env.py,
# can be acquired:
# my_important_option = config.get_main_option("my_important_option")
# ... etc.
def upload_data_and_update_db(csv,
login,
config,
nbr_workers=None,
overwrite=False):
"""
Takes a csv file in which each row represents a dataset, uploads the data
to storage and metadata to database. If 'frames' is selected as upload
type, each dataset will be split into individual 2D frames before moving
to storage.
TODO: Add logging instead of printing
:param str login: Full path to json file containing login credentials
:param str csv: Full path to csv file containing the following fields
for each file to be uploaded:
str dataset_id: Unique dataset ID <ID>-YYYY-MM-DD-HH-MM-SS-<SSSS>
str file_name: Full path to file to be uploaded
str description: Short description of file
str parent_dataset_id: Parent dataset unique ID if there is one
list positions: Which position files in folder to upload.
Uploads all if left empty and file_name is a folder.
Only valid for ome-tiff uploads.
:param str config: Full path to json config file containing the fields:
str upload_type: Specify if the file should be split prior to upload
Valid options: 'frames' or 'file'
str frames_format: Which file splitter class to use.
Valid options:
'ome_tiff' needs MicroManagerMetadata tag for each frame for metadata
'tif_folder' when each file is already an individual frame
and relies on MicroManager metadata
'tif_id' needs ImageDescription tag in first frame page for metadata
str storage: 'local' (default) - data will be stored locally and
synced to S3 the same day. Or 'S3' - data will be uploaded
directly to S3 then synced with local storage daily.
str storage_access: If not using predefined storage locations,
this parameter refers to mount_point for local storage and
bucket_name for S3 storage. (optional)
str json_meta: If splitting to frames, give full path to json
metadata schema for reading metadata (optional)
:param int, None nbr_workers: Number of workers for parallel uploads
:param bool overwrite: Use with caution if your upload if your upload was
interrupted and you want to overwrite existing data in database
and storage
"""
# Assert that csv file exists and load it
assert os.path.isfile(csv), \
"File doesn't exist: {}".format(csv)
files_data = pd.read_csv(csv)
# Get database connection URI
db_connection = db_utils.get_connection_str(login)
db_utils.check_connection(db_connection)
# Read and validate config json
config_json = json_ops.read_json_file(
json_filename=config,
schema_name="CONFIG_SCHEMA",
)
# Assert that upload type is valid
upload_type = config_json['upload_type'].lower()
assert upload_type in {"file", "frames"}, \
"upload_type should be 'file' or 'frames', not {}".format(
upload_type,
)
if nbr_workers is not None:
assert nbr_workers > 0, \
"Nbr of worker must be >0, not {}".format(nbr_workers)
# Import local or S3 storage class
storage = 'local'
if 'storage' in config_json:
storage = config_json['storage']
storage_class = aux_utils.get_storage_class(storage_type=storage)
storage_access = None
if 'storage_access' in config_json:
storage_access = config_json['storage_access']
# Make sure microscope is a string
microscope = None
if 'microscope' in config_json:
if isinstance(config_json['microscope'], str):
microscope = config_json['microscope']
if upload_type == 'frames':
# If upload type is frames, check from frames format
assert 'frames_format' in config_json, \
'You must specify the type of file(s)'
splitter_class = aux_utils.get_splitter_class(
config_json['frames_format'],
)
# Upload all files
for file_nbr, row in files_data.iterrows():
# Assert that ID is correctly formatted
dataset_serial = row.dataset_id
try:
cli_utils.validate_id(dataset_serial)
except AssertionError as e:
raise AssertionError("Invalid ID:", e)
# Get S3 directory based on upload type
if upload_type == "frames":
storage_dir = "/".join([FRAME_FOLDER_NAME, dataset_serial])
else:
storage_dir = "/".join([FILE_FOLDER_NAME, dataset_serial])
# Instantiate database operations class
db_inst = db_ops.DatabaseOperations(
dataset_serial=dataset_serial,
)
# Make sure dataset is not already in database
if not overwrite:
with db_ops.session_scope(db_connection) as session:
db_inst.assert_unique_id(session)
# Check for parent dataset
parent_dataset_id = 'None'
if 'parent_dataset_id' in row:
parent_dataset_id = row.parent_dataset_id
# Check for dataset description
description = None
if 'description' in row:
if row.description == row.description:
description = row.description
if upload_type == "frames":
# Instantiate splitter class
frames_inst = splitter_class(
data_path=row.file_name,
storage_dir=storage_dir,
storage_class=storage_class,
storage_access=storage_access,
overwrite=overwrite,
file_format=FRAME_FILE_FORMAT,
nbr_workers=nbr_workers,
)
# Get kwargs if any
kwargs = {}
if 'positions' in row:
positions = row['positions']
if not pd.isna(positions):
kwargs['positions'] = positions
if 'schema_filename' in config_json:
kwargs['schema_filename'] = config_json['schema_filename']
if 'filename_parser' in config_json:
filename_parser = config_json['filename_parser']
kwargs['filename_parser'] = filename_parser
# Extract metadata and split file into frames
frames_inst.get_frames_and_metadata(**kwargs)
# Add frames metadata to database
try:
with db_ops.session_scope(db_connection) as session:
db_inst.insert_frames(
session=session,
description=description,
frames_meta=frames_inst.get_frames_meta(),
frames_json_meta=frames_inst.get_frames_json(),
global_meta=frames_inst.get_global_meta(),
global_json_meta=frames_inst.get_global_json(),
microscope=microscope,
parent_dataset=parent_dataset_id,
)
except AssertionError as e:
print("Data set {} already in DB".format(dataset_serial), e)
# File upload
else:
# Just upload file without opening it
assert os.path.isfile(row.file_name), \
"File doesn't exist: {}".format(row.file_name)
data_uploader = storage_class(
storage_dir=storage_dir,
access_point=storage_access,
)
if not overwrite:
data_uploader.assert_unique_id()
try:
data_uploader.upload_file(file_path=row.file_name)
print("File {} uploaded to S3".format(row.file_name))
except AssertionError as e:
print("File already on S3, moving on to DB entry. {}".format(e))
sha = meta_utils.gen_sha256(row.file_name)
# Add file entry to DB once I can get it tested
global_json = {"file_origin": row.file_name}
file_name = row.file_name.split("/")[-1]
try:
with db_ops.session_scope(db_connection) as session:
db_inst.insert_file(
session=session,
description=description,
storage_dir=storage_dir,
file_name=file_name,
global_json_meta=global_json,
microscope=microscope,
parent_dataset=parent_dataset_id,
sha256=sha,
)
print("File info for {} inserted in DB".format(dataset_serial))
except AssertionError as e:
print("File {} already in database".format(dataset_serial))
