Skip to content

Commit 169613e

Browse files
committed
Fix indentation of function
1 parent 7cc70a6 commit 169613e

1 file changed

Lines changed: 55 additions & 56 deletions

File tree

src/imcflibs/imagej/omerotools.py

Lines changed: 55 additions & 56 deletions
Original file line numberDiff line numberDiff line change
@@ -226,68 +226,67 @@ def find_dataset(client, dataset_id):
226226
# Fetch the dataset from the OMERO server using the provided dataset ID
227227
return client.getDataset(Long(dataset_id))
228228

229-
def get_acquisition_metadata(user_client, image_wpr):
230-
"""Get acquisition metadata from OMERO based on an image ID.
231-
232-
Parameters
233-
----------
234-
user_client : fr.igred.omero.Client
235-
Client used for login to OMERO
236-
image_wpr : fr.igred.omero.repositor.ImageWrapper
237-
Wrapper to the image for the metadata
238-
239-
Returns
240-
-------
241-
dict
242-
243-
{
244-
objective_magnification : float,
245-
objective_na : float,
246-
acquisition_date : str,
247-
acquisition_date_number : str,
248-
}
249-
"""
250-
ctx = user_client.getCtx()
251-
instrument_data = (
252-
user_client.getGateway()
253-
.getMetadataService(ctx)
254-
.loadInstrument(image_wpr.asDataObject().getInstrumentId())
255-
)
256-
objective_data = instrument_data.copyObjective().get(0)
257-
metadata = {}
258229

259-
metadata["objective_magnification"] = (
260-
objective_data.getNominalMagnification().getValue()
261-
if objective_data.getNominalMagnification() is not None
262-
else 0
263-
)
264-
metadata["objective_na"] = (
265-
objective_data.getLensNA().getValue()
266-
if objective_data.getLensNA() is not None
267-
else 0
268-
)
230+
def get_acquisition_metadata(user_client, image_wpr):
231+
"""Get acquisition metadata from OMERO based on an image ID.
269232
270-
if image_wpr.getAcquisitionDate() is None:
271-
if image_wpr.asDataObject().getFormat() == "ZeissCZI":
272-
field = "Information|Document|CreationDate"
273-
date_field = get_info_from_original_metadata(
274-
user_client, image_wpr, field
275-
)
276-
metadata["acquisition_date"] = date_field.split("T")[0]
277-
metadata["acquisition_date_number"] = int(
278-
metadata["acquisition_date"].replace("-", "")
279-
)
280-
else:
281-
metadata["acquisition_date"] = "NA"
282-
metadata["acquisition_date_number"] = 0
283-
else:
284-
sdf = SimpleDateFormat("yyyy-MM-dd")
285-
metadata["acquisition_date"] = sdf.format(image_wpr.getAcquisitionDate())
233+
Parameters
234+
----------
235+
user_client : fr.igred.omero.Client
236+
Client used for login to OMERO
237+
image_wpr : fr.igred.omero.repositor.ImageWrapper
238+
Wrapper to the image for the metadata
239+
240+
Returns
241+
-------
242+
dict
243+
244+
{
245+
objective_magnification : float,
246+
objective_na : float,
247+
acquisition_date : str,
248+
acquisition_date_number : str,
249+
}
250+
"""
251+
ctx = user_client.getCtx()
252+
instrument_data = (
253+
user_client.getGateway()
254+
.getMetadataService(ctx)
255+
.loadInstrument(image_wpr.asDataObject().getInstrumentId())
256+
)
257+
objective_data = instrument_data.copyObjective().get(0)
258+
metadata = {}
259+
260+
metadata["objective_magnification"] = (
261+
objective_data.getNominalMagnification().getValue()
262+
if objective_data.getNominalMagnification() is not None
263+
else 0
264+
)
265+
metadata["objective_na"] = (
266+
objective_data.getLensNA().getValue()
267+
if objective_data.getLensNA() is not None
268+
else 0
269+
)
270+
271+
if image_wpr.getAcquisitionDate() is None:
272+
if image_wpr.asDataObject().getFormat() == "ZeissCZI":
273+
field = "Information|Document|CreationDate"
274+
date_field = get_info_from_original_metadata(user_client, image_wpr, field)
275+
metadata["acquisition_date"] = date_field.split("T")[0]
286276
metadata["acquisition_date_number"] = int(
287277
metadata["acquisition_date"].replace("-", "")
288278
)
279+
else:
280+
metadata["acquisition_date"] = "NA"
281+
metadata["acquisition_date_number"] = 0
282+
else:
283+
sdf = SimpleDateFormat("yyyy-MM-dd")
284+
metadata["acquisition_date"] = sdf.format(image_wpr.getAcquisitionDate())
285+
metadata["acquisition_date_number"] = int(
286+
metadata["acquisition_date"].replace("-", "")
287+
)
289288

290-
return metadata
289+
return metadata
291290

292291

293292
def get_info_from_original_metadata(user_client, image_wpr, field):

0 commit comments

Comments
 (0)