@@ -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
293292def get_info_from_original_metadata (user_client , image_wpr , field ):
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