diff --git a/minerva_analysis/server/models/data_model.py b/minerva_analysis/server/models/data_model.py index 7b5c612f4..4dbcc2d7d 100644 --- a/minerva_analysis/server/models/data_model.py +++ b/minerva_analysis/server/models/data_model.py @@ -664,25 +664,17 @@ def convertOmeTiff(filePath, channelFilePath=None, dataDirectory=None, isLabelIm channel_io = tf.TiffFile(str(channelFilePath), is_ome=False) channels = zarr.open(channel_io.series[0].aszarr()) write_path = None - # removing '.ome' from the name - directory = Path(dataDirectory + "/" + str(filePath.name).replace('.ome', '_pyramided')) - args = {} - args['in_paths'] = [Path(filePath)] - args['out_path'] = directory - args['is_mask'] = True - pyramid_assemble.main(py_args=args) - write_path = str(directory) - # TODO: Reintroduce when MCMICRO pipeline produces better masks - # segmentation_mask = tf.TiffFile(str(filePath), is_ome=False) - # if segmentation_mask.series[0].aszarr().is_multiscales is False: - # args = {} - # args['in_paths'] = [Path(filePath)] - # args['out_path'] = directory - # args['is_mask'] = True - # pyramid_assemble.main(py_args=args) - # write_path = str(directory) - # else: - # write_path = str(filePath) + directory = Path(dataDirectory + "/" + filePath.name) + segmentation_mask = tf.TiffFile(str(filePath), is_ome=False) + if segmentation_mask.series[0].aszarr().is_multiscales is False: + args = {} + args['in_paths'] = [Path(filePath)] + args['out_path'] = directory + args['is_mask'] = True + pyramid_assemble.main(py_args=args) + write_path = str(directory) + else: + write_path = str(filePath) return {'segmentation': write_path}