diff --git a/merfishing/core/__init__.py b/merfishing/core/__init__.py index 440159d..faecdbe 100644 --- a/merfishing/core/__init__.py +++ b/merfishing/core/__init__.py @@ -538,9 +538,11 @@ def plot_fov( # load gray image data fov_images = { - name: self.get_image_fov(name=name, fov=fov, projection="max", padding=padding, contrast=True) - if "+" not in name - else self.get_rgb_image(name, as_float=True, fov=fov, projection="max", padding=padding, contrast=True) + name: ( + self.get_image_fov(name=name, fov=fov, projection="max", padding=padding, contrast=True) + if "+" not in name + else self.get_rgb_image(name, as_float=True, fov=fov, projection="max", padding=padding, contrast=True) + ) for name in image_names } @@ -862,20 +864,20 @@ def cell_segmentation( temp_dir.mkdir(exist_ok=True) output_prefix_list = [] - + if debug is not None: try: debug = int(debug) except ValueError: print("Debug need to be None or an integer.") - transcript_df = pd.read_csv(f'{self.region_dir}/detected_transcripts.csv.gz') - fov_list = list(transcript_df['fov'].unique()) + transcript_df = pd.read_csv(f"{self.region_dir}/detected_transcripts.csv.gz") + fov_list = list(transcript_df["fov"].unique()) fov_list = fov_list[:debug] - #fov_list = self.fov_ids[:debug] + # fov_list = self.fov_ids[:debug] else: - transcript_df = pd.read_csv(f'{self.region_dir}/detected_transcripts.csv.gz') - fov_list = list(transcript_df['fov'].unique()) - #fov_list = self.fov_ids + transcript_df = pd.read_csv(f"{self.region_dir}/detected_transcripts.csv.gz") + fov_list = list(transcript_df["fov"].unique()) + # fov_list = self.fov_ids if gpu is False: with ProcessPoolExecutor(jobs) as executor: