chore: merge dev into release

chore: merge dev into release

moseq2_extract/__init__.py

@@ -1 +1 @@
-__version__ = "v1.1.2"
+__version__ = "v1.2.0"

moseq2_extract/cli.py

@@ -248,10 +248,16 @@ def download_flip_file(config_file, output_dir):
 
 @cli.command(name="generate-config", help="Generates a configuration file (config.yaml) that holds editable options for extraction parameters.")
 @click.option('--output-file', '-o', type=click.Path(), default='config.yaml')
-def generate_config(output_file):
+@click.option('--camera-type', default='k2', type=str, help='specify the camera type (k2 or azure), default is k2')
+
+def generate_config(output_file, camera_type):
 
     objs = extract.params
     params = {tmp.name: tmp.default for tmp in objs if not tmp.required}
+    if camera_type=='azure':
+        params['bg_roi_depth_range'] = [550, 650]
+        params['spatial_filter_size'] = [5]
+        params['tail_filter_size'] = [15, 15]
 
     with open(output_file, 'w') as f:
         yaml.safe_dump(params, f)

moseq2_extract/extract/extract.py

@@ -169,7 +169,7 @@ def extract_chunk(chunk, use_tracking_model=False, spatial_filter_size=(3,),
     # Orient mouse to face east
     if flip_classifier:
         # get frame indices of incorrectly orientation
-        flips = get_flips(cropped_frames, flip_classifier, flip_classifier_smoothing)
+        flips = get_flips(cropped_filtered_frames, flip_classifier, flip_classifier_smoothing)
         flip_indices = np.where(flips)
 
         # apply flips

moseq2_extract/gui.py

@@ -93,7 +93,7 @@ def parse_input(s):
     return ret_extract
 
 @filter_warnings
-def generate_config_command(output_file):
+def generate_config_command(output_file, camera_type='k2'):
     """
     Generate configuration file (config.yaml) to use throughout pipeline.
 
@@ -108,6 +108,10 @@ def generate_config_command(output_file):
     objs = extract.params
 
     params = {tmp.name: tmp.default for tmp in objs if not tmp.required}
+    if camera_type=='azure':
+        params['bg_roi_depth_range'] = [550, 650]
+        params['spatial_filter_size'] = [5]
+        params['tail_filter_size'] = [15, 15]
 
     # Check if the file already exists, and prompt user if they would like to overwrite pre-existing file
     if exists(output_file):

moseq2_extract/helpers/wrappers.py

@@ -164,6 +164,7 @@ def get_roi_wrapper(input_file, config_data, output_dir=None):
     config_data['output_dir'] = output_dir
 
     if config_data.get('finfo') is None:
+        # when depth video is .avi, frame_size/dim is read directly from the video
         config_data['finfo'] = get_movie_info(input_file, **config_data)
 
     # checks camera type to set appropriate bg_roi_weights
@@ -185,7 +186,8 @@ def get_roi_wrapper(input_file, config_data, output_dir=None):
         adjusted_bg_depth_range = bground_im[cY][cX]
         config_data['bg_roi_depth_range'] = [int(adjusted_bg_depth_range-50), int(adjusted_bg_depth_range+50)]
 
-    first_frame = load_movie_data(input_file, 0, **config_data) # there is a tar object flag that must be set!!
+    # pass in config_data['finfo']['dims'] for frame size otherwise frame size is hard coded to 512x424
+    first_frame = load_movie_data(input_file, 0, frame_size=config_data['finfo']['dims'], **config_data) # there is a tar object flag that must be set!!
     write_image(join(output_dir, 'first_frame.tiff'), first_frame, scale=True,
                 scale_factor=config_data['bg_roi_depth_range'])
 
@@ -402,12 +404,14 @@ def flip_file_wrapper(config_file, output_dir, selected_flip=None):
     """
 
     flip_files = {
-        'large mice with fibers':
+        'large mice with fibers (K2)':
             "https://storage.googleapis.com/flip-classifiers/flip_classifier_k2_largemicewithfiber.pkl",
-        'adult male c57s':
+        'adult male c57s (K2)':
             "https://storage.googleapis.com/flip-classifiers/flip_classifier_k2_c57_10to13weeks.pkl",
-        'mice with Inscopix cables':
-            "https://storage.googleapis.com/flip-classifiers/flip_classifier_k2_inscopix.pkl"
+        'mice with Inscopix cables (K2)':
+            "https://storage.googleapis.com/flip-classifiers/flip_classifier_k2_inscopix.pkl",
+        'adult male c57s (Azure)':
+            "https://moseq-data.s3.amazonaws.com/flip-classifier-azure-temp.pkl"
     }
 
     key_list = list(flip_files)