Parameters

developers/ground_truth_generation/bridges/extract_images_from_cell_counter.py

@@ -1,6 +1,7 @@
 import os
 import xmltodict
 from bigfish import stack
+from cut_detector.utils.parameters import Parameters
 from munch import Munch
 from cnn_framework.utils.tools import save_tiff
 
@@ -29,7 +30,8 @@ def extract_bridge_images(
     save_dir : str
         Path to the folder where to save the images.
     """
-    margin = MtCutDetectionFactory().margin
+    params = Parameters()
+    margin = MtCutDetectionFactory(params).margin
 
     # Create save_dir if not exists
     if not os.path.exists(save_dir):

developers/ground_truth_generation/bridges/semi_images_generation/generate_semi_images.py

@@ -6,6 +6,7 @@
 from cnn_framework.utils.readers.tiff_reader import TiffReader
 
 
+from cut_detector.utils.parameters import Parameters
 from developers.ground_truth_generation.bridges.semi_images_generation.micro_tubules_augmentations_advanced import (
     MicroTubulesAugmentationAdvanced,
 )
@@ -22,7 +23,8 @@
 
 def main(params, save_dir, debug_plot, circle_radius=11, diff_radius=4.54):
 
-    factory = MtCutDetectionFactoryAdvanced()
+    params = Parameters()
+    factory = MtCutDetectionFactoryAdvanced(params)
     file_paths = os.listdir(params.data_dir)
 
     # Create the save directory if it does not exist

playground/mid_body_detection.py

@@ -7,6 +7,7 @@
 from cnn_framework.utils.readers.tiff_reader import TiffReader
 
 from cut_detector.data.tools import get_data_path
+from cut_detector.utils.parameters import Parameters
 from cut_detector.utils.tools import re_organize_channels
 from cut_detector.widget_functions.mid_body_detection import (
     perform_mid_body_detection,
@@ -48,6 +49,7 @@ def main(
         video_name,
         mitoses_path,
         tracks_path,
+        Parameters(),
         save=save,
         movies_save_dir=movies_save_dir,
     )

playground/mitosis_track_generation.py

@@ -10,6 +10,7 @@
 from cut_detector.utils.cell_spot import CellSpot
 from cut_detector.utils.cell_track import CellTrack
 from cut_detector.utils.mitosis_track import MitosisTrack
+from cut_detector.utils.parameters import Parameters
 from cut_detector.utils.tools import re_organize_channels
 from cut_detector.widget_functions.mitosis_track_generation import (
     perform_mitosis_track_generation,
@@ -155,7 +156,7 @@ def main(
     image = re_organize_channels(image.squeeze())  # TYXC
 
     mitosis_tracks, cell_spots, cell_tracks = perform_mitosis_track_generation(
-        image, video_name, spots_dir, tracks_dir
+        image, video_name, spots_dir, tracks_dir, Parameters()
     )
 
     plot_predictions_evolution(cell_spots, cell_tracks, mitosis_tracks)

playground/mt_cut_detection.py

@@ -13,6 +13,7 @@
     MtCutDetectionFactory,
 )
 from cut_detector.utils.mitosis_track import MitosisTrack
+from cut_detector.utils.parameters import Parameters
 from cut_detector.utils.tools import re_organize_channels
 
 
@@ -57,7 +58,8 @@ def main(
 
     image = re_organize_channels(image.squeeze())  # TYXC
 
-    factory = MtCutDetectionFactory()
+    params = Parameters()
+    factory = MtCutDetectionFactory(params)
 
     results = factory.update_mt_cut_detection(
         [mitosis_track],

playground/napari_layer.py

@@ -8,6 +8,7 @@
 from cut_detector.factories.results_saving_factory import ResultsSavingFactory
 from cut_detector.utils.cell_track import CellTrack
 from cut_detector.utils.mitosis_track import MitosisTrack
+from cut_detector.utils.parameters import Parameters
 
 
 def main(
@@ -60,7 +61,8 @@ def main(
             mitosis_track = MitosisTrack.load(f)
         mitosis_tracks.append(mitosis_track)
 
-    ResultsSavingFactory().generate_napari_tracking_mask(
+    params = Parameters()
+    ResultsSavingFactory(params).generate_napari_tracking_mask(
         mitosis_tracks,
         video,
         viewer,

playground/results_saving.py

@@ -6,6 +6,7 @@
 from cnn_framework.utils.readers.tiff_reader import TiffReader
 
 from cut_detector.data.tools import get_data_path
+from cut_detector.utils.parameters import Parameters
 from cut_detector.utils.tools import re_organize_channels
 from cut_detector.widget_functions.save_results import perform_results_saving
 
@@ -33,6 +34,7 @@ def main(
 
     perform_results_saving(
         mitosis_path,
+        Parameters(),
         show=False,
         save_dir=results_dir,
         verbose=True,

src/cut_detector/_tests/test_micro_tubules_cut_detection.py

@@ -3,6 +3,7 @@
 
 from cut_detector._widget import micro_tubules_cut_detection
 from cut_detector.data.tools import get_data_path
+from cut_detector.utils.parameters import Parameters
 from cut_detector.widget_functions.mt_cut_detection import (
     perform_mt_cut_detection,
 )
@@ -25,6 +26,7 @@ def test_micro_tubules_cut_detection():
         video,
         "example_video",
         get_data_path("mitoses"),
+        Parameters(),
         save=False,
     )
 

src/cut_detector/_tests/test_mid_body_detection.py

@@ -3,6 +3,7 @@
 
 from cut_detector._widget import mid_body_detection
 from cut_detector.data.tools import get_data_path
+from cut_detector.utils.parameters import Parameters
 from cut_detector.widget_functions.mid_body_detection import (
     perform_mid_body_detection,
 )
@@ -29,6 +30,7 @@ def test_mid_body_detection():
         "example_video",
         get_data_path("mitoses"),
         get_data_path("tracks"),
+        params=Parameters(),
         save=False,
         parallel_detection=True,
     )
@@ -44,6 +46,7 @@ def test_mid_body_detection():
         "example_video",
         get_data_path("mitoses"),
         get_data_path("tracks"),
+        params=Parameters(),
         save=False,
         parallel_detection=False,
     )
@@ -52,6 +55,7 @@ def test_mid_body_detection():
         "example_video",
         get_data_path("mitoses"),
         get_data_path("tracks"),
+        params=Parameters(),
         save=False,
         parallel_detection=False,
         detection_method="h_maxima",

src/cut_detector/_tests/test_results_saving.py

@@ -3,6 +3,7 @@
 
 from cut_detector._widget import results_saving
 from cut_detector.data.tools import get_data_path
+from cut_detector.utils.parameters import Parameters
 from cut_detector.widget_functions.save_results import perform_results_saving
 
 import pytest
@@ -23,6 +24,7 @@ def test_results_saving():
 
     perform_results_saving(
         get_data_path("mitoses"),
+        Parameters(),
         show=False,
         save_dir=get_data_path("results"),
         verbose=True,

src/cut_detector/_tests/test_track_generation.py

@@ -3,6 +3,7 @@
 
 from cut_detector._widget import mitosis_track_generation
 from cut_detector.data.tools import get_data_path
+from cut_detector.utils.parameters import Parameters
 from cut_detector.widget_functions.mitosis_track_generation import (
     perform_mitosis_track_generation,
 )
@@ -27,6 +28,7 @@ def test_track_generation():
         "example_video",
         get_data_path("spots"),
         get_data_path("tracks"),
+        Parameters(),
         save=False,
     )