Use the same diameter for masking when doing derotations one after th…

…e other

derotation/analysis/full_rotation_pipeline.py

@@ -1,3 +1,4 @@
+import copy
 import logging
 import sys
 from pathlib import Path
@@ -57,7 +58,7 @@ def __call__(self):
         self.contrast_enhancement()
         self.process_analog_signals()
         rotated_images = self.rotate_frames_line_by_line()
-        masked = self.add_circle_mask(rotated_images)
+        masked = self.add_circle_mask(rotated_images, self.mask_diameter)
         self.save(masked)
         self.save_csv_with_derotation_data()
 
@@ -127,6 +128,7 @@ def load_data(self):
         self.num_frames = self.image_stack.shape[0]
         self.num_lines_per_frame = self.image_stack.shape[1]
         self.num_total_lines = self.num_frames * self.num_lines_per_frame
+        self.mask_diameter = copy.deepcopy(self.num_lines_per_frame)
 
         self.direction, self.speed = read_randomized_stim_table(
             self.config["paths_read"]["path_to_randperm"]

derotation/analysis/incremental_rotation_pipeline.py

@@ -50,10 +50,10 @@ def __call__(self):
             masked_unregistered, x_fitted, y_fitted
         )
 
-        new_diameter = self.num_lines_per_frame - 2 * max(
+        self.new_diameter = self.num_lines_per_frame - 2 * max(
             max(np.abs(shifts["x"])), max(np.abs(shifts["y"]))
         )
-        masked = self.add_circle_mask(registered_images, new_diameter)
+        masked = self.add_circle_mask(registered_images, self.new_diameter)
 
         self.save(masked)
         self.save_csv_with_derotation_data()

examples/derotation_slurm_job.py

@@ -9,6 +9,10 @@
     IncrementalPipeline,
 )
 
+# =====================================================================
+# Set up the config files
+# =====================================================================
+
 job_id = int(sys.argv[1:][0])
 dataset_path = sys.argv[1:][1]
 datasets = [path for path in os.listdir(dataset_path) if path.startswith("23")]
@@ -30,7 +34,6 @@
 full_rotation_image = [file for file in image_files if "rotation_0" in file][0]
 incremental_image = [file for file in image_files if "increment_0" in file][0]
 
-#  make debug_plots and logs and derotated folder in dataset
 Path(f"{dataset_path}/{dataset}/debug_plots_incremental/").mkdir(
     parents=True, exist_ok=True
 )
@@ -78,8 +81,13 @@
         yaml.dump(config, f)
 
 
-derotate = IncrementalPipeline(f"incremental_rotation_{job_id}")
-derotate()
+# =====================================================================
+# Run the pipeline
+# =====================================================================
+
+derotate_incremental = IncrementalPipeline(f"incremental_rotation_{job_id}")
+derotate_incremental()
 
 derotate_full = FullPipeline(f"full_rotation_{job_id}")
+derotate_full.mask_diameter = derotate_incremental.new_diameter
 derotate_full()