Add small fixes to improve handling of batch processing

Author: lauraporta

derotation/analysis/incremental_derotation_pipeline.py

@@ -14,7 +14,6 @@
 
 import matplotlib.pyplot as plt
 import numpy as np
-import pandas as pd
 
 from derotation.analysis.blob_detection import BlobDetection
 from derotation.analysis.fit_ellipse import (
@@ -40,8 +39,10 @@ def __init__(self, *args, **kwargs):
         """Initialize the IncrementalPipeline object."""
         super().__init__(*args, **kwargs)
 
-        self.small_rotations = 10
-        self.number_of_rotations = self.rot_deg // self.small_rotations
+        self.degrees_per_small_rotation = 10
+        self.number_of_rotations = (
+            self.rot_deg // self.degrees_per_small_rotation
+        )
 
     def __call__(self):
         """Overwrite the ``__call__`` method from the parent class to derotate
@@ -60,8 +61,6 @@ def __call__(self):
         self.save(self.masked_image_volume)
         self.save_csv_with_derotation_data()
 
-        self.center_of_rotation = self.find_center_of_rotation()
-
     def create_signed_rotation_array(self) -> np.ndarray:
         logging.info("Creating signed rotation array...")
         rotation_on = np.zeros(self.total_clock_time)
@@ -116,7 +115,9 @@ def adjust_rotation_increment(self) -> Tuple[np.ndarray, np.ndarray]:
                 self.rot_blocks_idx["end"],
             )
         ]
-        new_increments = [self.small_rotations / t for t in ticks_per_rotation]
+        new_increments = [
+            self.degrees_per_small_rotation / t for t in ticks_per_rotation
+        ]
 
         logging.info(f"New increment example: {new_increments[0]:.3f}")
 
@@ -257,34 +258,6 @@ def plot_rotation_speeds(self):
         #  rotation pipeline
         pass
 
-    def save_csv_with_derotation_data(self):
-        """Saves a csv file with the rotation angles by line and frame,
-        and the rotation on signal.
-        It is saved in the saving folder specified in the config file.
-        """
-        df = pd.DataFrame(
-            columns=[
-                "frame",
-                "rotation_angle",
-                "clock",
-            ]
-        )
-
-        df["frame"] = np.arange(self.num_frames)
-        df["rotation_angle"] = self.rot_deg_frame[: self.num_frames]
-        df["clock"] = self.frame_start[: self.num_frames]
-
-        Path(self.config["paths_write"]["derotated_tiff_folder"]).mkdir(
-            parents=True, exist_ok=True
-        )
-
-        df.to_csv(
-            self.config["paths_write"]["derotated_tiff_folder"]
-            + self.config["paths_write"]["saving_name"]
-            + ".csv",
-            index=False,
-        )
-
     ### ------- Methods unique to IncrementalPipeline ----------------- ###
 
     def find_center_of_rotation(self) -> Tuple[int, int]:

derotation/config/load_config.py

@@ -66,9 +66,7 @@ def update_config_paths(
     config["paths_write"]["logs_folder"] = str(
         Path(output_folder) / "derotation" / "logs"
     )
-    config["paths_write"]["derotated_tiff_folder"] = str(
-        Path(output_folder) / "derotation/"
-    )
+    config["paths_write"]["derotated_tiff_folder"] = str(Path(output_folder))
     config["paths_write"]["saving_name"] = (
         f"derotated{f'_{folder_suffix}' if folder_suffix else ''}"
     )

derotation/derotate_batch.py

@@ -51,7 +51,6 @@ def derotate(
     Exception
         If the pipeline fails.
     """
-    # FULL DEROTATION PIPELINE
     # find tif and bin files
     bin_path = list(dataset_folder.rglob(glob_naming_pattern_bin))[0]
     tif_path = list(dataset_folder.rglob(glob_naming_pattern_tif))[0]
@@ -67,7 +66,7 @@ def derotate(
         folder_suffix=folder_suffix,
     )
 
-    logging.info("Running full derotation pipeline")
+    logging.info(f"Running {folder_suffix} derotation pipeline")
 
     # Run the pipeline
     try:
@@ -77,7 +76,7 @@ def derotate(
             derotator = IncrementalPipeline(config)
         derotator()
     except Exception as e:
-        logging.error("Full derotation pipeline failed")
+        logging.error("Derotation pipeline failed")
         logging.error(e.args)
         logging.error(traceback.format_exc())
         raise e