octopi 1.1__py3-none-any.whl → 1.2.0__py3-none-any.whl

octopi/extract/membranebound_extract.py

@@ -1,5 +1,5 @@
 from scipy.spatial.transform import Rotation as R
-from octopi import utils, io
+from copick_utils.io import readers
 import scipy.ndimage as ndi
 from typing import Tuple
 import numpy as np
@@ -36,7 +36,7 @@ def process_membrane_bound_extract(run,
     new_session_id = str(int(save_session_id) + 1)  # Convert to string after increment                                  
 
     # Need Better Error Handing for Missing Picks
-    coordinates = io.get_copick_coordinates(
+    coordinates = readers.coordinates(
         run, 
         picks_info[0], picks_info[1], picks_info[2],
         voxel_size,
@@ -54,12 +54,13 @@ def process_membrane_bound_extract(run,
     if membrane_info is None:
         # Flag to distinguish between organelle and membrane segmentation
         membranes_provided = False
-        seg = io.get_segmentation_array(run, 
-                                    voxel_size, 
-                                    organelle_info[0],
-                                    user_id=organelle_info[1], 
-                                    session_id=organelle_info[2],
-                                    raise_error=False)
+        seg = readers.segmentation(
+            run, 
+            voxel_size, 
+            organelle_info[0],
+            user_id=organelle_info[1], 
+            session_id=organelle_info[2],
+            raise_error=False)
         # If No Segmentation is Found, Return
         if seg is None: return     
         elif nPoints == 0 or np.unique(seg).max() == 0:
@@ -68,7 +69,7 @@ def process_membrane_bound_extract(run,
     else:
         # Read both Organelle and Membrane Segmentations
         membranes_provided = True
-        seg = io.get_segmentation_array(
+        seg = readers.segmentation(
             run, 
             voxel_size, 
             membrane_info[0],
@@ -76,7 +77,7 @@ def process_membrane_bound_extract(run,
             session_id=membrane_info[2],
             raise_error=False)
 
-        organelle_seg = io.get_segmentation_array(
+        organelle_seg = readers.segmentation(
             run, 
             voxel_size, 
             organelle_info[0],

octopi/extract/midpoint_extract.py

@@ -1,6 +1,6 @@
 from octopi.extract import membranebound_extract as extract
 from scipy.spatial.transform import Rotation as R
-from octopi import io
+from copick_utils.io import readers
 from scipy.spatial import cKDTree
 from typing import Tuple
 import numpy as np
@@ -28,7 +28,7 @@ def process_midpoint_extract(
     """
 
     # Pull Picks that Are used for Midpoint Extraction
-    coordinates = io.get_copick_coordinates(
+    coordinates = readers.coordinates(
         run, 
         picks_info[0], picks_info[1], picks_info[2],
         voxel_size
@@ -40,7 +40,7 @@ def process_midpoint_extract(
     save_picks_info[2] = save_session_id
 
     # Get Organelle Segmentation
-    seg = io.get_segmentation_array(
+    seg = readers.segmentation(
         run, 
         voxel_size, 
         organelle_info[0],

octopi/models/common.py

@@ -1,5 +1,5 @@
 from monai.losses import FocalLoss, TverskyLoss
-from octopi import losses
+from octopi.utils import losses
 from octopi.models import (
     Unet, AttentionUnet, MedNeXt, SegResNet
 )

octopi/processing/create_targets_from_picks.py

@@ -1,6 +1,5 @@
 from octopi.processing.segmentation_from_picks import from_picks
-import octopi.processing.writers as write
-from octopi import io 
+from copick_utils.io import readers, writers
 from typing import List
 from tqdm import tqdm
 import numpy as np
@@ -56,7 +55,7 @@ def generate_targets(
         run = root.get_run(runID)
 
         # Get Tomogram 
-        tomo = io.get_tomogram_array(run, voxel_size, tomo_algorithm)
+        tomo = readers.tomogram(run, voxel_size, tomo_algorithm)
         
         # Initialize Target Volume
         target = np.zeros(tomo.shape, dtype=np.uint8)
@@ -107,7 +106,7 @@ def generate_targets(
         # Write Segmentation for non-empty targets
         if target.max() > 0 and numPicks > 0:
             tqdm.write(f'Annotating {numPicks} picks in {runID}...')    
-            write.segmentation(run, target, target_user_name, 
+            writers.segmentation(run, target, target_user_name, 
                                name = target_segmentation_name, session_id= target_session_id, 
                                voxel_size = voxel_size)
     print('Creation of targets complete!')

octopi/processing/evaluate.py

@@ -1,7 +1,7 @@
-from octopi import utils, io
+from copick_utils.io import readers
 from scipy.spatial import distance
+import copick, json, os, yaml   
 from typing import List
-import copick, json, os
 import numpy as np
 
 class evaluator:
@@ -95,12 +95,12 @@ class evaluator:
             for name, radius in self.objects:
                 
                 # Get Ground Truth and Predicted Coordinates
-                gt_coordinates = io.get_copick_coordinates(
+                gt_coordinates = readers.coordinates(
                     run, name, 
                     self.ground_truth_user_id, self.ground_truth_session_id, 
                     self.voxel_size, raise_error=False
                 )
-                pred_coordinates = io.get_copick_coordinates(
+                pred_coordinates = readers.coordinates(
                     run, name,
                     self.prediction_user_id, self.predict_session_id, 
                     self.voxel_size, raise_error=False
@@ -202,14 +202,27 @@ class evaluator:
             }    
             
             os.makedirs(save_path, exist_ok=True)
-            summary_metrics = { "input": self.input_params, "parameters": self.parameters, 
-                                    "summary_metrics": final_summary_metrics }
-            with open(os.path.join(save_path, 'average_metrics.json'), 'w') as f:
-                json.dump(summary_metrics, f, indent=4)
-            print(f'\nAverage Metrics saved to {os.path.join(save_path, "average_metrics.json")}')
+            summary_metrics = { "input": self.input_params, 
+                                "final_fbeta_score": final_fbeta,  
+                                "aggregated_particle_scores": {    # Optionally add per-particle details
+                                    name: {
+                                        "tp": counts['total_tp'],
+                                        "fp": counts['total_fp'], 
+                                        "fn": counts['total_fn'],
+                                        "weight": self.weights.get(name, 1)
+                                    } for name, counts in aggregated_counts.items()
+                                },
+                                "summary_metrics": final_summary_metrics, 
+                                "parameters": self.parameters,  }
+
+            # Save average metrics to YAML file
+            with open(os.path.join(save_path, 'average_metrics.yaml'), 'w') as f:
+                yaml.dump(summary_metrics, f, indent=4, default_flow_style=False, sort_keys=False)
+            print(f'\nAverage Metrics saved to {os.path.join(save_path, "average_metrics.yaml")}')
             
-            detailed_metrics = { "input": self.input_params, "parameters": self.parameters, 
-                                "metrics": metrics }
+            detailed_metrics = { "input": self.input_params,  
+                                  "metrics": metrics,
+                                 "parameters": self.parameters, }
             with open(os.path.join(save_path, 'metrics.json'), 'w') as f:
                 json.dump(detailed_metrics, f, indent=4)
             print(f'Metrics saved to {os.path.join(save_path, "metrics.json")}')

octopi/processing/importers.py

@@ -1,7 +1,7 @@
 from octopi.processing.downsample import FourierRescale
 import copick, argparse, mrcfile, glob, os
-import octopi.processing.writers as write
 from octopi.entry_points import common
+from copick_utils.io import writers
 from tqdm import tqdm
 
 def from_dataportal(
@@ -57,10 +57,10 @@ def from_dataportal(
 
             # If we want to save the tomograms at a different voxel size, we need to rescale the tomograms
             if output_voxel_size is None:
-                write.tomogram(run, vol, input_voxel_size, target_tomo_type)
+                writers.tomogram(run, vol, input_voxel_size, target_tomo_type)
             else:
                 vol = rescale.run(vol)
-                write.tomogram(run, vol, output_voxel_size, target_tomo_type)
+                writers.tomogram(run, vol, output_voxel_size, target_tomo_type)
     
     print(f'Downloading Complete!! Downloaded {len(root.runs)} runs')
 
@@ -168,7 +168,7 @@ def from_mrcs(
             voxel_size_to_write = input_voxel_size
 
         # Write the tomogram
-        write.tomogram(run, vol, voxel_size_to_write, target_tomo_type)
+        writers.tomogram(run, vol, voxel_size_to_write, target_tomo_type)
     print(f"Processed {len(mrc_files)} files from {mrcs_path}")
 
 

octopi/pytorch/hyper_search.py

@@ -1,10 +1,9 @@
-from monai.losses import FocalLoss, TverskyLoss
 from monai.metrics import ConfusionMatrixMetric
 from octopi.pytorch import trainer
 from mlflow.tracking import MlflowClient
 from octopi.models import common
-from octopi import io, losses
 import torch, mlflow, optuna, gc
+from octopi.utils import io
 
 class BayesianModelSearch:
 
@@ -207,7 +206,7 @@ class BayesianModelSearch:
         if score > best_score_so_far:
             torch.save(model_trainer.model_weights, f'{self.results_dir}/best_model.pth')
             io.save_parameters_to_yaml(self.model_builder, model_trainer, self.data_generator, 
-                                    f'{self.results_dir}/best_model_config.yaml')
+                                    f'{self.results_dir}/model_config.yaml')
 
     def get_best_score(self, trial):
         """Retrieve the best score from the trial."""

octopi/pytorch/model_search_submitter.py

@@ -1,7 +1,7 @@
 from octopi.datasets import generators, multi_config_generator
+from octopi.utils import config, parsers
 from octopi.pytorch import hyper_search
 import torch, mlflow, optuna
-from octopi import utils
 from typing import List
 import pandas as pd
 
@@ -75,7 +75,7 @@ class ModelSearchSubmit:
         self.data_generator = None
 
         # Set random seed for reproducibility
-        utils.set_seed(self.random_seed)
+        config.set_seed(self.random_seed)
 
         # Initialize dataset generator
         self._initialize_data_generator()
@@ -108,7 +108,7 @@ class ModelSearchSubmit:
             )
 
         # Split datasets into training and validation
-        ratios = utils.parse_data_split(self.data_split)
+        ratios = parsers.parse_data_split(self.data_split)
         self.data_generator.get_data_splits(
             trainRunIDs=self.trainRunIDs,
             validateRunIDs=self.validateRunIDs,
@@ -134,7 +134,7 @@ class ModelSearchSubmit:
 
         # Set up MLflow tracking
         try:
-            tracking_uri = utils.mlflow_setup()
+            tracking_uri = config.mlflow_setup()
             mlflow.set_tracking_uri(tracking_uri)
         except Exception as e:
             print(f'Failed to set up MLflow tracking: {e}')