WIP: saving images 🐛

calcium_imaging_automation/core/reader.py

@@ -20,12 +20,16 @@ def __init__(
     def get_folders_first_layer(self, file_path: Path) -> List[Path]:
         return list(file_path.glob(self.folder_read_pattern))
 
-    def get_files_paths_by_format(self, folder: Path, filetype="tif") -> List[Path]:
+    def get_files_paths_by_format(
+        self, folder: Path, filetype="tif"
+    ) -> List[Path]:
         return list(folder.rglob(filetype))
-    
+
     def total_objects_by_format(self, folder: Path) -> dict:
         return {
-            filetype.split(".")[-1]: len(self.get_files_paths_by_format(folder, filetype))
+            filetype.split(".")[-1]: len(
+                self.get_files_paths_by_format(folder, filetype)
+            )
             for filetype in self.file_read_pattern
         }
 

calcium_imaging_automation/core/writer.py

@@ -1,14 +1,17 @@
 from pathlib import Path
-from typing import List
+from typing import Dict, List
 
+import numpy as np
 from datashuttle.configs.config_class import Configs
 from datashuttle.utils import folders
+from PIL import Image
 
 
 class DatashuttleWrapper:
     def __init__(self, output_path: Path) -> None:
         # This is supposed to run in the cluster and have direct access
         # to the central storages
+        self.output_path = output_path
         self.datashuttle_cfg = Configs(
             project_name=output_path.name,
             file_path=output_path,
@@ -20,7 +23,8 @@ def __init__(self, output_path: Path) -> None:
         )
 
     def create_folders(self, dataset_names: List[str], session_number) -> None:
-        folders.create_folder_trees(
+        # all_paths is a dictionary with keys: sub, ses
+        self.all_paths: Dict[str, List[Path]] = folders.create_folder_trees(
             cfg=self.datashuttle_cfg,
             top_level_folder="derivatives",
             sub_names=[
@@ -30,3 +34,21 @@ def create_folders(self, dataset_names: List[str], session_number) -> None:
             ses_names=[f"ses-{i}" for i in range(session_number)],
             datatype="funcimg",
         )
+
+    def get_dataset_path(self, dataset_name: str) -> Path:
+        print((self.output_path / "derivatives"))
+        return next(
+            (self.output_path / "derivatives").glob(f"*{dataset_name}*"), None
+        )
+
+    def save_image(
+        self,
+        image: np.ndarray,
+        run_id: int,
+        dataset_name: str,
+        session_number: int,
+        filename: str,
+    ) -> None:
+        path = self.get_dataset_path(dataset_name)
+        image = Image.fromarray(image)
+        image.save(path / f"ses-{session_number}" / f"{filename}-{run_id}")

examples/debugging.py

@@ -1,10 +1,12 @@
-from example_usage import main
-from pathlib import Path   
+from pathlib import Path
 
+from example_usage import main
 
 main(
-    raw_data_path = Path('/nfs/winstor/margrie/SimonWeiler/RawData/Invivo_imaging/3photon_rotation/shared/'),
-    output_path = Path('/ceph/margrie/laura/cimaut/'),
-    folder_read_pattern = '2*',
-    file_read_pattern = ['rotation_00001.tif', '*.bin']
-)
+    raw_data_path=Path(
+        "/nfs/winstor/margrie/SimonWeiler/RawData/Invivo_imaging/3photon_rotation/shared/"
+    ),
+    output_path=Path("/ceph/margrie/laura/cimaut/"),
+    folder_read_pattern="2*",
+    file_read_pattern=["rotation_00001.tif", "*.bin"],
+)

examples/example_usage.py

@@ -3,9 +3,10 @@
 import logging
 from pathlib import Path
 from typing import List
-import wandb
+
 import numpy as np
 
+import wandb
 from calcium_imaging_automation.core.reader import ReadAllPathsInFolder
 from calcium_imaging_automation.core.writer import DatashuttleWrapper
 
@@ -35,7 +36,6 @@ def main(
     wandb.init(project="example_usage")
     run_id = wandb.run.id
 
-
     # --- Read folders and files ---
     reader = ReadAllPathsInFolder(
         raw_data_path,
@@ -48,12 +48,10 @@ def main(
     number_of_tiffs = reader.max_session_number(filetype="tif")
     logging.info(f"Max of tiffs found: {number_of_tiffs}")
 
-
     # --- Write folders and files ---
     writer = DatashuttleWrapper(output_path)
     writer.create_folders(reader.dataset_names, session_number=number_of_tiffs)
 
-
     for dataset in reader.datasets_paths:
         dataset = dataset.stem
         for session in range(1, number_of_tiffs + 1):
@@ -63,15 +61,25 @@ def main(
             data = np.random.rand(100, 100)
             metric_measured = np.random.rand()
 
-            wandb.log({
-                "dataset": dataset,
-                "session": session,
-                "metric_measured": metric_measured,
-                "image": wandb.Image(data),
-                "run_id": run_id
-            })
-
-    wandb.finish()     
+            wandb.log(
+                {
+                    "dataset": dataset,
+                    "session": session,
+                    "metric_measured": metric_measured,
+                    "run_id": run_id,
+                }
+            )
+
+            # save image in session folder
+            writer.save_image(
+                image=data,
+                run_id=run_id,
+                dataset_name=dataset,
+                session_number=session,
+                filename="image",
+            )
+
+    wandb.finish()
     logging.info("Pipeline finished.")
 
 

examples/example_usage.sh

@@ -6,4 +6,3 @@ python examples/example_usage.py \
     --folder_read_pattern '2*' \
     --file_read_pattern 'rotation_00001.tif' \
     --file_read_pattern '*.bin' \
-