Merge pull request #14 from catalystneuro/change_repo_structure

Separate conversion folder for benisty_2024 and lohani_2022

README.md

@@ -16,7 +16,7 @@ We recommend that you install the package inside a [virtual environment](https:/
 ### Running a specific conversion
 Once you have installed the package with pip, you can run any of the conversion scripts in a notebook or a python file:
 
-https://github.com/catalystneuro/higley-lab-to-nwb//tree/main/src/benisty_2022/benisty_2022_conversion_script.py
+https://github.com/catalystneuro/higley-lab-to-nwb//tree/main/src/lohani_2022/lohani_2022_conversion_script.py
 
 
 
@@ -49,12 +49,12 @@ both of the methods above install the repository in [editable mode](https://pip.
 ### Running a specific conversion
 To run a specific conversion, you might need to install first some conversion specific dependencies that are located in each conversion directory:
 ```
-pip install -r src/higley_lab_to_nwb/benisty_2022/benisty_2022_requirements.txt
+pip install -r src/higley_lab_to_nwb/lohani_2022/lohani_2022_requirements.txt
 ```
 
 You can run a specific conversion with the following command:
 ```
-python src/higley_lab_to_nwb/benisty_2022/benisty_2022_conversion_script.py
+python src/higley_lab_to_nwb/lohani_2022/lohani_2022_conversion_script.py
 ```
 
 ## Repository structure
@@ -70,26 +70,26 @@ Each conversion is organized in a directory of its own in the `src` directory:
     └── src
         ├── higley_lab_to_nwb
         │   ├── conversion_directory_1
-        │   └── benisty_2022
-        │       ├── benisty_2022behaviorinterface.py
-        │       ├── benisty_2022_convert_session.py
-        │       ├── benisty_2022_metadata.yml
-        │       ├── benisty_2022nwbconverter.py
-        │       ├── benisty_2022_requirements.txt
-        │       ├── benisty_2022_notes.md
+        │   └── lohani_2022
+        │       ├── lohani_2022behaviorinterface.py
+        │       ├── lohani_2022_convert_session.py
+        │       ├── lohani_2022_metadata.yml
+        │       ├── lohani_2022nwbconverter.py
+        │       ├── lohani_2022_requirements.txt
+        │       ├── lohani_2022_notes.md
 
         │       └── __init__.py
         │   ├── conversion_directory_b
 
         └── __init__.py
 
- For example, for the conversion `benisty_2022` you can find a directory located in `src/higley-lab-to-nwb/benisty_2022`. Inside each conversion directory you can find the following files:
+ For example, for the conversion `lohani_2022` you can find a directory located in `src/higley-lab-to-nwb/lohani_2022`. Inside each conversion directory you can find the following files:
 
-* `benisty_2022_convert_sesion.py`: this script defines the function to convert one full session of the conversion.
-* `benisty_2022_requirements.txt`: dependencies specific to this conversion.
-* `benisty_2022_metadata.yml`: metadata in yaml format for this specific conversion.
-* `benisty_2022behaviorinterface.py`: the behavior interface. Usually ad-hoc for each conversion.
-* `benisty_2022nwbconverter.py`: the place where the `NWBConverter` class is defined.
-* `benisty_2022_notes.md`: notes and comments concerning this specific conversion.
+* `lohani_2022_convert_sesion.py`: this script defines the function to convert one full session of the conversion.
+* `lohani_2022_requirements.txt`: dependencies specific to this conversion.
+* `lohani_2022_metadata.yml`: metadata in yaml format for this specific conversion.
+* `lohani_2022behaviorinterface.py`: the behavior interface. Usually ad-hoc for each conversion.
+* `lohani_2022nwbconverter.py`: the place where the `NWBConverter` class is defined.
+* `lohani_2022_notes.md`: notes and comments concerning this specific conversion.
 
 The directory might contain other files that are necessary for the conversion but those are the central ones.

src/higley_lab_to_nwb/benisty_2024/__init__.py

@@ -0,0 +1 @@
+from .benisty_2024_nwbconverter import Benisty2024NWBConverter

src/higley_lab_to_nwb/benisty_2024/benisty_2024_convert_all_sessions.py

@@ -0,0 +1,25 @@
+"""Primary script to run to convert an entire session for of data using the NWBConverter."""
+
+from pathlib import Path
+from typing import Union
+import os
+from .benisty_2024_convert_session import session_to_nwb
+
+
+
+# Parameters for conversion
+root_path = Path("/media/amtra/Samsung_T5/CN_data")
+data_dir_path = root_path / "Higley-CN-data-share"
+output_dir_path = root_path / "Higley-conversion_nwb/"
+
+session_ids = os.listdir(data_dir_path)
+stub_test = True
+for session_id in session_ids:
+    session_folder = data_dir_path / Path(session_id)
+    if os.path.isdir(session_folder):
+        session_to_nwb(
+            folder_path=session_folder,
+            output_dir_path=output_dir_path,
+            session_id=session_id,
+            stub_test=stub_test,
+        )

src/higley_lab_to_nwb/benisty_2024/benisty_2024_convert_session.py

@@ -0,0 +1,70 @@
+"""Primary script to run to convert an entire session for of data using the NWBConverter."""
+
+from pathlib import Path
+from typing import Union
+from neuroconv.utils import load_dict_from_file, dict_deep_update
+from higley_lab_to_nwb.benisty_2024 import Benisty2024NWBConverter
+import os
+import glob
+
+
+def session_to_nwb(
+    folder_path: Union[str, Path], output_dir_path: Union[str, Path], session_id: str, stub_test: bool = False
+):
+
+    output_dir_path = Path(output_dir_path)
+    if stub_test:
+        output_dir_path = output_dir_path / "nwb_stub"
+    output_dir_path.mkdir(parents=True, exist_ok=True)
+
+    nwbfile_path = output_dir_path / f"{session_id}_new.nwb"
+
+    source_data = dict()
+    conversion_options = dict()
+
+    search_pattern = "_".join(session_id.split("_")[:2])
+
+    converter = Benisty2024NWBConverter(
+        source_data=source_data,
+    )
+
+    # Add datetime to conversion
+    metadata = converter.get_metadata()
+    date = read_session_start_time(folder_path=folder_path)
+    metadata["NWBFile"]["session_start_time"] = date
+    subject_id = session_id.split("_")[1]
+    metadata["Subject"].update(subject_id=subject_id)
+    metadata["NWBFile"].update(session_id=session_id)
+
+    # Update default metadata with the editable in the corresponding yaml file
+    editable_metadata_path = Path(__file__).parent / "benisty_2024_metadata.yaml"
+    editable_metadata = load_dict_from_file(editable_metadata_path)
+    metadata = dict_deep_update(metadata, editable_metadata)
+
+    # Add ophys metadata
+    ophys_metadata_path = Path(__file__).parent / "metadata" / "benisty_2024_ophys_metadata.yaml"
+    ophys_metadata = load_dict_from_file(ophys_metadata_path)
+    metadata = dict_deep_update(metadata, ophys_metadata)
+
+    # Run conversion
+    converter.run_conversion(
+        metadata=metadata, nwbfile_path=nwbfile_path, conversion_options=conversion_options, overwrite=True
+    )
+
+
+if __name__ == "__main__":
+
+    # Parameters for conversion
+    root_path = Path("/media/amtra/Samsung_T5/CN_data")
+    data_dir_path = root_path / "Higley-CN-data-share"
+    output_dir_path = root_path / "Higley-conversion_nwb/"
+    stub_test = True
+    session_ids = os.listdir(data_dir_path)
+    session_id = "11222019_grabAM06_vis_stim"
+    folder_path = data_dir_path / Path(session_id)
+    session_to_nwb(
+        folder_path=folder_path,
+        output_dir_path=output_dir_path,
+        session_id=session_id,
+        stub_test=stub_test,
+    )

src/higley_lab_to_nwb/benisty_2024/benisty_2024_nwbconverter.py

@@ -0,0 +1,12 @@
+"""Primary NWBConverter class for this dataset."""
+
+from typing import Dict, List
+from neuroconv import NWBConverter
+
+
+
+class Benisty2024NWBConverter(NWBConverter):
+    """Primary conversion class."""
+
+    data_interface_classes = dict(
+    )

src/higley_lab_to_nwb/benisty_2024/benisty_2024_requirements.txt

@@ -0,0 +1,4 @@
+nwb-conversion-tools==0.11.1   # Example of specific pinned dependecy
+some-extra-package==1.11.3  # Example of another extra package that's necessary for the current conversion
+roiextractors
+neuroconv @ git+https://github.com/catalystneuro/neuroconv.git@facemap

src/higley_lab_to_nwb/benisty_2024/metadata/benisty_2024_ophys_metadata.yaml

@@ -0,0 +1,4 @@
+Ophys:
+  Device:
+  OnePhotonSeries:
+  ImagingPlane: