Merge pull request #2 from catalystneuro/add_fiber_photometry

Add fiber photometry interface

.github/workflows/test-install.yml

@@ -29,4 +29,3 @@ jobs:
       run: pip install -e .
     - name: Test module load
       run: python -c "import hnasko_lab_to_nwb"
-

.gitignore

@@ -146,4 +146,4 @@ dmypy.json
 .DS_Store
 
 # NWB files
-**.nwb
+**.nwb

.pre-commit-config.yaml

@@ -15,11 +15,11 @@ repos:
     rev: v2.3.0
     hooks:
     - id: codespell
-        additional_dependencies:
+    additional_dependencies:
         - tomli
 
 -   repo: https://github.com/astral-sh/ruff-pre-commit
     rev: v0.6.9
     hooks:
     - id: ruff
-        args: [ --fix ]
+    args: [ --fix ]

README.md

@@ -14,8 +14,8 @@ pip install hnasko-lab-to-nwb
 
 We recommend that you install the package inside a [virtual environment](https://docs.python.org/3/tutorial/venv.
 html). A simple way of doing this is to use a [conda environment](https://docs.conda.
-io/projects/conda/en/latest/user-guide/concepts/environments.html) from the `conda` package manager ([installation 
-instructions](https://docs.conda.io/en/latest/miniconda.html)). Detailed instructions on how to use conda 
+io/projects/conda/en/latest/user-guide/concepts/environments.html) from the `conda` package manager ([installation
+instructions](https://docs.conda.io/en/latest/miniconda.html)). Detailed instructions on how to use conda
 environments can be found in their [documentation](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html).
 
 ### Running a specific conversion
@@ -30,10 +30,10 @@ python convert_session.py
 ```
 
 ## Installation from GitHub
-Another option is to install the package directly from GitHub. This option has the advantage that the source code 
-can be modified if you need to amend some of the code we originally provided to adapt to future experimental 
-differences. To install the conversion from GitHub you will need to use `git` ([installation instructions] (https://github.com/git-guides/install-git)). 
-We also recommend the installation of `conda` ([installation instructions](https://docs.conda.io/en/latest/miniconda.html)) as it contains all the required 
+Another option is to install the package directly from GitHub. This option has the advantage that the source code
+can be modified if you need to amend some of the code we originally provided to adapt to future experimental
+differences. To install the conversion from GitHub you will need to use `git` ([installation instructions] (https://github.com/git-guides/install-git)).
+We also recommend the installation of `conda` ([installation instructions](https://docs.conda.io/en/latest/miniconda.html)) as it contains all the required
 machinery in a single and simple install.
 
 From a terminal (note that conda should install one in your system) you can do the following:
@@ -47,7 +47,7 @@ conda activate hnasko-lab-to-nwb-env
 
 This creates a [conda environment](https://docs.conda.io/projects/conda/en/latest/user-guide/concepts/environments.html) which isolates the conversion code from your system libraries.  We recommend that you run all your conversion related tasks and analysis from the created environment in order to minimize issues related to package dependencies.
 
-Alternatively, if you want to avoid conda altogether (for example if you use another virtual environment tool) you 
+Alternatively, if you want to avoid conda altogether (for example if you use another virtual environment tool) you
 can install the repository with the following commands using only pip:
 
 ```
@@ -94,11 +94,11 @@ Each conversion is organized in a directory of its own in the `src` directory:
 
         └── __init__.py
 
-For example, for the conversion `embargo_2025` you can find a directory located in `src/hnasko-lab-to-nwb/embargo_2025`. 
+For example, for the conversion `embargo_2025` you can find a directory located in `src/hnasko-lab-to-nwb/embargo_2025`.
 Inside each conversion directory you can find the following files:
 
 
-* `convert_sesion.py`: this script defines the function to convert one full session of the conversion. 
+* `convert_sesion.py`: this script defines the function to convert one full session of the conversion.
 * `metadata.yml`: metadata in yaml format for this specific conversion.
 * `behaviorinterface.py`: the behavior interface. Usually ad-hoc for each conversion.
 * `nwbconverter.py`: the place where the `NWBConverter` class is defined.

pyproject.toml

@@ -83,4 +83,3 @@ fixable = ["ALL"]
 [tool.ruff.lint.isort]
 relative-imports-order = "closest-to-furthest"
 known-first-party = ["neuroconv"]
-

src/hnasko_lab_to_nwb/embargo_2025/__init__.py

@@ -1,2 +0,0 @@
-from .behaviorinterface import Embargo2025BehaviorInterface
-from .nwbconverter import Embargo2025NWBConverter

src/hnasko_lab_to_nwb/embargo_2025/convert_all_sessions.py

@@ -1,9 +1,10 @@
 """Primary script to run to convert all sessions in a dataset using session_to_nwb."""
-from pathlib import Path
-from typing import Union
+import traceback
 from concurrent.futures import ProcessPoolExecutor, as_completed
+from pathlib import Path
 from pprint import pformat
-import traceback
+from typing import Union
+
 from tqdm import tqdm
 
 from .embargo_2025_convert_session import session_to_nwb
@@ -39,7 +40,7 @@ def dataset_to_nwb(
         for session_to_nwb_kwargs in session_to_nwb_kwargs_per_session:
             session_to_nwb_kwargs["output_dir_path"] = output_dir_path
             session_to_nwb_kwargs["verbose"] = verbose
-            exception_file_path = data_dir_path / f"ERROR_<nwbfile_name>.txt" # Add error file path here
+            exception_file_path = data_dir_path / f"ERROR_<nwbfile_name>.txt"  # Add error file path here
             futures.append(
                 executor.submit(
                     safe_session_to_nwb,
@@ -86,11 +87,11 @@ def get_session_to_nwb_kwargs_per_session(
     list[dict[str, Any]]
         A list of dictionaries containing the kwargs for session_to_nwb for each session.
     """
-     #####
-     # # Implement this function to return the kwargs for session_to_nwb for each session
-     # This can be a specific list with hard-coded sessions, a path expansion or any conversion specific logic that you might need
-     #####
-    raise NotImplementedError 
+    #####
+    # # Implement this function to return the kwargs for session_to_nwb for each session
+    # This can be a specific list with hard-coded sessions, a path expansion or any conversion specific logic that you might need
+    #####
+    raise NotImplementedError
 
 
 if __name__ == "__main__":

src/hnasko_lab_to_nwb/embargo_2025/convert_session.py

@@ -1,70 +1,101 @@
 """Primary script to run to convert an entire session for of data using the NWBConverter."""
+
 from pathlib import Path
 from typing import Union
-import datetime
-from zoneinfo import ZoneInfo
-
-from neuroconv.utils import load_dict_from_file, dict_deep_update
 
-from .embargo_2025 import Embargo2025NWBConverter
+from nwbconverter import Embargo2025NWBConverter
 
+from neuroconv.utils import dict_deep_update, load_dict_from_file
 
-def session_to_nwb(data_dir_path: Union[str, Path], output_dir_path: Union[str, Path], stub_test: bool = False):
 
-    data_dir_path = Path(data_dir_path)
+def session_to_nwb(
+    output_dir_path: Union[str, Path],
+    subject_id: str,
+    session_id: str,
+    tdt_folder_path: Union[str, Path],
+    protocol_type: 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)
 
-    session_id = "subject_identifier_usually"
-    nwbfile_path = output_dir_path / f"{session_id}.nwb"
-
+    nwbfile_path = output_dir_path / f"sub-{subject_id}_ses-{session_id}.nwb"
+
+    valid_protocols = {"Varying durations", "Varying frequencies", "Shocks"}
+    if protocol_type not in valid_protocols:
+        raise ValueError(f"Invalid protocol_type: {protocol_type}. Must be one of {valid_protocols}.")
+    if protocol_type == "Varying durations":
+        session_description = (
+            "The subject is placed in a plastic tub and is recorded for 3.5 minutes. "
+            "The subject receives a 40 Hz stimulation at various durations (i.e. 250ms, 1s and 4s) "
+            "5 times for each duration) with an inter-stimulus interval (ISI) of 10s. "
+        )
+    elif protocol_type == "Varying frequencies":
+        session_description = (
+            "The subject is placed in a plastic tub and undergoes 3 recording sessions corresponding "
+            "to a fixed duration of stimulation (i.e., 250ms, 1s, and 4s). Each session lasted 8 minutes. "
+            "The subject receives optogenetic stimulation at varying frequencies "
+            "(5 Hz, 10 Hz , 20 Hz and 40 Hz) 5 times for each duration with an ISI of 10s. "
+        )
+    elif protocol_type == "Shocks":
+        session_description = (
+            "The subject is placed in a shock chamber and recorded for 6 minutes. "
+            "Uncued shocks (0.3 mA) at various durations (250ms, 1s and 4s, 5 times for each duration) "
+            "are delivered in a randomized order and ISI."
+        )
     source_data = dict()
     conversion_options = dict()
 
-    # Add Recording
-    source_data.update(dict(Recording=dict()))
-    conversion_options.update(dict(Recording=dict(stub_test=stub_test)))
-
-    # Add Sorting
-    source_data.update(dict(Sorting=dict()))
-    conversion_options.update(dict(Sorting=dict()))
+    # Add FiberPhotometry
 
-    # Add Behavior
-    source_data.update(dict(Behavior=dict()))
-    conversion_options.update(dict(Behavior=dict()))
+    source_data.update(dict(FiberPhotometry=dict(folder_path=tdt_folder_path)))
+    conversion_options.update(dict(FiberPhotometry=dict()))
 
     converter = Embargo2025NWBConverter(source_data=source_data)
 
-    # Add datetime to conversion
-    metadata = converter.get_metadata()
-    date = datetime.datetime(year=2020, month=1, day=1, tzinfo=ZoneInfo("US/Eastern"))
-    metadata["NWBFile"]["session_start_time"] = date
-
     # Update default metadata with the editable in the corresponding yaml file
-    editable_metadata_path = Path(__file__).parent / "embargo_2025_metadata.yaml"
+    metadata = converter.get_metadata()
+    editable_metadata_path = Path(__file__).parent / "metadata.yaml"
     editable_metadata = load_dict_from_file(editable_metadata_path)
     metadata = dict_deep_update(metadata, editable_metadata)
 
-    metadata["Subject"]["subject_id"] = "a_subject_id"  # Modify here or in the yaml file
+    metadata["Subject"]["subject_id"] = subject_id
+    metadata["NWBFile"]["session_id"] = session_id
+    metadata["NWBFile"]["session_description"] = session_description
 
     # Run conversion
-    converter.run_conversion(metadata=metadata, nwbfile_path=nwbfile_path, conversion_options=conversion_options)
+    converter.run_conversion(
+        metadata=metadata, nwbfile_path=nwbfile_path, conversion_options=conversion_options, overwrite=True
+    )
 
 
 if __name__ == "__main__":
 
     # Parameters for conversion
-    data_dir_path = Path("/Directory/With/Raw/Formats/")
-    output_dir_path = Path("~/conversion_nwb/")
-    stub_test = False
-
-<<<<<<< HEAD:hnasko-lab-to-nwb/src/hnasko_lab_to_nwb/embargo_2025/convert_session.py
-    session_to_nwb(data_dir_path=data_dir_path, output_dir_path=output_dir_path, stub_test=stub_test)
-=======
-    session_to_nwb(data_dir_path=data_dir_path,
-                    output_dir_path=output_dir_path,
-                    stub_test=stub_test,
-                    )
->>>>>>> main:hnasko-lab-to-nwb/src/hnasko_lab_to_nwb/embargo_2025/embargo_2025_convert_session.py
+    data_dir_path = Path("D:/Hnasko-CN-data-share/SN pan GABA recordings/PPN/")
+    output_dir_path = Path("D:/hnasko_lab_conversion_nwb")
+    from neuroconv.tools.path_expansion import LocalPathExpander
+
+    data_dir_path = "D:/Hnasko-CN-data-share/SN pan GABA recordings/PPN/"
+    # Specify source data
+    source_data_spec = {
+        "FiberPhotometry": {
+            "base_directory": data_dir_path + "Fiber photometry_TDT",
+            "folder_path": "{protocol_type}/{subject_id}-{session_id}",
+        }
+    }
+    # Instantiate LocalPathExpander
+    path_expander = LocalPathExpander()
+    # Expand paths and extract metadata
+    metadata_list = path_expander.expand_paths(source_data_spec)
+    for metadata in metadata_list:
+        session_to_nwb(
+            output_dir_path=output_dir_path,
+            subject_id=metadata["metadata"]["Subject"]["subject_id"],
+            session_id=metadata["metadata"]["NWBFile"]["session_id"],
+            tdt_folder_path=metadata["source_data"]["FiberPhotometry"]["folder_path"],
+            protocol_type=metadata["metadata"]["extras"]["protocol_type"],
+            stub_test=True,
+        )