Merge branch 'main' into add_fox_lab_to_nwb

pyproject.toml

@@ -17,14 +17,16 @@ classifiers = [
 dependencies = [
   "neuroconv[video]",
   "nwbinspector",
-  #"roiextractors",
+  "roiextractors",
+  "tifffile",
+  "pymatreader",
 ]
 
 [project.urls]
 Repository="https://github.com/catalystneuro/cohen-lab-to-nwb"
 
 [build-system]
-requires = ["setuptools>=58.0.0", "wheel"]
+requires = ["setuptools>=64.0.0"]
 build-backend = "setuptools.build_meta"
 
 [tool.setuptools]

src/dickerson_lab_to_nwb/paye_conversion.py

@@ -10,7 +10,7 @@
 from roiextractors.extraction_tools import PathType
 from roiextractors.imagingextractor import ImagingExtractor
 
-from ..utils import match_paths
+from ..cohen_u01_utils.utils import match_paths
 
 
 def extract_experiment_details(xml_file_path: str):

src/kim_lab_to_nwb/conversion_notes.md

@@ -0,0 +1,13 @@
+
+
+## Structure of the matlab file
+
+
+# data(1,:) is time
+# data(2,:) is left wingbeat
+# data(3,:) is left-right wingbeat
+# data(4,:) is x-position of the visual pattern
+# data(5,:) is y-position of the visual pattern
+# data(6,:) is 2-photon frame synchronization signal (1 pulse corresponds to 1 frame)
+# data(7,:) is behavior camera signal (1 pulse corresponds to 1 frame)
+# data(8,:) indicates the start of a stimulus (it is empty in this example)

src/kim_lab_to_nwb/kim_conversion.py

@@ -0,0 +1,196 @@
+from datetime import datetime
+from pathlib import Path
+import uuid
+
+import numpy as np
+from neuroconv.tools.nwb_helpers import get_default_backend_configuration, configure_backend
+from neuroconv.datainterfaces import VideoInterface
+from pynwb import NWBFile, TimeSeries, NWBHDF5IO
+from pynwb.file import Subject
+from pymatreader import read_mat
+
+from kim_lab_to_nwb.ophys import MultiTiffMultiPageTiffImagingInterface
+from cohen_u01_nwb_conversion_utils.utils import detect_threshold_crossings
+
+
+def convert_session_to_nwb(
+    matlab_data_file_path: str | Path,
+    video_file_path: str | Path,
+    experiment_info_file_path: str | Path,
+    tiff_folder_path: str | Path,
+    output_dir: str | Path,
+    verbose: bool = False,
+) -> Path:
+    """
+    Convert a single experimental session from Kim Lab data to NWB format.
+
+    Parameters
+    ----------
+    matlab_data_file_path : str or Path
+        Path to the MATLAB data file
+    video_file_path : str or Path
+        Path to the video file
+    experiment_info_file_path : str or Path
+        Path to the experiment info file
+    tiff_folder_path : str or Path
+        Path to the folder containing TIFF files
+    output_dir : str or Path
+        Directory where the NWB file will be saved
+    verbose : bool, optional
+        Whether to print progress information, by default False
+    
+    Returns
+    -------
+    Path
+        Path to the created NWB file
+    
+    Raises
+    ------
+    FileNotFoundError
+        If any of the required input files are not found
+    """
+    # Convert all paths to Path objects
+    matlab_data_file_path = Path(matlab_data_file_path)
+    video_file_path = Path(video_file_path)
+    experiment_info_file_path = Path(experiment_info_file_path)
+    tiff_folder_path = Path(tiff_folder_path)
+    output_dir = Path(output_dir)
+
+    # Validate input files exist
+    if not matlab_data_file_path.is_file():
+        raise FileNotFoundError(f"Matlab data file not found at {matlab_data_file_path}")
+    if not video_file_path.is_file():
+        raise FileNotFoundError(f"Video file not found at {video_file_path}")
+    if not experiment_info_file_path.is_file():
+        raise FileNotFoundError(f"Experiment info file not found at {experiment_info_file_path}")
+    if not tiff_folder_path.exists():
+        raise FileNotFoundError(f"Tiff folder not found at {tiff_folder_path}")
+
+    # Load data
+    mat_data = read_mat(matlab_data_file_path)
+    data = mat_data["data"]
+    protocol = mat_data["protocol"]
+
+    experiment_info = read_mat(experiment_info_file_path)
+    age = experiment_info["age"]
+    genotype = experiment_info["cross"]
+
+    # Extract session ID from matlab file path
+    session_id = matlab_data_file_path.stem.split('data_')[1]
+    if verbose:
+        print(f"Processing {session_id=} ({age=}, {genotype=})")
+
+    session_start_time = datetime.strptime(session_id[:8], '%Y%m%d')
+    if verbose:
+        print(f"Session start time: {session_start_time}")
+
+    # Unpack data
+    time = data[0]
+    left_wingbeat = data[1]
+    left_right_wingbeat = data[2]
+    x_position = data[3]
+    y_position = data[4]
+    two_photon_frame_sync = data[5]
+    behavior_camera_sync = data[6]
+    stimulus_start = data[7]
+
+    # Create NWB file
+    nwbfile = NWBFile(
+        session_description=f"protocol: {protocol}",
+        identifier=str(uuid.uuid4()),
+        session_start_time=session_start_time,
+        session_id=session_id,
+    )
+
+    # Set up imaging interface
+    ophys_interface = MultiTiffMultiPageTiffImagingInterface(
+        tiff_folder_path,
+        pattern=session_id + "_{frame:05d}.tif",
+        sampling_frequency=30.0,
+        verbose=verbose
+    )
+
+    aligned_timestamps = time[detect_threshold_crossings(two_photon_frame_sync, 0.5)]
+    aligned_timestamps = aligned_timestamps[:ophys_interface.imaging_extractor.get_num_frames()]
+    ophys_interface.set_aligned_timestamps(aligned_timestamps=aligned_timestamps)
+    ophys_interface.add_to_nwbfile(nwbfile, metadata=dict())
+
+    # Set up video interface
+    video_interface = VideoInterface(
+        file_paths=[video_file_path],
+    )
+
+    video_timestamps = time[detect_threshold_crossings(behavior_camera_sync, 0.5)]
+    video_interface.set_aligned_timestamps([video_timestamps])
+    video_interface.add_to_nwbfile(nwbfile, metadata=dict())
+
+    # Add subject information
+    nwbfile.subject = Subject(
+        subject_id=session_id,
+        genotype=genotype,
+        age=f"P{age}D",
+    )
+
+    # Add timeseries data
+    timeseries_wingbeat = TimeSeries(
+        name="wingbeat",
+        data=left_wingbeat,
+        unit="n.a.",
+        timestamps=time,
+        description="wingbeat",
+    )
+    nwbfile.add_acquisition(timeseries_wingbeat)
+
+    timeseries_left_right_wingbeat = TimeSeries(
+        name="left_right_wingbeat",
+        data=left_right_wingbeat,
+        unit="n.a.",
+        timestamps=timeseries_wingbeat,
+        description="left-right wingbeat",
+    )
+    nwbfile.add_acquisition(timeseries_left_right_wingbeat)
+
+    timeseries_x_position = TimeSeries(
+        name="stimulus_position",
+        data=np.c_[x_position, y_position],
+        unit="n.a.",
+        timestamps=timeseries_wingbeat,
+        description="position of the visual pattern",
+    )
+    nwbfile.add_acquisition(timeseries_x_position)
+
+    # Configure and save the NWB file
+    backend_configuration = get_default_backend_configuration(nwbfile, backend="hdf5")
+    configure_backend(nwbfile=nwbfile, backend_configuration=backend_configuration)
+
+    nwbfile_path = output_dir / f"{session_id}.nwb"
+    with NWBHDF5IO(nwbfile_path, mode="w") as io:
+        io.write(nwbfile)
+
+    if verbose:
+        print(f"Created NWB file: {nwbfile_path}")
+
+    return nwbfile_path
+
+
+if __name__ == "__main__":
+    # Example usage with the original paths
+    data_folder_path = Path("/Users/heberto/project_data/Sample data-selected/Kim Lab")
+
+    # Define input paths
+    matlab_data_file_path = data_folder_path / "raw data" / "data_20240108b_00003.mat"
+    video_file_path = data_folder_path / "raw data" / "20240108b_00003.avi"
+    experiment_info_file_path = data_folder_path / "raw data" / "exp_info.mat"
+    tiff_folder_path = data_folder_path / "raw data"
+    output_dir = data_folder_path / "nwb"
+
+    output_dir.mkdir(exist_ok=True, parents=True)
+
+    nwbfile_path = convert_session_to_nwb(
+        matlab_data_file_path=matlab_data_file_path,
+        video_file_path=video_file_path,
+        experiment_info_file_path=experiment_info_file_path,
+        tiff_folder_path=tiff_folder_path,
+        output_dir=output_dir,
+        verbose=True  # Enable verbose output for demonstration
+    )

src/kim_lab/ophys.py → src/kim_lab_to_nwb/ophys.py

@@ -8,7 +8,7 @@
 from tifffile import TiffFile
 from tqdm import tqdm
 
-from ..utils import match_paths
+from cohen_u01_nwb_conversion_utils.utils import match_paths
 
 
 class MultiTiffMultiPageTiffImagingExtractor(ImagingExtractor):