Merge pull request #7 from catalystneuro/add_visual_stimulus_to_kim

Add visual stimulus to Kim lab II

src/kim_lab_to_nwb/stimuli.py

@@ -0,0 +1,68 @@
+from typing import Optional
+
+import numpy as np
+from neuroconv.basedatainterface import BaseDataInterface
+from neuroconv.utils import FilePathType, DeepDict
+from pynwb import NWBFile
+from pynwb.image import ImageSeries
+from pymatreader import read_mat
+
+
+class KimLabStimuliInterface(BaseDataInterface):
+    """Data interface for Kim Lab visual stimuli data."""
+
+    def __init__(self, file_path: FilePathType, sampling_frequency: float = 30.0, verbose: bool = False):
+        """Initialize the stimuli interface.
+        
+        Parameters
+        ----------
+        file_path : FilePathType
+            Path to the visual_stimuli.mat file
+        sampling_frequency : float
+            Sampling frequency in Hz
+        verbose : bool, default: False
+            Whether to print progress information
+        """
+        super().__init__(file_path=file_path)
+        self.file_path = file_path
+        self.sampling_frequency = sampling_frequency
+        self.verbose = verbose
+
+    def get_metadata(self) -> dict:
+        """Get metadata for the visual stimuli.
+        
+        Returns
+        -------
+        dict
+            The metadata dictionary
+        """
+        metadata = super().get_metadata()
+        return metadata
+
+    def add_to_nwbfile(self, nwbfile: NWBFile, metadata: Optional[DeepDict] = None):
+        """Add the visual stimuli data to the NWB file.
+        
+        Parameters
+        ----------
+        nwbfile : NWBFile
+            The NWB file to add the stimuli to
+        metadata : Optional[DeepDict], optional
+            Metadata dictionary
+        """
+        # Load the visual stimuli data
+        data = read_mat(self.file_path)["visual_stimuli"]
+
+        # Create an image series for the visual stimuli
+        # The data shape is (16, 80, 495000) where:
+        # - First two dimensions (16, 80) are the stimulus image at each timepoint
+        # - Last dimension (495000) is time
+        image_series = ImageSeries(
+            name="VisualStimuli",
+            data=np.moveaxis(data, -1, 0),  # Move time dimension to first axis (495000, 16, 80)
+            unit="n.a.",
+            rate=self.sampling_frequency,
+            description="Visual stimuli presented during the experiment"
+        )
+
+        # Add to the NWB file's stimulus presentation
+        nwbfile.add_stimulus(image_series)