Add Intan loader

CHANGELOG.md

@@ -3,6 +3,10 @@
 Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
 [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) convention.
 
+## [0.6.0] - 2023-02-13
+
++ Add - Intan loader
+
 ## [0.5.0] - 2023-01-09
 
 + Remove - `recursive_search` function
@@ -53,6 +57,7 @@ Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
 
 + Add - Readers for: `ScanImage`, `Suite2p`, `CaImAn`.
 
+[0.6.0]: https://github.com/datajoint/element-interface/releases/tag/0.6.0
 [0.5.0]: https://github.com/datajoint/element-interface/releases/tag/0.5.0
 [0.4.2]: https://github.com/datajoint/element-interface/releases/tag/0.4.2
 [0.4.1]: https://github.com/datajoint/element-interface/releases/tag/0.4.1

element_interface/rhs_perchannel_loader.py

@@ -0,0 +1,85 @@
+import numpy as np
+from pathlib import Path
+from intanrhsreader import read_header
+
+
+def load_rhs(folder: str, file_expr: str = "*"):
+    """Load rhs data
+
+    Data type and coversions are based on https://intantech.com/files/Intan_RHS2000_data_file_formats.pdf.
+
+    Example:
+        # Read data
+        >>> rhs_data = load_rhs("/home/inbox/organoids21/032520_US_885kHz_sham", file_expr="amp*dat")
+
+        # Plot data
+        >>> import matplotlib.pyplot as plt
+        >>> plt.plot(rhs_data["time"], rhs_data["recordings"]["amp-B-000.dat"])
+        >>> plt.xlabel("Time (s)")
+        >>> plt.ylabel("Reading")
+        >>> plt.show()
+
+    Args:
+        folder (str): Folder that contains info.rhs, time.dat, and *.dat files
+        file_expr (str): pattern matching of file names to be read. Defaults to "*" (read all files).
+
+    Returns:
+        rhs_data (dict): RHS data.
+            rhs_data["header"] (dict): Header.
+            rhs_data["recordings"] (dict): Readings from various files
+            rhs_data["timestamps"] (np.array_like): Relative timestamps in seconds.
+    """
+
+    rhs_data = {}
+
+    # Get header
+    header_filepath = next(Path(folder).glob("info.rhs"))
+    with open(header_filepath, "rb") as fid:
+        rhs_data["header"] = read_header(fid)
+
+    # Get timestamps
+    time_file = next(Path(folder).glob("time.dat"))
+
+    rhs_data["timestamps"] = (
+        np.memmap(time_file, dtype=np.int32)
+        / rhs_data["header"]["frequency_parameters"]["amplifier_sample_rate"]
+    )
+
+    # Get data files
+    file_paths = Path(folder).glob(file_expr)
+
+    exclude_list = ["time", "info", "Zone.Identifier"]
+
+    file_paths = [
+        file
+        for file in file_paths
+        if not any(string in file.as_posix() for string in exclude_list)
+    ]
+
+    # Get recording data
+    rhs_data["recordings"] = {}
+
+    for file_path in sorted(file_paths):
+        signal_type = file_path.stem.split("-")[0]
+
+        if signal_type == "amp":
+            signal = np.memmap(file_path, dtype=np.int16)
+            signal = signal * 0.195  # Convert to microvolts
+
+        elif signal_type == "board":
+            signal = np.memmap(file_path, dtype=np.uint16)
+            signal = (signal - 32768) * 0.0003125  # Convert to volts
+
+        elif signal_type == "dc":
+            signal = np.memmap(file_path, dtype=np.uint16)
+            signal = (signal - 512) * 19.23  # Convert to milivolts
+
+        elif signal_type == "stim":
+            signal = np.memmap(file_path, dtype=np.uint16)
+            # convert the signal from 9-bit one's complement to standard encoding
+            current = np.bitwise_and(signal, 255) * rhs_data["header"]["stim_step_size"]
+            sign = 1 - np.bitwise_and(signal, 256) // 128
+            signal = current * sign
+
+        rhs_data["recordings"][file_path.stem] = signal
+    return rhs_data

element_interface/version.py

@@ -1,3 +1,3 @@
 """Package metadata"""
 
-__version__ = "0.5.0"
+__version__ = "0.6.0"