Merge pull request #73 from tdincer/intan

Intan loader

Author: JaerongA

element_interface/intan_loader.py

@@ -0,0 +1,287 @@
+import numpy as np
+import os, sys, struct
+from pathlib import Path
+import matplotlib.pyplot as plt
+
+
+def read_qstring(fid):
+    """Read Qt style QString.
+
+    The first 32-bit unsigned number indicates the length of the string (in bytes).
+    If this number equals 0xFFFFFFFF, the string is null.
+
+    Strings are stored as unicode.
+    """
+
+    (length,) = struct.unpack("<I", fid.read(4))
+    if length == int("ffffffff", 16):
+        return ""
+
+    if length > (os.fstat(fid.fileno()).st_size - fid.tell() + 1):
+        print(length)
+        raise Exception("Length too long.")
+
+    # convert length from bytes to 16-bit Unicode words
+    length = int(length / 2)
+
+    data = []
+    for i in range(0, length):
+        (c,) = struct.unpack("<H", fid.read(2))
+        data.append(c)
+
+    if sys.version_info >= (3, 0):
+        a = "".join([chr(c) for c in data])
+    else:
+        a = "".join([unichr(c) for c in data])
+
+    return a
+
+
+def read_header(fid):
+    """Reads the Intan File Format header from the given file."""
+
+    # Check 'magic number' at beginning of file to make sure this is an Intan
+    # Technologies RHD2000 data file.
+    (magic_number,) = struct.unpack("<I", fid.read(4))
+
+    if magic_number != int("0xD69127AC", 16):
+        raise Exception("Unrecognized file type.")
+
+    header = {}
+    # Read version number.
+    version = {}
+    (version["major"], version["minor"]) = struct.unpack("<hh", fid.read(4))
+    header["version"] = version
+
+    print("")
+    print(
+        "Reading Intan Technologies RHS2000 Data File, Version {}.{}".format(
+            version["major"], version["minor"]
+        )
+    )
+    print("")
+
+    # Read information of sampling rate and amplifier frequency settings.
+    (header["sample_rate"],) = struct.unpack("<f", fid.read(4))
+    (
+        header["dsp_enabled"],
+        header["actual_dsp_cutoff_frequency"],
+        header["actual_lower_bandwidth"],
+        header["actual_lower_settle_bandwidth"],
+        header["actual_upper_bandwidth"],
+        header["desired_dsp_cutoff_frequency"],
+        header["desired_lower_bandwidth"],
+        header["desired_lower_settle_bandwidth"],
+        header["desired_upper_bandwidth"],
+    ) = struct.unpack("<hffffffff", fid.read(34))
+
+    # This tells us if a software 50/60 Hz notch filter was enabled during
+    # the data acquisition.
+    (notch_filter_mode,) = struct.unpack("<h", fid.read(2))
+    header["notch_filter_frequency"] = 0
+    if notch_filter_mode == 1:
+        header["notch_filter_frequency"] = 50
+    elif notch_filter_mode == 2:
+        header["notch_filter_frequency"] = 60
+
+    (
+        header["desired_impedance_test_frequency"],
+        header["actual_impedance_test_frequency"],
+    ) = struct.unpack("<ff", fid.read(8))
+    (header["amp_settle_mode"], header["charge_recovery_mode"]) = struct.unpack(
+        "<hh", fid.read(4)
+    )
+
+    frequency_parameters = {}
+    frequency_parameters["amplifier_sample_rate"] = header["sample_rate"]
+    frequency_parameters["board_adc_sample_rate"] = header["sample_rate"]
+    frequency_parameters["board_dig_in_sample_rate"] = header["sample_rate"]
+    frequency_parameters["desired_dsp_cutoff_frequency"] = header[
+        "desired_dsp_cutoff_frequency"
+    ]
+    frequency_parameters["actual_dsp_cutoff_frequency"] = header[
+        "actual_dsp_cutoff_frequency"
+    ]
+    frequency_parameters["dsp_enabled"] = header["dsp_enabled"]
+    frequency_parameters["desired_lower_bandwidth"] = header["desired_lower_bandwidth"]
+    frequency_parameters["desired_lower_settle_bandwidth"] = header[
+        "desired_lower_settle_bandwidth"
+    ]
+    frequency_parameters["actual_lower_bandwidth"] = header["actual_lower_bandwidth"]
+    frequency_parameters["actual_lower_settle_bandwidth"] = header[
+        "actual_lower_settle_bandwidth"
+    ]
+    frequency_parameters["desired_upper_bandwidth"] = header["desired_upper_bandwidth"]
+    frequency_parameters["actual_upper_bandwidth"] = header["actual_upper_bandwidth"]
+    frequency_parameters["notch_filter_frequency"] = header["notch_filter_frequency"]
+    frequency_parameters["desired_impedance_test_frequency"] = header[
+        "desired_impedance_test_frequency"
+    ]
+    frequency_parameters["actual_impedance_test_frequency"] = header[
+        "actual_impedance_test_frequency"
+    ]
+
+    header["frequency_parameters"] = frequency_parameters
+
+    (
+        header["stim_step_size"],
+        header["recovery_current_limit"],
+        header["recovery_target_voltage"],
+    ) = struct.unpack("fff", fid.read(12))
+
+    note1 = read_qstring(fid)
+    note2 = read_qstring(fid)
+    note3 = read_qstring(fid)
+    header["notes"] = {"note1": note1, "note2": note2, "note3": note3}
+
+    (header["dc_amplifier_data_saved"], header["eval_board_mode"]) = struct.unpack(
+        "<hh", fid.read(4)
+    )
+
+    header["ref_channel_name"] = read_qstring(fid)
+
+    # Create structure arrays for each type of data channel.
+    header["spike_triggers"] = []
+    header["amplifier_channels"] = []
+    header["board_adc_channels"] = []
+    header["board_dac_channels"] = []
+    header["board_dig_in_channels"] = []
+    header["board_dig_out_channels"] = []
+
+    # Read signal summary from data file header.
+    (number_of_signal_groups,) = struct.unpack("<h", fid.read(2))
+    print("n signal groups {}".format(number_of_signal_groups))
+
+    for signal_group in range(1, number_of_signal_groups + 1):
+        signal_group_name = read_qstring(fid)
+        signal_group_prefix = read_qstring(fid)
+        (
+            signal_group_enabled,
+            signal_group_num_channels,
+            signal_group_num_amp_channels,
+        ) = struct.unpack("<hhh", fid.read(6))
+
+        if (signal_group_num_channels > 0) and (signal_group_enabled > 0):
+            for signal_channel in range(0, signal_group_num_channels):
+                new_channel = {
+                    "port_name": signal_group_name,
+                    "port_prefix": signal_group_prefix,
+                    "port_number": signal_group,
+                }
+                new_channel["native_channel_name"] = read_qstring(fid)
+                new_channel["custom_channel_name"] = read_qstring(fid)
+                (
+                    new_channel["native_order"],
+                    new_channel["custom_order"],
+                    signal_type,
+                    channel_enabled,
+                    new_channel["chip_channel"],
+                    command_stream,
+                    new_channel["board_stream"],
+                ) = struct.unpack(
+                    "<hhhhhhh", fid.read(14)
+                )  # ignore command_stream
+                new_trigger_channel = {}
+                (
+                    new_trigger_channel["voltage_trigger_mode"],
+                    new_trigger_channel["voltage_threshold"],
+                    new_trigger_channel["digital_trigger_channel"],
+                    new_trigger_channel["digital_edge_polarity"],
+                ) = struct.unpack("<hhhh", fid.read(8))
+                (
+                    new_channel["electrode_impedance_magnitude"],
+                    new_channel["electrode_impedance_phase"],
+                ) = struct.unpack("<ff", fid.read(8))
+
+                if channel_enabled:
+                    if signal_type == 0:
+                        header["amplifier_channels"].append(new_channel)
+                        header["spike_triggers"].append(new_trigger_channel)
+                    elif signal_type == 1:
+                        raise Exception("Wrong signal type for the rhs format")
+                        # header['aux_input_channels'].append(new_channel)
+                    elif signal_type == 2:
+                        raise Exception("Wrong signal type for the rhs format")
+                        # header['supply_voltage_channels'].append(new_channel)
+                    elif signal_type == 3:
+                        header["board_adc_channels"].append(new_channel)
+                    elif signal_type == 4:
+                        header["board_dac_channels"].append(new_channel)
+                    elif signal_type == 5:
+                        header["board_dig_in_channels"].append(new_channel)
+                    elif signal_type == 6:
+                        header["board_dig_out_channels"].append(new_channel)
+                    else:
+                        raise Exception("Unknown channel type.")
+
+    # Summarize contents of data file.
+    header["num_amplifier_channels"] = len(header["amplifier_channels"])
+    header["num_board_adc_channels"] = len(header["board_adc_channels"])
+    header["num_board_dac_channels"] = len(header["board_dac_channels"])
+    header["num_board_dig_in_channels"] = len(header["board_dig_in_channels"])
+    header["num_board_dig_out_channels"] = len(header["board_dig_out_channels"])
+
+    return header
+
+
+def load_rhs(folder: str, file_expr: str):
+    """Load rhs data
+
+    Example:
+        # Read data
+        >>> rhs_data = load_rhs("/home/inbox/organoids21/032520_US_885kHz_sham", file_expr="amp*dat")
+
+        # Plot data
+        >>> 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): regex pattern of the file names to be read.
+
+    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.
+    """
+
+    header_filepath = next(Path(folder).glob("info.rhs"))
+    with open(header_filepath, "rb") as fid:
+        header = read_header(fid)
+
+    time_file = next(Path(folder).glob("time.dat"))
+
+    timestamps = (
+        np.memmap(time_file, dtype=np.int32)
+        / header["frequency_parameters"]["amplifier_sample_rate"]
+    )
+
+    rhs_data = dict(header=header, timestamps=timestamps, recordings={})
+
+    file_paths = Path(folder).glob(file_expr)
+    file_paths = [x for x in file_paths if x.as_posix() != "time.dat"]
+
+    for file_path in file_paths:
+        file_path = file_path.as_posix()
+        if "amp" in file_path:
+            signal = np.memmap(file_path, dtype=np.int16)
+            signal = signal * 0.195  # Convert to microvolts
+        elif "board-ANALOG-IN" in file_path or "board-ANALOG-OUT" in file_path:
+            signal = np.memmap(file_path, dtype=np.uint16)
+            signal = (signal - 32768) * 0.0003125  # Convert to volts
+        elif "dc-" in file_path:
+            signal = np.memmap(file_path, dtype=np.uint16)
+            signal = (signal - 512) * 19.23  # Convert to milivolts
+        elif "board-DIGITAL-IN" in file_path or "board-DIGITAL-OUT" in file_path:
+            signal = np.memmap(file_path, dtype=np.uint16)
+        elif "stim-" in file_path:
+            data = np.memmap(file_path, dtype=np.uint16)
+            i = np.bitwise_and(data, 255) * header["stim_step_size"]
+            sign = (128 - np.bitwise_and(data, 255)) / 128
+            signal = i * sign
+        rhs_data["recordings"][Path(file_path).relative_to(folder).stem] = signal
+
+    return rhs_data