ensemble-eeg 0.0.1__py3-none-any.whl

ensemble_eeg/brm_to_edf.py

@@ -0,0 +1,373 @@
+import glob
+import os
+import shutil
+import zipfile
+from collections import Counter, namedtuple
+from datetime import datetime, timezone
+
+import defusedxml.ElementTree as ET
+import numpy as np
+
+import src.ensemble_eeg.ensemble_eeg as ensemble_eeg
+
+
+def convert_brm_to_edf(fd, is_fs_64hz=None):
+    """
+    Converts a BRM file to EDF format.
+
+    Parameters:
+        fd (str): The path to the BRM file.
+        is_fs_64hz (bool, optional): Indicates whether the sampling frequency is 64 Hz. Defaults to None.
+
+    Raises:
+        ValueError: If the file is not found.
+
+    Returns:
+        None
+    """
+    filename = os.path.basename(fd)
+    file_exists = os.path.isfile(fd)
+
+    if file_exists:
+        file_dir = os.path.dirname(fd)
+        tmp_dir = os.path.join(file_dir, "tmp")
+        if os.path.isdir(tmp_dir):
+            shutil.rmtree(tmp_dir)
+
+        print(f"{filename}")
+        print("\tUnzipping to temporary directory")
+        with zipfile.ZipFile(fd, "r") as zip_ref:
+            zip_ref.extractall(tmp_dir)
+
+        index_xml = os.path.join(tmp_dir, "BRM_Index.xml")
+        index = parse_xml(index_xml)
+        device_xml = os.path.join(tmp_dir, "Device.xml")
+        device = parse_xml(device_xml)
+
+        dat_files_left = []
+        dat_files_right = []
+
+        if is_fs_64hz is None:
+            is_fs_64hz = (
+                input("is the sampling " "frequency 64 Hz? [y/N]: ").lower() == "y"
+            )
+
+        if is_fs_64hz:
+            dat_files_left = sorted(
+                glob.glob(os.path.join(tmp_dir, "DATA_RAW_EEG_LEFT*.dat"))
+            )
+            dat_files_right = sorted(
+                glob.glob(os.path.join(tmp_dir, "DATA_RAW_EEG_RIGHT*.dat"))
+            )
+
+        else:
+            dat_files_left = sorted(
+                glob.glob(os.path.join(tmp_dir, "DATA_RAW_EEG_ELECTRODE_LEFT*.dat"))
+            )
+            dat_files_right = sorted(
+                glob.glob(os.path.join(tmp_dir, "DATA_RAW_EEG_ELECTRODE_RIGHT*.dat"))
+            )
+
+        n_data_files_left = len(dat_files_left)
+        n_data_files_right = len(dat_files_right)
+
+        assert n_data_files_left == n_data_files_right
+
+        for i in range(0, n_data_files_left):
+            both_dat_files = [dat_files_left[i], dat_files_right[i]]
+            data = extract_brm_file(index, device, both_dat_files)
+
+            if i == 0:
+                output_filename = os.path.splitext(fd)[0] + ".edf"
+            else:
+                output_filename = os.path.splitext(fd)[0] + "_" + str(i) + ".edf"
+
+            hdr = prepare_edf_header(data)
+            signal_header = prepare_edf_signal_header(data, device)
+            header = ensemble_eeg.Header(*hdr, signal_header)
+
+            # write header to file
+            print(f"\tprint header to {output_filename}")
+            ensemble_eeg.write_edf_header(output_filename, header)
+
+            # write data to file
+            print(f"\tprint data records to {output_filename}")
+            write_brm_data_to_edf(output_filename, data)
+
+        print("\tremoving temporary directory")
+        shutil.rmtree(tmp_dir)
+    else:
+        raise ValueError("file not found")
+
+
+def parse_xml(xml):
+    """
+    Parse an XML file and return a named tuple representing the parsed XML.
+
+    Parameters:
+        xml (str): The path to the XML file to be parsed.
+
+    Returns:
+        Parsed_XML: A named tuple representing the parsed XML. The fields of the
+            named tuple correspond to the unique XML tags found in the file. If
+            a tag appears only once, the corresponding field of the named tuple
+            will contain the text content of the tag. If a tag appears multiple
+            times, the corresponding field of the named tuple will contain a
+            list of named tuples, each representing one occurrence of the tag.
+            The fields of the nested named tuples correspond to the unique tags
+            found within the repeated tag, and the values of the fields
+            correspond to the text content of the corresponding tags.
+
+    Raises:
+        ValueError: If the specified XML file does not exist.
+
+    Example:
+        >>> parse_xml('data.xml')
+        Parsed_XML(tag_names=['tag1', 'tag2'], tag1='text1', tag2=[Tag2(tag3='text3', tag4='text4')])
+    """
+    file_exists = os.path.isfile(xml)
+
+    if file_exists:
+        tree = ET.parse(xml)
+        root = tree.getroot()
+
+        all_tags = [child.tag for child in root]
+        tag_names = list(Counter(all_tags).keys())
+        tag_dict = list(Counter(all_tags).items())
+
+        Parsed_XML = namedtuple("ParsedXML", tag_names)
+        parsed_xml = []
+        counter = 0
+        for name, vals in tag_dict:
+            if vals == 1:
+                parsed_xml.append(root[counter].text)
+                counter = counter + 1
+            else:
+                parsed_child = []
+                child_elems = root.findall(name)
+                for child_elem in child_elems:
+                    child_elem_tags = [el.tag for el in child_elem]
+                    child_elem_vals = [el.text for el in child_elem]
+                    tup = namedtuple(child_elem.tag, child_elem_tags)
+                    parsed_child.append(tup(*child_elem_vals))
+                    counter = counter + 1
+                parsed_xml.append(parsed_child)
+
+    else:
+        raise ValueError("file not found")
+
+    return Parsed_XML(*parsed_xml)
+
+
+def extract_brm_file(index, device, dat_files):
+    """
+    Extracts data from BRM files based on the given index, device, and dat_files.
+
+    Parameters:
+        index (Index): The index object containing file descriptions.
+        device (Device): The device to extract data for.
+        dat_files (List[str]): The list of dat files to extract data from.
+
+    Returns:
+        List[List[Data]]: A list of data extracted from BRM files.
+    """
+    filenames = [fd.FileName for fd in index.FileDescription]
+
+    counter = 0
+    data = [[] for _ in dat_files]
+
+    for dat_file in dat_files:
+        df = os.path.basename(dat_file)
+        file = index.FileDescription[filenames.index(df)]
+        file = file._replace(FileName=dat_file)
+        print(f"\textracting {df} datastream")
+        data[counter] = get_brm_data(file, device)
+        counter = counter + 1
+
+    return data
+
+
+def get_brm_data(file, device):
+    """
+    Generates a named tuple containing the data from the given file and device.
+
+    Parameters:
+        file (namedtuple): The file containing the data.
+        device (str): The device associated with the data.
+
+    Returns:
+        Data: A named tuple containing the data from the file, the sample rate, and the numerical data.
+    """
+    DAUSampleHz = 512
+
+    Data = namedtuple("data", list(file._fields) + ["sampleHz", "data"])
+    data = list(file)
+    data.append(int(DAUSampleHz / int(file.SamplePeriod512thSeconds)))
+    data.append(get_numerical_data(file, device))
+
+    return Data(*data)
+
+
+def get_numerical_data(file, device):
+    """
+    Reads numerical data from a file and returns it.
+
+    Parameters:
+        file (File): The file object representing the file to read from.
+        device (str): The device to use for reading the file.
+
+    Returns:
+        np.ndarray: The numerical data read from the file.
+
+    Raises:
+        Exception: If the file format is unrecognized.
+    """
+    f = open(file.FileName, "rb")
+
+    match file.FileType:
+        case "FloatMappedToInt16" | "Int16":
+            data = np.fromfile(f, dtype=np.int16)
+        case "Float32":
+            data = np.fromfile(f, dtype=np.float32)
+        case _:
+            raise Exception(f"Unrecognized file format {file.FileType}")
+
+    return data
+
+
+def prepare_edf_header(data):
+    """
+    Generate the header for an EDF (European Data Format) file.
+
+    Args:
+        data: A list of objects containing the data for each channel.
+
+    Returns:
+        header: A list containing the header information for the EDF file.
+
+    Raises:
+        None.
+
+    Examples:
+        >>> data = [channel1, channel2]
+        >>> prepare_edf_header(data)
+        ['0', 'X X X X', 'Startdate X X X X', 'dd.mm.yy', 'hh.mm.ss',
+        header_size, None, n_records, '1', n_signals]
+    """
+    n_channels = 2
+    version = "0"
+    PID = "X X X X"
+    RID = "Startdate X X X X"
+    # start_date = datetime.strftime(
+    #     datetime.fromtimestamp(int(data[0].StartTime), timezone.utc), format="%d.%m.%y"
+    # )
+    # start_time = datetime.strftime(
+    #     datetime.fromtimestamp(int(data[0].StartTime), timezone.utc), format="%H.%M.%S"
+    # )
+
+    start_date = "01.01.85"
+    start_time = "00.00.00"
+
+    bytes_in_header = (
+        ensemble_eeg.HEADER_SIZE + n_channels * ensemble_eeg.SIGNAL_HEADER_SIZE
+    )
+    reserved = None
+    fs = data[0].sampleHz
+    n_records = int(np.floor(len(data[0].data) / fs))
+    dur_data_record = "1"
+    n_signals = len(data)
+    header = [
+        version,
+        PID,
+        RID,
+        start_date,
+        start_time,
+        bytes_in_header,
+        reserved,
+        n_records,
+        dur_data_record,
+        n_signals,
+    ]
+
+    return header
+
+
+def prepare_edf_signal_header(data, device):
+    """
+    Generate the signal headers for an EDF file based on the provided data and device.
+
+    Parameters:
+        data (list): A list of data objects.
+        device (Device): The device object.
+
+    Returns:
+        tuple: A tuple of signal headers.
+    """
+    channel_ids = [channel.ID for channel in device.Channel]
+    units = data[0].Units
+
+    # replace non-ascii characters
+    if "µ" in units:
+        units = units.replace("µ", "u")
+
+    signal_headers = [[] for _ in data]
+    for i in range(0, len(data)):
+        ichan = channel_ids.index(data[i].ChannelTitle)
+        if data[i].ChannelTitle == "Left":
+            label = "F3"
+        elif data[i].ChannelTitle == "Right":
+            label = "F4"
+
+        transducer_type = None
+        physical_dimension = units
+        physical_min = round(-5e6 / float(device.Channel[ichan].Gain) / 2)
+        physical_max = round(5e6 / float(device.Channel[ichan].Gain) / 2)
+        digital_min = -(2**15)
+        digital_max = 2**15 - 1
+        prefiltering = None
+        nr_samples = data[i].sampleHz
+        reserved = None
+        sig_header = [
+            label,
+            transducer_type,
+            physical_dimension,
+            physical_min,
+            physical_max,
+            digital_min,
+            digital_max,
+            prefiltering,
+            nr_samples,
+            reserved,
+        ]
+        signal_headers[i] = ensemble_eeg.SignalHeader(*sig_header)
+
+    return tuple(signal_headers)
+
+
+def write_brm_data_to_edf(filename, data):
+    """
+    Write BRM data to EDF file.
+
+    Args:
+        filename (str): The name of the file to write the data to.
+        data (list): A list of data objects.
+
+    Returns:
+        None
+    """
+    file_exists = os.path.isfile(filename)
+    dat1 = data[0].data
+    dat2 = data[1].data
+
+    if file_exists:
+        fs = data[0].sampleHz
+        n_records = int(np.floor(len(data[0].data) / fs))
+        fd = open(filename, "ab")
+
+        index = 0
+        for i_record in range(0, n_records):
+            fd.write(dat1[index : (index + fs)])
+            fd.write(dat2[index : (index + fs)])
+            index = (i_record + 1) * fs
+
+        fd.close()

ensemble_eeg/ensemble_edf.py

@@ -0,0 +1,600 @@
+import os
+import shutil
+import warnings
+from collections import namedtuple
+
+import numpy as np
+
+
+def _str(f, size, _):
+    s = f.read(size).decode("ascii", "ignore").strip()
+    while s.endswith("\x00"):
+        s = s[:-1]
+    return s
+
+
+def _int(f, size, name):
+    s = _str(f, size, name)
+    try:
+        return int(s)
+    except ValueError:
+        warnings.warn("{name}: Could not parse integer {s}.".format(name=name, s=s))
+
+
+def _float(f, size, name):
+    s = _str(f, size, name)
+    try:
+        return float(s)
+    except ValueError:
+        warnings.warn("{name}: Could not parse float {s}.".format(name=name, s=s))
+
+
+def _discard(f, size, _):
+    f.read(size)
+
+
+HEADER = (
+    ("version", 8, _str),
+    ("local_patient_identification", 80, _str),
+    ("local_recording_identification", 80, _str),
+    ("startdate_of_recording", 8, _str),
+    ("starttime_of_recording", 8, _str),
+    ("number_of_bytes_in_header_record", 8, _int),
+    ("reserved", 44, _discard),
+    ("number_of_data_records", 8, _int),
+    ("duration_of_a_data_record", 8, _float),
+    ("number_of_signals", 4, _int),
+)
+
+
+SIGNAL_HEADER = (
+    ("label", 16, _str),
+    ("transducer_type", 80, _str),
+    ("physical_dimension", 8, _str),
+    ("physical_minimum", 8, _float),
+    ("physical_maximum", 8, _float),
+    ("digital_minimum", 8, _int),
+    ("digital_maximum", 8, _int),
+    ("prefiltering", 80, _str),
+    ("nr_of_samples_in_each_data_record", 8, _int),
+    ("reserved", 32, _discard),
+)
+
+INT_SIZE = 2
+HEADER_SIZE = sum([size for _, size, _ in HEADER])
+SIGNAL_HEADER_SIZE = sum([size for _, size, _ in SIGNAL_HEADER])
+
+Header = namedtuple("Header", [name for name, _, _ in HEADER] + ["signals"])
+SignalHeader = namedtuple("SignalHeader", [name for name, _, _ in SIGNAL_HEADER])
+
+
+def read_edf_header(fd):
+    """
+    Reads the header of an EDF file.
+
+    Parameters:
+        fd (str or file-like object): The file descriptor or the path to the EDF file.
+
+    Returns:
+        Header: The header of the EDF file, including information about the signals.
+
+    Raises:
+        FileNotFoundError: If the file specified by `fd` does not exist.
+        ValueError: If `fd` is not a valid EDF file.
+    """
+    opened = False
+    if isinstance(fd, str):
+        opened = True
+        fd = open(fd, "rb")
+
+    header = [func(fd, size, name) for name, size, func in HEADER]
+    number_of_signals = header[-1]
+    signal_headers = [[] for _ in range(number_of_signals)]
+
+    for name, size, func in SIGNAL_HEADER:
+        for signal_header in signal_headers:
+            signal_header.append(func(fd, size, name))
+
+    header.append(
+        tuple(SignalHeader(*signal_header) for signal_header in signal_headers)
+    )
+
+    if opened:
+        fd.close()
+
+    return Header(*header)
+
+
+def read_edf_data(fd, header, chans="all"):
+    """
+    Reads EDF data from a file or file-like object.
+
+    Parameters:
+        fd (str or file-like object): The file path or file-like object to read the EDF data from.
+        header (Header): The EDF header object containing information about the data.
+
+    Returns:
+        generator: A generator that yields each data record as a list of signals.
+
+    Raises:
+        IOError: If there was an error opening or reading the EDF file.
+    """
+    opened = False
+    if isinstance(fd, str):
+        opened = True
+        fd = open(fd, "rb")
+
+        start = 0
+        end = header.number_of_data_records
+
+        if chans == "all":
+            chans = list(range(header.number_of_signals))
+
+        data_record_length = sum(
+            [signal.nr_of_samples_in_each_data_record for signal in header.signals]
+        )
+
+        if opened:
+            fd.seek(
+                HEADER_SIZE
+                + header.number_of_signals * SIGNAL_HEADER_SIZE
+                + start * data_record_length * INT_SIZE
+            )
+
+        for _ in range(start, end):
+            a = np.fromfile(fd, count=data_record_length, dtype=np.int16)
+
+            offset = 0
+            chan_nr = 0
+            data_record = []
+            for signal in header.signals:
+                if chan_nr in chans:
+                    data_record.append(
+                        a[offset : offset + signal.nr_of_samples_in_each_data_record]
+                    )
+
+                offset += signal.nr_of_samples_in_each_data_record
+                chan_nr += 1
+
+            yield data_record
+
+    if opened:
+        fd.close()
+
+
+def write_edf_header(fd, header):
+    """
+    Writes the EDF header to the specified file-like object or file path.
+
+    Args:
+        fd (str): (Relative) path to file to write.
+        header: The header information to write.
+
+    Raises:
+        AssertionError: If the length of the value to write is not equal to the expected size.
+
+    Returns:
+        None
+    """
+    opened = False
+    if isinstance(fd, str):
+        fd = open(fd, "wb")
+        opened = True
+
+        for val, (name, size, _) in zip(header, HEADER):
+            if val is None:
+                val = b"\x20" * size
+
+            if not isinstance(val, bytes):
+                if (
+                    name == "startdate_of_recording" or name == "starttime_of_recording"
+                ) and not isinstance(val, str):
+                    val = "{:02d}.{:02d}.{:02d}".format(val[0], val[1], val[2] % 100)
+                val = str(val).encode(encoding="ascii").ljust(size, b"\x20")
+
+            assert len(val) == size
+            fd.write(val)
+
+        for vals, (name, size, _) in zip(zip(*header.signals), SIGNAL_HEADER):
+            for val in vals:
+                if val is None:
+                    val = b"\x20" * size
+
+                if not isinstance(val, bytes):
+                    val = str(val).encode(encoding="ascii").ljust(size, b"\x20")
+
+                assert len(val) == size
+                fd.write(val)
+
+    if opened:
+        fd.close()
+
+
+def write_edf_data(fd, data_records):
+    """Function to check and fix edf files according to EDF plus standards
+
+    Args:
+        fd (str): (Relative) path to file to write.
+        data_records (array): Variable with data_records to write to edf file\
+            is output from read_edf_data function
+
+    """
+    opened = False
+    if isinstance(fd, str):
+        opened = True
+        fd = open(fd, "ab")
+        for data_record in data_records:
+            for signal in data_record:
+                signal.tofile(fd)
+    # try:
+
+    if opened:
+        fd.close()
+
+
+def fix_edf_header(fd):
+    """
+    Fix the EDF header.
+
+    Args:
+        fd (file object): The file descriptor for the EDF file.
+
+    Returns:
+        None
+    """
+
+    if not (os.path.isfile(fd)):
+        raise FileNotFoundError(fd)
+    else:
+        print(f"fixing header for {fd} ... ", end="", flush=True)
+
+    header = read_edf_header(fd)
+    data = read_edf_data(fd, header)
+
+    something_to_fix = False
+    if ":" in header.startdate_of_recording:
+        warnings.warn(
+            f"start date {header.startdate_of_recording} "
+            "contains colon (:), changing to dot (.)"
+        )
+        header = header._replace(
+            startdate_of_recording=header.startdate_of_recording.replace(":", ".")
+        )
+        something_to_fix = True
+
+    if ":" in header.starttime_of_recording:
+        warnings.warn(
+            f"start time {header.starttime_of_recording}"
+            "contains colon (:), changing to dot (.)"
+        )
+        header = header._replace(
+            starttime_of_recording=header.starttime_of_recording.replace(":", ".")
+        )
+        something_to_fix = True
+
+    for signal in header.signals:
+        if signal.physical_maximum <= signal.physical_minimum:
+            warnings.warn(
+                f"channel {signal.label}: physical maximum "
+                f"({signal.physical_maximum}) is smaller or equal "
+                f"to physical minimum ({signal.physical_minimum})"
+            )
+
+        if signal.digital_maximum <= signal.digital_minimum:
+            warnings.warn(
+                f"channel {signal.label}: digital maximum "
+                f"({signal.digital_maximum}) is smaller or equal "
+                f"to digital minimum ({signal.digital_minimum})"
+            )
+
+    if something_to_fix:
+        tmp_fd = fd + "tmp"
+        write_edf_header(tmp_fd, header)
+        write_edf_data(tmp_fd, data)
+
+        assert os.path.getsize(tmp_fd) == os.path.getsize(fd)
+        os.replace(tmp_fd, fd)
+
+    print("done")
+
+
+def anonymize_edf_header(fd):
+    """Function to anonymize edf files according to ENSEMBLE and BIDS standards.
+    The output file will be appended with ANONYMIZED in the filename. Please
+    make sure to only upload the anonymized files.
+
+
+    Args:
+    fd (str): (Relative) path to file to rename.
+
+    """
+    if not (os.path.isfile(fd)):
+        raise FileNotFoundError(fd)
+    else:
+        print(f"anonymizing {fd} ... ", end="", flush=True)
+
+    header = read_edf_header(fd)
+    data = read_edf_data(fd, header)
+
+    filename = os.path.splitext(os.path.basename(fd))[0]
+    ext = os.path.splitext(os.path.basename(fd))[1]
+    folder = os.path.dirname(fd)
+    split_filename = filename.split("_")
+    is_ensemble_approved = (
+        split_filename[0] == "subj"
+        and len(split_filename[1]) == 10
+        and ("E" in split_filename[1])
+    )
+
+    anonymized_rid = "Startdate X X X X"
+    if is_ensemble_approved:
+        pseudo_code = split_filename[1]
+        anonymized_pid = pseudo_code + " X X X"
+    else:
+        anonymized_pid = "X X X X"
+
+    anonymized_startdate = "01.01.85"
+    anonymized_starttime = "00.00.00"
+
+    header = header._replace(
+        local_patient_identification=anonymized_pid,
+        local_recording_identification=anonymized_rid,
+        startdate_of_recording=anonymized_startdate,
+        starttime_of_recording=anonymized_starttime,
+    )
+
+    fd_out = os.path.join(folder, filename + "_ANONYMIZED" + ext)
+    write_edf_header(fd_out, header)
+    write_edf_data(fd_out, data)
+
+    print("done")
+
+
+def rename_for_ensemble(fd):
+    """Function to rename edf files according to ENSEMBLE and BIDS standards
+
+    Args:
+        fd (str): (Relative) path to file to rename.
+
+    """
+    if not os.path.isfile(fd):
+        raise FileNotFoundError(fd)
+
+    filedir = os.path.expanduser(os.path.dirname(fd))
+    if not filedir:
+        filedir = os.getcwd()
+
+    while True:
+        print(f"changing name of {fd}")
+        filename = os.path.basename(fd)
+
+        # check whether filename needs to be changed
+        do_renaming = check_filename_ensemble(filename)
+
+        if do_renaming:
+            header = read_edf_header(fd)
+
+            # get the new subject code
+            subject_code = get_subject_code()
+
+            # check type of acquisition
+            acq = get_acquisition_type(header)
+
+            # check type of session
+            ses = get_session_type()
+
+        split_new_filename = [subject_code, ses, acq, "run-1_eeg.edf"]
+        new_filename = "_".join(split_new_filename)
+
+        print(f"new filename is {new_filename}")
+        correct_filename = input("Is this correct? [Y/n]: ")
+
+        if correct_filename.lower() == "y":
+            break
+
+    # Create new directory and copy renamed file
+    new_dirname = os.path.join(filedir, subject_code)
+    new_filename = os.path.join(new_dirname, new_filename)
+
+    if not os.path.isdir(new_dirname):
+        os.mkdir(new_dirname)
+
+    if os.path.isfile(new_filename):
+        print("File already exists, not overwriting")
+    else:
+        shutil.copy(fd, new_filename)
+
+
+def combine_aeeg_channels(fd_left, fd_right, new_filename="two_channel_aeeg"):
+    """
+    Combine left and right aEEG channels into a single edf file.
+
+    Args:
+        fd_left (str): The file path of the left aEEG channel.
+        fd_right (str): The file path of the right aEEG channel.
+        new_filename (str, optional): The name of the new combined file. Defaults to "two_channel_aeeg".
+
+    Raises:
+        FileNotFoundError: If fd_left or fd_right is not a valid file path.
+    """
+    if not os.path.isfile(fd_left):
+        raise FileNotFoundError(fd_left)
+    elif not os.path.isfile(fd_right):
+        raise FileNotFoundError(fd_right)
+
+    filename_left = os.path.basename(fd_left)
+    filename_right = os.path.basename(fd_right)
+    print(f"Combining {filename_left} and {filename_right} ... ", end="", flush=True)
+
+    output_dir = os.path.dirname(fd_left)
+    path_to_file = os.path.join(output_dir, new_filename + ".edf")
+
+    hdr_left = read_edf_header(fd_left)
+    hdr_right = read_edf_header(fd_right)
+
+    opened = False
+    if isinstance(fd_left, str):
+        opened = True
+        fd = open(fd_left, "rb")
+
+    # create new header by combining left and right channel headers, get the
+    # annotation channel from right channel
+    header = [func(fd, size, name) for name, size, func in HEADER]
+
+    # create new signal headers
+    signal_headers_left = [hdr_left.signals[0]]
+    signal_headers_right = [signal for signal in hdr_right.signals]
+    signal_headers = signal_headers_left + signal_headers_right
+    header[-1] = len(signal_headers)
+    header.append(
+        tuple(SignalHeader(*signal_header) for signal_header in signal_headers)
+    )
+
+    # calculate new header length
+    header_length = HEADER_SIZE + len(signal_headers) * SIGNAL_HEADER_SIZE
+    header[5] = header_length
+
+    # read in data from both left and right channels, read - if possible -
+    # annotation channel from right channel edf file
+    labels_left = [signal.label for signal in hdr_left.signals]
+    chans = list(range(hdr_left.number_of_signals))
+    if "EDF Annotations" in labels_left:
+        chans.remove(labels_left.index("EDF Annotations"))
+
+    data_left = list(read_edf_data(fd_left, hdr_left, chans=chans))
+    data_right = list(read_edf_data(fd_right, hdr_right))
+
+    # append channels
+    data_all = append_channels(data_left, data_right)
+
+    write_edf_header(path_to_file, Header(*header))
+    write_edf_data(path_to_file, data_all)
+
+    if opened:
+        fd.close()
+
+    print("done")
+
+
+def append_channels(data_left, data_right):
+    """
+    This function takes two lists of data and appends the corresponding elements from the second list to the elements in the first list. It yields the appended elements.
+    """
+    counter = 0
+    for _ in range(len(data_left)):
+        dat_out = data_left[counter]
+        dat_out.extend(data_right[counter])
+        counter += 1
+
+        yield dat_out
+
+
+def check_filename_ensemble(filename):
+    """
+    Helper function to check filename and compare to the ENSEMBLE standard
+
+     Args:
+        fd (str): (Relative) path to file to rename.
+
+    """
+    split_filename = filename.split("_")
+    do_renaming = True
+
+    if (
+        (split_filename[0] == "subj")
+        and ("ses" in split_filename[2])
+        and ("acq" in split_filename[3])
+        and ("run" in split_filename[4])
+        and (split_filename[-1] == "eeg.edf")
+    ):
+        do_renaming = False
+        warnings.warn(
+            "The filename already seems to adhere to the ensemble " "and BIDS standard "
+        )
+        continue_renaming = input("Are you sure you want to rename this file? " "[y/N]")
+        do_renaming = continue_renaming.lower() == "y"
+
+    return do_renaming
+
+
+def get_subject_code():
+    """
+    Helper code to get subject code with user input
+    """
+
+    # Get centre code
+    while True:
+        centre_code = input("Please input your centre code [xxx]: ")
+        if len(centre_code) != 3 or not centre_code.isdigit():
+            print("Centre code must consist of three digits")
+            continue
+        break
+
+    # Get subject number
+    while True:
+        subject_number = input("Please input your subject number [xxxxx]: ")
+        if len(subject_number) != 5 or not subject_number.isdigit():
+            print("Subject number must consist of five digits")
+            continue
+        break
+
+    # Get sibling number
+    while True:
+        sibling_number = input("Please input the sibling number [x]: ")
+        if len(sibling_number) != 1 or not sibling_number.isdigit():
+            print("Sibling number must consist of a single digit")
+            continue
+        break
+
+    subject_code = "sub-" + centre_code + "E" + subject_number + sibling_number
+
+    return subject_code
+
+
+def get_acquisition_type(header):
+    """
+    Helper code to get acquisition type with user input or header information.
+
+    Args:
+        header: The header information of the file.
+
+    Returns:
+        acq: The determined acquisition type.
+    """
+    # Check number of signals in file
+    if header.number_of_signals <= 4:
+        acq = "acq-aeeg"
+        print("file automatically determined to be aEEG")
+        correct_acq = input("is this correct? [Y/n]: ").lower()
+
+        if correct_acq == "n":
+            acq = "acq-ceeg"
+
+    else:
+        acq = "acq-ceeg"
+        print("file automatically determined to be cEEG")
+        correct_acq = input("is this correct? [Y/n]: ").lower()
+
+        if correct_acq == "n":
+            acq = "acq-aeeg"
+
+    return acq
+
+
+def get_session_type():
+    """
+    Helper code to get session type with user input
+    """
+    while 1:
+        ses_string = (
+            "During which session was this recordig taken? " + "[(d)iag/(t)erm]: "
+        )
+        ses = input(ses_string).lower()
+        if ses == "d" or ses == "diag":
+            ses = "ses-diag"
+            break
+        elif ses == "t" or ses == "term":
+            ses = "ses-term"
+            break
+
+    return ses

ensemble_eeg-0.0.1.dist-info/LICENSE

@@ -0,0 +1,189 @@
+GNU GENERAL PUBLIC LICENSE
+
+Version 3, 29 June 2007
+
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+
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+12. No Surrender of Others' Freedom.
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+If conditions are imposed on you (whether by court order, agreement or otherwise) that contradict the conditions of this License, they do not excuse you from the conditions of this License. If you cannot convey a covered work so as to satisfy simultaneously your obligations under this License and any other pertinent obligations, then as a consequence you may not convey it at all. For example, if you agree to terms that obligate you to collect a royalty for further conveying from those to whom you convey the Program, the only way you could satisfy both those terms and this License would be to refrain entirely from conveying the Program.
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+END OF TERMS AND CONDITIONS

ensemble_eeg-0.0.1.dist-info/METADATA

@@ -0,0 +1,92 @@
+Metadata-Version: 2.1
+Name: ensemble_eeg
+Version: 0.0.1
+Summary: Package used to analyze preprocess edf files for the ENSEMBLE2 study
+Author: Bauke van der Velde
+Author-email: Bauke van der Velde <b.vandervelde-3@umcutrecht.nl>
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
+Classifier: Operating System :: OS Independent
+Requires-Python: >3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+License-File: NOTICE
+Requires-Dist: numpy
+Requires-Dist: defusedxml
+
+# ENSEMBLE EEG
+
+Ensemble EEG is a library of EEG analyis tools for the ENSEMBLE study. As of
+today it is focuses on 4 seperate things:
+
+- **Anonymizing** EDF files in accordance with the ENSEMBLE study and the
+  requirements of EDF+
+- **Converting** BRM to EDF+ files
+- **Combining** seperate aEEG channels into one EDF+ file
+- **Renaming** EEG files according to ENSEMBLE and BIDS standards
+- **Fixing** EDF headers to adhere to the EDF+ standard
+
+## Installation
+##### Pip
+```
+python3 -m pip install ensemble_eeg
+```
+
+## Usage
+##### Anonymizing EDF-files
+```
+>>> import ensemble_eeg
+>>> ensemble_eeg.anonymize_edf_header('path/2/your/edf/file')
+```
+##### Fixing EDF headers
+```
+>>> import ensemble_eeg
+>>> ensemble_eeg.fix_edf_header('path/2/your/edf/file')
+```
+##### Converting BRM to EDF files
+```
+>>> import brm_to_edf
+>>> brm_to_edf.convert_brm_to_edf('path/2/your/brm/file')
+```
+##### Combine left and right aEEG channels into one single file
+```
+>>> import ensemble_eeg
+>>> ensemble_eeg.combine_aeeg_channels('path/2/your/left/channel', 'path/2/your/right/channel', 'new_filename')
+```
+##### Rename EDF-files according to BIDS and ENSEMBLE standards
+```
+>>> import ensemble_eeg
+>>> ensemble_eeg.rename_for_ensemble('path/2/your/edf/file')
+```
+### Situations
+##### 1) File is already EDF, but you do not know whether header is EDF+, the file is not anonymized, and not renamed
+```
+>>> import ensemble_eeg
+>>> file = 'path/2/your/edf/file'
+>>> ensemble_eeg.fix_edf_header(file)       # for header check
+>>> ensemble_eeg.anonymize_edf_header(file) # for anonymization
+>>> ensemble_eeg.rename_for_ensemble(file)  # for renaming
+
+```
+##### 2) File is BRM 
+```
+>>> import ensemble_eeg
+>>> brm_file = 'path/2/your/brm/file'
+>>> brm_to_edf.convert_brm_to_edf(brm_file)     # for conversion, output edf is already anonymized
+>>> edf_file = 'path/2/your/edf/file'           # check which file was made in previous step
+>>> ensemble_eeg.rename_for_ensemble(edf_file)  # for renaming
+
+```
+##### 3) Files are edf, but left and right channel are seperate 
+```
+>>> import ensemble_eeg
+>>> left_file = 'path/2/your/left/edf/file'
+>>> right_file = 'path/2/your/right/edf/file'
+>>> ensemble_eeg.combine_aeeg_channels(left_file, right_file) # output is automatically anonymized
+>>> ensemble_eeg.rename_for_ensemble(file)                    # for renaming
+
+```
+
+
+## Acknowledgements
+

ensemble_eeg-0.0.1.dist-info/NOTICE

@@ -0,0 +1,25 @@
+ensemble_eeg is a Python 3 software library to preprocess eeg data for the ENSEMBLE
+study, based - in part - on the edfrd library
+
+Copyright 2018 Christoph Jansen
+Copyright 2024 Bauke van der Velde
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU Lesser General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU Lesser General Public License for more details.
+
+You should have received a copy of the GNU Lesser General Public License
+along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
+Web:
+  - https://github.com/ensemble2/ensemble_eeg
+  - https://fondationparalysiecerebrale.org/projet-ensemble
+  
+E-Mail:
+  - b.vandervelde-3@umcutrecht.nl

ensemble_eeg-0.0.1.dist-info/RECORD

@@ -0,0 +1,9 @@
+ensemble_eeg/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+ensemble_eeg/brm_to_edf.py,sha256=0oUa92uCgYcnVaV-NoZhpLDdraDDXMTeCLrbNvrEvFI,11325
+ensemble_eeg/ensemble_edf.py,sha256=zCp2gSOP9LA6B-Lg7KQvaMteMNZ1uJpxfNwq1UStIUg,17502
+ensemble_eeg-0.0.1.dist-info/LICENSE,sha256=qXzAXUqPurJdhVIJzMejS0Qgs8zlMa9LWe8XyTBO9MA,32005
+ensemble_eeg-0.0.1.dist-info/METADATA,sha256=GNc6yNt6vu1p2kNkxUG6jWvd3ardtO1_zeAH5F0SW6Y,2926
+ensemble_eeg-0.0.1.dist-info/NOTICE,sha256=nHgkntXezqQ-K2wUhC-_jmiM6xl3Gc-9f6wNdcjjwIk,989
+ensemble_eeg-0.0.1.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
+ensemble_eeg-0.0.1.dist-info/top_level.txt,sha256=wZe3epOvL0kHDHu6RagQJUAE6TDvw-QTFz07xMcDzeY,37
+ensemble_eeg-0.0.1.dist-info/RECORD,,

ensemble_eeg-0.0.1.dist-info/WHEEL

@@ -0,0 +1,5 @@
+Wheel-Version: 1.0
+Generator: bdist_wheel (0.42.0)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

ensemble_eeg-0.0.1.dist-info/top_level.txt

@@ -0,0 +1,3 @@
+brm_to_edf
+ensemble_edf
+ensemble_eeg