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353 lines
8.9 KiB
353 lines
8.9 KiB
import os
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import struct
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import array
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from datetime import datetime
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import six
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import re
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from nd2reader.exceptions import InvalidVersionError
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def get_version(fh):
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"""Determines what version the ND2 is.
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Args:
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fh: File handle of the .nd2 file
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Returns:
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tuple: Major and minor version
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"""
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# the first 16 bytes seem to have no meaning, so we skip them
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fh.seek(16)
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# the next 38 bytes contain the string that we want to parse. Unlike most of the ND2, this is in UTF-8
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data = fh.read(38).decode("utf8")
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return parse_version(data)
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def parse_version(data):
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"""Parses a string with the version data in it.
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Args:
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data (unicode): the 19th through 54th byte of the ND2, representing the version
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Returns:
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tuple: Major and minor version
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"""
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match = re.search(r"""^ND2 FILE SIGNATURE CHUNK NAME01!Ver(?P<major>\d)\.(?P<minor>\d)$""", data)
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if match:
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# We haven't seen a lot of ND2s but the ones we have seen conform to this
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return int(match.group('major')), int(match.group('minor'))
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raise InvalidVersionError("The version of the ND2 you specified is not supported.")
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def read_chunk(fh, chunk_location):
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"""Reads a piece of data given the location of its pointer.
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Args:
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fh: an open file handle to the ND2
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chunk_location (int): location to read
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Returns:
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bytes: the data at the chunk location
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"""
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if chunk_location is None or fh is None:
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return None
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fh.seek(chunk_location)
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# The chunk metadata is always 16 bytes long
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chunk_metadata = fh.read(16)
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header, relative_offset, data_length = struct.unpack("IIQ", chunk_metadata)
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if header != 0xabeceda:
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raise ValueError("The ND2 file seems to be corrupted.")
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# We start at the location of the chunk metadata, skip over the metadata, and then proceed to the
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# start of the actual data field, which is at some arbitrary place after the metadata.
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fh.seek(chunk_location + 16 + relative_offset)
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return fh.read(data_length)
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def read_array(fh, kind, chunk_location):
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"""
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Args:
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fh: File handle of the nd2 file
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kind: data type, can be one of 'double', 'int' or 'float'
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chunk_location: the location of the array chunk in the binary nd2 file
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Returns:
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array.array: an array of the data
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"""
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kinds = {'double': 'd',
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'int': 'i',
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'float': 'f'}
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if kind not in kinds:
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raise ValueError('You attempted to read an array of an unknown type.')
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raw_data = read_chunk(fh, chunk_location)
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if raw_data is None:
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return None
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return array.array(kinds[kind], raw_data)
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def _parse_unsigned_char(data):
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"""
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Args:
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data: binary data
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Returns:
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char: the data converted to unsigned char
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"""
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return struct.unpack("B", data.read(1))[0]
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def _parse_unsigned_int(data):
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"""
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Args:
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data: binary data
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Returns:
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int: the data converted to unsigned int
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"""
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return struct.unpack("I", data.read(4))[0]
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def _parse_unsigned_long(data):
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"""
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Args:
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data: binary data
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Returns:
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long: the data converted to unsigned long
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"""
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return struct.unpack("Q", data.read(8))[0]
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def _parse_double(data):
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"""
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Args:
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data: binary data
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Returns:
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double: the data converted to double
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"""
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return struct.unpack("d", data.read(8))[0]
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def _parse_string(data):
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"""
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Args:
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data: binary data
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Returns:
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string: the data converted to string
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"""
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value = data.read(2)
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# the string ends at the first instance of \x00\x00
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while not value.endswith(six.b("\x00\x00")):
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next_data = data.read(2)
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if len(next_data) == 0:
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break
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value += next_data
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try:
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decoded = value.decode("utf16")[:-1].encode("utf8")
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except UnicodeDecodeError:
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decoded = value.decode('utf8').encode("utf8")
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return decoded
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def _parse_char_array(data):
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"""
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Args:
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data: binary data
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Returns:
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array.array: the data converted to an array
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"""
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array_length = struct.unpack("Q", data.read(8))[0]
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return array.array("B", data.read(array_length))
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def parse_date(text_info):
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"""
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The date and time when acquisition began.
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Args:
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text_info: the text that contains the date and time information
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Returns:
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datetime: the date and time of the acquisition
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"""
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for line in text_info.values():
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line = line.decode("utf8")
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# ND2s seem to randomly switch between 12- and 24-hour representations.
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possible_formats = ["%m/%d/%Y %H:%M:%S", "%m/%d/%Y %I:%M:%S %p", "%d/%m/%Y %H:%M:%S"]
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for date_format in possible_formats:
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try:
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absolute_start = datetime.strptime(line, date_format)
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except (TypeError, ValueError):
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continue
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return absolute_start
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return None
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def _parse_metadata_item(data, cursor_position):
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"""Reads hierarchical data, analogous to a Python dict.
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Args:
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data: the binary data that needs to be parsed
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cursor_position: the position in the binary nd2 file
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Returns:
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dict: a dictionary containing the metadata item
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"""
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new_count, length = struct.unpack("<IQ", data.read(12))
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length -= data.tell() - cursor_position
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next_data_length = data.read(length)
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value = read_metadata(next_data_length, new_count)
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# Skip some offsets
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data.read(new_count * 8)
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return value
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def _get_value(data, data_type, cursor_position):
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"""ND2s use various codes to indicate different data types, which we translate here.
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Args:
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data: the binary data
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data_type: the data type (unsigned char = 1, unsigned int = 2 or 3, unsigned long = 5, double = 6, string = 8,
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char array = 9, metadata item = 11)
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cursor_position: the cursor position in the binary nd2 file
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Returns:
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mixed: the parsed value
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"""
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parser = {1: _parse_unsigned_char,
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2: _parse_unsigned_int,
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3: _parse_unsigned_int,
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5: _parse_unsigned_long,
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6: _parse_double,
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8: _parse_string,
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9: _parse_char_array,
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11: _parse_metadata_item}
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try:
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value = parser[data_type](data) if data_type < 11 else parser[data_type](data, cursor_position)
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except (KeyError, struct.error):
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value = None
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return value
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def read_metadata(data, count):
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"""
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Iterates over each element of some section of the metadata and parses it.
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Args:
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data: the metadata in binary form
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count: the number of metadata elements
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Returns:
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dict: a dictionary containing the parsed metadata
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"""
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if data is None:
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return None
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data = six.BytesIO(data)
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metadata = {}
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for _ in range(count):
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cursor_position = data.tell()
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header = data.read(2)
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if not header:
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# We've reached the end of some hierarchy of data
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break
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data_type, name_length = struct.unpack('BB', header)
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name = data.read(name_length * 2).decode("utf16")[:-1].encode("utf8")
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value = _get_value(data, data_type, cursor_position)
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metadata = _add_to_metadata(metadata, name, value)
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return metadata
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def _add_to_metadata(metadata, name, value):
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"""
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Add the name value pair to the metadata dict
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Args:
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metadata (dict): a dictionary containing the metadata
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name (string): the dictionary key
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value: the value to add
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Returns:
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dict: the new metadata dictionary
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"""
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if name not in metadata.keys():
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metadata[name] = value
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else:
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if not isinstance(metadata[name], list):
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# We have encountered this key exactly once before. Since we're seeing it again, we know we
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# need to convert it to a list before proceeding.
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metadata[name] = [metadata[name]]
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# We've encountered this key before so we're guaranteed to be dealing with a list. Thus we append
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# the value to the already-existing list.
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metadata[name].append(value)
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return metadata
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def get_from_dict_if_exists(key, dictionary, convert_key_to_binary=True):
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"""
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Get the entry from the dictionary if it exists
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Args:
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key: key to lookup
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dictionary: dictionary to look in
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convert_key_to_binary: convert the key from string to binary if true
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Returns:
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the value of dictionary[key] or None
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"""
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if convert_key_to_binary:
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key = six.b(key)
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if key not in dictionary:
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return None
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return dictionary[key]
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def check_or_make_dir(directory):
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"""
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Check if a directory exists, if not, create it
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Args:
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directory: the path to the directory
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"""
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if not os.path.exists(directory):
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os.makedirs(directory)
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