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263 lines
7.9 KiB
263 lines
7.9 KiB
import numpy as np
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import skimage.io
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import logging
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from io import BytesIO
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import array
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import struct
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log = logging.getLogger("nd2reader")
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class Channel(object):
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def __init__(self, name, camera, exposure_time):
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self._name = name
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self._camera = camera
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self._exposure_time = exposure_time
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@property
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def name(self):
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return self._name
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@property
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def camera(self):
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return self._camera
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@property
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def exposure_time(self):
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return self._exposure_time
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class ImageSet(object):
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"""
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A group of images that share the same timestamp. NIS Elements doesn't store a unique timestamp for every
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image, rather, it stores one for each set of images that share the same field of view and z-axis level.
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"""
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def __init__(self):
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self._images = []
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def add(self, image):
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"""
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:type image: nd2reader.model.Image()
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"""
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self._images.append(image)
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def __iter__(self):
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for image in self._images:
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yield image
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class Image(object):
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def __init__(self, timestamp, raw_array, field_of_view, channel, z_level, height, width):
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self._timestamp = timestamp
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self._raw_data = raw_array
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self._field_of_view = field_of_view
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self._channel = channel
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self._z_level = z_level
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self._height = height
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self._width = width
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self._data = None
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@property
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def timestamp(self):
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"""
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The number of seconds after the beginning of the acquisition that the image was taken. Note that for a given field
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of view and z-level offset, if you have images of multiple channels, they will all be given the same timestamp.
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No, this doesn't make much sense. But that's how ND2s are structured, so if your experiment depends on millisecond
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accuracy, you need to find an alternative imaging system.
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"""
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return self._timestamp / 1000.0
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@property
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def channel(self):
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return self._channel
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@property
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def z_level(self):
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return self._z_level
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@property
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def data(self):
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if self._data is None:
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# The data is just a flat, 1-dimensional array. We convert it to a 2D array and cast the data points as 16-bit integers
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self._data = np.reshape(self._raw_data, (self._height, self._width)).astype(np.int64).astype(np.uint16)
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return self._data
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@property
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def is_valid(self):
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return np.any(self.data)
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def show(self):
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skimage.io.imshow(self.data)
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skimage.io.show()
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class MetadataItem(object):
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def __init__(self, start, data):
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self._datatype = ord(data[start])
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self._label_length = 2 * ord(data[start + 1])
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self._data = data
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@property
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def is_valid(self):
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return self._datatype > 0
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@property
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def key(self):
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return self._data[2:self._label_length].decode("utf16").encode("utf8")
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@property
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def length(self):
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return self._length
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@property
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def data_start(self):
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return self._label_length + 2
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@property
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def _body(self):
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"""
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All data after the header.
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"""
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return self._data[self.data_start:]
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def _get_bytes(self, count):
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return self._data[self.data_start: self.data_start + count]
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@property
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def value(self):
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parser = {1: self._parse_unsigned_char,
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2: self._parse_unsigned_int,
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3: self._parse_unsigned_int,
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5: self._parse_unsigned_long,
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6: self._parse_double,
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8: self._parse_string,
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9: self._parse_char_array,
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11: self._parse_metadata_item
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}
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return parser[self._datatype]()
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def _parse_unsigned_char(self):
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self._length = 1
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return self._unpack("B", self._get_bytes(self._length))
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def _parse_unsigned_int(self):
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self._length = 4
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return self._unpack("I", self._get_bytes(self._length))
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def _parse_unsigned_long(self):
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self._length = 8
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return self._unpack("Q", self._get_bytes(self._length))
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def _parse_double(self):
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self._length = 8
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return self._unpack("d", self._get_bytes(self._length))
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def _parse_string(self):
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# the string is of unknown length but ends at the first instance of \x00\x00
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stop = self._body.index("\x00\x00")
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self._length = stop
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return self._body[:stop - 1].decode("utf16").encode("utf8")
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def _parse_char_array(self):
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array_length = self._unpack("Q", self._get_bytes(8))
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self._length = array_length + 8
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return array.array("B", self._body[8:array_length])
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def _parse_metadata_item(self):
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count, length = struct.unpack("<IQ", self._get_bytes(12))
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metadata_set = MetadataSet(self._body, 0, count)
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def _unpack(self, kind, data):
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"""
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:param kind: the datatype to interpret the bytes as (see: https://docs.python.org/2/library/struct.html#struct-format-strings)
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:type kind: str
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:param data: the bytes to be converted
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:type data: bytes
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Parses a sequence of bytes and converts them to a Python data type.
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struct.unpack() returns a tuple but we only want the first element.
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"""
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return struct.unpack(kind, data)[0]
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class MetadataSet(object):
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"""
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A container of metadata items. Can contain other MetadataSet objects.
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"""
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def __init__(self, data, start, item_count):
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self._items = []
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self._parse(data, start, item_count)
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def _parse(self, data, start, item_count):
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for item in range(item_count):
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metadata_item = MetadataItem(start, data)
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if not metadata_item.is_valid:
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break
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start += metadata_item.length
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class Chunkmap(object):
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def __init__(self):
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pass
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def read(self, filename):
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with open(filename, "rb") as f:
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data = f.read(-1)
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self.parse(data, 1)
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def parse(self, data, count):
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data = BytesIO(data)
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res = {}
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total_count = 0
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for c in range(count):
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lastpos = data.tell()
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total_count += 1
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hdr = data.read(2)
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if not hdr:
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break
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typ = ord(hdr[0])
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bname = data.read(2*ord(hdr[1]))
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name = bname.decode("utf16")[:-1].encode("utf8")
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if typ == 1:
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value, = struct.unpack("B", data.read(1))
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elif typ in [2, 3]:
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value, = struct.unpack("I", data.read(4))
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elif typ == 5:
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value, = struct.unpack("Q", data.read(8))
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elif typ == 6:
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value, = struct.unpack("d", data.read(8))
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elif typ == 8:
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value = data.read(2)
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while value[-2:] != "\x00\x00":
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value += data.read(2)
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value = value.decode("utf16")[:-1].encode("utf8")
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elif typ == 9:
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cnt, = struct.unpack("Q", data.read(8))
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value = array.array("B", data.read(cnt))
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elif typ == 11:
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curpos = data.tell()
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newcount, length = struct.unpack("<IQ", data.read(12))
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curpos = data.tell()
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length -= data.tell()-lastpos
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nextdata = data.read(length)
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value = self.parse(nextdata, newcount)
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# Skip some offsets
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data.read(newcount * 8)
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else:
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assert 0, "%s hdr %x:%x unknown" % (name, ord(hdr[0]), ord(hdr[1]))
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if not name in res:
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res[name] = value
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else:
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if not isinstance(res[name], list):
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res[name] = [res[name]]
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res[name].append(value)
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x = data.read()
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assert not x, "skip %d %s" % (len(x), repr(x[:30]))
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return res
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