zolfa-nd2reader/nd2reader/service/__init__.py

import array
import numpy as np
import struct
from StringIO import StringIO
from collections import namedtuple
import logging
from nd2reader.model import Channel, ImageSet, Image

log = logging.getLogger("nd2reader")
log.setLevel(logging.DEBUG)
chunk = namedtuple('Chunk', ['location', 'length'])
field_of_view = namedtuple('FOV', ['number', 'x', 'y', 'z', 'pfs_offset'])


class BaseNd2(object):
    def __init__(self, filename):
        self._reader = Nd2Reader(filename)
        self._channel_offset = None

    @property
    def height(self):
        return self._metadata['ImageAttributes']['SLxImageAttributes']['uiHeight']

    @property
    def width(self):
        return self._metadata['ImageAttributes']['SLxImageAttributes']['uiWidth']

    @property
    def channels(self):
        metadata = self._metadata['ImageMetadataSeq']['SLxPictureMetadata']['sPicturePlanes']
        try:
            validity = self._metadata['ImageMetadata']['SLxExperiment']['ppNextLevelEx'][''][0]['ppNextLevelEx'][''][0]['pItemValid']
        except KeyError:
            # If none of the channels have been deleted, there is no validity list, so we just make one
            validity = [True for i in metadata]
        # Channel information is contained in dictionaries with the keys a0, a1...an where the number
        # indicates the order in which the channel is stored. So by sorting the dicts alphabetically
        # we get the correct order.
        for (label, chan), valid in zip(sorted(metadata['sPlaneNew'].items()), validity):
            if not valid:
                continue
            name = chan['sDescription']
            exposure_time = metadata['sSampleSetting'][label]['dExposureTime']
            camera = metadata['sSampleSetting'][label]['pCameraSetting']['CameraUserName']
            yield Channel(name, camera, exposure_time)

    @property
    def _image_count(self):
        return self._metadata['ImageAttributes']['SLxImageAttributes']['uiSequenceCount']

    @property
    def _sequence_count(self):
        return self._metadata['ImageEvents']['RLxExperimentRecord']['uiCount']

    @property
    def timepoint_count(self):
        return self._image_count / self.field_of_view_count / self.z_level_count

    @property
    def z_level_count(self):
        return self._image_count / self._sequence_count

    @property
    def field_of_view_count(self):
        """
        The metadata contains information about fields of view, but it contains it even if some fields
        of view were cropped. We can't find anything that states which fields of view are actually
        in the image data, so we have to calculate it. There probably is something somewhere, since
        NIS Elements can figure it out, but we haven't found it yet.

        """
        return sum(self._metadata['ImageMetadata']['SLxExperiment']['ppNextLevelEx'][''][0]['pItemValid'])

    @property
    def channel_count(self):
        return self._reader.channel_count

    @property
    def channel_offset(self):
        if self._channel_offset is None:
            self._channel_offset = {}
            for n, channel in enumerate(self.channels):
                self._channel_offset[channel.name] = n
        return self._channel_offset

    @property
    def _metadata(self):
        return self._reader.metadata

    def _calculate_image_set_number(self, timepoint, fov, z_level):
        return timepoint * self.field_of_view_count * self.z_level_count + (fov * self.z_level_count + z_level)


class Nd2Reader(object):
    """
    Reads .nd2 files, provides an interface to the metadata, and generates numpy arrays from the image data.

    """
    def __init__(self, filename):
        self._filename = filename
        self._file_handler = None
        self._chunk_map_start_location = None
        self._label_map = {}
        self._metadata = {}
        self._read_map()
        self._parse_dict_data()

    @property
    def fh(self):
        if self._file_handler is None:
            self._file_handler = open(self._filename, "rb")
        return self._file_handler

    @property
    def channel_count(self):
        return self._metadata['ImageAttributes']["SLxImageAttributes"]["uiComp"]

    def get_raw_image_data(self, image_set_number, channel_offset):
        chunk = self._label_map["ImageDataSeq|%d!" % image_set_number]
        data = self._read_chunk(chunk.location)
        timestamp = struct.unpack("d", data[:8])[0]
        # The images for the various channels are interleaved within each other. Yes, this is an incredibly unintuitive and nonsensical way
        # to store data.
        image_data = array.array("H", data)
        image_data_start = 4 + channel_offset
        return timestamp, image_data[image_data_start::self.channel_count]

    def _parse_dict_data(self):
        # TODO: Don't like this name
        for label in self._top_level_dict_labels:
            chunk_location = self._label_map[label].location
            data = self._read_chunk(chunk_location)
            stop = label.index("LV")
            self._metadata[label[:stop]] = self.read_lv_encoding(data, 1)

    @property
    def metadata(self):
        return self._metadata

    @property
    def _top_level_dict_labels(self):
        # TODO: I don't like this name either
        for label in self._label_map.keys():
            if label.endswith("LV!") or "LV|" in label:
                yield label

    def _read_map(self):
        """
        Every label ends with an exclamation point, however, we can't directly search for those to find all the labels
        as some of the bytes contain the value 33, which is the ASCII code for "!". So we iteratively find each label,
        grab the subsequent data (always 16 bytes long), advance to the next label and repeat.

        """
        raw_text = self._get_raw_chunk_map_text()
        label_start = self._find_first_label_offset(raw_text)
        while True:
            data_start = self._get_data_start(label_start, raw_text)
            label, value = self._extract_map_key(label_start, data_start, raw_text)
            if label == "ND2 CHUNK MAP SIGNATURE 0000001!":
                # We've reached the end of the chunk map
                break

            self._label_map[label] = value
            label_start = data_start + 16

    @staticmethod
    def _find_first_label_offset(raw_text):
        """
        The chunk map starts with some number of (seemingly) useless bytes, followed
        by "ND2 FILEMAP SIGNATURE NAME 0001!". We return the location of the first character after this sequence,
        which is the actual beginning of the chunk map.

        """
        return raw_text.index("ND2 FILEMAP SIGNATURE NAME 0001!") + 32

    @staticmethod
    def _get_data_start(label_start, raw_text):
        """
        The data for a given label begins immediately after the first exclamation point

        """
        return raw_text.index("!", label_start) + 1

    @staticmethod
    def _extract_map_key(label_start, data_start, raw_text):
        """
        Chunk map entries are a string label of arbitrary length followed by 16 bytes of data, which represent
        the byte offset from the beginning of the file where that data can be found.

        """
        key = raw_text[label_start: data_start]
        location, length = struct.unpack("QQ", raw_text[data_start: data_start + 16])
        return key, chunk(location=location, length=length)

    @property
    def chunk_map_start_location(self):
        """
        The position in bytes from the beginning of the file where the chunk map begins.
        The chunk map is a series of string labels followed by the position (in bytes) of the respective data.

        """
        if self._chunk_map_start_location is None:
            # Put the cursor 8 bytes before the end of the file
            self.fh.seek(-8, 2)
            # Read the last 8 bytes of the file
            self._chunk_map_start_location = struct.unpack("Q", self.fh.read(8))[0]
        return self._chunk_map_start_location

    def _read_chunk(self, chunk_location):
        """
        Gets the data for a given chunk pointer

        """
        self.fh.seek(chunk_location)
        chunk_data = self._read_chunk_metadata()
        header, relative_offset, data_length = self._parse_chunk_metadata(chunk_data)
        return self._read_chunk_data(chunk_location, relative_offset, data_length)

    def _read_chunk_metadata(self):
        """
        Gets the chunks metadata, which is always 16 bytes

        """
        return self.fh.read(16)

    def _read_chunk_data(self, chunk_location, relative_offset, data_length):
        """
        Reads the actual data for a given chunk

        """
        # We start at the location of the chunk metadata, skip over the metadata, and then proceed to the
        # start of the actual data field, which is at some arbitrary place after the metadata.
        self.fh.seek(chunk_location + 16 + relative_offset)
        return self.fh.read(data_length)

    @staticmethod
    def _parse_chunk_metadata(chunk_data):
        """
        Finds out everything about a given chunk. Every chunk begins with the same value, so if that's ever
        different we can assume the file has suffered some kind of damage.

        """
        header, relative_offset, data_length = struct.unpack("IIQ", chunk_data)
        if header != 0xabeceda:
            raise ValueError("The ND2 file seems to be corrupted.")
        return header, relative_offset, data_length

    def _get_raw_chunk_map_text(self):
        """
        Reads the entire chunk map and returns it as a string.

        """
        self.fh.seek(self.chunk_map_start_location)
        return self.fh.read(-1)

    @staticmethod
    def as_numpy_array(arr):
        return np.frombuffer(arr)

    def _z_level_count(self):
        """read the microscope coordinates and temperatures
        Missing: get chunknames and types from xml metadata"""
        res = {}
        name = "CustomData|Z!"
        st = self._read_chunk(self._label_map[name].location)
        res = array.array("d", st)
        return len(res)

    def read_lv_encoding(self, data, count):
        data = StringIO(data)
        res = {}
        total_count = 0
        for c in range(count):
            lastpos = data.tell()
            total_count += 1
            hdr = data.read(2)
            if not hdr:
                break
            typ = ord(hdr[0])
            bname = data.read(2*ord(hdr[1]))
            name = bname.decode("utf16")[:-1].encode("utf8")
            if typ == 1:
                value, = struct.unpack("B", data.read(1))
            elif typ in [2, 3]:
                value, = struct.unpack("I", data.read(4))
            elif typ == 5:
                value, = struct.unpack("Q", data.read(8))
            elif typ == 6:
                value, = struct.unpack("d", data.read(8))
            elif typ == 8:
                value = data.read(2)
                while value[-2:] != "\x00\x00":
                    value += data.read(2)
                value = value.decode("utf16")[:-1].encode("utf8")
            elif typ == 9:
                cnt, = struct.unpack("Q", data.read(8))
                value = array.array("B", data.read(cnt))
            elif typ == 11:
                newcount, length = struct.unpack("<IQ", data.read(12))
                length -= data.tell()-lastpos
                nextdata = data.read(length)
                value = self.read_lv_encoding(nextdata, newcount)
                # Skip some offsets
                data.read(newcount * 8)
            else:
                assert 0, "%s hdr %x:%x unknown" % (name, ord(hdr[0]),  ord(hdr[1]))
            if not name in res:
                res[name] = value
            else:
                if not isinstance(res[name], list):
                    res[name] = [res[name]]
                res[name].append(value)
        x = data.read()
        assert not x, "skip %d %s" % (len(x), repr(x[:30]))
        return res