From d0401fd8e414d7327064b914d4049941df44fd94 Mon Sep 17 00:00:00 2001 From: Jim Rybarski Date: Sat, 30 Aug 2014 19:39:35 -0500 Subject: [PATCH] identified some metadata to extract --- nd2reader/__init__.py | 159 ++++++++++++++++++++++++++++++++++++++++-- run.py | 17 +++++ 2 files changed, 172 insertions(+), 4 deletions(-) create mode 100644 run.py diff --git a/nd2reader/__init__.py b/nd2reader/__init__.py index 742aa95..3dd9ebc 100644 --- a/nd2reader/__init__.py +++ b/nd2reader/__init__.py @@ -1,9 +1,59 @@ import array import numpy as np import struct +from collections import namedtuple +from StringIO import StringIO +chunk = namedtuple('Chunk', ['location', 'length']) +field_of_view = namedtuple('FOV', ['x', 'y', 'z', 'pfs_offset']) +channel = namedtuple('Channel', ['name', 'camera', 'exposure_time']) -class Nd2Reader(object): + +class Nd2(object): + def __init__(self, filename): + self._parser = Nd2Parser(filename) + + @property + def height(self): + return self._parser.metadata['ImageAttributes']['SLxImageAttributes']['uiHeight'] + + @property + def width(self): + return self._parser.metadata['ImageAttributes']['SLxImageAttributes']['uiWidth'] + + @property + def fields_of_view(self): + for fov in self.metadata['ImageMetadata']['SLxExperiment']['ppNextLevelEx'][''][0]['uLoopPars']['Points']['']: + yield field_of_view(x=fov['dPosX'], y=fov['dPosY'], z=fov['dPosZ'], pfs_offset=fov['dPFSOffset']) + + @property + def fov_count(self): + return len(list(self.fields_of_view)) + + @property + def channels(self): + metadata = self.metadata['ImageMetadataSeq']['SLxPictureMetadata']['sPicturePlanes'] + for label, chan in metadata['sPlaneNew'].items(): + name = chan['sDescription'] + exposure_time = metadata['sSampleSetting'][label]['dExposureTime'] + camera = metadata['sSampleSetting'][label]['pCameraSetting']['CameraUserName'] + yield channel(name=name, exposure_time=exposure_time, camera=camera) + + @property + def metadata(self): + return self._parser.metadata + + + + + + + + + + + +class Nd2Parser(object): """ Reads .nd2 files, provides an interface to the metadata, and generates numpy arrays from the image data. @@ -13,7 +63,9 @@ class Nd2Reader(object): 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): @@ -21,6 +73,25 @@ class Nd2Reader(object): self._file_handler = open(self._filename, "rb") return self._file_handler + 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 @@ -36,6 +107,7 @@ class Nd2Reader(object): 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 @@ -65,8 +137,8 @@ class Nd2Reader(object): """ key = raw_text[label_start: data_start] - value = struct.unpack("QQ", raw_text[data_start: data_start + 16]) - return key, value + 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): @@ -131,4 +203,83 @@ class Nd2Reader(object): @staticmethod def as_numpy_array(arr): - return np.frombuffer(arr) \ No newline at end of file + return np.frombuffer(arr) + + def read_lv_encoding(self, data, count): + data = StringIO(data) + res = {} + for c in range(count): + lastpos = data.tell() + 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("