From bf35675022ceff52a43b6fd5fde006341ab8ba57 Mon Sep 17 00:00:00 2001 From: jim Date: Tue, 11 Nov 2014 11:20:07 -0600 Subject: [PATCH] solved missing fields of view issue --- nd2reader/__init__.py | 57 +++++++++++++++++++++++++++++-------- nd2reader/model/__init__.py | 24 ++++++++++++++++ run.py | 23 +++++++++++---- 3 files changed, 86 insertions(+), 18 deletions(-) create mode 100644 nd2reader/model/__init__.py diff --git a/nd2reader/__init__.py b/nd2reader/__init__.py index 420828c..d59fcee 100644 --- a/nd2reader/__init__.py +++ b/nd2reader/__init__.py @@ -3,16 +3,21 @@ import numpy as np import struct from collections import namedtuple from StringIO import StringIO +from nd2reader.model import Channel +from pprint import pprint chunk = namedtuple('Chunk', ['location', 'length']) field_of_view = namedtuple('FOV', ['number', 'x', 'y', 'z', 'pfs_offset']) -channel = namedtuple('Channel', ['name', 'camera', 'exposure_time']) class Nd2(object): def __init__(self, filename): self._parser = Nd2Parser(filename) + @property + def timepoint_count(self): + return len(self._parser.metadata['ImageEvents']['RLxExperimentRecord']['pEvents']['']) + @property def height(self): return self._parser.metadata['ImageAttributes']['SLxImageAttributes']['uiHeight'] @@ -23,21 +28,50 @@ class Nd2(object): @property def fields_of_view(self): - for number, fov in enumerate(self.metadata['ImageMetadata']['SLxExperiment']['ppNextLevelEx']['']['uLoopPars']['Points']['']): - yield field_of_view(number=number + 1, x=fov['dPosX'], y=fov['dPosY'], z=fov['dPosZ'], pfs_offset=fov['dPFSOffset']) + fov_data = self.metadata['ImageMetadata']['SLxExperiment']['ppNextLevelEx'][''] + valid_fields = list(fov_data['pItemValid']) + for number, (fov, valid) in enumerate(zip(fov_data['uLoopPars']['Points'][''], valid_fields)): + if valid: + yield field_of_view(number=number + 1, + 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)) + """ + 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']['']['pItemValid']) @property def channels(self): metadata = self.metadata['ImageMetadataSeq']['SLxPictureMetadata']['sPicturePlanes'] - for label, chan in metadata['sPlaneNew'].items(): + # 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 in sorted(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) + yield Channel(name, camera, exposure_time) + + @property + def channel_count(self): + return self.metadata['ImageAttributes']["SLxImageAttributes"]["uiComp"] + + @property + def z_level_count(self): + """ + The number of different z-axis levels. + + """ + return 1 @property def metadata(self): @@ -48,13 +82,12 @@ class Nd2(object): def get_image(self, nr): d = self._parser._read_chunk(self._parser._label_map["ImageDataSeq|%d!" % nr].location) - acqtime = struct.unpack("d", d[:8])[0] - res = [acqtime] - for i in range(self.metadata['ImageAttributes']["SLxImageAttributes"]["uiComp"]): + timestamp = struct.unpack("d", d[:8])[0] + res = [timestamp] + # The images for the various channels are interleaved within each other. + for i in range(self.channel_count): a = array.array("H", d) - - res.append(a[4+i::self.metadata['ImageAttributes']["SLxImageAttributes"]["uiComp"]]) - arr = np.reshape(res[1], (self.height, self.width)) + res.append(a[4+i::self.channel_count]) # TODO: Are you missing a zoom level? Is there extra data here? Can you get timestamps now? return res diff --git a/nd2reader/model/__init__.py b/nd2reader/model/__init__.py new file mode 100644 index 0000000..5415ecb --- /dev/null +++ b/nd2reader/model/__init__.py @@ -0,0 +1,24 @@ +class Channel(object): + def __init__(self, name, camera, exposure_time): + self._name = name + self._camera = camera + self._exposure_time = exposure_time + + @property + def name(self): + if self._name is not None and self._name != "": + return self._name + return "UnnamedChannel" + + @property + def camera(self): + return self._camera + + @property + def exposure_time(self): + return self._exposure_time + + +class Image(object): + def __init__(self): + self.timestamp = None \ No newline at end of file diff --git a/run.py b/run.py index c751aa9..3b8c2e4 100644 --- a/run.py +++ b/run.py @@ -1,16 +1,27 @@ from nd2reader import Nd2 from pprint import pprint +import numpy as np +from skimage import io +# n = Nd2("/home/jim/Desktop/nd2hacking/test-141111.nd2") +n = Nd2("/home/jim/Desktop/nd2hacking/YFP-dsRed-GFP-BF.nd2") -n = Nd2("/home/jim/Desktop/nd2hacking/BFonly.nd2") # print("Height: ", n.height) # print("Width: ", n.width) # for fov in n.fields_of_view: # print(fov.number, fov.x, fov.y, fov.z, fov.pfs_offset) # -# for channel in n.channels: -# print(channel.name) -# print(channel.camera) -# print(channel.exposure_time) +print(n.timepoint_count) +print(n.fov_count) +print(n.channel_count) +for fov in n.fields_of_view: + print(fov.number, fov.x, fov.y, fov.z) +# pprint(len(n.metadata['ImageMetadata']['SLxExperiment']['uLoopPars']['pPeriod'][''])) -n.get_image(3) \ No newline at end of file +# res = n.get_image(6) +# print(res[0]) +# arr = np.reshape(res[1], (n.height, n.width)) +# io.imshow(arr) +# io.show() + +# pprint(n.metadata) \ No newline at end of file