def __init__(self, filename = "", channel = -1, \
name = ""):
"""
Constructor
"""
DataSource.__init__(self)
self.channel = channel
if not name:
name = "Ch%d" % channel
self.bitdepth = 12
self.name = name
self.timepoint = 0
self.timepoints = 0
self.filename = filename
self.parser = ConfigParser.RawConfigParser()
if filename:
filepointer = codecs.open(self.convertFileName(filename), "r", "utf-16")
self.parser.readfp(filepointer)
dataName = self.parser.get("File Info","DataName")
if dataName[0] == '"':
dataName = dataName[1:]
if dataName[-1] == '"':
dataName = dataName[:-1]
directoryName, self.lutFileName = self.getLUTPath(self.channel)
newLut = os.path.join(directoryName, self.lutFileName)
newLut = os.path.join(os.path.dirname(self.filename), newLut)
if not os.path.exists(newLut):
self.path = "%s.files"%self.filename
print self.lutFileName
else:
self.path = os.path.join(os.path.dirname(filename), directoryName)
# when lutFileName is e.g. bro28_par3_07-04-18_LUT1.lut, we take the
# bro28_par3_07-04-18 and ignore the LUT1.lut, and use that as the basis of the filenames
# for the tiff files
self.fileNameBase = "_".join(self.lutFileName.split("_")[:-1])
#self.fileNameBase = dataName
self.reader = None
self.originalScalarRange = (0, 4095)
self.scalarRange = 0, 2 ** self.bitdepth - 1
self.dimensions = (0,0,0)
self.voxelsize = (1,1,1)
self.spacing = None
self.emission = 0
self.excitation = 0
self.color = None
self.shift = None
self.noZ = 0
self.reverseSlices = True
if channel >= 0:
self.ctf = self.readLUT()
self.setPath(filename)
# nm = nanometer, um = micrometer, mm = millimeter
self.unit_coeffs = {"nm":1e-9, "um":1e-6, "mm":0.001,"ms":0.001}
self.shortname = None
def __init__(self, filename = ""):
"""
Constructor
"""
DataSource.__init__(self)
# list of references to individual datasets (= timepoints) stored in
# vti-files
self.polydataReader = None
self.dataSets = []
self.polyTimepoint = -1
self.polyDataFiles = []
# filename of the .du-file
self.filename = filename
self.baseFilename = ""
self.setPath(filename)
# path to the .du-file and .vti-file(s)
self.path = ""
self.reader = None
# Number of datasets added to this datasource
self.counter = 0
self.parser = None
self.ctf = None
# TODO: what is this?
# self.dataUnitSettings = {}
self.settings = None
self.dimensions = None
self.spacing = None
self.voxelsizes = None
def __init__(self, filename = ""):
"""
Constructor
"""
DataSource.__init__(self)
self.setPath(filename)
dataSetName = os.path.basename(filename)
dataSetName = dataSetName.split(".")
dataSetName = ".".join(dataSetName[:-1])
self.dataSetName = dataSetName
self.io = itk.BioRadImageIO.New()
self.reader = itk.ImageFileReader[itk.Image.UC3].New()
self.reader.SetImageIO(self.io.GetPointer())
self.ctf = None
self.filename = filename
self.filepattern = None
self.dimensions = None
self.voxelsize = None
self.spacing = None
self.itkToVtk = None
self.color = None
self.shift = None
self.tps = -1
if filename:
self.path = os.path.dirname(filename)
self.getDataSetCount()
def __init__(self, source, component):
"""
Initialization
"""
DataSource.__init__(self)
self.source = source
self.component = component
self.extract = vtk.vtkImageExtractComponents()
self.extract.SetComponents(self.component)
self.setPath = source.setPath
self.getPath = source.getPath
self.setMask = source.setMask
self.getSpacing = source.getSpacing
self.getVoxelSize = source.getVoxelSize
self.setResampleDimensions = source.setResampleDimensions
self.getOriginalScalarRange = source.getOriginalScalarRange
self.getOriginalDimensions = source.getOriginalDimensions
self.getResampleFactors = source.getResampleFactors
self.getResampledVoxelSize = source.getResampledVoxelSize
self.getResampleDimensions = source.getResampleDimensions
self.setIntensityScale = source.setIntensityScale
self.getIntensityScaledData = source.getIntensityScaledData
self.getResampledData = source.getResampledData
self.getEmissionWavelength = source.getEmissionWavelength
self.getExcitationWavelength = source.getExcitationWavelength
self.getNumericalAperture = source.getNumericalAperture
self.getDataSetCount = source.getDataSetCount
self.getFileName = source.getFileName
self.getDimensions = source.getDimensions
self.getScalarRange = source.getScalarRange
self.ctf = None
def __init__(self, filename = "", experiment = "", channel = -1): """ Constructor """ DataSource.__init__(self) self.filename = filename self.reader = LeicaExperiment(filename, progressCallback = self.updateProgress) self.shortname = os.path.basename(filename) self.experiment = experiment if experiment: self.originalDimensions = self.reader.GetDimensions(self.experiment) duration = self.reader.GetDuration(self.experiment) numT = self.reader.GetNumberOfTimepoints(self.experiment) print "Number of Timepoints = ",numT print "Duration=",duration step = duration/float(numT) stamps = [] for t in range(0, numT): stamps.append(step*t) self.setTimeStamps(stamps) self.setAbsoluteTimeStamps(stamps) self.channel = channel self.dimensions = None self.voxelsize = None self.spacing = None self.color = None self.ctf = None self.setPath(filename) self.datasetCount = None
def __init__(self, filename = ""):
"""
Constructor of MRCDataSource
"""
DataSource.__init__(self)
self.filename = filename
self.setPath(filename)
self.bitDepth = 0
self.spacing = None
self.voxelSize = None
# Create vtkMRCReader for reading MRC files
self.reader = vtkbxd.vtkMRCReader()
self.reader.AddObserver('ProgressEvent', lib.messenger.send)
lib.messenger.connect(self.reader, 'ProgressEvent', self.updateProgress)
if self.filename:
self.reader.SetFileName(self.convertFileName(self.filename))
if self.reader.OpenFile():
if self.reader.ReadHeader():
self.setOriginalScalarRange()
else:
Logging.error("Failed to read the header of the MRC file correctly",
"Error in MRCDataSource.py in __init.py__, failed to read the header of the MRC file: %s" %(self.filename))
return
else:
Logging.error("Failed to open file",
"Error in MRCDataSource.py in __init__, failed to open file: %s" %(self.filename))
return
def __init__(self, filename = ""):
"""
Constructor
"""
DataSource.__init__(self)
name = os.path.basename(filename)
name = name.split(".")
name = ".".join(name[:-1])
self.name = name
self.setPath(filename)
self.filename = filename
self.reader = None
self.datatype = "Float"
self.dimensions = None
self.voxelsize = (1, 1, 1)
self.spacing = None
self.color = None
self.shift = None
self.tps = -1
self.numberOfImages = 0
self.dataFileName = ""
self.bytesPerPixel = 0
self.duration = 0.0
if filename:
self.path = os.path.dirname(filename)
self.getDataSetCount()
f = open(filename, "r")
self.readInfo(f)
f.close()
self.createTimeStamps()
def __init__(self, filename=""):
"""
Constructor of MRCDataSource
"""
DataSource.__init__(self)
self.filename = filename
self.setPath(filename)
self.bitDepth = 0
self.spacing = None
self.voxelSize = None
# Create vtkMRCReader for reading MRC files
self.reader = vtkbxd.vtkMRCReader()
self.reader.AddObserver('ProgressEvent', lib.messenger.send)
lib.messenger.connect(self.reader, 'ProgressEvent',
self.updateProgress)
if self.filename:
self.reader.SetFileName(self.convertFileName(self.filename))
if self.reader.OpenFile():
if self.reader.ReadHeader():
self.setOriginalScalarRange()
else:
Logging.error(
"Failed to read the header of the MRC file correctly",
"Error in MRCDataSource.py in __init.py__, failed to read the header of the MRC file: %s"
% (self.filename))
return
else:
Logging.error(
"Failed to open file",
"Error in MRCDataSource.py in __init__, failed to open file: %s"
% (self.filename))
return
def __init__(self, source, component): """ Initialization """ DataSource.__init__(self) self.source = source self.component = component self.extract = vtk.vtkImageExtractComponents() self.extract.SetComponents(self.component) self.setPath = source.setPath self.getPath = source.getPath self.setMask = source.setMask self.getSpacing = source.getSpacing self.getVoxelSize = source.getVoxelSize self.setResampleDimensions = source.setResampleDimensions self.getOriginalScalarRange = source.getOriginalScalarRange self.getOriginalDimensions = source.getOriginalDimensions self.getResampleFactors = source.getResampleFactors self.getResampledVoxelSize = source.getResampledVoxelSize self.getResampleDimensions = source.getResampleDimensions self.setIntensityScale = source.setIntensityScale self.getIntensityScaledData = source.getIntensityScaledData self.getResampledData = source.getResampledData self.getEmissionWavelength = source.getEmissionWavelength self.getExcitationWavelength = source.getExcitationWavelength self.getNumericalAperture = source.getNumericalAperture self.getDataSetCount = source.getDataSetCount self.getFileName = source.getFileName self.getDimensions = source.getDimensions self.getScalarRange = source.getScalarRange self.ctf = None
def __init__(self, filenames = [], callback = None):
"""
Constructor
"""
DataSource.__init__(self)
self.name = "Import"
self.extMapping = {"tif": "TIFF", "tiff": "TIFF", "png": "PNG", "jpg": "JPEG", "jpeg": "JPEG", \
"pnm": "PNM", "vti": "XMLImageData", "vtk": "DataSet", "bmp": "BMP"}
self.dimMapping = {"bmp":2, "tif":2, "tiff":2, "png":2, "jpg":2, "jpeg":2, "pnm":2, "vti":3, "vtk":3}
self.callback = callback
self.initialize()
def __init__(self, filename="", channelNum=-1):
"""
Constructor
"""
DataSource.__init__(self)
# Name and path of the lsm-file:
self.filename = filename
if len(os.path.basename(self.filename)) > 4:
self.imageName = os.path.basename(self.filename)[:-4]
self.numericalAperture = 0
self.excitationWavelength = 0
self.timepoint = -1
self.shortname = os.path.basename(filename)
self.path = ""
# An lsm-file may contain multiple channels. However, LsmDataSource only
# handles one channel. The following attribute indicates, which channel
# within the lsm-file is hadled by this LsmDataSource instance.
self.channelNum = channelNum
self.setPath(filename)
self.dataUnitSettings = {}
self.spacing = None
self.origin = None
self.voxelsize = None
# vtkLSMReader is used to do the actual reading:
self.reader = vtkbxd.vtkLSMReader()
#self.reader.DebugOn()
self.reader.AddObserver("ProgressEvent", lib.messenger.send)
lib.messenger.connect(self.reader, 'ProgressEvent',
self.updateProgress)
# If a filename was specified, the file is loaded
if self.filename:
self.path = os.path.dirname(filename)
Logging.info("LsmDataSource created with file %s and channelNum=%d"%\
(self.filename, channelNum), kw = "lsmreader")
try:
f = open(self.convertFileName(filename))
f.close()
except IOError, ex:
Logging.error(
"Failed to open LSM file",
"Failed to open file %s for reading: %s" %
(filename, str(ex)))
return
self.reader.SetFileName(self.convertFileName(self.filename))
self.reader.SetUpdateChannel(channelNum)
self.reader.UpdateInformation()
self.originalScalarRange = None
self.getBitDepth()
self.originalDimensions = self.reader.GetDimensions()[0:3]
self.readTimeStamps()
def __init__(self, filename = "", channelNum = -1):
"""
Constructor
"""
DataSource.__init__(self)
# Name and path of the lsm-file:
self.filename = filename
if len(os.path.basename(self.filename)) > 4:
self.imageName = os.path.basename(self.filename)[:-4]
self.numericalAperture = 0
self.excitationWavelength = 0
self.timepoint = -1
self.shortname = os.path.basename(filename)
self.path = ""
# An lsm-file may contain multiple channels. However, LsmDataSource only
# handles one channel. The following attribute indicates, which channel
# within the lsm-file is hadled by this LsmDataSource instance.
self.channelNum = channelNum
self.setPath(filename)
self.dataUnitSettings = {}
self.spacing = None
self.origin = None
self.voxelsize = None
# vtkLSMReader is used to do the actual reading:
self.reader = vtkbxd.vtkLSMReader()
#self.reader.DebugOn()
self.reader.AddObserver("ProgressEvent", lib.messenger.send)
lib.messenger.connect(self.reader, 'ProgressEvent', self.updateProgress)
# If a filename was specified, the file is loaded
if self.filename:
self.path = os.path.dirname(filename)
Logging.info("LsmDataSource created with file %s and channelNum=%d"%\
(self.filename, channelNum), kw = "lsmreader")
try:
f = open(self.convertFileName(filename))
f.close()
except IOError, ex:
Logging.error("Failed to open LSM file",
"Failed to open file %s for reading: %s" % (filename, str(ex)))
return
self.reader.SetFileName(self.convertFileName(self.filename))
self.reader.SetUpdateChannel(channelNum)
self.reader.UpdateInformation()
self.originalScalarRange = None
self.getBitDepth()
self.originalDimensions = self.reader.GetDimensions()[0:3]
self.readTimeStamps()
def __init__(self, filename="", imageNum=-1, channelNum=-1, reader=None):
"""
Constructor of LIF DataSource
"""
DataSource.__init__(self)
self.filename = filename
self.imageName = ""
self.setPath(filename)
# LIF file can contain multiple images with multiple channels.
# Define which image and channel is associated to this DataSource
self.imageNum = imageNum
self.channelNum = channelNum
self.bitDepth = 0
self.spacing = None
self.voxelSize = None
self.ctf = None
# Use vtkLIFReader
self.reader = vtkbxd.vtkLIFReader()
self.reader.AddObserver('ProgressEvent', lib.messenger.send)
lib.messenger.connect(self.reader, 'ProgressEvent',
self.updateProgress)
# Open file if defined
if self.filename:
self.reader.SetFileName(self.convertFileName(self.filename))
if self.reader.OpenFile():
if reader:
self.reader.CopyHeaderInfo(reader)
if self.reader.ReadLIFHeader():
self.reader.SetCurrentImage(self.imageNum)
self.reader.SetCurrentChannel(self.channelNum)
self.imageName = self.reader.GetImageName(self.imageNum)
self.createTimeStamps()
self.originalDimensions = self.internalGetDimensions()[0:3]
else:
Logging.error(
"Failed to read the header of the LIF file correctly",
"Error in LIFDataSource.py in __init__, failed to read the header of the LIF file: %s"
% (self.filename))
return
else:
Logging.error(
"Failed to open file",
"Error in LIFDataSource.py in __init__, failed to open file: %s"
% (self.filename))
return
def __init__(self, filenames=[], callback=None):
"""
Constructor
"""
DataSource.__init__(self)
self.name = "Import"
self.extMapping = {"tif": "TIFF", "tiff": "TIFF", "png": "PNG", "jpg": "JPEG", "jpeg": "JPEG", \
"pnm": "PNM", "vti": "XMLImageData", "vtk": "DataSet", "bmp": "BMP"}
self.dimMapping = {
"bmp": 2,
"tif": 2,
"tiff": 2,
"png": 2,
"jpg": 2,
"jpeg": 2,
"pnm": 2,
"vti": 3,
"vtk": 3
}
self.callback = callback
self.initialize()
def __init__(self, filename = "", imageNum = 0, channelNum = 0):
"""
Constructor
"""
DataSource.__init__(self)
self.filename = filename
self.numImages = 1
self.numChannels = 1
self.numTimePoints = 1
self.currentImage = imageNum
self.currentChannel = channelNum
self.currentTimepoint = 0
self.imageName = ""
self.reader = vtkbxd.vtkOMETIFFReader()
self.reader.AddObserver('ProgressEvent', lib.messenger.send)
lib.messenger.connect(self.reader, 'ProgressEvent', self.updateProgress)
self.ctf = None
if self.filename:
self.reader.SetFileName(self.convertFileName(self.filename))
if not self.reader.ReadOMEHeader():
Logging.error("Failed to open OME-TIFF file",
"Failed to open file %s for reading: %s"%(filename, str(ex)))
return
self.numImages = self.reader.GetNumberOfImages()
if self.currentImage < self.numImages:
self.reader.SetCurrentImage(self.currentImage)
self.numChannels = self.reader.GetNumberOfChannels()
if self.currentChannel < self.numChannels:
self.reader.SetCurrentChannel(self.currentChannel)
self.imageName = self.reader.GetImageName()
if self.imageName == "":
self.imageName = "Image-%d"%(self.currentImage+1)
self.numTimePoints = self.reader.GetNumberOfTimePoints()
self.createTimeStamps()
def __init__(self, filename = ""): """ Constructor """ DataSource.__init__(self) self.sourceUnits = []
def __init__(self, filename=""):
"""
Constructor
"""
DataSource.__init__(self)
self.sourceUnits = []
def __init__(self, filename = ""): DataSource.__init__(self)
def __init__(self, filename=""):
DataSource.__init__(self)