def setDataSource(self, dataSource):
"""
Sets a DataSource for this CombinedDataUnit
Parameters: dataSource A DataSource to manage actual
image data located on disk
"""
DataUnit.setDataSource(self, dataSource)
def setDataSource(self, dataSource): """ Sets a DataSource for this CombinedDataUnit Parameters: dataSource A DataSource to manage actual image data located on disk """ DataUnit.setDataSource(self, dataSource)
def loadFromFile(self, filename): """ Loads the specified .oif-file and imports data from it. Parameters: filename The .oif-file to be loaded """ dataunit = DataUnit() datasource = InterfileDataSource(filename) dataunit.setDataSource(datasource) return [dataunit]
def loadFromFile(self, filename): """ Loads image from MRC-file and generates own DataSource @param filename Path to MRC-file @return List of tuples of datasets in file (only one) """ self.filename = filename dataUnits = [] imageName = self.getShortName() dataSource = MRCDataSource(filename) dataUnit = DataUnit() dataUnit.setDataSource(dataSource) dataUnits.append((imageName,dataUnit)) return dataUnits
def loadFromFile(self, filename):
"""
Loads image from MRC-file and generates own DataSource
@param filename Path to MRC-file
@return List of tuples of datasets in file (only one)
"""
self.filename = filename
dataUnits = []
imageName = self.getShortName()
dataSource = MRCDataSource(filename)
dataUnit = DataUnit()
dataUnit.setDataSource(dataSource)
dataUnits.append((imageName, dataUnit))
return dataUnits
def loadFromFile(self, filename):
"""
Loads a directory of slices
"""
self.filename = filename
filebase, ext = os.path.splitext(filename)
directoryname = os.path.abspath(os.path.dirname(filename))
ext = ext[1:]
files = glob.glob(os.path.join(directoryname, "*.%s"%ext))
print "Loading files", files
datasource = FileListDataSource.FileListDataSource()
datasource.setSlicesPerTimepoint(len(files))
datasource.setFilenames(files)
dataunit = DataUnit()
dataunit.setDataSource(datasource)
settings = dataunit.getSettings()
dims = datasource.getDimensions()
settings.set("Dimensions", dims)
settings.set("Name", os.path.basename(os.path.dirname(filename)))
return [dataunit]
def loadFromFile(self, filename):
"""
Loads a directory of slices
"""
self.filename = filename
filebase, ext = os.path.splitext(filename)
directoryname = os.path.abspath(os.path.dirname(filename))
ext = ext[1:]
files = glob.glob(os.path.join(directoryname, "*.%s" % ext))
print "Loading files", files
datasource = FileListDataSource.FileListDataSource()
datasource.setSlicesPerTimepoint(len(files))
datasource.setFilenames(files)
dataunit = DataUnit()
dataunit.setDataSource(datasource)
settings = dataunit.getSettings()
dims = datasource.getDimensions()
settings.set("Dimensions", dims)
settings.set("Name", os.path.basename(os.path.dirname(filename)))
return [dataunit]
self.reader.SetFileName(self.convertFileName(filename))
#self.reader.Update()
self.reader.UpdateInformation()
dataunits = []
channelNum = self.reader.GetNumberOfChannels()
self.timepointAmnt = channelNum
Logging.info("There are %d channels" % channelNum, kw = "lsmreader")
for i in range(channelNum):
# We create a datasource with specific channel number that
# we can associate with the dataunit
datasource = LsmDataSource(filename, i)
datasource.setPath(filename)
dataunit = DataUnit()
dataunit.setDataSource(datasource)
dataunits.append(dataunit)
return dataunits
def getColorTransferFunction(self):
"""
Returns the ctf of the dataset series which this datasource
operates on
"""
if not self.ctf:
Logging.info("Using ctf based on LSM Color", kw = "lsmreader")
ctf = vtk.vtkColorTransferFunction()
r = self.reader.GetChannelColorComponent(self.channelNum, 0)
g = self.reader.GetChannelColorComponent(self.channelNum, 1)
def loadFromFile(self, filename):
"""
Loads the specified .bxc-file and imports data from it.
Also returns a DataUnit of the type stored in the loaded
.bxc-file or None if something goes wrong. The dataunit is
returned in a list with one item for interoperability with
LSM data source
"""
if not self.baseFilename:
self.baseFilename = filename
self.shortname = os.path.basename(filename)
dataUnitFormat = self.loadBxdFile(filename)
Logging.info("format of unit = ", dataUnitFormat, kw = "datasource")
if (not dataUnitFormat) or (not self.parser):
Logging.info("No dataUnitFormat or parser: %s and %s"%(dataUnitFormat, self.parser), kw = "datasource")
return None
# Then, the number of datasets/timepoints that belong to this dataset
# series
try:
count = self.parser.get("ImageData", "numberOfFiles")
except ConfigParser.NoOptionError:
count = self.parser.get("ImageData", "numberoffiles")
Logging.info("format = ", dataUnitFormat, "count = ", count, kw = "datasource")
# Then read the .vti-filenames and store them in the dataSets-list:
filedir = os.path.dirname(filename)
hasPolydata = self.parser.has_section("PolyData")
for i in range(int(count)):
currentFile = "file_%d"%i
filename = self.parser.get("ImageData", currentFile)
if hasPolydata:
print "GOT polydata"
polyFileName = self.parser.get("PolyData", currentFile)
self.polyDataFiles.append(polyFileName)
reader = vtk.vtkXMLImageDataReader()
filepath = os.path.join(filedir, filename)
if not reader.CanReadFile(filepath):
Logging.error("Cannot read file",
"Cannot read source XML Image Data File %s"%filename)
return
self.dataSets.append(filename)
# If everything went well, we create a new DataUnit-instance of the
# correct subclass, so that the DataUnit-instance can take over and
# resume data processing. First, we return the DataUnit to the caller,
# so it can set a reference to it:
dataunit = DataUnit()
settings = DataUnitSettings()
settings.setType("")
settings = settings.readFrom(self.parser)
self.originalDimensions = eval(settings.get("Dimensions"))
self.settings = settings
dataunit.setDataSource(self)
dataunit.setSettings(settings)
data = dataunit.getTimepoint(0)
dataunits = [dataunit]
if data.GetNumberOfScalarComponents() == 3:
for i in range(0, 3) :
dataSource = RGBComponentDataSource(self, i)
dataunit = DataUnit()
dataunit.setDataSource(dataSource)
settings = DataUnitSettings()
settings = settings.readFrom(self.parser)
dataunit.setSettings(settings)
dataunits.append(dataunit)
return dataunits
self.reader.SetFileName(self.convertFileName(filename))
#self.reader.Update()
self.reader.UpdateInformation()
dataunits = []
channelNum = self.reader.GetNumberOfChannels()
self.timepointAmnt = channelNum
Logging.info("There are %d channels" % channelNum, kw="lsmreader")
for i in range(channelNum):
# We create a datasource with specific channel number that
# we can associate with the dataunit
datasource = LsmDataSource(filename, i)
datasource.setPath(filename)
dataunit = DataUnit()
dataunit.setDataSource(datasource)
dataunits.append(dataunit)
return dataunits
def getColorTransferFunction(self):
"""
Returns the ctf of the dataset series which this datasource
operates on
"""
if not self.ctf:
Logging.info("Using ctf based on LSM Color", kw="lsmreader")
ctf = vtk.vtkColorTransferFunction()
r = self.reader.GetChannelColorComponent(self.channelNum, 0)
g = self.reader.GetChannelColorComponent(self.channelNum, 1)
b = self.reader.GetChannelColorComponent(self.channelNum, 2)
