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()
#! /usr/bin/env python
import vtk
import vtkbxd
import time
D = "/media/sda12/Data/sample2.lsm"
t = time.time()
def elapsed():
global t
return "(%.2fs elapsed)" % (time.time() - t)
r1 = vtkbxd.vtkLSMReader()
r1.SetFileName(D)
r1.SetUpdateChannel(0)
d1 = r1.GetOutput()
itf1 = vtkbxd.vtkIntensityTransferFunction()
itf1.SetBrightness(50.0)
ctf1 = vtkbxd.vtkColorTransferFunction()
ctf1.AddRGBPoint(0, 0, 0, 0)
ctf1.AddRGBPoint(255.0, 0, 1.0, 0)
print "Feeding channels to merge ", elapsed()
merge = vtkbxd.vtkImageColorMerge()
#merge.SetNumberOfThreads(5)
merge.AddInput(d1)
merge.AddLookupTable(ctf1)
#! /usr/bin/env python
import vtk
import vtkbxd
import time
D="/media/sda12/Data/sample2.lsm"
t=time.time()
def elapsed():
global t
return "(%.2fs elapsed)"%(time.time()-t)
r1=vtkbxd.vtkLSMReader()
r1.SetFileName(D)
r1.SetUpdateChannel(0)
d1=r1.GetOutput()
itf1=vtkbxd.vtkIntensityTransferFunction()
itf1.SetBrightness(50.0)
ctf1=vtkbxd.vtkColorTransferFunction()
ctf1.AddRGBPoint(0,0,0,0)
ctf1.AddRGBPoint(255.0,0,1.0,0)
print "Feeding channels to merge ",elapsed()
merge = vtkbxd.vtkImageColorMerge()
#merge.SetNumberOfThreads(5)
merge.AddInput(d1)
merge.AddLookupTable(ctf1)
merge.AddIntensityTransferFunction(itf1)
