def deserialize(name, value):
"""
Returns the value of a given key
"""
if "ColorTransferFunction" in name:
data = eval(value)
colorTransferFunction = vtk.vtkColorTransferFunction()
lib.ImageOperations.loadLUTFromString(data, colorTransferFunction)
return colorTransferFunction
# Annotations is a list of classes that can easily be
# pickled / unpickled
if "Annotations" in name:
Logging.info("deserializing Annotations", kw="dataunit")
#val = zlib.decompress(value)
val = pickle.loads(value)
Logging.info("unpickled %d annotations" % len(val), kw="dataunit")
return val
if name not in [
"IntensityTransferFunction", "IntensityTransferFunctions",
"AlphaTransferFunction"
]:
return eval(value)
transferFunction = vtkbxd.vtkIntensityTransferFunction()
lst = eval(value)
lib.ImageOperations.setFromParameterList(transferFunction, lst)
return transferFunction
def initialize(self, dataunit, channels, timepoints):
"""
Set initial values for settings based on
number of channels and timepoints
"""
DataUnitSettings.initialize(self, dataunit, channels, timepoints)
for i in range(channels):
tf = vtkbxd.vtkIntensityTransferFunction()
self.setCounted("IntensityTransferFunction", i, tf, 0)
self.set("PreviewChannel", 1)
def initialize(self, dataunit, channels, timepoints):
"""
Set initial values for settings based on
number of channels and timepoints
"""
DataUnitSettings.initialize(self, dataunit, channels, timepoints)
for i in range(channels):
tf = vtkbxd.vtkIntensityTransferFunction()
self.setCounted("IntensityTransferFunction", i, tf, 0)
self.set("PreviewChannel", 1)
def __init__(self, parent, tb):
"""
Initialization
Parameters:
parent Is the parent widget of this window
"""
self.alphaTF = vtkbxd.vtkIntensityTransferFunction()
self.operationName = "Merge"
self.createItemSelection = 1
TaskPanel.TaskPanel.__init__(self, parent, tb)
self.oldBg = self.GetBackgroundColour()
self.mainsizer.Layout()
self.mainsizer.Fit(self)
def __init__(self, parent, tb): """ Initialization Parameters: parent Is the parent widget of this window """ self.alphaTF = vtkbxd.vtkIntensityTransferFunction() self.operationName = "Merge" self.createItemSelection = 1 TaskPanel.TaskPanel.__init__(self, parent, tb) self.oldBg = self.GetBackgroundColour() self.mainsizer.Layout() self.mainsizer.Fit(self)
def setCombinedDataUnit(self, dataUnit):
"""
Sets the combined dataunit that is to be processed.
It is then used to get the names of all the source
data units and they are added to the menu.
"""
TaskPanel.TaskPanel.setCombinedDataUnit(self, dataUnit)
# We add entry "Alpha Channel" to the list of channels to allow
# the user to edit the alpha channel for the 24-bit color merging
#self.dataUnit.setOpacityTransfer(self.alphaTF)
self.settings.set("AlphaTransferFunction", self.alphaTF)
ctf = self.settings.get("ColorTransferFunction")
sources = dataUnit.getSourceDataUnits()
totmax = 0
for i in sources:
minval, maxval = i.getScalarRange()
ctf = i.getColorTransferFunction()
ctfmin, ctfmax = ctf.GetRange()
bitmax = 0
sBitDepth = i.getSingleComponentBitDepth()
if sBitDepth == 8 or sBitDepth == 12:
bitmax = (2**i.getSingleComponentBitDepth() - 1)
maxval = max(ctfmax, maxval, bitmax)
if maxval > totmax:
totmax = maxval
self.alphaTF.SetRangeMax(int(totmax))
for i in range(len(sources)):
tf = vtkbxd.vtkIntensityTransferFunction()
tf.SetRangeMax(int(totmax))
#self.settings.setCounted("IntensityTransferFunction",i,tf,0)
sources[i].getSettings().set("IntensityTransferFunction", tf)
tf = sources[0].getSettings().get("IntensityTransferFunction")
#print "\n\nSETTING ITF EDITOR FUNCTION"
self.intensityTransferEditor.setIntensityTransferFunction(tf)
for i in range(len(sources)):
self.dataUnit.setOutputChannel(i, 1)
if self.colorBtn:
#Logging.info("Setting ctf of colorbutton to ",ctf,kw="ctf")
self.colorBtn.setColorTransferFunction(ctf)
else:
Logging.info("No color button to set ctf to ", kw="ctf")
self.restoreFromCache()
def setCombinedDataUnit(self, dataUnit):
"""
Sets the combined dataunit that is to be processed.
It is then used to get the names of all the source
data units and they are added to the menu.
"""
TaskPanel.TaskPanel.setCombinedDataUnit(self, dataUnit)
# We add entry "Alpha Channel" to the list of channels to allow
# the user to edit the alpha channel for the 24-bit color merging
#self.dataUnit.setOpacityTransfer(self.alphaTF)
self.settings.set("AlphaTransferFunction", self.alphaTF)
ctf = self.settings.get("ColorTransferFunction")
sources = dataUnit.getSourceDataUnits()
totmax = 0
for i in sources:
minval, maxval = i.getScalarRange()
ctf = i.getColorTransferFunction()
ctfmin, ctfmax = ctf.GetRange()
bitmax = 0
sBitDepth = i.getSingleComponentBitDepth()
if sBitDepth == 8 or sBitDepth == 12:
bitmax = (2**i.getSingleComponentBitDepth()-1)
maxval = max(ctfmax, maxval, bitmax)
if maxval > totmax:
totmax = maxval
self.alphaTF.SetRangeMax(int(totmax))
for i in range(len(sources)):
tf = vtkbxd.vtkIntensityTransferFunction()
tf.SetRangeMax(int(totmax))
#self.settings.setCounted("IntensityTransferFunction",i,tf,0)
sources[i].getSettings().set("IntensityTransferFunction", tf)
tf = sources[0].getSettings().get("IntensityTransferFunction")
#print "\n\nSETTING ITF EDITOR FUNCTION"
self.intensityTransferEditor.setIntensityTransferFunction(tf)
for i in range(len(sources)):
self.dataUnit.setOutputChannel(i, 1)
if self.colorBtn:
#Logging.info("Setting ctf of colorbutton to ",ctf,kw="ctf")
self.colorBtn.setColorTransferFunction(ctf)
else:
Logging.info("No color button to set ctf to ", kw = "ctf")
self.restoreFromCache()
def __init__(self, n = -1):
"""
Constructor
"""
DataUnitSettings.__init__(self, n)
#self.registerCounted("MergingColorTransferFunction",1)
self.set("Type", "Merging")
self.registerCounted("IntensityTransferFunction", 1)
self.register("AlphaTransferFunction", 1)
self.register("AlphaMode")
self.registerCounted("PreviewChannel")
tf = vtkbxd.vtkIntensityTransferFunction()
self.set("AlphaTransferFunction", tf)
self.set("AlphaMode", [0, 0])
def __init__(self, n=-1):
"""
Constructor
"""
DataUnitSettings.__init__(self, n)
#self.registerCounted("MergingColorTransferFunction",1)
self.set("Type", "Merging")
self.registerCounted("IntensityTransferFunction", 1)
self.register("AlphaTransferFunction", 1)
self.register("AlphaMode")
self.registerCounted("PreviewChannel")
tf = vtkbxd.vtkIntensityTransferFunction()
self.set("AlphaTransferFunction", tf)
self.set("AlphaMode", [0, 0])
def resetTransferFunctions(self, event=None):
"""
A method to reset all the intensity transfer functions
"""
dataunits = self.dataUnit.getSourceDataUnits()
for unit in dataunits:
setting = unit.getSettings()
minval, maxval = unit.getScalarRange()
ctf = unit.getColorTransferFunction()
ctfmin, ctfmax = ctf.GetRange()
print "CTF range=", ctfmax
bitmax = (2**unit.getSingleComponentBitDepth() - 1)
print "bitmax=", bitmax
maxval = max(ctfmax, maxval, bitmax)
itf = vtkbxd.vtkIntensityTransferFunction()
itf.SetRangeMax(maxval)
self.alphaTF.SetRangeMax(maxval)
setting.set("IntensityTransferFunction", itf)
def resetTransferFunctions(self, event = None):
"""
A method to reset all the intensity transfer functions
"""
dataunits = self.dataUnit.getSourceDataUnits()
for unit in dataunits:
setting = unit.getSettings()
minval, maxval = unit.getScalarRange()
ctf = unit.getColorTransferFunction()
ctfmin, ctfmax = ctf.GetRange()
print "CTF range=",ctfmax
bitmax = (2**unit.getSingleComponentBitDepth()-1)
print "bitmax=",bitmax
maxval = max(ctfmax, maxval,bitmax)
itf = vtkbxd.vtkIntensityTransferFunction()
itf.SetRangeMax(maxval)
self.alphaTF.SetRangeMax(maxval)
setting.set("IntensityTransferFunction", itf)
def resetTransferFunctions(self, event=None):
"""
A method to reset all the intensity transfer functions
"""
l = self.dataUnit.getNumberOfTimepoints()
sources = self.dataUnit.getSourceDataUnits()
for i in range(l):
minval = min([a.getScalarRange()[0] for a in sources])
maxval = max([a.getScalarRange()[1] for a in sources])
bitdepth = sources[0].getBitDepth()
minval = min(0, minval)
maxval = max(2 ** bitdepth - 1, maxval)
itf = vtkbxd.vtkIntensityTransferFunction()
itf.SetRangeMax(maxval)
self.settings.setCounted("IntensityTransferFunctions", i, itf)
itf = self.settings.getCounted("IntensityTransferFunctions", self.timePoint)
self.iTFEditor.setIntensityTransferFunction(itf)
def resetTransferFunctions(self, event=None):
"""
A method to reset all the intensity transfer functions
"""
l = self.dataUnit.getNumberOfTimepoints()
sources = self.dataUnit.getSourceDataUnits()
for i in range(l):
minval = min([a.getScalarRange()[0] for a in sources])
maxval = max([a.getScalarRange()[1] for a in sources])
bitdepth = sources[0].getBitDepth()
minval = min(0, minval)
maxval = max(2**bitdepth - 1, maxval)
itf = vtkbxd.vtkIntensityTransferFunction()
itf.SetRangeMax(maxval)
self.settings.setCounted("IntensityTransferFunctions", i, itf)
itf = self.settings.getCounted("IntensityTransferFunctions",
self.timePoint)
self.iTFEditor.setIntensityTransferFunction(itf)
def initialize(self, dataunit, channels, timepoints):
"""
Set initial values for settings based on
number of channels and timepoints
"""
DataUnitSettings.initialize(self, dataunit, channels, timepoints)
ctf = self.get("ColorTransferFunction")
if hasattr(dataunit, "getScalarRange"):
minval, maxval = dataunit.getScalarRange()
bitdepth = dataunit.getBitDepth()
else:
minval, maxval = dataunit.getSourceDataUnits()[0].getScalarRange()
bitdepth = dataunit.getSourceDataUnits()[0].getBitDepth()
minval = min(0,minval)
maxval = max(2**bitdepth-1, maxval)
for i in range(timepoints):
tf = vtkbxd.vtkIntensityTransferFunction()
tf.SetRangeMax(maxval)
self.setCounted("IntensityTransferFunctions", i, tf, 0)
def initialize(self, dataunit, channels, timepoints):
"""
Set initial values for settings based on
number of channels and timepoints
"""
DataUnitSettings.initialize(self, dataunit, channels, timepoints)
ctf = self.get("ColorTransferFunction")
if hasattr(dataunit, "getScalarRange"):
minval, maxval = dataunit.getScalarRange()
bitdepth = dataunit.getBitDepth()
else:
minval, maxval = dataunit.getSourceDataUnits()[0].getScalarRange()
bitdepth = dataunit.getSourceDataUnits()[0].getBitDepth()
minval = min(0, minval)
maxval = max(2**bitdepth - 1, maxval)
for i in range(timepoints):
tf = vtkbxd.vtkIntensityTransferFunction()
tf.SetRangeMax(maxval)
self.setCounted("IntensityTransferFunctions", i, tf, 0)
def deserialize(name, value):
"""
Returns the value of a given key
"""
if "ColorTransferFunction" in name:
data = eval(value)
colorTransferFunction = vtk.vtkColorTransferFunction()
lib.ImageOperations.loadLUTFromString(data, colorTransferFunction)
return colorTransferFunction
# Annotations is a list of classes that can easily be
# pickled / unpickled
if "Annotations" in name:
Logging.info("deserializing Annotations", kw = "dataunit")
#val = zlib.decompress(value)
val = pickle.loads(value)
Logging.info("unpickled %d annotations" % len(val), kw = "dataunit")
return val
if name not in ["IntensityTransferFunction", "IntensityTransferFunctions", "AlphaTransferFunction"]:
return eval(value)
transferFunction = vtkbxd.vtkIntensityTransferFunction()
lst = eval(value)
lib.ImageOperations.setFromParameterList(transferFunction, lst)
return transferFunction
def __init__(self, parent, **kws):
"""
Initialization
"""
self.parent = parent
wx.Panel.__init__(self, parent, -1)
self.doyield = 1
self.calling = 0
self.guiupdate = 0
self.iTF = vtkbxd.vtkIntensityTransferFunction()
self.mainsizer = wx.BoxSizer(wx.VERTICAL)
self.canvasBox = wx.BoxSizer(wx.HORIZONTAL)
self.contrastBox = wx.BoxSizer(wx.VERTICAL)
self.gammaBox = wx.BoxSizer(wx.HORIZONTAL)
self.brightnessBox = wx.BoxSizer(wx.HORIZONTAL)
self.contrastSlider = RangedSlider.RangedSlider(self,
-1,
10000,
size=(-1, 280),
style=wx.SL_VERTICAL)
self.contrastSlider.setSnapPoint(1.0, 0.1)
self.contrastSlider.setRange(0, 50, 0.0001, 1.0)
self.contrastSlider.setRange(50.01, 100, 1.0, 20.0)
self.contrastSlider.setScaledValue(1.0)
self.contrastLbl = wx.StaticText(self, -1, "Contrast")
self.Bind(wx.EVT_COMMAND_SCROLL, self.setContrast, self.contrastSlider)
self.canvas = PaintPanel(self)
self.canvasBox.Add(self.canvas, 1, wx.ALL | wx.EXPAND, 10)
self.canvasBox.Add(self.contrastBox)
self.contrastEdit = wx.TextCtrl(self, -1, "1.00", size=(50, -1))
self.contrastBox.Add(self.contrastLbl)
self.contrastBox.Add(self.contrastEdit)
self.contrastBox.Add(self.contrastSlider, 1, wx.TOP | wx.BOTTOM, 0)
self.brightnessEdit = wx.TextCtrl(self,
-1,
"0.00",
size=(70, -1),
style=wx.TE_PROCESS_ENTER)
self.gammaEdit = wx.TextCtrl(self,
-1,
"1.00",
size=(70, -1),
style=wx.TE_PROCESS_ENTER)
self.gammaEdit.SetForegroundColour(scripting.COLOR_EXPERIENCED)
self.brightnessSlider = RangedSlider.RangedSlider(
self, -1, 5000, size=(260, -1), style=wx.SL_HORIZONTAL)
self.brightnessSlider.setRange(0, 100, -255, 255)
self.brightnessSlider.setSnapPoint(0.0, 0.1)
self.brightnessSlider.setScaledValue(0.1)
self.Bind(wx.EVT_COMMAND_SCROLL, self.setBrightness,
self.brightnessSlider)
self.gammaSlider = RangedSlider.RangedSlider(self,
-1,
10000,
size=(260, -1),
style=wx.SL_HORIZONTAL)
self.gammaSlider.setRange(0, 50, 0.0001, 1.0)
self.gammaSlider.setRange(50.01, 100, 1.0, 15.0)
self.gammaSlider.setScaledValue(1.0)
self.gammaSlider.setSnapPoint(1.0, 0.1)
self.Bind(wx.EVT_COMMAND_SCROLL, self.setGamma, self.gammaSlider)
self.gammaBox.Add(self.gammaSlider)
self.gammaBox.Add(self.gammaEdit, 0, wx.ALIGN_CENTER_VERTICAL | wx.ALL)
self.brightnessBox.Add(self.brightnessSlider)
self.brightnessBox.Add(self.brightnessEdit, 0,
wx.ALIGN_CENTER_VERTICAL | wx.ALL)
self.minValueLbl = wx.StaticText(self, wx.NewId(), "Min value:")
self.minValueLbl.SetForegroundColour(scripting.COLOR_EXPERIENCED)
self.maxValueLbl = wx.StaticText(self, wx.NewId(), "Max value:")
self.maxValueLbl.SetForegroundColour(scripting.COLOR_EXPERIENCED)
self.minValue = wx.TextCtrl(self,
-1,
style=wx.TE_PROCESS_ENTER,
size=(70, -1))
self.minValue.SetForegroundColour(scripting.COLOR_EXPERIENCED)
self.maxValue = wx.TextCtrl(self,
-1,
style=wx.TE_PROCESS_ENTER,
size=(70, -1))
self.maxValue.SetForegroundColour(scripting.COLOR_EXPERIENCED)
fieldsizer = wx.GridBagSizer(0, 5)
valuesizer = wx.BoxSizer(wx.HORIZONTAL)
fieldsizer.Add(self.minValueLbl, (0, 0))
fieldsizer.Add(self.minValue, (0, 1))
fieldsizer.Add(self.maxValueLbl, (0, 2))
fieldsizer.Add(self.maxValue, (0, 3))
self.minthresholdLbl = wx.StaticText(self, wx.NewId(),
"Min threshold:")
self.minthresholdLbl.SetForegroundColour(scripting.COLOR_EXPERIENCED)
self.maxthresholdLbl = wx.StaticText(self, wx.NewId(),
"Max threshold:")
self.maxthresholdLbl.SetForegroundColour(scripting.COLOR_EXPERIENCED)
self.minthreshold = wx.TextCtrl(self,
-1,
style=wx.TE_PROCESS_ENTER,
size=(70, -1))
self.minthreshold.SetForegroundColour(scripting.COLOR_EXPERIENCED)
self.maxthreshold = wx.TextCtrl(self,
-1,
style=wx.TE_PROCESS_ENTER,
size=(70, -1))
self.maxthreshold.SetForegroundColour(scripting.COLOR_EXPERIENCED)
fieldsizer.Add(self.minthresholdLbl, (1, 0))
fieldsizer.Add(self.minthreshold, (1, 1))
fieldsizer.Add(self.maxthresholdLbl, (1, 2))
fieldsizer.Add(self.maxthreshold, (1, 3))
#self.minProcessLbl=wx.StaticText(self,-1,"Processing\nthreshold:")
#TODO: is following line important? at the moment minProcess is used later in code. 19.7.2007 SS
#self.minProcess=wx.TextCtrl(self,-1,style=wx.TE_PROCESS_ENTER)
#fieldsizer.Add(self.minProcessLbl,(2,0))
#fieldsizer.Add(self.minProcess,(2,1))
self.ssThresholdLbl = wx.StaticText(self, -1, "Smooth start:")
self.ssThresholdLbl.SetForegroundColour(scripting.COLOR_EXPERIENCED)
self.ssThreshold = wx.TextCtrl(self,
-1,
"0",
style=wx.TE_PROCESS_ENTER,
size=(70, -1))
self.ssThreshold.SetForegroundColour(scripting.COLOR_EXPERIENCED)
self.ssgammaEdit = wx.TextCtrl(self,
-1,
"1.00",
size=(70, -1),
style=wx.TE_PROCESS_ENTER)
self.ssgammaEdit.SetForegroundColour(scripting.COLOR_EXPERIENCED)
self.ssgammaSlider = RangedSlider.RangedSlider(self,
-1,
10000,
size=(150, -1),
style=wx.SL_HORIZONTAL)
self.ssgammaSlider.setRange(0, 50, 0.0001, 1.0)
self.ssgammaSlider.setRange(50.01, 100, 1.0, 15.0)
self.ssgammaSlider.setScaledValue(1.0)
self.ssgammaSlider.setSnapPoint(1.0, 0.1)
self.ssgammaSlider.SetForegroundColour(scripting.COLOR_EXPERIENCED)
self.Bind(wx.EVT_COMMAND_SCROLL, self.setSSGamma, self.ssgammaSlider)
fieldsizer.Add(self.ssThresholdLbl, (2, 0))
fieldsizer.Add(self.ssThreshold, (2, 1))
fieldsizer.Add(self.ssgammaSlider, (2, 2))
fieldsizer.Add(self.ssgammaEdit, (2, 3))
self.seThresholdLbl = wx.StaticText(self, -1, "Smooth end:")
self.seThresholdLbl.SetForegroundColour(scripting.COLOR_EXPERIENCED)
self.seThreshold = wx.TextCtrl(self,
-1,
"255",
style=wx.TE_PROCESS_ENTER,
size=(70, -1))
self.seThreshold.SetForegroundColour(scripting.COLOR_EXPERIENCED)
self.segammaEdit = wx.TextCtrl(self,
-1,
"1.00",
size=(70, -1),
style=wx.TE_PROCESS_ENTER)
self.segammaEdit.SetForegroundColour(scripting.COLOR_EXPERIENCED)
self.segammaSlider = RangedSlider.RangedSlider(self,
-1,
10000,
size=(150, -1),
style=wx.SL_HORIZONTAL)
self.segammaSlider.setRange(0, 50, 0.0001, 1.0)
self.segammaSlider.setRange(50.01, 100, 1.0, 15.0)
self.segammaSlider.setScaledValue(1.0)
self.segammaSlider.setSnapPoint(1.0, 0.1)
self.segammaSlider.SetForegroundColour(scripting.COLOR_EXPERIENCED)
self.Bind(wx.EVT_COMMAND_SCROLL, self.setSEGamma, self.segammaSlider)
self.seThreshold.Bind(wx.EVT_KILL_FOCUS, self.updateSE)
self.seThreshold.Bind(wx.EVT_TEXT_ENTER, self.updateSE)
self.ssThreshold.Bind(wx.EVT_KILL_FOCUS, self.updateSS)
self.ssThreshold.Bind(wx.EVT_TEXT_ENTER, self.updateSS)
fieldsizer.Add(self.seThresholdLbl, (3, 0))
fieldsizer.Add(self.seThreshold, (3, 1))
fieldsizer.Add(self.segammaSlider, (3, 2))
fieldsizer.Add(self.segammaEdit, (3, 3))
self.gammaEdit.Bind(wx.EVT_KILL_FOCUS, self.updateGamma)
self.gammaEdit.Bind(wx.EVT_TEXT_ENTER, self.updateGamma)
self.contrastEdit.Bind(wx.EVT_KILL_FOCUS, self.updateContrast)
self.contrastEdit.Bind(wx.EVT_TEXT_ENTER, self.updateContrast)
self.brightnessEdit.Bind(wx.EVT_KILL_FOCUS, self.updateBrightness)
self.brightnessEdit.Bind(wx.EVT_TEXT_ENTER, self.updateBrightness)
self.minValue.Bind(wx.EVT_KILL_FOCUS, self.updateMinimumValue)
self.minValue.Bind(wx.EVT_TEXT_ENTER, self.updateMinimumValue)
self.maxValue.Bind(wx.EVT_KILL_FOCUS, self.updateMaximumValue)
self.maxValue.Bind(wx.EVT_TEXT_ENTER, self.updateMaximumValue)
self.minthreshold.Bind(wx.EVT_KILL_FOCUS, self.updateMinimumThreshold)
self.minthreshold.Bind(wx.EVT_TEXT_ENTER, self.updateMinimumThreshold)
self.maxthreshold.Bind(wx.EVT_KILL_FOCUS, self.updateMaximumThreshold)
self.maxthreshold.Bind(wx.EVT_TEXT_ENTER, self.updateMaximumThreshold)
self.setMinimumThreshold(0)
self.setMaximumThreshold(255)
self.setMinimumValue(0)
self.setMaximumValue(255)
self.mainsizer.Add(self.canvasBox)
self.gammaLbl = wx.StaticText(self, -1, "Gamma")
self.gammaLbl.SetForegroundColour(scripting.COLOR_EXPERIENCED)
self.brightnessLbl = wx.StaticText(self, -1, "Brightness")
self.mainsizer.Add(self.brightnessLbl)
self.mainsizer.Add(self.brightnessBox)
self.mainsizer.Add(self.gammaLbl)
self.mainsizer.Add(self.gammaBox)
self.mainsizer.Add(fieldsizer)
# self.mainsizer.Add(self.defaultBtn)
self.SetAutoLayout(True)
self.SetSizer(self.mainsizer)
self.mainsizer.SetSizeHints(self)
self.updateGraph()
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)
itfmap = vtkbxd.vtkImageMapToIntensities()
itfmap.SetInput(d1)
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)
itfmap = vtkbxd.vtkImageMapToIntensities()
def __init__(self, parent, **kws):
"""
Initialization
"""
self.parent = parent
wx.Panel.__init__(self, parent, -1)
self.doyield = 1
self.calling = 0
self.guiupdate = 0
self.iTF = vtkbxd.vtkIntensityTransferFunction()
self.mainsizer = wx.BoxSizer(wx.VERTICAL)
self.canvasBox = wx.BoxSizer(wx.HORIZONTAL)
self.contrastBox = wx.BoxSizer(wx.VERTICAL)
self.gammaBox = wx.BoxSizer(wx.HORIZONTAL)
self.brightnessBox = wx.BoxSizer(wx.HORIZONTAL)
self.contrastSlider = RangedSlider.RangedSlider(self, -1, 10000, size=(-1, 280), style=wx.SL_VERTICAL)
self.contrastSlider.setSnapPoint(1.0, 0.1)
self.contrastSlider.setRange(0, 50, 0.0001, 1.0)
self.contrastSlider.setRange(50.01, 100, 1.0, 20.0)
self.contrastSlider.setScaledValue(1.0)
self.contrastLbl = wx.StaticText(self, -1, "Contrast")
self.Bind(wx.EVT_COMMAND_SCROLL, self.setContrast, self.contrastSlider)
self.canvas = PaintPanel(self)
self.canvasBox.Add(self.canvas, 1, wx.ALL | wx.EXPAND, 10)
self.canvasBox.Add(self.contrastBox)
self.contrastEdit = wx.TextCtrl(self, -1, "1.00", size=(50, -1))
self.contrastBox.Add(self.contrastLbl)
self.contrastBox.Add(self.contrastEdit)
self.contrastBox.Add(self.contrastSlider, 1, wx.TOP | wx.BOTTOM, 0)
self.brightnessEdit = wx.TextCtrl(self, -1, "0.00", size=(70, -1), style=wx.TE_PROCESS_ENTER)
self.gammaEdit = wx.TextCtrl(self, -1, "1.00", size=(70, -1), style=wx.TE_PROCESS_ENTER)
self.gammaEdit.SetForegroundColour(scripting.COLOR_EXPERIENCED)
self.brightnessSlider = RangedSlider.RangedSlider(self, -1, 5000, size=(260, -1), style=wx.SL_HORIZONTAL)
self.brightnessSlider.setRange(0, 100, -255, 255)
self.brightnessSlider.setSnapPoint(0.0, 0.1)
self.brightnessSlider.setScaledValue(0.1)
self.Bind(wx.EVT_COMMAND_SCROLL, self.setBrightness, self.brightnessSlider)
self.gammaSlider = RangedSlider.RangedSlider(self, -1, 10000, size=(260, -1), style=wx.SL_HORIZONTAL)
self.gammaSlider.setRange(0, 50, 0.0001, 1.0)
self.gammaSlider.setRange(50.01, 100, 1.0, 15.0)
self.gammaSlider.setScaledValue(1.0)
self.gammaSlider.setSnapPoint(1.0, 0.1)
self.Bind(wx.EVT_COMMAND_SCROLL, self.setGamma, self.gammaSlider)
self.gammaBox.Add(self.gammaSlider)
self.gammaBox.Add(self.gammaEdit, 0, wx.ALIGN_CENTER_VERTICAL | wx.ALL)
self.brightnessBox.Add(self.brightnessSlider)
self.brightnessBox.Add(self.brightnessEdit, 0, wx.ALIGN_CENTER_VERTICAL | wx.ALL)
self.minValueLbl = wx.StaticText(self, wx.NewId(), "Min value:")
self.minValueLbl.SetForegroundColour(scripting.COLOR_EXPERIENCED)
self.maxValueLbl = wx.StaticText(self, wx.NewId(), "Max value:")
self.maxValueLbl.SetForegroundColour(scripting.COLOR_EXPERIENCED)
self.minValue = wx.TextCtrl(self, -1, style=wx.TE_PROCESS_ENTER, size=(70, -1))
self.minValue.SetForegroundColour(scripting.COLOR_EXPERIENCED)
self.maxValue = wx.TextCtrl(self, -1, style=wx.TE_PROCESS_ENTER, size=(70, -1))
self.maxValue.SetForegroundColour(scripting.COLOR_EXPERIENCED)
fieldsizer = wx.GridBagSizer(0, 5)
valuesizer = wx.BoxSizer(wx.HORIZONTAL)
fieldsizer.Add(self.minValueLbl, (0, 0))
fieldsizer.Add(self.minValue, (0, 1))
fieldsizer.Add(self.maxValueLbl, (0, 2))
fieldsizer.Add(self.maxValue, (0, 3))
self.minthresholdLbl = wx.StaticText(self, wx.NewId(), "Min threshold:")
self.minthresholdLbl.SetForegroundColour(scripting.COLOR_EXPERIENCED)
self.maxthresholdLbl = wx.StaticText(self, wx.NewId(), "Max threshold:")
self.maxthresholdLbl.SetForegroundColour(scripting.COLOR_EXPERIENCED)
self.minthreshold = wx.TextCtrl(self, -1, style=wx.TE_PROCESS_ENTER, size=(70, -1))
self.minthreshold.SetForegroundColour(scripting.COLOR_EXPERIENCED)
self.maxthreshold = wx.TextCtrl(self, -1, style=wx.TE_PROCESS_ENTER, size=(70, -1))
self.maxthreshold.SetForegroundColour(scripting.COLOR_EXPERIENCED)
fieldsizer.Add(self.minthresholdLbl, (1, 0))
fieldsizer.Add(self.minthreshold, (1, 1))
fieldsizer.Add(self.maxthresholdLbl, (1, 2))
fieldsizer.Add(self.maxthreshold, (1, 3))
# self.minProcessLbl=wx.StaticText(self,-1,"Processing\nthreshold:")
# TODO: is following line important? at the moment minProcess is used later in code. 19.7.2007 SS
# self.minProcess=wx.TextCtrl(self,-1,style=wx.TE_PROCESS_ENTER)
# fieldsizer.Add(self.minProcessLbl,(2,0))
# fieldsizer.Add(self.minProcess,(2,1))
self.ssThresholdLbl = wx.StaticText(self, -1, "Smooth start:")
self.ssThresholdLbl.SetForegroundColour(scripting.COLOR_EXPERIENCED)
self.ssThreshold = wx.TextCtrl(self, -1, "0", style=wx.TE_PROCESS_ENTER, size=(70, -1))
self.ssThreshold.SetForegroundColour(scripting.COLOR_EXPERIENCED)
self.ssgammaEdit = wx.TextCtrl(self, -1, "1.00", size=(70, -1), style=wx.TE_PROCESS_ENTER)
self.ssgammaEdit.SetForegroundColour(scripting.COLOR_EXPERIENCED)
self.ssgammaSlider = RangedSlider.RangedSlider(self, -1, 10000, size=(150, -1), style=wx.SL_HORIZONTAL)
self.ssgammaSlider.setRange(0, 50, 0.0001, 1.0)
self.ssgammaSlider.setRange(50.01, 100, 1.0, 15.0)
self.ssgammaSlider.setScaledValue(1.0)
self.ssgammaSlider.setSnapPoint(1.0, 0.1)
self.ssgammaSlider.SetForegroundColour(scripting.COLOR_EXPERIENCED)
self.Bind(wx.EVT_COMMAND_SCROLL, self.setSSGamma, self.ssgammaSlider)
fieldsizer.Add(self.ssThresholdLbl, (2, 0))
fieldsizer.Add(self.ssThreshold, (2, 1))
fieldsizer.Add(self.ssgammaSlider, (2, 2))
fieldsizer.Add(self.ssgammaEdit, (2, 3))
self.seThresholdLbl = wx.StaticText(self, -1, "Smooth end:")
self.seThresholdLbl.SetForegroundColour(scripting.COLOR_EXPERIENCED)
self.seThreshold = wx.TextCtrl(self, -1, "255", style=wx.TE_PROCESS_ENTER, size=(70, -1))
self.seThreshold.SetForegroundColour(scripting.COLOR_EXPERIENCED)
self.segammaEdit = wx.TextCtrl(self, -1, "1.00", size=(70, -1), style=wx.TE_PROCESS_ENTER)
self.segammaEdit.SetForegroundColour(scripting.COLOR_EXPERIENCED)
self.segammaSlider = RangedSlider.RangedSlider(self, -1, 10000, size=(150, -1), style=wx.SL_HORIZONTAL)
self.segammaSlider.setRange(0, 50, 0.0001, 1.0)
self.segammaSlider.setRange(50.01, 100, 1.0, 15.0)
self.segammaSlider.setScaledValue(1.0)
self.segammaSlider.setSnapPoint(1.0, 0.1)
self.segammaSlider.SetForegroundColour(scripting.COLOR_EXPERIENCED)
self.Bind(wx.EVT_COMMAND_SCROLL, self.setSEGamma, self.segammaSlider)
self.seThreshold.Bind(wx.EVT_KILL_FOCUS, self.updateSE)
self.seThreshold.Bind(wx.EVT_TEXT_ENTER, self.updateSE)
self.ssThreshold.Bind(wx.EVT_KILL_FOCUS, self.updateSS)
self.ssThreshold.Bind(wx.EVT_TEXT_ENTER, self.updateSS)
fieldsizer.Add(self.seThresholdLbl, (3, 0))
fieldsizer.Add(self.seThreshold, (3, 1))
fieldsizer.Add(self.segammaSlider, (3, 2))
fieldsizer.Add(self.segammaEdit, (3, 3))
self.gammaEdit.Bind(wx.EVT_KILL_FOCUS, self.updateGamma)
self.gammaEdit.Bind(wx.EVT_TEXT_ENTER, self.updateGamma)
self.contrastEdit.Bind(wx.EVT_KILL_FOCUS, self.updateContrast)
self.contrastEdit.Bind(wx.EVT_TEXT_ENTER, self.updateContrast)
self.brightnessEdit.Bind(wx.EVT_KILL_FOCUS, self.updateBrightness)
self.brightnessEdit.Bind(wx.EVT_TEXT_ENTER, self.updateBrightness)
self.minValue.Bind(wx.EVT_KILL_FOCUS, self.updateMinimumValue)
self.minValue.Bind(wx.EVT_TEXT_ENTER, self.updateMinimumValue)
self.maxValue.Bind(wx.EVT_KILL_FOCUS, self.updateMaximumValue)
self.maxValue.Bind(wx.EVT_TEXT_ENTER, self.updateMaximumValue)
self.minthreshold.Bind(wx.EVT_KILL_FOCUS, self.updateMinimumThreshold)
self.minthreshold.Bind(wx.EVT_TEXT_ENTER, self.updateMinimumThreshold)
self.maxthreshold.Bind(wx.EVT_KILL_FOCUS, self.updateMaximumThreshold)
self.maxthreshold.Bind(wx.EVT_TEXT_ENTER, self.updateMaximumThreshold)
self.setMinimumThreshold(0)
self.setMaximumThreshold(255)
self.setMinimumValue(0)
self.setMaximumValue(255)
self.mainsizer.Add(self.canvasBox)
self.gammaLbl = wx.StaticText(self, -1, "Gamma")
self.gammaLbl.SetForegroundColour(scripting.COLOR_EXPERIENCED)
self.brightnessLbl = wx.StaticText(self, -1, "Brightness")
self.mainsizer.Add(self.brightnessLbl)
self.mainsizer.Add(self.brightnessBox)
self.mainsizer.Add(self.gammaLbl)
self.mainsizer.Add(self.gammaBox)
self.mainsizer.Add(fieldsizer)
# self.mainsizer.Add(self.defaultBtn)
self.SetAutoLayout(True)
self.SetSizer(self.mainsizer)
self.mainsizer.SetSizeHints(self)
self.updateGraph()
