def createRescale(self):
"""
Creates the GUI for controlling the rescaling
"""
box = wx.StaticBox(self, -1, "Preview selected mapping")
previewBox = wx.StaticBoxSizer(box, wx.HORIZONTAL)
self.preview = PreviewFrame(self,
previewsize=(256, 256),
scrollbars=False)
previewBox.Add(self.preview)
self.zslider = wx.Slider(self,
value=1,
minValue=1,
maxValue=1,
style=wx.SL_VERTICAL | wx.SL_LABELS
| wx.SL_AUTOTICKS)
self.zslider.SetHelpText(
"Use this slider to select the displayed optical slice.")
self.zslider.Bind(wx.EVT_SCROLL, self.onChangeZSlice)
previewBox.Add(self.zslider, 1, wx.EXPAND)
box = wx.StaticBox(self, -1, "Channel histograms")
self.histogramSizer = wx.StaticBoxSizer(box, wx.HORIZONTAL)
self.sizer.Add(previewBox, (0, 0), flag=wx.EXPAND | wx.ALL)
self.sizer.Add(self.histogramSizer, (2, 0), flag=wx.EXPAND | wx.ALL)
def createRescale(self):
"""
Creates the GUI for controlling the rescaling
"""
box = wx.StaticBox(self, -1, "Preview selected mapping")
previewBox = wx.StaticBoxSizer(box, wx.HORIZONTAL)
self.preview = PreviewFrame(self, previewsize = (256, 256), scrollbars = False)
previewBox.Add(self.preview)
self.zslider = wx.Slider(self, value = 1, minValue = 1, maxValue = 1,
style = wx.SL_VERTICAL | wx.SL_LABELS | wx.SL_AUTOTICKS)
self.zslider.SetHelpText("Use this slider to select the displayed optical slice.")
self.zslider.Bind(wx.EVT_SCROLL, self.onChangeZSlice)
previewBox.Add(self.zslider, 1, wx.EXPAND)
box = wx.StaticBox(self, -1, "Channel histograms")
self.histogramSizer = wx.StaticBoxSizer(box, wx.HORIZONTAL)
self.sizer.Add(previewBox, (0, 0), flag = wx.EXPAND | wx.ALL)
self.sizer.Add(self.histogramSizer, (2, 0), flag = wx.EXPAND | wx.ALL)
class RescaleDialog(wx.Dialog):
"""
Description: A dialog for rescaling a dataset to 8-bit
"""
def __init__(self, parent):
"""
Initialize the dialog
"""
wx.Dialog.__init__(self,
parent,
-1,
'Select mapping to 8-bit values',
size=(640, 480))
self.sizer = wx.GridBagSizer()
self.btnsizer = wx.BoxSizer(wx.HORIZONTAL)
self.histograms = []
self.dataUnits = []
self.resampleDims = []
self.shift = 0
self.scale = 0
self.taskPanels = Modules.DynamicLoader.getTaskModules()
self.createRescale()
self.lbl = wx.StaticText(
self, -1,
"""BioImageXD recommends 8-bit images (intensity values between 0 and 255) for most purposes. This tool converts other bit depths to 8-bit.\nUse the histograms below to select how the intensities in your dataset are mapped to the range 0-255, then click "Convert".\nClick "Convert without mapping" to directly use only the values 0-255 in your original dataset for the resulting dataset.
""")
lblbox = wx.BoxSizer(wx.VERTICAL)
hdr = wx.StaticText(self, -1, "Select mapping to 8-bit values",
(20, 120))
font = wx.Font(14, wx.SWISS, wx.NORMAL, wx.NORMAL)
hdr.SetFont(font)
lblbox.Add(hdr)
lblbox.Add(self.lbl)
self.sizer.Add(lblbox, (1, 0), flag=wx.EXPAND | wx.LEFT | wx.RIGHT)
self.sizer.Add(self.btnsizer, (3, 0),
flag=wx.EXPAND | wx.RIGHT | wx.LEFT)
self.okButton = wx.Button(self, -1, "Convert")
self.noScalingButton = wx.Button(self, -1, "Convert without mapping")
self.cancelButton = wx.Button(self, -1, "Cancel")
self.okButton.Bind(wx.EVT_BUTTON, self.onOkButton)
self.noScalingButton.Bind(wx.EVT_BUTTON, self.onNoScaling)
self.cancelButton.Bind(wx.EVT_BUTTON, self.onCancelButton)
self.btnsizer.Add(self.okButton)
self.btnsizer.Add(self.noScalingButton)
self.btnsizer.Add(self.cancelButton)
self.result = 0
self.SetSizer(self.sizer)
self.SetAutoLayout(1)
self.sizer.Fit(self)
def onNoScaling(self, event):
"""
Do not use any intensity scaling
"""
self.result = 1
for i, dataUnit in enumerate(self.dataUnits):
ds = dataUnit.getDataSource()
ds.setIntensityScale(-1, -1)
self.EndModal(wx.ID_OK)
def onCancelButton(self, event):
"""
Cancel the procedure
"""
self.result = 0
self.EndModal(wx.ID_CANCEL)
def onOkButton(self, event):
"""
Executes the procedure
"""
for i, dataUnit in enumerate(self.dataUnits):
ds = dataUnit.getDataSource()
bitdepth = ds.getSingleComponentBitDepth()
self.scale = 255.0 / (2**bitdepth - 1)
print "Setting intensity scale", self.shift, self.scale
ds.setIntensityScale(self.shift, self.scale)
ds.resetColorTransferFunction()
dataUnit.resetColorTransferFunction()
self.result = 1
#self.Close()
self.EndModal(wx.ID_OK)
def zoomToFit(self):
self.preview.zoomToFit()
def setDataUnits(self, dataunits):
"""
Set the dataunits to be resampled
"""
self.dataUnits = dataunits
unitclass = self.taskPanels["Merging"][2].getDataUnit()
self.mergeUnit = unitclass("Preview for scaling intensity")
for dataUnit in dataunits:
#print "Creating histogram for ",dataUnit
self.mergeUnit.addSourceDataUnit(dataUnit)
x, y, z = dataUnit.getDimensions()
ds = dataUnit.getDataSource()
minval, maxval = ds.getOriginalScalarRange()
#print "Original scalar range = ",minval,maxval
self.resampleDims.append(ds.getResampleDimensions())
scale = maxval / 255.0
print "Scale for histograms = ", scale
#"Using scale",scale
histogram = Histogram.Histogram(self,
scale=scale,
lowerThreshold=minval,
upperThreshold=maxval)
self.histogramSizer.Add(histogram)
self.histograms.append(histogram)
histogram.setThresholdMode(1)
histogram.setDataUnit(dataUnit, noupdate=1)
lib.messenger.connect(histogram, "threshold_changed",
self.onSetThreshold)
x, y, z = dataUnit.getDimensions()
self.zslider.SetRange(1, z)
moduletype = self.taskPanels["Merging"][0]
module = moduletype()
self.mergeUnit.setModule(module)
self.preview.setDataUnit(self.mergeUnit)
self.preview.zoomToFit()
self.preview.updatePreview()
self.sizer.Fit(self)
self.Layout()
def onSetThreshold(self, obj, event, lower, upper):
"""
An event handler for updating the thresholds based on one of the histograms
"""
n = self.histograms.index(obj)
dataUnit = self.dataUnits[n]
minval, maxval = dataUnit.getDataSource().getOriginalScalarRange()
#print "Original scalar range=",minval,maxval
if lower == 0 and upper == 255:
self.shift = 0
self.scale = 255.0 / maxval
else:
upper = upper * (maxval / 255.0)
lower = lower * (maxval / 255.0)
self.shift = -int(lower)
self.scale = 255.0 / ((upper - lower))
dataUnit.getDataSource().setIntensityScale(self.shift, self.scale)
dataUnit.resetColorTransferFunction()
self.preview.updatePreview(1)
def createRescale(self):
"""
Creates the GUI for controlling the rescaling
"""
box = wx.StaticBox(self, -1, "Preview selected mapping")
previewBox = wx.StaticBoxSizer(box, wx.HORIZONTAL)
self.preview = PreviewFrame(self,
previewsize=(256, 256),
scrollbars=False)
previewBox.Add(self.preview)
self.zslider = wx.Slider(self,
value=1,
minValue=1,
maxValue=1,
style=wx.SL_VERTICAL | wx.SL_LABELS
| wx.SL_AUTOTICKS)
self.zslider.SetHelpText(
"Use this slider to select the displayed optical slice.")
self.zslider.Bind(wx.EVT_SCROLL, self.onChangeZSlice)
previewBox.Add(self.zslider, 1, wx.EXPAND)
box = wx.StaticBox(self, -1, "Channel histograms")
self.histogramSizer = wx.StaticBoxSizer(box, wx.HORIZONTAL)
self.sizer.Add(previewBox, (0, 0), flag=wx.EXPAND | wx.ALL)
self.sizer.Add(self.histogramSizer, (2, 0), flag=wx.EXPAND | wx.ALL)
def onChangeZSlice(self, event):
"""
Set the zslice displayed
"""
self.preview.setZSlice(self.zslider.GetValue() - 1)
self.preview.updatePreview(0)
class RescaleDialog(wx.Dialog):
"""
Description: A dialog for rescaling a dataset to 8-bit
"""
def __init__(self, parent):
"""
Initialize the dialog
"""
wx.Dialog.__init__(self, parent, -1, 'Select mapping to 8-bit values', size = (640, 480))
self.sizer = wx.GridBagSizer()
self.btnsizer = wx.BoxSizer(wx.HORIZONTAL)
self.histograms = []
self.dataUnits = []
self.resampleDims = []
self.shift = 0
self.scale = 0
self.taskPanels = Modules.DynamicLoader.getTaskModules()
self.createRescale()
self.lbl = wx.StaticText(self, -1,
"""BioImageXD recommends 8-bit images (intensity values between 0 and 255) for most purposes. This tool converts other bit depths to 8-bit.\nUse the histograms below to select how the intensities in your dataset are mapped to the range 0-255, then click "Convert".\nClick "Convert without mapping" to directly use only the values 0-255 in your original dataset for the resulting dataset.
""")
lblbox = wx.BoxSizer(wx.VERTICAL)
hdr = wx.StaticText(self, -1, "Select mapping to 8-bit values", (20, 120))
font = wx.Font(14, wx.SWISS, wx.NORMAL, wx.NORMAL)
hdr.SetFont(font)
lblbox.Add(hdr)
lblbox.Add(self.lbl)
self.sizer.Add(lblbox, (1, 0), flag = wx.EXPAND | wx.LEFT | wx.RIGHT)
self.sizer.Add(self.btnsizer, (3, 0), flag = wx.EXPAND | wx.RIGHT | wx.LEFT)
self.okButton = wx.Button(self, -1, "Convert")
self.noScalingButton = wx.Button(self, -1, "Convert without mapping")
self.cancelButton = wx.Button(self, -1, "Cancel")
self.okButton.Bind(wx.EVT_BUTTON, self.onOkButton)
self.noScalingButton.Bind(wx.EVT_BUTTON, self.onNoScaling)
self.cancelButton.Bind(wx.EVT_BUTTON, self.onCancelButton)
self.btnsizer.Add(self.okButton)
self.btnsizer.Add(self.noScalingButton)
self.btnsizer.Add(self.cancelButton)
self.result = 0
self.SetSizer(self.sizer)
self.SetAutoLayout(1)
self.sizer.Fit(self)
def onNoScaling(self, event):
"""
Do not use any intensity scaling
"""
self.result = 1
for i, dataUnit in enumerate(self.dataUnits):
ds = dataUnit.getDataSource()
ds.setIntensityScale(-1, -1)
self.EndModal(wx.ID_OK)
def onCancelButton(self, event):
"""
Cancel the procedure
"""
self.result = 0
self.EndModal(wx.ID_CANCEL)
def onOkButton(self, event):
"""
Executes the procedure
"""
for i, dataUnit in enumerate(self.dataUnits):
ds = dataUnit.getDataSource()
bitdepth = ds.getSingleComponentBitDepth()
self.scale = 255.0 / (2**bitdepth - 1)
print "Setting intensity scale",self.shift,self.scale
ds.setIntensityScale(self.shift, self.scale)
ds.resetColorTransferFunction()
dataUnit.resetColorTransferFunction()
self.result = 1
#self.Close()
self.EndModal(wx.ID_OK)
def zoomToFit(self):
self.preview.zoomToFit()
def setDataUnits(self, dataunits):
"""
Set the dataunits to be resampled
"""
self.dataUnits = dataunits
unitclass = self.taskPanels["Merging"][2].getDataUnit()
self.mergeUnit = unitclass("Preview for scaling intensity")
for dataUnit in dataunits:
#print "Creating histogram for ",dataUnit
self.mergeUnit.addSourceDataUnit(dataUnit)
x, y, z = dataUnit.getDimensions()
ds = dataUnit.getDataSource()
minval, maxval = ds.getOriginalScalarRange()
#print "Original scalar range = ",minval,maxval
self.resampleDims.append(ds.getResampleDimensions())
scale = maxval / 255.0
print "Scale for histograms = ",scale
#"Using scale",scale
histogram = Histogram.Histogram(self, scale = scale, lowerThreshold = minval, upperThreshold = maxval)
self.histogramSizer.Add(histogram)
self.histograms.append(histogram)
histogram.setThresholdMode(1)
histogram.setDataUnit(dataUnit, noupdate = 1)
lib.messenger.connect(histogram, "threshold_changed", self.onSetThreshold)
x, y, z = dataUnit.getDimensions()
self.zslider.SetRange(1, z)
moduletype = self.taskPanels["Merging"][0]
module = moduletype()
self.mergeUnit.setModule(module)
self.preview.setDataUnit(self.mergeUnit)
self.preview.zoomToFit()
self.preview.updatePreview()
self.sizer.Fit(self)
self.Layout()
def onSetThreshold(self, obj, event, lower, upper):
"""
An event handler for updating the thresholds based on one of the histograms
"""
n = self.histograms.index(obj)
dataUnit = self.dataUnits[n]
minval, maxval = dataUnit.getDataSource().getOriginalScalarRange()
#print "Original scalar range=",minval,maxval
if lower == 0 and upper == 255:
self.shift = 0
self.scale = 255.0 / maxval
else:
upper = upper * (maxval / 255.0)
lower = lower * (maxval / 255.0)
self.shift = -int(lower)
self.scale = 255.0 / ((upper - lower))
dataUnit.getDataSource().setIntensityScale(self.shift, self.scale)
dataUnit.resetColorTransferFunction()
self.preview.updatePreview(1)
def createRescale(self):
"""
Creates the GUI for controlling the rescaling
"""
box = wx.StaticBox(self, -1, "Preview selected mapping")
previewBox = wx.StaticBoxSizer(box, wx.HORIZONTAL)
self.preview = PreviewFrame(self, previewsize = (256, 256), scrollbars = False)
previewBox.Add(self.preview)
self.zslider = wx.Slider(self, value = 1, minValue = 1, maxValue = 1,
style = wx.SL_VERTICAL | wx.SL_LABELS | wx.SL_AUTOTICKS)
self.zslider.SetHelpText("Use this slider to select the displayed optical slice.")
self.zslider.Bind(wx.EVT_SCROLL, self.onChangeZSlice)
previewBox.Add(self.zslider, 1, wx.EXPAND)
box = wx.StaticBox(self, -1, "Channel histograms")
self.histogramSizer = wx.StaticBoxSizer(box, wx.HORIZONTAL)
self.sizer.Add(previewBox, (0, 0), flag = wx.EXPAND | wx.ALL)
self.sizer.Add(self.histogramSizer, (2, 0), flag = wx.EXPAND | wx.ALL)
def onChangeZSlice(self, event):
"""
Set the zslice displayed
"""
self.preview.setZSlice(self.zslider.GetValue() - 1)
self.preview.updatePreview(0)
