class MaskPreviewDialog(ImagePreviewDialog):
def _beforePreview(self):
self.dim = 256
self.samplingRate = 1
self.unit = getattr(self, 'unit', UNIT_PIXEL)
if self.unit != UNIT_PIXEL:
self.samplingRate = self.firstItem.getSamplingRate()
self.dim_par = self.firstItem.getDim()[0] * self.samplingRate
self.ratio = self.dim / float(self.dim_par)
self.previewLabel = 'Central slice'
def _createPreview(self, frame):
""" Should be implemented by subclasses to
create the items preview.
"""
from pyworkflow.gui.matplotlib_image import MaskPreview
if self.maskRadius == -1:
self.iniRadius = self.dim_par / 2
else:
self.iniRadius = self.maskRadius
self.preview = MaskPreview(frame,
self.dim,
label=self.previewLabel,
outerRadius=self.iniRadius * self.ratio)
self.preview.grid(row=0, column=0)
def _createControls(self, frame):
self.addRadiusBox(frame)
def addRadiusBox(self, parent):
self.radiusSlider = LabelSlider(
parent,
'Outer radius (%s)' % self.unit,
from_=0,
to=int(self.dim_par / 2),
value=self.iniRadius,
step=self.samplingRate,
callback=lambda a, b, c: self.updateRadius())
self.radiusSlider.grid(row=0, column=0, padx=5, pady=5)
def updateRadius(self):
self.preview.updateMask(self.radiusSlider.get() * self.ratio)
def getRadius(self):
return int(self.radiusSlider.get())
class MaskPreviewDialog(ImagePreviewDialog):
def _beforePreview(self):
self.dim = 256
self.samplingRate = 1
self.unit = getattr(self, 'unit', UNIT_PIXEL)
if self.unit != UNIT_PIXEL:
self.samplingRate = self.firstItem.getSamplingRate()
self.dim_par = self.firstItem.getDim()[0] * self.samplingRate
self.ratio = self.dim / float(self.dim_par)
self.previewLabel = 'Central slice'
def _createPreview(self, frame):
""" Should be implemented by subclasses to
create the items preview.
"""
from pyworkflow.gui.matplotlib_image import MaskPreview
if self.maskRadius == -1:
self.iniRadius = self.dim_par/2
else:
self.iniRadius = self.maskRadius
self.preview = MaskPreview(frame, self.dim, label=self.previewLabel,
outerRadius=self.iniRadius*self.ratio)
self.preview.grid(row=0, column=0)
def _createControls(self, frame):
self.addRadiusBox(frame)
def addRadiusBox(self, parent):
self.radiusSlider = LabelSlider(parent, 'Outer radius (%s)' % self.unit,
from_=0, to=int(self.dim_par/2),
value=self.iniRadius,
step=self.samplingRate,
callback=lambda a, b, c:self.updateRadius())
self.radiusSlider.grid(row=0, column=0, padx=5, pady=5)
def updateRadius(self):
self.preview.updateMask(self.radiusSlider.get() * self.ratio)
def getRadius(self):
return int(self.radiusSlider.get())
class PreWhiteningDialog(dialog.Dialog):
def __init__(self, form, workingDir, **kwargs):
"""
Params:
parent: parent windows of the dialog.
provider: the TreeProvider to populate items tree.
"""
self.form = form
self.workingDir = workingDir
buttons = [('Select', dialog.RESULT_YES), ('Cancel', dialog.RESULT_CANCEL)]
dialog.Dialog.__init__(self, form.root, "Pre-whitening", buttons=buttons, default='Select', **kwargs)
def _runBeforePreWhitening(self):
prot = self.form.protocol
# Convert input volumes
ih = ImageHandler()
if prot.useSplitVolume:
ih.convert(prot.volumeHalf1.get(), join(self.workingDir, 'volume1.map'))
ih.convert(prot.volumeHalf2.get(), join(self.workingDir, 'volume2.map'))
else:
ih.convert(prot.inputVolume.get(), join(self.workingDir, 'volume1.map'))
self.results = prot.runResmap(self.workingDir, wizardMode=True)
def _runPreWhitening(self, newElbowAngstrom, newRampWeight):
# Add resmap libraries to the path
results = self.results
self.figure.clear()
myCreatePrewhiteningFigure(results, self.figure, newElbowAngstrom, newRampWeight)
def body(self, bodyFrame):
figFrame = FigureFrame(bodyFrame, figsize=(18, 9))
figFrame.grid(row=0, column=0, columnspan=5)
#self._runBeforePreWhitening(self.prot)
dialog.FlashMessage(self.form.root, "Running Pre-Whitening tool...",
func=self._runBeforePreWhitening)
results = self.results
self.figure = figFrame.getFigure() #plt.figure(figsize=(18, 9))
self._runPreWhitening(results['newElbowAngstrom'],
results['newRampWeight'])
#bodyFrame.config()
bodyFrame.columnconfigure(0, weight=1)
bodyFrame.rowconfigure(0, weight=1)
controlsFrame = tk.Frame(bodyFrame)
controlsFrame.grid(row=1, column=0)
self.elbowSlider = LabelSlider(controlsFrame, "Angstroms", from_=2.1*results['vxSize'], to=100,
value=results['newElbowAngstrom'])
self.elbowSlider.grid(row=1, column=0, padx=5, pady=5)
self.rampSlider = LabelSlider(controlsFrame, "Ramp weight", from_=0.0, to=1.,
value=results['newRampWeight'])
self.rampSlider.grid(row=1, column=1, padx=5, pady=5)
self.updateBtn = HotButton(controlsFrame, " Update ",
command=self._onUpdate,
tooltip="Update plots with new pre-whitening parameters.")
self.updateBtn.grid(row=1, column=2, padx=10, pady=5)
def getElbowValue(self):
return self.elbowSlider.get()
def getRampValue(self):
return self.rampSlider.get()
def _onUpdate(self, e=None):
self._runPreWhitening(self.getElbowValue(), self.getRampValue())
class PreWhiteningDialog(dialog.Dialog):
def __init__(self, form, workingDir, **kwargs):
"""
Params:
parent: parent windows of the dialog.
provider: the TreeProvider to populate items tree.
"""
self.form = form
self.workingDir = workingDir
buttons = [('Select', dialog.RESULT_YES),
('Cancel', dialog.RESULT_CANCEL)]
dialog.Dialog.__init__(self,
form.root,
"Pre-whitening",
buttons=buttons,
default='Select',
**kwargs)
def _runBeforePreWhitening(self):
prot = self.form.protocol
# Convert input volumes
ih = ImageHandler()
if prot.useSplitVolume:
ih.convert(prot.volumeHalf1.get(),
join(self.workingDir, 'volume1.map'))
ih.convert(prot.volumeHalf2.get(),
join(self.workingDir, 'volume2.map'))
else:
ih.convert(prot.inputVolume.get(),
join(self.workingDir, 'volume1.map'))
self.results = prot.runResmap(self.workingDir, wizardMode=True)
def _runPreWhitening(self, newElbowAngstrom, newRampWeight):
# Add resmap libraries to the path
results = self.results
self.figure.clear()
myCreatePrewhiteningFigure(results, self.figure, newElbowAngstrom,
newRampWeight)
def body(self, bodyFrame):
figFrame = FigureFrame(bodyFrame, figsize=(18, 9))
figFrame.grid(row=0, column=0, columnspan=5)
#self._runBeforePreWhitening(self.prot)
dialog.FlashMessage(self.form.root,
"Running Pre-Whitening tool...",
func=self._runBeforePreWhitening)
results = self.results
self.figure = figFrame.getFigure() #plt.figure(figsize=(18, 9))
self._runPreWhitening(results['newElbowAngstrom'],
results['newRampWeight'])
#bodyFrame.config()
bodyFrame.columnconfigure(0, weight=1)
bodyFrame.rowconfigure(0, weight=1)
controlsFrame = tk.Frame(bodyFrame)
controlsFrame.grid(row=1, column=0)
self.elbowSlider = LabelSlider(controlsFrame,
"Angstroms",
from_=2.1 * results['vxSize'],
to=100,
value=results['newElbowAngstrom'])
self.elbowSlider.grid(row=1, column=0, padx=5, pady=5)
self.rampSlider = LabelSlider(controlsFrame,
"Ramp weight",
from_=0.0,
to=1.,
value=results['newRampWeight'])
self.rampSlider.grid(row=1, column=1, padx=5, pady=5)
self.updateBtn = HotButton(
controlsFrame,
" Update ",
command=self._onUpdate,
tooltip="Update plots with new pre-whitening parameters.")
self.updateBtn.grid(row=1, column=2, padx=10, pady=5)
def getElbowValue(self):
return self.elbowSlider.get()
def getRampValue(self):
return self.rampSlider.get()
def _onUpdate(self, e=None):
self._runPreWhitening(self.getElbowValue(), self.getRampValue())
class CtfDialog(DownsampleDialog):
def _createRightPreview(self, rightFrame):
self.isInnerRad = True
listeners = {
"<Button-4>": self.makeBigger,
"<Button-5>": self.makeSmaller,
"<Up>": self.upKeyPress,
"<Down>": self.downKeyPress
}
from pyworkflow.gui.matplotlib_image import PsdPreview
return PsdPreview(rightFrame,
self.dim,
self.lf,
self.hf,
label=self.rightPreviewLabel,
listenersDict=listeners)
def downKeyPress(self, event):
self.isInnerRad = False
self.highlightOuterSlider()
def upKeyPress(self, event):
self.isInnerRad = True
self.highlightInnerSlider()
def highlightOuterSlider(self):
self.hfSlider.highlightLabel()
self.lfSlider.removeHighlightFromLabel()
def highlightInnerSlider(self):
self.lfSlider.highlightLabel()
self.hfSlider.removeHighlightFromLabel()
def makeBigger(self, event):
self.isMakingBigger = True
if self.isInnerRad:
self.lf = self.lf + self.step
else:
new_val = self.hf + self.step
if new_val <= 0.5: # Don't make the mask bigger unless the is equal or lower than the max
self.hf = new_val
self.manageMaskVals()
def makeSmaller(self, event):
self.isMakingBigger = False
if self.isInnerRad:
new_val = self.lf - self.step
if new_val >= 0:
self.lf = new_val
else:
self.hf = self.hf - self.step
self.manageMaskVals()
def manageMaskVals(self):
if self.isMakingBigger:
if self.isInnerRad and self.lf >= self.hf: # Inner ring can't be bigger than outer ring
# Subtract one step to go back to the nearest lower value
self.lf = self.hf - self.step
else:
if not self.isInnerRad and self.hf <= self.lf: # Outer ring can't be smaller than inner
# ring
# Add one step to go back to the nearest higher value
self.hf = self.lf + self.step
# Set the ring sliders in case it comes from the mouse wheel
self.setFreq(self.lfSlider, self.lf)
self.setFreq(self.hfSlider, self.hf)
# Show values
self.showValues(self.hfVar, self.hfSlider)
self.showValues(self.lfVar, self.lfSlider)
# Update mask
self.rightPreview.updateFreq(self.lf, self.hf)
def _showInAngstroms(self):
return getattr(self, 'showInAngstroms', False)
def _createControls(self, frame):
frame.columnconfigure(0, weight=1)
frame.columnconfigure(1, weight=1)
frame.columnconfigure(2, weight=1)
self.step = 0.01
self.freqFrame = ttk.LabelFrame(frame, text="Frequencies")
self.freqFrame.columnconfigure(0, weight=3)
self.freqFrame.grid(row=0, column=2, sticky='news')
self.lfSlider = LabelSlider(
self.freqFrame,
'Low freq',
value=self.lf,
from_=0.01,
to=0.5,
length=178,
labelWidth=13,
step=self.step,
showvalue=0,
callback=lambda a, b, c: self.updateSliderInnerRadius(),
)
self.lfSlider.grid(row=0, column=0, padx=5, pady=5, sticky='news')
self.lfSlider.highlightLabel()
self.hfSlider = LabelSlider(
self.freqFrame,
'High freq',
value=self.lf,
from_=0.01,
to=0.5,
length=178,
labelWidth=13,
step=self.step,
showvalue=0,
callback=lambda a, b, c: self.updateSliderOuterRadius(),
)
self.hfSlider.grid(row=1, column=0, padx=5, pady=5, sticky='news')
# Pack and configure low freq slider
self.lfVar = tk.StringVar()
self.lfLabel = tk.Label(self.freqFrame,
textvariable=self.lfVar,
width=26)
self.lfLabel.grid(row=0, column=1, sticky='nse', padx=5, pady=5)
# Pack and configure high freq slider
self.hfVar = tk.StringVar()
self.hfLabel = tk.Label(self.freqFrame,
textvariable=self.hfVar,
width=26)
self.hfLabel.grid(row=1, column=1, sticky='nse', padx=5, pady=5)
# Update both mask and sliders with the initial values
self.manageMaskVals()
# def getDownsample(self):
# return 1.0 # Micrograph previously downsample, not taken into account here
def updateFreqRing(self):
self.rightPreview.updateFreq(self.getLowFreq(), self.getHighFreq())
self.showValues(self.lfVar, self.lfSlider)
self.showValues(self.hfVar, self.hfSlider)
def updateSliderOuterRadius(self):
new_val = self.getFreq(self.hfSlider)
# Carry out the action only if the slider is clicked & dragged (prevent from minimal variations when the mouse
# is on the slider but not clicking on it)
if abs(new_val - self.hf) >= self.step:
self.highlightOuterSlider()
self.isInnerRad = False
self.isMakingBigger = False
# Check if the user is making the ring bigger
if new_val > self.hf:
self.isMakingBigger = True
self.hf = new_val
self.manageMaskVals()
def updateSliderInnerRadius(self):
new_val = self.getFreq(self.lfSlider)
# Highlight only if the slider is clicked & dragged (prevent from minimal variations when the mouse is on the
# slider but not clicking on it)
if abs(new_val - self.lf) >= self.step:
self.highlightInnerSlider()
self.isInnerRad = True
self.isMakingBigger = False
# Check if the user is making the ring bigger
if new_val > self.lf:
self.isMakingBigger = True
self.lf = new_val
self.manageMaskVals()
def showValues(self, var2set, labSlider):
"""
Show the values selected for the inner and outer radius. If the units are angstroms (sampling_rate = 1,
it will show only one value to avoid redundancies
"""
sr = self.firstItem.getSamplingRate()
freqVal = max(self.getFreq(labSlider),
0.0001) # avoid division by zero
if sr == 1:
var2set.set('{:2.2f} {}'.format(labSlider.slider.get(),
emcts.UNIT_PIXEL))
else:
var2set.set('{:2.2f} rad/{} | {:5.1f} {}'.format(
labSlider.slider.get(), emcts.UNIT_ANGSTROM_SYMBOL,
self.getDownsample() * sr / freqVal,
emcts.UNIT_ANGSTROM_SYMBOL))
def getLowFreq(self):
return self.lfSlider.get()
def getHighFreq(self):
return self.hfSlider.get()
@staticmethod
def getFreq(freqSlider):
return freqSlider.get()
@staticmethod
def setFreq(freqSlider, val):
freqSlider.slider.set(val)