def show(self, form):
protocol = form.protocol
params = self._getParameters(protocol)
_value = params['value']
_label = params['label']
# form.setParamFromVar('inputMicrographs') # update selected input micrographs
provider = self._getProvider(protocol)
if provider is not None:
args = {
'unit': UNIT_PIXEL,
'downsample': _value[0],
'lf': _value[1],
'hf': _value[2],
'showInAngstroms': True
}
d = CtfDownsampleDialog(form.root, provider, **args)
if d.resultYes():
form.setVar(_label[0], d.getDownsample())
form.setVar(_label[1], d.getLowFreq())
form.setVar(_label[2], d.getHighFreq())
else:
dialog.showWarning("Empty input", "Select elements first",
form.root)
def show(self, form, *args):
protocol = form.protocol
provider = self._getProvider(protocol)
installErrors = Plugin.validateInstallation()
if installErrors:
dialog.showError("SPIDER not properly installed.",
"\n".join(installErrors), form.root)
return
if provider is not None:
d = SpiderFilterDialog(form.root,
provider,
protocolParent=protocol)
if d.resultYes():
if protocol.filterType <= FILTER_FERMI:
form.setVar('filterRadius', d.getRadius())
else:
form.setVar('lowFreq', d.getLowFreq())
form.setVar('highFreq', d.getHighFreq())
if protocol.filterType == FILTER_FERMI:
form.setVar('temperature', d.getTemperature())
else:
dialog.showWarning("Input particles", "Select particles first",
form.root)
def show(self, form, *params):
prot = form.protocol
acquisitionInfo = prot.loadAcquisitionInfo()
if prot.importFilePath:
if exists(prot.importFilePath):
if acquisitionInfo:
msg = ''
for k, v in acquisitionInfo.iteritems():
msg += '%s = %s\n' % (k, v)
msg += '\n*Do you want to use detected acquisition values?*'
response = dialog.askYesNo("Import acquisition", msg,
form.root)
if response:
for k, v in acquisitionInfo.iteritems():
form.setVar(k, v)
else:
dialog.showWarning("Import failed",
"Could not import acquisition info.",
form.root)
else:
dialog.showError(
"Input error", "*Import file doesn't exist.*\nFile:\n%s" %
prot.importFilePath, form.root)
else:
dialog.showError("Input error", "Select import file first",
form.root)
def show(self, form):
protocol = form.protocol
provider = self._getProvider(protocol)
params = self._getParameters(protocol)
if provider is not None:
args = {
'mode': params['mode'],
'lowFreq': params['value'][1],
'highFreq': params['value'][0],
'unit': UNIT_ANGSTROM
}
args['showDecay'] = False
d = emwiz.BandPassFilterDialog(form.root, provider, **args)
if d.resultYes():
form.setVar('lowPass', d.getHighFreq())
form.setVar('highPass', d.getLowFreq())
else:
dialog.showWarning("Input micrographs", "Select micrographs first",
form.root)
def show(self, form):
protocol = form.protocol
provider = self._getProvider(protocol)
if provider is not None:
d = BsoftFilterDialog(form.root, provider, protocolParent=protocol)
else:
dialog.showWarning("Input particles", "Select particles first", form.root)
def show(self, form):
protocol = form.protocol
provider = self._getProvider(protocol)
if provider is not None:
d = BsoftFilterDialog(form.root, provider, protocolParent=protocol)
else:
dialog.showWarning("Input particles", "Select particles first", form.root)
def show(self, form):
protocol = form.protocol
provider = self._getProvider(protocol)
if protocol.inputImage.get():
d = CustomMaskDialog(form.root, provider, protocolParent=protocol)
if d.resultYes():
for varName in CUSTOMMASK_VARS.iterkeys():
form.setVar(varName, d.getVarValue(varName))
else:
dialog.showWarning("Input error", "Select the input image first", form.root)
def show(self, form, *args):
protocol = form.protocol
provider = self._getProvider(protocol)
if protocol.inputImage.get():
d = CustomMaskDialog(form.root, provider, protocolParent=protocol)
if d.resultYes():
for varName in CUSTOMMASK_VARS:
form.setVar(varName, d.getVarValue(varName))
else:
dialog.showWarning("Input error", "Select the input image first",
form.root)
def show(self, form, value, label, units=UNIT_PIXEL):
protocol = form.protocol
provider = self._getProvider(protocol)
if provider is not None:
d = MaskPreviewDialog(form.root,
provider,
maskRadius=value,
unit=units)
if d.resultYes():
self.setVar(form, label, d.getRadius())
else:
dialog.showWarning("Empty input", "Select elements first", form.root)
def show(self, form, value, label, units=UNIT_PIXEL):
protocol = form.protocol
provider = self._getProvider(protocol)
if provider is not None:
args = {'unit': units, 'downsample': value}
d = DownsampleDialog(form.root, provider, **args)
if d.resultYes():
form.setVar(label, d.getDownsample())
else:
dialog.showWarning("Empty input", "Select elements first",
form.root)
def show(self, form, value, label, units=UNIT_PIXEL_FOURIER):
protocol = form.protocol
provider = self._getProvider(protocol)
if provider is not None:
args = {'freqSigma': value, 'unit': units}
d = GaussianFilterDialog(form.root, provider, **args)
if d.resultYes():
form.setVar(label, d.getFreqSigma())
else:
dialog.showWarning("Empty input", "Select elements first",
form.root)
def show(self, form, value, label, units=UNIT_PIXEL):
protocol = form.protocol
provider = self._getProvider(protocol)
if provider is not None:
d = MaskPreviewDialog(form.root,
provider,
maskRadius=value,
unit=units)
if d.resultYes():
self.setVar(form, label, d.getRadius())
else:
dialog.showWarning("Empty input", "Select elements first", form.root)
def show(self, form, value, label, units=UNIT_PIXEL):
protocol = form.protocol
provider = self._getProvider(protocol)
if provider is not None:
args = {'unit': units,
'downsample': value
}
d = DownsampleDialog(form.root, provider, **args)
if d.resultYes():
form.setVar(label, d.getDownsample())
else:
dialog.showWarning("Empty input", "Select elements first", form.root)
def show(self, form, value, label, units=UNIT_PIXEL_FOURIER):
protocol = form.protocol
provider = self._getProvider(protocol)
if provider is not None:
args = {'freqSigma': value,
'unit': units
}
d = GaussianFilterDialog(form.root, provider, **args)
if d.resultYes():
form.setVar(label, d.getFreqSigma())
else:
dialog.showWarning("Empty input", "Select elements first", form.root)
def show(self, form, value, label, units=UNIT_PIXEL):
protocol = form.protocol
provider = self._getProvider(protocol)
if provider is not None:
d = MaskRadiiPreviewDialog(form.root,
provider,
innerRadius=value[0],
outerRadius=value[1],
unit=units)
if d.resultYes():
form.setVar(label[0], d.getRadius(d.radiusSliderIn))
form.setVar(label[1], d.getRadius(d.radiusSliderOut))
else:
dialog.showWarning("Empty input", "Select elements first", form.root)
def show(self, form, value, label, units=UNIT_PIXEL):
protocol = form.protocol
# form.setParamFromVar('inputMicrographs') # update selected input micrographs
provider = self._getProvider(protocol)
if provider is not None:
args = {'unit': units, 'lf': value[0], 'hf': value[1]}
d = CtfDialog(form.root, provider, **args)
if d.resultYes():
form.setVar(label[0], d.getLowFreq())
form.setVar(label[1], d.getHighFreq())
else:
dialog.showWarning("Empty input", "Select elements first",
form.root)
def show(self, form, value, label, units=UNIT_PIXEL):
protocol = form.protocol
provider = self._getProvider(protocol)
if provider is not None:
d = MaskRadiiPreviewDialog(form.root,
provider,
innerRadius=value[0],
outerRadius=value[1],
unit=units)
if d.resultYes():
form.setVar(label[0], d.getRadius(d.radiusSliderIn))
form.setVar(label[1], d.getRadius(d.radiusSliderOut))
else:
dialog.showWarning("Empty input", "Select elements first", form.root)
def show(self, form):
self.prot = form.protocol
self.form = form
emptyInput = ((not self.prot.inputVolume.get().hasValue()) or
(self.prot.useSplitVolume == True and
not self.prot.splitVolume.get().hasValue()))
if emptyInput:
dialog.showWarning("Empty input", "Select input volume(s) first", self.form.root)
else:
d = PreWhiteningDialog(self.form, os.getcwd())
if d.resultYes():
print "result: ", d.getElbowValue(), d.getRampValue()
form.setVar('prewhitenAng', d.getElbowValue())
form.setVar('prewhitenRamp', d.getRampValue())
def show(self, form, value, label, units=UNIT_PIXEL):
protocol = form.protocol
# form.setParamFromVar('inputMicrographs') # update selected input micrographs
provider = self._getProvider(protocol)
if provider is not None:
args = {'unit': units,
'lf': value[0],
'hf': value[1]
}
d = CtfDialog(form.root, provider, **args)
if d.resultYes():
form.setVar(label[0], d.getLowFreq())
form.setVar(label[1], d.getHighFreq())
else:
dialog.showWarning("Empty input", "Select elements first", form.root)
def show(self, form):
protocol = form.protocol
provider = self._getProvider(protocol)
if provider is not None:
d = SpiderFilterDialog(form.root, provider,
protocolParent=protocol)
if d.resultYes():
if protocol.filterType <= FILTER_SPACE_REAL:
form.setVar('filterRadius', d.getRadius())
else:
form.setVar('lowFreq', d.getLowFreq())
form.setVar('highFreq', d.getHighFreq())
if protocol.filterType == FILTER_FERMI:
form.setVar('temperature', d.getTemperature())
else:
dialog.showWarning("Input particles", "Select particles first", form.root)
def show(self, form):
self.prot = form.protocol
self.form = form
if not self.prot.useSplitVolume:
emptyInput = self.prot.inputVolume.get() is None
else:
emptyInput = (self.prot.volumeHalf1.get() is None or
self.prot.volumeHalf2.get() is None)
if emptyInput:
dialog.showWarning("Empty input", "Select input volume(s) first", self.form.root)
else:
d = PreWhiteningDialog(self.form, os.getcwd())
if d.resultYes():
print "result: ", d.getElbowValue(), d.getRampValue()
form.setVar('prewhitenAng', d.getElbowValue())
form.setVar('prewhitenRamp', d.getRampValue())
def show(self, form, value, label, units=emcts.UNIT_PIXEL):
protocol = form.protocol
provider = self._getProvider(protocol)
if provider is not None:
d = MaskPreviewDialog(form.root,
provider,
maskRadius=value,
unit=units)
if d.resultYes():
if units == emcts.UNIT_ANGSTROM:
value = round(d.getRadiusAngstroms(
d.radiusSlider)) # Must be an integer
else:
value = d.getRadius(d.radiusSlider)
self.setVar(form, label, value)
else:
dialog.showWarning("Empty input", "Select elements first",
form.root)
def show(self, form, *args):
params = self._getParameters(form.protocol)
value = params['value']
label = params['label']
protocol = form.protocol
provider = self._getProvider(protocol)
if provider is not None:
d = MaskRadiiPreviewDialog(form.root,
provider,
innerRadius=value[0],
outerRadius=value[1],
unit=UNIT_PIXEL)
if d.resultYes():
form.setVar(label[0], int(d.getRadius(d.radiusSliderIn)))
form.setVar(label[1], int(d.getRadius(d.radiusSliderOut)))
else:
dialog.showWarning("Empty input", "Select elements first",
form.root)
def show(self, form):
self.prot = form.protocol
self.form = form
if not self.prot.useSplitVolume:
emptyInput = self.prot.inputVolume.get() is None
else:
emptyInput = (self.prot.volumeHalf1.get() is None
or self.prot.volumeHalf2.get() is None)
if emptyInput:
dialog.showWarning("Empty input", "Select input volume(s) first",
self.form.root)
else:
d = PreWhiteningDialog(self.form, os.getcwd())
if d.resultYes():
print "result: ", d.getElbowValue(), d.getRampValue()
form.setVar('prewhitenAng', d.getElbowValue())
form.setVar('prewhitenRamp', d.getRampValue())
def show(self, form):
protocol = form.protocol
provider = self._getProvider(protocol)
if provider is not None:
d = SpiderFilterDialog(form.root,
provider,
protocolParent=protocol)
if d.resultYes():
if protocol.filterType <= FILTER_FERMI:
form.setVar('filterRadius', d.getRadius())
else:
form.setVar('lowFreq', d.getLowFreq())
form.setVar('highFreq', d.getHighFreq())
if protocol.filterType == FILTER_FERMI:
form.setVar('temperature', d.getTemperature())
else:
dialog.showWarning("Input particles", "Select particles first",
form.root)
def show(self, form):
protocol = form.protocol
params = self._getParameters(protocol)
_value = params['value']
_label = params['label']
pix = params['pix']
provider = self._getProvider(protocol)
if provider is not None:
args = {'unit': UNIT_ANGSTROM,
'lf': "%0.2f" % (pix/_value[0]),
'hf': "%0.2f" % (pix/_value[1])
}
d = CtfDialog(form.root, provider, **args)
if d.resultYes():
form.setVar(_label[0], "%0.2f" % (pix/d.getLowFreq()))
form.setVar(_label[1], "%0.2f" % (pix/d.getHighFreq()))
else:
dialog.showWarning("Empty input", "Select elements first", form.root)
def show(self, form):
params = self._getParameters(form.protocol)
protocol = form.protocol
provider = self._getProvider(protocol)
if provider is not None:
args = {'mode': params['mode'],
'highFreq': params['value'],
'unit': UNIT_ANGSTROM
}
args['showLowFreq'] = False
args['showDecay'] = False
d = BandPassFilterDialog(form.root, provider, **args)
if d.resultYes():
form.setVar('resolution', d.samplingRate/d.getHighFreq())
else:
dialog.showWarning("Input volumes", "Select volumes first", form.root)
def show(self, form, value, label, mode, unit=UNIT_PIXEL, **args):
protocol = form.protocol
provider = self._getProvider(protocol)
if provider is not None:
self.mode = mode
args.update({'mode': self.mode, 'unit': unit})
if self.mode == FILTER_LOW_PASS:
args['showLowFreq'] = False
args['highFreq'] = value[1]
args['freqDecay'] = value[2]
elif self.mode == FILTER_HIGH_PASS:
args['showHighFreq'] = False
args['lowFreq'] = value[0]
args['freqDecay'] = value[2]
elif self.mode == FILTER_BAND_PASS:
args['lowFreq'] = value[0]
args['highFreq'] = value[1]
args['freqDecay'] = value[2]
else:
raise Exception("Unknown mode '%s'" % self.mode)
d = BandPassFilterDialog(form.root, provider, **args)
if d.resultYes():
def setFormValue(flag, value, index):
if args.get(flag, True):
if unit == UNIT_ANGSTROM:
value = d.samplingRate / (value)
form.setVar(label[index], value)
setFormValue('showLowFreq', d.getLowFreq(), 0)
setFormValue('showHighFreq', d.getHighFreq(), 1)
setFormValue('showDecay', d.getFreqDecay(), 2)
else:
dialog.showWarning("Empty input", "Select elements first",
form.root)
def show(self, form, *params):
prot = form.protocol
acquisitionInfo = prot.loadAcquisitionInfo()
if prot.importFilePath:
if exists(prot.importFilePath):
if acquisitionInfo:
msg = ''
for k, v in acquisitionInfo.iteritems():
msg += '%s = %s\n' % (k, v)
msg += '\n*Do you want to use detected acquisition values?*'
response = dialog.askYesNo("Import acquisition", msg, form.root)
if response:
for k, v in acquisitionInfo.iteritems():
form.setVar(k, v)
else:
dialog.showWarning("Import failed",
"Could not import acquisition info.", form.root)
else:
dialog.showError("Input error", "*Import file doesn't exist.*\nFile:\n%s" % prot.importFilePath, form.root)
else:
dialog.showError("Input error", "Select import file first", form.root)
def show(self, form, value, label, mode, unit=UNIT_PIXEL, **args):
protocol = form.protocol
provider = self._getProvider(protocol)
if provider is not None:
self.mode = mode
args.update({'mode': self.mode,
'unit': unit})
if self.mode == FILTER_LOW_PASS:
args['showLowFreq'] = False
args['highFreq'] = value[1]
args['freqDecay'] = value[2]
elif self.mode == FILTER_HIGH_PASS:
args['showHighFreq'] = False
args ['lowFreq'] = value[0]
args ['freqDecay'] = value[2]
elif self.mode == FILTER_BAND_PASS:
args['lowFreq'] = value[0]
args['highFreq'] = value[1]
args['freqDecay'] = value[2]
else:
raise Exception("Unknown mode '%s'" % self.mode)
d = BandPassFilterDialog(form.root, provider, **args)
if d.resultYes():
def setFormValue(flag, value, index):
if args.get(flag, True):
if unit == UNIT_ANGSTROM:
value = d.samplingRate / (value)
form.setVar(label[index], value)
setFormValue('showLowFreq', d.getLowFreq(), 0)
setFormValue('showHighFreq', d.getHighFreq(), 1)
setFormValue('showDecay', d.getFreqDecay(), 2)
else:
dialog.showWarning("Empty input", "Select elements first", form.root)
def show(self, form):
protocol = form.protocol
provider = self._getProvider(protocol)
params = self._getParameters(protocol)
if provider is not None:
args = {'mode': params['mode'],
'lowFreq': params['value'][1],
'highFreq': params['value'][0],
'unit': UNIT_ANGSTROM
}
args['showDecay'] = False
d = emwiz.BandPassFilterDialog(form.root, provider, **args)
if d.resultYes():
form.setVar('lowPass', d.getHighFreq())
form.setVar('highPass', d.getLowFreq())
else:
dialog.showWarning("Input micrographs", "Select micrographs first", form.root)
def show(self, form):
protocol = form.protocol
params = self._getParameters(protocol)
_value = params['value']
_label = params['label']
# form.setParamFromVar('inputMicrographs') # update selected input micrographs
provider = self._getProvider(protocol)
if provider is not None:
args = {'unit': UNIT_PIXEL,
'downsample': _value[0],
'lf': _value[1],
'hf': _value[2]
}
d = CtfDownsampleDialog(form.root, provider, **args)
if d.resultYes():
form.setVar(_label[0], d.getDownsample())
form.setVar(_label[1], d.getLowFreq())
form.setVar(_label[2], d.getHighFreq())
else:
dialog.showWarning("Empty input", "Select elements first", form.root)
def show(self, form):
protocol = form.protocol
params = self._getParameters(protocol)
_value = params['value']
_label = params['label']
pix = params['pix']
provider = self._getProvider(protocol)
if provider is not None:
args = {
'unit': UNIT_ANGSTROM,
'lf': "%0.2f" % (pix / _value[0]),
'hf': "%0.2f" % (pix / _value[1])
}
d = CtfDialog(form.root, provider, **args)
if d.resultYes():
form.setVar(_label[0], "%0.2f" % (pix / d.getLowFreq()))
form.setVar(_label[1], "%0.2f" % (pix / d.getHighFreq()))
else:
dialog.showWarning("Empty input", "Select elements first",
form.root)
def show(self, form):
params = self._getParameters(form.protocol)
protocol = form.protocol
provider = self._getProvider(protocol)
if provider is not None:
args = {
'mode': params['mode'],
'highFreq': params['value'],
'unit': UNIT_ANGSTROM
}
args['showLowFreq'] = False
args['showDecay'] = False
d = BandPassFilterDialog(form.root, provider, **args)
if d.resultYes():
form.setVar('resolution', d.samplingRate / d.getHighFreq())
else:
dialog.showWarning("Input volumes", "Select volumes first",
form.root)