def calcPixSize(self):
if self.useEst:
inputEst = self.inputEst.get().getOutputLog()
input_params = parseMagCorrInput(inputEst)
newPix = input_params[3]
return newPix
else:
return self.newPix.get()
def _getParams(self):
inputMics = self.inputCoords.get().getMicrographs()
mic_x, mic_y, _ = inputMics.getFirstItem().getDim()
if self.useEst:
inputEst = self.inputEst.get().getOutputLog()
input_params = parseMagCorrInput(inputEst)
ang = input_params[0]
major_scale = input_params[1]
minor_scale = input_params[2]
else:
ang = self.angDist.get()
major_scale = self.scaleMaj.get()
minor_scale = self.scaleMin.get()
return [mic_x, mic_y, ang, major_scale, minor_scale]
def _processMovie(self, movie):
inputMovies = self.inputMovies.get()
outputMovieFn = self._getAbsPath(self._getOutputMovieName(movie))
logFn = self._getAbsPath(self.getOutputLog(movie))
self._createLink(movie)
self._argsMagDistCor()
params = {'movieFn': self._getMovieFn(movie),
'outputMovieFn': outputMovieFn,
'logFn': logFn,
'nthr': self.numberOfThreads.get(),
'doGain': 'YES' if self.doGain else 'NO',
'doResample': 'YES' if self.doResample else 'NO'
}
if self.useEst:
inputEst = self.inputEst.get().getOutputLog()
input_params = parseMagCorrInput(inputEst)
params['angDist'] = input_params[0]
params['scaleMaj'] = input_params[1]
params['scaleMin'] = input_params[2]
else:
params['angDist'] = self.angDist.get()
params['scaleMaj'] = self.scaleMaj.get()
params['scaleMin'] = self.scaleMin.get()
if self.doGain:
params['gainFile'] = inputMovies.getGain()
if self.doResample:
params['newX'] = self.newX.get()
params['newY'] = self.newY.get()
self._storeSummary(movie)
try:
self.runJob(self._program % params, self._args % params)
except:
print("ERROR: Distortion correction for movie %s failed\n"
% movie.getFileName())
def _storeSummary(self):
if self.getAttributeValue('useEst', False):
inputFn = self.getAttributeValue('inputEst', None).getOutputLog()
input_params = parseMagCorrInput(inputFn)
self.summaryVar.set("The following magnification distortion parameters "
"were used for correction:\n\n"
"Distortion Angle: *%0.2f* degrees\n"
"Major Scale: *%0.3f*\n"
"Minor Scale: *%0.3f*\n"
% (input_params[0],
input_params[1],
input_params[2]))
else:
self.summaryVar.set("The following magnification distortion parameters "
"were used for correction:\n\n"
"Distortion Angle: *%0.2f* degrees\n"
"Major Scale: *%0.3f*\n"
"Minor Scale: *%0.3f*\n"
% (self.getAttributeValue('angDist', 1.0),
self.getAttributeValue('scaleMaj', 1.0),
self.getAttributeValue('scaleMin', 1.0)))
def _storeSummary(self, movie):
""" Implement this method if you want to store the summary. """
if self.getAttributeValue('useEst', False):
inputFn = self.getAttributeValue('inputEst', None).getOutputLog()
input_params = parseMagCorrInput(inputFn)
self.summaryVar.set("The following magnification distortion parameters "
"were used for correction:\n\n"
"Distortion Angle: *%0.2f* degrees\n"
"Major Scale: *%0.3f*\n"
"Minor Scale: *%0.3f*\n"
"Corrected pixel size: *%0.3f* A"
% (input_params[0], input_params[1],
input_params[2], input_params[3]))
else:
self.summaryVar.set("The following magnification distortion parameters "
"were used for correction:\n\n"
"Distortion Angle: *%0.2f* degrees\n"
"Major Scale: *%0.3f*\n"
"Minor Scale: *%0.3f*\n"
"Corrected pixel size: *%0.3f* A"
% (self.getAttributeValue('angDist', 1.0),
self.getAttributeValue('scaleMaj', 1.0),
self.getAttributeValue('scaleMin', 1.0),
self.newPix.get()))
