def _writeFreqsMetaData(self, pattern, outputFn):
""" Glob and read frequencies either from reconstruction
or noise and write the proper metadata file.
"""
fnFreqs = sorted(glob.glob(self._getExtraPath(pattern)))
subset = 0
numberOfParticles = getFloatListFromValues(
self.numberOfParticles.get())
validationMd = xmipp.MetaData()
for fnFreq in fnFreqs:
print fnFreq
data = []
fnFreqOpen = open(fnFreq, "r")
for line in fnFreqOpen:
fields = line.split()
rowdata = map(float, fields)
data.extend(rowdata)
meanRes = (sum(data) / len(data))
data[:] = [(x - meanRes)**2 for x in data]
varRes = (sum(data) / (len(data) - 1))
stdRes = sqrt(varRes)
objId = validationMd.addObject()
validationMd.setValue(xmipp.MDL_COUNT,
long(numberOfParticles[subset]), objId)
validationMd.setValue(xmipp.MDL_AVG, meanRes, objId)
validationMd.setValue(xmipp.MDL_STDDEV, stdRes, objId)
subset += 1
validationMd.write(outputFn)
def _writeFreqsMetaData(self, pattern, outputFn):
""" Glob and read frequencies either from reconstruction
or noise and write the proper metadata file.
"""
fnFreqs = sorted(glob.glob(self._getExtraPath(pattern)))
subset = 0
numberOfParticles = getFloatListFromValues(self.numberOfParticles.get())
validationMd = xmipp.MetaData()
for fnFreq in fnFreqs:
print fnFreq
data = []
fnFreqOpen = open(fnFreq, "r")
for line in fnFreqOpen:
fields = line.split()
rowdata = map(float, fields)
data.extend(rowdata)
meanRes = (sum(data) / len(data))
data[:] = [(x-meanRes) ** 2 for x in data]
varRes = (sum(data) / (len(data) - 1))
stdRes = sqrt(varRes)
objId = validationMd.addObject()
validationMd.setValue(xmipp.MDL_COUNT,
long(numberOfParticles[subset]),
objId)
validationMd.setValue(xmipp.MDL_AVG,meanRes, objId)
validationMd.setValue(xmipp.MDL_STDDEV,stdRes,objId)
subset += 1
validationMd.write(outputFn)
def itersFloatValues(self, attributeName, firstValue=-1):
""" Take the string of a given attribute and
create a list of floats that will be used by
the iteratioins. An special first value will be
added to the list for iteration 0.
"""
valuesStr = self.getAttributeValue(attributeName)
if valuesStr is None:
raise Exception('None value for attribute: %s' % attributeName)
return [firstValue] + getFloatListFromValues(valuesStr, length=self.numberOfIterations.get())
def itersFloatValues(self, attributeName, firstValue=-1):
""" Take the string of a given attribute and
create a list of floats that will be used by
the iteratioins. An special first value will be
added to the list for iteration 0.
"""
valuesStr = self.getAttributeValue(attributeName)
if valuesStr is None:
raise Exception('None value for attribute: %s' % attributeName)
return [firstValue] + getFloatListFromValues(valuesStr, length=self.numberOfIterations.get())
def _writeFreqsMetaData(self, pattern, outputFn):
""" Glob and read frequencies either from reconstruction
or noise and write the proper metadata file.
"""
fnFreqs = sorted(glob.glob(self._getExtraPath(pattern)))
subset = 0
numberOfParticles = getFloatListFromValues(
self.numberOfParticles.get())
validationMd = xmippLib.MetaData()
fnOut = open(outputFn, 'w')
for fnFreq in fnFreqs:
print fnFreq
data = []
dataInv = []
fnFreqOpen = open(fnFreq, "r")
for line in fnFreqOpen:
fields = line.split()
rowdata = map(float, fields)
print("rowdata", rowdata)
#AJ cambio
val = 1.0 / (float(rowdata[0]) * float(rowdata[0]))
dataInv.append(val)
#FIN AJ
data.extend(rowdata)
print("data", data, dataInv)
meanRes = (sum(data) / len(data))
data[:] = [(x - meanRes)**2 for x in data]
varRes = (sum(data) / (len(data) - 1))
stdRes = sqrt(varRes)
meanResInv = (sum(dataInv) / len(dataInv))
dataInv[:] = [(x - meanResInv)**2 for x in dataInv]
varResInv = (sum(dataInv) / (len(dataInv) - 1))
stdResInv = sqrt(varResInv)
fnOut.write(
str(numberOfParticles[subset]) + ' ' + str(meanRes) + ' ' +
str(stdRes) + ' ' + str(meanResInv) + ' ' + str(stdResInv) +
'\n')
#
# objId = validationMd.addObject()
# validationMd.setValue(xmippLib.MDL_COUNT,
# long(numberOfParticles[subset]),
# objId)
# validationMd.setValue(xmippLib.MDL_AVG, meanRes, objId)
# validationMd.setValue(xmippLib.MDL_STDDEV, stdRes, objId)
subset += 1
# validationMd.write(outputFn)
fnOut.close()
def _summary(self):
""" Should be overriden in subclasses to
return summary message for NORMAL EXECUTION.
"""
numberOfParticles = getFloatListFromValues(self.numberOfParticles.get())
maxNumberOfParticles = 0.5 * self.inputParticles.get().getSize()
intNumberOfParticles = [int(float(x)) for x in numberOfParticles]
particlesNumber = ''
for number in intNumberOfParticles:
if number <= maxNumberOfParticles:
particlesNumber += str(number)+' '
msg = []
msg.append("Number of particles: " + particlesNumber)
msg.append("Number of times that reconstruction is performed per each "
"particles subset: %d" % self.numberOfIterations)
return msg
def _summary(self):
""" Should be overriden in subclasses to
return summary message for NORMAL EXECUTION.
"""
numberOfParticles = getFloatListFromValues(
self.numberOfParticles.get())
maxNumberOfParticles = 0.5 * self.inputParticles.get().getSize()
intNumberOfParticles = [int(float(x)) for x in numberOfParticles]
particlesNumber = ''
for number in intNumberOfParticles:
if number <= maxNumberOfParticles:
particlesNumber += str(number) + ' '
msg = []
msg.append("Number of particles: " + particlesNumber)
msg.append("Number of times that reconstruction is performed per each "
"particles subset: %d" % self.numberOfIterations)
return msg
def _insertAllSteps(self):
self._createFilenameTemplates()
#convertInputStep
particlesMd = self._getFileName('input_xmd')
imgSet = self.inputParticles.get()
writeSetOfParticles(imgSet, particlesMd)
#for debugging purpose
debugging = False
inputNameRefVol = self.input3DReference.get().getFileName()
fnNewVol = self._getExtraPath('newVolume.vol')
fnNewImgStk = self._getExtraPath('newImages.stk')
fnNewImgMd = self._getExtraPath('newImages.xmd')
#do resizing
if self.doResize.get():
args = "-i %s " "-o %s --fourier %f " % (inputNameRefVol, fnNewVol,
self.newSize)
self.runJob("xmipp_image_resize", args)
args = "-i %s -o %s --fourier %f" % (particlesMd, fnNewImgStk,
self.newSize)
args += " --save_metadata_stack %s" % fnNewImgMd
args += " --keep_input_columns"
self.runJob("xmipp_image_resize", args)
oldSize = self.inputParticles.get().getDim()[0]
scaleFactor = oldSize / self.newSize.get()
args = "-i %s" % fnNewImgMd
args += " --operate modify_values 'shiftX=shiftX*%f'" % scaleFactor
self.runJob('xmipp_metadata_utilities', args)
args = "-i %s" % fnNewImgMd
args += " --operate modify_values 'shiftY=shiftY*%f'" % scaleFactor
self.runJob('xmipp_metadata_utilities', args)
#projections from reference volume
if self.doResize.get():
args = "-i %s -o %s" % (fnNewVol,
self._getExtraPath('Ref_Projections.stk'))
args += " --experimental_images %s" % fnNewImgMd
else:
args = "-i %s -o %s" % (self.input3DReference.get().getFileName(),
self._getExtraPath('Ref_Projections.stk'))
args += " --experimental_images %s" % particlesMd
args += " --sampling_rate %f --sym %s" % (self.angSampRate,
self.symmetryGroup.get())
args += " --min_tilt_angle 0 --max_tilt_angle 90"
args += " --compute_neighbors --angular_distance -1"
self.runJob("xmipp_angular_project_library",
args,
numberOfMpi=self.numberOfMpi.get() *
self.numberOfThreads.get())
numberOfParticles = getFloatListFromValues(
self.numberOfParticles.get())
fractionCounter = 0
maxNumberOfParticles = 0.5 * self.inputParticles.get().getSize()
for number in numberOfParticles:
if number <= maxNumberOfParticles:
for iteration in range(0, self.numberOfIterations.get()):
self._insertFunctionStep('reconstructionStep', number,
fractionCounter, iteration,
debugging, fnNewImgMd,
particlesMd)
fractionCounter += 1
self._insertFunctionStep('gatherResultsStep', debugging)
def _insertAllSteps(self):
self._createFilenameTemplates()
#convertInputStep
particlesMd = self._getFileName('input_xmd')
imgSet = self.inputParticles.get()
writeSetOfParticles(imgSet, particlesMd)
#for debugging purpose
debugging = False
inputNameRefVol = self.input3DReference.get().getFileName()
fnNewVol = self._getExtraPath('newVolume.vol')
fnNewImgStk = self._getExtraPath('newImages.stk')
fnNewImgMd = self._getExtraPath('newImages.xmd')
#do resizing
if self.doResize.get():
args = "-i %s ""-o %s --fourier %f " % (inputNameRefVol,
fnNewVol,
self.newSize)
self.runJob("xmipp_image_resize", args)
args = "-i %s -o %s --fourier %f" % (particlesMd,
fnNewImgStk,
self.newSize)
args += " --save_metadata_stack %s" % fnNewImgMd
args += " --keep_input_columns"
self.runJob("xmipp_image_resize", args)
oldSize = self.inputParticles.get().getDim()[0]
scaleFactor = float(self.newSize.get())/float(oldSize)
args = "-i %s" % fnNewImgMd
args += " --operate modify_values 'shiftX=shiftX*%f'" % scaleFactor
self.runJob('xmipp_metadata_utilities', args, numberOfMpi=1)
args = "-i %s" % fnNewImgMd
args += " --operate modify_values 'shiftY=shiftY*%f'" % scaleFactor
self.runJob('xmipp_metadata_utilities', args, numberOfMpi=1)
#projections from reference volume
if self.doResize.get():
args = "-i %s -o %s" % (fnNewVol,
self._getExtraPath('Ref_Projections.stk'))
args += " --experimental_images %s" % fnNewImgMd
else:
args = "-i %s -o %s" % (self.input3DReference.get().getFileName(),
self._getExtraPath('Ref_Projections.stk'))
args += " --experimental_images %s" % particlesMd
args += " --sampling_rate %f --sym %s" % (self.angSampRate,
self.symmetryGroup.get())
args += " --min_tilt_angle 0 --max_tilt_angle 90"
args += " --compute_neighbors --angular_distance -1"
self.runJob("xmipp_angular_project_library",
args,
numberOfMpi = self.numberOfMpi.get() * self.numberOfThreads.get())
numberOfParticles = getFloatListFromValues(self.numberOfParticles.get())
fractionCounter = 0
maxNumberOfParticles = 0.5 * self.inputParticles.get().getSize()
for number in numberOfParticles:
if number <= maxNumberOfParticles:
for iteration in range(0,self.numberOfIterations.get()):
self._insertFunctionStep('reconstructionStep', number,
fractionCounter, iteration,
debugging, fnNewImgMd,
particlesMd)
fractionCounter+=1
self._insertFunctionStep('gatherResultsStep', debugging)