def show(self, form):
autopickProt = form.protocol
micSet = autopickProt.getInputMicrographs()
if not micSet:
print 'must specify input micrographs'
return
project = autopickProt.getProject()
micfn = micSet.getFileName()
coordsDir = project.getTmpPath(micSet.getName())
cleanPath(coordsDir)
makePath(coordsDir)
pickerProps = os.path.join(coordsDir, 'picker.conf')
f = open(pickerProps, "w")
params = ['boxSize', 'lowerThreshold', 'higherThreshold', 'gaussWidth']
args = {
"params": ','.join(params),
"preprocess": "%s sxprocess.py" % pw.getScipionScript(),
"picker": "%s e2boxer.py" % pw.getScipionScript(),
"convert": pw.join('apps', 'pw_convert.py'),
'coordsDir': coordsDir,
'micsSqlite': micSet.getFileName(),
"boxSize": autopickProt.boxSize,
"lowerThreshold": autopickProt.lowerThreshold,
"higherThreshold": autopickProt.higherThreshold,
"gaussWidth": autopickProt.gaussWidth,
"extraParams": autopickProt.extraParams
}
f.write("""
parameters = %(params)s
boxSize.value = %(boxSize)s
boxSize.label = Box Size
boxSize.help = some help
lowerThreshold.value = %(lowerThreshold)s
lowerThreshold.label = Lower Threshold
lowerThreshold.help = some help
higherThreshold.help = some help
higherThreshold.value = %(higherThreshold)s
higherThreshold.label = Higher Threshold
gaussWidth.help = some help
gaussWidth.value = %(gaussWidth)s
gaussWidth.label = Gauss Width
runDir = %(coordsDir)s
preprocessCommand = %(preprocess)s demoparms --makedb=thr_low=%%(lowerThreshold):thr_hi=%%(higherThreshold):boxsize=%%(boxSize):gauss_width=%%(gaussWidth):%(extraParams)s
autopickCommand = %(picker)s --gauss_autoboxer=demoparms --write_dbbox --boxsize=%%(boxSize) --norm=normalize.ramp.normvar %%(micrograph)
convertCommand = %(convert)s --coordinates --from eman2 --to xmipp --input %(micsSqlite)s --output %(coordsDir)s
""" % args)
f.close()
process = CoordinatesObjectView(project,
micfn,
coordsDir,
autopickProt,
pickerProps=pickerProps).show()
process.wait()
myprops = readProperties(pickerProps)
if myprops['applyChanges'] == 'true':
for param in params:
form.setVar(param, myprops[param + '.value'])
def show(self, form):
autopickProt = form.protocol
micSet = autopickProt.getInputMicrographs()
if not micSet:
print 'must specify input micrographs'
return
project = autopickProt.getProject()
micfn = micSet.getFileName()
coordsDir = project.getTmpPath(micSet.getName())
cleanPath(coordsDir)
makePath(coordsDir)
# Get current values of the properties
# micfn = os.path.join(coordsDir, 'micrographs.xmd')
# writeSetOfMicrographs(micSet, micfn)
dogpickerProps = os.path.join(coordsDir, 'picker.conf')
f = open(dogpickerProps, "w")
args = {
"dogpicker":
os.path.join(os.environ['DOGPICKER_HOME'], "ApDogPicker.py"),
"convert":
os.path.join(os.environ['SCIPION_HOME'],
os.path.join('pyworkflow', 'apps', 'pw_convert.py')),
'coordsDir':
coordsDir,
'micsSqlite':
micSet.getFileName(),
"diameter":
autopickProt.diameter,
"threshold":
autopickProt.threshold,
"apix":
micSet.getSamplingRate()
}
f.write("""
parameters = diameter,threshold
diameter.value = %(diameter)s
diameter.label = Diameter
diameter.help = some help
threshold.value = %(threshold)s
threshold.label = Threshold
threshold.help = some help
autopickCommand = %(dogpicker)s --thresh=%%(threshold) --diam=%%(diameter) --apix=%(apix)s --image=%%(micrograph) --outfile=%(coordsDir)s/%%(micrographName).txt
convertCommand = %(convert)s --coordinates --from dogpicker --to xmipp --input %(micsSqlite)s --output %(coordsDir)s
""" % args)
f.close()
process = CoordinatesObjectView(project,
micfn,
coordsDir,
autopickProt,
pickerProps=dogpickerProps).show()
process.wait()
myprops = readProperties(dogpickerProps)
form.setVar('diameter', myprops['diameter.value'])
form.setVar('threshold', myprops['threshold.value'])
def show(self, form):
autopickProt = form.protocol
micSet = autopickProt.getInputMicrographs()
if not micSet:
print 'must specify input micrographs'
return
project = autopickProt.getProject()
micfn = micSet.getFileName()
coordsDir = project.getTmpPath(micSet.getName())
cleanPath(coordsDir)
makePath(coordsDir)
pickerProps = os.path.join(coordsDir, 'picker.conf')
f = open(pickerProps, "w")
params = ['boxSize', 'lowerThreshold', 'higherThreshold', 'gaussWidth']
args = {
"params": ','.join(params),
"preprocess" : os.path.join(os.environ['SCIPION_HOME'], "scipion sxprocess.py"),
"picker" : os.path.join(os.environ['SCIPION_HOME'], "scipion e2boxer.py"),
"convert" : os.path.join(os.environ['SCIPION_HOME'], os.path.join('pyworkflow','apps', 'pw_convert.py')),
'coordsDir':coordsDir,
'micsSqlite': micSet.getFileName(),
"boxSize": autopickProt.boxSize,
"lowerThreshold": autopickProt.lowerThreshold,
"higherThreshold": autopickProt.higherThreshold,
"gaussWidth": autopickProt.gaussWidth,
"extraParams":autopickProt.extraParams
}
f.write("""
parameters = %(params)s
boxSize.value = %(boxSize)s
boxSize.label = Box Size
boxSize.help = some help
lowerThreshold.value = %(lowerThreshold)s
lowerThreshold.label = Lower Threshold
lowerThreshold.help = some help
higherThreshold.help = some help
higherThreshold.value = %(higherThreshold)s
higherThreshold.label = Higher Threshold
gaussWidth.help = some help
gaussWidth.value = %(gaussWidth)s
gaussWidth.label = Gauss Width
runDir = %(coordsDir)s
preprocessCommand = %(preprocess)s demoparms --makedb=thr_low=%%(lowerThreshold):thr_hi=%%(higherThreshold):boxsize=%%(boxSize):gauss_width=%%(gaussWidth):%(extraParams)s
autopickCommand = %(picker)s --gauss_autoboxer=demoparms --write_dbbox --boxsize=%%(boxSize) --norm=normalize.ramp.normvar %%(micrograph)
convertCommand = %(convert)s --coordinates --from eman2 --to xmipp --input %(micsSqlite)s --output %(coordsDir)s
""" % args)
f.close()
process = CoordinatesObjectView(project, micfn, coordsDir, autopickProt, pickerProps=pickerProps).show()
process.wait()
myprops = readProperties(pickerProps)
for param in params:
form.setVar(param, myprops[param + '.value'])
def show(self, form):
autopickProt = form.protocol
autopickFomProt = autopickProt.getInputAutopick()
project = autopickProt.getProject()
micSet = autopickFomProt.getInputMicrographs()
micfn = micSet.getFileName()
coordsDir = project.getTmpPath(micSet.getName())
cleanPath(coordsDir)
makePath(coordsDir)
pickerProps = os.path.join(coordsDir, 'picker.conf')
f = open(pickerProps, "w")
args = {
"picker" : "%s relion_autopick" % pw.getScipionScript(),
"convert" : pw.join('apps', 'pw_convert.py'),
'coordsDir':coordsDir,
'micsSqlite': micSet.getFileName(),
"diameter": autopickFomProt.particleDiameter,
"threshold": autopickProt.pickingThreshold,
"apix": micSet.getSamplingRate(),
'ang': autopickFomProt.angularSampling,
'lowpass':autopickFomProt.lowpassFilterRefs,
'ref': 'input_references.star',
'min_distance': autopickProt.interParticleDistance,
'protDir': autopickFomProt.getWorkingDir()
}
autopickCommand = '%(picker)s --i extra/%%(micrographName).star --o autopick --particle_diameter %(diameter)s --angpix %(apix)s --ref %(ref)s --ang %(ang)s --lowpass %(lowpass)s --threshold %%(threshold) --min_distance %%(ipd) --read_fom_maps'%args
if autopickFomProt.refsHaveInvertedContrast:
autopickCommand += ' --invert'
if autopickFomProt.refsCtfCorrected:
autopickCommand += ' --ctf'
args['autopickCommand'] = autopickCommand
f.write("""
parameters = ipd,threshold
ipd.value = %(min_distance)s
ipd.label = Minimum inter-particles distance
ipd.help = some help
threshold.value = %(threshold)s
threshold.label = Threshold
threshold.help = some help
runDir = %(protDir)s
autopickCommand = %(autopickCommand)s
convertCommand = %(convert)s --coordinates --from relion --to xmipp --input %(micsSqlite)s --output %(coordsDir)s --extra %(protDir)s/extra
""" % args)
f.close()
process = CoordinatesObjectView(autopickProt.getProject(), micfn, coordsDir, autopickFomProt, pickerProps=pickerProps).show()
process.wait()
myprops = readProperties(pickerProps)
if myprops['applyChanges'] == 'true':
form.setVar('pickingThreshold', myprops['threshold.value'])
form.setVar('interParticleDistance', myprops['ipd.value'])
def show(self, form):
autopickProt = form.protocol
micSet = autopickProt.getInputMicrographs()
if not micSet:
print 'must specify input micrographs'
return
project = autopickProt.getProject()
micfn = micSet.getFileName()
coordsDir = project.getTmpPath(micSet.getName())
cleanPath(coordsDir)
makePath(coordsDir)
# Get current values of the properties
# micfn = os.path.join(coordsDir, 'micrographs.xmd')
# writeSetOfMicrographs(micSet, micfn)
dogpickerProps = os.path.join(coordsDir, 'picker.conf')
f = open(dogpickerProps, "w")
args = {
"dogpicker" : os.path.join(os.environ['DOGPICKER_HOME'], "ApDogPicker.py"),
"convert" : os.path.join(os.environ['SCIPION_HOME'], os.path.join('pyworkflow','apps', 'pw_convert.py')),
'coordsDir':coordsDir,
'micsSqlite': micSet.getFileName(),
"diameter": autopickProt.diameter,
"threshold": autopickProt.threshold,
"apix": micSet.getSamplingRate()
}
f.write("""
parameters = diameter,threshold
diameter.value = %(diameter)s
diameter.label = Diameter
diameter.help = some help
threshold.value = %(threshold)s
threshold.label = Threshold
threshold.help = some help
autopickCommand = %(dogpicker)s --thresh=%%(threshold) --diam=%%(diameter) --apix=%(apix)s --image=%%(micrograph) --outfile=%(coordsDir)s/%%(micrographName).txt
convertCommand = %(convert)s --coordinates --from dogpicker --to xmipp --input %(micsSqlite)s --output %(coordsDir)s
""" % args)
f.close()
process = CoordinatesObjectView(project, micfn, coordsDir, autopickProt, pickerProps=dogpickerProps).show()
process.wait()
myprops = readProperties(dogpickerProps)
form.setVar('diameter', myprops['diameter.value'])
form.setVar('threshold', myprops['threshold.value'])
def show(self, form):
autopickProt = form.protocol
autopickFomProt = autopickProt.getInputAutopick()
# Get current values of the properties
# _, values = self._getInputProtocol(self._targets, autopickProt)
# threshold, distance = values
# autopickFomProt.setStepsExecutor() # allow to use runJob
# autopickFomProt.autopickStep(threshold, distance, '--read_fom_maps')
# print "Writing Xmipp coordinate files."
# micFn, coordsDir = autopickFomProt.writeXmippCoords()
project = autopickProt.getProject()
micSet = autopickFomProt.getInputMicrographs()
micfn = micSet.getFileName()
coordsDir = project.getTmpPath(micSet.getName())
cleanPath(coordsDir)
makePath(coordsDir)
pickerProps = os.path.join(coordsDir, 'picker.conf')
f = open(pickerProps, "w")
args = {
"picker":
os.path.join(os.environ['SCIPION_HOME'],
"scipion relion_autopick"),
"convert":
os.path.join(os.environ['SCIPION_HOME'],
os.path.join('pyworkflow', 'apps', 'pw_convert.py')),
'coordsDir':
coordsDir,
'micsSqlite':
micSet.getFileName(),
"diameter":
autopickFomProt.particleDiameter,
"threshold":
autopickProt.pickingThreshold,
"apix":
micSet.getSamplingRate(),
'ang':
autopickFomProt.angularSampling,
'lowpass':
autopickFomProt.lowpassFilterRefs,
'ref':
'input_references.star',
'min_distance':
autopickProt.interParticleDistance,
'protDir':
autopickFomProt.getWorkingDir()
}
autopickCommand = '%(picker)s --i extra/%%(micrographName).star --o autopick --particle_diameter %(diameter)s --angpix %(apix)s --ref %(ref)s --ang %(ang)s --lowpass %(lowpass)s --threshold %%(threshold) --min_distance %%(ipd) --read_fom_maps' % args
if autopickFomProt.refsHaveInvertedContrast:
autopickCommand += ' --invert'
if autopickFomProt.refsCtfCorrected:
autopickCommand += ' --ctf'
args['autopickCommand'] = autopickCommand
f.write("""
parameters = ipd,threshold
ipd.value = %(min_distance)s
ipd.label = Minimum inter-particles distance
ipd.help = some help
threshold.value = %(threshold)s
threshold.label = Threshold
threshold.help = some help
runDir = %(protDir)s
autopickCommand = %(autopickCommand)s
convertCommand = %(convert)s --coordinates --from relion --to xmipp --input %(micsSqlite)s --output %(coordsDir)s --extra %(protDir)s/extra
""" % args)
f.close()
process = CoordinatesObjectView(autopickProt.getProject(),
micfn,
coordsDir,
autopickFomProt,
pickerProps=pickerProps).show()
process.wait()
myprops = readProperties(pickerProps)
form.setVar('pickingThreshold', myprops['threshold.value'])
form.setVar('interParticleDistance', myprops['ipd.value'])
def show(self, form):
autopickProt = form.protocol
if not autopickProt.hasAttribute('outputCoordinates'):
form.showWarning("You should run the procotol in 'Optimize' mode "
"at least once before opening the wizard.")
return
project = autopickProt.getProject()
micSet = autopickProt.outputMicrographs
micfn = micSet.getFileName()
coordsDir = project.getTmpPath(micSet.getName())
cleanPath(coordsDir)
makePath(coordsDir)
cmd = '%s relion_autopick ' % pw.getScipionScript()
cmd += '--i extra/%(micrographName).star '
cmd += '--threshold %(threshold) --min_distance %(ipd) '
cmd += ' --max_stddev_noise %(maxStddevNoise) '
cmd += ' --read_fom_maps'
cmd += autopickProt.getAutopickParams()
convertCmd = pw.join('apps', 'pw_convert.py')
convertCmd += ' --coordinates --from relion --to xmipp '
convertCmd += ' --input %s' % micSet.getFileName()
convertCmd += ' --output %s' % coordsDir
convertCmd += ' --extra %s' % autopickProt._getExtraPath()
args = {
"threshold": autopickProt.pickingThreshold,
'min_distance': autopickProt.interParticleDistance,
'autopickCommand': cmd,
'convertCmd': convertCmd,
'protDir': autopickProt.getWorkingDir(),
'maxStddevNoise': autopickProt.maxStddevNoise
}
pickerProps = os.path.join(coordsDir, 'picker.conf')
f = open(pickerProps, "w")
f.write("""
parameters = ipd,threshold,maxStddevNoise
ipd.value = %(min_distance)s
ipd.label = Inter-particles distance
ipd.help = Minimum distance (in Angstroms) between particles
threshold.value = %(threshold)s
threshold.label = Threshold
threshold.help = some help
maxStddevNoise.value = %(maxStddevNoise)s
maxStddevNoise.label = Max. stddev noise
maxStddevNoise.help = Prevent picking in carbon areas, useful values probably between 1.0 and 1.2, use -1 to switch it off
runDir = %(protDir)s
autopickCommand = %(autopickCommand)s
convertCommand = %(convertCmd)s
""" % args)
f.close()
process = CoordinatesObjectView(autopickProt.getProject(), micfn,
coordsDir, autopickProt,
pickerProps=pickerProps).show()
process.wait()
myprops = readProperties(pickerProps)
# Check if the wizard changes were accepted or just canceled
if myprops['applyChanges'] == 'true':
form.setVar('pickingThreshold', myprops['threshold.value'])
form.setVar('interParticleDistance', myprops['ipd.value'])
form.setVar('maxStddevNoise', myprops['maxStddevNoise.value'])
# Change the run type now to 'Compute' after using the wizard
# and (supposedly) optimized parameters
form.setVar('runType', RUN_COMPUTE)
# Mark the wizard was used
setattr(autopickProt, 'wizardExecuted', True)
def show(self, form):
autopickProt = form.protocol
autopickFomProt = autopickProt.getInputAutopick()
# Get current values of the properties
# _, values = self._getInputProtocol(self._targets, autopickProt)
# threshold, distance = values
# autopickFomProt.setStepsExecutor() # allow to use runJob
# autopickFomProt.autopickStep(threshold, distance, '--read_fom_maps')
# print "Writing Xmipp coordinate files."
# micFn, coordsDir = autopickFomProt.writeXmippCoords()
project = autopickProt.getProject()
micSet = autopickFomProt.getInputMicrographs()
micfn = micSet.getFileName()
coordsDir = project.getTmpPath(micSet.getName())
cleanPath(coordsDir)
makePath(coordsDir)
pickerProps = os.path.join(coordsDir, 'picker.conf')
f = open(pickerProps, "w")
args = {
"picker" : os.path.join(os.environ['SCIPION_HOME'], "scipion relion_autopick"),
"convert" : os.path.join(os.environ['SCIPION_HOME'], os.path.join('pyworkflow','apps', 'pw_convert.py')),
'coordsDir':coordsDir,
'micsSqlite': micSet.getFileName(),
"diameter": autopickFomProt.particleDiameter,
"threshold": autopickProt.pickingThreshold,
"apix": micSet.getSamplingRate(),
'ang': autopickFomProt.angularSampling,
'lowpass':autopickFomProt.lowpassFilterRefs,
'ref': 'input_references.star',
'min_distance': autopickProt.interParticleDistance,
'protDir': autopickFomProt.getWorkingDir()
}
autopickCommand = '%(picker)s --i extra/%%(micrographName).star --o autopick --particle_diameter %(diameter)s --angpix %(apix)s --ref %(ref)s --ang %(ang)s --lowpass %(lowpass)s --threshold %%(threshold) --min_distance %%(ipd) --read_fom_maps'%args
if autopickFomProt.refsHaveInvertedContrast:
autopickCommand += ' --invert'
if autopickFomProt.refsCtfCorrected:
autopickCommand += ' --ctf'
args['autopickCommand'] = autopickCommand
f.write("""
parameters = ipd,threshold
ipd.value = %(min_distance)s
ipd.label = Minimum inter-particles distance
ipd.help = some help
threshold.value = %(threshold)s
threshold.label = Threshold
threshold.help = some help
runDir = %(protDir)s
autopickCommand = %(autopickCommand)s
convertCommand = %(convert)s --coordinates --from relion --to xmipp --input %(micsSqlite)s --output %(coordsDir)s --extra %(protDir)s/extra
""" % args)
f.close()
process = CoordinatesObjectView(autopickProt.getProject(), micfn, coordsDir, autopickFomProt, pickerProps=pickerProps).show()
process.wait()
myprops = readProperties(pickerProps)
form.setVar('pickingThreshold', myprops['threshold.value'])
form.setVar('interParticleDistance', myprops['ipd.value'])
