def show(self, form):
prot = form.protocol
micSet = prot.getInputMicrographs()
if not micSet:
print 'must specify input micrographs'
return
project = prot.getProject()
micfn = micSet.getFileName()
# Prepare a temporary folder to convert some input files
# and put some of the intermediate result files
coordsDir = project.getTmpPath(micSet.getName())
pwutils.cleanPath(coordsDir)
pwutils.makePath(coordsDir)
prot.convertInputs(coordsDir)
pickerConfig = os.path.join(coordsDir, 'picker.conf')
f = open(pickerConfig, "w")
pickScript = pw.join('em', 'packages', 'igbmc', 'run_gempicker.py')
pickCmd = prot._getPickArgs(threshold=False, workingDir=coordsDir)[0]
convertCmd = pw.join('apps', 'pw_convert.py')
args = {
"pickScript": pickScript,
"pickCmd": pickCmd,
"convertCmd": convertCmd,
'coordsDir': coordsDir,
'micsSqlite': micSet.getFileName(),
'thresholdLow': prot.thresholdLow,
'thresholdHigh': prot.thresholdHigh,
"useGPU": prot.useGPU
}
f.write("""
parameters = thresholdLow,thresholdHigh
thresholdLow.value = %(thresholdLow)s
thresholdLow.label = Threshold Low
thresholdLow.help = Low value cut-off
thresholdHigh.value = %(thresholdHigh)s
thresholdHigh.label = Threshold High
thresholdHigh.help = High value cut-off
autopickCommand = %(pickScript)s %%(micrograph) %(coordsDir)s %(useGPU)s %(pickCmd)s --thresh=%%(thresholdLow) --threshHigh=%%(thresholdHigh)
convertCommand = %(convertCmd)s --coordinates --from gempicker --to xmipp --input %(micsSqlite)s --output %(coordsDir)s
""" % args)
f.close()
process = CoordinatesObjectView(project, micfn, coordsDir, prot,
mode=CoordinatesObjectView.MODE_AUTOMATIC,
pickerProps=pickerConfig).show()
process.wait()
myprops = pwutils.readProperties(pickerConfig)
if myprops['applyChanges'] == 'true':
form.setVar('thresholdLow', myprops['thresholdLow.value'])
form.setVar('thresholdHigh', myprops['thresholdHigh.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":
pw.join('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()
# Check if the wizard changes were accepted or just canceled
myprops = readProperties(dogpickerProps)
if myprops['applyChanges'] == 'true':
form.setVar('diameter', myprops['diameter.value'])
form.setVar('threshold', myprops['threshold.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()
}
autopickCmd = '%(picker)s --i extra/%%(micrographName).star --o autopick --particle_diameter %(diameter)s '
autopickCmd += '--angpix %(apix)s --ref %(ref)s --ang %(ang)s --lowpass %(lowpass)s --threshold %%(threshold) '
autopickCmd += '--min_distance %%(ipd) --read_fom_maps' % args
if autopickFomProt.refsHaveInvertedContrast:
autopickCmd += ' --invert'
if autopickFomProt.refsCtfCorrected:
autopickCmd += ' --ctf'
args['autopickCmd'] = autopickCmd
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
autopickCmd = %(autopickCmd)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 = pwutils.readProperties(pickerProps)
if myprops['applyChanges'] == 'true':
form.setVar('pickingThreshold', myprops['threshold.value'])
form.setVar('interParticleDistance', myprops['ipd.value'])
def show(self, form):
prot = form.protocol
micSet = prot.getInputMicrographs()
if not micSet:
print 'must specify input micrographs'
return
project = prot.getProject()
micfn = micSet.getFileName()
# Prepare a temporary folder to convert some input files
# and put some of the intermediate result files
coordsDir = project.getTmpPath(micSet.getName())
pwutils.cleanPath(coordsDir)
pwutils.makePath(coordsDir)
prot.convertInputs(coordsDir)
pickerConfig = os.path.join(coordsDir, 'picker.conf')
f = open(pickerConfig, "w")
pickScript = pw.join('em', 'packages', 'igbmc', 'run_gempicker.py')
pickCmd = prot.getArgs(threshold=False, workingDir=coordsDir)
convertCmd = pw.join('apps', 'pw_convert.py')
args = {
"pickScript": pickScript,
"pickCmd": pickCmd,
"convertCmd": convertCmd,
'coordsDir': coordsDir,
'micsSqlite': micSet.getFileName(),
'thresholdLow': prot.thresholdLow,
'thresholdHigh': prot.thresholdHigh,
"useGPU": prot.useGPU
}
f.write("""
parameters = thresholdLow,thresholdHigh
thresholdLow.value = %(thresholdLow)s
thresholdLow.label = Threshold Low
thresholdLow.help = Low value cut-off
thresholdHigh.value = %(thresholdHigh)s
thresholdHigh.label = Threshold High
thresholdHigh.help = High value cut-off
autopickCommand = %(pickScript)s %%(micrograph) %(coordsDir)s %(useGPU)s %(pickCmd)s --thresh=%%(thresholdLow) --threshHigh=%%(thresholdHigh)
convertCommand = %(convertCmd)s --coordinates --from gempicker --to xmipp --input %(micsSqlite)s --output %(coordsDir)s
""" % args)
f.close()
process = CoordinatesObjectView(project, micfn, coordsDir, prot,
pickerProps=pickerConfig).show()
process.wait()
myprops = pwutils.readProperties(pickerConfig)
if myprops['applyChanges'] == 'true':
form.setVar('thresholdLow', myprops['thresholdLow.value'])
form.setVar('thresholdHigh', myprops['thresholdHigh.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()
}
autopickCmd = '%(picker)s --i extra/%%(micrographName).star --o autopick --particle_diameter %(diameter)s '
autopickCmd += '--angpix %(apix)s --ref %(ref)s --ang %(ang)s --lowpass %(lowpass)s --threshold %%(threshold) '
autopickCmd += '--min_distance %%(ipd) --read_fom_maps' % args
if autopickFomProt.refsHaveInvertedContrast:
autopickCmd += ' --invert'
if autopickFomProt.refsCtfCorrected:
autopickCmd += ' --ctf'
args['autopickCmd'] = autopickCmd
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
autopickCmd = %(autopickCmd)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 = pwutils.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(Plugin.getHome(), "ApDogPicker.py"),
"convert": 'emconvert',
'coordsDir': coordsDir,
'micsSqlite': micSet.getFileName(),
"diameter": autopickProt.diameter,
"threshold": autopickProt.threshold,
"apix": micSet.getSamplingRate()
}
f.write("""
parameters = diameterA,threshold
diameterA.value = %(diameter)s
diameterA.label = Diameter in A
diameterA.help = Sampling rate is %(apix)s
threshold.value = %(threshold)s
threshold.label = Threshold
threshold.help = Threshold in standard deviations above the mean
autopickCommand = python2 %(dogpicker)s --thresh=%%(threshold) --diam=%%(diameterA) --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,
mode=CoordinatesObjectView.MODE_AUTOMATIC,
pickerProps=dogpickerProps).show()
process.wait()
# Check if the wizard changes were accepted or just canceled
myprops = readProperties(dogpickerProps)
if myprops['applyChanges'] == 'true':
form.setVar('diameter', myprops['diameterA.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)
# 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" : pw.join('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,
mode=CoordinatesObjectView.MODE_AUTOMATIC,
pickerProps=dogpickerProps).show()
process.wait()
# Check if the wizard changes were accepted or just canceled
myprops = readProperties(dogpickerProps)
if myprops['applyChanges'] == 'true':
form.setVar('diameter', myprops['diameter.value'])
form.setVar('threshold', myprops['threshold.value'])
def show(self, form):
prot = form.protocol
micSet = prot.getInputMicrographs()
gpus = prot.getGpuList()
if not gpus:
form.showWarning("You should select at least one GPU.")
return
if not micSet:
form.showWarning("You should select input micrographs "
"before opening the wizard.")
return
project = prot.getProject()
if prot.micrographsSelection == 0: # all micrographs
micFn = micSet.getFileName()
else:
# Create a subset based on defocus values
ctfs = prot.ctfRelations.get()
if ctfs is None:
form.showWarning("You should select CTFs if using a defocus "
"subset. ")
return
micSubset = prot._createSetOfMicrographs(suffix='subset')
for mic in getSubsetByDefocus(ctfs, micSet,
prot.micrographsNumber.get()):
micSubset.append(mic)
micSubset.write()
micSubset.close()
micFn = micSubset.getFileName()
# Prepare a temporary folder to convert some input files
# and put some of the intermediate result files
coordsDir = project.getTmpPath(micSet.getName())
pwutils.cleanPath(coordsDir)
pwutils.makePath(coordsDir)
refStack = os.path.join(coordsDir, 'references.mrcs')
prot.convertReferences(refStack)
# Get current values of the properties
# micFn = os.path.join(coordsDir, 'micrographs.xmd')
# writeSetOfMicrographs(micSet, micFn)
pickerConfig = os.path.join(coordsDir, 'picker.conf')
f = open(pickerConfig, "w")
pickScript = pw.join('em', 'packages', 'gautomatch',
'run_gautomatch.py')
# Let use the first selected gpu for the wizard
pickCmd = prot.getArgs(threshold=False, mindist=False) % {
'GPU': gpus[0]
}
convertCmd = pw.join('apps', 'pw_convert.py')
args = {
"pickScript": pickScript,
"pickCmd": pickCmd,
"convertCmd": convertCmd,
'coordsDir': coordsDir,
'micsSqlite': micSet.getFileName(),
'threshold': prot.threshold.get(),
"mindist": prot.minDist.get(),
"refStack": refStack
}
# If Gautomatch will guess advanced parameter we don't need to send
# the min distance to the wizard.
if prot.advanced:
f.write("""
parameters = threshold
threshold.value = %(threshold)s
threshold.label = Threshold
threshold.help = Particles with CCC above the threshold will be picked
autopickCommand = %(pickScript)s %%(micrograph) %(refStack)s %(coordsDir)s %(pickCmd)s --cc_cutoff %%(threshold)
convertCommand = %(convertCmd)s --coordinates --from gautomatch --to xmipp --input %(micsSqlite)s --output %(coordsDir)s
""" % args)
else:
f.write("""
parameters = threshold,mindist
threshold.value = %(threshold)s
threshold.label = Threshold
threshold.help = Particles with CCC above the threshold will be picked
mindist.value = %(mindist)s
mindist.label = Min search distance
mindist.help = Use value of 0.9~1.1X diameter
autopickCommand = %(pickScript)s %%(micrograph) %(refStack)s %(coordsDir)s %(pickCmd)s --cc_cutoff %%(threshold) --min_dist %%(mindist)
convertCommand = %(convertCmd)s --coordinates --from gautomatch --to xmipp --input %(micsSqlite)s --output %(coordsDir)s
""" % args)
f.close()
process = CoordinatesObjectView(
project,
micFn,
coordsDir,
prot,
mode=CoordinatesObjectView.MODE_AUTOMATIC,
pickerProps=pickerConfig).show()
process.wait()
myprops = pwutils.readProperties(pickerConfig)
if myprops['applyChanges'] == 'true':
form.setVar('threshold', myprops['threshold.value'])
if not prot.advanced:
form.setVar('minDist', myprops['mindist.value'])
else:
pass # TODO: We could even in future parse the 'guessed' params
def show(self, form):
prot = form.protocol
micSet = prot.getInputMicrographs()
if not micSet:
print 'must specify input micrographs'
return
project = prot.getProject()
micfn = micSet.getFileName()
# Prepare a temporary folder to convert some input files
# and put some of the intermediate result files
coordsDir = project.getTmpPath(micSet.getName())
pwutils.cleanPath(coordsDir)
pwutils.makePath(coordsDir)
refStack = os.path.join(coordsDir, 'references.mrcs')
prot.convertReferences(refStack)
# Get current values of the properties
# micfn = os.path.join(coordsDir, 'micrographs.xmd')
# writeSetOfMicrographs(micSet, micfn)
pickerConfig = os.path.join(coordsDir, 'picker.conf')
f = open(pickerConfig, "w")
pickScript = pw.join('em', 'packages', 'gautomatch',
'run_gautomatch.py')
pickCmd = prot.getArgs(threshold=False, mindist=False)
convertCmd = pw.join('apps', 'pw_convert.py')
args = {
"pickScript": pickScript,
"pickCmd": pickCmd,
"convertCmd": convertCmd,
'coordsDir': coordsDir,
'micsSqlite': micSet.getFileName(),
'threshold': prot.threshold.get(),
"mindist": prot.minDist.get(),
"refStack": refStack
}
# If Gautomatch will guess advanced parameter we don't need to send
# the min distance to the wizard.
if prot.advanced:
f.write("""
parameters = threshold
threshold.value = %(threshold)s
threshold.label = Threshold
threshold.help = Particles with CCC above the threshold will be picked
autopickCommand = %(pickScript)s %%(micrograph) %(refStack)s %(coordsDir)s %(pickCmd)s --cc_cutoff %%(threshold)
convertCommand = %(convertCmd)s --coordinates --from gautomatch --to xmipp --input %(micsSqlite)s --output %(coordsDir)s
""" % args)
else:
f.write("""
parameters = threshold,mindist
threshold.value = %(threshold)s
threshold.label = Threshold
threshold.help = Particles with CCC above the threshold will be picked
mindist.value = %(mindist)s
mindist.label = Min search distance
mindist.help = Use value of 0.9~1.1X diameter
autopickCommand = %(pickScript)s %%(micrograph) %(refStack)s %(coordsDir)s %(pickCmd)s --cc_cutoff %%(threshold) --min_dist %%(mindist)
convertCommand = %(convertCmd)s --coordinates --from gautomatch --to xmipp --input %(micsSqlite)s --output %(coordsDir)s
""" % args)
f.close()
process = CoordinatesObjectView(project,
micfn,
coordsDir,
prot,
pickerProps=pickerConfig).show()
process.wait()
myprops = pwutils.readProperties(pickerConfig)
if myprops['applyChanges'] == 'true':
form.setVar('threshold', myprops['threshold.value'])
if not prot.advanced:
form.setVar('minDist', myprops['mindist.value'])
else:
pass # TODO: We could even in future parse the 'guessed' params
def show(self, form):
autopickProt = form.protocol
if not autopickProt.hasAttribute('outputCoordinatesSubset'):
form.showWarning("You should run the procotol in 'Optimize' mode "
"at least once before opening the wizard.")
return
project = autopickProt.getProject()
micSet = autopickProt.outputMicrographsSubset
micfn = micSet.getFileName()
coordsDir = project.getTmpPath(micSet.getName())
cleanPath(coordsDir)
makePath(coordsDir)
from pyworkflow.em.packages.xmipp3.convert import writeSetOfMicrographs
micStarFn = os.path.join(coordsDir, 'micrographs.xmd')
# Set CTF information to the micrographs to be displayed in the
# picking list
autopickProt.micDict = OrderedDict()
micDict, _ = autopickProt._loadInputList()
def _preprocessMic(mic, micRow):
mic.setCTF(micDict[mic.getMicName()].getCTF())
writeSetOfMicrographs(micSet,
micStarFn,
preprocessImageRow=_preprocessMic)
# Create a folder in extra to backup the original autopick star files
backupDir = autopickProt._getExtraPath('wizard-backup')
cleanPath(backupDir)
makePath(backupDir)
pwutils.copyPattern(autopickProt._getExtraPath("*autopick.star"),
backupDir)
cmd = '%s relion_autopick ' % pw.getScipionScript()
#cmd += '--i extra/%(micrographName).star '
cmd += '--i input_micrographs.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,
'preprocessCommand': 'rm -rf %s/*.pos' % coordsDir,
'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 (A)
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
preprocessCommand = %(preprocessCommand)s
autopickCommand = %(autopickCommand)s
convertCommand = %(convertCmd)s
hasInitialCoordinates = true
doPickAll = true
""" % args)
f.close()
process = CoordinatesObjectView(
autopickProt.getProject(),
micStarFn,
coordsDir,
autopickProt,
mode=CoordinatesObjectView.MODE_AUTOMATIC,
pickerProps=pickerProps).show()
process.wait()
myprops = pwutils.readProperties(pickerProps)
# Check if the wizard changes were accepted or just canceled
if myprops.get('applyChanges', 'false') == '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)
else:
# If the wizard was not execute, we should restore the original
# autopick star files in case their were modified by the wizard
pwutils.copyPattern(os.path.join(backupDir, "*autopick.star"),
autopickProt._getExtraPath())
def show(self, form):
autopickProt = form.protocol
project = autopickProt.getProject()
micSet = autopickProt.getInputMicrographs()
micfn = micSet.getFileName()
coordsDir = project.getTmpPath(micSet.getName())
print("coordsDir: ", coordsDir)
params, minDiameter, maxDiameter, threshold = autopickProt._getPickArgs(
)
cleanPath(coordsDir)
makePath(coordsDir, 'extra')
pickerProps = os.path.join(coordsDir, 'picker.conf')
from pyworkflow.em.packages.relion.convert import writeSetOfMicrographs
micStarFn = os.path.join(coordsDir, 'input_micrographs.star')
def _postprocessMic(mic, micRow):
micFn = mic.getFileName()
micBase = os.path.basename(micFn)
createLink(micFn, os.path.join(coordsDir, micBase))
micRow.setValue(md.RLN_MICROGRAPH_NAME, micBase)
writeSetOfMicrographs(micSet,
micStarFn,
postprocessImageRow=_postprocessMic)
f = open(pickerProps, "w")
#params = params.replace('--odir ""', '--odir extra')
autopickCmd = "%s relion_autopick " % pw.getScipionScript()
autopickCmd += ' --i input_micrographs.star '
autopickCmd += params
autopickCmd += ' --LoG_diam_min %(mind) '
autopickCmd += ' --LoG_diam_max %(maxd) '
autopickCmd += ' --LoG_adjust_threshold %(threshold) '
args = {
"convert": pw.join('apps', 'pw_convert.py'),
'coordsDir': coordsDir,
'micsSqlite': micSet.getFileName(),
"minDiameter": minDiameter,
"maxDiameter": maxDiameter,
"threshold": threshold,
'projDir': project.getPath(), #autopickProt.getWorkingDir(),
"autopickCmd": autopickCmd
}
f.write("""
parameters = mind,maxd,threshold
mind.value = %(minDiameter)s
mind.label = Min. Diameter for LoG filter (A)
mind.help = The smallest allowed diameter for the blob-detection algorithm. This should correspond to the smallest size of your particles in Angstroms.
maxd.value = %(maxDiameter)s
maxd.label = Max. Diameter for LoG filter (A)
maxd.help = The largest allowed diameter for the blob-detection algorithm. This should correspond to the largest size of your particles in Angstroms.
threshold.value = %(threshold)s
threshold.label = Adjust default threshold
threshold.help = Lower threshold -> more particles
runDir = %(coordsDir)s
autopickCommand = %(autopickCmd)s
convertCommand = %(convert)s --coordinates --from relion --to xmipp --input %(micsSqlite)s --output %(coordsDir)s --extra %(coordsDir)s/
hasInitialCoordinates = false
doPickAll = true
""" % args)
f.close()
process = CoordinatesObjectView(autopickProt.getProject(),
micfn,
coordsDir,
autopickProt,
pickerProps=pickerProps).show()
process.wait()
myprops = pwutils.readProperties(pickerProps)
if myprops['applyChanges'] == 'true':
form.setVar('minDiameter', myprops['mind.value'])
form.setVar('maxDiameter', myprops['maxd.value'])
form.setVar('threshold', myprops['threshold.value'])
def show(self, form):
prot = form.protocol
micSet = prot.getInputMicrographs()
gpus = prot.getGpuList()
if not gpus:
form.showWarning("You should select at least one GPU.")
return
if not micSet:
form.showWarning("You should select input micrographs "
"before opening the wizard.")
return
project = prot.getProject()
if prot.micrographsSelection == 0: # all micrographs
micFn = micSet.getFileName()
else:
# Create a subset based on defocus values
ctfs = prot.ctfRelations.get()
if ctfs is None:
form.showWarning("You should select CTFs if using a defocus "
"subset. ")
return
micSubset = prot._createSetOfMicrographs(suffix='subset')
for mic in getSubsetByDefocus(ctfs, micSet,
prot.micrographsNumber.get()):
micSubset.append(mic)
micSubset.write()
micSubset.close()
micFn = micSubset.getFileName()
# Prepare a temporary folder to convert some input files
# and put some of the intermediate result files
coordsDir = project.getTmpPath(micSet.getName())
pwutils.cleanPath(coordsDir)
pwutils.makePath(coordsDir)
refStack = os.path.join(coordsDir, 'references.mrcs')
prot.convertReferences(refStack)
# Get current values of the properties
# micFn = os.path.join(coordsDir, 'micrographs.xmd')
# writeSetOfMicrographs(micSet, micFn)
pickerConfig = os.path.join(coordsDir, 'picker.conf')
f = open(pickerConfig, "w")
pickScript = pw.join('em', 'packages', 'gautomatch',
'run_gautomatch.py')
# Let use the first selected gpu for the wizard
pickCmd = prot.getArgs(threshold=False,
mindist=False) % {'GPU': gpus[0]}
convertCmd = pw.join('apps', 'pw_convert.py')
args = {
"pickScript": pickScript,
"pickCmd": pickCmd,
"convertCmd": convertCmd,
'coordsDir': coordsDir,
'micsSqlite': micSet.getFileName(),
'threshold': prot.threshold.get(),
"mindist": prot.minDist.get(),
"refStack": refStack
}
# If Gautomatch will guess advanced parameter we don't need to send
# the min distance to the wizard.
if prot.advanced:
f.write("""
parameters = threshold
threshold.value = %(threshold)s
threshold.label = Threshold
threshold.help = Particles with CCC above the threshold will be picked
autopickCommand = %(pickScript)s %%(micrograph) %(refStack)s %(coordsDir)s %(pickCmd)s --cc_cutoff %%(threshold)
convertCommand = %(convertCmd)s --coordinates --from gautomatch --to xmipp --input %(micsSqlite)s --output %(coordsDir)s
""" % args)
else:
f.write("""
parameters = threshold,mindist
threshold.value = %(threshold)s
threshold.label = Threshold
threshold.help = Particles with CCC above the threshold will be picked
mindist.value = %(mindist)s
mindist.label = Min search distance
mindist.help = Use value of 0.9~1.1X diameter
autopickCommand = %(pickScript)s %%(micrograph) %(refStack)s %(coordsDir)s %(pickCmd)s --cc_cutoff %%(threshold) --min_dist %%(mindist)
convertCommand = %(convertCmd)s --coordinates --from gautomatch --to xmipp --input %(micsSqlite)s --output %(coordsDir)s
""" % args)
f.close()
process = CoordinatesObjectView(project, micFn, coordsDir, prot,
mode=CoordinatesObjectView.MODE_AUTOMATIC,
pickerProps=pickerConfig).show()
process.wait()
myprops = pwutils.readProperties(pickerConfig)
if myprops['applyChanges'] == 'true':
form.setVar('threshold', myprops['threshold.value'])
if not prot.advanced:
form.setVar('minDist', myprops['mindist.value'])
else:
pass # TODO: We could even in future parse the 'guessed' params
def show(self, form):
autopickProt = form.protocol
micSet = autopickProt.getInputMicrographs()
if not micSet:
print('must specify input micrographs')
return
# ensuring a valid boxSize
if autopickProt.boxSize.get() is None:
autopickProt.boxSize.set(100)
project = autopickProt.getProject()
coordsDir = project.getTmpPath(micSet.getName())
cleanPath(coordsDir)
makePath(coordsDir)
micMdFn = os.path.join(coordsDir, "micrographs.xmd")
writeSetOfMicrographs(micSet, micMdFn)
pickerProps = os.path.join(coordsDir, 'picker.conf')
f = open(pickerProps, "w")
params = ['boxSize', 'lowerThreshold', 'higherThreshold', 'gaussWidth']
program = eman2.Plugin.getBoxerCommand(boxerVersion='old')
extraParams = "invert_contrast=%s:use_variance=%s:%s" % (
autopickProt.doInvert,
autopickProt.useVarImg,
autopickProt.extraParams)
args = {
"params": ','.join(params),
"preprocess": "%s %s" % (pw.getScipionScript(),
eman2.Plugin.getProgram('sxprocess.py')),
"picker": "%s %s" % (pw.getScipionScript(), program),
"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": extraParams
}
f.write("""
parameters = %(params)s
boxSize.value = %(boxSize)s
boxSize.label = Box Size
boxSize.help = Box size in pixels
lowerThreshold.value = %(lowerThreshold)s
lowerThreshold.label = Lower Threshold
lowerThreshold.help = Lower Threshold
higherThreshold.help = Higher Threshold
higherThreshold.value = %(higherThreshold)s
higherThreshold.label = Higher Threshold
gaussWidth.help = Width of the Gaussian kernel used
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, micMdFn, coordsDir, autopickProt,
mode=CoordinatesObjectView.MODE_AUTOMATIC,
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
if not autopickProt.hasAttribute('outputCoordinatesSubset'):
form.showWarning("You should run the procotol in 'Optimize' mode "
"at least once before opening the wizard.")
return
project = autopickProt.getProject()
micSet = autopickProt.outputMicrographsSubset
micfn = micSet.getFileName()
coordsDir = project.getTmpPath(micSet.getName())
cleanPath(coordsDir)
makePath(coordsDir)
from pyworkflow.em.packages.xmipp3.convert import writeSetOfMicrographs
micStarFn = os.path.join(coordsDir, 'micrographs.xmd')
# Set CTF information to the micrographs to be displayed in the
# picking list
autopickProt.micDict = OrderedDict()
micDict, _ = autopickProt._loadInputList()
def _preprocessMic(mic, micRow):
mic.setCTF(micDict[mic.getMicName()].getCTF())
writeSetOfMicrographs(micSet, micStarFn,
preprocessImageRow=_preprocessMic)
# Create a folder in extra to backup the original autopick star files
backupDir = autopickProt._getExtraPath('wizard-backup')
cleanPath(backupDir)
makePath(backupDir)
pwutils.copyPattern(autopickProt._getExtraPath("*autopick.star"),
backupDir)
cmd = '%s relion_autopick ' % pw.getScipionScript()
#cmd += '--i extra/%(micrographName).star '
cmd += '--i input_micrographs.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,
'preprocessCommand': 'rm -rf %s/*.pos' % coordsDir,
'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 (A)
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
preprocessCommand = %(preprocessCommand)s
autopickCommand = %(autopickCommand)s
convertCommand = %(convertCmd)s
hasInitialCoordinates = true
doPickAll = true
""" % args)
f.close()
process = CoordinatesObjectView(autopickProt.getProject(), micStarFn,
coordsDir, autopickProt,
mode=CoordinatesObjectView.MODE_AUTOMATIC,
pickerProps=pickerProps).show()
process.wait()
myprops = pwutils.readProperties(pickerProps)
# Check if the wizard changes were accepted or just canceled
if myprops.get('applyChanges', 'false') == '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)
else:
# If the wizard was not execute, we should restore the original
# autopick star files in case their were modified by the wizard
pwutils.copyPattern(os.path.join(backupDir, "*autopick.star"),
autopickProt._getExtraPath())