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":
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
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
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'])