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 createProjectFromWorkflow(workflow, projectName, argsList):
scipion = SCIPION_EP
scriptsPath = pw.join('project', 'scripts')
# Clean the project name as pyworkflow will do
projectName = Project.cleanProjectName(projectName)
# Create the project
print("Creating project %s" % projectName)
createProjectScript = os.path.join(scriptsPath, 'create.py')
os.system("python -m %s python %s %s %s" %
(scipion, createProjectScript, projectName, workflow))
# Wait 2 seconds to avoid activity
time.sleep(2)
if scheduleProject(argsList):
# Schedule the project
scheduleProjectScript = os.path.join(scriptsPath, 'schedule.py')
print("Scheduling project %s" % projectName)
subprocess.Popen([
"python", "-m", scipion, "python", scheduleProjectScript,
projectName
])
# Wait 5 seconds to avoid activity
time.sleep(5)
if launchGUI(argsList):
print("Showing project %s" % projectName)
# Launch scipion
subprocess.Popen(["python", "-m", scipion, MODE_PROJECT, projectName])
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 __init__(self, volfile, sendEnd=True,**kwargs):
if volfile.endswith('.mrc'):
volfile += ':mrc'
self.kwargs = kwargs
if volfile is None:
raise ValueError(volfile)
if '@' in volfile:
[index, file] = volfile.split('@');
else :
file = volfile
if ':' in file:
file = file[0: file.rfind(':')]
if not os.path.exists(file):
raise Exception("File %s does not exists"%file)
self.volfile = volfile
self.voxelSize = self.kwargs.get('voxelSize', None)
# ChimeraServer is the basic server. There are other
# than inherit from it.
serverName=self.kwargs.get('ChimeraServer','ChimeraServer')
self.address = ''
self.port = getFreePort()
serverfile = pw.join('em', 'chimera_server.py')
command = CommandView("chimera --script '%s %s %s' &" %
(serverfile, self.port,serverName),
env=getChimeraEnviron(),).show()
self.authkey = 'test'
self.client = Client((self.address, self.port), authkey=self.authkey)
self.initVolumeData()
self.openVolumeOnServer(self.vol,sendEnd)
self.initListenThread()
def __init__(self, volfile, sendEnd=True,**kwargs):
if volfile.endswith('.mrc'):
volfile += ':mrc'
self.kwargs = kwargs
if volfile is None:
raise ValueError(volfile)
if '@' in volfile:
[index, file] = volfile.split('@');
else :
file = volfile
if ':' in file:
file = file[0: file.rfind(':')]
if not os.path.exists(file):
raise Exception("File %s does not exists"%file)
self.volfile = volfile
self.voxelSize = self.kwargs.get('voxelSize', None)
# ChimeraServer is the basic server. There are other
# than inherit from it.
serverName=self.kwargs.get('ChimeraServer','ChimeraServer')
self.address = ''
self.port = getFreePort()
serverfile = pw.join('em', 'chimera_server.py')
command = CommandView("chimera --script '%s %s %s' &" %
(serverfile, self.port,serverName),
env=getChimeraEnviron(),).show()
self.authkey = 'test'
self.client = Client((self.address, self.port), authkey=self.authkey)
self.initVolumeData()
self.openVolumeOnServer(self.vol,sendEnd)
self.initListenThread()
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)
# 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 createEmanProcess(script='e2converter.py', args=None, direc="."):
""" Open a new Process with all EMAN environment (python...etc)
that will server as an adaptor to use EMAN library
"""
program = pw.join('em', 'packages', 'eman2', script)
cmd = getEmanCommand(program, args)
# gcmd = greenStr(cmd)
print "** Running: '%s'" % cmd
proc = subprocess.Popen(cmd, shell=True, env=getEnviron(),
stdin=subprocess.PIPE,
stdout=subprocess.PIPE, cwd=direc)
return proc
def createEmanProcess(script='e2converter.py', args=None, direc="."):
""" Open a new Process with all EMAN environment (python...etc)
that will server as an adaptor to use EMAN library
"""
program = pw.join('em', 'packages', 'eman2', script)
cmd = getEmanCommand(program, args)
# gcmd = greenStr(cmd)
print "** Running: '%s'" % cmd
proc = subprocess.Popen(cmd, shell=True, env=getEnviron(),
stdin=subprocess.PIPE,
stdout=subprocess.PIPE, cwd=direc)
return proc
def _launchLocal(protocol, wait, stdin=None, stdout=None, stderr=None):
# Check first if we need to launch with MPI or not
command = (
'%s %s "%s" "%s" %s' %
(pw.PYTHON, pw.join(pw.APPS, 'pw_protocol_run.py'),
protocol.getProject().path, protocol.getDbPath(), protocol.strId()))
hostConfig = protocol.getHostConfig()
useQueue = protocol.useQueue()
# Check if need to submit to queue
if useQueue and (protocol.getSubmitDict()["QUEUE_FOR_JOBS"] == "N"):
submitDict = dict(hostConfig.getQueuesDefault())
submitDict.update(protocol.getSubmitDict())
submitDict['JOB_COMMAND'] = command
jobId = _submit(hostConfig, submitDict)
else:
jobId = _run(command, wait, stdin, stdout, stderr)
return jobId
def a_testEmanConvert(self):
project = self.loadProject("TestXmippWorkflow")
particleList = project.mapper.selectByClass('SetOfParticles')
eman2.loadEnvironment()
program = pw.join('em', 'packages', 'eman2', 'e2converter.py')
cmd = eman2.getEmanCommand(program, 'myimage.hdf')
gcmd = greenStr(cmd)
print "** Running: '%s'" % gcmd
proc = subprocess.Popen(cmd, shell=True, stdin=subprocess.PIPE)
p = particleList[0]
for i, img in enumerate(p):
loc = img.getLocation()
index = loc.getIndex()
fn = loc.getFileName()
print >> proc.stdin, index, fn
p.wait()
def a_testEmanConvert(self):
project = self.loadProject("TestXmippWorkflow")
particleList = project.mapper.selectByClass('SetOfParticles')
eman2.loadEnvironment()
program = pw.join('em', 'packages', 'eman2', 'e2converter.py')
cmd = eman2.getEmanCommand(program, 'myimage.hdf')
gcmd = greenStr(cmd)
print "** Running: '%s'" % gcmd
proc = subprocess.Popen(cmd, shell=True, stdin=subprocess.PIPE)
p = particleList[0]
for i, img in enumerate(p):
loc = img.getLocation()
index = loc.getIndex()
fn = loc.getFileName()
print >> proc.stdin, index, fn
p.wait()
def createProjectFromWorkflow(self, workflow):
projectName = self._getValue(PROJECT_NAME)
scipion = pw.getScipionScript()
scriptsPath = pw.join('project', 'scripts')
# Download the required data
# pwutils.runCommand(scipion +
# " testdata --download jmbFalconMovies")
# Create the project
createProjectScript = os.path.join(scriptsPath, 'create.py')
pwutils.runCommand(scipion + " python " + createProjectScript + " " +
projectName + " " + workflow)
# Schedule the project
scheduleProjectScript = os.path.join(scriptsPath, 'schedule.py')
pwutils.runCommand(scipion + " python " + scheduleProjectScript + " " +
projectName)
# Launch scipion
pwutils.runCommand(scipion + " project " + projectName)
def openProject(self, projName):
from subprocess import Popen
script = pw.join('apps', 'pw_project.py')
Popen([os.environ['SCIPION_PYTHON'], script, projName])
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 _getAppsProgram(prog):
""" Get a command to launch a program under the apps folder.
"""
return "%s %s" % (pw.PYTHON, pw.join(pw.APPS, prog))
def openProject(self, projName):
from subprocess import Popen
script = pw.join('apps', 'pw_project.py')
Popen([pw.PYTHON, script, projName])
def _getAppsProgram(prog):
""" Get a command to launch a program under the apps folder.
And also using a different python if configured in SCIPION_PYTHON var.
"""
return os.environ.get("SCIPION_PYTHON", "python") + " " + pw.join("apps", prog)
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)
from pyworkflow.em.packages.xmipp3 import writeSetOfMicrographs
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']
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, 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'])
Usage: python -m pyworkflow.project.scripts.stop project_name
This script will stop all running protocols of the specified project.
e.g.
scipion python scripts/stop.py MyProject
""" % error)
sys.exit(1)
n = len(sys.argv)
if n > 2:
usage("This script accepts 1 mandatory parameter: the project name")
projName = sys.argv[1]
path = pw.join('gui', 'no-tkinter')
sys.path.insert(1, path)
manager = Manager()
if not manager.hasProject(projName):
usage("There is no project with this name: %s" % pwutils.red(projName))
# the project may be a soft link which may be unavailable to the cluster so get the real path
try:
projectPath = os.readlink(manager.getProjectPath(projName))
except:
projectPath = manager.getProjectPath(projName)
project = Project(path=projectPath)
project.load()
def _getAppsProgram(prog):
""" Get a command to launch a program under the apps folder.
And also using a different python if configured in SCIPION_PYTHON var.
"""
return os.environ.get('SCIPION_PYTHON', 'python') + ' ' + pw.join('apps', prog)
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):
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,
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 test_Process(self):
prog = pw.join('apps', 'pw_sleep.py')
p = Popen('xmipp_python %s 500' % prog, shell=True)
print "pid: ", p.pid
time.sleep(5)
killWithChilds(p.pid)
def openProject(self, projName):
from subprocess import Popen
script = pw.join('apps', 'pw_project.py')
Popen([os.environ['SCIPION_PYTHON'], script, projName])
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'])
