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 _launchLocal(protocol, wait, stdin=None, stdout=None, stderr=None):
# Check first if we need to launch with MPI or not
# zocalo_job_path = protocol.getProject().path
protStrId = protocol.strId()
python = pw.SCIPION_PYTHON
scipion = pw.getScipionScript()
command = '%s %s runprotocol pw_protocol_run.py "%s" "%s" %s' % (
python, scipion, protocol.getProject().path, protocol.getDbPath(),
protStrId)
hostConfig = protocol.getHostConfig()
useQueue = protocol.useQueue()
# our_params = ['runprotocol', 'pw_protocol_run.py', protocol.getProject().path, protocol.getDbPath(), protStrId]
# our_command = process.buildRunCommand(scipion, our_params, -1, hostConfig=hostConfig, env=python)
# print('+++++++++New Command++++++++++')
# print(our_command)
# Check if need to submit to queue
if useQueue:
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 openPath(self, path):
"Try to open the selected path"
path = expandPattern(path)
# If the path is a dir, open it with scipion browser dir <path>
if os.path.isdir(path):
dpath = (path if os.path.isabs(path)
else os.path.join(os.getcwd(), path))
subprocess.Popen([pw.getScipionScript(), 'view', dpath])
return
# If it is a file, interpret it correctly and open it with DataView
dirname = os.path.dirname(path)
fname = os.path.basename(path)
if '@' in fname:
path = os.path.join(dirname, fname.split('@', 1)[-1])
else:
path = os.path.join(dirname, fname)
if os.path.exists(path):
import xmippLib
fn = xmippLib.FileName(path)
if fn.isImage() or fn.isMetaData():
from pyworkflow.em.viewers import DataView
DataView(path).show()
else:
_open_cmd(path)
else:
# This is probably one special reference, like sci-open:... that
# can be interpreted with our handlers.
tag = path.split(':', 1)[0] if ':' in path else None
if tag in self.handlers:
self.handlers[tag](path.split(':', 1)[-1])
else:
print "Can't find %s" % path
def openPath(self, path):
"Try to open the selected path"
path = expandPattern(path)
# If the path is a dir, open it with scipion browser dir <path>
if os.path.isdir(path):
dpath = (path if os.path.isabs(path)
else os.path.join(os.getcwd(), path))
subprocess.Popen([pw.getScipionScript(), 'view', dpath])
return
# If it is a file, interpret it correctly and open it with DataView
dirname = os.path.dirname(path)
fname = os.path.basename(path)
if '@' in fname:
path = os.path.join(dirname, fname.split('@', 1)[-1])
else:
path = os.path.join(dirname, fname)
if os.path.exists(path):
import xmipp
fn = xmipp.FileName(path)
if fn.isImage() or fn.isMetaData():
from pyworkflow.em.viewer import DataView
DataView(path).show()
else:
_open_cmd(path)
else:
# This is probably one special reference, like sci-open:... that
# can be interpreted with our handlers.
tag = path.split(':', 1)[0] if ':' in path else None
if tag in self.handlers:
self.handlers[tag](path.split(':', 1)[-1])
else:
print "Can't find %s" % path
def schedule(protocol, wait=False):
""" Use this function to schedule protocols that are not ready to
run yet. Right now it only make sense to schedule jobs locally.
"""
cmd = '%s %s runprotocol pw_schedule_run.py' % (pw.PYTHON,
pw.getScipionScript())
cmd += ' "%s" "%s" %s' % (protocol.getProject().path, protocol.getDbPath(),
protocol.strId())
jobId = _run(cmd, wait)
protocol.setJobId(jobId)
return jobId
def _createScipionProject(self):
dataPath = self.getConfValue(DEPOSITION_PATTERN)
projectName = self.getConfValue(PROJECT_NAME)
projectPath = os.path.join(self.getConfValue(PROJECTS_PATH),
projectName)
print("")
print("Deposition Pattern: %s" % dataPath)
print("Project Name: %s" % projectName)
print("Project Path: %s" % projectPath)
# Launch the simulation
if self.getConfValue(SIMULATION):
rawData = self.getConfValue(RAWDATA_SIM)
gainGlob = os.path.join(rawData, self.getConfValue(GAIN_PAT))
gainPath = gainGlob[0] if len(gainGlob) > 0 else ''
rawDataPath = os.path.join(rawData, self.getConfValue(PATTERN))
subprocess.Popen('%s python %s "%s" %s %d %s &' %
(pw.getScipionScript(), 'simulate_acquisition.py',
rawDataPath, self.getConfValue(DEPOSITION_DIR),
self.getConfValue(TIMEOUT), gainPath),
shell=True)
time.sleep(1)
# Check if there are something to process
count = 1
while not len(pwutils.glob(dataPath)):
if count == 6:
self.windows.close()
string = ("No file found in %s.\n"
"Make sure that the acquisition has been started.\n\n" %
dataPath)
if count < 5:
str2 = "Retrying... (%s/5)" % count
else:
str2 = "Last try..."
try:
self.windows.showInfo(string + str2)
except: # When 'Cancel' is press
sys.exit(0)
time.sleep(3)
count += 1
preprocessWorkflow(self.configDict)
os.system('touch /tmp/scipion/project_%s' % projectName)
if self.getConfValue(WAIT2PICK, False):
os.system('touch /tmp/scipion/wait2pick_%s' % projectName)
def schedule(protocol, wait=False):
""" Use this function to schedule protocols that are not ready to
run yet. Right now it only make sense to schedule jobs locally.
"""
protStrId = protocol.strId()
python = pw.SCIPION_PYTHON
scipion = pw.getScipionScript()
cmd = '%s %s runprotocol pw_schedule_run.py' % (python, scipion)
cmd += ' "%s" "%s" %s' % (protocol.getProject().path,
protocol.getDbPath(),
protStrId)
jobId = _run(cmd, wait)
protocol.setJobId(jobId)
return jobId
def getDataSet(cls, name):
"""
This method is called every time the dataset want to be retrieved
"""
assert name in cls._datasetDict, "Dataset: %s dataset doesn't exist." % name
ds = cls._datasetDict[name]
folder = ds.folder
url = '' if ds.url is None else ' -u ' + ds.url
if not pw.utils.envVarOn('SCIPION_TEST_NOSYNC'):
command = ("%s %s testdata --download %s %s" %
(pw.PYTHON, pw.getScipionScript(), folder, url))
print(">>>> %s" % command)
os.system(command)
return cls._datasetDict[name]
def _launchLocal(protocol, wait, stdin=None, stdout=None, stderr=None):
# Check first if we need to launch with MPI or not
command = ('%s %s runprotocol pw_protocol_run.py "%s" "%s" %s' %
(pw.PYTHON, pw.getScipionScript(), 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 _launchLocal(protocol, wait, stdin=None, stdout=None, stderr=None):
# Check first if we need to launch with MPI or not
protStrId = protocol.strId()
python = pw.SCIPION_PYTHON
scipion = pw.getScipionScript()
command = '%s %s runprotocol pw_protocol_run.py "%s" "%s" %s' % (
python, scipion, protocol.getProject().path, protocol.getDbPath(),
protStrId)
hostConfig = protocol.getHostConfig()
useQueue = protocol.useQueue()
# Check if need to submit to queue
if useQueue:
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 _launchLocal(protocol, wait, stdin=None, stdout=None, stderr=None):
# Check first if we need to launch with MPI or not
protStrId = protocol.strId()
python = pw.SCIPION_PYTHON
scipion = pw.getScipionScript()
command = '%s %s runprotocol pw_protocol_run.py "%s" "%s" %s' % (python, scipion,
protocol.getProject().path,
protocol.getDbPath(),
protStrId)
hostConfig = protocol.getHostConfig()
useQueue = protocol.useQueue()
# Check if need to submit to queue
if useQueue:
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 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 _runNewItem(self, itemType, itemName):
if self._match(itemName):
spaces = (itemType * 2) * ' '
scipion = pw.getScipionScript()
cmd = "%s %s test %s" % (spaces, scipion, itemName)
run = ((itemType == MODULE and self.mode == 'module') or
(itemType == CLASS and self.mode == 'classes') or
(itemType == TEST and self.mode == 'all'))
if run:
if self.log:
logFile = join(self.testsDir, '%s.txt' % itemName)
cmdFull = cmd + " > %s 2>&1" % logFile
else:
logFile = ''
cmdFull = cmd
print(pwutils.green(cmdFull))
t = pwutils.Timer()
t.tic()
self.testCount += 1
result = os.system(cmdFull)
if self.log:
self._logTest(cmd.replace(scipion, 'scipion'),
t.getToc(), result, logFile)
def _createScipionProject(self, projName, projPath, scipionProjPath):
manager = Manager()
project = manager.createProject(projName, location=scipionProjPath)
self.lastProt = None
pattern = self._getConfValue(PATTERN)
smtpServer = self._getConfValue(SMTP_SERVER, '')
smtpFrom = self._getConfValue(SMTP_FROM, '')
smtpTo = self._getConfValue(SMTP_TO, '')
doMail = self._getValue(EMAIL_NOTIFICATION)
doPublish = self._getValue(HTML_REPORT)
protImport = project.newProtocol(em.ProtImportMovies,
objLabel='Import movies',
filesPath=projPath,
filesPattern=pattern,
sphericalAberration=self._getConfValue(CS),
dataStreaming=True)
# Should I publish html report?
if doPublish == 1:
publish = self._getConfValue('HTML_PUBLISH')
print("\n\nReport available at URL: %s/%s\n\n"
%('http://scipion.cnb.csic.es/scipionbox',projName))
else:
publish = ''
protMonitor = project.newProtocol(em.ProtMonitorSummary,
objLabel='Summary Monitor',
doMail=doMail,
emailFrom=smtpFrom,
emailTo=smtpTo,
smtp=smtpServer,
publishCmd=publish)
def _saveProtocol(prot, movies=True, monitor=True):
if movies:
prot.inputMovies.set(self.lastProt)
prot.inputMovies.setExtended('outputMovies')
project.saveProtocol(prot)
self.lastProt = prot
if monitor:
protMonitor.inputProtocols.append(prot)
_saveProtocol(protImport, movies=False)
useMC2 = self._getValue(MOTIONCOR2)
useMC = self._getValue(MOTIONCORR) or useMC2
useOF = self._getValue(OPTICAL_FLOW)
useSM = self._getValue(SUMMOVIE)
useCTF = self._getValue(CTFFIND4)
useGCTF = self._getValue(GCTF)
kwargs = {}
frames = self._getValue(FRAMES_RANGE).split()
if frames:
kwargs['alignFrame0'] = kwargs['sumFrame0'] = frames[0]
kwargs['alignFrameN'] = kwargs['sumFrameN'] = frames[1]
if useMC:
# Create motioncorr
from pyworkflow.em.packages.motioncorr import ProtMotionCorr
protMC = project.newProtocol(ProtMotionCorr,
objLabel='Motioncorr',
useMotioncor2=useMC2,
**kwargs)
_saveProtocol(protMC)
if useOF:
# Create Optical Flow protocol
from pyworkflow.em.packages.xmipp3 import XmippProtOFAlignment
protOF = project.newProtocol(XmippProtOFAlignment,
objLabel='Optical Flow',
doSaveMovie=useSM,
**kwargs)
_saveProtocol(protOF)
if useSM:
# If OF write the movie, then we need to reset frames count
if frames and useOF:
kwargs['alignFrame0'] = kwargs['sumFrame0'] = 1
kwargs['alignFrameN'] = kwargs['sumFrameN'] = 0
from pyworkflow.em.packages.grigoriefflab import ProtSummovie
protSM = project.newProtocol(ProtSummovie,
objLabel='Summovie',
cleanInputMovies=useOF,
numberOfThreads=1,
**kwargs)
_saveProtocol(protSM)
lastBeforeCTF = self.lastProt
if useCTF:
from pyworkflow.em.packages.grigoriefflab import ProtCTFFind
protCTF = project.newProtocol(ProtCTFFind,
objLabel='Ctffind',
numberOfThreads=1)
protCTF.inputMicrographs.set(lastBeforeCTF)
protCTF.inputMicrographs.setExtended('outputMicrographs')
_saveProtocol(protCTF, movies=False)
if useGCTF:
from pyworkflow.em.packages.gctf import ProtGctf
protGCTF = project.newProtocol(ProtGctf,
objLabel='Gctf')
protGCTF.inputMicrographs.set(lastBeforeCTF)
protGCTF.inputMicrographs.setExtended('outputMicrographs')
_saveProtocol(protGCTF, movies=False)
project.saveProtocol(protMonitor)
os.system('%s project %s &' % (pw.getScipionScript(), projName))
self.windows.close()
def _createScipionProject(self, projName, projPath, scipionProjPath):
manager = Manager()
project = manager.createProject(projName, location=scipionProjPath)
self.lastProt = None
pattern = self._getConfValue(PATTERN)
smtpServer = self._getConfValue(SMTP_SERVER, '')
smtpFrom = self._getConfValue(SMTP_FROM, '')
smtpTo = self._getConfValue(SMTP_TO, '')
doMail = self._getValue(EMAIL_NOTIFICATION)
doPublish = self._getValue(HTML_REPORT)
protImport = project.newProtocol(
em.ProtImportMovies,
objLabel='Import movies',
filesPath=projPath,
filesPattern=pattern,
sphericalAberration=self._getConfValue(CS),
dataStreaming=True)
# Should I publish html report?
if doPublish == 1:
publish = self._getConfValue('HTML_PUBLISH')
print("\n\nReport available at URL: %s/%s\n\n" %
('http://scipion.cnb.csic.es/scipionbox', projName))
else:
publish = ''
protMonitor = project.newProtocol(em.ProtMonitorSummary,
objLabel='Summary Monitor',
doMail=doMail,
emailFrom=smtpFrom,
emailTo=smtpTo,
smtp=smtpServer,
publishCmd=publish)
def _saveProtocol(prot, movies=True, monitor=True):
if movies:
prot.inputMovies.set(self.lastProt)
prot.inputMovies.setExtended('outputMovies')
project.saveProtocol(prot)
self.lastProt = prot
if monitor:
protMonitor.inputProtocols.append(prot)
_saveProtocol(protImport, movies=False)
useMC2 = self._getValue(MOTIONCOR2)
useMC = self._getValue(MOTIONCORR) or useMC2
useOF = self._getValue(OPTICAL_FLOW)
useSM = self._getValue(SUMMOVIE)
useCTF = self._getValue(CTFFIND4)
useGCTF = self._getValue(GCTF)
kwargs = {}
frames = self._getValue(FRAMES_RANGE).split()
if frames:
kwargs['alignFrame0'] = kwargs['sumFrame0'] = frames[0]
kwargs['alignFrameN'] = kwargs['sumFrameN'] = frames[1]
if useMC:
# Create motioncorr
from pyworkflow.em.packages.motioncorr import ProtMotionCorr
protMC = project.newProtocol(ProtMotionCorr,
objLabel='Motioncorr',
useMotioncor2=useMC2,
**kwargs)
_saveProtocol(protMC)
if useOF:
# Create Optical Flow protocol
from pyworkflow.em.packages.xmipp3 import XmippProtOFAlignment
protOF = project.newProtocol(XmippProtOFAlignment,
objLabel='Optical Flow',
doSaveMovie=useSM,
**kwargs)
_saveProtocol(protOF)
if useSM:
# If OF write the movie, then we need to reset frames count
if frames and useOF:
kwargs['alignFrame0'] = kwargs['sumFrame0'] = 1
kwargs['alignFrameN'] = kwargs['sumFrameN'] = 0
from pyworkflow.em.packages.grigoriefflab import ProtSummovie
protSM = project.newProtocol(ProtSummovie,
objLabel='Summovie',
cleanInputMovies=useOF,
numberOfThreads=1,
**kwargs)
_saveProtocol(protSM)
lastBeforeCTF = self.lastProt
if useCTF:
from pyworkflow.em.packages.grigoriefflab import ProtCTFFind
protCTF = project.newProtocol(ProtCTFFind,
objLabel='Ctffind',
numberOfThreads=1)
protCTF.inputMicrographs.set(lastBeforeCTF)
protCTF.inputMicrographs.setExtended('outputMicrographs')
_saveProtocol(protCTF, movies=False)
if useGCTF:
from pyworkflow.em.packages.gctf import ProtGctf
protGCTF = project.newProtocol(ProtGctf, objLabel='Gctf')
protGCTF.inputMicrographs.set(lastBeforeCTF)
protGCTF.inputMicrographs.setExtended('outputMicrographs')
_saveProtocol(protGCTF, movies=False)
project.saveProtocol(protMonitor)
os.system('%s project %s &' % (pw.getScipionScript(), projName))
self.windows.close()
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
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'])
