def __init__(self, parent, windows, **args):
tk.Frame.__init__(self, parent, bg='white', **args)
self.windows = windows
self.manager = windows.manager
self.root = windows.root
# tkFont.Font(size=12, family='verdana', weight='bold')
bigSize = pwgui.cfgFontSize + 2
smallSize = pwgui.cfgFontSize - 2
fontName = pwgui.cfgFontName
self.projNameFont = tkFont.Font(size=bigSize,
family=fontName,
weight='bold')
self.projDateFont = tkFont.Font(size=smallSize, family=fontName)
self.projDelFont = tkFont.Font(size=smallSize,
family=fontName,
weight='bold')
self.manager = Manager()
self.filter = tk.StringVar()
self.filterBox = None
self.addActionsFrame()
self.columnconfigure(0, weight=1)
self.rowconfigure(1, weight=1)
text = TaggedText(self, width=40, height=15, bd=0, bg='white')
text.grid(row=1, columnspan=2, column=0, sticky='news')
self.createProjectList(text)
text.setReadOnly(True)
self.text = text
self.filterBox.focus_set()
def main():
args = get_parser().parse_args()
projName = args.project
# Create a manager and load the project
manager = Manager()
cwd = os.getcwd() # Keep current directory to restore it later
project = manager.loadProject(projName)
# Export protocols as a dict
jsonDict = project.getProtocolsDict()
os.chdir(cwd) # Restore after project load
if args.output:
print("Writing workflow to file: ", args.output)
with open(args.output, 'w') as f:
json.dump(list(jsonDict.values()),
f,
indent=4,
separators=(',', ': '))
else:
print(
json.dumps(list(jsonDict.values()),
indent=4,
separators=(',', ': ')))
def testExportSteps(self):
manager = Manager()
stepsStats = dict()
for project in manager.listProjects():
projectFolder = manager.getProjectPath(project.projName)
project = Project(pyworkflow.Config.getDomain(), projectFolder)
project.load()
for prot in project.getRuns():
protName = prot.getClassName()
for step in prot.loadSteps():
stepName = "-".join([
prot.getClassPackageName(), protName,
step.funcName.get()
])
stepSeconds = step.getElapsedTime().total_seconds()
if stepName not in stepsStats:
stepsStats[stepName] = []
stepsStats[stepName].append(stepSeconds)
# average steps
for name in stepsStats:
plugin, protClass, step = name.split("-")
stepStats = stepsStats[name]
mean = sum(stepStats) / len(stepStats)
# DO not send mean values if higher than a threshold to keep chart in a decent visualization range
# We are loosing long duration steps, probably due to large
if mean < 30:
bm = Benchmark(time=mean, name="-".join([protClass, step]))
codespeed.sendData(bm)
def __init__(self):
projName = self.__class__.__name__
manager = Manager()
if manager.hasProject(projName):
self.project = manager.loadProject(projName)
else:
self.project = manager.createProject(projName)
# Use graph view as default
settings = self.project.getSettings()
settings.setRunsView(1) # graph view
settings.write()
self.loadWorkflow()
def setupTestProject(cls):
""" Create and setup a Project for a give Test class. """
projName = cls.__name__
if os.environ.get('SCIPION_TEST_CONTINUE', None) == '1':
proj = Manager().loadProject(projName)
else:
proj = Manager().createProject(
projName) # Now it will be loaded if exists
cls.outputPath = proj.path
# Create project does not change the working directory anymore
os.chdir(cls.outputPath)
cls.projName = projName
cls.proj = proj
def _select(self):
projName = self.projName.get().strip()
projLocation = self.projLocation.get().strip()
copyFiles = self.tkCheckVar.get() != 0
searchLocation = self.searchLocation.get().strip()
manager = Manager()
# If project name is empty we will use the same name as the source
if not projName:
projName = os.path.basename(projLocation)
errorMessage = ''
# Validate that project location is not empty
if not projLocation:
errorMessage = "Project location is empty\n"
# Validate that project location exists
elif not os.path.exists(projLocation):
errorMessage += "Project location does not exist\n"
# Validate that project location is a directory
elif not os.path.isdir(projLocation):
errorMessage += "Project location is not a directory\n"
# Validate that the project location is a scipion project folder
elif not os.path.exists(os.path.join(projLocation,
Project.getDbName())):
errorMessage += "Project location doesn't look like a scipion folder\n"
# Validate that there isn't already a project with the same name
if manager.hasProject(projName):
errorMessage += "Project [%s] already exists\n" % projName
# Validate that search location exists
if searchLocation:
if not os.path.exists(searchLocation):
errorMessage += "Raw files location does not exist\n"
# Validate that search location is a directory
elif not os.path.isdir(searchLocation):
errorMessage += "Raw files location is not a directory\n"
if errorMessage:
showError("Validation error", errorMessage, self.root)
else:
self.parent.importProject(projLocation, copyFiles, projName,
searchLocation)
self.close()
def __init__(self, parent, windows, **args):
tk.Frame.__init__(self, parent, bg='white', **args)
self.windows = windows
self.manager = windows.manager
self.root = windows.root
#tkFont.Font(size=12, family='verdana', weight='bold')
bigSize = pwgui.cfgFontSize + 2
smallSize = pwgui.cfgFontSize - 2
fontName = pwgui.cfgFontName
self.projNameFont = tkFont.Font(size=bigSize,
family=fontName,
weight='bold')
self.projDateFont = tkFont.Font(size=smallSize, family=fontName)
self.projDelFont = tkFont.Font(size=smallSize,
family=fontName,
weight='bold')
self.manager = Manager()
# Add the create project button
btnFrame = tk.Frame(self, bg='white')
btn = HotButton(btnFrame,
text=Message.LABEL_CREATE_PROJECT,
font=self.projNameFont,
command=self._onCreateProject)
btn.grid(row=0, column=0, sticky='nw', padx=10, pady=10)
# Add the Import project button
btn = Button(btnFrame,
text=Message.LABEL_IMPORT_PROJECT,
font=self.projNameFont,
command=self._onImportProject)
btn.grid(row=0, column=1, sticky='nw', padx=10, pady=10)
btnFrame.grid(row=0, column=0, sticky='nw')
self.columnconfigure(0, weight=1)
self.rowconfigure(1, weight=1)
text = TaggedText(self, width=40, height=15, bd=0, bg='white')
text.grid(row=1, columnspan=2, column=0, sticky='news')
self.createProjectList(text)
text.setReadOnly(True)
self.text = text
def main():
if len(sys.argv) != 3:
usage("Incorrect number of input parameters")
projName = sys.argv[1]
searchDir = os.path.abspath(sys.argv[2])
# Create a new project
manager = Manager()
if not manager.hasProject(projName):
usage("Nonexistent project: %s" % pwutils.red(projName))
if not os.path.exists(searchDir):
usage("Nonexistent SEARCH_DIR: %s" % pwutils.red(searchDir))
project = manager.loadProject(projName)
project.fixLinks(searchDir)
def _writeSubset(self, subset):
""" Generated the output of this subset. """
newSubsetName = 'outputParticles_%03d' % self._counter
self.info("Creating new subset: %s" % newSubsetName)
subset.write()
self._defineOutputs(**{newSubsetName: subset})
self._defineTransformRelation(self.inputParticles, subset)
# The following is required to commit the changes to the database
self._store(subset)
subset.close()
manager = Manager()
project = manager.loadProject(self.getProject().getName())
input2D = self.input2dProtocol.get()
copyProt = project.copyProtocol(project.getProtocol(input2D.getObjId()))
copyProt.inputParticles.set(project.getProtocol(self.getObjId()))
copyProt.inputParticles.setExtended(newSubsetName)
project.scheduleProtocol(copyProt, self._runPrerequisites)
# Next schedule will be after this one
self._runPrerequisites.append(copyProt.getObjId())
def setupTestProject(cls, writeLocalConfig=False):
""" Create and setup a Project for a give Test class. """
projName = cls.__name__
hostsConfig = None
if writeLocalConfig:
hostsConfig = '/tmp/hosts.conf'
print("Writing local config: %s" % hostsConfig)
import pyworkflow.protocol as pwprot
pwprot.HostConfig.writeBasic(hostsConfig)
if os.environ.get('SCIPION_TEST_CONTINUE', None) == '1':
proj = Manager().loadProject(projName)
else:
proj = Manager().createProject(projName, hostsConf=hostsConfig)
cls.outputPath = proj.path
# Create project does not change the working directory anymore
os.chdir(cls.outputPath)
cls.projName = projName
cls.proj = proj
def __init__(self, config, **kwargs):
windowTitle = config.get(WINDOWS_TITLE, 'Scipion wizard')
try:
title = '%s (%s on %s)' % (windowTitle, pwutils.getLocalUserName(),
pwutils.getLocalHostName())
except Exception:
title = windowTitle
settings = ProjectSettings()
self.generalCfg = settings.getConfig()
self.config = config
ProjectBaseWindow.__init__(self, title, minsize=(400, 550), **kwargs)
self.viewFuncs = {VIEW_WIZARD: BoxWizardView}
self.manager = Manager()
self.switchView(VIEW_WIZARD)
def openProject(projectName):
""" Opens a scipion project:
:param projectName: Name of a existing project to open,
or "here" to create a project in the current working dir,
or "last" to open the most recent project
"""
manager = Manager()
projName = os.path.basename(projectName)
# Handle special name 'here' to create a project
# from the current directory
if projName == 'here':
cwd = Config.SCIPION_CWD
if " " in cwd:
print("Projects can't have spaces in the name: %s" % cwd)
sys.exit(1)
print("\nYou are trying to create a project here:", pwutils.cyan(cwd))
if os.listdir(cwd):
print(pwutils.red('\nWARNING: this folder is not empty!!!'))
key = input("\nDo you want to create a project here? [y/N]?")
if key.lower().strip() != 'y':
print("\nAborting...")
sys.exit(0)
else:
print("\nCreating project....")
projName = os.path.basename(cwd)
projDir = os.path.dirname(cwd)
manager.createProject(projName, location=projDir)
elif projName == 'last': # Get last project
projects = manager.listProjects()
if not projects:
sys.exit("No projects yet, cannot open the last one.")
projName = projects[0].projName
projPath = manager.getProjectPath(projName)
projWindow = ProjectWindow(projPath)
projWindow.show()
n = len(sys.argv)
if n > 3:
usage("Incorrect number of input parameters")
delete = '--delete' in sys.argv
arg1 = sys.argv[1]
if n > 1 and arg1 != '--delete':
customUserData = arg1
else:
customUserData = pw.Config.SCIPION_USER_DATA
print("Loading projects from:\n %s" % customUserData)
# Create a new project
manager = Manager(workspace=customUserData)
for projInfo in manager.listProjects():
projName = projInfo.getName()
proj = manager.loadProject(projName)
settings = proj.getSettings()
leftTime = proj.getLeftTime()
if (leftTime is not None and leftTime.days < 0):
if delete:
print("Deleting: %s (%s) " % (projName, leftTime))
manager.deleteProject(projName)
else:
print("Should delete: %s (%s)" % (projName, leftTime))
def __init__(self, parent, windows, **kwargs):
tk.Frame.__init__(self, parent, bg='white', **kwargs)
self.windows = windows
self.manager = windows.manager
self.root = windows.root
self.vars = {}
self.checkvars = []
self.microscope = None
self.configDict = self.windows.config
# Regular expression to validate username and sample name
self.re = re.compile('\A[a-zA-Z0-9][a-zA-Z0-9_-]+[a-zA-Z0-9]\Z')
# tkFont.Font(size=12, family='verdana', weight='bold')
bigSize = pwgui.cfgFontSize + 2
smallSize = pwgui.cfgFontSize - 2
fontName = pwgui.cfgFontName
self.bigFont = tkFont.Font(size=bigSize, family=fontName)
self.bigFontBold = tkFont.Font(size=bigSize,
family=fontName,
weight='bold')
self.projDateFont = tkFont.Font(size=smallSize, family=fontName)
self.projDelFont = tkFont.Font(size=smallSize,
family=fontName,
weight='bold')
self.manager = Manager()
# Header section
headerFrame = tk.Frame(self, bg='white')
headerFrame.grid(row=0, column=0, sticky='new')
headerText = "Create New Session"
headerText += " %s" % pwutils.prettyTime(dateFormat='%Y-%m-%d')
label = tk.Label(headerFrame,
text=headerText,
font=self.bigFontBold,
borderwidth=0,
anchor='nw',
bg='white',
fg=pwgui.Color.DARK_GREY_COLOR)
label.grid(row=0, column=0, sticky='nw', padx=(20, 5), pady=10)
# Body section
bodyFrame = tk.Frame(self, bg='white')
bodyFrame.grid(row=1, column=0, sticky='news')
self._fillContent(bodyFrame)
# Add the create project button
btnFrame = tk.Frame(self, bg='white')
btn = HotButton(btnFrame,
text="Create New Session",
activebackground="dark grey",
activeforeground='black',
font=self.bigFontBold,
command=self._onAction)
btn.grid(row=0, column=1, sticky='ne', padx=10, pady=10)
# Add the Cancel project button
btn = Button(btnFrame,
Message.LABEL_BUTTON_CANCEL,
Icon.ACTION_CLOSE,
font=self.bigFontBold,
command=self.windows.close)
btn.grid(row=0, column=0, sticky='ne', padx=10, pady=10)
btnFrame.grid(row=2, column=0, sticky='sew')
btnFrame.columnconfigure(0, weight=1)
self.columnconfigure(0, weight=1)
self.rowconfigure(1, weight=1)
if n < 2:
usage("This script accepts 1 mandatory parameter: the project name.")
elif n > 2 and sys.argv[2] != '--ignore':
usage("The protocol class names to be ignored must be after a '--ignore' flag.")
projName = sys.argv[1]
# This fails, since it is triggering matplotlib.pyplot and then import error happens:
# ... pyworkflow/gui/no-tkinter/_tkinter.py: invalid ELF header. If we want this back we might need to
# invest some time "faking" tkinter again for python3.
# path = pw.join('gui', 'no-tkinter')
# sys.path.insert(1, path)
# Create a new project
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(pw.Config.getDomain(), projectPath)
project.load()
runs = project.getRuns()
This script show (or edit) some of the configuration of the project.
Use readOnly=True (or False) to set/unset read only property
Use lifeTime=X for setting X hours or None to unset life time of the project.
""" % error
sys.exit(1)
n = len(sys.argv)
if n < 2 or n > 4:
usage("Incorrect number of input parameters")
# Load the given project
projectsDir = os.path.join(pw.Config.SCIPION_USER_DATA, 'projects')
projName = sys.argv[1]
manager = Manager()
project = manager.loadProject(projName)
if project is None:
usage("Project '%s' does not exist in: \n %s" % (projName, projectsDir))
setReadOnly = False
setLifeTime = False
for arg in sys.argv:
if arg.startswith('readOnly='):
setReadOnly = True
value = arg.split('readOnly=')[1]
b = Boolean(value=value)
readOnlyValue = b.get()
elif arg.startswith('lifeTime='):
ALL_TUTORIALS = OrderedDict([('intro', TutorialIntro),
('betagal', TutorialBetagal)])
if __name__ == '__main__':
def printUsage(msg):
if msg:
print("ERROR: ", msg)
print("\nUSAGE: scipion tutorial [TUTORIAL_NAME]")
print("\nwhere TUTORIAL_NAME can be:")
print("\n".join([' %s' % k for k in ALL_TUTORIALS.keys()]))
if len(sys.argv) == 2:
manager = Manager()
tutorialName = sys.argv[1]
if tutorialName not in ALL_TUTORIALS:
printUsage("Invalid tutorial '%s'." % tutorialName)
else:
# Instantiate the proper tutorial class
tutorial = ALL_TUTORIALS[tutorialName]()
projWindow = ProjectWindow(tutorial.project.getName())
projWindow.show()
else:
msg = 'Too many arguments.' if len(sys.argv) > 2 else ''
printUsage(msg)
def _createSessionScipionProject(self, session):
microscope = session.getMicroscope()
camera = session.getCamera()
path = session.getPath()
manager = Manager()
project = manager.createProject(session.getScipionProjectName(),
location=path)
# A custom workflow can be selected and then we will not modify it
if 'workflow' in session.preprocessing:
jsonFile = session.preprocessing['workflow']
project.loadProtocols(jsonFile)
return
# If not, then we will customize the generic workflow
jsonFile = getDataFile('workflows/scipion3_generic_workflow.json')
project.loadProtocols(jsonFile)
runsGraph = project.getRunsGraph(refresh=True)
# Create a dict with class names and nodes for easier access
nodeNames = {}
for n in runsGraph.getNodes():
p = n.run
if p is not None:
nodeNames[p.getClassName()] = n
nodeImport = nodeNames['ProtImportMovies']
nodeCompress = nodeNames['ProtRelionCompressMovies']
nodeRelionMc = nodeNames['ProtRelionMotioncor']
nodeMc = nodeNames['ProtMotionCorr']
nodeCtffind = nodeNames['CistemProtCTFFind']
nodeGctf = nodeNames['ProtGctf']
# Update import parameters
protImport = nodeImport.run
protImport.setAttributesFromDict(
{
'filesPath': path,
'filesPattern': CAMERA_SETTINGS[camera][PATTERN]
},
setBasic=False)
project.saveProtocol(protImport)
def _moveChilds(parent, newParent, inputName, outputName):
for c in parent.getChilds():
prot = c.run
inputObj = getattr(prot, inputName)
inputObj.set(newParent.run)
inputObj.setExtended(outputName)
project.saveProtocol(prot)
# There is no need to compress if we are not using the
# falcon3, let's remove that step from the workflow
# and update the input for the dependent steps
if camera != FALCON3:
_moveChilds(nodeCompress, nodeImport, 'inputMovies',
'outputMovies')
project.deleteProtocol(nodeCompress.run)
opts = session.preprocessing['options']
if opts['Motion correction'] == 'motioncor2':
_moveChilds(nodeRelionMc, nodeMc, 'inputMicrographs',
'outputMicrographsDoseWeighted')
protCtffind = nodeCtffind.run
protCtffind.usePowerSpectra.set(False)
project.saveProtocol(protCtffind)
if opts['CTF estimation'] == 'gctf':
_moveChilds(nodeCtffind, nodeGctf, "ctfRelations", "outputCTF")
def usage(error):
print("""
ERROR: %s
Usage: fixlinks.py PROJECT SEARCH_DIR
PROJECT: provide the project name to fix broken links in the imports.
SEARCH_DIR: provide a directory where to look for the files.
and fix the links.
""" % error)
sys.exit(1)
if len(sys.argv) != 3:
usage("Incorrect number of input parameters")
projName = sys.argv[1]
searchDir = os.path.abspath(sys.argv[2])
# Create a new project
manager = Manager()
if not manager.hasProject(projName):
usage("Nonexistent project: %s" % pwutils.red(projName))
if not os.path.exists(searchDir):
usage("Nonexistent SEARCH_DIR: %s" % pwutils.red(searchDir))
project = manager.loadProject(projName)
project.fixLinks(searchDir)
def monitorStep(self):
self._runPrerequisites = []
manager = Manager()
project = manager.loadProject(self.getProject().getName())
percentage = [1.14, 2.29, 3.44, 5.74, 9.19, 14.94, 24.13, 39.08]
numGlobalIters = len(percentage) + 2
self.consecutiveBimodal = 2
self.listConsecutiveBimodal = []
targetResolution = self.minimumTargetResolution.get()
#Global iterations
for i in range(numGlobalIters):
self.convertInputStep(percentage, i)
print("Target resolution - group %s: %f " %
(chr(65 + i), float(targetResolution)))
sys.stdout.flush()
if i == 0:
previousProtVol = self
namePreviousVol = 'outputVolumesInit'
else:
previousProtVol = newHighRes
namePreviousVol = 'outputVolume'
newHighRes = project.newProtocol(
XmippProtReconstructHighRes,
objLabel='HighRes - group %s' % chr(65 + i),
symmetryGroup=self.symmetryGroup.get(),
numberOfIterations=1,
particleRadius=self.particleRadius.get(),
maximumTargetResolution=targetResolution,
alignmentMethod=XmippProtReconstructHighRes.GLOBAL_ALIGNMENT,
angularMaxShift=self.maxShift.get(),
angularMinTilt=self.angularMinTilt.get(),
angularMaxTilt=self.angularMaxTilt.get(),
postAdHocMask=self.postAdHocMask.get(),
postSymmetryWithinMask=self.postSymmetryWithinMask.get(),
postSymmetryWithinMaskType=self.postSymmetryWithinMaskType.get(
),
postSymmetryWithinMaskMask=self.postSymmetryWithinMaskMask.get(
),
postSymmetryHelical=self.postSymmetryHelical.get(),
postSymmetryHelicalRadius=self.postSymmetryHelicalRadius.get(),
postSymmetryHelicalDihedral=self.postSymmetryHelicalDihedral.
get(),
postSymmetryHelicalMinRot=self.postSymmetryHelicalMinRot.get(),
postSymmetryHelicalMaxRot=self.postSymmetryHelicalMaxRot.get(),
postSymmetryHelicalMinZ=self.postSymmetryHelicalMinZ.get(),
postSymmetryHelicalMaxZ=self.postSymmetryHelicalMaxZ.get(),
postScript=self.postScript.get(),
postSignificantDenoise=self.postSignificantDenoise.get(),
postFilterBank=self.postFilterBank.get(),
postLaplacian=self.postLaplacian.get(),
postDeconvolve=self.postDeconvolve.get(),
postSoftNeg=self.postSoftNeg.get(),
postSoftNegK=self.postSoftNegK.get(),
postDifference=self.postDifference.get(),
numberOfMpi=self.numberOfMpi.get(),
useGpu=self.useGpu.get(),
gpuList=self.gpuList.get())
previousProtPart = self
namePreviousParticles = 'outputParticles%s' % chr(65 + i)
newHighRes.inputParticles.set(previousProtPart)
newHighRes.inputParticles.setExtended(namePreviousParticles)
newHighRes.inputVolumes.set(previousProtVol)
newHighRes.inputVolumes.setExtended(namePreviousVol)
project.scheduleProtocol(newHighRes)
# Next schedule will be after this one
self._runPrerequisites.append(newHighRes.getObjId())
self.childs.append(newHighRes)
finishedIter = False
while finishedIter == False:
time.sleep(15)
newHighRes = self._updateProtocol(newHighRes)
if newHighRes.isFailed() or newHighRes.isAborted():
raise Exception('XmippProtReconstructHighRes has failed')
if newHighRes.isFinished():
finishedIter = True
fnDir = newHighRes._getExtraPath("Iter%03d" % 1)
fnFSCs = open(self._getExtraPath('fnFSCs.txt'), 'a')
fnFSCs.write(join(fnDir, "fsc.xmd") + " \n")
fnFSCs.close()
targetResolution = self.checkOutputsStep(newHighRes, i, False)
targetResolution = max(targetResolution,
self.maximumTargetResolution.get())
if i >= 7: #We are in the last three iterations
#Check the output particles and remove all the disabled ones
fnOutParticles = newHighRes._getPath('angles.xmd')
params = '-i %s --query select "enabled==1"' % (fnOutParticles)
self.runJob("xmipp_metadata_utilities", params, numberOfMpi=1)
fnFinal = self._getExtraPath('inputLocalHighRes1.xmd')
if i == 7:
copy(fnOutParticles, fnFinal)
else:
params = ' -i %s --set union %s -o %s' % (
fnFinal, fnOutParticles, fnFinal)
self.runJob("xmipp_metadata_utilities",
params,
numberOfMpi=1)
if i == 9:
outputinputSetOfParticles = self._createSetOfParticles(
)
outputinputSetOfParticles.copyInfo(
self.inputParticles.get())
readSetOfParticles(fnFinal, outputinputSetOfParticles)
self._defineOutputs(
outputParticlesLocal1=outputinputSetOfParticles)
self._store(outputinputSetOfParticles)
#Local iterations
numLocalIters = 5
for i in range(numLocalIters):
if i > 2:
minPrevRes = prevTargetResolution
if targetResolution > minPrevRes:
print("Target resolution is stuck")
sys.stdout.flush()
break
prevTargetResolution = targetResolution
print("Target resolution - INPUT local %d: %f " %
((i + 1), float(targetResolution)))
sys.stdout.flush()
previousProtVol = newHighRes
namePreviousVol = 'outputVolume'
#calling highres local with the new input set
newHighRes = project.newProtocol(
XmippProtReconstructHighRes,
objLabel='HighRes - local %d' % (i + 1),
symmetryGroup=self.symmetryGroup.get(),
numberOfIterations=1,
particleRadius=self.particleRadius.get(),
maximumTargetResolution=targetResolution,
alignmentMethod=XmippProtReconstructHighRes.LOCAL_ALIGNMENT,
angularMaxShift=self.maxShift.get(),
angularMinTilt=self.angularMinTilt.get(),
angularMaxTilt=self.angularMaxTilt.get(),
postAdHocMask=self.postAdHocMask.get(),
postSymmetryWithinMask=self.postSymmetryWithinMask.get(),
postSymmetryWithinMaskType=self.postSymmetryWithinMaskType.get(
),
postSymmetryWithinMaskMask=self.postSymmetryWithinMaskMask.get(
),
postSymmetryHelical=self.postSymmetryHelical.get(),
postSymmetryHelicalRadius=self.postSymmetryHelicalRadius.get(),
postSymmetryHelicalDihedral=self.postSymmetryHelicalDihedral.
get(),
postSymmetryHelicalMinRot=self.postSymmetryHelicalMinRot.get(),
postSymmetryHelicalMaxRot=self.postSymmetryHelicalMaxRot.get(),
postSymmetryHelicalMinZ=self.postSymmetryHelicalMinZ.get(),
postSymmetryHelicalMaxZ=self.postSymmetryHelicalMaxZ.get(),
postScript=self.postScript.get(),
postSignificantDenoise=self.postSignificantDenoise.get(),
postFilterBank=self.postFilterBank.get(),
postLaplacian=self.postLaplacian.get(),
postDeconvolve=self.postDeconvolve.get(),
postSoftNeg=self.postSoftNeg.get(),
postSoftNegK=self.postSoftNegK.get(),
postDifference=self.postDifference.get(),
numberOfMpi=self.numberOfMpi.get(),
useGpu=self.useGpu.get(),
gpuList=self.gpuList.get())
newHighRes.inputParticles.set(self)
namePreviousParticles = 'outputParticlesLocal%d' % (i + 1)
newHighRes.inputParticles.setExtended(namePreviousParticles)
newHighRes.inputVolumes.set(previousProtVol)
newHighRes.inputVolumes.setExtended(namePreviousVol)
project.scheduleProtocol(newHighRes, self._runPrerequisites)
# Next schedule will be after this one
self._runPrerequisites.append(newHighRes.getObjId())
self.childs.append(newHighRes)
finishedIter = False
while finishedIter == False:
time.sleep(15)
newHighRes = self._updateProtocol(newHighRes)
if newHighRes.isFailed() or newHighRes.isAborted():
raise Exception('XmippProtReconstructHighRes has failed')
if newHighRes.isFinished():
finishedIter = True
fnDir = newHighRes._getExtraPath("Iter%03d" % 1)
fnFSCs = open(self._getExtraPath('fnFSCs.txt'), 'a')
fnFSCs.write(join(fnDir, "fsc.xmd") + " \n")
fnFSCs.close()
targetResolution = self.checkOutputsStep(newHighRes,
numGlobalIters + i, True)
targetResolution = max(targetResolution,
self.maximumTargetResolution.get())
#Check the output particles and remove all the disabled ones
fnOutParticles = newHighRes._getPath('angles.xmd')
params = '-i %s --query select "enabled==1"' % (fnOutParticles)
self.runJob("xmipp_metadata_utilities", params, numberOfMpi=1)
fnFinal = self._getExtraPath('inputLocalHighRes%d.xmd' % (i + 2))
copy(fnOutParticles, fnFinal)
if i > 1:
#including the number of particles as stoppping criteria
mdFinal = emlib.MetaData(fnFinal)
Nfinal = mdFinal.size()
Ninit = self.inputParticles.get().getSize()
if Nfinal < Ninit * 0.3:
print("Image set size too small", Nfinal, Ninit)
sys.stdout.flush()
break
outputinputSetOfParticles = self._createSetOfParticles()
outputinputSetOfParticles.copyInfo(self.inputParticles.get())
readSetOfParticles(fnFinal, outputinputSetOfParticles)
result = {
'outputParticlesLocal%d' % (i + 2): outputinputSetOfParticles
}
self._defineOutputs(**result)
self._store(outputinputSetOfParticles)
#self = self._updateProtocol(self)
self.createOutputStep(project)
n = len(sys.argv)
if n < 2 or n > 4:
usage("Incorrect number of input parameters")
projName = sys.argv[1]
jsonFile = None if n < 3 else os.path.abspath(sys.argv[2])
location = None if n < 4 else sys.argv[3]
# This might not be working anymore for python3.
# I'm getting invalid ELF header triggered by matplotlib -->from . import _tkagg
# path = pw.join('gui', 'no-tkinter')
# sys.path.insert(1, path)
# Create a new project
manager = Manager()
if manager.hasProject(projName):
usage("There is already a project with this name: %s" %
pwutils.red(projName))
if jsonFile is not None and not os.path.exists(jsonFile):
usage("Nonexistent json file: %s" % pwutils.red(jsonFile))
project = manager.createProject(projName, location=location)
if jsonFile is not None:
protDict = project.loadProtocols(jsonFile)
def monitorStep(self):
self._runPrerequisites = []
manager = Manager()
project = manager.loadProject(self.getProject().getName())
self.numIter = self.maxNumClasses.get()
for iter in range(1, self.numIter):
if iter == 1:
self.convertInputStep()
newSplitProt = project.newProtocol(
XmippProtSplitVolumeHierarchical,
objLabel='split volume hierarchical - iter %d' % iter,
symmetryGroup=self.symmetryGroup.get(),
angularSampling=self.angularSampling.get(),
angularDistance=self.angularDistance.get(),
maxShift=self.maxShift.get(),
directionalClasses=self.directionalClasses.get(),
homogeneize=self.homogeneize.get(),
targetResolution=self.targetResolution.get(),
class2dIterations=self.class2dIterations.get(),
splitVolume=self.splitVolume.get(),
Niter=self.Niter.get(),
Nrec=self.Nrec.get(),
useGpu=self.useGpu.get(),
gpuList=self.gpuList.get())
previousSplitProt = self
newSubsetNameSplitVol = 'outputVolumesInit'
newSplitProt.inputVolume.set(previousSplitProt)
newSplitProt.inputVolume.setExtended(newSubsetNameSplitVol)
newSubsetNameSplitParts = 'outputParticlesInit'
newSplitProt.inputParticles.set(previousSplitProt)
newSplitProt.inputParticles.setExtended(
newSubsetNameSplitParts)
project.scheduleProtocol(newSplitProt, self._runPrerequisites)
# Next schedule will be after this one
self._runPrerequisites.append(newSplitProt.getObjId())
self.childs.append(newSplitProt)
newSignificantProt = project.newProtocol(
XmippProtReconstructHeterogeneous,
objLabel='significant heterogeneity - iter %d' % iter,
symmetryGroup=self.symmetryGroup.get(),
particleRadius=self.particleRadius.get(),
targetResolution=self.targetResolution.get(),
useGpu=self.useGpu.get(),
gpuList=self.gpuList.get(),
numberOfIterations=self.numberOfIterations.get(),
nxtMask=self.nextMask.get(),
angularMinTilt=self.angularMinTilt.get(),
angularMaxTilt=self.angularMaxTilt.get(),
numberOfReplicates=self.numberOfReplicates.get(),
angularMaxShift=self.angularMaxShift.get(),
numberVotes=self.numberVotes.get(),
stochastic=self.stochastic.get(),
stochasticAlpha=self.stochasticAlpha.get(),
stochasticN=self.stochasticN.get())
previousSignifProt = newSplitProt
newSubsetNameSignifParts = 'outputParticlesInit'
newSignificantProt.inputParticles.set(previousSplitProt)
newSignificantProt.inputParticles.setExtended(
newSubsetNameSignifParts)
newSubsetNameSignifVol = 'outputVolumes'
newSignificantProt.inputVolumes.set(previousSignifProt)
newSignificantProt.inputVolumes.setExtended(
newSubsetNameSignifVol)
project.scheduleProtocol(newSignificantProt,
self._runPrerequisites)
# Next schedule will be after this one
self._runPrerequisites.append(newSignificantProt.getObjId())
self.childs.append(newSignificantProt)
elif iter > 1 and not self.finished:
newSplitProt = project.newProtocol(
XmippProtSplitVolumeHierarchical,
objLabel='split volume hierarchical - iter %d' % iter,
symmetryGroup=self.symmetryGroup.get(),
angularSampling=self.angularSampling.get(),
angularDistance=self.angularDistance.get(),
maxShift=self.maxShift.get(),
directionalClasses=self.directionalClasses.get(),
homogeneize=self.homogeneize.get(),
targetResolution=self.targetResolution.get(),
class2dIterations=self.class2dIterations.get(),
splitVolume=self.splitVolume.get(),
Niter=self.Niter.get(),
Nrec=self.Nrec.get(),
useGpu=self.useGpu.get(),
gpuList=self.gpuList.get())
newSubsetNameSplitVol = 'outputAuxVolumes'
newSplitProt.inputVolume.set(previousSplitProt)
newSplitProt.inputVolume.setExtended(newSubsetNameSplitVol)
newSubsetNameSplitParts = 'outputAuxParticles'
newSplitProt.inputParticles.set(previousSplitProt)
newSplitProt.inputParticles.setExtended(
newSubsetNameSplitParts)
project.scheduleProtocol(newSplitProt, self._runPrerequisites)
# Next schedule will be after this one
self._runPrerequisites.append(newSplitProt.getObjId())
self.childs.append(newSplitProt)
newSignificantProt = project.newProtocol(
XmippProtReconstructHeterogeneous,
objLabel='significant heterogeneity - iter %d' % iter,
symmetryGroup=self.symmetryGroup.get(),
particleRadius=self.particleRadius.get(),
targetResolution=self.targetResolution.get(),
useGpu=self.useGpu.get(),
gpuList=self.gpuList.get(),
numberOfIterations=self.numberOfIterations.get(),
nxtMask=self.nextMask.get(),
angularMinTilt=self.angularMinTilt.get(),
angularMaxTilt=self.angularMaxTilt.get(),
numberOfReplicates=self.numberOfReplicates.get(),
angularMaxShift=self.angularMaxShift.get(),
numberVotes=self.numberVotes.get(),
stochastic=self.stochastic.get(),
stochasticAlpha=self.stochasticAlpha.get(),
stochasticN=self.stochasticN.get())
previousSignifProt = newSplitProt
newSubsetNameSignifParts = 'outputAuxParticles'
newSignificantProt.inputParticles.set(previousSplitProt)
newSignificantProt.inputParticles.setExtended(
newSubsetNameSignifParts)
newSubsetNameSignifVol = 'outputVolumes'
newSignificantProt.inputVolumes.set(previousSignifProt)
newSignificantProt.inputVolumes.setExtended(
newSubsetNameSignifVol)
project.scheduleProtocol(newSignificantProt,
self._runPrerequisites)
# Next schedule will be after this one
self._runPrerequisites.append(newSignificantProt.getObjId())
self.childs.append(newSignificantProt)
if not self.finished:
finishedIter = False
while finishedIter == False:
time.sleep(15)
newSplitProt = self._updateProtocol(newSplitProt)
newSignificantProt = self._updateProtocol(
newSignificantProt)
if newSplitProt.isFailed() or newSplitProt.isAborted():
raise Exception(
'XmippProtSplitVolumeHierarchical has failed')
if newSignificantProt.isFailed(
) or newSignificantProt.isAborted():
raise Exception(
'XmippProtReconstructHeterogeneous has failed')
if newSignificantProt.isFinished():
finishedIter = True
for classItem in newSignificantProt.outputClasses:
self.classListSizes.append(classItem.getSize())
self.classListIds.append(classItem.getObjId())
self.classListProtocols.append(newSignificantProt)
finishedSubset = False
finishedLast = False
if iter != self.numIter - 1:
subsetProt = self.checkOutputsStep(project, iter)
while finishedSubset == False and not self.finished:
time.sleep(5)
subsetProt = self._updateProtocol(subsetProt)
if subsetProt.isFailed() or subsetProt.isAborted():
raise Exception(
'XmippMetaProtCreateSubset has failed')
if subsetProt.isFinished():
finishedSubset = True
previousSplitProt = subsetProt
elif iter == self.numIter - 1:
outputMetaProt = self.createOutputStep(project)
while finishedLast == False:
time.sleep(5)
outputMetaProt = self._updateProtocol(outputMetaProt)
if outputMetaProt.isFailed():
raise Exception(
'XmippMetaProtCreateOutput has failed')
if outputMetaProt.isFinished():
finishedLast = True
if self.finished and iter == self.numIter - 1:
finishedLast = False
outputMetaProt = self.createOutputStep(project)
while finishedLast == False:
time.sleep(5)
outputMetaProt = self._updateProtocol(outputMetaProt)
if outputMetaProt.isFailed():
raise Exception('XmippMetaProtCreateOutput has failed')
if outputMetaProt.isFinished():
finishedLast = True
if self.finished and iter < self.numIter - 1:
continue
if n < 2 or n > 3:
usage("Incorrect number of input parameters")
jsonFn = os.path.abspath(sys.argv[1])
now = datetime.now()
tempSpace = "editor-%s" % now.strftime('%Y%m%d-%H%M%S')
customUserData = os.path.join(pw.Config.SCIPION_USER_DATA, 'tmp', tempSpace)
pwutils.makePath(os.path.join(customUserData, 'projects'))
print("Loading projects from:\n", customUserData)
# Create a new project
manager = Manager(workspace=customUserData)
projName = os.path.basename(jsonFn)
proj = manager.createProject(projName)
projPath = manager.getProjectPath(proj.getShortName())
proj.loadProtocols(jsonFn)
class EditorProjectWindow(ProjectWindow):
def close(self, e=None):
try:
print("Writing protocols to: ", jsonFn)
proj.getRunsGraph(refresh=True) # Build project runs graph
proj.exportProtocols(proj.getRuns(), jsonFn)
print("Deleting temporary folder: ", customUserData)
pwutils.cleanPath(customUserData)
class ProjectsView(tk.Frame):
def __init__(self, parent, windows, **args):
tk.Frame.__init__(self, parent, bg='white', **args)
self.windows = windows
self.manager = windows.manager
self.root = windows.root
#tkFont.Font(size=12, family='verdana', weight='bold')
bigSize = pwgui.cfgFontSize + 2
smallSize = pwgui.cfgFontSize - 2
fontName = pwgui.cfgFontName
self.projNameFont = tkFont.Font(size=bigSize,
family=fontName,
weight='bold')
self.projDateFont = tkFont.Font(size=smallSize, family=fontName)
self.projDelFont = tkFont.Font(size=smallSize,
family=fontName,
weight='bold')
self.manager = Manager()
# Add the create project button
btnFrame = tk.Frame(self, bg='white')
btn = HotButton(btnFrame,
text=Message.LABEL_CREATE_PROJECT,
font=self.projNameFont,
command=self._onCreateProject)
btn.grid(row=0, column=0, sticky='nw', padx=10, pady=10)
# Add the Import project button
btn = Button(btnFrame,
text=Message.LABEL_IMPORT_PROJECT,
font=self.projNameFont,
command=self._onImportProject)
btn.grid(row=0, column=1, sticky='nw', padx=10, pady=10)
btnFrame.grid(row=0, column=0, sticky='nw')
self.columnconfigure(0, weight=1)
self.rowconfigure(1, weight=1)
text = TaggedText(self, width=40, height=15, bd=0, bg='white')
text.grid(row=1, columnspan=2, column=0, sticky='news')
self.createProjectList(text)
text.setReadOnly(True)
self.text = text
def createProjectList(self, text):
"""Load the list of projects"""
r = 0
text.setReadOnly(False)
text.clear()
parent = tk.Frame(text, bg='white')
parent.columnconfigure(0, weight=1)
colors = ['white', '#EAEBFF']
for i, p in enumerate(self.manager.listProjects()):
try:
project = self.manager.loadProject(p.getName(),
chdir=False,
loadAllConfig=False)
# Add creation time to project info
p.cTime = project.getCreationTime()
# Add if it's a link
p.isLink = project.isLink()
# If it's a link, get the linked folder
if p.isLink:
p.linkedFolder = os.path.realpath(project.path)
frame = self.createProjectLabel(parent, p, color=colors[i % 2])
frame.grid(row=r, column=0, padx=10, pady=5, sticky='new')
r += 1
except Exception, ex:
print "ERROR loading project: %s" % p.getName()
print ex
text.window_create(tk.INSERT, window=parent)
text.bindWidget(parent)
text.setReadOnly(True)
# *
# **************************************************************************
"""
Launch main project window
"""
import pickle
import sys
import os
from pyworkflow.project import Manager, Label
from pyworkflow.gui.project import ProjectWindow
if __name__ == '__main__':
manager = Manager()
projName = os.path.basename(sys.argv[1])
projPath = manager.getProjectPath(projName)
projWindow = ProjectWindow(projPath)
proj = projWindow.project
sett = proj.getSettings()
sett.setColorMode(sett.COLOR_MODE_LABELS)
with open(proj.getPath('labels.pkl'), 'r') as f:
labelsDict, colorsDict = pickle.load(f)
for labelName, prots in labelsDict.iteritems():
label = Label(name=labelName, color=colorsDict[labelName])
sett.getLabels().addLabel(label)
class ProjectsView(tk.Frame):
_PROJ_CONTAINER = "projectsframe"
def __init__(self, parent, windows, **args):
tk.Frame.__init__(self, parent, bg='white', **args)
self.windows = windows
self.manager = windows.manager
self.root = windows.root
# tkFont.Font(size=12, family='verdana', weight='bold')
bigSize = pwgui.cfgFontSize + 2
smallSize = pwgui.cfgFontSize - 2
fontName = pwgui.cfgFontName
self.projNameFont = tkFont.Font(size=bigSize,
family=fontName,
weight='bold')
self.projDateFont = tkFont.Font(size=smallSize, family=fontName)
self.projDelFont = tkFont.Font(size=smallSize,
family=fontName,
weight='bold')
self.manager = Manager()
self.filter = tk.StringVar()
self.filterBox = None
self.addActionsFrame()
self.columnconfigure(0, weight=1)
self.rowconfigure(1, weight=1)
text = TaggedText(self, width=40, height=15, bd=0, bg='white')
text.grid(row=1, columnspan=2, column=0, sticky='news')
self.createProjectList(text)
text.setReadOnly(True)
self.text = text
self.filterBox.focus_set()
def addActionsFrame(self):
""" Add the "toolbar" for actions like create project, import
project or filter"""
# Add the create project button
bg = "white"
btnFrame = tk.Frame(self, bg=bg)
btn = HotButton(btnFrame,
text=Message.LABEL_CREATE_PROJECT,
font=self.projNameFont,
command=self._onCreateProject)
btn.grid(row=0, column=0, sticky='nw', padx=10, pady=10)
# Add the Import project button
btn = Button(btnFrame,
text=Message.LABEL_IMPORT_PROJECT,
font=self.projNameFont,
command=self._onImportProject)
btn.grid(row=0, column=1, sticky='nw', padx=10, pady=10)
btnFrame.grid(row=0, column=0, sticky='nw')
# Add a filter box
# Add the Import project button
btn = tk.Label(btnFrame, bg=bg, text="Filter:", font=self.projNameFont)
btn.grid(row=0, column=2, sticky='nse', padx=10, pady=10)
self.filterBox = tk.Entry(btnFrame,
font=self.projNameFont,
textvariable=self.filter)
self.filterBox.grid(row=0, column=3, sticky='ne', padx=10, pady=12)
self.filterBox.bind('<Return>', self._onFilter)
self.filterBox.bind('<KP_Enter>', self._onFilter)
def createProjectList(self, text):
"""Load the list of projects"""
r = 0
text.setReadOnly(False)
text.clear()
parent = tk.Frame(text, bg='white', name=self._PROJ_CONTAINER)
parent.columnconfigure(0, weight=1)
colors = ['white', '#EAEBFF']
for i, p in enumerate(self.manager.listProjects()):
try:
# Add creation time to project info
# Add if it's a link
p.index = "index%s" % i
# Consider the filter
if not self._doesProjectMatchFilter(p):
continue
frame = self.createProjectLabel(parent, p, color=colors[i % 2])
frame.grid(row=r, column=0, padx=10, pady=5, sticky='new')
r += 1
except Exception as ex:
print("ERROR loading project: %s" % p.getName())
print(ex)
text.window_create(tk.INSERT, window=parent)
text.bindWidget(parent)
text.setReadOnly(True)
def createProjectLabel(self, parent, projInfo, color):
frame = tk.Frame(parent, bg=color, name=projInfo.index)
# ROW1
# Project name
label = tk.Label(frame,
text=projInfo.projName,
anchor='nw',
bg=color,
justify=tk.LEFT,
font=self.projNameFont,
cursor='hand1',
width=50)
label.grid(row=0, column=0, padx=2, pady=2, sticky='nw')
label.bind('<Button-1>', lambda e: self.openProject(projInfo.projName))
# ROW2
# Timestamp line
dateMsg = '%s%s %s%s' % (
Message.LABEL_MODIFIED, prettyDate(projInfo.mTime),
Message.LABEL_CREATED, prettyTime(projInfo.cTime, time=False))
dateLabel = tk.Label(frame,
text=dateMsg,
font=self.projDateFont,
bg=color)
dateLabel.grid(row=1, column=0, sticky='nw')
# Delete action
delLabel = tk.Label(frame,
text=Message.LABEL_DELETE_PROJECT,
font=self.projDelFont,
bg=color,
cursor='hand1')
delLabel.grid(row=1, column=1, padx=10)
delLabel.bind('<Button-1>', lambda e: self.deleteProject(projInfo))
# Rename action
mvLabel = tk.Label(frame,
text=Message.LABEL_RENAME_PROJECT,
font=self.projDelFont,
bg=color,
cursor='hand1')
mvLabel.grid(row=1, column=2)
mvLabel.bind('<Button-1>',
lambda e: self.renameProject(projInfo.projName))
# ROW3
if projInfo.isLink():
linkMsg = 'link --> ' + projInfo.realPath()
lblLink = tk.Label(frame,
text=linkMsg,
font=self.projDateFont,
bg=color,
fg='grey',
justify=tk.LEFT)
lblLink.grid(row=2, column=0, columnspan=3, sticky='w')
return frame
def createNewProject(self, projName, projLocation):
proj = self.manager.createProject(projName, location=projLocation)
self.createProjectList(self.text)
self.openProject(proj.getShortName())
def _onCreateProject(self, e=None):
projWindow = ProjectCreateWindow("Create project", self)
projWindow.show()
def _onImportProject(self, e=None):
importProjWindow = ProjectImportWindow("Import project", self)
importProjWindow.show()
def _onFilter(self, e=None):
self.createProjectList(self.text)
def _setFocusToList(self, e=None):
self.text.focus_set()
def _doesProjectMatchFilter(self, project):
""" Returns true if the project matches the filter"""
# Lets' use the name anc creation date for now:
searchString = "~".join([
project.getName().lower(),
prettyDate(project.mTime),
prettyTime(project.cTime, time=False)
])
return self.filter.get().lower() in searchString
def importProject(self, projLocation, copyFiles, projName, searchLocation):
self.manager.importProject(projLocation, copyFiles, projName,
searchLocation)
self.createProjectList(self.text)
self.openProject(projName)
def openProject(self, projName):
from subprocess import Popen
script = pw.join(pw.APPS, 'pw_project.py')
Popen([pw.PYTHON, script, projName])
def deleteProject(self, projInfo):
projName = projInfo.projName
if askYesNo(
Message.TITLE_DELETE_PROJECT,
"Project *%s*. " % projName + Message.MESSAGE_DELETE_PROJECT,
self.root):
self.manager.deleteProject(projName)
#Delete the frame
self.text.children[self._PROJ_CONTAINER].children[
projInfo.index].grid_forget()
def renameProject(self, projName):
newName = askString("Rename project %s" % projName, "Enter new name:",
self.root)
if not newName or newName == projName:
return
if self.manager.hasProject(newName):
showError("Rename cancelled",
"Project name already exists: %s" % newName, self.root)
return
self.manager.renameProject(projName, newName)
self.createProjectList(self.text)
pathToProj = os.path.abspath(sys.argv[1])
now = datetime.now()
tempSpace = "loading-%s" % now.strftime('%Y%m%d-%H%M%S')
customUserData = os.path.join(pw.Config.SCIPION_USER_DATA, 'tmp', tempSpace)
projectsDir = os.path.join(customUserData, 'projects')
pwutils.makePath(projectsDir)
print("Loading projects from:\n", projectsDir)
projName = os.path.basename(pathToProj)
pwutils.createAbsLink(pathToProj, os.path.join(projectsDir, projName))
# Create a new project
manager = Manager(workspace=customUserData)
proj = manager.loadProject(projName)
projPath = manager.getProjectPath(projName)
class EditorProjectWindow(ProjectWindow):
def close(self, e=None):
try:
print("Deleting temporary folder: ", customUserData)
pwutils.cleanPath(customUserData)
except Exception as ex:
print("Error: ", ex)
ProjectWindow.close(self, e)
from pyworkflow.project import Manager
from pyworkflow.gui.project import ProjectWindow
import pyworkflow.utils as pwutils
if __name__ == '__main__':
# Add callback for remote debugging if available.
try:
from rpdb2 import start_embedded_debugger
from signal import signal, SIGUSR2
signal(SIGUSR2, lambda sig, frame: start_embedded_debugger('a'))
except ImportError:
pass
if len(sys.argv) > 1:
manager = Manager()
projName = os.path.basename(sys.argv[1])
# Handle special name 'here' to create a project
# from the current directory
if projName == 'here':
cwd = os.environ['SCIPION_CWD']
print "\nYou are trying to create a project here:", pwutils.cyan(
cwd)
if os.listdir(cwd):
print pwutils.red('\nWARNING: this folder is not empty!!!')
key = raw_input("\nDo you want to create a project here? [y/N]?")
if key.lower().strip() != 'y':
print "\nAborting..."