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)
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)
except Exception as ex:
print("Error saving the workflow: ", ex)
ProjectWindow.close(self, e)
class EditorProjectWindow(ProjectWindow):
def close(self, e=None):
try:
print "Deleting temporary folder: ", customUserData
pwutils.cleanPath(customUserData)
except Exception, ex:
print "Error: ", ex
ProjectWindow.close(self, e)
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()
class EditorProjectWindow(ProjectWindow):
def close(self, e=None):
try:
print "Writing protocols to: ", jsonFn
proj.getRunsGraph() # Build project runs graph
proj.exportProtocols(proj.getRuns(), jsonFn)
print "Deleting temporary folder: ", customUserData
pwutils.cleanPath(customUserData)
except Exception, ex:
print "Error saving the workflow: ", ex
ProjectWindow.close(self, e)
plotter.createSubPlot(title, 'atom index', ylabel)
plotter.plotMdFile(mdFn, None, xmippLib.MDL_NMA_ATOMSHIFT)
return plotter
def createDistanceProfilePlot(protocol, modeNumber):
vectorMdFn = protocol._getExtraPath("distanceProfiles",
"vec%d.xmd" % modeNumber)
plotter = createShiftPlot(vectorMdFn,
"Atom shifts for mode %d" % modeNumber, "shift")
return plotter
def createVmdView(protocol, modeNumber):
vmdFile = protocol._getExtraPath("animations",
"animated_mode_%03d.vmd" % modeNumber)
return VmdView('-e "%s"' % vmdFile)
def showDistanceProfilePlot(protocol, modeNumber):
createDistanceProfilePlot(protocol, modeNumber).show()
def showVmdView(protocol, modeNumber):
createVmdView(protocol, modeNumber).show()
ProjectWindow.registerObjectCommand(OBJCMD_NMA_PLOTDIST,
showDistanceProfilePlot)
ProjectWindow.registerObjectCommand(OBJCMD_NMA_VMD, showVmdView)
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 pwutils.envVarOn('SCIPION_DEBUG'):
# 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) == 2:
manager = Manager()
tutorialName = sys.argv[1]
if not tutorialName in ALL_TUTORIALS:
printUsage("Invalid tutorial '%s'." % tutorialName)
else:
# Instanciate 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)
# we only consider the 'doSaveUnweightedMic' flag if the
# weighted ones should be created.
return (self.doSaveAveMic and self.doSaveUnweightedMic)
def _createOutputWeightedMicrographs(self):
return (self.doSaveAveMic and self.doApplyDoseFilter)
def _getOutputMovieUnWtName(self, movie):
""" Returns the name of the output dose-weighted movie.
(relative to micFolder)
"""
return self._getMovieRoot(movie) + '_aligned_movie.mrcs'
def showCartesianShiftsPlot(inputSet, itemId):
item = inputSet[itemId]
if item.hasAttribute('_xmipp_OFMeanX'):
meanX = [float(x) for x in item._xmipp_OFMeanX]
meanY = [float(y) for y in item._xmipp_OFMeanY]
plotter = createAlignmentPlot(meanX, meanY)
plotter.show()
else:
print("These items do not have OF alignment set. ")
ProjectWindow.registerObjectCommand(OBJCMD_MOVIE_ALIGNCARTESIAN,
showCartesianShiftsPlot)
# Just for backwards compatibility
ProtMovieAlignment = XmippProtOFAlignment
"""
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)
for protId in prots:
node = sett.getNodeById(protId)
node.setLabels([labelName])
if i == 0:
res['freq'] = [float(x) for x in line.split()]
elif i == 2:
res['amp'] = [float(x) for x in line.split()]
elif i == 3:
res['fit'] = [float(x) for x in line.split()]
elif i == 4:
res['quality'] = [float(x) for x in line.split()]
break
i += 1
return res
OBJCMD_CTFFIND4 = "CTFFind plot results"
ProjectWindow.registerObjectCommand(OBJCMD_CTFFIND4, createCtfPlot)
class CtffindViewer(Viewer):
""" Specific way to visualize SetOfCtf. """
_environments = [DESKTOP_TKINTER]
_targets = [CistemProtCTFFind]
def _visualize(self, prot, **kwargs):
outputCTF = getattr(prot, 'outputCTF', None)
if outputCTF is not None:
ctfView = CtfView(self._project, outputCTF)
viewParams = ctfView.getViewParams()
viewParams[showj.OBJCMDS] = "'%s'" % OBJCMD_CTFFIND4
return [ctfView]
'CTF',
yformat=False)
a.invert_xaxis()
for i in range(1, 5):
_plotCurve(a, i, fn)
xplotter.showLegend([
'simulated CTF', 'equiphase avg.', 'equiphase avg. - bg',
'cross correlation'
])
a.grid(True)
xplotter.show()
OBJCMD_GCTF = "Display Ctf Analysis"
ProjectWindow.registerObjectCommand(OBJCMD_GCTF, createCtfPlot)
def _plotCurve(a, i, fn):
freqs = _getValues(fn, 0)
curv = _getValues(fn, i)
a.plot(freqs, curv)
def _getValues(fn, col):
f = open(fn)
values = []
for line in f:
if not line.startswith('Resolution', 2, 12):
column = line.split()
value = float(column[col])
def showExtraFile(volumeSet, volId, suffix):
vol = volumeSet[volId]
volFn = vol.getFileName().replace('.hdf', suffix)
vw.DataView(volFn).show()
def showClassAvgProjs(volumeSet, volId):
showExtraFile(volumeSet, volId, '_aptcl.hdf')
def showProjs(volumeSet, volId):
showExtraFile(volumeSet, volId, '_proj.hdf')
def showInitialRandomVolume(volumeSet, volId):
showExtraFile(volumeSet, volId, '_init.hdf')
ProjectWindow.registerObjectCommand(OBJCMD_CLASSAVG_PROJS, showClassAvgProjs)
ProjectWindow.registerObjectCommand(OBJCMD_PROJS, showProjs)
ProjectWindow.registerObjectCommand(OBJCMD_INITVOL, showInitialRandomVolume)
class RefineEasyViewer(ProtocolViewer):
""" Visualization of Refine Easy."""
_targets = [EmanProtRefine]
_environments = [DESKTOP_TKINTER, WEB_DJANGO]
_label = 'viewer Refine Easy'
def _defineParams(self, form):
self._env = os.environ.copy()
form.addSection(label='Results per Iteration')
form.addParam('iterToShow', EnumParam,
legendName = ['rotational avg. No Astg',
'rotational avg.',
'CTF Fit',
'Cross Correlation',
'2sigma cross correlation of noise']
for i in range(1, 6):
_plotCurve(a, i, fn)
xplotter.showLegend(legendName)
a.grid(True)
xplotter.show()
OBJCMD_CTFFIND4 = "Display Ctf Fitting"
ProjectWindow.registerObjectCommand(OBJCMD_CTFFIND4, createCtfPlot)
class CtffindViewer(Viewer):
""" Specific way to visualize SetOfCtf after Gctf. """
_environments = [DESKTOP_TKINTER, WEB_DJANGO]
_targets = [ProtCTFFind]
def _visualize(self, prot, **kwargs):
outputCTF = getattr(prot, 'outputCTF', None)
if outputCTF is not None:
ctfView = CtfView(self._project, outputCTF)
viewParams = ctfView.getViewParams()
viewParams[showj.OBJCMDS] = "'%s'" % OBJCMD_CTFFIND4
return [ctfView]
return (self.doSaveAveMic and self.doSaveUnweightedMic)
def _createOutputWeightedMicrographs(self):
return (self.doSaveAveMic and self.doApplyDoseFilter)
def _getOutputMovieWtName(self, movie):
""" Returns the name of the output dose-weighted movie.
(relative to micFolder)
"""
return self._getMovieRoot(movie) + '_aligned_movie_DW.mrcs'
def showCartesianShiftsPlot(inputSet, itemId):
item = inputSet[itemId]
if item.hasAttribute('_xmipp_OFMeanX'):
meanX = [float(x) for x in item._xmipp_OFMeanX]
meanY = [float(y) for y in item._xmipp_OFMeanY]
plotter = createAlignmentPlot(meanX, meanY)
plotter.show()
else:
print "These items do not have OF alignment set. "
ProjectWindow.registerObjectCommand(OBJCMD_MOVIE_ALIGNCARTESIAN,
showCartesianShiftsPlot)
# Just for backwards compatibility
ProtMovieAlignment = XmippProtOFAlignment
(PYTHON, os.path.join(getInstallPath(), PLUGIN_MANAGER_PY)))
def launchTemplates(window):
os.system("%s %s" % (PYTHON, os.path.join(getScriptsPath(), KICKOFF)))
# Cancel this for now to prevent an early import of Config and a false initialization
from pyworkflow.gui.project import ProjectManagerWindow, ProjectWindow
ProjectManagerWindow.registerPluginMenu("Plugin manager", launchPluginManager,
None)
ProjectManagerWindow.registerPluginMenu("Workflow templates", launchTemplates,
None)
def importFromTemplate(window):
templates = getTemplates()
chosenTemplate = chooseTemplate(templates, parentWindow=window.getRoot())
if chosenTemplate is not None and resolveTemplate(chosenTemplate, [],
showScheduleOption=False,
schedule=False,
showProjectOption=False,
showProject=False,
showProjectName=False):
importTemplate(chosenTemplate, window)
ProjectWindow.registerPluginMenu("Import workflow template",
importFromTemplate, None)
print "\nAborting..."
sys.exit(0)
else:
print "\nCreating project...."
projName = os.path.basename(cwd)
projDir = os.path.dirname(cwd)
proj = 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)
# try:
projWindow = ProjectWindow(projPath)
# except Exception as e:
# # Print any exception
# print("ERROR: At pw_project.py loading Project %s.\n"
# " Message: %s\n" % (projPath, e))
#
# import traceback
# traceback.print_exc(file=sys.stderr)
#
# sys.exit(e)
projWindow.show()
else:
print "usage: pw_project.py PROJECT_NAME"
DataView(volFn).show()
def showClassAvgProjs(volumeSet, volId):
showExtraFile(volumeSet, volId, '_aptcl.hdf')
def showProjs(volumeSet, volId):
showExtraFile(volumeSet, volId, '_proj.hdf')
def showInitialRandomVolume(volumeSet, volId):
showExtraFile(volumeSet, volId, '_init.hdf')
ProjectWindow.registerObjectCommand(OBJCMD_CLASSAVG_PROJS, showClassAvgProjs)
ProjectWindow.registerObjectCommand(OBJCMD_PROJS, showProjs)
ProjectWindow.registerObjectCommand(OBJCMD_INITVOL, showInitialRandomVolume)
class Refine2DViewer(ProtocolViewer):
""" Visualization of e2refine2d results. """
_targets = [EmanProtRefine2D, EmanProtRefine2DBispec]
_environments = [DESKTOP_TKINTER, WEB_DJANGO]
_label = 'viewer refine 2d'
def _defineParams(self, form):
self._env = os.environ.copy()
form.addSection(label='Results per Iteration')
form.addParam('iterToShow',
a = xplotter.createSubPlot(plot_title, 'Resolution (Angstroms)', 'CTF',
yformat=False)
a.invert_xaxis()
for i in range(1, 5):
_plotCurve(a, i, fn)
xplotter.showLegend(['simulated CTF',
'equiphase avg.',
'equiphase avg. - bg',
'cross correlation'])
a.grid(True)
xplotter.show()
OBJCMD_GCTF = "Display Ctf Analysis"
ProjectWindow.registerObjectCommand(OBJCMD_GCTF, createCtfPlot)
def _plotCurve(a, i, fn):
freqs = _getValues(fn, 0)
curv = _getValues(fn, i)
a.plot(freqs, curv)
def _getValues(fn, col):
f = open(fn)
values = []
for line in f:
if not line.startswith('Resolution', 2, 12):
column = line.split()
value = float(column[col])