def show(self, form, *params):
prot = form.protocol
acquisitionInfo = prot.loadAcquisitionInfo()
if prot.importFilePath:
if exists(prot.importFilePath):
if acquisitionInfo:
msg = ''
for k, v in acquisitionInfo.iteritems():
msg += '%s = %s\n' % (k, v)
msg += '\n*Do you want to use detected acquisition values?*'
response = dialog.askYesNo("Import acquisition", msg,
form.root)
if response:
for k, v in acquisitionInfo.iteritems():
form.setVar(k, v)
else:
dialog.showWarning("Import failed",
"Could not import acquisition info.",
form.root)
else:
dialog.showError(
"Input error", "*Import file doesn't exist.*\nFile:\n%s" %
prot.importFilePath, form.root)
else:
dialog.showError("Input error", "Select import file first",
form.root)
def show(self, form, *args):
protocol = form.protocol
provider = self._getProvider(protocol)
installErrors = Plugin.validateInstallation()
if installErrors:
dialog.showError("SPIDER not properly installed.",
"\n".join(installErrors), form.root)
return
if provider is not None:
d = SpiderFilterDialog(form.root,
provider,
protocolParent=protocol)
if d.resultYes():
if protocol.filterType <= FILTER_FERMI:
form.setVar('filterRadius', d.getRadius())
else:
form.setVar('lowFreq', d.getLowFreq())
form.setVar('highFreq', d.getHighFreq())
if protocol.filterType == FILTER_FERMI:
form.setVar('temperature', d.getTemperature())
else:
dialog.showWarning("Input particles", "Select particles first",
form.root)
def _select(self):
projName = self.projName.get().strip()
projLocation = self.projLocation.get().strip()
# Validate that project name is not empty
if not projName:
showError("Validation error", "Project name is empty", self.root)
# Validate that project location is not empty
elif not projLocation:
showError("Validation error", "Project location is empty",
self.root)
# Validate that project location exists
elif not os.path.exists(projLocation):
showError("Validation error", "Project location does not exist",
self.root)
# Validate that project location is a directory
elif not os.path.isdir(projLocation):
showError("Validation error",
"Project location is not a directory", self.root)
# Validate that project path (location + name) ddoes not exists
elif os.path.exists(os.path.join(projLocation, projName)):
showError("Validation error", "Project path already exists",
self.root)
else:
self.parent.createNewProject(projName, projLocation)
self.close()
def checkFileIntegrityGUI(fn, parent):
ok = verifyMD5(fn)
if ok:
showInfo("File integrity", "File is OK", parent)
else:
showError(
"File integrity",
"File seems to have been modified since its creation. Not OK",
parent)
def show(self, form, *params):
acquisitionInfo = form.protocol.loadAcquisitionInfo()
if isinstance(acquisitionInfo, dict):
# If acquisitionInfo is None means something is wrong.
# Now, let's try to show a meanful error message.
self._setAcquisition(form, acquisitionInfo)
else:
# If not dict, it should be an error message
dialog.showError("Input error", acquisitionInfo, form.root)
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)
def show(self, form, *params):
acquisitionInfo = form.protocol.loadAcquisitionInfo()
if isinstance(acquisitionInfo, dict):
# If acquisitionInfo is None means something is wrong.
# Now, let's try to show a meaningful error message.
self._setAcquisition(form, acquisitionInfo)
else:
# If not dict, it should be an error message
dialog.showError("Input error", acquisitionInfo, form.root)
def validate(self):
validationMsg = None
if len(self.textVar.get().strip()) == 0:
validationMsg = "Label name can't be empty.\n"
if validationMsg is not None:
dialog.showError("Validation error", validationMsg, self)
return False
return True
def validate(self):
validationMsg = None
if len(self.textVar.get().strip()) == 0:
validationMsg = "Label name can't be empty.\n"
if validationMsg is not None:
dialog.showError("Validation error", validationMsg, self)
return False
return True
def show(self, form, *params):
try:
acquisitionInfo = form.protocol.loadAcquisitionInfo()
if isinstance(acquisitionInfo, dict):
# If acquisitionInfo is None means something is wrong.
# Now, let's try to show a meaningful error message.
self._setAcquisition(form, acquisitionInfo)
else:
# If not dict, it should be an error message
dialog.showError("Input error", acquisitionInfo, form.root)
except FileNotFoundError as e:
dialog.showInfo(
"File not found",
"Metadata file with acquisition not found.\n\n %s" % e,
form.root)
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 _showPlot(self, paramName=None):
views = []
color = self.colozaxis
rmax = self.radcut.get()
if self.displayPlot == TILT_SCATTER:
views.append(self._createScatterPlot(rmax, colorzaxis=color))
elif self.displayPlot == TILT_CONTOUR:
plotFn = self.protocol._getFileName('outputContourPlot')
if os.path.exists(plotFn):
views.append(DataView(plotFn))
else:
showError("File not found",
"Contour plot file not found: %s" % plotFn,
self.getTkRoot())
return views
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_DBNAME)):
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 _itemSelected(self, obj):
index = obj.getIndex()
filename = obj.getFileName()
if index:
filename = "%03d@%s" % (index, filename)
# self.image = xmipp.Image()
self.image = ImageHandler()._img
try:
self.image.readPreview(filename, self.dim)
if filename.endswith('.psd'):
self.image.convertPSD()
self.Z = self.image.getData()
except Exception, e:
from pyworkflow.gui.matplotlib_image import getPngData
self.Z = getPngData(findResource('no-image.png'))
dialog.showError("Input particles", "Error reading image <%s>" % filename, self)
def _itemSelected(self, obj):
index = obj.getIndex()
filename = emlib.image.ImageHandler.fixXmippVolumeFileName(obj)
if index:
filename = "%03d@%s" % (index, filename)
self.image = emlib.image.ImageHandler()._img
try:
self.image.readPreview(filename, self.dim)
if filename.endswith('.psd'):
self.image.convertPSD()
self.Z = self.image.getData()
except Exception as e:
from pyworkflow.gui.matplotlib_image import getPngData
self.Z = getPngData(pw.findResource('no-image.gif'))
dialog.showError("Input particles",
"Error reading image <%s>" % filename, self)
self.preview.updateData(self.Z)
def _select(self):
projName = self.projName.get().strip()
projLocation = self.projLocation.get().strip()
# Validate that project name is not empty
if not projName:
showError("Validation error", "Project name is empty", self.root)
# Validate that project location is not empty
elif not projLocation:
showError("Validation error", "Project location is empty", self.root)
# Validate that project location exists
elif not os.path.exists(projLocation):
showError("Validation error", "Project location does not exist", self.root)
# Validate that project location is a directory
elif not os.path.isdir(projLocation):
showError("Validation error", "Project location is not a directory", self.root)
# Validate that project path (location + name) ddoes not exists
elif os.path.exists(os.path.join(projLocation, projName)):
showError("Validation error", "Project path already exists", self.root)
else:
self.parent.createNewProject(projName, projLocation)
self.close()
def show(self, form, *params):
prot = form.protocol
acquisitionInfo = prot.loadAcquisitionInfo()
if prot.importFilePath:
if exists(prot.importFilePath):
if acquisitionInfo:
msg = ''
for k, v in acquisitionInfo.iteritems():
msg += '%s = %s\n' % (k, v)
msg += '\n*Do you want to use detected acquisition values?*'
response = dialog.askYesNo("Import acquisition", msg, form.root)
if response:
for k, v in acquisitionInfo.iteritems():
form.setVar(k, v)
else:
dialog.showWarning("Import failed",
"Could not import acquisition info.", form.root)
else:
dialog.showError("Input error", "*Import file doesn't exist.*\nFile:\n%s" % prot.importFilePath, form.root)
else:
dialog.showError("Input error", "Select import file first", form.root)
def _createAngDistChimera(self, it):
radius = self.spheresScale.get()
volumes = self._getVolumeNames()
self.protocol._execEmanProcess(self.protocol._getRun(), it)
angularDist = self.protocol._getFileName("angles", iter=it)
def createSqlite(prefix):
nparts = self._getNumberOfParticles(it, prefix)
sqliteFn = self.protocol._getFileName('projections',
iter=it,
half=prefix)
self.createAngDistributionSqlite(sqliteFn,
nparts,
itemDataIterator=self._iterAngles(
it, prefix))
return sqliteFn
if len(volumes) > 1:
showError(
"Error",
"Please select a single volume to show it's angular distribution",
self.getTkRoot())
elif not os.path.exists(angularDist):
showError(
"Error",
"Please select a valid iteration to show the angular distribution",
self.getTkRoot())
else:
if self.showHalves.get() == HALF_EVEN:
sqliteFn = createSqlite('even')
elif self.showHalves.get() == HALF_ODD:
sqliteFn = createSqlite('odd')
elif self.showHalves.get() == FULL_MAP:
sqliteFn = createSqlite('full')
else:
showError(
"Error",
"Please select a single volume to show it's angular distribution",
self.getTkRoot())
vol = self.protocol.outputVolume
volOrigin = vol.getOrigin(force=True).getShifts()
samplingRate = vol.getSamplingRate()
return ChimeraAngDist(volumes[0],
self.protocol._getTmpPath(),
voxelSize=samplingRate,
volOrigin=volOrigin,
angularDistFile=sqliteFn,
spheresDistance=radius)
def _doPreview(self, e=None):
if self.lastObj is None:
dialog.showError("Empty selection", "Select an item first before preview", self)
else:
self._computeRightPreview()
def checkFileIntegrityGUI(fn,parent):
ok = verifyMD5(fn)
if ok:
showInfo("File integrity", "File is OK", parent)
else:
showError("File integrity","File seems to have been modified since its creation. Not OK", parent)
def _doPreview(self, e=None):
if self.lastObj is None:
dialog.showError("Empty selection",
"Select an item first before preview", self)
else:
self._itemSelected(self.lastObj)