def QuestionPopup( message ):
messageBox = qt.QMessageBox()
clickedButton = messageBox.question(None, '', message, qt.QMessageBox().Yes | qt.QMessageBox().No, qt.QMessageBox().Yes)
if clickedButton == qt.QMessageBox.Yes:
return True
else:
return False
def createExtensionModule(self):
if (self.extensionLocation is None):
# Action shouldn't be enabled if no extension is selected, but guard
# against that just in case...
return
dlg = CreateComponentDialog("module", self.parent.window())
dlg.setTemplates(self.templateManager.templates("modules"),
default="scripted")
dlg.showDestination = False
while dlg.exec_() == qt.QDialog.Accepted:
name = dlg.componentName
try:
self.templateManager.copyTemplate(self.extensionLocation,
"modules", dlg.componentType,
name)
except:
md = qt.QMessageBox(self.parent.window())
md.icon = qt.QMessageBox.Critical
md.text = "An error occurred while trying to create the module."
md.detailedText = traceback.format_exc()
md.standardButtons = qt.QMessageBox.Retry | qt.QMessageBox.Close
if md.exec_() != qt.QMessageBox.Retry:
return
continue
try:
self.extensionProject.addModule(name)
self.extensionProject.save()
except:
md = qt.QMessageBox(self.parent.window())
md.icon = qt.QMessageBox.Critical
md.text = "An error occurred while adding the module to the extension."
md.informativeText = "The module has been created, but the extension" \
" CMakeLists.txt could not be updated. In order" \
" to include the module in the extension build," \
" you will need to update the extension" \
" CMakeLists.txt by hand."
md.detailedText = traceback.format_exc()
md.standardButtons = qt.QMessageBox.Close
md.exec_()
self.loadModules(os.path.join(self.extensionLocation, name),
depth=0)
return
def createExtension(self):
dlg = CreateComponentDialog("extension", self.parent.window())
dlg.setTemplates(self.templateManager.templates("extensions"))
while dlg.exec_() == qt.QDialog.Accepted:
try:
path = self.templateManager.copyTemplate(
dlg.destination, "extensions", dlg.componentType,
dlg.componentName)
except:
md = qt.QMessageBox(self.parent.window())
md.icon = qt.QMessageBox.Critical
md.text = "An error occurred while trying to create the extension."
md.detailedText = traceback.format_exc()
md.standardButtons = qt.QMessageBox.Retry | qt.QMessageBox.Close
if md.exec_() != qt.QMessageBox.Retry:
return
continue
if self.selectExtension(path):
self.editExtensionMetadata()
return
def setNumDialogs(self, numDialogs=1, dialogType=None):
""" User can set the amount of dialogs in the
dialog sequence.
"""
for x in range(0, numDialogs):
try:
#
# Set dialog based on the 'dialogType' argument.
#
self.dialogs.append(dialogType[str(x)])
except Exception, e:
#
# Set default based on the default 'dialogType' argument.
#
dialog = qt.QMessageBox()
self.dialogs.append(dialog)
self.dialogs[x].connect('buttonClicked(QAbstractButton*)',
self.onButtonClicked)
self.dialogs[x].setTextFormat(1)
#
# NOTE: Need to keep the window modality
# always in front. Blocking out
# all other interactions.
#
self.dialogs[x].setWindowModality(2)
def uploadSnapshots(self):
"""Upload the checked snapshots to Picasa (avoiding upload the ones already uploaded).
Remember that """
# Store the albums that must be uploaded
ids = []
# Add to the list of uploads just the ones that are visible, checked and not have been already uploaded
for key,value in self.snapshotsCached.items():
cb = value[self.SNAPSHOT_WIDGET]
if cb.visible and cb.checked and not value[self.SNAPSHOT_UPLOADED]:
ids.append(key)
self.imagesToUploadCount = len(ids)
if self.imagesToUploadCount == 0:
# No albums to upload. Display information message
qt.QMessageBox.warning(slicer.util.mainWindow(), 'Warning', 'There are not any new snapshopts to upload to Picasa at this moment')
else:
self.imagesUploadedCount = 0
# Get the selected album id
albumId = self.albumNamesComboBox.itemData(self.albumNamesComboBox.currentIndex)
# Get the selected tags (pressed buttons)
tags = [b.text for b in [btn for btn in self.btnTags if btn.checked]]
self.progressBar.setMaximum(self.imagesToUploadCount)
self.progressBar.setValue(0)
self.progressBar.show()
# Upload
#self.logic.picasaUploadPictures(ids, albumId, tags, self.onImageUploaded)
for snapshotNodeId in ids:
self.progressBar.labelText = "Uploading %i / %i images..." % (self.imagesUploadedCount + 1, self.imagesToUploadCount)
slicer.app.processEvents()
self.logic.picasaUploadPicture(snapshotNodeId, self.snapshotsCached[snapshotNodeId][self.SNAPSHOT_NAME], self.snapshotsCached[snapshotNodeId][self.SNAPSHOT_DESCRIPTION], albumId, tags)
self.imagesUploadedCount += 1
# Update the state of the new uploaded snap
self.snapshotsCached[snapshotNodeId][self.SNAPSHOT_UPLOADED] = True
self.snapshotsCached[snapshotNodeId][self.SNAPSHOT_WIDGET].toolTip = "%s. Uploaded to Picasa: YES" % self.snapshotsCached[snapshotNodeId][self.SNAPSHOT_DESCRIPTION]
self.snapshotsCached[snapshotNodeId][self.SNAPSHOT_WIDGET].checked = True
self.snapshotsCached[snapshotNodeId][self.SNAPSHOT_WIDGET].enabled = False
slicer.app.processEvents()
if self.progressBar.wasCanceled:
# The process was cancelled by the user
qt.QMessageBox.warning(slicer.util.mainWindow(), 'Warning', 'The process was cancelled, but %i images were uploaded' % self.imagesUploadedCount)
return
self.progressBar.setValue(self.imagesUploadedCount)
#self.progressBar.setFormat("Uploading %i / %i images..." % (self.imagesUploadedCount + 1, self.imagesToUploadCount))
#self.progressBar.labelText = "Uploading %i / %i images..." % (self.imagesUploadedCount + 1, self.imagesToUploadCount)
#slicer.app.processEvents()
# Inform the user
self.msgBox = qt.QMessageBox(qt.QMessageBox.Information, 'Images uploaded', '%i images were uploaded succesfully' % self.imagesUploadedCount)
self.msgBox.setModal(True)
self.msgBox.show()
def messageBox(self, text, title='DICOM'):
self.mb = qt.QMessageBox(slicer.util.mainWindow())
self.mb.setWindowTitle(title)
self.mb.setText(text)
self.mb.setWindowModality(1)
self.mb.exec_()
return
def genMsg(self, title, text, info, detail, icon=qt.QMessageBox.Warning):
'''Returns a customised message box object'''
msg = qt.QMessageBox()
msg.setIcon(icon)
msg.setWindowTitle(title)
msg.setText(text)
msg.setInformativeText(info)
msg.setDetailedText(detail)
return msg
def confirmDialog(self, message):
self.dialog = qt.QMessageBox()
self.dialog.setWindowTitle("Editor")
self.dialog.setText(message)
self.dialogRejectButton = self.addButton("Cancel", 2)
self.dialogAcceptButton = self.addButton("Ok", 1)
# TODO: cannot call the exec() method from the pythonqt
#self.dialog.exec()
return True
def __init__(self, parent, helpString = ""):
self.helpString = helpString
self.message = qt.QMessageBox()
self.message.setWindowTitle("Editor Help")
self.button = qt.QPushButton("?", parent)
self.button.setMaximumWidth(15)
self.button.setToolTip("Bring up a help window")
parent.layout().addWidget(self.button)
self.button.connect('clicked()', self.showHelp)
def onDownloadButton(self):
"""Click in download button"""
# Check if there is a Study and Case introduced
self.CaseId = self.txtCaseId.text.strip()
if self.CaseId and self.StudyId:
self.lblDownloading.show()
slicer.app.processEvents()
# Get the selected image types and label maps
imageTypes = [
self.imageTypes[cb.text] for cb in
[check for check in self.cbsImageTypes if check.isChecked()]
]
labelMapExtensions = [
self.labelMapTypes[cb.text] for cb in [
check for check in self.cbsLabelMapTypes
if check.isChecked()
]
]
result = self.logic.loadCase(self.txtServer.text,
self.txtServerpath.text, self.StudyId,
self.txtCaseId.text, imageTypes,
labelMapExtensions,
self.localStoragePath,
self.cbCacheMode.checkState(),
self.rbSSH.isChecked(),
self.txtPrivateKeySSH.text)
self.lblDownloading.hide()
if (result == Util.ERROR):
self.msgBox = qt.QMessageBox(
qt.QMessageBox.Warning, 'Error',
"There was an error when downloading some of the images of this case. It is possible that some of the selected images where not available in the server. Please review the log console for more details.\nSuggested actions:\n-Empty cache\n-Restart Slicer"
)
self.msgBox.show()
else:
# Show info messsage
self.msgBox = qt.QMessageBox(
qt.QMessageBox.Information, 'Attention',
"Please make sure that you have selected a study and a case")
self.msgBox.show()
def createExtension(self):
dlg = CreateComponentDialog("extension", self.parent.window())
dlg.setTemplates(self.templateManager.templates("extensions"))
while dlg.exec_() == qt.QDialog.Accepted:
# If the selected destination is in a repository then use the root of that repository
# as destination
try:
repo = SlicerWizard.Utilities.getRepo(dlg.destination)
createInSubdirectory = True
requireEmptyDirectory = True
if repo is None:
destination = os.path.join(dlg.destination,
dlg.componentName)
if os.path.exists(dlg.destination):
raise IOError("create extension: refusing to overwrite"
" existing directory '%s'" %
dlg.destination)
else:
destination = SlicerWizard.Utilities.localRoot(repo)
cmakeFile = os.path.join(destination, "CMakeLists.txt")
createInSubdirectory = False # create the files in the destination directory
requireEmptyDirectory = False # we only check if no CMakeLists.txt file exists
if os.path.exists(cmakeFile):
raise IOError(
"create extension: refusing to overwrite"
" directory containing CMakeLists.txt file at '%s'"
% dlg.destination)
path = self.templateManager.copyTemplate(
destination, "extensions", dlg.componentType,
dlg.componentName, createInSubdirectory,
requireEmptyDirectory)
except:
md = qt.QMessageBox(self.parent.window())
md.icon = qt.QMessageBox.Critical
md.text = "An error occurred while trying to create the extension."
md.detailedText = traceback.format_exc()
md.standardButtons = qt.QMessageBox.Retry | qt.QMessageBox.Close
if md.exec_() != qt.QMessageBox.Retry:
return
continue
if self.selectExtension(path):
self.editExtensionMetadata()
return
def runPreProcessing(self):
'''
'''
# notify user
dialog = qt.QMessageBox()
dialog.setWindowTitle("Please wait")
dialog.setText("Please wait while pre-processing runs..")
dialog.setModal(False)
dialog.show()
# message = qt.QMessageBox( qt.QMessageBox.NoIcon, "Please wait", "Please wait while pre-processing runs..", qt.QMessageBox.Ignore )
# message.setModal( False )
# message.show()
slicer.app.processEvents()
# run preprocessing
returnValue = tcl("::EMSegmenterPreProcessingTcl::Run")
# message.hide()
dialog.hide()
slicer.app.processEvents()
if not returnValue or int(returnValue) != 0:
# something went wrong!
# error message!
messageBox = qt.QMessageBox.warning(
self, "Error", "Pre-processing did not execute correctly!")
return
workingDataNode = self.mrmlManager().GetWorkingDataNode()
if workingDataNode:
# set flags in the mrml nodes
workingDataNode.SetAlignedTargetNodeIsValid(1)
workingDataNode.SetAlignedAtlasNodeIsValid(1)
# show preprocessing output in sliceViews
volumeCollection = workingDataNode.GetInputTargetNode()
if volumeCollection:
outputNode = volumeCollection.GetNthVolumeNode(0)
# propagate to sliceViews
selectionNode = slicer.app.applicationLogic().GetSelectionNode(
)
selectionNode.SetReferenceActiveVolumeID(outputNode.GetID())
#selectionNode.SetReferenceSecondaryVolumeID( outputNode.GetID() )
slicer.app.applicationLogic().PropagateVolumeSelection()
Helper.Info('=============================================')
Helper.Info('Pre-processing completed successfully')
Helper.Info('=============================================')
def onApplyButton(self):
if self.applyButton.text == "Generate":
self.applyButton.setText("Cancel")
else:
self.reset()
return
configPath = self.configPathEdit.currentPath
targetDirectoryPath = self.targetDirectoryButton.directory
if configPath == "" or targetDirectoryPath == "":
self.message.showMessage(
"Must select config file and and output path")
self.reset()
return
self.logic.configure(configPath, targetDirectoryPath, self.myQObject)
self.logic.generate()
forceVal = False
if self.logic.errorMessage.startswith("AppExists:"):
targetDirectory = self.logic.errorMessage[len("AppExists:"):]
answer = self.showErrorMessage(
"Target Exists", "The application directory exists."
'\n\n%s\n\nClick Ok to overwrite.' % targetDirectory)
if answer == qt.QMessageBox.Ok:
self.logic.configure(configPath,
targetDirectoryPath,
self.myQObject,
force=True)
self.logic.generate()
forceVal = True
else:
self.reset()
if self.logic.errorMessage == "Extension Updates available":
answer = self.showErrorMessage( "Extension Updates available",
"Extension Updates are available. " \
"Click Ok to ignore, or update them manually.")
if answer == qt.QMessageBox.Ok:
self.logic.configure(configPath,
targetDirectoryPath,
self.myQObject,
ignoreUpdates=True,
force=forceVal)
self.logic.generate()
else:
self.reset()
if self.logic.errorMessage:
qt.QMessageBox().question(slicer.app.activeWindow(),
"CustomSlicerGenerator",
self.logic.errorMessage,
qt.QMessageBox.Ok)
self.reset(
) # Reset only if error found. Otherwise extensions might be installing
def killOtherListeners(self, osName, pid= None):
msgBox = qt.QMessageBox()
msgBox.setText('There are other DICOM listeners running.\n Do you want to end them?')
msgBox.setStandardButtons(qt.QMessageBox.Yes | qt.QMessageBox.No)
val = msgBox.exec_()
if(val == qt.QMessageBox.Yes):
if osName == 'nt':
os.popen('taskkill /f /im storescp.exe')
elif osName == 'posix':
import signal
os.kill(pid, signal.SIGKILL)
return True
else:
return False
def __init__(self, MODULE):
"""
Init function.
"""
self.MODULE = MODULE
self.ScenePackager = ScenePackager(self.MODULE)
#------------------------
# Set wait window
#------------------------
self.waitWindow = qt.QMessageBox(1, "Uploading", \
"Please wait while file uploads...")
def initClearDialog(self):
""" Initiates/resets dialog for window to clear the current scene.
"""
try:
self.clearSceneDialog.delete()
except:
pass
self.clearSceneDialog = qt.QMessageBox()
self.clearSceneDialog.setStandardButtons(qt.QMessageBox.Yes
| qt.QMessageBox.No)
self.clearSceneDialog.setDefaultButton(qt.QMessageBox.No)
self.clearSceneDialog.setText("In order to run tests " +
"you have to clear the current scene." +
"\nAre you sure you want to clear?")
def __makeDialog(self):
"""
The Dialog box. If the user 'OK's the delete
it calls on 'Workflow_Delete.beginWorkflow'
@return: The delete dialog.
@rtype: qt.QMessageBox
"""
deleteDialog = qt.QMessageBox()
deleteDialog.setIcon(qt.QMessageBox.Warning)
deleteDialog.setText("Are you sure you want to delete '%s' from Xnat?"\
%(self.MODULE.View.getItemName()))
deleteDialog.connect('buttonClicked(QAbstractButton*)',
self.beginWorkflow)
deleteDialog.addButton(qt.QMessageBox.Ok)
deleteDialog.addButton(qt.QMessageBox.Cancel)
return deleteDialog
def __init__(self, MODULE):
""" Init function.
"""
self.MODULE = MODULE
self.XnatScenePackager = XnatScenePackager(self.MODULE)
#------------------------
# Set wait window
#------------------------
self.waitWindow = qt.QMessageBox(1, "Uploading",
"Please wait while file uploads...")
self.waitWindow.setWindowModality(2)
#
# Remove the 'OK' button from the wait window.
#
self.waitWindow.setStandardButtons(0)
def __init__(self, MODULE, uriName):
""" Init function.
"""
#--------------------
# The MODULE
#--------------------
self.MODULE = MODULE
#--------------------
# The Dialog box. If the user 'OK's the delete
# it calls on 'XnatDeleteWorkflow.beginWorkflow'
#--------------------
self.deleteDialog = qt.QMessageBox()
self.deleteDialog.setIcon(qt.QMessageBox.Warning)
self.deleteDialog.setText(
"Are you sure you want to delete the '%s' from Xnat?" % (uriName))
self.deleteDialog.connect('buttonClicked(QAbstractButton*)',
self.beginWorkflow)
self.deleteDialog.addButton(qt.QMessageBox.Ok)
self.deleteDialog.addButton(qt.QMessageBox.Cancel)
def __init__(self, MODULE):
"""
@param MODULE: The XNATSlicer module.
@type MODULE: XnatSlicerWidget
"""
self.MODULE = MODULE
self.loadFile = None
self.newMRMLFile = None
self.currRemoteHost = None
self.skipEmptySceneCheck = False
self._src = None
self.loaders = {}
#--------------------------------
# Popups
#--------------------------------
self.areYouSureDialog = qt.QMessageBox()
self.areYouSureDialog.setIcon(4)
self.areYouSureDialog.setText(
"You are about to load all readable scans from '**HERE**'.\n" +
"This may take several minutes.\n" +
"Are you sure you want to continue?")
self.areYouSureDialog.addButton(qt.QMessageBox.Yes)
self.areYouSureDialog.addButton(qt.QMessageBox.No)
self.areYouSureDialog.connect('buttonClicked(QAbstractButton*)',
self.beginWorkflow)
self.XnatDownloadPopup = XnatDownloadPopup()
self.XnatDownloadPopup.setCancelCallback(
self.MODULE.XnatIo.cancelDownload)
self.clearScenePopup = XnatClearScenePopup()
self.clearScenePopup.connect('buttonClicked(QAbstractButton*)',
self.__clearSceneButtonClicked)
self.preDownloadPopup = XnatTextPopup('<b>Checking files...</b>')
self.postDownloadPopup = XnatTextPopup(
'<b>Processing. Data will load automatically.</b>')
def selectExtension(self, path=None):
if path is None or isinstance(path, bool):
path = qt.QFileDialog.getExistingDirectory(self.parent.window(),
"Select Extension...",
self.extensionLocation)
if not len(path):
return False
# Attempt to open extension
try:
repo = SlicerWizard.Utilities.getRepo(path)
if repo is None:
xd = SlicerWizard.ExtensionDescription(sourcedir=path)
else:
xd = SlicerWizard.ExtensionDescription(repo=repo)
path = SlicerWizard.Utilities.localRoot(repo)
xp = SlicerWizard.ExtensionProject(path)
except:
md = qt.QMessageBox(self.parent.window())
md.icon = qt.QMessageBox.Critical
md.text = "Failed to open extension '%s'." % path
md.detailedText = traceback.format_exc()
md.standardButtons = qt.QMessageBox.Close
md.exec_()
return False
# Enable and show edit section
self.editorCollapsibleButton.enabled = True
self.editorCollapsibleButton.collapsed = False
# Populate edit information
self.extensionNameField.text = xp.project
self.extensionLocationField.text = path
if xd.scmurl == "NA":
if repo is None:
repoText = "(none)"
elif hasattr(repo, "remotes"):
repoText = "(local git repository)"
else:
repoText = "(unknown local repository)"
self.extensionRepositoryField.clear()
self.extensionRepositoryField.placeholderText = repoText
else:
self.extensionRepositoryField.text = xd.scmurl
ri = self.extensionContentsModel.setRootPath(path)
self.extensionContentsView.setRootIndex(ri)
w = self.extensionContentsView.width
self.extensionContentsView.setColumnWidth(0, (w * 4) / 9)
# Prompt to load scripted modules from extension
self.loadModules(path)
# Store extension location, project and description for later use
self.extensionProject = xp
self.extensionDescription = xd
self.extensionLocation = path
return True
def showErrorMessage(self, windowTitle, text):
answer = qt.QMessageBox().question(
slicer.app.activeWindow(), windowTitle, text,
qt.QMessageBox.Ok | qt.QMessageBox.Cancel)
return answer
def setup(self):
"""Init the widget """
# ScriptedLoadableModuleWidget.setup(self)
settings = qt.QSettings()
if (SlicerUtil.IsDevelopment):
# reload button
self.reloadButton = qt.QPushButton("Reload")
self.reloadButton.toolTip = "Reload this module."
self.reloadButton.name = "Reload"
self.layout.addWidget(self.reloadButton)
self.reloadButton.connect('clicked()', self.onBtnReloadClicked)
self.logic = PicasaSnapLogic()
self.__addObservers__()
######## Credentials
self.credentialsCollapsibleButton = ctk.ctkCollapsibleButton()
self.credentialsCollapsibleButton.text = "Credentials"
self.layout.addWidget(self.credentialsCollapsibleButton)
self.credentialsLayout = qt.QFormLayout(
self.credentialsCollapsibleButton)
self.isUserLogged = False
self.loginLineEdit = qt.QLineEdit()
self.credentialsLayout.addRow("Login: "******"Password: "******"Remember my credentials")
self.rememberCredentialsCheckBox.toolTip = "Check for an automatic login when the application starts"
self.loginButton = qt.QPushButton("Login")
self.loginButton.toolTip = "Login in Picassa service (Google credentials)"
self.logoutButton = qt.QPushButton("Logout")
self.logoutButton.toolTip = "Logout to connect with another user's credentials"
# Add all the items, they will be shown/hidden in refreshCredentialsUI function
self.credentialsLayout.addRow(self.rememberCredentialsCheckBox,
self.loginButton)
self.credentialsLayout.addRow(None, self.logoutButton)
######## Snapshots (main frame)
self.mainCollapsibleButton = ctk.ctkCollapsibleButton()
self.mainCollapsibleButton.text = "Snapshots"
self.layout.addWidget(self.mainCollapsibleButton)
self.mainLayout = qt.QVBoxLayout(self.mainCollapsibleButton)
############### Current snapshots
self.currentSnapshotsFrame = qt.QFrame()
self.currentSnapshotsLayout = qt.QVBoxLayout()
self.currentSnapshotsFrame.setLayout(self.currentSnapshotsLayout)
self.currentSnapshotsFrame.setFrameShape(qt.QFrame.StyledPanel)
self.mainLayout.addWidget(self.currentSnapshotsFrame)
self.snapshotsLabel = qt.QLabel("Snapshots to upload:")
self.snapshotsLabel.setStyleSheet(
"font-weight:bold; font-size:14px; margin-bottom:10px")
self.currentSnapshotsLayout.addWidget(self.snapshotsLabel)
# Subframe that contains the checkbox list
self.currentSnapshotsInnerFrame = qt.QFrame()
self.currentSnapshotsInnerLayout = qt.QVBoxLayout()
self.currentSnapshotsInnerFrame.setLayout(
self.currentSnapshotsInnerLayout)
self.currentSnapshotsLayout.addWidget(self.currentSnapshotsInnerFrame)
self.noItemsLabel = qt.QLabel(
"(There are not any snapshots at the moment)")
# Add the label by default. It will be hidden if there is any snapshot
self.currentSnapshotsInnerLayout.addWidget(self.noItemsLabel)
self.loadExistingSnapshotsFirstLoad()
############### Albums
# Try to login before getting the albums
self.login()
msgBox = None
if self.isUserLogged:
# Show message box while loading the data
msgBox = qt.QMessageBox(qt.QMessageBox.Information, 'Login',
'Connecting with Picasa. Please wait...',
qt.QMessageBox.Cancel)
msgBox.show()
try:
self.albumNameFrame = qt.QFrame()
self.albumNameLayout = qt.QHBoxLayout()
self.albumNameFrame.setLayout(self.albumNameLayout)
self.albumNameFrame.setFrameShape(qt.QFrame.StyledPanel)
self.albumNameLabel = qt.QLabel("Album name:")
self.albumNameLabel.setStyleSheet("font-weight:bold;")
self.albumNamesComboBox = qt.QComboBox()
self.loadAlbums()
self.albumNameLayout.addWidget(self.albumNameLabel)
self.albumNameLayout.addWidget(self.albumNamesComboBox)
self.mainLayout.addWidget(self.albumNameFrame)
############### Tags
self.tagsFrame = qt.QFrame()
self.tagsLayout = qt.QGridLayout()
self.tagsFrame.setLayout(self.tagsLayout)
self.tagsFrame.setFrameShape(qt.QFrame.StyledPanel)
self.tagsLabel = qt.QLabel(
"Tags (select all that apply, you can filter o create new tags):"
)
self.tagsLabel.setStyleSheet(
"font-weight: bold; margin-bottom: 10px; margin-top: 5px")
self.tagsLayout.addWidget(self.tagsLabel, 0, 0, 1, 3)
# Add input to filter tags and button to add a new one
self.tagsFilterLineEdit = qt.QLineEdit()
self.tagsFilterLineEdit.toolTip = "Type here to filter your tags. If you press the return key all the visible tags will be checked"
#self.tagsFilterLineEdit.setStyleSheet(style)
self.tagsLayout.addWidget(self.tagsFilterLineEdit, 1, 0, 1, 2)
self.newTagButton = qt.QPushButton("New tag")
#self.newTagButton.setStyleSheet("background-color: #5D74C6; color:white")
self.newTagButton.setIconSize(qt.QSize(20, 20))
self.newTagButton.setIcon(
qt.QIcon(self.CIP_ICON_DIR + "/Plus - 48.png"))
self.newTagButton.setFixedWidth(75)
self.newTagButton.toolTip = "Add a new tag (the tag will not be created until you upload any picture with it)"
self.tagsLayout.addWidget(self.newTagButton, 1, 2)
self.loadTags()
############### Upload snapshots controls
self.uploadSnapsButtonFrame = qt.QFrame()
self.uploadSnapsLayout = qt.QHBoxLayout()
self.uploadSnapsButtonFrame.setLayout(self.uploadSnapsLayout)
#self(qt.QFrame.HLine)
self.mainLayout.addWidget(self.uploadSnapsButtonFrame)
self.uploadSnapshotsButton = qt.QPushButton()
self.uploadSnapshotsButton.text = "Upload to Picasa!"
self.uploadSnapshotsButton.toolTip = "Upload selected screenshots to Picassa"
self.uploadSnapshotsButton.setStyleSheet(
"background-color: #5D74C6; color: white; font-weight: bold; font-size:14px"
)
self.uploadSnapshotsButton.setIcon(
qt.QIcon(self.CIP_ICON_DIR + "/Upload - 64.png"))
self.uploadSnapshotsButton.setIconSize(qt.QSize(24, 24))
self.uploadSnapshotsButton.setFixedSize(170, 35)
self.uploadSnapsLayout.addWidget(self.uploadSnapshotsButton)
############### Progress bar
self.progressBar = qt.QProgressDialog()
self.progressBar.setMinimum(0)
self.progressBar.setMinimumDuration(0)
self.progressBar.setWindowModality(True)
# Check for updates in CIP
#autoUpdate = SlicerUtil.settingGetOrSetDefault("PicasaSnap", "AutoUpdate", 1)
#uw = AutoUpdateWidget(parent=self.parent, autoUpdate=autoUpdate)
#uw.addAutoUpdateCheckObserver(self.onAutoUpdateStateChanged)
# self.uploadProgressFrame = qt.QFrame()
# self.uploadProgressLayout = qt.QVBoxLayout()
# self.uploadProgressFrame.setLayout(self.uploadProgressLayout)
#
# # Gif image
# self.imUploading = qt.QMovie("%s/loading.gif" % self.CIP_ICON_DIR, qt.QByteArray())
# # Label to contain the gif
# self.lblImLoading = qt.QLabel()
# # Fix the dimensions of the image (by fixing the dimensions of the label that contains it)
# self.lblImLoading.setFixedWidth(40)
# # Other image parameters
# self.imUploading.setCacheMode(qt.QMovie.CacheAll)
# self.imUploading.setSpeed(100)
# # Assign the label to the image (don't start it yet, it will be started when we are uploading)
# self.lblImLoading.setMovie(self.imUploading)
# #self.imUploading.start()
# self.uploadProgressLayout.addWidget(self.lblImLoading)
#
# # Label that will show the progress
# self.lblUploading = qt.QLabel("Uploading %i/%i images...")
# self.uploadProgressLayout.addWidget(self.lblUploading)
#
# Cancel uploading button
# self.btnCancelUpload = qt.QPushButton("Cancel")
# self.btnCancelUpload.toolTip = "Cancel the process"
# self.btnCancelUpload.setFixedWidth(100)
# self.uploadProgressLayout.addWidget(self.btnCancelUpload)
# self.mainLayout.addWidget(self.uploadProgressFrame)
#
# # Hide the progress frame
# self.uploadProgressFrame.hide()
######## Connections
self.uploadSnapshotsButton.connect(
'clicked (bool)', self.onUploadSnapshotsButtonClicked)
self.loginButton.connect('clicked (bool)',
self.onLoginButtonClicked)
self.logoutButton.connect('clicked (bool)',
self.onLogoutButtonClicked)
self.loginLineEdit.returnPressed.connect(
self.onLoginPasswordReturnKeyPressed)
self.passwordLineEdit.returnPressed.connect(
self.onLoginPasswordReturnKeyPressed)
self.albumNamesComboBox.connect("currentIndexChanged (int)",
self.onAlbumsCurrentIndexChanged)
self.newTagButton.connect('clicked (bool)',
self.onNewTagButtonClicked)
self.tagsFilterLineEdit.connect('textEdited (QString)',
self.onFilterTagsEdited)
self.tagsFilterLineEdit.returnPressed.connect(
self.onFilterTagsReturnKeyPressed)
# Add vertical spacer
self.layout.addStretch(1)
finally:
# Hide MesageBox if it was visible
if msgBox:
msgBox.close()
def onStartStopDicomPeer(self, flag):
if flag:
import os
self.startStopDicomPeerButton.setEnabled(False)
dicomFilesDirectory = slicer.app.temporaryPath
configFilePath = dicomFilesDirectory + '/Dcmtk-db/dcmqrscp.cfg'
processCurrentPath = dicomFilesDirectory + '/Dcmtk-db/'
msgBox = qt.QMessageBox()
msgBox.setText(
'Do you want to choose local DCMTK database folder?')
msgBox.setStandardButtons(qt.QMessageBox.Yes | qt.QMessageBox.No)
val = msgBox.exec_()
if (val == qt.QMessageBox.Yes):
print 'Yes'
dicomFilesDirectory = qt.QFileDialog.getExistingDirectory(
None, 'Select DCMTK database folder')
configFilePath = dicomFilesDirectory + '/dcmqrscp.cfg'
processCurrentPath = dicomFilesDirectory
else:
downloads = (
('http://slicer.kitware.com/midas3/download?items=18822',
'Dcmtk-db.zip'), )
print 'Downloading'
import urllib
for url, name in downloads:
filePath = slicer.app.temporaryPath + '/' + name
if not os.path.exists(filePath) or os.stat(
filePath).st_size == 0:
print 'Requesting download %s from %s...\n' % (name,
url)
urllib.urlretrieve(url, filePath)
print 'Finished with download'
print 'Unzipping'
qt.QDir().mkpath(dicomFilesDirectory)
slicer.app.applicationLogic().Unzip(filePath,
dicomFilesDirectory)
import subprocess
dcmqrscpExeOptions = (
'/bin',
'/../CTK-build/CMakeExternals/Install/bin',
'/../DCMTK-install/bin',
'/../DCMTK-build/bin',
)
dcmqrscpExePath = None
dcmqrscpExeName = '/dcmqrscp'
if slicer.app.os == 'win':
dcmqrscpExeName = dcmqrscpExeName + '.exe'
for path in dcmqrscpExeOptions:
testPath = slicer.app.slicerHome + path + dcmqrscpExeName
if os.path.exists(testPath):
dcmqrscpExePath = testPath
break
if not dcmqrscpExePath:
raise (UserWarning("Could not find dcmqrscp executable"))
args = (dcmqrscpExePath, '-c', configFilePath)
print 'Start DICOM peer'
self.popen = subprocess.Popen(args,
stdout=subprocess.PIPE,
cwd=processCurrentPath)
self.startStopDicomPeerButton.setEnabled(True)
else:
print 'Stop DICOM peer'
self.popen.kill()
def init_fGrowCut(self):
self.emergencyStopFunc = None
self.dialogBox = qt.QMessageBox(
) #will display messages to draw users attention if he does anything wrong
self.dialogBox.setWindowTitle("Fast GrowCut Error")
self.dialogBox.setWindowModality(
qt.Qt.NonModal
) #will allow user to continue interacting with Slicer
# TODO: check this claim- might be causing leaks
# set the image, label nodes (this will not change although the user can
# alter what is bgrnd/frgrnd in editor)
# Confused about how info propagates UIarray to UIVol, not the other way, NEEDS AUTO TESTS
self.labelNode = self.editUtil.getLabelVolume(
) #labelLogic.GetVolumeNode()
self.backgroundNode = self.editUtil.getBackgroundVolume(
) #backgroundLogic.GetVolumeNode()
#perform safety check on right images/labels being selected, #set up images
#if red slice doesnt have a label or image, go no further
if type(self.backgroundNode) == type(None) or type(
self.labelNode) == type(None):
self.dialogBox.setText(
"Either Image (must be Background Image) or Label not set in slice views."
)
self.dialogBox.show()
if self.emergencyStopFunc:
self.emergencyStopFunc()
return
volumesLogic = slicer.modules.volumes.logic()
self.labelName = self.labelNode.GetName(
) # record name of label so user, cant trick us
self.imgName = self.backgroundNode.GetName()
if self.sliceViewMatchEditor(
self.sliceLogic
) == False: # do nothing, exit function if user has played with images
if self.emergencyStopFunc:
self.emergencyStopFunc()
return
# fast growcut shortcuts
resetFGC = qt.QKeySequence(qt.Qt.Key_R) # reset initialization flag
runFGC = qt.QKeySequence(qt.Qt.Key_G) # run fast growcut
editSeed = qt.QKeySequence(qt.Qt.Key_S) # edit seed labels
print " keys for reset init, run GC, edit seed are R,G, S"
self.qtkeyconnections = []
self.qtkeydefsGrowcut = [[resetFGC, self.resetFastGrowCutFlag],
[runFGC, self.runFastGrowCut],
[editSeed, self.editGrowCutSeed]]
for keydef in self.qtkeydefsGrowcut:
s = qt.QShortcut(keydef[0], slicer.util.mainWindow()
) # connect this qt event to mainWindow focus
#s.setContext(1)
s.connect('activated()', keydef[1])
#s.connect('activatedAmbiguously()', keydef[1])
self.qtkeyconnections.append(s)
self.fGCLabelMod_tag = self.sliceLogic.AddObserver(
"ModifiedEvent", self.FastGrowCutChangeLabelInput
) # put test listener on the whole window
# fast grow cut parameters
self.bSegmenterInitialized = "no"
self.bEditGrowCutSeed = True
self.currentMessage = ""
seedArray = slicer.util.array(self.labelName)
self.growCutSeedArray = seedArray.copy()
self.growCutSegArray = seedArray.copy()
self.growCutSeedArray[:] = 0
self.growCutSegArray[:] = 0
import vtkSlicerFastGrowCutModuleLogicPython
fastGCMod = vtkSlicerFastGrowCutModuleLogicPython.vtkFastGrowCutSeg()
fastGCMod.SetSourceVol(self.backgroundNode.GetImageData())
fastGCMod.SetSeedVol(self.labelNode.GetImageData())
fastGCMod.Initialization()
self.fastGCMod = fastGCMod
self.fastCrowCutCreated = True #tracks if completed the initializtion (so can do stop correctly) of KSlice
def ErrorPopup(message):
messageBox = qt.QMessageBox()
messageBox.critical(None, '', message)
def init_fCleverSeg(self):
slicer.util.showStatusMessage("Checking CleverSeg inputs...")
if not self.areInputsValid():
logging.warning(self.getInvalidInputsMessage())
background = self.editUtil.getBackgroundVolume()
labelInput = self.editUtil.getLabelVolume()
if not slicer.util.confirmOkCancelDisplay(
"Current image type is '{0}' and labelmap type is '{1}'. CleverSeg only works "
"reliably with 'short' type.\n\nIf the segmentation result is not satisfactory"
", then cast the image and labelmap to 'short' type (using Cast Scalar Volume "
"module) or install CleverSeg extension and use CleverSegEffect editor "
"tool.".format(
self.editUtil.getBackgroundVolume().GetImageData(
).GetScalarTypeAsString(),
self.editUtil.getLabelVolume().GetImageData().
GetScalarTypeAsString()),
windowTitle='Editor'):
logging.warning('CleverSeg is cancelled by the user')
return
self.emergencyStopFunc = None
self.dialogBox = qt.QMessageBox(
) # will display messages to draw users attention if he does anything wrong
self.dialogBox.setWindowTitle("CleverSeg Error")
self.dialogBox.setWindowModality(
qt.Qt.NonModal
) # will allow user to continue interacting with Slicer
# TODO: check this claim- might be causing leaks
# set the image, label nodes (this will not change although the user can
# alter what is bgrnd/frgrnd in editor)
# Confused about how info propagates UIarray to UIVol, not the other way, NEEDS AUTO TESTS
self.labelNode = self.editUtil.getLabelVolume(
) # labelLogic.GetVolumeNode()
self.backgroundNode = self.editUtil.getBackgroundVolume(
) # backgroundLogic.GetVolumeNode()
# perform safety check on right images/labels being selected, #set up images
# if red slice doesnt have a label or image, go no further
if type(self.backgroundNode) == type(None) or type(
self.labelNode) == type(None):
self.dialogBox.setText(
"Either Image (must be Background Image) or Label not set in slice views."
)
self.dialogBox.show()
if self.emergencyStopFunc:
self.emergencyStopFunc()
return
volumesLogic = slicer.modules.volumes.logic()
self.labelName = self.labelNode.GetName(
) # record name of label so user, cant trick us
self.imgName = self.backgroundNode.GetName()
if self.sliceViewMatchEditor(
self.sliceLogic
) == False: # do nothing, exit function if user has played with images
if self.emergencyStopFunc:
self.emergencyStopFunc()
return
# CleverSeg shortcuts
resetCS = qt.QKeySequence(qt.Qt.Key_R) # reset initialization flag
runCS = qt.QKeySequence(qt.Qt.Key_C) # run CleverSeg
editSeed = qt.QKeySequence(qt.Qt.Key_S) # edit seed labels
print " keys for reset init = R, run CS = C, edit seed = S"
self.qtkeyconnections = []
self.qtkeydefsCleverSeg = [[resetCS, self.resetCleverSegFlag],
[runCS, self.runCleverSeg],
[editSeed, self.editCleverSegSeed]]
for keydef in self.qtkeydefsCleverSeg:
s = qt.QShortcut(keydef[0], slicer.util.mainWindow()
) # connect this qt event to mainWindow focus
# s.setContext(1)
s.connect('activated()', keydef[1])
# s.connect('activatedAmbiguously()', keydef[1])
self.qtkeyconnections.append(s)
self.CSLabelMod_tag = self.sliceLogic.AddObserver(
"ModifiedEvent", self.CleverSegChangeLabelInput
) # put test listener on the whole window
# fast balanced growth parameters
self.bSegmenterInitialized = "no"
self.bEditCleverSegSeed = True
self.currentMessage = ""
seedArray = slicer.util.array(self.labelName)
self.CleverSegSeedArray = seedArray.copy()
self.CleverSegSegArray = seedArray.copy()
self.CleverSegSeedArray[:] = 0
self.CleverSegSegArray[:] = 0
import vtkSlicerCleverSegModuleLogicPython
cleverSegMod = vtkSlicerCleverSegModuleLogicPython.vtkCleverSeg()
cleverSegMod.SetSourceVol(self.backgroundNode.GetImageData())
cleverSegMod.SetSeedVol(self.labelNode.GetImageData())
cleverSegMod.Initialization()
self.cleverSegMod = cleverSegMod
self.cleverSegCreated = True # tracks if completed the initializtion (so can do stop correctly) of KSlice
def onEntry(self, comingFrom, transitionType):
'''
'''
super(EMSegmentStartSegmentationStep,
self).onEntry(comingFrom, transitionType)
targetNode = self.mrmlManager().GetWorkingDataNode(
).GetInputTargetNode()
alignedAtlasNode = self.mrmlManager().GetWorkingDataNode(
).GetAlignedAtlasNode()
if alignedAtlasNode and not self.mrmlManager(
).DoTargetAndAtlasDataTypesMatch(targetNode, alignedAtlasNode):
# error
messageBox = qt.QMessageBox.warning(
self, "Error",
"Scalar type mismatch for input images; all image scalar types must be the same (including input channels and aligned/resampled/casted atlas images)."
)
return
workingDirectory = self.mrmlManager().GetSaveWorkingDirectory()
if self.mrmlManager().GetSaveIntermediateResults():
# if we want to save the results directly, we have to check if the workingDirectory is setup correctly
if not workingDirectory:
# workingDirectory was not configured
messageBox = qt.QMessageBox.warning(
self, "Error",
"Saving intermediate results is turned on but no intermediate directory is selected."
)
return
elif not os.path.exists(workingDirectory):
# the workingDirectory path does not exist
messageBox = qt.QMessageBox.warning(
self, "Error",
"Saving intermediate results is turned on but the intermediate directory "
+ workingDirectory + " does not exist!")
return
if self.mrmlManager().GetAtlasNumberOfTrainingSamples() <= 0:
# compute the number of training samples
self.mrmlManager().ComputeAtlasNumberOfTrainingSamples()
# create output volumes
self.logic().CreateOutputVolumeNode()
# notify user
# qt.QMessageBox( qt.QMessageBox.NoIcon, "Please wait", "Please wait while the segmentation runs..", qt.QMessageBox.Ignore )
dialog = qt.QMessageBox()
dialog.setWindowTitle("Please wait")
dialog.setText("Please wait while the segmentation runs..")
dialog.setModal(False)
dialog.show()
slicer.app.processEvents()
# start the segmentation
returnValue = self.logic().StartSegmentationWithoutPreprocessing(
slicer.app.applicationLogic())
dialog.hide()
slicer.app.processEvents()
if returnValue != 0:
# something went wrong!
# error message!
messageBox = qt.QMessageBox.warning(
self, "Error", "Segmentation did not execute correctly!")
return
outputNode = self.mrmlManager().GetOutputVolumeNode()
if not outputNode:
messageBox = qt.QMessageBox.warning(self, "Error",
"Output node was not found!")
return
selectionNode = slicer.app.applicationLogic().GetSelectionNode()
#selectionNode.SetReferenceActiveVolumeID(bgVolumeID)
#selectionNode.SetReferenceSecondaryVolumeID( outputNode.GetID() )
selectionNode.SetReferenceActiveLabelVolumeID(outputNode.GetID())
slicer.app.applicationLogic().PropagateVolumeSelection()
# show foreground volume
numberOfCompositeNodes = slicer.mrmlScene.GetNumberOfNodesByClass(
'vtkMRMLSliceCompositeNode')
for n in xrange(numberOfCompositeNodes):
compositeNode = slicer.mrmlScene.GetNthNodeByClass(
n, 'vtkMRMLSliceCompositeNode')
if compositeNode:
# display a fade of foreground/background
compositeNode.SetForegroundOpacity(0.5)
Helper.Debug("All Done!")
workflow = self.workflow()
if not workflow:
Helper.Error("No valid workflow found!")
return False
# we go backward to display statistics
workflow.goBackward()
def checkVisSimTools(self):
# TODO: optimise this part to download only the missing files
# Check if elastix exist or download it
if isfile(self.elastixBinPath.strip()):
print("elastix binaries are found in " + self.elastixBinPath)
else:
print("elastix binaries are missing, trying to download ... ")
msg = qt.QMessageBox()
msg.setIcon(qt.QMessageBox.Information)
msg.setText("elastix binaries are missing!")
msg.setInformativeText(
"VisSimTools elastix binaries will be downloaded, this may take some time, please wait!"
)
msg.setWindowTitle("VisSimTools")
msg.exec_()
try:
print("Downloading VisSimTools elastix ...")
#cmd=" wget --no-check-certificate ""https://mtixnat.uni-koblenz.de/owncloud/index.php/s/3bYztVkSrJxdpDz/download"" -O ~/VisSimToolsTmp.zip"
vissimZip = expanduser("~/VisSimToolsTmp.zip")
with open(vissimZip, 'wb') as f:
uFile = urllib2.urlopen(self.elastixWebLink)
chunk = 10024096
while 1:
data = uFile.read(chunk)
f.write(data)
if not data:
f.close()
print "done!"
break
#endIf
print "Reading ... %s bytes" % len(data)
#endWhile
print("Extracting to user home ")
zip_ref = zipfile.ZipFile(vissimZip, 'r')
zip_ref.extractall(expanduser("~/"))
zip_ref.close()
#remove the downloaded zip file
os.remove(vissimZip)
except Exception as e:
print(
"Error: can not download and extract VisSimTools Elastix ..."
)
print(e)
return -1
#end try-except
#endif
# check if other files exist
if isfile(self.parsPath.strip()):
print("Other files are found !")
else:
print("Other files are missing, trying to download ... ")
msg = qt.QMessageBox()
msg.setIcon(qt.QMessageBox.Information)
msg.setText("Other files are missing!")
msg.setInformativeText(
"VisSimTools other files will be downloaded, this may take some time, please wait!"
)
msg.setWindowTitle("VisSimTools")
msg.exec_()
try:
print("Downloading VisSimTools others ...")
vissimZip = expanduser("~/VisSimToolsTmp.zip")
with open(vissimZip, 'wb') as f:
uFile = urllib2.urlopen(self.othersWebLink)
chunk = 10024096
while 1:
data = uFile.read(chunk)
f.write(data)
if not data:
f.close()
print "done!"
break
#endIf
print "Reading ... %s bytes" % len(data)
#endWhile
print("Extracting to user home ")
zip_ref = zipfile.ZipFile(vissimZip, 'r')
zip_ref.extractall(expanduser("~/"))
zip_ref.close()
#remove the downloaded zip file
os.remove(vissimZip)
# change permission of bin folder for Linux
if self.winOS == 0:
print("Making binaries executable for Linux ")
md = stat.S_IRWXU | stat.S_IRGRP | stat.S_IROTH | stat.S_IXGRP | stat.S_IXOTH
os.chmod(self.elastixBinPath.strip(), md)
os.chmod(self.transformixBinPath.strip(), md)
os.chmod(self.elxInvTransBinPath.strip(), md)
#endif
msg.setInformativeText(
"VisSimTools folder is downloaded and ready to use!")
msg.exec_()
except Exception as e:
print("Error: can not download and extract VisSimTools ...")
print(e)
return -1
def loadModules(self, path, depth=1):
# Get list of modules in specified path
modules = ModuleInfo.findModules(path, depth)
# Determine which modules in above are not already loaded
factory = slicer.app.moduleManager().factoryManager()
loadedModules = factory.instantiatedModuleNames()
candidates = [m for m in modules if m.key not in loadedModules]
# Prompt to load additional module(s)
if len(candidates):
dlg = LoadModulesDialog(self.parent.window())
dlg.setModules(candidates)
if dlg.exec_() == qt.QDialog.Accepted:
modulesToLoad = dlg.selectedModules
# Add module(s) to permanent search paths, if requested
if dlg.addToSearchPaths:
settings = slicer.app.revisionUserSettings()
rawSearchPaths = list(
settings.value("Modules/AdditionalPaths"))
searchPaths = [qt.QDir(path) for path in rawSearchPaths]
modified = False
for module in modulesToLoad:
rawPath = os.path.dirname(module.path)
path = qt.QDir(rawPath)
if not path in searchPaths:
searchPaths.append(path)
rawSearchPaths.append(rawPath)
modified = True
if modified:
settings.setValue("Modules/AdditionalPaths",
rawSearchPaths)
# Register requested module(s)
failed = []
for module in modulesToLoad:
factory.registerModule(qt.QFileInfo(module.path))
if not factory.isRegistered(module.key):
failed.append(module)
if len(failed):
md = qt.QMessageBox(self.parent.window())
md.icon = qt.QMessageBox.Critical
md.standardButtons = qt.QMessageBox.Close
md.windowTitle = "Module loading failed"
if len(failed) > 1:
md.text = "The following modules could not be registered:"
else:
md.text = "The '%s' module could not be registered:" % failed[
0].key
failedFormat = "<ul><li>%(key)s<br/>(%(path)s)</li></ul>"
md.informativeText = "".join(
[failedFormat % m.__dict__ for m in failed])
md.exec_()
return
# Instantiate and load requested module(s)
if not factory.loadModules(
[module.key for module in modulesToLoad]):
md = qt.QMessageBox(self.parent.window())
md.icon = qt.QMessageBox.Critical
md.standardButtons = qt.QMessageBox.Close
md.windowTitle = "Error loading module(s)"
md.text = (
"The module factory manager reported an error. "
"One or more of the requested module(s) and/or "
"dependencies thereof may not have been loaded.")
md.exec_()
