def __init__(self, parent):
ScriptedLoadableModuleWidget.__init__(self, parent)
self.logic = ProcessesLogic()
thisPath = qt.QFileInfo(__file__).path()
self.defaultPath = os.path.join(thisPath, "Resources",
"ProcessScripts", "filter.slicer.py")
self.nodeObserverTag = None
def registerSlicerURLHandler():
"""
Registers file associations and applicationName:// protocol (e.g., Slicer://)
with this executable. This allows Kheops (https://demo.kheops.online) open
images selected in the web browser directly in Slicer.
For now, only implemented on Windows.
"""
if os.name == 'nt':
launcherPath = qt.QDir.toNativeSeparators(
qt.QFileInfo(
slicer.app.launcherExecutableFilePath).absoluteFilePath())
reg = qt.QSettings(f"HKEY_CURRENT_USER\\Software\\Classes",
qt.QSettings.NativeFormat)
reg.setValue(f"{slicer.app.applicationName}/.",
f"{slicer.app.applicationName} supported file")
reg.setValue(f"{slicer.app.applicationName}/URL protocol", "")
reg.setValue(f"{slicer.app.applicationName}/shell/open/command/.",
f"\"{launcherPath}\" \"%1\"")
reg.setValue(f"{slicer.app.applicationName}/DefaultIcon/.",
f"{slicer.app.applicationName}.exe,0")
for ext in ['mrml', 'mrb']:
reg.setValue(f".{ext}/.", f"{slicer.app.applicationName}")
reg.setValue(f".{ext}/Content Type", f"application/x-{ext}")
else:
raise NotImplementedError()
def test_VolumeProcesses(self):
self.delayDisplay("Starting the Volume test")
import SampleData
volumeNode = SampleData.downloadSample("MRHead")
def onProcessesCompleted(testClass):
# when test finishes, we succeeded!
testClass.delayDisplay('Test passed!')
logic = ProcessesLogic(
completedCallback=lambda: onProcessesCompleted(self))
thisPath = qt.QFileInfo(__file__).path()
scriptPath = os.path.join(thisPath, "Resources", "ProcessScripts",
"volumeFilter.slicer.py")
for radius in range(5):
filterProcess = VolumeFilterProcess(scriptPath, volumeNode,
radius * 5)
logic.addProcess(
VolumeFilterProcess(scriptPath, volumeNode, radius))
logic.run()
logic.waitForFinished() # Optional
def createTempDirectory(self):
tempDir = qt.QDir(self.getTempDirectoryBase())
tempDirName = qt.QDateTime().currentDateTime().toString("yyyyMMdd_hhmmss_zzz")
fileInfo = qt.QFileInfo(qt.QDir(tempDir), tempDirName)
dirPath = fileInfo.absoluteFilePath()
qt.QDir().mkpath(dirPath)
return dirPath
def getTempDirectoryBase(self, bySlicer=True):
if bySlicer:
import qt, slicer
tempDir = qt.QDir(slicer.app.temporaryPath)
fileInfo = qt.QFileInfo(qt.QDir(tempDir), "RadPathFusion")
dirPath = fileInfo.absoluteFilePath()
qt.QDir().mkpath(dirPath)
return dirPath
def pathsFromMimeData(mimeData):
filesToAdd = []
acceptedFileExtensions = ['jpg', 'jpeg', 'tif', 'tiff', 'png', 'bmp']
if mimeData.hasFormat('text/uri-list'):
urls = mimeData.urls()
for url in urls:
localPath = url.toLocalFile() # convert QUrl to local path
pathInfo = qt.QFileInfo()
pathInfo.setFile(localPath) # information about the path
if pathInfo.isDir(
): # if it is a directory we add the files to the dialog
directory = qt.QDir(localPath)
nameFilters = [
'*.' + ext for ext in acceptedFileExtensions
]
filenamesInFolder = directory.entryList(
nameFilters, qt.QDir.Files, qt.QDir.Name)
for filenameInFolder in filenamesInFolder:
filesToAdd.append(
directory.absoluteFilePath(filenameInFolder))
else:
ext = pathInfo.suffix().lower()
if ext in acceptedFileExtensions:
filesToAdd.append(localPath)
# Filter out files that are known to cause complications
# Currently, there is only one rule, but it is expected that more filtering rules wil be added in the future.
filteredFilesToAdd = []
for filePath in filesToAdd:
fileName = qt.QFileInfo(filePath).fileName()
# Ignore cone-beam image in Bruker Skyscan folder
# such as `left_side_damaged__rec_spr.bmp`
if fileName.endswith("spr.bmp"):
# skip this file
logging.debug(
f"Skipping {filePath} - it looks like a Bruker Skyscan cone-beam image, not an image slice"
)
continue
filteredFilesToAdd.append(filePath)
return filteredFilesToAdd
def foldersFromMimeData(mimeData, acceptFiles=False):
directoriesToAdd = []
if mimeData.hasFormat('text/uri-list'):
urls = mimeData.urls()
for url in urls:
localPath = url.toLocalFile() # convert QUrl to local path
pathInfo = qt.QFileInfo()
pathInfo.setFile(localPath) # information about the path
if pathInfo.isDir(): # if it is a directory we add the files to the dialog
directoriesToAdd.append(localPath)
elif acceptFiles:
directoriesToAdd.append(pathInfo.absolutePath())
return directoriesToAdd
def isMimeDataAccepted(self):
"""Checks the dropped data and returns true if it is one or
more directories"""
self.directoriesToAdd = []
mimeData = self.qSlicerFileDialog.mimeData()
if mimeData.hasFormat('text/uri-list'):
urls = mimeData.urls()
for url in urls:
localPath = url.toLocalFile() # convert QUrl to local path
pathInfo = qt.QFileInfo()
pathInfo.setFile(localPath) # information about the path
if pathInfo.isDir(): # if it is a directory we add the files to the dialog
self.directoriesToAdd.append(localPath)
self.qSlicerFileDialog.acceptMimeData(len(self.directoriesToAdd) != 0)
def tempDirectory(self,key='__SlicerTestTemp__',tempDir=None,includeDateTime=False):
"""Come up with a unique directory name in the temp dir and make it and return it
# TODO: switch to QTemporaryDir in Qt5.
Note: this directory is not automatically cleaned up
"""
if not tempDir:
tempDir = qt.QDir(slicer.app.temporaryPath)
tempDirName = key
if includeDateTime:
key += qt.QDateTime().currentDateTime().toString("yyyy-MM-dd_hh+mm+ss.zzz")
fileInfo = qt.QFileInfo(qt.QDir(tempDir), tempDirName)
dirPath = fileInfo.absoluteFilePath()
qt.QDir().mkpath(dirPath)
return dirPath
def downloadFile(self, dlUrl):
import urllib
# Set download directory to a folder in Slicer cache
destinationDir = slicer.mrmlScene.GetCacheManager().GetRemoteCacheDirectory()
fileInfo = qt.QFileInfo(dlUrl.path())
destinationFilePath = destinationDir + "/" + fileInfo.fileName()
logging.info("Downloading model file: {0}".format(destinationFilePath))
self.downloadProgressBar.show()
urllib.urlretrieve(dlUrl.toString(), destinationFilePath, self.reportProgress)
self.downloadProgressBar.close()
return destinationFilePath
def createTempDirectory(self, bySlicer=True):
if bySlicer:
import qt, slicer
tempDir = qt.QDir(self.getTempDirectoryBase(bySlicer))
tempDirName = qt.QDateTime().currentDateTime().toString(
"yyyyMMdd_hhmmss_zzz")
fileInfo = qt.QFileInfo(qt.QDir(tempDir), tempDirName)
dirPath = fileInfo.absoluteFilePath()
qt.QDir().mkpath(dirPath)
# Write inputs
inputDir = os.path.join(dirPath, 'input')
qt.QDir().mkpath(inputDir)
resultTransformDir = os.path.join(dirPath, 'result-transform')
qt.QDir().mkpath(resultTransformDir)
resultResampleDir = os.path.join(dirPath, 'result-resample')
qt.QDir().mkpath(resultResampleDir)
return dirPath, inputDir, resultTransformDir, resultResampleDir
def test_ModelProcesses(self):
self.delayDisplay("Starting the Model test")
layoutManager = slicer.app.layoutManager()
layoutManager.setLayout(
slicer.vtkMRMLLayoutNode.SlicerLayoutOneUp3DView)
modelNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLModelNode")
modelNode.CreateDefaultDisplayNodes()
sphereSource = vtk.vtkSphereSource()
sphereSource.SetRadius(10)
sphereSource.SetThetaResolution(50)
sphereSource.SetPhiResolution(50)
sphereSource.Update()
modelNode.SetAndObservePolyData(sphereSource.GetOutputDataObject(0))
def onProcessesCompleted(testClass):
# when first test finishes, run second test
testClass.delayDisplay('Test passed!')
testClass.setUp()
testClass.test_VolumeProcesses()
logic = ProcessesLogic(
completedCallback=lambda: onProcessesCompleted(self))
thisPath = qt.QFileInfo(__file__).path()
scriptPath = os.path.join(thisPath, "Resources", "ProcessScripts",
"modelFilter.slicer.py")
for iteration in range(50):
filterProcess = ModelFilterProcess(scriptPath, modelNode,
iteration)
logic.addProcess(filterProcess)
logic.run()
def getTempDirectoryBase(self): tempDir = qt.QDir(slicer.app.temporaryPath) fileInfo = qt.QFileInfo(qt.QDir(tempDir), "Elastix") dirPath = fileInfo.absoluteFilePath() qt.QDir().mkpath(dirPath) return dirPath
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(
_settingsList(settings,
"Modules/AdditionalPaths",
convertToAbsolutePaths=True))
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",
slicer.app.toSlicerHomeRelativePaths(
rawSearchPaths))
# Enable developer mode (shows Reload&Test section, etc.), if requested
if dlg.enableDeveloperMode:
qt.QSettings().setValue('Developer/DeveloperMode', 'true')
# 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):
if len(failed) > 1:
text = "The following modules could not be registered:"
else:
text = "The '%s' module could not be registered:" % failed[
0].key
failedFormat = "<ul><li>%(key)s<br/>(%(path)s)</li></ul>"
detailedInformation = "".join(
[failedFormat % m.__dict__ for m in failed])
slicer.util.errorDisplay(
text,
parent=self.parent.window(),
windowTitle="Module loading failed",
standardButtons=qt.QMessageBox.Close,
informativeText=detailedInformation)
return
# Instantiate and load requested module(s)
if not factory.loadModules(
[module.key for module in modulesToLoad]):
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.")
slicer.util.errorDisplay(
text,
parent=self.parent.window(),
windowTitle="Error loading module(s)",
standardButtons=qt.QMessageBox.Close)
