class DataReaderTest(unittest.TestCase):
def setUp(self):
self.reader = DataReader()
def tearDown(self):
del self.reader
def testDataReader(self):
path = os.path.dirname(os.path.abspath(__file__))
fileName = path + "/data/hi-3.mhd"
imageData = self.reader.GetImageData(fileName)
self.assertIsNotNone(imageData)
dimensions = imageData.GetDimensions()
self.assertEquals(dimensions, (21, 15, 9))
def testUnsupportedDataTypes(self):
self.assertRaises(Exception, self.reader.GetImageData, "data/hi-3.mrb")
def testSupportedDataTypes(self):
self.assertTrue(self.reader.IsExtensionSupported("mhd"))
self.assertTrue(self.reader.IsExtensionSupported("vti"))
self.assertTrue(self.reader.IsExtensionSupported("dcm"))
self.assertFalse(self.reader.IsExtensionSupported("mrb"))
self.assertFalse(self.reader.IsExtensionSupported("vtk"))
self.assertFalse(self.reader.IsExtensionSupported("raw"))
self.assertFalse(self.reader.IsExtensionSupported("dat"))
# def testDatFileFormat(self):
# path = os.path.dirname(os.path.abspath(__file__))
# fileName = path + "/data/present492x492x442.dat"
# imageData = self.reader.GetImageData(fileName)
# dimensions = imageData.GetDimensions()
# self.assertEquals(dimensions, (492, 492, 442))
def testVTIFileFormat(self):
path = os.path.dirname(os.path.abspath(__file__))
fileName = path + "/data/modelSegmentation.vti"
imageData = self.reader.GetImageData(fileName)
dimensions = imageData.GetDimensions()
self.assertEquals(dimensions, (376, 245, 206))
def testEmptyDirectory(self):
path = os.path.dirname(os.path.abspath(__file__))
fileName = path + "/data"
imageData = self.reader.GetImageData(fileName)
self.assertIsNone(imageData)
def testDICOMFileFormat(self):
path = os.path.dirname(os.path.abspath(__file__))
fileName = path + "/data/DICOM"
imageData = self.reader.GetImageData(fileName)
self.assertIsNotNone(imageData)
dimensions = imageData.GetDimensions()
self.assertEquals(dimensions, (320, 384, 11))
def setFile(self, fileName):
"""
:type fileName: str
"""
if fileName is None:
self.imageData = None
self.visualization = None
self.renderWidget.setData(self.imageData)
self.renderWidget.setVolumeVisualization(self.visualization)
self.dataChanged.emit(self.imageData)
self.visualizationChanged.emit(self.visualization)
return
# Read image data
dataReader = DataReader()
imageData = dataReader.GetImageData(fileName)
resizer = DataResizer()
self.imageData = resizer.ResizeData(imageData, maximum=25000000)
# Give the image data to the widget
self.renderWidget.setData(self.imageData)
self.dataChanged.emit(self.imageData)
# Set the render type
self.setVisualizationType(self.visualizationType)
def setFixedFile(self, fileName):
"""
:type fileName: str
"""
if fileName is None:
self.fixedImageData = None
self.fixedVisualization = None
self.visualization = None
self.visualizations = dict()
self.visualizationType = None
self.multiRenderWidget.setFixedData(self.fixedImageData)
self.multiRenderWidget.setVolumeVisualization(
self.fixedVisualization)
self.fixedDataChanged.emit(self.fixedImageData)
self.visualizationChanged.emit(self.visualization)
return
# Read image data
dataReader = DataReader()
imageData = dataReader.GetImageData(fileName)
# TODO: there should be a setting for this, either in project, per loaded
# data file or a general setting
resizer = DataResizer()
self.fixedImageData = resizer.ResizeData(imageData, maximum=25000000)
# Give the image data to the widget
self.multiRenderWidget.setFixedData(self.fixedImageData)
self.fixedDataChanged.emit(self.fixedImageData)
# Set the visualization type
self.setVisualizationType(self.visualizationType)
def exportDataAs(self):
"""
Opens a file dialog so that the user can provide a filename
for saving the transformed dataset to.
"""
fileType = FileTypeDialog.getFileType(self,
"Choose file type for export")
if len(fileType) == 0:
return
extension = "(*." + fileType + ")"
fileName, other = QFileDialog.getSaveFileName(
self, "Save registration result to...", "", extension)
if len(fileName) == 0:
return
self.showProgressBar("Exporting data...")
transform = self.multiDataWidget.transformations.completeTransform()
dataReader = DataReader()
imageData = dataReader.GetImageData(
ProjectController.Instance().currentProject.movingData)
transformer = DataTransformer()
outputData = transformer.TransformImageData(imageData, transform)
writer = DataWriter()
writer.WriteToFile(outputData, fileName, fileType)
self.hideProgressBar()
def imageData(self):
if not self.filename:
return None
if not self.__imageData:
dataReader = DataReader()
self.__imageData = dataReader.GetImageData(self._filename)
return self.__imageData
def transformation(self):
transformation = ParameterList()
transformation.append(Parameter("Transform", "AffineTransform"))
transformMatrix = self.transform.GetMatrix()
matrix = vtkMatrix4x4()
matrix.DeepCopy(transformMatrix)
matrix.Invert()
if isIdentity(matrix):
return None
elemList = listFromMatrix(matrix)
imageReader = DataReader()
imageData = imageReader.GetImageData(self.dataset)
if not imageData:
raise Exception("Could not create image data")
scalarType = imageData.GetScalarTypeAsString()
dimensions = list(imageData.GetDimensions())
bounds = list(imageData.GetBounds())
spacing = list(imageData.GetSpacing())
if not scalarType or not bounds or not spacing:
raise Exception("Could not get the needed parameters")
center = [(bounds[0] + bounds[1]) / 2.0, (bounds[2] + bounds[3]) / 2.0,
(bounds[4] + bounds[5]) / 2.0]
transformation.append(Parameter("NumberOfParameters", len(elemList)))
transformation.append(Parameter("TransformParameters", elemList))
transformation.append(
Parameter("InitialTransformParametersFileName",
"NoInitialTransform"))
transformation.append(Parameter("HowToCombineTransforms", "Compose"))
transformation.append(Parameter("MovingImageDimension", 3))
transformation.append(Parameter("FixedImageDimension", 3))
# The following options are from the dataset
transformation.append(
Parameter("FixedInternalImagePixelType", scalarType))
transformation.append(
Parameter("MovingInternalImagePixelType", scalarType))
transformation.append(Parameter("Size", dimensions))
transformation.append(Parameter("Spacing", spacing))
transformation.append(Parameter("CenterOfRotation", center))
return transformation
def testDataWriter(self):
path = os.path.dirname(os.path.abspath(__file__))
fileName = path + "/data/hi-3.mhd"
outputFolder = path + "/data/DataWriter"
exportFileName = outputFolder + "/output.mhd"
dataReader = DataReader()
imageData = dataReader.GetImageData(fileName)
fileType = DataReader.TypeMHD
self.writer.WriteToFile(imageData, exportFileName, fileType)
# Cleanup test directory
try:
if os.path.exists(outputFolder):
import shutil
shutil.rmtree(outputFolder)
except Exception, e:
raise e
def setMovingFile(self, fileName):
if fileName is None:
self.movingImageData = None
self.movingVisualization = None
self.multiRenderWidget.setMovingData(self.movingImageData)
self.multiRenderWidget.setVolumeVisualization(self.visualization)
self.movingDataChanged.emit(self.movingImageData)
self.visualizationChanged.emit(self.movingVisualization)
return
# Read image data
dataReader = DataReader()
# self.movingImageData = dataReader.GetImageData(fileName)
imageData = dataReader.GetImageData(fileName)
resizer = DataResizer()
self.movingImageData = resizer.ResizeData(imageData, maximum=25000000)
# Give the image data to the widget
self.multiRenderWidget.setMovingData(self.movingImageData)
self.movingDataChanged.emit(self.movingImageData)
# Set the visualization type
self.setVisualizationType(self.visualizationType)
def setFile(self, fileName):
"""
Slot that reads properties of the dataset and displays them in a few widgets.
"""
if fileName is None:
return
self.fileName = fileName
# Read info from dataset
# TODO: read out the real world dimensions in inch or cm
# TODO: scalar type (int, float, short, etc.)
imageReader = DataReader()
imageData = imageReader.GetImageData(fileName)
directory, name = os.path.split(fileName)
dimensions = imageData.GetDimensions()
minimum, maximum = imageData.GetScalarRange()
scalarType = imageData.GetScalarTypeAsString()
bins = DataAnalyzer.histogramForData(imageData, 256)
self.histogram = Histogram()
self.histogram.bins = bins
self.histogram.enabled = True
self.histogramWidget = HistogramWidget()
self.histogramWidget.setMinimumHeight(100)
self.histogramWidget.setHistogram(self.histogram)
self.histogramWidget.setAxeMode(bottom=HistogramWidget.AxeClear,
left=HistogramWidget.AxeLog)
Style.styleWidgetForTab(self.histogramWidget)
nameText = name
dimsText = "(" + str(dimensions[0]) + ", " + str(dimensions[1]) + ", " + str(dimensions[2]) + ")"
voxsText = str(dimensions[0] * dimensions[1] * dimensions[2])
rangText = "[" + str(minimum) + " : " + str(maximum) + "]"
typeText = scalarType
layout = self.layout()
if not layout:
# Create a new layout
layout = QGridLayout()
layout.setAlignment(Qt.AlignTop)
# Create string representations
nameLabels = []
nameLabels.append(QLabel("File name:"))
nameLabels.append(QLabel("Dimensions:"))
nameLabels.append(QLabel("Voxels:"))
nameLabels.append(QLabel("Range:"))
nameLabels.append(QLabel("Data type:"))
for label in nameLabels:
label.setAlignment(Qt.AlignRight | Qt.AlignVCenter)
# Create 'dynamic' labels
self.labelTitle = QLabel(nameText)
self.labelDimensions = QLabel(dimsText)
self.labelVoxels = QLabel(voxsText)
self.labelRange = QLabel(rangText)
self.labelType = QLabel(typeText)
index = 0
for label in nameLabels:
layout.addWidget(label, index, 0)
index += 1
layout.addWidget(self.labelTitle, 0, 1)
layout.addWidget(self.labelDimensions, 1, 1)
layout.addWidget(self.labelVoxels, 2, 1)
layout.addWidget(self.labelRange, 3, 1)
layout.addWidget(self.labelType, 4, 1)
layout.addWidget(self.histogramWidget, 5, 0, 1, 2)
widget = QWidget()
widget.setLayout(layout)
Style.styleWidgetForTab(widget)
self.scrollArea.setWidget(widget)
scrollLayout = QGridLayout()
scrollLayout.setSpacing(0)
scrollLayout.setContentsMargins(0, 0, 0, 0)
scrollLayout.addWidget(self.scrollArea)
self.setLayout(scrollLayout)
else:
# Just update the text for the 'dynamic' labels
self.labelTitle.setText(nameText)
self.labelDimensions.setText(dimsText)
self.labelVoxels.setText(voxsText)
self.labelRange.setText(rangText)
self.labelType.setText(typeText)
def setFile(self, fileName):
"""
Slot that reads properties of the dataset and displays them in a few widgets.
"""
if fileName is None:
return
# Read info from dataset
# TODO: read out the real world dimensions in inch or cm
# TODO: scalar type (int, float, short, etc.)
imageReader = DataReader()
imageData = imageReader.GetImageData(fileName)
directory, name = os.path.split(fileName)
dimensions = imageData.GetDimensions()
minimum, maximum = imageData.GetScalarRange()
bins = DataAnalyzer.histogramForData(imageData, 256)
self.histogram = Histogram()
self.histogram.bins = bins
self.histogram.enabled = True
self.histogramWidget = HistogramWidget()
self.histogramWidget.setHistogram(self.histogram)
self.histogramWidget.setAxeMode(bottom=HistogramWidget.AxeClear,
left=HistogramWidget.AxeLog)
Style.styleWidgetForTab(self.histogramWidget)
nameText = name
dimsText = "(" + str(dimensions[0]) + ", " + str(dimensions[1]) + ", " + str(dimensions[2]) + ")"
voxsText = str(dimensions[0] * dimensions[1] * dimensions[2])
rangText = "[" + str(minimum) + " : " + str(maximum) + "]"
layout = self.layout()
if not layout:
# Create a new layout
layout = QGridLayout()
layout.setAlignment(Qt.AlignTop)
# Create string representations
nameField = QLabel("File name:")
dimsField = QLabel("Dimensions:")
voxsField = QLabel("Voxels:")
rangField = QLabel("Range:")
nameField.setAlignment(Qt.AlignRight | Qt.AlignVCenter)
dimsField.setAlignment(Qt.AlignRight | Qt.AlignVCenter)
voxsField.setAlignment(Qt.AlignRight | Qt.AlignVCenter)
rangField.setAlignment(Qt.AlignRight | Qt.AlignVCenter)
# Create 'dynamic' labels
self.labelTitle = QLabel(nameText)
self.labelDimensions = QLabel(dimsText)
self.labelVoxels = QLabel(voxsText)
self.labelRange = QLabel(rangText)
layout.addWidget(nameField, 0, 0)
layout.addWidget(dimsField, 1, 0)
layout.addWidget(voxsField, 2, 0)
layout.addWidget(rangField, 3, 0)
layout.addWidget(self.labelTitle, 0, 1)
layout.addWidget(self.labelDimensions, 1, 1)
layout.addWidget(self.labelVoxels, 2, 1)
layout.addWidget(self.labelRange, 3, 1)
layout.addWidget(self.histogramWidget, 4, 0, 1, 2)
self.setLayout(layout)
else:
# Just update the text for the 'dynamic' labels
self.labelTitle.setText(nameText)
self.labelDimensions.setText(dimsText)
self.labelVoxels.setText(voxsText)
self.labelRange.setText(rangText)