def load_image_dir(self, dicom_dir):
VTK_DATA_ROOT = vtkGetDataRoot()
self.reader.SetDirectoryName(dicom_dir)
# self.reader.SetFilePrefix(VTK_DATA_ROOT + "/Data/headsq/quarter") # UNIX FRIENDLY
self.reader.SetFilePrefix(VTK_DATA_ROOT +
r"\Data\headsq\quarter") # WINDOWS FRIENDLY
self.reader.SetDataExtent(0, 63, 0, 63, 1, 93)
self.reader.SetDataSpacing(3.2, 3.2, 1.5)
self.reader.SetDataOrigin(0.0, 0.0, 0.0)
self.reader.SetDataScalarTypeToUnsignedShort()
self.reader.UpdateWholeExtent()
self.reader.Update()
self.current_image = self.reader.getOutput()
def read_image(self, image_path=None, orientation="axial"):
if image_path is None:
# self.folder = "/Users/nandana/Downloads/image_ex" #NANDANA PATH
image_folder = r"O:\personal\wasil\supervise\dluximon\miu_viewer\image_ex"
else:
# dicom_seri = os.path.join(image_path, "dicom.seri")
# if os.path.exists(dicom_seri):
# QIA version of loading
self.image_folder = image_path
self.load_image_dir(image_folder)
### Temporary to try to change the voxel values
image = self.reader.GetOutput()
VTK_DATA_ROOT = vtkGetDataRoot()
# self.reader2.SetDirectoryName(dicom_dir)
# self.reader.SetFilePrefix(VTK_DATA_ROOT + "/Data/headsq/quarter") # UNIX FRIENDLY
# self.reader2.SetFilePrefix(VTK_DATA_ROOT + r"\Data\headsq\quarter") # WINDOWS FRIENDLY
# self.reader2.SetDataExtent(0, 63, 0, 63, 1, 93)
# self.reader2.SetDataSpacing(3.2, 3.2, 1.5)
# self.reader2.SetDataOrigin(0.0, 0.0, 0.0)
# self.reader2.SetDataScalarTypeToUnsignedShort()
# self.reader2.UpdateWholeExtent()
# self.reader2.Update()
# image_temp = self.reader2.GetOutput()
image2 = vtk.vtkImageData()
# image2.CopyStructure(image)
# image2.ShallowCopy(image_temp) # need this if i make from vtkimagedata
image2.ShallowCopy(image) # need this if i make from vtkimagedata
image2.SetSpacing(.6, .6, 1)
image2.SetExtent(0, 100, 0, 100, 0, 100) #
image2.SetOrigin(0, 0, 0)
image2.SetDirectionMatrix(image.GetDirectionMatrix()) # hhmmmm
extent = image2.GetExtent()
imageData = vtk.vtkImageData()
imageData.SetDimensions(100, 100, 100)
if vtk.VTK_MAJOR_VERSION <= 5:
imageData.SetNumberOfScalarComponents(1)
imageData.SetScalarTypeToDouble()
else:
imageData.AllocateScalars(vtk.VTK_DOUBLE, 1)
dims = imageData.GetDimensions()
# Fill every entry of the image data with "2.0"
for z in range(dims[2]):
for y in range(dims[1]):
for x in range(dims[0]):
if image.GetScalarComponentAsDouble(x, y, z, 0) > -100:
imageData.SetScalarComponentFromDouble(
x, y, z, 0, 1000)
else:
imageData.SetScalarComponentFromDouble(x, y, z, 0, 0)
imageData.SetSpacing(.6, .6, 1)
imageData.SetExtent(0, 100, 0, 100, 0, 100) #
imageData.SetOrigin(0, 0, 0)
imageData.SetDirectionMatrix(image.GetDirectionMatrix()) # hhmmmm
self.imageData = imageData
self.img_reslice.SetInputData(0, self.imageData)
self.img_reslice.SetOutputDimensionality(2)
self.img_reslice.SetInterpolationModeToLinear()
self.roi_reslice.SetInputData(0, self.reader.GetOutput())
self.roi_reslice.SetOutputDimensionality(2)
self.roi_reslice.SetInterpolationModeToLinear()
self.window.Render()
self.center = self.calculate_center()
self.update_view(
orientation=orientation) #TODO: it is not update_view anymore
if not self.image_loaded:
self.interactor_style.AddObserver("MouseWheelForwardEvent",
self.scroll_forward_callback)
self.interactor_style.AddObserver("MouseWheelBackwardEvent",
self.scroll_backward_callback)
self.interactor_style.AddObserver("MouseMoveEvent",
self.mouse_move_callback)
self.interactor_style.AddObserver("KeyPressEvent",
self.key_press_callback)
self.interactor_style.AddObserver("LeftButtonPressEvent",
self.left_press_callback)
self.window.AddObserver("ModifiedEvent", self.window_mod_callback)
self.image_loaded = True
def main():
VTK_DATA_ROOT = vtkGetDataRoot()
folder = "/Users/nandana/Downloads/image_ex"
#read dicom files from specified directory
reader = vtkDICOMImageReader()
reader.SetDirectoryName(folder)
reader.SetFilePrefix(VTK_DATA_ROOT + "/Data/headsq/quarter")
reader.SetDataExtent(0, 63, 0, 63, 1, 93)
reader.SetDataSpacing(3.2, 3.2, 1.5)
reader.SetDataOrigin(-150.0, 150.0, 3.0)
reader.SetDataScalarTypeToUnsignedShort()
reader.UpdateWholeExtent()
# Calculate the center of the volume
reader.Update()
(xMin, xMax, yMin, yMax, zMin,
zMax) = reader.GetExecutive().GetWholeExtent(
reader.GetOutputInformation(0))
(xSpacing, ySpacing, zSpacing) = reader.GetOutput().GetSpacing()
(x0, y0, z0) = reader.GetOutput().GetOrigin()
center = [
x0 + xSpacing * 0.5 * (xMin + xMax),
y0 + ySpacing * 0.5 * (yMin + yMax),
z0 + zSpacing * 0.5 * (zMin + zMax)
]
yd = ((yMax - yMin) + 1) * ySpacing
"""
# Matrices for axial, coronal, sagittal, oblique view orientations
axial = vtkMatrix4x4()
axial.DeepCopy((1, 0, 0, center[0],
0, 1, 0, center[1],
0, 0, 1, center[2],
0, 0, 0, 1))
coronal = vtkMatrix4x4()
coronal.DeepCopy((1, 0, 0, center[0],
0, 0, 1, center[1],
0,-1, 0, center[2],
0, 0, 0, 1))
sagittal = vtkMatrix4x4
sagittal.DeepCopy((0, 0,-1, center[0],
1, 0, 0, center[1],
0,-1, 0, center[2],
0, 0, 0, 1))
oblique = vtkMatrix4x4()
oblique.DeepCopy((1, 0, 0, center[0],
0, 0.866025, -0.5, center[1],
0, 0.5, 0.866025, center[2],
0, 0, 0, 1))
reslice = vtkImageReslice()
outputPort = reader.GetOutputPort()
#reslice.SetInputConnection(reader.GetOutputPort())
reslice.SetInputConnection(0, reader.GetOutputPort())
print(reader.GetOutput().GetExtent())
reslice.SetOutputExtent(reader.GetOutput().GetExtent())
reslice.SetOutputDimensionality(2)
reslice.SetResliceAxes(coronal)
reslice.SetInterpolationModeToLinear()
"""
# Visualize
imageViewer = vtkResliceImageViewer()
imageViewer.SetSliceOrientationToXY()
#imageViewer.SetSlice(9)
imageViewer.SetResliceModeToAxisAligned()
imageViewer.SliceScrollOnMouseWheelOff()
imageViewer.SetInputData(reader.GetOutput())
#imageViewer.Render()
camera = imageViewer.GetRenderer().GetActiveCamera()
print(camera.GetOrientationWXYZ())
# slice status message
sliceTextProp = vtkTextProperty()
sliceTextProp.SetFontFamilyToCourier()
sliceTextProp.SetFontSize(20)
sliceTextProp.SetVerticalJustificationToBottom()
sliceTextProp.SetJustificationToLeft()
sliceTextMapper = vtkTextMapper()
msg = "Slice {} out of {}".format(imageViewer.GetSlice() + 1, \
imageViewer.GetSliceMax() + 1)
sliceTextMapper.SetInput(msg)
sliceTextMapper.SetTextProperty(sliceTextProp)
sliceTextActor = vtkActor2D()
sliceTextActor.SetMapper(sliceTextMapper)
sliceTextActor.SetPosition(100, 10)
# coordinate display
coordTextProp = vtkTextProperty()
coordTextProp.SetFontFamilyToCourier()
coordTextProp.SetFontSize(20)
coordTextProp.SetVerticalJustificationToBottom()
coordTextProp.SetJustificationToLeft()
coordTextMapper = vtkTextMapper()
coordTextMapper.SetInput("Pixel Coordinates: (--, --)")
coordTextMapper.SetTextProperty(coordTextProp)
coordTextActor = vtkActor2D()
coordTextActor.SetMapper(coordTextMapper)
coordTextActor.SetPosition(500, 10)
worldCoordTextProp = vtkTextProperty()
worldCoordTextProp.SetFontFamilyToCourier()
worldCoordTextProp.SetFontSize(20)
worldCoordTextProp.SetVerticalJustificationToBottom()
worldCoordTextProp.SetJustificationToLeft()
worldCoordTextMapper = vtkTextMapper()
worldCoordTextMapper.SetInput("World Coordinates: (--, --)")
worldCoordTextMapper.SetTextProperty(worldCoordTextProp)
worldCoordTextActor = vtkActor2D()
worldCoordTextActor.SetMapper(worldCoordTextMapper)
worldCoordTextActor.SetPosition(500, 30)
# usage hint message
usageTextProp = vtkTextProperty()
usageTextProp.SetFontFamilyToCourier()
usageTextProp.SetFontSize(14)
usageTextProp.SetVerticalJustificationToTop()
usageTextProp.SetJustificationToLeft()
usageTextMapper = vtkTextMapper()
usageTextMapper.SetInput(
"- Slice with mouse wheel\n- Zoom with pressed right\n mouse button while dragging\n- Press i to toggle cursor line on/off"
)
usageTextMapper.SetTextProperty(usageTextProp)
usageTextActor = vtkActor2D()
usageTextActor.SetMapper(usageTextMapper)
usageTextActor.GetPositionCoordinate(
).SetCoordinateSystemToNormalizedDisplay()
usageTextActor.GetPositionCoordinate().SetValue(0.05, 0.95)
actor = imageViewer.GetImageActor()
#image = vtkImageActor()
#actor.GetMapper().SetInputData(reader.GetOutput())
image = imageViewer.GetInput()
roiData = vtkImageData()
roiImage = vtkImageActor()
roiData.DeepCopy(image)
extent = roiData.GetExtent()
for i in range(extent[0], extent[1]):
for j in range(extent[2], extent[3]):
for k in range(extent[4], extent[5]):
if image.GetScalarComponentAsDouble(i, j, k, 0) > -100:
roiData.SetScalarComponentFromDouble(i, j, k, 0, 1)
#roiData.SetScalarComponentFromDouble(0, i, j, k, 1)
else: #just in case
roiData.SetScalarComponentFromDouble(i, j, k, 0, 0.0)
#roiData.SetScalarComponentFromDouble(0, i, j, k, 0.0)
"""
for i in range(extent[0], extent[1]):
for j in range(extent[2], extent[3]):
#for k in range(extent[4], extent[5]):
#k = 0
roiData.SetScalarComponentFromDouble(i, j, k, 0, 0.0)
#roiData.SetScalarComponentFromDouble(0, i, j, k, 0.0)
"""
print(extent)
table = vtkLookupTable()
table.SetNumberOfTableValues(2)
table.SetRange(0.0, 1.0)
table.SetTableValue(0, 0.0, 0.0, 0.0, 0.0)
table.SetTableValue(1, 0.0, 1.0, 0.0, 1.0)
table.Build()
mapToColor = vtkImageMapToColors()
mapToColor.SetLookupTable(table)
mapToColor.PassAlphaToOutputOn()
mapToColor.SetInputData(roiData)
#actor.GetMapper().SetInputConnection(mapToColor.GetOutputPort())
roiImage.GetMapper().SetInputConnection(mapToColor.GetOutputPort())
imageViewer.SetInputData(image)
interactorStyle = vtkInteractorStyleImage()
interactor = vtkRenderWindowInteractor()
imageViewer.SetupInteractor(interactor)
interactor.SetInteractorStyle(interactorStyle)
# add slice status message and usage hint message to the renderer
imageViewer.GetRenderer().AddActor2D(coordTextActor)
imageViewer.GetRenderer().AddActor2D(sliceTextActor)
imageViewer.GetRenderer().AddActor2D(usageTextActor)
imageViewer.GetRenderer().AddActor2D(worldCoordTextActor)
imageViewer.GetRenderer().AddActor(roiImage)
#imageViewer.GetRenderer().AddViewProp(stack)
# initialize rendering and interaction
#imageViewer.SetSlice(35)
imageViewer.GetRenderWindow().SetSize(1000, 1000)
imageViewer.GetRenderer().SetBackground(0.2, 0.3, 0.4)
imageViewer.GetWindowLevel().SetWindow(1000)
imageViewer.GetWindowLevel().SetLevel(-1000)
imageViewer.Render()
yd = (yMax - yMin + 1) * ySpacing
xd = (xMax - xMin + 1) * xSpacing
d = camera.GetDistance()
camera.SetParallelScale(0.5 * xd)
camera.SetFocalPoint(center[0], center[1], 0)
camera.SetPosition(center[0], center[1], +d)
actions = {}
actions["Dolly"] = -1
actions["Cursor"] = 0
def middlePressCallback(obj, event):
# if middle + ctrl pressed, zoom in/out
# otherwise slice through image (handled by mouseMoveCallback)
if (interactor.GetControlKey()):
actions["Dolly"] = 0
interactorStyle.OnRightButtonDown()
else:
actions["Dolly"] = 1
def middleReleaseCallback(obj, event):
if (actions["Dolly"] == 0):
interactorStyle.OnRightButtonUp()
elif (actions["Dolly"] == 1):
actions["Dolly"] = 0
def mouseMoveCallback(obj, event):
# if the middle button is pressed + mouse is moved, slice through image
# otherwise, update world/pixel coords as mouse is moved
if (actions["Dolly"] == 1):
(lastX, lastY) = interactor.GetLastEventPosition()
(curX, curY) = interactor.GetEventPosition()
deltaY = curY - lastY
if (deltaY > 0):
imageViewer.IncrementSlice(1)
elif (deltaY < 0):
imageViewer.IncrementSlice(-1)
msg = "Slice {} out of {}".format(imageViewer.GetSlice() + 1, \
imageViewer.GetSliceMax() + 1)
sliceTextMapper.SetInput(msg)
imageViewer.Render()
else:
(mouseX, mouseY) = interactor.GetEventPosition()
bounds = actor.GetMapper().GetInput().GetBounds()
testCoord = vtkCoordinate()
testCoord.SetCoordinateSystemToDisplay()
testCoord.SetValue(mouseX, mouseY, 0)
(posX, posY,
posZ) = testCoord.GetComputedWorldValue(imageViewer.GetRenderer())
inBounds = True
if posX < bounds[0] or posX > bounds[1] or posY < bounds[
2] or posY > bounds[3]:
inBounds = False
if inBounds:
wMousePos = "World Coordinates: (" + "{:.2f}".format(
posX) + ", " + "{:.2f}".format(
posY) + ", " + "{:.2f}".format(posZ) + ")"
pMousePos = "Pixel Coordinates: (" + "{:.2f}".format(
mouseX) + ", " + "{:.2f}".format(mouseY) + ")"
worldCoordTextMapper.SetInput(wMousePos)
coordTextMapper.SetInput(pMousePos)
imageViewer.Render()
interactorStyle.OnMouseMove()
def scrollForwardCallback(obj, event):
# slice through image on scroll, update slice text
imageViewer.IncrementSlice(1)
msg = "Slice {} out of {}".format(imageViewer.GetSlice() + 1, \
imageViewer.GetSliceMax() + 1)
sliceTextMapper.SetInput(msg)
imageViewer.Render()
def scrollBackwardCallback(obj, event):
imageViewer.IncrementSlice(-1)
msg = "Slice {} out of {}".format(imageViewer.GetSlice() + 1, \
imageViewer.GetSliceMax() + 1)
sliceTextMapper.SetInput(msg)
imageViewer.Render()
def windowModifiedCallback(obj, event):
# track render window width so coordinate text aligns itself
# to the right side of the screen
width = imageViewer.GetRenderWindow().GetSize()[0]
coordTextActor.SetPosition(width - 550, 10)
worldCoordTextActor.SetPosition(width - 550, 30)
imageViewer.Render()
def keyPressCallback(obj, event):
# toggle cursor on/off when t key is pressed
key = interactor.GetKeySym()
if (key == "t"):
if (actions["Cursor"] == 0):
imageViewer.GetRenderWindow().HideCursor()
actions["Cursor"] = 1
elif (actions["Cursor"] == 1):
imageViewer.GetRenderWindow().ShowCursor()
actions["Cursor"] = 0
interactorStyle.AddObserver("MiddleButtonPressEvent", middlePressCallback)
interactorStyle.AddObserver("MiddleButtonReleaseEvent",
middleReleaseCallback)
interactorStyle.AddObserver("MouseMoveEvent", mouseMoveCallback)
interactorStyle.AddObserver("MouseWheelForwardEvent",
scrollForwardCallback)
interactorStyle.AddObserver("MouseWheelBackwardEvent",
scrollBackwardCallback)
interactorStyle.AddObserver("KeyPressEvent", keyPressCallback)
imageViewer.GetRenderWindow().AddObserver("ModifiedEvent",
windowModifiedCallback)
interactor.Start()
import numpy as np
from vtkmodules.vtkIOImage import vtkDICOMImageReader
from vtkmodules.util.misc import vtkGetDataRoot
from vtkmodules.vtkCommonMath import vtkMatrix4x4
from vtkmodules.vtkCommonCore import vtkLookupTable
from vtkmodules.vtkImagingColor import vtkImageMapToWindowLevelColors
from vtkmodules.vtkImagingCore import vtkImageMapToColors, vtkImageReslice
from vtkmodules.vtkRenderingCore import vtkImageActor, vtkRenderer, \
vtkRenderWindow, vtkRenderWindowInteractor, vtkCoordinate, vtkTextProperty, vtkTextMapper, vtkActor2D
from vtkmodules.vtkInteractionStyle import vtkInteractorStyleImage
from vtkmodules.vtkCommonDataModel import vtkImageData
from math import floor, sqrt
from timeit import default_timer as timer
Z_SLICE = None
VTK_DATA_ROOT = vtkGetDataRoot()
folder = "/Users/nandana/Downloads/image_ex"
# Start by loading some data.
reader = vtkDICOMImageReader()
reader.SetDirectoryName(folder)
reader.SetFilePrefix(VTK_DATA_ROOT + "/Data/headsq/quarter")
reader.SetDataExtent(0, 63, 0, 63, 1, 93)
reader.SetDataSpacing(3.2, 3.2, 1.5)
reader.SetDataOrigin(0.0, 0.0, 0.0)
reader.SetDataScalarTypeToUnsignedShort()
reader.UpdateWholeExtent()
# Calculate the center of the volume
reader.Update()
(xMin, xMax, yMin, yMax, zMin,
# Tests paraview/paraview#18391
from vtkmodules.util.misc import vtkGetDataRoot, vtkGetTempDir
from vtk import vtkXMLGenericDataObjectReader, vtkDoubleArray, vtkDataSetWriter, vtkPDataSetReader
from os.path import join
reader = vtkXMLGenericDataObjectReader()
reader.SetFileName(join(vtkGetDataRoot(), "Data/multicomb_0.vts"))
reader.Update()
a1 = vtkDoubleArray()
a1.SetName("field-1")
a1.SetNumberOfTuples(1)
a1.SetValue(0, 100.0)
a1.GetRange()
a2 = vtkDoubleArray()
a2.SetName("field-2")
a2.SetNumberOfTuples(2)
a2.SetValue(0, 1.0)
a2.SetValue(1, 2.0)
a2.GetRange()
dobj = reader.GetOutputDataObject(0)
dobj.GetFieldData().AddArray(a1)
dobj.GetFieldData().AddArray(a2)
writer = vtkDataSetWriter()
writer.SetFileName(join(vtkGetTempDir(), "TestPDataSetReaderWriterWithFieldData.vtk"))
# Tests paraview/paraview#18391
from vtkmodules.util.misc import vtkGetDataRoot, vtkGetTempDir
from vtk import vtkXMLGenericDataObjectReader, vtkDoubleArray, vtkDataSetWriter, vtkPDataSetReader
from os.path import join
reader = vtkXMLGenericDataObjectReader()
reader.SetFileName(join(vtkGetDataRoot(), "Data/multicomb_0.vts"))
reader.Update()
a1 = vtkDoubleArray()
a1.SetName("field-1")
a1.SetNumberOfTuples(1)
a1.SetValue(0, 100.0)
a1.GetRange()
a2 = vtkDoubleArray()
a2.SetName("field-2")
a2.SetNumberOfTuples(2)
a2.SetValue(0, 1.0)
a2.SetValue(1, 2.0)
a2.GetRange()
dobj = reader.GetOutputDataObject(0)
dobj.GetFieldData().AddArray(a1)
dobj.GetFieldData().AddArray(a2)
writer = vtkDataSetWriter()
writer.SetFileName(
join(vtkGetTempDir(), "TestPDataSetReaderWriterWithFieldData.vtk"))
def __init__(self):
VTK_DATA_ROOT = vtkGetDataRoot()
self.reader = vtkDICOMImageReader()
self.folder = "/Users/nandana/Downloads/image_ex"
self.reader.SetDirectoryName(self.folder)
self.reader.SetFilePrefix(VTK_DATA_ROOT + "/Data/headsq/quarter")
self.reader.SetDataExtent(0, 63, 0, 63, 1, 93)
self.reader.SetDataSpacing(3.2, 3.2, 1.5)
self.reader.SetDataOrigin(0.0, 0.0, 0.0)
self.reader.SetDataScalarTypeToUnsignedShort()
self.reader.UpdateWholeExtent()
self.reader.Update()
self.center = self.calculate_center()
self.axial = vtkMatrix4x4()
self.axial.DeepCopy((1, 0, 0, self.center[0], 0, 1, 0, self.center[1],
0, 0, 1, self.center[2], 0, 0, 0, 1))
self.coronal = vtkMatrix4x4()
self.coronal.DeepCopy(
(1, 0, 0, self.center[0], 0, 0, 1, self.center[1], 0, -1, 0,
self.center[2], 0, 0, 0, 1))
self.sagittal = vtkMatrix4x4()
self.sagittal.DeepCopy(
(0, 0, -1, self.center[0], 1, 0, 0, self.center[1], 0, -1, 0,
self.center[2], 0, 0, 0, 1))
self.oblique = vtkMatrix4x4()
self.oblique.DeepCopy(
(1, 0, 0, self.center[0], 0, 0.866025, -0.5, self.center[1], 0,
0.5, 0.866025, self.center[2], 0, 0, 0, 1))
self.img_reslice = vtkImageReslice()
self.roi_reslice = vtkImageReslice()
self.img_reslice.SetInputConnection(0, self.reader.GetOutputPort())
self.img_reslice.SetOutputDimensionality(2)
self.img_reslice.SetInterpolationModeToLinear()
self.roi_reslice.SetInputConnection(0, self.reader.GetOutputPort())
self.roi_reslice.SetOutputDimensionality(2)
self.roi_reslice.SetInterpolationModeToLinear()
self.set_orientation(self.axial)
self.img_table = vtkLookupTable()
self.roi_table = vtkLookupTable()
self.window_level = vtkImageMapToWindowLevelColors()
self.img_color = vtkImageMapToColors()
self.roi_color = vtkImageMapToColors()
self.img = self.map_img()
self.roi = self.map_roi()
self.px_coord_text_prop = vtkTextProperty()
self.px_coord_text_mapper = vtkTextMapper()
self.px_coord_text_actor = vtkActor2D()
self.world_coord_text_prop = vtkTextProperty()
self.world_coord_text_mapper = vtkTextMapper()
self.world_coord_text_actor = vtkActor2D()
self.usage_text_prop = vtkTextProperty()
self.usage_text_mapper = vtkTextMapper()
self.usage_text_actor = vtkActor2D()
self.renderer = vtkRenderer()
self.add_text()
self.renderer.AddActor(self.img)
self.renderer.AddActor(self.roi)
self.renderer.SetBackground(0.2, 0.3, 0.4)
self.window = vtkRenderWindow()
self.window.AddRenderer(self.renderer)
self.window.SetSize(1000, 1000)
self.interactor_style = vtkInteractorStyleImage()
self.interactor_style.SetInteractionModeToImageSlicing()
self.interactor = vtkRenderWindowInteractor()
self.interactor.SetInteractorStyle(self.interactor_style)
self.window.SetInteractor(self.interactor)
self.window_level.SetWindow(1000)
self.window_level.SetLevel(200)
self.window_level.Update()
self.window.Render()
self.interactor_style.AddObserver("MouseWheelForwardEvent",
self.scroll_forward_callback)
self.interactor_style.AddObserver("MouseWheelBackwardEvent",
self.scroll_backward_callback)
self.interactor_style.AddObserver("MouseMoveEvent",
self.mouse_move_callback)
self.interactor_style.AddObserver("KeyPressEvent",
self.key_press_callback)
self.interactor_style.AddObserver("LeftButtonPressEvent",
self.left_press_callback)
self.window.AddObserver("ModifiedEvent", self.window_mod_callback)
self.actions = {
"Slicing": 0,
"Cursor": 0,
"CurrentPos": -1,
"LastPos": -1,
"DoubleClick": 0
}
def load_image(self, file):
# (1) Read File
# (2) Get min, max, window-level
# (3) Update views
# (1)
if self.demo_mode:
print(file)
print("......")
self.reader = vtkDICOMImageReader()
VTK_DATA_ROOT = vtkGetDataRoot()
self.reader.SetDirectoryName(file)
self.reader.SetFilePrefix(VTK_DATA_ROOT + "/Data/headsq/quarter") # UNIX FRIENDLY
# self.reader.SetFilePrefix(VTK_DATA_ROOT + r"\Data\headsq\quarter") # WINDOWS FRIENDLY
### Extract
# TODO: double check that the image attributes are correct when using vtkDICOMimageReader
# self.reader.SetDataExtent(0, 63, 0, 63, 1, 93)
# self.reader.SetDataSpacing(3.2, 3.2, 1.5)
# self.reader.SetDataOrigin(0.0, 0.0, 0.0)
self.reader.SetDataScalarTypeToUnsignedShort()
# self.reader.UpdateWholeExtent()
self.reader.Update()
imageData = self.reader.GetOutput()
self.image = imageData
image_info = dict(image_data=imageData, spacing=imageData.GetSpacing(), origin=imageData.GetOrigin())
minv, maxv = (-1024, 1024) #close enough estimate
else:
if qia_loaded:
print(file)
self.image = qimage.read(file)
### QIA version
image_info = dict(image_data=self.image, spacing=self.image.get_spacing(), origin=self.image.get_origin())
dims = image_info["image_data"].get_size()
else: #assume numpy array
print("Not implemented yet")
# load numpy array
### numpy version >>> for future compatibility
# image_npy = np.array(self.image.get_array())
# image_npy = np.moveaxis(image_npy, 0, 2) #because I saved the numpy files (z, x, y) -_-
# image_npy = np.rot90(image_npy, 3)
# image_npy = np.flip(image_npy, 1)
# image_info = dict(image_data=image_npy, spacing=self.image.get_spacing(), origin=self.image.get_origin())
# dims = image_info["image_data"].shape
imageData = vtk.vtkImageData()
print("dims", dims)
#instantiating imageData obj
imageData.SetDimensions(dims[0], dims[1], dims[2])
if vtk.VTK_MAJOR_VERSION <= 5:
imageData.SetNumberOfScalarComponents(1)
imageData.SetScalarTypeToDouble()
else:
imageData.AllocateScalars(vtk.VTK_DOUBLE, 1)
# (2) Update the vtk obj image information
imageData.SetSpacing(image_info["spacing"][0], image_info["spacing"][1], image_info["spacing"][2])
### QIA Version
imageData.SetExtent(0, dims[0]-1, 0, dims[1]-1, 1, dims[2]) # with QIA it goes from [ 1 to z_max ] instead of [0 to z_max - 1]
imageData.SetOrigin(image_info["origin"][0], image_info["origin"][1], image_info["origin"][2]) #unsure if it's this one
# imageData.SetOrigin(image_info["origin"][0], image_info["origin"][1], 0) #unsure if it's this one
for z in range(dims[2]):
z+=1
for y in range(dims[1]):
for x in range(dims[0]):
# print(x,y, z)
# double check if x,y,z is the appropriate order after you get the numpy array
# imageData.SetScalarComponentFromDouble(x, y, z, 0, image_info["image_data"][x,y,z] ) # numpy
imageData.SetScalarComponentFromDouble(x, y, z, 0, image_info["image_data"].get_value((x,y,z)) ) # QIA
minv, maxv = self.image.get_min_max()
# (2)
self.window_level.SetWindow(maxv-minv)
self.window_level.SetLevel((maxv+minv)/2)
self.window_level.Update()
# (3)
# TODO: Make blockSignals useful (to avoid reloading things if we click too often, etc.)
for v in self.views:
v.blockSignals(True)
self.viewer_center = self.views[0].calculate_center(extent=imageData.GetExtent(), spacing=image_info["spacing"], origin=image_info["origin"])
print("viewer center", self.viewer_center)
for v in self.views:
v.update_image(imageData)
if not v.viewer_initialized:
# orientation = "axial"
orientation = "sagittal"
# before this, orientation has of the viewer has not been defined yet.
# aka it doesn't set the viewer orientation until the first image has loaded
v.init_view(orientation=orientation, center=self.viewer_center)
else:
# if viewer has been initialized already, then just update the center
v.set_position(self.viewer_center)
v.connect_window_level(self.window_level) #updating window level
# v.resetCamera() ### TODO: Implement and activate
for v in self.views:
v.blockSignals(False)
self.render()