"""

USAGE:

=============

loadDisplay = Display()

"""

def __init__(self):

""" initialize visualization with standard vtk actors, renders, windowsn, interactors """

# use cell picker for interacting with the image orthogonal views.

self.picker = vtk.vtkCellPicker()

self.picker.SetTolerance(0.005)

# Create 3 orthogonal view using the ImagePlaneWidget

self.xImagePlaneWidget = vtk.vtkImagePlaneWidget()

self.yImagePlaneWidget = vtk.vtkImagePlaneWidget()

self.zImagePlaneWidget = vtk.vtkImagePlaneWidget()

# The 3 image plane widgets

self.xImagePlaneWidget.DisplayTextOn();

self.xImagePlaneWidget.SetPicker(self.picker);

self.xImagePlaneWidget.RestrictPlaneToVolumeOn();

self.xImagePlaneWidget.SetKeyPressActivationValue('x');

self.xImagePlaneWidget.GetPlaneProperty().SetColor(1, 0, 0);

self.xImagePlaneWidget.SetResliceInterpolateToNearestNeighbour();

self.yImagePlaneWidget.DisplayTextOn();

self.yImagePlaneWidget.SetPicker(self.picker);

self.yImagePlaneWidget.RestrictPlaneToVolumeOn();

self.yImagePlaneWidget.SetKeyPressActivationValue('y');

self.yImagePlaneWidget.GetPlaneProperty().SetColor(0, 1, 0);

self.yImagePlaneWidget.SetLookupTable(self.xImagePlaneWidget.GetLookupTable());

self.zImagePlaneWidget.DisplayTextOn();

self.zImagePlaneWidget.SetPicker(self.picker);

self.zImagePlaneWidget.SetKeyPressActivationValue('z');

self.zImagePlaneWidget.GetPlaneProperty().SetColor(0, 0, 1);

self.zImagePlaneWidget.SetLookupTable(self.xImagePlaneWidget.GetLookupTable());

self.zImagePlaneWidget.SetRightButtonAutoModifier(1);

# Create a renderer, render window, and render window interactor to

# display the results.

self.renderer1 = vtk.vtkRenderer()

self.renWin1 = vtk.vtkRenderWindow()

self.iren1 = vtk.vtkRenderWindowInteractor()

self.renWin1.SetSize(1000, 800);

self.renWin1.AddRenderer(self.renderer1)

self.iren1.SetRenderWindow(self.renWin1)

self.xImagePlaneWidget.SetInteractor( self.iren1 )

self.yImagePlaneWidget.SetInteractor( self.iren1 )

self.zImagePlaneWidget.SetInteractor( self.iren1 )

# Set Up Camera view

self.camera = self.renderer1.GetActiveCamera()

self.renderer1.SetBackground(0.0, 0.0, 0.0)

self.iren1.SetPicker(self.picker)

self.T1origin = [0,0,0]

self.T2origin = [0,0,0]

self.T2extent = [0,0,0,0,0,0]

self.T1extent = [0,0,0,0,0,0]

self.T1spacing = [0,0,0]

def __call__(self):

""" Turn Class into a callable object """

Display()

def dicomTransform(self, image, image_pos_pat, image_ori_pat):

""" dicomTransform: transforms an image to a DICOM coordinate frame

INPUTS:

=======

image: (vtkImageData) Input image to Transform

image_pos_pat: (list(dicomInfo[0x0020,0x0032].value))) Image position patient Dicom Tag

image_ori_pat: (list(dicomInfo[0x0020,0x0037].value)) Image oreintation patient Dicom Tag

OUTPUTS:

=======

transformed_image (vtkImageData) Transformed imaged mapped to dicom coords frame

transform (vtkTransform) Transform used

"""

# If one considers the localizer plane as a "viewport" onto the DICOM 3D coordinate space, then that viewport is described by its origin, its row unit vector, column unit vector and a normal unit vector (derived from the row and column vectors by taking the cross product). Now if one moves the origin to 0,0,0 and rotates this viewing plane such that the row vector is in the +X direction, the column vector the +Y direction, and the normal in the +Z direction, then one has a situation where the X coordinate now represents a column offset in mm from the localizer's top left hand corner, and the Y coordinate now represents a row offset in mm from the localizer's top left hand corner, and the Z coordinate can be ignored. One can then convert the X and Y mm offsets into pixel offsets using the pixel spacing of the localizer imag

# Initialize Image orienation

"Image Orientation Patient Matrix"

IO = matrix( [[0, 0,-1, 1],

[1, 0, 0, 1],

[0,-1, 0, 1],

[0, 0, 0, 1]])

# Assign the 6-Image orientation patient coordinates (from Dicomtags)

IO[0,0] = image_ori_pat[0]; IO[0,1] = image_ori_pat[1]; IO[0,2] = image_ori_pat[2];

IO[1,0] = image_ori_pat[3]; IO[1,1] = image_ori_pat[4]; IO[1,2] = image_ori_pat[5];

# obtain thrid column as the cross product of column 1 y 2

IO_col1 = [image_ori_pat[0], image_ori_pat[1], image_ori_pat[2]]

IO_col2 = [image_ori_pat[3], image_ori_pat[4], image_ori_pat[5]]

IO_col3 = cross(IO_col1, IO_col2)

# assign column 3

IO[2,0] = IO_col3[0]; IO[2,1] = IO_col3[1]; IO[2,2] = IO_col3[2];

IP = array([0, 0, 0, 1]) # Initialization Image Position

IP[0] = image_pos_pat[0]; IP[1] = image_pos_pat[1]; IP[2] = image_pos_pat[2];

IO[0,3] = -image_pos_pat[0]; IO[1,3] = -image_pos_pat[1]; IO[2,3] = -image_pos_pat[2]

"Compute Volume Origin"

origin = IP*IO.I

# Create matrix 4x4

DICOM_mat = vtk.vtkMatrix4x4();

DICOM_mat.SetElement(0, 0, IO[0,0])

DICOM_mat.SetElement(0, 1, IO[0,1])

DICOM_mat.SetElement(0, 2, IO[0,2])

DICOM_mat.SetElement(0, 3, IO[0,3])

DICOM_mat.SetElement(1, 0, IO[1,0])

DICOM_mat.SetElement(1, 1, IO[1,1])

DICOM_mat.SetElement(1, 2, IO[1,2])

DICOM_mat.SetElement(1, 3, IO[1,3])

DICOM_mat.SetElement(2, 0, IO[2,0])

DICOM_mat.SetElement(2, 1, IO[2,1])

DICOM_mat.SetElement(2, 2, IO[2,2])

DICOM_mat.SetElement(2, 3, IO[2,3])

DICOM_mat.SetElement(3, 0, IO[3,0])

DICOM_mat.SetElement(3, 1, IO[3,1])

DICOM_mat.SetElement(3, 2, IO[3,2])

DICOM_mat.SetElement(3, 3, IO[3,3])

#DICOM_mat.Invert()

# Set up the axes

transform = vtk.vtkTransform()

transform.Concatenate(DICOM_mat)

transform.Update()

# Set up the cube (set up the translation back to zero

DICOM_mat_cube = vtk.vtkMatrix4x4();

DICOM_mat_cube.DeepCopy(DICOM_mat)

DICOM_mat_cube.SetElement(0, 3, 0)

DICOM_mat_cube.SetElement(1, 3, 0)

DICOM_mat_cube.SetElement(2, 3, 0)

transform_cube = vtk.vtkTransform()

transform_cube.Concatenate(DICOM_mat_cube)

transform_cube.Update()

# Change info

# Flip along Y-Z-axis: VTK uses computer graphics convention where the first pixel in memory is shown

# in the lower left of the displayed image.

flipZ_image = vtk.vtkImageFlip()

flipZ_image.SetInput(image)

flipZ_image.SetFilteredAxis(2)

flipZ_image.Update()

flipY_image = vtk.vtkImageFlip()

flipY_image.SetInput(flipZ_image.GetOutput())

flipY_image.SetFilteredAxis(1)

flipY_image.Update()

# Change info origin

flipY_origin_image = vtk.vtkImageChangeInformation()

flipY_origin_image.SetInput( flipY_image.GetOutput() );

flipY_origin_image.SetOutputOrigin(origin[0,0], origin[0,1], origin[0,2])

flipY_origin_image.Update()

transformed_image = flipY_origin_image.GetOutput()

transformed_image.UpdateInformation()

self.dims = transformed_image.GetDimensions()

print "Image Dimensions"

print self.dims

(xMin, xMax, yMin, yMax, zMin, zMax) = transformed_image.GetWholeExtent()

print "Image Extension"

print xMin, xMax, yMin, yMax, zMin, zMax

self.spacing = transformed_image.GetSpacing()

print "Image Spacing"

print self.spacing

self.origin = transformed_image.GetOrigin()

print "Image Origin"

print self.origin

return transformed_image, transform_cube

def addSegment(self, lesion3D, color, interact):

'''Add segmentation to current display'''

# Set the planes based on seg bounds

self.lesion_bounds = lesion3D.GetBounds()

print "\n Mesh DICOM bounds: "

print "xmin, xmax= [%d, %d]" % (self.lesion_bounds[0], self.lesion_bounds[1])

print "yin, ymax= [%d, %d]" % (self.lesion_bounds[2], self.lesion_bounds[3])

print "zmin, zmax= [%d, %d]" % (self.lesion_bounds[4], self.lesion_bounds[5])

### GEt semgnetation information

self.no_pts_segm = lesion3D.GetNumberOfPoints()

print "no pts %d" % self.no_pts_segm

# get VOI volume

VOI_massProperty = vtk.vtkMassProperties()

VOI_massProperty.SetInput(lesion3D)

VOI_massProperty.Update()

# VTK is unitless. The units you get out are the units you put in.

# If your input polydata has points defined in terms of millimetres, then

# the volume will be in cubic millimetres.

self.VOI_vol = VOI_massProperty.GetVolume() # mm3

self.VOI_surface = VOI_massProperty.GetSurfaceArea() # mm2

# just print the results

print "\nVolume lesion = ", self.VOI_vol

print "Surface lesion = ", self.VOI_surface

# Calculate the effective diameter of the surface D=2(sqrt3(3V/(4pi)))

diam_root = (3*self.VOI_vol)/(4*pi)

self.VOI_efect_diameter = 2*pow(diam_root,1.0/3)

print "VOI_efect_diameter = ", self.VOI_efect_diameter

centerOfMassFilter = vtk.vtkCenterOfMass()

centerOfMassFilter.SetInput( lesion3D )

centerOfMassFilter.SetUseScalarsAsWeights(False)

centerOfMassFilter.Update()

# centroid of lesion

self.lesion_centroid = [0,0,0]

self.lesion_centroid = centerOfMassFilter.GetCenter()

print "lesion_centroid = ", self.lesion_centroid

# Add ICPinit_mesh.vtk to the render

self.mapper_mesh = vtk.vtkPolyDataMapper()

self.mapper_mesh.SetInput( lesion3D )

self.mapper_mesh.ScalarVisibilityOff()

self.actor_mesh = vtk.vtkActor()

self.actor_mesh.SetMapper(self.mapper_mesh)

self.actor_mesh.GetProperty().SetColor(color) #R,G,B

self.actor_mesh.GetProperty().SetOpacity(0.3)

self.actor_mesh.GetProperty().SetPointSize(5.0)

self.actor_mesh.GetProperty().SetRepresentationToWireframe()

self.xImagePlaneWidget.SetSliceIndex(0)

self.yImagePlaneWidget.SetSliceIndex(0)

self.zImagePlaneWidget.SetSliceIndex( 0 )

self.renderer1.AddActor(self.actor_mesh)

# Initizalize

self.renderer1.Modified()

self.renWin1.Render()

self.renderer1.Render()

if(interact==True):

self.iren1.Start()

return

def subImage(self, Images2Sub, timep):

'''subtract volumes based on indicated postS'''

sub_preMat = vtk.vtkImageMathematics()

sub_preMat.SetOperationToSubtract()

sub_preMat.SetInput1(Images2Sub[timep])

sub_preMat.SetInput2(Images2Sub[0])

sub_preMat.Update()

sub_pre = vtk.vtkImageData()

sub_pre = sub_preMat.GetOutput()

# define image based on subtraction of postS -preS

subtractedImage = sub_pre

return subtractedImage

def display_pick(self, images, image_pos_pat, image_ori_pat, postS, LesionZslice):

'''Display a z-slice and use picker to pick coordinates with a mouse right-click'''

#subtract volumes based on indicated postS

# define image based on subtraction of postS -preS

image = self.subImage(images, postS)

# Proceed to build reference frame for display objects based on DICOM coords

[transformed_image, transform_cube] = self.dicomTransform(image, image_pos_pat, image_ori_pat)

# Calculate the center of the volume

transformed_image.UpdateInformation()

# Set up ortogonal planes

self.xImagePlaneWidget.SetInput( transformed_image )

self.yImagePlaneWidget.SetInput( transformed_image )

self.zImagePlaneWidget.SetInput( transformed_image )

self.zImagePlaneWidget.SetSliceIndex( LesionZslice )

self.xImagePlaneWidget.On()

self.yImagePlaneWidget.On()

self.zImagePlaneWidget.On()

############

self.textMapper = vtk.vtkTextMapper()

tprop = self.textMapper.GetTextProperty()

tprop.SetFontFamilyToArial()

tprop.SetFontSize(10)

tprop.BoldOn()

tprop.ShadowOn()

tprop.SetColor(1, 0, 0)

# initialize

self.seeds = vtk.vtkPoints()

self.textActor = vtk.vtkActor2D()

self.textActor.VisibilityOff()

self.textActor.SetMapper(self.textMapper)

# Initizalize

self.iren1.SetPicker(self.picker)

self.picker.AddObserver("EndPickEvent", self.annotatePick)

self.renWin1.Render()

self.renderer1.Render()

self.iren1.Start()

return self.seeds

def annotatePick(self, object, event):

'''Auxiliary function of picker, print coords chosen'''

if(self.picker.GetCellId() < 0):

self.textActor.VisibilityOff()

else:

selPt = self.picker.GetSelectionPoint()

pickPos = self.picker.GetPickPosition()

self.seeds.InsertNextPoint(pickPos[0], pickPos[1], pickPos[2] )

print pickPos

self.textMapper.SetInput("(%.6f, %.6f, %.6f)"%pickPos)

self.textActor.SetPosition(selPt[:2])

self.textActor.VisibilityOn()

return

def visualize(self, images, image_pos_pat, image_ori_pat, sub, postS, interact):

'''Display and render volumes, reference frames, actors and widgets'''

if(sub):

#subtract volumes based on indicated postS

# define image based on subtraction of postS -preS

image = self.subImage(images, postS)

else:

image = images[postS]

# Proceed to build reference frame for display objects based on DICOM coords

[self.transformed_image, transform_cube] = self.dicomTransform(image, image_pos_pat, image_ori_pat)

# get info from image before visualization

self.transformed_image.UpdateInformation()

self.dims = self.transformed_image.GetDimensions()

print "Image Dimensions"

print self.dims

self.T1spacing = self.transformed_image.GetSpacing()

print "Image Spacing"

print self.T1spacing

self.T1origin = self.transformed_image.GetOrigin()

print "Image Origin"

print self.T1origin

self.T1extent = list(self.transformed_image.GetWholeExtent())

print "Image Extent"

print self.T1extent

# Set up ortogonal planes

self.xImagePlaneWidget.SetInput( self.transformed_image )

self.xImagePlaneWidget.SetPlaneOrientationToXAxes()

self.xImagePlaneWidget.SetSliceIndex(0)

self.yImagePlaneWidget.SetInput( self.transformed_image )

self.yImagePlaneWidget.SetPlaneOrientationToYAxes()

self.yImagePlaneWidget.SetSliceIndex(0)

self.zImagePlaneWidget.SetInput( self.transformed_image )

self.zImagePlaneWidget.SetPlaneOrientationToZAxes()

self.zImagePlaneWidget.SetSliceIndex(0)

self.xImagePlaneWidget.On()

self.yImagePlaneWidget.On()

self.zImagePlaneWidget.On()

# set up cube actor with Orientation(A-P, S-I, L-R) using transform_cube

# Set up to ALS (+X=A, +Y=S, +Z=L) source:

cube = vtk.vtkAnnotatedCubeActor()

cube.SetXPlusFaceText( "L" );

cube.SetXMinusFaceText( "R" );

cube.SetYPlusFaceText( "A" );

cube.SetYMinusFaceText( "P" );

cube.SetZPlusFaceText( "S" );

cube.SetZMinusFaceText( "I" );

cube.SetFaceTextScale( 0.5 );

cube.GetAssembly().SetUserTransform( transform_cube );

# Set UP the axes

axes2 = vtk.vtkAxesActor()

axes2.SetShaftTypeToCylinder();

#axes2.SetUserTransform( transform_cube );

axes2.SetTotalLength( 1.5, 1.5, 1.5 );

axes2.SetCylinderRadius( 0.500 * axes2.GetCylinderRadius() );

axes2.SetConeRadius( 1.025 * axes2.GetConeRadius() );

axes2.SetSphereRadius( 1.500 * axes2.GetSphereRadius() );

tprop2 = axes2.GetXAxisCaptionActor2D()

tprop2.GetCaptionTextProperty();

assembly = vtk.vtkPropAssembly();

assembly.AddPart( axes2 );

assembly.AddPart( cube );

widget = vtk.vtkOrientationMarkerWidget();

widget.SetOutlineColor( 0.9300, 0.5700, 0.1300 );

widget.SetOrientationMarker( assembly );

widget.SetInteractor( self.iren1 );

widget.SetViewport( 0.0, 0.0, 0.4, 0.4 );

widget.SetEnabled( 1 );

widget.InteractiveOff();

# Create a text property for both cube axes

tprop = vtk.vtkTextProperty()

tprop.SetColor(1, 1, 1)

tprop.ShadowOff()

# Create a vtkCubeAxesActor2D. Use the outer edges of the bounding box to

# draw the axes. Add the actor to the renderer.

axes = vtk.vtkCubeAxesActor2D()

axes.SetInput(self.transformed_image)

axes.SetCamera(self.renderer1.GetActiveCamera())

axes.SetLabelFormat("%6.4g")

axes.SetFlyModeToOuterEdges()

axes.SetFontFactor(1.2)

axes.SetAxisTitleTextProperty(tprop)

axes.SetAxisLabelTextProperty(tprop)

self.renderer1.AddViewProp(axes)

############

# bounds and initialize camera

bounds = self.transformed_image.GetBounds()

self.renderer1.ResetCamera(bounds)

self.renderer1.ResetCameraClippingRange()

self.camera.SetViewUp(0.0,-1.0,0.0)

self.camera.Azimuth(315)

# Initizalize

self.renWin1.Modified()

self.renWin1.Render()

self.renderer1.Render()

if(interact==True):

interactor = self.renWin1.GetInteractor()

interactor.Start()

return

def addT2visualize(self, T2images, image_pos_pat, image_ori_pat, T2dims, T2spacing, interact):

'''Added to build second reference frame and display T2 overlayed into T1 reference frame'''

# Proceed to build reference frame for display objects based on DICOM coords

[transformed_T2image, transform_cube] = self.dicomTransform(T2images, image_pos_pat, image_ori_pat)

self.T2origin = list(transformed_T2image.GetOrigin())

print "T2 Extent"

self.T2extent = list(transformed_T2image.GetExtent())

print self.T2extent

# Set up ortogonal planes

self.xImagePlaneWidget.SetInput( transformed_T2image )

self.xImagePlaneWidget.SetSliceIndex(0)

self.yImagePlaneWidget.SetInput( transformed_T2image )

self.yImagePlaneWidget.SetSliceIndex(0)

self.zImagePlaneWidget.SetInput( transformed_T2image )

self.zImagePlaneWidget.SetSliceIndex(0)

# Create a text property for both cube axes

tprop = vtk.vtkTextProperty()

tprop.SetColor(0, 1, 1)

tprop.ShadowOff()

# Update the reneder window to receive new image !Important*****

self.renderer1.Modified()

self.renWin1.Modified()

# Create a vtkCubeAxesActor2D. Use the outer edges of the bounding box to

# draw the axes. Add the actor to the renderer.

axesT2 = vtk.vtkCubeAxesActor2D()

axesT2.SetInput(transformed_T2image)

axesT2.SetCamera(self.renderer1.GetActiveCamera())

axesT2.SetLabelFormat("%6.4g")

axesT2.SetFlyModeToOuterEdges()

axesT2.SetFontFactor(1.2)

axesT2.SetAxisTitleTextProperty(tprop)

axesT2.SetAxisLabelTextProperty(tprop)

self.renderer1.AddViewProp(axesT2)

############

if(interact==True):

interactor = self.renWin1.GetInteractor()

interactor.Start()

return

def addT2transvisualize(self, T2images, image_pos_pat, image_ori_pat, T2dims, T2spacing, sideBreast, interact):

'''Added to build second reference frame and display T2 overlayed into T1 reference frame'''

# Proceed to build reference frame for display objects based on DICOM coords

[transformed_T2image, transform_cube] = self.dicomTransform(T2images, image_pos_pat, image_ori_pat)

#alignR = int(raw_input('\nAlign right? Yes:1 No:0 : '))

#if alignR:

if(sideBreast=="Right"):

zf1 = self.T1spacing[2]*self.T1extent[5] + self.T1origin[2]

self.T2origin[2] = zf1 - T2spacing[2]*self.T2extent[5] # this is z-span

else:

self.T2origin[2] = self.T1origin[2]

# Change info origin

translated_T2image = vtk.vtkImageChangeInformation()

translated_T2image.SetInput( transformed_T2image )

translated_T2image.SetOutputOrigin(self.T2origin)

translated_T2image.Update()

# Set up ortogonal planes

self.xImagePlaneWidget.SetInput( translated_T2image.GetOutput() )

self.xImagePlaneWidget.SetSliceIndex(0)

self.yImagePlaneWidget.SetInput( translated_T2image.GetOutput() )

self.yImagePlaneWidget.SetSliceIndex(0)

self.zImagePlaneWidget.SetInput( translated_T2image.GetOutput() )

self.zImagePlaneWidget.SetSliceIndex(0)

# Create a text property for both cube axes

tprop = vtk.vtkTextProperty()

tprop.SetColor(0.5, 0.5, 0)

tprop.ShadowOff()

# Update the reneder window to receive new image !Important*****

self.renderer1.Modified()

self.renWin1.Modified()

# Create a vtkCubeAxesActor2D. Use the outer edges of the bounding box to

# draw the axes. Add the actor to the renderer.

axesT2 = vtk.vtkCubeAxesActor2D()

axesT2.SetInput(translated_T2image.GetOutput())

axesT2.SetCamera(self.renderer1.GetActiveCamera())

axesT2.SetLabelFormat("%6.4g")

axesT2.SetFlyModeToOuterEdges()

axesT2.SetFontFactor(1.2)

axesT2.SetAxisTitleTextProperty(tprop)

axesT2.SetAxisLabelTextProperty(tprop)

self.renderer1.AddViewProp(axesT2)

### Update T2Images

t_T2images = vtk.vtkImageChangeInformation()

t_T2images.SetInput( T2images )

t_T2images.SetOutputOrigin(self.T2origin)

t_T2images.Update()

############

if(interact==True):

interactor = self.renWin1.GetInteractor()

interactor.Start()

return

def extract_annot(self, list_annots):

'''Parse list of annotations, put markers according to notes and color code according to sequence order'''

annots_dict_list=[]

a_count = 1

for one_annot in list_annots:

annots_dict = {}

print one_annot

# iterate throuhg attributes of annotation

annots_dict['AccessionNumber'] = one_annot[one_annot.find("':")+4:one_annot.find("',")]

one_annot = one_annot[one_annot.find("',")+2:]

annots_dict['SeriesDate'] = one_annot[one_annot.find("':")+4:one_annot.find("',")]

one_annot = one_annot[one_annot.find("',")+2:]

annots_dict['SeriesNumber'] = one_annot[one_annot.find("':")+4:one_annot.find("',")]

one_annot = one_annot[one_annot.find("',")+2:]

annots_dict['SliceLocation'] = one_annot[one_annot.find("':")+4:one_annot.find("',")]

one_annot = one_annot[one_annot.find("',")+2:]

annots_dict['SeriesDescription'] = one_annot[one_annot.find("':")+4:one_annot.find("',")]

one_annot = one_annot[one_annot.find("',")+2:]

annots_dict['PatientID'] = one_annot[one_annot.find("':")+4:one_annot.find("',")]

one_annot = one_annot[one_annot.find("',")+2:]

annots_dict['StudyID'] = one_annot[one_annot.find("':")+4:one_annot.find("',")]

one_annot = one_annot[one_annot.find("',")+2:]

# get the type of annotation: e.g CALLIPER, ELLIPSE, ARROW

annots_dict['note'] = one_annot[one_annot.find("':")+4:one_annot.find("\\")]

# extract annotation coordinate location

coords_str = one_annot[one_annot.find("\\"):one_annot.find("',")]

non_dec = re.compile(r'[^\d.]+')

coords = non_dec.sub(',', coords_str).split(',')

print coords

if coords != ['']:

annots_dict['xi']=float(coords[1])

annots_dict['yi']=float(coords[2])

annots_dict['xf']=float(coords[3])

annots_dict['yf']=float(coords[4])

# finish last attribute of annotations

one_annot = one_annot[one_annot.find("',")+2:]

annots_dict['SeriesInstanceUID'] = one_annot[one_annot.find("':")+4:]

annots_dict_list.append(annots_dict)

a_count+=1

return annots_dict_list

def display_annot(self, images, image_pos_pat, image_ori_pat, annots_dict_list, interact):

'''Display list of annotations, put markers according to notes and color code according to sequence order'''

# define image based on subtraction of postS -preS

image = images[4]

# Proceed to build reference frame for display objects based on DICOM coords

[self.transformed_image, transform_cube] = self.dicomTransform(image, image_pos_pat, image_ori_pat)

# supports 56 annotations

color_list = [ [0,0,0], [1,0,0], [0,0,1], [0,1,1], [1,1,0], [1,0,1], [1,1,1], [0.5,0.5,0.5], [0.5,0.5,0], [1,0.2,0], [1,1,0], [0,1,1],[0,1,0.6], [0,1,1], [1,0.4,0], [0.6,0,0.2], [1,1,0], [0,1,1],[0,1,0], [0,1,1], [1,0,0.1], [1,0.4,0],[0,1,1],[0,1,0], [0,1,1], [1,0,0.1], [1,0.4,0],

[0,0,0], [1,0,0], [0,0,1], [0,1,1], [1,1,0], [1,0,1], [1,1,1], [0.5,0.5,0.5], [0.5,0.5,0], [1,0.2,0], [1,1,0], [0,1,1],[0,1,0.6], [0,1,1], [1,0.4,0], [0.6,0,0.2], [1,1,0], [0,1,1],[0,1,0], [0,1,1], [1,0,0.1], [1,0.4,0],[0,1,1],[0,1,0], [0,1,1], [1,0,0.1], [1,0.4,0] ]

a_count = 1

annot_pts_lbl = vtk.vtkPoints()

for annots_dict in annots_dict_list:

try:

float(annots_dict['SliceLocation'])

print '\n=========#'+str(a_count)

print annots_dict

######################

## Display in graphics

######################

im_pt = [0,0,0]

ijk = [0,0,0]

pco = [0,0,0]

pi_2display=[0,0,0]

pf_2display=[0,0,0]

# extract Slice locaton

pixId_sliceloc = self.transformed_image.FindPoint(self.origin[0], self.origin[1], float(annots_dict['SliceLocation']))

self.transformed_image.GetPoint(pixId_sliceloc, im_pt)

io = self.transformed_image.ComputeStructuredCoordinates( im_pt, ijk, pco)

# mark initial

print "Point init"

ijk[0] = int(annots_dict['xi'])

ijk[1] = int(annots_dict['yi'])

print ijk

annots_dict['pi_ijk']=ijk

pixId = self.transformed_image.ComputePointId(ijk)

pi_2display = self.transformed_image.GetPoint(pixId)

annots_dict['pi_2display']=pi_2display

print pi_2display

# mark final

print "Point final"

ijk[0] = int(annots_dict['xf'])

ijk[1] = int(annots_dict['yf'])

print ijk

annots_dict['pf_ijk']=ijk

pixId = self.transformed_image.ComputePointId(ijk)

pf_2display = self.transformed_image.GetPoint(pixId)

annots_dict['pf_2display']=pf_2display

print pf_2display

# Create a graphial line between the two points

annot_pts = vtk.vtkPoints()

annot_pts.InsertNextPoint(pi_2display)

annot_pts.InsertNextPoint(pf_2display)

annot_ln = vtk.vtkLine()

annot_ln.GetPointIds().SetId(0,0)

annot_ln.GetPointIds().SetId(1,1)

note_lines = vtk.vtkCellArray()

note_lines.InsertNextCell(annot_ln)

annot_poly = vtk.vtkPolyData()

annot_poly.SetPoints(annot_pts)

annot_poly.SetLines(note_lines)

annot_poly.Update()

# Create mappers and actors

annot_mapper_mesh = vtk.vtkPolyDataMapper()

annot_mapper_mesh.SetInput( annot_poly )

self.annot_actor = vtk.vtkActor()

self.annot_actor.SetMapper(annot_mapper_mesh)

self.annot_actor.GetProperty().SetColor(color_list[a_count])

self.annot_actor.GetProperty().SetLineWidth(3)

self.annot_actor.GetProperty().SetOpacity(0.6)

self.annot_actor.GetProperty().SetPointSize(7.0)

self.annot_actor.GetProperty().SetRepresentationToWireframe()

############

# Generate data arrays containing label ids

annot_pts_lbl.InsertPoint(a_count, pi_2display)

# add annotation to scene

print annots_dict

self.renderer1.AddActor(self.annot_actor)

# Initizalize

self.renWin1.Render()

self.renderer1.Render()

a_count +=1

except ValueError:

a_count +=1

pass

############

print annot_pts_lbl.GetNumberOfPoints()

annot_lbl_poly = vtk.vtkPolyData()

annot_lbl_poly.SetPoints(annot_pts_lbl)

annot_lbl_poly.Update()

# Generate data arrays containing label ids

ids = vtk.vtkIdFilter()

ids.SetInput(annot_lbl_poly)

ids.PointIdsOn()

ids.CellIdsOff()

# Create labels for points

visPts = vtk.vtkSelectVisiblePoints()

visPts.SetInput(ids.GetOutput())

visPts.SetRenderer(self.renderer1)

visPts.SelectionWindowOff()

# Create the mapper to display the point ids. Specify the format to

# use for the labels. Also create the associated actor.

ldm = vtk.vtkLabeledDataMapper()

ldm.SetInput(visPts.GetOutput())

ldm.SetLabelModeToLabelFieldData()

pointLabels = vtk.vtkActor2D()

pointLabels.SetMapper(ldm)

# initialize

self.renderer1.AddActor2D(pointLabels)

print "\n====== Color codes:\n "

print '\033[1;31m 1) Red '

print '\033[1;34m 2) Blue '

print '\033[1;36m 3) Cyan '

print '\033[1;33m 4) Yellow '

print '\033[1;35m 5) Fushia '

print '\033[1;37m 6) White '

print '\033[1;30m 7) Gray '

print '\033[1;0m'

############

if(interact==True):

interactor = self.renWin1.GetInteractor()

interactor.Start()

return

def extract_segment_dims(self, lesion3D):

'''Extract mayor dimensions of automatic lesion segmentation for validation'''

# define image based on subtraction of postS -preS

axis_lenghts = array( [0,0,0] ).astype(float)

l_bounds = lesion3D.GetBounds()

axis_lenghts[0] = (l_bounds[1]-l_bounds[0])**2

axis_lenghts[1] = (l_bounds[3]-l_bounds[2])**2

axis_lenghts[2] = (l_bounds[5]-l_bounds[4])**2