Source code for braviz.visualization.checkerboard_view
##############################################################################
# Braviz, Brain Data interactive visualization #
# Copyright (C) 2014 Diego Angulo #
# #
# This program is free software: you can redistribute it and/or modify #
# it under the terms of the GNU Lesser General Public License as #
# published by the Free Software Foundation, either version 3 of the #
# License, or (at your option) any later version. #
# #
# This program is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU Lesser General Public License for more details. #
# #
# You should have received a copy of the GNU Lesser General Public License#
# along with this program. If not, see <http://www.gnu.org/licenses/>. #
##############################################################################
import logging
import vtk
from vtk.qt4.QVTKRenderWindowInteractor import QVTKRenderWindowInteractor
from PyQt4.QtGui import QFrame, QHBoxLayout
from PyQt4.QtCore import pyqtSignal
from braviz.visualization.simple_vtk import OrientationAxes, persistentImagePlane, get_window_level
from braviz.visualization.subject_viewer import do_and_render
__author__ = 'Diego'
[docs]class CheckboardView(object):
"""
Viewer to compare two images
"""
def __init__(self, render_window_interactor, reader, widget):
"""
Construct the viewer
Args:
render_window_interactor (vtkRenderWindowInteractor) : Interactor for the image plane widget
reader (braviz.visualization.base_reader.BaseReader) : Braviz reader
widget (QObject) : Must implement *slice_change_handle*
"""
self.iren = render_window_interactor
self.ren_win = render_window_interactor.GetRenderWindow()
self.ren = vtk.vtkRenderer()
self.ren.SetBackground((0.75, 0.75, 0.75))
self.ren.GradientBackgroundOn()
self.ren.SetBackground2((0.5, 0.5, 0.5))
self.ren.SetBackground((0.2, 0.2, 0.2))
self.ren.SetUseDepthPeeling(1)
self.ren_win.SetMultiSamples(0)
self.ren_win.AlphaBitPlanesOn()
self.ren.SetOcclusionRatio(0.1)
self.ren_win.AddRenderer(self.ren)
self.iren.SetInteractorStyle(vtk.vtkInteractorStyleTrackballCamera())
self.axes = OrientationAxes()
self.axes.initialize(self.iren)
self.reader = reader
self.widget = widget
# pipeline
# img1 -> map_colors -------------- |checkboard view ---> plane widget
# img2 -> reslice -> map_colors -> |
self.__img1 = None
self.__img2 = None
self.__color_wl1 = vtk.vtkImageMapToWindowLevelColors()
self.__color_wl2 = vtk.vtkImageMapToWindowLevelColors()
self.__color_wl1.SetOutputFormatToRGB()
self.__color_wl2.SetOutputFormatToRGB()
self.__lut = self.reader.get("LABEL", None, lut=True, name="APARC")
self.__color_labels1 = vtk.vtkImageMapToColors()
self.__color_labels2 = vtk.vtkImageMapToColors()
self.__color_labels1.SetLookupTable(self.__lut)
self.__color_labels2.SetLookupTable(self.__lut)
self.__color_labels1.SetOutputFormatToRGB()
self.__color_labels2.SetOutputFormatToRGB()
# WL : Window Level, NOM: Nominal, PT: Pass Throug (no lut)
self.__color1_type = "WL"
self.__color2_type = "WL"
self.__reslice2 = vtk.vtkImageReslice()
self.__checkboard_view = vtk.vtkImageCheckerboard()
self.__plane_widget = None
self.__current_space = "subject"
self.__orientation = 2
self.__divs = 3
self.__img1_params = (None, "None", None)
self.__img2_params = (None, "None", None)
self.__outline = vtk.vtkOutlineFilter()
self.__outline_mapper = vtk.vtkPolyDataMapper()
self.__outline_mapper.SetInputConnection(
self.__outline.GetOutputPort())
self.__outline_actor = vtk.vtkActor()
self.__outline_actor.SetMapper(self.__outline_mapper)
self.ren.AddActor(self.__outline_actor)
self.reset_camera(0, skip_render=True)
self.set_number_of_divisions(self.__divs, skip_render=True)
__camera_positions_dict = {
0: ((-3.5, 0, 13), (157, 154, 130), (0, 0, 1)),
2: ((-3.5, 0, 10), (250, 0, 10), (0, 0, 1)),
1: ((-3.5, 0, 10), (-250, 0, 10), (0, 0, 1)),
4: ((-3.5, 0, 10), (-3.5, -200, 10), (0, 0, 1)),
3: ((-3.5, 0, 10), (-3.5, 200, 10), (0, 0, 1)),
5: ((-3, 0, 3), (-3, 0, 252), (0, 1, 0)),
6: ((-3, 0, 3), (-3, 0, -252), (0, 1, 0)),
}
@do_and_render
[docs] def reset_camera(self, position):
"""
resets the current camera to standard locations.
Args:
position (int) :
- 0: initial 3d view
- 1: left
- 2: right
- 3: front
- 4: back
- 5: top
- 6: bottom
"""
focal, position, viewup = self.__camera_positions_dict[position]
cam1 = self.ren.GetActiveCamera()
cam1.SetFocalPoint(focal)
cam1.SetPosition(position)
cam1.SetViewUp(viewup)
self.ren.ResetCameraClippingRange()
[docs] def update_pipeline(self):
"""
Updates the whole visualization pipeline
"""
if self.__plane_widget is None:
self._create_image_plane_widget()
if self.__img1 is None and self.__img2 is None:
self.__plane_widget.Off()
return
else:
self.__plane_widget.On()
if self.__img1 is not None:
self.__outline.SetInputData(self.__img1)
if self.__color1_type == "NOM":
self.__color_labels1.SetInputData(self.__img1)
if self.__img2 is None:
self.__color_labels1.Update()
self.__plane_widget.SetInputData(
self.__color_labels1.GetOutput())
else:
self.__color_labels1.Update()
self.__checkboard_view.SetInput1Data(
self.__color_labels1.GetOutput())
elif self.__color1_type == "WL":
self.__color_wl1.SetInputData(self.__img1)
w, l = get_window_level(self.__img1)
self.__color_wl1.SetWindow(w)
self.__color_wl1.SetLevel(l)
if self.__img2 is None:
self.__color_wl1.Update()
self.__plane_widget.SetInputData(
self.__color_wl1.GetOutput())
# self.__plane_widget.SetInputConnection(self.__color_wl1.GetOutputPort())
else:
self.__color_wl1.Update()
self.__checkboard_view.SetInput1Data(
self.__color_wl1.GetOutput())
elif self.__color1_type == "PT":
if self.__img2 is None:
self.__plane_widget.SetInputData(self.__img1)
else:
self.__checkboard_view.SetInput1Data(self.__img1)
else:
raise ValueError
if self.__img2 is not None:
if self.__img1 is not None:
self.__reslice2.SetOutputOrigin(self.__img1.GetOrigin())
self.__reslice2.SetOutputSpacing(self.__img1.GetSpacing())
self.__reslice2.SetOutputExtent(self.__img1.GetExtent())
if self.__color2_type:
self.__reslice2.SetInterpolationModeToNearestNeighbor()
else:
self.__reslice2.SetInterpolationModeToCubic()
self.__reslice2.SetInputData(self.__img2)
else:
self.__outline.SetInputData(self.__img2)
#----------------------------------
if self.__color2_type == "NOM":
if self.__img1 is None:
self.__color_labels2.SetInputData(self.__img2)
self.__color_labels2.Update()
self.__plane_widget.SetInputData(
self.__color_labels2.GetOutput())
else:
self.__color_labels2.SetInputConnection(
self.__reslice2.GetOutputPort())
self.__color_labels2.Update()
self.__checkboard_view.SetInput2Data(
self.__color_labels2.GetOutput())
elif self.__color2_type == "WL":
w, l = get_window_level(self.__img2)
self.__color_wl2.SetWindow(w)
self.__color_wl2.SetLevel(l)
if self.__img1 is None:
self.__color_wl2.SetInputData(self.__img2)
self.__color_wl2.Update()
self.__plane_widget.SetInputData(
self.__color_wl2.GetOutput())
else:
self.__color_wl2.SetInputConnection(
self.__reslice2.GetOutputPort())
self.__color_wl2.Update()
self.__checkboard_view.SetInput2Data(
self.__color_wl2.GetOutput())
elif self.__color2_type == "PT":
if self.__img1 is None:
self.__plane_widget.SetInputData(self.__img2)
else:
self.__reslice2.Update()
self.__checkboard_view.SetInput2Data(
self.__reslice2.GetOutput())
else:
raise ValueError
if self.__img1 is not None and self.__img2 is not None:
self.__checkboard_view.Update()
# print self.__checkboard_view.GetOutput()
self.__plane_widget.SetInputData(
self.__checkboard_view.GetOutput())
def _create_image_plane_widget(self):
"""
Creates the internal vtkImagePlaneWidget
"""
if self.__plane_widget is None:
self.__plane_widget = persistentImagePlane(self.__orientation)
self.__plane_widget.SetInteractor(self.iren)
self.__plane_widget.GetColorMap().SetLookupTable(None)
self.__plane_widget.On()
def slice_change_handler(source, event):
new_slice = self.__plane_widget.GetSliceIndex()
self.widget.slice_change_handle(new_slice)
self.__plane_widget.AddObserver(
self.__plane_widget.slice_change_event, slice_change_handler)
@do_and_render
[docs] def set_img1(self, subj, img_class, img_name, contrast=1, force=False):
"""
Sets the first image
Args:
subj : Subject image code
img_class (str) : image class (see :meth:`braviz.visualization.subject_viewer.ImageManager.change_image_modality`)
img_name (str) : image name (see :meth:`braviz.visualization.subject_viewer.ImageManager.change_image_modality`)
contrast (int) : contrast for fMRI images
force (bool) : if ``True`` force reloading the data
"""
if img_class is not None:
img_class = img_class.upper()
img_name = img_name.upper()
params = (subj, img_class, img_name, contrast)
if params == self.__img1_params and not force:
return
self.__img1_params = params
if img_class is None:
self.__img1 = None
else:
try:
self.__img1 = self.reader.get(img_class, subj, format="vtk",
space=self.__current_space, name=img_name)
except Exception as e:
log = logging.getLogger(__name__)
log.exception(e)
self.__img1 = None
if img_class == "LABEL":
self.__color1_type = "NOM"
elif img_class == "DTI":
self.__color1_type = "PT"
elif img_class == "IMAGE":
self.__color1_type = "WL"
elif img_class is None:
pass
else:
raise NotImplementedError
self.update_pipeline()
@do_and_render
[docs] def set_img2(self, subj, img_class, img_name, contrast=None, force=False):
"""
Sets the second image
Args:
subj : Subject image code
img_class (str) : image class (see :meth:`braviz.visualization.subject_viewer.ImageManager.change_image_modality`)
img_name (str) : image name (see :meth:`braviz.visualization.subject_viewer.ImageManager.change_image_modality`)
contrast (int) : contrast for fMRI images
force (bool) : if ``True`` force reloading the data
"""
if img_class is not None:
img_class = img_class.upper()
img_name = img_name.upper()
params = (subj, img_class, img_name, contrast)
if params == self.__img1_params and not force:
return
self.__img2_params = params
if img_class is None:
self.__img2 = None
else:
try:
self.__img2 = self.reader.get(img_class, subj, format="vtk",
space=self.__current_space, name=img_name)
except Exception as e:
log = logging.getLogger(__name__)
log.exception(e)
self.__img2 = None
if img_class == "LABEL":
self.__color2_type = "NOM"
elif img_class == "DTI":
self.__color2_type = "PT"
elif img_class == "IMAGE":
self.__color2_type = "WL"
else:
raise NotImplementedError
self.update_pipeline()
@do_and_render
[docs] def set_number_of_divisions(self, divs):
"""
Set number of divisions in the checkboard pattern
Args:
divs (int) : Number of divisions
"""
divs_ar = [divs] * 3
divs_ar[self.__orientation] = 1
self.__checkboard_view.SetNumberOfDivisions(divs_ar)
self.__divs = divs
if self.__img1 is not None and self.__img2 is not None:
self.__checkboard_view.Update()
self.__plane_widget.SetInputData(
self.__checkboard_view.GetOutput())
@do_and_render
[docs] def set_orientation(self, orientation_int):
"""
Sets orientation of the plane widget
Args:
orientation_int (int) : 0 is x, 1 is y, 2 is z
"""
self.__plane_widget.set_orientation(orientation_int)
self.__orientation = orientation_int
self.set_number_of_divisions(self.__divs, skip_render=True)
def _load_test_view(self):
"""
Test
"""
self.set_img1(119, "IMAGE", "MRI")
self.set_img2(119, "LABEL", "APARC")
@do_and_render
[docs] def change_space(self, new_space):
"""
Change current coordinate system
new_space (str) : new coordinate system, see :meth:`~braviz.readAndFilter.base_reader.BaseReader.get`
"""
self.__current_space = new_space
p1 = self.__img1_params
p2 = self.__img2_params
self.set_img1(*p1, force=True, skip_render=True)
self.set_img2(*p2, force=True, skip_render=True)
@do_and_render
[docs] def set_image_slice(self, new_slice):
"""
Set plane widget slice
Args:
new_slice (int) : Index of desired slice
"""
if self.__plane_widget is None:
return
self.__plane_widget.SetSliceIndex(int(new_slice))
self.__plane_widget.InvokeEvent(self.__plane_widget.slice_change_event)
[docs] def get_number_of_image_slices(self):
"""
Gets the number of slices available in the current direction
Returns:
The number of available slices
"""
if self.__plane_widget is None:
return 0
img = self.__plane_widget.GetInput()
if img is None:
return 0
dimensions = img.GetDimensions()
return dimensions[self.__orientation]
[docs]class QCheckViewer(QFrame):
"""
Wraps the :class:`CheckboardView` so that in can be connected to Qt applications.
"""
slice_changed = pyqtSignal(int)
def __init__(self, reader, parent):
"""
Constructs the widget
Args:
reader (braviz.visualization.base_reader.BaseReader) : Braviz reader
parent (QObject) : Parent
"""
QFrame.__init__(self, parent)
self.__qwindow_interactor = QVTKRenderWindowInteractor(self)
self.__reader = reader
self.__vtk_viewer = CheckboardView(
self.__qwindow_interactor, self.__reader, self)
self.__layout = QHBoxLayout()
self.__layout.addWidget(self.__qwindow_interactor)
self.__layout.setContentsMargins(0, 0, 0, 0)
self.setLayout(self.__layout)
[docs] def initialize_widget(self):
"""
Call this function **after** calling show on the widget or a parent
"""
self.__qwindow_interactor.Initialize()
self.__qwindow_interactor.Start()
@property
def viewer(self):
"""
Access to internal :class:`CheckboardView` object
"""
return self.__vtk_viewer
[docs] def slice_change_handle(self, new_slice):
"""
Emits a qt signal when the current slice is changed from vtk
"""
self.slice_changed.emit(new_slice)