def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.vtkImageLogarithmicScale(), 'Processing.',
('vtkImageData',), ('vtkImageData',),
replaceDoc=True,
inputFunctions=None, outputFunctions=None)
def fft(self, mode='magnitude', logscale=12, center=True):
"""Fast Fourier transform of a picture.
:param float logscale: if non-zero, take the logarithm of the
intensity and scale it by this factor.
:param str mode: either [magnitude, real, imaginary, complex], compute the
point array data accordingly.
:param bool center: shift constant zero-frequency to the center of the image for display.
(FFT converts spatial images into frequency space, but puts the zero frequency at the origin)
"""
ffti = vtk.vtkImageFFT()
ffti.SetInputData(self._data)
ffti.Update()
if 'mag' in mode:
mag = vtk.vtkImageMagnitude()
mag.SetInputData(ffti.GetOutput())
mag.Update()
out = mag.GetOutput()
elif 'real' in mode:
extractRealFilter = vtk.vtkImageExtractComponents()
extractRealFilter.SetInputData(ffti.GetOutput())
extractRealFilter.SetComponents(0)
extractRealFilter.Update()
out = extractRealFilter.GetOutput()
elif 'imaginary' in mode:
extractImgFilter = vtk.vtkImageExtractComponents()
extractImgFilter.SetInputData(ffti.GetOutput())
extractImgFilter.SetComponents(1)
extractImgFilter.Update()
out = extractImgFilter.GetOutput()
elif 'complex' in mode:
out = ffti.GetOutput()
else:
colors.printc("Error in fft(): unknown mode", mode)
raise RuntimeError()
if center:
center = vtk.vtkImageFourierCenter()
center.SetInputData(out)
center.Update()
out = center.GetOutput()
if 'complex' not in mode:
if logscale:
ils = vtk.vtkImageLogarithmicScale()
ils.SetInputData(out)
ils.SetConstant(logscale)
ils.Update()
out = ils.GetOutput()
return Picture(out)
def main():
# Initialize argument and constant variables
parser = ArgumentParser("Create isosurfacing of object")
parser.add_argument("infections")
parser.add_argument("recovered")
parser.add_argument("deaths")
parser.add_argument("density")
parser.add_argument("climate_max")
parser.add_argument("climate_min")
parser.add_argument("location")
parser.add_argument("migration")
parser.add_argument("sat")
parser.add_argument("--camera",
type=str,
help="Optional camera settings file")
args = parser.parse_args()
global sat_x
global sat_y
global max_cases
global max_radius
global infections_color
global recovered_color
global deaths_color
global infections_opacity
global recovered_opacity
global deaths_opacity
global infections_data
global recovered_data
global deaths_data
global legend_circle_actors
global legend_text_actors
global max_weight
global ren
app = QApplication([])
window = QMainWindow()
ui = Ui_MainWindow()
ui.setupUi(window)
# Read in data for global confirmed cases
with open(args.infections) as csvDataFile:
csv_reader = csv.reader(csvDataFile)
for row in csv_reader:
# We do not need country/province name, so we remove the first two columns
if (row[2] != 0 or row[3] != 0):
infections_data.append(row[2:])
infections_data = infections_data[1:]
# Read in data for global deaths
with open(args.deaths) as csvDataFile:
csv_reader = csv.reader(csvDataFile)
for row in csv_reader:
if (row[2] != 0 or row[3] != 0):
deaths_data.append(row[2:])
deaths_data = deaths_data[1:]
# Read in data for global recovered cases
with open(args.recovered) as csvDataFile:
csv_reader = csv.reader(csvDataFile)
for row in csv_reader:
if (row[2] != 0 or row[3] != 0):
recovered_data.append(row[2:])
recovered_data = recovered_data[1:]
numDates = len(infections_data[0]) - 3
max_cases = compute_max(date)
# Create reader for density file
density_reader = vtk.vtkTIFFReader()
density_reader.SetFileName(args.density)
density_reader.Update()
density_log = vtk.vtkImageLogarithmicScale()
density_log.SetInputConnection(density_reader.GetOutputPort())
density_log.SetConstant(0.435)
density_log.Update()
density_range = density_log.GetOutput().GetScalarRange()
climate_max_reader = vtk.vtkTIFFReader()
climate_max_reader.SetFileName(args.climate_max + "-" +
str(initial_date.month.real).zfill(2) +
".tif")
climate_max_reader.Update()
climate_max_range = [-40, 45]
climate_min_reader = vtk.vtkTIFFReader()
climate_min_reader.SetFileName(args.climate_min + "-" +
str(initial_date.month.real).zfill(2) +
".tif")
climate_min_reader.Update()
climate_min_range = [-50, 30]
sat_reader = vtk.vtkJPEGReader()
sat_reader.SetFileName(args.sat)
sat_reader.Update()
sat_dimensions = sat_reader.GetOutput().GetDimensions()
sat_x = sat_dimensions[0]
sat_y = sat_dimensions[1]
# Read in data for migration
location_map = create_long_lat(args.location)
migrations = []
for filename in os.listdir(args.migration):
if filename.endswith(".csv"):
with open(args.migration + "\\" + filename) as csvDataFile:
country = filename.split(".")[0]
if country not in location_map:
continue
loc_dst = location_map[country]
csv_reader = csv.reader(csvDataFile)
for row in csv_reader:
if row[2] not in location_map:
continue
loc_src = location_map[row[2]]
try:
migrations.append(
add_migration_info(loc_src, loc_dst, int(row[9])))
except ValueError:
continue
line_actors = process_migration_actors(migrations)
# Create a plane to map the satellite image onto
plane = vtk.vtkPlaneSource()
plane.SetCenter(0.0, 0.0, 0.0)
plane.SetNormal(0.0, 0.0, 1.0)
plane.SetPoint1(sat_x, 0, 0)
plane.SetPoint2(0, sat_y, 0)
# Create satellite image texture
texture = vtk.vtkTexture()
texture.SetInputConnection(sat_reader.GetOutputPort())
# Map satellite texture to plane
texturePlane = vtk.vtkTextureMapToPlane()
texturePlane.SetInputConnection(plane.GetOutputPort())
max_val = 100
color_count = 1000
density_ctf = vtk.vtkColorTransferFunction()
density_ctf.AddRGBPoint(0, 0, 0, 0)
density_ctf.AddRGBPoint(10, 0, 0, 1)
density_ctf.AddRGBPoint(30, 0, 1, 1)
density_ctf.AddRGBPoint(50, 1, 1, 0)
density_ctf.AddRGBPoint(65, 1, 0.5, 0)
density_ctf.AddRGBPoint(80, 1, 0, 0)
density_lut = vtk.vtkLookupTable()
density_lut.SetNumberOfTableValues(color_count)
density_lut.Build()
rgb = list(density_ctf.GetColor(0)) + [0]
density_lut.SetTableValue(0, rgb)
for i in range(1, color_count):
rgb = list(density_ctf.GetColor(
max_val * float(i) / color_count)) + [1]
density_lut.SetTableValue(i, rgb)
climate_ctf = vtk.vtkColorTransferFunction()
climate_ctf.AddRGBPoint(5, 0, 0, 1)
climate_ctf.AddRGBPoint(35, 0, 1, 1)
climate_ctf.AddRGBPoint(65, 1, 1, 0)
climate_ctf.AddRGBPoint(95, 1, 0, 0)
climate_lut = vtk.vtkLookupTable()
climate_lut.SetNumberOfTableValues(color_count)
climate_lut.Build()
for i in range(0, color_count):
rgb = list(climate_ctf.GetColor(
max_val * float(i) / color_count)) + [1]
climate_lut.SetTableValue(i, rgb)
# Create mappers
density_mapper = vtk.vtkDataSetMapper()
density_mapper.SetInputConnection(density_log.GetOutputPort())
density_mapper.SetLookupTable(density_lut)
density_mapper.SetScalarRange([0, density_range[1]])
density_mapper.Update()
climate_max_mapper = vtk.vtkDataSetMapper()
climate_max_mapper.SetInputConnection(climate_max_reader.GetOutputPort())
climate_max_mapper.SetLookupTable(climate_lut)
climate_max_mapper.SetScalarRange(climate_max_range)
climate_max_mapper.Update()
climate_min_mapper = vtk.vtkDataSetMapper()
climate_min_mapper.SetInputConnection(climate_min_reader.GetOutputPort())
climate_min_mapper.SetLookupTable(climate_lut)
climate_min_mapper.SetScalarRange(climate_min_range)
climate_min_mapper.Update()
sat_mapper = vtk.vtkPolyDataMapper()
sat_mapper.SetInputConnection(texturePlane.GetOutputPort())
density_actor = vtk.vtkActor()
density_actor.SetMapper(density_mapper)
density_actor.GetProperty().SetOpacity(0.99)
density_actor.VisibilityOn()
climate_max_actor = vtk.vtkActor()
climate_max_actor.SetMapper(climate_max_mapper)
climate_max_actor.GetProperty().SetOpacity(0.6)
climate_max_actor.VisibilityOff()
climate_min_actor = vtk.vtkActor()
climate_min_actor.SetMapper(climate_min_mapper)
climate_min_actor.GetProperty().SetOpacity(0.6)
climate_min_actor.VisibilityOff()
sat_actor = vtk.vtkActor()
sat_actor.SetMapper(sat_mapper)
sat_actor.SetTexture(texture)
sat_actor.GetProperty().SetOpacity(0.6)
# Make satellite image same size as contour map
crange = sat_actor.GetXRange()[0] - sat_actor.GetXRange()[1]
mrange = density_actor.GetXRange()[0] - density_actor.GetXRange()[1]
density_actor.SetScale(crange / mrange)
crange = sat_actor.GetXRange()[0] - sat_actor.GetXRange()[1]
mrange = climate_max_actor.GetXRange()[0] - climate_max_actor.GetXRange(
)[1]
climate_max_actor.SetScale(crange / mrange)
climate_min_actor.SetScale(crange / mrange)
# Initialize renderer and place actors
ren = vtk.vtkRenderer()
ren.AddActor(density_actor)
ren.AddActor(climate_max_actor)
ren.AddActor(climate_min_actor)
# Add legend actors
add_legend_actors()
# Add infections, recovered, and deaths actors
infections_actors = []
if (ui.infections_check.isChecked()):
add_case_actors(date, infections_data, infections_actors,
infections_color, infections_opacity)
recovered_actors = []
if (ui.recovered_check.isChecked()):
add_case_actors(date, recovered_data, recovered_actors,
recovered_color, recovered_opacity)
deaths_actors = []
if (ui.deaths_check.isChecked()):
add_case_actors(date, deaths_data, deaths_actors, deaths_color,
deaths_opacity)
for line_actor in line_actors:
line_actor.VisibilityOn()
ren.AddActor(line_actor)
ren.AddActor(sat_actor)
ren.ResetCamera()
ren.SetBackground(0, 0, 0)
# Initialize camera settings
cam1 = ren.GetActiveCamera()
cam1.Azimuth(0)
cam1.Elevation(0)
cam1.Roll(360)
cam1.Zoom(1.5)
ren.ResetCameraClippingRange()
if args.camera:
reader = open(args.camera, "r")
line = reader.readline().split(",")
cam1.SetPosition(float(line[0]), float(line[1]), float(line[2]))
line = reader.readline().split(",")
cam1.SetFocalPoint(float(line[0]), float(line[1]), float(line[2]))
line = reader.readline().split(",")
cam1.SetViewUp(float(line[0]), float(line[1]), float(line[2]))
line = reader.readline().split(",")
cam1.SetClippingRange(float(line[0]), float(line[1]))
line = reader.readline().split(",")
cam1.SetViewAngle(float(line[0]))
line = reader.readline().split(",")
cam1.SetParallelScale(float(line[0]))
# Initialize PyQT5 UI and link to renderer
ui.vtkWidget.GetRenderWindow().AddRenderer(ren)
ui.vtkWidget.GetRenderWindow().SetSize(1280, 720)
ui.vtkWidget.GetRenderWindow().AddRenderer(ren)
ui.vtkWidget.GetRenderWindow().SetAlphaBitPlanes(True)
ui.vtkWidget.GetRenderWindow().SetMultiSamples(False)
iren = ui.vtkWidget.GetRenderWindow().GetInteractor()
# create the scalar_bar
density_scalar_bar = vtk.vtkScalarBarActor()
density_scalar_bar.SetOrientationToHorizontal()
density_scalar_bar.SetMaximumNumberOfColors(color_count)
density_scalar_bar.SetLookupTable(density_lut)
density_scalar_bar.SetTitle("Density (Log 10)")
# create the scalar_bar_widget
density_scalar_bar_widget = vtk.vtkScalarBarWidget()
density_scalar_bar_widget.SetInteractor(iren)
density_scalar_bar_widget.SetScalarBarActor(density_scalar_bar)
density_scalar_bar_widget.On()
# create the scalar_bar
climate_scalar_bar = vtk.vtkScalarBarActor()
climate_scalar_bar.SetOrientationToHorizontal()
climate_scalar_bar.SetMaximumNumberOfColors(color_count)
climate_scalar_bar.SetLookupTable(climate_lut)
climate_scalar_bar.SetTitle("Temparature (Celsius)")
# create the scalar_bar_widget
climate_scalar_bar_widget = vtk.vtkScalarBarWidget()
climate_scalar_bar_widget.SetInteractor(iren)
climate_scalar_bar_widget.SetScalarBarActor(climate_scalar_bar)
climate_scalar_bar_widget.Off()
# Function to initialize slider settings
def slider_setup(slider, val, bounds, interv):
slider.setOrientation(QtCore.Qt.Horizontal)
slider.setValue(float(val))
slider.setSliderPosition(val)
slider.setTracking(False)
slider.setTickInterval(interv)
slider.setTickPosition(QSlider.TicksAbove)
slider.setRange(bounds[0], bounds[1])
slider_setup(ui.time_slider, 0, [0, numDates], 1)
window.show()
window.setWindowState(Qt.WindowMaximized)
iren.Initialize()
def time_slider_callback(val):
global max_cases
global date
date = val
new_date = initial_date + timedelta(val)
if new_date.month.real != ui.curr_month:
ui.curr_month = new_date.month.real
climate_max_reader.SetFileName(args.climate_max + "-" +
str(ui.curr_month).zfill(2) +
".tif")
climate_max_reader.Update()
climate_min_reader.SetFileName(args.climate_min + "-" +
str(ui.curr_month).zfill(2) +
".tif")
climate_min_reader.Update()
ui.date_label.setText("Date (" + new_date.strftime('%m/%d/%Y') + "):")
# Remove old infections, recovered, and deaths actors
remove_case_actors(infections_actors)
remove_case_actors(recovered_actors)
remove_case_actors(deaths_actors)
remove_legend_actors()
# Recompute max cases
max_cases = compute_max(date)
# Add infections, recovered, and deaths actors
if (ui.infections_check.isChecked()):
add_case_actors(date, infections_data, infections_actors,
infections_color, infections_opacity)
if (ui.recovered_check.isChecked()):
add_case_actors(date, recovered_data, recovered_actors,
recovered_color, recovered_opacity)
if (ui.deaths_check.isChecked()):
add_case_actors(date, deaths_data, deaths_actors, deaths_color,
deaths_opacity)
add_legend_actors()
ui.vtkWidget.GetRenderWindow().Render()
def infections_callback():
if (ui.infections_check.isChecked()):
add_case_actors(date, infections_data, infections_actors,
infections_color, infections_opacity)
else:
remove_case_actors(infections_actors)
ui.vtkWidget.GetRenderWindow().Render()
def recovered_callback():
if (ui.recovered_check.isChecked()):
add_case_actors(date, recovered_data, recovered_actors,
recovered_color, recovered_opacity)
else:
remove_case_actors(recovered_actors)
ui.vtkWidget.GetRenderWindow().Render()
def deaths_callback():
if (ui.deaths_check.isChecked()):
add_case_actors(date, deaths_data, deaths_actors, deaths_color,
deaths_opacity)
else:
remove_case_actors(deaths_actors)
ui.vtkWidget.GetRenderWindow().Render()
def density_callback():
if ui.density_check.isChecked():
ui.climate_max_check.setChecked(False)
ui.climate_min_check.setChecked(False)
density_actor.VisibilityOn()
density_scalar_bar_widget.On()
ui.vtkWidget.GetRenderWindow().Render()
else:
density_actor.VisibilityOff()
density_scalar_bar_widget.Off()
ui.vtkWidget.GetRenderWindow().Render()
def climate_max_callback():
if ui.climate_max_check.isChecked():
ui.density_check.setChecked(False)
ui.climate_min_check.setChecked(False)
climate_max_actor.VisibilityOn()
climate_scalar_bar_widget.On()
ui.vtkWidget.GetRenderWindow().Render()
else:
climate_max_actor.VisibilityOff()
climate_scalar_bar_widget.Off()
ui.vtkWidget.GetRenderWindow().Render()
def climate_min_callback():
if ui.climate_min_check.isChecked():
ui.density_check.setChecked(False)
ui.climate_max_check.setChecked(False)
climate_min_actor.VisibilityOn()
climate_scalar_bar_widget.On()
ui.vtkWidget.GetRenderWindow().Render()
else:
climate_min_actor.VisibilityOff()
climate_scalar_bar_widget.Off()
ui.vtkWidget.GetRenderWindow().Render()
def migration_callback():
if ui.migration_check.isChecked():
for line_actor in line_actors:
line_actor.VisibilityOn()
ui.vtkWidget.GetRenderWindow().Render()
else:
for line_actor in line_actors:
line_actor.VisibilityOff()
ui.vtkWidget.GetRenderWindow().Render()
# Handle screenshot button event
def screenshot_callback():
save_frame(ren.GetActiveCamera(), ui.vtkWidget.GetRenderWindow(),
ui.log)
# Handle show camera settings button event
def camera_callback():
print_camera_settings(ren.GetActiveCamera(), ui.camera_info, ui.log)
# Handle quit button event
def quit_callback():
sys.exit()
# Register callbacks to UI
ui.time_slider.valueChanged.connect(time_slider_callback)
ui.push_screenshot.clicked.connect(screenshot_callback)
ui.push_camera.clicked.connect(camera_callback)
ui.push_quit.clicked.connect(quit_callback)
ui.infections_check.stateChanged.connect(infections_callback)
ui.recovered_check.stateChanged.connect(recovered_callback)
ui.deaths_check.stateChanged.connect(deaths_callback)
ui.density_check.stateChanged.connect(density_callback)
ui.climate_max_check.stateChanged.connect(climate_max_callback)
ui.climate_min_check.stateChanged.connect(climate_min_callback)
ui.migration_check.stateChanged.connect(migration_callback)
# Terminate setup for PyQT5 interface
sys.exit(app.exec_())
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# This scripts shows a compressed spectrum of an image.
# Image pipeline
reader = vtk.vtkPNGReader()
reader.SetFileName("" + str(VTK_DATA_ROOT) + "/Data/fullhead15.png")
fft = vtk.vtkImageFFT()
fft.SetInputConnection(reader.GetOutputPort())
fft.ReleaseDataFlagOff()
#fft DebugOn
magnitude = vtk.vtkImageMagnitude()
magnitude.SetInputConnection(fft.GetOutputPort())
magnitude.ReleaseDataFlagOff()
center = vtk.vtkImageFourierCenter()
center.SetInputConnection(magnitude.GetOutputPort())
compress = vtk.vtkImageLogarithmicScale()
compress.SetInputConnection(center.GetOutputPort())
compress.SetConstant(15)
viewer = vtk.vtkImageViewer2()
viewer.SetInputConnection(compress.GetOutputPort())
viewer.SetColorWindow(150)
viewer.SetColorLevel(170)
viewInt = vtk.vtkRenderWindowInteractor()
viewer.SetupInteractor(viewInt)
viewer.Render()
# --- end of script --
def main():
colors = vtk.vtkNamedColors()
fileName = get_program_parameters()
# Read the image.
readerFactory = vtk.vtkImageReader2Factory()
reader = readerFactory.CreateImageReader2(fileName)
reader.SetFileName(fileName)
reader.Update()
fft = vtk.vtkImageFFT()
fft.SetInputConnection(reader.GetOutputPort())
mag = vtk.vtkImageMagnitude()
mag.SetInputConnection(fft.GetOutputPort())
center = vtk.vtkImageFourierCenter()
center.SetInputConnection(mag.GetOutputPort())
compress = vtk.vtkImageLogarithmicScale()
compress.SetInputConnection(center.GetOutputPort())
compress.SetConstant(15)
compress.Update()
# Create the actors.
originalActor = vtk.vtkImageActor()
originalActor.GetMapper().SetInputConnection(reader.GetOutputPort())
originalActor.GetProperty().SetInterpolationTypeToNearest()
compressedActor = vtk.vtkImageActor()
compressedActor.GetMapper().SetInputConnection(compress.GetOutputPort())
compressedActor.GetProperty().SetInterpolationTypeToNearest()
CreateImageActor(compressedActor, 160, 120)
# Define the viewport ranges.
# (xmin, ymin, xmax, ymax)
originalViewport = [0.0, 0.0, 0.5, 1.0]
compressedViewport = [0.5, 0.0, 1.0, 1.0]
# Setup the renderers.
originalRenderer = vtk.vtkRenderer()
originalRenderer.SetViewport(originalViewport)
originalRenderer.AddActor(originalActor)
originalRenderer.ResetCamera()
originalRenderer.SetBackground(colors.GetColor3d("SlateGray"))
compressedRenderer = vtk.vtkRenderer()
compressedRenderer.SetViewport(compressedViewport)
compressedRenderer.AddActor(compressedActor)
compressedRenderer.ResetCamera()
compressedRenderer.SetBackground(colors.GetColor3d("LightSlateGray"))
renderWindow = vtk.vtkRenderWindow()
renderWindow.SetSize(600, 300)
renderWindow.SetWindowName('VTKSpectrum')
renderWindow.AddRenderer(originalRenderer)
renderWindow.AddRenderer(compressedRenderer)
renderWindowInteractor = vtk.vtkRenderWindowInteractor()
style = vtk.vtkInteractorStyleImage()
renderWindowInteractor.SetInteractorStyle(style)
renderWindowInteractor.SetRenderWindow(renderWindow)
renderWindowInteractor.Initialize()
renderWindowInteractor.Start()
def scatterPlot(imagedata1, imagedata2, z, countVoxels=True, wholeVolume=True, logarithmic=True, bitDepth=8):
"""
Create scatterplot
"""
imagedata1.SetUpdateExtent(imagedata1.GetWholeExtent())
imagedata2.SetUpdateExtent(imagedata1.GetWholeExtent())
imagedata1.Update()
imagedata2.Update()
range1 = imagedata1.GetScalarRange()
range2 = imagedata2.GetScalarRange()
n = 255
# n = min(max(sc1max,sc2max),255)
# d = (n+1) / float(2**bitDepth)
if bitDepth is None:
spacing1 = float(abs(range1[1] - range1[0])) / (n + 1)
spacing2 = float(abs(range2[1] - range2[0])) / (n + 1)
else:
spacing1 = float(2 ** bitDepth) / (n + 1)
spacing2 = float(2 ** bitDepth) / (n + 1)
app = vtk.vtkImageAppendComponents()
app.AddInput(imagedata1)
app.AddInput(imagedata2)
# shiftscale = vtk.vtkImageShiftScale()
# shiftscale.SetOutputScalarTypeToUnsignedChar()
# shiftscale.SetScale(d)
# shiftscale.SetInputConnection(app.GetOutputPort())
acc = vtk.vtkImageAccumulate()
acc.SetComponentExtent(0, n, 0, n, 0, 0)
acc.SetComponentOrigin(range1[0], range2[0], 0)
acc.SetComponentSpacing(spacing1, spacing2, 0)
# acc.SetInputConnection(shiftscale.GetOutputPort())
acc.SetInputConnection(app.GetOutputPort())
acc.Update()
data = acc.GetOutput()
origData = data
originalRange = data.GetScalarRange()
if logarithmic:
Logging.info("Scaling scatterplot logarithmically", kw="imageop")
logscale = vtk.vtkImageLogarithmicScale()
logscale.SetInputConnection(acc.GetOutputPort())
logscale.Update()
data = logscale.GetOutput()
x0, x1 = data.GetScalarRange()
if countVoxels:
Logging.info("Scalar range of scatterplot = ", x0, x1, kw="imageop")
ctf = fire(x0, x1)
ctf = equalize(data, ctf, x1)
maptocolor = vtk.vtkImageMapToColors()
maptocolor.SetInputConnection(data.GetProducerPort())
maptocolor.SetLookupTable(ctf)
maptocolor.SetOutputFormatToRGB()
maptocolor.Update()
data = maptocolor.GetOutput()
ctf.originalRange = originalRange
Logging.info("Scatterplot has dimensions: ", data.GetDimensions(), data.GetExtent(), kw="imageop")
data.SetWholeExtent(data.GetExtent())
img = vtkImageDataToWxImage(data)
# w, h = img.GetWidth(), img.GetHeight()
# if w < 255 or h < 255:
# dh = 255-h
# img.Resize((255, 255),(0, 0), 0,0,0)
return img, ctf, origData
def scatterPlot(imagedata1,
imagedata2,
z,
countVoxels=True,
wholeVolume=True,
logarithmic=True,
bitDepth=8):
"""
Create scatterplot
"""
imagedata1.SetUpdateExtent(imagedata1.GetWholeExtent())
imagedata2.SetUpdateExtent(imagedata1.GetWholeExtent())
imagedata1.Update()
imagedata2.Update()
range1 = imagedata1.GetScalarRange()
range2 = imagedata2.GetScalarRange()
n = 255
#n = min(max(sc1max,sc2max),255)
#d = (n+1) / float(2**bitDepth)
if bitDepth is None:
spacing1 = float(abs(range1[1] - range1[0])) / (n + 1)
spacing2 = float(abs(range2[1] - range2[0])) / (n + 1)
else:
spacing1 = float(2**bitDepth) / (n + 1)
spacing2 = float(2**bitDepth) / (n + 1)
app = vtk.vtkImageAppendComponents()
app.AddInput(imagedata1)
app.AddInput(imagedata2)
#shiftscale = vtk.vtkImageShiftScale()
#shiftscale.SetOutputScalarTypeToUnsignedChar()
#shiftscale.SetScale(d)
#shiftscale.SetInputConnection(app.GetOutputPort())
acc = vtk.vtkImageAccumulate()
acc.SetComponentExtent(0, n, 0, n, 0, 0)
acc.SetComponentOrigin(range1[0], range2[0], 0)
acc.SetComponentSpacing(spacing1, spacing2, 0)
#acc.SetInputConnection(shiftscale.GetOutputPort())
acc.SetInputConnection(app.GetOutputPort())
acc.Update()
data = acc.GetOutput()
origData = data
originalRange = data.GetScalarRange()
if logarithmic:
Logging.info("Scaling scatterplot logarithmically", kw="imageop")
logscale = vtk.vtkImageLogarithmicScale()
logscale.SetInputConnection(acc.GetOutputPort())
logscale.Update()
data = logscale.GetOutput()
x0, x1 = data.GetScalarRange()
if countVoxels:
Logging.info("Scalar range of scatterplot = ", x0, x1, kw="imageop")
ctf = fire(x0, x1)
ctf = equalize(data, ctf, x1)
maptocolor = vtk.vtkImageMapToColors()
maptocolor.SetInputConnection(data.GetProducerPort())
maptocolor.SetLookupTable(ctf)
maptocolor.SetOutputFormatToRGB()
maptocolor.Update()
data = maptocolor.GetOutput()
ctf.originalRange = originalRange
Logging.info("Scatterplot has dimensions: ",
data.GetDimensions(),
data.GetExtent(),
kw="imageop")
data.SetWholeExtent(data.GetExtent())
img = vtkImageDataToWxImage(data)
#w, h = img.GetWidth(), img.GetHeight()
#if w < 255 or h < 255:
# dh = 255-h
# img.Resize((255, 255),(0, 0), 0,0,0)
return img, ctf, origData
def main():
# Initialize argument and constant variables
parser = ArgumentParser("Create isosurfacing of object")
parser.add_argument("density")
parser.add_argument("climate")
parser.add_argument("sat")
parser.add_argument("--camera",
type=str,
help="Optional camera settings file")
args = parser.parse_args()
# Create reader for ct scan
density_reader = vtk.vtkTIFFReader()
density_reader.SetFileName(args.density)
density_reader.Update()
print(density_reader.GetOutput().GetScalarRange()[1])
density_log = vtk.vtkImageLogarithmicScale()
density_log.SetInputConnection(density_reader.GetOutputPort())
density_log.SetConstant(0.435)
density_log.Update()
density_range = density_log.GetOutput().GetScalarRange()
climate_reader = vtk.vtkTIFFReader()
climate_reader.SetFileName(args.climate + "-" +
str(initial_date.month.real).zfill(2) + ".tif")
climate_reader.Update()
climate_range = climate_reader.GetOutput().GetScalarRange()
sat_reader = vtk.vtkJPEGReader()
sat_reader.SetFileName(args.sat)
max_val = 100
color_count = 1000
density_ctf = vtk.vtkColorTransferFunction()
density_ctf.AddRGBPoint(0, 0, 0, 0)
density_ctf.AddRGBPoint(10, 0, 0, 1)
density_ctf.AddRGBPoint(30, 0, 1, 1)
density_ctf.AddRGBPoint(50, 1, 1, 0)
density_ctf.AddRGBPoint(65, 1, 0.5, 0)
density_ctf.AddRGBPoint(80, 1, 0, 0)
density_lut = vtk.vtkLookupTable()
density_lut.SetNumberOfTableValues(color_count)
density_lut.Build()
rgb = list(density_ctf.GetColor(0)) + [0]
density_lut.SetTableValue(0, rgb)
for i in range(1, color_count):
rgb = list(density_ctf.GetColor(
max_val * float(i) / color_count)) + [1]
density_lut.SetTableValue(i, rgb)
climate_ctf = vtk.vtkColorTransferFunction()
climate_ctf.AddRGBPoint(5, 0, 0, 1)
climate_ctf.AddRGBPoint(35, 0, 1, 1)
climate_ctf.AddRGBPoint(65, 1, 1, 0)
climate_ctf.AddRGBPoint(95, 1, 0, 0)
climate_lut = vtk.vtkLookupTable()
climate_lut.SetNumberOfTableValues(color_count)
climate_lut.Build()
for i in range(0, color_count):
rgb = list(climate_ctf.GetColor(
max_val * float(i) / color_count)) + [1]
climate_lut.SetTableValue(i, rgb)
density_mapper = vtk.vtkDataSetMapper()
density_mapper.SetInputConnection(density_log.GetOutputPort())
density_mapper.SetLookupTable(density_lut)
density_mapper.SetScalarRange([0, density_range[1]])
density_mapper.Update()
climate_mapper = vtk.vtkDataSetMapper()
climate_mapper.SetInputConnection(climate_reader.GetOutputPort())
climate_mapper.SetLookupTable(climate_lut)
climate_mapper.SetScalarRange(climate_range)
climate_mapper.Update()
sat_mapper = vtk.vtkDataSetMapper()
sat_mapper.SetInputConnection(sat_reader.GetOutputPort())
density_actor = vtk.vtkActor()
density_actor.SetMapper(density_mapper)
density_actor.GetProperty().SetOpacity(0.99)
density_actor.VisibilityOn()
climate_actor = vtk.vtkActor()
climate_actor.SetMapper(climate_mapper)
climate_actor.GetProperty().SetOpacity(0.6)
climate_actor.VisibilityOff()
sat_actor = vtk.vtkActor()
sat_actor.SetMapper(sat_mapper)
sat_actor.GetProperty().SetOpacity(0.7)
# Make satellite image same size as contour map
crange = sat_actor.GetXRange()[0] - sat_actor.GetXRange()[1]
mrange = density_actor.GetXRange()[0] - density_actor.GetXRange()[1]
density_actor.SetScale(crange / mrange)
crange = sat_actor.GetXRange()[0] - sat_actor.GetXRange()[1]
mrange = climate_actor.GetXRange()[0] - climate_actor.GetXRange()[1]
climate_actor.SetScale(crange / mrange)
# Initialize renderer and place actors
ren = vtk.vtkRenderer()
ren.AddActor(density_actor)
ren.AddActor(climate_actor)
ren.AddActor(sat_actor)
ren.ResetCamera()
ren.SetBackground(0, 0, 0)
# Initialize camera settings
cam1 = ren.GetActiveCamera()
cam1.Azimuth(0)
cam1.Elevation(0)
cam1.Roll(360)
cam1.Zoom(1)
ren.ResetCameraClippingRange()
if args.camera:
reader = open(args.camera, "r")
line = reader.readline().split(",")
cam1.SetPosition(float(line[0]), float(line[1]), float(line[2]))
line = reader.readline().split(",")
cam1.SetFocalPoint(float(line[0]), float(line[1]), float(line[2]))
line = reader.readline().split(",")
cam1.SetViewUp(float(line[0]), float(line[1]), float(line[2]))
line = reader.readline().split(",")
cam1.SetClippingRange(float(line[0]), float(line[1]))
line = reader.readline().split(",")
cam1.SetViewAngle(float(line[0]))
line = reader.readline().split(",")
cam1.SetParallelScale(float(line[0]))
# Initialize PyQT5 UI and link to renderer
app = QApplication([])
window = QMainWindow()
ui = Ui_MainWindow()
ui.setupUi(window)
ui.vtkWidget.GetRenderWindow().AddRenderer(ren)
ui.vtkWidget.GetRenderWindow().SetSize(1280, 720)
ui.vtkWidget.GetRenderWindow().AddRenderer(ren)
ui.vtkWidget.GetRenderWindow().SetAlphaBitPlanes(True)
ui.vtkWidget.GetRenderWindow().SetMultiSamples(False)
iren = ui.vtkWidget.GetRenderWindow().GetInteractor()
# create the scalar_bar
density_scalar_bar = vtk.vtkScalarBarActor()
density_scalar_bar.SetOrientationToHorizontal()
density_scalar_bar.SetMaximumNumberOfColors(color_count)
density_scalar_bar.SetLookupTable(density_lut)
density_scalar_bar.SetTitle("Density (Log 10)")
# create the scalar_bar_widget
density_scalar_bar_widget = vtk.vtkScalarBarWidget()
density_scalar_bar_widget.SetInteractor(iren)
density_scalar_bar_widget.SetScalarBarActor(density_scalar_bar)
density_scalar_bar_widget.On()
# create the scalar_bar
climate_scalar_bar = vtk.vtkScalarBarActor()
climate_scalar_bar.SetOrientationToHorizontal()
climate_scalar_bar.SetMaximumNumberOfColors(color_count)
climate_scalar_bar.SetLookupTable(climate_lut)
climate_scalar_bar.SetTitle("Temparature (Celsius)")
# create the scalar_bar_widget
climate_scalar_bar_widget = vtk.vtkScalarBarWidget()
climate_scalar_bar_widget.SetInteractor(iren)
climate_scalar_bar_widget.SetScalarBarActor(climate_scalar_bar)
climate_scalar_bar_widget.Off()
# Function to initialize slider settings
def slider_setup(slider, val, bounds, interv):
slider.setOrientation(QtCore.Qt.Horizontal)
slider.setValue(float(val))
slider.setSliderPosition(val)
slider.setTracking(False)
slider.setTickInterval(interv)
slider.setTickPosition(QSlider.TicksAbove)
slider.setRange(bounds[0], bounds[1])
slider_setup(ui.time_slider, 0, [0, (curr_date - initial_date).days], 1)
window.show()
window.setWindowState(Qt.WindowMaximized)
iren.Initialize()
def time_slider_callback(val):
new_date = initial_date + timedelta(val)
if new_date.month.real != ui.curr_month:
ui.curr_month = new_date.month.real
climate_reader.SetFileName(args.climate + "-" +
str(ui.curr_month).zfill(2) + ".tif")
climate_reader.Update()
new_range = climate_reader.GetOutput().GetScalarRange()
climate_mapper.SetScalarRange(new_range)
ui.date_label.setText("Date (" + new_date.strftime('%m/%d/%Y') + "):")
def density_callback():
isOn = density_actor.GetVisibility()
if isOn:
density_actor.VisibilityOff()
density_scalar_bar_widget.Off()
ui.vtkWidget.GetRenderWindow().Render()
ui.push_density.setText('Enable Density')
else:
density_actor.VisibilityOn()
density_scalar_bar_widget.On()
ui.vtkWidget.GetRenderWindow().Render()
ui.push_density.setText('Disable Density')
def climate_callback():
isOn = climate_actor.GetVisibility()
if isOn:
climate_actor.VisibilityOff()
climate_scalar_bar_widget.Off()
ui.vtkWidget.GetRenderWindow().Render()
ui.push_climate.setText('Enable Temperature')
else:
climate_actor.VisibilityOn()
climate_scalar_bar_widget.On()
ui.vtkWidget.GetRenderWindow().Render()
ui.push_climate.setText('Disable Temperature')
# Handle screenshot button event
def screenshot_callback():
save_frame(ren.GetActiveCamera(), ui.vtkWidget.GetRenderWindow(),
ui.log)
# Handle show camera settings button event
def camera_callback():
print_camera_settings(ren.GetActiveCamera(), ui.camera_info, ui.log)
# Handle quit button event
def quit_callback():
sys.exit()
# Register callbacks to UI
ui.time_slider.valueChanged.connect(time_slider_callback)
ui.push_screenshot.clicked.connect(screenshot_callback)
ui.push_camera.clicked.connect(camera_callback)
ui.push_quit.clicked.connect(quit_callback)
ui.push_density.clicked.connect(density_callback)
ui.push_climate.clicked.connect(climate_callback)
# Terminate setup for PyQT5 interface
sys.exit(app.exec_())
