def __init__(self, directory):
self.basePath = directory
self.layers = []
self.data = []
self.imageReader = vtkPNGReader()
# Load JSON metadata
with open(os.path.join(directory, "config.json"), "r") as f:
self.config = json.load(f)
self.nbLayers = len(self.config['scene'])
while len(self.layers) < self.nbLayers:
self.layers.append({})
with open(os.path.join(directory, "index.json"), "r") as f:
self.info = json.load(f)
with open(os.path.join(directory, "offset.json"), "r") as f:
offsets = json.load(f)
for key, value in iteritems(offsets):
meta = key.split('|')
if len(meta) == 2:
self.layers[int(meta[0])][meta[1]] = value
elif meta[1] in self.layers[int(meta[0])]:
self.layers[int(meta[0])][meta[1]][int(meta[2])] = value
else:
self.layers[int(meta[0])][meta[1]] = [value, value, value]
self.composite = CompositeJSON(len(self.layers))
def __init__(self, directory):
self.basePath = directory
self.layers = []
self.data = []
self.imageReader = vtkPNGReader()
# Load JSON metadata
with open(os.path.join(directory, "config.json"), "r") as f:
self.config = json.load(f)
self.nbLayers = len(self.config["scene"])
while len(self.layers) < self.nbLayers:
self.layers.append({})
with open(os.path.join(directory, "index.json"), "r") as f:
self.info = json.load(f)
with open(os.path.join(directory, "offset.json"), "r") as f:
offsets = json.load(f)
for key, value in iteritems(offsets):
meta = key.split("|")
if len(meta) == 2:
self.layers[int(meta[0])][meta[1]] = value
elif meta[1] in self.layers[int(meta[0])]:
self.layers[int(meta[0])][meta[1]][int(meta[2])] = value
else:
self.layers[int(meta[0])][meta[1]] = [value, value, value]
self.composite = CompositeJSON(len(self.layers))
def __init__(self, isWriter=True, removePNG=True):
self.view = simple.CreateView('RenderView')
self.view.Background = [0.0, 0.0, 0.0]
self.view.CenterAxesVisibility = 0
self.view.OrientationAxesVisibility = 0
self.reader = vtkPNGReader()
self.cleanAfterMe = removePNG
self.canWrite = isWriter
def __init__(self, isWriter=True, removePNG=True):
self.view = simple.CreateView('RenderView')
self.view.Background = [0.0, 0.0, 0.0]
self.view.CenterAxesVisibility = 0
self.view.OrientationAxesVisibility = 0
self.reader = vtkPNGReader()
self.cleanAfterMe = removePNG
self.canWrite = isWriter
def VtkRead(filepath, t):
if not const.VTK_WARNING:
log_path = os.path.join(inv_paths.USER_LOG_DIR, "vtkoutput.txt")
fow = vtkFileOutputWindow()
fow.SetFileName(log_path.encode(const.FS_ENCODE))
ow = vtkOutputWindow()
ow.SetInstance(fow)
global no_error
if t == "bmp":
reader = vtkBMPReader()
elif t == "tiff" or t == "tif":
reader = vtkTIFFReader()
elif t == "png":
reader = vtkPNGReader()
elif t == "jpeg" or t == "jpg":
reader = vtkJPEGReader()
else:
return False
reader.AddObserver("ErrorEvent", VtkErrorToPy)
reader.SetFileName(filepath)
reader.Update()
if no_error:
image = reader.GetOutput()
dim = image.GetDimensions()
if reader.GetNumberOfScalarComponents() > 1:
luminanceFilter = vtkImageLuminance()
luminanceFilter.SetInputData(image)
luminanceFilter.Update()
image = vtkImageData()
image.DeepCopy(luminanceFilter.GetOutput())
img_array = numpy_support.vtk_to_numpy(
image.GetPointData().GetScalars())
img_array.shape = (dim[1], dim[0])
return img_array
else:
no_error = True
return False
def __init__(self, directory):
self.basePath = directory
self.layers = []
self.data = []
self.imageReader = vtkPNGReader()
# Load JSON metadata
with open(os.path.join(directory, "config.json"), "r") as f:
self.config = json.load(f)
self.nbLayers = len(self.config["scene"])
while len(self.layers) < self.nbLayers:
self.layers.append({})
with open(os.path.join(directory, "index.json"), "r") as f:
self.info = json.load(f)
def __init__(self, directory):
self.basePath = directory
self.layers = []
self.data = []
self.imageReader = vtkPNGReader()
# Load JSON metadata
with open(os.path.join(directory, "config.json"), "r") as f:
self.config = json.load(f)
self.nbLayers = len(self.config['scene'])
while len(self.layers) < self.nbLayers:
self.layers.append({})
with open(os.path.join(directory, "index.json"), "r") as f:
self.info = json.load(f)
def vtkRegressionTestImage( renWin ):
"""vtkRegressionTestImage(renWin) -- produce regression image for window
This function writes out a regression .png file for a vtkWindow.
Does anyone involved in testing care to elaborate?
"""
from vtkmodules.vtkRenderingCore import vtkWindowToImageFilter
from vtkmodules.vtkIOImage import vtkPNGReader
from vtkmodules.vtkImagingCore import vtkImageDifference
imageIndex=-1;
for i in range(0, len(sys.argv)):
if sys.argv[i] == '-V' and i < len(sys.argv)-1:
imageIndex = i+1
if imageIndex != -1:
fname = os.path.join(vtkGetDataRoot(), sys.argv[imageIndex])
rt_w2if = vtkWindowToImageFilter()
rt_w2if.SetInput(renWin)
if os.path.isfile(fname):
pass
else:
rt_pngw = vtkPNGWriter()
rt_pngw.SetFileName(fname)
rt_pngw.SetInputConnection(rt_w2if.GetOutputPort())
rt_pngw.Write()
rt_pngw = None
rt_png = vtkPNGReader()
rt_png.SetFileName(fname)
rt_id = vtkImageDifference()
rt_id.SetInputConnection(rt_w2if.GetOutputPort())
rt_id.SetImageConnection(rt_png.GetOutputPort())
rt_id.Update()
if rt_id.GetThresholdedError() <= 10:
return 1
else:
sys.stderr.write('Failed image test: %f\n'
% rt_id.GetThresholdedError())
return 0
return 2
def vtkRegressionTestImage(renWin):
"""vtkRegressionTestImage(renWin) -- produce regression image for window
This function writes out a regression .png file for a vtkWindow.
Does anyone involved in testing care to elaborate?
"""
from vtkmodules.vtkRenderingCore import vtkWindowToImageFilter
from vtkmodules.vtkIOImage import vtkPNGReader
from vtkmodules.vtkImagingCore import vtkImageDifference
imageIndex = -1
for i in range(0, len(sys.argv)):
if sys.argv[i] == '-V' and i < len(sys.argv) - 1:
imageIndex = i + 1
if imageIndex != -1:
fname = os.path.join(vtkGetDataRoot(), sys.argv[imageIndex])
rt_w2if = vtkWindowToImageFilter()
rt_w2if.SetInput(renWin)
if os.path.isfile(fname):
pass
else:
rt_pngw = vtkPNGWriter()
rt_pngw.SetFileName(fname)
rt_pngw.SetInputConnection(rt_w2if.GetOutputPort())
rt_pngw.Write()
rt_pngw = None
rt_png = vtkPNGReader()
rt_png.SetFileName(fname)
rt_id = vtkImageDifference()
rt_id.SetInputConnection(rt_w2if.GetOutputPort())
rt_id.SetImageConnection(rt_png.GetOutputPort())
rt_id.Update()
if rt_id.GetThresholdedError() <= 10:
return 1
else:
sys.stderr.write('Failed image test: %f\n' %
rt_id.GetThresholdedError())
return 0
return 2
def convertImageToFloat(srcPngImage, destFile, scalarRange=[0.0, 1.0]):
reader = vtkPNGReader()
reader.SetFileName(srcPngImage)
reader.Update()
rgbArray = reader.GetOutput().GetPointData().GetArray(0)
stackSize = rgbArray.GetNumberOfTuples()
size = reader.GetOutput().GetDimensions()
outputArray = vtkFloatArray()
outputArray.SetNumberOfComponents(1)
outputArray.SetNumberOfTuples(stackSize)
for idx in range(stackSize):
outputArray.SetTuple1(
idx, getScalarFromRGB(rgbArray.GetTuple(idx), scalarRange))
# Write float file
with open(destFile, "wb") as f:
f.write(memoryview(outputArray))
return size
def convertImageToFloat(srcPngImage, destFile, scalarRange=[0.0, 1.0]):
reader = vtkPNGReader()
reader.SetFileName(srcPngImage)
reader.Update()
rgbArray = reader.GetOutput().GetPointData().GetArray(0)
stackSize = rgbArray.GetNumberOfTuples()
size = reader.GetOutput().GetDimensions()
outputArray = vtkFloatArray()
outputArray.SetNumberOfComponents(1)
outputArray.SetNumberOfTuples(stackSize)
for idx in range(stackSize):
outputArray.SetTuple1(
idx,
getScalarFromRGB(rgbArray.GetTuple(idx), scalarRange)
)
# Write float file
with open(destFile, 'wb') as f:
f.write(buffer(outputArray))
return size
def convert(self, directory):
imagePaths = {}
depthPaths = {}
layerNames = []
for fileName in os.listdir(directory):
if "_rgb" in fileName or "_depth" in fileName:
fileId = fileName.split("_")[0][0]
if "_rgb" in fileName:
imagePaths[fileId] = os.path.join(directory, fileName)
else:
layerNames.append(fileId)
depthPaths[fileId] = os.path.join(directory, fileName)
layerNames.sort()
if len(layerNames) == 0:
return
# Load data in Memory
depthArrays = []
imageReader = vtkPNGReader()
numberOfValues = self.width * self.height * len(layerNames)
imageSize = self.width * self.height
self.layers = len(layerNames)
# Write all images as single memoryview
opacity = vtkUnsignedCharArray()
opacity.SetNumberOfComponents(1)
opacity.SetNumberOfTuples(numberOfValues)
intensity = vtkUnsignedCharArray()
intensity.SetNumberOfComponents(1)
intensity.SetNumberOfTuples(numberOfValues)
for layer in range(self.layers):
imageReader.SetFileName(imagePaths[layerNames[layer]])
imageReader.Update()
rgbaArray = imageReader.GetOutput().GetPointData().GetArray(0)
for idx in range(imageSize):
intensity.SetValue((layer * imageSize) + idx,
rgbaArray.GetValue(idx * 4))
opacity.SetValue((layer * imageSize) + idx,
rgbaArray.GetValue(idx * 4 + 3))
with open(depthPaths[layerNames[layer]], "rb") as depthFile:
depthArrays.append(depthFile.read())
# Apply pixel sorting
destOrder = vtkUnsignedCharArray()
destOrder.SetNumberOfComponents(1)
destOrder.SetNumberOfTuples(numberOfValues)
opacityOrder = vtkUnsignedCharArray()
opacityOrder.SetNumberOfComponents(1)
opacityOrder.SetNumberOfTuples(numberOfValues)
intensityOrder = vtkUnsignedCharArray()
intensityOrder.SetNumberOfComponents(1)
intensityOrder.SetNumberOfTuples(numberOfValues)
for pixelIdx in range(imageSize):
depthStack = []
for depthArray in depthArrays:
depthStack.append((depthArray[pixelIdx], len(depthStack)))
depthStack.sort(key=lambda tup: tup[0])
for destLayerIdx in range(len(depthStack)):
sourceLayerIdx = depthStack[destLayerIdx][1]
# Copy Idx
destOrder.SetValue((imageSize * destLayerIdx) + pixelIdx,
sourceLayerIdx)
opacityOrder.SetValue(
(imageSize * destLayerIdx) + pixelIdx,
opacity.GetValue((imageSize * sourceLayerIdx) + pixelIdx),
)
intensityOrder.SetValue(
(imageSize * destLayerIdx) + pixelIdx,
intensity.GetValue((imageSize * sourceLayerIdx) +
pixelIdx),
)
with open(os.path.join(directory, "alpha.uint8"), "wb") as f:
f.write(memoryview(opacityOrder))
with open(os.path.join(directory, "intensity.uint8"), "wb") as f:
f.write(memoryview(intensityOrder))
with open(os.path.join(directory, "order.uint8"), "wb") as f:
f.write(memoryview(destOrder))
def ShowSlice(self, index=0):
try:
dicom = self.dicom_list[index]
except IndexError:
dicom = self.dicom_list[0]
if self.actor is None:
self.__init_vtk()
# UPDATE GUI
## Text related to size
value = STR_SIZE % (dicom.image.size[0], dicom.image.size[1])
self.text_image_size.SetValue(value)
## Text related to slice position
if not (dicom.image.spacing):
value1 = ''
else:
value1 = STR_SPC % (dicom.image.spacing[2])
if dicom.image.orientation_label == 'AXIAL':
value2 = STR_LOCAL % (dicom.image.position[2])
elif dicom.image.orientation_label == 'CORONAL':
value2 = STR_LOCAL % (dicom.image.position[1])
elif dicom.image.orientation_label == 'SAGITTAL':
value2 = STR_LOCAL % (dicom.image.position[0])
else:
value2 = ''
value = "%s\n%s" % (value1, value2)
self.text_image_location.SetValue(value)
## Text related to patient/ acquisiiton data
value = STR_PATIENT %(dicom.patient.id,\
dicom.acquisition.protocol_name)
self.text_patient.SetValue(value)
## Text related to acquisition date and time
value = STR_ACQ % (dicom.acquisition.date, dicom.acquisition.time)
self.text_acquisition.SetValue(value)
if isinstance(dicom.image.thumbnail_path, list):
reader = vtkPNGReader()
if _has_win32api:
reader.SetFileName(
win32api.GetShortPathName(
dicom.image.thumbnail_path[index]).encode(
const.FS_ENCODE))
else:
reader.SetFileName(dicom.image.thumbnail_path[index])
reader.Update()
image = reader.GetOutput()
else:
filename = dicom.image.file
if _has_win32api:
filename = win32api.GetShortPathName(filename).encode(
const.FS_ENCODE)
np_image = imagedata_utils.read_dcm_slice_as_np2(filename)
vtk_image = converters.to_vtk(np_image, dicom.image.spacing, 0,
'AXIAL')
# ADJUST CONTRAST
window_level = dicom.image.level
window_width = dicom.image.window
colorer = vtkImageMapToWindowLevelColors()
colorer.SetInputData(vtk_image)
colorer.SetWindow(float(window_width))
colorer.SetLevel(float(window_level))
colorer.Update()
image = colorer.GetOutput()
flip = vtkImageFlip()
flip.SetInputData(image)
flip.SetFilteredAxis(1)
flip.FlipAboutOriginOn()
flip.ReleaseDataFlagOn()
flip.Update()
if self.actor is None:
self.actor = vtkImageActor()
self.renderer.AddActor(self.actor)
self.canvas.modified = True
# PLOT IMAGE INTO VIEWER
self.actor.SetInputData(flip.GetOutput())
self.renderer.ResetCamera()
self.interactor.Render()
# Setting slider position
self.slider.SetValue(index)
def compareImageWithSavedImage(src_img, img_fname, threshold=10):
"""Compares a source image (src_img, which is a vtkImageData) with
the saved image file whose name is given in the second argument.
If the image file does not exist the image is generated and
stored. If not the source image is compared to that of the
figure. This function also handles multiple images and finds the
best matching image.
"""
global _NO_IMAGE
if _NO_IMAGE:
return
f_base, f_ext = os.path.splitext(img_fname)
if not os.path.isfile(img_fname):
# generate the image
pngw = vtkPNGWriter()
pngw.SetFileName(_getTempImagePath(img_fname))
pngw.SetInputConnection(src_img.GetOutputPort())
pngw.Write()
_printCDashImageNotFoundError(img_fname)
msg = "Missing baseline image: " + img_fname + "\nTest image created: " + _getTempImagePath(img_fname)
sys.tracebacklimit = 0
raise RuntimeError(msg)
pngr = vtkPNGReader()
pngr.SetFileName(img_fname)
pngr.Update()
idiff = vtkImageDifference()
idiff.SetInputConnection(src_img.GetOutputPort())
idiff.SetImageConnection(pngr.GetOutputPort())
idiff.Update()
min_err = idiff.GetThresholdedError()
img_err = min_err
err_index = 0
count = 0
if min_err > threshold:
count = 1
test_failed = 1
err_index = -1
while 1: # keep trying images till we get the best match.
new_fname = f_base + "_%d.png"%count
if not os.path.exists(new_fname):
# no other image exists.
break
# since file exists check if it matches.
pngr.SetFileName(new_fname)
pngr.Update()
idiff.Update()
alt_err = idiff.GetThresholdedError()
if alt_err < threshold:
# matched,
err_index = count
test_failed = 0
min_err = alt_err
img_err = alt_err
break
else:
if alt_err < min_err:
# image is a better match.
err_index = count
min_err = alt_err
img_err = alt_err
count = count + 1
# closes while loop.
if test_failed:
_handleFailedImage(idiff, pngr, img_fname)
# Print for CDash.
_printCDashImageError(img_err, err_index, f_base)
msg = "Failed image test: %f\n"%idiff.GetThresholdedError()
sys.tracebacklimit = 0
raise RuntimeError(msg)
# output the image error even if a test passed
_printCDashImageSuccess(img_err, err_index)