def testOutputWindow(self):
a = vtk.vtkOutputWindow()
b = vtk.vtkOutputWindow()
self.assertNotEqual(a, b)
c = vtk.vtkOutputWindow.GetInstance()
d = vtk.vtkOutputWindow.GetInstance()
self.assertIs(c, d)
def OpenPlistProject(self, filename):
import invesalius.data.measures as ms
import invesalius.data.mask as msk
import invesalius.data.surface as srf
if not const.VTK_WARNING:
log_path = os.path.join(const.USER_LOG_DIR, 'vtkoutput.txt')
fow = vtk.vtkFileOutputWindow()
fow.SetFileName(log_path.encode(const.FS_ENCODE))
ow = vtk.vtkOutputWindow()
ow.SetInstance(fow)
filelist = Extract(filename, tempfile.mkdtemp())
dirpath = os.path.abspath(os.path.split(filelist[0])[0])
# Opening the main file from invesalius 3 project
main_plist = os.path.join(dirpath, 'main.plist')
project = plistlib.readPlist(main_plist)
# case info
self.name = project["name"]
self.modality = project["modality"]
self.original_orientation = project["orientation"]
self.window = project["window_width"]
self.level = project["window_level"]
self.threshold_range = project["scalar_range"]
self.spacing = project["spacing"]
# Opening the matrix containing the slices
filepath = os.path.join(dirpath, project["matrix"]["filename"])
self.matrix_filename = filepath
self.matrix_shape = project["matrix"]['shape']
self.matrix_dtype = project["matrix"]['dtype']
# Opening the masks
self.mask_dict = {}
for index in project["masks"]:
filename = project["masks"][index]
filepath = os.path.join(dirpath, filename)
m = msk.Mask()
m.OpenPList(filepath)
self.mask_dict[m.index] = m
# Opening the surfaces
self.surface_dict = {}
for index in project["surfaces"]:
filename = project["surfaces"][index]
filepath = os.path.join(dirpath, filename)
s = srf.Surface(int(index))
s.OpenPList(filepath)
self.surface_dict[s.index] = s
# Opening the measurements
self.measurement_dict = {}
measurements = plistlib.readPlist(
os.path.join(dirpath, project["measurements"]))
for index in measurements:
measure = ms.Measurement()
measure.Load(measurements[index])
self.measurement_dict[int(index)] = measure
def set_vtk_log():
import vtk
log_path = os.path.join("log.ini")
fow = vtk.vtkFileOutputWindow()
fow.SetFileName(log_path)
ow = vtk.vtkOutputWindow()
ow.SetInstance(fow)
def OpenPlistProject(self, filename):
import invesalius.data.measures as ms
import invesalius.data.mask as msk
import invesalius.data.surface as srf
if not const.VTK_WARNING:
log_path = os.path.join(const.LOG_FOLDER, 'vtkoutput.txt')
fow = vtk.vtkFileOutputWindow()
fow.SetFileName(log_path)
ow = vtk.vtkOutputWindow()
ow.SetInstance(fow)
filelist = Extract(filename, tempfile.mkdtemp())
dirpath = os.path.abspath(os.path.split(filelist[0])[0])
# Opening the main file from invesalius 3 project
main_plist = os.path.join(dirpath ,'main.plist')
project = plistlib.readPlist(main_plist)
# case info
self.name = project["name"]
self.modality = project["modality"]
self.original_orientation = project["orientation"]
self.window = project["window_width"]
self.level = project["window_level"]
self.threshold_range = project["scalar_range"]
self.spacing = project["spacing"]
# Opening the matrix containing the slices
filepath = os.path.join(dirpath, project["matrix"]["filename"])
self.matrix_filename = filepath
self.matrix_shape = project["matrix"]['shape']
self.matrix_dtype = project["matrix"]['dtype']
# Opening the masks
self.mask_dict = {}
for index in project["masks"]:
filename = project["masks"][index]
filepath = os.path.join(dirpath, filename)
m = msk.Mask()
m.OpenPList(filepath)
self.mask_dict[m.index] = m
# Opening the surfaces
self.surface_dict = {}
for index in project["surfaces"]:
filename = project["surfaces"][index]
filepath = os.path.join(dirpath, filename)
s = srf.Surface(int(index))
s.OpenPList(filepath)
self.surface_dict[s.index] = s
# Opening the measurements
self.measurement_dict = {}
measurements = plistlib.readPlist(os.path.join(dirpath,
project["measurements"]))
for index in measurements:
measure = ms.Measurement()
measure.Load(measurements[index])
self.measurement_dict[int(index)] = measure
def ReadOthers(dir_):
"""
Read the given Analyze, NIfTI, Compressed NIfTI or PAR/REC file,
remove singleton image dimensions and convert image orientation to
RAS+ canonical coordinate system. Analyze header does not support
affine transformation matrix, though cannot be converted automatically
to canonical orientation.
:param dir_: file path
:return: imagedata object
"""
if not const.VTK_WARNING:
log_path = os.path.join(const.USER_LOG_DIR, 'vtkoutput.txt')
fow = vtk.vtkFileOutputWindow()
fow.SetFileName(log_path.encode(const.FS_ENCODE))
ow = vtk.vtkOutputWindow()
ow.SetInstance(fow)
try:
imagedata = nib.squeeze_image(nib.load(dir_))
imagedata = nib.as_closest_canonical(imagedata)
imagedata.update_header()
except (nib.filebasedimages.ImageFileError):
return False
return imagedata
def OpenPlistProject(self, filename):
import data.measures as ms
if not const.VTK_WARNING:
log_path = os.path.join(const.LOG_FOLDER, 'vtkoutput.txt')
fow = vtk.vtkFileOutputWindow()
fow.SetFileName(log_path)
ow = vtk.vtkOutputWindow()
ow.SetInstance(fow)
filelist = Extract(filename, tempfile.mkdtemp())
main_plist = min(filter(lambda x: x.endswith('.plist'), filelist),
key=lambda x: len(x))
project = plistlib.readPlist(main_plist)
dirpath = os.path.abspath(os.path.split(filelist[0])[0])
for key in project:
if key == 'imagedata':
filepath = os.path.split(project[key]["$vti"])[-1]
path = os.path.join(dirpath, filepath)
self.imagedata = iu.Import(path)
elif key == 'presets':
filepath = os.path.split(project[key]["#plist"])[-1]
path = os.path.join(dirpath, filepath)
p = Presets()
p.OpenPlist(path)
self.presets = p
elif key == 'dicom_sample':
path = os.path.join(dirpath, project[key])
p = dicom.Parser()
p.SetFileName(path)
d = dicom.Dicom()
d.SetParser(p)
self.dicom_sample = d
elif key == 'mask_dict':
self.mask_dict = {}
for mask in project[key]:
filepath = os.path.split(project[key][mask]["#mask"])[-1]
path = os.path.join(dirpath, filepath)
m = msk.Mask()
m.OpenPList(path)
self.mask_dict[m.index] = m
elif key == 'surface_dict':
self.surface_dict = {}
for surface in project[key]:
filepath = os.path.split(project[key][surface]["#surface"])[-1]
path = os.path.join(dirpath, filepath)
s = srf.Surface()
s.OpenPList(path)
self.surface_dict[s.index] = s
elif key == 'measurement_dict':
self.measurement_dict = {}
d = project['measurement_dict']
for index in d:
measure = ms.Measurement()
measure.Load(d[index])
self.measurement_dict[int(index)] = measure
else:
setattr(self, key, project[key])
def __init__(self, config):
self.roi_physical_size = config["ROI_specs"]["roi_physical_size"]
self.roi_physical_nvoxel = config["ROI_specs"]["roi_physical_nvoxel"]
self.default_ct_value = config["ROI_specs"]["default_ct_value"]
vtk_out = vtk.vtkOutputWindow()
vtk_out.SetInstance(vtk_out)
def GetDicomGroups(self, path, recursive):
if not const.VTK_WARNING:
log_path = utils.encode(
os.path.join(const.USER_LOG_DIR, 'vtkoutput.txt'),
const.FS_ENCODE)
fow = vtk.vtkFileOutputWindow()
fow.SetFileName(log_path)
ow = vtk.vtkOutputWindow()
ow.SetInstance(fow)
y = yGetDicomGroups(path, recursive)
for value_progress in y:
print(">>>>", value_progress)
if not self.running:
break
if isinstance(value_progress, tuple):
self.UpdateLoadFileProgress(value_progress)
else:
self.EndLoadFile(value_progress)
self.UpdateLoadFileProgress(None)
#Is necessary in the case user cancel
#the load, ensure that dicomdialog is closed
if (self.stoped):
self.UpdateLoadFileProgress(None)
self.stoped = False
def ReadOthers(dir_):
"""
Read the given Analyze, NIfTI, Compressed NIfTI or PAR/REC file,
remove singleton image dimensions and convert image orientation to
RAS+ canonical coordinate system. Analyze header does not support
affine transformation matrix, though cannot be converted automatically
to canonical orientation.
:param dir_: file path
:return: imagedata object
"""
if not const.VTK_WARNING:
log_path = os.path.join(const.USER_LOG_DIR, 'vtkoutput.txt')
fow = vtk.vtkFileOutputWindow()
fow.SetFileName(log_path.encode(const.FS_ENCODE))
ow = vtk.vtkOutputWindow()
ow.SetInstance(fow)
try:
imagedata = nib.squeeze_image(nib.load(dir_))
imagedata = nib.as_closest_canonical(imagedata)
imagedata.update_header()
except(nib.filebasedimages.ImageFileError):
return False
return imagedata
def send_errors_to_logging():
"""Send all VTK error/warning messages to Python's logging module."""
error_output = vtk.vtkStringOutputWindow()
error_win = vtk.vtkOutputWindow()
error_win.SetInstance(error_output)
obs = Observer()
return obs.observe(error_output)
def GetDicomGroups(self, path, recursive):
if not const.VTK_WARNING:
log_path = utils.encode(os.path.join(const.USER_LOG_DIR, 'vtkoutput.txt'), const.FS_ENCODE)
fow = vtk.vtkFileOutputWindow()
fow.SetFileName(log_path)
ow = vtk.vtkOutputWindow()
ow.SetInstance(fow)
y = yGetDicomGroups(path, recursive)
for value_progress in y:
print(">>>>", value_progress)
if not self.running:
break
if isinstance(value_progress, tuple):
self.UpdateLoadFileProgress(value_progress)
else:
self.EndLoadFile(value_progress)
self.UpdateLoadFileProgress(None)
#Is necessary in the case user cancel
#the load, ensure that dicomdialog is closed
if(self.stoped):
self.UpdateLoadFileProgress(None)
self.stoped = False
def vis_bw(ax, a, facecolor='r'):
# verts, faces, normals, values = measure.marching_cubes_lewiner(a, 0)
# print(verts)
# mesh = Poly3DCollection(verts[faces], alpha=0.5)
# mesh.set_facecolor(facecolor)
# ax.add_collection3d(mesh)
# v_a = numpy_support.numpy_to_vtk(num_array=a.ravel(), deep=True, array_type=vtk.VTK_STRUCTURED_POINTS)
# v_a = vtk.vtkDataObject()
# v_a.SetInformation(v_bit_a)
# n2vtk = vtk.vtkImageImport() # Converter
# n2vtk.SetArr
#
# contour = vtk.vtkDiscreteMarchingCubes()
# contour.SetInputData(v_a)
# contour.SetValue(0, .5)
# contour.Update()
# writer = vtk.vtkPolyDataWriter()
# writer.SetInputData(contour)
# writer.SetFileName('contour.vtk')
# writer.Update()
# mc = vtk.vtkMarchingCubes(v_a)
# print(v_a)
n_a = np.ravel(sitk.GetArrayFromImage(a), order='C')
v_a = vtk.vtkImageData()
v_a.SetSpacing(a.GetSpacing())
v_a.SetOrigin(a.GetOrigin())
v_a.SetDimensions(a.GetSize())
print(a.GetPixelID())
v_a.SetScalarType(convertTypeITKtoVTK(sitk.sitkInt8), vtk.vtkInformation())
v_a.SetNumberOfScalarComponents(a.GetNumberOfComponentsPerPixel(),
vtk.vtkInformation())
print('a')
v_a_to_VTK = numpy_to_vtk(n_a,
deep=True,
array_type=convertTypeITKtoVTK(a.GetPixelID()))
print('b')
v_a.GetPointData().SetScalars(v_a_to_VTK)
fow = vtk.vtkFileOutputWindow()
fow.SetFileName('ow.txt')
ow = vtk.vtkOutputWindow()
ow.SetInstance(fow)
contour = vtk.vtkDiscreteMarchingCubes()
contour.SetInputData(v_a)
contour.SetValue(0, .5)
contour.Update()
writer = vtk.vtkPolyDataWriter()
writer.SetInputData(contour.GetOutput())
writer.SetFileName('contour.vtk')
writer.Update()
def setup_vtk_err(setup_qt):
""" Used to send VTK errors to file instead of screen. """
err_out = vtk.vtkFileOutputWindow()
err_out.SetFileName('tests/output/vtk.err.txt')
vtk_std_err = vtk.vtkOutputWindow()
vtk_std_err.SetInstance(err_out)
return vtk_std_err, setup_qt
def picker_callback(self, picker):
global LIST_AMF_OBJECTS, CURRENT_SELECTED_OBJECT, DICT_MATERIAL
# Catch the errors here
output = vtk.vtkFileOutputWindow()
output.SetFileName("log.txt")
vtk.vtkOutputWindow().SetInstance(output)
picker_outside = True
# Check if the object picked belongs to our LIST_AMF_OBJECTS
for i in range(len(LIST_AMF_OBJECTS)):
if picker.actor in LIST_AMF_OBJECTS[i].geometry.actor.actors:
# The user picked an object in our LIST_AMF_OBJECTS
picker_outside = False
# Update the visualization
LIST_AMF_OBJECTS[
i].geometry.actor.mapper.scalar_visibility = False # Disable the scalar colors assigned to the object
LIST_AMF_OBJECTS[i].geometry.actor.property.color = (
1, 0, 0) # Color the picked object in red
LIST_AMF_OBJECTS[
i].geometry.actor.property.line_width = 8 # Increase slighly the size of the wireframe edges
# Update the GUI
self.GUI_OBJECT_NAME = LIST_AMF_OBJECTS[i].name
self.GUI_ID = LIST_AMF_OBJECTS[i].xmlObjectID
self.GUI_MATERIAL_ID = LIST_AMF_OBJECTS[i].materialId
self.GUI_MATERIAL_NAME = DICT_MATERIAL[
LIST_AMF_OBJECTS[i].materialId]
CURRENT_SELECTED_OBJECT = i
# LIST_AMF_OBJECTS[i].geometry.actor.actor.scale = (1,1,2) # Just a placeholder in case we want to slightly increase the height of the selected object
else:
# The object was not picked - Reapply the original Scalar Color and line width
LIST_AMF_OBJECTS[
i].geometry.actor.mapper.scalar_visibility = True
LIST_AMF_OBJECTS[i].geometry.actor.property.line_width = 2
# LIST_AMF_OBJECTS[i].geometry.actor.actor.scale = (1,1,1) # Just a placeholder to assign the orignal height to the object
if picker_outside:
# The picker did not select an object belonging to our LIST_AMF_OBJECTS
self.GUI_MATERIAL_ID = ""
self.GUI_OBJECT_NAME = ""
self.GUI_ID = "No Object Selected"
self.GUI_MATERIAL_NAME = ""
CURRENT_SELECTED_OBJECT = -1
def set_error_output_file(filename):
"""Set a file to write out the VTK errors."""
filename = os.path.abspath(os.path.expanduser(filename))
fileOutputWindow = vtk.vtkFileOutputWindow()
fileOutputWindow.SetFileName(filename)
outputWindow = vtk.vtkOutputWindow()
outputWindow.SetInstance(fileOutputWindow)
return fileOutputWindow, outputWindow
def __init__(self, config):
self.config = config
# Get VTK errors to console instead of stupid flashing window
vtk_out = vtk.vtkOutputWindow()
vtk_out.SetInstance(vtk_out)
# self.device, self.model = self._get_device_and_load_model()
self.logger = config.get_logger('predict')
self.device, self.model = self._get_device_and_load_model_from_url()
def OpenPlistProject(self, filename):
if not const.VTK_WARNING:
log_path = os.path.join(inv_paths.USER_LOG_DIR, 'vtkoutput.txt')
fow = vtk.vtkFileOutputWindow()
fow.SetFileName(log_path.encode(const.FS_ENCODE))
ow = vtk.vtkOutputWindow()
ow.SetInstance(fow)
filelist = Extract(filename, tempfile.mkdtemp())
dirpath = os.path.abspath(os.path.split(filelist[0])[0])
self.load_from_folder(dirpath)
def setupLogging(self):
""" setup local login """
import os
temp = os.path.split(os.tempnam())[0]
app = ''.join(c for c in self.appName if 'a' <= c.lower() <= 'z') + '.log.'
logName = os.path.join(temp, app)
fileOutputWindow = vtk.vtkFileOutputWindow()
fileOutputWindow.SetFileName(logName)
outputWindow = vtk.vtkOutputWindow().GetInstance()
if outputWindow:
outputWindow.SetInstance(fileOutputWindow)
def test_ball_sim():
'''
Drawing the ball and animating with mlab
'''
from mayavi import mlab
import time
# to prevent error messages
import vtk
output = vtk.vtkFileOutputWindow()
output.SetFileName("log.txt")
vtk.vtkOutputWindow().SetInstance(output)
p = np.array([0.8197, -1.62, 0.32])
#init_vel = np.array([-2.2230, 5.7000, 2.8465])
orange = (0.9100, 0.4100, 0.1700)
s = mlab.points3d(p[0], p[1], p[2], color=orange, scale_factor=0.05)
for i in range(10):
#time.sleep(0.2)
p = p + 0.01
s.mlab_source.set(x=p[0], y=p[1], z=p[2])
def VtkRead(filepath, t):
if not const.VTK_WARNING:
log_path = os.path.join(const.USER_LOG_DIR, 'vtkoutput.txt')
fow = vtk.vtkFileOutputWindow()
fow.SetFileName(log_path.encode(const.FS_ENCODE))
ow = vtk.vtkOutputWindow()
ow.SetInstance(fow)
global no_error
if t == "bmp":
reader = vtk.vtkBMPReader()
elif t == "tiff" or t == "tif":
reader = vtk.vtkTIFFReader()
elif t == "png":
reader = vtk.vtkPNGReader()
elif t == "jpeg" or t == "jpg":
reader = vtk.vtkJPEGReader()
else:
return False
print ">>>> bmp reader", type(filepath)
reader.AddObserver("ErrorEvent", VtkErrorToPy)
reader.SetFileName(filepath.encode(const.FS_ENCODE))
reader.Update()
if no_error:
image = reader.GetOutput()
dim = image.GetDimensions()
if reader.GetNumberOfScalarComponents() > 1:
luminanceFilter = vtk.vtkImageLuminance()
luminanceFilter.SetInputData(image)
luminanceFilter.Update()
image = vtk.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, parent, id, style):
wx.Panel.__init__(self, parent, id, style=style)
self.build_gui()
self.__bind_events_wx()
#self.__bind_events_pb()
self.Show()
# funcão para escrever o erro
log_path = os.path.join('.' , 'vtkoutput.txt')
fow = vtk.vtkFileOutputWindow()
fow.SetFileName(log_path)
ow = vtk.vtkOutputWindow()
ow.SetInstance(fow)
def __init__(self, parent, id, style):
wx.Panel.__init__(self, parent, id, style=style)
self.build_gui()
self.__bind_events_wx()
self.__bind_events_pb()
self.Show()
# Error description
log_path = os.path.join('.', 'vtkoutput.txt')
fow = vtk.vtkFileOutputWindow()
fow.SetFileName(log_path)
ow = vtk.vtkOutputWindow()
ow.SetInstance(fow)
def VtkRead(filepath, t):
if not const.VTK_WARNING:
log_path = os.path.join(inv_paths.USER_LOG_DIR, 'vtkoutput.txt')
fow = vtk.vtkFileOutputWindow()
fow.SetFileName(log_path.encode(const.FS_ENCODE))
ow = vtk.vtkOutputWindow()
ow.SetInstance(fow)
global no_error
if t == "bmp":
reader = vtk.vtkBMPReader()
elif t == "tiff" or t == "tif":
reader = vtk.vtkTIFFReader()
elif t == "png":
reader = vtk.vtkPNGReader()
elif t == "jpeg" or t == "jpg":
reader = vtk.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 = vtk.vtkImageLuminance()
luminanceFilter.SetInputData(image)
luminanceFilter.Update()
image = vtk.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 _setupLogging(self):
""" setup local logging """
if not self.logFile:
import os
import tempfile
temp = tempfile.gettempdir()
app = "".join(c for c in self.appName if "a" <= c.lower() <= "z") + ".log."
self.logFile = os.path.join(temp, app)
fileOutputWindow = vtk.vtkFileOutputWindow()
fileOutputWindow.SetFileName(self.logFile)
outputWindow = vtk.vtkOutputWindow().GetInstance()
if outputWindow:
outputWindow.SetInstance(fileOutputWindow)
def _setupLogging(self):
""" setup local logging """
if not self.logFile:
import os
import tempfile
temp = tempfile.gettempdir()
app = ''.join(
c for c in self.appName if 'a' <= c.lower() <= 'z') + '.log.'
self.logFile = os.path.join(temp, app)
fileOutputWindow = vtk.vtkFileOutputWindow()
fileOutputWindow.SetFileName(self.logFile)
outputWindow = vtk.vtkOutputWindow().GetInstance()
if outputWindow:
outputWindow.SetInstance(fileOutputWindow)
def __init__(self, parent, id, style):
wx.Panel.__init__(self, parent, id, style=style)
# usa da wx com a vtk junto (colocação do vtk dentro de wx)
self.renderer = vtk.vtkRenderer()
self.Interactor = wxVTKRenderWindowInteractor(self,
-1,
size=self.GetSize())
self.Interactor.GetRenderWindow().AddRenderer(self.renderer)
self.Interactor.Render()
#-----------------------------------------------------------------------------
#------- ajeitaro estilo da camera
istyle = vtk.vtkInteractorStyleTrackballCamera()
self.Interactor.SetInteractorStyle(istyle)
#---------------------------------------------------------------
self.VerPlano = False # inicializar o plano, para usar como plano de corte
self.Bind(wx.EVT_IDLE,
self.Restabelecer) #para funcionar o editor de corte
# funcão para escrever o erro num ficheiro txt
log_path = os.path.join('.', 'vtkoutput.txt')
fow = vtk.vtkFileOutputWindow()
fow.SetFileName(log_path)
ow = vtk.vtkOutputWindow()
ow.SetInstance(fow)
#--------------------------------------------------------
#-------Criar a caixa de trabalho
hbox = wx.BoxSizer(wx.VERTICAL)
hbox.Add(wx.StaticText(self, -1, 'Area de Corte'))
hbox.Add(self.Interactor, 1,
wx.EXPAND) # juntar com o wx, numa so janela
self.SetSizer(hbox)
#------------------------------------------------------------------
self.adicionaeixos() #adiconar a função que chama o eixos
def CreateImageData(self, filelist, zspacing, size, bits):
message = _("Generating multiplanar visualization...")
if not const.VTK_WARNING:
log_path = os.path.join(const.USER_LOG_DIR, 'vtkoutput.txt')
fow = vtk.vtkFileOutputWindow()
fow.SetFileName(log_path)
ow = vtk.vtkOutputWindow()
ow.SetInstance(fow)
x,y = size
px, py = utils.predict_memory(len(filelist), x, y, bits)
utils.debug("Image Resized to >>> %f x %f" % (px, py))
if (x == px) and (y == py):
const.REDUCE_IMAGEDATA_QUALITY = 0
else:
const.REDUCE_IMAGEDATA_QUALITY = 1
if not(const.REDUCE_IMAGEDATA_QUALITY):
update_progress= vtk_utils.ShowProgress(1, dialog_type = "ProgressDialog")
array = vtk.vtkStringArray()
for x in range(len(filelist)):
if not self.running:
return False
array.InsertValue(x,filelist[x])
if not self.running:
return False
reader = vtkgdcm.vtkGDCMImageReader()
reader.SetFileNames(array)
reader.AddObserver("ProgressEvent", lambda obj,evt:
update_progress(reader,message))
reader.Update()
if not self.running:
reader.AbortExecuteOn()
return False
# The zpacing is a DicomGroup property, so we need to set it
imagedata = vtk.vtkImageData()
imagedata.DeepCopy(reader.GetOutput())
spacing = imagedata.GetSpacing()
imagedata.SetSpacing(spacing[0], spacing[1], zspacing)
else:
update_progress= vtk_utils.ShowProgress(2*len(filelist),
dialog_type = "ProgressDialog")
# Reformat each slice and future append them
appender = vtk.vtkImageAppend()
appender.SetAppendAxis(2) #Define Stack in Z
# Reformat each slice
for x in range(len(filelist)):
# TODO: We need to check this automatically according
# to each computer's architecture
# If the resolution of the matrix is too large
if not self.running:
return False
reader = vtkgdcm.vtkGDCMImageReader()
reader.SetFileName(filelist[x])
reader.AddObserver("ProgressEvent", lambda obj,evt:
update_progress(reader,message))
reader.Update()
#Resample image in x,y dimension
slice_imagedata = ResampleImage2D(reader.GetOutput(), px, py, update_progress)
#Stack images in Z axes
appender.AddInput(slice_imagedata)
#appender.AddObserver("ProgressEvent", lambda obj,evt:update_progress(appender))
appender.Update()
# The zpacing is a DicomGroup property, so we need to set it
if not self.running:
return False
imagedata = vtk.vtkImageData()
imagedata.DeepCopy(appender.GetOutput())
spacing = imagedata.GetSpacing()
imagedata.SetSpacing(spacing[0], spacing[1], zspacing)
imagedata.AddObserver("ProgressEvent", lambda obj,evt:
update_progress(imagedata,message))
imagedata.Update()
return imagedata
def OpenPlistProject(self, filename):
import invesalius.data.measures as ms
import invesalius.data.mask as msk
import invesalius.data.surface as srf
if not const.VTK_WARNING:
log_path = os.path.join(inv_paths.USER_LOG_DIR, 'vtkoutput.txt')
fow = vtk.vtkFileOutputWindow()
fow.SetFileName(log_path.encode(const.FS_ENCODE))
ow = vtk.vtkOutputWindow()
ow.SetInstance(fow)
filelist = Extract(filename, tempfile.mkdtemp())
dirpath = os.path.abspath(os.path.split(filelist[0])[0])
# Opening the main file from invesalius 3 project
main_plist = os.path.join(dirpath ,'main.plist')
project = plistlib.readPlist(main_plist)
format_version = project["format_version"]
if format_version > const.INVESALIUS_ACTUAL_FORMAT_VERSION:
from invesalius.gui.dialogs import ImportOldFormatInvFile
ImportOldFormatInvFile()
# case info
self.name = project["name"]
self.modality = project["modality"]
self.original_orientation = project["orientation"]
self.window = project["window_width"]
self.level = project["window_level"]
self.threshold_range = project["scalar_range"]
self.spacing = project["spacing"]
if project.get("affine"):
self.affine = project["affine"]
Publisher.sendMessage('Update affine matrix',
affine=self.affine, status=True)
self.compress = project.get("compress", True)
# Opening the matrix containing the slices
filepath = os.path.join(dirpath, project["matrix"]["filename"])
self.matrix_filename = filepath
self.matrix_shape = project["matrix"]['shape']
self.matrix_dtype = project["matrix"]['dtype']
# Opening the masks
self.mask_dict = {}
for index in project["masks"]:
filename = project["masks"][index]
filepath = os.path.join(dirpath, filename)
m = msk.Mask()
m.OpenPList(filepath)
self.mask_dict[m.index] = m
# Opening the surfaces
self.surface_dict = {}
for index in project["surfaces"]:
filename = project["surfaces"][index]
filepath = os.path.join(dirpath, filename)
s = srf.Surface(int(index))
s.OpenPList(filepath)
self.surface_dict[s.index] = s
# Opening the measurements
self.measurement_dict = {}
measurements = plistlib.readPlist(os.path.join(dirpath,
project["measurements"]))
for index in measurements:
if measurements[index]["type"] in (const.DENSITY_ELLIPSE, const.DENSITY_POLYGON):
measure = ms.DensityMeasurement()
else:
measure = ms.Measurement()
measure.Load(measurements[index])
self.measurement_dict[int(index)] = measure
"""
from __future__ import division
import numpy as np
npl = np.linalg
from mayavi import mlab
from tvtk.tools import visual
import motion
# Send pointlessly spammed mayavi warnings to the shadow realm
import os, vtk
if os.path.exists("/dev/null"): shadow_realm = "/dev/null"
else: shadow_realm = "c:\\nul"
mlab_warning_output = vtk.vtkFileOutputWindow()
mlab_warning_output.SetFileName(shadow_realm)
vtk.vtkOutputWindow().SetInstance(mlab_warning_output)
class Viz(object):
"""
Allows easy creation of a figure window with multicopter and environment visualization.
model: Model object for the multicopter
building_layout: array of booleans describing where buildings are in a grid
building_size: tuple of (length, width, height) that applies to all buildings
building_spacing: single number for the distance between adjacent buildings
fig: the Mayavi figure to draw to, a new one is made if left None
"""
def __init__(self,
model,
def pickOriginAndZone(self,x,y,z,substrateHeightGuess,altitude=0.001,pickZone=True):
# dirty hack to suppress VTK errors when setting origin's mlab_data
output=vtk.vtkFileOutputWindow()
output.SetFileName("log.txt")
vtk.vtkOutputWindow().SetInstance(output)
s = mlab.mesh(x, y, z)
s.components[1].property.lighting = False
maximumHeight = z.max()
safeHeight = maximumHeight+0.01
origin = mlab.points3d(float(x.min()), float(y.min()), 0.0, mode='axes',
color=(1, 0, 0),
scale_factor=0.03)
if pickZone:
scanZone = HorizontalRectangle((0,0,0),height=0,displayZOffset=self.calibration.mechanical.spotZ.asUnit('m'))
substrateHeightZone = HorizontalRectangle((1,0,0),height=0)
def updateSubstrateHeight(newHeight):
colorRangeHeight = altitude-self.calibration.mechanical.spotZ.asUnit('m')
s.module_manager.scalar_lut_manager.data_range = (newHeight-colorRangeHeight,newHeight+colorRangeHeight)
origin.mlab_source.set(z = newHeight)
if pickZone:
scanZone.height = newHeight+float(altitude)
substrateHeightZone.height = newHeight
updateSubstrateHeight(float(substrateHeightGuess))
def originSelectorCallBack(picker):
origin.mlab_source.set(x = picker.pick_position[0],
y = picker.pick_position[1])
selectedPosition = Position(picker.pick_position,unit='m')
try:
self.setProbeLocation(Position([selectedPosition[0],selectedPosition[1],safeHeight],'m'))
self.setProbeLocation(selectedPosition + Position([0,0,0.002],'m'))
except Warning:
pass
picker = mlab.gcf().on_mouse_pick(originSelectorCallBack,
type='cell',
button='Middle')
def zoneSelectorCallback(picker,zone):
pickedPosition = picker.pick_position[0:2]
if pickZone:
self.setProbeLocation(Position([pickedPosition[0],pickedPosition[1],safeHeight],'m'))
self.setProbeLocation(Position([pickedPosition[0],pickedPosition[1],scanZone.height],'m'))
if picker.topRightPicked:
zone.bottomLeft = pickedPosition
else:
zone.topRight = pickedPosition
picker.topRightPicked = not(picker.topRightPicked)
def scanZoneSelectorCallback(picker):
return zoneSelectorCallback(picker,scanZone)
def substrateHeightZoneSelectorCallback(picker):
zoneSelectorCallback(picker,substrateHeightZone)
if not(picker.topRightPicked):
substrateHeightZone.sort()
zValuesInZone = z[(x > substrateHeightZone.bottomLeft[0]) &
(x < substrateHeightZone.topRight[0]) &
(y > substrateHeightZone.bottomLeft[1]) &
(y < substrateHeightZone.topRight[1])]
print 'Estimating substrate height based on',zValuesInZone.shape,'values...'
if len(zValuesInZone) > 0:
heightEstimate = self.estimateSubstrateHeight(zValuesInZone)
updateSubstrateHeight(heightEstimate)
picker = mlab.gcf().on_mouse_pick(scanZoneSelectorCallback,
type='cell',
button='Right')
picker.add_trait('topRightPicked',api.Bool(False))
picker = mlab.gcf().on_mouse_pick(substrateHeightZoneSelectorCallback,
type='cell',
button='Left')
picker.add_trait('topRightPicked',api.Bool(False))
mlab.orientation_axes()
mlab.view(azimuth=0,elevation=0)
mlab.show()
originPosition = Position(origin.mlab_source.points[0][:],'m')
if pickZone:
scanZone.sort()
lastProbeLaserPosition = self.getProbeLocation()
lastProbeLaserPosition[2] = safeHeight
self.setProbeLocation(lastProbeLaserPosition)
return (originPosition,scanZone)
else:
return originPosition
def __init__(self, lattice, size, pos):
wx.Frame.__init__(self,
None,
-1,
"Lattice Preview",
size=size,
pos=pos)
self.lattice = lattice
# menu bar
menuBar = wx.MenuBar()
menuFile = wx.Menu()
menuFileAbout = menuFile.Append(-1, "About...", "About")
menuFile.AppendSeparator()
menuFileNew = menuFile.Append(-1, "&New...\tCtrl+N", "New Preview")
menuFileClose = menuFile.Append(-1, "&Close\tCtrl+W", "Close Window")
self.Bind(wx.EVT_MENU, self.ShowAbout, menuFileAbout)
self.Bind(wx.EVT_MENU, self.OnNew, menuFileNew)
self.Bind(wx.EVT_MENU, self.OnClose, menuFileClose)
menuBar.Append(menuFile, "Preview")
self.menuView = wx.Menu()
if len(lattice.vertexTypes) > 0:
self.menuView.Append(-1, "Vertex Type").Enable(False)
for t in lattice.vertexTypes:
m = self.menuView.AppendCheckItem(-1, " " + str(t))
m.Check(True)
self.Bind(wx.EVT_MENU, self.OnViewVertex, m)
if len(lattice.vertexTypes) > 0 and len(lattice.edgeTypes) > 0:
self.menuView.AppendSeparator()
if len(lattice.edgeTypes) > 0:
self.menuView.Append(-1, "Edge Type").Enable(False)
for t in lattice.edgeTypes:
m = self.menuView.AppendCheckItem(-1, " " + str(t))
m.Check(True)
self.Bind(wx.EVT_MENU, self.OnViewEdge, m)
if len(lattice.vertexTypes) > 0 or len(lattice.edgeTypes) > 0:
self.menuView.AppendSeparator()
m = self.menuView.Append(-1, "Show All")
self.Bind(wx.EVT_MENU, self.OnShowAll, m)
m = self.menuView.Append(-1, "Hide All")
self.Bind(wx.EVT_MENU, self.OnHideAll, m)
menuBar.Append(self.menuView, "View")
self.SetMenuBar(menuBar)
main = wx.BoxSizer(wx.VERTICAL)
self.SetBackgroundColour('#eeffff')
self.vtkwidget = wxVTKRenderWindowInteractor(self, -1)
main.Add(self.vtkwidget, 1, wx.EXPAND)
self.SetSizer(main)
self.Layout()
self.vtkwidget.Enable(1)
self.vtkwidget.AddObserver("ExitEvent", lambda o, e, f=self: f.Close())
self.vertexActors = []
self.vertexView = []
self.edgeActors = []
self.edgeView = []
self.InitColors()
self.renderer = vtk.vtkRenderer()
self.renderer.SetBackground(0.1, 0.2, 0.4)
self.vtkwidget.GetRenderWindow().AddRenderer(self.renderer)
vtk.vtkOutputWindow().PromptUserOff()
self.ShowPreview()
vtkDataReader,
vtkXMLFileReadTester,
vtkStringOutputWindow,
vtkOutputWindow,
)
from ogs5py.tools.types import PCS_TYP
from ogs5py.reader.vtkhelper import vtkreader_dict, XMLreader_dict
from ogs5py.tools.output import split_ply_path, split_pnt_path, readpvd_single
from ogs5py.reader.techelper import readtec_single_table, readtec_multi_table
from ogs5py.tools.tools import split_file_path
# redirect VTK error to a string
VTK_ERR = vtkStringOutputWindow()
"""VTK Error output. Accessible with ``VTK_ERR.GetOutput()``"""
VTK_STD_OUT = vtkOutputWindow()
VTK_STD_OUT.SetInstance(VTK_ERR)
###############################################################################
# vtk readers
###############################################################################
def readvtk_single(infile):
"""Read an arbitrary vtk/vtkXML file to a dictionary wtih its data."""
xml_checker = vtkXMLFileReadTester()
xml_checker.SetFileName(infile)
is_xml = bool(xml_checker.TestReadFile())
if is_xml:
# check for vtk-XML-type
def create_surface_piece(filename, shape, dtype, mask_filename, mask_shape,
mask_dtype, roi, spacing, mode, min_value, max_value,
decimate_reduction, smooth_relaxation_factor,
smooth_iterations, language, flip_image,
from_binary, algorithm, imagedata_resolution, fill_border_holes):
log_path = tempfile.mktemp('vtkoutput.txt')
fow = vtk.vtkFileOutputWindow()
fow.SetFileName(log_path)
ow = vtk.vtkOutputWindow()
ow.SetInstance(fow)
pad_bottom = (roi.start == 0)
pad_top = (roi.stop >= shape[0])
if fill_border_holes:
padding = (1, 1, pad_bottom)
else:
padding = (0, 0, 0)
if from_binary:
mask = numpy.memmap(mask_filename, mode='r',
dtype=mask_dtype,
shape=mask_shape)
if fill_border_holes:
a_mask = pad_image(mask[roi.start + 1: roi.stop + 1, 1:, 1:], 0, pad_bottom, pad_top)
else:
a_mask = numpy.array(mask[roi.start + 1: roi.stop + 1, 1:, 1:])
image = converters.to_vtk(a_mask, spacing, roi.start, "AXIAL", padding=padding)
del a_mask
else:
image = numpy.memmap(filename, mode='r', dtype=dtype,
shape=shape)
mask = numpy.memmap(mask_filename, mode='r',
dtype=mask_dtype,
shape=mask_shape)
if fill_border_holes:
a_image = pad_image(image[roi], numpy.iinfo(image.dtype).min, pad_bottom, pad_top)
else:
a_image = numpy.array(image[roi])
# if z_iadd:
# a_image[0, 1:-1, 1:-1] = image[0]
# if z_eadd:
# a_image[-1, 1:-1, 1:-1] = image[-1]
if algorithm == u'InVesalius 3.b2':
a_mask = numpy.array(mask[roi.start + 1: roi.stop + 1, 1:, 1:])
a_image[a_mask == 1] = a_image.min() - 1
a_image[a_mask == 254] = (min_value + max_value) / 2.0
image = converters.to_vtk(a_image, spacing, roi.start, "AXIAL", padding=padding)
gauss = vtk.vtkImageGaussianSmooth()
gauss.SetInputData(image)
gauss.SetRadiusFactor(0.3)
gauss.ReleaseDataFlagOn()
gauss.Update()
del image
image = gauss.GetOutput()
del gauss
del a_mask
else:
# if z_iadd:
# origin = -spacing[0], -spacing[1], -spacing[2]
# else:
# origin = 0, -spacing[1], -spacing[2]
image = converters.to_vtk(a_image, spacing, roi.start, "AXIAL", padding=padding)
del a_image
if imagedata_resolution:
image = ResampleImage3D(image, imagedata_resolution)
flip = vtk.vtkImageFlip()
flip.SetInputData(image)
flip.SetFilteredAxis(1)
flip.FlipAboutOriginOn()
flip.ReleaseDataFlagOn()
flip.Update()
# writer = vtk.vtkXMLImageDataWriter()
# writer.SetFileName('/tmp/camboja.vti')
# writer.SetInputData(flip.GetOutput())
# writer.Write()
del image
image = flip.GetOutput()
del flip
contour = vtk.vtkContourFilter()
contour.SetInputData(image)
if from_binary:
contour.SetValue(0, 127) # initial threshold
else:
contour.SetValue(0, min_value) # initial threshold
contour.SetValue(1, max_value) # final threshold
# contour.ComputeScalarsOn()
# contour.ComputeGradientsOn()
# contour.ComputeNormalsOn()
contour.ReleaseDataFlagOn()
contour.Update()
polydata = contour.GetOutput()
del image
del contour
filename = tempfile.mktemp(suffix='_%d_%d.vtp' % (roi.start, roi.stop))
writer = vtk.vtkXMLPolyDataWriter()
writer.SetInputData(polydata)
writer.SetFileName(filename)
writer.Write()
print("Writing piece", roi, "to", filename)
print("MY PID MC", os.getpid())
return filename
def simulate(self,
q0,
control,
tN=0,
dt=0.005,
goal=None,
override=None,
Des=None):
"""
Runs the simulation and displays / plots the results.
q0: array initial state condition [pos, ang1, ang2, vel, angvel1, angvel2]
control: function of array state, scalar time, and scalar goal that returns a scalar input force
tN: scalar duration in time units, set to 0 for realtime simulation
dt: scalar timestep for simulation
goal: optional scalar position to be passed to control and marked as "goal" in visualizations
override: optional function of scalar time that returns an array state that overrides
the actual simulation (allows you to visualize an arbitrary trajectory)
Des: tuple of time and state trajectories to be plotted as desired
"""
q0 = np.array(q0, dtype=np.float64)
# Positive tN means timeseries simulation
if tN > 0:
from matplotlib import pyplot
# Record real start time
print "----"
print "Simulating acrocart for a horizon of {}...".format(tN)
start_time = time.time()
# Run timeseries simulation and store results
T = np.arange(0, tN + dt, dt)
Q = np.zeros((len(T), self.dyn.n_q), dtype=np.float64)
U = np.zeros((len(T), self.dyn.n_u), dtype=np.float64)
Q[0] = np.copy(q0)
for i, t in enumerate(T[:-1]):
U[i] = control(Q[i], t, goal)
if override is None:
Q[i + 1] = self.dyn.step(Q[i], U[i], dt)
else:
Q[i + 1] = override(t)
print "Simulation finished in {} realtime seconds.".format(
np.round(time.time() - start_time, 3))
print "Final state: {}".format(np.round(Q[-1], 3))
print "Sum of squared input forces: {}".format(
np.round(np.sum(U[:, 0]**2), 3))
# Plot results
print "Plotting results... (close plots to continue)"
print "----"
fig = pyplot.figure()
fig.suptitle("AcroCart Simulation", fontsize=24)
ax = fig.add_subplot(2, 1, 1)
ax.plot(T, Q[:, 0], "k", label="pos")
ax.plot(T, Q[:, 1], "g", label="ang1")
ax.plot(T, Q[:, 2], "b", label="ang2")
if Des is not None:
ax.plot(Des[0], Des[1][:, 0], "k--")
ax.plot(Des[0], Des[1][:, 1], "g--")
ax.plot(Des[0], Des[1][:, 2], "b--")
ax.set_xlim([T[0], T[-1]])
ax.legend(fontsize=16)
ax.set_ylabel("Pose", fontsize=16)
ax.grid(True)
ax = fig.add_subplot(2, 1, 2)
ax.plot(T, U[:, 0], "r", label="input")
ax.set_xlim([T[0], T[-1]])
ax.set_ylabel("Input", fontsize=16)
ax.set_xlabel("Time", fontsize=16)
ax.grid(True)
pyplot.show() # blocking
# Nonpositive tN implies realtime simulation
else:
print "----"
print "Starting realtime acrocart simulation..."
print "Setting-up Mayavi graphics..."
from mayavi import mlab
import os, vtk
if os.path.exists("/dev/null"): shadow_realm = "/dev/null"
else: shadow_realm = "c:\\nul"
mlab_warning_output = vtk.vtkFileOutputWindow()
mlab_warning_output.SetFileName(shadow_realm)
vtk.vtkOutputWindow().SetInstance(mlab_warning_output)
# Generate visualization objects and initial figure view
fig = mlab.figure(size=(500, 500), bgcolor=(0.25, 0.25, 0.25))
rail = mlab.plot3d(self.dyn.rail_lims, (0, 0), (0, 0),
line_width=1,
color=(1, 1, 1))
cart = mlab.points3d(q0[0],
0,
0,
scale_factor=0.2,
mode="cube",
color=(0, 0, 1))
joint1 = mlab.points3d(q0[0],
-0.125,
0,
scale_factor=0.12,
color=(0, 1, 1))
x1, y1 = q0[0] + self.dyn.l1 * np.sin(
q0[1]), -self.dyn.l1 * np.cos(q0[1])
pole1 = mlab.plot3d((q0[0], x1), (-0.15, -0.15), (0, y1),
line_width=1,
color=(0, 1, 0))
joint2 = mlab.points3d(x1,
-0.175,
y1,
scale_factor=0.12,
color=(0, 1, 1))
pole2 = mlab.plot3d((x1, x1 + self.dyn.l2 * np.sin(q0[2])),
(-0.2, -0.2),
(y1, y1 - self.dyn.l2 * np.cos(q0[2])),
line_width=1,
color=(1, 0, 0))
disp = mlab.text3d(-0.6,
0,
1.2 * (self.dyn.l1 + self.dyn.l2),
"t = 0.0",
scale=0.45)
if goal is not None:
mlab.points3d(goal,
0,
-1.2 * (self.dyn.l1 + self.dyn.l2),
scale_factor=0.2,
mode="axes",
color=(1, 0, 0))
recenter = lambda: mlab.view(
azimuth=-90,
elevation=90,
focalpoint=(np.mean(self.dyn.rail_lims), 0, 0),
distance=1.8 * np.sum(np.abs(self.dyn.rail_lims)))
recenter()
# Setup user keyboard interactions
disturb = [0.0]
reset = [False]
def keyPressEvent(event):
k = str(event.text())
if k == '.': disturb[0] += 0.5
elif k == ',': disturb[0] -= 0.5
elif k == ' ': disturb[0] = 0.0
elif k == 'v': recenter()
elif k == 'r':
t[0] = 0.0
q[0] = np.copy(q0)
disturb[0] = 0.0
print "User triggered reset!"
reset[0] = True
start_time[0] = time.time()
fig.scene._vtk_control.keyPressEvent = keyPressEvent
print "--\nUSER KEYBOARD CONTROLS:"
if override is None:
print "Increment / decrement disturbance cart-force with '>' / '<' and cancel disturbance with ' ' (spacebar)."
print "Reset view with 'v'. Reset simulation with 'r'.\n--"
print "(close all Mayavi windows to continue...)"
# Wrap simulation in animation
@mlab.animate(delay=50) # 20 FPS is best Mayavi can do
def realtime_loop():
while True:
# Simulate physics up to realtime
while (t[0] <
time.time() - start_time[0]) and not reset[0]:
if override is None:
q[0] = self.dyn.step(q[0],
control(q[0], t[0],
goal), dt, disturb[0])
else:
q[0] = override(t[0])
t[0] += dt
# Update animation
reset[0] = False
cart.mlab_source.set(x=q[0][0])
joint1.mlab_source.set(x=q[0][0])
x1, y1 = q[0][0] + self.dyn.l1 * np.sin(
q[0][1]), -self.dyn.l1 * np.cos(q[0][1])
pole1.mlab_source.set(x=(q[0][0], x1), z=(0, y1))
joint2.mlab_source.set(x=x1, z=y1)
pole2.mlab_source.set(
x=(x1, x1 + self.dyn.l2 * np.sin(q[0][2])),
z=(y1, y1 - self.dyn.l2 * np.cos(q[0][2])))
disp.text = "t = " + str(np.round(t[0], 1))
yield
# Begin simulation and visualization
t = [0.0]
q = [np.copy(q0)]
start_time = [time.time()]
realtime_loop()
mlab.show() # blocking
print "----"
import sys
import os
import vtk
import igl
from vtk.util import numpy_support
import numpy as np
import math
import random
from scipy.sparse import csr_matrix, coo_matrix
vtk_out = vtk.vtkOutputWindow()
vtk_out.SetInstance(vtk_out)
#Make Shader
rootPath = os.path.dirname(os.path.abspath(__file__))
with open(os.path.join(rootPath, "shaders", "normalmap.glsl"),
'r') as shaderFile:
FragmentShaderText = shaderFile.read()
with open(os.path.join(rootPath, "shaders", "vertexShader.glsl"),
'r') as shaderFile:
VertexShaderText = shaderFile.read()
def tutte(V, F):
#Get Boundary and Edge
L = igl.boundary_loop(F)
sizeL = len(L)
def join_process_surface(filenames, algorithm, smooth_iterations, smooth_relaxation_factor, decimate_reduction, keep_largest, fill_holes, options, msg_queue):
def send_message(msg):
try:
msg_queue.put_nowait(msg)
except queue.Full as e:
print(e)
log_path = tempfile.mktemp('vtkoutput.txt')
fow = vtk.vtkFileOutputWindow()
fow.SetFileName(log_path)
ow = vtk.vtkOutputWindow()
ow.SetInstance(fow)
send_message('Joining surfaces ...')
polydata_append = vtk.vtkAppendPolyData()
for f in filenames:
reader = vtk.vtkXMLPolyDataReader()
reader.SetFileName(f)
reader.Update()
polydata = reader.GetOutput()
polydata_append.AddInputData(polydata)
del reader
del polydata
polydata_append.Update()
# polydata_append.GetOutput().ReleaseDataFlagOn()
polydata = polydata_append.GetOutput()
#polydata.Register(None)
# polydata.SetSource(None)
del polydata_append
send_message('Cleaning surface ...')
clean = vtk.vtkCleanPolyData()
# clean.ReleaseDataFlagOn()
# clean.GetOutput().ReleaseDataFlagOn()
clean_ref = weakref.ref(clean)
# clean_ref().AddObserver("ProgressEvent", lambda obj,evt:
# UpdateProgress(clean_ref(), _("Creating 3D surface...")))
clean.SetInputData(polydata)
clean.PointMergingOn()
clean.Update()
del polydata
polydata = clean.GetOutput()
# polydata.SetSource(None)
del clean
if algorithm == 'ca_smoothing':
send_message('Calculating normals ...')
normals = vtk.vtkPolyDataNormals()
normals_ref = weakref.ref(normals)
# normals_ref().AddObserver("ProgressEvent", lambda obj,evt:
# UpdateProgress(normals_ref(), _("Creating 3D surface...")))
normals.SetInputData(polydata)
# normals.ReleaseDataFlagOn()
#normals.SetFeatureAngle(80)
#normals.AutoOrientNormalsOn()
normals.ComputeCellNormalsOn()
# normals.GetOutput().ReleaseDataFlagOn()
normals.Update()
del polydata
polydata = normals.GetOutput()
# polydata.SetSource(None)
del normals
clean = vtk.vtkCleanPolyData()
# clean.ReleaseDataFlagOn()
# clean.GetOutput().ReleaseDataFlagOn()
clean_ref = weakref.ref(clean)
# clean_ref().AddObserver("ProgressEvent", lambda obj,evt:
# UpdateProgress(clean_ref(), _("Creating 3D surface...")))
clean.SetInputData(polydata)
clean.PointMergingOn()
clean.Update()
del polydata
polydata = clean.GetOutput()
# polydata.SetSource(None)
del clean
# try:
# polydata.BuildLinks()
# except TypeError:
# polydata.BuildLinks(0)
# polydata = ca_smoothing.ca_smoothing(polydata, options['angle'],
# options['max distance'],
# options['min weight'],
# options['steps'])
send_message('Context Aware smoothing ...')
mesh = cy_mesh.Mesh(polydata)
cy_mesh.ca_smoothing(mesh, options['angle'],
options['max distance'],
options['min weight'],
options['steps'])
# polydata = mesh.to_vtk()
# polydata.SetSource(None)
# polydata.DebugOn()
# else:
# #smoother = vtk.vtkWindowedSincPolyDataFilter()
# send_message('Smoothing ...')
# smoother = vtk.vtkSmoothPolyDataFilter()
# smoother_ref = weakref.ref(smoother)
# # smoother_ref().AddObserver("ProgressEvent", lambda obj,evt:
# # UpdateProgress(smoother_ref(), _("Creating 3D surface...")))
# smoother.SetInputData(polydata)
# smoother.SetNumberOfIterations(smooth_iterations)
# smoother.SetRelaxationFactor(smooth_relaxation_factor)
# smoother.SetFeatureAngle(80)
# #smoother.SetEdgeAngle(90.0)
# #smoother.SetPassBand(0.1)
# smoother.BoundarySmoothingOn()
# smoother.FeatureEdgeSmoothingOn()
# #smoother.NormalizeCoordinatesOn()
# #smoother.NonManifoldSmoothingOn()
# # smoother.ReleaseDataFlagOn()
# # smoother.GetOutput().ReleaseDataFlagOn()
# smoother.Update()
# del polydata
# polydata = smoother.GetOutput()
# #polydata.Register(None)
# # polydata.SetSource(None)
# del smoother
if not decimate_reduction:
print("Decimating", decimate_reduction)
send_message('Decimating ...')
decimation = vtk.vtkQuadricDecimation()
# decimation.ReleaseDataFlagOn()
decimation.SetInputData(polydata)
decimation.SetTargetReduction(decimate_reduction)
decimation_ref = weakref.ref(decimation)
# decimation_ref().AddObserver("ProgressEvent", lambda obj,evt:
# UpdateProgress(decimation_ref(), _("Creating 3D surface...")))
#decimation.PreserveTopologyOn()
#decimation.SplittingOff()
#decimation.BoundaryVertexDeletionOff()
# decimation.GetOutput().ReleaseDataFlagOn()
decimation.Update()
del polydata
polydata = decimation.GetOutput()
#polydata.Register(None)
# polydata.SetSource(None)
del decimation
#to_measure.Register(None)
# to_measure.SetSource(None)
if keep_largest:
send_message('Finding the largest ...')
conn = vtk.vtkPolyDataConnectivityFilter()
conn.SetInputData(polydata)
conn.SetExtractionModeToLargestRegion()
conn_ref = weakref.ref(conn)
# conn_ref().AddObserver("ProgressEvent", lambda obj,evt:
# UpdateProgress(conn_ref(), _("Creating 3D surface...")))
conn.Update()
# conn.GetOutput().ReleaseDataFlagOn()
del polydata
polydata = conn.GetOutput()
#polydata.Register(None)
# polydata.SetSource(None)
del conn
#Filter used to detect and fill holes. Only fill boundary edges holes.
#TODO: Hey! This piece of code is the same from
#polydata_utils.FillSurfaceHole, we need to review this.
if fill_holes:
send_message('Filling holes ...')
filled_polydata = vtk.vtkFillHolesFilter()
# filled_polydata.ReleaseDataFlagOn()
filled_polydata.SetInputData(polydata)
filled_polydata.SetHoleSize(300)
filled_polydata_ref = weakref.ref(filled_polydata)
# filled_polydata_ref().AddObserver("ProgressEvent", lambda obj,evt:
# UpdateProgress(filled_polydata_ref(), _("Creating 3D surface...")))
filled_polydata.Update()
# filled_polydata.GetOutput().ReleaseDataFlagOn()
del polydata
polydata = filled_polydata.GetOutput()
#polydata.Register(None)
# polydata.SetSource(None)
# polydata.DebugOn()
del filled_polydata
to_measure = polydata
normals = vtk.vtkPolyDataNormals()
# normals.ReleaseDataFlagOn()
# normals_ref = weakref.ref(normals)
# normals_ref().AddObserver("ProgressEvent", lambda obj,evt:
# UpdateProgress(normals_ref(), _("Creating 3D surface...")))
normals.SetInputData(polydata)
normals.SetFeatureAngle(80)
normals.SplittingOn()
normals.AutoOrientNormalsOn()
normals.NonManifoldTraversalOn()
normals.ComputeCellNormalsOn()
# normals.GetOutput().ReleaseDataFlagOn()
normals.Update()
del polydata
polydata = normals.GetOutput()
#polydata.Register(None)
# polydata.SetSource(None)
del normals
# # Improve performance
# stripper = vtk.vtkStripper()
# # stripper.ReleaseDataFlagOn()
# # stripper_ref = weakref.ref(stripper)
# # stripper_ref().AddObserver("ProgressEvent", lambda obj,evt:
# # UpdateProgress(stripper_ref(), _("Creating 3D surface...")))
# stripper.SetInputData(polydata)
# stripper.PassThroughCellIdsOn()
# stripper.PassThroughPointIdsOn()
# # stripper.GetOutput().ReleaseDataFlagOn()
# stripper.Update()
# del polydata
# polydata = stripper.GetOutput()
# #polydata.Register(None)
# # polydata.SetSource(None)
# del stripper
send_message('Calculating area and volume ...')
measured_polydata = vtk.vtkMassProperties()
measured_polydata.SetInputData(to_measure)
measured_polydata.Update()
volume = float(measured_polydata.GetVolume())
area = float(measured_polydata.GetSurfaceArea())
del measured_polydata
filename = tempfile.mktemp(suffix='_full.vtp')
writer = vtk.vtkXMLPolyDataWriter()
writer.SetInputData(polydata)
writer.SetFileName(filename)
writer.Write()
del writer
print("MY PID", os.getpid())
return filename, {'volume': volume, 'area': area}
- Read in XYZ point cloud mesh
- Read in Scalar values and apply a single one
- Create mesh from delaunay
- Export to VTK format for visualisation in Paraview
Updates:
- Read all 3 velocities in as a vector and apply to dataset (SetVectors?)
"""
# This example shows how to use Delaunay3D with alpha shapes.
import vtk
from vtk import *
# prevent error window from popping up
ow = vtk.vtkOutputWindow()
ow.DebugOff()
ow.GlobalWarningDisplayOff()
# flags
large = 1
subsamp = 0
if (large == 1):
filename = 'GT_3d.csv'
Name = 'Vol'
cols = [0, 1, 2, 3, 4, 5]
else:
filename = 'grid_vels.csv'
Name = 'Surf'
cols = [1, 2, 3, 4, 5, 6]
def setup_vtk_log(log_file: str = "vtk.log", append: bool = False):
fow = vtk.vtkFileOutputWindow()
fow.SetFileName(os.path.join(os.path.dirname(__file__), log_file))
fow.SetAppend(append)
ow = vtk.vtkOutputWindow()
ow.SetInstance(fow)
def CreateImageData(self, filelist, zspacing, size, bits):
message = _("Generating multiplanar visualization...")
if not const.VTK_WARNING:
log_path = os.path.join(const.LOG_FOLDER, 'vtkoutput.txt')
fow = vtk.vtkFileOutputWindow()
fow.SetFileName(log_path)
ow = vtk.vtkOutputWindow()
ow.SetInstance(fow)
x, y = size
px, py = utils.predict_memory(len(filelist), x, y, bits)
utils.debug("Image Resized to >>> %f x %f" % (px, py))
if (x == px) and (y == py):
const.REDUCE_IMAGEDATA_QUALITY = 0
else:
const.REDUCE_IMAGEDATA_QUALITY = 1
if not (const.REDUCE_IMAGEDATA_QUALITY):
update_progress = vtk_utils.ShowProgress(
1, dialog_type="ProgressDialog")
array = vtk.vtkStringArray()
for x in xrange(len(filelist)):
if not self.running:
return False
array.InsertValue(x, filelist[x])
if not self.running:
return False
reader = vtkgdcm.vtkGDCMImageReader()
reader.SetFileNames(array)
reader.AddObserver(
"ProgressEvent",
lambda obj, evt: update_progress(reader, message))
reader.Update()
if not self.running:
reader.AbortExecuteOn()
return False
# The zpacing is a DicomGroup property, so we need to set it
imagedata = vtk.vtkImageData()
imagedata.DeepCopy(reader.GetOutput())
spacing = imagedata.GetSpacing()
imagedata.SetSpacing(spacing[0], spacing[1], zspacing)
else:
update_progress = vtk_utils.ShowProgress(
2 * len(filelist), dialog_type="ProgressDialog")
# Reformat each slice and future append them
appender = vtk.vtkImageAppend()
appender.SetAppendAxis(2) #Define Stack in Z
# Reformat each slice
for x in xrange(len(filelist)):
# TODO: We need to check this automatically according
# to each computer's architecture
# If the resolution of the matrix is too large
if not self.running:
return False
reader = vtkgdcm.vtkGDCMImageReader()
reader.SetFileName(filelist[x])
reader.AddObserver(
"ProgressEvent",
lambda obj, evt: update_progress(reader, message))
reader.Update()
#Resample image in x,y dimension
slice_imagedata = ResampleImage2D(reader.GetOutput(), px, py,
update_progress)
#Stack images in Z axes
appender.AddInput(slice_imagedata)
#appender.AddObserver("ProgressEvent", lambda obj,evt:update_progress(appender))
appender.Update()
# The zpacing is a DicomGroup property, so we need to set it
if not self.running:
return False
imagedata = vtk.vtkImageData()
imagedata.DeepCopy(appender.GetOutput())
spacing = imagedata.GetSpacing()
imagedata.SetSpacing(spacing[0], spacing[1], zspacing)
imagedata.AddObserver(
"ProgressEvent",
lambda obj, evt: update_progress(imagedata, message))
imagedata.Update()
return imagedata
import vtk
# from vtk.util.misc import vtkGetDataRoot
# from vtk.util.misc import vtkGetTempDir
import sys
# import os
# VTK_DATA_ROOT = vtkGetDataRoot()
# VTK_TEMP_DIR = vtkGetTempDir()
output = vtk.vtkFileOutputWindow()
output.SetFileName("log.txt")
vtk.vtkOutputWindow().SetInstance(output)
test_files = [['minimal.nii.gz', 'out_minimal.nii.gz']]
display_file = 'data/flair.nii.gz'
def TestDisplay(file):
# in_path = os.path.join(str(VTK_DATA_ROOT), "Data", file)
in_path = "./data/flair.nii.gz"
reader = vtk.vtkNIFTIImageReader()
reader.SetFileName(in_path)
reader.Update()
# # marching cubes?
# contour = vtk.vtkMarchingCubes()
# contour.SetInput(brain_reader.GetOutput())
# contour.Update()
#
# mapper = vtk.vtkImageSliceMapper()
del self.vtk_widget_3
del self.vtk_widget_4
self.vtk_widget_2 = VTK_Widget2(0)
self.vtk_widget_3 = VTK_Widget2(1)
self.vtk_widget_4 = VTK_Widget2(2)
self.vtk_widget_1 = VTK_Widget1()
self.HSplitterTop.addWidget(self.vtk_widget_1)
self.HSplitterTop.addWidget(self.vtk_widget_2)
self.HSplitterBottom.addWidget(self.vtk_widget_3)
self.HSplitterBottom.addWidget(self.vtk_widget_4)
self.vtk_widget_1.SetSource(self.reader.GetOutput())
self.vtk_widget_2.SetSource(self.reader.GetOutput())
self.vtk_widget_3.SetSource(self.reader.GetOutput())
self.vtk_widget_4.SetSource(self.reader.GetOutput())
# START APPLICATION
app = QApplication(sys.argv)
ow = vtk.vtkOutputWindow()
ow.SetGlobalWarningDisplay(0)
mainwindow = MainVizWindow()
mainwindow.show()
if sys.argv.__len__() > 1:
source = sys.argv[1]
mainwindow.setSource(source)
sys.exit(app.exec_())
#!/usr/bin/python
from __future__ import division
import traits
import traitsui
from mayavi import mlab
import cv2
import numpy as np
import vtk
output = vtk.vtkFileOutputWindow()
# Throw the stupid vtk runtime errors into a burning pit
output.SetFileName("/dev/null")
vtk.vtkOutputWindow().SetInstance(output)
color_ranges = {
'hsv': np.array([
[0, 179], # Stupid OpenCV saving 1 bit...
[0, 255],
[0, 255]
]),
'bgr': np.array([
[0, 255],
[0, 255],
[0, 255]
])
}
def np_inrange(vector, lower_range, upper_range):
sat_lower = np.min(vector > lower_range, axis=1)
self.tabs.tabBar().setTabButton(1, QTabBar.RightSide, None)
self.tabs.addTab(self.tab_gad, icon_tab_loc, "Locate(GAD)")
self.tabs.tabBar().setTabButton(2, QTabBar.RightSide, None)
self.tabs.addTab(self.tab_jhd, icon_tab_rel, "Relocate(JHD)")
self.tabs.tabBar().setTabButton(3, QTabBar.RightSide, None)
self.tabs.addTab(self.tab_hdd, icon_tab_rel, "Relocate(DD)")
self.tabs.tabBar().setTabButton(4, QTabBar.RightSide, None)
self.tabs.addTab(self.tab_tg, icon_tab_tg, "Tomography")
self.tabs.tabBar().setTabButton(5, QTabBar.RightSide, None)
self.setCentralWidget(self.tabs)
def closeTab (self, currentIndex):
currentQWidget = self.tabs.widget(currentIndex)
currentQWidget.deleteLater()
self.tabs.removeTab(currentIndex)
if __name__ == '__main__':
app = QApplication(sys.argv)
main = MainWindow()
splash_pix = QPixmap(splash_screen)
splash = QSplashScreen(splash_pix, Qt.WindowStaysOnTopHint)
splash.show()
time.sleep(1)
splash.close()
main.showMaximized()
errOut = vtk.vtkFileOutputWindow()
errOut.SetFileName(os.path.join(os.getcwd(),'bug','vtk.bug'))
vtkStdErrOut = vtk.vtkOutputWindow()
vtkStdErrOut.SetInstance(errOut)
sys.exit(app.exec_())
def OpenPlistProject(self, filename):
import invesalius.data.measures as ms
import invesalius.data.mask as msk
import invesalius.data.surface as srf
if not const.VTK_WARNING:
log_path = os.path.join(const.USER_LOG_DIR, 'vtkoutput.txt')
fow = vtk.vtkFileOutputWindow()
fow.SetFileName(log_path.encode(const.FS_ENCODE))
ow = vtk.vtkOutputWindow()
ow.SetInstance(fow)
filelist = Extract(filename, tempfile.mkdtemp())
dirpath = os.path.abspath(os.path.split(filelist[0])[0])
# Opening the main file from invesalius 3 project
main_plist = os.path.join(dirpath ,'main.plist')
project = plistlib.readPlist(main_plist)
format_version = project["format_version"]
if format_version > const.INVESALIUS_ACTUAL_FORMAT_VERSION:
from invesalius.gui.dialogs import ImportOldFormatInvFile
ImportOldFormatInvFile()
# case info
self.name = project["name"]
self.modality = project["modality"]
self.original_orientation = project["orientation"]
self.window = project["window_width"]
self.level = project["window_level"]
self.threshold_range = project["scalar_range"]
self.spacing = project["spacing"]
if project.get("affine"):
self.affine = project["affine"]
Publisher.sendMessage('Update affine matrix',
affine=self.affine, status=True)
self.compress = project.get("compress", True)
# Opening the matrix containing the slices
filepath = os.path.join(dirpath, project["matrix"]["filename"])
self.matrix_filename = filepath
self.matrix_shape = project["matrix"]['shape']
self.matrix_dtype = project["matrix"]['dtype']
# Opening the masks
self.mask_dict = {}
for index in project["masks"]:
filename = project["masks"][index]
filepath = os.path.join(dirpath, filename)
m = msk.Mask()
m.OpenPList(filepath)
self.mask_dict[m.index] = m
# Opening the surfaces
self.surface_dict = {}
for index in project["surfaces"]:
filename = project["surfaces"][index]
filepath = os.path.join(dirpath, filename)
s = srf.Surface(int(index))
s.OpenPList(filepath)
self.surface_dict[s.index] = s
# Opening the measurements
self.measurement_dict = {}
measurements = plistlib.readPlist(os.path.join(dirpath,
project["measurements"]))
for index in measurements:
if measurements[index]["type"] in (const.DENSITY_ELLIPSE, const.DENSITY_POLYGON):
measure = ms.DensityMeasurement()
else:
measure = ms.Measurement()
measure.Load(measurements[index])
self.measurement_dict[int(index)] = measure