def load_image(self, *args):
if debug:
print "loc3djr_maintoolbar.load_image()"
debug = False
reader = None
pars = None
if debug:
reader = vtk.vtkImageReader2()
reader.SetDataScalarTypeToUnsignedShort()
reader.SetDataByteOrderToLittleEndian()
reader.SetFileNameSliceOffset(120)
reader.SetDataExtent(0, 511, 0, 511, 0, 106)
reader.SetFilePrefix('/home/jdhunter/seizure/data/ThompsonK/CT/raw/1.2.840.113619.2.55.1.1762864819.1957.1074338393.')
reader.SetFilePattern( '%s%d.raw')
reader.SetDataSpacing(25.0/512, 25.0/512, 0.125 )
reader.Update()
else:
dlg = widgets['dlgReader']
response = dlg.run()
if response == gtk.RESPONSE_OK:
try: reader = widgets.reader
except AttributeError:
pars = widgets.get_params()
pars = widgets.validate(pars)
if pars is None:
error_msg('Could not validate the parameters', dlg)
return
reader = widgets.get_reader(pars)
pars = widgets.get_params()
pars = widgets.validate(pars)
dlg.hide()
if debug:
print "reader=", reader
if not reader:
if debug:
print "hit cancel, see if we can survive"
else:
imageData = reader.GetOutput()
if debug:
print "pars=", pars
print "loc3djr_maintoolbar.load_image(): reader.GetOutput() is " , imageData
print "load_image(): imageData.SetSpacing(", reader.GetDataSpacing(), " )"
imageData.SetSpacing(reader.GetDataSpacing())
if debug:
print "calling EventHandler().notify('set image data', imageData)"
EventHandler().notify('set image data', imageData)
if type(reader) == vtkNiftiImageReader:
if debug:
print "calling EventHandler().setNifti()"
#XXX EventHandler().setNifti(reader.GetFilename())
EventHandler().setNifti(reader.GetQForm())
def load_image(self, *args):
print "loc3djr_maintoolbar.load_image()"
debug = False
reader = None
pars = None
if debug:
reader = vtk.vtkImageReader2()
reader.SetDataScalarTypeToUnsignedShort()
reader.SetDataByteOrderToLittleEndian()
reader.SetFileNameSliceOffset(120)
reader.SetDataExtent(0, 511, 0, 511, 0, 106)
reader.SetFilePrefix(
'/home/jdhunter/seizure/data/ThompsonK/CT/raw/1.2.840.113619.2.55.1.1762864819.1957.1074338393.'
)
reader.SetFilePattern('%s%d.raw')
reader.SetDataSpacing(25.0 / 512, 25.0 / 512, 0.125)
reader.Update()
else:
dlg = widgets['dlgReader']
response = dlg.run()
if response == gtk.RESPONSE_OK:
try:
reader = widgets.reader
except AttributeError:
pars = widgets.get_params()
pars = widgets.validate(pars)
if pars is None:
error_msg('Could not validate the parameters', dlg)
return
reader = widgets.get_reader(pars)
pars = widgets.get_params()
pars = widgets.validate(pars)
dlg.hide()
print "reader=", reader
if not reader:
print "hit cancel, see if we can survive"
else:
imageData = reader.GetOutput()
print "pars=", pars
print "loc3djr_maintoolbar.load_image(): reader.GetOutput() is ", imageData
print "load_image(): imageData.SetSpacing(", reader.GetDataSpacing(
), " )"
imageData.SetSpacing(reader.GetDataSpacing())
print "calling EventHandler().notify('set image data', imageData)"
EventHandler().notify('set image data', imageData)
if type(reader) == vtkNiftiImageReader:
print "calling EventHandler().setNifti()"
#XXX EventHandler().setNifti(reader.GetFilename())
EventHandler().setNifti(reader.GetQForm())
def __init__(self, xyz, radius=None, rgb=None):
# if radius is not defined, force it to be some percentage of
# the total dimensions of the scanz..
if (radius == None):
pars = widgets.get_params()
if debug:
print "pars.dfov is ", pars.dfov
if debug:
print "pars.dimensions[0] is" , pars.dimensions[0]
ratio = float(pars.dfov)/float(pars.dimensions[0])
radius = ratio * 3
if debug:
print "setting radius=", radius
if rgb is None: rgb = (0,0,1)
self.sphere = vtk.vtkSphereSource()
self.sphere.SetRadius(radius)
res = 20
self.sphere.SetThetaResolution(res)
self.sphere.SetPhiResolution(res)
self.sphere.SetCenter(xyz)
mapper = vtk.vtkPolyDataMapper()
mapper.SetInput(self.sphere.GetOutput())
mapper.ImmediateModeRenderingOn()
self.SetMapper(mapper)
self.GetProperty().SetColor( rgb )
self.label = ''
self.labelColor = (1,1,0)
def load_mri(self, *args):
print "loc3djr_maintoolbar.load_mri()"
if self.niftiFilename is not None:
fname=self.niftiFilename
else:
dialog = gtk.FileSelection('Choose nifti file')
dialog.set_transient_for(widgets['dlgReader'])
dialog.set_filename(shared.get_last_dir())
response = dialog.run()
fname = dialog.get_filename()
dialog.destroy()
if response == gtk.RESPONSE_OK:
print fname
else:
return
#reader = vtkNiftiImageReader()
#reader.SetFileName(fname)
#reader.Update()
pars = Params()
if fname.endswith(".nii.gz"):
pars.extension=".".join(fname.split(".")[-2:])
pars.pattern=".".join(fname.split(os.path.sep)[-1].split(".")[:-2])
#elif fname.endswith(".nii"):
# pars.extension=".nii"
else:
pars.extension=".".join(fname.split(".")[-1:])
pars.pattern=".".join(fname.split(os.path.sep)[-1].split(".")[:-1])
print "pars.extension", pars.extension
print "pars.pattern", pars.pattern
pars.dir=os.path.dirname(fname)#sep.join(fname.split(os.path.sep)[:-1])
print "pars.dir", pars.dir
pars.readerClass='vtkNiftiImageReader'
reader=widgets.get_reader(pars)
pars.first=1
pars.last=reader.GetDepth()
print "reader=", reader
if not reader:
print "hit cancel, see if we can survive"
else:
pars=widgets.get_params()
pars=widgets.validate(pars)
imageData = reader.GetOutput()
#stupid workaround, somehow imageData.Extent is not written. dunno why
#maybe its in vtkImageImportFromArray
imageData.SetExtent(reader.GetDataExtent())
print "loc3djr_maintoolbar.load_mri(): reader.GetOutput() is " , imageData
print "load_mri(): imageData.SetSpacing(", reader.GetDataSpacing(), " )"
imageData.SetSpacing(reader.GetDataSpacing())
print "calling EventHandler().notify('set image data', imageData)"
EventHandler().notify('set image data', imageData)
print "calling EventHandler().setNifti()"
EventHandler().setNifti(reader.GetQForm(),reader.GetDataSpacing())
def __init__(self, xyz, radius=None, rgb=None):
# if radius is not defined, force it to be some percentage of
# the total dimensions of the scanz..
if (radius == None):
pars = widgets.get_params()
print "pars.dfov is ", pars.dfov
print "pars.dimensions[0] is", pars.dimensions[0]
ratio = float(pars.dfov) / float(pars.dimensions[0])
radius = ratio * 3
print "setting radius=", radius
if rgb is None: rgb = (0, 0, 1)
self.sphere = vtk.vtkSphereSource()
self.sphere.SetRadius(radius)
res = 20
self.sphere.SetThetaResolution(res)
self.sphere.SetPhiResolution(res)
self.sphere.SetCenter(xyz)
mapper = vtk.vtkPolyDataMapper()
mapper.SetInput(self.sphere.GetOutput())
mapper.ImmediateModeRenderingOn()
self.SetMapper(mapper)
self.GetProperty().SetColor(rgb)
self.label = ''
self.labelColor = (1, 1, 0)
