def __init__(self, parent=None):
QtGui.QWidget.__init__(self, parent)
# Using composition to include the visual element of the GUI.
self.ui = Ui_GlyphExportDlg()
self.ui.setupUi(self)
'''Initialise a sceneviewer for viewing'''
self._context = Context('glyph_export')
self.ui.sceneviewerwidget.setContext(self._context)
self.setWindowIcon(QtGui.QIcon(":/cmiss_icon.ico"))
self.resize(620, 440)
self._context.getGlyphmodule().defineStandardGlyphs()
self._default_region = self._context.getDefaultRegion()
'''This set the prefix for the files to be exported'''
self._prefix = 'GlyphExport'
'''Read the file with the following function'''
self.readMesh()
'''Create material which is used to colour the to be exported surfaces'''
self.createMaterial()
'''Create surface graphics which will be viewed and exported'''
self.createSurfaceGraphics()
'''Create glyph graphics which will be viewed and exported'''
self.createGlyphGraphics()
'''Export glyph into JSON format'''
self.ui.sceneviewerwidget.graphicsInitialized.connect(
self.exportWebGLJson)
class SemiAutoModel(object):
'''
classdocs
'''
def __init__(self):
'''
Constructor
'''
self._context = Context('heartsurface')
glyph_module = self._context.getGlyphmodule()
glyph_module.defineStandardGlyphs()
material_module = self._context.getMaterialmodule()
material_module.defineStandardMaterials()
self.clear()
def clear(self):
self._region = None
self._image_data = None
def initialize(self):
self._region = self._context.createRegion()
def getRegion(self):
return self._region
def getContext(self):
return self._context
def getPointCloud(self):
return []
def setImageData(self, image_data):
self._image_data = image_data
def write_ex(file_name, data, options=None):
context = Context("Neurolucida")
region = context.getDefaultRegion()
load(region, data, options)
region.writeFile(file_name)
def __init__(self):
self._context = Context("LungModelView")
self._logger = self._context.getLogger()
self._initialize()
self._leftRegion = self.setRegion('leftRegion')
self._rightRegion = self.setRegion('rightRegion')
self._leftAirwayRegion = self.setRegion('leftAirwayRegion')
self._rightAirwayRegion = self.setRegion('rightAirwayRegion')
self._leftArteryRegion = self.setRegion('leftArteryRegion')
self._rightArteryRegion = self.setRegion('rightArteryRegion')
self._leftVeinRegion = self.setRegion('leftVeinRegion')
self._rightVeinRegion = self.setRegion('rightVeinRegion')
regions = {
self._leftRegion.getName(): self._leftRegion,
self._rightRegion.getName(): self._rightRegion,
self._leftAirwayRegion.getName(): self._leftAirwayRegion,
self._rightAirwayRegion.getName(): self._rightAirwayRegion,
self._leftArteryRegion.getName(): self._leftArteryRegion,
self._rightArteryRegion.getName(): self._rightArteryRegion,
self._leftVeinRegion.getName(): self._leftVeinRegion,
self._rightVeinRegion.getName(): self._rightVeinRegion
}
self._meshModel = MeshModel(regions, self._materialModule,
self._context)
def test_mousecolonsegment1(self):
"""
Test creation of mouse colon segment scaffold.
"""
options = MeshType_3d_colonsegment1.getDefaultOptions("Mouse 1")
context = Context("Test")
region = context.getDefaultRegion()
self.assertTrue(region.isValid())
annotationGroups = MeshType_3d_colonsegment1.generateBaseMesh(region, options)
self.assertEqual(7, len(annotationGroups))
fieldmodule = region.getFieldmodule()
self.assertEqual(RESULT_OK, fieldmodule.defineAllFaces())
mesh3d = fieldmodule.findMeshByDimension(3)
self.assertEqual(160, mesh3d.getSize())
coordinates = fieldmodule.findFieldByName("coordinates").castFiniteElement()
self.assertTrue(coordinates.isValid())
flatCoordinates = fieldmodule.findFieldByName("flat coordinates").castFiniteElement()
self.assertTrue(flatCoordinates.isValid())
with ChangeManager(fieldmodule):
one = fieldmodule.createFieldConstant(1.0)
faceMeshGroup = createFaceMeshGroupExteriorOnFace(fieldmodule, Element.FACE_TYPE_XI3_1)
surfaceAreaField = fieldmodule.createFieldMeshIntegral(one, coordinates, faceMeshGroup)
surfaceAreaField.setNumbersOfPoints(4)
flatSurfaceAreaField = fieldmodule.createFieldMeshIntegral(one, flatCoordinates, faceMeshGroup)
flatSurfaceAreaField.setNumbersOfPoints(4)
fieldcache = fieldmodule.createFieldcache()
result, surfaceArea = surfaceAreaField.evaluateReal(fieldcache, 1)
self.assertEqual(result, RESULT_OK)
self.assertAlmostEqual(surfaceArea, 468.17062489996886, delta=1.0E-6)
result, flatSurfaceArea = flatSurfaceAreaField.evaluateReal(fieldcache, 1)
self.assertEqual(result, RESULT_OK)
self.assertAlmostEqual(flatSurfaceArea, surfaceArea, delta=1.0E-3)
def __init__(self, ex_data_file, location, identifier):
self._context = Context('DataTrimmer')
self._region = self._context.createRegion()
self._region.setName('TrimRegion')
self._field_module = self._region.getFieldmodule()
self._ex_filename = ex_data_file
self._location = location
self._identifier = identifier
self._output_filename = None
self._coordinate_field = None
self._mesh = None
self._groups = None
self._group_fields = None
self._group_dct = None
self._settings = {}
# read the EX Zinc data file
self._initialise_ex_data(ex_data_file)
self._load_settings()
self._material_module = self._context.getMaterialmodule()
self._initialise_glyph_material()
self._init_graphics_module()
self._initialise_tessellation(12)
self._scene_change_callback = None
self._initialise_scene()
def __init__(self, parent=None):
'''
Initiaise the MaterialsAndTextureDlg first calling the QWidget __init__ function.
'''
QtGui.QWidget.__init__(self, parent)
# Using composition to include the visual element of the GUI.
self.ui = Ui_MaterialsAndTextureDlg()
self.ui.setupUi(self)
self._context = Context('selection')
self.ui.sceneviewerwidget.setContext(self._context)
self.setWindowIcon(QtGui.QIcon(":/cmiss_icon.ico"))
self.resize(620, 440)
self._prefix = "MaterialsAndTexture"
self._regions = []
default_region = self._context.getDefaultRegion()
for i in range(1, 6):
region_name = 'region_' + str(i)
region = default_region.createChild(region_name)
self._regions.append(region)
self.createMaterial()
self.createMaterialUsingImageField()
self.createFiniteElements()
self.createSurfaceGraphics()
''' the following function exports the camera settings'''
self.ui.sceneviewerwidget.graphicsInitialized.connect(
self.exportWebGLJson)
def create_fibre_values(self, out_file="fibre_values_spheroidal.txt"):
"""takes an .exfile document, extracts the prolate spheroidal coordinates at each nodes and write them in
order into a new file. The function works by creating a node iterator from the nodeset wich contains all
nodes """
if os.path.isfile("/tmp/" + out_file):
os.remove("/tmp/" + out_file)
out = open(out_file, "w+")
context = Context("heart")
region = context.getDefaultRegion()
region.readFile(self.in_file)
fieldmodule = region.getFieldmodule()
field = fieldmodule.findFieldByName("fibres")
cache = fieldmodule.createFieldcache()
node_set = fieldmodule.findNodesetByName("nodes")
mesh = fieldmodule.findMeshByDimension(3)
ele_iter = mesh.createElementiterator()
node_iter = node_set.createNodeiterator() #create the node iterator
counter = 0
node = node_iter.next()
while node.isValid():
cache.setNode(
node) #sets the fieldcache-position to the current node
result, out_values = field.evaluateReal(
cache, 3
) #evaluates real coordinates at the current position of cache
if result == ZINC_OK:
out.write(
str(out_values[0]) + " " + str(out_values[1]) + " " +
str(out_values[2]) + "\r\n")
else:
break
node = node_iter.next()
counter += 1
def create_node_connectivity(self, out_file="connectivity.txt"):
if os.path.isfile("/tmp/" + out_file):
os.remove("/tmp/" + out_file)
out = open(out_file, "w+")
context = Context("heart")
region = context.getDefaultRegion()
region.readFile(self.in_file)
fieldmodule = region.getFieldmodule()
field = fieldmodule.findFieldByName("coordinates")
cache = fieldmodule.createFieldcache()
mesh = fieldmodule.findMeshByDimension(3)
ele_iter = mesh.createElementiterator()
#d_ds1 = mesh.getChartDifferentialoperator(1, 2)
#print(d_ds1.isValid())
counter = 0
element = ele_iter.next()
ele_template = element.getElementfieldtemplate(field, 1)
n = ele_template.getNumberOfLocalNodes()
while element.isValid():
for i in range(1, n + 1):
current_node = element.getNode(ele_template, i)
cache.setElement(element)
#test = field.evaluateDerivative(d_ds1, cache, 1)
#print(test)
local_index = current_node.getIdentifier()
out.write(str(local_index) + " ")
out.write("\r\n")
element = ele_iter.next()
ele_template = element.getElementfieldtemplate(field, 1)
def find_standard_elements(self,):
"""
Returns the standard element numbers in mesh (ie meshes that have 8 nodes per element
"""
context = Context("Scaffold")
region = context.getDefaultRegion()
result = region.readFile(self.input_mesh)
if result != ZINC_OK:
raise ValueError('Error loading mesh in {0}'.format(self.input_mesh))
field_module = region.getFieldmodule()
mesh = field_module.findMeshByDimension(self.dim)
coordinates = field_module.findFieldByName('coordinates')
# Store elements in a dict
el_iter = mesh.createElementiterator()
elemDict = dict()
element = el_iter.next()
elem_list = []
while element.isValid():
elem_list.append(int(element.getIdentifier()))
elemDict[int(element.getIdentifier())] = element
element = el_iter.next()
mesh_elements = elemDict
for elem in elem_list:
mesh_element = mesh_elements[elem]
eft = mesh_element.getElementfieldtemplate(coordinates, -1) # assumes all components same
nodeIdentifiers = zinc_utils.getElementNodeIdentifiers8Node(mesh_element, eft)
a=1
def __init__(self):
'''
Constructor
'''
self._context = Context('surfacefit')
materialmodule = self._context.getMaterialmodule()
materialmodule.beginChange()
materialmodule.defineStandardMaterials()
self._surfaceMaterial = materialmodule.createMaterial()
self._surfaceMaterial.setName('fit-surface')
self._surfaceMaterial.setAttributeReal3(Material.ATTRIBUTE_AMBIENT,
[0.7, 0.7, 1.0])
self._surfaceMaterial.setAttributeReal3(Material.ATTRIBUTE_DIFFUSE,
[0.7, 0.7, 1.0])
self._surfaceMaterial.setAttributeReal3(Material.ATTRIBUTE_SPECULAR,
[0.5, 0.5, 0.5])
self._surfaceMaterial.setAttributeReal(Material.ATTRIBUTE_ALPHA, 0.5)
self._surfaceMaterial.setAttributeReal(Material.ATTRIBUTE_SHININESS,
0.3)
materialmodule.endChange()
glyphmodule = self._context.getGlyphmodule()
glyphmodule.defineStandardGlyphs()
tessellationmodule = self._context.getTessellationmodule()
defaultTessellation = tessellationmodule.getDefaultTessellation()
defaultTessellation.setRefinementFactors([12])
self._location = None
self._zincModelFile = None
self._zincPointCloudFile = None
self._pointCloudData = None
self._filterTopErrorProportion = 0.9
self._filterNonNormalProjectionLimit = 0.99
self._enableLoadPreviousSolution = False
self.clear()
class SemiAutoModel(object):
'''
classdocs
'''
def __init__(self):
'''
Constructor
'''
self._context = Context('heartsurface')
glyph_module = self._context.getGlyphmodule()
glyph_module.defineStandardGlyphs()
material_module = self._context.getMaterialmodule()
material_module.defineStandardMaterials()
self.clear()
def clear(self):
self._region = None
self._image_data = None
def initialize(self):
self._region = self._context.createRegion()
def getRegion(self):
return self._region
def getContext(self):
return self._context
def getPointCloud(self):
return []
def setImageData(self, image_data):
self._image_data = image_data
def __init__(self, filename, field_info, output_filename):
self._context = Context("AddField")
self._region = self._context.getDefaultRegion()
self._region.readFile(filename)
self._output_file = output_filename
self._add_field(field_info)
class AxisViewerDlg(QtGui.QWidget):
'''
Create a subclass of QWidget for our application. We could also have derived this
application from QMainWindow to give us a menu bar among other things, but a
QWidget is sufficient for our purposes.
'''
def __init__(self, parent=None):
'''
Initiaise the AxisViewerDlg first calling the QWidget __init__ function.
'''
QtGui.QWidget.__init__(self, parent)
# create instance of Zinc Context from which all other objects are obtained
self._context = ZincContext("Axis Viewer");
# set up standard materials and glyphs so we can use them elsewhere
# define standard materials first as some coloured glyphs use them
materialmodule = self._context.getMaterialmodule()
materialmodule.defineStandardMaterials()
# this example uses a standard axes glyph hence need the following:
glyphmodule = self._context.getGlyphmodule()
glyphmodule.defineStandardGlyphs()
# Using composition to include the visual element of the GUI.
self.ui = Ui_AxisViewerDlg()
self.ui.setupUi(self)
# Must pass the context to the ZincWidget to set it up
self.ui._zincwidget.setContext(self._context)
self.setWindowIcon(QtGui.QIcon(":/cmiss_icon.ico"))
self.resize(620, 440)
# set up content for this application
self.setupAxes()
# AxisViewerDlg end
# AxisViewerDlg.setupAxes start
def setupAxes(self):
region = self._context.getDefaultRegion()
# Graphics for visualising a region belong to its scene
scene = region.getScene()
# Call beginChange() to stop scene change messages being sent while
# making multiple changes to scene or its graphics.
# It's very important to call endChange() at the end!
scene.beginChange()
# Create Points graphics in scene and visualise with unit-sized solid 3-D axes
graphics = scene.createGraphicsPoints()
attributes = graphics.getGraphicspointattributes()
attributes.setGlyphShapeType(Glyph.SHAPE_TYPE_AXES_SOLID)
# Note: default base size of 0.0 would make axes invisible!
attributes.setBaseSize([1.0])
# Restart scene messaging and inform clients of changes.
# This ultimately triggers a redraw in the Zinc Widget.
scene.endChange()
def __init__(self, location, identifier):
self._location = location
self._identifier = identifier
self._filenameStem = os.path.join(self._location, self._identifier)
self._context = Context("MeshGenerator")
self._initialise()
self._region = self._context.createRegion()
self._generator_model = MeshGeneratorModel(self._region, self._materialmodule)
self._plane_model = MeshPlaneModel(self._region)
def define_standard_graphics_objects(context: Context):
"""
Defines Zinc standard objects for use in graphics, including
a number of graphical materials and glyphs.
"""
glyphmodule = context.getGlyphmodule()
glyphmodule.defineStandardGlyphs()
materialmodule = context.getMaterialmodule()
materialmodule.defineStandardMaterials()
class AxisViewerDlg(QtGui.QWidget):
'''
Create a subclass of QWidget for our application. We could also have derived this
application from QMainWindow to give us a menu bar among other things, but a
QWidget is sufficient for our purposes.
'''
def __init__(self, parent=None):
'''
Initiaise the AxisViewerDlg first calling the QWidget __init__ function.
'''
QtGui.QWidget.__init__(self, parent)
# create instance of Zinc Context from which all other objects are obtained
self._context = ZincContext("Axis Viewer")
# set up standard materials and glyphs so we can use them elsewhere
# define standard materials first as some coloured glyphs use them
materialmodule = self._context.getMaterialmodule()
materialmodule.defineStandardMaterials()
# this example uses a standard axes glyph hence need the following:
glyphmodule = self._context.getGlyphmodule()
glyphmodule.defineStandardGlyphs()
# Using composition to include the visual element of the GUI.
self.ui = Ui_AxisViewerDlg()
self.ui.setupUi(self)
# Must pass the context to the ZincWidget to set it up
self.ui._zincwidget.setContext(self._context)
self.setWindowIcon(QtGui.QIcon(":/cmiss_icon.ico"))
self.resize(620, 440)
# set up content for this application
self.setupAxes()
# AxisViewerDlg end
# AxisViewerDlg.setupAxes start
def setupAxes(self):
region = self._context.getDefaultRegion()
# Graphics for visualising a region belong to its scene
scene = region.getScene()
# Call beginChange() to stop scene change messages being sent while
# making multiple changes to scene or its graphics.
# It's very important to call endChange() at the end!
scene.beginChange()
# Create Points graphics in scene and visualise with unit-sized solid 3-D axes
graphics = scene.createGraphicsPoints()
attributes = graphics.getGraphicspointattributes()
attributes.setGlyphShapeType(Glyph.SHAPE_TYPE_AXES_SOLID)
# Note: default base size of 0.0 would make axes invisible!
attributes.setBaseSize([1.0])
# Restart scene messaging and inform clients of changes.
# This ultimately triggers a redraw in the Zinc Widget.
scene.endChange()
def __init__(self):
'''
Constructor
'''
self._context = Context('heartsurface')
glyph_module = self._context.getGlyphmodule()
glyph_module.defineStandardGlyphs()
material_module = self._context.getMaterialmodule()
material_module.defineStandardMaterials()
self.clear()
def __init__(self, parent=None):
'''
Call the super class init functions, create a Zinc context and set the scene viewer handle to None.
'''
QtOpenGL.QGLWidget.__init__(self, parent)
# Create a Zinc context from which all other objects can be derived either directly or indirectly.
# Each context requires a unique name to reference it.
self._context = Context("finiteelementcreation")
self._scene_viewer = None
def __init__(self):
self._context = Context('Segmentation')
self._undo_redo_stack = QtGui.QUndoStack()
self.defineStandardMaterials()
self._createModeMaterials()
self.defineStandardGlyphs()
self._image_model = ImageModel(self._context)
self._node_model = NodeModel(self._context)
def __init__(self, parent=None):
'''
Call the super class init functions, create a Zinc context and set the scene viewer handle to None.
'''
QtOpenGL.QGLWidget.__init__(self, parent)
# Create a Zinc context from which all other objects can be derived either directly or indirectly.
#print(opencmiss.zinc.__version__)
self._context = Context("axisviewer")
self._scene_viewer = None
def export_to_web_gl_json(mesh_description):
"""
Export graphics into JSON formats. Returns an array containing the
string buffers for each export
:param mesh_description:
:return:
"""
context = Context('web_gl')
if isinstance(mesh_description, dict):
region_description = mesh_description['_region_description']
scene_description = mesh_description['_scene_description']
time_array = mesh_description['_epochs']
start_time = time_array[0]
end_time = time_array[-1]
epoch_count = len(time_array)
else:
region_description = mesh_description.get_region_description()
scene_description = mesh_description.get_scene_description()
start_time = mesh_description.get_start_time()
end_time = mesh_description.get_end_time()
epoch_count = mesh_description.get_epoch_count()
region = context.createRegion()
scene = region.getScene()
_read_region_description(region, region_description)
_read_scene_description(scene, scene_description)
tessellation_module = scene.getTessellationmodule()
default_tessellation = tessellation_module.getDefaultTessellation()
default_tessellation.setRefinementFactors([4, 4, 1])
tessellation_module.setDefaultTessellation(default_tessellation)
stream_information = scene.createStreaminformationScene()
stream_information.setIOFormat(stream_information.IO_FORMAT_THREEJS)
stream_information.setInitialTime(start_time)
stream_information.setFinishTime(end_time)
stream_information.setNumberOfTimeSteps(epoch_count)
stream_information.setOutputTimeDependentVertices(1)
# Get the total number of graphics in a scene/region that can be exported
number = stream_information.getNumberOfResourcesRequired()
resources = []
# Write out each graphics into a json file which can be rendered with our
# WebGL script
for i in range(number):
resources.append(stream_information.createStreamresourceMemory())
scene.write(stream_information)
# Store all the resources in a buffer
resource_buffer = [resources[i].getBuffer()[1] for i in range(number)]
return resource_buffer
class Scene(object):
def __init__(self):
self._context = Context("Scene")
self._initialize()
def getContext(self):
return self._context
def getScene(self):
return self._context.getDefaultRegion().getScene()
def _initialize(self):
tess = self._context.getTessellationmodule().getDefaultTessellation()
tess.setRefinementFactors(12)
self._materialModule = self._context.getMaterialmodule()
self._materialModule.defineStandardMaterials()
material = self._materialModule.createMaterial()
material.setName('solidBlue')
material.setManaged(True)
material.setAttributeReal3(Material.ATTRIBUTE_AMBIENT, [0.0, 0.2, 0.6])
material.setAttributeReal3(Material.ATTRIBUTE_DIFFUSE, [0.0, 0.7, 1.0])
material.setAttributeReal3(Material.ATTRIBUTE_EMISSION,
[0.0, 0.0, 0.0])
material.setAttributeReal3(Material.ATTRIBUTE_SPECULAR,
[0.1, 0.1, 0.1])
material.setAttributeReal(Material.ATTRIBUTE_SHININESS, 0.2)
material = self._materialModule.createMaterial()
material.setName('transBlue')
material.setManaged(True)
material.setAttributeReal3(Material.ATTRIBUTE_AMBIENT, [0.0, 0.2, 0.6])
material.setAttributeReal3(Material.ATTRIBUTE_DIFFUSE, [0.0, 0.7, 1.0])
material.setAttributeReal3(Material.ATTRIBUTE_EMISSION,
[0.0, 0.0, 0.0])
material.setAttributeReal3(Material.ATTRIBUTE_SPECULAR,
[0.1, 0.1, 0.1])
material.setAttributeReal(Material.ATTRIBUTE_ALPHA, 0.3)
material.setAttributeReal(Material.ATTRIBUTE_SHININESS, 0.2)
material = self._materialModule.createMaterial()
material.setName('solidTissue')
material.setManaged(True)
material.setAttributeReal3(Material.ATTRIBUTE_AMBIENT, [0.9, 0.7, 0.5])
material.setAttributeReal3(Material.ATTRIBUTE_DIFFUSE, [0.9, 0.7, 0.5])
material.setAttributeReal3(Material.ATTRIBUTE_EMISSION,
[0.0, 0.0, 0.0])
material.setAttributeReal3(Material.ATTRIBUTE_SPECULAR,
[0.2, 0.2, 0.3])
material.setAttributeReal(Material.ATTRIBUTE_ALPHA, 1.0)
material.setAttributeReal(Material.ATTRIBUTE_SHININESS, 0.2)
glyphmodule = self._context.getGlyphmodule()
glyphmodule.defineStandardGlyphs()
def initialise(self):
'''
Ensure scene or other objects from old context are not in use before calling
'''
self._context = Context("SimpleViz")
# set up standard materials and glyphs so we can use them elsewhere
materialmodule = self._context.getMaterialmodule()
materialmodule.defineStandardMaterials()
glyphmodule = self._context.getGlyphmodule()
glyphmodule.defineStandardGlyphs()
self._rootRegion = self._context.createRegion()
def __init__(self, filename, output_filename, scale, marker_type='nodes'):
self._context = Context("TrasformMesh")
self._region = self._context.getDefaultRegion()
self._region.readFile(filename)
self._output_file = output_filename
self._marker_type = marker_type
self._scale = scale
self._scale_geometry()
def __init__(self, location, identifier):
'''
Constructor
'''
self._location = location
self._identifier = identifier
self._filenameStem = os.path.join(self._location, self._identifier)
self._context = Context("MeshGenerator")
tess = self._context.getTessellationmodule().getDefaultTessellation()
tess.setRefinementFactors(12)
self._sceneChangeCallback = None
# set up standard materials and glyphs so we can use them elsewhere
self._materialmodule = self._context.getMaterialmodule()
self._materialmodule.defineStandardMaterials()
solid_blue = self._materialmodule.createMaterial()
solid_blue.setName('solid_blue')
solid_blue.setManaged(True)
solid_blue.setAttributeReal3(Material.ATTRIBUTE_AMBIENT, [ 0.0, 0.2, 0.6 ])
solid_blue.setAttributeReal3(Material.ATTRIBUTE_DIFFUSE, [ 0.0, 0.7, 1.0 ])
solid_blue.setAttributeReal3(Material.ATTRIBUTE_EMISSION, [ 0.0, 0.0, 0.0 ])
solid_blue.setAttributeReal3(Material.ATTRIBUTE_SPECULAR, [ 0.1, 0.1, 0.1 ])
solid_blue.setAttributeReal(Material.ATTRIBUTE_SHININESS , 0.2)
trans_blue = self._materialmodule.createMaterial()
trans_blue.setName('trans_blue')
trans_blue.setManaged(True)
trans_blue.setAttributeReal3(Material.ATTRIBUTE_AMBIENT, [ 0.0, 0.2, 0.6 ])
trans_blue.setAttributeReal3(Material.ATTRIBUTE_DIFFUSE, [ 0.0, 0.7, 1.0 ])
trans_blue.setAttributeReal3(Material.ATTRIBUTE_EMISSION, [ 0.0, 0.0, 0.0 ])
trans_blue.setAttributeReal3(Material.ATTRIBUTE_SPECULAR, [ 0.1, 0.1, 0.1 ])
trans_blue.setAttributeReal(Material.ATTRIBUTE_ALPHA , 0.3)
trans_blue.setAttributeReal(Material.ATTRIBUTE_SHININESS , 0.2)
glyphmodule = self._context.getGlyphmodule()
glyphmodule.defineStandardGlyphs()
self._deleteElementRanges = []
self._scale = [ 1.0, 1.0, 1.0 ]
self._settings = {
'meshTypeName' : '',
'meshTypeOptions' : { },
'deleteElementRanges' : '',
'scale' : '*'.join(STRING_FLOAT_FORMAT.format(value) for value in self._scale),
'displayAxes' : True,
'displayElementNumbers' : True,
'displayLines' : True,
'displayNodeDerivatives' : False,
'displayNodeNumbers' : True,
'displaySurfaces' : True,
'displaySurfacesExterior' : True,
'displaySurfacesTranslucent' : True,
'displaySurfacesWireframe' : False,
'displayXiAxes' : False
}
self._discoverAllMeshTypes()
self._loadSettings()
self._generateMesh()
def export_vtk(self, filename):
context = Context("Scaffold")
region = context.getDefaultRegion()
result = region.readFile(self.input_mesh)
if result != ZINC_OK:
raise ValueError('Error loading mesh in {0}'.format(self.input_mesh))
from scaffoldmaker.utils.exportvtk import ExportVtk
export = ExportVtk(region, 'test')
export.writeFile(filename)
def setupZinc(self):
self.zincContext = Context(str('Radiation'))
#Zinc viewer setup
self.mvLayout = QtWidgets.QVBoxLayout(self.graphicsHost)
self.mvLayout.setSpacing(0)
self.mvLayout.setContentsMargins(0,0,0,0)
self.mvLayout.setObjectName("mvLayout")
self.meshWindow = SceneviewerWidget(self.graphicsHost)
self.meshWindow.setContext(self.zincContext)
self.mvLayout.addWidget(self.meshWindow)
self.meshWindow.graphicsInitialized.connect(self.setBackgroundColor)
def test_field_coordinates(self):
"""
Test creation of finite element coordinates field.
"""
context = Context("test")
region = context.createRegion()
fieldmodule = region.getFieldmodule()
coordinates = findOrCreateFieldCoordinates(fieldmodule)
self.assertTrue(coordinates.isValid())
self.assertEqual(3, coordinates.getNumberOfComponents())
self.assertTrue(coordinates.isManaged())
self.assertTrue(coordinates.isTypeCoordinate())
def test_cylinder1(self):
"""
Test creation of cylinder scaffold.
"""
scaffold = MeshType_3d_solidcylinder1
parameterSetNames = scaffold.getParameterSetNames()
self.assertEqual(parameterSetNames, ["Default"])
options = scaffold.getDefaultOptions("Default")
self.assertEqual(12, len(options))
self.assertEqual(4, options.get("Number of elements across major"))
self.assertEqual(4, options.get("Number of elements across minor"))
self.assertEqual(0, options.get("Number of elements across shell"))
self.assertEqual(1,
options.get("Number of elements across transition"))
self.assertEqual(1, options.get("Number of elements along"))
self.assertEqual(1.0,
options.get("Shell element thickness proportion"))
context = Context("Test")
region = context.getDefaultRegion()
self.assertTrue(region.isValid())
annotationGroups = scaffold.generateMesh(region, options)
self.assertEqual(0, len(annotationGroups))
fieldmodule = region.getFieldmodule()
mesh3d = fieldmodule.findMeshByDimension(3)
self.assertEqual(12, mesh3d.getSize())
mesh2d = fieldmodule.findMeshByDimension(2)
self.assertEqual(52, mesh2d.getSize())
mesh1d = fieldmodule.findMeshByDimension(1)
self.assertEqual(73, mesh1d.getSize())
nodes = fieldmodule.findNodesetByFieldDomainType(
Field.DOMAIN_TYPE_NODES)
self.assertEqual(34, nodes.getSize())
datapoints = fieldmodule.findNodesetByFieldDomainType(
Field.DOMAIN_TYPE_DATAPOINTS)
self.assertEqual(0, datapoints.getSize())
# check coordinates range, cylinder volume
coordinates = fieldmodule.findFieldByName(
"coordinates").castFiniteElement()
self.assertTrue(coordinates.isValid())
minimums, maximums = evaluateFieldNodesetRange(coordinates, nodes)
assertAlmostEqualList(self, minimums, [-1.0, -1.0, 0.0], 1.0E-6)
assertAlmostEqualList(self, maximums, [1.0, 1.0, 3.0], 1.0E-6)
with ChangeManager(fieldmodule):
one = fieldmodule.createFieldConstant(1.0)
volumeField = fieldmodule.createFieldMeshIntegral(
one, coordinates, mesh3d)
volumeField.setNumbersOfPoints(3)
fieldcache = fieldmodule.createFieldcache()
result, volume = volumeField.evaluateReal(fieldcache, 1)
self.assertEqual(result, RESULT_OK)
self.assertAlmostEqual(volume, 9.414866630615249, delta=1.0E-3)
def __init__(self, input_scaffold_file, groups):
self._context = Context('ScaffoldGroupManager')
self._region = self._context.createRegion()
self._region.setName('GroupManagerRegion')
self._field_module = self._region.getFieldmodule()
self._scaffold_file = input_scaffold_file
self._model_coordinates_field = None
self._output_filename = None
self._groups = groups
self._load()
for group in groups["groups"]:
self._manage_groups(group)
def __init__(self,
xi1Elements=4,
xi2Elements=1,
xi3Elements=1,
timepoints=1):
'''
Constructor
'''
self.context = Context('Tube')
self.lengthElements = xi2Elements
self.circumferentialElements = xi1Elements
self.wallElements = xi3Elements
self.numberOfTimePoints = timepoints
class PlainModelViewerWidget(QtGui.QWidget):
def __init__(self, parent=None):
super(PlainModelViewerWidget, self).__init__(parent)
self._ui = Ui_PlainModelViewerWidget()
self._ui.setupUi(self)
self._context = Context('view')
self._setupZinc()
self._callback = None
self._model_data = None
self._makeConnections()
def _setupZinc(self):
self._zinc = self._ui.widgetZinc
self._zinc.setContext(self._context)
self._defineStandardMaterials()
self._defineStandardGlyphs()
def _makeConnections(self):
self._ui.pushButtonDone.clicked.connect(self._doneButtonClicked)
def _doneButtonClicked(self):
self._callback()
def registerDoneExecution(self, callback):
self._callback = callback
def setModelData(self, model_data):
self._model_data = model_data
self._visualise()
def _defineStandardGlyphs(self):
'''
Helper method to define the standard glyphs
'''
glyph_module = self._context.getGlyphmodule()
glyph_module.defineStandardGlyphs()
def _defineStandardMaterials(self):
'''
Helper method to define the standard materials.
'''
material_module = self._context.getMaterialmodule()
material_module.defineStandardMaterials()
def _visualise(self):
''' Read model data
def __init__(self, parent=None):
'''
Initiaise the AxisViewerDlg first calling the QWidget __init__ function.
'''
QtGui.QWidget.__init__(self, parent)
# create instance of Zinc Context from which all other objects are obtained
self._context = ZincContext("Axis Viewer");
# set up standard materials and glyphs so we can use them elsewhere
# define standard materials first as some coloured glyphs use them
materialmodule = self._context.getMaterialmodule()
materialmodule.defineStandardMaterials()
# this example uses a standard axes glyph hence need the following:
glyphmodule = self._context.getGlyphmodule()
glyphmodule.defineStandardGlyphs()
# Using composition to include the visual element of the GUI.
self.ui = Ui_AxisViewerDlg()
self.ui.setupUi(self)
# Must pass the context to the ZincWidget to set it up
self.ui._zincwidget.setContext(self._context)
self.setWindowIcon(QtGui.QIcon(":/cmiss_icon.ico"))
self.resize(620, 440)
# set up content for this application
self.setupAxes()
def __init__(self, parent=None):
'''
Initiaise the MaterialsAndTextureDlg first calling the QWidget __init__ function.
'''
QtGui.QWidget.__init__(self, parent)
# Using composition to include the visual element of the GUI.
self.ui = Ui_MaterialsAndTextureDlg()
self.ui.setupUi(self)
self._context = Context('selection')
self.ui.sceneviewerwidget.setContext(self._context)
self.setWindowIcon(QtGui.QIcon(":/cmiss_icon.ico"))
self.resize(620, 440)
self._prefix = "MaterialsAndTexture"
self._regions = []
default_region = self._context.getDefaultRegion()
for i in range(1, 6):
region_name = 'region_' + str(i)
region = default_region.createChild(region_name)
self._regions.append(region)
self.createMaterial()
self.createMaterialUsingImageField()
self.createFiniteElements()
self.createSurfaceGraphics()
''' the following function exports the camera settings'''
self.ui.sceneviewerwidget.graphicsInitialized.connect(self.exportWebGLJson)
def __init__(self, parent=None):
'''
Initialise the ZincViewGraphics first calling the QMainWindow __init__ function.
'''
QtGui.QMainWindow.__init__(self, parent)
# create instance of Zinc Context from which all other objects are obtained
self._context = ZincContext("ZincViewGraphics");
# set up standard materials for colouring graphics
self._context.getMaterialmodule().defineStandardMaterials()
# set up standard glyphs, graphics to show at points e.g. spheres, arrows
self._context.getGlyphmodule().defineStandardGlyphs()
# Load the user interface controls
self._ui = Ui_ZincViewGraphics()
self._ui.setupUi(self)
self._makeConnections()
# Must pass the Context to the Zinc SceneviewerWidget
self._ui.sceneviewerWidget.setContext(self._context)
# must set other sceneviewer defaults once graphics are initialised
self._ui.sceneviewerWidget.graphicsInitialized.connect(self._graphicsInitialized)
# read the model and create some graphics to see it:
self.setupModel()
def __init__(self):
'''
Constructor
'''
self._context = Context('surfacefit')
materialmodule = self._context.getMaterialmodule()
materialmodule.beginChange()
materialmodule.defineStandardMaterials()
self._surfaceMaterial = materialmodule.createMaterial()
self._surfaceMaterial.setName('fit-surface')
self._surfaceMaterial.setAttributeReal3(Material.ATTRIBUTE_AMBIENT, [0.7, 0.7, 1.0])
self._surfaceMaterial.setAttributeReal3(Material.ATTRIBUTE_DIFFUSE, [0.7, 0.7, 1.0])
self._surfaceMaterial.setAttributeReal3(Material.ATTRIBUTE_SPECULAR, [0.5, 0.5, 0.5])
self._surfaceMaterial.setAttributeReal(Material.ATTRIBUTE_ALPHA, 0.5)
self._surfaceMaterial.setAttributeReal(Material.ATTRIBUTE_SHININESS, 0.3)
materialmodule.endChange()
glyphmodule = self._context.getGlyphmodule()
glyphmodule.defineStandardGlyphs()
tessellationmodule = self._context.getTessellationmodule()
defaultTessellation = tessellationmodule.getDefaultTessellation()
defaultTessellation.setRefinementFactors([12])
self._location = None
self._zincModelFile = None
self._zincPointCloudFile = None
self._pointCloudData = None
self._filterTopErrorProportion = 0.9
self._filterNonNormalProjectionLimit = 0.99
self.clear()
def __init__(self):
super(PelvisModel, self).__init__()
self._context = Context("pelvis")
glyph_module = self._context.getGlyphmodule()
glyph_module.defineStandardGlyphs()
material_module = self._context.getMaterialmodule()
material_module.defineStandardMaterials()
self._time_keeper = self._context.getTimekeepermodule().getDefaultTimekeeper()
self._time_keeper.setMaximumTime(324)
self._time_keeper.setMinimumTime(236)
self._nodes_start = []
self._nodes_end = []
self._elements = []
self._command = ['node', os.environ['IMU_BLE']]
self._process = None
self._stdout_reader = None
self._timer = QtCore.QTimer()
self._timer.setInterval(10)
self._timer.timeout.connect(self._readData)
self._timer_active = False
# First create coordinate field
self._male_region = self._context.getDefaultRegion().createSubregion("male")
self._setupMaleRegion(self._male_region)
self._female_region = self._context.getDefaultRegion().createSubregion("female")
self._setupFemaleRegion(self._female_region)
def __init__(self, parent = None):
'''
Call the super class init functions, create a Zinc context and set the scene viewer handle to None.
'''
QtOpenGL.QGLWidget.__init__(self, parent)
# Create a Zinc context from which all other objects can be derived either directly or indirectly.
#print(opencmiss.zinc.__version__)
self._context = Context("axisviewer")
self._scene_viewer = None
def __init__(self):
self._context = Context('Segmentation')
self._undo_redo_stack = QtGui.QUndoStack()
self.defineStandardMaterials()
self._createModeMaterials()
self.defineStandardGlyphs()
self._image_model = ImageModel(self._context)
self._node_model = NodeModel(self._context)
def __init__(self, parent = None):
'''
Call the super class init functions, create a Zinc context and set the scene viewer handle to None.
'''
QtOpenGL.QGLWidget.__init__(self, parent)
# Create a Zinc context from which all other objects can be derived either directly or indirectly.
# Each context requires a unique name to reference it.
self._context = Context("finiteelementcreation")
self._scene_viewer = None
def __init__(self):
'''
Constructor
'''
self._context = Context('heartsurface')
glyph_module = self._context.getGlyphmodule()
glyph_module.defineStandardGlyphs()
material_module = self._context.getMaterialmodule()
material_module.defineStandardMaterials()
self.clear()
def __init__(self, parent = None):
'''
Call the super class init functions, create a Zinc context and set the scene viewer handle to None.
'''
QtOpenGL.QGLWidget.__init__(self, parent)
# Create a Zinc context from which all other objects can be derived either directly or indirectly.
self._context = Context("autosegmenter")
self._scene_viewer = None
self._imageDataLocation = None
def __init__(self):
'''
Constructor
'''
self._context = Context('heartsurface')
self.defineStandardMaterials()
self.defineStandardGlyphs()
self._region = None
self._image_model = ImageModel(self._context)
self._node_model = NodeModel(self._context)
self._location = None
def __init__(self):
'''
Constructor
'''
self._context = Context('hearttransform')
self.defineStandardMaterials()
self.defineStandardGlyphs()
self._location = None
self._region = None
self._image_model = ImageModel(self._context)
self._transform_model = TransformModel(self._context)
def __init__(self, context_name):
'''
Constructor
'''
self._context = Context(context_name)
self._timeKeeper = self._context.getTimekeepermodule().getDefaultTimekeeper()
glyph_module = self._context.getGlyphmodule()
glyph_module.defineStandardGlyphs()
material_module = self._context.getMaterialmodule()
material_module.defineStandardMaterials()
self._setupSpectrum()
self.clear()
def __init__(self, parent=None):
super(PlainModelViewerWidget, self).__init__(parent)
self._ui = Ui_PlainModelViewerWidget()
self._ui.setupUi(self)
self._context = Context('view')
self._setupZinc()
self._callback = None
self._model_data = None
self._makeConnections()
def main():
'''
The entry point for the application, handle application arguments.
'''
# Create the context
context = Context("image")
# Name of the file we intend to read in.
image_name = 'drawing.png'
# Get a handle to the root region
default_region = context.getDefaultRegion()
# The field module allows us to create a field image to
# store the image data into.
field_module = default_region.getFieldmodule()
# Create an image field, we don't specify the domain here for this
# field even though it is a source field. A temporary xi source field
# is created for us.
image_field = field_module.createFieldImage()
image_field.setName('texture')
# Create a stream information object that we can use to read the
# image file from the disk
stream_information = image_field.createStreaminformationImage()
# Set the format for the image we want to read
stream_information.setFileFormat(stream_information.FILE_FORMAT_PNG)
# We are reading in a file from the local disk so our resource is a file.
stream_information.createStreamresourceFile(image_name)
# Actually read in the image file into the image field.
ret = image_field.read(stream_information)
if ret == 1: # CMISS_OK has the literal value 1
print('Image successfully read into image field.')
else:
print('Error: failed to read image into image field.')
def __init__(self, context_name):
'''
Constructor
'''
self._context = Context(context_name)
self._timeKeeper = self._context.getTimekeepermodule().getDefaultTimekeeper()
glyphmodule = self._context.getGlyphmodule()
glyphmodule.defineStandardGlyphs()
materialmodule = self._context.getMaterialmodule()
materialmodule.defineStandardMaterials()
tessellationmodule = self._context.getTessellationmodule()
default_tessellation = tessellationmodule.getDefaultTessellation()
default_tessellation.setMinimumDivisions(12)
self._setupSpectrum()
self.clear()
def __init__(self):
self._coordinate_description = None
self._file_location = None
self._location = None
self._context = Context("MeshImage")
defineStandardVisualisationTools(self._context)
self._image_model = ImageModel(self._context)
# First create coordinate field
self._elements = None
self._nodes = None
self._rotation_axis = [0, 1, 0]
self._reference_normal = [0, 0, 1]
self._region = self._context.getDefaultRegion()
self._coordinate_field = createFiniteElementField(self._region)
self._plane = self._setupDetectionPlane(self._region, self._coordinate_field)
self._iso_scalar_field = createIsoScalarField(self._region, self._coordinate_field, self._plane)
self._visibility_field = createVisibilityFieldForPlane(self._region, self._coordinate_field, self._plane)
def __init__(self, numberOfFrames,samplepointsPerElement=1):
'''
Load mesh and setup for model
'''
self.context = Context('heart')
self.numberOfFrames = numberOfFrames
self.samplepointsPerElement = samplepointsPerElement
region = self.context.getDefaultRegion()
sir = region.createStreaminformationRegion()
self.times = range(numberOfFrames)
path = os.path.abspath(__file__)
dirPath = os.path.dirname(path)
for t in self.times:
tfile = sir.createStreamresourceFile(os.path.join(dirPath,'heartmodel.exnode'))
sir.setResourceAttributeReal(tfile,sir.ATTRIBUTE_TIME,t)
sir.createStreamresourceFile(os.path.join(dirPath,'globalhermiteparam.exelem'))
region.read(sir)
self.region = region.findChildByName('heart')
fieldModule = self.region.getFieldmodule()
self.prolateSpheroidalCoordinatesField = fieldModule.findFieldByName('coordinates').castFiniteElement()
#Hold on to the nodes
nodeset = fieldModule.findNodesetByName('nodes')
nodeIterator = nodeset.createNodeiterator()
self.nodes = dict()
node = nodeIterator.next()
while node.isValid():
ni = node.getIdentifier()
self.nodes[ni] = node
node = nodeIterator.next()
# Hold on to elements to get boundary
mesh = fieldModule.findMeshByDimension(3)
ei = mesh.createElementiterator()
self.elemDict = dict()
elem = ei.next()
while elem.isValid():
self.elemDict[elem.getIdentifier()] = elem
elem = ei.next()
logging.info("Created LV Model")
def __init__(self, parent=None):
'''
Initiaise the ZincView first calling the QWidget __init__ function.
'''
QtGui.QMainWindow.__init__(self, parent)
self._context = ZincContext("ZincView");
# set up standard materials and glyphs so we can use them elsewhere
materialmodule = self._context.getMaterialmodule()
materialmodule.defineStandardMaterials()
glyphmodule = self._context.getGlyphmodule()
glyphmodule.defineStandardGlyphs()
# Using composition to include the visual element of the GUI.
self.ui = Ui_ZincView()
self.ui.setupUi(self)
self.ui.sceneviewerwidget.setContext(self._context)
self.ui.sceneviewerwidget.graphicsInitialized.connect(self._graphicsInitialized)
self.setWindowIcon(QtGui.QIcon(":/cmiss_icon.ico"))
self._maximumClippingDistance = 1
def __init__(self, parent=None):
'''
Initiaise the MaterialsDlg first calling the QWidget __init__ function.
'''
QtGui.QWidget.__init__(self, parent)
# Using composition to include the visual element of the GUI.
self._ui = Ui_SelectionDlg()
self._ui.setupUi(self)
self.setWindowIcon(QtGui.QIcon(":/cmiss_icon.ico"))
self.resize(620, 440)
self._context = Context('selection')
self._ui.zincWidget.setContext(self._context)
# Define some standard glyphs and materials
self._ui.zincWidget.defineStandardGlyphs()
self._ui.zincWidget.defineStandardMaterials()
self._readCube()
self._showCube()
def __init__(self, parent=None):
'''
Initiaise the ReadMeshDlg first calling the QWidget __init__ function.
'''
QtGui.QWidget.__init__(self, parent)
# create instance of Zinc Context from which all other objects are obtained
self._context = ZincContext("ModelViewer");
# set up standard materials and glyphs so we can use them elsewhere
self._materialmodule = self._context.getMaterialmodule()
self._materialmodule.defineStandardMaterials()
self._glyphmodule = self._context.getGlyphmodule()
self._glyphmodule.defineStandardGlyphs()
# improve tessellation quality
tessellationmodule = self._context.getTessellationmodule()
defaultTessellation = tessellationmodule.getDefaultTessellation()
defaultTessellation.setMinimumDivisions([6])
default_region = self._context.getDefaultRegion()
timekeepermodule = self._context.getTimekeepermodule()
self._timekeeper = timekeepermodule.getDefaultTimekeeper()
# create region to load mesh into
self._region = default_region.createChild('myregion')
# read the model and create some graphics to see it
self.readMesh()
self.createSurfaceGraphics()
# Using composition to include the visual element of the GUI.
self.ui = Ui_ReadMeshDlg()
self.ui.setupUi(self)
# Must pass the context to the ZincWidget for it to work
self.ui._zincwidget.setContext(self._context)
self.setWindowIcon(QtGui.QIcon(":/cmiss_icon.ico"))
# set up callbacks for changes in the time slider
self.ui.timeSlider.valueChanged.connect(self.timeChanged)
self.resize(620, 440)
def __init__(self, trc_data):
super(MOCAPViewer, self).__init__()
self._trc_data = trc_data
self._ui = Ui_MOCAPViewer()
self._ui.setupUi(self)
self._nodes = []
self._labels = self._trc_data['Labels'][2:]
frame_min = self._trc_data['Frame#'][0]
frame_max = self._trc_data['Frame#'][-1]
time_min = self._trc_data['Time'][0]
time_max = self._trc_data['Time'][-1]
self._ui.horizontalSlider.setMinimum(frame_min)
self._ui.horizontalSlider.setMaximum(frame_max)
self._ui.spinBox.setValue(10)
self._context = Context('MOCAP')
glyphmodule = self._context.getGlyphmodule()
glyphmodule.defineStandardGlyphs()
materialmodule = self._context.getMaterialmodule()
materialmodule.defineStandardMaterials()
self._ui.sceneviewerWidget.setContext(self._context)
self._timer = QtCore.QTimer(self)
self._timeKeeper = self._context.getTimekeepermodule().getDefaultTimekeeper()
self._timeKeeper.setMinimumTime(time_min)
self._timeKeeper.setMaximumTime(time_max)
self._region = self._context.getDefaultRegion()
self._createScene(self._region)
self._graphics = None
self._populateListWidget()
self._makeConnections()
def generateMesh(self,numtimepoints,zregion=None):
"""
:param zregion: Zinc region to define model in. Must be empty.
:param moptions: Dict containing options. See getDefaultOptions().
:return: None
"""
region = zregion
if zregion is None:
ctx = Context('gen')
region = ctx.getDefaultRegion()
self.context = ctx
self.region = region
self.numTimePoints = numtimepoints
elementsCountUp = 5
elementsCountAround = 6
useCrossDerivatives = False
fm = region.getFieldmodule()
fm.beginChange()
#Get time list
timeSequence = fm.getMatchingTimesequence(range(numtimepoints))
coordinates = fm.createFieldFiniteElement(3)
coordinates.setName('coordinates')
coordinates.setManaged(True)
coordinates.setTypeCoordinate(True)
coordinates.setCoordinateSystemType(Field.COORDINATE_SYSTEM_TYPE_RECTANGULAR_CARTESIAN)
coordinates.setComponentName(1, 'x')
coordinates.setComponentName(2, 'y')
coordinates.setComponentName(3, 'z')
nodes = fm.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_NODES)
nodetemplateApex = nodes.createNodetemplate()
nodetemplateApex.defineField(coordinates)
nodetemplateApex.setValueNumberOfVersions(coordinates, -1, Node.VALUE_LABEL_VALUE, 1)
nodetemplateApex.setValueNumberOfVersions(coordinates, -1, Node.VALUE_LABEL_D_DS1, 1)
nodetemplateApex.setValueNumberOfVersions(coordinates, -1, Node.VALUE_LABEL_D_DS2, 1)
if useCrossDerivatives:
nodetemplate = nodes.createNodetemplate()
nodetemplate.defineField(coordinates)
nodetemplate.setValueNumberOfVersions(coordinates, -1, Node.VALUE_LABEL_VALUE, 1)
nodetemplate.setValueNumberOfVersions(coordinates, -1, Node.VALUE_LABEL_D_DS1, 1)
nodetemplate.setValueNumberOfVersions(coordinates, -1, Node.VALUE_LABEL_D_DS2, 1)
nodetemplate.setValueNumberOfVersions(coordinates, -1, Node.VALUE_LABEL_D2_DS1DS2, 1)
else:
nodetemplate = nodetemplateApex
nodetemplate.setTimesequence(coordinates,timeSequence)
self.coordinates = coordinates
mesh = fm.findMeshByDimension(2)
bicubicHermiteBasis = fm.createElementbasis(2, Elementbasis.FUNCTION_TYPE_CUBIC_HERMITE)
eft = mesh.createElementfieldtemplate(bicubicHermiteBasis)
if not useCrossDerivatives:
for n in range(4):
eft.setFunctionNumberOfTerms(n*4 + 4, 0)
# Apex1: collapsed on xi1 = 0
eftApex1 = mesh.createElementfieldtemplate(bicubicHermiteBasis)
eftApex1.setNumberOfLocalNodes(3)
eftApex1.setNumberOfLocalScaleFactors(4)
for s in range(4):
si = s + 1
sid = (s // 2)*100 + s + 1 # add 100 for different 'version'
eftApex1.setScaleFactorType(si, Elementfieldtemplate.SCALE_FACTOR_TYPE_NODE_GENERAL)
eftApex1.setScaleFactorIdentifier(si, sid)
# basis node 1 -> local node 1
eftApex1.setTermNodeParameter(1, 1, 1, Node.VALUE_LABEL_VALUE, 1)
# 0 terms = zero parameter for d/dxi1 basis
eftApex1.setFunctionNumberOfTerms(2, 0)
# 2 terms for d/dxi2 via general linear map:
eftApex1.setFunctionNumberOfTerms(3, 2)
eftApex1.setTermNodeParameter(3, 1, 1, Node.VALUE_LABEL_D_DS1, 1)
eftApex1.setTermScaling(3, 1, [1])
eftApex1.setTermNodeParameter(3, 2, 1, Node.VALUE_LABEL_D_DS2, 1)
eftApex1.setTermScaling(3, 2, [2])
# 0 terms = zero parameter for cross derivative 1 2
eftApex1.setFunctionNumberOfTerms(4, 0)
# basis node 2 -> local node 1
eftApex1.setTermNodeParameter(5, 1, 1, Node.VALUE_LABEL_VALUE, 1)
# 0 terms = zero parameter for d/dxi1 basis
eftApex1.setFunctionNumberOfTerms(6, 0)
# 2 terms for d/dxi2 via general linear map:
eftApex1.setFunctionNumberOfTerms(7, 2)
eftApex1.setTermNodeParameter(7, 1, 1, Node.VALUE_LABEL_D_DS1, 1)
eftApex1.setTermScaling(7, 1, [3])
eftApex1.setTermNodeParameter(7, 2, 1, Node.VALUE_LABEL_D_DS2, 1)
eftApex1.setTermScaling(7, 2, [4])
# 0 terms = zero parameter for cross derivative 1 2
eftApex1.setFunctionNumberOfTerms(8, 0)
# basis nodes 3, 4 -> regular local nodes 2, 3
for bn in range(2,4):
fo = bn*4
ni = bn
eftApex1.setTermNodeParameter(fo + 1, 1, ni, Node.VALUE_LABEL_VALUE, 1)
eftApex1.setTermNodeParameter(fo + 2, 1, ni, Node.VALUE_LABEL_D_DS1, 1)
eftApex1.setTermNodeParameter(fo + 3, 1, ni, Node.VALUE_LABEL_D_DS2, 1)
if useCrossDerivatives:
eftApex1.setTermNodeParameter(fo + 4, 1, ni, Node.VALUE_LABEL_D2_DS1DS2, 1)
else:
eftApex1.setFunctionNumberOfTerms(fo + 4, 0)
elementtemplate = mesh.createElementtemplate()
elementtemplate.setElementShapeType(Element.SHAPE_TYPE_SQUARE)
elementtemplate.defineField(coordinates, -1, eft)
elementtemplateApex1 = mesh.createElementtemplate()
elementtemplateApex1.setElementShapeType(Element.SHAPE_TYPE_SQUARE)
elementtemplateApex1.defineField(coordinates, -1, eftApex1)
cache = fm.createFieldcache()
# create nodes
nodeIdentifier = 1
radiansPerElementAround = 2.0*np.pi/elementsCountAround
radiansPerElementUp = np.pi/elementsCountUp/2.0
x = [ 0.0, 0.0, 0.0 ]
dx_ds1 = [ 0.0, 0.0, 0.0 ]
dx_ds2 = [ 0.0, 0.0, 0.0 ]
zero = [ 0.0, 0.0, 0.0 ]
radius = 0.5
self.Nodes = dict()
# create apex1 node
node = nodes.createNode(nodeIdentifier, nodetemplateApex)
self.apexNode = node
self.coordinates = coordinates
self.radiansPerElementUp = radiansPerElementUp
cache.setNode(node)
self.Nodes[nodeIdentifier] = node
coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_VALUE, 1, [ 0.0, 0.0, -radius ])
coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_D_DS1, 1, [ 0.0, radius*radiansPerElementUp, 0.0 ])
coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_D_DS2, 1, [ radius*radiansPerElementUp, 0.0, 0.0 ])
nodeIdentifier = nodeIdentifier + 1
# create regular rows between apexes
for n2 in range(1, elementsCountUp):
radiansUp = n2*radiansPerElementUp
cosRadiansUp = np.cos(radiansUp);
sinRadiansUp = np.sin(radiansUp);
for n1 in range(elementsCountAround):
radiansAround = n1*radiansPerElementAround
cosRadiansAround = np.cos(radiansAround)
sinRadiansAround = np.sin(radiansAround)
x = [
radius*cosRadiansAround*sinRadiansUp,
radius*sinRadiansAround*sinRadiansUp,
-radius*cosRadiansUp
]
dx_ds1 = [
radius*-sinRadiansAround*sinRadiansUp*radiansPerElementAround,
radius*cosRadiansAround*sinRadiansUp*radiansPerElementAround,
0.0
]
dx_ds2 = [
radius*cosRadiansAround*cosRadiansUp*radiansPerElementUp,
radius*sinRadiansAround*cosRadiansUp*radiansPerElementUp,
radius*sinRadiansUp*radiansPerElementUp
]
node = nodes.createNode(nodeIdentifier, nodetemplate)
cache.setNode(node)
self.Nodes[nodeIdentifier] = node
coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_VALUE, 1, x)
coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_D_DS1, 1, dx_ds1)
coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_D_DS2, 1, dx_ds2)
if useCrossDerivatives:
coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_D2_DS1DS2, 1, zero)
nodeIdentifier = nodeIdentifier + 1
# create elements
elementIdentifier = 1
# create Apex1 elements, editing eft scale factor identifiers around apex
# scale factor identifiers follow convention of offsetting by 100 for each 'version'
bni1 = 1
for e1 in range(elementsCountAround):
va = e1
vb = (e1 + 1)%elementsCountAround
eftApex1.setScaleFactorIdentifier(1, va*100 + 1)
eftApex1.setScaleFactorIdentifier(2, va*100 + 2)
eftApex1.setScaleFactorIdentifier(3, vb*100 + 1)
eftApex1.setScaleFactorIdentifier(4, vb*100 + 2)
# redefine field in template for changes to eftApex1:
elementtemplateApex1.defineField(coordinates, -1, eftApex1)
element = mesh.createElement(elementIdentifier, elementtemplateApex1)
bni2 = e1 + 2
bni3 = (e1 + 1)%elementsCountAround + 2
nodeIdentifiers = [ bni1, bni2, bni3 ]
element.setNodesByIdentifier(eftApex1, nodeIdentifiers)
# set general linear map coefficients
radiansAround = e1*radiansPerElementAround
radiansAroundNext = ((e1 + 1)%elementsCountAround)*radiansPerElementAround
scalefactors = [
np.sin(radiansAround), np.cos(radiansAround), np.sin(radiansAroundNext), np.cos(radiansAroundNext)
]
element.setScaleFactors(eftApex1, scalefactors)
elementIdentifier = elementIdentifier + 1
# create regular rows between apexes
for e2 in range(elementsCountUp - 2):
for e1 in range(elementsCountAround):
element = mesh.createElement(elementIdentifier, elementtemplate)
bni1 = e2*elementsCountAround + e1 + 2
bni2 = e2*elementsCountAround + (e1 + 1)%elementsCountAround + 2
nodeIdentifiers = [ bni1, bni2, bni1 + elementsCountAround, bni2 + elementsCountAround ]
element.setNodesByIdentifier(eft, nodeIdentifiers)
elementIdentifier = elementIdentifier + 1
fm.defineAllFaces()
fm.endChange()
class SelectionDlg(QtGui.QWidget):
'''
Create a subclass of QWidget for our application. We could also have derived this
application from QMainApplication to give us a menu bar among other things, but a
QWidget is sufficient for our purposes.
'''
def __init__(self, parent=None):
'''
Initiaise the MaterialsDlg first calling the QWidget __init__ function.
'''
QtGui.QWidget.__init__(self, parent)
# Using composition to include the visual element of the GUI.
self._ui = Ui_SelectionDlg()
self._ui.setupUi(self)
self.setWindowIcon(QtGui.QIcon(":/cmiss_icon.ico"))
self.resize(620, 440)
self._context = Context('selection')
self._ui.zincWidget.setContext(self._context)
# Define some standard glyphs and materials
self._ui.zincWidget.defineStandardGlyphs()
self._ui.zincWidget.defineStandardMaterials()
self._readCube()
self._showCube()
def _readCube(self):
'''
Read in a basic cube mesh from an exformat file.
'''
region = self._context.getDefaultRegion()
region.readFile('cube.exformat')
def _showCube(self):
'''
Show the cube with surfaces and node points.
'''
region = self._context.getDefaultRegion()
scene = region.getScene()
field_module = region.getFieldmodule()
finite_element_field = field_module.findFieldByName('coordinates')
material_module = self._context.getMaterialmodule()
blue_material = material_module.findMaterialByName('blue')
red_material = material_module.findMaterialByName('red')
gold_material = material_module.findMaterialByName('gold')
silver_material = material_module.findMaterialByName('silver')
yellow_material = material_module.findMaterialByName('yellow')
green_material = material_module.findMaterialByName('green')
# We use the beginChange and endChange to wrap any immediate changes this will
# streamline the rendering of the scene.
scene.beginChange()
lines = scene.createGraphicsLines()
lines.setCoordinateField(finite_element_field)
lines.setMaterial(yellow_material)
lines.setSelectedMaterial(green_material)
surface = scene.createGraphicsSurfaces()
surface.setCoordinateField(finite_element_field)
surface.setMaterial(blue_material)
surface.setSelectedMaterial(red_material)
nodes = scene.createGraphicsPoints()
nodes.setCoordinateField(finite_element_field)
nodes.setFieldDomainType(finite_element_field.DOMAIN_TYPE_NODES)
nodes.setMaterial(gold_material)
nodes.setSelectedMaterial(silver_material)
attributes = nodes.getGraphicspointattributes()
attributes.setGlyphShapeType(Glyph.SHAPE_TYPE_SPHERE)
attributes.setBaseSize(0.1)
# Let the scene render the scene.
scene.endChange()
class MOCAPViewer(QtGui.QWidget):
def __init__(self, trc_data):
super(MOCAPViewer, self).__init__()
self._trc_data = trc_data
self._ui = Ui_MOCAPViewer()
self._ui.setupUi(self)
self._nodes = []
self._labels = self._trc_data['Labels'][2:]
frame_min = self._trc_data['Frame#'][0]
frame_max = self._trc_data['Frame#'][-1]
time_min = self._trc_data['Time'][0]
time_max = self._trc_data['Time'][-1]
self._ui.horizontalSlider.setMinimum(frame_min)
self._ui.horizontalSlider.setMaximum(frame_max)
self._ui.spinBox.setValue(10)
self._context = Context('MOCAP')
glyphmodule = self._context.getGlyphmodule()
glyphmodule.defineStandardGlyphs()
materialmodule = self._context.getMaterialmodule()
materialmodule.defineStandardMaterials()
self._ui.sceneviewerWidget.setContext(self._context)
self._timer = QtCore.QTimer(self)
self._timeKeeper = self._context.getTimekeepermodule().getDefaultTimekeeper()
self._timeKeeper.setMinimumTime(time_min)
self._timeKeeper.setMaximumTime(time_max)
self._region = self._context.getDefaultRegion()
self._createScene(self._region)
self._graphics = None
self._populateListWidget()
self._makeConnections()
def _makeConnections(self):
self._ui.listWidget.itemClicked.connect(self._labelClicked)
self._ui.listWidget.itemChanged.connect(self._labelChanged)
self._ui.sceneviewerWidget.graphicsInitialized.connect(self._sceneviewerReady)
self._ui.pushButtonPlay.clicked.connect(self._playClicked)
self._ui.spinBox.valueChanged.connect(self._sizeChanged)
self._ui.horizontalSlider.valueChanged.connect(self._timeChanged)
self._timer.timeout.connect(self._timeIncrement)
def _playClicked(self):
text = self._ui.pushButtonPlay.text()
if text == '&Play':
self._timer.start(10)
self._ui.pushButtonPlay.setText('&Stop')
else:
self._timer.stop()
self._ui.pushButtonPlay.setText('&Play')
def _timeIncrement(self):
time_increment = 1
current_value = self._ui.horizontalSlider.value()
current_value += time_increment
if current_value >= self._ui.horizontalSlider.maximum():
current_value = self._ui.horizontalSlider.minimum()
self._ui.horizontalSlider.setValue(current_value)
def _sizeChanged(self, value):
scene = self._region.getScene()
scene.beginChange()
for graphics in self._graphics:
attributes = graphics.getGraphicspointattributes()
attributes.setBaseSize(value)
scene.endChange()
def _timeChanged(self, frame_index):
time = self._trc_data['Time'][frame_index - 1]
self._timeKeeper.setTime(time)
def _sceneviewerReady(self):
self._graphics = createNodeGraphics(self._region)
self._ui.sceneviewerWidget.viewAll()
def getTRCData(self):
return self._trc_data
def _getNodeForLabel(self, label):
index = self._labels.index(label)
node = self._nodes[index]
return node
def _labelClicked(self, item):
# Set node selected.
node = self._getNodeForLabel(item.text())
nodeset = node.getNodeset()
selection_group = self._ui.sceneviewerWidget._selectionGroup#getSelectionGroup()
nodegroup = selection_group.getFieldNodeGroup(nodeset)
if not nodegroup.isValid():
nodegroup = selection_group.createFieldNodeGroup(nodeset)
group = nodegroup.getNodesetGroup()
if not group.containsNode(node):
group.removeAllNodes()
group.addNode(node)
def _labelChanged(self, item):
row = self._ui.listWidget.row(item)
node = self._getNodeForLabel(self._labels[row])
new_text = str(item.text())
old_text = self._labels[row]
fieldmodule = self._region.getFieldmodule()
fieldcache = fieldmodule.createFieldcache()
fieldmodule.beginChange()
fieldcache.setNode(node)
self._string_field.assignString(fieldcache, new_text)
self._labels[row] = new_text
self._trc_data[new_text] = self._trc_data.pop(old_text)
self._trc_data['Labels'][row + 2] = new_text
fieldmodule.endChange()
def _populateListWidget(self):
self._ui.listWidget.addItems(self._labels)
for index in xrange(self._ui.listWidget.count()):
item = self._ui.listWidget.item(index)
item.setFlags(item.flags() | QtCore.Qt.ItemIsEditable)
def _createScene(self, region):
coordinate_field = createFiniteElementField(region)
self._string_field = createStoredStringField(region)
fieldmodule = region.getFieldmodule()
fieldmodule.beginChange()
nodeset = fieldmodule.findNodesetByName('nodes')
node_template = nodeset.createNodetemplate()
time = self._trc_data['Time']
ts = fieldmodule.getMatchingTimesequence(0)
for index, t in enumerate(time):
ts.setTime(index + 1, t),
# Set the finite element coordinate field for the nodes to use
node_template.defineField(coordinate_field)
node_template.defineField(self._string_field)
node_template.setTimesequence(coordinate_field, ts)
fieldcache = fieldmodule.createFieldcache()
for label in self._labels:
node_coordinates = self._trc_data[label]
node = nodeset.createNode(-1, node_template)
self._nodes.append(node)
# Set the node coordinates, first set the field cache to use the current node
fieldcache.setNode(node)
for index, t in enumerate(time):
fieldcache.setTime(t)
# Pass in floats as an array
coordinate_field.assignReal(fieldcache, node_coordinates[index])
self._string_field.assignString(fieldcache, label)
fieldmodule.endChange()
class MeshImageModel(object):
def __init__(self):
self._coordinate_description = None
self._file_location = None
self._location = None
self._context = Context("MeshImage")
defineStandardVisualisationTools(self._context)
self._image_model = ImageModel(self._context)
# First create coordinate field
self._elements = None
self._nodes = None
self._rotation_axis = [0, 1, 0]
self._reference_normal = [0, 0, 1]
self._region = self._context.getDefaultRegion()
self._coordinate_field = createFiniteElementField(self._region)
self._plane = self._setupDetectionPlane(self._region, self._coordinate_field)
self._iso_scalar_field = createIsoScalarField(self._region, self._coordinate_field, self._plane)
self._visibility_field = createVisibilityFieldForPlane(self._region, self._coordinate_field, self._plane)
def load_mesh(self, mesh):
self._nodes = mesh['points']
self._elements = mesh['elements']
self._createMesh(self._nodes, self._elements)
extents = calculateExtents(self._nodes)
mid_point = [(extents[1] + extents[0])/2.0, (extents[3] + extents[2])/2.0, (extents[5] + extents[4])/2.0]
self._plane.setRotationPoint(mid_point)
def load_images(self, images_dir):
self._image_model.setImageData(images_dir)
def clear(self):
return
self._image_model.clear()
self._region = None
def initialise(self):
# return
# self._region = self._context.createRegion()
self._image_model.initialise(self._region)
def getImageModel(self):
return self._image_model
def getContext(self):
return self._context
def getCoordinateField(self):
return self._coordinate_field
def getRegion(self):
return self._region
def getVisibilityField(self):
return self._visibility_field
def getImageRegionNames(self):
return self._image_model.getRegionNames()
def setImageRegionVisibility(self, region_name, state):
self._image_model.setRegionVisibility(region_name, state)
def getIsoScalarField(self):
return self._iso_scalar_field
def setRotationAngle(self, angle):
c = cos(angle*pi/180.0)
s = sin(angle*pi/180.0)
C = 1 - c
x = self._rotation_axis[0]
y = self._rotation_axis[1]
z = self._rotation_axis[2]
Q = [[x*x*C+c, x*y*C-z*c, x*z*C+y*s],
[y*x*C+z*s, y*y*C+c, y*z*C-x*s ],
[z*x*C-y*s, z*y*C+x*s, z*z*C+c]]
n = mxvectormult(Q, self._reference_normal)
self._plane.setNormal(n)
def _setupDetectionPlane(self, region, coordinate_field):
'''
Adds a single finite element to the region and keeps a handle to the
fields created for the finite element in the following attributes(
self-documenting names):
'_coordinate_field'
'_scale_field'
'_scaled_coordinate_field'
'_iso_scalar_field'
'''
fieldmodule = region.getFieldmodule()
fieldmodule.beginChange()
plane = ZincPlane(fieldmodule)
fieldmodule.endChange()
return plane
def _createMesh(self, nodes, elements):
"""
Create a mesh from data extracted from a VRML file.
The nodes are given as a list of coordinates and the elements
are given as a list of indexes into the node list..
"""
# First create all the required nodes
createNodes(self._coordinate_field, self._nodes)
# then define elements using a list of node indexes
createElements(self._coordinate_field, self._elements)
# Define all faces also
fieldmodule = self._coordinate_field.getFieldmodule()
fieldmodule.defineAllFaces()
