def __init__(self): self.renderer = None self.window = None self.interactor = None self.image = None self.logger = logging.getLogger(get_logger_name()) self.initialize_graphics()
def read_header_file(cls, params): '''Read a header (.hdr) file. ''' logger = logging.getLogger(get_logger_name()) file_name = params.header_file_name # Remove 'format' tag from xml file. f = open(file_name, "r") lines = f.readlines() # Create string from xml file and parse it. xml_string = "".join(lines) tree = et.ElementTree(et.fromstring(xml_string)) root = tree.getroot() transform = root.find('transform_lps') logger.info("transform: " + str(transform.attrib)) header = Header() header.t00 = float(transform.attrib['t00']) header.t01 = float(transform.attrib['t01']) header.t02 = float(transform.attrib['t02']) header.t10 = float(transform.attrib['t10']) header.t11 = float(transform.attrib['t11']) header.t12 = float(transform.attrib['t12']) header.t20 = float(transform.attrib['t20']) header.t21 = float(transform.attrib['t21']) header.t22 = float(transform.attrib['t22']) return header
def __init__(self, mesh, graphics, params): self.mesh = mesh self.params = params self.graphics = graphics self.geometry = None self.branch_geometry = None self.logger = logging.getLogger(get_logger_name())
def __init__(self, params): self.params = params self.surface = None self.centerlines = None self.surface_caps = None self.graphics = None self.logger = logging.getLogger(get_logger_name())
def __init__(self): self.renderer = None self.window = None self.interactor = None self.colors = vtk.vtkNamedColors() self.logger = logging.getLogger(get_logger_name()) self.initialize_graphics()
def __init__(self, params): self.params = params self.file_base_name = None self.surface = None self.graphics = None self.boundary_edge_components = None self.logger = logging.getLogger(get_logger_name())
def __init__(self, params): self.params = params self.surface = None self.mesh_from_vtp = None self.graphics = None self.boundary_faces = None self.boundary_edges = None self.boundary_edge_components = None self.boundary_face_components = None self.logger = logging.getLogger(get_logger_name())
def __init__(self, params): self.params = params self.volume = None self.graphics = None self.paths = None self.logger = logging.getLogger(get_logger_name()) self.greyscale_lut = None self.hue_lut = None self.sat_lut = None self.colors = vtk.vtkNamedColors()
def __init__(self): self.inlet_face_name = None self.inlet_center = None self.outlet_centers = None self.outlet_face_names = None self.geometry = None self.branch_geometry = None self.logger = logging.getLogger(get_logger_name())
def __init__(self, params): self.params = params self.nodes = {} self.segments = {} self.graphics = None self.logger = logging.getLogger(get_logger_name()) self.points = vtk.vtkPoints() self.vertices = vtk.vtkCellArray() self.points_polydata = None self.lines_polydata = None
def __init__(self, params): self.params = params self.surface = None self.center = None self.mesh_from_vtp = None self.graphics = None self.boundary_faces = None self.boundary_edges = None self.boundary_edge_components = None self.boundary_face_components = None self.hue_lut = None self.area_list = None self.scalar_range = None self.logger = logging.getLogger(get_logger_name())
def __init__(self, params): self.params = params self.renderer = None self.window = None self.interactor = None self.segment_actors = {} self.solver = None self.picked_segment = None self.picked_segments = [] self.picked_actors = [] self.colors = vtk.vtkNamedColors() self.logger = logging.getLogger(get_logger_name()) self.initialize_graphics()
def __init__(self, params): self.params = params self.nodes = None self.segments = None self.times = None self.min_time_index = None self.max_time_index = None self.graphics = None self.logger = logging.getLogger(get_logger_name()) try: self.points = vtk.vtkPoints() self.vertices = vtk.vtkCellArray() except: self.points = None self.vertices = None self.params.display_geometry = False self.points_polydata = None self.lines_polydata = None self.lines_segment_names = None
def __init__(self): self.centerlines = None self.logger = logging.getLogger(get_logger_name()) self.num_cells = None self.num_paths = None self.path_elems = None self.group_elems = None self.materials = None self.num_seg = None self.seg_list = None self.group_seg = None self.group_terminal = None self.group_length = None self.group_Ain = None self.group_Aout = None self.connectivity = None self.seg_connectivity = None self.seg_head = None self.seg_rear = None self.nodes = None self.num_elements = None self.user_outlet_paths = None self.bc_list = None self.bc_map = None self.inflow_data = None self.outlet_face_names = None self.outlet_face_names_index = None self.centerlines = None self.centerlines_geometry = None # Some constansts for writing the solver file. self.solver_file_msg = "\n\n### DO NOT CHANGE THIS SECTION - generated automatically" self.space = " " self.endl = "\n"
#!/usr/bin/env python """This script extracts slices from a 3D image volume. """ import argparse import sys import os import logging from manage import get_logger_name, init_logging, get_log_file_name from parameters import Parameters from header import Header from image import Image from graphics import Graphics from path import Path logger = logging.getLogger(get_logger_name()) class Args(object): """ This class defines the command line arguments to the generate-1d-mesh script. """ PREFIX = "--" HEADER_FILE = "header_file_name" IMAGE_FILE = "image_file_name" PATH_FILE = "path_file_name" def cmd(name): """ Create an argparse command argument. """ return Args.PREFIX + name.replace("_", "-") def parse_args():
def read_path_file(cls, params, graphics): """ Read a path (.pth) file. """ logger = logging.getLogger(get_logger_name()) file_name = params.path_file_name # Remove 'format' tag from xml file. f = open(file_name, "r") lines = f.readlines() # Create string from xml file and parse it. xml_string = "".join(lines) tree = et.ElementTree(et.fromstring(xml_string)) #tree = et.parse(file_name) root = tree.getroot() ## Create paths. # paths = [] for path_t in root.iter('path'): path_id = path_t.attrib["id"] logger.info("Path ID: %s" % path_id) path = Path(path_id, graphics) pid = 1 for path_element_t in path_t.iter('path_element'): #pid = path_element_t.attrib["id"] path_element = PathElement(pid) logger.info(" Element ID: %s" % pid) pid += 1 for control_pts in path_element_t.iter('control_points'): for point in control_pts.iter('point'): x = point.attrib['x'] y = point.attrib['y'] z = point.attrib['z'] path_element.control_points.append([float(x),float(y),float(z)]) #_for point in control_pts logger.info(" Number of control points: %d" % len(path_element.control_points)) #_for control_pts in path_element_t.iter('control_points'): for path_pts in path_element_t.iter('path_points'): for path_pt in path_pts.iter('path_point'): pid = path_pt.attrib['id'] path_element.ids.append(pid) for pos in path_pt.iter('pos'): x = pos.attrib['x'] y = pos.attrib['y'] z = pos.attrib['z'] path_element.points.append([float(x),float(y),float(z)]) for tangent in path_pt.iter('tangent'): x = tangent.attrib['x'] y = tangent.attrib['y'] z = tangent.attrib['z'] path_element.tangents.append([float(x),float(y),float(z)]) for rotation in path_pt.iter('rotation'): x = rotation.attrib['x'] y = rotation.attrib['y'] z = rotation.attrib['z'] path_element.rotations.append([float(x),float(y),float(z)]) #_for path_pt in path_pts.iter('path_point') #_for path_pts in path_element_t.iter('path_points') logger.info(" Number of path points: %d" % len(path_element.points)) path.elements.append(path_element) #_for path_element_t in path_t.iter('path_element') length = path.get_length() logger.info("Path length: %g" % length) paths.append(path) #_for path_t in root.iter('path') return paths
def __init__(self, id, graphic): self.id = id self.elements = [] self.graphics = graphic self.logger = logging.getLogger(get_logger_name())