def main():
set_diagnostics_on(False)
#define model geometry and indices
perfusion_indices()
#Read in geometry files
define_node_geometry(get_default_geometry_path('Small.ipnode'))
define_1d_elements(get_default_geometry_path('Small.ipelem'))
append_units()
#define radius by Strahler order
s_ratio=1.5
inlet_rad=12.0
order_system = 'strahler'
order_options = 'all'
name = 'inlet'
define_rad_from_geom(order_system, s_ratio, name, inlet_rad, order_options,'')
#Call solve
evaluate_prq()
#export geometry
group_name = 'perf_model'
export_1d_elem_geometry(get_default_output_path('small.exnode'), group_name)
export_node_geometry(get_default_output_path('small.exelem'), group_name)
# export element field for radius
field_name = 'radius_perf'
ne_radius = get_ne_radius()
export_1d_elem_field(ne_radius, get_default_output_path('radius_perf.exelem'), name, field_name)
def main():
set_diagnostics_on(False)
# Read settings
ventilation_indices()
define_node_geometry(get_default_geometry_path('SmallTree.ipnode'))
define_1d_elements(get_default_geometry_path('SmallTree.ipelem'))
define_rad_from_file(get_default_geometry_path('SmallTree.ipfiel'))
append_units()
# Set the working directory to the this files directory and then reset after running simulation.
file_location = os.path.dirname(os.path.abspath(__file__))
cur_dir = os.getcwd()
os.chdir(file_location)
# Run simulation.
evaluate_vent()
# Set the working directory back to it's original location.
os.chdir(cur_dir)
# Output results
# Export airway nodes and elements
group_name = 'vent_model'
export_1d_elem_geometry(
get_default_output_path('Output/Ventilation/small_tree.exelem'),
group_name)
export_node_geometry(
get_default_output_path('Output/Ventilation/small_tree.exnode'),
group_name)
# Export flow element
field_name = 'flow'
export_elem_field(
get_default_output_path(
'Output/Ventilation/ventilation_fields.exelem'), group_name,
field_name)
# Export element field for radius
ne_radius = get_ne_radius()
field_name = 'radius'
export_1d_elem_field(
ne_radius,
get_default_output_path(
'Output/Ventilation/ventilation_radius_field.exelem'), group_name,
field_name)
# Export terminal solution
export_terminal_solution(
get_default_output_path('Output/Ventilation/terminal.exnode'),
group_name)
def main():
set_diagnostics_on(False)
#define model geometry and indices
perfusion_indices()
#Read in geometry files
define_node_geometry(get_default_geometry_path('Small.ipnode'))
define_1d_elements(get_default_geometry_path('Small.ipelem'))
append_units()
#define radius by Strahler order
s_ratio=1.5
inlet_rad=12.0
order_system = 'strahler'
order_options = 'all'
name = 'inlet'
define_rad_from_geom(order_system, s_ratio, name, inlet_rad, order_options,'')
#Call solve
evaluate_prq()
#export geometry
group_name = 'perf_model'
export_1d_elem_geometry(get_default_output_path('Output/Perfusion/small.exnode'), group_name)
export_node_geometry(get_default_output_path('Output/Perfusion/small.exelem'), group_name)
# export element field for radius
field_name = 'radius_perf'
ne_radius = get_ne_radius()
export_1d_elem_field(ne_radius, get_default_output_path('Output/Perfusion/radius_perf.exelem'), name, field_name)
# export element field for flow
field_name = 'flow_perf'
export_1d_elem_field(7, get_default_output_path('Output/Perfusion/flow_perf.exelem'), name, field_name)
# export node field for pressure
field_name = 'pressure_perf'
export_node_field(1,get_default_output_path('Output/Perfusion/pressure_perf.exnode'), name, field_name)
# export terminal solution
export_terminal_perfusion(get_default_output_path('Output/Perfusion/terminals.exnode'), 'terminal_q')
def main():
set_diagnostics_on(False)
# Read settings
ventilation_indices()
define_node_geometry(get_default_geometry_path('SmallTree.ipnode'))
define_1d_elements(get_default_geometry_path('SmallTree.ipelem'))
define_rad_from_file(get_default_geometry_path('SmallTree.ipfiel'))
append_units()
# Set the working directory to the this files directory and then reset after running simulation.
file_location = os.path.dirname(os.path.abspath(__file__))
cur_dir = os.getcwd()
os.chdir(file_location)
# Run simulation.
evaluate_vent()
# Set the working directory back to it's original location.
os.chdir(cur_dir)
# Output results
# Export airway nodes and elements
group_name = 'vent_model'
export_1d_elem_geometry(get_default_output_path('Output/Ventilation/small_tree.exelem'), group_name)
export_node_geometry(get_default_output_path('Output/Ventilation/small_tree.exnode'), group_name)
# Export flow element
field_name = 'flow'
export_elem_field(get_default_output_path('Output/Ventilation/ventilation_fields.exelem'), group_name, field_name)
# Export element field for radius
ne_radius = get_ne_radius()
field_name = 'radius'
export_1d_elem_field(ne_radius, get_default_output_path('Output/Ventilation/ventilation_radius_field.exelem'), group_name, field_name)
# Export terminal solution
export_terminal_solution(get_default_output_path('Output/Ventilation/terminal.exnode'), group_name)
import sys
import os
from PySide import QtGui
from src.view import View
from src.scene import Scene
from aether.diagnostics import set_diagnostics_on
from aether.indices import define_problem_type
from aether.geometry import *
from aether.exports import *
from aether.growtree import grow_tree
set_diagnostics_on(False)
define_problem_type('grow_tree')
def loadAirway(ipnode, ipelem):
exnode = os.path.splitext(ipnode)[0] + '.exnode'
exelem = os.path.splitext(ipelem)[0] + '.exelem'
define_node_geometry(ipnode)
define_1d_elements(ipelem)
export_node_geometry(exnode, 'airway')
export_1d_elem_geometry(exelem, 'airway')
airwayModel.load(exnode, exelem)
def loadSurface(ipnode, ipelem):
node = os.path.splitext(ipnode)[0]
elem = os.path.splitext(ipelem)[0]
def main():
set_diagnostics_on(False)
patientid = 'lung005'
protocal = 'baseline_cropped/GTV'
density_tag = raw_input('Do you want to read density file? [yes/no]')
constriction_tag = raw_input(
'Do you want to constrict the airways? [yes/no]')
densitytag = False
constrictiontag = False
if density_tag.lower() == "yes":
densitytag = True
else:
densitytag = False
if constriction_tag.lower() == "yes":
constrictiontag = True
else:
constrictiontag = False
# Read settings
ventilation_indices()
define_node_geometry(
get_default_geometry_path('AirwayTree_VF.ipnode', patientid, protocal))
define_1d_elements(
get_default_geometry_path('AirwayTree_VF.ipelem', patientid, protocal))
#define_rad_from_geom('horsfield', 1.16, 'inlet', 6.7)
define_rad_from_file(
get_default_geometry_path('AirwayTree_VF.ipfiel', patientid, protocal))
append_units()
if densitytag == True:
#read density file
cc_dir = get_default_output_path('unit_cc.txt', patientid, protocal)
get_terminal_density_from_file(
get_default_geometry_path(
'AirwayTree_VF_node_with_density_GTV.txt', patientid,
protocal), cc_dir)
# v_dir = solve_volume_from_cc(cc_dir)
# set_volume_fromrv(v_dir)
if constrictiontag == True:
constriction_dir = get_default_geometry_path('ElemToClose.txt',
patientid, protocal)
set_constriction_from_file(constriction_dir)
# Set the working directory to the this files directory and then reset after running simulation.
file_location = os.path.dirname(os.path.abspath(__file__))
cur_dir = os.getcwd()
os.chdir(file_location)
#print(file_location)
# Run simulation.
evaluate_vent()
# Set the working directory back to it's original location.
os.chdir(cur_dir)
# Output results
# Export airway nodes and elements
group_name = 'vent_model'
export_1d_elem_geometry(
get_default_output_path('AirwayTree_VF.exelem', patientid, protocal),
group_name)
export_node_geometry(
get_default_output_path('AirwayTree_VF.exnode', patientid, protocal),
group_name)
# Export flow element
field_name = 'flow'
export_elem_field(
get_default_output_path('ventilation_fields.exelem', patientid,
protocal), group_name, field_name)
# Export element field for radius
ne_radius = get_ne_radius()
field_name = 'radius'
export_1d_elem_field(
ne_radius,
get_default_output_path('ventilation_radius_field.exelem', patientid,
protocal), group_name, field_name)
# Export terminal solution
export_terminal_solution(
get_default_output_path('terminal.exnode', patientid, protocal),
group_name)
# Export bin results
export_bin_results(
get_default_output_path('bin_results.txt', patientid, protocal), 20)