Partial merge #174

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Merged

behdadebsh merged 14 commits into LungNoodle:develop from behdadebsh:partial_merge

Jun 3, 2025

.github/workflows/build_test.yml

            
                      Original file line number
                      Diff line number
                      Diff line change
                  
    @@ -24,15 +24,15 @@ jobs:
  
                os: windows-2022,

              }

            - {

                name: "Ubuntu 20.04",

                name: "Ubuntu 24.04",

                build_type: "Release",

                os: ubuntu-20.04,

                os: ubuntu-24.04,

              }

            - {

                name: "Ubuntu 20.04 with SuperLU",

                name: "Ubuntu 24.04 with SuperLU",

                build_type: "Release",

                super_lu: true,

                os: ubuntu-20.04,

                os: ubuntu-24.04,

              }

            - {

                name: "macOS Ventura",

src/bindings/c/geometry.c

-Original file line number
+Diff line change
@@ Expand Up @@
     void define_rad_from_geom_c(const char *order_system, int *order_system_len, double *control_param,
                                 const char *start_from, int *start_from_len, double *start_rad,
                                 const char *group_type, int *group_type_len, const char *group_options, int *group_options_len);
+    void occlude_vessel_c(int *VESSEL_NUMBER, double *RATIO);
     void element_connectivity_1d_c(void);
     void evaluate_ordering_c(void);
     void volume_of_mesh_c(double *volume_model, double *volume_tree);
@@ Expand Down Expand Up @@
     }
+    void occlude_vessel(int VESSEL_NUMBER, double RATIO)
+    {
+      occlude_vessel_c(&VESSEL_NUMBER, &RATIO);
+    }
     void element_connectivity_1d()
     {
       element_connectivity_1d_c();
@@ Expand Down @@

src/bindings/c/geometry.f90

            
                      Original file line number
                      Diff line number
                      Diff line change
                  
    @@ -4,7 +4,7 @@ module geometry_c
  
      use indices

      !use mesh_functions

      !use precision ! sets dp for precision

      !use math_constants !pi  

      !use math_constants !pi

    implicit none

      private

    @@ -184,7 +184,7 @@ subroutine list_tree_statistics_c(filename, filename_len) &
  
        integer,intent(in) :: filename_len

        type(c_ptr), value, intent(in) :: filename

        character(len=MAX_FILENAME_LEN) :: filename_f

        call strncpy(filename_f, filename, filename_len)

        call list_tree_statistics(filename_f)

    @@ -194,34 +194,34 @@ end subroutine list_tree_statistics_c
  
    !###################################################################################

    !

      subroutine internal_mesh_reorder_c() bind(C, name="internal_mesh_reorder_c")

        use geometry,only: internal_mesh_reorder

        implicit none

        call internal_mesh_reorder()

      end subroutine internal_mesh_reorder_c

    !

    !###################################################################################

    !

      subroutine make_data_grid_c(surface_elems_len, surface_elems, num_target, offset, spacing)&

           bind(C, name="make_data_grid_c")

        use arrays,only: dp

        use iso_c_binding, only: c_ptr

        use utils_c, only: strncpy

        use other_consts, only: MAX_FILENAME_LEN, MAX_STRING_LEN

        use geometry, only: make_data_grid

        implicit none

        integer,intent(in) :: surface_elems_len

        integer,intent(in) :: surface_elems(surface_elems_len)

        integer,intent(in) :: num_target

        real(dp),intent(in) :: offset, spacing

        call make_data_grid(surface_elems, num_target, offset, spacing)

      end subroutine make_data_grid_c

    !!!###################################################################################

    @@ -236,7 +236,7 @@ subroutine make_2d_vessel_from_1d_c(elemlist, elemlist_len) bind(C, name="make_2
  
        call make_2d_vessel_from_1d(elemlist)

      end subroutine make_2d_vessel_from_1d_c

    !

    !###################################################################################

    !

    @@ -329,6 +329,26 @@ subroutine define_rad_from_geom_c(order_system, order_system_len, control_param,
  
        call define_rad_from_geom(order_system_f, control_param, start_from_f, start_rad, group_type_f, group_options_f)

      end subroutine define_rad_from_geom_c

      !

      !##################################################################################

      !

      !*define_rad_from_geom:* Defines vessel or airway radius based on their geometric structure

        subroutine occlude_vessel_c(VESSEL_NUMBER, RATIO) bind(C, name="occlude_vessel_c")

          !use iso_c_binding, only: c_ptr

          !use utils_c, only: strncpy

          !use other_consts, only: MAX_STRING_LEN

          use arrays, only: dp

          use geometry, only: occlude_vessel

          implicit none

          integer,intent(in) :: VESSEL_NUMBER

          real(dp),intent(in) :: RATIO

          !character(len=MAX_STRING_LEN) :: order_system_f, start_from_f, group_type_f, group_options_f

          call occlude_vessel(VESSEL_NUMBER, RATIO)

        end subroutine occlude_vessel_c

    !

    !###########################################################################

    !

    @@ -373,10 +393,10 @@ function get_local_node_f_c(ndimension,np_global) result(get_local_node) bind(C,
  
        use arrays, only: dp

        use geometry, only: get_local_node_f

        implicit none

        integer :: ndimension,np_global

        integer :: get_local_node

        get_local_node=get_local_node_f(ndimension,np_global)

      end function get_local_node_f_c

    @@ -443,5 +463,3 @@ end subroutine write_node_geometry_2d_c
  
    !

    end module geometry_c

src/bindings/c/geometry.h

-Original file line number
+Diff line change
@@ Expand Up @@
     SHO_PUBLIC int get_local_node_f(const char *ndimenstion, const char *np_global);
     SHO_PUBLIC void define_rad_from_geom(const char *ORDER_SYSTEM, double CONTROL_PARAM, const char *START_FROM,
                                          double START_RAD, const char *GROUP_TYPE, const char *GROUP_OPTIONS);
+    SHO_PUBLIC void occlude_vessel(int VESSEL_NUMBER, double RATIO);
     SHO_PUBLIC void element_connectivity_1d();
     SHO_PUBLIC void evaluate_ordering();
     SHO_PUBLIC void volume_of_mesh(double *volume_model, double *volume_tree);
@@ Expand Down @@

src/bindings/c/pressure_resistance_flow.c

-Original file line number
+Diff line change
@@ -1,8 +1,21 @@
     #include "pressure_resistance_flow.h"
     #include <string.h>
+    extern void compliance_list_c(int *elemlist2_len, int elemlist2[]);
+    extern void occlusion_list_c(int *elemlist_len, int elemlist[]);
     void evaluate_prq_c(const char *mesh_type, int *mesh_type_len, const char *vessel_type, int *vessel_type_len,int *grav_dirn, double *grav_factor, const char *bc_type, int *bc_type_len,  double *inlet_bc, double *outlet_bc,  double *remodeling_grade);
+    void compliance_list(int elemlist2_len, int elemlist2[])
+    {
+      compliance_list_c(&elemlist2_len, elemlist2);
+    }
+    void occlusion_list(int elemlist_len, int elemlist[])
+    {
+      occlusion_list_c(&elemlist_len, elemlist);
+    }
     void evaluate_prq(const char *mesh_type, const char *vessel_type,int grav_dirn, double grav_factor, const char *bc_type, double inlet_bc, double outlet_bc, double remodeling_grade)
     {
         int mesh_type_len = strlen(mesh_type);
@@ Expand Down @@

src/bindings/c/pressure_resistance_flow.f90

-Original file line number
+Diff line change
@@ Expand Up / @@ -4,6 +4,47 @@ module pressure_resistance_flow_c @@
     contains
+      !
+      !###################################################################################
+      !
+      ! the main growing subroutine. Generates a volume-filling tree into a closed surface.
+      subroutine occlusion_list_c(surface_elems_len, surface_elems) bind(C, name="occlusion_list_c")
+        !use arrays,only: dp
+        !use iso_c_binding, only: c_ptr
+        !use utils_c, only: strncpy
+        !use other_consts, only: MAX_FILENAME_LEN
+        use pressure_resistance_flow,only: occlusion_list
+        implicit none
+        integer,intent(in) :: surface_elems_len
+        integer,intent(in) :: surface_elems(surface_elems_len)
+        call occlusion_list(surface_elems)
+      end subroutine occlusion_list_c
+      !
+      !###################################################################################
+      !
+      ! makes the vessels given rigid.
+      subroutine compliance_list_c(surface_elems_len, surface_elems) bind(C, name="compliance_list_c")
+        !use arrays,only: dp
+        !use iso_c_binding, only: c_ptr
+        !use utils_c, only: strncpy
+        !use other_consts, only: MAX_FILENAME_LEN
+        use pressure_resistance_flow,only: compliance_list
+        implicit none
+        integer,intent(in) :: surface_elems_len
+        integer,intent(in) :: surface_elems(surface_elems_len)
+        call compliance_list(surface_elems)
+      end subroutine compliance_list_c
     !!!###################################################################################
     subroutine evaluate_prq_c(mesh_type,mesh_type_len,vessel_type,vessel_type_len,grav_dirn,grav_factor,bc_type,bc_type_len,inlet_bc, &
@@ Expand Down @@

src/bindings/c/pressure_resistance_flow.h

-Original file line number
+Diff line change
@@ Expand Up / @@ -3,7 +3,8 @@ @@
     #include "symbol_export.h"
+    SHO_PUBLIC void occlusion_list(int elemlist_len, int elemlist[]);
+    SHO_PUBLIC void compliance_list(int elemlist2_len, int elemlist2[]);
     SHO_PUBLIC void evaluate_prq(const char *mesh_type, const char *vessel_type, int grav_dirn, double grav_factor, const char *bc_type, double inlet_bc, double outlet_bc, double remodeling_grade);
@@ Expand Down @@

src/bindings/interface/pressure_resistance_flow.i

-Original file line number
+Diff line change
@@ -1,8 +1,55 @@
     %module(package="aether") pressure_resistance_flow
     %include symbol_export.h
-    %include pressure_resistance_flow.h
+    %typemap(in) (int elemlist_len, int elemlist[]) {
+    int i;
+    if (!PyList_Check($input)) {
+      PyErr_SetString(PyExc_ValueError, "Expecting a list");
+      SWIG_fail;
+    }
+    $1 = PyList_Size($input);
+    $2 = (int *) malloc(($1)*sizeof(int));
+    for (i = 0; i < $1; i++) {
+      PyObject *o = PyList_GetItem($input, i);
+      if (!PyInt_Check(o)) {
+        free($2);
+        PyErr_SetString(PyExc_ValueError, "List items must be integers");
+        SWIG_fail;
+      }
+      $2[i] = PyInt_AsLong(o);
+    }
+    }
+    %typemap(in) (int elemlist2_len, int elemlist2[]) {
+    int i;
+    if (!PyList_Check($input)) {
+      PyErr_SetString(PyExc_ValueError, "Expecting a list");
+      SWIG_fail;
+    }
+    $1 = PyList_Size($input);
+    $2 = (int *) malloc(($1)*sizeof(int));
+    for (i = 0; i < $1; i++) {
+      PyObject *o = PyList_GetItem($input, i);
+      if (!PyInt_Check(o)) {
+        free($2);
+        PyErr_SetString(PyExc_ValueError, "List items must be integers");
+        SWIG_fail;
+      }
+      $2[i] = PyInt_AsLong(o);
+    }
+    }
+    %typemap(freearg) (int elemlist_len, int elemlist[]) {
+    if ($2) free($2);
+    }
+    %typemap(freearg) (int elemlist2_len, int elemlist2[]) {
+    if ($2) free($2);
+    }
     %{
     #include "pressure_resistance_flow.h"
     %}
+    %include pressure_resistance_flow.h

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