Improved the clima wrapper

clima/__init__.py

@@ -1,4 +1,5 @@
 import os
 os.environ['OMP_NUM_THREADS'] = '1'
-
-from ._clima import WaterAdiabatClimate
+
+from ._clima import WaterAdiabatClimate, ClimaException
+from ._clima import rebin # rebin routine from futils

clima/cython/CMakeLists.txt

@@ -7,6 +7,10 @@ endif()
 
 add_library(_clima MODULE ${_clima})
 set(_clima_deps
+  futils.pyx
+  OpticalProperties.pyx
+  ClimaRadtranWrk.pyx
+  Radtran.pyx
   WaterAdiabatClimate.pyx
 )
 foreach(PDEP ${_clima_deps})
@@ -15,5 +19,5 @@ endforeach()
 
 python_extension_module(_clima)
 
-target_link_libraries(_clima clima_wrapper)
+target_link_libraries(_clima clima_c_api)
 target_include_directories(_clima PUBLIC ${NumPy_INCLUDE_DIRS})

clima/cython/ClimaRadtranWrk.pyx

@@ -0,0 +1,44 @@
+cimport ClimaRadtranWrk_pxd as rwrk_pxd
+
+cdef class ClimaRadtranWrk:
+  cdef void *_ptr
+
+  def __init__(self):
+    pass
+
+  def __dealloc__(self):
+    pass
+
+  property fup_a:
+    def __get__(self):
+      cdef int dim1, dim2
+      rwrk_pxd.climaradtranwrk_fup_a_get_size(&self._ptr, &dim1, &dim2)
+      cdef ndarray arr = np.empty((dim1, dim2), np.double, order="F")
+      rwrk_pxd.climaradtranwrk_fup_a_get(&self._ptr, &dim1, &dim2, <double *>arr.data)
+      return arr
+
+  property fdn_a:
+    def __get__(self):
+      cdef int dim1, dim2
+      rwrk_pxd.climaradtranwrk_fdn_a_get_size(&self._ptr, &dim1, &dim2)
+      cdef ndarray arr = np.empty((dim1, dim2), np.double, order="F")
+      rwrk_pxd.climaradtranwrk_fdn_a_get(&self._ptr, &dim1, &dim2, <double *>arr.data)
+      return arr
+
+  property fup_n:
+    def __get__(self):
+      cdef int dim1
+      rwrk_pxd.climaradtranwrk_fup_n_get_size(&self._ptr, &dim1)
+      cdef ndarray arr = np.empty(dim1, np.double)
+      rwrk_pxd.climaradtranwrk_fup_n_get(&self._ptr, &dim1, <double *>arr.data)
+      return arr
+
+  property fdn_n:
+    def __get__(self):
+      cdef int dim1
+      rwrk_pxd.climaradtranwrk_fdn_n_get_size(&self._ptr, &dim1)
+      cdef ndarray arr = np.empty(dim1, np.double)
+      rwrk_pxd.climaradtranwrk_fdn_n_get(&self._ptr, &dim1, <double *>arr.data)
+      return arr
+
+

clima/cython/ClimaRadtranWrk_pxd.pxd

@@ -0,0 +1,14 @@
+
+# getters and setters
+
+cdef extern void climaradtranwrk_fup_a_get_size(void *ptr, int *dim1, int *dim2)
+cdef extern void climaradtranwrk_fup_a_get(void *ptr, int *dim1, int *dim2, double *arr)
+
+cdef extern void climaradtranwrk_fdn_a_get_size(void *ptr, int *dim1, int *dim2)
+cdef extern void climaradtranwrk_fdn_a_get(void *ptr, int *dim1, int *dim2, double *arr)
+
+cdef extern void climaradtranwrk_fup_n_get_size(void *ptr, int *dim1)
+cdef extern void climaradtranwrk_fup_n_get(void *ptr, int *dim1, double *arr)
+
+cdef extern void climaradtranwrk_fdn_n_get_size(void *ptr, int *dim1)
+cdef extern void climaradtranwrk_fdn_n_get(void *ptr, int *dim1, double *arr)

clima/cython/OpticalProperties.pyx

@@ -0,0 +1,26 @@
+cimport OpticalProperties_pxd as op_pxd
+
+cdef class OpticalProperties:
+  cdef void *_ptr
+
+  def __init__(self):
+    pass
+
+  def __dealloc__(self):
+    pass
+
+  property wavl:
+    def __get__(self):
+      cdef int dim1
+      op_pxd.opticalproperties_wavl_get_size(&self._ptr, &dim1)
+      cdef ndarray arr = np.empty(dim1, np.double)
+      op_pxd.opticalproperties_wavl_get(&self._ptr, &dim1, <double *>arr.data)
+      return arr
+
+  property freq:
+    def __get__(self):
+      cdef int dim1
+      op_pxd.opticalproperties_freq_get_size(&self._ptr, &dim1)
+      cdef ndarray arr = np.empty(dim1, np.double)
+      op_pxd.opticalproperties_freq_get(&self._ptr, &dim1, <double *>arr.data)
+      return arr

clima/cython/OpticalProperties_pxd.pxd

@@ -0,0 +1,8 @@
+
+# getters and setters
+
+cdef extern void opticalproperties_wavl_get_size(void *ptr, int *dim1)
+cdef extern void opticalproperties_wavl_get(void *ptr, int *dim1, double *arr)
+
+cdef extern void opticalproperties_freq_get_size(void *ptr, int *dim1)
+cdef extern void opticalproperties_freq_get(void *ptr, int *dim1, double *arr)

clima/cython/Radtran.pyx

@@ -0,0 +1,46 @@
+cimport Radtran_pxd as rad_pxd
+
+cdef class Radtran:
+  cdef void *_ptr
+
+  def __init__(self):
+    pass
+
+  def __dealloc__(self):
+    pass
+
+  property ir:
+    def __get__(self):
+      cdef void *ptr1;
+      rad_pxd.radtran_ir_get(&self._ptr, &ptr1)
+      var = OpticalProperties()
+      var._ptr = ptr1
+      return var
+
+  property sol:
+    def __get__(self):
+      cdef void *ptr1;
+      rad_pxd.radtran_sol_get(&self._ptr, &ptr1)
+      var = OpticalProperties()
+      var._ptr = ptr1
+      return var
+
+  property wrk_ir:
+    def __get__(self):
+      cdef void *ptr1;
+      rad_pxd.radtran_wrk_ir_get(&self._ptr, &ptr1)
+      var = ClimaRadtranWrk()
+      var._ptr = ptr1
+      return var
+
+  property wrk_sol:
+    def __get__(self):
+      cdef void *ptr1;
+      rad_pxd.radtran_wrk_sol_get(&self._ptr, &ptr1)
+      var = ClimaRadtranWrk()
+      var._ptr = ptr1
+      return var
+
+
+
+

clima/cython/Radtran_pxd.pxd

@@ -0,0 +1,9 @@
+
+# getters and setters
+cdef extern void radtran_ir_get(void *ptr, void *ptr1);
+
+cdef extern void radtran_sol_get(void *ptr, void *ptr1);
+
+cdef extern void radtran_wrk_ir_get(void *ptr, void *ptr1);
+
+cdef extern void radtran_wrk_sol_get(void *ptr, void *ptr1);

clima/cython/WaterAdiabatClimate.pyx

@@ -133,6 +133,14 @@ cdef class WaterAdiabatClimate:
       wa_pxd.wateradiabatclimate_species_names_get(&self._ptr, &dim1, <char *>species_names_c.data)
       return c2stringarr(species_names_c, S_STR_LEN, dim1)
 
+  property rad:
+    def __get__(self):
+      cdef void *ptr1
+      wa_pxd.wateradiabatclimate_rad_get(&self._ptr, &ptr1)
+      var = Radtran()
+      var._ptr = ptr1
+      return var
+
   property P:
     def __get__(self):
       cdef int dim1

clima/cython/WaterAdiabatClimate_pxd.pxd

@@ -6,6 +6,7 @@ cdef extern from "<stdbool.h>":
 cdef extern void allocate_wateradiabatclimate(void *ptr);
 cdef extern void deallocate_wateradiabatclimate(void *ptr);
 
+# wrappers for functions
 cdef extern void wateradiabatclimate_create_wrapper(void *ptr, char *data_dir, char *species_file,
                                                     char *settings_file, char *flux_file, char *err);
 
@@ -31,6 +32,7 @@ cdef extern void wateradiabatclimate_to_regular_grid_wrapper(void *ptr, char *er
 
 cdef extern void wateradiabatclimate_out2atmosphere_txt_wrapper(void *ptr, char *filename, int *nz, double *eddy, bool *overwrite, bool *clip, char *err)
 
+# getters and setters
 cdef extern void wateradiabatclimate_p_top_get(void *ptr, double *val)
 cdef extern void wateradiabatclimate_p_top_set(void *ptr, double *val)
 
@@ -61,4 +63,6 @@ cdef extern void wateradiabatclimate_dz_get(void *ptr, int *dim1, double *arr)
 cdef extern void wateradiabatclimate_densities_get_size(void *ptr, int *dim1, int *dim2)
 cdef extern void wateradiabatclimate_densities_get(void *ptr, int *dim1, int *dim2, double *arr)
 
+cdef extern void wateradiabatclimate_rad_get(void *ptr, void *ptr1)
+
 

clima/cython/_clima.pyx

@@ -6,6 +6,10 @@ import os
 DEF S_STR_LEN = 20;
 DEF ERR_LEN = 1024;
 
+include "futils.pyx"
+include "OpticalProperties.pyx"
+include "ClimaRadtranWrk.pyx"
+include "Radtran.pyx"
 include "WaterAdiabatClimate.pyx"
 
 # utils

clima/cython/futils.pyx

@@ -0,0 +1,19 @@
+cimport futils_pxd as f_pxd
+
+cpdef rebin(ndarray[double, ndim=1] old_bins, ndarray[double, ndim=1]  old_vals, ndarray[double, ndim=1]  new_bins):
+  cdef int n_old = old_bins.shape[0] - 1
+  cdef int n_new = new_bins.shape[0] - 1
+  cdef ndarray new_vals = np.empty(n_new, np.double)
+  cdef int ierr
+
+  if old_vals.shape[0] != n_old:
+    raise ValueError('"old_bins" and "old_vals" arguments to "rebin" have incompatible shapes')
+
+  f_pxd.futils_rebin_wrapper(&n_old, <double *> old_bins.data, <double *> old_vals.data, 
+                             &n_new, <double *> new_bins.data, <double *> new_vals.data, &ierr)
+  if ierr < 0:
+    raise Exception("rebin returned error code: "+str(ierr))
+
+  return new_vals
+
+

clima/cython/futils_pxd.pxd

@@ -0,0 +1,2 @@
+cdef extern void futils_rebin_wrapper(int *n_old, double *old_bins, double *old_vals, 
+                                      int *n_new, double *new_bins, double *new_vals, int *ierr)

clima/fortran/CMakeLists.txt

@@ -1,6 +1,15 @@
 
-add_library(clima_wrapper 
-  wrapper_utils.f90 
-  WaterAdiabatClimate_wrapper.f90 
+add_library(clima_c_api 
+  clima_c_api.f90 
 )
-target_link_libraries(clima_wrapper clima)
+set(clima_c_api_deps
+  futils.f90
+  OpticalProperties.f90
+  ClimaRadtranWrk.f90
+  Radtran.f90
+  WaterAdiabatClimate.f90
+)
+foreach(PDEP ${_clima_deps})
+  set_source_files_properties(clima_c_api.f90 PROPERTIES OBJECT_DEPENDS ${PDEP})
+endforeach()
+target_link_libraries(clima_c_api clima)

clima/fortran/ClimaRadtranWrk.f90

@@ -0,0 +1,84 @@
+! ClimaRadtranWrk
+
+!!!!!!!!!!!!!!!!!!!!!!!!!!!
+!!! getters and setters !!!
+!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
+subroutine climaradtranwrk_fup_a_get_size(ptr, dim1, dim2) bind(c)
+  use clima_radtran, only: ClimaRadtranWrk
+  type(c_ptr), intent(in) :: ptr
+  integer(c_int), intent(out) :: dim1, dim2
+  type(ClimaRadtranWrk), pointer :: w
+  call c_f_pointer(ptr, w)
+  dim1 = size(w%fup_a,1)
+  dim2 = size(w%fup_a,2)
+end subroutine
+
+subroutine climaradtranwrk_fup_a_get(ptr, dim1, dim2, arr) bind(c)
+  use clima_radtran, only: ClimaRadtranWrk
+  type(c_ptr), intent(in) :: ptr
+  integer(c_int), intent(in) :: dim1, dim2
+  real(c_double), intent(out) :: arr(dim1,dim2)
+  type(ClimaRadtranWrk), pointer :: w
+  call c_f_pointer(ptr, w)
+  arr = w%fup_a
+end subroutine
+
+subroutine climaradtranwrk_fdn_a_get_size(ptr, dim1, dim2) bind(c)
+  use clima_radtran, only: ClimaRadtranWrk
+  type(c_ptr), intent(in) :: ptr
+  integer(c_int), intent(out) :: dim1, dim2
+  type(ClimaRadtranWrk), pointer :: w
+  call c_f_pointer(ptr, w)
+  dim1 = size(w%fdn_a,1)
+  dim2 = size(w%fdn_a,2)
+end subroutine
+
+subroutine climaradtranwrk_fdn_a_get(ptr, dim1, dim2, arr) bind(c)
+  use clima_radtran, only: ClimaRadtranWrk
+  type(c_ptr), intent(in) :: ptr
+  integer(c_int), intent(in) :: dim1, dim2
+  real(c_double), intent(out) :: arr(dim1,dim2)
+  type(ClimaRadtranWrk), pointer :: w
+  call c_f_pointer(ptr, w)
+  arr = w%fdn_a
+end subroutine
+
+subroutine climaradtranwrk_fup_n_get_size(ptr, dim1) bind(c)
+  use clima_radtran, only: ClimaRadtranWrk
+  type(c_ptr), intent(in) :: ptr
+  integer(c_int), intent(out) :: dim1
+  type(ClimaRadtranWrk), pointer :: w
+  call c_f_pointer(ptr, w)
+  dim1 = size(w%fup_n,1)
+end subroutine
+
+subroutine climaradtranwrk_fup_n_get(ptr, dim1, arr) bind(c)
+  use clima_radtran, only: ClimaRadtranWrk
+  type(c_ptr), intent(in) :: ptr
+  integer(c_int), intent(in) :: dim1
+  real(c_double), intent(out) :: arr(dim1)
+  type(ClimaRadtranWrk), pointer :: w
+  call c_f_pointer(ptr, w)
+  arr = w%fup_n
+end subroutine
+
+subroutine climaradtranwrk_fdn_n_get_size(ptr, dim1) bind(c)
+  use clima_radtran, only: ClimaRadtranWrk
+  type(c_ptr), intent(in) :: ptr
+  integer(c_int), intent(out) :: dim1
+  type(ClimaRadtranWrk), pointer :: w
+  call c_f_pointer(ptr, w)
+  dim1 = size(w%fdn_n,1)
+end subroutine
+
+subroutine climaradtranwrk_fdn_n_get(ptr, dim1, arr) bind(c)
+  use clima_radtran, only: ClimaRadtranWrk
+  type(c_ptr), intent(in) :: ptr
+  integer(c_int), intent(in) :: dim1
+  real(c_double), intent(out) :: arr(dim1)
+  type(ClimaRadtranWrk), pointer :: w
+  call c_f_pointer(ptr, w)
+  arr = w%fdn_n
+end subroutine
+