Merge pull request #582 from LBL-EESA/mask_below_surface

add elevation mask

.travis.yml

@@ -17,7 +17,7 @@ env:
     - BUILD_TYPE=Debug
     - TECA_DIR=/travis_teca_dir
     - TECA_PYTHON_VERSION=3
-    - TECA_DATA_REVISION=112
+    - TECA_DATA_REVISION=115
   jobs:
     - DOCKER_IMAGE=ubuntu IMAGE_VERSION=20.04 IMAGE_NAME=ubuntu_20_04 REQUIRE_NETCDF_MPI=TRUE
     - DOCKER_IMAGE=ubuntu IMAGE_VERSION=20.04 IMAGE_NAME=ubuntu_20_04 REQUIRE_NETCDF_MPI=FALSE

alg/CMakeLists.txt

@@ -21,11 +21,13 @@ set(teca_alg_cxx_srcs
     teca_component_statistics.cxx
     teca_derived_quantity.cxx
     teca_descriptive_statistics.cxx
+    teca_elevation_mask.cxx
     teca_evaluate_expression.cxx
     teca_face_to_cell_centering.cxx
     teca_geography.cxx
     teca_indexed_dataset_cache.cxx
     teca_integrated_vapor_transport.cxx
+    teca_integrated_water_vapor.cxx
     teca_l2_norm.cxx
     teca_latitude_damper.cxx
     teca_laplacian.cxx

alg/teca_bayesian_ar_detect.cxx

@@ -608,7 +608,9 @@ void teca_bayesian_ar_detect::internals_t::clear()
 teca_bayesian_ar_detect::teca_bayesian_ar_detect() :
     min_component_area_variable("min_component_area"),
     min_ivt_variable("min_water_vapor"),
-    hwhm_latitude_variable("hwhm_latitude"), thread_pool_size(1),
+    hwhm_latitude_variable("hwhm_latitude"),
+    ar_probability_variable("ar_probability"),
+    thread_pool_size(1),
     internals(new internals_t)
 {
     this->set_number_of_input_connections(1);
@@ -631,18 +633,21 @@ void teca_bayesian_ar_detect::get_properties_description(
 
     opts.add_options()
         TECA_POPTS_GET(std::string, prefix, ivt_variable,
-            "name of the water vapor variable")
+            "Set the name of the integrated vaopr transport(IVT) variable to"
+            " compute AR probability from.")
         TECA_POPTS_GET(std::string, prefix, min_component_area_variable,
-            "name of the column in the parameter table containing the "
-            "component area threshold")
+            "Set the name of the column in the parameter table containing the "
+            "minimum feature area threshold.")
         TECA_POPTS_GET(std::string, prefix, min_ivt_variable,
-            "name of the column in the parameter table containing the "
-            "water vapor threshold")
+            "Set the name of the column in the parameter table containing the "
+            "minimum percentile IVT threshold.")
         TECA_POPTS_GET(std::string, prefix, hwhm_latitude_variable,
-            "name of the column in the parameter table containing the "
-            "half width at half max latitude")
+            "Set the name of the column in the parameter table containing the "
+            "half width at half max latitude mask value.")
+        TECA_POPTS_GET(std::string, prefix, ar_probability_variable,
+            "Set the name of the variable to store the computed AR probability in.")
         TECA_POPTS_GET(int, prefix, thread_pool_size,
-            "number of threads to parallelize execution over")
+            "Set the number of threads to parallelize execution over.")
         ;
 
     this->teca_algorithm::get_properties_description(prefix, opts);
@@ -660,6 +665,7 @@ void teca_bayesian_ar_detect::set_properties(const std::string &prefix,
     TECA_POPTS_SET(opts, std::string, prefix, min_component_area_variable)
     TECA_POPTS_SET(opts, std::string, prefix, min_ivt_variable)
     TECA_POPTS_SET(opts, std::string, prefix, hwhm_latitude_variable)
+    TECA_POPTS_SET(opts, std::string, prefix, ar_probability_variable)
     TECA_POPTS_SET(opts, int, prefix, thread_pool_size)
     TECA_POPTS_SET(opts, int, prefix, verbose)
 }
@@ -809,7 +815,7 @@ teca_metadata teca_bayesian_ar_detect::get_output_metadata(
     // report the variable that we compute, for each timestep from the
     // parameter tables.
     teca_metadata md(input_md[0]);
-    md.append("variables", std::string("ar_probability"));
+    md.append("variables", std::string(this->ar_probability_variable));
 
     // add attributes to enable CF I/O
     teca_metadata atts;
@@ -820,7 +826,7 @@ teca_metadata teca_bayesian_ar_detect::get_output_metadata(
         0, "unitless", "posterior AR flag",
         "the posterior probability of the presence of an atmospheric river");
 
-    atts.set("ar_probability", (teca_metadata)prob_atts);
+    atts.set(this->ar_probability_variable, (teca_metadata)prob_atts);
 
     unsigned long num_params =
         this->internals->parameter_table->get_number_of_rows();
@@ -879,7 +885,7 @@ std::vector<teca_metadata> teca_bayesian_ar_detect::get_upstream_request(
     arrays.insert(this->ivt_variable);
 
     // remove what we produce
-    arrays.erase("ar_probability");
+    arrays.erase(this->ar_probability_variable);
     arrays.erase("ar_count");
     arrays.erase("parameter_table_row");
 
@@ -1043,7 +1049,7 @@ const_p_teca_dataset teca_bayesian_ar_detect::execute(
     // set up the reduction which computes the average over runs of all control
     // parameter combinations provided in the parameter table
     ::parameter_table_reduction reduce(parameter_table_size,
-        "wv_cc", "ar_probability");
+        "wv_cc", this->ar_probability_variable);
 
     p_teca_programmable_reduce pr = teca_programmable_reduce::New();
     pr->set_name("parameter_table_reduce");

alg/teca_bayesian_ar_detect.h

@@ -62,6 +62,14 @@ class teca_bayesian_ar_detect : public teca_algorithm
     TECA_ALGORITHM_PROPERTY(std::string, min_component_area_variable)
     TECA_ALGORITHM_PROPERTY(std::string, hwhm_latitude_variable)
 
+    /** @anchor probability variable
+     * @name probability variable
+     * Set the name of the variable to store output probability as.
+     */
+    ///@{
+    TECA_ALGORITHM_PROPERTY(std::string, ar_probability_variable)
+    ///@}
+
     // set/get the number of threads in the pool. setting
     // to -1 results in a thread per core factoring in all MPI
     // ranks running on the node. the default is -1.
@@ -99,6 +107,7 @@ class teca_bayesian_ar_detect : public teca_algorithm
     std::string min_component_area_variable;
     std::string min_ivt_variable;
     std::string hwhm_latitude_variable;
+    std::string ar_probability_variable;
     int thread_pool_size;
 
     struct internals_t;

alg/teca_cartesian_mesh_source.cxx

@@ -549,7 +549,7 @@ teca_metadata teca_cartesian_mesh_source::get_output_metadata(
     z_atts.set("size", nz);
 
     teca_metadata t_atts = this->t_axis_attributes;
-    t_atts.set("type_code", z_axis->type_code());
+    t_atts.set("type_code", t_axis->type_code());
     t_atts.set("size", nt);
 
     teca_metadata atts;
@@ -707,7 +707,6 @@ const_p_teca_dataset teca_cartesian_mesh_source::execute(unsigned int port,
     std::string x_variable = this->x_axis_variable.empty() ? "x" : this->x_axis_variable;
     std::string y_variable = this->y_axis_variable.empty() ? "y" : this->y_axis_variable;
     std::string z_variable = this->z_axis_variable.empty() ? "z" : this->z_axis_variable;
-    std::string t_variable = this->t_axis_variable.empty() ? "t" : this->t_axis_variable;
 
     mesh->set_x_coordinates(x_variable, out_x);
     mesh->set_y_coordinates(y_variable, out_y);