add rename_variables

* adds teca_rename_variables an algorithm that could be used to rename
  arrays as they pass through.
* incldues a test and Python bindings.

.travis.yml

@@ -17,7 +17,7 @@ env:
     - BUILD_TYPE=Debug
     - TECA_DIR=/travis_teca_dir
     - TECA_PYTHON_VERSION=3
-    - TECA_DATA_REVISION=116
+    - TECA_DATA_REVISION=117
   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

@@ -34,6 +34,7 @@ set(teca_alg_cxx_srcs
     teca_mask.cxx
     teca_normalize_coordinates.cxx
     teca_parser.cxx
+    teca_rename_variables.cxx
     teca_table_calendar.cxx
     teca_table_reduce.cxx
     teca_table_region_mask.cxx

alg/teca_rename_variables.cxx

@@ -0,0 +1,225 @@
+#include "teca_rename_variables.h"
+
+#include "teca_mesh.h"
+#include "teca_array_collection.h"
+#include "teca_variant_array.h"
+#include "teca_metadata.h"
+#include "teca_array_attributes.h"
+
+#include <algorithm>
+#include <iostream>
+#include <string>
+#include <set>
+#include <cmath>
+
+#if defined(TECA_HAS_BOOST)
+#include <boost/program_options.hpp>
+#endif
+
+using std::string;
+using std::vector;
+using std::set;
+using std::cerr;
+using std::endl;
+
+//#define TECA_DEBUG
+
+// --------------------------------------------------------------------------
+teca_rename_variables::teca_rename_variables() :
+    original_variable_names(), new_variable_names()
+{
+    this->set_number_of_input_connections(1);
+    this->set_number_of_output_ports(1);
+}
+
+// --------------------------------------------------------------------------
+teca_rename_variables::~teca_rename_variables()
+{}
+
+#if defined(TECA_HAS_BOOST)
+// --------------------------------------------------------------------------
+void teca_rename_variables::get_properties_description(
+    const string &prefix, options_description &global_opts)
+{
+    options_description opts("Options for "
+        + (prefix.empty()?"teca_rename_variables":prefix));
+
+    opts.add_options()
+        TECA_POPTS_MULTI_GET(std::vector<std::string>, prefix, original_variable_names,
+            "Sets the list of original_variable_names to rename.")
+        TECA_POPTS_MULTI_GET(std::vector<std::string>, prefix, new_variable_names,
+            "Sets the list of new names, one for each variable to rename.")
+        ;
+
+    this->teca_algorithm::get_properties_description(prefix, opts);
+
+    global_opts.add(opts);
+}
+
+// --------------------------------------------------------------------------
+void teca_rename_variables::set_properties(
+    const string &prefix, variables_map &opts)
+{
+    this->teca_algorithm::set_properties(prefix, opts);
+
+    TECA_POPTS_SET(opts, std::vector<std::string>, prefix, original_variable_names)
+    TECA_POPTS_SET(opts, std::vector<std::string>, prefix, new_variable_names)
+
+}
+#endif
+
+// --------------------------------------------------------------------------
+teca_metadata teca_rename_variables::get_output_metadata(
+    unsigned int port,
+    const std::vector<teca_metadata> &input_md)
+{
+#ifdef TECA_DEBUG
+    cerr << teca_parallel_id()
+        << "teca_rename_variables::get_output_metadata" << endl;
+#endif
+    (void)port;
+
+    // validate the user provided values.
+    if (this->original_variable_names.size() != this->new_variable_names.size())
+    {
+        TECA_ERROR("Each variable to rename must have a "
+            " corresponding output_variable_name.")
+        return teca_metadata();
+    }
+
+    teca_metadata out_md(input_md[0]);
+
+    // update the list of original_variable_names to reflect the new names
+    std::set<std::string> out_vars;
+    if (out_md.get("variables", out_vars))
+    {
+        TECA_ERROR("Failed to get the list of variables")
+        return teca_metadata();
+    }
+
+    unsigned long n_vars = this->original_variable_names.size();
+    for (unsigned long i = 0; i < n_vars; ++i)
+    {
+        std::set<std::string>::iterator it = out_vars.find(this->original_variable_names[i]);
+        if (it == out_vars.end())
+        {
+            TECA_ERROR("No such variable \"" << this->original_variable_names[i]
+                << "\" to rename")
+            return teca_metadata();
+        }
+
+        out_vars.erase(it);
+        out_vars.insert(this->new_variable_names[i]);
+    }
+
+    // update the list of attributes to reflect the new names
+    teca_metadata attributes;
+    if (out_md.get("attributes", attributes))
+    {
+        TECA_ERROR("Failed to get attributes")
+        return teca_metadata();
+    }
+
+    for (unsigned long i = 0; i < n_vars; ++i)
+    {
+        const std::string &var_name = this->original_variable_names[i];
+
+        teca_metadata atts;
+        if (attributes.get(var_name, atts))
+        {
+            TECA_ERROR("Failed to get attributes for \"" << var_name << "\"")
+            return teca_metadata();
+        }
+
+        attributes.remove(var_name);
+
+        attributes.set(this->new_variable_names[i], atts);
+    }
+
+    out_md.set("attributes", attributes);
+
+    return out_md;
+}
+
+// --------------------------------------------------------------------------
+std::vector<teca_metadata> teca_rename_variables::get_upstream_request(
+    unsigned int port,
+    const std::vector<teca_metadata> &input_md,
+    const teca_metadata &request)
+{
+    (void)port;
+    (void)input_md;
+
+    vector<teca_metadata> up_reqs;
+
+    // copy the incoming request to preserve the downstream requirements.
+    // replace renamed original_variable_names with their original name
+    teca_metadata req(request);
+
+    std::set<std::string> arrays;
+    if (req.has("arrays"))
+        req.get("arrays", arrays);
+
+    unsigned long n_vars = this->new_variable_names.size();
+    for (unsigned long i = 0; i < n_vars; ++i)
+    {
+        std::set<std::string>::iterator it = arrays.find(this->new_variable_names[i]);
+        if (it != arrays.end())
+        {
+            arrays.erase(it);
+            arrays.insert(this->original_variable_names[i]);
+        }
+
+    }
+
+    req.set("arrays", arrays);
+    up_reqs.push_back(req);
+
+    return up_reqs;
+}
+
+// --------------------------------------------------------------------------
+const_p_teca_dataset teca_rename_variables::execute(
+    unsigned int port,
+    const std::vector<const_p_teca_dataset> &input_data,
+    const teca_metadata &request)
+{
+#ifdef TECA_DEBUG
+    cerr << teca_parallel_id() << "teca_rename_variables::execute" << endl;
+#endif
+    (void)port;
+    (void)request;
+
+    // get the input mesh
+    const_p_teca_mesh in_mesh
+        = std::dynamic_pointer_cast<const teca_mesh>(input_data[0]);
+
+    if (!in_mesh)
+    {
+        TECA_ERROR("The input dataset is not a teca_mesh")
+        return nullptr;
+    }
+
+    // create the output mesh, pass everything through.
+    p_teca_mesh out_mesh = std::static_pointer_cast<teca_mesh>
+        (std::const_pointer_cast<teca_mesh>(in_mesh)->new_shallow_copy());
+
+
+    // rename the arrays if they are found
+    p_teca_array_collection arrays = out_mesh->get_point_arrays();
+
+    unsigned long n_vars = this->original_variable_names.size();
+    for (unsigned long i = 0; i < n_vars; ++i)
+    {
+        const std::string var_name = this->original_variable_names[i];
+
+        p_teca_variant_array array = arrays->get(var_name);
+        if (array)
+        {
+            arrays->remove(var_name);
+            arrays->set(this->new_variable_names[i], array);
+        }
+    }
+
+    return out_mesh;
+}

alg/teca_rename_variables.h

@@ -0,0 +1,70 @@
+#ifndef teca_rename_variables_h
+#define teca_rename_variables_h
+
+#include "teca_shared_object.h"
+#include "teca_algorithm.h"
+#include "teca_metadata.h"
+
+#include <string>
+#include <vector>
+
+TECA_SHARED_OBJECT_FORWARD_DECL(teca_rename_variables)
+
+/// An algorithm that renames original_variable_names.
+class teca_rename_variables : public teca_algorithm
+{
+public:
+    TECA_ALGORITHM_STATIC_NEW(teca_rename_variables)
+    TECA_ALGORITHM_DELETE_COPY_ASSIGN(teca_rename_variables)
+    TECA_ALGORITHM_CLASS_NAME(teca_rename_variables)
+    ~teca_rename_variables();
+
+    // report/initialize to/from Boost program options
+    // objects.
+    TECA_GET_ALGORITHM_PROPERTIES_DESCRIPTION()
+    TECA_SET_ALGORITHM_PROPERTIES()
+
+    /** @anchor original_variable_names
+     * @name original_variable_names
+     * Set the list of variables to rename. For each variable to rename a new
+     * name must be specified at the same index in the @ref new_variable_names
+     * list. The two lists must be the same length.
+     */
+    ///@{
+    TECA_ALGORITHM_VECTOR_PROPERTY(std::string, original_variable_name)
+    ///@}
+
+    /** @anchor new_variable_names
+     * @name new_variable_names
+     * Set the names of the renamed variables. The new names are applied to the
+     * list of variables to rename in the same order and the two lists must be
+     * the same length.
+     */
+    ///@{
+    TECA_ALGORITHM_VECTOR_PROPERTY(std::string, new_variable_name)
+    ///@}
+
+protected:
+    teca_rename_variables();
+
+private:
+    teca_metadata get_output_metadata(
+        unsigned int port,
+        const std::vector<teca_metadata> &input_md) override;
+
+    std::vector<teca_metadata> get_upstream_request(
+        unsigned int port,
+        const std::vector<teca_metadata> &input_md,
+        const teca_metadata &request) override;
+
+    const_p_teca_dataset execute(
+        unsigned int port,
+        const std::vector<const_p_teca_dataset> &input_data,
+        const teca_metadata &request) override;
+
+private:
+    std::vector<std::string> original_variable_names;
+    std::vector<std::string> new_variable_names;
+};
+
+#endif

python/teca_py_alg.i

@@ -26,6 +26,7 @@
 #include "teca_latitude_damper.h"
 #include "teca_mask.h"
 #include "teca_normalize_coordinates.h"
+#include "teca_rename_variables.h"
 #include "teca_saffir_simpson.h"
 #include "teca_table_calendar.h"
 #include "teca_table_sort.h"
@@ -429,3 +430,11 @@ struct teca_tc_saffir_simpson
 %shared_ptr(teca_elevation_mask)
 %ignore teca_elevation_mask::operator=;
 %include "teca_elevation_mask.h"
+
+/***************************************************************************
+ rename_variables
+ ***************************************************************************/
+%ignore teca_rename_variables::shared_from_this;
+%shared_ptr(teca_rename_variables)
+%ignore teca_rename_variables::operator=;
+%include "teca_rename_variables.h"

test/CMakeLists.txt

@@ -748,3 +748,10 @@ teca_add_test(test_interval_iterator_yearly
     1
     FEATURES ${TECA_HAS_NETCDF}
     REQ_TECA_DATA)
+
+teca_add_test(test_rename_variables
+    SOURCES test_rename_variables.cpp
+    LIBS teca_core teca_data teca_io teca_alg ${teca_test_link}
+    COMMAND test_rename_variables "${TECA_DATA_ROOT}/test_rename_variables.nc"
+    FEATURES ${TECA_HAS_NETCDF}
+    REQ_TECA_DATA)