Merge pull request #1 from btschwertfeger/vectorized-computation

Vectorized computation
btschwertfeger · Oct 21, 2022 · 2041890 · 2041890
2 parents c575947 + 8ed1002
commit 2041890
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diff --git a/.vscode/c_cpp_properties.json b/.vscode/c_cpp_properties.json
@@ -9,7 +9,7 @@
             "defines": [],
             "compilerPath": "/usr/bin/g++",
             "cStandard": "c11",
-            "cppStandard": "c++17",
+            "cppStandard": "c++11",
             "intelliSenseMode": "macos-gcc-x64"
         }
     ],

diff --git a/README.md b/README.md
@@ -1,8 +1,11 @@
 # Bias-Adjustment-Cpp
 
-[![Generic badge](https://img.shields.io/badge/license-MIT-green.svg)](https://shields.io/)
+<div style="text-align: center">
+
 [![GitHub](https://badgen.net/badge/icon/github?icon=github&label)](https://github.com/btschwertfeger/Bias-Adjustment-Cpp)
+[![Generic badge](https://img.shields.io/badge/license-MIT-green.svg)](https://shields.io/)
 
+</div>
 Collection of different scale- and distribution-based bias adjustment techniques for climatic research. Many of these methods have also been implemented in Python. This can be found here: https://github.com/btschwertfeger/Bias-Adjustment-Python.
 
 ____

diff --git a/cmake/modules/FindNetCDFCxx.cmake b/cmake/modules/FindNetCDFCxx.cmake
@@ -11,6 +11,7 @@
 #   netCDFCxx_INCLUDE_DIRS - path of netCDFCxx includes
 #   netCDFCxx_LIBRARIES - netCDFCxx libraries
 
+message (STATUS "searching netCDFCxx...")
 find_package(netCDF REQUIRED)
 find_program(NCXX4_CONFIG "ncxx4-config")
 

diff --git a/example_adjust.run.sh b/example_adjust.run.sh
@@ -45,18 +45,18 @@ declare -a quant_methods=("quantile_mapping" "quantile_delta_mapping")
 { setopt KSH_ARRAYS || : ; } 2> /dev/null
 
 tmp_path=${work_dir}/tmp/$(uuidgen | tr '[:upper:]' '[:lower:]' | head -c 12)
-tmp_obs="${tmp_path}/obs"
+tmp_ref="${tmp_path}/ref"
 tmp_contr="${tmp_path}/contr"
 tmp_scen="${tmp_path}/scen"
 tmp_results="${tmp_path}/results"
 
-mkdir -p $tmp_obs
+mkdir -p $tmp_ref
 mkdir -p $tmp_contr
 mkdir -p $tmp_scen
 mkdir -p $tmp_results
 
 declare -a datasets=("${observations}" "${control}" "${scenario}")
-declare -a ds_paths=("${tmp_obs}" "${tmp_contr}" "${tmp_scen}")
+declare -a ds_paths=("${tmp_ref}" "${tmp_contr}" "${tmp_scen}")
 
 # * -------------------------------------------------------------------
 # *                         Computation
@@ -82,7 +82,7 @@ for method in "${month_methods[@]}"; do
     # ? Apply scaling-based bias adjustment per month
     for (( month=1; month<13; month++ )); do
         $exec_file                                          \
-            --ref "${tmp_obs}/${month}.nc"                  \
+            --ref "${tmp_ref}/${month}.nc"                  \
             --contr "${tmp_contr}/${month}.nc"              \
             --scen "${tmp_scen}/${month}.nc"                \
             -v $variable                                    \

diff --git a/examples.ipynb b/examples.ipynb
@@ -103,16 +103,16 @@
   {
    "cell_type": "code",
    "execution_count": 7,
-   "id": "8527dadf-3928-4cc1-8ac2-b7ca30afb7ad",
+   "id": "9dc582c9-acc7-40c9-9cbc-90467b6bd5c9",
    "metadata": {},
    "outputs": [],
    "source": [
-    "float* obs_one_loc = new float[ds_obs.n_time]; \n",
-    "float* simh_one_loc = new float[ds_simh.n_time];\n",
-    "float* simp_one_loc = new float[ds_simp.n_time];\n",
+    "std::vector<float> v_obs_one_loc(ds_obs.n_time);   // observations (control period)\n",
+    "std::vector<float> v_simh_one_loc(ds_obs.n_time);  // simulated (control period)\n",
+    "std::vector<float> v_simp_one_loc(ds_obs.n_time);  // simulated (scenario period)\n",
     "\n",
-    "float* ls_result = new float[ds_simp.n_time];\n",
-    "float* qdm_result = new float[ds_simp.n_time];"
+    "std::vector<float> v_ls_result(ds_obs.n_time);   // Lienar Scaling result\n",
+    "std::vector<float> v_qdm_result(ds_obs.n_time);  // Quantile Delta Mapping result"
    ]
   },
   {
@@ -132,9 +132,9 @@
    "outputs": [],
    "source": [
     "// select time series\n",
-    "ds_obs.fill_timeseries_for_location(obs_one_loc, 0, 0);\n",
-    "ds_simh.fill_timeseries_for_location(simh_one_loc, 0, 0);\n",
-    "ds_simp.fill_timeseries_for_location(simp_one_loc, 0, 0);"
+    "ds_obs.fill_timeseries_for_location(v_obs_one_loc, 0, 0);\n",
+    "ds_simh.fill_timeseries_for_location(v_simh_one_loc, 0, 0);\n",
+    "ds_simp.fill_timeseries_for_location(v_simp_one_loc, 0, 0);"
    ]
   },
   {
@@ -153,7 +153,7 @@
    "outputs": [],
    "source": [
     "// select metotds \n",
-    "CM_Func_ptr_simple apply_adjustment_ls = CMethods::get_cmethod_simple(\"linear_scaling\");\n",
+    "CM_Func_ptr_scaling apply_adjustment_ls = CMethods::get_cmethod_scaling(\"linear_scaling\");\n",
     "CM_Func_ptr_quantile apply_adjustment_qdm = CMethods::get_cmethod_quantile(\"quantile_delta_mapping\");"
    ]
   },
@@ -174,11 +174,10 @@
    "source": [
     "// apply linear scaling\n",
     "apply_adjustment_ls(\n",
-    "    ls_result, \n",
-    "    obs_one_loc, \n",
-    "    simh_one_loc, \n",
-    "    simp_one_loc, \n",
-    "    ds_simp.n_time,\n",
+    "    v_ls_result, \n",
+    "    v_obs_one_loc, \n",
+    "    v_simh_one_loc, \n",
+    "    v_simp_one_loc, \n",
     "    \"+\"\n",
     ")"
    ]
@@ -192,11 +191,10 @@
    "source": [
     "// apply quantile delta mapping\n",
     "apply_adjustment_qdm(\n",
-    "    qdm_result, \n",
-    "    obs_one_loc, \n",
-    "    simh_one_loc, \n",
-    "    simp_one_loc, \n",
-    "    ds_simp.n_time,\n",
+    "    v_qdm_result, \n",
+    "    v_obs_one_loc, \n",
+    "    v_simh_one_loc, \n",
+    "    v_simp_one_loc, \n",
     "    \"+\",\n",
     "    100\n",
     ")"
@@ -235,7 +233,7 @@
     }
    ],
    "source": [
-    "for(unsigned ts = start; ts < end; ts++) std::cout << obs_one_loc[ts] << \" \";"
+    "for(unsigned ts = start; ts < end; ts++) std::cout << v_obs_one_loc[ts] << \" \";"
    ]
   },
   {
@@ -253,7 +251,7 @@
     }
    ],
    "source": [
-    "std::cout << MyMath::mean(obs_one_loc, ds_obs.n_time);"
+    "std::cout << MyMath::mean(v_obs_one_loc);"
    ]
   },
   {
@@ -279,7 +277,7 @@
     }
    ],
    "source": [
-    "for(unsigned ts = start; ts < end; ts++) std::cout << simh_one_loc[ts] << \" \";"
+    "for(unsigned ts = start; ts < end; ts++) std::cout << v_simh_one_loc[ts] << \" \";"
    ]
   },
   {
@@ -297,7 +295,7 @@
     }
    ],
    "source": [
-    "std::cout << MyMath::mean(simh_one_loc, ds_simh.n_time);"
+    "std::cout << MyMath::mean(v_simh_one_loc);"
    ]
   },
   {
@@ -323,7 +321,7 @@
     }
    ],
    "source": [
-    "for(unsigned ts = start; ts < end; ts++) std::cout << simp_one_loc[ts] << \" \";"
+    "for(unsigned ts = start; ts < end; ts++) std::cout << v_simp_one_loc[ts] << \" \";"
    ]
   },
   {
@@ -341,7 +339,7 @@
     }
    ],
    "source": [
-    "std::cout << MyMath::mean(simp_one_loc, ds_simp.n_time);"
+    "std::cout << MyMath::mean(v_simp_one_loc);"
    ]
   },
   {
@@ -368,7 +366,7 @@
     }
    ],
    "source": [
-    "for(unsigned ts = 0; ts < 10; ts++) std::cout << ls_result[ts] << \" \";"
+    "for(unsigned ts = 0; ts < 10; ts++) std::cout << v_ls_result[ts] << \" \";"
    ]
   },
   {
@@ -386,7 +384,7 @@
     }
    ],
    "source": [
-    "std::cout << MyMath::mean(ls_result, ds_simp.n_time);"
+    "std::cout << MyMath::mean(v_ls_result);"
    ]
   },
   {
@@ -412,7 +410,7 @@
     }
    ],
    "source": [
-    "for(unsigned ts = 0; ts < 10; ts++) std::cout << qdm_result[ts] << \" \";"
+    "for(unsigned ts = 0; ts < 10; ts++) std::cout << v_qdm_result[ts] << \" \";"
    ]
   },
   {
@@ -430,7 +428,7 @@
     }
    ],
    "source": [
-    "std::cout << MyMath::mean(qdm_result, ds_simp.n_time);"
+    "std::cout << MyMath::mean(v_qdm_result);"
    ]
   },
   {
@@ -454,31 +452,32 @@
     "*    All time attributes are missing here, so one have to set them using some other variable.\n",
     "*/\n",
     "NcFileHandler ncSaver;\n",
-    "ncSaver.to_netcdf(\"qdm_result.nc\", variable_name, qdm_result, ds_simp.n_time) // n_time should be length of qdm_result"
+    "ncSaver.to_netcdf(\"qdm_result.nc\", variable_name, v_qdm_result) // n_time should be length of qdm_result"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 24,
+   "execution_count": 25,
    "id": "101f92fa-29a6-42fc-86f6-a4614c73e780",
    "metadata": {},
    "outputs": [],
    "source": [
     "// Saving can also be done by using the ds_simp instance to copy all time attributes and values to the full adjusted time series \n",
-    "ds_simp.to_netcdf(\"qdm_result.nc\", variable_name, qdm_result)"
+    "ds_simp.to_netcdf(\"qdm_result.nc\", variable_name, v_qdm_result)"
    ]
   },
   {
    "cell_type": "markdown",
    "id": "9e53e2b8-d7fc-4cc8-b52b-14ca4e5b7cda",
    "metadata": {},
    "source": [
-    "# 4. More usage examples"
+    "# 4. More usage examples based on Unidata Program Center's NetCDF data strucutres \n",
+    "References: http://doi.org/10.5065/D6H70CW6"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 25,
+   "execution_count": 26,
    "id": "c6563442-e2be-4f64-bc0e-494e79eb4646",
    "metadata": {},
    "outputs": [
@@ -496,7 +495,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 26,
+   "execution_count": 27,
    "id": "73227a54-95c6-40d5-bc22-5537e0cfe60b",
    "metadata": {},
    "outputs": [
@@ -514,7 +513,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 27,
+   "execution_count": 28,
    "id": "7f449f18-9bbb-4e0e-8e8f-fb78e6fc9bb8",
    "metadata": {},
    "outputs": [
@@ -532,7 +531,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 28,
+   "execution_count": 29,
    "id": "d1bdcab5-edb7-41d7-b038-b14b260d7c2b",
    "metadata": {},
    "outputs": [
@@ -568,17 +567,17 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 29,
+   "execution_count": 30,
    "id": "67e00d69-81a9-4a1f-8001-4ec1ddd43ee0",
    "metadata": {},
    "outputs": [
     {
      "data": {
       "text/plain": [
-       "{ \"calendar\" => @0x6000020ec9d8, \"units\" => @0x6000020ec7a8 }"
+       "{ \"calendar\" => @0x60000089f1a8, \"units\" => @0x60000089f138 }"
       ]
      },
-     "execution_count": 29,
+     "execution_count": 30,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -589,7 +588,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 30,
+   "execution_count": 31,
    "id": "093c24e1-3e99-4c56-a450-207ffa00e4b7",
    "metadata": {},
    "outputs": [

diff --git a/include/CMethods.hxx b/include/CMethods.hxx
@@ -14,28 +14,28 @@
 
 #include <iostream>
 
-typedef void (*CM_Func_ptr_simple)(float* output, float* ref, float* contr, float* scen, unsigned n_time, std::string kind);
-typedef void (*CM_Func_ptr_quantile)(float* output, float* ref, float* contr, float* scen, unsigned n_time, std::string kind, unsigned n_quantiles);
+typedef void (*CM_Func_ptr_scaling)(std::vector<float>& v_output, std::vector<float>& v_reference, std::vector<float>& v_control, std::vector<float>& v_scenario, std::string kind);
+typedef void (*CM_Func_ptr_quantile)(std::vector<float>& v_output, std::vector<float>& v_reference, std::vector<float>& v_control, std::vector<float>& v_scenario, std::string kind, unsigned n_quantiles);
 
 class CMethods {
    public:
     CMethods();
     ~CMethods();
 
-    static CM_Func_ptr_simple get_cmethod_simple(std::string method_name);
+    static CM_Func_ptr_scaling get_cmethod_scaling(std::string method_name);
     static CM_Func_ptr_quantile get_cmethod_quantile(std::string method_name);
 
-    static std::vector<std::string> simple_method_names;
+    static std::vector<std::string> scaling_method_names;
     static std::vector<std::string> quantile_method_names;
     static std::vector<std::string> all_method_names;
 
-    static void Linear_Scaling(float* output, float* reference, float* control, float* scenario, unsigned, std::string n_time);
-    static void Variance_Scaling(float* output, float* reference, float* control, float* scenario, unsigned, std::string n_time);
-    static void Delta_Method(float* output, float* reference, float* control, float* scenario, unsigned, std::string n_time);
+    static void Linear_Scaling(std::vector<float>& v_output, std::vector<float>& v_reference, std::vector<float>& v_control, std::vector<float>& v_scenario, std::string kind);
+    static void Variance_Scaling(std::vector<float>& v_output, std::vector<float>& v_reference, std::vector<float>& v_control, std::vector<float>& v_scenario, std::string kind);
+    static void Delta_Method(std::vector<float>& v_output, std::vector<float>& v_reference, std::vector<float>& v_control, std::vector<float>& v_scenario, std::string kind);
 
-    static std::vector<double> get_xbins(float* a, float* b, unsigned n_quantiles, unsigned length, std::string kind);
-    static void Quantile_Mapping(float* output, float* reference, float* control, float* scenario, unsigned n_time, std::string kind, unsigned n_quantiles);
-    static void Quantile_Delta_Mapping(float* output, float* reference, float* control, float* scenario, unsigned n_time, std::string kind, unsigned n_quantiles);
+    static std::vector<double> get_xbins(std::vector<float>& a, std::vector<float>& b, unsigned n_quantiles, std::string kind);
+    static void Quantile_Mapping(std::vector<float>& v_output, std::vector<float>& v_reference, std::vector<float>& v_control, std::vector<float>& v_scenario, std::string kind, unsigned n_quantiles);
+    static void Quantile_Delta_Mapping(std::vector<float>& v_output, std::vector<float>& v_reference, std::vector<float>& v_control, std::vector<float>& v_scenario, std::string kind, unsigned n_quantiles);
 };
 
 #endif