finished netCdf reader and added bathymetry reading support

config.json

@@ -1,11 +1,11 @@
 {
     "solver": "fwave",
-    "nx": 50,
-    "ny": 50,
-    "simulationSizeX": 100,
-    "simulationSizeY": 100,
+    "nx": 10,
+    "ny": 10,
+    "simulationSizeX": 10,
+    "simulationSizeY": 10,
     "setup":"CIRCULARDAMBREAK2D",
-    "bathymetry":"resources/bathymetry/singleWall2d_100x100.csv",
+    "bathymetry":"resources/netCdfTest.nc",
     "hasBoundaryL": false,
     "hasBoundaryR": false,
     "hasBoundaryU": false,

config.log

@@ -1,27 +1,26 @@
-file /Users/richardhofmann/Dropbox/Mac/Desktop/programming/uni/tsunami/tsunami_lab/SConstruct,line 36:
+file /Users/lpmg/Desktop/Uni/Sem5/Tsunami/tsunami_lab/SConstruct,line 36:
 	Configure(confdir = .sconf_temp)
 scons: Configure: Checking for C library netcdf... 
-scons: Configure: ".sconf_temp/conftest_292a485a87739177f630f5f17109eb40_0.c" is up to date.
+scons: Configure: ".sconf_temp/conftest_1ddd6b9627e69bc88093239e56660785_0.c" is up to date.
 scons: Configure: The original builder output was:
-  |.sconf_temp/conftest_292a485a87739177f630f5f17109eb40_0.c <-
+  |.sconf_temp/conftest_1ddd6b9627e69bc88093239e56660785_0.c <-
   |  |
   |  |
   |  |#include "netcdf.h"
   |  |
-  |  |int
-  |  |main() {
+  |  |int main(void) {
   |  |  
   |  |return 0;
   |  |}
   |  |
   |
-scons: Configure: ".sconf_temp/conftest_292a485a87739177f630f5f17109eb40_0.o" is up to date.
+scons: Configure: ".sconf_temp/conftest_1ddd6b9627e69bc88093239e56660785_0.o" is up to date.
 scons: Configure: The original builder output was:
-  |gcc -o .sconf_temp/conftest_292a485a87739177f630f5f17109eb40_0.o -c .sconf_temp/conftest_292a485a87739177f630f5f17109eb40_0.c
+  |gcc -o .sconf_temp/conftest_1ddd6b9627e69bc88093239e56660785_0.o -c .sconf_temp/conftest_1ddd6b9627e69bc88093239e56660785_0.c
   |
-scons: Configure: ".sconf_temp/conftest_292a485a87739177f630f5f17109eb40_0_6914dc1c61d7fa91c0e58be35491f622" is up to date.
+scons: Configure: ".sconf_temp/conftest_1ddd6b9627e69bc88093239e56660785_0_b592ebdd36f6be32a5b2ea6e1bd2921e" is up to date.
 scons: Configure: The original builder output was:
-  |gcc -o .sconf_temp/conftest_292a485a87739177f630f5f17109eb40_0_6914dc1c61d7fa91c0e58be35491f622 .sconf_temp/conftest_292a485a87739177f630f5f17109eb40_0.o -lnetcdf
+  |gcc -o .sconf_temp/conftest_1ddd6b9627e69bc88093239e56660785_0_b592ebdd36f6be32a5b2ea6e1bd2921e .sconf_temp/conftest_1ddd6b9627e69bc88093239e56660785_0.o -lnetcdf
   |
 scons: Configure: (cached) yes
 

resources/netcdfTest.cdl

@@ -0,0 +1,41 @@
+netcdf tsunamiNetCdf {
+dimensions:
+	x = 10 ;
+	y = 10 ;
+variables:
+	float x(x) ;
+		x:units = "meters" ;
+		x:axis = "X" ;
+	float y(y) ;
+		y:units = "meters" ;
+		y:axis = "Y" ;
+	float bathymetry(x, y) ;
+        bathymetry:units = "meters" ;
+data:
+
+ x = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;
+
+ y = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;
+
+ bathymetry =
+  // bathymetry(0, 0-9)
+    -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+  // bathymetry(1, 0-9)
+    -2, -2, -2, -2, -2, -2, -2, -2, -2, -2,
+  // bathymetry(2, 0-9)
+    -3, -3, -3, -3, -3, -3, -3, -3, -3, -3,
+  // bathymetry(3, 0-9)
+    -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+  // bathymetry(4, 0-9)
+    -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+  // bathymetry(5, 0-9)
+    -1, -1, 23, -1, -1, -1, -1, -1, -1, -1,
+  // bathymetry(6, 0-9)
+    -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+  // bathymetry(7, 0-9)
+    -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+  // bathymetry(8, 0-9)
+    -1, -1, -1, -1, -1, -1, 99, -1, -1, -1,
+  // bathymetry(9, 0-9)
+    -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 ;
+}

src/io/BathymetryLoader.cpp

@@ -18,7 +18,7 @@ tsunami_lab::io::BathymetryLoader::~BathymetryLoader()
 
 void tsunami_lab::io::BathymetryLoader::loadBathymetry(const std::string &i_file)
 {
-    std::cout << "Loading bathymetry from file: " << i_file << std::endl;
+    std::cout << "Loading bathymetry from csv file: " << i_file << std::endl;
     if (!std::filesystem::exists(i_file))
     {
         std::cerr << "Error: File not found!" << std::endl;

src/io/NetCdf.cpp

@@ -8,7 +8,6 @@
 #include <iostream>
 #include <netcdf.h>
 
-
 void tsunami_lab::io::NetCdf::checkNcErr(tsunami_lab::t_idx i_err)
 {
     if (i_err)
@@ -20,36 +19,36 @@ void tsunami_lab::io::NetCdf::checkNcErr(tsunami_lab::t_idx i_err)
     }
 }
 
-tsunami_lab::io::NetCdf::NetCdf(t_idx i_nx,
-                                const t_idx i_ny,
-                                t_idx i_stride,
-                                t_real const *i_b)
+tsunami_lab::io::NetCdf::NetCdf(const char *path,
+                                t_idx i_nx,
+                                t_idx i_ny,
+                                t_idx i_stride)
 {
 
     m_nx = i_nx;
     m_ny = i_ny;
     m_stride = i_stride;
 
-    m_err = nc_create("tsunamiNetCdf.nc", // path
-                      NC_CLOBBER,         // cmode
-                      &m_ncId);           // ncidp
+    if (path == nullptr)
+        return;
+
+    m_err = nc_create(path,       // path
+                      NC_CLOBBER, // cmode
+                      &m_ncId);   // ncidp
     checkNcErr(m_err);
 
-    t_real *m_bathymetryData = new t_real[i_nx * i_ny];
     t_real *m_x = new t_real[i_nx];
     t_real *m_y = new t_real[i_ny];
 
-    // loop for bathymetry
-    int i = 0;
+    // set x and y
     for (std::size_t l_ix = 0; l_ix < i_nx; l_ix++)
     {
-        for (std::size_t l_iy = 0; l_iy < i_ny; l_iy++)
-        {
-            m_bathymetryData[i++] = i_b[l_ix + l_iy * i_stride];
-            m_y[l_iy] = l_iy;
-        }
         m_x[l_ix] = l_ix;
     }
+    for (std::size_t l_iy = 0; l_iy < i_ny; l_iy++)
+    {
+        m_y[l_iy] = l_iy;
+    }
 
     // define dimensions
     int m_dimIds[3];
@@ -141,7 +140,8 @@ tsunami_lab::io::NetCdf::NetCdf(t_idx i_nx,
 
     // assign attributes
     m_err = nc_put_att_text(m_ncId, m_varTId, "units",
-                            strlen("seconds"), "seconds");
+                            strlen("seconds since the earthquake event"),
+                            "seconds since the earthquake event");
     checkNcErr(m_err);
 
     m_err = nc_put_att_text(m_ncId, m_varXId, "units",
@@ -164,17 +164,11 @@ tsunami_lab::io::NetCdf::NetCdf(t_idx i_nx,
     m_err = nc_put_att_text(m_ncId, m_varTHId, "units",
                             strlen("meters"), "meters");
     checkNcErr(m_err);
-    m_err = nc_put_att_text(m_ncId, m_varHuId, "units",
-                            strlen("Newton * seconds"), "meters");
-    checkNcErr(m_err);
-    m_err = nc_put_att_text(m_ncId, m_varHvId, "units",
-                            strlen("Newton * seconds"), "meters");
-    checkNcErr(m_err);
 
     m_err = nc_enddef(m_ncId); // ncid
     checkNcErr(m_err);
 
-    // write data 
+    // write data
     m_err = nc_put_var_float(m_ncId,   // ncid
                              m_varXId, // varid
                              &m_x[0]); // op
@@ -184,13 +178,6 @@ tsunami_lab::io::NetCdf::NetCdf(t_idx i_nx,
                              &m_y[0]); // op
     checkNcErr(m_err);
 
-    m_err = nc_put_var_float(m_ncId,            // ncid
-                             m_varBId,          // varid
-                             m_bathymetryData); // op
-    checkNcErr(m_err);
-
-
-    delete[] m_bathymetryData;
     delete[] m_x;
     delete[] m_y;
 }
@@ -226,6 +213,28 @@ void tsunami_lab::io::NetCdf::write(t_real const *i_h,
             l_i++;
         }
     }
+
+    // write bathymetry on first call
+    if (m_timeStepCount == 0)
+    {
+        t_real *l_b = new t_real[m_nx * m_ny];
+        for (t_idx l_x = 0; l_x < m_nx; l_x++)
+        {
+            for (t_idx l_y = 0; l_y < m_ny; l_y++)
+            {
+                l_b[l_i] = i_b[l_x + l_y * m_stride];
+                l_i++;
+            }
+        }
+
+        m_err = nc_put_var_float(m_ncId,
+                                 m_varBId,
+                                 l_b);
+        checkNcErr(m_err);
+        delete[] l_b;
+    }
+
+    //write values
     m_err = nc_put_var1_float(m_ncId,
                               m_varTId,
                               &m_timeStepCount,
@@ -238,6 +247,7 @@ void tsunami_lab::io::NetCdf::write(t_real const *i_h,
                               count,
                               l_h);
     checkNcErr(m_err);
+
     m_err = nc_put_vara_float(m_ncId,
                               m_varTHId,
                               start,
@@ -267,55 +277,48 @@ void tsunami_lab::io::NetCdf::write(t_real const *i_h,
     delete[] l_hv;
 }
 
-void tsunami_lab::io::NetCdf::read(const char* l_filename,
-                                    t_real * i_b,
-                                    t_real * i_d){
-    t_real x_in[m_nx], y_in[m_ny];
-    int x_varid, y_varid, b_varid;
-
-    t_real x_in[m_nx], y_in[m_ny];
-
-    int *l_data = new int[m_nx * m_ny];
-
-         m_err = nc_open(l_filename, NC_NOWRITE, &m_ncIdRead);
-        checkNcErr(m_err);
-
-        m_err = nc_inq_varid(m_ncIdRead, "x", &x_varid);
-        checkNcErr(m_err);
-        m_err = nc_inq_varid(m_ncIdRead, "y", &y_varid);
-        checkNcErr(m_err);
-
-        /* Read the coordinate variable data. */
-        m_err = nc_get_var_float(m_ncIdRead, x_varid, &x_in[0]);
-        checkNcErr(m_err);
-        m_err = nc_get_var_float(m_ncIdRead, y_varid, &y_in[0]);
-        checkNcErr(m_err);
+tsunami_lab::t_real *tsunami_lab::io::NetCdf::read(const char *i_file,
+                                                   const char *i_var,
+                                                   t_idx &o_nx,
+                                                   t_idx &o_ny)
+{
+    std::cout << "Loading "<< i_var << " from .nc file: " << i_file << std::endl;
 
-    if(i_b == nullptr){
-
-        /* Get the varids of the pressure and temperature netCDF
-         * variables. */
-         m_err = nc_inq_varid(m_ncIdRead, "bathymetry", &b_varid);
-        checkNcErr(m_err);
+    int l_ncIdRead, l_varXIdRead, l_varYIdRead, l_varDataIdRead = 0;
 
-        //read data
-        m_err  = nc_get_var_float(m_ncIdRead, b_varid, i_b);
-        checkNcErr(m_err);
+    m_err = nc_open(i_file, NC_NOWRITE, &l_ncIdRead);
+    checkNcErr(m_err);
 
-
-        m_err = nc_close(m_ncIdRead);
-        checkNcErr(m_err);
-    } else{
-        /* Get the varids of the pressure and temperature netCDF
-         * variables. */
-         m_err = nc_inq_varid(m_ncIdRead, "displacement", &b_varid);
-        checkNcErr(m_err);
+    // get dimension ids
+    m_err = nc_inq_dimid(l_ncIdRead, "x", &l_varXIdRead);
+    checkNcErr(m_err);
+    m_err = nc_inq_dimid(l_ncIdRead, "y", &l_varYIdRead);
+    checkNcErr(m_err);
+    // read dimension size
+    m_err = nc_inq_dimlen(l_ncIdRead, l_varXIdRead, &o_nx);
+    checkNcErr(m_err);
+    m_err = nc_inq_dimlen(l_ncIdRead, l_varYIdRead, &o_ny);
+    checkNcErr(m_err);
+    // get var id of desired variable
+    m_err = nc_inq_varid(l_ncIdRead, i_var, &l_varDataIdRead);
+    checkNcErr(m_err);
+    // read data
+    t_real l_data[o_nx][o_ny];
+    m_err = nc_get_var_float(l_ncIdRead, l_varDataIdRead, &l_data[0][0]);
+    checkNcErr(m_err);
 
-        //read data
-        m_err  = nc_get_var_float(m_ncIdRead, d_varid, i_d);
-        checkNcErr(m_err);
+    m_err = nc_close(l_ncIdRead);
+    checkNcErr(m_err);
 
-        m_err = nc_close(m_ncIdRead);
-        checkNcErr(m_err);
+    // convert to strided array
+    t_real *l_stridedArray = new t_real[o_nx * o_ny];
+    for (std::size_t l_ix = 0; l_ix < o_nx; l_ix++)
+    {
+        for (std::size_t l_iy = 0; l_iy < o_ny; l_iy++)
+        {
+            l_stridedArray[l_ix + l_iy * o_nx] = l_data[l_ix][l_iy];
+        }
     }
+    std::cout << "Done loading "<< i_var << std::endl;
+    return l_stridedArray;
 }