Modification to bathymetry.cpp/h to support more .grd metadata formats

gistfile1.txt

➜  MB-System git:(capstone-spring2024) ✗ git diff src/mbgrd2gltf/bathymetry.h src/mbgrd2gltf/bathymetry.cpp
diff --git a/src/mbgrd2gltf/bathymetry.cpp b/src/mbgrd2gltf/bathymetry.cpp
index 6287bee51..db8a17adc 100644
--- a/src/mbgrd2gltf/bathymetry.cpp
+++ b/src/mbgrd2gltf/bathymetry.cpp
@@ -40,6 +40,7 @@

 // external libraries
 #include <netcdf.h>
+#include <iostream>

 namespace mbgrd2gltf
 {
@@ -47,23 +48,96 @@ namespace mbgrd2gltf
 	{
 		int netcdf_id = get_netcdf_id(options.input_filepath().c_str());

-		try
+        // Support various arbitrary versions of metadata describing the grid through try-catch blocks
+		std::string x_name = "x";
+		std::string y_name = "y";
+        try
+        {
+            _side = get_dimension_length(netcdf_id, "side");
+        }
+		catch (const std::exception&)
 		{
-			_side = get_dimension_length(netcdf_id, "side");
+		    _side = 2;
+        }
+        try
+        {
 			_xysize = get_dimension_length(netcdf_id, "xysize");
+        }
+		catch (const std::exception&)
+		{
+			std::cout << "Failed to get xysize = " << std::string() << std::endl;
+			try
+			{
+				_x = get_dimension_length(netcdf_id, x_name.c_str());
+				_y = get_dimension_length(netcdf_id, y_name.c_str());
+				_xysize = _x * _y;
+			}
+			catch(const std::exception& e)
+			{
+				// As produced by `gmt6 grdproject` command
+				std::cout << "Trying lon and lat..." << e.what() << '\n';
+				_x = get_dimension_length(netcdf_id, "lon");
+				_y = get_dimension_length(netcdf_id, "lat");
+				_xysize = _x * _y;
+				x_name = "lon";
+				y_name = "lat";
+			}
+
+        }
+        try
+        {
 			get_variable_double_array(netcdf_id, "x_range", _x_range, _side);
 			get_variable_double_array(netcdf_id, "y_range", _y_range, _side);
 			get_variable_double_array(netcdf_id, "z_range", _z_range, _side);
+        }
+		catch (const std::exception&)
+		{
+            // Use actual_range variable attributes
+			get_variable_attribute_double(netcdf_id, x_name.c_str(), "actual_range", _x_range);
+			get_variable_attribute_double(netcdf_id, y_name.c_str(), "actual_range", _y_range);
+			get_variable_attribute_double(netcdf_id, "z", "actual_range", _z_range);
+			double temp = _y_range[0];
+			_y_range[0] = _y_range[1];
+			_y_range[1] = temp;
+        }
+        try
+        {
 			get_variable_double_array(netcdf_id, "spacing", _spacing, _side);
-			get_variable_uint_array(netcdf_id, "dimension", _dimension, _side);
-			_z = Matrix<float>(_dimension[0], _dimension[1]);
-			get_variable_float_array(netcdf_id, "z", _z.data(), _xysize);
+        }
+        catch (const std::exception&)
+        {
+            _spacing[0] = (_x_range[1] - _x_range[0]) / _x;
+            _spacing[1] = (_y_range[1] - _y_range[0]) / _y;
+        }
+        try
+        {
+            _start[0] = _xysize - _xysize;
+            _length[0] = _side;
+			get_variable_uint_array(netcdf_id, "dimension", _dimension, _start, _length);
+        }
+		catch (const std::exception&)
+		{
+            _dimension[0] = _x;
+            _dimension[1] = _y;
+        }
+		try
+		{
+            // The z array in Monterey25.grd is 1-dimensional array: float z(xysize)
+            _start[0] = _xysize - _xysize;
+            _length[0] = _xysize;
+            size_t _zero = 0;
+            _z = Matrix<float>(_dimension[0], _dimension[1]);
+			get_variable_float_array(netcdf_id, "z", _z.data(), &_zero, &_xysize);
 		}
 		catch (const std::exception&)
 		{
-			nc_close(netcdf_id);
-
-			throw;
+            // The z array is recent mbgrid generated .grd files is 2-dimensional array: float z(y, x)
+            _start[1] = _x - _x;
+            _start[0] = _y - _y;
+            _length[1] = _x;
+            _length[0] = _y;
+            _z = Matrix<float>(_length[1], _length[0]);
+			get_variable_float_array(netcdf_id, "z", _z.data(), _start, _length);
 		}

 		int return_value = nc_close(netcdf_id);
@@ -135,6 +209,19 @@ namespace mbgrd2gltf
 				+ "'");
 	}

+	void Bathymetry::get_variable_attribute_double(int netcdf_id, const char *var_name, const char *att_name, double *out)
+	{
+		int variable_id = get_variable_id(netcdf_id, var_name);
+		int return_value = nc_get_att_double(netcdf_id, variable_id, att_name, out);
+
+		if (return_value != NC_NOERR)
+			throw NetCdfError(return_value, "failed to get double value(s) for attribute '"
+				+ std::string(att_name)
+				+ "'"
+                + " for var_name "
+                + std::string(var_name));
+	}
+
 	size_t Bathymetry::get_dimension_length(int netcdf_id, const char *name)
 	{
 		size_t out;
@@ -162,11 +249,10 @@ namespace mbgrd2gltf
 				+ "'");
 	}

-	void Bathymetry::get_variable_float_array(int netcdf_id, const char *name, float *out, size_t length)
+	void Bathymetry::get_variable_float_array(int netcdf_id, const char *name, float *out, size_t *start, size_t *length)
 	{
-		size_t start = 0;
 		int variable_id = get_variable_id(netcdf_id, name);
-		int return_value = nc_get_vara_float(netcdf_id, variable_id, &start, &length, out);
+		int return_value = nc_get_vara_float(netcdf_id, variable_id, start, length, out);

 		if (return_value != NC_NOERR)
 			throw NetCdfError(return_value, "failed to get float array data for variable '"
@@ -174,11 +260,10 @@ namespace mbgrd2gltf
 				+ "'");
 	}

-	void Bathymetry::get_variable_uint_array(int netcdf_id, const char *name, unsigned *out, size_t length)
+	void Bathymetry::get_variable_uint_array(int netcdf_id, const char *name, unsigned int *out, size_t *start, size_t *length)
 	{
-		size_t start = 0;
 		int variable_id = get_variable_id(netcdf_id, name);
-		int return_value = nc_get_vara_uint(netcdf_id, variable_id, &start, &length, out);
+		int return_value = nc_get_vara_uint(netcdf_id, variable_id, start, length, out);

 		if (return_value != NC_NOERR)
 			throw NetCdfError(return_value, "failed to get uint array data for variable '"
@@ -197,8 +282,9 @@ namespace mbgrd2gltf
 		_xysize = _z.count();
 		_dimension[0] = _z.size_x();
 		_dimension[1] = _z.size_y();
-		_spacing[0] = std::abs(_x_range[1] - _x_range[0]) / (double)(_dimension[0] - 1);
-		_spacing[1] = std::abs(_y_range[1] - _y_range[0]) / (double)(_dimension[1] - 1);
+		// Allow negative values for when one or more grid axes are reversed
+		_spacing[0] = (_x_range[1] - _x_range[0]) / (double)(_dimension[0] - 1);
+		_spacing[1] = (_y_range[1] - _y_range[0]) / (double)(_dimension[1] - 1);
 	}

 	std::string Bathymetry::to_string() const
diff --git a/src/mbgrd2gltf/bathymetry.h b/src/mbgrd2gltf/bathymetry.h
index 72f2bdc0d..6d61b6009 100644
--- a/src/mbgrd2gltf/bathymetry.h
+++ b/src/mbgrd2gltf/bathymetry.h
@@ -78,7 +78,11 @@ namespace mbgrd2gltf
 		double _spacing[2];
 		size_t _side;
 		size_t _xysize;
-		unsigned _dimension[2];
+		size_t _x;
+		size_t _y;
+		size_t _start[2];
+		unsigned int _dimension[2];
+		size_t _length[2];

 	private: // methods

@@ -87,10 +91,11 @@ namespace mbgrd2gltf
 		static int get_dimension_id(int netcdf_id, const char *name);
 		static size_t get_attribute_length(int netcdf_id, const char *name);
 		static void get_attribute_text(int netcdf_id, const char *name, char *out);
+		static void get_variable_attribute_double(int netcdf_id, const char *var_name, const char *att_name, double *out);
 		static size_t get_dimension_length(int netcdf_id, const char *name);
 		static void get_variable_double_array(int netcdf_id, const char *name, double *out, size_t length);
-		static void get_variable_float_array(int netcdf_id, const char *name, float *out, size_t length);
-		static void get_variable_uint_array(int netcdf_id, const char *name, unsigned *out, size_t length);
+		static void get_variable_float_array(int netcdf_id, const char *name, float *out, size_t *start, size_t *length);
+		static void get_variable_uint_array(int netcdf_id, const char *name, unsigned int *out, size_t *start, size_t *length);

 		void compress(const Options& options);

@@ -109,8 +114,8 @@ namespace mbgrd2gltf
 		inline double altitude_max() const { return _z_range[1]; }
 		inline double longitude_spacing() const { return _spacing[0]; }
 		inline double latitude_spacing() const { return _spacing[1]; }
-		inline unsigned size_x() const { return _dimension[0]; }
-		inline unsigned size_y() const { return _dimension[1]; }
+		inline size_t size_x() const { return _dimension[0]; }
+		inline size_t size_y() const { return _dimension[1]; }
 		inline size_t side_count() const { return _side; }
 		inline size_t altitudes_length() const { return _xysize; }