diff --git a/Applications/Utils/FileConverter/NetCdfConverter.cpp b/Applications/Utils/FileConverter/NetCdfConverter.cpp
index aa3400245a54d899b0783bb3db2bf3adb32ad9ab..a1b305e78e123301cd91c1420d103fcb1fe04709 100644
--- a/Applications/Utils/FileConverter/NetCdfConverter.cpp
+++ b/Applications/Utils/FileConverter/NetCdfConverter.cpp
@@ -31,7 +31,8 @@
using namespace netCDF;
-const double no_data = -9999;
+static const double no_data_output = -9999;
+static double no_data_input = -9999;
enum class OutputType
{
@@ -163,35 +164,38 @@ static std::pair<double, double> getBoundaries(NcVar const& var)
}
static MathLib::Point3d getOrigin(NcFile const& dataset, NcVar const& var,
- std::vector<std::size_t> const& dim_idx_map,
- bool is_time_dep)
+ std::vector<std::size_t> const& dim_idx_map,
+ std::size_t const time_offset)
{
- std::size_t const temp_offset = (is_time_dep) ? 1 : 0;
MathLib::Point3d origin(MathLib::ORIGIN);
std::size_t const n_dims = var.getDimCount();
- for (std::size_t i = temp_offset; i < n_dims; ++i)
+ for (std::size_t i = time_offset; i < n_dims; ++i)
{
NcVar const& dim = getDimVar(dataset, var, dim_idx_map[i]);
auto const bounds = (dim.isNull()) ? getDimLength(var, dim_idx_map[i])
: getBoundaries(dim);
- origin[i - temp_offset] =
+ origin[i - time_offset] =
(bounds.first < bounds.second) ? bounds.first : bounds.second;
}
return origin;
}
-static void flipRaster(std::vector<double>& data, std::size_t const width,
- std::size_t const height)
+static void flipRaster(std::vector<double>& data, std::size_t const layers,
+ std::size_t const width, std::size_t const height)
{
std::size_t const length(data.size());
std::vector<double> tmp_vec;
tmp_vec.reserve(length);
- for (std::size_t i = 0; i < height; i++)
+ for (std::size_t k = 0; k < layers; k++)
{
- std::size_t const line_idx(length - (width * (i + 1)));
- for (std::size_t j = 0; j < width; j++)
+ std::size_t const layer_end = (k+1) * height * width;
+ for (std::size_t i = 0; i < height; i++)
{
- tmp_vec.push_back(data[line_idx + j]);
+ std::size_t const line_idx(layer_end - (width * (i + 1)));
+ for (std::size_t j = 0; j < width; j++)
+ {
+ tmp_vec.push_back(data[line_idx + j]);
+ }
}
}
std::copy(tmp_vec.cbegin(), tmp_vec.cend(), data.begin());
@@ -394,25 +398,24 @@ static double getResolution(NcFile const& dataset, NcVar const& var)
static GeoLib::RasterHeader createRasterHeader(
NcFile const& dataset, NcVar const& var,
std::vector<std::size_t> const& dim_idx_map,
- std::vector<std::size_t> const& length, bool is_time_dep)
+ std::vector<std::size_t> const& length, std::size_t const time_offset)
{
- MathLib::Point3d const origin = getOrigin(dataset, var, dim_idx_map, is_time_dep);
+ MathLib::Point3d const origin =
+ getOrigin(dataset, var, dim_idx_map, time_offset);
double const res = getResolution(dataset, var);
std::size_t n_dims = var.getDimCount();
- std::size_t temp_offset = (is_time_dep) ? 1 : 0;
std::size_t z_length =
- (n_dims - temp_offset == 3) ? length[dim_idx_map.back()] : 1;
- return {length[dim_idx_map[0 + temp_offset]],
- length[dim_idx_map[1 + temp_offset]],
- z_length, origin, res, no_data};
+ (n_dims - time_offset == 3) ? length[dim_idx_map.back()] : 1;
+ return {length[dim_idx_map[0 + time_offset]],
+ length[dim_idx_map[1 + time_offset]],
+ z_length, origin, res, no_data_output};
}
-static std::vector<std::size_t> getLength(NcVar const& var, bool const is_time_dep)
+static std::vector<std::size_t> getLength(NcVar const& var, std::size_t const time_offset)
{
- std::size_t const temp_offset = (is_time_dep) ? 1 : 0;
std::size_t const n_dims = (var.getDimCount());
std::vector<std::size_t> length(n_dims, 1);
- for (std::size_t i = temp_offset; i < n_dims; ++i)
+ for (std::size_t i = time_offset; i < n_dims; ++i)
{
length[i] = var.getDim(i).getSize();
}
@@ -429,16 +432,11 @@ static std::vector<double> getData(NcFile const& dataset, NcVar const& var,
offset[0] = time_step;
std::vector<double> data_vec(total_length, 0);
var.getVar(offset, length, data_vec.data());
- std::replace_if(data_vec.begin(), data_vec.end(),
- [](double& x) { return x <= no_data; }, no_data);
- // reverse lines in vertical direction if the original file has its origin
- // in the northwest corner
- NcVar const dim_var (getDimVar(dataset, var, n_dims - 1));
- auto const bounds = (dim_var.isNull()) ? getDimLength(var, n_dims - 1)
- : getBoundaries(dim_var);
- if (bounds.first > bounds.second)
- flipRaster(data_vec, length[n_dims - 1], length[n_dims - 2]);
+ std::replace_if(
+ data_vec.begin(), data_vec.end(),
+ [](double& x) { return x == no_data_input; }, no_data_output);
+
return data_vec;
}
@@ -531,14 +529,15 @@ static MeshLib::MeshElemType assignElemType(
}
static bool convert(NcFile const& dataset, NcVar const& var,
- std::string const& output_name,
- std::vector<std::size_t> const& dim_idx_map,
- bool const is_time_dep,
- std::pair<std::size_t, std::size_t> const& time_bounds,
- OutputType const output, MeshLib::MeshElemType const elem_type)
+ std::string const& output_name,
+ std::vector<std::size_t> const& dim_idx_map,
+ std::size_t const time_offset,
+ std::pair<std::size_t, std::size_t> const& time_bounds,
+ OutputType const output,
+ MeshLib::MeshElemType const elem_type)
{
std::unique_ptr<MeshLib::Mesh> mesh;
- std::vector<std::size_t> const length = getLength(var, is_time_dep);
+ std::vector<std::size_t> const length = getLength(var, time_offset);
std::size_t const array_length = std::accumulate(
length.cbegin(), length.cend(), 1, std::multiplies<std::size_t>());
for (std::size_t i = time_bounds.first; i <= time_bounds.second; ++i)
@@ -546,11 +545,24 @@ static bool convert(NcFile const& dataset, NcVar const& var,
std::string const step_str = (time_bounds.first != time_bounds.second)
? std::string(" time step " + std::to_string(i)) : "";
std::cout << "Converting" << step_str << "...\n";
- std::vector<double> const data_vec =
+ std::vector<double> data_vec =
getData(dataset, var, array_length, i, length);
+ // reverse lines in vertical direction if file has its origin in the
+ // northwest corner
+ std::size_t const n_dims = length.size();
+ NcVar const dim_var(getDimVar(dataset, var, n_dims - 2));
+ auto const bounds = (dim_var.isNull()) ? getDimLength(var, n_dims - 2)
+ : getBoundaries(dim_var);
+ if (bounds.first > bounds.second)
+ {
+ std::size_t n_layers =
+ (length.size() - time_offset == 3) ? length[n_dims - 3] : 1;
+ flipRaster(data_vec, n_layers, length[n_dims - 1], length[n_dims - 2]);
+ }
+
GeoLib::RasterHeader const header =
- createRasterHeader(dataset, var, dim_idx_map, length, is_time_dep);
+ createRasterHeader(dataset, var, dim_idx_map, length, time_offset);
MeshLib::UseIntensityAs const useIntensity =
MeshLib::UseIntensityAs::DATAVECTOR;
if (output == OutputType::MULTIMESH)
@@ -620,6 +632,12 @@ int main(int argc, char* argv[])
"(http://www.opengeosys.org)",
' ', GitInfoLib::GitInfo::ogs_version);
+ TCLAP::ValueArg<int> arg_nodata(
+ "n", "nodata",
+ "explicitly specifies the no data value used in the dataset (usually it is not necessary to set this)",
+ false, no_data_input, "integer specifying no data value");
+ cmd.add(arg_nodata);
+
std::vector<std::string> allowed_elems{"tri", "quad", "prism", "hex"};
TCLAP::ValuesConstraint<std::string> allowed_elem_vals(allowed_elems);
TCLAP::ValueArg<std::string> arg_elem_type(
@@ -785,6 +803,11 @@ int main(int argc, char* argv[])
elemSelectionLoop(n_dims - temp_offset);
}
+ if (arg_nodata.isSet())
+ {
+ no_data_input = arg_nodata.getValue();
+ }
+
if (!convert(dataset, var, output_name, dim_idx_map, is_time_dep,
time_bounds, output, elem_type))
return EXIT_FAILURE;
diff --git a/Tests/Data/FileConverter/slim_100897_198.vtu b/Tests/Data/FileConverter/slim_100897_198.vtu
index a81f426f1ecf049384fd858b906659e4f4ec6463..1ab68fd13204af261109f58da4a39dd7c0662534 100644
--- a/Tests/Data/FileConverter/slim_100897_198.vtu
+++ b/Tests/Data/FileConverter/slim_100897_198.vtu
@@ -1,3 +1,3 @@
version https://git-lfs.github.com/spec/v1
-oid sha256:8ceec1ea5ea0967e7111c945e5e41032a8351a60bddd5ecc8675ef40ab46432e
+oid sha256:cbc59239316835e389fec40bf758fe7d6a481a17fad9389f3fa0c24b453d6398
size 4462866