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Epoch time #1287

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Nov 9, 2023
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Epoch time #1287

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242 changes: 123 additions & 119 deletions Source/IO/NCInterface.H
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Original file line number Diff line number Diff line change
Expand Up @@ -58,120 +58,128 @@ struct NCVar
const int varid;

//! Name of this variable
[[nodiscard]] std::string name() const;
[[nodiscard]] std::string name () const;

//! Number of array dimensions for this variable
[[nodiscard]] int ndim() const;
[[nodiscard]] int ndim () const;

//! Shape of the array (size in each array dimension)
[[nodiscard]] std::vector<size_t> shape() const;
[[nodiscard]] std::vector<size_t> shape () const;

//! Write out the entire variable
void put(const double*) const;
void put(const float*) const;
void put(const int*) const;
void put (const double*) const;
void put (const float*) const;
void put (const int*) const;

//! Write out a slice of data
void
put(const double*,
const std::vector<size_t>&,
const std::vector<size_t>&) const;
put (const double*,
const std::vector<size_t>&,
const std::vector<size_t>&) const;

//! Write out a slice of data with with strides (see hyperslab definition in
//! NetCDF)
void
put(const double*,
const std::vector<size_t>&,
const std::vector<size_t>&,
const std::vector<ptrdiff_t>&) const;
put (const double*,
const std::vector<size_t>&,
const std::vector<size_t>&,
const std::vector<ptrdiff_t>&) const;
//! Write out a slice of data
void
put(const float*,
const std::vector<size_t>&,
const std::vector<size_t>&) const;
put (const float*,
const std::vector<size_t>&,
const std::vector<size_t>&) const;

//! Write out a slice of data with with strides (see hyperslab definition in
//! NetCDF)
void
put(const float*,
const std::vector<size_t>&,
const std::vector<size_t>&,
const std::vector<ptrdiff_t>&) const;
put (const float*,
const std::vector<size_t>&,
const std::vector<size_t>&,
const std::vector<ptrdiff_t>&) const;

void put (const int*, const std::vector<size_t>&, const std::vector<size_t>&) const;

void put(const int*, const std::vector<size_t>&, const std::vector<size_t>&) const;
void
put(const int*,
const std::vector<size_t>&,
const std::vector<size_t>&,
const std::vector<ptrdiff_t>&) const;
put (const int*,
const std::vector<size_t>&,
const std::vector<size_t>&,
const std::vector<ptrdiff_t>&) const;

void put (const char**, const std::vector<size_t>&, const std::vector<size_t>&) const;

void put(const char**, const std::vector<size_t>&, const std::vector<size_t>&) const;
void
put(
const char** dptr,
const std::vector<size_t>& start,
const std::vector<size_t>& count,
const std::vector<ptrdiff_t>& stride) const;
put (const char** dptr,
const std::vector<size_t>& start,
const std::vector<size_t>& count,
const std::vector<ptrdiff_t>& stride) const;

//! Read the entire variable from file
void get(double*) const;
void get(float*) const;
void get(int*) const;
void get (double*) const;
void get (float*) const;
void get (int*) const;

//! Read a chunk of data from the file
void
get(double*, const std::vector<size_t>&, const std::vector<size_t>&) const;
get (double*, const std::vector<size_t>&, const std::vector<size_t>&) const;

//! Read a chunk of data with strides
void
get(double*,
const std::vector<size_t>&,
const std::vector<size_t>&,
const std::vector<ptrdiff_t>&) const;
get (double*,
const std::vector<size_t>&,
const std::vector<size_t>&,
const std::vector<ptrdiff_t>&) const;

//! Read a chunk of data from the file
void
get(float*, const std::vector<size_t>&, const std::vector<size_t>&) const;
get (float*, const std::vector<size_t>&, const std::vector<size_t>&) const;

//! Read a chunk of data with strides
void
get(float*,
const std::vector<size_t>&,
const std::vector<size_t>&,
const std::vector<ptrdiff_t>&) const;
get (float*,
const std::vector<size_t>&,
const std::vector<size_t>&,
const std::vector<ptrdiff_t>&) const;

void
get(int*, const std::vector<size_t>&, const std::vector<size_t>&) const;
get (int*, const std::vector<size_t>&, const std::vector<size_t>&) const;

void
get(int*,
const std::vector<size_t>&,
const std::vector<size_t>&,
const std::vector<ptrdiff_t>&) const;
get (int*,
const std::vector<size_t>&,
const std::vector<size_t>&,
const std::vector<ptrdiff_t>&) const;

//! Read a chunk of data from the file
void
get(char*, const std::vector<size_t>&, const std::vector<size_t>&) const;
get (char*, const std::vector<size_t>&, const std::vector<size_t>&) const;

//! Read a chunk of data with strides
void
get(char*,
const std::vector<size_t>&,
const std::vector<size_t>&,
const std::vector<ptrdiff_t>&) const;
get (char*,
const std::vector<size_t>&,
const std::vector<size_t>&,
const std::vector<ptrdiff_t>&) const;

[[nodiscard]] bool has_attr (const std::string& name) const;

void put_attr (const std::string& name, const std::string& value) const;

[[nodiscard]] bool has_attr(const std::string& name) const;
void put_attr(const std::string& name, const std::string& value) const;
void
put_attr(const std::string& name, const std::vector<double>& value) const;
put_attr (const std::string& name, const std::vector<double>& value) const;

void
put_attr(const std::string& name, const std::vector<float>& value) const;
void put_attr(const std::string& name, const std::vector<int>& value) const;

[[nodiscard]] std::string get_attr(const std::string& name) const;
void get_attr(const std::string& name, std::vector<double>& value) const;
void get_attr(const std::string& name, std::vector<float>& value) const;
void get_attr(const std::string& name, std::vector<int>& value) const;
void par_access(int cmode) const; //Uncomment for parallel NetCDF
put_attr (const std::string& name, const std::vector<float>& value) const;

void put_attr (const std::string& name, const std::vector<int>& value) const;

[[nodiscard]] std::string get_attr (const std::string& name) const;

void get_attr (const std::string& name, std::vector<double>& value) const;
void get_attr (const std::string& name, std::vector<float>& value) const;
void get_attr (const std::string& name, std::vector<int>& value) const;

void par_access (int cmode) const; //Uncomment for parallel NetCDF
};

//! Representation of a NetCDF group
Expand All @@ -182,99 +190,97 @@ public:
const int ncid;

//! Name of this group
[[nodiscard]] std::string name() const;
[[nodiscard]] std::string name () const;

//! Full name for this group
[[nodiscard]] std::string full_name() const;
[[nodiscard]] std::string full_name () const;

//! Number of sub-groups within this group
[[nodiscard]] int num_groups() const;
[[nodiscard]] int num_groups () const;

//! Number of dimensions in this group
[[nodiscard]] int num_dimensions() const;
[[nodiscard]] int num_dimensions () const;

//! Number of variables within this group
[[nodiscard]] int num_variables() const;
[[nodiscard]] int num_variables () const;

//! Number of attributes within this group
[[nodiscard]] int num_attributes() const;
[[nodiscard]] int num_attributes () const;

//! Check if a group exists
[[nodiscard]] bool has_group(const std::string&) const;
[[nodiscard]] bool has_group (const std::string&) const;

//! Check if a dimension exists by name
[[nodiscard]] bool has_dim(const std::string&) const;
[[nodiscard]] bool has_dim (const std::string&) const;

//! Check if a variable exists by name
[[nodiscard]] bool has_var(const std::string&) const;
[[nodiscard]] bool has_var (const std::string&) const;

//! Check if an attribute exists
[[nodiscard]] bool has_attr(const std::string&) const;
[[nodiscard]] bool has_attr (const std::string&) const;

/** Get the group by name
*
* Throws error if the group doesn't exist, use `has_group` to check
*/
[[nodiscard]] NCGroup group(const std::string&) const;
[[nodiscard]] NCGroup group (const std::string&) const;

//! Get the dimension instance by name
[[nodiscard]] NCDim dim(const std::string&) const;
[[nodiscard]] NCDim dim (const std::string&) const;

//! Get the variable instance by name
[[nodiscard]] NCVar var(const std::string&) const;
[[nodiscard]] NCVar var (const std::string&) const;

//! Define new group
[[nodiscard]] NCGroup def_group(const std::string&) const;
[[nodiscard]] NCGroup def_group (const std::string&) const;

//! Define new dimension
[[nodiscard]] NCDim def_dim(const std::string&, size_t len) const;
[[nodiscard]] NCDim def_dim (const std::string&, size_t len) const;

//! Define a scalar variable, i.e., 0-dimensional array
[[nodiscard]] NCVar def_scalar(const std::string& name, nc_type dtype) const;
[[nodiscard]] NCVar def_scalar (const std::string& name, nc_type dtype) const;

//! Define an array
[[nodiscard]] NCVar def_array(
const std::string& name,
nc_type dtype,
const std::vector<std::string>&) const;
[[nodiscard]] NCVar def_array (const std::string& name,
nc_type dtype,
const std::vector<std::string>&) const;

//! Define a variable (wrapper for def_array)
[[nodiscard]] NCVar def_var(
const std::string& name,
const nc_type dtype,
const std::vector<std::string>& dnames) const
[[nodiscard]] NCVar def_var (const std::string& name,
const nc_type dtype,
const std::vector<std::string>& dnames) const
{
return def_array(name, dtype, dnames);
}

void put_attr(const std::string& name, const std::string& value) const;
void put_attr(const std::string& name, const std::vector<double>& value) const;
void put_attr(const std::string& name, const std::vector<float>& value) const;
void put_attr(const std::string& name, const std::vector<int>& value) const;
void put_attr (const std::string& name, const std::string& value) const;
void put_attr (const std::string& name, const std::vector<double>& value) const;
void put_attr (const std::string& name, const std::vector<float>& value) const;
void put_attr (const std::string& name, const std::vector<int>& value) const;

[[nodiscard]] std::string get_attr(const std::string& name) const;
void get_attr(const std::string& name, std::vector<double>& value) const;
void get_attr(const std::string& name, std::vector<float>& value) const;
void get_attr(const std::string& name, std::vector<int>& value) const;
[[nodiscard]] std::string get_attr (const std::string& name) const;
void get_attr (const std::string& name, std::vector<double>& value) const;
void get_attr (const std::string& name, std::vector<float>& value) const;
void get_attr (const std::string& name, std::vector<int>& value) const;

//! Return a list of all groups defined in this group
[[nodiscard]] std::vector<NCGroup> all_groups() const;
[[nodiscard]] std::vector<NCGroup> all_groups () const;

//! Return a list of all dimensions defined in this group
[[nodiscard]] std::vector<NCDim> all_dims() const;
[[nodiscard]] std::vector<NCDim> all_dims () const;

//! Return a list of all variables defined in this group
[[nodiscard]] std::vector<NCVar> all_vars() const;
[[nodiscard]] std::vector<NCVar> all_vars () const;

//! Enter definition mode (not needed for NetCDF4 format)
void enter_def_mode() const;
void enter_def_mode () const;

//! Exit definition mode
void exit_def_mode() const;
void exit_def_mode () const;

protected:
NCGroup(const int id) : ncid(id) {}
NCGroup(const int id, const NCGroup* /*par*/) : ncid(id) {}
NCGroup (const int id) : ncid(id) {}
NCGroup (const int id, const NCGroup* /*par*/) : ncid(id) {}
};

/** Representation of a NetCDF file
Expand All @@ -285,28 +291,26 @@ class NCFile : public NCGroup
{
public:
static NCFile
create(const std::string& name, const int cmode = NC_CLOBBER | NC_NETCDF4);
create (const std::string& name, const int cmode = NC_CLOBBER | NC_NETCDF4);

static NCFile open(const std::string& name, const int cmode = NC_NOWRITE);
static NCFile open (const std::string& name, const int cmode = NC_NOWRITE);

static NCFile create_par(
const std::string& name,
const int cmode = NC_CLOBBER | NC_NETCDF4 | NC_MPIIO,
MPI_Comm comm = MPI_COMM_WORLD,
MPI_Info info = MPI_INFO_NULL);
static NCFile create_par (const std::string& name,
const int cmode = NC_CLOBBER | NC_NETCDF4 | NC_MPIIO,
MPI_Comm comm = MPI_COMM_WORLD,
MPI_Info info = MPI_INFO_NULL);

static NCFile open_par(
const std::string& name,
const int cmode = NC_NOWRITE,
MPI_Comm comm = MPI_COMM_WORLD,
MPI_Info info = MPI_INFO_NULL);
static NCFile open_par (const std::string& name,
const int cmode = NC_NOWRITE,
MPI_Comm comm = MPI_COMM_WORLD,
MPI_Info info = MPI_INFO_NULL);

~NCFile();
~NCFile ();

void close();
void close ();

protected:
NCFile(const int id) : NCGroup(id), is_open{true} {}
NCFile (const int id) : NCGroup(id), is_open{true} {}

bool is_open{false};
};
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