int
main(int argc, char **argv)
{ /* create tst_classic_fills.nc */
printf("\n*** Testing fill values.\n");
printf("*** testing read of string record var with no data...");
{
#define STRING_VAR_NAME "blood_toil_tears_sweat"
#define NDIMS_STRING 1
#define DATA_START 1 /* Real data here. */
int ncid, varid, dimid, varid_in;
const char *data_out[1] = {
"We have before us an ordeal of the most grievous kind. We have before "
"us many, many long months of struggle and of suffering. You ask, what "
"is our policy? I can say: It is to wage war, by sea, land and air, "
"with all our might and with all the strength that God can give us; to "
"wage war against a monstrous tyranny, never surpassed in the dark, "
"lamentable catalogue of human crime. That is our policy. You ask, what "
"is our aim? "
"I can answer in one word: It is victory, victory at all costs, victory "
"in spite of all terror, victory, however long and hard the road may "
"be; for without victory, there is no survival."};
char *data_in;
size_t index = DATA_START;
/* Create file with a 1D string var. Set its fill value to the
* empty string. */
if (nc_create(FILE_NAME, NC_NETCDF4, &ncid)) ERR;
if (nc_def_dim(ncid, "sentence", NC_UNLIMITED, &dimid)) ERR;
if (nc_def_var(ncid, STRING_VAR_NAME, NC_STRING, NDIMS_STRING,
&dimid, &varid)) ERR;
/* Check it out. */
if (nc_inq_varid(ncid, STRING_VAR_NAME, &varid_in)) ERR;
/* Write one string, leaving some blank records which will then
* get the fill value. */
if (nc_put_var1_string(ncid, varid_in, &index, data_out)) ERR;
/* Get all the data from the variable. */
if (nc_get_var1_string(ncid, varid_in, &index, &data_in)) ERR;
if (strcmp(data_in, data_out[0])) ERR;
free(data_in);
if (nc_close(ncid)) ERR;
/* Now re-open file, read data, and check values again. */
if (nc_open(FILE_NAME, NC_NOWRITE, &ncid)) ERR;
data_in = NULL;
if (nc_get_var1_string(ncid, varid_in, &index, &data_in)) ERR;
if (strcmp(data_in, data_out[0])) ERR;
free(data_in);
if (nc_close(ncid)) ERR;
}
SUMMARIZE_ERR;
printf("*** testing read of string record var w/fill-value with no data...");
{
#undef STRING_VAR_NAME
#define STRING_VAR_NAME "I_Have_A_Dream"
#undef NDIMS_STRING
#define NDIMS_STRING 1
#define FILLVALUE_LEN 1 /* There is 1 string, the empty one. */
#undef DATA_START
#define DATA_START 2 /* Real data here. */
int ncid, varid, dimid, varid_in;
const char *missing_val[FILLVALUE_LEN] = {""};
const char *missing_val_in[FILLVALUE_LEN];
const char *data_out[1] = {
"With this faith, we will be able to hew out of the mountain of "
"despair a stone of hope. With this faith, we will be able to "
"transform the jangling discords of our nation into a beautiful "
"symphony of brotherhood. With this faith, we will be able to work "
"together, to pray together, to struggle together, to go to jail "
"together, to stand up for freedom together, knowing that we will "
"be free one day."};
char *data_in;
size_t index = DATA_START;
/* Create file with a 1D string var. Set its fill value to the
* empty string. */
if (nc_create(FILE_NAME, NC_NETCDF4, &ncid)) ERR;
if (nc_def_dim(ncid, "sentence", NC_UNLIMITED, &dimid)) ERR;
if (nc_def_var(ncid, STRING_VAR_NAME, NC_STRING, NDIMS_STRING,
&dimid, &varid)) ERR;
if (nc_put_att_string(ncid, varid, "_FillValue", FILLVALUE_LEN,
missing_val)) ERR;
/* Check it out. */
if (nc_inq_varid(ncid, STRING_VAR_NAME, &varid_in)) ERR;
if (nc_get_att_string(ncid, varid_in, "_FillValue",
(char **)missing_val_in)) ERR;
if (strcmp(missing_val[0], missing_val_in[0])) ERR;
if (nc_free_string(FILLVALUE_LEN, (char **)missing_val_in)) ERR;
/* Write one string, leaving some blank records which will then
* get the fill value. */
if (nc_put_var1_string(ncid, varid_in, &index, data_out)) ERR;
/* Get all the data from the variable. */
index = 0;
data_in = NULL;
if (nc_get_var1_string(ncid, varid_in, &index, &data_in)) ERR;
if (strcmp(data_in, missing_val[0])) ERR;
free(data_in);
index = 1;
data_in = NULL;
if (nc_get_var1_string(ncid, varid_in, &index, &data_in)) ERR;
if (strcmp(data_in, missing_val[0])) ERR;
free(data_in);
index = DATA_START;
data_in = NULL;
if (nc_get_var1_string(ncid, varid_in, &index, &data_in)) ERR;
if (strcmp(data_in, data_out[0])) ERR;
free(data_in);
if (nc_close(ncid)) ERR;
/* Now re-open file, read data, and check values again. */
if (nc_open(FILE_NAME, NC_NOWRITE, &ncid)) ERR;
if (nc_inq_varid(ncid, STRING_VAR_NAME, &varid_in)) ERR;
if (nc_get_att_string(ncid, varid_in, "_FillValue",
(char **)missing_val_in)) ERR;
if (strcmp(missing_val[0], missing_val_in[0])) ERR;
if (nc_free_string(FILLVALUE_LEN, (char **)missing_val_in)) ERR;
/* Get all the data from the variable. */
/* As of HDF5-1.8.12, reading from an unwritten chunk in a dataset with a
* variable-length datatype and a fill-value set will error, instead
* of retrieving the fill-value. -QAK
*/
#ifdef NOT_YET
index = 0;
data_in = NULL;
if (nc_get_var1_string(ncid, varid_in, &index, &data_in)) ERR;
if (strcmp(data_in, missing_val[0])) ERR;
free(data_in);
index = 1;
data_in = NULL;
if (nc_get_var1_string(ncid, varid_in, &index, &data_in)) ERR;
if (strcmp(data_in, missing_val[0])) ERR;
free(data_in);
#endif /* NOT_YET */
index = DATA_START;
data_in = NULL;
if (nc_get_var1_string(ncid, varid_in, &index, &data_in)) ERR;
if (strcmp(data_in, data_out[0])) ERR;
free(data_in);
if (nc_close(ncid)) ERR;
}
SUMMARIZE_ERR;
/* printf("*** testing empty fill values of a string var..."); */
/* { */
/* #define STRING_VAR_NAME "The_String" */
/* #define NDIMS_STRING 1 */
/* #define FILLVALUE_LEN 1 /\* There is 1 string, the empty one. *\/ */
/* #define DATA_START 2 /\* Real data here. *\/ */
/* int ncid, varid, dimid, varid_in; */
/* const char *missing_val[FILLVALUE_LEN] = {""}; */
/* const char *missing_val_in[FILLVALUE_LEN]; */
/* const char *data_out[1] = {"The evil that men do lives after them; " */
/* "the good is oft interred with their bones."}; */
/* char **data_in; */
/* size_t index = DATA_START; */
/* int i; */
/* /\* Create file with a 1D string var. Set its fill value to the */
/* * empty string. *\/ */
/* if (nc_create(FILE_NAME, NC_NETCDF4, &ncid)) ERR; */
/* if (nc_def_dim(ncid, "rec", NC_UNLIMITED, &dimid)) ERR; */
/* if (nc_def_var(ncid, STRING_VAR_NAME, NC_STRING, NDIMS_STRING, &dimid, &varid)) ERR; */
/* if (nc_put_att_string(ncid, varid, "_FillValue", FILLVALUE_LEN, missing_val)) ERR; */
/* /\* Check it out. *\/ */
/* if (nc_inq_varid(ncid, STRING_VAR_NAME, &varid_in)) ERR; */
/* if (nc_get_att_string(ncid, varid_in, "_FillValue", (char **)missing_val_in)) ERR; */
/* if (strcmp(missing_val[0], missing_val_in[0])) ERR; */
/* if (nc_free_string(FILLVALUE_LEN, (char **)missing_val_in)) ERR; */
/* /\* Write one string, leaving some blank records which will then */
/* * get the fill value. *\/ */
/* if (nc_put_var1_string(ncid, varid_in, &index, data_out)) ERR; */
/* /\* Get all the data from the variable. *\/ */
/* if (!(data_in = malloc((DATA_START + 1) * sizeof(char *)))) ERR; */
/* if (nc_get_var_string(ncid, varid_in, data_in)) ERR; */
/* /\* First there should be fill values, then the data value we */
/* * wrote. *\/ */
/* for (i = 0; i < DATA_START; i++) */
/* if (strcmp(data_in[i], "")) ERR; */
/* if (strcmp(data_in[DATA_START], data_out[0])) ERR; */
/* /\* Close everything up. Don't forget to free the string! *\/ */
/* if (nc_free_string(DATA_START + 1, data_in)) ERR; */
/* if (nc_close(ncid)) ERR; */
/* /\* Now re-open file, read data, and check values again. *\/ */
/* if (nc_open(FILE_NAME, NC_NOWRITE, &ncid)) ERR; */
/* if (nc_inq_varid(ncid, STRING_VAR_NAME, &varid_in)) ERR; */
/* if (nc_get_att_string(ncid, varid_in, "_FillValue", (char **)missing_val_in)) ERR; */
/* if (strcmp(missing_val[0], missing_val_in[0])) ERR; */
/* /\*if (nc_free_string(FILLVALUE_LEN, (char **)missing_val_in[0])) ERR;*\/ */
/* if (nc_close(ncid)) ERR; */
/* free(data_in); */
/* } */
/* SUMMARIZE_ERR; */
/* printf("*** testing non-empty fill values of a string var..."); */
/* { */
/* #define STRING_VAR_NAME2 "CASSIUS" */
/* #define FILLVALUE_LEN2 1 /\* There is 1 string in the fillvalue array. *\/ */
/* #define DATA_START2 9 /\* Real data starts here. *\/ */
/* int ncid, varid, dimid, varid_in; */
/* const char *missing_val[FILLVALUE_LEN2] = {"I know that virtue to be in you, Brutus"}; */
/* const char *missing_val_in[FILLVALUE_LEN2]; */
/* const char *data_out[1] = {"The evil that men do lives after them; " */
/* "the good is oft interred with their bones."}; */
/* char **data_in; */
/* size_t index = DATA_START2; */
/* int i; */
/* /\* Create file with a 1D string var. Set its fill value to the */
/* * a non-empty string. *\/ */
/* if (nc_create(FILE_NAME, NC_NETCDF4, &ncid)) ERR; */
/* if (nc_def_dim(ncid, "rec", NC_UNLIMITED, &dimid)) ERR; */
/* if (nc_def_var(ncid, STRING_VAR_NAME2, NC_STRING, NDIMS_STRING, &dimid, &varid)) ERR; */
/* if (nc_put_att_string(ncid, varid, "_FillValue", FILLVALUE_LEN2, missing_val)) ERR; */
/* /\* Check it out. *\/ */
/* if (nc_inq_varid(ncid, STRING_VAR_NAME2, &varid_in)) ERR; */
/* if (nc_get_att_string(ncid, varid_in, "_FillValue", (char **)missing_val_in)) ERR; */
/* if (strcmp(missing_val[0], missing_val_in[0])) ERR; */
/* if (nc_free_string(FILLVALUE_LEN2, (char **)missing_val_in)) ERR; */
/* /\* Write one string, leaving some blank records which will then */
/* * get the fill value. *\/ */
/* if (nc_put_var1_string(ncid, varid_in, &index, data_out)) ERR; */
/* /\* Get all the data from the variable. *\/ */
/* if (!(data_in = malloc((DATA_START2 + 1) * sizeof(char *)))) ERR; */
/* if (nc_get_var_string(ncid, varid_in, data_in)) ERR; */
/* /\* First there should be fill values, then the data value we */
/* * wrote. *\/ */
/* for (i = 0; i < DATA_START2; i++) */
/* if (strcmp(data_in[i], missing_val[0])) ERR; */
/* if (strcmp(data_in[DATA_START2], data_out[0])) ERR; */
/* /\* Close everything up. *\/ */
/* if (nc_close(ncid)) ERR; */
/* /\* Now re-open file, read data, and check values again. *\/ */
/* if (nc_open(FILE_NAME, NC_NOWRITE, &ncid)) ERR; */
/* if (nc_inq_varid(ncid, STRING_VAR_NAME2, &varid_in)) ERR; */
/* if (nc_get_att_string(ncid, varid_in, "_FillValue", (char **)missing_val_in)) ERR; */
/* if (strcmp(missing_val[0], missing_val_in[0])) ERR; */
/* if (nc_free_string(FILLVALUE_LEN2, (char **)missing_val_in)) ERR; */
/* if (nc_close(ncid)) ERR; */
/* free(data_in); */
/* } */
/* printf("*** testing read of string record var with no data..."); */
/* { */
/* #define STRING_VAR_NAME "Moon_Is_A_Harsh_Mistress" */
/* #define NDIMS_STRING 1 */
/* #define FILLVALUE_LEN 1 /\* There is 1 string, the empty one. *\/ */
/* #define DATA_START 2 /\* Real data here. *\/ */
/* int ncid, varid, dimid, varid_in; */
/* char *missing_val[FILLVALUE_LEN] = {""}; */
/* char *missing_val_in; */
/* /\* Create file with a 1D string var. Set its fill value to the */
/* * empty string. *\/ */
/* if (nc_create(FILE_NAME, NC_NETCDF4, &ncid)) ERR; */
/* if (nc_def_dim(ncid, "Lunar_Years", NC_UNLIMITED, &dimid)) ERR; */
/* if (nc_def_var(ncid, STRING_VAR_NAME, NC_STRING, NDIMS_STRING, */
/* &dimid, &varid)) ERR; */
/* if (nc_put_att_string(ncid, varid, "_FillValue", FILLVALUE_LEN, */
/* missing_val)) ERR; */
/* /\* Check it out. *\/ */
/* if (nc_inq_varid(ncid, STRING_VAR_NAME, &varid_in)) ERR; */
/* if (nc_get_att_string(ncid, varid_in, "_FillValue", &missing_val_in)) ERR; */
/* if (strcmp(missing_val[0], missing_val_in)) ERR; */
/* if (nc_free_string(FILLVALUE_LEN, &missing_val_in)) ERR; */
/* /\* Get all the data from the variable. There is none! *\/ */
/* if (nc_get_var_string(ncid, varid_in, NULL)) ERR; */
/* /\* Close file. *\/ */
/* if (nc_close(ncid)) ERR; */
/* /\* Now re-open file, and check again. *\/ */
/* if (nc_open(FILE_NAME, NC_NOWRITE, &ncid)) ERR; */
/* if (nc_inq_varid(ncid, STRING_VAR_NAME, &varid_in)) ERR; */
/* if (nc_get_att_string(ncid, varid_in, "_FillValue", &missing_val_in)) ERR; */
/* if (strcmp(missing_val[0], missing_val_in)) ERR; */
/* if (nc_free_string(FILLVALUE_LEN, &missing_val_in)) ERR; */
/* if (nc_close(ncid)) ERR; */
/* } */
/* SUMMARIZE_ERR; */
FINAL_RESULTS;
}
int main(int argc, char* argv[])
{
program_name = argv[0];
if (argc < 3) {
print_help();
exit(EXIT_FAILURE);
}
char binfile[50];
base = argv[1];
strapp(binfile, ".nc");
int total_ids = atoi(argv[2]);
FILE *fp;
if (argc > 2) {
infile = argv[3];
fp = fopen(infile, "r");
if (!fp)
error(1, errno, "%s", infile);
} else {
infile = "stdin";
fp = stdin;
}
/* Get the first line with the SNP names */
char *line = NULL;
size_t n = 0;
int read = getlin(&line, &n, fp);
if (read == -1)
error(1, errno, "%s", infile);
int nsnps = getsnps(line);
free(line);
line = NULL;
printf("%d markers\n", nsnps);
printf("Converting intensity values to binary\n");
int ncid, stat, sampid, varid;
size_t nids = 0, perkey;
size_t count[3] = { 1, 0, 0 };
size_t start[3] = { 0, 0, 0 };
char *id;
float *vals;
while (getlin(&line, &n, fp) != -1) {
if (nids == 0) {
/* Count number of vals in first line to alloc indv_dat */
read = getstrings(line, NULL, DELIM) - 1;
if (read < 1)
error(2, 0, "No values found");
if (read % nsnps != 0)
error(2, 0, "Not same number of values for each marker");
perkey = read / nsnps;
printf("%zu values per marker\n", perkey);
vals = malloc(sizeof(float) * read);
if (vals == NULL)
error(1, errno, "dat.vals");
/* Create netcdf file and write snp names */
ncid = create_nc(binfile, total_ids, nsnps, perkey);
stat = nc_inq_varid(ncid, "sample", &sampid);
check_err(stat,__LINE__,__FILE__);
stat = nc_inq_varid(ncid, "intensity", &varid);
check_err(stat,__LINE__,__FILE__);
writesnps(ncid, nsnps);
count[1] = nsnps;
count[2] = perkey;
}
/* Read valuess from line */
id = linevals(line, vals);
/* Write sample id */
stat = nc_put_var1_string(ncid, sampid, &nids, (const char **) &id);
check_err(stat,__LINE__,__FILE__);
/* Write intensity values */
start[0] = nids;
stat = nc_put_vara_float(ncid, varid, start, count, vals);
check_err(stat,__LINE__,__FILE__);
free(line);
line = NULL;
nids++;
printf("Read %zu\r", nids);
fflush(stdout);
}
fclose(fp);
stat = nc_close(ncid);
check_err(stat,__LINE__,__FILE__);
free(vals);
free(line);
printf("Wrote %zu samples to [ %s ]\n", nids, binfile);
exit(EXIT_SUCCESS);
}
int mov_session::save()
{
int ierr,ncid,i;
int dimid_ntimeseries,dimid_one;
int varid_filename,varid_colors,varid_units,varid_names;
int varid_xshift,varid_yshift,varid_type,varid_coldstart;
int varid_stationfile,varid_plottitle,varid_xlabel,varid_ylabel;
int varid_startdate,varid_enddate,varid_precision,varid_ymin,varid_ymax;
int varid_autodate,varid_autoy,varid_checkState;
int dims_1d[1];
int nTimeseries;
QString relPath,TempFile,Directory,tempString;
QByteArray tempByte;
size_t start[1];
size_t iu;
double mydatadouble[1];
int mydataint[1];
const char * mydatastring[1];
QFile Session(this->sessionFileName);
QVector<QString> filenames_ts;
QVector<QString> filetype_ts;
QVector<QString> colors_ts;
QVector<double> units_ts;
QVector<QString> seriesname_ts;
QVector<double> xshift_ts;
QVector<double> yshift_ts;
QVector<QString> date_ts;
QVector<QString> stationfile_ts;
QVector<int> checkStates_ts;
//Remove the old file
if(Session.exists())
Session.remove();
//Get the path of the session file so we can save a relative path later
mov_generic::splitPath(this->sessionFileName,TempFile,Directory);
QDir CurrentDir(Directory);
ierr = mov_generic::NETCDF_ERR(nc_create(this->sessionFileName.toUtf8(),NC_NETCDF4,&ncid));
if(ierr!=NC_NOERR)return 1;
//Start setting up the definitions
nTimeseries = this->tableWidget->rowCount();
filenames_ts.resize(nTimeseries);
colors_ts.resize(nTimeseries);
units_ts.resize(nTimeseries);
seriesname_ts.resize(nTimeseries);
xshift_ts.resize(nTimeseries);
yshift_ts.resize(nTimeseries);
date_ts.resize(nTimeseries);
stationfile_ts.resize(nTimeseries);
filetype_ts.resize(nTimeseries);
checkStates_ts.resize(nTimeseries);
for(i=0;i<nTimeseries;i++)
{
filenames_ts[i] = this->tableWidget->item(i,6)->text();
seriesname_ts[i] = this->tableWidget->item(i,1)->text();
colors_ts[i] = this->tableWidget->item(i,2)->text();
units_ts[i] = this->tableWidget->item(i,3)->text().toDouble();
xshift_ts[i] = this->tableWidget->item(i,4)->text().toDouble();
yshift_ts[i] = this->tableWidget->item(i,5)->text().toDouble();
date_ts[i] = this->tableWidget->item(i,7)->text();
filetype_ts[i] = this->tableWidget->item(i,8)->text();
stationfile_ts[i] = this->tableWidget->item(i,10)->text();
if(this->tableWidget->item(i,0)->checkState()==Qt::Checked)
checkStates_ts[i] = 1;
else
checkStates_ts[i] = 0;
}
ierr = mov_generic::NETCDF_ERR(nc_def_dim(ncid,"ntimeseries",static_cast<size_t>(nTimeseries),&dimid_ntimeseries));
if(ierr!=NC_NOERR)return 1;
ierr = mov_generic::NETCDF_ERR(nc_def_dim(ncid,"one",1,&dimid_one));
if(ierr!=NC_NOERR)return 1;
//Arrays
dims_1d[0] = dimid_ntimeseries;
ierr = mov_generic::NETCDF_ERR(nc_def_var(ncid,"timeseries_filename",NC_STRING,1,dims_1d,&varid_filename));
if(ierr!=NC_NOERR)return 1;
ierr = mov_generic::NETCDF_ERR(nc_def_var(ncid,"timeseries_colors",NC_STRING,1,dims_1d,&varid_colors));
if(ierr!=NC_NOERR)return 1;
ierr = mov_generic::NETCDF_ERR(nc_def_var(ncid,"timeseries_names",NC_STRING,1,dims_1d,&varid_names));
if(ierr!=NC_NOERR)return 1;
ierr = mov_generic::NETCDF_ERR(nc_def_var(ncid,"timeseries_filetype",NC_STRING,1,dims_1d,&varid_type));
if(ierr!=NC_NOERR)return 1;
ierr = mov_generic::NETCDF_ERR(nc_def_var(ncid,"timeseries_coldstartdate",NC_STRING,1,dims_1d,&varid_coldstart));
if(ierr!=NC_NOERR)return 1;
ierr = mov_generic::NETCDF_ERR(nc_def_var(ncid,"timeseries_stationfile",NC_STRING,1,dims_1d,&varid_stationfile));
if(ierr!=NC_NOERR)return 1;
ierr = mov_generic::NETCDF_ERR(nc_def_var(ncid,"timeseries_xshift",NC_DOUBLE,1,dims_1d,&varid_xshift));
if(ierr!=NC_NOERR)return 1;
ierr = mov_generic::NETCDF_ERR(nc_def_var(ncid,"timeseries_yshift",NC_DOUBLE,1,dims_1d,&varid_yshift));
if(ierr!=NC_NOERR)return 1;
ierr = mov_generic::NETCDF_ERR(nc_def_var(ncid,"timeseries_units",NC_DOUBLE,1,dims_1d,&varid_units));
if(ierr!=NC_NOERR)return 1;
ierr = mov_generic::NETCDF_ERR(nc_def_var(ncid,"timeseries_checkState",NC_INT,1,dims_1d,&varid_checkState));
if(ierr!=NC_NOERR)return 1;
//Scalars
dims_1d[0] = dimid_one;
ierr = mov_generic::NETCDF_ERR(nc_def_var(ncid,"timeseries_plottitle",NC_STRING,1,dims_1d,&varid_plottitle));
if(ierr!=NC_NOERR)return 1;
ierr = mov_generic::NETCDF_ERR(nc_def_var(ncid,"timeseries_xlabel",NC_STRING,1,dims_1d,&varid_xlabel));
if(ierr!=NC_NOERR)return 1;
ierr = mov_generic::NETCDF_ERR(nc_def_var(ncid,"timeseries_ylabel",NC_STRING,1,dims_1d,&varid_ylabel));
if(ierr!=NC_NOERR)return 1;
ierr = mov_generic::NETCDF_ERR(nc_def_var(ncid,"timeseries_precision",NC_INT,1,dims_1d,&varid_precision));
if(ierr!=NC_NOERR)return 1;
ierr = mov_generic::NETCDF_ERR(nc_def_var(ncid,"timeseries_startdate",NC_STRING,1,dims_1d,&varid_startdate));
if(ierr!=NC_NOERR)return 1;
ierr = mov_generic::NETCDF_ERR(nc_def_var(ncid,"timeseries_enddate",NC_STRING,1,dims_1d,&varid_enddate));
if(ierr!=NC_NOERR)return 1;
ierr = mov_generic::NETCDF_ERR(nc_def_var(ncid,"timeseries_ymin",NC_DOUBLE,1,dims_1d,&varid_ymin));
if(ierr!=NC_NOERR)return 1;
ierr = mov_generic::NETCDF_ERR(nc_def_var(ncid,"timeseries_ymax",NC_DOUBLE,1,dims_1d,&varid_ymax));
if(ierr!=NC_NOERR)return 1;
ierr = mov_generic::NETCDF_ERR(nc_def_var(ncid,"timeseries_autodate",NC_INT,1,dims_1d,&varid_autodate));
if(ierr!=NC_NOERR)return 1;
ierr = mov_generic::NETCDF_ERR(nc_def_var(ncid,"timeseries_autoy",NC_INT,1,dims_1d,&varid_autoy));
if(ierr!=NC_NOERR)return 1;
ierr = mov_generic::NETCDF_ERR(nc_enddef(ncid));
if(ierr!=NC_NOERR)return 1;
tempByte = this->plotTitleWidget->text().toUtf8();
mydatastring[0] = tempByte.data();
ierr = mov_generic::NETCDF_ERR(nc_put_var_string(ncid,varid_plottitle,mydatastring));
if(ierr!=NC_NOERR)return 1;
tempByte = this->xLabelWidget->text().toUtf8();
mydatastring[0] = tempByte.data();
ierr = mov_generic::NETCDF_ERR(nc_put_var_string(ncid,varid_xlabel,mydatastring));
if(ierr!=NC_NOERR)return 1;
tempByte = this->yLabelWidget->text().toUtf8();
mydatastring[0] = tempByte.data();
ierr = mov_generic::NETCDF_ERR(nc_put_var_string(ncid,varid_ylabel,mydatastring));
if(ierr!=NC_NOERR)return 1;
tempByte = this->startDateEdit->dateTime().toString("yyyy-MM-dd hh:mm:ss").toUtf8();
mydatastring[0] = tempByte.data();
ierr = mov_generic::NETCDF_ERR(nc_put_var_string(ncid,varid_startdate,mydatastring));
if(ierr!=NC_NOERR)return 1;
tempByte = this->endDateEdit->dateTime().toString("yyyy-MM-dd hh:mm:ss").toUtf8();
mydatastring[0] = tempByte.data();
ierr = mov_generic::NETCDF_ERR(nc_put_var_string(ncid,varid_enddate,mydatastring));
if(ierr!=NC_NOERR)return 1;
mydataint[0] = 3;
ierr = mov_generic::NETCDF_ERR(nc_put_var_int(ncid,varid_precision,mydataint));
if(ierr!=NC_NOERR)return 1;
mydatadouble[0] = this->yMinSpinBox->value();
ierr = mov_generic::NETCDF_ERR(nc_put_var_double(ncid,varid_ymin,mydatadouble));
if(ierr!=NC_NOERR)return 1;
mydatadouble[0] = this->yMaxSpinBox->value();
ierr = mov_generic::NETCDF_ERR(nc_put_var_double(ncid,varid_ymax,mydatadouble));
if(ierr!=NC_NOERR)return 1;
if(this->checkAllData->isChecked())
mydataint[0] = 1;
else
mydataint[0] = 0;
ierr = mov_generic::NETCDF_ERR(nc_put_var_int(ncid,varid_autodate,mydataint));
if(ierr!=NC_NOERR)return 1;
if(this->checkYAuto->isChecked())
mydataint[0] = 1;
else
mydataint[0] = 0;
ierr = mov_generic::NETCDF_ERR(nc_put_var_int(ncid,varid_autoy,mydataint));
if(ierr!=NC_NOERR)return 1;
for(iu=0;iu<static_cast<unsigned int>(nTimeseries);iu++)
{
start[0] = iu;
relPath = CurrentDir.relativeFilePath(filenames_ts[iu]);
tempByte = relPath.toUtf8();
mydatastring[0] = tempByte.data();
ierr = mov_generic::NETCDF_ERR(nc_put_var1_string(ncid,varid_filename,start,mydatastring));
if(ierr!=NC_NOERR)return 1;
mydatastring[0] = NULL;
tempString = seriesname_ts[iu];
tempByte = tempString.toUtf8();
mydatastring[0] = tempByte.data();
ierr = mov_generic::NETCDF_ERR(nc_put_var1_string(ncid,varid_names,start,mydatastring));
if(ierr!=NC_NOERR)return 1;
mydatastring[0] = NULL;
tempByte = colors_ts[iu].toUtf8();
mydatastring[0] = tempByte.data();
ierr = mov_generic::NETCDF_ERR(nc_put_var1_string(ncid,varid_colors,start,mydatastring));
if(ierr!=NC_NOERR)return 1;
mydatastring[0] = NULL;
tempByte = date_ts[iu].toUtf8();
mydatastring[0] = tempByte.data();
ierr = mov_generic::NETCDF_ERR(nc_put_var1_string(ncid,varid_coldstart,start,mydatastring));
if(ierr!=NC_NOERR)return 1;
mydatastring[0] = NULL;
relPath = CurrentDir.relativeFilePath(stationfile_ts[iu]);
tempByte = relPath.toUtf8();
mydatastring[0] = tempByte.data();
ierr = mov_generic::NETCDF_ERR(nc_put_var1_string(ncid,varid_stationfile,start,mydatastring));
if(ierr!=NC_NOERR)return 1;
mydatastring[0] = NULL;
tempByte = filetype_ts[iu].toUtf8();
mydatastring[0] = tempByte.data();
ierr = mov_generic::NETCDF_ERR(nc_put_var1_string(ncid,varid_type,start,mydatastring));
if(ierr!=NC_NOERR)return 1;
mydatastring[0] = NULL;
mydatadouble[0] = xshift_ts[iu];
ierr = mov_generic::NETCDF_ERR(nc_put_var1_double(ncid,varid_xshift,start,mydatadouble));
if(ierr!=NC_NOERR)return 1;
mydatadouble[0] = yshift_ts[iu];
ierr = mov_generic::NETCDF_ERR(nc_put_var1_double(ncid,varid_yshift,start,mydatadouble));
if(ierr!=NC_NOERR)return 1;
mydatadouble[0] = units_ts[iu];
ierr = mov_generic::NETCDF_ERR(nc_put_var1_double(ncid,varid_units,start,mydatadouble));
if(ierr!=NC_NOERR)return 1;
mydataint[0] = checkStates_ts[iu];
ierr = mov_generic::NETCDF_ERR(nc_put_var1_int(ncid,varid_checkState,start,mydataint));
if(ierr!=NC_NOERR)return 1;
}
ierr = mov_generic::NETCDF_ERR(nc_close(ncid));
if(ierr!=NC_NOERR)return 1;
}
int
main(int argc, char **argv)
{ /* create tst_classic_fills.nc */
printf("\n*** Testing fill values.\n");
printf("*** testing empty fill values of a string var...");
{
#define STRING_VAR_NAME "The_String"
#define NDIMS_STRING 1
#define FILLVALUE_LEN 1 /* There is 1 string, the empty one. */
#define DATA_START 2 /* Real data here. */
int ncid, varid, dimid, varid_in;
const char *missing_val[FILLVALUE_LEN] = {""};
const char *missing_val_in[FILLVALUE_LEN];
const char *data_out[1] = {"The evil that men do lives after them; "
"the good is oft interred with their bones."};
char **data_in;
size_t index = DATA_START;
int i;
/* Create file with a 1D string var. Set its fill value to the
* empty string. */
if (nc_create(FILE_NAME, NC_NETCDF4, &ncid)) ERR;
if (nc_def_dim(ncid, "rec", NC_UNLIMITED, &dimid)) ERR;
if (nc_def_var(ncid, STRING_VAR_NAME, NC_STRING, NDIMS_STRING, &dimid, &varid)) ERR;
if (nc_put_att_string(ncid, varid, "_FillValue", FILLVALUE_LEN, missing_val)) ERR;
/* Check it out. */
if (nc_inq_varid(ncid, STRING_VAR_NAME, &varid_in)) ERR;
if (nc_get_att_string(ncid, varid_in, "_FillValue", (char **)missing_val_in)) ERR;
if (strcmp(missing_val[0], missing_val_in[0])) ERR;
if (nc_free_string(FILLVALUE_LEN, (char **)missing_val_in)) ERR;
/* Write one string, leaving some blank records which will then
* get the fill value. */
if (nc_put_var1_string(ncid, varid_in, &index, data_out)) ERR;
/* Get all the data from the variable. */
if (!(data_in = malloc((DATA_START + 1) * sizeof(char *)))) ERR;
if (nc_get_var_string(ncid, varid_in, data_in)) ERR;
/* First there should be fill values, then the data value we
* wrote. */
for (i = 0; i < DATA_START; i++)
if (strcmp(data_in[i], "")) ERR;
if (strcmp(data_in[DATA_START], data_out[0])) ERR;
/* Close everything up. */
if (nc_close(ncid)) ERR;
/* Now re-open file, read data, and check values again. */
if (nc_open(FILE_NAME, NC_NOWRITE, &ncid)) ERR;
if (nc_inq_varid(ncid, STRING_VAR_NAME, &varid_in)) ERR;
if (nc_get_att_string(ncid, varid_in, "_FillValue", (char **)missing_val_in)) ERR;
if (strcmp(missing_val[0], missing_val_in[0])) ERR;
if (nc_free_string(FILLVALUE_LEN, (char **)missing_val_in)) ERR;
if (nc_close(ncid)) ERR;
free(data_in);
}
SUMMARIZE_ERR;
printf("*** testing non-empty fill values of a string var...");
{
#define STRING_VAR_NAME2 "CASSIUS"
#define FILLVALUE_LEN2 1 /* There is 1 string in the fillvalue array. */
#define DATA_START2 9 /* Real data starts here. */
int ncid, varid, dimid, varid_in;
const char *missing_val[FILLVALUE_LEN2] = {"I know that virtue to be in you, Brutus"};
const char *missing_val_in[FILLVALUE_LEN2];
const char *data_out[1] = {"The evil that men do lives after them; "
"the good is oft interred with their bones."};
char **data_in;
size_t index = DATA_START2;
int i;
/* Create file with a 1D string var. Set its fill value to the
* a non-empty string. */
if (nc_create(FILE_NAME, NC_NETCDF4, &ncid)) ERR;
if (nc_def_dim(ncid, "rec", NC_UNLIMITED, &dimid)) ERR;
if (nc_def_var(ncid, STRING_VAR_NAME2, NC_STRING, NDIMS_STRING, &dimid, &varid)) ERR;
if (nc_put_att_string(ncid, varid, "_FillValue", FILLVALUE_LEN2, missing_val)) ERR;
/* Check it out. */
if (nc_inq_varid(ncid, STRING_VAR_NAME2, &varid_in)) ERR;
if (nc_get_att_string(ncid, varid_in, "_FillValue", (char **)missing_val_in)) ERR;
if (strcmp(missing_val[0], missing_val_in[0])) ERR;
if (nc_free_string(FILLVALUE_LEN2, (char **)missing_val_in)) ERR;
/* Write one string, leaving some blank records which will then
* get the fill value. */
if (nc_put_var1_string(ncid, varid_in, &index, data_out)) ERR;
/* Get all the data from the variable. */
if (!(data_in = malloc((DATA_START2 + 1) * sizeof(char *)))) ERR;
if (nc_get_var_string(ncid, varid_in, data_in)) ERR;
/* First there should be fill values, then the data value we
* wrote. */
for (i = 0; i < DATA_START2; i++)
if (strcmp(data_in[i], missing_val[0])) ERR;
if (strcmp(data_in[DATA_START2], data_out[0])) ERR;
/* Close everything up. */
if (nc_close(ncid)) ERR;
/* Now re-open file, read data, and check values again. */
if (nc_open(FILE_NAME, NC_NOWRITE, &ncid)) ERR;
if (nc_inq_varid(ncid, STRING_VAR_NAME2, &varid_in)) ERR;
if (nc_get_att_string(ncid, varid_in, "_FillValue", (char **)missing_val_in)) ERR;
if (strcmp(missing_val[0], missing_val_in[0])) ERR;
if (nc_free_string(FILLVALUE_LEN2, (char **)missing_val_in)) ERR;
if (nc_close(ncid)) ERR;
free(data_in);
}
SUMMARIZE_ERR;
printf("*** testing fill values of one var...");
{
#define V1_NAME "v1"
#define MAX_VALS 10
int ncid, varid, rec_id, dims[2];
static int rec[1] = {1};
size_t start[2] = {0, 0};
size_t count[2] = {1, MAX_VALS};
char vals[MAX_VALS];
int i;
if (nc_create(FILE_NAME, NC_NETCDF4, &ncid)) ERR;
/* Define dimensions and two vars, a 1D coordinate var for
* unlimited dimension, and a 2D var which uses the unlimited
* dimension. */
if (nc_def_dim(ncid, "rec", NC_UNLIMITED, &dims[0])) ERR;
if (nc_def_dim(ncid, "len", MAX_VALS, &dims[1])) ERR;
if (nc_def_var(ncid, "rec", NC_INT, 1, dims, &rec_id)) ERR;
if (nc_def_var(ncid, V1_NAME, NC_CHAR, 2, dims, &varid)) ERR;
/* Extend record dimension by 1. */
if (nc_put_vara_int(ncid, rec_id, start, count, rec)) ERR;
/* Read the other variable; it must have only fill values. */
if (nc_get_vara_text(ncid, 1, start, count, vals)) ERR;
for (i = 0; i < MAX_VALS; i++)
if(vals[i] != NC_FILL_CHAR) ERR;
if (nc_close(ncid)) ERR;
/* Now re-open file, read data, and check values again. */
if (nc_open(FILE_NAME, NC_NOWRITE, &ncid)) ERR;
/* Read the other variable; it must have only fill values. */
if (nc_get_vara_text(ncid, 1, start, count, vals)) ERR;
for (i = 0; i < MAX_VALS; i++)
if(vals[i] != NC_FILL_CHAR) ERR;
if(nc_close(ncid)) ERR;
}
SUMMARIZE_ERR;
printf("*** testing fill values of lots of vars...");
{
int ncid; /* netCDF id */
#define NVALS 10 /* values per fixed-size variable or record */
#define NFIXVARS 6 /* number of fixed-size vars, one of each type */
#define NRECVARS 6 /* number of record vars, one of each type */
#define RANK_REC 1
#define RANK_FIXVARS 1
#define RANK_RECVARS 2
/* dimension ids */
int rec_dim;
int len_dim;
/* dimension lengths */
size_t rec_len = NC_UNLIMITED;
size_t len_len = NVALS;
/* variable ids */
int rec_id;
int fixvar_ids[NFIXVARS];
int recvar_ids[NRECVARS];
int rec_dims[RANK_REC];
int fixvar_dims[RANK_FIXVARS];
int recvar_dims[RANK_RECVARS];
int fixvar, recvar, i;
char *fnames[] = {"c", "b", "s", "i", "f", "d"};
char *rnames[] = {"cr", "br", "sr", "ir", "fr", "dr"};
nc_type types[] = {NC_CHAR, NC_BYTE, NC_SHORT, NC_INT, NC_FLOAT, NC_DOUBLE};
/*if (nc_set_default_format(format + 1, NULL)) ERR;*/
if (nc_create(FILE_NAME, NC_NETCDF4, &ncid)) ERR;
/* define dimensions */
if (nc_def_dim(ncid, "rec", rec_len, &rec_dim)) ERR;
if (nc_def_dim(ncid, "len", len_len, &len_dim)) ERR;
rec_dims[0] = rec_dim;
if (nc_def_var(ncid, "rec", NC_INT, RANK_REC, rec_dims, &rec_id)) ERR;
/* define fixed and record variables of all 6 primitive types */
fixvar_dims[0] = len_dim;
for (fixvar = 0; fixvar < NFIXVARS; fixvar++)
if (nc_def_var(ncid, fnames[fixvar], types[fixvar], RANK_FIXVARS,
fixvar_dims, &fixvar_ids[fixvar])) ERR;
recvar_dims[0] = rec_dim;
recvar_dims[1] = len_dim;
for (recvar = 0; recvar < NRECVARS; recvar++)
if (nc_def_var(ncid, rnames[recvar], types[recvar], RANK_RECVARS,
recvar_dims, &recvar_ids[recvar])) ERR;
/* leave define mode */
if (nc_enddef(ncid)) ERR;
{ /* store rec */
static size_t rec_start[RANK_REC];
static size_t rec_count[RANK_REC];
static int rec[] = {1};
rec_len = 1; /* number of records of rec data */
rec_start[0] = 0;
rec_count[0] = rec_len;
if (nc_put_vara_int(ncid, rec_id, rec_start, rec_count, rec)) ERR;
}
if (nc_close(ncid)) ERR;
/* Now re-open file, read data, and check values */
if (nc_open(FILE_NAME, NC_NOWRITE, &ncid)) ERR;
/* Check that fixed-size variables are full of fill values */
for (fixvar = 0; fixvar < NFIXVARS; fixvar++) {
int varid;
nc_type type;
if (nc_inq_varid(ncid, fnames[fixvar], &varid)) ERR;
if (nc_inq_vartype(ncid, varid, &type)) ERR;
switch(type) {
case NC_CHAR:
{
char vals[NVALS];
if (nc_get_var_text(ncid, varid, vals)) ERR;
for (i = 0; i < NVALS; i++)
if(vals[i] != NC_FILL_CHAR) ERR;
}
break;
case NC_BYTE:
{
signed char vals[NVALS];
if (nc_get_var_schar(ncid, varid, vals)) ERR;
for (i = 0; i < NVALS; i++)
if(vals[i] != NC_FILL_BYTE) ERR;
}
break;
case NC_SHORT:
{
short vals[NVALS];
if (nc_get_var_short(ncid, varid, vals)) ERR;
for (i = 0; i < NVALS; i++)
if(vals[i] != NC_FILL_SHORT) ERR;
}
break;
case NC_INT:
{
int vals[NVALS];
if (nc_get_var_int(ncid, varid, vals)) ERR;
for (i = 0; i < NVALS; i++)
if(vals[i] != NC_FILL_INT) ERR;
}
break;
case NC_FLOAT:
{
float vals[NVALS];
if (nc_get_var_float(ncid, varid, vals)) ERR;
for (i = 0; i < NVALS; i++)
if(vals[i] != NC_FILL_FLOAT) ERR;
}
break;
case NC_DOUBLE:
{
double vals[NVALS];
if (nc_get_var_double(ncid, varid, vals)) ERR;
for (i = 0; i < NVALS; i++)
if (vals[i] != NC_FILL_DOUBLE) ERR;
}
break;
default:
ERR;
}
}
/* Read record, check record variables have only fill values */
for (recvar = 0; recvar < NRECVARS; recvar++) {
int varid;
nc_type type;
size_t start[] = {0, 0};
size_t count[] = {1, NVALS};
if (nc_inq_varid(ncid, rnames[recvar], &varid)) ERR;
if (nc_inq_vartype(ncid, varid, &type)) ERR;
switch(type) {
case NC_CHAR:
{
char vals[NVALS];
if (nc_get_vara_text(ncid, varid, start, count, vals)) ERR;
for (i = 0; i < NVALS; i++)
if(vals[i] != NC_FILL_CHAR) ERR;
}
break;
case NC_BYTE:
{
signed char vals[NVALS];
if (nc_get_vara_schar(ncid, varid, start, count, vals)) ERR;
for (i = 0; i < NVALS; i++)
if(vals[i] != NC_FILL_BYTE) ERR;
}
break;
case NC_SHORT:
{
short vals[NVALS];
if (nc_get_vara_short(ncid, varid, start, count, vals)) ERR;
for (i = 0; i < NVALS; i++)
if(vals[i] != NC_FILL_SHORT) ERR;
}
break;
case NC_INT:
{
int vals[NVALS];
if (nc_get_vara_int(ncid, varid, start, count, vals)) ERR;
for (i = 0; i < NVALS; i++)
if(vals[i] != NC_FILL_INT) ERR;
}
break;
case NC_FLOAT:
{
float vals[NVALS];
if (nc_get_vara_float(ncid, varid, start, count, vals)) ERR;
for (i = 0; i < NVALS; i++)
if(vals[i] != NC_FILL_FLOAT) ERR;
}
break;
case NC_DOUBLE:
{
double vals[NVALS];
if (nc_get_vara_double(ncid, varid, start, count, vals)) ERR;
for (i = 0; i < NVALS; i++)
if(vals[i] != NC_FILL_DOUBLE) ERR;
}
break;
default:
ERR;
}
}
if (nc_close(ncid)) ERR;
}
SUMMARIZE_ERR;
FINAL_RESULTS;
return 0;
}