void getCommandLineParams(t_Params *ptParams,int argc,char *argv[])
{
char *szTemp = NULL;
char *pcError = NULL;
/*get parameter file name*/
ptParams->szDatFile = extractParameter(argc,argv,DAT_FILE,ALWAYS);
if(ptParams->szDatFile == NULL)
goto error;
/*get output filestub*/
ptParams->szTreeFile = extractParameter(argc,argv,TREE_FILE, ALWAYS);
if(ptParams->szTreeFile == NULL)
goto error;
ptParams->szMapFile = extractParameter(argc,argv,MAP_FILE, ALWAYS);
if(ptParams->szMapFile == NULL)
goto error;
szTemp = extractParameter(argc,argv,SPLIT,ALWAYS);
if(szTemp != NULL){
ptParams->nSplit = strtol(szTemp,&pcError,10);
if(*pcError != '\0'){
goto error;
}
}
else{
goto error;
}
szTemp = extractParameter(argc,argv,MIN_SIZE,ALWAYS);
if(szTemp != NULL){
ptParams->nMinSize = strtol(szTemp,&pcError,10);
if(*pcError != '\0'){
goto error;
}
}
else{
goto error;
}
return;
error:
writeUsage(stdout);
exit(EXIT_FAILURE);
}
void getCommandLineParams(t_Params *ptParams,int argc,char *argv[])
{
char *szTemp = NULL;
char *cError = NULL;
/*get parameter file name*/
ptParams->szInputFile = extractParameter(argc,argv, INPUT_FILE,ALWAYS);
if(ptParams->szInputFile == NULL)
goto error;
if(szTemp = extractParameter(argc,argv, LOOKUP_FILE_FLAG, OPTION)){
ptParams->szLookUpFile = szTemp;
}
else{
ptParams->szLookUpFile = getenv("SEQ_LOOKUP_FILE");
if(ptParams->szLookUpFile == NULL){
ptParams->szLookUpFile = LOOKUP_FILE;
}
}
/*identifiers*/
szTemp = extractParameter(argc, argv, IDENT, OPTION);
if(szTemp != NULL){
ptParams->bIdent = TRUE;
}
else{
ptParams->bIdent = FALSE;
}
szTemp = extractParameter(argc, argv, PHYLIP, OPTION);
if(szTemp != NULL){
ptParams->bPhylip = TRUE;
}
else{
ptParams->bPhylip = FALSE;
}
return;
error:
writeUsage(stdout);
exit(EXIT_FAILURE);
}
void getCommandLineParams(t_Params *ptParams,int argc,char *argv[])
{
char *szTemp = NULL;
char *cError = NULL;
/*get parameter file name*/
ptParams->szDataFile = extractParameter(argc,argv, DATA_FILE, ALWAYS);
if(ptParams->szDataFile == NULL)
goto error;
if(extractParameter(argc,argv, NO_INDEX, OPTION)){
ptParams->bNoIndex = TRUE;
}
else{
ptParams->bNoIndex = FALSE;
}
if(szTemp = extractParameter(argc,argv, LOOKUP_FILE_FLAG, OPTION)){
ptParams->szLookUpFile = szTemp;
}
else{
ptParams->szLookUpFile = getenv("PYRO_LOOKUP_FILE");
if(ptParams->szLookUpFile == NULL){
ptParams->szLookUpFile = LOOKUP_FILE;
}
}
ptParams->szOutFileStub = extractParameter(argc,argv, OUT_FILE_STUB, ALWAYS);
if(ptParams->szOutFileStub == NULL)
goto error;
return;
error:
writeUsage(stdout);
exit(EXIT_FAILURE);
}
void ArgumentHelper::handle_error() const {
writeUsage(std::cerr);
//exit(1);
}
bool ArgumentHelper::process(int argc, const char **argv){
name_= argv[0];
++argv;
--argc;
current_unnamed_= unnamed_arguments_.begin();
current_optional_unnamed_= optional_unnamed_arguments_.begin();
for ( int i=0; i< argc; ++i){
if (strcmp(argv[i], "--help") == 0){
writeUsage(std::cout);
exit(0);
}
}
while (argc != 0){
const char* cur_arg= argv[0];
if (cur_arg[0]=='-' && !seen_end_named_){
--argc; ++argv;
if (cur_arg[1]=='-'){
if (cur_arg[2] == '\0') {
//std::cout << "Ending flags " << std::endl;
seen_end_named_=true;
} else {
// long argument
LMap::iterator f= long_names_.find(cur_arg+2);
if ( f != long_names_.end()){
if (!f->second->process(argc, argv)) {
handle_error();
return false;
}
} else {
std::cerr<< "Invalid long argument "<< cur_arg << ".\n";
handle_error();
return false;
}
}
} else {
if (cur_arg[1]=='\0') {
std::cerr << "Invalid argument " << cur_arg << ".\n";
handle_error();
return false;
}
SMap::iterator f= short_names_.find(cur_arg[1]);
if ( f != short_names_.end()){
if (!f->second->process(argc, argv)) {
handle_error();
return false;
}
} else {
std::cerr<< "Invalid short argument "<< cur_arg << ".\n";
handle_error();
return false;
}
}
} else {
if (current_unnamed_ != unnamed_arguments_.end()){
Argument_target *t= *current_unnamed_;
t->process(argc, argv);
++current_unnamed_;
} else if (current_optional_unnamed_ != optional_unnamed_arguments_.end()){
Argument_target *t= *current_optional_unnamed_;
t->process(argc, argv);
++current_optional_unnamed_;
} else if (extra_arguments_!= NULL){
extra_arguments_->push_back(cur_arg);
--argc;
++argv;
} else {
std::cerr << "Invalid extra argument " << argv[0] << std::endl;
handle_error();
return false;
}
}
}
if (current_unnamed_ != unnamed_arguments_.end()){
std::cerr << "Missing required arguments:" << std::endl;
for (; current_unnamed_ != unnamed_arguments_.end(); ++current_unnamed_){
(*current_unnamed_)->write_name(std::cerr);
std::cerr << std::endl;
}
std::cerr << std::endl;
handle_error();
return false;
}
if (VERBOSE) verbose=true;
return true;
}
/****************************************************************************
Desc: Prints the web page for an SCACHEMGR struct
(The URL for this page requires no parameters since there is only
one SCACHE_MGR per copy of FLAIM.)
****************************************************************************/
RCODE F_SCacheMgrPage::display(
FLMUINT uiNumParams,
const char ** ppszParams)
{
RCODE rc = FERR_OK;
SCACHE_MGR LocalSCacheMgr;
FLMBOOL bAutoRefresh;
#define NUM_CACHE_REQ_STRINGS 4
char * pszSCacheRequestString[ NUM_CACHE_REQ_STRINGS];
char szOffsetTable[12][6];
char szAddressTable[2][20];
FLMBOOL bHighlight = FALSE;
char * pszTemp = NULL;
FLMUINT uiLoop;
// Note: The SCacheBlock requests need the following params:
// "BlockAddress", "File", "LowTransID" and "HighTransID"
// ex: <A href="SCacheBlock?BlockAddress=100?File=5?LowTransID=30?HighTransID=100"> pMRUCache </A>
if( RC_BAD( rc = f_alloc( 200, &pszTemp)))
{
printErrorPage( rc, TRUE, (char *)"Failed to allocate temporary buffer");
goto Exit;
}
// First thing that we need to do is grab a local copy of gv_FlmSysData.SCacheMgr,
// and of the data for the three SCache blocks that it has pointers to...
for (uiLoop = 0; uiLoop < NUM_CACHE_REQ_STRINGS; uiLoop++)
{
if( RC_BAD( rc = f_alloc( 150,
&pszSCacheRequestString[ uiLoop])))
{
printErrorPage( rc, TRUE, (char *)"Failed to allocate temporary buffer");
goto Exit;
}
}
f_mutexLock( gv_FlmSysData.hShareMutex);
f_memcpy (&LocalSCacheMgr, &gv_FlmSysData.SCacheMgr, sizeof (LocalSCacheMgr));
flmBuildSCacheBlockString( pszSCacheRequestString[0], LocalSCacheMgr.pMRUCache);
flmBuildSCacheBlockString( pszSCacheRequestString[1], LocalSCacheMgr.pLRUCache);
flmBuildSCacheBlockString( pszSCacheRequestString[2], LocalSCacheMgr.pFirstFree);
flmBuildSCacheBlockString( pszSCacheRequestString[3], LocalSCacheMgr.pLastFree);
f_mutexUnlock( gv_FlmSysData.hShareMutex);
bAutoRefresh = DetectParameter( uiNumParams, ppszParams, "Refresh");
// Now - are we being asked to display the usage stats? Or is this a regular page...
if (DetectParameter( uiNumParams, ppszParams, "Usage"))
{
// There's a function to handle display the usage info (because both
// RCacheMgr and SCacheMgr have usage stats).
writeUsage( &LocalSCacheMgr.Usage, bAutoRefresh,
"/SCacheMgr?Usage",
"Usage Statistics for the SCache");
}
else // This is a regular SCacheMgr page...
{
// Determine if we are being requested to refresh this page or not.
stdHdr();
fnPrintf( m_pHRequest, HTML_DOCTYPE "<HTML>\n");
if (bAutoRefresh)
{
// Send back the page with a refresh command in the header
fnPrintf( m_pHRequest,
"<HEAD>"
"<META http-equiv=\"refresh\" content=\"5; url=%s/SCacheMgr?Refresh\">"
"<TITLE>gv_FlmSysData.SCacheMgr</TITLE>\n", m_pszURLString);
printStyle();
popupFrame(); //Spits out a Javascript function that will open a new window..
fnPrintf( m_pHRequest, "\n</HEAD>\n<body>\n");
f_sprintf( (char *)pszTemp,
"<A HREF=%s/SCacheMgr>Stop Auto-refresh</A>", m_pszURLString);
}
else // bAutoRefresh == FALSE
{
// Send back a page without the refresh command
fnPrintf( m_pHRequest,
"<HEAD>"
"<TITLE>gv_FlmSysData.SCacheMgr</TITLE>\n");
printStyle();
popupFrame(); //Spits out a Javascript function that will open a new window..
fnPrintf( m_pHRequest, "\n</HEAD>\n<body>\n");
f_sprintf( (char *)pszTemp,
"<A HREF=%s/SCacheMgr?Refresh>Start Auto-refresh (5 sec.)</A>",
m_pszURLString);
}
// Write out the table headings
printTableStart( "SCache Manager Structure", 4);
printTableRowStart();
printColumnHeading( "", JUSTIFY_LEFT, FLM_IMON_COLOR_PUTTY_1, 4, 1, FALSE);
fnPrintf( m_pHRequest, "<A HREF=%s/SCacheMgr>Refresh</A>, %s\n", m_pszURLString, pszTemp);
printColumnHeadingClose();
printTableRowEnd();
// Write out the table headings.
printTableRowStart();
printColumnHeading( "Byte Offset (hex)");
printColumnHeading( "Field Name");
printColumnHeading( "Field Type");
printColumnHeading( "Value");
printTableRowEnd();
//Now - we have three rows in the table that may or may not have hyperlinks in them.
printTableRowStart( bHighlight = ~bHighlight);
flmPrintCacheLine(m_pHRequest, pszSCacheRequestString[0], "pMRUCache", &LocalSCacheMgr, &LocalSCacheMgr.pMRUCache);
printTableRowStart( bHighlight = ~bHighlight);
flmPrintCacheLine(m_pHRequest, pszSCacheRequestString[1], "pLRUCache", &LocalSCacheMgr, &LocalSCacheMgr.pLRUCache);
printTableRowStart( bHighlight = ~bHighlight);
flmPrintCacheLine(m_pHRequest, pszSCacheRequestString[2], "pFirstFree", &LocalSCacheMgr, &LocalSCacheMgr.pFirstFree);
printTableRowStart( bHighlight = ~bHighlight);
flmPrintCacheLine(m_pHRequest, pszSCacheRequestString[3], "pLastFree", &LocalSCacheMgr, &LocalSCacheMgr.pLastFree);
//Format the strings that are displayed in the Offset column on of the table
printOffset(&LocalSCacheMgr, &LocalSCacheMgr.ppHashTbl, szOffsetTable[0]);
printOffset(&LocalSCacheMgr, &LocalSCacheMgr.Usage, szOffsetTable[1]);
printOffset(&LocalSCacheMgr, &LocalSCacheMgr.bAutoCalcMaxDirty, szOffsetTable[2]);
printOffset(&LocalSCacheMgr, &LocalSCacheMgr.uiMaxDirtyCache, szOffsetTable[3]);
printOffset(&LocalSCacheMgr, &LocalSCacheMgr.uiLowDirtyCache, szOffsetTable[4]);
printOffset(&LocalSCacheMgr, &LocalSCacheMgr.uiTotalUses, szOffsetTable[5]);
printOffset(&LocalSCacheMgr, &LocalSCacheMgr.uiBlocksUsed, szOffsetTable[6]);
printOffset(&LocalSCacheMgr, &LocalSCacheMgr.uiPendingReads, szOffsetTable[7]);
printOffset(&LocalSCacheMgr, &LocalSCacheMgr.uiIoWaits, szOffsetTable[8]);
printOffset(&LocalSCacheMgr, &LocalSCacheMgr.uiHashTblSize, szOffsetTable[9]);
printOffset(&LocalSCacheMgr, &LocalSCacheMgr.uiHashTblBits, szOffsetTable[10]);
#ifdef FLM_DEBUG
printOffset(&LocalSCacheMgr, &LocalSCacheMgr.bDebug, szOffsetTable[11]);
#endif
printAddress( LocalSCacheMgr.ppHashTbl, szAddressTable[0]);
printAddress( &LocalSCacheMgr.Usage, szAddressTable[1]);
printTableRowStart( bHighlight = ~bHighlight);
fnPrintf( m_pHRequest, TD_s
"<td><A HREF=\"%s/SCacheHashTable?Start=0\">ppHashTbl</A></td>\n"
"<td>SCACHE **</td>\n"
"<td><A href=\"%s/SCacheHashTbl\">%s</A></td>\n",
szOffsetTable[0], m_pszURLString, m_pszURLString, szAddressTable[0]);
printTableRowEnd();
printTableRowStart( bHighlight = ~bHighlight);
fnPrintf( m_pHRequest, TD_s
"<td><A href=\"javascript:openPopup('%s/SCacheMgr?Usage')\">Usage</A></td>\n"
"<td>FLM_CACHE_USAGE</td>\n"
"<td><A href=\"javascript:openPopup('%s/SCacheMgr?Usage')\">%s</A></td>\n",
szOffsetTable[1], m_pszURLString, m_pszURLString, szAddressTable[1]);
printTableRowEnd();
// uiFreeCount
printHTMLUint(
(char *)"uiFreeCount",
(char *)"FLMUINT",
(void *)&LocalSCacheMgr,
(void *)&LocalSCacheMgr.uiFreeCount,
LocalSCacheMgr.uiFreeCount,
(bHighlight = ~bHighlight));
// uiFreeBytes
printHTMLUint(
(char *)"uiFreeBytes",
(char *)"FLMUINT",
(void *)&LocalSCacheMgr,
(void *)&LocalSCacheMgr.uiFreeBytes,
LocalSCacheMgr.uiFreeBytes,
(bHighlight = ~bHighlight));
// uiReplaceableCount
printHTMLUint(
(char *)"uiReplaceableCount",
(char *)"FLMUINT",
(void *)&LocalSCacheMgr,
(void *)&LocalSCacheMgr.uiReplaceableCount,
LocalSCacheMgr.uiReplaceableCount,
(bHighlight = ~bHighlight));
// uiReplaceableBytes
printHTMLUint(
(char *)"uiReplaceableBytes",
(char *)"FLMUINT",
(void *)&LocalSCacheMgr,
(void *)&LocalSCacheMgr.uiReplaceableBytes,
LocalSCacheMgr.uiReplaceableBytes,
(bHighlight = ~bHighlight));
printTableRowStart( bHighlight = ~bHighlight);
fnPrintf( m_pHRequest, TD_s "<td>bAutoCalcMaxDirty</td>\n"
"<td>FLMBOOL</td>\n" TD_i, szOffsetTable[2],
LocalSCacheMgr.bAutoCalcMaxDirty);
printTableRowEnd();
printTableRowStart( bHighlight = ~bHighlight);
fnPrintf( m_pHRequest, TD_s "<td>uiMaxDirtyCache</td>\n"
"<td>FLMUINT</td>\n" TD_lu, szOffsetTable[3],
LocalSCacheMgr.uiMaxDirtyCache);
printTableRowEnd();
printTableRowStart( bHighlight = ~bHighlight);
fnPrintf( m_pHRequest, TD_s "<td>uiLowDirtyCache</td>\n"
"<td>FLMUINT</td>\n" TD_lu, szOffsetTable[4],
LocalSCacheMgr.uiLowDirtyCache);
printTableRowEnd();
printTableRowStart( bHighlight = ~bHighlight);
fnPrintf( m_pHRequest, TD_s "<td>uiTotalUses</td>\n"
"<td>FLMUINT</td>\n" TD_lu, szOffsetTable[5],
LocalSCacheMgr.uiTotalUses);
printTableRowEnd();
printTableRowStart( bHighlight = ~bHighlight);
fnPrintf( m_pHRequest, TD_s "<td>uiBlocksUsed</td> <td>FLMUINT</td>\n"
TD_lu, szOffsetTable[6], LocalSCacheMgr.uiBlocksUsed);
printTableRowEnd();
printTableRowStart( bHighlight = ~bHighlight);
fnPrintf( m_pHRequest, TD_s "<td>uiPendingReads</td>\n"
"<td>FLMUINT</td>\n" TD_lu, szOffsetTable[7],
LocalSCacheMgr.uiPendingReads);
printTableRowEnd();
printTableRowStart( bHighlight = ~bHighlight);
fnPrintf( m_pHRequest, TD_s "<td>uiIoWaits</td>\n <td>FLMUINT</td>\n" TD_lu,
szOffsetTable[8], LocalSCacheMgr.uiIoWaits);
printTableRowEnd();
printTableRowStart( bHighlight = ~bHighlight);
fnPrintf( m_pHRequest, TD_s "<td>uiHashTableSize</td>\n"
"<td>FLMUINT</td>\n" TD_lu, szOffsetTable[9],
LocalSCacheMgr.uiHashTblSize);
printTableRowEnd();
printTableRowStart( bHighlight = ~bHighlight);
fnPrintf( m_pHRequest, TD_s "<td>uiHashTableBits</td>\n"
"<td>FLMUINT</td>\n" TD_lu, szOffsetTable[10],
LocalSCacheMgr.uiHashTblBits);
printTableRowEnd();
#ifdef FLM_DEBUG
printTableRowStart( bHighlight = ~bHighlight);
fnPrintf( m_pHRequest, TD_s "<td>bDebug</td>\n" "<td>FLMBOOL</td>\n"
TD_i, szOffsetTable[11], LocalSCacheMgr.bDebug);
printTableRowEnd();
#endif
printTableEnd();
fnPrintf( m_pHRequest, "</BODY></HTML>\n");
fnEmit();
}
Exit:
if (pszTemp)
{
f_free( &pszTemp);
}
for (uiLoop = 0; uiLoop < NUM_CACHE_REQ_STRINGS; uiLoop++)
{
if( pszSCacheRequestString[uiLoop])
{
f_free( &pszSCacheRequestString[uiLoop]);
}
}
return( rc);
}
int main(int argc, const char *argv[]) {
double startTime = Util::clock();
Util::setShowError(true);
Util::setShowWarning(true);
Util::setShowStatus(false);
if(argc <= 1) {
writeUsage();
return 0;
}
// Retrieve setup
std::vector<std::string> args;
for(int i = 1; i < argc; i++) {
args.push_back(std::string(argv[i]));
}
SetupTrain setup(args);
File* forecast = setup.forecasts[0];
File* observation = setup.observations[0];
File* ogrid = observation;
int nLat = ogrid->getNumLat();
int nLon = ogrid->getNumLon();
int nTime = ogrid->getNumTime();
vec2 lats = ogrid->getLats();
vec2 lons = ogrid->getLons();
vec2 elevs = ogrid->getElevs();
Variable::Type variable = setup.variable;
std::vector<double> offsets = forecast->getTimes();
int D = setup.forecasts.size();
std::cout << "Number of obs files: " << setup.observations.size() << std::endl;
std::cout << "Number of fcst files: " << setup.forecasts.size() << std::endl;
std::cout << "Number of lats: " << nLat << std::endl;
std::cout << "Number of lons: " << nLon << std::endl;
std::cout << "Number of times: " << nTime << std::endl;
std::cout << "Forecast reference times: ";
for(int f = 0; f < setup.forecasts.size(); f++) {
double timeF = setup.forecasts[f]->getReferenceTime();
std::cout << " " << timeF;
}
std::cout << std::endl;
std::cout << "Observation reference times: ";
for(int f = 0; f < setup.observations.size(); f++) {
double timeO = setup.observations[f]->getReferenceTime();
std::cout << " " << timeO;
}
std::cout << std::endl;
// figure out which files match
std::vector<int> indexF;
std::vector<int> indexO;
for(int f = 0; f < setup.forecasts.size(); f++) {
int io = Util::MV;
double timeF = setup.forecasts[f]->getReferenceTime();
for(int o = 0; o < setup.observations.size(); o++) {
double timeO = setup.observations[o]->getReferenceTime();
if(timeF == timeO) {
io = o;
}
}
if(Util::isValid(io)) {
indexF.push_back(f);
indexO.push_back(io);
}
}
int validD = indexF.size();
std::cout << "Number of valid days: " << validD << std::endl;
if(validD == 0) {
return -1;
}
// vec2Int Io2f, Jo2f;
// Downscaler::getNearestNeighbour(*observation, *forecast, Io2f, Jo2f);
vec2Int If2o, Jf2o;
Downscaler::getNearestNeighbour(*forecast, *observation, If2o, Jf2o);
std::cout << "Created nearest neighbour map" << std::endl;
std::vector<double> ftimes = forecast->getTimes();
std::vector<double> otimes = observation->getTimes();
double freftime = forecast->getReferenceTime();
double oreftime = observation->getReferenceTime();
std::cout << "Forecast offsets:";
for(int t = 0; t < ftimes.size(); t++) {
std::cout << " " << ftimes[t] - freftime;
}
std::cout << std::endl;
std::cout << "Observation offsets:";
for(int t = 0; t < otimes.size(); t++) {
std::cout << " " << otimes[t] - oreftime;
}
std::cout << std::endl;
for(int t = 0; t < offsets.size(); t++) {
double time0 = Util::clock();
std::cout << "Forecast time index: " << t << std::endl;
// If multiple available obstimes, then use the one with the lowest ftime
double ftime = ftimes[t] - freftime;
int fTimeIndex = t;
int oTimeIndex = Util::MV;
int fmaxDays = ftimes[ftimes.size()-1] / 86400;
/*
// Use the same leadtime in obs and forecast (probably not optimal obs for
// leadtimes above 24h)
for(int tt = 0; tt < otimes.size(); tt++) {
double otime = otimes[tt] - oreftime;
if(otime == ftime) {
oTimeIndex = tt;
break;
}
}
*/
for(int d = 0; d < fmaxDays; d++) {
// Find appropriate obs time
for(int tt = 0; tt < otimes.size(); tt++) {
double otime = otimes[tt] - oreftime + d * 86400;
if(otime == ftime && (t == 0 || tt != 0)) {
oTimeIndex = tt;
break;
}
}
}
assert(Util::isValid(oTimeIndex));
// Loop over all files
std::vector<FieldPtr> ffields;
std::vector<FieldPtr> ofields;
for(int d = 0; d < setup.forecasts.size(); d++) {
double ftime = setup.forecasts[d]->getTimes()[t];
int fDateIndex = d;
int oDateIndex = Util::MV;
// Find corresponding observation file
for(int dd = 0; dd < setup.observations.size(); dd++) {
double otime = setup.observations[dd]->getTimes()[oTimeIndex];
if(ftime == otime) {
oDateIndex = dd;
break;
}
}
if(Util::isValid(fDateIndex) && Util::isValid(oDateIndex)) {
std::cout << " Found matching: (" << fDateIndex << "," << fTimeIndex << ") "
<< " (" << oDateIndex << "," << oTimeIndex << ")" << std::endl;
assert(setup.forecasts.size() > fDateIndex);
assert(setup.observations.size() > oDateIndex);
ffields.push_back(setup.forecasts[fDateIndex]->getField(variable, fTimeIndex));
ofields.push_back(setup.observations[oDateIndex]->getField(variable, oTimeIndex));
}
}
if(ffields.size() == 0) {
std::stringstream ss;
ss << "Cannot find files with available data for timestep " << t << std::endl;
Util::error(ss.str());
}
assert(ffields.size() > 0);
////////////////////////
// Compute parameters
if(setup.output->isLocationDependent()) {
// Do this in parallel, inserting the values into a preallocated matrix
std::vector<std::vector<std::vector<float> > > parameters;
parameters.resize(nLat);
for(int i = 0; i < nLat; i++) {
parameters[i].resize(nLon);
}
#pragma omp parallel for
for(int i = 0; i < nLat; i++) {
for(int j = 0; j < nLon; j++) {
// Arrange data
std::vector<ObsEns> data;
for(int d = 0; d < ffields.size(); d++){
// Downscaling (currently nearest neighbour)
// float obs = (*ofields[d])(Io2f[i][j],Jo2f[i][j],0);
// const Ens& ens = (*ffields[d])(i,j);
float obs = (*ofields[d])(i,j,0);
Ens ens = (*ffields[d])(If2o[i][j],Jf2o[i][j]);
ObsEns obsens(obs, ens);
data.push_back(obsens);
}
Parameters par = setup.method->train(data);
parameters[i][j] = par.getValues();
}
}
// Then save values serially
for(int i = 0; i < nLat; i++) {
for(int j = 0; j < nLon; j++) {
float lat = lats[i][j];
float lon = lons[i][j];
float elev = elevs[i][j];
setup.output->setParameters(Parameters(parameters[i][j]), t, Location(lat, lon, elev));
}
}
}
else {
std::cout << "Location independent estimation" << std::endl;
// Arrange data
std::vector<ObsEns> data;
for(int i = 0; i < nLat; i++) {
for(int j = 0; j < nLon; j++) {
for(int d = 0; d < ffields.size(); d++){
// Downscaling (currently nearest neighbour)
// float obs = (*ofields[d])(Io2f[i][j],Jo2f[i][j],0);
// const Ens& ens = (*ffields[d])(i,j);
float obs = (*ofields[d])(i,j,0);
Ens ens = (*ffields[d])(If2o[i][j],Jf2o[i][j]);
if(Util::isValid(obs) && Util::isValid(ens[0])) {
ObsEns obsens(obs, ens);
data.push_back(obsens);
}
}
}
}
std::cout << "Using " << data.size() << " data points" << std::endl;
Parameters par = setup.method->train(data);
setup.output->setParameters(par, t, Location(Util::MV, Util::MV, Util::MV));
}
// Clear the memory of the files
// for(int f = 0; f < ofields.size(); f++) {
// ofields[f].reset();
// }
for(int f = 0; f < setup.forecasts.size(); f++) {
setup.forecasts[f]->clear();
}
for(int f = 0; f < setup.observations.size(); f++) {
setup.observations[f]->clear();
}
double time1 = Util::clock();
std::cout << " Time: " << time1 - time0 << " seconds" << std::endl;
}
std::cout << "Recomputing nearest neighbour tree" << std::endl;
setup.output->recomputeTree();
std::cout << "Writing to parameter file" << std::endl;
setup.output->write();
double endTime = Util::clock();
std::cout << "Total time: " << endTime - startTime << std::endl;
}
void getCommandLineParams(t_Params *ptParams,int argc,char *argv[])
{
char *szTemp = NULL;
char *cError = NULL;
/*get parameter file name*/
ptParams->szSeqInputFile = extractParameter(argc,argv, SEQ_INPUT_FILE,ALWAYS);
if(ptParams->szSeqInputFile == NULL)
goto error;
/*get parameter file name*/
ptParams->szRefInputFile = extractParameter(argc,argv, REF_INPUT_FILE,OPTION);
if(ptParams->szRefInputFile == NULL){
ptParams->szRefInputFile = ptParams->szSeqInputFile;
}
szTemp = extractParameter(argc,argv,SKEW,OPTION);
if(szTemp != NULL){
ptParams->nSkew = strtol(szTemp,&cError,10);
if(*cError!='\0'){
goto error;
}
}
else{
ptParams->nSkew = DEFAULT_SKEW;
}
if(extractParameter(argc,argv,USE_BALANCE,OPTION)){
ptParams->bImbalance = FALSE;
}
else{
ptParams->bImbalance = TRUE;
}
szTemp = extractParameter(argc,argv,CLASSIFY,OPTION);
if(szTemp != NULL){
char *szTok = strtok(szTemp, DELIM2);
ptParams->dAlpha = strtod(szTok,&cError);
if(*cError!='\0'){
goto error;
}
szTok = strtok(NULL, DELIM2);
ptParams->dBeta = strtod(szTok,&cError);
if(*cError!='\0'){
goto error;
}
}
else{
if(ptParams->bImbalance == FALSE){
ptParams->dAlpha = DEFAULT_ALPHA_1;
ptParams->dBeta = DEFAULT_BETA_1;
}
else{
ptParams->dAlpha = DEFAULT_ALPHA_2;
ptParams->dBeta = DEFAULT_BETA_2;
}
}
if(extractParameter(argc,argv,OUTPUT_ALIGNMENTS,OPTION)){
ptParams->bOutputAlignments = TRUE;
}
else{
ptParams->bOutputAlignments = FALSE;
}
if(szTemp = extractParameter(argc,argv, LOOKUP_FILE_FLAG, OPTION)){
ptParams->szLookUpFile = szTemp;
}
else{
ptParams->szLookUpFile = getenv("SEQ_LOOKUP_FILE");
if(ptParams->szLookUpFile == NULL){
ptParams->szLookUpFile = LOOKUP_FILE;
}
}
return;
error:
writeUsage(stdout);
exit(EXIT_FAILURE);
}
