HDFEOS5CFMissLLArray.cc

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// This file is part of the hdf5_handler implementing for the CF-compliant
// Copyright (c) 2011-2016 The HDF Group, Inc. and OPeNDAP, Inc.
//
// This is free software; you can redistribute it and/or modify it under the
// terms of the GNU Lesser General Public License as published by the Free
// Software Foundation; either version 2.1 of the License, or (at your
// option) any later version.
//
// This software is distributed in the hope that it will be useful, but
// WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
// or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
// License for more details.
//
// You should have received a copy of the GNU Lesser General Public
// License along with this library; if not, write to the Free Software
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
//
// You can contact OPeNDAP, Inc. at PO Box 112, Saunderstown, RI. 02874-0112.
// You can contact The HDF Group, Inc. at 1800 South Oak Street,
// Suite 203, Champaign, IL 61820  
 
 
#include "config_hdf5.h"
#include <sys/stat.h>
#include <iostream>
#include <sstream>
#include <cassert>
#include <BESDebug.h>
#include <libdap/InternalErr.h>
//#include <libdap/Array.h>
 
#include "HDFEOS5CFMissLLArray.h"
#include "HDF5RequestHandler.h"
 
using namespace std;
using namespace libdap;
 
BaseType *HDFEOS5CFMissLLArray::ptr_duplicate()
{
    return new HDFEOS5CFMissLLArray(*this);
}
 
bool HDFEOS5CFMissLLArray::read()
{
 
    BESDEBUG("h5","Coming to HDFEOS5CFMissLLArray read "<<endl);
    if(nullptr == HDF5RequestHandler::get_lrdata_mem_cache())
        read_data_NOT_from_mem_cache(false,nullptr);
    else {
        vector<string> cur_lrd_non_cache_dir_list;                                      
        HDF5RequestHandler::get_lrd_non_cache_dir_list(cur_lrd_non_cache_dir_list);     
                                                                                                    
        string cache_key;
        // Check if this file is included in the non-cache directory                    
        if( (cur_lrd_non_cache_dir_list.empty()) ||                                 
            ("" == check_str_sect_in_list(cur_lrd_non_cache_dir_list,filename,'/'))) {  
            short cache_flag = 2;
                        vector<string> cur_cache_dlist;                                                         
                        HDF5RequestHandler::get_lrd_cache_dir_list(cur_cache_dlist);                            
                        string cache_dir = check_str_sect_in_list(cur_cache_dlist,filename,'/');                
                        if(cache_dir != ""){                                                                     
                            cache_key = cache_dir + varname;                                                    
                    cache_flag = 3;
            }
                        else                                                                                    
                            cache_key = filename + varname;     
 
                // Need to obtain the total number of elements.
                // Currently only trivial geographic projection is supported.
                // So the total number of elements for LAT is ydimsize,
                //    the total number of elements for LON is xdimsize.
                if(cvartype == CV_LAT_MISS)
                    handle_data_with_mem_cache(H5FLOAT32,(size_t)ydimsize,cache_flag,cache_key,false);
                else 
                    handle_data_with_mem_cache(H5FLOAT32,(size_t)xdimsize,cache_flag,cache_key,false);
        }
        else 
                 read_data_NOT_from_mem_cache(false,nullptr);
    }
    return true;
}
 
void HDFEOS5CFMissLLArray::read_data_NOT_from_mem_cache(bool add_cache,void*buf){
 
    BESDEBUG("h5","Coming to read_data_NOT_from_mem_cache "<<endl);
 
    // First handle geographic projection. No GCTP is needed.Since the calculation
    // of lat/lon is really simple for this case. No need to provide the disk cache
    // unless the calculation takes too long. We will see.
    if(eos5_projcode == HE5_GCTP_GEO) {
        read_data_NOT_from_mem_cache_geo(add_cache,buf);
        return;
    }
 
    int nelms = -1;
    vector<int>offset;
    vector<int>count;
    vector<int>step;
 
    if (rank <=  0) 
       throw InternalErr (__FILE__, __LINE__,
                          "The number of dimension of this variable should be greater than 0");
    else {
         offset.resize(rank);
         count.resize(rank);
         step.resize(rank);
         nelms = format_constraint (offset.data(), step.data(), count.data());
    }
 
    if (nelms <= 0) 
       throw InternalErr (__FILE__, __LINE__,
                          "The number of elments is negative.");
 
    vector<size_t>pos(rank,0);
    for (int i = 0; i< rank; i++)
        pos[i] = offset[i];
 
    vector<size_t>dimsizes;
    dimsizes.push_back(ydimsize);
    dimsizes.push_back(xdimsize);
    int total_elms = xdimsize*ydimsize;
 
    double upleft[2];
    double lowright[2];
    vector<int>rows;
    vector<int>cols;
    vector<double>lon;
    vector<double>lat;
    rows.resize(xdimsize*ydimsize);
    cols.resize(xdimsize*ydimsize);
    lon.resize(xdimsize*ydimsize);
    lat.resize(xdimsize*ydimsize);
 
    upleft[0] = point_left;
    upleft[1] = point_upper;
    lowright[0] = point_right;
    lowright[1] = point_lower;
 
 
    int j = 0;
    int r = -1;
 
    for (int k = j = 0; j < ydimsize; ++j) {
        for (int i = 0; i < xdimsize; ++i) {
            rows[k] = j;
            cols[k] = i;
            ++k;
        }
    }
 
    BESDEBUG("h5", " Before calling GDij2ll, check all projection parameters. "  << endl);
    BESDEBUG("h5", " eos5_projcode is "  << eos5_projcode <<endl);
    BESDEBUG("h5", " eos5_zone is "  << eos5_zone <<endl);
    BESDEBUG("h5", " eos5_params[0] is "  << eos5_params[0] <<endl);
    BESDEBUG("h5", " eos5_params[1] is "  << eos5_params[1] <<endl);
    BESDEBUG("h5", " eos5_sphere is "  << eos5_sphere <<endl);
    BESDEBUG("h5", " xdimsize is "  << xdimsize <<endl);
    BESDEBUG("h5", " ydimsize is "  << ydimsize <<endl);
    BESDEBUG("h5", " eos5_pixelreg is "  << eos5_pixelreg <<endl);
    BESDEBUG("h5", " eos5_origin is "  << eos5_origin <<endl);
    BESDEBUG("h5", " upleft[0] is "  << upleft[0] <<endl);
    BESDEBUG("h5", " upleft[1] is "  << upleft[1] <<endl);
    BESDEBUG("h5", " lowright[0] is "  << lowright[0] <<endl);
    BESDEBUG("h5", " lowright[1] is "  << lowright[1] <<endl);
    
#if 0
    cerr<< " eos5_params[0] is "  << eos5_params[0] <<endl;
    cerr<< " eos5_params[1] is "  << eos5_params[1] <<endl;
    cerr<< " eos5_sphere is "  << eos5_sphere <<endl;
    cerr<<  " eos5_zone is "  << eos5_zone <<endl;
    cerr<< " Before calling GDij2ll, check all projection parameters. "  << endl;
    cerr<<  " eos5_zone is "  << eos5_zone <<endl;
    cerr<< " eos5_params[0] is "  << eos5_params[0] <<endl;
    cerr<< " eos5_params[1] is "  << eos5_params[1] <<endl;
    BESDEBUG("h5", " xdimsize is "  << xdimsize <<endl);
    BESDEBUG("h5", " ydimsize is "  << ydimsize <<endl);
    BESDEBUG("h5", " eos5_pixelreg is "  << eos5_pixelreg <<endl);
    BESDEBUG("h5", " eos5_origin is "  << eos5_origin <<endl);
    BESDEBUG("h5", " upleft[0] is "  << upleft[0] <<endl);
    BESDEBUG("h5", " upleft[1] is "  << upleft[1] <<endl);
    BESDEBUG("h5", " lowright[0] is "  << lowright[0] <<endl);
    BESDEBUG("h5", " lowright[1] is "  << lowright[1] <<endl);
#endif
 
    // boolean to mark if the value can be read from the cache. 
    // Not necessary from programming point of view. Use it to
    // make the code flow clear.
    bool ll_read_from_cache = true;
 
    // Check if geo-cache is turned on.
    bool use_latlon_cache = HDF5RequestHandler::get_use_eosgeo_cachefile();
 
 
    // Adding more code to read latlon from cache here.
    if(use_latlon_cache == true) {
 
        // Cache name is made in a special way to make sure the same lat/lon 
        // fall into the same cache file.
        string cache_fname = obtain_ll_cache_name();
 
        // Obtain eos-geo disk cache size, dir and prefix.
        long ll_disk_cache_size = HDF5RequestHandler::get_latlon_disk_cache_size();
        string ll_disk_cache_dir = HDF5RequestHandler::get_latlon_disk_cache_dir();
        string ll_disk_cache_prefix = HDF5RequestHandler::get_latlon_disk_cachefile_prefix();
 
        // Expected cache file size
        int expected_file_size = 2*xdimsize*ydimsize*sizeof(double);     
        HDF5DiskCache *ll_cache = HDF5DiskCache::get_instance(ll_disk_cache_size,ll_disk_cache_dir,ll_disk_cache_prefix);
        int fd = 0;
        ll_read_from_cache = ll_cache->get_data_from_cache(cache_fname, expected_file_size,fd);
 
        if(ll_read_from_cache == true) {
 
            BESDEBUG("h5", " Read latitude and longitude from a disk cache. "  <<endl);
            size_t var_offset = 0;
            // Longitude is stored after latitude.
            if(CV_LON_MISS == cvartype) 
                var_offset = xdimsize*ydimsize*sizeof(double);
 
            vector<double> var_value;
            var_value.resize(xdimsize*ydimsize);
 
#if 0
            //Latitude starts from 0, longitude starts from xdimsize*ydimsize*sizeof(double);
#endif
            off_t fpos = lseek(fd,var_offset,SEEK_SET);
            if(fpos == -1) {
                throw InternalErr (__FILE__, __LINE__,
                          "Cannot seek the cached file offset.");
 
            }
            ssize_t ret_val = HDF5CFUtil::read_buffer_from_file(fd,(void*)var_value.data(),var_value.size()*sizeof(double));
            ll_cache->unlock_and_close(cache_fname);
 
            // If the cached file is not read correctly, we should purge the file.
            if((-1 == ret_val) || ((size_t)ret_val != (xdimsize*ydimsize*sizeof(double)))) {
                ll_cache->purge_file(cache_fname);
                ll_read_from_cache = false; 
            }
            else {
                // short-cut, no need to do subset.
                if(total_elms == nelms)
                    set_value((dods_float64 *)var_value.data(),total_elms);
                else {
                    vector<double>val;
                    subset<double>(
                           var_value.data(),
                           rank,
                           dimsizes,
                           offset.data(),
                           step.data(),
                           count.data(),
                           &val,
                           pos,
                           0);
                    set_value((dods_float64 *)val.data(),nelms);
                }
                return;
            }
        }
        else 
            ll_read_from_cache = false;
    }
    
    // Calculate Lat/lon by using GCTP
    r = GDij2ll (eos5_projcode, eos5_zone, eos5_params.data(), eos5_sphere, xdimsize, ydimsize, upleft, lowright,
                 xdimsize * ydimsize, rows.data(), cols.data(), lon.data(), lat.data(), eos5_pixelreg, eos5_origin);
    if (r != 0) {
        ostringstream eherr;
        eherr << "cannot calculate grid latitude and longitude";
        throw InternalErr (__FILE__, __LINE__, eherr.str ());
    }
 
 
    // ll_read_from_cache may be redundant. It is good to remind that we will generate the cache file
    // when reading from the cache fails.
    // We are using cache and need to write data to the cache.
    if(use_latlon_cache == true && ll_read_from_cache == false) {
        string cache_fname = obtain_ll_cache_name();
        long ll_disk_cache_size = HDF5RequestHandler::get_latlon_disk_cache_size();
        string ll_disk_cache_dir = HDF5RequestHandler::get_latlon_disk_cache_dir();
        string ll_disk_cache_prefix = HDF5RequestHandler::get_latlon_disk_cachefile_prefix();
        
        BESDEBUG("h5", " Write EOS5 grid latitude and longitude to a disk cache. "  <<endl);
 
        HDF5DiskCache *ll_cache = HDF5DiskCache::get_instance(ll_disk_cache_size,ll_disk_cache_dir,ll_disk_cache_prefix);
        
        // Merge vector lat and lon. lat first.
        vector <double>latlon;
        latlon.reserve(xdimsize*ydimsize*2);
        latlon.insert(latlon.end(),lat.begin(),lat.end());
        latlon.insert(latlon.end(),lon.begin(),lon.end());
        ll_cache->write_cached_data(cache_fname,2*xdimsize*ydimsize*sizeof(double),latlon);
     
    }
    BESDEBUG("h5", " The first value of lon is "  << lon[0] <<endl);
    BESDEBUG("h5", " The first value of lat is "  << lat[0] <<endl);
 
#if 0
    vector<size_t>pos(rank,0);
    for (int i = 0; i< rank; i++)
        pos[i] = offset[i];
 
    vector<size_t>dimsizes;
    dimsizes.push_back(ydimsize);
    dimsizes.push_back(xdimsize);
    int total_elms = xdimsize*ydimsize;
#endif
 
    
    if(CV_LON_MISS == cvartype) {
        if(total_elms == nelms)
            set_value((dods_float64 *)lon.data(),total_elms);
        else {
            vector<double>val;
            subset<double>(
                           lon.data(),
                           rank,
                           dimsizes,
                           offset.data(),
                           step.data(),
                           count.data(),
                           &val,
                           pos,
                           0);
            set_value((dods_float64 *)val.data(),nelms);
        }
       
    }
    else if(CV_LAT_MISS == cvartype) {
 
        if(total_elms == nelms)
            set_value((dods_float64 *)lat.data(),total_elms);
        else {
            vector<double>val;
            subset<double>(
                           lat.data(),
                           rank,
                           dimsizes,
                           offset.data(),
                           step.data(),
                           count.data(),
                           &val,
                           pos,
                           0);
            set_value((dods_float64 *)val.data(),nelms);
        }
    }
    return;
 
}
 
string HDFEOS5CFMissLLArray::obtain_ll_cache_name() {
 
    BESDEBUG("h5","Coming to obtain_ll_cache_name "<<endl);
 
 
    // Here we have a sanity check for the cached parameters:Cached directory,file prefix and cached directory size.
    // Supposedly Hyrax BES cache feature should check this and the code exists. However, the
    string bescachedir = HDF5RequestHandler::get_latlon_disk_cache_dir();
    string bescacheprefix = HDF5RequestHandler::get_latlon_disk_cachefile_prefix();
    long cachesize = HDF5RequestHandler::get_latlon_disk_cache_size();
 
    if(("" == bescachedir)||(""==bescacheprefix)||(cachesize <=0)){
        throw InternalErr (__FILE__, __LINE__, "Either the cached dir is empty or the prefix is nullptr or the cache size is not set.");
    }
    else {
        struct stat sb;
        if(stat(bescachedir.c_str(),&sb) !=0) {
            string err_mesg="The cached directory " + bescachedir;
            err_mesg = err_mesg + " doesn't exist.  ";
            throw InternalErr(__FILE__,__LINE__,err_mesg);
                    
        }
        else { 
            if(true == S_ISDIR(sb.st_mode)) {
                if(access(bescachedir.c_str(),R_OK|W_OK|X_OK) == -1) {
                    string err_mesg="The cached directory " + bescachedir;
                    err_mesg = err_mesg + " can NOT be read,written or executable.";
                    throw InternalErr(__FILE__,__LINE__,err_mesg);
                }
            }
            else {
                string err_mesg="The cached directory " + bescachedir;
                err_mesg = err_mesg + " is not a directory.";
                throw InternalErr(__FILE__,__LINE__,err_mesg);
            }
        }
    }
 
    string cache_fname=HDF5RequestHandler::get_latlon_disk_cachefile_prefix();
 
    // Projection code,zone,sphere,pix,origin
    cache_fname +=HDF5CFUtil::get_int_str(eos5_projcode);
    cache_fname +=HDF5CFUtil::get_int_str(eos5_zone);
    cache_fname +=HDF5CFUtil::get_int_str(eos5_sphere);
    cache_fname +=HDF5CFUtil::get_int_str(eos5_pixelreg);
    cache_fname +=HDF5CFUtil::get_int_str(eos5_origin);
 
    cache_fname +=HDF5CFUtil::get_int_str(ydimsize);
    cache_fname +=HDF5CFUtil::get_int_str(xdimsize);
 
    // upleft,lowright
    // HDF-EOS upleft,lowright,params use DDDDMMMSSS.6 digits. So choose %17.6f.
    cache_fname +=HDF5CFUtil::get_double_str(point_left,17,6);
    cache_fname +=HDF5CFUtil::get_double_str(point_upper,17,6);
    cache_fname +=HDF5CFUtil::get_double_str(point_right,17,6);
    cache_fname +=HDF5CFUtil::get_double_str(point_lower,17,6);
 
    // According to HDF-EOS2 document, only 13 parameters are used.
    for(int ipar = 0; ipar<13;ipar++) {
        cache_fname+=HDF5CFUtil::get_double_str(eos5_params[ipar],17,6);
    }
            
    string cache_fpath = bescachedir + "/"+ cache_fname;
    return cache_fpath;
 
}
void HDFEOS5CFMissLLArray::read_data_NOT_from_mem_cache_geo(bool add_cache,void*buf){
 
    BESDEBUG("h5","Coming to read_data_NOT_from_mem_cache_geo "<<endl);
    int nelms = -1;
    vector<int>offset;
    vector<int>count;
    vector<int>step;
 
 
    if (rank <=  0) 
       throw InternalErr (__FILE__, __LINE__,
                          "The number of dimension of this variable should be greater than 0");
    else {
 
         offset.resize(rank);
         count.resize(rank);
         step.resize(rank);
         nelms = format_constraint (offset.data(), step.data(), count.data());
    }
 
    if (nelms <= 0) 
       throw InternalErr (__FILE__, __LINE__,
                          "The number of elments is negative.");
 
    float start = 0.0;
    float end   = 0.0;
 
    vector<float>val;
    val.resize(nelms);
    
 
    if (CV_LAT_MISS == cvartype) {
        
        if (HE5_HDFE_GD_UL == eos5_origin || HE5_HDFE_GD_UR == eos5_origin) {
 
            start = point_upper;
            end   = point_lower; 
 
        }
        else {// (gridorigin == HE5_HDFE_GD_LL || gridorigin == HE5_HDFE_GD_LR)
        
            start = point_lower;
            end = point_upper;
        }
 
        if(ydimsize <=0) 
            throw InternalErr (__FILE__, __LINE__,
                            "The number of elments should be greater than 0.");
           
        float lat_step = (end - start) /ydimsize;
 
        // Now offset,step and val will always be valid. line 74 and 85 assure this.
        if ( HE5_HDFE_CENTER == eos5_pixelreg ) {
            for (int i = 0; i < nelms; i++)
                val[i] = ((offset[0]+i*step[0] + 0.5F) * lat_step + start) / 1000000.0F;
 
            // If the memory cache is turned on, we have to save all values to the buf
            if(add_cache == true) {
                vector<float>total_val;
                total_val.resize(ydimsize);
                for (int total_i = 0; total_i < ydimsize; total_i++)
                    total_val[total_i] = ((total_i + 0.5F) * lat_step + start) / 1000000.0F;
                // Note: the float is size 4 
                memcpy(buf,total_val.data(),4*ydimsize);
            }
 
        }
        else { // HE5_HDFE_CORNER 
            for (int i = 0; i < nelms; i++)
                val[i] = ((float)(offset[0]+i * step[0])*lat_step + start) / 1000000.0F;
 
            // If the memory cache is turned on, we have to save all values to the buf
            if(add_cache == true) {
                vector<float>total_val;
                total_val.resize(ydimsize);
                for (int total_i = 0; total_i < ydimsize; total_i++)
                    total_val[total_i] = ((float)(total_i) * lat_step + start) / 1000000.0F;
                // Note: the float is size 4 
                memcpy(buf,total_val.data(),4*ydimsize);
            }
 
        }
    }
 
    if (CV_LON_MISS == cvartype) {
 
        if (HE5_HDFE_GD_UL == eos5_origin || HE5_HDFE_GD_LL == eos5_origin) {
 
            start = point_left;
            end   = point_right; 
 
        }
        else {// (gridorigin == HE5_HDFE_GD_UR || gridorigin == HE5_HDFE_GD_LR)
        
            start = point_right;
            end = point_left;
        }
 
        if(xdimsize <=0) 
            throw InternalErr (__FILE__, __LINE__,
                        "The number of elments should be greater than 0.");
        float lon_step = (end - start) /xdimsize;
 
        if (HE5_HDFE_CENTER == eos5_pixelreg) {
            for (int i = 0; i < nelms; i++)
                val[i] = ((offset[0] + i *step[0] + 0.5F) * lon_step + start ) / 1000000.0F;
 
            // If the memory cache is turned on, we have to save all values to the buf
            if(add_cache == true) {
                vector<float>total_val;
                total_val.resize(xdimsize);
                for (int total_i = 0; total_i < xdimsize; total_i++)
                    total_val[total_i] = ((total_i+0.5F) * lon_step + start) / 1000000.0F;
                // Note: the float is size 4 
                memcpy(buf,total_val.data(),4*xdimsize);
            }
 
        }
        else { // HE5_HDFE_CORNER 
            for (int i = 0; i < nelms; i++)
                val[i] = ((float)(offset[0]+i*step[0]) * lon_step + start) / 1000000.0F;
 
            // If the memory cache is turned on, we have to save all values to the buf
            if(add_cache == true) {
                vector<float>total_val;
                total_val.resize(xdimsize);
                for (int total_i = 0; total_i < xdimsize; total_i++)
                    total_val[total_i] = ((float)(total_i) * lon_step + start) / 1000000.0F;
                // Note: the float is size 4 
                memcpy(buf,total_val.data(),4*xdimsize);
            }
        }
    }
 
#if 0
for (int i =0; i <nelms; i++) 
"h5","final data val "<< i <<" is " << val[i] <<endl;
#endif
 
    set_value ((dods_float32 *) val.data(), nelms);
    
 
    return;
}
 
#if 0
// parse constraint expr. and make hdf5 coordinate point location.
// return number of elements to read. 
int
HDFEOS5CFMissLLArray::format_constraint (int *offset, int *step, int *count)
{
        long nels = 1;
        int id = 0;
 
        Dim_iter p = dim_begin ();
 
        while (p != dim_end ()) {
 
                int start = dimension_start (p, true);
                int stride = dimension_stride (p, true);
                int stop = dimension_stop (p, true);
 
                // Check for illegal  constraint
                if (start > stop) {
                   ostringstream oss;
 
                   oss << "Array/Grid hyperslab start point "<< start <<
                         " is greater than stop point " <<  stop <<".";
                   throw Error(malformed_expr, oss.str());
                }
 
 
 
                offset[id] = start;
                step[id] = stride;
                count[id] = ((stop - start) / stride) + 1;      // count of elements
                nels *= count[id];              // total number of values for variable
 
                BESDEBUG ("h5",
                         "=format_constraint():"
                         << "id=" << id << " offset=" << offset[id]
                         << " step=" << step[id]
                         << " count=" << count[id]
                         << endl);
 
                id++;
                p++;
        }
 
        return nels;
}
 
#endif