StareFunctions.cc

// This file is part of libdap, A C++ implementation of the OPeNDAP Data
// Access Protocol.
 
// Copyright (c) 2019 OPeNDAP, Inc.
// Authors: Kodi Neumiller <kneumiller@opendap.org>
//
// This library 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 library 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.
 
#include "config.h"
 
#include <sstream>
#include <memory>
#include <cassert>
 
#include <STARE.h>
 
#include <netcdf.h>
 
#include <libdap/BaseType.h>
#include <libdap/Float64.h>
#include <libdap/Str.h>
#include <libdap/Array.h>
#include <libdap/Grid.h>
#include <libdap/Structure.h>
 
#include <libdap/DMR.h>
#include <libdap/D4RValue.h>
 
#include <libdap/Byte.h>
#include <libdap/Int16.h>
#include <libdap/Int32.h>
#include <libdap/UInt16.h>
#include <libdap/UInt32.h>
#include <libdap/Float32.h>
#include <libdap/UInt64.h>
#include <libdap/Int64.h>
 
#include "BESDebug.h"
// #include "BESUtil.h"
#include "BESInternalError.h"
#include "BESSyntaxUserError.h"
 
#include "StareFunctions.h"
#include "GeoFile.h"
 
#define STARE_FUNC "stare"
 
using namespace libdap;
using namespace std;
 
namespace functions {
 
// These default values can be overridden using BES keys.
// See StareFunctions.h jhrg 5/21/20
// If stare_storage_path is empty, expect the sidecar file in the same
// place as the data file. jhrg 5/26/20
string stare_storage_path;
 
// TODO Remove this once change-over is complete. jhrg 6/17/21
string stare_sidecar_suffix = "_stare.nc";
 
ostream & operator << (ostream &out, const stare_matches &m)
{
    assert(m.stare_indices.size() == m.row_indices.size()
        && m.row_indices.size() == m.col_indices.size());
 
    auto ti = m.target_indices.begin();
    auto si = m.stare_indices.begin();
    auto xi = m.row_indices.begin();
    auto yi = m.col_indices.begin();
 
    while (si != m.stare_indices.end()) {
        out << "Target: " << *ti++ << ", Dataset Index: " << *si++ << ", coord: row: " << *xi++ << ", col: " << *yi++ << endl;
    }
 
    return out;
}
 
static void
extract_stare_index_array(Array *var, vector<STARE_ArrayIndexSpatialValue> &values)
{
    if (var->var()->type() != dods_uint64_c)
        throw BESSyntaxUserError("STARE server function passed an invalid Index array (" + var->name()
        + " is type: " + var->var()->type_name() + ").", __FILE__, __LINE__);
 
    values.resize(var->length());
    var->value((dods_uint64*)values.data());    // Extract the values of 'var' to 'values'
}
 
bool
target_in_dataset(const vector<STARE_ArrayIndexSpatialValue> &target_indices,
                  const vector<STARE_ArrayIndexSpatialValue> &data_stare_indices) {
#if 1
    // this took 0.23s and worked.
    // Changes to the range-for loop, fixed the type (was unsigned long long
    // which works on OSX but not CentOS7). jhrg 11/5/19
    for (const STARE_ArrayIndexSpatialValue &i : target_indices) {
        for (const STARE_ArrayIndexSpatialValue &j :data_stare_indices ) {
            // Check to see if the index 'i' overlaps the index 'j'. The cmpSpatial()
            // function returns -1, 0, 1 depending on i in j, no overlap or, j in i.
            // testing for !0 covers the general overlap case.
            int result = cmpSpatial(i, j);
            if (result != 0)
                return true;
        }
    }
#else
    // For one sample MOD05 file, this took 5.6s and failed to work.
    // Problem: seg fault.
 
    // Initialize the skiplists for the search
    auto r = SpatialRange(data_stare_indices);
    cerr << "built spatial range" << endl;
    for (const dods_uint64 &sid : target_indices) {
        if( r.contains(sid) ) { return true; }
    }
#endif
    return false;
}
 
unsigned int
count(const vector<STARE_ArrayIndexSpatialValue> &target_indices,
      const vector<STARE_ArrayIndexSpatialValue> &dataset_indices,
      bool all_dataset_matches /*= false*/) {
    unsigned int counter = 0;
    for (const auto &i : target_indices) {
        for (const auto &j : dataset_indices)
            // Here we are counting the number of target indices that overlap the
            // dataset indices.
            if (cmpSpatial(i, j) != 0) {
                counter++;
                BESDEBUG(STARE_FUNC, "Matching (dataset, target) indices: " << i << ", " << j << endl);
                if (!all_dataset_matches)
                    break;  // exit the inner loop
            }
    }
 
    return counter;
}
 
unique_ptr<stare_matches>
stare_subset_helper(const vector<STARE_ArrayIndexSpatialValue> &target_indices,
                    const vector<STARE_ArrayIndexSpatialValue> &dataset_indices,
                    size_t dataset_rows, size_t dataset_cols)
{
    unique_ptr<stare_matches> subset(new stare_matches());
 
   auto sid_iter = dataset_indices.begin();
    for (size_t i = 0; i < dataset_rows; ++i) {
        for (size_t j = 0; j < dataset_cols; ++j) {
            auto sid = *sid_iter++;
            for (const auto &target : target_indices) {
                if (cmpSpatial(sid, target) != 0) {     // != 0 --> sid is in target OR target is in sid
                    subset->add(i, j, sid, target);
                }
            }
        }
    }
 
    return subset;
}
 
void
read_stare_indices_from_function_argument(BaseType *raw_stare_indices,
                                          vector<STARE_ArrayIndexSpatialValue> &s_indices) {
 
    auto stare_indices = dynamic_cast<Array *>(raw_stare_indices);
    if (stare_indices == nullptr)
        throw BESSyntaxUserError(
                "Expected an Array but found a " + raw_stare_indices->type_name(), __FILE__, __LINE__);
 
    if (stare_indices->var()->type() != dods_uint64_c)
        throw BESSyntaxUserError(
                "Expected an Array of UInt64 values but found an Array of  " + stare_indices->var()->type_name(),
                __FILE__, __LINE__);
 
    stare_indices->read();
 
    extract_stare_index_array(stare_indices, s_indices);
}
 
BaseType *
StareIntersectionFunction::stare_intersection_dap4_function(D4RValueList *args, DMR &dmr)
{
    if (args->size() != 2) {
        ostringstream oss;
        oss << "stare_intersection(): Expected two arguments, but got " << args->size();
        throw BESSyntaxUserError(oss.str(), __FILE__, __LINE__);
    }
 
    const BaseType *dependent_var = args->get_rvalue(0)->value(dmr);
    BaseType *raw_stare_indices = args->get_rvalue(1)->value(dmr);
 
    unique_ptr<GeoFile> gf(new GeoFile(dmr.filename()));
 
    // Read the stare indices for the dependent var from the sidecar file.
    vector<STARE_ArrayIndexSpatialValue> dep_var_stare_indices;
    gf->get_stare_indices(dependent_var->name(), dep_var_stare_indices);
 
    // Put the stare indices passed into the function into a vector<>
    vector<STARE_ArrayIndexSpatialValue> target_s_indices;
    read_stare_indices_from_function_argument(raw_stare_indices, target_s_indices);
 
    // Are any of the target indices covered by this variable
    bool status = target_in_dataset(target_s_indices, dep_var_stare_indices);
 
    unique_ptr<Int32> result(new Int32("result"));
    if (status) {
        result->set_value(1);
    }
    else {
        result->set_value(0);
    }
 
    return result.release();
}
 
BaseType *
StareCountFunction::stare_count_dap4_function(D4RValueList *args, DMR &dmr)
{
    if (args->size() != 2) {
        ostringstream oss;
        oss << "stare_intersection(): Expected two arguments, but got " << args->size();
        throw BESSyntaxUserError(oss.str(), __FILE__, __LINE__);
    }
 
    const BaseType *dependent_var = args->get_rvalue(0)->value(dmr);
    BaseType *raw_stare_indices = args->get_rvalue(1)->value(dmr);
 
    unique_ptr<GeoFile> gf(new GeoFile(dmr.filename()));
 
    // Read the stare indices for the dependent var from the sidecar file.
    vector<STARE_ArrayIndexSpatialValue> dep_var_stare_indices;
    gf->get_stare_indices(dependent_var->name(), dep_var_stare_indices);
 
    // Put the stare indices passed into the function into a vector<>
    vector<STARE_ArrayIndexSpatialValue> target_s_indices;
    read_stare_indices_from_function_argument(raw_stare_indices, target_s_indices);
 
    unsigned int num = count(target_s_indices, dep_var_stare_indices, false);
 
    unique_ptr<Int32> result(new Int32("result"));
    result->set_value(static_cast<int>(num));
    return result.release();
}
 
BaseType *
StareSubsetFunction::stare_subset_dap4_function(D4RValueList *args, DMR &dmr)
{
    if (args->size() != 2) {
        ostringstream oss;
        oss << "stare_subset(): Expected two arguments, but got " << args->size();
        throw BESSyntaxUserError(oss.str(), __FILE__, __LINE__);
    }
 
    const BaseType *dependent_var = args->get_rvalue(0)->value(dmr);
    BaseType *raw_stare_indices = args->get_rvalue(1)->value(dmr);
 
    unique_ptr<GeoFile> gf(new GeoFile(dmr.filename()));
 
    // Read the stare indices for the dependent var from the sidecar file.
    vector<STARE_ArrayIndexSpatialValue> dep_var_stare_indices;
    gf->get_stare_indices(dependent_var->name(), dep_var_stare_indices);
 
    // Put the stare indices passed into the function into a vector<>
    vector<STARE_ArrayIndexSpatialValue> target_s_indices;
    read_stare_indices_from_function_argument(raw_stare_indices, target_s_indices);
 
    unique_ptr <stare_matches> subset = stare_subset_helper(target_s_indices, dep_var_stare_indices,
                                                            gf->get_variable_rows(dependent_var->name()),
                                                            gf->get_variable_cols(dependent_var->name()));
 
    // When no subset is found (none of the target indices match those in the dataset)
    if (subset->stare_indices.empty()) {
        subset->stare_indices.push_back(0);
        subset->target_indices.push_back(0);
        subset->row_indices.push_back(-1);
        subset->col_indices.push_back(-1);
    }
    // Transfer values to a Structure
    unique_ptr<Structure> result(new Structure("result"));
 
    unique_ptr<Array> stare(new Array("stare", new UInt64("stare")));
    // Various static analysis tools say the cast from STARE_SpatialIntervals to
    // dods_uint64 is not needed. FAIL. It is needed on various newer versions of
    // g++. jhrg 6/11/22
    stare->set_value((dods_uint64*)&(subset->stare_indices[0]), static_cast<int>(subset->stare_indices.size()));
    stare->append_dim(static_cast<int>(subset->stare_indices.size()));
    result->add_var_nocopy(stare.release());
 
    unique_ptr<Array> target(new Array("target", new UInt64("target")));
    target->set_value((dods_uint64*) &(subset->target_indices[0]), static_cast<int>(subset->target_indices.size()));
    target->append_dim(static_cast<int>(subset->target_indices.size()));
    result->add_var_nocopy(target.release());
 
    unique_ptr<Array> x(new Array("row", new Int32("row")));
    x->set_value(subset->row_indices, static_cast<int>(subset->row_indices.size()));
    x->append_dim(static_cast<int>(subset->row_indices.size()));
    result->add_var_nocopy(x.release());
 
    unique_ptr<Array> y(new Array("col", new Int32("col")));
    y->set_value(subset->col_indices, static_cast<int>(subset->col_indices.size()));
    y->append_dim(static_cast<int>(subset->col_indices.size()));
    result->add_var_nocopy(y.release());
 
    return result.release();
}
 
double get_double_value(BaseType *btp)
{
    switch (btp->type()) {
        case libdap::dods_float64_c:
            return dynamic_cast<Float64*>(btp)->value();
        case libdap::dods_int64_c:
            return static_cast<double>(dynamic_cast<Int64*>(btp)->value());
        case libdap::dods_uint64_c:
            return static_cast<double>(dynamic_cast<UInt64*>(btp)->value());
        default: {
            throw BESSyntaxUserError(string("Expected a constant value, but got ").append(btp->type_name())
                                            .append(" instead."), __FILE__, __LINE__);
        }
    }
}
 
BaseType *
StareSubsetArrayFunction::stare_subset_array_dap4_function(D4RValueList *args, DMR &dmr)
{
    if (args->size() != 3) {
        ostringstream oss;
        oss << "stare_subset_array(): Expected three arguments, but got " << args->size();
        throw BESSyntaxUserError(oss.str(), __FILE__, __LINE__);
    }
 
    auto dependent_var = dynamic_cast<Array*>(args->get_rvalue(0)->value(dmr));
    if (!dependent_var)
        throw BESSyntaxUserError("Expected an Array as teh first argument to stare_subset_array()", __FILE__, __LINE__);
 
    BaseType *mask_val_var = args->get_rvalue(1)->value(dmr);
    double mask_value = get_double_value(mask_val_var);
 
    BaseType *raw_stare_indices = args->get_rvalue(2)->value(dmr);
 
    unique_ptr<GeoFile> gf(new GeoFile(dmr.filename()));
 
    // Read the stare indices for the dependent var from the sidecar file.
    vector<STARE_ArrayIndexSpatialValue> dep_var_stare_indices;
    gf->get_stare_indices(dependent_var->name(), dep_var_stare_indices);
 
    // Put the stare indices passed into the function into a vector<>
    vector<STARE_ArrayIndexSpatialValue> target_s_indices;
    read_stare_indices_from_function_argument(raw_stare_indices, target_s_indices);
 
    // ptr_duplicate() does not copy data values
    unique_ptr<Array> result(dynamic_cast<Array*>(dependent_var->ptr_duplicate()));
 
    // FIXME Add more types. jhrg 6/17/20
    switch(dependent_var->var()->type()) {
        case dods_int16_c: {
            build_masked_data<dods_int16>(dependent_var, dep_var_stare_indices, target_s_indices,
                                          static_cast<short>(mask_value), result);
            break;
        }
        case dods_float32_c: {
            build_masked_data<dods_float32>(dependent_var, dep_var_stare_indices, target_s_indices,
                                            static_cast<float>(mask_value), result);
            break;
        }
 
        default:
            throw BESInternalError(string("stare_subset_array() failed: Unsupported array element type (")
                + dependent_var->var()->type_name() + ").", __FILE__, __LINE__);
    }
 
    return result.release();
}
 
STARE_SpatialIntervals
stare_box_helper(const vector<point> &points, int resolution) {
    LatLonDegrees64ValueVector latlonbox;
    for (auto &p: points) {
        latlonbox.push_back(LatLonDegrees64(p.lat, p.lon));
    }
 
    STARE index(27, 6);
    return index.CoverBoundingBoxFromLatLonDegrees(latlonbox, resolution);
}
 
STARE_SpatialIntervals
stare_box_helper(const point &top_left, const point &bottom_right, int resolution) {
    LatLonDegrees64ValueVector latlonbox;
    latlonbox.push_back(LatLonDegrees64(top_left.lat, top_left.lon));
    latlonbox.push_back(LatLonDegrees64(top_left.lat, bottom_right.lon));
    latlonbox.push_back(LatLonDegrees64(bottom_right.lat, bottom_right.lon));
    latlonbox.push_back(LatLonDegrees64(bottom_right.lat, top_left.lon));
 
    STARE index(27, 6); // Hack values.
    return index.CoverBoundingBoxFromLatLonDegrees(latlonbox, resolution);
}
 
BaseType *
StareBoxFunction::stare_box_dap4_function(libdap::D4RValueList *args, libdap::DMR &dmr)
{
    STARE_SpatialIntervals sivs;
 
    if (args->size() == 4) {
        // build cover from simple box
        double tl_lat = get_double_value(args->get_rvalue(0)->value(dmr));
        double tl_lon = get_double_value(args->get_rvalue(1)->value(dmr));
        double br_lat = get_double_value(args->get_rvalue(2)->value(dmr));
        double br_lon = get_double_value(args->get_rvalue(3)->value(dmr));
 
        sivs = stare_box_helper(point(tl_lat, tl_lon), point(br_lat, br_lon));
    }
    else if (args->size() >= 6 && (args->size() % 2) == 0) {
        // build cover from list of three or more points (lat, lon)
        bool flip_flop = false;
        double lat_value = -90;
        vector<point> points;
        for (auto &arg: *args) {
            if (flip_flop) {
                point pt(lat_value, get_double_value(arg->value(dmr)));
                points.push_back(pt);
                flip_flop = false;
            }
            else {
                lat_value = get_double_value(arg->value(dmr));
                flip_flop = true;
            }
        }
 
        sivs = stare_box_helper(points);
    }
    else {
        ostringstream oss;
        oss << "stare_box(): Expected four corner lat/lon values or a list of three or more points, but got "
            << args->size() << " values.";
        throw BESSyntaxUserError(oss.str(), __FILE__, __LINE__);
    }
 
    unique_ptr<Array> cover(new Array("cover", new UInt64("cover")));
    cover->set_value((dods_uint64*)(sivs.data()), static_cast<int>(sivs.size()));
    cover->append_dim(static_cast<int>(sivs.size()));
 
    return cover.release();
}
 
 
 
 
} // namespace functions