ObsFrameRead.cc

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/*
 * (C) Copyright 2017-2019 UCAR
 * 
 * This software is licensed under the terms of the Apache Licence Version 2.0
 * which can be obtained at http://www.apache.org/licenses/LICENSE-2.0. 
 */
 
#include "oops/util/abor1_cpp.h"
 
#include "oops/util/Logger.h"
 
#include "ioda/distribution/DistributionFactory.h"
#include "ioda/io/ObsFrameRead.h"
#include "ioda/io/ObsIoFactory.h"
 
namespace ioda {
 
//--------------------------- public functions ---------------------------------------
//------------------------------------------------------------------------------------
ObsFrameRead::ObsFrameRead(const ObsSpaceParameters & params) :
    ObsFrame(params) {
    // Create the ObsIo object
    obs_io_ = ObsIoFactory::create(ObsIoModes::READ, params);
 
    // Create an MPI distribution
    each_process_reads_separate_obs_ = obs_io_->eachProcessGeneratesSeparateObs();
    if (each_process_reads_separate_obs_) {
      // On each process the obs_io_ object will produce a separate series of observations, so
      // we need to use a non-overlapping distribution. The RoundRobin will do.
      eckit::LocalConfiguration distConf;
      distConf.set("distribution", "RoundRobin");
      dist_ = DistributionFactory::create(params.comm(), distConf);
    } else {
      dist_ = DistributionFactory::create(params.comm(), params.top_level_.toConfiguration());
    }
 
    max_frame_size_ = params.top_level_.obsIoInParameters().maxFrameSize;
    oops::Log::debug() << "ObsFrameRead: maximum frame size: " << max_frame_size_ << std::endl;
}
 
ObsFrameRead::~ObsFrameRead() {}
 
//------------------------------------------------------------------------------------
void ObsFrameRead::frameInit() {
    // reset counters, etc.
    frame_start_ = 0;
    if (each_process_reads_separate_obs_) {
      // Ensure record numbers assigned on different processes don't overlap
      next_rec_num_ = params_.comm().rank();
      rec_num_increment_ = params_.comm().size();
    } else {
      next_rec_num_ = 0;
      rec_num_increment_ = 1;
    }
    unique_rec_nums_.clear();
    max_var_size_ = obs_io_->maxVarSize();
    nlocs_ = 0;
    adjusted_nlocs_frame_start_ = 0;
    gnlocs_ = 0;
 
    // create an ObsGroup based frame with an in-memory backend
    createFrameFromObsGroup(obs_io_->varList(), obs_io_->dimVarList(), obs_io_->varDimMap());
 
    // record the variable name <-> dim names associations.
    dims_attached_to_vars_ = this->ioVarDimMap();
}
 
//------------------------------------------------------------------------------------
void ObsFrameRead::frameNext() {
    frame_start_ += max_frame_size_;
    adjusted_nlocs_frame_start_ += adjusted_nlocs_frame_count_;
}
 
//------------------------------------------------------------------------------------
bool ObsFrameRead::frameAvailable() {
    bool haveAnotherFrame = (frame_start_ < max_var_size_);
    // If there is another frame, then read it into obs_frame_
    if (haveAnotherFrame) {
        // Resize along the nlocs dimension
        Variable nlocsVar = obs_frame_.vars.open("nlocs");
        obs_frame_.resize(
            { std::pair<Variable, Dimensions_t>(nlocsVar, frameCount("nlocs")) });
 
        // Transfer all variable data
        Dimensions_t frameStart = this->frameStart();
        for (auto & varNameObject : obs_io_->varList()) {
            std::string varName = varNameObject.first;
            Variable sourceVar = varNameObject.second;
            Dimensions_t frameCount = this->basicFrameCount(sourceVar);
            if (frameCount > 0) {
                // Transfer the variable data for this frame. Do this in two steps:
                //    ObsIo --> memory buffer --> frame storage
 
                // Selection objects for transfer;
                std::vector<Dimensions_t> varShape = sourceVar.getDimensions().dimsCur;
                Selection obsIoSelect = createObsIoSelection(varShape, frameStart, frameCount);
                Selection memBufferSelect = createMemSelection(varShape, frameCount);
                Selection obsFrameSelect = createEntireFrameSelection(varShape, frameCount);
 
                // Transfer the data
                Variable destVar = obs_frame_.vars.open(varName);
                if (destVar.isA<int>()) {
                    std::vector<int> varValues;
                    sourceVar.read<int>(varValues, memBufferSelect, obsIoSelect);
                    destVar.write<int>(varValues, memBufferSelect, obsFrameSelect);
                } else if (destVar.isA<float>()) {
                    std::vector<float> varValues;
                    sourceVar.read<float>(varValues, memBufferSelect, obsIoSelect);
                    destVar.write<float>(varValues, memBufferSelect, obsFrameSelect);
                } else if (destVar.isA<std::string>()) {
                    std::vector<std::string> varValues;
                    sourceVar.read<std::string>(varValues, memBufferSelect, obsIoSelect);
                    destVar.write<std::string>(varValues, memBufferSelect, obsFrameSelect);
                }
            }
        }
 
        // generate the frame index and record numbers for this frame
        genFrameIndexRecNums(dist_);
 
        // clear the selection caches
        known_frame_selections_.clear();
        known_mem_selections_.clear();
    } else {
      if (obs_io_->eachProcessGeneratesSeparateObs()) {
        // sum up global location counts on all PEs
        params_.comm().allReduceInPlace(gnlocs_, eckit::mpi::sum());
        params_.comm().allReduceInPlace(gnlocs_outside_timewindow_, eckit::mpi::sum());
      }
      // assign each record to the patch of a unique PE
      dist_->computePatchLocs();
    }
    return (haveAnotherFrame);
}
 
//------------------------------------------------------------------------------------
Dimensions_t ObsFrameRead::frameStart() {
    return frame_start_;
}
 
//------------------------------------------------------------------------------------
Dimensions_t ObsFrameRead::frameCount(const std::string & varName) {
    Variable var = obs_io_->vars().open(varName);
    Dimensions_t  fCount;
    if (var.isDimensionScale()) {
        fCount = basicFrameCount(var);
    } else {
        if (obs_io_->isVarDimByNlocs(varName)) {
            fCount = adjusted_nlocs_frame_count_;
        } else {
            fCount = basicFrameCount(var);
        }
    }
    return fCount;
}
 
//-----------------------------------------------------------------------------------
bool ObsFrameRead::readFrameVar(const std::string & varName, std::vector<int> & varData) {
    return readFrameVarHelper<int>(varName, varData);
}
bool ObsFrameRead::readFrameVar(const std::string & varName, std::vector<float> & varData) {
    return readFrameVarHelper<float>(varName, varData);
}
bool ObsFrameRead::readFrameVar(const std::string & varName,
                                std::vector<std::string> & varData) {
    return readFrameVarHelper<std::string>(varName, varData);
}
 
//--------------------------- private functions --------------------------------------
//-----------------------------------------------------------------------------------
void ObsFrameRead::print(std::ostream & os) const {
    os << "ObsFrameRead: " << std::endl;
}
 
//------------------------------------------------------------------------------------
Dimensions_t ObsFrameRead::basicFrameCount(const Variable & var) {
    Dimensions_t count;
    Dimensions_t varSize0 = var.getDimensions().dimsCur[0];
    if ((frame_start_ + max_frame_size_) > varSize0) {
        count = varSize0 - frame_start_;
        if (count < 0) { count = 0; }
    } else {
        count = max_frame_size_;
    }
    return count;
}
 
//------------------------------------------------------------------------------------
Selection ObsFrameRead::createIndexedFrameSelection(const std::vector<Dimensions_t> & varShape) {
    // frame_loc_index_ contains the indices for the first dimension. Subsequent
    // dimensions, we want to select all indices.
    Selection indexedFrameSelect;
    indexedFrameSelect.extent(varShape)
        .select({ SelectionOperator::SET, 0, frame_loc_index_ });
    for (std::size_t i = 1; i < varShape.size(); ++i) {
        std::vector<Dimensions_t> dimIndex(varShape[i]);
        std::iota(dimIndex.begin(), dimIndex.end(), 0);
        indexedFrameSelect.extent(varShape).select({ SelectionOperator::AND, i, dimIndex });
    }
    return indexedFrameSelect;
}
 
// -----------------------------------------------------------------------------
void ObsFrameRead::genFrameIndexRecNums(std::shared_ptr<Distribution> & dist) {
    // Generate location indices relative to the obs source (locIndex) and relative
    // to the current frame (frameIndex).
    std::vector<Dimensions_t> locIndex;
    std::vector<Dimensions_t> frameIndex;
 
    // Apply the timing window. Need to filter out locations that are outside the
    // timing window before generating record numbers. This is because
    // we are generating record numbers on the fly since we want to get to the point where
    // we can do the MPI distribution without knowing how many obs (and records) we are going
    // to encounter. Only apply the timing window in the case of reading from a file.
    if (obs_io_->applyTimingWindow()) {
        genFrameLocationsTimeWindow(locIndex, frameIndex);
    } else {
        genFrameLocationsAll(locIndex, frameIndex);
    }
 
    // Generate record numbers for this frame. Consider obs grouping.
    std::vector<Dimensions_t> records;
    const std::vector<std::string> &obsGroupVarList = obs_io_->obsGroupingVars();
    if (obsGroupVarList.empty()) {
        genRecordNumbersAll(locIndex, records);
    } else {
        genRecordNumbersGrouping(obsGroupVarList, frameIndex, records);
    }
 
    // Apply the MPI distribution to the records
    applyMpiDistribution(dist, locIndex, records);
 
    // New frame count is the number of entries in the frame_loc_index_ vector
    // This will be handed to callers through the frameCount function for all
    // variables with nlocs as their first dimension.
    adjusted_nlocs_frame_count_ = frame_loc_index_.size();
}
 
//------------------------------------------------------------------------------------
void ObsFrameRead::genFrameLocationsAll(std::vector<Dimensions_t> & locIndex,
                                        std::vector<Dimensions_t> & frameIndex) {
    Dimensions_t locSize = this->frameCount("nlocs");
    gnlocs_ += locSize;
 
    locIndex.resize(locSize);
    std::iota(locIndex.begin(), locIndex.end(), this->frameStart());
 
    frameIndex.resize(locSize);
    std::iota(frameIndex.begin(), frameIndex.end(), 0);
}
 
//------------------------------------------------------------------------------------
void ObsFrameRead::genFrameLocationsTimeWindow(std::vector<Dimensions_t> & locIndex,
                                               std::vector<Dimensions_t> & frameIndex) {
    Dimensions_t frameCount = this->frameCount("nlocs");
    Dimensions_t frameStart = this->frameStart();
 
    // Prefer MetaData/datetime. Eventually "MetaData/time" will be obsoleted.
    std::string dtVarName;
    if (obs_frame_.vars.exists("MetaData/datetime")) {
        dtVarName = std::string("MetaData/datetime");
    } else if (obs_frame_.vars.exists("MetaData/time")) {
        dtVarName = std::string("MetaData/time");
    } else {
        std::string ErrMsg =
            std::string("ERROR: ObsFrameRead::genFrameLocationsTimeWindow: ") +
            std::string("date time information does not exist, ") +
            std::string("cannot perform time window filtering");
        throw eckit::UserError(ErrMsg, Here());
    }
 
    // Build the selection objects
    Variable dtVar = obs_frame_.vars.open(dtVarName);
    std::vector<Dimensions_t> varShape = dtVar.getDimensions().dimsCur;
    Selection memSelect = createMemSelection(varShape, frameCount);
    Selection frameSelect = createEntireFrameSelection(varShape, frameCount);
 
    // convert ref, offset time to datetime objects
    std::vector<util::DateTime> dtimeVals;
    if (dtVarName == "MetaData/datetime") {
        std::vector<std::string> dtValues;
        dtVar.read<std::string>(dtValues, memSelect, frameSelect);
        dtValues.resize(frameCount);
 
        dtimeVals = convertDtStringsToDtime(dtValues);
    } else {
        std::vector<float> dtValues;
        dtVar.read<float>(dtValues, memSelect, frameSelect);
        dtValues.resize(frameCount);
 
        int refDtime;
        this->obs_io_->atts().open("date_time").read<int>(refDtime);
        dtimeVals = convertRefOffsetToDtime(refDtime, dtValues);
    }
 
    // Keep all locations that fall inside the timing window. Note iloc will be set
    // to the number of locations stored in the output vectors after exiting the
    // following for loop.
    locIndex.resize(frameCount);
    frameIndex.resize(frameCount);
    std::size_t iloc = 0;
    for (std::size_t i = 0; i < frameCount; ++i) {
      if (this->insideTimingWindow(dtimeVals[i])) {
        locIndex[iloc] = frameStart + i;
        frameIndex[iloc] = i;
        iloc++;
      } else {
        gnlocs_outside_timewindow_++;
      }
    }
    locIndex.resize(iloc);
    frameIndex.resize(iloc);
    gnlocs_ += iloc;
}
 
//------------------------------------------------------------------------------------
void ObsFrameRead::genRecordNumbersAll(const std::vector<Dimensions_t> & locIndex,
                                       std::vector<Dimensions_t> & records) {
    // No obs grouping. Assign each location to a separate record.
    Dimensions_t locSize = locIndex.size();
    records.assign(locSize, 0);
    for (std::size_t i = 0; i < locSize; ++i) {
        records[i] = next_rec_num_;
        next_rec_num_ += rec_num_increment_;
    }
}
 
//------------------------------------------------------------------------------------
void ObsFrameRead::genRecordNumbersGrouping(const std::vector<std::string> & obsGroupVarList,
                                            const std::vector<Dimensions_t> & frameIndex,
                                     std::vector<Dimensions_t> & records) {
    // Form the selection objects for reading the variables
 
    // Applying obs grouping. First convert all of the group variable data values for this
    // frame into string key values. This is done in one call to minimize accessing the
    // frame data for the grouping variables.
    std::size_t locSize = frameIndex.size();
    records.assign(locSize, 0);
    std::vector<std::string> obsGroupingKeys(locSize);
    buildObsGroupingKeys(obsGroupVarList, frameIndex, obsGroupingKeys);
 
    for (std::size_t i = 0; i < locSize; ++i) {
      if (obs_grouping_.find(obsGroupingKeys[i]) == obs_grouping_.end()) {
        // key is not present in the map
        // assign current record number to the current key, and move to the next record number
        obs_grouping_.insert(
            std::pair<std::string, std::size_t>(obsGroupingKeys[i], next_rec_num_));
        next_rec_num_ += rec_num_increment_;
      }
      records[i] = obs_grouping_.at(obsGroupingKeys[i]);
    }
}
 
//------------------------------------------------------------------------------------
void ObsFrameRead::buildObsGroupingKeys(const std::vector<std::string> & obsGroupVarList,
                                        const std::vector<Dimensions_t> & frameIndex,
                                        std::vector<std::string> & groupingKeys) {
    // Walk though each variable and construct the segments of the key values (strings)
    // Append the segments as each variable is encountered.
    for (std::size_t i = 0; i < obsGroupVarList.size(); ++i) {
        // Retrieve the variable values from the obs frame and convert
        // those values to strings. Then append those "value" strings from each
        // variable to form the grouping keys.
        std::string obsGroupVarName = obsGroupVarList[i];
        std::string varName = std::string("MetaData/") + obsGroupVarName;
        Variable groupVar = obs_frame_.vars.open(varName);
        if (!obs_io_->isVarDimByNlocs(varName)) {
            std::string ErrMsg =
                std::string("ERROR: ObsFrameRead::genRecordNumbersGrouping: ") +
                std::string("obs grouping variable (") + obsGroupVarName +
                std::string(") must have 'nlocs' as first dimension");
            ABORT(ErrMsg);
        }
 
        // Form selection objects to grab the current frame values
        Dimensions_t frameStart = this->frameStart();
        Dimensions_t frameCount = this->frameCount("nlocs");
 
        std::vector<Dimensions_t> varShape = groupVar.getDimensions().dimsCur;
        Selection memSelect = createMemSelection(varShape, frameCount);
        Selection frameSelect = createEntireFrameSelection(varShape, frameCount);
 
        std::string keySegment;
        if (groupVar.isA<int>()) {
            std::vector<int> groupVarValues;
            groupVar.read<int>(groupVarValues, memSelect, frameSelect);
            groupVarValues.resize(frameCount);
            for (std::size_t j = 0; j < frameIndex.size(); ++j) {
                keySegment = std::to_string(groupVarValues[frameIndex[j]]);
                if (i == 0) {
                    groupingKeys[j] = keySegment;
                } else {
                    groupingKeys[j] += ":";
                    groupingKeys[j] += keySegment;
                }
            }
        } else if (groupVar.isA<float>()) {
            std::vector<float> groupVarValues;
            groupVar.read<float>(groupVarValues, memSelect, frameSelect);
            groupVarValues.resize(frameCount);
            for (std::size_t j = 0; j < frameIndex.size(); ++j) {
                keySegment = std::to_string(groupVarValues[frameIndex[j]]);
                if (i == 0) {
                    groupingKeys[j] = keySegment;
                } else {
                    groupingKeys[j] += ":";
                    groupingKeys[j] += keySegment;
                }
            }
        } else if (groupVar.isA<std::string>()) {
            std::vector<std::string> groupVarValues;
            groupVar.read<std::string>(groupVarValues, memSelect, frameSelect);
            groupVarValues.resize(frameCount);
            for (std::size_t j = 0; j < frameIndex.size(); ++j) {
                keySegment = groupVarValues[frameIndex[j]];
                if (i == 0) {
                    groupingKeys[j] = keySegment;
                } else {
                    groupingKeys[j] += ":";
                    groupingKeys[j] += keySegment;
                }
            }
        }
    }
}
 
//------------------------------------------------------------------------------------
void ObsFrameRead::applyMpiDistribution(const std::shared_ptr<Distribution> & dist,
                                        const std::vector<Dimensions_t> & locIndex,
                                        const std::vector<Dimensions_t> & records) {
    // Read lat/lon for this frame
    Dimensions_t locSize = locIndex.size();
    std::vector<float> lats(locSize, 0);
    std::vector<float> lons(locSize, 0);
    Dimensions_t frameStart = this->frameStart();
    // Form selection objects to grab the current frame values
    Dimensions_t frameCount = this->frameCount("nlocs");
 
    // Assume that lat and lon variables are shaped the same
    if (!obs_frame_.vars.exists("MetaData/longitude")) {
        throw eckit::UserError("MetaData/longitude not found in observations file", Here());
    }
    Variable latLonVar = obs_frame_.vars.open("MetaData/longitude");
    std::vector<Dimensions_t> varShape = latLonVar.getDimensions().dimsCur;
    Selection memSelect = createMemSelection(varShape, frameCount);
    Selection frameSelect = createEntireFrameSelection(varShape, frameCount);
 
    latLonVar.read(lons, memSelect, frameSelect);
    lons.resize(frameCount);
 
    if (!obs_frame_.vars.exists("MetaData/latitude")) {
        throw eckit::UserError("MetaData/latitude not found in observations file", Here());
    }
    latLonVar = obs_frame_.vars.open("MetaData/latitude");
    latLonVar.read(lats, memSelect, frameSelect);
    lats.resize(frameCount);
 
    // Generate the index and recnums for this frame.
    const std::size_t commSize = params_.comm().size();
    const std::size_t commRank = params_.comm().rank();
    frame_loc_index_.clear();
    for (std::size_t i = 0; i < locSize; ++i) {
        std::size_t rowNum = locIndex[i];
        std::size_t recNum = records[i];
        // The current frame storage always starts at zero so frameIndex
        // needs to be the offset from the ObsIo frame start.
        std::size_t frameIndex = rowNum - frameStart;
        eckit::geometry::Point2 point(lons[frameIndex], lats[frameIndex]);
 
        std::size_t globalLocIndex = rowNum;
        if (each_process_reads_separate_obs_) {
          // Each process reads a different set of observations. Make sure all of them are assigned
          // different global location indices
          globalLocIndex = rowNum * commSize + commRank;
        }
        dist_->assignRecord(recNum, globalLocIndex, point);
 
        if (dist->isMyRecord(recNum)) {
            indx_.push_back(globalLocIndex);
            recnums_.push_back(recNum);
            unique_rec_nums_.insert(recNum);
            frame_loc_index_.push_back(frameIndex);
            nlocs_++;
        }
    }
    nrecs_ = unique_rec_nums_.size();
}
 
// -----------------------------------------------------------------------------
bool ObsFrameRead::insideTimingWindow(const util::DateTime & obsDt) {
    return ((obsDt > params_.windowStart()) && (obsDt <= params_.windowEnd()));
}
 
}  // namespace ioda