FitsWriter.cc

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// -*- lsst-c++ -*-
 
#include <memory>
 
#include "lsst/afw/table/io/FitsWriter.h"
#include "lsst/afw/table/BaseTable.h"
#include "lsst/afw/table/BaseRecord.h"
 
namespace lsst {
namespace afw {
namespace table {
namespace io {
 
namespace {
 
using Fits = FitsWriter::Fits;
 
//----- Code to write FITS headers --------------------------------------------------------------------------
 
// The driver code is at the bottom of this section; it's easier to understand if you start there
// and work your way up.
 
// A Schema::forEach functor that writes FITS header keys for a field when it is called.
struct ProcessSchema {
    template <typename T>
    void operator()(SchemaItem<T> const& item) const {
        std::string name = item.field.getName();
        int n = fits->addColumn<typename Field<T>::Element>(name, item.field.getElementCount(),
                                                            item.field.getDoc());
        if (!item.field.getDoc().empty()) {
            // We use a separate key TDOCn for documentation (in addition to the TTYPEn comments)
            // so we can have long strings via the CONTINUE convention.
            // When reading, if there is no TDOCn, we'll just use the TTYPEn comment.
            fits->writeColumnKey("TDOC", n, item.field.getDoc());
        }
        specialize(item, n);  // delegate to other member functions that are specialized on field tag types
    }
 
    void operator()(SchemaItem<std::string> const& item) const {
        std::string name = item.field.getName();
        std::size_t n = fits->addColumn<std::string>(name, item.field.getElementCount(), item.field.getDoc());
        if (!item.field.getDoc().empty()) {
            fits->writeColumnKey("TDOC", n, item.field.getDoc());
        }
        specialize(item, n);
    }
 
    void operator()(SchemaItem<Flag> const& item) const {
        std::string name = item.field.getName();
        fits->writeColumnKey("TFLAG", nFlags, name);
        if (!item.field.getDoc().empty()) {
            // We use a separate key TFDOCn for documentation instead of the comment on TFLAGn so
            // we can have long strings via the CONTINUE convention.
            // When reading, if there is no TFDOCn, we'll use the TTYPEn comment.
            fits->writeColumnKey("TFDOC", nFlags, item.field.getDoc());
        }
        ++nFlags;
    }
 
    // Create and apply the functor to a schema.
    static void apply(Fits& fits, Schema const& schema) {
        ProcessSchema f = {&fits, 0};
        schema.forEach(f);
    }
 
    template <typename T>
    void specialize(SchemaItem<T> const& item, int n) const {
        if (!item.field.getUnits().empty()) fits->writeColumnKey("TUNIT", n, item.field.getUnits());
        fits->writeColumnKey("TCCLS", n, "Scalar", "Field template used by lsst.afw.table");
    }
 
    void specialize(SchemaItem<lsst::geom::Angle> const& item, int n) const {
        // Always write units for lsst::geom::Angles as radians (in-memory lsst::geom::Angles field don't use
        // the unit attribute, single lsst::geom::Angle abstracts that away).
        fits->writeColumnKey("TUNIT", n, "rad");
        fits->writeColumnKey("TCCLS", n, "Angle", "Field template used by lsst.afw.table");
    }
 
    template <typename T>
    void specialize(SchemaItem<Array<T> > const& item, int n) const {
        if (!item.field.getUnits().empty()) fits->writeColumnKey("TUNIT", n, item.field.getUnits());
        fits->writeColumnKey("TCCLS", n, "Array", "Field template used by lsst.afw.table");
    }
 
    void specialize(SchemaItem<std::string> const& item, std::size_t n) const {
        if (!item.field.getUnits().empty()) fits->writeColumnKey("TUNIT", n, item.field.getUnits());
        fits->writeColumnKey("TCCLS", n, "String", "Field template used by lsst.afw.table");
    }
 
    Fits* fits;
    mutable int nFlags;
};
 
void writeAliasMap(Fits& fits, AliasMap const& aliases) {
    for (auto const &aliase : aliases) {
        fits.writeKey("ALIAS", aliase.first + ":" + aliase.second);
    }
}
 
}  // namespace
 
// the driver for all the above machinery
void FitsWriter::_writeTable(std::shared_ptr<BaseTable const> const& table, std::size_t nRows) {
    Schema schema = table->getSchema();
    _fits->createTable();
    LSST_FITS_CHECK_STATUS(*_fits, "creating table");
    std::size_t nFlags = schema.getFlagFieldCount();
    if (nFlags > 0) {
        int n = _fits->addColumn<bool>("flags", nFlags, "bits for all Flag fields; see also TFLAGn");
        _fits->writeKey("FLAGCOL", n + 1, "Column number for the bitflags.");
    }
    ProcessSchema::apply(*_fits, schema);
    writeAliasMap(*_fits, *schema.getAliasMap());
    // write the version number to the fits header, plus any other metadata
    std::shared_ptr<daf::base::PropertyList> metadata = table->getMetadata();
    if (!metadata) {
        metadata = std::make_shared<daf::base::PropertyList>();
    }
    metadata->set<int>("AFW_TABLE_VERSION", Schema::VERSION);
    _fits->writeMetadata(*metadata);
    // In case the metadata was attached to the table, clean it up.
    metadata->remove("AFW_TABLE_VERSION");
    _row = -1;
    _fits->addRows(nRows);
    _processor = std::make_shared<ProcessRecords>(_fits, schema, nFlags, _row);
}
 
//----- Code for writing FITS records -----------------------------------------------------------------------
 
// The driver code is at the bottom of this section; it's easier to understand if you start there
// and work your way up.
 
// A Schema::forEach functor that writes table data for a single record when it is called.
// We instantiate one of these, then reuse it on all the records after updating the data
// members that tell it which record and row number it's on.
struct FitsWriter::ProcessRecords {
    template <typename T>
    void operator()(SchemaItem<T> const& item) const {
        fits->writeTableArray(row, col, item.key.getElementCount(), record->getElement(item.key));
        ++col;
    }
 
    template <typename T>
    void operator()(SchemaItem<Array<T> > const& item) const {
        if (item.key.isVariableLength()) {
            ndarray::Array<T const, 1, 1> array = record->get(item.key);
            fits->writeTableArray(row, col, array.template getSize<0>(), array.getData());
        } else {
            fits->writeTableArray(row, col, item.key.getElementCount(), record->getElement(item.key));
        }
        ++col;
    }
 
    void operator()(SchemaItem<std::string> const& item) const {
        // Write fixed-length and variable-length strings the same way
        fits->writeTableScalar(row, col, record->get(item.key));
        ++col;
    }
 
    void operator()(SchemaItem<Flag> const& item) const {
        flags[bit] = record->get(item.key);
        ++bit;
    }
 
    ProcessRecords(Fits* fits_, Schema const& schema_, int nFlags_, std::size_t const& row_)
            : row(row_), col(0), bit(0), nFlags(nFlags_), fits(fits_), schema(schema_) {
        if (nFlags) flags.reset(new bool[nFlags]);
    }
 
    void apply(BaseRecord const* r) {
        record = r;
        col = 0;
        bit = 0;
        if (nFlags) ++col;
        schema.forEach(*this);
        if (nFlags) fits->writeTableArray(row, 0, nFlags, flags.get());
    }
 
    std::size_t const& row;
    mutable int col;
    mutable int bit;
    int nFlags;
    Fits* fits;
    std::unique_ptr<bool[]> flags;
    BaseRecord const* record;
    Schema schema;
};
 
void FitsWriter::_writeRecord(BaseRecord const& record) {
    ++_row;
    _processor->apply(&record);
}
}  // namespace io
}  // namespace table
}  // namespace afw
}  // namespace lsst