DataView retrieveFeatureData(const Tag &tag, size_t feature_index) {
if (tag.featureCount() == 0) {
throw nix::OutOfBounds("There are no features associated with this tag!", 0);
}
if (feature_index > tag.featureCount()) {
throw nix::OutOfBounds("Feature index out of bounds.", 0);
}
Feature feat = tag.getFeature(feature_index);
DataArray data = feat.data();
if (data == nix::none) {
throw nix::UninitializedEntity();
//return NDArray(nix::DataType::Float,{0});
}
if (feat.linkType() == nix::LinkType::Tagged) {
NDSize offset, count;
getOffsetAndCount(tag, data, offset, count);
if (!positionAndExtentInData(data, offset, count)) {
throw nix::OutOfBounds("Requested data slice out of the extent of the Feature!", 0);
}
DataView io = DataView(data, count, offset);
return io;
}
// for untagged and indexed return the full data
NDSize offset(data.dataExtent().size(), 0);
DataView io = DataView(data, data.dataExtent(), offset);
return io;
}
void OpMsg::replaceFlags(Message* message, uint32_t flags) {
invariant(!message->empty());
invariant(message->operation() == dbMsg);
invariant(message->dataSize() >= static_cast<int>(sizeof(uint32_t)));
DataView(message->singleData().data()).write<LittleEndian<uint32_t>>(flags);
}
Message OpMsgBuilder::finish() {
invariant(_state == kBody);
invariant(_bodyStart);
invariant(!_openBuilder);
_state = kDone;
// TODO figure out where checksums should be calculated. It needs to be *after* we set the
// messageID and replyTo fields in the header, which is currently done deep in the network
// stack. That will either need to move closer to here, or the checksumming will need to be
// done there.
invariant(!(_flags & OpMsg::kChecksumPresent)); // TODO SERVER-28679 compute checksum.
// If this fails, it means some internal user set an invalid flag.
invariant(!containsUnknownRequiredFlags(_flags));
DataView(_buf.buf())
.write<LittleEndian<uint32_t>>(_flags, /*offset=*/sizeof(MSGHEADER::Layout));
const auto size = _buf.len();
MSGHEADER::View header(_buf.buf());
header.setMessageLength(size);
// header.setRequestMsgId(...); // These are currently filled in by the networking layer.
// header.setResponseToMsgId(...);
header.setOpCode(dbMsg);
return Message(_buf.release());
}
void OpMsgBuilder::finishDocumentStream(DocSequenceBuilder* docSequenceBuilder) {
invariant(_state == kDocSequence);
invariant(_openBuilder);
_openBuilder = false;
const int32_t size = _buf.len() - docSequenceBuilder->_sizeOffset;
invariant(size > 0);
DataView(_buf.buf()).write<LittleEndian<int32_t>>(size, docSequenceBuilder->_sizeOffset);
}
DataView retrieveFeatureData(const MultiTag &tag, size_t position_index, size_t feature_index) {
if (tag.featureCount() == 0) {
throw nix::OutOfBounds("There are no features associated with this tag!", 0);
}
if (feature_index >= tag.featureCount()) {
throw nix::OutOfBounds("Feature index out of bounds.", 0);
}
Feature feat = tag.getFeature(feature_index);
DataArray data = feat.data();
if (data == nix::none) {
throw nix::UninitializedEntity();
//return NDArray(nix::DataType::Float,{0});
}
if (feat.linkType() == nix::LinkType::Tagged) {
NDSize offset, count;
getOffsetAndCount(tag, data, position_index, offset, count);
if (!positionAndExtentInData(data, offset, count)) {
throw nix::OutOfBounds("Requested data slice out of the extent of the Feature!", 0);
}
DataView io = DataView(data, count, offset);
return io;
} else if (feat.linkType() == nix::LinkType::Indexed) {
//FIXME does the feature data to have a setdimension in the first dimension for the indexed case?
//For now it will just be a slice across the first dim.
if (position_index > data.dataExtent()[0]){
throw nix::OutOfBounds("Position is larger than the data stored in the feature.", 0);
}
NDSize offset(data.dataExtent().size(), 0);
offset[0] = position_index;
NDSize count(data.dataExtent());
count[0] = 1;
if (!positionAndExtentInData(data, offset, count)) {
throw nix::OutOfBounds("Requested data slice out of the extent of the Feature!", 0);
}
DataView io = DataView(data, count, offset);
return io;
}
// FIXME is this expected behavior? In the untagged case all data is returned
NDSize offset(data.dataExtent().size(), 0);
DataView io = DataView(data, data.dataExtent(), offset);
return io;
}
TEST(DataRangeCursor, ConstDataRangeCursor) {
char buf[14];
DataView(buf).write<uint16_t>(1);
DataView(buf).write<LittleEndian<uint32_t>>(2, sizeof(uint16_t));
DataView(buf).write<BigEndian<uint64_t>>(3, sizeof(uint16_t) + sizeof(uint32_t));
ConstDataRangeCursor cdrc(buf, buf + sizeof(buf));
ConstDataRangeCursor backup(cdrc);
ASSERT_EQUALS(static_cast<uint16_t>(1), cdrc.readAndAdvance<uint16_t>());
ASSERT_EQUALS(static_cast<uint32_t>(2), cdrc.readAndAdvance<LittleEndian<uint32_t>>());
ASSERT_EQUALS(static_cast<uint64_t>(3), cdrc.readAndAdvance<BigEndian<uint64_t>>());
ASSERT_NOT_OK(cdrc.readAndAdvanceNoThrow<char>());
// test skip()
cdrc = backup;
ASSERT_OK(cdrc.skipNoThrow<uint32_t>());
ASSERT_OK(cdrc.advanceNoThrow(10));
ASSERT_NOT_OK(cdrc.readAndAdvanceNoThrow<char>());
}
TEST(DataRangeCursor, ConstDataRangeCursor) {
char buf[14];
DataView(buf).write<uint16_t>(1);
DataView(buf).write<LittleEndian<uint32_t>>(2, sizeof(uint16_t));
DataView(buf).write<BigEndian<uint64_t>>(3, sizeof(uint16_t) + sizeof(uint32_t));
ConstDataRangeCursor cdrc(buf, buf + sizeof(buf));
ConstDataRangeCursor backup(cdrc);
ASSERT_EQUALS(static_cast<uint16_t>(1), cdrc.readAndAdvance<uint16_t>().getValue());
ASSERT_EQUALS(static_cast<uint32_t>(2),
cdrc.readAndAdvance<LittleEndian<uint32_t>>().getValue());
ASSERT_EQUALS(static_cast<uint64_t>(3), cdrc.readAndAdvance<BigEndian<uint64_t>>().getValue());
ASSERT_EQUALS(false, cdrc.readAndAdvance<char>().isOK());
// test skip()
cdrc = backup;
ASSERT_EQUALS(true, cdrc.skip<uint32_t>().isOK());
;
ASSERT_EQUALS(true, cdrc.advance(10).isOK());
ASSERT_EQUALS(false, cdrc.readAndAdvance<char>().isOK());
}
void writeDocument(char* start) const {
char* buf = start;
memcpy(buf, _frame.objdata(), _frame.objsize() - 1); // don't copy final EOO
DataView(buf).write<LittleEndian<int>>(documentSize());
buf += (_frame.objsize() - 1);
buf[0] = (char)Object;
buf[1] = 'o';
buf[2] = 0;
memcpy(buf + 3, _oField.objdata(), _oField.objsize());
buf += 3 + _oField.objsize();
buf[0] = EOO;
verify(static_cast<size_t>((buf + 1) - start) == documentSize()); // DEV?
}
DataView retrieveData(const Tag &tag, size_t reference_index) {
vector<double> positions = tag.position();
vector<double> extents = tag.extent();
vector<DataArray> refs = tag.references();
if (refs.size() == 0) {
throw nix::OutOfBounds("There are no references in this tag!", 0);
}
if (!(reference_index < tag.referenceCount())) {
throw nix::OutOfBounds("Reference index out of bounds.", 0);
}
size_t dimension_count = refs[reference_index].dimensionCount();
if (positions.size() != dimension_count || (extents.size() > 0 && extents.size() != dimension_count)) {
throw nix::IncompatibleDimensions("Number of dimensions in position or extent do not match dimensionality of data","util::retrieveData");
}
NDSize offset, count;
getOffsetAndCount(tag, refs[reference_index], offset, count);
if (!positionAndExtentInData(refs[reference_index], offset, count)) {
throw nix::OutOfBounds("Referenced data slice out of the extent of the DataArray!", 0);
}
DataView io = DataView(refs[reference_index], count, offset);
return io;
}
DataView retrieveData(const MultiTag &tag, size_t position_index, size_t reference_index) {
DataArray positions = tag.positions();
DataArray extents = tag.extents();
vector<DataArray> refs = tag.references();
if (refs.size() == 0) { // Do I need this?
throw nix::OutOfBounds("There are no references in this tag!", 0);
}
if (position_index >= positions.dataExtent()[0] ||
(extents && position_index >= extents.dataExtent()[0])) {
throw nix::OutOfBounds("Index out of bounds of positions or extents!", 0);
}
if (!(reference_index < tag.referenceCount())) {
throw nix::OutOfBounds("Reference index out of bounds.", 0);
}
size_t dimension_count = refs[reference_index].dimensionCount();
if (positions.dataExtent().size() == 1 && dimension_count != 1) {
throw nix::IncompatibleDimensions("Number of dimensions in position or extent do not match dimensionality of data",
"util::retrieveData");
} else if (positions.dataExtent().size() > 1) {
if (positions.dataExtent()[1] > dimension_count ||
(extents && extents.dataExtent()[1] > dimension_count)) {
throw nix::IncompatibleDimensions("Number of dimensions in position or extent do not match dimensionality of data",
"util::retrieveData");
}
}
NDSize offset, count;
getOffsetAndCount(tag, refs[reference_index], position_index, offset, count);
if (!positionAndExtentInData(refs[reference_index], offset, count)) {
throw nix::OutOfBounds("References data slice out of the extent of the DataArray!", 0);
}
DataView io = DataView(refs[reference_index], count, offset);
return io;
}
