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;
}
RangeDimension::RangeDimension(const DataArray &array)
: ImplContainer()
{
if (array.dataExtent().size() > 1) {
throw InvalidRank("Error creating RangeDimension with DataArray: array must be 1-D!");
}
}
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;
}
bool positionInData(const DataArray &data, const NDSize &position) {
NDSize data_size = data.dataExtent();
bool valid = true;
if (!(data_size.size() == position.size())) {
return false;
}
for (size_t i = 0; i < data_size.size(); i++) {
valid &= position[i] < data_size[i];
}
return valid;
}
Result validate(const DataArray &data_array) {
Result result_base = validate_entity_with_sources(data_array);
Result result = validator({
must(data_array, &DataArray::dataType, notEqual<DataType>(DataType::Nothing), "data type is not set!"),
must(data_array, &DataArray::dimensionCount, isEqual<size_t>(data_array.dataExtent().size()), "data dimensionality does not match number of defined dimensions!", {
could(data_array, &DataArray::dimensions, notEmpty(), {
must(data_array, &DataArray::dimensions, dimTicksMatchData(data_array), "in some of the Range dimensions the number of ticks differs from the number of data entries along the corresponding data dimension!"),
must(data_array, &DataArray::dimensions, dimLabelsMatchData(data_array), "in some of the Set dimensions the number of labels differs from the number of data entries along the corresponding data dimension!") }) }),
could(data_array, &DataArray::unit, notFalse(), {
should(data_array, &DataArray::unit, isValidUnit(), "Unit is not SI or composite of SI units.") }),
could(data_array, &DataArray::polynomCoefficients, notEmpty(), {
should(data_array, &DataArray::expansionOrigin, notFalse(), "polynomial coefficients for calibration are set, but expansion origin is missing!") }),
could(data_array, &DataArray::expansionOrigin, notFalse(), {
should(data_array, &DataArray::polynomCoefficients, notEmpty(), "expansion origin for calibration is set, but polynomial coefficients are missing!") })
});
return result.concat(result_base);
}
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;
}
void BaseTestDataArray::testData() {
typedef boost::multi_array<double, 3> array_type;
typedef array_type::index index;
array_type A(boost::extents[3][4][2]);
int values = 0;
for(index i = 0; i != 3; ++i)
for(index j = 0; j != 4; ++j)
for(index k = 0; k != 2; ++k)
A[i][j][k] = values++;
CPPUNIT_ASSERT_EQUAL(array1.dataType(), nix::DataType::Double);
CPPUNIT_ASSERT_EQUAL(array1.dataExtent(), nix::NDSize({0, 0, 0}));
CPPUNIT_ASSERT(array1.getDimension(1) == false);
array1.setData(A);
array_type B(boost::extents[1][1][1]);
array1.getData(B);
int verify = 0;
int errors = 0;
for(index i = 0; i != 3; ++i) {
for(index j = 0; j != 4; ++j) {
for(index k = 0; k != 2; ++k) {
int v = verify++;
errors += B[i][j][k] != v;
}
}
}
CPPUNIT_ASSERT_EQUAL(errors, 0);
DataArray direct = block.createDataArray("da_direct", "double", A);
array_type Adirect(boost::extents[3][4][2]);
direct.getData(Adirect);
errors = 0;
verify = 0;
for(index i = 0; i != 3; ++i) {
for(index j = 0; j != 4; ++j) {
for(index k = 0; k != 2; ++k) {
int v = verify++;
errors += Adirect[i][j][k] != v;
}
}
}
CPPUNIT_ASSERT_EQUAL(0, errors);
//test createDataArray overload that takes data but specify an storage datat type
DataArray directFloat = block.createDataArray("da_direct_int", "int", A, DataType::Int32);
CPPUNIT_ASSERT_EQUAL(DataType::Int32, directFloat.dataType());
boost::multi_array<int, 3> AdirectFloat(boost::extents[3][4][2]);
direct.getData(AdirectFloat);
errors = 0;
verify = 0;
for(index i = 0; i != 3; ++i) {
for(index j = 0; j != 4; ++j) {
for(index k = 0; k != 2; ++k) {
int v = verify++;
errors += AdirectFloat[i][j][k] != v;
}
}
}
CPPUNIT_ASSERT_EQUAL(0, errors);
typedef boost::multi_array<double, 2> array2D_type;
typedef array_type::index index;
array2D_type C(boost::extents[5][5]);
for(index i = 0; i != 5; ++i)
for(index j = 0; j != 5; ++j)
C[i][j] = 42.0;
CPPUNIT_ASSERT_EQUAL(array2.dataExtent(), nix::NDSize({20, 20}));
array2.setData(C, nix::NDSize({0, 0}));
array2.dataExtent(nix::NDSize({40, 40}));
CPPUNIT_ASSERT_EQUAL(array2.dataExtent(), nix::NDSize({40, 40}));
array2D_type D(boost::extents[5][5]);
for(index i = 0; i != 5; ++i)
for(index j = 0; j != 5; ++j)
D[i][j] = 42.0;
array2.setData(D, nix::NDSize({ 20, 20 }));
array2D_type E(boost::extents[1][1]);
array2.getData(E, nix::NDSize({ 5, 5 }), nix::NDSize({ 20, 20 }));
for(index i = 0; i != 5; ++i)
for(index j = 0; j != 5; ++j)
CPPUNIT_ASSERT_DOUBLES_EQUAL(D[i][j], E[i][j],
std::numeric_limits<double>::epsilon());
array2D_type F(boost::extents[5][5]);
array2.getData(F, nix::NDSize({ 20, 20 }));
for(index i = 0; i != 5; ++i)
for(index j = 0; j != 5; ++j)
CPPUNIT_ASSERT_DOUBLES_EQUAL(D[i][j], F[i][j],
std::numeric_limits<double>::epsilon());
nix::DataArray da3 = block.createDataArray("direct-vector",
"double",
nix::DataType::Double,
nix::NDSize({5}));
CPPUNIT_ASSERT(da3.dataExtent() == nix::NDSize{5});
CPPUNIT_ASSERT(da3.getDimension(1) == false);
std::vector<double> dv = {1.0, 2.0, 3.0, 4.0, 5.0};
da3.setData(nix::DataType::Double, dv.data(), nix::NDSize({ 5 }), nix::NDSize({ 0 }));
std::vector<double> dvin;
dvin.resize(5);
da3.getData(nix::DataType::Double, dvin.data(), nix::NDSize({ 5 }), nix::NDSize({ 0 }));
for(size_t i = 0; i < dvin.size(); i++) {
CPPUNIT_ASSERT_DOUBLES_EQUAL(dv[i], dvin[i],
std::numeric_limits<double>::epsilon());
}
// test IO of a scalar
double scalar = -1.0;
//value + offset + count
// nix::NDSize({}) indicates a scalar
scalar = -1.0;
da3.getData(scalar, nix::NDSize({}), nix::NDSize({0}));
CPPUNIT_ASSERT_DOUBLES_EQUAL(dv[0], scalar,
std::numeric_limits<double>::epsilon());
// nix::NDSize({1, 1, ..., 1}) has a number of elemts == 1
// so that should work too
scalar = -1.0;
da3.getData(scalar, nix::NDSize({1}), nix::NDSize({0}));
CPPUNIT_ASSERT_DOUBLES_EQUAL(dv[0], scalar,
std::numeric_limits<double>::epsilon());
scalar = -1.0;
da3.getData(scalar, nix::NDSize({1, 1}), nix::NDSize({0}));
CPPUNIT_ASSERT_DOUBLES_EQUAL(dv[0], scalar,
std::numeric_limits<double>::epsilon());
//value + offset
scalar = -1.0;
da3.getData(scalar, nix::NDSize({0}));
CPPUNIT_ASSERT_DOUBLES_EQUAL(dv[0], scalar,
std::numeric_limits<double>::epsilon());
//TODO: setData(scalar) + getData(scalar)
DataArray daA = block.createDataArray("append", "double", DataType::Double , NDSize({0, 4, 5}));
CPPUNIT_ASSERT_THROW(daA.appendData(DataType::Double, nullptr, NDSize({2, 4, 5}), 3), InvalidRank);
CPPUNIT_ASSERT_THROW(daA.appendData(DataType::Double, nullptr, NDSize({2, 4, 5, 6}), 0), IncompatibleDimensions);
CPPUNIT_ASSERT_THROW(daA.appendData(DataType::Double, nullptr, NDSize({4, 4, 6}), 0), IncompatibleDimensions);
std::vector<double> append_data(3*4*5, 1);
daA.appendData(DataType::Double, append_data.data(), {3, 4, 5}, 0);
CPPUNIT_ASSERT_EQUAL(NDSize({3, 4, 5}), daA.dataExtent());
std::fill(append_data.begin(), append_data.end(), 2);
daA.appendData(DataType::Double, append_data.data(), {3, 4, 5}, 0);
CPPUNIT_ASSERT_EQUAL(NDSize({6, 4, 5}), daA.dataExtent());
std::vector<double> append_check(6*4*5, 0);
daA.getData(DataType::Double, append_check.data(), {6, 4, 5}, {});
for(size_t i = 0; i < 6*4*5; i++) {
CPPUNIT_ASSERT_EQUAL(i > 3*4*5-1 ? 2.0 : 1.0, append_check[i]);
}
}
void getOffsetAndCount(const MultiTag &tag, const DataArray &array, size_t index, NDSize &offsets, NDSize &counts) {
DataArray positions = tag.positions();
DataArray extents = tag.extents();
NDSize position_size, extent_size;
size_t dimension_count = array.dimensionCount();
if (positions) {
position_size = positions.dataExtent();
}
if (extents) {
extent_size = extents.dataExtent();
}
if (!positions || index >= position_size[0]) {
throw nix::OutOfBounds("Index out of bounds of positions!", 0);
}
if (extents && index >= extent_size[0]) {
throw nix::OutOfBounds("Index out of bounds of positions or extents!", 0);
}
if (position_size.size() == 1 && dimension_count != 1) {
throw nix::IncompatibleDimensions("Number of dimensions in positions does not match dimensionality of data",
"util::getOffsetAndCount");
}
if (position_size.size() > 1 && position_size[1] > dimension_count) {
throw nix::IncompatibleDimensions("Number of dimensions in positions does not match dimensionality of data",
"util::getOffsetAndCount");
}
if (extents && extent_size.size() > 1 && extent_size[1] > dimension_count) {
throw nix::IncompatibleDimensions("Number of dimensions in extents does not match dimensionality of data",
"util::getOffsetAndCount");
}
NDSize temp_offset = NDSize{static_cast<NDSize::value_type>(index), static_cast<NDSize::value_type>(0)};
NDSize temp_count{static_cast<NDSize::value_type>(1), static_cast<NDSize::value_type>(dimension_count)};
vector<double> offset;
positions.getData(offset, temp_count, temp_offset);
NDSize data_offset(dimension_count, static_cast<size_t>(0));
NDSize data_count(dimension_count, static_cast<size_t>(1));
vector<string> units = tag.units();
for (size_t i = 0; i < offset.size(); ++i) {
Dimension dimension = array.getDimension(i+1);
string unit = "none";
if (i <= units.size() && units.size() > 0) {
unit = units[i];
}
data_offset[i] = positionToIndex(offset[i], unit, dimension);
}
if (extents) {
vector<double> extent;
extents.getData(extent, temp_count, temp_offset);
for (size_t i = 0; i < extent.size(); ++i) {
Dimension dimension = array.getDimension(i+1);
string unit = "none";
if (i <= units.size() && units.size() > 0) {
unit = units[i];
}
ndsize_t c = positionToIndex(offset[i] + extent[i], unit, dimension) - data_offset[i];
data_count[i] = (c > 1) ? c : 1;
}
}
offsets = data_offset;
counts = data_count;
}