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more testing of the data access methods and some fixing #838

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more testing of the data access methods and some fixing #838

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b4bc440
[data_access] refactor positionAndExtentInData
jgrewe May 23, 2021
cee3f71
[data access] debug code
jgrewe May 9, 2022
f1c03cd
[dimensions] more tests for dimensions
jgrewe May 14, 2022
120dad7
[Dimensions/dataaccess] delegate range matching handling to dataAccess
jgrewe May 14, 2022
0f41b27
[cleanup] remove cerr and commnets
jgrewe May 25, 2022
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5 changes: 2 additions & 3 deletions include/nix/DataView.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,6 @@ class NIXAPI DataView : public DataSet {
public:
DataView(DataArray da, NDSize count, NDSize offset)
: array(std::move(da)), offset(std::move(offset)), count(std::move(count)) {

if (this->offset.size() != array.dataExtent().size()) {
throw IncompatibleDimensions("DataView offset dimensionality does not match dimensionality of data", "nix::DataView");
}
Expand All @@ -28,7 +27,7 @@ class NIXAPI DataView : public DataSet {
}
if (this->offset + this->count > array.dataExtent()) {
throw OutOfBounds("Trying to create DataView which is out of bounds");
}
}
}

// the DataIO interface implementation
Expand Down Expand Up @@ -59,4 +58,4 @@ class NIXAPI DataView : public DataSet {

} // nix::

#endif // DATA_VIEW_HPP
#endif // DATA_VIEW_HPP
12 changes: 6 additions & 6 deletions include/nix/util/dataAccess.hpp
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Expand Up @@ -397,23 +397,23 @@ NIXAPI DEPRECATED DataView retrieveData(const Tag &tag, const DataArray &array,
/**
* @brief Checks whether a given position is in the extent of the given DataArray.
*
* @param data The data array.
* @param data_size The extent of the data array.
* @param position The position.
*
* @return True if the position is in the extent of the data array, false otherwise.
*/
NIXAPI bool positionInData(const DataArray &data, const NDSize &position);
NIXAPI bool positionInData(const NDSize &data_size, const NDSize &position);

/**
* @brief Checks whether a given position plus count is in the extent of the given DataArray.
* @brief Checks whether a given offset plus count is in the extent of the given DataArray.
*
* @param data The DataArray.
* @param position The position
* @param offset The offset
* @param count The number of elements per dimension.
*
* @return True if position and count are in the extent of the data array, false otherwise.
* @return True if offset and offset + count are in the extent of the data array, false otherwise.
*/
NIXAPI bool positionAndExtentInData(const DataArray &data, const NDSize &position, const NDSize &count);
NIXAPI bool positionAndExtentInData(const DataArray &data, const NDSize &offset, const NDSize &count);

/**
* @brief Retruns the feature data associated with a Tag.
Expand Down
23 changes: 13 additions & 10 deletions src/Dimensions.cpp
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Expand Up @@ -263,14 +263,15 @@ boost::optional<std::pair<ndsize_t, ndsize_t>> SampledDimension::indexOf(const d
boost::optional<std::pair<ndsize_t, ndsize_t>> SampledDimension::indexOf(double start, double end, const double sampling_interval,
const double offset, const RangeMatch match) const {
boost::optional<std::pair<ndsize_t, ndsize_t>> indices;
PositionMatch pos_match = match == RangeMatch::Inclusive ? PositionMatch::LessOrEqual : PositionMatch::Less;

if (start > end) {
return indices;
}
PositionMatch end_matching;
end_matching = (match == RangeMatch::Inclusive) ? PositionMatch::LessOrEqual : PositionMatch::Less;

boost::optional<ndsize_t> si = getSampledIndex(start, offset, sampling_interval, PositionMatch::GreaterOrEqual);
boost::optional<ndsize_t> ei = getSampledIndex(end, offset, sampling_interval, pos_match);
boost::optional<ndsize_t> ei = getSampledIndex(end, offset, sampling_interval, end_matching);

if (si && ei && *si <= *ei) {
indices = std::pair<ndsize_t, ndsize_t>(*si, *ei);
}
Expand Down Expand Up @@ -453,10 +454,12 @@ boost::optional<std::pair<ndsize_t, ndsize_t>> SetDimension::indexOf(double star
if (start > end) {
return index;
}
PositionMatch end_match = match == RangeMatch::Inclusive ? PositionMatch::LessOrEqual : PositionMatch::Less;

PositionMatch end_matching;
end_matching = (match == RangeMatch::Inclusive) ? PositionMatch::LessOrEqual : PositionMatch::Less;

boost::optional<ndsize_t> si = getSetIndex(start, set_labels, PositionMatch::GreaterOrEqual);
boost::optional<ndsize_t> ei = getSetIndex(end, set_labels, end_match);
boost::optional<ndsize_t> ei = getSetIndex(end, set_labels, end_matching);

if (si && ei && *si <= *ei) {
index = std::pair<ndsize_t, ndsize_t>(*si, *ei);
}
Expand Down Expand Up @@ -662,8 +665,9 @@ boost::optional<std::pair<ndsize_t, ndsize_t>> RangeDimension::indexOf(double st
if (!si) {
return range;
}
PositionMatch endMatching = (match == RangeMatch::Inclusive) ? PositionMatch::LessOrEqual : PositionMatch::Less;
boost::optional<ndsize_t> ei = getIndex(end, ticks, endMatching);
PositionMatch end_matching;
end_matching = (match == RangeMatch::Inclusive) ? PositionMatch::LessOrEqual : PositionMatch::Less;
boost::optional<ndsize_t> ei = getIndex(end, ticks, end_matching);
if (ei && *si <= *ei) {
range = std::pair<ndsize_t, ndsize_t>(*si, *ei);
}
Expand Down Expand Up @@ -716,7 +720,6 @@ std::vector<boost::optional<std::pair<ndsize_t, ndsize_t>>> RangeDimension::inde
if (start_positions.size() != end_positions.size()) {
throw runtime_error("Dimension::IndexOf - Number of start and end positions must match!");
}

std::vector<boost::optional<std::pair<ndsize_t, ndsize_t>>> indices;
vector<double> ticks = this->ticks();
for (size_t i = 0; i < start_positions.size(); ++i) {
Expand Down
38 changes: 22 additions & 16 deletions src/util/dataAccess.cpp
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Expand Up @@ -480,9 +480,16 @@ void getOffsetAndCount(const MultiTag &tag, const DataArray &array, const vector
vector<vector<optional<pair<ndsize_t, ndsize_t>>>> data_indices;
for (size_t dim_index = 0; dim_index < dimensions.size(); ++dim_index) {
vector<string> temp_units(start_positions[dim_index].size(), units[dim_index]);
vector<optional<pair<ndsize_t, ndsize_t>>> ranges = positionToIndex(start_positions[dim_index], end_positions[dim_index],
temp_units, match, dimensions[dim_index]);

vector<optional<pair<ndsize_t, ndsize_t>>> ranges;
RangeMatch rm; // The range match needs to be adjusted if the extent is 0.0 in that case we want have an inclusive matching
if (start_positions[dim_index] == end_positions[dim_index]) {
rm = RangeMatch::Inclusive;
} else {
rm = match;
}
ranges = positionToIndex(start_positions[dim_index], end_positions[dim_index],
temp_units, rm, dimensions[dim_index]);

data_indices.push_back(ranges);
}
// at this point we do have all the start and end indices of the tagged positions that the caller wants the data of.
Expand All @@ -497,15 +504,17 @@ void getOffsetAndCount(const MultiTag &tag, const DataArray &array, const vector
ndsize_t count = (*opt_range).second - (*opt_range).first;
data_count[dim_index] += count;
} else {
data_count[dim_index] = 0;
if (end_positions[dim_index][i] == start_positions[dim_index][i]) {
optional<ndsize_t> ofst = positionToIndex(end_positions[dim_index][i], units[dim_index], PositionMatch::GreaterOrEqual, dimensions[dim_index]);
if (!ofst) {
throw nix::OutOfBounds("util::offsetAndCount:An invalid range was encountered!");
}
temp_offset[i] = *ofst;
temp_offset[i] = *ofst; // I do not remember what this might be good for...
}
}
}

offsets.push_back(data_offset);
counts.push_back(data_count);
}
Expand All @@ -519,24 +528,24 @@ void getOffsetAndCount(const MultiTag &tag, const DataArray &array, ndsize_t ind
}


bool positionInData(const DataArray &data, const NDSize &position) {
NDSize data_size = data.dataExtent();
bool positionInData(const NDSize &data_size, const NDSize &position) {
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];
valid &= position[i] <= data_size[i];
}
return valid;
}


bool positionAndExtentInData(const DataArray &data, const NDSize &position, const NDSize &count) {
NDSize pos = position + count;
pos -= 1;
return positionInData(data, pos);
bool positionAndExtentInData(const DataArray &data, const NDSize &offset, const NDSize &count) {
NDSize end_pos = offset + count;
NDSize data_size = data.dataExtent();
bool valid = positionInData(data_size, offset);
valid &= positionInData(data_size, end_pos);
return valid;
}


Expand Down Expand Up @@ -675,6 +684,7 @@ vector<DataView> taggedData(const MultiTag &tag, vector<ndsize_t> &position_indi
vector<NDSize> counts, offsets;
vector<DataView> views;

// if no positions are given, we will return dataviews for all positions
if (position_indices.size() < 1) {
size_t pos_count = check::fits_in_size_t(tag.positions().dataExtent()[0],
"Number of positions > size_t.");
Expand All @@ -683,11 +693,7 @@ vector<DataView> taggedData(const MultiTag &tag, vector<ndsize_t> &position_indi
}

getOffsetAndCount(tag, array, position_indices, offsets, counts, match);

for (size_t i = 0; i < offsets.size(); ++i) {
if (!positionAndExtentInData(array, offsets[i], counts[i])) {
throw OutOfBounds("References data slice out of the extent of the DataArray!", 0);
}
DataView io = DataView(array, counts[i], offsets[i]);
views.push_back(io);
}
Expand Down
23 changes: 15 additions & 8 deletions test/BaseTestDataAccess.cpp
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Expand Up @@ -198,7 +198,8 @@ void BaseTestDataAccess::testPositionToIndexSetDimension() {

CPPUNIT_ASSERT_THROW(util::positionToIndex({5.0, 0.}, {10.5}, RangeMatch::Inclusive, setDim), std::runtime_error);

vector<optional<pair<ndsize_t, ndsize_t>>> ranges = util::positionToIndex({5.0, 0.}, {10.5, 1.0}, RangeMatch::Inclusive, setDim);
vector<optional<pair<ndsize_t, ndsize_t>>> ranges;
ranges = util::positionToIndex({5.0, 0.}, {10.5, 1.0}, RangeMatch::Inclusive, setDim);
CPPUNIT_ASSERT(ranges.size() == 2);
CPPUNIT_ASSERT(!ranges[0]);
CPPUNIT_ASSERT(ranges[1] && (*ranges[1]).first == 0 && (*ranges[1]).second == 1);
Expand Down Expand Up @@ -288,19 +289,18 @@ void BaseTestDataAccess::testOffsetAndCount() {
CPPUNIT_ASSERT_THROW(util::getOffsetAndCount(multi_tag, data_array, -1, offsets, counts), nix::OutOfBounds); // not a valid position index
CPPUNIT_ASSERT_THROW(util::getOffsetAndCount(multi_tag, data_array, 3, offsets, counts), nix::OutOfBounds); // not a valid position index

util::getOffsetAndCount(multi_tag, data_array, 0, offsets, counts);
util::getOffsetAndCount(multi_tag, data_array, 0, offsets, counts, RangeMatch::Inclusive);
CPPUNIT_ASSERT(offsets.size() == 4);
CPPUNIT_ASSERT(counts.size() == 4);
CPPUNIT_ASSERT(offsets[0] == 0 && offsets[1] == 3 && offsets[2] == 2 && offsets[3] == 1);
CPPUNIT_ASSERT(counts[0] == 1 && counts[1] == 7 && counts[2] == 2 && counts[3] == 3);

util::getOffsetAndCount(multi_tag, data_array, 0, offsets, counts, RangeMatch::Exclusive);
CPPUNIT_ASSERT(offsets.size() == 4);
CPPUNIT_ASSERT(counts.size() == 4);
CPPUNIT_ASSERT(offsets[0] == 0 && offsets[1] == 3 && offsets[2] == 2 && offsets[3] == 1);
CPPUNIT_ASSERT(counts[0] == 1 && counts[1] == 6 && counts[2] == 2 && counts[3] == 2);
CPPUNIT_ASSERT(counts[0] == 1 && counts[1] == 7 && counts[2] == 2 && counts[3] == 3);

util::getOffsetAndCount(multi_tag, data_array, 1, offsets, counts);
util::getOffsetAndCount(multi_tag, data_array, 1, offsets, counts, RangeMatch::Inclusive);
CPPUNIT_ASSERT(offsets.size() == 4);
CPPUNIT_ASSERT(counts.size() == 4);
CPPUNIT_ASSERT(offsets[0] == 0 && offsets[1] == 8 && offsets[2] == 1 && offsets[3] == 1);
Expand All @@ -317,11 +317,19 @@ void BaseTestDataAccess::testOffsetAndCount() {
void BaseTestDataAccess::testPositionInData() {
NDSize offsets, counts;
util::getOffsetAndCount(multi_tag, data_array, 0, offsets, counts);
CPPUNIT_ASSERT(util::positionInData(data_array, offsets));
CPPUNIT_ASSERT(util::positionInData(data_array.dataExtent(), offsets));
CPPUNIT_ASSERT(util::positionAndExtentInData(data_array, offsets, counts));

util::getOffsetAndCount(multi_tag, data_array, 1, offsets, counts);
CPPUNIT_ASSERT(util::positionInData(data_array, offsets));
CPPUNIT_ASSERT(util::positionInData(data_array.dataExtent(), offsets));
CPPUNIT_ASSERT(!util::positionAndExtentInData(data_array, offsets, counts));

util::getOffsetAndCount(multi_tag, data_array, 0, offsets, counts, RangeMatch::Exclusive);
CPPUNIT_ASSERT(util::positionInData(data_array.dataExtent(), offsets));
CPPUNIT_ASSERT(util::positionAndExtentInData(data_array, offsets, counts));

util::getOffsetAndCount(multi_tag, data_array, 1, offsets, counts, RangeMatch::Exclusive);
CPPUNIT_ASSERT(util::positionInData(data_array.dataExtent(), offsets));
CPPUNIT_ASSERT(!util::positionAndExtentInData(data_array, offsets, counts));
}

Expand Down Expand Up @@ -454,7 +462,6 @@ void BaseTestDataAccess::testMultiTagFeatureData() {
}
}
index_data.setData(data1);

DataArray tagged_data = block.createDataArray("tagged feature data", "test", nix::DataType::Double, {10, 20, 10, 10});
dim1 = tagged_data.appendSampledDimension(1.0);
dim1.unit("ms");
Expand Down
7 changes: 6 additions & 1 deletion test/BaseTestDimension.cpp
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Expand Up @@ -661,7 +661,7 @@ void BaseTestDimension::testRangeDimUnit() {

std::vector<double> ticks;
for (size_t i = 0; i < 5; i++) {
ticks.push_back(i * boost::math::constants::pi<double>());
ticks.push_back(i * boost::math::constants::pi<double>());
}
Dimension d = data_array.appendRangeDimension(ticks);
CPPUNIT_ASSERT(d.dimensionType() == DimensionType::Range);
Expand Down Expand Up @@ -822,6 +822,11 @@ void BaseTestDimension::testRangeDimIndexOf() {
CPPUNIT_ASSERT(!range);
range = rd.indexOf(100., -100., {}, RangeMatch::Exclusive);
CPPUNIT_ASSERT(!range);
range = rd.indexOf(-100., -100, {}, RangeMatch::Inclusive);
CPPUNIT_ASSERT(range);
CPPUNIT_ASSERT(range && (*range).first == 0 && (*range).second == 0);
range = rd.indexOf(-100., -100, {}, RangeMatch::Exclusive);
CPPUNIT_ASSERT(!range);

range = rd.indexOf(100., -100., rd.ticks(), RangeMatch::Exclusive);
CPPUNIT_ASSERT(!range);
Expand Down