diff --git a/CMakeLists.txt b/CMakeLists.txt index 236e323..b3d7377 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -427,6 +427,7 @@ if(AARE_TESTS) set(TestSources ${CMAKE_CURRENT_SOURCE_DIR}/src/algorithm.test.cpp ${CMAKE_CURRENT_SOURCE_DIR}/src/defs.test.cpp + ${CMAKE_CURRENT_SOURCE_DIR}/src/decode.test.cpp ${CMAKE_CURRENT_SOURCE_DIR}/src/Dtype.test.cpp ${CMAKE_CURRENT_SOURCE_DIR}/src/Frame.test.cpp ${CMAKE_CURRENT_SOURCE_DIR}/src/geo_helpers.test.cpp diff --git a/include/aare/NDView.hpp b/include/aare/NDView.hpp index 55b442b..ddb5d1c 100644 --- a/include/aare/NDView.hpp +++ b/include/aare/NDView.hpp @@ -184,4 +184,9 @@ std::ostream& operator <<(std::ostream& os, const NDView& arr){ } +template +NDView make_view(std::vector& vec){ + return NDView(vec.data(), {static_cast(vec.size())}); +} + } // namespace aare \ No newline at end of file diff --git a/include/aare/decode.hpp b/include/aare/decode.hpp index 1c3c479..e784c4a 100644 --- a/include/aare/decode.hpp +++ b/include/aare/decode.hpp @@ -1,6 +1,7 @@ #pragma once #include +#include #include namespace aare { @@ -10,4 +11,16 @@ uint16_t adc_sar_04_decode64to16(uint64_t input); void adc_sar_05_decode64to16(NDView input, NDView output); void adc_sar_04_decode64to16(NDView input, NDView output); -} // namespace aare \ No newline at end of file + +/** + * @brief Apply custom weights to a 16-bit input value. Will sum up weights[i]**i + * for each bit i that is set in the input value. + * @throws std::out_of_range if weights.size() < 16 + * @param input 16-bit input value + * @param weights vector of weights, size must be less than or equal to 16 + */ +double apply_custom_weights(uint16_t input, const NDView weights); + +void apply_custom_weights(NDView input, NDView output, const NDView weights); + +} // namespace aare diff --git a/python/aare/__init__.py b/python/aare/__init__.py index 98e8c72..db9672f 100644 --- a/python/aare/__init__.py +++ b/python/aare/__init__.py @@ -13,6 +13,10 @@ from ._aare import ClusterFinderMT, ClusterCollector, ClusterFileSink, ClusterVe from ._aare import fit_gaus, fit_pol1 from ._aare import Interpolator + + +from ._aare import apply_custom_weights + from .CtbRawFile import CtbRawFile from .RawFile import RawFile from .ScanParameters import ScanParameters diff --git a/python/src/ctb_raw_file.hpp b/python/src/ctb_raw_file.hpp index 56e571b..a88a9d1 100644 --- a/python/src/ctb_raw_file.hpp +++ b/python/src/ctb_raw_file.hpp @@ -10,6 +10,8 @@ #include "aare/decode.hpp" // #include "aare/fClusterFileV2.hpp" +#include "np_helper.hpp" + #include #include #include @@ -65,35 +67,54 @@ m.def("adc_sar_04_decode64to16", [](py::array_t input) { return output; }); - py::class_(m, "CtbRawFile") - .def(py::init()) - .def("read_frame", - [](CtbRawFile &self) { - size_t image_size = self.image_size_in_bytes(); - py::array image; - std::vector shape; - shape.reserve(2); - shape.push_back(1); - shape.push_back(image_size); +m.def( + "apply_custom_weights", + [](py::array_t &input, + py::array_t + &weights) { + - py::array_t header(1); + // Create new array with same shape as the input array (uninitialized values) + py::buffer_info buf = input.request(); + py::array_t output(buf.shape); - // always read bytes - image = py::array_t(shape); + // Use NDViews to call into the C++ library + auto weights_view = make_view_1d(weights); + NDView input_view(input.mutable_data(), {input.size()}); + NDView output_view(output.mutable_data(), {output.size()}); - self.read_into( - reinterpret_cast(image.mutable_data()), - header.mutable_data()); + apply_custom_weights(input_view, output_view, weights_view); + return output; + }); - return py::make_tuple(header, image); - }) - .def("seek", &CtbRawFile::seek) - .def("tell", &CtbRawFile::tell) - .def("master", &CtbRawFile::master) +py::class_(m, "CtbRawFile") + .def(py::init()) + .def("read_frame", + [](CtbRawFile &self) { + size_t image_size = self.image_size_in_bytes(); + py::array image; + std::vector shape; + shape.reserve(2); + shape.push_back(1); + shape.push_back(image_size); - .def_property_readonly("image_size_in_bytes", - &CtbRawFile::image_size_in_bytes) + py::array_t header(1); - .def_property_readonly("frames_in_file", &CtbRawFile::frames_in_file); + // always read bytes + image = py::array_t(shape); -} \ No newline at end of file + self.read_into(reinterpret_cast(image.mutable_data()), + header.mutable_data()); + + return py::make_tuple(header, image); + }) + .def("seek", &CtbRawFile::seek) + .def("tell", &CtbRawFile::tell) + .def("master", &CtbRawFile::master) + + .def_property_readonly("image_size_in_bytes", + &CtbRawFile::image_size_in_bytes) + + .def_property_readonly("frames_in_file", &CtbRawFile::frames_in_file); + +} diff --git a/src/NDView.test.cpp b/src/NDView.test.cpp index 3070de6..6bc8eef 100644 --- a/src/NDView.test.cpp +++ b/src/NDView.test.cpp @@ -190,4 +190,16 @@ TEST_CASE("compare two views") { NDView view2(vec2.data(), Shape<2>{3, 4}); REQUIRE((view1 == view2)); +} + + +TEST_CASE("Create a view over a vector"){ + std::vector vec; + for (int i = 0; i != 12; ++i) { + vec.push_back(i); + } + auto v = aare::make_view(vec); + REQUIRE(v.shape()[0] == 12); + REQUIRE(v[0] == 0); + REQUIRE(v[11] == 11); } \ No newline at end of file diff --git a/src/decode.cpp b/src/decode.cpp index 17c033d..8ac7bc0 100644 --- a/src/decode.cpp +++ b/src/decode.cpp @@ -1,5 +1,5 @@ #include "aare/decode.hpp" - +#include namespace aare { uint16_t adc_sar_05_decode64to16(uint64_t input){ @@ -22,6 +22,10 @@ uint16_t adc_sar_05_decode64to16(uint64_t input){ } void adc_sar_05_decode64to16(NDView input, NDView output){ + if(input.shape() != output.shape()){ + throw std::invalid_argument(LOCATION + " input and output shapes must match"); + } + for(int64_t i = 0; i < input.shape(0); i++){ for(int64_t j = 0; j < input.shape(1); j++){ output(i,j) = adc_sar_05_decode64to16(input(i,j)); @@ -49,6 +53,9 @@ uint16_t adc_sar_04_decode64to16(uint64_t input){ } void adc_sar_04_decode64to16(NDView input, NDView output){ + if(input.shape() != output.shape()){ + throw std::invalid_argument(LOCATION + " input and output shapes must match"); + } for(int64_t i = 0; i < input.shape(0); i++){ for(int64_t j = 0; j < input.shape(1); j++){ output(i,j) = adc_sar_04_decode64to16(input(i,j)); @@ -56,6 +63,40 @@ void adc_sar_04_decode64to16(NDView input, NDView outpu } } +double apply_custom_weights(uint16_t input, const NDView weights) { + if(weights.size() > 16){ + throw std::invalid_argument("weights size must be less than or equal to 16"); + } + + double result = 0.0; + for (ssize_t i = 0; i < weights.size(); ++i) { + result += ((input >> i) & 1) * std::pow(weights[i], i); + } + return result; + +} + +void apply_custom_weights(NDView input, NDView output, const NDView weights) { + if(input.shape() != output.shape()){ + throw std::invalid_argument(LOCATION + " input and output shapes must match"); + } + + //Calculate weights to avoid repeatedly calling std::pow + std::vector weights_powers(weights.size()); + for (ssize_t i = 0; i < weights.size(); ++i) { + weights_powers[i] = std::pow(weights[i], i); + } + + // Apply custom weights to each element in the input array + for (ssize_t i = 0; i < input.shape(0); i++) { + double result = 0.0; + for (size_t bit_index = 0; bit_index < weights_powers.size(); ++bit_index) { + result += ((input(i) >> bit_index) & 1) * weights_powers[bit_index]; + } + output(i) = result; + } +} + } // namespace aare diff --git a/src/decode.test.cpp b/src/decode.test.cpp new file mode 100644 index 0000000..a90213c --- /dev/null +++ b/src/decode.test.cpp @@ -0,0 +1,80 @@ +#include "aare/decode.hpp" + +#include +#include +#include "aare/NDArray.hpp" +using Catch::Matchers::WithinAbs; +#include + +TEST_CASE("test_adc_sar_05_decode64to16"){ + uint64_t input = 0; + uint16_t output = aare::adc_sar_05_decode64to16(input); + CHECK(output == 0); + + + // bit 29 on th input is bit 0 on the output + input = 1UL << 29; + output = aare::adc_sar_05_decode64to16(input); + CHECK(output == 1); + + // test all bits by iteratting through the bitlist + std::vector bitlist = {29, 19, 28, 18, 31, 21, 27, 20, 24, 23, 25, 22}; + for (size_t i = 0; i < bitlist.size(); i++) { + input = 1UL << bitlist[i]; + output = aare::adc_sar_05_decode64to16(input); + CHECK(output == (1 << i)); + } + + + // test a few "random" values + input = 0; + input |= (1UL << 29); + input |= (1UL << 19); + input |= (1UL << 28); + output = aare::adc_sar_05_decode64to16(input); + CHECK(output == 7UL); + + + input = 0; + input |= (1UL << 18); + input |= (1UL << 27); + input |= (1UL << 25); + output = aare::adc_sar_05_decode64to16(input); + CHECK(output == 1096UL); + + input = 0; + input |= (1UL << 25); + input |= (1UL << 22); + output = aare::adc_sar_05_decode64to16(input); + CHECK(output == 3072UL); + } + + + TEST_CASE("test_apply_custom_weights") { + + uint16_t input = 1; + aare::NDArray weights_data({3}, 0.0); + weights_data(0) = 1.7; + weights_data(1) = 2.1; + weights_data(2) = 1.8; + + auto weights = weights_data.view(); + + + double output = aare::apply_custom_weights(input, weights); + CHECK_THAT(output, WithinAbs(1.0, 0.001)); + + input = 1UL << 1; + output = aare::apply_custom_weights(input, weights); + CHECK_THAT(output, WithinAbs(2.1, 0.001)); + + + input = 1UL << 2; + output = aare::apply_custom_weights(input, weights); + CHECK_THAT(output, WithinAbs(3.24, 0.001)); + + input = 0b111; + output = aare::apply_custom_weights(input, weights); + CHECK_THAT(output, WithinAbs(6.34, 0.001)); + + } \ No newline at end of file