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Commit fd919a8d authored by Samuel Debionne's avatar Samuel Debionne
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Merge branch '111-add-reader-mode' into 'develop' 

Resolve "Add Reader Mode"

Closes #111

See merge request !110
parents 1f3c3e80 613aa2e0
Pipeline #75269 passed with stages
in 9 minutes and 11 seconds
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bench/io/bench_io_hdf5.cpp
View file @ fd919a8d
......@@ -105,7 +105,9 @@ static void graph_io_hdf5_raw(benchmark::State& state)
const int nb_frames = 10000;
auto src = input_node(g, nb_frames);
lima::io::h5::writer writer("test_raw.h5", nb_frames, 1, dimensions_t{512, 512}, lima::pixel_enum::gray8);
lima::io::h5::saving_params params;
params.nb_frames_per_file = nb_frames;
lima::io::h5::writer writer("test_writer_raw.h5", params, dimensions_t{512, 512}, lima::pixel_enum::gray8);
flow::function_node<frame_t> write_view(
g, flow::serial, [&writer](frame_t in) { writer.write_view(lima::view(in), in.metadata.idx); });
......@@ -157,8 +159,10 @@ static void graph_io_hdf5_chunk_raw(benchmark::State& state)
}
});
lima::io::h5::writer writer("test_raw.h5", nb_frames, nb_frames_per_chunk, dimensions_t{512, 512},
lima::pixel_enum::gray8);
lima::io::h5::saving_params params;
params.nb_frames_per_file = nb_frames;
params.nb_frames_per_chunk = nb_frames_per_chunk;
lima::io::h5::writer writer("test_writer_raw.h5", params, dimensions_t{512, 512}, lima::pixel_enum::gray8);
flow::function_node<chunk_ptr_t> write_chunk(
g, flow::serial, [&writer](chunk_ptr_t in) { writer.write_chunk(in->data.data(), in->data.size(), in->id); });
......@@ -210,8 +214,10 @@ static void graph_io_hdf5_comp(benchmark::State& state)
return res;
});
lima::io::h5::writer writer("test_comp.h5", nb_frames, 1, dimensions_t{512, 512}, lima::pixel_enum::gray8,
lima::io::h5::compression_enum::bshuf_lz4);
lima::io::h5::saving_params params;
params.nb_frames_per_file = nb_frames;
params.compression = lima::io::h5::compression_enum::bshuf_lz4;
lima::io::h5::writer writer("test_writer_raw.h5", params, dimensions_t{512, 512}, lima::pixel_enum::gray8);
flow::function_node<chunk_ptr_t> write_chunk(
g, flow::serial, [&writer](chunk_ptr_t in) { writer.write_chunk(in->data.data(), in->data.size(), in->id); });
......@@ -290,8 +296,11 @@ static void graph_io_hdf5_chunk_comp(benchmark::State& state)
return res;
});
lima::io::h5::writer writer("test_chunk_comp.h5", nb_frames, nb_frames_per_chunk, dimensions_t{512, 512},
lima::pixel_enum::gray8, lima::io::h5::compression_enum::bshuf_lz4);
lima::io::h5::saving_params params;
params.nb_frames_per_file = nb_frames;
params.nb_frames_per_chunk = nb_frames_per_chunk;
params.compression = lima::io::h5::compression_enum::bshuf_lz4;
lima::io::h5::writer writer("test_writer_raw.h5", params, dimensions_t{512, 512}, lima::pixel_enum::gray8);
flow::function_node<chunk_ptr_t> write_chunk(g, flow::serial, [&writer, &nb_frames_per_chunk](chunk_ptr_t in) {
writer.write_chunk(in->data.data(), in->data.size(), in->id);
......
detectors/simulator/include/lima/detectors/simulator/hw/enums.describe.hpp
View file @ fd919a8d
......@@ -11,13 +11,13 @@
#include <boost/describe/io_enums.hpp>
#include <lima/detectors/simulator/hw/enums.hpp>
#include <lima/detectors/simulator/hw/generator/enums.describe.hpp>
namespace lima
{
namespace detectors::simulator::hw
{
BOOST_DESCRIBE_ENUM(generator_type_enum, gauss, diffraction)
BOOST_DESCRIBE_ENUM(channel_depth_enum, uint8, uint16, uint32, float32)
BOOST_DESCRIBE_ENUM(image_source_enum, generator, loader)
using boost::describe::operator<<;
using boost::describe::operator>>;
......
detectors/simulator/include/lima/detectors/simulator/hw/enums.hpp
View file @ fd919a8d
......@@ -6,25 +6,17 @@
#pragma once
#include <lima/detectors/simulator/hw/generator/enums.hpp>
namespace lima
{
namespace detectors::simulator::hw
{
/// Generator type
enum class generator_type_enum : int
{
gauss,
diffraction
};
/// Pixel bit depth
enum class channel_depth_enum : int
/// Image source type
enum class image_source_enum : int
{
unknown,
uint8,
uint16,
uint32,
float32
generator,
loader
};
} // namespace detectors::simulator::hw
......
detectors/simulator/include/lima/detectors/simulator/hw/generator.hpp
View file @ fd919a8d
......@@ -6,147 +6,75 @@
#pragma once
#include <cmath>
#include <vector>
#include <lima/core/pixel.hpp>
#include <lima/core/image/typedefs.hpp>
#include <lima/processing/serial/generator.hpp>
#include <lima/detectors/simulator/hw/params.hpp>
#include <lima/detectors/simulator/hw/generator/params.hpp>
namespace lima
{
namespace detectors::simulator::hw
namespace detectors::simulator::hw::generator
{
/// Calculates Gauss(x,y) for a given peak
///
/// \param[in] x X-coord
/// \param[in] y Y-coord
/// \param[in] x0 X-coord of the center
/// \param[in] y0 Y-coord of the center
/// \param[in] fwhm Full Width at Half Maximum
/// \param[in] max the central maximum value
/// \return Gauss(x,y)
inline double gauss_2d(std::ptrdiff_t x, std::ptrdiff_t y, double x0, double y0, double fwhm, double max)
// The default channel converter maps the range of the value of the source to the destination,
// this is not what we want here
struct channel_converter_round
{
const double SGM_FWHM = 0.42466090014400952136075141705144; // 1/(2*sqrt(2*ln(2)))
double sigma = SGM_FWHM * std::fabs(fwhm);
return max * std::exp(-((x - x0) * (x - x0) + (y - y0) * (y - y0)) / (2 * sigma * sigma));
}
/// Calculates the summary intensity at certain point
///
/// \param[in] x X-coord
/// \param[in] y Y-coord
/// \return intensity
///
inline double diffract(boost::gil::point<std::ptrdiff_t> dim, double x, double y)
{
const double pi = 3.14159265358979323846;
x -= dim.x / 2;
y -= dim.y / 2;
double r = std::sqrt(x * x + y * y);
double w = (2 * pi / 100 * (0.5 + r / 500));
double ar = (r >= 300) ? (r - 300) : 0;
double a = std::exp(-std::pow(ar / 500, 4.0)) / (r / 5000 + 0.1);
return a * std::pow(std::cos(r * w), 20.0);
}
struct generate_gauss
{
using point_t = boost::gil::point<std::ptrdiff_t>;
using const_t = generate_gauss;
using value_type = boost::gil::pixel<float, boost::gil::gray_layout_t>;
using reference = value_type;
using const_reference = value_type;
using argument_type = point_t;
using result_type = reference;
static const bool is_mutable = false;
generate_gauss(int frame_nr, double grow_factor) : m_frame_nr(frame_nr), m_grow_factor(grow_factor) {}
result_type operator()(const point_t& p) const
template <typename Ch1, typename Ch2>
void operator()(const Ch1& src, Ch2& dst) const
{
double res = 0.0;
// For each peaks
for (auto&& peak : m_peaks)
// Add gaussian
res += gauss_2d(p.x, p.y, peak.x0, peak.y0, peak.fwhm, peak.max);
// Apply grow factor
res *= (1.0 + m_grow_factor * m_frame_nr);
return value_type(res);
dst = std::round(src);
}
std::vector<gauss_peak> m_peaks;
int m_frame_nr = 0;
double m_grow_factor = 0.0;
};
typedef generate_gauss::point_t point_t;
typedef boost::gil::virtual_2d_locator<generate_gauss, false> generate_gauss_locator_t;
typedef boost::gil::image_view<generate_gauss_locator_t> generate_gauss_view_t;
struct generate_diffraction
struct generator
{
using point_t = boost::gil::point<std::ptrdiff_t>;
using const_t = generate_diffraction;
using value_type = boost::gil::pixel<float, boost::gil::gray_layout_t>;
using reference = value_type;
using const_reference = value_type;
using argument_type = point_t;
using result_type = reference;
static const bool is_mutable = false;
generate_diffraction(int frame_nr, double grow_factor, double diffract_x, double diffract_y,
double diffract_sx = 0.0, double diffract_sy = 0.0) :
m_frame_nr(frame_nr),
m_grow_factor(grow_factor),
m_diffract_x(diffract_x),
m_diffract_y(diffract_y),
m_diffract_sx(diffract_sx),
m_diffract_sy(diffract_sy)
generator(init_params const& init_pars, exec_params const& exec_pars) :
m_init_params(init_pars), m_exec_params(exec_pars)
{
}
result_type operator()(const point_t& p) const
{
double res = 0.0;
double gx = m_diffract_x + m_frame_nr * m_diffract_sx;
double gy = m_diffract_y + m_frame_nr * m_diffract_sy;
point_t dimensions() { return {m_init_params.width, m_init_params.height}; }
// For each peaks
for (auto&& peak : m_peaks)
// Add gaussian
res += gauss_2d(gx, gy, peak.x0, peak.y0, peak.fwhm, peak.max);
pixel_enum pixel_type() { return m_exec_params.pixel_type; }
// Apply grow factor
res *= (1 + m_grow_factor * m_frame_nr);
res *= diffract(m_dim, p.x, p.y);
return value_type(res);
// visitor will be called with generated image view
template <typename Visitor>
void frame_getter_visit(int frame_nr, Visitor&& visitor)
{
auto pixel_visitor = [&](auto pixel) {
auto image_dims = dimensions();
auto converter = [image_dims, pixel, chan_conv = channel_converter_round()](auto&& gen) {
auto src = make_generated_view(image_dims, gen);
using Channel = typename std::decay_t<decltype(pixel)>::type;
return boost::gil::color_converted_view<Channel>(src, chan_conv);
};
switch (m_exec_params.generator_type) {
case generator_type_enum::gauss: {
generate_gauss func(frame_nr, m_exec_params.gauss);
visitor(converter(func));
break;
}
case generator_type_enum::diffraction: {
generate_diffraction func(frame_nr, m_exec_params.diffraction);
visitor(converter(func));
break;
}
default:
//TODO: Normalize exceptions
throw std::runtime_error("Invalid generator mode");
}
};
auto pixel_type = typeof_pixel(m_exec_params.pixel_type);
std::visit(pixel_visitor, pixel_type);
}
point_t m_dim;
std::vector<gauss_peak> m_peaks;
int m_frame_nr = 0;
double m_grow_factor = 0.0;
double m_diffract_x;
double m_diffract_y;
double m_diffract_sx;
double m_diffract_sy;
init_params m_init_params;
exec_params m_exec_params;
};
using point_t = generate_gauss::point_t;
using generate_diffraction_locator_t = boost::gil::virtual_2d_locator<generate_diffraction, false>;
using generate_diffraction_view_t = boost::gil::image_view<generate_diffraction_locator_t>;
} // namespace detectors::simulator::hw
} // namespace detectors::simulator::hw::generator
} // namespace lima
detectors/simulator/include/lima/detectors/simulator/hw/generator/enums.describe.hpp 0 → 100644
View file @ fd919a8d
// Copyright (C) 2018 Samuel Debionne, ESRF.
// Use, modification and distribution is subject to the Boost Software
// License, Version 1.0. (See accompanying file LICENSE_1_0.txt or copy at
// http://www.boost.org/LICENSE_1_0.txt)
#pragma once
#include <boost/describe.hpp>
#include <boost/describe/io_enums.hpp>
#include <lima/detectors/simulator/hw/generator/enums.hpp>
namespace lima
{
namespace detectors::simulator::hw::generator
{
BOOST_DESCRIBE_ENUM(generator_type_enum, gauss, diffraction)
} // namespace detectors::simulator::hw::generator
} // namespace lima
detectors/simulator/include/lima/detectors/simulator/hw/generator/enums.hpp 0 → 100644
View file @ fd919a8d
// Copyright (C) 2020 Alejandro Homs Puron, ESRF.
// Use, modification and distribution is subject to the Boost Software
// License, Version 1.0. (See accompanying file LICENSE_1_0.txt or copy at
// http://www.boost.org/LICENSE_1_0.txt)
#pragma once
namespace lima
{
namespace detectors::simulator::hw::generator
{
/// Generator type
enum class generator_type_enum : int
{
gauss,
diffraction
};
} // namespace detectors::simulator::hw::generator
} // namespace lima
detectors/simulator/include/lima/detectors/simulator/hw/generator/params.describe.hpp 0 → 100644
View file @ fd919a8d
// Copyright (C) 2018 Samuel Debionne, ESRF.
// Use, modification and distribution is subject to the Boost Software
// License, Version 1.0. (See accompanying file LICENSE_1_0.txt or copy at
// http://www.boost.org/LICENSE_1_0.txt)
#pragma once
#include <boost/describe/annotations.hpp>
#include <boost/describe/io_structs.hpp>
#include <lima/processing/serial/generator/params.describe.hpp>
#include <lima/detectors/simulator/hw/generator/enums.describe.hpp>
#include <lima/detectors/simulator/hw/generator/params.hpp>
namespace lima
{
namespace detectors::simulator::hw::generator
{
BOOST_DESCRIBE_STRUCT(init_params, (), (width, height))
// clang-format off
BOOST_ANNOTATE_MEMBER(init_params, width,
(desc, "frame width"),
(doc, "The width of the frame in pixel"))
BOOST_ANNOTATE_MEMBER(init_params, height,
(desc, "frame height"),
(doc, "The height of the frame in pixel"))
// clang-format on
BOOST_DESCRIBE_STRUCT(exec_params, (), (generator_type, gauss, diffraction, pixel_type))
// clang-format off
BOOST_ANNOTATE_MEMBER(exec_params, generator_type,
(desc, "type of generator"),
(doc, "The type of generator [gauss, diffraction]"))
BOOST_ANNOTATE_MEMBER(exec_params, gauss,
(desc, "Gauss generator params"),
(doc, "The configuration of the Gauss generator"))
BOOST_ANNOTATE_MEMBER(exec_params, diffraction,
(desc, "Diffraction generator params"),
(doc, "The configuration of the Diffraction generator"))
BOOST_ANNOTATE_MEMBER(exec_params, pixel_type,
(desc, "pixel type"),
(doc, "The pixel type (channel, color space and layout) [gray8, gray16, gray32, gray32f]"))
// clang-format on
using boost::describe::operator<<;
} // namespace detectors::simulator::hw::generator
} // namespace lima
detectors/simulator/include/lima/detectors/simulator/hw/generator/params.hpp 0 → 100644
View file @ fd919a8d
// Copyright (C) 2020 Alejandro Homs Puron, ESRF.
// Use, modification and distribution is subject to the Boost Software
// License, Version 1.0. (See accompanying file LICENSE_1_0.txt or copy at
// http://www.boost.org/LICENSE_1_0.txt)
#pragma once
#include <vector>
#include <lima/core/enums.hpp>
#include <lima/processing/serial/generator/params.hpp>
#include <lima/detectors/simulator/hw/generator/enums.hpp>
namespace lima
{
namespace detectors::simulator::hw::generator
{
using namespace lima::processing::generator;
/// Initialization parameters: defined once in the application
struct init_params
{
int width = 2048;
int height = 2048;
};
/// Execution parameters: defined each time the generator is instantiated
struct exec_params
{
generator_type_enum generator_type = generator_type_enum::gauss; //!< The type of generator
gauss_params gauss = {2048, 2048}; //!< The Gauss generator parameters
diffraction_params diffraction = {2048, 2048}; //!< The Diffraction generator parameters
pixel_enum pixel_type = pixel_enum::gray8; //!< The pixel type (layout, bitdepth)
};
} // namespace detectors::simulator::hw::generator
} // namespace lima
detectors/simulator/include/lima/detectors/simulator/hw/loader.hpp 0 → 100644
View file @ fd919a8d
// Copyright (C) 2020 Alejandro Homs Puron, ESRF.
// Use, modification and distribution is subject to the Boost Software
// License, Version 1.0. (See accompanying file LICENSE_1_0.txt or copy at
// http://www.boost.org/LICENSE_1_0.txt)
#pragma once
#include <boost/gil/extension/dynamic_image/apply_operation.hpp>
#include <lima/core/pixel.hpp>
#include <lima/io/multi.hpp>
#include <lima/io/hdf5.hpp>
#include <lima/detectors/simulator/hw/loader/params.hpp>
namespace lima
{
namespace detectors::simulator::hw::loader
{
struct loader
{
using reader_t = io::multi<io::h5::reader>;
loader(exec_params const& exec_pars, int rank, int nb_frames) :
m_reader(exec_pars, rank, nb_frames),
m_dimensions(m_reader.dimensions()),
m_pixel_type(m_reader.pixel_type())
{
}
point_t dimensions() { return m_dimensions; }
pixel_enum pixel_type() { return m_pixel_type; }
// visitor will be called with generated image view
template <typename Visitor>
void frame_getter_visit(int frame_nr, Visitor&& visitor)
{
auto frame = m_reader.read_frame(frame_nr);
boost::gil::apply_operation(const_view(frame), visitor);
}
reader_t m_reader;
point_t m_dimensions;
pixel_enum m_pixel_type;
};
} // namespace detectors::simulator::hw::loader
} // namespace lima
detectors/simulator/include/lima/detectors/simulator/hw/loader/params.describe.hpp 0 → 100644
View file @ fd919a8d
// Copyright (C) 2020 Alejandro Homs Puron, ESRF.
// Use, modification and distribution is subject to the Boost Software
// License, Version 1.0. (See accompanying file LICENSE_1_0.txt or copy at
// http://www.boost.org/LICENSE_1_0.txt)
#pragma once
#include <boost/describe/annotations.hpp>
#include <boost/describe/io_structs.hpp>
#include <lima/io/h5/params.describe.hpp>
#include <lima/detectors/simulator/hw/loader/params.hpp>
namespace lima
{
namespace detectors::simulator::hw::loader
{
BOOST_DESCRIBE_STRUCT(exec_params, (io::h5::reader::params_t), ())
using boost::describe::operator<<;
} // namespace detectors::simulator::hw::loader
} // namespace lima
detectors/simulator/include/lima/detectors/simulator/hw/loader/params.hpp 0 → 100644
View file @ fd919a8d
// Copyright (C) 2020 Alejandro Homs Puron, ESRF.
// Use, modification and distribution is subject to the Boost Software
// License, Version 1.0. (See accompanying file LICENSE_1_0.txt or copy at
// http://www.boost.org/LICENSE_1_0.txt)
#pragma once
#include <vector>
#include <lima/io/h5/reader.hpp>
namespace lima
{
namespace detectors::simulator::hw::loader
{
using namespace std::string_literals;
/// Execution parameters: defined each time the loader is instantiated
struct exec_params : io::h5::reader::params_t // loading_params
{
};
} // namespace detectors::simulator::hw::loader
} // namespace lima
detectors/simulator/include/lima/detectors/simulator/hw/params.describe.hpp
View file @ fd919a8d
......@@ -11,6 +11,8 @@
#include <lima/hw/params.describe.hpp>
#include <lima/detectors/simulator/hw/generator/params.describe.hpp>
#include <lima/detectors/simulator/hw/loader/params.describe.hpp>
#include <lima/detectors/simulator/hw/enums.describe.hpp>
#include <lima/detectors/simulator/hw/params.hpp>
......@@ -18,60 +20,32 @@ namespace lima
{
namespace detectors::simulator::hw
{
BOOST_DESCRIBE_STRUCT(init_params, (), (width, height))
BOOST_DESCRIBE_STRUCT(init_params, (), (generator))
// clang-format off
BOOST_ANNOTATE_MEMBER(init_params, width,
(desc, "frame width"),
(doc, "The width of the frame in pixel"))
BOOST_ANNOTATE_MEMBER(init_params, height,
(desc, "frame height"),
(doc, "The height of the frame in pixel"))
BOOST_ANNOTATE_MEMBER(init_params, generator,
(desc, "generator init params"),
(