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[TASK] volume of different integer types with internal range check #3

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Sep 25, 2024
Merged

[TASK] volume of different integer types with internal range check #3

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43 changes: 22 additions & 21 deletions examples/plot_simple.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,39 +2,40 @@
from pathlib import Path
import numpy as np
import matplotlib.pyplot as plt
from timepix_sort.config import TDC2TriggerMode
from timepix_sort.data_model import PixelEvent
from timepix_sort.read import read_chunks
from timepix_sort.process_chunks import process_chunks
from timepix_sort.config import TDC2TriggerMode, TDC1TriggerMode
from timepix_sort.read import read_chunks, read_file_to_buffer
from timepix_sort.process import process_chunks
from timepix_sort.post_process import data_to_volume

data_dir = Path(__file__).parent.parent / "tests" / "data"
filename = data_dir / "Co_pos_0000.tpx3"
# filename = data_dir / "Co_test_0000.tpx3"


start = datetime.datetime.now()
events = [
ev
for ev in process_chunks(
read_chunks(filename), trigger_mode=TDC2TriggerMode.rising_edge, tot_min=1
)
if ev is not None
]
chunks = read_chunks(read_file_to_buffer(filename))
events, event_statistics = process_chunks(chunks, TDC1TriggerMode.rising_edge, 6)
end = datetime.datetime.now()
dt = (end - start).total_seconds()
print(f"Processing {len(events)} events required {dt:.3f} seconds")

result = np.zeros([515, 514])
for ev in events:
if isinstance(ev, PixelEvent):
x, y = ev.pos.x, ev.pos.y
assert x >= 0
assert y >= 0
x = int(round(x))
y = int(round(y))
result[x, y] += 1
si_buf = events.sorted_indices()
sorted_indices = np.array(si_buf, copy=False)

pixels_diff = events.pixel_events_with_difference_time(si_buf)
pixels_diff.sort()
assert pixels_diff.is_sorted

tmp = np.arange(0, 20)
lut = np.array([tmp, tmp]).T
lut[:, 0] *= int(1.6e6 / 20)
volume = np.zeros([525, 524, len(tmp)], dtype=np.int16)
data_to_volume(pixels_diff, lut, volume)
result = np.sum(volume, axis=-1)
largest_hit = np.max(result.ravel())
lowest_hit = np.min(result.ravel())
np.save("image_data.npy", result)
plt.imshow(result[100:350, :400])
print(f"hit range {lowest_hit} {largest_hit}")
plt.imshow(result[100:350, :400], vmax=largest_hit/3)
plt.axis("equal")
plt.savefig("rough_data_result.png")
8 changes: 4 additions & 4 deletions examples/use_ext.py
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Original file line number Diff line number Diff line change
Expand Up @@ -44,9 +44,9 @@
events_statistics.n_control_indications
)
txt = f"""Event statistics
# of events {events_statistics.n_events: 8d}
# of events {events_statistics.n_events: 8d}

consisting of
consisting of
pixel {events_statistics.n_pixels: 8d}
timestamps {events_statistics.n_timestamps: 8d}
global time {events_statistics.n_global_time: 8d}
Expand All @@ -70,9 +70,9 @@
toc_pixels_sorted = _now()

tmp = np.arange(0, 20)
lut = np.array([tmp, tmp]).T
lut = np.array([tmp, tmp], dtype=np.uint64).T
lut[:, 0] *= int(1.6e6 / 20)
volume = np.zeros([525, 524, len(tmp)], dtype=np.uint16)
volume = np.zeros([525, 524, len(tmp)], dtype=np.int32)
data_to_volume(pixels_diff, lut, volume)
# print("volume sum", np.sum(np.sum(volume)))

Expand Down
71 changes: 65 additions & 6 deletions src/c++/volume.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -3,16 +3,19 @@
#include <pybind11/numpy.h>
#include <timepix_sort/events.h>
#include <iostream>
#include <boost/numeric/conversion/cast.hpp>

namespace py = pybind11;
namespace dm = timepix::data_model;
namespace tpp = timepix::python;
namespace tps = timepix::sort;


template<typename array_base_t>
static void
data_to_volume(const tps::PixelEventsDiffTime& pd, const py::array_t<uint64_t>& lut, py::array_t<uint16_t> volume)
data_to_volume(const tps::PixelEventsDiffTime& pd, const py::array_t<uint64_t>& lut, py::array& volume)
{

auto lut_r = lut.unchecked<2>();
if (lut_r.shape(1) != 2)
throw std::runtime_error("Lut last dimension must be 2");
Expand All @@ -24,9 +27,11 @@ data_to_volume(const tps::PixelEventsDiffTime& pd, const py::array_t<uint64_t>&
lutt.insert(lut_r(i, 0), lut_r(i, 1));
}

auto r = volume.mutable_unchecked<3>();
auto r = volume.mutable_unchecked<array_base_t, 3>();
// fill the buffer
size_t event_nr = -1;
for(const auto& ev: pd){
event_nr++;
const auto pos = tps::map_pixel_and_chip_nr_to_global_pixel(ev.pos(), ev.chip_nr());
if (pos.x() < 0){
throw std::range_error("x < 0");
Expand All @@ -40,7 +45,7 @@ data_to_volume(const tps::PixelEventsDiffTime& pd, const py::array_t<uint64_t>&
}
if (pos.y() >= r.shape(1) - 1){
throw std::range_error("y >= r.shape(1) -1");
}
}
const auto tmp = lutt.linear_interp(ev.time_of_arrival());
const auto ti = int64_t(std::round(tmp));
if (ti < 0){
Expand All @@ -49,14 +54,36 @@ data_to_volume(const tps::PixelEventsDiffTime& pd, const py::array_t<uint64_t>&
if (ti >= r.shape(2) - 1){
throw std::range_error("ti >= r.shape(2) - 1");
}
r(pos.x(), pos.y(), ti) += ev.time_over_threshold();
const int64_t tot = ev.time_over_threshold();
const int64_t prev_tot = r(pos.x(), pos.y(), ti);
const int64_t tot_s = tot + prev_tot;

try {
r(pos.x(), pos.y(), ti) = boost::numeric_cast<array_base_t>(tot_s);
}
catch(boost::numeric::negative_overflow& e) {
std::stringstream strm;
strm << "event nr " << event_nr << ": tot = " << tot
<< " old value = " << prev_tot
<< " total " << tot_s
<< ": " << e.what();
throw std::overflow_error(strm.str());
}
catch(boost::numeric::positive_overflow& e) {
std::stringstream strm;
strm << "event nr " << event_nr << ": tot = " << tot
<< " old value = " << prev_tot
<< " total " << tot_s
<< ": " << e.what();
throw std::overflow_error(strm.str());
}
}
}

static auto
data_to_points(const tps::PixelEventsDiffTime& pd)
{
std::vector<py::ssize_t> dims = {pd.size(), 3};
std::vector<py::ssize_t> dims = {boost::numeric_cast<py::ssize_t>(pd.size()), 3};
py::array_t<uint64_t> res(dims);
auto r = res.mutable_unchecked<2>();

Expand All @@ -75,9 +102,41 @@ data_to_points(const tps::PixelEventsDiffTime& pd)
}


static void
data_to_volume_gateway(const tps::PixelEventsDiffTime& pd, const py::array_t<uint64_t>& lut, py::array& volume)
{

const auto dtype = volume.dtype();
const auto dtype_num = dtype.num();
if(dtype_num == py::dtype::of<uint8_t>().num()){
data_to_volume<uint8_t>(pd, lut, volume);
} else if (dtype_num == py::dtype::of<int8_t>().num()){
data_to_volume<int8_t>(pd, lut, volume);
} else if(dtype_num == py::dtype::of<uint16_t>().num()){
data_to_volume<uint16_t>(pd, lut, volume);
} else if (dtype_num == py::dtype::of<int16_t>().num()){
data_to_volume<int16_t>(pd, lut, volume);
} else if(dtype_num == py::dtype::of<uint32_t>().num()){
data_to_volume<uint32_t>(pd, lut, volume);
} else if (dtype_num == py::dtype::of<int32_t>().num()){
data_to_volume<int32_t>(pd, lut, volume);
} else if(dtype_num == py::dtype::of<uint64_t>().num()){
data_to_volume<uint64_t>(pd, lut, volume);
} else if (dtype_num == py::dtype::of<int64_t>().num()){
data_to_volume<int64_t>(pd, lut, volume);
} else {
std::stringstream strm;
strm << "data to gateway dtype: " << dtype.char_()
<< ", dtype num " << dtype.num()
<< "not handled!";
throw std::runtime_error(strm.str());
}
}


void tpp::volume_init(pybind11::module &m)
{

m.def("data_to_volume", data_to_volume);
m.def("data_to_volume", &data_to_volume_gateway);
m.def("data_to_points", data_to_points);
}
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