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Brining in changes (#93)

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This commit is contained in:
Erik Fröjdh
2024-11-11 19:59:55 +01:00
committed by GitHub
parent d8d1f0c517
commit 349e3af8e1
23 changed files with 674 additions and 140 deletions
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7
python/aare/__init__.py
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@ -1,7 +1,10 @@
# Make the compiled classes that live in _aare available from aare.
from . import _aare
from ._aare import VarClusterFinder, File, RawMasterFile
from ._aare import Pedestal, ClusterFinder
from ._aare import File, RawFile, RawMasterFile, RawSubFile
from ._aare import Pedestal, ClusterFinder, VarClusterFinder
from ._aare import DetectorType
from .CtbRawFile import CtbRawFile
from .ScanParameters import ScanParameters

94
python/examples/play.py
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@ -53,84 +53,36 @@ def get_Mh02_frames(fname):
# plt.imshow(data[0,0])
# p = Path('/Users/erik/data/aare_test_data/jungfrau/jungfrau_single_master_0.json')
base = Path('/mnt/sls_det_storage/matterhorn_data/aare_test_data/ci/aare_test_data')
# p = Path(base / 'jungfrau/jungfrau_single_master_0.json')
# f = aare.File(p)
# frame = f.read_frame()
# fig, ax = plt.subplots()
# im = ax.imshow(frame, cmap='viridis')
# fpath = Path('/Users/erik/data/Moench03old/test_034_irradiated_noise_g4_hg_exptime_2000us_master_0.json')
# # fpath = Path('/Users/erik/data/Moench05/moench05_multifile_master_0.json')
# # f = aare.CtbRawFile(fpath, transform = transform.moench05)
# # with CtbRawFile(fpath, transform = transform.moench05) as f:
# # for header, image in f:
# # print(f'Frame number: {header["frameNumber"]}')
# # m = aare.RawMasterFile(fpath)
# f = aare.File(fpath)
# for i in range(10):
# frame = f.read_frame()
# cf = aare.ClusterFinder((400,400),(3,3))
# for i in range(100):
# cf.push_pedestal_frame(f.read_frame())
# f.seek(0)
# pd = f.read_n(100).mean(axis=0)
# clusters = cf.find_clusters_without_threshold(f.read_frame())
# # f2 = aare.CtbRawFile(fpath, transform=transform.matterhorn02)
# # header, data = f2.read()
# # plt.plot(data[:,0,20,20])
# from aare import RawMasterFile, File, RawSubFile, DetectorType, RawFile
# base = Path('/mnt/sls_det_storage/matterhorn_data/aare_test_data/Jungfrau10/Jungfrau_DoubleModule_1UDP_ROI/SideBySide/')
# fpath = Path('241019_JF_12keV_Si_FF_GaAs_FF_7p88mmFilter_PedestalStart_ZPos_5.5_master_0.json')
# raw = Path('241019_JF_12keV_Si_FF_GaAs_FF_7p88mmFilter_PedestalStart_ZPos_5.5_d0_f0_0.raw')
base = Path('/Users/erik/data/matterhorn/raw')
fpath = Path(base / 'scan_15keV_vrf700_vrsh700_th0_master_0.json')
f = aare.CtbRawFile(fpath, transform=transform.matterhorn02)
f.seek(100)
header1, image1 = f.read_frame()
# m = RawMasterFile(base / fpath)
# # roi = m.roi
# # rows = roi.ymax-roi.ymin+1
# # cols = 1024-roi.xmin
# # sf = RawSubFile(base / raw, DetectorType.Jungfrau, rows, cols, 16)
# fpath = Path(base / 'scan_all15keV_vrf500_vrsh700_th0_master_0.json')
# f = aare.CtbRawFile(fpath, transform=transform.matterhorn02)
# f.seek(100)
# header4, image4 = f.read_frame()
# n_counters = image.shape[1] / 48**2 / 2
# for i in range(100):
# header, image = f.read_frame()
# print(header['frameNumber'])
#Data come in "blocks" of 4 pixels/receiver
# data = get_Mh02_frames(fpath.as_posix())
# rawi = np.zeros(48*48*4+56, dtype = np.uint16)
# for i,v in enumerate(rawi[56:]):
# rawi[i+56] = i
# raw = image.view(np.uint16)
# pixel_map = decode(1, rawi)
# # img = np.take(raw, pixel_map)
# pm = np.zeros((4, 48,48), dtype = np.int64)
# for counter in range(4):
# for row in range(48):
# for col in range(48):
# pm[counter, row, col] = row*48 + col+counter*48*48
# f2 = aare.CtbRawFile(fpath, transform=transform.matterhorn02)
# header, data = f2.read()
# plt.plot(data[:,0,20,20])
from aare import RawFile
base = Path('/mnt/sls_det_storage/matterhorn_data/aare_test_data/Jungfrau10/Jungfrau_DoubleModule_1UDP_ROI/SideBySide/')
fname = base / Path('241019_JF_12keV_Si_FF_GaAs_FF_7p88mmFilter_PedestalStart_ZPos_5.5_master_0.json')
# fname = Path(base / 'jungfrau/jungfrau_single_master_0.json')
f = RawFile(fname)
h,img = f.read_frame()
print(f'{h["frameNumber"]}')

116
python/src/file.hpp
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@ -1,7 +1,10 @@
#include "aare/CtbRawFile.hpp"
#include "aare/RawMasterFile.hpp"
#include "aare/File.hpp"
#include "aare/Frame.hpp"
#include "aare/RawFile.hpp"
#include "aare/RawMasterFile.hpp"
#include "aare/RawSubFile.hpp"
#include "aare/defs.hpp"
// #include "aare/fClusterFileV2.hpp"
@ -19,6 +22,18 @@ using namespace ::aare;
void define_file_io_bindings(py::module &m) {
py::enum_<DetectorType>(m, "DetectorType")
.value("Jungfrau", DetectorType::Jungfrau)
.value("Eiger", DetectorType::Eiger)
.value("Mythen3", DetectorType::Mythen3)
.value("Moench", DetectorType::Moench)
.value("Moench03", DetectorType::Moench03)
.value("Moench03_old", DetectorType::Moench03_old)
.value("ChipTestBoard", DetectorType::ChipTestBoard)
.value("Unknown", DetectorType::Unknown);
PYBIND11_NUMPY_DTYPE(DetectorHeader, frameNumber, expLength, packetNumber,
bunchId, timestamp, modId, row, column, reserved,
debug, roundRNumber, detType, version, packetMask);
@ -36,7 +51,6 @@ void define_file_io_bindings(py::module &m) {
py::array_t<DetectorHeader> header(1);
// always read bytes
image = py::array_t<uint8_t>(shape);
@ -49,7 +63,10 @@ void define_file_io_bindings(py::module &m) {
.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("image_size_in_bytes",
&CtbRawFile::image_size_in_bytes)
.def_property_readonly("frames_in_file", &CtbRawFile::frames_in_file);
py::class_<File>(m, "File")
@ -169,26 +186,107 @@ void define_file_io_bindings(py::module &m) {
.def_property_readonly("frame_padding", &RawMasterFile::frame_padding)
.def_property_readonly("frame_discard_policy",
&RawMasterFile::frame_discard_policy)
.def_property_readonly("total_frames_expected", &RawMasterFile::total_frames_expected)
.def_property_readonly("total_frames_expected",
&RawMasterFile::total_frames_expected)
.def_property_readonly("geometry", &RawMasterFile::geometry)
.def_property_readonly("analog_samples", &RawMasterFile::analog_samples)
.def_property_readonly("digital_samples",
&RawMasterFile::digital_samples)
.def_property_readonly("transceiver_samples", &RawMasterFile::transceiver_samples)
.def_property_readonly("transceiver_samples",
&RawMasterFile::transceiver_samples)
.def_property_readonly("number_of_rows", &RawMasterFile::number_of_rows)
.def_property_readonly("quad", &RawMasterFile::quad)
.def_property_readonly("scan_parameters", &RawMasterFile::scan_parameters);
.def_property_readonly("scan_parameters",
&RawMasterFile::scan_parameters)
.def_property_readonly("roi", &RawMasterFile::roi);
py::class_<ScanParameters>(m, "ScanParameters")
.def(py::init<const std::string &>())
.def(py::init<const ScanParameters&>())
.def(py::init<const ScanParameters &>())
.def_property_readonly("enabled", &ScanParameters::enabled)
.def_property_readonly("dac", &ScanParameters::dac)
.def_property_readonly("start", &ScanParameters::start)
.def_property_readonly("stop", &ScanParameters::stop)
.def_property_readonly("step", &ScanParameters::step);
py::class_<ROI>(m, "ROI")
.def(py::init<>())
.def_readwrite("xmin", &ROI::xmin)
.def_readwrite("xmax", &ROI::xmax)
.def_readwrite("ymin", &ROI::ymin)
.def_readwrite("ymax", &ROI::ymax)
.def("__str__", [](const ROI& self){
return fmt::format("ROI: xmin: {} xmax: {} ymin: {} ymax: {}", self.xmin, self.xmax, self.ymin, self.ymax);
});
py::class_<RawFile>(m, "RawFile")
.def(py::init<const std::filesystem::path &>())
.def("read_frame",
[](RawFile &self) {
size_t image_size = self.bytes_per_frame();
const uint8_t item_size = self.bytes_per_pixel();
py::array image;
std::vector<ssize_t> shape;
shape.reserve(2);
shape.push_back(self.rows());
shape.push_back(self.cols());
//return headers from all subfiles
py::array_t<DetectorHeader> header(self.n_mod());
if (item_size == 1) {
image = py::array_t<uint8_t>(shape);
} else if (item_size == 2) {
image = py::array_t<uint16_t>(shape);
} else if (item_size == 4) {
image = py::array_t<uint32_t>(shape);
}
fmt::print("item_size: {} rows: {} cols: {}\n", item_size, self.rows(), self.cols());
self.read_into(
reinterpret_cast<std::byte *>(image.mutable_data()),
header.mutable_data());
return py::make_tuple(header, image);
});
py::class_<RawSubFile>(m, "RawSubFile")
.def(py::init<const std::filesystem::path &, DetectorType, size_t,
size_t, size_t>())
.def_property_readonly("bytes_per_frame", &RawSubFile::bytes_per_frame)
.def_property_readonly("pixels_per_frame",
&RawSubFile::pixels_per_frame)
.def("seek", &RawSubFile::seek)
.def("tell", &RawSubFile::tell)
.def_property_readonly("rows", &RawSubFile::rows)
.def_property_readonly("cols", &RawSubFile::cols)
.def("read_frame",
[](RawSubFile &self) {
const uint8_t item_size = self.bytes_per_pixel();
py::array image;
std::vector<ssize_t> shape;
shape.reserve(2);
shape.push_back(self.rows());
shape.push_back(self.cols());
if (item_size == 1) {
image = py::array_t<uint8_t>(shape);
} else if (item_size == 2) {
image = py::array_t<uint16_t>(shape);
} else if (item_size == 4) {
image = py::array_t<uint32_t>(shape);
}
fmt::print("item_size: {} rows: {} cols: {}\n", item_size, self.rows(), self.cols());
self.read_into(
reinterpret_cast<std::byte *>(image.mutable_data()));
return image;
});
// py::class_<ClusterHeader>(m, "ClusterHeader")
// .def(py::init<>())
// .def_readwrite("frame_number", &ClusterHeader::frame_number)