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ImageStreamIOWrap.cpp
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executable file
·1207 lines (1124 loc) · 46.5 KB
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#include <pybind11/chrono.h>
#include <pybind11/numpy.h>
#include <pybind11/pybind11.h>
#include <pybind11/stl.h>
#include <ctime>
#include "ImageStreamIO.h"
#include "ImageStruct.h"
namespace py = pybind11;
std::string toString(const IMAGE_KEYWORD &kw) {
std::ostringstream tmp_str;
// tmp_str << kw.name << ": ";
switch (kw.type) {
case 'L':
tmp_str << kw.value.numl;
break;
case 'D':
tmp_str << kw.value.numf;
break;
case 'S':
tmp_str << kw.value.valstr;
break;
default:
tmp_str << "Unknown format";
break;
}
tmp_str << " " << kw.comment;
return tmp_str.str();
}
struct ImageStreamIOType {
enum Type : uint64_t {
CIRCULAR_BUFFER_TYPE = CIRCULAR_BUFFER,
MATH_DATA_TYPE = MATH_DATA,
IMG_RECV_TYPE = IMG_RECV,
IMG_SENT_TYPE = IMG_SENT,
ZAXIS_UNDEF_TYPE = ZAXIS_UNDEF,
ZAXIS_SPACIAL_TYPE = ZAXIS_SPACIAL,
ZAXIS_TEMPORAL_TYPE = ZAXIS_TEMPORAL,
ZAXIS_WAVELENGTH_TYPE = ZAXIS_WAVELENGTH,
ZAXIS_MAPPING_TYPE = ZAXIS_MAPPING
};
Type type;
ImageStreamIOType() : type(MATH_DATA_TYPE){};
ImageStreamIOType(uint64_t type)
: type(static_cast<ImageStreamIOType::Type>(type)){};
enum Type get_type() const {
return static_cast<ImageStreamIOType::Type>(type & 0xF);
}
enum Type get_axis() const {
return static_cast<ImageStreamIOType::Type>(type & 0xF0000);
}
};
struct ImageStreamIODataType {
enum DataType : uint8_t {
UINT8 = _DATATYPE_UINT8,
INT8 = _DATATYPE_INT8,
UINT16 = _DATATYPE_UINT16,
INT16 = _DATATYPE_INT16,
UINT32 = _DATATYPE_UINT32,
INT32 = _DATATYPE_INT32,
UINT64 = _DATATYPE_UINT64,
INT64 = _DATATYPE_INT64,
FLOAT = _DATATYPE_FLOAT,
DOUBLE = _DATATYPE_DOUBLE,
COMPLEX_FLOAT = _DATATYPE_COMPLEX_FLOAT,
COMPLEX_DOUBLE = _DATATYPE_COMPLEX_DOUBLE,
HALF = _DATATYPE_HALF
};
static const std::vector<uint8_t> Size;
DataType datatype;
uint8_t asize;
ImageStreamIODataType() : datatype(FLOAT), asize(Size[FLOAT]){};
ImageStreamIODataType(uint8_t datatype)
: datatype(static_cast<ImageStreamIODataType::DataType>(datatype)),
asize(Size[datatype]){};
operator uint8_t() const { return datatype; }
};
const std::vector<uint8_t> ImageStreamIODataType::Size(
{0, SIZEOF_DATATYPE_UINT8, SIZEOF_DATATYPE_INT8, SIZEOF_DATATYPE_UINT16,
SIZEOF_DATATYPE_INT16, SIZEOF_DATATYPE_UINT32, SIZEOF_DATATYPE_INT32,
SIZEOF_DATATYPE_UINT64, SIZEOF_DATATYPE_INT64, SIZEOF_DATATYPE_FLOAT,
SIZEOF_DATATYPE_DOUBLE, SIZEOF_DATATYPE_COMPLEX_FLOAT,
SIZEOF_DATATYPE_COMPLEX_DOUBLE, SIZEOF_DATATYPE_HALF});
std::string ImageStreamIODataTypeToPyFormat(ImageStreamIODataType dt) {
switch (dt.datatype) {
case ImageStreamIODataType::DataType::UINT8:
return py::format_descriptor<uint8_t>::format();
case ImageStreamIODataType::DataType::INT8:
return py::format_descriptor<int8_t>::format();
case ImageStreamIODataType::DataType::UINT16:
return py::format_descriptor<uint16_t>::format();
case ImageStreamIODataType::DataType::INT16:
return py::format_descriptor<int16_t>::format();
case ImageStreamIODataType::DataType::UINT32:
return py::format_descriptor<uint32_t>::format();
case ImageStreamIODataType::DataType::INT32:
return py::format_descriptor<int32_t>::format();
case ImageStreamIODataType::DataType::UINT64:
return py::format_descriptor<uint64_t>::format();
case ImageStreamIODataType::DataType::INT64:
return py::format_descriptor<int64_t>::format();
case ImageStreamIODataType::DataType::FLOAT:
return py::format_descriptor<float>::format();
case ImageStreamIODataType::DataType::DOUBLE:
return py::format_descriptor<double>::format();
// case ImageStreamIODataType::DataType::COMPLEX_FLOAT: return
// py::format_descriptor<(std::complex<float>>::format(); case
// ImageStreamIODataType::DataType::COMPLEX_DOUBLE: return
// py::format_descriptor<(std::complex<double>>::format();
default:
throw std::runtime_error("Not implemented");
}
}
ImageStreamIODataType PyFormatToImageStreamIODataType(const py::buffer_info &info) {
if (info.item_type_is_equivalent_to<uint8_t>()) {
return ImageStreamIODataType::DataType::UINT8;
}
if (info.item_type_is_equivalent_to<int8_t>()) {
return ImageStreamIODataType::DataType::INT8;
}
if (info.item_type_is_equivalent_to<uint16_t>()) {
return ImageStreamIODataType::DataType::UINT16;
}
if (info.item_type_is_equivalent_to<int16_t>()) {
return ImageStreamIODataType::DataType::INT16;
}
if (info.item_type_is_equivalent_to<uint32_t>()) {
return ImageStreamIODataType::DataType::UINT32;
}
if (info.item_type_is_equivalent_to<int32_t>()) {
return ImageStreamIODataType::DataType::INT32;
}
if (info.item_type_is_equivalent_to<uint64_t>()) {
return ImageStreamIODataType::DataType::UINT64;
}
if (info.item_type_is_equivalent_to<int64_t>()) {
return ImageStreamIODataType::DataType::INT64;
}
if (info.item_type_is_equivalent_to<float>()) {
return ImageStreamIODataType::DataType::FLOAT;
}
if (info.item_type_is_equivalent_to<double>()) {
return ImageStreamIODataType::DataType::DOUBLE;
}
// case ImageStreamIODataType::DataType::COMPLEX_FLOAT: return
// py::format_descriptor<(std::complex<float>>::format(); case
// ImageStreamIODataType::DataType::COMPLEX_DOUBLE: return
// py::format_descriptor<(std::complex<double>>::format();
throw std::runtime_error("Not implemented");
}
template <typename T>
py::array_t<T> convert_img(const IMAGE &img) {
if (ImageStreamIO_typesize(img.md->datatype) != sizeof(T)) {
throw std::runtime_error("IMAGE is not compatible with output format");
}
std::vector<ssize_t> shape(img.md->naxis);
std::vector<ssize_t> strides(img.md->naxis);
ssize_t stride = sizeof(T);
// Row Major representation
// for (int8_t axis(img.md->naxis-1); axis >= 0; --axis) {
// Col Major representation
for (int8_t axis(0); axis < img.md->naxis; ++axis) {
shape[axis] = img.md->size[axis];
strides[axis] = stride;
stride *= shape[axis];
}
auto ret_buffer = py::array_t<T>(shape, strides);
void *current_image = img.array.raw;
size_t size_data = img.md->nelement * sizeof(T);
if (img.md->location == -1) {
memcpy(ret_buffer.mutable_data(), current_image, size_data);
} else {
#ifdef HAVE_CUDA
cudaSetDevice(img.md->location);
cudaMemcpy(ret_buffer.mutable_data(), current_image, size_data,
cudaMemcpyDeviceToHost);
#else
throw std::runtime_error(
"unsupported location, CACAO needs to be compiled with -DUSE_CUDA=ON");
#endif
}
return ret_buffer;
}
template <typename T>
void write(IMAGE &img,
py::array_t<T, py::array::f_style | py::array::forcecast> b) {
if (img.array.raw == nullptr) {
throw std::runtime_error("image not initialized");
}
/* Request a buffer descriptor from Python */
py::buffer_info info = b.request();
if (img.md->datatype !=
PyFormatToImageStreamIODataType(info)) {
throw std::invalid_argument("incompatible type");
}
if (info.ndim != img.md->naxis) {
throw std::invalid_argument("incompatible number of axis");
}
const uint32_t *size_ptr = img.md->size;
for (auto &dim : info.shape) {
if (*size_ptr != dim) {
throw std::invalid_argument("incompatible shape");
}
++size_ptr;
}
ImageStreamIODataType dt(img.md->datatype);
uint8_t *buffer_ptr = (uint8_t *)info.ptr;
uint64_t size = img.md->nelement * dt.asize;
img.md->write = 1; // set this flag to 1 when writing data
void *current_image = img.array.raw;
if (img.md->location == -1) {
memcpy(current_image, buffer_ptr, size);
} else {
#ifdef HAVE_CUDA
cudaSetDevice(img.md->location);
cudaMemcpy(current_image, buffer_ptr, size, cudaMemcpyHostToDevice);
#else
throw std::runtime_error(
"unsupported location, CACAO needs to be compiled with -DUSE_CUDA=ON");
#endif
}
ImageStreamIO_sempost(&img, -1);
clock_gettime(CLOCK_ISIO, &img.md->lastaccesstime);
img.md->write = 0; // Done writing data
img.md->cnt0++;
img.md->cnt1++;
}
PYBIND11_MODULE(ImageStreamIOWrap, m) {
m.doc() = "CACAO ImageStreamIO python module";
auto imageDatatype =
py::class_<ImageStreamIODataType>(m, "ImageStreamIODataType")
.def(py::init([](uint8_t datatype) {
return std::unique_ptr<ImageStreamIODataType>(
new ImageStreamIODataType(datatype));
}))
.def_readonly("size", &ImageStreamIODataType::asize)
.def_readonly("type", &ImageStreamIODataType::datatype)
.def("__repr__", [](const ImageStreamIODataType &img_datatype) {
std::ostringstream tmp_str;
tmp_str << "datatype: " << img_datatype.datatype << std::endl;
tmp_str << "size: " << img_datatype.asize << std::endl;
return tmp_str.str();
});
py::enum_<ImageStreamIODataType::DataType>(imageDatatype, "Type")
.value("UINT8", ImageStreamIODataType::DataType::UINT8)
.value("INT8", ImageStreamIODataType::DataType::INT8)
.value("UINT16", ImageStreamIODataType::DataType::UINT16)
.value("INT16", ImageStreamIODataType::DataType::INT16)
.value("UINT32", ImageStreamIODataType::DataType::UINT32)
.value("INT32", ImageStreamIODataType::DataType::INT32)
.value("UINT64", ImageStreamIODataType::DataType::UINT64)
.value("INT64", ImageStreamIODataType::DataType::INT64)
.value("HALF", ImageStreamIODataType::DataType::HALF)
.value("FLOAT", ImageStreamIODataType::DataType::FLOAT)
.value("DOUBLE", ImageStreamIODataType::DataType::DOUBLE)
.value("COMPLEX_FLOAT", ImageStreamIODataType::DataType::COMPLEX_FLOAT)
.value("COMPLEX_DOUBLE", ImageStreamIODataType::DataType::COMPLEX_DOUBLE)
.export_values();
auto imagetype =
py::class_<ImageStreamIOType>(m, "ImageStreamIOType")
.def(py::init([](uint8_t type) {
return std::unique_ptr<ImageStreamIOType>(
new ImageStreamIOType(type));
}))
.def_property_readonly("axis", &ImageStreamIOType::get_axis)
.def_property_readonly("type", &ImageStreamIOType::get_type)
.def("__repr__", [](const ImageStreamIOType &image_type) {
std::ostringstream tmp_str;
tmp_str << "type: " << image_type.get_type() << std::endl;
tmp_str << "axis: " << image_type.get_axis() << std::endl;
return tmp_str.str();
});
py::enum_<ImageStreamIOType::Type>(imagetype, "Type")
.value("CIRCULAR_BUFFER_TYPE",
ImageStreamIOType::Type::CIRCULAR_BUFFER_TYPE)
.value("MATH_DATA_TYPE", ImageStreamIOType::Type::MATH_DATA_TYPE)
.value("IMG_RECV_TYPE", ImageStreamIOType::Type::IMG_RECV_TYPE)
.value("IMG_SENT_TYPE", ImageStreamIOType::Type::IMG_SENT_TYPE)
.value("ZAXIS_UNDEF_TYPE", ImageStreamIOType::Type::ZAXIS_UNDEF_TYPE)
.value("ZAXIS_SPACIAL_TYPE", ImageStreamIOType::Type::ZAXIS_SPACIAL_TYPE)
.value("ZAXIS_TEMPORAL_TYPE",
ImageStreamIOType::Type::ZAXIS_TEMPORAL_TYPE)
.value("ZAXIS_WAVELENGTH_TYPE",
ImageStreamIOType::Type::ZAXIS_WAVELENGTH_TYPE)
.value("ZAXIS_MAPPING_TYPE", ImageStreamIOType::Type::ZAXIS_MAPPING_TYPE)
.export_values();
// IMAGE_KEYWORD interface
py::class_<IMAGE_KEYWORD>(m, "Image_kw")
.def(py::init(
[]() { return std::unique_ptr<IMAGE_KEYWORD>(new IMAGE_KEYWORD()); }))
.def(py::init([](std::string name, int64_t numl, std::string comment) {
if (name.size() > KEYWORD_MAX_STRING) {
throw std::invalid_argument("name too long");
}
if (comment.size() > KEYWORD_MAX_COMMENT) {
throw std::invalid_argument("comment too long");
}
auto kw = std::unique_ptr<IMAGE_KEYWORD>(new IMAGE_KEYWORD());
std::copy(name.begin(), name.end(), kw->name);
kw->type = 'L';
kw->value.numl = numl;
std::copy(comment.begin(), comment.end(), kw->comment);
return kw;
}),
py::arg("name"), py::arg("numl"), py::arg("comment") = "")
.def(py::init([](std::string name, double numf, std::string comment) {
if (name.size() > KEYWORD_MAX_STRING) {
throw std::invalid_argument("name too long");
}
if (comment.size() > KEYWORD_MAX_COMMENT) {
throw std::invalid_argument("comment too long");
}
auto kw = std::unique_ptr<IMAGE_KEYWORD>(new IMAGE_KEYWORD());
std::copy(name.begin(), name.end(), kw->name);
kw->type = 'D';
kw->value.numf = numf;
std::copy(comment.begin(), comment.end(), kw->comment);
return kw;
}),
py::arg("name"), py::arg("numf"), py::arg("comment") = "")
.def(py::init(
[](std::string name, std::string valstr, std::string comment) {
if (name.size() > KEYWORD_MAX_STRING) {
throw std::invalid_argument("name too long");
}
if (valstr.size() > KEYWORD_MAX_STRING) {
throw std::invalid_argument("valstr too long");
}
if (comment.size() > KEYWORD_MAX_COMMENT) {
throw std::invalid_argument("comment too long");
}
auto kw = std::unique_ptr<IMAGE_KEYWORD>(new IMAGE_KEYWORD());
std::copy(name.begin(), name.end(), kw->name);
kw->type = 'S';
std::copy(valstr.begin(), valstr.end(), kw->value.valstr);
std::copy(comment.begin(), comment.end(), kw->comment);
return kw;
}),
py::arg("name"), py::arg("valstr"), py::arg("comment") = "")
.def_readonly("name", &IMAGE_KEYWORD::name)
.def_readonly("type", &IMAGE_KEYWORD::type)
.def_property_readonly("value",
[](const IMAGE_KEYWORD &kw) -> py::object {
switch (kw.type) {
case 'L':
return py::int_(kw.value.numl);
case 'D':
return py::float_(kw.value.numf);
case 'S':
return py::str(kw.value.valstr);
default:
throw std::runtime_error("Unknown format");
}
})
.def("__str__", [](const IMAGE_KEYWORD &kw) { return toString(kw); })
.def("__repr__", [](const IMAGE_KEYWORD &kw) { return toString(kw); })
.def_readonly("comment", &IMAGE_KEYWORD::comment);
// STREAM_PROC_TRACE interface
py::class_<STREAM_PROC_TRACE>(m, "Proc_trace")
.def_readonly("triggermode", &STREAM_PROC_TRACE::triggermode)
.def_readonly("pid_write", &STREAM_PROC_TRACE::procwrite_PID)
.def_readonly("trigger_inode", &STREAM_PROC_TRACE::trigger_inode)
.def_readonly("ts_procstart", &STREAM_PROC_TRACE::ts_procstart)
.def_readonly("ts_streamupdate", &STREAM_PROC_TRACE::ts_streamupdate)
.def_readonly("trigger_semindex", &STREAM_PROC_TRACE::trigsemindex)
.def_readonly("trigger_status", &STREAM_PROC_TRACE::triggerstatus)
.def_readonly("cnt0", &STREAM_PROC_TRACE::cnt0);
// IMAGE_METADATA interface
py::class_<IMAGE_METADATA>(m, "Image_md")
// .def(py::init([]() {
// return std::unique_ptr<IMAGE_METADATA>(new IMAGE_METADATA());
// }))
.def_readonly("version", &IMAGE_METADATA::version)
.def_readonly("name", &IMAGE_METADATA::name)
.def_readonly("naxis", &IMAGE_METADATA::naxis)
.def_property_readonly("size",
[](const IMAGE_METADATA &md) {
std::vector<uint32_t> dims(md.naxis);
const uint32_t *ptr = md.size;
for (auto &&dim : dims) {
dim = *ptr;
++ptr;
}
return dims;
})
.def_readonly("nelement", &IMAGE_METADATA::nelement)
.def_property_readonly(
"datatype",
[](const IMAGE_METADATA &md) {
return ImageStreamIODataType(md.datatype).datatype;
})
.def_property_readonly(
"imagetype",
[](const IMAGE_METADATA &md) {
return ImageStreamIOType(md.imagetype).get_type();
})
.def_property_readonly(
"creationtime",
[](const IMAGE_METADATA &md) {
auto creation_time =
std::chrono::seconds{md.creationtime.tv_sec} +
std::chrono::nanoseconds{md.creationtime.tv_nsec};
std::chrono::system_clock::time_point tp{creation_time};
return tp;
})
.def_property_readonly(
"lastaccesstime",
[](const IMAGE_METADATA &md) {
auto creation_time =
std::chrono::seconds{md.lastaccesstime.tv_sec} +
std::chrono::nanoseconds{md.lastaccesstime.tv_nsec};
std::chrono::system_clock::time_point tp{creation_time};
return tp;
})
.def_property_readonly(
"acqtime",
[](const IMAGE_METADATA &md) {
auto acqtime = std::chrono::seconds{md.atime.tv_sec} +
std::chrono::nanoseconds{md.atime.tv_nsec};
std::chrono::system_clock::time_point tp{acqtime};
return tp;
})
.def_property_readonly(
"writetime",
[](const IMAGE_METADATA &md) {
auto writetime = std::chrono::seconds{md.writetime.tv_sec} +
std::chrono::nanoseconds{md.writetime.tv_nsec};
std::chrono::system_clock::time_point tp{writetime};
return tp;
})
.def_readonly("shared", &IMAGE_METADATA::shared)
.def_readonly("location", &IMAGE_METADATA::location)
.def_property_readonly("location_str",
[](const IMAGE_METADATA &md) {
if (md.location < 0) {
return std::string("CPU RAM");
}
std::ostringstream tmp_str;
tmp_str << "GPU" << int(md.location) << " RAM";
return tmp_str.str();
})
.def_readonly("status", &IMAGE_METADATA::status)
.def_readonly("inode", &IMAGE_METADATA::inode)
.def_readonly("logflag", &IMAGE_METADATA::logflag)
.def_readonly("sem", &IMAGE_METADATA::sem)
.def_readonly("cnt0", &IMAGE_METADATA::cnt0)
.def_readonly("cnt1", &IMAGE_METADATA::cnt1)
.def_readonly("cnt2", &IMAGE_METADATA::cnt2)
.def_readonly("write", &IMAGE_METADATA::write)
.def_readonly("flag", &IMAGE_METADATA::flag)
.def_readonly("NBkw", &IMAGE_METADATA::NBkw)
.def("__repr__", [](const IMAGE_METADATA &md) {
std::ostringstream tmp_str;
tmp_str << "Name: " << md.name << std::endl;
tmp_str << "Version: " << md.version << std::endl;
tmp_str << "Size: [" << md.size[0];
for (int i = 1; i < md.naxis; ++i) {
tmp_str << ", " << md.size[i];
}
tmp_str << "]" << std::endl;
tmp_str << "nelement: " << md.nelement << std::endl;
// tmp_str << "datatype: " << md.datatype << std::endl;
// tmp_str << "imagetype: " << md.imagetype << std::endl;
{
auto creationtime = std::chrono::seconds{md.creationtime.tv_sec} +
std::chrono::nanoseconds{md.creationtime.tv_nsec};
std::chrono::system_clock::time_point tp{creationtime};
std::time_t t = std::chrono::system_clock::to_time_t(tp);
tmp_str << "creationtime: " << std::ctime(&t);
}
{
auto lastaccesstime =
std::chrono::seconds{md.lastaccesstime.tv_sec} +
std::chrono::nanoseconds{md.lastaccesstime.tv_nsec};
std::chrono::system_clock::time_point tp{lastaccesstime};
std::time_t t = std::chrono::system_clock::to_time_t(tp);
tmp_str << "lastaccesstime: " << std::ctime(&t);
}
{
auto acqtime = std::chrono::seconds{md.atime.tv_sec} +
std::chrono::nanoseconds{md.atime.tv_nsec};
std::chrono::system_clock::time_point tp{acqtime};
std::time_t t = std::chrono::system_clock::to_time_t(tp);
tmp_str << "acqtime: " << std::ctime(&t);
}
tmp_str << "shared: " << int(md.shared) << std::endl;
tmp_str << "location: ";
if (md.location < 0) {
tmp_str << "CPU RAM" << std::endl;
} else {
tmp_str << "GPU" << int(md.location) << " RAM" << std::endl;
}
tmp_str << "flag: " << md.flag << std::endl;
tmp_str << "logflag: " << int(md.logflag) << std::endl;
tmp_str << "sem: " << md.sem << std::endl;
tmp_str << "cnt0: " << md.cnt0 << std::endl;
tmp_str << "cnt1: " << md.cnt1 << std::endl;
tmp_str << "cnt2: " << md.cnt2;
return tmp_str.str();
});
// IMAGE interface
py::class_<IMAGE>(m, "Image", py::buffer_protocol())
.def(py::init([]() { return std::unique_ptr<IMAGE>(new IMAGE()); }))
.def_readonly("used", &IMAGE::used)
.def_readonly("memsize", &IMAGE::memsize)
.def_readonly("md", &IMAGE::md)
.def_readonly("streamproctrace0", &IMAGE::streamproctrace)
.def_property_readonly(
"shape",
[](const IMAGE &img) {
if (img.array.raw == nullptr) {
throw std::runtime_error("image not initialized");
}
py::tuple dims(img.md->naxis);
const uint32_t *ptr = img.md->size;
// std::copy(ptr, ptr + img.md->naxis, dims);
for (int i{}; i < img.md->naxis; ++i) {
dims[i] = ptr[i];
}
return dims;
})
.def_property_readonly(
"semReadPID",
[](const IMAGE &img) {
if (img.array.raw == nullptr) {
throw std::runtime_error("image not initialized");
}
std::vector<pid_t> semReadPID(img.md->sem);
for (int i = 0; i < img.md->sem; ++i) {
semReadPID[i] = img.semReadPID[i];
}
return semReadPID;
})
.def_property_readonly(
"acqtimearray",
[](const IMAGE &img) {
if (img.array.raw == nullptr) {
throw std::runtime_error("image not initialized");
}
if (img.atimearray == NULL) {
throw std::runtime_error("acqtimearray not initialized");
}
std::vector<std::chrono::system_clock::time_point> acqtimearray(
img.md->size[2]);
for (int i = 0; i < img.md->size[2]; ++i) {
auto acqtime =
std::chrono::seconds{img.atimearray[i].tv_sec} +
std::chrono::nanoseconds{img.atimearray[i].tv_nsec};
std::chrono::system_clock::time_point tp{acqtime};
acqtimearray[i] = tp;
}
return acqtimearray;
})
.def_property_readonly(
"writetimearray",
[](const IMAGE &img) {
if (img.array.raw == nullptr) {
throw std::runtime_error("image not initialized");
}
if (img.writetimearray == NULL) {
throw std::runtime_error("writetimearray not initialized");
}
std::vector<std::chrono::system_clock::time_point> writetimearray(
img.md->size[2]);
for (int i = 0; i < img.md->size[2]; ++i) {
auto writetime =
std::chrono::seconds{img.writetimearray[i].tv_sec} +
std::chrono::nanoseconds{img.writetimearray[i].tv_nsec};
std::chrono::system_clock::time_point tp{writetime};
writetimearray[i] = tp;
}
return writetimearray;
})
.def_property_readonly(
"cntarray",
[](const IMAGE &img) {
if (img.array.raw == nullptr) {
throw std::runtime_error("image not initialized");
}
if (img.cntarray == NULL) {
throw std::runtime_error("cntarray not initialized");
}
std::vector<uint64_t> cntarray(img.md->size[2]);
for (int i = 0; i < img.md->size[2]; ++i) {
cntarray[i] = img.cntarray[i];
}
return cntarray;
})
// TODO: fix flagarray never allocated and cause segfaults
// .def_property_readonly(
// "flagarray",
// [](const IMAGE &img) {
// if (img.array.raw == nullptr) {
// throw std::runtime_error("image not initialized");
// }
// if (img.flagarray == NULL) {
// throw std::runtime_error("flagarray not initialized");
// }
// std::vector<uint64_t> flagarray(img.md->size[2]);
// for (int i = 0; i < img.md->size[2]; ++i) {
// flagarray[i] = img.flagarray[i];
// }
// return flagarray;
// })
.def_property_readonly(
"semWritePID",
[](const IMAGE &img) {
if (img.array.raw == nullptr) {
throw std::runtime_error("image not initialized");
}
std::vector<pid_t> semWritePID(img.md->sem);
for (int i = 0; i < img.md->sem; ++i) {
semWritePID[i] = img.semWritePID[i];
}
return semWritePID;
})
.def("get_kws",
[](const IMAGE &img) {
if (img.array.raw == nullptr) {
throw std::runtime_error("image not initialized");
}
std::map<std::string, IMAGE_KEYWORD> keywords;
for (int i = 0; i < img.md->NBkw; ++i) {
if (strcmp(img.kw[i].name, "") == 0) {
break;
}
std::string key(img.kw[i].name);
keywords[key] = img.kw[i];
}
return keywords;
})
.def("get_kws_list",
[](const IMAGE &img) {
if (img.array.raw == nullptr) {
throw std::runtime_error("image not initialized");
}
std::list<IMAGE_KEYWORD> keywords;
for (int i = 0; i < img.md->NBkw; ++i) {
if (strcmp(img.kw[i].name, "") == 0) {
break;
}
keywords.push_back(img.kw[i]);
}
return keywords;
})
.def("set_kws",
[](const IMAGE &img, std::map<std::string, IMAGE_KEYWORD> &keywords) {
if (img.array.raw == nullptr) {
throw std::runtime_error("image not initialized");
}
std::map<std::string, IMAGE_KEYWORD>::iterator it =
keywords.begin();
int cnt = 0;
while (it != keywords.end()) {
if (cnt >= img.md->NBkw)
throw std::runtime_error("Too many keywords provided");
img.kw[cnt] = it->second;
it++;
cnt++;
}
// Pad with empty keywords
if (cnt < img.md->NBkw) {
img.kw[cnt] = IMAGE_KEYWORD();
}
})
.def("set_kws_list",
[](const IMAGE &img, std::list<IMAGE_KEYWORD> &keywords) {
if (img.array.raw == nullptr) {
throw std::runtime_error("image not initialized");
}
std::list<IMAGE_KEYWORD>::iterator it =
keywords.begin();
int cnt = 0;
while (it != keywords.end()) {
if (cnt >= img.md->NBkw)
throw std::runtime_error("Too many keywords provided");
img.kw[cnt] = *it;
it++;
cnt++;
}
// Pad with empty keywords
if (cnt < img.md->NBkw) {
img.kw[cnt] = IMAGE_KEYWORD();
}
})
.def_buffer([](const IMAGE &img) -> py::buffer_info {
if (img.array.raw == nullptr) {
py::print("image not initialized");
return py::buffer_info();
}
if (img.md->location >= 0) {
py::print("Can not use this with a GPU buffer");
return py::buffer_info();
}
ImageStreamIODataType dt(img.md->datatype);
std::string format = ImageStreamIODataTypeToPyFormat(dt);
std::vector<ssize_t> shape(img.md->naxis);
std::vector<ssize_t> strides(img.md->naxis);
ssize_t stride = dt.asize;
// Row Major representation
// for (int8_t axis(img.md->naxis-1); axis >= 0; --axis) {
// Col Major representation
for (int8_t axis(0); axis < img.md->naxis; ++axis) {
shape[axis] = img.md->size[axis];
strides[axis] = stride;
stride *= shape[axis];
}
return py::buffer_info(
img.array.raw, /* Pointer to buffer */
dt.asize, /* Size of one scalar */
format, /* Python struct-style format descriptor */
img.md->naxis, /* Number of dimensions */
shape, /* Buffer dimensions */
strides /* Strides (in bytes) for each index */
);
})
.def("copy",
[](const IMAGE &img) -> py::object {
if (img.array.raw == nullptr)
throw std::runtime_error("image not initialized");
ImageStreamIODataType dt(img.md->datatype);
switch (dt.datatype) {
case ImageStreamIODataType::DataType::UINT8:
return convert_img<uint8_t>(img);
case ImageStreamIODataType::DataType::INT8:
return convert_img<int8_t>(img);
case ImageStreamIODataType::DataType::UINT16:
return convert_img<uint16_t>(img);
case ImageStreamIODataType::DataType::INT16:
return convert_img<int16_t>(img);
case ImageStreamIODataType::DataType::UINT32:
return convert_img<uint32_t>(img);
case ImageStreamIODataType::DataType::INT32:
return convert_img<int32_t>(img);
case ImageStreamIODataType::DataType::UINT64:
return convert_img<uint64_t>(img);
case ImageStreamIODataType::DataType::INT64:
return convert_img<int64_t>(img);
case ImageStreamIODataType::DataType::FLOAT:
return convert_img<float>(img);
case ImageStreamIODataType::DataType::DOUBLE:
return convert_img<double>(img);
// case ImageStreamIODataType::DataType::COMPLEX_FLOAT: return ;
// case ImageStreamIODataType::DataType::COMPLEX_DOUBLE: return ;
default:
throw std::runtime_error("Not implemented");
}
})
.def("update", [](IMAGE &img) {
if (img.array.raw == nullptr)
throw std::runtime_error("image not initialized");
return ImageStreamIO_UpdateIm(&img);
})
.def("update_atime", [](IMAGE &img, std::chrono::system_clock::time_point &tp) {
if (img.array.raw == nullptr)
throw std::runtime_error("image not initialized");
auto secs = std::chrono::time_point_cast<std::chrono::seconds>(tp);
auto ns = std::chrono::time_point_cast<std::chrono::nanoseconds>(tp) -
std::chrono::time_point_cast<std::chrono::nanoseconds>(secs);
struct timespec atime = {secs.time_since_epoch().count(), ns.count()};
return ImageStreamIO_UpdateIm_atime(&img, &atime);
})
.def("write", &write<uint8_t>,
R"pbdoc(
Write into memory image stream
Parameters:
buffer [in]: buffer to put into memory image stream
)pbdoc",
py::arg("buffer"))
.def("write", &write<uint16_t>,
R"pbdoc(
Write into memory image stream
Parameters:
buffer [in]: buffer to put into memory image stream
)pbdoc",
py::arg("buffer"))
.def("write", &write<uint32_t>,
R"pbdoc(
Write into memory image stream
Parameters:
buffer [in]: buffer to put into memory image stream
)pbdoc",
py::arg("buffer"))
.def("write", &write<uint64_t>,
R"pbdoc(
Write into memory image stream
Parameters:
buffer [in]: buffer to put into memory image stream
)pbdoc",
py::arg("buffer"))
.def("write", &write<int8_t>,
R"pbdoc(
Write into memory image stream
Parameters:
buffer [in]: buffer to put into memory image stream
)pbdoc",
py::arg("buffer"))
.def("write", &write<int16_t>,
R"pbdoc(
Write into memory image stream
Parameters:
buffer [in]: buffer to put into memory image stream
)pbdoc",
py::arg("buffer"))
.def("write", &write<int32_t>,
R"pbdoc(
Write into memory image stream
Parameters:
buffer [in]: buffer to put into memory image stream
)pbdoc",
py::arg("buffer"))
.def("write", &write<int64_t>,
R"pbdoc(
Write into memory image stream
Parameters:
buffer [in]: buffer to put into memory image stream
)pbdoc",
py::arg("buffer"))
.def("write", &write<float>,
R"pbdoc(
Write into memory image stream
Parameters:
buffer [in]: buffer to put into memory image stream
)pbdoc",
py::arg("buffer"))
.def("write", &write<double>,
R"pbdoc(
Write into memory image stream
Parameters:
buffer [in]: buffer to put into memory image stream
)pbdoc",
py::arg("buffer"))
.def(
"create",
[](IMAGE &img, const std::string &name, const py::buffer &buffer,
int8_t location, uint8_t shared, int NBsem, int NBkw,
uint64_t imagetype, uint32_t CBsize) {
py::buffer_info info = buffer.request();
auto buf = pybind11::array::ensure(buffer);
if (!buf) {
throw std::invalid_argument("input buffer is not an np.array");
}
uint8_t datatype = PyFormatToImageStreamIODataType(info);
uint32_t dims[buf.ndim()];
for (int i = 0; i < buf.ndim(); ++i) {
dims[i] = buf.shape()[i];
}
int res = ImageStreamIO_createIm_gpu(
&img, name.c_str(), buf.ndim(), dims, datatype, location,
shared, NBsem, NBkw, imagetype, CBsize);
if (res == 0) {
if (buf.dtype() == pybind11::dtype::of<uint8_t>()) {
write<uint8_t>(img, buffer);
} else if (buf.dtype() == pybind11::dtype::of<int8_t>()) {
write<int8_t>(img, buffer);
} else if (buf.dtype() == pybind11::dtype::of<uint16_t>()) {
write<uint16_t>(img, buffer);
} else if (buf.dtype() == pybind11::dtype::of<int16_t>()) {
write<int16_t>(img, buffer);
} else if (buf.dtype() == pybind11::dtype::of<uint32_t>()) {
write<uint32_t>(img, buffer);
} else if (buf.dtype() == pybind11::dtype::of<int32_t>()) {
write<int32_t>(img, buffer);
} else if (buf.dtype() == pybind11::dtype::of<uint64_t>()) {
write<uint64_t>(img, buffer);
} else if (buf.dtype() == pybind11::dtype::of<int64_t>()) {
write<int64_t>(img, buffer);
} else if (buf.dtype() == pybind11::dtype::of<float>()) {
write<float>(img, buffer);
} else if (buf.dtype() == pybind11::dtype::of<double>()) {
write<double>(img, buffer);
} else {
throw std::invalid_argument("unsupported array datatype");
}
}
return res;
},
R"pbdoc(
Create shared memory image stream
Parameters:
name [in]: the name of the shared memory file will be SHAREDMEMDIR/<name>_im.shm
buffer [in]: np.array of the image.
location [in]: location of allocate the image (-1 for CPU or GPU number)
shared [in]: if true then a shared memory buffer is allocated. If false, only local storage is used.
NBkw [in]: the number of keywords to allocate.
NBsem [in]: the number of semaphore to attach.
imagetype[in]: the type of the image to create (ImageStreamIOType).
CBsize [in]: fast circular buffer size
Return:
ret [out]: error code
)pbdoc",
py::arg("name"), py::arg("buffer"), py::arg("location") = -1,
py::arg("shared") = 1, py::arg("NBsem") = IMAGE_NB_SEMAPHORE,
py::arg("NBkw") = 1, py::arg("imagetype") = MATH_DATA,
py::arg("CBsize") = 0)
// .def(
// "create",
// [](IMAGE &img, std::string name, py::array_t<uint32_t> dims,
// uint8_t datatype, uint8_t shared, uint16_t NBkw) {
// /* Request a buffer descriptor from Python */
// py::buffer_info info = dims.request();
// // uint8_t datatype =
// // PyFormatToImageStreamIODataType(info);
// // std::vector<uint32_t> ushape(info.ndim);
// // std::copy(info.shape.begin(), info.shape.end(),
// ushape.begin());
// return ImageStreamIO_createIm(&img, name.c_str(), info.size,
// (uint32_t *)info.ptr, datatype,
// shared, NBkw);
// },
// R"pbdoc(
// Create shared memory image stream
// Parameters:
// name [in]: the name of the shared memory file will be
// SHAREDMEMDIR/<name>_im.shm dims [in]: np.array of the
// image. datatype [in]: data type code,
// pyImageStreamIO.Datatype shared [in]: if true then a
// shared memory buffer is allocated. If false, only local
// storage is used. NBkw [in]: the number of keywords to
// allocate.
// Return:
// ret [out]: error code
// )pbdoc",
// py::arg("name"), py::arg("dims"),
// py::arg("datatype") = ImageStreamIODataType::DataType::FLOAT,
// py::arg("shared") = 1, py::arg("NBkw") = 1)
// .def(
// "create",
// [](IMAGE &img, std::string name, py::array_t<uint32_t> dims,
// uint8_t datatype, int8_t location, uint8_t shared, int NBsem,
// int NBkw, uint64_t imagetype) {
// /* Request a buffer descriptor from Python */