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Adding support for streaming through the input arrays of a pipeline #182

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merged 3 commits into from
Dec 17, 2024
Merged

Adding support for streaming through the input arrays of a pipeline #182

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aa3f7b6
Adding support for streaming the input arrays of a pipeline
joaori Nov 6, 2024
5b88cf4
Code cleanup based on code review.
joaori Nov 26, 2024
59fbb02
Updated documentation to include mention to reading with stream handler.
joaori Dec 17, 2024
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78 changes: 56 additions & 22 deletions src/pdal/PyArray.cpp
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Expand Up @@ -34,7 +34,6 @@

#include "PyArray.hpp"
#include <pdal/io/MemoryViewReader.hpp>
#include <numpy/arrayobject.h>

namespace pdal
{
Expand Down Expand Up @@ -95,7 +94,8 @@ std::string pyObjectToString(PyObject *pname)
#define PyDataType_NAMES(descr) ((descr)->names)
#endif

Array::Array(PyArrayObject* array) : m_array(array), m_rowMajor(true)
Array::Array(PyArrayObject* array, std::shared_ptr<ArrayStreamHandler> stream_handler)
: m_array(array), m_rowMajor(true), m_stream_handler(std::move(stream_handler))
{
Py_XINCREF(array);

Expand Down Expand Up @@ -164,51 +164,85 @@ Array::~Array()
Py_XDECREF(m_array);
}


ArrayIter& Array::iterator()
std::shared_ptr<ArrayIter> Array::iterator()
{
ArrayIter *it = new ArrayIter(m_array);
m_iterators.emplace_back((it));
return *it;
return std::make_shared<ArrayIter>(m_array, m_stream_handler);
}

ArrayIter::ArrayIter(PyArrayObject* np_array, std::shared_ptr<ArrayStreamHandler> stream_handler)
: m_stream_handler(std::move(stream_handler))
{
resetIterator(np_array);
}

ArrayIter::ArrayIter(PyArrayObject* np_array)
void ArrayIter::resetIterator(std::optional<PyArrayObject*> np_array = {})
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It seems like there are really two separate cases here. An initialize case and a reset case, variously triggered by the optional argument. Perhaps more clear to have two functions?

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Hmm. This didn't come out as nicely as I was thinking, so I may regret my comment ;)

{
m_iter = NpyIter_New(np_array,
NPY_ITER_EXTERNAL_LOOP | NPY_ITER_READONLY | NPY_ITER_REFS_OK,
NPY_KEEPORDER, NPY_NO_CASTING, NULL);
if (!m_iter)
throw pdal_error("Unable to create numpy iterator.");
std::optional<int> stream_chunk_size = std::nullopt;
if (m_stream_handler) {
stream_chunk_size = (*m_stream_handler)();
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The handler returns uint64_t, but assigns to int.

Is there any reason for optional? Seems like initializing to 0 would work fine.

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I've changed type to int64_t instead of uint64_t just for the sake of presenting a clearer error message to the python developer in case they mistakenly return a negative number.

Will be this:
RuntimeError: Stream chunk size not in the range of array length: -1

Instead of this:
RuntimeError: Unable to cast Python instance of type <class 'int'> to C++ type '?' (#define PYBIND11_DETAILED_ERROR_MESSAGES or compile in debug mode for details)

if (*stream_chunk_size == 0) {
m_done = true;
return;
}
}

if (np_array) {
// Init iterator
m_iter = NpyIter_New(np_array.value(),
NPY_ITER_EXTERNAL_LOOP | NPY_ITER_READONLY | NPY_ITER_REFS_OK,
NPY_KEEPORDER, NPY_NO_CASTING, NULL);
if (!m_iter)
throw pdal_error("Unable to create numpy iterator.");
} else {
// Otherwise, reset the iterator to the initial state
if (NpyIter_Reset(m_iter, NULL) != NPY_SUCCEED) {
NpyIter_Deallocate(m_iter);
throw pdal_error("Unable to reset numpy iterator.");
}
}
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set m_iter to nullptr here?

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Good catch. I've fixed it for the error case of m_iterNext below as well.


char *itererr;
m_iterNext = NpyIter_GetIterNext(m_iter, &itererr);
if (!m_iterNext)
{
NpyIter_Deallocate(m_iter);
throw pdal_error(std::string("Unable to create numpy iterator: ") +
itererr);
throw pdal_error(std::string("Unable to create numpy iterator: ") + itererr);
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This seems like a misleading error message.

}
m_data = NpyIter_GetDataPtrArray(m_iter);
m_stride = NpyIter_GetInnerStrideArray(m_iter);
m_size = NpyIter_GetInnerLoopSizePtr(m_iter);
m_stride = *NpyIter_GetInnerStrideArray(m_iter);
m_size = *NpyIter_GetInnerLoopSizePtr(m_iter);
if (stream_chunk_size) {
if (0 <= *stream_chunk_size && *stream_chunk_size <= m_size) {
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Seems you could use 0 as a sentinel since a chunk size of 0 seems pointless.

m_size = *stream_chunk_size;
} else {
throw pdal_error(std::string("Stream chunk size not in the range of array length: ") +
std::to_string(*stream_chunk_size));
}
}
m_done = false;
}

ArrayIter::~ArrayIter()
{
NpyIter_Deallocate(m_iter);
if (m_iter != nullptr) {
NpyIter_Deallocate(m_iter);
}
}

ArrayIter& ArrayIter::operator++()
{
if (m_done)
return *this;

if (--(*m_size))
*m_data += *m_stride;
else if (!m_iterNext(m_iter))
m_done = true;
if (--m_size) {
*m_data += m_stride;
} else if (!m_iterNext(m_iter)) {
if (m_stream_handler) {
resetIterator();
} else {
m_done = true;
}
}
return *this;
}

Expand Down
19 changes: 12 additions & 7 deletions src/pdal/PyArray.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -49,6 +49,7 @@

#include <vector>
#include <memory>
#include <optional>

namespace pdal
{
Expand All @@ -58,14 +59,15 @@ namespace python

class ArrayIter;

using ArrayStreamHandler = std::function<int64_t()>;

class PDAL_DLL Array
{
public:
using Shape = std::array<size_t, 3>;
using Fields = std::vector<MemoryViewReader::Field>;

Array(PyArrayObject* array);
Array(PyArrayObject* array, std::shared_ptr<ArrayStreamHandler> stream_handler = {});
~Array();

Array(Array&& a) = default;
Expand All @@ -77,14 +79,14 @@ class PDAL_DLL Array
bool rowMajor() const { return m_rowMajor; };
Shape shape() const { return m_shape; }
const Fields& fields() const { return m_fields; };
ArrayIter& iterator();
std::shared_ptr<ArrayIter> iterator();
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private:
PyArrayObject* m_array;
Fields m_fields;
bool m_rowMajor;
Shape m_shape {};
std::vector<std::unique_ptr<ArrayIter>> m_iterators;
std::shared_ptr<ArrayStreamHandler> m_stream_handler;
};


Expand All @@ -94,20 +96,23 @@ class PDAL_DLL ArrayIter
ArrayIter(const ArrayIter&) = delete;
ArrayIter() = delete;

ArrayIter(PyArrayObject*);
ArrayIter(PyArrayObject*, std::shared_ptr<ArrayStreamHandler>);
~ArrayIter();

ArrayIter& operator++();
operator bool () const { return !m_done; }
char* operator*() const { return *m_data; }

private:
NpyIter *m_iter;
NpyIter *m_iter = nullptr;
NpyIter_IterNextFunc *m_iterNext;
char **m_data;
npy_intp *m_size;
npy_intp *m_stride;
npy_intp m_size;
npy_intp m_stride;
bool m_done;

std::shared_ptr<ArrayStreamHandler> m_stream_handler;
void resetIterator(std::optional<PyArrayObject*> np_array);
};

} // namespace python
Expand Down
14 changes: 10 additions & 4 deletions src/pdal/PyPipeline.cpp
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Expand Up @@ -245,14 +245,20 @@ void PipelineExecutor::addArrayReaders(std::vector<std::shared_ptr<Array>> array
for (auto f : array->fields())
r.pushField(f);

ArrayIter& iter = array->iterator();
auto incrementer = [&iter](PointId id) -> char *
auto arrayIter = array->iterator();
auto incrementer = [arrayIter, firstPoint = true](PointId id) mutable -> char *
{
if (! iter)
ArrayIter& iter = *arrayIter;
if (!firstPoint && iter) {
++iter;
} else {
firstPoint = false;
}

if (!iter)
return nullptr;

char *c = *iter;
++iter;
return c;
};

Expand Down
20 changes: 16 additions & 4 deletions src/pdal/libpdalpython.cpp
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
#include <pybind11/pybind11.h>
#include <pybind11/stl.h>
#include <pybind11/numpy.h>
#include <pybind11/functional.h>
#include <pybind11/stl/filesystem.h>
#include <iostream>

Expand Down Expand Up @@ -189,11 +190,22 @@ namespace pdal {
));
}

void setInputs(std::vector<py::array> ndarrays) {
void setInputs(const std::vector<py::object>& inputs) {
_inputs.clear();
for (const auto& ndarray: ndarrays) {
PyArrayObject* ndarray_ptr = (PyArrayObject*)ndarray.ptr();
_inputs.push_back(std::make_shared<pdal::python::Array>(ndarray_ptr));
for (const auto& input_obj: inputs) {
if (py::isinstance<py::array>(input_obj)) {
// Backward compatibility for accepting list of numpy arrays
auto ndarray = input_obj.cast<py::array>();
_inputs.push_back(std::make_shared<pdal::python::Array>((PyArrayObject*)ndarray.ptr()));
} else {
// Now expected to be a list of pairs: (numpy array, <optional> stream handler)
auto input = input_obj.cast<std::pair<py::array, pdal::python::ArrayStreamHandler>>();
_inputs.push_back(std::make_shared<pdal::python::Array>(
(PyArrayObject*)input.first.ptr(),
input.second ?
std::make_shared<pdal::python::ArrayStreamHandler>(input.second)
: nullptr));
}
}
delExecutor();
}
Expand Down
12 changes: 10 additions & 2 deletions src/pdal/pipeline.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@

import json
import logging
from typing import Any, Container, Dict, Iterator, List, Optional, Sequence, Union, cast
from typing import Any, Container, Dict, Iterator, List, Optional, Sequence, Union, cast, Callable

import numpy as np
import pathlib
Expand Down Expand Up @@ -41,6 +41,7 @@ def __init__(
loglevel: int = logging.ERROR,
json: Optional[str] = None,
dataframes: Sequence[DataFrame] = (),
stream_handlers: Sequence[Callable[[], int]] = (),
):

if json:
Expand All @@ -58,7 +59,14 @@ def __init__(
stages = _parse_stages(spec) if isinstance(spec, str) else spec
for stage in stages:
self |= stage
self.inputs = arrays

if stream_handlers:
if len(stream_handlers) != len(arrays):
raise RuntimeError("stream_handlers must match the number of specified input arrays / dataframes")
self.inputs = [(a, h) for a, h in zip(arrays, stream_handlers)]
else:
self.inputs = [(a, None) for a in arrays]

self.loglevel = loglevel

def __getstate__(self):
Expand Down
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