Permit creation of NumPy arrays with a "base" object that owns the data #440

wjakob · 2016-10-12T23:05:03Z

This patch adds an extra base handle parameter to most py::array and
py::array_t<> constructors. If specified along with a pointer to
data, the base object will be registered within NumPy, which increases
the base's reference count. This feature is useful to create shallow
copies of C++ or Python arrays while ensuring that the owners of the
underlying can't be garbage collected while referenced by NumPy.

The commit also adds a simple test function involving a wrap()
function that creates shallow copies of various N-D arrays.

This patch adds an extra base handle parameter to most ``py::array`` and ``py::array_t<>`` constructors. If specified along with a pointer to data, the base object will be registered within NumPy, which increases the base's reference count. This feature is useful to create shallow copies of C++ or Python arrays while ensuring that the owners of the underlying can't be garbage collected while referenced by NumPy. The commit also adds a simple test function involving a ``wrap()`` function that creates shallow copies of various N-D arrays.

wjakob · 2016-10-12T23:09:35Z

This feature is related to discussions on #383 and is up for review (one of my projects needed the ability to create shallow copies of NumPy arrays, so I just went ahead and implemented it.)

cc @aldanor -- does it look reasonable to you?

aldanor · 2016-10-12T23:41:20Z

include/pybind11/numpy.h

@@ -156,8 +156,10 @@ NAMESPACE_END(detail)
    (reinterpret_cast<::pybind11::detail::PyArray_Proxy*>(ptr)->attr)
 #define PyArrayDescr_GET_(ptr, attr) \
    (reinterpret_cast<::pybind11::detail::PyArrayDescr_Proxy*>(ptr)->attr)
+#define PyArray_FLAGS_(ptr) \
+    (reinterpret_cast<::pybind11::detail::PyArray_Proxy*>(ptr)->flags)


Or rather just PyArray_GET_(flags) :)

aldanor · 2016-10-12T23:42:09Z

include/pybind11/numpy.h

-            tmp = object(api.PyArray_NewCopy_(tmp.ptr(), -1 /* any order */), false);
+        if (ptr) {
+            if (base) {
+                PyArray_GET_(tmp.ptr(), base) = base.inc_ref().ptr();


I haven't read this part of numpy api in detail, but my guess is that it's our job to incref the owner, and it's numpy's job to decref it when the array dies, is that correct?

that's right.

aldanor · 2016-10-12T23:44:59Z

include/pybind11/numpy.h

+                flags = base_array.flags() & ~detail::npy_api::NPY_ARRAY_OWNDATA_;
+            else
+                /* Writable by default, easy to downgrade later on if needed */
+                flags = detail::npy_api::NPY_ARRAY_WRITEABLE_;


Yea, agreed, writeable should probably be the default when constructing arrays as we discussed earlier (and read-only a default when passing them around as args).

I interpret this comment as an observation with no action items :)

aldanor · 2016-10-12T23:47:02Z

include/pybind11/numpy.h

@@ -319,6 +345,11 @@ class array : public buffer {
        return (size_t) PyArray_GET_(m_ptr, nd);
    }

+    /// Base object
+    object base() const {


Just wondering, is there a use case for exposing the base?

NumPy has a .base flag, so I thought it would be nice to expose it in the C++ API as well.

This feature (pointer into memory owned by a "base") is really neat for exposing a NumPy "view" into a data structure that may be implemented in a completely different programming language. The base pointer lets you get back from the numpy view to the parent class, which can be useful in a function that is called without knowing the latter.

(whether that last approach is a good design pattern is another matter)

aldanor · 2016-10-12T23:48:22Z

tests/test_numpy_array.py

@@ -158,3 +159,53 @@ def test_make_c_f_array():
    assert not make_c_array().flags.f_contiguous
    assert make_f_array().flags.f_contiguous
    assert not make_f_array().flags.c_contiguous
+
+
+@pytest.requires_numpy


Maybe a separate test for base lifetime? E.g., create base, bind array to it, del/decref base, make sure the array and base are still alive, kill array, make sure the base is also dead?

Ok, will add one.

wjakob · 2016-10-13T08:51:18Z

merged -- thanks for the feedback.

wjakob · 2016-10-13T08:52:10Z

include/pybind11/pybind11.h

+        try {
+            file = module::import("sys").attr("stdout");
+        } catch (const import_error &) {
+            /* If print() is called from code that is executed as


@dean0x7d : FYI

That's an interesting situation. I guess that comes up with the ConstructorStats output from destructors. Wouldn't it be better to add the try/catch to ConstructorStats rather than penalize every py::print call?

In general, any Python code executed in a destructor can throw an exception, so this isn't really isolated to py::print. Even with pure C++ code it's up to the destructor to make sure that no exceptions escape -- the called functions don't need to be aware if they are running from a destructor or not.

It came up when I added py::print to a destructor that (as part of implementing a new testcase) got called during interpreter shutdown. Many Python calls will still work in that situation, but importing new things is definitely forbidden. py::print is special in this regard that it needs to import sys, and then stdout, hence the decision to modify it.

aldanor · 2016-10-13T08:52:17Z

This is great, thanks! :)

aldanor reviewed Oct 12, 2016

View reviewed changes

wjakob added 2 commits October 13, 2016 10:34

py::print robustness improvements, added import exception class

c49d6e5

NumPy "base" feature: integrated feedback by @aldanor

fac7c09

wjakob force-pushed the master branch from d4e9822 to fac7c09 Compare October 13, 2016 08:50

wjakob merged commit 00488a3 into pybind:master Oct 13, 2016

wjakob commented Oct 13, 2016

View reviewed changes

rwgk mentioned this pull request Feb 9, 2023

FWD pybind11 google/pybind11k#440

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Permit creation of NumPy arrays with a "base" object that owns the data #440

Permit creation of NumPy arrays with a "base" object that owns the data #440

wjakob commented Oct 12, 2016

wjakob commented Oct 12, 2016

aldanor Oct 12, 2016

wjakob Oct 13, 2016

aldanor Oct 12, 2016

wjakob Oct 13, 2016

aldanor Oct 12, 2016

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wjakob commented Oct 13, 2016

wjakob Oct 13, 2016

dean0x7d Oct 13, 2016 •

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wjakob Oct 13, 2016

aldanor commented Oct 13, 2016

Permit creation of NumPy arrays with a "base" object that owns the data #440

Permit creation of NumPy arrays with a "base" object that owns the data #440

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aldanor commented Oct 13, 2016

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