Fix locked Java buffer copy for array conversions

elevans · elevans · commit a62ec75b1b8e · 2022-10-24T12:02:21.000-05:00
`memoryview` of Java arrays (jarr) exposes the jarr's
buffer protocol and copies the buffer into a page
which then is referenced locked by `memoryview` and
things that are created from it (e.g. numpy.frombuffer). Changing
the underlying jarr's memory and requesting a new `memoryview`
does not return an updated view with the jarr's data change as
we expect, but instead the initial `memoryview` data state. This is bad.
In order to get `memoryview` to reflect the correct jarr data changes
you need to dereference (e.g. del or set to None) the `memoryview`
and objects that depend on it (e.g. a numpy array created from the
view).

This patch resolves this issue by obtaining the buffer
that `memoryview` is getting and wrapping the buffer
with numpy as we want. We can then safely release the buffer
(preserving memory) and return a copy to the user. If
_jarray_to_ndarray is called again on the same Java array
a new buffer is obtained, wrapped with numpy and released. The end
result is an updated view of the Java array upon request.
diff --git a/src/scyjava/_convert.py b/src/scyjava/_convert.py
@@ -618,7 +618,9 @@ def _jarray_to_ndarray(jarr):
     }
     # fmt: on
     dtype = jarraytype_map[element_type]
-    ndarray = np.frombuffer(memoryview(jarr), dtype=dtype)
+    bb = bytes(jarr)
+    ndarray = np.frombuffer(bb, dtype=dtype)
+    del bb  # release the buffer
     return ndarray.reshape(_jarray_shape(jarr))
 
 

Original file line number	Diff line number	Diff line change
`@@ -618,7 +618,9 @@ def _jarray_to_ndarray(jarr):`
`618`	`618`	`}`
`619`	`619`	`# fmt: on`
`620`	`620`	`dtype = jarraytype_map[element_type]`
`621`		`- ndarray = np.frombuffer(memoryview(jarr), dtype=dtype)`
	`621`	`+ bb = bytes(jarr)`
	`622`	`+ ndarray = np.frombuffer(bb, dtype=dtype)`
	`623`	`+ del bb # release the buffer`
`622`	`624`	`return ndarray.reshape(_jarray_shape(jarr))`
`623`	`625`
`624`	`626`