binary format I/O fails on big-endian architectures like s390x due to endianness bugs #2511
Description
The following four tests fail on s390x (big-endian) under Alpine Linux 3.23 with errors related to endianness:
=================================== FAILURES ===================================
____________________________ PlyTest.test_uv_export ____________________________
[gw6] linux -- Python 3.12.12 /builds/strophy/aports/testing/py3-trimesh/src/trimesh-4.11.2/.testenv/bin/python3
self = <tests.test_ply.PlyTest testMethod=test_uv_export>
def test_uv_export(self):
m = g.get_mesh("fuze.ply")
assert hasattr(m, "visual") and hasattr(m.visual, "uv")
assert m.visual.uv.shape[0] == m.vertices.shape[0]
# create empty file to export to
with g.TemporaryDirectory() as D:
name = g.os.path.join(D, "file.ply")
# export should contain the uv data
m.export(name)
m2 = g.trimesh.load(name)
assert hasattr(m2, "visual") and hasattr(m2.visual, "uv")
> assert g.np.allclose(m.visual.uv, m2.visual.uv)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
tests/test_ply.py:234:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/usr/lib/python3.12/site-packages/numpy/_core/numeric.py:2376: in allclose
res = all(isclose(a, b, rtol=rtol, atol=atol, equal_nan=equal_nan))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
a = TrackedArray([[0.62901198864 , 0.417026013136],
[0.62901198864 , 0.442966014147],
[0.66143...8642],
[0.565362989902, 0.991708993912],
[0.520901024342, 0.780556023121]], shape=(664, 2))
b = TrackedArray([[4.092561360438e-312, 4.765015389936e-312],
[4.092561360438e-312, 4.765015389936e-312],
... [4.092561360438e-312, 4.765015389936e-312],
[4.092561360438e-312, 4.765015389936e-312]], shape=(502, 2))
rtol = 1e-05, atol = 1e-08, equal_nan = False
@array_function_dispatch(_isclose_dispatcher)
def isclose(a, b, rtol=1.e-5, atol=1.e-8, equal_nan=False):
"""
Returns a boolean array where two arrays are element-wise equal within a
tolerance.
The tolerance values are positive, typically very small numbers. The
relative difference (`rtol` * abs(`b`)) and the absolute difference
`atol` are added together to compare against the absolute difference
between `a` and `b`.
.. warning:: The default `atol` is not appropriate for comparing numbers
with magnitudes much smaller than one (see Notes).
Parameters
----------
a, b : array_like
Input arrays to compare.
rtol : array_like
The relative tolerance parameter (see Notes).
atol : array_like
The absolute tolerance parameter (see Notes).
equal_nan : bool
Whether to compare NaN's as equal. If True, NaN's in `a` will be
considered equal to NaN's in `b` in the output array.
Returns
-------
y : array_like
Returns a boolean array of where `a` and `b` are equal within the
given tolerance. If both `a` and `b` are scalars, returns a single
boolean value.
See Also
--------
allclose
math.isclose
Notes
-----
For finite values, isclose uses the following equation to test whether
two floating point values are equivalent.::
absolute(a - b) <= (atol + rtol * absolute(b))
Unlike the built-in `math.isclose`, the above equation is not symmetric
in `a` and `b` -- it assumes `b` is the reference value -- so that
`isclose(a, b)` might be different from `isclose(b, a)`.
The default value of `atol` is not appropriate when the reference value
`b` has magnitude smaller than one. For example, it is unlikely that
``a = 1e-9`` and ``b = 2e-9`` should be considered "close", yet
``isclose(1e-9, 2e-9)`` is ``True`` with default settings. Be sure
to select `atol` for the use case at hand, especially for defining the
threshold below which a non-zero value in `a` will be considered "close"
to a very small or zero value in `b`.
`isclose` is not defined for non-numeric data types.
:class:`bool` is considered a numeric data-type for this purpose.
Examples
--------
>>> import numpy as np
>>> np.isclose([1e10,1e-7], [1.00001e10,1e-8])
array([ True, False])
>>> np.isclose([1e10,1e-8], [1.00001e10,1e-9])
array([ True, True])
>>> np.isclose([1e10,1e-8], [1.0001e10,1e-9])
array([False, True])
>>> np.isclose([1.0, np.nan], [1.0, np.nan])
array([ True, False])
>>> np.isclose([1.0, np.nan], [1.0, np.nan], equal_nan=True)
array([ True, True])
>>> np.isclose([1e-8, 1e-7], [0.0, 0.0])
array([ True, False])
>>> np.isclose([1e-100, 1e-7], [0.0, 0.0], atol=0.0)
array([False, False])
>>> np.isclose([1e-10, 1e-10], [1e-20, 0.0])
array([ True, True])
>>> np.isclose([1e-10, 1e-10], [1e-20, 0.999999e-10], atol=0.0)
array([False, True])
"""
# Turn all but python scalars into arrays.
x, y, atol, rtol = (
a if isinstance(a, (int, float, complex)) else asanyarray(a)
for a in (a, b, atol, rtol))
# Make sure y is an inexact type to avoid bad behavior on abs(MIN_INT).
# This will cause casting of x later. Also, make sure to allow subclasses
# (e.g., for numpy.ma).
# NOTE: We explicitly allow timedelta, which used to work. This could
# possibly be deprecated. See also gh-18286.
# timedelta works if `atol` is an integer or also a timedelta.
# Although, the default tolerances are unlikely to be useful
if (dtype := getattr(y, "dtype", None)) is not None and dtype.kind != "m":
dt = multiarray.result_type(y, 1.)
y = asanyarray(y, dtype=dt)
elif isinstance(y, int):
y = float(y)
# atol and rtol can be arrays
if not (np.all(np.isfinite(atol)) and np.all(np.isfinite(rtol))):
err_s = np.geterr()["invalid"]
err_msg = f"One of rtol or atol is not valid, atol: {atol}, rtol: {rtol}"
if err_s == "warn":
warnings.warn(err_msg, RuntimeWarning, stacklevel=2)
elif err_s == "raise":
raise FloatingPointError(err_msg)
elif err_s == "print":
print(err_msg)
with errstate(invalid='ignore'):
> result = (less_equal(abs(x - y), atol + rtol * abs(y))
^^^^^
& isfinite(y)
| (x == y))
E ValueError: operands could not be broadcast together with shapes (664,2) (502,2)
/usr/lib/python3.12/site-packages/numpy/_core/numeric.py:2507: ValueError
________________________ PlyTest.test_vertex_attributes ________________________
[gw6] linux -- Python 3.12.12 /builds/strophy/aports/testing/py3-trimesh/src/trimesh-4.11.2/.testenv/bin/python3
self = <tests.test_ply.PlyTest testMethod=test_vertex_attributes>
def test_vertex_attributes(self):
"""
Test writing vertex attributes to a ply, by reading them back and asserting the
written attributes array matches
"""
m = g.get_mesh("box.STL")
test_1d_attribute = g.np.copy(m.vertices[:, 0])
test_nd_attribute = g.np.copy(m.vertices)
m.vertex_attributes["test_1d_attribute"] = test_1d_attribute
m.vertex_attributes["test_nd_attribute"] = test_nd_attribute
export = m.export(file_type="ply")
reconstructed = g.roundtrip(export, file_type="ply")
vertex_attributes = reconstructed.metadata["_ply_raw"]["vertex"]["data"]
result_1d = vertex_attributes["test_1d_attribute"]
result_nd = vertex_attributes["test_nd_attribute"]["f1"]
> g.np.testing.assert_almost_equal(result_1d, test_1d_attribute)
E AssertionError:
E Arrays are not almost equal to 7 decimals
E
E Mismatched elements: 4455 / 4455 (100%)
E First 5 mismatches are at indices:
E [0]: 6.8986592767e-313 (ACTUAL), 6.4057698249816895 (DESIRED)
E [1]: 6.8986592767e-313 (ACTUAL), 6.4057698249816895 (DESIRED)
E [2]: 6.8986592767e-313 (ACTUAL), 6.4057698249816895 (DESIRED)
E [3]: 6.8986592767e-313 (ACTUAL), 6.4057698249816895 (DESIRED)
E [4]: 3.414826356378e-312 (ACTUAL), 6.4647698402404785 (DESIRED)
E Max absolute difference among violations: 6.523769855499
E Max relative difference among violations: 1.
E ACTUAL: array([6.8986593e-313, 6.8986593e-313, 6.8986593e-313, ...,
E 1.2470836e-314, 1.2470836e-314, 6.8986593e-313],
E shape=(4455,), dtype='<f8')
E DESIRED: array([6.4057698, 6.4057698, 6.4057698, ..., 6.1128769, 6.1128769,
E 6.4057698], shape=(4455,))
tests/test_ply.py:106: AssertionError
_________________________ PlyTest.test_face_attributes _________________________
[gw4] linux -- Python 3.12.12 /builds/strophy/aports/testing/py3-trimesh/src/trimesh-4.11.2/.testenv/bin/python3
self = <tests.test_ply.PlyTest testMethod=test_face_attributes>
def test_face_attributes(self):
# Test writing face attributes to a ply, by reading
# them back and asserting the written attributes array matches
for encoding in ["binary", "ascii"]:
for dt in [g.np.float32, g.np.float64]:
m = g.get_mesh("box.STL")
test_1d_attribute = g.np.copy(m.face_angles[:, 0])
test_nd_attribute = g.np.copy(m.face_angles)
m.face_attributes["test_1d_attribute"] = test_1d_attribute.astype(dt)
m.face_attributes["test_nd_attribute"] = test_nd_attribute.astype(dt)
export = m.export(
file_type="ply", include_attributes=True, encoding=encoding
)
reconstructed = g.roundtrip(export, file_type="ply", process=False)
face_attributes = reconstructed.metadata["_ply_raw"]["face"]["data"]
result_1d = face_attributes["test_1d_attribute"]
if encoding == "binary":
# only binary format allows this
result_nd = face_attributes["test_nd_attribute"]["f1"]
else:
result_nd = face_attributes["test_nd_attribute"]
> g.np.testing.assert_almost_equal(result_1d, test_1d_attribute)
E AssertionError:
E Arrays are not almost equal to 7 decimals
E
E nan location mismatch:
E ACTUAL: array([-4.0472194e+16, -2.0552418e-08, 8.8456492e+04, ...,
E -2.9970339e+22, -4.0331457e+16, -4.0331457e+16],
E shape=(8954,), dtype='<f4')
E DESIRED: array([1.5707963, 1.0913298, 1.5365074, ..., 2.3561945, 0.7853982,
E 0.7853982], shape=(8954,))
tests/test_ply.py:134: AssertionError
____________________ GLTFTest.test_export_custom_attributes ____________________
[gw7] linux -- Python 3.12.12 /builds/strophy/aports/testing/py3-trimesh/src/trimesh-4.11.2/.testenv/bin/python3
self = <tests.test_gltf.GLTFTest testMethod=test_export_custom_attributes>
def test_export_custom_attributes(self):
# Write and read custom vertex attributes to gltf
sphere = g.trimesh.primitives.Sphere()
v_count, _ = sphere.vertices.shape
sphere.vertex_attributes["_CustomFloat32Scalar"] = g.np.random.rand(
v_count, 1
).astype(g.np.float32)
sphere.vertex_attributes["_CustomFloat32Vec3"] = g.np.random.rand(
v_count, 3
).astype(g.np.float32)
sphere.vertex_attributes["_CustomFloat32Mat4"] = g.np.random.rand(
v_count, 4, 4
).astype(g.np.float32)
# export as GLB bytes
export = sphere.export(file_type="glb")
# this should validate just fine
validate_glb(export)
# uint32 is slightly off-label and may cause
# validators to fail but if you're a bad larry who
# doesn't follow the rules it should be fine
sphere.vertex_attributes["_CustomUInt32Scalar"] = g.np.random.randint(
0, 1000, size=(v_count, 1)
).astype(g.np.uint32)
# when you add a uint16/int16 the gltf-validator
# complains about the 4-byte boundaries even though
# all their lengths and offsets mod 4 are zero
# not sure if that's a validator bug or what
sphere.vertex_attributes["_CustomUInt16Scalar"] = g.np.random.randint(
0, 1000, size=(v_count, 1)
).astype(g.np.uint16)
sphere.vertex_attributes["_CustomInt16Scalar"] = g.np.random.randint(
0, 1000, size=(v_count, 1)
).astype(g.np.int16)
# export as GLB then re-load
export = sphere.export(file_type="glb")
r = g.trimesh.load(g.trimesh.util.wrap_as_stream(export), file_type="glb")
for _, val in r.geometry.items():
assert set(val.vertex_attributes.keys()) == set(
sphere.vertex_attributes.keys()
)
for key in val.vertex_attributes:
# the vertex attribute before round-tripping
ori = sphere.vertex_attributes[key]
# non 4-byte aligned attributes would have been padded
check = val.vertex_attributes[key][:, : ori.shape[1]]
> assert g.np.allclose(ori, check), key
E AssertionError: _CustomFloat32Scalar
E assert False
E + where False = <function allclose at 0x3ff4c81e130>(array([[1.78557485e-01],\n [7.64179289e-01],\n [4.88104403e-01],\n [2.13032410e-01],\n [6.76045477e-01],\n [1.72032222e-01],\n [1.05292611e-01],\n [2.76651591e-01],\n [9.32412148e-02],\n [7.08671927e-01],\n [8.45383883e-01],\n [1.59452073e-02],\n [6.11236751e-01],\n [1.41733764e-02],\n [9.26103219e-02],\n [8.46374512e-01],\n [8.07372808e-01],\n [9.98835623e-01],\n [5.66610694e-01],\n [3.46271455e-01],\n [7.11632669e-01],\n [4.38893676e-01],\n [9.66912448e-01],\n [2.80399650e-01],\n [8.15345109e-01],\n [5.29560089e-01],\n [1.23304993e-01],\n [3.16784412e-01],\n [5.66678345e-01],\n [7.68971503e-01],\n [7.21466839e-01],\n [8.83644596e-02],\n [7.66119838e-01],\n [6.53052032e-02],\n [7.29488581e-02],\n [6.81485474e-01],\n [8.88428450e-01],\n [1.64339975e-01],\n [3.55258644e-01],\n [1.83149964e-01],\n [6.87364638e-01],\n [1.81428939e-01],\n [4.45469558e-01],\n [6.06894433e-01],\n [3.53891730e-01],\n [7.51811802e-01],\n [8.33294153e-01],\n [6.00830078e-01]...02e-01],\n [6.41341627e-01],\n [5.26171684e-01],\n [1.33700415e-01],\n [8.70324314e-01],\n [1.72386259e-01],\n [8.53354275e-01],\n [2.25214228e-01],\n [1.62106991e-01],\n [4.36152726e-01],\n [3.61672640e-02],\n [7.96875656e-01],\n [6.67929173e-01],\n [5.78643441e-01],\n [7.40894735e-01],\n [9.90205944e-01],\n [2.56226361e-01],\n [2.54459549e-02],\n [5.68959832e-01],\n [9.10290778e-01],\n [7.77455688e-01],\n [1.36427194e-01],\n [8.35757494e-01],\n [5.25348485e-01],\n [2.21652582e-01],\n [1.23829611e-01],\n [3.85971099e-01],\n [6.22173011e-01],\n [7.30783820e-01],\n [1.51006445e-01],\n [6.43105805e-01],\n [2.59271204e-01],\n [4.73210156e-01],\n [1.77116930e-01],\n [2.27904990e-01],\n [4.35855895e-01],\n [5.64736485e-01],\n [7.26099133e-01],\n [3.84750277e-01],\n [6.39364302e-01],\n [3.96793246e-01],\n [9.07050520e-02],\n [6.05722189e-01],\n [2.98411578e-01],\n [2.82684505e-01],\n [1.85717955e-01],\n [1.68054730e-01],\n [6.84710860e-01]], dtype=float32), array([[-2.75471211e+04],\n [ 2.01578350e+01],\n [-5.00307001e+11],\n [ 5.87450119e-13],\n [ 3.89705851e+10],\n [ 1.00844172e-05],\n [-4.54749501e-15],\n [ 8.47624844e+04],\n [ 7.67947245e+00],\n [-4.42377066e-35],\n [ 1.18818715e-26],\n [-6.00005148e-35],\n [ 7.35008219e-37],\n [ 1.45310127e+31],\n [ 1.77305735e+36],\n [ 1.58273621e-38],\n [-7.28191176e+36],\n [-5.22405186e-09],\n [ 1.66542952e+23],\n [ 6.73560873e+37],\n [-8.54000596e-30],\n [-5.19764700e-12],\n [-3.41963768e-27],\n [-5.56823093e-32],\n [ 4.72360742e+32],\n [ 4.53213453e+00],\n [ 4.67241953e+12],\n [-1.40128328e-28],\n [-9.96895359e+12],\n [ 1.17717852e+11],\n [ 1.09836377e-30],\n [ 9.62127214e+27],\n [ 1.24000265e+28],\n [-2.32568923e-02],\n [ 3.43595389e-06],\n [-1.68486859e+13],\n [ 1.85187933e-31],\n [-4.88665029e-02],\n [ 2.31937444e+33],\n [-2.47324676e-13],\n [ 1.67498770e-18],\n [-2.94202142e-37],\n [-1.20273653e-25],\n [ 6.84291257e+28],\n [ 4.65850800e+07],\n [-6.01198636e-02],\n ....30257394e-09],\n [-4.64064392e+02],\n [-5.18422092e-27],\n [ 5.04760833e-35],\n [ 4.74580801e+27],\n [-1.56193851e-29],\n [ 1.47081354e+20],\n [ 1.57063673e+25],\n [ 1.38980366e-19],\n [ 2.47092645e-32],\n [ 9.56430418e+24],\n [-2.09092608e+35],\n [ 8.76744922e+04],\n [ 1.37958895e-17],\n [ 3.65019635e-23],\n [ 2.94683430e-33],\n [ 2.35126417e+16],\n [-3.66175805e+10],\n [ 3.71850173e+13],\n [-1.12992596e-27],\n [ 4.55105663e-07],\n [ 6.17735349e-02],\n [-1.46619892e+23],\n [ 3.57380791e+20],\n [ 5.83230622e-38],\n [-3.02310265e-03],\n [-5.14281083e-16],\n [ 9.97176229e+28],\n [-6.54884652e-26],\n [ 2.22954633e-08],\n [-4.15547123e-23],\n [ 4.81836743e-17],\n [-4.32139920e+27],\n [-3.10168951e-38],\n [-9.21790034e-28],\n [-6.10469839e-18],\n [-4.21642038e+37],\n [ 3.99228309e+20],\n [ 3.50571245e+36],\n [-1.23518949e-27],\n [-4.76808180e-22],\n [ 1.90400807e+24],\n [ 7.09296850e-35],\n [-3.03013325e+15],\n [-7.23055832e-33],\n [ 2.99788348e-06]], dtype='<f4'))
E + where <function allclose at 0x3ff4c81e130> = <module 'numpy' from '/usr/lib/python3.12/site-packages/numpy/__init__.py'>.allclose
E + where <module 'numpy' from '/usr/lib/python3.12/site-packages/numpy/__init__.py'> = g.np
tests/test_gltf.py:599: AssertionError