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-rw-r--r--silx/io/commonh5.py8
-rw-r--r--silx/io/fabioh5.py4
-rw-r--r--silx/io/specfile.c55
-rw-r--r--silx/io/test/test_specfile.py13
-rw-r--r--silx/io/test/test_spech5.py11
-rw-r--r--silx/io/test/test_spectoh5.py4
-rw-r--r--silx/io/test/test_utils.py20
-rw-r--r--silx/io/utils.py7
8 files changed, 100 insertions, 22 deletions
diff --git a/silx/io/commonh5.py b/silx/io/commonh5.py
index 2956714..b624816 100644
--- a/silx/io/commonh5.py
+++ b/silx/io/commonh5.py
@@ -1,6 +1,6 @@
# coding: utf-8
# /*##########################################################################
-# Copyright (C) 2016-2018 European Synchrotron Radiation Facility
+# Copyright (C) 2016-2019 European Synchrotron Radiation Facility
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
@@ -29,6 +29,10 @@ files. They are used in :mod:`spech5` and :mod:`fabioh5`.
library, which is not a mandatory dependency for `silx`.
"""
import collections
+try:
+ from collections import abc
+except ImportError: # Python2 support
+ import collections as abc
import weakref
import h5py
@@ -42,7 +46,7 @@ __license__ = "MIT"
__date__ = "02/07/2018"
-class _MappingProxyType(collections.MutableMapping):
+class _MappingProxyType(abc.MutableMapping):
"""Read-only dictionary
This class is available since Python 3.3, but not on earlyer Python
diff --git a/silx/io/fabioh5.py b/silx/io/fabioh5.py
index 27ef3fd..351b981 100644
--- a/silx/io/fabioh5.py
+++ b/silx/io/fabioh5.py
@@ -1,6 +1,6 @@
# coding: utf-8
# /*##########################################################################
-# Copyright (C) 2016-2018 European Synchrotron Radiation Facility
+# Copyright (C) 2016-2019 European Synchrotron Radiation Facility
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
@@ -474,7 +474,7 @@ class FabioReader(object):
while len(location) < max_dim:
location.append(0)
normalized_image = numpy.zeros(max_shape, dtype=image.dtype)
- normalized_image[location] = image
+ normalized_image[tuple(location)] = image
images[index] = normalized_image
# create a cube
diff --git a/silx/io/specfile.c b/silx/io/specfile.c
index 0cc1195..f8e7ed8 100644
--- a/silx/io/specfile.c
+++ b/silx/io/specfile.c
@@ -1,4 +1,4 @@
-/* Generated by Cython 0.29.7 */
+/* Generated by Cython 0.29.11 */
/* BEGIN: Cython Metadata
{
@@ -41,8 +41,8 @@ END: Cython Metadata */
#elif PY_VERSION_HEX < 0x02060000 || (0x03000000 <= PY_VERSION_HEX && PY_VERSION_HEX < 0x03030000)
#error Cython requires Python 2.6+ or Python 3.3+.
#else
-#define CYTHON_ABI "0_29_7"
-#define CYTHON_HEX_VERSION 0x001D07F0
+#define CYTHON_ABI "0_29_11"
+#define CYTHON_HEX_VERSION 0x001D0BF0
#define CYTHON_FUTURE_DIVISION 1
#include <stddef.h>
#ifndef offsetof
@@ -344,8 +344,16 @@ END: Cython Metadata */
#define __Pyx_DefaultClassType PyClass_Type
#else
#define __Pyx_BUILTIN_MODULE_NAME "builtins"
+#if PY_VERSION_HEX < 0x030800A4
#define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\
PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
+#elif PY_VERSION_HEX >= 0x030800B2
+ #define __Pyx_PyCode_New(a, p, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\
+ PyCode_NewWithPosOnlyArgs(a, p, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
+#else
+ #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\
+ PyCode_New(a, 0, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
+#endif
#define __Pyx_DefaultClassType PyType_Type
#endif
#ifndef Py_TPFLAGS_CHECKTYPES
@@ -28176,6 +28184,9 @@ static PyTypeObject __pyx_type_4silx_2io_8specfile_SpecFile = {
#if PY_VERSION_HEX >= 0x030400a1
0, /*tp_finalize*/
#endif
+ #if PY_VERSION_HEX >= 0x030800b1
+ 0, /*tp_vectorcall*/
+ #endif
};
static struct __pyx_obj_4silx_2io_8specfile___pyx_scope_struct____iter__ *__pyx_freelist_4silx_2io_8specfile___pyx_scope_struct____iter__[8];
@@ -28271,6 +28282,9 @@ static PyTypeObject __pyx_type_4silx_2io_8specfile___pyx_scope_struct____iter__
#if PY_VERSION_HEX >= 0x030400a1
0, /*tp_finalize*/
#endif
+ #if PY_VERSION_HEX >= 0x030800b1
+ 0, /*tp_vectorcall*/
+ #endif
};
static struct __pyx_obj_4silx_2io_8specfile___pyx_scope_struct_1___iter__ *__pyx_freelist_4silx_2io_8specfile___pyx_scope_struct_1___iter__[8];
@@ -28366,6 +28380,9 @@ static PyTypeObject __pyx_type_4silx_2io_8specfile___pyx_scope_struct_1___iter__
#if PY_VERSION_HEX >= 0x030400a1
0, /*tp_finalize*/
#endif
+ #if PY_VERSION_HEX >= 0x030800b1
+ 0, /*tp_vectorcall*/
+ #endif
};
static struct __pyx_vtabstruct_array __pyx_vtable_array;
@@ -28544,6 +28561,9 @@ static PyTypeObject __pyx_type___pyx_array = {
#if PY_VERSION_HEX >= 0x030400a1
0, /*tp_finalize*/
#endif
+ #if PY_VERSION_HEX >= 0x030800b1
+ 0, /*tp_vectorcall*/
+ #endif
};
static PyObject *__pyx_tp_new_Enum(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
@@ -28652,6 +28672,9 @@ static PyTypeObject __pyx_type___pyx_MemviewEnum = {
#if PY_VERSION_HEX >= 0x030400a1
0, /*tp_finalize*/
#endif
+ #if PY_VERSION_HEX >= 0x030800b1
+ 0, /*tp_vectorcall*/
+ #endif
};
static struct __pyx_vtabstruct_memoryview __pyx_vtable_memoryview;
@@ -28902,6 +28925,9 @@ static PyTypeObject __pyx_type___pyx_memoryview = {
#if PY_VERSION_HEX >= 0x030400a1
0, /*tp_finalize*/
#endif
+ #if PY_VERSION_HEX >= 0x030800b1
+ 0, /*tp_vectorcall*/
+ #endif
};
static struct __pyx_vtabstruct__memoryviewslice __pyx_vtable__memoryviewslice;
@@ -29037,6 +29063,9 @@ static PyTypeObject __pyx_type___pyx_memoryviewslice = {
#if PY_VERSION_HEX >= 0x030400a1
0, /*tp_finalize*/
#endif
+ #if PY_VERSION_HEX >= 0x030800b1
+ 0, /*tp_vectorcall*/
+ #endif
};
static PyMethodDef __pyx_methods[] = {
@@ -30192,7 +30221,9 @@ static int __Pyx_modinit_type_init_code(void) {
__Pyx_RefNannySetupContext("__Pyx_modinit_type_init_code", 0);
/*--- Type init code ---*/
if (PyType_Ready(&__pyx_type_4silx_2io_8specfile_SpecFile) < 0) __PYX_ERR(0, 629, __pyx_L1_error)
+ #if PY_VERSION_HEX < 0x030800B1
__pyx_type_4silx_2io_8specfile_SpecFile.tp_print = 0;
+ #endif
if ((CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP) && likely(!__pyx_type_4silx_2io_8specfile_SpecFile.tp_dictoffset && __pyx_type_4silx_2io_8specfile_SpecFile.tp_getattro == PyObject_GenericGetAttr)) {
__pyx_type_4silx_2io_8specfile_SpecFile.tp_getattro = __Pyx_PyObject_GenericGetAttr;
}
@@ -30240,13 +30271,17 @@ static int __Pyx_modinit_type_init_code(void) {
if (__Pyx_setup_reduce((PyObject*)&__pyx_type_4silx_2io_8specfile_SpecFile) < 0) __PYX_ERR(0, 629, __pyx_L1_error)
__pyx_ptype_4silx_2io_8specfile_SpecFile = &__pyx_type_4silx_2io_8specfile_SpecFile;
if (PyType_Ready(&__pyx_type_4silx_2io_8specfile___pyx_scope_struct____iter__) < 0) __PYX_ERR(0, 300, __pyx_L1_error)
+ #if PY_VERSION_HEX < 0x030800B1
__pyx_type_4silx_2io_8specfile___pyx_scope_struct____iter__.tp_print = 0;
+ #endif
if ((CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP) && likely(!__pyx_type_4silx_2io_8specfile___pyx_scope_struct____iter__.tp_dictoffset && __pyx_type_4silx_2io_8specfile___pyx_scope_struct____iter__.tp_getattro == PyObject_GenericGetAttr)) {
__pyx_type_4silx_2io_8specfile___pyx_scope_struct____iter__.tp_getattro = __Pyx_PyObject_GenericGetAttrNoDict;
}
__pyx_ptype_4silx_2io_8specfile___pyx_scope_struct____iter__ = &__pyx_type_4silx_2io_8specfile___pyx_scope_struct____iter__;
if (PyType_Ready(&__pyx_type_4silx_2io_8specfile___pyx_scope_struct_1___iter__) < 0) __PYX_ERR(0, 680, __pyx_L1_error)
+ #if PY_VERSION_HEX < 0x030800B1
__pyx_type_4silx_2io_8specfile___pyx_scope_struct_1___iter__.tp_print = 0;
+ #endif
if ((CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP) && likely(!__pyx_type_4silx_2io_8specfile___pyx_scope_struct_1___iter__.tp_dictoffset && __pyx_type_4silx_2io_8specfile___pyx_scope_struct_1___iter__.tp_getattro == PyObject_GenericGetAttr)) {
__pyx_type_4silx_2io_8specfile___pyx_scope_struct_1___iter__.tp_getattro = __Pyx_PyObject_GenericGetAttrNoDict;
}
@@ -30254,12 +30289,16 @@ static int __Pyx_modinit_type_init_code(void) {
__pyx_vtabptr_array = &__pyx_vtable_array;
__pyx_vtable_array.get_memview = (PyObject *(*)(struct __pyx_array_obj *))__pyx_array_get_memview;
if (PyType_Ready(&__pyx_type___pyx_array) < 0) __PYX_ERR(1, 105, __pyx_L1_error)
+ #if PY_VERSION_HEX < 0x030800B1
__pyx_type___pyx_array.tp_print = 0;
+ #endif
if (__Pyx_SetVtable(__pyx_type___pyx_array.tp_dict, __pyx_vtabptr_array) < 0) __PYX_ERR(1, 105, __pyx_L1_error)
if (__Pyx_setup_reduce((PyObject*)&__pyx_type___pyx_array) < 0) __PYX_ERR(1, 105, __pyx_L1_error)
__pyx_array_type = &__pyx_type___pyx_array;
if (PyType_Ready(&__pyx_type___pyx_MemviewEnum) < 0) __PYX_ERR(1, 279, __pyx_L1_error)
+ #if PY_VERSION_HEX < 0x030800B1
__pyx_type___pyx_MemviewEnum.tp_print = 0;
+ #endif
if ((CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP) && likely(!__pyx_type___pyx_MemviewEnum.tp_dictoffset && __pyx_type___pyx_MemviewEnum.tp_getattro == PyObject_GenericGetAttr)) {
__pyx_type___pyx_MemviewEnum.tp_getattro = __Pyx_PyObject_GenericGetAttr;
}
@@ -30274,7 +30313,9 @@ static int __Pyx_modinit_type_init_code(void) {
__pyx_vtable_memoryview.convert_item_to_object = (PyObject *(*)(struct __pyx_memoryview_obj *, char *))__pyx_memoryview_convert_item_to_object;
__pyx_vtable_memoryview.assign_item_from_object = (PyObject *(*)(struct __pyx_memoryview_obj *, char *, PyObject *))__pyx_memoryview_assign_item_from_object;
if (PyType_Ready(&__pyx_type___pyx_memoryview) < 0) __PYX_ERR(1, 330, __pyx_L1_error)
+ #if PY_VERSION_HEX < 0x030800B1
__pyx_type___pyx_memoryview.tp_print = 0;
+ #endif
if ((CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP) && likely(!__pyx_type___pyx_memoryview.tp_dictoffset && __pyx_type___pyx_memoryview.tp_getattro == PyObject_GenericGetAttr)) {
__pyx_type___pyx_memoryview.tp_getattro = __Pyx_PyObject_GenericGetAttr;
}
@@ -30287,7 +30328,9 @@ static int __Pyx_modinit_type_init_code(void) {
__pyx_vtable__memoryviewslice.__pyx_base.assign_item_from_object = (PyObject *(*)(struct __pyx_memoryview_obj *, char *, PyObject *))__pyx_memoryviewslice_assign_item_from_object;
__pyx_type___pyx_memoryviewslice.tp_base = __pyx_memoryview_type;
if (PyType_Ready(&__pyx_type___pyx_memoryviewslice) < 0) __PYX_ERR(1, 961, __pyx_L1_error)
+ #if PY_VERSION_HEX < 0x030800B1
__pyx_type___pyx_memoryviewslice.tp_print = 0;
+ #endif
if ((CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP) && likely(!__pyx_type___pyx_memoryviewslice.tp_dictoffset && __pyx_type___pyx_memoryviewslice.tp_getattro == PyObject_GenericGetAttr)) {
__pyx_type___pyx_memoryviewslice.tp_getattro = __Pyx_PyObject_GenericGetAttr;
}
@@ -35245,6 +35288,9 @@ static PyTypeObject __pyx_CyFunctionType_type = {
#if PY_VERSION_HEX >= 0x030400a1
0,
#endif
+#if PY_VERSION_HEX >= 0x030800b1
+ 0,
+#endif
};
static int __pyx_CyFunction_init(void) {
__pyx_CyFunctionType = __Pyx_FetchCommonType(&__pyx_CyFunctionType_type);
@@ -37223,6 +37269,9 @@ static PyTypeObject __pyx_GeneratorType_type = {
#elif PY_VERSION_HEX >= 0x030400a1
0,
#endif
+#if PY_VERSION_HEX >= 0x030800b1
+ 0,
+#endif
};
static int __pyx_Generator_init(void) {
__pyx_GeneratorType_type.tp_getattro = __Pyx_PyObject_GenericGetAttrNoDict;
diff --git a/silx/io/test/test_specfile.py b/silx/io/test/test_specfile.py
index 55850f1..79d5544 100644
--- a/silx/io/test/test_specfile.py
+++ b/silx/io/test/test_specfile.py
@@ -1,6 +1,6 @@
# coding: utf-8
# /*##########################################################################
-# Copyright (C) 2016-2017 European Synchrotron Radiation Facility
+# Copyright (C) 2016-2019 European Synchrotron Radiation Facility
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
@@ -224,14 +224,21 @@ class TestSpecFile(unittest.TestCase):
with self.assertRaises(specfile.SfErrScanNotFound):
self.sf.index(99)
+ def assertRaisesRegex(self, *args, **kwargs):
+ # Python 2 compatibility
+ if sys.version_info.major >= 3:
+ return super(TestSpecFile, self).assertRaisesRegex(*args, **kwargs)
+ else:
+ return self.assertRaisesRegexp(*args, **kwargs)
+
def test_getitem(self):
self.assertIsInstance(self.sf[2], Scan)
self.assertIsInstance(self.sf["1.2"], Scan)
# int out of range
- with self.assertRaisesRegexp(IndexError, 'Scan index must be in ran'):
+ with self.assertRaisesRegex(IndexError, 'Scan index must be in ran'):
self.sf[107]
# float indexing not allowed
- with self.assertRaisesRegexp(TypeError, 'The scan identification k'):
+ with self.assertRaisesRegex(TypeError, 'The scan identification k'):
self.sf[1.2]
# non existant scan with "N.M" indexing
with self.assertRaises(KeyError):
diff --git a/silx/io/test/test_spech5.py b/silx/io/test/test_spech5.py
index 7c8ed5d..0263c3c 100644
--- a/silx/io/test/test_spech5.py
+++ b/silx/io/test/test_spech5.py
@@ -1,6 +1,6 @@
# coding: utf-8
# /*##########################################################################
-# Copyright (C) 2016-2018 European Synchrotron Radiation Facility
+# Copyright (C) 2016-2019 European Synchrotron Radiation Facility
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
@@ -272,6 +272,13 @@ class TestSpecH5(unittest.TestCase):
self.assertEqual(self.sfh5["25.1/start_time"],
u"2015-03-14T03:53:50")
+ def assertRaisesRegex(self, *args, **kwargs):
+ # Python 2 compatibility
+ if sys.version_info.major >= 3:
+ return super(TestSpecH5, self).assertRaisesRegex(*args, **kwargs)
+ else:
+ return self.assertRaisesRegexp(*args, **kwargs)
+
def testDatasetInstanceAttr(self):
"""The SpecH5Dataset objects must implement some dummy attributes
to improve compatibility with widgets dealing with h5py datasets."""
@@ -279,7 +286,7 @@ class TestSpecH5(unittest.TestCase):
self.assertIsNone(self.sfh5["1.1"]["measurement"]["MRTSlit UP"].chunks)
# error message must be explicit
- with self.assertRaisesRegexp(
+ with self.assertRaisesRegex(
AttributeError,
"SpecH5Dataset has no attribute tOTo"):
dummy = self.sfh5["/1.1/start_time"].tOTo
diff --git a/silx/io/test/test_spectoh5.py b/silx/io/test/test_spectoh5.py
index 2b79704..44b59e0 100644
--- a/silx/io/test/test_spectoh5.py
+++ b/silx/io/test/test_spectoh5.py
@@ -1,6 +1,6 @@
# coding: utf-8
# /*##########################################################################
-# Copyright (C) 2016-2018 European Synchrotron Radiation Facility
+# Copyright (C) 2016-2019 European Synchrotron Radiation Facility
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
@@ -132,7 +132,7 @@ class TestConvertSpecHDF5(unittest.TestCase):
def testTitle(self):
"""Test the value of a dataset"""
- title12 = self.h5f["/1.2/title"].value
+ title12 = self.h5f["/1.2/title"][()]
self.assertEqual(title12,
u"aaaaaa")
diff --git a/silx/io/test/test_utils.py b/silx/io/test/test_utils.py
index 5a4c629..56f89fc 100644
--- a/silx/io/test/test_utils.py
+++ b/silx/io/test/test_utils.py
@@ -1,6 +1,6 @@
# coding: utf-8
# /*##########################################################################
-# Copyright (C) 2016-2018 European Synchrotron Radiation Facility
+# Copyright (C) 2016-2019 European Synchrotron Radiation Facility
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
@@ -30,6 +30,7 @@ import re
import shutil
import tempfile
import unittest
+import sys
from .. import utils
import silx.io.url
@@ -102,6 +103,13 @@ class TestSave(unittest.TestCase):
os.unlink(self.npy_fname)
shutil.rmtree(self.tempdir)
+ def assertRegex(self, *args, **kwargs):
+ # Python 2 compatibility
+ if sys.version_info.major >= 3:
+ return super(TestSave, self).assertRegex(*args, **kwargs)
+ else:
+ return self.assertRegexpMatches(*args, **kwargs)
+
def test_save_csv(self):
utils.save1D(self.csv_fname, self.x, self.y,
xlabel=self.xlab, ylabels=self.ylabs,
@@ -112,7 +120,7 @@ class TestSave(unittest.TestCase):
actual_csv = csvf.read()
csvf.close()
- self.assertRegexpMatches(actual_csv, expected_csv)
+ self.assertRegex(actual_csv, expected_csv)
def test_save_npy(self):
"""npy file is saved with numpy.save after building a numpy array
@@ -138,7 +146,7 @@ class TestSave(unittest.TestCase):
actual_spec = specf.read()
specf.close()
- self.assertRegexpMatches(actual_spec, expected_spec1)
+ self.assertRegex(actual_spec, expected_spec1)
def test_savespec_file_handle(self):
"""Save SpecFile using savespec(), passing a file handle"""
@@ -158,7 +166,7 @@ class TestSave(unittest.TestCase):
actual_spec = specf.read()
specf.close()
- self.assertRegexpMatches(actual_spec, expected_spec2)
+ self.assertRegex(actual_spec, expected_spec2)
def test_save_spec(self):
"""Save SpecFile using save()"""
@@ -168,7 +176,7 @@ class TestSave(unittest.TestCase):
specf = open(self.spec_fname)
actual_spec = specf.read()
specf.close()
- self.assertRegexpMatches(actual_spec, expected_spec2)
+ self.assertRegex(actual_spec, expected_spec2)
def test_save_csv_no_labels(self):
"""Save csv using save(), with autoheader=True but
@@ -189,7 +197,7 @@ class TestSave(unittest.TestCase):
csvf = open(self.csv_fname)
actual_csv = csvf.read()
csvf.close()
- self.assertRegexpMatches(actual_csv, expected_csv2)
+ self.assertRegex(actual_csv, expected_csv2)
def assert_match_any_string_in_list(test, pattern, list_of_strings):
diff --git a/silx/io/utils.py b/silx/io/utils.py
index 930c84e..f294101 100644
--- a/silx/io/utils.py
+++ b/silx/io/utils.py
@@ -52,7 +52,7 @@ except ImportError as e:
logger = logging.getLogger(__name__)
-NEXUS_HDF5_EXT = [".h5", ".nx5", ".nxs", ".hdf", ".hdf5", ".cxi"]
+NEXUS_HDF5_EXT = [".h5", ".nx5", ".nxs", ".hdf", ".hdf5", ".cxi"]
"""List of possible extensions for HDF5 file formats."""
@@ -460,7 +460,10 @@ def _open_local_file(filename):
"File '%s' can't be read as a numpy file." % filename))
if h5py.is_hdf5(filename):
- return h5py.File(filename, "r")
+ try:
+ return h5py.File(filename, "r")
+ except OSError:
+ return h5py.File(filename, "r", libver='latest', swmr=True)
try:
from . import fabioh5
generated by cgit v1.2.3 (git 2.25.1) at 2024-05-29 05:03:57 +0000