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# coding: utf-8
# /*##########################################################################
# Copyright (C) 2016-2017 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
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
#
# ############################################################################*/
"""Tests for fabioh5 wrapper"""
__authors__ = ["V. Valls"]
__license__ = "MIT"
__date__ = "11/04/2017"
import logging
import numpy
import unittest
_logger = logging.getLogger(__name__)
try:
import fabio
except ImportError:
fabio = None
try:
import h5py
except ImportError:
h5py = None
if fabio is not None and h5py is not None:
from .. import fabioh5
class TestFabioH5(unittest.TestCase):
def setUp(self):
if fabio is None:
self.skipTest("fabio is needed")
if h5py is None:
self.skipTest("h5py is needed")
header = {
"integer": "-100",
"float": "1.0",
"string": "hi!",
"list_integer": "100 50 0",
"list_float": "1.0 2.0 3.5",
"string_looks_like_list": "2000 hi!",
}
data = numpy.array([[10, 11], [12, 13], [14, 15]], dtype=numpy.int64)
self.fabio_image = fabio.numpyimage.NumpyImage(data, header)
self.h5_image = fabioh5.File(fabio_image=self.fabio_image)
def test_main_groups(self):
self.assertEquals(self.h5_image.h5py_class, h5py.File)
self.assertEquals(self.h5_image["/"].h5py_class, h5py.File)
self.assertEquals(self.h5_image["/scan_0"].h5py_class, h5py.Group)
self.assertEquals(self.h5_image["/scan_0/instrument"].h5py_class, h5py.Group)
self.assertEquals(self.h5_image["/scan_0/measurement"].h5py_class, h5py.Group)
def test_wrong_path_syntax(self):
# result tested with a default h5py file
self.assertRaises(ValueError, lambda: self.h5_image[""])
def test_wrong_root_name(self):
# result tested with a default h5py file
self.assertRaises(KeyError, lambda: self.h5_image["/foo"])
def test_wrong_root_path(self):
# result tested with a default h5py file
self.assertRaises(KeyError, lambda: self.h5_image["/foo/foo"])
def test_wrong_name(self):
# result tested with a default h5py file
self.assertRaises(KeyError, lambda: self.h5_image["foo"])
def test_wrong_path(self):
# result tested with a default h5py file
self.assertRaises(KeyError, lambda: self.h5_image["foo/foo"])
def test_frames(self):
dataset = self.h5_image["/scan_0/instrument/detector_0/data"]
self.assertEquals(dataset.h5py_class, h5py.Dataset)
self.assertTrue(isinstance(dataset[()], numpy.ndarray))
self.assertEquals(dataset.dtype.kind, "i")
self.assertEquals(dataset.shape, (1, 3, 2))
self.assertEquals(dataset.attrs["interpretation"], "image")
def test_metadata_int(self):
dataset = self.h5_image["/scan_0/instrument/detector_0/others/integer"]
self.assertEquals(dataset.h5py_class, h5py.Dataset)
self.assertEquals(dataset[()], -100)
self.assertEquals(dataset.dtype.kind, "i")
self.assertEquals(dataset.shape, (1,))
def test_metadata_float(self):
dataset = self.h5_image["/scan_0/instrument/detector_0/others/float"]
self.assertEquals(dataset.h5py_class, h5py.Dataset)
self.assertEquals(dataset[()], 1.0)
self.assertEquals(dataset.dtype.kind, "f")
self.assertEquals(dataset.shape, (1,))
def test_metadata_string(self):
dataset = self.h5_image["/scan_0/instrument/detector_0/others/string"]
self.assertEquals(dataset.h5py_class, h5py.Dataset)
self.assertEquals(dataset[()], numpy.string_("hi!"))
self.assertEquals(dataset.dtype.type, numpy.string_)
self.assertEquals(dataset.shape, (1,))
def test_metadata_list_integer(self):
dataset = self.h5_image["/scan_0/instrument/detector_0/others/list_integer"]
self.assertEquals(dataset.h5py_class, h5py.Dataset)
self.assertEquals(dataset.dtype.kind, "u")
self.assertEquals(dataset.shape, (1, 3))
self.assertEquals(dataset[0, 0], 100)
self.assertEquals(dataset[0, 1], 50)
def test_metadata_list_float(self):
dataset = self.h5_image["/scan_0/instrument/detector_0/others/list_float"]
self.assertEquals(dataset.h5py_class, h5py.Dataset)
self.assertEquals(dataset.dtype.kind, "f")
self.assertEquals(dataset.shape, (1, 3))
self.assertEquals(dataset[0, 0], 1.0)
self.assertEquals(dataset[0, 1], 2.0)
def test_metadata_list_looks_like_list(self):
dataset = self.h5_image["/scan_0/instrument/detector_0/others/string_looks_like_list"]
self.assertEquals(dataset.h5py_class, h5py.Dataset)
self.assertEquals(dataset[()], numpy.string_("2000 hi!"))
self.assertEquals(dataset.dtype.type, numpy.string_)
self.assertEquals(dataset.shape, (1,))
def test_float_32(self):
float_list = [u'1.2', u'1.3', u'1.4']
data = numpy.array([[0, 0], [0, 0]], dtype=numpy.int8)
fabio_image = None
for float_item in float_list:
header = {"float_item": float_item}
if fabio_image is None:
fabio_image = fabio.edfimage.EdfImage(data=data, header=header)
else:
fabio_image.appendFrame(data=data, header=header)
h5_image = fabioh5.File(fabio_image=fabio_image)
data = h5_image["/scan_0/instrument/detector_0/others/float_item"]
# There is no equality between items
self.assertEqual(len(data), len(set(data)))
# At worst a float32
self.assertIn(data.dtype.char, ['d', 'f'])
self.assertLessEqual(data.dtype.itemsize, 32 / 8)
def test_float_64(self):
float_list = [
u'1469117129.082226',
u'1469117136.684986', u'1469117144.312749', u'1469117151.892507',
u'1469117159.474265', u'1469117167.100027', u'1469117174.815799',
u'1469117182.437561', u'1469117190.094326', u'1469117197.721089']
data = numpy.array([[0, 0], [0, 0]], dtype=numpy.int8)
fabio_image = None
for float_item in float_list:
header = {"time_of_day": float_item}
if fabio_image is None:
fabio_image = fabio.edfimage.EdfImage(data=data, header=header)
else:
fabio_image.appendFrame(data=data, header=header)
h5_image = fabioh5.File(fabio_image=fabio_image)
data = h5_image["/scan_0/instrument/detector_0/others/time_of_day"]
# There is no equality between items
self.assertEqual(len(data), len(set(data)))
# At least a float64
self.assertIn(data.dtype.char, ['d', 'f'])
self.assertGreaterEqual(data.dtype.itemsize, 64 / 8)
def test_ub_matrix(self):
"""Data from mediapix.edf"""
header = {}
header["UB_mne"] = 'UB0 UB1 UB2 UB3 UB4 UB5 UB6 UB7 UB8'
header["UB_pos"] = '1.99593e-16 2.73682e-16 -1.54 -1.08894 1.08894 1.6083e-16 1.08894 1.08894 9.28619e-17'
header["sample_mne"] = 'U0 U1 U2 U3 U4 U5'
header["sample_pos"] = '4.08 4.08 4.08 90 90 90'
data = numpy.array([[0, 0], [0, 0]], dtype=numpy.int8)
fabio_image = fabio.edfimage.EdfImage(data=data, header=header)
h5_image = fabioh5.File(fabio_image=fabio_image)
sample = h5_image["/scan_0/sample"]
self.assertIsNotNone(sample)
self.assertEquals(sample.attrs["NXclass"], "NXsample")
d = sample['unit_cell_abc']
expected = numpy.array([4.08, 4.08, 4.08])
self.assertIsNotNone(d)
self.assertEquals(d.shape, (3, ))
self.assertIn(d.dtype.char, ['d', 'f'])
numpy.testing.assert_array_almost_equal(d[...], expected)
d = sample['unit_cell_alphabetagamma']
expected = numpy.array([90.0, 90.0, 90.0])
self.assertIsNotNone(d)
self.assertEquals(d.shape, (3, ))
self.assertIn(d.dtype.char, ['d', 'f'])
numpy.testing.assert_array_almost_equal(d[...], expected)
d = sample['ub_matrix']
expected = numpy.array([[[1.99593e-16, 2.73682e-16, -1.54],
[-1.08894, 1.08894, 1.6083e-16],
[1.08894, 1.08894, 9.28619e-17]]])
self.assertIsNotNone(d)
self.assertEquals(d.shape, (1, 3, 3))
self.assertIn(d.dtype.char, ['d', 'f'])
numpy.testing.assert_array_almost_equal(d[...], expected)
def suite():
test_suite = unittest.TestSuite()
test_suite.addTest(
unittest.defaultTestLoader.loadTestsFromTestCase(TestFabioH5))
return test_suite
if __name__ == '__main__':
unittest.main(defaultTest="suite")
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