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#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Project: Fable Input Output
# https://github.com/silx-kit/fabio
#
# Copyright (C) European Synchrotron Radiation Facility, Grenoble, France
#
# Principal author: Jérôme Kieffer (Jerome.Kieffer@ESRF.eu)
#
# 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.
#
"""
Unit tests for the d*TREK format.
"""
import unittest
import os
import logging
import numpy
import shutil
from ..utilstest import UtilsTest
logger = logging.getLogger(__name__)
import fabio
from fabio.dtrekimage import DtrekImage
from fabio.edfimage import EdfImage
from fabio.utils import testutils
# statistics come from fit2d I think
# filename dim1 dim2 min max mean stddev
TESTIMAGES = [("mb_LP_1_001.img", (3072, 3072), 0.0000, 65535., 120.33, 147.38,
{"BEAM_CENTER_Y": "157.500000"}),
("mb_LP_1_001.img.gz", (3072, 3072), 0.0000, 65535., 120.33, 147.38,
{"BEAM_CENTER_Y": "157.500000"}),
("mb_LP_1_001.img.bz2", (3072, 3072), 0.0000, 65535., 120.33, 147.38,
{"BEAM_CENTER_Y": "157.500000"}),
("HSA_1_5mg_C1_0004.img", (385, 775), -2, 2127, 69.25, 59.52,
{"WAVELENGTH": "1.0 1.541870"}),
]
class TestMatch(unittest.TestCase):
"""
check the ??fit2d?? conversion to edf gives same numbers
"""
def setUp(self):
""" Download images """
self.fn_adsc = UtilsTest.getimage("mb_LP_1_001.img.bz2")[:-4]
self.fn_edf = UtilsTest.getimage("mb_LP_1_001.edf.bz2")[:-4]
def testsame(self):
"""test ADSC image match to EDF"""
im1 = EdfImage()
im1.read(self.fn_edf)
im2 = DtrekImage()
im2.read(self.fn_adsc)
diff = (im1.data.astype("float32") - im2.data.astype("float32"))
logger.debug("type: %s %s shape %s %s " % (im1.data.dtype, im2.data.dtype, im1.data.shape, im2.data.shape))
logger.debug("im1 min %s %s max %s %s " % (im1.data.min(), im2.data.min(), im1.data.max(), im2.data.max()))
logger.debug("delta min %s max %s mean %s" % (diff.min(), diff.max(), diff.mean()))
self.assertEqual(abs(diff).max(), 0.0, "asdc data == edf data")
class TestDtrekImplementation(testutils.ParametricTestCase):
@classmethod
def setUpClass(cls):
cls.tmp_directory = os.path.join(UtilsTest.tempdir, cls.__name__)
os.makedirs(cls.tmp_directory)
@classmethod
def tearDownClass(cls):
shutil.rmtree(cls.tmp_directory)
def setUp(self):
unittest.TestCase.setUp(self)
def test_write_and_read_cube(self):
input_type = numpy.uint16
data = numpy.arange(5 * 10 * 2).reshape(5, 10, 2)
data = data.astype(input_type)
obj = DtrekImage(data=data)
filename = os.path.join(self.tmp_directory, "cube.img")
obj.save(filename)
self.assertEqual(obj.data.dtype.type, input_type)
obj2 = fabio.open(filename)
self.assertEqual(obj2.data.dtype.type, input_type)
self.assertEqual(obj.shape, obj2.shape)
numpy.testing.assert_array_almost_equal(obj.data, obj2.data)
def test_write_and_read_empty(self):
obj = DtrekImage(data=None)
filename = os.path.join(self.tmp_directory, "cube.img")
obj.save(filename)
obj2 = fabio.open(filename)
self.assertEqual(obj2.data, None)
self.assertEqual(obj.data, obj2.data)
def test_write_and_read(self):
configs = [
(numpy.uint16, "little_endian", None),
(numpy.uint16, "big_endian", None),
(numpy.uint32, "little_endian", None),
(numpy.int32, "little_endian", None),
(numpy.float32, "little_endian", None),
(numpy.float32, "little_endian", None),
# Data have to be converted before storage
(numpy.uint64, "little_endian", numpy.uint32),
(numpy.int64, "little_endian", numpy.int32),
(numpy.float16, "little_endian", numpy.float32),
]
for config in configs:
with self.subTest(config=config):
input_type, byte_order, output_type = config
if output_type is None:
output_type = input_type
header = {}
header["BYTE_ORDER"] = byte_order
data = numpy.arange(5 * 10).reshape(5, 10)
data = data.astype(input_type)
obj = DtrekImage(data=data, header=header)
filename = os.path.join(self.tmp_directory, "saved_%s.img" % hash(config))
obj.save(filename)
self.assertEqual(obj.data.dtype.type, input_type)
obj2 = fabio.open(filename)
self.assertEqual(obj2.data.dtype.type, output_type)
self.assertEqual(obj.shape, obj2.shape)
if input_type == output_type:
numpy.testing.assert_array_almost_equal(obj.data, obj2.data)
class TestRealSamples(testutils.ParametricTestCase):
"""
Test real samples stored in our archive.
"""
@classmethod
def setUpClass(cls):
"""Prefetch images"""
download = []
for datainfo in TESTIMAGES:
name = datainfo[0]
if name.endswith(".bz2"):
download.append(name)
elif name.endswith(".gz"):
download.append(name[:-3] + ".bz2")
else:
download.append(name + ".bz2")
download = list(set(download))
for name in download:
os.path.dirname(UtilsTest.getimage(name))
cls.im_dir = UtilsTest.resources.data_home
def test_read(self):
""" check we can read flat ADSC images"""
for datainfo in TESTIMAGES:
with self.subTest(datainfo=datainfo):
name, shape, mini, maxi, mean, stddev, keys = datainfo
obj = DtrekImage()
obj.read(os.path.join(self.im_dir, name))
self.assertAlmostEqual(mini, obj.getmin(), 2, "getmin")
self.assertAlmostEqual(maxi, obj.getmax(), 2, "getmax")
got_mean = obj.getmean()
self.assertAlmostEqual(mean, got_mean, 2, "getmean exp %s != got %s" % (mean, got_mean))
self.assertAlmostEqual(stddev, obj.getstddev(), 2, "getstddev")
for key, value in keys.items():
self.assertIn(key, obj.header)
self.assertEqual(value, obj.header[key])
self.assertEqual(shape, obj.shape)
def suite():
loadTests = unittest.defaultTestLoader.loadTestsFromTestCase
testsuite = unittest.TestSuite()
testsuite.addTest(loadTests(TestMatch))
testsuite.addTest(loadTests(TestRealSamples))
testsuite.addTest(loadTests(TestDtrekImplementation))
return testsuite
if __name__ == '__main__':
runner = unittest.TextTestRunner()
runner.run(suite())
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