#!/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. # """ 2011: Jerome Kieffer for ESRF. Unit tests for CBF images based on references images taken from: http://pilatus.web.psi.ch/DATA/DATASETS/insulin_0.2/ 19/01/2015 """ import unittest import os import time import logging logger = logging.getLogger(__name__) import numpy import fabio from fabio.cbfimage import CbfImage from fabio.compression import decByteOffset_numpy, decByteOffset_cython from ..utilstest import UtilsTest class TestCbfReader(unittest.TestCase): """ test cbf image reader """ def setUp(self): """Download images""" self.edf_filename = "run2_1_00148.edf.bz2" self.edf_filename = UtilsTest.getimage(self.edf_filename)[:-4] self.cbf_filename = "run2_1_00148.cbf.bz2" self.cbf_filename = UtilsTest.getimage(self.cbf_filename)[:-4] def test_read(self): """ check whole reader""" times = [] times.append(time.time()) cbf = fabio.open(self.cbf_filename) times.append(time.time()) edf = fabio.open(self.edf_filename) times.append(time.time()) self.assertAlmostEqual(0, abs(cbf.data - edf.data).max()) logger.info("Reading CBF took %.3fs whereas the same EDF took %.3fs" % (times[1] - times[0], times[2] - times[1])) def test_write(self): "Rest writing with self consistency at the fabio level" name = os.path.basename(self.cbf_filename) obj = CbfImage() obj.read(self.cbf_filename) obj.write(os.path.join(UtilsTest.tempdir, name)) other = CbfImage() other.read(os.path.join(UtilsTest.tempdir, name)) self.assertEqual(abs(obj.data - other.data).max(), 0, "data are the same") for key in obj.header: if key in["filename", "X-Binary-Size-Padding"]: continue self.assertTrue(key in other.header, "Key %s is in header" % key) self.assertEqual(obj.header[key], other.header[key], "value are the same for key %s" % key) # By destroying the object, one actually closes the file, which is needed under windows. del obj del other if os.path.exists(os.path.join(UtilsTest.tempdir, name)): os.unlink(os.path.join(UtilsTest.tempdir, name)) def test_byte_offset(self): """ check byte offset algorithm""" cbf = fabio.open(self.cbf_filename) starter = b"\x0c\x1a\x04\xd5" cbs = cbf.cbs startPos = cbs.find(starter) + 4 data = cbs[startPos: startPos + int(cbf.header["X-Binary-Size"])] startTime = time.time() size = cbf.shape[0] * cbf.shape[1] numpyRes = decByteOffset_numpy(data, size=size) tNumpy = time.time() - startTime logger.info("Timing for Numpy method : %.3fs" % tNumpy) startTime = time.time() cythonRes = decByteOffset_cython(stream=data, size=size) tCython = time.time() - startTime delta = abs(numpyRes - cythonRes).max() self.assertAlmostEqual(0, delta) logger.info("Timing for Cython method : %.3fs, max delta= %s" % (tCython, delta)) def test_consitency_manual(self): """ Test if an image can be read and saved and the results are "similar" """ name = os.path.basename(self.cbf_filename) obj = fabio.open(self.cbf_filename) new = CbfImage(data=obj.data, header=obj.header) new.write(os.path.join(UtilsTest.tempdir, name)) other = fabio.open(os.path.join(UtilsTest.tempdir, name)) self.assertEqual(abs(obj.data - other.data).max(), 0, "data are the same") for key in obj.header: if key in["filename", "X-Binary-Size-Padding"]: continue self.assertTrue(key in other.header, "Key %s is in header" % key) self.assertEqual(obj.header[key], other.header[key], "value are the same for key %s [%s|%s]" % (key, obj.header[key], other.header[key])) def test_consitency_convert(self): """ Test if an image can be read and saved and the results are "similar" """ name = os.path.basename(self.cbf_filename) obj = fabio.open(self.cbf_filename) new = obj.convert("cbf") new.write(os.path.join(UtilsTest.tempdir, name)) other = fabio.open(os.path.join(UtilsTest.tempdir, name)) self.assertEqual(abs(obj.data - other.data).max(), 0, "data are the same") for key in obj.header: if key in["filename", "X-Binary-Size-Padding"]: continue self.assertTrue(key in other.header, "Key %s is in header" % key) self.assertEqual(obj.header[key], other.header[key], "value are the same for key %s [%s|%s]" % (key, obj.header[key], other.header[key])) def test_unicode(self): """ Test if an image can be read and saved to an unicode named """ name = u"%s" % os.path.basename(self.cbf_filename) obj = fabio.open(self.cbf_filename) obj.write(os.path.join(UtilsTest.tempdir, name)) other = fabio.open(os.path.join(UtilsTest.tempdir, name)) self.assertEqual(abs(obj.data - other.data).max(), 0, "data are the same") for key in obj.header: if key in["filename", "X-Binary-Size-Padding"]: continue self.assertTrue(key in other.header, "Key %s is in header" % key) self.assertEqual(obj.header[key], other.header[key], "value are the same for key %s [%s|%s]" % (key, obj.header[key], other.header[key])) def test_bug_388(self): data = numpy.random.randint(0, 100, size=(27, 31)).astype(numpy.int32) im = CbfImage(data=data, header={}) filename = os.path.join(UtilsTest.tempdir, "bad_name.edf") im.write(filename) res = fabio.open(filename) self.assertEqual(abs(data-res.data).max(), 0, "Data are the same despite the wrong name") def test_bug_408(self): "Bug when reading files generated by XDS" xds_filename = UtilsTest.getimage("XDS.cbf.bz2")[:-4] f = fabio.open(xds_filename) def suite(): loadTests = unittest.defaultTestLoader.loadTestsFromTestCase testsuite = unittest.TestSuite() testsuite.addTest(loadTests(TestCbfReader)) return testsuite if __name__ == '__main__': runner = unittest.TextTestRunner() runner.run(suite())