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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)
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
"""
Test for MRC file format imagess.
"""
from __future__ import print_function, with_statement, division, absolute_import
import unittest
import os
import logging
logger = logging.getLogger(__name__)
import fabio
from ..mrcimage import MrcImage
from ..openimage import openimage
from .utilstest import UtilsTest
class TestMrc(unittest.TestCase):
"""basic test"""
mrcfilename = 'EMD-3001.map'
npyfilename = 'EMD-3001.npy'
results = """EMD-3001.map 73 43 -0.36814222 0.678705 0.006804995 0.1630334"""
def setUp(self):
"""Download files"""
self.fn = {}
for i in [self.mrcfilename, self.npyfilename]:
self.fn[i] = UtilsTest.getimage(i + ".bz2")[:-4]
for i in self.fn:
assert os.path.exists(self.fn[i])
def test_read(self):
""" check we can read kcd images"""
vals = self.results.split()
dim1, dim2 = [int(x) for x in vals[1:3]]
mini, maxi, mean, stddev = [float(x) for x in vals[3:]]
for ext in ["", ".gz", ".bz2"]:
try:
obj = openimage(self.fn[self.mrcfilename] + ext)
except Exception as err:
logger.error("unable to read: %s", self.fn[self.mrcfilename] + ext)
raise err
self.assertAlmostEqual(mini, obj.getmin(), 4, "getmin" + ext)
self.assertAlmostEqual(maxi, obj.getmax(), 4, "getmax" + ext)
self.assertAlmostEqual(mean, obj.getmean(), 4, "getmean" + ext)
self.assertAlmostEqual(stddev, obj.getstddev(), 4, "getstddev" + ext)
self.assertEqual(dim1, obj.dim1, "dim1" + ext)
self.assertEqual(dim2, obj.dim2, "dim2" + ext)
def test_same(self):
""" see if we can read kcd images and if they are the same as the EDF """
mrc = MrcImage()
mrc.read(self.fn[self.mrcfilename])
npy = fabio.open(self.fn[self.npyfilename])
diff = (mrc.data - npy.data)
self.assertAlmostEqual(abs(diff).sum(), 0, 4)
def suite():
loadTests = unittest.defaultTestLoader.loadTestsFromTestCase
testsuite = unittest.TestSuite()
testsuite.addTest(loadTests(TestMrc))
return testsuite
if __name__ == '__main__':
runner = unittest.TextTestRunner()
runner.run(suite())
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