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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/>.
#
"""
# Unit tests
# builds on stuff from ImageD11.test.testpeaksearch
28/11/2014
"""
import unittest
import os
import numpy
import logging
logger = logging.getLogger(__name__)
import fabio
from fabio.mar345image import mar345image
from ..utilstest import UtilsTest
# filename dim1 dim2 min max mean stddev
TESTIMAGES = """example.mar2300 2300 2300 0 999999 180.15 4122.67
example.mar2300.bz2 2300 2300 0 999999 180.15 4122.67
example.mar2300.gz 2300 2300 0 999999 180.15 4122.67
Fe3O4_023_101.mar2560 2560 3072 0 258253 83.61749 198.29895739775
Fe3O4_023_101.mar2560.bz2 2560 3072 0 258253 83.61749 198.29895739775
Fe3O4_023_101.mar2560.gz 2560 3072 0 258253 83.61749 198.29895739775"""
# Fe3O4_023_101.mar2560 is a pathological file from Mar555
class TestMar345(unittest.TestCase):
def setUp(self):
"""
download images
"""
self.mar345 = UtilsTest.getimage("example.mar2300.bz2")[:-4]
self.mar555 = UtilsTest.getimage("Fe3O4_023_101.mar2560.bz2")[:-4]
def tearDown(self):
unittest.TestCase.tearDown(self)
self.mar345 = self.mar555 = None
def test_read(self):
"""
Test the reading of Mar345 images
"""
for line in TESTIMAGES.split('\n'):
vals = line.strip().split()
name = vals[0]
dim1, dim2 = [int(x) for x in vals[1:3]]
shape = dim2, dim1
mini, maxi, mean, stddev = [float(x) for x in vals[3:]]
obj = mar345image()
obj.read(UtilsTest.getimage(name))
self.assertAlmostEqual(mini, obj.getmin(), 2, "getmin [%s,%s]" % (mini, obj.getmin()))
self.assertAlmostEqual(maxi, obj.getmax(), 2, "getmax [%s,%s]" % (maxi, obj.getmax()))
self.assertAlmostEqual(mean, obj.getmean(), 2, "getmean [%s,%s]" % (mean, obj.getmean()))
self.assertAlmostEqual(stddev, obj.getstddev(), 2, "getstddev [%s,%s]" % (stddev, obj.getstddev()))
self.assertEqual(shape, obj.shape, "shape")
def test_write(self):
"Test writing with self consistency at the fabio level"
for line in TESTIMAGES.split("\n"):
logger.debug("Processing file: %s" % line)
vals = line.split()
name = vals[0]
obj = mar345image()
obj.read(os.path.join(os.path.dirname(self.mar345), name))
obj.write(os.path.join(UtilsTest.tempdir, name))
other = mar345image()
other.read(os.path.join(UtilsTest.tempdir, name))
if abs(obj.data - other.data).max():
logger.error("data for %s are not the same %s", line, numpy.where(obj.data - other.data))
self.assertEqual(abs(obj.data - other.data).max(), 0, "data are the same")
for key in obj.header:
if key == "filename":
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]))
os.unlink(os.path.join(UtilsTest.tempdir, name))
def test_byteswap_write(self):
"Test writing with self consistency at the fabio level"
for line in TESTIMAGES.split("\n"):
logger.debug("Processing file: %s" % line)
vals = line.split()
name = vals[0]
obj = mar345image()
obj.read(os.path.join(os.path.dirname(self.mar345), name))
obj.swap_needed = not (obj.swap_needed)
obj.write(os.path.join(UtilsTest.tempdir, name))
other = mar345image()
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 == "filename":
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]))
os.unlink(os.path.join(UtilsTest.tempdir, name))
@unittest.skip("very slow test")
def test_memoryleak(self):
"""
This test takes a lot of time, so only in debug mode.
"""
N = 1000
if logger.getEffectiveLevel() <= logging.INFO:
logger.debug("Testing for memory leak")
for i in range(N):
_img = fabio.open(self.mar345)
print("reading #%s/%s" % (i, N))
def test_aux(self):
"""test auxillary functions
"""
from fabio.ext import mar345_IO
shape = 120, 130
size = shape[0] * shape[1]
img = numpy.random.randint(0, 32000, size).astype("int16")
b = mar345_IO.precomp(img, shape[-1])
c = mar345_IO.postdec(b, shape[-1])
self.assertEqual(abs(c - img).max(), 0, "pre-compression and post-decompression works")
a = mar345_IO.calc_nb_bits(numpy.arange(8).astype("int32"), 0, 8)
self.assertEqual(a, 32, "8*4")
a = mar345_IO.calc_nb_bits(numpy.arange(10).astype("int32"), 0, 10)
self.assertEqual(a, 50, "10*5")
a = mar345_IO.calc_nb_bits(numpy.arange(50).astype("int32"), 0, 50)
self.assertEqual(a, 350, 50 * 7)
img.shape = shape
cmp_ccp4 = mar345_IO.compress_pck(img, use_CCP4=True)
cmp_fab = mar345_IO.compress_pck(img, use_CCP4=False)
delta = abs(len(cmp_fab) - len(cmp_ccp4))
if len(cmp_fab) > len(cmp_ccp4):
logger.error("len(fabio): %s len(ccp4):%s", len(cmp_fab), len(cmp_ccp4))
self.assertLessEqual(delta, 10, "Compression by FabIO is similar to CCP4")
img_c_c = mar345_IO.uncompress_pck(cmp_ccp4, overflowPix=False, use_CCP4=True)
delta = img_c_c - img
ok = abs(delta).ravel()
if ok.max() > 0:
logger.error("img_c_c: %s %s" % numpy.where(delta))
self.assertEqual(ok.max(), 0, "Compression CCP4 decompression CCP4")
img_c_f = mar345_IO.uncompress_pck(cmp_ccp4, overflowPix=False, use_CCP4=False)
delta = img_c_f - img
ok = abs(delta).ravel()
if ok.max() > 0:
logger.error("img_c_f: %s %s" % numpy.where(delta))
self.assertEqual(ok.max(), 0, "Compression CCP4 decompression Cython")
img_f_c = mar345_IO.uncompress_pck(cmp_fab, overflowPix=False, use_CCP4=True)
delta = img_f_c - img
ok = abs(delta).ravel()
if ok.max() > 0:
logger.error("img_f_c: %s %s" % numpy.where(delta))
self.assertEqual(ok.max(), 0, "Compression Cython decompression CCP4")
img_f_f = mar345_IO.uncompress_pck(cmp_fab, overflowPix=False, use_CCP4=False)
delta = img_f_f - img
ok = abs(delta).ravel()
if ok.max() > 0:
logger.error("img_f_f: %s %s" % numpy.where(delta))
self.assertEqual(ok.max(), 0, "Compression Cython decompression Cython")
def suite():
loadTests = unittest.defaultTestLoader.loadTestsFromTestCase
testsuite = unittest.TestSuite()
testsuite.addTest(loadTests(TestMar345))
return testsuite
if __name__ == '__main__':
runner = unittest.TextTestRunner()
runner.run(suite)
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