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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
"""
from __future__ import print_function, with_statement, division, absolute_import
import unittest
import sys
import os
import numpy
import gzip
import bz2
if __name__ == '__main__':
import pkgutil
__path__ = pkgutil.extend_path([os.path.dirname(__file__)], "fabio.test")
from .utilstest import UtilsTest
logger = UtilsTest.get_logger(__file__)
fabio = sys.modules["fabio"]
from fabio.edfimage import edfimage
from fabio.third_party import six
class TestFlatEdfs(unittest.TestCase):
""" test some flat images """
def common_setup(self):
self.BYTE_ORDER = "LowByteFirst" if numpy.little_endian else "HighByteFirst"
self.MYHEADER = six.b("{\n%-1020s}\n" % (
"""Omega = 0.0 ;
Dim_1 = 256 ;
Dim_2 = 256 ;
DataType = FloatValue ;
ByteOrder = %s ;
Image = 1;
History-1 = something=something else;
\n\n""" % self.BYTE_ORDER))
self.MYIMAGE = numpy.ones((256, 256), numpy.float32) * 10
self.MYIMAGE[0, 0] = 0
self.MYIMAGE[1, 1] = 20
assert len(self.MYIMAGE[0:1, 0:1].tostring()) == 4, \
len(self.MYIMAGE[0:1, 0:1].tostring())
def setUp(self):
""" initialize"""
self.common_setup()
self.filename = os.path.join(UtilsTest.tempdir, "im0000.edf")
if not os.path.isfile(self.filename):
outf = open(self.filename, "wb")
assert len(self.MYHEADER) % 1024 == 0
outf.write(self.MYHEADER)
outf.write(self.MYIMAGE.tostring())
outf.close()
def tearDown(self):
unittest.TestCase.tearDown(self)
self.BYTE_ORDER = self.MYHEADER = self.MYIMAGE = None
def test_read(self):
""" check readable"""
obj = edfimage()
obj.read(self.filename)
self.assertEqual(obj.dim1, 256, msg="dim1!=256 for file: %s" % self.filename)
self.assertEqual(obj.dim2, 256, msg="dim2!=256 for file: %s" % self.filename)
self.assertEqual(obj.bpp, 4, msg="bpp!=4 for file: %s" % self.filename)
self.assertEqual(obj.bytecode, numpy.float32, msg="bytecode!=flot32 for file: %s" % self.filename)
self.assertEqual(obj.data.shape, (256, 256), msg="shape!=(256,256) for file: %s" % self.filename)
self.assertEqual(obj.header['History-1'],
"something=something else")
def test_getstats(self):
""" test statistics"""
obj = edfimage()
obj.read(self.filename)
self.assertEqual(obj.getmean(), 10)
self.assertEqual(obj.getmin(), 0)
self.assertEqual(obj.getmax(), 20)
class TestBzipEdf(TestFlatEdfs):
""" same for bzipped versions """
def setUp(self):
"""set it up"""
TestFlatEdfs.setUp(self)
if not os.path.isfile(self.filename + ".bz2"):
bz2.BZ2File(self.filename + ".bz2", "wb").write(open(self.filename, "rb").read())
self.filename += ".bz2"
class TestGzipEdf(TestFlatEdfs):
""" same for gzipped versions """
def setUp(self):
""" set it up """
TestFlatEdfs.setUp(self)
if not os.path.isfile(self.filename + ".gz"):
gzip.open(self.filename + ".gz", "wb").write(open(self.filename, "rb").read())
self.filename += ".gz"
# statistics come from fit2d I think
# filename dim1 dim2 min max mean stddev
TESTIMAGES = """F2K_Seb_Lyso0675.edf 2048 2048 982 17467 1504.29 217.61
F2K_Seb_Lyso0675.edf.bz2 2048 2048 982 17467 1504.29 217.61
F2K_Seb_Lyso0675.edf.gz 2048 2048 982 17467 1504.29 217.61
id13_badPadding.edf 512 512 85 61947 275.62 583.44 """
class TestEdfs(unittest.TestCase):
"""
Read some test images
"""
def setUp(self):
self.im_dir = os.path.dirname(UtilsTest.getimage("F2K_Seb_Lyso0675.edf.bz2"))
UtilsTest.getimage("id13_badPadding.edf.bz2")
def test_read(self):
""" check we can read these images"""
for line in TESTIMAGES.split("\n"):
vals = line.split()
name = vals[0]
dim1, dim2 = [int(x) for x in vals[1:3]]
mini, maxi, mean, stddev = [float(x) for x in vals[3:]]
obj = edfimage()
try:
obj.read(os.path.join(self.im_dir, name))
except:
print ("Cannot read image", name)
raise
self.assertAlmostEqual(mini, obj.getmin(), 2, "testedfs: %s getmin()" % name)
self.assertAlmostEqual(maxi, obj.getmax(), 2, "testedfs: %s getmax" % name)
logger.info("%s Mean: exp=%s, obt=%s" % (name, mean, obj.getmean()))
self.assertAlmostEqual(mean, obj.getmean(), 2, "testedfs: %s getmean" % name)
logger.info("%s StdDev: exp=%s, obt=%s" % (name, stddev, obj.getstddev()))
self.assertAlmostEqual(stddev, obj.getstddev(), 2, "testedfs: %s getstddev" % name)
self.assertEqual(dim1, obj.dim1, "testedfs: %s dim1" % name)
self.assertEqual(dim2, obj.dim2, "testedfs: %s dim2" % name)
obj = None
def test_rebin(self):
"""test the rebin of edfdata"""
f = edfimage()
f.read(os.path.join(self.im_dir, "F2K_Seb_Lyso0675.edf"))
f.rebin(1024, 1024)
self.assertEqual(abs(numpy.array([[1547, 1439], [1536, 1494]]) - f.data).max(), 0, "data are the same after rebin")
def tearDown(self):
unittest.TestCase.tearDown(self)
self.im_dir = None
class testedfcompresseddata(unittest.TestCase):
"""
Read some test images with their data-block compressed.
Z-Compression and Gzip compression are implemented Bzip2 and byte offet are experimental
"""
def setUp(self):
self.im_dir = os.path.dirname(UtilsTest.getimage("edfGzip_U16.edf.bz2"))
UtilsTest.getimage("edfCompressed_U16.edf.bz2")
UtilsTest.getimage("edfUncompressed_U16.edf.bz2")
def test_read(self):
""" check we can read these images"""
ref = edfimage()
gzipped = edfimage()
compressed = edfimage()
refFile = "edfUncompressed_U16.edf"
gzippedFile = "edfGzip_U16.edf"
compressedFile = "edfCompressed_U16.edf"
try:
ref.read(os.path.join(self.im_dir, refFile))
except:
raise RuntimeError("Cannot read image Uncompressed image %s" % refFile)
try:
gzipped.read(os.path.join(self.im_dir, gzippedFile))
except:
raise RuntimeError("Cannot read image gzippedFile image %s" % gzippedFile)
try:
compressed.read(os.path.join(self.im_dir, compressedFile))
except:
raise RuntimeError("Cannot read image compressedFile image %s" % compressedFile)
self.assertEqual((ref.data - gzipped.data).max(), 0, "Gzipped data block is correct")
self.assertEqual((ref.data - compressed.data).max(), 0, "Zlib compressed data block is correct")
class TestEdfMultiFrame(unittest.TestCase):
"""
Read some test images with their data-block compressed.
Z-Compression and Gzip compression are implemented Bzip2 and byte offet are experimental
"""
def setUp(self):
self.multiFrameFilename = UtilsTest.getimage("MultiFrame.edf.bz2")[:-4]
self.Frame0Filename = UtilsTest.getimage("MultiFrame-Frame0.edf.bz2")[:-4]
self.Frame1Filename = UtilsTest.getimage("MultiFrame-Frame1.edf.bz2")[:-4]
self.ref = edfimage()
self.frame0 = edfimage()
self.frame1 = edfimage()
try:
self.ref.read(self.multiFrameFilename)
except:
raise RuntimeError("Cannot read image multiFrameFilename image %s" % self.multiFrameFilename)
try:
self.frame0.read(self.Frame0Filename)
except:
raise RuntimeError("Cannot read image Frame0File image %s" % self.Frame0File)
try:
self.frame1.read(self.Frame1Filename)
except:
raise RuntimeError("Cannot read image Frame1File image %s" % self.Frame1File)
def tearDown(self):
unittest.TestCase.tearDown(self)
self.multiFrameFilename = self.Frame0Filename = self.Frame1Filename = self.ref = self.frame0 = self.frame1 = None
def test_getFrame_multi(self):
"""testedfmultiframe.test_getFrame_multi"""
self.assertEqual((self.ref.data - self.frame0.data).max(), 0, "getFrame_multi: Same data for frame 0")
f1_multi = self.ref.getframe(1)
# logger.warning("f1_multi.header=%s\nf1_multi.data= %s" % (f1_multi.header, f1_multi.data))
self.assertEqual((f1_multi.data - self.frame1.data).max(), 0, "getFrame_multi: Same data for frame 1")
def test_getFrame_mono(self):
"testedfmultiframe.test_getFrame_mono"
self.assertEqual((self.ref.data - self.frame0.data).max(), 0, "getFrame_mono: Same data for frame 0")
f1_mono = self.frame0.getframe(1)
self.assertEqual((f1_mono.data - self.frame1.data).max(), 0, "getFrame_mono: Same data for frame 1")
def test_next_multi(self):
"""testedfmultiframe.test_getFrame_mono"""
self.assertEqual((self.ref.data - self.frame0.data).max(), 0, "next_multi: Same data for frame 0")
next_ = self.ref.next()
self.assertEqual((next_.data - self.frame1.data).max(), 0, "next_multi: Same data for frame 1")
def text_next_mono(self):
"testedfmultiframe.text_next_mono"
self.assertEqual((self.ref.data - self.frame0.data).max(), 0, "next_mono: Same data for frame 0")
next_ = self.frame0.next()
self.assertEqual((next_.data - self.frame1.data).max(), 0, "next_mono: Same data for frame 1")
def test_previous_multi(self):
"""testedfmultiframe.test_previous_multi"""
f1 = self.ref.getframe(1)
self.assertEqual((f1.data - self.frame1.data).max(), 0, "previous_multi: Same data for frame 1")
f0 = f1.previous()
self.assertEqual((f0.data - self.frame1.data).max(), 0, "previous_multi: Same data for frame 0")
def test_previous_mono(self):
"testedfmultiframe.test_previous_mono"
f1 = self.ref.getframe(1)
self.assertEqual((f1.data - self.frame1.data).max(), 0, "previous_mono: Same data for frame 1")
prev = self.frame1.previous()
self.assertEqual((prev.data - self.frame0.data).max(), 0, "previous_mono: Same data for frame 0")
def test_openimage_multiframes(self):
"test if openimage can directly read first or second frame of a multi-frame"
self.assertEqual((fabio.open(self.multiFrameFilename).data - self.frame0.data).max(), 0, "openimage_multiframes: Same data for default ")
self.assertEqual((fabio.open(self.multiFrameFilename, 0).data - self.frame0.data).max(), 0, "openimage_multiframes: Same data for frame 0")
self.assertEqual((fabio.open(self.multiFrameFilename, 1).data - self.frame1.data).max(), 0, "openimage_multiframes: Same data for frame 1")
class TestEdfFastRead(unittest.TestCase):
"""
Read some test images with their data-block compressed.
Z-Compression and Gzip compression are implemented Bzip2 and byte offet are experimental
"""
def setUp(self):
self.refFilename = UtilsTest.getimage("MultiFrame-Frame0.edf.bz2")
self.fastFilename = self.refFilename[:-4]
def test_fastread(self):
ref = fabio.open(self.refFilename)
refdata = ref.data
obt = ref.fastReadData(self.fastFilename)
self.assertEqual(abs(obt - refdata).max(), 0, "testedffastread: Same data")
class TestEdfWrite(unittest.TestCase):
"""
Write dummy edf files with various compression schemes
"""
tmpdir = UtilsTest.tempdir
def setUp(self):
self.data = numpy.arange(100).reshape((10, 10))
self.header = {"toto": "tutu"}
def testFlat(self):
self.filename = os.path.join(self.tmpdir, "merged.azim")
e = edfimage(data=self.data, header=self.header)
e.write(self.filename)
r = fabio.open(self.filename)
self.assert_(r.header["toto"] == self.header["toto"], "header are OK")
self.assert_(abs(r.data - self.data).max() == 0, "data are OK")
self.assertEqual(int(r.header["EDF_HeaderSize"]), 512, "header size is one 512 block")
def testGzip(self):
self.filename = os.path.join(self.tmpdir, "merged.azim.gz")
e = edfimage(data=self.data, header=self.header)
e.write(self.filename)
r = fabio.open(self.filename)
self.assert_(r.header["toto"] == self.header["toto"], "header are OK")
self.assert_(abs(r.data - self.data).max() == 0, "data are OK")
self.assertEqual(int(r.header["EDF_HeaderSize"]), 512, "header size is one 512 block")
def testBzip2(self):
self.filename = os.path.join(self.tmpdir, "merged.azim.gz")
e = edfimage(data=self.data, header=self.header)
e.write(self.filename)
r = fabio.open(self.filename)
self.assert_(r.header["toto"] == self.header["toto"], "header are OK")
self.assert_(abs(r.data - self.data).max() == 0, "data are OK")
self.assertEqual(int(r.header["EDF_HeaderSize"]), 512, "header size is one 512 block")
def tearDown(self):
os.unlink(self.filename)
class TestEdfRegression(unittest.TestCase):
"""
Test suite to prevent regression
"""
def bug_27(self):
"""
import fabio
obj = fabio.open("any.edf")
obj.header["missing"]="blah"
obj.write("any.edf")
"""
# create dummy image:
shape = (32, 32)
data = numpy.random.randint(0, 6500, size=shape[0] * shape[1]).astype("uint16").reshape(shape)
fname = os.path.join(UtilsTest.tempdir, "bug27.edf")
e = edfimage(data=data, header={"key1": "value1"})
e.write(fname)
del e
obj = fabio.open(fname)
obj.header["missing"] = "blah"
obj.write(fname)
del obj
# os.unlink(fname)
def suite():
testsuite = unittest.TestSuite()
testsuite.addTest(TestFlatEdfs("test_read"))
testsuite.addTest(TestFlatEdfs("test_getstats"))
testsuite.addTest(TestBzipEdf("test_read"))
testsuite.addTest(TestBzipEdf("test_getstats"))
testsuite.addTest(TestGzipEdf("test_read"))
testsuite.addTest(TestGzipEdf("test_getstats"))
testsuite.addTest(TestEdfs("test_read"))
testsuite.addTest(TestEdfs("test_rebin"))
testsuite.addTest(testedfcompresseddata("test_read"))
testsuite.addTest(TestEdfMultiFrame("test_getFrame_multi"))
testsuite.addTest(TestEdfMultiFrame("test_getFrame_mono"))
testsuite.addTest(TestEdfMultiFrame("test_next_multi"))
testsuite.addTest(TestEdfMultiFrame("text_next_mono"))
testsuite.addTest(TestEdfMultiFrame("test_previous_multi"))
testsuite.addTest(TestEdfMultiFrame("test_openimage_multiframes"))
testsuite.addTest(TestEdfFastRead("test_fastread"))
testsuite.addTest(TestEdfWrite("testFlat"))
testsuite.addTest(TestEdfWrite("testGzip"))
testsuite.addTest(TestEdfWrite("testBzip2"))
testsuite.addTest(TestEdfRegression("bug_27"))
return testsuite
if __name__ == '__main__':
runner = unittest.TextTestRunner()
runner.run(suite())
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