File: testedfimage.py

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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())