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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)
#
# 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.
#
"""
# Unit tests
# builds on stuff from ImageD11.test.testpeaksearch
28/11/2014
"""
import unittest
import os
import numpy
import shutil
import io
import logging
logger = logging.getLogger(__name__)
import fabio
from ...edfimage import edfimage
from ...fabioutils import GzipFile, BZ2File
from ..utilstest import UtilsTest
class TestFlatEdfs(unittest.TestCase):
""" test some flat images """
def common_setup(self):
self.BYTE_ORDER = "LowByteFirst" if numpy.little_endian else "HighByteFirst"
self.MYHEADER = ("{\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)).encode("latin-1")
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].tobytes()) == 4, self.MYIMAGE[0:1, 0:1].tobytes()
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.tobytes())
outf.close()
obj = edfimage()
obj.read(self.filename)
self.obj = obj
def tearDown(self):
self.obj.close()
self.obj = None
unittest.TestCase.tearDown(self)
self.BYTE_ORDER = self.MYHEADER = self.MYIMAGE = None
def test_read(self):
""" check readable"""
self.assertEqual(self.obj.shape, (256, 256), msg="File %s has wrong shape " % self.filename)
self.assertEqual(self.obj.bpp, 4, msg="bpp!=4 for file: %s" % self.filename)
self.assertEqual(self.obj.bytecode, numpy.float32, msg="bytecode!=flot32 for file: %s" % self.filename)
self.assertEqual(self.obj.data.shape, (256, 256), msg="shape!=(256,256) for file: %s" % self.filename)
def test_getstats(self):
""" test statistics"""
self.assertEqual(self.obj.getmean(), 10)
self.assertEqual(self.obj.getmin(), 0)
self.assertEqual(self.obj.getmax(), 20)
def test_headers(self):
self.assertEqual(len(self.obj.header), 7)
expected_keys = ["Omega", "Dim_1", "Dim_2", "DataType", "ByteOrder", "Image", "History-1"]
self.assertEqual(expected_keys, list(self.obj.header.keys()))
expected_values = {
"Omega": "0.0",
"Dim_1": "256",
"Dim_2": "256",
"DataType": "FloatValue",
"Image": "1",
"History-1": "something=something else"
}
for k, expected_value in expected_values.items():
self.assertEqual(self.obj.header[k], expected_value)
class TestBzipEdf(TestFlatEdfs):
""" same for bzipped versions """
def setUp(self):
"""set it up"""
TestFlatEdfs.setUp(self)
if not os.path.isfile(self.filename + ".bz2"):
with BZ2File(self.filename + ".bz2", "wb") as f:
with open(self.filename, "rb") as d:
f.write(d.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"):
with GzipFile(self.filename + ".gz", "wb") as f:
with open(self.filename, "rb") as d:
f.write(d.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]]
shape = dim2, dim1
mini, maxi, mean, stddev = [float(x) for x in vals[3:]]
obj = edfimage()
try:
obj.read(os.path.join(self.im_dir, name))
except Exception:
logger.error("Cannot read image %s", 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(obj.shape, shape, "testedfs: %s shape" % 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"
ref.read(os.path.join(self.im_dir, refFile))
gzipped.read(os.path.join(self.im_dir, gzippedFile))
compressed.read(os.path.join(self.im_dir, 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()
self.ref.read(self.multiFrameFilename)
self.frame0.read(self.Frame0Filename)
self.frame1.read(self.Frame1Filename)
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):
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):
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):
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):
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):
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):
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 ")
# print(fabio.open(self.multiFrameFilename, 0).data)
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.fast_read_data(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.assertTrue(r.header["toto"] == self.header["toto"], "header are OK")
self.assertTrue(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.assertTrue(r.header["toto"] == self.header["toto"], "header are OK")
self.assertTrue(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.assertTrue(r.header["toto"] == self.header["toto"], "header are OK")
self.assertTrue(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 test_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
def test_remove_metadata_header(self):
filename = UtilsTest.getimage("face.edf.bz2")[0:-4]
output_filename = os.path.join(UtilsTest.tempdir, "test_remove_metadata_header.edf")
image = fabio.open(filename)
del image.header["Dim_1"]
image.write(output_filename)
image2 = fabio.open(output_filename)
self.assertEqual(image.shape, image2.shape)
class TestBadFiles(unittest.TestCase):
filename_template = "%s.edf"
@classmethod
def setUpClass(cls):
cls.tmp_directory = os.path.join(UtilsTest.tempdir, cls.__name__)
os.makedirs(cls.tmp_directory)
cls.create_resources()
@classmethod
def tearDownClass(cls):
shutil.rmtree(cls.tmp_directory)
@classmethod
def create_resources(cls):
filename = os.path.join(cls.tmp_directory, cls.filename_template % "base")
cls.base_filename = filename
with io.open(filename, "wb") as fd:
cls.write_header(fd, 1)
cls.header1 = fd.tell()
cls.write_data(fd)
cls.data1 = fd.tell()
cls.write_header(fd, 2)
cls.header2 = fd.tell()
cls.write_data(fd)
cls.data2 = fd.tell()
@classmethod
def write_header(cls, fd, image_number):
byte_order = "LowByteFirst" if numpy.little_endian else "HighByteFirst"
byte_order = byte_order.encode("latin-1")
fd.write(b"{\n")
fd.write(b"Omega = 0.0 ;\n")
fd.write(b"Dim_1 = 256 ;\n")
fd.write(b"Dim_2 = 256 ;\n")
fd.write(b"DataType = FloatValue ;\n")
fd.write(b"ByteOrder = %s ;\n" % byte_order)
fd.write(b"Image = %d ;\n" % image_number)
fd.write(b"History-1 = something=something else;\n")
fd.write(b"}\n")
@classmethod
def write_data(cls, fd):
data = numpy.ones((256, 256), numpy.float32) * 10
data[0, 0] = 0
data[1, 1] = 20
fd.write(data.tobytes())
@classmethod
def copy_base(cls, filename, size):
with io.open(cls.base_filename, "rb") as fd_base:
with io.open(filename, "wb") as fd_result:
fd_result.write(fd_base.read(size))
@classmethod
def open(cls, filename):
image = fabio.edfimage.EdfImage()
image.read(filename)
return image
def test_base(self):
filename = os.path.join(self.tmp_directory, self.filename_template % str(self.id()))
size = self.data2
self.copy_base(filename, size)
image = self.open(filename)
self.assertEqual(image.nframes, 2)
frame = image.getframe(0)
self.assertEqual(frame.header["Image"], "1")
self.assertEqual(frame.data[-1].sum(), 2560)
frame = image.getframe(1)
self.assertEqual(frame.header["Image"], "2")
self.assertEqual(frame.data[-1].sum(), 2560)
def test_empty(self):
filename = os.path.join(self.tmp_directory, self.filename_template % str(self.id()))
f = io.open(filename, "wb")
f.close()
self.assertRaises(IOError, self.open, filename)
def test_wrong_magic(self):
filename = os.path.join(self.tmp_directory, self.filename_template % str(self.id()))
f = io.open(filename, "wb")
f.write(b"\x10\x20\x30")
f.close()
self.assertRaises(IOError, self.open, filename)
def test_half_header(self):
filename = os.path.join(self.tmp_directory, self.filename_template % str(self.id()))
size = self.header1 // 2
self.copy_base(filename, size)
self.assertRaises(IOError, self.open, filename)
def test_header_with_no_data(self):
filename = os.path.join(self.tmp_directory, self.filename_template % str(self.id()))
size = self.header1
self.copy_base(filename, size)
image = self.open(filename)
self.assertIn(image.nframes, [0, 1])
self.assertTrue(image.incomplete_file)
def test_header_with_half_data(self):
filename = os.path.join(self.tmp_directory, self.filename_template % str(self.id()))
size = (self.header1 + self.data1) // 2
self.copy_base(filename, size)
image = self.open(filename)
self.assertEqual(image.nframes, 1)
self.assertTrue(image.incomplete_file)
frame = image
self.assertEqual(frame.header["Image"], "1")
self.assertEqual(frame.data[-1].sum(), 0)
self.assertTrue(frame.incomplete_data)
def test_full_frame_plus_half_header(self):
filename = os.path.join(self.tmp_directory, self.filename_template % str(self.id()))
size = (self.data1 + self.header2) // 2
self.copy_base(filename, size)
image = self.open(filename)
self.assertEqual(image.nframes, 1)
self.assertTrue(image.incomplete_file)
frame = image
self.assertEqual(frame.header["Image"], "1")
self.assertEqual(frame.data[-1].sum(), 2560)
self.assertFalse(frame.incomplete_data)
def test_full_frame_plus_header_with_no_data(self):
filename = os.path.join(self.tmp_directory, self.filename_template % str(self.id()))
size = self.header2
self.copy_base(filename, size)
image = self.open(filename)
self.assertIn(image.nframes, [1, 2])
self.assertTrue(image.incomplete_file)
frame = image
self.assertEqual(frame.header["Image"], "1")
self.assertEqual(frame.data[-1].sum(), 2560)
self.assertFalse(frame.incomplete_data)
def test_full_frame_plus_header_with_half_data(self):
filename = os.path.join(self.tmp_directory, self.filename_template % str(self.id()))
size = (self.header2 + self.data2) // 2
self.copy_base(filename, size)
image = self.open(filename)
self.assertEqual(image.nframes, 2)
self.assertTrue(image.incomplete_file)
frame = image.getframe(0)
self.assertEqual(frame.header["Image"], "1")
self.assertEqual(frame.data[-1].sum(), 2560)
self.assertFalse(frame.incomplete_data)
frame = image.getframe(1)
self.assertEqual(frame.header["Image"], "2")
self.assertEqual(frame.data[-1].sum(), 0)
self.assertTrue(frame.incomplete_data)
class TestBadGzFiles(TestBadFiles):
filename_template = "%s.edf.gz"
@classmethod
def write_header(cls, fd, image_number):
with GzipFile(fileobj=fd, mode="wb") as gzfd:
TestBadFiles.write_header(gzfd, image_number)
@classmethod
def write_data(cls, fd):
with GzipFile(fileobj=fd, mode="wb") as gzfd:
TestBadFiles.write_data(gzfd)
class TestSphere2SaxsSamples(unittest.TestCase):
"""Test some samples from sphere2saxs"""
def setUp(self):
unittest.TestCase.setUp(self)
self.samples = UtilsTest.resources.getdir("sphere2saxs_output.tar.bz2")
SAMPLES = {
"multi.edf": (5, (200, 100), numpy.float32, (6.292408e-05, 0.5594252, 3.2911296, 0.82902604)),
"multi.edf.gz": (5, (200, 100), numpy.float32, (6.292408e-05, 0.5594252, 3.2911296, 0.82902604)),
"sphere.edf": (1, (200, 100), numpy.float32, (6.292408e-05, 0.5594252, 3.2911296, 0.82902604)),
"sphere.edf.gz": (1, (200, 100), numpy.float32, (6.292408e-05, 0.5594252, 3.2911296, 0.82902604)),
}
def test_all_images(self):
for filename in self.samples:
if not os.path.isfile(filename):
continue
with fabio.open(filename) as f:
logger.debug("Reading file %s", filename)
expected_data = self.SAMPLES[os.path.basename(filename)]
nframes, shape, dtype, datainfo = expected_data
self.assertEqual(f.nframes, nframes)
self.assertEqual(f.shape, shape)
self.assertEqual(f.dtype, dtype)
vmin, vmean, vmax, vstd = datainfo
self.assertEqual(f.dtype, dtype)
self.assertAlmostEqual(f.data.min(), vmin, places=4)
self.assertAlmostEqual(f.data.mean(), vmean, places=4)
self.assertAlmostEqual(f.data.max(), vmax, places=4)
self.assertAlmostEqual(f.data.std(), vstd, places=4)
class TestEdfIterator(unittest.TestCase):
"""Read different EDF files with lazy iterator
"""
def test_multi_frame(self):
"""Test iterator on a multi-frame EDF"""
filename = UtilsTest.getimage("MultiFrame.edf.bz2")
iterator = fabio.edfimage.EdfImage.lazy_iterator(filename)
ref = fabio.open(filename)
for index in range(ref.nframes):
frame = next(iterator)
ref_frame = ref.getframe(index)
self.assertEqual(numpy.abs(ref_frame.data - frame.data).max(), 0, 'Test frame %d data' % index)
self.assertEqual(ref_frame.header, frame.header, 'Test frame %d header' % index)
with self.assertRaises(StopIteration):
next(iterator)
def test_single_frame(self):
"""Test iterator on a single frame EDF"""
filename = UtilsTest.getimage("edfCompressed_U16.edf")
iterator = fabio.edfimage.EdfImage.lazy_iterator(filename)
frame = next(iterator)
ref = fabio.open(filename)
self.assertEqual((ref.data - frame.data).max(), 0, "Test data")
self.assertEqual(ref.header, frame.header, "Test header")
with self.assertRaises(StopIteration):
next(iterator)
class TestEdfBadHeader(unittest.TestCase):
"""Test reader behavior with corrupted header file"""
def setUp(self):
self.fgood = os.path.join(UtilsTest.tempdir, "TestEdfGoodHeaderPadding.edf")
self.fbad = os.path.join(UtilsTest.tempdir, "TestEdfBadHeaderPadding.edf")
self.fzero = os.path.join(UtilsTest.tempdir, "TestEdfZeroHeaderPadding.edf")
self.fnonascii = os.path.join(UtilsTest.tempdir, "TestEdfNonAsciiItem.edf")
self.data = numpy.zeros((10, 11), numpy.uint8)
self.hdr = {"mykey": "myvalue", "title": "ok"}
good = fabio.edfimage.edfimage(self.data, self.hdr)
good.write(self.fgood)
with fabio.open(self.fgood) as good:
self.good_header = good.header
with open(self.fgood, "rb") as fh:
hdr = bytearray(fh.read(512))
while hdr.find(b"}") < 0:
hdr += fh.read(512)
data = fh.read()
with open( self.fbad, "wb") as fb:
start = hdr.rfind(b";") + 1
end = hdr.find(b"}") - 1
hdr[start:end] = [ord('\n')] + [0xcd] * (end - start - 1)
fb.write(hdr)
fb.write(data)
with open( self.fzero, "wb") as fb:
# insert some 0x00 to be stripped
key = b"myvalue"
z = hdr.find(key)
hdr[z + len(key)] = 0
fb.write(hdr)
fb.write(data)
with open( self.fnonascii, "wb") as fb:
hdr[z:z + 1]= 0xc3, 0xa9 # e-acute in utf-8 ??
with open(self.fnonascii, "wb") as fb:
fb.write(hdr)
fb.write(data)
def tearDown(self):
os.remove(self.fgood)
os.remove(self.fbad)
os.remove(self.fzero)
os.remove(self.fnonascii)
def testReadBadPadding(self):
"""
Some old data were found with headers padded with 0xcd (issue #373)
"""
with fabio.open(self.fbad) as im:
self.assertTrue((im.data == 0).all())
self.assertEqual(im.header, self.good_header)
def testReadGoodPadding(self):
with fabio.open(self.fgood) as im:
self.assertTrue((im.data == 0).all())
self.assertEqual(im.header, self.good_header)
def testReadZeroPadding(self):
with fabio.open(self.fzero) as im:
self.assertTrue((im.data == 0).all())
self.assertEqual(im.header, self.good_header)
def testNonAsciiHeader(self):
"""Non-ascii characters are skipped."""
with fabio.open(self.fnonascii) as im:
self.assertTrue((im.data == 0).all())
expected = dict(self.good_header)
expected.pop("mykey")
self.assertEqual(im.header, expected)
def suite():
loadTests = unittest.defaultTestLoader.loadTestsFromTestCase
testsuite = unittest.TestSuite()
testsuite.addTest(loadTests(TestFlatEdfs))
testsuite.addTest(loadTests(TestBzipEdf))
testsuite.addTest(loadTests(TestGzipEdf))
testsuite.addTest(loadTests(TestEdfs))
testsuite.addTest(loadTests(TestEdfCompressedData))
testsuite.addTest(loadTests(TestEdfMultiFrame))
testsuite.addTest(loadTests(TestEdfFastRead))
testsuite.addTest(loadTests(TestEdfWrite))
testsuite.addTest(loadTests(TestEdfRegression))
testsuite.addTest(loadTests(TestBadFiles))
testsuite.addTest(loadTests(TestBadGzFiles))
testsuite.addTest(loadTests(TestEdfIterator))
testsuite.addTest(loadTests(TestSphere2SaxsSamples))
testsuite.addTest(loadTests(TestEdfBadHeader))
return testsuite
if __name__ == '__main__':
runner = unittest.TextTestRunner()
runner.run(suite())
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