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 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 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")
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 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(dim1, obj.dim1, "testedfs: %s dim1" % name)
self.assertEqual(dim2, obj.dim2, "testedfs: %s dim2" % name)
obj = None
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)
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")
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 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 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 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()
obj = edfimage()
obj.read(self.filename)
self.obj = obj
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()
obj = edfimage()
obj.read(self.filename)
self.obj = obj
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_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_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_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 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(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 imread(self, filepath, plugin=None):
return fabio.edfimage(filepath).data
