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Merge branch 'issue96' into devel

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This commit is contained in:
John Evans 2013-08-07 16:55:12 -04:00
commit 4c90b321b3
12 changed files with 134 additions and 113 deletions
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4
glymur/codestream.py
View file

@ -556,8 +556,8 @@ class Codestream(object):
mantissa_exponent_buffer_length = length - 4
cqcc, sqcc = struct.unpack(fmt, read_buffer)
if cqcc >= self._csiz:
msg = "Invalid component number (%d), "
msg += "number of components is only %d."
msg = "Invalid component number ({0}), "
msg += "number of components is only {1}."
msg = msg.format(cqcc, self._csiz)
warnings.warn(msg)

4
glymur/jp2box.py
View file

@ -1792,14 +1792,14 @@ class XMLBox(Jp2kBox):
text = read_buffer.decode('utf-8')
# Strip out any trailing nulls, as they can foul up XML parsing.
text = text.rstrip('\0')
text = text.rstrip(chr(0))
try:
elt = ET.fromstring(text)
xml = ET.ElementTree(elt)
except ParseError as parse_error:
msg = 'A problem was encountered while parsing an XML box:'
msg += '\n\n\t"{0}"\n\nNo XML was retrieved.'
msg += '\n\n\t"{0}"\n\nNo XML was retrieved.'
msg = msg.format(str(parse_error))
warnings.warn(msg, UserWarning)
xml = None

24
glymur/jp2dump.py
View file

@ -1,6 +1,7 @@
"""
Entry point for jp2dump script.
"""
import warnings
from .jp2k import Jp2k
@ -15,8 +16,21 @@ def jp2dump(filename, codestream=False):
codestream : optional, logical scalar
Whether or not to dump codestream contents.
"""
j = Jp2k(filename)
if codestream:
print(j.get_codestream(header_only=False))
else:
print(j)
with warnings.catch_warnings(record=True) as wctx:
# JP2 metadata can be extensive, so don't print any warnings until we
# are done with the metadata.
j = Jp2k(filename)
if codestream:
print(j.get_codestream(header_only=False))
else:
print(j)
# Re-emit any warnings that may have been suppressed.
if len(wctx) > 0:
print("\n")
for warning in wctx:
print("{0}:{1}: {2}: {3}".format(warning.filename,
warning.lineno,
warning.category.__name__,
warning.message))

6
glymur/jp2k.py
View file

@ -966,8 +966,10 @@ class Jp2k(Jp2kBox):
dparam.nb_tile_to_decode = 1
with ExitStack() as stack:
if hasattr(_opj2.OPENJP2, 'opj_stream_create_default_file_stream_v3'):
stream = _opj2.stream_create_default_file_stream_v3(self.filename,
if hasattr(_opj2.OPENJP2,
'opj_stream_create_default_file_stream_v3'):
filename = self.filename
stream = _opj2.stream_create_default_file_stream_v3(filename,
True)
stack.callback(_opj2.stream_destroy_v3, stream)
else:

3
glymur/test/__init__.py
View file

@ -0,0 +1,3 @@
"""
Test suite for glymur high-level functionality.
"""

98
glymur/test/fixtures.py
View file

@ -1,5 +1,9 @@
"""
Test fixtures common to more than one test point.
"""
import re
import sys
import warnings
import numpy as np
@ -20,6 +24,28 @@ if glymur.lib.openjp2.OPENJP2 is not None:
OPENJP2_IS_V2_OFFICIAL = True
NO_READ_BACKEND_MSG = "Matplotlib with the PIL backend must be available in "
NO_READ_BACKEND_MSG += "order to run the tests in this suite."
try:
from matplotlib.pyplot import imread
NO_READ_BACKEND = False
except ImportError:
NO_READ_BACKEND = True
def read_image(infile):
"""Read image using matplotlib backend.
Hopefully PIL(low) is installed as matplotlib's backend. It issues
warnings which we do not care about, so suppress them.
"""
with warnings.catch_warnings():
warnings.simplefilter("ignore")
data = imread(infile)
return data
def mse(amat, bmat):
"""Mean Square Error"""
diff = amat.astype(np.double) - bmat.astype(np.double)
@ -36,28 +62,10 @@ def peak_tolerance(amat, bmat):
def read_pgx(pgx_file):
"""Helper function for reading the PGX comparison files.
Open the file in ascii mode and read the header line.
Will look something like
PG ML + 8 128 128
PG%[ \t]%c%c%[ \t+-]%d%[ \t]%d%[ \t]%d"
"""
header = ''
with open(pgx_file, 'rb') as fptr:
while True:
char = fptr.read(1)
if char[0] == 10 or char == '\n':
pos = fptr.tell()
break
else:
if sys.hexversion < 0x03000000:
header += char
else:
header += chr(char[0])
header, pos = read_pgx_header(pgx_file)
header = header.rstrip()
tokens = re.split('\s', header)
tokens = re.split(r'\s', header)
if (tokens[1][0] == 'M') and (sys.byteorder == 'little'):
swapbytes = True
@ -81,6 +89,28 @@ def read_pgx(pgx_file):
nrows = int(tokens[4])
ncols = int(tokens[3])
dtype = determine_pgx_datatype(signed, bitdepth)
shape = [nrows, ncols]
# Reopen the file in binary mode and seek to the start of the binary
# data
with open(pgx_file, 'rb') as fptr:
fptr.seek(pos)
data = np.fromfile(file=fptr, dtype=dtype).reshape(shape)
return(data.byteswap(swapbytes))
def determine_pgx_datatype(signed, bitdepth):
"""Determine the datatype of the PGX file.
Parameters
----------
signed : bool
True if the datatype is signed, false otherwise
bitdepth : int
How many bits are used to make up an image plane. Should be 8 or 16.
"""
if signed:
if bitdepth <= 8:
dtype = np.int8
@ -96,12 +126,28 @@ def read_pgx(pgx_file):
else:
raise RuntimeError("unhandled bitdepth")
shape = [nrows, ncols]
return dtype
# Reopen the file in binary mode and seek to the start of the binary
# data
def read_pgx_header(pgx_file):
"""Open the file in ascii mode (not really) and read the header line.
Will look something like
PG ML + 8 128 128
PG%[ \t]%c%c%[ \t+-]%d%[ \t]%d%[ \t]%d"
"""
header = ''
with open(pgx_file, 'rb') as fptr:
fptr.seek(pos)
data = np.fromfile(file=fptr, dtype=dtype).reshape(shape)
while True:
char = fptr.read(1)
if char[0] == 10 or char == '\n':
pos = fptr.tell()
break
else:
if sys.hexversion < 0x03000000:
header += char
else:
header += chr(char[0])
header = header.rstrip()
return header, pos
return(data.byteswap(swapbytes))

2
glymur/test/test_callbacks.py
View file

@ -88,7 +88,7 @@ class TestCallbacks15(unittest.TestCase):
with patch('sys.stdout', new=StringIO()) as fake_out:
d = j.read(rlevel=1, verbose=True)
actual = fake_out.getvalue().strip()
regex = re.compile(r"""\[INFO\]\stile\s1\sof\s1\s+
\[INFO\]\s-\stiers-1\stook\s
[0-9]+\.[0-9]+\ss\s+

9
glymur/test/test_jp2k.py
View file

@ -7,6 +7,7 @@ import struct
import sys
import tempfile
import uuid
from xml.etree import cElementTree as ET
if sys.hexversion < 0x02070000:
import unittest2 as unittest
@ -65,7 +66,7 @@ class TestConfig(unittest.TestCase):
"""Don't have either openjp2 or openjpeg libraries? Must error out.
"""
with patch('glymur.lib.openjp2.OPENJP2', new=None):
with patch('glymur.lib.openjpeg.OPENJPEG', new=None):
with patch('glymur.lib.openjpeg.OPENJPEG', new=None):
with self.assertRaises(glymur.jp2k.LibraryNotFoundError):
d = glymur.Jp2k(self.jp2file).read()
@ -73,7 +74,7 @@ class TestConfig(unittest.TestCase):
"""Don't have openjp2 library? Must error out.
"""
with patch('glymur.lib.openjp2.OPENJP2', new=None):
with patch('glymur.lib.openjpeg.OPENJPEG', new=None):
with patch('glymur.lib.openjpeg.OPENJPEG', new=None):
with self.assertRaises(glymur.jp2k.LibraryNotFoundError):
d = glymur.Jp2k(self.jp2file).read_bands()
@ -83,7 +84,7 @@ class TestConfig(unittest.TestCase):
"""
data = glymur.Jp2k(self.j2kfile).read()
with patch('glymur.lib.openjp2.OPENJP2', new=None):
with patch('glymur.lib.openjpeg.OPENJPEG', new=None):
with patch('glymur.lib.openjpeg.OPENJPEG', new=None):
with self.assertRaises(glymur.jp2k.LibraryNotFoundError):
with tempfile.NamedTemporaryFile(suffix='.jp2') as tfile:
ofile = Jp2k(tfile.name, 'wb')
@ -623,6 +624,8 @@ class TestJp2k(unittest.TestCase):
self.assertEqual(jp2k.box[3].box_id, 'xml ')
self.assertEqual(jp2k.box[3].offset, 77)
self.assertEqual(jp2k.box[3].length, 36)
self.assertEqual(ET.tostring(jp2k.box[3].xml.getroot()),
b'<test>this is a test</test>')
@unittest.skipIf(os.name == "nt", "NamedTemporaryFile issue on windows")
def test_asoc_label_box(self):

51
glymur/test/test_opj_suite.py
View file

@ -66,11 +66,10 @@ class TestSuite(unittest.TestCase):
def test_ETS_C0P0_p0_02_j2k(self):
jfile = os.path.join(data_root, 'input/conformance/p0_02.j2k')
jp2k = Jp2k(jfile)
with warnings.catch_warnings():
# There's a 0xff30 marker segment. Not illegal, but we don't
# really know what to do with it. Just ignore.
# Invalid marker ID.
warnings.simplefilter("ignore")
jp2k = Jp2k(jfile)
jpdata = jp2k.read(rlevel=0)
pgxfile = os.path.join(data_root, 'baseline/conformance/c0p0_02.pgx')
@ -385,11 +384,7 @@ class TestSuite(unittest.TestCase):
def test_ETS_C1P0_p0_02_j2k(self):
jfile = os.path.join(data_root, 'input/conformance/p0_02.j2k')
with warnings.catch_warnings():
# There's a 0xff30 marker segment. Not illegal, but we don't
# really know what to do with it. Just ignore.
warnings.simplefilter("ignore")
jp2k = Jp2k(jfile)
jp2k = Jp2k(jfile)
jpdata = jp2k.read(rlevel=0)
pgxfile = os.path.join(data_root, 'baseline/conformance/c1p0_02_0.pgx')
@ -830,7 +825,7 @@ class TestSuite(unittest.TestCase):
jfile = os.path.join(data_root, 'input/nonregression/broken2.jp2')
with self.assertRaises(IOError):
with warnings.catch_warnings():
# Library warning, invalid number of subbands.
# Invalid marker ID.
warnings.simplefilter("ignore")
data = Jp2k(jfile).read()
self.assertTrue(True)
@ -852,7 +847,7 @@ class TestSuite(unittest.TestCase):
'input/nonregression/broken4.jp2')
with self.assertRaises(IOError):
with warnings.catch_warnings():
# Library warning, invalid number of subbands.
# invalid number of subbands, bad marker ID
warnings.simplefilter("ignore")
data = Jp2k(jfile).read()
self.assertTrue(True)
@ -1053,6 +1048,7 @@ class TestSuite(unittest.TestCase):
f = 'input/nonregression/gdal_fuzzer_unchecked_numresolutions.jp2'
jfile = os.path.join(data_root, f)
with warnings.catch_warnings():
# Invalid number of resolutions.
warnings.simplefilter("ignore")
j = Jp2k(jfile)
with self.assertRaises(IOError):
@ -1066,6 +1062,7 @@ class TestSuite(unittest.TestCase):
'gdal_fuzzer_assert_in_opj_j2k_read_SQcd_SQcc.patch.jp2')
jfile = os.path.join(data_root, '/'.join(lst))
with warnings.catch_warnings():
# Invalid component number.
warnings.simplefilter("ignore")
j = Jp2k(jfile)
with self.assertRaises(IOError):
@ -1077,6 +1074,7 @@ class TestSuite(unittest.TestCase):
relpath = 'input/nonregression/gdal_fuzzer_check_number_of_tiles.jp2'
jfile = os.path.join(data_root, relpath)
with warnings.catch_warnings():
# Invalid number of tiles.
warnings.simplefilter("ignore")
j = Jp2k(jfile)
with self.assertRaises(IOError):
@ -1088,6 +1086,7 @@ class TestSuite(unittest.TestCase):
relpath = 'input/nonregression/gdal_fuzzer_check_comp_dx_dy.jp2'
jfile = os.path.join(data_root, relpath)
with warnings.catch_warnings():
# Invalid subsampling value
warnings.simplefilter("ignore")
with self.assertRaises(IOError):
j = Jp2k(jfile).read()
@ -1220,36 +1219,28 @@ class TestSuite(unittest.TestCase):
def test_NR_DEC_p1_04_j2k_57_decode(self):
jfile = os.path.join(data_root, 'input/conformance/p1_04.j2k')
jp2k = Jp2k(jfile)
with warnings.catch_warnings():
warnings.simplefilter("ignore")
tdata = jp2k.read(tile=63) # last tile
tdata = jp2k.read(tile=63) # last tile
odata = jp2k.read()
np.testing.assert_array_equal(tdata, odata[896:1024, 896:1024])
def test_NR_DEC_p1_04_j2k_58_decode(self):
jfile = os.path.join(data_root, 'input/conformance/p1_04.j2k')
jp2k = Jp2k(jfile)
with warnings.catch_warnings():
warnings.simplefilter("ignore")
tdata = jp2k.read(tile=63, rlevel=2) # last tile
tdata = jp2k.read(tile=63, rlevel=2) # last tile
odata = jp2k.read(rlevel=2)
np.testing.assert_array_equal(tdata, odata[224:256, 224:256])
def test_NR_DEC_p1_04_j2k_59_decode(self):
jfile = os.path.join(data_root, 'input/conformance/p1_04.j2k')
jp2k = Jp2k(jfile)
with warnings.catch_warnings():
warnings.simplefilter("ignore")
tdata = jp2k.read(tile=12) # 2nd row, 5th column
tdata = jp2k.read(tile=12) # 2nd row, 5th column
odata = jp2k.read()
np.testing.assert_array_equal(tdata, odata[128:256, 512:640])
def test_NR_DEC_p1_04_j2k_60_decode(self):
jfile = os.path.join(data_root, 'input/conformance/p1_04.j2k')
jp2k = Jp2k(jfile)
with warnings.catch_warnings():
warnings.simplefilter("ignore")
tdata = jp2k.read(tile=12, rlevel=1) # 2nd row, 5th column
tdata = jp2k.read(tile=12, rlevel=1) # 2nd row, 5th column
odata = jp2k.read(rlevel=1)
np.testing.assert_array_equal(tdata, odata[64:128, 256:320])
@ -1366,9 +1357,7 @@ class TestSuite(unittest.TestCase):
jfile = os.path.join(data_root, 'input/conformance/p1_06.j2k')
jp2k = Jp2k(jfile)
fulldata = jp2k.read()
with warnings.catch_warnings():
warnings.simplefilter("ignore")
tiledata = jp2k.read(tile=0)
tiledata = jp2k.read(tile=0)
np.testing.assert_array_equal(tiledata, fulldata[0:3, 0:3])
@unittest.skip("fprintf stderr output in r2343.")
@ -1376,9 +1365,7 @@ class TestSuite(unittest.TestCase):
jfile = os.path.join(data_root, 'input/conformance/p1_06.j2k')
jp2k = Jp2k(jfile)
fulldata = jp2k.read()
with warnings.catch_warnings():
warnings.simplefilter("ignore")
tiledata = jp2k.read(tile=5)
tiledata = jp2k.read(tile=5)
np.testing.assert_array_equal(tiledata, fulldata[3:6, 3:6])
@unittest.skip("fprintf stderr output in r2343.")
@ -3809,7 +3796,7 @@ class TestSuiteDump(unittest.TestCase):
32, 32, 131, 2002, 2002, 1888])
self.assertEqual(c.segment[3]._exponent,
[17, 17, 17, 17, 16, 16, 16, 15, 15, 15, 14, 14,
14, 13, 13, 13, 11, 11, 11, 11, 11, 11])
14, 13, 13, 13, 11, 11, 11, 11, 11, 11])
# COM: comment
# Registration
@ -4596,10 +4583,10 @@ class TestSuiteDump(unittest.TestCase):
self.assertEqual(c.segment[7].sqcc & 0x1f, 2) # none
self.assertEqual(c.segment[7]._mantissa,
[1824, 1776, 1776, 1728, 1792, 1792, 1760, 1872,
1872, 1896, 5, 5, 71, 2003, 2003, 1890])
1872, 1896, 5, 5, 71, 2003, 2003, 1890])
self.assertEqual(c.segment[7]._exponent,
[18, 18, 18, 18, 17, 17, 17, 16, 16, 16, 14, 14,
14, 14, 14, 14])
14, 14, 14, 14])
# COM: comment
# Registration
@ -5634,7 +5621,7 @@ class TestSuiteDump(unittest.TestCase):
self.assertEqual(c.segment[3]._mantissa, [0] * 16)
self.assertEqual(c.segment[3]._exponent,
[18, 19, 19, 20, 19, 19, 20, 19, 19, 20, 19, 19, 20,
19, 19, 20])
19, 19, 20])
# COM: comment
# Registration

22
glymur/test/test_opj_suite_neg.py
View file

@ -12,22 +12,12 @@ if sys.hexversion < 0x02070000:
else:
import unittest
import warnings
import numpy as np
import pkg_resources
from glymur.lib import openjp2 as opj2
msg = "Matplotlib with the PIL backend must be available in order to run the "
msg += "tests in this suite."
no_read_backend_msg = msg
try:
from PIL import Image
from matplotlib.pyplot import imread
no_read_backend = False
except:
no_read_backend = True
from .fixtures import read_image, NO_READ_BACKEND, NO_READ_BACKEND_MSG
from glymur import Jp2k
import glymur
@ -40,17 +30,9 @@ except:
raise
def read_image(infile):
# PIL issues warnings which we do not care about, so suppress them.
with warnings.catch_warnings():
warnings.simplefilter("ignore")
data = imread(infile)
return data
@unittest.skipIf(glymur.lib.openjp2.OPENJP2 is None,
"Missing openjp2 library.")
@unittest.skipIf(no_read_backend, no_read_backend_msg)
@unittest.skipIf(NO_READ_BACKEND, NO_READ_BACKEND_MSG)
@unittest.skipIf(data_root is None,
"OPJ_DATA_ROOT environment variable not set")
class TestSuiteNegative(unittest.TestCase):

22
glymur/test/test_opj_suite_write.py
View file

@ -13,21 +13,11 @@ if sys.hexversion < 0x02070000:
else:
import unittest
import warnings
import numpy as np
from glymur.lib import openjp2 as opj2
msg = "Matplotlib with the PIL backend must be available in order to run the "
msg += "tests in this suite."
no_read_backend_msg = msg
try:
from PIL import Image
from matplotlib.pyplot import imread
no_read_backend = False
except:
no_read_backend = True
from .fixtures import read_image, NO_READ_BACKEND, NO_READ_BACKEND_MSG
from glymur import Jp2k
import glymur
@ -40,18 +30,10 @@ except:
raise
def read_image(infile):
# PIL issues warnings which we do not care about, so suppress them.
with warnings.catch_warnings():
warnings.simplefilter("ignore")
data = imread(infile)
return data
@unittest.skipIf(os.name == "nt", "no write support on windows, period")
@unittest.skipIf(glymur.lib.openjp2.OPENJP2 is None,
"Missing openjp2 library.")
@unittest.skipIf(no_read_backend, no_read_backend_msg)
@unittest.skipIf(NO_READ_BACKEND, NO_READ_BACKEND_MSG)
@unittest.skipIf(data_root is None,
"OPJ_DATA_ROOT environment variable not set")
class TestSuiteWrite(unittest.TestCase):

2
glymur/test/test_printing.py
View file

@ -1,6 +1,7 @@
#pylint: disable-all
import os
import pkg_resources
import re
import struct
import sys
import tempfile
@ -1026,5 +1027,6 @@ class TestPrinting(unittest.TestCase):
self.assertEqual(actual, expected)
if __name__ == "__main__":
unittest.main()