def test_open_http():
url = "https://github.com/CellProfiler/python-bioformats/raw/39f2aa8360324b4129284d4f647d4f7ee7797518" \
"/tests/resources/Channel1-01-A-01.tif"
image, scale = bioformats.load_image_url(url,
rescale=False,
wants_max_intensity=True)
assert image.shape[0] == 640
def test_open_file():
path = os.path.join(os.path.dirname(__file__), 'resources',
'Channel1-01-A-01.tif')
url = "file:" + future.moves.urllib.request.pathname2url(path)
image, scale = bioformats.load_image_url(url,
rescale=False,
wants_max_intensity=True)
assert image.shape[0] == 640
def test_unicode_url():
#
# Regression test of issue #17: ensure that this does not
# raise an exception when converting URL to string
#
path = os.path.join(os.path.dirname(__file__), 'resources', 'Channel1-01-A-01.tif')
url = "file:" + future.moves.urllib.request.pathname2url(path)
image, scale = bioformats.load_image_url(url, rescale=False, wants_max_intensity=True)
assert image.shape[0] == 640
def test_01_03_unicode_url(self):
#
# Regression test of issue #17: ensure that this does not
# raise an exception when converting URL to string
#
path = os.path.join(os.path.dirname(__file__), 'Channel1-01-A-01.tif')
url = u"file:" + urllib.pathname2url(path).encode("utf-8")
image, scale = load_image_url(
url, rescale=False, wants_max_intensity=True)
self.assertEqual(image.shape[0], 640)
def test_01_03_unicode_url(self):
#
# Regression test of issue #17: ensure that this does not
# raise an exception when converting URL to string
#
path = os.path.join(os.path.dirname(__file__), 'Channel1-01-A-01.tif')
url = "file:" + pathname2url(path)
image, scale = load_image_url(
url, rescale=False, wants_max_intensity=True)
self.assertEqual(image.shape[0], 640)
def test_unicode_url():
#
# Regression test of issue #17: ensure that this does not
# raise an exception when converting URL to string
#
path = os.path.join(os.path.dirname(__file__), 'resources',
'Channel1-01-A-01.tif')
url = "file:" + future.moves.urllib.request.pathname2url(path)
image, scale = bioformats.load_image_url(url,
rescale=False,
wants_max_intensity=True)
assert image.shape[0] == 640
def fn():
from bioformats import load_image_url
import javabridge
from scipy.io.matlab.mio import loadmat
from cellprofiler.modules.loadimages import url2pathname
javabridge.attach()
with self.image_dict_lock:
generation = self.image_dict_generation
for k, v in well.iteritems():
sd = {}
with self.image_dict_lock:
if self.image_dict_generation > generation:
return
self.image_dict[k] = sd
for c, fd in enumerate(v):
if PlateData.D_CHANNEL in fd:
channel = fd[PlateData.D_CHANNEL]
else:
channel = str(c+1)
url = fd[PlateData.D_FILENAME]
try:
if url.lower().endswith(".mat"):
img = loadmat(
url2pathname(url),
struct_as_record=True)["Image"]
else:
img = load_image_url(url)
with self.image_dict_lock:
if self.image_dict_generation > generation:
return
sd[channel] = img
except:
traceback.print_exc()
pass
wx.CallAfter(self.update_figure)
javabridge.static_call(
"java/lang/System", "gc", "()V")
javabridge.detach()
def fn():
from bioformats import load_image_url
import javabridge
from scipy.io.matlab.mio import loadmat
from cellprofiler.modules.loadimages import url2pathname
javabridge.attach()
with self.image_dict_lock:
generation = self.image_dict_generation
for k, v in well.iteritems():
sd = {}
with self.image_dict_lock:
if self.image_dict_generation > generation:
return
self.image_dict[k] = sd
for c, fd in enumerate(v):
if PlateData.D_CHANNEL in fd:
channel = fd[PlateData.D_CHANNEL]
else:
channel = str(c + 1)
url = fd[PlateData.D_FILENAME]
try:
if url.lower().endswith(".mat"):
img = loadmat(
url2pathname(url),
struct_as_record=True)["Image"]
else:
img = load_image_url(url)
with self.image_dict_lock:
if self.image_dict_generation > generation:
return
sd[channel] = img
except:
traceback.print_exc()
pass
wx.CallAfter(self.update_figure)
javabridge.static_call(
"java/lang/System", "gc", "()V")
javabridge.detach()
def test_open_http():
url = "https://github.com/CellProfiler/python-bioformats/raw/39f2aa8360324b4129284d4f647d4f7ee7797518" \
"/tests/resources/Channel1-01-A-01.tif"
image, scale = bioformats.load_image_url(url, rescale=False, wants_max_intensity=True)
assert image.shape[0] == 640
def test_open_file():
path = os.path.join(os.path.dirname(__file__), 'resources', 'Channel1-01-A-01.tif')
url = "file:" + future.moves.urllib.request.pathname2url(path)
image, scale = bioformats.load_image_url(url, rescale=False, wants_max_intensity=True)
assert image.shape[0] == 640
def test_01_02_open_http(self):
url = "https://github.com/CellProfiler/python-bioformats"+\
"/raw/master/bioformats/tests/Channel1-01-A-01.tif"
image, scale = load_image_url(
url, rescale=False, wants_max_intensity=True)
self.assertEqual(image.shape[0], 640)
def test_01_01_open_file(self):
path = os.path.join(os.path.dirname(__file__), 'Channel1-01-A-01.tif')
url = "file:" + urllib.pathname2url(path).encode("utf-8")
image, scale = load_image_url(
url, rescale=False, wants_max_intensity=True)
self.assertEqual(image.shape[0], 640)
def test_01_02_open_http(self):
url = "https://github.com/CellProfiler/python-bioformats"+\
"/raw/master/bioformats/tests/Channel1-01-A-01.tif"
image, scale = load_image_url(
url, rescale=False, wants_max_intensity=True)
self.assertEqual(image.shape[0], 640)
def test_01_01_open_file(self):
path = os.path.join(os.path.dirname(__file__), 'Channel1-01-A-01.tif')
url = "file:" + pathname2url(path)
image, scale = load_image_url(
url, rescale=False, wants_max_intensity=True)
self.assertEqual(image.shape[0], 640)