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 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_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_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)