def initialise(self, directory):
self.directories = [os.path.join(directory, d)
for d in _sorted_listdir(directory)
if d.endswith(".stack")]
self.current = 0
stack = self.get_stack()
OpenGL.GLUT.glutSetWindowTitle(self.get_title())
self.renderer = VolumeRenderer()
self.renderer.make_volume_obj(stack, (1, 1, 1))
def manifest(self, entry):
"""Returns manifest as a list.
:param entry: :class:`jicbioimage.core.io.FileBackend.Entry`
:returns: :class:`jicbioimage.core.io.Manifest`
"""
m = Manifest()
for fname in _sorted_listdir(entry.directory):
if fname == 'manifest.json':
continue
fpath = os.path.join(entry.directory, fname)
md5_hexdigest = _md5_hexdigest_from_file(fpath)
metadata = self.metadata_from_fname(fname, md5_hexdigest)
m.add(**metadata)
return m
def manifest(self, entry):
"""Returns manifest as a list.
:param entry: :class:`jicbioimage.core.io.FileBackend.Entry`
:returns: :class:`jicbioimage.core.io.Manifest`
"""
m = Manifest()
for fname in _sorted_listdir(entry.directory):
if fname == 'manifest.json':
continue
fpath = os.path.join(entry.directory, fname)
md5_hexdigest = _md5_hexdigest_from_file(fpath)
metadata = self.metadata_from_fname(fname, md5_hexdigest)
m.add(**metadata)
return m
def from_directory(cls, directory):
skimage.io.use_plugin('freeimage')
def is_image_fname(fname):
"Return True if fname is '.png', '.tif' or '.tiff'."""
image_exts = set([".png", ".tif", ".tiff"])
base, ext = os.path.splitext(fname)
return ext in image_exts
fnames = [fn for fn in _sorted_listdir(directory)
if is_image_fname(fn)]
fpaths = [os.path.join(directory, fn) for fn in fnames]
images = [cls._rgb_to_identifier(skimage.io.imread(fp))
for fp in fpaths]
stack = np.dstack(images)
return stack.view(cls)
def test_sorted_lisdir(self, patch_listdir):
patch_listdir.return_value = ["z20.png", "z3.png", "z1.png"]
from jicbioimage.core.image import _sorted_listdir
l = _sorted_listdir(".")
patch_listdir.assert_called_with(".")
self.assertEqual(l, ["z1.png", "z3.png", "z20.png"])
def test_sorted_lisdir(self, patch_listdir):
patch_listdir.return_value = ["z20.png", "z3.png", "z1.png"]
from jicbioimage.core.image import _sorted_listdir
l = _sorted_listdir(".")
patch_listdir.assert_called_with(".")
self.assertEqual(l, ["z1.png", "z3.png", "z20.png"])
