def test_manual_addition_of_ImageCollection_to_DataManager(self):
# We start off by creating a :class:`jicbioimage.core.io.DataManager`.
# This takes a backend argument. The backend provides a means to store
# unpacked image files.
from jicbioimage.core.io import DataManager, FileBackend
backend = FileBackend(directory=TMP_DIR)
data_manager = DataManager(backend=backend)
# The :func:`jicbioimage.core.image.DataManager.conver` function is be
# default an instance of the callable
# :class:`jicbioimage.core.io.BFConvertWrapper` class.
from jicbioimage.core.io import BFConvertWrapper, _md5_hexdigest_from_file
self.assertTrue(isinstance(data_manager.convert, BFConvertWrapper))
# We also need to import an ImageCollection
from jicbioimage.core.image import ImageCollection
# If the input file has not already been converted with do so.
fpath = os.path.join(DATA_DIR, 'z-series.ome.tif')
self.assertFalse(data_manager.convert.already_converted(fpath))
if not data_manager.convert.already_converted(fpath):
path_to_manifest = data_manager.convert(fpath) # unpacks and creates manifests
self.assertEqual(path_to_manifest, os.path.join(TMP_DIR,
_md5_hexdigest_from_file(fpath),
'manifest.json'))
image_collection = ImageCollection()
image_collection.parse_manifest(path_to_manifest)
self.assertEqual(len(image_collection), 5)
data_manager.append(image_collection)
self.assertEqual(len(data_manager), 1)
self.assertTrue(data_manager.convert.already_converted(fpath))
def test_parse_manifest_raises_runtime_error_if_no_filename(self):
# Create manifest.json file without fpath.
manifest_fp = os.path.join(TMP_DIR, 'manifest.json')
with open(manifest_fp, 'w') as fh:
json.dump({"nofpath": "/tmp"}, fh)
from jicbioimage.core.image import ImageCollection
image_collection = ImageCollection()
with self.assertRaises(RuntimeError):
image_collection.parse_manifest(manifest_fp)
def test_parse_manifest_raises_runtime_error_if_no_filename(self):
# Create manifest.json file without fpath.
manifest_fp = os.path.join(TMP_DIR, 'manifest.json')
with open(manifest_fp, 'w') as fh:
json.dump({"nofpath": "/tmp"}, fh)
from jicbioimage.core.image import ImageCollection
image_collection = ImageCollection()
with self.assertRaises(RuntimeError):
image_collection.parse_manifest(manifest_fp)
def load(self, fpath):
"""Load a microscopy file.
:param fpath: path to microscopy file
"""
def is_microscopy_item(fpath):
"""Return True if the fpath is likely to be microscopy data.
:param fpath: file path to image
:returns: :class:`bool`
"""
l = fpath.split('.')
ext = l[-1]
pre_ext = l[-2]
if ((ext == 'tif' or ext == 'tiff') and pre_ext != 'ome'):
return False
return True
if not self.convert.already_converted(fpath):
path_to_manifest = self.convert(fpath)
else:
path_to_manifest = os.path.join(self.backend.directory,
_md5_hexdigest_from_file(fpath),
'manifest.json')
collection = None
if is_microscopy_item(fpath):
collection = MicroscopyCollection(path_to_manifest)
else:
collection = ImageCollection(path_to_manifest)
self.append(collection)
return collection
def test_parse_manifest_raises_backwards_compatible_with_abs_paths(self):
# Create manifest.json file without fpath.
manifest_fp = os.path.join(TMP_DIR, 'manifest.json')
shutil.copy(os.path.join(DATA_DIR, "tjelvar.png"), TMP_DIR)
abs_im_fpath = os.path.join(TMP_DIR, 'tjelvar.png')
entry = dict(filename=abs_im_fpath, series=0, channel=0, zslice=0,
timepoint=0)
with open(manifest_fp, 'w') as fh:
json.dump([entry], fh)
from jicbioimage.core.image import ImageCollection, Image
image_collection = ImageCollection()
image_collection.parse_manifest(manifest_fp)
im = image_collection[0].image
expected_im = Image.from_file(abs_im_fpath)
import numpy as np
self.assertTrue(np.array_equal(im, expected_im))
def test_repr_html(self):
from jicbioimage.core.image import ImageCollection, ProxyImage, Image
image_collection = ImageCollection()
image = Image((50,50))
image.png = MagicMock(return_value=bytearray('image', encoding='utf-8'))
with patch('jicbioimage.core.image.Image.from_file', return_value=image) as patched_image:
image_collection.append(ProxyImage('test0.tif'))
html = image_collection._repr_html_()
self.assertEqual(html.strip().replace(' ', '').replace('\n', ''),
'''
<div style="float: left; padding: 2px;" >
<p>
<table><tr><th>Index</th><td>0</td></tr></table>
</p>
<img style="margin-left: auto; margin-right: auto;" src="data:image/png;base64,aW1hZ2U=" />
</div>
'''.strip().replace(' ', '').replace('\n', ''))
image.png.assert_called_once_with(width=300)
def test_parse_manifest_raises_backwards_compatible_with_abs_paths(self):
# Create manifest.json file without fpath.
manifest_fp = os.path.join(TMP_DIR, 'manifest.json')
shutil.copy(os.path.join(DATA_DIR, "tjelvar.png"), TMP_DIR)
abs_im_fpath = os.path.join(TMP_DIR, 'tjelvar.png')
entry = dict(filename=abs_im_fpath,
series=0,
channel=0,
zslice=0,
timepoint=0)
with open(manifest_fp, 'w') as fh:
json.dump([entry], fh)
from jicbioimage.core.image import ImageCollection, Image
image_collection = ImageCollection()
image_collection.parse_manifest(manifest_fp)
im = image_collection[0].image
expected_im = Image.from_file(abs_im_fpath)
import numpy as np
self.assertTrue(np.array_equal(im, expected_im))
def test_proxy_image(self):
from jicbioimage.core.image import ImageCollection, ProxyImage
image_collection = ImageCollection()
image_collection.append(ProxyImage('test0.tif'))
image_collection.append(ProxyImage('test1.tif'))
proxy_image = image_collection.proxy_image()
self.assertEqual(proxy_image.fpath, 'test0.tif')
proxy_image = image_collection.proxy_image(index=1)
self.assertEqual(proxy_image.fpath, 'test1.tif')
def test_has_proxy_image(self):
from jicbioimage.core.image import ImageCollection
image_collection = ImageCollection()
self.assertTrue(callable(image_collection.proxy_image))
def test_len(self):
from jicbioimage.core.image import ImageCollection
image_collection = ImageCollection()
self.assertEqual(len(image_collection), 0)