def test_repr_html(self):
from jicbioimage.core.image import MicroscopyCollection, MicroscopyImage, Image
microscopy_collection = MicroscopyCollection()
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:
microscopy_collection.append(MicroscopyImage('test0.tif',
dict(series=1, channel=2, zslice=3, timepoint=4)))
html = microscopy_collection._repr_html_()
self.assertEqual(html.strip().replace(' ', '').replace('\n', ''),
'''
<div style="float: left; padding: 2px;" >
<p>
<table>
<tr>
<th>Index</th>
<th>Series</th>
<th>Channel</th>
<th>Z-slice</th>
<th>Time point</th>
</tr>
<tr>
<td>0</td>
<td>1</td>
<td>2</td>
<td>3</td>
<td>4</td>
</tr>
</table>
</p>
<img style="margin-left: auto; margin-right: auto;" src="data:image/png;base64,aW1hZ2U=" />
</div>
'''.strip().replace(' ', '').replace('\n', ''))
def test_zstack_proxy_iterator_is_iterable(self):
import collections
from jicbioimage.core.image import MicroscopyCollection
microscopy_collection = MicroscopyCollection()
self.assertTrue(isinstance(microscopy_collection.zstack_proxy_iterator(),
collections.Iterable))
self.assertTrue(isinstance(microscopy_collection.zstack_proxy_iterator(),
collections.Iterable))
def test_zstack_proxy_iterator_is_iterable(self):
import collections
from jicbioimage.core.image import MicroscopyCollection
microscopy_collection = MicroscopyCollection()
self.assertTrue(
isinstance(microscopy_collection.zstack_proxy_iterator(),
collections.Iterable))
self.assertTrue(
isinstance(microscopy_collection.zstack_proxy_iterator(),
collections.Iterable))
def get_microscopy_collection_from_tiff(input_file):
"""Return microscopy collection from tiff file."""
data_manager, backend_dir = get_data_manager()
data_manager.load(input_file)
md5_hex = _md5_hexdigest_from_file(input_file)
manifest_path = os.path.join(backend_dir, md5_hex, "manifest.json")
microscopy_collection = MicroscopyCollection()
microscopy_collection.parse_manifest(manifest_path)
return microscopy_collection
def get_microscopy_collection_from_tiff(input_file):
"""Return microscopy collection from tiff file."""
data_manager, backend_dir = get_data_manager()
data_manager.load(input_file)
md5_hex = _md5_hexdigest_from_file(input_file)
manifest_path = os.path.join(backend_dir, md5_hex, "manifest.json")
microscopy_collection = MicroscopyCollection()
microscopy_collection.parse_manifest(manifest_path)
return microscopy_collection
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 analyse_dir(args):
"""Analyse all images in an input directory."""
for fname in os.listdir(args.input_dir):
if not fname.lower().endswith(".nd2"):
continue
logger.info("Analysing image: {}".format(fname))
def get_dir_name(fname):
no_suffix_list = fname.split(".")[0:-1]
return ".".join(no_suffix_list)
dir_name = get_dir_name(fname)
specific_out_dir = os.path.join(args.output_dir, dir_name)
# Skip analysis of image if output directory exists.
if os.path.isdir(specific_out_dir):
logger.info("Directory exists: {}".format(specific_out_dir))
logger.info("Skipping: {}".format(fname))
continue
os.mkdir(specific_out_dir)
fpath = os.path.join(args.input_dir, fname)
manifest_path = convert_and_split(fpath, 'nikon_backend')
microscopy_collection = MicroscopyCollection(manifest_path)
analyse_all(microscopy_collection, specific_out_dir, args.threshold,
args.min_voxel, args.max_voxel)
def test_proxy_image(self):
from jicbioimage.core.image import MicroscopyCollection, MicroscopyImage
microscopy_collection = MicroscopyCollection()
microscopy_collection.append(
MicroscopyImage('test0.tif',
dict(series=0, channel=0, zslice=0, timepoint=0)))
microscopy_collection.append(
MicroscopyImage('test1.tif',
dict(series=1, channel=1, zslice=1, timepoint=1)))
proxy_image = microscopy_collection.proxy_image()
self.assertEqual(proxy_image.fpath, 'test0.tif')
proxy_image = microscopy_collection.proxy_image(s=1, c=1, z=1, t=1)
self.assertEqual(proxy_image.fpath, 'test1.tif')
def test_repr_html(self):
from jicbioimage.core.image import MicroscopyCollection, MicroscopyImage, Image
microscopy_collection = MicroscopyCollection()
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:
microscopy_collection.append(
MicroscopyImage(
'test0.tif',
dict(series=1, channel=2, zslice=3, timepoint=4)))
html = microscopy_collection._repr_html_()
self.assertEqual(
html.strip().replace(' ', '').replace('\n', ''), '''
<div style="float: left; padding: 2px;" >
<p>
<table>
<tr>
<th>Index</th>
<th>Series</th>
<th>Channel</th>
<th>Z-slice</th>
<th>Time point</th>
</tr>
<tr>
<td>0</td>
<td>1</td>
<td>2</td>
<td>3</td>
<td>4</td>
</tr>
</table>
</p>
<img style="margin-left: auto; margin-right: auto;" src="data:image/png;base64,aW1hZ2U=" />
</div>
'''.strip().replace(' ', '').replace('\n', ''))
def test_proxy_image(self):
from jicbioimage.core.image import MicroscopyCollection, MicroscopyImage
microscopy_collection = MicroscopyCollection()
microscopy_collection.append(MicroscopyImage('test0.tif',
dict(series=0, channel=0, zslice=0, timepoint=0)))
microscopy_collection.append(MicroscopyImage('test1.tif',
dict(series=1, channel=1, zslice=1, timepoint=1)))
proxy_image = microscopy_collection.proxy_image()
self.assertEqual(proxy_image.fpath, 'test0.tif')
proxy_image = microscopy_collection.proxy_image(s=1, c=1, z=1, t=1)
self.assertEqual(proxy_image.fpath, 'test1.tif')
def test_image(self):
from jicbioimage.core.image import MicroscopyCollection
microscopy_collection = MicroscopyCollection()
self.assertTrue(callable(microscopy_collection.image))
def test_zstack_array(self):
from jicbioimage.core.image import MicroscopyCollection
microscopy_collection = MicroscopyCollection()
self.assertTrue(callable(microscopy_collection.zstack_array))
def test_zstack_proxy_iterator(self):
from jicbioimage.core.image import MicroscopyCollection
microscopy_collection = MicroscopyCollection()
self.assertTrue(callable(microscopy_collection.zstack_proxy_iterator))
def test_manifest_data(self):
from jicbioimage.core.image import MicroscopyCollection, MicroscopyImage
microscopy_collection = MicroscopyCollection()
microscopy_collection.append(
MicroscopyImage('test0.tif',
dict(series=0, channel=0, zslice=0, timepoint=0)))
microscopy_collection.append(
MicroscopyImage('test0.tif',
dict(series=0, channel=1, zslice=2, timepoint=3)))
microscopy_collection.append(
MicroscopyImage('test1.tif',
dict(series=1, channel=2, zslice=3, timepoint=4)))
self.assertEqual(microscopy_collection.series, [0, 1])
self.assertEqual(microscopy_collection.channels(), [0, 1])
self.assertEqual(microscopy_collection.channels(s=1), [2])
self.assertEqual(microscopy_collection.zslices(), [0, 2])
self.assertEqual(microscopy_collection.zslices(s=1), [3])
self.assertEqual(microscopy_collection.timepoints(), [0, 3])
self.assertEqual(microscopy_collection.timepoints(s=1), [4])
def test_len(self):
from jicbioimage.core.image import MicroscopyCollection
microscopy_collection = MicroscopyCollection()
self.assertEqual(len(microscopy_collection), 0)
def test_manifest_data(self):
from jicbioimage.core.image import MicroscopyCollection, MicroscopyImage
microscopy_collection = MicroscopyCollection()
microscopy_collection.append(MicroscopyImage('test0.tif',
dict(series=0, channel=0, zslice=0, timepoint=0)))
microscopy_collection.append(MicroscopyImage('test0.tif',
dict(series=0, channel=1, zslice=2, timepoint=3)))
microscopy_collection.append(MicroscopyImage('test1.tif',
dict(series=1, channel=2, zslice=3, timepoint=4)))
self.assertEqual(microscopy_collection.series, [0, 1])
self.assertEqual(microscopy_collection.channels(), [0, 1])
self.assertEqual(microscopy_collection.channels(s=1), [2])
self.assertEqual(microscopy_collection.zslices(), [0, 2])
self.assertEqual(microscopy_collection.zslices(s=1), [3])
self.assertEqual(microscopy_collection.timepoints(), [0, 3])
self.assertEqual(microscopy_collection.timepoints(s=1), [4])
