def test_info_html_table(self):
from jicbioimage.core.image import MicroscopyImage
microscopy_image = MicroscopyImage('dummy.tif',
dict(series=0, channel=1, zslice=2, timepoint=3))
self.assertEqual(
microscopy_image.__info_html_table__(30).strip().replace(' ', ''),
'''
<table>
<tr>
<th>Index</th>
<th>Series</th>
<th>Channel</th>
<th>Z-slice</th>
<th>Time point</th>
</tr>
<tr>
<td>30</td>
<td>0</td>
<td>1</td>
<td>2</td>
<td>3</td>
</tr>
</table>
'''.strip().replace(' ', '')
)
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(self):
from jicbioimage.core.image import MicroscopyImage
microscopy_image = MicroscopyImage(
'dummy.tif', dict(series=0, channel=1, zslice=2, timepoint=3))
self.assertEqual(
repr(microscopy_image),
'<MicroscopyImage(s=0, c=1, z=2, t=3) object at {}>'.format(
hex(id(microscopy_image))))
def test_instantiation(self):
from jicbioimage.core.image import MicroscopyImage
microscopy_image = MicroscopyImage(
'dummy.tif', dict(series=0, channel=1, zslice=2, timepoint=3))
self.assertEqual(microscopy_image.fpath, 'dummy.tif')
self.assertEqual(microscopy_image.series, 0)
self.assertEqual(microscopy_image.channel, 1)
self.assertEqual(microscopy_image.zslice, 2)
self.assertEqual(microscopy_image.timepoint, 3)
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_info_html_table(self):
from jicbioimage.core.image import MicroscopyImage
microscopy_image = MicroscopyImage(
'dummy.tif', dict(series=0, channel=1, zslice=2, timepoint=3))
self.assertEqual(
microscopy_image.__info_html_table__(30).strip().replace(' ', ''),
'''
<table>
<tr>
<th>Index</th>
<th>Series</th>
<th>Channel</th>
<th>Z-slice</th>
<th>Time point</th>
</tr>
<tr>
<td>30</td>
<td>0</td>
<td>1</td>
<td>2</td>
<td>3</td>
</tr>
</table>
'''.strip().replace(' ', ''))
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_repr_png_return_type(self):
from jicbioimage.core.image import MicroscopyImage
fpath = os.path.join(DATA_DIR, 'tjelvar.png')
microscopy_image = MicroscopyImage(
fpath, dict(series=0, channel=0, zslice=0, timepoint=0))
self.assertEqual(type(microscopy_image._repr_png_()), bytes)
def test_in_zstack(self):
from jicbioimage.core.image import MicroscopyImage
microscopy_image = MicroscopyImage('dummy.tif',
dict(series=0, channel=1, zslice=2, timepoint=3))
self.assertTrue(microscopy_image.in_zstack(s=0, c=1, t=3))
self.assertFalse(microscopy_image.in_zstack(s=5, c=1, t=3))
def test_repr_png_return_type(self):
from jicbioimage.core.image import MicroscopyImage
fpath = os.path.join(DATA_DIR, 'tjelvar.png')
microscopy_image = MicroscopyImage(fpath,
dict(series=0, channel=0, zslice=0, timepoint=0))
self.assertEqual(type(microscopy_image._repr_png_()), bytes)
def test_in_zstack(self):
from jicbioimage.core.image import MicroscopyImage
microscopy_image = MicroscopyImage(
'dummy.tif', dict(series=0, channel=1, zslice=2, timepoint=3))
self.assertTrue(microscopy_image.in_zstack(s=0, c=1, t=3))
self.assertFalse(microscopy_image.in_zstack(s=5, c=1, t=3))