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_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_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_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])