def test_02_04_set_text(self): o = O.OMEXML(TIFF_XML) ad = o.root_node.find("/".join( [O.qn(o.get_ns('ome'), x) for x in ("Image", "AcquisitionDate")])) im = o.root_node.find(O.qn(o.get_ns("ome"), "Image")) O.set_text(im, "Foo") self.assertEqual(O.get_text(im), "Foo") O.set_text(ad, "Bar") self.assertEqual(O.get_text(ad), "Bar")
def test_02_04_set_text(self): o = O.OMEXML(TIFF_XML) ad = o.root_node.find("/".join( [O.qn(o.get_ns('ome'), x) for x in ("Image", "AcquiredDate")])) im = o.root_node.find(O.qn(o.get_ns("ome"), "Image")) O.set_text(im, "Foo") self.assertEqual(O.get_text(im), "Foo") O.set_text(ad, "Bar") self.assertEqual(O.get_text(ad), "Bar")
def test_07_01_sa_get_item(self): o = O.OMEXML(TIFF_XML) a = o.structured_annotations["Annotation:4"] self.assertEqual(a.tag, O.qn(o.get_ns("sa"), "XMLAnnotation")) values = a.findall(O.qn(o.get_ns("sa"), "Value")) self.assertEqual(len(values), 1) oms = values[0].findall(O.qn(O.NS_ORIGINAL_METADATA, "OriginalMetadata")) self.assertEqual(len(oms), 1) keys = oms[0].findall(O.qn(O.NS_ORIGINAL_METADATA, "Key")) self.assertEqual(len(keys), 1) self.assertEqual(O.get_text(keys[0]), "XResolution") values = oms[0].findall(O.qn(O.NS_ORIGINAL_METADATA, "Value")) self.assertEqual(len(values), 1) self.assertEqual(O.get_text(values[0]), "72")
def test_07_01_sa_get_item(self): o = O.OMEXML(TIFF_XML) a = o.structured_annotations["Annotation:4"] self.assertEqual(a.tag, O.qn(O.NS_SA, "XMLAnnotation")) values = a.findall(O.qn(O.NS_SA, "Value")) self.assertEqual(len(values), 1) oms = values[0].findall( O.qn(O.NS_ORIGINAL_METADATA, "OriginalMetadata")) self.assertEqual(len(oms), 1) keys = oms[0].findall(O.qn(O.NS_ORIGINAL_METADATA, "Key")) self.assertEqual(len(keys), 1) self.assertEqual(O.get_text(keys[0]), "XResolution") values = oms[0].findall(O.qn(O.NS_ORIGINAL_METADATA, "Value")) self.assertEqual(len(values), 1) self.assertEqual(O.get_text(values[0]), "72")
def test_14_02_set_plane_count(self): o = O.OMEXML() pixels = o.image(0).Pixels self.assertTrue(isinstance(pixels, O.OMEXML.Pixels)) pixels.plane_count = 2 self.assertEqual( len(pixels.node.findall(O.qn(o.get_ns('ome'), "Plane"))), 2)
def test_07_05_om_setitem(self): o = O.OMEXML() o.structured_annotations.OriginalMetadata["Foo"] = "Bar" sa = o.structured_annotations.node a = sa.findall(O.qn(O.NS_SA, "XMLAnnotation")) self.assertEqual(len(a), 1) vs = a[0].findall(O.qn(O.NS_SA, "Value")) self.assertEqual(len(vs), 1) om = vs[0].findall(O.qn(O.NS_ORIGINAL_METADATA, "OriginalMetadata")) self.assertEqual(len(om), 1) k = om[0].findall(O.qn(O.NS_ORIGINAL_METADATA, "Key")) self.assertEqual(len(k), 1) self.assertEqual(O.get_text(k[0]), "Foo") v = om[0].findall(O.qn(O.NS_ORIGINAL_METADATA, "Value")) self.assertEqual(len(v), 1) self.assertEqual(O.get_text(v[0]), "Bar")
def test_13_11_get_image_ref(self): o = O.OMEXML(self.GROUPFILES_XML) ws = o.plates[0].Well['A02'].Sample[3] self.assertEqual(ws.ImageRef, "Image:9") ref = ws.node.find(O.qn(o.get_ns("spw"), "ImageRef")) ws.node.remove(ref) self.assertTrue(ws.ImageRef is None)
def test_05_18_pixels_set_channel_count(self): o = O.OMEXML(TIFF_XML) o.image(0).Pixels.channel_count = 2 self.assertEqual( len( o.image(0).Pixels.node.findall(O.qn(o.get_ns("ome"), "Channel"))), 2)
def test_07_05_om_setitem(self): o = O.OMEXML() o.structured_annotations.OriginalMetadata["Foo"] = "Bar" sa = o.structured_annotations.node a = sa.findall(O.qn(o.get_ns("sa"), "XMLAnnotation")) self.assertEqual(len(a), 1) vs = a[0].findall(O.qn(o.get_ns("sa"), "Value")) self.assertEqual(len(vs), 1) om = vs[0].findall(O.qn(O.NS_ORIGINAL_METADATA, "OriginalMetadata")) self.assertEqual(len(om), 1) k = om[0].findall(O.qn(O.NS_ORIGINAL_METADATA, "Key")) self.assertEqual(len(k), 1) self.assertEqual(O.get_text(k[0]), "Foo") v = om[0].findall(O.qn(O.NS_ORIGINAL_METADATA, "Value")) self.assertEqual(len(v), 1) self.assertEqual(O.get_text(v[0]), "Bar")
def test_13_11_get_image_ref(self): o = O.OMEXML(self.GROUPFILES_XML) ws = o.plates[0].Well['A02'].Sample[3] self.assertEqual(ws.ImageRef, "Image:9") ref = ws.node.find(O.qn(O.NS_SPW, "ImageRef")) ws.node.remove(ref) self.assertTrue(ws.ImageRef is None)
def test_12_05_new_sample_item(self): o = O.OMEXML() plate = o.plates.newPlate("foo","bar") w = plate.Well.new(4,5, "xyz") w.Sample.new("ooo") w.Sample.new("ppp") sample_nodes = w.node.findall(O.qn(o.get_ns("spw"), "WellSample")) self.assertEqual(len(sample_nodes), 2) self.assertEqual(sample_nodes[0].get("ID"), "ooo") self.assertEqual(sample_nodes[1].get("ID"), "ppp") self.assertEqual(sample_nodes[0].get("Index"), "0") self.assertEqual(sample_nodes[1].get("Index"), "1")
def test_12_05_new_sample_item(self): o = O.OMEXML() plate = o.plates.newPlate("foo", "bar") w = plate.Well.new(4, 5, "xyz") w.Sample.new("ooo") w.Sample.new("ppp") sample_nodes = w.node.findall(O.qn(O.NS_SPW, "WellSample")) self.assertEqual(len(sample_nodes), 2) self.assertEqual(sample_nodes[0].get("ID"), "ooo") self.assertEqual(sample_nodes[1].get("ID"), "ppp") self.assertEqual(sample_nodes[0].get("Index"), "0") self.assertEqual(sample_nodes[1].get("Index"), "1")
def test_13_12_set_image_ref(self): o = O.OMEXML(self.GROUPFILES_XML) ws = o.plates[0].Well['A02'].Sample[3] ws.ImageRef = "Foo" self.assertEqual( ws.node.find(O.qn(O.NS_SPW, "ImageRef")).get("ID"), "Foo")
def test_02_02_get_text(self): o = O.OMEXML(TIFF_XML) ad = o.root_node.find("/".join( [O.qn(o.get_ns('ome'), x) for x in ("Image", "AcquisitionDate")])) self.assertEqual(O.get_text(ad), "2008-02-05T17:24:46")
def test_02_02_get_text(self): o = O.OMEXML(TIFF_XML) ad = o.root_node.find( "/".join([O.qn(o.get_ns('ome'), x) for x in ("Image", "AcquiredDate")])) self.assertEqual(O.get_text(ad), "2008-02-05T17:24:46")
def test_02_01_iter_children(self): o = O.OMEXML(TIFF_XML) for node, expected_tag in zip( o.root_node, (O.qn(o.get_ns("ome"), "Image"), O.qn(o.get_ns("sa"), "StructuredAnnotations"))): self.assertEqual(node.tag, expected_tag)
def test_00_00_init(self): o = O.OMEXML() self.assertEquals(o.root_node.tag, O.qn(o.get_ns("ome"), "OME")) self.assertEquals(o.image_count, 1)
def test_03_02_set_image_count(self): o = O.OMEXML(TIFF_XML) o.image_count = 2 self.assertEqual( len(o.root_node.findall(O.qn(o.get_ns("ome"), "Image"))), 2)
def test_03_02_set_image_count(self): o = O.OMEXML(TIFF_XML) o.image_count = 2 self.assertEqual(len(o.root_node.findall(O.qn(o.get_ns("ome"), "Image"))), 2)
def test_13_12_set_image_ref(self): o = O.OMEXML(self.GROUPFILES_XML) ws = o.plates[0].Well['A02'].Sample[3] ws.ImageRef = "Foo" self.assertEqual(ws.node.find(O.qn(o.get_ns("spw"), "ImageRef")).get("ID"), "Foo")
def test_02_01_iter_children(self): o = O.OMEXML(TIFF_XML) for node, expected_tag in zip( o.root_node, (O.qnome("Image"), O.qn(O.NS_SA, "StructuredAnnotations"))): self.assertEqual(node.tag, expected_tag)
def test_14_02_set_plane_count(self): o = O.OMEXML() pixels = o.image(0).Pixels self.assertTrue(isinstance(pixels, O.OMEXML.Pixels)) pixels.plane_count = 2 self.assertEqual(len(pixels.node.findall(O.qn(o.get_ns('ome'), "Plane"))), 2)
def test_03_04_structured_annotations(self): o = O.OMEXML(TIFF_XML) self.assertEqual(o.structured_annotations.node.tag, O.qn(O.NS_SA, "StructuredAnnotations"))
def test_03_04_structured_annotations(self): o = O.OMEXML(TIFF_XML) self.assertEqual(o.structured_annotations.node.tag, O.qn(o.get_ns("sa"), "StructuredAnnotations"))
def test_05_18_pixels_set_channel_count(self): o = O.OMEXML(TIFF_XML) o.image(0).Pixels.channel_count = 2 self.assertEqual( len(o.image(0).Pixels.node.findall(O.qn(o.get_ns("ome"), "Channel"))), 2)