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_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_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)
