Merge pull request #39 from HackerMD/acquisition_date

Fix bug that prevented setting values for "AcquiredDate" attribute

Author: LeeKamentsky

bioformats/omexml.py

@@ -36,7 +36,7 @@ def xsd_now():
      xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" 
      xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2013-06 http://www.openmicroscopy.org/Schemas/OME/2012-03/ome.xsd">
   <Image ID="Image:0" Name="default.png">
-    <AcquiredDate>%(DEFAULT_NOW)s</AcquiredDate>
+    <AcquisitionDate>%(DEFAULT_NOW)s</AcquisitionDate>
     <Pixels DimensionOrder="XYCTZ" 
             ID="Pixels:0" 
             SizeC="1" 
@@ -278,7 +278,7 @@ class OMEXML(object):
     derived objects. For instance:
     
     >>> o = OMEXML()
-    >>> print o.image().AcquiredDate
+    >>> print o.image().AcquisitionDate
     
     will get you the date that image # 0 was acquired.
     
@@ -354,7 +354,7 @@ def set_image_count(self, value):
             new_image = self.Image(ElementTree.SubElement(root, qn(self.ns['ome'], "Image")))
             new_image.ID = str(uuid.uuid4())
             new_image.Name = "default.png"
-            new_image.AcquiredDate = xsd_now()
+            new_image.AcquisitionDate = xsd_now()
             new_pixels = self.Pixels(
                 ElementTree.SubElement(new_image.node, qn(self.ns['ome'], "Pixels")))
             new_pixels.ID = str(uuid.uuid4())
@@ -411,20 +411,21 @@ def set_Name(self, value):
             self.node.set("Name", value)
         Name = property(get_Name, set_Name)
 
-        def get_AcquiredDate(self):
+        def get_AcquisitionDate(self):
             '''The date in ISO-8601 format'''
-            acquired_date = self.node.find(qn(self.ns["ome"], "AcquiredDate"))
+            acquired_date = self.node.find(qn(self.ns["ome"], "AcquisitionDate"))
             if acquired_date is None:
                 return None
             return get_text(acquired_date)
 
-        def set_AcquiredDate(self, date):
-            acquired_date = self.node.find(qn(self.ns["ome"], "AcquiredDate"))
+        def set_AcquisitionDate(self, date):
+            acquired_date = self.node.find(qn(self.ns["ome"], "AcquisitionDate"))
             if acquired_date is None:
                 acquired_date = ElementTree.SubElement(
-                    self.node, qn(self.ns, "AcquiredDate"))
+                    self.node, qn(self.ns["ome"], "AcquisitionDate"))
             set_text(acquired_date, date)
-        AcquiredDate = property(get_AcquiredDate, set_AcquiredDate)
+        AcquisitionDate = property(get_AcquisitionDate, set_AcquisitionDate)
+
 
         @property
         def Pixels(self):

bioformats/tests/test_omexml.py

@@ -46,13 +46,13 @@ def test_02_01_iter_children(self):
     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")]))
+            "/".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_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")]))
+            [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")
@@ -99,14 +99,25 @@ def test_04_04_image_set_name(self):
         o.image(0).Name = "Foo"
         self.assertEquals(o.image(0).node.get("Name"), "Foo")
 
-    def test_04_05_image_get_acquired_date(self):
+    def test_04_05_image_get_acquisition_date(self):
         o = O.OMEXML(TIFF_XML)
-        self.assertEqual(o.image(0).AcquiredDate, "2008-02-05T17:24:46")
+        self.assertEqual(o.image(0).AcquisitionDate, "2008-02-05T17:24:46")
 
-    def test_04_06_image_set_acquired_date(self):
+    def test_04_06_image_set_acquisition_date(self):
         o = O.OMEXML(TIFF_XML)
-        o.image(0).AcquiredDate = "2011-12-21T11:04:14.903000"
-        self.assertEqual(o.image(0).AcquiredDate, "2011-12-21T11:04:14.903000")
+        o.image(0).AcquisitionDate = "2011-12-21T11:04:14.903000"
+        self.assertEqual(o.image(0).AcquisitionDate, "2011-12-21T11:04:14.903000")
+        
+    def test_04_07_image_1_acquisition_date(self):
+        # regression test of #38
+        o = O.OMEXML()
+        o.set_image_count(2)
+        date_1 = "2011-12-21T11:04:14.903000"
+        date_2 = "2015-10-13T09:57:00.000000"
+        o.image(0).AcquisitionDate = date_1
+        o.image(1).AcquisitionDate = date_2
+        self.assertEqual(o.image(0).AcquisitionDate, date_1)
+        self.assertEqual(o.image(1).AcquisitionDate, date_2)
 
     def test_05_01_pixels_get_id(self):
         o = O.OMEXML(TIFF_XML)
@@ -736,7 +747,7 @@ def test_14_17_set_position_z(self):
 	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
 	xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2013-06 http://www.openmicroscopy.org/Schemas/OME/2013-06/ome.xsd">
 	<Image ID="Image:0" Name="Channel1-01-A-01.tif">
-		<AcquiredDate>2008-02-05T17:24:46</AcquiredDate>
+		<AcquisitionDate>2008-02-05T17:24:46</AcquisitionDate>
 		<Pixels DimensionOrder="XYCZT" ID="Pixels:0" PhysicalSizeX="352.77777777777777"
 			PhysicalSizeY="352.77777777777777" SizeC="2" SizeT="3" SizeX="640"
 			SizeY="512" SizeZ="1" Type="uint8">