def create_nominal(cls, name, labels):
"""
Creates a nominal attribute.
:param name: the name of the attribute
:type name: str
:param labels: the list of string labels to use
:type labels: list
"""
return Attribute(
javabridge.make_instance("weka/core/Attribute",
"(Ljava/lang/String;Ljava/util/List;)V",
name, javabridge.make_list(labels)))
def test_11_06_select_overlay(self):
display_svc = ij2.get_display_service(self.context)
overlay_svc = ij2.get_overlay_service(self.context)
i, j = np.mgrid[0:15, 0:1900:100]
image = i + j
ds = ij2.create_dataset(self.context, image, "Foo")
display = display_svc.createDisplay("Foo", ds)
d2 = display_svc.createDisplay("Bar", ij2.create_dataset(self.context, image, "Bar"))
mask = np.zeros(i.shape, bool)
islice = slice(2, -3)
jslice = slice(3, -4)
mask[islice, jslice] = True
overlay = ij2.create_overlay(self.context, mask)
overlay_svc.addOverlays(display, J.make_list([overlay]))
ij2.select_overlay(display.o, overlay)
def test_11_06_select_overlay(self):
display_svc = ij2.get_display_service(self.context)
overlay_svc = ij2.get_overlay_service(self.context)
i, j = np.mgrid[0:15, 0:1900:100]
image = i+j
ds = ij2.create_dataset(self.context, image, "Foo")
display = display_svc.createDisplay("Foo", ds)
d2 = display_svc.createDisplay("Bar", ij2.create_dataset(self.context, image, "Bar"))
mask = np.zeros(i.shape, bool)
islice = slice(2,-3)
jslice = slice(3,-4)
mask[islice, jslice] = True
overlay = ij2.create_overlay(self.context, mask)
overlay_svc.addOverlays(display, J.make_list([overlay]))
ij2.select_overlay(display.o, overlay)
def test_11_07_get_selection_bounds(self):
display_svc = ij2.get_display_service(self.context)
overlay_svc = ij2.get_overlay_service(self.context)
i, j = np.mgrid[0:15, 0:1900:100]
image = i+j
ds = ij2.create_dataset(self.context, image, "Foo")
display = display_svc.createDisplay("Foo", ds)
mask = np.zeros(i.shape, bool)
islice = slice(2,-3)
jslice = slice(3,-4)
mask[islice, jslice] = True
overlay = ij2.create_overlay(self.context, mask)
overlay_svc.addOverlays(display, J.make_list([overlay]))
ij2.select_overlay(display.o, overlay)
rect = overlay_svc.getSelectionBounds(display)
self.assertEqual(J.get_field(rect, "x", "D"), 3)
self.assertEqual(J.get_field(rect, "y", "D"), 2)
self.assertEqual(J.get_field(rect, "width", "D"), 11)
self.assertEqual(J.get_field(rect, "height", "D"), 9)
def test_09_09_check_overlay(self):
svc = ij2.get_display_service(self.context)
r = np.random.RandomState()
i, j = np.mgrid[0:11, 0:1300:100]
image = i+j
ds = ij2.create_dataset(self.context, image, "Foo")
display = svc.createDisplay("Foo", ds)
mask = np.zeros(image.shape, bool)
mask[2:-1, 3:-4] = 1
overlay = ij2.create_overlay(self.context, mask)
ij2.get_overlay_service(self.context).addOverlays(
display.o, J.make_list([overlay]))
ij2.select_overlay(display.o, overlay)
self.run_command("net.imagej.plugins.commands.imglib.CropImage",
dict(display=display), {})
dataset = ij2.wrap_dataset(display.getActiveView().getData())
image_out = dataset.get_pixel_data()
self.assertSequenceEqual(image_out.shape, [7, 5])
np.testing.assert_array_equal(image[2:-2, 3:-5], image_out)
def test_11_07_get_selection_bounds(self):
display_svc = ij2.get_display_service(self.context)
overlay_svc = ij2.get_overlay_service(self.context)
i, j = np.mgrid[0:15, 0:1900:100]
image = i + j
ds = ij2.create_dataset(self.context, image, "Foo")
display = display_svc.createDisplay("Foo", ds)
mask = np.zeros(i.shape, bool)
islice = slice(2, -3)
jslice = slice(3, -4)
mask[islice, jslice] = True
overlay = ij2.create_overlay(self.context, mask)
overlay_svc.addOverlays(display, J.make_list([overlay]))
ij2.select_overlay(display.o, overlay)
rect = overlay_svc.getSelectionBounds(display)
self.assertEqual(J.get_field(rect, "x", "D"), 3)
self.assertEqual(J.get_field(rect, "y", "D"), 2)
self.assertEqual(J.get_field(rect, "width", "D"), 11)
self.assertEqual(J.get_field(rect, "height", "D"), 9)
def test_09_09_check_overlay(self):
svc = ij2.get_display_service(self.context)
r = np.random.RandomState()
i, j = np.mgrid[0:11, 0:1300:100]
image = i + j
ds = ij2.create_dataset(self.context, image, "Foo")
display = svc.createDisplay("Foo", ds)
mask = np.zeros(image.shape, bool)
mask[2:-1, 3:-4] = 1
overlay = ij2.create_overlay(self.context, mask)
ij2.get_overlay_service(self.context).addOverlays(
display.o, J.make_list([overlay]))
ij2.select_overlay(display.o, overlay)
self.run_command("net.imagej.plugins.commands.imglib.CropImage",
dict(display=display), {})
dataset = ij2.wrap_dataset(display.getActiveView().getData())
image_out = dataset.get_pixel_data()
self.assertSequenceEqual(image_out.shape, [7, 5])
np.testing.assert_array_equal(image[2:-2, 3:-5], image_out)
def create_instances(cls, name, atts, capacity):
"""
Creates a new Instances.
:param name: the relation name
:type name: str
:param atts: the list of attributes to use for the dataset
:type atts: list of Attribute
:param capacity: how many data rows to reserve initially (see compactify)
:type capacity: int
:return: the dataset
:rtype: Instances
"""
attributes = []
for att in atts:
attributes.append(att.jobject)
return Instances(
javabridge.make_instance(
"weka/core/Instances", "(Ljava/lang/String;Ljava/util/ArrayList;I)V",
name, javabridge.make_list(attributes), capacity))
def create_instances(cls, name, atts, capacity):
"""
Creates a new Instances.
:param name: the relation name
:type name: str
:param atts: the list of attributes to use for the dataset
:type atts: list of Attribute
:param capacity: how many data rows to reserve initially (see compactify)
:type capacity: int
:return: the dataset
:rtype: Instances
"""
attributes = []
for att in atts:
attributes.append(att.jobject)
return Instances(
javabridge.make_instance(
"weka/core/Instances",
"(Ljava/lang/String;Ljava/util/ArrayList;I)V", name,
javabridge.make_list(attributes), capacity))
def test_06_01_get_mask_data(self):
# Get the overlay data from a display
#
display_svc = ij2.get_display_service(self.context)
overlay_svc = ij2.get_overlay_service(self.context)
image = np.zeros((30, 30))
ds = ij2.create_dataset(self.context, image, "Foo")
display = display_svc.createDisplay("Foo", ds)
d2 = display_svc.createDisplay("Bar", ij2.create_dataset(self.context, image, "Bar"))
overlay = J.run_script(
"""var o = new Packages.net.imagej.overlay.RectangleOverlay(context.getContext());
o.setOrigin(5, 0);
o.setOrigin(3, 1);
o.setExtent(6, 0);
o.setExtent(7, 1);
o;""", dict(context=self.context))
overlay_svc.addOverlays(display, J.make_list([overlay]))
ij2.select_overlay(display.o, overlay)
mask = ij2.create_mask(display)
i, j = np.mgrid[0:mask.shape[0], 0:mask.shape[1]]
np.testing.assert_equal(mask, (j >= 5) & (j < 11) & (i >= 3) & (i < 10))
def test_06_01_get_mask_data(self):
# Get the overlay data from a display
#
display_svc = ij2.get_display_service(self.context)
overlay_svc = ij2.get_overlay_service(self.context)
image = np.zeros((30, 30))
ds = ij2.create_dataset(self.context, image, "Foo")
display = display_svc.createDisplay("Foo", ds)
d2 = display_svc.createDisplay("Bar", ij2.create_dataset(self.context, image, "Bar"))
overlay = J.run_script(
"""var o = new Packages.net.imagej.overlay.RectangleOverlay(context.getContext());
o.setOrigin(5, 0);
o.setOrigin(3, 1);
o.setExtent(6, 0);
o.setExtent(7, 1);
o;""", dict(context=self.context))
overlay_svc.addOverlays(display, J.make_list([overlay]))
ij2.select_overlay(display.o, overlay)
mask = ij2.create_mask(display)
i, j = np.mgrid[0:mask.shape[0], 0:mask.shape[1]]
np.testing.assert_equal(mask, (j >= 5) & (j < 11) & (i >= 3) & (i < 10))
def __init__(self):
if service_classes is None:
classes = None
ctxt_fn = J.run_script(
"""new java.util.concurrent.Callable() {
call: function() {
return new Packages.net.imagej.ImageJ(false);
}
}""")
else:
classes = [
J.class_for_name(x)
for x in service_classes or REQUIRED_SERVICES]
classes = J.make_list(classes)
ctxt_fn = J.run_script(
"""new java.util.concurrent.Callable() {
call: function() {
return new Packages.net.imagej.ImageJ(classes);
}
}""", dict(classes = classes.o))
self.o = J.call(ctxt_fn, 'call', '()Ljava/lang/Object;')
def __init__(self):
if service_classes is None:
classes = None
ctxt_fn = J.run_script(
"""new java.util.concurrent.Callable() {
call: function() {
return new Packages.net.imagej.ImageJ(false);
}
}""")
else:
classes = [
J.class_for_name(x)
for x in service_classes or REQUIRED_SERVICES]
classes = J.make_list(classes)
ctxt_fn = J.run_script(
"""new java.util.concurrent.Callable() {
call: function() {
return new Packages.net.imagej.ImageJ(classes);
}
}""", dict(classes = classes.o))
self.o = J.execute_future_in_main_thread(
J.make_future_task(ctxt_fn))
def __init__(self):
if service_classes is None:
classes = None
ctxt_fn = J.run_script("""new java.util.concurrent.Callable() {
call: function() {
return new Packages.net.imagej.ImageJ(false);
}
}""")
else:
classes = [
J.class_for_name(x)
for x in service_classes or REQUIRED_SERVICES
]
classes = J.make_list(classes)
ctxt_fn = J.run_script(
"""new java.util.concurrent.Callable() {
call: function() {
return new Packages.net.imagej.ImageJ(classes);
}
}""", dict(classes=classes.o))
self.o = J.execute_future_in_main_thread(
J.make_future_task(ctxt_fn))
def test_08_14_addAllI(self):
l = javabridge.make_list(["Foo", "Bar"])
l.addAllI(1, javabridge.make_list(["Baz"]))
self.assertSequenceEqual(l, ["Foo", "Baz", "Bar"])
def test_08_12_make_list(self):
l = javabridge.make_list(["Foo", "Bar"])
self.assertSequenceEqual(l, ["Foo", "Bar"])
self.assertTrue(hasattr(l, "addI"))
def test_08_21__delitem__(self):
l = javabridge.make_list(["Foo", "Bar", "Baz"])
del l[1]
self.assertSequenceEqual(l, ["Foo", "Baz"])
def fn():
list(javabridge.iterate_java(javabridge.make_list(range(10)).o))
def test_08_19__getitem__(self):
l = javabridge.make_list(["Foo", "Bar", "Baz", "Hello", "World"])
self.assertEqual(l[1], "Bar")
self.assertEqual(l[-2], "Hello")
self.assertSequenceEqual(l[1:3], ["Bar", "Baz"])
self.assertSequenceEqual(l[::3], ["Foo", "Hello"])
def test_08_20__setitem__(self):
l = javabridge.make_list(["Foo", "Bar"])
l[1] = "Baz"
self.assertEqual(l.get(1), "Baz")
def test_08_17_set(self):
l = javabridge.make_list(["Foo", "Bar"])
l.set(1, "Baz")
self.assertEqual(l.get(1), "Baz")
def test_08_18_subList(self):
l = javabridge.make_list(["Foo", "Bar", "Baz", "Hello", "World"])
self.assertSequenceEqual(l.subList(1, 3), ["Bar", "Baz"])
def create_nominal(cls, name, labels):
"""
Creates a nominal attribute.
:param name: the name of the attribute
:type name: str
:param labels: the list of string labels to use
:type labels: list
"""
return Attribute(
javabridge.make_instance(
"weka/core/Attribute", "(Ljava/lang/String;Ljava/util/List;)V", name, javabridge.make_list(labels)))
def test_08_21__delitem__(self):
l = javabridge.make_list(["Foo", "Bar", "Baz"])
del l[1]
self.assertSequenceEqual(l, ["Foo", "Baz"])
def test_08_19__getitem__(self):
l = javabridge.make_list(["Foo", "Bar", "Baz", "Hello", "World"])
self.assertEqual(l[1], "Bar")
self.assertEqual(l[-2], "Hello")
self.assertSequenceEqual(l[1:3], ["Bar", "Baz"])
self.assertSequenceEqual(l[::3], ["Foo", "Hello"])
def test_08_17_set(self):
l = javabridge.make_list(["Foo", "Bar"])
l.set(1, "Baz")
self.assertEqual(l.get(1), "Baz")
def test_08_15_indexOf(self):
l = javabridge.make_list(["Foo", "Bar"])
self.assertEqual(l.indexOf("Bar"), 1)
self.assertEqual(l.lastIndexOf("Foo"), 0)
def test_08_16_get(self):
l = javabridge.make_list(["Foo", "Bar"])
self.assertEqual(l.get(1), "Bar")
def test_08_12_make_list(self):
l = javabridge.make_list(["Foo", "Bar"])
self.assertSequenceEqual(l, ["Foo", "Bar"])
self.assertTrue(hasattr(l, "addI"))
def test_08_18_subList(self):
l = javabridge.make_list(["Foo", "Bar", "Baz", "Hello", "World"])
self.assertSequenceEqual(l.subList(1, 3), ["Bar", "Baz"])
def test_08_14_addAllI(self):
l = javabridge.make_list(["Foo", "Bar"])
l.addAllI(1, javabridge.make_list(["Baz"]))
self.assertSequenceEqual(l, ["Foo", "Baz", "Bar"])
def test_08_20__setitem__(self):
l = javabridge.make_list(["Foo", "Bar"])
l[1] = "Baz"
self.assertEqual(l.get(1), "Baz")
def test_08_15_indexOf(self):
l = javabridge.make_list(["Foo", "Bar"])
self.assertEqual(l.indexOf("Bar"), 1)
self.assertEqual(l.lastIndexOf("Foo"), 0)
def fn():
list(javabridge.iterate_java(javabridge.make_list(range(10)).o))
def test_08_16_get(self):
l = javabridge.make_list(["Foo", "Bar"])
self.assertEqual(l.get(1), "Bar")
