def test_fromCartesian(self):
"""MageList fromCartesian() should return new list with ACG coordinates
"""
point = MagePoint([.1,.2,.3])
m = MageList([point]*5,Color='green')
res = m.toCartesian().fromCartesian()
self.assertEqual(str(m),str(res))
def test_fromCartesian(self):
"""MageList fromCartesian() should return new list with ACG coordinates
"""
point = MagePoint([.1, .2, .3])
m = MageList([point] * 5, Color='green')
res = m.toCartesian().fromCartesian()
self.assertEqual(str(m), str(res))
def test_toCartesian(self):
"""MageList toCartesian should return new list"""
m = MageList([self.null],Color='green')
res = m.toCartesian()
self.assertEqual(len(m), len(res))
self.assertEqual(m.Color,res.Color)
self.assertEqual(res[0].Coordinates,[1,1,1])
m.Color='red'
self.assertEqual(res.Color,'green')
m = MageList([self.properties])
self.assertRaises(ValueError,m.toCartesian)
def test_toArray_coords_only(self):
"""MageList toArray should return the correct array"""
m = MageList(self.empty_list)
self.assertEqual(m.toArray(include_radius=False), array(()))
m = MageList(self.first_list, Radius=0.3)
self.assertEqual(m.toArray(include_radius=False), array([[0, 0, 0], [2.0, 4.0, 6.0]]))
m = MageList(self.radii)
self.assertEqual(m.toArray(include_radius=False), array([[2, 2, 2], [3, 3, 3]]))
m = MageList(self.radii, Radius=0.4)
self.assertEqual(m.toArray(include_radius=False), array([[2, 2, 2], [3, 3, 3]]))
m = MageList(self.single_list) # radius = None
self.assertEqual(m.toArray(include_radius=False), array([[1, 1, 1]]))
def test_init(self):
"""MageList should init correctly with data"""
m = MageList(self.minimal_list)
self.assertEqual(str(m), "@dotlist\n" + str(self.null))
m = MageList(self.multi_list,
'x',
Off=True,
Color='green',
NoButton=True)
self.assertEqual(str(m), "@dotlist {x} off nobutton color=green\n" + \
'\n'.join(10 * [str(self.properties)]))
m = MageList(self.first_list,NoButton=True,Color='red', \
Style='vector', Radius=0.03, Width=3, Label='test')
self.assertEqual(str(m), "@vectorlist {test} nobutton color=red " + \
"radius=0.03 width=3\n" + str(self.null) + '\n' + str(self.properties))
def test_toArray_radii(self):
"""MageList toArray should return the correct array"""
m = MageList(self.empty_list)
self.assertEqual(m.toArray(),array(()))
m = MageList(self.first_list,Radius=.3)
self.assertEqual(m.toArray(),array([[0,0,0,0.3],[2.0,4.0,6.0,0.3]]))
m = MageList(self.radii)
self.assertEqual(m.toArray(), array([[2,2,2,.1],[3,3,3,.5]]))
m = MageList(self.radii,Radius=.4)
self.assertEqual(m.toArray(), array([[2,2,2,.1],[3,3,3,.5]]))
m = MageList(self.single_list) #radius = None
self.assertRaises(ValueError,m.toArray)
def setUp(self):
self.point = MagePoint([0, 0, 0], 'x')
self.ml = MageList([self.point], Label='y', Color='green')
self.mg1 = MageGroup([self.ml], Label='z')
self.mg2 = MageGroup([self.ml, self.ml], Label='b')
self.kin = Kinemage(1)
self.kin.Groups = [self.mg1, self.mg2]
def test_fromCartesian(self):
"""MageGroup fromCartesian should return a new MageGroup"""
point = MagePoint([.1, .2, .3])
l = MageList([point] * 5, Color='red')
m = MageGroup([l], Radius=0.02, Subgroup=True)
mg = MageGroup([m])
res = mg.toCartesian().fromCartesian()
self.assertEqual(str(mg), str(res))
def test_iterPoints(self):
"""MageList iterPoints should yield all points in self"""
m = MageList(self.single_list)
for point in m.iterPoints():
assert isinstance(point, MagePoint)
self.assertEqual(len(list(m.iterPoints())), 1)
m = MageList(self.multi_list)
for point in m.iterPoints():
assert isinstance(point, MagePoint)
self.assertEqual(len(list(m.iterPoints())), 10)
def test_fromCartesian(self):
"""Kinemage fromCartesian should return Kinemage with A,C,G(,U) coords
"""
point = MagePoint([.1, .2, .3])
l = MageList([point] * 5, Color='red')
m1 = MageGroup([l], Radius=0.02, Subgroup=True)
m2 = MageGroup([l], Radius=0.02)
mg = MageGroup([m1])
k = Kinemage(Count=1, Groups=[mg, m2])
res = k.toCartesian().fromCartesian()
self.assertEqual(str(k), str(res))
def setUp(self):
"""Define some standard lists and groups."""
self.p1 = MagePoint([0, 1, 0], Color='green', Label='x')
self.p0 = MagePoint([0, 0, 0])
self.min_list = MageList([self.p0] * 2, 'y')
self.max_list = MageList([self.p1]*5,'z',Color='blue',Off=True, \
Style='ball')
self.min_group = MageGroup([self.min_list], Label="min_group")
self.max_group = MageGroup([self.min_list, self.max_list],
Color='red',
Label="max_group",
Style='dot')
self.nested = MageGroup([self.min_group, self.max_group],
Label='nest',
Color='orange',
Radius=0.3,
Style='vector')
self.empty = MageGroup(Label='empty',
Color='orange',
NoButton=True,
Style='vector',
RecessiveOn=False)
def MageListFromString(line):
"""Returns a new MageList, created from a string representation"""
result = MageList()
trans = {'off':('Off',True),\
'on':('Off',False),\
'color':'Color',\
'radius':'Radius',\
'nobutton':('NoButton',True),\
'angle':'Angle',\
'width':'Width',\
'face':'Face',\
'font':'Font',\
'size':'Size'}
line = re.sub('=\s*','=',line)
label = extract_delimited(line, '{', '}')
if label is not None:
pieces = line.replace('{'+label+'}', '').split()
else:
pieces = line.split()
style = pieces[0].strip('@')[:-4] #take off the 'list' part
if style in MageList.KnownStyles:
result.Style = style
else:
raise ValueError,"Unknown style: %s"%(style)
result.Label = label
#process all optional pieces
for piece in pieces[1:]:
try:
key,value = [item.strip() for item in piece.split('=')]
key = trans[key]
except ValueError: #unpack list of wrong size
key,value = trans[piece][0],trans[piece][1]
#KeyError will be raised in case of an unkown key
setattr(result,key,value)
return result
def test_iterPoints(self):
"""MageList iterPoints should yield all points in self"""
m = MageList(self.single_list)
for point in m.iterPoints():
assert isinstance(point,MagePoint)
self.assertEqual(len(list(m.iterPoints())),1)
m = MageList(self.multi_list)
for point in m.iterPoints():
assert isinstance(point,MagePoint)
self.assertEqual(len(list(m.iterPoints())),10)
def test_toCartesian(self):
"""MageList toCartesian should return new list"""
m = MageList([self.null], Color='green')
res = m.toCartesian()
self.assertEqual(len(m), len(res))
self.assertEqual(m.Color, res.Color)
self.assertEqual(res[0].Coordinates, [1, 1, 1])
m.Color = 'red'
self.assertEqual(res.Color, 'green')
m = MageList([self.properties])
self.assertRaises(ValueError, m.toCartesian)
def test_toArray_coords_only(self):
"""MageList toArray should return the correct array"""
m = MageList(self.empty_list)
self.assertEqual(m.toArray(include_radius=False), array(()))
m = MageList(self.first_list, Radius=.3)
self.assertEqual(m.toArray(include_radius=False),
array([[0, 0, 0], [2.0, 4.0, 6.0]]))
m = MageList(self.radii)
self.assertEqual(m.toArray(include_radius=False),
array([[2, 2, 2], [3, 3, 3]]))
m = MageList(self.radii, Radius=.4)
self.assertEqual(m.toArray(include_radius=False),
array([[2, 2, 2], [3, 3, 3]]))
m = MageList(self.single_list) #radius = None
self.assertEqual(m.toArray(include_radius=False), array([[1, 1, 1]]))
def test_init_empty(self):
"""MageList should init correctly with no data"""
m = MageList()
self.assertEqual(str(m), "@dotlist")
m = MageList(self.empty_list)
self.assertEqual(str(m), "@dotlist")
def test_toArray_radii(self):
"""MageList toArray should return the correct array"""
m = MageList(self.empty_list)
self.assertEqual(m.toArray(), array(()))
m = MageList(self.first_list, Radius=.3)
self.assertEqual(m.toArray(),
array([[0, 0, 0, 0.3], [2.0, 4.0, 6.0, 0.3]]))
m = MageList(self.radii)
self.assertEqual(m.toArray(), array([[2, 2, 2, .1], [3, 3, 3, .5]]))
m = MageList(self.radii, Radius=.4)
self.assertEqual(m.toArray(), array([[2, 2, 2, .1], [3, 3, 3, .5]]))
m = MageList(self.single_list) #radius = None
self.assertRaises(ValueError, m.toArray)
