class JSpiralGenerator(JavaIteratorWrapper):
"""
Create a SpiralGenerator and wrap the points into java Point objects
"""
def __init__(self, names, units, centre, radius, scale=1.0, alternate_direction=False):
super(JSpiralGenerator, self).__init__()
self.names = names
self.generator = SpiralGenerator(names, units, centre, radius, scale, alternate_direction)
logging.debug(self.generator.to_dict())
def _iterator(self):
x_name = self.names[0]
y_name = self.names[1]
for point in self.generator.iterator():
index = point.indexes[0]
x_position = point.positions[x_name]
y_position = point.positions[y_name]
java_point = Point(x_name, index, x_position,
y_name, index, y_position, False)
# Set is2D=False
yield java_point
class JSpiralGenerator(JavaIteratorWrapper):
"""
Create a SpiralGenerator and wrap the points into java Point objects
"""
def __init__(self, names, units, centre, radius, scale=1.0, alternate_direction=False):
super(JSpiralGenerator, self).__init__()
self.names = names
self.generator = SpiralGenerator(names, units, centre, radius, scale, alternate_direction)
logging.debug(self.generator.to_dict())
def _iterator(self):
x_name = self.names[0]
y_name = self.names[1]
for point in self.generator.iterator():
index = point.indexes[0]
x_position = point.positions[x_name]
y_position = point.positions[y_name]
java_point = Point(x_name, index, x_position,
y_name, index, y_position, False)
# Set is2D=False
yield java_point
def test_double_spiral_scan(self):
line1 = LineGenerator(["l1"], "mm", -1, 2, 5)
spiral_s = SpiralGenerator(["s1", "s2"], "mm", [1, 2], 5, 2.5, True)
spiral_t = SpiralGenerator(["t1", "t2"], "mm", [0, 0], 5, 2.5, True)
line2 = LineGenerator(["l2"], "mm", -1, 2, 5, True)
r = CircularROI([0, 0], 1)
e1 = ROIExcluder([r], ["s1", "l1"])
e2 = ROIExcluder([r], ["l2", "t1"])
g = CompoundGenerator([line1, spiral_s, spiral_t, line2], [e1, e2], [])
g.prepare()
points = []
l1s = []
tl2 = []
s_f = True
for l1 in line1.positions["l1"]:
sp = zip(spiral_s.positions['s1'], spiral_s.positions['s2'])
sp = sp if s_f else list(sp)[::-1]
s_f = not s_f
l1s += [(s1, s2, l1) for (s1, s2) in sp]
l2_f = True
for (t1, t2) in zip(spiral_t.positions['t1'], spiral_t.positions['t2']):
l2p = line2.positions['l2'] if l2_f else line2.positions['l2'][::-1]
l2pu = line2.bounds['l2'][1:len(line2.positions['l2'])+1]
l2pl = line2.bounds['l2'][0:len(line2.positions['l2'])]
if not l2_f:
l2pu, l2pl = l2pl[::-1], l2pu[::-1]
l2_f = not l2_f
tl2 += [(l2, l2u, l2l, t1, t2) for (l2, l2u, l2l) in
zip(l2p, l2pu, l2pl) if l2*l2 + t1*t1 <= 1]
t_f = True
for (s1, s2, l1) in l1s:
inner = tl2 if t_f else tl2[::-1]
t_f = not t_f
points += [(l2, l2u, l2l, t1, t2, s1, s2, l1)
for (l2, l2u, l2l, t1, t2) in inner if s1*s1 + l1*l1 <= 1]
l1s_original = l1s
l1s = [(s1, s2, l1) for (s1, s2, l1) in l1s if s1*s1 + l1*l1 <= 1]
expected = [{"l2":l2, "t1":t1, "t2":t2, "s1":s1, "s2":s2, "l1":l1}
for (l2, l2u, l2l, t1, t2, s1, s2, l1) in points]
expected_idx = []
t_f = (l1s_original.index(l1s[0])) % 2 == 0 # t_f is False
for d1 in range_(len(l1s)):
expected_idx += [[d1, d2] for d2 in (range_(len(tl2)) if t_f else
range_(len(tl2) - 1, -1, -1))]
t_f = not t_f
expected_l2_lower = [l2l for (l2, l2u, l2l, t1, t2, s1, s2, l1) in points]
expected_l2_upper = [l2u for (l2, l2u, l2l, t1, t2, s1, s2, l1) in points]
gpoints = list(g.iterator())
self.assertEqual(expected, [p.positions for p in gpoints])
self.assertEqual(expected_idx, [p.indexes for p in gpoints])
self.assertEqual(expected_l2_lower, [p.lower["l2"] for p in gpoints])
self.assertEqual(expected_l2_upper, [p.upper["l2"] for p in gpoints])
def test_three_dim_middle_alternates(self):
tg = LineGenerator("t", "mm", 1, 5, 5)
zg = LineGenerator("z", "mm", -1, 3, 5, True)
spiral = SpiralGenerator(["s1", "s2"], "mm", [1, 1], 2, 1, True)
yg = LineGenerator("y", "mm", 0, 4, 5)
xg = LineGenerator("x", "mm", 0, 4, 5)
r1 = CircularROI([0, 0], 1)
e1 = ROIExcluder([r1], ["s1", "z"])
e2 = ROIExcluder([r1], ["y", "x"])
g = CompoundGenerator([tg, zg, spiral, yg, xg], [e2, e1], [])
g.prepare()
it = 0
iz = 0
iy = 0
ix = 0
tzs = []
points = []
for t in range_(1, 6):
for z in (range_(-1, 4) if it % 2 == 0 else range_(3, -2, -1)):
s1p = spiral.positions["s1"] if iz % 2 == 0 else spiral.positions["s1"][::-1]
s2p = spiral.positions["s2"] if iz % 2 == 0 else spiral.positions["s2"][::-1]
points += [(x, y, s1, s2, z, t) for (s1, s2) in zip(s1p, s2p)
for y in range(0, 5) for x in range(0, 5)
if s1*s1 + z*z <= 1 and y*y + x*x <= 1]
iz += 1
it += 1
expected = [{"x":float(x), "y":float(y), "s1":s1, "s2":s2, "z":float(z), "t":float(t)}
for (x, y, s1, s2, z, t) in points]
actual = [p.positions for p in list(g.iterator())]
for e, a in zip(expected, actual):
self.assertEqual(e, a)
def test_excluder_spread_axes(self):
sp = SpiralGenerator(["s1", "s2"], ["mm", "mm"], centre=[0, 0], radius=1, scale=0.5, alternate=True)
y = LineGenerator("y", "mm", 0, 1, 3, True)
z = LineGenerator("z", "mm", -2, 3, 6, True)
e = ROIExcluder([CircularROI([0., 0.], 1.0)], ["s1", "z"])
g = CompoundGenerator([z, y, sp], [e], [])
g.prepare()
s1_pos, s2_pos = sp.positions["s1"], sp.positions["s2"]
s1_pos = np.tile(np.append(s1_pos, s1_pos[::-1]), 9)
s2_pos = np.tile(np.append(s2_pos, s2_pos[::-1]), 9)
y_pos = np.tile(np.repeat(np.array([0, 0.5, 1.0, 1.0, 0.5, 0]), sp.size), 3)
z_pos = np.repeat(np.array([-2, -1, 0, 1, 2, 3]), sp.size * 3)
mask_func = lambda ps1, pz: ps1**2 + pz**2 <= 1
mask = mask_func(s1_pos, z_pos)
expected_s1 = s1_pos[mask]
expected_s2 = s2_pos[mask]
expected_y = y_pos[mask]
expected_z = z_pos[mask]
expected_positions = [{'s1':ps1, 's2':ps2, 'y':py, 'z':pz}
for (ps1, ps2, py, pz) in zip(expected_s1, expected_s2, expected_y, expected_z)]
positions = [point.positions for point in list(g.iterator())]
self.assertEqual(positions, expected_positions)
def test_line_spiral(self):
expected = [
{
'y': -0.3211855677650875,
'x': 0.23663214944574582,
'z': 0.0
},
{
'y': -0.25037538922751695,
'x': -0.6440318266552169,
'z': 0.0
},
{
'y': 0.6946549630820702,
'x': -0.5596688286164636,
'z': 0.0
},
{
'y': 0.6946549630820702,
'x': -0.5596688286164636,
'z': 2.0
},
{
'y': -0.25037538922751695,
'x': -0.6440318266552169,
'z': 2.0
},
{
'y': -0.3211855677650875,
'x': 0.23663214944574582,
'z': 2.0
},
{
'y': -0.3211855677650875,
'x': 0.23663214944574582,
'z': 4.0
},
{
'y': -0.25037538922751695,
'x': -0.6440318266552169,
'z': 4.0
},
{
'y': 0.6946549630820702,
'x': -0.5596688286164636,
'z': 4.0
},
]
z = LineGenerator("z", "mm", 0.0, 4.0, 3)
spiral = SpiralGenerator(['x', 'y'],
"mm", [0.0, 0.0],
0.8,
alternate=True)
g = CompoundGenerator([z, spiral], [], [])
g.prepare()
self.assertEqual(g.axes, ["z", "x", "y"])
points = list(g.iterator())
self.assertEqual(len(expected), len(points))
for i, p in enumerate(points):
self.assertEqual(expected[i], p.positions)
def test_get_point_large_scan(self):
s = SpiralGenerator(["x", "y"], "mm", [0, 0], 6, 1) #114 points
z = LineGenerator("z", "mm", 0, 1, 100)
w = LineGenerator("w", "mm", 0, 1, 5)
t = LineGenerator("t", "mm", 0, 1, 5)
rad1 = 2.8
r1 = CircularROI([1., 1.], rad1)
e1 = ROIExcluder([r1], ["x", "y"])
rad2 = 2
r2 = CircularROI([0.5, 0.5], rad2)
e2 = ROIExcluder([r2], ["y", "z"])
rad3 = 0.5
r3 = CircularROI([0.5, 0.5], rad3)
e3 = ROIExcluder([r3], ["w", "t"])
g = CompoundGenerator([t, w, z, s], [e1, e2, e3], [])
g.prepare()
spiral = [(x, y) for (x, y) in zip(s.positions["x"], s.positions["y"])]
zwt = [(z/99., w/4., t/4.) for t in range_(0, 5)
for w in range_(0, 5)
for z in range_(0, 100)]
expected = [(x, y, z, w, t) for (z, w, t) in zwt for (x, y) in spiral]
expected = [{"x":x, "y":y, "z":z, "w":w, "t":t}
for (x,y,z,w,t) in expected if
(x-1)*(x-1) + (y-1)*(y-1) <= rad1*rad1 and
(y-0.5)*(y-0.5) + (z-0.5)*(z-0.5) <= rad2*rad2 and
(w-0.5)*(w-0.5) + (t-0.5)*(t-0.5) <= rad3*rad3]
points = [g.get_point(n) for n in range_(0, g.size)]
pos = [p.positions for p in points]
# assertEqual on a sequence of dicts is *really* slow
for (e, p) in zip(expected, pos):
self.assertEquals(e.keys(), p.keys())
for k in e.keys():
self.assertAlmostEqual(e[k], p[k])
def __init__(self, names, units, centre, radius, scale=1.0, alternate_direction=False):
super(JSpiralGenerator, self).__init__()
self.names = names
spiral_gen = SpiralGenerator(names, units, centre, radius, scale, alternate_direction)
self.generator = CompoundGenerator([spiral_gen], [], [])
self.generator.prepare()
logging.debug(self.generator.to_dict())
def spiral_rectangle_check():
spiral = SpiralGenerator(['x', 'y'], ["mm", "mm"], [0.0, 0.0], 10.0)
rectangle = ROIExcluder([RectangularROI([0.0, 0.0], 10.0, 10.0)],
['x', 'y'])
gen = CompoundGenerator([spiral], [rectangle], [])
plot_generator(gen, rectangle)
def test_horrible_scan(self):
lissajous = LissajousGenerator(["j1", "j2"], "mm", [-0.5, 0.7],
[2, 3.5], 7, 100)
line2 = LineGenerator(["l2"], "mm", -3, 3, 7, True)
line1 = LineGenerator(["l1"], "mm", -1, 2, 5, True)
spiral = SpiralGenerator(["s1", "s2"], "mm", [1, 2], 5, 2.5, True)
r1 = CircularROI([1, 1], 2)
r2 = CircularROI([-1, -1], 4)
r3 = CircularROI([1, 1], 2)
e1 = ROIExcluder([r1], ["j1", "l2"])
e2 = ROIExcluder([r2], ["s2", "l1"])
e3 = ROIExcluder([r3], ["s1", "s2"])
g = CompoundGenerator([lissajous, line2, line1, spiral], [e1, e2, e3],
[])
g.prepare()
l2_f = True
l1_f = True
s_f = True
points = []
for (j1, j2) in zip(lissajous.positions["j1"],
lissajous.positions["j2"]):
l2p = line2.positions["l2"] if l2_f else line2.positions["l2"][::-1]
l2_f = not l2_f
for l2 in l2p:
l1p = line1.positions["l1"] if l1_f else line1.positions[
"l1"][::-1]
l1_f = not l1_f
for l1 in l1p:
sp = zip(spiral.positions["s1"], spiral.positions["s2"]) if s_f \
else zip(spiral.positions["s1"][::-1], spiral.positions["s2"][::-1])
s_f = not s_f
for (s1, s2) in sp:
points.append((s1, s2, l1, l2, j1, j2))
self.assertEqual(
lissajous.size * line2.size * line1.size * spiral.size,
len(points))
points = [(s1, s2, l1, l2, j1, j2)
for (s1, s2, l1, l2, j1, j2) in points
if (j1 - 1)**2 + (l2 - 1)**2 <= 4 and (s2 + 1)**2 +
(l1 + 1)**2 <= 16 and (s1 - 1)**2 + (s2 - 1)**2 <= 4]
self.assertEqual(len(points), g.size)
generated_points = list(g.iterator())
self.assertEqual(len(points), len(generated_points))
actual = [p.positions for p in generated_points]
expected = [{
"j1": j1,
"j2": j2,
"l2": l2,
"l1": l1,
"s1": s1,
"s2": s2
} for (s1, s2, l1, l2, j1, j2) in points]
for e, a in zip(expected, actual):
self.assertEqual(e, a)
self.assertEqual((181, 10), g.shape)
def test_simple_mask_alternating_spiral(self):
z = LineGenerator("z", "mm", 0.0, 4.0, 5)
spiral = SpiralGenerator(['x', 'y'], "mm", [0.0, 0.0], 3, alternate=True) #29 points
r = RectangularROI([-2, -2], 3, 4)
e = ROIExcluder([r], ["x", "y"])
g = CompoundGenerator([z, spiral], [e], [])
g.prepare()
p = list(zip(spiral.positions['x'], spiral.positions['y']))
expected = [x >= -2 and x < 1 and y >= -2 and y < 2 for (x, y) in p]
expected_r = [x >= -2 and x < 1 and y >= -2 and y < 2 for (x, y) in p[::-1]]
actual = g.dimensions[1].mask.tolist()
self.assertEqual(expected, actual)
def test_double_mask_spiral(self):
zgen = LineGenerator("z", "mm", 0.0, 4.0, 5)
spiral = SpiralGenerator(['x', 'y'], "mm", [0.0, 0.0], 3) #29 points
r1 = RectangularROI([-2, -2], 4, 3)
r2 = RectangularROI([-2, 0], 4, 3)
e1 = ROIExcluder([r1], ["y", "x"])
e2 = ROIExcluder([r2], ["y", "z"])
g = CompoundGenerator([zgen, spiral], [e1, e2], [])
g.prepare()
p = list(zip(spiral.positions['x'], spiral.positions['y']))
p = [(x, y, z) for z in range_(0, 5) for (x, y) in p]
expected = [x >= -2 and x <= 1 and y >= -2 and y <= 2
and z >= 0 and z <= 3 for (x, y, z) in p]
actual = g.dimensions[0].mask.tolist()
self.assertEqual(expected, actual)
def test_from_dict(self):
_dict = dict()
_dict['axes'] = ["x", "y"]
_dict['units'] = ["mm", "cm"]
_dict['centre'] = [0.0, 0.0]
_dict['radius'] = 1.4
_dict['scale'] = 1
_dict['alternate'] = True
units_dict = dict()
units_dict['x'] = "mm"
units_dict['y'] = "cm"
gen = SpiralGenerator.from_dict(_dict)
self.assertEqual(["x", "y"], gen.axes)
self.assertEqual(units_dict, gen.axis_units())
self.assertEqual([0.0, 0.0], gen.centre)
self.assertEqual(1.4, gen.radius)
self.assertEqual(1, gen.scale)
def test_200_million_time_constraint(self):
start_time = time.time()
s = SpiralGenerator(
["x", "y"], "mm", [0, 0], 6, 0.02, True) # ~2e5 points
z = LineGenerator("z", "mm", 0, 1, ZSIZE, True) #1e2 points or 1e1 for Jython
w = LineGenerator("w", "mm", 0, 1, 10, True) #1e1 points
r1 = CircularROI([-0.7, 4], 0.5)
r2 = CircularROI([0.5, 0.5], 0.3)
r3 = CircularROI([0.2, 4], 0.5)
e1 = ROIExcluder([r1], ["x", "y"])
e2 = ROIExcluder([r2], ["w", "z"])
e3 = ROIExcluder([r3], ["z", "y"])
om = RandomOffsetMutator(0, ["x", "y"], {"x":0.2, "y":0.2})
g = CompoundGenerator([w, z, s], [e1, e3, e2], [om])
g.prepare() # g.size ~3e5
end_time = time.time()
# if this test becomes problematic then we'll just have to remove it
self.assertLess(end_time - start_time, TIMELIMIT)
def test_time_constraint_complex(self):
a = LineGenerator("a", "eV", 0, 1, 10)
b = LineGenerator("b", "rad", 0, 1, 10)
c = LissajousGenerator(["c", "d"], ["mm", "cm"], [0, 0], [5, 5], 3, 10)
d = SpiralGenerator(["e", "f"], ["mm", "s"], [10, 5], 7, 0.6)
e = LineGenerator("g", "mm", 0, 1, 10)
f = LineGenerator("h", "mm", 0, 5, 20)
r1 = CircularROI([0.2, 0.2], 0.1)
r2 = CircularROI([0.4, 0.2], 0.1)
r3 = CircularROI([0.6, 0.2], 0.1)
e1 = ROIExcluder([r1, r2, r3], ["a", "b"])
m1 = RandomOffsetMutator(12, ["a"], [0.1])
m2 = RandomOffsetMutator(200, ["c", "f"], [0.01, 0.5])
g = CompoundGenerator([c, d, e, f, b, a], [e1], [m1, m2])
g.prepare() # 1e6 points
for i in [1, 2, 3, 4, 5, 6]:
p = 10**i
start_time = time.time()
g.get_points(0, p)
end_time = time.time()
self.assertLess(end_time - start_time, TIMELIMIT * p / 1e4)
def test_configure(self):
task = MagicMock()
params = MagicMock()
energy = LineGenerator("energy", "kEv", 13.0, 15.2, 2)
spiral = SpiralGenerator(["x", "y"], ["mm", "mm"], [0., 0.],
5.,
scale=2.0)
params.generator = CompoundGenerator([energy, spiral], [], [], 0.1)
params.filePath = "/tmp/file.h5"
params.generator.prepare()
completed_steps = 0
steps_to_do = 38
part_info = {
"DET": [NDArrayDatasetInfo("xspress3", 2)],
"STAT": [CalculatedNDAttributeDatasetInfo("sum", "StatsTotal")],
}
infos = self.o.configure(task, completed_steps, steps_to_do, part_info,
params)
self.assertEqual(len(infos), 5)
self.assertEquals(infos[0].name, "xspress3.data")
self.assertEquals(infos[0].filename, "file.h5")
self.assertEquals(infos[0].type, "primary")
self.assertEquals(infos[0].rank, 4)
self.assertEquals(infos[0].path, "/entry/detector/detector")
self.assertEquals(infos[0].uniqueid,
"/entry/NDAttributes/NDArrayUniqueId")
self.assertEquals(infos[1].name, "xspress3.sum")
self.assertEquals(infos[1].filename, "file.h5")
self.assertEquals(infos[1].type, "secondary")
self.assertEquals(infos[1].rank, 4)
self.assertEquals(infos[1].path, "/entry/sum/sum")
self.assertEquals(infos[1].uniqueid,
"/entry/NDAttributes/NDArrayUniqueId")
self.assertEquals(infos[2].name, "energy.value_set")
self.assertEquals(infos[2].filename, "file.h5")
self.assertEquals(infos[2].type, "position_set")
self.assertEquals(infos[2].rank, 1)
self.assertEquals(infos[2].path, "/entry/detector/energy_set")
self.assertEquals(infos[2].uniqueid, "")
self.assertEquals(infos[3].name, "x.value_set")
self.assertEquals(infos[3].filename, "file.h5")
self.assertEquals(infos[3].type, "position_set")
self.assertEquals(infos[3].rank, 1)
self.assertEquals(infos[3].path, "/entry/detector/x_set")
self.assertEquals(infos[3].uniqueid, "")
self.assertEquals(infos[4].name, "y.value_set")
self.assertEquals(infos[4].filename, "file.h5")
self.assertEquals(infos[4].type, "position_set")
self.assertEquals(infos[4].rank, 1)
self.assertEquals(infos[4].path, "/entry/detector/y_set")
self.assertEquals(infos[4].uniqueid, "")
self.assertEqual(task.put.call_args_list, [
call(self.child["positionMode"], True),
call(self.child["numCapture"], 0),
call('flushDataPerNFrames', 10.0),
call('flushAttrPerNFrames', 10.0)
])
self.assertEqual(task.put_many_async.call_count, 2)
self.assertEqual(
task.put_many_async.call_args_list[0],
call(
self.child,
dict(enableCallbacks=True,
fileWriteMode="Stream",
swmrMode=True,
positionMode=True,
dimAttDatasets=True,
lazyOpen=True,
arrayCounter=0,
filePath="/tmp/",
fileName="file.h5",
fileTemplate="%s%s")))
self.assertEqual(
task.put_many_async.call_args_list[1],
call(
self.child,
dict(numExtraDims=1,
posNameDimN="d1",
extraDimSizeN=20,
posNameDimX="d0",
extraDimSizeX=2,
posNameDimY="",
extraDimSizeY=1,
posNameDim3="",
extraDimSize3=1,
posNameDim4="",
extraDimSize4=1,
posNameDim5="",
extraDimSize5=1,
posNameDim6="",
extraDimSize6=1,
posNameDim7="",
extraDimSize7=1,
posNameDim8="",
extraDimSize8=1,
posNameDim9="",
extraDimSize9=1)))
expected_xml = """<?xml version="1.0" ?>
<hdf5_layout>
<group name="entry">
<attribute name="NX_class" source="constant" type="string" value="NXentry" />
<group name="detector">
<attribute name="signal" source="constant" type="string" value="detector" />
<attribute name="axes" source="constant" type="string" value="energy_set,.,.,." />
<attribute name="NX_class" source="constant" type="string" value="NXdata" />
<attribute name="energy_set_indices" source="constant" type="string" value="0" />
<dataset name="energy_set" source="constant" type="float" value="13,15.2">
<attribute name="units" source="constant" type="string" value="kEv" />
</dataset>
<attribute name="x_set_indices" source="constant" type="string" value="1" />
<dataset name="x_set" source="constant" type="float" value="0.473264298891,-1.28806365331,-1.11933765723,0.721339144968,2.26130106714,2.3717213098,1.08574712174,-0.863941392256,-2.59791589857,-3.46951769442,-3.22399679412,-1.98374931946,-0.132541097885,1.83482458567,3.45008680308,4.36998121172,4.42670524204,3.63379270355,2.15784413199,0.269311496406">
<attribute name="units" source="constant" type="string" value="mm" />
</dataset>
<attribute name="y_set_indices" source="constant" type="string" value="1" />
<dataset name="y_set" source="constant" type="float" value="-0.64237113553,-0.500750778455,1.38930992616,1.98393756064,0.784917470231,-1.17377831157,-2.66405897615,-2.9669684623,-2.01825893141,-0.24129368636,1.72477821509,3.27215424484,3.98722048131,3.71781556747,2.5610299588,0.799047653518,-1.18858453138,-3.01284626565,-4.34725663835,-4.9755042398">
<attribute name="units" source="constant" type="string" value="mm" />
</dataset>
<dataset det_default="true" name="detector" source="detector">
<attribute name="NX_class" source="constant" type="string" value="SDS" />
</dataset>
</group>
<group name="sum">
<attribute name="signal" source="constant" type="string" value="sum" />
<attribute name="axes" source="constant" type="string" value="energy_set,.,.,." />
<attribute name="NX_class" source="constant" type="string" value="NXdata" />
<attribute name="energy_set_indices" source="constant" type="string" value="0" />
<hardlink name="energy_set" target="/entry/detector/energy_set" />
<attribute name="x_set_indices" source="constant" type="string" value="1" />
<hardlink name="x_set" target="/entry/detector/x_set" />
<attribute name="y_set_indices" source="constant" type="string" value="1" />
<hardlink name="y_set" target="/entry/detector/y_set" />
<dataset name="sum" ndattribute="StatsTotal" source="ndattribute" />
</group>
<group name="NDAttributes" ndattr_default="true">
<attribute name="NX_class" source="constant" type="string" value="NXcollection" />
</group>
</group>
</hdf5_layout>"""
expected_filename = "/tmp/BLOCK-HDF5-layout.xml"
self.assertEqual(task.put_async.call_args_list[0][0][1],
expected_filename)
actual_xml = open(expected_filename).read().replace(">", ">\n")
self.assertEqual(actual_xml.splitlines(), expected_xml.splitlines())
def test_configure(self):
energy = LineGenerator("energy", "kEv", 13.0, 15.2, 2)
spiral = SpiralGenerator(["x", "y"], ["mm", "mm"], [0., 0.],
5.,
scale=2.0)
generator = CompoundGenerator([energy, spiral], [], [], 0.1)
generator.prepare()
fileDir = "/tmp"
formatName = "xspress3"
fileTemplate = "thing-%s.h5"
completed_steps = 0
steps_to_do = 38
part_info = {
"DET": [NDArrayDatasetInfo(2)],
"PANDA": [
NDAttributeDatasetInfo("I0", AttributeDatasetType.DETECTOR,
"COUNTER1.COUNTER", 2),
NDAttributeDatasetInfo("It", AttributeDatasetType.MONITOR,
"COUNTER2.COUNTER", 2),
NDAttributeDatasetInfo("t1x", AttributeDatasetType.POSITION,
"INENC1.VAL", 2)
],
"STAT": [CalculatedNDAttributeDatasetInfo("sum", "StatsTotal")],
}
infos = self.o.configure(self.context, completed_steps, steps_to_do,
part_info, generator, fileDir, formatName,
fileTemplate)
assert len(infos) == 8
assert infos[0].name == "xspress3.data"
assert infos[0].filename == "thing-xspress3.h5"
assert infos[0].type == DatasetType.PRIMARY
assert infos[0].rank == 4
assert infos[0].path == "/entry/detector/detector"
assert infos[0].uniqueid == "/entry/NDAttributes/NDArrayUniqueId"
assert infos[1].name == "xspress3.sum"
assert infos[1].filename == "thing-xspress3.h5"
assert infos[1].type == DatasetType.SECONDARY
assert infos[1].rank == 4
assert infos[1].path == "/entry/sum/sum"
assert infos[1].uniqueid == "/entry/NDAttributes/NDArrayUniqueId"
assert infos[2].name == "I0.data"
assert infos[2].filename == "thing-xspress3.h5"
assert infos[2].type == DatasetType.PRIMARY
assert infos[2].rank == 4
assert infos[2].path == "/entry/I0/I0"
assert infos[2].uniqueid == "/entry/NDAttributes/NDArrayUniqueId"
assert infos[3].name == "It.data"
assert infos[3].filename == "thing-xspress3.h5"
assert infos[3].type == DatasetType.MONITOR
assert infos[3].rank == 4
assert infos[3].path == "/entry/It/It"
assert infos[3].uniqueid == "/entry/NDAttributes/NDArrayUniqueId"
assert infos[4].name == "t1x.value"
assert infos[4].filename == "thing-xspress3.h5"
assert infos[4].type == DatasetType.POSITION_VALUE
assert infos[4].rank == 4
assert infos[4].path == "/entry/t1x/t1x"
assert infos[4].uniqueid == "/entry/NDAttributes/NDArrayUniqueId"
assert infos[5].name == "energy.value_set"
assert infos[5].filename == "thing-xspress3.h5"
assert infos[5].type == DatasetType.POSITION_SET
assert infos[5].rank == 1
assert infos[5].path == "/entry/detector/energy_set"
assert infos[5].uniqueid == ""
assert infos[6].name == "x.value_set"
assert infos[6].filename == "thing-xspress3.h5"
assert infos[6].type == DatasetType.POSITION_SET
assert infos[6].rank == 1
assert infos[6].path == "/entry/detector/x_set"
assert infos[6].uniqueid == ""
assert infos[7].name == "y.value_set"
assert infos[7].filename == "thing-xspress3.h5"
assert infos[7].type == DatasetType.POSITION_SET
assert infos[7].rank == 1
assert infos[7].path == "/entry/detector/y_set"
assert infos[7].uniqueid == ""
expected_xml_filename = "/tmp/BLOCK-HDF5-layout.xml"
# Wait for the start_future so the post gets through to our child
# even on non-cothread systems
self.o.start_future.result(timeout=1)
assert self.child.handled_requests.mock_calls == [
call.put('positionMode', True),
call.put('arrayCounter', 0),
call.put('dimAttDatasets', True),
call.put('enableCallbacks', True),
call.put('fileName', 'xspress3'),
call.put('filePath', '/tmp/'),
call.put('fileTemplate', '%sthing-%s.h5'),
call.put('fileWriteMode', 'Stream'),
call.put('lazyOpen', True),
call.put('positionMode', True),
call.put('swmrMode', True),
call.put('extraDimSize3', 1),
call.put('extraDimSize4', 1),
call.put('extraDimSize5', 1),
call.put('extraDimSize6', 1),
call.put('extraDimSize7', 1),
call.put('extraDimSize8', 1),
call.put('extraDimSize9', 1),
call.put('extraDimSizeN', 20),
call.put('extraDimSizeX', 2),
call.put('extraDimSizeY', 1),
call.put('numExtraDims', 1),
call.put('posNameDim3', ''),
call.put('posNameDim4', ''),
call.put('posNameDim5', ''),
call.put('posNameDim6', ''),
call.put('posNameDim7', ''),
call.put('posNameDim8', ''),
call.put('posNameDim9', ''),
call.put('posNameDimN', 'd1'),
call.put('posNameDimX', 'd0'),
call.put('posNameDimY', ''),
call.put('flushAttrPerNFrames', 10.0),
call.put('flushDataPerNFrames', 10.0),
call.put('xml', expected_xml_filename),
call.put('numCapture', 0),
call.post('start')
]
expected_xml = """<?xml version="1.0" ?>
<hdf5_layout>
<group name="entry">
<attribute name="NX_class" source="constant" type="string" value="NXentry" />
<group name="detector">
<attribute name="signal" source="constant" type="string" value="detector" />
<attribute name="axes" source="constant" type="string" value="energy_set,.,.,." />
<attribute name="NX_class" source="constant" type="string" value="NXdata" />
<attribute name="energy_set_indices" source="constant" type="string" value="0" />
<dataset name="energy_set" source="constant" type="float" value="13,15.2">
<attribute name="units" source="constant" type="string" value="kEv" />
</dataset>
<attribute name="x_set_indices" source="constant" type="string" value="1" />
<dataset name="x_set" source="constant" type="float" value="0.473264298891,-1.28806365331,-1.11933765723,0.721339144968,2.26130106714,2.3717213098,1.08574712174,-0.863941392256,-2.59791589857,-3.46951769442,-3.22399679412,-1.98374931946,-0.132541097885,1.83482458567,3.45008680308,4.36998121172,4.42670524204,3.63379270355,2.15784413199,0.269311496406">
<attribute name="units" source="constant" type="string" value="mm" />
</dataset>
<attribute name="y_set_indices" source="constant" type="string" value="1" />
<dataset name="y_set" source="constant" type="float" value="-0.64237113553,-0.500750778455,1.38930992616,1.98393756064,0.784917470231,-1.17377831157,-2.66405897615,-2.9669684623,-2.01825893141,-0.24129368636,1.72477821509,3.27215424484,3.98722048131,3.71781556747,2.5610299588,0.799047653518,-1.18858453138,-3.01284626565,-4.34725663835,-4.9755042398">
<attribute name="units" source="constant" type="string" value="mm" />
</dataset>
<dataset det_default="true" name="detector" source="detector">
<attribute name="NX_class" source="constant" type="string" value="SDS" />
</dataset>
</group>
<group name="sum">
<attribute name="signal" source="constant" type="string" value="sum" />
<attribute name="axes" source="constant" type="string" value="energy_set,.,.,." />
<attribute name="NX_class" source="constant" type="string" value="NXdata" />
<attribute name="energy_set_indices" source="constant" type="string" value="0" />
<hardlink name="energy_set" target="/entry/detector/energy_set" />
<attribute name="x_set_indices" source="constant" type="string" value="1" />
<hardlink name="x_set" target="/entry/detector/x_set" />
<attribute name="y_set_indices" source="constant" type="string" value="1" />
<hardlink name="y_set" target="/entry/detector/y_set" />
<dataset name="sum" ndattribute="StatsTotal" source="ndattribute" />
</group>
<group name="I0">
<attribute name="signal" source="constant" type="string" value="I0" />
<attribute name="axes" source="constant" type="string" value="energy_set,.,.,." />
<attribute name="NX_class" source="constant" type="string" value="NXdata" />
<attribute name="energy_set_indices" source="constant" type="string" value="0" />
<hardlink name="energy_set" target="/entry/detector/energy_set" />
<attribute name="x_set_indices" source="constant" type="string" value="1" />
<hardlink name="x_set" target="/entry/detector/x_set" />
<attribute name="y_set_indices" source="constant" type="string" value="1" />
<hardlink name="y_set" target="/entry/detector/y_set" />
<dataset name="I0" ndattribute="COUNTER1.COUNTER" source="ndattribute" />
</group>
<group name="It">
<attribute name="signal" source="constant" type="string" value="It" />
<attribute name="axes" source="constant" type="string" value="energy_set,.,.,." />
<attribute name="NX_class" source="constant" type="string" value="NXdata" />
<attribute name="energy_set_indices" source="constant" type="string" value="0" />
<hardlink name="energy_set" target="/entry/detector/energy_set" />
<attribute name="x_set_indices" source="constant" type="string" value="1" />
<hardlink name="x_set" target="/entry/detector/x_set" />
<attribute name="y_set_indices" source="constant" type="string" value="1" />
<hardlink name="y_set" target="/entry/detector/y_set" />
<dataset name="It" ndattribute="COUNTER2.COUNTER" source="ndattribute" />
</group>
<group name="t1x">
<attribute name="signal" source="constant" type="string" value="t1x" />
<attribute name="axes" source="constant" type="string" value="energy_set,.,.,." />
<attribute name="NX_class" source="constant" type="string" value="NXdata" />
<attribute name="energy_set_indices" source="constant" type="string" value="0" />
<hardlink name="energy_set" target="/entry/detector/energy_set" />
<attribute name="x_set_indices" source="constant" type="string" value="1" />
<hardlink name="x_set" target="/entry/detector/x_set" />
<attribute name="y_set_indices" source="constant" type="string" value="1" />
<hardlink name="y_set" target="/entry/detector/y_set" />
<dataset name="t1x" ndattribute="INENC1.VAL" source="ndattribute" />
</group>
<group name="NDAttributes" ndattr_default="true">
<attribute name="NX_class" source="constant" type="string" value="NXcollection" />
</group>
</group>
</hdf5_layout>"""
with open(expected_xml_filename) as f:
actual_xml = f.read().replace(">", ">\n")
assert actual_xml.splitlines() == expected_xml.splitlines()
def __init__(self, names, units, centre, radius, scale=1.0, alternate_direction=False):
super(JSpiralGenerator, self).__init__()
self.names = names
self.generator = SpiralGenerator(names, units, centre, radius, scale, alternate_direction)
logging.debug(self.generator.to_dict())
def __init__(self, names, units, centre, radius, scale=1.0, alternate_direction=False):
super(JSpiralGenerator, self).__init__()
self.names = names
self.generator = SpiralGenerator(names, units, centre, radius, scale, alternate_direction)
logging.debug(self.generator.to_dict())
def configure_and_check_output(self, on_windows=False):
energy = LineGenerator("energy", "kEv", 13.0, 15.2, 2)
spiral = SpiralGenerator(["x", "y"], ["mm", "mm"], [0.0, 0.0],
5.0,
scale=2.0)
generator = CompoundGenerator([energy, spiral], [], [], 0.1)
generator.prepare()
fileDir = "/tmp"
formatName = "xspress3"
fileTemplate = "thing-%s.h5"
completed_steps = 0
steps_to_do = 38
part_info = {
"DET": [NDArrayDatasetInfo(2)],
"PANDA": [
NDAttributeDatasetInfo.from_attribute_type(
"I0", AttributeDatasetType.DETECTOR, "COUNTER1.COUNTER"),
NDAttributeDatasetInfo.from_attribute_type(
"It", AttributeDatasetType.MONITOR, "COUNTER2.COUNTER"),
NDAttributeDatasetInfo.from_attribute_type(
"t1x", AttributeDatasetType.POSITION, "INENC1.VAL"),
],
"STAT": [CalculatedNDAttributeDatasetInfo("sum", "StatsTotal")],
}
if on_windows:
part_info["WINPATH"] = [FilePathTranslatorInfo("Y", "/tmp", "")]
infos = self.o.on_configure(
self.context,
completed_steps,
steps_to_do,
part_info,
generator,
fileDir,
formatName,
fileTemplate,
)
assert len(infos) == 8
assert infos[0].name == "xspress3.data"
assert infos[0].filename == "thing-xspress3.h5"
assert infos[0].type == DatasetType.PRIMARY
assert infos[0].rank == 4
assert infos[0].path == "/entry/detector/detector"
assert infos[0].uniqueid == "/entry/NDAttributes/NDArrayUniqueId"
assert infos[1].name == "xspress3.sum"
assert infos[1].filename == "thing-xspress3.h5"
assert infos[1].type == DatasetType.SECONDARY
assert infos[1].rank == 2
assert infos[1].path == "/entry/sum/sum"
assert infos[1].uniqueid == "/entry/NDAttributes/NDArrayUniqueId"
assert infos[2].name == "I0.data"
assert infos[2].filename == "thing-xspress3.h5"
assert infos[2].type == DatasetType.PRIMARY
assert infos[2].rank == 2
assert infos[2].path == "/entry/I0.data/I0.data"
assert infos[2].uniqueid == "/entry/NDAttributes/NDArrayUniqueId"
assert infos[3].name == "It.data"
assert infos[3].filename == "thing-xspress3.h5"
assert infos[3].type == DatasetType.MONITOR
assert infos[3].rank == 2
assert infos[3].path == "/entry/It.data/It.data"
assert infos[3].uniqueid == "/entry/NDAttributes/NDArrayUniqueId"
assert infos[4].name == "t1x.value"
assert infos[4].filename == "thing-xspress3.h5"
assert infos[4].type == DatasetType.POSITION_VALUE
assert infos[4].rank == 2
assert infos[4].path == "/entry/t1x.value/t1x.value"
assert infos[4].uniqueid == "/entry/NDAttributes/NDArrayUniqueId"
assert infos[5].name == "energy.value_set"
assert infos[5].filename == "thing-xspress3.h5"
assert infos[5].type == DatasetType.POSITION_SET
assert infos[5].rank == 1
assert infos[5].path == "/entry/detector/energy_set"
assert infos[5].uniqueid == ""
assert infos[6].name == "x.value_set"
assert infos[6].filename == "thing-xspress3.h5"
assert infos[6].type == DatasetType.POSITION_SET
assert infos[6].rank == 1
assert infos[6].path == "/entry/detector/x_set"
assert infos[6].uniqueid == ""
assert infos[7].name == "y.value_set"
assert infos[7].filename == "thing-xspress3.h5"
assert infos[7].type == DatasetType.POSITION_SET
assert infos[7].rank == 1
assert infos[7].path == "/entry/detector/y_set"
assert infos[7].uniqueid == ""
expected_xml_filename_local = "/tmp/BLOCK_HDF5-layout.xml"
if on_windows:
expected_xml_filename_remote = "Y:\\BLOCK_HDF5-layout.xml"
expected_filepath = "Y:" + os.sep
else:
expected_xml_filename_remote = expected_xml_filename_local
expected_filepath = "/tmp" + os.sep
# Wait for the start_future so the post gets through to our child
# even on non-cothread systems
self.o.start_future.result(timeout=1)
assert self.child.handled_requests.mock_calls == [
call.put("positionMode", True),
call.put("arrayCounter", 0),
call.put("dimAttDatasets", True),
call.put("enableCallbacks", True),
call.put("fileName", "xspress3"),
call.put("filePath", expected_filepath),
call.put("fileTemplate", "%sthing-%s.h5"),
call.put("fileWriteMode", "Stream"),
call.put("lazyOpen", True),
call.put("storeAttr", True),
call.put("swmrMode", True),
call.put("extraDimSize3", 1),
call.put("extraDimSize4", 1),
call.put("extraDimSize5", 1),
call.put("extraDimSize6", 1),
call.put("extraDimSize7", 1),
call.put("extraDimSize8", 1),
call.put("extraDimSize9", 1),
call.put("extraDimSizeN", 20),
call.put("extraDimSizeX", 2),
call.put("extraDimSizeY", 1),
call.put("numExtraDims", 1),
call.put("posNameDim3", ""),
call.put("posNameDim4", ""),
call.put("posNameDim5", ""),
call.put("posNameDim6", ""),
call.put("posNameDim7", ""),
call.put("posNameDim8", ""),
call.put("posNameDim9", ""),
call.put("posNameDimN", "d1"),
call.put("posNameDimX", "d0"),
call.put("posNameDimY", ""),
call.put("flushAttrPerNFrames", 0),
call.put("flushDataPerNFrames", 38),
call.put("xmlLayout", expected_xml_filename_remote),
call.put("numCapture", 0),
call.post("start"),
call.when_value_matches("arrayCounterReadback", greater_than_zero,
None),
]
with open(expected_xml_filename_local) as f:
actual_xml = f.read().replace(">", ">\n")
# Check the layout filename Malcolm uses for file creation
assert self.o.layout_filename == expected_xml_filename_local
return actual_xml
def setUp(self):
self.g = SpiralGenerator(['x', 'y'], ["cm", "mm"], [0.0, 0.0],
1.4,
alternate=True)
def test_duplicate_name_raises(self):
with self.assertRaises(ValueError):
SpiralGenerator(["x", "x"], ["mm", "mm"], [0.0, 0.0], 1.0)
class SpiralGeneratorTest(ScanPointGeneratorTest):
def setUp(self):
self.g = SpiralGenerator(['x', 'y'], ["cm", "mm"], [0.0, 0.0],
1.4,
alternate=True)
def test_init(self):
self.assertEqual(self.g.units, dict(x="cm", y="mm"))
self.assertEqual(self.g.axes, ["x", "y"])
def test_duplicate_name_raises(self):
with self.assertRaises(ValueError):
SpiralGenerator(["x", "x"], ["mm", "mm"], [0.0, 0.0], 1.0)
def test_array_positions(self):
expected_x = [
0.23663214944574582, -0.6440318266552169, -0.5596688286164636,
0.36066957248394327, 1.130650533568409, 1.18586065489788,
0.5428735608675326
]
expected_y = [
-0.3211855677650875,
-0.25037538922751695,
0.6946549630820702,
0.9919687803189761,
0.3924587351155914,
-0.5868891557832875,
-1.332029488076613,
]
expected_bx = [
0.0, -0.2214272368007088, -0.7620433832656455,
-0.13948222773063082, 0.8146440851904461, 1.2582363345925418,
0.9334439933089926, 0.06839234794968006
]
expected_by = [
0.0, -0.5189218293602549, 0.23645222432582483, 0.9671992383675001,
0.7807653675717078, -0.09160107657707395, -1.0190886264001306,
-1.4911377166541206
]
self.g.prepare_positions()
self.g.prepare_bounds()
self.assertListAlmostEqual(expected_x, self.g.positions['x'].tolist())
self.assertListAlmostEqual(expected_y, self.g.positions['y'].tolist())
self.assertListAlmostEqual(expected_bx, self.g.bounds['x'].tolist())
self.assertListAlmostEqual(expected_by, self.g.bounds['y'].tolist())
def test_to_dict(self):
expected_dict = dict()
expected_dict[
'typeid'] = "scanpointgenerator:generator/SpiralGenerator:1.0"
expected_dict['axes'] = ['x', 'y']
expected_dict['units'] = ['cm', 'mm']
expected_dict['centre'] = [0.0, 0.0]
expected_dict['radius'] = 1.4
expected_dict['scale'] = 1
expected_dict['alternate'] = True
d = self.g.to_dict()
self.assertEqual(expected_dict, d)
def test_from_dict(self):
_dict = dict()
_dict['type'] = "SpiralGenerator"
_dict['axes'] = ["x", "y"]
_dict['units'] = ["mm", "cm"]
_dict['centre'] = [0.0, 0.0]
_dict['radius'] = 1.4
_dict['scale'] = 1
_dict['alternate'] = True
units_dict = dict()
units_dict['x'] = "mm"
units_dict['y'] = "cm"
gen = SpiralGenerator.from_dict(_dict)
self.assertEqual(["x", "y"], gen.axes)
self.assertEqual(units_dict, gen.units)
self.assertEqual([0.0, 0.0], gen.centre)
self.assertEqual(1.4, gen.radius)
self.assertEqual(1, gen.scale)
def spiral_check():
spiral = SpiralGenerator(['x', 'y'], ["mm", "mm"], [0.0, 0.0], 10.0)
gen = CompoundGenerator([spiral], [], [])
plot_generator(gen)
