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 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)