class Analysis_test(unittest.TestCase):
"""Path to sample Data File"""
datadir=path.join(pth,"sample-data")
def setUp(self):
self.d1=Data(path.join(self.datadir,"OVF1.ovf"))
self.d2=Data(path.join(self.datadir,"TDI_Format_RT.txt"))
self.d3=Data(path.join(self.datadir,"New-XRay-Data.dql"))
self.d4=Data(np.column_stack([np.ones(100),np.ones(100)*2]),setas="xy")
def test_functions(self):
#Test section:
self.s1=self.d1.section(z=(12,13))
self.assertTrue(142.710<self.d2.mean("Temp")<142.711,"Failed on the mean test.")
self.assertTrue(round(self.d2.span("Temp")[0],1)==4.3 and round(self.d2.span("Temp")[1],1)==291.6,"Span test failed.")
f=self.d2.split(lambda r:r["Temp"]<150)
self.assertTrue(len(f[0])==838,"Split failed to work.")
self.assertEqual(len(self.d3.threshold(2000,rising=True,falling=True,all_vals=True)),5,"Threshold failure.")
self.d4.add(0,1,"Add")
self.d4.subtract(1,0,header="Subtract")
self.d4.multiply(0,1,header="Multiply")
self.d4.divide(0,1,header="Divide")
self.d4.diffsum(0,1,header="Diffsum")
self.assertTrue(np.all(self.d4[0]==np.array([-0.5,-1,-3,3,-1,2])),"Test column ops failed.")
d=Data(np.zeros((100,1)))
d.add(0,1.0)
self.assertEqual(np.sum(d[:,0]),100.,"Add with a flot didn't work")
d.add(0,np.ones(100))
self.assertEqual(np.sum(d[:,0]),200.,"Add with an array failed.")
def test_peaks(self):
d=self.d3.clone
d.peaks(width=8,poly=4,significance=100,modify=True)
self.assertEqual(len(d),11,"Failed on peaks test.")
def test_threshold(self):
#set up some zigzag data
#mins at 0,100,200,300,400, max at 50, 150, 250, 350 and zeros in between
ar = np.zeros((400,2))
ar[:,0]=np.arange(0,len(ar))
for i in range(4):
ar[i*100:i*100+50,1] = np.linspace(-1,1,50)
for i in range(4):
ar[i*100+50:i*100+100,1] = np.linspace(1,-1,50)
d = Data(ar, setas='xy')
self.assertTrue(len(d.threshold(0,rising=True,falling=False,all_vals=True)==4))
self.assertTrue(len(d.threshold(0,rising=False,falling=True,all_vals=True)==4))
self.assertTrue(len(d.threshold(0,interpolate=False,rising=False,falling=True,all_vals=True)==4))
self.assertTrue(d.threshold(0,all_vals=True)[1]==124.5)
self.thresh=d
self.assertTrue(np.sum(d.threshold([0.0,0.5,1.0])-np.array([[24.5,36.74999999, 49.]]))<1E-6,"Multiple threshold failed.")
self.assertAlmostEqual(d.threshold(0,interpolate=False,all_vals=True)[1],124.5,6,"Threshold without interpolation failed.")
result=d.threshold(0,interpolate=False,all_vals=True,xcol=False)
self.assertTrue(np.allclose(result,np.array([[ 24.5, 0. ],[124.5, 0. ],[224.5, 0. ],[324.5, 0. ]])),
"Failed threshold with False scol - result was {}".format(result))
def test_apply(self):
self.app=Data(np.zeros((100,1)),setas="y")
self.app.apply(lambda r:r.i[0],header="Counter")
def calc(r,omega=1.0,k=1.0):
return np.sin(r.y*omega)
self.app.apply(calc,replace=False,header="Sin",_extra={"omega":0.1},k=1.0)
self.app.apply(lambda r:r.__class__([r[1],r[0]]),replace=True,header=["Index","Sin"])
self.app.setas="xy"
self.assertAlmostEqual(self.app.integrate(),-64.1722191259037,msg="Integrate after aplies failed.")
t=Data(d.interpolate(d.peaks(significance=sensitivity,width=8,poly=4)))
t.column_headers=copy(d.column_headers)
d%='peaks'
t%='peaks'
d.setas="xy"
d.labels[d.find_col('Angle')]=r"Reflection Angle $\theta$"
t.del_rows(0, lambda x,y: x<critical_edge)
t.setas="xy"
t.template.fig_width=7.0
t.template.fig_height=5.0
t.plot(fmt='go', plotter=pyplot.semilogy)
main_fig=d.plot(figure=t.fig, plotter=pyplot.semilogy)
d.show()
#Now convert the angle to sin^2
t.apply(lambda x: np.sin(np.radians(x[0]/2.0))**2, 0,header=r"$sin^2\theta$")
# Now create the m^2 order
m=np.arange(len(t))+fringe_offset
m=m**2
#And add it to t
t.add_column(m, column_header='$m^2$')
#Now we can it a straight line
t.setas="x..y"
fit=t.lmfit(Linear,result=True,replace=False,header="Fit")
g=t["LinearModel:slope"]
gerr=t["LinearModel:slope err"]/g
g=np.sqrt(1.0/g)
gerr/=2.0
l=float(d['Lambda'])
th=l/(2*g)
therr=th*(gerr)
t = Data(d.interpolate(d.peaks(significance=sensitivity, width=8, poly=4)))
t.column_headers = copy(d.column_headers)
d %= "peaks"
t %= "peaks"
d.setas = "xy"
d.labels[d.find_col("Angle")] = r"Reflection Angle $\theta$"
t.del_rows(0, lambda x, y: x < critical_edge)
t.setas = "xy"
t.template.fig_width = 7.0
t.template.fig_height = 5.0
t.plot(fmt="go", plotter=pyplot.semilogy)
main_fig = d.plot(figure=t.fig, plotter=pyplot.semilogy)
d.show()
# Now convert the angle to sin^2
t.apply(lambda x: np.sin(np.radians(x[0] / 2.0)) ** 2, 0, header=r"$sin^2\theta$")
# Now create the m^2 order
m = np.arange(len(t)) + fringe_offset
m = m ** 2
# And add it to t
t.add_column(m, column_header="$m^2$")
# Now we can it a straight line
t.setas = "x..y"
fit = t.lmfit(Linear, result=True, replace=False, header="Fit")
g = t["LinearModel:slope"]
gerr = t["LinearModel:slope err"] / g
g = np.sqrt(1.0 / g)
gerr /= 2.0
l = float(d["Lambda"])
th = l / (2 * g)
therr = th * (gerr)
class Analysis_test(unittest.TestCase):
"""Path to sample Data File"""
datadir=path.join(pth,"sample-data")
def setUp(self):
self.d1=Data(path.join(self.datadir,"OVF1.ovf"))
self.d2=Data(path.join(self.datadir,"TDI_Format_RT.txt"))
self.d3=Data(path.join(self.datadir,"New-XRay-Data.dql"))
self.d4=Data(np.column_stack([np.ones(100),np.ones(100)*2]),setas="xy")
def test_functions(self):
#Test section:
self.s1=self.d1.section(z=(12,13))
f=self.d2.split(lambda r:r["Temp"]<150)
self.assertTrue(len(f[0])==838,"Split failed to work.")
self.assertEqual(len(self.d3.threshold(2000,rising=True,falling=True,all_vals=True)),5,"Threshold failure.")
def test_peaks(self):
d=self.d3.clone
d.peaks(width=8,poly=4,significance=100,modify=True)
self.assertEqual(len(d),11,"Failed on peaks test.")
def test_threshold(self):
#set up some zigzag data
#mins at 0,100,200,300,400, max at 50, 150, 250, 350 and zeros in between
ar = np.zeros((400,2))
ar[:,0]=np.arange(0,len(ar))
for i in range(4):
ar[i*100:i*100+50,1] = np.linspace(-1,1,50)
for i in range(4):
ar[i*100+50:i*100+100,1] = np.linspace(1,-1,50)
d = Data(ar, setas='xy')
self.assertTrue(len(d.threshold(0,rising=True,falling=False,all_vals=True)==4))
self.assertTrue(len(d.threshold(0,rising=False,falling=True,all_vals=True)==4))
self.assertTrue(len(d.threshold(0,interpolate=False,rising=False,falling=True,all_vals=True)==4))
self.assertTrue(d.threshold(0,all_vals=True)[1]==124.5)
self.thresh=d
self.assertTrue(np.sum(d.threshold([0.0,0.5,1.0])-np.array([[24.5,36.74999999, 49.]]))<1E-6,"Multiple threshold failed.")
self.assertAlmostEqual(d.threshold(0,interpolate=False,all_vals=True)[1],124.5,6,"Threshold without interpolation failed.")
result=d.threshold(0,interpolate=False,all_vals=True,xcol=False)
self.assertTrue(np.allclose(result,np.array([[ 24.5, 0. ],[124.5, 0. ],[224.5, 0. ],[324.5, 0. ]])),
"Failed threshold with False scol - result was {}".format(result))
def test_apply(self):
self.app=Data(np.zeros((100,1)),setas="y")
self.app.apply(lambda r:r.i[0],header="Counter")
def calc(r,omega=1.0,k=1.0):
return np.sin(r.y*omega)
self.app.apply(calc,replace=False,header="Sin",_extra={"omega":0.1},k=1.0)
self.app.apply(lambda r:r.__class__([r[1],r[0]]),replace=True,header=["Index","Sin"])
self.app.setas="xy"
self.assertAlmostEqual(self.app.integrate(output="result"),18.87616564214,msg="Integrate after aplies failed.")
def test_scale(self):
x=np.linspace(-5,5,101)
y=np.sin(x)
orig=Data(x+np.random.normal(size=101,scale=0.025),y+np.random.normal(size=101,scale=0.01))
orig.setas="xy"
XTests=[[(0,0,0.5),(0,2,-0.1)],
[(0,0,0.5)],
[(0,2,-0.2)]]
YTests=[[(1,1,0.5),(1,2,-0.1)],
[(1,1,0.5)],
[(1,2,-0.2)]]
for xmode,xdata,xtests in zip(["linear","scale","offset"],[x*2+0.2,x*2,x+0.2],XTests):
for ymode,ydata,ytests in zip(["linear","scale","offset"],[y*2+0.2,y*2,y+0.2],YTests):
to_scale=Data(xdata+np.random.normal(size=101,scale=0.025),ydata+np.random.normal(size=101,scale=0.01))
to_scale.setas="xy"
to_scale.scale(orig,xmode=xmode,ymode=ymode)
transform=to_scale["Transform"]
t_err=to_scale["Transform Err"]
for i,j,v in xtests+ytests:
self.assertLessEqual(np.abs(transform[i,j]-v),5*t_err[i,j],"Failed to get correct trandorm factor for {}:{} ({} vs {}".format(xmode,ymode,transform[i,j],v))
to_scale=Data(x*5+0.1+np.random.normal(size=101,scale=0.025),y*0.5+0.1+0.5*x+np.random.normal(size=101,scale=0.01))
to_scale.setas="xy"
to_scale.scale(orig,xmode="affine")
a_tranform=np.array([[0.2,0.,-0.02],[-0.2, 2.,-0.17]])
t_delta=np.abs(to_scale["Transform"]-a_tranform)
t_in_range=t_delta<to_scale["Transform Err"]*5
self.assertTrue(np.all(t_in_range),"Failed to produce correct affine scaling {} vs {}".format(to_scale["Transform"],a_tranform))
def test_clip(self):
x=np.linspace(0,np.pi*10,1001)
y=np.sin(x)
z=np.cos(x)
d=Data(x,y,z,setas="xyz")
d.clip((-0.1,0.2),"Column 2")
self.assertTrue((d.z.min()>=-0.1) and (d.z.max()<=0.2),"Clip with a column specified failed.")
d=Data(x,y,z,setas="xyz")
d.clip((-0.5,0.7))
self.assertTrue((d.y.min()>=-0.5) and (d.y.max()<=0.7),"Clip with no column specified failed.")
def test_integrate(self):
d=Data(path.join(self.datadir,"SLD_200919.dat"))
d.setas="x..y"
d.integrate(result=True,header="Total_M")
result=d["Total_M"]
self.assertAlmostEqual(result,4.19687459365,7,"Integrate returned the wrong result!")
d.setas[-1]="y"
d.plot(multiple="y2")
self.assertEqual(len(d.axes),2,"Failed to produce plot with double y-axis")
d.close("all")
d.setas="x..y"
fx=d.interpolate(None)
self.assertEqual(fx(np.linspace(1,1500,101)).shape,(101,7),"Failed to get the interpolated shape right")
def test_sg_filter(self):
x=np.linspace(0,10*np.pi,1001)
y=np.sin(x)+np.random.normal(size=1001,scale=0.05)
d=Data(x,y,column_headers=["Time","Signal"],setas="xy")
d.SG_Filter(order=1,result=True)
d.setas="x.y"
d.y=d.y-np.cos(x)
self.assertAlmostEqual(d.y[5:-5].mean(), 0,places=2,msg="Failed to differentiate correctly")
class Analysis_test(unittest.TestCase):
"""Path to sample Data File"""
datadir = path.join(pth, "sample-data")
def setUp(self):
self.d1 = Data(path.join(self.datadir, "OVF1.ovf"))
self.d2 = Data(path.join(self.datadir, "TDI_Format_RT.txt"))
self.d3 = Data(path.join(self.datadir, "New-XRay-Data.dql"))
self.d4 = Data(np.column_stack([np.ones(100),
np.ones(100) * 2]),
setas="xy")
def test_functions(self):
#Test section:
self.s1 = self.d1.section(z=(12, 13))
self.assertTrue(142.710 < self.d2.mean("Temp") < 142.711,
"Failed on the mean test.")
self.assertTrue(
round(self.d2.span("Temp")[0], 1) == 4.3
and round(self.d2.span("Temp")[1], 1) == 291.6,
"Span test failed.")
f = self.d2.split(lambda r: r["Temp"] < 150)
self.assertTrue(len(f[0]) == 838, "Split failed to work.")
self.assertEqual(
len(
self.d3.threshold(2000,
rising=True,
falling=True,
all_vals=True)), 5, "Threshold failure.")
self.d4.add(0, 1, "Add")
self.d4.subtract(1, 0, header="Subtract")
self.d4.multiply(0, 1, header="Multiply")
self.d4.divide(0, 1, header="Divide")
self.d4.diffsum(0, 1, header="Diffsum")
self.assertTrue(
np.all(self.d4[0] == np.array([-0.5, -1, -3, 3, -1, 2])),
"Test column ops failed.")
d = Data(np.zeros((100, 1)))
d.add(0, 1.0)
self.assertEqual(np.sum(d[:, 0]), 100., "Add with a flot didn't work")
d.add(0, np.ones(100))
self.assertEqual(np.sum(d[:, 0]), 200., "Add with an array failed.")
def test_peaks(self):
d = self.d3.clone
d.peaks(width=8, poly=4, significance=100, modify=True)
self.assertEqual(len(d), 11, "Failed on peaks test.")
def test_threshold(self):
#set up some zigzag data
#mins at 0,100,200,300,400, max at 50, 150, 250, 350 and zeros in between
ar = np.zeros((400, 2))
ar[:, 0] = np.arange(0, len(ar))
for i in range(4):
ar[i * 100:i * 100 + 50, 1] = np.linspace(-1, 1, 50)
for i in range(4):
ar[i * 100 + 50:i * 100 + 100, 1] = np.linspace(1, -1, 50)
d = Data(ar, setas='xy')
self.assertTrue(
len(
d.threshold(0, rising=True, falling=False, all_vals=True) ==
4))
self.assertTrue(
len(
d.threshold(0, rising=False, falling=True, all_vals=True) ==
4))
self.assertTrue(
len(
d.threshold(0,
interpolate=False,
rising=False,
falling=True,
all_vals=True) == 4))
self.assertTrue(d.threshold(0, all_vals=True)[1] == 124.5)
self.thresh = d
self.assertTrue(
np.sum(
d.threshold([0.0, 0.5, 1.0]) -
np.array([[24.5, 36.74999999, 49.]])) < 1E-6,
"Multiple threshold failed.")
self.assertAlmostEqual(
d.threshold(0, interpolate=False, all_vals=True)[1], 124.5, 6,
"Threshold without interpolation failed.")
result = d.threshold(0, interpolate=False, all_vals=True, xcol=False)
self.assertTrue(
np.allclose(
result,
np.array([[24.5, 0.], [124.5, 0.], [224.5, 0.], [324.5, 0.]])),
"Failed threshold with False scol - result was {}".format(result))
def test_apply(self):
self.app = Data(np.zeros((100, 1)), setas="y")
self.app.apply(lambda r: r.i[0], header="Counter")
def calc(r, omega=1.0, k=1.0):
return np.sin(r.y * omega)
self.app.apply(calc,
replace=False,
header="Sin",
_extra={"omega": 0.1},
k=1.0)
self.app.apply(lambda r: r.__class__([r[1], r[0]]),
replace=True,
header=["Index", "Sin"])
self.app.setas = "xy"
self.assertAlmostEqual(self.app.integrate(),
-64.1722191259037,
msg="Integrate after aplies failed.")
