more cleanup

tests/bottom_reference/generate.py

@@ -58,7 +58,7 @@
 
 # Calculate the exact reflection coefficient (not the reflectivity!)
 ampl = models[3].amplitude()
-numpy.savetxt("sim/reflection.dat", zip(ampl[0], ampl[1].real, -ampl[1].imag))
+np.savetxt("sim/reflection.dat", zip(ampl[0], ampl[1].real, -ampl[1].imag))
 
 # plot the reflectivity
 problem = MultiFitProblem([models[0], models[1], models[2]])

tests/bottom_reference/test_reconstruction.py

@@ -1,31 +1,36 @@
+from os.path import dirname, realpath, join as joinpath
 import pylab
-import numpy
+import numpy as np
 
 from refl1d.names import *
 
 from direfl.api.reference_layer import BottomReferenceVariation
 from direfl.api.sld_profile import ConcatSLDProfile, ConstantSLDProfile, FunctionSLDProfile
 
+ROOT = dirname(realpath(__file__))
+def getdata(filename):
+    return joinpath(ROOT, "sim", filename)
+
 # SLD: Si: ~2.1 (2.1 is set precisely in generate.py)
 #      Air: 0
 var = BottomReferenceVariation(0e-6, 2.1e-6)
 
 sld = FunctionSLDProfile(lambda x: 4e-6 if x < 15 else 5e-6, [0, 30], 15)
 sld_concat = ConcatSLDProfile([ConstantSLDProfile(5.0e-6, 15), ConstantSLDProfile(5.5e-6, 35)])
 
-var.load('sim/generate-1-refl.datA', sld)
-var.load('sim/generate-2-refl.datA', sld_concat)
-# var.load('sim/generate-3-refl.datA', ConstantSLDProfile(6.0e-6, 70))
+var.load(getdata("generate-1-refl.datA"), sld)
+var.load(getdata("generate-2-refl.datA"), sld_concat)
+# var.load(getdata("generate-3-refl.datA"), ConstantSLDProfile(6.0e-6, 70))
 var.run()
 
 def load_reflection(file):
-    q, real, imag = numpy.loadtxt(file).T
+    q, real, imag = np.loadtxt(file).T
     return q, real + 1j * imag
 
-q, r = load_reflection("sim/reflection.dat")
+q, r = load_reflection(getdata("reflection.dat"))
 
 # Load the exact reflection coefficient
-# exact_amplitude = numpy.loadtxt('sim/reflection.dat').T
+# exact_amplitude = np.loadtxt('sim/reflection.dat').T
 
 pylab.plot(q, 1e4 * r.real * q ** 2)
 pylab.plot(q, 1e4 * r.imag * q ** 2)
@@ -50,7 +55,7 @@ def load_reflection(file):
 # fourier.method = fourier.cosine_transform
 rec = PotentialReconstruction(250, 4, cutoff=2)
 pot = rec.reconstruct(fourier)
-x_space = numpy.linspace(0, 250, 1001)
+x_space = np.linspace(0, 250, 1001)
 
 pylab.plot(x_space, [pot(x) for x in x_space])
 pylab.show()

tests/rough_reference/generate.py

@@ -4,7 +4,7 @@
 
 # Call via: refl1d generate.py --store=sim --steps=0 --simulate --noise=1e-10
 data = load4("sim/generate-1-refl.datA", name="data", columns="Q dQ R dR", radiation="neutron",
-             L=4, dL=1e-9, simulation_range=numpy.linspace(0, 1, 5001))
+             L=4, dL=1e-9, simulation_range=np.linspace(0, 1, 5001))
 
 Si = Material("Si", name="Si")
 Cu = Material("Cu")

tests/rough_reference/test_reconstruction.py

@@ -1,11 +1,16 @@
+from os.path import dirname, realpath, join as joinpath
 import pylab
-import numpy
+import numpy as np
 
 from refl1d.names import *
 
 from direfl.api.reference_layer import BottomReferenceVariation
 from direfl.api.sld_profile import ConcatSLDProfile, ConstantSLDProfile, FunctionSLDProfile, MircoSlabSLDProfile
 
+ROOT = dirname(realpath(__file__))
+def getdata(filename):
+    return joinpath(ROOT, "sim", filename)
+
 # SLD: Si: ~2.1 (2.1 is set precisely in generate.py)
 #      Air: 0
 b = 1.5e-6
@@ -26,26 +31,26 @@
 t6 = MircoSlabSLDProfile([0, 30.1], [7], [b, 5e-6], 4)
 
 
-var.load('sim/generate-1-refl.datA', ConcatSLDProfile([t1, t5]))
-#var.load('sim/generate-1-refl.datA', t1)
-#var.load('sim/generate-2-refl.datA', t2)
-#var.load('sim/generate-3-refl.datA', t3)
-#var.load('sim/generate-2-refl.datA', ConcatSLDProfile([t2, t5]))
-#var.load('sim/generate-3-refl.datA', ConcatSLDProfile([t3, t5]))
-var.load('sim/generate-4-refl.datA', ConcatSLDProfile([t4, t5]))
-var.load('sim/generate-5-refl.datA', t6)
+var.load(getdata("generate-1-refl.datA"), ConcatSLDProfile([t1, t5]))
+#var.load(getdata("generate-1-refl.datA"), t1)
+#var.load(getdata("generate-2-refl.datA"), t2)
+#var.load(getdata("generate-3-refl.datA"), t3)
+#var.load(getdata("generate-2-refl.datA"), ConcatSLDProfile([t2, t5]))
+#var.load(getdata("generate-3-refl.datA"), ConcatSLDProfile([t3, t5]))
+var.load(getdata("generate-4-refl.datA"), ConcatSLDProfile([t4, t5]))
+var.load(getdata("generate-5-refl.datA"), t6)
 var.run()
 
 
 def load_reflection(file):
-    q, real, imag = numpy.loadtxt(file).T
+    q, real, imag = np.loadtxt(file).T
     return q, real + 1j * imag
 
 
-q, r = load_reflection("sim/reflection.dat")
+q, r = load_reflection(getdata("reflection.dat"))
 
 # Load the exact reflection coefficient
-# exact_amplitude = numpy.loadtxt('sim/reflection.dat').T
+# exact_amplitude = np.loadtxt('sim/reflection.dat').T
 
 pylab.plot(q, 1e4 * r.real * q ** 2)
 pylab.plot(q, 1e4 * r.imag * q ** 2)
@@ -72,7 +77,7 @@ def load_reflection(file):
 # fourier.method = fourier.cosine_transform
 rec = PotentialReconstruction(250, 4, cutoff=2)
 pot = rec.reconstruct(fourier)
-x_space = numpy.linspace(0, 250, 1001)
+x_space = np.linspace(0, 250, 1001)
 
 pylab.plot(x_space, [pot(x) for x in x_space])
 pylab.show()

tests/top_reference/test_reconstruction.py

@@ -1,31 +1,36 @@
+from os.path import dirname, realpath, join as joinpath
 import pylab
-import numpy
+import numpy as np
 
 from refl1d.names import *
 
 from direfl.api.reference_layer import TopReferenceVariation
 from direfl.api.sld_profile import ConcatSLDProfile, ConstantSLDProfile, FunctionSLDProfile
 
+ROOT = dirname(realpath(__file__))
+def getdata(filename):
+    return joinpath(ROOT, "sim", filename)
+
 # SLD: Si: ~2.1 (2.1 is set precisely in generate.py)
 #      Air: 0
 var = TopReferenceVariation(0e-6, 1.5e-6)
 
-var.load('sim/generate-1-refl.datA', ConstantSLDProfile(4e-6, 0))
-var.load('sim/generate-2-refl.datA', ConstantSLDProfile(4e-6, 35))
-var.load('sim/generate-3-refl.datA', ConstantSLDProfile(4e-6, 36))
-var.load('sim/generate-4-refl.datA', ConstantSLDProfile(5.64e-6, 38.35))
+var.load(getdata("generate-1-refl.datA"), ConstantSLDProfile(4e-6, 0))
+var.load(getdata("generate-2-refl.datA"), ConstantSLDProfile(4e-6, 35))
+var.load(getdata("generate-3-refl.datA"), ConstantSLDProfile(4e-6, 36))
+var.load(getdata("generate-4-refl.datA"), ConstantSLDProfile(5.64e-6, 38.35))
 var.run()
 
 
 def load_reflection(file):
-    q, real, imag = numpy.loadtxt(file).T
+    q, real, imag = np.loadtxt(file).T
     return q, real + 1j * imag
 
 
-q, r = load_reflection("sim/reflection.dat")
+q, r = load_reflection(getdata("reflection.dat"))
 
 # Load the exact reflection coefficient
-# exact_amplitude = numpy.loadtxt('sim/reflection.dat').T
+# exact_amplitude = np.loadtxt('sim/reflection.dat').T
 
 pylab.plot(q, 1e4 * r.real * q ** 2)
 pylab.plot(q, 1e4 * r.imag * q ** 2)
@@ -55,7 +60,7 @@ def load_reflection(file):
 # fourier.method = fourier.cosine_transform
 rec = PotentialReconstruction(400, 4, cutoff=2)
 pot = rec.reconstruct(fourier)
-x_space = numpy.linspace(0, 400, 1001)
+x_space = np.linspace(0, 400, 1001)
 
 pylab.plot(x_space, [pot(x) for x in x_space])
 pylab.show()