def testZeros(self):
importOp("Zeros")
v = Vec(32, False)
op = Zeros()
op.eval(v)
self.isAlmostEqualTo(v.getList(), 0.0, 9)
def testTriInverse(self):
from org.nmrfx.processor.operations import Tri
op = Tri(0, 1.0, 1.0, False)
v = Vec(1000, False)
v.ones()
op.eval(v)
iop = op.getInverseOp()
iop.eval(v)
self.isAlmostEqualTo(v.getList(), 1.0)
def testAdd(self):
importOp('Add')
v = Vec(256, True)
temp = v.getList()
real, imag = 1, 3
op = Add(real, imag, 0, -1)
op.eval(v)
for i, v in enumerate(v.getList()):
self.assertAlmostEqual(v.real, temp[i].real + real)
self.assertAlmostEqual(v.imag, temp[i].imag + imag)
def testSinebellApodInverseComplex(self):
v = Vec(1024, True)
v.ones()
offset = 0.5
end = 0.98
power = 1.0
c = 1.0
apodSize = 0
op = SinebellApod(offset, end, power, c, apodSize, False)
op.eval(v)
iop = op.getInverseOp()
iop.eval(v)
self.isAlmostEqualTo(v.getList(), 1.0)
def testOperation(self):
importOp("Operation")
class TestOperation(Operation):
__slots__ = ['a', 'b', 'c']
def __init__(self, a, b, c):
self.a = a
self.b = b
self.c = c
def eval(self, vector):
if len(vector) > 3:
vector.set(0, self.a, 0)
vector.set(1, self.b, 0)
vector.set(2, self.c, 0)
vector.set(3, self.a * self.b, self.c)
a, b, c = 2, 3, 4
op = TestOperation(a, b, c)
v = Vec(32, True)
op.eval(v)
self.assertEqual(v[0].real, a)
self.assertEqual(v[1].real, b)
self.assertEqual(v[2].real, c)
self.assertEqual(v[3].real, a * b)
self.assertEqual(v[3].imag, c)
def genSpectrum(self, size=1024):
importOp("Gen")
importOp("Ft")
v = Vec(size, True)
sw = 1000.0
dwell = 1.0 / sw
v.setDwellTime(dwell)
freq = sw / 4.0
lw = 10.0
amp = 100
ph = 0.0
op = Gen(freq, lw, amp, ph)
op.eval(v)
op = Ft(False, False)
op.eval(v)
return v
def testZFInverse(self):
from org.nmrfx.processor.operations import Zf
size = 31
newSize = 64
factor = None
pad = None
v = Vec(size, False)
op = Zf(factor, newSize, pad)
op.eval(v)
size2 = v.getSize()
self.assert_(newSize == size2)
iop = op.getInverseOp()
iop.eval(v)
size3 = v.getSize()
self.assert_(size == size3)
def test_case(size, pt1, pt2):
'''Pass in pt1, pt2, and vector size and verify that it is correct'''
v = Vec(size, False)
v.ones()
op = Tm(pt1, pt2)
op.eval(v)
for i in range(0, pt1):
self.assert_(v[i] < v[i + 1])
for i in range(pt1, pt2):
self.assert_(v[i] == v[i + 1])
for i in range(pt2, size - 1):
self.assert_(v[i] > v[i + 1])
self.assertAlmostEqual(v[pt1], 1.0)
self.assertAlmostEqual(v[pt1 / 2], 0.5, 5)
self.assertAlmostEqual(v[pt2], 1.0)
self.assertAlmostEqual(v[pt2 + (size - pt2) / 2], 0.5, 5)
def testIft(self):
importOp("Ft")
importOp("Ift")
importOp("Gen")
size = 1024
v = Vec(size, True)
vSave = Vec(size, True)
sw = 1000.0
dwell = 1.0 / sw
v.setDwellTime(dwell)
op = Gen(1000.0, 10.0, 100.0, 0.0)
op.eval(v)
v.copy(vSave)
op = Ft(False, False)
op.eval(v)
op = Ift()
op.eval(v)
v.subtract(vSave)
self.isAlmostEqualTo(v.getList(), 0.0)
def testApodization(self):
importOp('Apodization')
class MultByLineApod(Apodization):
def __init__(self, size):
self.resize(size)
self.setApodVec([float(i) / 256 for i in range(256)])
def eval(self, vector):
self.applyApod(vector)
return self
v = Vec(256, True)
v.ones()
op = MultByLineApod(256)
op.eval(v)
temp = v.getList()
for i, v in enumerate(temp):
self.assertEqual(i / 256.0, v)
def testFtInverse(self):
importOp("Ft")
importOp("Gen")
size = 1024
v = self.genSpectrum(size)
vSave = Vec(size, True)
v.copy(vSave)
op = Ft(False, False)
op.eval(v)
iop = op.getInverseOp()
iop.eval(v)
v.subtract(vSave)
self.isAlmostEqualTo(v.getList(), 0.0)
vSave.copy(v)
op = Ft(True, False)
op.eval(v)
iop = op.getInverseOp()
iop.eval(v)
v.subtract(vSave)
self.isAlmostEqualTo(v.getList(), 0.0)
vSave.copy(v)
op = Ft(False, True)
op.eval(v)
iop = op.getInverseOp()
iop.eval(v)
v.subtract(vSave)
self.isAlmostEqualTo(v.getList(), 0.0)
def testHft(self):
importOp("Hft")
size = 1024
v = self.genSpectrum(size)
vSave = Vec(size, True)
v.copy(vSave)
v.makeReal()
op = Hft()
op.eval(v)
v.subtract(vSave)
# fixme Hft generates some wiggle in baseline which requires relatively large tolerance here
self.isAlmostEqualTo(v.getList(), 0.0, 3)
def test_case(size=10, shift=1, complex=False, useApache=False):
v = Vec(10, complex)
if (useApache):
v.makeApache()
v.ones()
v.rand()
temp = v.getList()
shift = 3
op = Shift(shift)
op.eval(v)
for index, val in enumerate(v.getList()):
if index < shift:
self.assertEqual(val.real, 0)
if complex:
self.assertEqual(val.imag, 0)
else:
self.assertEqual(val.real, temp[index - shift].real)
if complex:
self.assertEqual(val.imag, temp[index - shift].imag)
def testOnes(self):
importOp("Ones")
v = Vec(32, False)
op = Ones()
op.eval(v)
self.isAlmostEqualTo(v.getList(), 1.0, 9)
v = Vec(32, True)
op.eval(v)
self.isAlmostEqualTo(v.getList(), 1.0, 9)
def testImag(self):
importOp("Imag")
size = 8
v = Vec(size, True)
v.set(0, 1.0, 2.0)
v.set(1, 3.0, 4.0)
values = v.getList()
op = Imag()
op.eval(v)
values = v.getList()
self.assert_(not v.isComplex())
self.assert_(values[0].real == 2.0)
self.assert_(values[1].real == 4.0)
def testZF(self):
from org.nmrfx.processor.operations import Zf
import math
log2 = lambda x: int(math.log(x) / math.log(2))
size = 32
newSize = 63
factor = None
pad = None
v = Vec(size, False)
op = Zf(factor, newSize, pad)
op.eval(v)
self.assert_(len(v) == newSize)
self.assert_(v.getSize() == newSize)
size = 64
v = Vec(size, False)
newSize = None
factor = 2
pad = None
op = Zf(factor, newSize, pad)
op.eval(v)
self.assert_(len(v) == 2**(2 + log2(size)))
self.assert_(v.getSize() == 2**(2 + log2(size)))
size = 100
v = Vec(size, False)
newSize = None
factor = None
pad = 15
op = Zf(factor, newSize, pad)
op.eval(v)
self.assert_(len(v) == size + pad)
self.assert_(v.getSize() == size + pad)
def testExpdInverse(self):
importOp("Expd")
from math import pi, exp
v = Vec(1025, False)
v.ones()
dwell = 1.0 / 1000.0
v.setDwellTime(dwell)
lb = 2.0
fPoint = 1.0
op = Expd(lb, fPoint, False)
op.eval(v)
iop = op.getInverseOp()
iop.eval(v)
self.isAlmostEqualTo(v.getList(), 1.0)
def testSinebellApod(self):
importOp("SinebellApod")
from math import pi, sin
#from 0 to Pi inclusive
v = Vec(1025, False)
v.ones()
#offset = 0.5
offset = 0.0
end = 1.0
power = 1.0
c = 1.0
apodSize = 0
temp = v.getList()
op = SinebellApod(offset, end, power, c, apodSize, False)
op.eval(v)
for val, index in zip([sin(i) for i in [pi * j / 4 for j in range(5)]],
[0, 256, 512, 768, 1024]):
self.assertAlmostEqual(val, v[index])
offset = 0.5
end = 1.5
v = Vec(1025, False)
v.ones()
op = SinebellApod(offset, end, power, c, apodSize, False)
op.eval(v)
for val, index in zip(
[sin(i) for i in [.5 * pi + pi * j / 4 for j in range(5)]],
[0, 256, 512, 768, 1024]):
self.assertAlmostEqual(val, v[index])
def testExpd(self):
importOp("Expd")
from math import pi, exp
v = Vec(1025, False)
v.ones()
dwell = 1.0 / 1000.0
v.setDwellTime(dwell)
lb = 2.0
fPoint = 1.0
op = Expd(lb, fPoint, False)
op.eval(v)
decay = pi * lb
for index, val in enumerate(v.getList()):
testVal = exp(-1.0 * index * decay * dwell)
self.assertAlmostEqual(val, testVal)
def testGf(self):
importOp("Gf")
from math import pi, exp
v = Vec(1025, False)
v.ones()
dwell = 1.0 / 1000.0
v.setDwellTime(dwell)
gf = 0.5
gfs = 0.1
fPoint = 1.0
op = Gf(gf, gfs, fPoint)
op.eval(v)
def testGmbInverse(self):
importOp("Gmb")
from math import pi, exp
v = Vec(1025, False)
v.ones()
dwell = 1.0 / 1000.0
v.setDwellTime(dwell)
gb = 0.1
lb = 2.0
fPoint = 1.0
op = Gmb(gb, lb, fPoint)
op.eval(v)
iop = op.getInverseOp()
iop.eval(v)
self.isAlmostEqualTo(v.getList(), 1.0)
def testGfInverse(self):
importOp("Gf")
from math import pi, exp
v = Vec(1025, False)
v.ones()
dwell = 1.0 / 1000.0
v.setDwellTime(dwell)
gf = 0.5
gfs = 0.1
fPoint = 1.0
op = Gf(gf, gfs, fPoint)
op.eval(v)
iop = op.getInverseOp()
iop.eval(v)
self.isAlmostEqualTo(v.getList(), 1.0)
def testDx(self):
v = Vec(1000, False)
v = v.rand()
def testGen(self):
importOp("Gen")
size = 1024
v = Vec(size, True)
sw = 1000.0
dwell = 1.0 / sw
v.setDwellTime(dwell)
freq = sw / 4.0
lw = 10.0
amp = 100
ph = 0.0
op = Gen(freq, lw, amp, ph)
op.eval(v)
values = v.getList()
# check amplitude is amp
self.assertAlmostEqual(values[0], amp)
v.zeros()
op = Gen(freq, lw, amp, 90.0)
op.eval(v)
values = v.getList()
# check imaginary amplitude is amp when phase is 90
self.assertAlmostEqual(values[0].imag, amp)
v.zeros()
op = Gen(freq, lw, amp, 0.0)
op.eval(v)
v.ft()
peakCenter = size * 3 / 4
values = v.getList()
# check if expected peak position is max
self.assert_(v[peakCenter - 1].real < v[peakCenter].real)
self.assert_(v[peakCenter + 1].real < v[peakCenter].real)
# check if peak is symmetrical
self.assertAlmostEqual(values[peakCenter - 2].real,
values[peakCenter + 2].real)
v.zeros()
op = Gen(freq, lw, amp, 0.0)
op.eval(v)
op.eval(v)
values = v.getList()
# check if additive (successive calls don't zero first)
self.assertAlmostEqual(values[0].real, 2.0 * amp)
def offtestIstCL(self):
importOp("IstCL")
importOp("Ft")
importOp("Add")
import pyproc
from java.util import ArrayList
#testing single Vector FFT with JavaCL and comparing the result to
#the vector.ft method
vec = Vec(1024, True)
self.assert_(vec.useApache())
pyproc.GEN(vector=vec)
vectors = ArrayList()
vectors.add(vec)
op = IstCL(1)
op.initializeVectors(vectors)
op.initializeBuffers()
#op.onePass(vectors)
op.parallelfft(False)
op.copyBack(vectors, False)
op.finish()
vec2 = Vec(1024, True)
pyproc.GEN(vector=vec2)
op = Ft(False, False)
op.eval(vec2)
#vec2.ft()
#testing fft
for (v1, v2) in zip(vec.getList(), vec2.getList()):
self.assertAlmostEqual(v1.real, v2.real, 12)
self.assertAlmostEqual(v1.imag, v2.imag, 12)
'''
test norm
'''
vec1 = Vec(32, True)
vec2 = Vec(32, True)
add = Add(100.0, 100.0)
add.eval(vec1)
add.eval(vec2)
set_max_index = 31
vec1.set(set_max_index, 101.0, 101.0)
vec2.set(set_max_index, 101.0, 101.0)
op = IstCL(1)
vectors = ArrayList()
vectors.add(vec1)
op.initializeVectors(vectors)
op.initializeBuffers()
op.declareComplexNorm()
op.declareReduceMax()
op.norm()
norms = op.copyBackNormBuffer()
op.reduceMax()
m = op.copyBackMaxBuffer()
index = op.copyBackMaxIndexBuffer()
print index
op.finish()
vec2norm = [i.real**2 + i.imag**2 for i in vec2.getList()]
for v1, v2 in zip(norms, vec2norm):
self.assertEqual(v1, v2)
self.assertEqual(m, 101 * 101 + 101 * 101)
self.assertAlmostEqual(index, set_max_index)
#for (v1, v2) in zip(vec1.getList(), vec2.getList()):
# self.assertAlmostEqual(v1.real, v2.real, 12)
# self.assertAlmostEqual(v1.imag, v2.imag, 12)
'''Test thresholding without fft'''
vec1 = Vec(256, True)
vec2 = Vec(256, True)
vec1.ones()
vec2.ones()
vec1.multiply(100.0, 0)
vec2.multiply(3.04, 0)
#vec2.ft();
#vec2.ift();
#if we have a threshold of .96, then all values will be thresholded by
#96.96 and will be reduced to 3.04
vec1.setComplex(2, 101.0, 0.0)
vec2.setComplex(2, 3.04, 0.0)
op = IstCL(1)
vectors = ArrayList()
vectors.add(vec1)
op.initializeVectors(vectors)
op.initializeBuffers()
op.norm()
op.reduceMax()
op.threshold()
op.copyBack(vectors, True)
op.finish()
for (i, (v1, v2)) in enumerate(zip(vec1.getList(), vec2.getList())):
print i
self.assertAlmostEqual(v1.real, v2.real, 12)
self.assertAlmostEqual(v1.imag, v2.imag, 12)
'''
def testTri(self):
from org.nmrfx.processor.operations import Tri
op = Tri(0, 1.0, 1.0, False)
v = Vec(1000, False)
v.ones()
op.eval(v)
for i in range(v.getSize()):
self.assertAlmostEqual(v[i], 1.0)
self.assertEqual(v.getReal(0), 1.0)
self.assertEqual(v.getReal(999), 1.0)
op = Tri(500, -10.0, 10.0, False)
v1 = Vec(1000, False)
v1.ones()
op.eval(v1)
self.assertAlmostEqual(v1.getReal(0), -10.0)
self.assertAlmostEqual(v1.getReal(999), 10.0)
for i in range(v.getSize() - 1):
self.assert_(v[i] <= v[i + 1])
v2 = Vec(100, False)
v2.ones()
op = Tri(0, 0.0, 2.0, False)
op.eval(v2)
self.assertAlmostEqual(v2.getReal(0), 1.0)
self.assertAlmostEqual(v2.getReal(49), 1.5, 1)
self.assertAlmostEqual(v2.getReal(99), 2.0)
for i in range(v.getSize() - 1):
self.assert_(v[i] <= v[i + 1])