def testDdsSubdAttributes(self):
"""
Test :prop:`Dds.subd` and :prop:`Dds.subd_h` objects.
"""
dds = mango.zeros(shape=self.shape, dtype="uint16", mpidims=(0, 1, 1))
self.assertEqual(0, dds[0, 0, 0])
dds[0, 0, 0] = 1
self.assertEqual(1, dds[0, 0, 0])
self.assertEqual(1, dds.subd[0, 0, 0])
self.assertEqual(1, dds.subd_h[0, 0, 0])
for h in (0, 1, 2, 3):
for halo in ((h, h, h), (2 * h, h // 2, h), (h, 2 * h, h // 2)):
dds = mango.zeros(shape=self.shape, dtype="uint16", halo=halo)
rootLogger.info("====")
rootLogger.info(
"dds.halo = %s" %
(dds.halo, ))
rootLogger.info(
"dds.subd.origin = %s" %
(dds.subd.origin, ))
rootLogger.info(
"dds.subd.shape = %s" %
(dds.subd.shape, ))
rootLogger.info(
"dds.subd.asarray().shape = %s" %
(dds.subd.asarray().shape, ))
rootLogger.info(
"dds.subd_h.asarray().shape = %s" %
(dds.subd_h.asarray().shape, ))
rootLogger.info(
"dds.subd_h.asarray().shape-(2*dds.halo) = %s" %
(dds.subd_h.asarray().shape - (2 * dds.halo), ))
rootLogger.info(
"dds.subd_h.origin = %s" %
(dds.subd_h.origin, ))
rootLogger.info(
"dds.subd_h.shape = %s" %
(dds.subd_h.shape, ))
self.assertTrue(
sp.all(dds.subd.origin == (dds.subd_h.origin + dds.halo)))
self.assertTrue(
sp.all(dds.subd.shape == (dds.subd_h.shape -
(2 * dds.halo))))
self.assertTrue(
sp.all(dds.subd.asarray().shape == (
dds.subd_h.asarray().shape - (2 * dds.halo))))
self.assertEqual(
0,
dds.subd_h.asarray()[halo[0], halo[1], halo[2]])
self.assertEqual(0, dds.subd.asarray()[0, 0, 0])
dds.subd.asarray()[0, 0, 0] = 1
self.assertEqual(1, dds.subd.asarray()[0, 0, 0])
self.assertEqual(
1,
dds.subd_h.asarray()[halo[0], halo[1], halo[2]])
def testCircularCylinderFill(self):
dir = self.createTmpDir("testCircularCylinderFill")
#dir = "."
dds = mango.zeros(shape=self.shape, dtype="uint16")
c = dds.shape*0.5
r = np.min(dds.shape-3)*0.5
axislen = dds.shape[0]*2
mango.data.fill_circular_cylinder(dds, c, r, axislen, fill=1)
mango.io.writeDds(os.path.join(dir, "tomoCyl0.nc"), dds)
dds1 = mango.zeros(shape=self.shape, dtype="uint16", origin=(100, 55, 13))
c = dds.shape*0.5
r = np.min(dds.shape-3)*0.5
axislen = dds.shape[0]*2
mango.data.fill_circular_cylinder(dds1, c, r, axislen, fill=1)
mango.io.writeDds(os.path.join(dir, "tomoCyl1.nc"), dds1)
self.assertTrue(sp.all(dds.subd.asarray() == dds1.subd.asarray()))
del dds1
dds2 = mango.zeros(shape=self.shape, mtype="tomo", origin=(100, 55, 13))
dds2.md.setVoxelSize((0.1,0.1,0.1), "cm")
c = dds.shape*0.5
r = np.min(dds.shape-3)*0.5
axislen = dds.shape[0]*2
mango.data.fill_circular_cylinder(dds2, c, r, axislen, fill=1, unit="mm")
mango.io.writeDds(os.path.join(dir, "tomoCyl2.nc"), dds2)
self.assertTrue(sp.all(dds.subd.asarray() == dds2.subd.asarray()))
del dds2
dds3 = mango.zeros(shape=self.shape, mtype="tomo", origin=(100, 55, 13))
dds3.md.setVoxelSize((2.5,2.5,2.5), "um")
c = dds.shape*0.5*dds3.md.getVoxelSize("mm")
r = np.min(dds.shape-3)*0.5*dds3.md.getVoxelSize("mm")[0]
axislen = dds.shape[0]*2*dds3.md.getVoxelSize("mm")[0]
mango.data.fill_circular_cylinder(dds3, c, r, axislen, fill=1, unit="mm")
mango.io.writeDds(os.path.join(dir, "tomoCyl3.nc"), dds3)
self.assertTrue(sp.all(dds.subd.asarray() == dds3.subd.asarray()))
del dds3
dds4 = mango.zeros(shape=self.shape, mtype="tomo", origin=(100, 55, 13))
dds4.md.setVoxelSize((2.5,2.5,2.5), "um")
c = (dds4.origin + dds.shape*0.5)*dds4.md.getVoxelSize("mm")
r = np.min(dds.shape-3)*0.5*dds4.md.getVoxelSize("mm")[0]
axislen = dds.shape[0]*2*dds4.md.getVoxelSize("mm")[0]
mango.data.fill_circular_cylinder(dds4, c, r, axislen, fill=1, unit="mm", coordsys="abs")
mango.io.writeDds(os.path.join(dir, "tomoCyl4.nc"), dds4)
self.assertTrue(sp.all(dds.subd.asarray() == dds4.subd.asarray()))
del dds4
def testDdsAsArray(self):
"""
Test the :meth:`Dds.asarray` method.
"""
dds = mango.zeros(shape=self.shape, dtype="uint16", mpidims=(0, 1, 1))
self.assertEqual(0, dds[0, 0, 0])
a = dds.asarray()
a += 10
self.assertEqual(10, dds[0, 0, 0])
a -= 10
self.assertEqual(0, dds[0, 0, 0])
a = dds.asarray()
del dds
a += 10
self.assertEqual(10, a[0, 0, 0])
a0 = self.createTmpArrayFromDds()
self.assertEqual(0, a0[0, 0, 0])
a0 += 16
self.assertEqual(16, a0[0, 0, 0])
a += 20
self.assertEqual(30, a[0, 0, 0])
def testDdsCreateFloat16(self):
"""
Test the :func:`mango.empty` and :func:`mango.ones`
and :func:`mango.zeros` methods for :samp:`dtype="float16"`
and :samp:`mtype="float16"`.
"""
if (mango.haveFloat16):
dds = mango.empty(shape=self.shape, dtype="float16")
fVal = np.float16(2.25)
dds.setAllToValue(fVal)
self.assertEqual(fVal, dds[0])
self.assertEqual(fVal, dds[0, 0, 0])
self.assertEqual(fVal, dds[(0, 0, 0)])
dds = mango.zeros(shape=self.shape, mtype="float16")
fVal = np.float16(2.25)
dds.asarray()[...] += fVal
self.assertEqual(fVal, dds[0])
self.assertEqual(fVal, dds[0, 0, 0])
self.assertEqual(fVal, dds[(0, 0, 0)])
dds = mango.ones(shape=self.shape, mtype="float16")
fVal = np.float16(2.25)
dds.asarray()[...] *= fVal
self.assertEqual(fVal, dds[0])
self.assertEqual(fVal, dds[0, 0, 0])
self.assertEqual(fVal, dds[(0, 0, 0)])
def testNonDistributedMetric(self):
if ((mpi.world == None) or (mpi.world.Get_size() == 1)):
img = mango.zeros((128, 64, 64), mtype="tomo")
img.md.setVoxelSize((1, 1, 1), "voxel")
c = img.origin + img.shape * 0.5
r = np.min(img.shape) * 0.4
a = (1, 0, 0)
mango.data.fill_circular_cylinder(img,
c,
r,
img.shape[0] * 1.1,
fill=32000,
coordsys="abs",
unit="voxel")
metric = cylinder_fit_gradient_metric()
metric.setGradientFromImage(img)
x = metric.getDefaultX()
rootLogger.info("Default x = %s" % (x, ))
x[metric.CENTRE_X_IDX] = c[2]
x[metric.CENTRE_Y_IDX] = c[1]
x[metric.CENTRE_Z_IDX] = c[0]
x[metric.AXIS_X_IDX] = a[2]
x[metric.AXIS_Y_IDX] = a[1]
x[metric.AXIS_Z_IDX] = a[0]
bestSoln = (0, 0)
for rr in range(-5, 6):
x[metric.RADIUS_IDX] = r + rr
val = metric(x)
if (val > bestSoln[0]):
bestSoln = (val, x[metric.RADIUS_IDX])
rootLogger.info("metric[%s] = %16.2f" % (x, val))
self.assertEqual(bestSoln[1], r)
self.assertLess(0, bestSoln[0])
def testMultiResFit1(self):
dir = self.createTmpDir("CylinderFitMultiResTest_testMultiResFit1")
#dir = "."
rootLogger.info("Generating synthetic image...")
#img = mango.zeros((128+((mpi.size//8)*16),64,64), mtype="tomo")
img = mango.zeros((512+((mpi.size//8)*16),256,256), mtype="tomo")
#img = mango.zeros((1024,512,512), mtype="tomo")
img.md.setVoxelSize((0.002,0.002,0.002), "mm")
c = (img.origin + img.shape*0.5)*img.md.getVoxelSize()
r = np.min(img.shape*img.md.getVoxelSize())*0.4
a = (1,0,0)
img.subd_h.asarray()[...] = 10000
mango.data.fill_circular_cylinder(img, c, r, img.shape[0]*1.1, fill=25000, coordsys="abs", unit=img.md.getVoxelSizeUnit())
img.subd.asarray()[...] += mango.data.gaussian_noise_like(img, mean=0, stdd=300).subd.asarray()
mango.io.writeDds(os.path.join(dir,"tomoCyl1.nc"), img)
rootLogger.info("Done generating synthetic image.")
fit, cylImg = cylinder_fit_multi_res(img, 1, resolutions=[64, 128, 512], retcylimg=True, metricThreshRelTol=0.50)
mango.io.writeDds(os.path.join(dir,"segmentedCyl1AnnularMsk.nc"), cylImg)
rootLogger.info("Img voxel size = %s %s" % (img.md.getVoxelSize(), img.md.getVoxelSizeUnit()))
rootLogger.info("Cyl img voxel size = %s %s" % (cylImg.md.getVoxelSize(), cylImg.md.getVoxelSizeUnit()))
rootLogger.info("c=%s, r=%s, a=%s" % (c,r,a))
rootLogger.info("Fit Results:\n%s" % ("\n".join(map(str,fit)),))
f0 = fit[0]
self.assertAlmostEqual(c[1], f0[1][0][1], 3)
self.assertAlmostEqual(c[2], f0[1][0][2], 3)
self.assertAlmostEqual(r, f0[1][1], 3)
self.assertAlmostEqual(sp.absolute(sp.dot(a, f0[1][3])), 1.0, 3)
def testNonDistributedMetric(self):
if ((mpi.world == None) or (mpi.world.Get_size() == 1)):
img = mango.zeros((128,64,64), mtype="tomo")
img.md.setVoxelSize((1,1,1), "voxel")
c = img.origin + img.shape*0.5
r = np.min(img.shape)*0.4
a = (1,0,0)
mango.data.fill_circular_cylinder(img, c, r, img.shape[0]*1.1, fill=32000, coordsys="abs", unit="voxel")
metric = cylinder_fit_gradient_metric()
metric.setGradientFromImage(img)
x = metric.getDefaultX()
rootLogger.info("Default x = %s" % (x,))
x[metric.CENTRE_X_IDX] = c[2]
x[metric.CENTRE_Y_IDX] = c[1]
x[metric.CENTRE_Z_IDX] = c[0]
x[metric.AXIS_X_IDX] = a[2]
x[metric.AXIS_Y_IDX] = a[1]
x[metric.AXIS_Z_IDX] = a[0]
bestSoln = (0,0)
for rr in range(-5, 6):
x[metric.RADIUS_IDX] = r + rr
val = metric(x)
if (val > bestSoln[0]):
bestSoln = (val, x[metric.RADIUS_IDX])
rootLogger.info("metric[%s] = %16.2f" % (x, val))
self.assertEqual(bestSoln[1], r)
self.assertLess(0, bestSoln[0])
def testNonDistributedOptimization(self):
if ((mpi.world == None) or (mpi.world.Get_size() == 1)):
img = mango.zeros((128, 64, 64), mtype="tomo")
img.md.setVoxelSize((1, 1, 1), "voxel")
c = img.origin + img.shape * 0.5
r = np.min(img.shape) * 0.4
a = (1, 0, 0)
mango.data.fill_circular_cylinder(img,
c,
r,
img.shape[0] * 1.1,
fill=32000,
coordsys="abs",
unit="voxel")
metric = cylinder_fit_gradient_metric()
metric.setGradientFromImage(img)
x = metric.getDefaultX()
rootLogger.info("Default x = %s" % (x, ))
x[metric.RADIUS_IDX] = r
x[metric.CENTRE_X_IDX] = c[2]
x[metric.CENTRE_Y_IDX] = c[1]
x[metric.CENTRE_Z_IDX] = c[0]
x[metric.AXIS_X_IDX] = a[2]
x[metric.AXIS_Y_IDX] = a[1]
x[metric.AXIS_Z_IDX] = a[0]
solnX = x.copy()
bestRes = None
for rr in range(-5, 6):
x[metric.RADIUS_IDX] = r + rr
res = sp.optimize.minimize(
lambda x: -sp.absolute(metric(x)),
x[0:6],
method="Powell",
options={
'xtol': 1.0e-1,
'ftol': 1.0e-2
})
#res = sp.optimize.minimize(metric, x[0:6], jac=False, method="BFGS", options={'gtol':1.0e3, 'eps':(0.05,0.05,0.05,0.001,0.001,0.001)})
rootLogger.info(
"result.success = %s, result.message = %s" %
(res.success, res.message))
rootLogger.info(
"optimized (metric_val, x) = (%16.2f, %s) = " %
(res.fun, res.x))
rootLogger.info("res.nfev = %8d" % (res.nfev, ))
if ((bestRes == None) or (res.fun < bestRes.fun)):
bestRes = res
bestRes.x[3:] /= sp.sqrt(sp.sum(bestRes.x[3:] * bestRes.x[3:]))
rootLogger.info("soln x = %s" % (solnX[0:bestRes.x.size], ))
rootLogger.info("best x = %s" % (bestRes.x, ))
self.assertTrue(
sp.all(
sp.absolute(bestRes.x -
solnX[0:bestRes.x.size]) < 0.1))
self.assertGreater(0, bestRes.fun)
def testCircularAnnularCylinderFillRotated(self):
dir = self.createTmpDir("testCircularAnnularCylinderFillRotated")
#dir = "."
dds = mango.zeros(shape=self.shape, mtype="segmented")
c = dds.shape*0.5
r = np.min(dds.shape-3)*0.35
w = np.min(dds.shape-3)*0.1
axislen = dds.shape[0]*2.
rm = np.dot(mango.math.rotation_matrix(-10, 1), mango.math.rotation_matrix(20, 2))
mango.data.fill_annular_circular_cylinder(dds, c, r, w, axislen, fill=1, rotation=rm)
mango.io.writeDds(os.path.join(dir, "segmentedAnnularCyl0_rotmtx.nc"), dds)
(axis, angle) = mango.math.axis_angle_from_rotation_matrix(rm)
rm = mango.math.axis_angle_to_rotation_matrix(axis, angle)
dds = mango.zeros(shape=self.shape, mtype="segmented")
mango.data.fill_annular_circular_cylinder(dds, c, r, w, axislen, fill=1, rotation=rm)
mango.io.writeDds(os.path.join(dir, "segmentedAnnularCyl0_rotmtxaa.nc"), dds)
dds1 = mango.zeros(shape=self.shape, mtype="segmented")
mango.data.fill_annular_circular_cylinder(dds1, c, r, w, axislen, fill=1, rotation=(axis, angle))
mango.io.writeDds(os.path.join(dir, "segmentedAnnularCyl1_axang.nc"), dds1)
self.assertTrue(sp.all(dds.subd.asarray() == dds1.subd.asarray()))
del dds1
dds1 = mango.zeros(shape=self.shape, mtype="segmented")
mango.data.fill_annular_circular_cylinder(dds1, c, r, w, axislen, fill=1, rotation=(axis.tolist(), angle))
mango.io.writeDds(os.path.join(dir, "segmentedAnnularCyl2_axlistang.nc"), dds1)
self.assertTrue(sp.all(dds.subd.asarray() == dds1.subd.asarray()))
del dds1
dds2 = mango.zeros(shape=self.shape, mtype="segmented")
mango.data.fill_annular_circular_cylinder(dds2, c, r, w, axislen, fill=1, rotation=(angle, axis.tolist()))
mango.io.writeDds(os.path.join(dir, "segmentedAnnularCyl3_angaxlist.nc"), dds2)
self.assertTrue(sp.all(dds.subd.asarray() == dds2.subd.asarray()))
del dds2
dds3 = mango.zeros(shape=self.shape, mtype="segmented")
mango.data.fill_annular_circular_cylinder(dds3, c, r, w, axislen, fill=1, rotation=(angle, axis))
mango.io.writeDds(os.path.join(dir, "segmentedAnnularCyl4_angax.nc"), dds3)
self.assertTrue(sp.all(dds.subd.asarray() == dds3.subd.asarray()))
del dds3
dds4 = mango.zeros(shape=self.shape, mtype="segmented")
mango.data.fill_annular_circular_cylinder(dds4, c, r, w, axislen, fill=1, rotation=angle*axis)
mango.io.writeDds(os.path.join(dir, "segmentedAnnularCyl5_axis.nc"), dds4)
self.assertTrue(sp.all(dds.subd.asarray() == dds4.subd.asarray()))
del dds4
dds5 = mango.zeros(shape=self.shape, mtype="segmented")
mango.data.fill_annular_circular_cylinder(dds5, c, r, w, axislen, fill=1, rotation=(angle*axis).tolist())
mango.io.writeDds(os.path.join(dir, "segmentedAnnularCyl4_axislist.nc"), dds5)
self.assertTrue(sp.all(dds.subd.asarray() == dds5.subd.asarray()))
del dds5
def _testNonDistributedMetricFit3(self):
dir = self.createTmpDir(
"CylinderFitTest_testNonDistributedMetricFit3")
#dir = "."
rootLogger.info("Generating synthetic image...")
#img = mango.zeros((128+((mpi.size//8)*16),64,64), mtype="tomo")
img = mango.zeros((256 + ((mpi.size // 8) * 16), 128, 128),
mtype="tomo")
#img = mango.zeros((1024,512,512), mtype="tomo")
img.md.setVoxelSize((0.002, 0.002, 0.002), "mm")
c = (img.origin + img.shape * 0.5) * img.md.getVoxelSize()
r = np.min(img.shape * img.md.getVoxelSize()) * 0.4
a = sp.array((1., 0., 0.))
cList = [c, c, c + (img.shape * 0.02) * img.md.getVoxelSize()]
rList = [r, 0.8 * r, 0.65 * r]
aList = [a, a, sp.array([1.0, 0.01, 0.02])]
fList = [20000, 15000, 18000]
img.subd_h.asarray()[...] = 10000
for i in range(len(cList)):
rMtx = mango.math.rotation_matrix_from_cross_prod(
sp.array([1., 0., 0.]), aList[i])
mango.data.fill_circular_cylinder(
img,
cList[i],
rList[i],
img.shape[0] * 1.25,
fill=fList[i],
rotation=rMtx,
coordsys="abs",
unit=img.md.getVoxelSizeUnit())
img.subd.asarray()[...] += mango.data.gaussian_noise_like(
img, mean=0, stdd=300).subd.asarray()
mango.io.writeDds(os.path.join(dir, "tomoCyl3.nc"), img)
rootLogger.info("Done generating synthetic image.")
fit, cylImg = \
cylinder_fit(
img,
numcyl=3,
retcylimg=True,
distributedMetricEvaluation=False,
metricThreshRelTol=0.5
)
mango.io.writeDds(os.path.join(dir, "segmentedCyl3AnnularMsk.nc"),
cylImg)
rootLogger.info("Voxel size = %s %s" %
(img.md.getVoxelSize(), img.md.getVoxelSizeUnit()))
for i in range(len(cList)):
rootLogger.info("c%s=%s, r%s=%s, a%s=%s" %
(i, cList[i], i, rList[i], i, aList[i]))
rootLogger.info("Fit Results:\n%s" % ("\n".join(map(str, fit)), ))
def testDdsCreateComplex(self):
"""
Test the :func:`mango.empty` and :func:`mango.ones`
and :func:`mango.zeros` methods for dtype=complex64/complex128.
"""
dds = mango.empty(shape=self.shape, dtype="complex64")
cVal = np.complex64(2 + 1j * 4)
dds.setAllToValue(cVal)
self.assertEqual(cVal, dds[0])
self.assertEqual(cVal, dds[0, 0, 0])
self.assertEqual(cVal, dds[(0, 0, 0)])
dds = mango.zeros(shape=self.shape, dtype="complex64")
self.assertEqual(np.complex64(0), dds[0])
self.assertEqual(np.complex64(0), dds[0, 0, 0])
self.assertEqual(np.complex64(0), dds[(0, 0, 0)])
dds = mango.ones(shape=self.shape, dtype="complex64")
self.assertEqual(np.complex64(1), dds[0])
self.assertEqual(np.complex64(1), dds[0, 0, 0])
self.assertEqual(np.complex64(1), dds[(0, 0, 0)])
dds = mango.empty(shape=self.shape, dtype="complex128")
cVal = np.complex128(2 + 1j * 4)
dds.setAllToValue(cVal)
self.assertEqual(cVal, dds[0])
self.assertEqual(cVal, dds[0, 0, 0])
self.assertEqual(cVal, dds[(0, 0, 0)])
dds = mango.zeros(shape=self.shape, dtype="complex128")
self.assertEqual(np.complex128(0), dds[0])
self.assertEqual(np.complex128(0), dds[0, 0, 0])
self.assertEqual(np.complex128(0), dds[(0, 0, 0)])
dds = mango.ones(shape=self.shape, dtype="complex128")
self.assertEqual(np.complex128(1), dds[0])
self.assertEqual(np.complex128(1), dds[0, 0, 0])
self.assertEqual(np.complex128(1), dds[(0, 0, 0)])
def testDdsSubdProperty(self):
"""
Test :prop:`Dds.subd` object.
"""
dds = mango.zeros(shape=self.shape, dtype="uint16", mpidims=(0, 1, 1))
self.assertEqual(0, dds[0, 0, 0])
rootLogger.info("dds.shape=%s, dds.mpi.shape=%s" %
(dds.shape, dds.mpi.shape))
logger.info("dds.mpi.rank=%s, dds.mpi.index=%s" %
(dds.mpi.rank, dds.mpi.index))
logger.info("dds.subd.origin=%s, dds.subd.shape=%s" %
(dds.subd.origin, dds.subd.shape))
dds = mango.zeros(shape=self.shape, dtype="uint16", mpidims=(0, 0, 0))
self.assertEqual(0, dds[0, 0, 0])
rootLogger.info("dds.shape=%s, dds.mpi.shape=%s" %
(dds.shape, dds.mpi.shape))
logger.info("dds.mpi.rank=%s, dds.mpi.index=%s" %
(dds.mpi.rank, dds.mpi.index))
logger.info("dds.subd.origin=%s, dds.subd.shape=%s" %
(dds.subd.origin, dds.subd.shape))
def testDdsClassAttr(self):
dds = mango.zeros(shape=self.shape)
rootLogger.info(str(dir(dds)))
self.assertTrue(hasattr(dds.__class__, "dtype"))
self.assertTrue(hasattr(dds.__class__, "__getitem__"))
self.assertTrue(hasattr(dds.__class__, "__setitem__"))
self.assertTrue(hasattr(dds.__class__, "fill"))
self.assertTrue(hasattr(dds, "mtype"))
self.assertTrue(hasattr(dds, "shape"))
self.assertTrue(hasattr(dds, "origin"))
self.assertTrue(hasattr(dds, "halo"))
self.assertTrue(hasattr(dds, "subd"))
self.assertTrue(hasattr(dds, "mpi"))
self.assertTrue(hasattr(dds, "md"))
def testDdsCommunicator(self):
"""
Test :prop:`Dds.mpi.comm` object.
"""
dds = mango.zeros(shape=self.shape, dtype="uint16", mpidims=(0, 1, 1))
self.assertEqual(0, dds[0, 0, 0])
comm = dds.mpi.comm
if (mango.mpi.haveMpi4py):
self.assertNotEqual(None, comm)
rootLogger.info("dds.mpi.comm=%s" % (dds.mpi.comm, ))
self.assertEqual(mango.mpi.world.size, dds.mpi.comm.size)
self.assertEqual(mango.mpi.world.rank, dds.mpi.comm.rank)
else:
self.assertEqual(None, comm)
def testDdsIndexingSetAndGet(self):
"""
Test the :meth:`Dds.__getitem__` and :meth:`Dds.__setitem__` methods.
"""
dds = mango.zeros(shape=self.shape, dtype="uint16")
dds[0, 0, 0] = 5
self.assertEqual(5, dds[0])
self.assertEqual(5, dds[0, 0, 0])
self.assertEqual(5, dds[(0, 0, 0)])
dds = mango.ones(shape=self.shape, dtype="uint8")
self.assertEqual(1, dds[0])
self.assertEqual(1, dds[0, 0, 0])
self.assertEqual(1, dds[(0, 0, 0)])
def testDdsMirrorOuterLayersToBorder(self):
"""
Test the :meth:`Dds.mirrorOuterLayersToBorder` method.
"""
dds = mango.zeros(shape=self.shape,
dtype="uint16",
mpidims=(0, 1, 1),
halo=2)
dds.setBorderToValue(1)
self.assertTrue(sp.sum(sp.where(dds.asarray() != 0, 1, 0)) > 0)
dds.mirrorOuterLayersToBorder(False)
logger.info("Num non-zero = %s" %
sp.sum(sp.where(dds.asarray() != 0, 1, 0)))
logger.info("Idx non-zero = %s" % (sp.where(dds.asarray() != 0), ))
self.assertTrue(sp.all(dds.asarray() == 0))
def testDistributedOptimization(self):
if ((mpi.size % 4) == 0):
mpidims = (0,2,2)
elif ((mpi.size % 2) == 0):
mpidims = (0,0,2)
else:
mpidims = (0,0,0)
img = mango.zeros((120+8*mpi.size,64,64), mtype="tomo", mpidims=mpidims)
img.md.setVoxelSize((1,1,1), "voxel")
c = img.origin + img.shape*0.5
r = np.min(img.shape)*0.4
a = (1,0,0)
mango.data.fill_circular_cylinder(img, c, r, img.shape[0]*1.1, fill=32000, coordsys="abs", unit="voxel")
metric = cylinder_fit_gradient_metric()
metric = DistributedGradCylFitMetric(metric, comm=img.mpi.comm, root=0)
metric.setGradientFromImage(img)
x = metric.getDefaultX()
rootLogger.info("Default x = %s" % (x,))
x[metric.RADIUS_IDX] = r
x[metric.CENTRE_X_IDX] = c[2]
x[metric.CENTRE_Y_IDX] = c[1]
x[metric.CENTRE_Z_IDX] = c[0]
x[metric.AXIS_X_IDX] = a[2]
x[metric.AXIS_Y_IDX] = a[1]
x[metric.AXIS_Z_IDX] = a[0]
solnX = x.copy()
bestRes = None
for rr in range(-5, 6):
x[metric.RADIUS_IDX] = r + rr
res = mango.optimize.distributed_minimize(metric, x[0:5], method="Powell", options={'xtol':1.0e-1, 'ftol':1.0e-2})
#res = sp.optimize.minimize(metric, x[0:6], jac=False, method="BFGS", options={'gtol':1.0e3, 'eps':(0.05,0.05,0.05,0.001,0.001,0.001)})
rootLogger.info("result.success = %s, result.message = %s" % (res.success, res.message))
rootLogger.info("optimized (metric_val, x) = (%16.2f, %s) = " % (res.fun, res.x))
rootLogger.info("res.nfev = %8d" % (res.nfev,))
if ((bestRes == None) or (res.fun < bestRes.fun)):
bestRes = res
#bestRes.x[3:] /= sp.sqrt(sp.sum(bestRes.x[3:]*bestRes.x[3:]))
rootLogger.info("soln x = %s" % (solnX[0:bestRes.x.size],))
rootLogger.info("best x = %s" % (bestRes.x,))
self.assertTrue(sp.all(sp.absolute(bestRes.x - solnX[0:bestRes.x.size]) < 0.1))
self.assertGreater(0, bestRes.fun)
def testDdsFill(self):
"""
Test the :meth:`Dds.fill` method.
"""
ddsDst = mango.zeros(shape=self.shape,
dtype="uint16",
mpidims=(0, 1, 1))
self.assertEqual(0, ddsDst[0, 0, 0])
ddsSrc = mango.ones(shape=self.shape,
dtype="uint16",
mpidims=(1, 0, 1))
self.assertEqual(1, ddsSrc[0, 0, 0])
ddsDst.fill(ddsSrc)
self.assertEqual(1, ddsDst[0, 0, 0])
def testMultiResFit1(self):
dir = self.createTmpDir("CylinderFitMultiResTest_testMultiResFit1")
#dir = "."
rootLogger.info("Generating synthetic image...")
#img = mango.zeros((128+((mpi.size//8)*16),64,64), mtype="tomo")
img = mango.zeros((512 + ((mpi.size // 8) * 16), 256, 256),
mtype="tomo")
#img = mango.zeros((1024,512,512), mtype="tomo")
img.md.setVoxelSize((0.002, 0.002, 0.002), "mm")
c = (img.origin + img.shape * 0.5) * img.md.getVoxelSize()
r = np.min(img.shape * img.md.getVoxelSize()) * 0.4
a = (1, 0, 0)
img.subd_h.asarray()[...] = 10000
mango.data.fill_circular_cylinder(img,
c,
r,
img.shape[0] * 1.1,
fill=25000,
coordsys="abs",
unit=img.md.getVoxelSizeUnit())
img.subd.asarray()[...] += mango.data.gaussian_noise_like(
img, mean=0, stdd=300).subd.asarray()
mango.io.writeDds(os.path.join(dir, "tomoCyl1.nc"), img)
rootLogger.info("Done generating synthetic image.")
fit, cylImg = cylinder_fit_multi_res(img,
1,
resolutions=[64, 128, 512],
retcylimg=True,
metricThreshRelTol=0.50)
mango.io.writeDds(os.path.join(dir, "segmentedCyl1AnnularMsk.nc"),
cylImg)
rootLogger.info("Img voxel size = %s %s" %
(img.md.getVoxelSize(), img.md.getVoxelSizeUnit()))
rootLogger.info(
"Cyl img voxel size = %s %s" %
(cylImg.md.getVoxelSize(), cylImg.md.getVoxelSizeUnit()))
rootLogger.info("c=%s, r=%s, a=%s" % (c, r, a))
rootLogger.info("Fit Results:\n%s" % ("\n".join(map(str, fit)), ))
f0 = fit[0]
self.assertAlmostEqual(c[1], f0[1][0][1], 3)
self.assertAlmostEqual(c[2], f0[1][0][2], 3)
self.assertAlmostEqual(r, f0[1][1], 3)
self.assertAlmostEqual(sp.absolute(sp.dot(a, f0[1][3])), 1.0, 3)
def testDdsCreate(self):
"""
Test the :func:`mango.empty` and :func:`mango.ones`
and :func:`mango.zeros` methods.
"""
dds = mango.zeros(shape=self.shape, dtype="uint16")
self.assertEqual(0, dds[0])
self.assertEqual(0, dds[0, 0, 0])
self.assertEqual(0, dds[(0, 0, 0)])
dds = mango.ones(shape=self.shape, dtype="uint8")
self.assertEqual(1, dds[0])
self.assertEqual(1, dds[0, 0, 0])
self.assertEqual(1, dds[(0, 0, 0)])
self.assertEqual(tuple(self.shape), tuple(dds.shape))
self.assertEqual(None, dds.mtype)
dds = mango.ones(shape=self.shape, mtype="tomo_float")
self.assertEqual(tuple(self.shape), tuple(dds.shape))
self.assertEqual(mango.mtype("tomo_float").dtype, dds.dtype)
self.assertEqual(mango.mtype("tomo_float"), dds.mtype)
dds = mango.ones(shape=self.shape,
mtype="tomo_float",
origin=(20, 50, -100))
elDds = mango.empty_like(dds)
self.assertTrue(sp.all(elDds.origin == dds.origin))
self.assertTrue(sp.all(elDds.shape == dds.shape))
self.assertTrue(sp.all(elDds.subd.origin == dds.subd.origin))
self.assertTrue(sp.all(elDds.subd.shape == dds.subd.shape))
elDds = mango.empty_like(dds, origin=dds.origin + (10, 20, 40))
self.assertTrue(sp.all(elDds.origin == dds.origin + (10, 20, 40)))
self.assertTrue(sp.all(elDds.shape == dds.shape))
self.assertTrue(
sp.all(elDds.subd.origin == dds.subd.origin + (10, 20, 40)))
self.assertTrue(sp.all(elDds.subd.shape == dds.subd.shape))
self.assertNotEqual(dds.mtype, None)
self.assertEqual(dds.mtype, elDds.mtype)
def testDdsMetaData(self):
dds = mango.zeros(shape=self.shape, dtype="uint16")
self.assertNotEqual(None, dds.md)
rootLogger.info(
"dds.md.getVoxelSize()=%s, dds.md.getVoxelSizeUnit()=%s" %
(dds.md.getVoxelSize(), dds.md.getVoxelSizeUnit()))
vSz = (0.5, 0.125, 0.25)
dds.md.setVoxelSize(vSz)
dds.md.setVoxelSizeUnit("um")
rootLogger.info(
"dds.md.getVoxelSize()=%s, dds.md.getVoxelSizeUnit()=%s" %
(dds.md.getVoxelSize(), dds.md.getVoxelSizeUnit()))
self.assertEqual("micrometre", dds.md.getVoxelSizeUnit())
self.assertTrue(sp.all(dds.md.getVoxelSize() - vSz < 1.0e-6))
dds.md.setVoxelSize(1)
dds.md.setVoxelSizeUnit("millimetre")
rootLogger.info(
"dds.md.getVoxelSize()=%s, dds.md.getVoxelSizeUnit()=%s" %
(dds.md.getVoxelSize(), dds.md.getVoxelSizeUnit()))
self.assertEqual("millimetre", dds.md.getVoxelSizeUnit())
self.assertTrue(sp.all(dds.md.getVoxelSize() == 1))
def testDdsAsArrayMemoryDealloc(self):
"""
Alloc and dealloc :obj:`Dds` objects and check memory
consumption.
"""
for i in range(0, 16):
rootLogger.info("Creating Dds...")
dds = mango.zeros(shape=(256, 512, 512),
dtype="uint16",
mpidims=(0, 0, 0))
rootLogger.info("Done creating Dds.")
self.assertEqual(0, dds[0, 0, 0])
a = dds.asarray()
rootLogger.info("Deleting Dds...")
del dds
rootLogger.info("Done deleting Dds.")
a += 10
self.assertEqual(10, a[0, 0, 0])
a -= 10
self.assertEqual(0, a[0, 0, 0])
def _testMultiResFit3(self):
dir = self.createTmpDir("CylinderFitMultiResTest_testMultiResFit3")
#dir = "."
rootLogger.info("Generating synthetic image...")
#img = mango.zeros((128+((world.size//8)*16),64,64), mtype="tomo")
img = mango.zeros((256+((world.size//8)*16),128,128), mtype="tomo")
#img = mango.zeros((1024,512,512), mtype="tomo")
img.md.setVoxelSize((0.002,0.002,0.002), "mm")
c = (img.origin + img.shape*0.5)*img.md.getVoxelSize()
r = np.min(img.shape*img.md.getVoxelSize())*0.4
a = sp.array((1.,0.,0.))
cList = [c, c, c+(img.shape*0.02)*img.md.getVoxelSize()]
rList = [r, 0.8*r, 0.65*r]
aList = [a, a, sp.array([1.0, 0.01,0.02])]
fList = [20000, 15000, 18000]
img.subd_h.asarray()[...] = 10000
for i in range(len(cList)):
rMtx = mango.math.rotation_matrix_from_cross_prod(sp.array([1.,0.,0.]), aList[i])
mango.data.fill_circular_cylinder(img, cList[i], rList[i], img.shape[0]*1.25, fill=fList[i], rotation=rMtx, coordsys="abs", unit=img.md.getVoxelSizeUnit())
img.subd.asarray()[...] += mango.data.gaussian_noise_like(img, mean=0, stdd=300).subd.asarray()
mango.io.writeDds(os.path.join(dir, "tomoCyl3.nc"), img)
rootLogger.info("Done generating synthetic image.")
fit, cylImg = \
cylinder_fit_multi_res(
img,
3,
resolutions=[64, 128, 512],
retcylimg=True,
metricThreshRelTol=0.50
)
mango.io.writeDds(os.path.join(dir,"segmentedCyl3AnnularMsk.nc"), cylImg)
rootLogger.info("Voxel size = %s %s" % (img.md.getVoxelSize(), img.md.getVoxelSizeUnit()))
for i in range(len(cList)):
rootLogger.info("c%s=%s, r%s=%s, a%s=%s" % (i,cList[i],i,rList[i],i,aList[i]))
rootLogger.info("Fit Results:\n%s" % ("\n".join(map(str,fit)),))
def createTmpArrayFromDds(self):
dds = mango.zeros(shape=self.shape, dtype="uint16", mpidims=(0, 1, 1))
a = dds.asarray()
del dds
return a
def testDdsSetGlobalFaceValue(self):
"""
Test the :meth:`mango.Dds.setFacesToValue` method.
"""
outDir = self.createTmpDir("testDdsSetGlobalFaceValue")
ddsorig = mango.zeros(shape=self.shape,
mtype="tomo",
origin=(-8, 5, -32))
for depth in (1, int(np.min(ddsorig.shape) // 2)):
for axis in (0, 1, 2):
dds = mango.copy(ddsorig)
vallo = 16 + axis
rootLogger.info("LO: axis=%s, val=%s, depth=%s" %
(axis, vallo, depth))
dds.setFacesToValue(vallo, axislo=axis, depth=depth)
#mango.io.writeDds(os.path.join(outDir, "tomoLoFaceAxis%s.nc" % axis), dds)
shpFace = dds.shape
shpFace[axis] = depth
mpidimsFace = [0, 0, 0]
mpidimsFace[axis] = 1
rootLogger.info("LO: shpFace=%s, mpidimsFace=%s" %
(shpFace, mpidimsFace))
ddsFace = mango.copy(dds, shape=shpFace, mpidims=mpidimsFace)
self.assertTrue(sp.all(ddsFace.subd.asarray() == vallo))
shpNotFace = dds.shape
shpNotFace[axis] = dds.shape[axis] - depth
orgNotFace = dds.origin
orgNotFace[axis] = dds.origin[axis] + depth
mpidimsNotFace = [0, 0, 0]
mpidimsNotFace[axis] = 1
rootLogger.info(
"LO: shpNotFace=%s, mpidimsNotFace=%s, orgNotFace=%s" %
(shpNotFace, mpidimsNotFace, orgNotFace))
ddsNotFace = mango.copy(dds,
origin=orgNotFace,
shape=shpNotFace,
mpidims=mpidimsNotFace)
self.assertTrue(sp.all(ddsNotFace.subd.asarray() == 0))
dds = mango.copy(ddsorig)
valhi = 2 * vallo
rootLogger.info("HI: axis=%s, val=%s, depth=%s" %
(axis, valhi, depth))
dds.setFacesToValue(valhi, axishi=axis, depth=depth)
#mango.io.writeDds(os.path.join(outDir, "tomoLoFaceAxis%s.nc" % axis), dds)
shpFace = dds.shape
shpFace[axis] = depth
mpidimsFace = [0, 0, 0]
mpidimsFace[axis] = 1
orgFace = dds.origin
orgFace[axis] = dds.origin[axis] + dds.shape[axis] - depth
rootLogger.info("HI: shpFace=%s, mpidimsFace=%s, orgFace=%s" %
(shpFace, mpidimsFace, orgFace))
ddsFace = mango.copy(dds,
origin=orgFace,
shape=shpFace,
mpidims=mpidimsFace)
self.assertTrue(sp.all(ddsFace.subd.asarray() == valhi))
shpNotFace = dds.shape
shpNotFace[axis] = dds.shape[axis] - depth
mpidimsNotFace = [0, 0, 0]
mpidimsNotFace[axis] = 1
rootLogger.info(
"HI: shpNotFace=%s, mpidimsNotFace=%s, orgNotFace=%s" %
(shpNotFace, mpidimsNotFace, orgNotFace))
ddsNotFace = mango.copy(dds,
shape=shpNotFace,
mpidims=mpidimsNotFace)
self.assertTrue(sp.all(ddsNotFace.subd.asarray() == 0))