def test_DataContainerFilter(self):
"""
"""
data = pg.DataContainer()
data.resize(5)
data.markValid([0, 4])
self.assertEqual(data('valid'), [1.0, 0.0, 0.0, 0.0, 1.0])
data.markInvalid(pg.IndexArray(np.arange(5, dtype="long")))
self.assertEqual(data('valid'), [0.0, 0.0, 0.0, 0.0, 0.0])
data.markValid(np.arange(5, dtype="long"))
self.assertEqual(data('valid'), [1.0, 1.0, 1.0, 1.0, 1.0])
data.markInvalid(range(5))
self.assertEqual(data('valid'), [0.0, 0.0, 0.0, 0.0, 0.0])
x = np.arange(5, dtype='float')
data.markValid(pg.Vector(x) > 2.0)
self.assertEqual(data('valid'), [0.0, 0.0, 0.0, 1.0, 1.0])
data.markValid(pg.BVector(x < 2.0))
self.assertEqual(data('valid'), [1.0, 1.0, 0.0, 1.0, 1.0])
data.markInvalid(pg.find(x > 3.0))
self.assertEqual(data('valid'), [1.0, 1.0, 0.0, 1.0, 0.0])
data.markInvalid(x < 1.0)
self.assertEqual(data('valid'), [0.0, 1.0, 0.0, 1.0, 0.0])
def test_DataContainerFilter(self):
"""
"""
data = pg.DataContainer()
data.resize(5)
data.markValid([0, 4])
self.assertEqual(data('valid'), [1.0, 0.0, 0.0, 0.0, 1.0])
data.markInvalid(pg.IndexArray(np.arange(5, dtype="long")))
self.assertEqual(data('valid'), [0.0, 0.0, 0.0, 0.0, 0.0])
data.markValid(np.arange(5, dtype="long"))
self.assertEqual(data('valid'), [1.0, 1.0, 1.0, 1.0, 1.0])
data.markInvalid(range(5))
self.assertEqual(data('valid'), [0.0, 0.0, 0.0, 0.0, 0.0])
x = np.arange(5, dtype='float')
data.markValid(pg.Vector(x) > 2.0)
self.assertEqual(data('valid'), [0.0, 0.0, 0.0, 1.0, 1.0])
data.markValid(pg.BVector(x < 2.0))
self.assertEqual(data('valid'), [1.0, 1.0, 0.0, 1.0, 1.0])
data.markInvalid(pg.find(x > 3.0))
self.assertEqual(data('valid'), [1.0, 1.0, 0.0, 1.0, 0.0])
data.markInvalid(x < 1.0)
self.assertEqual(data('valid'), [0.0, 1.0, 0.0, 1.0, 0.0])
def test_createPartMesh(self):
mesh = pg.meshtools.createMesh1D(np.linspace(0, 1, 10))
self.assertEqual(mesh.cellCount(), 9)
mesh2 = mesh.createMeshByCellIdx(
pg.find(pg.x(mesh.cellCenters()) < 0.5))
self.assertEqual(mesh2.cellCount(), 4)
self.assertEqual(mesh2.cellCenters()[-1][0] < 0.5, True)
def test_createPartMesh(self):
mesh = pg.createMesh1D(np.linspace(0, 1, 10))
self.assertEqual(mesh.cellCount(), 9)
mesh2 = mesh.createMeshByCellIdx(
pg.find(pg.x(mesh.cellCenters()) < 0.5))
self.assertEqual(mesh2.cellCount(), 4)
self.assertEqual(mesh2.cellCenters()[-1][0] < 0.5, True)
def parseMapToCellArray(attributeMap, mesh, default=0.0):
"""
Parse a value map to cell attributes.
A map should consist of pairs of marker and value.
A marker is an integer and corresponds to the cell.marker().
Parameters
----------
mesh : :gimliapi:`GIMLI::Mesh`
For each cell of mesh a value will be returned.
attributeMap : list | dict
List of pairs [marker, value] ] || [[marker, value]],
or dictionary with marker keys
default : float [0.0]
Fill all unmapped atts to this default.
Returns
-------
atts : array
Array of length mesh.cellCount()
"""
atts = pg.RVector(mesh.cellCount(), default)
if isinstance(attributeMap, dict):
raise Exception("Please implement me!")
elif hasattr(attributeMap, '__len__'):
if not hasattr(attributeMap[0], '__len__'):
# assuming [marker, value]
attributeMap = [attributeMap]
for pair in attributeMap:
if hasattr(pair, '__len__'):
idx = pg.find(mesh.cellMarkers() == pair[0])
if len(idx) == 0:
print("Warning! parseMapToCellArray: cannot find marker " +
str(pair[0]) + " within mesh.")
else:
#print('---------------------')
#print(atts, idx, pair[1], type(pair[1]), float(pair[1]))
if isinstance(pair[1], np.complex):
#print('+++++++++++++++++')
if not isinstance(atts, pg.CVector):
atts = pg.toComplex(atts)
atts[idx] = pair[1]
else:
atts[idx] = float(pair[1])
else:
raise Exception("Please provide a list of [int, value] pairs" +
str(pair))
else:
print("attributeMap: ", attributeMap)
raise Exception("Cannot interpret attributeMap!")
return atts
def calcInvBlock(mesh, dens, out='gravInv'):
# extract block delta density
densBlock = pg.RVector(dens)
densMarker2 = dens[pg.find(mesh.cellMarker() == 2)[0]]
# densBlock[(mesh.cellMarker() == 1)|(mesh.cellMarker() == 3)] = densMarker2
densBlock[pg.find((mesh.cellMarker() == 1) | (mesh.cellMarker() == 3))] = \
densMarker2
densBlock -= densMarker2
# define meausrement positions
gravPointsX = np.linspace(-20, 20, 41)
sensorPositions = np.vstack((gravPointsX, np.zeros(len(gravPointsX)))).T
# solve analytical
gz = solveGravimetry(mesh, densBlock, pnts=sensorPositions, complete=False)
# noisyfy
errAbs = 0.00001
dzerr = np.random.randn(len(sensorPositions)) * errAbs
gz = gz + dzerr
# createParamesh
paraMesh = pg.createGrid(x=np.linspace(-20, 20, 41),
y=np.linspace(-20, 0, 21))
# init Gravimetry manager (should do meshing, simulation and noisying)
Grav = Gravimetry(verbose=True)
model = Grav.invert(sensorPositions, gz, errAbs, verbose=1, mesh=paraMesh)
fig, ax = plt.subplots()
ax.plot(pg.x(sensorPositions), gz, label='gz')
ax.plot(pg.x(sensorPositions), Grav.inv.response(), label='response')
ax.legend()
ax.grid()
ax.set_xlabel('$x$ [m]')
ax.set_ylabel('$\partial u / \partial z$ [mGal]')
plt.show(block=False)
ax.figure.savefig(out, bbox_inches='tight')
return Grav, densBlock
def calcInvBlock(mesh, dens, out='gravInv'):
# extract block delta density
densBlock = pg.RVector(dens)
densMarker2 = dens[pg.find(mesh.cellMarker() == 2)[0]]
#densBlock[(mesh.cellMarker() == 1) | (mesh.cellMarker() == 3)] = densMarker2
densBlock[pg.find((mesh.cellMarker() == 1)
| (mesh.cellMarker() == 3))] = densMarker2
densBlock -= densMarker2
# define meausrement positions
gravPointsX = np.linspace(-20, 20, 41)
sensorPositions = np.vstack((gravPointsX, np.zeros(len(gravPointsX)))).T
# solve analytical
gz = solveGravimetry(mesh, densBlock, pnts=sensorPositions, complete=False)
# noisyfy
errAbs = 0.00001
dzerr = np.random.randn(len(sensorPositions)) * errAbs
gz = gz + dzerr
# createParamesh
paraMesh = pg.createGrid(x=np.linspace(-20, 20, 41),
y=np.linspace(-20, 0, 21))
# init Gravimetry manager (should do meshing, simulation and noisying)
Grav = Gravimetry(verbose=True)
model = Grav.invert(sensorPositions, gz, errAbs, verbose=1, mesh=paraMesh)
fig, ax = plt.subplots()
ax.plot(pg.x(sensorPositions), gz, label='gz')
ax.plot(pg.x(sensorPositions), Grav.inv.response(), label='response')
ax.legend()
ax.grid()
ax.set_xlabel('$x$ [m]')
ax.set_ylabel('$\partial u / \partial z$ [mGal]')
plt.show(block=False)
ax.figure.savefig(out, bbox_inches='tight')
return Grav, densBlock
def drawTravelTimeData(ax, data, t=None):
"""Draw first arrival traveltime data into mpl ax a.
data of type pg.DataContainer must contain sensorIdx 's' and 'g'
and thus being numbered internally [0..n)
"""
x = pg.x(data.sensorPositions())
# z = pg.z(data.sensorPositions())
shots = pg.unique(pg.sort(data('s')))
geoph = pg.unique(pg.sort(data('g')))
startOffsetIDX = 0
if min(min(shots), min(geoph)) == 1:
startOffsetIDX = 1
tShow = data('t')
if t is not None:
tShow = t
ax.set_xlim([min(x), max(x)])
ax.set_ylim([max(tShow), -0.002])
ax.figure.show()
for shot in shots:
gIdx = pg.find(data('s') == shot)
sensorIdx = [int(i__ - startOffsetIDX) for i__ in data('g')[gIdx]]
ax.plot(x[sensorIdx], tShow[gIdx], 'x-')
yPixel = ax.transData.inverted().transform_point((1, 1))[1] - \
ax.transData.inverted().transform_point((0, 0))[1]
xPixel = ax.transData.inverted().transform_point((1, 1))[0] - \
ax.transData.inverted().transform_point((0, 0))[0]
# draw shot points
ax.plot(x[[int(i__ - startOffsetIDX) for i__ in shots]],
np.zeros(len(shots)) + 8. * yPixel,
'gv',
markersize=8)
# draw geophone points
ax.plot(x[[int(i__ - startOffsetIDX) for i__ in geoph]],
np.zeros(len(geoph)) + 3. * yPixel,
'r^',
markersize=8)
ax.grid()
ax.set_ylim([max(tShow), +16. * yPixel])
ax.set_xlim([min(x) - 5. * xPixel, max(x) + 5. * xPixel])
ax.set_xlabel('x-Coordinate [m]')
ax.set_ylabel('Traveltime [ms]')
def checkData(self, data=None):
"""Return data from container.
THINKABOUT: Data will be changed, or should the manager keep a copy?
"""
data = data or pg.DataContainerERT(self.data)
if isinstance(data, pg.DataContainer):
if not data.allNonZero('k'):
pg.warn("Data file contains no geometric factors (token='k').")
data['k'] = createGeometricFactors(data, verbose=True)
if self.fop.complex():
if not data.haveData('rhoa'):
pg.critical('Datacontainer have no "rhoa" values.')
if not data.haveData('ip'):
pg.critical('Datacontainer have no "ip" values.')
# pg.warn('check sign of phases')
rhoa = data['rhoa']
phia = -data['ip'] / 1000 # 'ip' is defined for neg mrad.
# we should think about some 'phia' in rad
return pg.utils.squeezeComplex(pg.utils.toComplex(rhoa, phia))
else:
if not data.haveData('rhoa'):
if data.allNonZero('r'):
pg.info("Creating apparent resistivies from "
"impedences rhoa = r * k")
data['rhoa'] = data['r'] * data['k']
elif data.allNonZero('u') and data.allNonZero('i'):
pg.info("Creating apparent resistivies from "
"voltage and currrent rhoa = u/i * k")
data['rhoa'] = data['u'] / data['i'] * data['k']
else:
pg.critical("Datacontainer have neither: "
"apparent resistivies 'rhoa', "
"or impedances 'r', "
"or voltage 'u' along with current 'i'.")
if any(data['rhoa'] < 0) and \
isinstance(self.inv.dataTrans, pg.core.TransLog):
print(pg.find(data['rhoa'] < 0))
print(data['rhoa'][data['rhoa'] < 0])
pg.critical("Found negative apparent resistivities. "
"These can't be processed with logarithmic "
"data transformation. You should consider to "
"filter them out using "
"data.remove(data['rhoa'] < 0).")
return data['rhoa']
return data
def parseMapToCellArray(attributeMap, mesh, default=0.0):
"""
Parse a value map to cell attributes.
A map should consist of pairs of marker and value.
A marker is an integer and corresponds to the cell.marker().
Parameters
----------
mesh : :gimliapi:`GIMLI::Mesh`
For each cell of mesh a value will be returned.
attributeMap : list | dict
List of pairs [marker, value] ] || [[marker, value]],
or dictionary with marker keys
default : float [0.0]
Fill all unmapped atts to this default.
Returns
-------
atts : array
Array of length mesh.cellCount()
"""
atts = pg.RVector(mesh.cellCount(), default)
if isinstance(attributeMap, dict):
raise Exception("Please implement me!")
elif hasattr(attributeMap, '__len__'):
if not hasattr(attributeMap[0], '__len__'):
# assuming [marker, value]
attributeMap = [attributeMap]
for pair in attributeMap:
if hasattr(pair, '__len__'):
idx = pg.find(mesh.cellMarker() == pair[0])
if len(idx) == 0:
print("Warning! parseMapToCellArray: cannot find marker " +
str(pair[0]) + " within mesh.")
else:
#print(atts, idx, pair[1], float(pair[1]))
atts[idx] = float(pair[1])
else:
raise Exception("Please provide a list of [int, value] pairs!" +
str(pair))
else:
print("attributeMap: ", attributeMap)
raise Exception("Cannot interpret attributeMap!")
return atts
def drawTravelTimeData(axes, data, t=None):
"""
Draw first arrival traveltime data into mpl axes a.
data of type \ref DataContainer must contain sensorIdx 's' and 'g'
and thus being numbered internally [0..n)
"""
x = pg.x(data.sensorPositions())
# z = pg.z(data.sensorPositions())
shots = pg.unique(pg.sort(data('s')))
geoph = pg.unique(pg.sort(data('g')))
startOffsetIDX = 0
if min(min(shots), min(geoph)) == 1:
startOffsetIDX = 1
tShow = data('t')
if t is not None:
tShow = t
axes.set_xlim([min(x), max(x)])
axes.set_ylim([max(tShow), -0.002])
axes.figure.show()
for shot in shots:
gIdx = pg.find(data('s') == shot)
sensorIdx = [int(i__ - startOffsetIDX) for i__ in data('g')[gIdx]]
axes.plot(x[sensorIdx], tShow[gIdx], 'x-')
yPixel = axes.transData.inverted().transform_point((1, 1))[1] - \
axes.transData.inverted().transform_point((0, 0))[1]
xPixel = axes.transData.inverted().transform_point((1, 1))[0] - \
axes.transData.inverted().transform_point((0, 0))[0]
# draw shot points
axes.plot(x[[int(i__ - startOffsetIDX) for i__ in shots]],
np.zeros(len(shots)) + 8. * yPixel, 'gv', markersize=8)
# draw geophone points
axes.plot(x[[int(i__ - startOffsetIDX) for i__ in geoph]],
np.zeros(len(geoph)) + 3. * yPixel, 'r^', markersize=8)
axes.grid()
axes.set_ylim([max(tShow), +16. * yPixel])
axes.set_xlim([min(x) - 5. * xPixel, max(x) + 5. * xPixel])
axes.set_xlabel('x-Coordinate [m]')
axes.set_ylabel('Traveltime [ms]')
def logDropTol( p, droptol = 1e-3 ):
""""""
tmp = pg.RVector( p );
tmp = pg.abs( tmp / droptol )
tmp.setVal( 1.0, pg.find( tmp < 1.0 ) )
#for i, v in enumerate( tmp ):
#tmp[ i ] = abs( tmp[ i ] / droptol );
#if tmp[ i ] < 1.0: tmp[ i ] = 1.0;
tmp = pg.log10( tmp );
tmp *= pg.sign( p );
return tmp;
def logDropTol(p, droptol=1e-3):
"""
Example
-------
>>> from pygimli.utils import logDropTol
>>> x = logDropTol((-10,-1,0,1,100))
>>> print(x.array())
[-4. -3. 0. 3. 5.]
"""
tmp = pg.RVector(p)
tmp = pg.abs(tmp / droptol)
tmp.setVal(1.0, pg.find(tmp < 1.0))
tmp = pg.log10(tmp)
tmp *= pg.sign(p)
return tmp
def logDropTol(p, droptol=1e-3):
"""Create logarithmic scaled copy of p.
Examples
--------
>>> from pygimli.utils import logDropTol
>>> x = logDropTol((-10, -1, 0, 1, 100))
>>> print(x.array())
[-4. -3. 0. 3. 5.]
"""
tmp = pg.RVector(p)
tmp = pg.abs(tmp / droptol)
tmp.setVal(1.0, pg.find(tmp < 1.0))
tmp = pg.log10(tmp)
tmp *= pg.sign(p)
return tmp
def test_RVectorIndexRW(self):
v = pg.Vector(5, 2.0)
np.testing.assert_array_equal(v, [2, 2, 2, 2, 2])
v += 1.0
np.testing.assert_array_equal(v, [3, 3, 3, 3, 3])
v += 1
np.testing.assert_array_equal(v, [4, 4, 4, 4, 4])
v[1] = 1.0
np.testing.assert_array_equal(v, [4, 1, 4, 4, 4])
v[1] += 1.0
np.testing.assert_array_equal(v, [4, 2, 4, 4, 4])
v[[1,2]] = 2.0
np.testing.assert_array_equal(v, [4, 2, 2, 4, 4])
v[pg.IVector(1,3)] = 3.0
np.testing.assert_array_equal(v, [4, 2, 2, 3, 4])
v[pg.IVector(5,2)] = 1.0
np.testing.assert_array_equal(v, [4, 2, 1, 3, 4])
v[pg.find(v==4.0)] = 5.0
np.testing.assert_array_equal(v, [5, 2, 1, 3, 5])
v[v==5.0] = 4.0
np.testing.assert_array_equal(v, [4, 2, 1, 3, 4])
v[v==4.0] = 5.0
np.testing.assert_array_equal(v, [5, 2, 1, 3, 5])
#this will work only if we overwrite __iadd__
#v[v==4.0] += 1.0
#np.testing.assert_array_equal(v, [6, 2, 1, 3, 6])
v.setVal(1.0, 1)
np.testing.assert_array_equal(v, [5, 1, 1, 3, 5])
def test_RVectorIndexRW(self):
v = pg.RVector(5, 2.0)
np.testing.assert_array_equal(v, [2, 2, 2, 2, 2])
v += 1.0
np.testing.assert_array_equal(v, [3, 3, 3, 3, 3])
v += 1
np.testing.assert_array_equal(v, [4, 4, 4, 4, 4])
v[1] = 1.0
np.testing.assert_array_equal(v, [4, 1, 4, 4, 4])
v[1] += 1.0
np.testing.assert_array_equal(v, [4, 2, 4, 4, 4])
v[[1,2]] = 2.0
np.testing.assert_array_equal(v, [4, 2, 2, 4, 4])
v[pg.IVector(1,3)] = 3.0
np.testing.assert_array_equal(v, [4, 2, 2, 3, 4])
v[pg.IVector(5,2)] = 1.0
np.testing.assert_array_equal(v, [4, 2, 1, 3, 4])
v[pg.find(v==4.0)] = 5.0
np.testing.assert_array_equal(v, [5, 2, 1, 3, 5])
v[v==5.0] = 4.0
np.testing.assert_array_equal(v, [4, 2, 1, 3, 4])
v[v==4.0] = 5.0
np.testing.assert_array_equal(v, [5, 2, 1, 3, 5])
#this will work only if we overwrite __iadd__
#v[v==4.0] += 1.0
#np.testing.assert_array_equal(v, [6, 2, 1, 3, 6])
v.setVal(1.0, 1)
np.testing.assert_array_equal(v, [5, 1, 1, 3, 5])
def parseArgPairToBoundaryArray(pair, mesh):
"""
Parse boundary related pair argument to
[ :gimliapi:`GIMLI::Boundary`, value|callable ] list.
Parameters
----------
pair : tuple
- [marker, arg]
- [[marker, ...], arg]
- [boundary, arg]
- [[boundary,...], arg]
- [node, arg]
arg will be parsed by
:py:mod:`pygimli.solver.solver.generateBoundaryValue`
and distributed to each boundary.
Callable functions will be executed at runtime.
mesh : :gimliapi:`GIMLI::Mesh`
Used to find boundaries by marker
Returns
-------
boundaries : list()
[ :gimliapi:`GIMLI::Boundary`, value|callable ]
"""
boundaries = []
bounds = []
# print('+'*30, pair)
if isinstance(pair[0], int):
bounds = mesh.findBoundaryByMarker(pair[0])
if isinstance(pair[0], list):
# [[,,..], ]
for b in pair[0]:
for bi in mesh.boundaries(pg.find(mesh.boundaryMarkers() == b)):
bounds.append(bi)
elif isinstance(pair[0], pg.stdVectorBounds):
bounds = pair[0]
elif isinstance(pair[0], pg.Boundary):
boundaries.append(pair)
return boundaries
elif isinstance(pair[0], pg.Node):
boundaries.append(pair)
return boundaries
for b in bounds:
val = None
if hasattr(pair[1], '__call__'):
# don't execute the callable here in init,
# we want to call them at runtime
val = pair[1]
else:
val = generateBoundaryValue(b, pair[1])
boundaries.append([b, val])
return boundaries
[vel_layered, vel_gradient])):
pg.boxprint(case)
if case is "gradient":
ana = analyticalSolutionGradient
elif case is "layered":
ana = analyticalSolution2Layer
for boundary in mesh.boundaries():
boundary.setMarker(0)
xmin, xmax = mesh.xmin(), mesh.xmax()
mesh.createNeighbourInfos()
# In order to use the Dijkstra, we extract the surface positions >0
mx = pg.x(mesh.positions())
my = pg.y(mesh.positions())
fi = pg.find((my == 0.0))
px = np.sort(mx(fi))
# A data container with index arrays named s (shot) and g (geophones) is
# created and filled with the positions and shot/geophone indices.
data = pg.DataContainer()
data.registerSensorIndex('s')
data.registerSensorIndex('g')
for i, pxi in enumerate(px):
data.createSensor([pxi, 0.0])
if pxi == 0:
source = i
ndata = len(px) - 1
data.resize(ndata)
def fillEmptyToCellArray(mesh, vals, slope=True):
"""
Prolongate empty cell values to complete cell attributes.
It is possible that you have zero values that need to be filled with
appropriate attributes. This function tries to fill the empty values
successive prolongation of the non zeros.
Parameters
----------
mesh : :gimliapi:`GIMLI::Mesh`
For each cell of mesh a value will be returned.
vals : array
Array of size cellCount().
Returns
-------
atts : array
Array of length mesh.cellCount()
"""
atts = pg.RVector(mesh.cellCount(), 0.0)
oldAtts = mesh.cellAttributes()
mesh.setCellAttributes(vals)
mesh.createNeighbourInfos()
# std::vector< Cell * >
# empties = []
if slope:
# search all cells with empty neighbours
ids = pg.find(mesh.cellAttributes() != 0.0)
for c in mesh.cells(ids):
for i in range(c.neighbourCellCount()):
nc = c.neighbourCell(i)
if nc:
if nc.attribute() == 0.0:
# c.setAttribute(99999)
b = pg.findCommonBoundary(c, nc)
# search along a slope
pos = b.center() - b.norm() * 1000.
sf = pg.RVector()
startCell = c
while startCell:
startCell.shape().isInside(pos, sf, False)
nextC = startCell.neighbourCell(sf)
if nextC:
if nextC.attribute() == 0.0:
nextC.setAttribute(c.attribute())
else:
break
startCell = nextC
mesh.fillEmptyCells(mesh.findCellByAttribute(0.0), background=-1)
atts = mesh.cellAttributes()
mesh.setCellAttributes(oldAtts)
return atts
def test2d():
mesh = pg.Mesh("mesh/world2d.bms")
print (mesh)
xMin = mesh.boundingBox().min()[0]
yMax = mesh.boundingBox().max()[0]
x = np.arange(xMin, yMax, 1.0)
mesh.createNeighbourInfos()
rho = pg.RVector(len(mesh.cellAttributes()), 1.0) * 2000.0
rho.setVal(0.0, pg.find(mesh.cellAttributes() == 1.0))
swatch = pg.Stopwatch(True)
pnts = []
spnts = pg.stdVectorRVector3()
for i in x:
pnts.append(pg.RVector3(i, 0.0001))
spnts.append(pg.RVector3(i, 0.0001))
# gzC, GC = calcGCells(pnts, mesh, rho, 1)
gzC = pg.calcGCells(spnts, mesh, rho, 1)
print ("calcGCells", swatch.duration(True))
# gzB, GB = calcGBounds(pnts, mesh, rho)
# gzB = pg.calcGBounds(spnts, mesh, rho)
# print("calcGBounds", swatch.duration(True))
gZ_Mesh = gzC
ax1, ax2 = getaxes()
# sphere analytical solution
gAna = analyticalCircle2D(spnts, radius=2.0, pos=pg.RVector3(0.0, -5.0), dDensity=2000)
gAna2 = analyticalCircle2D(spnts, radius=2.0, pos=pg.RVector3(5.0, -5.0), dDensity=2000)
gAna = gAna + gAna2
ax1.plot(x, gAna, "-x", label="analytical")
ax1.plot(x, gZ_Mesh, label="WonBevis1987-mesh")
print (gAna / gZ_Mesh)
# rho=GB[0]/mesh.cellSizes()
drawModel(ax2, mesh, rho)
for i in (0, 1):
drawSelectedMeshBoundaries(ax2, mesh.findBoundaryByMarker(i), color=(1.0, 1.0, 1.0, 1.0), linewidth=0.3)
# sphere polygone
radius = 2.0
depth = 5.0
poly1 = pg.stdVectorRVector3()
poly2 = pg.stdVectorRVector3()
nSegment = 124
for i in range(nSegment):
xp = np.sin((i + 1) * (2.0 * np.pi) / nSegment)
yp = np.cos((i + 1) * (2.0 * np.pi) / nSegment)
poly1.append(pg.RVector3(xp * radius, yp * radius - depth))
poly2.append(pg.RVector3(xp * radius + 5.0, yp * radius - depth))
gZ_Poly = calcPolydgdz(spnts, poly1, 2000)
gZ_Poly += calcPolydgdz(spnts, poly2, 2000)
ax1.plot(x, gZ_Poly, label="WonBevis1987-Poly")
ax2.plot(pg.x(poly1), pg.y(poly1), color="red")
ax2.plot(pg.x(poly2), pg.y(poly2), color="red")
ax2.plot(pg.x(spnts), pg.y(spnts), marker="x", color="black")
# test some special case
for i, p in enumerate(poly1):
poly1[i] = pg.RVector3(poly1[i] - pg.RVector3(5.0, -6.0))
ax2.plot(pg.x(poly1), pg.y(poly1), color="green")
gz = calcPolydgdz(spnts, poly1, 2000)
ax1.plot(x, gz, label="Special Case", color="green")
ax1.set_ylabel("dg/dz [mGal]")
ax2.set_ylabel("Tiefe [m]")
ax1.legend()
ax2.set_xlim([x[0], x[-1]])
ax2.grid()
def drawShapes(ax, mesh, u):
'''
'''
ax.set_aspect('equal')
Nx = 21
Ny = 21
nLevels = 12
tix = np.linspace(-1.0, 1.0, Nx)
tiy = np.linspace(-1.0, 1.0, Ny)
(X,Y) = np.meshgrid(tix, tiy)
uc = g.RVector(len(X.flat))
pnts = []
c = mesh.cell(0)
imax = g.find(u == max(u))[0]
for i in range(c.nodeCount()):
print c.rst(i)
print imax
print c.createShapeFunctions()[imax]
print "dx", c.createShapeFunctions()[imax].derive(0)
print "dy", c.createShapeFunctions()[imax].derive(1)
# draw nodes
for i in range(c.nodeCount()):
col = 'black'
if i == imax:
col = 'red'
ax.plot(c.node(i).pos()[0], c.node(i).pos()[1], '.', markersize = 12, linewidth=0, color=col)
# draw boundary
drawMeshBoundaries(ax, mesh)
ptns = []
grads = []
swatch = g.Stopwatch(True)
for i, x in enumerate(X.flat):
p = c.shape().xyz(g.RVector3(X.flat[i], Y.flat[i]))
X.flat[i] = p[0]
Y.flat[i] = p[1]
#ax.plot(p[0], p[1], '.', zorder=10, color='black', markersize = 1)
if not c.shape().isInside(p):
uc[i] = -99.0
continue
uc[i] = c.pot(p, u)
gr = c.grad(p, u)
ptns.append(p)
grads.append(gr)
print swatch.duration(True)
for i, p in enumerate(ptns):
#print p, grads[i]
ax.quiver(p[0], p[1], grads[i][0], grads[i][1], zorder=10)
Z = np.ma.masked_where(uc == -99., uc)
Z = Z.reshape(Ny, Nx)
cs = ax.contourf(X, Y, Z, nLevels)
def rrmswitherr(a, b, err, errtol=1):
"""Compute root mean square of values with error above a threshold"""
fi = pg.find(err < errtol)
return pg.rrms(a[fi], b[fi])
def harmfit(y,
x=None,
error=None,
nc=42,
resample=None,
lam=0.1,
window=None,
verbose=False,
dosave=False,
lineSearch=True,
robust=False,
maxiter=20):
"""HARMFIT - GIMLi based curve-fit by harmonic functions
Parameters
----------
y : 1d-array - values to be fitted
x : 1d-array(len(y)) - data abscissa data. default: [0 .. len(y))
error : 1d-array(len(y)) error of y. default (absolute error = 0.01)
nc : int - Number of harmonic coefficients
resample : 1d-array - resample y to x using fitting coeffients
window : int - just fit data inside window bounds
Returns
-------
response : 1d-array(len(resample) or len(x)) - smoothed values
coefficients : 1d-array - fitting coefficients
"""
if x is None:
x = np.arange(len(y))
# else:
# if not isinstance(x, pg.RVector):
# x = pg.asvector(x)
#
# if not isinstance(y, pg.RVector):
# y = pg.asvector(y)
xToFit = None
yToFit = None
if window is not None:
idx = pg.find((x >= window[0]) & (x < window[1]))
# idx = getIndex(x , lambda v: v > window[0] and v < window[1])
xToFit = x(idx)
yToFit = y(idx)
if error is not None:
error = error(idx)
else:
xToFit = x
yToFit = y
# print xToFit
# print yToFit
fop = pg.HarmonicModelling(nc, xToFit, verbose)
inv = pg.RInversion(yToFit, fop, verbose, dosave)
if error is not None:
inv.setAbsoluteError(error)
else:
inv.setAbsoluteError(0.01)
inv.setMarquardtScheme(0.8)
if error is not None:
inv.stopAtChi1(True)
inv.setLambda(lam)
inv.setMaxIter(maxiter)
inv.setLineSearch(lineSearch)
inv.setRobustData(robust)
# inv.setConstraintType(0)
coeff = inv.run()
print(inv.chi2())
if resample is not None:
if not isinstance(resample, pg.RVector):
resample = pg.asvector(resample)
ret = fop.response(coeff, resample)
if window is not None:
# print pg.find((resample < window[0]) | (resample >= window[1]))
ret.setVal(
0.0, pg.find((resample < window[0]) | (resample >= window[1])))
# idx = getIndex(resample,
# lambda v: v <= window[0] or v >= window[1])
# for i in idx: ret[i] = 0.0
return ret, coeff
else:
return inv.response(), coeff
# The second problem for pure Neumann domains is the non-uniqueness of
# the partial differential equation (there are only partial derivatives of the
# electric potential so an arbitrary value might be added, i.e. calibrated).
#
# Therefore we add calibration node with marker -1000 where the potential is
# fixed , somewhere on the boundary and far from the electrodes.
plc.createNode([0.75, 0.25, 0.5], marker=-1000)
###############################################################################
# For sufficient numerical accuracy it is generally a good idea to refine the
# mesh in the vicinity of the electrodes positions.
# We force the local mesh refinement by an additional node at 1/2 mm
# distance in -z-direction.
for s in plc.positions(pg.find(plc.nodeMarkers() == -99)):
plc.createNode(s - [0.0, 0.0, 1e-3 / 2])
# Also refine the reference node
plc.createNode([0.5, 0.5, -0.5 - 1e-3 / 2])
###############################################################################
# Create the tetrahedron mesh (calling the tetgen mesh generator)
mesh = mt.createMesh(plc)
###############################################################################
# First we want to simulate our ERT response for a homogeneous resistivity
# of 1 :math:`\Omega`m. Usually, simulate will calculate apparent resistivities
# (rhoa) and put them into the returned DataContainerERT.
# However, for the calculation of rhoa, geometric factors (k) are expected in
def fillEmptyToCellArray(mesh, vals):
"""
Prolongate empty cell values to complete cell attributes.
It is possible that you have zero values that need to be filled with
appropriate attributes. This function tries to fill the empty values
successive prolongation of the non zeros.
Parameters
----------
mesh : :gimliapi:`GIMLI::Mesh`
For each cell of mesh a value will be returned.
vals : array
Array of size cellCount().
Returns
-------
atts : array
Array of length mesh.cellCount()
"""
atts = pg.RVector(mesh.cellCount(), 0.0)
oldAtts = mesh.cellAttributes()
mesh.setCellAttributes(vals)
mesh.createNeighbourInfos()
# std::vector< Cell * >
#empties = []
#! search all cells with empty neighbours
ids = pg.find(mesh.cellAttributes() != 0.0)
for c in mesh.cells(ids):
for i in range(c.neighbourCellCount()):
nc = c.neighbourCell(i)
if nc:
if nc.attribute() == 0.0:
#c.setAttribute(99999)
b = pg.findCommonBoundary(c, nc)
### search along a slope
pos = b.center() - b.norm()*1000.
sf = pg.RVector()
startCell = c
while startCell:
startCell.shape().isInside(pos, sf, False)
nextC = startCell.neighbourCell(sf)
if nextC:
if nextC.attribute()==0.0:
nextC.setAttribute(c.attribute())
else:
break
startCell = nextC
mesh.fillEmptyCells(mesh.findCellByAttribute(0.0), background=-1 )
atts = mesh.cellAttributes()
mesh.setCellAttributes(oldAtts)
return atts
def test_IndexAccess(self):
# (double) array/vector
an = np.arange(10.)
ag = pg.Vector(an)
# bn = nd.array(bool)
bn = (an > 4.)
self.assertEqual(type(bn), np.ndarray)
self.assertEqual(bn.dtype, 'bool')
self.assertEqual(sum(bn), 5)
# bg = BVector
bg = (ag > 4.)
self.assertEqual(type(bg), pg.BVector)
self.assertEqual(sum(bg), 5)
# BVector(nd.array(bool))
self.assertEqual(len(bg), len(pg.BVector(bn)))
self.assertEqual(sum(bg), sum(pg.BVector(bn)))
self.assertEqual(bg[0], pg.BVector(bn)[0])
np.testing.assert_array_equal(bg, pg.BVector(bn))
# In = nd.array(int)
In = np.nonzero(bn)[0]
self.assertEqual(type(In), np.ndarray)
self.assertEqual(In.dtype, 'int64')
self.assertEqual(len(In), 5)
self.assertEqual(In[0], 5)
# np.nonzero(bg)
np.testing.assert_array_equal(In, np.nonzero(bg)[0])
# Ig = IndexArray
Ig = pg.find(bg)
self.assertEqual(type(Ig), pg.core.IndexArray)
self.assertEqual(len(Ig), 5)
self.assertEqual(Ig[0], 5)
# pg.find(nd.array(bool))
np.testing.assert_array_equal(Ig, pg.find(bn))
## Indexoperators ##
# ndarray [nd.array(bool)] == ndarray [nd.array(int)]
np.testing.assert_equal(an[bn], an[In])
self.assertEqual(len(an[bn]), 5)
self.assertEqual(an[bn][0], 5)
# ndarray[IndexArray] == ndarray [nd.array(int)]
np.testing.assert_equal(an[Ig], an[In])
# ndarray[BVector] == ndarray [nd.array(bool)]
np.testing.assert_array_equal(an[np.array(bg, dtype='bool')], an[bn])
np.testing.assert_array_equal(an[np.array(bg)], an[bn])
np.testing.assert_array_equal(an[bg.array()], an[bn])
np.testing.assert_array_equal(an[an>5], [6, 7, 8, 9])
np.testing.assert_array_equal(ag[bg], ag[Ig])
self.assertEqual(len(ag[bg]), 5)
self.assertEqual(ag[bg][0], 5)
# RVector [BVector] == RVector [nd.array(bool)]
np.testing.assert_array_equal(ag[bg], ag[bn])
np.testing.assert_equal(sum(ag[bg]), sum(ag[bn]))
# RVector [IndexArray] == RVector [nd.array(int)]
np.testing.assert_array_equal(ag[Ig], ag[In])
# RVector(BVector) == RVector(nd.array(bool))
# RVector(IndexArray) == RVector(nd.array(int))
I = pg.core.IndexArray([0,1,1,0])
np.testing.assert_array_equal(pg.sum(I), 2)
np.testing.assert_array_equal(sum(I), 2)
np.testing.assert_array_equal(np.sum(I), 2)
# -*- coding: utf-8 -*- import numpy as np import pygimli as pg # (double) array/vector an = np.arange(10.) ag = pg.RVector(an) # boolean array/vector bn = (an > 4.) bg = (ag > 4.) # index vectors from bools fn = np.nonzero(bn)[0] fg = pg.find(bg) # pure numpy indexing print((an[bn])) print((an[fn])) # pure pygimli indexing print((ag(bg))) print((ag(fg))) # work print((ag[bg])) print((ag[fg])) print((ag[fn])) print((ag[bn]))
def test_IndexAccess(self):
# (double) array/vector
an = np.arange(10.)
ag = pg.RVector(an)
# bn = nd.array(bool)
bn = (an > 4.)
self.assertEqual(type(bn), np.ndarray)
self.assertEqual(bn.dtype, 'bool')
self.assertEqual(sum(bn), 5)
# bg = BVector
bg = (ag > 4.)
self.assertEqual(type(bg), pg.BVector)
self.assertEqual(sum(bg), 5)
# BVector(nd.array(bool))
self.assertEqual(len(bg), len(pg.BVector(bn)))
self.assertEqual(sum(bg), sum(pg.BVector(bn)))
self.assertEqual(bg[0], pg.BVector(bn)[0])
np.testing.assert_array_equal(bg, pg.BVector(bn))
# In = nd.array(int)
In = np.nonzero(bn)[0]
self.assertEqual(type(In), np.ndarray)
self.assertEqual(In.dtype, 'int')
self.assertEqual(len(In), 5)
self.assertEqual(In[0], 5)
# np.nonzero(bg)
np.testing.assert_array_equal(In, np.nonzero(bg)[0])
# Ig = IndexArray
Ig = pg.find(bg)
self.assertEqual(type(Ig), pg.IndexArray)
self.assertEqual(len(Ig), 5)
self.assertEqual(Ig[0], 5)
# pg.find(nd.array(bool))
np.testing.assert_array_equal(Ig, pg.find(bn))
## Indexoperators ##
# ndarray [nd.array(bool)] == ndarray [nd.array(int)]
np.testing.assert_equal(an[bn], an[In])
self.assertEqual(len(an[bn]), 5)
self.assertEqual(an[bn][0], 5)
# ndarray[IndexArray] == ndarray [nd.array(int)]
np.testing.assert_equal(an[Ig], an[In])
# ndarray[BVector] == ndarray [nd.array(bool)]
np.testing.assert_array_equal(an[np.array(bg, dtype='bool')], an[bn])
np.testing.assert_array_equal(an[np.array(bg)], an[bn])
np.testing.assert_array_equal(an[bg.array()], an[bn])
## this fails because it is interpreted as an[[0,0,0,1,1,1]] ..
#np.testing.assert_equal(an[bg], an[bn])
# RVector [BVector] == RVector [IndexArray]
np.testing.assert_array_equal(ag[bg], ag[Ig])
self.assertEqual(len(ag[bg]), 5)
self.assertEqual(ag[bg][0], 5)
# RVector [BVector] == RVector [nd.array(bool)]
np.testing.assert_array_equal(ag[bg], ag[bn])
np.testing.assert_equal(sum(ag[bg]), sum(ag[bn]))
# RVector [IndexArray] == RVector [nd.array(int)]
np.testing.assert_array_equal(ag[Ig], ag[In])
def harmfit(y, x=None, error=None, nc=42, resample=None, lam=0.1,
window=None, verbose=False, dosave=False,
lineSearch=True, robust=False, maxiter=20):
"""HARMFIT - GIMLi based curve-fit by harmonic functions
Parameters
----------
y : 1d-array - values to be fitted
x : 1d-array(len(y)) - data abscissa data. default: [0 .. len(y))
error : 1d-array(len(y)) error of y. default (absolute error = 0.01)
nc : int - Number of harmonic coefficients
resample : 1d-array - resample y to x using fitting coeffients
window : int - just fit data inside window bounds
Returns
-------
response : 1d-array(len(resample) or len(x)) - smoothed values
coefficients : 1d-array - fitting coefficients
"""
if x is None:
x = np.arange(len(y))
xToFit = None
yToFit = None
if window is not None:
idx = pg.find((x >= window[0]) & (x < window[1]))
# idx = getIndex(x , lambda v: v > window[0] and v < window[1])
xToFit = x(idx)
yToFit = y(idx)
if error is not None:
error = error(idx)
else:
xToFit = x
yToFit = y
fop = pg.HarmonicModelling(nc, xToFit, verbose)
inv = pg.RInversion(yToFit, fop, verbose, dosave)
if error is not None:
inv.setAbsoluteError(error)
else:
inv.setAbsoluteError(0.01)
inv.setMarquardtScheme(0.8)
if error is not None:
inv.stopAtChi1(True)
inv.setLambda(lam)
inv.setMaxIter(maxiter)
inv.setLineSearch(lineSearch)
inv.setRobustData(robust)
# inv.setConstraintType(0)
coeff = inv.run()
if resample is not None:
ret = fop.response(coeff, resample)
if window is not None:
# print pg.find((resample < window[0]) | (resample >= window[1]))
ret.setVal(0.0, pg.find((resample < window[0]) |
(resample >= window[1])))
# idx = getIndex(resample,
# lambda v: v <= window[0] or v >= window[1])
# for i in idx: ret[i] = 0.0
return ret, coeff
else:
return inv.response(), coeff
pg.show(mesh, times, cMap='Spectral', fillContour=True, ax=ax)
drawStreamLines(ax, mesh, -times, nx=50, ny=50)
###############################################################################
# We compare the result with the analytical solution along the x axis
x = np.arange(0., 140., 0.5)
tFMM = pg.interpolate(mesh, times, x, x * 0., x * 0.)
tAna = analyticalSolution2Layer(x, zlay, v[0], v[1])
print("min(dt)={} ms max(dt)={} ms".format(min(tFMM - tAna) * 1000,
max(tFMM - tAna) * 1000))
###############################################################################
# In order to use the Dijkstra, we extract the surface positions >0
mx = pg.x(mesh.positions())
my = pg.y(mesh.positions())
fi = pg.find((my == 0.0) & (mx >= 0))
px = np.sort(mx(fi))
###############################################################################
# A data container with index arrays named s (shot) and g (geophones) is
# created and filled with the positions and shot/geophone indices.
data = pg.DataContainer()
data.registerSensorIndex('s')
data.registerSensorIndex('g')
for pxi in px:
data.createSensor(pg.RVector3(pxi, 0.0))
ndata = len(px) - 1
data.resize(ndata)
data.set('s', pg.RVector(ndata, 0)) # only one shot at first sensor
data.set('g', pg.utils.grange(1, ndata, 1)) # all others and geophones
def fillEmptyToCellArray(mesh, vals, slope=True):
"""
Prolongate empty cell values to complete cell attributes.
It is possible to have zero values that are filled with appropriate
attributes. This function tries to fill empty values successively by
prolongation of the non-zeros.
Parameters
----------
mesh : :gimliapi:`GIMLI::Mesh`
For each cell of mesh a value will be returned.
vals : array
Array of size cellCount().
Returns
-------
atts : array
Array of length mesh.cellCount()
Examples
--------
>>> import pygimli as pg
>>> import numpy as np
>>> import matplotlib.pyplot as plt
>>>
>>> # Create a mesh with 3 layers and an outer region for extrapolation
>>> layers = pg.meshtools.createWorld([0,-50],[100,0], layers=[-15,-35])
>>> inner = pg.meshtools.createMesh(layers, area=3)
>>> mesh = pg.meshtools.appendTriangleBoundary(inner, xbound=120, ybound=50,
... area=20, marker=0)
>>>
>>> # Create data for the inner region only
>>> layer_vals = [20,30,50]
>>> data = np.array(layer_vals)[inner.cellMarkers() - 1]
>>>
>>> # The following fails since len(data) != mesh.cellCount(), extrapolate
>>> # pg.show(mesh, data)
>>>
>>> # Create data vector, where zeros fill the outer region
>>> data_with_outer = np.array([0] + layer_vals)[mesh.cellMarkers()]
>>>
>>> # Actual extrapolation
>>> extrapolated_data = pg.meshtools.fillEmptyToCellArray(mesh,
... data_with_outer, slope=False)
>>> extrapolated_data_with_slope = pg.meshtools.fillEmptyToCellArray(mesh,
... data_with_outer, slope=True)
>>>
>>> # Visualization
>>> fig, (ax1, ax2, ax3) = plt.subplots(1,3, figsize=(10,8), sharey=True)
>>> _ = pg.show(mesh, data_with_outer, ax=ax1, cMin=0)
>>> _ = pg.show(mesh, extrapolated_data, ax=ax2, cMin=0)
>>> _ = pg.show(mesh, extrapolated_data_with_slope, ax=ax3, cMin=0)
>>> _ = ax1.set_title("Original data")
>>> _ = ax2.set_title("Extrapolated with slope=False")
>>> _ = ax3.set_title("Extrapolated with slope=True")
"""
# atts = pg.Vector(mesh.cellCount(), 0.0) # not used
# oldAtts = mesh.cellAttributes() # not used
mesh.setCellAttributes(vals)
mesh.createNeighborInfos()
# std::vector< Cell * >
# empties = []
if slope:
# search all cells with empty neighbors
ids = pg.find(mesh.cellAttributes() != 0.0)
for c in mesh.cells(ids):
for i in range(c.neighborCellCount()):
nc = c.neighborCell(i)
if nc:
if nc.attribute() == 0.0:
# c.setAttribute(99999)
b = pg.core.findCommonBoundary(c, nc)
# search along a slope
pos = b.center() - b.norm() * 1000.
sf = pg.Vector()
startCell = c
while startCell:
startCell.shape().isInside(pos, sf, False)
nextC = startCell.neighborCell(sf)
if nextC:
if nextC.attribute() == 0.0:
nextC.setAttribute(c.attribute())
else:
break
startCell = nextC
vals = mesh.cellAttributes()
mesh.prolongateEmptyCellsValues(vals, background=-9e99)
mesh.setCellAttributes(vals)
return vals
def test2d():
mesh = g.Mesh( 'mesh/world2d.bms' )
print mesh
xMin = mesh.boundingBox( ).min()[0]
yMax = mesh.boundingBox( ).max()[0]
x = P.arange( xMin, yMax, 1. );
mesh.createNeighbourInfos()
rho = g.RVector( len( mesh.cellAttributes() ), 1. ) * 2000.0
rho.setVal( 0.0, g.find( mesh.cellAttributes() == 1.0 ) )
swatch = g.Stopwatch( True )
pnts = []
spnts = g.stdVectorRVector3()
for i in x:
pnts.append( g.RVector3( i, 0.0001 ) )
spnts.append( g.RVector3( i, 0.0001 ) )
#gzC, GC = calcGCells( pnts, mesh, rho, 1 )
gzC = g.calcGCells( spnts , mesh, rho, 1 )
print "calcGCells", swatch.duration( True )
#gzB, GB = calcGBounds( pnts, mesh, rho )
gzB = g.calcGBounds( spnts , mesh, rho )
print "calcGBounds", swatch.duration( True )
gZ_Mesh = gzC
ax1, ax2 = getaxes()
# sphere analytical solution
gAna = analyticalCircle2D( spnts, radius = 2.0, pos = g.RVector3( 0.0, -5.0 ), dDensity = 2000 )
gAna2 = analyticalCircle2D( spnts, radius = 2.0, pos = g.RVector3( 5.0, -5.0 ), dDensity = 2000 )
gAna = gAna + gAna2
ax1.plot( x, gAna, '-x', label= 'Analytisch' )
ax1.plot( x, gZ_Mesh, label= 'WonBevis1987-mesh' )
print gAna / gZ_Mesh
#rho=GB[0]/mesh.cellSizes()
gci = drawModel( ax2, mesh, rho )
drawSelectedMeshBoundaries( ax2, mesh.findBoundaryByMarker( 0 )
, color = ( 1.0, 1.0, 1.0, 1.0 )
, linewidth = 0.3 )
drawSelectedMeshBoundaries( ax2, mesh.findBoundaryByMarker( 1 )
, color = ( 1.0, 1.0, 1.0, 1.0 )
, linewidth = 0.3 )
# sphere polygone
radius = 2.
depth = 5.
poly1 = g.stdVectorRVector3()
poly2 = g.stdVectorRVector3()
nSegment=124
for i in range( nSegment ):
xp = np.sin( (i+1) * ( 2. * np.pi ) / nSegment )
yp = np.cos( (i+1) * ( 2. * np.pi ) / nSegment )
poly1.append( g.RVector3( xp * radius, yp * radius - depth ) )
poly2.append( g.RVector3( xp * radius + 5., yp * radius - depth ) )
gZ_Poly = calcPolydgdz( spnts, poly1, 2000 )
gZ_Poly += calcPolydgdz( spnts, poly2, 2000 )
ax1.plot( x, gZ_Poly, label= 'WonBevis1987-Poly' )
ax2.plot( g.x( poly1 ), g.y( poly1 ), color = 'red' )
ax2.plot( g.x( poly2 ), g.y( poly2 ), color = 'red' )
ax2.plot( g.x( spnts ), g.y( spnts ), marker = 'x', color = 'black' )
# test some special case
for i, p in enumerate( poly1 ):
poly1[i] = g.RVector3( poly1[i] - g.RVector3( 5.0, -6. ) )
ax2.plot( g.x( poly1 ), g.y( poly1 ), color = 'green' )
gz = calcPolydgdz( spnts, poly1, 2000 )
ax1.plot( x, gz, label= 'Special Case', color = 'green' )
ax1.set_ylabel( 'dg/dz [mGal]' )
ax2.set_ylabel( 'Tiefe [m]' )
ax1.legend()
ax2.set_xlim( [ x[0], x[-1] ] )
ax2.grid()
drawStreamLines(ax, mesh, -times, nx=50, ny=50)
###############################################################################
# We compare the result with the analytical solution along the x axis
x = np.arange(0., 140., 0.5)
tFMM = pg.interpolate(mesh, times, x, x * 0., x * 0.)
tAna = analyticalSolution2Layer(x)
print("min(dt)={} ms max(dt)={} ms".format(
min(tFMM - tAna) * 1000,
max(tFMM - tAna) * 1000))
###############################################################################
# In order to use the Dijkstra, we extract the surface positions >0
mx = pg.x(mesh.positions())
my = pg.y(mesh.positions())
fi = pg.find((my == 0.0) & (mx >= 0))
px = np.sort(mx(fi))
###############################################################################
# A data container with index arrays named s (shot) and g (geophones) is
# created and filled with the positions and shot/geophone indices.
data = pg.DataContainer()
data.registerSensorIndex('s')
data.registerSensorIndex('g')
for pxi in px:
data.createSensor(pg.RVector3(pxi, 0.0))
ndata = len(px) - 1
data.resize(ndata)
data.set('s', pg.RVector(ndata, 0)) # only one shot at first sensor
data.set('g', pg.utils.grange(1, ndata, 1)) # all others and geophones
def drawShapes(ax, mesh, u):
'''
'''
ax.set_aspect('equal')
Nx = 21
Ny = 21
nLevels = 12
tix = np.linspace(-1.0, 1.0, Nx)
tiy = np.linspace(-1.0, 1.0, Ny)
X, Y = np.meshgrid(tix, tiy)
uc = pg.RVector(len(X.flat))
c = mesh.cell(0)
imax = pg.find(u == max(u))[0]
for i in range(c.nodeCount()):
print(c.rst(i))
print(imax)
print(c.createShapeFunctions()[imax])
print("dx", c.createShapeFunctions()[imax].derive(0))
print("dy", c.createShapeFunctions()[imax].derive(1))
# draw nodes
for i in range(c.nodeCount()):
col = 'black'
if i == imax:
col = 'red'
ax.plot(c.node(i).pos()[0], c.node(i).pos()[1], '.', markersize=12,
linewidth=0, color=col)
# draw boundary
drawMeshBoundaries(ax, mesh)
ptns = []
grads = []
swatch = pg.Stopwatch(True)
for i, x in enumerate(X.flat):
p = c.shape().xyz(pg.RVector3(X.flat[i], Y.flat[i]))
X.flat[i] = p[0]
Y.flat[i] = p[1]
# ax.plot(p[0], p[1], '.', zorder=10, color='black', markersize = 1)
if not c.shape().isInside(p):
uc[i] = -99.0
continue
uc[i] = c.pot(p, u)
gr = c.grad(p, u)
ptns.append(p)
grads.append(gr)
print(swatch.duration(True))
for i, p in enumerate(ptns):
ax.quiver(p[0], p[1], grads[i][0], grads[i][1], zorder=10)
Z = np.ma.masked_where(uc == -99., uc)
Z = Z.reshape(Ny, Nx)
ax.contourf(X, Y, Z, nLevels)
def drawStreamLine_(ax, mesh, c, data, dataMesh=None, linewidth=1.0,
dropTol=0.0, **kwargs):
"""Draw a single streamline.
Draw a single streamline into a given mesh for given data stating at
the center of cell c.
The Streamline will be enlarged until she reached a cell that
already contains a streamline.
TODO
linewidth and color depends on absolute velocity
or background color saturation
Parameters
----------
ax : matplotlib.ax
ax to draw into
mesh : :gimliapi:`GIMLI::Mesh`
2d Mesh to draw the streamline
c : :gimliapi:`GIMLI::Cell`
start cell
data : iterable float | [float, float]
If data is an array (per cell or node) gradients are calculated
otherwise the data will be interpreted as vector field.
dataMesh : :gimliapi:`GIMLI::Mesh` [None]
Optional mesh for the data. If you want high resolution
data to plot on coarse draw mesh.
linewidth : float [1.0]
Streamline linewidth
dropTol : float [0.0]
Don't draw stream lines with velocity lower than drop tolerance.
"""
x, y, v = streamline(mesh, data, startCoord=c.center(), dLengthSteps=5,
dataMesh=dataMesh, maxSteps=10000, verbose=False,
coords=[0, 1])
if 'color' not in kwargs:
kwargs['color'] = 'black'
lines = None
if len(x) > 2:
points = np.array([x, y]).T.reshape(-1, 1, 2)
segments = np.concatenate([points[:-1], points[1:]], axis=1)
lwidths = pg.RVector(len(v), linewidth)
lwidths[pg.find(pg.RVector(v) < dropTol)] = 0.0
lines = mpl.collections.LineCollection(
segments, linewidths=lwidths, **kwargs)
ax.add_collection(lines)
# probably the limits are wrong without plot call
# lines = ax.plot(x, y, **kwargs)
# updateAxes_(ax, lines)
# ax.plot(x, y, '.-', color='black', **kwargs)
if len(x) > 3:
xmid = int(len(x) / 2)
ymid = int(len(y) / 2)
dx = x[xmid + 1] - x[xmid]
dy = y[ymid + 1] - y[ymid]
c = mesh.findCell([x[xmid], y[ymid]])
# dLength = c.center().dist(c.node(0).pos()) / 4. # NOT USED
if v[xmid] > dropTol:
# ax.arrow(x[xmid], y[ymid], dx, dy,
# #width=dLength / 3.,
# width=0,
# head_width=0.01,
# head_length=0.02
# # head_width=dLength / 3.,
# # head_length=dLength / 3.,
# head_starts_at_zero=True,
# length_includes_head=False,
# lw=4,
# ls=None,
# **kwargs)
dx90 = -dy
dy90 = dx
aLen = 3
aWid = 1
xy = list(zip([x[xmid] + dx90*aWid, x[xmid] + dx*aLen,
x[xmid] - dx90*aWid],
[y[ymid] + dy90*aWid, y[ymid] + dy*aLen,
y[ymid] - dy90*aWid]))
arrow = mpl.patches.Polygon(xy, ls=None, lw=0, closed=True,
**kwargs)
# arrow = mpl.collections.PolyCollection(xy, lines=None,
# closed=True, **kwargs)
ax.add_patch(arrow)
return lines
def drawStreamLine_(ax, mesh, c, data, dataMesh=None, linewidth=1.0,
dropTol=0.0, **kwargs):
"""Draw a single streamline.
Draw a single streamline into a given mesh for given data stating at
the center of cell c.
The Streamline will be enlarged until she reached a cell that
already contains a streamline.
TODO
linewidth and color depends on absolute velocity
or background color saturation
Parameters
----------
ax : matplotlib.ax
ax to draw into
mesh : :gimliapi:`GIMLI::Mesh`
2d Mesh to draw the streamline
c : :gimliapi:`GIMLI::Cell`
start cell
data : iterable float | [float, float]
If data is an array (per cell or node) gradients are calculated
otherwise the data will be interpreted as vector field.
dataMesh : :gimliapi:`GIMLI::Mesh` [None]
Optional mesh for the data. If you want high resolution
data to plot on coarse draw mesh.
linewidth : float [1.0]
Streamline linewidth
dropTol : float [0.0]
Don't draw stream lines with velocity lower than drop tolerance.
"""
x, y, v = streamline(mesh, data, startCoord=c.center(), dLengthSteps=5,
dataMesh=dataMesh, maxSteps=10000, verbose=False,
coords=[0, 1])
if 'color' not in kwargs:
kwargs['color'] = 'black'
lines = None
if len(x) > 2:
points = np.array([x, y]).T.reshape(-1, 1, 2)
segments = np.concatenate([points[:-1], points[1:]], axis=1)
lwidths = pg.RVector(len(v), linewidth)
lwidths[pg.find(pg.RVector(v) < dropTol)] = 0.0
lines = mpl.collections.LineCollection(
segments, linewidths=lwidths, **kwargs)
ax.add_collection(lines)
# probably the limits are wrong without plot call
# lines = ax.plot(x, y, **kwargs)
# updateAxes_(ax, lines)
# ax.plot(x, y, '.-', color='black', **kwargs)
if len(x) > 3:
xmid = int(len(x) / 2)
ymid = int(len(y) / 2)
dx = x[xmid + 1] - x[xmid]
dy = y[ymid + 1] - y[ymid]
c = mesh.findCell([x[xmid], y[ymid]])
# dLength = c.center().dist(c.node(0).pos()) / 4. # NOT USED
if v[xmid] > dropTol:
# ax.arrow(x[xmid], y[ymid], dx, dy,
# #width=dLength / 3.,
# width=0,
# head_width=0.01,
# head_length=0.02
# # head_width=dLength / 3.,
# # head_length=dLength / 3.,
# head_starts_at_zero=True,
# length_includes_head=False,
# lw=4,
# ls=None,
# **kwargs)
dx90 = -dy
dy90 = dx
aLen = 3
aWid = 1
xy = list(zip([x[xmid] + dx90*aWid, x[xmid] + dx*aLen,
x[xmid] - dx90*aWid],
[y[ymid] + dy90*aWid, y[ymid] + dy*aLen,
y[ymid] - dy90*aWid]))
arrow = mpl.patches.Polygon(xy, ls=None, lw=0, closed=True,
**kwargs)
# arrow = mpl.collections.PolyCollection(xy, lines=None,
# closed=True, **kwargs)
ax.add_patch(arrow)
return lines
def test2d():
mesh = pg.Mesh('mesh/world2d.bms')
print(mesh)
xMin = mesh.boundingBox().min()[0]
yMax = mesh.boundingBox().max()[0]
x = np.arange(xMin, yMax, 1.)
mesh.createNeighbourInfos()
rho = pg.RVector(len(mesh.cellAttributes()), 1.) * 2000.0
rho.setVal(0.0, pg.find(mesh.cellAttributes() == 1.0))
swatch = pg.Stopwatch(True)
pnts = []
spnts = pg.stdVectorRVector3()
for i in x:
pnts.append(pg.RVector3(i, 0.0001))
spnts.append(pg.RVector3(i, 0.0001))
# gzC, GC = calcGCells(pnts, mesh, rho, 1)
gzC = pg.calcGCells(spnts, mesh, rho, 1)
print("calcGCells", swatch.duration(True))
# gzB, GB = calcGBounds(pnts, mesh, rho)
# gzB = pg.calcGBounds(spnts, mesh, rho)
# print("calcGBounds", swatch.duration(True))
gZ_Mesh = gzC
ax1, ax2 = getaxes()
# sphere analytical solution
gAna = analyticalCircle2D(spnts,
radius=2.0,
pos=pg.RVector3(0.0, -5.0),
dDensity=2000)
gAna2 = analyticalCircle2D(spnts,
radius=2.0,
pos=pg.RVector3(5.0, -5.0),
dDensity=2000)
gAna = gAna + gAna2
ax1.plot(x, gAna, '-x', label='analytical')
ax1.plot(x, gZ_Mesh, label='WonBevis1987-mesh')
print(gAna / gZ_Mesh)
# rho=GB[0]/mesh.cellSizes()
drawModel(ax2, mesh, rho)
for i in (0, 1):
drawSelectedMeshBoundaries(ax2,
mesh.findBoundaryByMarker(i),
color=(1.0, 1.0, 1.0, 1.0),
linewidth=0.3)
# sphere polygone
radius = 2.
depth = 5.
poly1 = pg.stdVectorRVector3()
poly2 = pg.stdVectorRVector3()
nSegment = 124
for i in range(nSegment):
xp = np.sin((i + 1) * (2. * np.pi) / nSegment)
yp = np.cos((i + 1) * (2. * np.pi) / nSegment)
poly1.append(pg.RVector3(xp * radius, yp * radius - depth))
poly2.append(pg.RVector3(xp * radius + 5., yp * radius - depth))
gZ_Poly = calcPolydgdz(spnts, poly1, 2000)
gZ_Poly += calcPolydgdz(spnts, poly2, 2000)
ax1.plot(x, gZ_Poly, label='WonBevis1987-Poly')
ax2.plot(pg.x(poly1), pg.y(poly1), color='red')
ax2.plot(pg.x(poly2), pg.y(poly2), color='red')
ax2.plot(pg.x(spnts), pg.y(spnts), marker='x', color='black')
# test some special case
for i, p in enumerate(poly1):
poly1[i] = pg.RVector3(poly1[i] - pg.RVector3(5.0, -6.))
ax2.plot(pg.x(poly1), pg.y(poly1), color='green')
gz = calcPolydgdz(spnts, poly1, 2000)
ax1.plot(x, gz, label='Special Case', color='green')
ax1.set_ylabel('dg/dz [mGal]')
ax2.set_ylabel('Tiefe [m]')
ax1.legend()
ax2.set_xlim([x[0], x[-1]])
ax2.grid()
def harmfit(y, x=None, error=None, nCoefficients=42, resample=None,
window=None, verbose=False, dosave=False,
lineSearch=True, robust=False, maxiter=20):
"""
HARMFIT - GIMLi based curve-fit by harmonic functions
y .. 1d-array(len(y)) values to be fitted
x .. 1d-array(len(y)) abscissa data spacing. if not given: 1 * [0 .. len(y))
error .. 1d-array(len(y)) data error of y (fit y into the range of error). if not given (absolute err = 1%)
nCoefficients .. int Number of harmonic coefficients
resample .. 1d-array(len(resample)) resample y based on fitting coeffients
window .. just fit data inside window bounds
return response, coefficients
response .. 1d-array(len(y)) if no resample given, else 1d-array(len(resample))
coefficients .. coefficients for harmic functions that fit y
"""
if x is None:
x = pg.asvector(np.arange(len(y)))
else:
if not isinstance(x, pg.RVector):
x = pg.asvector(x)
if not isinstance(y, pg.RVector):
y = pg.asvector(y)
xToFit = None
yToFit = None
if window is not None:
idx = pg.find((x >= window[0]) & (x < window[1]))
#idx = getIndex(x , lambda v: v > window[0] and v < window[1])
xToFit = x(idx)
yToFit = y(idx)
if error is not None:
error = error(idx)
else:
xToFit = x
yToFit = y
# print xToFit
# print yToFit
fop = pg.HarmonicModelling(nCoefficients, xToFit, verbose)
inv = pg.RInversion(yToFit, fop, verbose, dosave)
if error is not None:
if not isinstance(error, pg.RVector):
error = pg.asvector(error)
inv.setRelativeError(error)
else:
inv.setAbsoluteError(0.01)
inv.setLambda(000.0)
inv.setLocalRegularization(True)
inv.setMaxIter(maxiter)
inv.setLineSearch(lineSearch)
inv.setRobustData(robust)
# inv.setConstraintType(0)
coeff = inv.run()
if resample is not None:
if not isinstance(resample, pg.RVector):
resample = pg.asvector(resample)
ret = fop.response(coeff, resample)
# print ret
if window is not None:
# print resample
# print window[0], window[1]
# print pg.find((resample < window[0]) | (resample >= window[1]))
ret.setVal(
0.0, pg.find(
(resample < window[0]) | (
resample >= window[1])))
# idx = getIndex(resample, lambda v: v <= window[0] or v >= window[1])
# for i in idx: ret[i] = 0.0
# print ret
# sys.exit
return ret, coeff
else:
return inv.response(), coeff
def drawStreamLine_(ax,
mesh,
c,
data,
dataMesh=None,
linewidth=1.0,
dropTol=0.0,
**kwargs):
"""Draw a single streamline.
Draw a single streamline into a given mesh for given data stating at
the center of cell c.
The Streamline will be enlarged until she reached a cell that
already contains a streamline.
TODO
linewidth and color depends on absolute velocity
or background color saturation
Parameters
----------
ax : matplotlib.ax
ax to draw into
mesh : :gimliapi:`GIMLI::Mesh`
2d mesh
c : :gimliapi:`GIMLI::Cell`
Start point is c.center()
data : iterable float | [float, float]
If data is an array (per cell or node) gradients are calculated
otherwise the data will be interpreted as vector field per nodes or
cell centers.
dataMesh : :gimliapi:`GIMLI::Mesh` [None]
Optional mesh for the data. If you want high resolution
data to plot on coarse draw mesh.
linewidth : float [1.0]
Streamline linewidth
dropTol : float [0.0]
Don't draw stream lines with velocity lower than drop tolerance.
Keyword Arguments
-----------------
**kwargs
arrowSize: int
Size of the arrow's head.
arrowColor: str
Color of the arrow's head.
Additional kwargs are being forwarded to mpl.LineCollection, mpl.Polygon
"""
x, y, v = streamline(mesh,
data,
startCoord=c.center(),
dLengthSteps=5,
dataMesh=dataMesh,
maxSteps=10000,
verbose=False,
coords=[0, 1])
if 'color' not in kwargs:
kwargs['color'] = 'black'
arrowSize = kwargs.pop('arrowSize', 12)
arrowColor = kwargs.pop('arrowColor', 'black')
lines = None
if len(x) > 2:
points = np.array([x, y]).T.reshape(-1, 1, 2)
segments = np.concatenate([points[:-1], points[1:]], axis=1)
lwidths = pg.Vector(len(v), linewidth)
lwidths[pg.find(pg.Vector(v) < dropTol)] = 0.0
lines = mpl.collections.LineCollection(segments,
linewidths=lwidths,
**kwargs)
ax.add_collection(lines)
# probably the limits are wrong without plot call
# lines = ax.plot(x, y, **kwargs)
# updateAxes_(ax, lines)
# ax.plot(x, y, '.-', color='black', **kwargs)
if len(x) > 3:
xmid = int(len(x) / 2)
ymid = int(len(y) / 2)
dx = x[xmid + 1] - x[xmid]
dy = y[ymid + 1] - y[ymid]
c = mesh.findCell([x[xmid], y[ymid]])
if v[xmid] > dropTol:
absArrowSize = True
if absArrowSize:
ax.annotate(
'',
xytext=(x[xmid] - dx, y[ymid] - dy),
xy=(x[xmid], y[ymid]),
arrowprops=dict(arrowstyle="-|>", color=arrowColor),
size=arrowSize,
**kwargs,
)
else:
ax.arrow(x[xmid],
y[ymid],
dx,
dy,
shape='full',
lw=0,
length_includes_head=True,
fc=arrowColor,
head_width=.35,
**kwargs)
# dx90 = -dy
# dy90 = dx
# aLen = 3
# aWid = 1
# xy = list(zip([x[xmid] + dx90*aWid, x[xmid] + dx*aLen,
# x[xmid] - dx90*aWid],
# [y[ymid] + dy90*aWid, y[ymid] + dy*aLen,
# y[ymid] - dy90*aWid]))
# arrow = mpl.patches.Polygon(xy, ls=None, lw=0, closed=True,
# **kwargs)
#ax.add_patch(arrow)
return lines
def rmswitherr(a, b, err, errtol=1):
"""Compute (abs-)root mean square of values with error above a threshold"""
fi = pg.find(err < errtol)
return sqrt(pg.mean(pg.pow(a[fi] - b[fi], 2)))
def rrmsWithErr(a, b, err, errtol=1):
"""Compute root mean square of values with error above a threshold"""
fi = pg.find(err < errtol)
return rms((a[fi]-b[fi])/a[fi])
def showMesh(mesh,
data=None,
hold=False,
block=False,
colorBar=None,
label=None,
coverage=None,
ax=None,
savefig=None,
showMesh=False,
showBoundary=None,
markers=False,
**kwargs):
"""2D Mesh visualization.
Create an axis object and plot a 2D mesh with given node or cell data.
Returns the axis and the color bar. The type of data determine the
appropriate draw method.
Parameters
----------
mesh : :gimliapi:`GIMLI::Mesh`
2D or 3D GIMLi mesh
data : iterable [None]
Optionally data to visualize.
. None (draw mesh only)
forward to :py:mod:`pygimli.mplviewer.drawMesh`
or if no cells are given:
forward to :py:mod:`pygimli.mplviewer.drawPLC`
. [[marker, value], ...]
List of Cellvalues per cell marker
forward to :py:mod:`pygimli.mplviewer.drawModel`
. float per cell -- model, patch
forward to :py:mod:`pygimli.mplviewer.drawModel`
. float per node -- scalar field
forward to :py:mod:`pygimli.mplviewer.drawField`
. iterable of type [float, float] -- vector field
forward to :py:mod:`pygimli.mplviewer.drawStreams`
. pg.R3Vector -- vector field
forward to :py:mod:`pygimli.mplviewer.drawStreams`
. pg.stdVectorRVector3 -- sensor positions
forward to :py:mod:`pygimli.mplviewer.drawSensors`
hold : bool [false]
Set interactive plot mode for matplotlib.
If this is set to false [default] your script will open
a window with the figure and draw your content.
If set to true nothing happens until you either force another show with
hold=False, you call plt.show() or pg.wait().
If you want show with stopping your script set block = True.
block : bool [false]
Force show drawing your content and block the script until you
close the current figure.
colorBar : bool [None], Colorbar
Create and show a colorbar. If colorBar is a valid colorbar then only
its values will be updated.
label : str
Set colorbar label. If set colorbar is toggled to True. [None]
coverage : iterable [None]
Weight data by the given coverage array and fadeout the color.
ax : matplotlib.Axes [None]
Instead of create a new and empty ax, just draw into the a given.
Useful to combine draws.
savefig: string
Filename for a direct save to disc.
The matplotlib pdf-output is a little bit big so we try
an epstopdf if the .eps suffix is found in savefig
showMesh : bool [False]
Shows the mesh itself aditional.
showBoundary : bool [None]
Shows all boundary with marker != 0. A value None means automatic
True for cell data and False for node data.
marker : bool [False]
Show mesh and boundary marker.
**kwargs :
* xlabel : str [None]
Add label to the x axis
* ylabel : str [None]
Add label to the y axis
* all remaining
Will be forwarded to the draw functions and matplotlib methods,
respectively.
Examples
--------
>>> import pygimli as pg
>>> import pygimli.meshtools as mt
>>> world = mt.createWorld(start=[-10, 0], end=[10, -10],
... layers=[-3, -7], worldMarker=False)
>>> mesh = mt.createMesh(world, quality=32, area=0.2, smooth=[1, 10])
>>> _ = pg.viewer.showMesh(mesh, markers=True)
Returns
-------
ax : matplotlib.axes
colobar : matplotlib.colorbar
"""
pg.renameKwarg('cmap', 'cMap', kwargs)
if ax is None:
ax = plt.subplots()[1]
# print('1*'*50)
# print(locale.localeconv())
# plt.subplots() resets locale setting to system default .. this went
# horrible wrong for german 'decimal_point': ','
pg.checkAndFixLocaleDecimal_point(verbose=False)
# print('2*'*50)
# print(locale.localeconv())
if block:
hold = True
if hold:
lastHoldStatus = pg.mplviewer.utils.holdAxes__
pg.mplviewer.hold(val=1)
gci = None
validData = False
if markers:
kwargs["boundaryMarker"] = True
if mesh.cellCount() > 0:
uniquemarkers, uniqueidx = np.unique(np.array(mesh.cellMarkers()),
return_inverse=True)
label = "Cell markers"
kwargs["cMap"] = plt.cm.get_cmap("Set3", len(uniquemarkers))
kwargs["logScale"] = False
kwargs["cMin"] = -0.5
kwargs["cMax"] = len(uniquemarkers) - 0.5
data = np.arange(len(uniquemarkers))[uniqueidx]
if data is None:
showMesh = True
if showBoundary is None:
showBoundary = True
elif isinstance(data, pg.stdVectorRVector3):
drawSensors(ax, data, **kwargs)
elif isinstance(data, pg.R3Vector):
drawStreams(ax, mesh, data, **kwargs)
else:
#print('-----------------------------')
#print(data, type(data))
#print('-----------------------------')
### data=[[marker, val], ....]
if isinstance(data, list) and \
isinstance(data[0], list) and instance(data[0][0], int):
data = pg.solver.parseMapToCellArray(data, mesh)
if hasattr(data[0], '__len__') and not \
isinstance(data, np.ma.core.MaskedArray):
if len(data) == 2: # [u,v] x N
data = np.array(data).T
if data.shape[1] == 2:
drawStreams(ax, mesh, data, **kwargs)
elif data.shape[1] == 3: # probably N x [u,v,w]
# if sum(data[:, 0]) != sum(data[:, 1]):
# drawStreams(ax, mesh, data, **kwargs)
drawStreams(ax, mesh, data[:, 0:2], **kwargs)
else:
pg.warn("No valid stream data:", data.shape, data.ndim)
showMesh = True
elif min(data) == max(data): # or pg.haveInfNaN(data):
pg.warn("No valid data: ", min(data), max(data),
pg.haveInfNaN(data))
showMesh = True
else:
validData = True
try:
if len(data) == mesh.cellCount():
gci = drawModel(ax, mesh, data, **kwargs)
if showBoundary is None:
showBoundary = True
elif len(data) == mesh.nodeCount():
gci = drawField(ax, mesh, data, **kwargs)
cMap = kwargs.pop('cMap', None)
if cMap is not None:
gci.set_cmap(cmapFromName(cMap))
except BaseException as e:
print("Exception occured: ", e)
print("Data: ", min(data), max(data), pg.haveInfNaN(data))
print("Mesh: ", mesh)
drawMesh(ax, mesh, **kwargs)
if mesh.cellCount() == 0:
showMesh = False
if mesh.boundaryCount() == 0:
pg.mplviewer.drawPLC(ax,
mesh,
showNodes=True,
fillRegion=False,
showBoundary=False,
**kwargs)
showBoundary = False
#ax.plot(pg.x(mesh), pg.y(mesh), '.', color='black')
else:
pg.mplviewer.drawPLC(ax, mesh, **kwargs)
if showMesh:
if gci is not None and hasattr(gci, 'set_antialiased'):
gci.set_antialiased(True)
gci.set_linewidth(0.3)
gci.set_edgecolor("0.1")
else:
pg.mplviewer.drawSelectedMeshBoundaries(ax,
mesh.boundaries(),
color="0.1",
linewidth=0.3)
#drawMesh(ax, mesh, **kwargs)
if showBoundary is True or showBoundary is 1:
b = mesh.boundaries(mesh.boundaryMarkers() != 0)
pg.mplviewer.drawSelectedMeshBoundaries(ax,
b,
color=(0.0, 0.0, 0.0, 1.0),
linewidth=1.4)
if kwargs.pop('fitView', True):
ax.set_xlim(mesh.xmin(), mesh.xmax())
ax.set_ylim(mesh.ymin(), mesh.ymax())
ax.set_aspect('equal')
cbar = None
if label is not None and colorBar is None:
colorBar = True
if colorBar and validData:
# , **kwargs) # causes problems!
labels = ['cMin', 'cMax', 'nLevs', 'cMap', 'logScale']
subkwargs = {key: kwargs[key] for key in labels if key in kwargs}
subkwargs['label'] = label
if colorBar is True or colorBar is 1:
cbar = createColorBar(gci,
orientation=kwargs.pop(
'orientation', 'horizontal'),
size=kwargs.pop('size', 0.2),
pad=kwargs.pop('pad', None))
updateColorBar(cbar, **subkwargs)
elif colorBar is not False:
cbar = updateColorBar(colorBar, **subkwargs)
if markers:
ticks = np.arange(len(uniquemarkers))
#print('show.ticks ********************', ticks)
cbar.set_ticks(ticks)
labels = []
for marker in uniquemarkers:
labels.append(str((marker)))
#print('show.labels ********************', labels)
cbar.set_ticklabels(labels)
if coverage is not None:
if len(data) == mesh.cellCount():
addCoverageAlpha(gci, coverage)
else:
raise BaseException('toImplement')
# addCoverageAlpha(gci, pg.cellDataToPointData(mesh, coverage))
if showMesh:
drawMesh(ax, mesh, **kwargs)
if showBoundary is True or showBoundary is 1:
b = mesh.boundaries(pg.find(mesh.boundaryMarkers() != 0))
pg.mplviewer.drawSelectedMeshBoundaries(ax,
b,
color=(0.0, 0.0, 0.0, 1.0),
linewidth=1.4)
if not hold or block is not False and plt.get_backend() is not "Agg":
if data is not None:
if len(data) == mesh.cellCount():
cb = CellBrowser(mesh, data, ax=ax)
plt.show(block=block)
try:
plt.pause(0.01)
except BaseException as _:
pass
if hold:
pg.mplviewer.hold(val=lastHoldStatus)
if savefig:
print('saving: ' + savefig + ' ...')
if '.' not in savefig:
savefig += '.pdf'
ax.figure.savefig(savefig, bbox_inches='tight')
# rc params savefig.format=pdf
if '.eps' in savefig:
try:
print("trying eps2pdf ... ")
os.system('epstopdf ' + savefig)
except BaseException as _:
pass
print('..done')
return ax, cbar
def test_IndexAccess(self):
# (double) array/vector
an = np.arange(10.)
ag = pg.RVector(an)
# bn = nd.array(bool)
bn = (an > 4.)
self.assertEqual(type(bn), np.ndarray)
self.assertEqual(bn.dtype, 'bool')
self.assertEqual(sum(bn), 5)
# bg = BVector
bg = (ag > 4.)
self.assertEqual(type(bg), pg.BVector)
self.assertEqual(sum(bg), 5)
# BVector(nd.array(bool))
self.assertEqual(len(bg), len(pg.BVector(bn)))
self.assertEqual(sum(bg), sum(pg.BVector(bn)))
self.assertEqual(bg[0], pg.BVector(bn)[0])
np.testing.assert_array_equal(bg, pg.BVector(bn))
# In = nd.array(int)
In = np.nonzero(bn)[0]
self.assertEqual(type(In), np.ndarray)
self.assertEqual(In.dtype, 'int')
self.assertEqual(len(In), 5)
self.assertEqual(In[0], 5)
# np.nonzero(bg)
np.testing.assert_array_equal(In, np.nonzero(bg)[0])
# Ig = IndexArray
Ig = pg.find(bg)
self.assertEqual(type(Ig), pg.IndexArray)
self.assertEqual(len(Ig), 5)
self.assertEqual(Ig[0], 5)
# pg.find(nd.array(bool))
np.testing.assert_array_equal(Ig, pg.find(bn))
## Indexoperators ##
# ndarray [nd.array(bool)] == ndarray [nd.array(int)]
np.testing.assert_equal(an[bn], an[In])
self.assertEqual(len(an[bn]), 5)
self.assertEqual(an[bn][0], 5)
# ndarray[IndexArray] == ndarray [nd.array(int)]
np.testing.assert_equal(an[Ig], an[In])
# ndarray[BVector] == ndarray [nd.array(bool)]
np.testing.assert_array_equal(an[np.array(bg, dtype='bool')], an[bn])
np.testing.assert_array_equal(an[np.array(bg)], an[bn])
np.testing.assert_array_equal(an[bg.array()], an[bn])
## this fails because it is interpreted as an[[0,0,0,1,1,1]] ..
#np.testing.assert_equal(an[bg], an[bn])
# RVector [BVector] == RVector [IndexArray]
np.testing.assert_array_equal(ag[bg], ag[Ig])
self.assertEqual(len(ag[bg]), 5)
self.assertEqual(ag[bg][0], 5)
# RVector [BVector] == RVector [nd.array(bool)]
np.testing.assert_array_equal(ag[bg], ag[bn])
np.testing.assert_equal(sum(ag[bg]), sum(ag[bn]))
# RVector [IndexArray] == RVector [nd.array(int)]
np.testing.assert_array_equal(ag[Ig], ag[In])
def rmsWithErr(a, b, err, errtol=1):
"""Compute (abs-)root mean square of values with error above a threshold"""
fi = pg.find(err < errtol)
return rms(a[fi] - b[fi])
def drawShapes( ax, mesh, u ):
#ax.set_aspect( 'equal' )
N = 11
mesh3 = g.createMesh3D( g.asvector( np.linspace( 0, 1, N ) ),
g.asvector( np.linspace( 0, 1, N ) ),
g.asvector( np.linspace( 0, 1, N ) ) )
uc = g.RVector( mesh3.nodeCount( ) )
grads = g.stdVectorRVector3( )
pnts = g.stdVectorRVector3( )
c = mesh.cell( 0 )
imax=g.find( u == max( u ) )[0]
N = c.createShapeFunctions()[ imax ]
print imax, N
# print imax, c.shape().createShapeFunctions()[imax]
for i in range( c.nodeCount() ):
print c.rst( i ), N( c.rst( i ) )
# draw nodes
for i in range( c.nodeCount() ):
col = 'black'
if i == imax:
col = 'red'
#ax.plot( [c.node( i ).pos()[0], c.node( i ).pos()[0] ],
#[c.node( i ).pos()[1], c.node( i ).pos()[1] ],
#[c.node( i ).pos()[2], c.node( i ).pos()[2] ],
#'.', markersize = 15, linewidth=0, color=col )
newNode = []
for i in range( mesh3.nodeCount( ) ):
p = c.shape().xyz( mesh3.node( i ).pos() )
newNode.append( p )
#ax.plot( p[0], p[1], '.', zorder=10, color='black', markersize = 1 )
if not c.shape().isInside( p ):
uc[ i ] = -99.0
grads.append( g.RVector3( 0.0, 0.0 ) )
continue
uc[ i ] = c.pot( p, u )
gr = c.grad( p, u ).normalise()
grads.append( gr )
#ax.plot( [ p[ 0 ], p[ 0 ] + gr[ 0 ]*0.1 ],
#[ p[ 1 ], p[ 1 ] + gr[ 1 ]*0.1 ],
#[ p[ 2 ], p[ 2 ] + gr[ 2 ]*0.1 ], '-', color='black' )
#pnts.append( p )
#print len(pnts)
#Z = np.ma.masked_where( uc == -99., uc )
##ax.plot( g.x(pnts), g.y(pnts), g.z(pnts), '.' )
for i, n in enumerate( mesh3.nodes() ):
n.setPos( newNode[ i ] )
mesh3.addExportData( 'u', uc.setVal( 0.0, g.find( uc == -99 ) ) )
name = 'cell' + str( c.nodeCount() ) + '-' + str( imax )
print "write ", name
mesh3.exportVTK( name, grads )