pygimli.utils

Useful utility functions.

Overview

Functions

GKtoUTM(ea[, no, zone, gk, gkzone])	Transform any Gauss-Krueger to UTM autodetect GK zone from offset.
KramersKronig(f, re, im[, usezero])	Return real/imaginary parts retrieved by Kramers-Kronig relations.
boxprint(s[, width, sym])	Print string centered in a box.
cMap(name)	Return default colormap for physical quantity name.
cache(funct)	Cache decorator.
chi2(a, b, err[, trans])	Return chi square value.
cmap(name)	Return default colormap for physical quantity name.
computeInverseRootMatrix(CM[, thrsh, verbose])	Compute inverse square root (C^{-0.5} of matrix.
convertCRSIndex2Map(rowIdx, colPtr)	Converts CRS indices to uncompressed indices (row, col).
covarianceMatrix(mesh[, nodes])	Geostatistical covariance matrix (cell or node) for given mesh.
createDateTimeString([now])	Return datetime as string (e.g.
createFolders(*args, **kwargs)
createResultFolder(*args, **kwargs)
createResultPath(subfolder[, now])	Create a result Folder.
createfolders(*args, **kwargs)
cumDist(p)	The progressive, i.e., cumulative length for a path p.
cut(v[, n])	Cuts the array v into n parts
diff(v)	Calculate approximate derivative.
dist(p[, c])	Calculate the distance for each position in p relative to pos c(x,y,z).
filterIndex(seq, idx)	TODO DOCUMENTME.
filterLinesByCommentStr(lines[, comment_str])	Filter all lines from a file.readlines output which begins with one of the symbols in the comment_str.
findNearest(x, y, xp, yp[, radius])	TODO DOCUMENTME.
findUTMZone(lon, lat)	Find utm zone for lon and lat values.
generateGeostatisticalModel(mesh, **kwargs)	Generate geostatistical model (cell or node) for given mesh.
getIndex(seq, f)	TODO DOCUMENTME.
getProjection(name[, ref])	Syntactic sugar to get some default Projections.
getSavePath([folder, subfolder, now])	TODO.
getUTMProjection(zone[, ellps])	Create and return the current coordinate projection.
gmat2numpy(mat)	Convert pygimli matrix into numpy.array.
grange(start, end[, dx, n, log])	Create array with possible increasing spacing.
hankelFC(order)	Filter coefficients for Hankel transformation.
interpExtrap(x, xp, yp)	numpy.interp interpolation function extended by linear extrapolation.
interperc(a[, trimval, islog, bins])	Return symmetric interpercentiles for alpha-trim outliers, e.g.
inthist(a, vals[, bins, islog])	Return point of integral (cumulative) histogram, e.g.
isComplex(vals)	Check numpy or pg.Vector if have complex data type
iterateBounds(inv[, dchi2, maxiter, change])	Find parameter bounds by iterating model parameter.
logDropTol(p[, dropTol])	Create logarithmic scaled copy of p.
modCovar(inv)	Formal model covariance matrix (MCM) from inversion.
nanrms(v[, axis])	Compute the root mean square excluding nan values.
niceLogspace(vMin, vMax[, nDec])	Create nice logarithmic space from the next decade lower to vMin to decade larger then vMax.
num2str(a[, fmtstr])	List of strings (deprecated, for backward-compatibility).
numpy2gmat(nmat)	Convert numpy.array into pygimli RMatrix.
prettify(value[, roundValue])	Return prettified string for value ..
prettyFloat(value[, roundValue])	Return prettified string for a float value.
rand(n[, minVal, maxVal, seed])	Create RVector of length n with normally distributed random numbers.
randN(n[, minVal, maxVal])	Create RVector of length n with normally distributed random numbers.
randn(n[, seed])	Create n normally distributed random numbers with optional seed.
readGPX(fileName)	Extract GPS Waypoint from GPS Exchange Format (GPX).
rms(v[, axis])	Compute the root mean square.
rmsWithErr(a, b, err[, errtol])	Compute (abs-)root mean square of values with error above a threshold
rmswitherr(a, b, err[, errtol])	Compute (abs-)root mean square of values with error above a threshold
rndig(a[, ndig])	Round float using a number of counting digits.
rrms(a, b[, axis])	Compute the relative (regarding a) root mean square.
saveResult(fname, data[, rrms, chi2, mode])	Save rms/chi2 results into filename.
sparseMatrix2Array(matrix[, indices, getInCRS])	Extract indices and value from sparse matrix (SparseMap or CRS)
sparseMatrix2coo(A[, rowOffset, colOffset])	Convert SparseMatrix to scipy.coo_matrix.
sparseMatrix2csr(A)	Convert SparseMatrix to scipy.csr_matrix.
squeezeComplex(z[, polar, conj])	Squeeze complex valued array into [real, imag] or [amp, phase(rad)]
strHash(string)
streamline(mesh, field, startCoord, dLengthSteps)	Create a streamline from startCoord and following a vector field in up and down direction.
streamlineDir(mesh, field, startCoord, …)	down = -1, up = 1, both = 0
toComplex(amp[, phi])	Convert real values into complex (z = a + ib) valued array.
toPolar(z)	Convert complex (z = a + ib) values array into amplitude and phase in radiant
toRealMatrix(C[, conj])	Convert complex valued matrix into a real valued Blockmatrix
trimDocString(docstring)	Return properly formatted docstring.
unicodeToAscii(text)	TODO DOCUMENTME.
unique(a)	Return list of unique elements ever seen with preserving order.
uniqueAndSum(indices, to_sum[, …])	Sum double values found by indices in a various number of arrays.
unique_everseen(iterable[, key])	Return iterator of unique elements ever seen with preserving order.
unique_rows(array)	Return unique rows in a 2D array.
unit(name[, unit])	Return the name of a physical quantity with its unit.

Classes

ProgressBar(its[, width, sign])

Animated text-based progressbar.

Functions

GKtoUTM

pygimli.utils.GKtoUTM(ea, no=None, zone=32, gk=None, gkzone=None)

Transform any Gauss-Krueger to UTM autodetect GK zone from offset.

KramersKronig

pygimli.utils.KramersKronig(f, re, im, usezero=False)

Return real/imaginary parts retrieved by Kramers-Kronig relations.

formulas including singularity removal according to Boukamp (1993)

boxprint

pygimli.utils.boxprint(s, width=80, sym='#')

Print string centered in a box.

Examples

>>> from pygimli.utils import boxprint
>>> boxprint("This is centered in a box.", width=40, sym='+')
++++++++++++++++++++++++++++++++++++++++
+      This is centered in a box.      +
++++++++++++++++++++++++++++++++++++++++

cMap

pygimli.utils.cMap(name)

Return default colormap for physical quantity name.

cache

pygimli.utils.cache(funct)

Cache decorator.

chi2

pygimli.utils.chi2(a, b, err, trans=None)

Return chi square value.

cmap

pygimli.utils.cmap(name)

Return default colormap for physical quantity name.

computeInverseRootMatrix

pygimli.utils.computeInverseRootMatrix(CM, thrsh=0.001, verbose=False)

Compute inverse square root (C^{-0.5} of matrix.

convertCRSIndex2Map

pygimli.utils.convertCRSIndex2Map(rowIdx, colPtr)

Converts CRS indices to uncompressed indices (row, col).

covarianceMatrix

pygimli.utils.covarianceMatrix(mesh, nodes=False, **kwargs)

Geostatistical covariance matrix (cell or node) for given mesh.

Parameters

• mesh (gimliapi:GIMLI::Mesh) – Mesh

• nodes (bool [False]) – use node positions, otherwise (default) cell centers are used

• **kwargs –

  Ifloat or list of floats

  correlation lengths (range) in individual directions

  dipfloat

  dip angle (in degree) of major axis (I[0])

  strikefloat

  strike angle (for 3D)

Returns

Cm – covariance matrix

Return type

np.array (square matrix of size cellCount/nodeCount)

createDateTimeString

pygimli.utils.createDateTimeString(now=None)

Return datetime as string (e.g. for saving results).

createFolders

pygimli.utils.createFolders(*args, **kwargs)

createResultFolder

pygimli.utils.createResultFolder(*args, **kwargs)

createResultPath

pygimli.utils.createResultPath(subfolder, now=None)

Create a result Folder.

createfolders

pygimli.utils.createfolders(*args, **kwargs)

cumDist

pygimli.utils.cumDist(p)

The progressive, i.e., cumulative length for a path p.

d = [0.0, d[0]+ | p[1]-p[0] |, d[1] + | p[2]-p[1] | + …]

Parameters

p (ndarray(N,2) | ndarray(N,3) | pg.core.R3Vector) – Position array

Returns

d – Distance array

Return type

ndarray(N)

Examples

>>> import pygimli as pg
>>> from pygimli.utils import cumDist
>>> import numpy as np
>>> p = pg.core.R3Vector(4)
>>> p[0] = [0.0, 0.0]
>>> p[1] = [0.0, 1.0]
>>> p[2] = [0.0, 1.0]
>>> p[3] = [0.0, 0.0]
>>> print(cumDist(p))
[0. 1. 1. 2.]

cut

pygimli.utils.cut(v, n=2)

Cuts the array v into n parts

diff

pygimli.utils.diff(v)

Calculate approximate derivative.

Calculate approximate derivative from v as d = [v_1-v_0, v2-v_1, …]

Parameters

v (array(N) | pg.core.R3Vector(N)) – Array of double values or positions

Returns

d – derivative array

Return type

[type(v)](N-1) |

Examples

>>> import pygimli as pg
>>> from pygimli.utils import diff
>>> p = pg.core.R3Vector(4)
>>> p[0] = [0.0, 0.0]
>>> p[1] = [0.0, 1.0]
>>> print(diff(p)[0])
RVector3: (0.0, 1.0, 0.0)
>>> print(diff(p)[1])
RVector3: (0.0, -1.0, 0.0)
>>> print(diff(p)[2])
RVector3: (0.0, 0.0, 0.0)
>>> p = pg.Vector(3)
>>> p[0] = 0.0
>>> p[1] = 1.0
>>> p[2] = 2.0
>>> print(diff(p))
2 [1.0, 1.0]

dist

pygimli.utils.dist(p, c=None)

Calculate the distance for each position in p relative to pos c(x,y,z).

Parameters

• p (ndarray(N,2) | ndarray(N,3) | pg.core.R3Vector) – Position array

• c ([x,y,z] [None]) – relative origin. default = [0, 0, 0]

Returns

d – Distance array

Return type

ndarray(N)

Examples

>>> import pygimli as pg
>>> from pygimli.utils import dist
>>> import numpy as np
>>> p = pg.core.R3Vector(4)
>>> p[0] = [0.0, 0.0]
>>> p[1] = [0.0, 1.0]
>>> print(dist(p))
[0. 1. 0. 0.]
>>> x = pg.Vector(4, 0)
>>> y = pg.Vector(4, 1)
>>> print(dist(np.array([x, y]).T))
[1. 1. 1. 1.]

filterIndex

pygimli.utils.filterIndex(seq, idx)

TODO DOCUMENTME.

filterLinesByCommentStr

pygimli.utils.filterLinesByCommentStr(lines, comment_str='#')

Filter all lines from a file.readlines output which begins with one of the symbols in the comment_str.

findNearest

pygimli.utils.findNearest(x, y, xp, yp, radius=- 1)

TODO DOCUMENTME.

findUTMZone

pygimli.utils.findUTMZone(lon, lat)

Find utm zone for lon and lat values.

lon -180 – -174 -> 1 … 174 – 180 -> 60 lat < 0 hemisphere = S, > 0 hemisphere = N

Parameters

• lon (float) –

• lat (float) –

Returns

zone + hemisphere

Return type

str

generateGeostatisticalModel

pygimli.utils.generateGeostatisticalModel(mesh, **kwargs)

Generate geostatistical model (cell or node) for given mesh.

Parameters

• mesh (gimliapi:GIMLI::Mesh) – Mesh

• nodes (bool [False]) – use node positions, otherwise (default) cell centers are used

• **kwargs –

  Ifloat or list of floats

  correlation lengths (range) in individual directions

  dipfloat

  dip angle of major axis (I[0])

  strikefloat

  strike angle (for 3D)

Returns

res

Return type

np.array of size cellCount or nodeCount (nodes=True)

Examples using pygimli.utils.generateGeostatisticalModel

Geostatistical regularization

getIndex

pygimli.utils.getIndex(seq, f)

TODO DOCUMENTME.

getProjection

pygimli.utils.getProjection(name, ref=None, **kwargs)

Syntactic sugar to get some default Projections.

getSavePath

pygimli.utils.getSavePath(folder=None, subfolder='', now=None)

TODO.

getUTMProjection

pygimli.utils.getUTMProjection(zone, ellps='WGS84')

Create and return the current coordinate projection.

This is a proxy for pyproj.

Parameters

• utmZone (str) – Zone for for UTM

• ellipsoid (str) – ellipsoid based on [‘wgs84’]

Returns

Return type

Pyproj Projection

gmat2numpy

pygimli.utils.gmat2numpy(mat)

Convert pygimli matrix into numpy.array.

TODO implement correct rval

grange

pygimli.utils.grange(start, end, dx=0, n=0, log=False)

Create array with possible increasing spacing.

Create either array from start step-wise filled with dx until end reached [start, end] (like np.array with defined end). Fill the array from start to end with n steps. [start, end] (like np.linespace) Fill the array from start to end with n steps but logarithmic increasing, dx will be ignored.

Parameters

• start (float) – First value of the resulting array

• end (float) – Last value of the resulting array

• dx (float) – Linear step length, n will be ignored

• n (int) – Amount of steps

• log (bool) – Logarithmic increasing range of length = n from start to end. dx will be ignored.

Examples

>>> from pygimli.utils import grange
>>> v1 = grange(start=0, end=10, dx=3)
>>> v2 = grange(start=0, end=10, n=3)
>>> print(v1)
4 [0.0, 3.0, 6.0, 9.0]
>>> print(v2)
3 [0.0, 5.0, 10.0]

Returns

ret – Return resulting array

Return type

GIMLI::RVector

Examples using pygimli.utils.grange

2D ERT modeling and inversion

2D FEM modelling on two-layer example

Hydrogeophysical modeling

hankelFC

pygimli.utils.hankelFC(order)

Filter coefficients for Hankel transformation.

10 data points per decade.

DOCUMENTME .. Author RUB?

Parameters

order (int) – order=1: NY=+0.5 (SIN) order=2: NY=-0.5 (COS) order=3: NY=0.0 (J0) order=4: NY=1.0 (J1)

Returns

• fc (np.array()) – Filter coefficients

• nc0 (int) – fc[nc0] refers to zero argument

interpExtrap

pygimli.utils.interpExtrap(x, xp, yp)

numpy.interp interpolation function extended by linear extrapolation.

interperc

pygimli.utils.interperc(a, trimval=3.0, islog=False, bins=None)

Return symmetric interpercentiles for alpha-trim outliers, e.g. interperc(a, 3) returns range of inner 94% (useful for colorscales).

inthist

pygimli.utils.inthist(a, vals, bins=None, islog=False)

Return point of integral (cumulative) histogram, e.g. inthist(a, [25, 50, 75]) provides quartiles and median of an array

isComplex

pygimli.utils.isComplex(vals)

Check numpy or pg.Vector if have complex data type

iterateBounds

pygimli.utils.iterateBounds(inv, dchi2=0.5, maxiter=100, change=1.02)

Find parameter bounds by iterating model parameter.

Find parameter bounds by iterating model parameter until error bound is reached

Parameters

• inv – gimli inversion object

• dchi2 – allowed variation of chi^2 values [0.5]

• maxiter – maximum iteration number for parameter iteration [100]

• change – changing factor of parameters [1.02, i.e. 2%]

logDropTol

pygimli.utils.logDropTol(p, dropTol=0.001)

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.]

Examples using pygimli.utils.logDropTol

Four-point sensitivities

modCovar

pygimli.utils.modCovar(inv)

Formal model covariance matrix (MCM) from inversion.

var, MCMs = modCovar(inv)

Parameters

inv (pygimli inversion object) –

Returns

• var (variances (inverse square roots of MCM matrix))

• MCMs (scaled MCM (such that diagonals are 1.0))

>>> # import pygimli as pg
>>> # import matplotlib.pyplot as plt
>>> # from matplotlib.cm import bwr
>>> # INV = pg.Inversion(data, f)
>>> # par = INV.run()
>>> # var, MCM = modCovar(INV)
>>> # i = plt.imshow(MCM, interpolation='nearest',
>>> #                 cmap=bwr, vmin=-1, vmax=1)
>>> # plt.colorbar(i)

nanrms

pygimli.utils.nanrms(v, axis=None)

Compute the root mean square excluding nan values.

niceLogspace

pygimli.utils.niceLogspace(vMin, vMax, nDec=10)

Create nice logarithmic space from the next decade lower to vMin to decade larger then vMax.

Parameters

• vMin (float) – lower limit need to be > 0

• vMax (float) – upper limit need to be >= vMin

• nDec (int) – Amount of logarithmic equidistant steps for one decade

Examples

>>> from pygimli.utils import niceLogspace
>>> v1 = niceLogspace(vMin=0.1, vMax=0.1, nDec=1)
>>> print(v1)
[0.1 1. ]
>>> v1 = niceLogspace(vMin=0.09, vMax=0.11, nDec=1)
>>> print(v1)
[0.01 0.1  1.  ]
>>> v1 = niceLogspace(vMin=0.09, vMax=0.11, nDec=10)
>>> print(len(v1))
21
>>> print(v1)
[0.01       0.01258925 0.01584893 0.01995262 0.02511886 0.03162278
 0.03981072 0.05011872 0.06309573 0.07943282 0.1        0.12589254
 0.15848932 0.19952623 0.25118864 0.31622777 0.39810717 0.50118723
 0.63095734 0.79432823 1.        ]

num2str

pygimli.utils.num2str(a, fmtstr='%g')

List of strings (deprecated, for backward-compatibility).

numpy2gmat

pygimli.utils.numpy2gmat(nmat)

Convert numpy.array into pygimli RMatrix.

TODO implement correct rval

prettify

pygimli.utils.prettify(value, roundValue=False)

Return prettified string for value .. if possible.

prettyFloat

pygimli.utils.prettyFloat(value, roundValue=False)

Return prettified string for a float value.

rand

pygimli.utils.rand(n, minVal=0.0, maxVal=1.0, seed=None)

Create RVector of length n with normally distributed random numbers.

randN

pygimli.utils.randN(n, minVal=0.0, maxVal=1.0)

Create RVector of length n with normally distributed random numbers.

randn

pygimli.utils.randn(n, seed=None)

Create n normally distributed random numbers with optional seed.

Parameters

• n (long) – length of random numbers array.

• seed (int[None]) – Optional seed for random number generator

Returns

r – Random numbers.

Return type

np.array

Examples

>>> import numpy as np
>>> from pygimli.utils import randn
>>> a = randn(5, seed=1337)
>>> b = randn(5)
>>> c = randn(5, seed=1337)
>>> print(np.array_equal(a, b))
False
>>> print(np.array_equal(a, c))
True

readGPX

pygimli.utils.readGPX(fileName)

Extract GPS Waypoint from GPS Exchange Format (GPX).

Currently only simple waypoint extraction is supported.

<gpx version=”1.0” creator=”creator”>

<metadata> <name>Name</name> </metadata> <wpt lat=”51.” lon=”11.”> <name>optional</name> <time>optional</time> <description>optional</description> </wpt>

</gpx>

rms

pygimli.utils.rms(v, axis=None)

Compute the root mean square.

rmsWithErr

pygimli.utils.rmsWithErr(a, b, err, errtol=1)

Compute (abs-)root mean square of values with error above a threshold

rmswitherr

pygimli.utils.rmswitherr(a, b, err, errtol=1)

Compute (abs-)root mean square of values with error above a threshold

rndig

pygimli.utils.rndig(a, ndig=3)

Round float using a number of counting digits.

rrms

pygimli.utils.rrms(a, b, axis=None)

Compute the relative (regarding a) root mean square.

saveResult

pygimli.utils.saveResult(fname, data, rrms=None, chi2=None, mode='w')

Save rms/chi2 results into filename.

sparseMatrix2Array

pygimli.utils.sparseMatrix2Array(matrix, indices=True, getInCRS=True)

Extract indices and value from sparse matrix (SparseMap or CRS)

Get python Arrays from SparseMatrix or SparseMapMatrix in either CRS convention (row index, column Start_End, values) or row index, column index, values.

Parameters

• matrix (pg.matrix.SparseMapMatrix or pg.matrix.SparseMatrix) – Input matrix to be transformed to numpy arrays.

• indices (boolean (True)) – Decides weather the indices of the matrix will be returned or not.

• getInCSR (boolean (True)) – If returned, the indices can have the format of a compressed row storage (CSR), the default or uncompressed lists with column and row indices.

Returns

• vals (numpy.ndarray) – Entries of the matrix.

• indices (list, list) – Optional. Returns additional array with the indices for reconstructing the matrix in the defined format.

sparseMatrix2coo

pygimli.utils.sparseMatrix2coo(A, rowOffset=0, colOffset=0)

Convert SparseMatrix to scipy.coo_matrix.

Parameters

A (pg.matrix.SparseMapMatrix | pg.matrix.SparseMatrix) – Matrix to convert from.

Returns

mat – Matrix to convert into.

Return type

scipy.coo_matrix

Examples using pygimli.utils.sparseMatrix2coo

Naive complex-valued electrical inversion

sparseMatrix2csr

pygimli.utils.sparseMatrix2csr(A)

Convert SparseMatrix to scipy.csr_matrix.

Compressed Sparse Row matrix, i.e., Compressed Row Storage (CRS)

Parameters

A (pg.matrix.SparseMapMatrix | pg.matrix.SparseMatrix) – Matrix to convert from.

Returns

mat – Matrix to convert into.

Return type

scipy.csr_matrix

squeezeComplex

pygimli.utils.squeezeComplex(z, polar=False, conj=False)

Squeeze complex valued array into [real, imag] or [amp, phase(rad)]

Examples using pygimli.utils.squeezeComplex

Naive complex-valued electrical inversion

strHash

pygimli.utils.strHash(string)

streamline

pygimli.utils.streamline(mesh, field, startCoord, dLengthSteps, dataMesh=None, maxSteps=1000, verbose=False, coords=0, 1)

Create a streamline from startCoord and following a vector field in up and down direction.

streamlineDir

pygimli.utils.streamlineDir(mesh, field, startCoord, dLengthSteps, dataMesh=None, maxSteps=1000, down=True, verbose=False, coords=0, 1)

down = -1, up = 1, both = 0

toComplex

pygimli.utils.toComplex(amp, phi=None)

Convert real values into complex (z = a + ib) valued array.

If no phases phi are given, assuming z = amp[0:N] + i amp[N:2N].

If phi is given in (rad) complex values are generated: z = amp*(cos(phi) + i sin(phi))

Parameters

• amp (iterable (float)) – Amplitudes or real unsqueezed real valued array.

• phi (iterable (float)) – Phases in neg radiant

Returns

z – Complex values

Return type

ndarray(dtype=np.complex)

Examples using pygimli.utils.toComplex

Complex-valued electrical modeling

Naive complex-valued electrical inversion

toPolar

pygimli.utils.toPolar(z)

Convert complex (z = a + ib) values array into amplitude and phase in radiant

If z is real valued we assume its squeezed.

Parameters

z (iterable (floats, complex)) – If z contains of floats and squeezedComplex is assumed [real, imag]

Returns

amp, phi – Amplitude amp and phase angle phi in radiant.

Return type

ndarray

toRealMatrix

pygimli.utils.toRealMatrix(C, conj=False)

Convert complex valued matrix into a real valued Blockmatrix

Parameters

• C (CMatrix) – Complex valued matrix

• conj (bool [False]) – Fill the matrix as complex conjugated matrix

Returns

R

Return type

pg.matrix.BlockMatrix()

trimDocString

pygimli.utils.trimDocString(docstring)

Return properly formatted docstring.

From: https://www.python.org/dev/peps/pep-0257/

Examples

>>> from pygimli.utils import trimDocString
>>> docstring = '    This is a string with indention and whitespace.   '
>>> trimDocString(docstring).replace('with', 'without')
'This is a string without indention and whitespace.'

unicodeToAscii

pygimli.utils.unicodeToAscii(text)

TODO DOCUMENTME.

unique

pygimli.utils.unique(a)

Return list of unique elements ever seen with preserving order.

Examples

>>> from pygimli.utils import unique
>>> unique((1,1,2,2,3,1))
[1, 2, 3]

See also

unique_everseen(), unique_rows()

uniqueAndSum

pygimli.utils.uniqueAndSum(indices, to_sum, return_index=False, verbose=False)

Sum double values found by indices in a various number of arrays.

Returns the sorted unique elements of a column_stacked array of indices. Another column_stacked array is returned with values at the unique indices, while values at double indices are properly summed.

Parameters

• ar (array_like) – Input array. This will be flattened if it is not already 1-D.

• to_sum (array_like) – Input array to be summed over axis 0. Other existing axes will be broadcasted remain untouched.

• return_index (bool, optional) – If True, also return the indices of ar (along the specified axis, if provided, or in the flattened array) that result in the unique array.

Returns

• unique (ndarray) – The sorted unique values.

• summed_array (ndarray) – The summed array, whereas all values for a specific index is the sum over all corresponding nonunique values.

• unique_indices (ndarray, optional) – The indices of the first occurrences of the unique values in the original array. Only provided if return_index is True.

Examples

>>> import numpy as np
>>> from pygimli.utils import uniqueAndSum
>>> idx1 = np.array([0, 0, 1, 1, 2, 2])
>>> idx2 = np.array([0, 0, 1, 2, 3, 3])
>>> # indices at positions 0 and 1 and at positions 5 and 6 are not unique
>>> to_sort = np.column_stack((idx1, idx2))
>>> # its possible to stack more than two array
>>> # you need for example 3 array to find unique node positions in a mesh
>>> values = np.arange(0.1, 0.7, 0.1)
>>> print(values)
[0.1 0.2 0.3 0.4 0.5 0.6]
>>> # some values to be summed together (for example attributes of nodes)
>>> unique_idx, summed_vals = uniqueAndSum(to_sort, values)
>>> print(unique_idx)
[[0 0]
 [1 1]
 [1 2]
 [2 3]]
>>> print(summed_vals)
[0.3 0.3 0.4 1.1]

unique_everseen

pygimli.utils.unique_everseen(iterable, key=None)

Return iterator of unique elements ever seen with preserving order.

Return iterator of unique elements ever seen with preserving order.

From: https://docs.python.org/3/library/itertools.html#itertools-recipes

Examples

>>> from pygimli.utils import unique_everseen
>>> s1 = 'AAAABBBCCDAABBB'
>>> s2 = 'ABBCcAD'
>>> list(unique_everseen(s1))
['A', 'B', 'C', 'D']
>>> list(unique_everseen(s2, key=str.lower))
['A', 'B', 'C', 'D']

See also

unique(), unique_rows()

unique_rows

pygimli.utils.unique_rows(array)

Return unique rows in a 2D array.

Examples

>>> from pygimli.utils import unique_rows
>>> import numpy as np
>>> A = np.array(([1,2,3],[3,2,1],[1,2,3]))
>>> unique_rows(A)
array([[1, 2, 3],
       [3, 2, 1]])

unit

pygimli.utils.unit(name, unit='auto')

Return the name of a physical quantity with its unit.

Classes

ProgressBar

class pygimli.utils.ProgressBar(its, width=80, sign=':')

Bases: object

Animated text-based progressbar.

Animated text-based progressbar for intensive loops. Should work in the console and in the IPython Notebook.

• optional: ‘estimated time’ instead of ‘x of y complete’

itsint

Number of iterations of the process.

widthint

Width of the ProgressBar, default is 80.

signstr

Sign used to fill the bar.

>>> from pygimli.utils import ProgressBar
>>> pBar = ProgressBar(its=20, width=40, sign='+')
>>> pBar.update(5)

[+++++++++++ 30% ] 6 of 20 complete

__init__(its, width=80, sign=':')

Constructor.

update(iteration, msg='')

Update ProgressBar by iteration number starting at 0 with optional message.