diff --git a/docs/source/algorithms/CrystalFieldEnergies-v1.rst b/docs/source/algorithms/CrystalFieldEnergies-v1.rst
index 90d81130f6004a9a81a518b2096b5c91d58fd2fd..9750f4703ab85d24dda130151ec53b26b2618177 100644
--- a/docs/source/algorithms/CrystalFieldEnergies-v1.rst
+++ b/docs/source/algorithms/CrystalFieldEnergies-v1.rst
@@ -21,30 +21,30 @@ The algorithm calculates the crystal field energies and wave functions. The exam
en, wf, ham = energies(1, B20=0.37737, B22=3.9770, B40=-0.031787, B42=-0.11611, B44=-0.12544)
# a list of crystal field energies
- print('energies:\n{}'.format(en))
+ print('energies:\n{}'.format(en[2:]))
# a complex-valued matrix with wave functions
print('wave functions:\n{}'.format(wf))
# a complex-valued matrix with the Hamiltonian
print('Hamiltonian:\n{}'.format(ham))
.. testoutput::
+ :options: +ELLIPSIS +NORMALIZE_WHITESPACE
energies:
- [ 0.00000000e+00 4.97379915e-14 2.93261118e+01 2.93261118e+01
- 4.43412485e+01 4.43412485e+01]
+ [ 29.32611185 29.32611185 44.3412485 44.3412485 ]
wave functions:
- [[ -6.93889390e-17+0.j -3.38877312e-01+0.j 6.80756336e-01+0.j
- -6.25169857e-01+0.j 1.74683643e-01+0.j -1.95256823e-02+0.j]
- [ 5.42213428e-01+0.j -7.97569062e-17+0.j -2.33045938e-01+0.j
- -2.53767032e-01+0.j 8.51307403e-02+0.j 7.61609638e-01+0.j]
- [ 5.55111512e-17+0.j 7.68873700e-01+0.j 1.21082286e-01+0.j
- -1.11195433e-01+0.j 6.14081735e-01+0.j -6.86404558e-02+0.j]
- [ -7.68873700e-01+0.j 6.77450070e-17+0.j 1.11195433e-01+0.j
- 1.21082286e-01+0.j 6.86404558e-02+0.j 6.14081735e-01+0.j]
- [ -5.55111512e-17+0.j -5.42213428e-01+0.j -2.53767032e-01+0.j
- 2.33045938e-01+0.j 7.61609638e-01+0.j -8.51307403e-02+0.j]
- [ 3.38877312e-01+0.j -2.36325596e-17+0.j 6.25169857e-01+0.j
- 6.80756336e-01+0.j 1.95256823e-02+0.j 1.74683643e-01+0.j]]
+ [[ ... ... ...
+ ... ... ...]
+ [ ... ... ...
+ ... ... ...]
+ [ ... ... ...
+ ... ... ...]
+ [ ... ... ...
+ ... ... ...]
+ [ ... ... ...
+ ... ... ...]
+ [ ... ... ...
+ ... ... ...]]
Hamiltonian:
[[ 1.86648000+0.j 0.00000000+0.j 9.27182972+0.j 0.00000000+0.j
-3.36590841+0.j 0.00000000+0.j]
diff --git a/docs/source/algorithms/MaxEnt-v1.rst b/docs/source/algorithms/MaxEnt-v1.rst
index ffcb57b43c6aa21135531d4c2f9a53b94c8e677a..f3d4a78544dfbcc309cd0793b14dd88362c0375c 100644
--- a/docs/source/algorithms/MaxEnt-v1.rst
+++ b/docs/source/algorithms/MaxEnt-v1.rst
@@ -174,13 +174,14 @@ and the reconstructed image, i.e. Fourier transform (right).
Output:
.. testoutput:: ExFourierCoeffs
+ :options: +ELLIPSIS +NORMALIZE_WHITESPACE
First reconstructed coefficient: 0.847
Second reconstructed coefficient: 0.846
Third reconstructed coefficient: 0.846
Fourth reconstructed coefficient: 0.896
Fifth reconstructed coefficient: 0.896
- Number of iterations: 3495
+ Number of iterations: ...
.. figure:: ../images/MaxEntFourierCoefficients.png
:align: center
@@ -223,13 +224,14 @@ and :ref:`algm-FFT` (right).
Output:
.. testoutput:: ExMUSR00022725
+ :options: +ELLIPSIS +NORMALIZE_WHITESPACE
Image at -1.359: 0.100
Image at 0.000: 0.009
Image at 1.359: 0.100
Negative background 0.006431
Positive background 0.006431
- Number of iterations: 22
+ Number of iterations: ...
.. figure:: ../images/MaxEntMUSR00022725.png
:align: center
@@ -258,6 +260,7 @@ and its imaginary part (right).
Output:
.. testoutput:: ExEMU00020884
+ :options: +ELLIPSIS +NORMALIZE_WHITESPACE
Image (real part) at -1.389: -0.063
Image (real part) at 0.000: 0.035
@@ -265,7 +268,7 @@ Output:
Image (imaginary part) at -1.389: -0.277
Image (imaginary part) at 0.000: 0.000
Image (imaginary part) at 1.389: 0.277
- Number of iterations: 33
+ Number of iterations: ...
.. figure:: ../images/MaxEntMUSR00020884.png
@@ -304,11 +307,12 @@ the original and reconstructed data (left), and the reconstructed image (right).
Output:
.. testoutput:: ExRealImage
+ :options: +ELLIPSIS +NORMALIZE_WHITESPACE
Image (real part) at 0.318: 0.000
Image (real part) at 0.477: 5.862
Image (real part) at 0.637: 0.000
- Number of iterations: 20000
+ Number of iterations: ...
.. figure:: ../images/MaxEntComplexData.png
:align: center
@@ -359,12 +363,13 @@ image in order to obtain smooth results).
Output:
.. testoutput:: ExRealPosImage
+ :options: +ELLIPSIS +NORMALIZE_WHITESPACE
Image at 0.318: 0.000 (PositiveImage=False), 0.000 (PositiveImage=True)
Image at 0.477: 5.862 (PositiveImage=False), 5.913 (PositiveImage=True)
Image at 0.637: 0.000 (PositiveImage=False), 0.000 (PositiveImage=True)
- Number of iterations: 20000
- Number of iterations: 11
+ Number of iterations: ...
+ Number of iterations: ...
.. figure:: ../images/MaxEntPositiveImage.png
:align: center
@@ -443,11 +448,12 @@ shows how to combine two workspaces with complex data.
Output:
.. testoutput:: ExComplexData
+ :options: +ELLIPSIS +NORMALIZE_WHITESPACE
- Number of iterations dataset1 separate: 11
- Number of iterations dataset2 separate: 7
- Number of iterations dataset1 combined: 11
- Number of iterations dataset2 combined: 7
+ Number of iterations dataset1 separate: ...
+ Number of iterations dataset2 separate: ...
+ Number of iterations dataset1 combined: ...
+ Number of iterations dataset2 combined: ...
Increasing the number of points in the image
@@ -479,11 +485,12 @@ from the default 1.0; the dataset contains 270 data points and here set to be sl
Output:
.. testoutput:: ExResolutionFactor
+ :options: +ELLIPSIS +NORMALIZE_WHITESPACE
Image at 0.000: 0.035 (ResolutionFactor=1)
Image at 0.000: 0.068 (ResolutionFactor=2)
- Number of iterations: 33
- Number of iterations: 20
+ Number of iterations: ...
+ Number of iterations: ...
.. figure:: ../images/MaxEntResolutionFactor.png
:align: center
@@ -510,11 +517,12 @@ a zoom into the region :math:`0.82 < x < 1.44` and :math:`-0.187 < y < 0.004`.
Output:
.. testoutput:: ExResolutionFactor2
+ :options: +ELLIPSIS +NORMALIZE_WHITESPACE
- Number of iterations: 41
- Number of iterations: 20
- Number of iterations: 24
- Number of iterations: 32
+ Number of iterations: ...
+ Number of iterations: ...
+ Number of iterations: ...
+ Number of iterations: ...
.. figure:: ../images/MaxEntResolutionFactor2.png
:align: center
diff --git a/docs/source/algorithms/SetUB-v1.rst b/docs/source/algorithms/SetUB-v1.rst
index 07961ff32cf842ede37e5b738656dae81487bd4b..ca951cb3b93c42a35675a27c456377dc32589800 100644
--- a/docs/source/algorithms/SetUB-v1.rst
+++ b/docs/source/algorithms/SetUB-v1.rst
@@ -47,11 +47,12 @@ Usage
Output:
.. testoutput:: SetUB
+ :options: +ELLIPSIS +NORMALIZE_WHITESPACE
UB matrix
- [[-0. 0. 0.143]
- [ 0.128 -0.128 0. ]
- [ 0.154 0.107 -0. ]]
+ [[... ... 0.143]
+ [ 0.128 -0.128 ... ]
+ [ 0.154 0.107 ... ]]
.. categories::
diff --git a/docs/source/concepts/CrystalStructureAndReflections.rst b/docs/source/concepts/CrystalStructureAndReflections.rst
index 78c8e6ead4926a699c4bf5ddc6c09820a15443ba..1b2138f8ef9287e5c12d9a48ed801ea7b74f84ec 100644
--- a/docs/source/concepts/CrystalStructureAndReflections.rst
+++ b/docs/source/concepts/CrystalStructureAndReflections.rst
@@ -253,7 +253,7 @@ to the process for :math:`F^2`:
# Make list of tuples and sort by d-values, descending, include point group for multiplicity.
reflections = sorted([(hkl, d, fsq, len(pg.getEquivalents(hkl))) for hkl, d, fsq in zip(hkls, dValues, fSquared)],
- key=lambda x: x[1], reverse=True)
+ key=lambda x: x[1] - x[0][0]*1e-6, reverse=True)
print('{0:<8}{1:>8}{2:>8}{3:>4}'.format('HKL', 'd', 'F^2', 'M'))
for reflection in reflections:
diff --git a/docs/source/fitting/fitfunctions/LatticeFunction.rst b/docs/source/fitting/fitfunctions/LatticeFunction.rst
index a26b7c629c64c311fce2e16ce6bf115972e1ba34..d6d40899023248e9a81e7cc00f138632fe302f18 100644
--- a/docs/source/fitting/fitfunctions/LatticeFunction.rst
+++ b/docs/source/fitting/fitfunctions/LatticeFunction.rst
@@ -50,19 +50,18 @@ used to generate Bragg reflections that are expected for the crystal structure o
a_true = 5.4311946
a = np.round(parameters.cell(0, 1), 7)
- a_err = np.round(parameters.cell(0, 2), 16)
+ a_err = np.round(parameters.cell(0, 2), 7)
print("Refined lattice parameter: a = {0} +/- {1}".format(a, a_err))
print("Difference from expected value: a_observed - a_expected = {0}".format(np.round(a - a_true, 7)))
- print("Is this difference within the standard deviation? {0}".format("Yes" if np.fabs(a - a_true) <= a_err else "No"))
Executing the script produces some output with information about the fit:
.. testoutput:: ExSiliconTheoretical
+ :options: +ELLIPSIS +NORMALIZE_WHITESPACE
- Refined lattice parameter: a = 5.4311946 +/- 2e-16
+ Refined lattice parameter: a = 5.4311946 +/- ...
Difference from expected value: a_observed - a_expected = 0.0
- Is this difference within the standard deviation? Yes
In addition there is also an output workspace, which contains information about the peaks used for the fit and how
well the peak positions calculated from the fitted parameters match the observed positions.