diff --git a/Code/Mantid/Framework/Crystal/src/OptimizeCrystalPlacement.cpp b/Code/Mantid/Framework/Crystal/src/OptimizeCrystalPlacement.cpp
index 9ec4798ee931860e79b9e6bab302c77db63f0737..793c6a5d90122723566a321d53398fc8cc876166 100644
--- a/Code/Mantid/Framework/Crystal/src/OptimizeCrystalPlacement.cpp
+++ b/Code/Mantid/Framework/Crystal/src/OptimizeCrystalPlacement.cpp
@@ -70,9 +70,6 @@ namespace Mantid
bool isEnabled (const IPropertyManager *algo) const
{
- bool P1= Prop1->isEnabled( algo);
- bool P2=Prop2->isEnabled(algo);
- std::cout<<"isEnabled="<<P1<<","<<P2<<std::endl;
return Prop1->isEnabled( algo)&& Prop2->isEnabled(algo);
}
private:
diff --git a/Code/Mantid/MantidQt/CustomDialogs/inc/MantidQtCustomDialogs/SlicingAlgorithmDialog.h b/Code/Mantid/MantidQt/CustomDialogs/inc/MantidQtCustomDialogs/SlicingAlgorithmDialog.h
index 524177fc9501179da01d68153ac4dbd90a96618d..cbf45bd91840f22387adb4f1cdb5e5390584b58c 100644
--- a/Code/Mantid/MantidQt/CustomDialogs/inc/MantidQtCustomDialogs/SlicingAlgorithmDialog.h
+++ b/Code/Mantid/MantidQt/CustomDialogs/inc/MantidQtCustomDialogs/SlicingAlgorithmDialog.h
@@ -87,7 +87,7 @@ private:
void makeDimensionInputs(const QString& propertyPrefix, QLayout* owningLayout, QString(*format)(Mantid::Geometry::IMDDimension_const_sptr), History history);
/// Determine if history should be used.
- SlicingAlgorithmDialog::History useHistory(const HistoryChanged& criticalChange, const bool bForceForget);
+ History useHistory(const HistoryChanged& criticalChange, const bool bForceForget);
/// Cleans a given layout.
void cleanLayoutOfDimensions(QLayout* layout);
diff --git a/Code/Mantid/MantidQt/CustomDialogs/src/SlicingAlgorithmDialog.cpp b/Code/Mantid/MantidQt/CustomDialogs/src/SlicingAlgorithmDialog.cpp
index b3deb5a4c11ba9d306cea32f07c01fdff1834ebf..2ea031255630579ce0f92b789272f174bebf91ec 100644
--- a/Code/Mantid/MantidQt/CustomDialogs/src/SlicingAlgorithmDialog.cpp
+++ b/Code/Mantid/MantidQt/CustomDialogs/src/SlicingAlgorithmDialog.cpp
@@ -61,7 +61,6 @@ namespace MantidQt
//Configure workspace selector
ui.workspace_selector->setValidatingAlgorithm(m_algName);
- connect(ui.workspace_selector, SIGNAL(clicked()), this, SLOT(createMDWorkspaceClicked()));
ui.workspace_selector->clear();
typedef std::set<std::string> WorkspaceNames;
WorkspaceNames names = AnalysisDataService::Instance().getObjectNames();
diff --git a/Code/Mantid/docs/source/algorithms/AnvredCorrection-v1.rst b/Code/Mantid/docs/source/algorithms/AnvredCorrection-v1.rst
index e2b6b8ecbe7391fe946c0ab92727cda4facdd76d..e489e5afe7d1c2c49d42e034308155d56a5dd410 100644
--- a/Code/Mantid/docs/source/algorithms/AnvredCorrection-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/AnvredCorrection-v1.rst
@@ -11,28 +11,28 @@ Description
Following A.J.Schultz's anvred, the weight factors should be:
-:math:`sin^2(theta) / (lamda^4 * spec * eff * trans)`
+:math:`sin^2(theta) / (lambda^4 * spec * eff * trans)`
where
-- theta = scattering\_angle/2
+- theta = scattering_angle/2
- lamda = wavelength (in angstroms?)
- spec = incident spectrum correction
- eff = pixel efficiency
- trans = absorption correction
The quantity: :math:`sin^2(theta) / eff` depends only on the pixel and can be
-pre-calculated for each pixel. It could be saved in array pix\_weight[].
+pre-calculated for each pixel. It could be saved in array pix_weight[].
-For now, pix\_weight[] is calculated by the method: BuildPixWeights()
-and just holds the :math:`sin^2(theta)`values. The wavelength dependent portion
-of the correction is saved in the array lamda\_weight[].
+For now, pix_weight[] is calculated by the method ``BuildPixWeights()``
+and just holds the :math:`sin^2(theta)` values. The wavelength dependent portion
+of the correction is saved in the array lamda_weight[].
The time-of-flight is converted to wave length by multiplying by
-tof\_to\_lamda[id], then (int)STEPS\_PER\_ANGSTROM \* lamda gives an
-index into the table lamda\_weight[]. The lamda\_weight[] array contains
+tof_to_lamda[id], then (int)STEPS_PER_ANGSTROM \* lamda gives an
+index into the table lamda_weight[]. The lamda_weight[] array contains
values like: 1/(lamda^power \* spec(lamda)) which are pre-calculated for
-each lamda. These values are saved in the array lamda\_weight[]. The
+each lamda. These values are saved in the array lamda_weight[]. The
optimal value to use for the power should be determined when a good
incident spectrum has been determined. Currently, power=3 when used with
an incident spectrum and power=2.4 when used without an incident
diff --git a/Code/Mantid/docs/source/algorithms/CalculateTransmission-v1.rst b/Code/Mantid/docs/source/algorithms/CalculateTransmission-v1.rst
index 0d52ebaa304b41238243bc93f4ac13fac83d515e..411864a76cb0d03c73e161da5287af1bf528fac0 100644
--- a/Code/Mantid/docs/source/algorithms/CalculateTransmission-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/CalculateTransmission-v1.rst
@@ -14,13 +14,14 @@ sample using detected counts from two monitors, one in front and one
behind the sample. A data workspace can be corrected for transmission by
`dividing <http://www.mantidproject.org/Divide>`_ by the output of this algorithm.
-| Because the detection efficiency of the monitors can be different the
+Because the detection efficiency of the monitors can be different the
transmission calculation is done using two runs, one run with the sample
(represented by :math:`S` below) and a direct run without
-it(\ :math:`D`). The fraction transmitted through the sample :math:`f`
-is calculated from this formula:
-| :math:`p = \frac{S_T}{D_T}\frac{D_I}{S_I}`
-| where :math:`S_I` is the number of counts from the monitor in front of
+it (:math:`D`). The fraction transmitted through the sample :math:`f` is calculated from this formula:
+
+.. math::p = \frac{S_T}{D_T}\frac{D_I}{S_I}
+
+where :math:`S_I` is the number of counts from the monitor in front of
the sample (the incident beam monitor), :math:`S_T` is the transmission
monitor after the sample, etc.
@@ -36,7 +37,7 @@ the data to be corrected.
ChildAlgorithms used
####################
-Uses the algorithm `linear <http://www.mantidproject.org/linear>`_ to fit to the calculated
+Uses the algorithm `Fit <algm-Fit>`_ to fit to the calculated
transmission fraction.
.. categories::
diff --git a/Code/Mantid/docs/source/algorithms/CalculateUMatrix-v1.rst b/Code/Mantid/docs/source/algorithms/CalculateUMatrix-v1.rst
index 63aab89c20bb1550a5c5a61efd12ef00b1c3e0e1..118c21e30c734cf79c97e8e39650bb55cd8fe0ea 100644
--- a/Code/Mantid/docs/source/algorithms/CalculateUMatrix-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/CalculateUMatrix-v1.rst
@@ -23,87 +23,100 @@ goniometer, :math:`\rm Q_{gon}`, indexed by :math:`(h_i, k_i, l_i)`, we
want to find the U matrix that maps peaks in the reciprocal space of the
sample to the peaks in the goniometer frame
-:math:`\rm U \rm B \left(
+.. math::
+ :label:
+ \rm U \rm B \left(
\begin{array}{c}
-
h_i \\
-
k_i \\
-
l_i \\
-
\end{array}
-
- \right) = \rm Q_{gon,i}` (1)
+ \right) = \rm Q_{gon,i}
For simplicity, we define
-:math:`\rm Q_{hkl,i} = \rm B \left(
+.. math::
+ :label:
+ \rm Q_{hkl,i} = \rm B \left(
\begin{array}{c}
-
h_i \\
-
k_i \\
-
l_i \\
-
\end{array}
-
- \right)` (2)
+ \right)
In the real world, such a matrix is not always possible to find.
Therefore we just try minimize the difference between the two sets of p
-:math:`\sum_i |\rm U \rm Q_{hkl,i} - \rm Q_{gon,i}|^2 = \sum_i \left(|\rm U \rm Q_{hkl,i}|^2 + |\rm Q_{gon,i}|^2 -2 \rm U \rm Q_{hkl,i} \cdot \rm Q_{gon,i}\right)`
-(3)
+.. math::
+ :label: pdiff
+
+ \sum_i |\rm U \rm Q_{hkl,i} - \rm Q_{gon,i}|^2 = \sum_i \left(|\rm U \rm Q_{hkl,i}|^2 + |\rm Q_{gon,i}|^2 -2 \rm U \rm Q_{hkl,i} \cdot \rm Q_{gon,i}\right)
-In equation (3)
-:math:`\left|\rm U \rm Q_{hkl,i}\right|^2 = |\rm Q_{hkl,i}|^2`, so the
+In equation :eq:`pdiff`, :math:`\left|\rm U \rm Q_{hkl,i}\right|^2 = |\rm Q_{hkl,i}|^2`, so the
first two terms on the left side are U independent. Therefore we want to
maximize
-:math:`\sum_i \left(\rm U \rm Q_{hkl,i} \cdot \rm Q_{gon,i}\right)` (4)
+.. math::
+ :label: uqdotqsum
+
+ \sum_i \left(\rm U \rm Q_{hkl,i} \cdot \rm Q_{gon,i}\right)
We are going to write the scalar product of the vectors in terms of
-quaternions\ `2 <http://en.wikipedia.org/wiki/Quaternion>`__. We define
+quaternions `2 <http://en.wikipedia.org/wiki/Quaternion>`__. We define
:math:`q_{hkl,i} = \left(0, Q_{hkl,i}\right)`,
:math:`q_{gon,i} = \left(0, Q_{gon,i}\right)` and the rotation U is
described by quaternion :math:`u = \left(w,x,y,z\right)`
-Then equation (4) will be written as
+Then equation :eq:`uqdotqsum` will be written as
+
+.. math::
+ :label: uqdotq
+
+ \sum_i \left(\rm U \rm Q_{hkl,i} \cdot \rm Q_{gon,i}\right) = 0.5 \cdot \left(u q_{hkl,i} u^*\right) q_{gon,i}\ + 0.5 \cdot q_{gon,i} \left(u q_{hkl,i} u^*\right)
+
+We define matrices
+
+.. math::
+ :label: quat_h
-:math:`\sum_i \left(\rm U \rm Q_{hkl,i} \cdot \rm Q_{gon,i}\right) = 0.5 \cdot \left(u q_{hkl,i} u^*\right) q_{gon,i}\ + 0.5 \cdot q_{gon,i} \left(u q_{hkl,i} u^*\right)`
-(5)
+ H_i= \left(\begin{array}{cccc}
+ 0 & -q_{hkl,i,x} & -q_{hkl,i,y} & -q_{hkl,i,z} \\
+ q_{hkl,i,x} & 0 & q_{hkl,i,z} & -q_{hkl,i,y} \\
+ q_{hkl,i,y} & -q_{hkl,i,z} & 0 & q_{hkl,i,x} \\
+ q_{hkl,i,z} & q_{hkl,i,y} & -q_{hkl,i,x} & 0
+ \end{array} \right)
-We define matrices :math:`H_i= \left(\begin{array}{cccc}
-0 & -q_{hkl,i,x} & -q_{hkl,i,y} & -q_{hkl,i,z} \\
-q_{hkl,i,x} & 0 & q_{hkl,i,z} & -q_{hkl,i,y} \\
-q_{hkl,i,y} & -q_{hkl,i,z} & 0 & q_{hkl,i,x} \\
-q_{hkl,i,z} & q_{hkl,i,y} & -q_{hkl,i,x} & 0
-\end{array} \right)` (6)
+and
-and :math:`S_i= \left(\begin{array}{cccc}
-0 & -q_{gonl,i,x} & -q_{gon,i,y} & -q_{gon,i,z} \\
-q_{gon,i,x} & 0 & -q_{gon,i,z} & q_{gon,i,y} \\
-q_{gon,i,y} & q_{gon,i,z} & 0 & -q_{gon,i,x} \\
-q_{gon,i,z} & -q_{gon,i,y} & q_{gon,i,x} & 0
-\end{array} \right)` (7)
+.. math::
+ :label: quat_s
-Then, we can rewrite equation (5) using
-matrices\ `3 <http://en.wikipedia.org/wiki/Quaternions_and_spatial_rotation#Pairs_of_unit_quaternions_as_rotations_in_4D_space>`__,\ `4 <http://www.cs.iastate.edu/~cs577/handouts/quaternion.pdf>`__:
+ S_i= \left(\begin{array}{cccc}
+ 0 & -q_{gonl,i,x} & -q_{gon,i,y} & -q_{gon,i,z} \\
+ q_{gon,i,x} & 0 & -q_{gon,i,z} & q_{gon,i,y} \\
+ q_{gon,i,y} & q_{gon,i,z} & 0 & -q_{gon,i,x} \\
+ q_{gon,i,z} & -q_{gon,i,y} & q_{gon,i,x} & 0
+ \end{array} \right)
-:math:`\sum_i \left(\rm U \rm Q_{hkl,i} \cdot \rm Q_{gon,i}\right) = \left(\begin{array}{cccc}
-w & x & y & z\end{array} \right) \sum_i H_i S_i \left(
+Then, we can rewrite equation :eq:`uqdotq` using
+matrices `3 <http://en.wikipedia.org/wiki/Quaternions_and_spatial_rotation#Pairs_of_unit_quaternions_as_rotations_in_4D_space>`_,
+`4 <http://www.cs.iastate.edu/~cs577/handouts/quaternion.pdf>`_:
+
+.. math::
+ :label:
+
+ \sum_i \left(\rm U \rm Q_{hkl,i} \cdot \rm Q_{gon,i}\right) = \left(\begin{array}{cccc}
+ w & x & y & z\end{array} \right) \sum_i H_i S_i \left(
\begin{array}{c}
w \\
x \\
y \\
-z
+ z
\end{array}
-
- \right)` (8)
+ \right)
The problem of finding :math:`\left(w,x,y,z\right)` that maximizes the
sum can now be rewritten in terms of eigenvectors of
@@ -114,29 +127,35 @@ sum can now be rewritten in terms of eigenvectors of
any vector :math:`(w,x,y,z)` as a linear combination of the eigenvectors
of :math:`HS`:
-:math:`\left(w,x,y,z\right) = \delta_0 \nu_0 +\delta_1 \nu_1 +\delta_2 \nu_2 +\delta_3 \nu_3`
-(9)
+.. math::
+ :label:
+
+ \left(w,x,y,z\right) = \delta_0 \nu_0 +\delta_1 \nu_1 +\delta_2 \nu_2 +\delta_3 \nu_3
+
+.. math::
+ :label:
-:math:`\left(\begin{array}{cccc}
-w & x & y & z\end{array} \right) HS \left(
+ \left(\begin{array}{cccc}
+ w & x & y & z\end{array} \right) HS \left(
\begin{array}{c}
w \\
x \\
y \\
-z
+ z
\end{array}
+ \right) = \delta_0^2 \nu_0 HS \nu_0 + \delta_1^2 \nu_1 HS \nu_1 +\delta_2^2 \nu_2 HS \nu_2 +\delta_3 \nu_3 HS \nu_3
- \right) = \delta_0^2 \nu_0 HS \nu_0 + \delta_1^2 \nu_1 HS \nu_1 +\delta_2^2 \nu_2 HS \nu_2 +\delta_3 \nu_3 HS \nu_3`
-(10)
+.. math::
+ :label: quatsum
-:math:`= \delta_0^2 \epsilon_0 + \delta_1^2 \epsilon_1 +\delta_2^2 \epsilon_2 +\delta_3 ^2 \epsilon_3`
-(11)
+ \begin{split}
+ & = \delta_0^2 \epsilon_0 + \delta_1^2 \epsilon_1 +\delta_2^2 \epsilon_2 +\delta_3 ^2 \epsilon_3
+ \end{split}
-:math:`u` is a unit quaternion,
+where :math:`u` is a unit quaternion,
:math:`\delta_0^2 + \delta_1^2 +\delta_2^2 +\delta_3 ^2=1` (12)
-Then the sum in equation (11) is maximized for
-:math:`\epsilon_0 =1, \epsilon_1 =0, \epsilon_2 =0 \epsilon_3 =0` (13)
+Then the sum in equation :eq:`quatsum` is maximized for :math:`\epsilon_0 =1, \epsilon_1 =0, \epsilon_2 =0 \epsilon_3 =0`
Therefore U is the rotation represented by the quaternion :math:`u`,
which is the eigenvector corresponding to the largest eigenvalue of
diff --git a/Code/Mantid/docs/source/algorithms/CatalogDownloadDataFiles-v1.rst b/Code/Mantid/docs/source/algorithms/CatalogDownloadDataFiles-v1.rst
index 3f21115aeb30c9d2e1c5136302e28b0b6b6cacc1..d9adc7808eaea78fb55d685afb06b87ce724f14e 100644
--- a/Code/Mantid/docs/source/algorithms/CatalogDownloadDataFiles-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/CatalogDownloadDataFiles-v1.rst
@@ -18,7 +18,7 @@ Usage
**Example - downloading a single datafile from ICAT.**
-.. code:: python
+.. code-block:: python
# Assuming you have previously logged into the catalog
# and stored the session return value in the variable 'session'
@@ -30,7 +30,7 @@ Usage
Output:
-.. code:: python
+.. code-block:: python
# Outputs a list locations of the datafiles downloaded.
# USERNAME will be your username on your system.
@@ -38,7 +38,7 @@ Output:
**Example - downloading multiple datafiles from ICAT.**
-.. code:: python
+.. code-block:: python
# The ids of the datafiles to download.
# These could be obtained from CatalogGetDataFiles or entered manually.
@@ -57,7 +57,7 @@ Output:
Output:
-.. code:: python
+.. code-block:: python
['/home/USERNAME/Desktop/33127010.nxs', '/home/USERNAME/Desktop/33127011.nxs']
diff --git a/Code/Mantid/docs/source/algorithms/CatalogGetDataFiles-v1.rst b/Code/Mantid/docs/source/algorithms/CatalogGetDataFiles-v1.rst
index f0f907008d0cf37e7f0649d8b909818e4ad40009..5629dbd026cc9620c7f388eaa297da45ae60a146 100644
--- a/Code/Mantid/docs/source/algorithms/CatalogGetDataFiles-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/CatalogGetDataFiles-v1.rst
@@ -16,7 +16,7 @@ Usage
**Example - obtain datafile information for all datafiles in a given ICAT investigation.**
-.. code:: python
+.. code-block:: python
# Assumes you have logged in and stored the session information that is
# returned from CatalogLogin() inside the session variable.
@@ -31,7 +31,7 @@ Usage
Output:
-.. code:: python
+.. code-block:: python
The number of datafiles in this investigation is: 22
diff --git a/Code/Mantid/docs/source/algorithms/CatalogGetDataSets-v1.rst b/Code/Mantid/docs/source/algorithms/CatalogGetDataSets-v1.rst
index be3b38408cf79b47735d9b751e74ec28b477caba..02c29638859eda90d49f60489d5dde17caab45ce 100644
--- a/Code/Mantid/docs/source/algorithms/CatalogGetDataSets-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/CatalogGetDataSets-v1.rst
@@ -16,7 +16,7 @@ Usage
**Example - obtain the datasets for a given catalog investigation.**
-.. code:: python
+.. code-block:: python
# Assumes you have logged in and stored the session information that is
# returned from CatalogLogin() inside the session variable.
@@ -27,7 +27,7 @@ Usage
Output:
-.. code:: python
+.. code-block:: python
The number of datafiles in this investigation is: 2
diff --git a/Code/Mantid/docs/source/algorithms/CatalogKeepAlive-v1.rst b/Code/Mantid/docs/source/algorithms/CatalogKeepAlive-v1.rst
index 0c408128170f20130f8a345b9eee0867af8e941a..6352d16a847bb4708d009bebdc3b5a4fcf4c2f94 100644
--- a/Code/Mantid/docs/source/algorithms/CatalogKeepAlive-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/CatalogKeepAlive-v1.rst
@@ -16,7 +16,7 @@ Usage
**Example - keeps the current session alive.**
-.. code:: python
+.. code-block:: python
# Attempts to keep ALL sessions alive indefinitely.
CatalogKeepALive()
diff --git a/Code/Mantid/docs/source/algorithms/CatalogListInstruments-v1.rst b/Code/Mantid/docs/source/algorithms/CatalogListInstruments-v1.rst
index e7f80ba5f442c34ca1a881d7ddcf775a964e7a3f..2b420ce258a9aedfc5e45b7326722d3ca4bab4ca 100644
--- a/Code/Mantid/docs/source/algorithms/CatalogListInstruments-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/CatalogListInstruments-v1.rst
@@ -16,7 +16,7 @@ Usage
**Example - obtaining instrument names from current active catalogs.**
-.. code:: python
+.. code-block:: python
# Assuming you have previously logged into the ISIS catalog.
instruments = CatalogListInstruments()
@@ -33,7 +33,7 @@ Usage
Output:
-.. code:: python
+.. code-block:: python
The number of instruments at ISIS is: 38
diff --git a/Code/Mantid/docs/source/algorithms/CatalogListInvestigationTypes-v1.rst b/Code/Mantid/docs/source/algorithms/CatalogListInvestigationTypes-v1.rst
index 68c48c369f7a8b0c88b0d0a8e651cc68a899be03..a2c8dee0f9aae6bde541570979c86ab9a70b555e 100644
--- a/Code/Mantid/docs/source/algorithms/CatalogListInvestigationTypes-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/CatalogListInvestigationTypes-v1.rst
@@ -16,7 +16,7 @@ Usage
**Example - obtain the investigation types from current catalogs.**
-.. code:: python
+.. code-block:: python
# Assuming you have previously logged into the ISIS catalog.
investigation_types = CatalogListInvestigations()
@@ -30,7 +30,7 @@ Usage
Output:
-.. code:: python
+.. code-block:: python
The number of instruments at ISIS is: 9
diff --git a/Code/Mantid/docs/source/algorithms/CatalogLogin-v1.rst b/Code/Mantid/docs/source/algorithms/CatalogLogin-v1.rst
index caccb5f32e2d5f20c6cf84c2672afd34b8344dd5..e851f2a26b23731d46d9d2f80d32148762ae6601 100644
--- a/Code/Mantid/docs/source/algorithms/CatalogLogin-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/CatalogLogin-v1.rst
@@ -16,7 +16,7 @@ Usage
**Example - log a user into the catalog.**
-.. code:: python
+.. code-block:: python
# Attempts to authenticate the user against the ISIS catalog.
# When logging into the catalog the session class is returned.
@@ -28,7 +28,7 @@ Usage
Output:
-.. code:: python
+.. code-block:: python
The session ID is: b931877c-3cfb-460e-9e88-ed4257020477
diff --git a/Code/Mantid/docs/source/algorithms/CatalogLogout-v1.rst b/Code/Mantid/docs/source/algorithms/CatalogLogout-v1.rst
index 9fdd1760f07eca0ea2d82665a6dabef65db1481b..5b41ec436da175870c472a7e259e92631e27c9a5 100644
--- a/Code/Mantid/docs/source/algorithms/CatalogLogout-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/CatalogLogout-v1.rst
@@ -16,7 +16,7 @@ Usage
**Example - logs a user out of the catalog.**
-.. code:: python
+.. code-block:: python
# Logs the user out of the catalog and kills CatalogKeepAlive()
CatalogLogout()
diff --git a/Code/Mantid/docs/source/algorithms/CatalogMyDataSearch-v1.rst b/Code/Mantid/docs/source/algorithms/CatalogMyDataSearch-v1.rst
index d4db9b293effbf132267986419d98d7c6aca4c56..1803d0cf7b2262eb9558c5b1bf83a273daadc630 100644
--- a/Code/Mantid/docs/source/algorithms/CatalogMyDataSearch-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/CatalogMyDataSearch-v1.rst
@@ -16,7 +16,7 @@ Usage
**Example - obtaining 'My data' from ICAT.**
-.. code:: python
+.. code-block:: python
# Assuming you have previously logged into the catalog.
my_data = CatalogMyDataSearch()
@@ -30,7 +30,7 @@ Usage
Output:
-.. code:: python
+.. code-block:: python
The number of investigations in 'My data' is: 1
diff --git a/Code/Mantid/docs/source/algorithms/CatalogPublish-v1.rst b/Code/Mantid/docs/source/algorithms/CatalogPublish-v1.rst
index c70cbe69e18e8d8722d3d04009cfff1b214d99e9..e1339fc557e232404ce1d5698be2310113eeafe7 100644
--- a/Code/Mantid/docs/source/algorithms/CatalogPublish-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/CatalogPublish-v1.rst
@@ -33,7 +33,7 @@ Usage
**CAUTION:** This usage example will only work if you are an investigator on the given investigation.
-.. code:: python
+.. code-block:: python
# To ensure the datafile is published to the correct catalog,
# store the session returned when logging in for use later.
diff --git a/Code/Mantid/docs/source/algorithms/CatalogSearch-v1.rst b/Code/Mantid/docs/source/algorithms/CatalogSearch-v1.rst
index 82e519581d2e8176e64737d39f8e0351ba556d53..a8f58ca7aa7830006d8b5c47ce9563d136ea7ed7 100644
--- a/Code/Mantid/docs/source/algorithms/CatalogSearch-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/CatalogSearch-v1.rst
@@ -16,7 +16,7 @@ Usage
**Example - searches for investigations in the catalog based on parameters set.**
-.. code:: python
+.. code-block:: python
# When logging into the catalog the session class is returned.
# This can then be used throughout to perform other ICAT routines.
@@ -36,7 +36,7 @@ Usage
Output:
-.. code:: python
+.. code-block:: python
The number of investigations returned was: 3
@@ -46,7 +46,7 @@ Output:
**Example - paging results returned.**
-.. code:: python
+.. code-block:: python
# When CountOnly is set to True a separate COUNT query is performed to see the total
# number of investigations that will be returned by this search. This is used for paging functionality.
@@ -59,7 +59,7 @@ Output:
Output:
-.. code:: python
+.. code-block:: python
The number of search results returned was: 109
diff --git a/Code/Mantid/docs/source/algorithms/ChopData-v1.rst b/Code/Mantid/docs/source/algorithms/ChopData-v1.rst
index 6f3dd09ff5c0df12528df303eea05e3738b48409..04a04f7d077fc3eb77586f9c6c53345886196ea1 100644
--- a/Code/Mantid/docs/source/algorithms/ChopData-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/ChopData-v1.rst
@@ -21,6 +21,7 @@ Identifying Extended Frames
:alt: Figure 1: Example Monitor Spectrum with Extended Frames
Figure 1: Example Monitor Spectrum with Extended Frames
+
If the parameters *IntegrationRangeLower*, *IntegrationRangeUpper* and
*MonitorWorkspaceIndex* are provided to the algorithm, then it will
attempt to identify where in the workspace the frames have been
diff --git a/Code/Mantid/docs/source/algorithms/ConvertToDetectorFaceMD-v1.rst b/Code/Mantid/docs/source/algorithms/ConvertToDetectorFaceMD-v1.rst
index 7111ec696e0c096d8ddf879c661c7f728ddc68a8..a74dacd75cfe1912e8cc2886afb5b4994f84f9a6 100644
--- a/Code/Mantid/docs/source/algorithms/ConvertToDetectorFaceMD-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/ConvertToDetectorFaceMD-v1.rst
@@ -9,12 +9,12 @@
Description
-----------
-This algorithm takes a a `MatrixWorkspace <http://www.mantidproject.org/MatrixWorkspace>`__ and
-converts it into a `MDEventWorkspace <http://www.mantidproject.org/MDEventWorkspace>`__ that can be
-viewed in the `SliceViewer <http://www.mantidproject.org/SliceViewer>`__.
+This algorithm takes a a `MatrixWorkspace <http://www.mantidproject.org/MatrixWorkspace>`_ and
+converts it into a `MDEventWorkspace <http://www.mantidproject.org/MDEventWorkspace>`_ that can be
+viewed in the `SliceViewer <http://www.mantidproject.org/SliceViewer>`_.
The algorithm currently only works for instruments with
-`RectangularDetectors <http://www.mantidproject.org/InstrumentDefinitionFile#Creating_Rectangular_Area_Detectors>`__. The coordinates of the
+`RectangularDetectors <http://www.mantidproject.org/InstrumentDefinitionFile#Creating_Rectangular_Area_Detectors>`_. The coordinates of the
output workspace are:
- Pixel X coordinate (integer starting at 0)
@@ -25,8 +25,8 @@ output workspace are:
Each MDEvent created has a weight given by the number of counts in that
bin. Zero bins are not converted to events (saving memory).
-Once created, the `MDEventWorkspace <http://www.mantidproject.org/MDEventWorkspace>`__ can be viewed
-in the `SliceViewer <http://www.mantidproject.org/SliceViewer>`__. It can also be rebinned with
+Once created, the `MDEventWorkspace <http://www.mantidproject.org/MDEventWorkspace>`_ can be viewed
+in the `SliceViewer <http://www.mantidproject.org/SliceViewer>`_. It can also be rebinned with
different parameters using :ref:`algm-BinMD`. This allows you to view
the data in detector-space. For example, you might use this feature to
look at your detector's sensitivity as a function of position, as well
@@ -39,16 +39,17 @@ screenshot for example:
:width: 600 px
SliceViewer-DetectorFace.png
+
BankNumbers Parameter
#####################
-If your instrument has several `RectangularDetectors <http://www.mantidproject.org/InstrumentDefinitionFile#Creating_Rectangular_Area_Detectors>`__, you can use the
+If your instrument has several `RectangularDetectors <http://www.mantidproject.org/InstrumentDefinitionFile#Creating_Rectangular_Area_Detectors>`_, you can use the
*BankNumbers* property to specify which one(s) to convert. The algorithm
-looks for `RectangularDetectors <http://www.mantidproject.org/InstrumentDefinitionFile#Creating_Rectangular_Area_Detectors>`__ with the name 'bankXX' where XX is the
+looks for `RectangularDetectors <http://www.mantidproject.org/InstrumentDefinitionFile#Creating_Rectangular_Area_Detectors>`_ with the name 'bankXX' where XX is the
bank number.
If you specify more than one bank number, then the algorithm will create
-a 4D `MDEventWorkspace <http://www.mantidproject.org/MDEventWorkspace>`__. The fourth dimension will be equal to the bank
+a 4D `MDEventWorkspace <http://www.mantidproject.org/MDEventWorkspace>`_. The fourth dimension will be equal to the bank
number, allowing you to easily pick a bank to view.
.. categories::
diff --git a/Code/Mantid/docs/source/algorithms/CreateCalFileByNames-v1.rst b/Code/Mantid/docs/source/algorithms/CreateCalFileByNames-v1.rst
index 675d868dacfd0a97fff7b1e6da7c9b371794363b..615a8d62fb84fdbe83a55704a158be3022078575 100644
--- a/Code/Mantid/docs/source/algorithms/CreateCalFileByNames-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/CreateCalFileByNames-v1.rst
@@ -13,6 +13,7 @@ Description
:alt: Instrument Tree
Instrument Tree
+
Create a `calibration file <http://www.mantidproject.org/CalFile>`_ for diffraction focusing based
on list of names of the instrument tree.
diff --git a/Code/Mantid/docs/source/algorithms/CreateDummyCalFile-v1.rst b/Code/Mantid/docs/source/algorithms/CreateDummyCalFile-v1.rst
index e3384106518b58f21933312e6e7caedd8c157d92..98d4ad65baf48c9739aedb29aabb00cca06f235e 100644
--- a/Code/Mantid/docs/source/algorithms/CreateDummyCalFile-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/CreateDummyCalFile-v1.rst
@@ -13,6 +13,7 @@ Description
:alt: Instrument Tree
Instrument Tree
+
Create a dummy `calibration file <http://www.mantidproject.org/CalFile>`_ for diffraction focusing
with one group.
diff --git a/Code/Mantid/docs/source/algorithms/CreateGroupingWorkspace-v1.rst b/Code/Mantid/docs/source/algorithms/CreateGroupingWorkspace-v1.rst
index e64d7b82c12a166f00efb114adcad361a16e4873..fc9cc6c5c4dc9d001ab51226469a537801ac547a 100644
--- a/Code/Mantid/docs/source/algorithms/CreateGroupingWorkspace-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/CreateGroupingWorkspace-v1.rst
@@ -26,6 +26,7 @@ number the groups in the output.
Usage
-----
+
**Example - CreateGoupingWorkspace for MUSR Instrument**
.. testcode:: ExCreateGroupingWorkspaceSimple
@@ -68,6 +69,7 @@ Output:
.. testoutput:: ExCreateGroupingWorkspaceFromWorkspace
Instrument name = MUSR
+
**Example - CreateGoupingWorkspace from GEM Instrument Definition**
.. testcode:: ExCreateGroupingWorkspaceFromIDF
diff --git a/Code/Mantid/docs/source/algorithms/FFT-v1.rst b/Code/Mantid/docs/source/algorithms/FFT-v1.rst
index 7debf3991362ddac760ca85cd75513e2c96b2c3f..8324c5ce746d3b4c2dd2822aa47954cb1497c1e4 100644
--- a/Code/Mantid/docs/source/algorithms/FFT-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/FFT-v1.rst
@@ -84,6 +84,7 @@ In this example the input data were calculated using function
:alt: FFT of a Gaussian
FFT of a Gaussian
+
Because the :math:`x=0` is in the middle of the data array the transform
shown is the exact DFT of the input data.
@@ -97,10 +98,12 @@ In this example the input data were calculated using function
:alt: Gaussian
Gaussian
+
.. figure:: /images/FFTGaussian1FFT.png
:alt: FFT of a Gaussian
FFT of a Gaussian
+
Because the :math:`x=0` is not in the middle of the data array the
transform shown includes a shifting factor of :math:`\exp(2\pi i\xi)`.
To remove it the output must be mulitplied by :math:`\exp(-2\pi i\xi)`.
@@ -110,6 +113,7 @@ The corrected transform will be:
:alt: FFT of a Gaussian
FFT of a Gaussian
+
It should be noted that in a case like this, i.e. when the input is a
real positive even function, the correction can be done by finding the
transform's modulus :math:`(Re^2+Im^2)^{1/2}`. The output workspace
diff --git a/Code/Mantid/docs/source/algorithms/FindPeaks-v1.rst b/Code/Mantid/docs/source/algorithms/FindPeaks-v1.rst
index cb1dc9415defbc003a8de6ca30a4cf965dbedd70..65804b22354b704994f3c90fdeef3c99a701e8e9 100644
--- a/Code/Mantid/docs/source/algorithms/FindPeaks-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/FindPeaks-v1.rst
@@ -64,30 +64,26 @@ x-max) is confined by this window.
If FitWindows is defined, starting peak centres are NOT user's input,
but found by highest value within peak window. (Is this correct???)
+Estimation of peak's background and range
+#########################################
+
+If FindPeaksBackground fails, then it is necessary to estimate a rough peak range and background according to
+observed data.
+
+#. Assume the local background (within the given fitting window) is close to linear;
+#. Take the first 3 and last 3 data points to calcualte the linear background;
+#. Remove background (rougly) and calcualte peak's height, width, and centre;
+#. If the peak centre (starting value) uses observed value, then set peakcentre to that value. Otherwise, set it to given value;
+#. Get the bin indexes of xmin, xmax and peakcentre;
+#. Calcualte peak range, i.e., left and right boundary;
+#. If any peak boundary exceeds or too close to the boundary, there will be 2 methods to solve this issue;
+
+ #. If peak centre is restricted to given value, then the peak range will be from 1/6 to 5/6 of the given data points;
+ #. If peak centre is set to observed value, then the 3 leftmost data points will be used for background.
+
References
-##########
+----------
-#. M.A.Mariscotti, *A method for automatic identification of peaks in
- the presence of background and its application to spectrum analysis*,
- NIM **50** (1967) 309.
-
-| ``==== Estimation of peak's background and range ====``
-| ``If FindPeaksBackground fails, then it is necessary to estimate a rough peak range and background according to``
-| ``observed data.``
-| ``1. Assume the local background (within the given fitting window) is close to linear;``
-| ``2. Take the first 3 and last 3 data points to calcualte the linear background;``
-| ``3. Remove background (rougly) and calcualte peak's height, width, and centre;``
-| ``4. If the peak centre (starting value) uses observed value, then set peakcentre to that value.  Otherwise, set it to given value;``
-| ``5. Get the bin indexes of xmin, xmax and peakcentre;``
-| ``6. Calcualte peak range, i.e., left and right boundary;``
-| ``7. If any peak boundary exceeds or too close to the boundary, there will be 2 methods to solve this issue;``
-| ``7.1 If peak centre is restricted to given value, then the peak range will be from 1/6 to 5/6 of the given data points;``
-| ``7.2 If peak centre is set to observed value, then the 3 leftmost data points will be used for background.``
-
-| ``==== References ====``
-| ``# M.A.Mariscotti, ``\ *``A`` ``method`` ``for`` ``automatic``
-``identification`` ``of`` ``peaks`` ``in`` ``the`` ``presence`` ``of``
-``background`` ``and`` ``its`` ``application`` ``to`` ``spectrum``
-``analysis``*\ ``, NIM ``\ **``50``**\ `` (1967) 309.``
+#. M.A.Mariscotti, *A method for automatic identification of peaks in the presence of background and its application to spectrum analysis , NIM 50 (1967) 309.*
.. categories::
diff --git a/Code/Mantid/docs/source/algorithms/FitPowderDiffPeaks-v1.rst b/Code/Mantid/docs/source/algorithms/FitPowderDiffPeaks-v1.rst
index eda542f3996129f492efe754e436c4618dd015c6..2ab58d8b154e388f0f3315b355c4858cb140e9c5 100644
--- a/Code/Mantid/docs/source/algorithms/FitPowderDiffPeaks-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/FitPowderDiffPeaks-v1.rst
@@ -16,13 +16,8 @@ It serves as the first step to fit/refine instrumental parameters that
will be introduced in `Le Bail Fit <Le Bail Fit>`__. The second step is
realized by algorithm RefinePowderInstrumentParameters.
-Version
-=======
-
-Current implementation of FitPowderDiffPeaks is version 2.
-
Peak Fitting Algorithms
-=======================
+-----------------------
Peak Fitting Mode
#################
@@ -60,17 +55,17 @@ the starting values of one peak will be the fitted peak profile
parameters of its right neighbour.
Use Cases
-=========
+---------
Several use cases are listed below about how to use this algorithm.
Use case 1: robust fitting
##########################
-| ``1. User wants to use the starting values of peaks parameters from input thermal neutron peak parameters such as Alph0, Alph1, and etc;``
-| ``2. User specifies the right most peak range and its Miller index;``
-| ``3. "FitPowderDiffPeaks" calculates Alpha, Beta and Sigma for each peak from parameter values from InstrumentParameterTable;``
-| ``4. "FitPowderDiffPeaks" fits peak parameters of each peak from high TOF to low TOF.``
+#. User wants to use the starting values of peaks parameters from input thermal neutron peak parameters such as Alph0, Alph1, and etc;
+#. User specifies the right most peak range and its Miller index;
+#. "FitPowderDiffPeaks" calculates Alpha, Beta and Sigma for each peak from parameter values from InstrumentParameterTable;
+#. "FitPowderDiffPeaks" fits peak parameters of each peak from high TOF to low TOF.
Use Case 2: Fitting Peak Parameters From Scratch
@@ -78,10 +73,8 @@ Use Case 2: Fitting Peak Parameters From Scratch
This is the extreme case such that
-| ``1. Input instrumental geometry parameters, including Dtt1, Dtt1t, Dtt2t, Zero, Zerot, Tcross and Width, have roughly-guessed values;``
-| ``2. There is no pre-knowledge for each peak's peak parameters, including Alpha, Beta, and Sigma.``
-
-
+#. Input instrumental geometry parameters, including Dtt1, Dtt1t, Dtt2t, Zero, Zerot, Tcross and Width, have roughly-guessed values;
+#. There is no pre-knowledge for each peak's peak parameters, including Alpha, Beta, and Sigma.
How to use algorithm with other algorithms
------------------------------------------
@@ -95,19 +88,16 @@ Example of Working With Other Algorithms
*FitPowderDiffPeaks* is designed to work with other algorithms, such
*RefinePowderInstrumentParameters*, and *LeBailFit*. See `Le Bail
-Fit <Le Bail Fit>`__ for full list of such algorithms.
+Fit <http://www.mantidproject.org/Le_Bail_Fit>`_ for full list of such algorithms.
A common scenario is that the starting values of instrumental geometry
related parameters (Dtt1, Dtt1t, and etc) are enough far from the real
values.
-| ``1. "FitPowderDiffPeaks" fits the single peaks from high TOF region in robust mode;``
-| ``2. "RefinePowderInstrumentParameters" refines the instrumental geometry related parameters by using the d-TOF function;``
-| ``3. Repeat step 1 and 2 for more single peaks incrementally. The predicted peak positions are more accurate in this step.``
-
+#. "FitPowderDiffPeaks" fits the single peaks from high TOF region in robust mode;
+#. "RefinePowderInstrumentParameters" refines the instrumental geometry related parameters by using the d-TOF function;
+#. Repeat step 1 and 2 for more single peaks incrementally. The predicted peak positions are more accurate in this step.
-Usage
------
.. categories::
diff --git a/Code/Mantid/docs/source/algorithms/GetEi-v1.rst b/Code/Mantid/docs/source/algorithms/GetEi-v1.rst
index 0b1facaa57a53b346ee1b89fe56b94ea8924c983..82845da4cbe0bc351b4d6c3aa71c40b46e6ae564 100644
--- a/Code/Mantid/docs/source/algorithms/GetEi-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/GetEi-v1.rst
@@ -9,8 +9,7 @@
Description
-----------
-Uses :math:`E=\frac{1}{2}mv^2`
-to calculate the energy of neutrons leaving the
+Uses :math:`E=\frac{1}{2}mv^2` to calculate the energy of neutrons leaving the
source. The velocity is calculated from the time it takes for the
neutron pulse to travel between the two monitors whose spectra were
specified.
@@ -48,7 +47,6 @@ The distances between the monitors are read from the instrument
definition file. It is assumed that the source and the monitors all lie
on one line and that the monitors have the same delay time.
-=======
.. warning::
This version is an older algorithm and is no longer in current use, although
diff --git a/Code/Mantid/docs/source/algorithms/InvertMask-v1.rst b/Code/Mantid/docs/source/algorithms/InvertMask-v1.rst
index 2012255db007aa5d0a98aa4e272e6376a845cfe4..0c645186b64b05f89527274f03b78e2e5f0c4001 100644
--- a/Code/Mantid/docs/source/algorithms/InvertMask-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/InvertMask-v1.rst
@@ -49,11 +49,6 @@ Usage
print "Source Mask workspace # Detectors masked = ", nummasked
print "Source Mask workspace # Detectors masked = ", nummasked2
-.. cleantestcode:: ExInvertPG3
-
- DeleteWorkspace(maskws)
- DeleteWorkspace(invmaskws)
-
Output:
.. testoutput:: ExInvertPG3
diff --git a/Code/Mantid/docs/source/algorithms/LoadParameterFile-v1.rst b/Code/Mantid/docs/source/algorithms/LoadParameterFile-v1.rst
index 559b44a5560a1f00821ee784f43d7d3f28fba49f..eb53c17ad839d534382af7be8c283e4ef37c4cf7 100644
--- a/Code/Mantid/docs/source/algorithms/LoadParameterFile-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/LoadParameterFile-v1.rst
@@ -9,16 +9,16 @@
Description
-----------
-.. role:: xml(code)
- :language: xml
+.. role:: xml(literal)
+ :class: highlight
This algorithm allows instrument parameters to be specified in a
separate file from the `IDF <http://www.mantidproject.org/InstrumentDefinitionFile>`__. The required
format for this file is identical to that used for defining parameters
-through :xml:`<component-link>` s in an
-`IDF <http://www.mantidproject.org/InstrumentDefinitionFile>`__. Below is an example of how to define a parameter
+through :xml:`<component-link>` tags in an
+`IDF <http://www.mantidproject.org/InstrumentDefinitionFile>`_. Below is an example of how to define a parameter
named 'test' to be associated with a component named 'bank\_90degnew'
-defined in the `IDF <http://www.mantidproject.org/InstrumentDefinitionFile>`__ of the HRPD instrument:
+defined in the `IDF <http://www.mantidproject.org/InstrumentDefinitionFile>`_ of the HRPD instrument:
.. code-block:: xml
diff --git a/Code/Mantid/docs/source/algorithms/LoadSQW-v1.rst b/Code/Mantid/docs/source/algorithms/LoadSQW-v1.rst
index 4fdae35008c8ef06753678fa64f37915fbd224d0..057e1744c9bdc13d4e7ae8b1d02da569bf026794 100644
--- a/Code/Mantid/docs/source/algorithms/LoadSQW-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/LoadSQW-v1.rst
@@ -34,8 +34,7 @@ Sqw objects comes in two flavours:
The former has the four main fields fully filled. The fields description
is given below. The latter has:
-- **main\_header**, **header**, **detpar** as empty structures (0x0
-struct array with no fields)
+- **main\_header**, **header**, **detpar** as empty structures (0x0 struct array with no fields)
- data.urange and data.pix do not exist.
@@ -47,37 +46,38 @@ DND-type object can not be currently read or understood by Mantid.
Structure of sqw class with remarks on what is currently used and what is ignored
#################################################################################
-String started by:
-
-| ``%Â --Â ignored``
-| ``*Â --Â used``
-
-| ``Â ``\ **``Main_header``**\ ``:``
-| `` %   main_headerfilename   Name of sqw file that is being read, excluding path``
-| `` %   main_headerfilepath   Path to sqw file that is being read, including terminating file separator``
-| `` %   main_headertitle      Title of sqw data structure``
-| `` %   main_headernfiles     Number of spe files that contribute to the sqw object``
-
-| `` ``\ **``Header``**\ ``: (scalar structure, or cellarray of scalar structures if more than one spe file)``
-| `` %   header{i}.filename   Name of sqw file excluding path``
-| `` %   header{i}.filepath   Path to sqw file including terminating file separator``
-| `` %   header{i}.efix       Fixed energy (ei or ef depending on emode)``
-| `` %   header{i}.emode      Emode=1 direct geometry, =2 indirect geometry, =0 if diffraction ''' Only emode 1 have ever been tried '''``
-| `` %   header{i}.alatt      Lattice parameters (Angstroms)``
-| `` %   header{i}.angdeg     Lattice angles (deg)``
-| `` %   header{i}.cu         First vector defining scattering plane (r.l.u.)``
-| `` %   header{i}.cv         Second vector defining scattering plane (r.l.u.)``
-| `` %   header{i}.psi        Orientation angle (rad)``
-| `` %   header{i}.omega      --|``
-| `` %   header{i}.dpsi         |  Crystal misorientation description (rad)``
-| `` %   header{i}.gl           |  (See notes elsewhere e.g. Tobyfit manual``
-| `` %   header{i}.gs         --|``
-| `` %   header{i}.en         Energy bin boundaries (meV) in the input spe file [column vector]``
-| `` %   header{i}.uoffset    Offset of origin of pixel projection axes in r.l.u. and energy i.e. [h; k; l; en] [column vector]``
-| `` %   header{i}.u_to_rlu   Matrix (4x4) of pixel projection axes in hkle representation``
-| `` %                      u(:,1) first vector - u(1:3,1) r.l.u., u(4,1) energy etc.``
-| `` %   header{i}.ulen       Length of pixel projection axes vectors in Ang^-1 or meV [row vector]``
-| `` %   header{i}.ulabel     Labels of the pixel projection axes [1x4 cell array of character strings]``
+::
+
+ String started by:
+ % -- ignored
+ * -- used
+
+ Main_header:
+ % main_headerfilename Name of sqw file that is being read, excluding path
+ % main_headerfilepath Path to sqw file that is being read, including terminating file separator
+ % main_headertitle Title of sqw data structure
+ % main_headernfiles Number of spe files that contribute to the sqw object
+
+ Header: (scalar structure, or cellarray of scalar structures if more than one spe file)
+ % header{i}.filename Name of sqw file excluding path
+ % header{i}.filepath Path to sqw file including terminating file separator
+ % header{i}.efix Fixed energy (ei or ef depending on emode)
+ % header{i}.emode Emode=1 direct geometry, =2 indirect geometry, =0 if diffraction ''' Only emode 1 have ever been tried '''
+ % header{i}.alatt Lattice parameters (Angstroms)
+ % header{i}.angdeg Lattice angles (deg)
+ % header{i}.cu First vector defining scattering plane (r.l.u.)
+ % header{i}.cv Second vector defining scattering plane (r.l.u.)
+ % header{i}.psi Orientation angle (rad)
+ % header{i}.omega --|
+ % header{i}.dpsi | Crystal misorientation description (rad)
+ % header{i}.gl | (See notes elsewhere e.g. Tobyfit manual
+ % header{i}.gs --|
+ % header{i}.en Energy bin boundaries (meV) in the input spe file [column vector]
+ % header{i}.uoffset Offset of origin of pixel projection axes in r.l.u. and energy i.e. [h; k; l; en] [column vector]
+ % header{i}.u_to_rlu Matrix (4x4) of pixel projection axes in hkle representation
+ % u(:,1) first vector - u(1:3,1) r.l.u., u(4,1) energy etc.
+ % header{i}.ulen Length of pixel projection axes vectors in Ang^-1 or meV [row vector]
+ % header{i}.ulabel Labels of the pixel projection axes [1x4 cell array of character strings]
The pixel projection axes, u1, u2, u3 are the orthonormal vectors of the
crystal Cartesian coordinate frame i.e. u1 \|\| a\*, u2 in plane of a\*,
@@ -85,63 +85,65 @@ and b\*, and u3 \|\| a\* x b\*. They form the coordinate frame in which
the pixel coordinates are stored in data.pix. The pixel projection axes
must necessarily be identical for all contributing spe files.
-| ``Â ``\ **``Detpar``**\ ``:``
-| `` %   detpar.filename    Name of file excluding path``
-| `` %   detpar.filepath    Path to file including terminating file separator``
-| `` %   detpar.group       Row vector of detector group number``
-| `` %   detpar.x2          Row vector of secondary flightpaths (m)``
-| `` %   detpar.phi         Row vector of scattering angles (deg)``
-| `` %   detpar.azim        Row vector of azimuthal angles (deg)``
-| `` %                  (West bank=0 deg, North bank=90 deg etc.)``
-| `` %   detpar.width       Row vector of detector widths (m)``
-| `` %   detpar.height      Row vector of detector heights (m)``
-
-| ``Â ``\ **``Data``**\ ``:``
-| `` %   data.filename   Name of sqw file that is being read, excluding path``
-| `` %   data.filepath   Path to sqw file that is being read, including terminating file separator``
-| `` %   data.title      Title of sqw data structure``
-| `` *   data.alatt      Lattice parameters for data field (Ang^-1)``
-| `` *   data.angdeg     Lattice angles for data field (degrees)``
-| `` %   data.uoffset    Offset of origin of projection axes in r.l.u. and energy ie. [h; k; l; en] [column vector]``
-| `` %   data.u_to_rlu   Matrix (4x4) of projection axes in hkle representation``
-| `` %                      u(:,1) first vector - u(1:3,1) r.l.u., u(4,1) energy etc.``
-| `` %   data.ulen       Length of projection axes vectors in Ang^-1 or meV [row vector]``
-| `` %   data.ulabel     Labels of the projection axes [1x4 cell array of character strings]``
-| `` %   data.iax        Index of integration axes into the projection axes  [row vector]``
-| `` %                  Always in increasing numerical order``
-| `` %                       e.g. if data is 2D, data.iax=[1,3] means summation has been performed along u1 and u3 axes``
-| `` %   data.iint       Integration range along each of the integration axes. [iint(2,length(iax))]``
-| `` %                       e.g. in 2D case above, is the matrix vector [u1_lo, u3_lo; u1_hi, u3_hi]``
-| `` %   data.pax        Index of plot axes into the projection axes  [row vector]``
-| `` %                  Always in increasing numerical order``
-| `` %                       e.g. if data is 3D, data.pax=[1,2,4] means u1, u2, u4 axes are x,y,z in any plotting``
-| `` %                                       2D, data.pax=[2,4]     "   u2, u4,    axes are x,y   in any plotting``
-| `` %   data.p          Call array containing bin boundaries along the plot axes [column vectors]``
-| `` %                       i.e. row cell array {data.p{1}, data.p{2} ...} (for as many axes as length of data.pax)``
-| `` %   data.dax        Index into data.pax of the axes for display purposes. For example we may have ``
-| `` %                  data.pax=[1,3,4] and data.dax=[3,1,2] This means that the first display axis is data.pax(3)=4,``
-| `` %                  the second is data.pax(1)=1, the third is data.pax(2)=3. The reason for data.dax is to allow``
-| `` %                  the display axes to be permuted but without the contents of the fields p, s,..pix needing to``
-| `` %                  be reordered [row vector]``
-| `` -----> Large data fields, data for MD image``
-| `` %   data.s          Cumulative signal.  [size(data.s)=(length(data.p1)-1, length(data.p2)-1, ...)]``
-| `` %   data.e          Cumulative variance [size(data.e)=(length(data.p1)-1, length(data.p2)-1, ...)]``
-| `` %   data.npix       No. contributing pixels to each bin of the plot axes.``
-| `` %                  [size(data.pix)=(length(data.p1)-1, length(data.p2)-1, ...)]``
-| ``Â ----->Â ``
-| `` *   data.urange     True range of the data along each axis [urange(2,4)] ``
-| `` ----> Pixels or events data ``
-| `` *   data.pix        Array containing data for each pixel:``
-| `` *                  If npixtot=sum(npix), then pix(9,npixtot) contains:``
-| ``Â *Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â u1Â Â Â Â Â Â -|``
-| `` *                   u2       |  Coordinates of pixel in the pixel projection axes``
-| ``Â *Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â u3Â Â Â Â Â Â Â |``
-| ``Â *Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â u4Â Â Â Â Â Â -|``
-| `` *                   irun        Run index in the header block from which pixel came``
-| `` *                   idet        Detector group number in the detector listing for the pixel``
-| `` *                   ien         Energy bin number for the pixel in the array in the (irun)th header``
-| `` *                   signal      Signal array``
-| `` *                   err         Error array (variance i.e. error bar squared)``
+::
+
+ \ **Detpar**\ :
+ % detpar.filename Name of file excluding path
+ % detpar.filepath Path to file including terminating file separator
+ % detpar.group Row vector of detector group number
+ % detpar.x2 Row vector of secondary flightpaths (m)
+ % detpar.phi Row vector of scattering angles (deg)
+ % detpar.azim Row vector of azimuthal angles (deg)
+ % (West bank=0 deg, North bank=90 deg etc.)
+ % detpar.width Row vector of detector widths (m)
+ % detpar.height Row vector of detector heights (m)
+
+ \ **Data**\ :
+ % data.filename Name of sqw file that is being read, excluding path
+ % data.filepath Path to sqw file that is being read, including terminating file separator
+ % data.title Title of sqw data structure
+ * data.alatt Lattice parameters for data field (Ang^-1)
+ * data.angdeg Lattice angles for data field (degrees)
+ % data.uoffset Offset of origin of projection axes in r.l.u. and energy ie. [h; k; l; en] [column vector]
+ % data.u_to_rlu Matrix (4x4) of projection axes in hkle representation
+ % u(:,1) first vector - u(1:3,1) r.l.u., u(4,1) energy etc.
+ % data.ulen Length of projection axes vectors in Ang^-1 or meV [row vector]
+ % data.ulabel Labels of the projection axes [1x4 cell array of character strings]
+ % data.iax Index of integration axes into the projection axes [row vector]
+ % Always in increasing numerical order
+ % e.g. if data is 2D, data.iax=[1,3] means summation has been performed along u1 and u3 axes
+ % data.iint Integration range along each of the integration axes. [iint(2,length(iax))]
+ % e.g. in 2D case above, is the matrix vector [u1_lo, u3_lo; u1_hi, u3_hi]
+ % data.pax Index of plot axes into the projection axes [row vector]
+ % Always in increasing numerical order
+ % e.g. if data is 3D, data.pax=[1,2,4] means u1, u2, u4 axes are x,y,z in any plotting
+ % 2D, data.pax=[2,4] " u2, u4, axes are x,y in any plotting
+ % data.p Call array containing bin boundaries along the plot axes [column vectors]
+ % i.e. row cell array {data.p{1}, data.p{2} ...} (for as many axes as length of data.pax)
+ % data.dax Index into data.pax of the axes for display purposes. For example we may have
+ % data.pax=[1,3,4] and data.dax=[3,1,2] This means that the first display axis is data.pax(3)=4,
+ % the second is data.pax(1)=1, the third is data.pax(2)=3. The reason for data.dax is to allow
+ % the display axes to be permuted but without the contents of the fields p, s,..pix needing to
+ % be reordered [row vector]
+ -----> Large data fields, data for MD image
+ % data.s Cumulative signal. [size(data.s)=(length(data.p1)-1, length(data.p2)-1, ...)]
+ % data.e Cumulative variance [size(data.e)=(length(data.p1)-1, length(data.p2)-1, ...)]
+ % data.npix No. contributing pixels to each bin of the plot axes.
+ % [size(data.pix)=(length(data.p1)-1, length(data.p2)-1, ...)]
+ ----->
+ * data.urange True range of the data along each axis [urange(2,4)]
+ ----> Pixels or events data
+ * data.pix Array containing data for each pixel:
+ * If npixtot=sum(npix), then pix(9,npixtot) contains:
+ * u1 -|
+ * u2 | Coordinates of pixel in the pixel projection axes
+ * u3 |
+ * u4 -|
+ * irun Run index in the header block from which pixel came
+ * idet Detector group number in the detector listing for the pixel
+ * ien Energy bin number for the pixel in the array in the (irun)th header
+ * signal Signal array
+ * err Error array (variance i.e. error bar squared)
data.s is normalized by the number of pixels, as is the variance data.e.
For those elements where data.npix==0, data.s=0 and data.e=0
@@ -152,13 +154,13 @@ General notes about SQW file assumptions
Parts of the code were written with the idea of generalising
functionality at a later stage. However, we can now assume that:
-| `` - the lattice parameters are all the same for all contributing spe files``
-| `` - the energy offset is zero in cuts``
-| `` Requires that all sqw files that are to be combined have``
-| `` (1)   each been created from only one spe file``
-| `` (2)   the same lattice parameters and pixel projection axes as held in the header block``
-| `` (3)   the same projection axes and offsets, as held in the data block``
-| `` (4)   the same plot and integration axes, with same bins and integration ranges``
-| `` The display axes will be taken from the first sqw object in the list to be combined   ```
+- the lattice parameters are all the same for all contributing spe files
+- the energy offset is zero in cuts
+- requires that all sqw files that are to be combined have
+ #. each been created from only one spe file
+ #. the same lattice parameters and pixel projection axes as held in the header block
+ #. the same projection axes and offsets, as held in the data block
+ #. the same plot and integration axes, with same bins and integration ranges
+- the display axes will be taken from the first sqw object in the list to be combined
.. categories::
diff --git a/Code/Mantid/docs/source/algorithms/MaskPeaksWorkspace-v1.rst b/Code/Mantid/docs/source/algorithms/MaskPeaksWorkspace-v1.rst
index 3cbdc13bad8e4b2a80a4f327b4952eb749f834a3..7fbdac5fe09b7f2dd0f12b23a6577df8fb7bc29c 100644
--- a/Code/Mantid/docs/source/algorithms/MaskPeaksWorkspace-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/MaskPeaksWorkspace-v1.rst
@@ -19,13 +19,12 @@ Usage
**Example:**
-.. comment::
- To usage test this properly you need a matching dataset and peaks workspace,
- the unit tests do this, but that functionality is not available in algorithms.
- You could load files, but the basic data would be too big to download sensisbly.
- Therefore this is an untested code block just showing usage
+.. To usage test this properly you need a matching dataset and peaks workspace,
+ the unit tests do this, but that functionality is not available in algorithms.
+ You could load files, but the basic data would be too big to download sensisbly.
+ Therefore this is an untested code block just showing usage
-.. code:: python
+.. code-block:: python
#the files for this example are not available for download
#This is to illustrate usage only
diff --git a/Code/Mantid/docs/source/algorithms/MonteCarloAbsorption-v1.rst b/Code/Mantid/docs/source/algorithms/MonteCarloAbsorption-v1.rst
index 57dce38cdd82f9b48b76e92a71f81d80f9c912f9..9beab7ac1ca59dc8e2551c22acbb80a3336dc136 100644
--- a/Code/Mantid/docs/source/algorithms/MonteCarloAbsorption-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/MonteCarloAbsorption-v1.rst
@@ -77,7 +77,7 @@ Output:
.. Ticket 9644 is in place to improve the python exports and expand this example
-.. code:: python
+.. code-block:: python
# The algorithm does allow you to set a complex sample environment
# of different materials and shapes, but some of the required methods
diff --git a/Code/Mantid/docs/source/algorithms/PoldiProjectRun-v1.rst b/Code/Mantid/docs/source/algorithms/PoldiProjectRun-v1.rst
index fb591ee2c1ce4ab48d0700d7cafbac6817778e12..a772c99e14e8f82d6ac90f58c6629be7ea4221a3 100644
--- a/Code/Mantid/docs/source/algorithms/PoldiProjectRun-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/PoldiProjectRun-v1.rst
@@ -29,7 +29,7 @@ Manager <PoldiProjectRun#Data_Manager>`__ paragraph.
The algorithm is used the classical way. Only one parameter is
compulsory.
-.. code:: python
+.. code-block:: python
OutputWorkspace = PoldiProjectRun(InputWorkspace=sample_manager_ws)
@@ -91,7 +91,7 @@ sample-manager TableWorkspace.
The raw data are loaded in a 2DWorkspace, using the generic file-loader
for SINQ data, given the instrument name *POLDI* as parameter.
-.. code:: python
+.. code-block:: python
LoadSINQFile(Instrument = "POLDI",
Filename = sample_file_path,
@@ -106,7 +106,7 @@ information. More specifically, the acquisition starting time is
extracted and store in the sample WS to initialize the *run\_start*
variable.
-.. code:: python
+.. code-block:: python
PoldiLoadLog(InputWorkspace = sample_output_ws,
Filename = sample_file_path,
@@ -118,7 +118,7 @@ variable.
For each raw data WS, the corresponding IDF is loaded, based on the
acquisition starting time.
-.. code:: python
+.. code-block:: python
LoadInstrument(Workspace = sample_output_ws,
InstrumentName = "Poldi",
@@ -135,7 +135,7 @@ should not differ more than *BadWiresThreshold*\ (\*100)%. One by one,
the most deviant wires are checks and removed until they all fit the
condition.
-.. code:: python
+.. code-block:: python
PoldiRemoveDeadWires(InputWorkspace = sample_output_ws,
RemoveExcludedWires = True,
@@ -156,7 +156,7 @@ they are now all extracted, using an example sample for each of them.
The chopper configuration is loaded in a dedicated Workspace, one per
*Poldi IPP* setup detected.
-.. code:: python
+.. code-block:: python
PoldiLoadChopperSlits(InputWorkspace = ex_of_sample_ws,
PoldiChopperSlits = ipp_chopper_slits)
@@ -166,7 +166,7 @@ The chopper configuration is loaded in a dedicated Workspace, one per
The characteristic Poldi spectra (*Intensity=f(wavelength)*) is
extracted from each IDF.
-.. code:: python
+.. code-block:: python
PoldiLoadSpectra(InputWorkspace = ex_of_sample_ws,
PoldiSpectra = ipp_Poldi_spectra)
@@ -176,7 +176,7 @@ extracted from each IDF.
Local setup information (such as the detector position, chopper offset,
etc...) are extracted and stores in a dedicated workspace.
-.. code:: python
+.. code-block:: python
PoldiLoadIPP(InputWorkspace = ex_of_sample_ws,
PoldiIPP = ipp_ipp_data)
@@ -211,7 +211,7 @@ the previously created *sample\_correlated\_ws*: on row (1) the detected
peak, on row (2) the fitted peak.
-.. code:: python
+.. code-block:: python
PoldiPeakDetection(InputWorkspace = sample_correlated_ws,
PeakDetectionThreshold = PeakDetectionThreshold,
diff --git a/Code/Mantid/docs/source/algorithms/PredictFractionalPeaks-v1.rst b/Code/Mantid/docs/source/algorithms/PredictFractionalPeaks-v1.rst
index e4116219d509ff05870160d36b3ec8b6eaa866be..e42ee0405d39092f6e4b3f8a765af73ce42c8e4d 100644
--- a/Code/Mantid/docs/source/algorithms/PredictFractionalPeaks-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/PredictFractionalPeaks-v1.rst
@@ -29,7 +29,7 @@ Usage
.. This test is not run at the moment as it creates an exception in python. Ticket 9642 is in place to fix this and reinstate the test
-.. code:: Python
+.. code-block:: python
ws=LoadIsawPeaks("TOPAZ_3007.peaks")
LoadIsawUB(ws,"ls5637.mat")
diff --git a/Code/Mantid/docs/source/algorithms/Q1D-v2.rst b/Code/Mantid/docs/source/algorithms/Q1D-v2.rst
index 4bc467f4deab1e1e3a176f27fbe2f543d9fd01e8..0fe23cefa3a364e467932f808b6ea576e5ccc625 100644
--- a/Code/Mantid/docs/source/algorithms/Q1D-v2.rst
+++ b/Code/Mantid/docs/source/algorithms/Q1D-v2.rst
@@ -49,8 +49,12 @@ is calculated from the sum of all input wavelength bins, n, that
evaluate to the same Q using the formula for Q at the top of this page.
In equations this relationship between the input bins and the output
bins is represented by :math:`n \supset I` and an example of a set of
-two bins is shown diagrammatically below. |Each Q bin contains the sum
-of many, one, or no wavelength bins\|centre|
+two bins is shown diagrammatically below.
+
+.. figure:: /images/Wav_Q_bins.png
+ :align: center
+
+ Each Q bin contains the sum of many, one, or no wavelength bins
In the equation the number of counts in the input spectrum number is
denoted by :math:`S(n)`, :math:`N(n)` is the wavelength dependent
@@ -203,6 +207,4 @@ Properties
| 5 | AccountForGravity | Input | Boolean | False | Whether to correct for the effects of gravity. |
+---------+---------------------+-------------+-------------------+-------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------+
-.. |Each Q bin contains the sum of many, one, or no wavelength bins\|centre| image:: /images/Wav_Q_bins.png
-
.. categories::
diff --git a/Code/Mantid/docs/source/algorithms/Q1DWeighted-v1.rst b/Code/Mantid/docs/source/algorithms/Q1DWeighted-v1.rst
index 9da2a77079b4c1f620078158b93a7c4140ab673c..8e9c1ddf6c32b6765f84a6303a14f62d98fe76f0 100644
--- a/Code/Mantid/docs/source/algorithms/Q1DWeighted-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/Q1DWeighted-v1.rst
@@ -12,23 +12,20 @@ Description
Performs azimuthal averaging for a 2D SANS data set by going through
each detector pixel, determining its Q-value, and adding its amplitude
:math:`I` to the appropriate Q bin. For greater precision, each detector
-pixel can be sub-divided in sub-pixels by setting the *NPixelDivision*
+pixel can be sub-divided in sub-pixels by setting the ``NPixelDivision``
parameters. Each pixel has a weight of 1 by default, but the weight of
each pixel can be set to :math:`1/\Delta I^2` by setting the
-*ErrorWeighting* parameter to True.
+``ErrorWeighting`` parameter to True.
-See the :ref:`algm-Rebin`__ documentation for
-details about choosing the *OutputBinning* parameter.
+See the :ref:`Rebin <algm-Rebin>` documentation for details about choosing the ``OutputBinning`` parameter.
-See `SANS
-Reduction <http://www.mantidproject.org/Reduction_for_HFIR_SANS>`__
+See `SANSReduction <http://www.mantidproject.org/Reduction_for_HFIR_SANS>`__
documentation for calculation details.
Usage
-----
-This algorithm is not intended to be run individually, rather as a part of the `SANS
-Reduction <http://www.mantidproject.org/Reduction_for_HFIR_SANS>`__.
+This algorithm is not intended to be run individually, rather as a part of the `SANSReduction <http://www.mantidproject.org/Reduction_for_HFIR_SANS>`_.
.. categories::
diff --git a/Code/Mantid/docs/source/algorithms/RadiusSum-v1.rst b/Code/Mantid/docs/source/algorithms/RadiusSum-v1.rst
index 737e72f74d4549bd186fb1b44f1fbeebdd828ec8..9245a89e7a1f7c07c78d9547bb2bb35353822099 100644
--- a/Code/Mantid/docs/source/algorithms/RadiusSum-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/RadiusSum-v1.rst
@@ -16,16 +16,12 @@ Workspace2D where the position of the pixels are not associated to
detector positions, but it is derived from the Axes.
.. figure:: /images/ExecuteRadiusSum.png
- :alt: 800px
- 800px
The image below shows a visual interpretation for the inputs of the
algorithm
.. figure:: /images/RadiusSumInputs.png
- :alt: 300px
- 300px
The Algorithm create **NumBins** rings around the **Centre** point each
one with :math:`width = BinSize` for
:math:`BinSize=\frac{MaxRadius-MinRadius}{NumBins}`.
@@ -38,16 +34,11 @@ below, shows what does this means. An ideal solution for RadiusSum is
the left image, while the right image is what is current implemented.
.. figure:: /images/RadiusSumSolutions.png
- :alt: 300px
- 300px
Although the images were applied to an image
`Workspace2D <http://www.mantidproject.org/Workspace2D>`_, the image below shows that it is possible
to apply this algorithm to Workspaces attached to instruments.
.. figure:: /images/RadiusSumInstrument.png
- :alt: 800 px
-
- 800 px
.. categories::
diff --git a/Code/Mantid/docs/source/algorithms/ResizeRectangularDetector-v1.rst b/Code/Mantid/docs/source/algorithms/ResizeRectangularDetector-v1.rst
index 64c87ac20fe418257de5fe1c64524569a9f43347..456bbfc064c99135f7524af01f1a93a516bbd861 100644
--- a/Code/Mantid/docs/source/algorithms/ResizeRectangularDetector-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/ResizeRectangularDetector-v1.rst
@@ -52,6 +52,7 @@ Usage
print ("bank 1 was scaled and is now %.2f by %.2f" % (bank1.xsize(), bank1.ysize()))
print ("bank 2 was not scaled and remains %.2f by %.2f" % (bank2.xsize(), bank2.ysize()))
+
Output:
.. testoutput:: ExScaleBank1
diff --git a/Code/Mantid/docs/source/algorithms/RetrieveRunInfo-v1.rst b/Code/Mantid/docs/source/algorithms/RetrieveRunInfo-v1.rst
index 1e9a2a1e81b1f8a7422397b4cf7d49c5272012ff..7e40b66034bba6ae7d4ebdce58fd776ca58af90c 100644
--- a/Code/Mantid/docs/source/algorithms/RetrieveRunInfo-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/RetrieveRunInfo-v1.rst
@@ -22,6 +22,7 @@ result table.
Output workspace generated by inspecting runs 12218-12229 and having
the default instrument set to TOSCA.
+
Limitations
-----------
diff --git a/Code/Mantid/docs/source/algorithms/SaveGSASInstrumentFile-v1.rst b/Code/Mantid/docs/source/algorithms/SaveGSASInstrumentFile-v1.rst
index 53727556063a53b60cbc8427e2b6ee1bc1e7bcf6..15cea7377bd2c7c0c7e8a9e87e56d266cd2a7831 100644
--- a/Code/Mantid/docs/source/algorithms/SaveGSASInstrumentFile-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/SaveGSASInstrumentFile-v1.rst
@@ -42,9 +42,9 @@ There are several places in this algorithm that can set the value of
:math:`2\theta`. From the highest priority, here is the list how
:math:`2\theta` is set up.
-| ``1. Algorithms' input property "TwoTheta";``
-| ``2. Either input TableWorkspace or input Fullprof resolution (.irf) file;``
-| ``3. Hard coded default "TwoTheta" of a certain instrument.``
+1. Algorithms' input property ``TwoTheta``;
+2. Either input TableWorkspace or input Fullprof resolution (.irf) file;
+3. Hard coded default "TwoTheta" of a certain instrument.
Set up :math:`L_1`
##################
@@ -53,8 +53,8 @@ There are 2 places in this algorithm that can set the value of
:math:`L_1`. From the highest priority, here is the list how
:math:`2\theta` is set up.
-| ``1. Algorithms' input property "L1"; ``
-| ``2. Hard coded default "TwoTheta" of a certain instrument.``
+1. Algorithms' input property ``L1``;
+2. Hard coded default "TwoTheta" of a certain instrument.
Calculation of :math:`L_2`
##########################
diff --git a/Code/Mantid/docs/source/algorithms/SaveMask-v1.rst b/Code/Mantid/docs/source/algorithms/SaveMask-v1.rst
index 97ae11d1cae3e4777860cf8ad0ebb63cb150c280..c398c9b829b52e0b22f14ee3ea51baef3716fbfc 100644
--- a/Code/Mantid/docs/source/algorithms/SaveMask-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/SaveMask-v1.rst
@@ -18,13 +18,13 @@ file. This algorithm has previously been renamed from SaveDetectorMasks.
There are two types of mask workspace that can serve as input.
1. `MaskWorkspace <http://www.mantidproject.org/MaskWorkspace>`__
-####################################
+##################################################################
In this case, :ref:`algm-SaveMask` will read Y values to determine
which detectors are masked;
2. A non-\ `MaskWorkspace <http://www.mantidproject.org/MaskWorkspace>`__ `MatrixWorkspace <http://www.mantidproject.org/MatrixWorkspace>`__ containing `Instrument <http://www.mantidproject.org/Instrument>`__
-#########################################################################################################################
+################################################################################################################################################################################################################
In this case, :ref:`algm-SaveMask` will scan through all detectors to
determine which are masked.
@@ -32,11 +32,11 @@ determine which are masked.
Definition of Mask
------------------
-If a pixel is **masked**, it means that the data from this pixel won't be used.
-In the masking workspace (i.e., `SpecialWorkspace2D <http://www.mantidproject.org/SpecialWorkspace2D>`__), the corresponding value is 1.Â
+If a pixel is **masked**, it means that the data from this pixel won't be used.
+In the masking workspace (i.e., `SpecialWorkspace2D <http://www.mantidproject.org/SpecialWorkspace2D>`__), the corresponding value is 1.
-If a pixel is **NOT masked**, it means that the data from this pixel will be used.  ``
-In the masking workspace (i.e., `SpecialWorkspace2D <http://www.mantidproject.org/SpecialWorkspace2D>`__), the corresponding value is 0.
+If a pixel is **NOT masked**, it means that the data from this pixel will be used. ``
+In the masking workspace (i.e., `SpecialWorkspace2D <http://www.mantidproject.org/SpecialWorkspace2D>`__), the corresponding value is 0.
XML File Format
---------------
@@ -45,13 +45,13 @@ Example 1:
.. code-block:: xml
- <?xml version="1.0" encoding="UTF-8" ?>
- <detector-masking">
- <group">
- <detids>3,34-44,47</detids>
- <component>bank123</component>
- <component>bank124</component>
- </group>
- </detector-masking>
+ <?xml version="1.0" encoding="UTF-8" ?>
+ <detector-masking">
+ <group">
+ <detids>3,34-44,47</detids>
+ <component>bank123</component>
+ <component>bank124</component>
+ </group>
+ </detector-masking>
.. categories::
diff --git a/Code/Mantid/docs/source/algorithms/UserFunction1D-v1.rst b/Code/Mantid/docs/source/algorithms/UserFunction1D-v1.rst
index 3121153c0e88092fce3886c339957a2f12a47da7..954f06c9652b73fff5132887a0a710afd365d6f9 100644
--- a/Code/Mantid/docs/source/algorithms/UserFunction1D-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/UserFunction1D-v1.rst
@@ -72,7 +72,7 @@ underscore symbol '\_'. The internal functions are:
| avg | var. | mean value of all arguments |
+---------+---------+-------------------------------------+
-An example of *Function* property is "a + b\*x + c\*x^2". Valiable *x*
+An example of *Function* property is "a + b\*x + c\*x^2". Variable *x*
is used to represent the values of the X-vector of the input spectrum.
All other variable names are treated as fitting parameters. A parameter
can be given an initial value in the *InitialParameters* property. For
@@ -82,7 +82,7 @@ with 0.0. If some of the parameters should be fixed in the fit list them
in the *Fix* property in any order, e.g. "a,c".
The resulting parameters are returned in a
-`TableWorkspace <http://www.mantidproject.org/TableWorkspace>`_ set in *OutputParameters* property.
+`TableWorkspace <http://www.mantidproject.org/TableWorkspace>`_ set in ``OutputParameters`` property.
Also for displaying purposes *OutputWorkspace* is returned. It contains
the initial spectrum, the fitted spectrum and their difference.
@@ -90,9 +90,7 @@ Example
-------
.. figure:: /images/UserFunction1D.gif
- :alt: UserFunction1D.gif
- UserFunction1D.gif
In this example the fitting function is a\*exp(-(x-c)^2\*s). The
parameter *s* is fixed.