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Fix a few more docs errors.
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Refs #9749
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@martyngigg
martyngigg committed Jun 25, 2014
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4 changes: 1 addition & 3 deletions Code/Mantid/docs/source/algorithms/GetEi-v1.rst
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Expand Up @@ -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.
Expand Down Expand Up @@ -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
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5 changes: 0 additions & 5 deletions Code/Mantid/docs/source/algorithms/InvertMask-v1.rst
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Expand Up @@ -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
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198 changes: 100 additions & 98 deletions Code/Mantid/docs/source/algorithms/LoadSQW-v1.rst
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Expand Up @@ -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.

Expand All @@ -47,101 +46,104 @@ 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:

| ``% -- 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]``
::

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\*,
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.

| `` ``\ **``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)``
::

\ **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
Expand All @@ -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::
9 changes: 4 additions & 5 deletions Code/Mantid/docs/source/algorithms/MaskPeaksWorkspace-v1.rst
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Expand Up @@ -19,11 +19,10 @@ 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-block:: python
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