Algorithm Usage Examples

Introduction

A usage example is part of the documentation page of an algorithm.

From a user’s point of view, the main purposes of usage examples are:

  • Getting started using the algorithm as part of a Python script
  • Understanding the algorithm
  • Showing hints/comments etc. that help understand Mantid Python scripting in general

The usage examples are written in reStructuredText, which can be converted to HTML and the code in the usage examples can be tested.

Guide

The example below show the proposed way to format an usage example in reStructuredText.

Usage
-----

**Example - simple rebin of a histogram workspace:**

.. testcode:: ExHistSimple

   # create histogram workspace
   dataX = [0,1,2,3,4,5,6,7,8,9] # or use dataX=range(0,10)
   dataY = [1,1,1,1,1,1,1,1,1] # or use dataY=[1]*9
   ws = CreateWorkspace(dataX, dataY)

   # rebin from min to max with size bin = 2
   ws = Rebin(ws, 2)

   print "The rebinned X values are: " + str(ws.readX(0))
   print "The rebinned Y values are: " + str(ws.readY(0))


Output:

.. testoutput:: ExHistSimple

   The rebinned X values are: [ 0.  2.  4.  6.  8.  9.]
   The rebinned Y values are: [ 2.  2.  2.  2.  1.]

What is required is:

  • Short description explaining the example, formatted as shown above, i.e. using ** to embolden the text.
  • A .. testcode:: section, with a unique ‘namespace’ name, here ExHistSimple. This ‘namespace’ is not shown when converted to HTML, but is used in testing the code. This section contains the actual Python code demonstrating a usage of the algorithm. This code block contains commented code, finishing with one or more Python print lines as shown
  • A .. testoutput:: section. This section must have a matching ‘namespace’ name to the ..testcode:: section. It simply contains a copy of the text that is printed out in the ..testcode:: section.
  • Include the “Output:” string above the ..testoutput:: directive.

What is optional:

  • A ..testcleanup:: section. This section must have a matching ‘namespace’ name to the ..testcode:: section. Here, add Python code to do any cleanup of files etc. that were created by the tests. See the notes below for things that are cleaned automatically.

Notes:

  • The configuration has a global “testcleanup” implemented which calls FrameworkManager::clear() to clear algorithms, workspaces & instruments so these are dealt with automatically.
  • There must be a clear blank line before the .. testcode:: and .. testoutput directives or the test is ignored. As with unit tests you should write a failing test first to ensure it is running.

What is worth keeping in mind is:

  • Assume the user is new to Python. Consider giving hints to more advanced Python in comments, or introduce a simple example first.
  • Use comments.
  • Use Python print to output results, which, where possible, helps to understand the algorithm.

A Jenkins job tests that the usage examples are not broken, i.e. that they continue to provide a working demonstration against the current build. It is vital to stress that the purpose of usage testing is not to replace unit testing (or system testing). The purpose of usage testing (better described as demonstration examples), is to provide some happy-path examples, which, where this is possible, can assist the user understanding of the Python code. This is very different from the purposes of testing in general, see here.

Additional benefits of usage examples:

  • Quick look-up for developers on how to use a certain algorithm in Python scripting
  • Allow the user to test that scripts return expected output in their installed Mantid versions
  • Additional test coverage of Mantid Python API

Using CreateSampleWorkspace and CreateWorkspace

There are many ways to create sample workspaces. For example CreateMDHistoWorkspace, CreateSampleWorkspace and CreateWorkspace. CreateSampleWorkspace creates a fully defined workspace (either event or histogram) but for creating simple histogram workspace CreateWorkspace may be a better option. Above is shown an example where CreateWorkspace is used. Below is a more complex use of CreateSampleWorkspace:

Usage
-----

**Example - Fit a Gaussian to a peak in a spectrum:**

.. testcode:: ExFitPeak

   # create a workspace with a gaussian peak sitting on top of a linear (here flat) background
   ws = CreateSampleWorkspace(Function="User Defined", UserDefinedFunction="name=LinearBackground, \
      A0=0.3;name=Gaussian, PeakCentre=5, Height=10, Sigma=0.7", NumBanks=1, BankPixelWidth=1, XMin=0, XMax=10, BinWidth=0.1)

   # Setup the data to fit:
   workspaceIndex = 0  # the spectrum with which WorkspaceIndex to fit
   startX = 1      # specify fitting region
   endX = 9      #

   # Setup the model, here a Gaussian, to fit to data
   tryCentre = '4'   # A start guess on peak centre
   sigma = '1'          # A start guess on peak width
   height = '8'         # A start guess on peak height
   myFunc = 'name=Gaussian, Height='+height+', PeakCentre='+tryCentre+', Sigma='+sigma
   # here purposely haven't included a linear background which mean fit will not be spot on
   # to include a linear background uncomment the line below
   #myFunc = 'name=LinearBackground, A0=0.3;name=Gaussian, Height='+height+', PeakCentre='+tryCentre+', Sigma='+sigma

   # Do the fitting
   fitStatus, chiSq, covarianceTable, paramTable, fitWorkspace = Fit(InputWorkspace='ws', \
      WorkspaceIndex=0, StartX = startX, EndX=endX, Output='fit', Function=myFunc)

   print "The fit was: " + fitStatus
   print("chi-squared of fit is: %.2f" % chiSq)
   print("Fitted Height value is: %.2f" % paramTable.column(1)[0])
   print("Fitted centre value is: %.2f" % paramTable.column(1)[1])
   print("Fitted sigma value is: %.2f" % paramTable.column(1)[2])
   # fitWorkspace contains the data, the calculated and the difference patterns
   print "Number of spectra in fitWorkspace is: " +  str(fitWorkspace.getNumberHistograms())
   print("The 20th y-value of the calculated pattern: %.4f" % fitWorkspace.readY(1)[19])

.. testcleanup:: ExFitPeak

   DeleteWorkspace(ws)

Output:

.. testoutput:: ExFitPeak

   The fit was: success
   chi-squared of fit is: 0.14
   Fitted Height value is: 9.79
   Fitted centre value is: 5.05
   Fitted sigma value is: 0.77
   Number of spectra in fitWorkspace is: 3
   The 20th y-value of the calculated pattern: 0.2361

For a more simple use of CreateSampleWorkspace see example below (note if no arguments are given then a histogram workspace is created):

Usage
-----

**Example - use option PreserveEvents:**

.. testcode:: ExEventRebin

   # create some event workspace
   ws = CreateSampleWorkspace(WorkspaceType="Event")

   print "What type is the workspace before 1st rebin: " + str(type(ws))
   # rebin from min to max with size bin = 2 preserving event workspace (default behaviour)
   ws = Rebin(ws, 2)
   print "What type is the workspace after 1st rebin: " + str(type(ws))
   ws = Rebin(ws, 2, PreserveEvents=False)
   print "What type is the workspace after 2nd rebin: " + str(type(ws))
   # note you can also check the type of a workspace using: print isinstance(ws, IEventWorkspace)

.. testcleanup:: ExEventRebin

   DeleteWorkspace(ws)

Output:

.. testoutput:: ExEventRebin

   What type is the workspace before 1st rebin: <class 'mantid.api._api.IEventWorkspace'>
   What type is the workspace after 1st rebin: <class 'mantid.api._api.IEventWorkspace'>
   What type is the workspace after 2nd rebin: <class 'mantid.api._api.MatrixWorkspace'>

When needing to load a data file

Instructions to add a new data file to the repository are available here. Files from the repository will be bundled up into a .zip file, and this .zip made available for download from the Mantid download page.

If you use files you must add the line

.. include:: ../usagedata-note.txt

as shown in the example below. This will generate a note to the user explaining how to download the UsageData.

Usage
-----

.. include:: ../usagedata-note.txt

**Example - Load ISIS histogram Nexus file:**
(see :ref:`LoadISISNexus <algm-LoadISISNexus>` for more options)

.. testcode:: ExLoadISISnexusHist

   # Load ISIS LOQ histogram dataset
   ws = Load('LOQ49886.nxs')

   print "The 1st x-value of the first spectrum is: " + str(ws.readX(0)[0])

.. testcleanup:: ExLoadISISnexusHist

   DeleteWorkspace(ws)

Output:

.. testoutput:: ExLoadISISnexusHist

   The 1st x-value of the first spectrum is: 5.0

Running the Tests

See here for how to run and test the usage examples locally.