re #9612 done 1-9 inclusive

Code/Mantid/docs/source/algorithms/AddLogDerivative-v1.rst

@@ -23,4 +23,50 @@ If any of the times in the logs are repeated, then those repeated time
 values will be skipped, and the output derivative log will have fewer
 points than the input.
 
+Usage
+-----
+
+**Example: Taking the derivative of logs**
+
+.. testcode:: AddLogDerivative
+
+    ws = CreateSampleWorkspace()
+    AddTimeSeriesLog(ws,"MyLog","2010-01-01T00:00:00",1.0,DeleteExisting=False)
+    AddTimeSeriesLog(ws,"MyLog","2010-01-01T00:00:10",2.0,DeleteExisting=False)
+    AddTimeSeriesLog(ws,"MyLog","2010-01-01T00:00:20",0.0,DeleteExisting=False)
+    AddTimeSeriesLog(ws,"MyLog","2010-01-01T00:00:30",5.0,DeleteExisting=False)
+
+    AddLogDerivative(ws,"MyLog",derivative=1,NewLogName="Derivative1")
+    AddLogDerivative(ws,"MyLog",derivative=2,NewLogName="Derivative2")
+    AddLogDerivative(ws,"MyLog",derivative=3,NewLogName="Derivative3")
+
+    for logName in ["MyLog","Derivative1","Derivative2","Derivative3"]:
+        print "Log: " + logName
+        print ws.getRun().getProperty(logName).valueAsString()
+
+
+Output:
+
+.. testoutput:: AddLogDerivative
+    :options: +NORMALIZE_WHITESPACE
+
+    Log: MyLog
+    2010-Jan-01 00:00:00  1
+    2010-Jan-01 00:00:10  2
+    2010-Jan-01 00:00:20  0
+    2010-Jan-01 00:00:30  5
+
+    Log: Derivative1
+    2010-Jan-01 00:00:05  0.1
+    2010-Jan-01 00:00:15  -0.2
+    2010-Jan-01 00:00:25  0.5
+
+    Log: Derivative2
+    2010-Jan-01 00:00:10  -0.03
+    2010-Jan-01 00:00:20  0.07
+
+    Log: Derivative3
+    2010-Jan-01 00:00:15  0.01
+
+
 .. categories::

Code/Mantid/docs/source/algorithms/CreateFlatEventWorkspace-v1.rst

@@ -13,4 +13,42 @@ This creates a new event workspace from an existing one by sampling an area of t
 source workspaces background and then using this to create a new workspace that covers 
 the same data range as the input workspace.
 
+Usage
+-----
+
+**Example: Extract the background into another workspace**
+
+.. testcode:: Extractbackground
+
+    ws = CreateSampleWorkspace("Event","Multiple Peaks")
+    wsOut=CreateFlatEventWorkspace(ws,RangeStart=15000,RangeEnd=18000)
+
+    #to compare we need to match the bins
+    wsOut=RebinToWorkspace(wsOut,ws,PreserveEvents=True)
+
+    print "The values for every 10th bin."
+    print "bin\tws\twsOut"
+    for i in range (0,ws.blocksize(),10):
+        print "%i\t%.2f\t%.2f" % (i,ws.readY(0)[i],wsOut.readY(0)[i])
+
+Output:
+
+.. testoutput:: Extractbackground
+    :options: +NORMALIZE_WHITESPACE
+
+    The values for every 10th bin.
+    bin     ws      wsOut
+    0       16.00   16.00
+    10      16.00   16.00
+    20      16.00   16.00
+    30      572.00  16.00
+    40      16.00   16.00
+    50      16.00   16.00
+    60      461.00  16.00
+    70      16.00   16.00
+    80      16.00   16.00
+    90      16.00   16.00
+
+
+
 .. categories::

Code/Mantid/docs/source/algorithms/CuboidGaugeVolumeAbsorption-v1.rst

@@ -42,4 +42,36 @@ shape must have been defined using, e.g.,
 :ref:`algm-CreateSampleShape` and the gauge volume must be
 fully within the sample.
 
+
+Usage
+-----
+
+**Example: A simple spherical sample with a cuboid guage volume**
+
+.. testcode:: ExCuboidGuageSimpleSpere
+
+    #setup the sample shape
+    sphere = '''<sphere id="sample-sphere">
+          <centre x="0" y="0" z="0"/>
+          <radius val=".2" />
+      </sphere>'''
+    ws = CreateSampleWorkspace("Histogram",NumBanks=1,BankPixelWidth=1)
+    ws = ConvertUnits(ws,"Wavelength")
+    ws = Rebin(ws,Params=[1])
+    CreateSampleShape(ws,sphere)
+    SetSampleMaterial(ws,ChemicalFormula="V")
+
+    #restrict the number of wavelength points to speed up the example
+    wsOut = CuboidGaugeVolumeAbsorption(ws, NumberOfWavelengthPoints=5, ElementSize=3,
+        SampleHeight=1,SampleWidth=2,SampleThickness=3)
+
+    print "The created workspace has one entry for each spectra: %i" % wsOut.getNumberHistograms()
+
+Output:
+
+.. testoutput:: ExCuboidGuageSimpleSpere
+
+    The created workspace has one entry for each spectra: 1
+
+
 .. categories::

Code/Mantid/docs/source/algorithms/FilterByLogValue-v1.rst

@@ -60,12 +60,55 @@ nexus file. Some of these files have a sample log called
 "veto\_pulse\_time" that only contains times of the pulses to be
 rejected. For example, this call will filter out veto pulses:
 
-``FilterByLogValue(InputWorkspace="ws", OutputWorkspace="ws", LogName="veto_pulse_time", PulseFilter="1")``
+.. testsetup:: VetoPulseTime
+
+   ws=CreateSampleWorkspace("Event")
+   AddTimeSeriesLog(ws, Name="veto_pulse_time", Time="2010-01-01T00:00:00", Value=1) 
+   AddTimeSeriesLog(ws, Name="veto_pulse_time", Time="2010-01-01T00:10:00", Value=0)
+   AddTimeSeriesLog(ws, Name="veto_pulse_time", Time="2010-01-01T00:20:00", Value=1)
+   AddTimeSeriesLog(ws, Name="veto_pulse_time", Time="2010-01-01T00:30:00", Value=0)
+   AddTimeSeriesLog(ws, Name="veto_pulse_time", Time="2010-01-01T00:40:00", Value=1)
+   AddTimeSeriesLog(ws, Name="veto_pulse_time", Time="2010-01-01T00:50:00", Value=0)
+
+.. testcode:: VetoPulseTime
+
+   ws = FilterByLogValue(ws, LogName="veto_pulse_time", PulseFilter="1")
 
 Comparing with other event filtering algorithms
 ###############################################
 
 Wiki page `EventFiltering <http://www.mantidproject.org/EventFiltering>`__ has a detailed
 introduction on event filtering in MantidPlot.
 
+
+Usage
+-----
+
+**Example - Filtering by a simple time series Log**  
+
+.. testcode:: Filter
+
+   ws = CreateSampleWorkspace("Event",BankPixelWidth=1)
+   AddTimeSeriesLog(ws, Name="proton_charge", Time="2010-01-01T00:00:00", Value=100) 
+   AddTimeSeriesLog(ws, Name="proton_charge", Time="2010-01-01T00:10:00", Value=100)
+   AddTimeSeriesLog(ws, Name="proton_charge", Time="2010-01-01T00:20:00", Value=100)
+   AddTimeSeriesLog(ws, Name="proton_charge", Time="2010-01-01T00:30:00", Value=100)
+   AddTimeSeriesLog(ws, Name="proton_charge", Time="2010-01-01T00:40:00", Value=15)
+   AddTimeSeriesLog(ws, Name="proton_charge", Time="2010-01-01T00:50:00", Value=100)
+
+   print "The unfiltered workspace %s has %i events and a peak value of %.2f" % (ws, ws.getNumberEvents(),ws.readY(0)[50])     
+
+   wsOut = FilterByLogValue(ws,"proton_charge",MinimumValue=75, MaximumValue=150)
+
+   print "The filtered workspace %s has %i events and a peak value of %.2f" % (wsOut, wsOut.getNumberEvents(),wsOut.readY(0)[50])     
+
+
+Output:
+
+.. testoutput:: Filter
+
+   The unfiltered workspace ws has 8000 events and a peak value of 1030.00
+   The filtered workspace wsOut has 4058 events and a peak value of 502.00
+
+
 .. categories::

Code/Mantid/docs/source/algorithms/GetEi-v1.rst

@@ -48,4 +48,5 @@ 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.
 
+
 .. categories::

Code/Mantid/docs/source/algorithms/GetEi-v2.rst

@@ -51,4 +51,79 @@ 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.
 
+Usage
+-----
+
+**Example: Calculating the Ei**
+
+.. testcode:: calcEi
+
+    import numpy as np
+    import math
+
+    #create a workspace wth two pixels to act as monitors
+    ws = CreateSampleWorkspace(bankPixelWidth=1,binWidth=10)
+
+    #set the data values
+    peakOneCentre = 8500.0
+    sigmaSqOne = 250.0*250.0
+    peakTwoCentre = 10800.0
+    sigmaSqTwo = 50*50
+    peakOneHeight = 3000.0
+    peakTwoHeight = 1000.0
+    xArray = []
+    yArray0 = []
+    yArray1 = []
+    for i in range (ws.blocksize()):
+        xValue = 5.0 + 5.5*i
+        xArray.append(xValue)
+        yArray0.append(peakOneHeight * math.exp(-0.5*pow(xValue - peakOneCentre, 2.)/sigmaSqOne))
+        yArray1.append(peakTwoHeight * math.exp(-0.5*pow(xValue - peakTwoCentre, 2.)/sigmaSqTwo))
+    xArray.append(5.0 + 5.5*ws.blocksize()) 
+
+    ws.setX(0, np.array(xArray))
+    ws.setX(1, np.array(xArray))   
+    ws.setY(0, np.array(yArray0))
+    ws.setY(1, np.array(yArray1))
+
+    (ei, firstMonitorPeak, FirstMonitorIndex, tzero) = GetEi(ws,Monitor1Spec=1,Monitor2Spec=2,EnergyEstimate=15.0)
+
+    print "ei: %.2f" % ei
+    print "firstMonitorPeak: %.2f" % firstMonitorPeak
+    print "FirstMonitorIndex: %i" % FirstMonitorIndex
+    print "tzero: %.2f" % tzero
+
+Output:
+
+.. testoutput:: calcEi
+    :options: +NORMALIZE_WHITESPACE
+
+    ei: 24.99
+    firstMonitorPeak: 8516.03
+    FirstMonitorIndex: 0
+    tzero: 1655.69
+
+**Example: Fixing the Ei**
+
+.. testcode:: fixEi
+
+    ws = CreateSampleWorkspace(bankPixelWidth=1,binWidth=10)
+
+    (ei, firstMonitorPeak, FirstMonitorIndex, tzero) = GetEi(ws,Monitor1Spec=1,Monitor2Spec=2,EnergyEstimate=15.0,FixEi=True)
+
+    print "ei: %.2f" % ei
+    print "firstMonitorPeak: %.2f" % firstMonitorPeak
+    print "FirstMonitorIndex: %i" % FirstMonitorIndex
+    print "tzero: %.2f" % tzero
+
+Output:
+
+.. testoutput:: fixEi
+    :options: +NORMALIZE_WHITESPACE
+
+    ei: 15.00
+    firstMonitorPeak: 8854.69
+    FirstMonitorIndex: 0
+    tzero: 0.00
+
 .. categories::

Code/Mantid/docs/source/algorithms/HRPDSlabCanAbsorption-v1.rst

@@ -34,7 +34,7 @@ Restrictions on the input workspace
 ###################################
 
 The input workspace must have units of wavelength. The
-`instrument <instrument>`__ associated with the workspace must be fully
+`instrument <http://www.mantidproject.org/instrument>`__ associated with the workspace must be fully
 defined because detector, source & sample position are needed.
 
 ChildAlgorithms used
@@ -43,4 +43,26 @@ ChildAlgorithms used
 The :ref:`algm-FlatPlateAbsorption` algorithm is used to
 calculate the correction due to the sample itself.
 
+Usage
+-----
+
+**Example:**
+
+.. testcode:: ExSimpleHRPDSlab
+
+    ws = CreateSampleWorkspace("Histogram",NumBanks=1,BankPixelWidth=1)
+    ws = ConvertUnits(ws,"Wavelength")
+    ws = Rebin(ws,Params=[1])
+    SetSampleMaterial(ws,ChemicalFormula="V")
+
+    wsOut = HRPDSlabCanAbsorption (ws,Thickness='0.2',ElementSize=3)
+
+    print "The created workspace has one entry for each spectra: %i" % wsOut.getNumberHistograms()
+
+Output:
+
+.. testoutput:: ExSimpleHRPDSlab
+
+    The created workspace has one entry for each spectra: 1
+
 .. categories::

Code/Mantid/docs/source/algorithms/RecordPythonScript-v1.rst

@@ -6,6 +6,45 @@
 
 .. properties::
 
+This algorithm records the python commans of any algoithms that execute while it is running and saves them out to a file.
+
+This is similar to extracting the history of a workspace, but outputs evey algorithm that occurs during it's execution rather than just for a specific workspace.
+
+The file is written out once this algotithm is cancelled, either using the running algorithm details button or via python.
+
+
+Usage
+-----
+
+**Example:**
+
+.. This example is written as code blocks as it would require multi threading to run singly
+.. Which is too complicated for a usage example
+
+.. code-block:: python
+    
+    RecordPythonScript("MyRecording.py")
+
+    # Run some algorithms in another python tab or via the GUI
+    # For example:
+    # ws = CreateSampleWorkspace("Event","Multiple Peaks")
+    # wsOut=CreateFlatEventWorkspace(ws,RangeStart=15000,RangeEnd=18000)
+    # wsOut=RebinToWorkspace(wsOut,ws,PreserveEvents=True)
+
+    # Then cancel the algorithm either using the GUI
+    # or executing this in another python tab
+    # AlgorithmManager.cancelAll()
+
+
+Output:
+
+.. code-block:: python
+
+    #a file containing the following:
+    CreateSampleWorkspace(OutputWorkspace='ws',WorkspaceType='Event',Function='Multiple Peaks',UserDefinedFunction='',NumBanks='2',BankPixelWidth='10',NumEvents='1000',Random='0',XUnit='TOF',XMin='0',XMax='20000',BinWidth='200')
+    CreateFlatEventWorkspace(InputWorkspace='ws',RangeStart='15000',RangeEnd='18000',OutputWorkspace='wsOut')
+    RebinToWorkspace(WorkspaceToRebin='wsOut',WorkspaceToMatch='ws',OutputWorkspace='wsOut',PreserveEvents='1')
+
 
 
 .. categories::

Code/Mantid/docs/source/algorithms/SignalOverError-v1.rst

@@ -12,4 +12,40 @@ Description
 Take a `MatrixWorkspace <http://www.mantidproject.org/MatrixWorkspace>`__ as input, and replaces the
 Y values by Y/E (signal divided by error)
 
+
+Usage
+-----
+
+**Example: Taking the derivative of logs**
+
+.. testcode:: AddLogDerivative
+
+    ws = CreateSampleWorkspace("Event")
+    wsOut = SignalOverError(ws)
+
+    print "Values from every 10th bin"
+    print "bin\tY\tE\tY_New"
+    for i in range (0,ws.blocksize(),10):
+        print "%i\t%.2f\t%.2f\t%.2f" % (i,ws.readY(0)[i],ws.readE(0)[i],wsOut.readY(0)[i])
+
+
+Output:
+
+.. testoutput:: AddLogDerivative
+    :options: +NORMALIZE_WHITESPACE
+
+    Values from every 10th bin
+    bin     Y       E       Y_New
+    0       30.00   5.48    5.48
+    10      30.00   5.48    5.48
+    20      30.00   5.48    5.48
+    30      30.00   5.48    5.48
+    40      30.00   5.48    5.48
+    50      1030.00 32.09   32.09
+    60      30.00   5.48    5.48
+    70      30.00   5.48    5.48
+    80      30.00   5.48    5.48
+    90      30.00   5.48    5.48
+
+
 .. categories::