From 58607d3757e6000dc8868cfe11b99409080c868f Mon Sep 17 00:00:00 2001
From: Antti Soininen <soininen@ill.fr>
Date: Wed, 30 May 2018 13:17:11 +0200
Subject: [PATCH] ReflectometrySumInQ: Add sphinx documentation. Re #22315
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+
+.. algorithm::
+
+.. summary::
+
+.. relatedalgorithms::
+
+.. properties::
+
+Description
+-----------
+
+This algorithm sums the Y values of histograms given by *InputWorkspaceIndexSet* into a single single histogram. The summation is done using the method proposed by Cubitt et al. [#CUBITT]_ This involves a projection to an
+arbitrary reference angle, :math:`2\theta_R`, with a "virtual" wavelength,
+:math:`\lambda_v`. This is the wavelength the neutron would have had if it had
+arrived at :math:`2\theta_R` with the same momentum transfer (:math:`Q`).
+
+Counts are considered to be spread evenly over the input pixel, and the
+top-left and bottom-right corner of the pixel are projected onto
+:math:`2\theta_R` giving a range in :math:`\lambda_v` to project onto. Counts
+are shared out proportionally into the output bins that overlap this range, and
+the projected counts from all pixels are summed into the appropriate output
+bins.
+
+The input workspace should have wavelength as the X units as well as an instrument.
+
+To produce a reflectivity, the input workspace has to be the reflected beam workspace where each histogram is individually divided by the summed (in lambda) direct beam data.
+
+Usage
+-----
+
+**Example - basic usage with reflectometry-like data**
+
+.. plot::
+ :include-source:
+
+ import numpy as np
+ from mantid.simpleapi import *
+ import matplotlib.pyplot as plt
+
+ # Direct beam
+ noBackground = 'name=LinearBackground, A0=0'
+ direct = CreateSampleWorkspace(
+ Function='User Defined',
+ UserDefinedFunction=noBackground,
+ NumBanks=1,
+ XUnit='Wavelength',
+ XMin=0., XMax=20., BinWidth=1.)
+ # Move the detector such that the beam is right at its center.
+ MoveInstrumentComponent(
+ Workspace=direct,
+ ComponentName='bank1',
+ X=-0.008 * 4.5, Y= -0.008 * 4.5, Z=0.)
+ # Fill intensity for pixels in the beam
+ for i in [44, 45, 54, 55]:
+ direct.dataY(i).fill(1.)
+ direct.dataE(i).fill(0.1)
+ # Group detectors to form a 'line detector'. The line is vertical in this case.
+ groupingPattern=''
+ for row in range(10):
+ for column in range(10):
+ groupingPattern = groupingPattern + str(column * 10 + row)
+ if column < 9:
+ groupingPattern = groupingPattern + '+'
+ if row < 9:
+ groupingPattern = groupingPattern + ','
+ direct = GroupDetectors(
+ InputWorkspace=direct,
+ GroupingPattern=groupingPattern,
+ Behaviour='Sum')
+
+ #Reflected beam
+ reflected = CreateSampleWorkspace(
+ Function='User Defined',
+ UserDefinedFunction=noBackground,
+ NumBanks=1,
+ XUnit='Wavelength',
+ XMin=0., XMax=20., BinWidth=1.)
+ # Move the detector. This reflectometer moves vertically.
+ MoveInstrumentComponent(
+ Workspace=reflected,
+ ComponentName='bank1',
+ X=-0.008 * 4.5, Y= 0.008 * 4, Z=0.)
+ # Create some fake reflected beam data.
+ Xs = reflected.readX(0)
+ Xs = (Xs[1:] + Xs[:-1]) / 2 # Bin edges -> points
+ decay = np.exp(-(Xs - 4.) / 3.)
+ span = decay < 1.
+ for i in [44, 45, 54, 55]:
+ Ys = reflected.dataY(i)
+ Ys.fill(1.)
+ Ys[span] = decay[span]
+ reflected = GroupDetectors(
+ InputWorkspace=reflected,
+ GroupingPattern=groupingPattern,
+ Behaviour='Sum')
+
+ # Now we have somewhat realistic data.
+ # Sum the direct beam (in lambda).
+ direct=SumSpectra(direct, ListOfWorkspaceIndices=[4, 5])
+ # Calculate (sum in Q) the reflectivity.
+ reflected /= direct
+ reflectivity = ReflectometrySumInQ(
+ InputWorkspace=reflected,
+ InputWorkspaceIndexSet=[4, 5],
+ BeamCentre=4,
+ WavelengthMin=0.1,
+ WavelengthMax=19.)
+
+ fig, axes = plt.subplots(subplot_kw={'projection': 'mantid'})
+ axes.plot(reflectivity)
+ axes.set_ylabel('"Reflectivity"')
+ # Uncomment to show the plot window.
+ #fig.show()
+
+References
+----------
+
+.. [#CUBITT] Cubitt et al., *J. Appl. Crystallogr.*, **6** 2006 (2015)
+ `doi: 10.1107/S1600576715019500 <http://dx.doi.org/10.1107/S1600576715019500>`_
+
+.. categories::
+
+.. sourcelink::
+
--
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