This directory contains data from the NCNR 2002 summer school.

ss02 contains the raw data directly from ICP.

ss02-fit/ssgpb001.log contains the reduced data.
ss02-fit/ssgpb001.staj is an attempt to model the data.

Data Analysis
=============

This section will give a brief walk-through for fitting a model to a
reduced reflectometry signal.  The basic model is a set of layers,
a repeated section and another set of layers.

* start
First start reflpak and choose the Fit... program.  How you do this
varies from system to system.  The initial screen shows a very simple
model and no data.  Use the Layer menu to add the number of layers
you want in your model. Use the Beam tab to set beam characteristics
such as intensity, wavelength and divergence.

* adjust profile
You can play with the model by clicking and dragging the parameters and 
interfaces in the profile.  The corresponding reflectivity is 
constinuously updated as you drag.  For fine control, press Ctrl+Arrow.  
This will move the most recently selected handle by a fifth of a pixel.  
Alternatively, click, move and click in the profile graph to zoom in on 
a portion. Now dragging will be easier to control. Alternatively, you 
can enter values directly into the model from the "Layers" tab.

* load model
Select  "File Open" from the menu, and navigate to the ss02-fit
directory.  Select ssgpb001.staj. This loads the five layer model
associated with the sample ssgpb and overlays it on the data for
that sample. You can change the data associated with a model using
the File Data menu.

* fitting
In the Layers tab, adjust a parameter.  E.g., set M1 QC to 4.2e-6.
Now go to the Fit tab, select MQC1 and click Fit.  You will see the
reflectivity adjust to match the data.

This is enough information to get you started.  For more details,
use the help system.


Data Reduction
==============

This section gives a brief walk-through for data reduction for a set
of NCNR data.  If you are only interested in the analysis software,
you may skip this section.

We are assuming that you already have octave+octave-forge installed,
and that octave is started with listen(1515)<Return> type at the
prompt.  Octave is only needed for data reduction, not for subsequent
analysis.

* start 
First start reflpak and choose the Reduce... program.  How you do this
varies from system to system. If you started the program in the ss02 
data directory, you will now see your dataset.  If not, you will see
the Reflred Choose window.  Navigate to the ss02 directory and click Ok.

* data tree
The SS02 dataset consists of a slit scan (i5282) and the data (ssgpb).
Initially the slit scan is showing, but you can open the whole tree
by clicking the '+' signs at the left, or using the arrow keys (right
arrow opens up a subtree).

* rocking curve
Let's first look at the rocking curves, NG-1 rock.  Click on each bar
004, 007, 013, ..., or use your arrow keys and Enter to display graphs
of the individual rocking curves.  Each curve should be centered about 
the red bar and symmetric (it is for this dataset).  If not, then it 
is possible that your sample shifted during the experiment.  Right
click in the tree, or press Delete to clear all the rocking curves.
The raw data for the curves is displayed in the text window above
the graph.

* specular
Next lets look at our data.  Scroll to the NG-1 spec section in the
ssgpb tree. Double-click or press Ctrl-Enter on section 001 to select 
sections 001-006. All sections show up in the graph.  The graph starts 
out linear, but you can change it to log scale by clicking the y-axis.  
Click, move and click on the graph to zoom.  Right click on the graph 
to unzoom.  Select the remaining data sets.  Click accept to sum the
data.

* background
Now you are ready to select the background.  There are at least two
different approaches to background estimation in use at the NCNR.
One is based on a detector offset relative to A3 and the other has
the detector offset from A4.  The fact that our dataset displays a
different range for the plus and minus offset background datasets 
(as indicated by the + and - signs in the ssgpb back section), suggests
that we are using the wrong convention.  Either select the other
convention for all datasets from the menu (Options Background), or
click the "NG1 back Q(A4)" label to change the convention for that
dataset only.  

Select the plus and minus offset backgrounds.  Note that one point in
the background overlaps the specular line still displayed on the screen.
Thats because the Q(A3) convention has the background measurement crossing
the specular ridge.  This point will be excluded from the dataset, as
indicated by the red circle around the data point.  You can exclude other
data points from the dataset by clicking them with the center mouse
button, but only do so if you have a good reason to believe the values
are bad (such as having a very long counting time in the raw data 
window because the beam shutter wasn't open or the reactor had a
power bump).  Click Accept to save the data.  Note that the excluded
data point is indeed excluded.

* Tcl console
When select the first section of slit scan data (i5282 001), you are 
greeted by the rather rude message:

	ICP recorded a wavelength of 1.5402 in i5252001.ng1.  We 
	will instead use 4.75.  If this is not correct, enter
	'set wavelength(i5282,NG-1) 1.5402' in the Tcl console
	and reload the file.

The message is self-explanatory: for some reason during summer
school of 2002, the wavelength recorded in the data file was
incorrect.  Rather than silently correct this, Reflred lets
you know what is going on.  Since the default behaviour is
almost certainly correct, that is the only choice we allow.
However, you as a user can override our choice by starting up
the Tcl Console from the Options menu and change the internal
variables of the program so that it does what you want.  Everything
about the program can be controlled from the Tcl console.  A
full description is beyond the scope of this document, but will
(eventually) be available via the help system.

* slit scan
Let's continue selecting the slit scan.  The thing you will notice
is that the data points do not all line up.  In particular, the
low Q end of the slit scan (i5282 001) has many thousands of counts
more than the rest of the scan.  This is because an attenuator was
placed in the beam, letting less than 1% of the neutrons through.
In this particular case, the attenuation factor is 122.1241.
Select Attenuators... from the menu and enter this value for Run 001.
The standard cut and paste keys (Ctrl-C and Ctrl-V) can be used to
propogate this value to the rest of the runs (all but run 6).  Now
the slit scan should more or less form a line.  Click Accept.

* reduction
Since we have built specular, background and slit scans, we can
now start the data reduction process.  Select Reduce... from the
menu.  This opens up the reduce screen.  Across the top of the
screen are three columns (Specular, Background and Slit Scan).
Select all these scans.  The program automatically calculates
(specular-background)/slit.  Note that we are using both left and
right y-axis.  We need to do this because the scale of the divided
data is significantly lower than the scale of raw data.

* footprint correction
The last step in data reduction is footprint correction.  Because
we are using fixed slits at low Q, the sample area illuminated by
the beam changes as we change angle.  First zoom the data so that
it shows all of the reflectivity line in the fixed slit region.
Click the right y-axis to change to linear scale.  

Now click the footprint correction Parameters... button at the bottom 
of the screen.  This opens up the footprint dialog.  Select "Fit 
footprint correction" and click "From graph...".  Choose the left 
and right end of the linear region after the first dip.  Now click 
correct from Qz to Qz "From graph..." and choose the bottom of the
dip and the last point in the fixed slit region.  Click Apply.
Look at the value of Qz where the correction is 1.0.  If this is
less than the Qz at the end of the fixed slit region, use that
value instead as the end of the 'to' range.

For more details, press F1 on the footprint dialog to view the help.

* save your results

You are now done the data reduction.  Save the results using the Save
or Save as... button on the Reduce screen.  The name of the saved
file shows up in the message bar, but it is immediately overwritten
when you move the mouse.  If you have subtracted but not divided data,
it will be the name of the first specular file with the extension replaced
by .sub.  If you have divided but not footprint corrected, the extension
will be .div.  If you have footprint corrected, the extension will be .refl.


Paul Kienzle
2004-03-29