# Changeset 267

Ignore:
Timestamp:
Nov 4, 2012 11:24:12 PM (7 years ago)
Message:

re-arrange and add to SAS basics

Location:
canSAS2012
Files:
10 edited
4 moved

Unmodified
Removed
• ## canSAS2012/.project

 r260 canSAS2012canSAS multi-dimensional data standard org.python.pydev.PyDevBuilder org.python.pydev.pythonNature
• ## canSAS2012/docs/source/basics.rst

 r230 ================================================== Define the terms here Definitions ================================================== such as Q and the meaning of reduced data .. sidebar:: work in progress... This document is under construction. Many parts have yet to be written. For the general case of small-angle scattering data, all that is required is to have measurements of reduced intensity :math:I as a function scattering vector, :math:Q.  Some techniques may require additional information, such as wavelength. .. index:: ! reduced data .. _reduced data: Reduced Data ========================= What is *reduced data*?  Consider this figure of the scientific workflow presented at the *2006 Advanced Photon Source Workshop on Scientific Software* (*ANL-APS-TB-51*, Argonne National Laboratory): .. figure:: graphics/2006-10-09-scientific-workflow.jpg :alt: scientific workflow :height: 400 px .. note:: *Reduced data* is the data presented for analysis after all instrument-specific artifacts and corrections have been applied. An *experiment* is constructed from a sequence of *measurements* by a scientific instrument.  Raw data from those measurements must be converted from the format received by components of the instrument (detectors, amplifiers, motors, encoders, thermocouples, etc.) into a form suitable for analysis particular to the scientific investigation.  Part of the conversion process involves the removal of artifacts and the correction of distortions of the signal by the measurement process (such as detector dead-time corrections or removal of dead pixels from an area detector image) and the combination of parameters describing the instrument configuration and even the possibility of an applied mask to remove parts of the measurement that contain no useful observations. The data that results after all these conversion steps have been applied is termed **reduced data**. In broad terms, the steps involved in the process of data reduction are particular to a specific scientific instrument as it existed at a specific time.  For many scientific instruments, such as those at large user facilities, it is not possible to generalize the process of data reduction and identify all the parameters necessary for data reduction in advance. .. note:: It is, and will always be, the responsibility of the instrument team to provide the process of converting the data measurements into **reduced data**. Requirements for Reduced SAS Data ---------------------------------------------- The absolute minimum information required for the standard analysis of small-angle scattering measurements is intensity as a function of scattering vector, :math:I(Q). :ref:Intensity  is expressed in absolute units of cross-section or in units directly convertible by a scaling constant :ref:scattering vector  is expressed as :ref:scattering vector magnitude  (:math:|Q|) or :ref:scattering vector   (:math:\vec{Q}) Some analyses may require additional information such as the estimation of experimental uncertainties, the wavelength and type of the radiation probe, or the instrumental resolution.  These should be provided, where possible.  Note that, for example, reduced SAS data does not *require* a number representing the distance from sample to detector as this common instrument-specific term has already been factored into the data reduction process. .. index:: ! Q .. _Q: Definition of :math:Q ========================= :math:Q may be represented either as the magnitude of the scattering vector, :math:|Q| or by the three-dimensional scattering vector :math:\vec{Q}. When we write :math:Q, we may refer to either or both of :math:|Q| or :math:\vec{Q},  depending on the context. .. _Q scalar: Q vector magnitude: :math:|Q|=(4 \pi / \lambda) \sin(\theta) ------------------------------------------------------------------ where :math:\lambda is the wavelength of the radiation, and :math:2\theta is the angle through which the detected radiation has been scattered. This is a one-dimensional reduction of the general case below. .. _Q geometry: .. figure:: graphics/Q-geometry.jpg :alt: Q geometry :height: 200 px definition of :math:|Q| geometry for small-angle scattering .. _Q vector: Q vector: :math:\vec{Q}=\vec{k'}-\vec{k} ---------------------------------------------- where :math:\vec{k} is the wave vector of the incident radiation and :math:\vec{k'} is the wave vector of the scattered radiation. Here, :math:\vec{k} is a vector of magnitude :math:2\pi/\lambda that points along the trajectory of the radiation. .. _Q vector geometry: .. figure:: graphics/q-vector.png :alt: Q vector geometry :height: 400 px definition of :math:\vec{Q} geometry for small-angle scattering [#]_ .. [#] A hearty nod for this graphic is given to the guide: **neutron scattering: A Primer**, by Roger Pynn (LANSCE), published in the Summer 1990 edition of *Los Alamos Science*. .. index:: ! I .. _I: Definition of Intensity: :math:I ========================================== The intensity may be represented in one of these forms: **absolute units**: :math:d\Sigma/d\Omega(Q) differential cross-section per unit volume per unit solid angle (typical units: 1/cm/sr) **absolute units**: :math:d\sigma/d\Omega(Q) differential cross-section per unit atom per unit solid angle (typical units: cm^2) **arbitrary units**: :math:I(Q) usually a ratio of two detectors but units are meaningless (typical units: a.u.) This presents a few problems for analysis software to sort out when reading the data. Fortunately, it is possible to analyze the *units* to determine which type of intensity is being reported and make choices at the time the file is read. But this is an area for consideration and possible improvement. One problem arises with software that automatically converts data into some canonical units used by that software. The software should not convert units between these different types of intensity indiscriminately. .. index:: I(Q) A second problem is that when arbitrary units are used, then the set of possible analytical results is restricted.  With such units, no meaningful volume fraction or number density can be determined directly from :math:I(Q). In some cases, it is possible to apply a factor to convert the arbitrary units to an absolute scale.  This should be considered as a possibility of the analysis process. .. index:: ! coordinate axes .. _coordinate axes: Coordinate Axes =========================== The canSAS standard assumes a right-hand rule coordinate system, consistent with a variety of software packages and data formats. See, for example: http://www.nexusformat.org/Coordinate_Systems :z: :math:z is along the trajectory of the radiation (positive value in the direction towards the detector) :x: :math:x is orthogonal to :math:z in the horizontal plane (positive values increase to the right when viewed towards the incoming radiation) :y: :math:y is orthogonal to :math:z and :math:x in the vertical plane (positive values increase upwards) .. index:: ! orientation roll pitch yaw .. _orientation: Orientation =========================== Orientation (angles) describes single-axis rotations (rotations about multiple axes require more information): **roll** is a rotation about the :math:z axis **pitch** is a rotation about the :math:x axis **yaw** is a rotation about the :math:y axis
• ## canSAS2012/docs/source/conf.py

 r230 # of the sidebar. #html_logo = None html_logo = 'cswikilogo.png' html_logo = 'graphics/cswikilogo.png' # The name of an image file (within the static path) to use as favicon of the
• ## canSAS2012/docs/source/contents.rst

 r230 subversion repository, available for world-readable checkout:: svn co http://svn.smallangles.net/svn/canSAS/canSAS2012 ./canSAS2012 svn co http://www.cansas.org/svn/canSAS2012 ./canSAS2012 Look in the docs/source directory for the source code files. .. rubric:: Index :ref:genindex .. rubric:: Search :ref:search
• ## canSAS2012/docs/source/framework.rst

 r227 ================================================== .. sidebar:: work in progress... This document is under construction. Many parts have yet to be written. .. describe the framework .. figure:: 2012-minimum.png .. figure:: graphics/2012-minimum.png :alt: Absolute minimum requirement for analysis of SAS data .. figure:: 2012-recommended-minimum.png .. figure:: graphics/2012-recommended-minimum.png :alt: Minimum content recommended for reduced SAS data :language: guess .. figure:: example1.png .. figure:: graphics/example1.png :alt: view of original hkl_ioc.mac HTML documentation
• ## canSAS2012/docs/source/hdf5.rst

 r225 .. $Id$ .. index:: ! HDF5 implementation; HDF5 .. _hdf5_implementation: ================================================== HDF5 Implementation Binary: HDF5 ================================================== .. sidebar:: work in progress... This document is under construction. Many parts have yet to be written. It is expected that small-angle scattering data will be stored in binary HDF5 files (http://www.hdfgroup.org/HDF5/). To store SAS data in text files, see the chapter titled :ref:xml_implementation. The basic plan here is to describe the implementation of the canSAS multi-dimensional format within the NeXus HDF5 format (http://www.nexusformat.org) by creating a new NeXus :index:NXcansas application definition, expressed as a NXDL file (http://download.nexusformat.org/doc/html/nxdl.html). The effort to create this NXDL definition will commence once the basics of the canSAS multi-dimensional format are set forth. Contents:
• ## canSAS2012/docs/source/implementation.rst

 r227 .. $Id$ .. index:: ! implementation .. _implementation:
• ## canSAS2012/docs/source/index.rst

 r230 outcome of that meeting. .. sidebar:: work in progress... This document is under construction. Many parts have yet to be written. .. toctree:: .. [#]  http://www.cansas.org .. [#]  http://svn.smallangles.net/trac/canSAS/browser/1dwg/tags/v1.0/doc/cansas-1d-1_0-manual.pdf .. [#]  http://www.smallangles.net/wgwiki/index.php/canSAS-2012 .. [#]  http://www.smallangles.net/wgwiki/index.php/2012_Data_Discussion .. [#]  http://www.cansas.org/trac/export/265/1dwg/tags/v1.0/doc/cansas-1d-1_0-manual.pdf .. [#]  http://www.cansas.org/wgwiki/index.php/canSAS-2012 .. [#]  http://www.cansas.org/wgwiki/index.php/2012_Data_Discussion
 r225 .. $Id$ .. index:: ! XML implementation; XML .. _xml_implementation: ================================================== XML Implementation Text: XML ================================================== .. sidebar:: work in progress... This document is under construction. Many parts have yet to be written. It is expected that small-angle scattering data will be stored in text files formatted as XML (http://www.w3schools.com/xml). To store SAS data in binary  files, see the chapter titled :ref:hdf5_implementation. The basic plan here is to describe the implementation of the canSAS multi-dimensional format in an XML file by creating an :index:XML Schema file (http://www.w3.org/XML/Schema, http://www.w3schools.com/schema) or similar schema specification (such as :index:schematron - http://www.schematron.com). The effort to create this XML Schema specification will commence once the basics of the canSAS multi-dimensional format are set forth. Contents: