Changeset 282 for canSAS2012


Ignore:
Timestamp:
Dec 29, 2012 12:52:14 AM (7 years ago)
Author:
prjemian
Message:

Building out the docs for the specification of the standard. Work still in progress.

Location:
canSAS2012/docs/source
Files:
6 added
7 edited

Legend:

Unmodified
Added
Removed
  • canSAS2012/docs/source/basics.rst

    r270 r282  
    188188=========================== 
    189189 
    190 The canSAS standard assumes a right-hand rule coordinate system,  
    191 consistent with a variety of software packages and data formats. 
    192 See, for example: http://www.nexusformat.org/Coordinate_Systems 
     190The canSAS standard assumes a right-hand rule coordinate system, [#]_, [#]_, [#]_ 
     191consistent with a variety of software packages and data formats. [#]_ 
    193192 
    194193:z: 
    195         :math:`z` is along the trajectory of the radiation 
     194        :math:`z` is along the trajectory of the incident radiation 
    196195        (positive value in the direction towards the detector) 
    197196:x: 
     
    202201        :math:`y` is orthogonal to :math:`z` and :math:`x`  
    203202        in the vertical plane (positive values increase upwards) 
    204                  
    205  
    206  
     203 
     204.. [#] http://en.wikipedia.org/wiki/Coordinate_system#Cartesian_coordinate_system 
     205.. [#] http://en.wikipedia.org/wiki/Polar_coordinate_system 
     206.. [#] http://en.wikipedia.org/wiki/Spherical_coordinate_system 
     207.. [#] http://www.nexusformat.org/Coordinate_Systems 
     208         
     209        .. _Coordinate Axes geometry: 
     210         
     211        .. figure:: graphics/translation-orientation-geometry-2.png 
     212            :alt: Coordinate Axes 
     213            :height: 400 px 
     214             
     215            definition of the coordinate axes for translations and rotations 
    207216 
    208217.. index:: 
     
    215224 
    216225Orientation 
    217 =========================== 
    218  
    219 Orientation (angles) describes single-axis rotations (rotations about 
    220 multiple axes require more information): 
    221          
    222 **roll** 
    223         is a rotation about the :math:`z` axis 
    224  
    225 **pitch** 
    226         is a rotation about the :math:`x` axis 
    227  
    228 **yaw** 
    229         is a rotation about the :math:`y` axis 
     226----------- 
     227 
     228Orientation angles [#]_ in the canSAS standard describe single-axis rotations.  
     229Rotations about multiple axes require more information. 
     230The rotations are described in terms of roll, pitch, and yaw [#]_ : 
     231         
     232:**roll**: 
     233        a rotation about the :math:`z` axis,  
     234        where zero rotation is along the positive :math:`x` axis 
     235 
     236:**pitch**: 
     237        a rotation about the :math:`x` axis,  
     238        where zero rotation is along the positive :math:`z` axis 
     239 
     240:**yaw**: 
     241        a rotation about the :math:`y` axis,  
     242        where zero rotation is along the positive :math:`z` axis 
     243  
     244.. [#] http://en.wikipedia.org/wiki/Orientation_%28geometry%29 
     245.. [#] http://en.wikipedia.org/wiki/Tait-Bryan_angles#Aircraft_attitudes 
     246  
  • canSAS2012/docs/source/contents.rst

    r270 r282  
    1515   basics 
    1616   framework 
     17   structure 
     18   sasdata 
    1719   implementation 
    1820   examples 
     21   notation 
    1922 
    2023About this documentation 
  • canSAS2012/docs/source/examples.rst

    r277 r282  
    143143        Qz: float[256, 256] 
    144144 
     145.. _example 2-D masked image: 
     146 
    1451472-D masked image 
    146148---------------- 
     
    425427        P: float[nPressure] 
    426428 
    427 .. _2-D.images.with.varied.T.t.P: 
     429.. _example 2-D.images.with.varied.T.t.P: 
    428430 
    4294312-D  :math:`I(T,t,P,Q(t))` images 
  • canSAS2012/docs/source/framework.rst

    r267 r282  
    11.. $Id$ 
    22 
    3 .. _structure: 
     3.. _framework overview: 
    44 
    55================================================== 
    6 Structure of the canSAS2012 data format 
     6Overview of the canSAS2012 data format 
    77================================================== 
    88 
     
    1717============== 
    1818 
     19Describe the structure of data to be presented for small-angle scattering analysis. 
     20Make the structure sufficiently general that it may be used for analysis of any form 
     21of reduced SAS data. 
     22 
     23The hierarchical structure of the canSAS standard has been designed to be  
     24compatible with the NeXus data format. 
     25 
    1926Description 
    2027============== 
    2128 
     29Absolute minimum requirement for analysis of SAS data 
     30------------------------------------------------------- 
     31 
     32The *least* amount of information necessary for meaningful  
     33small-angle scattering analysis is the presentation of  
     34the :math:`I(Q)` SAS data.  In the canSAS standard, 
     35this data is presented within  
     36a *SASdata* group (holding the data from a single experiment),  
     37inside of *SASentry* group (holding the data from a single sample), 
     38inside of a *SASroot* group (holding one or more experiments). 
     39 
     40.. note:: It is recommended to store more metadata than this absolute minimum standard shows. 
     41   See the section :ref:`minimum recommended content` for more details. 
    2242 
    2343.. figure:: graphics/2012-minimum.png 
    24     :alt: Absolute minimum requirement for analysis of SAS data  
    25  
    26     Absolute minimum requirement for analysis of SAS data . 
    27  
     44 
     45    Absolute minimum requirement for analysis of SAS data. 
     46     
     47Alternatively, this may be shown using a more condensed :ref:`notation <notation>`, as: 
     48 
     49.. code-block:: text 
     50  :linenos: 
     51   
     52  SASroot 
     53    SASentry 
     54      SASdata 
     55        @Q_indices=0 
     56        @I_axes="Q" 
     57        I: float[] 
     58        Q: float[] 
     59 
     60.. _minimum recommended content: 
     61 
     62Minimum content recommended for reduced SAS data 
     63-------------------------------------------------- 
     64 
     65It is recommended that instruments provide at least the information described  
     66in this section to satisfy the needs of data analysis and visualization software. 
    2867 
    2968.. figure:: graphics/2012-recommended-minimum.png 
    30     :alt: Minimum content recommended for reduced SAS data 
    3169 
    3270    Minimum content recommended for reduced SAS data. 
    3371 
     72.. code-block:: text 
     73  :linenos: 
     74   
     75  SASroot 
     76    SASentry 
     77      Title: string 
     78      SASdata 
     79        @Q_indices=0 
     80        @I_axes="Q" 
     81        I: float[] 
     82        Q: float[] 
     83        probe_type: string 
     84        wavelength: float (or possibly float[]) 
     85        Idev: float[] 
     86        Qdev: float[] 
     87        SASnote 
     88          anything: string, float, float[], ... 
     89      SASsample 
     90        name: string 
     91         
     92-------------- 
     93 
     94.. caution:: re-write from this point downward on this page 
    3495 
    3596Terms 
     
    3899.. index:: ! SASroot 
    39100        groups; SASroot 
     101         
     102.. sidebar:: TODO! 
     103 
     104        break this up into tables for each group 
    40105 
    41106**SASroot**: 
     
    107172                        use attributes similar to ``@Mask_indices`` (such as ``@Temperature_indices`` 
    108173                        or ``@Pressure_indices``). 
     174                 
     175                **SASsample**: 
     176                        derived from original 1D format, content and attributes have changed 
     177                         
     178                        .. caution:: needs full write-up 
     179 
     180                .. index:: ! Title 
     181 
     182                **Title**: 
     183                        (string) Title of this *SASentry*.   
     184                        Optional attribute:  *name={short-Run-identifier}*. 
     185                        Example:: 
     186                         
     187                                Glassy Carbon C4 12keV 
    109188 
    110189 
     
    132211        Unidata UDunits 
    133212        UDunits 
     213 
     214.. _units: 
    134215 
    135216:@units: (required for all numerical objects)  
     
    152233The **names** for data objects should follow a standard  
    153234convention that starts with a letter (upper or lower case) and  
    154 then letters, numbers, and "_". The length of the name is limited  
    155 to no more than 63 characters (imposed by the rule HDF5 for names). 
    156  
    157 This standard convention may be described by the regular expression:: 
    158  
    159         [A-Za-z][\\w_]*  
     235then a sequence composed of letters, numbers, and/or "_".  
     236The length of the name is limited  
     237to no more than 63 characters (imposed by the HDF5 rule for names). 
     238 
     239        .. index:: ! naming standard; regular expression 
     240         
     241        This standard convention for object names may be  
     242        described by this regular expression:: 
     243         
     244                [A-Za-z][\\w_]*  
    160245 
    161246 
     
    190275 
    191276 
    192 .. [#data_object] Such as an array or scalar or text. HDF5 calls this a *dataset*,    
     277.. [#data_object] Such as text, a scalar, or an array. HDF5 calls this a *dataset*,    
    193278        Not a folder or a group or an object that contain other objects. 
    194279.. _Unidata UDunits: http://www.unidata.ucar.edu/software/udunits/udunits-2-units.html 
  • canSAS2012/docs/source/implementation.rst

    r267 r282  
    122122-------------------------- 
    123123 
    124 See the model for 2-D  :math:`I(T,t,P,Q(t))` :ref:`images <2-D.images.with.varied.T.t.P>`. 
     124See the model for 2-D  :math:`I(T,t,P,Q(t))` :ref:`images <example 2-D.images.with.varied.T.t.P>`. 
    125125 
    126126        Given the indices ``i,j,k,l,m``, return all values for this datum:: 
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