Jan 5, 2014 9:22:22 AM (8 years ago)

fixup number formatting; update produced doc files

1 edited


  • trunk/sphinxdocs/build/html/GSASIIobj.html

    r1168 r1183  
    871871<table border="1" class="docutils">
    873 <col width="25%" />
     873<col width="24%" />
    874874<col width="17%" />
    875 <col width="58%" />
     875<col width="59%" />
    877877<thead valign="bottom">
    883883<tbody valign="top">
    884 <tr class="row-even"><td>Limits</td>
     884<tr class="row-even"><td>Comments</td>
     886<td>Text strings extracted from the original powder
     887data header. These cannot be changed by the user;
     888it may be empty.</td>
     890<tr class="row-odd"><td>Limits</td>
    886892<td>A list of two two element lists, as [[Ld,Hd],[L,H]]
    890896two-theta value to be used.</td>
    892 <tr class="row-odd"><td>Reflection Lists</td>
     898<tr class="row-even"><td>Reflection Lists</td>
    894900<td>A dict with an entry for each phase in the
    900 <tr class="row-even"><td>Instrument Parameters</td>
     906<tr class="row-odd"><td>Instrument Parameters</td>
    902908<td>A list containing two dicts where the possible
    910916Items in the first dict are noted as [1]</td>
    912 <tr class="row-odd"><td></td>
     918<tr class="row-even"><td></td>
    914920<td>Specifies a wavelength in Angstroms [1]</td>
    916 <tr class="row-even"><td></td>
     922<tr class="row-odd"><td></td>
    918924<td>Specifies the primary wavelength in
    920926source is used [1]</td>
    922 <tr class="row-odd"><td></td>
     928<tr class="row-even"><td></td>
    923929<td><p class="first">Lam2</p>
    924930<p class="last">I(L2)/I(L1)</p>
    929935Ratio of Lam2 to Lam1 [1]</td>
    931 <tr class="row-even"><td></td>
     937<tr class="row-odd"><td></td>
    933939<td><dl class="first last docutils">
    944 <tr class="row-odd"><td></td>
     950<tr class="row-even"><td></td>
    946952<td>Two-theta zero correction in <em>degrees</em> [1]</td>
    948 <tr class="row-even"><td></td>
     954<tr class="row-odd"><td></td>
    950956<td>Azimuthal setting angle for data recorded
    951957with differing setting angles [1]</td>
    953 <tr class="row-odd"><td></td>
     959<tr class="row-even"><td></td>
    954960<td>U, V, W</td>
    955961<td>Cagliotti profile coefficients
    958964<span class="math">\(U \tan^2\theta + V \tan\theta + W\)</span> [1]</td>
    960 <tr class="row-even"><td></td>
     966<tr class="row-odd"><td></td>
    961967<td>X, Y</td>
    962968<td>Cauchy (Lorentzian) instrumental broadening
    963969coefficients [1]</td>
    965 <tr class="row-odd"><td></td>
     971<tr class="row-even"><td></td>
    967973<td>Variant of the Finger-Cox-Jephcoat asymmetric
    971977L is the goniometer diameter. [1]</td>
    973 <tr class="row-even"><td></td>
     979<tr class="row-odd"><td></td>
    975981<td>Polarization coefficient. [1]</td>
    977 <tr class="row-odd"><td>wtFactor</td>
     983<tr class="row-even"><td>wtFactor</td>
    979985<td>A weighting factor to increase or decrease
    984990to decreasing the uncertainties).</td>
    986 <tr class="row-even"><td>Sample Parameters</td>
     992<tr class="row-odd"><td>Sample Parameters</td>
    988994<td>Specifies a dict with parameters that describe how
    993999the value is a float unless otherwise noted.</td>
    995 <tr class="row-odd"><td></td>
     1001<tr class="row-even"><td></td>
    9971003<td>The histogram scale factor (refinable)</td>
    999 <tr class="row-even"><td></td>
     1005<tr class="row-odd"><td></td>
    10011007<td>The sample absorption coefficient as
    10021008<span class="math">\(\mu r\)</span> where r is the radius
    1003 (refinable).</td>
    1004 </tr>
    1005 <tr class="row-odd"><td></td>
     1009(refinable). Only valid for Debye-Scherrer geometry.</td>
     1011<tr class="row-even"><td></td>
     1013<td>Surface roughness parameter A as defined by
     1014Surotti,J. Appl. Cryst, 5,325-331, 1972.(refinable -
     1015only valid for Bragg-Brentano geometry)</td>
     1017<tr class="row-odd"><td></td>
     1019<td>Surface roughness parameter B (refinable -
     1020only valid for Bragg-Brentano geometry)</td>
     1022<tr class="row-even"><td></td>
    1013 <tr class="row-even"><td></td>
     1030<tr class="row-odd"><td></td>
    10141031<td>Phi, Chi,
    10161033<td>Goniometer sample setting angles, in degrees.</td>
    1018 <tr class="row-odd"><td></td>
     1035<tr class="row-even"><td></td>
    10191036<td>Gonio. radius</td>
    10201037<td>Radius of the diffractometer in mm</td>
    1022 <tr class="row-even"><td></td>
     1039<tr class="row-odd"><td></td>
    10241041<td>A name for the instrument, used in preparing
    10251042a CIF (str).</td>
    1027 <tr class="row-odd"><td></td>
     1044<tr class="row-even"><td></td>
    10351052any computations.</td>
    1037 <tr class="row-even"><td></td>
     1054<tr class="row-odd"><td></td>
    10391056<td>The random-number Id for the histogram
    10401057(same value as where top-level key is ranId)</td>
    1042 <tr class="row-odd"><td></td>
     1059<tr class="row-even"><td></td>
    10441061<td>Type of diffraction data, may be &#8216;Debye-Scherrer&#8217;
    10451062or &#8216;Bragg-Brentano&#8217; (str).</td>
    1047 <tr class="row-even"><td></td>
     1064<tr class="row-odd"><td></td>
    10491066<td>not in use?</td>
    1051 <tr class="row-odd"><td>hId</td>
     1068<tr class="row-even"><td>hId</td>
    10531070<td>The number assigned to the histogram when
    10541071the project is loaded or edited (can change)</td>
    1056 <tr class="row-even"><td>ranId</td>
     1073<tr class="row-odd"><td>ranId</td>
    10581075<td>A random number id for the histogram
    10591076that does not change</td>
    1061 <tr class="row-odd"><td>Background</td>
     1078<tr class="row-even"><td>Background</td>
    10631080<td>The background is stored as a list with where
    10681085(TODO: this needs to be expanded.)</td>
    1070 <tr class="row-even"><td>Data</td>
     1087<tr class="row-odd"><td>Data</td>
    10721089<td><p class="first">The data consist of a list of 6 np.arrays
     1292<div class="section" id="image-data-structure">
     1293<h2>Image Data Structure<a class="headerlink" href="#image-data-structure" title="Permalink to this headline">¶</a></h2>
     1294<span class="target" id="image-table"></span><p id="index-12">Every 2-dimensional image is stored in the GSAS-II data tree
     1295with a top-level entry named beginning with the string &#8220;IMG &#8221;. The
     1296image data are directly associated with that tree item and there
     1297are a series of children to that item. The routines <a class="reference internal" href="GSASII.html#GSASII.GSASII.GetUsedHistogramsAndPhasesfromTree" title="GSASII.GSASII.GetUsedHistogramsAndPhasesfromTree"><tt class="xref py py-func docutils literal"><span class="pre">GSASII.GSASII.GetUsedHistogramsAndPhasesfromTree()</span></tt></a>
     1298and <a class="reference internal" href="GSASIIstruc.html#GSASIIstrIO.GetUsedHistogramsAndPhases" title="GSASIIstrIO.GetUsedHistogramsAndPhases"><tt class="xref py py-func docutils literal"><span class="pre">GSASIIstrIO.GetUsedHistogramsAndPhases()</span></tt></a> will
     1299load this information into a dictionary where the child tree name is
     1300used as a key, and the information in the main entry is assigned
     1301a key of <tt class="docutils literal"><span class="pre">Data</span></tt>, as outlined below.</p>
     1302<table border="1" class="docutils">
     1304<col width="12%" />
     1305<col width="12%" />
     1306<col width="76%" />
     1308<thead valign="bottom">
     1309<tr class="row-odd"><th class="head">key</th>
     1310<th class="head">sub-key</th>
     1311<th class="head">explanation</th>
     1314<tbody valign="top">
     1315<tr class="row-even"><td>Comments</td>
     1317<td>Text strings extracted from the original image data
     1318header or a metafile. These cannot be changed by
     1319the user; it may be empty.</td>
     1321<tr class="row-odd"><td>Image Controls</td>
     1323<td>(float) The offset to be applied to an azimuthal
     1324value. Accomodates
     1325detector orientations other than with the detector
     1329<tr class="row-even"><td></td>
     1330<td>background image</td>
     1331<td>(list:str,float) The name of a tree item (&#8220;IMG ...&#8221;) that is to be subtracted
     1332during image integration multiplied by value. It must have the same size/shape as
     1333the integrated image. NB: value &lt; 0 for subtraction.</td>
     1335<tr class="row-odd"><td></td>
     1337<td>(str) The material used for determining the position/orientation
     1338of the image. The data is obtained from <a class="reference internal" href="GSASIIutil.html#module-ImageCalibrants" title="ImageCalibrants"><tt class="xref py py-func docutils literal"><span class="pre">ImageCalibrants()</span></tt></a>
     1339and UserCalibrants.py (supplied by user).</td>
     1341<tr class="row-even"><td></td>
     1343<td>(float) The minimum d-spacing used during the last calibration run.</td>
     1345<tr class="row-odd"><td></td>
     1347<td>(int) The number of expected diffraction lines skipped during the last
     1348calibration run.</td>
     1350<tr class="row-even"><td></td>
     1352<td>(list:floats) The [X,Y] point in detector coordinates (mm) where the direct beam
     1353strikes the detector plane as determined by calibration. This point
     1354does not have to be within the limits of the detector boundaries.</td>
     1356<tr class="row-odd"><td></td>
     1358<td>(bool) If True then the azimuth reported for the integrated slice
     1359of the image is at the center line otherwise it is at the leading edge.</td>
     1361<tr class="row-even"><td></td>
     1363<td>(str) The name of the colormap used to display the image. Default = &#8216;Paired&#8217;.</td>
     1365<tr class="row-odd"><td></td>
     1367<td>(float) The minimum value of I/Ib for a point selected in a diffraction ring for
     1368calibration calculations. See pixLimit for details as how point is found.</td>
     1370<tr class="row-even"><td></td>
     1372<td>(float) Coefficient for penetration correction to distance; accounts for diffraction
     1373ring offset at higher angles. Optionally determined by calibration.</td>
     1375<tr class="row-odd"><td></td>
     1377<td>(bool) If True then refine DetDepth during calibration/recalibration calculation.</td>
     1379<tr class="row-even"><td></td>
     1381<td>(float) The distance (mm) from sample to detector plane.</td>
     1383<tr class="row-odd"><td></td>
     1385<td>(list:lists) Each object in ellipses is a list [center,phi,radii,color] where
     1386center (list) is location (mm) of the ellipse center on the detector plane, phi is the
     1387rotation of the ellipse minor axis from the x-axis, and radii are the minor &amp; major
     1388radii of the ellipse. If radii[0] is negative then parameters describe a hyperbola. Color
     1389is the selected drawing color (one of &#8216;b&#8217;, &#8216;g&#8217; ,&#8217;r&#8217;) for the ellipse/hyperbola.</td>
     1391<tr class="row-even"><td></td>
     1393<td>(float) Not used;  parameter in EdgeFinder code.</td>
     1395<tr class="row-odd"><td></td>
     1397<td>(bool) If True then integrate over full 360 deg azimuthal range.</td>
     1399<tr class="row-even"><td></td>
     1401<td>(list:floats) The &#8216;Omega&#8217;,&#8217;Chi&#8217;,&#8217;Phi&#8217; goniometer angles used for this image.
     1402Required for texture calculations.</td>
     1404<tr class="row-odd"><td></td>
     1406<td>(bool) If True display the image with the x-axis inverted.</td>
     1408<tr class="row-even"><td></td>
     1410<td>(bool) If True display the image with the y-axis inverted.</td>
     1412<tr class="row-odd"><td></td>
     1414<td>(list:floats) The minimum and maximum 2-theta values to be used for integration.</td>
     1416<tr class="row-even"><td></td>
     1418<td>(list:floats) The minimum and maximum azimuth values to be used for integration.</td>
     1420<tr class="row-odd"><td></td>
     1422<td>(list:float,bool) If True apply a detector absorption correction using the value to the
     1423intensities obtained during integration.</td>
     1425<tr class="row-even"><td></td>
     1427<td>(int) The number of azimuth pie slices.</td>
     1429<tr class="row-odd"><td></td>
     1431<td>(int) The number of 2-theta steps.</td>
     1433<tr class="row-even"><td></td>
     1435<td>(list:ints) The X,Y dimensions (microns) of each pixel.</td>
     1437<tr class="row-odd"><td></td>
     1439<td>(int) A box in the image with 2*pixLimit+1 edges is searched to find the maximum.
     1440This value (I) along with the minimum (Ib) in the box is reported by <a class="reference internal" href="GSASIIimage.html#GSASIIimage.ImageLocalMax" title="GSASIIimage.ImageLocalMax"><tt class="xref py py-func docutils literal"><span class="pre">GSASIIimage.ImageLocalMax()</span></tt></a>
     1441and subject to cutoff in <a class="reference internal" href="GSASIIimage.html#GSASIIimage.makeRing" title="GSASIIimage.makeRing"><tt class="xref py py-func docutils literal"><span class="pre">GSASIIimage.makeRing()</span></tt></a>.
     1442Locations are used to construct rings of points for calibration calcualtions.</td>
     1444<tr class="row-even"><td></td>
     1446<td>(list:float,bool) If type=&#8217;SASD&#8217; and if True, apply polarization correction to intensities from
     1447integration using value.</td>
     1449<tr class="row-odd"><td></td>
     1451<td>(list:lists) Each entry is [X,Y,dsp] where X &amp; Y are lists of x,y coordinates around a
     1452diffraction ring with the same d-spacing (dsp)</td>
     1454<tr class="row-even"><td></td>
     1456<td>(list) The x,y coordinates of the &gt;5 points on an inner ring
     1457selected by the user,</td>
     1459<tr class="row-odd"><td></td>
     1461<td>(list) The minimum &amp; maximum values of the image</td>
     1463<tr class="row-even"><td></td>
     1465<td>(float) The angle between the x-axis and the vector about which the
     1466detector is tilted. Constrained to -180 to 180 deg.</td>
     1468<tr class="row-odd"><td></td>
     1470<td>(str) Currently only &#8216;Cylinder&#8217;. Sample shape for Debye-Scherrer experiments; used for absorption
     1473<tr class="row-even"><td></td>
     1475<td>(list: float,bool) Value of absorption coefficient for Debye-Scherrer experimnents, flag if True
     1476to cause correction to be applied.</td>
     1478<tr class="row-odd"><td></td>
     1480<td>(bool) If True the use the image controls values for all new images to be read. (might be removed)</td>
     1482<tr class="row-even"><td></td>
     1484<td>(bool) If True then display all the selected x,y ring positions (vida supra rings) used in the calibration.</td>
     1486<tr class="row-odd"><td></td>
     1488<td>(bool) If True then isplay the integration limits to be used.</td>
     1490<tr class="row-even"><td></td>
     1492<td>(list:int) The number of pixels on the image x &amp; y axes</td>
     1494<tr class="row-odd"><td></td>
     1496<td>(str) One of &#8216;PWDR&#8217;, &#8216;SASD&#8217; or &#8216;REFL&#8217; for powder, small angle or reflectometry data, respectively.</td>
     1498<tr class="row-even"><td></td>
     1500<td>(float) The angle the detector normal makes with the incident beam; range -90 to 90.</td>
     1502<tr class="row-odd"><td></td>
     1504<td>(float) Tha radiation wavelength (Angstroms) as entered by the user (or someday obtained from the image header).</td>
     1506<tr class="row-even"><td>Masks</td>
     1508<td>(list: lists) Each entry [2-theta,[azimuth[0],azimuth[1]],thickness] describes an arc mask
     1509to be excluded from integration</td>
     1511<tr class="row-odd"><td></td>
     1513<td>(list:lists) Each entry describes the x,y points (3 or more - mm) that describe a frame outside
     1514of which is excluded from recalibration and integration. Only one frame is allowed.</td>
     1516<tr class="row-even"><td></td>
     1518<td>(list:lists) Each entry [x,y,radius] (mm) describes an excluded spot on the image to be excluded
     1519from integration.</td>
     1521<tr class="row-odd"><td></td>
     1523<td>(list:lists) Each entry is a list of 3+ [x,y] points (mm) that describe a polygon on the image
     1524to be excluded from integration.</td>
     1526<tr class="row-even"><td></td>
     1528<td>(list: lists) Each entry [2-theta,thickness] describes a ring mask
     1529to be excluded from integration.</td>
     1531<tr class="row-odd"><td></td>
     1533<td>(list:[tuple,list]) [(Imin,Imax),[Imin,Imax]] This gives lower and upper limits for points on the image to be included
     1534in integrsation. The tuple is the image intensity limits and the list are those set by the user.</td>
     1536<tr class="row-even"><td>Stress/Strain</td>
     1537<td>Sample phi</td>
     1538<td>(float) Sample rotation about vertical axis.</td>
     1540<tr class="row-odd"><td></td>
     1541<td>Sample z</td>
     1542<td>(float) Sample translation from the calibration sample position (for Sample phi = 0)</td>
     1544<tr class="row-even"><td></td>
     1546<td>(list: 3x3 array of float) The strain tensor coefficients [[&#8216; e11&#8217;,&#8217;e12&#8217;,&#8217;e13&#8217;],[&#8216; e21&#8217;,&#8217;e22&#8217;,&#8217;e23&#8217;],[&#8216; e31&#8217;,&#8217;e32&#8217;,&#8217;e33&#8217;]].
     1547These will be restricted by space group symmetry; result of strain fit refinement.</td>
     1549<tr class="row-odd"><td></td>
     1551<td>(str) &#8216;True&#8217; or &#8216;Conventional&#8217;: The strain model used for the calculation.</td>
     1553<tr class="row-even"><td></td>
     1555<td>(list:dict) Each item is for a diffraction ring on the image; all items are from the same phase and are used to determine the strain tensor.
     1556The dictionary items are:
     1557&#8216;Dset&#8217;: (float) True d-spacing for the diffraction ring; entered by the user.
     1558&#8216;Dcalc&#8217;: (float) d-spacing...
     1559&#8216;pixLimit&#8217;: (int) Search range to find highest point on ring for each data point
     1560&#8216;cutoff&#8217;: (float) I/Ib cutoff for searching.
     1561&#8216;ImxyObs&#8217;: (list:lists) [[X],[Y]] observed points to be used for strain calculations.
     1562&#8216;ImxyCalc&#8217;:(list:lists) [[X],[Y]] calculated points based on refined strain.</td>
     1567<div class="section" id="parameter-dictionary">
     1568<h2>Parameter Dictionary<a class="headerlink" href="#parameter-dictionary" title="Permalink to this headline">¶</a></h2>
     1569<span class="target" id="parmdict-table"></span><p id="index-13">The parameter dictionary contains all of the variable parameters for the refinement.
     1570The dictionary keys are the name of the parameter (&lt;phase&gt;:&lt;hist&gt;:&lt;name&gt;:&lt;atom&gt;).
     1571It is prepared in two ways. When loaded from the tree
     1572(in <a class="reference internal" href="GSASII.html#GSASII.GSASII.MakeLSParmDict" title="GSASII.GSASII.MakeLSParmDict"><tt class="xref py py-meth docutils literal"><span class="pre">GSASII.GSASII.MakeLSParmDict()</span></tt></a> and
     1573<a class="reference internal" href="GSASIIGUIr.html#GSASIIIO.ExportBaseclass.loadParmDict" title="GSASIIIO.ExportBaseclass.loadParmDict"><tt class="xref py py-meth docutils literal"><span class="pre">GSASIIIO.ExportBaseclass.loadParmDict()</span></tt></a>),
     1574the values are lists with two elements: <tt class="docutils literal"><span class="pre">[value,</span> <span class="pre">refine</span> <span class="pre">flag]</span></tt></p>
     1575<p>When loaded from the GPX file (in
     1576<a class="reference internal" href="GSASIIstruc.html#GSASIIstrMain.Refine" title="GSASIIstrMain.Refine"><tt class="xref py py-func docutils literal"><span class="pre">GSASIIstrMain.Refine()</span></tt></a> and <a class="reference internal" href="GSASIIstruc.html#GSASIIstrMain.SeqRefine" title="GSASIIstrMain.SeqRefine"><tt class="xref py py-func docutils literal"><span class="pre">GSASIIstrMain.SeqRefine()</span></tt></a>), the value in the
     1577dict is the actual parameter value (usually a float, but sometimes a
     1578letter or string flag value (such as I or A for iso/anisotropic).</p>
    12751580<div class="section" id="classes-and-routines">
    12761581<h2><em>Classes and routines</em><a class="headerlink" href="#classes-and-routines" title="Permalink to this headline">¶</a></h2>
    14031708<p>This is called in two places (only) <a class="reference internal" href="GSASIIstruc.html#GSASIIstrIO.GetUsedHistogramsAndPhases" title="GSASIIstrIO.GetUsedHistogramsAndPhases"><tt class="xref py py-func docutils literal"><span class="pre">GSASIIstrIO.GetUsedHistogramsAndPhases()</span></tt></a>
    14041709(which loads the histograms and phases from a GPX file) and
    1405 <tt class="xref py py-meth docutils literal"><span class="pre">GSASII.GSASII.GetUsedHistogramsAndPhases()</span></tt>
     1710<a class="reference internal" href="GSASII.html#GSASII.GSASII.GetUsedHistogramsAndPhasesfromTree" title="GSASII.GSASII.GetUsedHistogramsAndPhasesfromTree"><tt class="xref py py-meth docutils literal"><span class="pre">GSASII.GSASII.GetUsedHistogramsAndPhasesfromTree()</span></tt></a>
    14061711(which loads the histograms and phases from the data tree.)</p>
    14071712<p>TODO: do we need a lookup for rigid body variables?</p>
    1533 <tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">lbl if not found in labellist or lbl with <tt class="docutils literal"><span class="pre">_1-9`</span> <span class="pre">(or</span>
    1534 <span class="pre">``_10-99</span></tt>, etc.) appended at the end</p>
     1838<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">lbl if not found in labellist or lbl with <tt class="docutils literal"><span class="pre">_1-9</span></tt> (or
     1839<tt class="docutils literal"><span class="pre">_10-99</span></tt>, etc.) appended at the end</p>
    16651970<li><a class="reference internal" href="#single-crystal-tree-items">Single Crystal Tree Items</a></li>
    16661971<li><a class="reference internal" href="#single-crystal-reflection-data-structure">Single Crystal Reflection Data Structure</a></li>
     1972<li><a class="reference internal" href="#image-data-structure">Image Data Structure</a></li>
     1973<li><a class="reference internal" href="#parameter-dictionary">Parameter Dictionary</a></li>
    16671974<li><a class="reference internal" href="#classes-and-routines"><em>Classes and routines</em></a></li>
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