Changeset 1183 for trunk/sphinxdocs/build/html/_modules/GSASIIobj.html
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- Jan 5, 2014 9:22:22 AM (8 years ago)
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trunk/sphinxdocs/build/html/_modules/GSASIIobj.html
r1168 r1183 54 54 <span class="c">#GSASIIobj - data objects for GSAS-II</span> 55 55 <span class="c">########### SVN repository information ###################</span> 56 <span class="c"># $Date: 201 3-11-22 16:24:29 -0600 (Fri, 22 Nov 2013) $</span>56 <span class="c"># $Date: 2014-01-02 14:18:25 -0600 (Thu, 02 Jan 2014) $</span> 57 57 <span class="c"># $Author: toby $</span> 58 <span class="c"># $Revision: 11 47$</span>58 <span class="c"># $Revision: 1181 $</span> 59 59 <span class="c"># $URL: https://subversion.xor.aps.anl.gov/pyGSAS/trunk/GSASIIobj.py $</span> 60 <span class="c"># $Id: GSASIIobj.py 11 47 2013-11-22 22:24:29Z toby $</span>60 <span class="c"># $Id: GSASIIobj.py 1181 2014-01-02 20:18:25Z toby $</span> 61 61 <span class="c">########### SVN repository information ###################</span> 62 62 … … 509 509 <span class="sd"> key sub-key explanation</span> 510 510 <span class="sd">====================== =============== ====================================================</span> 511 <span class="sd">Comments \ Text strings extracted from the original powder </span> 512 <span class="sd"> data header. These cannot be changed by the user; </span> 513 <span class="sd"> it may be empty.</span> 511 514 <span class="sd">Limits \ A list of two two element lists, as [[Ld,Hd],[L,H]]</span> 512 515 <span class="sd"> where L and Ld are the current and default lowest</span> … … 570 573 <span class="sd">\ Absorption The sample absorption coefficient as</span> 571 574 <span class="sd"> :math:`\\mu r` where r is the radius</span> 572 <span class="sd"> (refinable).</span> 575 <span class="sd"> (refinable). Only valid for Debye-Scherrer geometry.</span> 576 <span class="sd">\ SurfaceRoughA Surface roughness parameter A as defined by</span> 577 <span class="sd"> Surotti,J. Appl. Cryst, 5,325-331, 1972.(refinable - </span> 578 <span class="sd"> only valid for Bragg-Brentano geometry) </span> 579 <span class="sd">\ SurfaceRoughB Surface roughness parameter B (refinable - </span> 580 <span class="sd"> only valid for Bragg-Brentano geometry) </span> 573 581 <span class="sd">\ DisplaceX, Sample displacement from goniometer center</span> 574 582 <span class="sd"> DisplaceY where Y is along the beam direction and</span> … … 707 715 <span class="sd"> single: Data object descriptions; Single Crystal Reflections</span> 708 716 <span class="sd"> </span> 709 <span class="sd">For every si mgle crystal a histogram, the ``'Data'`` item contains</span>717 <span class="sd">For every single crystal a histogram, the ``'Data'`` item contains</span> 710 718 <span class="sd">the structure factors as an np.array in item `'RefList'`.</span> 711 719 <span class="sd">The columns in that array are documented below.</span> … … 728 736 <span class="sd">========== ====================================================</span> 729 737 738 <span class="sd">Image Data Structure</span> 739 <span class="sd">--------------------</span> 740 741 <span class="sd">.. _Image_table:</span> 742 743 <span class="sd">.. index::</span> 744 <span class="sd"> image: Image data object description</span> 745 <span class="sd"> image: Image object descriptions</span> 746 <span class="sd"> </span> 747 <span class="sd">Every 2-dimensional image is stored in the GSAS-II data tree</span> 748 <span class="sd">with a top-level entry named beginning with the string "IMG ". The</span> 749 <span class="sd">image data are directly associated with that tree item and there </span> 750 <span class="sd">are a series of children to that item. The routines :func:`GSASII.GSASII.GetUsedHistogramsAndPhasesfromTree`</span> 751 <span class="sd">and :func:`GSASIIstrIO.GetUsedHistogramsAndPhases` will</span> 752 <span class="sd">load this information into a dictionary where the child tree name is</span> 753 <span class="sd">used as a key, and the information in the main entry is assigned</span> 754 <span class="sd">a key of ``Data``, as outlined below.</span> 755 756 <span class="sd">.. tabularcolumns:: |l|l|p{4in}|</span> 757 758 <span class="sd">====================== ====================== ====================================================</span> 759 <span class="sd"> key sub-key explanation</span> 760 <span class="sd">====================== ====================== ====================================================</span> 761 <span class="sd">Comments \ Text strings extracted from the original image data </span> 762 <span class="sd"> header or a metafile. These cannot be changed by </span> 763 <span class="sd"> the user; it may be empty. </span> 764 <span class="sd">Image Controls azmthOff (float) The offset to be applied to an azimuthal </span> 765 <span class="sd"> value. Accomodates </span> 766 <span class="sd"> detector orientations other than with the detector </span> 767 <span class="sd"> X-axis</span> 768 <span class="sd"> horizontal.</span> 769 <span class="sd">\ background image (list:str,float) The name of a tree item ("IMG ...") that is to be subtracted</span> 770 <span class="sd"> during image integration multiplied by value. It must have the same size/shape as </span> 771 <span class="sd"> the integrated image. NB: value < 0 for subtraction.</span> 772 <span class="sd">\ calibrant (str) The material used for determining the position/orientation</span> 773 <span class="sd"> of the image. The data is obtained from :func:`ImageCalibrants` </span> 774 <span class="sd"> and UserCalibrants.py (supplied by user).</span> 775 <span class="sd">\ calibdmin (float) The minimum d-spacing used during the last calibration run.</span> 776 <span class="sd">\ calibskip (int) The number of expected diffraction lines skipped during the last</span> 777 <span class="sd"> calibration run.</span> 778 <span class="sd">\ center (list:floats) The [X,Y] point in detector coordinates (mm) where the direct beam</span> 779 <span class="sd"> strikes the detector plane as determined by calibration. This point </span> 780 <span class="sd"> does not have to be within the limits of the detector boundaries. </span> 781 <span class="sd">\ centerAzm (bool) If True then the azimuth reported for the integrated slice</span> 782 <span class="sd"> of the image is at the center line otherwise it is at the leading edge.</span> 783 <span class="sd">\ color (str) The name of the colormap used to display the image. Default = 'Paired'.</span> 784 <span class="sd">\ cutoff (float) The minimum value of I/Ib for a point selected in a diffraction ring for </span> 785 <span class="sd"> calibration calculations. See pixLimit for details as how point is found. </span> 786 <span class="sd">\ DetDepth (float) Coefficient for penetration correction to distance; accounts for diffraction</span> 787 <span class="sd"> ring offset at higher angles. Optionally determined by calibration.</span> 788 <span class="sd">\ DetDepthRef (bool) If True then refine DetDepth during calibration/recalibration calculation.</span> 789 <span class="sd">\ distance (float) The distance (mm) from sample to detector plane.</span> 790 <span class="sd">\ ellipses (list:lists) Each object in ellipses is a list [center,phi,radii,color] where</span> 791 <span class="sd"> center (list) is location (mm) of the ellipse center on the detector plane, phi is the </span> 792 <span class="sd"> rotation of the ellipse minor axis from the x-axis, and radii are the minor & major</span> 793 <span class="sd"> radii of the ellipse. If radii[0] is negative then parameters describe a hyperbola. Color</span> 794 <span class="sd"> is the selected drawing color (one of 'b', 'g' ,'r') for the ellipse/hyperbola.</span> 795 <span class="sd">\ edgemin (float) Not used; parameter in EdgeFinder code.</span> 796 <span class="sd">\ fullIntegrate (bool) If True then integrate over full 360 deg azimuthal range.</span> 797 <span class="sd">\ GonioAngles (list:floats) The 'Omega','Chi','Phi' goniometer angles used for this image. </span> 798 <span class="sd"> Required for texture calculations.</span> 799 <span class="sd">\ invert_x (bool) If True display the image with the x-axis inverted.</span> 800 <span class="sd">\ invert_y (bool) If True display the image with the y-axis inverted.</span> 801 <span class="sd">\ IOtth (list:floats) The minimum and maximum 2-theta values to be used for integration.</span> 802 <span class="sd">\ LRazimuth (list:floats) The minimum and maximum azimuth values to be used for integration.</span> 803 <span class="sd">\ Oblique (list:float,bool) If True apply a detector absorption correction using the value to the</span> 804 <span class="sd"> intensities obtained during integration.</span> 805 <span class="sd">\ outAzimuths (int) The number of azimuth pie slices.</span> 806 <span class="sd">\ outChannels (int) The number of 2-theta steps. </span> 807 <span class="sd">\ pixelSize (list:ints) The X,Y dimensions (microns) of each pixel.</span> 808 <span class="sd">\ pixLimit (int) A box in the image with 2*pixLimit+1 edges is searched to find the maximum.</span> 809 <span class="sd"> This value (I) along with the minimum (Ib) in the box is reported by :func:`GSASIIimage.ImageLocalMax`</span> 810 <span class="sd"> and subject to cutoff in :func:`GSASIIimage.makeRing`. </span> 811 <span class="sd"> Locations are used to construct rings of points for calibration calcualtions.</span> 812 <span class="sd">\ PolaVal (list:float,bool) If type='SASD' and if True, apply polarization correction to intensities from </span> 813 <span class="sd"> integration using value.</span> 814 <span class="sd">\ rings (list:lists) Each entry is [X,Y,dsp] where X & Y are lists of x,y coordinates around a </span> 815 <span class="sd"> diffraction ring with the same d-spacing (dsp)</span> 816 <span class="sd">\ ring (list) The x,y coordinates of the >5 points on an inner ring </span> 817 <span class="sd"> selected by the user,</span> 818 <span class="sd">\ Range (list) The minimum & maximum values of the image</span> 819 <span class="sd">\ rotation (float) The angle between the x-axis and the vector about which the </span> 820 <span class="sd"> detector is tilted. Constrained to -180 to 180 deg. </span> 821 <span class="sd">\ SampleShape (str) Currently only 'Cylinder'. Sample shape for Debye-Scherrer experiments; used for absorption</span> 822 <span class="sd"> calculations.</span> 823 <span class="sd">\ SampleAbs (list: float,bool) Value of absorption coefficient for Debye-Scherrer experimnents, flag if True</span> 824 <span class="sd"> to cause correction to be applied.</span> 825 <span class="sd">\ setDefault (bool) If True the use the image controls values for all new images to be read. (might be removed)</span> 826 <span class="sd">\ setRings (bool) If True then display all the selected x,y ring positions (vida supra rings) used in the calibration. </span> 827 <span class="sd">\ showLines (bool) If True then isplay the integration limits to be used.</span> 828 <span class="sd">\ size (list:int) The number of pixels on the image x & y axes</span> 829 <span class="sd">\ type (str) One of 'PWDR', 'SASD' or 'REFL' for powder, small angle or reflectometry data, respectively.</span> 830 <span class="sd">\ tilt (float) The angle the detector normal makes with the incident beam; range -90 to 90.</span> 831 <span class="sd">\ wavelength (float) Tha radiation wavelength (Angstroms) as entered by the user (or someday obtained from the image header).</span> 832 <span class="sd"> </span> 833 <span class="sd">Masks Arcs (list: lists) Each entry [2-theta,[azimuth[0],azimuth[1]],thickness] describes an arc mask</span> 834 <span class="sd"> to be excluded from integration</span> 835 <span class="sd">\ Frames (list:lists) Each entry describes the x,y points (3 or more - mm) that describe a frame outside</span> 836 <span class="sd"> of which is excluded from recalibration and integration. Only one frame is allowed.</span> 837 <span class="sd">\ Points (list:lists) Each entry [x,y,radius] (mm) describes an excluded spot on the image to be excluded</span> 838 <span class="sd"> from integration.</span> 839 <span class="sd">\ Polygons (list:lists) Each entry is a list of 3+ [x,y] points (mm) that describe a polygon on the image</span> 840 <span class="sd"> to be excluded from integration.</span> 841 <span class="sd">\ Rings (list: lists) Each entry [2-theta,thickness] describes a ring mask</span> 842 <span class="sd"> to be excluded from integration.</span> 843 <span class="sd">\ Thresholds (list:[tuple,list]) [(Imin,Imax),[Imin,Imax]] This gives lower and upper limits for points on the image to be included</span> 844 <span class="sd"> in integrsation. The tuple is the image intensity limits and the list are those set by the user. </span> 845 <span class="sd"> </span> 846 <span class="sd">Stress/Strain Sample phi (float) Sample rotation about vertical axis.</span> 847 <span class="sd">\ Sample z (float) Sample translation from the calibration sample position (for Sample phi = 0)</span> 848 <span class="sd">\ strain (list: 3x3 array of float) The strain tensor coefficients [[' e11','e12','e13'],[' e21','e22','e23'],[' e31','e32','e33']].</span> 849 <span class="sd"> These will be restricted by space group symmetry; result of strain fit refinement.</span> 850 <span class="sd">\ Type (str) 'True' or 'Conventional': The strain model used for the calculation.</span> 851 <span class="sd">\ d-zero (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.</span> 852 <span class="sd"> The dictionary items are:</span> 853 <span class="sd"> 'Dset': (float) True d-spacing for the diffraction ring; entered by the user.</span> 854 <span class="sd"> 'Dcalc': (float) d-spacing...</span> 855 <span class="sd"> 'pixLimit': (int) Search range to find highest point on ring for each data point</span> 856 <span class="sd"> 'cutoff': (float) I/Ib cutoff for searching.</span> 857 <span class="sd"> 'ImxyObs': (list:lists) [[X],[Y]] observed points to be used for strain calculations.</span> 858 <span class="sd"> 'ImxyCalc':(list:lists) [[X],[Y]] calculated points based on refined strain. </span> 859 <span class="sd"> </span> 860 <span class="sd">====================== ====================== ====================================================</span> 861 862 <span class="sd">Parameter Dictionary</span> 863 <span class="sd">-------------------------</span> 864 865 <span class="sd">.. _parmDict_table:</span> 866 867 <span class="sd">.. index::</span> 868 <span class="sd"> single: Parameter dictionary</span> 869 870 <span class="sd">The parameter dictionary contains all of the variable parameters for the refinement.</span> 871 <span class="sd">The dictionary keys are the name of the parameter (<phase>:<hist>:<name>:<atom>). </span> 872 <span class="sd">It is prepared in two ways. When loaded from the tree</span> 873 <span class="sd">(in :meth:`GSASII.GSASII.MakeLSParmDict` and</span> 874 <span class="sd">:meth:`GSASIIIO.ExportBaseclass.loadParmDict`), </span> 875 <span class="sd">the values are lists with two elements: ``[value, refine flag]``</span> 876 877 <span class="sd">When loaded from the GPX file (in</span> 878 <span class="sd">:func:`GSASIIstrMain.Refine` and :func:`GSASIIstrMain.SeqRefine`), the value in the</span> 879 <span class="sd">dict is the actual parameter value (usually a float, but sometimes a </span> 880 <span class="sd">letter or string flag value (such as I or A for iso/anisotropic). </span> 881 730 882 731 883 <span class="sd">*Classes and routines*</span> … … 738 890 <span class="kn">import</span> <span class="nn">GSASIImath</span> <span class="kn">as</span> <span class="nn">G2mth</span> 739 891 740 <span class="n">GSASIIpath</span><span class="o">.</span><span class="n">SetVersionNumber</span><span class="p">(</span><span class="s">"$Revision: 11 47$"</span><span class="p">)</span>892 <span class="n">GSASIIpath</span><span class="o">.</span><span class="n">SetVersionNumber</span><span class="p">(</span><span class="s">"$Revision: 1181 $"</span><span class="p">)</span> 741 893 742 894 <span class="n">DefaultControls</span> <span class="o">=</span> <span class="p">{</span> … … 759 911 <span class="sd"> :param str lbl: the input label</span> 760 912 <span class="sd"> :param list labellist: the labels that have already been encountered</span> 761 <span class="sd"> :returns: lbl if not found in labellist or lbl with ``_1-9` (or</span>913 <span class="sd"> :returns: lbl if not found in labellist or lbl with ``_1-9`` (or</span> 762 914 <span class="sd"> ``_10-99``, etc.) appended at the end</span> 763 915 <span class="sd"> '''</span> … … 842 994 <span class="sd"> This is called in two places (only) :func:`GSASIIstrIO.GetUsedHistogramsAndPhases`</span> 843 995 <span class="sd"> (which loads the histograms and phases from a GPX file) and</span> 844 <span class="sd"> :meth:`GSASII.GSASII.GetUsedHistogramsAndPhases `</span>996 <span class="sd"> :meth:`GSASII.GSASII.GetUsedHistogramsAndPhasesfromTree`</span> 845 997 <span class="sd"> (which loads the histograms and phases from the data tree.)</span> 846 998
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