Changeset 1179
- Timestamp:
- Dec 30, 2013 1:02:16 PM (9 years ago)
- Location:
- trunk
- Files:
-
- 2 edited
-
GSASIIimage.py (modified) (2 diffs)
-
GSASIIobj.py (modified) (3 diffs)
Legend:
- Unmodified
- Added
- Removed
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trunk/GSASIIimage.py
r1178 r1179 579 579 Ring = makeRing(1.0,ellipse,pixLimit,cutoff,scalex,scaley,self.ImageZ) 580 580 if Ring: 581 ellipse = FitEllipse( ring)581 ellipse = FitEllipse(Ring) 582 582 Ring = makeRing(1.0,ellipse,pixLimit,cutoff,scalex,scaley,self.ImageZ) #do again 583 ellipse = FitEllipse( ring)583 ellipse = FitEllipse(Ring) 584 584 else: 585 585 print '1st ring not sufficiently complete to proceed' … … 861 861 'Needs a doc string' 862 862 863 # print 'Masks:',Masks864 863 StaControls = copy.deepcopy(Controls) 865 864 phi = StrSta['Sample phi'] -
trunk/GSASIIobj.py
r1168 r1179 457 457 key sub-key explanation 458 458 ====================== =============== ==================================================== 459 Comments \ Text strings extracted from the original powder 460 data header. These cannot be changed by the user; 461 it may be empty. 459 462 Limits \ A list of two two element lists, as [[Ld,Hd],[L,H]] 460 463 where L and Ld are the current and default lowest … … 518 521 \ Absorption The sample absorption coefficient as 519 522 :math:`\\mu r` where r is the radius 520 (refinable). 523 (refinable). Only valid for Debye-Scherrer geometry. 524 \ SurfaceRoughA Surface roughness parameter A as defined by 525 Surotti,J. Appl. Cryst, 5,325-331, 1972.(refinable - 526 only valid for Bragg-Brentano geometry) 527 \ SurfaceRoughB Surface roughness parameter B (refinable - 528 only valid for Bragg-Brentano geometry) 521 529 \ DisplaceX, Sample displacement from goniometer center 522 530 DisplaceY where Y is along the beam direction and … … 676 684 ========== ==================================================== 677 685 686 Image Data Structure 687 -------------------- 688 689 .. _Image_table: 690 691 .. index:: 692 image: Image data object description 693 image: Image object descriptions 694 695 Every 2-dimensional image is stored in the GSAS-II data tree 696 with a top-level entry named beginning with the string "IMG ". The 697 image data are directly associated with that tree item and there 698 are a series of children to that item. The routines :func:`GSASII.GSASII.GetUsedHistogramsAndPhasesfromTree` 699 and :func:`GSASIIstrIO.GetUsedHistogramsAndPhases` will 700 load this information into a dictionary where the child tree name is 701 used as a key, and the information in the main entry is assigned 702 a key of ``Data``, as outlined below. 703 704 .. tabularcolumns:: |l|l|p{4in}| 705 706 ====================== ====================== ==================================================== 707 key sub-key explanation 708 ====================== ====================== ==================================================== 709 Comments \ Text strings extracted from the original image data 710 header or a metafile. These cannot be changed by 711 the user; it may be empty. 712 Image Controls azmthOff (float) The offset to be applied to an azimuthal 713 value. Accomodates 714 detector orientations other than with the detector 715 X-axis 716 horizontal. 717 \ background image (list:str,float) The name of a tree item ("IMG ...") that is to be subtracted 718 during image integration multiplied by value. It must have the same size/shape as 719 the integrated image. NB: value < 0 for subtraction. 720 \ calibrant (str) The material used for determining the position/orientation 721 of the image. The data is obtained from :func:`ImageCalibrants` 722 and UserCalibrants.py (supplied by user). 723 \ calibdmin (float) The minimum d-spacing used during the last calibration run. 724 \ calibskip (int) The number of expected diffraction lines skipped during the last 725 calibration run. 726 \ center (list:floats) The [X,Y] point in detector coordinates (mm) where the direct beam 727 strikes the detector plane as determined by calibration. This point 728 does not have to be within the limits of the detector boundaries. 729 \ centerAzm (bool) If True then the azimuth reported for the integrated slice 730 of the image is at the center line otherwise it is at the leading edge. 731 \ color (str) The name of the colormap used to display the image. Default = 'Paired'. 732 \ cutoff (float) The minimum value of I/Ib for a point selected in a diffraction ring for 733 calibration calculations. See pixLimit for details as how point is found. 734 \ DetDepth (float) Coefficient for penetration correction to distance; accounts for diffraction 735 ring offset at higher angles. Optionally determined by calibration. 736 \ DetDepthRef (bool) If True then refine DetDepth during calibration/recalibration calculation. 737 \ distance (float) The distance (mm) from sample to detector plane. 738 \ ellipses (list:lists) Each object in ellipses is a list [center,phi,radii,color] where 739 center (list) is location (mm) of the ellipse center on the detector plane, phi is the 740 rotation of the ellipse minor axis from the x-axis, and radii are the minor & major 741 radii of the ellipse. If radii[0] is negative then parameters describe a hyperbola. Color 742 is the selected drawing color (one of 'b', 'g' ,'r') for the ellipse/hyperbola. 743 \ edgemin (float) Not used; parameter in EdgeFinder code. 744 \ fullIntegrate (bool) If True then integrate over full 360 deg azimuthal range. 745 \ GonioAngles (list:floats) The 'Omega','Chi','Phi' goniometer angles used for this image. 746 Required for texture calculations. 747 \ invert_x (bool) If True display the image with the x-axis inverted. 748 \ invert_y (bool) If True display the image with the y-axis inverted. 749 \ IOtth (list:floats) The minimum and maximum 2-theta values to be used for integration. 750 \ LRazimuth (list:floats) The minimum and maximum azimuth values to be used for integration. 751 \ Oblique (list:float,bool) If True apply a detector absorption correction using the value to the 752 intensities obtained during integration. 753 \ outAzimuths (int) The number of azimuth pie slices. 754 \ outChannels (int) The number of 2-theta steps. 755 \ pixelSize (list:ints) The X,Y dimensions (microns) of each pixel. 756 \ pixLimit (int) A box in the image with 2*pixLimit+1 edges is searched to find the maximum. 757 This value (I) along with the minimum (Ib) in the box is reported by :func:`GSASIIimage.ImageLocalMax` 758 and subject to cutoff in :func:`GSASIIimage.makeRing`. 759 Locations are used to construct rings of points for calibration calcualtions. 760 \ PolaVal (list:float,bool) If type='SASD' and if True, apply polarization correction to intensities from 761 integration using value. 762 \ rings (list:lists) Each entry is [X,Y,dsp] where X & Y are lists of x,y coordinates around a 763 diffraction ring with the same d-spacing (dsp) 764 \ ring (list) The x,y coordinates of the >5 points on an inner ring 765 selected by the user, 766 \ Range (list) The minimum & maximum values of the image 767 \ rotation (float) The angle between the x-axis and the vector about which the 768 detector is tilted. Constrained to -180 to 180 deg. 769 \ SampleShape (str) Currently only 'Cylinder'. Sample shape for Debye-Scherrer experiments; used for absorption 770 calculations. 771 \ SampleAbs (list: float,bool) Value of absorption coefficient for Debye-Scherrer experimnents, flag if True 772 to cause correction to be applied. 773 \ setDefault (bool) If True the use the image controls values for all new images to be read. (might be removed) 774 \ setRings (bool) If True then display all the selected x,y ring positions (vida supra rings) used in the calibration. 775 \ showLines (bool) If True then isplay the integration limits to be used. 776 \ size (list:int) The number of pixels on the image x & y axes 777 \ type (str) One of 'PWDR', 'SASD' or 'REFL' for powder, small angle or reflectometry data, respectively. 778 \ tilt (float) The angle the detector normal makes with the incident beam; range -90 to 90. 779 \ wavelength (float) Tha radiation wavelength (Angstroms) as entered by the user (or someday obtained from the image header). 780 781 Masks Arcs (list: lists) Each entry [2-theta,[azimuth[0],azimuth[1]],thickness] describes an arc mask 782 to be excluded from integration 783 \ Frames (list:lists) Each entry describes the x,y points (3 or more - mm) that describe a frame outside 784 of which is excluded from recalibration and integration. Only one frame is allowed. 785 \ Points (list:lists) Each entry [x,y,radius] (mm) describes an excluded spot on the image to be excluded 786 from integration. 787 \ Polygons (list:lists) Each entry is a list of 3+ [x,y] points (mm) that describe a polygon on the image 788 to be excluded from integration. 789 \ Rings (list: lists) Each entry [2-theta,thickness] describes a ring mask 790 to be excluded from integration. 791 \ Thresholds (list:[tuple,list]) [(Imin,Imax),[Imin,Imax]] This gives lower and upper limits for points on the image to be included 792 in integrsation. The tuple is the image intensity limits and the list are those set by the user. 793 794 Stress/Strain Sample phi (float) Sample rotation about vertical axis. 795 \ Sample z (float) Sample translation from the calibration sample position (for Sample phi = 0) 796 \ strain (list: 3x3 array of float) The strain tensor coefficients [[' e11','e12','e13'],[' e21','e22','e23'],[' e31','e32','e33']]. 797 These will be restricted by space group symmetry; result of strain fit refinement. 798 \ Type (str) 'True' or 'Conventional': The strain model used for the calculation. 799 \ 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. 800 The dictionary items are: 801 'Dset': (float) True d-spacing for the diffraction ring; entered by the user. 802 'Dcalc': (float) d-spacing... 803 'pixLimit': (int) Search range to find highest point on ring for each data point 804 'cutoff': (float) I/Ib cutoff for searching. 805 'ImxyObs': (list:lists) [[X],[Y]] observed points to be used for strain calculations. 806 'ImxyCalc':(list:lists) [[X],[Y]] calculated points based on refined strain. 807 808 ====================== ====================== ==================================================== 678 809 679 810 *Classes and routines*
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