Changeset 1179


Ignore:
Timestamp:
Dec 30, 2013 1:02:16 PM (8 years ago)
Author:
vondreele
Message:
 
Location:
trunk
Files:
2 edited

Legend:

Unmodified
Added
Removed
  • trunk/GSASIIimage.py

    r1178 r1179  
    579579    Ring = makeRing(1.0,ellipse,pixLimit,cutoff,scalex,scaley,self.ImageZ)
    580580    if Ring:
    581         ellipse = FitEllipse(ring)
     581        ellipse = FitEllipse(Ring)
    582582        Ring = makeRing(1.0,ellipse,pixLimit,cutoff,scalex,scaley,self.ImageZ)    #do again
    583         ellipse = FitEllipse(ring)
     583        ellipse = FitEllipse(Ring)
    584584    else:
    585585        print '1st ring not sufficiently complete to proceed'
     
    861861    'Needs a doc string'
    862862   
    863 #    print 'Masks:',Masks
    864863    StaControls = copy.deepcopy(Controls)
    865864    phi = StrSta['Sample phi']
  • trunk/GSASIIobj.py

    r1168 r1179  
    457457  key                      sub-key        explanation
    458458======================  ===============  ====================================================
     459Comments                      \           Text strings extracted from the original powder
     460                                          data header. These cannot be changed by the user;
     461                                          it may be empty.
    459462Limits                       \            A list of two two element lists, as [[Ld,Hd],[L,H]]
    460463                                          where L and Ld are the current and default lowest
     
    518521\                         Absorption      The sample absorption coefficient as
    519522                                          :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)                                         
    521529\                         DisplaceX,      Sample displacement from goniometer center
    522530                          DisplaceY       where Y is along the beam direction and
     
    676684==========  ====================================================
    677685
     686Image Data Structure
     687--------------------
     688
     689.. _Image_table:
     690
     691.. index::
     692   image: Image data object description
     693   image: Image object descriptions
     694   
     695Every 2-dimensional image is stored in the GSAS-II data tree
     696with a top-level entry named beginning with the string "IMG ". The
     697image data are directly associated with that tree item and there
     698are a series of children to that item. The routines :func:`GSASII.GSASII.GetUsedHistogramsAndPhasesfromTree`
     699and :func:`GSASIIstrIO.GetUsedHistogramsAndPhases` will
     700load this information into a dictionary where the child tree name is
     701used as a key, and the information in the main entry is assigned
     702a key of ``Data``, as outlined below.
     703
     704.. tabularcolumns:: |l|l|p{4in}|
     705
     706======================  ======================  ====================================================
     707  key                      sub-key              explanation
     708======================  ======================  ====================================================
     709Comments                       \                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.                                               
     712Image 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                                               
     781Masks                       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                                               
     794Stress/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======================  ======================  ====================================================
    678809
    679810*Classes and routines*
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