diff --git a/demo/code/TinyDetector.m b/demo/code/TinyDetector.m
deleted file mode 100644
index 319dc06..0000000
--- a/demo/code/TinyDetector.m
+++ /dev/null
@@ -1,50 +0,0 @@
-classdef TinyDetector < geom.Detector
-    % 201-by-201 1 mm pixels with no gaps and no chips
-    methods
-        function obj = TinyDetector(varargin)
-            obj@geom.Detector(varargin{:});
-            a = defaultArgs();
-            n = fieldnames(a);
-            for j=1:length(n)
-                nj = n{j};
-                aj = a.(nj);
-                if isempty(obj.(nj))
-                    obj.(nj) = aj;
-                else
-                    if  ~isa(obj.(nj),class(aj)) || ...
-                            (ischar(aj) && ~strcmpi(aj,obj.(nj))) ||...
-                            (isnumeric(aj) && obj.(nj)~=aj)
-                        warning(['argument ''%s'' incompatible with',...
-                            'TinyDetector and may cause problems'],nj);
-                    end
-                end
-            end
-        end
-    end
-    methods (Static=true)
-        
-        function ind = chipIndex(ix,iy,mode)
-            % This mimics the behavior of geom.Pilatus6M, but always
-            % returns an index of 1
-            if nargin==0
-                mode = 'all';
-            elseif nargin==2
-                mode = 'pixels';
-            end
-            switch lower(mode)
-                case 'all'
-                    ind = ones(201,201);                    
-                case 'pixels'
-                    ind = ones(size(ix));
-                case 'nearest'
-                    ind = ones(size(ix));
-                otherwise
-                    error('did not recognize mode %s',mode);
-            end
-        end
-    end
-end
-
-function args = defaultArgs()
-args = struct('name','TinyDetector','nx',201,'ny',201,'qx',1,'qy',1);
-end
\ No newline at end of file
diff --git a/demo/code/custom_read_header.m b/demo/code/custom_read_header.m
deleted file mode 100644
index 8593860..0000000
--- a/demo/code/custom_read_header.m
+++ /dev/null
@@ -1,11 +0,0 @@
-function h = custom_read_header(fn)
-info = imfinfo(fn);
-header_text = info.ImageDescription;
-parsed_header = regexp(header_text,'(?<name>\S+)\s*:\s*(?<value>\S*)','names');
-
-h = struct();
-for j=1:numel(parsed_header)
-    h.(parsed_header(j).name) = str2double(parsed_header(j).value);
-end
-
-end
\ No newline at end of file
diff --git a/demo/code/custom_read_image.m b/demo/code/custom_read_image.m
deleted file mode 100644
index d22b214..0000000
--- a/demo/code/custom_read_image.m
+++ /dev/null
@@ -1,6 +0,0 @@
-function [im,h] = custom_read_image(fn)
-im = imread(fn);
-if nargout==2
-    h = custom_read_header(fn);
-end
-end
\ No newline at end of file
diff --git a/demo/code/input_geometry.m b/demo/code/input_geometry.m
deleted file mode 100644
index 2b255ad..0000000
--- a/demo/code/input_geometry.m
+++ /dev/null
@@ -1,116 +0,0 @@
-function input_geometry()
-% create input geometry objects 
-
-% diffraction geometry 
-Source = geom.Source(...
-        'wavelength',1,...
-        'direction',[0,0,1],...
-        'fractionOfPolarization',0.5,...
-        'polarizationPlaneNormal',[0,1,0]);
-
-Detector = TinyDetector(...
-        'nx',201,...
-        'ny',201,...
-        'qx',1,...
-        'qy',1,...
-        'f',200,...
-        'orgx',100,...
-        'orgy',100,...
-        'xShift',0,...
-        'yShift',0,...
-        'sensorMaterial','Si',...
-        'sensorThickness',1,...
-        'mask',true(201,201));
-    
-Crystal = geom.Crystal(...
-        'a',30.4897,...
-        'b',10,...
-        'c',10,...
-        'alpha',90,...
-        'beta',90,...
-        'gamma',90,...
-        'a_axis',[30.4897,0,0],...
-        'b_axis',[0,10,0],...
-        'c_axis',[0,0,10]);
-    
-Spindle = geom.Spindle(...
-        'rotationAxis',[-1,0,0],...
-        'startingFrame',1,...
-        'startingAngle',0,...
-        'oscillationRange',1);
-
-BkgSpindle = Spindle;
-BkgSpindle.oscillationRange = 10; % same as Spindle, but 10 degrees per image
-
-
-% geometry objects for reading images
-
-CrystalImageSeries = io.ImageSeries(...
-    'fileNameTemplate','images/crystal%04d.tif',...
-    'fileReadFunction', @custom_read_image,...
-    'headerReadFunction',@custom_read_header,...
-    'frameRange',[1,360]);
-
-BkgImageSeries = io.ImageSeries(...
-    'fileNameTemplate','images/background%04d.tif',...
-    'fileReadFunction', @custom_read_image,...
-    'headerReadFunction',@custom_read_header,...
-    'frameRange',[1,36]);
-
-
-% divide dataset into wedges
-
-frameStart = 1:10:360;
-frameEnd = frameStart + 10 - 1;
-
-frameStartBkg = 1:36;
-frameEndBkg = 1:36;
-
-IS = io.ImageSeries.empty();
-RS = geom.RotationSeries.empty();
-
-for j=1:numel(frameStart)
-    frameRange = [frameStart(j),frameEnd(j)];
-    IS(j) = io.ImageSeries(...
-        'frameRange',frameRange,...
-        'fileReadFunction',[],...
-        'headerReadFunction',[]);
-    RS(j) = geom.RotationSeries(Spindle);
-    RS(j).seriesFrameRange = frameRange;
-end
-
-BkgIS = io.ImageSeries.empty();
-
-for j=1:length(frameStart)
-    BkgIS(j) = io.ImageSeries(...
-        'frameRange',[frameStartBkg(j),frameEndBkg(j)],...
-        'fileReadFunction',[],...
-        'headerReadFunction',[]);
-end
-
-
-% prepare crystal geometry objects and save to proc/geom.mat
-
-InputGeometry = geom.DiffractionExperiment(...
-    'Crystal',Crystal,...
-    'Detector',Detector,...
-    'Source',Source,...
-    'Spindle',Spindle);
-
-RefinedGeometry = arrayfun(@(rs) geom.DiffractionExperiment('Spindle',rs),RS);
-
-InputImageSeries = CrystalImageSeries;
-
-WedgeImageSeries = IS;
-
-save proc/geom.mat InputGeometry RefinedGeometry InputImageSeries WedgeImageSeries
-
-
-% prepare background geometry objects and save to proc/geomBkg.mat
-
-InputImageSeries = BkgImageSeries;
-
-WedgeImageSeries = BkgIS;
-
-save proc/geomBkg.mat InputImageSeries WedgeImageSeries
-
diff --git a/demo/expected_results/process.html b/demo/expected_results/process.html
deleted file mode 100644
index 186b06e..0000000
--- a/demo/expected_results/process.html
+++ /dev/null
@@ -1,4400 +0,0 @@
-
-<!DOCTYPE html
-  PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
-<html><head>
-      <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
-   <!--
-This HTML was auto-generated from MATLAB code.
-To make changes, update the MATLAB code and republish this document.
-      --><title>Process</title><meta name="generator" content="MATLAB 9.4"><link rel="schema.DC" href="http://purl.org/dc/elements/1.1/"><meta name="DC.date" content="2020-01-17"><meta name="DC.source" content="process.m"><style type="text/css">
-html,body,div,span,applet,object,iframe,h1,h2,h3,h4,h5,h6,p,blockquote,pre,a,abbr,acronym,address,big,cite,code,del,dfn,em,font,img,ins,kbd,q,s,samp,small,strike,strong,sub,sup,tt,var,b,u,i,center,dl,dt,dd,ol,ul,li,fieldset,form,label,legend,table,caption,tbody,tfoot,thead,tr,th,td{margin:0;padding:0;border:0;outline:0;font-size:100%;vertical-align:baseline;background:transparent}body{line-height:1}ol,ul{list-style:none}blockquote,q{quotes:none}blockquote:before,blockquote:after,q:before,q:after{content:'';content:none}:focus{outine:0}ins{text-decoration:none}del{text-decoration:line-through}table{border-collapse:collapse;border-spacing:0}
-
-html { min-height:100%; margin-bottom:1px; }
-html body { height:100%; margin:0px; font-family:Arial, Helvetica, sans-serif; font-size:10px; color:#000; line-height:140%; background:#fff none; overflow-y:scroll; }
-html body td { vertical-align:top; text-align:left; }
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-h1 { padding:0px; margin:0px 0px 25px; font-family:Arial, Helvetica, sans-serif; font-size:1.5em; color:#d55000; line-height:100%; font-weight:normal; }
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-h3 { padding:0px; margin:0px 0px 5px; font-family:Arial, Helvetica, sans-serif; font-size:1.1em; color:#000; font-weight:bold; line-height:140%; }
-
-a { color:#005fce; text-decoration:none; }
-a:hover { color:#005fce; text-decoration:underline; }
-a:visited { color:#004aa0; text-decoration:none; }
-
-p { padding:0px; margin:0px 0px 20px; }
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-p img, pre img, tt img, li img, h1 img, h2 img { margin-bottom:0px; } 
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-ul { padding:0px; margin:0px 0px 20px 23px; list-style:square; }
-ul li { padding:0px; margin:0px 0px 7px 0px; }
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-ol li ul { padding-top:7px; }
-ol li ul li { list-style:square; }
-
-.content { font-size:1.2em; line-height:140%; padding: 20px; }
-
-pre, code { font-size:12px; }
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-pre { margin:0px 0px 20px; }
-pre.codeinput { padding:10px; border:1px solid #d3d3d3; background:#f7f7f7; }
-pre.codeoutput { padding:10px 11px; margin:0px 0px 20px; color:#4c4c4c; }
-pre.error { color:red; }
-
-@media print { pre.codeinput, pre.codeoutput { word-wrap:break-word; width:100%; } }
-
-span.keyword { color:#0000FF }
-span.comment { color:#228B22 }
-span.string { color:#A020F0 }
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-.footer { width:auto; padding:10px 0px; margin:25px 0px 0px; border-top:1px dotted #878787; font-size:0.8em; line-height:140%; font-style:italic; color:#878787; text-align:left; float:none; }
-.footer p { margin:0px; }
-.footer a { color:#878787; }
-.footer a:hover { color:#878787; text-decoration:underline; }
-.footer a:visited { color:#878787; }
-
-table th { padding:7px 5px; text-align:left; vertical-align:middle; border: 1px solid #d6d4d4; font-weight:bold; }
-table td { padding:7px 5px; text-align:left; vertical-align:top; border:1px solid #d6d4d4; }
-
-
-
-
-
-  </style></head><body><div class="content"><h1>Process</h1><!--introduction--><!--/introduction--><h2>Contents</h2><div><ul><li><a href="#2">Create input geometry objects</a></li><li><a href="#3">Integrate on a coarse grid (for scaling)</a></li><li><a href="#10">Plot of overall scale factor vs. frame number (b)</a></li><li><a href="#12">Plot of coarse map intensity vs. resolution (1/d)</a></li><li><a href="#13">Plot of coarse map intensity slice (l = 0)</a></li><li><a href="#14">Integrate on a fine grid</a></li><li><a href="#18">Plot of fine grid intensity vs. resolution (1/d)</a></li><li><a href="#19">Plot of fine grid intensity slice (l = 0)</a></li><li><a href="#20">Plot of CC* vs. resolution (1/d)</a></li></ul></div><p>check that mdx is on path</p><pre class="codeinput"><span class="keyword">try</span>
-    geom.Detector();
-<span class="keyword">catch</span>
-    error(<span class="string">'mdx is not on the path! edit setup_environment.m and run'</span>);
-<span class="keyword">end</span>
-</pre><h2 id="2">Create input geometry objects</h2><p>hote: The normal workflow is to run XDS and import the geometry using proc.Batch.xds2geom() and proc.Batch.cbf2geom(). However, for this demo the simulated diffraction images are small and lack Bragg peaks, so XDS cannot be run beforehand. Running the input_geometry script creates the objects directly.</p><pre class="codeinput"><span class="keyword">if</span> ~isfolder(<span class="string">'proc'</span>), mkdir(<span class="string">'proc'</span>); <span class="keyword">end</span>
-
-input_geometry(); <span class="comment">% creates proc/geom.mat and proc/geomBkg.mat</span>
-</pre><h2 id="3">Integrate on a coarse grid (for scaling)</h2><p><b>proc.Batch.filter</b></p><pre class="codeinput">[tf, errorMessage] = proc.Batch.filter(<span class="keyword">...</span>
-    <span class="string">'workingDirectory'</span>,<span class="string">'proc'</span>,<span class="keyword">...</span>
-    <span class="string">'ndiv'</span>,[3,5,5],<span class="keyword">...</span><span class="comment"> % coarse grid divisions</span>
-    <span class="string">'maxCount'</span>,50,<span class="keyword">...</span><span class="comment">  % histogram up to maxCount</span>
-    <span class="string">'parallel'</span>,false<span class="keyword">...</span><span class="comment"> % true requires parallel processing toolbox</span>
-    );
-
-<span class="keyword">if</span> ~tf, rethrow(errorMessage);<span class="keyword">end</span>
-</pre><pre class="codeoutput">
-proc.Batch.filter
-date: 17-Jan-2020 15:47:40
-workingDirectory: proc
-geometryIn: geom.mat
-matOut: filter.mat
-logOut: filter.log
-ndiv: [3 5 5]
-window: 2
-maxCount: 50
-smax: Inf
-refineGrid: 1
-parallel: 0
-
-  checking input file geom.mat
-  reading workspace variables from file proc/geom.mat
-    InputGeometry
-    RefinedGeometry
-    InputImageSeries
-    WedgeImageSeries
-  reading first image (to update bad pixel mask)
-  processing wedge 1 of 36
-    initializing the Integrater
-    initializing the reference grid
-    reading images and accumulating count histogram
-    initializing the Filter
-    designing moving window
-    calculating moving weighted median
-    calculating KL divergence of count histograms and Poisson distribution
-    identifying outliers
-    generating integration mask
-  processing wedge 2 of 36
-    initializing the Integrater
-    initializing the reference grid
-    reading images and accumulating count histogram
-    initializing the Filter
-    designing moving window
-    calculating moving weighted median
-    calculating KL divergence of count histograms and Poisson distribution
-    identifying outliers
-    generating integration mask
-  processing wedge 3 of 36
-    initializing the Integrater
-    initializing the reference grid
-    reading images and accumulating count histogram
-    initializing the Filter
-    designing moving window
-    calculating moving weighted median
-    calculating KL divergence of count histograms and Poisson distribution
-    identifying outliers
-    generating integration mask
-  processing wedge 4 of 36
-    initializing the Integrater
-    initializing the reference grid
-    reading images and accumulating count histogram
-    initializing the Filter
-    designing moving window
-    calculating moving weighted median
-    calculating KL divergence of count histograms and Poisson distribution
-    identifying outliers
-    generating integration mask
-  processing wedge 5 of 36
-    initializing the Integrater
-    initializing the reference grid
-    reading images and accumulating count histogram
-    initializing the Filter
-    designing moving window
-    calculating moving weighted median
-    calculating KL divergence of count histograms and Poisson distribution
-    identifying outliers
-    generating integration mask
-  processing wedge 6 of 36
-    initializing the Integrater
-    initializing the reference grid
-    reading images and accumulating count histogram
-    initializing the Filter
-    designing moving window
-    calculating moving weighted median
-    calculating KL divergence of count histograms and Poisson distribution
-    identifying outliers
-    generating integration mask
-  processing wedge 7 of 36
-    initializing the Integrater
-    initializing the reference grid
-    reading images and accumulating count histogram
-    initializing the Filter
-    designing moving window
-    calculating moving weighted median
-    calculating KL divergence of count histograms and Poisson distribution
-    identifying outliers
-    generating integration mask
-  processing wedge 8 of 36
-    initializing the Integrater
-    initializing the reference grid
-    reading images and accumulating count histogram
-    initializing the Filter
-    designing moving window
-    calculating moving weighted median
-    calculating KL divergence of count histograms and Poisson distribution
-    identifying outliers
-    generating integration mask
-  processing wedge 9 of 36
-    initializing the Integrater
-    initializing the reference grid
-    reading images and accumulating count histogram
-    initializing the Filter
-    designing moving window
-    calculating moving weighted median
-    calculating KL divergence of count histograms and Poisson distribution
-    identifying outliers
-    generating integration mask
-  processing wedge 10 of 36
-    initializing the Integrater
-    initializing the reference grid
-    reading images and accumulating count histogram
-    initializing the Filter
-    designing moving window
-    calculating moving weighted median
-    calculating KL divergence of count histograms and Poisson distribution
-    identifying outliers
-    generating integration mask
-  processing wedge 11 of 36
-    initializing the Integrater
-    initializing the reference grid
-    reading images and accumulating count histogram
-    initializing the Filter
-    designing moving window
-    calculating moving weighted median
-    calculating KL divergence of count histograms and Poisson distribution
-    identifying outliers
-    generating integration mask
-  processing wedge 12 of 36
-    initializing the Integrater
-    initializing the reference grid
-    reading images and accumulating count histogram
-    initializing the Filter
-    designing moving window
-    calculating moving weighted median
-    calculating KL divergence of count histograms and Poisson distribution
-    identifying outliers
-    generating integration mask
-  processing wedge 13 of 36
-    initializing the Integrater
-    initializing the reference grid
-    reading images and accumulating count histogram
-    initializing the Filter
-    designing moving window
-    calculating moving weighted median
-    calculating KL divergence of count histograms and Poisson distribution
-    identifying outliers
-    generating integration mask
-  processing wedge 14 of 36
-    initializing the Integrater
-    initializing the reference grid
-    reading images and accumulating count histogram
-    initializing the Filter
-    designing moving window
-    calculating moving weighted median
-    calculating KL divergence of count histograms and Poisson distribution
-    identifying outliers
-    generating integration mask
-  processing wedge 15 of 36
-    initializing the Integrater
-    initializing the reference grid
-    reading images and accumulating count histogram
-    initializing the Filter
-    designing moving window
-    calculating moving weighted median
-    calculating KL divergence of count histograms and Poisson distribution
-    identifying outliers
-    generating integration mask
-  processing wedge 16 of 36
-    initializing the Integrater
-    initializing the reference grid
-    reading images and accumulating count histogram
-    initializing the Filter
-    designing moving window
-    calculating moving weighted median
-    calculating KL divergence of count histograms and Poisson distribution
-    identifying outliers
-    generating integration mask
-  processing wedge 17 of 36
-    initializing the Integrater
-    initializing the reference grid
-    reading images and accumulating count histogram
-    initializing the Filter
-    designing moving window
-    calculating moving weighted median
-    calculating KL divergence of count histograms and Poisson distribution
-    identifying outliers
-    generating integration mask
-  processing wedge 18 of 36
-    initializing the Integrater
-    initializing the reference grid
-    reading images and accumulating count histogram
-    initializing the Filter
-    designing moving window
-    calculating moving weighted median
-    calculating KL divergence of count histograms and Poisson distribution
-    identifying outliers
-    generating integration mask
-  processing wedge 19 of 36
-    initializing the Integrater
-    initializing the reference grid
-    reading images and accumulating count histogram
-    initializing the Filter
-    designing moving window
-    calculating moving weighted median
-    calculating KL divergence of count histograms and Poisson distribution
-    identifying outliers
-    generating integration mask
-  processing wedge 20 of 36
-    initializing the Integrater
-    initializing the reference grid
-    reading images and accumulating count histogram
-    initializing the Filter
-    designing moving window
-    calculating moving weighted median
-    calculating KL divergence of count histograms and Poisson distribution
-    identifying outliers
-    generating integration mask
-  processing wedge 21 of 36
-    initializing the Integrater
-    initializing the reference grid
-    reading images and accumulating count histogram
-    initializing the Filter
-    designing moving window
-    calculating moving weighted median
-    calculating KL divergence of count histograms and Poisson distribution
-    identifying outliers
-    generating integration mask
-  processing wedge 22 of 36
-    initializing the Integrater
-    initializing the reference grid
-    reading images and accumulating count histogram
-    initializing the Filter
-    designing moving window
-    calculating moving weighted median
-    calculating KL divergence of count histograms and Poisson distribution
-    identifying outliers
-    generating integration mask
-  processing wedge 23 of 36
-    initializing the Integrater
-    initializing the reference grid
-    reading images and accumulating count histogram
-    initializing the Filter
-    designing moving window
-    calculating moving weighted median
-    calculating KL divergence of count histograms and Poisson distribution
-    identifying outliers
-    generating integration mask
-  processing wedge 24 of 36
-    initializing the Integrater
-    initializing the reference grid
-    reading images and accumulating count histogram
-    initializing the Filter
-    designing moving window
-    calculating moving weighted median
-    calculating KL divergence of count histograms and Poisson distribution
-    identifying outliers
-    generating integration mask
-  processing wedge 25 of 36
-    initializing the Integrater
-    initializing the reference grid
-    reading images and accumulating count histogram
-    initializing the Filter
-    designing moving window
-    calculating moving weighted median
-    calculating KL divergence of count histograms and Poisson distribution
-    identifying outliers
-    generating integration mask
-  processing wedge 26 of 36
-    initializing the Integrater
-    initializing the reference grid
-    reading images and accumulating count histogram
-    initializing the Filter
-    designing moving window
-    calculating moving weighted median
-    calculating KL divergence of count histograms and Poisson distribution
-    identifying outliers
-    generating integration mask
-  processing wedge 27 of 36
-    initializing the Integrater
-    initializing the reference grid
-    reading images and accumulating count histogram
-    initializing the Filter
-    designing moving window
-    calculating moving weighted median
-    calculating KL divergence of count histograms and Poisson distribution
-    identifying outliers
-    generating integration mask
-  processing wedge 28 of 36
-    initializing the Integrater
-    initializing the reference grid
-    reading images and accumulating count histogram
-    initializing the Filter
-    designing moving window
-    calculating moving weighted median
-    calculating KL divergence of count histograms and Poisson distribution
-    identifying outliers
-    generating integration mask
-  processing wedge 29 of 36
-    initializing the Integrater
-    initializing the reference grid
-    reading images and accumulating count histogram
-    initializing the Filter
-    designing moving window
-    calculating moving weighted median
-    calculating KL divergence of count histograms and Poisson distribution
-    identifying outliers
-    generating integration mask
-  processing wedge 30 of 36
-    initializing the Integrater
-    initializing the reference grid
-    reading images and accumulating count histogram
-    initializing the Filter
-    designing moving window
-    calculating moving weighted median
-    calculating KL divergence of count histograms and Poisson distribution
-    identifying outliers
-    generating integration mask
-  processing wedge 31 of 36
-    initializing the Integrater
-    initializing the reference grid
-    reading images and accumulating count histogram
-    initializing the Filter
-    designing moving window
-    calculating moving weighted median
-    calculating KL divergence of count histograms and Poisson distribution
-    identifying outliers
-    generating integration mask
-  processing wedge 32 of 36
-    initializing the Integrater
-    initializing the reference grid
-    reading images and accumulating count histogram
-    initializing the Filter
-    designing moving window
-    calculating moving weighted median
-    calculating KL divergence of count histograms and Poisson distribution
-    identifying outliers
-    generating integration mask
-  processing wedge 33 of 36
-    initializing the Integrater
-    initializing the reference grid
-    reading images and accumulating count histogram
-    initializing the Filter
-    designing moving window
-    calculating moving weighted median
-    calculating KL divergence of count histograms and Poisson distribution
-    identifying outliers
-    generating integration mask
-  processing wedge 34 of 36
-    initializing the Integrater
-    initializing the reference grid
-    reading images and accumulating count histogram
-    initializing the Filter
-    designing moving window
-    calculating moving weighted median
-    calculating KL divergence of count histograms and Poisson distribution
-    identifying outliers
-    generating integration mask
-  processing wedge 35 of 36
-    initializing the Integrater
-    initializing the reference grid
-    reading images and accumulating count histogram
-    initializing the Filter
-    designing moving window
-    calculating moving weighted median
-    calculating KL divergence of count histograms and Poisson distribution
-    identifying outliers
-    generating integration mask
-  processing wedge 36 of 36
-    initializing the Integrater
-    initializing the reference grid
-    reading images and accumulating count histogram
-    initializing the Filter
-    designing moving window
-    calculating moving weighted median
-    calculating KL divergence of count histograms and Poisson distribution
-    identifying outliers
-    generating integration mask
-  Refining the integration masks
-  checking output file filter.mat
-
-WARNING: Output file already exists and will be overwritten.
-
-  saving workspace variables to file: proc/filter.mat
-    options
-    Grid
-    pixelMask
-
-proc.Batch.filter
-date: 17-Jan-2020 15:48:09
-Done!
-</pre><p><b>proc.Batch.integrate</b></p><pre class="codeinput">[tf,errorMessage] = proc.Batch.integrate(<span class="keyword">...</span>
-    <span class="string">'workingDirectory'</span>,<span class="string">'proc'</span>,<span class="keyword">...</span>
-    <span class="string">'parallel'</span>,false<span class="keyword">...</span><span class="comment"> % requires parallel processing toolbox</span>
-    );
-
-<span class="keyword">if</span> ~tf, rethrow(errorMessage);<span class="keyword">end</span>
-</pre><pre class="codeoutput">
-proc.Batch.integrate
-date: 17-Jan-2020 15:48:09
-workingDirectory: proc
-geometryIn: geom.mat
-gridIn: filter.mat
-matOut: integrate.mat
-logOut: integrate.log
-binMode: coarse
-binExcludedVoxels: 1
-parallel: 0
-
-  checking input file geom.mat
-  reading workspace variables from file proc/geom.mat
-    InputGeometry
-    RefinedGeometry
-    InputImageSeries
-    WedgeImageSeries
-  checking input file filter.mat
-  reading workspace variables from file proc/filter.mat
-    Grid
-    pixelMask
-  processing wedge 1 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 2 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 3 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 4 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 5 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 6 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 7 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 8 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 9 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 10 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 11 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 12 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 13 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 14 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 15 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 16 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 17 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 18 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 19 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 20 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 21 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 22 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 23 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 24 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 25 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 26 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 27 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 28 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 29 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 30 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 31 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 32 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 33 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 34 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 35 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 36 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  checking output file integrate.mat
-
-WARNING: Output file already exists and will be overwritten.
-
-  saving workspace variables to file: proc/integrate.mat
-    options
-    bin
-    binExcl
-
-proc.Batch.integrate
-date: 17-Jan-2020 15:48:11
-Done!
-</pre><p><b>proc.Batch.correct</b></p><pre class="codeinput">[tf,errorMessage] = proc.Batch.correct(<span class="keyword">...</span>
-    <span class="string">'workingDirectory'</span>,<span class="string">'proc'</span>,<span class="keyword">...</span>
-    <span class="string">'parallel'</span>,false<span class="keyword">...</span><span class="comment"> % requires parallel processing toolbox</span>
-    );
-
-<span class="keyword">if</span> ~tf, rethrow(errorMessage);<span class="keyword">end</span>
-</pre><pre class="codeoutput">
-proc.Batch.correct
-date: 17-Jan-2020 15:48:11
-workingDirectory: proc
-geometryIn: geom.mat
-gridIn: filter.mat
-bkgGeometryIn: geomBkg.mat
-matOut: correct.mat
-logOut: correct.log
-binMode: coarse
-readBackground: 1
-readImageHeaders: 1
-exposureTimeField: Exposure_time
-parallel: 0
-binExcludedVoxels: 1
-
-  checking input file geom.mat
-  reading workspace variables from file proc/geom.mat
-    InputGeometry
-    RefinedGeometry
-    InputImageSeries
-    WedgeImageSeries
-  checking input file filter.mat
-  reading workspace variables from file proc/filter.mat
-    Grid
-    pixelMask
-  checking input file geomBkg.mat
-  reading workspace variables from file proc/geomBkg.mat
-    InputImageSeries
-    WedgeImageSeries
-  processing wedge 1 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 2 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 3 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 4 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 5 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 6 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 7 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 8 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 9 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 10 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 11 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 12 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 13 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 14 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 15 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 16 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 17 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 18 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 19 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 20 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 21 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 22 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 23 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 24 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 25 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 26 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 27 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 28 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 29 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 30 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 31 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 32 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 33 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 34 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 35 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 36 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  checking output file correct.mat
-
-WARNING: Output file already exists and will be overwritten.
-
-  saving workspace variables to file: proc/correct.mat
-    options
-    corr
-    corrExcl
-
-proc.Batch.correct
-date: 17-Jan-2020 15:48:14
-Done!
-</pre><p><b>proc.Batch.export</b></p><pre class="codeinput">[tf,errorMessage] = proc.Batch.export(<span class="keyword">...</span>
-    <span class="string">'workingDirectory'</span>,<span class="string">'proc'</span>);
-
-<span class="keyword">if</span> ~tf, rethrow(errorMessage);<span class="keyword">end</span>
-</pre><pre class="codeoutput">
-proc.Batch.export
-date: 17-Jan-2020 15:48:14
-workingDirectory: proc
-geometryIn: geom.mat
-gridIn: filter.mat
-integrateIn: integrate.mat
-correctIn: correct.mat
-matOut: export.mat
-logOut: export.log
-minimumCounts: 0
-minimumPixels: 1
-binExcludedVoxels: 1
-
-  checking input file geom.mat
-  reading workspace variables from file proc/geom.mat
-    InputGeometry
-    RefinedGeometry
-  checking input file filter.mat
-  reading workspace variables from file proc/filter.mat
-    Grid
-  checking input file integrate.mat
-  reading workspace variables from file proc/integrate.mat
-    bin
-    binExcl
-  checking input file correct.mat
-  reading workspace variables from file proc/correct.mat
-    corr
-    corrExcl
-  averaging geometry object
-  checking output file export.mat
-
-WARNING: Output file already exists and will be overwritten.
-
-  saving workspace variables to file: proc/export.mat
-    options
-    AverageGeometry
-    diffuseTable
-    braggTable
-
-proc.Batch.export
-date: 17-Jan-2020 15:48:15
-Done!
-</pre><p><b>proc.Batch.combine</b></p><pre class="codeinput">[tf,errorMessage] = proc.Batch.combine(<span class="keyword">...</span>
-    <span class="string">'workingDirectory'</span>,<span class="string">'proc'</span>,<span class="keyword">...</span>
-    <span class="string">'exportIn'</span>,{<span class="string">'export.mat'</span>},<span class="keyword">...</span>
-    <span class="string">'mergeNeighbors'</span>,true,<span class="keyword">...</span>
-    <span class="string">'combineBragg'</span>,false,<span class="keyword">...</span>
-    <span class="string">'nwx'</span>,4,<span class="keyword">...</span><span class="comment"> % some default parameters for ScalingModel</span>
-    <span class="string">'nwy'</span>,4);
-
-<span class="keyword">if</span> ~tf, rethrow(errorMessage);<span class="keyword">end</span>
-</pre><pre class="codeoutput">
-proc.Batch.combine
-date: 17-Jan-2020 15:48:15
-workingDirectory: proc
-exportIn: export.mat
-matOut: combine.mat
-logOut: combine.log
-mergeNeighbors: 1
-combineBragg: 0
-neighborMaxSep: 0.5
-fractionRangeBragg: [0.95 1.05]
-nws: 100
-nwx: 4
-nwy: 4
-
-  checking input file export.mat
-  reading workspace variables from file proc/export.mat
-    diffuseTable
-    AverageGeometry
-  pre-processing batch 1
-    merging equivalent observations within 5 frames of each other
-      24 observations merged in diffuse table, 16560 remaining
-  loading diffuse data from batch 1 into table
-  checking output file combine.mat
-
-WARNING: Output file already exists and will be overwritten.
-
-  saving workspace variables to file: proc/combine.mat
-    options
-    diffuseTable
-    ScalingModel
-
-proc.Batch.combine
-date: 17-Jan-2020 15:48:15
-Done!
-</pre><p><b>proc.Batch.scale</b></p><pre class="codeinput">[tf,errorMessage] = proc.Batch.scale(<span class="keyword">...</span>
-    <span class="string">'workingDirectory'</span>,<span class="string">'proc'</span>,<span class="keyword">...</span>
-    <span class="string">'scaleIn'</span>,<span class="string">'combine.mat'</span>,<span class="keyword">...</span>
-    <span class="string">'bizMult'</span>,5,<span class="keyword">...</span><span class="comment"> % regularization parameter for smoothness of b</span>
-    <span class="string">'program'</span>,{<span class="string">'b'</span>,50,1E-4,<span class="string">'o'</span>,[],10,<span class="string">'a'</span>,20,1E-3});
-
-<span class="keyword">if</span> ~tf, rethrow(errorMessage);<span class="keyword">end</span>
-</pre><pre class="codeoutput">
-proc.Batch.scale
-date: 17-Jan-2020 15:48:15
-workingDirectory: proc
-combineIn: combine.mat
-scaleIn: combine.mat
-matOut: scale.mat
-logOut: scale.log
-mergeByColumns: hasu, kasu, lasu
-program: b, 50, 0.0001, o, [], 10, a, 20, 0.001
-cMin: 0
-bizMult: 5
-csMult: 100
-cizMult: 10
-cMult: 0.001
-aixiyMult: 10
-aizMult: 1
-dipMult: 0.01
-
-  checking input file combine.mat
-  reading workspace variables from file proc/combine.mat
-    diffuseTable
-  checking input file combine.mat
-  reading workspace variables from file proc/combine.mat
-    ScalingModel
-  initializing proc.scale.MultiBatchScaler
-  calculating regularization parameters
-  refining scales
-    refining scale vs. frame number
-      1 of 50: x2 = 19.8571
-      2 of 50: x2 = 18.8523
-      3 of 50: x2 = 18.3843
-      4 of 50: x2 = 18.1649
-      5 of 50: x2 = 18.0612
-      6 of 50: x2 = 18.0117
-      7 of 50: x2 = 17.9876
-      8 of 50: x2 = 17.9758
-      9 of 50: x2 = 17.9698
-      10 of 50: x2 = 17.9667
-      11 of 50: x2 = 17.965
-      12 of 50: x2 = 17.9641
-      13 of 50: x2 = 17.9635
-      14 of 50: x2 = 17.9632
-      15 of 50: x2 = 17.963
-      16 of 50: x2 = 17.9629
-      17 of 50: x2 = 17.9628 &lt;-- reached tolerance
-    removing outliers
-      0 outliers removed from batch 1
-    refining scale vs. frame number and detector position
-      1 of 20: x2 = 17.523
-      2 of 20: x2 = 17.4625
-      3 of 20: x2 = 17.4456
-      4 of 20: x2 = 17.4383
-      5 of 20: x2 = 17.4345
-      6 of 20: x2 = 17.4323
-      7 of 20: x2 = 17.4308
-      8 of 20: x2 = 17.4297
-      9 of 20: x2 = 17.4288 &lt;-- reached tolerance
-  done refining scales
-  checking output file scale.mat
-
-WARNING: Output file already exists and will be overwritten.
-
-  saving workspace variables to file: proc/scale.mat
-    options
-    ScalingModel
-
-proc.Batch.scale
-date: 17-Jan-2020 15:48:15
-Done!
-</pre><h2 id="10">Plot of overall scale factor vs. frame number (b)</h2><pre class="codeinput">load <span class="string">proc/scale.mat</span> <span class="string">ScalingModel</span>
-
-figure;plot(ScalingModel.Ia.wz,ScalingModel.b);
-xlabel(<span class="string">'Frame Number'</span>);ylabel(<span class="string">'Scale Factor (b)'</span>);
-
-clear <span class="string">ScalingModel</span>
-</pre><img vspace="5" hspace="5" src="process_01.png" alt=""> <p><b>proc.Batch.merge</b></p><pre class="codeinput">[tf,errorMessage] = proc.Batch.merge(<span class="keyword">...</span>
-    <span class="string">'workingDirectory'</span>,<span class="string">'proc'</span>);
-
-<span class="keyword">if</span> ~tf, rethrow(errorMessage);<span class="keyword">end</span>
-</pre><pre class="codeoutput">
-proc.Batch.merge
-date: 17-Jan-2020 15:48:17
-workingDirectory: proc
-combineIn: combine.mat
-scaleIn: scale.mat
-matOut: merge.mat
-logOut: merge.log
-mergeBragg: 0
-sigmaCutoff: 5
-mergeByColumns: hasu, kasu, lasu
-
-  checking input file scale.mat
-  reading workspace variables from file proc/scale.mat
-    ScalingModel
-  checking input file combine.mat
-  reading workspace variables from file proc/combine.mat
-    diffuseTable
-  calculating scale factors
-  scaling intensities
-  merging intensities
-  removing outliers
-    mean reduced chi-squared of equivalent reflections (1 is ideal): 4.17476
-    removing observations with abs(resid/sigma) &gt; 20.8738
-    23 outliers removed, 16537 observations remaining
-  merging intensities
-  checking output file merge.mat
-
-WARNING: Output file already exists and will be overwritten.
-
-  saving workspace variables to file: proc/merge.mat
-    options
-    hklMerge
-    ih
-    isOutlier
-
-proc.Batch.merge
-date: 17-Jan-2020 15:48:17
-Done!
-</pre><h2 id="12">Plot of coarse map intensity vs. resolution (1/d)</h2><pre class="codeinput">load <span class="string">proc/merge.mat</span> <span class="string">hklMerge</span>
-
-figure;plot(hklMerge.s,hklMerge.I,<span class="string">'.'</span>);
-xlabel(<span class="string">'1/d (&Aring;^{-1})'</span>);ylabel(<span class="string">'Intensity'</span>);title(<span class="string">'Coarse Map intensity vs. resolution'</span>);
-clear <span class="string">hklMerge</span>
-</pre><img vspace="5" hspace="5" src="process_02.png" alt=""> <h2 id="13">Plot of coarse map intensity slice (l = 0)</h2><pre class="codeinput">load <span class="string">proc/merge.mat</span> <span class="string">hklMerge</span>
-
-<span class="comment">% create 3D array from hkl table</span>
-E2A = proc.script.ExpandTableToArray(<span class="keyword">...</span>
-    <span class="string">'hklcols'</span>,{<span class="string">'hasu'</span>,<span class="string">'kasu'</span>,<span class="string">'lasu'</span>,<span class="string">'I'</span>},<span class="keyword">...</span>
-    <span class="string">'SpaceGroup'</span>,symm.SpaceGroup(1),<span class="keyword">...</span>
-    <span class="string">'symexpand'</span>,true,<span class="keyword">...</span>
-    <span class="string">'ndiv'</span>,[1,1,1]);
-
-[P,I] = E2A.run(hklMerge);
-[~,~,nl0] = P.frac2ind(0,0,0);
-[h,~,~] = P.ind2frac(1:P.N(1),0,0);
-[~,k,~] = P.ind2frac(0,1:P.N(2),0);
-
-figure;imagesc(h,k,I(:,:,nl0)');
-xlabel(<span class="string">'h'</span>);ylabel(<span class="string">'k'</span>);title(<span class="string">'Coarse Map Intensity (l = 0)'</span>);colormap <span class="string">hot</span>;colorbar
-
-clear <span class="string">h</span> <span class="string">k</span> <span class="string">nl0</span> <span class="string">P</span> <span class="string">I</span> <span class="string">E2A</span> <span class="string">hklMerge</span>
-</pre><img vspace="5" hspace="5" src="process_03.png" alt=""> <h2 id="14">Integrate on a fine grid</h2><p><b>proc.Batch.grid</b></p><p>make a fine grid</p><pre class="codeinput">ndiv = [5,15,15]; <span class="comment">% number of divisions for the fine grid</span>
-
-[tf,errorMessage] = proc.Batch.grid(<span class="keyword">...</span>
-    <span class="string">'workingDirectory'</span>,<span class="string">'proc'</span>,<span class="keyword">...</span>
-    <span class="string">'matOut'</span>,<span class="string">'grid.mat'</span>,<span class="keyword">...</span>
-    <span class="string">'smax'</span>,Inf,<span class="keyword">...</span>
-    <span class="string">'getSymmetryEquivalents'</span>,true,<span class="keyword">...</span>
-    <span class="string">'ndiv'</span>,ndiv,<span class="keyword">...</span>
-    <span class="string">'excludeBraggPosition'</span>,true,<span class="keyword">...</span>
-    <span class="string">'parallel'</span>,false<span class="keyword">...</span><span class="comment"> % true requires parallel computing toolbox</span>
-    );
-
-<span class="keyword">if</span> ~tf, rethrow(errorMessage);<span class="keyword">end</span>
-</pre><pre class="codeoutput">Warning: parallel is not a valid option 
-
-proc.Batch.grid
-date: 17-Jan-2020 15:48:18
-workingDirectory: proc
-geometryIn: geom.mat
-matOut: grid.mat
-logOut: grid.log
-ndiv: [5 15 15]
-smax: Inf
-hLim: [-Inf Inf]
-kLim: [-Inf Inf]
-lLim: [-Inf Inf]
-h: []
-k: []
-l: []
-getSymmetryEquivalents: 1
-excludeBraggPosition: 1
-
-  checking input file geom.mat
-  reading workspace variables from file proc/geom.mat
-    InputGeometry
-    RefinedGeometry
-    InputImageSeries
-    WedgeImageSeries
-  reading first image (to update bad pixel mask)
-  processing wedge 1 of 36
-    initializing the Integrater
-    initializing the reference grid
-  processing wedge 2 of 36
-    initializing the Integrater
-    initializing the reference grid
-  processing wedge 3 of 36
-    initializing the Integrater
-    initializing the reference grid
-  processing wedge 4 of 36
-    initializing the Integrater
-    initializing the reference grid
-  processing wedge 5 of 36
-    initializing the Integrater
-    initializing the reference grid
-  processing wedge 6 of 36
-    initializing the Integrater
-    initializing the reference grid
-  processing wedge 7 of 36
-    initializing the Integrater
-    initializing the reference grid
-  processing wedge 8 of 36
-    initializing the Integrater
-    initializing the reference grid
-  processing wedge 9 of 36
-    initializing the Integrater
-    initializing the reference grid
-  processing wedge 10 of 36
-    initializing the Integrater
-    initializing the reference grid
-  processing wedge 11 of 36
-    initializing the Integrater
-    initializing the reference grid
-  processing wedge 12 of 36
-    initializing the Integrater
-    initializing the reference grid
-  processing wedge 13 of 36
-    initializing the Integrater
-    initializing the reference grid
-  processing wedge 14 of 36
-    initializing the Integrater
-    initializing the reference grid
-  processing wedge 15 of 36
-    initializing the Integrater
-    initializing the reference grid
-  processing wedge 16 of 36
-    initializing the Integrater
-    initializing the reference grid
-  processing wedge 17 of 36
-    initializing the Integrater
-    initializing the reference grid
-  processing wedge 18 of 36
-    initializing the Integrater
-    initializing the reference grid
-  processing wedge 19 of 36
-    initializing the Integrater
-    initializing the reference grid
-  processing wedge 20 of 36
-    initializing the Integrater
-    initializing the reference grid
-  processing wedge 21 of 36
-    initializing the Integrater
-    initializing the reference grid
-  processing wedge 22 of 36
-    initializing the Integrater
-    initializing the reference grid
-  processing wedge 23 of 36
-    initializing the Integrater
-    initializing the reference grid
-  processing wedge 24 of 36
-    initializing the Integrater
-    initializing the reference grid
-  processing wedge 25 of 36
-    initializing the Integrater
-    initializing the reference grid
-  processing wedge 26 of 36
-    initializing the Integrater
-    initializing the reference grid
-  processing wedge 27 of 36
-    initializing the Integrater
-    initializing the reference grid
-  processing wedge 28 of 36
-    initializing the Integrater
-    initializing the reference grid
-  processing wedge 29 of 36
-    initializing the Integrater
-    initializing the reference grid
-  processing wedge 30 of 36
-    initializing the Integrater
-    initializing the reference grid
-  processing wedge 31 of 36
-    initializing the Integrater
-    initializing the reference grid
-  processing wedge 32 of 36
-    initializing the Integrater
-    initializing the reference grid
-  processing wedge 33 of 36
-    initializing the Integrater
-    initializing the reference grid
-  processing wedge 34 of 36
-    initializing the Integrater
-    initializing the reference grid
-  processing wedge 35 of 36
-    initializing the Integrater
-    initializing the reference grid
-  processing wedge 36 of 36
-    initializing the Integrater
-    initializing the reference grid
-  checking output file grid.mat
-
-WARNING: Output file already exists and will be overwritten.
-
-  saving workspace variables to file: proc/grid.mat
-    options
-    Grid
-    pixelMask
-
-proc.Batch.grid
-date: 17-Jan-2020 15:48:19
-Done!
-</pre><p><b>proc.Batch.reintegrate</b></p><pre class="codeinput">[tf,errorMessage] = proc.Batch.reintegrate(<span class="keyword">...</span>
-    <span class="string">'workingDirectory'</span>,<span class="string">'proc'</span>,<span class="keyword">...</span>
-    <span class="string">'geometryIn'</span>,<span class="string">'geom.mat'</span>,<span class="keyword">...</span>
-    <span class="string">'bkgGeometryIn'</span>,<span class="string">'geomBkg.mat'</span>,<span class="keyword">...</span>
-    <span class="string">'gridIn'</span>,<span class="string">'grid.mat'</span>,<span class="keyword">...</span>
-    <span class="string">'scaleIn'</span>,<span class="string">'scale.mat'</span>,<span class="keyword">...</span>
-    <span class="string">'matOut'</span>,<span class="string">'reintegrate.mat'</span>,<span class="keyword">...</span>
-    <span class="string">'logOut'</span>,<span class="string">'reintegrate.log'</span>,<span class="keyword">...</span>
-    <span class="string">'minimumCounts'</span>,0,<span class="keyword">...</span>
-    <span class="string">'minimumPixels'</span>,1,<span class="keyword">...</span>
-    <span class="string">'parallel'</span>,false<span class="keyword">...</span><span class="comment"> % true requires parallel computing toolbox</span>
-    );
-
-<span class="keyword">if</span> ~tf, rethrow(errorMessage);<span class="keyword">end</span>
-</pre><pre class="codeoutput">
-proc.Batch.reintegrate
-date: 17-Jan-2020 15:48:19
-workingDirectory: proc
-geometryIn: geom.mat
-readBackground: 1
-bkgGeometryIn: geomBkg.mat
-gridIn: grid.mat
-scaleIn: scale.mat
-matOut: reintegrate.mat
-logOut: reintegrate.log
-exposureTimeField: Exposure_time
-minimumCounts: 0
-minimumPixels: 1
-parallel: 0
-binExcludedVoxels: 0
-
-  checking input file geom.mat
-  reading workspace variables from file proc/geom.mat
-    InputGeometry
-    RefinedGeometry
-    InputImageSeries
-    WedgeImageSeries
-  checking input file grid.mat
-  reading workspace variables from file proc/grid.mat
-    Grid
-    pixelMask
-  checking input file scale.mat
-  reading workspace variables from file proc/scale.mat
-    ScalingModel
-  checking input file geomBkg.mat
-  reading workspace variables from file proc/geomBkg.mat
-    InputImageSeries
-    WedgeImageSeries
-  processing wedge 1 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 2 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 3 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 4 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 5 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 6 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 7 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 8 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 9 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 10 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 11 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 12 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 13 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 14 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 15 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 16 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 17 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 18 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 19 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 20 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 21 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 22 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 23 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 24 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 25 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 26 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 27 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 28 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 29 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 30 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 31 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 32 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 33 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 34 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 35 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 36 of 36
-    initializing the Integrater
-    reading images and accumulating counts
-  processing wedge 1 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 2 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 3 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 4 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 5 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 6 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 7 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 8 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 9 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 10 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 11 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 12 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 13 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 14 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 15 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 16 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 17 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 18 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 19 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 20 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 21 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 22 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 23 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 24 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 25 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 26 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 27 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 28 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 29 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 30 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 31 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 32 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 33 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 34 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 35 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  processing wedge 36 of 36
-    initializing the Integrater
-    calculating image corrections
-    reading exposure times from crystal image headers
-    reading background images
-    calculating the pixel multiplicity
-    accumulating image corrections
-  checking output file reintegrate.mat
-
-WARNING: Output file already exists and will be overwritten.
-
-  saving workspace variables to file: proc/reintegrate.mat
-    options
-    diffuseTable
-    AverageGeometry
-
-proc.Batch.reintegrate
-date: 17-Jan-2020 15:48:38
-Done!
-</pre><p><b>MergeScaledDiffuse</b></p><pre class="codeinput"><span class="comment">% get crystal info</span>
-load <span class="string">proc/export.mat</span> <span class="string">AverageGeometry</span>
-
-M = proc.script.MergeScaledDiffuse(<span class="keyword">...</span>
-    <span class="string">'Grid'</span>,grid.Sub3d(<span class="string">'ndiv'</span>,ndiv),<span class="keyword">...</span>
-    <span class="string">'Crystal'</span>,AverageGeometry.Crystal,<span class="keyword">...</span>
-    <span class="string">'nMin'</span>,2,<span class="keyword">...</span>
-    <span class="string">'workingDirectory'</span>,<span class="string">'proc'</span>);
-
-AverageGeometry
-
-<span class="comment">% run the script on reintegrate.mat</span>
-fn = M.mapToColumns({<span class="string">'reintegrate.mat'</span>});
-
-[hklMerge,isincl] = M.mergeColumns(fn);
-
-<span class="comment">% save table to mat file</span>
-save(<span class="string">'proc/mergeFine.mat'</span>,<span class="string">'hklMerge'</span>);
-
-<span class="comment">% split and merge for calculating cc1/2, cc*</span>
-rng(0,<span class="string">'twister'</span>); <span class="comment">% set random number generator for reproducibility</span>
-[hklMerge] = M.mergeRandomHalfSets(fn,isincl);
-
-save(<span class="string">'proc/mergeFineSplit.mat'</span>,<span class="string">'hklMerge'</span>);
-
-M.clearTmp(fn); <span class="comment">% clear files from temporary directory</span>
-
-clear <span class="string">hklMerge</span> <span class="string">isincl</span> <span class="string">M</span>
-</pre><pre class="codeoutput">
-AverageGeometry = 
-
-  DiffractionExperiment with properties:
-
-      Source: [1&times;1 geom.Source]
-     Spindle: [1&times;1 geom.RotationSeries]
-     Crystal: [1&times;1 geom.Crystal]
-    Detector: [1&times;1 TinyDetector]
-
-START
-making temporary directory /private/var/folders/24/ns8c5m4j5pn5ws4d8j9pjr680000gn/T/mdx-kit-20200117154839
-loading diffuseTable from proc/reintegrate.mat
-  mapping hkl to asu
-  get rows of diffuseTable to put in each binary file
-  append to binary files
-DONE: 1125 tmp files written (94.801 Mb total)
-START: mergeColumns
-
-processing file 1 of 1125
-processing file 2 of 1125
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-constructing hklTable
-sorting hklTable
-DONE: 3950028 reflections, 1266 rejected, merged to 981296
-START: mergeRandomHalfSets
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-constructing hklTable
-sorting hklTable
-DONE
-</pre><h2 id="18">Plot of fine grid intensity vs. resolution (1/d)</h2><pre class="codeinput">load <span class="string">proc/mergeFine.mat</span> <span class="string">hklMerge</span>
-load <span class="string">proc/export.mat</span> <span class="string">AverageGeometry</span>
-
-h = hklMerge.h + hklMerge.dh/ndiv(1);
-k = hklMerge.k + hklMerge.dk/ndiv(2);
-l = hklMerge.l + hklMerge.dl/ndiv(3);
-
-[sx,sy,sz] = AverageGeometry.hkl2s(h,k,l);
-hklMerge.s = sqrt(sx.^2 + sy.^2 + sz.^2);
-
-figure;plot(hklMerge.s,hklMerge.I,<span class="string">'.'</span>);
-xlabel(<span class="string">'1/d (&Aring;^{-1})'</span>);ylabel(<span class="string">'Intensity'</span>);title(<span class="string">'Fine Map intensity vs. resolution'</span>);
-clear <span class="string">hklMerge</span> <span class="string">sx</span> <span class="string">sy</span> <span class="string">sz</span> <span class="string">h</span> <span class="string">k</span> <span class="string">l</span> <span class="string">AverageGeometry</span>
-</pre><img vspace="5" hspace="5" src="process_04.png" alt=""> <h2 id="19">Plot of fine grid intensity slice (l = 0)</h2><pre class="codeinput">load <span class="string">proc/mergeFine.mat</span> <span class="string">hklMerge</span>
-
-hklMerge.hfrac = hklMerge.h + hklMerge.dh/ndiv(1);
-hklMerge.kfrac = hklMerge.k + hklMerge.dk/ndiv(2);
-hklMerge.lfrac = hklMerge.l + hklMerge.dl/ndiv(3);
-
-<span class="comment">% create 3D array from hkl table</span>
-E2A = proc.script.ExpandTableToArray(<span class="keyword">...</span>
-    <span class="string">'hklcols'</span>,{<span class="string">'hfrac'</span>,<span class="string">'kfrac'</span>,<span class="string">'lfrac'</span>,<span class="string">'I'</span>},<span class="keyword">...</span>
-    <span class="string">'SpaceGroup'</span>,symm.SpaceGroup(1),<span class="keyword">...</span>
-    <span class="string">'symexpand'</span>,true,<span class="keyword">...</span>
-    <span class="string">'ndiv'</span>,ndiv);
-
-[P,I] = E2A.run(hklMerge);
-[~,~,nl0] = P.frac2ind(0,0,0);
-[h,~,~] = P.ind2frac(1:P.N(1),0,0);
-[~,k,~] = P.ind2frac(0,1:P.N(2),0);
-
-figure;imagesc(h,k,I(:,:,nl0)');colormap <span class="string">hot</span>
-xlabel(<span class="string">'h'</span>);ylabel(<span class="string">'k'</span>);title(<span class="string">'Fine Map Intensity (l = 0)'</span>);colorbar
-
-clear <span class="string">h</span> <span class="string">k</span> <span class="string">nl0</span> <span class="string">P</span> <span class="string">I</span> <span class="string">E2A</span> <span class="string">hklMerge</span>
-</pre><img vspace="5" hspace="5" src="process_05.png" alt=""> <h2 id="20">Plot of CC* vs. resolution (1/d)</h2><pre class="codeinput">load <span class="string">proc/mergeFineSplit.mat</span> <span class="string">hklMerge</span>
-load <span class="string">proc/export.mat</span> <span class="string">AverageGeometry</span>
-C = AverageGeometry.Crystal;
-
-hklMerge.hfrac = hklMerge.h + hklMerge.dh/ndiv(1);
-hklMerge.kfrac = hklMerge.k + hklMerge.dk/ndiv(2);
-hklMerge.lfrac = hklMerge.l + hklMerge.dl/ndiv(3);
-
-ET2A = proc.script.ExpandTableToArray(<span class="keyword">...</span>
-        <span class="string">'hklcols'</span>,{<span class="string">'hfrac'</span>,<span class="string">'kfrac'</span>,<span class="string">'lfrac'</span>,<span class="string">'I1'</span>,<span class="string">'I2'</span>},<span class="keyword">...</span>
-        <span class="string">'SpaceGroup'</span>,symm.SpaceGroup(1),<span class="keyword">...</span>
-        <span class="string">'symexpand'</span>,false,<span class="keyword">...</span>
-        <span class="string">'ndiv'</span>,ndiv);
-
-[P,I1,I2] = ET2A.run(hklMerge);
-
-B = latt.Basis(C.a,C.b,C.c,C.alpha,C.beta,C.gamma);
-B = latt.OrientedBasis.realign(B,C.a_axis,C.b_axis,C.c_axis);
-SVR = proc.script.StatisticsVsRadius(<span class="keyword">...</span>
-        <span class="string">'edges'</span>,0:.01:.6,<span class="keyword">...</span>
-        <span class="string">'Basis'</span>,B.invert,<span class="keyword">...</span>
-        <span class="string">'PeriodicGrid'</span>,P);
-
-sr12 = SVR.run(I1,I2);
-
-<span class="comment">% ccstar:</span>
-cc12 = sr12.cc;
-ccstar = sqrt(2*cc12./(1+cc12));
-
-figure;plot(sr12.r,ccstar,<span class="string">'-'</span>,<span class="string">'DisplayName'</span>,<span class="string">'CC*'</span>);hold <span class="string">on</span>;
-plot(sr12.r,cc12,<span class="string">'-'</span>,<span class="string">'DisplayName'</span>,<span class="string">'CC_{1/2}'</span>);
-set(gca,<span class="string">'Ylim'</span>,[0,1]);
-xlabel(<span class="string">'1/d (&Aring;^{-1})'</span>);ylabel(<span class="string">'Correlation Coefficient (CC)'</span>);legend <span class="string">show</span>
-
-title(<span class="string">'Fine map, correlation of random half-sets vs. resolution'</span>);
-
-clear <span class="string">hklMerge</span> <span class="string">C</span> <span class="string">AverageGeometry</span> <span class="string">P</span> <span class="string">I1</span> <span class="string">I2</span> <span class="string">B</span> <span class="string">SVR</span> <span class="string">sr12</span> <span class="comment">% save ccstar for next cell</span>
-</pre><pre class="codeoutput">Warning: Imaginary parts of complex X and/or Y arguments ignored 
-</pre><img vspace="5" hspace="5" src="process_06.png" alt=""> <p class="footer"><br><a href="https://www.mathworks.com/products/matlab/">Published with MATLAB&reg; R2018a</a><br></p></div><!--
-##### SOURCE BEGIN #####
-%% Process
-
-%%
-% check that mdx is on path
-try
-    geom.Detector();
-catch
-    error('mdx is not on the path! edit setup_environment.m and run');
-end
-
-%% Create input geometry objects
-% hote: The normal workflow is to run XDS and import the geometry using
-% proc.Batch.xds2geom() and proc.Batch.cbf2geom(). However, for this demo
-% the simulated diffraction images are small and lack Bragg peaks, so
-% XDS cannot be run beforehand. Running the input_geometry script
-% creates the objects directly.
-
-if ~isfolder('proc'), mkdir('proc'); end
-
-input_geometry(); % creates proc/geom.mat and proc/geomBkg.mat
-
-%% Integrate on a coarse grid (for scaling)
-
-%% 
-% *proc.Batch.filter*
-
-[tf, errorMessage] = proc.Batch.filter(...
-    'workingDirectory','proc',...
-    'ndiv',[3,5,5],... % coarse grid divisions
-    'maxCount',50,...  % histogram up to maxCount
-    'parallel',false... % true requires parallel processing toolbox
-    );  
-
-if ~tf, rethrow(errorMessage);end
-%% 
-% *proc.Batch.integrate*
-
-[tf,errorMessage] = proc.Batch.integrate(...
-    'workingDirectory','proc',...
-    'parallel',false... % requires parallel processing toolbox
-    ); 
-
-if ~tf, rethrow(errorMessage);end
-%% 
-% *proc.Batch.correct*
-
-[tf,errorMessage] = proc.Batch.correct(...
-    'workingDirectory','proc',...
-    'parallel',false... % requires parallel processing toolbox
-    );
-
-if ~tf, rethrow(errorMessage);end
-%% 
-% *proc.Batch.export*
-[tf,errorMessage] = proc.Batch.export(...
-    'workingDirectory','proc');
-
-if ~tf, rethrow(errorMessage);end
-%% 
-% *proc.Batch.combine*
-[tf,errorMessage] = proc.Batch.combine(...
-    'workingDirectory','proc',...
-    'exportIn',{'export.mat'},...
-    'mergeNeighbors',true,...
-    'combineBragg',false,...
-    'nwx',4,... % some default parameters for ScalingModel
-    'nwy',4);
-
-if ~tf, rethrow(errorMessage);end
-%% 
-% *proc.Batch.scale*
-
-[tf,errorMessage] = proc.Batch.scale(...
-    'workingDirectory','proc',...
-    'scaleIn','combine.mat',...
-    'bizMult',5,... % regularization parameter for smoothness of b
-    'program',{'b',50,1E-4,'o',[],10,'a',20,1E-3}); 
-
-if ~tf, rethrow(errorMessage);end
-
-%% Plot of overall scale factor vs. frame number (b)
-
-load proc/scale.mat ScalingModel
-
-figure;plot(ScalingModel.Ia.wz,ScalingModel.b);
-xlabel('Frame Number');ylabel('Scale Factor (b)');
-
-clear ScalingModel
-%% 
-% *proc.Batch.merge*
-
-[tf,errorMessage] = proc.Batch.merge(...
-    'workingDirectory','proc');
-
-if ~tf, rethrow(errorMessage);end
-
-%% Plot of coarse map intensity vs. resolution (1/d)
-load proc/merge.mat hklMerge
-
-figure;plot(hklMerge.s,hklMerge.I,'.');
-xlabel('1/d (Ã…^{-1})');ylabel('Intensity');title('Coarse Map intensity vs. resolution');
-clear hklMerge
-
-%% Plot of coarse map intensity slice (l = 0)
-
-load proc/merge.mat hklMerge
-
-% create 3D array from hkl table
-E2A = proc.script.ExpandTableToArray(...
-    'hklcols',{'hasu','kasu','lasu','I'},...
-    'SpaceGroup',symm.SpaceGroup(1),...
-    'symexpand',true,...
-    'ndiv',[1,1,1]);
-
-[P,I] = E2A.run(hklMerge);
-[~,~,nl0] = P.frac2ind(0,0,0);
-[h,~,~] = P.ind2frac(1:P.N(1),0,0);
-[~,k,~] = P.ind2frac(0,1:P.N(2),0);
-
-figure;imagesc(h,k,I(:,:,nl0)');
-xlabel('h');ylabel('k');title('Coarse Map Intensity (l = 0)');colormap hot;colorbar
-
-clear h k nl0 P I E2A hklMerge
-%% Integrate on a fine grid
-
-%% 
-% *proc.Batch.grid*
-%
-% make a fine grid
-
-ndiv = [5,15,15]; % number of divisions for the fine grid
-
-[tf,errorMessage] = proc.Batch.grid(...
-    'workingDirectory','proc',...
-    'matOut','grid.mat',...
-    'smax',Inf,...
-    'getSymmetryEquivalents',true,...
-    'ndiv',ndiv,...
-    'excludeBraggPosition',true,...
-    'parallel',false... % true requires parallel computing toolbox
-    );
-
-if ~tf, rethrow(errorMessage);end
-
-%% 
-% *proc.Batch.reintegrate*
-
-[tf,errorMessage] = proc.Batch.reintegrate(...
-    'workingDirectory','proc',...
-    'geometryIn','geom.mat',...
-    'bkgGeometryIn','geomBkg.mat',...
-    'gridIn','grid.mat',...
-    'scaleIn','scale.mat',...
-    'matOut','reintegrate.mat',...
-    'logOut','reintegrate.log',...
-    'minimumCounts',0,...
-    'minimumPixels',1,...
-    'parallel',false... % true requires parallel computing toolbox
-    );
-
-if ~tf, rethrow(errorMessage);end
-
-%% 
-% *MergeScaledDiffuse*
-
-% get crystal info
-load proc/export.mat AverageGeometry
-
-M = proc.script.MergeScaledDiffuse(...
-    'Grid',grid.Sub3d('ndiv',ndiv),...
-    'Crystal',AverageGeometry.Crystal,...
-    'nMin',2,...
-    'workingDirectory','proc');
-
-AverageGeometry
-
-% run the script on reintegrate.mat
-fn = M.mapToColumns({'reintegrate.mat'});
-
-[hklMerge,isincl] = M.mergeColumns(fn);
-
-% save table to mat file
-save('proc/mergeFine.mat','hklMerge');
-
-% split and merge for calculating cc1/2, cc*
-rng(0,'twister'); % set random number generator for reproducibility
-[hklMerge] = M.mergeRandomHalfSets(fn,isincl);
-
-save('proc/mergeFineSplit.mat','hklMerge');
-
-M.clearTmp(fn); % clear files from temporary directory
-
-clear hklMerge isincl M
-
-%% Plot of fine grid intensity vs. resolution (1/d)
-load proc/mergeFine.mat hklMerge
-load proc/export.mat AverageGeometry
-
-h = hklMerge.h + hklMerge.dh/ndiv(1);
-k = hklMerge.k + hklMerge.dk/ndiv(2);
-l = hklMerge.l + hklMerge.dl/ndiv(3);
-
-[sx,sy,sz] = AverageGeometry.hkl2s(h,k,l);
-hklMerge.s = sqrt(sx.^2 + sy.^2 + sz.^2);
-
-figure;plot(hklMerge.s,hklMerge.I,'.');
-xlabel('1/d (Ã…^{-1})');ylabel('Intensity');title('Fine Map intensity vs. resolution');
-clear hklMerge sx sy sz h k l AverageGeometry
-
-%% Plot of fine grid intensity slice (l = 0)
-load proc/mergeFine.mat hklMerge
-
-hklMerge.hfrac = hklMerge.h + hklMerge.dh/ndiv(1);
-hklMerge.kfrac = hklMerge.k + hklMerge.dk/ndiv(2);
-hklMerge.lfrac = hklMerge.l + hklMerge.dl/ndiv(3);
-
-% create 3D array from hkl table
-E2A = proc.script.ExpandTableToArray(...
-    'hklcols',{'hfrac','kfrac','lfrac','I'},...
-    'SpaceGroup',symm.SpaceGroup(1),...
-    'symexpand',true,...
-    'ndiv',ndiv);
-
-[P,I] = E2A.run(hklMerge);
-[~,~,nl0] = P.frac2ind(0,0,0);
-[h,~,~] = P.ind2frac(1:P.N(1),0,0);
-[~,k,~] = P.ind2frac(0,1:P.N(2),0);
-
-figure;imagesc(h,k,I(:,:,nl0)');colormap hot
-xlabel('h');ylabel('k');title('Fine Map Intensity (l = 0)');colorbar
-
-clear h k nl0 P I E2A hklMerge
-
-%% Plot of CC* vs. resolution (1/d)
-
-load proc/mergeFineSplit.mat hklMerge
-load proc/export.mat AverageGeometry
-C = AverageGeometry.Crystal;
-
-hklMerge.hfrac = hklMerge.h + hklMerge.dh/ndiv(1);
-hklMerge.kfrac = hklMerge.k + hklMerge.dk/ndiv(2);
-hklMerge.lfrac = hklMerge.l + hklMerge.dl/ndiv(3);
-
-ET2A = proc.script.ExpandTableToArray(...
-        'hklcols',{'hfrac','kfrac','lfrac','I1','I2'},...
-        'SpaceGroup',symm.SpaceGroup(1),...
-        'symexpand',false,...
-        'ndiv',ndiv);
-
-[P,I1,I2] = ET2A.run(hklMerge);
-    
-B = latt.Basis(C.a,C.b,C.c,C.alpha,C.beta,C.gamma);
-B = latt.OrientedBasis.realign(B,C.a_axis,C.b_axis,C.c_axis);
-SVR = proc.script.StatisticsVsRadius(...
-        'edges',0:.01:.6,... 
-        'Basis',B.invert,...
-        'PeriodicGrid',P);
-
-sr12 = SVR.run(I1,I2);
-
-% ccstar:
-cc12 = sr12.cc;
-ccstar = sqrt(2*cc12./(1+cc12));
-
-figure;plot(sr12.r,ccstar,'-','DisplayName','CC*');hold on;
-plot(sr12.r,cc12,'-','DisplayName','CC_{1/2}');
-set(gca,'Ylim',[0,1]);
-xlabel('1/d (Ã…^{-1})');ylabel('Correlation Coefficient (CC)');legend show
-
-title('Fine map, correlation of random half-sets vs. resolution');
-
-clear hklMerge C AverageGeometry P I1 I2 B SVR sr12 % save ccstar for next cell
-
-##### SOURCE END #####
---></body></html>
\ No newline at end of file
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diff --git a/demo/process.m b/demo/process.m
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--- a/demo/process.m
+++ /dev/null
@@ -1,272 +0,0 @@
-%% Process
-
-%%
-% check that mdx is on path
-try
-    geom.Detector();
-catch
-    error('mdx is not on the path! edit setup_environment.m and run');
-end
-
-%% Create input geometry objects
-% hote: The normal workflow is to run XDS and import the geometry using
-% proc.Batch.xds2geom() and proc.Batch.cbf2geom(). However, for this demo
-% the simulated diffraction images are small and lack Bragg peaks, so
-% XDS cannot be run beforehand. Running the input_geometry script
-% creates the objects directly.
-
-if ~isfolder('proc'), mkdir('proc'); end
-
-input_geometry(); % creates proc/geom.mat and proc/geomBkg.mat
-
-%% Integrate on a coarse grid (for scaling)
-
-%% 
-% *proc.Batch.filter*
-
-[tf, errorMessage] = proc.Batch.filter(...
-    'workingDirectory','proc',...
-    'ndiv',[3,5,5],... % coarse grid divisions
-    'maxCount',50,...  % histogram up to maxCount
-    'parallel',false... % true requires parallel processing toolbox
-    );  
-
-if ~tf, rethrow(errorMessage);end
-%% 
-% *proc.Batch.integrate*
-
-[tf,errorMessage] = proc.Batch.integrate(...
-    'workingDirectory','proc',...
-    'parallel',false... % requires parallel processing toolbox
-    ); 
-
-if ~tf, rethrow(errorMessage);end
-%% 
-% *proc.Batch.correct*
-
-[tf,errorMessage] = proc.Batch.correct(...
-    'workingDirectory','proc',...
-    'parallel',false... % requires parallel processing toolbox
-    );
-
-if ~tf, rethrow(errorMessage);end
-%% 
-% *proc.Batch.export*
-[tf,errorMessage] = proc.Batch.export(...
-    'workingDirectory','proc');
-
-if ~tf, rethrow(errorMessage);end
-%% 
-% *proc.Batch.combine*
-[tf,errorMessage] = proc.Batch.combine(...
-    'workingDirectory','proc',...
-    'exportIn',{'export.mat'},...
-    'mergeNeighbors',true,...
-    'combineBragg',false,...
-    'nwx',4,... % some default parameters for ScalingModel
-    'nwy',4);
-
-if ~tf, rethrow(errorMessage);end
-%% 
-% *proc.Batch.scale*
-
-[tf,errorMessage] = proc.Batch.scale(...
-    'workingDirectory','proc',...
-    'scaleIn','combine.mat',...
-    'bizMult',5,... % regularization parameter for smoothness of b
-    'program',{'b',50,1E-4,'o',[],10,'a',20,1E-3}); 
-
-if ~tf, rethrow(errorMessage);end
-
-%% Plot of overall scale factor vs. frame number (b)
-
-load proc/scale.mat ScalingModel
-
-figure;plot(ScalingModel.Ib.w,ScalingModel.b);
-xlabel('Frame Number');ylabel('Scale Factor (b)');
-
-clear ScalingModel
-%% 
-% *proc.Batch.merge*
-
-[tf,errorMessage] = proc.Batch.merge(...
-    'workingDirectory','proc');
-
-if ~tf, rethrow(errorMessage);end
-
-%% Plot of coarse map intensity vs. resolution (1/d)
-load proc/merge.mat hklMerge
-
-figure;plot(hklMerge.s,hklMerge.I,'.');
-xlabel('1/d (Å^{-1})');ylabel('Intensity');title('Coarse Map intensity vs. resolution');
-clear hklMerge
-
-%% Plot of coarse map intensity slice (l = 0)
-
-load proc/merge.mat hklMerge
-
-% create 3D array from hkl table
-E2A = proc.script.ExpandTableToArray(...
-    'hklcols',{'hasu','kasu','lasu','I'},...
-    'SpaceGroup',symm.SpaceGroup(1),...
-    'symexpand',true,...
-    'ndiv',[1,1,1]);
-
-[P,I] = E2A.run(hklMerge);
-[~,~,nl0] = P.frac2ind(0,0,0);
-[h,~,~] = P.ind2frac(1:P.N(1),0,0);
-[~,k,~] = P.ind2frac(0,1:P.N(2),0);
-
-figure;imagesc(h,k,I(:,:,nl0)');
-xlabel('h');ylabel('k');title('Coarse Map Intensity (l = 0)');colormap hot;colorbar
-
-clear h k nl0 P I E2A hklMerge
-%% Integrate on a fine grid
-
-%% 
-% *proc.Batch.grid*
-%
-% make a fine grid
-
-ndiv = [5,15,15]; % number of divisions for the fine grid
-
-[tf,errorMessage] = proc.Batch.grid(...
-    'workingDirectory','proc',...
-    'matOut','grid.mat',...
-    'smax',Inf,...
-    'getSymmetryEquivalents',true,...
-    'ndiv',ndiv,...
-    'excludeBraggPosition',true,...
-    'parallel',false... % true requires parallel computing toolbox
-    );
-
-if ~tf, rethrow(errorMessage);end
-
-%% 
-% *proc.Batch.reintegrate*
-
-[tf,errorMessage] = proc.Batch.reintegrate(...
-    'workingDirectory','proc',...
-    'geometryIn','geom.mat',...
-    'bkgGeometryIn','geomBkg.mat',...
-    'gridIn','grid.mat',...
-    'scaleIn','scale.mat',...
-    'matOut','reintegrate.mat',...
-    'logOut','reintegrate.log',...
-    'minimumCounts',0,...
-    'minimumPixels',1,...
-    'parallel',false... % true requires parallel computing toolbox
-    );
-
-if ~tf, rethrow(errorMessage);end
-
-%% 
-% *MergeScaledDiffuse*
-
-% get crystal info
-load proc/export.mat AverageGeometry
-
-M = proc.script.MergeScaledDiffuse(...
-    'Grid',grid.Sub3d('ndiv',ndiv),...
-    'Crystal',AverageGeometry.Crystal,...
-    'nMin',2,...
-    'workingDirectory','proc');
-
-AverageGeometry
-
-% run the script on reintegrate.mat
-fn = M.mapToColumns({'reintegrate.mat'});
-
-[hklMerge,isincl] = M.mergeColumns(fn);
-
-% save table to mat file
-save('proc/mergeFine.mat','hklMerge');
-
-% split and merge for calculating cc1/2, cc*
-rng(0,'twister'); % set random number generator for reproducibility
-[hklMerge] = M.mergeRandomHalfSets(fn,isincl);
-
-save('proc/mergeFineSplit.mat','hklMerge');
-
-M.clearTmp(fn); % clear files from temporary directory
-
-clear hklMerge isincl M
-
-%% Plot of fine grid intensity vs. resolution (1/d)
-load proc/mergeFine.mat hklMerge
-load proc/export.mat AverageGeometry
-
-h = hklMerge.h + hklMerge.dh/ndiv(1);
-k = hklMerge.k + hklMerge.dk/ndiv(2);
-l = hklMerge.l + hklMerge.dl/ndiv(3);
-
-[sx,sy,sz] = AverageGeometry.hkl2s(h,k,l);
-hklMerge.s = sqrt(sx.^2 + sy.^2 + sz.^2);
-
-figure;plot(hklMerge.s,hklMerge.I,'.');
-xlabel('1/d (Å^{-1})');ylabel('Intensity');title('Fine Map intensity vs. resolution');
-clear hklMerge sx sy sz h k l AverageGeometry
-
-%% Plot of fine grid intensity slice (l = 0)
-load proc/mergeFine.mat hklMerge
-
-hklMerge.hfrac = hklMerge.h + hklMerge.dh/ndiv(1);
-hklMerge.kfrac = hklMerge.k + hklMerge.dk/ndiv(2);
-hklMerge.lfrac = hklMerge.l + hklMerge.dl/ndiv(3);
-
-% create 3D array from hkl table
-E2A = proc.script.ExpandTableToArray(...
-    'hklcols',{'hfrac','kfrac','lfrac','I'},...
-    'SpaceGroup',symm.SpaceGroup(1),...
-    'symexpand',true,...
-    'ndiv',ndiv);
-
-[P,I] = E2A.run(hklMerge);
-[~,~,nl0] = P.frac2ind(0,0,0);
-[h,~,~] = P.ind2frac(1:P.N(1),0,0);
-[~,k,~] = P.ind2frac(0,1:P.N(2),0);
-
-figure;imagesc(h,k,I(:,:,nl0)');colormap hot
-xlabel('h');ylabel('k');title('Fine Map Intensity (l = 0)');colorbar
-
-clear h k nl0 P I E2A hklMerge
-
-%% Plot of CC* vs. resolution (1/d)
-
-load proc/mergeFineSplit.mat hklMerge
-load proc/export.mat AverageGeometry
-C = AverageGeometry.Crystal;
-
-hklMerge.hfrac = hklMerge.h + hklMerge.dh/ndiv(1);
-hklMerge.kfrac = hklMerge.k + hklMerge.dk/ndiv(2);
-hklMerge.lfrac = hklMerge.l + hklMerge.dl/ndiv(3);
-
-ET2A = proc.script.ExpandTableToArray(...
-        'hklcols',{'hfrac','kfrac','lfrac','I1','I2'},...
-        'SpaceGroup',symm.SpaceGroup(1),...
-        'symexpand',false,...
-        'ndiv',ndiv);
-
-[P,I1,I2] = ET2A.run(hklMerge);
-    
-B = latt.Basis(C.a,C.b,C.c,C.alpha,C.beta,C.gamma);
-B = latt.OrientedBasis.realign(B,C.a_axis,C.b_axis,C.c_axis);
-SVR = proc.script.StatisticsVsRadius(...
-        'edges',0:.01:.6,... 
-        'Basis',B.invert,...
-        'PeriodicGrid',P);
-
-sr12 = SVR.run(I1,I2);
-
-% ccstar:
-cc12 = sr12.cc;
-ccstar = sqrt(2*cc12./(1+cc12));
-
-figure;plot(sr12.r,ccstar,'-','DisplayName','CC*');hold on;
-plot(sr12.r,cc12,'-','DisplayName','CC_{1/2}');
-set(gca,'Ylim',[0,1]);
-xlabel('1/d (Å^{-1})');ylabel('Correlation Coefficient (CC)');legend show
-
-title('Fine map, correlation of random half-sets vs. resolution');
-
-clear hklMerge C AverageGeometry P I1 I2 B SVR sr12 % save ccstar for next cell
diff --git a/demo/setup_environment.m b/demo/setup_environment.m
deleted file mode 100644
index 7850e62..0000000
--- a/demo/setup_environment.m
+++ /dev/null
@@ -1,13 +0,0 @@
-function tf = setup_environment()
-
-mdx_lib_path = '../'; % change if demo folder is moved elsewhere (recommended)
-
-% 1) add mdx-kit to (global) MATLAB path
-addpath(mdx_lib_path);
-
-% 2) add code directory to (global) MATLAB path
-addpath('code');
-
-tf = true;
-
-end