plotOrientationsIPF.m

function plotOrientationsIPF(input, varargin)
% Function to load and plot grain orientations in inverse pole figures
%
% Points in the inverse pole figure can be colored accoring to the intensity of 
% the inverse pole figure or the ODF at the corresponding orientation
%
% Usage
%
%    plotOrientationsIPF(inputfile,'cs',cs_ppv,'ss',ss, 'directions', [vector3d.X, vector3d.Y, vector3d.Z])
%    plotOrientationsIPF(inputfile,'cs',cs_ppv,'ss',ss, 'directions', [vector3d.X, vector3d.Y, vector3d.Z], 'minpf',0.0, 'maxpf',5.)
%    plotOrientationsIPF(inputfile,'cs',cs_ppv,'ss',ss, 'directions', [vector3d.X, vector3d.Y, vector3d.Z], 'halfwidth', 10)
%    plotOrientationsIPF(inputfile,'cs',cs_ppv,'ss',ss, 'directions', [vector3d.X, vector3d.Y, vector3d.Z], 'odfColor', true)
%    plotOrientationsIPF(inputfile,'cs',cs_ppv,'ss',ss, 'directions', [vector3d.X, vector3d.Y, vector3d.Z], 'output', outputfile)
%
%
% Input
%
%  input can either 
%		- the full path to the file with the list of euler angles, or, (see loadOrientations.m for file format)
%		- a list of orientations if they are already known
%
%
% Required parameters 
%
%    cs: crystal system
%    ss: sample system
%    directions: list of sample directions for the inverse pole figures
%
%
% Optional parameters
%    outputfile : full path to name of file in which to save the image
%    odfColor: color points according to ODF intensity. Otherwise, points are colored according to PF intensity
%    halfwidth: halfwidth for ODF calculation, in degrees, default is 15
%    minpf: minimum for intensity plot (max should be set as well)
%    maxpf: minimum for intensity plot (min should be set as well)
%    hem: hemisphere (upper or lower, upper by default)
%    markersize: 7 by default
%    colormap: name of colormap, between single quotes, default is 'plasma', you can use 'WhiteJet', for instance
% 
% See also loadOrientations
%
% This is part of the TIMEleSS tools
% http://timeless.texture.rocks/
%
% Copyright (C) S. Merkel, Universite de Lille, France
%
% This program is free software; you can redistribute it and/or
% modify it under the terms of the GNU General Public License
% as published by the Free Software Foundation; either version 2
% of the License, or (at your option) any later version.

	% default parameters and parser
	p = inputParser;
	addParameter(p,'cs',false);
	addParameter(p,'ss',false);
	addParameter(p,'directions',false);
	addParameter(p,'outputfile',false);
	addParameter(p,'odfColor',false,@islogical);
	addParameter(p,'halfwidth',15., @isfloat);
	addParameter(p,'minpf',false, @isfloat);
	addParameter(p,'maxpf',false, @isfloat);
	addParameter(p,'hem','upper', @isstring);
	addParameter(p,'markersize',7, @isfloat);
	addParameter(p,'colormap','plasma', @ischar);
	parse(p,varargin{:});
	odfColor = p.Results.odfColor;
	outputfile = p.Results.outputfile;
	cs = p.Results.cs;
	ss = p.Results.ss;
	directions = p.Results.directions;
	minpf = p.Results.minpf;
	maxpf = p.Results.maxpf;
	halfwidth = p.Results.halfwidth;
	hem = p.Results.hem;
	markersize = p.Results.markersize;
	colormap = p.Results.colormap;
	
	if (islogical(cs))
		fprintf('\nError: no crystal symmetry provided\n')
		return
	end
	if (islogical(ss))
		fprintf('\nError: no crystal sample provided\n')
		return
	end
	if (islogical(directions))
		fprintf('\nError: no list of directions for IPF provided\n')
		return
	end
	
	% Use Beartex convention for axes
	setMTEXpref('bAxisDirection','north')
	setMTEXpref('aAxisDirection','east')
	
	% If input parameter is a char,
	% load file and create the corresponding list of orientations
	if (ischar(input))
		ori0 = loadOrientations(input, cs, ss);
		n = size(ori0);
	% Else, if input is a list of orientations, just copy them
	elseif (isa(input,'orientation'))
		ori0 = reshape(input,[],1); % Put all orientations as a vertical vector
		n = size(ori0);
		fprintf('\nStarting from %d orientations\n', n(1))
	end
		
	% Fit an ODF to the data
	odf = calcDensity(ori0,'halfwidth',halfwidth*degree);
	fprintf('\nCalculated an ODF based on grain orientations\n')
	
	if (not(odfColor))
		% Plot orientations, colors according to pole figure
		% Working on each pole figure individually
		ndirections = size(directions,2);
		f=newMtexFigure('figSize','large','layout',[1,ndirections]);
		for i =1:ndirections
			thisdirection = directions(i);
			fprintf('\nCalculating colors for inverse pole figure %d\n', i);
			clear colors
			h = inv(ori0)*thisdirection;
			where = [thisdirection,thisdirection]; % Need to calculate it twice, otherwise, does not return a list of intensities
			pf = calcPoleFigure(odf,h,where);
			colors = pf.intensities(1:2:end); % Removing one in 2 values
			%colors = pf.intensities
			fprintf('\nPlotting antipodal inverse pole figure %d\n', i);
			if i == 1
				plotIPDF(ori0,colors,thisdirection,'MarkerSize',markersize,'antipodal','all',hem);
			else
				mtexFig = gcm;
				plotIPDF(ori0,colors,thisdirection,'MarkerSize',markersize,'antipodal','all',hem,'parent',mtexFig.nextAxis);
			end
		end
		f.drawNow;
		if (islogical(minpf) || islogical(maxpf)) 
			CLim(gcm,'equal');
		else
			CLim(gcm,[minpf,maxpf]);
		end
		mtexColorMap(char(colormap));
		mtexColorbar;
	else
		% Plot orientations, colored based on ODF
		fprintf('\Plotting antipodal inverse pole figures. Color based on ODF value for each grain.\n');
		plotIPDF(ori0,eval(odf,ori0),directions,'MarkerSize',markersize,'antipodal','all',hem);
		if (islogical(minpf) || islogical(maxpf)) 
			CLim(gcm,'equal');
		else
			CLim(gcm,[minpf,maxpf]);
		end
		mtexColorMap(char(colormap));
		mtexColorbar;
	end
	if (not (outputfile==false))
		% Save plot to the output file
		saveas(gcf,outputfile);
		fprintf('\nSaved plot of grain orientations in \n\t%s\n', outputfile)
	end
end