initial commit

+utils/get_att_length.m

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+% GET_ATT_LENGTH returns attenuation length of a material for a given energy (range)
+%   formula...              chemical formula
+%   energy...               single value in keV or energy range in keV
+%   (optional) dens...      density, negative number for default values
+%   (optional) ang...       grazing angle (default 90)
+%   (optional) npts...      number of points
+%   (optional) plot...      set to 1 for plotting
+%
+%   returns 
+%       att...            (energy in keV, transmission)
+%       req_density...      density in g/cm^3
+%
+%   examples:
+%   get_att_length('Au', 8.7, -1, 45)
+%   get_att_length('Pb', [11.2 24], 0.1, -1, 100)
+%
+%   03/2017
+
+%*-----------------------------------------------------------------------*
+%|                                                                       |
+%|  Except where otherwise noted, this work is licensed under a          |
+%|  Creative Commons Attribution-NonCommercial-ShareAlike 4.0            |
+%|  International (CC BY-NC-SA 4.0) license.                             |
+%|                                                                       |
+%|  Copyright (c) 2017 by Paul Scherrer Institute (http://www.psi.ch)    |
+%|                                                                       |
+%|       Author: CXS group, PSI                                          |
+%*-----------------------------------------------------------------------*
+% You may use this code with the following provisions:
+%
+% If the code is fully or partially redistributed, or rewritten in another
+%   computing language this notice should be included in the redistribution.
+%
+% If this code, or subfunctions or parts of it, is used for research in a 
+%   publication or if it is fully or partially rewritten for another 
+%   computing language the authors and institution should be acknowledged 
+%   in written form in the publication: “Data processing was carried out 
+%   using the “cSAXS matlab package” developed by the CXS group,
+%   Paul Scherrer Institut, Switzerland.” 
+%   Variations on the latter text can be incorporated upon discussion with 
+%   the CXS group if needed to more specifically reflect the use of the package 
+%   for the published work.
+%
+% A publication that focuses on describing features, or parameters, that
+%    are already existing in the code should be first discussed with the
+%    authors.
+%   
+% This code and subroutines are part of a continuous development, they 
+%    are provided “as they are” without guarantees or liability on part
+%    of PSI or the authors. It is the user responsibility to ensure its 
+%    proper use and the correctness of the results.
+
+function [ att, req_density ] = get_att_length( formula, energy, varargin )
+
+% check density
+if nargin < 3
+    dens = -1;
+else
+    dens = varargin{1};
+end
+
+% check angle
+if nargin < 4
+    ang = 90;
+else
+    ang = varargin{2};
+end
+
+% check specified number of points
+if nargin < 5
+    npts = 99;
+else
+    npts = varargin{3}-1;
+end
+
+% check if plotting is requested
+if nargin < 6
+    plot_att = false;
+else
+    plot_att = varargin{4};
+end
+
+
+% convert to keV
+energy = energy * 1000;
+
+if size(energy) ==1
+    emin = energy-1;
+    emax = energy+1;
+    npts = 2;
+    req_range = false;
+elseif size(energy,2) == 2
+    emin = energy(1);
+    emax = energy(2);
+    req_range = true;
+else
+    error('Only one specific energy or an energy range is supported.')
+    
+end
+
+% check the energy range
+if emin < 30 || emax > 30000
+    error('Energies must be in the range 0.03 keV to 30 keV.')
+end
+
+% request the data
+server = 'http://henke.lbl.gov/';
+req = sprintf('Material=Enter+Formula&Formula=%s&Density=%f&Scan=Energy&Min=%d&Max=%d&Npts=%d&Fixed=%f&Plot=Log&Output=Plot', formula, dens, emin, emax, npts, ang);
+data_req = webwrite('http://henke.lbl.gov/cgi-bin/atten.pl', req);
+
+% find and read dat file
+f_pos = strfind(data_req, '/tmp');
+data_req = strsplit(data_req(f_pos(1):end), '.');
+data = webread([server data_req{1} '.dat']);
+
+% split data by line breaks
+data = strsplit(data, '\n');
+
+% extract density
+req_density = data{1};
+req_density = strsplit(req_density, '=');
+req_density = strsplit(req_density{2}, ' ');
+req_density = str2double(req_density{1});
+
+
+% output
+if npts==2 && ~req_range
+    att = zeros(1,2);
+    req_att = data{4};
+    req_att = strsplit(req_att,' ');
+    att(1,1) = str2double(req_att{2})/1000;
+    att(1,2) = str2double(req_att{3});
+else
+    att = zeros(npts+1,2);
+    for i=1:npts+1
+        req_att = data{i+2};
+        req_att = strsplit(req_att,' ');
+        att(i,1) = str2double(req_att{2})/1000;
+        att(i,2) = str2double(req_att{3});
+    end
+end
+
+% plot attenuation
+if plot_att
+    if ~req_range
+        fprintf('Requested plot for a single point.')
+    end
+    figure(76);
+    plot(att(:,1), att(:,2))
+    ylabel('attenuation length')
+    xlabel('energy in keV')
+    grid on;
+    
+end
+
+end
+