├── .gitignore
├── README.md
├── UnitTest.m
├── CalcGamma.m
└── LICENSE


/.gitignore:
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1 | *.smbdelete*
2 | .DS_STORE
3 | *.m~
4 | log.txt
5 | test_data/
6 | 


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/README.md:
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 1 | # CalcGamma
 2 | 
 3 | [![DOI](https://zenodo.org/badge/26833173.svg)](https://zenodo.org/doi/10.5281/zenodo.12735617)
 4 | 
 5 | by Mark Geurts <mark.w.geurts@gmail.com>
 6 | <br>Copyright &copy; 2015, University of Wisconsin Board of Regents
 7 | 
 8 | ## Description
 9 | 
10 | `CalcGamma()` computes a 1-D, 2-D, or 3-D local or global Gamma index between two datasets (reference and target) given a defined coordinate space using MATLAB.  The Gamma analysis is performed based on the formalism presented by D. A. Low et. al., [A technique for the quantitative evaluation of dose distributions.](http://www.ncbi.nlm.nih.gov/pubmed/9608475), Med Phys. 1998 May; 25(5): 656-61.
11 | 
12 | ## Installation
13 | 
14 | To install this function, copy `CalcGamma.m` from this repository into your MATLAB path. If installing as a submodule into another git repository, execute `git submodule add https://github.com/mwgeurts/gamma`.  
15 | 
16 | ## Usage and Documentation
17 | 
18 | ```matlab
19 | gamma = CalcGamma(reference, target, percent, dta);
20 | gamma = CalcGamma(..., 'OptionName', OptionValue);
21 | ```
22 | 
23 | See the [wiki](../../wiki) for information on the format of the input and arguments as well options and examples.
24 | 
25 | ## License
26 | 
27 | Released under the GNU GPL v3.0 License.  See the [LICENSE](LICENSE) file for further details.
28 | 


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/UnitTest.m:
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  1 | function varargout = UnitTest(varargin)
  2 | % UnitTest executes the unit tests for this application, and can be called 
  3 | % either independently (when testing just the latest version) or via 
  4 | % UnitTestHarness (when testing for regressions between versions).  Either 
  5 | % two or three input arguments can be passed to UnitTest as described 
  6 | % below.
  7 | %
  8 | % The following variables are required for proper execution: 
  9 | %   varargin{1}: string containing the path to the main function. This is
 10 | %       only required if UnitTest is to be operated across multiple file 
 11 | %       names; otherwise it can be an empty string.
 12 | %   varargin{2}: variable containing the test data.  this can be a string
 13 | %       to a file, a structure, or any MATLAB variable.
 14 | %   varargin{3} (optional): variable containing reference data to be used
 15 | %       for comparison.  If not provided, it is assumed that this version
 16 | %       is the reference and therefore all comparison tests will "Pass".
 17 | %
 18 | % The following variables are returned upon succesful completion when input 
 19 | % arguments are provided. If no return variables are given, the results
 20 | % will be printed to stdout.
 21 | %   varargout{1}: cell array of strings containing preamble text that
 22 | %       summarizes the test, where each cell is a line. This text will
 23 | %       precede the results table in the report.
 24 | %   varargout{2}: n x 3 cell array of strings containing the test ID in
 25 | %       the first column, name in the second, and result (Pass/Fail or 
 26 | %       numerical values typically) of the test in the third.
 27 | %   varargout{3}: cell array of strings containing footnotes referenced by
 28 | %       the tests, where each cell is a line.  This text will follow the
 29 | %       results table in the report.
 30 | %   varargout{4} (optional): variable containing reference data created by 
 31 | %       executing this version.  This variable can be passed back into 
 32 | %       subsequent executions of UnitTest as varargin{3} to compare results
 33 | %       between versions (or to a priori validated reference data).
 34 | %
 35 | % The following variables are returned when no input arguments are
 36 | % provided (required only if called by UnitTestHarness):
 37 | %   varargout{1}: string containing the application name (with .m 
 38 | %       extension)
 39 | %   varargout{2}: string containing the path to the version application 
 40 | %       whose results will be used as reference
 41 | %   varargout{3}: 1 x n cell array of strings containing paths to the other 
 42 | %       applications which will be tested
 43 | %   varargout{4}: 2 x m cell array of strings containing the name of each 
 44 | %       test suite (first column) and path to the test data (second column)
 45 | %   varargout{5}: string containing the path and name of report file (will 
 46 | %       be appended by _R201XX.md based on the MATLAB version)
 47 | %
 48 | % Below is an example of how this function is used:
 49 | %
 50 | %   % Start profiler
 51 | %   profile on -history
 52 | %
 53 | %   % Execute unit test, printing the test results to stdout
 54 | %   UnitTest('', load('../test_data/InputData.mat'), ...
 55 | %       load('../test_data/OutputData.mat'));
 56 | %
 57 | %   % Stop and view the profiler results
 58 | %   profile viewer
 59 | %
 60 | %   % Execute unit test, storing the test results
 61 | %   [preamble, table, footnotes] = UnitTest('', ...
 62 | %       load('../test_data/InputData.mat'), ...
 63 | %       load('../test_data/OutputData.mat'));
 64 | %
 65 | %   % Execute unit test again but without reference data, this time storing 
 66 | %   % the output from UnitTest as a new reference file
 67 | %   [preamble, table, footnotes, newreference] = ...
 68 | %       UnitTest('', load('../test_data/InputData.mat'));
 69 | %
 70 | % Author: Mark Geurts, mark.w.geurts@gmail.com
 71 | % Copyright (C) 2015 University of Wisconsin Board of Regents
 72 | %
 73 | % This program is free software: you can redistribute it and/or modify it 
 74 | % under the terms of the GNU General Public License as published by the  
 75 | % Free Software Foundation, either version 3 of the License, or (at your 
 76 | % option) any later version.
 77 | %
 78 | % This program is distributed in the hope that it will be useful, but 
 79 | % WITHOUT ANY WARRANTY; without even the implied warranty of 
 80 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General 
 81 | % Public License for more details.
 82 | % 
 83 | % You should have received a copy of the GNU General Public License along 
 84 | % with this program. If not, see http://www.gnu.org/licenses/.
 85 | 
 86 | %% Return Application Information
 87 | % If UnitTest was executed without input arguments
 88 | if nargin == 0
 89 |     
 90 |     % Declare the application filename
 91 |     varargout{1} = '';
 92 | 
 93 |     % Declare current version directory
 94 |     varargout{2} = '';
 95 | 
 96 |     % Declare prior version directories
 97 |     varargout{3} = {};
 98 | 
 99 |     % Declare location of test data. Column 1 is the name of the 
100 |     % test suite, column 2 is the absolute path to the file(s)
101 |     varargout{4} = {};
102 | 
103 |     % Declare name of report file (will be appended by _R201XX.md based on 
104 |     % the MATLAB version)
105 |     varargout{5} = '';
106 |     
107 |     % Return to invoking function
108 |     return;
109 | end
110 | 
111 | %% Initialize Unit Testing
112 | % Initialize static test result text variables
113 | pass = 'Pass';
114 | fail = 'Fail';
115 | unk = 'N/A'; %#ok<NASGU>
116 | 
117 | % Initialize preamble text
118 | preamble = {
119 |     '| Input Data | Value |'
120 |     '|------------|-------|'
121 | };
122 | 
123 | % Initialize results cell array
124 | results = cell(0,3);
125 | 
126 | % Initialize footnotes cell array
127 | footnotes = cell(0,1);
128 | 
129 | % Initialize reference structure
130 | if nargout == 4
131 |     reference = struct;
132 | end
133 | 
134 | %% TEST 1/2/3/4: Analytic 1D Gamma
135 | %
136 | % DESCRIPTION: This unit test creates a large analytic reference dataset, 
137 | %   modifies it by a known amount, and executes CalcGamma.  The gamma
138 | %   result is then compared to a known solution
139 | %
140 | % RELEVANT REQUIREMENTS: none
141 | %
142 | % INPUT DATA: varargin{3}.gammaA
143 | %
144 | % CONDITION A (+): When computed using identical criteria, CalcGamma
145 | %   produces an identical array to the reference with GPU Calculation
146 | %
147 | % CONDITION B (+): When computed using identical criteria, CalcGamma
148 | %   produces an identical array to the reference with CPU Calculation
149 | %
150 | % CONDITION C (-): When computed using modified criteria, CalcGamma
151 | %   produces a different result
152 | 
153 | % Add path to Event() function (to test Event calls function)
154 | addpath('../test_data/');
155 | 
156 | % Declare gamma criteria
157 | percent = 3;
158 | dta = 0.3;
159 | local = 1;
160 | 
161 | % Declare size of data arrays
162 | n = 2000;
163 | 
164 | % Create reference structure (sine function)
165 | ref.start = 0;
166 | ref.width = pi / 1000;
167 | ref.data = sin(ref.start:ref.width:...
168 |     ref.start + ref.width * n) + 2;
169 | 
170 | % Declare modification values (to be applied to target data)
171 | shift = 0.1;
172 | scale = 1.01;
173 | 
174 | % Modify reference data, saving to target structure
175 | target.start = ref.start + shift;
176 | target.width = ref.width;
177 | target.data = ref.data * scale;
178 | 
179 | % Execute in try/catch statement
180 | try
181 | 
182 |     % Execute CalcGamma using test dataset
183 |     t = tic;
184 |     gamma = CalcGamma(ref, target, percent, dta, 'local', local);
185 |     gtime = sprintf('%0.1f sec', toc(t));
186 |     gpf = pass;
187 |     cpf = pass;
188 | 
189 |     % If reference data exists
190 |     if nargin == 3
191 |         
192 |         % If current value does not equal the reference
193 |         if max(abs(gamma - varargin{3}.gammaA)) > 1e-5
194 |             gpf = fail;
195 |         end
196 |         
197 |         % Execute CalcGamma again using CPU
198 |         t = tic;
199 |         gamma = CalcGamma(ref, target, percent, dta, 'cpu', 1, ...
200 |             'local', local);
201 |         ctime = sprintf('%0.1f sec', toc(t));
202 |         
203 |         % If CPU value does not equal the reference
204 |         if max(abs(gamma - varargin{3}.gammaA)) > 1e-5
205 |             cpf = fail;
206 |         end
207 |         
208 |         % Execute CalcGamma again, this time using modified criteria
209 |         gamma = CalcGamma(ref, target, percent, dta * 2, ...
210 |             'local', local);
211 |         
212 |         % If modified value equals the reference, the test fails
213 |         if max(abs(gamma - varargin{3}.gammaA)) < 1e-5
214 |             gpf = fail;
215 |         end
216 |         
217 |         % Execute CalcGamma again, this time using modified criteria
218 |         gamma = CalcGamma(ref, target, percent * 2, dta, ...
219 |             'local', local);
220 |         
221 |         % If modified value equals the reference, the test fails
222 |         if max(abs(gamma - varargin{3}.gammaA)) < 1e-5
223 |             gpf = fail;
224 |         end
225 |         
226 |     % Otherwise, set reference    
227 |     elseif nargout == 4
228 |         reference.gammaA = gamma;
229 |         gpf = pass;
230 |         cpf = pass;
231 |     end
232 |     
233 | catch
234 |     gpf = fail;
235 |     cpf = fail;
236 | end
237 | 
238 | % Add the dataset size to the preamble
239 | preamble{length(preamble)+1} = ...
240 |     sprintf('| Analytic 1D Gamma Array | %i x %i  |', size(gamma));
241 | 
242 | % Add header to results table
243 | results{size(results,1)+1,1} = 'ID';
244 | results{size(results,1),2} = 'Test Case';
245 | results{size(results,1),3} = 'Result';
246 | 
247 | % Add GPU computation result
248 | results{size(results,1)+1,1} = '1';
249 | results{size(results,1),2} = 'Analytic 1D Gamma GPU Result within 1e-5';
250 | results{size(results,1),3} = gpf;
251 | 
252 | % Add computation time
253 | results{size(results,1)+1,1} = '2';
254 | results{size(results,1),2} = 'Analytic 1D Gamma GPU Computation Time';
255 | results{size(results,1),3} = gtime;
256 | 
257 | % Add CPU computation result
258 | results{size(results,1)+1,1} = '3';
259 | results{size(results,1),2} = 'Analytic 1D Gamma CPU Result within 1e-5';
260 | results{size(results,1),3} = cpf;
261 | 
262 | % Add computation time
263 | results{size(results,1)+1,1} = '4';
264 | results{size(results,1),2} = 'Analytic 1D Gamma CPU Computation Time';
265 | results{size(results,1),3} = ctime;
266 | 
267 | %% TEST 5/6/7/8: Beam Profile 1D Gamma
268 | %
269 | % DESCRIPTION: This unit test creates a real world profile dataset 
270 | %   and executes CalcGamma.  The gamma result is then compared to a known 
271 | %   solution
272 | %
273 | % RELEVANT REQUIREMENTS: none
274 | %
275 | % INPUT DATA: varargin{2}.referenceB, varargin{2}.targetB, 
276 | %   varargin{3}.gammaB
277 | %
278 | % CONDITION A (+): When computed using identical criteria, CalcGamma
279 | %   produces an identical array to the reference with GPU Calculation
280 | %
281 | % CONDITION B (+): When computed using identical criteria, CalcGamma
282 | %   produces an identical array to the reference with CPU Calculation
283 | %
284 | % CONDITION C (-): When computed using modified criteria, CalcGamma
285 | %   produces a different result
286 | 
287 | % Declare gamma criteria
288 | percent = 2;
289 | dta = 0.1;
290 | local = 0;
291 | 
292 | % Load reference and target data from varargin
293 | ref = varargin{2}.referenceB;
294 | target = varargin{2}.targetB;
295 | 
296 | % Determine location and value of maximum
297 | [C, I] = max(target.data);
298 |     
299 | % Search left side for half-maximum value
300 | for x = 1:I-1
301 |     if target.data(x) == C/2
302 |         left = target.start + target.width * (x-1);
303 |         break;
304 |     elseif target.data(x) < C/2 && target.data(x+1) > C/2
305 |         left = interp1(target.data(x:x+1), target.start + ...
306 |             target.width * (x-1:x), C/2);
307 |         break;
308 |     end
309 | end
310 | 
311 | % Search right side for half-maximum value
312 | for x = I:size(target.data,1)-1
313 |     if target.data(x) == C/2
314 |         right = target.start + target.width * (x-1);
315 |         break;
316 |     elseif target.data(x) > C/2 && target.data(x+1) < C/2
317 |         right = interp1(target.data(x:x+1), target.start + ...
318 |             target.width * (x-1:x), C/2);
319 |         break;
320 |     end
321 | end     
322 | 
323 | % Center target profile on FWHM
324 | target.start = target.start - (right + left)/2;
325 | 
326 | % Execute in try/catch statement
327 | try
328 | 
329 |     % Execute CalcGamma using test dataset
330 |     t = tic;
331 |     gamma = CalcGamma(ref, target, percent, dta, 'local', local);
332 |     gtime = sprintf('%0.1f sec', toc(t));
333 |     gpf = pass;
334 |     cpf = pass;
335 | 
336 |     % If reference data exists
337 |     if nargin == 3
338 |         
339 |         % If current value does not equal the reference
340 |         if max(abs(gamma - varargin{3}.gammaB)) > 1e-5
341 |             gpf = fail;
342 |         end
343 |         
344 |         % Execute CalcGamma again using CPU
345 |         t = tic;
346 |         gamma = CalcGamma(ref, target, percent, dta, 'cpu', 1, ...
347 |             'local', local);
348 |         ctime = sprintf('%0.1f sec', toc(t));
349 |         
350 |         % If CPU value does not equal the reference
351 |         if max(abs(gamma - varargin{3}.gammaB)) > 1e-5
352 |             cpf = fail;
353 |         end
354 |         
355 |         % Execute CalcGamma again, this time using modified criteria
356 |         gamma = CalcGamma(ref, target, percent, dta, ...
357 |             'local', local, 'limit', 0.1);
358 |         
359 |         % If modified value equals the reference, the test fails
360 |         if max(abs(gamma - varargin{3}.gammaB)) < 1e-5
361 |             gpf = fail;
362 |         end
363 |         
364 |         % Execute CalcGamma again, this time using modified criteria
365 |         gamma = CalcGamma(ref, target, percent, dta, ...
366 |             'local', local, 'refval', 10);
367 |         
368 |         % If modified value equals the reference, the test fails
369 |         if max(abs(gamma - varargin{3}.gammaB)) < 1e-5
370 |             gpf = fail;
371 |         end
372 |         
373 |     % Otherwise, set reference    
374 |     elseif nargout == 4
375 |         reference.gammaB = gamma;
376 |         gpf = pass;
377 |         cpf = pass;
378 |     end
379 |     
380 | catch
381 |     gpf = fail;
382 |     cpf = fail;
383 | end
384 | 
385 | % Add the dataset size to the preamble
386 | preamble{length(preamble)+1} = ...
387 |     sprintf('| Beam Profile 1D Gamma Array | %i x %i  |', size(gamma));
388 | 
389 | % Add GPU computation result
390 | results{size(results,1)+1,1} = '5';
391 | results{size(results,1),2} = 'Beam Profile 1D Gamma GPU Result within 1e-5';
392 | results{size(results,1),3} = gpf;
393 | 
394 | % Add computation time
395 | results{size(results,1)+1,1} = '6';
396 | results{size(results,1),2} = 'Beam Profile 1D Gamma GPU Computation Time';
397 | results{size(results,1),3} = gtime;
398 | 
399 | % Add CPU computation result
400 | results{size(results,1)+1,1} = '7';
401 | results{size(results,1),2} = 'Beam Profile 1D Gamma CPU Result within 1e-5';
402 | results{size(results,1),3} = cpf;
403 | 
404 | % Add computation time
405 | results{size(results,1)+1,1} = '8';
406 | results{size(results,1),2} = 'Beam Profile 1D Gamma CPU Computation Time';
407 | results{size(results,1),3} = ctime;
408 | 
409 | %% TEST 9/10/11/12: Simple 2D Gamma
410 | %
411 | % DESCRIPTION: This unit test creates a simple analytic reference dataset, 
412 | %   modifies it by a known amount, and executes CalcGamma.  The gamma
413 | %   result is then compared to a known solution
414 | %
415 | % RELEVANT REQUIREMENTS: none
416 | %
417 | % INPUT DATA: varargin{3}.gammaC
418 | %
419 | % CONDITION A (+): When computed using identical criteria, CalcGamma
420 | %   produces an identical array to the reference with GPU Calculation
421 | %
422 | % CONDITION B (+): When computed using identical criteria, CalcGamma
423 | %   produces an identical array to the reference with CPU Calculation
424 | %
425 | % CONDITION C (-): When computed using modified criteria, CalcGamma
426 | %   produces a different result
427 | 
428 | % Declare Gamma criteria
429 | percent = 3;
430 | dta = 0.3;
431 | local = 0;
432 | res = 20;
433 | 
434 | % Declare size of data arrays
435 | n = 100;
436 | 
437 | % Create reference data structure (peaks function)
438 | ref.start = [0 0];
439 | ref.width = [0.01 0.01];
440 | ref.data = peaks(n) + 5;
441 | 
442 | % Declare modification values (to be applied to reference data)
443 | shift = [0.05 0.05];
444 | scale = 1.03;
445 | 
446 | % Modify reference data, saving to target structure
447 | target.start = ref.start + shift;
448 | target.width = ref.width;
449 | target.data = ref.data * scale;
450 | 
451 | % Execute in try/catch statement
452 | try
453 | 
454 |     % Execute CalcGamma using test dataset
455 |     t = tic;
456 |     gamma = CalcGamma(ref, target, percent, dta, 'local', local, ...
457 |         'res', res);
458 |     gtime = sprintf('%0.1f sec', toc(t));
459 |     gpf = pass;
460 |     cpf = pass;
461 | 
462 |     % If reference data exists
463 |     if nargin == 3
464 |         
465 |         % If current value does not equal the reference
466 |         if max(max(abs(gamma - varargin{3}.gammaC))) > 1e-5
467 |             gpf = fail;
468 |         end
469 |         
470 |         % Execute CalcGamma again using CPU
471 |         t = tic;
472 |         gamma = CalcGamma(ref, target, percent, dta, 'cpu', 1, ...
473 |             'local', local, 'res', res);
474 |         ctime = sprintf('%0.1f sec', toc(t));
475 |         
476 |         % If CPU value does not equal the reference
477 |         if max(max(abs(gamma - varargin{3}.gammaC))) > 1e-5
478 |             cpf = fail;
479 |         end
480 |         
481 |         % Execute CalcGamma again, this time using modified criteria
482 |         gamma = CalcGamma(ref, target, percent, dta * 2, ...
483 |             'local', local, 'res', res);
484 |         
485 |         % If modified value equals the reference, the test fails
486 |         if max(max(abs(gamma - varargin{3}.gammaC))) < 1e-5
487 |             gpf = fail;
488 |         end
489 |         
490 |         % Execute CalcGamma again, this time using modified criteria
491 |         gamma = CalcGamma(ref, target, percent * 2, dta, ...
492 |             'local', local, 'res', res);
493 |         
494 |         % If modified value equals the reference, the test fails
495 |         if max(max(abs(gamma - varargin{3}.gammaC))) < 1e-5
496 |             gpf = fail;
497 |         end
498 |         
499 |     % Otherwise, set reference    
500 |     elseif nargout == 4
501 |         reference.gammaC = gamma;
502 |         gpf = pass;
503 |         cpf = pass;
504 |     end
505 |     
506 | catch
507 |     gpf = fail;
508 |     cpf = fail;
509 | end
510 | 
511 | % Add the dataset size to the preamble
512 | preamble{length(preamble)+1} = ...
513 |     sprintf('| Simple 2D Gamma Array | %i x %i  |', size(gamma));
514 | 
515 | % Add GPU computation result
516 | results{size(results,1)+1,1} = '9';
517 | results{size(results,1),2} = 'Simple 2D Gamma GPU Result within 1e-5';
518 | results{size(results,1),3} = gpf;
519 | 
520 | % Add computation time
521 | results{size(results,1)+1,1} = '10';
522 | results{size(results,1),2} = 'Simple 2D Gamma GPU Computation Time';
523 | results{size(results,1),3} = gtime;
524 | 
525 | % Add CPU computation result
526 | results{size(results,1)+1,1} = '11';
527 | results{size(results,1),2} = 'Simple 2D Gamma CPU Result within 1e-5';
528 | results{size(results,1),3} = cpf;
529 | 
530 | % Add computation time
531 | results{size(results,1)+1,1} = '12';
532 | results{size(results,1),2} = 'Simple 2D Gamma CPU Computation Time';
533 | results{size(results,1),3} = ctime;
534 | 
535 | %% TEST 13/14/15/16: Dose Volume 3D Gamma
536 | %
537 | % DESCRIPTION: This unit test creates a real world dose volume dataset 
538 | %   and executes CalcGamma.  The gamma result is then compared to a known 
539 | %   solution
540 | %
541 | % RELEVANT REQUIREMENTS: none
542 | %
543 | % INPUT DATA: varargin{2}.referenceD, varargin{2}.targetD, 
544 | %   varargin{3}.gammaD
545 | %
546 | % CONDITION A (+): When computed using identical criteria, CalcGamma
547 | %   produces an identical array to the reference with GPU Calculation
548 | %
549 | % CONDITION B (+): When computed using identical criteria, CalcGamma
550 | %   produces an identical array to the reference with CPU Calculation
551 | 
552 | % Declare gamma criteria
553 | percent = 3;
554 | dta = 3;
555 | local = 0;
556 | restrict = 1;
557 | 
558 | % Load reference and target data from varargin
559 | ref = varargin{2}.referenceD;
560 | target = varargin{2}.targetD;
561 | 
562 | % Execute in try/catch statement
563 | try
564 | 
565 |     % Execute CalcGamma using test dataset
566 |     t = tic;
567 |     gamma = CalcGamma(ref, target, percent, dta, 'local', local, ...
568 |         'restrict', restrict);
569 |     gtime = sprintf('%0.1f sec', toc(t));
570 |     gpf = pass;
571 |     cpf = pass;
572 | 
573 |     % If reference data exists
574 |     if nargin == 3
575 |         
576 |         % If current value does not equal the reference
577 |         if max(max(max(abs(gamma - varargin{3}.gammaD)))) > 1e-5
578 |             gpf = fail;
579 |         end
580 |         
581 |         % Execute CalcGamma again using CPU
582 |         t = tic;
583 |         gamma = CalcGamma(ref, target, percent, dta, 'cpu', 1, ...
584 |             'local', local, 'restrict', restrict);
585 |         ctime = sprintf('%0.1f sec', toc(t));
586 |         
587 |         % If CPU value does not equal the reference
588 |         if max(max(max(abs(gamma - varargin{3}.gammaD)))) > 1e-5
589 |             cpf = fail;
590 |         end
591 |         
592 |     % Otherwise, set reference    
593 |     elseif nargout == 4
594 |         reference.gammaD = gamma;
595 |         gpf = pass;
596 |         cpf = pass;
597 |     end
598 |     
599 | catch
600 |     gpf = fail;
601 |     cpf = fail;
602 | end
603 | 
604 | % Add the dataset size to the preamble
605 | preamble{length(preamble)+1} = ...
606 |     sprintf('| Dose Volume 3D Gamma Array | %i x %i x %i |', size(gamma));
607 | 
608 | % Add GPU computation result
609 | results{size(results,1)+1,1} = '13';
610 | results{size(results,1),2} = 'Dose Volume 3D Gamma GPU Result within 1e-5';
611 | results{size(results,1),3} = gpf;
612 | 
613 | % Add computation time
614 | results{size(results,1)+1,1} = '14';
615 | results{size(results,1),2} = 'Dose Volume 3D Gamma GPU Computation Time';
616 | results{size(results,1),3} = gtime;
617 | 
618 | % Add CPU computation result
619 | results{size(results,1)+1,1} = '15';
620 | results{size(results,1),2} = 'Dose Volume 3D Gamma CPU Result within 1e-5';
621 | results{size(results,1),3} = cpf;
622 | 
623 | % Add computation time
624 | results{size(results,1)+1,1} = '16';
625 | results{size(results,1),2} = 'Dose Volume 3D Gamma CPU Computation Time';
626 | results{size(results,1),3} = ctime;
627 | 
628 | %% TEST 17: Data Validity
629 | %
630 | % DESCRIPTION: This test verifies that CalcGamma correctly fails when input
631 | %   data is not valid.  This function tests error messages both with an
632 | %   without the Event() function.
633 | %
634 | % RELEVANT REQUIREMENTS: none 
635 | %
636 | % INPUT DATA: No input data required
637 | %
638 | % CONDITION A (-): CalcGamma fails with too few arguments
639 | %
640 | % CONDITION B (-): CalcGamma fails if the reference structure is poorly
641 | %   formatted
642 | %
643 | % CONDITION C (-): CalcGamma fails if the target structure is poorly
644 | %   formatted
645 | %
646 | % CONDITION D (-): CalcGamma fails if the reference and target dimensions
647 | %   differ
648 | %
649 | % CONDITION E (-): CalcGamma fails if the reference structure contains more
650 | %   than three dimensions
651 | %
652 | % CONDITION F (-): CalcGamma fails if the target structure contains more
653 | %   than three dimensions
654 | 
655 | % Start with passing result
656 | pf = pass;
657 | 
658 | % Try to execute CalcGamma with too few arguments
659 | try
660 |     CalcGamma();
661 |     pf = fail;
662 | catch
663 |     % The test passes if an error is thrown
664 | end
665 | 
666 | % Initialize bad data
667 | ref.data = rand(5);
668 | ref.start = [0 0];
669 | ref.width = [1 1 1];
670 | target.data = rand(5);
671 | target.start = [0 0];
672 | target.width = [1 1 1];
673 | 
674 | % Try to execute CalcGamma with bad reference structure
675 | try
676 |     CalcGamma(ref, target, 1, 1);
677 |     pf = fail;
678 | catch
679 |     % The test passes if an error is thrown
680 | end
681 | 
682 | % Fix reference
683 | ref.width = [1 1];
684 | 
685 | % Try to execute CalcGamma with bad target structure
686 | try
687 |     CalcGamma(ref, target, 1, 1);
688 |     pf = fail;
689 | catch
690 |     % The test passes if an error is thrown
691 | end
692 | 
693 | % Fix target
694 | target.data = rand(5, 5, 5);
695 | target.start = [0 0 0];
696 | target.width = [1 1 1];
697 | 
698 | % Try to execute CalcGamma with different dimensions
699 | try
700 |     CalcGamma(ref, target, 1, 1);
701 |     pf = fail;
702 | catch
703 |     % The test passes if an error is thrown
704 | end
705 | 
706 | % Create 4-D datasets
707 | ref.data = rand(5, 5, 5, 5);
708 | ref.start = [0 0 0 0];
709 | ref.width = [1 1 1 1];
710 | target.data = rand(5, 5, 5, 5);
711 | target.start = [0 0 0 0];
712 | target.width = [1 1 1 1];
713 | 
714 | % Try to execute CalcGamma with different dimensions
715 | try
716 |     CalcGamma(ref, target, 1, 1);
717 |     pf = fail;
718 | catch
719 |     % The test passes if an error is thrown
720 | end
721 | 
722 | % Repeat without Event()
723 | restoredefaultpath
724 | 
725 | % Try to execute CalcGamma with too few arguments
726 | try
727 |     CalcGamma();
728 |     pf = fail;
729 | catch
730 |     % The test passes if an error is thrown
731 | end
732 | 
733 | % Initialize bad data
734 | ref.data = rand(5);
735 | ref.start = [0 0];
736 | ref.width = [1 1 1];
737 | target.data = rand(5);
738 | target.start = [0 0];
739 | target.width = [1 1 1];
740 | 
741 | % Try to execute CalcGamma with bad reference structure
742 | try
743 |     CalcGamma(ref, target, 1, 1);
744 |     pf = fail;
745 | catch
746 |     % The test passes if an error is thrown
747 | end
748 | 
749 | % Fix reference
750 | ref.width = [1 1];
751 | 
752 | % Try to execute CalcGamma with bad target structure
753 | try
754 |     CalcGamma(ref, target, 1, 1);
755 |     pf = fail;
756 | catch
757 |     % The test passes if an error is thrown
758 | end
759 | 
760 | % Fix target
761 | target.data = rand(5, 5, 5);
762 | target.start = [0 0 0];
763 | target.width = [1 1 1];
764 | 
765 | % Try to execute CalcGamma with different dimensions
766 | try
767 |     CalcGamma(ref, target, 1, 1);
768 |     pf = fail;
769 | catch
770 |     % The test passes if an error is thrown
771 | end
772 | 
773 | % Create 4-D datasets
774 | ref.data = rand(5, 5, 5, 5);
775 | ref.start = [0 0 0 0];
776 | ref.width = [1 1 1 1];
777 | target.data = rand(5, 5, 5, 5);
778 | target.start = [0 0 0 0];
779 | target.width = [1 1 1 1];
780 | 
781 | % Try to execute CalcGamma with different dimensions
782 | try
783 |     CalcGamma(ref, target, 1, 1);
784 |     pf = fail;
785 | catch
786 |     % The test passes if an error is thrown
787 | end
788 | 
789 | % Add test result
790 | results{size(results,1)+1,1} = '17';
791 | results{size(results,1),2} = 'Data Validation Checks Functional';
792 | results{size(results,1),3} = pf;
793 | 
794 | %% TEST 18/19: Code Analyzer Messages, Cyclomatic Complexity
795 | %
796 | % DESCRIPTION: This unit test uses the checkcode() MATLAB function to check
797 | %   each function used by the application and return any Code Analyzer
798 | %   messages that result.  The cumulative cyclomatic complexity is also
799 | %   computed for each function and summed to determine the total
800 | %   application complexity.  Although this test does not reference any
801 | %   particular requirements, it is used during development to help identify
802 | %   high risk code.
803 | %
804 | % RELEVANT REQUIREMENTS: none 
805 | %
806 | % INPUT DATA: No input data required
807 | %
808 | % CONDITION A (+): Report any code analyzer messages for all functions
809 | %   called by CalcGamma
810 | %
811 | % CONDITION B (+): Report the cumulative cyclomatic complexity for all
812 | %   functions called by CalcGamma
813 | 
814 | % Search for required functions
815 | fList = matlab.codetools.requiredFilesAndProducts('CalcGamma.m');
816 | 
817 | % Initialize complexity and messages counters
818 | comp = 0;
819 | mess = 0;
820 | 
821 | % Loop through each dependency
822 | for i = 1:length(fList)
823 |     
824 |     % Execute checkcode
825 |     inform = checkcode(fList{i}, '-cyc');
826 |     
827 |     % Loop through results
828 |     for j = 1:length(inform)
829 |        
830 |         % Check for McCabe complexity output
831 |         c = regexp(inform(j).message, ...
832 |             '^The McCabe complexity .+ is ([0-9]+)\.$', 'tokens');
833 |         
834 |         % If regular expression was found
835 |         if ~isempty(c)
836 |             
837 |             % Add complexity
838 |             comp = comp + str2double(c{1});
839 |             
840 |         else
841 |             
842 |             % If not an invalid code message
843 |             if ~strncmp(inform(j).message, 'Filename', 8)
844 |                 
845 |                 % Log message
846 |                 Event(sprintf('%s in %s', inform(j).message, fList{i}), ...
847 |                     'CHCK');
848 | 
849 |                 % Add as code analyzer message
850 |                 mess = mess + 1;
851 |             end
852 |         end
853 |         
854 |     end
855 | end
856 | 
857 | % Add code analyzer messages counter to results
858 | results{size(results,1)+1,1} = '18';
859 | results{size(results,1),2} = 'Code Analyzer Messages';
860 | results{size(results,1),3} = sprintf('%i', mess);
861 | 
862 | % Add complexity results
863 | results{size(results,1)+1,1} = '19';
864 | results{size(results,1),2} = 'Cumulative Cyclomatic Complexity';
865 | results{size(results,1),3} = sprintf('%i', comp);
866 | 
867 | %% Finish up
868 | % Close all figures
869 | close all force;
870 | 
871 | % If no return variables are present, print the results
872 | if nargout == 0
873 |     
874 |     % Print preamble
875 |     for j = 1:length(preamble)
876 |         fprintf('%s\n', preamble{j});
877 |     end
878 |     fprintf('\n');
879 |     
880 |     % Loop through each table row
881 |     for j = 1:size(results,1)
882 |         
883 |         % Print table row
884 |         fprintf('| %s |\n', strjoin(results(j,:), ' | '));
885 |        
886 |         % If this is the first column
887 |         if j == 1
888 |             
889 |             % Also print a separator row
890 |             fprintf('|%s\n', repmat('----|', 1, size(results,2)));
891 |         end
892 | 
893 |     end
894 |     fprintf('\n');
895 |     
896 |     % Print footnotes
897 |     for j = 1:length(footnotes) 
898 |         fprintf('%s<br>\n', footnotes{j});
899 |     end
900 |     
901 | % Otherwise, return the results as variables    
902 | else
903 | 
904 |     % Store return variables
905 |     if nargout >= 1; varargout{1} = preamble; end
906 |     if nargout >= 2; varargout{2} = results; end
907 |     if nargout >= 3; varargout{3} = footnotes; end
908 |     if nargout >= 4; varargout{4} = reference; end
909 | end
910 | 


--------------------------------------------------------------------------------
/CalcGamma.m:
--------------------------------------------------------------------------------
  1 | function gamma = CalcGamma(varargin)
  2 | % CalcGamma computes 1-D, 2-D, or 3-D global or absolute gamma between two
  3 | % datasets (reference and target) given a defined coordinate space. The 
  4 | % datasets must have the same number of dimensions, although they can be 
  5 | % different sizes. Gamma will be computed for each target dose point by
  6 | % shifting the reference image (using linear interpolation) and determining
  7 | % the minimum Gamma index across all shifts.
  8 | %
  9 | % This function optionally uses the Parallel Computing Toolbox GPU interp
 10 | % functions to increase computation speed. A try-catch statement is used
 11 | % to test for GPU support. In addition, for memory management, the
 12 | % meshgrid and data arrays are converted to single precision during
 13 | % interpolation. This function calls Event() to log execution status, if 
 14 | % available.
 15 | %
 16 | % For more information on the Gamma evaluation function, see D. A. Low et 
 17 | % al., "A technique for the quantitative evaluation of dose distributions", 
 18 | % Med Phys. 1998 May; 25(5): 656-61.
 19 | %
 20 | % The following variables are required for proper execution: 
 21 | %   varargin{1}: structure containing the reference data, where the field
 22 | %       start is an array containing the coordinates along each dimension
 23 | %       of the first voxel, width is an array containing the width of each
 24 | %       voxel along each dimension, and data is an n-dimensional array
 25 | %   varargin{2}: structure containing the target data, where the field
 26 | %       start is an array containing the coordinates along each dimension
 27 | %       of the first voxel, width is an array containing the width of each
 28 | %       voxel along each dimension, and data is an n-dimensional array
 29 | %   varargin{3}: Gamma absolute criterion percentage
 30 | %   varargin{4}: Gamma Distance To Agreement (DTA) criterion, in the same
 31 | %       units as the reference and target width structure fields  
 32 | %   varargin{5:end} (optional): additional parameters preceded by option
 33 | %       flags.  The available options are 'local', 'refval', 'restrict',
 34 | %       'res', and 'limit'.
 35 | %
 36 | % The following options can be passed to this argument as name/value pairs:
 37 | %   local: boolean, indicates whether to perform a local (1) or global (0) 
 38 | %       Gamma computation. If not present, the function will assume a 
 39 | %       global Gamma computation.
 40 | %   refval: reference value for the global absolute criterion. Is used with 
 41 | %       the percentage from varargin{3} to compute absolute value. If not 
 42 | %       present, the maximum value in the reference data is used.
 43 | %   restrict: restricted search flag. If 1 or not provided, only the gamma  
 44 | %       values along the X/Y/Z axes are computed during 3D comptation. If 
 45 | %       0, the entire rectangular/volumetric search space is computed.
 46 | %   res: DTA resolution factor.  The number of distance steps equal the
 47 | %       resolution factor multiplied by the limit.  If not provided, the
 48 | %       factor is 100 for 1D/2D and 20 for 3D calculations.
 49 | %   limit: The DTA limit.  This number determines how far the function will 
 50 | %       search in the distance axes when computing Gamma.  This also 
 51 | %       therefore specifies the maximum "real" Gamma Index value. 
 52 | %   cpu: boolean, set to 1 to force CPU computation.
 53 | %
 54 | % The following variables are returned upon succesful completion:
 55 | %   gamma: array of the same dimensions as varargin{2}.data containing the
 56 | %       computed gamma values
 57 | %
 58 | % Below is an example of how the function is used:
 59 | %
 60 | %   reference.start = [-10 -10]; % mm
 61 | %   reference.width = [0.1 0.1]; % mm
 62 | %   reference.data = rand(200);
 63 | %
 64 | %   target.start = [-10 -10]; % mm
 65 | %   target.width = [0.1 0.1]; % mm
 66 | %   target.data = rand(200);
 67 | %
 68 | %   percent = 3;
 69 | %   dta = 0.5; % mm
 70 | %   local = 0; % Perform global gamma
 71 | %   
 72 | %   gamma = CalcGamma(reference, target, percent, dta, 'local', local);
 73 | %
 74 | % Author: Mark Geurts, mark.w.geurts@gmail.com
 75 | % Copyright (C) 2014 University of Wisconsin Board of Regents
 76 | %
 77 | % This program is free software: you can redistribute it and/or modify it 
 78 | % under the terms of the GNU General Public License as published by the  
 79 | % Free Software Foundation, either version 3 of the License, or (at your 
 80 | % option) any later version.
 81 | %
 82 | % This program is distributed in the hope that it will be useful, but 
 83 | % WITHOUT ANY WARRANTY; without even the implied warranty of 
 84 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General 
 85 | % Public License for more details.
 86 | % 
 87 | % You should have received a copy of the GNU General Public License along 
 88 | % with this program. If not, see http://www.gnu.org/licenses/.
 89 | 
 90 | %% Validate Inputs
 91 | % Verify at least four input arguments are provided
 92 | if nargin < 4
 93 |     
 94 |     % If not, throw an error and stop execution
 95 |     if exist('Event', 'file') == 2
 96 |         Event('Too few input argumenst passed to CalcGamma', 'ERROR');
 97 |     else
 98 |         error('Too few input argumenst passed to CalcGamma');
 99 |     end
100 | end
101 | 
102 | % Check if the reference structure contains width, start, and data fields,
103 | % and if the size of the width and start vectors are equal
104 | if ~isfield(varargin{1}, 'width') || ~isfield(varargin{1}, 'start') || ...
105 |         ~isfield(varargin{1}, 'data') || ~isequal(length(varargin{1}.width), ...
106 |         length(varargin{1}.start))
107 |     
108 |     % If not, throw an error and stop execution
109 |     if exist('Event', 'file') == 2
110 |         Event(['Incorrect reference data format.  Must contain width, ', ...
111 |             'start, and data fields and be of equal dimensions'], 'ERROR');
112 |     else
113 |         error(['Incorrect reference data format.  Must contain width, ', ...
114 |             'start, and data fields and be of equal dimensions']);
115 |     end
116 |     
117 | % Check if the target structure contains width, start, and data fields,
118 | % and if the size of the width and start vectors are equal
119 | elseif ~isfield(varargin{2}, 'width') || ~isfield(varargin{2}, 'start') || ...
120 |         ~isfield(varargin{2}, 'data') || ~isequal(length(varargin{2}.width), ...
121 |         length(varargin{2}.start))
122 |     
123 |     % If not, throw an error and stop execution
124 |     if exist('Event', 'file') == 2
125 |         Event(['Incorrect target data format.  Must contain width, ', ...
126 |             'start, and data fields and be of equal dimensions'], 'ERROR');
127 |     else
128 |         error(['Incorrect target data format.  Must contain width, ', ...
129 |             'start, and data fields and be of equal dimensions']);
130 |     end
131 |     
132 | % Check if the reference and target data arrays are the same number of
133 | % dimensions.  Calculating the gamma from a lower dimensional dataset to a
134 | % higher dimensional reference is currently not supported
135 | elseif ~isequal(size(size(varargin{1}.data)), size(size(varargin{2}.data)))
136 |     
137 |     % If not, throw an error and stop execution
138 |     if exist('Event', 'file') == 2
139 |         Event(['The fixed and target data arrays must be of the same', ...
140 |             ' dimensions'], 'ERROR');
141 |     else
142 |         error(['The fixed and target data arrays must be of the same', ...
143 |             ' dimensions']);
144 |     end
145 | end
146 | 
147 | % Log validation completed
148 | if exist('Event', 'file') == 2
149 |     Event('Data validation completed, beginning Gamma computation');
150 |     tic;
151 | end
152 | 
153 | %% Declare default options
154 | % local indicates whether to perform a local (1) or global (0) Gamma 
155 | % computation. If not present, the function will assume a global Gamma 
156 | % computation.
157 | local = 0;
158 | 
159 | % refval is the reference value for the global absolute criterion. Is used 
160 | % with the percentage from varargin{3} to compute absolute value. If not 
161 | % present, the maximum value in the reference data is used.
162 | refval = max(max(max(varargin{1}.data)));
163 | 
164 | % restricted search flag. If 1, only the gamma values along the X/Y/Z axes 
165 | % are computed during 3D comptation. If 0, the entire rectangular/
166 | % volumetric search space is computed.
167 | restrict = 1;
168 | 
169 | % The resolution parameter determines the number of steps (relative to 
170 | % the distance to agreement) that each reference voxel will be
171 | % interpolated to and gamma calculated.  A value of 5 with a DTA of 3
172 | % mm means that gamma will be calculated at intervals of 3/5 = 0.6 mm.
173 | % Different resolutions can be set for different dimensions of data. 
174 | if size(varargin{2}.width,2) == 1
175 | 
176 |     % Set 1-D resolution
177 |     res = 100;
178 |     
179 | elseif size(varargin{2}.width,2) == 2
180 | 
181 |     % Set 2-D resolution
182 |     res = 50;
183 |     
184 | elseif size(varargin{2}.width,2) == 3
185 | 
186 |     % Set 3-D resolution
187 |     res = 20;
188 |     
189 | end
190 | 
191 | % The search limit parameter determines how far the function will search in
192 | % the distance axes when computing Gamma.  This also therefore specifies
193 | % the maximum believable Gamma Index value.  Typically this value is 2.
194 | % This should always be set to an integer.
195 | limit = 2;
196 | 
197 | %% Search for provided options
198 | % Load data structure from varargin
199 | for i = 5:nargin
200 |     
201 |     % If the local option is set
202 |     if strcmp(varargin{i}, 'local')
203 |         local = varargin{i+1}; 
204 |         
205 |     % If the refval option is set
206 |     elseif strcmp(varargin{i}, 'refval')
207 |         refval = varargin{i+1}; 
208 |         
209 |     % If the restrict option is set
210 |     elseif strcmp(varargin{i}, 'restrict')
211 |         restrict = varargin{i+1}; 
212 |         
213 |     % If the res option is set
214 |     elseif strcmp(varargin{i}, 'res')
215 |         res = varargin{i+1}; 
216 |         
217 |     % If the limit option is set
218 |     elseif strcmp(varargin{i}, 'limit')
219 |         limit = varargin{i+1}; 
220 |     
221 |     % If the cpu option is set
222 |     elseif strcmp(varargin{i}, 'cpu')
223 |         cpu = varargin{i+1}; 
224 |     end
225 | end
226 | 
227 | %% Log options
228 | % If Event reporting is enabled
229 | if exist('Event', 'file') == 2
230 |     
231 |     % Log local
232 |     if local == 1
233 |         Event('Gamma calculation set to local');  
234 |     else
235 |         Event('Gamma calculation assumed to global');
236 |     end
237 |     
238 |     % Log refval
239 |     Event(sprintf('Reference value set to %g', refval));
240 |     
241 |     % Log restrict
242 |     if restrict == 1
243 |         Event('Restricted search enabled');  
244 |     else
245 |         Event('Restricted search disabled');
246 |     end
247 | 
248 |     % Log res
249 |     Event(sprintf('Resolution set to %g', res));
250 |     
251 |     % Log limit
252 |     Event(sprintf('DTA limit set to %g', limit));
253 | end
254 | 
255 | %% Compute mesh grids
256 | % If the reference dataset is 1-D
257 | if length(varargin{1}.width) == 1
258 | 
259 |     % Log event
260 |     if exist('Event', 'file') == 2
261 |         Event('Reference dataset is 1-D');
262 |     end
263 |     
264 |     % Check if the data is in rows or columns (this is only needed for 1-D)
265 |     if size(varargin{1}.data,1) > size(varargin{1}.data,2)
266 |         
267 |         % If in rows, transpose
268 |         varargin{1}.data = varargin{1}.data';
269 |     end
270 |     
271 |     % Compute the reference X coordinates using the start and width values
272 |     refX = single(varargin{1}.start(1):varargin{1}.width(1):varargin{1}.start(1) ...
273 |         + varargin{1}.width(1) * (size(varargin{1}.data,2) - 1));
274 |     
275 | % Otherwise, if the reference dataset is 2-D
276 | elseif length(varargin{1}.width) == 2
277 | 
278 |     % Log event
279 |     if exist('Event', 'file') == 2
280 |         Event('Reference dataset is 2-D');
281 |     end
282 |     
283 |     % Compute X and Y meshgrids for the reference dataset positions using 
284 |     % the start and width values
285 |     [refX, refY] = meshgrid(single(varargin{1}.start(2): ...
286 |         varargin{1}.width(2):varargin{1}.start(2) + varargin{1}.width(2) * ...
287 |         (size(varargin{1}.data,2) - 1)), single(varargin{1}.start(1): ...
288 |         varargin{1}.width(1):varargin{1}.start(1) + varargin{1}.width(1)...
289 |         * (size(varargin{1}.data,1) - 1)));
290 |     
291 | % Otherwise, if the reference dataset is 3-D
292 | elseif length(varargin{1}.width) == 3
293 | 
294 |     % Log event
295 |     if exist('Event', 'file') == 2
296 |         Event('Reference dataset is 3-D');
297 |     end
298 |     
299 |     % Compute X, Y, and Z meshgrids for the reference dataset positions
300 |     % using the start and width values, permuting X/Y
301 |     [refX, refY, refZ] = meshgrid(single(varargin{1}.start(2): ...
302 |         varargin{1}.width(2):varargin{1}.start(2) + varargin{1}.width(2) * ...
303 |         (size(varargin{1}.data,2) - 1)), single(varargin{1}.start(1): ...
304 |         varargin{1}.width(1):varargin{1}.start(1) + varargin{1}.width(1)...
305 |         * (size(varargin{1}.data,1) - 1)), single(varargin{1}.start(3):...
306 |         varargin{1}.width(3):varargin{1}.start(3) + varargin{1}.width(3)...
307 |         * (size(varargin{1}.data,3) - 1)));
308 | 
309 | % Otherwise, if the reference data is of higher dimension
310 | else
311 | 
312 |     % Throw an error and stop execution
313 |     if exist('Event', 'file') == 2
314 |         Event('The fixed data structure contains too many dimensions', ...
315 |             'ERROR');
316 |     else
317 |         error('The fixed data structure contains too many dimensions');
318 |     end
319 | end
320 | 
321 | % If the target dataset is 1-D
322 | if length(varargin{2}.width) == 1
323 | 
324 |     % Log event
325 |     if exist('Event', 'file') == 2
326 |         Event('Target dataset is 1-D');
327 |     end
328 |     
329 |     % Check if the data is in rows or columns (this is only needed for 1-D)
330 |     if size(varargin{2}.data,1) > size(varargin{2}.data,2)
331 |         
332 |         % If in rows, transpose
333 |         varargin{2}.data = varargin{2}.data';
334 |     end
335 |     
336 |     % Compute the target X coordinates using the start and width values
337 |     tarX = single(varargin{2}.start(1):varargin{2}.width(1):varargin{2}.start(1) ...
338 |         + varargin{2}.width(1) * (size(varargin{2}.data,2) - 1));
339 |     
340 | % Otherwise, if the target dataset is 2-D
341 | elseif length(varargin{2}.width) == 2
342 | 
343 |     % Log event
344 |     if exist('Event', 'file') == 2
345 |         Event('Target dataset is 2-D');
346 |     end
347 |     
348 |     % Compute X and Y meshgrids for the target dataset positions using the
349 |     % start and width values
350 |     [tarX, tarY] = meshgrid(single(varargin{2}.start(2):...
351 |         varargin{2}.width(2):varargin{2}.start(2) + varargin{2}.width(2) * ...
352 |         (size(varargin{2}.data,2) - 1)), single(varargin{2}.start(1): ...
353 |         varargin{2}.width(1):varargin{2}.start(1) + varargin{2}.width(1) ...
354 |         * (size(varargin{2}.data,1) - 1)));
355 |     
356 | % Otherwise, if the target dataset is 3-D
357 | elseif length(varargin{2}.width) == 3
358 | 
359 |     % Log event
360 |     if exist('Event', 'file') == 2
361 |         Event('Target dataset is 3-D');
362 |     end
363 |     
364 |     % Compute X, Y, and Z meshgrids for the target dataset positions using
365 |     % the start and width values, permuting X/Y
366 |     [tarX, tarY, tarZ] = meshgrid(single(varargin{2}.start(2):...
367 |         varargin{2}.width(2):varargin{2}.start(2) + varargin{2}.width(2) * ...
368 |         (size(varargin{2}.data,2) - 1)), single(varargin{2}.start(1): ...
369 |         varargin{2}.width(1):varargin{2}.start(1) + varargin{2}.width(1) ...
370 |         * (size(varargin{2}.data,1) - 1)), single(varargin{2}.start(3):...
371 |         varargin{2}.width(3):varargin{2}.start(3) + varargin{2}.width(3) ...
372 |         * (size(varargin{2}.data,3) - 1)));
373 |     
374 | end
375 | 
376 | %% Initialize variables
377 | % Generate an initial gamma volume with values of 2^2 (this is the maximum
378 | % reliable value of gamma, see description of limit above).  Note that
379 | % gamma-squared is stored during computation; sqrt is computed at the end.
380 | gamma = ones(size(varargin{2}.data)) * (limit ^ 2);
381 | 
382 | % Log number of gamma calculations (for status updates on 3D calcs)
383 | if restrict == 1
384 | 
385 |     % Compute number of restricted search calcs
386 |     num = (res * (limit * 2) + 1) * length(varargin{2}.width);
387 | else
388 | 
389 |     % Compute total number of calcs
390 |     num = (res * (limit * 2) + 1) ^ length(varargin{2}.width);
391 | end
392 | 
393 | % num is the number of iterations, num * numel the total number of
394 | % interpolations being performed
395 | if exist('Event', 'file') == 2
396 |     Event(sprintf('Number of gamma calculations = %g', num * numel(gamma)));
397 | end
398 | 
399 | % Initialize counter (for progress indicator)
400 | n = 0;
401 | 
402 | %% Begin computation
403 | % Start try-catch block to safely test for CUDA functionality
404 | try
405 |     % If the cpu option is set, throw an error to force CPU computation
406 |     if exist('cpu', 'var') == 1 && cpu == 1
407 |         error('Reverting to CPU computation');
408 |     end
409 |     
410 |     % Clear and initialize GPU memory.  If CUDA is not enabled, or if the
411 |     % Parallel Computing Toolbox is not installed, this will error, and the
412 |     % function will automatically rever to CPU computation via the catch
413 |     % statement
414 |     gpuDevice(1);
415 |     
416 |     % Start a for loop to interpolate the dose array along the x-direction.  
417 |     % Note to support parfor loops indices must be integers, so x varies 
418 |     % from -2 to +2 multiplied by the number of interpolation steps.  
419 |     % Effectively, this evaluates gamma from -2 * DTA to +2 * DTA.
420 |     for x = -limit*res:limit*res
421 |         
422 |         % i is the x axis step value
423 |         i = x/res * varargin{4};
424 |         
425 |         % Initialize j and k as zero (they will be updated if the data is
426 |         % of higher dimension)
427 |         j = 0;
428 |         k = 0;
429 |         
430 |         % If the data contains a second dimension
431 |         if length(varargin{1}.width) > 1
432 |    
433 |             % Start a for loop to interpolate the dose array along the
434 |             % y-direction.  Note to support parfor loops indices must be
435 |             % integers, so y varies from -2 to +2 multiplied by the number
436 |             % of interpolation steps.  Effectively, this evaluates gamma
437 |             % from -2 * DTA to +2 * DTA.
438 |             for y = -limit*res:limit*res
439 |                 
440 |                 % j is the y axis step value
441 |                 j = y/res * varargin{4};
442 |                 
443 |                 % Initialize k as zero (it will be updated if the data is
444 |                 % of higher dimension)
445 |                 k = 0;
446 |                 
447 |                 % If the data contains a third dimension
448 |                 if length(varargin{1}.width) > 2
449 |                     
450 |                     % Start a for loop to interpolate the dose array along 
451 |                     % the z-direction.  Note to support parfor loops 
452 |                     % indices must be integers, so z varies from -2 to +2 
453 |                     % multiplied by the number of interpolation steps.
454 |                     % Effectively, this evaluates gamma from -2 * DTA to 
455 |                     % +2 * DTA.
456 |                     for z = -limit*res:limit*res
457 |                         
458 |                         % k is the z axis step value
459 |                         k = z/res * varargin{4};
460 | 
461 |                         % Check restricted search flag
462 |                         if restrict == 0 || sum(abs([x y z]) > 0) == 1
463 |                             
464 |                             % Run GPU interp3 function to compute the reference
465 |                             % values at the specified target coordinate points
466 |                             interp = gather(interp3(gpuArray(refX), gpuArray(refY), ...
467 |                                 gpuArray(refZ), gpuArray(single(varargin{1}.data)), ...
468 |                                 gpuArray(tarX + i), gpuArray(tarY + j), ...
469 |                                 gpuArray(tarZ + k), 'linear', 0));
470 | 
471 |                             % Update the gamma array by returning the minimum
472 |                             % of the existing value or the new value
473 |                             gamma = min(gamma, GammaEquation(interp, ...
474 |                                 varargin{2}.data, i, j, k, varargin{3}, varargin{4}, ...
475 |                                 refval, local));
476 |                             
477 |                             % Update counter 
478 |                             n = n + 1;
479 |                             
480 |                             % If counter is at an even %, display progress
481 |                             if mod((n-1)/num, 0.01) > 0.005 && ...
482 |                                     mod(n/num, 0.01) < 0.005
483 |                                 fprintf('%0.1f%%\n', n/num*100);
484 |                             end
485 |                         end
486 |                     end
487 |                     
488 |                 % Otherwise, the data is 2-D
489 |                 else
490 |                 
491 |                     % Run GPU interp2 function to compute the reference
492 |                     % values at the specified target coordinate points
493 |                     interp = gather(interp2(gpuArray(refX), gpuArray(refY), ...
494 |                         gpuArray(single(varargin{1}.data)), gpuArray(tarX + i), ...
495 |                         gpuArray(tarY + j), 'linear', 0));
496 |                     
497 |                     % Update the gamma array by returning the minimum
498 |                     % of the existing value or the new value
499 |                     gamma = min(gamma, GammaEquation(interp, varargin{2}.data, ...
500 |                         i, j, k, varargin{3}, varargin{4}, ...
501 |                         refval, local));
502 |                 end
503 |             end
504 |             
505 |         % Otherwise, the data is 1-D
506 |         else
507 |         
508 |             % Run GPU interp function to compute the reference values at 
509 |             % the specified target coordinate points
510 |             interp = gather(interp1(gpuArray(refX), ...
511 |                 gpuArray(single(varargin{1}.data)), gpuArray(tarX + i), ...
512 |                 'linear', 0));
513 |             
514 |             % Update the gamma array by returning the minimum of the 
515 |             % existing value or the new value
516 |             gamma = min(gamma, GammaEquation(interp, varargin{2}.data, ...
517 |                 i, j, k, varargin{3}, varargin{4}, ...
518 |                 refval, local));
519 |         end
520 |     end
521 |     
522 | % If GPU fails, revert to CPU computation
523 | catch
524 | 
525 |     % Log GPU failure (if cpu flag is not set)
526 |     if exist('Event', 'file') == 2 && exist('cpu', 'var') ~= 1
527 |         Event('GPU failed, reverting to CPU method', 'WARN'); 
528 |     end
529 |     
530 |     % Start a for loop to interpolate the dose array along the x-direction.  
531 |     % Note to support parfor loops indices must be integers, so x varies 
532 |     % from -2 to +2 multiplied by the number of interpolation steps.  
533 |     % Effectively, this evaluates gamma from -2 * DTA to +2 * DTA.
534 |     for x = -limit*res:limit*res
535 |     
536 |         % i is the x axis step value
537 |         i = x/res * varargin{4};
538 |         
539 |         % Initialize j and k as zero (they will be updated if the data is
540 |         % of higher dimension)
541 |         j = 0;
542 |         k = 0;
543 |         
544 |         % If the data contains a second dimension
545 |         if length(varargin{1}.width) > 1
546 |             
547 |             % Start a for loop to interpolate the dose array along the
548 |             % y-direction.  Note to support parfor loops indices must be
549 |             % integers, so y varies from -2 to +2 multiplied by the number
550 |             % of interpolation steps.  Effectively, this evaluates gamma
551 |             % from -2 * DTA to +2 * DTA.
552 |             for y = -limit*res:limit*res
553 |                 
554 |                 % j is the y axis step value
555 |                 j = y/res * varargin{4};
556 |                 
557 |                 % Initialize k as zero (it will be updated if the data is
558 |                 % of higher dimension)
559 |                 k = 0;
560 |                 
561 |                 % If the data contains a third dimension
562 |                 if length(varargin{1}.width) > 2
563 |                     
564 |                     % Start a for loop to interpolate the dose array along 
565 |                     % the z-direction.  Note to support parfor loops 
566 |                     % indices must be integers, so z varies from -2 to +2 
567 |                     % multiplied by the number of interpolation steps.
568 |                     % Effectively, this evaluates gamma from -2 * DTA to 
569 |                     % +2 * DTA.
570 |                     for z = -limit*res:limit*res
571 |                         
572 |                         % k is the z axis step value
573 |                         k = z/res * varargin{4};
574 | 
575 |                         % Check restricted search flag
576 |                         if restrict == 0 || sum(abs([x y z]) > 0) == 1
577 |                             
578 |                             % Run CPU interp3 function to compute the reference
579 |                             % values at the specified target coordinate points
580 |                             interp = interp3(refX, refY, refZ, ...
581 |                                 single(varargin{1}.data), tarX + i, ...
582 |                                 tarY + j, tarZ + k, '*linear', 0);
583 | 
584 |                             % Update the gamma array by returning the minimum
585 |                             % of the existing value or the new value
586 |                             gamma = min(gamma, GammaEquation(interp, ...
587 |                                 varargin{2}.data, i, j, k, varargin{3}, ...
588 |                                 varargin{4}, refval, local));
589 |                             
590 |                             % Update counter 
591 |                             n = n + 1;
592 |                             
593 |                             % If counter is at an even %, display progress
594 |                             if mod((n-1)/num, 0.01) > 0.005 && ...
595 |                                     mod(n/num, 0.01) < 0.005
596 |                                 fprintf('%0.1f%%\n', n/num*100);
597 |                             end
598 |                         end
599 |                     end
600 |                     
601 |                 % Otherwise, the data is 2-D
602 |                 else
603 |                 
604 |                     % Run CPU interp2 function to compute the reference
605 |                     % values at the specified target coordinate points
606 |                     interp = interp2(refX, refY, single(varargin{1}.data), ...
607 |                         tarX + i, tarY + j, '*linear', 0);
608 |                     
609 |                     % Update the gamma array by returning the minimum
610 |                     % of the existing value or the new value
611 |                     gamma = min(gamma, GammaEquation(interp, ...
612 |                         varargin{2}.data, i, j, k, varargin{3}, ...
613 |                         varargin{4}, refval, local));
614 |                 end
615 |             end
616 |             
617 |         % Otherwise, the data is 1-D
618 |         else
619 |         
620 |             % Run CPU interp function to compute the reference values at 
621 |             % the specified target coordinate points
622 |             interp = interp1(refX, single(varargin{1}.data), tarX + i, ...
623 |                 '*linear', 0);
624 |             
625 |             % Update the gamma array by returning the minimum of the 
626 |             % existing value or the new value
627 |             gamma = min(gamma, GammaEquation(interp, varargin{2}.data, ...
628 |                 i, j, k, varargin{3}, varargin{4}, ...
629 |                 refval, local));
630 |         end
631 |     end
632 | end
633 |     
634 | %% Finish up
635 | % Take square root of result
636 | gamma = sqrt(gamma);
637 | 
638 | % Log completion
639 | if exist('Event', 'file') == 2
640 |     Event(sprintf(['Gamma calculation completed successfully in ', ...
641 |         '%0.3f seconds'], toc));
642 | end
643 | 
644 | % Clear temporary variables
645 | clear refX refY refZ tarX tarY tarZ interp;
646 | 
647 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
648 | function gamma = GammaEquation(ref, tar, i, j, k, perc, dta, refval, local)
649 | % GammaEquation is the programmatic form of the Gamma definition as given
650 | % by Low et al in matrix form.  This function computes both local and
651 | % global Gamma, and is a subfunction for CalcGamma.  Note that this
652 | % equation returns Gamma-squared instead of Gamma.
653 | %
654 | % The following inputs are used for computation and are required:
655 | %   ref: the reference 3D array.  Must be the same size as tar
656 | %   tar: the target 3D array.  Must be the same size as ref
657 | %   i: magnitude of x position offset of tar to ref, relative to dta
658 | %   j: magnitude of y position offset of tar to ref, relative to dta
659 | %   k: magnitude of z position offset of tar to ref, relative to dta
660 | %   perc: the percent Gamma criterion, given in % (i.e. 3 for 3%)
661 | %   dta: the distance to agreement Gamma criterion, unitless but relative
662 | %       to i, j, and k
663 | %   refval: if global, the reference value to base the % criterion from 
664 | %   local: boolean, indicates whether to perform a local (1) or global (0)
665 | %       Gamma computation
666 | %
667 | % The following variables are returned:
668 | %   gamma: a 3D array of the same dimensions as ref and interp of the
669 | %       computed gamma-squared value for each voxel based on interp and 
670 | %       i, j, k
671 | 
672 | % If local is set to 1, perform a local Gamma computation
673 | if local == 1
674 |     
675 |     % Gamma is defined as the sqrt((abs difference/relative tolerance)^2 +
676 |     % sum((voxel offset/dta)^2)).  The sqrt is removed for computational
677 |     % efficiency.
678 |     gamma = ((tar - ref) ./ (ref * perc / 100)).^2 + ...
679 |         (i/dta)^2 + (j/dta)^2 + (k/dta)^2;
680 | else
681 |     
682 |     % Gamma is defined as the sqrt((abs difference/absolute  tolerance)^2 +
683 |     % sum((voxel offset/dta)^2)). The sqrt is removed for computational
684 |     % efficiency.
685 |     gamma = ((tar - ref) ./ (refval * perc / 100)).^2 + ...
686 |         (i/dta)^2 + (j/dta)^2 + (k/dta)^2;
687 | end
688 | 


--------------------------------------------------------------------------------
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227 |     permission to license the work in any other way, but it does not
228 |     invalidate such permission if you have separately received it.
229 | 
230 |     d) If the work has interactive user interfaces, each must display
231 |     Appropriate Legal Notices; however, if the Program has interactive
232 |     interfaces that do not display Appropriate Legal Notices, your
233 |     work need not make them do so.
234 | 
235 |   A compilation of a covered work with other separate and independent
236 | works, which are not by their nature extensions of the covered work,
237 | and which are not combined with it such as to form a larger program,
238 | in or on a volume of a storage or distribution medium, is called an
239 | "aggregate" if the compilation and its resulting copyright are not
240 | used to limit the access or legal rights of the compilation's users
241 | beyond what the individual works permit.  Inclusion of a covered work
242 | in an aggregate does not cause this License to apply to the other
243 | parts of the aggregate.
244 | 
245 |   6. Conveying Non-Source Forms.
246 | 
247 |   You may convey a covered work in object code form under the terms
248 | of sections 4 and 5, provided that you also convey the
249 | machine-readable Corresponding Source under the terms of this License,
250 | in one of these ways:
251 | 
252 |     a) Convey the object code in, or embodied in, a physical product
253 |     (including a physical distribution medium), accompanied by the
254 |     Corresponding Source fixed on a durable physical medium
255 |     customarily used for software interchange.
256 | 
257 |     b) Convey the object code in, or embodied in, a physical product
258 |     (including a physical distribution medium), accompanied by a
259 |     written offer, valid for at least three years and valid for as
260 |     long as you offer spare parts or customer support for that product
261 |     model, to give anyone who possesses the object code either (1) a
262 |     copy of the Corresponding Source for all the software in the
263 |     product that is covered by this License, on a durable physical
264 |     medium customarily used for software interchange, for a price no
265 |     more than your reasonable cost of physically performing this
266 |     conveying of source, or (2) access to copy the
267 |     Corresponding Source from a network server at no charge.
268 | 
269 |     c) Convey individual copies of the object code with a copy of the
270 |     written offer to provide the Corresponding Source.  This
271 |     alternative is allowed only occasionally and noncommercially, and
272 |     only if you received the object code with such an offer, in accord
273 |     with subsection 6b.
274 | 
275 |     d) Convey the object code by offering access from a designated
276 |     place (gratis or for a charge), and offer equivalent access to the
277 |     Corresponding Source in the same way through the same place at no
278 |     further charge.  You need not require recipients to copy the
279 |     Corresponding Source along with the object code.  If the place to
280 |     copy the object code is a network server, the Corresponding Source
281 |     may be on a different server (operated by you or a third party)
282 |     that supports equivalent copying facilities, provided you maintain
283 |     clear directions next to the object code saying where to find the
284 |     Corresponding Source.  Regardless of what server hosts the
285 |     Corresponding Source, you remain obligated to ensure that it is
286 |     available for as long as needed to satisfy these requirements.
287 | 
288 |     e) Convey the object code using peer-to-peer transmission, provided
289 |     you inform other peers where the object code and Corresponding
290 |     Source of the work are being offered to the general public at no
291 |     charge under subsection 6d.
292 | 
293 |   A separable portion of the object code, whose source code is excluded
294 | from the Corresponding Source as a System Library, need not be
295 | included in conveying the object code work.
296 | 
297 |   A "User Product" is either (1) a "consumer product", which means any
298 | tangible personal property which is normally used for personal, family,
299 | or household purposes, or (2) anything designed or sold for incorporation
300 | into a dwelling.  In determining whether a product is a consumer product,
301 | doubtful cases shall be resolved in favor of coverage.  For a particular
302 | product received by a particular user, "normally used" refers to a
303 | typical or common use of that class of product, regardless of the status
304 | of the particular user or of the way in which the particular user
305 | actually uses, or expects or is expected to use, the product.  A product
306 | is a consumer product regardless of whether the product has substantial
307 | commercial, industrial or non-consumer uses, unless such uses represent
308 | the only significant mode of use of the product.
309 | 
310 |   "Installation Information" for a User Product means any methods,
311 | procedures, authorization keys, or other information required to install
312 | and execute modified versions of a covered work in that User Product from
313 | a modified version of its Corresponding Source.  The information must
314 | suffice to ensure that the continued functioning of the modified object
315 | code is in no case prevented or interfered with solely because
316 | modification has been made.
317 | 
318 |   If you convey an object code work under this section in, or with, or
319 | specifically for use in, a User Product, and the conveying occurs as
320 | part of a transaction in which the right of possession and use of the
321 | User Product is transferred to the recipient in perpetuity or for a
322 | fixed term (regardless of how the transaction is characterized), the
323 | Corresponding Source conveyed under this section must be accompanied
324 | by the Installation Information.  But this requirement does not apply
325 | if neither you nor any third party retains the ability to install
326 | modified object code on the User Product (for example, the work has
327 | been installed in ROM).
328 | 
329 |   The requirement to provide Installation Information does not include a
330 | requirement to continue to provide support service, warranty, or updates
331 | for a work that has been modified or installed by the recipient, or for
332 | the User Product in which it has been modified or installed.  Access to a
333 | network may be denied when the modification itself materially and
334 | adversely affects the operation of the network or violates the rules and
335 | protocols for communication across the network.
336 | 
337 |   Corresponding Source conveyed, and Installation Information provided,
338 | in accord with this section must be in a format that is publicly
339 | documented (and with an implementation available to the public in
340 | source code form), and must require no special password or key for
341 | unpacking, reading or copying.
342 | 
343 |   7. Additional Terms.
344 | 
345 |   "Additional permissions" are terms that supplement the terms of this
346 | License by making exceptions from one or more of its conditions.
347 | Additional permissions that are applicable to the entire Program shall
348 | be treated as though they were included in this License, to the extent
349 | that they are valid under applicable law.  If additional permissions
350 | apply only to part of the Program, that part may be used separately
351 | under those permissions, but the entire Program remains governed by
352 | this License without regard to the additional permissions.
353 | 
354 |   When you convey a copy of a covered work, you may at your option
355 | remove any additional permissions from that copy, or from any part of
356 | it.  (Additional permissions may be written to require their own
357 | removal in certain cases when you modify the work.)  You may place
358 | additional permissions on material, added by you to a covered work,
359 | for which you have or can give appropriate copyright permission.
360 | 
361 |   Notwithstanding any other provision of this License, for material you
362 | add to a covered work, you may (if authorized by the copyright holders of
363 | that material) supplement the terms of this License with terms:
364 | 
365 |     a) Disclaiming warranty or limiting liability differently from the
366 |     terms of sections 15 and 16 of this License; or
367 | 
368 |     b) Requiring preservation of specified reasonable legal notices or
369 |     author attributions in that material or in the Appropriate Legal
370 |     Notices displayed by works containing it; or
371 | 
372 |     c) Prohibiting misrepresentation of the origin of that material, or
373 |     requiring that modified versions of such material be marked in
374 |     reasonable ways as different from the original version; or
375 | 
376 |     d) Limiting the use for publicity purposes of names of licensors or
377 |     authors of the material; or
378 | 
379 |     e) Declining to grant rights under trademark law for use of some
380 |     trade names, trademarks, or service marks; or
381 | 
382 |     f) Requiring indemnification of licensors and authors of that
383 |     material by anyone who conveys the material (or modified versions of
384 |     it) with contractual assumptions of liability to the recipient, for
385 |     any liability that these contractual assumptions directly impose on
386 |     those licensors and authors.
387 | 
388 |   All other non-permissive additional terms are considered "further
389 | restrictions" within the meaning of section 10.  If the Program as you
390 | received it, or any part of it, contains a notice stating that it is
391 | governed by this License along with a term that is a further
392 | restriction, you may remove that term.  If a license document contains
393 | a further restriction but permits relicensing or conveying under this
394 | License, you may add to a covered work material governed by the terms
395 | of that license document, provided that the further restriction does
396 | not survive such relicensing or conveying.
397 | 
398 |   If you add terms to a covered work in accord with this section, you
399 | must place, in the relevant source files, a statement of the
400 | additional terms that apply to those files, or a notice indicating
401 | where to find the applicable terms.
402 | 
403 |   Additional terms, permissive or non-permissive, may be stated in the
404 | form of a separately written license, or stated as exceptions;
405 | the above requirements apply either way.
406 | 
407 |   8. Termination.
408 | 
409 |   You may not propagate or modify a covered work except as expressly
410 | provided under this License.  Any attempt otherwise to propagate or
411 | modify it is void, and will automatically terminate your rights under
412 | this License (including any patent licenses granted under the third
413 | paragraph of section 11).
414 | 
415 |   However, if you cease all violation of this License, then your
416 | license from a particular copyright holder is reinstated (a)
417 | provisionally, unless and until the copyright holder explicitly and
418 | finally terminates your license, and (b) permanently, if the copyright
419 | holder fails to notify you of the violation by some reasonable means
420 | prior to 60 days after the cessation.
421 | 
422 |   Moreover, your license from a particular copyright holder is
423 | reinstated permanently if the copyright holder notifies you of the
424 | violation by some reasonable means, this is the first time you have
425 | received notice of violation of this License (for any work) from that
426 | copyright holder, and you cure the violation prior to 30 days after
427 | your receipt of the notice.
428 | 
429 |   Termination of your rights under this section does not terminate the
430 | licenses of parties who have received copies or rights from you under
431 | this License.  If your rights have been terminated and not permanently
432 | reinstated, you do not qualify to receive new licenses for the same
433 | material under section 10.
434 | 
435 |   9. Acceptance Not Required for Having Copies.
436 | 
437 |   You are not required to accept this License in order to receive or
438 | run a copy of the Program.  Ancillary propagation of a covered work
439 | occurring solely as a consequence of using peer-to-peer transmission
440 | to receive a copy likewise does not require acceptance.  However,
441 | nothing other than this License grants you permission to propagate or
442 | modify any covered work.  These actions infringe copyright if you do
443 | not accept this License.  Therefore, by modifying or propagating a
444 | covered work, you indicate your acceptance of this License to do so.
445 | 
446 |   10. Automatic Licensing of Downstream Recipients.
447 | 
448 |   Each time you convey a covered work, the recipient automatically
449 | receives a license from the original licensors, to run, modify and
450 | propagate that work, subject to this License.  You are not responsible
451 | for enforcing compliance by third parties with this License.
452 | 
453 |   An "entity transaction" is a transaction transferring control of an
454 | organization, or substantially all assets of one, or subdividing an
455 | organization, or merging organizations.  If propagation of a covered
456 | work results from an entity transaction, each party to that
457 | transaction who receives a copy of the work also receives whatever
458 | licenses to the work the party's predecessor in interest had or could
459 | give under the previous paragraph, plus a right to possession of the
460 | Corresponding Source of the work from the predecessor in interest, if
461 | the predecessor has it or can get it with reasonable efforts.
462 | 
463 |   You may not impose any further restrictions on the exercise of the
464 | rights granted or affirmed under this License.  For example, you may
465 | not impose a license fee, royalty, or other charge for exercise of
466 | rights granted under this License, and you may not initiate litigation
467 | (including a cross-claim or counterclaim in a lawsuit) alleging that
468 | any patent claim is infringed by making, using, selling, offering for
469 | sale, or importing the Program or any portion of it.
470 | 
471 |   11. Patents.
472 | 
473 |   A "contributor" is a copyright holder who authorizes use under this
474 | License of the Program or a work on which the Program is based.  The
475 | work thus licensed is called the contributor's "contributor version".
476 | 
477 |   A contributor's "essential patent claims" are all patent claims
478 | owned or controlled by the contributor, whether already acquired or
479 | hereafter acquired, that would be infringed by some manner, permitted
480 | by this License, of making, using, or selling its contributor version,
481 | but do not include claims that would be infringed only as a
482 | consequence of further modification of the contributor version.  For
483 | purposes of this definition, "control" includes the right to grant
484 | patent sublicenses in a manner consistent with the requirements of
485 | this License.
486 | 
487 |   Each contributor grants you a non-exclusive, worldwide, royalty-free
488 | patent license under the contributor's essential patent claims, to
489 | make, use, sell, offer for sale, import and otherwise run, modify and
490 | propagate the contents of its contributor version.
491 | 
492 |   In the following three paragraphs, a "patent license" is any express
493 | agreement or commitment, however denominated, not to enforce a patent
494 | (such as an express permission to practice a patent or covenant not to
495 | sue for patent infringement).  To "grant" such a patent license to a
496 | party means to make such an agreement or commitment not to enforce a
497 | patent against the party.
498 | 
499 |   If you convey a covered work, knowingly relying on a patent license,
500 | and the Corresponding Source of the work is not available for anyone
501 | to copy, free of charge and under the terms of this License, through a
502 | publicly available network server or other readily accessible means,
503 | then you must either (1) cause the Corresponding Source to be so
504 | available, or (2) arrange to deprive yourself of the benefit of the
505 | patent license for this particular work, or (3) arrange, in a manner
506 | consistent with the requirements of this License, to extend the patent
507 | license to downstream recipients.  "Knowingly relying" means you have
508 | actual knowledge that, but for the patent license, your conveying the
509 | covered work in a country, or your recipient's use of the covered work
510 | in a country, would infringe one or more identifiable patents in that
511 | country that you have reason to believe are valid.
512 | 
513 |   If, pursuant to or in connection with a single transaction or
514 | arrangement, you convey, or propagate by procuring conveyance of, a
515 | covered work, and grant a patent license to some of the parties
516 | receiving the covered work authorizing them to use, propagate, modify
517 | or convey a specific copy of the covered work, then the patent license
518 | you grant is automatically extended to all recipients of the covered
519 | work and works based on it.
520 | 
521 |   A patent license is "discriminatory" if it does not include within
522 | the scope of its coverage, prohibits the exercise of, or is
523 | conditioned on the non-exercise of one or more of the rights that are
524 | specifically granted under this License.  You may not convey a covered
525 | work if you are a party to an arrangement with a third party that is
526 | in the business of distributing software, under which you make payment
527 | to the third party based on the extent of your activity of conveying
528 | the work, and under which the third party grants, to any of the
529 | parties who would receive the covered work from you, a discriminatory
530 | patent license (a) in connection with copies of the covered work
531 | conveyed by you (or copies made from those copies), or (b) primarily
532 | for and in connection with specific products or compilations that
533 | contain the covered work, unless you entered into that arrangement,
534 | or that patent license was granted, prior to 28 March 2007.
535 | 
536 |   Nothing in this License shall be construed as excluding or limiting
537 | any implied license or other defenses to infringement that may
538 | otherwise be available to you under applicable patent law.
539 | 
540 |   12. No Surrender of Others' Freedom.
541 | 
542 |   If conditions are imposed on you (whether by court order, agreement or
543 | otherwise) that contradict the conditions of this License, they do not
544 | excuse you from the conditions of this License.  If you cannot convey a
545 | covered work so as to satisfy simultaneously your obligations under this
546 | License and any other pertinent obligations, then as a consequence you may
547 | not convey it at all.  For example, if you agree to terms that obligate you
548 | to collect a royalty for further conveying from those to whom you convey
549 | the Program, the only way you could satisfy both those terms and this
550 | License would be to refrain entirely from conveying the Program.
551 | 
552 |   13. Use with the GNU Affero General Public License.
553 | 
554 |   Notwithstanding any other provision of this License, you have
555 | permission to link or combine any covered work with a work licensed
556 | under version 3 of the GNU Affero General Public License into a single
557 | combined work, and to convey the resulting work.  The terms of this
558 | License will continue to apply to the part which is the covered work,
559 | but the special requirements of the GNU Affero General Public License,
560 | section 13, concerning interaction through a network will apply to the
561 | combination as such.
562 | 
563 |   14. Revised Versions of this License.
564 | 
565 |   The Free Software Foundation may publish revised and/or new versions of
566 | the GNU General Public License from time to time.  Such new versions will
567 | be similar in spirit to the present version, but may differ in detail to
568 | address new problems or concerns.
569 | 
570 |   Each version is given a distinguishing version number.  If the
571 | Program specifies that a certain numbered version of the GNU General
572 | Public License "or any later version" applies to it, you have the
573 | option of following the terms and conditions either of that numbered
574 | version or of any later version published by the Free Software
575 | Foundation.  If the Program does not specify a version number of the
576 | GNU General Public License, you may choose any version ever published
577 | by the Free Software Foundation.
578 | 
579 |   If the Program specifies that a proxy can decide which future
580 | versions of the GNU General Public License can be used, that proxy's
581 | public statement of acceptance of a version permanently authorizes you
582 | to choose that version for the Program.
583 | 
584 |   Later license versions may give you additional or different
585 | permissions.  However, no additional obligations are imposed on any
586 | author or copyright holder as a result of your choosing to follow a
587 | later version.
588 | 
589 |   15. Disclaimer of Warranty.
590 | 
591 |   THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
592 | APPLICABLE LAW.  EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
593 | HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
594 | OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
595 | THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
596 | PURPOSE.  THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
597 | IS WITH YOU.  SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
598 | ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
599 | 
600 |   16. Limitation of Liability.
601 | 
602 |   IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
603 | WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
604 | THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
605 | GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
606 | USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
607 | DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
608 | PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
609 | EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
610 | SUCH DAMAGES.
611 | 
612 |   17. Interpretation of Sections 15 and 16.
613 | 
614 |   If the disclaimer of warranty and limitation of liability provided
615 | above cannot be given local legal effect according to their terms,
616 | reviewing courts shall apply local law that most closely approximates
617 | an absolute waiver of all civil liability in connection with the
618 | Program, unless a warranty or assumption of liability accompanies a
619 | copy of the Program in return for a fee.
620 | 
621 |                      END OF TERMS AND CONDITIONS
622 | 
623 |             How to Apply These Terms to Your New Programs
624 | 
625 |   If you develop a new program, and you want it to be of the greatest
626 | possible use to the public, the best way to achieve this is to make it
627 | free software which everyone can redistribute and change under these terms.
628 | 
629 |   To do so, attach the following notices to the program.  It is safest
630 | to attach them to the start of each source file to most effectively
631 | state the exclusion of warranty; and each file should have at least
632 | the "copyright" line and a pointer to where the full notice is found.
633 | 
634 |     {one line to give the program's name and a brief idea of what it does.}
635 |     Copyright (C) {year}  {name of author}
636 | 
637 |     This program is free software: you can redistribute it and/or modify
638 |     it under the terms of the GNU General Public License as published by
639 |     the Free Software Foundation, either version 3 of the License, or
640 |     (at your option) any later version.
641 | 
642 |     This program is distributed in the hope that it will be useful,
643 |     but WITHOUT ANY WARRANTY; without even the implied warranty of
644 |     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
645 |     GNU General Public License for more details.
646 | 
647 |     You should have received a copy of the GNU General Public License
648 |     along with this program.  If not, see <http://www.gnu.org/licenses/>.
649 | 
650 | Also add information on how to contact you by electronic and paper mail.
651 | 
652 |   If the program does terminal interaction, make it output a short
653 | notice like this when it starts in an interactive mode:
654 | 
655 |     {project}  Copyright (C) {year}  {fullname}
656 |     This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
657 |     This is free software, and you are welcome to redistribute it
658 |     under certain conditions; type `show c' for details.
659 | 
660 | The hypothetical commands `show w' and `show c' should show the appropriate
661 | parts of the General Public License.  Of course, your program's commands
662 | might be different; for a GUI interface, you would use an "about box".
663 | 
664 |   You should also get your employer (if you work as a programmer) or school,
665 | if any, to sign a "copyright disclaimer" for the program, if necessary.
666 | For more information on this, and how to apply and follow the GNU GPL, see
667 | <http://www.gnu.org/licenses/>.
668 | 
669 |   The GNU General Public License does not permit incorporating your program
670 | into proprietary programs.  If your program is a subroutine library, you
671 | may consider it more useful to permit linking proprietary applications with
672 | the library.  If this is what you want to do, use the GNU Lesser General
673 | Public License instead of this License.  But first, please read
674 | <http://www.gnu.org/philosophy/why-not-lgpl.html>.
675 | 
676 | 


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