Commit e06b2e0b9baef16482ac532da90c5c70b9f29259
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797f8ab0
removed functions not in use
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stim/biomodels/fiber.h
... | ... | @@ -281,39 +281,6 @@ public: |
281 | 281 | T radius(int idx){ |
282 | 282 | return r[idx]; |
283 | 283 | } |
284 | - /// get index of a node on a fiber | |
285 | - // by matching the node on fiber to already set vertices (both strings) | |
286 | - // used in obj file conversion | |
287 | - int | |
288 | - getIndexes(std::string* input, std::string searched, int sizeV) | |
289 | - { | |
290 | - int result = 0; | |
291 | - for (int i = 0; i < sizeV; i++) | |
292 | - { | |
293 | - if (input[i] == searched) | |
294 | - { | |
295 | - result = i + 1; | |
296 | - } | |
297 | - } | |
298 | - return result; | |
299 | - } | |
300 | - // strObj returns a string of fiber indices corresponding to vectors of positions in the fiber including intermediate nodes | |
301 | - std::string | |
302 | - strObj(std::string* strArray, int sizeV) | |
303 | - { | |
304 | - std::stringstream ss; | |
305 | - std::stringstream oss; | |
306 | - for(unsigned int i = 0; i < N; i++) | |
307 | - { | |
308 | - ss.str(std::string()); | |
309 | - for(unsigned int d = 0; d < 3; d++) | |
310 | - { | |
311 | - ss<<c[i][d]; | |
312 | - } | |
313 | - oss<<getIndexes(strArray, ss.str(), sizeV)<<" "; | |
314 | - } | |
315 | - return oss.str(); | |
316 | - } | |
317 | 284 | |
318 | 285 | /// Return the point on the fiber closest to q |
319 | 286 | /// @param q is the query point used to locate the nearest point on the fiber centerline | ... | ... |
stim/biomodels/network.h
... | ... | @@ -207,66 +207,19 @@ class network{ |
207 | 207 | } |
208 | 208 | |
209 | 209 | |
210 | - // this function gives sum of lengths of all the fibers in the network | |
211 | - float lengthOfNetwork(){ | |
212 | - stim::fiber<T> FIBER; // initialize a fiber used in looping through all edges casting into fibers in the network | |
213 | - float networkLength=0;float N=0; // initialize variables for finding total length of all the fibers | |
214 | - // for each edge in the network | |
215 | - for (unsigned int i=0; i < E.size(); i ++) | |
216 | - { | |
217 | - FIBER = get_fiber(i); // cast each edge to fiber | |
218 | - N= FIBER.length(); // find length of the fiber | |
219 | - networkLength = networkLength + N; // running sum of fiber lengths | |
220 | - } | |
221 | - return networkLength; | |
222 | - } | |
223 | - | |
224 | - | |
225 | - // list of all the points after resampling -- function used only on a resampled network | |
226 | - std::vector<stim::vec<T> > points_afterResampling(){ | |
227 | - std::vector<stim::vec<T> > pointsVector; // points in the resampled network | |
228 | - stim::fiber<T> FIBER; // initialize a fiber used in looping through all edges casting into fibers in the network | |
229 | - std::vector<stim::vec<T> > pointsFiber; // resampled points on each fiber of the network | |
230 | - for(unsigned e = 0; e < E.size(); e++){ // for each edge in the edge list | |
231 | - FIBER = get_fiber(e); // Cast edge to a fiber | |
232 | - pointsFiber = FIBER.centerline(); // find points on the edge returns a stim vec | |
233 | - for (unsigned v = 0; v < FIBER.n_pts(); v++){ // iterate one point at a time from the stim::vec | |
234 | - pointsVector.push_back(pointsFiber[v]);} //add the points on centerline to the stim::vec points list | |
235 | - } | |
236 | - return pointsVector; | |
237 | - } | |
238 | - | |
239 | 210 | |
240 | 211 | // total number of points on all fibers after resampling -- function used only on a resampled network |
241 | 212 | unsigned total_points(){ |
242 | 213 | unsigned n = 0; |
243 | 214 | for(unsigned e = 0; e < E.size(); e++) |
244 | 215 | n += E[e].size(); |
245 | - //unsigned int n = points_afterResampling().size(); | |
246 | 216 | return n; |
247 | 217 | } |
248 | 218 | |
249 | 219 | // gaussian function |
250 | 220 | float gaussianFunction(float x, float std=25){ return exp(-x/(2*std*std));} // by default std = 25 |
251 | 221 | |
252 | - // sum of values in a stim vector | |
253 | - float sum(stim::vec<T> metricList){ | |
254 | - float sumMetricList = 0; // Initialize variable to calculate sum | |
255 | - for (unsigned int count=0; count<metricList.size(); count++) // for each element in the stim vector | |
256 | - { sumMetricList += metricList[count];} // running sum of values | |
257 | - return sumMetricList; | |
258 | - } | |
259 | - | |
260 | - | |
261 | - // distance between two points | |
262 | - double dist(stim::vec<T> p0, stim::vec<T> p1){ | |
263 | - double sum = 0; // initialize variables | |
264 | - stim::vec<T> v = p1 - p0;; // direction vector | |
265 | - for(unsigned int d = 0; d < 3; d++){ // for each dimension | |
266 | - sum += v[d] * v[d];} // running sum of modulus of direction vector | |
267 | - return sqrt(sum); | |
268 | - } | |
269 | - | |
222 | + // stim 3d vector to annpoint of 3 dimensions | |
270 | 223 | void stim2ann(ANNpoint &a, stim::vec<T> b){ |
271 | 224 | a[0] = b[0]; |
272 | 225 | a[1] = b[1]; |
... | ... | @@ -333,43 +286,6 @@ class network{ |
333 | 286 | } |
334 | 287 | |
335 | 288 | return M/L; |
336 | - | |
337 | - | |
338 | - /*int N; // number of points on the fiber in the second network | |
339 | - float totalNetworkLength = A.lengthOfNetwork(); | |
340 | - stim::vec<float> fiberMetric(A.edges()); // allocate space for accumulating fiber metric as each fiber is evaluated | |
341 | - stim::fiber<T> FIBER; // Initialize a fiber will be used in calculating the metric | |
342 | - //for each fiber in the second network, find nearest distance in the kd tree | |
343 | - for (unsigned int i=0; i < A.edges(); i ++) // loop through all the edges/fibers in the network | |
344 | - { | |
345 | - FIBER = A.get_fiber(i); // Get the fiber corresponding to the index i | |
346 | - std::vector< stim::vec<T> > fiberPoints = FIBER.centerline(); // Get the points on the fiber | |
347 | - N = FIBER.size(); // number of points on the fiber | |
348 | - stim::vec<float> segmentMetric(N-1); // allocate space for a vec array that stores metric for each segmen in the fiber | |
349 | - // for each segment in the fiber | |
350 | - for (unsigned j = 0; j < N - 1; j++) | |
351 | - { | |
352 | - stim::vec<T> p1 = fiberPoints[j];stim::vec<T> p2 = fiberPoints[j+1]; // starting and ending points on the segments | |
353 | - ANNpoint queryPt1; queryPt1 = annAllocPt(3); // allocate memory for query points | |
354 | - ANNpoint queryPt2; queryPt2 = annAllocPt(3); | |
355 | - | |
356 | - //for each dimension of the points connecting segment | |
357 | - for (unsigned d = 0; d < 3; d++){ | |
358 | - queryPt1[d] = double(fiberPoints[j][d]); // starting point on segment in network whose closest distance on KD tree should be found | |
359 | - queryPt2[d] = double(fiberPoints[j + 1][d]); // ending point on segment in network whose closest distance on KD tree should be found | |
360 | - } | |
361 | - kdt->annkSearch( queryPt1, 1, nnIdx1, dists1, eps); // search the nearest point in KD tree to query point(point on network), find the distance | |
362 | - kdt->annkSearch( queryPt2, 1, nnIdx2, dists2, eps); // search the nearest point in KD tree to query point(point on network), find the distance | |
363 | - // find the gaussian of the distance and subtract it from 1 to calculate the error | |
364 | - float error1 = 1.0f - gaussianFunction(float(dists1[0]), sigma);float error2 = 1.0f - gaussianFunction(float(dists2[0]), sigma); | |
365 | - // average the error and scale it with distance between the points | |
366 | - segmentMetric[j] = ((error1 + error2) / 2) * dist(p1, p2) ; | |
367 | - } | |
368 | - fiberMetric[i] = sum(segmentMetric); | |
369 | - } | |
370 | - metric = sum(fiberMetric)/totalNetworkLength; //normalize the scaled error of all the points with total length of the network | |
371 | - assert (0<=metric <=1); //assert metroc os always less than or equal to one and greater than or equal to zero | |
372 | - return metric;*/ | |
373 | 289 | } |
374 | 290 | }; //end stim::network class |
375 | 291 | }; //end stim namespace | ... | ... |