codebase / stimlib

Commit e0edbe1317a40526ff0bc4e06ad8fd38e8c62b50

Authored by Laila Saadatifard
2 parents 03428452 9f5c0d4a

Merge branch 'master' of git.stim.ee.uh.edu:codebase/stimlib

Showing 17 changed files with 1315 additions and 391 deletions   Show diff stats
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stim/biomodels/network.h
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... ... @@ -33,7 +33,10 @@ class network{
33 33 public:
34 34 unsigned v[2]; //unique id's designating the starting and ending
35 35 // default constructor
36   - edge() : cylinder<T>(){v[1] = -1; v[0] = -1;}
  36 + edge() : cylinder<T>()
  37 + {
  38 + v[1] = -1; v[0] = -1;
  39 + }
37 40 /// Constructor - creates an edge from a list of points by calling the stim::fiber constructor
38 41  
39 42 ///@param p is an array of positions in space
... ... @@ -54,7 +57,7 @@ class network{
54 57 /// Output the edge information as a string
55 58 std::string str(){
56 59 std::stringstream ss;
57   - ss<<"("<<cylinder<T>::size()<<")\tl = "<<length()<<"\t"<<v[0]<<"----"<<v[1];
  60 + ss<<"("<<cylinder<T>::size()<<")\tl = "<<this.length()<<"\t"<<v[0]<<"----"<<v[1];
58 61 return ss.str();
59 62 }
60 63  
... ... @@ -64,9 +67,9 @@ class network{
64 67 class vertex : public stim::vec3<T>
65 68 {
66 69 public:
67   - //std::vector<unsigned int> edges; //indices of edges connected to this node.
68   - std::vector<unsigned int> e[2]; //indices of edges going out (e[0]) and coming in (e[1])
69   - //stim::vec3<T> p; //position of this node in physical space.
  70 + //std::vector<unsigned int> edges; //indices of edges connected to this node.
  71 + std::vector<unsigned int> e[2]; //indices of edges going out (e[0]) and coming in (e[1])
  72 + //stim::vec3<T> p; //position of this node in physical space.
70 73  
71 74 //constructor takes a stim::vec
72 75 vertex(stim::vec3<T> p) : stim::vec3<T>(p){}
... ... @@ -90,6 +93,7 @@ class network{
90 93 return ss.str();
91 94 }
92 95  
  96 +
93 97 };
94 98  
95 99 protected:
... ... @@ -99,6 +103,18 @@ protected:
99 103  
100 104 public:
101 105  
  106 + ///default constructor
  107 + network()
  108 + {
  109 +
  110 + }
  111 +
  112 + ///constructor with a file to load.
  113 + network(std::string fileLocation)
  114 + {
  115 + load_obj(fileLocation);
  116 + }
  117 +
102 118 ///Returns the number of edges in the network.
103 119 unsigned int edges(){
104 120 return E.size();
... ... @@ -109,72 +125,219 @@ public:
109 125 return V.size();
110 126 }
111 127  
  128 + std::vector<vertex> operator*(T s){
  129 + for (unsigned i=0; i< vertices; i ++ ){
  130 + V[i] = V[i] * s;
  131 + }
  132 + return V;
  133 + }
  134 +
  135 + std::vector<vertex> operator*(vec<T> s){
  136 + for (unsigned i=0; i< vertices; i ++ ){
  137 + for (unsigned dim = 0 ; dim< 3; dim ++){
  138 + V[i][dim] = V[i][dim] * s[dim];
  139 + }
  140 + }
  141 + return V;
  142 + }
  143 +
  144 + // Returns an average of branching index in the network
  145 +
  146 + double BranchingIndex(){
  147 + double B=0;
  148 + for(unsigned v=0; v < V.size(); v ++){
  149 + B += ((V[v].e[0].size()) + (V[v].e[1].size()));
  150 + }
  151 + B = B / V.size();
  152 + return B;
  153 +
  154 + }
  155 +
  156 + // Returns number of branch points in thenetwork
  157 +
  158 + unsigned int BranchP(){
  159 + unsigned int B=0;
  160 + unsigned int c;
  161 + for(unsigned v=0; v < V.size(); v ++){
  162 + c = ((V[v].e[0].size()) + (V[v].e[1].size()));
  163 + if (c > 2){
  164 + B += 1;}
  165 + }
  166 + return B;
  167 +
  168 + }
  169 +
  170 + // Returns number of end points (tips) in thenetwork
  171 +
  172 + unsigned int EndP(){
  173 + unsigned int B=0;
  174 + unsigned int c;
  175 + for(unsigned v=0; v < V.size(); v ++){
  176 + c = ((V[v].e[0].size()) + (V[v].e[1].size()));
  177 + if (c == 1){
  178 + B += 1;}
  179 + }
  180 + return B;
  181 +
  182 + }
  183 +
  184 + //// Returns a dictionary with the key as the vertex
  185 + //std::map<std::vector<vertex>,unsigned int> DegreeDict(){
  186 + // std::map<std::vector<vertex>,unsigned int> dd;
  187 + // unsigned int c = 0;
  188 + // for(unsigned v=0; v < V.size(); v ++){
  189 + // c = ((V[v].e[0].size()) + (V[v].e[1].size()));
  190 + // dd[V[v]] = c;
  191 + // }
  192 + // return dd;
  193 + //}
  194 +
  195 + //// Return number of branching stems
  196 + //unsigned int Stems(){
  197 + // unsigned int s = 0;
  198 + // std::map<std::vector<vertex>,unsigned int> dd;
  199 + // dd = DegreeDict();
  200 + // //for(unsigned v=0; v < V.size(); v ++){
  201 + // // V[v].e[0].
  202 + // return s;
  203 + //}
  204 +
  205 +
  206 + // Returns an average of fiber/edge lengths in the network
  207 + double Lengths(){
  208 + stim::vec<T> L;double sumLength = 0;
  209 + for(unsigned e = 0; e < E.size(); e++){ //for each edge in the network
  210 + L.push_back(E[e].length()); //append the edge length
  211 + sumLength = sumLength + E[e].length();
  212 + }
  213 + double avg = sumLength / E.size();
  214 + return avg;
  215 + }
  216 +
  217 +
  218 + // Returns an average of tortuosities in the network
  219 + double Tortuosities(){
  220 + stim::vec<T> t;
  221 + stim::vec<T> id1, id2; // starting and ending vertices of the edge
  222 + double distance;double tortuosity;double sumTortuosity = 0;
  223 + for(unsigned e = 0; e < E.size(); e++){ //for each edge in the network
  224 + id1 = E[e][0]; //get the edge starting point
  225 + id2 = E[e][E[e].size() - 1]; //get the edge ending point
  226 + distance = (id1 - id2).len(); //displacement between the starting and ending points
  227 + if(distance > 0){
  228 + tortuosity = E[e].length()/ distance ; // tortuoisty = edge length / edge displacement
  229 + }
  230 + else{
  231 + tortuosity = 0;}
  232 + t.push_back(tortuosity);
  233 + sumTortuosity += tortuosity;
  234 + }
  235 + double avg = sumTortuosity / E.size();
  236 + return avg;
  237 + }
  238 +
  239 + // Returns average contraction of the network
  240 + double Contractions(){
  241 + stim::vec<T> t;
  242 + stim::vec<T> id1, id2; // starting and ending vertices of the edge
  243 + double distance;double contraction;double sumContraction = 0;
  244 + for(unsigned e = 0; e < E.size(); e++){ //for each edge in the network
  245 + id1 = E[e][0]; //get the edge starting point
  246 + id2 = E[e][E[e].size() - 1]; //get the edge ending point
  247 + distance = (id1 - id2).len(); //displacement between the starting and ending points
  248 + contraction = distance / E[e].length(); // tortuoisty = edge length / edge displacement
  249 + t.push_back(contraction);
  250 + sumContraction += contraction;
  251 + }
  252 + double avg = sumContraction / E.size();
  253 + return avg;
  254 + }
  255 +
  256 + // returns average fractal dimension of the branches of the network
  257 + double FractalDimensions(){
  258 + stim::vec<T> t;
  259 + stim::vec<T> id1, id2; // starting and ending vertices of the edge
  260 + double distance;double fract;double sumFractDim = 0;
  261 + for(unsigned e = 0; e < E.size(); e++){ //for each edge in the network
  262 + id1 = E[e][0]; //get the edge starting point
  263 + id2 = E[e][E[e].size() - 1]; //get the edge ending point
  264 + distance = (id1 - id2).len(); //displacement between the starting and ending points
  265 + fract = std::log(distance) / std::log(E[e].length()); // tortuoisty = edge length / edge displacement
  266 + t.push_back(sumFractDim);
  267 + sumFractDim += fract;
  268 + }
  269 + double avg = sumFractDim / E.size();
  270 + return avg;
  271 + }
112 272 stim::cylinder<T> get_cylinder(unsigned f){
113   - return E[f]; //return the specified edge (casting it to a fiber)
  273 + return E[f]; //return the specified edge (casting it to a fiber)
114 274 }
115 275  
116 276 //load a network from an OBJ file
117 277 void load_obj(std::string filename){
118 278  
119   - stim::obj<T> O; //create an OBJ object
120   - O.load(filename); //load the OBJ file as an object
  279 + stim::obj<T> O; //create an OBJ object
  280 + O.load(filename); //load the OBJ file as an object
121 281  
122   - std::vector<unsigned> id2vert; //this list stores the OBJ vertex ID associated with each network vertex
  282 + std::vector<unsigned> id2vert; //this list stores the OBJ vertex ID associated with each network vertex
123 283  
124   - unsigned i[2]; //temporary, IDs associated with the first and last points in an OBJ line
  284 + unsigned i[2]; //temporary, IDs associated with the first and last points in an OBJ line
125 285  
126 286 //for each line in the OBJ object
127 287 for(unsigned int l = 1; l <= O.numL(); l++){
128 288  
129   - std::vector< stim::vec<T> > c; //allocate an array of points for the vessel centerline
  289 + std::vector< stim::vec<T> > c; //allocate an array of points for the vessel centerline
130 290 O.getLine(l, c); //get the fiber centerline
131 291  
132 292 std::vector< stim::vec3<T> > c3(c.size());
133 293 for(size_t j = 0; j < c.size(); j++)
134 294 c3[j] = c[j];
135 295  
136   - edge new_edge = c3; //create an edge from the given centerline
137   - unsigned int I = new_edge.size(); //calculate the number of points on the centerline
  296 + // edge new_edge = c3; ///This is dangerous.
  297 + edge new_edge(c3);
  298 +
  299 + //create an edge from the given centerline
  300 + unsigned int I = new_edge.size(); //calculate the number of points on the centerline
138 301  
139 302 //get the first and last vertex IDs for the line
140   - std::vector< unsigned > id; //create an array to store the centerline point IDs
  303 + std::vector< unsigned > id; //create an array to store the centerline point IDs
141 304 O.getLinei(l, id); //get the list of point IDs for the line
142 305 i[0] = id.front(); //get the OBJ ID for the first element of the line
143 306 i[1] = id.back(); //get the OBJ ID for the last element of the line
144 307  
145   - std::vector<unsigned>::iterator it; //create an iterator for searching the id2vert array
  308 + std::vector<unsigned>::iterator it; //create an iterator for searching the id2vert array
146 309 unsigned it_idx; //create an integer for the id2vert entry index
147 310  
148 311 //find out if the nodes for this fiber have already been created
149 312 it = find(id2vert.begin(), id2vert.end(), i[0]); //look for the first node
150   - it_idx = std::distance(id2vert.begin(), it);
151 313 if(it == id2vert.end()){ //if i[0] hasn't already been used
152 314 vertex new_vertex = new_edge[0]; //create a new vertex, assign it a position
153   - new_vertex.e[0].push_back(E.size()); //add the current edge as outgoing
154   - new_edge.v[0] = V.size(); //add the new vertex to the edge
155   - V.push_back(new_vertex); //add the new vertex to the vertex list
156   - id2vert.push_back(i[0]); //add the ID to the ID->vertex conversion list
  315 + new_vertex.e[0].push_back(E.size()); //add the current edge as outgoing
  316 + new_edge.v[0] = V.size(); //add the new edge to the edge
  317 + V.push_back(new_vertex); //add the new vertex to the vertex list
  318 + id2vert.push_back(i[0]); //add the ID to the ID->vertex conversion list
157 319 }
158   - else{ //if the vertex already exists
  320 + else{ //if the vertex already exists
  321 + it_idx = std::distance(id2vert.begin(), it);
159 322 V[it_idx].e[0].push_back(E.size()); //add the current edge as outgoing
160 323 new_edge.v[0] = it_idx;
161 324 }
162 325  
163   - it = find(id2vert.begin(), id2vert.end(), i[1]); //look for the second ID
164   - it_idx = std::distance(id2vert.begin(), it);
165   - if(it == id2vert.end()){ //if i[1] hasn't already been used
166   - vertex new_vertex = new_edge[I-1]; //create a new vertex, assign it a position
167   - new_vertex.e[1].push_back(E.size()); //add the current edge as incoming
168   - new_edge.v[1] = V.size();
169   - V.push_back(new_vertex); //add the new vertex to the vertex list
170   - id2vert.push_back(i[1]); //add the ID to the ID->vertex conversion list
  326 + it = find(id2vert.begin(), id2vert.end(), i[1]); //look for the second ID
  327 + if(it == id2vert.end()){ //if i[1] hasn't already been used
  328 + vertex new_vertex = new_edge[I-1]; //create a new vertex, assign it a position
  329 + new_vertex.e[1].push_back(E.size()); //add the current edge as incoming
  330 + new_edge.v[1] = V.size(); //add the new vertex to the edge
  331 + V.push_back(new_vertex); //add the new vertex to the vertex list
  332 + id2vert.push_back(i[1]); //add the ID to the ID->vertex conversion list
171 333 }
172   - else{ //if the vertex already exists
  334 + else{ //if the vertex already exists
  335 + it_idx = std::distance(id2vert.begin(), it);
173 336 V[it_idx].e[1].push_back(E.size()); //add the current edge as incoming
174 337 new_edge.v[1] = it_idx;
175 338 }
176 339  
177   - E.push_back(new_edge); //push the edge to the list
  340 + E.push_back(new_edge); //push the edge to the list
178 341  
179 342 }
180 343 }
... ... @@ -199,17 +362,17 @@ public:
199 362 /// This function resamples all fibers in a network given a desired minimum spacing
200 363 /// @param spacing is the minimum distance between two points on the network
201 364 stim::network<T> resample(T spacing){
202   - stim::network<T> n; //create a new network that will be an exact copy, with resampled fibers
203   - n.V = V; //copy all vertices
  365 + stim::network<T> n; //create a new network that will be an exact copy, with resampled fibers
  366 + n.V = V; //copy all vertices
204 367  
205   - n.E.resize(edges()); //allocate space for the edge list
  368 + n.E.resize(edges()); //allocate space for the edge list
206 369  
207 370 //copy all fibers, resampling them in the process
208   - for(unsigned e = 0; e < edges(); e++){ //for each edge in the edge list
209   - n.E[e] = E[e].resample(spacing); //resample the edge and copy it to the new network
  371 + for(unsigned e = 0; e < edges(); e++){ //for each edge in the edge list
  372 + n.E[e] = E[e].resample(spacing); //resample the edge and copy it to the new network
210 373 }
211 374  
212   - return n; //return the resampled network
  375 + return n; //return the resampled network
213 376 }
214 377  
215 378  
... ... @@ -236,14 +399,14 @@ public:
236 399 /// @param m is the magnitude value to use. The default is 0 (usually radius).
237 400 T average(unsigned m = 0){
238 401  
239   - T M, L; //allocate space for the total magnitude and length
240   - M = L = 0; //initialize both the initial magnitude and length to zero
241   - for(unsigned e = 0; e < E.size(); e++){ //for each edge in the network
  402 + T M, L; //allocate space for the total magnitude and length
  403 + M = L = 0; //initialize both the initial magnitude and length to zero
  404 + for(unsigned e = 0; e < E.size(); e++){ //for each edge in the network
242 405 M += E[e].integrate(m); //get the integrated magnitude
243   - L += E[e].length(); //get the edge length
  406 + L += E[e].length(); //get the edge length
244 407 }
245 408  
246   - return M / L; //return the average magnitude
  409 + return M / L; //return the average magnitude
247 410 }
248 411  
249 412 /// This function compares two networks and returns the percentage of the current network that is missing from A.
... ... @@ -256,17 +419,17 @@ public:
256 419 R = (*this); //initialize the result with the current network
257 420  
258 421 //generate a KD-tree for network A
259   - float metric = 0.0; // initialize metric to be returned after comparing the networks
260   - ANNkd_tree* kdt; // initialize a pointer to a kd tree
261   - double **c; // centerline (array of double pointers) - points on kdtree must be double
262   - unsigned int n_data = A.total_points(); // set the number of points
263   - c = (double**) malloc(sizeof(double*) * n_data); // allocate the array pointer
264   - for(unsigned int i = 0; i < n_data; i++) // allocate space for each point of 3 dimensions
  422 + float metric = 0.0; // initialize metric to be returned after comparing the networks
  423 + ANNkd_tree* kdt; // initialize a pointer to a kd tree
  424 + double **c; // centerline (array of double pointers) - points on kdtree must be double
  425 + unsigned int n_data = A.total_points(); // set the number of points
  426 + c = (double**) malloc(sizeof(double*) * n_data); // allocate the array pointer
  427 + for(unsigned int i = 0; i < n_data; i++) // allocate space for each point of 3 dimensions
265 428 c[i] = (double*) malloc(sizeof(double) * 3);
266 429  
267 430 unsigned t = 0;
268 431 for(unsigned e = 0; e < A.E.size(); e++){ //for each edge in the network
269   - for(unsigned p = 0; p < A.E[e].size(); p++){ //for each point in the edge
  432 + for(unsigned p = 0; p < A.E[e].size(); p++){ //for each point in the edge
270 433 for(unsigned d = 0; d < 3; d++){ //for each coordinate
271 434  
272 435 c[t][d] = A.E[e][p][d];
... ... @@ -276,27 +439,27 @@ public:
276 439 }
277 440  
278 441 //compare each point in the current network to the field produced by A
279   - ANNpointArray pts = (ANNpointArray)c; // create an array of data points of type double
280   - kdt = new ANNkd_tree(pts, n_data, 3); // build a KD tree using the annpointarray
  442 + ANNpointArray pts = (ANNpointArray)c; // create an array of data points of type double
  443 + kdt = new ANNkd_tree(pts, n_data, 3); // build a KD tree using the annpointarray
281 444 double eps = 0; // error bound
282   - ANNdistArray dists = new ANNdist[1]; // near neighbor distances
283   - ANNidxArray nnIdx = new ANNidx[1]; // near neighbor indices // allocate near neigh indices
  445 + ANNdistArray dists = new ANNdist[1]; // near neighbor distances
  446 + ANNidxArray nnIdx = new ANNidx[1]; // near neighbor indices // allocate near neigh indices
284 447  
285 448 stim::vec3<T> p0, p1;
286 449 float m1;
287   - float M = 0; //stores the total metric value
288   - float L = 0; //stores the total network length
  450 + float M = 0; //stores the total metric value
  451 + float L = 0; //stores the total network length
289 452 ANNpoint queryPt = annAllocPt(3);
290 453 for(unsigned e = 0; e < R.E.size(); e++){ //for each edge in A
291   - R.E[e].add_mag(0); //add a new magnitude for the metric
  454 + R.E[e].add_mag(0); //add a new magnitude for the metric
292 455  
293   - for(unsigned p = 0; p < R.E[e].size(); p++){ //for each point in the edge
  456 + for(unsigned p = 0; p < R.E[e].size(); p++){ //for each point in the edge
294 457  
295   - p1 = R.E[e][p]; //get the next point in the edge
  458 + p1 = R.E[e][p]; //get the next point in the edge
296 459 stim2ann(queryPt, p1);
297   - kdt->annkSearch( queryPt, 1, nnIdx, dists, eps); //find the distance between A and the current network
  460 + kdt->annkSearch( queryPt, 1, nnIdx, dists, eps); //find the distance between A and the current network
298 461 m1 = 1.0f - gaussianFunction((float)dists[0], sigma); //calculate the metric value based on the distance
299   - R.E[e].set_mag(m1, p, 1); //set the error for the second point in the segment
  462 + R.E[e].set_mag(m1, p, 1); //set the error for the second point in the segment
300 463  
301 464 }
302 465 }
... ... @@ -308,8 +471,106 @@ public:
308 471 unsigned nmags(){
309 472 return E[0].nmags();
310 473 }
  474 + // split a string in text by the character sep
  475 + stim::vec<T> split(std::string &text, char sep)
  476 + {
  477 + stim::vec<T> tokens;
  478 + std::size_t start = 0, end = 0;
  479 + while ((end = text.find(sep, start)) != std::string::npos) {
  480 + tokens.push_back(atof(text.substr(start, end - start).c_str()));
  481 + start = end + 1;
  482 + }
  483 + tokens.push_back(atof(text.substr(start).c_str()));
  484 + return tokens;
  485 + }
  486 + // load a network in text file to a network class
  487 + void load_txt(std::string filename)
  488 + {
  489 + std::vector <std::string> file_contents;
  490 + std::ifstream file(filename);
  491 + std::string line;
  492 + std::vector<unsigned> id2vert; //this list stores the vertex ID associated with each network vertex
  493 + //for each line in the text file, store them as strings in file_contents
  494 + while (std::getline(file, line))
  495 + {
  496 + std::stringstream ss(line);
  497 + file_contents.push_back(ss.str());
  498 + }
  499 + unsigned int numEdges = atoi(file_contents[0].c_str()); //number of edges in the network
  500 + unsigned int I = atoi(file_contents[1].c_str()) ; //calculate the number of points3d on the first edge
  501 + unsigned int count = 1; unsigned int k = 2; // count is global counter through the file contents, k is for the vertices on the edges
  502 + // for each edge in the network.
  503 + for (unsigned int i = 0; i < numEdges; i ++ )
  504 + {
  505 + // pre allocate a position vector p with number of points3d on the edge p
  506 + std::vector< stim::vec<T> > p(0, I);
  507 + // for each point on the nth edge
  508 + for (unsigned int j = k; j < I + k; j++)
  509 + {
  510 + // split the points3d of floats with separator space and form a float3 position vector out of them
  511 + p.push_back(split(file_contents[j], ' '));
  512 + }
  513 + count += p.size() + 1; // increment count to point at the next edge in the network
  514 + I = atoi(file_contents[count].c_str()); // read in the points3d at the next edge and convert it to an integer
  515 + k = count + 1;
  516 + edge new_edge = p; // create an edge with a vector of points3d on the edge
  517 + E.push_back(new_edge); // push the edge into the network
  518 + }
  519 + unsigned int numVertices = atoi(file_contents[count].c_str()); // this line in the text file gives the number of distinct vertices
  520 + count = count + 1; // this line of text file gives the first verrtex
  521 + // push each vertex into V
  522 + for (unsigned int i = 0; i < numVertices; i ++)
  523 + {
  524 + vertex new_vertex = split(file_contents[count], ' ');
  525 + V.push_back(new_vertex);
  526 + count += atoi(file_contents[count + 1].c_str()) + 2; // Skip number of edge ids + 2 to point to the next vertex
  527 + }
  528 + } // end load_txt function
311 529  
312   -
  530 + // strTxt returns a string of edges
  531 + std::string
  532 + strTxt(std::vector< stim::vec<T> > p)
  533 + {
  534 + std::stringstream ss;
  535 + std::stringstream oss;
  536 + for(unsigned int i = 0; i < p.size(); i++){
  537 + ss.str(std::string());
  538 + for(unsigned int d = 0; d < 3; d++){
  539 + ss<<p[i][d];
  540 + }
  541 + ss < "\n";
  542 + }
  543 + return ss.str();
  544 + }
  545 + // removes specified character from string
  546 + void removeCharsFromString(std::string &str, char* charsToRemove ) {
  547 + for ( unsigned int i = 0; i < strlen(charsToRemove); ++i ) {
  548 + str.erase( remove(str.begin(), str.end(), charsToRemove[i]), str.end() );
  549 + }
  550 + }
  551 + //exports network to txt file
  552 + void
  553 + to_txt(std::string filename)
  554 + {
  555 + std::ofstream ofs(filename, std::ofstream::out | std::ofstream::app);
  556 + int num;
  557 + ofs << (E.size()).str() << "\n";
  558 + for(unsigned int i = 0; i < E.size(); i++)
  559 + {
  560 + std::string str;
  561 + ofs << (E[i].size()).str() << "\n";
  562 + str = E[i].strTxt();
  563 + ofs << str << "\n";
  564 + }
  565 + for(int i = 0; i < V.size(); i++)
  566 + {
  567 + std::string str;
  568 + str = V[i].str();
  569 + removeCharsFromString(str, "[],");
  570 + ofs << str << "\n";
  571 + }
  572 + ofs.close();
  573 + }
313 574 }; //end stim::network class
314 575 }; //end stim namespace
315 576 #endif
... ...
stim/cuda/cuda_texture.cuh
  Show/Hide comments   View file @e0edbe1
... ... @@ -134,15 +134,15 @@ namespace stim
134 134 void
135 135 UnmapCudaTexture()
136 136 {
137   - HANDLE_ERROR(
138   - cudaGraphicsUnmapResources(1, &resource)
139   - );
140   - HANDLE_ERROR(
141   - cudaGraphicsUnregisterResource(resource)
142   - );
143   - HANDLE_ERROR(
144   - cudaDestroyTextureObject(tObj)
145   - );
  137 + // HANDLE_ERROR(
  138 + // cudaGraphicsUnmapResources(1, &resource)
  139 + // );
  140 + // HANDLE_ERROR(
  141 + // cudaGraphicsUnregisterResource(resource)
  142 + // );
  143 + // HANDLE_ERROR(
  144 + // cudaDestroyTextureObject(tObj)
  145 + // );
146 146 // HANDLE_ERROR(
147 147 // cudaFreeArray(srcArray)
148 148 // );
... ...
stim/cuda/filter.cuh
  Show/Hide comments   View file @e0edbe1
... ... @@ -7,6 +7,7 @@
7 7 #include <stdio.h>
8 8 #include <stim/visualization/colormap.h>
9 9 #include <sstream>
  10 +#include <stim/math/constants.h>
10 11 #include <stim/cuda/cudatools/devices.h>
11 12 #include <stim/cuda/cudatools/threads.h>
12 13 #include <stim/cuda/cuda_texture.cuh>
... ... @@ -14,7 +15,6 @@
14 15 #include <stim/cuda/arraymath.cuh>
15 16  
16 17 #define IMAD(a,b,c) ( __mul24((a), (b)) + (c) )
17   -#define M_PI 3.141592654f
18 18  
19 19  
20 20 namespace stim
... ... @@ -73,7 +73,7 @@ namespace stim
73 73 idx = j*kl+i;
74 74 x = i - kr - 0.5;
75 75 y = j - kr - 0.5;
76   - LoG[idx] = (-1.0/M_PI/powf(sigma, 4))* (1 - (powf(x,2)+powf(y,2))/2.0/powf(sigma, 2))
  76 + LoG[idx] = (-1.0/PI/powf(sigma, 4))* (1 - (powf(x,2)+powf(y,2))/2.0/powf(sigma, 2))
77 77 *expf(-(powf(x,2)+powf(y,2))/2/powf(sigma,2));
78 78 t +=LoG[idx];
79 79 }
... ... @@ -98,7 +98,7 @@ namespace stim
98 98 int y = blockIdx.y;
99 99 int xi = threadIdx.x;
100 100 int yi = threadIdx.y;
101   - float val = 0;
  101 + // float val = 0;
102 102 float tu = (x-kr+xi)/(float)DIM_X;
103 103 float tv = (y-kr+yi)/(float)DIM_Y;
104 104 shared[xi][yi] = gpuLoG[yi*kl+xi]*(255.0-(float)tex2D<unsigned char>(texIn, tu, tv));
... ... @@ -111,7 +111,7 @@ namespace stim
111 111 //y = min(y, height - 1);
112 112  
113 113 int idx = y*DIM_X+x;
114   - int k_idx;
  114 + // int k_idx;
115 115 for(unsigned int step = blockDim.x/2; step >= 1; step >>= 1)
116 116 {
117 117 __syncthreads();
... ...
stim/cuda/ivote/down_sample.cuh
  Show/Hide comments   View file @e0edbe1
... ... @@ -44,7 +44,7 @@ namespace stim{
44 44 unsigned int y_ds = (y/sigma_ds + (y %sigma_ds == 0 ? 0:1));
45 45  
46 46 //get the number of pixels in the image
47   - unsigned int pixels_ds = x_ds * y_ds;
  47 +// unsigned int pixels_ds = x_ds * y_ds;
48 48  
49 49 unsigned int max_threads = stim::maxThreadsPerBlock();
50 50 dim3 threads(max_threads, 1);
... ... @@ -97,4 +97,4 @@ namespace stim{
97 97 }
98 98 }
99 99  
100   -#endif
101 100 \ No newline at end of file
  101 +#endif
... ...
stim/envi/agilent_binary.h 0 → 100644
  Show/Hide comments   View file @e0edbe1
  1 +//make sure that this header file is only loaded once
  2 +#ifndef STIM_AGILENT_BINARY_H
  3 +#define STIM_AGILENT_BINARY_H
  4 +
  5 +#include <string>
  6 +#include <fstream>
  7 +
  8 +//CUDA
  9 +#ifdef CUDA_FOUND
  10 + #include <cuda_runtime.h>
  11 + #include "cufft.h"
  12 + #include <stim/cuda/cudatools/error.h>
  13 +#endif
  14 +
  15 +namespace stim{
  16 +
  17 +template<typename T>
  18 +class agilent_binary{
  19 +
  20 +protected:
  21 + std::string fname;
  22 + T* ptr;
  23 + size_t R[3];
  24 + static const size_t header = 1020;
  25 + double Z[2];
  26 +
  27 +public:
  28 + size_t size(){
  29 + return (size_t)R[0] * (size_t)R[1] * (size_t)R[2];
  30 + }
  31 +
  32 + size_t bytes(){
  33 + return size() * sizeof(T);
  34 + }
  35 + void alloc(){
  36 + ptr = (T*) malloc(bytes());
  37 + }
  38 + void alloc(short x, short y, short z){
  39 + R[0] = x;
  40 + R[1] = y;
  41 + R[2] = z;
  42 + alloc();
  43 + }
  44 +
  45 + void deep_copy(agilent_binary<T>* dst, const agilent_binary<T>* src){
  46 + dst->alloc(src->R[0], src->R[1], src->R[2]); //allocate memory
  47 + memcpy(dst->ptr, src->ptr, bytes()); //copy the data
  48 + memcpy(dst->Z, src->Z, sizeof(double) * 2); //copy the data z range
  49 + }
  50 +
  51 + agilent_binary(){
  52 + memset(R, 0, sizeof(short) * 3); //set the resolution to zero
  53 + ptr = NULL;
  54 + }
  55 +
  56 + /// Constructor with resolution
  57 + agilent_binary(short x, short y, short z){
  58 + alloc(x, y, z);
  59 + }
  60 +
  61 + /// Constructor with filename
  62 + agilent_binary(std::string filename){
  63 + ptr = NULL;
  64 + load(filename);
  65 + }
  66 +
  67 + /// Copy constructor
  68 + agilent_binary(const agilent_binary<T> &obj){
  69 + deep_copy(this, &obj);
  70 + }
  71 +
  72 + agilent_binary<T>& operator=(const agilent_binary<T> rhs){
  73 + if(this != &rhs){ //check for self-assignment
  74 + deep_copy(this, &rhs); //make a deep copy
  75 + }
  76 + return *this; //return the result
  77 + }
  78 +
  79 + ~agilent_binary(){
  80 + free(ptr);
  81 + }
  82 +
  83 + void load(std::string filename){
  84 + if(ptr != NULL) free(ptr); //if memory has been allocated, free it
  85 +
  86 + fname = filename; //save the filename
  87 +
  88 + short x, y, z;
  89 +
  90 + std::ifstream infile(fname, std::ios::binary); //open the input file
  91 + infile.seekg(9, std::ios::beg); //seek past 9 bytes from the beginning of the file
  92 +
  93 + infile.read((char*)(&z), 2); //read two bytes of data (the number of samples is stored as a 16-bit integer)
  94 +
  95 + infile.seekg(13, std::ios::cur); //skip another 13 bytes
  96 + infile.read((char*)(&x), 2); //read the X and Y dimensions
  97 + infile.read((char*)(&y), 2);
  98 +
  99 + infile.seekg(header, std::ios::beg); //seek to the start of the data
  100 +
  101 + alloc(x, y, z);
  102 + ptr = (T*) malloc(bytes()); //allocate space for the data
  103 + infile.read((char*)ptr, bytes()); //read the data
  104 + infile.close();
  105 + }
  106 +
  107 + void save(std::string filename){
  108 + std::ofstream outfile(filename, std::ios::binary); //create an output file
  109 +
  110 + char zero = 0;
  111 + for(size_t i = 0; i < 9; i++) outfile.write(&zero, 1); //write 9 zeros
  112 + outfile.write((char*)&R[0], 2);
  113 + for(size_t i = 0; i < 13; i++) outfile.write(&zero, 1); //write 13 zeros
  114 + outfile.write((char*)&R[1], 2);
  115 + outfile.write((char*)&R[2], 2);
  116 + for(size_t i = 0; i < 992; i++) outfile.write(&zero, 1); //write 992 zeros
  117 + //char zerovec[1020];
  118 + //outfile.write((char*)zerovec, 1020);
  119 +
  120 + size_t b = bytes();
  121 + outfile.write((char*)ptr, b); //write the data to the output file
  122 + outfile.close();
  123 + }
  124 +
  125 + stim::envi_header create_header(){
  126 + stim::envi_header header;
  127 + header.samples = R[0];
  128 + header.lines = R[1];
  129 + header.bands = R[2];
  130 +
  131 + double z_delta = (double)(Z[1] - Z[0]) / (double)(R[2] - 1);
  132 + header.wavelength.resize(R[2]);
  133 + for(size_t i = 0; i < R[2]; i++)
  134 + header.wavelength[i] = i * z_delta + Z[0];
  135 +
  136 + return header;
  137 + }
  138 +
  139 + /// Calculate the absorbance spectrum from the transmission spectrum given a background
  140 + void absorbance(stim::agilent_binary<T>* background){
  141 + size_t N = size(); //calculate the number of values to be ratioed
  142 + if(N != background->size()){
  143 + std::cerr<<"ERROR in stim::agilent_binary::absorbance() - transmission image size doesn't match background"<<std::endl;
  144 + exit(1);
  145 + }
  146 + for(size_t i = 0; i < N; i++)
  147 + ptr[i] = -log10(ptr[i] / background->ptr[i]);
  148 + }
  149 +
  150 +#ifdef CUDA_FOUND
  151 + /// Perform an FFT and return a binary file with bands in the specified range
  152 + agilent_binary<T> fft(float band_min, float band_max){
  153 + auto total_start = std::chrono::high_resolution_clock::now();
  154 +
  155 + auto start = std::chrono::high_resolution_clock::now();
  156 + T* cpu_data = (T*) malloc( bytes() ); //allocate space for the transposed data
  157 + for(size_t b = 0; b < R[2]; b++){
  158 + for(size_t x = 0; x < R[0] * R[1]; x++){
  159 + cpu_data[x * R[2] + b] = ptr[b * R[0] * R[1] + x];
  160 + }
  161 + }
  162 + auto end = std::chrono::high_resolution_clock::now();
  163 + std::chrono::duration<double> diff = end-start;
  164 + // std::cout << "Transpose data: " << diff.count() << " s\n";
  165 +
  166 + start = std::chrono::high_resolution_clock::now();
  167 + cufftHandle plan; //allocate space for a cufft plan
  168 + cufftReal* gpu_data; //create a pointer to the data
  169 + size_t batch = R[0] * R[1]; //calculate the batch size (X * Y)
  170 + HANDLE_ERROR(cudaMalloc((void**)&gpu_data, bytes())); //allocate space on the GPU
  171 + HANDLE_ERROR(cudaMemcpy(gpu_data, cpu_data, bytes(), cudaMemcpyHostToDevice)); //copy the data to the GPU
  172 + cufftComplex* gpu_fft;
  173 + HANDLE_ERROR(cudaMalloc((void**)&gpu_fft, R[0] * R[1] * (R[2]/2 + 1) * sizeof(cufftComplex)));
  174 + end = std::chrono::high_resolution_clock::now();
  175 + diff = end-start;
  176 + //std::cout << "Allocate/copy: " << diff.count() << " s\n";
  177 +
  178 + start = std::chrono::high_resolution_clock::now();
  179 + int N[1]; //create an array with the interferogram size (required for cuFFT input)
  180 + N[0] = R[2]; //set the only array value to the interferogram size
  181 + if(cufftPlanMany(&plan, 1, N, NULL, 1, R[2], NULL, 1, R[2], CUFFT_R2C, batch) != CUFFT_SUCCESS){
  182 + std::cout<<"cuFFT Error: unable to create 1D plan."<<std::endl;
  183 + exit(1);
  184 + }
  185 + end = std::chrono::high_resolution_clock::now();
  186 + diff = end-start;
  187 + //std::cout << "Create a plan: " << diff.count() << " s\n";
  188 +
  189 + start = std::chrono::high_resolution_clock::now();
  190 + if (cufftExecR2C(plan, gpu_data, gpu_fft) != CUFFT_SUCCESS){ //execute the (implicitly forward) transform
  191 + std::cout<<"CUFFT error: ExecR2C Forward failed";
  192 + exit(1);
  193 + }
  194 + end = std::chrono::high_resolution_clock::now();
  195 + diff = end-start;
  196 + //std::cout << "Perform FFT: " << diff.count() << " s\n";
  197 +
  198 + start = std::chrono::high_resolution_clock::now();
  199 + std::complex<T>* cpu_fft = (std::complex<T>*) malloc( R[0] * R[1] * (R[2]/2+1) * sizeof(std::complex<T>) );
  200 + HANDLE_ERROR(cudaMemcpy(cpu_fft, gpu_fft, R[0] * R[1] * (R[2]/2+1) * sizeof(cufftComplex), cudaMemcpyDeviceToHost)); //copy data from the host to the device
  201 +
  202 + double int_delta = 0.00012656; //interferogram sample spacing in centimeters
  203 + double int_length = int_delta * R[2]; //interferogram length in centimeters
  204 + double fft_delta = 1/int_length; //spectrum spacing (in inverse centimeters, wavenumber
  205 +
  206 + size_t start_i = std::ceil(band_min / fft_delta); //calculate the first band to store
  207 + size_t size_i = std::floor(band_max / fft_delta) - start_i; //calculate the number of bands to store
  208 + size_t end_i = start_i + size_i; //last band number
  209 + agilent_binary<T> result(R[0], R[1], size_i);
  210 + result.Z[0] = start_i * fft_delta; //set the range for the FFT result
  211 + result.Z[1] = end_i * fft_delta;
  212 +
  213 + for(size_t b = start_i; b < end_i; b++){
  214 + for(size_t x = 0; x < R[0] * R[1]; x++){
  215 + result.ptr[(b - start_i) * R[0] * R[1] + x] = abs(cpu_fft[x * (R[2]/2+1) + b]);
  216 + }
  217 + }
  218 + end = std::chrono::high_resolution_clock::now();
  219 + diff = end-start;
  220 + //std::cout << "Transpose/Crop: " << diff.count() << " s\n";
  221 +
  222 + auto total_end = std::chrono::high_resolution_clock::now();
  223 + diff = total_end-total_start;
  224 +
  225 + cufftDestroy(plan);
  226 + HANDLE_ERROR(cudaFree(gpu_data));
  227 + HANDLE_ERROR(cudaFree(gpu_fft));
  228 + free(cpu_data);
  229 + free(cpu_fft);
  230 +
  231 + return result;
  232 + }
  233 +#endif
  234 +
  235 +};
  236 +
  237 +}
  238 +
  239 +#endif
0 240 \ No newline at end of file
... ...
stim/envi/bip.h
  Show/Hide comments   View file @e0edbe1
... ... @@ -235,6 +235,7 @@ public:
235 235  
236 236 for(unsigned long long i = 0; i < B; i++) //for each element of the spectrum
237 237 p[i] = (double) temp[i]; //cast each element to a double value
  238 + free(temp); //free temporary memory
238 239 return true;
239 240 }
240 241  
... ...
stim/gl/gl_spider.h
  Show/Hide comments   View file @e0edbe1
... ... @@ -14,6 +14,7 @@
14 14 #include <stim/math/vec3.h>
15 15 #include <stim/math/rect.h>
16 16 #include <stim/math/matrix.h>
  17 +#include <stim/math/constants.h>
17 18 #include <stim/cuda/spider_cost.cuh>
18 19 #include <stim/cuda/cudatools/glbind.h>
19 20 #include <stim/cuda/arraymath.cuh>
... ... @@ -369,7 +370,7 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
369 370 ///Stored in a display list.
370 371 ///uses the default d vector <0,0,1>
371 372 void
372   - genDirectionVectors(float solidAngle = 5/M_PI*4)
  373 + genDirectionVectors(float solidAngle = M_PI/2)
373 374 {
374 375  
375 376 //Set up the vectors necessary for Rectangle creation.
... ... @@ -584,7 +585,7 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
584 585 glDeleteFramebuffers(1, &framebufferID);
585 586 glGenFramebuffers(1, &framebufferID);
586 587 glBindFramebuffer(GL_FRAMEBUFFER, framebufferID);
587   - int numChannels = 1;
  588 +// int numChannels = 1;
588 589 // unsigned char* texels = new unsigned char[width * height * numChannels];
589 590 glGenTextures(1, &textureID);
590 591 glBindTexture(GL_TEXTURE_2D, textureID);
... ... @@ -609,7 +610,7 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
609 610 {
610 611 glGenFramebuffers(1, &fboID);
611 612 glBindFramebuffer(GL_FRAMEBUFFER, fboID);
612   - int numChannels = 1;
  613 +// int numChannels = 1;
613 614 // unsigned char* texels = new unsigned char[width * height * numChannels];
614 615 glGenTextures(1, &texbufferID);
615 616 glBindTexture(GL_TEXTURE_2D, texbufferID);
... ... @@ -938,7 +939,7 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
938 939 network_time = 0;
939 940 hit_time = 0;
940 941 #endif
941   - stepsize = 3.0;
  942 + stepsize = 2.5;
942 943 t_length = 16.0;
943 944  
944 945 srand(100);
... ... @@ -1392,13 +1393,9 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
1392 1393  
1393 1394 Z[0] = cos(PHI[0]);
1394 1395 Z[1] = cos(PHI[1]);
1395   -
1396 1396  
1397 1397 range = Z[0] - Z[1];
1398 1398  
1399   -
1400   - float z, theta, phi;
1401   -
1402 1399 std::vector<stim::vec3<float> > vecsUni;
1403 1400 for(int i = 0; i < numSamplesPos; i++)
1404 1401 {
... ... @@ -1490,8 +1487,6 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
1490 1487 void
1491 1488 trace(int min_cost)
1492 1489 {
1493   - bool sEmpty = true;
1494   - float lastmag = 16.0;;
1495 1490 stim::vec3<float> curSeed;
1496 1491 stim::vec3<float> curSeedVec;
1497 1492 float curSeedMag;
... ... @@ -1527,7 +1522,7 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
1527 1522 gpuStartTimer();
1528 1523 #endif
1529 1524  
1530   - float s = 3.0;
  1525 +// float s = 3.0;
1531 1526 GLuint selectBuf[2048];
1532 1527 GLint hits;
1533 1528 glSelectBuffer(2048, selectBuf);
... ... @@ -1541,17 +1536,17 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
1541 1536 CHECK_OPENGL_ERROR
1542 1537 //What would that vessel see in front of it.
1543 1538 camSel.setPosition(loc);
1544   - camSel.setFocalDistance(mag/s);
1545   - camSel.LookAt((loc[0]+dir[0]*mag/s),
1546   - (loc[1]+dir[1]*mag/s),
1547   - (loc[2]+dir[2]*mag/s));
  1539 + camSel.setFocalDistance(mag/stepsize);
  1540 + camSel.LookAt((loc[0]+dir[0]*mag/stepsize),
  1541 + (loc[1]+dir[1]*mag/stepsize),
  1542 + (loc[2]+dir[2]*mag/stepsize));
1548 1543 ps = camSel.getPosition();
1549 1544 ups = camSel.getUp();
1550 1545 ds = camSel.getLookAt();
1551 1546 glMatrixMode(GL_PROJECTION);
1552 1547 glPushMatrix();
1553 1548 glLoadIdentity();
1554   - glOrtho(-mag/s/2.0, mag/s/2.0, -mag/s/2.0, mag/s/2.0, 0.0, mag/s/2.0);
  1549 + glOrtho(-mag/stepsize/2.0, mag/stepsize/2.0, -mag/stepsize/2.0, mag/stepsize/2.0, 0.0, mag/stepsize/2.0);
1555 1550 glMatrixMode(GL_MODELVIEW);
1556 1551 glPushMatrix();
1557 1552 glLoadIdentity();
... ... @@ -1597,21 +1592,11 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
1597 1592 int
1598 1593 processHits(GLint hits, GLuint buffer[])
1599 1594 {
1600   - GLuint names, *ptr;
1601   - //printf("hits = %u\n", hits);
  1595 + GLuint *ptr;
1602 1596 ptr = (GLuint *) buffer;
1603   - // for (int i = 0; i < hits; i++) { /* for each hit */
1604   - names = *ptr;
1605   - // printf (" number of names for hit = %u\n", names);
1606 1597 ptr++;
1607 1598 ptr++; //Skip the minimum depth value.
1608 1599 ptr++; //Skip the maximum depth value.
1609   - // printf (" the name is ");
1610   - // for (int j = 0; j < names; j++) { /* for each name */
1611   - // printf ("%u ", *ptr); ptr++;
1612   - // }
1613   - // printf ("\n");
1614   - // }
1615 1600  
1616 1601  
1617 1602 if(hits == 0)
... ... @@ -1675,11 +1660,18 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
1675 1660 }
1676 1661  
1677 1662 #ifdef TIMING
1678   - double network_time = (std::clock() - s) / (double) CLOCKS_PER_SEC;
1679   - network_time += network_time * 1000.0;
  1663 + double nt = (std::clock() - s) / (double) CLOCKS_PER_SEC;
  1664 + network_time += nt * 1000.0;
1680 1665 #endif
1681 1666 }
1682 1667  
  1668 +// void
  1669 +// addToNetwork(pair<stim::fiber<float>, int> in, stim::vec3<float> spos,
  1670 +// stim::vec<float> smag, stim::vec3<float> sdir)
  1671 +// {
  1672 +//
  1673 +// }
  1674 +
1683 1675  
1684 1676 void
1685 1677 printSizes()
... ... @@ -1783,9 +1775,6 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
1783 1775 }
1784 1776 }
1785 1777 }
1786   -
1787   -
1788   -
1789 1778 };
1790 1779 }
1791 1780 #endif
... ...
stim/grids/image_stack.h
  Show/Hide comments   View file @e0edbe1
... ... @@ -33,10 +33,10 @@ public:
33 33 stim::filename file_path(file_mask);
34 34  
35 35 //if the file path is relative, update it with the current working directory
36   - if(file_path.is_relative()){
37   - stim::filename wd = stim::filename::cwd();
38   - file_path = wd.get_relative(file_mask);
39   - }
  36 +// if(file_path.is_relative()){
  37 +// stim::filename wd = stim::filename::cwd();
  38 +// file_path = wd.get_relative(file_mask);
  39 +// }
40 40  
41 41 //get the list of files
42 42 std::vector<stim::filename> file_list = file_path.get_list();
... ... @@ -134,10 +134,10 @@ public:
134 134 stim::filename file_path(file_mask);
135 135  
136 136 //if the file path is relative, update it with the current working directory
137   - if(file_path.is_relative()){
138   - stim::filename wd = stim::filename::cwd();
139   - file_path = wd.get_relative(file_mask);
140   - }
  137 +// if(file_path.is_relative()){
  138 +// stim::filename wd = stim::filename::cwd();
  139 +// file_path = wd.get_relative(file_mask);
  140 +// }
141 141  
142 142 //create a list of file names
143 143 std::vector<std::string> file_list = stim::wildcards::increment(file_path.str(), 0, R[3]-1, 1);
... ...
stim/math/matrix.h
  Show/Hide comments   View file @e0edbe1
... ... @@ -53,13 +53,13 @@ struct matrix
53 53  
54 54 template<typename Y>
55 55 vec<Y> operator*(vec<Y> rhs){
56   - unsigned int N = rhs.size();
  56 + unsigned int M = rhs.size();
57 57  
58 58 vec<Y> result;
59   - result.resize(N);
  59 + result.resize(M);
60 60  
61   - for(int r=0; r<N; r++)
62   - for(int c=0; c<N; c++)
  61 + for(int r=0; r<M; r++)
  62 + for(int c=0; c<M; c++)
63 63 result[r] += (*this)(r, c) * rhs[c];
64 64  
65 65 return result;
... ...
stim/math/vec3.h
  Show/Hide comments   View file @e0edbe1
... ... @@ -3,6 +3,7 @@
3 3  
4 4  
5 5 #include <stim/cuda/cudatools/callable.h>
  6 +#include <cmath>
6 7  
7 8  
8 9 namespace stim{
... ... @@ -216,7 +217,6 @@ public:
216 217 return result;
217 218 }
218 219  
219   -#ifndef __NVCC__
220 220 /// Outputs the vector as a string
221 221 std::string str() const{
222 222 std::stringstream ss;
... ... @@ -234,7 +234,6 @@ public:
234 234  
235 235 return ss.str();
236 236 }
237   -#endif
238 237  
239 238 size_t size(){ return 3; }
240 239  
... ...
stim/optics/scalarbeam.h
  Show/Hide comments   View file @e0edbe1
... ... @@ -121,12 +121,12 @@ CUDA_CALLABLE void lut_lookup(T* lut_values, T* lut, T val, size_t N, T min_val,
121 121  
122 122 template <typename T>
123 123 CUDA_CALLABLE stim::complex<T> clerp(stim::complex<T> v0, stim::complex<T> v1, T t) {
124   - return stim::complex<T>( fma(t, v1.r, fma(-t, v0.r, v0.r)), fma(t, v1.i, fma(-t, v0.i, v0.i)) );
  124 + return stim::complex<T>( fmaf(t, v1.r, fmaf(-t, v0.r, v0.r)), fmaf(t, v1.i, fmaf(-t, v0.i, v0.i)) );
125 125 }
126 126  
127 127 template <typename T>
128 128 CUDA_CALLABLE T lerp(T v0, T v1, T t) {
129   - return fma(t, v1, fma(-t, v0, v0));
  129 + return fmaf(t, v1, fmaf(-t, v0, v0));
130 130 }
131 131  
132 132 #ifdef CUDA_FOUND
... ...
stim/optics/scalarfield.h
  Show/Hide comments   View file @e0edbe1
... ... @@ -293,6 +293,8 @@ protected:
293 293 stim::complex<T>* E;
294 294 size_t R[2];
295 295 locationType loc;
  296 + using rect<T>::X;
  297 + using rect<T>::Y;
296 298  
297 299 T* p[3]; //scalar position for each point in E
298 300  
... ...
stim/parser/filename.h
  Show/Hide comments   View file @e0edbe1
... ... @@ -2,218 +2,295 @@
2 2 #define STIM_FILENAME_H
3 3  
4 4 #include <stdio.h> /* defines FILENAME_MAX */
  5 +#include <sstream>
  6 +#include <vector>
  7 +#include <algorithm>
  8 +#include <iostream>
  9 +#include <iomanip>
  10 +
  11 +#include <stim/parser/parser.h>
  12 +
  13 +// set OS dependent defines, including:
  14 +// 1) path division character ('/' or '\') used for output only
  15 +// 2) command for getting the current working directory
  16 +// 3) header files for getting the current working directory
  17 +// 4) include BOOST filesystem class if compiling on GCC
  18 +#define STIM_DIV '/'
5 19 #ifdef _WIN32
6 20 #include <windows.h>
7   - #include <direct.h>
8   - #define GetCurrentDir _getcwd
9   - #define STIM_FILENAME_DIV '/'
  21 + #include <direct.h>
  22 + #define GetCurrentDir _getcwd
  23 + #define STIM_FILENAME_DIV '\\'
10 24 #else
11   - #include <unistd.h>
12   - #define GetCurrentDir getcwd
  25 + #ifdef BOOST_PRECOMPILED
  26 + #include <boost/filesystem.hpp>
  27 + #endif
  28 + #include <unistd.h>
  29 + #define GetCurrentDir getcwd
13 30 #define STIM_FILENAME_DIV '/'
14 31 #endif
15 32  
16   -#include <string>
17   -#include <sstream>
18   -#include <iomanip>
19   -#include <vector>
20   -#include <stack>
21   -#include <algorithm>
22   -#include <iostream>
23   -
24   -#include "../parser/parser.h"
25   -#ifdef BOOST_PRECOMPILED
26   -#include <boost/filesystem.hpp>
27   -#endif
28 33 namespace stim{
29 34  
30   -//filename class designed to work with both Windows and Unix
  35 +class filepath{
  36 +protected:
  37 + std::string _drive; //drive on which the file is located (used for Windows)
  38 + std::vector<std::string> _path; //path for the specified file (list of hierarchical directories)
31 39  
32   -class filename{
  40 + /// replaces win32 dividers with the Linux standard (used internally by default)
  41 + std::string unix_div(std::string s) {
  42 + std::replace( s.begin(), s.end(), '\\', '/');
  43 + return s;
  44 + }
33 45  
34   -private:
35   - void init(){
  46 + /// gets the directory hierarchy for the current working directory
  47 + static std::string cwd(){
  48 + char cCurrentPath[FILENAME_MAX];
36 49  
37   - absolute = false;
  50 + if (!GetCurrentDir(cCurrentPath, sizeof(cCurrentPath))){
  51 + std::cout<<"ERROR getting current working directory."<<std::endl;
  52 + exit(1);
  53 + }
38 54  
  55 + std::stringstream ss;
  56 + ss<<cCurrentPath;
  57 + return ss.str();
39 58 }
40 59  
41   -protected:
  60 + /// convert a relative path to an absolute path
  61 + void get_absolute(std::string &drive, std::vector<std::string> &absolute, std::vector<std::string> relative){
42 62  
43   - std::string drive; //drive letter (for Windows)
44   - std::vector<std::string> path; //directory hierarchy
45   - std::string prefix; //file prefix (without extension)
46   - std::string ext; //file extension
  63 + std::string current = cwd(); //get the current directory as a string
47 64  
48   - bool absolute; //filename is an absolute path
  65 + std::string current_drive;
  66 + std::vector<std::string> current_dir;
  67 + parse_path(current_drive, current_dir, current); //get the current drive and directories
49 68  
50   - //replaces win32 dividers with the Linux standard
51   - std::string unix_div(std::string s) {
52   - std::replace( s.begin(), s.end(), '\\', '/');
53   - return s;
54   - }
55   -
56   - //break up a filename into a prefix and extension
57   - void parse_name(std::string fname){
  69 + // step through each directory in the relative path, adjusting the current directory
  70 + // index depending on whether the relative path is specified with '.' or '..'
  71 + int current_i = (int)current_dir.size() - 1;
  72 + int relative_i;
  73 + for(relative_i = 0; relative_i < relative.size(); relative_i++){
  74 + if(relative[relative_i] == "..") current_i--;
  75 + else if(relative[relative_i] != ".") break;
  76 + }
  77 + if(current_i < 0){
  78 + std::cerr<<"ERROR stim::filepath - relative path is incompatible with working directory"<<std::endl;
  79 + exit(1);
  80 + }
58 81  
59   - //find the extension
60   - size_t xpos = fname.find_last_of('.'); //find the position of the extension period (if there is one)
61   - if(xpos != std::string::npos){ //split the prefix and extension
62   - prefix = fname.substr(0, xpos);
63   - ext = fname.substr(xpos + 1);
  82 + absolute.clear();
  83 + for(size_t i = 0; i <= current_i; i++){
  84 + absolute.push_back(current_dir[i]);
  85 + }
  86 + for(size_t i = relative_i; i < relative.size(); i++){
  87 + absolute.push_back(relative[i]);
64 88 }
65   - else
66   - prefix = fname;
67 89 }
68 90  
69   - //parse a file locator string
70   - void parse(std::string loc){
71   - if(loc.size() == 0) return;
72   -
73   - loc = unix_div(loc);
74   -
75   - //determine the drive (if Windows)
76   - drive = "";
77   - #ifdef _WIN32
78   - //if the second character is a colon, the character right before it is the drive
79   - if(loc[1] == ':'){
80   - absolute = true; //this is an absolute path
81   - drive = loc[0]; //copy the drive letter
82   - loc = loc.substr(3); //remove the drive information from the locator string
  91 + /// Parses a directory string into a drive (NULL if not Windows) and list of hierarchical directories
  92 + /// Returns true if the path is relative, false if it is absolute
  93 + void parse_path(std::string &drive, std::vector<std::string> &absolute, std::string dir){
  94 + drive = ""; //initialize the drive to NULL (it will stay that way for Windows)
  95 + std::vector<std::string> path;
  96 + bool relative = true; //the default path is relative
  97 +
  98 + if(dir.length() == 0) return; //return if the file locator is empty
  99 + std::string unix_dir = unix_div(dir); //replace any Windows division characters with Unix
  100 +
  101 + if(unix_dir.length() > 1 && unix_dir[1] == ':'){ //if a drive identifier is given
  102 + if(unix_dir[0] > 64 && unix_dir[0] < 91) //if the drive letter is upper case
  103 + _drive = unix_dir[0] + 32; //convert it to lower case
  104 + else if(unix_dir[0] > 96 && unix_dir[0] < 123) //if the drive character is lower case
  105 + _drive = unix_dir[0]; //store it as-is
  106 + else{ //otherwise throw an error
  107 + std::cerr<<"ERROR stim::filename - drive letter is invalid: "<<unix_dir[0]<<std::endl;
  108 + exit(1);
83 109 }
84   - #else
85   - if(loc[0] == STIM_FILENAME_DIV){
86   - absolute = true;
87   - loc = loc.substr(1);
88   - }
89   - #endif
90   -
91   - //determine the file name
92   - std::string fname = loc.substr( loc.find_last_of('/') + 1 ); //find the file name (including extension)
  110 + unix_dir = unix_dir.substr(2, unix_dir.length()-2); //extract the directory structure
  111 + }
93 112  
94   - //parse the file name
95   - parse_name(fname);
  113 + if(unix_dir.front() == '/'){ //if there is a leading slash
  114 + relative = false; //the path is not relative
  115 + unix_dir = unix_dir.substr(1, unix_dir.length() - 1); //remove the slash
  116 + }
  117 + if(unix_dir.back() == '/')
  118 + unix_dir = unix_dir.substr(0, unix_dir.length() - 1);
96 119  
97   - //find the directory hierarchy
98   - std::string dir = loc.substr(0, loc.find_last_of('/') + 1 );
99   - path = stim::parser::split(dir, '/');
  120 + path = stim::parser::split(unix_dir, '/'); //split up the directory structure
  121 +
  122 + if(relative)
  123 + get_absolute(drive, absolute, path);
  124 + else
  125 + absolute = path;
100 126 }
101 127  
102   -public:
  128 +
103 129  
104   - filename(){
105   - init();
  130 +public:
  131 + filepath(){
  132 + _drive = "";
106 133 }
107 134  
108   - filename(std::string loc){
109   - init();
110   - parse(loc);
  135 + filepath(const stim::filepath& p){
  136 + *this = p;
111 137 }
112 138  
  139 + filepath(const std::string s){
  140 + parse_path(_drive, _path, s);
  141 + }
113 142  
114   - /// Outputs the file name (including prefix and extension)
115   - std::string get_name(){
116   - if(prefix == "" && ext == "")
117   - return "";
118   - else
119   - return prefix + "." + ext;
  143 + stim::filepath& operator=(const std::string s){
  144 + parse_path(_drive, _path, s); //parse the string to get the drive and relative path
  145 + return *this;
120 146 }
121 147  
122   - /// Output the file extension only (usually three characters after a '.')
123   - std::string get_extension(){
124   - return ext;
  148 + std::string str(){
  149 + std::stringstream ss;
  150 + if(_drive != "") //if a drive letter is specified
  151 + ss<<_drive<<":"; //add it to the string
  152 + for(size_t i = 0; i < _path.size(); i++)
  153 + ss<<STIM_FILENAME_DIV<<_path[i];
  154 + ss<<STIM_FILENAME_DIV;
  155 + return ss.str();
  156 + }
  157 +}; //end filepath
  158 +
  159 +class filename : public filepath{
  160 +protected:
  161 + std::string _prefix; //filename prefix
  162 + std::string _extension; //filename extension
  163 +
  164 + void set_filename(std::string fname){
  165 + size_t ext_i = fname.find_last_of('.'); //calculate the index of the '.'
  166 + if(ext_i != std::string::npos){ //if there is an extension
  167 + _prefix = fname.substr(0, ext_i); //store the prefix
  168 + _extension = fname.substr(ext_i + 1, fname.size() - ext_i - 1); //store the extension
  169 + }
  170 + else //otherwise just store the prefix
  171 + _prefix = fname;
125 172 }
126 173  
127   - /// Output the file prefix only (name before the extension)
128   - std::string get_prefix(){
129   - return prefix;
  174 +public:
  175 + filename(){}
  176 +
  177 + filename(stim::filepath p, std::string fname) : stim::filepath(p){
  178 + set_filename(fname);
130 179 }
131 180  
132   - /// Output the entire path (not including the filename)
133   - /// ex. "c:\this\is\the\directory\"
134   - std::string dir(){
135   - std::stringstream ss;
  181 + stim::filename& operator=(const std::string s){
  182 + std::string unix_s = unix_div(s); //convert dividers to unix
  183 + size_t name_i = unix_s.find_last_of('/'); //find the index of the last divider
136 184  
137   - //if the path is absolute
138   - if(absolute){
139   - //output the drive letter if in Windows
140   - #ifdef _WIN32
141   - ss<<drive<<":";
142   - #endif
143   - ss<<STIM_FILENAME_DIV;
  185 + if(name_i == std::string::npos){ //if there is no divider, this is just a filename
  186 + unix_s = "./" + unix_s; //append a ./ to the beginning so that the working directory is used
  187 + name_i = 1;
144 188 }
145 189  
146   - //output the directory
147   - for(unsigned int d = 0; d < path.size(); d++)
148   - ss<<path[d]<<STIM_FILENAME_DIV;
  190 + name_i++;
149 191  
150   - return ss.str();
151 192  
  193 + std::string filename = unix_s.substr(name_i, unix_s.size() - name_i); //extract the filename
  194 + std::string filepath = unix_s.substr(0, name_i-1); //extract the filepath
  195 +
  196 + filepath::operator=(filepath); //parse and store the file path
  197 +
  198 + set_filename(filename);
  199 + return *this;
152 200 }
153 201  
154   - void clear()
155   - {
156   - drive = ""; //drive letter (for Windows)
157   - path.resize(0);
158   - prefix= ""; //file prefix (without extension)
159   - ext = ""; //file extension
  202 + filename(std::string s){
  203 + operator=(s);
160 204 }
161 205  
162   - /// Output the entire string, including the path and filename
163   - /// ex. "c:\this\is\a\directory\file.txt"
164   - std::string str(){
165   - std::stringstream ss; //create a string stream
166   - ss<<dir()<<get_name(); //push the directory and filename to that stream
167   - return ss.str(); //convert the stream to a string and return it
  206 + bool is_relative(){
  207 + return false;
168 208 }
169 209  
170   - //*****************************************************************************************************************
171   - // output is the directory and the prefix and the extension of the files, which are looking for in that directory.
172   - /// David: I have no idea what this is doing. It looks identical to dir()
173   - std::string dir_fname(){
174   - std::stringstream ss;
175 210  
176   - //if the path is absolute
177   - if(absolute){
178   - //output the drive letter if in Windows
179   - #ifdef _WIN32
180   - ss<<drive<<":";
181   - #endif
182   - ss<<STIM_FILENAME_DIV;
183   - }
  211 + std::string str(){
  212 + std::stringstream ss;
  213 + ss<<filepath::str()<<_prefix;
  214 + if(_extension.size() != 0)
  215 + ss<<"."<<_extension;
  216 + return ss.str();
  217 + }
184 218  
  219 + /// Create a matching file locator with a prefix s
  220 + stim::filename prefix(std::string s){
  221 + stim::filename result = *this;
  222 + result._prefix = s;
  223 + return result;
  224 + }
185 225  
186   - for(unsigned int d = 0; d < path.size(); d++)
187   - ss<<path[d]<<STIM_FILENAME_DIV;
188   - ss<<get_name();
  226 + std::string prefix(){
  227 + return _prefix;
  228 + }
189 229  
190   - return ss.str();
  230 + std::string get_prefix(){
  231 + return _prefix;
  232 + }
191 233  
  234 + /// Create a matching file locator with the extension changed to s
  235 + stim::filename extension(std::string s){
  236 + stim::filename result = *this;
  237 + result._extension = s;
  238 + return result;
192 239 }
193 240  
194   - // output is the directory and the name of the file which are found in that given directory
195   - std::string f_name(std::string file_name){
196   - std::stringstream ss;
  241 + std::string extension(){
  242 + return _extension;
  243 + }
197 244  
198   - if(absolute){ //if the path is absolute
199   - #ifdef _WIN32
200   - ss<<drive<<":"; //output the drive letter if in Windows
201   - #endif
202   - ss<<STIM_FILENAME_DIV; //output a path divider
  245 + stim::filename fname(std::string s){
  246 + stim::filename result = *this;
  247 + size_t ext_i = s.find_last_of('.'); //calculate the index of the '.'
  248 + if(ext_i != std::string::npos){ //if there is an extension
  249 + result._prefix = s.substr(0, ext_i); //store the prefix
  250 + result._extension = s.substr(ext_i + 1, s.size() - ext_i - 1); //store the extension
203 251 }
  252 + else //otherwise just store the prefix
  253 + result._prefix = s;
  254 + return result;
  255 + }
  256 +
  257 + /// create a matching file locator with the path changed to s
  258 + stim::filename path(std::string s){
  259 + stim::filename result = *this;
  260 + result.parse_path(result._drive, result._path, s);
  261 + return result;
  262 + }
204 263  
205   - for(unsigned int d = 0; d < path.size(); d++) //for each directory in the current path
206   - ss<<path[d]<<STIM_FILENAME_DIV; //add that directory, interspersing path dividers
  264 + std::string path(){
  265 + return filepath::str();
  266 + }
207 267  
208   - stim::filename fn = file_name;
209   - std::string fn_prefix = fn.prefix;
210   - std::string fn_ext = fn.ext;
211   - ss<<fn_prefix + '.' + fn_ext;
  268 + /// Casting operator, casts to a string
  269 + operator std::string(){
  270 + return str();
  271 + }
212 272  
213   - return ss.str();
  273 + /// This function replaces a wildcard in the prefix with the specified string
  274 + stim::filename insert(std::string str){
214 275  
  276 + stim::filename result = *this; //initialize the result filename to the current filename
  277 + size_t loc = result._prefix.find('*'); //find a wild card in the string
  278 + if(loc == std::string::npos) //if a wildcard isn't found
  279 + result._prefix += str; //append the value to the prefix
  280 + else
  281 + result._prefix.replace(loc, 1, str); //replace the wildcard with the string
  282 + return result; //return the result
215 283 }
216 284  
  285 + /// This function replaces a wildcard in the prefix with the specified integer (with a padding of n)
  286 + stim::filename insert(size_t i, size_t n = 2){
  287 +
  288 + std::stringstream ss;
  289 + ss << std::setw(n) << std::setfill('0') << i;
  290 + return insert(ss.str());
  291 + }
  292 +
  293 +
217 294 /// Returns a list of files using the current filename as a template.
218 295 /// For example:
219 296 /// C:\this\is\a\path\file*.txt
... ... @@ -223,28 +300,33 @@ public:
223 300 //the Unix version requires Boost
224 301  
225 302 #ifdef _WIN32
226   - stim::filename filepath(dir_fname()); //initialize filepath with the mask
227 303  
228 304 HANDLE hFind = INVALID_HANDLE_VALUE; //allocate data structures for looping through files
229 305 WIN32_FIND_DATAA FindFileData;
230 306 std::vector<stim::filename> file_list; //initialize a list to hold all matching filenames
231 307  
232   - hFind = FindFirstFileA((filepath.str().c_str()), &FindFileData); //find the first file that matches the specified file path
  308 + std::string path_string = str();
  309 + hFind = FindFirstFileA(path_string.c_str(), &FindFileData); //find the first file that matches the specified file path
233 310  
234 311 if (hFind == INVALID_HANDLE_VALUE) { //if there are no matching files
235   - printf ("Invalid file handle. Error is %u.\n", GetLastError()); //print an error
  312 + //printf ("Invalid file handle. Error is %u.\n", GetLastError()); //print an error
  313 + return file_list;
236 314 }
237 315 else {
238 316 std::string file_name = FindFileData.cFileName; //save the file name
239   - std::string file_path = dir(); //the file is in the specified directory, so save it
  317 + std::string file_path = path(); //the file is in the specified directory, so save it
240 318 stim::filename current_file(file_path + file_name); //create a stim::filename structure representing this file
241   - file_list.push_back(current_file); //push the new stim::filename to the file list
  319 + if(!(FindFileData.cFileName[0] == '.' && FindFileData.cFileName[1] == '\0'))
  320 + file_list.push_back(current_file); //push the new stim::filename to the file list
  321 +
242 322  
243 323 // List all the other files in the directory.
244 324 while (FindNextFileA(hFind, &FindFileData) != 0){ //iterate until there are no more matching files
245   - file_name = FindFileData.cFileName; //save the next file
246   - current_file = (f_name(file_name)); //append the directory
247   - file_list.push_back(current_file); //push it to the list
  325 + if(!(FindFileData.cFileName[0] == '.' && FindFileData.cFileName[1] == '.' && FindFileData.cFileName[2] == '\0')){ //account for the possibility of the '..' filename
  326 + file_name = FindFileData.cFileName; //save the next file
  327 + current_file = fname(file_name); //append the directory
  328 + file_list.push_back(current_file); //push it to the list
  329 + }
248 330 }
249 331 FindClose(hFind); //close the file data structure
250 332 }
... ... @@ -252,7 +334,7 @@ public:
252 334  
253 335 #elif BOOST_PRECOMPILED
254 336  
255   - boost::filesystem::path p(dir()); //create a path from the current filename
  337 + boost::filesystem::path p(path()); //create a path from the current filename
256 338 std::vector<stim::filename> file_list;
257 339 if(boost::filesystem::exists(p)){
258 340 if(boost::filesystem::is_directory(p)){
... ... @@ -265,9 +347,9 @@ public:
265 347 for (vec::const_iterator it(v.begin()), it_end(v.end()); it != it_end; ++it)
266 348 {
267 349 //if the filename is a wild card *or* it matches the read file name
268   - if( prefix == "*" || prefix == (*it).filename().stem().string()){
  350 + if( _prefix == "*" || _prefix == (*it).filename().stem().string()){
269 351 //if the extension is a wild card *or* it matches the read file extension
270   - if( ext == "*" || "." + ext == (*it).filename().extension().string()){
  352 + if( _extension == "*" || "." + _extension == (*it).filename().extension().string()){
271 353 file_list.push_back((*it).string()); //include it in the final list
272 354 }
273 355  
... ... @@ -287,108 +369,6 @@ public:
287 369 #endif
288 370  
289 371 }
290   - //**************************************************************************************************
291   -
292   - //gets the current working directory
293   - static stim::filename cwd(){
294   -
295   -
296   - char cCurrentPath[FILENAME_MAX];
297   -
298   - if (!GetCurrentDir(cCurrentPath, sizeof(cCurrentPath))){
299   - std::cout<<"ERROR getting current working directory."<<std::endl;
300   - exit(1);
301   - }
302   -
303   - std::cout<<cCurrentPath<<std::endl;
304   - return stim::filename(std::string(cCurrentPath) + STIM_FILENAME_DIV);
305   - }
306   -
307   - void set_name(std::string fname){
308   - parse_name(fname);
309   - }
310   -
311   - //append a string to the filename and return a new filename
312   - stim::filename append(std::string s){
313   - stim::filename result = *this; //create a new filename, copy the current filename
314   - result.prefix = prefix + s; //append the string to the filename
315   - return result;
316   - }
317   -
318   - //get a path relative to the current one
319   - stim::filename get_relative(std::string rel){
320   -
321   - std::vector<std::string> rel_path = stim::parser::split(rel, STIM_FILENAME_DIV);
322   -
323   - //if the relative path doesn't contain a file, add a blank string to be used as the filename
324   - if(rel[rel.size()-1] == STIM_FILENAME_DIV)
325   - rel_path.push_back("");
326   -
327   - //create a stack representing the current absolute path
328   - std::stack<std::string, std::vector<std::string> > s(path);
329   -
330   - //for each token in the relative path
331   - for(int d=0; d<rel_path.size() - 1; d++){
332   -
333   - //if the token is a double-dot, pop a directory off of the stack
334   - if(rel_path[d] == "..")
335   - s.pop();
336   - else
337   - s.push(rel_path[d]);
338   - }
339   -
340   - std::string* end = &s.top() + 1;
341   - std::string* begin = end - s.size();
342   - std::vector<std::string> result_path(begin, end);
343   -
344   - //create a new path to be returned
345   - stim::filename result = *this;
346   - result.path = result_path;
347   - result.set_name(rel_path.back());
348   -
349   - return result;
350   - }
351   -
352   - /// This function replaces a wildcard in the prefix with the specified string
353   - stim::filename insert(std::string str){
354   -
355   - stim::filename result = *this; //initialize the result filename to the current filename
356   - size_t loc = result.prefix.find('*'); //find a wild card in the string
357   - if(loc == std::string::npos) //if a wildcard isn't found
358   - result.prefix += str; //append the value to the prefix
359   - else
360   - result.prefix.replace(loc, 1, str); //replace the wildcard with the string
361   - return result; //return the result
362   - }
363   -
364   - stim::filename insert(size_t i, size_t n = 2){
365   -
366   - std::stringstream ss;
367   - ss << std::setw(n) << std::setfill('0') << i;
368   - return insert(ss.str());
369   - }
370   -
371   - bool is_relative(){
372   - return !absolute;
373   - }
374   -
375   - bool is_absolute(){
376   - return absolute;
377   - }
378   -
379   -
380   -
381   -
382   -
383   -
384   -
385   -
386   -
387   -};
388   -
389   -
390   -} //end namespace stim
391   -
392   -
  372 +}; //end filename
  373 +} //end namespace stim
393