1 #ifdef HAVE_CONFIG_H
2 #include <config.h>
3 #endif
4 #include "SUMA_suma.h"
5 #include "thd_segtools_fNM.h"
6 #include "SUMA_SegOpts.h"
7 #include "SUMA_SegFunc.h"
8 #include "SUMA_CoordMatch.h"
9 #include "SUMA_gts.h"
10
usage_SurfMatch(SUMA_GENERIC_ARGV_PARSE * ps,int detail)11 void usage_SurfMatch (SUMA_GENERIC_ARGV_PARSE *ps, int detail)
12 {
13 static char FuncName[]={"usage_SurfMatch"};
14 char * s = NULL, *sio=NULL, *st = NULL, *sts = NULL;
15 int i;
16 s = SUMA_help_basics();
17 sio = SUMA_help_IO_Args(ps);
18 printf (
19 "\n"
20 "Usage: SurfMatch <-i_TYPE BASE> <-i_TYPE INSURF> <-prefix PREFIX> \n"
21 " [-sv SURF_VOL] [-warp WARP]\n"
22 " -i_TYPE BASE: BASE is the reference surface to which nodes will be\n"
23 " registered. The BASE surface is the first surface on the\n"
24 " command line.\n"
25 " -i_TYPE INSURF: Surface whose nodes will be affine transformed as to\n"
26 " minimize their shortest distance to BASE.\n"
27 " -depthlimit DL: Exclude from cost computations nodes in INSURF that \n"
28 " are more than DL from the top node along the principal\n"
29 " direction closest to the Z axis.\n"
30 " -reduce_ref RED: Reduce first mesh to speed up computations.\n"
31 " If RED is between 0 and 1.0, then the new surface\n"
32 " will approximately have RED * N_Nodes\n"
33 " If RED > 1.0 then RED is the approximate number of\n"
34 " nodes in the reduced mesh.\n"
35 " -warp WARP: Set the type of affine warp allowed. \n"
36 " Choose from the following:\n"
37 " sho: For shift only.\n"
38 " sro: For shift + rotate\n"
39 " srs: For shift + rotate + scale\n"
40 /* " aff: For affine general.\n" */
41 " -city: Use City Block instead of Euclidian distance\n"
42 "\n"
43 /* Need an option that just takes point, not necessarily a second
44 surface.
45 Need an option to provide cmask */
46 "Example:\n"
47 " SurfMatch -i std.6rh.pial.asc -i std.6lh.pial.asc -warp sro\n"
48 " suma -onestate -i std.6rh.pial.asc -i std.6lh.pial.asc \\\n"
49 " -i SurfMatch.gii \n"
50 "\n");
51 SUMA_free(s); s = NULL; SUMA_free(st); st = NULL;
52 SUMA_free(sio); sio = NULL;
53
54 printf(" Ziad S. Saad SSCC/NIMH/NIH saadz@mail.nih.gov \n");
55 exit(0);
56 }
57
58 SUMA_GENERIC_PROG_OPTIONS_STRUCT *
SUMA_SurfMatch_ParseInput(char * argv[],int argc,SUMA_GENERIC_ARGV_PARSE * ps)59 SUMA_SurfMatch_ParseInput( char *argv[], int argc,
60 SUMA_GENERIC_ARGV_PARSE *ps)
61 {
62 static char FuncName[]={"SUMA_SurfMatch_ParseInput"};
63 SUMA_GENERIC_PROG_OPTIONS_STRUCT *Opt=NULL;
64 int kar;
65 SUMA_Boolean brk;
66 SUMA_Boolean LocalHead = NOPE;
67
68 SUMA_ENTRY;
69
70 Opt = SUMA_Alloc_Generic_Prog_Options_Struct();
71 Opt->s=NULL;
72 Opt->flt1 = 1.0;
73 Opt->b1 = 0;
74 Opt->efrac = 0.0;
75 kar = 1;
76 brk = NOPE;
77 while (kar < argc) { /* loop accross command ine options */
78 /*fprintf(stdout, "%s verbose: Parsing command line...\n", FuncName);*/
79 if (strcmp(argv[kar], "-h") == 0 || strcmp(argv[kar], "-help") == 0) {
80 usage_SurfMatch(ps, strlen(argv[kar])>3?1:0);
81 exit (0);
82 }
83
84 SUMA_SKIP_COMMON_OPTIONS(brk, kar);
85
86
87 if (!brk && (strcmp(argv[kar], "-warp") == 0))
88 {
89 if (kar+1 >= argc)
90 {
91 fprintf (SUMA_STDERR, "need a string after -warp \n");
92 exit (1);
93 }
94 ++kar;
95 if (!strcmp(argv[kar],"shift_only") ||
96 !strcmp(argv[kar],"sho")) {
97 Opt->s = SUMA_copy_string("shft");
98 } else if (!strcmp(argv[kar],"shift_rotate") ||
99 !strcmp(argv[kar],"sro")) {
100 Opt->s = SUMA_copy_string("shft+rot");
101 } else if (!strcmp(argv[kar],"shift_rotate_scale") ||
102 !strcmp(argv[kar],"srs")) {
103 Opt->s = SUMA_copy_string("shft+rot+scl");
104 } else if (!strcmp(argv[kar],"affine_general") ||
105 !strcmp(argv[kar],"aff")) {
106 Opt->s = SUMA_copy_string("shft+rot+scl+shr");
107 } else {
108 SUMA_S_Errv("Bad -warp parameter of %s\n"
109 "Choose from sho, sro, srs, or aff\n",
110 argv[kar]);
111 exit(1);
112 }
113 brk = YUP;
114 }
115
116 if (!brk && (strcmp(argv[kar], "-city") == 0))
117 {
118 Opt->b1 = 1;
119 brk = YUP;
120 }
121
122 if (!brk && (strcmp(argv[kar], "-prefix") == 0))
123 {
124 if (kar+1 >= argc)
125 {
126 fprintf (SUMA_STDERR, "need a number after -prefix \n");
127 exit (1);
128 }
129 Opt->out_prefix = SUMA_copy_string(argv[++kar]);
130
131 brk = YUP;
132 }
133
134 if (!brk && (strcmp(argv[kar], "-depthlimit") == 0))
135 {
136 if (kar+1 >= argc)
137 {
138 fprintf (SUMA_STDERR, "need a number after -depthlimit \n");
139 exit (1);
140 }
141 Opt->flt1 = atof(argv[++kar]);
142 brk = YUP;
143 }
144
145 if (!brk && (strcmp(argv[kar], "-reduce_ref") == 0))
146 {
147 if (kar+1 >= argc)
148 {
149 fprintf (SUMA_STDERR, "need a number after -reduce_ref \n");
150 exit (1);
151 }
152 Opt->efrac = atof(argv[++kar]);
153 brk = YUP;
154 }
155
156 if (!brk && (strcmp(argv[kar], "-debug") == 0))
157 {
158 if (kar+1 >= argc)
159 {
160 fprintf (SUMA_STDERR, "need a number after -debug \n");
161 exit (1);
162 }
163
164 Opt->debug = atoi(argv[++kar]);
165 brk = YUP;
166 }
167
168 if (!brk && !ps->arg_checked[kar]) {
169 fprintf (SUMA_STDERR,
170 "Error SurfMatch: Option %s not understood\n", argv[kar]);
171 suggest_best_prog_option(argv[0], argv[kar]);
172 exit (1);
173 } else {
174 brk = NOPE;
175 kar ++;
176 }
177 }
178
179 if (!Opt->out_prefix) {
180 Opt->out_prefix = SUMA_copy_string("SurfMatch.gii");
181 THD_force_ok_overwrite(1) ;
182 }
183
184 if (!Opt->s) {
185 Opt->s = SUMA_copy_string("shft");
186 }
187 SUMA_RETURN(Opt);
188 }
189
main(int argc,char * argv[])190 int main (int argc,char *argv[])
191 {/* Main */
192 static char FuncName[]={"SurfMatch"};
193 SUMA_GENERIC_PROG_OPTIONS_STRUCT *Opt;
194 SUMA_GENERIC_ARGV_PARSE *ps=NULL;
195 SUMA_SurfSpecFile *Spec = NULL;
196 int N_Spec=0, N_inmask;
197 byte *cmask=NULL;
198 SUMA_SurfaceObject *SO = NULL, *SOr=NULL;
199 SUMA_Boolean LocalHead = NOPE;
200
201 SUMA_STANDALONE_INIT;
202 SUMA_mainENTRY;
203
204 /* Allocate space for DO structure */
205 SUMAg_DOv = SUMA_Alloc_DisplayObject_Struct (SUMA_MAX_DISPLAYABLE_OBJECTS);
206 ps = SUMA_Parse_IO_Args(argc, argv, "-i;-t;-spec;-s;-sv;");
207
208 if (argc < 2) {
209 usage_SurfMatch(ps, 0);
210 exit (1);
211 }
212
213 Opt = SUMA_SurfMatch_ParseInput (argv, argc, ps);
214
215 if (Opt->debug > 2) LocalHead = YUP;
216
217 /* check on inputs */
218 if (ps->s_N_surfnames + ps->i_N_surfnames + ps->t_N_surfnames != 2) {
219 SUMA_S_Err("Must have two surfaces");
220 exit(1);
221 }
222
223 Spec = SUMA_IO_args_2_spec(ps, &N_Spec);
224 if (N_Spec == 0) {
225 SUMA_S_Err("No surfaces found.");
226 exit(1);
227 }
228 if (N_Spec != 1) {
229 SUMA_S_Err("Multiple spec at input.");
230 exit(1);
231 }
232
233 SOr = SUMA_Load_Spec_Surf_with_Metrics(Spec, 0, ps->sv[0], 1);
234 if (!SOr) {
235 fprintf (SUMA_STDERR,"Error %s:\n"
236 "Failed to find surface\n"
237 "in spec file. \n",
238 FuncName );
239 exit(1);
240
241 }
242
243 if (Opt->efrac>0.0) {
244 SUMA_SurfaceObject *SOrr=NULL;
245 if (!(SOrr = SUMA_Mesh_Resample_nodes(SOr, Opt->efrac))) {
246 SUMA_S_Errv("Failed to resample initial mesh at %f\n",Opt->efrac);
247 exit(1);
248 }
249 SUMA_Free_Surface_Object(SOr); SOr=SOrr; SOrr=NULL;
250 SUMA_SurfaceMetrics_eng(SOr, "EdgeList|MemberFace", NULL, 0,
251 SUMAg_CF->DsetList);
252 if (!SOr->Label && !(SUMA_SurfaceFileName(SOr, NOPE))) {
253 SOr->Label = SUMA_copy_string("Le_Remaille");
254 }
255 }
256
257 SO = SUMA_Load_Spec_Surf_with_Metrics(Spec, 1, ps->sv[0], 1);
258
259 if (Opt->flt1 != 1.0) {
260 SUMA_LHv("Masking out nodes deeper than %f mm", Opt->flt1);
261 N_inmask = SUMA_NodeDepth(SO->NodeList, SO->N_Node, prjdir, NULL,
262 Opt->flt1, &cmask, NULL);
263 } else {
264 N_inmask = SO->N_Node;
265 }
266
267 SUMA_S_Notev("Have Reference %s %d nodes, input %s, %d nodes (%d in mask)\n",
268 SOr->Label, SOr->N_Node, SO->Label, SO->N_Node, N_inmask);
269 if (Opt->b1) {
270 Opt->s = SUMA_append_replace_string(Opt->s,"City", " ; ", 1);
271 }
272 SUMA_AlignCoords(SO->NodeList, SO->N_Node, cmask, 1, SOr, Opt->s);
273
274 /* write surface */
275 if (!SUMA_Save_Surface_Object_Wrap (Opt->out_prefix, NULL, SO,
276 SUMA_FT_NOT_SPECIFIED, SUMA_FF_NOT_SPECIFIED,
277 NULL)) {
278 SUMA_S_Err("Failed to write surface of whole head");
279 exit (1);
280 }
281
282 if (SOr) SUMA_Free_Surface_Object(SOr); SOr = NULL;
283 if (SO) SUMA_Free_Surface_Object(SO); SO = NULL;
284
285 if (cmask) SUMA_free(cmask); cmask=NULL;
286 if (ps) SUMA_FreeGenericArgParse(ps); ps = NULL;
287 if (N_Spec) {
288 int k=0;
289 for (k=0; k<N_Spec; ++k) {
290 if (!SUMA_FreeSpecFields(&(Spec[k]))) {
291 SUMA_S_Err("Failed to free spec fields");
292 }
293 }
294 SUMA_free(Spec); Spec = NULL; N_Spec = 0;
295 }
296 if (Opt) Opt = SUMA_Free_Generic_Prog_Options_Struct(Opt);
297 if (!SUMA_Free_CommonFields(SUMAg_CF))
298 SUMA_error_message(FuncName,"SUMAg_CF Cleanup Failed!",1);
299 exit(0);
300
301 }
302