/usr/include/teem/pull.h is in libteem-dev 1.12.0~20160122-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 813 814 815 816 817 818 819 820 821 822 823 824 825 826 827 828 829 830 831 832 833 834 835 836 837 838 839 840 841 842 843 844 845 846 847 848 849 850 851 852 853 854 855 856 857 858 859 860 861 862 863 864 865 866 867 868 869 870 871 872 873 874 875 876 877 878 879 880 881 882 883 884 885 886 887 888 889 890 891 892 893 894 895 896 897 898 899 900 901 902 903 904 905 906 907 908 909 910 911 912 913 914 915 916 917 918 919 920 921 922 923 924 925 926 927 928 929 930 931 932 933 934 935 936 937 938 939 940 941 942 943 944 945 946 947 948 949 950 951 952 953 954 955 956 957 958 959 960 961 962 963 964 965 966 967 968 969 970 971 972 973 974 975 976 977 978 979 980 981 982 983 984 985 986 987 988 989 990 991 992 993 994 995 996 997 998 999 1000 1001 1002 1003 1004 1005 1006 1007 1008 1009 1010 1011 1012 1013 1014 1015 1016 1017 1018 1019 1020 1021 1022 1023 1024 1025 1026 1027 1028 1029 1030 1031 1032 1033 1034 1035 1036 1037 1038 1039 1040 1041 1042 1043 1044 1045 1046 1047 1048 1049 1050 1051 1052 1053 1054 1055 1056 1057 1058 1059 1060 1061 1062 1063 1064 1065 1066 1067 1068 1069 1070 1071 1072 1073 1074 1075 1076 1077 1078 1079 1080 1081 1082 1083 1084 1085 1086 1087 1088 1089 1090 1091 1092 1093 1094 1095 1096 1097 1098 1099 1100 1101 1102 1103 1104 1105 1106 1107 1108 1109 1110 1111 1112 1113 1114 1115 1116 1117 1118 1119 1120 1121 1122 1123 1124 1125 1126 1127 1128 1129 1130 1131 1132 1133 1134 1135 1136 1137 1138 1139 1140 1141 1142 1143 1144 1145 1146 1147 1148 1149 1150 1151 1152 1153 1154 1155 1156 1157 1158 1159 1160 1161 1162 1163 1164 1165 1166 1167 1168 1169 1170 1171 1172 1173 1174 1175 1176 1177 1178 1179 1180 1181 1182 1183 1184 1185 1186 1187 1188 1189 1190 1191 1192 1193 1194 1195 1196 1197 1198 1199 1200 1201 1202 1203 1204 1205 1206 1207 1208 1209 1210 1211 1212 1213 1214 1215 1216 1217 1218 1219 1220 1221 1222 1223 1224 1225 1226 1227 1228 1229 1230 1231 1232 1233 1234 1235 1236 | /*
Teem: Tools to process and visualize scientific data and images .
Copyright (C) 2013, 2012, 2011, 2010, 2009 University of Chicago
Copyright (C) 2008, 2007, 2006, 2005 Gordon Kindlmann
Copyright (C) 2004, 2003, 2002, 2001, 2000, 1999, 1998 University of Utah
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public License
(LGPL) as published by the Free Software Foundation; either
version 2.1 of the License, or (at your option) any later version.
The terms of redistributing and/or modifying this software also
include exceptions to the LGPL that facilitate static linking.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public License
along with this library; if not, write to Free Software Foundation, Inc.,
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
*/
#ifndef PULL_HAS_BEEN_INCLUDED
#define PULL_HAS_BEEN_INCLUDED
#include <teem/air.h>
#include <teem/hest.h>
#include <teem/biff.h>
#include <teem/nrrd.h>
#include <teem/ell.h>
#include <teem/gage.h>
#include <teem/limn.h>
#include <teem/ten.h>
/*
** This library was created to implement the research and methods of:
**
** Gordon L. Kindlmann, Ra{\'u}l San Jos{\'e} Est{\'e}par,
** Stephen M. Smith, Carl-Fredrik Westin.
** Sampling and Visualizing Creases with Scale-Space Particles.
** IEEE Trans. on Visualization and Computer Graphics,
** 15(6):1415-1424 (2009)
**
** Further information and usage examples:
** http://people.cs.uchicago.edu/~glk/ssp/
**
** The library is still being actively developed to support research on
** particle systems for general feature sampling. At some point, for
** example, it should subsume the "push" library for glyph packing in
** tensor fields.
*/
#if defined(_WIN32) && !defined(__CYGWIN__) && !defined(TEEM_STATIC)
# if defined(TEEM_BUILD) || defined(pull_EXPORTS) || defined(teem_EXPORTS)
# define PULL_EXPORT extern __declspec(dllexport)
# else
# define PULL_EXPORT extern __declspec(dllimport)
# endif
#else /* TEEM_STATIC || UNIX */
# define PULL_EXPORT extern
#endif
#ifdef __cplusplus
extern "C" {
#endif
#define PULL pullBiffKey
#define PULL_THREAD_MAXNUM 512
#define PULL_VOLUME_MAXNUM 4
#define PULL_POINT_NEIGH_INCR 16
#define PULL_BIN_MAXNUM 40000000 /* sanity check on max number bins */
#define PULL_PHIST 0 /* can compile history of positions,
with tuples of length PULL_PHIST_NUM */
#define PULL_PHIST_NUM 6 /* doubles saved per history point:
0 1 2 3 4 5
X Y Z Scl cond val
where Scl is just scale coordinate,
cond is from pullCond* enum,
and val is anything the caller wanted to
remember at that point */
#define PULL_HINTER 0
#define PULL_TANCOVAR 1
/*
******** pullInfo enum
**
** all the things that might be *learned* about the local neighborhood
** that are used as ingredients in the computation of particle motion.
** This info was originally learned only from gage, but now (according
** to value of pullSource) can come from other kinds of information.
**
** There are multiple scalars (and associated) derivatives that can
** be used for dynamics:
** - Inside: just for nudging things to stay inside a mask
** - Height: value for computer-vision-y features of ridges, valleys,
** and edges. Setting pullInfoHeight as a constraint does valley
** sampling (flip the sign to get ridges), based on the various
** "tangents" Setting pullInfoHeightLaplacian as a constraint
* does zero-crossing edge detection.
** - Isovalue: just for implicit surfaces f=0
** - Strength: some measure of feature strength, with the assumption
** that it can't be analytically differentiated in space or scale.
*/
enum {
pullInfoUnknown, /* 0 */
pullInfoTensor, /* 1: [7] tensor here */
pullInfoTensorInverse, /* 2: [7] inverse of tensor here */
pullInfoHessian, /* 3: [9] hessian used for force distortion */
pullInfoInside, /* 4: [1] containment scalar */
pullInfoInsideGradient, /* 5: [3] containment vector */
pullInfoHeight, /* 6: [1] for gravity, and edge and crease
feature detection */
pullInfoHeightGradient, /* 7: [3] */
pullInfoHeightHessian, /* 8: [9] */
pullInfoHeightLaplacian, /* 9: [1] for zero-crossing edge detection */
pullInfoSeedPreThresh, /* 10: [1] scalar for pre-thresholding seeding,
so that points can be quickly eliminated
(e.g. prior to constraint satisfaction) */
pullInfoSeedThresh, /* 11: [1] scalar for thresholding seeding */
pullInfoLiveThresh, /* 12: [1] scalar for thresholding extant
particles, AND for future additions from
population control */
pullInfoLiveThresh2, /* 13: [1] another pullInfoLiveThresh */
pullInfoLiveThresh3, /* 14: [1] yet another pullInfoLiveThresh */
pullInfoTangent1, /* 15: [3] first tangent to motion allowed
for constraint satisfaction */
pullInfoTangent2, /* 16: [3] second tangent to motion allowed
for constraint satisfaction */
pullInfoNegativeTangent1, /* 17: [3] like the tangents, but with a negated
objective function */
pullInfoNegativeTangent2, /* 18: [3] second negative tangent */
pullInfoIsovalue, /* 19: [1] for isosurface extraction */
pullInfoIsovalueGradient, /* 20: [3] */
pullInfoIsovalueHessian, /* 21: [9] */
pullInfoStrength, /* 22: [1] */
pullInfoQuality, /* 23: [1] */
pullInfoLast
};
#define PULL_INFO_MAX 23
/*
********* pullProp* enum: the various properties of particles in the system
**
** These are things that are not learned from the image data, but are
** descriptions of a particle, its neighborhood of particles in the
** system, and the current state of system computation. As of revision
** 5080, these may refer to information *computed* from the per-particle
** info, but which may not itself be saved as a field in pullPoint.
**
** consider adding: dot between normalized directions of force and movmt
*/
enum {
pullPropUnknown, /* 0: nobody knows */
pullPropIdtag, /* 1: [1] idtag (unsigned int) */
pullPropIdCC, /* 2: [1] idcc (unsigned int) */
pullPropEnergy, /* 3: [1] energy from last iteration */
pullPropStepEnergy, /* 4: [1] step size for minimizing energy */
pullPropStepConstr, /* 5: [1] step size for constraint satis. */
pullPropStuck, /* 6: [1] how many iters its been stuck */
pullPropPosition, /* 7: [4] position */
pullPropForce, /* 8: [4] force accumulation */
pullPropNeighDistMean, /* 9: [1] "mean distance" to neighbors */
pullPropScale, /* 10: [1] scale position */
pullPropNeighCovar, /* 11: [10] unique coeffs of covariance matrix
of offsets to all interacting neighbors,
in rs-normalized space, updated only during
pullProcessModeNeighLearn. The layout is:
0:xx 1:xy 2:xz 3:xs
. 4:yy 5:yz 6:ys
. 7:zz 8:zs
. 9:ss */
pullPropNeighCovar7Ten, /* 12: [7] spatial 3x3 submatrix of covariance,
formatted as ten-compatible 7-tensor */
pullPropNeighTanCovar, /* 13: [6] covariance of "tangents" of neighbors,
(e.g. pullInfoTangent1 for crease surfaces)
including point itself */
pullPropNeighInterNum, /* 14: [1] # neighbors last iter */
pullPropNeighCovarTrace, /* 15: [1] trace of NeighCovar */
pullPropNeighCovarDet, /* 16: [1] det of NeighCovar */
pullPropStability, /* 17: [1] some measure of NeighCovar */
pullPropLast
};
#define PULL_PROP_MAX 17
/*
** the components of a point's status that are set as a bitflag
** in point->status
*/
enum {
pullStatusUnknown, /* 0: nobody knows */
pullStatusStuck, /* 1: couldn't move to decrease energy */
#define PULL_STATUS_STUCK_BIT (1<< 1)
pullStatusNewbie, /* 2: not binned, testing if the system
would be better with me in it */
#define PULL_STATUS_NEWBIE_BIT (1<< 2)
pullStatusNixMe, /* 3: nix me at the *end* of this iter,
and don't look at me for energy
during this iteration */
#define PULL_STATUS_NIXME_BIT (1<< 3)
pullStatusEdge, /* 4: at the spatial edge of one of the
volumes: gage had to invent values for
some samples in the kernel support */
#define PULL_STATUS_EDGE_BIT (1<< 4)
pullStatusLast
};
/*
******** pullInterType* enum
**
** the different types of scale-space interaction that can happen
** in scale-space. The descriptions here overlook the normalization
** by radiusScale and radiusSpace
*/
enum {
pullInterTypeUnknown, /* 0 */
pullInterTypeJustR, /* 1: phi(r,s) = phi_r(r) */
pullInterTypeUnivariate, /* 2: phi(r,s) = phi_r(u); u = sqrt(r*r+s*s) */
pullInterTypeSeparable, /* 3: phi(r,s) = phi_r(r)*phi_s(s) */
pullInterTypeAdditive, /* 4: phi(r,s) = beta*phi_r(r)*win(s)
+ (1-beta)*win(r)*phi_s(s) */
pullInterTypeLast
};
#define PULL_INTER_TYPE_MAX 4
/*
******** pullEnergyType* enum
**
** the different shapes of potential energy profiles that can be used
*/
enum {
pullEnergyTypeUnknown, /* 0 */
pullEnergyTypeSpring, /* 1 */
pullEnergyTypeGauss, /* 2 */
pullEnergyTypeBspln, /* 3 */
pullEnergyTypeButterworth, /* 4 */
pullEnergyTypeCotan, /* 5 */
pullEnergyTypeCubic, /* 6 */
pullEnergyTypeQuartic, /* 7 */
pullEnergyTypeCubicWell, /* 8 */
pullEnergyTypeBetterCubicWell, /* 9 */
pullEnergyTypeQuarticWell, /* 10 */
pullEnergyTypeHepticWell, /* 11 */
pullEnergyTypeZero, /* 12 */
pullEnergyTypeButterworthParabola, /* 13 */
pullEnergyTypeLast
};
#define PULL_ENERGY_TYPE_MAX 13
#define PULL_ENERGY_PARM_NUM 3
enum {
pullProcessModeUnknown, /* 0 */
pullProcessModeDescent, /* 1 */
pullProcessModeNeighLearn, /* 2 */
pullProcessModeAdding, /* 3 */
pullProcessModeNixing, /* 4 */
pullProcessModeLast
};
#define PULL_PROCESS_MODE_MAX 4
/*
** the conditions under which a point may find itself at some position
*/
enum {
pullCondUnknown, /* 0 */
pullCondOld, /* 1 */
pullCondConstraintSatA, /* 2 */
pullCondConstraintSatB, /* 3 */
pullCondEnergyTry, /* 4 */
pullCondConstraintFail, /* 5 */
pullCondConstraintSuccess, /* 6 */
pullCondEnergyBad, /* 7 */
pullCondNew, /* 8 */
pullCondLast
};
/*
** the places that "info" can be learned from. Originally this was
** strictly from gage and no where else; it can be handy to allow it
** to originate from different places as well, but still flow through
** the channels now organized around pullInfo
*/
enum {
pullSourceUnknown, /* 0 */
pullSourceGage, /* 1: measured from gage */
pullSourceProp, /* 2: copied from a pullProp */
pullSourceLast
};
#define PULL_SOURCE_MAX 2
/*
** the different kinds of computations and entities that one can
** count, for book-keeping and meta-optimization purposes
*/
enum {
pullCountUnknown, /* 0 */
pullCountDescent, /* 1 */
pullCountTestStep, /* 2 */
pullCountEnergyFromImage, /* 3 */
pullCountForceFromImage, /* 4 */
pullCountEnergyFromPoints, /* 5 */
pullCountForceFromPoints, /* 6 */
pullCountProbe, /* 7 */
pullCountConstraintSatisfy, /* 8 */
pullCountAdding, /* 9 */
pullCountNixing, /* 10 */
pullCountPointsStuck, /* 11 */
pullCountPoints, /* 12 */
pullCountCC, /* 13 */
pullCountIteration, /* 14 */
pullCountLast
};
#define PULL_COUNT_MAX 14
/*
** reasons for pullTraceSet to stop (or go nowhere)
*/
enum {
pullTraceStopUnknown, /* 0 */
pullTraceStopSpeeding, /* 1 */
pullTraceStopConstrFail, /* 2 */
pullTraceStopBounds, /* 3 */
pullTraceStopLength, /* 4 */
pullTraceStopStub, /* 5 */
pullTraceStopLast
};
#define PULL_TRACE_STOP_MAX 5
/*
** Defines how par-particle information can be learned. This is
** typically via measurements in the image by gage, but other sources
** are possible (as indicated by the source field).
**
** There is a basic design decision in whether to make pullInfos the
** most general representation of information (including referring to
** pullProps), or, whether pullProps should be the general thing,
** which can then refer to some pullInfo. In the long run, these
** should probably be merged. In the short term, there is better
** infrastructure for representing and parsing pullInfos, so that has
** been leveraged to include other things as well.
*/
typedef struct pullInfoSpec_t {
/* ------ INPUT ------ */
int info, /* from the pullInfo* enum: what is the
"info" that this infospec defines */
source; /* from the pullSource* enum: where does
this information come from */
char *volName; /* volume name */
int item, /* which gage item (for pullSourceGage) */
prop; /* which pull property (for pullSourceProp) */
double scale, /* scaling factor (including sign) */
zero; /* for height and inside: where is zero,
for seedThresh, threshold value */
int constraint; /* (for scalar items) minimizing this
is a constraint to enforce per-point
per-iteration, not merely a contribution
to the point's energy */
/* ------ INTERNAL ------ */
unsigned int volIdx; /* which volume (for pullSourceGage) */
} pullInfoSpec;
/*
******** pullPoint
**
*/
typedef struct pullPoint_t {
unsigned int idtag, /* unique point ID */
idCC; /* id for connected component analysis */
struct pullPoint_t **neighPoint; /* list of neighboring points */
unsigned int neighPointNum;
airArray *neighPointArr; /* airArray around neighPoint and neighNum
(no callbacks used here) */
double neighDistMean; /* average of distance to neighboring
points with whom this point interacted,
in rs-normalized space */
float neighCovar[10], /* unique coeffs in 4x4 covariance matrix of
neighbors with whom this point interacted */
#if PULL_TANCOVAR
neighTanCovar[6], /* covariance of "tangent" info of neighbors */
#endif
stability; /* the scalar stability measure */
unsigned int neighInterNum, /* number of particles with which I had some
non-zero interaction on last iteration */
stuckIterNum; /* how many iterations I've been stuck */
#if PULL_PHIST
double *phist; /* history of positions tried in the last iter,
in sets of 5 doubles: (x,y,z,t,info) */
unsigned int phistNum; /* number of positions stored */
airArray *phistArr; /* airArray around phist */
#endif
int status; /* bit-flag of status info */
double pos[4], /* position in space and scale */
energy, /* energy accumulator for this iteration */
force[4], /* force accumulator for this iteration */
stepEnergy, /* step size for energy minimization */
stepConstr, /* step size for constraint satisfaction;
HEY: this doens't seem to be really used? */
info[1]; /* all information learned from gage that matters
for particle dynamics. This is sneakily
allocated for *more*, depending on needs,
so this MUST be last field */
} pullPoint;
/*
******** pullBin
**
** the data structure for doing spatial binning.
*/
typedef struct pullBin_t {
pullPoint **point; /* dyn. alloc. array of point pointers */
unsigned int pointNum; /* # of points in this bin */
airArray *pointArr; /* airArray around point and pointNum
(no callbacks used here) */
struct pullBin_t **neighBin; /* NULL-terminated list of all
neighboring bins, including myself */
} pullBin;
/*
******** pullEnergy
**
** the functions which determine inter-point forces
**
** NOTE: the eval() function probably does NOT check to see it was passed
** a non-NULL pointer into which to store the derivative of energy ("denr")
**
** Thu Apr 10 12:40:08 EDT 2008: nixed the "support" function, since it
** was annoying to deal with variable support potentials. Now everything
** cuts off at dist=1. You can still use the parm vector to change the
** shape inside the support.
*/
typedef struct {
char name[AIR_STRLEN_SMALL];
unsigned int parmNum;
double (*well)(double *wx, const double parm[PULL_ENERGY_PARM_NUM]);
double (*eval)(double *denr, double dist,
const double parm[PULL_ENERGY_PARM_NUM]);
} pullEnergy;
typedef struct {
const pullEnergy *energy;
double parm[PULL_ENERGY_PARM_NUM];
} pullEnergySpec;
/*
** In the interests of simplicity (and with the cost of some redundancy),
** this is going to copied per-task, which is why it contains the gageContext
** The idea is that the first of these is somehow set up by the user
** or something, and the rest of them are created within pull per-task.
*/
typedef struct {
int verbose; /* blah blah blah */
char *name; /* how the volume will be identified
(like its a variable name) */
const gageKind *kind;
const Nrrd *ninSingle; /* don't own */
const Nrrd *const *ninScale; /* don't own;
NOTE: only one of ninSingle and ninScale
can be non-NULL */
unsigned int scaleNum; /* number of scale-space samples (volumes) */
double *scalePos; /* location of all samples in scale */
int scaleDerivNorm; /* normalize derivatives based on scale */
double scaleDerivNormBias; /* bias on derivative normalization by scale */
NrrdKernelSpec *ksp00, /* for sampling tensor field */
*ksp11, /* for gradient of mask, other 1st derivs */
*ksp22, /* for 2nd derivatives */
*kspSS; /* for reconstructing from scale-space
samples */
gageQuery pullValQuery; /* if this is a pullValGageKind volume,
then we don't have a real gageContext,
and we have to manage our own query */
gageContext *gctx; /* do own, and set based on info here */
gagePerVolume *gpvl, /* stupid gage API . . . */
**gpvlSS; /* stupid gage API . . . */
int seedOnly, /* volume only required for seeding, for
either pullInfoSeedThresh or
pullInfoSeedPreThresh */
forSeedPreThresh; /* we learn pullInfoSeedPreThresh from this */
} pullVolume;
/*
******** pullTask
**
** The information specific for a thread.
*/
typedef struct pullTask_t {
struct pullContext_t
*pctx; /* parent's context; not const because the
tasks assign themselves bins to do work */
pullVolume
*vol[PULL_VOLUME_MAXNUM]; /* volumes copied from parent */
const double
*ans[PULL_INFO_MAX+1]; /* answer *pointers* for all possible infos,
pointing into per-task per-volume gctxs
(or into above per-task pullValAnswer),
OR: NULL if that info is not being used */
int processMode, /* what kind of point processing is being
done by this task right now */
probeSeedPreThreshOnly; /* hack-ish flag to communicate to pullProbe
that we only care about SeedPreThresh */
airThread *thread; /* my thread */
unsigned int threadIdx; /* which thread am I */
airRandMTState *rng; /* state for my RNG */
pullPoint *pointBuffer, /* place for copying point into during
strength ascent computation; can't be
statically allocated because pullPoint
size is known only at run-time */
**neighPoint; /* array of point pointers, either all
possible points from neighbor bins, or
last learned interacting neighbors */
pullPoint **addPoint; /* points to add before next iter */
unsigned int addPointNum; /* # of points to add */
airArray *addPointArr; /* airArray around addPoint, addPointNum */
pullPoint **nixPoint; /* points to nix before next iter */
unsigned int nixPointNum; /* # of points to nix */
airArray *nixPointArr; /* airArray around nixPoint, nixPointNum */
void *returnPtr; /* for airThreadJoin */
unsigned int stuckNum; /* # stuck particles seen by this task */
} pullTask;
/*
******** pullInitMethod* enum
**
** the different ways pull can be initialized
*/
enum {
pullInitMethodUnknown, /* 0 */
pullInitMethodRandom, /* 1 */
pullInitMethodHalton, /* 2 */
pullInitMethodPointPerVoxel, /* 3 */
pullInitMethodGivenPos, /* 4 */
pullInitMethodLast
};
#define PULL_INIT_METHOD_MAX 4
/*
******** pullInitParm
**
** none of this is directly user-set; set with pullInit*Set function
** (note that there is no pullInit* enum; these values are too diverse)
*/
typedef struct {
int method; /* from pullInitMethod* enum */
int liveThreshUse, /* use the liveThresh info as a criterion
for seeding */
unequalShapesAllow; /* when taking in volumes, allow their shapes
to be unuequal. Some confusing usage problems
are due to using differently shaped volumes */
double jitter; /* w/ PointPerVoxel,
how much to jitter index space positions */
unsigned int numInitial, /* w/ Random OR Halton, # points to start with */
haltonStartIndex, /* w/ Halton, first index to use */
samplesAlongScaleNum, /* w/ PointPerVoxel,
# of samples along scale (distributed
uniformly in scale's *index* space*/
ppvZRange[2]; /* (hack to permit seeding only in part of
volume, when initialization is painfully
the main bottleneck) w/ PointPerVoxel,
range of indices along Z to do seeding
by pointPerVoxel, or, {1,0} to do the
whole volume as normal */
int pointPerVoxel; /* w/ PointPerVoxel,
if this (ppv) is > 0, then use
ppv points per voxel. If ppv < 0, then jitter
point point every -ppv'th voxel
(so ppv=-1 is same as ppv=1) */
const Nrrd *npos; /* positions (4xN array) to start with */
} pullInitParm;
/*
******** pullIterParm* enum
**
** parameters related to iterations and their periods
*/
enum {
pullIterParmUnknown,
/* if non-zero, minimum number of iterations for whole system. */
pullIterParmMin,
/* if non-zero, max number of iterations for whole system.
if zero: no explicit limit on the number of iterations */
pullIterParmMax,
/* if non-zero, max number of iterations we allow something to be
continuously stuck before nixing it */
pullIterParmStuckMax,
/* if non-zero, max number of iterations for enforcing each constraint */
pullIterParmConstraintMax,
/* how many intervals to wait between attemps at population control,
or, 0 to say: "no pop cntl" */
pullIterParmPopCntlPeriod,
/* how many iterations for which to run descent on tentative new
points during population control, so that they end up at a good
location, at which we can meaningfully test whether adding the
point will reducing system energy */
pullIterParmAddDescent,
/* periodicity with which to call the pullContext->iter_cb */
pullIterParmCallback,
/* if non-zero, interval between iters at which output snapshots are saved */
pullIterParmSnap,
/* the half-life of energyIncreasePermit, in terms of iterations, or
0 if no such decay is wanted */
pullIterParmEnergyIncreasePermitHalfLife,
pullIterParmLast
};
typedef struct {
unsigned int min, max,
popCntlPeriod,
addDescent,
constraintMax,
stuckMax,
callback,
snap,
energyIncreasePermitHalfLife;
} pullIterParm;
/*
******** pullSysParm* enum
**
** various continuous parameters. It should be understood that the number
** of these is a reflection of the experimentation and exploration that
** went into the creation of these particles systems, rather than a need
** for onerous parameter tweaking in order to get something useful done.
** Except for alpha, beta, and gamma, these have reasonable defaults.
*/
enum {
pullSysParmUnknown,
/* balance between particle-image energy E_i and inter-particle energy E_ij,
the most important parameter in the governing equation of the system.
alpha = 0: only particle-image; alpha = 1: only inter-particle */
pullSysParmAlpha,
/* when using pullInterAdditive ("Phi_2") inter-particle energy, beta
sets the balance between spatial repulsion and scale attraction.
(if not using this energy, this is moot)
beta = 0: only spatial repulsion; beta = 1: only scale attraction */
pullSysParmBeta,
/* when energyFromStrength is non-zero: scaling factor on energy
from strength */
pullSysParmGamma,
/* when learning a suitable gamma from data (via pullGammaLearn)
in the context of separable energy functions, how much to
scale the learned gamma. Making this greater than 1.0 helps
let the energy from strength overpower the slight repulsion
along scale that might exist by the separable phi construction. */
pullSysParmSeparableGammaLearnRescale,
/* to be more selective for pullInfoSeedThresh and
pullInfoLiveThresh at higher scales, set theta > 0, and the
effective threshold will be base threshold + theta*scale.
HOWEVER, the way this is implemented is a hack:
the probed strength value is decremented by theta*scale */
pullSysParmTheta,
/* initial (time) step for dynamics */
pullSysParmStepInitial,
/* radius/scaling of inter-particle interactions in the spatial domain */
pullSysParmRadiusSpace,
/* radius/scaling of inter-particle interactions in the scale domain */
pullSysParmRadiusScale,
/* spatial width of bin, as multiple of pullSysParmRadiusSpace (the
width along scale is set to pullSysParmRadiusScale). Can't be
lower than 1, but may be usefully set greater that 1 to reduce
the total number of bins, especially if caching neighbor lists */
pullSysParmBinWidthSpace,
/* probability that we find the true neighbors of the particle, as
opposed to using a cached list */
pullSysParmNeighborTrueProb,
/* probability that we do image probing to find out what's really going on */
pullSysParmProbeProb,
/* (>= 1.0) how much to opportunistically scale up step size (for
energy minimization) with every iteration */
pullSysParmOpporStepScale,
/* (< 1.0) when energy goes up instead of down, or when constraint
satisfaction seems to be going the wrong way, how to scale (down)
step size */
pullSysParmBackStepScale,
/* pseudo-convergence threshold that controls when population control is
activated (has to be higher than (less strict) energyDecreaseMin */
pullSysParmEnergyDecreasePopCntlMin,
/* epsilon amount by which its okay for particle energy to increase,
in the context of gradient descent */
pullSysParmEnergyIncreasePermit,
/* convergence threshold: stop when fractional improvement
(decrease) in total system energy dips below this */
pullSysParmEnergyDecreaseMin,
/* convergence threshold for constraint satisfaction: finished if
stepsize goes below this times pctx->voxelSizeSpace */
pullSysParmConstraintStepMin,
/* spring constant on bbox wall */
pullSysParmWall,
/* when doing population control nixing, don't nix a particle if this
fraction of its neighbors have already been nixed (Section 3.5 of
paper implies that this value should be 0.5; lower values also work) */
pullSysParmFracNeighNixedMax,
pullSysParmLast
};
typedef struct {
double alpha, beta, gamma, separableGammaLearnRescale, theta, wall,
radiusSpace, radiusScale, binWidthSpace,
neighborTrueProb, probeProb,
stepInitial, opporStepScale, backStepScale, constraintStepMin,
energyDecreaseMin,
energyDecreasePopCntlMin,
energyIncreasePermit,
fracNeighNixedMax;
} pullSysParm;
/*
******** pullConstraintFail* enum
**
** the various ways constriant satisfaction can fail
*/
enum {
pullConstraintFailUnknown, /* 0 */
pullConstraintFailHessZeroA, /* 1 */
pullConstraintFailHessZeroB, /* 2 */
pullConstraintFailProjGradZeroA, /* 3 */
pullConstraintFailProjGradZeroB, /* 4 */
pullConstraintFailIterMaxed, /* 5 */
pullConstraintFailTravel, /* 6 */
pullConstraintFailLast
};
#define PULL_CONSTRAINT_FAIL_MAX 6
/*
******** pullFlag* enum
**
** the various booleans
*/
enum {
pullFlagUnknown,
/* permute points during rebinning between iters, to randomize their
ordering within their bin (bins are still processed in scanline
order) */
pullFlagPermuteOnRebin,
/* when alpha is exactly zero, probably with the purpose of migrating
particles along scale towards the scale of maximal strength while
avoiding all inter-particle interaction, don't try any population
control */
pullFlagNoPopCntlWithZeroAlpha,
/* when learning gamma via Eq. 26 of the paper, also use beta to
more accurately reflect the 2nd derivative of energy wrt scale */
pullFlagUseBetaForGammaLearn,
/* whether or not to deny adding points to bins where there are
close points already */
pullFlagRestrictiveAddToBins,
/* if non-zero, strength is a particle-image energy term that is
minimized by motion along scale, which in turn requires extra
probing to determine the strength gradient along scale. */
pullFlagEnergyFromStrength,
/* if non-zero, nix points that got near enough to the volume edge
that gage had to invent values for the kernel support */
pullFlagNixAtVolumeEdgeSpace,
/* if non-zero, during initialization, try constraint satisfaction
(if there is a constraint) before testing whether the seedThresh
is met. Doing the constraint will take longer, but a point is
more likely to meet a threshold based on feature strength */
pullFlagConstraintBeforeSeedThresh,
/* do no adding during population control */
pullFlagNoAdd,
/* use the targetDim-based "enough" heuristic to guess whether
adding a point could usefully reduce system energy. On by
default; turn this off when using a large-support energy that
involves more neighbors than the single-neighbor-deep energies
that are normally used (like cwell:0.66,x or qwell:0.64) */
pullFlagPopCntlEnoughTest,
/* if this is true, then the convergence test ignores whether or
not there have been adds or nixes with the last round of pop cntl;
otherwise (the default, for backwards compatibility), any adds or
nixes would prevent convergence */
pullFlagConvergenceIgnoresPopCntl,
/* no binning: all particles can potentially interact (for debugging) */
pullFlagBinSingle,
/* whether to allow codimension-3 (point) constraint manifolds.
Typical uses of constraints are for extracting lines and surfaces */
pullFlagAllowCodimension3Constraints,
/* what we call scale is not sigma but rather the tau of gage */
pullFlagScaleIsTau,
/* pullStart should skip initializing the points */
pullFlagStartSkipsPoints,
/* constrain the third world-space coordinate ("z") to be zero, at all
times, so that pull can be used to process 2D images */
pullFlagZeroZ,
pullFlagLast
};
typedef struct {
int permuteOnRebin,
noPopCntlWithZeroAlpha,
useBetaForGammaLearn,
restrictiveAddToBins,
energyFromStrength,
nixAtVolumeEdgeSpace,
constraintBeforeSeedThresh,
popCntlEnoughTest,
convergenceIgnoresPopCntl,
noAdd,
binSingle,
allowCodimension3Constraints,
scaleIsTau,
startSkipsPoints,
zeroZ;
} pullFlag;
/*
******** pullContext
**
** everything for doing one computation
**
*/
typedef struct pullContext_t {
/* INPUT ----------------------------- */
pullInitParm initParm; /* parms for initialization, set with
the pullInit*Set() functions */
pullIterParm iterParm; /* parms about iterations and periods, set
with pullIterParmSet() */
pullSysParm sysParm; /* continuous parameters for system,
set with pullSysParmSet() */
pullFlag flag; /* all flags, set with pullFlagSet() */
int verbose; /* verbosity level, set with
pullVerboseSet() */
unsigned int threadNum, /* number of threads to use, set with
pullThreadNumSet() */
rngSeed, /* seed value for random number generator,
NOT directly related to seed point
placement (as name might suggest),
set with pullRngSeedSet() */
progressBinMod; /* if non-zero, progress indication by
printing "." is given when the bin index
is a multiple of this; higher numbers
give less feedback, set with
pullProgressBinModSet() */
void (*iter_cb)(void *data_cb); /* callback to call from pullRun() every
iterParm.callback iterations. This and
data_cb are set w/ pullCallbackSet() */
void *data_cb; /* data to pass to callback */
pullVolume
*vol[PULL_VOLUME_MAXNUM]; /* the volumes we analyze (we DO OWN),
set by either pullVolumeSingleAdd()
or pullVolumeStackAdd() */
unsigned int volNum; /* actual length of vol[] used */
pullInfoSpec
*ispec[PULL_INFO_MAX+1]; /* info ii is in effect if ispec[ii] is
non-NULL (and we DO OWN ispec[ii]),
set by pullInfoSpecAdd() */
int interType; /* from the pullInterType* enum. This
and the energy specs below are set by
pullInterEnergySet() */
pullEnergySpec *energySpecR, /* starting point for radial potential
energy function, phi_r */
*energySpecS, /* second energy potential function, for
scale-space behavior, phi_s */
*energySpecWin; /* function used to window phi_r along s,
and phi_s along r, for use with
pullInterTypeAdditive */
/* INTERNAL -------------------------- */
unsigned int haltonOffset; /* with pullInitMethodHalton, add this to
the index to sequence generation, to
account for the points previously
generated (which did not meet the
constraint satisfaction) */
double bboxMin[4], bboxMax[4]; /* scale-space bounding box of all volumes:
region over which binning is defined.
In 3-D space, the bbox is axis aligned,
even when the volume is not so aligned,
which means that some bins might be
under- or un- utilized, oh well.
bboxMin[3] and bboxMax[3] are the
bounds of the volume in *scale* (sigma),
not t, or tau */
unsigned int infoTotalLen, /* total length of the info buffers needed,
which determines size of allocated
binPoint */
infoIdx[PULL_INFO_MAX+1], /* index of answer within pullPoint->info */
idtagNext; /* next per-point igtag value */
int haveScale, /* non-zero iff one of the volumes is in
scale-space */
constraint, /* if non-zero, we have a constraint to
satisfy, and this is its info number */
constraintDim, /* dimension of *spatial* constraint
manifold we're working on; or
-1 if unknown/unset */
targetDim, /* dimension of total constraint manifold
which can be different than constraintDim
because of scale-space, and either
repulsive (+1) or attractive (+0)
behavior along scale; or
-1 if unknown/unset */
finished; /* used to signal all threads to return */
double maxDistSpace, /* max dist of point-point interaction in
the spatial axes.*/
maxDistScale, /* max dist of point-point interaction
along scale */
voxelSizeSpace, /* mean spatial voxel edge length, for
limiting travel distance for descent
and constraint satisfaction */
voxelSizeScale, /* mean voxel edge length in space, for
limiting travel (along scale) distance
during descent */
eipScale; /* how to scale energyIncreasePermit
at each iteration, in accordance with
energyIncreasePermitHalfLife */
pullBin *bin; /* volume of bins (see binsEdge, binNum) */
unsigned int binsEdge[4], /* # bins along each volume edge,
determined by maxEval and scale */
binNum, /* total # bins in grid */
binNextIdx; /* next bin of points to be processed,
we're done when binNextIdx == binNum */
unsigned int *tmpPointPerm; /* storing points during rebinning */
pullPoint **tmpPointPtr;
unsigned int tmpPointNum;
airThreadMutex *binMutex; /* mutex around bin, needed because bins
are the unit of work for the tasks */
pullTask **task; /* dynamically allocated array of tasks */
airThreadBarrier *iterBarrierA; /* barriers between iterations */
airThreadBarrier *iterBarrierB; /* barriers between iterations */
#if PULL_HINTER
Nrrd *nhinter; /* 2-D histogram of (r,s)-space relative
locations of interacting particles
(NOT thread safe) */
#endif
FILE *logAdd; /* text-file record of all the particles
that have been added
(NOT thread-safe) */
/* OUTPUT ---------------------------- */
double timeIteration, /* time needed for last (single) iter */
timeRun, /* total time spent in pullRun() */
energy; /* final energy of system */
unsigned int addNum, /* # prtls added by PopCntl in last iter */
nixNum, /* # prtls nixed by PopCntl in last iter */
stuckNum, /* # stuck particles in last iter */
pointNum, /* total # particles */
CCNum, /* # connected components */
iter, /* how many iterations were needed
(this is updated per iteration) */
/* HEY: this should really be per-task, to be thread-safe!! */
count[PULL_COUNT_MAX+1]; /* all possible kinds of counts */
} pullContext;
/*
******** pullTrace
*/
typedef struct {
double seedPos[4]; /* where was the seed point */
/* ------- output ------- */
Nrrd *nvert, /* locations of tract vertices */
*nstrn, /* if non-NULL, 1-D array of strengths */
*nvelo; /* 1-D list of velocities */
unsigned int seedIdx; /* which index in nvert is for seedpoint */
int whyStop[2], /* why backward/forward (0/1) tracing stopped
(from pullTraceStop* enum) */
whyNowhere; /* why trace never started (from pullTraceStop*) */
} pullTrace;
/*
******** pullTraceMulti
*/
typedef struct {
pullTrace **trace;
unsigned int traceNum;
airArray *traceArr;
} pullTraceMulti;
/*
******** pullPtrPtrUnion
**
** deal with "dereferencing type-punned pointer will
** break strict-aliasing rules"
*/
typedef union {
pullPoint ***points; /* address of array of point pointers */
void **v;
} pullPtrPtrUnion;
/* defaultsPull.c */
PULL_EXPORT const int pullPresent;
PULL_EXPORT const int pullPhistEnabled;
PULL_EXPORT const char *pullBiffKey;
/* initPull.c */
PULL_EXPORT int pullInitRandomSet(pullContext *pctx, unsigned int numInitial);
PULL_EXPORT int pullInitHaltonSet(pullContext *pctx, unsigned int numInitial,
unsigned int start);
PULL_EXPORT int pullInitPointPerVoxelSet(pullContext *pctx, int pointPerVoxel,
unsigned int zSlcMin,
unsigned int zSlcMax,
unsigned int alongScaleNum,
double jitter);
PULL_EXPORT int pullInitGivenPosSet(pullContext *pctx, const Nrrd *npos);
PULL_EXPORT int pullInitLiveThreshUseSet(pullContext *pctx, int liveThreshUse);
PULL_EXPORT int pullInitUnequalShapesAllowSet(pullContext *pctx, int allow);
/* parmPull.c */
PULL_EXPORT int pullIterParmSet(pullContext *pctx, int which,
unsigned int pval);
PULL_EXPORT int pullSysParmSet(pullContext *pctx, int which,
double pval);
PULL_EXPORT int pullFlagSet(pullContext *pctx, int which, int flag);
PULL_EXPORT int pullVerboseSet(pullContext *pctx, int verbose);
PULL_EXPORT int pullThreadNumSet(pullContext *pctx, unsigned int threadNum);
PULL_EXPORT int pullRngSeedSet(pullContext *pctx, unsigned int rngSeed);
PULL_EXPORT int pullProgressBinModSet(pullContext *pctx, unsigned int bmod);
PULL_EXPORT int pullCallbackSet(pullContext *pctx,
void (*iter_cb)(void *data_cb),
void *data_cb);
PULL_EXPORT int pullInterEnergySet(pullContext *pctx, int interType,
const pullEnergySpec *enspR,
const pullEnergySpec *enspS,
const pullEnergySpec *enspWin);
PULL_EXPORT int pullLogAddSet(pullContext *pctx, FILE *log);
/* energy.c */
PULL_EXPORT const airEnum *const pullInterType;
PULL_EXPORT const airEnum *const pullEnergyType;
PULL_EXPORT const pullEnergy *const pullEnergyUnknown;
PULL_EXPORT const pullEnergy *const pullEnergySpring;
PULL_EXPORT const pullEnergy *const pullEnergyGauss;
PULL_EXPORT const pullEnergy *const pullEnergyBspln;
PULL_EXPORT const pullEnergy *const pullEnergyButterworth;
PULL_EXPORT const pullEnergy *const pullEnergyCotan;
PULL_EXPORT const pullEnergy *const pullEnergyCubic;
PULL_EXPORT const pullEnergy *const pullEnergyQuartic;
PULL_EXPORT const pullEnergy *const pullEnergyCubicWell;
PULL_EXPORT const pullEnergy *const pullEnergyBetterCubicWell;
PULL_EXPORT const pullEnergy *const pullEnergyQuarticWell;
PULL_EXPORT const pullEnergy *const pullEnergyHepticWell;
PULL_EXPORT const pullEnergy *const pullEnergyZero;
PULL_EXPORT const pullEnergy *const pullEnergyButterworthParabola;
PULL_EXPORT const pullEnergy *const pullEnergyAll[PULL_ENERGY_TYPE_MAX+1];
PULL_EXPORT pullEnergySpec *pullEnergySpecNew(void);
PULL_EXPORT void pullEnergySpecSet(pullEnergySpec *ensp,
const pullEnergy *energy,
const double parm[PULL_ENERGY_PARM_NUM]);
PULL_EXPORT void pullEnergySpecCopy(pullEnergySpec *esDst,
const pullEnergySpec *esSrc);
PULL_EXPORT pullEnergySpec *pullEnergySpecNix(pullEnergySpec *ensp);
PULL_EXPORT int pullEnergySpecParse(pullEnergySpec *ensp, const char *str);
PULL_EXPORT hestCB *pullHestEnergySpec;
/* volumePull.c */
PULL_EXPORT pullVolume *pullVolumeNew(void);
PULL_EXPORT pullVolume *pullVolumeNix(pullVolume *vol);
PULL_EXPORT int pullVolumeSingleAdd(pullContext *pctx,
const gageKind *kind,
char *name, const Nrrd *nin,
const NrrdKernelSpec *ksp00,
const NrrdKernelSpec *ksp11,
const NrrdKernelSpec *ksp22);
PULL_EXPORT int pullVolumeStackAdd(pullContext *pctx,
const gageKind *kind,
char *name,
const Nrrd *nin,
const Nrrd *const *ninSS,
double *scalePos,
unsigned int ninNum,
int scaleDerivNorm,
double scaleDerivNormBias,
const NrrdKernelSpec *ksp00,
const NrrdKernelSpec *ksp11,
const NrrdKernelSpec *ksp22,
const NrrdKernelSpec *kspSS);
PULL_EXPORT const pullVolume *pullVolumeLookup(const pullContext *pctx,
const char *volName);
PULL_EXPORT int pullConstraintScaleRange(pullContext *pctx,
double ssrange[2]);
/* enumsPull.c */
PULL_EXPORT const airEnum *const pullInfo;
PULL_EXPORT const airEnum *const pullSource;
PULL_EXPORT const airEnum *const pullProp;
PULL_EXPORT const airEnum *const pullProcessMode;
PULL_EXPORT const airEnum *const pullTraceStop;
PULL_EXPORT const airEnum *const pullInitMethod;
PULL_EXPORT const airEnum *const pullCount;
PULL_EXPORT const airEnum *const pullConstraintFail;
/* infoPull.c */
PULL_EXPORT unsigned int pullPropLen(int prop);
PULL_EXPORT unsigned int pullInfoLen(int info);
PULL_EXPORT pullInfoSpec *pullInfoSpecNew(void);
PULL_EXPORT pullInfoSpec *pullInfoSpecNix(pullInfoSpec *ispec);
PULL_EXPORT int pullInfoSpecAdd(pullContext *pctx, pullInfoSpec *ispec);
PULL_EXPORT int pullInfoGet(Nrrd *ninfo, int info, pullContext *pctx);
PULL_EXPORT int pullInfoSpecSprint(char str[AIR_STRLEN_LARGE],
const pullContext *pctx,
const pullInfoSpec *ispec);
/* contextPull.c */
PULL_EXPORT pullContext *pullContextNew(void);
PULL_EXPORT pullContext *pullContextNix(pullContext *pctx);
PULL_EXPORT int pullOutputGet(Nrrd *nPosOut, Nrrd *nTenOut,
Nrrd *nStrengthOut,
const double scaleVec[3], double scaleRad,
pullContext *pctx);
PULL_EXPORT int pullOutputGetFilter(Nrrd *nPosOut, Nrrd *nTenOut,
Nrrd *nStrengthOut,
const double scaleVec[3], double scaleRad,
pullContext *pctx,
unsigned int idtagMin,
unsigned int idtagMax);
PULL_EXPORT int pullPositionHistoryPolydataGet(limnPolyData *pld,
pullContext *pctx);
PULL_EXPORT int pullPositionHistoryNrrdGet(Nrrd *nhist, pullContext *pctx,
pullPoint *point);
PULL_EXPORT int pullPropGet(Nrrd *nprop, int prop, pullContext *pctx);
/* pointPull.c */
PULL_EXPORT int pullPointInitializePerVoxel(const pullContext *pctx,
const unsigned int pointIdx,
pullPoint *point,
pullVolume *scaleVol,
int *createFailP);
PULL_EXPORT int pullPointInitializeRandomOrHalton(pullContext *pctx,
const unsigned int pointIdx,
pullPoint *point,
pullVolume *scaleVol);
PULL_EXPORT int pullPointInitializeGivenPos(pullContext *pctx,
const double *posData,
const unsigned int pointIdx,
pullPoint *point,
int *createFailP);
PULL_EXPORT double pullPointScalar(const pullContext *pctx,
const pullPoint *point, int sclInfo,
double grad[4], double hess[9]);
PULL_EXPORT unsigned int pullPointNumber(const pullContext *pctx);
PULL_EXPORT unsigned int pullPointNumberFilter(const pullContext *pctx,
unsigned int idtagMin,
unsigned int idtagMax);
PULL_EXPORT pullPoint *pullPointNew(pullContext *pctx);
PULL_EXPORT pullPoint *pullPointNix(pullPoint *pnt);
PULL_EXPORT int pullProbe(pullTask *task, pullPoint *point);
/* binningPull.c */
PULL_EXPORT int pullBinsPointAdd(pullContext *pctx, pullPoint *point,
/* output */
pullBin **binUsed);
PULL_EXPORT int pullBinsPointMaybeAdd(pullContext *pctx, pullPoint *point,
/* output */
pullBin **binUsed, int *added);
/* trace.c */
PULL_EXPORT pullTrace *pullTraceNew(void);
PULL_EXPORT pullTrace *pullTraceNix(pullTrace *pts);
PULL_EXPORT size_t pullTraceMultiSizeof(const pullTraceMulti *mtrc);
PULL_EXPORT int pullTraceSet(pullContext *pctx, pullTrace *trc,
int recordStrength, int sigmaNorm,
double scaleDelta, double halfScaleWin,
double velocityMax, unsigned int arrIncr,
const double seedPos[4]);
PULL_EXPORT pullTraceMulti *pullTraceMultiNew(void);
PULL_EXPORT pullTraceMulti *pullTraceMultiNix(pullTraceMulti *mtrc);
PULL_EXPORT int pullTraceMultiAdd(pullTraceMulti *mtrc, pullTrace *trc,
int *addedP);
PULL_EXPORT int pullTraceMultiFilterConcaveDown(Nrrd *nfilt,
const pullTraceMulti *mtrc,
double winLenFrac);
PULL_EXPORT int pullTraceMultiPlotAdd(Nrrd *nplot,
const pullTraceMulti *mtrc,
const Nrrd *nfilt, int strengthUse,
unsigned int trcIdxMin,
unsigned int trcNum);
PULL_EXPORT int pullTraceMultiWrite(FILE *file, const pullTraceMulti *mtrc);
PULL_EXPORT int pullTraceMultiRead(pullTraceMulti *mtrc, FILE *file);
/* actionPull.c */
PULL_EXPORT int pullEnergyPlot(pullContext *pctx, Nrrd *nplot,
double xx, double yy, double zz,
unsigned int res);
PULL_EXPORT int pullBinProcess(pullTask *task, unsigned int myBinIdx);
PULL_EXPORT int pullGammaLearn(pullContext *pctx);
/* corePull.c */
PULL_EXPORT int pullStart(pullContext *pctx);
PULL_EXPORT int pullRun(pullContext *pctx);
PULL_EXPORT int pullFinish(pullContext *pctx);
/* ccPull.c */
PULL_EXPORT int pullCCFind(pullContext *pctx);
PULL_EXPORT int pullCCMeasure(pullContext *pctx, Nrrd *nmeas,
int measrInfo, double rho);
PULL_EXPORT int pullCCSort(pullContext *pctx, int measrInfo, double rho);
#ifdef __cplusplus
}
#endif
#endif /* PULL_HAS_BEEN_INCLUDED */
|