├── .gitignore ├── BoneTexture ├── BoneTexture.py ├── CMakeLists.txt ├── Resources │ ├── Icons │ │ └── BoneTexture.png │ └── UI │ │ └── BoneTexture.ui └── Testing │ ├── CMakeLists.txt │ └── Python │ └── CMakeLists.txt ├── BoneTextureExtension.png ├── CMakeLists.txt ├── ComputeBMFeatureMaps ├── CMakeLists.txt ├── ComputeBMFeatureMaps.cxx ├── ComputeBMFeatureMaps.xml └── Testing │ ├── CMakeLists.txt │ └── Cxx │ └── CMakeLists.txt ├── ComputeBMFeatures ├── CMakeLists.txt ├── ComputeBMFeatures.cxx ├── ComputeBMFeatures.xml └── Testing │ ├── CMakeLists.txt │ └── Cxx │ └── CMakeLists.txt ├── ComputeGLCMFeatureMaps ├── CMakeLists.txt ├── ComputeGLCMFeatureMaps.cxx ├── ComputeGLCMFeatureMaps.xml └── Testing │ ├── CMakeLists.txt │ └── Cxx │ └── CMakeLists.txt ├── ComputeGLCMFeatures ├── CMakeLists.txt ├── ComputeGLCMFeatures.cxx ├── ComputeGLCMFeatures.xml └── Testing │ ├── CMakeLists.txt │ └── Cxx │ └── CMakeLists.txt ├── ComputeGLRLMFeatureMaps ├── CMakeLists.txt ├── ComputeGLRLMFeatureMaps.cxx ├── ComputeGLRLMFeatureMaps.xml └── Testing │ ├── CMakeLists.txt │ └── Cxx │ └── CMakeLists.txt ├── ComputeGLRLMFeatures ├── CMakeLists.txt ├── ComputeGLRLMFeatures.cxx ├── ComputeGLRLMFeatures.xml └── Testing │ ├── CMakeLists.txt │ └── Cxx │ └── CMakeLists.txt ├── CreateLabelMapFromCSV ├── CMakeLists.txt ├── CreateLabelMapFromCSV.cxx ├── CreateLabelMapFromCSV.xml └── Testing │ ├── CMakeLists.txt │ └── Cxx │ └── CMakeLists.txt ├── Docs └── BoneTextureExtensionTutorial_2017.pdf ├── LICENSE.txt ├── README.md ├── SaveVectorImageAsCSV ├── CMakeLists.txt ├── SaveVectorImageAsCSV.cxx ├── SaveVectorImageAsCSV.xml └── Testing │ ├── CMakeLists.txt │ └── Cxx │ └── CMakeLists.txt ├── SeparateVectorImage ├── CMakeLists.txt ├── SeparateVectorImage.cxx ├── SeparateVectorImage.xml └── Testing │ ├── CMakeLists.txt │ └── Cxx │ └── CMakeLists.txt ├── SuperBuild.cmake └── SuperBuild ├── External_ITKBoneMorphometry.cmake └── External_ITKTextureFeature.cmake /.gitignore: -------------------------------------------------------------------------------- 1 | BoneTexture/BoneTexture.pyc 2 | BoneTextureSerializer/BoneTextureSerializer.pyc 3 | CMakeLists.txt.user 4 | -------------------------------------------------------------------------------- /BoneTexture/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | #----------------------------------------------------------------------------- 2 | set(MODULE_NAME BoneTexture) 3 | 4 | #----------------------------------------------------------------------------- 5 | set(MODULE_PYTHON_SCRIPTS 6 | ${MODULE_NAME}.py 7 | ) 8 | 9 | set(MODULE_PYTHON_RESOURCES 10 | Resources/Icons/${MODULE_NAME}.png 11 | Resources/UI/${MODULE_NAME}.ui 12 | ) 13 | 14 | #----------------------------------------------------------------------------- 15 | slicerMacroBuildScriptedModule( 16 | NAME ${MODULE_NAME} 17 | SCRIPTS ${MODULE_PYTHON_SCRIPTS} 18 | RESOURCES ${MODULE_PYTHON_RESOURCES} 19 | WITH_GENERIC_TESTS 20 | ) 21 | 22 | #----------------------------------------------------------------------------- 23 | if(BUILD_TESTING) 24 | 25 | # Register the unittest subclass in the main script as a ctest. 26 | # Note that the test will also be available at runtime. 27 | slicer_add_python_unittest(SCRIPT ${MODULE_NAME}.py) 28 | 29 | # Additional build-time testing 30 | add_subdirectory(Testing) 31 | endif() 32 | -------------------------------------------------------------------------------- /BoneTexture/Resources/Icons/BoneTexture.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Kitware/BoneTextureExtension/3410506efaa404131f7b02aa70769f537b1f2b3d/BoneTexture/Resources/Icons/BoneTexture.png -------------------------------------------------------------------------------- /BoneTexture/Resources/UI/BoneTexture.ui: -------------------------------------------------------------------------------- 1 | 2 | 3 | BoneTexture 4 | 5 | 6 | 7 | 0 8 | 0 9 | 416 10 | 1437 11 | 12 | 13 | 14 | 15 | 16 | 17 | Single Image Mode 18 | 19 | 20 | 21 | 22 | 23 | 24 | Serializer Mode 25 | 26 | 27 | 28 | 29 | 30 | 31 | Inputs 32 | 33 | 34 | 35 | 36 | 37 | 0 38 | 39 | 40 | 41 | 42 | 43 | 44 | Input data folder: 45 | 46 | 47 | 48 | 49 | 50 | 51 | ctkPathLineEdit::Dirs|ctkPathLineEdit::Drives|ctkPathLineEdit::NoDot|ctkPathLineEdit::NoDotDot|ctkPathLineEdit::Readable 52 | 53 | 54 | 55 | 56 | 57 | 58 | Note: The input data should be named: Scan_{ID} for the input scan and Seg_{ID} for the corresponding label map (if a region mask exists) 59 | 60 | 61 | true 62 | 63 | 64 | 65 | 66 | 67 | 68 | 69 | 70 | 71 | 72 | Input volume: 73 | 74 | 75 | 76 | 77 | 78 | 79 | Input labelmap: 80 | 81 | 82 | 83 | 84 | 85 | 86 | Pick the input to the algorithm. 87 | 88 | 89 | 90 | vtkMRMLScalarVolumeNode 91 | 92 | 93 | 94 | false 95 | 96 | 97 | false 98 | 99 | 100 | false 101 | 102 | 103 | inputVolume 104 | 105 | 106 | 107 | 108 | 109 | 110 | Specify Mask 111 | 112 | 113 | 114 | 115 | 116 | 117 | 118 | 7 119 | 120 | 121 | 122 | This defines region over which texture features will be computed (Note: This option will greatly improve computation time) 123 | 124 | 125 | true 126 | 127 | 128 | 129 | 130 | 131 | 132 | 133 | vtkMRMLLabelMapVolumeNode 134 | 135 | 136 | 137 | 138 | 139 | 140 | false 141 | 142 | 143 | false 144 | 145 | 146 | 147 | 148 | 149 | inputLabelMap 150 | 151 | 152 | 153 | 154 | 155 | 156 | 157 | 158 | 159 | 160 | Conversion: Vector Input Scan to Scalar 161 | 162 | 163 | 164 | 165 | 166 | Convert Input Scan to Scalar 167 | 168 | 169 | 170 | 171 | 172 | 173 | 174 | 175 | 176 | 3 177 | 0 178 | 179 | 180 | 181 | 182 | 183 | 184 | 185 | 186 | 1 187 | 0 188 | 189 | 190 | 191 | 192 | 193 | 194 | 195 | 196 | 197 | Convert Input Scan to Scalar 198 | 199 | 200 | 201 | 202 | 203 | 204 | 205 | 206 | 207 | Process Inputs 208 | 209 | 210 | 211 | 212 | 213 | 214 | 215 | 216 | 217 | 218 | 219 | 220 | 221 | 222 | 223 | 224 | Computation 225 | 226 | 227 | 228 | 229 | 230 | Features choice 231 | 232 | 233 | 234 | 235 | 236 | 237 | 238 | 239 | 240 | 241 | 242 | 243 | 244 | 245 | 246 | 247 | 248 | 249 | 250 | Gray Level Co-occurrences (GLCM) features 251 | 252 | 253 | 254 | 255 | 256 | 257 | 258 | 259 | 260 | 261 | 262 | 263 | 264 | Gray Level Run Length (GLRLM) features 265 | 266 | 267 | 268 | 269 | 270 | 271 | Bone Morphometry (BM) features 272 | 273 | 274 | 275 | 276 | 277 | 278 | 279 | 280 | 281 | Populate Parameters Based on Inputs 282 | 283 | 284 | 285 | 286 | 287 | 288 | true 289 | 290 | 291 | GLCM parameters 292 | 293 | 294 | true 295 | 296 | 297 | true 298 | 299 | 300 | false 301 | 302 | 303 | 304 | QLayout::SetMinimumSize 305 | 306 | 307 | 9 308 | 309 | 310 | 311 | 312 | QFormLayout::AllNonFixedFieldsGrow 313 | 314 | 315 | 316 | 317 | Mask "inside" value: 318 | 319 | 320 | 321 | 322 | 323 | 324 | 1000 325 | 326 | 327 | 1 328 | 329 | 330 | 1 331 | 332 | 333 | GLCMFeaturesValue.insideMask 334 | 335 | 336 | 337 | 338 | 339 | 340 | Number of bins: 341 | 342 | 343 | 344 | 345 | 346 | 347 | 1 348 | 349 | 350 | 1200 351 | 352 | 353 | 10 354 | 355 | 356 | GLCMFeaturesValue.binNumber 357 | 358 | 359 | 360 | 361 | 362 | 363 | Voxel Intensity Range: 364 | 365 | 366 | 367 | 368 | 369 | 370 | 371 | 372 | min: 373 | 374 | 375 | 376 | 377 | 378 | 379 | max: 380 | 381 | 382 | 383 | 384 | 385 | 386 | -1000000 387 | 388 | 389 | 1000000 390 | 391 | 392 | 4000 393 | 394 | 395 | GLCMFeaturesValue.pixelIntensityMax 396 | 397 | 398 | 399 | 400 | 401 | 402 | -1000000 403 | 404 | 405 | 1000000 406 | 407 | 408 | GLCMFeaturesValue.pixelIntensityMin 409 | 410 | 411 | 412 | 413 | 414 | 415 | 416 | 417 | Neighborhood Radius: 418 | 419 | 420 | 421 | 422 | 423 | 424 | 100 425 | 426 | 427 | 4 428 | 429 | 430 | GLCMFeaturesValue.neighborhoodRadius 431 | 432 | 433 | 434 | 435 | 436 | 437 | 438 | 439 | 440 | 441 | 442 | true 443 | 444 | 445 | GLRLM parameters 446 | 447 | 448 | true 449 | 450 | 451 | true 452 | 453 | 454 | false 455 | 456 | 457 | 458 | QLayout::SetMinimumSize 459 | 460 | 461 | 9 462 | 463 | 464 | 465 | 466 | QFormLayout::AllNonFixedFieldsGrow 467 | 468 | 469 | 470 | 471 | Number of bins: 472 | 473 | 474 | 475 | 476 | 477 | 478 | Voxel Intensity Range: 479 | 480 | 481 | 482 | 483 | 484 | 485 | Distance range: 486 | 487 | 488 | 489 | 490 | 491 | 492 | 493 | 494 | min: 495 | 496 | 497 | 498 | 499 | 500 | 501 | max: 502 | 503 | 504 | 505 | 506 | 507 | 508 | -1000000 509 | 510 | 511 | 1000000 512 | 513 | 514 | 4000 515 | 516 | 517 | GLRLMFeaturesValue.pixelIntensityMax 518 | 519 | 520 | 521 | 522 | 523 | 524 | -1000000 525 | 526 | 527 | 1000000 528 | 529 | 530 | GLRLMFeaturesValue.pixelIntensityMin 531 | 532 | 533 | 534 | 535 | 536 | 537 | 538 | 539 | QFormLayout::AllNonFixedFieldsGrow 540 | 541 | 542 | 543 | 544 | min: 545 | 546 | 547 | 548 | 549 | 550 | 551 | max: 552 | 553 | 554 | 555 | 556 | 557 | 558 | 1000.000000000000000 559 | 560 | 561 | 0.100000000000000 562 | 563 | 564 | 1.000000000000000 565 | 566 | 567 | GLRLMFeaturesValue.distanceMax 568 | 569 | 570 | 571 | 572 | 573 | 574 | 5.000000000000000 575 | 576 | 577 | 0.100000000000000 578 | 579 | 580 | GLRLMFeaturesValue.distanceMin 581 | 582 | 583 | 584 | 585 | 586 | 587 | 588 | 589 | 1 590 | 591 | 592 | 1200 593 | 594 | 595 | 10 596 | 597 | 598 | GLRLMFeaturesValue.binNumber 599 | 600 | 601 | 602 | 603 | 604 | 605 | Neighborhood Radius: 606 | 607 | 608 | 609 | 610 | 611 | 612 | 100 613 | 614 | 615 | 4 616 | 617 | 618 | GLRLMFeaturesValue.neighborhoodRadius 619 | 620 | 621 | 622 | 623 | 624 | 625 | Mask "inside" value: 626 | 627 | 628 | 629 | 630 | 631 | 632 | 1000 633 | 634 | 635 | 1 636 | 637 | 638 | 1 639 | 640 | 641 | GLRLMFeaturesValue.insideMask 642 | 643 | 644 | 645 | 646 | 647 | 648 | 649 | 650 | 651 | 652 | 653 | BM parameters 654 | 655 | 656 | true 657 | 658 | 659 | false 660 | 661 | 662 | 663 | 664 | 665 | 666 | 667 | Threshold: 668 | 669 | 670 | 671 | 672 | 673 | 674 | Neighborhood Radius: 675 | 676 | 677 | 678 | 679 | 680 | 681 | -1000000 682 | 683 | 684 | 1000000 685 | 686 | 687 | 0 688 | 689 | 690 | 1 691 | 692 | 693 | BMFeaturesValue.threshold 694 | 695 | 696 | 697 | 698 | 699 | 700 | 100 701 | 702 | 703 | 4 704 | 705 | 706 | BMFeaturesValue.neighborhoodRadius 707 | 708 | 709 | 710 | 711 | 712 | 713 | 714 | 715 | 716 | 717 | 718 | 719 | 720 | 721 | Qt::StrongFocus 722 | 723 | 724 | Export 725 | 726 | 727 | false 728 | 729 | 730 | 731 | 732 | 733 | 734 | 735 | 736 | Output folder: 737 | 738 | 739 | 740 | 741 | 742 | 743 | ctkPathLineEdit::Dirs|ctkPathLineEdit::Drives|ctkPathLineEdit::Executable|ctkPathLineEdit::NoDot|ctkPathLineEdit::NoDotDot|ctkPathLineEdit::PermissionMask|ctkPathLineEdit::Readable|ctkPathLineEdit::Writable 744 | 745 | 746 | 747 | 748 | 749 | 750 | 751 | 752 | 753 | Separate feature maps 754 | 755 | 756 | 757 | 758 | 759 | 760 | Save feature values table 761 | 762 | 763 | 764 | 765 | 766 | 767 | 768 | 769 | Filename: 770 | 771 | 772 | 773 | 774 | 775 | 776 | 777 | 778 | 779 | 780 | 781 | Export Results 782 | 783 | 784 | 785 | 786 | 787 | 788 | 789 | 790 | 791 | Results 792 | 793 | 794 | true 795 | 796 | 797 | false 798 | 799 | 800 | 801 | 802 | 803 | Feature Values 804 | 805 | 806 | true 807 | 808 | 809 | 810 | 811 | 812 | 813 | 0 814 | 0 815 | 816 | 817 | 818 | 819 | 0 820 | 326 821 | 822 | 823 | 824 | Qt::ScrollBarAsNeeded 825 | 826 | 827 | true 828 | 829 | 830 | QAbstractItemView::NoEditTriggers 831 | 832 | 833 | QAbstractItemView::ExtendedSelection 834 | 835 | 836 | true 837 | 838 | 839 | 100 840 | 841 | 842 | true 843 | 844 | 845 | false 846 | 847 | 848 | true 849 | 850 | 851 | true 852 | 853 | 854 | 855 | 1 856 | 857 | 858 | 859 | 860 | 2 861 | 862 | 863 | 864 | 865 | 3 866 | 867 | 868 | 869 | 870 | 4 871 | 872 | 873 | 874 | 875 | 5 876 | 877 | 878 | 879 | 880 | 6 881 | 882 | 883 | 884 | 885 | 7 886 | 887 | 888 | 889 | 890 | 8 891 | 892 | 893 | 894 | 895 | 9 896 | 897 | 898 | 899 | 900 | 10 901 | 902 | 903 | 904 | 905 | GLCM Features 906 | 907 | 908 | 909 | 910 | Values 911 | 912 | 913 | 914 | 915 | GLRLM Features 916 | 917 | 918 | 919 | 920 | Values 921 | 922 | 923 | 924 | 925 | BM Features 926 | 927 | 928 | 929 | 930 | Values 931 | 932 | 933 | 934 | 935 | Energy 936 | 937 | 938 | 939 | 940 | 0.0 941 | 942 | 943 | 944 | 945 | Short Run Emphasis 946 | 947 | 948 | 949 | 950 | 0.0 951 | 952 | 953 | 954 | 955 | Bone Volume Density 956 | 957 | 958 | 959 | 960 | 0.0 961 | 962 | 963 | 964 | 965 | Entropy 966 | 967 | 968 | 969 | 970 | 0.0 971 | 972 | 973 | 974 | 975 | Long Run Emphasis 976 | 977 | 978 | 979 | 980 | 0.0 981 | 982 | 983 | 984 | 985 | Trabecular Thickness 986 | 987 | 988 | 989 | 990 | 0.0 991 | 992 | 993 | 994 | 995 | Correlation 996 | 997 | 998 | 999 | 1000 | 0.0 1001 | 1002 | 1003 | 1004 | 1005 | Grey Level Nonuniformity 1006 | 1007 | 1008 | 1009 | 1010 | 0.0 1011 | 1012 | 1013 | 1014 | 1015 | Trabecular Separation 1016 | 1017 | 1018 | 1019 | 1020 | 0.0 1021 | 1022 | 1023 | 1024 | 1025 | Inverse Difference Moment 1026 | 1027 | 1028 | 1029 | 1030 | 0.0 1031 | 1032 | 1033 | 1034 | 1035 | Run Length Nonuniformity 1036 | 1037 | 1038 | 1039 | 1040 | 0.0 1041 | 1042 | 1043 | 1044 | 1045 | Trabecular Number 1046 | 1047 | 1048 | 1049 | 1050 | 0.0 1051 | 1052 | 1053 | 1054 | 1055 | Inertia 1056 | 1057 | 1058 | 1059 | 1060 | 0.0 1061 | 1062 | 1063 | 1064 | 1065 | Low Grey Level Run Emphasis 1066 | 1067 | 1068 | 1069 | 1070 | 0.0 1071 | 1072 | 1073 | 1074 | 1075 | Bone Surface Density 1076 | 1077 | 1078 | 1079 | 1080 | 0.0 1081 | 1082 | 1083 | 1084 | 1085 | Cluster Shade 1086 | 1087 | 1088 | 1089 | 1090 | 0.0 1091 | 1092 | 1093 | 1094 | 1095 | High Grey Level Run Emphasis 1096 | 1097 | 1098 | 1099 | 1100 | 0.0 1101 | 1102 | 1103 | 1104 | 1105 | Cluster Prominence 1106 | 1107 | 1108 | 1109 | 1110 | 0.0 1111 | 1112 | 1113 | 1114 | 1115 | Short Run Low Grey Level Emphasis 1116 | 1117 | 1118 | 1119 | 1120 | 0.0 1121 | 1122 | 1123 | 1124 | 1125 | Haralick Correlation 1126 | 1127 | 1128 | 1129 | 1130 | 0.0 1131 | 1132 | 1133 | 1134 | 1135 | Short Run High Grey Level Emphasis 1136 | 1137 | 1138 | 1139 | 1140 | 0.0 1141 | 1142 | 1143 | 1144 | 1145 | Long Run Low Grey Level Emphasis 1146 | 1147 | 1148 | 1149 | 1150 | 0.0 1151 | 1152 | 1153 | 1154 | 1155 | Long Run High Grey Level Emphasis 1156 | 1157 | 1158 | 1159 | 1160 | 0.0 1161 | 1162 | 1163 | 1164 | 1165 | 1166 | 1167 | 1168 | 1169 | 1170 | 1171 | Display Colormaps 1172 | 1173 | 1174 | true 1175 | 1176 | 1177 | 1178 | 1179 | 1180 | Feature set: 1181 | 1182 | 1183 | 1184 | 1185 | 1186 | 1187 | Feature: 1188 | 1189 | 1190 | 1191 | 1192 | 1193 | 1194 | 1195 | 1196 | 1197 | 1198 | 1199 | 1200 | 1201 | 1202 | 1203 | 1204 | 1205 | 1206 | Compute Texture Maps 1207 | 1208 | 1209 | 1210 | 1211 | 1212 | 1213 | 1214 | 0 1215 | 0 1216 | 1217 | 1218 | 1219 | 24 1220 | 1221 | 1222 | 1223 | 1224 | 1225 | 1226 | Compute Texture Feature Set 1227 | 1228 | 1229 | 1230 | 1231 | 1232 | 1233 | 1234 | 0 1235 | 0 1236 | 1237 | 1238 | 1239 | 24 1240 | 1241 | 1242 | 1243 | 1244 | 1245 | 1246 | Qt::Vertical 1247 | 1248 | 1249 | 1250 | 20 1251 | 40 1252 | 1253 | 1254 | 1255 | 1256 | 1257 | 1258 | 1259 | 1260 | qMRMLNodeComboBox 1261 | QWidget 1262 |
qMRMLNodeComboBox.h
1263 | 1264 | 1265 | qMRMLWidget 1266 | QWidget 1267 |
qMRMLWidget.h
1268 | 1 1269 | 1270 | 1271 | ctkCollapsibleButton 1272 | QWidget 1273 |
ctkCollapsibleButton.h
1274 | 1 1275 | 1276 | 1277 | ctkCollapsibleGroupBox 1278 | QGroupBox 1279 |
ctkCollapsibleGroupBox.h
1280 | 1 1281 | 1282 | 1283 | ctkPathLineEdit 1284 | QWidget 1285 |
ctkPathLineEdit.h
1286 | 1287 | 1288 | 1289 | 1290 | 1291 | BoneTexture 1292 | mrmlSceneChanged(vtkMRMLScene*) 1293 | inputScanComboBox 1294 | setMRMLScene(vtkMRMLScene*) 1295 | 1296 | 1297 | 122 1298 | 132 1299 | 1300 | 1301 | 248 1302 | 61 1303 | 1304 | 1305 | 1306 | 1307 | BoneTexture 1308 | mrmlSceneChanged(vtkMRMLScene*) 1309 | inputSegmentationComboBox 1310 | setMRMLScene(vtkMRMLScene*) 1311 | 1312 | 1313 | 130 1314 | 331 1315 | 1316 | 1317 | 182 1318 | 252 1319 | 1320 | 1321 | 1322 | 1323 | 1324 | -------------------------------------------------------------------------------- /BoneTexture/Testing/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | add_subdirectory(Python) 2 | -------------------------------------------------------------------------------- /BoneTexture/Testing/Python/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | 2 | #slicer_add_python_unittest(SCRIPT ${MODULE_NAME}ModuleTest.py) 3 | -------------------------------------------------------------------------------- /BoneTextureExtension.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Kitware/BoneTextureExtension/3410506efaa404131f7b02aa70769f537b1f2b3d/BoneTextureExtension.png -------------------------------------------------------------------------------- /CMakeLists.txt: -------------------------------------------------------------------------------- 1 | cmake_minimum_required(VERSION 3.16.3) 2 | 3 | project(BoneTextureExtension) 4 | 5 | #----------------------------------------------------------------------------- 6 | # Extension meta-information 7 | set(EXTENSION_HOMEPAGE "https://www.slicer.org/wiki/Documentation/Nightly/Extensions/BoneTextureExtension") 8 | set(EXTENSION_CATEGORY "Quantification") 9 | set(EXTENSION_CONTRIBUTORS "Jean-Baptiste VIMORT (Kitware Inc.)") 10 | set(EXTENSION_DESCRIPTION "This extensions contain several modules that can be used to compute feature maps of N-Dimensional images using well-known texture analysis methods. Key Features: 8 coocurrence textural features: energy, entropy, correlation, inertia, cluster Shade... / 10 run length textural features: run length emphasis, grey level non uniformity, run length non uniformity, low grey level long run emphasis... / Input configurable parameters: locality of the texture, offset directions for co-ocurrence and run length computation, the number of bins for the intensity histograms, and the intensity range or the range of run lengths.") 11 | set(EXTENSION_ICONURL "https://www.slicer.org/w/img_auth.php/0/09/Logo-BoneTextureExtension.png") 12 | set(EXTENSION_SCREENSHOTURLS "https://www.slicer.org/w/img_auth.php/7/70/BoneTextureExtension-Slicer.png") 13 | set(EXTENSION_DEPENDS "NA") # Specified as a list or "NA" if no dependencies 14 | set(EXTENSION_BUILD_SUBDIRECTORY inner-build) 15 | 16 | set(SUPERBUILD_TOPLEVEL_PROJECT inner) 17 | 18 | #----------------------------------------------------------------------------- 19 | # Extension dependencies 20 | find_package(Slicer REQUIRED) 21 | include(${Slicer_USE_FILE}) 22 | mark_as_superbuild(Slicer_DIR) 23 | 24 | find_package(Git REQUIRED) 25 | mark_as_superbuild(GIT_EXECUTABLE) 26 | 27 | #----------------------------------------------------------------------------- 28 | # SuperBuild setup 29 | option(${EXTENSION_NAME}_SUPERBUILD "Build ${EXTENSION_NAME} and the projects it depends on." ON) 30 | mark_as_advanced(${EXTENSION_NAME}_SUPERBUILD) 31 | if(${EXTENSION_NAME}_SUPERBUILD) 32 | include("${CMAKE_CURRENT_SOURCE_DIR}/SuperBuild.cmake") 33 | return() 34 | endif() 35 | 36 | #----------------------------------------------------------------------------- 37 | # Extension modules 38 | add_subdirectory(ComputeGLCMFeatures) 39 | add_subdirectory(ComputeGLRLMFeatures) 40 | add_subdirectory(ComputeBMFeatures) 41 | add_subdirectory(ComputeGLCMFeatureMaps) 42 | add_subdirectory(ComputeGLRLMFeatureMaps) 43 | add_subdirectory(ComputeBMFeatureMaps) 44 | add_subdirectory(BoneTexture) 45 | add_subdirectory(SeparateVectorImage) 46 | add_subdirectory(SaveVectorImageAsCSV) 47 | add_subdirectory(CreateLabelMapFromCSV) 48 | 49 | #----------------------------------------------------------------------------- 50 | set(EXTENSION_CPACK_INSTALL_CMAKE_PROJECTS) 51 | set(CPACK_INSTALL_CMAKE_PROJECTS "${CPACK_INSTALL_CMAKE_PROJECTS};${ITKBoneMorphometry_DIR};ITKBoneMorphometry;RuntimeLibraries;/") 52 | set(CPACK_INSTALL_CMAKE_PROJECTS "${CPACK_INSTALL_CMAKE_PROJECTS};${ITKTextureFeature_DIR};ITKTextureFeature;RuntimeLibraries;/") 53 | set(${EXTENSION_NAME}_CPACK_INSTALL_CMAKE_PROJECTS "${EXTENSION_CPACK_INSTALL_CMAKE_PROJECTS}" CACHE STRING "List of external projects to install" FORCE) 54 | 55 | #----------------------------------------------------------------------------- 56 | list(APPEND CPACK_INSTALL_CMAKE_PROJECTS "${CMAKE_BINARY_DIR};${EXTENSION_NAME};ALL;/") 57 | list(APPEND CPACK_INSTALL_CMAKE_PROJECTS "${${EXTENSION_NAME}_CPACK_INSTALL_CMAKE_PROJECTS}") 58 | include(${Slicer_EXTENSION_GENERATE_CONFIG}) 59 | include(${Slicer_EXTENSION_CPACK}) 60 | -------------------------------------------------------------------------------- /ComputeBMFeatureMaps/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | #----------------------------------------------------------------------------- 2 | set(MODULE_NAME ComputeBMFeatureMaps) 3 | 4 | #----------------------------------------------------------------------------- 5 | 6 | # 7 | # SlicerExecutionModel 8 | # 9 | find_package(SlicerExecutionModel REQUIRED) 10 | include(${SlicerExecutionModel_USE_FILE}) 11 | 12 | # 13 | # ITK 14 | # 15 | set(${PROJECT_NAME}_ITK_COMPONENTS 16 | ITKIOImageBase 17 | ITKCommon 18 | ITKStatistics 19 | ITKImageGrid 20 | ITKImageSources 21 | ITKTestKernel 22 | ITKMetaIO 23 | ITKImageIntensity 24 | BoneMorphometry 25 | ) 26 | find_package(ITK 4.9 COMPONENTS ${${PROJECT_NAME}_ITK_COMPONENTS} REQUIRED) 27 | if(ITK_VERSION VERSION_GREATER_EQUAL "5.3") 28 | foreach(factory_uc IN ITEMS "IMAGEIO" "MESHIO" "TRANSFORMIO") 29 | set(ITK_NO_${factory_uc}_FACTORY_REGISTER_MANAGER 1) 30 | endforeach() 31 | else() 32 | set(ITK_NO_IO_FACTORY_REGISTER_MANAGER 1) # See Libs/ITKFactoryRegistration/CMakeLists.txt 33 | endif() 34 | include(${ITK_USE_FILE}) 35 | 36 | #----------------------------------------------------------------------------- 37 | set(MODULE_INCLUDE_DIRECTORIES 38 | ${CMAKE_CURRENT_SOURCE_DIR}/../include 39 | ) 40 | 41 | set(MODULE_SRCS 42 | ) 43 | 44 | set(MODULE_TARGET_LIBRARIES 45 | ${ITK_LIBRARIES} 46 | ) 47 | 48 | #----------------------------------------------------------------------------- 49 | SEMMacroBuildCLI( 50 | NAME ${MODULE_NAME} 51 | TARGET_LIBRARIES ${MODULE_TARGET_LIBRARIES} 52 | INCLUDE_DIRECTORIES ${MODULE_INCLUDE_DIRECTORIES} 53 | ADDITIONAL_SRCS ${MODULE_SRCS} 54 | ) 55 | 56 | #----------------------------------------------------------------------------- 57 | if(BUILD_TESTING) 58 | add_subdirectory(Testing) 59 | endif() 60 | -------------------------------------------------------------------------------- /ComputeBMFeatureMaps/ComputeBMFeatureMaps.cxx: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | * 3 | * Copyright Insight Software Consortium 4 | * 5 | * Licensed under the Apache License, Version 2.0 (the "License"); 6 | * you may not use this file except in compliance with the License. 7 | * You may obtain a copy of the License at 8 | * 9 | * http://www.apache.org/licenses/LICENSE-2.0.txt 10 | * 11 | * Unless required by applicable law or agreed to in writing, software 12 | * distributed under the License is distributed on an "AS IS" BASIS, 13 | * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 14 | * See the License for the specific language governing permissions and 15 | * limitations under the License. 16 | * 17 | *=========================================================================*/ 18 | 19 | 20 | // Use an anonymous namespace to keep class types and function names 21 | // from colliding when module is used as shared object module. Every 22 | // thing should be in an anonymous namespace except for the module 23 | // entry point, e.g. main() 24 | // 25 | 26 | #include "itkImageFileReader.h" 27 | #include "itkImageFileWriter.h" 28 | #include "itkFloatingPointExceptions.h" 29 | #include "itkImage.h" 30 | #include "itkVector.h" 31 | #include "itkNeighborhood.h" 32 | #include "itkMetaDataDictionary.h" 33 | #include "itkMetaDataObject.h" 34 | 35 | #include "itkBoneMorphometryFeaturesImageFilter.h" 36 | #include "itkReplaceFeatureMapNanInfImageFilter.h" 37 | 38 | #include "itkPluginUtilities.h" 39 | 40 | #include "ComputeBMFeatureMapsCLP.h" 41 | 42 | namespace 43 | { 44 | 45 | template< typename TPixel > 46 | int DoIt( int argc, char * argv[] ) 47 | { 48 | PARSE_ARGS; 49 | 50 | const unsigned int Dimension = 3; 51 | 52 | typedef TPixel PixelType; 53 | typedef itk::Image< PixelType, Dimension > InputImageType; 54 | typedef itk::VectorImage< float, Dimension > OutputImageType; 55 | 56 | typedef itk::Neighborhood NeighborhoodType; 57 | NeighborhoodType hood; 58 | 59 | typedef itk::ImageFileReader< InputImageType > ReaderType; 60 | typename ReaderType::Pointer reader = ReaderType::New(); 61 | reader->SetFileName( inputVolume ); 62 | reader->Update(); 63 | 64 | typedef itk::BoneMorphometryFeaturesImageFilter FilterType; 65 | typename FilterType::Pointer filter = FilterType::New(); 66 | filter->SetInput(reader->GetOutput()); 67 | 68 | if(inputMask != "") 69 | { 70 | typename ReaderType::Pointer maskReader = ReaderType::New(); 71 | maskReader->SetFileName( inputMask ); 72 | maskReader->Update(); 73 | filter->SetMaskImage(maskReader->GetOutput()); 74 | } 75 | 76 | hood.SetRadius(neighborhoodRadius); 77 | filter->SetNeighborhoodRadius(hood.GetRadius()); 78 | filter->SetThreshold( threshold ); 79 | filter->Update(); 80 | 81 | typedef itk::ReplaceFeatureMapNanInfImageFilter PostProcessingFilterType; 82 | PostProcessingFilterType::Pointer postProcessingFilter = PostProcessingFilterType::New(); 83 | 84 | postProcessingFilter->SetInput( filter->GetOutput() ); 85 | postProcessingFilter->Update(); 86 | 87 | itk::MetaDataDictionary dictionary; 88 | itk::EncapsulateMetaData(dictionary,"DWMRI_b-value","1.0"); 89 | itk::EncapsulateMetaData(dictionary,"modality","DWMRI"); 90 | postProcessingFilter->GetOutput()->SetMetaDataDictionary(dictionary); 91 | 92 | typedef itk::ImageFileWriter< OutputImageType > WriterType; 93 | typename WriterType::Pointer writer = WriterType::New(); 94 | writer->SetFileName( outputVolume ); 95 | writer->SetInput( postProcessingFilter->GetOutput() ); 96 | writer->SetUseCompression( true ); 97 | writer->Update(); 98 | 99 | return EXIT_SUCCESS; 100 | } 101 | 102 | } // end of anonymous namespace 103 | 104 | int main( int argc, char * argv[] ) 105 | { 106 | PARSE_ARGS; 107 | 108 | itk::ImageIOBase::IOPixelType inputPixelType; 109 | itk::ImageIOBase::IOComponentType inputComponentType; 110 | itk::FloatingPointExceptions::Enable(); 111 | itk::FloatingPointExceptions::SetExceptionAction( itk::FloatingPointExceptions::ABORT ); 112 | 113 | try 114 | { 115 | 116 | itk::GetImageType(inputVolume, inputPixelType, inputComponentType); 117 | 118 | switch( inputComponentType ) 119 | { 120 | case itk::ImageIOBase::UCHAR: 121 | return DoIt< int >( argc, argv ); 122 | break; 123 | case itk::ImageIOBase::USHORT: 124 | return DoIt< int >( argc, argv ); 125 | break; 126 | case itk::ImageIOBase::SHORT: 127 | return DoIt< int >( argc, argv ); 128 | break; 129 | case itk::ImageIOBase::FLOAT: 130 | return DoIt< float >( argc, argv ); 131 | break; 132 | case itk::ImageIOBase::INT: 133 | return DoIt< int >( argc, argv ); 134 | break; 135 | default: 136 | std::cerr << "Unknown input image pixel component type: " 137 | << itk::ImageIOBase::GetComponentTypeAsString( inputComponentType ) 138 | << std::endl; 139 | return EXIT_FAILURE; 140 | break; 141 | } 142 | } 143 | catch( itk::ExceptionObject & excep ) 144 | { 145 | std::cerr << argv[0] << ": exception caught !" << std::endl; 146 | std::cerr << excep << std::endl; 147 | return EXIT_FAILURE; 148 | } 149 | return EXIT_SUCCESS; 150 | } 151 | -------------------------------------------------------------------------------- /ComputeBMFeatureMaps/ComputeBMFeatureMaps.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | Quantification.Bone Morphometry Features 4 | Compute BM Feature Maps 5 | 1.0 6 | http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/ComputeBMFeatureMaps 7 | 8 | Jean-Baptiste Vimort, Kitware Inc. 9 | This work was supported by the National Institute of Health (NIH) National Institute for Dental and Craniofacial Research (NIDCR) R01EB021391 (Textural Biomarkers of Arthritis for the Subchondral Bone in the Temporomandibular Joint) 10 | 11 | 12 | Input/output parameters 13 | 14 | inputVolume 15 | 16 | input 17 | 0 18 | Input Volume 19 | 20 | 21 | outputVolume 22 | 23 | output 24 | 1 25 | Output Volume 26 | 27 | 28 | inputMask 29 | 30 | inputMask 31 | input 32 | s 33 | A mask defining the region over which texture features will be calculated 34 | 35 | 36 | 37 | threshold 38 | 39 | threshold 40 | t 41 | The threshold that will separate the inside and outside of the Bone (everything superior to the threshold is considered as part of the bone) 42 | 1 43 | 44 | 45 | neighborhoodRadius 46 | 47 | neighborhoodRadius 48 | n 49 | The size of the neighborhood radius 50 | 4 51 | 52 | 53 | 54 | -------------------------------------------------------------------------------- /ComputeBMFeatureMaps/Testing/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | add_subdirectory(Cxx) 2 | -------------------------------------------------------------------------------- /ComputeBMFeatureMaps/Testing/Cxx/CMakeLists.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Kitware/BoneTextureExtension/3410506efaa404131f7b02aa70769f537b1f2b3d/ComputeBMFeatureMaps/Testing/Cxx/CMakeLists.txt -------------------------------------------------------------------------------- /ComputeBMFeatures/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | #----------------------------------------------------------------------------- 2 | set(MODULE_NAME ComputeBMFeatures) 3 | 4 | #----------------------------------------------------------------------------- 5 | 6 | # 7 | # SlicerExecutionModel 8 | # 9 | find_package(SlicerExecutionModel REQUIRED) 10 | include(${SlicerExecutionModel_USE_FILE}) 11 | 12 | # 13 | # ITK 14 | # 15 | set(${PROJECT_NAME}_ITK_COMPONENTS 16 | ITKIOImageBase 17 | ITKCommon 18 | ITKStatistics 19 | ITKImageGrid 20 | ITKImageSources 21 | ITKTestKernel 22 | ITKMetaIO 23 | ITKImageIntensity 24 | BoneMorphometry 25 | ) 26 | find_package(ITK 4.9 COMPONENTS ${${PROJECT_NAME}_ITK_COMPONENTS} REQUIRED) 27 | if(ITK_VERSION VERSION_GREATER_EQUAL "5.3") 28 | foreach(factory_uc IN ITEMS "IMAGEIO" "MESHIO" "TRANSFORMIO") 29 | set(ITK_NO_${factory_uc}_FACTORY_REGISTER_MANAGER 1) 30 | endforeach() 31 | else() 32 | set(ITK_NO_IO_FACTORY_REGISTER_MANAGER 1) # See Libs/ITKFactoryRegistration/CMakeLists.txt 33 | endif() 34 | include(${ITK_USE_FILE}) 35 | 36 | #----------------------------------------------------------------------------- 37 | set(MODULE_INCLUDE_DIRECTORIES 38 | ${CMAKE_CURRENT_SOURCE_DIR}/../include 39 | ) 40 | 41 | set(MODULE_SRCS 42 | ) 43 | 44 | set(MODULE_TARGET_LIBRARIES 45 | ${ITK_LIBRARIES} 46 | ) 47 | 48 | #----------------------------------------------------------------------------- 49 | SEMMacroBuildCLI( 50 | NAME ${MODULE_NAME} 51 | TARGET_LIBRARIES ${MODULE_TARGET_LIBRARIES} 52 | INCLUDE_DIRECTORIES ${MODULE_INCLUDE_DIRECTORIES} 53 | ADDITIONAL_SRCS ${MODULE_SRCS} 54 | ) 55 | 56 | #----------------------------------------------------------------------------- 57 | if(BUILD_TESTING) 58 | add_subdirectory(Testing) 59 | endif() 60 | -------------------------------------------------------------------------------- /ComputeBMFeatures/ComputeBMFeatures.cxx: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | * 3 | * Copyright Insight Software Consortium 4 | * 5 | * Licensed under the Apache License, Version 2.0 (the "License"); 6 | * you may not use this file except in compliance with the License. 7 | * You may obtain a copy of the License at 8 | * 9 | * http://www.apache.org/licenses/LICENSE-2.0.txt 10 | * 11 | * Unless required by applicable law or agreed to in writing, software 12 | * distributed under the License is distributed on an "AS IS" BASIS, 13 | * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 14 | * See the License for the specific language governing permissions and 15 | * limitations under the License. 16 | * 17 | *=========================================================================*/ 18 | 19 | 20 | // Use an anonymous namespace to keep class types and function names 21 | // from colliding when module is used as shared object module. Every 22 | // thing should be in an anonymous namespace except for the module 23 | // entry point, e.g. main() 24 | // 25 | 26 | #include "itkImageFileReader.h" 27 | #include "itkImageFileWriter.h" 28 | #include "itkFloatingPointExceptions.h" 29 | #include "itkImage.h" 30 | #include "itkVector.h" 31 | #include "itkNeighborhood.h" 32 | #include "itkMetaDataDictionary.h" 33 | #include "itkMetaDataObject.h" 34 | 35 | #include "itkBoneMorphometryFeaturesFilter.h" 36 | 37 | #include "itkPluginUtilities.h" 38 | 39 | #include "ComputeBMFeaturesCLP.h" 40 | 41 | namespace 42 | { 43 | 44 | template< typename TPixel > 45 | int DoIt( int argc, char * argv[] ) 46 | { 47 | PARSE_ARGS; 48 | 49 | const unsigned int Dimension = 3; 50 | 51 | typedef TPixel PixelType; 52 | typedef itk::Image< PixelType, Dimension > InputImageType; 53 | 54 | typedef itk::ImageFileReader< InputImageType > ReaderType; 55 | typename ReaderType::Pointer reader = ReaderType::New(); 56 | reader->SetFileName( inputVolume ); 57 | reader->Update(); 58 | 59 | typedef itk::BoneMorphometryFeaturesFilter FilterType; 60 | typename FilterType::Pointer filter = FilterType::New(); 61 | filter->SetInput(reader->GetOutput()); 62 | 63 | if(inputMask != "") 64 | { 65 | typename ReaderType::Pointer maskReader = ReaderType::New(); 66 | maskReader->SetFileName( inputMask ); 67 | maskReader->Update(); 68 | filter->SetMaskImage(maskReader->GetOutput()); 69 | } 70 | 71 | filter->SetThreshold( threshold ); 72 | filter->Update(); 73 | 74 | std::ofstream rts; 75 | rts.open(returnParameterFile.c_str() ); 76 | rts << "outputVector = "<GetBVTV()<<"," 77 | <GetTbTh()<<"," 78 | <GetTbSp()<<"," 79 | <GetTbN()<<"," 80 | <GetBSBV()<< std::endl; 81 | rts<<"BVTV = "<< filter->GetBVTV() << std::endl; 82 | rts<<"TbTh = "<< filter->GetTbTh() << std::endl; 83 | rts<<"TbSp = "<< filter->GetTbSp() << std::endl; 84 | rts<<"TbN = "<< filter->GetTbN() << std::endl; 85 | rts<<"BSBV = "<< filter->GetBSBV() << std::endl; 86 | 87 | return EXIT_SUCCESS; 88 | } 89 | 90 | } // end of anonymous namespace 91 | 92 | int main( int argc, char * argv[] ) 93 | { 94 | PARSE_ARGS; 95 | 96 | itk::ImageIOBase::IOPixelType inputPixelType; 97 | itk::ImageIOBase::IOComponentType inputComponentType; 98 | itk::FloatingPointExceptions::Enable(); 99 | itk::FloatingPointExceptions::SetExceptionAction( itk::FloatingPointExceptions::ABORT ); 100 | 101 | try 102 | { 103 | 104 | itk::GetImageType(inputVolume, inputPixelType, inputComponentType); 105 | 106 | switch( inputComponentType ) 107 | { 108 | case itk::ImageIOBase::UCHAR: 109 | return DoIt< int >( argc, argv ); 110 | break; 111 | case itk::ImageIOBase::USHORT: 112 | return DoIt< int >( argc, argv ); 113 | break; 114 | case itk::ImageIOBase::SHORT: 115 | return DoIt< int >( argc, argv ); 116 | break; 117 | case itk::ImageIOBase::FLOAT: 118 | return DoIt< float >( argc, argv ); 119 | break; 120 | case itk::ImageIOBase::INT: 121 | return DoIt< int >( argc, argv ); 122 | break; 123 | default: 124 | std::cerr << "Unknown input image pixel component type: " 125 | << itk::ImageIOBase::GetComponentTypeAsString( inputComponentType ) 126 | << std::endl; 127 | return EXIT_FAILURE; 128 | break; 129 | } 130 | } 131 | catch( itk::ExceptionObject & excep ) 132 | { 133 | std::cerr << argv[0] << ": exception caught !" << std::endl; 134 | std::cerr << excep << std::endl; 135 | return EXIT_FAILURE; 136 | } 137 | return EXIT_SUCCESS; 138 | } 139 | -------------------------------------------------------------------------------- /ComputeBMFeatures/ComputeBMFeatures.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | Quantification.Bone Morphometry Features 4 | Compute BM Features 5 | 1.0 6 | http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/ComputeGLRLMFeatures 7 | 8 | Jean-Baptiste Vimort, Kitware Inc. 9 | This work was supported by the National Institute of Health (NIH) National Institute for Dental and Craniofacial Research (NIDCR) R01EB021391 (Textural Biomarkers of Arthritis for the Subchondral Bone in the Temporomandibular Joint) 10 | 11 | 12 | 13 | inputVolume 14 | 15 | input 16 | 0 17 | Input Volume 18 | 19 | 20 | inputMask 21 | 22 | inputMask 23 | input 24 | s 25 | A mask defining the region over which texture features will be calculated 26 | 27 | 28 | 29 | threshold 30 | 31 | threshold 32 | t 33 | The threshold that will separate the inside and outside of the Bone (everything superior to the threshold is considered as part of the bone) 34 | 1 35 | 36 | 37 | 38 | 39 | Output parameters 40 | 41 | BVTV 42 | 43 | output 44 | 45 | 46 | TbTh 47 | 48 | output 49 | 50 | 51 | TbSp 52 | 53 | output 54 | 55 | 56 | TbN 57 | 58 | output 59 | 60 | 61 | BSBV 62 | 63 | output 64 | 65 | 66 | 67 | 68 | Advanced parameters 69 | 70 | outputVector 71 | 72 | output 73 | Output Vector 74 | 75 | 76 | 77 | -------------------------------------------------------------------------------- /ComputeBMFeatures/Testing/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | add_subdirectory(Cxx) 2 | -------------------------------------------------------------------------------- /ComputeBMFeatures/Testing/Cxx/CMakeLists.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Kitware/BoneTextureExtension/3410506efaa404131f7b02aa70769f537b1f2b3d/ComputeBMFeatures/Testing/Cxx/CMakeLists.txt -------------------------------------------------------------------------------- /ComputeGLCMFeatureMaps/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | #----------------------------------------------------------------------------- 2 | set(MODULE_NAME ComputeGLCMFeatureMaps) 3 | 4 | #----------------------------------------------------------------------------- 5 | 6 | # 7 | # SlicerExecutionModel 8 | # 9 | find_package(SlicerExecutionModel REQUIRED) 10 | include(${SlicerExecutionModel_USE_FILE}) 11 | 12 | # 13 | # ITK 14 | # 15 | set(${PROJECT_NAME}_ITK_COMPONENTS 16 | ITKIOImageBase 17 | ITKCommon 18 | ITKStatistics 19 | ITKImageGrid 20 | ITKImageSources 21 | ITKTestKernel 22 | ITKMetaIO 23 | ITKImageIntensity 24 | TextureFeatures 25 | ) 26 | find_package(ITK 4.9 COMPONENTS ${${PROJECT_NAME}_ITK_COMPONENTS} REQUIRED) 27 | if(ITK_VERSION VERSION_GREATER_EQUAL "5.3") 28 | foreach(factory_uc IN ITEMS "IMAGEIO" "MESHIO" "TRANSFORMIO") 29 | set(ITK_NO_${factory_uc}_FACTORY_REGISTER_MANAGER 1) 30 | endforeach() 31 | else() 32 | set(ITK_NO_IO_FACTORY_REGISTER_MANAGER 1) # See Libs/ITKFactoryRegistration/CMakeLists.txt 33 | endif() 34 | include(${ITK_USE_FILE}) 35 | 36 | #----------------------------------------------------------------------------- 37 | set(MODULE_INCLUDE_DIRECTORIES 38 | ${CMAKE_CURRENT_SOURCE_DIR}/../include 39 | ) 40 | 41 | set(MODULE_SRCS 42 | ) 43 | 44 | set(MODULE_TARGET_LIBRARIES 45 | ${ITK_LIBRARIES} 46 | ) 47 | 48 | #----------------------------------------------------------------------------- 49 | SEMMacroBuildCLI( 50 | NAME ${MODULE_NAME} 51 | TARGET_LIBRARIES ${MODULE_TARGET_LIBRARIES} 52 | INCLUDE_DIRECTORIES ${MODULE_INCLUDE_DIRECTORIES} 53 | ADDITIONAL_SRCS ${MODULE_SRCS} 54 | ) 55 | 56 | #----------------------------------------------------------------------------- 57 | if(BUILD_TESTING) 58 | add_subdirectory(Testing) 59 | endif() 60 | -------------------------------------------------------------------------------- /ComputeGLCMFeatureMaps/ComputeGLCMFeatureMaps.cxx: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | * 3 | * Copyright Insight Software Consortium 4 | * 5 | * Licensed under the Apache License, Version 2.0 (the "License"); 6 | * you may not use this file except in compliance with the License. 7 | * You may obtain a copy of the License at 8 | * 9 | * http://www.apache.org/licenses/LICENSE-2.0.txt 10 | * 11 | * Unless required by applicable law or agreed to in writing, software 12 | * distributed under the License is distributed on an "AS IS" BASIS, 13 | * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 14 | * See the License for the specific language governing permissions and 15 | * limitations under the License. 16 | * 17 | *=========================================================================*/ 18 | 19 | 20 | // Use an anonymous namespace to keep class types and function names 21 | // from colliding when module is used as shared object module. Every 22 | // thing should be in an anonymous namespace except for the module 23 | // entry point, e.g. main() 24 | // 25 | 26 | #include "itkImageFileReader.h" 27 | #include "itkImageFileWriter.h" 28 | #include "itkFloatingPointExceptions.h" 29 | #include "itkImage.h" 30 | #include "itkVector.h" 31 | #include "itkNeighborhood.h" 32 | #include "itkMetaDataDictionary.h" 33 | #include "itkMetaDataObject.h" 34 | 35 | #include "itkCoocurrenceTextureFeaturesImageFilter.h" 36 | 37 | #include "itkPluginUtilities.h" 38 | 39 | #include "ComputeGLCMFeatureMapsCLP.h" 40 | 41 | namespace 42 | { 43 | 44 | template< typename TPixel > 45 | int DoIt( int argc, char * argv[] ) 46 | { 47 | PARSE_ARGS; 48 | 49 | const unsigned int Dimension = 3; 50 | 51 | typedef TPixel PixelType; 52 | typedef itk::Image< PixelType, Dimension > InputImageType; 53 | typedef itk::VectorImage< float, Dimension > OutputImageType; 54 | 55 | typedef itk::Neighborhood NeighborhoodType; 56 | NeighborhoodType hood; 57 | 58 | typedef itk::ImageFileReader< InputImageType > ReaderType; 59 | typename ReaderType::Pointer reader = ReaderType::New(); 60 | reader->SetFileName( inputVolume ); 61 | reader->Update(); 62 | 63 | typedef itk::Statistics::CoocurrenceTextureFeaturesImageFilter< InputImageType, OutputImageType, InputImageType > FilterType; 64 | typename FilterType::Pointer filter = FilterType::New(); 65 | filter->SetInput(reader->GetOutput()); 66 | 67 | if(inputMask != "") 68 | { 69 | typename ReaderType::Pointer maskReader = ReaderType::New(); 70 | maskReader->SetFileName( inputMask ); 71 | maskReader->Update(); 72 | filter->SetMaskImage(maskReader->GetOutput()); 73 | } 74 | 75 | filter->SetInsidePixelValue(insideMask); 76 | filter->SetNumberOfBinsPerAxis(binNumber); 77 | hood.SetRadius(neighborhoodRadius); 78 | filter->SetNeighborhoodRadius(hood.GetRadius()); 79 | filter->SetHistogramMinimum( pixelIntensityMin ); 80 | filter->SetHistogramMaximum( pixelIntensityMax ); 81 | filter->Update(); 82 | 83 | itk::MetaDataDictionary dictionary; 84 | itk::EncapsulateMetaData(dictionary,"DWMRI_b-value","1.0"); 85 | itk::EncapsulateMetaData(dictionary,"modality","DWMRI"); 86 | filter->GetOutput()->SetMetaDataDictionary(dictionary); 87 | 88 | typedef itk::ImageFileWriter< OutputImageType > WriterType; 89 | typename WriterType::Pointer writer = WriterType::New(); 90 | writer->SetFileName( outputVolume ); 91 | writer->SetInput( filter->GetOutput() ); 92 | writer->SetUseCompression( true ); 93 | writer->Update(); 94 | 95 | return EXIT_SUCCESS; 96 | } 97 | 98 | } // end of anonymous namespace 99 | 100 | int main( int argc, char * argv[] ) 101 | { 102 | PARSE_ARGS; 103 | 104 | itk::ImageIOBase::IOPixelType inputPixelType; 105 | itk::ImageIOBase::IOComponentType inputComponentType; 106 | itk::FloatingPointExceptions::Enable(); 107 | itk::FloatingPointExceptions::SetExceptionAction( itk::FloatingPointExceptions::ABORT ); 108 | 109 | try 110 | { 111 | 112 | itk::GetImageType(inputVolume, inputPixelType, inputComponentType); 113 | 114 | switch( inputComponentType ) 115 | { 116 | case itk::ImageIOBase::UCHAR: 117 | return DoIt< int >( argc, argv ); 118 | break; 119 | case itk::ImageIOBase::USHORT: 120 | return DoIt< int >( argc, argv ); 121 | break; 122 | case itk::ImageIOBase::SHORT: 123 | return DoIt< int >( argc, argv ); 124 | break; 125 | case itk::ImageIOBase::FLOAT: 126 | return DoIt< float >( argc, argv ); 127 | break; 128 | case itk::ImageIOBase::INT: 129 | return DoIt< int >( argc, argv ); 130 | break; 131 | default: 132 | std::cerr << "Unknown input image pixel component type: " 133 | << itk::ImageIOBase::GetComponentTypeAsString( inputComponentType ) 134 | << std::endl; 135 | return EXIT_FAILURE; 136 | break; 137 | } 138 | } 139 | catch( itk::ExceptionObject & excep ) 140 | { 141 | std::cerr << argv[0] << ": exception caught !" << std::endl; 142 | std::cerr << excep << std::endl; 143 | return EXIT_FAILURE; 144 | } 145 | return EXIT_SUCCESS; 146 | } 147 | -------------------------------------------------------------------------------- /ComputeGLCMFeatureMaps/ComputeGLCMFeatureMaps.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | Quantification.Texture Features 4 | Compute GLCM Feature Maps 5 | 1.0 6 | http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/ComputeGLCMFeatureMaps 7 | 8 | Jean-Baptiste Vimort, Kitware Inc. 9 | This work was supported by the National Institute of Health (NIH) National Institute for Dental and Craniofacial Research (NIDCR) R01EB021391 (Textural Biomarkers of Arthritis for the Subchondral Bone in the Temporomandibular Joint) 10 | 11 | 12 | Input/output parameters 13 | 14 | inputVolume 15 | 16 | input 17 | 0 18 | Input Volume 19 | 20 | 21 | outputVolume 22 | 23 | output 24 | 1 25 | Output Volume 26 | 27 | 28 | inputMask 29 | 30 | inputMask 31 | input 32 | s 33 | A mask defining the region over which texture features will be calculated 34 | 35 | 36 | 37 | insideMask 38 | 39 | insideMask 40 | i 41 | The pixel value that defines the ”inside” of the mask 42 | 1 43 | 44 | 45 | binNumber 46 | 47 | binNumber 48 | b 49 | The number of intensity bins 50 | 10 51 | 52 | 53 | neighborhoodRadius 54 | 55 | neighborhoodRadius 56 | n 57 | The size of the neighborhood radius 58 | 4 59 | 60 | 61 | pixelIntensityMin 62 | 63 | pixelIntensityMin 64 | p 65 | Minnimum of the pixel intensity range over which the features will be calculated 66 | 0 67 | 68 | 69 | pixelIntensityMax 70 | 71 | pixelIntensityMax 72 | P 73 | Maximum of the pixel intensity range over which the features will be calculated 74 | 4000 75 | 76 | 77 | 78 | -------------------------------------------------------------------------------- /ComputeGLCMFeatureMaps/Testing/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | add_subdirectory(Cxx) 2 | -------------------------------------------------------------------------------- /ComputeGLCMFeatureMaps/Testing/Cxx/CMakeLists.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Kitware/BoneTextureExtension/3410506efaa404131f7b02aa70769f537b1f2b3d/ComputeGLCMFeatureMaps/Testing/Cxx/CMakeLists.txt -------------------------------------------------------------------------------- /ComputeGLCMFeatures/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | #----------------------------------------------------------------------------- 2 | set(MODULE_NAME ComputeGLCMFeatures) 3 | 4 | #----------------------------------------------------------------------------- 5 | 6 | # 7 | # SlicerExecutionModel 8 | # 9 | find_package(SlicerExecutionModel REQUIRED) 10 | include(${SlicerExecutionModel_USE_FILE}) 11 | 12 | # 13 | # ITK 14 | # 15 | set(${PROJECT_NAME}_ITK_COMPONENTS 16 | ITKIOImageBase 17 | ITKCommon 18 | ITKStatistics 19 | ITKImageGrid 20 | ITKImageSources 21 | ITKTestKernel 22 | ITKMetaIO 23 | ITKImageIntensity 24 | ) 25 | find_package(ITK 4.9 COMPONENTS ${${PROJECT_NAME}_ITK_COMPONENTS} REQUIRED) 26 | if(ITK_VERSION VERSION_GREATER_EQUAL "5.3") 27 | foreach(factory_uc IN ITEMS "IMAGEIO" "MESHIO" "TRANSFORMIO") 28 | set(ITK_NO_${factory_uc}_FACTORY_REGISTER_MANAGER 1) 29 | endforeach() 30 | else() 31 | set(ITK_NO_IO_FACTORY_REGISTER_MANAGER 1) # See Libs/ITKFactoryRegistration/CMakeLists.txt 32 | endif() 33 | include(${ITK_USE_FILE}) 34 | 35 | #----------------------------------------------------------------------------- 36 | set(MODULE_INCLUDE_DIRECTORIES 37 | ${CMAKE_CURRENT_SOURCE_DIR}/../include 38 | ) 39 | 40 | set(MODULE_SRCS 41 | ) 42 | 43 | set(MODULE_TARGET_LIBRARIES 44 | ${ITK_LIBRARIES} 45 | ) 46 | 47 | #----------------------------------------------------------------------------- 48 | SEMMacroBuildCLI( 49 | NAME ${MODULE_NAME} 50 | TARGET_LIBRARIES ${MODULE_TARGET_LIBRARIES} 51 | INCLUDE_DIRECTORIES ${MODULE_INCLUDE_DIRECTORIES} 52 | ADDITIONAL_SRCS ${MODULE_SRCS} 53 | ) 54 | 55 | #----------------------------------------------------------------------------- 56 | if(BUILD_TESTING) 57 | add_subdirectory(Testing) 58 | endif() 59 | -------------------------------------------------------------------------------- /ComputeGLCMFeatures/ComputeGLCMFeatures.cxx: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | * 3 | * Copyright Insight Software Consortium 4 | * 5 | * Licensed under the Apache License, Version 2.0 (the "License"); 6 | * you may not use this file except in compliance with the License. 7 | * You may obtain a copy of the License at 8 | * 9 | * http://www.apache.org/licenses/LICENSE-2.0.txt 10 | * 11 | * Unless required by applicable law or agreed to in writing, software 12 | * distributed under the License is distributed on an "AS IS" BASIS, 13 | * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 14 | * See the License for the specific language governing permissions and 15 | * limitations under the License. 16 | * 17 | *=========================================================================*/ 18 | 19 | 20 | // Use an anonymous namespace to keep class types and function names 21 | // from colliding when module is used as shared object module. Every 22 | // thing should be in an anonymous namespace except for the module 23 | // entry point, e.g. main() 24 | // 25 | 26 | #include "itkImageFileReader.h" 27 | #include "itkImageFileWriter.h" 28 | #include "itkFloatingPointExceptions.h" 29 | #include "itkImage.h" 30 | #include "itkVector.h" 31 | #include "itkNeighborhood.h" 32 | #include "itkMetaDataDictionary.h" 33 | #include "itkMetaDataObject.h" 34 | 35 | #include "itkScalarImageToTextureFeaturesFilter.h" 36 | 37 | #include "itkPluginUtilities.h" 38 | 39 | #include "ComputeGLCMFeaturesCLP.h" 40 | 41 | namespace 42 | { 43 | 44 | template< typename TPixel > 45 | int DoIt( int argc, char * argv[] ) 46 | { 47 | PARSE_ARGS; 48 | 49 | const unsigned int Dimension = 3; 50 | 51 | typedef TPixel PixelType; 52 | typedef itk::Image< PixelType, Dimension > InputImageType; 53 | 54 | typedef itk::ImageFileReader< InputImageType > ReaderType; 55 | typename ReaderType::Pointer reader = ReaderType::New(); 56 | reader->SetFileName( inputVolume ); 57 | reader->Update(); 58 | 59 | typedef itk::Statistics::ScalarImageToTextureFeaturesFilter< InputImageType> FilterType; 60 | typename FilterType::Pointer filter = FilterType::New(); 61 | filter->SetInput(reader->GetOutput()); 62 | 63 | if(inputMask != "") 64 | { 65 | typename ReaderType::Pointer maskReader = ReaderType::New(); 66 | maskReader->SetFileName( inputMask ); 67 | maskReader->Update(); 68 | filter->SetMaskImage(maskReader->GetOutput()); 69 | } 70 | 71 | filter->SetInsidePixelValue(insideMask); 72 | filter->SetNumberOfBinsPerAxis(binNumber); 73 | filter->SetPixelValueMinMax(pixelIntensityMin, pixelIntensityMax); 74 | 75 | typename FilterType::FeatureNameVectorPointer requestedFeatures = FilterType::FeatureNameVector::New(); 76 | requestedFeatures->push_back(static_cast(FilterType::TextureFeaturesFilterType::Energy)); 77 | requestedFeatures->push_back(static_cast(FilterType::TextureFeaturesFilterType::Entropy)); 78 | requestedFeatures->push_back(static_cast(FilterType::TextureFeaturesFilterType::Correlation)); 79 | requestedFeatures->push_back(static_cast(FilterType::TextureFeaturesFilterType::InverseDifferenceMoment)); 80 | requestedFeatures->push_back(static_cast(FilterType::TextureFeaturesFilterType::Inertia)); 81 | requestedFeatures->push_back(static_cast(FilterType::TextureFeaturesFilterType::ClusterShade)); 82 | requestedFeatures->push_back(static_cast(FilterType::TextureFeaturesFilterType::ClusterProminence)); 83 | requestedFeatures->push_back(static_cast(FilterType::TextureFeaturesFilterType::HaralickCorrelation)); 84 | filter->SetRequestedFeatures(requestedFeatures); 85 | 86 | filter->Update(); 87 | 88 | typename FilterType::FeatureValueVector::ConstIterator mIt; 89 | typename FilterType::FeatureValueVectorPointer meanVector = filter->GetFeatureMeans(); 90 | std::ofstream rts; 91 | rts.open(returnParameterFile.c_str() ); 92 | rts << "outputVector = "; 93 | for(mIt = meanVector->Begin(); mIt != meanVector->End(); mIt++) 94 | { 95 | if(mIt != meanVector->Begin()) 96 | { 97 | rts << ","; 98 | } 99 | rts << mIt.Value(); 100 | } 101 | rts << std::endl; 102 | 103 | mIt = meanVector->Begin(); 104 | 105 | rts<<"Energy = "<< mIt.Value() << std::endl; 106 | mIt++; 107 | rts<<"Entropy = "<< mIt.Value() << std::endl; 108 | mIt++; 109 | rts<<"Correlation = "<< mIt.Value() << std::endl; 110 | mIt++; 111 | rts<<"InverseDifferenceMoment = "<< mIt.Value() << std::endl; 112 | mIt++; 113 | rts<<"Inertia = "<< mIt.Value() << std::endl; 114 | mIt++; 115 | rts<<"ClusterShade = "<< mIt.Value() << std::endl; 116 | mIt++; 117 | rts<<"ClusterProminence = "<< mIt.Value() << std::endl; 118 | mIt++; 119 | rts<<"HaralickCorrelation = "<< mIt.Value() << std::endl; 120 | 121 | return EXIT_SUCCESS; 122 | } 123 | 124 | } // end of anonymous namespace 125 | 126 | int main( int argc, char * argv[] ) 127 | { 128 | PARSE_ARGS; 129 | 130 | itk::ImageIOBase::IOPixelType inputPixelType; 131 | itk::ImageIOBase::IOComponentType inputComponentType; 132 | itk::FloatingPointExceptions::Enable(); 133 | itk::FloatingPointExceptions::SetExceptionAction( itk::FloatingPointExceptions::ABORT ); 134 | 135 | try 136 | { 137 | 138 | itk::GetImageType(inputVolume, inputPixelType, inputComponentType); 139 | 140 | switch( inputComponentType ) 141 | { 142 | case itk::ImageIOBase::UCHAR: 143 | return DoIt< int >( argc, argv ); 144 | break; 145 | case itk::ImageIOBase::USHORT: 146 | return DoIt< int >( argc, argv ); 147 | break; 148 | case itk::ImageIOBase::SHORT: 149 | return DoIt< int >( argc, argv ); 150 | break; 151 | case itk::ImageIOBase::FLOAT: 152 | return DoIt< float >( argc, argv ); 153 | break; 154 | case itk::ImageIOBase::INT: 155 | return DoIt< int >( argc, argv ); 156 | break; 157 | default: 158 | std::cerr << "Unknown input image pixel component type: " 159 | << itk::ImageIOBase::GetComponentTypeAsString( inputComponentType ) 160 | << std::endl; 161 | return EXIT_FAILURE; 162 | break; 163 | } 164 | } 165 | catch( itk::ExceptionObject & excep ) 166 | { 167 | std::cerr << argv[0] << ": exception caught !" << std::endl; 168 | std::cerr << excep << std::endl; 169 | return EXIT_FAILURE; 170 | } 171 | return EXIT_SUCCESS; 172 | } 173 | -------------------------------------------------------------------------------- /ComputeGLCMFeatures/ComputeGLCMFeatures.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | Quantification.Texture Features 4 | Compute GLCM Features 5 | 1.0 6 | http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/ComputeGLCMFeatures 7 | 8 | Jean-Baptiste Vimort, Kitware Inc. 9 | This work was supported by the National Institute of Health (NIH) National Institute for Dental and Craniofacial Research (NIDCR) R01EB021391 (Textural Biomarkers of Arthritis for the Subchondral Bone in the Temporomandibular Joint) 10 | 11 | 12 | Input parameters 13 | 14 | inputVolume 15 | 16 | input 17 | 0 18 | Input Volume 19 | 20 | 21 | inputMask 22 | 23 | inputMask 24 | input 25 | s 26 | A mask defining the region over which texture features will be calculated 27 | 28 | 29 | 30 | insideMask 31 | 32 | insideMask 33 | i 34 | The pixel value that defines the ”inside” of the mask 35 | 1 36 | 37 | 38 | binNumber 39 | 40 | binNumber 41 | b 42 | The number of intensity bins 43 | 10 44 | 45 | 46 | pixelIntensityMin 47 | 48 | pixelIntensityMin 49 | p 50 | Minnimum of the pixel intensity range over which the features will be calculated 51 | 0 52 | 53 | 54 | pixelIntensityMax 55 | 56 | pixelIntensityMax 57 | P 58 | Maximum of the pixel intensity range over which the features will be calculated 59 | 4000 60 | 61 | 62 | 63 | 64 | Output parameters 65 | 66 | Energy 67 | 68 | output 69 | 70 | 71 | Entropy 72 | 73 | output 74 | 75 | 76 | Correlation 77 | 78 | output 79 | 80 | 81 | InverseDifferenceMoment 82 | 83 | output 84 | 85 | 86 | Inertia 87 | 88 | output 89 | 90 | 91 | ClusterShade 92 | 93 | output 94 | 95 | 96 | ClusterProminence 97 | 98 | output 99 | 100 | 101 | HaralickCorrelation 102 | 103 | output 104 | 105 | 106 | 107 | 108 | Advanced parameters 109 | 110 | outputVector 111 | 112 | output 113 | Output Vector 114 | 115 | 116 | 117 | -------------------------------------------------------------------------------- /ComputeGLCMFeatures/Testing/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | add_subdirectory(Cxx) 2 | -------------------------------------------------------------------------------- /ComputeGLCMFeatures/Testing/Cxx/CMakeLists.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Kitware/BoneTextureExtension/3410506efaa404131f7b02aa70769f537b1f2b3d/ComputeGLCMFeatures/Testing/Cxx/CMakeLists.txt -------------------------------------------------------------------------------- /ComputeGLRLMFeatureMaps/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | #----------------------------------------------------------------------------- 2 | set(MODULE_NAME ComputeGLRLMFeatureMaps) 3 | 4 | #----------------------------------------------------------------------------- 5 | 6 | # 7 | # SlicerExecutionModel 8 | # 9 | find_package(SlicerExecutionModel REQUIRED) 10 | include(${SlicerExecutionModel_USE_FILE}) 11 | 12 | # 13 | # ITK 14 | # 15 | set(${PROJECT_NAME}_ITK_COMPONENTS 16 | ITKIOImageBase 17 | ITKCommon 18 | ITKStatistics 19 | ITKImageGrid 20 | ITKImageSources 21 | ITKTestKernel 22 | ITKMetaIO 23 | ITKImageIntensity 24 | TextureFeatures 25 | ) 26 | find_package(ITK 4.9 COMPONENTS ${${PROJECT_NAME}_ITK_COMPONENTS} REQUIRED) 27 | if(ITK_VERSION VERSION_GREATER_EQUAL "5.3") 28 | foreach(factory_uc IN ITEMS "IMAGEIO" "MESHIO" "TRANSFORMIO") 29 | set(ITK_NO_${factory_uc}_FACTORY_REGISTER_MANAGER 1) 30 | endforeach() 31 | else() 32 | set(ITK_NO_IO_FACTORY_REGISTER_MANAGER 1) # See Libs/ITKFactoryRegistration/CMakeLists.txt 33 | endif() 34 | include(${ITK_USE_FILE}) 35 | 36 | #----------------------------------------------------------------------------- 37 | set(MODULE_INCLUDE_DIRECTORIES 38 | ${CMAKE_CURRENT_SOURCE_DIR}/../include 39 | ) 40 | 41 | set(MODULE_SRCS 42 | ) 43 | 44 | set(MODULE_TARGET_LIBRARIES 45 | ${ITK_LIBRARIES} 46 | ) 47 | 48 | #----------------------------------------------------------------------------- 49 | SEMMacroBuildCLI( 50 | NAME ${MODULE_NAME} 51 | TARGET_LIBRARIES ${MODULE_TARGET_LIBRARIES} 52 | INCLUDE_DIRECTORIES ${MODULE_INCLUDE_DIRECTORIES} 53 | ADDITIONAL_SRCS ${MODULE_SRCS} 54 | ) 55 | 56 | #----------------------------------------------------------------------------- 57 | if(BUILD_TESTING) 58 | add_subdirectory(Testing) 59 | endif() 60 | -------------------------------------------------------------------------------- /ComputeGLRLMFeatureMaps/ComputeGLRLMFeatureMaps.cxx: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | * 3 | * Copyright Insight Software Consortium 4 | * 5 | * Licensed under the Apache License, Version 2.0 (the "License"); 6 | * you may not use this file except in compliance with the License. 7 | * You may obtain a copy of the License at 8 | * 9 | * http://www.apache.org/licenses/LICENSE-2.0.txt 10 | * 11 | * Unless required by applicable law or agreed to in writing, software 12 | * distributed under the License is distributed on an "AS IS" BASIS, 13 | * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 14 | * See the License for the specific language governing permissions and 15 | * limitations under the License. 16 | * 17 | *=========================================================================*/ 18 | 19 | 20 | // Use an anonymous namespace to keep class types and function names 21 | // from colliding when module is used as shared object module. Every 22 | // thing should be in an anonymous namespace except for the module 23 | // entry point, e.g. main() 24 | // 25 | 26 | #include "itkImageFileReader.h" 27 | #include "itkImageFileWriter.h" 28 | #include "itkFloatingPointExceptions.h" 29 | #include "itkImage.h" 30 | #include "itkVector.h" 31 | #include "itkNeighborhood.h" 32 | #include "itkMetaDataDictionary.h" 33 | #include "itkMetaDataObject.h" 34 | 35 | #include "itkRunLengthTextureFeaturesImageFilter.h" 36 | 37 | #include "itkPluginUtilities.h" 38 | 39 | #include "ComputeGLRLMFeatureMapsCLP.h" 40 | 41 | namespace 42 | { 43 | 44 | template< typename TPixel > 45 | int DoIt( int argc, char * argv[] ) 46 | { 47 | PARSE_ARGS; 48 | 49 | const unsigned int Dimension = 3; 50 | 51 | typedef TPixel PixelType; 52 | typedef itk::Image< PixelType, Dimension > InputImageType; 53 | typedef itk::VectorImage< float, Dimension > OutputImageType; 54 | 55 | typedef itk::Neighborhood NeighborhoodType; 56 | NeighborhoodType hood; 57 | 58 | typedef itk::ImageFileReader< InputImageType > ReaderType; 59 | typename ReaderType::Pointer reader = ReaderType::New(); 60 | reader->SetFileName( inputVolume ); 61 | reader->Update(); 62 | 63 | typedef itk::Statistics::RunLengthTextureFeaturesImageFilter< InputImageType, OutputImageType ,InputImageType > FilterType; 64 | typename FilterType::Pointer filter = FilterType::New(); 65 | filter->SetInput(reader->GetOutput()); 66 | 67 | if(inputMask != "") 68 | { 69 | typename ReaderType::Pointer maskReader = ReaderType::New(); 70 | maskReader->SetFileName( inputMask ); 71 | maskReader->Update(); 72 | filter->SetMaskImage(maskReader->GetOutput()); 73 | } 74 | 75 | filter->SetInsidePixelValue(insideMask); 76 | filter->SetNumberOfBinsPerAxis(binNumber); 77 | hood.SetRadius(neighborhoodRadius); 78 | filter->SetNeighborhoodRadius(hood.GetRadius()); 79 | filter->SetHistogramValueMinimum( pixelIntensityMin ); 80 | filter->SetHistogramValueMaximum( pixelIntensityMax ); 81 | filter->SetHistogramDistanceMinimum( distanceMin ); 82 | filter->SetHistogramDistanceMaximum( distanceMax ); 83 | filter->Update(); 84 | 85 | itk::MetaDataDictionary dictionary; 86 | itk::EncapsulateMetaData(dictionary,"DWMRI_b-value","1.0"); 87 | itk::EncapsulateMetaData(dictionary,"modality","DWMRI"); 88 | filter->GetOutput()->SetMetaDataDictionary(dictionary); 89 | 90 | typedef itk::ImageFileWriter< OutputImageType > WriterType; 91 | typename WriterType::Pointer writer = WriterType::New(); 92 | writer->SetFileName( outputVolume ); 93 | writer->SetInput( filter->GetOutput() ); 94 | writer->SetUseCompression( true ); 95 | writer->Update(); 96 | 97 | return EXIT_SUCCESS; 98 | } 99 | 100 | } // end of anonymous namespace 101 | 102 | int main( int argc, char * argv[] ) 103 | { 104 | PARSE_ARGS; 105 | 106 | itk::ImageIOBase::IOPixelType inputPixelType; 107 | itk::ImageIOBase::IOComponentType inputComponentType; 108 | itk::FloatingPointExceptions::Enable(); 109 | itk::FloatingPointExceptions::SetExceptionAction( itk::FloatingPointExceptions::ABORT ); 110 | 111 | try 112 | { 113 | 114 | itk::GetImageType(inputVolume, inputPixelType, inputComponentType); 115 | 116 | switch( inputComponentType ) 117 | { 118 | case itk::ImageIOBase::UCHAR: 119 | return DoIt< int >( argc, argv ); 120 | break; 121 | case itk::ImageIOBase::USHORT: 122 | return DoIt< int >( argc, argv ); 123 | break; 124 | case itk::ImageIOBase::SHORT: 125 | return DoIt< int >( argc, argv ); 126 | break; 127 | case itk::ImageIOBase::FLOAT: 128 | return DoIt< float >( argc, argv ); 129 | break; 130 | case itk::ImageIOBase::INT: 131 | return DoIt< int >( argc, argv ); 132 | break; 133 | default: 134 | std::cerr << "Unknown input image pixel component type: " 135 | << itk::ImageIOBase::GetComponentTypeAsString( inputComponentType ) 136 | << std::endl; 137 | return EXIT_FAILURE; 138 | break; 139 | } 140 | } 141 | catch( itk::ExceptionObject & excep ) 142 | { 143 | std::cerr << argv[0] << ": exception caught !" << std::endl; 144 | std::cerr << excep << std::endl; 145 | return EXIT_FAILURE; 146 | } 147 | return EXIT_SUCCESS; 148 | } 149 | -------------------------------------------------------------------------------- /ComputeGLRLMFeatureMaps/ComputeGLRLMFeatureMaps.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | Quantification.Texture Features 4 | Compute GLRLM Feature Maps 5 | 1.0 6 | http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/ComputeGLRLMFeatureMaps 7 | 8 | Jean-Baptiste Vimort, Kitware Inc. 9 | This work was supported by the National Institute of Health (NIH) National Institute for Dental and Craniofacial Research (NIDCR) R01EB021391 (Textural Biomarkers of Arthritis for the Subchondral Bone in the Temporomandibular Joint) 10 | 11 | 12 | Input/output parameters 13 | 14 | inputVolume 15 | 16 | input 17 | 0 18 | Input Volume 19 | 20 | 21 | outputVolume 22 | 23 | output 24 | 1 25 | Output Volume 26 | 27 | 28 | inputMask 29 | 30 | inputMask 31 | input 32 | s 33 | A mask defining the region over which texture features will be calculated 34 | 35 | 36 | 37 | insideMask 38 | 39 | insideMask 40 | i 41 | The pixel value that defines the ”inside” of the mask 42 | 1 43 | 44 | 45 | binNumber 46 | 47 | binNumber 48 | b 49 | The number of intensity bins 50 | 10 51 | 52 | 53 | neighborhoodRadius 54 | 55 | neighborhoodRadius 56 | n 57 | The size of the neighborhood radius 58 | 4 59 | 60 | 61 | pixelIntensityMin 62 | 63 | pixelIntensityMin 64 | p 65 | Minnimum of the pixel intensity range over which the features will be calculated 66 | 0 67 | 68 | 69 | pixelIntensityMax 70 | 71 | pixelIntensityMax 72 | P 73 | Maximum of the pixel intensity range over which the features will be calculated 74 | 4000 75 | 76 | 77 | distanceMin 78 | 79 | distanceMin 80 | d 81 | Minnimum of the distance range over which the features will be calculated 82 | 0.0 83 | 84 | 85 | distanceMax 86 | 87 | distanceMax 88 | D 89 | Maximum of the distance range over which the features will be calculated 90 | 1.0 91 | 92 | 93 | 94 | -------------------------------------------------------------------------------- /ComputeGLRLMFeatureMaps/Testing/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | add_subdirectory(Cxx) 2 | -------------------------------------------------------------------------------- /ComputeGLRLMFeatureMaps/Testing/Cxx/CMakeLists.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Kitware/BoneTextureExtension/3410506efaa404131f7b02aa70769f537b1f2b3d/ComputeGLRLMFeatureMaps/Testing/Cxx/CMakeLists.txt -------------------------------------------------------------------------------- /ComputeGLRLMFeatures/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | #----------------------------------------------------------------------------- 2 | set(MODULE_NAME ComputeGLRLMFeatures) 3 | 4 | #----------------------------------------------------------------------------- 5 | 6 | # 7 | # SlicerExecutionModel 8 | # 9 | find_package(SlicerExecutionModel REQUIRED) 10 | include(${SlicerExecutionModel_USE_FILE}) 11 | 12 | # 13 | # ITK 14 | # 15 | set(${PROJECT_NAME}_ITK_COMPONENTS 16 | ITKIOImageBase 17 | ITKCommon 18 | ITKStatistics 19 | ITKImageGrid 20 | ITKImageSources 21 | ITKTestKernel 22 | ITKMetaIO 23 | ITKImageIntensity 24 | ) 25 | find_package(ITK 4.9 COMPONENTS ${${PROJECT_NAME}_ITK_COMPONENTS} REQUIRED) 26 | if(ITK_VERSION VERSION_GREATER_EQUAL "5.3") 27 | foreach(factory_uc IN ITEMS "IMAGEIO" "MESHIO" "TRANSFORMIO") 28 | set(ITK_NO_${factory_uc}_FACTORY_REGISTER_MANAGER 1) 29 | endforeach() 30 | else() 31 | set(ITK_NO_IO_FACTORY_REGISTER_MANAGER 1) # See Libs/ITKFactoryRegistration/CMakeLists.txt 32 | endif() 33 | include(${ITK_USE_FILE}) 34 | 35 | #----------------------------------------------------------------------------- 36 | set(MODULE_INCLUDE_DIRECTORIES 37 | ${CMAKE_CURRENT_SOURCE_DIR}/../include 38 | ) 39 | 40 | set(MODULE_SRCS 41 | ) 42 | 43 | set(MODULE_TARGET_LIBRARIES 44 | ${ITK_LIBRARIES} 45 | ) 46 | 47 | #----------------------------------------------------------------------------- 48 | SEMMacroBuildCLI( 49 | NAME ${MODULE_NAME} 50 | TARGET_LIBRARIES ${MODULE_TARGET_LIBRARIES} 51 | INCLUDE_DIRECTORIES ${MODULE_INCLUDE_DIRECTORIES} 52 | ADDITIONAL_SRCS ${MODULE_SRCS} 53 | ) 54 | 55 | #----------------------------------------------------------------------------- 56 | if(BUILD_TESTING) 57 | add_subdirectory(Testing) 58 | endif() 59 | -------------------------------------------------------------------------------- /ComputeGLRLMFeatures/ComputeGLRLMFeatures.cxx: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | * 3 | * Copyright Insight Software Consortium 4 | * 5 | * Licensed under the Apache License, Version 2.0 (the "License"); 6 | * you may not use this file except in compliance with the License. 7 | * You may obtain a copy of the License at 8 | * 9 | * http://www.apache.org/licenses/LICENSE-2.0.txt 10 | * 11 | * Unless required by applicable law or agreed to in writing, software 12 | * distributed under the License is distributed on an "AS IS" BASIS, 13 | * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 14 | * See the License for the specific language governing permissions and 15 | * limitations under the License. 16 | * 17 | *=========================================================================*/ 18 | 19 | 20 | // Use an anonymous namespace to keep class types and function names 21 | // from colliding when module is used as shared object module. Every 22 | // thing should be in an anonymous namespace except for the module 23 | // entry point, e.g. main() 24 | // 25 | 26 | #include "itkImageFileReader.h" 27 | #include "itkImageFileWriter.h" 28 | #include "itkFloatingPointExceptions.h" 29 | #include "itkImage.h" 30 | #include "itkVector.h" 31 | #include "itkNeighborhood.h" 32 | #include "itkMetaDataDictionary.h" 33 | #include "itkMetaDataObject.h" 34 | 35 | #include "itkScalarImageToRunLengthFeaturesFilter.h" 36 | 37 | #include "itkPluginUtilities.h" 38 | 39 | #include "ComputeGLRLMFeaturesCLP.h" 40 | 41 | namespace 42 | { 43 | 44 | template< typename TPixel > 45 | int DoIt( int argc, char * argv[] ) 46 | { 47 | PARSE_ARGS; 48 | 49 | const unsigned int Dimension = 3; 50 | 51 | typedef TPixel PixelType; 52 | typedef itk::Image< PixelType, Dimension > InputImageType; 53 | 54 | typedef itk::ImageFileReader< InputImageType > ReaderType; 55 | typename ReaderType::Pointer reader = ReaderType::New(); 56 | reader->SetFileName( inputVolume ); 57 | reader->Update(); 58 | 59 | typedef itk::Statistics::ScalarImageToRunLengthFeaturesFilter< InputImageType> FilterType; 60 | typename FilterType::Pointer filter = FilterType::New(); 61 | filter->SetInput(reader->GetOutput()); 62 | 63 | if(inputMask != "") 64 | { 65 | typename ReaderType::Pointer maskReader = ReaderType::New(); 66 | maskReader->SetFileName( inputMask ); 67 | maskReader->Update(); 68 | filter->SetMaskImage(maskReader->GetOutput()); 69 | } 70 | 71 | filter->SetInsidePixelValue(insideMask); 72 | filter->SetNumberOfBinsPerAxis(binNumber); 73 | filter->SetPixelValueMinMax(pixelIntensityMin, pixelIntensityMax); 74 | filter->SetDistanceValueMinMax(distanceMin, distanceMax); 75 | 76 | typename FilterType::FeatureNameVectorPointer requestedFeatures = FilterType::FeatureNameVector::New(); 77 | requestedFeatures->push_back(static_cast(FilterType::RunLengthFeaturesFilterType::ShortRunEmphasis)); 78 | requestedFeatures->push_back(static_cast(FilterType::RunLengthFeaturesFilterType::LongRunEmphasis)); 79 | requestedFeatures->push_back(static_cast(FilterType::RunLengthFeaturesFilterType::GreyLevelNonuniformity)); 80 | requestedFeatures->push_back(static_cast(FilterType::RunLengthFeaturesFilterType::RunLengthNonuniformity)); 81 | requestedFeatures->push_back(static_cast(FilterType::RunLengthFeaturesFilterType::LowGreyLevelRunEmphasis)); 82 | requestedFeatures->push_back(static_cast(FilterType::RunLengthFeaturesFilterType::HighGreyLevelRunEmphasis)); 83 | requestedFeatures->push_back(static_cast(FilterType::RunLengthFeaturesFilterType::ShortRunLowGreyLevelEmphasis)); 84 | requestedFeatures->push_back(static_cast(FilterType::RunLengthFeaturesFilterType::ShortRunHighGreyLevelEmphasis)); 85 | requestedFeatures->push_back(static_cast(FilterType::RunLengthFeaturesFilterType::LongRunLowGreyLevelEmphasis)); 86 | requestedFeatures->push_back(static_cast(FilterType::RunLengthFeaturesFilterType::LongRunHighGreyLevelEmphasis)); 87 | filter->SetRequestedFeatures(requestedFeatures); 88 | 89 | filter->Update(); 90 | 91 | typename FilterType::FeatureValueVector::ConstIterator mIt; 92 | typename FilterType::FeatureValueVectorPointer meanVector = filter->GetFeatureMeans(); 93 | std::ofstream rts; 94 | rts.open(returnParameterFile.c_str() ); 95 | rts << "outputVector = "; 96 | for(mIt = meanVector->Begin(); mIt != meanVector->End(); mIt++) 97 | { 98 | if(mIt != meanVector->Begin()) 99 | { 100 | rts << ","; 101 | } 102 | rts << mIt.Value(); 103 | } 104 | rts << std::endl; 105 | 106 | mIt = meanVector->Begin(); 107 | 108 | rts<<"ShortRunEmphasis = "<< mIt.Value() << std::endl; 109 | mIt++; 110 | rts<<"LongRunEmphasis = "<< mIt.Value() << std::endl; 111 | mIt++; 112 | rts<<"GreyLevelNonuniformity = "<< mIt.Value() << std::endl; 113 | mIt++; 114 | rts<<"RunLengthNonuniformity = "<< mIt.Value() << std::endl; 115 | mIt++; 116 | rts<<"LowGreyLevelRunEmphasis = "<< mIt.Value() << std::endl; 117 | mIt++; 118 | rts<<"HighGreyLevelRunEmphasis = "<< mIt.Value() << std::endl; 119 | mIt++; 120 | rts<<"ShortRunLowGreyLevelEmphasis = "<< mIt.Value() << std::endl; 121 | mIt++; 122 | rts<<"ShortRunHighGreyLevelEmphasis = "<< mIt.Value() << std::endl; 123 | mIt++; 124 | rts<<"LongRunLowGreyLevelEmphasis = "<< mIt.Value() << std::endl; 125 | mIt++; 126 | rts<<"LongRunHighGreyLevelEmphasis = "<< mIt.Value() << std::endl; 127 | 128 | return EXIT_SUCCESS; 129 | } 130 | 131 | } // end of anonymous namespace 132 | 133 | int main( int argc, char * argv[] ) 134 | { 135 | PARSE_ARGS; 136 | 137 | itk::ImageIOBase::IOPixelType inputPixelType; 138 | itk::ImageIOBase::IOComponentType inputComponentType; 139 | itk::FloatingPointExceptions::Enable(); 140 | itk::FloatingPointExceptions::SetExceptionAction( itk::FloatingPointExceptions::ABORT ); 141 | 142 | try 143 | { 144 | 145 | itk::GetImageType(inputVolume, inputPixelType, inputComponentType); 146 | 147 | switch( inputComponentType ) 148 | { 149 | case itk::ImageIOBase::UCHAR: 150 | return DoIt< int >( argc, argv ); 151 | break; 152 | case itk::ImageIOBase::USHORT: 153 | return DoIt< int >( argc, argv ); 154 | break; 155 | case itk::ImageIOBase::SHORT: 156 | return DoIt< int >( argc, argv ); 157 | break; 158 | case itk::ImageIOBase::FLOAT: 159 | return DoIt< float >( argc, argv ); 160 | break; 161 | case itk::ImageIOBase::INT: 162 | return DoIt< int >( argc, argv ); 163 | break; 164 | default: 165 | std::cerr << "Unknown input image pixel component type: " 166 | << itk::ImageIOBase::GetComponentTypeAsString( inputComponentType ) 167 | << std::endl; 168 | return EXIT_FAILURE; 169 | break; 170 | } 171 | } 172 | catch( itk::ExceptionObject & excep ) 173 | { 174 | std::cerr << argv[0] << ": exception caught !" << std::endl; 175 | std::cerr << excep << std::endl; 176 | return EXIT_FAILURE; 177 | } 178 | return EXIT_SUCCESS; 179 | } 180 | -------------------------------------------------------------------------------- /ComputeGLRLMFeatures/ComputeGLRLMFeatures.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | Quantification.Texture Features 4 | Compute GLRLM Features 5 | 1.0 6 | http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/ComputeGLRLMFeatures 7 | 8 | Jean-Baptiste Vimort, Kitware Inc. 9 | This work was supported by the National Institute of Health (NIH) National Institute for Dental and Craniofacial Research (NIDCR) R01EB021391 (Textural Biomarkers of Arthritis for the Subchondral Bone in the Temporomandibular Joint) 10 | 11 | 12 | Input parameters 13 | 14 | inputVolume 15 | 16 | input 17 | 0 18 | Input Volume 19 | 20 | 21 | inputMask 22 | 23 | inputMask 24 | input 25 | s 26 | A mask defining the region over which texture features will be calculated 27 | 28 | 29 | 30 | insideMask 31 | 32 | insideMask 33 | i 34 | The pixel value that defines the ”inside” of the mask 35 | 1 36 | 37 | 38 | binNumber 39 | 40 | binNumber 41 | b 42 | The number of intensity bins 43 | 10 44 | 45 | 46 | pixelIntensityMin 47 | 48 | pixelIntensityMin 49 | p 50 | Minnimum of the pixel intensity range over which the features will be calculated 51 | 0 52 | 53 | 54 | pixelIntensityMax 55 | 56 | pixelIntensityMax 57 | P 58 | Maximum of the pixel intensity range over which the features will be calculated 59 | 4000 60 | 61 | 62 | distanceMin 63 | 64 | distanceMin 65 | d 66 | Minnimum of the distance range over which the features will be calculated 67 | 0.0 68 | 69 | 70 | distanceMax 71 | 72 | distanceMax 73 | D 74 | Maximum of the distance range over which the features will be calculated 75 | 1.0 76 | 77 | 78 | 79 | 80 | Output parameters 81 | 82 | ShortRunEmphasis 83 | 84 | output 85 | 86 | 87 | LongRunEmphasis 88 | 89 | output 90 | 91 | 92 | GreyLevelNonuniformity 93 | 94 | output 95 | 96 | 97 | RunLengthNonuniformity 98 | 99 | output 100 | 101 | 102 | LowGreyLevelRunEmphasis 103 | 104 | output 105 | 106 | 107 | HighGreyLevelRunEmphasis 108 | 109 | output 110 | 111 | 112 | ShortRunLowGreyLevelEmphasis 113 | 114 | output 115 | 116 | 117 | ShortRunHighGreyLevelEmphasis 118 | 119 | output 120 | 121 | 122 | LongRunLowGreyLevelEmphasis 123 | 124 | output 125 | 126 | 127 | LongRunHighGreyLevelEmphasis 128 | 129 | output 130 | 131 | 132 | 133 | 134 | Advanced parameters 135 | 136 | outputVector 137 | 138 | output 139 | Output Vector 140 | 141 | 142 | 143 | -------------------------------------------------------------------------------- /ComputeGLRLMFeatures/Testing/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | add_subdirectory(Cxx) 2 | -------------------------------------------------------------------------------- /ComputeGLRLMFeatures/Testing/Cxx/CMakeLists.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Kitware/BoneTextureExtension/3410506efaa404131f7b02aa70769f537b1f2b3d/ComputeGLRLMFeatures/Testing/Cxx/CMakeLists.txt -------------------------------------------------------------------------------- /CreateLabelMapFromCSV/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | #----------------------------------------------------------------------------- 2 | set(MODULE_NAME CreateLabelMapFromCSV) 3 | 4 | #----------------------------------------------------------------------------- 5 | 6 | # 7 | # SlicerExecutionModel 8 | # 9 | find_package(SlicerExecutionModel REQUIRED) 10 | include(${SlicerExecutionModel_USE_FILE}) 11 | 12 | # 13 | # ITK 14 | # 15 | set(${PROJECT_NAME}_ITK_COMPONENTS 16 | ITKIOImageBase 17 | ITKCommon 18 | ITKStatistics 19 | ITKImageGrid 20 | ITKImageSources 21 | ITKTestKernel 22 | ITKMetaIO 23 | ITKImageIntensity 24 | ) 25 | find_package(ITK 4.9 COMPONENTS ${${PROJECT_NAME}_ITK_COMPONENTS} REQUIRED) 26 | if(ITK_VERSION VERSION_GREATER_EQUAL "5.3") 27 | foreach(factory_uc IN ITEMS "IMAGEIO" "MESHIO" "TRANSFORMIO") 28 | set(ITK_NO_${factory_uc}_FACTORY_REGISTER_MANAGER 1) 29 | endforeach() 30 | else() 31 | set(ITK_NO_IO_FACTORY_REGISTER_MANAGER 1) # See Libs/ITKFactoryRegistration/CMakeLists.txt 32 | endif() 33 | include(${ITK_USE_FILE}) 34 | 35 | #----------------------------------------------------------------------------- 36 | set(MODULE_INCLUDE_DIRECTORIES 37 | ${CMAKE_CURRENT_SOURCE_DIR}/../include 38 | ) 39 | 40 | set(MODULE_SRCS 41 | ) 42 | 43 | set(MODULE_TARGET_LIBRARIES 44 | ${ITK_LIBRARIES} 45 | ) 46 | 47 | #----------------------------------------------------------------------------- 48 | SEMMacroBuildCLI( 49 | NAME ${MODULE_NAME} 50 | TARGET_LIBRARIES ${MODULE_TARGET_LIBRARIES} 51 | INCLUDE_DIRECTORIES ${MODULE_INCLUDE_DIRECTORIES} 52 | ADDITIONAL_SRCS ${MODULE_SRCS} 53 | ) 54 | 55 | #----------------------------------------------------------------------------- 56 | if(BUILD_TESTING) 57 | add_subdirectory(Testing) 58 | endif() 59 | -------------------------------------------------------------------------------- /CreateLabelMapFromCSV/CreateLabelMapFromCSV.cxx: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | * 3 | * Copyright Insight Software Consortium 4 | * 5 | * Licensed under the Apache License, Version 2.0 (the "License"); 6 | * you may not use this file except in compliance with the License. 7 | * You may obtain a copy of the License at 8 | * 9 | * http://www.apache.org/licenses/LICENSE-2.0.txt 10 | * 11 | * Unless required by applicable law or agreed to in writing, software 12 | * distributed under the License is distributed on an "AS IS" BASIS, 13 | * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 14 | * See the License for the specific language governing permissions and 15 | * limitations under the License. 16 | * 17 | *=========================================================================*/ 18 | 19 | 20 | // Use an anonymous namespace to keep class types and function names 21 | // from colliding when module is used as shared object module. Every 22 | // thing should be in an anonymous namespace except for the module 23 | // entry point, e.g. main() 24 | // 25 | #include 26 | #include 27 | #include "itkImageFileReader.h" 28 | #include "itkImageFileWriter.h" 29 | #include "itkFloatingPointExceptions.h" 30 | #include "itkImage.h" 31 | #include "itkVector.h" 32 | #include "itkNeighborhood.h" 33 | #include "itkMetaDataDictionary.h" 34 | #include "itkMetaDataObject.h" 35 | 36 | #include "itkVectorIndexSelectionCastImageFilter.h" 37 | 38 | #include "itkPluginUtilities.h" 39 | 40 | #include "CreateLabelMapFromCSVCLP.h" 41 | 42 | namespace 43 | { 44 | 45 | template< typename TPixel > 46 | int DoIt( int argc, char * argv[] ) 47 | { 48 | 49 | PARSE_ARGS; 50 | 51 | const unsigned int Dimension = 3; 52 | 53 | typedef TPixel PixelType; 54 | typedef itk::Image< PixelType, Dimension > InputImageType; 55 | typedef itk::ImageFileReader< InputImageType > ReaderType; 56 | typedef itk::Image< unsigned int, Dimension > OutImageType; 57 | typedef itk::ImageFileWriter< OutImageType > WriterType; 58 | 59 | typename ReaderType::Pointer reader = ReaderType::New(); 60 | reader->SetFileName( inputVolume ); 61 | reader->Update(); 62 | 63 | OutImageType::Pointer output = OutImageType::New(); 64 | output->SetRegions(reader->GetOutput()->GetRequestedRegion()); 65 | output->SetOrigin(reader->GetOutput()->GetOrigin()); 66 | output->SetDirection(reader->GetOutput()->GetDirection()); 67 | output->SetSpacing(reader->GetOutput()->GetSpacing()); 68 | output->Allocate(); 69 | 70 | typename OutImageType::IndexType pixelIndex; 71 | 72 | std::ifstream inputFile; 73 | inputFile.open(inputFileName.c_str(), std::ios::in); 74 | 75 | std::string line; 76 | while(std::getline(inputFile, line)) 77 | { 78 | 79 | std::istringstream s(line); 80 | std::string field; 81 | 82 | getline(s, field,','); 83 | pixelIndex[0] = std::atoi(field.c_str()); 84 | getline(s, field,','); 85 | pixelIndex[1] = std::atoi(field.c_str()); 86 | getline(s, field,','); 87 | pixelIndex[2] = std::atoi(field.c_str()); 88 | getline(s, field,','); 89 | 90 | std::string label = field.substr(0, field.size()-1); 91 | 92 | if(label == Label1.c_str()) 93 | { 94 | output->SetPixel (pixelIndex, 1); 95 | } 96 | else if(label == Label2.c_str()) 97 | { 98 | output->SetPixel (pixelIndex, 2); 99 | } 100 | else if(label == Label3.c_str()) 101 | { 102 | output->SetPixel (pixelIndex, 3); 103 | } 104 | else if(label == Label4.c_str()) 105 | { 106 | output->SetPixel (pixelIndex, 4); 107 | } 108 | else if(label == Label5.c_str()) 109 | { 110 | output->SetPixel (pixelIndex, 5); 111 | } 112 | else 113 | { 114 | output->SetPixel (pixelIndex, 0); 115 | } 116 | 117 | } 118 | typename WriterType::Pointer writer = WriterType::New(); 119 | writer->SetFileName( outputLabeMap ); 120 | writer->SetInput( output ); 121 | writer->Update(); 122 | 123 | return EXIT_SUCCESS; 124 | } 125 | 126 | } // end of anonymous namespace 127 | 128 | int main( int argc, char * argv[] ) 129 | { 130 | PARSE_ARGS; 131 | 132 | itk::ImageIOBase::IOPixelType inputPixelType; 133 | itk::ImageIOBase::IOComponentType inputComponentType; 134 | itk::FloatingPointExceptions::Enable(); 135 | itk::FloatingPointExceptions::SetExceptionAction( itk::FloatingPointExceptions::ABORT ); 136 | 137 | try 138 | { 139 | 140 | itk::GetImageType(inputVolume, inputPixelType, inputComponentType); 141 | 142 | switch( inputComponentType ) 143 | { 144 | case itk::ImageIOBase::UCHAR: 145 | return DoIt< int >( argc, argv ); 146 | break; 147 | case itk::ImageIOBase::USHORT: 148 | return DoIt< int >( argc, argv ); 149 | break; 150 | case itk::ImageIOBase::SHORT: 151 | return DoIt< int >( argc, argv ); 152 | break; 153 | case itk::ImageIOBase::FLOAT: 154 | return DoIt< float >( argc, argv ); 155 | break; 156 | case itk::ImageIOBase::INT: 157 | return DoIt< int >( argc, argv ); 158 | break; 159 | default: 160 | std::cerr << "Unknown input image pixel component type: " 161 | << itk::ImageIOBase::GetComponentTypeAsString( inputComponentType ) 162 | << std::endl; 163 | return EXIT_FAILURE; 164 | break; 165 | } 166 | } 167 | catch( itk::ExceptionObject & excep ) 168 | { 169 | std::cerr << argv[0] << ": exception caught !" << std::endl; 170 | std::cerr << excep << std::endl; 171 | return EXIT_FAILURE; 172 | } 173 | return EXIT_SUCCESS; 174 | } 175 | -------------------------------------------------------------------------------- /CreateLabelMapFromCSV/CreateLabelMapFromCSV.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | Quantification.Texture Features 4 | Create label map from CSV 5 | 1.0 6 | http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/SaveVectorImageAsCSV 7 | 8 | Jean-Baptiste Vimort, Kitware Inc. 9 | This work was supported by the National Institute of Health (NIH) National Institute for Dental and Craniofacial Research (NIDCR) R01EB021391 (Textural Biomarkers of Arthritis for the Subchondral Bone in the Temporomandibular Joint) 10 | 11 | 12 | Input/output parameters 13 | 14 | inputVolume 15 | 16 | input 17 | 0 18 | Input Volume 19 | 20 | 21 | inputFileName 22 | 23 | input 24 | 1 25 | Input File Name 26 | 27 | 28 | outputLabeMap 29 | 30 | output 31 | 2 32 | Label Map created from the CSV 33 | 34 | 35 | Label1 36 | 37 | input 38 | 3 39 | 1 40 | 41 | 42 | Label2 43 | 44 | input 45 | L2 46 | 47 | 48 | 49 | Label3 50 | 51 | input 52 | L3 53 | 54 | 55 | 56 | Label4 57 | 58 | input 59 | L4 60 | 61 | 62 | 63 | Label5 64 | 65 | input 66 | L5 67 | 68 | 69 | 70 | 71 | -------------------------------------------------------------------------------- /CreateLabelMapFromCSV/Testing/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | add_subdirectory(Cxx) 2 | -------------------------------------------------------------------------------- /CreateLabelMapFromCSV/Testing/Cxx/CMakeLists.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Kitware/BoneTextureExtension/3410506efaa404131f7b02aa70769f537b1f2b3d/CreateLabelMapFromCSV/Testing/Cxx/CMakeLists.txt -------------------------------------------------------------------------------- /Docs/BoneTextureExtensionTutorial_2017.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Kitware/BoneTextureExtension/3410506efaa404131f7b02aa70769f537b1f2b3d/Docs/BoneTextureExtensionTutorial_2017.pdf -------------------------------------------------------------------------------- /LICENSE.txt: -------------------------------------------------------------------------------- 1 | Apache License 2 | Version 2.0, January 2004 3 | http://www.apache.org/licenses/ 4 | 5 | 6 | TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION 7 | 8 | 1. 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However, in accepting such obligations, You may act only 171 | on Your own behalf and on Your sole responsibility, not on behalf 172 | of any other Contributor, and only if You agree to indemnify, 173 | defend, and hold each Contributor harmless for any liability 174 | incurred by, or claims asserted against, such Contributor by reason 175 | of your accepting any such warranty or additional liability. 176 | 177 | END OF TERMS AND CONDITIONS 178 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # Bone Texture 2 | 3 | This slicer extension uses work contributed as external modules for ITK. 4 | 5 | ### ITKBoneMorphometry 6 | - Module: [ITKBoneMorphometry](https://github.com/InsightSoftwareConsortium/ITKBoneMorphometry) 7 | - Insight Journal: [Computing Bone Morphometric Feature Maps from 3-Dimensional Images](http://www.insight-journal.org/browse/publication/988) 8 | 9 | ### ITKTextureFeatures 10 | - Module: [ITKTextureFeatures](https://github.com/InsightSoftwareConsortium/ITKTextureFeatures) 11 | - Insight Journal: [Computing Textural Feature Maps for N-Dimensional images](http://www.insight-journal.org/browse/publication/985) 12 | 13 | A tutorial of how to use this module can be found in [pdf](./Docs/BoneTextureExtensionTutorial_2017.pdf). 14 | 15 | 16 | -------------------------------------------------------------------------------- /SaveVectorImageAsCSV/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | #----------------------------------------------------------------------------- 2 | set(MODULE_NAME SaveVectorImageAsCSV) 3 | 4 | #----------------------------------------------------------------------------- 5 | 6 | # 7 | # SlicerExecutionModel 8 | # 9 | find_package(SlicerExecutionModel REQUIRED) 10 | include(${SlicerExecutionModel_USE_FILE}) 11 | 12 | # 13 | # ITK 14 | # 15 | set(${PROJECT_NAME}_ITK_COMPONENTS 16 | ITKIOImageBase 17 | ITKCommon 18 | ITKStatistics 19 | ITKImageGrid 20 | ITKImageSources 21 | ITKTestKernel 22 | ITKMetaIO 23 | ITKImageIntensity 24 | ) 25 | find_package(ITK 4.9 COMPONENTS ${${PROJECT_NAME}_ITK_COMPONENTS} REQUIRED) 26 | if(ITK_VERSION VERSION_GREATER_EQUAL "5.3") 27 | foreach(factory_uc IN ITEMS "IMAGEIO" "MESHIO" "TRANSFORMIO") 28 | set(ITK_NO_${factory_uc}_FACTORY_REGISTER_MANAGER 1) 29 | endforeach() 30 | else() 31 | set(ITK_NO_IO_FACTORY_REGISTER_MANAGER 1) # See Libs/ITKFactoryRegistration/CMakeLists.txt 32 | endif() 33 | include(${ITK_USE_FILE}) 34 | 35 | #----------------------------------------------------------------------------- 36 | set(MODULE_INCLUDE_DIRECTORIES 37 | ${CMAKE_CURRENT_SOURCE_DIR}/../include 38 | ) 39 | 40 | set(MODULE_SRCS 41 | ) 42 | 43 | set(MODULE_TARGET_LIBRARIES 44 | ${ITK_LIBRARIES} 45 | ) 46 | 47 | #----------------------------------------------------------------------------- 48 | SEMMacroBuildCLI( 49 | NAME ${MODULE_NAME} 50 | TARGET_LIBRARIES ${MODULE_TARGET_LIBRARIES} 51 | INCLUDE_DIRECTORIES ${MODULE_INCLUDE_DIRECTORIES} 52 | ADDITIONAL_SRCS ${MODULE_SRCS} 53 | ) 54 | 55 | #----------------------------------------------------------------------------- 56 | if(BUILD_TESTING) 57 | add_subdirectory(Testing) 58 | endif() 59 | -------------------------------------------------------------------------------- /SaveVectorImageAsCSV/SaveVectorImageAsCSV.cxx: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | * 3 | * Copyright Insight Software Consortium 4 | * 5 | * Licensed under the Apache License, Version 2.0 (the "License"); 6 | * you may not use this file except in compliance with the License. 7 | * You may obtain a copy of the License at 8 | * 9 | * http://www.apache.org/licenses/LICENSE-2.0.txt 10 | * 11 | * Unless required by applicable law or agreed to in writing, software 12 | * distributed under the License is distributed on an "AS IS" BASIS, 13 | * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 14 | * See the License for the specific language governing permissions and 15 | * limitations under the License. 16 | * 17 | *=========================================================================*/ 18 | 19 | 20 | // Use an anonymous namespace to keep class types and function names 21 | // from colliding when module is used as shared object module. Every 22 | // thing should be in an anonymous namespace except for the module 23 | // entry point, e.g. main() 24 | // 25 | #include 26 | #include "itkImageFileReader.h" 27 | #include "itkImageFileWriter.h" 28 | #include "itkFloatingPointExceptions.h" 29 | #include "itkImage.h" 30 | #include "itkVector.h" 31 | #include "itkNeighborhood.h" 32 | #include "itkMetaDataDictionary.h" 33 | #include "itkMetaDataObject.h" 34 | 35 | #include "itkVectorIndexSelectionCastImageFilter.h" 36 | 37 | #include "itkPluginUtilities.h" 38 | 39 | #include "SaveVectorImageAsCSVCLP.h" 40 | 41 | namespace 42 | { 43 | 44 | template< typename TPixel > 45 | int DoIt( int argc, char * argv[] ) 46 | { 47 | 48 | PARSE_ARGS; 49 | 50 | const unsigned int Dimension = 3; 51 | 52 | typedef TPixel PixelType; 53 | typedef itk::VectorImage< PixelType, Dimension > InputImageType; 54 | typedef itk::Image< PixelType, Dimension > InputMaskType; 55 | typedef itk::ImageFileReader< InputImageType > ReaderType; 56 | typedef itk::ImageFileReader< InputMaskType > MaskReaderType; 57 | 58 | typename ReaderType::Pointer reader = ReaderType::New(); 59 | reader->SetFileName( inputVolume ); 60 | reader->Update(); 61 | 62 | std::ofstream outputFile; 63 | const char *outputFilename = outputFileBaseName.c_str(); 64 | outputFile.open(outputFilename, std::ios::out); 65 | 66 | if(predefineTitle) 67 | { 68 | outputFile<<"X"<<","; 69 | outputFile<<"Y"<<","; 70 | outputFile<<"Z"<<","; 71 | outputFile<<"Energy"<<","; 72 | outputFile<<"Entropy"<<","; 73 | outputFile<<"Correlation"<<","; 74 | outputFile<<"InverseDifferenceMoment"<<","; 75 | outputFile<<"Inertia"<<","; 76 | outputFile<<"ClusterShade"<<","; 77 | outputFile<<"ClusterProminence"<<","; 78 | outputFile<<"HarralickCorrelation"<<","; 79 | outputFile<<"ShortRunEmphasis"<<","; 80 | outputFile<<"LongRunEmpasis"<<","; 81 | outputFile<<"GreyLevelNonUniformity"<<","; 82 | outputFile<<"RunLengthNonUniformity"<<","; 83 | outputFile<<"LowGreyLevelRunEmphasis"<<","; 84 | outputFile<<"HighGreyLevelRunEmphasis"<<","; 85 | outputFile<<"ShortRunLowGreyLevelEmphasis"<<","; 86 | outputFile<<"ShortRunHighGreyLevelEmphasis"<<","; 87 | outputFile<<"LongRunLowGreyLevelEmphasis"<<","; 88 | outputFile<<"LongRunHighGreyLevelEmphasis"<<","; 89 | outputFile<<"BVTV"<<","; 90 | outputFile<<"TbN"<<","; 91 | outputFile<<"TbTh"<<","; 92 | outputFile<<"TbSp"<<","; 93 | outputFile<<"BSBV"<<","; 94 | 95 | 96 | outputFile< inIt( reader->GetOutput(), reader->GetOutput()->GetRequestedRegion()); 100 | inIt.GoToBegin (); 101 | typename InputImageType::PixelType inputPixel; 102 | typename InputImageType::IndexType inputIndex; 103 | const unsigned int VectorComponentDimension = reader->GetOutput()->GetNumberOfComponentsPerPixel(); 104 | 105 | if(inputMask != "") 106 | { 107 | typename MaskReaderType::Pointer maskReader = MaskReaderType::New(); 108 | maskReader->SetFileName( inputMask ); 109 | maskReader->Update(); 110 | typename itk::ImageRegionConstIterator< InputMaskType > maskIt( maskReader->GetOutput(), maskReader->GetOutput()->GetRequestedRegion()); 111 | maskIt.GoToBegin (); 112 | if(secondInputVolume != "") 113 | { 114 | typename ReaderType::Pointer secondReader = ReaderType::New(); 115 | secondReader->SetFileName( secondInputVolume ); 116 | secondReader->Update(); 117 | typename itk::ImageRegionConstIterator< InputImageType > secInIt( secondReader->GetOutput(), secondReader->GetOutput()->GetRequestedRegion()); 118 | secInIt.GoToBegin (); 119 | const unsigned int SecondVectorComponentDimension = secondReader->GetOutput()->GetNumberOfComponentsPerPixel(); 120 | 121 | if(thirdInputVolume != "") 122 | { 123 | typename ReaderType::Pointer thirdReader = ReaderType::New(); 124 | thirdReader->SetFileName( thirdInputVolume ); 125 | thirdReader->Update(); 126 | typename itk::ImageRegionConstIterator< InputImageType > thirdInIt( thirdReader->GetOutput(), thirdReader->GetOutput()->GetRequestedRegion()); 127 | thirdInIt.GoToBegin (); 128 | const unsigned int ThirdVectorComponentDimension = thirdReader->GetOutput()->GetNumberOfComponentsPerPixel(); 129 | 130 | /// Mask + Input Volume + second and third Input Volume /// 131 | while ( !inIt.IsAtEnd() ) 132 | { 133 | if(maskIt.Get() != 0) 134 | { 135 | inputIndex = inIt.GetIndex(); 136 | for( unsigned int i = 0; i < Dimension; i++ ) 137 | { 138 | outputFile<SetFileName( secondInputVolume ); 231 | secondReader->Update(); 232 | typename itk::ImageRegionConstIterator< InputImageType > secInIt( secondReader->GetOutput(), secondReader->GetOutput()->GetRequestedRegion()); 233 | secInIt.GoToBegin (); 234 | const unsigned int SecondVectorComponentDimension = reader->GetOutput()->GetNumberOfComponentsPerPixel(); 235 | 236 | if(thirdInputVolume != "") 237 | { 238 | typename ReaderType::Pointer thirdReader = ReaderType::New(); 239 | thirdReader->SetFileName( thirdInputVolume ); 240 | thirdReader->Update(); 241 | typename itk::ImageRegionConstIterator< InputImageType > thirdInIt( thirdReader->GetOutput(), thirdReader->GetOutput()->GetRequestedRegion()); 242 | thirdInIt.GoToBegin (); 243 | const unsigned int ThirdVectorComponentDimension = thirdReader->GetOutput()->GetNumberOfComponentsPerPixel(); 244 | 245 | /// Input Volume + second and third Input Volume /// 246 | while ( !inIt.IsAtEnd() ) 247 | { 248 | inputIndex = inIt.GetIndex(); 249 | for( unsigned int i = 0; i < Dimension; i++ ) 250 | { 251 | outputFile<( argc, argv ); 357 | break; 358 | case itk::ImageIOBase::USHORT: 359 | return DoIt< int >( argc, argv ); 360 | break; 361 | case itk::ImageIOBase::SHORT: 362 | return DoIt< int >( argc, argv ); 363 | break; 364 | case itk::ImageIOBase::FLOAT: 365 | return DoIt< float >( argc, argv ); 366 | break; 367 | case itk::ImageIOBase::INT: 368 | return DoIt< int >( argc, argv ); 369 | break; 370 | default: 371 | std::cerr << "Unknown input image pixel component type: " 372 | << itk::ImageIOBase::GetComponentTypeAsString( inputComponentType ) 373 | << std::endl; 374 | return EXIT_FAILURE; 375 | break; 376 | } 377 | } 378 | catch( itk::ExceptionObject & excep ) 379 | { 380 | std::cerr << argv[0] << ": exception caught !" << std::endl; 381 | std::cerr << excep << std::endl; 382 | return EXIT_FAILURE; 383 | } 384 | return EXIT_SUCCESS; 385 | } 386 | -------------------------------------------------------------------------------- /SaveVectorImageAsCSV/SaveVectorImageAsCSV.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | Quantification.Texture Features 4 | Save Vector Image As CSV 5 | 1.0 6 | http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/SaveVectorImageAsCSV 7 | 8 | Jean-Baptiste Vimort, Kitware Inc. 9 | This work was supported by the National Institute of Health (NIH) National Institute for Dental and Craniofacial Research (NIDCR) R01EB021391 (Textural Biomarkers of Arthritis for the Subchondral Bone in the Temporomandibular Joint) 10 | 11 | 12 | Input/output parameters 13 | 14 | inputVolume 15 | 16 | input 17 | 0 18 | Input Volume 19 | 20 | 21 | secondInputVolume 22 | 23 | input 24 | secondInputVolume 25 | a 26 | 2nd Input Volume (Optional) 27 | 28 | 29 | thirdInputVolume 30 | 31 | input 32 | thirdInputVolume 33 | b 34 | Third Input Volume (Optional) 35 | 36 | 37 | inputMask 38 | 39 | inputMask 40 | input 41 | s 42 | A mask defining the region over which texture features will be calculated 43 | 44 | 45 | 46 | predefineTitle 47 | 48 | predefineTitle 49 | input 50 | p 51 | Add the names of the features computed in BoneTextureExtension (GLCM the GLRLM) 52 | 53 | 54 | 55 | outputFileBaseName 56 | 57 | output 58 | 1 59 | Output File Base Name 60 | 61 | 62 | 63 | -------------------------------------------------------------------------------- /SaveVectorImageAsCSV/Testing/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | add_subdirectory(Cxx) 2 | -------------------------------------------------------------------------------- /SaveVectorImageAsCSV/Testing/Cxx/CMakeLists.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Kitware/BoneTextureExtension/3410506efaa404131f7b02aa70769f537b1f2b3d/SaveVectorImageAsCSV/Testing/Cxx/CMakeLists.txt -------------------------------------------------------------------------------- /SeparateVectorImage/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | #----------------------------------------------------------------------------- 2 | set(MODULE_NAME SeparateVectorImage) 3 | 4 | #----------------------------------------------------------------------------- 5 | 6 | # 7 | # SlicerExecutionModel 8 | # 9 | find_package(SlicerExecutionModel REQUIRED) 10 | include(${SlicerExecutionModel_USE_FILE}) 11 | 12 | # 13 | # ITK 14 | # 15 | set(${PROJECT_NAME}_ITK_COMPONENTS 16 | ITKIOImageBase 17 | ITKCommon 18 | ITKStatistics 19 | ITKImageGrid 20 | ITKImageSources 21 | ITKTestKernel 22 | ITKMetaIO 23 | ITKImageIntensity 24 | ) 25 | find_package(ITK 4.9 COMPONENTS ${${PROJECT_NAME}_ITK_COMPONENTS} REQUIRED) 26 | if(ITK_VERSION VERSION_GREATER_EQUAL "5.3") 27 | foreach(factory_uc IN ITEMS "IMAGEIO" "MESHIO" "TRANSFORMIO") 28 | set(ITK_NO_${factory_uc}_FACTORY_REGISTER_MANAGER 1) 29 | endforeach() 30 | else() 31 | set(ITK_NO_IO_FACTORY_REGISTER_MANAGER 1) # See Libs/ITKFactoryRegistration/CMakeLists.txt 32 | endif() 33 | include(${ITK_USE_FILE}) 34 | 35 | #----------------------------------------------------------------------------- 36 | set(MODULE_INCLUDE_DIRECTORIES 37 | ${CMAKE_CURRENT_SOURCE_DIR}/../include 38 | ) 39 | 40 | set(MODULE_SRCS 41 | ) 42 | 43 | set(MODULE_TARGET_LIBRARIES 44 | ${ITK_LIBRARIES} 45 | ) 46 | 47 | #----------------------------------------------------------------------------- 48 | SEMMacroBuildCLI( 49 | NAME ${MODULE_NAME} 50 | TARGET_LIBRARIES ${MODULE_TARGET_LIBRARIES} 51 | INCLUDE_DIRECTORIES ${MODULE_INCLUDE_DIRECTORIES} 52 | ADDITIONAL_SRCS ${MODULE_SRCS} 53 | ) 54 | 55 | #----------------------------------------------------------------------------- 56 | if(BUILD_TESTING) 57 | add_subdirectory(Testing) 58 | endif() 59 | -------------------------------------------------------------------------------- /SeparateVectorImage/SeparateVectorImage.cxx: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | * 3 | * Copyright Insight Software Consortium 4 | * 5 | * Licensed under the Apache License, Version 2.0 (the "License"); 6 | * you may not use this file except in compliance with the License. 7 | * You may obtain a copy of the License at 8 | * 9 | * http://www.apache.org/licenses/LICENSE-2.0.txt 10 | * 11 | * Unless required by applicable law or agreed to in writing, software 12 | * distributed under the License is distributed on an "AS IS" BASIS, 13 | * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 14 | * See the License for the specific language governing permissions and 15 | * limitations under the License. 16 | * 17 | *=========================================================================*/ 18 | 19 | 20 | // Use an anonymous namespace to keep class types and function names 21 | // from colliding when module is used as shared object module. Every 22 | // thing should be in an anonymous namespace except for the module 23 | // entry point, e.g. main() 24 | // 25 | 26 | #include "itkImageFileReader.h" 27 | #include "itkImageFileWriter.h" 28 | #include "itkFloatingPointExceptions.h" 29 | #include "itkImage.h" 30 | #include "itkVector.h" 31 | #include "itkNeighborhood.h" 32 | #include "itkMetaDataDictionary.h" 33 | #include "itkMetaDataObject.h" 34 | 35 | #include "itkVectorIndexSelectionCastImageFilter.h" 36 | 37 | #include "itkPluginUtilities.h" 38 | 39 | #include "SeparateVectorImageCLP.h" 40 | 41 | // Feature name lists for GLCM, GLRM, and BM 42 | std::vector GLCMFeatures = {"Energy", "Entropy", "Correlation", "InverseDifferenceMoment", 43 | "Inertia", "ClusterShade", "ClusterProminence", "HaralickCorrelation"}; 44 | 45 | std::vector RLFeatures = {"ShortRunEmphasis", "LongRunEmphasis", 46 | "GreyLevelNonuniformity", "RunLengthNonuniformity", 47 | "LowGreyLevelRunEmphasis", "HighGreyLevelRunEmphasis", 48 | "ShortRunLowGreyLevelEmphasis", "ShortRunHighGreyLevelEmphasis", 49 | "LongRunLowGreyLevelEmphasis", "LongRunHighGreyLevelEmphasis"}; 50 | 51 | std::vector BMFeatures = {"BoneVolumeDensity", "TrabecularThickness", 52 | "TrabecularSeparation", "TrabecularNumber", "BoneSurfaceDensity"}; 53 | 54 | namespace 55 | { 56 | 57 | template< typename TPixel > 58 | int DoIt( int argc, char * argv[] ) 59 | { 60 | PARSE_ARGS; 61 | 62 | const unsigned int Dimension = 3; 63 | 64 | typedef TPixel PixelType; 65 | typedef itk::VectorImage< PixelType, Dimension > InputImageType; 66 | typedef itk::Image< PixelType, Dimension > OutputImageType; 67 | 68 | typedef itk::ImageFileReader< InputImageType > ReaderType; 69 | typename ReaderType::Pointer reader = ReaderType::New(); 70 | reader->SetFileName( inputVolume ); 71 | reader->Update(); 72 | 73 | unsigned int VectorComponentDimension = reader->GetOutput()->GetNumberOfComponentsPerPixel(); 74 | 75 | typedef itk::VectorIndexSelectionCastImageFilter< InputImageType, OutputImageType > IndexSelectionType; 76 | typename IndexSelectionType::Pointer indexSelectionFilter = IndexSelectionType::New(); 77 | indexSelectionFilter->SetInput( reader->GetOutput() ); 78 | 79 | // Select the appropriate feature name list based on VectorComponentDimension 80 | std::vector featureNames; 81 | 82 | if (VectorComponentDimension == 8) { 83 | featureNames = GLCMFeatures; 84 | } else if (VectorComponentDimension == 10) { 85 | featureNames = RLFeatures; 86 | } else if (VectorComponentDimension == 5) { 87 | featureNames = BMFeatures; 88 | } else { 89 | for (unsigned int i = 1; i <= VectorComponentDimension; ++i) { 90 | std::ostringstream ss; 91 | ss << i; 92 | featureNames.push_back(ss.str()); 93 | } 94 | } 95 | 96 | for( unsigned int i = 0; i < VectorComponentDimension; i++ ) 97 | { 98 | indexSelectionFilter->SetIndex(i); 99 | 100 | // Create and set up a writer 101 | typedef itk::ImageFileWriter< OutputImageType > WriterType; 102 | typename WriterType::Pointer writer = WriterType::New(); 103 | std::string outputFilename = outputFileBaseName.c_str();; 104 | std::string suffix = featureNames[i]; 105 | writer->SetFileName( outputFilename + "_" + suffix + ".nrrd" ); 106 | writer->SetInput( indexSelectionFilter->GetOutput() ); 107 | 108 | writer->Update(); 109 | } 110 | 111 | 112 | 113 | return EXIT_SUCCESS; 114 | } 115 | 116 | } // end of anonymous namespace 117 | 118 | int main( int argc, char * argv[] ) 119 | { 120 | PARSE_ARGS; 121 | 122 | itk::ImageIOBase::IOPixelType inputPixelType; 123 | itk::ImageIOBase::IOComponentType inputComponentType; 124 | itk::FloatingPointExceptions::Enable(); 125 | itk::FloatingPointExceptions::SetExceptionAction( itk::FloatingPointExceptions::ABORT ); 126 | 127 | try 128 | { 129 | 130 | itk::GetImageType(inputVolume, inputPixelType, inputComponentType); 131 | 132 | switch( inputComponentType ) 133 | { 134 | case itk::ImageIOBase::UCHAR: 135 | return DoIt< int >( argc, argv ); 136 | break; 137 | case itk::ImageIOBase::USHORT: 138 | return DoIt< int >( argc, argv ); 139 | break; 140 | case itk::ImageIOBase::SHORT: 141 | return DoIt< int >( argc, argv ); 142 | break; 143 | case itk::ImageIOBase::FLOAT: 144 | return DoIt< float >( argc, argv ); 145 | break; 146 | case itk::ImageIOBase::INT: 147 | return DoIt< int >( argc, argv ); 148 | break; 149 | default: 150 | std::cerr << "Unknown input image pixel component type: " 151 | << itk::ImageIOBase::GetComponentTypeAsString( inputComponentType ) 152 | << std::endl; 153 | return EXIT_FAILURE; 154 | break; 155 | } 156 | } 157 | catch( itk::ExceptionObject & excep ) 158 | { 159 | std::cerr << argv[0] << ": exception caught !" << std::endl; 160 | std::cerr << excep << std::endl; 161 | return EXIT_FAILURE; 162 | } 163 | return EXIT_SUCCESS; 164 | } 165 | -------------------------------------------------------------------------------- /SeparateVectorImage/SeparateVectorImage.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | Quantification.Texture Features 4 | Separate Vector Image 5 | 1.0 6 | http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/SeparateVectorImage 7 | 8 | Jean-Baptiste Vimort, Kitware Inc. 9 | This work was supported by the National Institute of Health (NIH) National Institute for Dental and Craniofacial Research (NIDCR) R01EB021391 (Textural Biomarkers of Arthritis for the Subchondral Bone in the Temporomandibular Joint) 10 | 11 | 12 | Input/output parameters 13 | 14 | inputVolume 15 | 16 | input 17 | 0 18 | Input Volume 19 | 20 | 21 | outputFileBaseName 22 | 23 | output 24 | 1 25 | Output File Base Name 26 | 27 | 28 | 29 | -------------------------------------------------------------------------------- /SeparateVectorImage/Testing/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | add_subdirectory(Cxx) 2 | -------------------------------------------------------------------------------- /SeparateVectorImage/Testing/Cxx/CMakeLists.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Kitware/BoneTextureExtension/3410506efaa404131f7b02aa70769f537b1f2b3d/SeparateVectorImage/Testing/Cxx/CMakeLists.txt -------------------------------------------------------------------------------- /SuperBuild.cmake: -------------------------------------------------------------------------------- 1 | #----------------------------------------------------------------------------- 2 | # Enable and setup External project global properties 3 | #----------------------------------------------------------------------------- 4 | 5 | set(ep_common_c_flags "${CMAKE_C_FLAGS_INIT} ${ADDITIONAL_C_FLAGS}") 6 | set(ep_common_cxx_flags "${CMAKE_CXX_FLAGS_INIT} ${ADDITIONAL_CXX_FLAGS}") 7 | 8 | #----------------------------------------------------------------------------- 9 | # Project dependencies 10 | #----------------------------------------------------------------------------- 11 | 12 | # Extension dependencies 13 | foreach(dep ${EXTENSION_DEPENDS}) 14 | mark_as_superbuild(${dep}_DIR) 15 | endforeach() 16 | 17 | set(proj ${SUPERBUILD_TOPLEVEL_PROJECT}) 18 | 19 | # Project dependencies 20 | set(${proj}_DEPENDS 21 | ITKBoneMorphometry 22 | ITKTextureFeature 23 | ) 24 | 25 | ExternalProject_Include_Dependencies(${proj} 26 | PROJECT_VAR proj 27 | SUPERBUILD_VAR ${EXTENSION_NAME}_SUPERBUILD 28 | ) 29 | 30 | ExternalProject_Add(${proj} 31 | ${${proj}_EP_ARGS} 32 | DOWNLOAD_COMMAND "" 33 | INSTALL_COMMAND "" 34 | SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR} 35 | BINARY_DIR ${EXTENSION_BUILD_SUBDIRECTORY} 36 | BUILD_ALWAYS 1 37 | CMAKE_CACHE_ARGS 38 | # Compiler settings 39 | -DCMAKE_C_COMPILER:FILEPATH=${CMAKE_C_COMPILER} 40 | -DCMAKE_C_FLAGS:STRING=${ep_common_c_flags} 41 | -DCMAKE_CXX_COMPILER:FILEPATH=${CMAKE_CXX_COMPILER} 42 | -DCMAKE_CXX_FLAGS:STRING=${ep_common_cxx_flags} 43 | -DCMAKE_CXX_STANDARD:STRING=${CMAKE_CXX_STANDARD} 44 | -DCMAKE_CXX_STANDARD_REQUIRED:BOOL=${CMAKE_CXX_STANDARD_REQUIRED} 45 | -DCMAKE_CXX_EXTENSIONS:BOOL=${CMAKE_CXX_EXTENSIONS} 46 | # Output directories 47 | -DCMAKE_RUNTIME_OUTPUT_DIRECTORY:PATH=${CMAKE_RUNTIME_OUTPUT_DIRECTORY} 48 | -DCMAKE_LIBRARY_OUTPUT_DIRECTORY:PATH=${CMAKE_LIBRARY_OUTPUT_DIRECTORY} 49 | -DCMAKE_ARCHIVE_OUTPUT_DIRECTORY:PATH=${CMAKE_ARCHIVE_OUTPUT_DIRECTORY} 50 | # Packaging 51 | -DMIDAS_PACKAGE_EMAIL:STRING=${MIDAS_PACKAGE_EMAIL} 52 | -DMIDAS_PACKAGE_API_KEY:STRING=${MIDAS_PACKAGE_API_KEY} 53 | # Superbuild 54 | -D${EXTENSION_NAME}_SUPERBUILD:BOOL=OFF 55 | -DEXTENSION_SUPERBUILD_BINARY_DIR:PATH=${${EXTENSION_NAME}_BINARY_DIR} 56 | DEPENDS 57 | ${${proj}_DEPENDS} 58 | ) 59 | 60 | -------------------------------------------------------------------------------- /SuperBuild/External_ITKBoneMorphometry.cmake: -------------------------------------------------------------------------------- 1 | 2 | set(proj ITKBoneMorphometry) 3 | 4 | # Set dependency list 5 | set(${proj}_DEPENDS 6 | "" 7 | ) 8 | 9 | # Include dependent projects if any 10 | ExternalProject_Include_Dependencies(${proj} PROJECT_VAR proj DEPENDS_VAR ${proj}_DEPENDENCIES) 11 | 12 | if(${SUPERBUILD_TOPLEVEL_PROJECT}_USE_SYSTEM_${proj}) 13 | message(FATAL_ERROR "Enabling ${SUPERBUILD_TOPLEVEL_PROJECT}_USE_SYSTEM_${proj} is not supported !") 14 | endif() 15 | 16 | # Sanity checks 17 | if(DEFINED ITKBoneMorphometry_DIR AND NOT EXISTS ${ITKBoneMorphometry_DIR}) 18 | message(FATAL_ERROR "ITKBoneMorphometry_DIR [${ITKBoneMorphometry_DIR}] variable is defined but corresponds to nonexistent directory") 19 | endif() 20 | 21 | 22 | if(NOT DEFINED ${proj}_DIR AND NOT ${SUPERBUILD_TOPLEVEL_PROJECT}_USE_SYSTEM_${proj}) 23 | 24 | ExternalProject_SetIfNotDefined( 25 | ${SUPERBUILD_TOPLEVEL_PROJECT}_${proj}_GIT_REPOSITORY 26 | "${EP_GIT_PROTOCOL}://github.com/InsightSoftwareConsortium/ITKBoneMorphometry.git" 27 | QUIET 28 | ) 29 | 30 | ExternalProject_SetIfNotDefined( 31 | ${SUPERBUILD_TOPLEVEL_PROJECT}_${proj}_GIT_TAG 32 | "7d4314f12a4682b2d995a628610eb7986d2e55de" 33 | QUIET 34 | ) 35 | 36 | set(EP_SOURCE_DIR ${CMAKE_BINARY_DIR}/${proj}) 37 | set(EP_BINARY_DIR ${CMAKE_BINARY_DIR}/${proj}-build) 38 | 39 | ExternalProject_Add(${proj} 40 | ${${proj}_EP_ARGS} 41 | GIT_REPOSITORY "${${SUPERBUILD_TOPLEVEL_PROJECT}_${proj}_GIT_REPOSITORY}" 42 | GIT_TAG "${${SUPERBUILD_TOPLEVEL_PROJECT}_${proj}_GIT_TAG}" 43 | SOURCE_DIR ${EP_SOURCE_DIR} 44 | BINARY_DIR ${EP_BINARY_DIR} 45 | CMAKE_CACHE_ARGS 46 | # Compiler settings 47 | -DCMAKE_C_COMPILER:FILEPATH=${CMAKE_C_COMPILER} 48 | -DCMAKE_C_FLAGS:STRING=${ep_common_c_flags} 49 | -DCMAKE_CXX_COMPILER:FILEPATH=${CMAKE_CXX_COMPILER} 50 | -DCMAKE_CXX_FLAGS:STRING=${ep_common_cxx_flags} 51 | -DCMAKE_CXX_STANDARD:STRING=${CMAKE_CXX_STANDARD} 52 | -DCMAKE_CXX_STANDARD_REQUIRED:BOOL=${CMAKE_CXX_STANDARD_REQUIRED} 53 | -DCMAKE_CXX_EXTENSIONS:BOOL=${CMAKE_CXX_EXTENSIONS} 54 | # Output directories 55 | -DCMAKE_RUNTIME_OUTPUT_DIRECTORY:PATH=${CMAKE_BINARY_DIR}/${Slicer_THIRDPARTY_BIN_DIR} 56 | -DCMAKE_LIBRARY_OUTPUT_DIRECTORY:PATH=${CMAKE_BINARY_DIR}/${Slicer_THIRDPARTY_LIB_DIR} 57 | # Install directories 58 | -DITK_INSTALL_RUNTIME_DIR:STRING=${Slicer_INSTALL_THIRDPARTY_LIB_DIR} 59 | -DITK_INSTALL_LIBRARY_DIR:STRING=${Slicer_INSTALL_THIRDPARTY_LIB_DIR} 60 | # Options 61 | -DBUILD_TESTING:BOOL=OFF 62 | # Dependencies 63 | -DITK_DIR:PATH=${ITK_DIR} 64 | -DPYTHON_EXECUTABLE:FILEPATH=${PYTHON_EXECUTABLE} 65 | -DPYTHON_INCLUDE_DIR:PATH=${PYTHON_INCLUDE_DIR} 66 | -DPYTHON_LIBRARY:FILEPATH=${PYTHON_LIBRARY} 67 | INSTALL_COMMAND "" 68 | DEPENDS 69 | ${${proj}_DEPENDS} 70 | ) 71 | set(${proj}_DIR ${EP_BINARY_DIR}) 72 | 73 | else() 74 | ExternalProject_Add_Empty(${proj} DEPENDS ${${proj}_DEPENDS}) 75 | endif() 76 | 77 | mark_as_superbuild(${proj}_DIR:PATH) 78 | ExternalProject_Message(${proj} "${proj}_DIR:${${proj}_DIR}") 79 | -------------------------------------------------------------------------------- /SuperBuild/External_ITKTextureFeature.cmake: -------------------------------------------------------------------------------- 1 | 2 | set(proj ITKTextureFeature) 3 | 4 | # Set dependency list 5 | set(${proj}_DEPENDS 6 | "" 7 | ) 8 | 9 | # Include dependent projects if any 10 | ExternalProject_Include_Dependencies(${proj} PROJECT_VAR proj DEPENDS_VAR ${proj}_DEPENDENCIES) 11 | 12 | if(${SUPERBUILD_TOPLEVEL_PROJECT}_USE_SYSTEM_${proj}) 13 | message(FATAL_ERROR "Enabling ${SUPERBUILD_TOPLEVEL_PROJECT}_USE_SYSTEM_${proj} is not supported !") 14 | endif() 15 | 16 | # Sanity checks 17 | if(DEFINED ITKTextureFeature_DIR AND NOT EXISTS ${ITKTextureFeature_DIR}) 18 | message(FATAL_ERROR "ITKTextureFeature_DIR [${ITKTextureFeature_DIR}] variable is defined but corresponds to nonexistent directory") 19 | endif() 20 | 21 | 22 | if(NOT DEFINED ${proj}_DIR AND NOT ${SUPERBUILD_TOPLEVEL_PROJECT}_USE_SYSTEM_${proj}) 23 | 24 | ExternalProject_SetIfNotDefined( 25 | ${SUPERBUILD_TOPLEVEL_PROJECT}_${proj}_GIT_REPOSITORY 26 | "${EP_GIT_PROTOCOL}://github.com/InsightSoftwareConsortium/ITKTextureFeatures.git" 27 | QUIET 28 | ) 29 | 30 | ExternalProject_SetIfNotDefined( 31 | ${SUPERBUILD_TOPLEVEL_PROJECT}_${proj}_GIT_TAG 32 | "7643fb34ced0b40ad7eb0f2a28d56a3a2941cc0f" 33 | QUIET 34 | ) 35 | 36 | set(EP_SOURCE_DIR ${CMAKE_BINARY_DIR}/${proj}) 37 | set(EP_BINARY_DIR ${CMAKE_BINARY_DIR}/${proj}-build) 38 | 39 | ExternalProject_Add(${proj} 40 | ${${proj}_EP_ARGS} 41 | GIT_REPOSITORY "${${SUPERBUILD_TOPLEVEL_PROJECT}_${proj}_GIT_REPOSITORY}" 42 | GIT_TAG "${${SUPERBUILD_TOPLEVEL_PROJECT}_${proj}_GIT_TAG}" 43 | SOURCE_DIR ${EP_SOURCE_DIR} 44 | BINARY_DIR ${EP_BINARY_DIR} 45 | CMAKE_CACHE_ARGS 46 | # Compiler settings 47 | -DCMAKE_C_COMPILER:FILEPATH=${CMAKE_C_COMPILER} 48 | -DCMAKE_C_FLAGS:STRING=${ep_common_c_flags} 49 | -DCMAKE_CXX_COMPILER:FILEPATH=${CMAKE_CXX_COMPILER} 50 | -DCMAKE_CXX_FLAGS:STRING=${ep_common_cxx_flags} 51 | -DCMAKE_CXX_STANDARD:STRING=${CMAKE_CXX_STANDARD} 52 | -DCMAKE_CXX_STANDARD_REQUIRED:BOOL=${CMAKE_CXX_STANDARD_REQUIRED} 53 | -DCMAKE_CXX_EXTENSIONS:BOOL=${CMAKE_CXX_EXTENSIONS} 54 | # Install directories 55 | -DITK_INSTALL_RUNTIME_DIR:STRING=${Slicer_INSTALL_LIB_DIR} 56 | -DITK_INSTALL_LIBRARY_DIR:STRING=${Slicer_INSTALL_LIB_DIR} 57 | # Options 58 | -DBUILD_TESTING:BOOL=OFF 59 | # Dependencies 60 | -DITK_DIR:PATH=${ITK_DIR} 61 | -DPYTHON_EXECUTABLE:FILEPATH=${PYTHON_EXECUTABLE} 62 | -DPYTHON_INCLUDE_DIR:PATH=${PYTHON_INCLUDE_DIR} 63 | -DPYTHON_LIBRARY:FILEPATH=${PYTHON_LIBRARY} 64 | INSTALL_COMMAND "" 65 | DEPENDS 66 | ${${proj}_DEPENDS} 67 | ) 68 | set(${proj}_DIR ${EP_BINARY_DIR}) 69 | 70 | else() 71 | ExternalProject_Add_Empty(${proj} DEPENDS ${${proj}_DEPENDS}) 72 | endif() 73 | 74 | mark_as_superbuild(${proj}_DIR:PATH) 75 | ExternalProject_Message(${proj} "${proj}_DIR:${${proj}_DIR}") 76 | --------------------------------------------------------------------------------