[med-svn] [plastimatch] branch upstream updated (fd55a83 -> e1533f5)
Greg Sharp
gregsharp-guest at moszumanska.debian.org
Mon Dec 5 23:38:17 UTC 2016
This is an automated email from the git hooks/post-receive script.
gregsharp-guest pushed a change to branch upstream
in repository plastimatch.
from fd55a83 New upstream version 1.6.4+dfsg1
new e1533f5 New upstream version 1.6.5+dfsg.1
The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
.gitignore | 2 +
AUTHORS.TXT | 48 +-
CMakeLists.txt | 176 +-
Testing/CMakeLists.txt | 96 +-
cmake/FindDlib.cmake | 19 +-
cmake/FindF2C.cmake | 51 -
cmake/PLM_FindFortran.cmake | 23 -
cmake/PlmMacros.cmake | 17 +-
cmake/language_support.cmake | 80 -
doc/NOTES.TXT | 181 +-
doc/STYLE_GUIDE_2.TXT | 5 +
doc/man/drr.1 | 2 +-
doc/man/fdk.1 | 6 +-
doc/man/landmark_warp.1 | 2 +-
doc/man/plastimatch.1 | 43 +-
libs/dlib-18.7/dlib/CMakeLists.txt | 429 --
libs/dlib-18.7/dlib/LICENSE.txt | 23 -
libs/dlib-18.7/dlib/README.txt | 41 -
libs/dlib-18.7/dlib/add_python_module | 111 -
libs/dlib-18.7/dlib/algs.h | 1033 ---
libs/dlib-18.7/dlib/all/source.cpp | 76 -
libs/dlib-18.7/dlib/all_console.cpp | 9 -
libs/dlib-18.7/dlib/all_gui.cpp | 9 -
libs/dlib-18.7/dlib/any.h | 13 -
libs/dlib-18.7/dlib/any/any.h | 181 -
libs/dlib-18.7/dlib/any/any_abstract.h | 210 -
libs/dlib-18.7/dlib/any/any_decision_function.h | 210 -
.../dlib/any/any_decision_function_abstract.h | 224 -
libs/dlib-18.7/dlib/any/any_function.h | 381 --
libs/dlib-18.7/dlib/any/any_function_abstract.h | 292 -
libs/dlib-18.7/dlib/any/any_function_impl.h | 516 --
libs/dlib-18.7/dlib/any/any_function_impl2.h | 44 -
libs/dlib-18.7/dlib/any/any_trainer.h | 218 -
libs/dlib-18.7/dlib/any/any_trainer_abstract.h | 234 -
libs/dlib-18.7/dlib/array.h | 10 -
libs/dlib-18.7/dlib/array/array_kernel.h | 780 ---
libs/dlib-18.7/dlib/array/array_kernel_abstract.h | 336 -
libs/dlib-18.7/dlib/array/array_tools.h | 38 -
libs/dlib-18.7/dlib/array/array_tools_abstract.h | 33 -
libs/dlib-18.7/dlib/array2d.h | 11 -
libs/dlib-18.7/dlib/array2d/array2d_kernel.h | 486 --
.../dlib/array2d/array2d_kernel_abstract.h | 287 -
.../dlib/array2d/serialize_pixel_overloads.h | 371 --
libs/dlib-18.7/dlib/assert.h | 155 -
libs/dlib-18.7/dlib/base64.h | 9 -
libs/dlib-18.7/dlib/base64/base64_kernel_1.cpp | 403 --
libs/dlib-18.7/dlib/base64/base64_kernel_1.h | 92 -
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libs/dlib-18.7/dlib/bayes_utils.h | 11 -
libs/dlib-18.7/dlib/bayes_utils/bayes_utils.h | 1677 -----
.../dlib/bayes_utils/bayes_utils_abstract.h | 1042 ---
libs/dlib-18.7/dlib/bigint.h | 43 -
libs/dlib-18.7/dlib/bigint/bigint_kernel_1.cpp | 1720 -----
libs/dlib-18.7/dlib/bigint/bigint_kernel_1.h | 541 --
libs/dlib-18.7/dlib/bigint/bigint_kernel_2.cpp | 1945 ------
libs/dlib-18.7/dlib/bigint/bigint_kernel_2.h | 567 --
.../dlib-18.7/dlib/bigint/bigint_kernel_abstract.h | 667 --
libs/dlib-18.7/dlib/bigint/bigint_kernel_c.h | 1130 ----
libs/dlib-18.7/dlib/binary_search_tree.h | 50 -
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libs/dlib-18.7/dlib/bit_stream.h | 42 -
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libs/dlib-18.7/dlib/bound_function_pointer.h | 10 -
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libs/dlib-18.7/dlib/bridge/bridge.h | 667 --
libs/dlib-18.7/dlib/bridge/bridge_abstract.h | 347 -
libs/dlib-18.7/dlib/bsp.h | 12 -
libs/dlib-18.7/dlib/bsp/bsp.cpp | 495 --
libs/dlib-18.7/dlib/bsp/bsp.h | 1041 ---
libs/dlib-18.7/dlib/bsp/bsp_abstract.h | 912 ---
libs/dlib-18.7/dlib/byte_orderer.h | 10 -
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libs/dlib-18.7/dlib/cassert | 1 -
libs/dlib-18.7/dlib/clustering.h | 11 -
libs/dlib-18.7/dlib/clustering/chinese_whispers.h | 135 -
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libs/dlib-18.7/dlib/cmake | 73 -
libs/dlib-18.7/dlib/cmake_find_blas.txt | 227 -
libs/dlib-18.7/dlib/cmd_line_parser.h | 84 -
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libs/dlib-18.7/dlib/cmd_line_parser/get_option.h | 181 -
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libs/dlib-18.7/dlib/compress_stream.h | 133 -
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libs/dlib-18.7/dlib/config_reader.h | 39 -
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.../config_reader/config_reader_kernel_abstract.h | 363 --
.../config_reader/config_reader_thread_safe_1.h | 456 --
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libs/dlib-18.7/dlib/console_progress_indicator.h | 202 -
libs/dlib-18.7/dlib/cpp_pretty_printer.h | 39 -
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libs/dlib-18.7/dlib/cpp_tokenizer.h | 40 -
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libs/dlib-18.7/dlib/crc32.h | 10 -
libs/dlib-18.7/dlib/crc32/crc32_kernel_1.h | 200 -
libs/dlib-18.7/dlib/crc32/crc32_kernel_abstract.h | 104 -
libs/dlib-18.7/dlib/cstring | 1 -
libs/dlib-18.7/dlib/data_io.h | 17 -
.../dlib/data_io/image_dataset_metadata.cpp | 387 --
.../dlib/data_io/image_dataset_metadata.h | 152 -
libs/dlib-18.7/dlib/data_io/libsvm_io.h | 274 -
libs/dlib-18.7/dlib/data_io/libsvm_io_abstract.h | 125 -
libs/dlib-18.7/dlib/data_io/load_image_dataset.h | 324 -
.../dlib/data_io/load_image_dataset_abstract.h | 285 -
libs/dlib-18.7/dlib/dir_nav.h | 21 -
libs/dlib-18.7/dlib/dir_nav/dir_nav_extensions.cpp | 87 -
libs/dlib-18.7/dlib/dir_nav/dir_nav_extensions.h | 158 -
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libs/dlib-18.7/dlib/dir_nav/dir_nav_kernel_1.cpp | 252 -
libs/dlib-18.7/dlib/dir_nav/dir_nav_kernel_1.h | 618 --
libs/dlib-18.7/dlib/dir_nav/dir_nav_kernel_2.cpp | 248 -
libs/dlib-18.7/dlib/dir_nav/dir_nav_kernel_2.h | 645 --
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libs/dlib-18.7/dlib/dir_nav/posix.h | 6 -
libs/dlib-18.7/dlib/dir_nav/windows.h | 6 -
libs/dlib-18.7/dlib/directed_graph.h | 37 -
.../dlib/directed_graph/directed_graph_kernel_1.h | 703 --
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libs/dlib-18.7/dlib/disjoint_subsets.h | 11 -
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libs/dlib-18.7/dlib/dlib_include_path_tutorial.txt | 20 -
libs/dlib-18.7/dlib/enable_if.h | 140 -
libs/dlib-18.7/dlib/entropy_decoder.h | 44 -
.../entropy_decoder/entropy_decoder_kernel_1.cpp | 220 -
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libs/dlib-18.7/dlib/entropy_encoder.h | 43 -
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libs/dlib-18.7/dlib/entropy_encoder_model.h | 146 -
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.../entropy_encoder_model_kernel_abstract.h | 118 -
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libs/dlib-18.7/dlib/error.h | 420 --
libs/dlib-18.7/dlib/external/libjpeg/README | 385 --
libs/dlib-18.7/dlib/external/libjpeg/jcomapi.cpp | 106 -
libs/dlib-18.7/dlib/external/libjpeg/jconfig.h | 45 -
libs/dlib-18.7/dlib/external/libjpeg/jdapimin.cpp | 395 --
libs/dlib-18.7/dlib/external/libjpeg/jdapistd.cpp | 275 -
libs/dlib-18.7/dlib/external/libjpeg/jdatasrc.cpp | 212 -
libs/dlib-18.7/dlib/external/libjpeg/jdcoefct.cpp | 736 ---
libs/dlib-18.7/dlib/external/libjpeg/jdcolor.cpp | 396 --
libs/dlib-18.7/dlib/external/libjpeg/jdct.h | 176 -
libs/dlib-18.7/dlib/external/libjpeg/jddctmgr.cpp | 269 -
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libs/dlib-18.7/dlib/external/libjpeg/jdhuff.h | 201 -
libs/dlib-18.7/dlib/external/libjpeg/jdinput.cpp | 381 --
libs/dlib-18.7/dlib/external/libjpeg/jdmainct.cpp | 512 --
libs/dlib-18.7/dlib/external/libjpeg/jdmarker.cpp | 1360 ----
libs/dlib-18.7/dlib/external/libjpeg/jdmaster.cpp | 557 --
libs/dlib-18.7/dlib/external/libjpeg/jdmerge.cpp | 400 --
libs/dlib-18.7/dlib/external/libjpeg/jdphuff.cpp | 668 --
libs/dlib-18.7/dlib/external/libjpeg/jdpostct.cpp | 290 -
libs/dlib-18.7/dlib/external/libjpeg/jdsample.cpp | 478 --
libs/dlib-18.7/dlib/external/libjpeg/jerror.cpp | 252 -
libs/dlib-18.7/dlib/external/libjpeg/jerror.h | 291 -
libs/dlib-18.7/dlib/external/libjpeg/jidctflt.cpp | 242 -
libs/dlib-18.7/dlib/external/libjpeg/jidctfst.cpp | 368 --
libs/dlib-18.7/dlib/external/libjpeg/jidctint.cpp | 389 --
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libs/dlib-18.7/dlib/external/libjpeg/jmemmgr.cpp | 1118 ----
libs/dlib-18.7/dlib/external/libjpeg/jmemnobs.cpp | 109 -
libs/dlib-18.7/dlib/external/libjpeg/jmemsys.h | 198 -
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libs/dlib-18.7/dlib/external/libjpeg/jpegint.h | 392 --
libs/dlib-18.7/dlib/external/libjpeg/jpeglib.h | 1096 ----
libs/dlib-18.7/dlib/external/libjpeg/jquant1.cpp | 856 ---
libs/dlib-18.7/dlib/external/libjpeg/jquant2.cpp | 1310 ----
libs/dlib-18.7/dlib/external/libjpeg/jutils.cpp | 179 -
libs/dlib-18.7/dlib/external/libjpeg/jversion.h | 14 -
libs/dlib-18.7/dlib/external/libpng/LICENSE | 111 -
libs/dlib-18.7/dlib/external/libpng/README | 202 -
libs/dlib-18.7/dlib/external/libpng/png.c | 4299 -------------
libs/dlib-18.7/dlib/external/libpng/png.h | 3319 ----------
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libs/dlib-18.7/dlib/external/libpng/pngerror.c | 932 ---
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libs/dlib-18.7/dlib/external/libpng/pngpread.c | 1291 ----
libs/dlib-18.7/dlib/external/libpng/pngpriv.h | 2047 ------
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libs/dlib-18.7/dlib/external/libpng/pngrio.c | 118 -
libs/dlib-18.7/dlib/external/libpng/pngrtran.c | 5110 ---------------
libs/dlib-18.7/dlib/external/libpng/pngrutil.c | 4475 -------------
libs/dlib-18.7/dlib/external/libpng/pngset.c | 1597 -----
libs/dlib-18.7/dlib/external/libpng/pngstruct.h | 489 --
libs/dlib-18.7/dlib/external/libpng/pngtrans.c | 841 ---
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libs/dlib-18.7/dlib/external/libpng/pngwtran.c | 637 --
libs/dlib-18.7/dlib/external/libpng/pngwutil.c | 3023 ---------
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libs/dlib-18.7/dlib/external/zlib/adler32.c | 179 -
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libs/dlib-18.7/dlib/external/zlib/crc32.h | 441 --
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libs/dlib-18.7/dlib/test/matrix4.cpp | 1095 ----
libs/dlib-18.7/dlib/test/matrix_chol.cpp | 182 -
libs/dlib-18.7/dlib/test/matrix_eig.cpp | 224 -
libs/dlib-18.7/dlib/test/matrix_lu.cpp | 223 -
libs/dlib-18.7/dlib/test/matrix_qr.cpp | 208 -
libs/dlib-18.7/dlib/test/max_cost_assignment.cpp | 157 -
libs/dlib-18.7/dlib/test/max_sum_submatrix.cpp | 177 -
libs/dlib-18.7/dlib/test/md5.cpp | 71 -
.../dlib/test/member_function_pointer.cpp | 553 --
libs/dlib-18.7/dlib/test/metaprogramming.cpp | 94 -
libs/dlib-18.7/dlib/test/multithreaded_object.cpp | 313 -
libs/dlib-18.7/dlib/test/numerical_integration.cpp | 228 -
libs/dlib-18.7/dlib/test/object_detector.cpp | 1002 ---
libs/dlib-18.7/dlib/test/oca.cpp | 236 -
libs/dlib-18.7/dlib/test/one_vs_all_trainer.cpp | 305 -
libs/dlib-18.7/dlib/test/one_vs_one_trainer.cpp | 218 -
libs/dlib-18.7/dlib/test/opt_qp_solver.cpp | 476 --
libs/dlib-18.7/dlib/test/optimization.cpp | 1208 ----
.../dlib/test/optimization_test_functions.cpp | 425 --
.../dlib/test/optimization_test_functions.h | 310 -
libs/dlib-18.7/dlib/test/parallel_for.cpp | 334 -
libs/dlib-18.7/dlib/test/parse.cpp | 233 -
libs/dlib-18.7/dlib/test/pipe.cpp | 688 --
libs/dlib-18.7/dlib/test/pixel.cpp | 545 --
libs/dlib-18.7/dlib/test/probabilistic.cpp | 123 -
libs/dlib-18.7/dlib/test/pyramid_down.cpp | 393 --
libs/dlib-18.7/dlib/test/queue.cpp | 426 --
libs/dlib-18.7/dlib/test/rand.cpp | 409 --
libs/dlib-18.7/dlib/test/ranking.cpp | 367 --
libs/dlib-18.7/dlib/test/read_write_mutex.cpp | 190 -
libs/dlib-18.7/dlib/test/reference_counter.cpp | 122 -
libs/dlib-18.7/dlib/test/rls.cpp | 196 -
libs/dlib-18.7/dlib/test/sammon.cpp | 211 -
libs/dlib-18.7/dlib/test/scan_image.cpp | 713 --
libs/dlib-18.7/dlib/test/sequence.cpp | 312 -
libs/dlib-18.7/dlib/test/sequence_labeler.cpp | 461 --
libs/dlib-18.7/dlib/test/sequence_segmenter.cpp | 294 -
libs/dlib-18.7/dlib/test/serialize.cpp | 961 ---
libs/dlib-18.7/dlib/test/set.cpp | 464 --
libs/dlib-18.7/dlib/test/sldf.cpp | 296 -
libs/dlib-18.7/dlib/test/sliding_buffer.cpp | 439 --
libs/dlib-18.7/dlib/test/smart_pointers.cpp | 440 --
libs/dlib-18.7/dlib/test/sockets.cpp | 245 -
libs/dlib-18.7/dlib/test/sockets2.cpp | 202 -
libs/dlib-18.7/dlib/test/sockstreambuf.cpp | 253 -
libs/dlib-18.7/dlib/test/sparse_vector.cpp | 282 -
libs/dlib-18.7/dlib/test/stack.cpp | 294 -
libs/dlib-18.7/dlib/test/static_map.cpp | 323 -
libs/dlib-18.7/dlib/test/static_set.cpp | 206 -
libs/dlib-18.7/dlib/test/statistics.cpp | 720 ---
libs/dlib-18.7/dlib/test/std_vector_c.cpp | 101 -
libs/dlib-18.7/dlib/test/string.cpp | 269 -
libs/dlib-18.7/dlib/test/svm.cpp | 661 --
libs/dlib-18.7/dlib/test/svm_c_linear.cpp | 314 -
libs/dlib-18.7/dlib/test/svm_c_linear_dcd.cpp | 484 --
libs/dlib-18.7/dlib/test/svm_multiclass_linear.cpp | 109 -
libs/dlib-18.7/dlib/test/svm_struct.cpp | 641 --
libs/dlib-18.7/dlib/test/svr_linear_trainer.cpp | 161 -
.../dlib-18.7/dlib/test/symmetric_matrix_cache.cpp | 212 -
libs/dlib-18.7/dlib/test/tester.cpp | 175 -
libs/dlib-18.7/dlib/test/tester.h | 187 -
libs/dlib-18.7/dlib/test/thread_pool.cpp | 395 --
libs/dlib-18.7/dlib/test/threads.cpp | 128 -
libs/dlib-18.7/dlib/test/timer.cpp | 347 -
libs/dlib-18.7/dlib/test/tokenizer.cpp | 378 --
libs/dlib-18.7/dlib/test/trust_region.cpp | 329 -
libs/dlib-18.7/dlib/test/tuple.cpp | 186 -
libs/dlib-18.7/dlib/test/type_safe_union.cpp | 442 --
libs/dlib-18.7/dlib/test/vectorstream.cpp | 142 -
libs/dlib-18.7/dlib/threads.h | 22 -
libs/dlib-18.7/dlib/threads/auto_mutex_extension.h | 135 -
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.../dlib-18.7/dlib/threads/auto_unlock_extension.h | 116 -
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libs/dlib-18.7/dlib/threads/posix.h | 6 -
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libs/dlib-18.7/dlib/threads/rmutex_extension.h | 109 -
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libs/dlib-18.7/dlib/threads/rsignaler_extension.h | 90 -
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.../dlib/threads/thread_specific_data_extension.h | 141 -
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libs/dlib-18.7/dlib/threads/threads_kernel.h | 18 -
libs/dlib-18.7/dlib/threads/threads_kernel_1.cpp | 83 -
libs/dlib-18.7/dlib/threads/threads_kernel_1.h | 267 -
libs/dlib-18.7/dlib/threads/threads_kernel_2.cpp | 75 -
libs/dlib-18.7/dlib/threads/threads_kernel_2.h | 180 -
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.../dlib/threads/threads_kernel_shared.cpp | 329 -
.../dlib-18.7/dlib/threads/threads_kernel_shared.h | 284 -
libs/dlib-18.7/dlib/threads/windows.h | 6 -
libs/dlib-18.7/dlib/time_this.h | 77 -
libs/dlib-18.7/dlib/timeout.h | 10 -
libs/dlib-18.7/dlib/timeout/timeout.h | 200 -
libs/dlib-18.7/dlib/timeout/timeout_abstract.h | 188 -
libs/dlib-18.7/dlib/timer.h | 10 -
libs/dlib-18.7/dlib/timer/timer.cpp | 208 -
libs/dlib-18.7/dlib/timer/timer.h | 426 --
libs/dlib-18.7/dlib/timer/timer_abstract.h | 190 -
libs/dlib-18.7/dlib/timer/timer_heavy.h | 392 --
libs/dlib-18.7/dlib/timing.h | 195 -
libs/dlib-18.7/dlib/tokenizer.h | 33 -
.../dlib/tokenizer/tokenizer_kernel_1.cpp | 295 -
libs/dlib-18.7/dlib/tokenizer/tokenizer_kernel_1.h | 155 -
.../dlib/tokenizer/tokenizer_kernel_abstract.h | 289 -
libs/dlib-18.7/dlib/tokenizer/tokenizer_kernel_c.h | 167 -
libs/dlib-18.7/dlib/tuple.h | 10 -
libs/dlib-18.7/dlib/tuple/tuple.h | 410 --
libs/dlib-18.7/dlib/tuple/tuple_abstract.h | 302 -
libs/dlib-18.7/dlib/type_safe_union.h | 11 -
.../dlib/type_safe_union/type_safe_union_kernel.h | 678 --
.../type_safe_union_kernel_abstract.h | 293 -
libs/dlib-18.7/dlib/uintn.h | 96 -
libs/dlib-18.7/dlib/unicode.h | 9 -
libs/dlib-18.7/dlib/unicode/unicode.cpp | 175 -
libs/dlib-18.7/dlib/unicode/unicode.h | 616 --
libs/dlib-18.7/dlib/unicode/unicode_abstract.h | 233 -
libs/dlib-18.7/dlib/unordered_pair.h | 176 -
libs/dlib-18.7/dlib/vectorstream.h | 10 -
libs/dlib-18.7/dlib/vectorstream/vectorstream.h | 138 -
.../dlib/vectorstream/vectorstream_abstract.h | 62 -
libs/dlib-18.7/dlib/windows_magic.h | 45 -
libs/dlib-18.7/dlib/xml_parser.h | 13 -
.../dlib/xml_parser/xml_parser_kernel_1.h | 1520 -----
.../dlib/xml_parser/xml_parser_kernel_abstract.h | 277 -
.../dlib/xml_parser/xml_parser_kernel_interfaces.h | 229 -
libs/nocedal/CMakeLists.txt | 20 -
libs/nocedal/README | 4 -
libs/nocedal/lbfgsb_2_1.c | 5622 ----------------
libs/nocedal/lbfgsb_2_1.f | 4429 -------------
libs/nocedal/lbfgsb_2_1_ori.f | 4423 -------------
libs/specfun/CMakeLists.txt | 16 +-
src/CMakeLists.txt | 23 +-
src/plastimatch/CHANGELOG.TXT | 8 +
src/plastimatch/CMakeLists.txt | 26 +-
src/plastimatch/base/CMakeLists.txt | 12 +-
src/plastimatch/base/bspline_xform.cxx | 119 -
src/plastimatch/base/bspline_xform.h | 2 +-
src/plastimatch/base/bspline_xform_legacy.cxx | 120 +
.../base/{dcmtk_uid.h => bspline_xform_legacy.h} | 9 +-
src/plastimatch/base/cxt_io.cxx | 5 +-
src/plastimatch/base/dcmtk_image.cxx | 193 +-
src/plastimatch/base/dcmtk_loader.cxx | 258 -
src/plastimatch/base/dcmtk_loader.h | 50 -
src/plastimatch/base/dcmtk_loader_p.h | 51 -
src/plastimatch/base/dcmtk_metadata.cxx | 10 +-
src/plastimatch/base/dcmtk_module.cxx | 105 +
src/plastimatch/base/dcmtk_module.h | 35 +
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src/plastimatch/base/dcmtk_module_general_series.h | 19 -
.../base/dcmtk_module_general_study.cxx | 29 -
src/plastimatch/base/dcmtk_module_general_study.h | 19 -
src/plastimatch/base/dcmtk_module_patient.cxx | 20 -
src/plastimatch/base/dcmtk_module_patient.h | 18 -
src/plastimatch/base/dcmtk_rdd.cxx | 8 +-
src/plastimatch/base/dcmtk_rt_study.cxx | 244 +-
src/plastimatch/base/dcmtk_rt_study.h | 32 +-
src/plastimatch/base/dcmtk_rt_study_p.cxx | 8 +
src/plastimatch/base/dcmtk_rt_study_p.h | 7 +
src/plastimatch/base/dcmtk_rtdose.cxx | 75 +-
src/plastimatch/base/dcmtk_rtplan.cxx | 428 ++
.../base/{dcmtk_rtss.h => dcmtk_rtplan.h} | 6 +-
src/plastimatch/base/dcmtk_rtss.cxx | 30 +-
src/plastimatch/base/dcmtk_series_map.h | 15 +
src/plastimatch/base/dcmtk_sro.cxx | 124 +-
src/plastimatch/base/dcmtk_util.cxx | 21 +-
src/plastimatch/base/dcmtk_util.h | 8 +
src/plastimatch/base/dicom_probe.cxx | 14 +
src/plastimatch/base/dicom_probe.h | 4 +
src/plastimatch/base/gdcm1_dose.cxx | 4 +-
src/plastimatch/base/gdcm1_series.cxx | 2 +-
src/plastimatch/base/gdcm1_series.h | 2 +-
src/plastimatch/base/metadata.cxx | 76 +-
src/plastimatch/base/metadata.h | 21 +-
src/plastimatch/base/plm_file_format.cxx | 54 +-
src/plastimatch/base/plm_file_format.h | 2 +
src/plastimatch/base/plm_image.cxx | 9 +-
src/plastimatch/base/plm_image.h | 6 +-
src/plastimatch/base/pwlut.cxx | 180 +-
src/plastimatch/base/pwlut.h | 76 +-
src/plastimatch/base/rpl_volume.cxx | 64 +-
src/plastimatch/base/rt_study.cxx | 115 +-
src/plastimatch/base/rt_study.h | 19 +-
src/plastimatch/base/rt_study_metadata.cxx | 200 +-
src/plastimatch/base/rt_study_metadata.h | 48 +-
src/plastimatch/base/rt_study_p.h | 2 +-
src/plastimatch/base/rtds_dcmtk.cxx | 13 +-
src/plastimatch/base/rtds_gdcm.cxx | 10 +-
src/plastimatch/base/rtplan.cxx | 121 +
src/plastimatch/base/rtplan.h | 55 +
src/plastimatch/base/rtplan_beam.cxx | 100 +
src/plastimatch/base/rtplan_beam.h | 45 +
src/plastimatch/base/rtplan_control_pt.cxx | 51 +
src/plastimatch/base/rtplan_control_pt.h | 57 +
src/plastimatch/base/rtss.cxx | 51 +-
src/plastimatch/base/rtss_contour.cxx | 2 +-
src/plastimatch/base/segmentation.cxx | 12 +-
src/plastimatch/base/segmentation.h | 1 +
src/plastimatch/base/thumbnail.cxx | 206 +-
src/plastimatch/base/vf_jacobian.cxx | 198 +-
src/plastimatch/base/volume_fill.cxx | 46 +-
src/plastimatch/base/volume_fill.h | 34 +-
src/plastimatch/base/xform.cxx | 6 +
src/plastimatch/base/xio_ct.cxx | 38 +-
src/plastimatch/base/xio_structures.cxx | 10 +-
src/plastimatch/cli/CMakeLists.txt | 2 +
src/plastimatch/cli/pcmd_gamma.cxx | 508 +-
src/plastimatch/cli/pcmd_maximum.cxx | 131 +
.../cli/{pcmd_crop.h => pcmd_maximum.h} | 6 +-
src/plastimatch/cli/pcmd_multiply.cxx | 166 +
.../cli/{pcmd_crop.h => pcmd_multiply.h} | 6 +-
src/plastimatch/cli/pcmd_synth.cxx | 10 +-
src/plastimatch/cli/pcmd_warp.cxx | 9 +-
src/plastimatch/cli/plastimatch_main.cxx | 16 +-
.../cmake/PlastimatchBuildTreeSettings.cmake.in | 1 +
src/plastimatch/cuda/cuda_probe.cu | 122 +-
src/plastimatch/cuda/cuda_util.cu | 270 +-
src/plastimatch/dose/CMakeLists.txt | 103 +-
src/plastimatch/dose/rt_mebs.cxx | 3 +-
src/plastimatch/dose/rt_plan.cxx | 443 +-
src/plastimatch/opencl/CMakeLists.txt | 54 +-
src/plastimatch/reconstruct/drr.cxx | 10 +-
src/plastimatch/reconstruct/drr.h | 9 +-
src/plastimatch/register/CMakeLists.txt | 7 -
src/plastimatch/register/bspline_optimize.cxx | 329 +-
.../register/bspline_optimize_liblbfgs.cxx | 218 +-
.../register/bspline_optimize_nlopt.cxx | 200 +-
.../register/bspline_optimize_steepest.cxx | 910 +--
src/plastimatch/register/cuda/CMakeLists.txt | 2 +-
.../register/registration_metric_type.h | 36 +-
src/plastimatch/script/lua_tty_commands_pcmd.cxx | 8 +
src/plastimatch/script/lua_tty_commands_pcmd.h | 4 +
src/plastimatch/segment/autolabel_trainer.cxx | 708 +-
src/plastimatch/segment/mabs.cxx | 79 +-
src/plastimatch/segment/mabs.h | 1 -
src/plastimatch/segment/mabs_parms.cxx | 3 +
src/plastimatch/segment/mabs_parms.h | 1 +
src/plastimatch/standalone/BeamDataRFA.cxx | 81 +
src/plastimatch/standalone/BeamDataRFA.h | 46 +
src/plastimatch/standalone/CMakeLists.txt | 739 ++-
src/plastimatch/standalone/beamdata_gen_gui.cpp | 2390 +++++++
src/plastimatch/standalone/beamdata_gen_gui.h | 137 +
src/plastimatch/standalone/beamdata_gen_gui.ui | 1993 ++++++
...onverter_main.cpp => beamdata_gen_gui_main.cpp} | 4 +-
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src/plastimatch/standalone/colormap_jet.txt | 64 -
src/plastimatch/standalone/dice_stats_main.cxx | 1 -
src/plastimatch/standalone/drr_main.cxx | 4 +-
src/plastimatch/standalone/drr_opts.cxx | 17 +-
src/plastimatch/standalone/gamma_gui.cpp | 19 +-
src/plastimatch/standalone/gamma_gui.h | 2 +-
src/plastimatch/standalone/gamma_gui.ui | 20 +-
src/plastimatch/standalone/qcustomplot.h | 2 +-
src/plastimatch/standalone/qt_util.cxx | 135 +-
src/plastimatch/standalone/qt_util.h | 191 +-
src/plastimatch/standalone/register_gui.cpp | 529 +-
src/plastimatch/standalone/register_gui.h | 210 +-
src/plastimatch/standalone/register_gui.ui | 715 +-
src/plastimatch/standalone/xvi_archive.cxx | 95 +-
src/plastimatch/standalone/xvi_archive.h | 5 +
src/plastimatch/standalone/yk_config.h | 10 +
src/plastimatch/sys/CMakeLists.txt | 1 -
src/plastimatch/sys/dlib_threads.cxx | 308 +-
src/plastimatch/sys/dlib_threads.h | 96 +-
src/plastimatch/sys/plm_config.h.in | 6 +-
src/plastimatch/sys/plm_fortran.h.in | 77 -
src/plastimatch/sys/plm_math.h | 8 +
src/plastimatch/sys/plm_return_code.h | 32 +-
src/plastimatch/sys/plm_sleep.cxx | 42 +-
src/plastimatch/sys/plm_sleep.h | 22 +-
src/plastimatch/sys/plm_timer.cxx | 1 +
src/plastimatch/sys/string_util.cxx | 3 +
src/plastimatch/test/CMakeLists.txt | 3 +
src/plastimatch/test/cpp_sizeof_test.cxx | 36 +-
src/plastimatch/test/dcmtk_test.cxx | 12 +-
src/plastimatch/test/dlib_thread_test.cxx | 124 +-
src/plastimatch/test/gabor_test.cxx | 68 +-
src/plastimatch/test/itk_thread_test.cxx | 200 +-
src/plastimatch/test/plm_restart_test.cxx | 172 +-
src/plastimatch/test/ransac_test.cxx | 176 +-
src/plastimatch/test/rtplan_test.cxx | 99 +
src/plastimatch/util/dicom_sro_save.cxx | 318 +-
src/plastimatch/util/dicom_sro_save.h | 116 +-
src/plastimatch/util/distance_map.cxx | 904 +--
src/plastimatch/util/gamma_dose_comparison.cxx | 2194 +++----
src/plastimatch/util/gamma_dose_comparison.h | 354 +-
src/plastimatch/util/itk_distance_map.cxx | 240 +-
src/plastimatch/util/rt_study_warp.cxx | 41 +-
src/plastimatch/util/simplify_points.cxx | 4 +-
src/plastimatch/util/synthetic_mha.cxx | 8 +-
src/plastimatch/util/warp_parms.h | 4 +-
1323 files changed, 14458 insertions(+), 442274 deletions(-)
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delete mode 100644 src/plastimatch/base/dcmtk_module_general_series.h
delete mode 100644 src/plastimatch/base/dcmtk_module_general_study.cxx
delete mode 100644 src/plastimatch/base/dcmtk_module_general_study.h
delete mode 100644 src/plastimatch/base/dcmtk_module_patient.cxx
delete mode 100644 src/plastimatch/base/dcmtk_module_patient.h
create mode 100755 src/plastimatch/base/dcmtk_rtplan.cxx
copy src/plastimatch/base/{dcmtk_rtss.h => dcmtk_rtplan.h} (75%)
mode change 100755 => 100644
create mode 100644 src/plastimatch/base/dcmtk_series_map.h
create mode 100644 src/plastimatch/base/rtplan.cxx
create mode 100644 src/plastimatch/base/rtplan.h
create mode 100644 src/plastimatch/base/rtplan_beam.cxx
create mode 100644 src/plastimatch/base/rtplan_beam.h
create mode 100644 src/plastimatch/base/rtplan_control_pt.cxx
create mode 100755 src/plastimatch/base/rtplan_control_pt.h
create mode 100644 src/plastimatch/cli/pcmd_maximum.cxx
copy src/plastimatch/cli/{pcmd_crop.h => pcmd_maximum.h} (72%)
mode change 100755 => 100644
create mode 100644 src/plastimatch/cli/pcmd_multiply.cxx
copy src/plastimatch/cli/{pcmd_crop.h => pcmd_multiply.h} (72%)
mode change 100755 => 100644
mode change 100644 => 100755 src/plastimatch/register/cuda/CMakeLists.txt
create mode 100644 src/plastimatch/standalone/BeamDataRFA.cxx
create mode 100644 src/plastimatch/standalone/BeamDataRFA.h
create mode 100644 src/plastimatch/standalone/beamdata_gen_gui.cpp
create mode 100644 src/plastimatch/standalone/beamdata_gen_gui.h
create mode 100644 src/plastimatch/standalone/beamdata_gen_gui.ui
copy src/plastimatch/standalone/{nki2mha_converter_main.cpp => beamdata_gen_gui_main.cpp} (68%)
delete mode 100644 src/plastimatch/standalone/colormap_customgamma.txt
delete mode 100644 src/plastimatch/standalone/colormap_jet.txt
delete mode 100644 src/plastimatch/sys/plm_fortran.h.in
mode change 100644 => 100755 src/plastimatch/sys/string_util.cxx
create mode 100755 src/plastimatch/test/rtplan_test.cxx
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