RNifti Fast R and C++ Access to NIfTI Images

NiftiImage.h
1 #ifndef _NIFTI_IMAGE_H_
2 #define _NIFTI_IMAGE_H_
3
4
5 #ifdef USING_R
6
7 #include <Rcpp.h>
8
9 #else
10
11 #define R_NegInf -INFINITY
12
13 #include <stdint.h>
14 #include <cstddef>
15 #include <cmath>
16 #include <string>
17 #include <sstream>
18 #include <vector>
19 #include <stdexcept>
20 #include <algorithm>
21 #include <map>
22 #include <locale>
23 #include <limits>
24
25 #endif
26
27
28 #include "niftilib/nifti1_io.h"
29
38 namespace RNifti {
39
40 namespace internal {
41
42 struct vec3
43 {
44 float v[3];
45
46 vec3 operator-() const
47 {
48 vec3 r;
49 r.v[0] = -v[0];
50 r.v[1] = -v[1];
51 r.v[2] = -v[2];
52 return r;
53 }
54 };
55
56 inline mat33 topLeftCorner (const mat44 &matrix)
57 {
58 mat33 newMatrix;
59 for (int i=0; i<3; i++)
60 {
61 for (int j=0; j<3; j++)
62 newMatrix.m[i][j] = matrix.m[i][j];
63 }
64 return newMatrix;
65 }
66
67 inline vec3 matrixVectorProduct (const mat33 &matrix, const vec3 &vector)
68 {
69 vec3 newVector;
70 for (int i=0; i<3; i++)
71 {
72 newVector.v[i] = 0.0;
73 for (int j=0; j<3; j++)
74 newVector.v[i] += matrix.m[i][j] * vector.v[j];
75 }
76 return newVector;
77 }
78
79 } // internal namespace
80
85 class NiftiImage
86 {
87 public:
92 struct Block
93 {
94 const NiftiImage &image;
95 const int dimension;
96 const int index;
105 Block (const NiftiImage &image, const int dimension, const int index)
106 : image(image), dimension(dimension), index(index)
107 {
108 if (dimension != image->ndim)
109 throw std::runtime_error("Blocks must be along the last dimension in the image");
110 }
111
120 Block & operator= (const NiftiImage &source)
121 {
122 if (source->datatype != image->datatype)
123 throw std::runtime_error("New data does not have the same datatype as the target block");
124 if (source->scl_slope != image->scl_slope || source->scl_inter != image->scl_inter)
125 throw std::runtime_error("New data does not have the same scale parameters as the target block");
126
127 size_t blockSize = 1;
128 for (int i=1; i<dimension; i++)
129 blockSize *= image->dim[i];
130
131 if (blockSize != source->nvox)
132 throw std::runtime_error("New data does not have the same size as the target block");
133
134 blockSize *= image->nbyper;
135 memcpy(static_cast<char*>(image->data) + blockSize*index, source->data, blockSize);
136 return *this;
137 }
138
146 template <typename TargetType>
147 std::vector<TargetType> getData (const bool useSlope = true) const;
148 };
149
150 #ifdef USING_R
151
157 static short sexpTypeToNiftiType (const int sexpType)
158 {
159 if (sexpType == INTSXP || sexpType == LGLSXP)
160 return DT_INT32;
161 else if (sexpType == REALSXP)
162 return DT_FLOAT64;
163 else
164 throw std::runtime_error("Array elements must be numeric");
165 }
166 #endif
167
173 static mat33 xformToRotation (const mat44 matrix)
174 {
175 float qb, qc, qd, qfac;
176 nifti_mat44_to_quatern(matrix, &qb, &qc, &qd, NULL, NULL, NULL, NULL, NULL, NULL, &qfac);
177 mat44 rotationMatrix = nifti_quatern_to_mat44(qb, qc, qd, 0.0, 0.0, 0.0, 1.0, 1.0, 1.0, qfac);
178 return internal::topLeftCorner(rotationMatrix);
179 }
180
186 static std::string xformToString (const mat44 matrix)
187 {
188 int icode, jcode, kcode;
189 nifti_mat44_to_orientation(matrix, &icode, &jcode, &kcode);
190
191 int codes[3] = { icode, jcode, kcode };
192 std::string result("---");
193 for (int i=0; i<3; i++)
194 {
195 switch (codes[i])
196 {
197 case NIFTI_L2R: result[i] = 'R'; break;
198 case NIFTI_R2L: result[i] = 'L'; break;
199 case NIFTI_P2A: result[i] = 'A'; break;
200 case NIFTI_A2P: result[i] = 'P'; break;
201 case NIFTI_I2S: result[i] = 'S'; break;
202 case NIFTI_S2I: result[i] = 'I'; break;
203 }
204 }
205 return result;
206 }
207
214 static int fileVersion (const std::string &path)
215 {
216 nifti_1_header *header = nifti_read_header(path.c_str(), NULL, false);
217 if (header == NULL)
218 return -1;
219 else
220 {
221 int version = NIFTI_VERSION(*header);
222 if (version == 0)
223 {
224 // NIfTI-2 has a 540-byte header - check for this or its byte-swapped equivalent
225 if (header->sizeof_hdr == 540 || header->sizeof_hdr == 469893120)
226 {
227 // The magic number has moved in NIfTI-2, so find it by byte offset
228 const char *magic = (char *) header + 4;
229 if (strncmp(magic,"ni2",3) == 0 || strncmp(magic,"n+2",3) == 0)
230 version = 2;
231 }
232 else if (!nifti_hdr_looks_good(header))
233 {
234 // Not plausible as ANALYZE, so return -1
235 version = -1;
236 }
237 }
238 return version;
239 }
240 }
241
242
243 protected:
244 nifti_image *image;
245 bool persistent;
251 void copy (const nifti_image *source);
252
257 void copy (const NiftiImage &source);
258
263 void copy (const Block &source);
264
265
266 #ifdef USING_R
267
273 void initFromNiftiS4 (const Rcpp::RObject &object, const bool copyData = true);
274
280 void initFromMriImage (const Rcpp::RObject &object, const bool copyData = true);
281
286 void initFromList (const Rcpp::RObject &object);
287
293 void initFromArray (const Rcpp::RObject &object, const bool copyData = true);
294
295 #endif
296
301 void updatePixdim (const std::vector<float> &pixdim);
302
307 void setPixunits (const std::vector<std::string> &pixunits);
308
309 public:
313 NiftiImage ()
314 : image(NULL), persistent(false) {}
315
320 NiftiImage (const NiftiImage &source)
321 : image(NULL), persistent(false)
322 {
323 this->copy(source);
324 #ifndef NDEBUG
325 Rprintf("Creating NiftiImage with pointer %p (from NiftiImage)\n", this->image);
326 #endif
327 }
328
333 NiftiImage (const Block &source)
334 : image(NULL), persistent(false)
335 {
336 this->copy(source);
337 #ifndef NDEBUG
338 Rprintf("Creating NiftiImage with pointer %p (from Block)\n", this->image);
339 #endif
340 }
341
348 NiftiImage (nifti_image * const image, const bool copy = false)
349 : image(NULL), persistent(false)
350 {
351 if (copy)
352 this->copy(image);
353 else
354 this->image = image;
355 #ifndef NDEBUG
356 Rprintf("Creating NiftiImage with pointer %p (from pointer)\n", this->image);
357 #endif
358 }
359
366 NiftiImage (const std::string &path, const bool readData = true)
367 : persistent(false)
368 {
369 this->image = nifti_image_read(path.c_str(), readData);
370 if (this->image == NULL)
371 throw std::runtime_error("Failed to read image from path " + path);
372 #ifndef NDEBUG
373 Rprintf("Creating NiftiImage with pointer %p (from string)\n", this->image);
374 #endif
375 }
376
383 NiftiImage (const std::string &path, const std::vector<int> &volumes);
384
385 #ifdef USING_R
386
391 NiftiImage (const SEXP object, const bool readData = true);
392 #endif
393
397 virtual ~NiftiImage ()
398 {
399 if (!persistent)
400 {
401 #ifndef NDEBUG
402 Rprintf("Freeing NiftiImage with pointer %p\n", this->image);
403 #endif
404 nifti_image_free(image);
405 }
406 }
407
411 operator const nifti_image* () const { return image; }
412
416 operator nifti_image* () { return image; }
417
421 const nifti_image * operator-> () const { return image; }
422
426 nifti_image * operator-> () { return image; }
427
432 NiftiImage & operator= (const NiftiImage &source)
433 {
434 copy(source);
435 #ifndef NDEBUG
436 Rprintf("Creating NiftiImage with pointer %p (from NiftiImage)\n", this->image);
437 #endif
438 return *this;
439 }
440
446 NiftiImage & operator= (const Block &source)
447 {
448 copy(source);
449 #ifndef NDEBUG
450 Rprintf("Creating NiftiImage with pointer %p (from Block)\n", this->image);
451 #endif
452 return *this;
453 }
454
459 NiftiImage & setPersistence (const bool persistent)
460 {
461 this->persistent = persistent;
462 #ifndef NDEBUG
463 if (persistent)
464 Rprintf("Setting NiftiImage with pointer %p to be persistent\n", this->image);
465 #endif
466 return *this;
467 }
468
472 bool isNull () const { return (image == NULL); }
473
477 bool isPersistent () const { return persistent; }
478
482 bool isDataScaled () const { return (image != NULL && image->scl_slope != 0.0 && (image->scl_slope != 1.0 || image->scl_inter != 0.0)); }
483
487 int nDims () const
488 {
489 if (image == NULL)
490 return 0;
491 else
492 return image->ndim;
493 }
494
499 std::vector<int> dim () const
500 {
501 if (image == NULL)
502 return std::vector<int>();
503 else
504 return std::vector<int>(image->dim+1, image->dim+image->ndim+1);
505 }
506
511 std::vector<float> pixdim () const
512 {
513 if (image == NULL)
514 return std::vector<float>();
515 else
516 return std::vector<float>(image->pixdim+1, image->pixdim+image->ndim+1);
517 }
518
525 NiftiImage & drop ()
526 {
527 int ndim = image->ndim;
528 while (image->dim[ndim] < 2)
529 ndim--;
530 image->dim[0] = image->ndim = ndim;
531
532 return *this;
533 }
534
542 template <typename TargetType>
543 std::vector<TargetType> getData (const bool useSlope = true) const;
544
551 NiftiImage & changeDatatype (const short datatype, const bool useSlope = false);
552
559 NiftiImage & changeDatatype (const std::string &datatype, const bool useSlope = false);
560
568 template <typename SourceType>
569 NiftiImage & replaceData (const std::vector<SourceType> &data, const short datatype = DT_NONE);
570
574 NiftiImage & dropData ()
575 {
576 nifti_image_unload(image);
577 return *this;
578 }
579
585 NiftiImage & rescale (const std::vector<float> &scales);
586
594 NiftiImage & reorient (const int i, const int j, const int k);
595
603 NiftiImage & reorient (const std::string &orientation);
604
605 #ifdef USING_R
606
610 NiftiImage & update (const Rcpp::RObject &object);
611 #endif
612
618 mat44 xform (const bool preferQuaternion = true) const;
619
623 int nBlocks () const
624 {
625 if (image == NULL)
626 return 0;
627 else
628 return image->dim[image->ndim];
629 }
630
638 const Block block (const int i) const { return Block(*this, nDims(), i); }
639
647 Block block (const int i) { return Block(*this, nDims(), i); }
648
654 const Block slice (const int i) const { return Block(*this, 3, i); }
655
661 Block slice (const int i) { return Block(*this, 3, i); }
662
668 const Block volume (const int i) const { return Block(*this, 4, i); }
669
675 Block volume (const int i) { return Block(*this, 4, i); }
676
682 void toFile (const std::string fileName, const short datatype = DT_NONE) const;
683
689 void toFile (const std::string fileName, const std::string &datatype) const;
690
691 #ifdef USING_R
692
697 Rcpp::RObject toArray () const;
698
704 Rcpp::RObject toPointer (const std::string label) const;
705
712 Rcpp::RObject toArrayOrPointer (const bool internal, const std::string label) const;
713
718 Rcpp::RObject headerToList () const;
719
720 #endif
721
722 };
723
724 // Include helper functions
725 #include "lib/NiftiImage_internal.h"
726
727 inline void NiftiImage::copy (const nifti_image *source)
728 {
729 if (image != NULL && !persistent)
730 nifti_image_free(image);
731
732 if (source == NULL)
733 image = NULL;
734 else
735 {
736 image = nifti_copy_nim_info(source);
737 if (source->data != NULL)
738 {
739 size_t dataSize = nifti_get_volsize(source);
740 image->data = calloc(1, dataSize);
741 memcpy(image->data, source->data, dataSize);
742 }
743 }
744
745 persistent = false;
746 }
747
748 inline void NiftiImage::copy (const NiftiImage &source)
749 {
750 const nifti_image *sourceStruct = source;
751 copy(sourceStruct);
752 }
753
754 inline void NiftiImage::copy (const Block &source)
755 {
756 if (image != NULL && !persistent)
757 nifti_image_free(image);
758
759 const nifti_image *sourceStruct = source.image;
760 if (sourceStruct == NULL)
761 image = NULL;
762 else
763 {
764 image = nifti_copy_nim_info(sourceStruct);
765 image->dim[0] = source.image->dim[0] - 1;
766 image->dim[source.dimension] = 1;
767 image->pixdim[source.dimension] = 1.0;
768 nifti_update_dims_from_array(image);
769
770 if (sourceStruct->data != NULL)
771 {
772 size_t blockSize = nifti_get_volsize(image);
773 image->data = calloc(1, blockSize);
774 memcpy(image->data, static_cast<char*>(source.image->data) + blockSize*source.index, blockSize);
775 }
776 }
777
778 persistent = false;
779 }
780
781 #ifdef USING_R
782
783 // Convert an S4 "nifti" object, as defined in the oro.nifti package, to a "nifti_image" struct
784 inline void NiftiImage::initFromNiftiS4 (const Rcpp::RObject &object, const bool copyData)
785 {
786 nifti_1_header header;
787 header.sizeof_hdr = 348;
788
789 const std::vector<short> dims = object.slot("dim_");
790 for (int i=0; i<8; i++)
791 header.dim[i] = dims[i];
792
793 header.intent_p1 = object.slot("intent_p1");
794 header.intent_p2 = object.slot("intent_p2");
795 header.intent_p3 = object.slot("intent_p3");
796 header.intent_code = object.slot("intent_code");
797
798 header.datatype = object.slot("datatype");
799 header.bitpix = object.slot("bitpix");
800
801 header.slice_start = object.slot("slice_start");
802 header.slice_end = object.slot("slice_end");
803 header.slice_code = Rcpp::as<int>(object.slot("slice_code"));
804 header.slice_duration = object.slot("slice_duration");
805
806 const std::vector<float> pixdims = object.slot("pixdim");
807 for (int i=0; i<8; i++)
808 header.pixdim[i] = pixdims[i];
809 header.xyzt_units = Rcpp::as<int>(object.slot("xyzt_units"));
810
811 header.vox_offset = object.slot("vox_offset");
812
813 header.scl_slope = object.slot("scl_slope");
814 header.scl_inter = object.slot("scl_inter");
815 header.toffset = object.slot("toffset");
816
817 header.cal_max = object.slot("cal_max");
818 header.cal_min = object.slot("cal_min");
819 header.glmax = header.glmin = 0;
820
821 strncpy(header.descrip, Rcpp::as<std::string>(object.slot("descrip")).c_str(), 79);
822 header.descrip[79] = '\0';
823 strncpy(header.aux_file, Rcpp::as<std::string>(object.slot("aux_file")).c_str(), 23);
824 header.aux_file[23] = '\0';
825 strncpy(header.intent_name, Rcpp::as<std::string>(object.slot("intent_name")).c_str(), 15);
826 header.intent_name[15] = '\0';
827 strncpy(header.magic, Rcpp::as<std::string>(object.slot("magic")).c_str(), 3);
828 header.magic[3] = '\0';
829
830 header.qform_code = object.slot("qform_code");
831 header.sform_code = object.slot("sform_code");
832
833 header.quatern_b = object.slot("quatern_b");
834 header.quatern_c = object.slot("quatern_c");
835 header.quatern_d = object.slot("quatern_d");
836 header.qoffset_x = object.slot("qoffset_x");
837 header.qoffset_y = object.slot("qoffset_y");
838 header.qoffset_z = object.slot("qoffset_z");
839
840 const std::vector<float> srow_x = object.slot("srow_x");
841 const std::vector<float> srow_y = object.slot("srow_y");
842 const std::vector<float> srow_z = object.slot("srow_z");
843 for (int i=0; i<4; i++)
844 {
845 header.srow_x[i] = srow_x[i];
846 header.srow_y[i] = srow_y[i];
847 header.srow_z[i] = srow_z[i];
848 }
849
850 if (header.datatype == DT_UINT8 || header.datatype == DT_INT16 || header.datatype == DT_INT32 || header.datatype == DT_INT8 || header.datatype == DT_UINT16 || header.datatype == DT_UINT32)
851 header.datatype = DT_INT32;
852 else if (header.datatype == DT_FLOAT32 || header.datatype == DT_FLOAT64)
853 header.datatype = DT_FLOAT64; // This assumes that sizeof(double) == 8
854 else
855 throw std::runtime_error("Data type is not supported");
856
857 this->image = nifti_convert_nhdr2nim(header, NULL);
858
859 const SEXP data = PROTECT(object.slot(".Data"));
860 if (!copyData || Rf_length(data) <= 1)
861 this->image->data = NULL;
862 else
863 {
864 const size_t dataSize = nifti_get_volsize(this->image);
865 this->image->data = calloc(1, dataSize);
866 if (header.datatype == DT_INT32)
867 {
868 Rcpp::IntegerVector intData(data);
869 std::copy(intData.begin(), intData.end(), static_cast<int32_t*>(this->image->data));
870 }
871 else
872 {
873 Rcpp::DoubleVector doubleData(data);
874 std::copy(doubleData.begin(), doubleData.end(), static_cast<double*>(this->image->data));
875 }
876 }
877 UNPROTECT(1);
878 }
879
880 inline void NiftiImage::initFromMriImage (const Rcpp::RObject &object, const bool copyData)
881 {
882 Rcpp::Reference mriImage(object);
883 Rcpp::Function getXform = mriImage.field("getXform");
884 Rcpp::NumericMatrix xform = getXform();
885
886 this->image = NULL;
887
888 if (Rf_length(mriImage.field("tags")) > 0)
889 initFromList(mriImage.field("tags"));
890
891 Rcpp::RObject data = mriImage.field("data");
892 if (data.inherits("SparseArray"))
893 {
894 Rcpp::Language call("as.array", data);
895 data = call.eval();
896 }
897
898 const short datatype = (Rf_isNull(data) ? DT_INT32 : sexpTypeToNiftiType(data.sexp_type()));
899
900 int dims[8] = { 0, 0, 0, 0, 0, 0, 0, 0 };
901 const std::vector<int> dimVector = mriImage.field("imageDims");
902 const int nDims = std::min(7, int(dimVector.size()));
903 dims[0] = nDims;
904 size_t nVoxels = 1;
905 for (int i=0; i<nDims; i++)
906 {
907 dims[i+1] = dimVector[i];
908 nVoxels *= dimVector[i];
909 }
910
911 if (this->image == NULL)
912 this->image = nifti_make_new_nim(dims, datatype, FALSE);
913 else
914 {
915 std::copy(dims, dims+8, this->image->dim);
916 this->image->datatype = datatype;
917 nifti_datatype_sizes(image->datatype, &image->nbyper, NULL);
918 }
919
920 if (copyData && !Rf_isNull(data))
921 {
922 // NB: nifti_get_volsize() will not be right here if there were tags
923 const size_t dataSize = nVoxels * image->nbyper;
924 this->image->data = calloc(1, dataSize);
925 if (datatype == DT_INT32)
926 memcpy(this->image->data, INTEGER(data), dataSize);
927 else
928 memcpy(this->image->data, REAL(data), dataSize);
929 }
930 else
931 this->image->data = NULL;
932
933 const std::vector<float> pixdimVector = mriImage.field("voxelDims");
934 const int pixdimLength = pixdimVector.size();
935 for (int i=0; i<std::min(pixdimLength,nDims); i++)
936 this->image->pixdim[i+1] = std::abs(pixdimVector[i]);
937
938 const std::vector<std::string> pixunitsVector = mriImage.field("voxelDimUnits");
939 setPixunits(pixunitsVector);
940
941 if (xform.rows() != 4 || xform.cols() != 4)
942 this->image->qform_code = this->image->sform_code = 0;
943 else
944 {
945 mat44 matrix;
946 for (int i=0; i<4; i++)
947 {
948 for (int j=0; j<4; j++)
949 matrix.m[i][j] = static_cast<float>(xform(i,j));
950 }
951
952 this->image->qto_xyz = matrix;
953 this->image->qto_ijk = nifti_mat44_inverse(image->qto_xyz);
954 nifti_mat44_to_quatern(image->qto_xyz, &image->quatern_b, &image->quatern_c, &image->quatern_d, &image->qoffset_x, &image->qoffset_y, &image->qoffset_z, NULL, NULL, NULL, &image->qfac);
955
956 this->image->sto_xyz = matrix;
957 this->image->sto_ijk = nifti_mat44_inverse(image->sto_xyz);
958
959 this->image->qform_code = this->image->sform_code = 2;
960 }
961 }
962
963 inline void NiftiImage::initFromList (const Rcpp::RObject &object)
964 {
965 Rcpp::List list(object);
966 nifti_1_header *header = nifti_make_new_header(NULL, DT_FLOAT64);
967
968 internal::updateHeader(header, list);
969
970 this->image = nifti_convert_nhdr2nim(*header, NULL);
971 this->image->data = NULL;
972 free(header);
973 }
974
975 inline void NiftiImage::initFromArray (const Rcpp::RObject &object, const bool copyData)
976 {
977 int dims[8] = { 0, 0, 0, 0, 0, 0, 0, 0 };
978 const std::vector<int> dimVector = object.attr("dim");
979
980 const int nDims = std::min(7, int(dimVector.size()));
981 dims[0] = nDims;
982 for (int i=0; i<nDims; i++)
983 dims[i+1] = dimVector[i];
984
985 const short datatype = sexpTypeToNiftiType(object.sexp_type());
986 this->image = nifti_make_new_nim(dims, datatype, int(copyData));
987
988 if (copyData)
989 {
990 const size_t dataSize = nifti_get_volsize(image);
991 if (datatype == DT_INT32)
992 memcpy(this->image->data, INTEGER(object), dataSize);
993 else
994 memcpy(this->image->data, REAL(object), dataSize);
995 }
996 else
997 this->image->data = NULL;
998
999 if (object.hasAttribute("pixdim"))
1000 {
1001 const std::vector<float> pixdimVector = object.attr("pixdim");
1002 const int pixdimLength = pixdimVector.size();
1003 for (int i=0; i<std::min(pixdimLength,nDims); i++)
1004 this->image->pixdim[i+1] = pixdimVector[i];
1005 }
1006
1007 if (object.hasAttribute("pixunits"))
1008 {
1009 const std::vector<std::string> pixunitsVector = object.attr("pixunits");
1010 setPixunits(pixunitsVector);
1011 }
1012 }
1013
1014 inline NiftiImage::NiftiImage (const SEXP object, const bool readData)
1015 : persistent(false)
1016 {
1017 Rcpp::RObject imageObject(object);
1018 bool resolved = false;
1019
1020 if (imageObject.hasAttribute(".nifti_image_ptr"))
1021 {
1022 Rcpp::XPtr<NiftiImage> imagePtr(SEXP(imageObject.attr(".nifti_image_ptr")));
1023 NiftiImage *ptr = imagePtr;
1024 if (ptr != NULL)
1025 {
1026 this->image = ptr->image;
1027 this->persistent = true;
1028 resolved = true;
1029
1030 if (imageObject.hasAttribute("dim"))
1031 update(imageObject);
1032 }
1033 else if (Rf_isString(object))
1034 throw std::runtime_error("Internal image is not valid");
1035 else
1036 Rf_warning("Ignoring invalid internal pointer");
1037 }
1038
1039 if (!resolved)
1040 {
1041 if (Rf_isNull(object))
1042 this->image = NULL;
1043 else if (Rf_isString(object))
1044 {
1045 const std::string path = Rcpp::as<std::string>(object);
1046 this->image = nifti_image_read(path.c_str(), readData);
1047 if (this->image == NULL)
1048 throw std::runtime_error("Failed to read image from path " + path);
1049 }
1050 else if (imageObject.inherits("nifti"))
1051 initFromNiftiS4(imageObject, readData);
1052 else if (imageObject.inherits("anlz"))
1053 throw std::runtime_error("Cannot currently convert objects of class \"anlz\"");
1054 else if (imageObject.inherits("MriImage"))
1055 initFromMriImage(imageObject, readData);
1056 else if (Rf_isVectorList(object))
1057 initFromList(imageObject);
1058 else if (imageObject.hasAttribute("dim"))
1059 initFromArray(imageObject, readData);
1060 else
1061 throw std::runtime_error("Cannot convert object of class \"" + Rcpp::as<std::string>(imageObject.attr("class")) + "\" to a nifti_image");
1062 }
1063
1064 if (this->image != NULL)
1065 nifti_update_dims_from_array(this->image);
1066
1067 #ifndef NDEBUG
1068 Rprintf("Creating NiftiImage with pointer %p (from SEXP)\n", this->image);
1069 #endif
1070 }
1071
1072 #endif // USING_R
1073
1074 inline NiftiImage::NiftiImage (const std::string &path, const std::vector<int> &volumes)
1075 : persistent(false)
1076 {
1077 if (volumes.empty())
1078 throw std::runtime_error("The vector of volumes is empty");
1079
1080 nifti_brick_list brickList;
1081 this->image = nifti_image_read_bricks(path.c_str(), volumes.size(), &volumes[0], &brickList);
1082 if (this->image == NULL)
1083 throw std::runtime_error("Failed to read image from path " + path);
1084
1085 size_t brickSize = image->nbyper * image->nx * image->ny * image->nz;
1086 image->data = calloc(1, nifti_get_volsize(image));
1087 for (int i=0; i<brickList.nbricks; i++)
1088 memcpy((char *) image->data + i * brickSize, brickList.bricks[i], brickSize);
1089 nifti_free_NBL(&brickList);
1090
1091 #ifndef NDEBUG
1092 Rprintf("Creating NiftiImage with pointer %p (from string and volume vector)\n", this->image);
1093 #endif
1094 }
1095
1096 inline void NiftiImage::updatePixdim (const std::vector<float> &pixdim)
1097 {
1098 const int nDims = image->dim[0];
1099 const std::vector<float> origPixdim(image->pixdim+1, image->pixdim+4);
1100
1101 for (int i=1; i<8; i++)
1102 image->pixdim[i] = 0.0;
1103
1104 const int pixdimLength = pixdim.size();
1105 for (int i=0; i<std::min(pixdimLength,nDims); i++)
1106 image->pixdim[i+1] = pixdim[i];
1107
1108 if (!std::equal(origPixdim.begin(), origPixdim.begin() + std::min(3,nDims), pixdim.begin()))
1109 {
1110 mat33 scaleMatrix;
1111 for (int i=0; i<3; i++)
1112 {
1113 for (int j=0; j<3; j++)
1114 {
1115 if (i != j)
1116 scaleMatrix.m[i][j] = 0.0;
1117 else if (i >= nDims)
1118 scaleMatrix.m[i][j] = 1.0;
1119 else
1120 scaleMatrix.m[i][j] = pixdim[i] / origPixdim[i];
1121 }
1122 }
1123
1124 if (image->qform_code > 0)
1125 {
1126 mat33 prod = nifti_mat33_mul(scaleMatrix, internal::topLeftCorner(image->qto_xyz));
1127 for (int i=0; i<3; i++)
1128 {
1129 for (int j=0; j<3; j++)
1130 image->qto_xyz.m[i][j] = prod.m[i][j];
1131 }
1132 image->qto_ijk = nifti_mat44_inverse(image->qto_xyz);
1133 nifti_mat44_to_quatern(image->qto_xyz, &image->quatern_b, &image->quatern_c, &image->quatern_d, &image->qoffset_x, &image->qoffset_y, &image->qoffset_z, NULL, NULL, NULL, &image->qfac);
1134 }
1135
1136 if (image->sform_code > 0)
1137 {
1138 mat33 prod = nifti_mat33_mul(scaleMatrix, internal::topLeftCorner(image->sto_xyz));
1139 for (int i=0; i<3; i++)
1140 {
1141 for (int j=0; j<3; j++)
1142 image->sto_xyz.m[i][j] = prod.m[i][j];
1143 }
1144 image->sto_ijk = nifti_mat44_inverse(image->sto_xyz);
1145 }
1146 }
1147 }
1148
1149 inline void NiftiImage::setPixunits (const std::vector<std::string> &pixunits)
1150 {
1151 for (size_t i=0; i<pixunits.size(); i++)
1152 {
1153 if (pixunits[i] == "m")
1154 image->xyz_units = NIFTI_UNITS_METER;
1155 else if (pixunits[i] == "mm")
1156 image->xyz_units = NIFTI_UNITS_MM;
1157 else if (pixunits[i] == "um")
1158 image->xyz_units = NIFTI_UNITS_MICRON;
1159 else if (pixunits[i] == "s")
1160 image->time_units = NIFTI_UNITS_SEC;
1161 else if (pixunits[i] == "ms")
1162 image->time_units = NIFTI_UNITS_MSEC;
1163 else if (pixunits[i] == "us")
1164 image->time_units = NIFTI_UNITS_USEC;
1165 else if (pixunits[i] == "Hz")
1166 image->time_units = NIFTI_UNITS_HZ;
1167 else if (pixunits[i] == "ppm")
1168 image->time_units = NIFTI_UNITS_PPM;
1169 else if (pixunits[i] == "rad/s")
1170 image->time_units = NIFTI_UNITS_RADS;
1171 }
1172 }
1173
1174 inline NiftiImage & NiftiImage::rescale (const std::vector<float> &scales)
1175 {
1176 std::vector<float> pixdim(image->pixdim+1, image->pixdim+4);
1177
1178 for (int i=0; i<std::min(3, int(scales.size())); i++)
1179 {
1180 if (scales[i] != 1.0)
1181 {
1182 pixdim[i] /= scales[i];
1183 image->dim[i+1] = static_cast<int>(std::floor(image->dim[i+1] * scales[i]));
1184 }
1185 }
1186
1187 updatePixdim(pixdim);
1188 nifti_update_dims_from_array(image);
1189
1190 // Data vector is now the wrong size, so drop it
1191 if (!persistent)
1192 nifti_image_unload(image);
1193
1194 image->scl_slope = 0.0;
1195 image->scl_inter = 0.0;
1196
1197 return *this;
1198 }
1199
1200 inline NiftiImage & NiftiImage::reorient (const int icode, const int jcode, const int kcode)
1201 {
1202 if (this->isNull())
1203 return *this;
1204 if (image->qform_code == 0 && image->sform_code == 0)
1205 {
1206 Rf_warning("Image qform and sform codes are both zero, so it cannot be reoriented");
1207 return *this;
1208 }
1209
1210 int used[6] = { 0, 0, 0, 0, 0, 0 };
1211 used[icode-1] = 1;
1212 used[jcode-1] = 1;
1213 used[kcode-1] = 1;
1214 if (used[0]+used[1] != 1 || used[2]+used[3] != 1 || used[4]+used[5] != 1)
1215 throw std::runtime_error("Each canonical axis should be used exactly once");
1216
1217 const int codes[3] = { icode, jcode, kcode };
1218 const mat44 native = this->xform();
1219
1220 // Calculate the origin, which requires inverting the current xform
1221 // Here we use a simplified formula that exploits blockwise inversion and the nature of xforms
1222 internal::vec3 origin;
1223 for (int i=0; i<3; i++)
1224 origin.v[i] = native.m[i][3];
1225 origin = -internal::matrixVectorProduct(nifti_mat33_inverse(internal::topLeftCorner(native)), origin);
1226
1227 // Create a target xform (rotation matrix only)
1228 mat33 target;
1229 for (int j=0; j<3; j++)
1230 {
1231 for (int i=0; i<3; i++)
1232 target.m[i][j] = 0.0;
1233
1234 switch (codes[j])
1235 {
1236 case NIFTI_L2R: target.m[0][j] = 1.0; break;
1237 case NIFTI_R2L: target.m[0][j] = -1.0; break;
1238 case NIFTI_P2A: target.m[1][j] = 1.0; break;
1239 case NIFTI_A2P: target.m[1][j] = -1.0; break;
1240 case NIFTI_I2S: target.m[2][j] = 1.0; break;
1241 case NIFTI_S2I: target.m[2][j] = -1.0; break;
1242 }
1243 }
1244
1245 // Extract (inverse of) canonical axis matrix from native xform
1246 int nicode, njcode, nkcode;
1247 nifti_mat44_to_orientation(native, &nicode, &njcode, &nkcode);
1248 int ncodes[3] = { nicode, njcode, nkcode };
1249 mat33 nativeAxesTransposed;
1250 for (int i=0; i<3; i++)
1251 {
1252 for (int j=0; j<3; j++)
1253 nativeAxesTransposed.m[i][j] = 0.0;
1254
1255 switch (ncodes[i])
1256 {
1257 case NIFTI_L2R: nativeAxesTransposed.m[i][0] = 1.0; break;
1258 case NIFTI_R2L: nativeAxesTransposed.m[i][0] = -1.0; break;
1259 case NIFTI_P2A: nativeAxesTransposed.m[i][1] = 1.0; break;
1260 case NIFTI_A2P: nativeAxesTransposed.m[i][1] = -1.0; break;
1261 case NIFTI_I2S: nativeAxesTransposed.m[i][2] = 1.0; break;
1262 case NIFTI_S2I: nativeAxesTransposed.m[i][2] = -1.0; break;
1263 }
1264 }
1265
1266 // Check for no-op case
1267 if (icode == nicode && jcode == njcode && kcode == nkcode)
1268 return *this;
1269
1270 // The transform is t(approx_old_xform) %*% target_xform
1271 // The new xform is old_xform %*% transform
1272 // NB: "transform" is really 4x4, but the last row is simple and the last column is filled below
1273 mat33 transform = nifti_mat33_mul(nativeAxesTransposed, target);
1274 mat44 result;
1275 for (int i=0; i<4; i++)
1276 {
1277 for (int j=0; j<3; j++)
1278 result.m[i][j] = native.m[i][0] * transform.m[0][j] + native.m[i][1] * transform.m[1][j] + native.m[i][2] * transform.m[2][j];
1279
1280 result.m[3][i] = i == 3 ? 1.0 : 0.0;
1281 }
1282
1283 // Extract the mapping between dimensions and the signs
1284 // These vectors are all indexed in the target space, except "revsigns"
1285 int locs[3], signs[3], newdim[3], revsigns[3];
1286 float newpixdim[3];
1287 double maxes[3] = { R_NegInf, R_NegInf, R_NegInf };
1288 internal::vec3 offset;
1289 for (int j=0; j<3; j++)
1290 {
1291 // Find the largest absolute value in each column, which gives the old dimension corresponding to each new dimension
1292 for (int i=0; i<3; i++)
1293 {
1294 const double value = static_cast<double>(transform.m[i][j]);
1295 if (fabs(value) > maxes[j])
1296 {
1297 maxes[j] = fabs(value);
1298 signs[j] = value > 0.0 ? 1 : -1;
1299 locs[j] = i;
1300 }
1301 }
1302
1303 // Obtain the sign for the reverse mapping
1304 revsigns[locs[j]] = signs[j];
1305
1306 // Permute dim and pixdim
1307 newdim[j] = image->dim[locs[j]+1];
1308 newpixdim[j] = image->pixdim[locs[j]+1];
1309
1310 // Flip and/or permute the origin
1311 if (signs[j] < 0)
1312 offset.v[j] = image->dim[locs[j]+1] - origin.v[locs[j]] - 1.0;
1313 else
1314 offset.v[j] = origin.v[locs[j]];
1315 }
1316
1317 // Convert the origin back to an xform offset and insert it
1318 offset = -internal::matrixVectorProduct(internal::topLeftCorner(result), offset);
1319 for (int i=0; i<3; i++)
1320 result.m[i][3] = offset.v[i];
1321
1322 // Update the xforms with nonzero codes
1323 if (image->qform_code > 0)
1324 {
1325 image->qto_xyz = result;
1326 image->qto_ijk = nifti_mat44_inverse(image->qto_xyz);
1327 nifti_mat44_to_quatern(image->qto_xyz, &image->quatern_b, &image->quatern_c, &image->quatern_d, &image->qoffset_x, &image->qoffset_y, &image->qoffset_z, NULL, NULL, NULL, &image->qfac);
1328 }
1329 if (image->sform_code > 0)
1330 {
1331 image->sto_xyz = result;
1332 image->sto_ijk = nifti_mat44_inverse(image->sto_xyz);
1333 }
1334
1335 // Calculate strides: the step in target space associated with each dimension in source space
1336 ptrdiff_t strides[3];
1337 strides[locs[0]] = 1;
1338 strides[locs[1]] = strides[locs[0]] * image->dim[locs[0]+1];
1339 strides[locs[2]] = strides[locs[1]] * image->dim[locs[1]+1];
1340
1341 // Permute the data (if present)
1342 if (image->data != NULL)
1343 {
1344 size_t volSize = size_t(image->nx * image->ny * image->nz);
1345 size_t nVolumes = std::max(size_t(1), image->nvox / volSize);
1346
1347 const std::vector<double> oldData = this->getData<double>();
1348 std::vector<double> newData(image->nvox);
1349
1350 // Where the sign is negative we need to start at the end of the dimension
1351 size_t volStart = 0;
1352 for (int i=0; i<3; i++)
1353 {
1354 if (revsigns[i] < 0)
1355 volStart += (image->dim[i+1] - 1) * strides[i];
1356 }
1357
1358 // Iterate over the data and place it into a new vector
1359 std::vector<double>::const_iterator it = oldData.begin();
1360 for (size_t v=0; v<nVolumes; v++)
1361 {
1362 for (int k=0; k<image->nz; k++)
1363 {
1364 ptrdiff_t offset = k * strides[2] * revsigns[2];
1365 for (int j=0; j<image->ny; j++)
1366 {
1367 for (int i=0; i<image->nx; i++)
1368 {
1369 newData[volStart + offset] = *it++;
1370 offset += strides[0] * revsigns[0];
1371 }
1372 offset += strides[1] * revsigns[1] - image->nx * strides[0] * revsigns[0];
1373 }
1374 }
1375 volStart += volSize;
1376 }
1377
1378 // Replace the existing data in the image
1379 this->replaceData(newData);
1380 }
1381
1382 // Copy new dims and pixdims in
1383 // NB: Old dims are used above, so this must happen last
1384 std::copy(newdim, newdim+3, image->dim+1);
1385 std::copy(newpixdim, newpixdim+3, image->pixdim+1);
1386 nifti_update_dims_from_array(image);
1387
1388 return *this;
1389 }
1390
1391 inline NiftiImage & NiftiImage::reorient (const std::string &orientation)
1392 {
1393 if (orientation.length() != 3)
1394 throw std::runtime_error("Orientation string should have exactly three characters");
1395
1396 int codes[3];
1397 for (int i=0; i<3; i++)
1398 {
1399 switch(orientation[i])
1400 {
1401 case 'r': case 'R': codes[i] = NIFTI_L2R; break;
1402 case 'l': case 'L': codes[i] = NIFTI_R2L; break;
1403 case 'a': case 'A': codes[i] = NIFTI_P2A; break;
1404 case 'p': case 'P': codes[i] = NIFTI_A2P; break;
1405 case 's': case 'S': codes[i] = NIFTI_I2S; break;
1406 case 'i': case 'I': codes[i] = NIFTI_S2I; break;
1407
1408 default:
1409 throw std::runtime_error("Orientation string is invalid");
1410 }
1411 }
1412
1413 return reorient(codes[0], codes[1], codes[2]);
1414 }
1415
1416 #ifdef USING_R
1417
1418 inline NiftiImage & NiftiImage::update (const Rcpp::RObject &object)
1419 {
1420 if (Rf_isVectorList(object))
1421 {
1422 Rcpp::List list(object);
1423 nifti_1_header *header = NULL;
1424 if (this->isNull())
1425 {
1426 header = nifti_make_new_header(NULL, DT_FLOAT64);
1427 internal::updateHeader(header, list, true);
1428 }
1429 else
1430 {
1431 header = (nifti_1_header *) calloc(1, sizeof(nifti_1_header));
1432 *header = nifti_convert_nim2nhdr(image);
1433 internal::updateHeader(header, list, true);
1434 }
1435
1436 if (header != NULL)
1437 {
1438 nifti_image *newImage = nifti_convert_nhdr2nim(*header, NULL);
1439 if (this->image->data != NULL)
1440 {
1441 size_t dataSize = nifti_get_volsize(image);
1442 newImage->data = calloc(1, dataSize);
1443 memcpy(newImage->data, image->data, dataSize);
1444 }
1445 if (!persistent)
1446 nifti_image_free(image);
1447 this->image = newImage;
1448 }
1449 }
1450 else if (object.hasAttribute("dim"))
1451 {
1452 for (int i=0; i<8; i++)
1453 image->dim[i] = 0;
1454 const std::vector<int> dimVector = object.attr("dim");
1455
1456 const int nDims = std::min(7, int(dimVector.size()));
1457 image->dim[0] = nDims;
1458 for (int i=0; i<nDims; i++)
1459 image->dim[i+1] = dimVector[i];
1460
1461 if (object.hasAttribute("pixdim"))
1462 {
1463 const std::vector<float> pixdimVector = object.attr("pixdim");
1464 updatePixdim(pixdimVector);
1465 }
1466
1467 if (object.hasAttribute("pixunits"))
1468 {
1469 const std::vector<std::string> pixunitsVector = object.attr("pixunits");
1470 setPixunits(pixunitsVector);
1471 }
1472
1473 // This NIfTI-1 library function clobbers dim[0] if the last dimension is unitary; we undo that here
1474 nifti_update_dims_from_array(image);
1475 image->dim[0] = image->ndim = nDims;
1476
1477 image->datatype = NiftiImage::sexpTypeToNiftiType(object.sexp_type());
1478 nifti_datatype_sizes(image->datatype, &image->nbyper, NULL);
1479
1480 if (!persistent)
1481 nifti_image_unload(image);
1482
1483 const size_t dataSize = nifti_get_volsize(image);
1484 image->data = calloc(1, dataSize);
1485 if (image->datatype == DT_INT32)
1486 memcpy(image->data, INTEGER(object), dataSize);
1487 else
1488 memcpy(image->data, REAL(object), dataSize);
1489
1490 image->scl_slope = 0.0;
1491 image->scl_inter = 0.0;
1492 }
1493
1494 return *this;
1495 }
1496
1497 #endif // USING_R
1498
1499 inline mat44 NiftiImage::xform (const bool preferQuaternion) const
1500 {
1501 if (image == NULL)
1502 {
1503 mat44 matrix;
1504 for (int i=0; i<4; i++)
1505 {
1506 for (int j=0; j<4; j++)
1507 matrix.m[i][j] = 0.0;
1508 }
1509 return matrix;
1510 }
1511 else if (image->qform_code <= 0 && image->sform_code <= 0)
1512 {
1513 // No qform or sform so use pixdim (NB: other software may assume differently)
1514 mat44 matrix;
1515 for (int i=0; i<4; i++)
1516 {
1517 for (int j=0; j<4; j++)
1518 {
1519 if (i != j)
1520 matrix.m[i][j] = 0.0;
1521 else if (i == 3)
1522 matrix.m[3][3] = 1.0;
1523 else
1524 matrix.m[i][j] = (image->pixdim[i+1]==0.0 ? 1.0 : image->pixdim[i+1]);
1525 }
1526 }
1527 return matrix;
1528 }
1529 else if ((preferQuaternion && image->qform_code > 0) || image->sform_code <= 0)
1530 return image->qto_xyz;
1531 else
1532 return image->sto_xyz;
1533 }
1534
1535 template <typename TargetType>
1536 inline std::vector<TargetType> NiftiImage::Block::getData (const bool useSlope) const
1537 {
1538 if (image.isNull())
1539 return std::vector<TargetType>();
1540
1541 size_t blockSize = 1;
1542 for (int i=1; i<dimension; i++)
1543 blockSize *= image->dim[i];
1544
1545 std::vector<TargetType> data(blockSize);
1546 internal::DataConverter<TargetType> *converter = NULL;
1547 if (useSlope && image.isDataScaled())
1548 converter = new internal::DataConverter<TargetType>(image->scl_slope, image->scl_inter);
1549
1550 internal::convertData<TargetType>(image->data, image->datatype, blockSize, data.begin(), blockSize*index, converter);
1551
1552 delete converter;
1553 return data;
1554 }
1555
1556 template <typename TargetType>
1557 inline std::vector<TargetType> NiftiImage::getData (const bool useSlope) const
1558 {
1559 if (this->isNull())
1560 return std::vector<TargetType>();
1561
1562 std::vector<TargetType> data(image->nvox);
1563 internal::DataConverter<TargetType> *converter = NULL;
1564 if (useSlope && this->isDataScaled())
1565 converter = new internal::DataConverter<TargetType>(image->scl_slope, image->scl_inter);
1566
1567 internal::convertData<TargetType>(image->data, image->datatype, image->nvox, data.begin(), 0, converter);
1568
1569 delete converter;
1570 return data;
1571 }
1572
1573 inline NiftiImage & NiftiImage::changeDatatype (const short datatype, const bool useSlope)
1574 {
1575 if (this->isNull() || image->datatype == datatype)
1576 return *this;
1577
1578 if (useSlope && this->isDataScaled())
1579 throw std::runtime_error("Resetting the slope and intercept for an image with them already set is not supported");
1580
1581 if (image->data != NULL)
1582 {
1583 int bytesPerPixel;
1584 nifti_datatype_sizes(datatype, &bytesPerPixel, NULL);
1585 void *data = calloc(image->nvox, bytesPerPixel);
1586
1587 switch (datatype)
1588 {
1589 case DT_UINT8:
1590 {
1591 internal::DataConverter<uint8_t> converter(useSlope ? internal::DataConverter<uint8_t>::IndexMode : internal::DataConverter<uint8_t>::CastMode);
1592 internal::convertData(image->data, image->datatype, image->nvox, static_cast<uint8_t *>(data), 0, &converter);
1593 image->scl_slope = static_cast<float>(converter.getSlope());
1594 image->scl_inter = static_cast<float>(converter.getIntercept());
1595 break;
1596 }
1597
1598 case DT_INT16:
1599 {
1600 internal::DataConverter<int16_t> converter(useSlope ? internal::DataConverter<int16_t>::IndexMode : internal::DataConverter<int16_t>::CastMode);
1601 internal::convertData(image->data, image->datatype, image->nvox, static_cast<int16_t *>(data), 0, &converter);
1602 image->scl_slope = static_cast<float>(converter.getSlope());
1603 image->scl_inter = static_cast<float>(converter.getIntercept());
1604 break;
1605 }
1606
1607 case DT_INT32:
1608 {
1609 internal::DataConverter<int32_t> converter(useSlope ? internal::DataConverter<int32_t>::IndexMode : internal::DataConverter<int32_t>::CastMode);
1610 internal::convertData(image->data, image->datatype, image->nvox, static_cast<int32_t *>(data), 0, &converter);
1611 image->scl_slope = static_cast<float>(converter.getSlope());
1612 image->scl_inter = static_cast<float>(converter.getIntercept());
1613 break;
1614 }
1615
1616 case DT_FLOAT32:
1617 {
1618 internal::DataConverter<float> converter(useSlope ? internal::DataConverter<float>::IndexMode : internal::DataConverter<float>::CastMode);
1619 internal::convertData(image->data, image->datatype, image->nvox, static_cast<float *>(data), 0, &converter);
1620 image->scl_slope = static_cast<float>(converter.getSlope());
1621 image->scl_inter = static_cast<float>(converter.getIntercept());
1622 break;
1623 }
1624
1625 case DT_FLOAT64:
1626 {
1627 internal::DataConverter<double> converter(useSlope ? internal::DataConverter<double>::IndexMode : internal::DataConverter<double>::CastMode);
1628 internal::convertData(image->data, image->datatype, image->nvox, static_cast<double *>(data), 0, &converter);
1629 image->scl_slope = static_cast<float>(converter.getSlope());
1630 image->scl_inter = static_cast<float>(converter.getIntercept());
1631 break;
1632 }
1633
1634 case DT_INT8:
1635 {
1636 internal::DataConverter<int8_t> converter(useSlope ? internal::DataConverter<int8_t>::IndexMode : internal::DataConverter<int8_t>::CastMode);
1637 internal::convertData(image->data, image->datatype, image->nvox, static_cast<int8_t *>(data), 0, &converter);
1638 image->scl_slope = static_cast<float>(converter.getSlope());
1639 image->scl_inter = static_cast<float>(converter.getIntercept());
1640 break;
1641 }
1642
1643 case DT_UINT16:
1644 {
1645 internal::DataConverter<uint16_t> converter(useSlope ? internal::DataConverter<uint16_t>::IndexMode : internal::DataConverter<uint16_t>::CastMode);
1646 internal::convertData(image->data, image->datatype, image->nvox, static_cast<uint16_t *>(data), 0, &converter);
1647 image->scl_slope = static_cast<float>(converter.getSlope());
1648 image->scl_inter = static_cast<float>(converter.getIntercept());
1649 break;
1650 }
1651
1652 case DT_UINT32:
1653 {
1654 internal::DataConverter<uint32_t> converter(useSlope ? internal::DataConverter<uint32_t>::IndexMode : internal::DataConverter<uint32_t>::CastMode);
1655 internal::convertData(image->data, image->datatype, image->nvox, static_cast<uint32_t *>(data), 0, &converter);
1656 image->scl_slope = static_cast<float>(converter.getSlope());
1657 image->scl_inter = static_cast<float>(converter.getIntercept());
1658 break;
1659 }
1660
1661 case DT_INT64:
1662 {
1663 internal::DataConverter<int64_t> converter(useSlope ? internal::DataConverter<int64_t>::IndexMode : internal::DataConverter<int64_t>::CastMode);
1664 internal::convertData(image->data, image->datatype, image->nvox, static_cast<int64_t *>(data), 0, &converter);
1665 image->scl_slope = static_cast<float>(converter.getSlope());
1666 image->scl_inter = static_cast<float>(converter.getIntercept());
1667 break;
1668 }
1669
1670 case DT_UINT64:
1671 {
1672 internal::DataConverter<uint64_t> converter(useSlope ? internal::DataConverter<uint64_t>::IndexMode : internal::DataConverter<uint64_t>::CastMode);
1673 internal::convertData(image->data, image->datatype, image->nvox, static_cast<uint64_t *>(data), 0, &converter);
1674 image->scl_slope = static_cast<float>(converter.getSlope());
1675 image->scl_inter = static_cast<float>(converter.getIntercept());
1676 break;
1677 }
1678
1679 default:
1680 throw std::runtime_error("Unsupported data type (" + std::string(nifti_datatype_string(datatype)) + ")");
1681 }
1682
1683 nifti_image_unload(image);
1684 image->data = data;
1685 }
1686
1687 image->datatype = datatype;
1688 nifti_datatype_sizes(datatype, &image->nbyper, &image->swapsize);
1689
1690 return *this;
1691 }
1692
1693 inline NiftiImage & NiftiImage::changeDatatype (const std::string &datatype, const bool useSlope)
1694 {
1695 return changeDatatype(internal::stringToDatatype(datatype), useSlope);
1696 }
1697
1698 template <typename SourceType>
1699 inline NiftiImage & NiftiImage::replaceData (const std::vector<SourceType> &data, const short datatype)
1700 {
1701 if (this->isNull())
1702 return *this;
1703 else if (data.size() != image->nvox)
1704 throw std::runtime_error("New data length does not match the number of voxels in the image");
1705
1706 if (datatype != DT_NONE)
1707 {
1708 nifti_image_unload(image);
1709 image->datatype = datatype;
1710 nifti_datatype_sizes(datatype, &image->nbyper, &image->swapsize);
1711 }
1712
1713 if (image->data == NULL)
1714 image->data = calloc(image->nvox, image->nbyper);
1715 internal::replaceData<SourceType>(data.begin(), data.end(), image->data, image->datatype);
1716
1717 image->scl_slope = 0.0;
1718 image->scl_inter = 0.0;
1719 image->cal_min = static_cast<float>(*std::min_element(data.begin(), data.end()));
1720 image->cal_max = static_cast<float>(*std::max_element(data.begin(), data.end()));
1721
1722 return *this;
1723 }
1724
1725 inline void NiftiImage::toFile (const std::string fileName, const short datatype) const
1726 {
1727 const bool changingDatatype = (datatype != DT_NONE && !this->isNull() && datatype != image->datatype);
1728
1729 // Copy the source image only if the datatype will be changed
1730 NiftiImage imageToWrite(image, changingDatatype);
1731
1732 if (changingDatatype)
1733 imageToWrite.changeDatatype(datatype, true);
1734 else
1735 imageToWrite.setPersistence(true);
1736
1737 const int status = nifti_set_filenames(imageToWrite, fileName.c_str(), false, true);
1738 if (status != 0)
1739 throw std::runtime_error("Failed to set filenames for NIfTI object");
1740 nifti_image_write(imageToWrite);
1741 }
1742
1743 inline void NiftiImage::toFile (const std::string fileName, const std::string &datatype) const
1744 {
1745 toFile(fileName, internal::stringToDatatype(datatype));
1746 }
1747
1748 #ifdef USING_R
1749
1750 inline Rcpp::RObject NiftiImage::toArray () const
1751 {
1752 Rcpp::RObject array;
1753
1754 if (this->isNull())
1755 return array;
1756 else if (this->isDataScaled())
1757 {
1758 array = internal::imageDataToArray<REALSXP>(image);
1759 std::transform(REAL(array), REAL(array)+Rf_length(array), REAL(array), internal::DataConverter<double>(image->scl_slope,image->scl_inter));
1760 }
1761 else
1762 {
1763 switch (image->datatype)
1764 {
1765 case DT_UINT8:
1766 case DT_INT16:
1767 case DT_INT32:
1768 case DT_INT8:
1769 case DT_UINT16:
1770 case DT_UINT32:
1771 case DT_INT64:
1772 case DT_UINT64:
1773 array = internal::imageDataToArray<INTSXP>(image);
1774 break;
1775
1776 case DT_FLOAT32:
1777 case DT_FLOAT64:
1778 array = internal::imageDataToArray<REALSXP>(image);
1779 break;
1780
1781 default:
1782 throw std::runtime_error("Unsupported data type (" + std::string(nifti_datatype_string(image->datatype)) + ")");
1783 }
1784 }
1785
1786 internal::addAttributes(array, image);
1787 array.attr("class") = Rcpp::CharacterVector::create("niftiImage", "array");
1788 return array;
1789 }
1790
1791 inline Rcpp::RObject NiftiImage::toPointer (const std::string label) const
1792 {
1793 if (this->isNull())
1794 return Rcpp::RObject();
1795 else
1796 {
1797 Rcpp::RObject string = Rcpp::wrap(label);
1798 internal::addAttributes(string, image, false);
1799 string.attr("class") = Rcpp::CharacterVector::create("internalImage", "niftiImage");
1800 return string;
1801 }
1802 }
1803
1804 inline Rcpp::RObject NiftiImage::toArrayOrPointer (const bool internal, const std::string label) const
1805 {
1806 return (internal ? toPointer(label) : toArray());
1807 }
1808
1809 inline Rcpp::RObject NiftiImage::headerToList () const
1810 {
1811 if (this->image == NULL)
1812 return Rcpp::RObject();
1813
1814 nifti_1_header header = nifti_convert_nim2nhdr(this->image);
1815 Rcpp::List result;
1816
1817 result["sizeof_hdr"] = header.sizeof_hdr;
1818
1819 result["dim_info"] = int(header.dim_info);
1820 result["dim"] = std::vector<short>(header.dim, header.dim+8);
1821
1822 result["intent_p1"] = header.intent_p1;
1823 result["intent_p2"] = header.intent_p2;
1824 result["intent_p3"] = header.intent_p3;
1825 result["intent_code"] = header.intent_code;
1826
1827 result["datatype"] = header.datatype;
1828 result["bitpix"] = header.bitpix;
1829
1830 result["slice_start"] = header.slice_start;
1831 result["pixdim"] = std::vector<float>(header.pixdim, header.pixdim+8);
1832 result["vox_offset"] = header.vox_offset;
1833 result["scl_slope"] = header.scl_slope;
1834 result["scl_inter"] = header.scl_inter;
1835 result["slice_end"] = header.slice_end;
1836 result["slice_code"] = int(header.slice_code);
1837 result["xyzt_units"] = int(header.xyzt_units);
1838 result["cal_max"] = header.cal_max;
1839 result["cal_min"] = header.cal_min;
1840 result["slice_duration"] = header.slice_duration;
1841 result["toffset"] = header.toffset;
1842 result["descrip"] = std::string(header.descrip, 80);
1843 result["aux_file"] = std::string(header.aux_file, 24);
1844
1845 result["qform_code"] = header.qform_code;
1846 result["sform_code"] = header.sform_code;
1847 result["quatern_b"] = header.quatern_b;
1848 result["quatern_c"] = header.quatern_c;
1849 result["quatern_d"] = header.quatern_d;
1850 result["qoffset_x"] = header.qoffset_x;
1851 result["qoffset_y"] = header.qoffset_y;
1852 result["qoffset_z"] = header.qoffset_z;
1853 result["srow_x"] = std::vector<float>(header.srow_x, header.srow_x+4);
1854 result["srow_y"] = std::vector<float>(header.srow_y, header.srow_y+4);
1855 result["srow_z"] = std::vector<float>(header.srow_z, header.srow_z+4);
1856
1857 result["intent_name"] = std::string(header.intent_name, 16);
1858 result["magic"] = std::string(header.magic, 4);
1859
1860 result.attr("class") = Rcpp::CharacterVector::create("niftiHeader");
1861
1862 return result;
1863 }
1864
1865 #endif // USING_R
1866
1867 } // namespace
1868
1869 #endif
RNifti::NiftiImage::reorient
NiftiImage & reorient(const int i, const int j, const int k)
Reorient the image by permuting dimensions and potentially reversing some.
Definition: NiftiImage.h:1200
RNifti::NiftiImage::NiftiImage
NiftiImage()
Default constructor.
Definition: NiftiImage.h:313
RNifti::NiftiImage::Block::index
const int index
The location along dimension.
Definition: NiftiImage.h:96
RNifti::NiftiImage::xformToString
static std::string xformToString(const mat44 matrix)
Convert a 4x4 xform matrix to a string describing its canonical axes.
Definition: NiftiImage.h:186
RNifti::NiftiImage::dim
std::vector< int > dim() const
Return the dimensions of the image.
Definition: NiftiImage.h:499
RNifti::NiftiImage::operator->
const nifti_image * operator->() const
Allows a NiftiImage object to be treated as a pointer to a const nifti_image.
Definition: NiftiImage.h:421
RNifti::NiftiImage::persistent
bool persistent
Marker of persistence, which determines whether the nifti_image should be freed on destruction...
Definition: NiftiImage.h:245
RNifti::NiftiImage::pixdim
std::vector< float > pixdim() const
Return the dimensions of the pixels or voxels in the image.
Definition: NiftiImage.h:511
RNifti::NiftiImage::NiftiImage
NiftiImage(const std::string &path, const bool readData=true)
Initialise using a path string.
Definition: NiftiImage.h:366
RNifti::NiftiImage::rescale
NiftiImage & rescale(const std::vector< float > &scales)
Rescale the image, changing its image dimensions and pixel dimensions.
Definition: NiftiImage.h:1174
RNifti::NiftiImage::NiftiImage
NiftiImage(nifti_image *const image, const bool copy=false)
Initialise using an existing nifti_image pointer.
Definition: NiftiImage.h:348
RNifti
Definition: NiftiImage.h:38
RNifti::NiftiImage::Block::operator=
Block & operator=(const NiftiImage &source)
Copy assignment operator, which allows a block in one image to be replaced with the contents of anoth...
Definition: NiftiImage.h:120
RNifti::NiftiImage::isNull
bool isNull() const
Determine whether or not the internal pointer is NULL.
Definition: NiftiImage.h:472
RNifti::NiftiImage::Block
Inner class referring to a subset of an image.
Definition: NiftiImage.h:92
RNifti::NiftiImage::slice
Block slice(const int i)
Extract a slice block from a 3D image.
Definition: NiftiImage.h:661
RNifti::NiftiImage::replaceData
NiftiImage & replaceData(const std::vector< SourceType > &data, const short datatype=DT_NONE)
Replace the pixel data in the image with the contents of a vector.
Definition: NiftiImage.h:1699
RNifti::NiftiImage::isDataScaled
bool isDataScaled() const
Determine whether nontrivial scale and slope parameters are set.
Definition: NiftiImage.h:482
RNifti::NiftiImage::slice
const Block slice(const int i) const
Extract a slice block from a 3D image.
Definition: NiftiImage.h:654
RNifti::NiftiImage::volume
const Block volume(const int i) const
Extract a volume block from a 4D image.
Definition: NiftiImage.h:668
RNifti::NiftiImage::isPersistent
bool isPersistent() const
Determine whether or not the image is marked as persistent.
Definition: NiftiImage.h:477
RNifti::NiftiImage::getData
std::vector< TargetType > getData(const bool useSlope=true) const
Extract a vector of data from the image, casting it to any required element type. ...
Definition: NiftiImage.h:1557
RNifti::NiftiImage::Block::getData
std::vector< TargetType > getData(const bool useSlope=true) const
Extract a vector of data from a block, casting it to any required element type.
Definition: NiftiImage.h:1536
RNifti::NiftiImage::setPixunits
void setPixunits(const std::vector< std::string > &pixunits)
Modify the pixel dimension units.
Definition: NiftiImage.h:1149
RNifti::NiftiImage::NiftiImage
NiftiImage(const Block &source)
Initialise from a block, copying in the data.
Definition: NiftiImage.h:333
RNifti::NiftiImage::~NiftiImage
virtual ~NiftiImage()
Destructor which frees the wrapped pointer, unless the object is marked as persistent.
Definition: NiftiImage.h:397
RNifti::NiftiImage
Thin wrapper around a C-style nifti_image struct that allows C++-style destruction.
Definition: NiftiImage.h:85
RNifti::NiftiImage::NiftiImage
NiftiImage(const NiftiImage &source)
Copy constructor.
Definition: NiftiImage.h:320
RNifti::NiftiImage::nBlocks
int nBlocks() const
Return the number of blocks in the image.
Definition: NiftiImage.h:623
RNifti::NiftiImage::Block::dimension
const int dimension
The dimension along which the block applies (which should be the last)
Definition: NiftiImage.h:95
RNifti::NiftiImage::Block::image
const NiftiImage & image
The parent image.
Definition: NiftiImage.h:94
RNifti::NiftiImage::operator=
NiftiImage & operator=(const NiftiImage &source)
Copy assignment operator, which copies from its argument.
Definition: NiftiImage.h:432
RNifti::NiftiImage::fileVersion
static int fileVersion(const std::string &path)
Get the NIfTI format version used by the file at the specified path.
Definition: NiftiImage.h:214
RNifti::NiftiImage::xformToRotation
static mat33 xformToRotation(const mat44 matrix)
Extract the pure rotation part of a 4x4 xform matrix.
Definition: NiftiImage.h:173
RNifti::NiftiImage::toFile
void toFile(const std::string fileName, const short datatype=DT_NONE) const
Write the image to a NIfTI-1 file.
Definition: NiftiImage.h:1725
RNifti::NiftiImage::updatePixdim
void updatePixdim(const std::vector< float > &pixdim)
Modify the pixel dimensions, and potentially the xform matrices to match.
Definition: NiftiImage.h:1096
RNifti::NiftiImage::block
const Block block(const int i) const
Extract a block from the image.
Definition: NiftiImage.h:638
RNifti::NiftiImage::setPersistence
NiftiImage & setPersistence(const bool persistent)
Marked the image as persistent, so that it can be passed back to R.
Definition: NiftiImage.h:459
RNifti::internal::vec3
Definition: NiftiImage.h:42
RNifti::NiftiImage::changeDatatype
NiftiImage & changeDatatype(const short datatype, const bool useSlope=false)
Change the datatype of the image, casting the pixel data if present.
Definition: NiftiImage.h:1573
RNifti::NiftiImage::copy
void copy(const nifti_image *source)
Copy the contents of a nifti_image to create a new image.
Definition: NiftiImage.h:727
RNifti::NiftiImage::xform
mat44 xform(const bool preferQuaternion=true) const
Obtain an xform matrix, indicating the orientation of the image.
Definition: NiftiImage.h:1499
RNifti::NiftiImage::image
nifti_image * image
The wrapped nifti_image pointer.
Definition: NiftiImage.h:244
RNifti::NiftiImage::nDims
int nDims() const
Return the number of dimensions in the image.
Definition: NiftiImage.h:487
RNifti::NiftiImage::volume
Block volume(const int i)
Extract a volume block from a 4D image.
Definition: NiftiImage.h:675
RNifti::NiftiImage::drop
NiftiImage & drop()
Drop unitary dimensions.
Definition: NiftiImage.h:525
RNifti::NiftiImage::Block::Block
Block(const NiftiImage &image, const int dimension, const int index)
Standard constructor for this class.
Definition: NiftiImage.h:105
RNifti::NiftiImage::dropData
NiftiImage & dropData()
Drop the data from the image, retaining only the metadata.
Definition: NiftiImage.h:574
RNifti::NiftiImage::block
Block block(const int i)
Extract a block from the image.
Definition: NiftiImage.h:647