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7a734598f9792fee943b70b6da8d932f *src/zlib/compress.c @@ -60,6 +190,6 @@ fff257bc1656eb60fc585a7dc35f963d *src/zlib/zutil.c de91a463004fd5b944c3d37eab0c1794 *src/zlib/zutil.h db1082070d31f780ebd9c051b74adc17 *src/znzlib/znzlib.c d4a2abbb6217055b8900c8d86ac6aa53 *tests/testthat.R -6e33415014a093811ff7efe7978236b0 *tests/testthat/test-05-nifti.R -335c27208d42142e57e497a1ad377b04 *tests/testthat/test-10-xform.R -934d2a677b2cc72e54788cfc7dfcadf4 *tests/testthat/test-15-foreign.R +bddc785f9d73227aa87d79ba5618e5b7 *tests/testthat/test-05-nifti.R +88c4645aeded119b6027c7280aad2b11 *tests/testthat/test-10-xform.R +7b55076655f51ffecc4a9425ed94f668 *tests/testthat/test-15-foreign.R diff --git a/NAMESPACE b/NAMESPACE index c2fa0fe..a63cddf 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -16,6 +16,7 @@ export("qform<-") export("sform<-") export(dumpNifti) export(ndim) +export(niftiVersion) export(orientation) export(origin) export(pixdim) diff --git a/NEWS b/NEWS index a20579a..43e6a53 100644 --- a/NEWS +++ b/NEWS @@ -2,6 +2,26 @@ Significant changes to the RNifti package are laid out below for each release. =============================================================================== +VERSION 0.8.0 + +- The new niftiVersion() function identifies the NIfTI format variant used by + files on disk. +- The readNifti() function gains an option which allows only certain volumes + to be read from disk. +- The updateNifti() function gains an option to set the internal datatype, for + advanced usage only (issue #8). +- Calling updateNifti() with a list containing only a few fields could + previously reset the remaining metadata to the defaults. This has been + corrected. +- It is now possible to change the cal_min and cal_max fields with the + updateNifti() function (issue #9). The scl_slope and scl_inter fields cannot + be changed, but this is now documented. +- R packages using the RNifti API must now ensure that the USING_R symbol is + defined (which it is by the main R header, R.h). Conversely, standalone use + of RNifti as a C++ library no longer requires _NO_R__ to be defined. + +=============================================================================== + VERSION 0.7.1 - The package is now more careful about handling NaNs when converting to diff --git a/R/nifti.R b/R/nifti.R index 6540e26..b6d7b25 100644 --- a/R/nifti.R +++ b/R/nifti.R @@ -10,8 +10,13 @@ #' class \code{"internalImage"}, which contains only minimal metadata about #' the image. Either way, the return value has an attribute which points to a #' C data structure containing the full image. -#' @return An array or internal image, with class \code{"niftiImage"}, and -#' possibly also \code{"internalImage"}. +#' @param volumes An integer vector giving the volumes to read (counting along +#' all dimensions beyond the third jointly), or \code{NULL}, the default, in +#' which case every volume is read. This cannot currently be set differently +#' for each file read. +#' @return An array or internal image, with class \code{"niftiImage"} (and +#' possibly also \code{"internalImage"}), or a list of such objects if +#' \code{file} has length greater than one. #' #' @note If the \code{internal} argument is \code{FALSE} (the default), the #' data type of the image pointer will be set to match one of R's native @@ -30,16 +35,16 @@ #' @seealso \code{\link{writeNifti}} #' @references The NIfTI-1 standard (\url{http://www.nitrc.org/docman/view.php/26/64/nifti1.h}). #' @export -readNifti <- function (file, internal = FALSE) +readNifti <- function (file, internal = FALSE, volumes = NULL) { if (!is.character(file)) stop("File name(s) must be specified in a character vector") if (length(file) == 0) stop("File name vector is empty") else if (length(file) > 1) - lapply(file, function(f) .Call("readNifti", path.expand(f), internal, PACKAGE="RNifti")) + lapply(file, function(f) .Call("readNifti", path.expand(f), internal, volumes, PACKAGE="RNifti")) else - .Call("readNifti", path.expand(file), internal, PACKAGE="RNifti") + .Call("readNifti", path.expand(file), internal, volumes, PACKAGE="RNifti") } #' Write a NIfTI-1 format file @@ -94,7 +99,7 @@ writeNifti <- function (image, file, template = NULL, datatype = "auto") #' @export retrieveNifti <- function (object) { - .Call("readNifti", object, TRUE, PACKAGE="RNifti") + .Call("readNifti", object, TRUE, NULL, PACKAGE="RNifti") } #' Update an internal NIfTI-1 object using a template @@ -103,19 +108,46 @@ retrieveNifti <- function (object) #' using metadata from the template. The dimensions and, if available, pixel #' dimensions, from the \code{image} will replace those from the template. #' +#' If \code{template} is a complete list of NIfTI-1 header fields, like that +#' produced by \code{\link{dumpNifti}}, or an image, then it will be used to +#' create the internal object, and then the data and metadata associated with +#' the \code{image} will overwrite the appropriate parts. If \code{template} +#' is an incomplete list, the \code{image} will be used to create the internal +#' object, and then the specified fields will be overwritten from the list. +#' This allows users to selectively update certain fields while leaving others +#' alone (but see the note below). +#' +#' Datatype information in a list \code{template} is ignored. The datatype can +#' only be changed using the \code{datatype} argument, but in this case the +#' internal object gets out of sync with the R array, so an internal image is +#' returned to avoid the mismatch. Changing the internal datatype in this way +#' is for advanced usage only. +#' #' @param image A numeric array. #' @param template An image, in any acceptable form (see #' \code{\link{retrieveNifti}}), or a named list of NIfTI-1 properties like #' that produced by \code{\link{dumpNifti}}. The default of \code{NULL} will #' have no effect. +#' @param datatype The NIfTI datatype to use within the internal image. The +#' default, \code{"auto"} uses the R type. Other possibilities are +#' \code{"float"}, \code{"int16"}, etc., which may be preferred to reduce +#' object size. However, no checks are done to ensure that the coercion +#' maintains precision, and this option is for advanced usage only. #' @return A copy of the original \code{image}, with its internal image -#' attribute set or updated appropriately. +#' attribute set or updated appropriately. If \code{datatype} is not +#' \code{"auto"} then the result is an internal image. +#' +#' @note The \code{scl_slope} and \code{scl_inter} fields affect the numerical +#' interpretation of the pixel data, so it is impossible in general to change +#' them without also changing the array values on both the C and the R side. +#' Therefore, to avoid unexpected side-effects, these fields are not affected +#' by this function. #' #' @author Jon Clayden #' @export -updateNifti <- function (image, template = NULL) +updateNifti <- function (image, template = NULL, datatype = "auto") { - .Call("updateNifti", image, template, PACKAGE="RNifti") + .Call("updateNifti", image, template, datatype, PACKAGE="RNifti") } #' Dump the contents of an internal NIfTI-1 object @@ -156,6 +188,33 @@ print.niftiHeader <- function (x, ...) cat(paste0(paste(rep(" ",maxWidth-widths[i]),collapse=""), names(x)[i], ": ", paste(format(x[[i]],trim=TRUE),collapse=" "), "\n")) } +#' Check the format version of a file +#' +#' This function identifies the likely NIfTI format variant used by one or more +#' files on disk. +#' +#' @param file A character vector of file names. +#' @return A vector of integers, of the same length as \code{file}. Each +#' element will be 0 for ANALYZE format (the precursor to NIfTI-1), 1 for +#' NIfTI-1 (which is now most common), 2 for NIfTI-2, or -1 if the file +#' doesn't exist or doesn't look plausible in any of these formats. +#' +#' @note NIfTI-2 format, mostly a variant of NIfTI-1 with wider datatypes used +#' for many fields, is not currently supported for reading, but it is +#' detected by this function. +#' +#' @examples +#' path <- system.file("extdata", "example.nii.gz", package="RNifti") +#' niftiVersion(path) # 1 +#' +#' @author Jon Clayden +#' @seealso \code{\link{readNifti}} +#' @export +niftiVersion <- function (file) +{ + sapply(file, function(f) .Call("niftiVersion", path.expand(f), PACKAGE="RNifti")) +} + rescaleNifti <- function (image, scales) { .Call("rescaleImage", image, scales, PACKAGE="RNifti") diff --git a/README.md b/README.md index 4f17654..7bcaa89 100644 --- a/README.md +++ b/README.md @@ -5,7 +5,7 @@ The [NIfTI-1 format](http://www.nitrc.org/docman/view.php/26/64/nifti1.h) is a p There are several packages available for reading and writing NIfTI-1 files in R, and these are summarised in the [Medical Imaging task view](https://cran.r-project.org/view=MedicalImaging). However, `RNifti` is distinguished by its - [extremely strong performance](#performance), in terms of speed; -- [C/C++ API](#api), allowing access to NIfTI images even in compiled code in other packages; and +- [C/C++ API](#api), allowing access to NIfTI images in compiled code in other R packages, or even in [standalone C++ code](#use-in-pure-c-projects); and - modest dependencies, consisting of only R itself and the very widely-used [Rcpp](https://cran.r-project.org/package=Rcpp) C++ wrapper library. The latest development version of the package can always be installed from GitHub using the `devtools` package. @@ -186,7 +186,7 @@ void myfunction (SEXP image_) ## Use in pure C++ projects -Thanks to contributions from @soolijoo, it is possible (as of package version 0.7.0) to use the `NiftiImage` C++ class in standalone C++ projects. You will need the following files: +Thanks to contributions from [@soolijoo](https://github.com/soolijoo), it is possible (as of package version 0.7.0) to use the `NiftiImage` C++ class in standalone C++ projects. You will need the following files: | Path | Purpose | | ------------------------------- | --------------------------------------------------------------------------------------------------- | @@ -198,4 +198,10 @@ Thanks to contributions from @soolijoo, it is possible (as of package version 0. | `src/znzlib/znzlib.c` | Source for I/O functions from the NIfTI-1 reference implementation | | `src/zlib/*` | `zlib` source files for reading and writing gzipped files (optional, as above) | -Note that the `NiftiImage` class is header-only, but C code from the NIfTI-1 reference implementation will need to be compiled and linked into the project. The constant `_NO_R__` should be defined, and `print.h` included, before including `NiftiImage.h`, so that the R API is not used. +Note that the `NiftiImage` class is header-only, but C code from the NIfTI-1 reference implementation will need to be compiled and linked into the project. The `print.h` header should be included before including `NiftiImage.h`, so that the R API is not used for printing error messages. The [`standalone` directory](https://github.com/jonclayden/RNifti/tree/master/standalone) provides a minimal example. + +## The NIfTI-2 format + +The [NIfTI-2 format](https://nifti.nimh.nih.gov/nifti-2) is a evolution of the far more widely-used NIfTI-1. It primarily [uses wider types for various fields](https://www.nitrc.org/forum/forum.php?thread_id=2148&forum_id=1941), to support large datasets and improve precision. + +Unfortunately, the NIfTI-1 version of the reference library is not forwards-compatible with NIfTI-2, and does not recognise NIfTI-2 files as valid, while the NIfTI-2 version changes the definition of the `nifti_image` data structure, and hence the return type of several core functions, rendering it potentially incompatible with software written for the original library. As a result, adding full NIfTI-2 support to `RNifti` without breaking existing code is not straightforward. Nevertheless, as of `RNifti` version 0.8.0, R function `niftiVersion()` and C++ static method `NiftiImage::fileVersion()` offer a forwards-compatible way to determine the version of the format used by a particular file, so that calling functions can take action accordingly. diff --git a/inst/doxygen/html/_nifti_image_8h_source.html b/inst/doxygen/html/_nifti_image_8h_source.html new file mode 100644 index 0000000..1eb30a2 --- /dev/null +++ b/inst/doxygen/html/_nifti_image_8h_source.html @@ -0,0 +1,128 @@ + + + + + + + +RNifti: inst/include/lib/NiftiImage.h Source File + + + + + + + + + +
+
+ + + + + + +
+
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 #define ISNAN(x) (x != x)
13 
14 #include <stdint.h>
15 #include <cstddef>
16 #include <cmath>
17 #include <string>
18 #include <sstream>
19 #include <vector>
20 #include <stdexcept>
21 #include <algorithm>
22 #include <map>
23 #include <locale>
24 #include <limits>
25 
26 #endif
27 
28 
29 #include "niftilib/nifti1_io.h"
30 
39 namespace RNifti {
40 
45 class NiftiImage
46 {
47 public:
52  struct Block
53  {
54  const NiftiImage &image;
55  const int dimension;
56  const int index;
65  Block (const NiftiImage &image, const int dimension, const int index)
66  : image(image), dimension(dimension), index(index)
67  {
68  if (dimension != image->ndim)
69  throw std::runtime_error("Blocks must be along the last dimension in the image");
70  }
71 
80  Block & operator= (const NiftiImage &source)
81  {
82  if (source->datatype != image->datatype)
83  throw std::runtime_error("New data does not have the same datatype as the target block");
84  if (source->scl_slope != image->scl_slope || source->scl_inter != image->scl_inter)
85  throw std::runtime_error("New data does not have the same scale parameters as the target block");
86 
87  size_t blockSize = 1;
88  for (int i=1; i<dimension; i++)
89  blockSize *= image->dim[i];
90 
91  if (blockSize != source->nvox)
92  throw std::runtime_error("New data does not have the same size as the target block");
93 
94  blockSize *= image->nbyper;
95  memcpy(static_cast<char*>(image->data) + blockSize*index, source->data, blockSize);
96  return *this;
97  }
98 
102  template <typename TargetType>
103  std::vector<TargetType> getData () const;
104  };
105 
106 #ifdef USING_R
107 
113  static short sexpTypeToNiftiType (const int sexpType)
114  {
115  if (sexpType == INTSXP || sexpType == LGLSXP)
116  return DT_INT32;
117  else if (sexpType == REALSXP)
118  return DT_FLOAT64;
119  else
120  throw std::runtime_error("Array elements must be numeric");
121  }
122 #endif
123 
129  static std::string xformToString (const mat44 matrix)
130  {
131  int icode, jcode, kcode;
132  nifti_mat44_to_orientation(matrix, &icode, &jcode, &kcode);
133 
134  int codes[3] = { icode, jcode, kcode };
135  std::string result("---");
136  for (int i=0; i<3; i++)
137  {
138  switch (codes[i])
139  {
140  case NIFTI_L2R: result[i] = 'R'; break;
141  case NIFTI_R2L: result[i] = 'L'; break;
142  case NIFTI_P2A: result[i] = 'A'; break;
143  case NIFTI_A2P: result[i] = 'P'; break;
144  case NIFTI_I2S: result[i] = 'S'; break;
145  case NIFTI_S2I: result[i] = 'I'; break;
146  }
147  }
148  return result;
149  }
150 
157  static int fileVersion (const std::string &path)
158  {
159  nifti_1_header *header = nifti_read_header(path.c_str(), NULL, false);
160  if (header == NULL)
161  return -1;
162  else
163  {
164  int version = NIFTI_VERSION(*header);
165  if (version == 0)
166  {
167  // NIfTI-2 has a 540-byte header - check for this or its byte-swapped equivalent
168  if (header->sizeof_hdr == 540 || header->sizeof_hdr == 469893120)
169  {
170  // The magic number has moved in NIfTI-2, so find it by byte offset
171  const char *magic = (char *) header + 4;
172  if (strncmp(magic,"ni2",3) == 0 || strncmp(magic,"n+2",3) == 0)
173  version = 2;
174  }
175  else if (!nifti_hdr_looks_good(header))
176  {
177  // Not plausible as ANALYZE, so return -1
178  version = -1;
179  }
180  }
181  return version;
182  }
183  }
184 
185 
186 protected:
187  nifti_image *image;
188  bool persistent;
194  void copy (const nifti_image *source);
195 
200  void copy (const NiftiImage &source);
201 
206  void copy (const Block &source);
207 
208 
209 #ifdef USING_R
210 
216  void initFromNiftiS4 (const Rcpp::RObject &object, const bool copyData = true);
217 
223  void initFromMriImage (const Rcpp::RObject &object, const bool copyData = true);
224 
229  void initFromList (const Rcpp::RObject &object);
230 
236  void initFromArray (const Rcpp::RObject &object, const bool copyData = true);
237 
238 #endif
239 
244  void updatePixdim (const std::vector<float> &pixdim);
245 
250  void setPixunits (const std::vector<std::string> &pixunits);
251 
252 public:
256  NiftiImage ()
257  : image(NULL), persistent(false) {}
258 
263  NiftiImage (const NiftiImage &source)
264  : image(NULL), persistent(false)
265  {
266  this->copy(source);
267 #ifndef NDEBUG
268  Rprintf("Creating NiftiImage with pointer %p (from NiftiImage)\n", this->image);
269 #endif
270  }
271 
276  NiftiImage (const Block &source)
277  : image(NULL), persistent(false)
278  {
279  this->copy(source);
280 #ifndef NDEBUG
281  Rprintf("Creating NiftiImage with pointer %p (from Block)\n", this->image);
282 #endif
283  }
284 
291  NiftiImage (nifti_image * const image, const bool copy = false)
292  : image(NULL), persistent(false)
293  {
294  if (copy)
295  this->copy(image);
296  else
297  this->image = image;
298 #ifndef NDEBUG
299  Rprintf("Creating NiftiImage with pointer %p (from pointer)\n", this->image);
300 #endif
301  }
302 
309  NiftiImage (const std::string &path, const bool readData = true)
310  : persistent(false)
311  {
312  this->image = nifti_image_read(path.c_str(), readData);
313  if (this->image == NULL)
314  throw std::runtime_error("Failed to read image from path " + path);
315 #ifndef NDEBUG
316  Rprintf("Creating NiftiImage with pointer %p (from string)\n", this->image);
317 #endif
318  }
319 
326  NiftiImage (const std::string &path, const std::vector<int> &volumes);
327 
328 #ifdef USING_R
329 
334  NiftiImage (const SEXP object, const bool readData = true);
335 #endif
336 
340  virtual ~NiftiImage ()
341  {
342  if (!persistent)
343  {
344 #ifndef NDEBUG
345  Rprintf("Freeing NiftiImage with pointer %p\n", this->image);
346 #endif
347  nifti_image_free(image);
348  }
349  }
350 
354  operator const nifti_image* () const { return image; }
355 
359  operator nifti_image* () { return image; }
360 
364  const nifti_image * operator-> () const { return image; }
365 
369  nifti_image * operator-> () { return image; }
370 
375  NiftiImage & operator= (const NiftiImage &source)
376  {
377  copy(source);
378 #ifndef NDEBUG
379  Rprintf("Creating NiftiImage with pointer %p (from NiftiImage)\n", this->image);
380 #endif
381  return *this;
382  }
383 
389  NiftiImage & operator= (const Block &source)
390  {
391  copy(source);
392 #ifndef NDEBUG
393  Rprintf("Creating NiftiImage with pointer %p (from Block)\n", this->image);
394 #endif
395  return *this;
396  }
397 
402  NiftiImage & setPersistence (const bool persistent)
403  {
404  this->persistent = persistent;
405 #ifndef NDEBUG
406  if (persistent)
407  Rprintf("Setting NiftiImage with pointer %p to be persistent\n", this->image);
408 #endif
409  return *this;
410  }
411 
415  bool isNull () const { return (image == NULL); }
416 
420  bool isPersistent () const { return persistent; }
421 
425  bool isDataScaled () const { return (image != NULL && image->scl_slope != 0.0 && (image->scl_slope != 1.0 || image->scl_inter != 0.0)); }
426 
430  int nDims () const
431  {
432  if (image == NULL)
433  return 0;
434  else
435  return image->ndim;
436  }
437 
442  std::vector<int> dim () const
443  {
444  if (image == NULL)
445  return std::vector<int>();
446  else
447  return std::vector<int>(image->dim+1, image->dim+image->ndim+1);
448  }
449 
454  std::vector<float> pixdim () const
455  {
456  if (image == NULL)
457  return std::vector<float>();
458  else
459  return std::vector<float>(image->pixdim+1, image->pixdim+image->ndim+1);
460  }
461 
468  NiftiImage & drop ()
469  {
470  int ndim = image->ndim;
471  while (image->dim[ndim] < 2)
472  ndim--;
473  image->dim[0] = image->ndim = ndim;
474 
475  return *this;
476  }
477 
481  template <typename TargetType>
482  std::vector<TargetType> getData () const;
483 
488  NiftiImage & changeDatatype (const short datatype);
489 
494  NiftiImage & changeDatatype (const std::string &datatype);
495 
503  template <typename SourceType>
504  NiftiImage & replaceData (const std::vector<SourceType> &data, const short datatype = DT_NONE);
505 
509  NiftiImage & dropData ()
510  {
511  nifti_image_unload(image);
512  return *this;
513  }
514 
520  NiftiImage & rescale (const std::vector<float> &scales);
521 
529  NiftiImage & reorient (const int i, const int j, const int k);
530 
538  NiftiImage & reorient (const std::string &orientation);
539 
540 #ifdef USING_R
541 
545  NiftiImage & update (const Rcpp::RObject &object);
546 #endif
547 
553  mat44 xform (const bool preferQuaternion = true) const;
554 
558  int nBlocks () const
559  {
560  if (image == NULL)
561  return 0;
562  else
563  return image->dim[image->ndim];
564  }
565 
573  const Block block (const int i) const { return Block(*this, nDims(), i); }
574 
582  Block block (const int i) { return Block(*this, nDims(), i); }
583 
589  const Block slice (const int i) const { return Block(*this, 3, i); }
590 
596  Block slice (const int i) { return Block(*this, 3, i); }
597 
603  const Block volume (const int i) const { return Block(*this, 4, i); }
604 
610  Block volume (const int i) { return Block(*this, 4, i); }
611 
617  void toFile (const std::string fileName, const short datatype = DT_NONE) const;
618 
624  void toFile (const std::string fileName, const std::string &datatype) const;
625 
626 #ifdef USING_R
627 
632  Rcpp::RObject toArray () const;
633 
639  Rcpp::RObject toPointer (const std::string label) const;
640 
647  Rcpp::RObject toArrayOrPointer (const bool internal, const std::string label) const;
648 
653  Rcpp::RObject headerToList () const;
654 
655 #endif
656 
657 };
658 
659 // Include helper functions
660 #include "lib/NiftiImage_internal.h"
661 
662 inline void NiftiImage::copy (const nifti_image *source)
663 {
664  if (image != NULL && !persistent)
665  nifti_image_free(image);
666 
667  if (source == NULL)
668  image = NULL;
669  else
670  {
671  image = nifti_copy_nim_info(source);
672  if (source->data != NULL)
673  {
674  size_t dataSize = nifti_get_volsize(source);
675  image->data = calloc(1, dataSize);
676  memcpy(image->data, source->data, dataSize);
677  }
678  }
679 
680  persistent = false;
681 }
682 
683 inline void NiftiImage::copy (const NiftiImage &source)
684 {
685  const nifti_image *sourceStruct = source;
686  copy(sourceStruct);
687 }
688 
689 inline void NiftiImage::copy (const Block &source)
690 {
691  if (image != NULL && !persistent)
692  nifti_image_free(image);
693 
694  const nifti_image *sourceStruct = source.image;
695  if (sourceStruct == NULL)
696  image = NULL;
697  else
698  {
699  image = nifti_copy_nim_info(sourceStruct);
700  image->dim[0] = source.image->dim[0] - 1;
701  image->dim[source.dimension] = 1;
702  image->pixdim[source.dimension] = 1.0;
703  nifti_update_dims_from_array(image);
704 
705  if (sourceStruct->data != NULL)
706  {
707  size_t blockSize = nifti_get_volsize(image);
708  image->data = calloc(1, blockSize);
709  memcpy(image->data, static_cast<char*>(source.image->data) + blockSize*source.index, blockSize);
710  }
711  }
712 
713  persistent = false;
714 }
715 
716 #ifdef USING_R
717 
718 // Convert an S4 "nifti" object, as defined in the oro.nifti package, to a "nifti_image" struct
719 inline void NiftiImage::initFromNiftiS4 (const Rcpp::RObject &object, const bool copyData)
720 {
721  nifti_1_header header;
722  header.sizeof_hdr = 348;
723 
724  const std::vector<short> dims = object.slot("dim_");
725  for (int i=0; i<8; i++)
726  header.dim[i] = dims[i];
727 
728  header.intent_p1 = object.slot("intent_p1");
729  header.intent_p2 = object.slot("intent_p2");
730  header.intent_p3 = object.slot("intent_p3");
731  header.intent_code = object.slot("intent_code");
732 
733  header.datatype = object.slot("datatype");
734  header.bitpix = object.slot("bitpix");
735 
736  header.slice_start = object.slot("slice_start");
737  header.slice_end = object.slot("slice_end");
738  header.slice_code = Rcpp::as<int>(object.slot("slice_code"));
739  header.slice_duration = object.slot("slice_duration");
740 
741  const std::vector<float> pixdims = object.slot("pixdim");
742  for (int i=0; i<8; i++)
743  header.pixdim[i] = pixdims[i];
744  header.xyzt_units = Rcpp::as<int>(object.slot("xyzt_units"));
745 
746  header.vox_offset = object.slot("vox_offset");
747 
748  header.scl_slope = object.slot("scl_slope");
749  header.scl_inter = object.slot("scl_inter");
750  header.toffset = object.slot("toffset");
751 
752  header.cal_max = object.slot("cal_max");
753  header.cal_min = object.slot("cal_min");
754  header.glmax = header.glmin = 0;
755 
756  strncpy(header.descrip, Rcpp::as<std::string>(object.slot("descrip")).c_str(), 79);
757  header.descrip[79] = '\0';
758  strncpy(header.aux_file, Rcpp::as<std::string>(object.slot("aux_file")).c_str(), 23);
759  header.aux_file[23] = '\0';
760  strncpy(header.intent_name, Rcpp::as<std::string>(object.slot("intent_name")).c_str(), 15);
761  header.intent_name[15] = '\0';
762  strncpy(header.magic, Rcpp::as<std::string>(object.slot("magic")).c_str(), 3);
763  header.magic[3] = '\0';
764 
765  header.qform_code = object.slot("qform_code");
766  header.sform_code = object.slot("sform_code");
767 
768  header.quatern_b = object.slot("quatern_b");
769  header.quatern_c = object.slot("quatern_c");
770  header.quatern_d = object.slot("quatern_d");
771  header.qoffset_x = object.slot("qoffset_x");
772  header.qoffset_y = object.slot("qoffset_y");
773  header.qoffset_z = object.slot("qoffset_z");
774 
775  const std::vector<float> srow_x = object.slot("srow_x");
776  const std::vector<float> srow_y = object.slot("srow_y");
777  const std::vector<float> srow_z = object.slot("srow_z");
778  for (int i=0; i<4; i++)
779  {
780  header.srow_x[i] = srow_x[i];
781  header.srow_y[i] = srow_y[i];
782  header.srow_z[i] = srow_z[i];
783  }
784 
785  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)
786  header.datatype = DT_INT32;
787  else if (header.datatype == DT_FLOAT32 || header.datatype == DT_FLOAT64)
788  header.datatype = DT_FLOAT64; // This assumes that sizeof(double) == 8
789  else
790  throw std::runtime_error("Data type is not supported");
791 
792  this->image = nifti_convert_nhdr2nim(header, NULL);
793 
794  const SEXP data = PROTECT(object.slot(".Data"));
795  if (!copyData || Rf_length(data) <= 1)
796  this->image->data = NULL;
797  else
798  {
799  const size_t dataSize = nifti_get_volsize(this->image);
800  this->image->data = calloc(1, dataSize);
801  if (header.datatype == DT_INT32)
802  {
803  Rcpp::IntegerVector intData(data);
804  std::copy(intData.begin(), intData.end(), static_cast<int32_t*>(this->image->data));
805  }
806  else
807  {
808  Rcpp::DoubleVector doubleData(data);
809  std::copy(doubleData.begin(), doubleData.end(), static_cast<double*>(this->image->data));
810  }
811  }
812  UNPROTECT(1);
813 }
814 
815 inline void NiftiImage::initFromMriImage (const Rcpp::RObject &object, const bool copyData)
816 {
817  Rcpp::Reference mriImage(object);
818  Rcpp::Function getXform = mriImage.field("getXform");
819  Rcpp::NumericMatrix xform = getXform();
820 
821  this->image = NULL;
822 
823  if (Rf_length(mriImage.field("tags")) > 0)
824  initFromList(mriImage.field("tags"));
825 
826  Rcpp::RObject data = mriImage.field("data");
827  if (data.inherits("SparseArray"))
828  {
829  Rcpp::Language call("as.array", data);
830  data = call.eval();
831  }
832 
833  const short datatype = (Rf_isNull(data) ? DT_INT32 : sexpTypeToNiftiType(data.sexp_type()));
834 
835  int dims[8] = { 0, 0, 0, 0, 0, 0, 0, 0 };
836  const std::vector<int> dimVector = mriImage.field("imageDims");
837  const int nDims = std::min(7, int(dimVector.size()));
838  dims[0] = nDims;
839  size_t nVoxels = 1;
840  for (int i=0; i<nDims; i++)
841  {
842  dims[i+1] = dimVector[i];
843  nVoxels *= dimVector[i];
844  }
845 
846  if (this->image == NULL)
847  this->image = nifti_make_new_nim(dims, datatype, FALSE);
848  else
849  {
850  std::copy(dims, dims+8, this->image->dim);
851  this->image->datatype = datatype;
852  nifti_datatype_sizes(image->datatype, &image->nbyper, NULL);
853  }
854 
855  if (copyData && !Rf_isNull(data))
856  {
857  // NB: nifti_get_volsize() will not be right here if there were tags
858  const size_t dataSize = nVoxels * image->nbyper;
859  this->image->data = calloc(1, dataSize);
860  if (datatype == DT_INT32)
861  memcpy(this->image->data, INTEGER(data), dataSize);
862  else
863  memcpy(this->image->data, REAL(data), dataSize);
864  }
865  else
866  this->image->data = NULL;
867 
868  const std::vector<float> pixdimVector = mriImage.field("voxelDims");
869  const int pixdimLength = pixdimVector.size();
870  for (int i=0; i<std::min(pixdimLength,nDims); i++)
871  this->image->pixdim[i+1] = std::abs(pixdimVector[i]);
872 
873  const std::vector<std::string> pixunitsVector = mriImage.field("voxelDimUnits");
874  setPixunits(pixunitsVector);
875 
876  if (xform.rows() != 4 || xform.cols() != 4)
877  this->image->qform_code = this->image->sform_code = 0;
878  else
879  {
880  mat44 matrix;
881  for (int i=0; i<4; i++)
882  {
883  for (int j=0; j<4; j++)
884  matrix.m[i][j] = static_cast<float>(xform(i,j));
885  }
886 
887  this->image->qto_xyz = matrix;
888  this->image->qto_ijk = nifti_mat44_inverse(image->qto_xyz);
889  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);
890 
891  this->image->sto_xyz = matrix;
892  this->image->sto_ijk = nifti_mat44_inverse(image->sto_xyz);
893 
894  this->image->qform_code = this->image->sform_code = 2;
895  }
896 }
897 
898 inline void NiftiImage::initFromList (const Rcpp::RObject &object)
899 {
900  Rcpp::List list(object);
901  nifti_1_header *header = nifti_make_new_header(NULL, DT_FLOAT64);
902 
903  internal::updateHeader(header, list);
904 
905  this->image = nifti_convert_nhdr2nim(*header, NULL);
906  this->image->data = NULL;
907  free(header);
908 }
909 
910 inline void NiftiImage::initFromArray (const Rcpp::RObject &object, const bool copyData)
911 {
912  int dims[8] = { 0, 0, 0, 0, 0, 0, 0, 0 };
913  const std::vector<int> dimVector = object.attr("dim");
914 
915  const int nDims = std::min(7, int(dimVector.size()));
916  dims[0] = nDims;
917  for (int i=0; i<nDims; i++)
918  dims[i+1] = dimVector[i];
919 
920  const short datatype = sexpTypeToNiftiType(object.sexp_type());
921  this->image = nifti_make_new_nim(dims, datatype, int(copyData));
922 
923  if (copyData)
924  {
925  const size_t dataSize = nifti_get_volsize(image);
926  if (datatype == DT_INT32)
927  memcpy(this->image->data, INTEGER(object), dataSize);
928  else
929  memcpy(this->image->data, REAL(object), dataSize);
930  }
931  else
932  this->image->data = NULL;
933 
934  if (object.hasAttribute("pixdim"))
935  {
936  const std::vector<float> pixdimVector = object.attr("pixdim");
937  const int pixdimLength = pixdimVector.size();
938  for (int i=0; i<std::min(pixdimLength,nDims); i++)
939  this->image->pixdim[i+1] = pixdimVector[i];
940  }
941 
942  if (object.hasAttribute("pixunits"))
943  {
944  const std::vector<std::string> pixunitsVector = object.attr("pixunits");
945  setPixunits(pixunitsVector);
946  }
947 }
948 
949 inline NiftiImage::NiftiImage (const SEXP object, const bool readData)
950  : persistent(false)
951 {
952  Rcpp::RObject imageObject(object);
953  bool resolved = false;
954 
955  if (imageObject.hasAttribute(".nifti_image_ptr"))
956  {
957  Rcpp::XPtr<NiftiImage> imagePtr(SEXP(imageObject.attr(".nifti_image_ptr")));
958  NiftiImage *ptr = imagePtr;
959  if (ptr != NULL)
960  {
961  this->image = ptr->image;
962  this->persistent = true;
963  resolved = true;
964 
965  if (imageObject.hasAttribute("dim"))
966  update(imageObject);
967  }
968  else if (Rf_isString(object))
969  throw std::runtime_error("Internal image is not valid");
970  else
971  Rf_warning("Ignoring invalid internal pointer");
972  }
973 
974  if (!resolved)
975  {
976  if (Rf_isNull(object))
977  this->image = NULL;
978  else if (Rf_isString(object))
979  {
980  const std::string path = Rcpp::as<std::string>(object);
981  this->image = nifti_image_read(path.c_str(), readData);
982  if (this->image == NULL)
983  throw std::runtime_error("Failed to read image from path " + path);
984  }
985  else if (imageObject.inherits("nifti"))
986  initFromNiftiS4(imageObject, readData);
987  else if (imageObject.inherits("anlz"))
988  throw std::runtime_error("Cannot currently convert objects of class \"anlz\"");
989  else if (imageObject.inherits("MriImage"))
990  initFromMriImage(imageObject, readData);
991  else if (Rf_isVectorList(object))
992  initFromList(imageObject);
993  else if (imageObject.hasAttribute("dim"))
994  initFromArray(imageObject, readData);
995  else
996  throw std::runtime_error("Cannot convert object of class \"" + Rcpp::as<std::string>(imageObject.attr("class")) + "\" to a nifti_image");
997  }
998 
999  if (this->image != NULL)
1000  nifti_update_dims_from_array(this->image);
1001 
1002 #ifndef NDEBUG
1003  Rprintf("Creating NiftiImage with pointer %p (from SEXP)\n", this->image);
1004 #endif
1005 }
1006 
1007 #endif // USING_R
1008 
1009 inline NiftiImage::NiftiImage (const std::string &path, const std::vector<int> &volumes)
1010  : persistent(false)
1011 {
1012  if (volumes.empty())
1013  throw std::runtime_error("The vector of volumes is empty");
1014 
1015  nifti_brick_list brickList;
1016  this->image = nifti_image_read_bricks(path.c_str(), volumes.size(), &volumes[0], &brickList);
1017  if (this->image == NULL)
1018  throw std::runtime_error("Failed to read image from path " + path);
1019 
1020  size_t brickSize = image->nbyper * image->nx * image->ny * image->nz;
1021  image->data = calloc(1, nifti_get_volsize(image));
1022  for (int i=0; i<brickList.nbricks; i++)
1023  memcpy((char *) image->data + i * brickSize, brickList.bricks[i], brickSize);
1024  nifti_free_NBL(&brickList);
1025 
1026 #ifndef NDEBUG
1027  Rprintf("Creating NiftiImage with pointer %p (from string and volume vector)\n", this->image);
1028 #endif
1029 }
1030 
1031 inline void NiftiImage::updatePixdim (const std::vector<float> &pixdim)
1032 {
1033  const int nDims = image->dim[0];
1034  const std::vector<float> origPixdim(image->pixdim+1, image->pixdim+4);
1035 
1036  for (int i=1; i<8; i++)
1037  image->pixdim[i] = 0.0;
1038 
1039  const int pixdimLength = pixdim.size();
1040  for (int i=0; i<std::min(pixdimLength,nDims); i++)
1041  image->pixdim[i+1] = pixdim[i];
1042 
1043  if (!std::equal(origPixdim.begin(), origPixdim.begin() + std::min(3,nDims), pixdim.begin()))
1044  {
1045  mat33 scaleMatrix;
1046  for (int i=0; i<3; i++)
1047  {
1048  for (int j=0; j<3; j++)
1049  {
1050  if (i != j)
1051  scaleMatrix.m[i][j] = 0.0;
1052  else if (i >= nDims)
1053  scaleMatrix.m[i][j] = 1.0;
1054  else
1055  scaleMatrix.m[i][j] = pixdim[i] / origPixdim[i];
1056  }
1057  }
1058 
1059  if (image->qform_code > 0)
1060  {
1061  mat33 prod = nifti_mat33_mul(scaleMatrix, internal::topLeftCorner(image->qto_xyz));
1062  for (int i=0; i<3; i++)
1063  {
1064  for (int j=0; j<3; j++)
1065  image->qto_xyz.m[i][j] = prod.m[i][j];
1066  }
1067  image->qto_ijk = nifti_mat44_inverse(image->qto_xyz);
1068  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);
1069  }
1070 
1071  if (image->sform_code > 0)
1072  {
1073  mat33 prod = nifti_mat33_mul(scaleMatrix, internal::topLeftCorner(image->sto_xyz));
1074  for (int i=0; i<3; i++)
1075  {
1076  for (int j=0; j<3; j++)
1077  image->sto_xyz.m[i][j] = prod.m[i][j];
1078  }
1079  image->sto_ijk = nifti_mat44_inverse(image->sto_xyz);
1080  }
1081  }
1082 }
1083 
1084 inline void NiftiImage::setPixunits (const std::vector<std::string> &pixunits)
1085 {
1086  for (size_t i=0; i<pixunits.size(); i++)
1087  {
1088  if (pixunits[i] == "m")
1089  image->xyz_units = NIFTI_UNITS_METER;
1090  else if (pixunits[i] == "mm")
1091  image->xyz_units = NIFTI_UNITS_MM;
1092  else if (pixunits[i] == "um")
1093  image->xyz_units = NIFTI_UNITS_MICRON;
1094  else if (pixunits[i] == "s")
1095  image->time_units = NIFTI_UNITS_SEC;
1096  else if (pixunits[i] == "ms")
1097  image->time_units = NIFTI_UNITS_MSEC;
1098  else if (pixunits[i] == "us")
1099  image->time_units = NIFTI_UNITS_USEC;
1100  else if (pixunits[i] == "Hz")
1101  image->time_units = NIFTI_UNITS_HZ;
1102  else if (pixunits[i] == "ppm")
1103  image->time_units = NIFTI_UNITS_PPM;
1104  else if (pixunits[i] == "rad/s")
1105  image->time_units = NIFTI_UNITS_RADS;
1106  }
1107 }
1108 
1109 inline NiftiImage & NiftiImage::rescale (const std::vector<float> &scales)
1110 {
1111  std::vector<float> pixdim(image->pixdim+1, image->pixdim+4);
1112 
1113  for (int i=0; i<std::min(3, int(scales.size())); i++)
1114  {
1115  if (scales[i] != 1.0)
1116  {
1117  pixdim[i] /= scales[i];
1118  image->dim[i+1] = static_cast<int>(std::floor(image->dim[i+1] * scales[i]));
1119  }
1120  }
1121 
1122  updatePixdim(pixdim);
1123  nifti_update_dims_from_array(image);
1124 
1125  // Data vector is now the wrong size, so drop it
1126  if (!persistent)
1127  nifti_image_unload(image);
1128 
1129  image->scl_slope = 0.0;
1130  image->scl_inter = 0.0;
1131 
1132  return *this;
1133 }
1134 
1135 inline NiftiImage & NiftiImage::reorient (const int icode, const int jcode, const int kcode)
1136 {
1137  if (this->isNull())
1138  return *this;
1139  if (image->qform_code == 0 && image->sform_code == 0)
1140  {
1141  Rf_warning("Image qform and sform codes are both zero, so it cannot be reoriented");
1142  return *this;
1143  }
1144 
1145  int used[6] = { 0, 0, 0, 0, 0, 0 };
1146  used[icode-1] = 1;
1147  used[jcode-1] = 1;
1148  used[kcode-1] = 1;
1149  if (used[0]+used[1] != 1 || used[2]+used[3] != 1 || used[4]+used[5] != 1)
1150  throw std::runtime_error("Each canonical axis should be used exactly once");
1151 
1152  const int codes[3] = { icode, jcode, kcode };
1153  const mat44 native = this->xform();
1154 
1155  // Create a target xform (rotation matrix only)
1156  mat33 target;
1157  for (int j=0; j<3; j++)
1158  {
1159  for (int i=0; i<3; i++)
1160  target.m[i][j] = 0.0;
1161 
1162  switch (codes[j])
1163  {
1164  case NIFTI_L2R: target.m[0][j] = 1.0; break;
1165  case NIFTI_R2L: target.m[0][j] = -1.0; break;
1166  case NIFTI_P2A: target.m[1][j] = 1.0; break;
1167  case NIFTI_A2P: target.m[1][j] = -1.0; break;
1168  case NIFTI_I2S: target.m[2][j] = 1.0; break;
1169  case NIFTI_S2I: target.m[2][j] = -1.0; break;
1170  }
1171  }
1172 
1173  // Extract (inverse of) canonical axis matrix from native xform
1174  int nicode, njcode, nkcode;
1175  nifti_mat44_to_orientation(native, &nicode, &njcode, &nkcode);
1176  int ncodes[3] = { nicode, njcode, nkcode };
1177  mat33 nativeAxesTransposed;
1178  for (int i=0; i<3; i++)
1179  {
1180  for (int j=0; j<3; j++)
1181  nativeAxesTransposed.m[i][j] = 0.0;
1182 
1183  switch (ncodes[i])
1184  {
1185  case NIFTI_L2R: nativeAxesTransposed.m[i][0] = 1.0; break;
1186  case NIFTI_R2L: nativeAxesTransposed.m[i][0] = -1.0; break;
1187  case NIFTI_P2A: nativeAxesTransposed.m[i][1] = 1.0; break;
1188  case NIFTI_A2P: nativeAxesTransposed.m[i][1] = -1.0; break;
1189  case NIFTI_I2S: nativeAxesTransposed.m[i][2] = 1.0; break;
1190  case NIFTI_S2I: nativeAxesTransposed.m[i][2] = -1.0; break;
1191  }
1192  }
1193 
1194  // Check for no-op case
1195  if (icode == nicode && jcode == njcode && kcode == nkcode)
1196  return *this;
1197 
1198  // The transform is t(approx_old_xform) %*% target_xform
1199  // The new xform is old_xform %*% transform
1200  // NB: "transform" is really 4x4, but the last row and column are filled implicitly during the multiplication loop
1201  mat33 transform = nifti_mat33_mul(nativeAxesTransposed, target);
1202  mat44 result;
1203  for (int i=0; i<4; i++)
1204  {
1205  for (int j=0; j<3; j++)
1206  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];
1207 
1208  result.m[i][3] = native.m[i][3];
1209  }
1210 
1211  // Update the xforms with nonzero codes
1212  if (image->qform_code > 0)
1213  {
1214  image->qto_xyz = result;
1215  image->qto_ijk = nifti_mat44_inverse(image->qto_xyz);
1216  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);
1217  }
1218  if (image->sform_code > 0)
1219  {
1220  image->sto_xyz = result;
1221  image->sto_ijk = nifti_mat44_inverse(image->sto_xyz);
1222  }
1223 
1224  // Extract the mapping between dimensions and the signs
1225  int locs[3], signs[3], newdim[3];
1226  float newpixdim[3];
1227  double maxes[3] = { R_NegInf, R_NegInf, R_NegInf };
1228  for (int j=0; j<3; j++)
1229  {
1230  for (int i=0; i<3; i++)
1231  {
1232  const double value = static_cast<double>(transform.m[i][j]);
1233  if (fabs(value) > maxes[j])
1234  {
1235  maxes[j] = fabs(value);
1236  signs[j] = value > 0.0 ? 1 : -1;
1237  locs[j] = i;
1238  }
1239  }
1240 
1241  // Permute dim and pixdim
1242  newdim[j] = image->dim[locs[j]+1];
1243  newpixdim[j] = image->pixdim[locs[j]+1];
1244  }
1245 
1246  // Calculate strides in target space
1247  ptrdiff_t strides[3];
1248  strides[locs[0]] = 1;
1249  for (int n=1; n<3; n++)
1250  strides[locs[n]] = strides[locs[n-1]] * image->dim[locs[n-1]+1];
1251 
1252  if (image->data != NULL)
1253  {
1254  size_t volSize = size_t(image->nx * image->ny * image->nz);
1255  size_t nVolumes = std::max(size_t(1), image->nvox / volSize);
1256 
1257  const std::vector<double> oldData = this->getData<double>();
1258  std::vector<double> newData(image->nvox);
1259 
1260  // Where the sign is negative we need to start at the end of the dimension
1261  size_t volStart = 0;
1262  for (int i=0; i<3; i++)
1263  {
1264  if (signs[i] < 0)
1265  volStart += (image->dim[i+1] - 1) * strides[i];
1266  }
1267 
1268  // Iterate over the data and place it into a new vector
1269  std::vector<double>::const_iterator it = oldData.begin();
1270  for (size_t v=0; v<nVolumes; v++)
1271  {
1272  for (int k=0; k<image->nz; k++)
1273  {
1274  ptrdiff_t offset = k * strides[2] * signs[2];
1275  for (int j=0; j<image->ny; j++)
1276  {
1277  for (int i=0; i<image->nx; i++)
1278  {
1279  newData[volStart + offset] = *it++;
1280  offset += strides[0] * signs[0];
1281  }
1282  offset += strides[1] * signs[1] - image->nx * strides[0] * signs[0];
1283  }
1284  }
1285  volStart += volSize;
1286  }
1287 
1288  // Replace the existing data in the image
1289  this->replaceData(newData);
1290  }
1291 
1292  // Copy new dims and pixdims in
1293  // NB: Old dims are used above, so this must happen last
1294  std::copy(newdim, newdim+3, image->dim+1);
1295  std::copy(newpixdim, newpixdim+3, image->pixdim+1);
1296  nifti_update_dims_from_array(image);
1297 
1298  return *this;
1299 }
1300 
1301 inline NiftiImage & NiftiImage::reorient (const std::string &orientation)
1302 {
1303  if (orientation.length() != 3)
1304  throw std::runtime_error("Orientation string should have exactly three characters");
1305 
1306  int codes[3];
1307  for (int i=0; i<3; i++)
1308  {
1309  switch(orientation[i])
1310  {
1311  case 'r': case 'R': codes[i] = NIFTI_L2R; break;
1312  case 'l': case 'L': codes[i] = NIFTI_R2L; break;
1313  case 'a': case 'A': codes[i] = NIFTI_P2A; break;
1314  case 'p': case 'P': codes[i] = NIFTI_A2P; break;
1315  case 's': case 'S': codes[i] = NIFTI_I2S; break;
1316  case 'i': case 'I': codes[i] = NIFTI_S2I; break;
1317 
1318  default:
1319  throw std::runtime_error("Orientation string is invalid");
1320  }
1321  }
1322 
1323  return reorient(codes[0], codes[1], codes[2]);
1324 }
1325 
1326 #ifdef USING_R
1327 
1328 inline NiftiImage & NiftiImage::update (const Rcpp::RObject &object)
1329 {
1330  if (Rf_isVectorList(object))
1331  {
1332  Rcpp::List list(object);
1333  nifti_1_header *header = NULL;
1334  if (this->isNull())
1335  {
1336  header = nifti_make_new_header(NULL, DT_FLOAT64);
1337  internal::updateHeader(header, list, true);
1338  }
1339  else
1340  {
1341  header = (nifti_1_header *) calloc(1, sizeof(nifti_1_header));
1342  *header = nifti_convert_nim2nhdr(image);
1343  internal::updateHeader(header, list, true);
1344  }
1345 
1346  if (header != NULL)
1347  {
1348  nifti_image *newImage = nifti_convert_nhdr2nim(*header, NULL);
1349  if (this->image->data != NULL)
1350  {
1351  size_t dataSize = nifti_get_volsize(image);
1352  newImage->data = calloc(1, dataSize);
1353  memcpy(newImage->data, image->data, dataSize);
1354  }
1355  if (!persistent)
1356  nifti_image_free(image);
1357  this->image = newImage;
1358  }
1359  }
1360  else if (object.hasAttribute("dim"))
1361  {
1362  for (int i=0; i<8; i++)
1363  image->dim[i] = 0;
1364  const std::vector<int> dimVector = object.attr("dim");
1365 
1366  const int nDims = std::min(7, int(dimVector.size()));
1367  image->dim[0] = nDims;
1368  for (int i=0; i<nDims; i++)
1369  image->dim[i+1] = dimVector[i];
1370 
1371  if (object.hasAttribute("pixdim"))
1372  {
1373  const std::vector<float> pixdimVector = object.attr("pixdim");
1374  updatePixdim(pixdimVector);
1375  }
1376 
1377  if (object.hasAttribute("pixunits"))
1378  {
1379  const std::vector<std::string> pixunitsVector = object.attr("pixunits");
1380  setPixunits(pixunitsVector);
1381  }
1382 
1383  // This NIfTI-1 library function clobbers dim[0] if the last dimension is unitary; we undo that here
1384  nifti_update_dims_from_array(image);
1385  image->dim[0] = image->ndim = nDims;
1386 
1387  image->datatype = NiftiImage::sexpTypeToNiftiType(object.sexp_type());
1388  nifti_datatype_sizes(image->datatype, &image->nbyper, NULL);
1389 
1390  if (!persistent)
1391  nifti_image_unload(image);
1392 
1393  const size_t dataSize = nifti_get_volsize(image);
1394  image->data = calloc(1, dataSize);
1395  if (image->datatype == DT_INT32)
1396  memcpy(image->data, INTEGER(object), dataSize);
1397  else
1398  memcpy(image->data, REAL(object), dataSize);
1399 
1400  image->scl_slope = 0.0;
1401  image->scl_inter = 0.0;
1402  }
1403 
1404  return *this;
1405 }
1406 
1407 #endif // USING_R
1408 
1409 inline mat44 NiftiImage::xform (const bool preferQuaternion) const
1410 {
1411  if (image == NULL)
1412  {
1413  mat44 matrix;
1414  for (int i=0; i<4; i++)
1415  {
1416  for (int j=0; j<4; j++)
1417  matrix.m[i][j] = 0.0;
1418  }
1419  return matrix;
1420  }
1421  else if (image->qform_code <= 0 && image->sform_code <= 0)
1422  {
1423  // No qform or sform so use pixdim (NB: other software may assume differently)
1424  mat44 matrix;
1425  for (int i=0; i<4; i++)
1426  {
1427  for (int j=0; j<4; j++)
1428  {
1429  if (i != j)
1430  matrix.m[i][j] = 0.0;
1431  else if (i == 3)
1432  matrix.m[3][3] = 1.0;
1433  else
1434  matrix.m[i][j] = (image->pixdim[i+1]==0.0 ? 1.0 : image->pixdim[i+1]);
1435  }
1436  }
1437  return matrix;
1438  }
1439  else if ((preferQuaternion && image->qform_code > 0) || image->sform_code <= 0)
1440  return image->qto_xyz;
1441  else
1442  return image->sto_xyz;
1443 }
1444 
1445 template <typename TargetType>
1446 inline std::vector<TargetType> NiftiImage::Block::getData () const
1447 {
1448  if (image.isNull())
1449  return std::vector<TargetType>();
1450 
1451  size_t blockSize = 1;
1452  for (int i=1; i<dimension; i++)
1453  blockSize *= image->dim[i];
1454 
1455  std::vector<TargetType> data(blockSize);
1456  internal::convertData<TargetType>(image->data, image->datatype, blockSize, data.begin(), blockSize*index);
1457 
1458  if (image.isDataScaled())
1459  std::transform(data.begin(), data.end(), data.begin(), internal::DataRescaler<TargetType>(image->scl_slope,image->scl_inter));
1460 
1461  return data;
1462 }
1463 
1464 template <typename TargetType>
1465 inline std::vector<TargetType> NiftiImage::getData () const
1466 {
1467  if (this->isNull())
1468  return std::vector<TargetType>();
1469 
1470  std::vector<TargetType> data(image->nvox);
1471  internal::convertData<TargetType>(image->data, image->datatype, image->nvox, data.begin());
1472 
1473  if (this->isDataScaled())
1474  std::transform(data.begin(), data.end(), data.begin(), internal::DataRescaler<TargetType>(image->scl_slope,image->scl_inter));
1475 
1476  return data;
1477 }
1478 
1479 inline NiftiImage & NiftiImage::changeDatatype (const short datatype)
1480 {
1481  if (this->isNull() || image->datatype == datatype)
1482  return *this;
1483 
1484  if (image->data != NULL)
1485  {
1486  int bytesPerPixel;
1487  nifti_datatype_sizes(datatype, &bytesPerPixel, NULL);
1488  void *data = calloc(image->nvox, bytesPerPixel);
1489 
1490  switch (datatype)
1491  {
1492  case DT_UINT8:
1493  internal::convertData<uint8_t>(image->data, image->datatype, image->nvox, static_cast<uint8_t *>(data));
1494  break;
1495 
1496  case DT_INT16:
1497  internal::convertData<int16_t>(image->data, image->datatype, image->nvox, static_cast<int16_t *>(data));
1498  break;
1499 
1500  case DT_INT32:
1501  internal::convertData<int32_t>(image->data, image->datatype, image->nvox, static_cast<int32_t *>(data));
1502  break;
1503 
1504  case DT_FLOAT32:
1505  internal::convertData<float>(image->data, image->datatype, image->nvox, static_cast<float *>(data));
1506  break;
1507 
1508  case DT_FLOAT64:
1509  internal::convertData<double>(image->data, image->datatype, image->nvox, static_cast<double *>(data));
1510  break;
1511 
1512  case DT_INT8:
1513  internal::convertData<int8_t>(image->data, image->datatype, image->nvox, static_cast<int8_t *>(data));
1514  break;
1515 
1516  case DT_UINT16:
1517  internal::convertData<uint16_t>(image->data, image->datatype, image->nvox, static_cast<uint16_t *>(data));
1518  break;
1519 
1520  case DT_UINT32:
1521  internal::convertData<uint32_t>(image->data, image->datatype, image->nvox, static_cast<uint32_t *>(data));
1522  break;
1523 
1524  case DT_INT64:
1525  internal::convertData<int64_t>(image->data, image->datatype, image->nvox, static_cast<int64_t *>(data));
1526  break;
1527 
1528  case DT_UINT64:
1529  internal::convertData<uint64_t>(image->data, image->datatype, image->nvox, static_cast<uint64_t *>(data));
1530  break;
1531 
1532  default:
1533  throw std::runtime_error("Unsupported data type (" + std::string(nifti_datatype_string(datatype)) + ")");
1534  }
1535 
1536  nifti_image_unload(image);
1537  image->data = data;
1538  }
1539 
1540  image->datatype = datatype;
1541  nifti_datatype_sizes(datatype, &image->nbyper, &image->swapsize);
1542 
1543  return *this;
1544 }
1545 
1546 inline NiftiImage & NiftiImage::changeDatatype (const std::string &datatype)
1547 {
1548  return changeDatatype(internal::stringToDatatype(datatype));
1549 }
1550 
1551 template <typename SourceType>
1552 inline NiftiImage & NiftiImage::replaceData (const std::vector<SourceType> &data, const short datatype)
1553 {
1554  if (this->isNull())
1555  return *this;
1556  else if (data.size() != image->nvox)
1557  throw std::runtime_error("New data length does not match the number of voxels in the image");
1558 
1559  if (datatype != DT_NONE)
1560  {
1561  nifti_image_unload(image);
1562  image->datatype = datatype;
1563  nifti_datatype_sizes(datatype, &image->nbyper, &image->swapsize);
1564  }
1565 
1566  if (image->data == NULL)
1567  image->data = calloc(image->nvox, image->nbyper);
1568  internal::replaceData<SourceType>(data.begin(), data.end(), image->data, image->datatype);
1569 
1570  image->scl_slope = 0.0;
1571  image->scl_inter = 0.0;
1572  image->cal_min = static_cast<float>(*std::min_element(data.begin(), data.end()));
1573  image->cal_max = static_cast<float>(*std::max_element(data.begin(), data.end()));
1574 
1575  return *this;
1576 }
1577 
1578 inline void NiftiImage::toFile (const std::string fileName, const short datatype) const
1579 {
1580  // Copy the source image only if the datatype will be changed
1581  NiftiImage imageToWrite(image, datatype != DT_NONE);
1582 
1583  if (datatype == DT_NONE)
1584  imageToWrite.setPersistence(true);
1585  else
1586  imageToWrite.changeDatatype(datatype);
1587 
1588  const int status = nifti_set_filenames(imageToWrite, fileName.c_str(), false, true);
1589  if (status != 0)
1590  throw std::runtime_error("Failed to set filenames for NIfTI object");
1591  nifti_image_write(imageToWrite);
1592 }
1593 
1594 inline void NiftiImage::toFile (const std::string fileName, const std::string &datatype) const
1595 {
1596  toFile(fileName, internal::stringToDatatype(datatype));
1597 }
1598 
1599 #ifdef USING_R
1600 
1601 inline Rcpp::RObject NiftiImage::toArray () const
1602 {
1603  Rcpp::RObject array;
1604 
1605  if (this->isNull())
1606  return array;
1607  else if (this->isDataScaled())
1608  {
1609  array = internal::imageDataToArray<REALSXP>(image);
1610  std::transform(REAL(array), REAL(array)+Rf_length(array), REAL(array), internal::DataRescaler<double>(image->scl_slope,image->scl_inter));
1611  }
1612  else
1613  {
1614  switch (image->datatype)
1615  {
1616  case DT_UINT8:
1617  case DT_INT16:
1618  case DT_INT32:
1619  case DT_INT8:
1620  case DT_UINT16:
1621  case DT_UINT32:
1622  case DT_INT64:
1623  case DT_UINT64:
1624  array = internal::imageDataToArray<INTSXP>(image);
1625  break;
1626 
1627  case DT_FLOAT32:
1628  case DT_FLOAT64:
1629  array = internal::imageDataToArray<REALSXP>(image);
1630  break;
1631 
1632  default:
1633  throw std::runtime_error("Unsupported data type (" + std::string(nifti_datatype_string(image->datatype)) + ")");
1634  }
1635  }
1636 
1637  internal::addAttributes(array, image);
1638  array.attr("class") = Rcpp::CharacterVector::create("niftiImage", "array");
1639  return array;
1640 }
1641 
1642 inline Rcpp::RObject NiftiImage::toPointer (const std::string label) const
1643 {
1644  if (this->isNull())
1645  return Rcpp::RObject();
1646  else
1647  {
1648  Rcpp::RObject string = Rcpp::wrap(label);
1649  internal::addAttributes(string, image, false);
1650  string.attr("class") = Rcpp::CharacterVector::create("internalImage", "niftiImage");
1651  return string;
1652  }
1653 }
1654 
1655 inline Rcpp::RObject NiftiImage::toArrayOrPointer (const bool internal, const std::string label) const
1656 {
1657  return (internal ? toPointer(label) : toArray());
1658 }
1659 
1660 inline Rcpp::RObject NiftiImage::headerToList () const
1661 {
1662  if (this->image == NULL)
1663  return Rcpp::RObject();
1664 
1665  nifti_1_header header = nifti_convert_nim2nhdr(this->image);
1666  Rcpp::List result;
1667 
1668  result["sizeof_hdr"] = header.sizeof_hdr;
1669 
1670  result["dim_info"] = int(header.dim_info);
1671  result["dim"] = std::vector<short>(header.dim, header.dim+8);
1672 
1673  result["intent_p1"] = header.intent_p1;
1674  result["intent_p2"] = header.intent_p2;
1675  result["intent_p3"] = header.intent_p3;
1676  result["intent_code"] = header.intent_code;
1677 
1678  result["datatype"] = header.datatype;
1679  result["bitpix"] = header.bitpix;
1680 
1681  result["slice_start"] = header.slice_start;
1682  result["pixdim"] = std::vector<float>(header.pixdim, header.pixdim+8);
1683  result["vox_offset"] = header.vox_offset;
1684  result["scl_slope"] = header.scl_slope;
1685  result["scl_inter"] = header.scl_inter;
1686  result["slice_end"] = header.slice_end;
1687  result["slice_code"] = int(header.slice_code);
1688  result["xyzt_units"] = int(header.xyzt_units);
1689  result["cal_max"] = header.cal_max;
1690  result["cal_min"] = header.cal_min;
1691  result["slice_duration"] = header.slice_duration;
1692  result["toffset"] = header.toffset;
1693  result["descrip"] = std::string(header.descrip, 80);
1694  result["aux_file"] = std::string(header.aux_file, 24);
1695 
1696  result["qform_code"] = header.qform_code;
1697  result["sform_code"] = header.sform_code;
1698  result["quatern_b"] = header.quatern_b;
1699  result["quatern_c"] = header.quatern_c;
1700  result["quatern_d"] = header.quatern_d;
1701  result["qoffset_x"] = header.qoffset_x;
1702  result["qoffset_y"] = header.qoffset_y;
1703  result["qoffset_z"] = header.qoffset_z;
1704  result["srow_x"] = std::vector<float>(header.srow_x, header.srow_x+4);
1705  result["srow_y"] = std::vector<float>(header.srow_y, header.srow_y+4);
1706  result["srow_z"] = std::vector<float>(header.srow_z, header.srow_z+4);
1707 
1708  result["intent_name"] = std::string(header.intent_name, 16);
1709  result["magic"] = std::string(header.magic, 4);
1710 
1711  result.attr("class") = Rcpp::CharacterVector::create("niftiHeader");
1712 
1713  return result;
1714 }
1715 
1716 #endif // USING_R
1717 
1718 } // namespace
1719 
1720 #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:1135
+
RNifti::NiftiImage::NiftiImage
NiftiImage()
Default constructor.
Definition: NiftiImage.h:256
+
RNifti::NiftiImage::Block::index
const int index
The location along dimension.
Definition: NiftiImage.h:56
+
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:129
+
RNifti::NiftiImage::dim
std::vector< int > dim() const
Return the dimensions of the image.
Definition: NiftiImage.h:442
+
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:364
+
RNifti::NiftiImage::persistent
bool persistent
Marker of persistence, which determines whether the nifti_image should be freed on destruction...
Definition: NiftiImage.h:188
+
RNifti::NiftiImage::pixdim
std::vector< float > pixdim() const
Return the dimensions of the pixels or voxels in the image.
Definition: NiftiImage.h:454
+
RNifti::NiftiImage::NiftiImage
NiftiImage(const std::string &path, const bool readData=true)
Initialise using a path string.
Definition: NiftiImage.h:309
+
RNifti::NiftiImage::rescale
NiftiImage & rescale(const std::vector< float > &scales)
Rescale the image, changing its image dimensions and pixel dimensions.
Definition: NiftiImage.h:1109
+
RNifti::NiftiImage::NiftiImage
NiftiImage(nifti_image *const image, const bool copy=false)
Initialise using an existing nifti_image pointer.
Definition: NiftiImage.h:291
+
RNifti
Definition: NiftiImage.h:39
+
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:80
+
RNifti::NiftiImage::isNull
bool isNull() const
Determine whether or not the internal pointer is NULL.
Definition: NiftiImage.h:415
+
RNifti::NiftiImage::Block
Inner class referring to a subset of an image.
Definition: NiftiImage.h:52
+
RNifti::NiftiImage::slice
Block slice(const int i)
Extract a slice block from a 3D image.
Definition: NiftiImage.h:596
+
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:1552
+
RNifti::NiftiImage::getData
std::vector< TargetType > getData() const
Extract a vector of data from the image, casting it to any required element type. ...
Definition: NiftiImage.h:1465
+
RNifti::NiftiImage::isDataScaled
bool isDataScaled() const
Determine whether nontrivial scale and slope parameters are set.
Definition: NiftiImage.h:425
+
RNifti::NiftiImage::slice
const Block slice(const int i) const
Extract a slice block from a 3D image.
Definition: NiftiImage.h:589
+
RNifti::NiftiImage::volume
const Block volume(const int i) const
Extract a volume block from a 4D image.
Definition: NiftiImage.h:603
+
RNifti::NiftiImage::isPersistent
bool isPersistent() const
Determine whether or not the image is marked as persistent.
Definition: NiftiImage.h:420
+
RNifti::NiftiImage::setPixunits
void setPixunits(const std::vector< std::string > &pixunits)
Modify the pixel dimension units.
Definition: NiftiImage.h:1084
+
RNifti::NiftiImage::NiftiImage
NiftiImage(const Block &source)
Initialise from a block, copying in the data.
Definition: NiftiImage.h:276
+
RNifti::NiftiImage::~NiftiImage
virtual ~NiftiImage()
Destructor which frees the wrapped pointer, unless the object is marked as persistent.
Definition: NiftiImage.h:340
+
RNifti::NiftiImage
Thin wrapper around a C-style nifti_image struct that allows C++-style destruction.
Definition: NiftiImage.h:45
+
RNifti::NiftiImage::NiftiImage
NiftiImage(const NiftiImage &source)
Copy constructor.
Definition: NiftiImage.h:263
+
RNifti::NiftiImage::nBlocks
int nBlocks() const
Return the number of blocks in the image.
Definition: NiftiImage.h:558
+
RNifti::NiftiImage::Block::dimension
const int dimension
The dimension along which the block applies (which should be the last)
Definition: NiftiImage.h:55
+
RNifti::NiftiImage::Block::image
const NiftiImage & image
The parent image.
Definition: NiftiImage.h:54
+
RNifti::NiftiImage::operator=
NiftiImage & operator=(const NiftiImage &source)
Copy assignment operator, which copies from its argument.
Definition: NiftiImage.h:375
+
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:157
+
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:1578
+
RNifti::NiftiImage::updatePixdim
void updatePixdim(const std::vector< float > &pixdim)
Modify the pixel dimensions, and potentially the xform matrices to match.
Definition: NiftiImage.h:1031
+
RNifti::NiftiImage::block
const Block block(const int i) const
Extract a block from the image.
Definition: NiftiImage.h:573
+
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:402
+
RNifti::NiftiImage::copy
void copy(const nifti_image *source)
Copy the contents of a nifti_image to create a new image.
Definition: NiftiImage.h:662
+
RNifti::NiftiImage::xform
mat44 xform(const bool preferQuaternion=true) const
Obtain an xform matrix, indicating the orientation of the image.
Definition: NiftiImage.h:1409
+
RNifti::NiftiImage::image
nifti_image * image
The wrapped nifti_image pointer.
Definition: NiftiImage.h:187
+
RNifti::NiftiImage::changeDatatype
NiftiImage & changeDatatype(const short datatype)
Change the datatype of the image, casting the pixel data if present.
Definition: NiftiImage.h:1479
+
RNifti::NiftiImage::Block::getData
std::vector< TargetType > getData() const
Extract a vector of data from a block, casting it to any required element type.
Definition: NiftiImage.h:1446
+
RNifti::NiftiImage::nDims
int nDims() const
Return the number of dimensions in the image.
Definition: NiftiImage.h:430
+
RNifti::NiftiImage::volume
Block volume(const int i)
Extract a volume block from a 4D image.
Definition: NiftiImage.h:610
+
RNifti::NiftiImage::drop
NiftiImage & drop()
Drop unitary dimensions.
Definition: NiftiImage.h:468
+
RNifti::NiftiImage::Block::Block
Block(const NiftiImage &image, const int dimension, const int index)
Standard constructor for this class.
Definition: NiftiImage.h:65
+
RNifti::NiftiImage::dropData
NiftiImage & dropData()
Drop the data from the image, retaining only the metadata.
Definition: NiftiImage.h:509
+
RNifti::NiftiImage::block
Block block(const int i)
Extract a block from the image.
Definition: NiftiImage.h:582
+
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Fast R and C++ Access to NIfTI Images
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Class List
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Here are the classes, structs, unions and interfaces with brief descriptions:
+
[detail level 123]
+ + + +
 ▼NRNifti
 ▼CNiftiImageThin wrapper around a C-style nifti_image struct that allows C++-style destruction
 CBlockInner class referring to a subset of an image
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+ + diff --git a/inst/doxygen/html/bc_s.png b/inst/doxygen/html/bc_s.png new file mode 100644 index 0000000000000000000000000000000000000000..224b29aa9847d5a4b3902efd602b7ddf7d33e6c2 GIT binary patch literal 676 zcmV;V0$crwP)y__>=_9%My z{n931IS})GlGUF8K#6VIbs%684A^L3@%PlP2>_sk`UWPq@f;rU*V%rPy_ekbhXT&s z(GN{DxFv}*vZp`F>S!r||M`I*nOwwKX+BC~3P5N3-)Y{65c;ywYiAh-1*hZcToLHK ztpl1xomJ+Yb}K(cfbJr2=GNOnT!UFA7Vy~fBz8?J>XHsbZoDad^8PxfSa0GDgENZS zuLCEqzb*xWX2CG*b&5IiO#NzrW*;`VC9455M`o1NBh+(k8~`XCEEoC1Ybwf;vr4K3 zg|EB<07?SOqHp9DhLpS&bzgo70I+ghB_#)K7H%AMU3v}xuyQq9&Bm~++VYhF09a+U zl7>n7Jjm$K#b*FONz~fj;I->Bf;ule1prFN9FovcDGBkpg>)O*-}eLnC{6oZHZ$o% zXKW$;0_{8hxHQ>l;_*HATI(`7t#^{$(zLe}h*mqwOc*nRY9=?Sx4OOeVIfI|0V(V2 zBrW#G7Ss9wvzr@>H*`r>zE z+e8bOBgqIgldUJlG(YUDviMB`9+DH8n-s9SXRLyJHO1!=wY^79WYZMTa(wiZ!zP66 zA~!21vmF3H2{ngD;+`6j#~6j;$*f*G_2ZD1E;9(yaw7d-QnSCpK(cR1zU3qU0000< KMNUMnLSTYoA~SLT literal 0 HcmV?d00001 diff --git a/inst/doxygen/html/bdwn.png b/inst/doxygen/html/bdwn.png new file mode 100644 index 0000000000000000000000000000000000000000..940a0b950443a0bb1b216ac03c45b8a16c955452 GIT binary patch literal 147 zcmeAS@N?(olHy`uVBq!ia0vp^>_E)H!3HEvS)PKZC{Gv1kP61Pb5HX&C2wk~_T + + + + + + +RNifti: Member List + + + + + + + + + +
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Fast R and C++ Access to NIfTI Images
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NiftiImage Member List
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This is the complete list of members for NiftiImage, including all inherited members.

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copy(nifti_image *const source)NiftiImageinlineprotected
copy(const NiftiImage &source)NiftiImageinlineprotected
copy(const Block &source)NiftiImageinlineprotected
drop()NiftiImageinline
headerToList() constNiftiImageinline
imageNiftiImageprotected
initFromArray(const Rcpp::RObject &object, const bool copyData=true)NiftiImageinlineprotected
initFromList(const Rcpp::RObject &object)NiftiImageinlineprotected
initFromMriImage(const Rcpp::RObject &object, const bool copyData=true)NiftiImageinlineprotected
initFromNiftiS4(const Rcpp::RObject &object, const bool copyData=true)NiftiImageinlineprotected
isNull() constNiftiImageinline
isPersistent() constNiftiImageinline
nDims() constNiftiImageinline
NiftiImage()NiftiImageinline
NiftiImage(const NiftiImage &source)NiftiImageinline
NiftiImage(nifti_image *const image, const bool copy=false)NiftiImageinline
NiftiImage(const std::string &path, const bool readData=true)NiftiImageinline
NiftiImage(const SEXP object, const bool readData=true)NiftiImageinline
operator nifti_image *() constNiftiImageinline
operator->() constNiftiImageinline
operator=(const NiftiImage &source)NiftiImageinline
operator=(const Block &source)NiftiImageinline
persistentNiftiImageprotected
rescale(const std::vector< float > &scales)NiftiImageinline
setPersistence(const bool persistent)NiftiImageinline
setPixunits(const std::vector< std::string > &pixunits)NiftiImageinlineprotected
sexpTypeToNiftiType(const int sexpType)NiftiImageinlinestatic
slice(const int i) constNiftiImageinline
slice(const int i)NiftiImageinline
toArray() constNiftiImageinline
toArrayOrPointer(const bool internal, const std::string label) constNiftiImageinline
toFile(const std::string fileName, const short datatype) constNiftiImageinline
toFile(const std::string fileName, const std::string &datatype) constNiftiImageinline
toPointer(const std::string label) constNiftiImageinline
update(const SEXP array)NiftiImageinline
updatePixdim(const std::vector< float > &pixdim)NiftiImageinlineprotected
volume(const int i) constNiftiImageinline
volume(const int i)NiftiImageinline
xform(const bool preferQuaternion=true) constNiftiImageinline
~NiftiImage()NiftiImageinline
+ +
+Generated by   +doxygen + 1.8.12 +
+ + diff --git a/inst/doxygen/html/class_nifti_image.html b/inst/doxygen/html/class_nifti_image.html new file mode 100644 index 0000000..9adaf4d --- /dev/null +++ b/inst/doxygen/html/class_nifti_image.html @@ -0,0 +1,1399 @@ + + + + + + + +RNifti: NiftiImage Class Reference + + + + + + + + + +
+
+ + + + + + +
+
RNifti +
+
Fast R and C++ Access to NIfTI Images
+
+
+ + + + + + + + +
+
+ + +
+ +
+ +
+
+
+Classes | +Public Member Functions | +Static Public Member Functions | +Protected Member Functions | +Protected Attributes | +List of all members
+
+
NiftiImage Class Reference
+
+
+ +

Thin wrapper around a C-style nifti_image struct that allows C++-style destruction. + More...

+ +

#include <NiftiImage.h>

+ + + + + +

+Classes

struct  Block
 Inner class referring to a subset of an image. More...
 
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+Public Member Functions

+ NiftiImage ()
 Default constructor.
 
 NiftiImage (const NiftiImage &source)
 Copy constructor. More...
 
 NiftiImage (nifti_image *const image, const bool copy=false)
 Initialise using an existing nifti_image pointer. More...
 
 NiftiImage (const std::string &path, const bool readData=true)
 Initialise using a path string. More...
 
 NiftiImage (const SEXP object, const bool readData=true)
 Initialise from an R object. More...
 
+ ~NiftiImage ()
 Destructor which frees the wrapped pointer, unless the object is marked as persistent.
 
+ operator nifti_image * () const
 Allows a NiftiImage object to be treated as a pointer to a nifti_image.
 
+nifti_image * operator-> () const
 Allows a NiftiImage object to be treated as a pointer to a nifti_image.
 
NiftiImage & operator= (const NiftiImage &source)
 Copy assignment operator, which copies from its argument. More...
 
NiftiImage & operator= (const Block &source)
 Copy assignment operator, which allows a block to be used to replace the contents of a suitably sized image. More...
 
void setPersistence (const bool persistent)
 Allows the image to be marked as persistent, so that it can be passed back to R. More...
 
+bool isNull () const
 Determines whether or not the internal pointer is NULL.
 
+bool isPersistent () const
 Determines whether or not the image is marked as persistent.
 
+int nDims () const
 Returns the number of dimensions in the image.
 
NiftiImage & drop ()
 Drop unitary dimensions. More...
 
void rescale (const std::vector< float > &scales)
 Rescales the image, changing its image dimensions and pixel dimensions. More...
 
void update (const SEXP array)
 Update the image from an R array. More...
 
mat44 xform (const bool preferQuaternion=true) const
 Obtain an xform matrix, indicating the orientation of the image. More...
 
const Block slice (const int i) const
 Extract a slice block from a 3D image. More...
 
Block slice (const int i)
 Extract a slice block from a 3D image. More...
 
const Block volume (const int i) const
 Extract a volume block from a 4D image. More...
 
Block volume (const int i)
 Extract a volume block from a 4D image. More...
 
void toFile (const std::string fileName, const short datatype) const
 Write the image to a NIfTI-1 file. More...
 
void toFile (const std::string fileName, const std::string &datatype) const
 Write the image to a NIfTI-1 file. More...
 
Rcpp::RObject toArray () const
 Create an R array from the image. More...
 
Rcpp::RObject toPointer (const std::string label) const
 Create an internal image to pass back to R. More...
 
Rcpp::RObject toArrayOrPointer (const bool internal, const std::string label) const
 A conditional method that calls either toArray or toPointer. More...
 
Rcpp::RObject headerToList () const
 Create an R list containing raw image metadata. More...
 
+ + + + +

+Static Public Member Functions

static short sexpTypeToNiftiType (const int sexpType)
 Convert between R SEXP object type and nifti_image datatype codes. More...
 
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+Protected Member Functions

void copy (nifti_image *const source)
 Copy the contents of a nifti_image to create a new image. More...
 
void copy (const NiftiImage &source)
 Copy the contents of another NiftiImage to create a new image. More...
 
void copy (const Block &source)
 Copy the contents of a Block to create a new image. More...
 
void initFromNiftiS4 (const Rcpp::RObject &object, const bool copyData=true)
 Initialise the object from an S4 object of class "nifti". More...
 
void initFromMriImage (const Rcpp::RObject &object, const bool copyData=true)
 Initialise the object from a reference object of class "MriImage". More...
 
void initFromList (const Rcpp::RObject &object)
 Initialise the object from an R list with named elements, which can only contain metadata. More...
 
void initFromArray (const Rcpp::RObject &object, const bool copyData=true)
 Initialise the object from an R array. More...
 
void updatePixdim (const std::vector< float > &pixdim)
 Modify the pixel dimensions, and potentially the xform matrices to match. More...
 
void setPixunits (const std::vector< std::string > &pixunits)
 Modify the pixel dimension units. More...
 
+ + + + + + + +

+Protected Attributes

+nifti_image * image
 The wrapped nifti_image pointer.
 
+bool persistent
 Marker of persistence, which determines whether the nifti_image should be freed on destruction.
 
+

Detailed Description

+

Thin wrapper around a C-style nifti_image struct that allows C++-style destruction.

+
Author
Jon Clayden
+

Constructor & Destructor Documentation

+ +

§ NiftiImage() [1/4]

+ +
+
+ + + + + +
+ + + + + + + + +
NiftiImage::NiftiImage (const NiftiImage & source)
+ 		+inline
+
+ +

Copy constructor.

+
Parameters
+ + +
sourceAnother NiftiImage object
+
+
+ +
+
+ +

§ NiftiImage() [2/4]

+ +
+
+ + + + + +
+ + + + + + + + + + + + + + + + + + +
NiftiImage::NiftiImage (nifti_image *const image,
const bool copy = false 
)
+ 		+inline
+
+ +

Initialise using an existing nifti_image pointer.

+
Parameters
+ + + +
imageAn existing nifti_image pointer, possibly NULL
copyIf true, the image data will be copied; otherwise this object just wraps the pointer passed to it
+
+
+ +
+
+ +

§ NiftiImage() [3/4]

+ +
+
+ + + + + +
+ + + + + + + + + + + + + + + + + + +
NiftiImage::NiftiImage (const std::string & path,
const bool readData = true 
)
+ 		+inline
+
+ +

Initialise using a path string.

+
Parameters
+ + + +
pathA string specifying a path to a valid NIfTI-1 file, possibly gzipped
readDataIf true, the data will be read as well as the metadata
+
+
+
Exceptions
+ + +
runtime_errorIf reading from the file fails
+
+
+ +
+
+ +

§ NiftiImage() [4/4]

+ +
+
+ + + + + +
+ + + + + + + + + + + + + + + + + + +
NiftiImage::NiftiImage (const SEXP object,
const bool readData = true 
)
+ 		+inline
+
+ +

Initialise from an R object.

+
Parameters
+ + + +
objectThe source object
readDataIf true, the data will be copied as well as the metadata
+
+
+ +
+
+

Member Function Documentation

+ +

§ copy() [1/3]

+ +
+
+ + + + + +
+ + + + + + + + +
void NiftiImage::copy (nifti_image *const source)
+ 		+inlineprotected
+
+ +

Copy the contents of a nifti_image to create a new image.

+
Parameters
+ + +
sourceA pointer to a nifti_image
+
+
+ +
+
+ +

§ copy() [2/3]

+ +
+
+ + + + + +
+ + + + + + + + +
void NiftiImage::copy (const NiftiImage & source)
+ 		+inlineprotected
+
+ +

Copy the contents of another NiftiImage to create a new image.

+
Parameters
+ + +
sourceA reference to a NiftiImage
+
+
+ +
+
+ +

§ copy() [3/3]

+ +
+
+ + + + + +
+ + + + + + + + +
void NiftiImage::copy (const Block & source)
+ 		+inlineprotected
+
+ +

Copy the contents of a Block to create a new image.

+
Parameters
+ + +
sourceA reference to a Block
+
+
+ +
+
+ +

§ drop()

+ +
+
+ + + + + +
+ + + + + + + +
NiftiImage& NiftiImage::drop ()
+ 		+inline
+
+ +

Drop unitary dimensions.

+
Returns
Self, after possibly reducing the dimensionality of the image
+
Note
This function differs from its R equivalent in only dropping unitary dimensions after the last nonunitary one
+ +
+
+ +

§ headerToList()

+ +
+
+ + + + + +
+ + + + + + + +
Rcpp::RObject NiftiImage::headerToList () const
+ 		+inline
+
+ +

Create an R list containing raw image metadata.

+
Returns
An R list
+ +
+
+ +

§ initFromArray()

+ +
+
+ + + + + +
+ + + + + + + + + + + + + + + + + + +
void NiftiImage::initFromArray (const Rcpp::RObject & object,
const bool copyData = true 
)
+ 		+inlineprotected
+
+ +

Initialise the object from an R array.

+
Parameters
+ + + +
objectThe source object
copyDataIf true, the data are copied in; otherwise just the metadata is extracted
+
+
+ +
+
+ +

§ initFromList()

+ +
+
+ + + + + +
+ + + + + + + + +
void NiftiImage::initFromList (const Rcpp::RObject & object)
+ 		+inlineprotected
+
+ +

Initialise the object from an R list with named elements, which can only contain metadata.

+
Parameters
+ + +
objectThe source object
+
+
+ +
+
+ +

§ initFromMriImage()

+ +
+
+ + + + + +
+ + + + + + + + + + + + + + + + + + +
void NiftiImage::initFromMriImage (const Rcpp::RObject & object,
const bool copyData = true 
)
+ 		+inlineprotected
+
+ +

Initialise the object from a reference object of class "MriImage".

+
Parameters
+ + + +
objectThe source object
copyDataIf true, the data are copied in; otherwise just the metadata is extracted
+
+
+ +
+
+ +

§ initFromNiftiS4()

+ +
+
+ + + + + +
+ + + + + + + + + + + + + + + + + + +
void NiftiImage::initFromNiftiS4 (const Rcpp::RObject & object,
const bool copyData = true 
)
+ 		+inlineprotected
+
+ +

Initialise the object from an S4 object of class "nifti".

+
Parameters
+ + + +
objectThe source object
copyDataIf true, the data are copied in; otherwise just the metadata is extracted
+
+
+ +
+
+ +

§ operator=() [1/2]

+ +
+
+ + + + + +
+ + + + + + + + +
NiftiImage& NiftiImage::operator= (const NiftiImage & source)
+ 		+inline
+
+ +

Copy assignment operator, which copies from its argument.

+
Parameters
+ + +
sourceAnother NiftiImage
+
+
+ +
+
+ +

§ operator=() [2/2]

+ +
+
+ + + + + +
+ + + + + + + + +
NiftiImage& NiftiImage::operator= (const Block & source)
+ 		+inline
+
+ +

Copy assignment operator, which allows a block to be used to replace the contents of a suitably sized image.

+
Parameters
+ + +
sourceA reference to a suitable Block object
+
+
+ +
+
+ +

§ rescale()

+ +
+
+ + + + + +
+ + + + + + + + +
void NiftiImage::rescale (const std::vector< float > & scales)
+ 		+inline
+
+ +

Rescales the image, changing its image dimensions and pixel dimensions.

+
Parameters
+ + +
scalesVector of scale factors along each dimension
+
+
+
Note
No interpolation is performed on the pixel data, which is simply dropped
+ +
+
+ +

§ setPersistence()

+ +
+
+ + + + + +
+ + + + + + + + +
void NiftiImage::setPersistence (const bool persistent)
+ 		+inline
+
+ +

Allows the image to be marked as persistent, so that it can be passed back to R.

+
Parameters
+ + +
persistentThe new persistence state of the object
+
+
+ +
+
+ +

§ setPixunits()

+ +
+
+ + + + + +
+ + + + + + + + +
void NiftiImage::setPixunits (const std::vector< std::string > & pixunits)
+ 		+inlineprotected
+
+ +

Modify the pixel dimension units.

+
Parameters
+ + +
pixunitsVector of new pixel units, specified using their standard abbreviations
+
+
+ +
+
+ +

§ sexpTypeToNiftiType()

+ +
+
+ + + + + +
+ + + + + + + + +
static short NiftiImage::sexpTypeToNiftiType (const int sexpType)
+ 		+inlinestatic
+
+ +

Convert between R SEXP object type and nifti_image datatype codes.

+
Parameters
+ + +
sexpTypeA numeric R SEXP type code
+
+
+
Returns
A nifti_image datatype code
+
Exceptions
+ + +
runtime_errorIf a non-numeric type is passed
+
+
+ +
+
+ +

§ slice() [1/2]

+ +
+
+ + + + + +
+ + + + + + + + +
const Block NiftiImage::slice (const int i) const
+ 		+inline
+
+ +

Extract a slice block from a 3D image.

+
Parameters
+ + +
iThe slice number required
+
+
+
Returns
A Block object
+ +
+
+ +

§ slice() [2/2]

+ +
+
+ + + + + +
+ + + + + + + + +
Block NiftiImage::slice (const int i)
+ 		+inline
+
+ +

Extract a slice block from a 3D image.

+
Parameters
+ + +
iThe slice number required
+
+
+
Returns
A Block object
+ +
+
+ +

§ toArray()

+ +
+
+ + + + + +
+ + + + + + + +
Rcpp::RObject NiftiImage::toArray () const
+ 		+inline
+
+ +

Create an R array from the image.

+
Returns
A numeric array object with an external pointer attribute
+ +
+
+ +

§ toArrayOrPointer()

+ +
+
+ + + + + +
+ + + + + + + + + + + + + + + + + + +
Rcpp::RObject NiftiImage::toArrayOrPointer (const bool internal,
const std::string label 
) const
+ 		+inline
+
+ +

A conditional method that calls either toArray or toPointer.

+
Parameters
+ + + +
internalIf true, toPointer will be called; otherwise toArray
labelA string labelling the image
+
+
+
Returns
An R object
+ +
+
+ +

§ toFile() [1/2]

+ +
+
+ + + + + +
+ + + + + + + + + + + + + + + + + + +
void NiftiImage::toFile (const std::string fileName,
const short datatype 
) const
+ 		+inline
+
+ +

Write the image to a NIfTI-1 file.

+
Parameters
+ + + +
fileNameThe file name to write to, with appropriate suffix (e.g. ".nii.gz")
datatypeThe datatype to use when writing the file
+
+
+ +
+
+ +

§ toFile() [2/2]

+ +
+
+ + + + + +
+ + + + + + + + + + + + + + + + + + +
void NiftiImage::toFile (const std::string fileName,
const std::string & datatype 
) const
+ 		+inline
+
+ +

Write the image to a NIfTI-1 file.

+
Parameters
+ + + +
fileNameThe file name to write to, with appropriate suffix (e.g. ".nii.gz")
datatypeThe datatype to use when writing the file, or "auto"
+
+
+ +
+
+ +

§ toPointer()

+ +
+
+ + + + + +
+ + + + + + + + +
Rcpp::RObject NiftiImage::toPointer (const std::string label) const
+ 		+inline
+
+ +

Create an internal image to pass back to R.

+
Parameters
+ + +
labelA string labelling the image
+
+
+
Returns
An R character string with additional attributes
+ +
+
+ +

§ update()

+ +
+
+ + + + + +
+ + + + + + + + +
void NiftiImage::update (const SEXP array)
+ 		+inline
+
+ +

Update the image from an R array.

+
Parameters
+ + +
arrayAn R array object
+
+
+ +
+
+ +

§ updatePixdim()

+ +
+
+ + + + + +
+ + + + + + + + +
void NiftiImage::updatePixdim (const std::vector< float > & pixdim)
+ 		+inlineprotected
+
+ +

Modify the pixel dimensions, and potentially the xform matrices to match.

+
Parameters
+ + +
pixdimVector of new pixel dimensions
+
+
+ +
+
+ +

§ volume() [1/2]

+ +
+
+ + + + + +
+ + + + + + + + +
const Block NiftiImage::volume (const int i) const
+ 		+inline
+
+ +

Extract a volume block from a 4D image.

+
Parameters
+ + +
iThe volume number required
+
+
+
Returns
A Block object
+ +
+
+ +

§ volume() [2/2]

+ +
+
+ + + + + +
+ + + + + + + + +
Block NiftiImage::volume (const int i)
+ 		+inline
+
+ +

Extract a volume block from a 4D image.

+
Parameters
+ + +
iThe volume number required
+
+
+
Returns
A Block object
+ +
+
+ +

§ xform()

+ +
+
+ + + + + +
+ + + + + + + + +
mat44 NiftiImage::xform (const bool preferQuaternion = true) const
+ 		+inline
+
+ +

Obtain an xform matrix, indicating the orientation of the image.

+
Parameters
+ + +
preferQuaternionIf true, use the qform matrix in preference to the sform
+
+
+
Returns
A 4x4 matrix
+ +
+
+
The documentation for this class was generated from the following file: +
+ +
+Generated by   +doxygen + 1.8.12 +
+ + diff --git a/inst/doxygen/html/class_r_nifti_1_1_nifti_image-members.html b/inst/doxygen/html/class_r_nifti_1_1_nifti_image-members.html new file mode 100644 index 0000000..397b961 --- /dev/null +++ b/inst/doxygen/html/class_r_nifti_1_1_nifti_image-members.html @@ -0,0 +1,132 @@ + + + + + + + +RNifti: Member List + + + + + + + + + +
+
+ + + + + + +
+
RNifti +
+
Fast R and C++ Access to NIfTI Images
+
+
+ + + + + + + + +
+
+ + +
+ +
+ + +
+
+
+
RNifti::NiftiImage Member List
+
+
+ +

This is the complete list of members for RNifti::NiftiImage, including all inherited members.

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
block(const int i) constRNifti::NiftiImageinline
block(const int i)RNifti::NiftiImageinline
changeDatatype(const short datatype)RNifti::NiftiImageinline
changeDatatype(const std::string &datatype)RNifti::NiftiImageinline
copy(const nifti_image *source)RNifti::NiftiImageinlineprotected
copy(const NiftiImage &source)RNifti::NiftiImageinlineprotected
copy(const Block &source)RNifti::NiftiImageinlineprotected
dim() constRNifti::NiftiImageinline
drop()RNifti::NiftiImageinline
dropData()RNifti::NiftiImageinline
fileVersion(const std::string &path)RNifti::NiftiImageinlinestatic
getData() constRNifti::NiftiImageinline
imageRNifti::NiftiImageprotected
isDataScaled() constRNifti::NiftiImageinline
isNull() constRNifti::NiftiImageinline
isPersistent() constRNifti::NiftiImageinline
nBlocks() constRNifti::NiftiImageinline
nDims() constRNifti::NiftiImageinline
NiftiImage()RNifti::NiftiImageinline
NiftiImage(const NiftiImage &source)RNifti::NiftiImageinline
NiftiImage(const Block &source)RNifti::NiftiImageinline
NiftiImage(nifti_image *const image, const bool copy=false)RNifti::NiftiImageinline
NiftiImage(const std::string &path, const bool readData=true)RNifti::NiftiImageinline
NiftiImage(const std::string &path, const std::vector< int > &volumes)RNifti::NiftiImageinline
operator const nifti_image *() constRNifti::NiftiImageinline
operator nifti_image *()RNifti::NiftiImageinline
operator->() constRNifti::NiftiImageinline
operator->()RNifti::NiftiImageinline
operator=(const NiftiImage &source)RNifti::NiftiImageinline
operator=(const Block &source)RNifti::NiftiImageinline
persistentRNifti::NiftiImageprotected
pixdim() constRNifti::NiftiImageinline
reorient(const int i, const int j, const int k)RNifti::NiftiImageinline
reorient(const std::string &orientation)RNifti::NiftiImageinline
replaceData(const std::vector< SourceType > &data, const short datatype=DT_NONE)RNifti::NiftiImageinline
rescale(const std::vector< float > &scales)RNifti::NiftiImageinline
setPersistence(const bool persistent)RNifti::NiftiImageinline
setPixunits(const std::vector< std::string > &pixunits)RNifti::NiftiImageinlineprotected
slice(const int i) constRNifti::NiftiImageinline
slice(const int i)RNifti::NiftiImageinline
toFile(const std::string fileName, const short datatype=DT_NONE) constRNifti::NiftiImageinline
toFile(const std::string fileName, const std::string &datatype) constRNifti::NiftiImageinline
updatePixdim(const std::vector< float > &pixdim)RNifti::NiftiImageinlineprotected
volume(const int i) constRNifti::NiftiImageinline
volume(const int i)RNifti::NiftiImageinline
xform(const bool preferQuaternion=true) constRNifti::NiftiImageinline
xformToString(const mat44 matrix)RNifti::NiftiImageinlinestatic
~NiftiImage()RNifti::NiftiImageinlinevirtual
+ +
+Generated by   +doxygen + 1.8.14 +
+ + diff --git a/inst/doxygen/html/class_r_nifti_1_1_nifti_image.html b/inst/doxygen/html/class_r_nifti_1_1_nifti_image.html new file mode 100644 index 0000000..e1ae3df --- /dev/null +++ b/inst/doxygen/html/class_r_nifti_1_1_nifti_image.html @@ -0,0 +1,1496 @@ + + + + + + + +RNifti: RNifti::NiftiImage Class Reference + + + + + + + + + +
+
+ + + + + + +
+
RNifti +
+
Fast R and C++ Access to NIfTI Images
+
+
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+ +
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+
+Classes | +Public Member Functions | +Static Public Member Functions | +Protected Member Functions | +Protected Attributes | +List of all members
+
+
RNifti::NiftiImage Class Reference
+
+
+ +

Thin wrapper around a C-style nifti_image struct that allows C++-style destruction. + More...

+ +

#include <NiftiImage.h>

+ + + + + +

+Classes

struct  Block
 Inner class referring to a subset of an image. More...
 
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+Public Member Functions

+ NiftiImage ()
 Default constructor.
 
 NiftiImage (const NiftiImage &source)
 Copy constructor. More...
 
 NiftiImage (const Block &source)
 Initialise from a block, copying in the data. More...
 
 NiftiImage (nifti_image *const image, const bool copy=false)
 Initialise using an existing nifti_image pointer. More...
 
 NiftiImage (const std::string &path, const bool readData=true)
 Initialise using a path string. More...
 
 NiftiImage (const std::string &path, const std::vector< int > &volumes)
 Initialise using a path string and sequence of required volumes. More...
 
+virtual ~NiftiImage ()
 Destructor which frees the wrapped pointer, unless the object is marked as persistent.
 
+ operator const nifti_image * () const
 Allows a NiftiImage object to be treated as a pointer to a const nifti_image.
 
+ operator nifti_image * ()
 Allows a NiftiImage object to be treated as a pointer to a nifti_image.
 
+const nifti_image * operator-> () const
 Allows a NiftiImage object to be treated as a pointer to a const nifti_image.
 
+nifti_image * operator-> ()
 Allows a NiftiImage object to be treated as a pointer to a nifti_image.
 
NiftiImage & operator= (const NiftiImage &source)
 Copy assignment operator, which copies from its argument. More...
 
NiftiImage & operator= (const Block &source)
 Copy assignment operator, which allows a block to be used to replace the contents of a suitably sized image. More...
 
NiftiImage & setPersistence (const bool persistent)
 Marked the image as persistent, so that it can be passed back to R. More...
 
+bool isNull () const
 Determine whether or not the internal pointer is NULL.
 
+bool isPersistent () const
 Determine whether or not the image is marked as persistent.
 
+bool isDataScaled () const
 Determine whether nontrivial scale and slope parameters are set.
 
+int nDims () const
 Return the number of dimensions in the image.
 
std::vector< int > dim () const
 Return the dimensions of the image. More...
 
std::vector< float > pixdim () const
 Return the dimensions of the pixels or voxels in the image. More...
 
NiftiImage & drop ()
 Drop unitary dimensions. More...
 
+template<typename TargetType >
std::vector< TargetType > getData () const
 Extract a vector of data from the image, casting it to any required element type.
 
NiftiImage & changeDatatype (const short datatype)
 Change the datatype of the image, casting the pixel data if present. More...
 
NiftiImage & changeDatatype (const std::string &datatype)
 Change the datatype of the image, casting the pixel data if present. More...
 
template<typename SourceType >
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. More...
 
+NiftiImage & dropData ()
 Drop the data from the image, retaining only the metadata.
 
NiftiImage & rescale (const std::vector< float > &scales)
 Rescale the image, changing its image dimensions and pixel dimensions. More...
 
NiftiImage & reorient (const int i, const int j, const int k)
 Reorient the image by permuting dimensions and potentially reversing some. More...
 
NiftiImage & reorient (const std::string &orientation)
 Reorient the image by permuting dimensions and potentially reversing some. More...
 
mat44 xform (const bool preferQuaternion=true) const
 Obtain an xform matrix, indicating the orientation of the image. More...
 
+int nBlocks () const
 Return the number of blocks in the image.
 
const Block block (const int i) const
 Extract a block from the image. More...
 
Block block (const int i)
 Extract a block from the image. More...
 
const Block slice (const int i) const
 Extract a slice block from a 3D image. More...
 
Block slice (const int i)
 Extract a slice block from a 3D image. More...
 
const Block volume (const int i) const
 Extract a volume block from a 4D image. More...
 
Block volume (const int i)
 Extract a volume block from a 4D image. More...
 
void toFile (const std::string fileName, const short datatype=DT_NONE) const
 Write the image to a NIfTI-1 file. More...
 
void toFile (const std::string fileName, const std::string &datatype) const
 Write the image to a NIfTI-1 file. More...
 
+ + + + + + + +

+Static Public Member Functions

static std::string xformToString (const mat44 matrix)
 Convert a 4x4 xform matrix to a string describing its canonical axes. More...
 
static int fileVersion (const std::string &path)
 Get the NIfTI format version used by the file at the specified path. More...
 
+ + + + + + + + + + + + + + + + +

+Protected Member Functions

void copy (const nifti_image *source)
 Copy the contents of a nifti_image to create a new image. More...
 
void copy (const NiftiImage &source)
 Copy the contents of another NiftiImage to create a new image. More...
 
void copy (const Block &source)
 Copy the contents of a Block to create a new image. More...
 
void updatePixdim (const std::vector< float > &pixdim)
 Modify the pixel dimensions, and potentially the xform matrices to match. More...
 
void setPixunits (const std::vector< std::string > &pixunits)
 Modify the pixel dimension units. More...
 
+ + + + + + + +

+Protected Attributes

+nifti_image * image
 The wrapped nifti_image pointer.
 
+bool persistent
 Marker of persistence, which determines whether the nifti_image should be freed on destruction.
 
+

Detailed Description

+

Thin wrapper around a C-style nifti_image struct that allows C++-style destruction.

+
Author
Jon Clayden
+

Constructor & Destructor Documentation

+ +

◆ NiftiImage() [1/5]

+ +
+
+ + + + + +
+ + + + + + + + +
RNifti::NiftiImage::NiftiImage (const NiftiImage & source)
+ 		+inline
+
+ +

Copy constructor.

+
Parameters
+ + +
sourceAnother NiftiImage object
+
+
+ +
+
+ +

◆ NiftiImage() [2/5]

+ +
+
+ + + + + +
+ + + + + + + + +
RNifti::NiftiImage::NiftiImage (const Block & source)
+ 		+inline
+
+ +

Initialise from a block, copying in the data.

+
Parameters
+ + +
sourceA Block object, referring to part of another NiftiImage
+
+
+ +
+
+ +

◆ NiftiImage() [3/5]

+ +
+
+ + + + + +
+ + + + + + + + + + + + + + + + + + +
RNifti::NiftiImage::NiftiImage (nifti_image *const image,
const bool copy = false 
)
+ 		+inline
+
+ +

Initialise using an existing nifti_image pointer.

+
Parameters
+ + + +
imageAn existing nifti_image pointer, possibly NULL
copyIf true, the image data will be copied; otherwise this object just wraps the pointer passed to it
+
+
+ +
+
+ +

◆ NiftiImage() [4/5]

+ +
+
+ + + + + +
+ + + + + + + + + + + + + + + + + + +
RNifti::NiftiImage::NiftiImage (const std::string & path,
const bool readData = true 
)
+ 		+inline
+
+ +

Initialise using a path string.

+
Parameters
+ + + +
pathA string specifying a path to a valid NIfTI-1 file, possibly gzipped
readDataIf true, the data will be read as well as the metadata
+
+
+
Exceptions
+ + +
runtime_errorIf reading from the file fails
+
+
+ +
+
+ +

◆ NiftiImage() [5/5]

+ +
+
+ + + + + +
+ + + + + + + + + + + + + + + + + + +
RNifti::NiftiImage::NiftiImage (const std::string & path,
const std::vector< int > & volumes 
)
+ 		+inline
+
+ +

Initialise using a path string and sequence of required volumes.

+
Parameters
+ + + +
pathA string specifying a path to a valid NIfTI-1 file, possibly gzipped
volumesThe volumes to read in (squashing all dimensions above the third together)
+
+
+
Exceptions
+ + +
runtime_errorIf reading from the file fails, or volumes is empty
+
+
+ +
+
+

Member Function Documentation

+ +

◆ block() [1/2]

+ +
+
+ + + + + +
+ + + + + + + + +
const Block RNifti::NiftiImage::block (const int i) const
+ 		+inline
+
+ +

Extract a block from the image.

+
Parameters
+ + +
iThe block number required
+
+
+
Returns
A Block object
+
Note
slice and volume are variants of this function specific to 3D and 4D images, respectively, which may be preferred in some cases for clarity
+ +
+
+ +

◆ block() [2/2]

+ +
+
+ + + + + +
+ + + + + + + + +
Block RNifti::NiftiImage::block (const int i)
+ 		+inline
+
+ +

Extract a block from the image.

+
Parameters
+ + +
iThe block number required
+
+
+
Returns
A Block object
+
Note
slice and volume are variants of this function specific to 3D and 4D images, respectively, which may be preferred in some cases for clarity
+ +
+
+ +

◆ changeDatatype() [1/2]

+ +
+
+ + + + + +
+ + + + + + + + +
NiftiImage & RNifti::NiftiImage::changeDatatype (const short datatype)
+ 		+inline
+
+ +

Change the datatype of the image, casting the pixel data if present.

+
Parameters
+ + +
datatypeA NIfTI datatype code
+
+
+ +
+
+ +

◆ changeDatatype() [2/2]

+ +
+
+ + + + + +
+ + + + + + + + +
NiftiImage & RNifti::NiftiImage::changeDatatype (const std::string & datatype)
+ 		+inline
+
+ +

Change the datatype of the image, casting the pixel data if present.

+
Parameters
+ + +
datatypeA string specifying the new datatype
+
+
+ +
+
+ +

◆ copy() [1/3]

+ +
+
+ + + + + +
+ + + + + + + + +
void RNifti::NiftiImage::copy (const nifti_image * source)
+ 		+inlineprotected
+
+ +

Copy the contents of a nifti_image to create a new image.

+
Parameters
+ + +
sourceA pointer to a nifti_image
+
+
+ +
+
+ +

◆ copy() [2/3]

+ +
+
+ + + + + +
+ + + + + + + + +
void RNifti::NiftiImage::copy (const NiftiImage & source)
+ 		+inlineprotected
+
+ +

Copy the contents of another NiftiImage to create a new image.

+
Parameters
+ + +
sourceA reference to a NiftiImage
+
+
+ +
+
+ +

◆ copy() [3/3]

+ +
+
+ + + + + +
+ + + + + + + + +
void RNifti::NiftiImage::copy (const Block & source)
+ 		+inlineprotected
+
+ +

Copy the contents of a Block to create a new image.

+
Parameters
+ + +
sourceA reference to a Block
+
+
+ +
+
+ +

◆ dim()

+ +
+
+ + + + + +
+ + + + + + + +
std::vector<int> RNifti::NiftiImage::dim () const
+ 		+inline
+
+ +

Return the dimensions of the image.

+
Returns
A vector of integers giving the width in each dimension
+ +
+
+ +

◆ drop()

+ +
+
+ + + + + +
+ + + + + + + +
NiftiImage& RNifti::NiftiImage::drop ()
+ 		+inline
+
+ +

Drop unitary dimensions.

+
Returns
Self, after possibly reducing the dimensionality of the image
+
Note
This function differs from its R equivalent in only dropping unitary dimensions after the last nonunitary one
+ +
+
+ +

◆ fileVersion()

+ +
+
+ + + + + +
+ + + + + + + + +
static int RNifti::NiftiImage::fileVersion (const std::string & path)
+ 		+inlinestatic
+
+ +

Get the NIfTI format version used by the file at the specified path.

+
Parameters
+ + +
pathA string specifying a file path
+
+
+
Returns
An integer: -1 if the file is not present or not valid, 0 for ANALYZE-7.5, or a value greater than 0 for NIfTI
+ +
+
+ +

◆ operator=() [1/2]

+ +
+
+ + + + + +
+ + + + + + + + +
NiftiImage& RNifti::NiftiImage::operator= (const NiftiImage & source)
+ 		+inline
+
+ +

Copy assignment operator, which copies from its argument.

+
Parameters
+ + +
sourceAnother NiftiImage
+
+
+ +
+
+ +

◆ operator=() [2/2]

+ +
+
+ + + + + +
+ + + + + + + + +
NiftiImage& RNifti::NiftiImage::operator= (const Block & source)
+ 		+inline
+
+ +

Copy assignment operator, which allows a block to be used to replace the contents of a suitably sized image.

+
Parameters
+ + +
sourceA reference to a suitable Block object
+
+
+ +
+
+ +

◆ pixdim()

+ +
+
+ + + + + +
+ + + + + + + +
std::vector<float> RNifti::NiftiImage::pixdim () const
+ 		+inline
+
+ +

Return the dimensions of the pixels or voxels in the image.

+
Returns
A vector of floating-point values giving the pixel width in each dimension
+ +
+
+ +

◆ reorient() [1/2]

+ +
+
+ + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + +
NiftiImage & RNifti::NiftiImage::reorient (const int i,
const int j,
const int k 
)
+ 		+inline
+
+ +

Reorient the image by permuting dimensions and potentially reversing some.

+
Parameters
+ + +
i,j,kConstants such as NIFTI_L2R, NIFTI_P2A and NIFTI_I2S, giving the canonical axes to reorient to
+
+
+
Note
The pixel data is reordered, but not resampled. The xform matrices will also be adjusted in line with the transformation
+ +
+
+ +

◆ reorient() [2/2]

+ +
+
+ + + + + +
+ + + + + + + + +
NiftiImage & RNifti::NiftiImage::reorient (const std::string & orientation)
+ 		+inline
+
+ +

Reorient the image by permuting dimensions and potentially reversing some.

+
Parameters
+ + +
orientationA string containing some permutation of the letters L or R, P or A, I or S, giving the canonical axes to reorient to
+
+
+
Note
The pixel data is reordered, but not resampled. The xform matrices will also be adjusted in line with the transformation
+ +
+
+ +

◆ replaceData()

+ +
+
+
+template<typename SourceType >
+ + + + + +
+ + + + + + + + + + + + + + + + + + +
NiftiImage & RNifti::NiftiImage::replaceData (const std::vector< SourceType > & data,
const short datatype = DT_NONE 
)
+ 		+inline
+
+ +

Replace the pixel data in the image with the contents of a vector.

+
Parameters
+ + + +
dataA data vector, whose elements will be cast to match the datatype of the image. An exception will be raised if this does not have a length matching the image
datatypeThe final datatype required. By default the existing datatype of the image is used
+
+
+ +
+
+ +

◆ rescale()

+ +
+
+ + + + + +
+ + + + + + + + +
NiftiImage & RNifti::NiftiImage::rescale (const std::vector< float > & scales)
+ 		+inline
+
+ +

Rescale the image, changing its image dimensions and pixel dimensions.

+
Parameters
+ + +
scalesVector of scale factors along each dimension
+
+
+
Note
No interpolation is performed on the pixel data, which is simply dropped
+ +
+
+ +

◆ setPersistence()

+ +
+
+ + + + + +
+ + + + + + + + +
NiftiImage& RNifti::NiftiImage::setPersistence (const bool persistent)
+ 		+inline
+
+ +

Marked the image as persistent, so that it can be passed back to R.

+
Parameters
+ + +
persistentThe new persistence state of the object
+
+
+ +
+
+ +

◆ setPixunits()

+ +
+
+ + + + + +
+ + + + + + + + +
void RNifti::NiftiImage::setPixunits (const std::vector< std::string > & pixunits)
+ 		+inlineprotected
+
+ +

Modify the pixel dimension units.

+
Parameters
+ + +
pixunitsVector of new pixel units, specified using their standard abbreviations
+
+
+ +
+
+ +

◆ slice() [1/2]

+ +
+
+ + + + + +
+ + + + + + + + +
const Block RNifti::NiftiImage::slice (const int i) const
+ 		+inline
+
+ +

Extract a slice block from a 3D image.

+
Parameters
+ + +
iThe slice number required
+
+
+
Returns
A Block object
+ +
+
+ +

◆ slice() [2/2]

+ +
+
+ + + + + +
+ + + + + + + + +
Block RNifti::NiftiImage::slice (const int i)
+ 		+inline
+
+ +

Extract a slice block from a 3D image.

+
Parameters
+ + +
iThe slice number required
+
+
+
Returns
A Block object
+ +
+
+ +

◆ toFile() [1/2]

+ +
+
+ + + + + +
+ + + + + + + + + + + + + + + + + + +
void RNifti::NiftiImage::toFile (const std::string fileName,
const short datatype = DT_NONE 
) const
+ 		+inline
+
+ +

Write the image to a NIfTI-1 file.

+
Parameters
+ + + +
fileNameThe file name to write to, with appropriate suffix (e.g. ".nii.gz")
datatypeThe datatype to use when writing the file
+
+
+ +
+
+ +

◆ toFile() [2/2]

+ +
+
+ + + + + +
+ + + + + + + + + + + + + + + + + + +
void RNifti::NiftiImage::toFile (const std::string fileName,
const std::string & datatype 
) const
+ 		+inline
+
+ +

Write the image to a NIfTI-1 file.

+
Parameters
+ + + +
fileNameThe file name to write to, with appropriate suffix (e.g. ".nii.gz")
datatypeThe datatype to use when writing the file, or "auto"
+
+
+ +
+
+ +

◆ updatePixdim()

+ +
+
+ + + + + +
+ + + + + + + + +
void RNifti::NiftiImage::updatePixdim (const std::vector< float > & pixdim)
+ 		+inlineprotected
+
+ +

Modify the pixel dimensions, and potentially the xform matrices to match.

+
Parameters
+ + +
pixdimVector of new pixel dimensions
+
+
+ +
+
+ +

◆ volume() [1/2]

+ +
+
+ + + + + +
+ + + + + + + + +
const Block RNifti::NiftiImage::volume (const int i) const
+ 		+inline
+
+ +

Extract a volume block from a 4D image.

+
Parameters
+ + +
iThe volume number required
+
+
+
Returns
A Block object
+ +
+
+ +

◆ volume() [2/2]

+ +
+
+ + + + + +
+ + + + + + + + +
Block RNifti::NiftiImage::volume (const int i)
+ 		+inline
+
+ +

Extract a volume block from a 4D image.

+
Parameters
+ + +
iThe volume number required
+
+
+
Returns
A Block object
+ +
+
+ +

◆ xform()

+ +
+
+ + + + + +
+ + + + + + + + +
mat44 RNifti::NiftiImage::xform (const bool preferQuaternion = true) const
+ 		+inline
+
+ +

Obtain an xform matrix, indicating the orientation of the image.

+
Parameters
+ + +
preferQuaternionIf true, use the qform matrix in preference to the sform
+
+
+
Returns
A 4x4 matrix
+ +
+
+ +

◆ xformToString()

+ +
+
+ + + + + +
+ + + + + + + + +
static std::string RNifti::NiftiImage::xformToString (const mat44 matrix)
+ 		+inlinestatic
+
+ +

Convert a 4x4 xform matrix to a string describing its canonical axes.

+
Parameters
+ + +
matrixAn xform matrix
+
+
+
Returns
A string containing three characters
+ +
+
+
The documentation for this class was generated from the following file: +
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+ + diff --git a/inst/doxygen/html/dir_98a44f28b9ced65c076c4e168f5923c6.html b/inst/doxygen/html/dir_98a44f28b9ced65c076c4e168f5923c6.html new file mode 100644 index 0000000..b928e7b --- /dev/null +++ b/inst/doxygen/html/dir_98a44f28b9ced65c076c4e168f5923c6.html @@ -0,0 +1,81 @@ + + + + + + + +RNifti: inst/include/lib Directory Reference + + + + + + + + + +
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+
RNifti +
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Fast R and C++ Access to NIfTI Images
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+
lib Directory Reference
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+} + +#powerTip.n:after, #powerTip.ne:after, #powerTip.nw:after { + border-top-color: #ffffff; + border-width: 10px; + margin: 0px -10px; +} +#powerTip.n:before { + border-top-color: #808080; + border-width: 11px; + margin: 0px -11px; +} +#powerTip.n:after, #powerTip.n:before { + left: 50%; +} + +#powerTip.nw:after, #powerTip.nw:before { + right: 14px; +} + +#powerTip.ne:after, #powerTip.ne:before { + left: 14px; +} + +#powerTip.s:after, #powerTip.s:before, +#powerTip.se:after, #powerTip.se:before, +#powerTip.sw:after, #powerTip.sw:before { + bottom: 100%; +} + +#powerTip.s:after, #powerTip.se:after, #powerTip.sw:after { + border-bottom-color: #ffffff; + border-width: 10px; + margin: 0px -10px; +} + +#powerTip.s:before, #powerTip.se:before, #powerTip.sw:before { + border-bottom-color: #808080; + border-width: 11px; + margin: 0px -11px; +} + +#powerTip.s:after, #powerTip.s:before { + left: 50%; +} + +#powerTip.sw:after, #powerTip.sw:before { + right: 14px; +} + +#powerTip.se:after, #powerTip.se:before { + left: 14px; +} + +#powerTip.e:after, #powerTip.e:before { + left: 100%; +} +#powerTip.e:after { + border-left-color: #ffffff; + border-width: 10px; + top: 50%; + margin-top: -10px; +} +#powerTip.e:before { + border-left-color: #808080; + border-width: 11px; + top: 50%; + margin-top: -11px; +} + +#powerTip.w:after, #powerTip.w:before { + right: 100%; +} +#powerTip.w:after { + border-right-color: #ffffff; + border-width: 10px; + top: 50%; + margin-top: -10px; +} +#powerTip.w:before { + border-right-color: #808080; + border-width: 11px; + top: 50%; + margin-top: -11px; +} + +@media print +{ + #top { display: none; } + #side-nav { display: none; } + #nav-path { display: none; } + body { overflow:visible; } + h1, h2, h3, h4, h5, h6 { page-break-after: avoid; } + .summary { display: none; } + .memitem { page-break-inside: avoid; } + #doc-content + { + margin-left:0 !important; + height:auto !important; + width:auto !important; + overflow:inherit; + display:inline; + } +} + +/* @group Markdown */ + +/* +table.markdownTable { + border-collapse:collapse; + margin-top: 4px; + margin-bottom: 4px; +} + +table.markdownTable td, table.markdownTable th { + border: 1px solid #2D4068; + padding: 3px 7px 2px; +} + +table.markdownTableHead tr { +} + +table.markdownTableBodyLeft td, table.markdownTable th { + border: 1px solid #2D4068; + padding: 3px 7px 2px; +} + +th.markdownTableHeadLeft th.markdownTableHeadRight th.markdownTableHeadCenter th.markdownTableHeadNone { + background-color: #374F7F; + color: #FFFFFF; + font-size: 110%; + padding-bottom: 4px; + padding-top: 5px; +} + +th.markdownTableHeadLeft { + text-align: left +} + +th.markdownTableHeadRight { + text-align: right +} + +th.markdownTableHeadCenter { + text-align: center +} +*/ + +table.markdownTable { + border-collapse:collapse; + margin-top: 4px; + margin-bottom: 4px; +} + +table.markdownTable td, table.markdownTable th { + border: 1px solid #2D4068; + padding: 3px 7px 2px; +} + +table.markdownTable tr { +} + +th.markdownTableHeadLeft, th.markdownTableHeadRight, th.markdownTableHeadCenter, th.markdownTableHeadNone { + background-color: #374F7F; 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you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation; either version 2 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License along + with this program; if not, write to the Free Software Foundation, Inc., + 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. + + @licend The above is the entire license notice + for the JavaScript code in this file + */ +function toggleVisibility(linkObj) +{ + var base = $(linkObj).attr('id'); + var summary = $('#'+base+'-summary'); + var content = $('#'+base+'-content'); + var trigger = $('#'+base+'-trigger'); + var src=$(trigger).attr('src'); + if (content.is(':visible')===true) { + content.hide(); + summary.show(); + $(linkObj).addClass('closed').removeClass('opened'); + $(trigger).attr('src',src.substring(0,src.length-8)+'closed.png'); + } else { + content.show(); + summary.hide(); + $(linkObj).removeClass('closed').addClass('opened'); + $(trigger).attr('src',src.substring(0,src.length-10)+'open.png'); + } + return false; +} + +function updateStripes() +{ + $('table.directory tr'). + removeClass('even').filter(':visible:even').addClass('even'); +} + +function toggleLevel(level) +{ + $('table.directory tr').each(function() { + var l = this.id.split('_').length-1; + var i = $('#img'+this.id.substring(3)); + var a = $('#arr'+this.id.substring(3)); + if (l + + + + + + +RNifti: File List + + + + + + + + + +
+
+ + + + + + +
+
RNifti +
+
Fast R and C++ Access to NIfTI Images
+
+
+ + + + + + + +
+ +
+
+ + +
+ +
+ +
+
+
File List
+
+
+
Here is a list of all documented files with brief descriptions:
+
[detail level 1234]
+ + + + +
 ▼ inst
 ▼ include
 ▼ lib
 NiftiImage.h
+
+
+ +
+Generated by   +doxygen + 1.8.14 +
+ + diff --git a/inst/doxygen/html/folderclosed.png b/inst/doxygen/html/folderclosed.png new file mode 100644 index 0000000000000000000000000000000000000000..bb8ab35edce8e97554e360005ee9fc5bffb36e66 GIT binary patch literal 616 zcmV-u0+;=XP)a9#ETzayK)T~Jw&MMH>OIr#&;dC}is*2Mqdf&akCc=O@`qC+4i z5Iu3w#1M@KqXCz8TIZd1wli&kkl2HVcAiZ8PUn5z_kG@-y;?yK06=cA0U%H0PH+kU zl6dp}OR(|r8-RG+YLu`zbI}5TlOU6ToR41{9=uz^?dGTNL;wIMf|V3`d1Wj3y!#6` zBLZ?xpKR~^2x}?~zA(_NUu3IaDB$tKma*XUdOZN~c=dLt_h_k!dbxm_*ibDM zlFX`g{k$X}yIe%$N)cn1LNu=q9_CS)*>A zsX_mM4L@`(cSNQKMFc$RtYbx{79#j-J7hk*>*+ZZhM4Hw?I?rsXCi#mRWJ=-0LGV5a-WR0Qgt<|Nqf)C-@80`5gIz45^_20000IqP)X=#(TiCT&PiIIVc55T}TU}EUh*{q$|`3@{d>{Tc9Bo>e= zfmF3!f>fbI9#GoEHh0f`i5)wkLpva0ztf%HpZneK?w-7AK@b4Itw{y|Zd3k!fH?q2 zlhckHd_V2M_X7+)U&_Xcfvtw60l;--DgZmLSw-Y?S>)zIqMyJ1#FwLU*%bl38ok+! zh78H87n`ZTS;uhzAR$M`zZ`bVhq=+%u9^$5jDplgxd44}9;IRqUH1YHH|@6oFe%z( zo4)_>E$F&^P-f(#)>(TrnbE>Pefs9~@iN=|)Rz|V`sGfHNrJ)0gJb8xx+SBmRf@1l zvuzt=vGfI)<-F9!o&3l?>9~0QbUDT(wFdnQPv%xdD)m*g%!20>Bc9iYmGAp<9YAa( z0QgYgTWqf1qN++Gqp z8@AYPTB3E|6s=WLG?xw0tm|U!o=&zd+H0oRYE;Dbx+Na9s^STqX|Gnq%H8s(nGDGJ j8vwW|`Ts`)fSK|Kx=IK@RG@g200000NkvXXu0mjfauFEA literal 0 HcmV?d00001 diff --git a/inst/doxygen/html/functions.html b/inst/doxygen/html/functions.html new file mode 100644 index 0000000..828a5a9 --- /dev/null +++ b/inst/doxygen/html/functions.html @@ -0,0 +1,248 @@ + + + + + + + +RNifti: Class Members + + + + + + + + + +
+
+ + + + + + +
+
RNifti +
+
Fast R and C++ Access to NIfTI Images
+
+
+ + + + + + + +
+ +
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+ + +
+ +
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+
Here is a list of all documented class members with links to the class documentation for each member:
+ +

- b -

+ + +

- c -

+ + +

- d -

+ + +

- f -

+ + +

- g -

+ + +

- i -

+ + +

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+ + +

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+ + +

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+ + +

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+ + +

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+ + +

- u -

+ + +

- v -

+ + +

- x -

+ + +

- ~ -

+
+ +
+Generated by   +doxygen + 1.8.14 +
+ + diff --git a/inst/doxygen/html/functions_func.html b/inst/doxygen/html/functions_func.html new file mode 100644 index 0000000..2aa2015 --- /dev/null +++ b/inst/doxygen/html/functions_func.html @@ -0,0 +1,235 @@ + + + + + + + +RNifti: Class Members - Functions + + + + + + + + + +
+
+ + + + + + +
+
RNifti +
+
Fast R and C++ Access to NIfTI Images
+
+
+ + + + + + + +
+ +
+
+ + +
+ +
+ +
+  + +

- b -

+ + +

- c -

+ + +

- d -

+ + +

- f -

+ + +

- g -

+ + +

- i -

+ + +

- n -

+ + +

- o -

+ + +

- p -

+ + +

- r -

+ + +

- s -

+ + +

- t -

+ + +

- u -

+ + +

- v -

+ + +

- x -

+ + +

- ~ -

+
+ +
+Generated by   +doxygen + 1.8.14 +
+ + diff --git a/inst/doxygen/html/functions_vars.html b/inst/doxygen/html/functions_vars.html new file mode 100644 index 0000000..9010ed1 --- /dev/null +++ b/inst/doxygen/html/functions_vars.html @@ -0,0 +1,88 @@ + + + + + + + +RNifti: Class Members - Variables + + + + + + + + + +
+
+ + + + + + +
+
RNifti +
+
Fast R and C++ Access to NIfTI Images
+
+
+ + + + + + + +
+ +
+
+ + +
+ +
+ +
+  +
+ +
+Generated by   +doxygen + 1.8.14 +
+ + diff --git a/inst/doxygen/html/index.html b/inst/doxygen/html/index.html new file mode 100644 index 0000000..70b0bbb --- /dev/null +++ b/inst/doxygen/html/index.html @@ -0,0 +1,78 @@ + + + + + + + +RNifti: RNifti: Fast R and C++ Access to NIfTI Images + + + + + + + + + +
+
+ + + + + + +
+
RNifti +
+
Fast R and C++ Access to NIfTI Images
+
+
+ + + + + + + +
+ +
+
+ + +
+ +
+ +
+
+
RNifti: Fast R and C++ Access to NIfTI Images
+
+
+

A more extensive overview of the RNifti package, and its usage from R, is provided on the package's GitHub page at https://github.com/jonclayden/RNifti. The primary role of these pages is to document the RNifti::NiftiImage C++ class for package developers linking to RNifti.

+
+ +
+Generated by   +doxygen + 1.8.14 +
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http://jquery.org/license + * + * http://docs.jquery.com/UI/Mouse + * + * Depends: + * jquery.ui.widget.js + */ +(function(b,c){var a=false;b(document).mouseup(function(d){a=false});b.widget("ui.mouse",{options:{cancel:":input,option",distance:1,delay:0},_mouseInit:function(){var d=this;this.element.bind("mousedown."+this.widgetName,function(e){return d._mouseDown(e)}).bind("click."+this.widgetName,function(e){if(true===b.data(e.target,d.widgetName+".preventClickEvent")){b.removeData(e.target,d.widgetName+".preventClickEvent");e.stopImmediatePropagation();return false}});this.started=false},_mouseDestroy:function(){this.element.unbind("."+this.widgetName)},_mouseDown:function(f){if(a){return}(this._mouseStarted&&this._mouseUp(f));this._mouseDownEvent=f;var e=this,g=(f.which==1),d=(typeof this.options.cancel=="string"&&f.target.nodeName?b(f.target).closest(this.options.cancel).length:false);if(!g||d||!this._mouseCapture(f)){return true}this.mouseDelayMet=!this.options.delay;if(!this.mouseDelayMet){this._mouseDelayTimer=setTimeout(function(){e.mouseDelayMet=true},this.options.delay)}if(this._mouseDistanceMet(f)&&this._mouseDelayMet(f)){this._mouseStarted=(this._mouseStart(f)!==false);if(!this._mouseStarted){f.preventDefault();return true}}if(true===b.data(f.target,this.widgetName+".preventClickEvent")){b.removeData(f.target,this.widgetName+".preventClickEvent")}this._mouseMoveDelegate=function(h){return e._mouseMove(h)};this._mouseUpDelegate=function(h){return e._mouseUp(h)};b(document).bind("mousemove."+this.widgetName,this._mouseMoveDelegate).bind("mouseup."+this.widgetName,this._mouseUpDelegate);f.preventDefault();a=true;return true},_mouseMove:function(d){if(b.browser.msie&&!(document.documentMode>=9)&&!d.button){return this._mouseUp(d)}if(this._mouseStarted){this._mouseDrag(d);return d.preventDefault()}if(this._mouseDistanceMet(d)&&this._mouseDelayMet(d)){this._mouseStarted=(this._mouseStart(this._mouseDownEvent,d)!==false);(this._mouseStarted?this._mouseDrag(d):this._mouseUp(d))}return !this._mouseStarted},_mouseUp:function(d){b(document).unbind("mousemove."+this.widgetName,this._mouseMoveDelegate).unbind("mouseup."+this.widgetName,this._mouseUpDelegate);if(this._mouseStarted){this._mouseStarted=false;if(d.target==this._mouseDownEvent.target){b.data(d.target,this.widgetName+".preventClickEvent",true)}this._mouseStop(d)}return false},_mouseDistanceMet:function(d){return(Math.max(Math.abs(this._mouseDownEvent.pageX-d.pageX),Math.abs(this._mouseDownEvent.pageY-d.pageY))>=this.options.distance)},_mouseDelayMet:function(d){return this.mouseDelayMet},_mouseStart:function(d){},_mouseDrag:function(d){},_mouseStop:function(d){},_mouseCapture:function(d){return true}})})(jQuery);(function(c,d){c.widget("ui.resizable",c.ui.mouse,{widgetEventPrefix:"resize",options:{alsoResize:false,animate:false,animateDuration:"slow",animateEasing:"swing",aspectRatio:false,autoHide:false,containment:false,ghost:false,grid:false,handles:"e,s,se",helper:false,maxHeight:null,maxWidth:null,minHeight:10,minWidth:10,zIndex:1000},_create:function(){var f=this,k=this.options;this.element.addClass("ui-resizable");c.extend(this,{_aspectRatio:!!(k.aspectRatio),aspectRatio:k.aspectRatio,originalElement:this.element,_proportionallyResizeElements:[],_helper:k.helper||k.ghost||k.animate?k.helper||"ui-resizable-helper":null});if(this.element[0].nodeName.match(/canvas|textarea|input|select|button|img/i)){this.element.wrap(c('
').css({position:this.element.css("position"),width:this.element.outerWidth(),height:this.element.outerHeight(),top:this.element.css("top"),left:this.element.css("left")}));this.element=this.element.parent().data("resizable",this.element.data("resizable"));this.elementIsWrapper=true;this.element.css({marginLeft:this.originalElement.css("marginLeft"),marginTop:this.originalElement.css("marginTop"),marginRight:this.originalElement.css("marginRight"),marginBottom:this.originalElement.css("marginBottom")});this.originalElement.css({marginLeft:0,marginTop:0,marginRight:0,marginBottom:0});this.originalResizeStyle=this.originalElement.css("resize");this.originalElement.css("resize","none");this._proportionallyResizeElements.push(this.originalElement.css({position:"static",zoom:1,display:"block"}));this.originalElement.css({margin:this.originalElement.css("margin")});this._proportionallyResize()}this.handles=k.handles||(!c(".ui-resizable-handle",this.element).length?"e,s,se":{n:".ui-resizable-n",e:".ui-resizable-e",s:".ui-resizable-s",w:".ui-resizable-w",se:".ui-resizable-se",sw:".ui-resizable-sw",ne:".ui-resizable-ne",nw:".ui-resizable-nw"});if(this.handles.constructor==String){if(this.handles=="all"){this.handles="n,e,s,w,se,sw,ne,nw"}var l=this.handles.split(",");this.handles={};for(var g=0;g
');if(/sw|se|ne|nw/.test(j)){h.css({zIndex:++k.zIndex})}if("se"==j){h.addClass("ui-icon ui-icon-gripsmall-diagonal-se")}this.handles[j]=".ui-resizable-"+j;this.element.append(h)}}this._renderAxis=function(q){q=q||this.element;for(var n in this.handles){if(this.handles[n].constructor==String){this.handles[n]=c(this.handles[n],this.element).show()}if(this.elementIsWrapper&&this.originalElement[0].nodeName.match(/textarea|input|select|button/i)){var o=c(this.handles[n],this.element),p=0;p=/sw|ne|nw|se|n|s/.test(n)?o.outerHeight():o.outerWidth();var m=["padding",/ne|nw|n/.test(n)?"Top":/se|sw|s/.test(n)?"Bottom":/^e$/.test(n)?"Right":"Left"].join("");q.css(m,p);this._proportionallyResize()}if(!c(this.handles[n]).length){continue}}};this._renderAxis(this.element);this._handles=c(".ui-resizable-handle",this.element).disableSelection();this._handles.mouseover(function(){if(!f.resizing){if(this.className){var i=this.className.match(/ui-resizable-(se|sw|ne|nw|n|e|s|w)/i)}f.axis=i&&i[1]?i[1]:"se"}});if(k.autoHide){this._handles.hide();c(this.element).addClass("ui-resizable-autohide").hover(function(){if(k.disabled){return}c(this).removeClass("ui-resizable-autohide");f._handles.show()},function(){if(k.disabled){return}if(!f.resizing){c(this).addClass("ui-resizable-autohide");f._handles.hide()}})}this._mouseInit()},destroy:function(){this._mouseDestroy();var e=function(g){c(g).removeClass("ui-resizable ui-resizable-disabled ui-resizable-resizing").removeData("resizable").unbind(".resizable").find(".ui-resizable-handle").remove()};if(this.elementIsWrapper){e(this.element);var f=this.element;f.after(this.originalElement.css({position:f.css("position"),width:f.outerWidth(),height:f.outerHeight(),top:f.css("top"),left:f.css("left")})).remove()}this.originalElement.css("resize",this.originalResizeStyle);e(this.originalElement);return this},_mouseCapture:function(f){var g=false;for(var e in this.handles){if(c(this.handles[e])[0]==f.target){g=true}}return !this.options.disabled&&g},_mouseStart:function(g){var j=this.options,f=this.element.position(),e=this.element;this.resizing=true;this.documentScroll={top:c(document).scrollTop(),left:c(document).scrollLeft()};if(e.is(".ui-draggable")||(/absolute/).test(e.css("position"))){e.css({position:"absolute",top:f.top,left:f.left})}this._renderProxy();var k=b(this.helper.css("left")),h=b(this.helper.css("top"));if(j.containment){k+=c(j.containment).scrollLeft()||0;h+=c(j.containment).scrollTop()||0}this.offset=this.helper.offset();this.position={left:k,top:h};this.size=this._helper?{width:e.outerWidth(),height:e.outerHeight()}:{width:e.width(),height:e.height()};this.originalSize=this._helper?{width:e.outerWidth(),height:e.outerHeight()}:{width:e.width(),height:e.height()};this.originalPosition={left:k,top:h};this.sizeDiff={width:e.outerWidth()-e.width(),height:e.outerHeight()-e.height()};this.originalMousePosition={left:g.pageX,top:g.pageY};this.aspectRatio=(typeof j.aspectRatio=="number")?j.aspectRatio:((this.originalSize.width/this.originalSize.height)||1);var i=c(".ui-resizable-"+this.axis).css("cursor");c("body").css("cursor",i=="auto"?this.axis+"-resize":i);e.addClass("ui-resizable-resizing");this._propagate("start",g);return true},_mouseDrag:function(e){var h=this.helper,g=this.options,m={},q=this,j=this.originalMousePosition,n=this.axis;var r=(e.pageX-j.left)||0,p=(e.pageY-j.top)||0;var i=this._change[n];if(!i){return false}var l=i.apply(this,[e,r,p]),k=c.browser.msie&&c.browser.version<7,f=this.sizeDiff;this._updateVirtualBoundaries(e.shiftKey);if(this._aspectRatio||e.shiftKey){l=this._updateRatio(l,e)}l=this._respectSize(l,e);this._propagate("resize",e);h.css({top:this.position.top+"px",left:this.position.left+"px",width:this.size.width+"px",height:this.size.height+"px"});if(!this._helper&&this._proportionallyResizeElements.length){this._proportionallyResize()}this._updateCache(l);this._trigger("resize",e,this.ui());return false},_mouseStop:function(h){this.resizing=false;var i=this.options,m=this;if(this._helper){var g=this._proportionallyResizeElements,e=g.length&&(/textarea/i).test(g[0].nodeName),f=e&&c.ui.hasScroll(g[0],"left")?0:m.sizeDiff.height,k=e?0:m.sizeDiff.width;var n={width:(m.helper.width()-k),height:(m.helper.height()-f)},j=(parseInt(m.element.css("left"),10)+(m.position.left-m.originalPosition.left))||null,l=(parseInt(m.element.css("top"),10)+(m.position.top-m.originalPosition.top))||null;if(!i.animate){this.element.css(c.extend(n,{top:l,left:j}))}m.helper.height(m.size.height);m.helper.width(m.size.width);if(this._helper&&!i.animate){this._proportionallyResize()}}c("body").css("cursor","auto");this.element.removeClass("ui-resizable-resizing");this._propagate("stop",h);if(this._helper){this.helper.remove()}return false},_updateVirtualBoundaries:function(g){var j=this.options,i,h,f,k,e;e={minWidth:a(j.minWidth)?j.minWidth:0,maxWidth:a(j.maxWidth)?j.maxWidth:Infinity,minHeight:a(j.minHeight)?j.minHeight:0,maxHeight:a(j.maxHeight)?j.maxHeight:Infinity};if(this._aspectRatio||g){i=e.minHeight*this.aspectRatio;f=e.minWidth/this.aspectRatio;h=e.maxHeight*this.aspectRatio;k=e.maxWidth/this.aspectRatio;if(i>e.minWidth){e.minWidth=i}if(f>e.minHeight){e.minHeight=f}if(hl.width),s=a(l.height)&&i.minHeight&&(i.minHeight>l.height);if(h){l.width=i.minWidth}if(s){l.height=i.minHeight}if(t){l.width=i.maxWidth}if(m){l.height=i.maxHeight}var f=this.originalPosition.left+this.originalSize.width,p=this.position.top+this.size.height;var k=/sw|nw|w/.test(q),e=/nw|ne|n/.test(q);if(h&&k){l.left=f-i.minWidth}if(t&&k){l.left=f-i.maxWidth}if(s&&e){l.top=p-i.minHeight}if(m&&e){l.top=p-i.maxHeight}var n=!l.width&&!l.height;if(n&&!l.left&&l.top){l.top=null}else{if(n&&!l.top&&l.left){l.left=null}}return l},_proportionallyResize:function(){var k=this.options;if(!this._proportionallyResizeElements.length){return}var g=this.helper||this.element;for(var f=0;f');var e=c.browser.msie&&c.browser.version<7,g=(e?1:0),h=(e?2:-1);this.helper.addClass(this._helper).css({width:this.element.outerWidth()+h,height:this.element.outerHeight()+h,position:"absolute",left:this.elementOffset.left-g+"px",top:this.elementOffset.top-g+"px",zIndex:++i.zIndex});this.helper.appendTo("body").disableSelection()}else{this.helper=this.element}},_change:{e:function(g,f,e){return{width:this.originalSize.width+f}},w:function(h,f,e){var j=this.options,g=this.originalSize,i=this.originalPosition;return{left:i.left+f,width:g.width-f}},n:function(h,f,e){var j=this.options,g=this.originalSize,i=this.originalPosition;return{top:i.top+e,height:g.height-e}},s:function(g,f,e){return{height:this.originalSize.height+e}},se:function(g,f,e){return c.extend(this._change.s.apply(this,arguments),this._change.e.apply(this,[g,f,e]))},sw:function(g,f,e){return c.extend(this._change.s.apply(this,arguments),this._change.w.apply(this,[g,f,e]))},ne:function(g,f,e){return c.extend(this._change.n.apply(this,arguments),this._change.e.apply(this,[g,f,e]))},nw:function(g,f,e){return c.extend(this._change.n.apply(this,arguments),this._change.w.apply(this,[g,f,e]))}},_propagate:function(f,e){c.ui.plugin.call(this,f,[e,this.ui()]);(f!="resize"&&this._trigger(f,e,this.ui()))},plugins:{},ui:function(){return{originalElement:this.originalElement,element:this.element,helper:this.helper,position:this.position,size:this.size,originalSize:this.originalSize,originalPosition:this.originalPosition}}});c.extend(c.ui.resizable,{version:"1.8.18"});c.ui.plugin.add("resizable","alsoResize",{start:function(f,g){var e=c(this).data("resizable"),i=e.options;var h=function(j){c(j).each(function(){var k=c(this);k.data("resizable-alsoresize",{width:parseInt(k.width(),10),height:parseInt(k.height(),10),left:parseInt(k.css("left"),10),top:parseInt(k.css("top"),10)})})};if(typeof(i.alsoResize)=="object"&&!i.alsoResize.parentNode){if(i.alsoResize.length){i.alsoResize=i.alsoResize[0];h(i.alsoResize)}else{c.each(i.alsoResize,function(j){h(j)})}}else{h(i.alsoResize)}},resize:function(g,i){var f=c(this).data("resizable"),j=f.options,h=f.originalSize,l=f.originalPosition;var k={height:(f.size.height-h.height)||0,width:(f.size.width-h.width)||0,top:(f.position.top-l.top)||0,left:(f.position.left-l.left)||0},e=function(m,n){c(m).each(function(){var q=c(this),r=c(this).data("resizable-alsoresize"),p={},o=n&&n.length?n:q.parents(i.originalElement[0]).length?["width","height"]:["width","height","top","left"];c.each(o,function(s,u){var t=(r[u]||0)+(k[u]||0);if(t&&t>=0){p[u]=t||null}});q.css(p)})};if(typeof(j.alsoResize)=="object"&&!j.alsoResize.nodeType){c.each(j.alsoResize,function(m,n){e(m,n)})}else{e(j.alsoResize)}},stop:function(e,f){c(this).removeData("resizable-alsoresize")}});c.ui.plugin.add("resizable","animate",{stop:function(i,n){var p=c(this).data("resizable"),j=p.options;var h=p._proportionallyResizeElements,e=h.length&&(/textarea/i).test(h[0].nodeName),f=e&&c.ui.hasScroll(h[0],"left")?0:p.sizeDiff.height,l=e?0:p.sizeDiff.width;var g={width:(p.size.width-l),height:(p.size.height-f)},k=(parseInt(p.element.css("left"),10)+(p.position.left-p.originalPosition.left))||null,m=(parseInt(p.element.css("top"),10)+(p.position.top-p.originalPosition.top))||null;p.element.animate(c.extend(g,m&&k?{top:m,left:k}:{}),{duration:j.animateDuration,easing:j.animateEasing,step:function(){var o={width:parseInt(p.element.css("width"),10),height:parseInt(p.element.css("height"),10),top:parseInt(p.element.css("top"),10),left:parseInt(p.element.css("left"),10)};if(h&&h.length){c(h[0]).css({width:o.width,height:o.height})}p._updateCache(o);p._propagate("resize",i)}})}});c.ui.plugin.add("resizable","containment",{start:function(f,r){var t=c(this).data("resizable"),j=t.options,l=t.element;var g=j.containment,k=(g instanceof c)?g.get(0):(/parent/.test(g))?l.parent().get(0):g;if(!k){return}t.containerElement=c(k);if(/document/.test(g)||g==document){t.containerOffset={left:0,top:0};t.containerPosition={left:0,top:0};t.parentData={element:c(document),left:0,top:0,width:c(document).width(),height:c(document).height()||document.body.parentNode.scrollHeight}}else{var n=c(k),i=[];c(["Top","Right","Left","Bottom"]).each(function(p,o){i[p]=b(n.css("padding"+o))});t.containerOffset=n.offset();t.containerPosition=n.position();t.containerSize={height:(n.innerHeight()-i[3]),width:(n.innerWidth()-i[1])};var q=t.containerOffset,e=t.containerSize.height,m=t.containerSize.width,h=(c.ui.hasScroll(k,"left")?k.scrollWidth:m),s=(c.ui.hasScroll(k)?k.scrollHeight:e);t.parentData={element:k,left:q.left,top:q.top,width:h,height:s}}},resize:function(g,q){var t=c(this).data("resizable"),i=t.options,f=t.containerSize,p=t.containerOffset,m=t.size,n=t.position,r=t._aspectRatio||g.shiftKey,e={top:0,left:0},h=t.containerElement;if(h[0]!=document&&(/static/).test(h.css("position"))){e=p}if(n.left<(t._helper?p.left:0)){t.size.width=t.size.width+(t._helper?(t.position.left-p.left):(t.position.left-e.left));if(r){t.size.height=t.size.width/i.aspectRatio}t.position.left=i.helper?p.left:0}if(n.top<(t._helper?p.top:0)){t.size.height=t.size.height+(t._helper?(t.position.top-p.top):t.position.top);if(r){t.size.width=t.size.height*i.aspectRatio}t.position.top=t._helper?p.top:0}t.offset.left=t.parentData.left+t.position.left;t.offset.top=t.parentData.top+t.position.top;var l=Math.abs((t._helper?t.offset.left-e.left:(t.offset.left-e.left))+t.sizeDiff.width),s=Math.abs((t._helper?t.offset.top-e.top:(t.offset.top-p.top))+t.sizeDiff.height);var k=t.containerElement.get(0)==t.element.parent().get(0),j=/relative|absolute/.test(t.containerElement.css("position"));if(k&&j){l-=t.parentData.left}if(l+t.size.width>=t.parentData.width){t.size.width=t.parentData.width-l;if(r){t.size.height=t.size.width/t.aspectRatio}}if(s+t.size.height>=t.parentData.height){t.size.height=t.parentData.height-s;if(r){t.size.width=t.size.height*t.aspectRatio}}},stop:function(f,n){var q=c(this).data("resizable"),g=q.options,l=q.position,m=q.containerOffset,e=q.containerPosition,i=q.containerElement;var j=c(q.helper),r=j.offset(),p=j.outerWidth()-q.sizeDiff.width,k=j.outerHeight()-q.sizeDiff.height;if(q._helper&&!g.animate&&(/relative/).test(i.css("position"))){c(this).css({left:r.left-e.left-m.left,width:p,height:k})}if(q._helper&&!g.animate&&(/static/).test(i.css("position"))){c(this).css({left:r.left-e.left-m.left,width:p,height:k})}}});c.ui.plugin.add("resizable","ghost",{start:function(g,h){var e=c(this).data("resizable"),i=e.options,f=e.size;e.ghost=e.originalElement.clone();e.ghost.css({opacity:0.25,display:"block",position:"relative",height:f.height,width:f.width,margin:0,left:0,top:0}).addClass("ui-resizable-ghost").addClass(typeof i.ghost=="string"?i.ghost:"");e.ghost.appendTo(e.helper)},resize:function(f,g){var e=c(this).data("resizable"),h=e.options;if(e.ghost){e.ghost.css({position:"relative",height:e.size.height,width:e.size.width})}},stop:function(f,g){var e=c(this).data("resizable"),h=e.options;if(e.ghost&&e.helper){e.helper.get(0).removeChild(e.ghost.get(0))}}});c.ui.plugin.add("resizable","grid",{resize:function(e,m){var p=c(this).data("resizable"),h=p.options,k=p.size,i=p.originalSize,j=p.originalPosition,n=p.axis,l=h._aspectRatio||e.shiftKey;h.grid=typeof h.grid=="number"?[h.grid,h.grid]:h.grid;var g=Math.round((k.width-i.width)/(h.grid[0]||1))*(h.grid[0]||1),f=Math.round((k.height-i.height)/(h.grid[1]||1))*(h.grid[1]||1);if(/^(se|s|e)$/.test(n)){p.size.width=i.width+g;p.size.height=i.height+f}else{if(/^(ne)$/.test(n)){p.size.width=i.width+g;p.size.height=i.height+f;p.position.top=j.top-f}else{if(/^(sw)$/.test(n)){p.size.width=i.width+g;p.size.height=i.height+f;p.position.left=j.left-g}else{p.size.width=i.width+g;p.size.height=i.height+f;p.position.top=j.top-f;p.position.left=j.left-g}}}}});var b=function(e){return parseInt(e,10)||0};var a=function(e){return !isNaN(parseInt(e,10))}})(jQuery);/*! + * jQuery hashchange event - v1.3 - 7/21/2010 + * http://benalman.com/projects/jquery-hashchange-plugin/ + * + * Copyright (c) 2010 "Cowboy" Ben Alman + * Dual licensed under the MIT and GPL licenses. + * http://benalman.com/about/license/ + */ +(function($,e,b){var c="hashchange",h=document,f,g=$.event.special,i=h.documentMode,d="on"+c in e&&(i===b||i>7);function a(j){j=j||location.href;return"#"+j.replace(/^[^#]*#?(.*)$/,"$1")}$.fn[c]=function(j){return j?this.bind(c,j):this.trigger(c)};$.fn[c].delay=50;g[c]=$.extend(g[c],{setup:function(){if(d){return false}$(f.start)},teardown:function(){if(d){return false}$(f.stop)}});f=(function(){var j={},p,m=a(),k=function(q){return q},l=k,o=k;j.start=function(){p||n()};j.stop=function(){p&&clearTimeout(p);p=b};function n(){var r=a(),q=o(m);if(r!==m){l(m=r,q);$(e).trigger(c)}else{if(q!==m){location.href=location.href.replace(/#.*/,"")+q}}p=setTimeout(n,$.fn[c].delay)}$.browser.msie&&!d&&(function(){var q,r;j.start=function(){if(!q){r=$.fn[c].src;r=r&&r+a();q=$(' + + + + +
+
+
NiftiImage::Block Member List
+
+
+ +

This is the complete list of members for NiftiImage::Block, including all inherited members.

+
+ + + + + +
Block(const NiftiImage &image, const int dimension, const int index)NiftiImage::Blockinline
dimensionNiftiImage::Block
imageNiftiImage::Block
indexNiftiImage::Block
operator=(const NiftiImage &source)NiftiImage::Blockinline
+ +
+Generated by   +doxygen + 1.8.12 +
+ + diff --git a/inst/doxygen/html/struct_nifti_image_1_1_block.html b/inst/doxygen/html/struct_nifti_image_1_1_block.html new file mode 100644 index 0000000..f0ebf03 --- /dev/null +++ b/inst/doxygen/html/struct_nifti_image_1_1_block.html @@ -0,0 +1,219 @@ + + + + + + + +RNifti: NiftiImage::Block Struct Reference + + + + + + + + + +
+
+ + + + + + +
+
RNifti +
+
Fast R and C++ Access to NIfTI Images
+
+
+ + + + + + + + +
+
+ + +
+ +
+ + +
+
+
+Public Member Functions | +Public Attributes | +List of all members
+
+
NiftiImage::Block Struct Reference
+
+
+ +

Inner class referring to a subset of an image. + More...

+ +

#include <NiftiImage.h>

+ + + + + + + + +

+Public Member Functions

 Block (const NiftiImage &image, const int dimension, const int index)
 Standard constructor for this class. More...
 
Block & operator= (const NiftiImage &source)
 Copy assignment operator, which allows a block in one image to be replaced with the contents of another image. More...
 
+ + + + + + + + + + +

+Public Attributes

+const NiftiImage & image
 The parent image.
 
+const int dimension
 The dimension along which the block applies (which should be the last)
 
+const int index
 The location along dimension.
 
+

Detailed Description

+

Inner class referring to a subset of an image.

+

Currently must refer to the last dimension in the image, i.e., a volume in a 4D parent image, or a slice in a 3D image

+

Constructor & Destructor Documentation

+ +

§ Block()

+ +
+
+ + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + +
NiftiImage::Block::Block (const NiftiImage & image,
const int dimension,
const int index 
)
+ 		+inline
+
+ +

Standard constructor for this class.

+
Parameters
+ + + + +
imageThe parent image
dimensionThe dimension along which the block applies (which should be the last)
indexThe location along dimension
+
+
+
Exceptions
+ + +
runtime_errorIf dimension is not the last dimension in the image
+
+
+ +
+
+

Member Function Documentation

+ +

§ operator=()

+ +
+
+ + + + + +
+ + + + + + + + +
Block& NiftiImage::Block::operator= (const NiftiImage & source)
+ 		+inline
+
+ +

Copy assignment operator, which allows a block in one image to be replaced with the contents of another image.

+
Parameters
+ + +
sourceA NiftiImage, containing the data to replace the block with
+
+
+
Returns
A reference to the block
+
Exceptions
+ + +
runtime_errorIf the source is incompatible with the block in size or datatype
+
+
+ +
+
+
The documentation for this struct was generated from the following file: +
+ +
+Generated by   +doxygen + 1.8.12 +
+ + diff --git a/inst/doxygen/html/struct_r_nifti_1_1_nifti_image_1_1_block-members.html b/inst/doxygen/html/struct_r_nifti_1_1_nifti_image_1_1_block-members.html new file mode 100644 index 0000000..a0e6581 --- /dev/null +++ b/inst/doxygen/html/struct_r_nifti_1_1_nifti_image_1_1_block-members.html @@ -0,0 +1,90 @@ + + + + + + + +RNifti: Member List + + + + + + + + + +
+
+ + + + + + +
+
RNifti +
+
Fast R and C++ Access to NIfTI Images
+
+
+ + + + + + + + +
+
+ + +
+ +
+ + +
+
+
+
RNifti::NiftiImage::Block Member List
+
+
+ +

This is the complete list of members for RNifti::NiftiImage::Block, including all inherited members.

+ + + + + + + +
Block(const NiftiImage &image, const int dimension, const int index)RNifti::NiftiImage::Blockinline
dimensionRNifti::NiftiImage::Block
getData() constRNifti::NiftiImage::Blockinline
imageRNifti::NiftiImage::Block
indexRNifti::NiftiImage::Block
operator=(const NiftiImage &source)RNifti::NiftiImage::Blockinline
+ +
+Generated by   +doxygen + 1.8.14 +
+ + diff --git a/inst/doxygen/html/struct_r_nifti_1_1_nifti_image_1_1_block.html b/inst/doxygen/html/struct_r_nifti_1_1_nifti_image_1_1_block.html new file mode 100644 index 0000000..9d0df4f --- /dev/null +++ b/inst/doxygen/html/struct_r_nifti_1_1_nifti_image_1_1_block.html @@ -0,0 +1,227 @@ + + + + + + + +RNifti: RNifti::NiftiImage::Block Struct Reference + + + + + + + + + +
+
+ + + + + + +
+
RNifti +
+
Fast R and C++ Access to NIfTI Images
+
+
+ + + + + + + + +
+
+ + +
+ +
+ + +
+
+
+Public Member Functions | +Public Attributes | +List of all members
+
+
RNifti::NiftiImage::Block Struct Reference
+
+
+ +

Inner class referring to a subset of an image. + More...

+ +

#include <NiftiImage.h>

+ + + + + + + + + + + + +

+Public Member Functions

 Block (const NiftiImage &image, const int dimension, const int index)
 Standard constructor for this class. More...
 
Block & operator= (const NiftiImage &source)
 Copy assignment operator, which allows a block in one image to be replaced with the contents of another image. More...
 
+template<typename TargetType >
std::vector< TargetType > getData () const
 Extract a vector of data from a block, casting it to any required element type.
 
+ + + + + + + + + + +

+Public Attributes

+const NiftiImage & image
 The parent image.
 
+const int dimension
 The dimension along which the block applies (which should be the last)
 
+const int index
 The location along dimension.
 
+

Detailed Description

+

Inner class referring to a subset of an image.

+

Currently must refer to the last dimension in the image, i.e., a volume in a 4D parent image, or a slice in a 3D image

+

Constructor & Destructor Documentation

+ +

◆ Block()

+ +
+
+ + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + +
RNifti::NiftiImage::Block::Block (const NiftiImage & image,
const int dimension,
const int index 
)
+ 		+inline
+
+ +

Standard constructor for this class.

+
Parameters
+ + + + +
imageThe parent image
dimensionThe dimension along which the block applies (which should be the last)
indexThe location along dimension
+
+
+
Exceptions
+ + +
runtime_errorIf dimension is not the last dimension in the image
+
+
+ +
+
+

Member Function Documentation

+ +

◆ operator=()

+ +
+
+ + + + + +
+ + + + + + + + +
Block& RNifti::NiftiImage::Block::operator= (const NiftiImage & source)
+ 		+inline
+
+ +

Copy assignment operator, which allows a block in one image to be replaced with the contents of another image.

+
Parameters
+ + +
sourceA NiftiImage, containing the data to replace the block with
+
+
+
Returns
A reference to the block
+
Exceptions
+ + +
runtime_errorIf the source is incompatible with the block in size or datatype
+
+
+ +
+
+
The documentation for this struct was generated from the following file: +
+ +
+Generated by   +doxygen + 1.8.14 +
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zdhYtk=T~nRRp;;0`TqaM%hmU;mtVDS4fwid`IE)F_P3pl{`@;|8j?$wcK>ZN7FxABOEIZWP29Klj&QJUg%Q*|qC!K$O k;y?8*9W`+@1mGbMdvep6;Zy{E_`i=)w))$?gg{9K0Dkw2jsO4v literal 0 HcmV?d00001 diff --git a/inst/include/RNifti.h b/inst/include/RNifti.h index 3138e66..eef2bc0 100644 --- a/inst/include/RNifti.h +++ b/inst/include/RNifti.h @@ -1,6 +1,11 @@ #ifndef _RNIFTI_H_ #define _RNIFTI_H_ +// RNiftyReg and divest have used HAVE_R, so accept this variant for compatibility +#if !defined(USING_R) && defined(HAVE_R) +#define USING_R +#endif + #include "niftilib/nifti1_io.h" #ifdef __cplusplus diff --git a/inst/include/lib/NiftiImage.h b/inst/include/lib/NiftiImage.h index d2ee60b..cfd1112 100644 --- a/inst/include/lib/NiftiImage.h +++ b/inst/include/lib/NiftiImage.h @@ -2,13 +2,14 @@ #define _NIFTI_IMAGE_H_ -#ifndef _NO_R__ +#ifdef USING_R #include #else #define R_NegInf -INFINITY +#define ISNAN(x) (x != x) #include #include @@ -20,6 +21,7 @@ #include #include #include +#include #endif @@ -101,7 +103,7 @@ class NiftiImage std::vector getData () const; }; -#ifndef _NO_R__ +#ifdef USING_R /** * Convert between R \c SEXP object type and \c nifti_image datatype codes * @param sexpType A numeric R \c SEXP type code @@ -146,6 +148,40 @@ class NiftiImage return result; } + /** + * Get the NIfTI format version used by the file at the specified path + * @param path A string specifying a file path + * @return An integer: -1 if the file is not present or not valid, 0 for ANALYZE-7.5, or + * a value greater than 0 for NIfTI + **/ + static int fileVersion (const std::string &path) + { + nifti_1_header *header = nifti_read_header(path.c_str(), NULL, false); + if (header == NULL) + return -1; + else + { + int version = NIFTI_VERSION(*header); + if (version == 0) + { + // NIfTI-2 has a 540-byte header - check for this or its byte-swapped equivalent + if (header->sizeof_hdr == 540 || header->sizeof_hdr == 469893120) + { + // The magic number has moved in NIfTI-2, so find it by byte offset + const char *magic = (char *) header + 4; + if (strncmp(magic,"ni2",3) == 0 || strncmp(magic,"n+2",3) == 0) + version = 2; + } + else if (!nifti_hdr_looks_good(header)) + { + // Not plausible as ANALYZE, so return -1 + version = -1; + } + } + return version; + } + } + protected: nifti_image *image; /**< The wrapped \c nifti_image pointer */ @@ -170,7 +206,7 @@ class NiftiImage void copy (const Block &source); -#ifndef _NO_R__ +#ifdef USING_R /** * Initialise the object from an S4 object of class \c "nifti" @@ -281,7 +317,15 @@ class NiftiImage #endif } -#ifndef _NO_R__ + /** + * Initialise using a path string and sequence of required volumes + * @param path A string specifying a path to a valid NIfTI-1 file, possibly gzipped + * @param volumes The volumes to read in (squashing all dimensions above the third together) + * @exception runtime_error If reading from the file fails, or \c volumes is empty + **/ + NiftiImage (const std::string &path, const std::vector &volumes); + +#ifdef USING_R /** * Initialise from an R object * @param object The source object @@ -493,12 +537,12 @@ class NiftiImage **/ NiftiImage & reorient (const std::string &orientation); -#ifndef _NO_R__ +#ifdef USING_R /** * Update the image from an R array - * @param array An R array object + * @param array An R array or list object **/ - NiftiImage & update (const SEXP array); + NiftiImage & update (const Rcpp::RObject &object); #endif /** @@ -579,7 +623,7 @@ class NiftiImage **/ void toFile (const std::string fileName, const std::string &datatype) const; -#ifndef _NO_R__ +#ifdef USING_R /** * Create an R array from the image @@ -669,7 +713,7 @@ inline void NiftiImage::copy (const Block &source) persistent = false; } -#ifndef _NO_R__ +#ifdef USING_R // Convert an S4 "nifti" object, as defined in the oro.nifti package, to a "nifti_image" struct inline void NiftiImage::initFromNiftiS4 (const Rcpp::RObject &object, const bool copyData) @@ -856,84 +900,7 @@ inline void NiftiImage::initFromList (const Rcpp::RObject &object) Rcpp::List list(object); nifti_1_header *header = nifti_make_new_header(NULL, DT_FLOAT64); - const Rcpp::CharacterVector _names = list.names(); - std::set names; - for (Rcpp::CharacterVector::const_iterator it=_names.begin(); it!=_names.end(); it++) - names.insert(Rcpp::as(*it)); - - internal::copyIfPresent(list, names, "sizeof_hdr", header->sizeof_hdr); - - internal::copyIfPresent(list, names, "dim_info", header->dim_info); - if (names.count("dim") == 1) - { - std::vector dim = list["dim"]; - for (size_t i=0; idim[i] = dim[i]; - } - - internal::copyIfPresent(list, names, "intent_p1", header->intent_p1); - internal::copyIfPresent(list, names, "intent_p2", header->intent_p2); - internal::copyIfPresent(list, names, "intent_p3", header->intent_p3); - internal::copyIfPresent(list, names, "intent_code", header->intent_code); - - internal::copyIfPresent(list, names, "datatype", header->datatype); - internal::copyIfPresent(list, names, "bitpix", header->bitpix); - - internal::copyIfPresent(list, names, "slice_start", header->slice_start); - if (names.count("pixdim") == 1) - { - std::vector pixdim = list["pixdim"]; - for (size_t i=0; ipixdim[i] = pixdim[i]; - } - internal::copyIfPresent(list, names, "vox_offset", header->vox_offset); - internal::copyIfPresent(list, names, "scl_slope", header->scl_slope); - internal::copyIfPresent(list, names, "scl_inter", header->scl_inter); - internal::copyIfPresent(list, names, "slice_end", header->slice_end); - internal::copyIfPresent(list, names, "slice_code", header->slice_code); - internal::copyIfPresent(list, names, "xyzt_units", header->xyzt_units); - internal::copyIfPresent(list, names, "cal_max", header->cal_max); - internal::copyIfPresent(list, names, "cal_min", header->cal_min); - internal::copyIfPresent(list, names, "slice_duration", header->slice_duration); - internal::copyIfPresent(list, names, "toffset", header->toffset); - - if (names.count("descrip") == 1) - strcpy(header->descrip, Rcpp::as(list["descrip"]).substr(0,79).c_str()); - if (names.count("aux_file") == 1) - strcpy(header->aux_file, Rcpp::as(list["aux_file"]).substr(0,23).c_str()); - - internal::copyIfPresent(list, names, "qform_code", header->qform_code); - internal::copyIfPresent(list, names, "sform_code", header->sform_code); - internal::copyIfPresent(list, names, "quatern_b", header->quatern_b); - internal::copyIfPresent(list, names, "quatern_c", header->quatern_c); - internal::copyIfPresent(list, names, "quatern_d", header->quatern_d); - internal::copyIfPresent(list, names, "qoffset_x", header->qoffset_x); - internal::copyIfPresent(list, names, "qoffset_y", header->qoffset_y); - internal::copyIfPresent(list, names, "qoffset_z", header->qoffset_z); - - if (names.count("srow_x") == 1) - { - std::vector srow_x = list["srow_x"]; - for (size_t i=0; isrow_x[i] = srow_x[i]; - } - if (names.count("srow_y") == 1) - { - std::vector srow_y = list["srow_y"]; - for (size_t i=0; isrow_y[i] = srow_y[i]; - } - if (names.count("srow_z") == 1) - { - std::vector srow_z = list["srow_z"]; - for (size_t i=0; isrow_z[i] = srow_z[i]; - } - - if (names.count("intent_name") == 1) - strcpy(header->intent_name, Rcpp::as(list["intent_name"]).substr(0,15).c_str()); - if (names.count("magic") == 1) - strcpy(header->magic, Rcpp::as(list["magic"]).substr(0,3).c_str()); + internal::updateHeader(header, list); this->image = nifti_convert_nhdr2nim(*header, NULL); this->image->data = NULL; @@ -996,7 +963,7 @@ inline NiftiImage::NiftiImage (const SEXP object, const bool readData) resolved = true; if (imageObject.hasAttribute("dim")) - update(object); + update(imageObject); } else if (Rf_isString(object)) throw std::runtime_error("Internal image is not valid"); @@ -1037,7 +1004,29 @@ inline NiftiImage::NiftiImage (const SEXP object, const bool readData) #endif } -#endif // _NO_R__ +#endif // USING_R + +inline NiftiImage::NiftiImage (const std::string &path, const std::vector &volumes) + : persistent(false) +{ + if (volumes.empty()) + throw std::runtime_error("The vector of volumes is empty"); + + nifti_brick_list brickList; + this->image = nifti_image_read_bricks(path.c_str(), volumes.size(), &volumes[0], &brickList); + if (this->image == NULL) + throw std::runtime_error("Failed to read image from path " + path); + + size_t brickSize = image->nbyper * image->nx * image->ny * image->nz; + image->data = calloc(1, nifti_get_volsize(image)); + for (int i=0; idata + i * brickSize, brickList.bricks[i], brickSize); + nifti_free_NBL(&brickList); + +#ifndef NDEBUG + Rprintf("Creating NiftiImage with pointer %p (from string and volume vector)\n", this->image); +#endif +} inline void NiftiImage::updatePixdim (const std::vector &pixdim) { @@ -1334,67 +1323,88 @@ inline NiftiImage & NiftiImage::reorient (const std::string &orientation) return reorient(codes[0], codes[1], codes[2]); } -#ifndef _NO_R__ +#ifdef USING_R -inline NiftiImage & NiftiImage::update (const SEXP array) +inline NiftiImage & NiftiImage::update (const Rcpp::RObject &object) { - Rcpp::RObject object(array); - if (!object.hasAttribute("dim")) - return *this; + if (Rf_isVectorList(object)) + { + Rcpp::List list(object); + nifti_1_header *header = NULL; + if (this->isNull()) + { + header = nifti_make_new_header(NULL, DT_FLOAT64); + internal::updateHeader(header, list, true); + } + else + { + header = (nifti_1_header *) calloc(1, sizeof(nifti_1_header)); + *header = nifti_convert_nim2nhdr(image); + internal::updateHeader(header, list, true); + } + + if (header != NULL) + { + nifti_image *newImage = nifti_convert_nhdr2nim(*header, NULL); + if (this->image->data != NULL) + { + size_t dataSize = nifti_get_volsize(image); + newImage->data = calloc(1, dataSize); + memcpy(newImage->data, image->data, dataSize); + } + if (!persistent) + nifti_image_free(image); + this->image = newImage; + } + } + else if (object.hasAttribute("dim")) + { + for (int i=0; i<8; i++) + image->dim[i] = 0; + const std::vector dimVector = object.attr("dim"); - for (int i=0; i<8; i++) - image->dim[i] = 0; - const std::vector dimVector = object.attr("dim"); + const int nDims = std::min(7, int(dimVector.size())); + image->dim[0] = nDims; + for (int i=0; idim[i+1] = dimVector[i]; - const int nDims = std::min(7, int(dimVector.size())); - image->dim[0] = nDims; - for (int i=0; idim[i+1] = dimVector[i]; + if (object.hasAttribute("pixdim")) + { + const std::vector pixdimVector = object.attr("pixdim"); + updatePixdim(pixdimVector); + } - if (object.hasAttribute("pixdim")) - { - const std::vector pixdimVector = object.attr("pixdim"); - updatePixdim(pixdimVector); - } + if (object.hasAttribute("pixunits")) + { + const std::vector pixunitsVector = object.attr("pixunits"); + setPixunits(pixunitsVector); + } - if (object.hasAttribute("pixunits")) - { - const std::vector pixunitsVector = object.attr("pixunits"); - setPixunits(pixunitsVector); - } + // This NIfTI-1 library function clobbers dim[0] if the last dimension is unitary; we undo that here + nifti_update_dims_from_array(image); + image->dim[0] = image->ndim = nDims; - // This NIfTI-1 library function clobbers dim[0] if the last dimension is unitary; we undo that here - nifti_update_dims_from_array(image); - image->dim[0] = image->ndim = nDims; + image->datatype = NiftiImage::sexpTypeToNiftiType(object.sexp_type()); + nifti_datatype_sizes(image->datatype, &image->nbyper, NULL); - image->datatype = NiftiImage::sexpTypeToNiftiType(object.sexp_type()); - nifti_datatype_sizes(image->datatype, &image->nbyper, NULL); + if (!persistent) + nifti_image_unload(image); - if (!persistent) - nifti_image_unload(image); + const size_t dataSize = nifti_get_volsize(image); + image->data = calloc(1, dataSize); + if (image->datatype == DT_INT32) + memcpy(image->data, INTEGER(object), dataSize); + else + memcpy(image->data, REAL(object), dataSize); - const size_t dataSize = nifti_get_volsize(image); - image->data = calloc(1, dataSize); - if (image->datatype == DT_INT32) - { - memcpy(image->data, INTEGER(object), dataSize); - image->cal_min = static_cast(*std::min_element(INTEGER(object), INTEGER(object)+image->nvox)); - image->cal_max = static_cast(*std::max_element(INTEGER(object), INTEGER(object)+image->nvox)); + image->scl_slope = 0.0; + image->scl_inter = 0.0; } - else - { - memcpy(image->data, REAL(object), dataSize); - image->cal_min = static_cast(*std::min_element(REAL(object), REAL(object)+image->nvox)); - image->cal_max = static_cast(*std::max_element(REAL(object), REAL(object)+image->nvox)); - } - - image->scl_slope = 0.0; - image->scl_inter = 0.0; return *this; } -#endif// _NO_R__ +#endif // USING_R inline mat44 NiftiImage::xform (const bool preferQuaternion) const { @@ -1586,7 +1596,7 @@ inline void NiftiImage::toFile (const std::string fileName, const std::string &d toFile(fileName, internal::stringToDatatype(datatype)); } -#ifndef _NO_R__ +#ifdef USING_R inline Rcpp::RObject NiftiImage::toArray () const { @@ -1703,7 +1713,7 @@ inline Rcpp::RObject NiftiImage::headerToList () const return result; } -#endif // _NO_R__ +#endif // USING_R } // namespace diff --git a/inst/include/lib/NiftiImage_internal.h b/inst/include/lib/NiftiImage_internal.h index ac20767..f2478d2 100644 --- a/inst/include/lib/NiftiImage_internal.h +++ b/inst/include/lib/NiftiImage_internal.h @@ -203,7 +203,7 @@ inline short stringToDatatype (const std::string &datatype) return datatypeCodes[lowerCaseDatatype]; } -#ifndef _NO_R__ +#ifdef USING_R template inline void copyIfPresent (const Rcpp::List &list, const std::set names, const std::string &name, TargetType &target) @@ -220,7 +220,95 @@ inline void copyIfPresent (const Rcpp::List &list, const std::set n target = static_cast(Rcpp::as(list[name])); } -#endif // _NO_R__ +inline void updateHeader (nifti_1_header *header, const Rcpp::List &list, const bool ignoreDatatype = false) +{ + if (header == NULL) + return; + + const Rcpp::CharacterVector _names = list.names(); + std::set names; + for (Rcpp::CharacterVector::const_iterator it=_names.begin(); it!=_names.end(); it++) + names.insert(Rcpp::as(*it)); + + copyIfPresent(list, names, "sizeof_hdr", header->sizeof_hdr); + + copyIfPresent(list, names, "dim_info", header->dim_info); + if (names.count("dim") == 1) + { + std::vector dim = list["dim"]; + for (size_t i=0; idim[i] = dim[i]; + } + + copyIfPresent(list, names, "intent_p1", header->intent_p1); + copyIfPresent(list, names, "intent_p2", header->intent_p2); + copyIfPresent(list, names, "intent_p3", header->intent_p3); + copyIfPresent(list, names, "intent_code", header->intent_code); + + if (!ignoreDatatype) + { + copyIfPresent(list, names, "datatype", header->datatype); + copyIfPresent(list, names, "bitpix", header->bitpix); + } + + copyIfPresent(list, names, "slice_start", header->slice_start); + if (names.count("pixdim") == 1) + { + std::vector pixdim = list["pixdim"]; + for (size_t i=0; ipixdim[i] = pixdim[i]; + } + copyIfPresent(list, names, "vox_offset", header->vox_offset); + copyIfPresent(list, names, "scl_slope", header->scl_slope); + copyIfPresent(list, names, "scl_inter", header->scl_inter); + copyIfPresent(list, names, "slice_end", header->slice_end); + copyIfPresent(list, names, "slice_code", header->slice_code); + copyIfPresent(list, names, "xyzt_units", header->xyzt_units); + copyIfPresent(list, names, "cal_max", header->cal_max); + copyIfPresent(list, names, "cal_min", header->cal_min); + copyIfPresent(list, names, "slice_duration", header->slice_duration); + copyIfPresent(list, names, "toffset", header->toffset); + + if (names.count("descrip") == 1) + strcpy(header->descrip, Rcpp::as(list["descrip"]).substr(0,79).c_str()); + if (names.count("aux_file") == 1) + strcpy(header->aux_file, Rcpp::as(list["aux_file"]).substr(0,23).c_str()); + + copyIfPresent(list, names, "qform_code", header->qform_code); + copyIfPresent(list, names, "sform_code", header->sform_code); + copyIfPresent(list, names, "quatern_b", header->quatern_b); + copyIfPresent(list, names, "quatern_c", header->quatern_c); + copyIfPresent(list, names, "quatern_d", header->quatern_d); + copyIfPresent(list, names, "qoffset_x", header->qoffset_x); + copyIfPresent(list, names, "qoffset_y", header->qoffset_y); + copyIfPresent(list, names, "qoffset_z", header->qoffset_z); + + if (names.count("srow_x") == 1) + { + std::vector srow_x = list["srow_x"]; + for (size_t i=0; isrow_x[i] = srow_x[i]; + } + if (names.count("srow_y") == 1) + { + std::vector srow_y = list["srow_y"]; + for (size_t i=0; isrow_y[i] = srow_y[i]; + } + if (names.count("srow_z") == 1) + { + std::vector srow_z = list["srow_z"]; + for (size_t i=0; isrow_z[i] = srow_z[i]; + } + + if (names.count("intent_name") == 1) + strcpy(header->intent_name, Rcpp::as(list["intent_name"]).substr(0,15).c_str()); + if (names.count("magic") == 1) + strcpy(header->magic, Rcpp::as(list["magic"]).substr(0,3).c_str()); +} + +#endif // USING_R inline mat33 topLeftCorner (const mat44 &matrix) { @@ -234,7 +322,7 @@ inline mat33 topLeftCorner (const mat44 &matrix) return newMatrix; } -#ifndef _NO_R__ +#ifdef USING_R template inline Rcpp::RObject imageDataToArray (const nifti_image *source) @@ -304,7 +392,7 @@ inline void addAttributes (Rcpp::RObject &object, nifti_image *source, const boo object.attr(".nifti_image_ptr") = xptr; } -#endif // _NO_R__ +#endif // USING_R } // namespace diff --git a/inst/include/lib/print.h b/inst/include/lib/print.h index 6b4456b..7e49100 100644 --- a/inst/include/lib/print.h +++ b/inst/include/lib/print.h @@ -1,11 +1,12 @@ #ifndef _PRINT_H_ #define _PRINT_H_ -#ifndef _NO_R__ +#ifdef USING_R #define R_USE_C99_IN_CXX #include +#include #define Rc_printf Rprintf #define Rc_fprintf_stdout(...) Rprintf(__VA_ARGS__) @@ -27,6 +28,6 @@ #define Rf_warning(str) fprintf(stderr, "%s\n", str) #define Rprintf(...) fprintf(stderr, __VA_ARGS__) -#endif// _NO_R__ +#endif // USING_R -#endif// _PRINT_H_ +#endif // _PRINT_H_ diff --git a/inst/include/niftilib/nifti1_io.h b/inst/include/niftilib/nifti1_io.h index ebb22b7..900f048 100644 --- a/inst/include/niftilib/nifti1_io.h +++ b/inst/include/niftilib/nifti1_io.h @@ -510,8 +510,13 @@ typedef struct { } nifti_type_ele; #undef LNI_FERR /* local nifti file error, to be compact and repetative */ +#ifdef USING_R +#define LNI_FERR(func,msg,file) \ + Rf_warning("%s: %s '%s'\n",func,msg,file) +#else #define LNI_FERR(func,msg,file) \ Rc_fprintf_stderr("** ERROR (%s): %s '%s'\n",func,msg,file) +#endif #undef swap_2 #undef swap_4 diff --git a/man/niftiVersion.Rd b/man/niftiVersion.Rd new file mode 100644 index 0000000..0bf0988 --- /dev/null +++ b/man/niftiVersion.Rd @@ -0,0 +1,37 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/nifti.R +\name{niftiVersion} +\alias{niftiVersion} +\title{Check the format version of a file} +\usage{ +niftiVersion(file) +} +\arguments{ +\item{file}{A character vector of file names.} +} +\value{ +A vector of integers, of the same length as \code{file}. Each + element will be 0 for ANALYZE format (the precursor to NIfTI-1), 1 for + NIfTI-1 (which is now most common), 2 for NIfTI-2, or -1 if the file + doesn't exist or doesn't look plausible in any of these formats. +} +\description{ +This function identifies the likely NIfTI format variant used by one or more +files on disk. +} +\note{ +NIfTI-2 format, mostly a variant of NIfTI-1 with wider datatypes used + for many fields, is not currently supported for reading, but it is + detected by this function. +} +\examples{ +path <- system.file("extdata", "example.nii.gz", package="RNifti") +niftiVersion(path) # 1 + +} +\seealso{ +\code{\link{readNifti}} +} +\author{ +Jon Clayden +} diff --git a/man/readNifti.Rd b/man/readNifti.Rd index da5b487..ffb286d 100644 --- a/man/readNifti.Rd +++ b/man/readNifti.Rd @@ -4,7 +4,7 @@ \alias{readNifti} \title{Read a NIfTI-1 format file} \usage{ -readNifti(file, internal = FALSE) +readNifti(file, internal = FALSE, volumes = NULL) } \arguments{ \item{file}{A character vector of file names.} @@ -15,10 +15,16 @@ will be returned. If \code{TRUE}, the return value will be an object of class \code{"internalImage"}, which contains only minimal metadata about the image. Either way, the return value has an attribute which points to a C data structure containing the full image.} + +\item{volumes}{An integer vector giving the volumes to read (counting along +all dimensions beyond the third jointly), or \code{NULL}, the default, in +which case every volume is read. This cannot currently be set differently +for each file read.} } \value{ -An array or internal image, with class \code{"niftiImage"}, and - possibly also \code{"internalImage"}. +An array or internal image, with class \code{"niftiImage"} (and + possibly also \code{"internalImage"}), or a list of such objects if + \code{file} has length greater than one. } \description{ This function reads one or more NIfTI-1 files into R, using the standard diff --git a/man/updateNifti.Rd b/man/updateNifti.Rd index e2bb28c..a681378 100644 --- a/man/updateNifti.Rd +++ b/man/updateNifti.Rd @@ -4,7 +4,7 @@ \alias{updateNifti} \title{Update an internal NIfTI-1 object using a template} \usage{ -updateNifti(image, template = NULL) +updateNifti(image, template = NULL, datatype = "auto") } \arguments{ \item{image}{A numeric array.} @@ -13,16 +13,46 @@ updateNifti(image, template = NULL) \code{\link{retrieveNifti}}), or a named list of NIfTI-1 properties like that produced by \code{\link{dumpNifti}}. The default of \code{NULL} will have no effect.} + +\item{datatype}{The NIfTI datatype to use within the internal image. The +default, \code{"auto"} uses the R type. Other possibilities are +\code{"float"}, \code{"int16"}, etc., which may be preferred to reduce +object size. However, no checks are done to ensure that the coercion +maintains precision, and this option is for advanced usage only.} } \value{ A copy of the original \code{image}, with its internal image - attribute set or updated appropriately. + attribute set or updated appropriately. If \code{datatype} is not + \code{"auto"} then the result is an internal image. } \description{ This function adds or updates the internal NIfTI-1 object for an array, using metadata from the template. The dimensions and, if available, pixel dimensions, from the \code{image} will replace those from the template. } +\details{ +If \code{template} is a complete list of NIfTI-1 header fields, like that +produced by \code{\link{dumpNifti}}, or an image, then it will be used to +create the internal object, and then the data and metadata associated with +the \code{image} will overwrite the appropriate parts. If \code{template} +is an incomplete list, the \code{image} will be used to create the internal +object, and then the specified fields will be overwritten from the list. +This allows users to selectively update certain fields while leaving others +alone (but see the note below). + +Datatype information in a list \code{template} is ignored. The datatype can +only be changed using the \code{datatype} argument, but in this case the +internal object gets out of sync with the R array, so an internal image is +returned to avoid the mismatch. Changing the internal datatype in this way +is for advanced usage only. +} +\note{ +The \code{scl_slope} and \code{scl_inter} fields affect the numerical + interpretation of the pixel data, so it is impossible in general to change + them without also changing the array values on both the C and the R side. + Therefore, to avoid unexpected side-effects, these fields are not affected + by this function. +} \author{ Jon Clayden } diff --git a/src/Makevars b/src/Makevars index 8ec6ed2..e2375e1 100644 --- a/src/Makevars +++ b/src/Makevars @@ -1,4 +1,4 @@ -PKG_CPPFLAGS = -DNDEBUG -DHAVE_ZLIB -I../inst/include -Izlib +PKG_CPPFLAGS = -DNDEBUG -DHAVE_ZLIB -DUSING_R -I../inst/include -Izlib OBJECTS_ZLIB = zlib/adler32.o zlib/compress.o zlib/crc32.o zlib/deflate.o zlib/gzclose.o zlib/gzlib.o zlib/gzread.o zlib/gzwrite.o zlib/infback.o zlib/inffast.o zlib/inflate.o zlib/inftrees.o zlib/trees.o zlib/uncompr.o zlib/zutil.o diff --git a/src/main.cpp b/src/main.cpp index 3f35c7c..48c742a 100644 --- a/src/main.cpp +++ b/src/main.cpp @@ -25,11 +25,31 @@ bool isInternal (RObject object) return false; } -RcppExport SEXP readNifti (SEXP _object, SEXP _internal) +RcppExport SEXP niftiVersion (SEXP _path) { BEGIN_RCPP - NiftiImage image(_object); - return image.toArrayOrPointer(as(_internal), "NIfTI image"); + int version = NiftiImage::fileVersion(as(_path)); + return wrap(version); +END_RCPP +} + +RcppExport SEXP readNifti (SEXP _object, SEXP _internal, SEXP _volumes) +{ +BEGIN_RCPP + if (Rf_isNull(_volumes)) + { + NiftiImage image(_object); + return image.toArrayOrPointer(as(_internal), "NIfTI image"); + } + else + { + std::vector volumes; + IntegerVector volumesR(_volumes); + for (int i=0; i(_object), volumes); + return image.toArrayOrPointer(as(_internal), "NIfTI image"); + } END_RCPP } @@ -42,20 +62,40 @@ BEGIN_RCPP END_RCPP } -RcppExport SEXP updateNifti (SEXP _image, SEXP _reference) +RcppExport SEXP updateNifti (SEXP _image, SEXP _reference, SEXP _datatype) { BEGIN_RCPP - const NiftiImage reference(_reference); - RObject image(_image); + const std::string datatype = as(_datatype); + const bool willChangeDatatype = (datatype != "auto"); - if (!reference.isNull()) + if (Rf_isVectorList(_reference) && Rf_length(_reference) < 36) { - NiftiImage updatedImage = reference; - updatedImage.update(image); - return updatedImage.toArray(); + NiftiImage image(_image); + image.update(_reference); + if (willChangeDatatype) + image.changeDatatype(datatype); + return image.toArrayOrPointer(willChangeDatatype, "NIfTI image"); } else - return image; + { + const NiftiImage reference(_reference); + if (reference.isNull() && willChangeDatatype) + { + NiftiImage image(_image); + image.changeDatatype(datatype); + return image.toPointer("NIfTI image"); + } + else if (reference.isNull() && !willChangeDatatype) + return _image; + else + { + NiftiImage image = reference; + image.update(_image); + if (willChangeDatatype) + image.changeDatatype(datatype); + return image.toArrayOrPointer(willChangeDatatype, "NIfTI image"); + } + } END_RCPP } @@ -179,9 +219,10 @@ END_RCPP extern "C" { static R_CallMethodDef callMethods[] = { - { "readNifti", (DL_FUNC) &readNifti, 2 }, + { "niftiVersion", (DL_FUNC) &niftiVersion, 1 }, + { "readNifti", (DL_FUNC) &readNifti, 3 }, { "writeNifti", (DL_FUNC) &writeNifti, 3 }, - { "updateNifti", (DL_FUNC) &updateNifti, 2 }, + { "updateNifti", (DL_FUNC) &updateNifti, 3 }, { "dumpNifti", (DL_FUNC) &dumpNifti, 1 }, { "getXform", (DL_FUNC) &getXform, 2 }, { "setXform", (DL_FUNC) &setXform, 3 }, diff --git a/tests/testthat/test-05-nifti.R b/tests/testthat/test-05-nifti.R index a1c58f0..8f377f1 100644 --- a/tests/testthat/test-05-nifti.R +++ b/tests/testthat/test-05-nifti.R @@ -1,43 +1,76 @@ -context("Reading and writing NIfTI files") +context("Reading, writing and manipulating NIfTI objects") + +test_that("NIfTI objects can be created from data", { + data <- array(rnorm(24), dim=c(3L,2L,4L)) + image <- retrieveNifti(data) + + expect_equal(ndim(data), 3L) + expect_is(image, "internalImage") + expect_equal(dim(image), c(3L,2L,4L)) + expect_equal(pixdim(data), c(1,1,1)) + expect_equal(pixdim(image), c(1,1,1)) + expect_equal(pixunits(data), "Unknown") + expect_equal(pixunits(image), "Unknown") + expect_equal(dumpNifti(image)$datatype, 64L) +}) test_that("NIfTI files can be read and written", { imagePath <- system.file("extdata", "example.nii.gz", package="RNifti") + volumeImagePath <- system.file("extdata", "example_4d.nii.gz", package="RNifti") compressedImagePath <- system.file("extdata", "example_compressed.nii.gz", package="RNifti") tempPath <- paste(tempfile(), "nii.gz", sep=".") - expect_that(dim(readNifti(imagePath,internal=FALSE)), equals(c(96L,96L,60L))) - expect_that(dim(readNifti(imagePath,internal=TRUE)), equals(c(96L,96L,60L))) - expect_that(print(readNifti(imagePath,internal=TRUE)), prints_text("2.5 mm per voxel",fixed=TRUE)) + expect_equal(niftiVersion(imagePath), structure(1L,names=imagePath)) + expect_equal(dim(readNifti(imagePath,internal=FALSE)), c(96L,96L,60L)) + expect_equal(dim(readNifti(imagePath,internal=TRUE)), c(96L,96L,60L)) + expect_output(print(readNifti(imagePath,internal=TRUE)), "2.5 mm per voxel") image <- readNifti(imagePath) - expect_that(pixunits(image), equals(c("mm","s"))) + expect_equal(image[40,40,30], 368) + expect_equal(pixunits(image), c("mm","s")) writeNifti(image, tempPath) - expect_that(pixdim(readNifti(tempPath)), equals(c(2.5,2.5,2.5))) + expect_equal(pixdim(readNifti(tempPath)), c(2.5,2.5,2.5)) unlink(tempPath) + expect_output(print(dumpNifti(image)), "NIfTI-1 header") + expect_equal(dumpNifti(image)$bitpix, 32L) writeNifti(image, tempPath, datatype="short") - expect_that(dumpNifti(tempPath)$bitpix, equals(16L)) + expect_equal(dumpNifti(tempPath)$bitpix, 16L) unlink(tempPath) - expect_that(dumpNifti(image)$dim, equals(c(3L,96L,96L,60L,1L,1L,1L,1L))) + expect_equal(dumpNifti(compressedImagePath)$datatype, 2L) + compressedImage <- readNifti(compressedImagePath) + expect_equal(dumpNifti(compressedImage)$datatype, 64L) + expect_equal(round(compressedImage[40,40,30]), 363) + + image <- readNifti(imagePath, internal=TRUE) + expect_equal(as.array(image)[40,40,30], 368) + expect_error(dim(image) <- c(60L,96L,96L)) + + image <- readNifti(volumeImagePath, volumes=1:2) + expect_equal(dim(image), c(96L,96L,60L,2L)) + expect_equal(max(image), 2) + expect_output(print(image), "x 1 s") # time units only appear for 4D+ images +}) + +test_that("image objects can be manipulated", { + imagePath <- system.file("extdata", "example.nii.gz", package="RNifti") + image <- readNifti(imagePath) + + expect_equal(dumpNifti(image)$dim, c(3L,96L,96L,60L,1L,1L,1L,1L)) pixdim(image) <- c(5,5,5) - expect_that(dumpNifti(image)$pixdim, equals(c(-1,5,5,5,0,0,0,0))) + expect_equal(dumpNifti(image)$pixdim, c(-1,5,5,5,0,0,0,0)) pixunits(image) <- c("m","ms") - expect_that(dumpNifti(image)$xyzt_units, equals(17L)) + expect_equal(dumpNifti(image)$xyzt_units, 17L) image <- updateNifti(image, list(intent_code=1000L)) - expect_that(dumpNifti(image)$intent_code, equals(1000L)) + expect_equal(dumpNifti(image)$intent_code, 1000L) + image <- updateNifti(image, datatype="float") + expect_equal(dumpNifti(image)$datatype, 16L) - expect_that(image[40,40,30], equals(368)) image <- readNifti(imagePath, internal=TRUE) - expect_that(as.array(image)[40,40,30], equals(368)) image <- RNifti:::rescaleNifti(image, c(0.5,0.5,0.5)) - expect_that(pixdim(image), equals(c(5,5,5))) - expect_that(as.array(image), gives_warning("no data")) - - expect_that(dumpNifti(compressedImagePath)$datatype, equals(2L)) - compressedImage <- readNifti(compressedImagePath) - expect_that(dumpNifti(compressedImage)$datatype, equals(64L)) - expect_that(round(compressedImage[40,40,30]), equals(363)) + expect_equal(pixdim(image), c(5,5,5)) + expect_warning(as.array(image), "no data") }) diff --git a/tests/testthat/test-10-xform.R b/tests/testthat/test-10-xform.R index d36e116..d55317d 100644 --- a/tests/testthat/test-10-xform.R +++ b/tests/testthat/test-10-xform.R @@ -4,32 +4,33 @@ test_that("NIfTI sform/qform operations work", { imagePath <- system.file("extdata", "example.nii.gz", package="RNifti") image <- readNifti(imagePath) - expect_that(diag(xform(image)), equals(c(-2.5,2.5,2.5,1))) - expect_that(diag(xform(image,useQuaternionFirst=FALSE)), equals(c(-2.5,2.5,2.5,1))) + expect_equal(diag(xform(image)), c(-2.5,2.5,2.5,1)) + expect_equal(diag(xform(image,useQuaternionFirst=FALSE)), c(-2.5,2.5,2.5,1)) + expect_equal(round(origin(image)), c(50,39,23)) point <- c(40, 40, 20) - expect_that(round(voxelToWorld(point,image)), equals(c(25,2,-8))) - expect_that(voxelToWorld(point,image,simple=TRUE), equals(c(97.5,97.5,47.5))) - expect_that(worldToVoxel(voxelToWorld(point,image),image), equals(point)) - expect_that(worldToVoxel(voxelToWorld(point,image,simple=TRUE),image,simple=TRUE), equals(point)) + expect_equal(round(voxelToWorld(point,image)), c(25,2,-8)) + expect_equal(voxelToWorld(point,image,simple=TRUE), c(97.5,97.5,47.5)) + expect_equal(worldToVoxel(voxelToWorld(point,image),image), point) + expect_equal(worldToVoxel(voxelToWorld(point,image,simple=TRUE),image,simple=TRUE), point) # NB: indexing into the image currently discards the metadata, including the xforms - expect_that(voxelToWorld(point[1:2],image[,,20L]), equals(c(39,39))) + expect_equal(voxelToWorld(point[1:2],image[,,20L]), c(39,39)) # Copy image object to check copy semantics originalImage <- image xform <- structure(round(xform(image)), code=4) qform(image) <- xform sform(image) <- xform - expect_that(dumpNifti(image)$qform_code, equals(4L)) - expect_that(dumpNifti(image)$sform_code, equals(4L)) - expect_that(dumpNifti(image)$srow_x, equals(c(-2,0,0,122))) - expect_that(dumpNifti(originalImage)$qform_code, equals(2L)) + expect_equal(dumpNifti(image)$qform_code, 4L) + expect_equal(dumpNifti(image)$sform_code, 4L) + expect_equal(dumpNifti(image)$srow_x, c(-2,0,0,122)) + expect_equal(dumpNifti(originalImage)$qform_code, 2L) image <- readNifti(imagePath, internal=FALSE) reorientedImage <- image orientation(reorientedImage) <- "PIR" - expect_that(orientation(image), equals("LAS")) - expect_that(orientation(reorientedImage), equals("PIR")) - expect_that(image[40,40,30], equals(reorientedImage[57,31,57])) + expect_equal(orientation(image), "LAS") + expect_equal(orientation(reorientedImage), "PIR") + expect_equal(image[40,40,30], reorientedImage[57,31,57]) }) diff --git a/tests/testthat/test-15-foreign.R b/tests/testthat/test-15-foreign.R index b9ef140..48bcb16 100644 --- a/tests/testthat/test-15-foreign.R +++ b/tests/testthat/test-15-foreign.R @@ -1,27 +1,25 @@ context("Working with objects from other packages") -test_that("image objects from other packages can be read", { +test_that("image objects from oro.nifti can be read", { imagePath <- system.file("extdata", "example.nii.gz", package="RNifti") - if (system.file(package="oro.nifti") == "") - skip("The \"oro.nifti\" package is not available") - else - { - # The oro.nifti package warns about nonzero slope, which is nothing to worry about - image <- suppressWarnings(oro.nifti::readNIfTI(imagePath)) - expect_that(dumpNifti(image)$bitpix, equals(32L)) - } + skip_if_not_installed("oro.nifti") - if (system.file(package="tractor.base") == "") - skip("The \"tractor.base\" package is not available") - else - { - reportr::setOutputLevel(reportr::OL$Warning) - - image <- tractor.base::readImageFile(imagePath) - expect_that(dumpNifti(image)$bitpix, equals(32L)) - - image <- tractor.base::readImageFile(imagePath, sparse=TRUE) - expect_that(dumpNifti(image)$bitpix, equals(32L)) - } -}) \ No newline at end of file + # The oro.nifti package warns about nonzero slope, which is nothing to worry about + image <- suppressWarnings(oro.nifti::readNIfTI(imagePath)) + expect_equal(dumpNifti(image)$bitpix, 32L) +}) + +test_that("image objects from tractor.base can be read", { + imagePath <- system.file("extdata", "example.nii.gz", package="RNifti") + + skip_if_not_installed("tractor.base") + + reportr::setOutputLevel(reportr::OL$Warning) + + image <- tractor.base::readImageFile(imagePath) + expect_equal(dumpNifti(image)$bitpix, 32L) + + image <- tractor.base::readImageFile(imagePath, sparse=TRUE) + expect_equal(dumpNifti(image)$bitpix, 32L) +})