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github | tomdoel/pulmonarytoolkit-master | rri_orient.m | .m | pulmonarytoolkit-master/External/Nifti_tools/rri_orient.m | 2,251 | utf_8 | 4253fb96b9189a8a4bad49661d9ecac3 | % Convert image of different orientations to standard Analyze orientation
%
% Usage: nii = rri_orient(nii);
% Jimmy Shen (jimmy@rotman-baycrest.on.ca), 26-APR-04
%___________________________________________________________________
function [nii, orient, pattern] = rri_orient(nii, varargin)
if nargin > 1
... |
github | tomdoel/pulmonarytoolkit-master | save_untouch0_nii_hdr.m | .m | pulmonarytoolkit-master/External/Nifti_tools/save_untouch0_nii_hdr.m | 8,594 | utf_8 | 7e8b1b327e1924837820f75780d52d01 | % internal function
% - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
function save_nii_hdr(hdr, fid)
if ~isequal(hdr.hk.sizeof_hdr,348),
error('hdr.hk.sizeof_hdr must be 348.');
end
write_header(hdr, fid);
return; % save_nii_hdr
%---------------------------------------------------------------... |
github | tomdoel/pulmonarytoolkit-master | rri_zoom_menu.m | .m | pulmonarytoolkit-master/External/Nifti_tools/rri_zoom_menu.m | 737 | utf_8 | d8151523470b0fba970eb1d98ba56030 | % Imbed a zoom menu to any figure.
%
% Usage: rri_zoom_menu(fig);
%
% - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
%
%--------------------------------------------------------------------
function menu_hdl = rri_zoom_menu(fig)
if isnumeric(fig)
menu_hdl = uimenu('Parent',fig, ...
'Label','Zoom on', ..... |
github | tomdoel/pulmonarytoolkit-master | rri_select_file.m | .m | pulmonarytoolkit-master/External/Nifti_tools/rri_select_file.m | 16,599 | utf_8 | e349954ca803370f62ceeabdbab5912e | function [selected_file, selected_path] = rri_select_file(varargin)
%
% USAGE: [selected_file, selected_path] = ...
% rri_select_file(dir_name, fig_title)
%
% Allow user to select a file from a list of Matlab competible
% file format
%
% Example:
%
% [selected_file, selected_path] = ...
% rri_select_... |
github | tomdoel/pulmonarytoolkit-master | clip_nii.m | .m | pulmonarytoolkit-master/External/Nifti_tools/clip_nii.m | 3,306 | utf_8 | a70bdbed5a0813312d4c83f94b99a710 | % CLIP_NII: Clip the NIfTI volume from any of the 6 sides
%
% Usage: nii = clip_nii(nii, [option])
%
% Inputs:
%
% nii - NIfTI volume.
%
% option - struct instructing how many voxel to be cut from which side.
%
% option.cut_from_L = ( number of voxel )
% option.cut_from_R = ( number of voxel )
% option.cut_from_P ... |
github | tomdoel/pulmonarytoolkit-master | affine.m | .m | pulmonarytoolkit-master/External/Nifti_tools/affine.m | 16,110 | utf_8 | 768d2303e551a9584685bdb01abf6f8b | % Using 2D or 3D affine matrix to rotate, translate, scale, reflect and
% shear a 2D image or 3D volume. 2D image is represented by a 2D matrix,
% 3D volume is represented by a 3D matrix, and data type can be real
% integer or floating-point.
%
% You may notice that MATLAB has a function called 'imtransform.m' fo... |
github | tomdoel/pulmonarytoolkit-master | load_untouch_nii_img.m | .m | pulmonarytoolkit-master/External/Nifti_tools/load_untouch_nii_img.m | 14,756 | utf_8 | 688b2a42f8071c6402a037c7ca923689 | % internal function
% - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
function [img,hdr] = load_untouch_nii_img(hdr,filetype,fileprefix,machine,img_idx,dim5_idx,dim6_idx,dim7_idx,old_RGB,slice_idx)
if ~exist('hdr','var') | ~exist('filetype','var') | ~exist('fileprefix','var') | ~exist('machine','var')
error('U... |
github | tomdoel/pulmonarytoolkit-master | load_untouch_nii.m | .m | pulmonarytoolkit-master/External/Nifti_tools/load_untouch_nii.m | 6,182 | utf_8 | 93108a725d2e357d773c8aa0acf71328 | % Load NIFTI or ANALYZE dataset, but not applying any appropriate affine
% geometric transform or voxel intensity scaling.
%
% Although according to NIFTI website, all those header information are
% supposed to be applied to the loaded NIFTI image, there are some
% situations that people do want to leave the origi... |
github | tomdoel/pulmonarytoolkit-master | collapse_nii_scan.m | .m | pulmonarytoolkit-master/External/Nifti_tools/collapse_nii_scan.m | 6,778 | utf_8 | 64b1cb0f7cd9e095d3c11ca66453df69 | % Collapse multiple single-scan NIFTI files into a multiple-scan NIFTI file
%
% Usage: collapse_nii_scan(scan_file_pattern, [collapsed_fileprefix], [scan_file_folder])
%
% Here, scan_file_pattern should look like: 'myscan_0*.img'
% If collapsed_fileprefix is omit, 'multi_scan' will be used
% If scan_file_folder is... |
github | tomdoel/pulmonarytoolkit-master | rri_orient_ui.m | .m | pulmonarytoolkit-master/External/Nifti_tools/rri_orient_ui.m | 5,384 | utf_8 | e1196b81940d9f93fbdb43c33799e587 | % Return orientation of the current image:
% orient is orientation 1x3 matrix, in that:
% Three elements represent: [x y z]
% Element value: 1 - Left to Right; 2 - Posterior to Anterior;
% 3 - Inferior to Superior; 4 - Right to Left;
% 5 - Anterior to Posterior; 6 - Superior to Inferior;
% e.g.:
% Standard RAS Or... |
github | tomdoel/pulmonarytoolkit-master | load_untouch0_nii_hdr.m | .m | pulmonarytoolkit-master/External/Nifti_tools/load_untouch0_nii_hdr.m | 8,093 | utf_8 | 3de9ff6a1da47b56ae680e7660eaa041 | % internal function
% - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
function hdr = load_nii_hdr(fileprefix, machine)
fn = sprintf('%s.hdr',fileprefix);
fid = fopen(fn,'r',machine);
if fid < 0,
msg = sprintf('Cannot open file %s.',fn);
error(msg);
else
fseek(fid,0,'bof');
hdr =... |
github | tomdoel/pulmonarytoolkit-master | load_nii.m | .m | pulmonarytoolkit-master/External/Nifti_tools/load_nii.m | 6,808 | utf_8 | d098a5dbea3cd4ad76cea624ffbef9db | % Load NIFTI or ANALYZE dataset. Support both *.nii and *.hdr/*.img
% file extension. If file extension is not provided, *.hdr/*.img will
% be used as default.
%
% A subset of NIFTI transform is included. For non-orthogonal rotation,
% shearing etc., please use 'reslice_nii.m' to reslice the NIFTI file.
% It will... |
github | tomdoel/pulmonarytoolkit-master | unxform_nii.m | .m | pulmonarytoolkit-master/External/Nifti_tools/unxform_nii.m | 1,181 | utf_8 | a77d113be34b09d588b2eb326a3c65c8 | % Undo the flipping and rotations performed by xform_nii; spit back only
% the raw img data block. Initial cut will only deal with 3D volumes
% strongly assume we have called xform_nii to write down the steps used
% in xform_nii.
%
% Usage: a = load_nii('original_name');
% manipulate a.img to make array... |
github | tomdoel/pulmonarytoolkit-master | load_untouch_nii_hdr.m | .m | pulmonarytoolkit-master/External/Nifti_tools/load_untouch_nii_hdr.m | 8,522 | utf_8 | 2d4bc8c8ffb83b37daf1e8dd87c108e6 | % internal function
% - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
function hdr = load_nii_hdr(fileprefix, machine, filetype)
if filetype == 2
fn = sprintf('%s.nii',fileprefix);
if ~exist(fn)
msg = sprintf('Cannot find file "%s.nii".', fileprefix);
error(msg);
end
else
... |
github | tomdoel/pulmonarytoolkit-master | save_nii_ext.m | .m | pulmonarytoolkit-master/External/Nifti_tools/save_nii_ext.m | 977 | utf_8 | b60a98ab7537a883dc3ffef3175f19ae | % Save NIFTI header extension.
%
% Usage: save_nii_ext(ext, fid)
%
% ext - struct with NIFTI header extension fields.
%
% NIFTI data format can be found on: http://nifti.nimh.nih.gov
%
% - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
%
function save_nii_ext(ext, fid)
if ~exist('ext','var') | ~exist('fid','var')
... |
github | tomdoel/pulmonarytoolkit-master | view_nii_menu.m | .m | pulmonarytoolkit-master/External/Nifti_tools/view_nii_menu.m | 14,415 | utf_8 | 32dd591fa1070721f0255f47f6e02510 | % Imbed Zoom, Interp, and Info menu to view_nii window.
%
% Usage: view_nii_menu(fig);
%
% - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
%
%--------------------------------------------------------------------
function menu_hdl = view_nii_menu(fig, varargin)
if isnumeric(fig)
menu_hdl = init(fig);
retur... |
github | tomdoel/pulmonarytoolkit-master | save_untouch_header_only.m | .m | pulmonarytoolkit-master/External/Nifti_tools/save_untouch_header_only.m | 2,132 | utf_8 | 5f0515ef6a35f171bc8371d0f3fd365d | % This function is only used to save Analyze or NIfTI header that is
% ended with .hdr and loaded by load_untouch_header_only.m. If you
% have NIfTI file that is ended with .nii and you want to change its
% header only, you can use load_untouch_nii / save_untouch_nii pair.
%
% Usage: save_untouch_header_only(hd... |
github | tomdoel/pulmonarytoolkit-master | pad_nii.m | .m | pulmonarytoolkit-master/External/Nifti_tools/pad_nii.m | 3,712 | utf_8 | 0b9de8feba6840e2d8ea1ab1752747c7 | % PAD_NII: Pad the NIfTI volume from any of the 6 sides
%
% Usage: nii = pad_nii(nii, [option])
%
% Inputs:
%
% nii - NIfTI volume.
%
% option - struct instructing how many voxel to be padded from which side.
%
% option.pad_from_L = ( number of voxel )
% option.pad_from_R = ( number of voxel )
% option.pad_from_P ... |
github | tomdoel/pulmonarytoolkit-master | load_nii_hdr.m | .m | pulmonarytoolkit-master/External/Nifti_tools/load_nii_hdr.m | 10,031 | utf_8 | e95839e314863f7ee463cc2626dd447c | % internal function
% - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
function [hdr, filetype, fileprefix, machine] = load_nii_hdr(fileprefix)
if ~exist('fileprefix','var'),
error('Usage: [hdr, filetype, fileprefix, machine] = load_nii_hdr(filename)');
end
machine = 'ieee-le';
new_ext = 0;
if fin... |
github | tomdoel/pulmonarytoolkit-master | save_untouch_slice.m | .m | pulmonarytoolkit-master/External/Nifti_tools/save_untouch_slice.m | 19,683 | utf_8 | 364468e5dbd3790c1aadf9a768534f1f | % Save back to the original image with a portion of slices that was
% loaded by "load_untouch_nii". You can process those slices matrix
% in any way, as long as their dimension is not altered.
%
% Usage: save_untouch_slice(slice, filename, ...
% slice_idx, [img_idx], [dim5_idx], [dim6_idx], [dim7_idx])
%
% slice ... |
github | tomdoel/pulmonarytoolkit-master | load_nii_img.m | .m | pulmonarytoolkit-master/External/Nifti_tools/load_nii_img.m | 12,328 | utf_8 | b1b9dd2838a8f217b10fefdc8a931d5e | % internal function
% - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
function [img,hdr] = load_nii_img(hdr,filetype,fileprefix,machine,img_idx,dim5_idx,dim6_idx,dim7_idx,old_RGB)
if ~exist('hdr','var') | ~exist('filetype','var') | ~exist('fileprefix','var') | ~exist('machine','var')
error('Usage: [img,hdr] = ... |
github | tomdoel/pulmonarytoolkit-master | bresenham_line3d.m | .m | pulmonarytoolkit-master/External/Nifti_tools/bresenham_line3d.m | 4,493 | utf_8 | c19f06df423676afeb59762ac55c0c2f | % Generate X Y Z coordinates of a 3D Bresenham's line between
% two given points.
%
% A very useful application of this algorithm can be found in the
% implementation of Fischer's Bresenham interpolation method in my
% another program that can rotate three dimensional image volume
% with an affine matrix:
% http... |
github | tomdoel/pulmonarytoolkit-master | make_nii.m | .m | pulmonarytoolkit-master/External/Nifti_tools/make_nii.m | 6,842 | utf_8 | 2ce600a040fdea42e96aeab2aaac0fbb | % Make NIfTI structure specified by an N-D matrix. Usually, N is 3 for
% 3D matrix [x y z], or 4 for 4D matrix with time series [x y z t].
% Optional parameters can also be included, such as: voxel_size,
% origin, datatype, and description.
%
% Once the NIfTI structure is made, it can be saved into NIfTI fil... |
github | tomdoel/pulmonarytoolkit-master | verify_nii_ext.m | .m | pulmonarytoolkit-master/External/Nifti_tools/verify_nii_ext.m | 1,676 | utf_8 | db3d32ecba688905185f5ed01b409fd1 | % Verify NIFTI header extension to make sure that each extension section
% must be an integer multiple of 16 byte long that includes the first 8
% bytes of esize and ecode. If the length of extension section is not the
% above mentioned case, edata should be padded with all 0.
%
% Usage: [ext, esize_total] = verif... |
github | tomdoel/pulmonarytoolkit-master | get_nii_frame.m | .m | pulmonarytoolkit-master/External/Nifti_tools/get_nii_frame.m | 4,333 | utf_8 | 8b0cba9d07733a6f82753b0c40b51107 | % Return time frame of a NIFTI dataset. Support both *.nii and
% *.hdr/*.img file extension. If file extension is not provided,
% *.hdr/*.img will be used as default.
%
% It is a lightweighted "load_nii_hdr", and is equivalent to
% hdr.dime.dim(5)
%
% Usage: [ total_scan ] = get_nii_frame(filename)
%
% filen... |
github | tomdoel/pulmonarytoolkit-master | flip_lr.m | .m | pulmonarytoolkit-master/External/Nifti_tools/flip_lr.m | 3,484 | utf_8 | a0b2d0189d90339a841863efeb60681a | % When you load any ANALYZE or NIfTI file with 'load_nii.m', and view
% it with 'view_nii.m', you may find that the image is L-R flipped.
% This is because of the confusion of radiological and neurological
% convention in the medical image before NIfTI format is adopted. You
% can find more details from:
%
% http... |
github | tomdoel/pulmonarytoolkit-master | save_nii.m | .m | pulmonarytoolkit-master/External/Nifti_tools/save_nii.m | 9,404 | utf_8 | 88aa93174482539fe993ac335fb01541 | % Save NIFTI dataset. Support both *.nii and *.hdr/*.img file extension.
% If file extension is not provided, *.hdr/*.img will be used as default.
%
% Usage: save_nii(nii, filename, [old_RGB])
%
% nii.hdr - struct with NIFTI header fields (from load_nii.m or make_nii.m)
%
% nii.img - 3D (or 4D) matrix of NIFTI... |
github | tomdoel/pulmonarytoolkit-master | rri_file_menu.m | .m | pulmonarytoolkit-master/External/Nifti_tools/rri_file_menu.m | 3,974 | utf_8 | 1ec91620ceb4108dde9a63945380028f | % Imbed a file menu to any figure. If file menu exist, it will append
% to the existing file menu. This file menu includes: Copy to clipboard,
% print, save, close etc.
%
% Usage: rri_file_menu(fig);
%
% rri_file_menu(fig,0) means no 'Close' menu.
%
% - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
%
%---------... |
github | tomdoel/pulmonarytoolkit-master | reslice_nii.m | .m | pulmonarytoolkit-master/External/Nifti_tools/reslice_nii.m | 9,817 | utf_8 | 05783cd4f127a22486db67a9cc89ad2a | % The basic application of the 'reslice_nii.m' program is to perform
% any 3D affine transform defined by a NIfTI format image.
%
% In addition, the 'reslice_nii.m' program can also be applied to
% generate an isotropic image from either a NIfTI format image or
% an ANALYZE format image.
%
% The resliced NIfTI fi... |
github | tomdoel/pulmonarytoolkit-master | save_untouch_nii.m | .m | pulmonarytoolkit-master/External/Nifti_tools/save_untouch_nii.m | 6,494 | utf_8 | 50fa95cbb847654356241a853328f912 | % Save NIFTI or ANALYZE dataset that is loaded by "load_untouch_nii.m".
% The output image format and file extension will be the same as the
% input one (NIFTI.nii, NIFTI.img or ANALYZE.img). Therefore, any file
% extension that you specified will be ignored.
%
% Usage: save_untouch_nii(nii, filename)
%
% nii -... |
github | tomdoel/pulmonarytoolkit-master | view_nii.m | .m | pulmonarytoolkit-master/External/Nifti_tools/view_nii.m | 139,608 | utf_8 | 74f9dea7539a45a7993beb22becf2fa2 | % VIEW_NII: Create or update a 3-View (Front, Top, Side) of the
% brain data that is specified by nii structure
%
% Usage: status = view_nii([h], nii, [option]) or
% status = view_nii(h, [option])
%
% Where, h is the figure on which the 3-View will be plotted;
% nii is the brain data in NIFTI format;
% option is... |
github | tomdoel/pulmonarytoolkit-master | mat_into_hdr.m | .m | pulmonarytoolkit-master/External/Nifti_tools/mat_into_hdr.m | 2,608 | utf_8 | d53006b93ff90a4a5561d16ff2f4e9a6 | %MAT_INTO_HDR The old versions of SPM (any version before SPM5) store
% an affine matrix of the SPM Reoriented image into a matlab file
% (.mat extension). The file name of this SPM matlab file is the
% same as the SPM Reoriented image file (.img/.hdr extension).
%
% This program will convert the ANALYZE 7.5 SPM Reor... |
github | tomdoel/pulmonarytoolkit-master | xform_nii.m | .m | pulmonarytoolkit-master/External/Nifti_tools/xform_nii.m | 18,107 | utf_8 | 29a1cff91c944d6a93e5101946a5da4d | % internal function
% 'xform_nii.m' is an internal function called by "load_nii.m", so
% you do not need run this program by yourself. It does simplified
% NIfTI sform/qform affine transform, and supports some of the
% affine transforms, including translation, reflection, and
% orthogonal rotation (N*90 degree... |
github | tomdoel/pulmonarytoolkit-master | make_ana.m | .m | pulmonarytoolkit-master/External/Nifti_tools/make_ana.m | 5,455 | utf_8 | 2f62999cbcad72129c892135ff492a1e | % Make ANALYZE 7.5 data structure specified by a 3D or 4D matrix.
% Optional parameters can also be included, such as: voxel_size,
% origin, datatype, and description.
%
% Once the ANALYZE structure is made, it can be saved into ANALYZE 7.5
% format data file using "save_untouch_nii" command (for more detail,... |
github | tomdoel/pulmonarytoolkit-master | extra_nii_hdr.m | .m | pulmonarytoolkit-master/External/Nifti_tools/extra_nii_hdr.m | 7,830 | utf_8 | 853f39f00cbf133e90d0f2cf08d79488 | % Decode extra NIFTI header information into hdr.extra
%
% Usage: hdr = extra_nii_hdr(hdr)
%
% hdr can be obtained from load_nii_hdr
%
% NIFTI data format can be found on: http://nifti.nimh.nih.gov
%
% - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
%
function hdr = extra_nii_hdr(hdr)
switch hdr.dime.datatype
ca... |
github | tomdoel/pulmonarytoolkit-master | rri_xhair.m | .m | pulmonarytoolkit-master/External/Nifti_tools/rri_xhair.m | 2,208 | utf_8 | b3ae9df90d43e5d9538b6b135fa8af20 | % rri_xhair: create a pair of full_cross_hair at point [x y] in
% axes h_ax, and return xhair struct
%
% Usage: xhair = rri_xhair([x y], xhair, h_ax);
%
% If omit xhair, rri_xhair will create a pair of xhair; otherwise,
% rri_xhair will update the xhair. If omit h_ax, current axes will
% be used.... |
github | tomdoel/pulmonarytoolkit-master | save_untouch_nii_hdr.m | .m | pulmonarytoolkit-master/External/Nifti_tools/save_untouch_nii_hdr.m | 8,514 | utf_8 | 582f82c471a9a8826eda59354f61dd1a | % internal function
% - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
function save_nii_hdr(hdr, fid)
if ~isequal(hdr.hk.sizeof_hdr,348),
error('hdr.hk.sizeof_hdr must be 348.');
end
write_header(hdr, fid);
return; % save_nii_hdr
%---------------------------------------------------------------... |
github | tomdoel/pulmonarytoolkit-master | expand_nii_scan.m | .m | pulmonarytoolkit-master/External/Nifti_tools/expand_nii_scan.m | 1,333 | utf_8 | 748da05d09c1a005401c67270c4b94ab | % Expand a multiple-scan NIFTI file into multiple single-scan NIFTI files
%
% Usage: expand_nii_scan(multi_scan_filename, [img_idx], [path_to_save])
%
% NIFTI data format can be found on: http://nifti.nimh.nih.gov
%
% - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
%
function expand_nii_scan(filename, img_idx, newpath)
... |
github | tomdoel/pulmonarytoolkit-master | load_untouch_header_only.m | .m | pulmonarytoolkit-master/External/Nifti_tools/load_untouch_header_only.m | 7,068 | utf_8 | 8996c72db42b01029c92a4ecd88f4b21 | % Load NIfTI / Analyze header without applying any appropriate affine
% geometric transform or voxel intensity scaling. It is equivalent to
% hdr field when using load_untouch_nii to load dataset. Support both
% *.nii and *.hdr file extension. If file extension is not provided,
% *.hdr will be used as default.
% ... |
github | tomdoel/pulmonarytoolkit-master | bipolar.m | .m | pulmonarytoolkit-master/External/Nifti_tools/bipolar.m | 2,145 | utf_8 | 295f87ece96ca4c5dff8dce4cd912a34 | %BIPOLAR returns an M-by-3 matrix containing a blue-red colormap, in
% in which red stands for positive, blue stands for negative,
% and white stands for 0.
%
% Usage: cmap = bipolar(M, lo, hi, contrast); or cmap = bipolar;
%
% cmap: output M-by-3 matrix for BIPOLAR colormap.
% M: number of shades in the color... |
github | tomdoel/pulmonarytoolkit-master | save_nii_hdr.m | .m | pulmonarytoolkit-master/External/Nifti_tools/save_nii_hdr.m | 9,270 | utf_8 | f97c194f5bfc667eb4f96edf12be02a7 | % internal function
% - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
function save_nii_hdr(hdr, fid)
if ~exist('hdr','var') | ~exist('fid','var')
error('Usage: save_nii_hdr(hdr, fid)');
end
if ~isequal(hdr.hk.sizeof_hdr,348),
error('hdr.hk.sizeof_hdr must be 348.');
end
if hdr.h... |
github | tomdoel/pulmonarytoolkit-master | MimSaveAs.m | .m | pulmonarytoolkit-master/External/mim/Gui/Controllers/MimSaveAs.m | 4,369 | utf_8 | deb135d8b21745a678354c23aa82d952 | function path_name = MimSaveAs(image_data, patient_name, path_name, is_secondary_capture, dicom_metadata, reporting)
% MimSaveAs. Prompts the user for a filename and file type, and saves the image
%
% Syntax
% ------
%
% MimSaveAs(image_data, patient_name, path_name, is_secondar... |
github | tomdoel/pulmonarytoolkit-master | MimSavePatchAs.m | .m | pulmonarytoolkit-master/External/mim/Gui/Controllers/MimSavePatchAs.m | 2,004 | utf_8 | 0785ad7055ad711560f7055d80d76370 | function path_name = MimSavePatchAs(patch_object, path_name, reporting)
% MimSavePatchAs. Prompts the user for a filename, and saves the patch object
%
% Syntax
% ------
%
% MimSavePatchAs(patch_object, path_name, reporting)
%
% patch_object is a PTKPatch o... |
github | tomdoel/pulmonarytoolkit-master | MimSaveMarkersAs.m | .m | pulmonarytoolkit-master/External/mim/Gui/Controllers/MimSaveMarkersAs.m | 2,153 | utf_8 | 862636fb14ace7b015bac1480e74fb18 | function path_name = MimSaveMarkersAs(markers_struct, path_name, reporting)
% MimSaveMarkersAs. Prompts the user for a filename, and saves the markers object
%
% Syntax
% ------
%
% MimSaveMarkersAs(patch_object, path_name, reporting)
%
% markers_struct is ... |
github | tomdoel/pulmonarytoolkit-master | MimFillHolesForDualColourImageColours.m | .m | pulmonarytoolkit-master/External/mim/Library/Segmentation/MimFillHolesForDualColourImageColours.m | 2,436 | utf_8 | c39e39664f6db6a1bb3b14d736d8da82 | function filled_image = MimFillHolesForDualColourImageColours(original_image, colour_1, colour_2)
% MimFillHolesForDualColourImageColours. Fills in holes in a colourmap image
%
% MimFillHolesForDualColourImageColours takes in a indexed image and fills in any completely
% enclosed holes, where ho... |
github | tomdoel/pulmonarytoolkit-master | MimFillHolesForMultiColourImage.m | .m | pulmonarytoolkit-master/External/mim/Library/Segmentation/MimFillHolesForMultiColourImage.m | 2,514 | utf_8 | 1c1f441b2fdbe39138716297f80e8939 | function filled_image_raw = MimFillHolesForMultiColourImage(filled_image_raw, allow_fill_with_background)
% MimFillHolesForMultiColourImage. Fills in holes in a colourmap image
%
% MimFillHolesForMultiColourImage takes in a indexed image and fills in any completely
% enclosed holes, where holes ... |
github | tomdoel/pulmonarytoolkit-master | MimLoad.m | .m | pulmonarytoolkit-master/External/mim/Library/File/MimLoad.m | 2,795 | utf_8 | 0388260a4317bf126812e696bb44bc96 | function image_data = MimLoad(file_path, filename_base, reporting)
% MimLoad. Loads an image or a structure previously saved with MimSave
%
% MimLoad allows you to load a structure from .mat and .raw files
% that have previously been saved using MimSave. MimLoad will
% decompress the images... |
github | tomdoel/pulmonarytoolkit-master | MimGetSingleImageInfo.m | .m | pulmonarytoolkit-master/External/mim/Library/File/MimGetSingleImageInfo.m | 4,078 | utf_8 | 83628d4a8847bea3b2bc8dbc5884f54c | function single_image_info = MimGetSingleImageInfo(file_path, file_name, file_format, tags_to_get, reporting)
% MimGetSingleImageInfo. Populates a DMSingleImageMetaInfo object with meta
% information derived from an image file
%
% file_format (optional) - an enum of type MimImageFileFormat, or
... |
github | tomdoel/pulmonarytoolkit-master | MimSaveImageAsDicom.m | .m | pulmonarytoolkit-master/External/mim/Library/File/MimSaveImageAsDicom.m | 9,010 | utf_8 | 6664b01a677e62ca52a04438257d8e37 | function MimSaveImageAsDicom(image_data, path, filename, patient_name, is_secondary_capture, dicom_metadata, reporting)
% MimSaveImageAsDicom. Saves an image in DICOM format, using Matlab's image processing toolbox
%
% Syntax
% ------
%
% MimSaveImageAsDicom(image_data, path, fil... |
github | tomdoel/pulmonarytoolkit-master | MimSave.m | .m | pulmonarytoolkit-master/External/mim/Library/File/MimSave.m | 3,797 | utf_8 | 5123226c6c84b1fbf1a6a6a7cc88d583 | function MimSave(file_path, filename_base, image_data, compression, reporting)
% MimSave. Saves an image or a structure containing images, with compression support
%
% MimSave allows you to save a structure as a .mat file, where every
% PTKImage in the structure has its raw data saved as a separat... |
github | tomdoel/pulmonarytoolkit-master | MimSaveTableAsCSV.m | .m | pulmonarytoolkit-master/External/mim/Library/File/MimSaveTableAsCSV.m | 4,899 | utf_8 | 7b7ffc5f223e04994cecb5d1df56a84c | function MimSaveTableAsCSV(file_path, file_name, table, file_dim, row_dim, col_dim, filters, context_list, reporting)
% MimSaveTableAsCSV.
%
% filters is used to filter each of the four dimensions of patient name,
% metric name, context name and slice number
%
% Licence
% ---... |
github | tomdoel/pulmonarytoolkit-master | MimConvertMetricsToTable.m | .m | pulmonarytoolkit-master/External/mim/Library/Conversion/MimConvertMetricsToTable.m | 2,847 | utf_8 | 64335b9846b2748d8dc146abf0ba2809 | function results_table = MimConvertMetricsToTable(results, patient_name, patient_id, reporting, context_mapping_function, results_table)
% MimConvertMetricsToTable.
%
%
% Licence
% -------
% Part of the TD MIM Toolkit. https://github.com/tomdoel
% Author: Tom Doel, 2013. www... |
github | tomdoel/pulmonarytoolkit-master | MimImageImporter.m | .m | pulmonarytoolkit-master/External/mim/Framework/MimImageImporter.m | 4,078 | utf_8 | b5652a919d756272c78308d9ec634cbf | function [uids, patient_ids] = MimImageImporter(filename_or_root_directory, database, reporting)
% MimImageImporter. Recrusively imports image files into a MimImageDatabase object
%
%
%
% Licence
% -------
% Part of the TD MIM Toolkit. https://github.com/tomdoel
% Author:... |
github | tomdoel/pulmonarytoolkit-master | biharmonic2DSolve.m | .m | pulmonarytoolkit-master/External/npReg/biharmonic2DSolve.m | 4,780 | utf_8 | abb22778085438a3b7ecda2f04518544 | function U = biharmonic2DSolve(varargin)
% biharmonic2DSolve: solve Biharmonic equation in 2D
% usage: U = biharmonic2DSolve(F);
% or: U = biharmonic2DSolve(F,BoundCond);
%
% Biharmonic equation is given by:
% (del^4) U = F
%
% arguments:
% F (MxNx2) - force field
% BoundCond - boundary conditions, can be... |
github | tomdoel/pulmonarytoolkit-master | poisson2DSolve.m | .m | pulmonarytoolkit-master/External/npReg/poisson2DSolve.m | 4,764 | utf_8 | 9aedc49846b79e798b1317fac6a19bc2 | function U = poisson2DSolve(varargin)
% poisson2DSolve: solve Poisson's equation in 2D
% usage: U = poisson2DSolve(F);
% or: U = poisson2DSolve(F,BoundCond);
%
% Poisson's equation is given by:
% (del^2) U = F
%
% arguments:
% F (MxNx2) - force field
% BoundCond - boundary conditions, can be one of:
% ... |
github | tomdoel/pulmonarytoolkit-master | genRegularizer2DSolve.m | .m | pulmonarytoolkit-master/External/npReg/genRegularizer2DSolve.m | 4,415 | utf_8 | b3301f9acc0e0f3432f017ac0d5377ce | function U = genRegularizer2DSolve(varargin)
% genRegularizer2DSolve: solve registration equation in 2D using general
% regularizer
% usage: U = genRegularizer2DSolve(F);
% or: U = genRegularizer2DSolve(F,Alpha);
% or: U = genRegularizer2DSolve(F,Alpha,BoundCond);
%
% arguments:
% F (MxNx2) - force field
... |
github | tomdoel/pulmonarytoolkit-master | npRegGet.m | .m | pulmonarytoolkit-master/External/npReg/npRegGet.m | 3,999 | utf_8 | fbb0334d1408d4e6e00b4f46ebbd1aa2 | function o = npRegGet(options,name,default,flag)
%NPREGGET Get NPREG OPTIONS parameters.
% VAL = NPREGGET(OPTIONS,'NAME') extracts the value of the named
% parameter from npReg options structure OPTIONS, returning an empty
% matrix if the parameter value is not specified in OPTIONS. It is
% sufficient to typ... |
github | tomdoel/pulmonarytoolkit-master | npRegSet.m | .m | pulmonarytoolkit-master/External/npReg/npRegSet.m | 19,631 | utf_8 | 890110331fa75b259f238d3cb534ba72 | function options = npRegSet(varargin)
%NPREGSET Create/alter npReg OPTIONS structure.
% OPTIONS = npRegSet('PARAM1',VALUE1,'PARAM2',VALUE2,...) creates a
% npable registration options structure OPTIONS in which the named
% parameters have the specified values. Any unspecified parameters are
% set to [] (para... |
github | tomdoel/pulmonarytoolkit-master | diffusionPeriodic3D.m | .m | pulmonarytoolkit-master/External/npReg/npRegLib/diffusionPeriodic3D.m | 2,800 | utf_8 | 915fb6dabe1e970ed3d1d48cd1426f74 | function UNew = diffusionPeriodic3D(varargin);
% diffusionPeriodic3D: solve diffusion registration in 3D with periodic
% boundary conditions
%
%
% author: Nathan D. Cahill
% email: nathan.cahill@rit.edu
% affiliation: Rochester Institute of Technology
% date: January 2014
% licence: GNU GPL v3
%
% Copyright Nath... |
github | tomdoel/pulmonarytoolkit-master | elasticDirichlet2D.m | .m | pulmonarytoolkit-master/External/npReg/npRegLib/elasticDirichlet2D.m | 2,551 | utf_8 | d3d421f97ca843672ecb0152d94cca68 | function UNew = elasticDirichlet2D(varargin);
% elasticDirichlet2D: solve elastic registraion in 2D with Dirichlet
% boundary conditions
%
%
% author: Nathan D. Cahill
% email: nathan.cahill@rit.edu
% affiliation: Rochester Institute of Technology
% date: January 2014
% licence: GNU GPL v3
%
% Copyright Nathan D... |
github | tomdoel/pulmonarytoolkit-master | npRegOptionCheckField.m | .m | pulmonarytoolkit-master/External/npReg/npRegLib/npRegOptionCheckField.m | 8,166 | utf_8 | 9a668cd5798f875c51b906da25e678c8 | function [validvalue, errmsg, errid, validfield] = npRegOptionCheckField(field,value)
%NPREGOPTIONCHECKFIELD Check validity of structure field contents.
%
% This is a helper function for NPREGSET and NPREGGET.
% [VALIDVALUE, ERRMSG, ERRID, VALIDFIELD] = NPREGOPTIONCHECKFIELD('field',V)
% checks the contents of the... |
github | tomdoel/pulmonarytoolkit-master | curvaturePeriodic2D.m | .m | pulmonarytoolkit-master/External/npReg/npRegLib/curvaturePeriodic2D.m | 1,508 | utf_8 | d12fe489fc0652cd636737a75470b599 | function UNew = curvaturePeriodic2D(varargin);
% curvaturePeriodic2D: solve curvature registraion in 2D with periodic
% boundary conditions
%
%
% author: Nathan D. Cahill
% email: nathan.cahill@rit.edu
% affiliation: Rochester Institute of Technology
% date: January 2014
% licence: GNU GPL v3 licence.
%
% Copyri... |
github | tomdoel/pulmonarytoolkit-master | dbquiy.m | .m | pulmonarytoolkit-master/External/npReg/npRegLib/dbquiy.m | 1,893 | utf_8 | 3dd24ccb5a4ad1b7034123397da5ad74 | function UNew = diffusionDirichlet2D(varargin);
% diffusionDirichlet2D: solve diffusion registraion in 2D with Dirichlet
% boundary conditions
%
%
% author: Nathan D. Cahill
% email: nathan.cahill@rit.edu
% affiliation: Rochester Institute of Technology
% date: January 2014
% licence: GNU GPL v3
%
% Copyright N... |
github | tomdoel/pulmonarytoolkit-master | diffusionNeumann3D.m | .m | pulmonarytoolkit-master/External/npReg/npRegLib/diffusionNeumann3D.m | 2,358 | utf_8 | 2abaa24208d50e60e876d83bbd3f8b94 | function UNew = diffusionNeumann3D(varargin);
% diffusionDirichlet3D: solve diffusion registraion in 3D with Neumann
% boundary conditions
%
%
% author: Nathan D. Cahill
% email: nathan.cahill@rit.edu
% affiliation: Rochester Institute of Technology
% date: January 2014
% licence: GNU GPL v3
%
% Copyright Nathan... |
github | tomdoel/pulmonarytoolkit-master | elasticNeumann3D.m | .m | pulmonarytoolkit-master/External/npReg/npRegLib/elasticNeumann3D.m | 4,070 | utf_8 | 5fe0fa5b6cab0a93bea8bc7982817027 | function UNew = elasticNeumann3D(varargin)
% elasticNeumann3D: solve elastic registration in 3D with Neumann
% boundary conditions
%
%
% author: Nathan D. Cahill
% email: nathan.cahill@rit.edu
% affiliation: Rochester Institute of Technology
% date: January 2014
% licence: GNU GPL v3
%
% Copyright Nathan D. Cahi... |
github | tomdoel/pulmonarytoolkit-master | fluidPeriodic2D.m | .m | pulmonarytoolkit-master/External/npReg/npRegLib/fluidPeriodic2D.m | 2,693 | utf_8 | 9db84ca227ce093fee0668659e0ae264 | function UNew = fluidPeriodic2D(varargin);
% fluidPeriodic2D: solve fluid registraion in 2D with Periodic
% boundary conditions
%
%
% author: Nathan D. Cahill
% email: nathan.cahill@rit.edu
% affiliation: Rochester Institute of Technology
% date: January 2014
% licence: GNU GPL v3
%
% Copyright Nathan D. Cahill
... |
github | tomdoel/pulmonarytoolkit-master | elasticDirichlet3D.m | .m | pulmonarytoolkit-master/External/npReg/npRegLib/elasticDirichlet3D.m | 4,066 | utf_8 | a2a7bd8c204ab65f291ffb1f66399799 | function UNew = elasticDirichlet3D(varargin);
% elasticDirichlet3D: solve elastic registraion in 3D with Dirichlet
% boundary conditions
%
%
% author: Nathan D. Cahill
% email: nathan.cahill@rit.edu
% affiliation: Rochester Institute of Technology
% date: January 2014
% licence: GNU GPL v3
%
% Copyright Nathan D... |
github | tomdoel/pulmonarytoolkit-master | fluidNeumann2D.m | .m | pulmonarytoolkit-master/External/npReg/npRegLib/fluidNeumann2D.m | 3,023 | utf_8 | 544c8ed6c9812c927b05ce0b618001b3 | function UNew = fluidNeumann2D(varargin);
% fluidNeumann2D: solve fluid registraion in 2D with Neumann
% boundary conditions
%
%
% author: Nathan D. Cahill
% email: nathan.cahill@rit.edu
% affiliation: Rochester Institute of Technology
% date: January 2014
% licence: GNU GPL v3
%
% Copyright Nathan D. Cahill
% C... |
github | tomdoel/pulmonarytoolkit-master | elasticPeriodic3D.m | .m | pulmonarytoolkit-master/External/npReg/npRegLib/elasticPeriodic3D.m | 4,435 | utf_8 | 0355bb6146b2001b32c7bd58422ec153 | function UNew = elasticPeriodic3D(varargin);
% elasticPeriodic3D: solve elastic registraion in 3D with periodic
% boundary conditions
%
%
% author: Nathan D. Cahill
% email: nathan.cahill@rit.edu
% affiliation: Rochester Institute of Technology
% date: January 2014
% licence: GNU GPL v3
%
% Copyright Nathan D. C... |
github | tomdoel/pulmonarytoolkit-master | elasticPeriodic2D.m | .m | pulmonarytoolkit-master/External/npReg/npRegLib/elasticPeriodic2D.m | 2,315 | utf_8 | 2135d0a13713767848feaeaa64909641 | function UNew = elasticPeriodic2D(varargin);
% elasticPeriodic2D: solve elastic registraion in 2D with periodic
% boundary conditions
%
%
% author: Nathan D. Cahill
% email: nathan.cahill@rit.edu
% affiliation: Rochester Institute of Technology
% date: January 2014
% licence: GNU GPL v3
%
% Copyright Nathan D. C... |
github | tomdoel/pulmonarytoolkit-master | curvatureNeumann2D.m | .m | pulmonarytoolkit-master/External/npReg/npRegLib/curvatureNeumann2D.m | 1,891 | utf_8 | 5b09aa3bf59e0e5b00a36f617750ecc3 | function UNew = curvatureNeumann2D(varargin);
% curvatureNeumann2D: solve curvature registraion in 2D with Neumann
% boundary conditions
%
%
% author: Nathan D. Cahill
% email: nathan.cahill@rit.edu
% affiliation: Rochester Institute of Technology
% date: January 2014
% licence: GNU GPL v3 licence.
%
% Copyright... |
github | tomdoel/pulmonarytoolkit-master | diffusionDirichlet3D.m | .m | pulmonarytoolkit-master/External/npReg/npRegLib/diffusionDirichlet3D.m | 2,348 | utf_8 | 375f3faa2444c1a86d07ba6b3ad26871 | function UNew = diffusionDirichlet3D(varargin);
% diffusionDirichlet3D: solve diffusion registraion in 3D with Dirichlet
% boundary conditions
%
%
% author: Nathan D. Cahill
% email: nathan.cahill@rit.edu
% affiliation: Rochester Institute of Technology
% date: January 2014
% licence: GNU GPL v3
%
% Copyright Na... |
github | tomdoel/pulmonarytoolkit-master | curvatureNeumann3D.m | .m | pulmonarytoolkit-master/External/npReg/npRegLib/curvatureNeumann3D.m | 2,368 | utf_8 | 78ca1925c071f3451a10938a3ced1cea | function UNew = curvatureNeumann3D(varargin);
% curvatureNeumann3D: solve curvature registration in 3D with Neumann
% boundary conditions
%
%
% author: Nathan D. Cahill
% email: nathan.cahill@rit.edu
% affiliation: Rochester Institute of Technology
% date: January 2014
% licence: GNU GPL v3 licence.
%
% Copyrigh... |
github | tomdoel/pulmonarytoolkit-master | diffusionNeumann2D.m | .m | pulmonarytoolkit-master/External/npReg/npRegLib/diffusionNeumann2D.m | 1,875 | utf_8 | bf385eb980adfaaa39c4f93013f0744e | function UNew = diffusionNeumann2D(varargin);
% diffusionNeumann2D: solve diffusion registraion in 2D with Neumann
% boundary conditions
%
%
% author: Nathan D. Cahill
% email: nathan.cahill@rit.edu
% affiliation: Rochester Institute of Technology
% date: January 2014
% licence: GNU GPL v3
%
% Copyright Nathan D... |
github | tomdoel/pulmonarytoolkit-master | genNpReg.m | .m | pulmonarytoolkit-master/External/npReg/npRegLib/genNpReg.m | 12,432 | utf_8 | e7d586911bf78ea00db243eb16c5a04d | function [BNEW,U,EXITFLAG,OUTPUT] = genNpReg(A,B,options,defaultopt,regDim,varargin);
%GENNPREG solves general nonparametric image registration problems
%using a fixed point iteration
%
%
% author: Nathan D. Cahill
% email: nathan.cahill@rit.edu
% affiliation: Rochester Institute of Technology
% date: January 2014
% li... |
github | tomdoel/pulmonarytoolkit-master | curvatureDirichlet2D.m | .m | pulmonarytoolkit-master/External/npReg/npRegLib/curvatureDirichlet2D.m | 1,843 | utf_8 | 77bffcbf865c113c425711d6c7507f1e | function UNew = curvatureDirichlet2D(varargin);
% curvatureDirichlet2D: solve curvature registraion in 2D with Dirichlet
% boundary conditions
%
%
% author: Nathan D. Cahill
% email: nathan.cahill@rit.edu
% affiliation: Rochester Institute of Technology
% date: January 2014
% licence: GNU GPL v3 licence.
%
% Co... |
github | tomdoel/pulmonarytoolkit-master | fluidDirichlet2D.m | .m | pulmonarytoolkit-master/External/npReg/npRegLib/fluidDirichlet2D.m | 2,991 | utf_8 | 458ca2389d19cf946ddeebad586d03c9 | function UNew = fluidDirichlet2D(varargin);
% fluidDirichlet2D: solve fluid registraion in 2D with Dirichlet
% boundary conditions
%
%
% author: Nathan D. Cahill
% email: nathan.cahill@rit.edu
% affiliation: Rochester Institute of Technology
% date: January 2014
% licence: GNU GPL v3
%
% Copyright Nathan D. Cahi... |
github | tomdoel/pulmonarytoolkit-master | curvaturePeriodic3D.m | .m | pulmonarytoolkit-master/External/npReg/npRegLib/curvaturePeriodic3D.m | 2,806 | utf_8 | 116beb3fef6c9514327e478880d8b1a9 | function UNew = curvaturePeriodic3D(varargin);
% curvaturePeriodic3D: solve curvature registration in 3D with periodic
% boundary conditions
%
%
% author: Nathan D. Cahill
% email: nathan.cahill@rit.edu
% affiliation: Rochester Institute of Technology
% date: January 2014
% licence: GNU GPL v3
%
% Copyright Nath... |
github | tomdoel/pulmonarytoolkit-master | elasticNeumann2D.m | .m | pulmonarytoolkit-master/External/npReg/npRegLib/elasticNeumann2D.m | 2,585 | utf_8 | 246d2e4876ea9766c6a2918ad08a476b | function UNew = elasticNeumann2D(varargin);
% elasticNeumann2D: solve elastic registraion in 2D with Neumann
% boundary conditions
%
%
% author: Nathan D. Cahill
% email: nathan.cahill@rit.edu
% affiliation: Rochester Institute of Technology
% date: January 2014
% licence: GNU GPL v3
%
% Copyright Nathan D. Cahi... |
github | tomdoel/pulmonarytoolkit-master | genNpReg2.m | .m | pulmonarytoolkit-master/External/npReg/npRegLib/genNpReg2.m | 12,575 | utf_8 | 13538332a4b615eaf670168539a3c460 | function [BNEW,U,EXITFLAG,OUTPUT] = genNpReg2(A,B,options,defaultopt,regDim,varargin);
%GENNPREG2 solves general nonparametric image registration problems
%using a fixed point iteration
%
%
% author: Nathan D. Cahill
% email: nathan.cahill@rit.edu
% affiliation: Rochester Institute of Technology
% date: January 2014
% ... |
github | tomdoel/pulmonarytoolkit-master | fluidNeumann3D.m | .m | pulmonarytoolkit-master/External/npReg/npRegLib/fluidNeumann3D.m | 4,723 | utf_8 | 3b54ca82309710e118d9af538c7ca478 | function UNew = fluidNeumann3D(varargin);
% fluidNeumann3D: solve fluid registraion in 3D with Neumann
% boundary conditions
%
%
% author: Nathan D. Cahill
% email: nathan.cahill@rit.edu
% affiliation: Rochester Institute of Technology
% date: January 2014
% licence: GNU GPL v3
%
% Copyright Nathan D. Cahill
% C... |
github | tomdoel/pulmonarytoolkit-master | fluidDirichlet3D.m | .m | pulmonarytoolkit-master/External/npReg/npRegLib/fluidDirichlet3D.m | 4,715 | utf_8 | f068207746f9a2f6dcad6e480a4fdd2a | function UNew = fluidDirichlet3D(varargin);
% fluidDirichlet3D: solve fluid registraion in 3D with Dirichlet
% boundary conditions
%
%
% author: Nathan D. Cahill
% email: nathan.cahill@rit.edu
% affiliation: Rochester Institute of Technology
% date: January 2014
% licence: GNU GPL v3
%
% Copyright Nathan D. Cahi... |
github | tomdoel/pulmonarytoolkit-master | fluidPeriodic3D.m | .m | pulmonarytoolkit-master/External/npReg/npRegLib/fluidPeriodic3D.m | 5,096 | utf_8 | 6b4fa87bc3bef8b0fdaa9fc9eb71c805 | function UNew = fluidPeriodic3D(varargin)
% fluidPeriodic3D: solve fluid registraion in 3D with Periodic
% boundary conditions
%
%
% author: Nathan D. Cahill
% email: nathan.cahill@rit.edu
% affiliation: Rochester Institute of Technology
% date: January 2014
% licence: GNU GPL v3
%
% Copyright Nathan D. Cahill
%... |
github | tomdoel/pulmonarytoolkit-master | curvatureDirichlet3D.m | .m | pulmonarytoolkit-master/External/npReg/npRegLib/curvatureDirichlet3D.m | 2,362 | utf_8 | b7af7ba41cb7a60a2ee4ddb4187cad34 | function UNew = curvatureDirichlet3D(varargin)
% curvatureDirichlet3D: solve curvature registraion in 3D with Dirichlet
% boundary conditions
%
%
% author: Nathan D. Cahill
% email: nathan.cahill@rit.edu
% affiliation: Rochester Institute of Technology
% date: January 2014
% licence: GNU GPL v3 licence.
%
% Copy... |
github | tomdoel/pulmonarytoolkit-master | diffusionPeriodic2D.m | .m | pulmonarytoolkit-master/External/npReg/npRegLib/diffusionPeriodic2D.m | 1,492 | utf_8 | d4cb994bb71d66336a6463ab953e0e86 | function UNew = diffusionPeriodic2D(varargin);
% diffusionPeriodic2D: solve diffusion registraion in 2D with Periodic
% boundary conditions
%
%
% author: Nathan D. Cahill
% email: nathan.cahill@rit.edu
% affiliation: Rochester Institute of Technology
% date: January 2014
% licence: GNU GPL v3
%
% Copyright Natha... |
github | tomdoel/pulmonarytoolkit-master | MatNatAddPaths.m | .m | pulmonarytoolkit-master/External/matnat/MatNatAddPaths.m | 1,688 | utf_8 | 8fab7c9105c687310698486e22aa357f | function MatNatAddPaths(varargin)
% Adds paths for MatNat
%
% Licence
% -------
% Part of MatNat. https://github.com/tomdoel/matnat
% Author: Tom Doel, 2015. www.tomdoel.com
% Distributed under the GNU GPL v3 licence. Please see website for details.
%
... |
github | tomdoel/pulmonarytoolkit-master | savejson.m | .m | pulmonarytoolkit-master/External/jsonlab-1.5/jsonlab-1.5/savejson.m | 19,005 | utf_8 | 2abe93f113a0cff486589165c908511d | function json=savejson(rootname,obj,varargin)
%
% json=savejson(rootname,obj,filename)
% or
% json=savejson(rootname,obj,opt)
% json=savejson(rootname,obj,'param1',value1,'param2',value2,...)
%
% convert a MATLAB object (cell, struct or array) into a JSON (JavaScript
% Object Notation) string
%
% author: Qianqian Fa... |
github | tomdoel/pulmonarytoolkit-master | loadjson.m | .m | pulmonarytoolkit-master/External/jsonlab-1.5/jsonlab-1.5/loadjson.m | 16,682 | ibm852 | 7eead0aa7db35c892d9233e6fa63cc05 | function data = loadjson(fname,varargin)
%
% data=loadjson(fname,opt)
% or
% data=loadjson(fname,'param1',value1,'param2',value2,...)
%
% parse a JSON (JavaScript Object Notation) file or string
%
% authors:Qianqian Fang (q.fang <at> neu.edu)
% created on 2011/09/09, including previous works from
%
% Nedial... |
github | tomdoel/pulmonarytoolkit-master | loadubjson.m | .m | pulmonarytoolkit-master/External/jsonlab-1.5/jsonlab-1.5/loadubjson.m | 13,272 | utf_8 | 6b84fc36f88b25a5db2515a93b6f23bc | function data = loadubjson(fname,varargin)
%
% data=loadubjson(fname,opt)
% or
% data=loadubjson(fname,'param1',value1,'param2',value2,...)
%
% parse a JSON (JavaScript Object Notation) file or string
%
% authors:Qianqian Fang (q.fang <at> neu.edu)
% created on 2013/08/01
%
% $Id$
%
% input:
% fname: input file... |
github | tomdoel/pulmonarytoolkit-master | saveubjson.m | .m | pulmonarytoolkit-master/External/jsonlab-1.5/jsonlab-1.5/saveubjson.m | 17,757 | utf_8 | 865a3f4e074323a42f75910b868ff3fb | function json=saveubjson(rootname,obj,varargin)
%
% json=saveubjson(rootname,obj,filename)
% or
% json=saveubjson(rootname,obj,opt)
% json=saveubjson(rootname,obj,'param1',value1,'param2',value2,...)
%
% convert a MATLAB object (cell, struct or array) into a Universal
% Binary JSON (UBJSON) binary string
%
% author... |
github | tomdoel/pulmonarytoolkit-master | DMImportRecursive.m | .m | pulmonarytoolkit-master/External/dicomat/DMImportRecursive.m | 5,279 | utf_8 | f90f1fb6fb84f86b978ca3708e839c29 | function fileGrouper = DMImportRecursive(filenameOrRootDirectory, dicomLibrary, reporting)
% DMImportRecursive. Loads metadata from a series of DICOM files
%
% Syntax
% ------
%
% file_grouper = DMLoadMetaDMImportRecursivedataFromDicomFiles(filenameOrRootDirectory, dicomLibrary, ... |
github | tomdoel/pulmonarytoolkit-master | DMSaveDicomSeries.m | .m | pulmonarytoolkit-master/External/dicomat/DMSaveDicomSeries.m | 4,613 | utf_8 | 3a455978ff974121733e61f74eec6035 | function DMSaveDicomSeries(base_filename, ordered_image, dicom_coordinates_list, metadata, image_type, software_info, reporting)
%
% Licence
% -------
% Part of DicoMat. https://github.com/tomdoel/dicomat
% Author: Tom Doel, 2013. www.tomdoel.com
% Distributed under the BSD ... |
github | tomdoel/pulmonarytoolkit-master | DMAddPaths.m | .m | pulmonarytoolkit-master/External/dicomat/DMAddPaths.m | 1,398 | utf_8 | c6dcc2c81a9f5d46ea5b59f5350eb597 | function DMAddPaths(varargin)
force = nargin > 0 && strcmp(varargin{1}, 'force');
% This version number should be incremented whenever new paths are added to
% the list
DMAddPaths_Version_Number = 1;
persistent DM_PathsHaveBeenSet
full_path = mfilename('fullpath');
[path_... |
github | tomdoel/pulmonarytoolkit-master | DMReadDicomTags.m | .m | pulmonarytoolkit-master/External/dicomat/DMReadDicomTags.m | 16,236 | utf_8 | 2a38a0989f4523af70a64fa26aa3b11c | function header = DMReadDicomTags(fileName, dictionary)
% DMReadDicomTags Reads in metainformation from a Dicom file.
%
% Usage:
% header = DMReadDicomTags(fileName, dictionary)
%
% fileName: path and filename of the Dicom file to read
%
% dictionary - an object of class DMDi... |
github | tomdoel/pulmonarytoolkit-master | DMAreImagesInSameGroup.m | .m | pulmonarytoolkit-master/External/dicomat/DMAreImagesInSameGroup.m | 4,858 | utf_8 | fab4823246b32e84dbb181b7ad546eb5 | function match = DMAreImagesInSameGroup(this_metadata, other_metadata, this_metadata_2)
% DMAreImagesInSameGroup. Determines whether two Dicom images form a coherent sequence
%
% DMAreImagesInSameGroup compares the metadata from two Dicom images. If
% the images are from the same patient, study and seri... |
github | tomdoel/pulmonarytoolkit-master | stlwrite.m | .m | pulmonarytoolkit-master/External/stlwrite/stlwrite.m | 8,854 | utf_8 | a08029a093548b0287838d73c8796e33 | function stlwrite(filename, varargin)
%STLWRITE Write STL file from patch or surface data.
%
% STLWRITE(FILE,fv) writes a stereolithography (STL) file to FILE for a triangulated
% patch defined by FV (a structure with fields 'vertices' and 'faces').
%
% STLWRITE(FILE,FACES,VERTICES) takes faces and vertices sep... |
github | tomdoel/pulmonarytoolkit-master | DepMatUpdate.m | .m | pulmonarytoolkit-master/External/depmat/DepMatUpdate.m | 1,128 | utf_8 | da7c7925d74b90a75a49dc600136031a | function DepMatUpdate(repoList, varargin)
% DepMatUpdate. Clones or updates all repositories in a DepMatRepo list
%
%
%
% Licence
% -------
% Part of DepMat. https://github.com/tomdoel/depmat
% Author: Tom Doel, 2015. www.tomdoel.com
% Distributed under the MIT ... |
github | tomdoel/pulmonarytoolkit-master | DepMatAddPaths.m | .m | pulmonarytoolkit-master/External/depmat/DepMatAddPaths.m | 2,784 | utf_8 | a772d4758e19b1f6938522b7cee72753 | function DepMatAddPaths(baseFolderList, repoNameList, forceUpdate)
% DepMatAddPaths. Adds paths for all subfolders in given repositories
%
%
%
% Licence
% -------
% Part of DepMat. https://github.com/tomdoel/depmat
% Author: Tom Doel, 2015. www.tomdoel.com
% Dist... |
github | swami1995/vo-slam-master | makehomogeneous.m | .m | vo-slam-master/src/display_ftr/makehomogeneous.m | 649 | utf_8 | 19d1cac5b6483d4dd545ef8b6bca5dcb | % MAKEHOMOGENEOUS - Appends a scale of 1 to array inhomogeneous coordinates
%
% Usage: hx = makehomogeneous(x)
%
% Argument:
% x - an N x npts array of inhomogeneous coordinates.
%
% Returns:
% hx - an (N+1) x npts array of homogeneous coordinates with the
% homogeneous scale set to 1
%
... |
github | swami1995/vo-slam-master | hnormalise.m | .m | vo-slam-master/src/display_ftr/hnormalise.m | 1,010 | utf_8 | 40eeebb3462ab60fb05b133bf0055baf | % HNORMALISE - Normalises array of homogeneous coordinates to a scale of 1
%
% Usage: nx = hnormalise(x)
%
% Argument:
% x - an Nxnpts array of homogeneous coordinates.
%
% Returns:
% nx - an Nxnpts array of homogeneous coordinates rescaled so
% that the scale values nx(N,:) are all 1.
%
... |
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