constructor for phiw_wvimg object - a container for a wt'ed image
FORMAT wvimg = phiw_wvimg(inpimg,input_options,waveobj,scales)
Function call takes four forms
wvimg = phiw_wvimg; no args, returns default object
wvimg = phiw_wvimg(wv_img); object passed, object returned
wvimg = phiw_wvimg(inpimg,input_options,wavelet,scales)
(Four imput arguments)
Creates wavelet structure from _untransformed_ data
in inpimg (either SPM vol struct, or data matrix)
and (possibly queues) transform with wavelet, scales
wvimg = phiw_wvimg(inpimg, [input_options], [twvimg])
(between one and three input arguments, where first argument is
not a wvimg object already)
Puts previously _transformed_ data from inpimg into wvimg object
This can have three forms:
1) If no third arg - try to derive info from inpimg .mat file
(return empty if not successful)
2) If third arg is phiw_wvimg object, use this as template
3) If third arg is vol struct, try and get info from that .mat
file (return empty if not successful)
object fields are:
ovol = SPM vol struct describing not wt'ed data
with fields: dim, mat, fname, pinfo
wvol = wavelet transformed SPM vol struct representing dimensions,
.mat data, filename for image data, datatype;
options = struct with options, with fields below. Options fall
into two categories; permanent, and object creation
options (noproc, remap); the latter are reset to 0 by
this routine
img = contains matrix data, or SPM vol struct representing
data
wtf = set if data has been wavelet transformed
changef = set if data has been changed since passed
wavelet = phiw_wavelet object giving wavelet for transform;
scales = number of coarsest scale for wt;
descrip = extended text description field;
passed options can be empty, or one or more fields from this list
defaults in [], OCO = object creation option
datatype - datatype for transformed data ['float']
wtprefix - default prefix for transformed file ['wt_']
verbose - flag to output feedback in matlab window [1]
descrip - description (appended to fulldescrip obj field)
[''] OCO
noproc - if not zero defer vol struct load and any wavelet
transform [0] OCO
remap - forces remap of passed vol struct [0] OCO
find_similar - when trying to create a wavelet image, first
look for a compatible image that already exists [0]
OCO
wvimg returned is empty if inputs are incorrect
Routine does little filling of fields, and relies on methods filling
the fields that they need, or complaining if appropriate
The constructor can also be called to give class functions, where the
name of the class function is a character string which is one of:
'orig_vol' returns original vol struct from wt'ed vol
'is_wted' returns 1 is this vol appears to be be WT'ed
'wtinfo' returns wtinfo, if available, empty otherwise
This class relies on lots of SPM routines
(spm_read_vols, spm_write_vol, spm_type, spm_vol, etc)
Matthew Brett 21/5/01 (C/NZD)
$Id: phiw_wvimg.m,v 1.11 2005/06/21 04:01:04 matthewbrett Exp $0001 function wvimg = phiw_wvimg(inpimg,input_options,waveobj,scales) 0002 % constructor for phiw_wvimg object - a container for a wt'ed image 0003 % FORMAT wvimg = phiw_wvimg(inpimg,input_options,waveobj,scales) 0004 % 0005 % Function call takes four forms 0006 % wvimg = phiw_wvimg; no args, returns default object 0007 % wvimg = phiw_wvimg(wv_img); object passed, object returned 0008 % wvimg = phiw_wvimg(inpimg,input_options,wavelet,scales) 0009 % (Four imput arguments) 0010 % Creates wavelet structure from _untransformed_ data 0011 % in inpimg (either SPM vol struct, or data matrix) 0012 % and (possibly queues) transform with wavelet, scales 0013 % wvimg = phiw_wvimg(inpimg, [input_options], [twvimg]) 0014 % (between one and three input arguments, where first argument is 0015 % not a wvimg object already) 0016 % Puts previously _transformed_ data from inpimg into wvimg object 0017 % This can have three forms: 0018 % 1) If no third arg - try to derive info from inpimg .mat file 0019 % (return empty if not successful) 0020 % 2) If third arg is phiw_wvimg object, use this as template 0021 % 3) If third arg is vol struct, try and get info from that .mat 0022 % file (return empty if not successful) 0023 % 0024 % object fields are: 0025 % ovol = SPM vol struct describing not wt'ed data 0026 % with fields: dim, mat, fname, pinfo 0027 % wvol = wavelet transformed SPM vol struct representing dimensions, 0028 % .mat data, filename for image data, datatype; 0029 % options = struct with options, with fields below. Options fall 0030 % into two categories; permanent, and object creation 0031 % options (noproc, remap); the latter are reset to 0 by 0032 % this routine 0033 % img = contains matrix data, or SPM vol struct representing 0034 % data 0035 % wtf = set if data has been wavelet transformed 0036 % changef = set if data has been changed since passed 0037 % wavelet = phiw_wavelet object giving wavelet for transform; 0038 % scales = number of coarsest scale for wt; 0039 % descrip = extended text description field; 0040 % 0041 % passed options can be empty, or one or more fields from this list 0042 % defaults in [], OCO = object creation option 0043 % 0044 % datatype - datatype for transformed data ['float'] 0045 % wtprefix - default prefix for transformed file ['wt_'] 0046 % verbose - flag to output feedback in matlab window [1] 0047 % descrip - description (appended to fulldescrip obj field) 0048 % [''] OCO 0049 % noproc - if not zero defer vol struct load and any wavelet 0050 % transform [0] OCO 0051 % remap - forces remap of passed vol struct [0] OCO 0052 % find_similar - when trying to create a wavelet image, first 0053 % look for a compatible image that already exists [0] 0054 % OCO 0055 % 0056 % wvimg returned is empty if inputs are incorrect 0057 % 0058 % Routine does little filling of fields, and relies on methods filling 0059 % the fields that they need, or complaining if appropriate 0060 % 0061 % The constructor can also be called to give class functions, where the 0062 % name of the class function is a character string which is one of: 0063 % 'orig_vol' returns original vol struct from wt'ed vol 0064 % 'is_wted' returns 1 is this vol appears to be be WT'ed 0065 % 'wtinfo' returns wtinfo, if available, empty otherwise 0066 % 0067 % This class relies on lots of SPM routines 0068 % (spm_read_vols, spm_write_vol, spm_type, spm_vol, etc) 0069 % 0070 % Matthew Brett 21/5/01 (C/NZD) 0071 % 0072 % $Id: phiw_wvimg.m,v 1.11 2005/06/21 04:01:04 matthewbrett Exp $ 0073 0074 myclass = 'phiw_wvimg'; 0075 0076 % default object struct; all fields are empty to allow fill below 0077 % it has to be this way to make sure all fields are in the same order 0078 defstruct = struct(... 0079 'ovol', [], ... 0080 'wvol', [], ... 0081 'options', [], ... 0082 'img', [], ... 0083 'wavelet', [], ... 0084 'scales', [], ... 0085 'oimgi', [], ... 0086 'descrip', '', ... 0087 'wtf', [], ... 0088 'changef', []); 0089 0090 % no args, return default object 0091 if nargin < 1 0092 wvimg = class(defstruct,myclass); 0093 return 0094 end 0095 0096 % wvimg object passed as first arg, return it unaltered 0097 if isa(inpimg, myclass) 0098 wvimg = inpimg; 0099 return 0100 end 0101 0102 % set unpassed inputs to empty 0103 if nargin < 2, input_options = [];end 0104 if nargin < 3, waveobj = [];end 0105 if nargin < 4, scales = [];end 0106 0107 % overall default options 0108 defopts = struct('datatype','float', ... 0109 'wtprefix','wt_',... 0110 'verbose',1,... 0111 'descrip','', ... 0112 'noproc',0, ... 0113 'remap',0, ... 0114 'find_similar',0); 0115 0116 % parse out string action calls (class functions) 0117 if ischar(inpimg) 0118 s_def = struct('noproc',1); 0119 switch inpimg 0120 case 'orig_vol' 0121 % Second argument is (array of) vol structs 0122 VY = input_options; 0123 if nargin < 2, error('Need vol struct'); end 0124 for v = 1:prod(size(VY)) 0125 wvobj = phiw_wvimg(VY(v), s_def); 0126 if isempty(wvobj), oVY(v) = VY(v); else oVY(v) = wvobj(v).ovol; end 0127 end 0128 wvimg = reshape(oVY, size(VY)); 0129 return 0130 case 'is_wted' 0131 % Second argument is (array of) vol structs 0132 VY = input_options; 0133 is_wtf = zeros(size(VY)); 0134 for v = 1:prod(size(VY)) 0135 is_wtf(v) = ~isempty(pr_getwave(VY(v))); 0136 end 0137 wvimg = is_wtf; 0138 return 0139 case 'wtinfo' 0140 % Second argument is a single vol struct 0141 VY = input_options; 0142 if prod(size(VY)) > 1, error('Can only handle one vol'); end 0143 wvimg = pr_getwave(VY); 0144 if ~ismempty(wvimg) 0145 wvimg = wtinfo(wvimg); 0146 end 0147 return 0148 end 0149 end 0150 0151 % process passed options 0152 if isfield(input_options,'datatype') 0153 if ~ischar(input_options.datatype) 0154 input_options.datatype = spm_type(input_options.datatype); 0155 end 0156 end 0157 0158 % get passed options from input 0159 filled_opts = mars_struct('ffillsplit', defopts, input_options); 0160 0161 % process inpimg argument 0162 % ---------------------------------------------- 0163 % remap volume if specified and is vol struct 0164 if isstruct(inpimg) & filled_opts.remap 0165 inpimg = inpimg.fname; 0166 end 0167 % convert string inpimg input to SPM vol struct 0168 if ischar(inpimg) 0169 inpimg = spm_vol(inpimg); 0170 end 0171 0172 % process different types of function call 0173 if nargin > 3 % must be untransformed data with wavelet and scales 0174 0175 % insert necessary data into wvimg structure to start 0176 [wvimg others] = mars_struct('ffillsplit', defstruct, ... 0177 struct(... 0178 'img', inpimg, ... 0179 'options', filled_opts, ... 0180 'wtf', 0, ... 0181 'descrip', filled_opts.descrip)); 0182 0183 if ~isa(waveobj,'phiw_wavelet') | isempty(scales) 0184 error('Need wavelet and scales for untransformed data'); 0185 end 0186 0187 % set ovol and ouput filename 0188 if isstruct(inpimg) % got a vol struct 0189 % set output file name by adding wt prefix 0190 [p f e] = fileparts(inpimg.fname); 0191 out_fname = fullfile(p, [wvimg.options.wtprefix f e]); 0192 0193 % look for a similar image that exists already 0194 if filled_opts.find_similar 0195 if exist(out_fname, 'file') 0196 Vw = spm_vol(out_fname); 0197 if phiw_wvimg('is_wted', Vw) 0198 Wo = phiw_wvimg(Vw, struct('noproc', 1)); 0199 if same_wtinfo(Wo, struct(... 0200 'wavelet', waveobj, ... 0201 'scales', scales)) 0202 wvimg = Wo; 0203 if ~filled_opts.noproc 0204 wvimg = doproc(wvimg); 0205 end 0206 return 0207 end 0208 end 0209 end 0210 end 0211 0212 % No found similar image - make afresh 0213 wvimg.ovol = inpimg; 0214 if ~isempty(wvimg.descrip) 0215 wvimg.descrip = [wvimg.descrip '; ' wvimg.ovol.descrip]; 0216 end 0217 wvimg.wvol.fname = out_fname; 0218 elseif ~isempty(inpimg) & isnumeric(inpimg) 0219 % maybe data passed was a matrix, we'll do our best 0220 sz = ones(1,3); 0221 sz(1:length(size(inpimg))) = size(inpimg); 0222 offs = -(sz+1)/2; 0223 wvimg.ovol = struct('dim', [sz spm_type(wvimg.options.datatype)],... 0224 'pinfo',[1 0 0]',... 0225 'fname',[],... 0226 'mat', [1 0 0 offs(1); 0 1 0 offs(2); 0 0 1 offs(3); ... 0227 0 0 0 1]); 0228 end 0229 0230 % last two args are wavelet and scales 0231 wvimg.wavelet = waveobj; 0232 wvimg.scales = scales; 0233 0234 % set bits for output image struct 0235 wvimg.wvol = mars_struct('fillafromb', wvimg.wvol, wvimg.ovol); 0236 wvimg.wvol.dim(1:3) = outdim(wvimg.wavelet, wvimg.ovol.dim(1:3)); 0237 0238 else % i.e nargin <= 3 0239 0240 % this must be a wt'ed vol struct for putting into object 0241 wvimg.wtf = 1; 0242 0243 % We need phiw_wvimg template information. We can get it from the input 0244 % vol struct, or from the third argument. Third argument can be empty 0245 % (missing), vol struct, or phiw_wvimg object... 0246 0247 % if no third argument, try and get template from .mat file 0248 if isempty(waveobj), waveobj = inpimg; end 0249 0250 % look for wavelet information in vol struct 0251 if isstruct(waveobj) 0252 waveobj = pr_getwave(waveobj); 0253 end 0254 0255 % no template obtainable -> give up and return empty 0256 if isempty(waveobj), wvimg = []; return, end 0257 0258 % Fill any missing input stuff from the template object 0259 wvimg = mars_struct('fillafromb', ... 0260 struct(... 0261 'img', inpimg, ... 0262 'options', input_options), ... 0263 struct(waveobj)); 0264 0265 % fill any missing / empty object fields from defaults 0266 wvimg.options = mars_struct('ffillsplit', defopts, wvimg.options); 0267 [wvimg others] = mars_struct('ffillsplit', defstruct, wvimg); 0268 0269 % input vol struct overrides template vol struct 0270 if isstruct(inpimg) 0271 wvimg.wvol = inpimg; 0272 else % input image dimensions override template 0273 wvimg.wvol.dim(1:3) = size(wvimg.img); 0274 end; 0275 0276 end 0277 0278 % set any options passed, overriding previous 0279 if mars_struct('isthere', input_options, 'datatype') 0280 wvimg.wvol.dim(4) = spm_type(input_options.datatype); 0281 end 0282 0283 % fill the vol structs with empty fields 0284 evol = struct('fname','','mat',eye(4),'dim',[1 1 1], ... 0285 'pinfo',ones(3,1),'descrip',''); 0286 wvimg.ovol = mars_struct('fillafromb', wvimg.ovol,evol); 0287 wvimg.wvol = mars_struct('fillafromb', wvimg.wvol,evol); 0288 0289 % set datatypes if missing 0290 if length(wvimg.ovol.dim) < 4 0291 wvimg.ovol.dim(4) = spm_type(wvimg.options.datatype); 0292 end 0293 if length(wvimg.wvol.dim) < 4 0294 wvimg.wvol.dim(4) = spm_type(wvimg.options.datatype); 0295 end 0296 0297 % bless (as we say in perl) 0298 wvimg = class(wvimg,myclass); 0299 0300 % do processing as necessary 0301 if ~wvimg.options.noproc 0302 wvimg = doproc(wvimg); 0303 end 0304 0305 % unset first pass options 0306 wvimg.options.noproc = 0; 0307 wvimg.options.remap = 0; 0308 wvimg.options.find_similar = 0; 0309 wvimg.options.descrip = ''; 0310 0311 return 0312 0313