class constructor for slice overlay (slover) object
FORMAT [o, others] = slover(params, others, varargin)
Inputs
params - either:
- action string implementing class methods (see below)
- array of image names / vol structs to display
- structure with some fields for object (see below)
others - structure, containing extra fields for object (or children)
varargin - maybe some other parameters for action calls (see below)
Outputs
o - slover object
others - any unrecognized fields from params, others
Object fields are:
- img - array of structs with information for images to display
- img structs contain fields
type - one of {'truecolour' 'split', 'contour'};
truecolour - displays transparent (see prop) image
overlaid with any previous
split - in defined area, replaces image present (SPM
type activation display)
contour - contour map of image overlaid. See help
for contours function in matlab
vol - vol struct info (see spm_vol)
can also be vol containing image as 3d matrix
set with add_blobs method
cmap - colormap for this image
nancol - color for NaN. If scalar, this is an index into
the image cmap. If 1x3 vector, it's a colour
prop - proportion of intensity for this cmap/img
func - function to apply to image before scaling to cmap
(and therefore before min/max thresholding. E.g. a func of
'i1(i1==0)=NaN' would convert zeros to NaNs
range - 2x1 vector of values for image to distribute colormap across
the first row of the colormap applies to the first
value in 'range', and the last value to the second
value in 'range'
outofrange - behavior for image values to the left and
right of image limits in 'range'. Left means
colormap values < 1, i.e for image values <
range(1), if (range(1)<range(2)), and image values >
range(1) where (range(1)>range(2)). If missing,
display min (for Left) and max (for Right) value from colormap.
Otherwise should be a 2 element cell array, where
the first element is the colour value for image values
left of 'range', and the second is for image values
right of 'range'. Scalar values for
colour index the colormap, 3x1 vectors are colour
values. An empty array attracts default settings
appropriate to the mode - i.e. transparent colour (where
img(n).type is truecolour), or split colour. Empty cells
default to 0. 0 specifies that voxels with this
colour do not influence the image (split =
background, true = black)
hold - resampling order for image (see spm_sample_vol) -
default 1
background - value when resampling outside image - default
NaN
linespec - string, applies only to contour map,
e.g. 'w-' for white continuous lines
contours - vector, applies to contour map only, defines
values in image for which to show contours
(see help contours)
linewidth - scalar, width in points of contour lines
- transform - either - 4x4 transformation to apply to image slice position,
relative to mm given by slicedef, before display
or - text string, one of axial, coronal, sagittal
These orientations assume the image is currently
(after its mat file has been applied) axially
oriented
- slicedef - 2x3 array specifying dimensions for slice images in mm
where rows are x,and y of slice image, and cols are neg max dim,
slice separation and pos max dim
- slices - vector of slice positions in mm in z (of transformed image)
- figure - figure handle for slice display figure
The object used for the display is attached as 'UserData'
to this figure
- figure_struct - stored figure parameters (in case figure dies and
needs to be recreated)
- refreshf - flag - if set or empty, refresh axis info for figure
else assume this is OK
- clf - flag, non zero -> clear figure before display. Redundant
if refreshf == 0
- resurrectf - if not zero, and figure (above) does not exist, will
attempt to recreate figure with same area properties.
Otherwise painting will give an error.
- userdata - flag, non zero -> attaches object to figure when ploting,
for use by callbacks (default is 1)
- area - struct with fields
position - bottom left, x size y size 1x4 vector of
area in which to display slices
units - one of
inches,centimeters,normalized,points,{pixels}
halign - one of left,{center},right
valign - one of top,{middle},bottom
- xslices - no of slices to display across figure (defaults to an optimum)
- cbar - if empty, missing, no colourbar. If an array of integers, then
indexes img array, and makes colourbar for each cmap for
that img. Cbars specified in order of appearance L->R
- labels - struct can be:
- empty (-> default numerical labels)
- 'none' (string) (no labels)
- or contain fields:
colour - colour for label text
size - font size in units normalized to slice axes
format - if = cell array of strings =
labels for each slice in Z. If is string, specifies
sprintf format string for labelling in distance of the
origin (Xmm=0, Ymm=0) of each slice from plane containing
the AC, in mm, in the space of the transformed image
- callback - callback string for button down on image panels. THe
following examples assume that you have the 'userdata'
field set to 1, giving you access to underlying object
To print to the matlab window the equivalent position in
mm of the position of a mouse click on one of the image
slices, set callback to:
'get_pos(get(gcf, ''UserData''))'
To print the intensity values of the images at the clicked point:
['so_obj = get(gcf, ''UserData''); ' ...
'point_vals(so_obj, get_pos(so_obj))']
- printstr - string for printing slice overlay figure window, e.g.
'print -dpsc -painters -noui' (the default)
- printfile - name of file to print output to; default 'slices.ps'
Action string formats:
FORMAT [cmap warnstr] = slover('getcmap', cmapname)
Gets colormap named in cmapname string
FORMAT [mx mn] = slover('volmaxmin', vol)
Returns maximum and minimum finite values from vol struct 'vol'
FORMAT vol = slover('blobs2vol', XYZ, vals, mat)
returns (pseudo) vol struct for 3d blob volume specified
in matrices as above
FORMAT vol = slover('matrix2vol', mat3d, mat)
returns (pseudo) vol struct for 3d matrix
input matrices as above
FORMAT obj = slover('basic_ui' [,dispf])
Runs basic UI to fetch some parameters, does display, returns object
If optional dispf parameter = 0, supresses display
$Id: slover.m,v 1.2 2005/05/06 22:59:56 matthewbrett Exp $0001 function [o, others] = slover(params, others, varargin) 0002 % class constructor for slice overlay (slover) object 0003 % FORMAT [o, others] = slover(params, others, varargin) 0004 % 0005 % Inputs 0006 % params - either: 0007 % - action string implementing class methods (see below) 0008 % - array of image names / vol structs to display 0009 % - structure with some fields for object (see below) 0010 % others - structure, containing extra fields for object (or children) 0011 % varargin - maybe some other parameters for action calls (see below) 0012 % 0013 % Outputs 0014 % o - slover object 0015 % others - any unrecognized fields from params, others 0016 % 0017 % Object fields are: 0018 % - img - array of structs with information for images to display 0019 % - img structs contain fields 0020 % type - one of {'truecolour' 'split', 'contour'}; 0021 % truecolour - displays transparent (see prop) image 0022 % overlaid with any previous 0023 % split - in defined area, replaces image present (SPM 0024 % type activation display) 0025 % contour - contour map of image overlaid. See help 0026 % for contours function in matlab 0027 % vol - vol struct info (see spm_vol) 0028 % can also be vol containing image as 3d matrix 0029 % set with add_blobs method 0030 % cmap - colormap for this image 0031 % nancol - color for NaN. If scalar, this is an index into 0032 % the image cmap. If 1x3 vector, it's a colour 0033 % prop - proportion of intensity for this cmap/img 0034 % func - function to apply to image before scaling to cmap 0035 % (and therefore before min/max thresholding. E.g. a func of 0036 % 'i1(i1==0)=NaN' would convert zeros to NaNs 0037 % range - 2x1 vector of values for image to distribute colormap across 0038 % the first row of the colormap applies to the first 0039 % value in 'range', and the last value to the second 0040 % value in 'range' 0041 % outofrange - behavior for image values to the left and 0042 % right of image limits in 'range'. Left means 0043 % colormap values < 1, i.e for image values < 0044 % range(1), if (range(1)<range(2)), and image values > 0045 % range(1) where (range(1)>range(2)). If missing, 0046 % display min (for Left) and max (for Right) value from colormap. 0047 % Otherwise should be a 2 element cell array, where 0048 % the first element is the colour value for image values 0049 % left of 'range', and the second is for image values 0050 % right of 'range'. Scalar values for 0051 % colour index the colormap, 3x1 vectors are colour 0052 % values. An empty array attracts default settings 0053 % appropriate to the mode - i.e. transparent colour (where 0054 % img(n).type is truecolour), or split colour. Empty cells 0055 % default to 0. 0 specifies that voxels with this 0056 % colour do not influence the image (split = 0057 % background, true = black) 0058 % hold - resampling order for image (see spm_sample_vol) - 0059 % default 1 0060 % background - value when resampling outside image - default 0061 % NaN 0062 % linespec - string, applies only to contour map, 0063 % e.g. 'w-' for white continuous lines 0064 % contours - vector, applies to contour map only, defines 0065 % values in image for which to show contours 0066 % (see help contours) 0067 % linewidth - scalar, width in points of contour lines 0068 % 0069 % - transform - either - 4x4 transformation to apply to image slice position, 0070 % relative to mm given by slicedef, before display 0071 % or - text string, one of axial, coronal, sagittal 0072 % These orientations assume the image is currently 0073 % (after its mat file has been applied) axially 0074 % oriented 0075 % - slicedef - 2x3 array specifying dimensions for slice images in mm 0076 % where rows are x,and y of slice image, and cols are neg max dim, 0077 % slice separation and pos max dim 0078 % - slices - vector of slice positions in mm in z (of transformed image) 0079 % - figure - figure handle for slice display figure 0080 % The object used for the display is attached as 'UserData' 0081 % to this figure 0082 % - figure_struct - stored figure parameters (in case figure dies and 0083 % needs to be recreated) 0084 % - refreshf - flag - if set or empty, refresh axis info for figure 0085 % else assume this is OK 0086 % - clf - flag, non zero -> clear figure before display. Redundant 0087 % if refreshf == 0 0088 % - resurrectf - if not zero, and figure (above) does not exist, will 0089 % attempt to recreate figure with same area properties. 0090 % Otherwise painting will give an error. 0091 % - userdata - flag, non zero -> attaches object to figure when ploting, 0092 % for use by callbacks (default is 1) 0093 % - area - struct with fields 0094 % position - bottom left, x size y size 1x4 vector of 0095 % area in which to display slices 0096 % units - one of 0097 % inches,centimeters,normalized,points,{pixels} 0098 % halign - one of left,{center},right 0099 % valign - one of top,{middle},bottom 0100 % - xslices - no of slices to display across figure (defaults to an optimum) 0101 % - cbar - if empty, missing, no colourbar. If an array of integers, then 0102 % indexes img array, and makes colourbar for each cmap for 0103 % that img. Cbars specified in order of appearance L->R 0104 % - labels - struct can be: 0105 % - empty (-> default numerical labels) 0106 % - 'none' (string) (no labels) 0107 % - or contain fields: 0108 % colour - colour for label text 0109 % size - font size in units normalized to slice axes 0110 % format - if = cell array of strings = 0111 % labels for each slice in Z. If is string, specifies 0112 % sprintf format string for labelling in distance of the 0113 % origin (Xmm=0, Ymm=0) of each slice from plane containing 0114 % the AC, in mm, in the space of the transformed image 0115 % - callback - callback string for button down on image panels. THe 0116 % following examples assume that you have the 'userdata' 0117 % field set to 1, giving you access to underlying object 0118 % To print to the matlab window the equivalent position in 0119 % mm of the position of a mouse click on one of the image 0120 % slices, set callback to: 0121 % 'get_pos(get(gcf, ''UserData''))' 0122 % To print the intensity values of the images at the clicked point: 0123 % ['so_obj = get(gcf, ''UserData''); ' ... 0124 % 'point_vals(so_obj, get_pos(so_obj))'] 0125 % - printstr - string for printing slice overlay figure window, e.g. 0126 % 'print -dpsc -painters -noui' (the default) 0127 % - printfile - name of file to print output to; default 'slices.ps' 0128 % 0129 % Action string formats: 0130 % FORMAT [cmap warnstr] = slover('getcmap', cmapname) 0131 % Gets colormap named in cmapname string 0132 % 0133 % FORMAT [mx mn] = slover('volmaxmin', vol) 0134 % Returns maximum and minimum finite values from vol struct 'vol' 0135 % 0136 % FORMAT vol = slover('blobs2vol', XYZ, vals, mat) 0137 % returns (pseudo) vol struct for 3d blob volume specified 0138 % in matrices as above 0139 % 0140 % FORMAT vol = slover('matrix2vol', mat3d, mat) 0141 % returns (pseudo) vol struct for 3d matrix 0142 % input matrices as above 0143 % 0144 % FORMAT obj = slover('basic_ui' [,dispf]) 0145 % Runs basic UI to fetch some parameters, does display, returns object 0146 % If optional dispf parameter = 0, supresses display 0147 % 0148 % $Id: slover.m,v 1.2 2005/05/06 22:59:56 matthewbrett Exp $ 0149 0150 myclass = 'slover'; 0151 0152 % Default object structure 0153 defstruct = struct('img', [], ... 0154 'transform', 'axial', ... 0155 'slicedef', [], ... 0156 'slices', [], ... 0157 'figure', [], ... 0158 'figure_struct', [], ... 0159 'refreshf', 1, ... 0160 'clf', 1, ... 0161 'resurrectf', 1, ... 0162 'userdata', 1, ... 0163 'area', [], ... 0164 'xslices', [], ... 0165 'cbar', [], ... 0166 'labels', [], ... 0167 'callback', ';', ... 0168 'printstr', 'print -dpsc -painters -noui', ... 0169 'printfile', 'slices.ps'); 0170 0171 if nargin < 1 0172 o = class(defstruct, myclass); 0173 others = []; 0174 return 0175 end 0176 if nargin < 2 0177 others = []; 0178 end 0179 0180 % parse out string action calls (class functions) 0181 if ischar(params) 0182 switch params 0183 case 'getcmap' 0184 if nargin < 2 0185 error('Need colormap name'); 0186 end 0187 o = pr_getcmap(others); 0188 return 0189 case 'volmaxmin' 0190 if nargin < 2 0191 error('Need volume to calculate max/min'); 0192 end 0193 [o others] = pr_volmaxmin(others); 0194 return 0195 case 'blobs2vol' 0196 if nargin < 4 0197 error('Need XYZ, vals, mat'); 0198 end 0199 o = pr_blobs2vol(others, varargin{:}); 0200 return 0201 case 'matrix2vol' 0202 if nargin < 3 0203 error('Need matrix and mat'); 0204 end 0205 o = pr_matrix2vol(others, varargin{:}); 0206 return 0207 case 'basic_ui' 0208 o = pr_basic_ui(others, varargin{:}); 0209 if ~isempty(o), o = paint(o); end 0210 return 0211 end 0212 0213 % if not action string, must be filename(s) 0214 params = spm_vol(params); 0215 end 0216 0217 % Could these just be image vol structs? 0218 if isfield(params, 'fname') 0219 for i = 1:prod(size(params)) 0220 obj.img(i).vol = params(i); 0221 end 0222 params = obj; 0223 end 0224 0225 % Deal with passed objects of this (or child) class 0226 if isa(params, myclass) 0227 o = params; 0228 % Check for simple form of call 0229 if isempty(others), return, end 0230 0231 % Otherwise, we are being asked to set fields of object 0232 [p others] = mars_struct('split', others, defstruct); 0233 o = mars_struct('ffillmerge', o, p); 0234 return 0235 end 0236 0237 % fill params with defaults, parse into fields for this object, children 0238 params = mars_struct('fillafromb', params, others); 0239 [params, others] = mars_struct('ffillsplit', defstruct, params); 0240 0241 % set the slover object 0242 o = class(params, myclass); 0243 0244 % refill with defaults 0245 o = fill_defaults(o); 0246 0247 return