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<Guido> <Hesselmann> wrote:
> Dear SPMers,
>
> I would like to select 4d NIFTI files using spm_select without the GUI. I
> understand that
> [files,dirs]=spm_select('List',direc,filt)
> should do the trick, but where is the frame filter? Has anyone solved the
> problem elegantly?
Hi Guido,
I think you need to hack the code a bit to get this to work. I
wouldn't claim to have done it elegantly, but the attached modified
spm_select (new lines 93-95 inserted) now has an option 'extlist',
which you can use like:
spm_select_mod('extlist', direc, filt, frames)
e.g. the following seems to do what I'd expect...
spm_select_mod('extlist', 'testdir', '\.nii', [1:3,5,7:9])
Best,
Ged.
function [t,sts] = spm_select(varargin)
% File selector
% FORMAT [t,sts] = spm_select(n,typ,mesg,sel,wd,filt,frames)
% n - Number of files
% A single value or a range. e.g.
% 1 - Select one file
% Inf - Select any number of files
% [1 Inf] - Select 1 to Inf files
% [0 1] - select 0 or 1 files
% [10 12] - select from 10 to 12 files
% typ - file type
% 'any' - all files
% 'image' - Image files (".img" and ".nii")
% Note that it gives the option to select
% individual volumes of the images.
% 'xml' - XML files
% 'mat' - Matlab .mat files
% 'batch' - SPM batch files (.mat and XML)
% 'dir' - select a directory
% Other strings act as a filter to regexp. This means
% that e.g. DCM*.mat files should have a typ of '^DCM.*\.mat$'
% mesg - a prompt (default 'Select files...')
% sel - list of already selected files
% wd - Directory to start off in
% filt - value for user-editable filter (default '.*')
% frames - Image frame numbers to include (default '1')
%
% t - selected files
% sts - status (1 means OK, 0 means window quit)
%
% Files can be selected from disk, but "virtual" files can also be selected.
% Virtual filenames are passed by
% spm_select('addvfiles',list)
% where list is a cell array of filenames
% The list can be cleared by
% spm_select('clearvfiles')
%
% FORMAT [t,sts] = spm_select('Filter',files,typ,filt,frames)
% filter the list of files (cell or char array) in the same way as the GUI would do.
% There is an additional typ 'extimage' which will match images with
% frame specifications, too. Also, there is a typ 'extdir', which will
% match canonicalised directory names.
%
% FORMAT cpath = spm_select('CPath',path,cwd)
% function to canonicalise paths: Prepends cwd to relative paths, processes
% '..' & '.' directories embedded in path.
% path - string matrix containing path name
% cwd - current working directory [defaut '.']
% cpath - conditioned paths, in same format as input path argument
%
% FORMAT [files,dirs]=spm_select('List',direc,filt)
% Returns files matching the filter (filt) and directories within dire
% direc - directory to search
% filt - filter to select files with (see regexp) e.g. '^w.*\.img$'
% files - files matching 'filt' in directory 'direc'
% dirs - subdirectories of 'direc'
%____________________________________________________________________________
% Copyright (C) 2005 Wellcome Department of Imaging Neuroscience
% John Ashburner
% $Id: spm_select.m 661 2006-10-20 14:50:58Z john $
if nargin > 0 && ischar(varargin{1})
switch lower(varargin{1})
case 'addvfiles'
error(nargchk(2,Inf,nargin));
vfiles('add',varargin{2:end});
case 'clearvfiles'
error(nargchk(1,1,nargin));
vfiles('clear');
case 'vfiles'
error(nargchk(1,1,nargin));
t = vfiles('all');
case 'cpath'
error(nargchk(2,Inf,nargin));
t = cpath(varargin{2:end});
case 'filter'
filt = mk_filter(varargin{3:end});
cs = iscell(varargin{2});
if ~cs
t = cellstr(varargin{2});
else
t = varargin{2};
end;
[t,sts] = do_filter(t,filt.ext);
[t,sts] = do_filter(t,filt.filt);
if ~cs
t = strvcat(t);
end;
case 'list'
filt = mk_filter('any',varargin{3}, []);
[t,sts] = listfiles(varargin{2},filt);
case 'extlist'
filt = mk_filter('extimage',varargin{3:end});
[t,sts] = listfiles(varargin{2},filt);
otherwise
error('Inappropriate usage.');
end
else
[t,sts] = selector(varargin{:});
end
%=======================================================================
%=======================================================================
function [t,ok] = selector(n,typ,mesg,already,wd,filt,frames,varargin)
if nargin<7, frames = '1'; end;
if nargin<6, filt = '.*'; end;
if nargin<5, wd = pwd; end;
if nargin<4, already = {''}; end;
if nargin<3, mesg = 'Select files...'; end;
if nargin<2, typ = 'any'; end;
if nargin<1, n = [0 Inf]; end;
ok = 0;
if numel(n)==1, n = [n n]; end;
if n(1)>n(2), n = n([2 1]); end;
if ~finite(n(1)), n(1) = 0; end;
already = strvcat(already);
t = '';
sfilt = mk_filter(typ,filt,frames);
[col1,col2,col3,fs] = colours;
fg = figure('IntegerHandle','off',...
'Tag','Select',...
'Name',strvcat(mesg),...
'NumberTitle','off',...
'Units','Pixels',...
'MenuBar','none',...
'DefaultTextInterpreter','none',...
'DefaultUicontrolInterruptible','on',...
'ResizeFcn',@resize_fun,...
'KeyPressFcn',@hitkey);
% Code from Brian Lenoski for dealing with multiple monitors
if spm_matlab_version_chk('7') >=0
S = get(0, 'MonitorPosition');
Rect = get(fg,'Position');
pointer_loc = get(0,'PointerLocation');
for i = 1:size(S,1), % Loop over monitors
h_min = S(i,1);
h_width = S(i,3);
h_max = h_width + h_min - 1;
v_min = S(i,2);
v_len = S(i,4);
v_max = v_min + v_len;
% Use the monitor containing the pointer
if pointer_loc(1) >= h_min && pointer_loc(1) < h_max && ...
pointer_loc(2) >= v_min && pointer_loc(2) < v_max,
hor_min = h_min;
hor_width = h_width;
hor_max = h_max;
ver_min = v_min;
ver_len = v_len;
ver_max = v_max;
end
end
Rect(1) = (hor_max - 0.5*hor_width) - 0.5*Rect(3); % Horizontal
Rect(2) = (ver_max - 0.5*ver_len) - 0.5*Rect(4); % Vertical
set(fg,'Position',Rect);
end
fh = 0.05;
%fs = 10;
sbh = 0.03; % Scroll-bar height. This should be worked out properly
h1 = (0.96-4*fh-5*0.01)/2;
if n(2)*fh+sbh<h1,
h1 = min([max([n(2) size(already,1)+.2])*fh+sbh, h1]);
end;
h2 = 0.96-4*fh-5*0.01-h1;
SPMdir = fileparts(which(mfilename));
if ( spm_matlab_version_chk('7') >= 0 ) && isdeployed,
ind = findstr(SPMdir,'_mcr')-1;
[SPMdir,junk] = fileparts(SPMdir(1:ind(1)));
end;
prevdirs([SPMdir filesep]);
[pd,vl] = prevdirs([wd filesep]);
% Selected Files
hp = 0.02;
sel = uicontrol(fg,...
'style','listbox',...
'units','normalized',...
'Position',[0.02 hp 0.96 h1],...
'FontSize',fs,...
'Callback',@unselect,...
'tag','selected',...
'BackgroundColor',col1,...
'ForegroundColor',col3,...
'Max',10000,...
'Min',0,...
'String',already,...
'Value',1);
c0 = uicontextmenu('Parent',fg);
set(sel,'uicontextmenu',c0);
uimenu('Label','Unselect All', 'Parent',c0,'Callback',@unselect_all);
% Messages
hp = hp+h1+0.01;
uicontrol(fg,...
'style','text',...
'units','normalized',...
'Position',[0.02 hp 0.96 fh],...
'FontSize',fs,...
'BackgroundColor',get(fg,'Color'),...
'ForegroundColor',col3,...
'HorizontalAlignment','left',...
'Tag','msg',...
'String',mesg);
if strcmpi(typ,'image'),
uicontrol(fg,...
'style','edit',...
'units','normalized',...
'Position',[0.61 hp 0.37 fh],...
'Callback',@update_frames,...
'tag','frame',...
'FontSize',fs,...
'BackgroundColor',col1,...
'String',frames,'UserData',eval(frames));
% 'ForegroundGolor',col3,...
end;
% Help
hp = hp+fh+0.01;
uicontrol(fg,...
'Style','pushbutton',...
'units','normalized',...
'Position',[0.02 hp fh fh],...
'FontSize',fs,...
'Callback',@heelp,...
'tag','?',...
'ForegroundColor',col3,...
'BackgroundColor',col1,...
'String','?',...
'FontWeight','bold',...
'ToolTipString','Show Help',...
'FontSize',fs);
uicontrol(fg,...
'Style','pushbutton',...
'units','normalized',...
'Position',[0.03+fh hp fh fh],...
'FontSize',fs,...
'Callback',@editwin,...
'tag','Ed',...
'ForegroundColor',col3,...
'BackgroundColor',col1,...
'String','Ed',...
'FontWeight','bold',...
'ToolTipString','Edit Selected Files',...
'FontSize',fs);
uicontrol(fg,...
'Style','pushbutton',...
'units','normalized',...
'Position',[0.04+2*fh hp fh fh],...
'FontSize',fs,...
'Callback',@select_rec,...
'tag','Rec',...
'ForegroundColor',col3,...
'BackgroundColor',col1,...
'String','Rec',...
'FontWeight','bold',...
'ToolTipString','Recursively Select Files with Current Filter',...
'FontSize',fs);
% Done
dne = uicontrol(fg,...
'Style','pushbutton',...
'units','normalized',...
'Position',[0.05+3*fh hp 0.45-3*fh fh],...
'FontSize',fs,...
'Callback',@delete,...
'tag','D',...
'ForegroundColor',col3,...
'BackgroundColor',col1,...
'String','Done',...
'FontWeight','bold',...
'FontSize',fs,...
'Enable','off',...
'DeleteFcn',@null);
if size(already,1)>=n(1) && size(already,1)<=n(2),
set(dne,'Enable','on');
end;
% Filter Button
uicontrol(fg,...
'Style','pushbutton',...
'units','normalized',...
'Position',[0.51 hp 0.1 fh],...
'FontSize',fs,...
'ForegroundColor',col3,...
'BackgroundColor',col1,...
'Callback',@clearfilt,...
'String','Filt',...
'FontSize',fs);
% Filter
uicontrol(fg,...
'style','edit',...
'units','normalized',...
'Position',[0.61 hp 0.37 fh],...
'ForegroundColor',col3,...
'BackgroundColor',col1,...
'FontSize',fs,...
'Callback',@update,...
'tag','regexp',...
'String',filt,...
'UserData',sfilt);
% Directories
hp = hp + fh+0.01;
db = uicontrol(fg,...
'style','listbox',...
'units','normalized',...
'Position',[0.02 hp 0.47 h2],...
'FontSize',fs,...
'Callback',@click_dir_box,...
'tag','dirs',...
'BackgroundColor',col1,...
'ForegroundColor',col3,...
'Max',1,...
'Min',0,...
'String','',...
'UserData',wd,...
'Value',1);
% Files
tmp = uicontrol(fg,...
'style','listbox',...
'units','normalized',...
'Position',[0.51 hp 0.47 h2],...
'FontSize',fs,...
'Callback',@click_file_box,...
'tag','files',...
'BackgroundColor',col1,...
'ForegroundColor',col3,...
'UserData',n,...
'Max',10240,...
'Min',0,...
'String','',...
'Value',1);
c0 = uicontextmenu('Parent',fg);
set(tmp,'uicontextmenu',c0);
uimenu('Label','Select All', 'Parent',c0,'Callback',@select_all);
% Drives
if strcmpi(computer,'PCWIN') || strcmpi(computer,'PCWIN64'),
dr = spm_platform('drives');
drivestr = cell(1,numel(dr));
for i=1:numel(dr),
drivestr{i} = [dr(i) ':'];
end;
%drivestr = {'A:','B:','C:','D:'};
sz = get(db,'Position');
sz(4) = sz(4)-fh-2*0.01;
set(db,'Position',sz);
uicontrol(fg,...
'style','text',...
'units','normalized',...
'Position',[0.02 hp+h2-fh-0.01 0.10 fh],...
'FontSize',fs,...
'BackgroundColor',get(fg,'Color'),...
'ForegroundColor',col3,...
'String','Drive');
uicontrol(fg,...
'style','popupmenu',...
'units','normalized',...
'Position',[0.12 hp+h2-fh-0.01 0.37 fh],...
'FontSize',fs,...
'Callback',@setdrive,...
'tag','drive',...
'BackgroundColor',col1,...
'ForegroundColor',col3,...
'String',drivestr,...
'Value',1);
end;
% Previous dirs
hp = hp+h2+0.01;
uicontrol(fg,...
'style','popupmenu',...
'units','normalized',...
'Position',[0.12 hp 0.86 fh],...
'FontSize',fs,...
'Callback',@click_dir_list,...
'tag','previous',...
'BackgroundColor',col1,...
'ForegroundColor',col3,...
'String',pd,...
'Value',vl);
uicontrol(fg,...
'style','text',...
'units','normalized',...
'Position',[0.02 hp 0.10 fh],...
'FontSize',fs,...
'BackgroundColor',get(fg,'Color'),...
'ForegroundColor',col3,...
'String','Prev');
% Directory
hp = hp + fh+0.01;
uicontrol(fg,...
'style','edit',...
'units','normalized',...
'Position',[0.12 hp 0.86 fh],...
'FontSize',fs,...
'Callback',@edit_dir,...
'tag','edit',...
'BackgroundColor',col1,...
'ForegroundColor',col3,...
'String','');
uicontrol(fg,...
'style','text',...
'units','normalized',...
'Position',[0.02 hp 0.10 fh],...
'FontSize',fs,...
'BackgroundColor',get(fg,'Color'),...
'ForegroundColor',col3,...
'String','Dir');
resize_fun(fg);
update(sel,wd)
waitfor(dne);
drawnow;
if ishandle(sel),
t = get(sel,'String');
if sfilt.code == -1
t = cellstr(t);
for k = 1:numel(t);
t{k} = cpath(t{k},pwd);
end;
t = char(t);
end;
ok = 1;
end;
if ishandle(fg), delete(fg); end;
drawnow;
return;
%=======================================================================
%=======================================================================
function null(varargin)
%=======================================================================
%=======================================================================
function msg(ob,str)
ob = sib(ob,'msg');
set(ob,'String',str);
if nargin>=3,
set(ob,'ForegroundColor',[1 0 0],'FontWeight','bold');
else
set(ob,'ForegroundColor',[0 0 0],'FontWeight','normal');
end;
drawnow;
return;
%=======================================================================
%=======================================================================
function setdrive(ob,varargin)
st = get(ob,'String');
vl = get(ob,'Value');
update(ob,st{vl});
return;
%=======================================================================
%=======================================================================
function resize_fun(fg,varargin)
ob = findobj(fg,'String','Filt','Style','pushbutton');
if ~isempty(ob),
ofs = get(ob,'FontSize');
ex = get(ob,'Extent');
ps = get(ob,'Position');
fs = floor(ofs*min(ps(4)./ex(4))+1);
fs = max(min(fs,30),4);
ob = findobj(fg,'Fontsize',ofs);
set(ob,'FontSize',fs);
end;
return;
%=======================================================================
%=======================================================================
function [d,mch] = prevdirs(d)
persistent pd
if ~iscell(pd), pd = {}; end;
d = deblank(d);
mch = find(strcmp(d,pd));
if isempty(mch),
pd = {pd{:},d};
mch = length(pd);
end;
d = pd;
return;
%=======================================================================
%=======================================================================
function clearfilt(ob,varargin)
set(sib(ob,'regexp'),'String','.*');
update(ob);
return;
%=======================================================================
%=======================================================================
function click_dir_list(ob,varargin)
vl = get(ob,'Value');
ls = get(ob,'String');
update(ob,deblank(ls{vl}));
return;
%=======================================================================
%=======================================================================
function edit_dir(ob,varargin)
update(ob,get(ob,'String'));
return;
%=======================================================================
%=======================================================================
function click_dir_box(lb,varargin)
update(lb,current_dir(lb));
return;
%=======================================================================
%=======================================================================
function dr = current_dir(lb,varargin)
vl = get(lb,'Value');
str = get(lb,'String');
pd = get(sib(lb,'edit'),'String');
while ~isempty(pd) & strcmp(pd(end),filesep)
pd=pd(1:end-1); % Remove any trailing fileseps
end
sel = deblank(str(vl,:));
if strcmp(sel,'..'), % Parent directory
dr = fileparts(pd);
elseif strcmp(sel,'.'), % Current directory
dr = pd;
else
dr = fullfile(pd,sel);
end;
return;
%=======================================================================
%=======================================================================
function re = getfilt(ob)
ob = sib(ob,'regexp');
ud = get(ob,'UserData');
re = struct('code',ud.code,...
'frames',get(sib(ob,'frame'),'UserData'),...
'ext',{ud.ext},...
'filt',{{get(sib(ob,'regexp'),'String')}});
return;
%=======================================================================
%=======================================================================
function update(lb,dr)
lb = sib(lb,'dirs');
if nargin<2 || isempty(dr),
dr = get(lb,'UserData');
end;
if ~(strcmpi(computer,'PCWIN') || strcmpi(computer,'PCWIN64'))
dr = [filesep dr filesep];
else
dr = [dr filesep];
end;
dr(findstr([filesep filesep],dr)) = [];
[f,d] = listfiles(dr,getfilt(lb));
if isempty(d),
dr = get(lb,'UserData');
[f,d] = listfiles(dr,getfilt(lb));
else
set(lb,'UserData',dr);
end;
set(lb,'Value',1,'String',d);
set(sib(lb,'files'),'Value',1,'String',f);
[ls,mch] = prevdirs(dr);
set(sib(lb,'previous'),'String',ls,'Value',mch);
set(sib(lb,'edit'),'String',dr);
if numel(dr)>1 && dr(2)==':',
str = get(sib(lb,'drive'),'String');
str = cat(1,char(str));
mch = find(lower(str(:,1))==lower(dr(1)));
if ~isempty(mch),
set(sib(lb,'drive'),'Value',mch);
end;
end;
return;
%=======================================================================
%=======================================================================
function update_frames(lb,varargin)
str = get(lb,'String');
%r = get(lb,'UserData');
try
r = eval(['[',str,']']);
catch
msg(lb,['Failed to evaluate "' str '".'],'r');
beep;
return;
end;
if ~isnumeric(r),
msg(lb,['Expression non-numeric "' str '".'],'r');
beep;
else
set(lb,'UserData',r);
msg(lb,'');
update(lb);
end;
%=======================================================================
%=======================================================================
function select_all(ob,varargin)
lb = findobj(get(get(ob,'Parent'),'Parent'),'Tag','files');
str = get(lb,'String');
set(lb,'Value',1:size(str,1));
drawnow;
click_file_box(lb);
return;
%=======================================================================
%=======================================================================
function click_file_box(lb,varargin)
lim = get(lb,'UserData');
ob = sib(lb,'selected');
str3 = get(ob,'String');
str = get(lb,'String');
vlo = get(lb,'Value');
lim1 = min(max(lim(2)-size(str3,1),0),length(vlo));
if isempty(vlo),
msg(lb,'Nothing selected');
return;
end;
if lim1==0,
msg(lb,['Selected ' num2str(size(str3,1)) '/' num2str(lim(2)) ' already.']);
beep;
set(sib(lb,'D'),'Enable','on');
return;
end;
vl = vlo(1:lim1);
msk = false(size(str,1),1);
if vl>0, msk(vl) = true; else msk = []; end;
str1 = str( msk,:);
str2 = str(~msk,:);
dr = [current_dir(sib(lb,'dirs')) filesep];
str1 = [repmat(dr,size(str1,1),1) str1];
set(lb,'Value',min(vl(1),size(str2,1)),'String',str2);
r = (1:size(str1,1))+size(str3,1);
str3 = deblank(strvcat(str3,str1));
set(ob,'String',str3,'Value',r);
if length(vlo)>lim1,
msg(lb,['Retained ' num2str(lim1) '/' num2str(length(vlo))...
' of selection.']);
beep;
elseif finite(lim(2))
if lim(1)==lim(2),
msg(lb,['Selected ' num2str(size(str3,1)) '/' num2str(lim(2)) ' files.']);
else
msg(lb,['Selected ' num2str(size(str3,1)) '/' num2str(lim(1)) '-' num2str(lim(2)) ' files.']);
end;
else
if size(str3,1) == 1, ss = ''; else ss = 's'; end;
msg(lb,['Selected ' num2str(size(str3,1)) ' file' ss '.']);
end;
if ~finite(lim(1)) || size(str3,1)>=lim(1),
set(sib(lb,'D'),'Enable','on');
end;
return;
%=======================================================================
%=======================================================================
function obj = sib(ob,tag)
obj = findobj(get(ob,'Parent'),'Tag',tag);
return;
%if isempty(obj),
% error(['Can''t find object with tag "' tag '".']);
%elseif length(obj)>1,
% error(['Found ' num2str(length(obj)) ' objects with tag "' tag '".']);
%end;
%return;
%=======================================================================
%=======================================================================
function unselect(lb,varargin)
vl = get(lb,'Value');
if isempty(vl), return; end;
str = get(lb,'String');
msk = ones(size(str,1),1);
if vl~=0, msk(vl) = 0; end;
str2 = str(logical(msk),:);
set(lb,'Value',min(vl(1),size(str2,1)),'String',str2);
lim = get(sib(lb,'files'),'UserData');
if size(str2,1)>= lim(1) && size(str2,1)<= lim(2),
set(sib(lb,'D'),'Enable','on');
else
set(sib(lb,'D'),'Enable','off');
end;
if size(str2,1) == 1, ss1 = ''; else ss1 = 's'; end;
%msg(lb,[num2str(size(str2,1)) ' file' ss ' remaining.']);
if numel(vl) == 1, ss = ''; else ss = 's'; end;
msg(lb,['Unselected ' num2str(numel(vl)) ' file' ss '. ' ...
num2str(size(str2,1)) ' file' ss1 ' remaining.']);
return;
%=======================================================================
%=======================================================================
function unselect_all(ob,varargin)
lb = findobj(get(get(ob,'Parent'),'Parent'),'Tag','selected');
set(lb,'Value',[],'String','','ListBoxTop',1);
msg(lb,'Unselected all files.');
lim = get(sib(lb,'files'),'UserData');
if lim(1)>0, set(sib(lb,'D'),'Enable','off'); end;
return;
%=======================================================================
%=======================================================================
function varargout = vfiles(option,varargin)
persistent vfs
if isempty(vfs),
vfs = newvfs;
end;
switch option,
case {'clear'}
vfs = newvfs;
case {'add'}
for j=1:numel(varargin),
pth = {};
fle = {};
if ischar(varargin{j}),
for i=1:size(varargin{j},1),
[pth{i} n e v] = spm_fileparts(deblank(varargin{j}(i,:)));
fle{i} = [n e v];
end;
elseif iscell(varargin{j}),
for i=1:numel(varargin{j}),
[pth{i} n e v] = spm_fileparts(deblank(varargin{j}{i}));
fle{i} = [n e v];
end;
end;
[pu pi pj] = unique(pth);
for k = 1:numel(pu)
vfs = addvfile(vfs,pu{k},fle(pj==k));
end;
end;
case {'list'}
[varargout{1:3}] = listvfiles(vfs,varargin{:});
case {'all'}
varargout{1} = vfs;
otherwise
error('Unknown option.');
end;
return;
%=======================================================================
%=======================================================================
function vfs = newvfs(nam)
if nargin==0, nam = ''; end;
vfs = struct('name',nam,'dirs',struct('name',{},'dirs',{},'files',{}),'files',struct('name',{},'ind',{}));
return;
%=======================================================================
%=======================================================================
function vfs = addvfile(vfs,pth,fle)
if isempty(pth),
for k = 1:numel(fle)
[unused,nam,ext,num] = spm_fileparts(fle{k});
if ~isempty(num),
ind = [str2num(num) 1 1];
ind = ind(1);
else
ind = [];
end;
fname = [nam ext];
mch = strcmp(fname,{vfs.files.name});
if any(mch),
mch = find(mch);
vfs.files(mch).ind = [vfs.files(mch).ind ind];
else
vfs.files(end+1).name = fname;
vfs.files(end).ind = ind;
end;
end;
else
ind = find(pth==filesep);
if isempty(ind)
dr = pth;
pth = '';
else
if any(ind==1),
ind = ind(2:end)-1;
pth = pth(2:end);
end;
if isempty(ind)
dr = pth;
pth = '';
else
dr = pth(1:(ind(1)-1));
pth = pth((ind(1)+1):end);
end;
end;
mch = strcmp(dr,{vfs.dirs.name});
if any(mch),
mch = find(mch);
else
mch = numel(vfs.dirs)+1;
vfs.dirs(mch) = newvfs(dr);
end;
vfs.dirs(mch) = addvfile(vfs.dirs(mch),pth,fle);
end;
return;
%=======================================================================
%=======================================================================
function [f,d] = listfiles(dr,filt)
ob = gco;
msg(ob,'Listing directory...');
if nargin<2, filt = ''; end;
if nargin<1, dr = '.'; end;
de = dir(dr);
if ~isempty(de),
d = {de([de.isdir]).name};
if ~any(strcmp(d, '.'))
d = {'.', d{:}};
end;
if filt.code~=-1,
f = {de(~[de.isdir]).name};
else
% f = d(3:end);
f = d;
end;
else
d = {'.','..'};
f = {};
end;
msg(ob,['Filtering ' num2str(numel(f)) ' files...']);
f = do_filter(f,filt.ext);
f = do_filter(f,filt.filt);
ii = cell(1,numel(f));
if filt.code==1 && (numel(filt.frames)~=1 || filt.frames(1)~=1),
msg(ob,['Reading headers of ' num2str(numel(f)) ' images...']);
for i=1:numel(f),
try
ni = nifti(fullfile(dr,f{i}));
dm = [ni.dat.dim 1 1 1 1 1];
d4 = (1:dm(4))';
catch
d4 = 1;
end;
msk = false(size(filt.frames));
for j=1:numel(msk), msk(j) = any(d4==filt.frames(j)); end;
ii{i} = filt.frames(msk);
end;
elseif filt.code==1 && (numel(filt.frames)==1 && filt.frames(1)==1),
for i=1:numel(f),
ii{i} = 1;
end;
end;
msg(ob,'Listing virtual files...');
[fv,dv,iv] = vfiles('list',dr);
if filt.code==-1,
fv = dv;
iv = cell(size(fv));
end;
msg(ob,['Filtering ' num2str(numel(fv)) ' virtual files...']);
[fv,ind] = do_filter(fv,filt.ext);
iv = iv(ind);
[fv,ind] = do_filter(fv,filt.filt);
iv = iv(ind);
if filt.code==1,
for i=1:numel(iv),
msk = false(size(filt.frames));
for j=1:numel(msk), msk(j) = any(iv{i}==filt.frames(j)); end;
iv{i} = filt.frames(msk);
end;
end;
d = { d{:},dv{:}};
f = { f{:},fv{:}};
ii = {ii{:},iv{:}};
msg(ob,['Listing ' num2str(numel(f)) ' files...']);
[f,ind] = sortrows(f(:));
ii = ii(ind);
msk = true(1,numel(f));
if ~isempty(f), f{1} = deblank(f{1}); end;
for i=2:numel(f),
f{i} = deblank(f{i});
if strcmp(f{i-1},f{i}),
if filt.code==1,
tmp = sort([ii{i}(:) ; ii{i-1}(:)]);
tmp(~diff(tmp,1)) = [];
ii{i} = tmp;
end;
msk(i-1) = false;
end;
end;
f = f(msk);
if filt.code==1,
ii = ii(msk);
c = cell(size(f));
for i=1:numel(f),
c{i} = [repmat([f{i} ','],numel(ii{i}),1) num2str(ii{i}(:)) ];
end;
f = c;
elseif filt.code==-1,
fs = filesep;
for i=1:numel(f),
f{i} = [f{i} fs];
end;
end;
f = strvcat(f{:});
d = sortrows(d(:));
d = strvcat(d);
sam = find(~any(diff(d+0,1),2));
d(sam,:) = [];
msg(ob,'');
return;
%=======================================================================
%=======================================================================
function [f,ind] = do_filter(f,filt)
t2 = false(numel(f),1);
% This would be a speedup, but does not work on MATLAB < R14SP3 due to
% changes in regexp handling
% filt_or = sprintf('(%s)|',filt{:});
% t1 = regexp(f,filt_or(1:end-1));
% if numel(f)==1 && ~iscell(t1), t1 = {t1}; end;
% for i=1:numel(t1),
% t2(i) = ~isempty(t1{i});
% end;
for j=1:numel(filt),
t1 = regexp(f,filt{j});
if numel(f)==1 && ~iscell(t1), t1 = {t1}; end;
for i=1:numel(t1),
t2(i) = t2(i) || ~isempty(t1{i});
end;
end;
ind = find(t2);
f = f(ind);
return;
%=======================================================================
%=======================================================================
function [f,d,ii] = listvfiles(vfs,dr)
f = {};
d = {};
ii = {};
if isempty(dr),
f = {vfs.files.name};
ii = {vfs.files.ind};
d = {vfs.dirs.name};
else
if dr(1)==filesep, dr = dr(2:end); end;
ind = find(dr==filesep);
if isempty(ind),
d1 = dr;
d2 = '';
else
d1 = dr(1:(ind(1)-1));
d2 = dr((ind(1)+1):end);
end;
for i=1:length(vfs.dirs),
if strcmp(d1,vfs.dirs(i).name),
[f,d,ii] = listvfiles(vfs.dirs(i),d2);
break;
end;
end;
end;
return;
%=======================================================================
%=======================================================================
function heelp(ob,varargin)
[col1,col2,col3,fs] = colours;
fg = get(ob,'Parent');
t = uicontrol(fg,...
'style','listbox',...
'units','normalized',...
'Position',[0.01 0.01 0.98 0.98],...
'FontSize',fs,...
'FontName','FixedWidthFont',...
'BackgroundColor',col2,...
'ForegroundColor',col3,...
'Max',0,...
'Min',0,...
'tag','HelpWin',...
'String',' ');
c0 = uicontextmenu('Parent',fg);
set(t,'uicontextmenu',c0);
uimenu('Label','Done', 'Parent',c0,'Callback',@helpclear);
ext = get(t,'Extent');
pw = floor(0.98/ext(3)*20-4);
str = spm_justify(pw,{[...
'File Selection help. You can return to selecting files via the right mouse button (the "Done" option). ',...
'Because of a bug in Matlab (on some machines), don''t resize this window when viewing the help.'],...
'',[...
'The panel at the bottom shows files that are already selected. ',...
'Clicking a selected file will un-select it. To un-select several, you can ',...
'drag the cursor over the files, and they will be gone on release. ',...
'You can use the right mouse button to un-select everything.'],...
'',[...
'Directories are navigated by editing the name of the current directory (where it says "Dir"), ',...
'by going to one of the previously entered directories ("Prev"), or by navigating around ',...
'the parent or subdirectories listed in the left side panel.'],...
'',[...
'Files matching the filter ("Filt") are shown in the panel on the right. ',...
'These can be selected by clicking or dragging. Use the right mouse button if ',...
'you would like to select all files. Note that when selected, the files disappear ',...
'from this panel. They can be made to reappear by re-specifying the directory ',...
'or the filter. ',...
'Note that the syntax of the filter differs from that used by previous versions of ',...
'SPM. The following is a list of symbols with special meaning for filtering the filenames:'],...
' ^ start of string',...
' $ end of string',...
' . any character',...
' \ quote next character',...
' * match zero or more',...
' + match one or more',...
' ? match zero or one, or match minimally',...
' {} match a range of occurrances',...
' [] set of characters',...
' [^] exclude a set of characters',...
' () group subexpression',...
' \w match word [a-z_A-Z0-9]',...
' \W not a word [^a-z_A-Z0-9]',...
' \d match digit [0-9]',...
' \D not a digit [^0-9]',...
' \s match white space [ \t\r\n\f]',...
' \S not a white space [^ \t\r\n\f]',...
' \<WORD\> exact word match',...
'',[...
'Individual time frames of image files can also be selected. The frame filter ',...
'allows specified frames to be shown, which is useful for image files that ',...
'contain multiple time points. If your images are only single time point, then ',...
'reading all the image headers can be avoided by specifying a frame filter of "1". ',...
'The filter should contain a list of integers indicating the frames to be used. ',...
'This can be generated by e.g. "1:100", or "1:2:100".'],...
'',[...
'The recursive selection button (Rec) allows files matching the regular expression to ',...
'be recursively selected. If there are many directories to search, then this can take ',...
'a while to run.'],...
'',[...
'There is also an edit button (Ed), which allows you to edit your selection of files. ',...
'When you are done, then use the menu-button of your mouse to either cancel or accept your changes'],''});
pad = cellstr(char(zeros(max(0,floor(1.2/ext(4) - numel(str))),1)));
str = {str{:}, pad{:}};
set(t,'String',str);
return;
%=======================================================================
%=======================================================================
function helpclear(ob,varargin)
ob = get(ob,'Parent');
ob = get(ob,'Parent');
ob = findobj(ob,'Tag','HelpWin');
delete(ob);
%=======================================================================
%=======================================================================
function hitkey(fg,varargin)
ch = get(fg,'CurrentCharacter');
if isempty(ch), return; end;
ob = findobj(fg,'Tag','files');
if ~isempty(ob),
f = get(ob,'String');
f = f(:,1);
fset = find(f>=ch);
if ~isempty(fset),
fset = fset(1);
%cb = get(ob,'Callback');
%set(ob,'Callback',[]);
set(ob,'ListboxTop',fset);
%set(ob,'Callback',cb);
else
set(ob,'ListboxTop',length(f));
end;
end;
return;
%=======================================================================
%=======================================================================
function t = cpath(t,d)
switch spm_platform('filesys'),
case 'unx',
mch = '^/';
fs = '/';
fs1 = '/';
case 'win',
mch = '^.:\\';
fs = '\';
fs1 = '\\';
otherwise;
error('What is this filesystem?');
end
if isempty(regexp(t,mch,'once')),
if nargin<2, d = pwd; end;
t = [d fs t];
end;
% Replace occurences of '/./' by '/' (problems with e.g. /././././././')
re = [fs1 '\.' fs1];
while ~isempty(regexp(t,re)),
t = regexprep(t,re,fs);
end;
t = regexprep(t,[fs1 '\.' '$'], fs);
% Replace occurences of '/abc/../' by '/'
re = [fs1 '[^' fs1 ']+' fs1 '\.\.' fs1];
while ~isempty(regexp(t,re)),
t = regexprep(t,re,fs,'once');
end;
t = regexprep(t,[fs1 '[^' fs1 ']+' fs1 '\.\.' '$'],fs,'once');
% Replace '//'
t = regexprep(t,[fs1 '+'], fs);
%=======================================================================
%=======================================================================
function editwin(ob,varargin)
[col1,col2,col3,fs] = colours;
fg = get(ob,'Parent');
lb = findobj(fg,'Tag','selected');
str = get(lb,'String');
str = cellstr(str);
h = uicontrol(fg,'Style','Edit',...
'units','normalized',...
'String',str,...
'FontSize',16,...
'Max',2,...
'Tag','EditWindow',...
'HorizontalAlignment','Left',...
'ForegroundColor',col3,...
'BackgroundColor',col1,...
'Position',[0.01 0.01 0.98 0.98]);
c0 = uicontextmenu('Parent',fg);
set(h,'uicontextmenu',c0);
uimenu('Label','Cancel', 'Parent',c0,'Callback',@editclear);
uimenu('Label','Accept', 'Parent',c0,'Callback',@editdone);
%=======================================================================
%=======================================================================
function editdone(ob,varargin)
ob = get(ob,'Parent');
ob = sib(ob,'EditWindow');
str = get(ob,'String');
str = deblank(cellstr(strvcat(str)));
if isempty(str{1}), str = {}; end;
lim = get(sib(ob,'files'),'UserData');
if numel(str)>lim(2),
msg(ob,['Retained ' num2str(lim(2)) ' of the ' num2str(numel(str)) ' files.']);
beep;
str = str(1:lim(2));
elseif finite(lim(2)),
if lim(1)==lim(2),
msg(ob,['Specified ' num2str(numel(str)) '/' num2str(lim(2)) ' files.']);
else
msg(ob,['Selected ' num2str(numel(str)) '/' num2str(lim(1)) '-' num2str(lim(2)) ' files.']);
end;
else
if numel(str) == 1, ss = ''; else ss = 's'; end;
msg(ob,['Specified ' num2str(numel(str)) ' file' ss '.']);
end;
if ~finite(lim(1)) || numel(str)>=lim(1),
set(sib(ob,'D'),'Enable','on');
else
set(sib(ob,'D'),'Enable','off');
end;
set(sib(ob,'selected'),'String',strvcat(str),'Value',[]);
delete(ob);
%=======================================================================
%=======================================================================
function editclear(ob,varargin)
ob = get(ob,'Parent');
ob = get(ob,'Parent');
ob = findobj(ob,'Tag','EditWindow');
delete(ob);
%=======================================================================
%=======================================================================
function [c1,c2,c3,fs] = colours
global defaults
c1 = [1 1 1];
c2 = [1 1 1];
c3 = [0 0 0];
fs = 14;
if isfield(defaults,'ui'),
ui = defaults.ui;
if isfield(ui,'colour1'), c1 = ui.colour1; end;
if isfield(ui,'colour2'), c2 = ui.colour2; end;
if isfield(ui,'colour3'), c3 = ui.colour3; end;
if isfield(ui,'fs'), fs = ui.fs; end;
end;
%=======================================================================
%=======================================================================
function select_rec(ob, varargin)
sel = [];
top = get(ob,'Parent');
start = get(findobj(top,'Tag','edit'),'String');
filt = get(findobj(top,'Tag','regexp'),'Userdata');
filt.filt = {get(findobj(top,'Tag','regexp'), 'String')};
fob = findobj(top,'Tag','frame');
if ~isempty(fob)
filt.frames = get(fob,'Userdata');
else
filt.frames = [];
end;
ptr = get(top,'Pointer');
try,
set(top,'Pointer','watch');
sel = select_rec1(start,filt);
catch,
set(top,'Pointer',ptr);
sel = '';
end;
set(top,'Pointer',ptr);
already= get(findobj(top,'Tag','selected'),'String');
fb = sib(ob,'files');
lim = get(fb,'Userdata');
limsel = min(lim(2)-size(already,1),size(sel,1));
set(findobj(top,'Tag','selected'),'String',strvcat(already,sel(1:limsel,:)),'Value',[]);
msg(ob,sprintf('Added %d/%d matching files to selection.', limsel, size(sel,1)));
if ~finite(lim(1)) || size(sel,1)>=lim(1),
set(sib(ob,'D'),'Enable','on');
else
set(sib(ob,'D'),'Enable','off');
end;
%=======================================================================
%=======================================================================
function sel=select_rec1(cdir,filt)
sel='';
[t,d] = listfiles(cdir,filt);
if ~isempty(t)
sel = [repmat([cdir,filesep],size(t,1),1),t];
end;
for k = 1:size(d,1)
if ~strcmp(deblank(d(k,:)),'.') && ~strcmp(deblank(d(k,:)),'..')
sel1 = select_rec1(fullfile(cdir,deblank(d(k,:))),filt);
if ~isempty(sel1) && ~isempty(sel),
sel = strvcat(sel, sel1);
elseif ~isempty(sel1),
sel = sel1;
end;
end;
end;
%=======================================================================
%=======================================================================
function sfilt=mk_filter(typ,filt,frames)
if nargin<3, frames = '1'; end;
if nargin<2, filt = '.*'; end;
if nargin<1, typ = 'any'; end;
switch lower(typ),
case {'any','*'}, code = 0; ext = {'.*'};
case {'image'}, code = 1; ext = {'.*\.nii$','.*\.img$','.*\.NII$','.*\.IMG$'};
case {'extimage'}, code = 1; ext = {'.*\.nii(,[0-9]*){0,1}$',...
'.*\.img(,[0-9]*){0,1}$',...
'.*\.NII(,[0-9]*){0,1}$',...
'.*\.IMG(,[0-9]*){0,1}$'};
case {'xml'}, code = 0; ext = {'.*\.xml$','.*\.XML$'};
case {'mat'}, code = 0; ext = {'.*\.mat$','.*\.MAT$'};
case {'batch'}, code = 0; ext = {'.*\.mat$','.*\.MAT$','.*\.m$','.*\.M$','.*\.xml$','.*\.XML$'};
case {'dir'}, code =-1; ext = {'.*'};
case {'extdir'}, code =-1; ext = {['.*' filesep '$']};
otherwise, code = 0; ext = {typ};
end;
sfilt = struct('code',code,'frames',frames,'ext',{ext},...
'filt',{{filt}});
%=======================================================================
%=======================================================================
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