Changeset 80 for misclib


Ignore:
Timestamp:
Feb 20, 2009, 3:06:07 PM (10 years ago)
Author:
tjniskan
Message:
  • Changed the historical "an2_" prefix to "aedes_" in all files. NOTE:

Any script or function relying to Aedes functions will be broken
because of this. Just do a search/replace from "an2_" to "aedes_" in
your files and all should be well...

  • Changed the name of an2_readtab.m to a more informative

aedes_readphasetable.m

Location:
misclib
Files:
12 edited

Legend:

Unmodified
Added
Removed
  • misclib/addicon.m

    r45 r80  
    3030
    3131% Load icon cdata
    32 S=load('an2_cdata.mat');
     32S=load('aedes_cdata.mat');
    3333cdata = S.cdata;
    3434 
  • misclib/filter_fmri_data.m

    r37 r80  
    2525
    2626% Read the data
    27 data = an2_read_nifti(infile);
     27data = aedes_read_nifti(infile);
    2828if length(size(data.FTDATA))<4
    2929  error('Input data has to be 4D data!')
     
    4242
    4343% Waitbar
    44 wbh=an2_wbar(0,'Filtering image data...');
     44wbh=aedes_wbar(0,'Filtering image data...');
    4545
    4646counter=1;
     
    5252          tmp = squeeze(double(data.FTDATA(ii,kk,zz,:)));
    5353          data.FTDATA(ii,kk,zz,:) = filtfilt(B_lo,A_lo,filtfilt(B_hi,A_hi,tmp))+mean(tmp);
    54           an2_wbar(counter/nVox,wbh)
     54          aedes_wbar(counter/nVox,wbh)
    5555          counter=counter+1;
    5656        end
     
    6161
    6262% Write new 4D NIfTI  image
    63 cwh = an2_calc_wait(sprintf('Writing 4D NIfTI file:\n%s',outfile));
    64 an2_write_nifti(data,outfile);
     63cwh = aedes_calc_wait(sprintf('Writing 4D NIfTI file:\n%s',outfile));
     64aedes_write_nifti(data,outfile);
    6565delete(cwh)
    6666
  • misclib/fmri_analysis.m

    r75 r80  
    225225if all(smooth_kernel)
    226226  if show_wbar
    227     wbh = an2_calc_wait('Smoothing data...');
     227    wbh = aedes_calc_wait('Smoothing data...');
    228228    drawnow
    229229  end
     
    260260end
    261261if show_wbar
    262   wbh = an2_wbar(0,sprintf('Estimating parameters. Processing plane 0/%d',nPlanes));
     262  wbh = aedes_wbar(0,sprintf('Estimating parameters. Processing plane 0/%d',nPlanes));
    263263  drawnow
    264264end
     
    268268  for kk=1:nCols
    269269    if show_wbar
    270       an2_wbar(ii/nPlanes,wbh,sprintf('Estimating parameters. Processing plane %d/%d, column %d/%d',ii,nPlanes,kk,nCols));
     270      aedes_wbar(ii/nPlanes,wbh,sprintf('Estimating parameters. Processing plane %d/%d, column %d/%d',ii,nPlanes,kk,nCols));
    271271    end
    272272    col_data = squeeze(smooth_data(:,kk,ii,:)).';
     
    291291
    292292if show_wbar
    293   wbh = an2_calc_wait('Calculating threshold...');
     293  wbh = aedes_calc_wait('Calculating threshold...');
    294294  drawnow
    295295end
  • misclib/fmri_blob_overlay.m

    r61 r80  
    128128  ImBlob = ImBlob.FTDATA;
    129129elseif ischar(ImBlob)
    130   data = an2_data_read(ImBlob);
     130  data = aedes_data_read(ImBlob);
    131131  ImBlob = double(data.FTDATA);
    132132  clear data;
     
    137137  ImAnat = ImAnat.FTDATA;
    138138elseif ischar(ImAnat)
    139   data = an2_data_read(ImAnat);
     139  data = aedes_data_read(ImAnat);
    140140  ImAnat = data.FTDATA;
    141141  clear data;
  • misclib/fmri_corr.m

    r73 r80  
    44
    55if ischar(data)
    6   data=an2_data_read(data);
     6  data=aedes_data_read(data);
    77  data = data.FTDATA;
    88elseif isstruct(data)
  • misclib/fmri_filter.m

    r75 r80  
    4040  data = data.FTDATA;
    4141elseif ischar(data)
    42   data = an2_data_read(data);
     42  data = aedes_data_read(data);
    4343  data = data.FTDATA;
    4444end
     
    8080 
    8181  % Waitbar
    82   wbh=an2_wbar(0,'Filtering image data...');
     82  wbh=aedes_wbar(0,'Filtering image data...');
    8383 
    8484  counter=1;
     
    109109                end
    110110                filtered_data(ii,kk,zz,:) = tmp;
    111                 an2_wbar(counter/nVox,wbh)
     111                aedes_wbar(counter/nVox,wbh)
    112112                counter=counter+1;
    113113          end
     
    123123% Write output to file
    124124if ~isempty(out_file)
    125   an2_write_nifti(filtered_data,out_file);
     125  aedes_write_nifti(filtered_data,out_file);
    126126end
    127127
  • misclib/fmri_smooth.m

    r63 r80  
    1717  data = data.FTDATA;
    1818elseif ischar(data)
    19   data = an2_data_read(data);
     19  data = aedes_data_read(data);
    2020  data = data.FTDATA;
    2121end
     
    7979% Write output files
    8080if writeSmoothedData
    81   an2_write_nifti(smooth_data,out_file)
     81  aedes_write_nifti(smooth_data,out_file)
    8282end
  • misclib/fmri_spm_volumes.m

    r62 r80  
    6363
    6464% Read the fMRI data
    65 data = an2_readfid(infile,'FastRead','on');
     65data = aedes_readfid(infile,'FastRead','on');
    6666if isempty(data)
    6767  disp('FMRI_SPM_VOLUMES: Action canceled...')
     
    9898nVols = length(StartVolume:EndVolume);
    9999
    100 wbh = an2_wbar(0,['Writing volumes...']);
     100wbh = aedes_wbar(0,['Writing volumes...']);
    101101
    102102% Write output images
     
    105105  count=count+1;
    106106 
    107   an2_wbar(count/nVols,wbh,'Writing volumes...');
     107  aedes_wbar(count/nVols,wbh,'Writing volumes...');
    108108 
    109109  % Check if volume should be omitted
     
    117117  % Rotate and flip volumes VNMR EPI and RASER to right orientations
    118118  if isEPI
    119     vol = flipdim(an2_rot3d(vol,1,3),2);
     119    vol = flipdim(aedes_rot3d(vol,1,3),2);
    120120  elseif isRASER
    121121    vol = flipdim(vol,2);
     
    126126 
    127127  % Write the NIfTI file
    128   done=an2_write_nifti(vol,[outdir,fname],...
     128  done=aedes_write_nifti(vol,[outdir,fname],...
    129129    'VoxelSize',VoxelSize,...
    130130    'XYZUnits',XYZUnits,...
  • misclib/makelcmraw.m

    r45 r80  
    3333if nargin==0
    3434  %% Ask for a file
    35   [DATA,msg] = an2_readfid('','return',3);
     35  [DATA,msg] = aedes_readfid('','return',3);
    3636  if isempty(DATA)
    3737    error(msg)
  • misclib/nifti3dto4d.m

    r66 r80  
    3636if nargin==0 || isempty(infiles)
    3737  % Prompt files to read
    38   [fname,fpath,findex] = an2_juigetfiles({'*.nii','NIfTI files (*.nii)';...
     38  [fname,fpath,findex] = aedes_juigetfiles({'*.nii','NIfTI files (*.nii)';...
    3939        '*.*','All Files (*.*)'},'Select volumes',pwd);
    4040 
     
    6363
    6464% Read the first image and get header parameters
    65 tmp_data = an2_read_nifti(infiles{1});
     65tmp_data = aedes_read_nifti(infiles{1});
    6666TimeUnits = tmp_data.HDR.timeunits;
    6767xyzunits = tmp_data.HDR.xyzunits;
     
    108108
    109109if showWbar
    110   wbh=an2_wbar(1/length(infiles),...
     110  wbh=aedes_wbar(1/length(infiles),...
    111111        sprintf('Reading 3D NIfTI files...1/%d',length(infiles)));
    112112end
    113113for ii=2:length(infiles)
    114114  % Read the nifti file
    115   tmp_data = an2_read_nifti(infiles{ii});
     115  tmp_data = aedes_read_nifti(infiles{ii});
    116116  sz(1)=size(tmp_data.FTDATA,1);
    117117  sz(2)=size(tmp_data.FTDATA,2);
     
    122122  DATA.FTDATA(:,:,:,ii) = tmp_data.FTDATA;
    123123  if showWbar
    124         an2_wbar(ii/length(infiles),wbh,...
     124        aedes_wbar(ii/length(infiles),wbh,...
    125125          sprintf('Reading 3D NIfTI files...%d/%d',ii,length(infiles)))
    126126  end
     
    154154% Write the resulting 4D NIfTI file
    155155if showWbar
    156   cwh = an2_calc_wait(sprintf('Writing 4D NIfTI file:\n%s',outfile));
     156  cwh = aedes_calc_wait(sprintf('Writing 4D NIfTI file:\n%s',outfile));
    157157end
    158 an2_write_nifti(DATA,outfile,...
     158aedes_write_nifti(DATA,outfile,...
    159159  'VoxelSize',vox_size,...
    160160  'XYZUnits',xyzunits,...
  • misclib/nifti4dto3d.m

    r53 r80  
    6161
    6262% Read the 4D NIfTI file
    63 DATA = an2_read_nifti(infile);
     63DATA = aedes_read_nifti(infile);
    6464nVol = size(DATA.FTDATA,4);
    6565
     
    7171% Write new 3D NIfTI volumes
    7272if showWbar
    73   wbh=an2_wbar(1/nVol,...
     73  wbh=aedes_wbar(1/nVol,...
    7474        sprintf('Writing 3D NIfTI files...1/%d',nVol));
    7575end
     
    8282  tmp_data.FTDATA = DATA.FTDATA(:,:,:,ii);
    8383  tmp_data.HDR.FileHeader = FileHeader;
    84   done=an2_write_nifti(tmp_data,filename);
     84  done=aedes_write_nifti(tmp_data,filename);
    8585 
    8686  if ~done
     
    8989 
    9090  if showWbar
    91         an2_wbar(ii/nVol,wbh,...
     91        aedes_wbar(ii/nVol,wbh,...
    9292          sprintf('Writing 3D NIfTI files...%d/%d',ii,nVol))
    9393  end
  • misclib/spectrsum.m

    r45 r80  
    2727
    2828if nargin==0
    29   DATA = an2_readfid('','return',3);
     29  DATA = aedes_readfid('','return',3);
    3030  if isempty(DATA)
    3131    % Canceled
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