Cleanup some old and redundant functions

git-svn-id: https://svn.code.sf.net/p/dct/code/trunk@792 4c865b51-4357-4376-afb4-474e03ccb993

1_preprocessing/gtApplyDrifts_xxx.m

-function gtApplyDrifts(first, last, copymode, dirpath, scanname, parameterfile)
-
-% FUNCTION gtApplyDrifts(first, last, copymode, dirpath, scanname, parameterfile)
-%
-% Shifts edf images in the 'dirpath' with a value given in the parameterfile corresponding to the edf number.  folder OverwritesCopies, corrects and undistorts full images online.
-%
-% INPUT
-%   copymode       = 'online' or 'parallel' 
-%   dirpath        = full path of the folder containing edf-s
-%   scanname       = name of scan
-%   parameterfile  = full path and name of the parameterfile (drifts has to be stored as
-%                     parameters.prep.ydrifts, parameters.prep.zdrifts)
-%
-
-
-%% Extract parameters
-
-if ~exist(dirpath,'dir')
-  gtError('Cannot find directory!')
-end
-
-if ~exist(parameterfile,'file')
-  gtError('Cannot find parameterfile!')
-end
-
-if isdeployed
-  global GT_DB
-  global GT_MATLAB_HOME
-  load('workspaceGlobal.mat');
-  first=str2num(first);
-  last=str2num(last);
-end
-  
-disp(' ')
-disp('Shifting and overwriting images with the following filenames...')
-disp('    - ref*.edf')
-disp(sprintf('    - %s*.edf',scanname))
-disp(' shifted = true/false field is added to edf header')
-disp(' /dark images are not modified/')
-disp(' ')
-
-%% Copymode online
-if strcmpi(copymode,'online')
-
-  disp('Online version is not yet implemented...')
-  return
-
-%   % read drifts from parameterfile first (or get in from a function), 
-%   % by that time those files must exist, so just overwrite them
-%   check if pfWaitToRead(fname) is ever needed
-
-%   filesdone=[];
-%   counter=0;
-%   
-%   while counter<250
-%     sfiles=dir([dirname '/*']);
-%     n=1;
-%     while n<=length(sfiles)
-%       sfname=sfiles(n).name;
-%       if strcmp('.',sfname(1)) || ~strcmp('.edf',sfname(end-3:end))
-%         sfiles(n)=[];
-%       else
-%         n=n+1;
-%       end
-%     end
-% 
-%
-%     if found==1
-%       counter=0;
-%     else
-%       counter=counter+1;
-%       disp('Sleeping')
-%       pause(5)
-%     end
-
-  
-%% Copymode parallel - do all from first to last
-elseif strcmpi(copymode,'parallel')
-  load(parameterfile)
-  yshift=parameters.prep.ydrift; % !! im0000 -> yshift(0001) , etc.
-  zshift=parameters.prep.zdrift; % !! im0000 -> zshift(0001) , etc.
-
-  if isempty(yshift)
-    gtError('parameters.prep.ydrift is empty, check parameter file!')
-  end
-  
-  if isempty(zshift)
-    gtError('parameters.prep.zdrift is empty, check parameter file!')
-  end
-  
-  % Images
-  ims=dir([dirpath '/' scanname '*.edf']);
-  for i=first:last
-    fname=[dirpath '/' ims(i).name];
-    disp(sprintf('Shifting %s',fname))
-    fnum=ims(i).name;
-    fnum=str2num(fnum(end-7:end-4));
-    if length(yshift)>=fnum+1
-      sfOverwrite(fname,yshift(fnum+1),zshift(fnum+1)); % !! im0000 -> yshift(0001) , etc.
-    else
-      %disp(sprintf('File: %s',fname))
-      gtError('No drift(s) are specified for this image.')
-    end
-
-    % Refs with the same number if exists
-    refs=dir(sprintf('%s/ref*%0.4d.edf',dirpath,fnum));
-    if ~isempty(refs)
-      for j=1:length(refs)
-        fname=[dirpath '/' refs(j).name];
-        disp(sprintf('Shifting %s',fname))
-        sfOverwrite(fname,yshift(fnum+1),zshift(fnum+1)); % !! im0000 -> yshift(0001) , etc.
-      end
-    end
-    
-  end
-  
-else
-  disp('Copymode must be either "online" or "parallel".')
-  gtError('Copymode is not recognized!')
-end % copymode
-
-end % of function
-
-
-%% Sub-functions
-
-function sfOverwrite(fname, yshift, zshift)
-
-  im=edf_read(fname); % pfWaitToRead(fname);
-  info=edf_info(fname);
-  
-  %if isfield(info,'istranslated')
-    %yshift=yshift-info.yshift;
-    %zshift=zshift-info.zshift;
-  %end
-  %info.yshift=info.yshift+yshift;
-  %info.zshift=info.zshift+zshift;
-
-  info.istranslated=true;
-  
-  im=gtShift(im,yshift,zshift);  % gtShift(im,x(horizontal_right),y(vertical_downwards))
-  
-  edf_write(im,fname,info);
-
-end

3_pairmatching/gtGetDifImage_old.m

-function im=gtGetDifImage(ndx,struct_id)
-%returns the full image requested, cropped to the specified difspot bounding box
-
-global difspot
-
-if isempty(difspot)
-  disp('Loading difspot file')
-  load('2_difspot/difspot.mat');
-end
-
-im = edf_read(sprintf('1_preprocessed/full/full%04d.edf',ndx),difspot(struct_id).BoundingBox);

3_pairmatching/gtGetDifImage_test.m

-function im=gtGetDifImage(ndx,struct_id)
-%returns the full image requested, cropped to the specified difspot bounding box
-
-%global difspot
-gtDBconnect
-
-% if isempty(difspot)
- % disp('Loading difspot file')
- % load('2_difspot/difspot.mat');
-% end
-
-% im = edf_read(sprintf('1_preprocessed/full/full%04d.edf',ndx),difspot(struct_id).BoundingBox);
-im=mysqlcmd(sprintf('1_preprocessed/full/full%04d.edf',ndx),'select BoundingBoxXorigin, BoundingBoxYorigin, BoundingBoxXsize, BoundingBoxYsize from %sdifspot where difspotID=%d',parameters.acq.name, struct_id)
\ No newline at end of file

3_pairmatching/old_gtGetSummedDifSpot_360.m

-function spot=gtGetSummedDifSpot_360(pair_id)
-%returns the summed difspot image (saved as difspot%05d.edf)
-%for 360 datasets, given a pair ID it returns the A difspot, if one exists,
-%else the B difspot
-
-parameters=[];
-if isempty(parameters)
-  disp('Loading parameter file')
-  load('parameters.mat');
-end
-acq=parameters.acq;
-
-%get the root of the pair name
-pair_name=parameters.acq.pair_tablename;
-pair_name(end-8:end)=[];
-
-%is there an A difspot in the pair table?
-  mysqlcmd = sprintf(['select !isnull(difAID), ifnull(difAID,difBID) from %s where pairID=%d'],...
-    acq.pair_tablename,pair_id);
-[A,difID]=mym(mysqlcmd);
-
-if A %if the first half of the scan
-  name=parameters.acq.difA_name;
-  disp('reading difspot from A')
-else
-  name=parameters.acq.difB_name;
-  disp('reading difspot from B')
-end
-path=sprintf('../%s/',name);
-
-
-spot=edf_read(sprintf('%s2_difspot/difspot/difspot%05d.edf',path,difID));
-
-
-
-end

zUtil_Imaging/gtShift_xxx.m

-function im=gtShift(imorig,x,y)
-
-xpad=zeros(size(imorig,1),abs(x));
-ypad=zeros(abs(y),size(imorig,2));
-
-if x>0
- 
-  tmp=[xpad imorig];
-  im=tmp(:,1:size(imorig,2));
-else
-  tmp=[imorig xpad];
-  im=tmp(:,abs(x)+1:end);
-
-end
-
-if y>0
-  tmp=[ypad;im];
-  im=tmp(1:size(imorig,1),:);
-else
-  tmp=[im;ypad];
-  im=tmp(abs(y)+1:end,:);
-end
-
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