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diffs20070621.txt
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diff -rw ./scripts/batch_processor/ProcessSession.m /Volumes/cortex/matlab/npt/scripts/batch_processor/ProcessSession.m
144c144
< if ~isempty(chunkSize) && ~isspace(chunkSize)
---
> if ~isempty(chunkSize) & ~isspace(chunkSize)
153c153
< if ~isempty(groups) && ~isspace(groups)
---
> if ~isempty(groups) & ~isspace(groups)
259,262d258
< % read sorter header to get chunckSize
< hdrfilename = nptDir(['..' filesep 'sort' filesep '*.hdr'],'CaseInsensitive');
< [max_duration,min_duration, trials,waves,rawfile,fs,channels, ...
< means,thresholds,numChunks,chunkSize] = nptReadSorterHdr(hdrfilename.name);
312c308
< if (smtrials~=0) && (smtrials~=trials)
---
> if (smtrials~=0) & (smtrials~=trials)
610c606
< if single_flag && ~highpassflag && strcmp(dtype,'Streamer')
---
> if single_flag & ~highpassflag & strcmp(dtype,'Streamer')
634c630
< if (~extracthighpass) && (~highpassflag)
---
> if (~extracthighpass) & (~highpassflag)
741c737
< if single_flag && ( strcmp(dtype,'Streamer') || strcmp(dtype,'UEI') )
---
> if single_flag & strcmp(dtype,'Streamer')
751c747
< elseif (~isempty(broadband) || extracthighpass==1)
---
> elseif (~isempty(broadband) | extracthighpass==1)
785c781
< elseif isempty(wavelist) && isdir('sort')
---
> elseif isempty(wavelist) & isdir('sort')
795c791
< if(sort && ~strcmp(sort_algo,'none'))
---
> if(sort & ~strcmp(sort_algo,'none'))
diff -rw ./scripts/batch_processor/ProcessSession.m~ /Volumes/cortex/matlab/npt/scripts/batch_processor/ProcessSession.m~
144c144
< if ~isempty(chunkSize) && ~isspace(chunkSize)
---
> if ~isempty(chunkSize) & ~isspace(chunkSize)
153c153
< if ~isempty(groups) && ~isspace(groups)
---
> if ~isempty(groups) & ~isspace(groups)
259,262d258
< % read sorter header to get chunckSize
< hdrfilename = nptDir(['..' filesep 'sort' filesep '*.hdr'],'CaseInsensitive');
< [max_duration,min_duration, trials,waves,rawfile,fs,channels, ...
< means,thresholds,numChunks,chunkSize] = nptReadSorterHdr(hdrfilename.name);
312c308
< if (smtrials~=0) && (smtrials~=trials)
---
> if (smtrials~=0) & (smtrials~=trials)
382c378,379
< % just put the data in unit since presumably we have checked the
---
> % just put the data in unit since presumably we have
> % checked the
610c607
< if single_flag && ~highpassflag && strcmp(dtype,'Streamer')
---
> if single_flag & ~highpassflag & strcmp(dtype,'Streamer')
634c631
< if (~extracthighpass) && (~highpassflag)
---
> if (~extracthighpass) & (~highpassflag)
741c738
< if single_flag && ( strcmp(dtype,'Streamer') || strcmp(dtype,'UEI') )
---
> if single_flag & strcmp(dtype,'Streamer')
751c748
< elseif (~isempty(broadband) || extracthighpass==1)
---
> elseif (~isempty(broadband) | extracthighpass==1)
785c782
< elseif isempty(wavelist) && isdir('sort')
---
> elseif isempty(wavelist) & isdir('sort')
795c792
< if(sort && ~strcmp(sort_algo,'none'))
---
> if(sort & ~strcmp(sort_algo,'none'))
diff -rw ./scripts/miscellaneous/checkObjCreate.m /Volumes/cortex/matlab/npt/scripts/miscellaneous/checkObjCreate.m
1c1
< function n = checkObjCreate(objArgs,numArgs,varargin)
---
> function n = checkObjCreate(varargin)
4c4
< Args = struct('firstVarargin','');
---
> Args = struct('ArgsC','','narginC','','firstVarargin','');
8c8
< if (objArgs.ArgsOnly)
---
> if (getfield(Args.ArgsC,'ArgsOnly'))
13c13
< if(numArgs==0)
---
> if(Args.narginC==0)
16c16
< elseif( (numArgs==1) && isa(Args.firstVarargin{1},objArgs.classname) )
---
> elseif( (Args.narginC==1) & isa(Args.firstVarargin{1},getfield(Args.ArgsC,'classname')))
20,26c20,28
< if(objArgs.Auto)
< if( (ispresent(objArgs.matname,'file','CaseInsensitive')) ...
< && (objArgs.RedoLevels==0) )
< fprintf('Loading saved %s object...\n',objArgs.classname);
< l = load(objArgs.matname);
< robj = eval(['l.' objArgs.matvarname]);
< fprintf('\tComparing saved %s object arguments with new arguments specified...\n',Args.classname);
---
> if(getfield(Args.ArgsC,'Auto'))
> % check for saved object
> %[pdir,cdir] = getDataOrder('session','relative','CDNow');
> if(ispresent(getfield(Args.ArgsC,'matname'),'file','CaseInsensitive') ...
> & (getfield(Args.ArgsC,'RedoLevels')==0))
> fprintf('Loading saved %s object...\n',getfield(Args.ArgsC,'classname'));
> l = load(getfield(Args.ArgsC,'matname'));
> robj = eval(['l.' getfield(Args.ArgsC,'matvarname')]);
> fprintf('\tComparing saved %s object arguments with new arguments specified...\n',getfield(Args.ArgsC,'classname'));
28c30
< sameFlag = checkArguments(objArgs,robj.data.Args);
---
> sameFlag = checkArguments(Args.ArgsC,robj.data.Args);
30c32
< fprintf('\tSaved %s object has same requested arguments...\n',objArgs.classname);
---
> fprintf('\tSaved %s object has same requested arguments...\n',getfield(Args.ArgsC,'classname'));
33c35
< fprintf('\tDifferent requested arguments, creating new %s object...\n',objArgs.classname);
---
> fprintf('\tDifferent requested arguments, creating new %s object...\n',getfield(Args.ArgsC,'classname'));
diff -rw ./scripts/miscellaneous/getDataOrder.m /Volumes/cortex/matlab/npt/scripts/miscellaneous/getDataOrder.m
91a92,93
> end
> cd(cwd)
107,108d108
< cd(cwd)
< end
Only in /Volumes/cortex/matlab/npt/scripts/miscellaneous: getReturnVal.m
Only in ./scripts/miscellaneous: separateAxis.m~
Binary files ./scripts/view/.DS_Store and /Volumes/cortex/matlab/npt/scripts/view/.DS_Store differ
diff -rw ./scripts/view/@dirfiles/dirfiles.m /Volumes/cortex/matlab/npt/scripts/view/@dirfiles/dirfiles.m
32,34c32
< % change to proper directory to check for saved object
< [pdir,cdir] = getDataOrder('cluster','relative','CDNow');
< command = checkObjCreate(Args,nargin,varargin);
---
> command = checkObjCreate('ArgsC',Args,'narginC',nargin,'firstVarargin',varargin);
53,55d50
< % return to previous directory
< cd(cdir);
<
81c76
< saveObject(obj,Args);
---
> saveObject(obj,'ArgsC',Args);
diff -rw ./scripts/view/@dirfiles/plot.m /Volumes/cortex/matlab/npt/scripts/view/@dirfiles/plot.m
12a13
> Args = rmfield (Args, 'ArgsOnly');
36,44c37,39
< rvarl = length(Args.ReturnVars);
< if(rvarl>0)
< % assign requested variables to varargout
< for rvi = 1:rvarl
< rvidx = rvi * 2;
< varargout{1}{rvidx-1} = Args.ReturnVars{rvi};
< varargout{1}{rvidx} = eval(Args.ReturnVars{rvi});
< end
< end
---
> RR = eval('Args.ReturnVars');
> for i=1:length(RR) RR1{i}=eval(RR{i}); end
> varargout = getReturnVal(Args.ReturnVars, RR1);
Binary files ./scripts/view/@ispikes/.DS_Store and /Volumes/cortex/matlab/npt/scripts/view/@ispikes/.DS_Store differ
diff -rw ./scripts/view/@ispikes/plot.m /Volumes/cortex/matlab/npt/scripts/view/@ispikes/plot.m
27c27
< chunkSize = vi.data.chunkSize * 1000;
---
> chunkSize = vi.data.chunkSize;
29c29
< chunkSize = Args.chunkSize * 1000;
---
> chunkSize = Args.chunkSize;
57c57
< line([chunkSize*(n-1) chunkSize*n],[lineY lineY],'Color',Args.Color);
---
> line([chunkSize*1000*(n-1) chunkSize*1000*n],[lineY lineY],'Color',Args.Color);
61c61
< [y,ind] = find(spiketime>chunkSize*(n-1) & spiketime<chunkSize*n);
---
> [y,ind] = find(spiketime>chunkSize*1000*(n-1) & spiketime<chunkSize*1000*n);
67c67
< xlim([chunkSize*(n-1) chunkSize*n])
---
> xlim([chunkSize*1000*(n-1) chunkSize*1000*n])
139c139
< line([chunkSize*(n-1) chunkSize*n],[lineY lineY],'Color',Args.Color);
---
> line([chunkSize*1000*(n-1) chunkSize*1000*n],[lineY lineY],'Color',Args.Color);
143c143
< [y,ind]=find(spiketime>chunkSize*(n-1) & spiketime<chunkSize*n);
---
> [y,ind]=find(spiketime>chunkSize*1000*(n-1) & spiketime<chunkSize*1000*n);
diff -rw ./scripts/view/@nptdata/saveObject.m /Volumes/cortex/matlab/npt/scripts/view/@nptdata/saveObject.m
1c1
< function n = saveObject(obj,Args)
---
> function n = saveObject(obj,varargin)
2a3,5
> % Args = struct('SaveLevelsC','','classnameC','','matnameC','','matvarnameC','');
> Args = struct('ArgsC','');
> [Args,varargin] = getOptArgs(varargin,Args);
4,10c7,11
< if(Args.SaveLevels)
< fprintf('Saving %s object...\n',Args.classname);
< % check to make sure the Args structure is a field in Args
< if(~ismember(obj.data,'Args'))
< obj.data.Args = Args;
< end
< eval([Args.matvarname ' = obj;']);
---
> robj = obj;
> n = 0;
> if(getfield(Args.ArgsC,'SaveLevels'))
> fprintf('Saving %s object...\n',getfield(Args.ArgsC,'classname'));
> eval([getfield(Args.ArgsC,'matvarname') ' = robj;']);
12c13,14
< eval(['save ' Args.matname ' ' Args.matvarname]);
---
> eval(['save ' getfield(Args.ArgsC,'matname') ' ' getfield(Args.ArgsC,'matvarname')]);
> n = 1;
diff -rw ./scripts/view/@nptgroup/nptgroup.m /Volumes/cortex/matlab/npt/scripts/view/@nptgroup/nptgroup.m
139c139
< ndg = ProcessLevel(nptdata,'Levels','Group',varargin{:});
---
> ndg = ProcessLevel(nptdata,varargin{:});
diff -rw ./scripts/view/@nptgroup/plot.m /Volumes/cortex/matlab/npt/scripts/view/@nptgroup/plot.m
86,87c86
< h=zeros(numDirs,1);
< delete(gca); %bug in R2006b with subplot requires this.
---
> h=[];
93,94c92,93
< h(i) = subplot('Position',axesPositions(i,:));
< % h = [h hc];
---
> hc = subplot('Position',axesPositions(i,:));
> h = [h hc];
102c101
< plot(thisObj,cellN,plotOptions{:},'GroupPlots',numDirs, ...
---
> thisObj = plot(thisObj,cellN,plotOptions{:},'GroupPlots',numDirs, ...
107,109c106,108
< % if(strcmp(version('-release'),'14'))
< % set(hc,'Position',axesPositions(i,:));
< % end
---
> if(strcmp(version('-release'),'14'))
> set(hc,'Position',axesPositions(i,:));
> end
113,116c112,114
< % if exist('outputs','var')
< % varargout{1} = {outputs{:},'handle',h};
< % end
<
---
> if exist('outputs','var')
> varargout{1} = {outputs{:},'handle',h};
> end
131,133d128
< rvidx = (rvi + 1) * 2;
< varargout{1}{rvidx-1} = 'handle';
< varargout{1}{rvidx} = h;
Only in ./scripts/view/@nptgroup: plot.m~
diff -rw ./scripts/view/gui/InspectFn.m /Volumes/cortex/matlab/npt/scripts/view/gui/InspectFn.m
42,45c42,43
< s.obj{ii} = plot(s.obj{ii}, s.optArgs{ii}{:});
< outputs = '';
< display(['Please add the argument ''ReturnVars'' to the ' ...
< 'respective plot function. Refer to @dirfiles/PLOT.']);
---
> display(['Error: please add the argument ''ReturnVars'' to the ' ...
> 'respective plot function! Refer to @dirfiles/PLOT.']);
53,56c51,52
< s.obj{ii} = plot(s.obj{ii},n,s.optArgs{ii}{:});
< outputs = '';
< display(['Please add the argument ''ReturnVars'' to the ' ...
< 'respective plot function. Refer to @dirfiles/PLOT.']);
---
> display(['Error: please add the argument ''ReturnVars'' to the ' ...
> 'respective plot function! Refer to @dirfiles/PLOT.']);
82c78
< if isfield(s.Arg(ii).Args,'LinkedZoom') && s.Arg(ii).Args.LinkedZoom==1
---
> if isfield(s.Arg(ii).Args,'LinkedZoom') & s.Arg(ii).Args.LinkedZoom==1
84c80
< % axes(h(1))
---
> axes(h(1))
89,100c85,87
< % linkedzoom(h,'onx')
< linkaxes(h,'x');
< elseif s.LinkedZoom
< % && length(findobj(h0,'Type','axes'))>1
< % % linkedzoom(h0,'onx')
< % linkaxes(h0,'x')
< h0axes = findobj(h0,'Type','axes');
< if(length(h0axes)>1)
< linkaxes(circshift(h0axes,1),'x');
< else
< zoom xon
< end
---
> LinkedZoom(h,'onx')
> elseif s.LinkedZoom & length(findobj(h0,'Type','axes'))>1
> LinkedZoom(h0,'onx')
114,116d100
< removefields = {'NumericArguments','GroupPlots', 'GroupPlotIndex', ...
< 'ReturnVars', 'ArgsOnly'};
< rmfnum = size(removefields,2);
118,128c102,104
< tmpstruct = s.Arg(ii).Args;
< if(isstruct(tmpstruct))
< for i = 1:rmfnum
< rmf = removefields{1};
< % check which arguments are present
< if(isfield(tmpstruct,rmf))
< % remove arguments that are present
< s.Arg(ii).Args = rmfield(tmpstruct,rmf);
< end
< end
< end
---
> s.Arg(ii).Args = rmfield(s.Arg(ii).Args, {'NumericArguments', ...
> 'GroupPlots', 'GroupPlotIndex', ...
> 'ReturnVars', 'ArgsOnly'});
Only in ./scripts/view/gui: InspectFn.m~
diff -rw ./scripts/view/gui/ObjectCB.m /Volumes/cortex/matlab/npt/scripts/view/gui/ObjectCB.m
61d60
< conArgs = {'Args',''};
237c236
< 'FontUnits','normalized', 'FontSize',.8, 'FontWeight','bold', ...
---
> 'FontUnits','normalized', 'FontSize',.9, 'FontWeight','bold', ...
266c265
< 'FontUnits','normalized', 'FontSize',.8, ...
---
> 'FontUnits','normalized', 'FontSize',.6, ...
335c334
< 'FontUnits','normalized', 'FontSize',.8, 'FontWeight','bold', ...
---
> 'FontUnits','normalized', 'FontSize',.9, 'FontWeight','bold', ...
473c472
< 'FontUnits','normalized', 'FontSize',.8, 'FontWeight','bold', ...
---
> 'FontUnits','normalized', 'FontSize',.9, 'FontWeight','bold', ...
Binary files ./scripts/view/gui/PlotOptions.fig and /Volumes/cortex/matlab/npt/scripts/view/gui/PlotOptions.fig differ
diff -rw ./scripts/view/gui/PlotOptions.m /Volumes/cortex/matlab/npt/scripts/view/gui/PlotOptions.m
25c25
< % Last Modified by GUIDE v2.5 08-Jun-2007 14:51:14
---
> % Last Modified by GUIDE v2.5 02-Jun-2006 17:52:39
30c30
< gui_Singleton = 1;
---
> gui_Singleton = 0;
78,81d77
< if(isempty(pud.Arg(ii).Args))
< flagsCollect{ii} = {};
< numOptions = 0;
< else
90d85
< end
131c126
< 'FontUnits','normalized','FontSize',.8, ...
---
> 'FontUnits','normalized','FontSize',.9, ...
156c151
< 'FontUnits','normalized','FontSize',.8, ...
---
> 'FontUnits','normalized','FontSize',.9, ...
diff -rw ./scripts/view/gui/old/PlotOptions.m /Volumes/cortex/matlab/npt/scripts/view/gui/old/PlotOptions.m
49,51c49,50
< numObjects = size(pud.obj,2);
< vert=1;
< % vert = 46;
---
> numObjects = size(pud.obj,2)
> vert=1
56d54
< % vert = vert - 2;
77,80d74
< % hf = uicontrol('Parent',gcf,'Units','normalized','Position',[.05 vert .9 .02], ...
< % 'FontUnits','normalized','FontSize',.15, ...
< % 'FontWeight','bold', ...
< % 'String',optionNames(jj),'Style','checkbox','Value',value);
82c76
< 'FontUnits','normalized', ...
---
> 'FontUnits','normalized','FontSize',.15, ...
90,97d83
< % ho = uicontrol('Parent',gcf,'Units','normalized','Position',[.05 vert .5 .02], ...
< % 'FontUnits','normalized','FontSize',.15, ...
< % 'FontWeight','bold', ...
< % 'String',optionNames(jj),'Style','text');
< % hv = uicontrol('Parent', gcf,'Units','normalized','Position',[.6 vert .4 .02], ...
< % 'FontUnits','normalized','FontSize',.15, ...
< % 'FontWeight','bold', ...
< % 'String',value,'Style','edit');
99c85
< 'FontUnits','normalized', ...
---
> 'FontUnits','normalized','FontSize',.15, ...
103c89
< 'FontUnits','normalized', ...
---
> 'FontUnits','normalized','FontSize',.15, ...
Only in ./scripts/view/gui/old: PlotOptions.m~
diff -rw ./scripts/view/gui/optionsGUI.m /Volumes/cortex/matlab/npt/scripts/view/gui/optionsGUI.m
33,35d32
< if(isempty(hArgs))
< numOptions = 0;
< else
38d34
< end
56c52
< 'FontUnits','normalized', 'FontSize',.8, ...
---
> 'FontUnits','normalized', 'FontSize',.9, ...
76c72
< 'FontUnits','normalized', 'FontSize',.8, ...
---
> 'FontUnits','normalized', 'FontSize',.9, ...
Only in ./scripts/view/gui: optionsGUI.m~
diff -rw ./scripts/view/gui/updatebutton_Callback.m /Volumes/cortex/matlab/npt/scripts/view/gui/updatebutton_Callback.m
32d31
< h_Obj = {};
Removed code to add numChunks and chunkSize to header files for polytrode data since it will be
easier to inspect the spike trains in trial-based mode. The data are combined back into one long
trial in adjspikes.