Fix 'normsetting' being overwritten in cluster or exported job.

Close #118. Also includes a bunch of other fixes and optimizations.
netstim · Aug 17, 2017 · 4f87288 · 4f87288
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commit 4f87288
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diff --git a/cluster/ea_run_HMS_Orchestra.m b/cluster/ea_run_HMS_Orchestra.m
@@ -4,10 +4,15 @@ function ea_run_HMS_Orchestra(options)
 % to be adapted to suit your needs. Then, you can "Export code" using
 % Lead-DBS and simply change the command ea_run to ea_run_cluster.
 
+jobFile = [options.root, options.patientname, filesep, 'job_', ea_generate_guid];
+save(jobFile, 'options');
+
+setenv('ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS', '1');
+
+cmdstring=['cd ', options.earoot, ' &&' ...
+           ' bsub -q short -W 12:0 -R "rusage[mem=50000]" -R "select[scratch2]"' ...
+           ' -o ', jobFile, '.out' ...
+           ' -e ', jobFile, '.err' ...
+           ' matlab -singleCompThread -nodisplay -r "ea_run runcluster ', jobFile, '"'];
 
-jobID=ea_generate_guid;
-options.spmdir=spm('dir');
-save([options.root,options.patientname,filesep,'job_',jobID],'options')
-setenv('ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS','1')
-cmdstring=['cd ',options.earoot,' && bsub -q short -W 12:0 -R "rusage[mem=50000]" -R "select[scratch2]" -o ',[options.root,options.patientname,filesep,'job_',jobID],'.out -e ',[options.root,options.patientname,filesep,'job_',jobID],'.err matlab -singleCompThread -nodisplay -r "ea_run runcluster ',[options.root,options.patientname,filesep,'job_',jobID],'"'];
 system(cmdstring);
diff --git a/cluster/ea_run_HMS_Orchestra_long.m b/cluster/ea_run_HMS_Orchestra_long.m
@@ -4,10 +4,15 @@ function ea_run_HMS_Orchestra_long(options)
 % to be adapted to suit your needs. Then, you can "Export code" using
 % Lead-DBS and simply change the command ea_run to ea_run_cluster.
 
+jobFile = [options.root, options.patientname, filesep, 'job_', ea_generate_guid];
+save(jobFile, 'options');
+
+setenv('ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS', '1');
+
+cmdstring=['cd ',options.earoot,' &&' ...
+           ' bsub -q long -R "rusage[mem=50000]" -R "select[scratch2]" -W 168:0' ...
+           ' -o ', jobFile, '.out' ...
+           ' -e ', jobFile, '.err' ...
+           ' matlab -singleCompThread -nodisplay -r "ea_run runcluster ', jobFile, '"'];
 
-jobID=ea_generate_guid;
-options.spmdir=spm('dir');
-save([options.root,options.patientname,filesep,'job_',jobID],'options')
-setenv('ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS','1')
-cmdstring=['cd ',options.earoot,' && bsub -q long -R "rusage[mem=50000]" -R "select[scratch2]" -W 168:0 -o ',[options.root,options.patientname,filesep,'job_',jobID],'.out -e ',[options.root,options.patientname,filesep,'job_',jobID],'.err matlab -singleCompThread -nodisplay -r "ea_run runcluster ',[options.root,options.patientname,filesep,'job_',jobID],'"'];
 system(cmdstring);
diff --git a/cluster/ea_run_HMS_Orchestra_max.m b/cluster/ea_run_HMS_Orchestra_max.m
@@ -4,10 +4,15 @@ function ea_run_HMS_Orchestra_max(options)
 % to be adapted to suit your needs. Then, you can "Export code" using
 % Lead-DBS and simply change the command ea_run to ea_run_cluster.
 
+jobFile = [options.root, options.patientname, filesep, 'job_', ea_generate_guid];
+save(jobFile, 'options');
+
+setenv('ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS', '1');
+
+cmdstring=['cd ', options.earoot, ' &&' ...
+           ' bsub -q long -R "rusage[mem=20000]" -R "select[scratch2]" -W 720:0' ...
+           ' -o ', jobFile, '.out' ...
+           ' -e ', jobFile, '.err' ...
+           ' matlab -singleCompThread -nodisplay -r "ea_run runcluster ', jobFile, '"'];
 
-jobID=ea_generate_guid;
-options.spmdir=spm('dir');
-save([options.root,options.patientname,filesep,'job_',jobID],'options')
-setenv('ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS','1')
-cmdstring=['cd ',options.earoot,' && bsub -q long -R "rusage[mem=20000]" -R "select[scratch2]" -W 720:0 -o ',[options.root,options.patientname,filesep,'job_',jobID],'.out -e ',[options.root,options.patientname,filesep,'job_',jobID],'.err matlab -singleCompThread -nodisplay -r "ea_run runcluster ',[options.root,options.patientname,filesep,'job_',jobID],'"'];
 system(cmdstring);
diff --git a/cluster/ea_run_HMS_Orchestra_medium.m b/cluster/ea_run_HMS_Orchestra_medium.m
@@ -4,10 +4,15 @@ function ea_run_HMS_Orchestra_medium(options)
 % to be adapted to suit your needs. Then, you can "Export code" using
 % Lead-DBS and simply change the command ea_run to ea_run_cluster.
 
+jobFile = [options.root, options.patientname, filesep, 'job_', ea_generate_guid];
+save(jobFile, 'options');
+
+setenv('ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS', '1');
+
+cmdstring=['cd ', options.earoot, ' &&' ...
+           ' bsub -q medium -R "rusage[mem=70000]" -R "select[scratch2]" -W 119:0' ...
+           ' -o ', jobFile,'.out' ...
+           ' -e ', jobFile,'.err' ...
+           ' matlab -singleCompThread -nodisplay -r "ea_run runcluster ', jobFile, '"'];
 
-jobID=ea_generate_guid;
-options.spmdir=spm('dir');
-save([options.root,options.patientname,filesep,'job_',jobID],'options')
-setenv('ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS','1')
-cmdstring=['cd ',options.earoot,' && bsub -q medium -R "rusage[mem=70000]" -R "select[scratch2]" -W 119:0 -o ',[options.root,options.patientname,filesep,'job_',jobID],'.out -e ',[options.root,options.patientname,filesep,'job_',jobID],'.err matlab -singleCompThread -nodisplay -r "ea_run runcluster ',[options.root,options.patientname,filesep,'job_',jobID],'"'];
 system(cmdstring);
diff --git a/cluster/ea_run_Martinos_Launchpad.m b/cluster/ea_run_Martinos_Launchpad.m
@@ -4,11 +4,15 @@ function ea_run_Martinos_Launchpad(options)
 % to be adapted to suit your needs. Then, you can "Export code" using
 % Lead-DBS and simply change the command ea_run to ea_run_cluster.
 
+jobFile = [options.root, options.patientname, filesep, 'job_', ea_generate_guid];
+save(jobFile, 'options');
 
-jobID=ea_generate_guid;
-options.spmdir=spm('dir');
-save([options.root,options.patientname,filesep,'job_',jobID],'options')
-setenv('ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS','1')
-cmdstring=['cd ',options.earoot,' && pbsubmit -q matlab -O ',[options.root,options.patientname,filesep,'job_',jobID],'.out -E ',[options.root,options.patientname,filesep,'job_',jobID],'.err -c "matlab.new -singleCompThread -nodisplay -r "''ea_run runcluster ',[options.root,options.patientname,filesep,'job_',jobID],'''"'];
+setenv('ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS', '1');
+
+cmdstring=['cd ', options.earoot, ' &&' ...
+           ' pbsubmit -q matlab' ...
+           ' -O ', jobFile, '.out' ...
+           ' -E ', jobFile, '.err' ...
+           ' -c "matlab.new -singleCompThread -nodisplay -r "''ea_run runcluster ', jobFile, '''"'];
 
 system(cmdstring);
diff --git a/cluster/ea_run_Martinos_Launchpad_compile.m b/cluster/ea_run_Martinos_Launchpad_compile.m
@@ -4,22 +4,24 @@ function ea_run_Martinos_Launchpad_compile(options)
 % to be adapted to suit your needs. Then, you can "Export code" using
 % Lead-DBS and simply change the command ea_run to ea_run_cluster.
 
+jobFile = [options.root, options.patientname, filesep, 'job_', ea_generate_guid];
+save(jobFile, 'options');
 
-jobID=ea_generate_guid;
-options.spmdir=spm('dir');
-save([options.root,options.patientname,filesep,'job_',jobID],'options')
-setenv('ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS','1')
+setenv('ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS', '1');
 
-cmdstring=['cd ',options.earoot,' && pbsubmit -q highio -O ',[options.root,options.patientname,filesep,'job_',jobID],'.out',...
-    ' -E ',[options.root,options.patientname,filesep,'job_',jobID],'.err',...
-    ' -c "',[ea_getearoot,'cluster',filesep,'run_ea_run_binary.sh'],...
-    ' ','/usr/pubsw/common/matlab/8.6',...
-    ' runcluster ''',ea_path_helper([options.root,options.patientname,filesep,'job_',jobID]),'''"'];
+cmdstring=['cd ', options.earoot, ' &&' ...
+           ' pbsubmit -q highio' ...
+           ' -O ',jobFile,'.out', ...
+           ' -E ', jobFile, '.err', ...
+           ' -c "', [ea_getearoot, 'cluster', filesep, 'run_ea_run_binary.sh'], ...
+           ' /usr/pubsw/common/matlab/8.6',...
+           ' runcluster ''', ea_path_helper(jobFile), '''"'];
 
-if ~exist([ea_getearoot,'cluster',filesep,'ea_run_binary'],'file');
-mcc('-m','ea_run','-o',['ea_run_binary']);
-movefile('ea_run_binary',['cluster',filesep,'ea_run_binary']);
-movefile('run_ea_run_binary.sh',['cluster',filesep,'run_ea_run_binary.sh']);
+if ~exist([ea_getearoot, 'cluster', filesep, 'ea_run_binary'],'file')
+    mcc('-m', 'ea_run', '-o', 'ea_run_binary');
+    movefile('ea_run_binary', ['cluster', filesep, 'ea_run_binary']);
+    movefile('run_ea_run_binary.sh', ['cluster', filesep, 'run_ea_run_binary.sh']);
 end
+
 keyboard
 system(cmdstring);
diff --git a/common/ea_prefs_default.m b/common/ea_prefs_default.m
@@ -1,4 +1,4 @@
-function prefs=ea_prefs(patientname)
+function prefs = ea_prefs(patientname)
 
 % determine preferences here. For filenames, the variable 'patientname' can
 % be used in string-handling. This variable will be a string with the same name as the patient
@@ -7,7 +7,7 @@
 % load loaded prefs (-> prefs.lp)
 try
     load([ea_getearoot,'ea_prefs']);
-    prefs.lp=lp;
+    prefs.lp = lp;
 end
 
 %% adjust to user
@@ -46,9 +46,6 @@
 prefs.gctnii='glpostop_ct.nii';
 prefs.tp_gctnii=['tp_',prefs.gctnii];
 
-
-
-
 %% connectome files:
 prefs.rest_prefix='res*.nii'; % raw resting state fMRI data search string
 prefs.rest_default='rest.nii'; % default for dcm2nii export.
@@ -81,7 +78,6 @@
 prefs.bvec='dti.bvec';
 prefs.sampledtidicom='sample_dti_dicom.dcm'; % sample DICOM file of DTI image (used for trackvis export).
 
-
 prefs.normmatrix='lmat.txt';
 
 %% Normalization:
@@ -179,7 +175,6 @@
 prefs.native.warp='inverse'; % set to 'tpm' in case you wish to create a atlas-specific tpm to warp atlases, set to 'inverse' to apply the inverse transform of your normalization.
 
 %% lead server:
-
 prefs.ls.autosave=0;
 
 %% environment
@@ -189,8 +184,6 @@
 %% xelatex executable path:
 prefs.ltx.pdfconverter=''; % set path to xelatex here (for PDF export)
 
-
-
 prefs.ls.dir=''; % set path to lead server here (for web export)
 prefs.ixi.dir=''; % set path to ixi database here
-prefs.ixi.meanage=60; % mean age used if no patient/subject age is specified in folder.
+prefs.ixi.meanage=60; % mean age used if no patient/subject age is specified in folder.
diff --git a/connectomics/lead_connectome.m b/connectomics/lead_connectome.m
@@ -305,20 +305,19 @@ function runsavebutn_Callback(hObject, eventdata, handles)
 
 % check wether this is run or save (independent or dependent mode)
 
-cfig=handles.leadfigure;
 options=ea_handles2options(handles);
+options.uipatdirs=getappdata(handles.leadfigure,'uipatdir');
 options.leadprod = 'connectome';
-isindependent=getappdata(handles.leadfigure,'isindependent');
-options.uipatdirs=getappdata(cfig,'uipatdir');
 ea_savelcopts(handles)
 
 % run execution:
-ea_busyaction('on',cfig,'connectome');
+ea_busyaction('on', handles.leadfigure, 'connectome');
 
-if isindependent
+if getappdata(handles.leadfigure,'isindependent')
     ea_run('run',options);
 end
-ea_busyaction('off',cfig,'connectome');
+
+ea_busyaction('off', handles.leadfigure, 'connectome');
 
 
 % --- Executes on button press in degree_centrality.

diff --git a/dev/lead_md/leadMD.m b/dev/lead_md/leadMD.m
@@ -66,30 +66,23 @@ function leadMD_OpeningFcn(hObject, eventdata, handles, varargin)
 options.prefs=ea_prefs('');
 
 % load atlassets
-as = dir(ea_space(options,'atlases'));
-asc=cell(0);
-cnt=1;
-for i=1:length(as)
-    if as(i).isdir
-        asc{cnt}=as(i).name;
-        cnt=cnt+1;
-    end
-end
+atlases = dir(ea_space(options,'atlases'));
+atlases = {atlases(cell2mat({atlases.isdir})).name};
+atlases = atlases(cellfun(@(x) ~strcmp(x(1),'.'), atlases));
 
-excludes={'.','..'};
-asc(ismember(asc,excludes))=[];
 if options.prefs.env.dev
-    asc{end+1}='Segment patient anatomy';
+    atlases{end+1} = 'Segment patient anatomy';
 end
-asc{end+1}='Use none';
 
-set(handles.atlassetpopup,'String',asc);
+atlases{end+1} = 'Use none';
 
-set(handles.atlassetpopup,'String',asc);
-[~,defix]=ismember(options.prefs.atlases.default,asc);
-set(handles.atlassetpopup,'Value',defix);
+set(handles.atlassetpopup, 'String', atlases);
 
-set(handles.versiontxt,'String',['v',ea_getvsn('local')]);
+set(handles.atlassetpopup, 'String', atlases);
+[~,defix]=ismember(options.prefs.atlases.default, atlases);
+set(handles.atlassetpopup, 'Value', defix);
+
+set(handles.versiontxt, 'String', ['v', ea_getvsn('local')]);
 
 
 % get electrode model specs and place in popup
@@ -102,8 +95,6 @@ function leadMD_OpeningFcn(hObject, eventdata, handles, varargin)
 axis off;
 axis equal;
 
-
-
 % UIWAIT makes leadMD wait for user response (see UIRESUME)
 % uiwait(handles.figure1);
 

diff --git a/ea_amendtoolboxoptions.m b/ea_amendtoolboxoptions.m
@@ -2,11 +2,11 @@
 
 if ~isfield(options,'lc') % might be predefined from an exported script..
     try
-        options.lc=options.prefs.machine.lc;
+        options.lc = options.prefs.machine.lc;
     catch
-        options.lc=[];
+        options.lc = [];
     end
 end
 
 % append 2D options.
-options.d2=ea_tdhandles2options([],options.d2);
+options.d2 = ea_tdhandles2options([], options.d2);
diff --git a/ea_autocoord.m b/ea_autocoord.m
@@ -10,9 +10,11 @@ function ea_autocoord(options)
 % Copyright (C) 2014 Charite University Medicine Berlin, Movement Disorders Unit
 % Andreas Horn
 
+% set patientdir
+options.prefs.patientdir = options.patientname;
+
 % get accurate electrode specifications and save it in options.
 options=ea_resolve_elspec(options);
-options.prefs=ea_prefs(options.patientname);
 
 directory = [options.root,options.patientname,filesep];
 
@@ -83,7 +85,7 @@ function ea_autocoord(options)
         end
 
         % Reslice(interpolate) preoperative anatomical image if needed
-        try        ea_resliceanat(options); end
+        try ea_resliceanat(options); end
 
         try
             fs = fopen([directory,'.pp'],'w');
@@ -113,14 +115,10 @@ function ea_autocoord(options)
         % 1. coreg all available preop MRI
         ea_checkcoregallmri(options,0,1); % check and coregister all preoperative MRIs here.
 
-        % 2. then coreg post to pre MRI:
-        %try % fix me - can we get rid of this try/catch here?
+        % 2. then coreg postop MRI to preop MRI
         ea_coregmr(options);
 
-        %end
-
-        % 3. finally perform normalization based on dominant or all preop
-        % MRIs:
+        % 3. finally perform normalization based on dominant or all preop MRIs
         ea_dumpnormmethod(options,options.normalize.method,'normmethod'); % has to come first due to applynormalization.
         eval([options.normalize.method,'(options)']); % triggers the normalization function and passes the options struct to it.
 
@@ -156,8 +154,7 @@ function ea_autocoord(options)
 
     if options.doreconstruction
         ea_checkfiles(options);
-        prefs=ea_prefs;
-        if ~prefs.env.dev % hard set to TRAC/CORE if not in dev mode.
+        if ~options.prefs.env.dev % hard set to TRAC/CORE if not in dev mode.
             options.reconmethod=1;
         end