Forward Simulation : formatting (remove sprintf with strings) and change...

Forward Simulation : formatting (remove sprintf with strings) and change gtFsimCheckMissingGrains output, differing missing grains and old grains.

Signed-off-by: Laura Nervo <laura.nervo@esrf.fr>

git-svn-id: https://svn.code.sf.net/p/dct/code/trunk@759 4c865b51-4357-4376-afb4-474e03ccb993

5_reconstruction/gtFsimCheckMissingGrains.m

@@ -7,82 +7,82 @@ function missing = gtFsimCheckMissingGrains(phase_num)
 %
 %     OUTPUT:
 %       missing = structure with:
-%                 ind        = grainid of missing grain from
-%                              ForwardSimulation
-%                 is_grain   = for each grain true if grain_[id].mat
-%                              exists
-%                 is_grain_r = is_grain reshaped as 
-%                              [nof_grain_per_job,njobs]
+%                 ind         = grainid of missing grain from
+%                               ForwardSimulation
+%                 is_grain    = for each grain true if grain_[id].mat
+%                               exists
+%                 is_uptodate = true if date(grain_####.mat) >= date(last job
+%                               submitted to OAR)
 
-% get number of jobs for that functions from OAR
-arrays=logviewOar('gtForwardSimulate_v2',[],false);
-% if ~isempty(arrays.fname)
-%     if ~isempty(arrays.('gtForwardSimulate_v2').logs)
-%        filename = arrays.('gtForwardSimulate_v2').logs;
-%        [~,njobs] = unix(['grep "njobs" ' filename ' | awk -F" = " ''{print $2}''']);
-%       nof_jobs = str2double(njobs);
-%     end
-% else
-    nof_jobs = 1;
+% get last gtForwardSimulate_v2 run date from oar.log file
+fid = fopen('oar.log');
+o=textscan(fid,'%s %s %d %s %s');
+fclose(fid);
+datemax=max(datenum(o{4}(:)));
 
-% end
 
-% get last gtForwardSimulate_v2 run date from oar.log file
-o=fileread('oar.log');
-o2=textscan(o,'%s %s %d %s %s');
-datemax=max(datenum(o2{4}(:)));
+grain=[];
+load(fullfile( '4_grains',['phase_' sprintf('%02d',phase_num)],'index.mat' ),'grain');
+% total number of grains
+nof_grains = length(grain);
 
-count=[];
 list_grains=dir(fullfile( '4_grains',['phase_' sprintf('%02d',phase_num)],'grain_*.mat'));
-for i=1:length(list_grains)
-    num = str2double(list_grains(i).name(7:10));
-    if datenum(list_grains(i).date,'dd-mmm-yyyy')>=datemax
-        count(num) = true; 
+for ii=1:length(list_grains)
+    if datenum(list_grains(ii).date,'dd-mmm-yyyy')>=datemax
+        is_uptodate(ii) = true;
     else
-        count(num) = false;
+        is_uptodate(ii) = false;
     end
 end
 
+nof_grains_fsim = length(list_grains);
 
-grain=load(fullfile( '4_grains',['phase_' sprintf('%02d',phase_num)],'index.mat' ),'grain');
-grain=grain.grain;
-
-% total number of grains
-nof_grains = length(grain);
-
-% is_grain contains true if grain_#.mat exists, false if doesn't exist
-is_grain=[];
-for i=1:nof_grains
-    if exist(fullfile( '4_grains',['phase_' sprintf('%02d',phase_num)],['grain_' sprintf('%04d.mat',i)] ),'file')
-        if count(i)
-            is_grain(i) = true;
-        else
-            disp(['grain # ' num2str(i) ' may not be updated'])
-            is_grain(i) = false;
-        end
+for ii = 1: nof_grains
+    if exist(fullfile( '4_grains',['phase_' sprintf('%02d',phase_num)],sprintf('grain_%04d.mat',ii)),'file')
+        is_grain(ii) = true;
     else
-        is_grain(i) = false;
+        disp(['grain # ' num2str(ii) ' does not exist.'])
+        is_grain(ii) = false;
     end
 end
 
-% grains per each job
-grains = ceil(nof_grains/nof_jobs);
-
-% fill with NaN to have exact division of nof_grains by nof_jobs
-tot_n = nof_jobs * grains;
-is_grain(nof_grains+1:tot_n)=NaN;
-
-% grain number of missing files
-ind=find(is_grain==0);
+missing.ind         = find(is_grain==false);
+missing.is_grain    = is_grain;
+missing.old         = find(is_uptodate==false);
+missing.is_uptodate = is_uptodate;
+
+if nof_grains ~= nof_grains_fsim
+    disp('Check number of grains from forward simulation: it differs from the total number of grains from INDEXTER')
+    disp(['Indexter : ' num2str(nof_grains)])
+    disp(['Forward Simulation : ' num2str(nof_grains_fsim)])
+    disp(['There should be ' num2str(nof_grains_fsim - nof_grains) ' grains to be removed. Run the following commands:'])
+    for ii=missing.old(1):missing.old(end)
+        if ii > nof_grains && ii <= nof_grains_fsim
+            disp(['   delete( ''' fullfile( '4_grains',['phase_' sprintf('%02d',phase_num)],sprintf('grain_%04d.mat',ii)) ''' )'])
+        end
+    end 
+end
 
-% reshape is_grain to have in each column each job status
-% column  = job number, row = grain number for that job
-is_grain_r = reshape(is_grain,tot_n/nof_jobs,nof_jobs);
+% check id in grain_####.mat
+checkId_fsim = [];
+for kk=1:nof_grains_fsim 
+    load(fullfile( '4_grains',['phase_' sprintf('%02d',phase_num)],sprintf('grain_%04d.mat',kk)),'id');
+    check = [kk id];
+    if kk ~= id
+        checkId_fsim{end+1} = check;
+    end
+end
 
-missing.ind = ind;
-missing.is_grain = is_grain;
-missing.is_grain_r = is_grain_r;
+checkId = [];
+for ii=1:nof_grains
+    check = [ii grain{ii}.id];
+    if ii ~= grain{ii}.id
+        checkId{end+1} = check;
+    end
+end
 
+missing.checkFsim = cell2mat(checkId_fsim');
+missing.checkIndex = cell2mat(checkId');
 
 clear grain
 

5_reconstruction/gtSetupForwardSimulation.m

-function gtSetupForwardSimulation
-% simple helper function to run gtForwardSimulate
-% whatever the current version is ;-)
+function gtSetupForwardSimulation()
+% GTSETUPFORWARDSIMULATION  Simple helper function to run gtForwardSimulate_v2
+%     gtSetupForwardSimulation()
+%     --------------------------
 
 
 parameters = [];
@@ -23,42 +24,45 @@ end
 phaseID_str = sprintf('%02d',phaseID);
 
 disp(['Setting up Forward Simulation for phase ' phaseID_str ' ' parameters.cryst(phaseID).name]);
-filetable = sprintf('%s_filetable', parameters.acq.name);
-% get the latest version of indexter output
-grain = [];
+filetable = [parameters.acq.name '_filetable'];
 
+% get the latest version of indexter output
+ngrains = [];
 for ii = 1 : nof_phases
-    filename = fullfile(parameters.acq.dir, '4_grains', sprintf('phase_%02d', ii), 'index.mat');
-    load(filename, 'grain');
+    grain = [];
+    index_filename = fullfile(parameters.acq.dir, '4_grains', sprintf('phase_%02d',ii), 'index.mat');
+    load(index_filename, 'grain');
     % how many grains in this dataset?
     ngrains(ii) = length(grain);
 end    
 
 
-%create / reset sample.mat spot2grain.mat
-filename = fullfile(parameters.acq.dir, '4_grains', 'sample.mat');
-if exist(filename, 'file') && (nof_phases > 1)
-    sample = GtSample.loadFromFile(filename);     % do not create from scratch - we want to keep information related to other phases
+% create / reset sample.mat spot2grain.mat
+sample_filename = fullfile(parameters.acq.dir, '4_grains', 'sample.mat');
+if ( exist(sample_filename, 'file') && nof_phases > 1 )
+    sample = GtSample.loadFromFile(sample_filename);     % do not create from scratch - we want to keep information related to other phases
 else
     sample = GtSample(nof_phases);
-    sample.fileTable = sprintf('%s_filetable',parameters.acq.name);
+    sample.fileTable = [parameters.acq.name '_filetable'];
     for ii = 1 : nof_phases
         phase = GtPhase(parameters.cryst(ii).name, ngrains(ii));
         sample.phases{ii} = phase;
     end
-    save(filename, 'sample');
+    save(sample_filename, 'sample');
 end
 
 
-disp(['Reset phase number ' num2str(phaseID) ' in the sample.mat:'])
-disp(['Name : ' parameters.cryst(phaseID).name])
-disp(['nof_grains: ' num2str(ngrains(phaseID))])
+disp(['Reset phase number ' phaseID_str ' in the sample.mat:'])
+disp(['  Phase name : ' parameters.cryst(phaseID).name])
+disp(['  Nof_grains : ' num2str(ngrains(phaseID))])
 
+% check number of grain_####.mat :
+missing = gtFsimCheckMissingGrains(phaseID);
 
 filename    = fullfile(parameters.acq.dir,'4_grains','spot2grain.mat');
-difspot_num  = mym(sprintf('select count(*) from %sdifspot', parameters.acq.name));
+difspot_num  = mym(['select count(*) from ' parameters.acq.name 'difspot']);
 
-if exist(filename, 'file') && nof_phases>1 
+if ( exist(filename, 'file') && nof_phases > 1 ) 
     check = inputwdefault('Do you want to reset spot2grain? [y/n]', 'n');
     if ~strcmpi(check, 'y')
         spot2grain  = cell(difspot_num, 1); % cell array linking difspots with grainids
@@ -75,7 +79,7 @@ check = inputwdefault('Use default parameters? [y/n]', 'y');
 if ~strcmpi(check, 'y')
     list = build_list_v2();
     parameters.fsim = gtModifyStructure(parameters.fsim, list.fsim(:, 1:2));
-    save([parameters.acq.dir '/parameters.mat'],'parameters');
+    save(fullfile(parameters.acq.dir,'parameters.mat'),'parameters');
 end
 
 % launch forward simulation process to OAR - split to two jobs
@@ -95,13 +99,12 @@ if strcmpi(check, 'y')
     OAR_list{1,1}='njobs'; OAR_list{1,2}='How many OAR jobs?';
     OAR_list{2,1}='walltime'; OAR_list{2,2}='Walltime for OAR jobs (hh:mm:ss)'; 
     
-    OAR_parameters=gtModifyStructure(OAR_parameters, OAR_list, 'Parameters for OAR');
+    OAR_parameters = gtModifyStructure(OAR_parameters, OAR_list, 'Parameters for OAR');
     
 
     OAR_make('gtForwardSimulate_v2', 1, ngrains(phaseID), OAR_parameters.njobs, ...
-        [parameters.acq.dir ' ' num2str(phaseID)], true, ...
+        [parameters.acq.dir ' ' phaseID_str], true, ...
         'walltime', OAR_parameters.walltime);
-    
 else
     gtForwardSimulate_v2(1, ngrains(phaseID), pwd, phaseID);
 end