*** NewSegmentationGUI ***

  gtSegmentationInitialise : Set segmentation method to 'doublethr_new' to be distinguished from 'doublethr' (standard segmentation routine)
  NewSegmentationPreGUI    : Check existence of difspot images before running segmentation and asking for their deletion.
  gtSegmentationLaunchOAR  : implemented the OAR submission using more cores on a single machine (default are 6 cores on one machine with 8000 Mb/core)
                             Difspot images should be saved in 2_difspot/00000, 2_difspot/10000, etc...

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

2_difspot/NewSegmentationDoubleThreshold.m

 function NewSegmentationDoubleThreshold(first_img, last_img, workingdir)
-
 % NEWSEGMENTATIONDOUBLETHRESHOLD  Faster, more efficient segmentation of
-% blobs and spots
+%                                 blobs and spots
 %
 % NewSegmentationDoubleThreshold(first_img, last_img, workingdir)
-%
+% ---------------------------------------------------------------
 % Replaces previous double threshold segmentation, keeping essentially the
 % same parameters and functionality.  Designed to work on a single large
 % machine, or a few machines.  Reduces file I/O time by reading a stack of
@@ -468,7 +467,7 @@ fprintf('blobID %d output, blob %d from this block \n', blob.difblobID, blob.blo
             'graylevel', vals);
     end
     
-    if stack.writespots
+    if (stack.writespots)
         gtSegmentationBlob2SpotTable(blob, stack)
     end
     

2_difspot/NewSegmentationGUI.m

@@ -60,7 +60,7 @@ function NewSegmentationGUI_OpeningFcn(hObject, eventdata, handles, varargin)
 % varargin   command line arguments to NewSegmentationGUI (see VARARGIN)
 
 % deal with tables, etc
-NewSegmentationPreGUI
+NewSegmentationPreGUI();
 
 % get segmentation parameters and populate figure
 handles = gtSegmentationInitialise(handles);

2_difspot/NewSegmentationPreGUI.m

@@ -151,6 +151,7 @@ else
     dbInsertMultiple([parameters.acq.name 'fullmedianvals'], 'ndx', 0:totproj)
 end
 
+parameters.seg.method = 'doublethr_new';
 
 % one question - does user want to subtract the background before
 % segmentation?
@@ -161,4 +162,18 @@ parameters.seg.background_subtract = strcmpi(check, 'y');
 
 save(parameters_name, 'parameters')
 
+% create the first '00000' folder by default
+[~,msg] = mkdir(fullfile(parameters.acq.name,'2_difspot','00000')); disp(msg)
+if exist(fullfile(parameters.acq.name,'2_difspot','00000','difspot00000.edf'),'file')
+    check = inputwdefault('Do you want to remove all the difspot images before going on? [y/n]','y');
+    if strcmpi(check, 'y')
+        delete(fullfile(parameters.acq.name,'2_difspot','*0000','*.edf'));
+    end
+elseif exist(fullfile(parameters.acq.name,'2_difspot','difspot00000.edf'),'file')
+    check = inputwdefault('Do you want to remove all the difspot images before going on? [y/n]','y');
+    if strcmpi(check, 'y')
+        delete(fullfile(parameters.acq.name,'2_difspot','*.edf'));
+    end
+end
+
 end % end of NewSegmentationPreGUI

2_difspot/gtSegmentationInitialise.m

@@ -17,6 +17,9 @@ load parameters
 handles.parameters = parameters;
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
+if ~strcmp(handles.parameters.seg.method, 'doublethr_new')
+handles.parameters.seg.method = 'doublethr_new';
+end
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % how many images in this scan?

2_difspot/gtSegmentationLaunchOAR.m

@@ -2,14 +2,16 @@ function handles = gtSegmentationLaunchOAR(handles)
 % launch OAR jobs
 
 set(handles.status_label, 'string', 'Launching OAR', 'backgroundColor', 'y')
-drawnow
+drawnow()
+
+handles.parameters.seg.segmentation_stack_size = 1000;
 
-OARtime = str2num(get(handles.OAR_walltime, 'string'));
-OARtmp  = ceil(OARtime/60); % minutes
-OARm    = mod(OARtmp, 60);  % minutes
-OARh    = (OARtmp-OARm)/60; % hours
-OAR_walltime = sprintf('%02d:%02d:00', OARh, OARm);
-OAR_njobs = str2num(get(handles.OAR_njobs, 'string'));
+list = build_list_v2();
+ind_tmp = findValueIntoCell(list.seg(:,1), {'segmentation_stack_size'});
+list.seg{ind_tmp(1),4} = 2;
+handles.parameters.seg = gtModifyStructure(handles.parameters.seg, list.seg, 2, 'Segmentation stack size:');
+
+handles = gtSegmentationSaveParameters(handles);
 
 if strcmpi(handles.parameters.acq.type, '360degree')
     totproj = handles.parameters.acq.nproj*2;
@@ -18,33 +20,74 @@ else
 end
 totproj = totproj-1;
 
-disp('%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%')
-disp(' ')
-disp('You should try running this in a single, large, interactive OAR job')
-disp(' ')
-disp('I suggest something like this:')
-disp(' ')
-disp('From rnice6, get an interactive OAR job:')
-disp('oarsub -I -p "mem_core_mb=8000" -l nodes=1/core=6,walltime=2')
-disp(' ')
-disp('then start matlab as normal via python')
-disp(' ')
-disp('You should have enough RAM to use >1000 images in memory')
-disp('Set parameters.seg.segmentation_stack_size = 1000')
-disp('Otherwise, default is a conservative 250')
-disp(' ')
-disp('In the dataset directory, run:')
-disp(sprintf('NewSegmentationDoubleThreshold(0, %d, pwd)', totproj))
-disp(' ')
-disp('...and see what happens.  Best of luck!')
-disp(' ')
-disp('If things work, we can automate properly...')
-disp('Andy, 30/08/2013')
-disp('%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%')
-
-
-
-set(handles.status_label, 'string', 'OAR (not!) launched', 'backgroundColor', 'g')
-drawnow()
+check = inputwdefault('Launch Segmentation with OAR? [y/n]', 'y');
+if strcmpi(check,'y')
+
+  % should be one big job
+    handles.parameters.oar.njobs    = str2num(get(handles.OAR_njobs, 'string'));
+    OARtime = str2num(get(handles.OAR_walltime, 'string'));
+    OARtmp  = ceil(OARtime/60); % minutes
+    OARm    = mod(OARtmp, 60);  % minutes
+    OARh    = (OARtmp-OARm)/60; % hours
+    handles.parameters.oar.walltime = sprintf('%02d:%02d:00', OARh, OARm);
+    
+    handles.parameters.oar.mem_core_mb = 8000; %Mb
+    handles.parameters.oar.node = 1;
+    handles.parameters.oar.core = 6;
+    
+    list = build_list_v2();
+
+    list.oar(end+1,:) = {'mem_core_mb','Memory for each core in Mb','double', 2};
+    list.oar(end+1,:) = {'node','Number of nodes','double', 2};
+    list.oar(end+1,:) = {'core','Number of cores per node','double', 2};
+
+    handles.parameters.oar = gtModifyStructure(handles.parameters.oar, list.oar, 2, 'OAR parameters:');
+
+    parameters = handles.parameters;
+    save('parameters.mat','parameters')
+    
+    disp('Using OAR parameters:')
+    disp(handles.parameters.oar)
+
+    pause(0.5);
+    OAR_make('NewSegmentationDoubleThreshold', 0, totproj, ...
+        handles.parameters.oar.njobs, handles.parameters.acq.dir, 1, ...
+        'mem_core_mb', handles.parameters.oar.mem_core_mb, ...
+        'node', handles.parameters.oar.node, ...
+        'core', handles.parameters.oar.core, ...
+        'walltime', handles.parameters.oar.walltime);
+
+    set(handles.status_label, 'string', 'OAR launched', 'backgroundColor', 'g')
+    drawnow()
+
+else
+
+    disp('%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%')
+    disp(' ')
+    disp('You should try running this in a single, large, interactive OAR job')
+    disp(' ')
+    disp('I suggest something like this:')
+    disp(' ')
+    disp('From rnice6, get an interactive OAR job:')
+    disp('oarsub -I -p "mem_core_mb=8000" -l nodes=1/core=6,walltime=2')
+    disp(' ')
+    disp('then start matlab as normal via python')
+    disp(' ')
+    disp('You should have enough RAM to use >1000 images in memory')
+    disp('Set parameters.seg.segmentation_stack_size = 1000')
+    disp('Otherwise, default is a conservative 250')
+    disp(' ')
+    disp('In the dataset directory, run:')
+    fprintf('NewSegmentationDoubleThreshold(0, %d, pwd)\n', totproj)
+    disp(' ')
+    disp('...and see what happens.  Best of luck!')
+    disp(' ')
+    disp('If things work, we can automate properly...')
+    disp('Andy, 30/08/2013')
+    disp('%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%')
+
+    set(handles.status_label, 'string', 'OAR (not!) launched', 'backgroundColor', 'g')
+    drawnow()
+end
 
 end