Merge pull request #53 from kschan0214/no_gpu

enabling option of GPU processing for FANSI and NDI
kschan0214 · Dec 12, 2022 · 941cd5b · 941cd5b
2 parents 190dd44 + 906611f
commit 941cd5b
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Showing 11 changed files with 71 additions and 11 deletions.
diff --git a/README.md b/README.md
@@ -41,11 +41,14 @@ If you have a more general question regarding the usage of SEPIA and/or other QS
 
 For full update log, please visit https://sepia-documentation.readthedocs.io/en/latest/getting_started/Release-note.html.
 
-### 1.2.1 (current master)
+### 1.2.1.1 (current master)
+* Enable option of GPU processing for FANSI and NDI
+
+### 1.2.1 (current 190dd44)
 * Fix bug for data with odd-number matrix size
 * Fix bug for missing file when using R2* mapping with NLLS algorithm
 
-### 1.2 (current d2f54a3)
+### 1.2 (commit d2f54a3)
 * Support several deep learning based methods (BFRnet, xQSM, QSMnet+ and LP-CNN) on Linux
 * Support atlas-based subcortical structure segmentation (CIT168 Reinforcement learning atlas, MuSus-100 and AHEAD) on Linux and Mac
 * Integrate R2* mapping toolbox into SEPIA
@@ -54,7 +57,7 @@ For full update log, please visit https://sepia-documentation.readthedocs.io/en/
 
 Please visit the documentation website for more info regarding the newly supported methods and functions.
 
-### 1.1.1 (current a7680bb)
+### 1.1.1 (commit a7680bb)
 * ROMEO is now packaged together with CLEAR-SWI. To accompany these changes, ROMEO_HOME is renamed to MRITOOLS_HOME
 * Supported CLEAR-SWI
 * Fixed bug: bipolar readout correction implementation in full processing pipeline is different from the one in Phase unwrapping standalone 

diff --git a/addons/qsm/ndi/NDI.m b/addons/qsm/ndi/NDI.m
@@ -42,7 +42,7 @@
 matrixSize = size(mask);
 
 % check optional input and set default
-[tolerance,stepSize,iteration,weight,b0dir] = parse_varargin_NDI(varargin);
+[tolerance,stepSize,iteration,weight,b0dir,isGPU] = parse_varargin_NDI(varargin);
 
 % verbose
 disp('Non-linear Dipole Inversion (NDI)');
@@ -67,6 +67,7 @@
 chi = zeros(matrixSize, 'like',localField);
 grad_prev = zeros(matrixSize, 'like',localField);
 
+if isGPU
 try
     % add gpu compatibility
     weight          = gpuArray(weight);
@@ -79,6 +80,7 @@
 catch
     isGPU = false;
 end
+end
 
 % case of one B0 direction
 tic

diff --git a/addons/qsm/ndi/Wrapper_QSM_NDI.m b/addons/qsm/ndi/Wrapper_QSM_NDI.m
@@ -20,6 +20,7 @@
 % Date created: 8 March 2020
 % Date modified: 16 August 2021
 % Date modified: 20 Feb 2022 (v1.0)
+% Date modified: 8 Dec 2022 (v1.2.2)
 %
 %
 function [chi] = Wrapper_QSM_NDI(localField,mask,matrixSize,voxelSize,algorParam, headerAndExtraData)
@@ -31,6 +32,7 @@
 tol         = algorParam.qsm.tol;
 stepSize    = algorParam.qsm.stepSize;
 maxiter     = algorParam.qsm.maxiter;
+isGPU       = algorParam.qsm.isGPU;
 
 % get extra data such as magnitude/weights/B0 direction/TE/etc.
 headerAndExtraData = check_and_set_SEPIA_header_data(headerAndExtraData);
@@ -84,7 +86,7 @@
 localField = localField/(b0*gyro);
 
 chi = NDI(localField,mask,voxelSize,'b0dir',b0dir,'weight',wmap,...
-          'iteration',maxiter,'stepsize',stepSize,'tol',tol);
+          'iteration',maxiter,'stepsize',stepSize,'tol',tol,'isGPU',isGPU);
 
 end
 
@@ -96,5 +98,6 @@
 try algorParam2.qsm.tol         = algorParam.qsm.tol;       catch; algorParam2.qsm.tol      = 1; end
 try algorParam2.qsm.stepSize    = algorParam.qsm.stepSize;  catch; algorParam2.qsm.stepSize = 1; end
 try algorParam2.qsm.maxiter     = algorParam.qsm.maxiter;   catch; algorParam2.qsm.maxiter  = 200; end
+try algorParam2.qsm.isGPU       = algorParam.qsm.isGPU;     catch; algorParam2.qsm.isGPU    = false; end
 
 end
diff --git a/addons/qsm/ndi/get_set_qsm_ndi.m b/addons/qsm/ndi/get_set_qsm_ndi.m
@@ -20,21 +20,27 @@ function get_set_qsm_ndi(h,mode,input)
 
 str_pattern = {'.qsm.tol',...
                '.qsm.maxiter',...
-               '.qsm.stepSize'};
+               '.qsm.stepSize',...
+               '.qsm.isGPU'};
 
 action_handle = {h.qsm.NDI.edit.tol,...
                  h.qsm.NDI.edit.maxIter,...
-                 h.qsm.NDI.edit.stepSize};
+                 h.qsm.NDI.edit.stepSize,...
+                 h.qsm.NDI.checkbox.isGPU};
 
 
 switch lower(mode)
     case 'set'
         fid = input;
 
-        for k = 1:length(action_handle)
+        for k = 1:3
             fprintf(fid,'algorParam%s = %s ;\n'	,str_pattern{k},get(action_handle{k},	'String'));
         end
 
+        % is GPU
+        k = k+1;
+        fprintf(fid,'algorParam%s = %i ;\n'             ,str_pattern{k},get(action_handle{k},	'Value'));
+
     case 'get'
 
         config_txt = input;
@@ -45,5 +51,11 @@ function get_set_qsm_ndi(h,mode,input)
             val             = get_num_as_string(config_txt, pattern_curr, '=', ';');
             set_non_nan_value(action_handle{k},'String',val)
         end
+
+        % isGPU
+        k = k+1;
+        pattern_curr    = str_pattern{k};
+        val             = get_num_as_string(config_txt, pattern_curr, '=', ';');
+        set_non_nan_value(action_handle{k}, 'Value', str2double(val))
 
 end
diff --git a/addons/qsm/ndi/sepia_handle_panel_qsm_NDI.m b/addons/qsm/ndi/sepia_handle_panel_qsm_NDI.m
@@ -24,6 +24,7 @@
 defaultTol      = 1;
 defaultMaxIter  = 200;
 defaultStepSize = 1;
+defaultIsGPU    = 0;
 
 %% Tooltips
 tooltip.qsm.NDI.tol   	 = 'Relative tolerance to stop NDI iteration.';
@@ -65,6 +66,14 @@
     % text|edit field pair: gradient step size
     [h.qsm.NDI.text.stepSize,h.qsm.NDI.edit.stepSize] = sepia_construct_text_edit(...
         panelParent,'Step size:',       defaultStepSize, [left(1) bottom(3) width height], wratio);
+
+    % col 1, row 4
+    % checkbox field pair: isGPU
+    h.qsm.NDI.checkbox.isGPU = uicontrol('Parent',h.qsm.panel.NDI,'Style','checkbox',...
+        'String','Enable GPU',...
+        'units','normalized','position',[left(1) bottom(4) width height],...
+        'HorizontalAlignment','left',...
+        'backgroundcolor',get(h.fig,'color'));
 
 
 %% set tooltips

diff --git a/gui_func/callback/config/get_set_qsm_fansi.m b/gui_func/callback/config/get_set_qsm_fansi.m
@@ -26,6 +26,7 @@ function get_set_qsm_fansi(h,mode,input)
                '.qsm.solver',...
                '.qsm.constraint',...
                '.qsm.gradient_mode',...
+               '.qsm.isGPU',...
                '.qsm.isWeakHarmonic',...
                '.qsm.beta',...
                '.qsm.muh'};
@@ -38,6 +39,7 @@ function get_set_qsm_fansi(h,mode,input)
                  h.qsm.FANSI.popup.solver,...
                  h.qsm.FANSI.popup.constraints,...
                  h.qsm.FANSI.popup.gradientMode,...
+                 h.qsm.FANSI.checkbox.isGPU,...
                  h.qsm.FANSI.checkbox.isWeakHarmonic,...
                  h.qsm.FANSI.edit.beta,...
                  h.qsm.FANSI.edit.muh};
@@ -54,6 +56,10 @@ function get_set_qsm_fansi(h,mode,input)
         for k = 6:8
             fprintf(fid,'algorParam%s = ''%s'' ;\n'     ,str_pattern{k},action_handle{k}.String{action_handle{k}.Value,1});
         end
+
+        % is GPU
+        k = k+1;
+        fprintf(fid,'algorParam%s = %i ;\n'             ,str_pattern{k},get(action_handle{k},	'Value'));
 
         k = k+1;
         fprintf(fid,'algorParam%s = %i ;\n'             ,str_pattern{k},get(action_handle{k},	'Value'));
@@ -110,6 +116,12 @@ function get_set_qsm_fansi(h,mode,input)
             case 'none'
                 set_non_nan_value(action_handle{k},'Value',4)
         end
+
+        % isGPU
+        k = k+1;
+        pattern_curr    = str_pattern{k};
+        val             = get_num_as_string(config_txt, pattern_curr, '=', ';');
+        set_non_nan_value(action_handle{k}, 'Value', str2double(val))
 
         % weak field harmonic
         k = k+1;
@@ -124,5 +136,5 @@ function get_set_qsm_fansi(h,mode,input)
             val             = get_num_as_string(config_txt, pattern_curr, '=', ';');
             set_non_nan_value(action_handle{k},'String',val);
         end
-
+        
 end
diff --git a/gui_func/panel/QSM_method/sepia_handle_panel_qsm_FANSI.m b/gui_func/panel/QSM_method/sepia_handle_panel_qsm_FANSI.m
@@ -131,6 +131,14 @@
     [h.qsm.FANSI.text.muh,h.qsm.FANSI.edit.muh] = sepia_construct_text_edit(...
         panelParent,'Harmonic consistency:',    defaultMuh,         [left(3) bottom(3) width height], wratio);
     set(h.qsm.FANSI.edit.muh, 'Enable', 'off');
+
+    % col 3, row 4
+    % checkbox field pair: isGPU
+    h.qsm.FANSI.checkbox.isGPU = uicontrol('Parent',h.qsm.panel.FANSI,'Style','checkbox',...
+        'String','Enable GPU',...
+        'units','normalized','position',[left(3) bottom(4) width height],...
+        'HorizontalAlignment','left',...
+        'backgroundcolor',get(h.fig,'color'));
 
 
 %% set tooltips

diff --git a/misc/qsm_algorithm/FANSI/FANSI_4sepia_v3.m b/misc/qsm_algorithm/FANSI/FANSI_4sepia_v3.m
@@ -85,6 +85,9 @@
 if isfield(options,'update')
     params.tolUpdate = options.update; % This variable was renamed in release 3.0
 end
+if isfield(options,'isGPU')
+    params.isGPU = options.isGPU; % This variable available in release 3.0
+end
 
 % Launch the desired solver
 isNonlinear = true; % This variable was renamed in release 3.0

diff --git a/sepia_universal_variables.m b/sepia_universal_variables.m
@@ -14,7 +14,7 @@
 % DO NOT change the order of the entities, add a new one at the end instead
 %
 %% Version
-SEPIA_version = 'v1.2.1';
+SEPIA_version = 'v1.2.1.1';
 
 %% PATH
 SEPIA_HOME = fileparts(mfilename('fullpath'));

diff --git a/wrapper/WrapperQSM/Wrapper_QSM_FANSI.m b/wrapper/WrapperQSM/Wrapper_QSM_FANSI.m
@@ -35,6 +35,7 @@
 options.muh             = algorParam.qsm.muh;
 alpha1                  = algorParam.qsm.lambda;
 mu1                     = algorParam.qsm.mu1;
+isGPU                   = algorParam.qsm.isGPU;
 
 % need further decision
 gradient_mode   = algorParam.qsm.gradient_mode;
@@ -77,6 +78,8 @@
     options.nonlinear = true;   % non-linear
 end
 
+options.isGPU = logical(isGPU);
+
 % data 
 % if both data are loaded
 if ~isempty(magn) && ~isempty(wmap)
@@ -189,5 +192,6 @@
 try algorParam2.qsm.isWeakHarmonic  = algorParam.qsm.isWeakHarmonic;catch; algorParam2.qsm.isWeakHarmonic	= 0; end
 try algorParam2.qsm.beta            = algorParam.qsm.beta;          catch; algorParam2.qsm.beta             = 150; end
 try algorParam2.qsm.muh             = algorParam.qsm.muh;           catch; algorParam2.qsm.muh              = 3; end
+try algorParam2.qsm.isGPU        	= algorParam.qsm.isGPU;       	catch; algorParam2.qsm.isGPU            = false; end
 
 end
diff --git a/wrapper/parser/deprecated/parse_varargin_NDI.m b/wrapper/parser/deprecated/parse_varargin_NDI.m
@@ -7,14 +7,15 @@
 % Date created: 5 June 2019
 % Date last modified: 27 Feb 2020 (v0.8.0)
 %
-function [tolerance,stepSize,iteration,weight,b0dir] = parse_varargin_NDI(arg)
+function [tolerance,stepSize,iteration,weight,b0dir,isGPU] = parse_varargin_NDI(arg)
 
 % predefine parameters
 tolerance   = 1;
 stepSize    = 1;
 iteration   = 200;
 b0dir       = [0,0,1];
 weight      = [];
+isGPU       = false;
 
 % use user defined input if any
 if ~isempty(arg)
@@ -34,6 +35,9 @@
         if strcmpi(arg{kvar},'b0dir')
             b0dir = arg{kvar+1};
         end
+        if strcmpi(arg{kvar},'isGPU')
+            isGPU = arg{kvar+1};
+        end
     end
 end