Added an option to specify plastimatch build directory

cerr · Dec 18, 2018 · 4851679 · 4851679
1 parent 6659379
commit 4851679
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Showing 4 changed files with 36 additions and 2 deletions.
diff --git a/CERR_core/CERROptions.json b/CERR_core/CERROptions.json
@@ -147,7 +147,7 @@
 
 "ROISampleRate" : 1,
 
-"DVHBinWidth" : 0.2,
+"DVHBinWidth" : 0.1,
 
 "DVHBlockSize" : 5000, 
 
@@ -217,6 +217,7 @@
 "sinc_filter_on_display" : 0,
 
 "plastimatch_command_file" : "bspline_register_cmd_dir.txt",
+"plastimatch_build_dir" : "~/software/plastimatch-build",
 
 "linePoolSize" : 30,
 

diff --git a/CERR_core/ImageRegistration/warp_dose.m b/CERR_core/ImageRegistration/warp_dose.m
@@ -3,6 +3,8 @@
 %
 % APA, 07/19/2012
 
+global stateS
+
 indexMovS = movPlanC{end};
 indexS = planC{end};
 
@@ -24,6 +26,12 @@
 % Generate name for the output .mha file
 warpedMhaFileName = fullfile(getCERRPath,'ImageRegistration','tmpFiles',['warped_dose_',baseScanUID,'_',movScanUID,'.mha']);
 
+% Switch to plastimatch directory if it exists
+prevDir = pwd;
+if exist(stateS.optS.plastimatch_build_dir,'dir')    
+    cd(stateS.optS.plastimatch_build_dir)
+end
+
 % Issue plastimatch warp command with nearest neighbor interpolation
 %system(['plastimatch warp --input ', escapeSlashes(movDoseFileName), ' --output-img ', escapeSlashes(warpedMhaFileName), ' --xf ', escapeSlashes(bspFileName)])
 system(['plastimatch warp --input ', movDoseFileName, ' --output-img ', warpedMhaFileName, ' --xf ', bspFileName])
@@ -41,3 +49,6 @@
     delete(warpedMhaFileName)
     delete(bspFileName)
 end
+
+% Switch back to the previous directory
+cd(prevDir)
diff --git a/CERR_core/ImageRegistration/warp_scan.m b/CERR_core/ImageRegistration/warp_scan.m
@@ -3,6 +3,8 @@
 %
 % APA, 07/19/2012
 
+global stateS
+
 % Create b-spline coefficients file
 if isstruct(deformS)
     baseScanUID = deformS.baseScanUID;
@@ -31,6 +33,12 @@
 % Generate name for the output .mha file
 warpedMhaFileName = fullfile(getCERRPath,'ImageRegistration','tmpFiles',['warped_scan_',baseScanUID,'_',movScanUID,'.mha']);
 
+% Switch to plastimatch directory if it exists
+prevDir = pwd;
+if exist(stateS.optS.plastimatch_build_dir,'dir')    
+    cd(stateS.optS.plastimatch_build_dir)
+end
+
 % Issue plastimatch warp command
 fail = system(['plastimatch warp --input ', movScanFileName, ' --output-img ', warpedMhaFileName, ' --xf ', bspFileName]);
 if fail % try escaping slashes
@@ -50,4 +58,7 @@
     end
     delete(movScanFileName)
     delete(warpedMhaFileName)
-end
+end
+
+% Switch back to the previous directory
+cd(prevDir)
diff --git a/CERR_core/ImageRegistration/warp_structures.m b/CERR_core/ImageRegistration/warp_structures.m
@@ -3,6 +3,8 @@
 %
 % APA, 07/20/2012
 
+global stateS
+
 indexMovS = movPlanC{end};
 
 % Create b-spline coefficients file
@@ -20,6 +22,12 @@
     baseScanUID = planC{indexS.scan}(strCreationScanNum).scanUID;    
 end
 
+% Switch to plastimatch directory if it exists
+prevDir = pwd;
+if exist(stateS.optS.plastimatch_build_dir,'dir')    
+    cd(stateS.optS.plastimatch_build_dir)
+end
+
 for structNum = movStructNumsV
 
     % Convert structure mask to .mha
@@ -68,3 +76,6 @@
         delete(bspFileName)
     end
 end
+
+% Switch back to the previous directory
+cd(prevDir)