* added helper function to use temporary directory

* temorary directory used for dicom export and reimport
* removed GUI elements from folder scanning

Author: wahln

matRad/dicom/@matRad_DicomImporter/matRad_DicomImporter.m

@@ -70,12 +70,10 @@
                     matRad_cfg.dispError('The DICOM export requires the octave-forge package "dicom"!\n');
                 end
             end
-            disp(pathToFolder)
-            if isempty(pathToFolder)
-                obj.patDir = uigetdir(pwd);
-            end
-            
-            obj = matRad_scanDicomImportFolder(obj);
+
+            obj.patDir = pathToFolder;
+                        
+            obj.matRad_scanDicomImportFolder();
 
             % matRad_DicomImporter imports only one structure, to select
             % patients and structures within a single patient the

matRad/dicom/@matRad_DicomImporter/matRad_scanDicomImportFolder.m

@@ -211,7 +211,7 @@
     numOfFiles = numel(obj.allfiles(:,1));
 
     if numel(Thickness) > 1
-        msgbox('Slices are not equidistant! CT will be interpolate with the lowest value of resolution is given by CT slices.', 'Warning');
+        matRad_cfg.dispWarning('Slices are not equidistant! CT will be interpolate with the lowest value of resolution is given by CT slices.');
         Thickness = Thickness(1); % min thickness
         ThBool = []; % in this case we will also create ct cube with the same resolution for all slices 
         PriorThicknesses = flip(rmmissing(diff(FiltredLocArray))); % prior values of spacing, which are needed for interpolation
@@ -241,16 +241,15 @@
         obj.patient = unique(obj.allfiles(:,3));
 
         if isempty(obj.patient)
-            msgbox('No patient found with DICOM CT _and_ RT structure set in patient directory!', 'Error','error');
+             matRad_cfg.dispError('No patient found with DICOM CT _and_ RT structure set in patient directory!');
         end
     else
-        msgbox('No DICOM files found in patient directory!', 'Error','error');
+         matRad_cfg.dispError('No DICOM files found in patient directory!');
         %h.WindowStyle = 'Modal';
         %error('No DICOM files found in patient directory');
     end
 else
-    msgbox('Search folder empty!', 'Error','error');
-    
+    matRad_cfg.dispError('Folder is empty!');
 end
 
 clear warnDlgDICOMtagShown;

test/importTest/test_DicomImporter.m renamed to test/dicom/test_dicomIO.m

@@ -1,4 +1,4 @@
-function test_suite = test_DicomImporter
+function test_suite = test_dicomIO
 %The output should always be test_suite, and the function name the same as
 %your file name
 
@@ -26,14 +26,33 @@
 % assertExceptionThrown(f,id) - test if exception of id is thrown. Take care of Octave issues with exception id (or don't provide id)
 % Check MOxUnit for more information or look at other tests
 
-function test_DicomImporter_classattachment
-    path = 'C:\Users\r114m\Documents\GitHub\matRad\userdata\dicomExport\HEAD_AND_NECK';
-    h = matRad_DicomImporter(path);
-    assertTrue(isa(h,'matRad_DicomImporter'));
+function test_DicomImporter_emptyfolder    
+    path = helper_temporaryFolder('dicomIOtest');
+    assertExceptionThrown(@() matRad_DicomImporter(path));
+
+function test_DicomExporter
+    testpatient = load('photons_testData.mat');
+    path = helper_temporaryFolder('dicomIOtest');
+    
+    dummyResultGUI = struct('physicalDose',rand(testpatient.ct.cubeDim),'w',ones(sum([testpatient.stf.totalNumOfBixels]),1));
+    for i = 1:numel(testpatient.stf)
+        dummyResultGUI.(['physicalDose_beam' num2str(i)]) = rand(testpatient.ct.cubeDim);
+    end
+    dummyResultGUI.wUnsequenced = dummyResultGUI.w;
+    
+    h = matRad_DicomExporter(testpatient.ct,testpatient.cst,testpatient.pln,testpatient.stf,dummyResultGUI);
+    assertTrue(isa(h,'matRad_DicomExporter'));
     assertTrue(isa(h,'handle'));
 
+    h.dicomDir = path;
+    h.matRad_exportDicom();
+
+    dircontents = dir([path filesep '*.dcm']);
+    assertTrue(numel(dircontents) > 0)
+
+
 function test_DicomImporter_loadFiles
-    path = 'C:\Users\r114m\Documents\GitHub\matRad\userdata\dicomExport\HEAD_AND_NECK';
+    path = helper_temporaryFolder('dicomIOtest',false);
     h = matRad_DicomImporter(path);
     assertTrue(isequal(h.patDir, path));
     assertTrue(~isempty(h.allfiles));

test/helper_temporaryFolder.m

@@ -0,0 +1,31 @@
+function [tmpPath,status] = helper_temporaryFolder(folderName,clearIfExists)
+%helper_temporaryFolder Creates a temporary folder for test data in the
+%  users temporary systemdirectory. 
+
+if nargin < 2
+    clearIfExists = true;
+end
+
+tmpPath = fullfile(tempdir(),folderName);
+
+if isfolder(tmpPath) && clearIfExists    
+    status = rmdir(tmpPath,'s');    
+    if status
+        status = mkdir(tmpPath);
+    else
+        status = double(isfolder(tmpPath));
+    end
+elseif ~isfolder(tmpPath)
+    status = mkdir(tmpPath);
+else
+    status = 1;
+end
+
+if ~status
+    tmpPath = pwd();
+    warning('temporary directory invalid - using wokring directory!');
+end
+
+
+end
+