Merge branch 'dev' of https://github.com/e0404/matRad into dev

AUTHORS.txt

@@ -20,6 +20,7 @@
 * Emily Heath
 * Cindy Hermann
 * Noa Homolka
+* Raed Ibragim
 * Fabian Jäger
 * Fernando Hueso-González
 * Navid Khaledi

examples/matRad_example13_fitAnalyticalParticleBaseData.m

@@ -167,7 +167,7 @@
 
 
 %% generate steering file
-stf = matRad_generateStfSinglePencilBeam(ct,cst,pln);
+stf = matRad_generateSingleBixelStf(ct,cst,pln);
 
 % Select existing BDL file to load and fit
 pln.loadExistingBDL = 'BDL_matRad.txt';

matRad/dicom/@matRad_DicomExporter/matRad_exportDicomCt.m

@@ -69,12 +69,6 @@
 nSlices = ct.cubeDim(3);
 %Create X Y Z vectors if not present
 if ~any(isfield(ct,{'x','y','z'}))
-    %positionOffset = transpose(ct.cubeDim ./ 2);
-    %positionOffset = ct.cubeDim .* [ct.resolution.y, ct.resolution.x, ct.resolution.z] ./ 2;
-%     positionOffset = [ct.resolution.y, ct.resolution.x, ct.resolution.z] ./ 2;
-%     ct.x = ct.resolution.x*[0:ct.cubeDim(2)-1] - positionOffset(2);
-%     ct.y = ct.resolution.y*[0:ct.cubeDim(1)-1] - positionOffset(1);
-%     ct.z = ct.resolution.z*[0:ct.cubeDim(3)-1] - positionOffset(3);
     ct = matRad_getWorldAxes(ct);
 end
 

matRad/dicom/@matRad_DicomExporter/matRad_exportDicomRTDoses.m

@@ -82,7 +82,7 @@
 %Now image meta
 resolution = ct.resolution;
 meta.PixelSpacing = [resolution.y; resolution.x];
-meta.SliceThickness = resolution.z;
+meta.SliceThickness = num2str(resolution.z);
 
 meta.ImagePositionPatient = [ct.x(1); ct.y(1); ct.z(1)];
 meta.ImageOrientationPatient = [1;0;0;0;1;0];

matRad/dicom/@matRad_DicomExporter/matRad_exportDicomRTStruct.m

@@ -96,9 +96,9 @@
 
 
 %Since we are exporting HU directly --> no rescaling in any case
-%meta.SliceThickness = ct.resolution.z;
-%meta.PixelSpacing = [ct.resolution.y; ct.resolution.x];
-%meta.ImageOrientationPatient = [1;0;0;0;1;0]; %lps
+meta.SliceThickness = num2str(ct.resolution.z);
+meta.PixelSpacing = [ct.resolution.y; ct.resolution.x];
+meta.ImageOrientationPatient = [1;0;0;0;1;0]; %lps
 
 %meta.RescaleSlope = 1;
 %meta.RescaleIntercept = 0;    

matRad/dicom/@matRad_DicomImporter/matRad_DicomImporter.m

@@ -0,0 +1,133 @@
+classdef matRad_DicomImporter < handle
+    % matRad_DicomImporter matRad class to handle a dicom import.  
+    %
+    % Example on how to use the matRad_DicomImport class
+    %
+    % dcmImpObj = matRad_DicomImporter('pathToFolder');          % create instance of matRad_DicomImporter
+    % dcmImpObj.matRad_importDicom(dcmImpObj);                   % run the import
+    %
+    %
+    % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+    %
+    % Copyright 2020 the matRad development team. 
+    % 
+    % This file is part of the matRad project. It is subject to the license 
+    % terms in the LICENSE file found in the top-level directory of this 
+    % distribution and at https://github.com/e0404/matRad/LICENSE.md. No part 
+    % of the matRad project, including this file, may be copied, modified, 
+    % propagated, or distributed except according to the terms contained in the 
+    % LICENSE file.
+    %
+    % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+    properties
+
+       % path to DICOM file 
+       patDir;
+
+       % lists of all files
+       allfiles;
+       patient;
+       importFiles; % all the names (directories) of files, that will be imported
+
+       % properties with data for import functions
+       importCT;
+       importRtss;
+       importRTDose;
+
+       % structures for .mat file
+       ct = [];
+       cst = [];
+       stf = [];
+       pln = [];
+       resultGUI = [];
+
+       ImportGrid;
+
+       % bools 
+       dicomMetaBool;
+       visBool;
+
+
+
+    end
+
+    methods
+
+        function obj = matRad_DicomImporter(pathToFolder)
+
+            %matRad_DicomImporter Construct an instance of this class
+            %   Can be called with the structures. If no argument is given,
+            %   all structures will be read from the base workspace
+
+            obj.patDir = pathToFolder;
+            matRad_cfg = MatRad_Config.instance();
+
+            if matRad_cfg.isOctave
+                %Octave needs the DICOM package
+                try
+                    pkg load dicom;
+                catch
+                    matRad_cfg.dispError('The DICOM export requires the octave-forge package "dicom"!\n');
+                end
+            end
+
+            obj.patDir = pathToFolder;
+
+            obj.matRad_scanDicomImportFolder();
+
+            % matRad_DicomImporter imports only one structure, to select
+            % patients and structures within a single patient the
+            % matRad_importDicomWidget is used
+
+            ctFiles = strcmp(obj.allfiles(:,2),'CT');
+            rtssFiles = strcmpi(obj.allfiles(:,2),'rtstruct'); %note we can have multiple RT structure sets, matRad will always import the firstit finds
+            rtPlanFiles = strcmpi(obj.allfiles(:,2),'rtplan');
+            rtDoseFiles = strcmpi(obj.allfiles(:,2),'rtdose');
+
+            obj.importFiles.ct = obj.allfiles(ctFiles,:);%All CT slice filepaths stored in a cell array like {'CTSlice1.dcm','CTSlice2.dcm'};
+            obj.importFiles.rtss = obj.allfiles(rtssFiles,:); 
+            obj.importFiles.rtplan = obj.allfiles(rtPlanFiles,:);
+            obj.importFiles.rtdose = obj.allfiles(rtDoseFiles,:);
+
+            for i = numel(obj.allfiles(:,1)):-1:1
+                if strcmp(obj.allfiles(i,2),'CT')
+                    obj.importFiles.resx = obj.allfiles{i,9}; 
+                    obj.importFiles.resy = obj.allfiles{i,10};
+                    obj.importFiles.resz = obj.allfiles{i,11}; %some CT dicoms do not follow  the standard and use SpacingBetweenSlices 
+                    break
+                end
+            end 
+
+            obj.importFiles.useImportGrid = false;
+
+
+        end
+
+        matRad_importDicom(obj)
+
+        obj = matRad_importDicomCt(obj)
+
+        obj = matRad_importDicomRTDose(obj)
+
+        obj = matRad_importDicomRTPlan(obj)
+
+        obj = matRad_importDicomRtss(obj)
+
+        obj = matRad_importDicomSteeringPhotons(obj)
+
+        obj = matRad_importDicomSteeringParticles(obj)
+
+        obj = matRad_scanDicomImportFolder(obj)
+
+        obj = matRad_calcHU(obj)
+
+        obj = matRad_createCst(obj)
+
+        obj = matRad_dummyCst(obj)
+
+        % matRad_saveImport(obj);
+
+    end
+
+end
+

matRad/dicom/matRad_calcHU.m → matRad/dicom/@matRad_DicomImporter/matRad_calcHU.m

@@ -1,17 +1,17 @@
-function ct = matRad_calcHU(ct)
+function obj = matRad_calcHU(obj)
 % matRad function to calculate Hounsfield units from a dicom ct 
 % that originally uses intensity values
 %
-% call
-%   ct = matRad_calcHU(ct)
+% In your object, there must be a property that contains unprocessed 
+% dicom ct data which are stored as intensity values (IV)
+%
+% Output - ct structure with cube with HU
 %
-% input
-%   ct: unprocessed dicom ct data which are stored as intensity values (IV)
+% HU = IV * slope + intercept
 %
-%                      HU = IV * slope + intercept
+% call
+%   obj = matRad_calcHU(obj)
 %
-% output
-%   ct:                 ct struct with cube with HU
 %
 % References
 %   -
@@ -29,10 +29,10 @@
 %
 % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
-for i = 1:ct.numOfCtScen
-    ct.cubeHU{i} = double(ct.cubeIV{i}) * double(ct.dicomInfo.RescaleSlope) + double(ct.dicomInfo.RescaleIntercept);
+for i = 1:obj.ct.numOfCtScen
+    obj.ct.cubeHU{i} = double(obj.ct.cubeIV{i}) * double(obj.ct.dicomInfo.RescaleSlope) + double(obj.ct.dicomInfo.RescaleIntercept);
 end
 
-ct = rmfield(ct,'cubeIV');
+obj.ct = rmfield(obj.ct,'cubeIV');
 
 end

matRad/dicom/@matRad_DicomImporter/matRad_createCst.m

@@ -0,0 +1,82 @@
+function obj = matRad_createCst(obj)
+% matRad function to create a cst struct upon dicom import
+% 
+% In your object, there must be a property that contains matlab structure 
+% containing information about rt structure set (generated with 
+% matRad_importDicomRtss and matRad_convRtssContours2Indices)
+%
+% Output - matRad cst structure
+%
+% call
+%   obj = matRad_createCst(obj)
+%
+%
+% References
+%   -
+%
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2015 the matRad development team. 
+% 
+% This file is part of the matRad project. It is subject to the license 
+% terms in the LICENSE file found in the top-level directory of this 
+% distribution and at https://github.com/e0404/matRad/LICENSE.md. No part 
+% of the matRad project, including this file, may be copied, modified, 
+% propagated, or distributed except according to the terms contained in the 
+% LICENSE file.
+%
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+matRad_cfg = MatRad_Config.instance();
+
+nStructures = size(obj.importRtss.structures,2);
+obj.cst = cell(nStructures,6);
+
+%Create set of default colors
+defaultColors = colorcube(nStructures);
+
+for i = 1:size(obj.importRtss.structures,2)
+    obj.cst{i,1} = i - 1; % first organ has number 0    
+    obj.cst{i,2} = obj.importRtss.structures(i).structName;
+
+    if ~isempty(regexpi(obj.cst{i,2},'tv', 'once')) || ...
+       ~isempty(regexpi(obj.cst{i,2},'target', 'once')) || ...
+       ~isempty(regexpi(obj.cst{i,2},'gtv', 'once')) || ...
+       ~isempty(regexpi(obj.cst{i,2},'ctv', 'once')) || ...
+       ~isempty(regexpi(obj.cst{i,2},'ptv', 'once')) || ...
+       ~isempty(regexpi(obj.cst{i,2},'boost', 'once')) || ...
+       ~isempty(regexpi(obj.cst{i,2},'tumor', 'once'))
+
+        obj.cst{i,3} = 'TARGET';
+
+        obj.cst{i,5}.Priority = 1;
+
+        % default objectives for targets
+        objective = DoseObjectives.matRad_SquaredDeviation;
+        objective.penalty = 800;
+        objective.parameters = {30};  %Default reference Dose
+        obj.cst{i,6}{1} = struct(objective);
+
+    else
+
+        obj.cst{i,3} = 'OAR';
+
+        obj.cst{i,5}.Priority = 2;
+
+        obj.cst{i,6} = []; % define no OAR dummy objcetives   
+
+    end
+
+    obj.cst{i,4}{1} = obj.importRtss.structures(i).indices;
+
+    % set default parameter for biological planning
+    obj.cst{i,5}.alphaX  = 0.1;
+    obj.cst{i,5}.betaX   = 0.05;
+    obj.cst{i,5}.Visible = 1;
+    if isfield(obj.importRtss.structures(i),'structColor') && ~isempty(obj.importRtss.structures(i).structColor)
+        obj.cst{i,5}.visibleColor = obj.importRtss.structures(i).structColor' ./ 255;
+    else
+        obj.cst{i,5}.visibleColor = defaultColors(i,:);
+        matRad_cfg.dispInfo('No color information for structure %d "%s". Assigned default color [%f %f %f]\n',i,obj.cst{i,2},defaultColors(i,1),defaultColors(i,2),defaultColors(i,3));
+    end
+end

matRad/dicom/matRad_dummyCst.m → matRad/dicom/@matRad_DicomImporter/matRad_dummyCst.m

@@ -1,14 +1,14 @@
-function cst = matRad_dummyCst(ct)
+function obj = matRad_dummyCst(obj)
 % matRad function to create a dummy cst struct for a ct
-% 
-% call
-%   cst = matRad_dummyCst(ct)
 %
-% input
-%   ct: matRad ct struct
+% In your object, there should be properties that contain:
+%   - ct structure;
+%   - cst structure.
 %
-% output
-%   cst: matRad cst struct
+% Output - matRad cst structure
+%
+% call
+%   obj = matRad_dummyCst(obj)
 %
 % References
 %   -
@@ -29,21 +29,21 @@
 warning('Did not find RTSS. Creating dummy segmentation for matRad.');
 
 % allocate
-cst = cell(1,6);
+obj.cst = cell(1,6);
 
 % fill
-cst{1,1}          = 0; % first organ has number 0
-cst{1,2}          = 'dummyContour';
-cst{1,3}          = 'OAR';
-cst{1,4}{1}       = find(ct.cubeHU{1}>0.1);        
-cst{1,5}.Priority = 1;       
+obj.cst{1,1}          = 0; % first organ has number 0
+obj.cst{1,2}          = 'dummyContour';
+obj.cst{1,3}          = 'OAR';
+obj.cst{1,4}{1}       = find(obj.ct.cubeHU{1}>0.1);        
+obj.cst{1,5}.Priority = 1;       
 
 % set default parameter for biological planning
-cst{1,5}.alphaX   = 0.1;
-cst{1,5}.betaX    = 0.05;
-cst{1,5}.Visible  = 1;
-cst{1,5}.visibleColor = [0 0 0];
+obj.cst{1,5}.alphaX   = 0.1;
+obj.cst{1,5}.betaX    = 0.05;
+obj.cst{1,5}.Visible  = 1;
+obj.cst{1,5}.visibleColor = [0 0 0];
 
 % define no objcetives   
-cst{1,6}          = [];
+obj.cst{1,6}          = [];