How to compile CERR

[Martin]

I am using CERR and made some minor changes. Now I want to use it at
another PC which has no Matlab. I tried to compile CERR using the
deploytool, but when I start the “exe” I get the following error:
??? Index exceeds matrix dimensions.
Error in ==> setOptsExe at 54
Error in ==> OptsExe at 36
Error in ==> CERR at 39
MATLAB:badsubscript

Is there a standard way to compile CERR?

Many thanks
Martin

[ap...@mskcc.org]

Hi Martin,

You can download the compile-able version of CERR from https://github.com/adityaapte/CERR/tree/compiled

i.e. the "compiled" branch of the CERR project on GitHub. Then, use compile_CERR.m function to create a compile.

Workflow to compile CERR:
STEP 1> Download CERR from https://github.com/adityaapte/CERR/tree/compiled
STEP 2> Add all files and folders under CERR to Matlab path.
STEP 3> Create the compile:
compile_CERR('G:\Projects\CERR_compile\CERR_git\CERR','G:\Projects\CERR_compile\CERR_git\compiled');

The above command will create a directory named "compiled" will all necessary contents to run the compiled code. CERR can be launched from the "CERR"-executable file in the newly created "compiled" folder.

If you want to distribute to the machines that do not have Matlab, you need to provide the MCR used to create this compile. Further instructions about the MCR are included in the README file under the "compiled" folder.

Regards,
Aditya

Many thanks
Martin

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[Martin]

Hi Aditya,

Thank you for your answer.
I downloaded the files and used the "compile_CERR('G:\Projects

\CERR_compile\CERR_git\CERR','G:\Projects\CERR_compile\CERR_git

\compiled');" command.
Everything compiled without a major error, but after I start the
"CERR.exe" i get the following weird error message:

??? Invalid field name: 'U:QiB3 (and a lot of other symbols like
arrows and so on).
Error in ==> setfield at 35
Error in ==> setOptsExe at 90
Error in ==> opts4Exe at 49
Error in ==> CERR at 52
MATLAB:Addfield:InvalidFieldName

I used Matlab 2010a und WinXp with standard Matlab compiler.
I didn' t change the files.

Do you have any idea what went wrong?

Many thanks
Martin

[ap...@mskcc.org]

Hi Martin,

The error implies that some field-names in CERROptions.m were not valid. Do
you see CERROptions.m in the same folder as CERR.exe? Can you open
CERROptions.m and make sure it looks valid?

Thanks,
Aditya

[Martin]

Hi Aditya,

Thank you for your answer.

I opened the CERROptions.m which is located in the same folder as
CERR.exe.
I think it is valid. I pasted it below.

Many thanks
Martin


function optS = CERROptions
%function optS = CERROptions
%Initialize all user-defined options for CERR.
%See CERRInstructions.doc (or pdf) for more information about options.

%
%Note: option settings must fit on one line and can contain one
semicolon
%at most.
%Options can be strings, cell arrays of strings, or numerical arrays.
%
%Author: J. O. Deasy, de...@radonc.wustl.edu
%
%Last specifications modified:
% 13 Jan 03, CZ, Added visualReferenceDose.
% 16 Jan 03, JOD, added optS.nudgeDistance.
% 27 Jan 03, JOD, added optS.uniformizeExcludeStructs
% 19 Mar 03, JOD, changed uniformization options (see
below).
% 17 Apr 03, CZ, add downsample parameter for 3D
display.
% 29 Apr 03, JOD, typo.
%
% Copyright 2010, Joseph O. Deasy, on behalf of the CERR development
team.
%
% This file is part of The Computational Environment for Radiotherapy
Research (CERR).
%
% CERR development has been led by: Aditya Apte, Divya Khullar, James
Alaly, and Joseph O. Deasy.
%
% CERR has been financially supported by the US National Institutes of
Health under multiple grants.
%
% CERR is distributed under the terms of the Lesser GNU Public
License.
%
% This version of CERR is free software: you can redistribute it
and/or modify
% it under the terms of the GNU General Public License as
published by
% the Free Software Foundation, either version 3 of the License,
or
% (at your option) any later version.
%
% CERR is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY;
% without even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.
% See the GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with CERR. If not, see <http://www.gnu.org/licenses/>.


%--Import
options----------------------------------------------------------------------
%

optS.loadCT = 'yes'; %('yes' or 'no') Load CT scans into planC?

optS.loadDoseSet = 'any' ; %'final'; %Fraction Group ID (will
match with any Fx Grp ID with the
%same initial letters, independent of case); or to load all this
should be 'any'

optS.loadStructures = {'any'}; %
{'lung','ipsi','contra','gtv','gvt','esoph','gross'};
%({'any'} or cell array of structure names) to load all this should be
{'any'}

optS.CTEndian = 'big'; %('big' or 'little') Byte ordering of CT
scans and digital films.

optS.loadFilm = 'none'; %('any' or 'none') Load digital films?

optS.zipSave = 'yes'; % 'yes' or 'no'; zip the resulting planC
file using bzip2.

optS.scanStructures = {'any'}; %
{'lung','ipsi','contra','gtv','gvt','esoph','gross'};
%{'any'} or {'none'} or a cell array of structure names to convert
%to raster/scan segment format for DVH calculations.

optS.DSHMaxPointInterval = 0.2; %Maximum interval (in cm)
between surface sampling points for dose-surface histograms.

optS.surfPtStructures = {''}; %Any structure whose name matches this
name, up to the number
%of letters given, will have surface points generated
%during import. That is, 'lun' will match 'lung' or 'lung_all'.

%--Dose Import
options-------------------------------------------------------------%
optS.downsampleLargeDoses = 'yes'; %If 'yes', downsamples doses
that are exceptionally large. For example, Corvis
%doses are usually defined at all points on the CT, which can lead to
dose
%distributions that are 300MB+ in size.

optS.doseSizeThreshold = 100; %Maximum size in MB of a dose
array before it will be downsampled. Only active if
%optS.downsampleLargeDoses is 'yes'.

optS.promptForNewSize = 'no'; %If 'yes', prompts the user to input
a voxel size, to be used for the downsampled
%dose distribution. If 'no', uses the value specifed in
optS.downsampledVoxelSize.

optS.downsampledVoxelSize = [.2 .2 .3];%Size of a voxel in the
downsampled dose distribution, [dx, dy, dz].




%--Scan uniformization
options---------------------------------------------------------%

%Given a set of CT values, we choose the largest block which CT slice
spacing which
%falls within the limits of optS.lowerLimitUniformCTSliceSpacing and
optS.upperLimitUniformCTSliceSpacing.
%Otherwise we create a set with a spacing equal to
optS.alternateUniformCTSliceSpacing. If the user desires
%a uniformized scan with a spacing of exactly
optS.alternateUniformCTSliceSpacing, then set
optS.lowerLimitUniformCTSliceSpacing
%to be larger than optS.upperLimitUniformCTSliceSpacing.

optS.createUniformizedDataset = 'yes'; %'yes' or 'no'. Create
uniformized & registered CT and structures datasets
%during import. The uniformized scan set has a uniform axial (z)
spacing
%and the same transverse resolution as the normal CT-scan (usually,
but
%not always, 512 x 512).

optS.uniformizeExcludeStructs = {'normaltissue', 'CT_EXTERNAL'};
% optS.uniformizeExcludeStructs = {'normaltissue', 'skin',
'CT_EXTERNAL'};
%cell array of structures to leave out of uniformization process. In
particular,
%leaving out skin increases program speed and decreases memory
requirements.

optS.uniformizedDataType = 'uint16'; %'uint8' or 'uint16'.
Datatype for uniformized dataset.

optS.structureArrayDataType = 'uint32'; %'uint32' or 'double'.
Datatype used to create uniformized structure array. Effectively sets
%max structures in a plan to 32 or 52 -- the number of bits in the
respective datatypes.

optS.lowerLimitUniformCTSliceSpacing = 0.05; %Smallest allowed
uniformized slice spacing. We take the largest block which is
%within the smallest and largest slice spacing requirements, inclusive
of the endpoints.

optS.upperLimitUniformCTSliceSpacing = 10; %Largest allowed
uniformized slice spacing.

optS.alternateLimitUniformCTSliceSpacing = 0.3; %If there are no
initial CT slices between the largest and smallest slice
%width allowed, make a uniformized dataset with this width.

%--Slice viewer
options----------------------------------------------------------------
%

optS.useOpenGL = 1; %1 to use openGL, 0 to avoid openGL.

optS.isodoseLevelMode = 'auto'; %'auto' or 'manual'. Auto
calculates isodose lines automatically.

optS.isodoseLevels = [70, 65, 60, 55, 50, 45, 40, 20, 10]; %Isodose
levels to show if optS.isodoseLevelMode = 'manual'.

optS.autoIsodoseLevels = 6; %Number of levels displayed if
optS.isodoseLevelMode = 'auto'.

optS.autoIsodoseRangeMode = 1; %Range used for
autoIsodoseLevels. Takes 1 or 2, where 1 is max/min, and 2 is user
defined.

optS.autoIsodoseRange = [0 100]; %Default range used for
autoIsodoseLevels if optS.autoIsodoseRangeMode = 'User'.

optS.isodoseLevelType = 'absolute'; %or 'absolute'

optS.isodoseUseColormap = 1; %1 if isodose lines should take
use colorbar values to determine their color.

optS.isodoseThickness = 1; %Thickness of isodose lines

optS.structureThickness = 2; %Thickness of structure lines

optS.structureDots = 1; %Set to 0 to disable black dots on
structure lines.

optS.displayDoseSet = ''; %The dose distribution to be displayed.
Defaults to the
%first dose distribution if this is not available.

optS.tickInterval = 1; %Ruler tick interval in cm.

optS.CTLevel = 0; %Beginning CT level and width

optS.CTWidth = 300;

optS.fontsize = 8; %user-interface font size

optS.UIColor = [1 1 1]*0.9;%Color of ui buttons

optS.colorOrder = reshape([1.0 0.7 0 0 1 0 1 0 0 0 0.9 0.9 0.75 0
0.75 0.75 0.75 0 0.6 0.75 1 0.8 0.25 0.25 1 0 1 0.75 0.5 0 0 1 0.50
1 0.5 1 0.5 1 0 0.3 0 0.9 0 0.7 0.3 0.7 0.3 0 0 0.8 0.9 0.7 0 0.8
0.9 0.6 0 0.33 0.66 1 1 0.33 0.33 1 0 0.9 0.9 0.5 0 0 1 0.40 0.9 0.6
0.9 0.6 0.9 0 0.7 0.4 0.8 0.6 0.9 0.2] * 0.9,3,28)';
%set color of contours. Each 3 number triple is r, g, b. Note: do
not put commas into the colorOrder

optS.inactiveSegStyle = '--'; %Style for inactive contouring
segments

optS.activeSegStyle = '-'; %Style for active contouring
segments

optS.displayPatientName = 0; %1 ('on') or 0 ('off').

optS.initialZoomTrans = 1.7; %Initial transverse zoom factor

optS.initialZoomSag = 1.0; %Initial saggital zoom factor

optS.initialZoomCor = 1.0; %Initial coronal zoom factor

optS.zoomFactor = 2.0; %x-y scale factor when zooming.

optS.dosePlotType = 'colorwash';%Method of dose distribution display:
'isodose' or 'colorwash'.

optS.doseColormap = 'starinterp'; %Colormap for dose colorwash. It
is read from CERRColormap.m.
%Options: 'jetmod' (modified jet), 'full' (full rainbow), 'ppt'
%(powerpoint based) 'star (14 non-blending colors)', 'starinterp',
'gray' or 'gray256'.

optS.CTColormap = 'gray256'; %CT colormap, usually grayscale. Also
read from CERRColormap.m.
%Same choices as optS.doseColormap.

optS.colorbarChoices = {'jetmod', 'ppt', 'full', 'full2', 'star',
'starinterp', 'gray', 'gray256', 'grayud64', 'doublecolorinvert',
'thedrewspecial', 'graycenter0width300', 'hotcold', 'copper'};

optS.staticColorbar = 0; %Set to 1 to have the same colors
represent the same dose values when switching between does
distributions.

optS.transparentZeroDose = 1; %If 1, dose that is zero is
always transparent even if the colorbar suggests it should have color.

optS.doubleSidedColorbar = 0; %If 1, the colorbar is inverted
onto itself to create a double headed colorbar that is useful for
viewing negative values.

optS.negativeTexture = 1; %If 1, negative values (those <
doseOffset) are displayed with a raster texture.

optS.colorbarMarks = []; %Ticks on colorbar to indicate these
doses, in Gy. Examples: [70], [50,70].
%To leave it empty, type [].

optS.visualRefColormapRows = 256; %Number of rows in visual
reference colorwash colormap.

optS.visualRefTopColormap = 'grayud64';%Colormap between
optS.visualRefDose and max dose.

optS.visualRefBottomColormap = 'full2'; %Colormap between zero dose
and optS.visualRefDose.

optS.visualRefDose = 65; %If optS.visualReferenceDoseMode is
'on', the color in the dose colorwash
%at this dose will be white. The colormap above this dose will be
modified.
%That is, it will be easy to pick out this dose.

optS.visualRefDoseMode = 'off'; %['on' or 'off'] If 'on', the
color in the dose colorwash at
%optS.visualReferenceDose will be white. The colormap above that dose
will be
%modified. That is, it will be easy to pick out the reference dose.

optS.initialTransparency = .5; %0-1, percentage of alpha for
colorwash. 1 is opaque, 0 transparent. Allows
%CT to be seen through wash.

optS.calcDoseInsideSkinOnly = 0; %only calculate dose inside
the skin on the transverse viewer. Enable for increased speed.

optS.CERRStatusStringEnabled = 1; %Change to zero to mute all
CERRStatusString outputs to GUI and Matlab prompt.

%--Image Fusion
options----------------------------------------------------------------
%

optS.fusionDisplayMode = 'colorblend'; %'colorblend', 'checked',
'max', or 'canny'.

optS.fusionCheckSize = 2; %size in cm of each side of
checkerboard elements.

optS.fusionAlgorithms = {'Manual', 'ControlPts - Affine', 'ControlPts
- Perspective', 'Exhaustive Search - MI', 'Stocastic - MI', 'Contour
Based'};
optS.fusionTemplates = {@Manual, @CTP_Affine, @CTP_Perspective,
@Exhaustive, @Stocastic, @ContourBased};


%--3D display
option-------------------------------------------------------------------
%

optS.visual3DxyDownsampleIndex = 128; %e.g., 128. Downsample to
this resolution in the transverse plane for 3D display

%--Dose Profile
option-----------------------------------------------------------------
%

optS.numDoseProfileSamples = 200; %The number of samples to take
along dose profile lines.


%--DVH/DSH
options---------------------------------------------------------------------
%

optS.ROISampleRate = 1; %(integer >= 1) Rate of ROI sampling
compared to CT spacing, for DVH computations.


optS.DVHBinWidth = 0.2; %Store and display DVHs with this width,
in units of Gy.


optS.DVHBlockSize = 5000; %Block processing parameter. 5000 is
the default. This results in much less temporary
%storage for large structure DVH computations. If there is disk-
thrashing during
%the DVH calculation, try reducing this number first.

optS.DVHLineWidth = 1.5; %Line thickness of DVH and DSH lines.

%--IVH (Intensity Volume Histogram)
options---------------------------------------------------------------------
%

%optS.ROISampleRate = 1; Uses the same as DVH


optS.IVHBinWidth = .2; %Store and display IVHs with this width,
in units of Gy.


optS.IVHBlockSize = 5000; %Block processing parameter. 5000 is
the default. This results in much less temporary
%storage for large structure IVH computations. If there is disk-
thrashing during
%the IVH calculation, try reducing this number first.

optS.IVHLineWidth = 1.5; %Line thickness of IVH lines.

%List of standard VOI names for renaming DVH's for export.
optS.defaultVOINames = {'GTV', 'CTV', 'PTV', 'spinal cord', 'heart',
'total lung', 'rt kidney', 'lt
kidney','aaaaaaaaaaaaaaaaaaaaa','b','c','d','e','f','g','h','i','j','k','l','m'};


%--Contouring
options------------------------------------------------------------------
%

optS.nudgeDistance = 0.5; %Number of voxel widths to nudge the
active contour.


%--Navigation montage
options----------------------------------------------------------%

optS.navigationMontageColormap = 'grayCenter0Width300';
optS.navigationMontageOnImport = 'no'; %'yes' or 'no'. Do or do
not create thumbnails on import.
optS.navigationMontage = 'no'; %'yes' or 'no'. Do or do not
display navigation montage when the CERR viewer is started.


%--Wavelet dose compression
options----------------------------------------------------%

optS.wavletcompresthreshpersent = 1; % CZ add wavelet
compression parameters 04-24-03
optS.wavletcompressiondecomplevel = 5;


%--IMRT
options------------------------------------------------------------------------
%
optS.IMRTCheckResolution = 'on'; %If original plan is 512x512,
downsample by factor of 2 if 'on'.

%List of installed dose calculation algorithms. First is the string
to
%describe the algorithm, second is a function handle pointing to code
%that returns a template of options required for the algorithm, and
last
%is the function handle to execute the algorithm. The function will
get
%an IM structure and the structure of its options on execution.
optS.IMRTDoseCalculationAlgorithms = {'QIB', 'VMC++'};
optS.IMRTDoseCalculationTemplates = {@getQIBTemplate,
@getVMCTemplate};
optS.IMRTDoseCalculationFunction = {@generateQIBInfluence,
@generateVMCInfluence};

optS.IMRTScatterReductionAlgorithms = {'Exponential', 'Probabilistic',
'Threshold', 'None'};
optS.IMRTScatterReductionTemplates = {@ExponentialTemplate,
@ProbabilisticTemplate, @ThresholdTemplate, @NoneTemplate};

optS.IMRTAutoIsocenterAlgorithms = {'GeometricCOM','Manual'};
optS.IMRTAutoIsocenterFunctions = {@isocenterGeometricCOM,
@isocenterManual};




%--planMetrics
options-----------------------------------------------------------------
%

optS.planMetrics = {'meanDose', 'maxDose', 'minDose', 'Vx', 'Dx',
'EUD', 'ERP', 'LKB', 'stdDevDose','MOCx','MOHx'};
%Installed metrics. Metrics must be added to metricSelection.m in the
"%function"
%command for the compiled version


%--Window presets - name, center, width !do not remove Manual dummy
preset! (#1) ----%

optS.windowPresets = [struct('name', '--Manual--', 'center', 0,
'width', 0) struct('name', 'Abd/Med', 'center', -10, 'width', 330)
struct('name', 'Head', 'center', 45, 'width', 125) struct('name',
'Liver', 'center', 80, 'width', 305) struct('name', 'Lung', 'center',
-500, 'width', 1500) struct('name', 'Spine', 'center', 30, 'width',
300) struct('name', 'Vrt/Bone', 'center', 400, 'width', 1500)
struct('name', 'PET', 'center', 4500, 'width', 11000) struct('name',
'MR', 'center', -500, 'width', 1350) struct('name', 'SPECT', 'center',
400, 'width', 1000) struct('name', 'Top 90', 'center', 400, 'width',
1000)];

%--Color Map base
scan----------------------------------------------------%
optS.scanColorMap = [struct('name', 'Gray') struct('name', 'copper')
struct('name', 'Red') struct('name', 'Green') struct('name', 'Blue')
struct('name', 'StarInterp')];

%--Caching
Options--------------------------------------------------------%
optS.cachingEnabled = 0; % set to 1 to enable caching, 0 to disable.
optS.colorWashCacheSize = 64; %Amount of memory to use per dose for
caching colorwash. In megabytes.


%--Matlab 7 compatibility
Options-----------------------------------------%
optS.saveFormat = '-V6'; %Set to [] to use default, '-V6' to save all
files in Matlab6 readable format.
%V6 is used to maintain Matlab 7 backwards compatibility with version
6+.

optS.plotObjFormat = 'v6'; %Flags for plotObjects that changed, and
introduced incompability between
%Matlab 7 and old versions.


%--Lab Book email
options-------------------------------------------------%
% setpref('Internet', 'E_mail', 'jal...@radonc.wustl.edu');
% setpref('Internet', 'SMTP_Server', 'mail.artsci.wustl.edu');
% optS.emailAddresses =
{'dkhu...@radonc.wustl.edu','aa...@radonc.wustl.edu','de...@radonc.wustl.edu'};

%--microRT
options--------------------------------------------------------%
optS.chkMicroRT = 0;

%--Compression-type
options-----------------------------------------------%
optS.CompressType = 'bz2'; %set to 'zip' or 'bz2'

%--Batch
Process----------------------------------------------------------%
optS.format = 'DICOM';

%--Initial Panel
Layout--------------------------------------------------------------%
optS.layout = 5; %1:1-Large, 2:1-Large+Bar, 3:2-Medium, 4:4-Medium,
5:1-Large+3-Small

%--Generate Log on Start-
up--------------------------------------------------------------%
optS.logOnStartup = 0; %1:yes - generate log, 0:No - don't generate
log

%--Temporary Directory to extract
bz2--------------------------------------------------------------%
optS.tmpDecompressDir = ''; %'': tempdir, 'C:\tempCERRExtract'

%--ROI Interpreted Type
optS.ROIInterpretedType = initROIInterpretedType;
%--RPC film
options-------------------------------------------------------%

%-- Option to convert PET to SUV
optS.convert_PET_to_SUV = 0; % 0: Do not convert to SUV, 1: Convert to
SUV


%-------------------------------------------
fini--------------------------%

On Apr 9, 4:46 pm, ap...@mskcc.org wrote:
> Hi Martin,
>
> The error implies that some field-names in CERROptions.m were not valid. Do
> you see CERROptions.m in the same folder as CERR.exe? Can you open
> CERROptions.m and make sure it looks valid?
>
> Thanks,
> Aditya
>

> On 4/9/12 10:30 AM, "Martin" <mm.wittm...@googlemail.com> wrote:
>