Creating mask of the structure from contour data points

[Suman Gautam]

Hello 

How to plot the mask of the structure from three dimension contour data points? I have three dimesional data points of the structure file. I wnat to plot the structure of that file and say that the oixel value inside the contour points is 0 and outside the contour points is 1. I have attached belwo the contour points.

Thank you 

[Stephen Terry]

For me, the most straightforward way is to use the Shapely library to convert the contour to a Shapely Polygon. You can see it used this way in the CalculateStructureVolume method of the dicomparser class in dicompylercore. A Shapely Polygon has a contains() method that tests if another shapely object (like a Point) lies within it. It can even be vectorized so you can use a 2D numpy array of coordinates. See https://gist.github.com/pelson/9785576

Steve  

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[Suman Gautam]

Thank you very much for the information. 

I have seen some examples for 2D but not for 3D. Calculating structure volume from the class  Dicomplyercore is not obvious for me. I am struggling a lot in spite of these references you provided. Could you please help me creating from those contour data points? 

I appreciate your help.

Thank you very much.

With Best Regards

Suman Gautam

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[Stephen Terry]

Whoops, sorry. I missed that the contour type in your first example was nonplanar. I've only worked with contours like in the example you just posted where the contour is entirely in the z=-52.5 plane. If the contour is entirely in one plane, you can just create a 2D mask for each z slice and stack them together to make a 3D mask. But for non-coplanar contours, I'm not sure how you would do that.

Steve

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[Andrew Miller]

within the python code for DICOMpyler and OnkoDICOM you will find coding examples of how to calculate volumes (i.e., 3D) from RTSTRUCT files which give 2D coordinates.

A

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Prof. Andrew Miller
B.Med, B.Sc, Grad.Dip.Ed, M.Inf.Comm.Tech(Res), FRANZCR, FAIDH, PHF

• Radiation Oncologist, Illawarra Cancer Care Centre, Wollongong, NSW 2500 Australia
• Adjunct Professor of Informatics, School of Informatics, University of Wollongong
  
• Adjunct Professor, Faculty of Health Sciences, University of Ontario Institute of Technology
  
• Director, Centre for Oncology Informatics, University of Wollongong
• Journal Manager, Journal for Radiation Oncology Informatics

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[Andrew Miller]

DICOMpyler does the calculation and displays it on the GUI.

OnkoDICOM does the calculation and saves it inside RTDOSE, and can output it into a CSV file for a single study or a directory of studies.

A

[Suman Gautam]

Hi 

I have an issues in creating a mask for tandem and ovoid in BT. The error is attached below. 

[Andrew Miller]

Are you trying to create ROIs?

A

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[Suman Gautam]

I am trying to create binary mask for tandem and ovoids. ROIs in my restructure files are shown.

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----------------

Regards,

Suman Gautam 

PhD Student

Department of Radiation Oncology.

Division of Medical Physics

VIRGINIA COMMONWEALTH UNIVERSITY

[Suman Gautam]

Hi 

I have an issue creating mask with the DICOM files.

With Best Regards

Suman Gautam

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