IO data in FreeART

Main inputs and outputs data for FreeART are : They are structured as presented :

• sinogram : This is the output of a projector (forward projection) and the input of a reconstruction algorithm.

  It is a 3D vector but for now we only take into account 2D sinograms. Shape should be :

  • first dimension for now should always be 1 until we stay in 2D.
  • second dimension is the number of projections.
  • third dimension is the definition of the detector (number of cell). We will simulate one ray per cell during the reconstruction.

• phantom : This is the input of a projector and the output of a reconstruction. This is a voxelisation of the sample. Shape is the following :

  • first dimension : represents the x axis of the phantom voxelisation (should be equal to the third dimension of the sinogram )
  • second dimension : represents the y axis of the phantom voxelisation (should be equal to the third dimension of the sinogram and to the first dimension of the phantom )
  • third dimension : for now should always be 1 until we stay in 2D.

• absorption matrices : In the case of fluorescence we can add the effect of the incoming beam absorption (with the absorption matrix)) AND the outgoing beam absorption (with the self absorption matrix).

  This can be an input for the sinogram generation (in compton or in fluorescence) or during a reconstuction. The shape of those matrices are mimicking the phantom structure. At each voxel we set the absorption in \(g.cm^{-2}\).