freeart.interpreter

Python module to build and run a freeart reconstruction from a configuraton file (.cfg file).

freeart.interpreter.configinterpreter: config file management

Create the link between freeart and a configuration file. Basically set up a reconstruction

class freeart.interpreter.configinterpreter.AbsConfInterpreter(filePath, _config)

Abstract class from which each interpreter (fluorescence, tx…) should inherit

resetAngles()

Reset all angles

iterate()

Iterate on the reconstruction. Each iteration generate a backward projection for each angle of acquisition (in a random order).

getFile()

Returns:the current configuratioin file

setLimitParallelReconstruction(val)

Limit the number of parallel reconstruction we can run

Parameters:val – the new limitation of parallel reconstructions to run

setLimitVoxels(val)

Limit the maximal number of voxel we can run during one iteration

Parameters:val – the maximal number of voxel to run during one step.

adaptSinogramData(data, isI0=False)

center, reduce sinogram (X definition and number of projection) and pick the range of projection requested.

Parameters:

• data –
• computeAngles – If true then compute self.angles

Returns:

data adapted to constrain

getSinograms()

Returns:A dictionnary of the sinograms to treat

class freeart.interpreter.configinterpreter.TxConfInterpreter(filePath, _config=None)

Interpreter for tx reconstruction

Parameters:filePath – the path of the cfg file

getReconstructionAlgorithms()

Returns:the dictionay of the freeart reconstruction.

iterate(nbIteration)

Iterate on the reconstruction. Each iteration generate a backward projection for each angle of acquisition (in a random order).

class freeart.interpreter.configinterpreter.FluoConfInterpreter(filePath, _config=None)

FreeART interpreter for fluorescence reconstruction. Basicall y take a .cfg file containing the description of the reconstruction in input and create all corresponding ARTAlgorithm for such reconstructions

Parameters:filePath – the configuration file to be interpreted.

fisxMaterials = None

Dict to associate at each material in the sample the corresponding fisx materials

selfAbsMatFile = None

File where to get the selfAbsMat file in case the user give them

absMatrixFile = None

The file of the absorption matrix file

fluoSinogramsAlgorithms = None

all the art algorithm to fit the configuration file

fluoSinograms = None

sinograms to treat

interactionMatrice = None

the interaction matrices

static getProbabilityOfEmission(energy, element, fisxElements, shell=None)

compute the probability of emission of the element for a specific energy and material.

Parameters:

• fisxMat – the fisx material of the interaction
• energy – the nergy of the incomng beam
• element – the generated element
• shell – the targetted shell of the interaction.

Returns:

the probability of emission of the element for a specific energy and material.

getReconstructionAlgorithms()

Returns:all the algorithm created for reconstructions

iterate(nbIteration)

Iterate on the reconstruction. Each iteration generate a backward projection for each angle of acquisition (in a random order).

getDensityPhantoms()

Return the phantom taking into account the probability of generation of the physical element