utils

freeart.utils

Python utils for freeart.

freeart.utils.reconstrutils: some utils linked to the reconstruction

freeart.utils.reconstrutils.decreaseMatSize(mat)

will decrease the matrice size if possible where one dimension has only one element

freeart.utils.reconstrutils.increaseMatSize(mat, firstPos)

Simple function which will add a dimension to the current matrice

Parameters:

• mat – the matrice for which we want to remove a dimension
• firstPos – if true remove the first position else remove the last

freeart.utils.reconstrutils.savePhantom(data, fileName, overwrite=False)

will create an edf file to store the given data

Parameters:

• data – the data to save
• fileName – the localisation to know where to save the data

freeart.utils.reconstrutils.LoadEdf_2D(fName, frame=0)

Load data from the given edf file

Parameters:

• fName – the name of the file
• frame – if multiple frame file, will use theis parameter to load a specific frame

freeart.utils.reconstrutils.makeFreeARTFluoSinogram(phantom, absMat, selfAbsMat, numAngle, detSetup, oversampling, beamCalcMeth, outRayPtCalcMeth, minAngle=0.0, maxAngle=6.283185307179586, subdivisionValue=3, turnOffSolidAngle=False, I0=1.0, voxelSize=1.0)

Generate the fluorescence sinogram

Parameters:

• phantom – The initial phantom (density * probability of emission of photon...)
• absMat – absorption of the incoming. Aka \({\mu}_{E_0}{\rho}x\)

Returns:

• sinogram (numpy array of float64 )
• angles list of angles of projection

Warning

all angle values must be given in rad

freeart.utils.reconstrutils.convertToFisxMaterial(materialName, material)

convert a material defined in a dictionnary (from tomoGUI for example. Used to be saved and loaded ) in a fisx Material. Won’t do the registration

Parameters:

• materialName – the name to attribute to the fisx material
• material – the material defined in a dictionary

Returns:

the fisx material

initial material structure looks like : materialName = “My_mat” material = {‘Comment’:”No comment”,

‘CompoundList’:[‘Cr’, ‘Fe’, ‘Ni’], ‘CompoundFraction’:[18.37, 69.28, 12.35], ‘Density’:1.0, ‘Thickness’:1.0}

Final structure is a fisx Material : steel = {“Cr”:18.37,

“Fe”:69.28, # calculated by subtracting the sum of all other elements “Ni”:12.35 }

material = Material(“My_mat”, 1.0, 1.0) material.setComposition(steel)

freeart.utils.genph: phantom generator

class freeart.utils.genph.PhantomGenerator

Bases: object

Class for generating different Phantoms

get3DPhantomSheppLogan(n)

Parameters:n – The width (and height) of the phantom to generate Returns:A numpy array of dimension n*n fit with the sheppLogan phantom

get2DPhantomSheppLogan(n, ellipsoidID=None)

Parameters:

• n – The width (and height) of the phantom to generate
• ellipsoidID – The Id of the ellipsoid to pick. If None will produce all the ellipsoid

get2DPhantomMetal(n, ellipsoidID=None)

Parameters:

• n – The width (and height) of the phantom to generate
• ellipsoidID – The Id of the ellipsoid to pick. If None will produce all the ellipsoid

freeart.utils.benchmark: tool for benchmarking

Benchmark file.

freeart.utils.benchmark.benchmark_tx_projection(oversamplings, widthsToTest, nbAngle)

Create a graph for benchmarking the transmission forward projector

Parameters:

• oversamplings – the list of oversamplings to test
• widthsToTest – the list of phantom width to test
• nbAngle – the number of projection to test

freeart.utils.benchmark.benchmark_tx_reconstruction(oversamplings, widthsToTest, nbAngle, nbIter)

Create a graph for benchmarking the transmission reconstructor

Parameters:

• oversamplings – the list of oversamplings to test
• widthsToTest – the list of phantom width to test
• nbAngle – the number of projection to test
• nbIter – the number of iteration to test (one iteration launch nbAngle back projection)

freeart.utils.benchmark.benchmark_fluo_projection(oversamplings, widthsToTest, nbAngle, outgoingraypointsmethods)

Benchmark the fluo projection

Parameters:

• oversamplings – the list of oversamplings to test
• widthsToTest – the list of phantom width to test
• nbAngle – the number of projection to test
• outgoingraypointsmethods – the list of outgoingrayalgorithm to test

freeart.utils.benchmark.benchmark_fluo_reconstruction(oversamplings, widthsToTest, nbAngle, outgoingraypointsmethods, nbIter)

benchmark the fluo reconstruction

Parameters:

• oversamplings – the list of oversamplings to test
• widthsToTest – the list of phantom width to test
• nbAngle – the number of projection to test
• outgoingraypointsmethods – the list of outgoingrayalgorithm to test
• nbIter – the number of iteration to test (one iteration launch nbAngle back projection)