cerr.registration package

Submodules

cerr.registration.register module

The register module defines routines for registering and deforming scans, structures and does distributions. It also provies routines for calculating vector field and Jacobian from deformation transformation.

cerr.registration.register.registerScans(basePlanC, baseScanIndex, movPlanC, movScanIndex, transformSaveDir, deforAlgorithm='bsplines', registrationTool='plastimatch', baseMask3M=None, movMask3M=None, inputCmdFile=None)[source]
Parameters:

  • basePlanC (cerr.plan_container.PlanC) – pyCERR plan container containing fixed target scan

  • baseScanIndex (int) – integer, identifies target scan in basePlanC

  • movPlanC (cerr.plan_container.PlanC) – pyCERR plan container containing moving scan

  • movScanIndex (int) – integer, identifies moving scan in movPlanC

  • transformSaveDir (str) – Directory to save transformation file

  • registration_tool (str) – registration software to use (‘PLASTIMATCH’,’ELASTIX’,’ANTS’)

  • baseMask3M (numpy.ndarray) – optional, 3D or 4D binary mask(s) in target space

  • movMask3M (numpy.ndarray) – optional, 3D or 4D binary mask(s) in moving space

  • inputCmdFile (str) – optional, path to registration command file

Returns:

plan container object basePlanC with an element added to planC.deform attribute

Return type:

cerr.plan_container.PlanC

cerr.registration.register.warpScan(basePlanC, baseScanIndex, movPlanC, movScanIndex, deformS)[source]

Routine to deform moving scan to fixed scan based on input transformation

Parameters:
Returns:

plan container object basePlanC with the deformed scan added to planC.scan attribute

Return type:

cerr.plan_container.PlanC

cerr.registration.register.warpDose(basePlanC, baseScanIndex, movPlanC, movDoseIndex, deformS)[source]

Routine to deform moving dose to fixed scan based on input transformation

Parameters:
Returns:

plan container object basePlanC with the deformed dose added to planC.dose attribute

Return type:

cerr.plan_container.PlanC

cerr.registration.register.warpStructures(basePlanC, baseScanIndex, movPlanC, movStrNumV, deformS)[source]

Routine to deform moving structures to fixed scan based on input transformation

Parameters:

  • basePlanC (cerr.plan_container.PlanC) – pyCERR plan container containing fixed target scan

  • baseScanIndex (int) – index of fixed scan in planC.scan

  • movPlanC (cerr.plan_container.PlanC) – pyCERR plan container containing moving scan

  • movStrNumV (int) – list of indices of moving structures in planC.structure

  • deformS (cerr.dataclasses.deform.Deform) – pyCERR’s deformation transformation object

Returns:

plan container object basePlanC with the deformed structures added to planC.structure attribute

Return type:

cerr.plan_container.PlanC

cerr.registration.register.calcVectorField(deformS, planC, baseScanNum, transformSaveDir)[source]

Routine to generate a vector field file from input pyCERR transformation object

Parameters:

  • deformS (cerr.dataclasses.deform.Deform) – pyCERR’s deformation transformation object

  • planC (cerr.plan_container.PlanC) – pyCERR’s plan container

  • baseScanNum (int) – index of fixed scan from planC.scan

  • transformSaveDir (str) – path to directory for storing the vector field file

Returns:

plan container object basePlanC with the deformed structures added to planC.structure attribute

Return type:

cerr.plan_container.PlanC

cerr.registration.register.calcJacobian(deformS, planC, tool='plastimatch')[source]

Routine to compute Jacobian of vector field

Parameters:

Returns:

cerr.registration.register.getDvfVectors(deformS, planC, scanNum, outputResV=[0, 0, 0], structNum=None, surfFlag=False)[source]

Routine to obtain dvf vectors

Parameters:

  • deformS (cerr.dataclasses.deform.Deform) – pyCERR’s deformation transformation object

  • planC (cerr.plan_container.PlanC) – pyCERR’s plan container

  • scanNum (int) – index for scan in planC.scan

  • outputResV (ist) – optional, grid resolution for output vectors. Used only when surfFlag is False.

  • structNum (int) – optional, index of planC.structure to restrict the vector calculation

  • surfFlag (bool) – optional, flag to calculate vectors on the surface of structNum

Returns:

(n x 2 x 3) vectors where 1st element in the 2nd dimension represents the start coordinates in

pyCERR r,c,s units and 2nd element in the 2nd dimension represents deformation y,x,z in cm in pyCERR virtual coordinates.

Return type:

(numpy.ndarray)

Module contents