Victre.Pipeline.Pipeline Class Reference

Victre Pipeline class. More...

Public Member Functions
def	__init__
	Object constructor for the Victre pipeline class. More...
def	project
	Method that runs MCGPU to project the phantom. More...
def	reconstruct
	Method that runs the reconstruction code for the DBT volume. More...
def	get_coordinates_dbt
	Method to get the corresponding coordinates in the DBT volume from the voxelized coordinates. More...
def	get_coordinates_dm
	Method to get the corresponding coordinates in the DM volume from the voxelized coordinates. More...
def	save_DICOM
	Saves the DBT generated reconstruction (if available) in DICOM format. More...
def	save_ROIs
	Saves the generated ROIs (absent and present) in RAW and HDF5 formats. More...
def	get_folder_contents
	Gets a list of files in the given folder. More...
def	generate_spiculated
	Generates a spiculated mass using the breastMass software. More...
def	insert_lesions
	Inserts the specified number of lesions in the phantom. More...
def	add_absent_ROIs
	Adds the specified number of absent regions of interest. More...

Public Attributes
	seed
	ip
	lesion_file
	lesions
	lesion_locations
	arguments_mcgpu
	materials
	flatfield_file
	arguments_recon
	recon_size

Detailed Description

Victre Pipeline class.

This is all you need!

Constructor & Destructor Documentation

def Victre.Pipeline.Pipeline.__init__	(		self,
			ip,
			seed = None,
			phantom_file = "phantom/pcl_2132574818_crop.raw.gz",
			spectrum_file = "./Victre/projection/spectrum/W28kVp_Rh50um_Be1mm.spc",
			lesion_file = None,
			materials = None,
			arguments_mcgpu = dict(),
			arguments_recon = dict(),
			flatfield_file = None
	)

Object constructor for the Victre pipeline class.

Parameters

ip	IP address to run the projection (GPU enabled)
seed	Random seed used to generate or read the phantom
phantom_file	Path to file containing the phantom to be loaded
spectrum_file	Path to file containing the spectrum used to project in MCGPU
lesion_file	Path to file containing the lesion to be inserted (in HDF5 format)
materials	Dictionary including the materials to be used during projection
arguments_mcgpu	Arguments to be overridden for the projection in MCGPU
arguments_recon	Arguments to be overridden for the reconstruction algorithm
flatfield_file	Path to the flatfield file for projection

Returns

None

Member Function Documentation

def Victre.Pipeline.Pipeline.add_absent_ROIs	(		self,
			lesion_type,
			n = 1,
			locations = None,
			roi_sizes = None
	)

Adds the specified number of absent regions of interest.

Parameters

lesion_type	Constant with the desired lesion type. Check available lesion types and materials in the Constants file.
n	Number of lesions to be added
locations	List of coordinates in the voxel/phantom space where the lesions will be inserted. If not specified, random locations will be generated.
roi_sizes	Size of the region of interest to be calculated to avoid overlapping with other tissues and check out of bounds locations

Returns

None. A location file will be saved inside the phantom folder with the corresponding seed. Negative lesion type means absent ROI.

def Victre.Pipeline.Pipeline.generate_spiculated	(		self,
			seed,
			size
	)

Generates a spiculated mass using the breastMass software.

Parameters

seed	Seed to be used when generating the mass
size	Size of the mass to be used in the breastMass config file

Returns

None. The result is saved in the lesions subfolder

def Victre.Pipeline.Pipeline.get_coordinates_dbt	(		self,
			vx_location
	)

Method to get the corresponding coordinates in the DBT volume from the voxelized coordinates.

Parameters

vx_location

Coordinates in the voxel/phantom space

Returns

Coordinates in the DBT space

def Victre.Pipeline.Pipeline.get_coordinates_dm	(		self,
			vx_location
	)

Method to get the corresponding coordinates in the DM volume from the voxelized coordinates.

Parameters

vx_location

Coordinates in the voxel/phantom space

Returns

Coordinates in the DM space

def Victre.Pipeline.Pipeline.get_folder_contents	(		self,
			folder
	)

Gets a list of files in the given folder.

Parameters

folder

Path to the folder to be processed

Returns

List with files inside the given folder

def Victre.Pipeline.Pipeline.insert_lesions	(		self,
			lesion_type,
			n = 1,
			lesion_file = None,
			locations = None,
			roi_sizes = None
	)

Inserts the specified number of lesions in the phantom.

Parameters

lesion_type	Constant with the desired lesion type. Check available lesion types and materials in the Constants file.
n	Number of lesions to be added
lesion_file	Path to file including the lesion to be inserted (in HDF5 format). If specified, it will overrite the lesion file specified in the constructor.
locations	List of coordinates in the voxel/phantom space where the lesions will be inserted. If not specified, random locations will be generated.
roi_sizes	Size of the region of interest to be calculated to avoid overlapping with other tissues and check out of bounds locations

Returns

None. A location file will be saved inside the phantom folder with the corresponding seed. Positive lesion type means absent ROI.

def Victre.Pipeline.Pipeline.project

(

self

)

Method that runs MCGPU to project the phantom.

def Victre.Pipeline.Pipeline.reconstruct

(

self

)

Method that runs the reconstruction code for the DBT volume.

def Victre.Pipeline.Pipeline.save_DICOM

(

self

)

Saves the DBT generated reconstruction (if available) in DICOM format.

def Victre.Pipeline.Pipeline.save_ROIs	(		self,
			roi_sizes
	)

Saves the generated ROIs (absent and present) in RAW and HDF5 formats.

Parameters

roi_sizes

Size of the ROIs for the defined lesion types

Member Data Documentation

Victre.Pipeline.Pipeline.arguments_mcgpu

Victre.Pipeline.Pipeline.arguments_recon

Victre.Pipeline.Pipeline.flatfield_file

Victre.Pipeline.Pipeline.ip

Victre.Pipeline.Pipeline.lesion_file

Victre.Pipeline.Pipeline.lesion_locations

Victre.Pipeline.Pipeline.lesions

Victre.Pipeline.Pipeline.materials

Victre.Pipeline.Pipeline.recon_size

Victre.Pipeline.Pipeline.seed

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The documentation for this class was generated from the following file:

• Victre/Pipeline.py