opentps.core.io package

Submodules

opentps.core.io.dataExporter module

class DataType(name: str, exportTypes: Sequence)

Bases: object

Class to store the export types for a specific data type

Variables:

  • name (str) – The name of the data type

  • exportTypes (Sequence) – The export types for this data type

  • exportType (ExportTypes) – The export type to use

class ExportConfig

Bases: object

gives all the export configuration to store the data (depending on the data type)

Variables:

  • imageConfig (DataType) – The image data type configuration

  • doseConfig (DataType) – The dose data type configuration

  • planConfig (DataType) – The plan data type configuration

  • contoursConfig (DataType) – The contours data type configuration

  • otherConfig (DataType) – The other data type configuration

property contoursConfig: DataType
property doseConfig: DataType
property imageConfig: DataType
property otherConfig: DataType
property planConfig: DataType
class ExportTypes(value)

Bases: Enum

Enumeration of the different export types

DICOM = 'Dicom'
MCSQUARE = 'MCsquare'
MHD = 'MHD'
PICKLE = 'Pickle'
exportImage(image: Image3D, folderPath: str, imageConfig: ExportTypes)

Exports the image to the given folder path.

Parameters:

  • image (Image3D) – The image to export

  • folderPath (str) – The folder path to export to

  • imageConfig (ExportTypes) – The export configuration

exportPatient(patient: Patient, folderPath: str, config: ExportConfig)

Exports the patient data to the given folder path.

Parameters:

  • patient (Patient) – The patient to export

  • folderPath (str) – The folder path to export to

  • config (ExportConfig) – The export configuration

exportPatientAsDicom(patient: Patient, folderPath: str)

Exports the patient data to the given folder path as dicom.

Parameters:

  • patient (Patient) – The patient to export

  • folderPath (str) – The folder path to export to

exportPlan(plan: RTPlan, folderPath: str, planConfig: ExportTypes)

Exports the plan to the given folder path.

Parameters:

  • plan (RTPlan) – The plan to export

  • folderPath (str) – The folder path to export to

  • planConfig (ExportTypes) – The export configuration

opentps.core.io.dataLoader module

get_file_type(filePath)
listAllFiles(inputPaths, maxDepth=-1)

List all files of compatible data format from given input paths.

Parameters:

  • inputPaths (str or list) – Path or list of paths pointing to the data to be listed.

  • maxDepth (int, optional) – Maximum subfolder depth where the function will check for files to be listed. Default is -1, which implies recursive search over infinite subfolder depth.

Returns:

fileLists – The function returns a dictionary containing lists of data files classified according to their file format (Dicom, MHD).

Return type:

dictionary

loadData(patientList: PatientList, dataPath: str, maxDepth=-1, ignoreExistingData: bool = True, importInPatient: Patient | None = None)

Load all data found at the given input path.

Parameters:

  • patientList (PatientList) – The patient list to which the data will be added.

  • dataPath (str or list) – Path or list of paths pointing to the data to be loaded.

  • maxDepth (int, optional) – Maximum subfolder depth where the function will check for data to be loaded. Default is -1, which implies recursive search over infinite subfolder depth.

  • ignoreExistingData (bool, optional) – If True, the function will not load data that is already present in the patient list. Default is True. (not implemented yet)

  • importInPatient (Patient, optional) – If given, the data will be imported into the given patient. Default is None, which implies that the data will be imported into a new patient.

Returns:

dataList – The function returns a list of data objects containing the imported data.

Return type:

list of data objects

readData(inputPaths, maxDepth=-1) → Sequence[PatientData | Patient]

Load all data found at the given input path.

Parameters:

  • inputPaths (str or list) – Path or list of paths pointing to the data to be loaded.

  • maxDepth (int, optional) – Maximum subfolder depth where the function will check for data to be loaded. Default is -1, which implies recursive search over infinite subfolder depth.

Returns:

dataList – The function returns a list of data objects containing the imported data.

Return type:

list of data objects

readSingleData(filePath, dicomCT={})

Load a single data object from the given input path.

Parameters:

  • filePath (str) – Path pointing to the data to be loaded.

  • dicomCT (dict, optional) – Dictionary containing the Dicom CT data already loaded. This is used to load the CT slices in the correct order.

opentps.core.io.dicomAnonymizer module

anonymiseDicom(dataPath, patientName)

Basic dicom anonymizer without options except to specify the new patient name The dicom file is replaced by the anonymised one ! Be careful if you want to keep the original you need a copy ;)

opentps.core.io.dicomIO module

arrayToDS(ls)
floatToDS(v)
readDicomCT(dcmFiles)

Generate a CT image object from a list of dicom CT slices.

Parameters:

dcmFiles (list) – List of paths for Dicom CT slices to be imported.

Returns:

image – The function returns the imported CT image

Return type:

ctImage object

readDicomDose(dcmFile)

Read a Dicom dose file and generate a dose image object.

Parameters:

dcmFile (str) – Path of the Dicom dose file.

Returns:

image – The function returns the imported dose image

Return type:

doseImage object

readDicomMRI(dcmFiles)

Generate a MR image object from a list of dicom MR slices.

Parameters:

dcmFiles (list) – List of paths for Dicom MR slices to be imported.

Returns:

image – The function returns the imported MR image

Return type:

mrImage object

readDicomPlan(dcmFile) → RTPlan

Read a Dicom plan file and generate a RTPlan object.

Parameters:

dcmFile (str) – Path of the Dicom plan file.

Returns:

plan – The function returns the imported plan

Return type:

RTPlan object

readDicomStruct(dcmFile)

Read a Dicom structure set file and generate a RTStruct object.

Parameters:

dcmFile (str) – Path of the Dicom RTstruct file.

Returns:

struct – The function returns the imported structure set

Return type:

RTStruct object

readDicomVectorField(dcmFile)

Read a Dicom vector field file and generate a vector field object.

Parameters:

dcmFile (str) – Path of the Dicom vector field file.

Returns:

field – The function returns the imported vector field

Return type:

vectorField3D object

setFrameOfReferenceUID(value)
writeDicomCT(ct: CTImage, outputFolderPath: str)

Write image and generate the DICOM file

Parameters:

  • ct (CTImage object) – The ct image object

  • outputFolderPath (str) – The output folder path

Returns:

The function returns the series instance UID for these images.

Return type:

SeriesInstanceUID

writeRTDose(dose: DoseImage, outputFile)

Export the dose data as a Dicom dose file

Parameters:

  • dose (DoseImage) – The dose image object.

  • outputFile – The output file path

writeRTPlan(plan: RTPlan, filePath, struct: RTStruct | None = None)

Write a RTPlan object to a dicom file

Parameters:

  • plan (RTPlan) – the RTPlan object to be written.

  • filePath (str) – path to the dicom file

writeRTStruct(struct: RTStruct, outputFile)

Export of TR structure data as a Dicom dose file.

Parameters:

  • struct (RTStruct) – The RTStruct object

  • ctSeriesInstanceUID (str) – The serial instance UID of the CT associated with this RT structure.

  • outputFile (str) – The output folde path

  • NOTE (Get the CT serial instance UID by calling the ‘writeDicomCT’ function.)

opentps.core.io.mcsquareIO module

class MCsquareIOTestCase(methodName='runTest')

Bases: TestCase

Test case for the MCsquareIO module.

testWrite()

Test the write function.

readBDL(path, materialsPath='default') → BDL

Read a BDL file

Parameters:

  • path (str) – The file path

  • materialsPath (str, optional) – The path to the materials

Returns:

bdl – The BDL object to be used

Return type:

BDL

readBeamlets(file_path, beamletRescaling: Sequence[float], origin, roi: ROIMask | None = None)

Read sparse beamlets from a file and return a beamlet dose image

Parameters:

  • file_path (str) – The path to the sparse beamlets file

  • beamletRescaling (Sequence[float]) – The beamlet dose image grid rescaling factors [r,s,t]

  • origin (Sequence[float]) – The origin of the dose grid [x,y,z]

  • roi (Optional[ROIMask], optional) – The ROI mask, by default None

Returns:

The beamlets dose image

Return type:

BeamletDose

readDose(filePath) → DoseImage

Read a dose file from MCsquare (MHD format) and give the dose Image

Parameters:

filePath (str) – Path to the dose file

Returns:

The dose image

Return type:

DoseImage

readMCsquareMHD(filePath) → Image3D

Read MHD file from MCsquare and give the 3D image

Parameters:

filePath (str) – Path to the MHD file

Returns:

image – The 3D image

Return type:

Image3D

readMCsquarePlan(ct: CTImage, file_path)

Read a plan file from MCsquare and give the plan

Parameters:

  • ct (CTImage) – The CT image

  • file_path (str) – Path to the plan file

Returns:

plan – The RT plan

Return type:

RTPlan

updateWeightsFromPlanPencil(ct: CTImage, initialPlan: RTPlan, file_path, bdl)

Update the weights of the initial plan with those from PlanPencil

Parameters:

  • ct (CTImage) – The CT image

  • initialPlan (RTPlan) – The initial plan

  • file_path (str) – Path to the MCsquare Plan file (PlanPencil)

writeBin(destFolder)

Write MCsquare binaries to the given folder

Parameters:

destFolder (str) – The folder where the binaries will be written

writeCT(ct: CTImage, filtePath, overwriteOutsideROI=None)

Write a CT image to a file

Parameters:

  • ct (CTImage) – The CT image

  • filtePath (str) – The file path

  • overwriteOutsideROI (ROI, optional) – The ROI to use for cropping the CT image

writeCTCalibrationAndBDL(calibration: AbstractCTCalibration, scannerPath, materialPath, bdl: BDL, bdlFileName)

Write a CT calibration and a BDL to a file

Parameters:

  • calibration (AbstractCTCalibration) – The CT calibration

  • scannerPath (str) – The path to the scanner

  • materialPath (str) – The path to the material

  • bdl (BDL) – The BDL

  • bdlFileName (str) – The BDL file name

writeConfig(config: MCsquareConfig, file_path)

Write a MCsquare configuration to a file

Parameters:

  • config (MCsquareConfig) – The MCsquare configuration

  • file_path (str) – The file path

writeContours(contour: ROIMask, folder_path)

Write a MHD contour file into a given folder

Parameters:

  • contour (ROIMask) – The contour to write

  • folder_path (str) – The path to the folder where the contour will be written

writeObjectives(objectives: ObjectivesList, file_path)

Write Objectives file at the given path

Parameters:

  • objectives (ObjectivesList) – The objectives list to write

  • file_path (str) – The path to the file where the objectives will be written

writePlan(plan: RTPlan, file_path, CT: CTImage, bdl: BDL)

Write a treatement plan file

Parameters:

  • plan (RTPlan) – The plan to write

  • file_path (str) – The file path to store the plan

  • CT (CTImage) – The CT image

  • bdl (BDL) – The BDL object

opentps.core.io.mhdIO module

exportImageMHD(outputPath, image)

Export image in MHD format (header + binary files).

Parameters:

  • outputPath (str) – Path of the MHD header file that will be generated.

  • image (image3D (or sub-class) object) – Image to be exported.

generateDefaultMetaData()

Generate a Python dictionary with default values for MHD header parameters.

Returns:

metaData – The function returns a Python dictionary with default MHD header information

Return type:

dictionary

importImageMHD(headerFile)

Import image from a pair of MHD header and binary files.

Parameters:

headerFile (str) – Path of the MHD header file to be imported.

Returns:

image – The function returns the imported image if successfully imported, or None in case of error.

Return type:

image3D object

readBinaryMHD(inputPath, metaData=None)

Read and the MHD binary file.

Parameters:

  • inputPath (str) – Path of the input binary file

  • metaData (dictionary) – Python dictionary with the MHD header information

Returns:

image – The function returns the imported image if successfully imported, or None in case of error.

Return type:

image3D object

readHeaderMHD(headerFile)

Read and parse the MHD header file.

Parameters:

headerFile (str) – Path of the MHD header file to be loaded.

Returns:

metaData – The function returns a Python dictionary with the header information

Return type:

dictionary

writeBinaryMHD(outputPath, data, metaData=None)

Write MHD binary file.

Parameters:

  • outputPath (str) – Path of the output binary file.

  • data (Numpy array) – Numpy array with the image to be exported.

  • metaData (dictionary) – Python dictionary with the MHD header information.

writeHeaderMHD(outputPath, metaData=None)

Write MHD header file.

Parameters:

  • outputPath (str) – Path of the MHD header file to be exported.

  • metaData (dictionary) – Python dictionary with the header information

opentps.core.io.scannerReader module

readScanner(scannerFolder, materialsPath='default') → AbstractCTCalibration

Read the CT calibration curve from a scanner folder

Parameters:

scannerFolder (str) – The path to the scanner folder

Returns:

The CT calibration curve for the given scanner

Return type:

AbstractCTCalibration

opentps.core.io.serializedObjectIO module

Made by damien (damien.dasnoy@uclouvain.be / damien.dasnoy@gmail.com)

copyIntoNewObject(sourceObject)

Copy the content of a source object into a new object of the same class

Parameters:

sourceObject (object) – The object to copy

Returns:

newObject – The new object with the same content as the source object

Return type:

object

dictionarizeData(data)

Convert an OpenTPS object into a dictionary

Parameters:

data (object) – The OpenTPS object to convert

Returns:

newDict – The dictionary containing the data of the OpenTPS object

Return type:

dict

loadBeamlets(file_path)

Load a beamlets object from a file

Parameters:

file_path (str) – The path of the file to load the beamlets

Returns:

beamlets – The beamlets object loaded from the file

Return type:

SparseBeamlets

loadData(file_path, cls)

Load a data object from a file (pickle)

Parameters:

  • file_path (str) – The path of the file to load the data

  • cls (class) – The class of the data object to load

loadDataStructure(filePath)

Load a OpenTPS data structure from the hard drive

Parameters:

filePath (str) – Path where to load the data structure

Returns:

dataList – List of OpenTPS objects loaded.

Return type:

list

loadRTPlan(file_path)

Load a RTPlan object from a file

Parameters:

file_path (str) – The path of the file to load the RTPlan

Returns:

plan – The RTPlan object loaded from the file

Return type:

RTPlan

loadSerializedObject(filePath)

TODO to do in the same way as for saving (object - structure)

saveBeamlets(beamlets, file_path)

Save the beamlets object in a file

Parameters:

  • beamlets (SparseBeamlets) – The beamlets object to save

  • file_path (str) – The path of the file where to save the beamlets object

saveData(data, file_path)

Save the data object in a file (pickle)

Parameters:

  • data (object) – The data object to save

  • file_path (str) – The path of the file where to save the data object

saveDataStructure(patientList, savingPath, compressedBool=False, splitPatientsBool=False)

Save OpenTPS data structures of a list of patient in the hard drive

Parameters:

  • patientList (list) – List of patients to save

  • savingPath (str) – Path where to save the data structure

  • compressedBool (bool, optional) – If True, the data structure is compressed before saving. The default is False.

  • splitPatientsBool (bool, optional) – If True, each patient is saved in a separate file. The default is False.

saveRTPlan(plan, file_path)

Save the RTPlan object in a file

Parameters:

  • plan (RTPlan) – The RTPlan object to save

  • file_path (str) – The path of the file where to save the RTPlan object

saveSerializedObjects(dataList, savingPath, compressedBool=False, dictionarized=False)

Save a list of OpenTPS objects in the hard drive

Parameters:

  • dataList (list) – List of OpenTPS objects to save

  • savingPath (str) – Path where to save the data structures

  • compressedBool (bool, optional) – If True, the data structure is compressed before saving. The default is False.

  • dictionarized (bool, optional) –

    If True, the data structure is dictionarized before saving to avoid loss

    of information over long-term storage due to class objects modifications. The default is False.

unDictionarize(dataDict)

Convert a dictionary into an OpenTPS object

Parameters:

dataDict (dict) – The dictionary containing the data of the OpenTPS object

Returns:

data – The OpenTPS object

Return type:

object

Module contents