Sisyphe.core.sisypheDicom

External packages/modules

Numpy, scientific computing, https://numpy.org/

pandas, data analysis and manipulation tool, https://pandas.pydata.org/

pydicom, DICOM library, https://pydicom.github.io/pydicom/stable/

PyQt5,Qt GUI, https://www.riverbankcomputing.com/software/pyqt/

SimpleITK, medical image processing, https://simpleitk.org/

skimage, image processing, https://scikit-image.org/

class Sisyphe.core.sisypheDicom.DicomToXmlDicom

Description

Dicom file to XmlDicom file conversion. XmlDicom file stores DICOM fields in a key/value XML file.

Inheritance

object -> DicomToXmlDicom

Creation: 08/09/2022 Last Revision: 27/03/2025

addDicomSeriesFilenames(filenames: list[str]) → None

Add a list of DICOM file names to the list of conversion.

Parameters

filenameslist[str]: list of DICOM file names

clear() → None: Reset all DicomToXmlDicom attributes.

clearDicomSeriesFilenames() → None: Clear the list of DICOM file names to convert.

execute() → None: Run Dicom to XmlDicom conversion.

getBackupXmlDicomDirectory() → str

Get path of the XmlDicom backup folder.

Returns

str: path of the backup folder

classmethod getDefaultXmlDicomFilename(ds: Dataset) → str

Get default XmlDicom file name from DICOM fields.

Parameters

dspydicom.Dataset: DICOM fields

Returns

str: ‘{lastname}_{firstname}_{birth_date}_{modality}_{acquisition_date}_{series_description}.xdcm’

getDicomSeriesFilenames() → list[str]

Get the list of DICOM file names to convert.

Returns

list[str]: list of DICOM file names

classmethod getFileExt() → str

Get XmlDicom file extension.

Returns

str: ‘.xdcm’

getXmlDicomFilename() → str

Get name of converted XmlDicom file.

Returns

str: XmlDicom file name

hasDicomSeriesFilenames() → bool

Check that the list of DICOM file names is not empty.

Returns

bool: True if list is not empty

isDefaultBackupXmlDicomDirectory() → bool

Checks whether path of the backup folder is defined. In this case, backup folder is the path of the Dicom files.

Returns

bool: True if backup folder path is not defined

setBackupXmlDicomDirectory(path: str) → None

Set the path of the XmlDicom backup folder.

Parameters

pathstr: path of the backup folder

setDicomSeriesFilenames(filenames: list[str]) → None

Set the list of DICOM file names to convert in XmlDicom format.

Parameters

filenameslist[str]: list of DICOM file names

setXmlDicomFilename(filename: str) → None

Set name of converted XmlDicom file.

Parameters

filenamestr: XmlDicom file name

class Sisyphe.core.sisypheDicom.DicomUIDGenerator

Description

Class to generate Dicom UID (study UID, series UID, instance UID, FrameOfReference UID) and Date/Time for various Dicom fields. This UID generator is used by DICOM import/export classes. UID is a Dicom ID code compliant with ISO-8824 standard.

Inheritance

object -> DicomUIDGenerator

Creation: 08/09/2022 Last revision: 11/12/2023

classmethod getCTSOPClassUID() → str

Get UID of the CT modality. UID = Dicom ID, ISO8824 format.

Returns

str: ‘1.2.840.10008.5.1.4.1.1.2’

getCurrentFrameOfReferenceUID() → str

Get current FrameOfReferenceUID.

Returns

str: FrameOfReference UID

getCurrentInstanceIndex() → int

Get current instance index.

Returns

int: instance index

getCurrentInstanceUID() → str

Get current InstanceUID.

Returns

str: Instance UID

getCurrentSeriesIndex() → int

Get current series index.

Returns

int: series index

getCurrentSeriesUID() → str

Get current SeriesUID.

Returns

str: Series UID

getCurrentStudyID() → str

Get current StudyID.

Returns

str: Study ID

getCurrentStudyUID() → str

Get current StudyUID.

Returns

str: Study UID

classmethod getImplementationClassUID() → str

Get implementation class UID (i.e. ID of the application/service class user) UID = Dicom ID, ISO8824 format.

Returns

str: ‘1.2.826.0.1.3680043.1.2.100.6.40.0.76’

classmethod getImplementationVersionName() → str

Get implementation version name (i.e. name of the application/service class user)

Returns

str: ‘PySisyphe’

getInstanceTime() → str

Get instance time.

Returns

str: instance time

classmethod getMRSOPClassUID() → str

Get UID of the MR modality. UID = Dicom ID, ISO8824 format.

Returns

str: ‘1.2.840.10008.5.1.4.1.1.4’

classmethod getNMSOPClassUID() → str

Get UID of the NM modality. UID = Dicom ID, ISO8824 format.

Returns

str: ‘1.2.840.10008.5.1.4.1.1.20’

classmethod getOTSOPClassUID() → str

Get UID of the OT modality. UID = Dicom ID, ISO8824 format.

Returns

str: ‘1.2.840.10008.5.1.4.1.1.7’

classmethod getPTSOPClassUID() → str

Get UID of the PT modality. UID = Dicom ID, ISO8824 format.

Returns

str: ‘1.2.840.10008.5.1.4.1.1.128’

classmethod getRTDoseSOPClassUID() → str

Get UID of the RTDOSE modality. UID = Dicom ID, ISO8824 format.

Returns

str: ‘1.2.840.10008.5.1.4.1.1.481.2’

classmethod getRTImageSOPClassUID() → str

Get UID of the RTIMAGE modality. UID = Dicom ID, ISO8824 format.

Returns

str: ‘1.2.840.10008.5.1.4.1.1.481.1’

classmethod getRTStructSOPClassUID() → str

Get UID of the RTSTRUCT modality. UID = Dicom ID, ISO8824 format.

Returns

str: ‘1.2.840.10008.5.1.4.1.1.481.3’

classmethod getRootUID() → str

Get root UID, str Prefix used to generate various UID codes. UID = Dicom ID, ISO8824 format.

Returns

str: UID prefix ‘1.2.840.12052’

classmethod getSOPClassUIDFromModality(modality: str) → str

Get modality UID. UID = Dicom ID, ISO8824 format.

Parameters

modalitystr: Dicom modality (‘CT’, ‘MR’, ‘NM’, ‘PT’, ‘OT’, ‘RTDOSE’, ‘RTSTRUCT’)

Returns

str: modality UID

getSeriesTime() → str

Get series time.

Returns

str: series time

getStudyDate() → str

Get study date.

Returns

str: study date

getStudyTime() → str

Get study time.

Returns

str: study time

newInstance() → None: Generates current InstanceUID and increments instance index.

newSeries() → None: Generates current SeriesUID and FrameOfReferenceUID, increments series index.

newStudy() → None: Generates current StudyUID.

class Sisyphe.core.sisypheDicom.ExportToDicom

Description

Class to convert PySisyphe volume (.xvol) to Dicom format.

Inheritance

object -> ExportToDicom

Creation: 08/09/2022 Last revision: 27/03/2025

clear() → None: Reset all ExportToDicom instance attributes.

execute(progress: DialogWait | None = None) → None

Run PySisyphe volume (.xvol) to Dicom conversion.

Parameters

progressSisyphe.gui.dialogWait.DialogWait | None: progress bar dialog (optional)

getBackupDicomDirectory() → str

Get the path of the backup folder. Dicom files are saved in this directory.

Returns

str: path of the backup folder

classmethod getSettingsDirectory() → str

Get PySisyphe user settings path (~/.PySisyphe/settings.xml in user folder).

Returns

str: PySisyphe user settings path

getVolume() → SisypheVolume

Get PySisyphe volume (.xvol) to convert.

Returns

Sisyphe.core.sisypheVolume.SisypheVolume: volume (.xvol) to convert

getXmlDicomReference() → str

Get XmlDicom reference (.xdcm). Dicom fields of the XmlDicom reference are used as a template for writing Dicom file.

Returns

str: XmlDicom file name

hasVolume() → bool

Checks whether PySisyphe volume to convert is defined.

Returns

bool: True if PySisyphe volume to convert is defined

hasXmlDicomReference() → bool

Checks whether XmlDicom reference is defined.

Returns

bool: True if PySisyphe volume to convert is defined

isDefaultBackupDicomDirectory() → bool

Checks whether backup folder is defined. The default backup folder is the path of the PySisyphe volume.

Returns

bool: True if backup folder is not defined

setBackupDicomDirectory(path: str) → None

Set the path of the backup folder. Dicom files are saved in this directory.

Parameters

pathstr: path of the backup folder

setVolume(vol: SisypheVolume) → None

Set PySisyphe volume (.xvol) to convert.

Parameters

volSisyphe.core.sisypheVolume.SisypheVolume: volume (.xvol) to convert

setXmlDicomReference(filename: str) → None

Set XmlDicom reference (.xdcm). Dicom fields of the XmlDicom reference are used as a template for writing Dicom file.

Parameters

filenamestr: XmlDicom file name

class Sisyphe.core.sisypheDicom.ExportToRTStruct

ExportToRTStruct class

Description

Class to convert PySisyphe ROI (.xroi) to Dicom RTSTRUCT.

Inheritance

object -> ExportToRTStruct

Creation: 08/09/2022 Last revision: 27/03/2025

addROI(roi: str | SisypheROI) → None

Add PySisyphe ROI to the list of conversion. PySisyphe ROI must have the same ID as the PySisyphe reference volume.

Parameters

roistr | Sisyphe.core.sisypheROI.SisypheROI: PySisyphe ROI file name or instance

clear() → None: Reset all ExportToRTStruct instance attributes.

execute(progress: DialogWait | None = None) → None

Run PySisyphe ROI (.xroi) to Dicom RTSTRUCT conversion.

Parameters

progressSisyphe.gui.dialogWait.DialogWait: progress bar dialog (optional)

getExportFolder() → str

Get the path of the backup folder. Dicom RTSTRUCT file is saved in this directory.

Returns

str: path of the backup folder

getROI() → SisypheROICollection

Get PySisyphe ROI(s) to convert.

Returns

Sisyphe.core.sisypheROI.SisypheROICollection: ROIs list to convert

getReferenceVolume() → SisypheVolume: Get PySisyphe reference volume (.xvol). Dicom RTSTRUCT is always associated to a reference anatomical volume. PySisyphe reference is also converted to Dicom format during execute method. PySisyphe ROI to convert must have the same ID as the PySisyphe reference volume.

Returns

Sisyphe.core.sisypheVolume.SisypheVolume

classmethod getSettingsDirectory() → str

Get PySisyphe user settings folder (~/.PySisyphe/settings.xml in user folder).

Returns

str: PySisyphe user settings folder

hasExportFolder() → bool

Checks whether backup folder is defined.

Returns

bool: True if backup folder is defined

hasROI() → bool

Checks whether PySisyphe ROIs list of conversion is not empty.

Returns

bool: True if PySisyphe ROIs list of conversion is not empty

hasReferenceVolume() → bool

Checks whether PySisyphe reference volume is defined.

Returns

bool: True if PySisyphe volume is defined

setExportFolder(folder: str) → None

Set the path of the backup folder. Dicom RTStruct file is saved in this directory.

Parameters

folderstr: path of the backup folder

setReferenceVolume(vol: str | SisypheVolume) → None

Set PySisyphe reference volume (.xvol). Dicom RTSTRUCT is always associated to a reference anatomical volume. PySisyphe reference is also converted to Dicom format during conversion. PySisyphe ROI to convert must have the same ID as the PySisyphe reference volume.

Parameters

volstr | Sisyphe.core.sisypheVolume.SisypheVolume: PySisyphe reference volume file name (.xvol) or instance

class Sisyphe.core.sisypheDicom.ImportFromDicom

Description

Class to convert Dicom files to PySisyphe volume (.xvol).

Inheritance

object -> ImportFromDicom

Creation: 08/09/2022 Last revision: 07/03/2025

clear() → None: Reset all ImportFromDicom instance attributes.

execute(progress: DialogWait | None = None, getdirs: bool = False) → SisypheVolume | None

Run Dicom to PySisyphe volume (.xvol) conversion.

Parameters

progressSisyphe.gui.dialogWait.DialogWait: progress bar dialog (optional)
getdirsbool: if True, copy PySisyphe volume origin and direction attributes from Dicom fields, otherwise set PySisyphe volume origin and direction attributes to default

Returns

Sisyphe.core.sisypheVolume.SisypheVolume: converted PySisyphe volume

getDicomFilenames() → list[str]

Get Dicom file names to convert.

Returns

str: list of Dicom file names

getDicomImagePositionPatient() → list[float]

Get PositionPatient Dicom field values from Dicom Files to convert.

Returns

list[float]: list of PositionPatient Dicom field values

getImportFolder() → str

Get path of the backup folder. PySisyphe volume is saved in this directory.

Returns

str: path of the backup folder

getReferenceUID() → str

Get Dicom files reference UID (i.e. FrameOfReferenceUID)

Returns

str: Dicom files reference UID

getReferenceVolume() → SisypheVolume: Get converted PySisyphe volume.

Returns

Sisyphe.core.sisypheVolume.SisypheVolume

getSaveTag() → bool

Get save tag value. If tag is True, PySisyphe volume is saved during execute method.

Returns

bool: save tag value

getSeriesUID() → str

Get Dicom files seriesUID.

Returns

str: Dicom files seriesUID

hasImportFolder() → bool

Checks whether backup folder is defined. The default backup folder is the path of the Dicom files.

Returns

bool: True if backup folder is defined

hasReferenceUID() → bool

Checks whether Dicom files reference UID is defined.

Returns

bool: True if Dicom files reference UID is defined

hasReferenceVolume() → bool

Checks whether converted PySisyphe volume exists (False before calling execute method).

Returns

bool: True if PySisyphe volume exists

isEmpty() → bool

Checks if ImportFromDicom is empty, Dicom files to convert are not defined.

Returns

bool: True if Dicom files to convert are not defined

saveReferenceVolume(progress: DialogWait | None = None) → None

Save converted PySisyphe volume.

Parameters

progressSisyphe.gui.dialogWait.DialogWait | None: progress bar dialog (optional)

setDicomFilenames(filenames: list[str]) → None

Set Dicom file names to convert. All files must belong to the same Dicom series. Dicom fields used to detect Dicom series:

(0x0008, 0x0018) SOPInstanceUID
(0x0020, 0x000e) SeriesInstanceUID
(0x0020, 0x0032) ImagePositionPatient
(0x0020, 0x0052) FrameOfReferenceUID

Parameters

filenamesstr: list of Dicom file names

setImportFolder(folder: str) → None

Set path of the backup folder. PySisyphe volume is saved in this directory.

Parameters

folderstr: path of the backup folder

setSaveTag(v: bool) → None

Set save tag value. If tag is True, PySisyphe volume is saved during execute method.

Parameters

vbool: save tag value

class Sisyphe.core.sisypheDicom.ImportFromRTDose

Description

Class to convert Dicom RTDose to PySisyphe volume (.xvol).

Inheritance

object -> ImportFromDicom -> ImportFromRTDose

Creation: 08/09/2022 Last revision: 07/03/2025

addRTDoseFilename(filenames: str | list[str]) → None

Add Dicom RTDose file names to convert. Dicom fields used:

(0x0008, 0x0060) Modality
(0x0020, 0x0052) FrameOfReferenceUID

Parameters

filenamesstr | list[str]: list of Dicom RTDose file names

clear() → None: Reset all ImportFromRTDose instance attributes.

execute(progress: DialogWait | None = None, getdirs: bool = False) → SisypheVolumeCollection | None

Run Dicom RTDose to PySisyphe volume (.xvol) conversion.

Parameters

progressSisyphe.gui.dialogWait.DialogWait: progress bar dialog
getdirsbool: if True, copy PySisyphe volume origin and direction attributes from Dicom fields, otherwise set PySisyphe volume origin and direction attributes to default

Returns

Sisyphe.core.sisypheVolume.SisypheVolumeCollection: converted PySisyphe volumes

getRTDoseFilename() → list[str]

Get Dicom RTDose file names to convert.

Returns

list[str]: list of Dicom RTDose file names

getRTDoseVolume() → SisypheVolumeCollection: Get converted PySisyphe volumes.

Returns

Sisyphe.core.sisypheVolume.SisypheVolumeCollection

hasRTDoseFilename() → bool

Checks whether Dicom RTDose files to convert are defined.

Returns

bool: True if Dicom RTDose files to convert are defined

hasRTDoseVolume() → bool

Checks whether converted PySisyphe volumes exists (False before calling execute method).

Returns

bool: True if PySisyphe volume exists

saveRTDoseVolume() → None: Save converted PySisyphe volumes.

class Sisyphe.core.sisypheDicom.ImportFromRTStruct

Description

Class to convert Dicom RTSTRUCT to PySisyphe ROI (.xroi).

Inheritance

object -> ImportFromDicom -> ImportFromRTStruct

Creation: 08/09/2022 Last revision: 07/03/2025

addRTStructFilename(filenames: str | list[str]) → None

Add Dicom RTStruct file names to convert. Dicom fields used:

(0x0008, 0x0060) Modality
(0x0020, 0x0052) FrameOfReferenceUID

Parameters

filenamesstr: list of Dicom RTDose file names

clear() → None: Reset all ImportFromRTStruct instance attributes.

execute(progress: DialogWait | None = None, getdirs: bool = False) → SisypheROICollection

Run Dicom RTStruct to PySisyphe roi (.xroi) conversion.

Parameters

progressSisyphe.gui.dialogWait.DialogWait: progress bar dialog (optional)
getdirsbool: if True, copy PySisyphe volume origin and direction attributes from Dicom fields, otherwise set PySisyphe volume origin and direction attributes to default

Returns

Sisyphe.core.sisypheROI.SisypheROICollection: converted PySisyphe rois

getRTStructFilename() → list[str]

Get Dicom RTStruct file names to convert.

Returns

list[str]: list of Dicom RTStruct file names

getRTStructLabel() → SisypheVolume

Get converted PySisyphe label volume.

Returns

Sisyphe.core.sisypheVolume.SisypheVolume: label volume

getRTStructROI() → SisypheROICollection: Get converted PySisyphe ROIs.

Returns

Sisyphe.core.sisypheROI.SisypheROICollection

hasRTStructFilename() → bool

Checks whether Dicom RTStruct files to convert are defined.

Returns

bool: True if Dicom RTStruct files to convert are defined

hasRTStructROI() → bool

Checks whether converted PySisyphe rois exists (False before calling execute method).

Returns

bool: True if PySisyphe rois exists

saveRTStructLabel() → None: Save converted PySisyphe label volume.

saveRTStructROI() → None: Save converted PySisyphe ROIs.

class Sisyphe.core.sisypheDicom.XmlDicom

Description

Class to get field values from XmlDicom file. XmlDicom file stores DICOM fields in a key/value XML file.

Scope of methods:

container-like methods for accessing DICOM fields
IO methods (Xml, Text, Matfile, CSV, Excel, Latex)

Inheritance

object -> XmlDicom

Creation: 08/09/2022 Last revisions: 11/12/2023

clear() → None: Delete all Dicom fields.

copyDataElementValuesToClipboard(keys: list[str], sep: str = '\t') → None

Copy a list of Dicom fields to clipboard.

Parameters

keyslist[str]: list of Dicom field names to copy
sepstr: separator char between Dicom fields (default ‘ ‘)

findKeywords(flt: str) → list[str] | None

Search for Dicom fields from a string or substring.

Parameters

fltstr: string to search Dicom fields names

Returns

list[str]: list of Dicom field names

getDataElement(keyword: str) → DataElement | list[DataElement] | None

Copy a Dicom field in a pydicom.DataElement. Returns a list of pydicom.DataElement if Dicom field value is not constant in all Dicom instances of a series. In this case, there is a pydicom.Element for each Dicom instance.

Parameters

keywordstr: Dicom field name

Returns

pydicom.Element | list[pydicom.Element]

getDataElementVM(keyword: str) → int | None

Get Dicom field VM attribute (Value multiplicity) from field name as str key. Some dicom fields have multiple values (vector), VM gives value count of the field.

Parameters

keywordstr: Dicom field name

Returns

str: VM value count of the DICOM field

getDataElementVR(keyword: str) → str | None

Get Dicom field VR attribute (Value representation i.e. Dicom datatype code) from field name as str key. Dicom datatype is a two-chars str code.

Parameters

keywordstr: Dicom field name

Returns

str: VR Dicom datatype code

Get Dicom field (Data element) value from field name as str key.

Parameters

keywordstr: Dicom field name

Returns

int | float | str | list[int] | list[float]: Dicom field value

getDataset(index: int = 0) → Dataset

Copy all Dicom Fields in a pydicom.Dataset.

Parameters

indexint: Dicom instance index to copy (default 0)

Returns

pydicom.Dataset

classmethod getFileExt() → str

Get XmlDicom file extension.

Returns

str: ‘.xdcm’

classmethod getFilterExt() → str

Get XmlDicom filter used by QFileDialog.getOpenFileName() and QFileDialog.getSaveFileName().

Returns

str: ‘PySisyphe XmlDicom (.xdcm)’

getKeywords() → list[str] | None

Get list of all Dicom field names in XmlDicom instance.

Returns

list[str]: list of Dicom field names

getKeywordsWithConstantValue() → list[str] | None

Get list of Dicom fields with constant value (same value in all Dicom instances).

Returns

list[str]: list of Dicom field names

getKeywordsWithValueVariation() → list[str] | None

Get list of Dicom fields having a value variation with Dicom instances (one value for each Dicom instance).

Returns

list[str]: list of Dicom field names

getNumerOfDatasets() → int

Get the number of Dicom instances in the current XmlDicom instance.

Returns

int: Dicom instance count

getSheet(keys: list[str]) → SisypheSheet

Copy a list of Dicom fields to a Sisyphe.core.sisypheSheet.SisypheSheet.

Parameters

keyslist[str]: list of Dicom fields

Returns

Sisyphe.core.sisypheSheet.SisypheSheet

hasKeyword(keyword: str) → bool

Checks whether a Dicom field is in XmlDicom instance.

Parameters

keywordstr: Dicom field name

Returns

bool: True if field is in XmlDicom instance

isEmpty() → bool

Checks if XmlInstance is empty (no Dicom field).

Returns

bool: True if XmlInstance is empty

loadXmlDicomFilename(filename: str) → None

Load XmlDicom file.

Parameters

filenamestr: XmlDicom file name

saveDataElementValuesToCSV(keys: list[str], filename: str) → None

Save a list of Dicom fields in a CSV file.

Parameters

keyslist[str]: list of Dicom field names to save
filenamestr: CSV file name

saveDataElementValuesToExcel(keys: list[str], filename: str) → None

Save a list of Dicom fields in an Excel file.

Parameters

keyslist[str]: list of Dicom field names to save
filenamestr: Excel file name

saveDataElementValuesToLATEX(keys: list[str], filename: str) → None

Save a list of Dicom fields in a LaTeX file.

Parameters

keyslist[str]: list of Dicom field names to save

filename : str, LaTeX file name

saveDataElementValuesToMatfile(keys: list[str], filename: str) → None

Save a list of Dicom fields in a Matlab file.

Parameters

keyslist[str]: list of Dicom field names to save
filenamestr: Matlab file name

saveDataElementValuesToTxt(keys: list[str], filename: str, sep: str = '\t') → None

Save a list of Dicom fields in a text file.

Parameters

keyslist[str]: list of Dicom field names to save
filenamestr: text file name
sepstr: separator char between Dicom fields (default ‘ ‘)

saveDataElementValuesToXml(keys: list[str], filename: str) → None

Save a list of Dicom fields in an XML file.

Parameters

keyslist[str]: list of Dicom field names to save
filenamestr: XML file name

Sisyphe.core.sisypheDicom.getAcquisitionFromDicom(filename: str, useacqnumber: bool = False) → SisypheAcquisition

Get acquisition attributes (Sisyphe.core.SisypheImageAttributes.SisypheAcquisition) in DICOM file.

Dicom fields used:

0x0008, 0x0020 Study Date

0x0008, 0x0021 Series Date

0x0008, 0x0022 Acquisition Date

0x0008, 0x0023 Content Date

0x0008, 0x0060 Modality

0x0008, 0x103e Series Description

0x0018, 0x0010 Contrast/Bolus Agent

0x0018, 0x0023 MR Acquisition Type (2D or 3D)

0x0020, 0x0012 Acquisition Number

Parameters

filenamestr: Dicom file name
useacqnumberbool: Add acquisition number in the SisypheAcquisition sequence attribute

Returns

Sisyphe.core.SisypheImageAttributes.SisypheIdentity: patient identity

Sisyphe.core.sisypheDicom.getDicomImageModalities() → list[str]

Get list of DICOM image modalities. DICOM modality format is two-chars str for images.

Returns

list[str]: [‘CT’, ‘MR’, ‘NM’, ‘PT’, ‘OT’]

Sisyphe.core.sisypheDicom.getDicomModalities() → list[str]

Get list of DICOM modalities. DICOM modality format is two-chars str for images.

Returns

list[str]: [‘CT’, ‘MR’, ‘NM’, ‘PT’, ‘OT’, ‘RTDOSE’, ‘RTSTRUCT’]

Sisyphe.core.sisypheDicom.getDicomRTModalities() → list[str]

Get list of DICOM radiotherapy modalities.

Returns

list[str]: [‘RTDOSE’, ‘RTSTRUCT’]

Sisyphe.core.sisypheDicom.getDiffusionParametersFromDicom(filename: str) → dict[slice(<class 'str'>, <class 'float'>, None), slice(<class 'str'>, list[float], None)]

Get diffusion attributes B-value and gradient direction in DICOM file.

Parameters

filenamestr: Dicom file name

Returns

dict[str: float, str: list[float]]

Key/Value

‘bval’: float, B-value
‘bvec’: list[float], gradient direction vector

Sisyphe.core.sisypheDicom.getIdentityFromDicom(filename: str) → SisypheIdentity

Get patient identity information (Sisyphe.core.SisypheImageAttributes.SisypheIdentity) from DICOM file.

Dicom fields used:

PatientName

PatientBirthDate

PatientSex

Parameters

filenamestr: Dicom file name

Returns

Sisyphe.core.SisypheImageAttributes.SisypheIdentity: patient identity

Sisyphe.core.sisypheDicom.loadBVal(filename: str, format='txt', numpy=False) → dict[slice(<class 'str'>, <class 'float'>, None)] | ~numpy.ndarray

Load gradient B-values.

Parameters

filenamestr

file name (.bval, .xbval or .txt)

formatstr

‘xml’, xml format <bvalue file=filename>v</bvector>
‘txt’, txt format, v[0] -> v[1] … -> v[n]

numpybool

return type is ndarray (True) or dict (False)

Returns

ndarray | dict[str: float]

if numpy parameter is False:

key str, diffusion weighted image file name (.xvol) or index number
value float, B-value

Sisyphe.core.sisypheDicom.loadBVec(filename: str, format='txtbydim', numpy=False) → dict[slice(<class 'str'>, [<class 'float'>, <class 'float'>, <class 'float'>], None)] | ~numpy.ndarray

Load gradient direction vector.

Parameters

filenamestr

file name (.bvec, .xbvec or .txt)

formatstr

‘xml’, xml format <bvector file=filename>v0[0] v0[1] v0[2]</bvector>
‘txtbyvec’, txt format, vector order, v0[0] -> v0[1] -> v0[2] -> … -> vn[0] -> vn[1] -> vn[2]
‘txtbydim’, txt format, dimension order, v0[0] -> … -> vn[0], v0[1] -> … -> vn[1], v0[2] -> … -> vn[2]

numpybool

return type is ndarray (True) or dict (False)

Returns

ndarray | dict[str: [float, float, float]]

if numpy parameter is False:

key str, diffusion weighted image file name (.xvol) or index number,
value [float, float, float], gradient direction vector

Sisyphe.core.sisypheDicom.mosaicImageToVolume(slc: ndarray, n: int) → ndarray

Siemens Mosaic 2D image to 3D volume conversion. Mosaic is a grid of n^2 images (n columns x n rows), all the slices of a volume are stored in a single DICOM mosaic file.

Parameters

slcnumpy.ndarray: 2D mosaic image (ndarray, ndim=2)
nint: columns/rows count

Returns

numpy.ndarray: 3D volume

Sisyphe.core.sisypheDicom.removeSuffixNumberFromFilename(filename: str) → str

Remove numerical suffix from a file name. ex: ‘../image_01.xvol’ -> ‘../image.xvol’

Parameters

filenamestr: file name

Returns

str: file name

Sisyphe.core.sisypheDicom.saveBVal(filename: str, bval: dict[slice(<class 'str'>, <class 'float'>, None)], format: str = 'txt') → None

Save gradient B-values.

Parameters

filenamestr

file name (.bval, .xbval or .txt)

bvaldict[str: float]

key str, diffusion weighted image file name (.xvol) or index number
value float, B value

formatstr

‘xml’, xml format <bvalue file=filename>v</bvector>
‘txt’, txt format, v[0] -> v[1] … -> v[n]

Sisyphe.core.sisypheDicom.saveBVec(filename: str, bvec: dict[slice(<class 'str'>, [<class 'float'>, <class 'float'>, <class 'float'>], None)], format='txtbydim') → None

Save gradient direction vector.

Parameters

filenamestr

file name (.bvec, .xbvec or .txt)

bvecdict[str: [float, float, float]],

key str, diffusion weighted image file name (.xvol) or index number
value [float, float, float], gradient direction vector

formatstr

‘xml’, xml format <bvector file=filename>v0[0] v0[1] v0[2]</bvector>
‘txtbyvec’, txt format, vector order, v0[0] -> v0[1] -> v0[2] -> … -> vn[0] -> vn[1] -> vn[2]
‘txtbydim’, txt format, dimension order, v0[0] -> … -> vn[0], v0[1] -> … -> vn[1], v0[2] -> … -> vn[2]