convert_source.imgio package

Submodules

convert_source.imgio.dcmio module

DICOM specific functions for convert_source. Primarily intended for converting and renaming DICOM files to BIDS NIFTI.

exception convert_source.imgio.dcmio.DICOMerror

Bases: Exception

convert_source.imgio.dcmio.get_bwpppe(dcm_file)

Reads the Bandwidth Per Pixel PhaseEncode value from a DICOM header.

Note

This DICOM field is usually left blank on Philips DICOM headers.

Parameters

dcm_file (str) – DICOM file.

Return type

Union[float, str]

Returns

Bandwidth Per Pixel PhaseEncode value as a float, or empty string otherwise.

convert_source.imgio.dcmio.get_mb(dcm_file)

Extracts multi-band acceleration factor from file description in the DICOM header for (philips MR scanners). If this information cannont be inferred from the DICOM header file description - then it is assumed to be 1.

Note

This is done via a regEx search as no DICOM tag stores this information explicitly.

Parameters

dcm_file (str) – DICOM file.

Return type

int

Returns

Multi-band acceleration factor.

convert_source.imgio.dcmio.get_red_fact(dcm_file)

Extracts parallel reduction factor in-plane value (GRAPPA/SENSE) from file description in the DICOM header for Philips MR scanners. This reduction factor is assumed to be 1 if a value cannot be found from witin the DICOM header.

Parameters

dcm_file (str) – DICOM file.

Return type

float

Returns

Parallel reduction factor in-plane value (e.g. SENSE/GRAPPA factor), or 1.0 if not specified.

convert_source.imgio.dcmio.get_scan_time(dcm_file)

Reads the scan time from the DICOM header.

Parameters

dcm_file (str) – DICOM file.

Return type

Union[float, str]

Returns

Acquisition duration (scan time, in s) as a float if it exists, or an empty string otherwise.

convert_source.imgio.dcmio.is_valid_dcm(dcm_file, raise_exc=False, verbose=False)

Checks for a valid DICOM file by inspecting the conversion type label in the DICOM file header. This field should be blank. If this label is populated, then it is likely a secondary capture image and thus is not likely to contain meaningful image information.

Parameters

  • dcm_file (str) – DICOM file.

  • raise_exc (Optional[bool]) – Raises exception in the case that execution needs to be halted.

  • verbose (Optional[bool]) – Enable verbosity.

Return type

bool

Returns

True if DICOM file is not a secondary capture (or does not have text in the conversion type label field), and False otherwise.

Raises

DICOMerror – Error that arises if the DICOM in question is not a valid DICOM, and the ‘raise_exc’ option is set to True.

convert_source.imgio.niio module

NIFTI specific functions for convert_source. Primarily intended for renaming NIFTI to be BIDS compliant.

convert_source.imgio.niio.get_data_params(file, json_file='')

Creates a dictionary of key mapped parameter items that are often not written to the BIDS JSON sidecar when converting Philips DICOM and PAR REC files.

Parameters

  • file (str) – Filepath to raw image data file (DICOM or PAR REC).

  • json_file (Optional[str]) – Corresponding JSON sidecare file.

Return type

Dict

Returns

Dictionary of BIDS related key mapped items/values.

convert_source.imgio.niio.get_nii_tr(nii_file)

Reads the NIFTI file header and returns the repetition time (TR, sec) as a value if it is not zero, otherwise this function returns an string.

Parameters

nii_file (str) – NIFTI image filename.

Return type

Union[float, str]

Returns

Repetition time (TR, sec), if not zero, or an empty string otherwise.

convert_source.imgio.niio.get_num_frames(nii_file)

Determines the number of frames/volumes/TRs in a NIFTI-2 file.

Parameters

nii_file (str) – NIFTI image file.

Return type

int

Returns

Number of temporal frames or volumes in NIFTI file.

convert_source.imgio.pario module

PAR REC specific functions for convert_source. Primarily intended for converting and renaming PAR REC files to BIDS NIFTI.

exception convert_source.imgio.pario.PARfileReadError

Bases: Exception

convert_source.imgio.pario.get_echo_time(par_file, tmp_dir=None, raise_exc=False)

Reads the echo time (TE, in sec.) from a PAR header file.

Note

Echo time is obtained from the PAR file header by reading in the PAR header file as a pandas dataframe, followed by saving the resulting dataframe as a M x N | N = 35. The echo times are stored in the resulting matrix (constructed from numpy as a numpy multi-dimensional array) in row 16 (count starts at 0).

Usage example:
>>> get_echo_time(par_file="File.PAR")
88.0
Parameters

  • par_file (str) – PAR header file.

  • tmp_dir (Optional[str]) – Path to temporary directory.

  • raise_exc (Optional[bool]) – Raise exception in the case of multi-echo acquisitions.

Return type

float

Returns

Echo time as a float or None in the case of multi-echo data.

Raises

PARfileReadError – Exception that is raised if multi-echo PAR files are used as inputs.

convert_source.imgio.pario.get_etl(par_file)

Gets EPI factor (Echo Train Length) from Philips’ PAR Header.

Note

This is done via a regEx search as the PAR header is not assumed to change significantly between scanners.

Parameters

par_file (str) – PAR header file.

Return type

int

Returns

Echo Train Length as integer.

convert_source.imgio.pario.get_flip_angle(par_file, tmp_dir=None, raise_exc=False)

Reads the flip angle (in degrees) from a PAR header file.

Note

Flip angle is obtained from the PAR file header by reading in the PAR header file as a pandas dataframe, followed by saving the resulting dataframe as a M x N | N = 35. The flip angles are stored in the resulting matrix (constructed from numpy as a numpy multi-dimensional array) in row 21 (count starts at 0).

Usage example:
>>> get_flip_angle(par_file="File.PAR")
90.0
Parameters

  • par_file (str) – PAR header file.

  • tmp_dir (Optional[str]) – Path to temporary directory.

  • raise_exc (Optional[bool]) – Raise exception in the case of multiple flip angles are found.

Return type

float

Returns

Flip angle as a float or None if multiple flip angles are found.

Raises

PARfileReadError – Exception that is raised if input PAR file contains multiple flip angles.

convert_source.imgio.pario.get_mb(par_file)

Extracts multi-band acceleration factor from from Philips’ PAR Header.

Note

This is done via a regEx search as the PAR header does not normally store this value.

Parameters

par_file (str) – Absolute filepath to PAR header file

Return type

int

Returns

Multi-band acceleration factor (as an int).

convert_source.imgio.pario.get_red_fact(par_file)

Extracts parallel reduction factor in-plane value (SENSE factor) from the file description in the PAR REC header for Philips MR scanners. This reduction factor is assumed to be 1 if a value cannot be found from witin the PAR REC header.

Note

This is done via a regEx search as the PAR header is not assumed to change significantly between scanners.

Parameters

par_file (str) – PAR header file.

Return type

float

Returns

Parallel reduction factor in-plane value (e.g. SENSE factor, as a float).

convert_source.imgio.pario.get_scan_time(par_file)

Gets the acquisition duration (scan time, in s) from the PAR header.

Note

This is done via a regEx search as the PAR header is not assumed to change significantly between scanners.

Parameters

par_file (str) – PAR header file.

Return type

Union[float, str]

Returns

Acquisition duration (scan time, in s). If not in header, an empty string is returned.

convert_source.imgio.pario.get_wfs(par_file)

Gets Water Fat Shift from Philips’ PAR Header.

Note

This is done via a regEx search as the PAR header is not assumed to change significantly between scanners.

Parameters

par_file (str) – PAR header file.

Return type

float

Returns

Water Fat Shift as a float.

Module contents