Pinnacle Export Tool

Summary

A tool to export DICOM objects from raw Pinnacle data:

Warning

The DICOM objects exported by this tool are not the same as the DICOM objects exported from within the Pinnacle application. Certain DICOM modalities correspond fairly well to the Pinnacle exported objects for some versions of Pinnacle. Others are not working as expected or have not been validated.

The first step when using this tool is to compare the output generated to the ‘ground truth’ generated by your version(s) of Pinnacle. You can then determine if this tool currently meets your export needs, or if some adjustments need to be made. Please create an issue on the PyMedPhys GitHub describing the circumstances where the tool is not working, providing some sample raw Pinnacle data where possible. If you’re up for a challenge, clone the PyMedPhys repository and attempt to solve the problem yourself! Don’t be afraid to ask for help when contributing your changes. The more developers we can encourage to contribute to this tool, the sooner it will become stable and reliable.

Finally, note that while this tool can be extremely useful for exporting large amounts of Pinnacle data to DICOM, we recommend that this should only be used for research purposes and not clinically.

API

class pymedphys.experimental.pinnacle.PinnacleExport(path, logger=None)[source]

Handle Pinnacle data to allow export of DICOM objects

This class is used to export the various DICOM objects from Pinnacle data found within the given path.

Parameters
  • path (str) – Path to raw Pinnacle data (directory containing ‘Patient’ file).

  • logger (Logger) – Logger the tool will log to.

static export_dose(plan, export_path='.')[source]

Exports the RTDOSE DICOM modality.

Parameters
  • plan (PinnaclePlan) – The plan for which dose should be exported.

  • export_path (str, optional) – The file system path where the DICOM object should be exported to.

export_image(image=None, series_uid='', export_path='.')[source]

Exports an image from the Pinnacle data.

Parameters
  • image (PinnacleImage, optional) – The image to export.

  • series_uid (str, optional) – The SeriesInstanceUID of the image to export.

  • export_path (str, optional) – The file system path where the DICOM objects should be exported to.

static export_plan(plan, export_path='.')[source]

Exports the RTPLAN DICOM modality.

Parameters
  • plan (PinnaclePlan) – The plan for which dose should be exported.

  • export_path (str, optional) – The file system path where the DICOM object should be exported to.

static export_struct(plan, export_path='.')[source]

Exports the RTSTRUCT DICOM modality.

Parameters
  • plan (PinnaclePlan) – The plan for which structures should be exported.

  • export_path (str, optional) – The file system path where the DICOM object should be exported to.

property images

Get the images available.

Returns

images – List of PinnacleImage’s available within the Pinnacle raw data in the path configured.

Return type

list

log_images()[source]

Outputs all images found in the Pinnacle data to the log.

log_plan_names()[source]

Outputs all plans found in the Pinnacle data to the log.

log_trial_names()[source]

Outputs all trials found in the Pinnacle data to the log.

log_trial_names_in_plan(plan)[source]

Outputs all trials found within a plan to the log.

Parameters

plan (PinnaclePlan) – The plan for which to log the trials.

property logger

Gets the configured logger.

Returns

logger – Logger configured.

Return type

Logger

property patient_info

Gets the patient info.

Returns

patient_info – Dictionary object containing the data found in the ‘Patient’ file within the raw Pinnacle data.

Return type

dict

property plans

Get the plans available.

Returns

plans – List of PinnaclePlan’s available within the Pinnacle raw data in the path configured.

Return type

list

class pymedphys.experimental.pinnacle.PinnaclePlan(pinnacle, path, plan)[source]

Represents a plan within the Pinnacle data.

This class manages the data specific to a plan within a Pinnacle dataset.

Parameters
  • pinnacle (PinnacleExport) – PinnacleExport object representing the dataset.

  • path (str) – Path to raw Pinnacle data (directoy containing ‘Patient’ file).

  • plan (dict) – Plan info dict from ‘Patient’ file.

property active_trial

Get and set the active trial for this plan.

When DICOM objects are exported, data from the active trial is used to generate the output.

convert_point(point)[source]

Convert a point from Pinnacle coordinates to DICOM coordinates.

Parameters

point (list) – The point to convert.

Returns

Return type

The converted point.

property dose_inst_uid

Gets the instance UID for RTDOSE.

Returns

uid – The UID to use for the dose.

Return type

str

generate_uids(uid_type='HASH')[source]

Generates UIDs to be used for exporting this plan.

Parameters

uid_type (str, optional) – If ‘HASH’, the entropy will be generated to hash to consistant UIDs. If not then random UIDs will be generated. Default: ‘HASH’

static is_prefix_valid(prefix)[source]

Check if a UID prefix is valid.

Parameters

prefix (str) – The UID prefix to check.

Returns

True if valid, False otherwise.

property iso_center

Gets and sets the iso center for this plan.

property logger

Gets the configured logger.

Returns

logger – Logger configured.

Return type

Logger

property machine_info

Gets the machine info for this plan.

Returns

machine_info – Machine info read from ‘plan.Pinnacle.Machines’ file.

Return type

dict

property path

Gets the path of the Pinnacle data.

Returns

path – Path containing the Pinnacle data.

Return type

str

property patient_position

Gets the patient position

Returns

patient_position – The patient position for this plan.

Return type

str

property pinnacle

Gets the PinnacleExport object.

Returns

pinnacle – PinnacleExport object for this dataset.

Return type

PinnacleExport

property plan_info

Gets the plan information for this plan.

Returns

plan_info – Plan info as found in the Pinnacle ‘Patient’ file.

Return type

dict

property plan_inst_uid

Gets the instance UID for RTPLAN.

Returns

uid – The UID to use for the plan.

Return type

str

property points

Gets the points defined within the plan.

Returns

points – List of points read from the ‘plan.Points’ file.

Return type

list

property primary_image

Gets the primary image for this plan.

Returns

primary_image – PinnacleImage representing the primary image for this plan.

Return type

PinnacleImage

property struct_inst_uid

Gets the instance UID for RTSTRUCT.

Returns

uid – The UID to use for the struct.

Return type

str

property trial_info

Gets the trial information of the active trial.

Returns

trial_info – Trial info from the ‘plan.Trial’ file.

Return type

dict

property trials

Gets the trials within this plan.

Returns

trials – List of all trials found within this plan.

Return type

list

class pymedphys.experimental.pinnacle.PinnacleImage(pinnacle, path, image)[source]

Represents an image within the Pinnacle data.

This class manages the data specific to an image within a Pinnacle dataset.

Parameters
  • pinnacle (PinnacleExport) – PinnacleExport object representing the dataset.

  • path (str) – Path to raw Pinnacle data (directoy containing ‘Patient’ file).

  • image (dict) – Image info dict from ‘Patient’ file.

property image

Gets the image information from the ‘Patient’ file.

Returns

image – Image info as found in the Pinnacle ‘Patient’ file.

Return type

dict

property image_header

Gets the image header from the ‘.header’ file.

Returns

image_header – Image info as found in the Pinnacle ‘.header’ file.

Return type

dict

property image_info

Gets the image information from the ‘.ImageInfo’ file.

Returns

image_info – Image info as found in the Pinnacle ‘.ImageInfo’ file.

Return type

dict

property image_set

Gets the image set from the ‘.ImageSet’ file.

Returns

image_set – Image set as found in the Pinnacle ‘.ImageSet’ file.

Return type

dict

property logger

Gets the configured logger.

Returns

logger – Logger configured.

Return type

Logger

property path

Gets the path of the Pinnacle data.

Returns

path – Path containing the Pinnacle data.

Return type

str

property pinnacle

Gets the PinnacleExport object.

Returns

pinnacle – PinnacleExport object for this dataset.

Return type

PinnacleExport

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