# Copyright (C) 2019 South Western Sydney Local Health District,
# University of New South Wales
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
# This work is derived from:
# https://github.com/AndrewWAlexander/Pinnacle-tar-DICOM
# which is released under the following license:
# Copyright (c) [2017] [Colleen Henschel, Andrew Alexander]
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
# The above copyright notice and this permission notice shall be included in all
# copies or substantial portions of the Software.
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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# SOFTWARE.
import logging
import os
import sys
import warnings
from .image import convert_image
from .pinn_yaml import pinn_to_dict
from .pinnacle_image import PinnacleImage
from .pinnacle_plan import PinnaclePlan
from .rtdose import convert_dose
from .rtplan import convert_plan
from .rtstruct import convert_struct
[docs]class PinnacleExport:
"""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.
"""
def __init__(self, path, logger=None):
# Show a warning to ensure that this module is used with caution
warnings.warn(
"The Pinnacle Export Module is intended for research purposes only. Parts "
"of the DICOM conversion are hard-coded and completely ignore your data. "
"This has proven useful for research applications but is not appropriate "
"for clinical use.",
category=UserWarning,
stacklevel=2,
)
self._logger = logger # Logger to use for all logging
self._path = path # Path to the root directory of the dataset
# (containing the Patient file)
self._patient_info = None # The patient data read from
self._plans = None # Pinnacle plans for this path
self._images = None # Images found in image.info
if not self._logger:
self._logger = logging.getLogger(__name__)
self._logger.setLevel(logging.DEBUG)
if len(self._logger.handlers) == 0:
ch = logging.StreamHandler(sys.stdout)
formatter = logging.Formatter(
"%(asctime)s - %(levelname)s - %(message)s"
)
ch.setFormatter(formatter)
ch.setLevel(logging.DEBUG)
self._logger.addHandler(ch)
@property
def logger(self):
"""Gets the configured logger.
Returns
-------
logger : Logger
Logger configured.
"""
return self._logger
@property
def patient_info(self):
"""Gets the patient info.
Returns
-------
patient_info : dict
Dictionary object containing the data found in the 'Patient'
file within the raw Pinnacle data.
"""
if not self._patient_info:
path_patient = os.path.join(self._path, "Patient")
self.logger.debug("Reading patient data from: %s", path_patient)
self._patient_info = pinn_to_dict(path_patient)
# Set the full patient name
last_name = self._patient_info["LastName"]
first_name = self._patient_info["FirstName"]
middle_name = self._patient_info["MiddleName"]
self._patient_info["FullName"] = f"{last_name}^{first_name}^{middle_name}^"
# gets birthday string with numbers and dashes
dobstr = self._patient_info["DateOfBirth"]
if "-" in dobstr:
dob_list = dobstr.split("-")
elif "/" in dobstr:
dob_list = dobstr.split("/")
else:
dob_list = dobstr.split(" ")
dob = ""
for num in dob_list:
if len(num) == 1:
num = f"0{num}"
dob = f"{dob}{num}"
self._patient_info["DOB"] = dob
return self._patient_info
@property
def plans(self):
"""Get the plans available.
Returns
-------
plans : list
List of PinnaclePlan's available within the Pinnacle raw data in the path
configured.
"""
# Read patient info to populate patients plans
if not self._plans:
self._plans = []
for plan in self.patient_info["PlanList"]:
path_plan = os.path.join(self._path, f"Plan_{plan['PlanID']}")
self._plans.append(PinnaclePlan(self, path_plan, plan))
return self._plans
@property
def images(self):
"""Get the images available.
Returns
-------
images : list
List of PinnacleImage's available within the Pinnacle raw data in the path
configured.
"""
# Read patient info to populate patients images
if not self._images:
self._images = []
for image in self.patient_info["ImageSetList"]:
pi = PinnacleImage(self, self._path, image)
# Check that image info exists to ensure the image is really available
if pi.image_info:
self._images.append(pi)
return self._images
@staticmethod
def export_struct(plan, export_path=".", skip_pattern="^$"):
"""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.
skip_pattern : str, optional
A regular expression specifying which ROIs to skip
For example: RadCalc|normal_tissue
"""
# Export Structures for plan
convert_struct(plan, export_path, skip_pattern)
@staticmethod
def export_dose(plan, export_path="."):
"""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 dose for plan
convert_dose(plan, export_path)
@staticmethod
def export_plan(plan, export_path="."):
"""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.
"""
# Export rtplan for plan
convert_plan(plan, export_path)
def export_image(self, image=None, series_uid="", export_path="."):
"""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.
"""
if not image and not series_uid:
self.logger.error("No image to export")
for im in self.images:
im_info = im.image_info[0]
im_suid = im_info["SeriesUID"]
if len(series_uid) > 0 and im_suid == series_uid:
convert_image(im, export_path)
break
if image:
convert_image(image, export_path)
def log_images(self):
"""Outputs all images found in the Pinnacle data to the log."""
for i in self.images:
image_header = i.image_header
if not image_header:
# If no ImageHeader is available then we can ignore this
continue
modality = "?"
if "modality" in image_header.keys():
modality = image_header["modality"]
series_uid = "?"
if "series_UID" in image_header.keys():
series_uid = image_header["series_UID"]
series_date_time = "?"
if "SeriesDateTime" in image_header.keys():
series_date_time = image_header["SeriesDateTime"]
self.logger.info("%s: %s %s", modality, series_uid, series_date_time)
def log_plan_names(self):
"""Outputs all plans found in the Pinnacle data to the log."""
for p in self.plans:
self.logger.info(p.plan_info["PlanName"])
def log_trial_names(self):
"""Outputs all trials found in the Pinnacle data to the log."""
for p in self.plans:
self.logger.info("### %s ###", p.plan_info["PlanName"])
for t in p.trials:
self.logger.info("- %s", t["Name"])
def log_trial_names_in_plan(self, plan):
"""Outputs all trials found within a plan to the log.
Parameters
----------
plan : PinnaclePlan
The plan for which to log the trials.
"""
self.logger.info("### %s ###", plan.plan_info["PlanName"])
self.logger.info(plan.path)
for trial in plan.trials:
self.logger.info("- %s", trial["Name"])
