Source code for pymedphys._pinnacle.pinnacle_image
# 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.
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# http://www.apache.org/licenses/LICENSE-2.0
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# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# 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]
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# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
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import os
from .pinn_yaml import pinn_to_dict
[docs]class PinnacleImage:
"""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.
"""
def __init__(self, pinnacle, path, image):
self._pinnacle = pinnacle
self._path = path
self._image = image
self._image_info = None # Data from ImageInfo
self._image_header = None # Data from .header file
self._image_set = None # Data from .ImageSet file
@property
def logger(self):
"""Gets the configured logger.
Returns
-------
logger : Logger
Logger configured.
"""
return self._pinnacle.logger
@property
def pinnacle(self):
"""Gets the PinnacleExport object.
Returns
-------
pinnacle : PinnacleExport
PinnacleExport object for this dataset.
"""
return self._pinnacle
@property
def path(self):
"""Gets the path of the Pinnacle data.
Returns
-------
path : str
Path containing the Pinnacle data.
"""
return self._path
@property
def image(self):
"""Gets the image information from the 'Patient' file.
Returns
-------
image : dict
Image info as found in the Pinnacle 'Patient' file.
"""
return self._image
@property
def image_info(self):
"""Gets the image information from the '.ImageInfo' file.
Returns
-------
image_info : dict
Image info as found in the Pinnacle '.ImageInfo' file.
"""
if not self._image_info:
path_image_info = os.path.join(
self._path, f"ImageSet_{self._image['ImageSetID']}.ImageInfo"
)
# Make sure the ImageInfo file really exists
if not os.path.exists(path_image_info):
self.logger.warning("ImageInfo path doesn't exist: %s", path_image_info)
return None
self.logger.debug("Reading image data from: %s", path_image_info)
self._image_info = pinn_to_dict(path_image_info)
return self._image_info
@property
def image_header(self):
"""Gets the image header from the '.header' file.
Returns
-------
image_header : dict
Image info as found in the Pinnacle '.header' file.
"""
if not self._image_header:
path_image_header = os.path.join(
self._path, f"ImageSet_{self._image['ImageSetID']}.header"
)
# Make sure the ImageInfo file really exists
if not os.path.exists(path_image_header):
self.logger.warning(
"ImageHeader path doesn't exist: %s", path_image_header
)
return None
self.logger.debug("Reading image data from: %s", path_image_header)
self._image_header = {}
with open(path_image_header) as f:
for line in f:
parts = line.split(" = ")
if len(parts) < 2:
parts = line.split(" : ")
if len(parts) > 1:
self._image_header[parts[0].strip()] = (
parts[1].replace(";", "").replace("\n", "")
)
return self._image_header
@property
def image_set(self):
"""Gets the image set from the '.ImageSet' file.
Returns
-------
image_set : dict
Image set as found in the Pinnacle '.ImageSet' file.
"""
if not self._image_set:
path_image_set = os.path.join(
self._path, f"ImageSet_{self._image['ImageSetID']}.ImageSet"
)
# Make sure the ImageInfo file really exists
if not os.path.exists(path_image_set):
self.logger.warning("ImageSet path doesn't exist: %s", path_image_set)
return None
self.logger.debug("Reading image data from: %s", path_image_set)
self._image_set = pinn_to_dict(path_image_set)
parts = self._image_set["ScanTimeFromScanner"].split(" ")
self._image_set["scan_date"] = parts[0].replace("-", "")
self._image_set["scan_time"] = parts[1].replace(":", "")
return self._image_set
