Source code for pymedphys._experimental.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");
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# 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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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, "rt") 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

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