Source code for modelhublib.processor

import numpy as np

from .imageloaders import PilImageLoader, SitkImageLoader
from .imageconverters import PilToNumpyConverter, SitkToNumpyConverter


[docs]class ImageProcessorBase(object): """ Abstract base class for image pre- and postprocessing, thus handeling all data processing before and after the inference. Several methods of this class have to be implemented in a contributed model. Follow the "Contribute Your Model to Modelhub" guide for detailed instructions. An image processor handles: 1. Loading of the input image(s). 2. Converting the loaded images to a numpy array 3. Preprocessing the image data (either on the image object or on the numpy array) After this step the data should be prepared to be directly feed to the inference step. 4. Processing the inference result and convert it to the expected output format. This class already provides loading and conversion of images using PIL and SimpleITK. If you need to support image formats which are not covered by those two, you should implement an additional :class:`~modelhublib.imageloaders.imageLoader.ImageLoader` and :class:`~modelhublib.imageconverters.imageConverter.ImageConverter`. If you do so, you will also need to overwrite the constructor (__init__) to instantiate your loader and converter and include them in the chain of responsibility. Best practice would be to call the original constructor from your derived class and then change what you need to change. Args: config (dict): Model configuration (loaded from model's config.json) """ def __init__(self, config): self._config = config self._imageLoader = PilImageLoader(self._config) self._imageLoader.setSuccessor(SitkImageLoader(self._config)) self._imageToNumpyConverter = PilToNumpyConverter() self._imageToNumpyConverter.setSuccessor(SitkToNumpyConverter())
[docs] def loadAndPreprocess(self, input): """ Loads input, preprocesses it and returns a numpy array appropriate to feed into the inference model (4 dimensions: [batchsize, z/color, height, width]). There should be no need to overwrite this method in a derived class! Rather overwrite the individual preprocessing steps used by this method! Args: input (str): Name of the input file to be loaded Returns: numpy array appropriate to feed into the inference model (4 dimensions: [batchsize, z/color, height, width]) """ image = self._load(input) image = self._preprocessBeforeConversionToNumpy(image) npArr = self._convertToNumpy(image) npArr = self._preprocessAfterConversionToNumpy(npArr) return npArr
[docs] def computeOutput(self, inferenceResults): """ Abstract method. Overwrite this method to define how to postprocess the inference results computed by the model into a proper output as defined in the model configuration file. Args: inferenceResults: Results of the inference as computed by the model. Returns: Converted inference results into format as defined in the model configuration. """ raise NotImplementedError("This is a method of an abstract class.")
[docs] def _load(self, input): """ Performs the actual loading of the image. There should be no need to overwrite this method in a derived class! Rather implement an additional :class:`~modelhublib.imageloaders.imageLoader.ImageLoader` to support further image formats. See also documentation of :class:`~ImageProcessorBase` above. Args: input (str): Name of the input file to be loaded Returns: Image object which type will be the native image object type of the library/handler used for loading (default implementation uses PIL or SimpleITK). Hence it might not always be the same. """ image = self._imageLoader.load(input) return image
[docs] def _preprocessBeforeConversionToNumpy(self, image): """ Perform preprocessing on the loaded image object (see :func:`~modelhublib.processor.ImageProcessorBase._load`). Overwrite this to implement image preprocessing using the loaded image object. If not overwritten, just returns the image object unchanged. When overwriting this, make sure to handle the possible types appropriately and throw an IOException if you cannot preprocess a certain type. Args: image (type = return of :func:`~modelhublib.processor.ImageProcessorBase._load`): Loaded image object Returns: Image object which must be of the same type as input image object. """ return image
[docs] def _convertToNumpy(self, image): """ Converts the image object into a corresponding numpy array with 4 dimensions: [batchsize, z/color, height, width]. There should be no need to overwrite this method in a derived class! Rather implement an additional :class:`~modelhublib.imageconverters.imageConverter.ImageConverter` to support further image format conversions. See also documentation of :class:`~ImageProcessorBase` above. Args: image: (type = return of :func:`~modelhublib.processor.ImageProcessorBase._preprocessBeforeConversionToNumpy`): Loaded and preproceesed image object. Returns: Representation of the input image as numpy array with 4 dimensions [batchsize, z/color, height, width]. """ npArr = self._imageToNumpyConverter.convert(image) return npArr
[docs] def _preprocessAfterConversionToNumpy(self, npArr): """ Perform preprocessing on the numpy array (the result of _convertToNumpy()). Overwrite this to implement preprocessing on the converted numpy array. If not overwritten, just returns the input array unchanged. Args: npArr (numpy array): input data after conversion by :func:`~modelhublib.processor.ImageProcessorBase._convertToNumpy` Returns: Preprocessed numpy array with 4 dimensions [batchsize, z/color, height, width]. """ return npArr