PrognosAIs

Documentation

Quick start

This page will show a quick-start of using prognosais, including installation and a simple toy experiment.

Installation

Prognosais can be installed using pip. It is recommended to install prognosais in a virtual environment: The following code block creates a virtual environment and installs prognosais in a linux environment.

mkdir ~/prognosais && cd ~/prognosais
python3 -m venv env
source env/bin/activate
pip install prognosais

Example experiment

We will now set up an example experiment to show how prognosais works and to explain the settings of prognosais. First we set up the experiment by installing the additionaly required packages and obtain the code of the examples: (This assumes that the virtual environment has been set-up as specified under installation)

cd ~/prognosais
source env/bin/activate
pip install xlrd
git clone https://github.com/Svdvoort/prognosais_examples
cd prognosais_examples

Now, we need to download the data for the example experiment. This data is part of the ‘LGG-1p19qDeletion’ collection on TCIA More information can be found in the accompanying publication.

We will now download the data to a directory of our choosing:

python download_1p19q_data.py

You will now be prompted for a directory in which to save the data. Wait untill the data is done downloading and extracting. The script will have prepared the input data and the download data, you can have a look in the download folder you specified.

The script will provide the input folder and label file that need to be specified. Open the config.yml file (in the prognosais_examples folder), you can have a look here at the different settings, which are explained more in depth in the file itself. For now we need to change three parameters:

1. input_folder under general, which is set to /path/to/input/, needs to be changed to the input folder provided by the download script

2. label_file under preprocessing > labeling which is set to \path\to\label_file, needs to be changed to the label file provided by the download script

3. output_folder under general, which is set to /path/to/output, needs to be changed to a folder of your choice in which the output will be saved.

If you want to speed-up the pre-processing you can also change the ‘max_cpus’ setting in preprocessing > general. By default, this is set to 1 which means that only 1 cpu core will be used, increase this if you have multiple cores available.

Once this is done the experiment can simply be run with

python example_pipeline.py

This will run the pipeline, including the pre-processing of the scans, the training of the model (a ResNet) and the evaluation of the model on the validation and test set. The results will be placed in the folder you specified under ‘output_folder’, in a subfolder starting with ResNet_18. This folder contains the pre-processed samples, the trained model (including logs from callbacks), and the evaluated results.

Custom network example

This page will continue the quick-start by showing how to implement and train your own network. It is assumed that you already followed the quick-start and set up the example there.

Implementing your own network

Prognosais was designed to make designing and training your own network as simple as possible.

Basic example: classification network

The simplest case is that of a ‘classification’ network, where samples belong to a discrete class (this can be either a single output label or a segmentation). In this case, only the model itself needs to be implemented.

We start by going to the directory with examples created earlier and creating the virtual environment. Here we will also create file my_definitions.py to contain our custom network

cd ~/prognosais
source env/bin/activate
cd prognosais_examples/
touch my_definitions.py

Now open my_definitions.py in your favorite editor and past the following into the file and save it:

from tensorflow.keras.layers import Concatenate, Conv3D, Dense, Flatten, ReLU
from tensorflow.keras.models import Model
from PrognosAIs.Model.Architectures.Architecture import ClassificationNetworkArchitecture, NetworkArchitecture

class SimpleNetwork_3D(ClassificationNetworkArchitecture):
    # We derive this class from the base class of the classification network
    # The class should be name as followed: {arbitrary_name}_2D for a 2D network or {arbitrary_name}_3D for a 3D network
    # In this way Prognosais will automatically chose the appropriate network based on the input dimensions

    def create_model(self):
        # Since we use the ClassificationNetworkArchitecture, we only need to define the function create_model
        # This function should construct the model and return it.

        # The inputs are already automatically defined, we can get them from `self`
        # In this case we assume there is only 1 input (for multiple inputs see more complicated examples later)
        inputs = self.inputs

        # We will now create a very simple model
        conv_1 = Conv3D(filters=4, kernel_size=(2, 2, 2))(inputs)

        relu_1 = ReLU()(conv_1)

        flatten_1 = Flatten()(relu_1)

        dense_1 = Dense(units=256)(flatten_1)

        # Since we use a ClassificationNetworkArchitecture, the outputs are defined already as well
        # In this case by default we get softmax output
        predictions = self.outputs(dense_1)

        # We construct the model and return it

        return Model(inputs=self.inputs, outputs=predictions)

Now we need to edit the config.yml file in two places:

1. Under general add the following: custom_definitions_file: my_definitions.py. This will make prognosais load your file with custom definitions

2. Under model change model_name to SimpleNetwork, this will make sure we use our just defined network.

For the model_name parameter you never need to add the _2D or _3D part, prognosais will add this automatically based on the dimensions of the input.

The pipeline can now be run again and this new model will be trained:

python example_pipeline.py

Of course the model will perform very poorly since it is quite simple, but of course you can make the model as complex as you want.

Advanced example: multiple inputs/outputs

Creating a network that accepts multiple inputs or outputs is not much more complicated than creating the simple network shown in the previous example. We will expand the previous simple network to deal with multiple inputs and outputs. Once again open the my_definitions.py file and add the following code:

class NetworkMultiInputMultiOutput_3D(ClassificationNetworkArchitecture):
    def create_model(self):
        # Once again the inputs are automatically created
        # However, since in our toy example data we only have one input and one output, we need to override the default settings
        self.inputs = self.make_inputs(self.input_shapes, self.input_data_type, squeeze_inputs=False)
        self.outputs = self.make_outputs(self.output_info, self.output_data_type, squeeze_outputs=False)
        # By setting squeeze to False, we ensure that even though we do not have multiple inputs/outputs, the inputs and outputs will
        # still be created as if there were actually multiple inputs and outputs
        # If you are sure that you always have multiple inputs/outputs you can use the self.inputs and self.outputs variables directly
        # Otherwise the above two lines are a safe alternative, making sure your model works regardless of the number of inputs/outputs

        # Now the self.inputs variable is actually a dictionary, where the keys are the different input names and the values the actual inputs
        # In this case apply a different convolutional filter to each input, and then concatenate all the inputs

        input_branches = []
        for i_input in self.inputs.values():
            input_branches.append(Conv3D(filters=4, kernel_size=(2, 2, 2))(i_input))

        # Only concatenate if there is more than 1 input
        if len(input_branches) > 1:
            concat_1 = Concatenate()(input_branches)
        else:
            concat_1 = input_branches[0]

        relu_1 = ReLU()(concat_1)

        flatten_1 = Flatten()(relu_1)

        dense_1 = Dense(units=256)(flatten_1)

        # The output are defined similarly, a dictionary with the keys the names of the outputs
        # Thus we can easily create multiple outputs in the following way:
        predictions = []
        for i_output in self.outputs.values():
            predictions.append(i_output(dense_1))

        # If you want to do different things with your outputs you can of course also do something like:
        # predictions = []
        # predictions.append(Dense(units=5, activation="softmax", name="output_1")
        # predictions.append(Dense(units=15, activation="relu", name="output_2")
        # Make sure that the name matches the output labels as defined in your label file!
        # You can also get the output labels from self.output_info.keys()

        # We construct the model and return it

        return Model(inputs=self.inputs, outputs=predictions)

We now need to change the config.yml file to train this new network. Simply change model_name under model to NetworkMultiInputMultiOutput, this will make sure we use our just defined network. The model can now be trained:

python example_pipeline.py

Of course in this example nothing will change compared to the previous example, since our data only has one input and one output.

Advanced example: non-classification network

In the above examples we have always used a ClassificationNetworkArchitecture, which makes it easier to implement our own network. However, it is possible to implement any arbitrary network using the more basic NetworkArchitecture, of which we present an example here.

Once again open my_definitions.py and add the following:

class NonClassificationNetwork_3D(NetworkArchitecture):
    # We have now used the NetworkArchitecture as the base class
    # We use the same model as the first basic example, nothing changed here
    def create_model(self):
        # Since we use the ClassificationNetworkArchitecture, we only need to define the function create_model
        # This function should construct the model and return it.

        # We need to load the inputs and outputs, they are not automatically generated in this case
        self.inputs = self.make_inputs(self.input_shapes, self.input_data_type)
        self.outputs = self.make_outputs(self.output_info, self.output_data_type)

        # We will now create a very simple model
        conv_1 = Conv3D(filters=4, kernel_size=(2, 2, 2))(self.inputs)

        relu_1 = ReLU()(conv_1)

        flatten_1 = Flatten()(relu_1)

        dense_1 = Dense(units=256)(flatten_1)

        # Since we use a ClassificationNetworkArchitecture, the outputs are defined already as well
        # In this case by default we get softmax output
        predictions = self.outputs(dense_1)

        # We construct the model and return it

        return Model(inputs=self.inputs, outputs=predictions)

    # However, we now also need to define a make_outputs function, since we do not have default for this for this basic architecture
    @staticmethod
    def make_outputs(
        output_info: dict,
        output_data_type: str,
        activation_type: str = "linear",
        squeeze_outputs: bool = True,
    ) -> dict:
        # The variables output_info and output_date_type are required in any make_outputs function, however apart from that you can
        # create any additional parameters that you want

        # The below code will create a dictionary of outputs (one item for each output) and we create a dense layer with one node and linear activation
        # The dtype is float32 but can be adjusted if required for your problem
        outputs = {}
        for i_output_name in output_info.keys():
            outputs[i_output_name] = Dense(
                1, name=i_output_name, activation="linear", dtype="float32",
            )

        # To make it easier for cases where there is only one output we will squeeze the output
        # Returning only that output instead of a dict
        if squeeze_outputs and len(outputs) == 1:
            outputs = list(outputs.values())[0]

        return outputs

We cannot train this model as the toy example dataset only has discrete data. However, this shows how a model can be implemented that has arbitrary outputs.

API documentation

PrognosAIs.IO package

Submodules

PrognosAIs.IO.ConfigLoader module

class PrognosAIs.IO.ConfigLoader.ConfigLoader(config_file)

Bases: object

copy_config(output_folder, save_name=None)

get_N_classes()

get_N_epoch()

get_N_jobs()

get_N_max_patches()

get_batch_size()

get_cache_in_memory()

get_callback_settings()

get_center_patch_around_mask()

get_class_weights()

get_cluster_setting()

get_cluster_type()

get_combine_patch_predictions()

get_config_file()

get_copy_files()

get_custom_definitions_file()

get_data_augmentation()

get_data_augmentation_factor()

get_data_augmentation_settings()

get_data_folder()

get_dataset_distribution()

get_do_augmentation()

get_dtype()

get_evaluate_metrics()

get_evaluate_train_set()

get_evaluation_mask_labels()

get_evaluation_metric_settings()

get_extra_input_file()

get_filter_missing()

get_float16_epsilon()

get_float_policy()

get_fsl_reorient_bin()

get_fsl_val_bin()

get_gpu_workers()

get_image_size()

get_input_folder()

get_keep_rejected_patches()

get_label_combination_type()

get_label_file()

get_loss_settings()

get_loss_weights()

get_make_one_hot()

get_make_patches()

get_mask_file()

get_mask_keyword()

get_max_steps_per_epoch()

get_metric_settings()

get_min_patch_voxels()

get_model_file()

get_model_name()

get_model_settings()

get_multi_channels_patches()

get_optimizer_settings()

get_output_folder()

get_patch_predictions()

get_patch_size()

get_preprocessings_settings()

get_processed_samples_folder()

get_random_state()

get_reject_patches()

get_resample_images()

get_resample_size()

get_rescale_mask_intensity()

get_resume_training_from_model()

get_save_name()

get_shuffle()

get_shuffle_evaluation()

get_shuffle_val()

get_size_string()

get_specific_output_folder()

get_stratify_index()

get_test_data_folder()

get_test_label_file()

get_test_model_file()

get_training_multi_processing()

get_use_class_weights()

get_use_class_weights_in_losses()

get_use_labels_from_rejection()

get_use_mask_as_channel()

get_use_mask_as_label()

get_write_predictions()

PrognosAIs.IO.Configs module

class PrognosAIs.IO.Configs.bias_field_correcting_config(config_settings: dict)

Bases: PrognosAIs.IO.Configs.config

property mask

property mask_file

class PrognosAIs.IO.Configs.config(config_settings: Optional[dict])

Bases: object

static get_step_type(config: Optional[dict]) → Tuple[bool, bool, dict]

class PrognosAIs.IO.Configs.general_config(config_settings: dict)

Bases: PrognosAIs.IO.Configs.config

class PrognosAIs.IO.Configs.labeling_config(config_settings: dict)

Bases: PrognosAIs.IO.Configs.config

class PrognosAIs.IO.Configs.masking_config(config_settings: dict)

Bases: PrognosAIs.IO.Configs.config

property mask

property mask_file

class PrognosAIs.IO.Configs.multi_dimension_extracting_config(config_settings: dict)

Bases: PrognosAIs.IO.Configs.config

class PrognosAIs.IO.Configs.normalizing_config(config_settings: dict)

Bases: PrognosAIs.IO.Configs.config

property mask

property mask_file

class PrognosAIs.IO.Configs.patching_config(config_settings: dict)

Bases: PrognosAIs.IO.Configs.config

property patch_size

class PrognosAIs.IO.Configs.rejecting_config(config_settings: dict)

Bases: PrognosAIs.IO.Configs.config

property mask

property mask_file

class PrognosAIs.IO.Configs.resampling_config(config_settings: dict)

Bases: PrognosAIs.IO.Configs.config

class PrognosAIs.IO.Configs.saving_config(config_settings: dict)

Bases: PrognosAIs.IO.Configs.config

PrognosAIs.IO.DataGenerator module

class PrognosAIs.IO.DataGenerator.Augmentor(example_sample: tensorflow.python.framework.ops.Tensor, brightness_probability: float = 0, brightness_delta: float = 0, contrast_probability: float = 0, contrast_min_factor: float = 1, contrast_max_factor: float = 1, flip_probability: float = 0, to_flip_axis: Union[int, list] = 0, crop_probability: float = 0, crop_size: list = None, rotate_probability: float = 0, max_rotate_angle: float = 0, to_rotate_axis: Union[int, list] = 0)

Bases: object

__init__(example_sample: tensorflow.python.framework.ops.Tensor, brightness_probability: float = 0, brightness_delta: float = 0, contrast_probability: float = 0, contrast_min_factor: float = 1, contrast_max_factor: float = 1, flip_probability: float = 0, to_flip_axis: Union[int, list] = 0, crop_probability: float = 0, crop_size: list = None, rotate_probability: float = 0, max_rotate_angle: float = 0, to_rotate_axis: Union[int, list] = 0) → None

Augmentor to randomly augment the features of a sample.

Parameters

• example_sample (tf.Tensor) – Example sample from which settings for augmentation will be derived

• brightness_probability (float, optional) – Probability of augmenting brightness. Defaults to 0.

• brightness_delta (float, optional) – Brightness will be adjusted with value from -delta to delta. Defaults to 0.

• contrast_probability (float, optional) – Probability of augmenting contrast. Defaults to 0.

• contrast_min_factor (float, optional) – Minimum contrast adjustment factor. Defaults to 1.

• contrast_max_factor (float, optional) – Maximum contrast adjustment factor. Defaults to 1.

• flip_probability (float, optional) – Probability of a random flip. Defaults to 0.

• to_flip_axis (Union[int, list], optional) – Axis to flip the feature over. Defaults to 0.

• crop_probability (float, optional) – Probability of cropping the feature. Defaults to 0.

• crop_size (list, optional) – Size to crop the feature to. Defaults to None.

apply_augmentation(augmentation_probability: float, seed: tensorflow.python.framework.ops.Tensor = None) → bool

Whether the the augmentation step should be applied based on the probability.

Parameters

• augmentation_probability (float) – The probability with which the step should be applied

• seed (tf.Tensor) – Seed to make operation repeatable. Defaults to None.

Returns

bool – Whether the step should be applied

augment_sample(sample: tensorflow.python.framework.ops.Tensor, seed=None, is_mask=False) → tensorflow.python.framework.ops.Tensor

Apply random augmentations to the sample based on the config.

Parameters

sample (tf.Tensor) – sample to be augmented

Returns

tf.Tensor – augmented sample

get_seed() → tensorflow.python.framework.ops.Tensor

Get a random seed that can be used to make other operation repeatable.

Returns

tf.Tensor – The seed

pad_to_original_size(sample: tensorflow.python.framework.ops.Tensor) → tensorflow.python.framework.ops.Tensor

Pad back a (potentially) augmented sample to its original size.

Parameters

sample (tf.Tensor) – The sample to pad

Returns

tf.Tensor – The padded sample with the same size as before any augmentation steps

random_brightness(sample: tensorflow.python.framework.ops.Tensor, seed: tensorflow.python.framework.ops.Tensor = None) → tensorflow.python.framework.ops.Tensor

Randomly adjusts the brightness of a sample.

Brightness is adjusted by a constact factor over the whole image, drawn from a distribution between -delta and delta as set during the initialization of the augmentator.

Parameters

• sample (tf.Tensor) – Sample for which to adjust brightness.

• seed (tf.Tensor) – Seed to make operation repeatable. Defaults to None.

Returns

tf.Tensor – The augmented sample.

random_contrast(sample: tensorflow.python.framework.ops.Tensor, seed: tensorflow.python.framework.ops.Tensor = None) → tensorflow.python.framework.ops.Tensor

Randomly adjust the contrast of a sample.

The contrast is adjusted by keeping the mean of the sample the same as for the original sample, and squeezing or expending the distribution of the intensities around the mean. The amount of squeezing or expanding is randomly drawn from the minimum and maximum contrast set during initialization.

Parameters

• sample (tf.Tensor) – Sample for which to adjust contrast

• seed (tf.Tensor) – Seed to make operation repeatable. Defaults to None.

Returns

tf.Tensor – The augmented sample

random_cropping(sample: tensorflow.python.framework.ops.Tensor, seed: tensorflow.python.framework.ops.Tensor = None) → tensorflow.python.framework.ops.Tensor

Randomly crop a part of the sample.

The crop will have the size of the crop size defined upon initialization of the augmentator. The crop will happen for all channels in the same way, but will not crop out channels. The location of the crop will be randomly drawn from throughout the whole image.

Parameters

• sample (tf.Tensor) – The sample to be cropped

• seed (tf.Tensor) – Seed to make operation repeatable. Defaults to None.

Returns

tf.Tensor – The augmented sample

random_flipping(sample: tensorflow.python.framework.ops.Tensor, seed: tensorflow.python.framework.ops.Tensor = None) → tensorflow.python.framework.ops.Tensor

Randomly flip the sample along one or multiple axis.

Parameters

• sample (tf.Tensor) – Sample for which to apply flipping

• seed (tf.Tensor) – Seed to make operation repeatable. Defaults to None.

Returns

tf.Tensor – The augmented sample

random_rotate(feature: tensorflow.python.framework.ops.Tensor, seed: tensorflow.python.framework.ops.Tensor = None, interpolation_order: int = 3) → tensorflow.python.framework.ops.Tensor

class PrognosAIs.IO.DataGenerator.HDF5Generator(root_folder: str, batch_size: int = 16, shuffle: bool = False, max_steps: int = - 1, drop_batch_remainder: bool = True, labels_only: bool = False)

Bases: object

__init__(root_folder: str, batch_size: int = 16, shuffle: bool = False, max_steps: int = - 1, drop_batch_remainder: bool = True, labels_only: bool = False) → None

Generate data from HDF5 files to be used in a TensorFlow pipeline.

This generator loads sample data from HDF5 files, and does this efficiently making us of TensorFlow dataset functions. The inputs and outputs are dict, which allows for easy us in a multi-input and/or multi-output model

Parameters

• root_folder (str) – Folder in which the HDF5 files are stored

• batch_size (int, optional) – Batch size of the generator. Defaults to 16.

• shuffle (bool, optional) – Whether datset should be shuffled. Defaults to False.

• data_augmentation (bool, optional) – Whether data augmentation should be applied. Defaults to False.

• augmentation_factor (int, optional) – Number of times dataset should be repeated for augmentation. Defaults to 5.

• augmentation_settings (dict, optional) – Setting for the data augmenation. Defaults to None.

• max_steps (int, optional) – Maximum number of (iteration) steps to provide. Defaults to -1, in which case all samples are provied.

• drop_batch_remainder (bool, optional) – Whether to drop the remainder of the batch if it does not fit perfectly. Defaults to True.

• labels_only (bool, optional) – Whether to only provide labels. Defaults to False.

• feature_index (str, optional) – Name of the feature group in the HDF5 file. Defaults to “sample”.

• label_index (str, optional) – Name of the label group in the HDF5 file. Defaults to “label”.

_get_all_dataset_attributes(h5py_object: Union[h5py._hl.files.File, h5py._hl.dataset.Dataset, h5py._hl.group.Group]) → dict

Run through al groups and dataset to get the attributes.

Parameters

h5py_object (Union[h5py.File, h5py.Dataset, h5py.Group]) – Object for which to return the attributes

Returns

dict – Mapping between feature/label name and its attributes

_get_dataset_names(h5py_object: Union[h5py._hl.files.File, h5py._hl.dataset.Dataset, h5py._hl.group.Group]) → list

Run through all groups and dataset to get the names.

Parameters

h5py_object (Union[h5py.File, h5py.Dataset, h5py.Group]) – Object for which to return the dataset names

Returns

list – Dataset names in object

apply_augmentation(features: dict, labels: dict) → Tuple[dict, dict]

feature_loader(sample_location: tensorflow.python.framework.ops.Tensor) → dict

Load the features from a hdf5 sample file.

This loader only loads the labels, instead of the features and labels as done by features_and_labels_loader

Parameters

sample_location (tf.Tensor) – Location of the sample file

Returns

dict – Features loaded from the sample file

features_and_labels_loader(sample_location: tensorflow.python.framework.ops.Tensor) → Tuple[dict, dict, tensorflow.python.framework.ops.Tensor]

Load the features and labels from a hdf5 file to be used in a TensorFlow dataset pipeline.

This loader loads the features and labels from a hdf5 file using TensorFlowIO. The outputs are therefor directly cast to tensor and can be used in a TensorFlow graph. All features and labels from the file are loaded, and a dict is returned mapping the name of each feature and label to its respective value

Parameters

sample_location (tf.Tensor) – Location of the sample file

Returns

Tuple[dict, dict] –

The features (first output) and labels (second output) loaded

from the sample.

fits_in_memory(used_memory: int = 0)

get_all_dataset_attributes(sample_file: str = None) → dict

Get the attributes of the features and labels stored in the file.

Returns

dict – Mapping of the feature/label name to its attributes

get_dataset_attribute(dataset_name: str, attribute_name: str) → Any

Get the attribute of a specific dataset

Parameters

• dataset_name (str) – Name of dataset for which to get the attribute

• attribute_name (str) – Name of attribute to get

Returns

Any – The value of the attribute

get_dataset_names() → list

Get the names of all datasets in the sample.

Returns

list – Dataset names in the sample

get_feature_attribute(attribute_name: str) → dict

Get a specific attribute for all features.

Parameters

attribute_name (str) – Name of attribute to get

Returns

dict – Mapping between feature names and the attribute value

get_feature_dimensionality() → dict

Get the dimensionality of each feature.

Returns

dict – Dimensionality of each feature

get_feature_metadata() → dict

Get all metadata of all features.

Returns

dict – The metadata of all features

get_feature_metadata_from_sample(sample_location: str) → dict

Get the feature metadata of a specific sample.

Parameters

sample_location (str) – The file location of the sample

Returns

dict – The feature metadata of the sample

get_feature_shape() → dict

Get the shape of each feature.

Returns

dict – Shape of each feature

get_feature_size() → dict

Get the size of each feature.

The size only of the feature does not take into account the number of channels and only represents the size of an individual channel of the feature.

Returns

dict – Size of each feature

get_label_attribute(attribute_name: str) → dict

Get a specific attribute for all labels.

Parameters

attribute_name (str) – Name of attribute to get

Returns

dict – Mapping between label names and the attribute value

get_labels_are_one_hot() → dict

Get whether labels are one-hot encoded.

Returns

dict – One-hot encoding status of each label

get_number_of_channels() → dict

Get the number of feature channels.

Returns

dict – Number of channels for each feature

get_number_of_classes() → dict

Get the number of output classes.

Returns

dict – Number of output classes for each label

get_numpy_iterator() → numpy.nditer

Construct a numpy iterator instead of TensorFlow dataset.

The numpy iterator will provide exactly the same data as the TensorFlow dataset. However, it might be easier to inspect the data when using a numpy iterator instead of a TensorFlow dataset

Returns

np.nditer – The dataset

get_spec() → dict

Get the TensorSpec for all input features.

Returns

dict – Maps the name of each input feature to the TensorSpec of the input.

get_tf_dataset(num_parallel_calls: int = - 1) → tensorflow.python.data.ops.dataset_ops.DatasetV2

Construct a TensorFlow dataset.

The dataset is constructed based on the settings supplied to the DataGenerator. The dataset can then directly be used to train or evaluate a TensorFlow model

Parameters

num_parallel_calls (int) – Number of parallel process to use. Defaults to tf.data.experimental.AUTOTUNE.

Returns

tf.data.Dataset – The constructed dataset

label_loader(sample_location: tensorflow.python.framework.ops.Tensor) → dict

Load the labels from a hdf5 sample file.

This loader only loads the labels, instead of the features and labels as done by features_and_labels_loader

Parameters

sample_location (tf.Tensor) – Location of the sample file

Returns

dict – Labels loaded from the sample file

load_features(loaded_hdf5: tensorflow_io.core.python.ops.io_tensor.IOTensor) → dict

Load the features from a HDF5 tensor.

Parameters

loaded_hdf5 (tfio.IOTensor) – Tensor from which to load features

Returns

dict – Mapping between feature names and features

load_labels(loaded_hdf5: tensorflow_io.core.python.ops.io_tensor.IOTensor) → dict

Load the labels from a HDF5 tensor.

Parameters

loaded_hdf5 (tfio.IOTensor) – Tensor from which to load labels

Returns

dict – Mapping between label names and labels

setup_augmentation(augmentation_factor: int = 1, augmentation_settings: dict = {}) → None

Set up data augmentation in the generator.

Parameters

• augmentation_factor (int) – Repeat dataset this many times in augmentation. Defaults to 1.

• augmentation_settings (dict) – Setting to parse to augmentation instance. Defaults to {}.

setup_caching(cache_in_memory: Union[bool, str] = 'AUTO', used_memory: int = 0) → None

Set up caching of the dataset in RAM.

Parameters

• cache_in_memory (Union[bool, str]) – Whether dataset should be cached in memory. Defaults to PrognosAIs.Constants.AUTO, in which case the dataset will be cached in memory if it fits, otherwise it will not be cached

• used_memory (int) – Amount of RAM (in bytes) that is already being used. Defaults to 0.

Raises

ValueError – If an unknown cache setting is requested

setup_caching_shuffling_steps(dataset: tensorflow.python.data.ops.dataset_ops.DatasetV2) → tensorflow.python.data.ops.dataset_ops.DatasetV2

Set-up caching, shuffling and the iteration step in the dataset pipeline.

This function helps to ensure that caching, shuffling and step limiting is done properly and efficiently, no matter where in the dataset pipeline it is included.

Parameters

dataset (tf.data.Dataset) – Datset for which to include the steps

Returns

tf.data.Dataset – Datset with caching, shuffling and iteration steps included

setup_sharding(n_workers: int, worker_index: int) → None

Shard the dataset according to the number of workers and worker index

Parameters

• n_workers (int) – number of workers

• worker_index (int) – worker index

PrognosAIs.IO.LabelParser module

class PrognosAIs.IO.LabelParser.LabelLoader(label_file: str, filter_missing: bool = False, missing_value: int = - 1, make_one_hot: bool = False, new_root_path: str = None)

Bases: object

__init__(label_file: str, filter_missing: bool = False, missing_value: int = - 1, make_one_hot: bool = False, new_root_path: str = None) → None

Create a label loader, that can load the image paths and labels from a text file to be used for a data generator

Parameters

• label_file – The label file from which to read the labels

• filter_missing – Whether missing values should be masked when generating one hot labels and class weights

• missing_value – If filter_missing is True, this value is used to mask

• make_one_hot – Whether labels should be transformed to one hot labels

• new_root_path – If you want to move the files, this will be the new root path

encode_labels_one_hot() → None

Encode sample labels as one hot

Parameters

None

Returns

None

get_class_weights(json_serializable=False) → dict

Get class weights for unbalanced labels

Parameters

None

Returns

Scaled_weights –

the weights for each class of each label category, scaled

such that the total weights*number of samples of each class approximates the total number of samples

get_data() → dict

Get all data from the label file

Parameters

None

Returns

data – Dictionary mapping each sample to each label

get_label_categories() → list

Get categories of labels

Parameters

None

Returns

label_categories – Category names

get_label_category_type(category_name: str) → type

Get the type of a label of a specific category/class

Parameters

category_name – Name of the category/class to get type of

Returns

type – Type of the labels of the category

get_label_from_sample(sample: str) → dict

Get label from a sample

Parameters

sample – The sample from which to get the label

Returns

label – Label of the sample

get_labels() → list

Get all labels of all samples

Parameters

None

Returns

labels – List of labels

get_labels_from_category(category_name: str) → list

Get labels of a specific category/class

Parameters

category_name – Name of the category/class to get

Returns

list – Labels of the category

get_number_of_classes() → dict

Get number of classes for all categories

Parameters

None

Returns

number_of_classes – The number of classes for each category

get_number_of_classes_from_category(category_name: str) → int

Get number of classes for a label category

Parameters

category_name – Category to get number of classes for

Returns

number_of_classes – The number of classes for the category

get_number_of_samples() → int

Get number of samples

Parameters

None

Returns

number_of_samples – The number of samples

get_original_label_category_type(category_name: str) → type

Get the original type of a label of a specific category/class

Parameters

category_name – Name of the category/class to get type of

Returns

type – Type of the labels of the category

get_original_labels_from_category(category_name: str) → list

Get original labels of a specific category/class

Parameters

category_name – Name of the category/class to get

Returns

list – Original labels of the category

get_samples() → list

Get all labels of all samples

Parameters

None

Returns

samples – List of samples

replace_root_path() → None

Replace the root path of the sample files in case they have been moved to a different a different directory.

Parameters

new_root_path – Path in which the files are now located

Returns

None

PrognosAIs.IO.utils module

PrognosAIs.IO.utils.copy_directory(original_directory, out_directory)

PrognosAIs.IO.utils.create_directory(file_path, exist_ok=True)

PrognosAIs.IO.utils.delete_directory(file_path)

PrognosAIs.IO.utils.find_files_with_extension(file_path, file_extension)

PrognosAIs.IO.utils.get_available_ram(used_memory: int = 0) → int

Get the available RAM in bytes.

Returns

int – available in RAM in bytes

PrognosAIs.IO.utils.get_cpu_devices() → list

PrognosAIs.IO.utils.get_dir_size(root_dir)

Returns total size of all files in dir (and subdirs)

PrognosAIs.IO.utils.get_file_name(file_path, file_extension)

PrognosAIs.IO.utils.get_file_name_from_full_path(file_path)

PrognosAIs.IO.utils.get_file_path(file_path)

PrognosAIs.IO.utils.get_gpu_compute_capability(gpu: tensorflow.python.eager.context.PhysicalDevice) → tuple

PrognosAIs.IO.utils.get_gpu_devices() → list

PrognosAIs.IO.utils.get_number_of_cpus()

PrognosAIs.IO.utils.get_number_of_gpu_devices() → int

PrognosAIs.IO.utils.get_number_of_slurm_nodes() → int

PrognosAIs.IO.utils.get_parent_directory(file_path)

PrognosAIs.IO.utils.get_root_name(file_path)

PrognosAIs.IO.utils.get_subdirectories(root_dir: str) → list

PrognosAIs.IO.utils.gpu_supports_float16(gpu: tensorflow.python.eager.context.PhysicalDevice) → bool

PrognosAIs.IO.utils.gpu_supports_mixed_precision(gpu: tensorflow.python.eager.context.PhysicalDevice) → bool

PrognosAIs.IO.utils.load_module_from_file(module_path)

PrognosAIs.IO.utils.normalize_path(path)

PrognosAIs.IO.utils.setup_logger()

Module contents

PrognosAIs.Model package

Subpackages

PrognosAIs.Model.Architectures package

Submodules

PrognosAIs.Model.Architectures.AlexNet module

class PrognosAIs.Model.Architectures.AlexNet.AlexNet_2D(input_shapes: dict, output_info: dict, input_data_type='float32', output_data_type='float32', model_config={})

Bases: PrognosAIs.Model.Architectures.Architecture.ClassificationNetworkArchitecture

create_model()

Here the code to create the actual model

padding_type = 'valid'

class PrognosAIs.Model.Architectures.AlexNet.AlexNet_3D(input_shapes: dict, output_info: dict, input_data_type='float32', output_data_type='float32', model_config={})

Bases: PrognosAIs.Model.Architectures.Architecture.ClassificationNetworkArchitecture

create_model()

Here the code to create the actual model

padding_type = 'valid'

PrognosAIs.Model.Architectures.Architecture module

class PrognosAIs.Model.Architectures.Architecture.ClassificationNetworkArchitecture(input_shapes: dict, output_info: dict, input_data_type='float32', output_data_type='float32', model_config={})

Bases: PrognosAIs.Model.Architectures.Architecture.NetworkArchitecture

static make_outputs(output_info: dict, output_data_type: str, activation_type: str = 'softmax', squeeze_outputs: bool = True) → dict

Make the outputs

class PrognosAIs.Model.Architectures.Architecture.NetworkArchitecture(input_shapes: dict, output_info: dict, input_data_type='float32', output_data_type='float32', model_config: dict = {})

Bases: abc.ABC

static check_minimum_input_size(input_layer: tensorflow.python.keras.engine.input_layer.Input, minimum_input_size: numpy.ndarray)

abstract create_model()

Here the code to create the actual model

static get_corrected_stride_size(layer: <module 'tensorflow.keras.layers' from '/home/docs/checkouts/readthedocs.org/user_builds/prognosais/envs/latest/lib/python3.7/site-packages/tensorflow/keras/layers/__init__.py'>, stride_size: list, conv_size: list)

Ensure that the stride is never bigger than the actual input In this way any network can keep working, indepedent of size

make_dropout_layer(layer)

make_inputs(input_shapes: dict, input_dtype: str, squeeze_inputs: bool = True) → Union[dict, tensorflow.python.keras.engine.input_layer.Input]

abstract make_outputs(output_info: dict, output_data_type: str) → <module ‘tensorflow.keras.layers’ from ‘/home/docs/checkouts/readthedocs.org/user_builds/prognosais/envs/latest/lib/python3.7/site-packages/tensorflow/keras/layers/__init__.py’>

Make the outputs

PrognosAIs.Model.Architectures.DDSNet module

class PrognosAIs.Model.Architectures.DDSNet.DDSNet(input_shapes: dict, output_info: dict, input_data_type='float32', output_data_type='float32', model_config={})

Bases: PrognosAIs.Model.Architectures.Architecture.ClassificationNetworkArchitecture

get_DDS_block(layer, N_filters)

init_dimensionality(N_dimension)

class PrognosAIs.Model.Architectures.DDSNet.DDSNet_2D(input_shapes: dict, output_info: dict, input_data_type='float32', output_data_type='float32', model_config={})

Bases: PrognosAIs.Model.Architectures.DDSNet.DDSNet

create_model()

Here the code to create the actual model

dims = 2

class PrognosAIs.Model.Architectures.DDSNet.DDSNet_3D(input_shapes: dict, output_info: dict, input_data_type='float32', output_data_type='float32', model_config={})

Bases: PrognosAIs.Model.Architectures.DDSNet.DDSNet

create_model()

Here the code to create the actual model

dims = 3

PrognosAIs.Model.Architectures.DenseNet module

class PrognosAIs.Model.Architectures.DenseNet.DenseNet(input_shapes: dict, output_info: dict, input_data_type='float32', output_data_type='float32', model_config={})

Bases: PrognosAIs.Model.Architectures.Architecture.ClassificationNetworkArchitecture

get_dense_block(layer, N_filters, N_conv_layers)

get_dense_stem(layer, N_filters)

get_transition_block(layer, N_filters, theta)

init_dimensionality(N_dimension)

class PrognosAIs.Model.Architectures.DenseNet.DenseNet_121_2D(input_shapes: dict, output_info: dict, input_data_type='float32', output_data_type='float32', model_config={})

Bases: PrognosAIs.Model.Architectures.DenseNet.DenseNet

GROWTH_RATE = 32

INITIAL_FILTERS = 64

THETA = 0.5

create_model()

Here the code to create the actual model

dims = 2

class PrognosAIs.Model.Architectures.DenseNet.DenseNet_121_3D(input_shapes: dict, output_info: dict, input_data_type='float32', output_data_type='float32', model_config={})

Bases: PrognosAIs.Model.Architectures.DenseNet.DenseNet

GROWTH_RATE = 32

INITIAL_FILTERS = 64

THETA = 0.5

create_model()

Here the code to create the actual model

dims = 3

class PrognosAIs.Model.Architectures.DenseNet.DenseNet_169_2D(input_shapes: dict, output_info: dict, input_data_type='float32', output_data_type='float32', model_config={})

Bases: PrognosAIs.Model.Architectures.DenseNet.DenseNet

GROWTH_RATE = 32

INITIAL_FILTERS = 64

THETA = 0.5

create_model()

Here the code to create the actual model

dims = 2

class PrognosAIs.Model.Architectures.DenseNet.DenseNet_169_3D(input_shapes: dict, output_info: dict, input_data_type='float32', output_data_type='float32', model_config={})

Bases: PrognosAIs.Model.Architectures.DenseNet.DenseNet

GROWTH_RATE = 32

INITIAL_FILTERS = 64

THETA = 0.5

create_model()

Here the code to create the actual model

dims = 3

class PrognosAIs.Model.Architectures.DenseNet.DenseNet_201_2D(input_shapes: dict, output_info: dict, input_data_type='float32', output_data_type='float32', model_config={})

Bases: PrognosAIs.Model.Architectures.DenseNet.DenseNet

GROWTH_RATE = 32

INITIAL_FILTERS = 64

THETA = 0.5

create_model()

Here the code to create the actual model

dims = 2

class PrognosAIs.Model.Architectures.DenseNet.DenseNet_201_3D(input_shapes: dict, output_info: dict, input_data_type='float32', output_data_type='float32', model_config={})

Bases: PrognosAIs.Model.Architectures.DenseNet.DenseNet

GROWTH_RATE = 32

INITIAL_FILTERS = 64

THETA = 0.5

create_model()

Here the code to create the actual model

dims = 3

class PrognosAIs.Model.Architectures.DenseNet.DenseNet_264_2D(input_shapes: dict, output_info: dict, input_data_type='float32', output_data_type='float32', model_config={})

Bases: PrognosAIs.Model.Architectures.DenseNet.DenseNet

GROWTH_RATE = 32

INITIAL_FILTERS = 64

THETA = 0.5

create_model()

Here the code to create the actual model

dims = 2

class PrognosAIs.Model.Architectures.DenseNet.DenseNet_264_3D(input_shapes: dict, output_info: dict, input_data_type='float32', output_data_type='float32', model_config={})

Bases: PrognosAIs.Model.Architectures.DenseNet.DenseNet

GROWTH_RATE = 32

INITIAL_FILTERS = 64

THETA = 0.5

create_model()

Here the code to create the actual model

dims = 3

PrognosAIs.Model.Architectures.InceptionNet module

class PrognosAIs.Model.Architectures.InceptionNet.InceptionNet_InceptionResNetV2_2D(input_shapes: dict, output_info: dict, input_data_type='float32', output_data_type='float32', model_config={})

Bases: PrognosAIs.Model.Architectures.InceptionNet.InceptionResNet

create_model()

Here the code to create the actual model

class PrognosAIs.Model.Architectures.InceptionNet.InceptionNet_InceptionResNetV2_3D(input_shapes: dict, output_info: dict, input_data_type='float32', output_data_type='float32', model_config={})

Bases: PrognosAIs.Model.Architectures.InceptionNet.InceptionResNet

create_model()

Here the code to create the actual model

class PrognosAIs.Model.Architectures.InceptionNet.InceptionResNet(input_shapes: dict, output_info: dict, input_data_type='float32', output_data_type='float32', model_config={})

Bases: PrognosAIs.Model.Architectures.Architecture.ClassificationNetworkArchitecture

get_inception_resnet_A(layer)

get_inception_resnet_B(layer)

get_inception_resnet_C(layer)

get_inception_resnet_reduction_A(layer)

get_inception_resnet_reduction_B(layer)

get_inception_stem(layer)

init_dimensionality(N_dimension)

PrognosAIs.Model.Architectures.ResNet module

class PrognosAIs.Model.Architectures.ResNet.ResNet(input_shapes: dict, output_info: dict, input_data_type='float32', output_data_type='float32', model_config={})

Bases: PrognosAIs.Model.Architectures.Architecture.ClassificationNetworkArchitecture

get_residual_conv_block(layer: <module 'tensorflow.keras.layers' from '/home/docs/checkouts/readthedocs.org/user_builds/prognosais/envs/latest/lib/python3.7/site-packages/tensorflow/keras/layers/__init__.py'>, N_filters: int, kernel_size: list)

get_residual_identity_block(layer, N_filters, kernel_size)

class PrognosAIs.Model.Architectures.ResNet.ResNet_18_2D(input_shapes: dict, output_info: dict, input_data_type='float32', output_data_type='float32', model_config={})

Bases: PrognosAIs.Model.Architectures.ResNet.ResNet

create_model()

Here the code to create the actual model

class PrognosAIs.Model.Architectures.ResNet.ResNet_18_3D(input_shapes: dict, output_info: dict, input_data_type='float32', output_data_type='float32', model_config={})

Bases: PrognosAIs.Model.Architectures.ResNet.ResNet

create_model()

Here the code to create the actual model

class PrognosAIs.Model.Architectures.ResNet.ResNet_18_multioutput_3D(input_shapes: dict, output_info: dict, input_data_type='float32', output_data_type='float32', model_config={})

Bases: PrognosAIs.Model.Architectures.ResNet.ResNet

create_model()

Here the code to create the actual model

class PrognosAIs.Model.Architectures.ResNet.ResNet_34_2D(input_shapes: dict, output_info: dict, input_data_type='float32', output_data_type='float32', model_config={})

Bases: PrognosAIs.Model.Architectures.ResNet.ResNet

create_model()

Here the code to create the actual model

class PrognosAIs.Model.Architectures.ResNet.ResNet_34_3D(input_shapes: dict, output_info: dict, input_data_type='float32', output_data_type='float32', model_config={})

Bases: PrognosAIs.Model.Architectures.ResNet.ResNet

create_model()

Here the code to create the actual model

PrognosAIs.Model.Architectures.UNet module

class PrognosAIs.Model.Architectures.UNet.UNet_2D(input_shapes: dict, output_info: dict, input_data_type='float32', output_data_type='float32', model_config: dict = {})

Bases: PrognosAIs.Model.Architectures.UNet.Unet

create_model()

Here the code to create the actual model

dims = 2

class PrognosAIs.Model.Architectures.UNet.UNet_3D(input_shapes: dict, output_info: dict, input_data_type='float32', output_data_type='float32', model_config: dict = {})

Bases: PrognosAIs.Model.Architectures.UNet.Unet

create_model()

Here the code to create the actual model

dims = 3

class PrognosAIs.Model.Architectures.UNet.Unet(input_shapes: dict, output_info: dict, input_data_type='float32', output_data_type='float32', model_config: dict = {})

Bases: PrognosAIs.Model.Architectures.Architecture.NetworkArchitecture

get_conv_block(layer, N_filters, kernel_size=3, activation='relu', kernel_regularizer=None)

get_cropping_block(conv_layer, upsampling_layer)

get_depth()

get_number_of_filters()

get_padding_block(layer)

get_pool_block(layer)

get_upsampling_block(layer, N_filters, activation='relu', kernel_regularizer=None)

init_dimensionality(N_dimension)

make_outputs(output_info: dict, output_data_type: str, activation_type: str = 'softmax')

Make the outputs

PrognosAIs.Model.Architectures.VGG module

class PrognosAIs.Model.Architectures.VGG.VGG(input_shapes: dict, output_info: dict, input_data_type='float32', output_data_type='float32', model_config={})

Bases: PrognosAIs.Model.Architectures.Architecture.ClassificationNetworkArchitecture

get_VGG_block(layer, N_filters, N_conv_layer)

init_dimensionality(N_dimension)

class PrognosAIs.Model.Architectures.VGG.VGG_16_2D(input_shapes: dict, output_info: dict, input_data_type='float32', output_data_type='float32', model_config={})

Bases: PrognosAIs.Model.Architectures.VGG.VGG

create_model()

Here the code to create the actual model

dims = 2

class PrognosAIs.Model.Architectures.VGG.VGG_16_3D(input_shapes: dict, output_info: dict, input_data_type='float32', output_data_type='float32', model_config={})

Bases: PrognosAIs.Model.Architectures.VGG.VGG

create_model()

Here the code to create the actual model

dims = 3

class PrognosAIs.Model.Architectures.VGG.VGG_19_2D(input_shapes: dict, output_info: dict, input_data_type='float32', output_data_type='float32', model_config={})

Bases: PrognosAIs.Model.Architectures.VGG.VGG

create_model()

Here the code to create the actual model

dims = 2

class PrognosAIs.Model.Architectures.VGG.VGG_19_3D(input_shapes: dict, output_info: dict, input_data_type='float32', output_data_type='float32', model_config={})

Bases: PrognosAIs.Model.Architectures.VGG.VGG

create_model()

Here the code to create the actual model

dims = 3

Module contents

Submodules

PrognosAIs.Model.Callbacks module

class PrognosAIs.Model.Callbacks.ConcordanceIndex(validation_generator)

Bases: tensorflow.python.keras.callbacks.Callback

A custom callback function to evaluate the concordance index on the whole validation set

on_epoch_end(epoch, logs=None)

Called at the end of an epoch.

Subclasses should override for any actions to run. This function should only be called during TRAIN mode.

Parameters

• epoch – Integer, index of epoch.

• logs – Dict, metric results for this training epoch, and for the validation epoch if validation is performed. Validation result keys are prefixed with val_.

class PrognosAIs.Model.Callbacks.Timer

Bases: tensorflow.python.keras.callbacks.Callback

A custom callback function to evaluate the elapsed time of training

on_epoch_end(epoch, logs=None)

Called at the end of an epoch.

Subclasses should override for any actions to run. This function should only be called during TRAIN mode.

Parameters

• epoch – Integer, index of epoch.

• logs – Dict, metric results for this training epoch, and for the validation epoch if validation is performed. Validation result keys are prefixed with val_.

PrognosAIs.Model.Callbacks.calculate_concordance_index(y_true, y_pred)

This function determine the concordance index for two numpy arrays

y_true contains a label to indicate whether events occurred, and time to events (or time to right censored data if no event occurred)

y_pred is beta*x in the cox model

PrognosAIs.Model.Evaluators module

class PrognosAIs.Model.Evaluators.Evaluator(model_file, data_folder, config_file, output_folder)

Bases: object

_combine_config_and_model_metrics(model_metrics: dict, config_metrics: dict) → dict

Combine the metrics specified in the model and those specified in the config.

Parameters

• model_metrics (dict) – Metrics as defined by the model

• config_metrics (dict) – Metrics defined in the config

Returns

dict – Combined metrics

static _fake_fit(model: tensorflow.python.keras.engine.training.Model) → tensorflow.python.keras.engine.training.Model

Fit of the model on fake date to properly initialize the model.

Parameters

model (tf.keras.Model) – Model to initialize

Returns

tf.keras.Model – Initalized model.

_format_predictions(predictions: Union[list, numpy.ndarray]) → dict

Format the predictions to match them with the output names

Parameters

predictions (Union[list, np.ndarray]) – The predictions from the model

Raises

ValueError – If the predictions do not match with the expected output names

Returns

dict – Output predictions matched with the output names

_init_data_generators(labels_only: bool) → dict

Initialize data generators for all sample folders.

Parameters

labels_only (bool) – Whether to only load labels

Returns

dict – initalized data generators

static _load_model(model_file: str, custom_objects: dict) → Tuple[tensorflow.python.keras.engine.training.Model, ValueError]

Try to load a model, if it doesnt work parse the error.

Parameters

• model_file (str) – Location of the model file

• custom_objects (dict) – Potential custom objects to use during model loading

Returns

Tuple[tf.keras.Model, ValueError] – The model if successfully loaded, otherwise the error

static combine_predictions(predictions: numpy.ndarray, are_one_hot: bool, label_combination_type: str) → numpy.ndarray

evaluate()

evaluate_metrics() → dict

Evaluate all metrics for all samples

Returns

dict – The evaluated metrics

evaluate_metrics_from_predictions(predictions: dict, real_labels: dict) → dict

Evaluate the metrics based on the model predictions

Parameters

• predictions (dict) – Predictions obtained from the model

• real_labels (dict) – The true labels of the samples for the different outputs

Returns

dict – The different evaluated metrics

evaluate_sample_metrics() → dict

Evaluate the metrics based on a full sample instead of based on individual batches

Returns

dict – The evaluated metrics

get_image_output_labels() → dict

Whether an output label is a simple class, the label is actually an image.

Returns

dict – Output labels that are image outputs

get_real_labels() → dict

get_real_labels_of_sample_subset(subset_name: str) → dict

Get the real labels corresponding of all samples from a subset.

Parameters

subset_name (str) – Name of subset to get labels for

Returns

dict – Real labels for each dataset and output

get_sample_labels_from_patch_labels()

get_sample_predictions_from_patch_predictions()

get_sample_result_from_patch_results(patch_results)

get_to_evaluate_metrics() → dict

Get the metrics functions which should be evaluated.

Returns

dict – Metric function to be evaluated for the different outputs

image_array_to_sitk(image_array: numpy.ndarray, input_name: str) → SimpleITK.SimpleITK.Image

init_data_generators() → dict

Initialize the data generators.

Returns

dict – DataGenerator for each subfolder of samples

classmethod init_from_sys_args(args_in)

init_label_generators() → dict

Initialize the data generators which only give labels.

Returns

dict – DataGenerator for each subfolder of samples

init_model_parameters() → None

Initialize the parameters from the model.

static load_model(model_file: str, custom_module: module = None) → tensorflow.python.keras.engine.training.Model

Load the model, including potential custom losses.

Parameters

• model_file (str) – Location of the model file

• custom_module (ModuleType) – Custom module from which to load losses or metrics

Raises

error – If the model could not be loaded and the problem is not due to a missing loss or metric function.

Returns

tf.keras.Model – The loaded model

make_dataframe(sample_names, predictions, labels) → pandas.core.frame.DataFrame

make_metric_dataframe(metrics: dict) → pandas.core.frame.DataFrame

static one_hot_labels_to_flat_labels(labels: numpy.ndarray) → numpy.ndarray

patches_to_sample_image(datagenerator: PrognosAIs.IO.DataGenerator.HDF5Generator, filenames: list, output_name: str, predictions: numpy.ndarray, labels_are_one_hot: bool, label_combination_type: str) → numpy.ndarray

predict() → dict

Get predictions from the model

Returns

dict – Predictions for the different outputs of the model for all samples

write_image_predictions_to_files(sample_names, predictions, labels_one_hot) → None

write_metrics_to_file() → None

write_predictions_to_file() → None

PrognosAIs.Model.Losses module

class PrognosAIs.Model.Losses.CoxLoss(**kwargs)

Bases: tensorflow.python.keras.losses.Loss

Cox loss as defined in https://arxiv.org/pdf/1606.00931.pdf.

call(y_true: tensorflow.python.framework.ops.Tensor, y_pred: tensorflow.python.framework.ops.Tensor) → tensorflow.python.framework.ops.Tensor

Calculate the cox loss.

Parameters

• y_true (tf.Tensor) – Tensor of shape (batch_size, 2), with the first index containing whether and event occurred for each sample, and the second index containing the time to event, or follow-up time if no event has occurred

• y_pred (tf.Tensor) – The \(\hat{h}_{\sigma\}\) as predicted by the network

Returns

tf.Tensor – The cox loss for each sample in the batch

get_config() → dict

Get the configuration of the loss.

Returns

dict – configuration of the loss

class PrognosAIs.Model.Losses.DICE_loss(name: str = 'dice_loss', weighted: bool = False, foreground_only: bool = False, **kwargs)

Bases: tensorflow.python.keras.losses.Loss

Loss class for the Sørensen–Dice coefficient.

call(y_true: tensorflow.python.framework.ops.Tensor, y_pred: tensorflow.python.framework.ops.Tensor) → tensorflow.python.framework.ops.Tensor

Calculate the DICE loss.

This functions calculates the DICE loss defined as:

\[1 - 2 * \frac{|A \cap B|}{|A| + |B|}\]

When no positive labels are found in both A and B the loss returns 0 by default. The loss works both for one-hot predicted labels and binary labels.

Parameters

• y_true (tf.Tensor) – The ground truth labels, shape: (batch_size, N_1, N_2 … N_d) where N_d is the number of channels (can be 1). For a 3D tensor with 1 channel (binary class) and batch size of 1 it will have a shape of (1, N_1, N_2, N_3, 1)

• y_pred (tf.Tensor) – The predicted labels. shape: (batch_size, N_1, N_2 … N_d) where N_d is the number of channels. When a binary prediction is done (last activation function is sigmoid), N_d = 1. When one-hot prediction are done (last activation function is softmax) N_d = number of classes

Returns

tf.Tensor – Tensor of length batch_size with the DICE loss for each sample

get_config() → dict

Get the configuration of the loss.

Returns

dict – configuration of the loss

class PrognosAIs.Model.Losses.MaskedCategoricalCrossentropy(name: str = 'masked_categorical_crossentropy', class_weight: dict = None, mask_value: int = - 1, **kwargs)

Bases: tensorflow.python.keras.losses.CategoricalCrossentropy

Caterogical crossentropy loss which takes into account missing values.

__call__(y_true: tensorflow.python.framework.ops.Tensor, y_pred: tensorflow.python.framework.ops.Tensor, sample_weight: tensorflow.python.framework.ops.Tensor = None) → tensorflow.python.framework.ops.Tensor

Obtain the total masked categorical crossentropy loss for the batch.

Parameters

• y_true (tf.Tensor) – Ground-truth labels, one-hot encoded (batch_size, N_1, N_2, …. N_d) tensor, with N_d the number of outputs

• y_pred (tf.Tensor) – Predictions one-hot encoded, for example from softmax, (batch_size, N_1, N_2, …. N_d) tensor, with N_d the number of outputs

• sample_weight (tf.Tensor) – Sample weight for each indidvidual label to be used in reduction of sample loss to overal batch loss

Returns

tf.Tensor – The total masked categorial crossentropy loss, scalar tensor with rank 0

__init__(name: str = 'masked_categorical_crossentropy', class_weight: dict = None, mask_value: int = - 1, **kwargs) → None

Caterogical crossentropy loss which takes into account missing values.

For the samples with masked values a cross entropy of 0 will be used, for the other samples the standard cross entropy loss will be calculated

Parameters

• name (str) – Optional name for the op

• class_weight (dict) – Weights for each class

• mask_value (int) – The value that indicates that a sample is missing

• **kwargs – arguments to pass the default CategoricalCrossentropy loss

call(y_true: tensorflow.python.framework.ops.Tensor, y_pred: tensorflow.python.framework.ops.Tensor) → tensorflow.python.framework.ops.Tensor

Obtain the masked categorical crossentropy loss for each sample.

Parameters

• y_true (tf.Tensor) – Ground-truth labels, one-hot encoded (batch_size, N_1, N_2, …. N_d) tensor, with N_d the number of outputs

• y_pred (tf.Tensor) – Predictions one-hot encoded, for example from softmax, (batch_size, N_1, N_2, …. N_d) tensor, with N_d the number of outputs

Returns

tf.Tensor –

The masked categorial crossentropy loss for each sample, has rank

one less than the inputs tensors

get_config() → dict

Get the configuration of the loss.

Returns

dict – Configuration parameters of the loss

is_unmasked_sample(y_true: tensorflow.python.framework.ops.Tensor) → tensorflow.python.framework.ops.Tensor

Get whether the samples are unmasked (i.e. have real label data).

Parameters

y_true (tf.Tensor) – Tensor of the true labels

Returns

tf.Tensor – Tensor of 0s and 1s indicating whether that sample is unmasked.

PrognosAIs.Model.Metrics module

class PrognosAIs.Model.Metrics.ConcordanceIndex(name='ConcordanceIndex', **kwargs)

Bases: tensorflow.python.keras.metrics.Metric

result()

Computes and returns the metric value tensor.

Result computation is an idempotent operation that simply calculates the metric value using the state variables.

update_state(y_true, y_pred, sample_weight=None)

Accumulates statistics for the metric.

Note: This function is executed as a graph function in graph mode. This means:

1. Operations on the same resource are executed in textual order. This should make it easier to do things like add the updated value of a variable to another, for example.

2. You don’t need to worry about collecting the update ops to execute. All update ops added to the graph by this function will be executed.

As a result, code should generally work the same way with graph or eager execution.

Parameters

• *args

• **kwargs – A mini-batch of inputs to the Metric.

class PrognosAIs.Model.Metrics.DICE(name='dice_coefficient', foreground_only=True, **kwargs)

Bases: tensorflow.python.keras.metrics.Metric

get_config()

Returns the serializable config of the metric.

result()

Computes and returns the metric value tensor.

Result computation is an idempotent operation that simply calculates the metric value using the state variables.

update_state(y_true, y_pred, sample_weight=None)

Accumulates statistics for the metric.

Note: This function is executed as a graph function in graph mode. This means:

1. Operations on the same resource are executed in textual order. This should make it easier to do things like add the updated value of a variable to another, for example.

2. You don’t need to worry about collecting the update ops to execute. All update ops added to the graph by this function will be executed.

As a result, code should generally work the same way with graph or eager execution.

Parameters

• *args

• **kwargs – A mini-batch of inputs to the Metric.

class PrognosAIs.Model.Metrics.MaskedAUC(name='MaskedAUC', mask_value=- 1, **kwargs)

Bases: tensorflow.python.keras.metrics.AUC

get_config()

Returns the serializable config of the metric.

update_state(y_true, y_pred, sample_weight=None)

Accumulates confusion matrix statistics.

Parameters

• y_true – The ground truth values.

• y_pred – The predicted values.

• sample_weight – Optional weighting of each example. Defaults to 1. Can be a Tensor whose rank is either 0, or the same rank as y_true, and must be broadcastable to y_true.

Returns

Update op.

class PrognosAIs.Model.Metrics.MaskedCategoricalAccuracy(name='MaskedCategoricalAccuracy', mask_value=- 1, **kwargs)

Bases: tensorflow.python.keras.metrics.CategoricalAccuracy

get_config()

Returns the serializable config of the metric.

update_state(y_true, y_pred, sample_weight=None)

Accumulates metric statistics.

y_true and y_pred should have the same shape.

Parameters

• y_true – Ground truth values. shape = [batch_size, d0, .. dN].

• y_pred – The predicted values. shape = [batch_size, d0, .. dN].

• sample_weight – Optional sample_weight acts as a coefficient for the metric. If a scalar is provided, then the metric is simply scaled by the given value. If sample_weight is a tensor of size [batch_size], then the metric for each sample of the batch is rescaled by the corresponding element in the sample_weight vector. If the shape of sample_weight is [batch_size, d0, .. dN-1] (or can be broadcasted to this shape), then each metric element of y_pred is scaled by the corresponding value of sample_weight. (Note on dN-1: all metric functions reduce by 1 dimension, usually the last axis (-1)).

Returns

Update op.

class PrognosAIs.Model.Metrics.MaskedSensitivity(name='masked_sensitivity', mask_value=- 1, **kwargs)

Bases: tensorflow.python.keras.metrics.Metric

reset_states()

Resets all of the metric state variables.

This function is called between epochs/steps, when a metric is evaluated during training.

result()

Computes and returns the metric value tensor.

Result computation is an idempotent operation that simply calculates the metric value using the state variables.

update_state(y_true, y_pred, sample_weight=None)

Accumulates statistics for the metric.

Note: This function is executed as a graph function in graph mode. This means:

1. Operations on the same resource are executed in textual order. This should make it easier to do things like add the updated value of a variable to another, for example.

2. You don’t need to worry about collecting the update ops to execute. All update ops added to the graph by this function will be executed.

As a result, code should generally work the same way with graph or eager execution.

Parameters

• *args

• **kwargs – A mini-batch of inputs to the Metric.

class PrognosAIs.Model.Metrics.MaskedSpecificity(name='masked_specificity', mask_value=- 1, **kwargs)

Bases: tensorflow.python.keras.metrics.Metric

reset_states()

Resets all of the metric state variables.

This function is called between epochs/steps, when a metric is evaluated during training.

result()

Computes and returns the metric value tensor.

Result computation is an idempotent operation that simply calculates the metric value using the state variables.

update_state(y_true, y_pred, sample_weight=None)

Accumulates statistics for the metric.

Note: This function is executed as a graph function in graph mode. This means:

1. Operations on the same resource are executed in textual order. This should make it easier to do things like add the updated value of a variable to another, for example.

2. You don’t need to worry about collecting the update ops to execute. All update ops added to the graph by this function will be executed.

As a result, code should generally work the same way with graph or eager execution.

Parameters

• *args

• **kwargs – A mini-batch of inputs to the Metric.

class PrognosAIs.Model.Metrics.Sensitivity(name='Sensitivity_custom', **kwargs)

Bases: tensorflow.python.keras.metrics.Metric

reset_states()

Resets all of the metric state variables.

This function is called between epochs/steps, when a metric is evaluated during training.

result()

Computes and returns the metric value tensor.

Result computation is an idempotent operation that simply calculates the metric value using the state variables.

update_state(y_true, y_pred, sample_weight=None)

Accumulates statistics for the metric.

Note: This function is executed as a graph function in graph mode. This means:

1. Operations on the same resource are executed in textual order. This should make it easier to do things like add the updated value of a variable to another, for example.

2. You don’t need to worry about collecting the update ops to execute. All update ops added to the graph by this function will be executed.

As a result, code should generally work the same way with graph or eager execution.

Parameters

• *args

• **kwargs – A mini-batch of inputs to the Metric.

class PrognosAIs.Model.Metrics.Specificity(name='Specificity_custom', **kwargs)

Bases: tensorflow.python.keras.metrics.Metric

reset_states()

Resets all of the metric state variables.

This function is called between epochs/steps, when a metric is evaluated during training.

result()

Computes and returns the metric value tensor.

Result computation is an idempotent operation that simply calculates the metric value using the state variables.

update_state(y_true, y_pred, sample_weight=None)

Accumulates statistics for the metric.

Note: This function is executed as a graph function in graph mode. This means:

1. Operations on the same resource are executed in textual order. This should make it easier to do things like add the updated value of a variable to another, for example.

2. You don’t need to worry about collecting the update ops to execute. All update ops added to the graph by this function will be executed.

As a result, code should generally work the same way with graph or eager execution.

Parameters

• *args

• **kwargs – A mini-batch of inputs to the Metric.

PrognosAIs.Model.Metrics.concordance_index(y_true, y_pred)

This function determines the concordance index given two tensorflow tensors

y_true contains a label to indicate whether events occurred, and time to events (or time to right censored data if no event occurred)

y_pred is beta*x in the cox model

PrognosAIs.Model.Parsers module

class PrognosAIs.Model.Parsers.CallbackParser(callback_settings: dict, root_path: str = None, module_paths=None, save_name=None)

Bases: PrognosAIs.Model.Parsers.StandardParser

__init__(callback_settings: dict, root_path: str = None, module_paths=None, save_name=None)

Parse callback settings to actual callbacks

Parameters

callback_settings – Settings for the callbacks

Returns

None

get_callbacks()

replace_root_path(settings, root_path)

class PrognosAIs.Model.Parsers.LossParser(loss_settings: dict, class_weights: dict = None, module_paths=None)

Bases: PrognosAIs.Model.Parsers.StandardParser

__init__(loss_settings: dict, class_weights: dict = None, module_paths=None)

Parse loss settings to actual losses

Parameters

loss_settings – Settings for the losses

Returns

None

get_losses()

class PrognosAIs.Model.Parsers.MetricParser(metric_settings: dict, label_names: list = None, module_paths=None)

Bases: PrognosAIs.Model.Parsers.StandardParser

__init__(metric_settings: dict, label_names: list = None, module_paths=None) → None

Parse metrics settings to actual metrics

Parameters

loss_settings – Settings for the losses

convert_metrics_list_to_dict(metrics: list) → dict

get_metrics()

class PrognosAIs.Model.Parsers.OptimizerParser(optimizer_settings: dict, module_paths=None)

Bases: PrognosAIs.Model.Parsers.StandardParser

__init__(optimizer_settings: dict, module_paths=None) → None

Interfacing class to easily get a tf.keras.optimizers optimizer

Parameters

optimizer_settings – Arguments to be passed to the optimizer

Returns

None

get_optimizer()

class PrognosAIs.Model.Parsers.StandardParser(config: dict, module_paths: list)

Bases: object

get_class(class_name)

parse_settings()

PrognosAIs.Model.Trainer module

class PrognosAIs.Model.Trainer.Trainer(config: PrognosAIs.IO.ConfigLoader.ConfigLoader, sample_folder: str, output_folder: str, tmp_data_folder: Optional[str] = None, save_name: Optional[str] = None)

Bases: object

Trainer to be used for training a model.

__init__(config: PrognosAIs.IO.ConfigLoader.ConfigLoader, sample_folder: str, output_folder: str, tmp_data_folder: Optional[str] = None, save_name: Optional[str] = None) → None

Trainer to be used for training a model.

Parameters

• config (ConfigLoader.ConfigLoader) – Config to be used

• sample_folder (str) – Folder containing the train and validation samples

• output_folder (str) – Folder to put the resulting model

• tmp_data_folder (str) – Folder to copy samples to and load from. Defaults to None.

• save_name (str) – Specify a name to save the model as instead of using a automatically generated one. Defaults to None.

static _get_architecture_name(model_name: str, input_dimensionality: dict) → Tuple[str, str]

Get the full architecture name from the model name and input dimensionality.

Parameters

• model_name (str) – Name of the model

• input_dimensionality (dict) – Dimensionality of the different inputs

Returns

Tuple[str, str] – Class name of architecture and full achitecture name

_setup_model() → tensorflow.python.keras.engine.training.Model

Get the model architecture from the architecture name (not yet compiled).

Raises

ValueError – If architecture is not known

Returns

tf.keras.Model – The loaded architecture

get_distribution_strategy() → tensorflow.python.distribute.distribute_lib.Strategy

Get the appropiate distribution strategy.

A strategy will be returned that can either distribute the training over multiple SLURM nodes, over multi GPUs, train on a single GPU or on a single CPU (in that order).

Returns

tf.distribute.Strategy – The distribution strategy to be used in training.

classmethod init_from_sys_args(args_in: list) → PrognosAIs.Model.Trainer.Trainer

Initialize a Trainer object from the command line.

Parameters

args_in (list) – Arguments to parse to the trainer

Returns

Trainer – The trainer object

load_class_weights() → Union[None, dict]

Load the class weight from the class weight file.

Returns

Union[None, dict] –

Class weights if requested and the class weight file exists,

otherwise None.

property model

Model to be used in training.

Returns

tf.keras.Model – The model

move_data_to_temporary_folder(data_folder: str) → str

Move the data to a temporary directory before loading.

Parameters

data_folder (str) – The original data folder

Returns

str – Folder to which the data has been moved

set_precision_strategy(float_policy_setting: Union[str, bool]) → None

Set the appropiate precision strategy for GPUs.

If the GPUs support it a mixed float16 precision will be used (see tf.keras.mixe_precision for more information), which reduces the memory overhead of the training, while doing computation in float32. If GPUs dont support mixed precision, we will try a float16 precision setting. If that doesn’t work either the normal policy is used. If you get NaN values for loss or loss doesn’t converge it might be because of the policy. Try running the model without a policy setting.

Parameters

float_policy_setting (float_policy_setting – Union[str, bool]): Which policy to select if set to PrognosAIs.Constants.AUTO, we will automatically determine what can be done. “mixed” will only consider mixed precision, “float16” only considers float16 policy. Set to False to not use a policy

static set_tf_config(cluster_resolver: tensorflow.python.distribute.cluster_resolver.cluster_resolver.ClusterResolver, environment: Optional[str] = None) → None

Set the TF_CONFIG env variable from the given cluster resolver.

From https://github.com/tensorflow/tensorflow/issues/37693

Parameters

• cluster_resolver (tf.distribute.cluster_resolver.ClusterResolver) – cluster resolver to use.

• environment (str) – Environment to set in TF_CONFIG. Defaults to None.

setup_callbacks() → list

Set up callbacks to be used during training.

Returns

list – the callbacks

setup_data_generator(sample_folder: str) → PrognosAIs.IO.DataGenerator.HDF5Generator

Set up a data generator for a folder containg train samples.

Parameters

sample_folder (str) – The path to the folder containing the sample files.

Raises

ValueError – If the sample folder does not exist or does not contain any samples.

Returns

DataGenerator.HDF5Generator – Datagenerator of the sample in the sample folder.

setup_model() → tensorflow.python.keras.engine.training.Model

Set up model to be used during train.

Returns

tf.keras.Model – The compiled model to be trained.

property train_data_generator

The train data generator to be used in training.

Returns

DataGenerator.HDF5Generator – The train data generator

train_model() → str

Train the model.

Returns

str – The location where the model has been saved

property validation_data_generator

The validation data generator to be used in training.

Returns

DataGenerator.HDF5Generator – The validation data generator

Module contents

PrognosAIs.Preprocessing package

Submodules

PrognosAIs.Preprocessing.Preprocessors module

class PrognosAIs.Preprocessing.Preprocessors.BatchPreprocessor(samples_path: str, output_directory: str, config: dict)

Bases: object

classmethod init_from_sys_args(args_in)

split_into_subsets(samples: list, sample_labels: list) → dict

start()

class PrognosAIs.Preprocessing.Preprocessors.SingleSamplePreprocessor(sample: PrognosAIs.Preprocessing.Samples.ImageSample, config: dict, output_directory: str = None)

Bases: object

static _get_all_images_from_sequence(image: SimpleITK.SimpleITK.Image, max_dims: int) → list

Get all of the images from a sequence of images.

Parameters

• image (sitk.Image) – Multi-dimensional image containg the sequence.

• max_dims (int) – The number of dimension of each individual image. This should be equal to the dimensionality of the input image - 1. Otherwise, we do not know how to extract the appropiate images

Raises

ValueError – If the maximum number of dimensions does not fit with the sequences.

Returns

list – All images extracted from the sequence.

static _get_first_image_from_sequence(image: SimpleITK.SimpleITK.Image, max_dims: int) → SimpleITK.SimpleITK.Image

Extract the first image from a sequence of images

Parameters

• image (sitk.Image) – Multi-dimensional image containg the sequence.

• max_dims (int) – The maximum number of dimension the output can be.

Returns

sitk.Image – The first image extracted from the sequence

apply_pipeline(pipeline=None)

bias_field_correcting()

build_pipeline() → list

channel_imputation(sample_channels)

channels_to_float16(sample_channels)

crop_to_mask(ROI_mask: SimpleITK.SimpleITK.Image, process_masks: bool = True, apply_to_output: bool = False)

mask_background(ROI_mask: SimpleITK.SimpleITK.Image, background_value: float = 0.0, process_masks: bool = True, apply_to_output: bool = False)

static mask_background_to_min(image, mask)

masking()

multi_dimension_extracting()

Extract invidiual images from a multi-dimensional sequence.

Raises

NotImplementedError – If an extraction type is requested that is not supported.

normalizing()

patching() → None

rejecting()

resampling()

saving()

PrognosAIs.Preprocessing.Samples module

class PrognosAIs.Preprocessing.Samples.ImageSample(root_path: str, extension_keyword: str = None, mask_keyword: str = None, labels: dict = None, number_of_label_classes: dict = None, are_labels_one_hot: bool = False, output_channel_names: list = [], input_channel_names: list = [])

Bases: abc.ABC

ImageSample base class

To be implemented by subclasses:

• init_image_files: Contains logic for retrieval of channel filepaths

• load_channels: Contains logic for loading of channels from filepaths

• load_output_channels: Contains logic for loading of output channels from filepaths

• load_masks: Contains logic of loading masks from filepaths

Parameters

• root_path – Path of the sample. Should contain folders or directories of channels and masks

• extension_keyword – Extension of the files to load

• mask_keyword (optional) – Keyword to identify which filepaths are masks. Defaults to None.

_identify_channel_file(image_file: str) → bool

Identify whether an image file should be included as channel

Parameters

image_file – Image file to check

Returns

bool – True if image_file is channel, False otherwise

_identify_mask_file(image_file: str) → bool

Identify whether an image file is a mask based on the mask keyword

Parameters

image_file – Image file to check

Returns

bool – True if image_file is mask, False otherwise

_identify_output_channel_file(image_file: str) → bool

Identify whether an image file is a output channel

Parameters

image_file – Image file to check

Returns

bool – True if image_file is output channel, False otherwise

_init_channel_files(image_files: list) → list

Get only the channel files from the image files, filtering out masks.

Parameters

image_files (list) – Paths to the image files

Returns

list – The paths to the channel files

_init_mask_files(image_files: list) → list

Get only the mask files from the image files, filtering out channels.

Parameters

image_files (list) – Paths to the image files

Returns

list – The paths to the mask files

_init_output_channel_files(image_files: list) → list

Get the output channel files from the image files.

Parameters

image_files (list) – Paths to the image files

Returns

list – The paths to the output channel files

_parse_function_parameters(function_parameters)

Parse the function parameters

Parameters

function_parameters (function or tuple) – Function and possible args and kw_args.

Returns

tuple – function, args, and kw_args

_perform_sanity_checks()

Automatic sanity check to see if we can process the sample

Raises

NotImplementedError – If the configuration has not been implemented

add_to_labels(to_add_labels: List[dict], to_add_number_of_label_classes: dict) → None

assert_all_channels_same_size()

Check wheter all channels have the same size

Raises

ValueError – Raised when not all channels have same size

assert_all_masks_same_size()

Check wheter all masks have the same size

Raises

ValueError – Raised when not all masks have same size

property channel_names

Names of the channels

Returns

list – Channel names

property channel_size

The image size of the channels

property channels

The channels present in the sample

Channels of a sample can be set by providing either a function,

or a tuple consisting of a function, possible function argument and function keyword arguments.

This function will then be applied to all channels in the sample. The function has to output either a SimpleITK Image or a list. In the last case it is assumed that these are patches and the class is updated accordingly

Returns

list – Channels present in the sample

copy()

Returns a (deep) copy of the instance

Returns

ImageSample – Deep copy of the instance

static get_appropiate_dtype_from_image(image: SimpleITK.SimpleITK.Image) → int

Find the minimum SimpleITK type need to represent the value

Parameters

value (float) – The value to check

Returns

int – The appropiate SimpleITK to which the value can be casted

static get_appropiate_dtype_from_scalar(value: Union[int, float], return_np_type: bool = False) → Union[int, numpy.dtype]

Find the minimum SimpleITK type need to represent the value

Parameters

• value (float) – The value to check

• return_np_type (bool) – If True returns the numpy type instead of the SimpleITK type. Defaults to False.

Returns

int – The appropiate SimpleITK to which the value can be casted

get_example_channel() → SimpleITK.SimpleITK.Image

Provides an example channel of the samples

Returns

sitk.Image – Single channel of the sample

get_example_channel_patches() → list

Provides an example of all patches of a channel, even if there is only one patch

Returns

list – Patch(es) of a single channel of the sample

get_example_mask() → SimpleITK.SimpleITK.Image

Provides an example mask of the samples

Returns

sitk.Image – Single mask of the sample

get_example_mask_patches() → list

Provides an example of all patches of a mask, even if there is only one patch

Returns

list – Patch(es) of a single mask of the sample

get_example_output_channel() → SimpleITK.SimpleITK.Image

Provides an example output channel of the samples

Returns

sitk.Image – Single channel of the sample

get_example_output_channel_patches() → list

Provides an example of all patches of a output channel, even if there is only one patch

Returns

list – Patch(es) of a single output channel of the sample

get_grouped_channels() → list

Groups the channels on a per-patch basis instead of a per-channel basis

The channels property indexes first by channel and then by (possibly) patches. This function instead first indexes by patches (or the whole sample of no patches). This can be handy when all channels are needed at the same time

Returns

list – Grouped channels for each patch

get_grouped_masks() → list

Groups the masks on a per-patch basis instead of a per-channel basis

The masks property indexes first by channel and then by (possibly) patches. This function instead first indexes by patches (or the whole sample of no patches). This can be handy when all masks are needed at the same time

Returns

list – Grouped channels for each patch. Empty lists if sample doesn’t have mask

get_grouped_output_channels() → list

Groups the output channels on a per-patch basis instead of a per-channel basis

The channels property indexes first by channel and then by (possibly) patches. This function instead first indexes by patches (or the whole sample of no patches). This can be handy when all channels are needed at the same time

Returns

list – Grouped channels for each patch

static get_numpy_type_from_sitk_type(sitk_type: int) → numpy.dtype

static get_sitk_type_from_numpy_type(numpy_type: numpy.dtype) → int

abstract init_image_files() → list

Get the filepaths (folders or files) of the channels for a single sample. To be implemented by the subclass

Returns

list – The filepaths of the channels

abstract load_channels(channel_files: list) → dict

Load the channels from the channel files. To be implemented by the subclass

Example subclass implementation:

def load_channels(self, channel_files):
    channels = {}

    nifti_reader = sitk.ImageFileReader()
    nifti_reader.SetImageIO("NiftiImageIO")
    for i_channel_file in channel_files:
        nifti_reader.SetFileName(i_channel_file)
        i_channel = nifti_reader.Execute()
        i_channel_name = os.path.basename(i_channel_file)
        channels[i_channel_name] = i_channel
    return channels

Parameters

channel_files (list) – Paths to the channels to be loaded

Returns

dict – mapping the channel file to the loaded image

abstract load_masks(mask_files: list) → dict

Load the masks from the mask files. To be implemented by the subclass

Example subclass implementation:

def load_masks(self, mask_files):
    masks = {}
    nifti_reader = sitk.ImageFileReader()
    nifti_reader.SetImageIO("NiftiImageIO")
    for i_mask_file in mask_files:
        nifti_reader.SetFileName(i_mask_file)
        i_mask = nifti_reader.Execute()
        i_mask = sitk.Cast(i_mask, sitk.sitkUInt8)
        i_mask_name = IO_utils.get_file_name(i_mask_file, self.image_extension)
        masks[i_mask_name] = i_mask
    return masks

Parameters

mask_files (list) – Paths to the masks to be loaded

Returns

dict – mapping the mask file to the loaded mask

property mask_names

Names of the masks

Returns

list – Mask names

property mask_size

The image size of the masks.

property masks

The masks present in the sample

Masks of a sample can be set by providing either a function,

or a tuple consisting of a function, possible function argument and function keyword arguments.

This function will then be applied to all masks in the sample. The function has to output either a SimpleITK Image or a list. In the last case it is assumed that these are patches and the class is updated accordingly

Returns

list – masks present in the sample

property output_channel_size

The image size of the channels

property output_channels

The output channels present in the sample

Output channels of a sample can be set by providing either a function,

or a tuple consisting of a function, possible function argument and function keyword arguments.

This function will then be applied to all output channels in the sample. The function has to output either a SimpleITK Image or a list. In the last case it is assumed that these are patches and the class is updated accordingly

Returns

list – Channels present in the sample

static promote_simpleitk_types(type_1: int, type_2: int) → int

Get the datatype that can represent both datatypes

Parameters

• type_1 (int) – SimpleITK datype of variable 1

• type_2 (int) – SimpleITK datatype of variable 2

Returns

int – SimpleITK datatype that can represent both datatypes

update_channel_size()

Update the channel size according to the current channels

update_labels() → None

update_mask_size() → None

Update the mask size according to the current masks

update_metadata() → None

update_output_channel_size()

Update the channel size according to the current channels

class PrognosAIs.Preprocessing.Samples.NIFTISample(**kwds)

Bases: PrognosAIs.Preprocessing.Samples.ImageSample

init_image_files()

Get the filepaths (folders or files) of the channels for a single sample. To be implemented by the subclass

Returns

list – The filepaths of the channels

load_channels(channel_files)

Load the channels from the channel files. To be implemented by the subclass

Example subclass implementation:

def load_channels(self, channel_files):
    channels = {}

    nifti_reader = sitk.ImageFileReader()
    nifti_reader.SetImageIO("NiftiImageIO")
    for i_channel_file in channel_files:
        nifti_reader.SetFileName(i_channel_file)
        i_channel = nifti_reader.Execute()
        i_channel_name = os.path.basename(i_channel_file)
        channels[i_channel_name] = i_channel
    return channels

Parameters

channel_files (list) – Paths to the channels to be loaded

Returns

dict – mapping the channel file to the loaded image

load_masks(mask_files)

Load the masks from the mask files. To be implemented by the subclass

Example subclass implementation:

def load_masks(self, mask_files):
    masks = {}
    nifti_reader = sitk.ImageFileReader()
    nifti_reader.SetImageIO("NiftiImageIO")
    for i_mask_file in mask_files:
        nifti_reader.SetFileName(i_mask_file)
        i_mask = nifti_reader.Execute()
        i_mask = sitk.Cast(i_mask, sitk.sitkUInt8)
        i_mask_name = IO_utils.get_file_name(i_mask_file, self.image_extension)
        masks[i_mask_name] = i_mask
    return masks

Parameters

mask_files (list) – Paths to the masks to be loaded

Returns

dict – mapping the mask file to the loaded mask

PrognosAIs.Preprocessing.Samples.get_sample_class(sample_type_name: str)

Module contents

Submodules

PrognosAIs.Constants module

PrognosAIs.Pipeline module

class PrognosAIs.Pipeline.Pipeline(config_file: str, preprocess: bool = True, train: bool = True, evaluate: bool = True, samples_folder: str = None)

Bases: object

classmethod init_from_sys_args(args_in)

start_local_pipeline()

start_slurm_pipeline(preprocess_job: slurmpie.slurmpie.Job, train_job: slurmpie.slurmpie.Job, evaluate_job: slurmpie.slurmpie.Job)

Module contents