LUME-model

LUME-model holds data structures used in the LUME modeling toolset. Variables and models built using LUME-model will be compatible with other tools. LUME-model uses pydantic models to enforce typed attributes upon instantiation.

Requirements

Python >= 3.7
pydantic
numpy

Install

LUME-model can be installed with conda using the command:

$ conda install lume-model -c conda-forge

Developer

A development environment may be created using the packaged dev-environment.yml file.

$ conda env create -f dev-environment.yml

Variables

The LUME-model variables are intended to enforce requirements for input and output variables by variable type. Current variable implementations are scalar (float) or image (numpy array) type.

Example of minimal implementation of scalar input and output variables:

from lume_model.variables import ScalarInputVariable, ScalarOutputVariable

input_variable = ScalarInputVariable(name="test_input", default=0.1, value_range=[1, 2])
output_variable = ScalarOutputVariable(name="test_output")

Example of minimal implementation of image input and output variables:

from lume_model.variables import ImageInputVariable, ImageOutputVariable
import numpy as np

input_variable = ImageInputVariable(
    name="test_input",
    default= np.array([[1, 2,], [3, 4]]),
    value_range=[1, 10],
    axis_labels=["count_1", "count_2"],
    x_min=0,
    y_min=0,
    x_max=5,
    y_max=5,
)

output_variable = ImageOutputVariable(
    name="test_output",
    axis_labels=["count_1", "count_2"],
)

All input variables may be made into constants by passing the is_constant=True keyword argument. Value assingments on these constant variables will raise an error message.

Models

LUME-model model classes are intended to guide user development while allowing for flexibility and customizability. The base class lume_model.models.BaseModel is used to enforce LUME tool compatable classes for the execution of trained models. For this case, model loading and execution should be organized into class methods.

Model Requirements:

input_variables, output_variables: LUME-model input and output variables are required for use with lume-epics tools. The user can optionally define these as class attributes or design the subclass so that these are passed during initialization . Names of all variables must be unique in order to be served using the EPICS tools. A utility function for saving these variables, which also enforces the uniqueness constraint, is provided (lume_model.utils.save_variables).
evaluate: The evaluate method is called by the serving model. Subclasses must implement the method, accepting a list of input variables and returning a list of the model's output variables with value attributes updated based on model execution.

Example model implementation:

from lume_model.models import BaseModel

class ExampleModel(BaseModel):
    input_variables = {
        "input1": ScalarInputVariable(name="input1", default=1, range=[0.0, 5.0]),
        "input2": ScalarInputVariable(name="input2", default=2, range=[0.0, 5.0]),
    }

    output_variables = {
        "output1": ScalarOutputVariable(name="output1"),
        "output2": ScalarOutputVariable(name="output2"),
    }

    def evaluate(self, input_variables):

        self.input_variables = {
            variable.name: variable for variable in input_variables
        }

        self.output_variables["output1"].value = (
            self.input_variables["input1"].value * 2
        )
        self.output_variables["output2"].value = (
            self.input_variables["input2"].value * 2
        )

        # return inputs * 2
        return list(self.output_variables.values())

Configuration files

Models and variables may be constructed using a yaml configuration file. The configuration file consists of three sections:

model (optional, can alternatively pass a custom model class into the model_from_yaml method)
input_variables
output_variables

The model section is used for the initialization of model classes. The model_class entry is used to specify the model class to initialize. The model_from_yaml method will attempt to import the specified class. Additional model-specific requirements may be provided. These requirements will be checked before model construction. Model keyword arguments may be passed via the config file or with the function kwarg model_kwargs. All models are assumed to accept input_variables and output_variables as keyword arguments.

The below example outlines the specification for a model compatible with the lume-model keras/tensorflow toolkit.

model:
    model_class: lume_model.keras.KerasModel
    requirements:
      tensorflow: 2.3.1
    args:
      model_file: examples/files/iris_model.h5
    input_format:
        order:
            - SepalLength
            - SepalWidth
            - PetalLength
            - PetalWidth
        shape: [1, 4]
    output_format:
        type: softmax

Variables are constructed the minimal data requirements for inputs/outputs.

An example ScalarInputVariable:

input_variables:
    SepalLength:
        name: SepalLength
        type: scalar
        default: 4.3
        lower: 4.3
        upper: 7.9

For image variables, default values must point to files associated with a default numpy array representation. The file import will be relative to PYTHONPATH.

An example ImageInputVariable:

input_variables:
    InputImage:
        name: test
        type: image
        default: examples/files/example_input_image.npy
        range: [0, 100]
        x_min: 0
        x_max: 10
        y_min: 0
        y_max: 10
        axis_labels: ["x", "y"]
        x_min_variable: xmin_pv
        y_min_variable: ymin_pv
        x_max_variable: xmax_pv
        y_max_variable: ymax_pv

Keras/tensorflow toolkit

At present, only the tensorflow v2 backend is supported for this toolkit.

The KerasModel packaged in the toolkit will be compatible with models saved using the keras.save_model() method.

Development requirements:

The model must be trained using the custom scaling layers provided in lume_model.keras.layers OR using preprocessing layers packaged with Keras OR the custom layers must be defined during build and made accessible during loading by the user. Custom layers are not supported out-of-the box by this toolkit.
The keras model must use named input layers such that the model will accept a dictionary input OR the KerasModel must be subclassed and the format_input and format_output member functions must be overwritten with proper formatting of model input from a dictionary mapping input variable names to values and proper output parsing into a dictionary, respectively. This will require use of the Keras functional API for model construction.

An example of a model built using the functional API is given below:

from tensorflow import keras
import tensorflow as tf

sepal_length_input = keras.Input(shape=(1,), name="SepalLength")
sepal_width_input = keras.Input(shape=(1,), name="SepalWidth")
petal_length_input = keras.Input(shape=(1,), name="PetalLength")
petal_width_input = keras.Input(shape=(1,), name="PetalWidth")
inputs = [sepal_length_input, sepal_width_input, petal_length_input, petal_width_input]
merged = keras.layers.concatenate(inputs)
dense1 = Dense(8, activation='relu')(merged)
output = Dense(3, activation='softmax', name="Species")(dense1)

# Compile model
model = keras.Model(inputs=inputs, outputs=[output])
optimizer = tf.keras.optimizers.Adam()
model.compile(loss='categorical_crossentropy', optimizer=optimizer, metrics=['accuracy'])

Models built in this way will accept inputs in dictionary form mapping variable name to a numpy array of values.

Configuration file

The KerasModel can be instantiated using the utility function lume_model.utils.model_from_yaml method.

KerasModel can be specified in the model_class of the model configuration.

model:
    model_class: lume_model.keras.KerasModel

Custom parsing will require a custom model class.

jacquelinegarrahan/lume-model