djcdata

djcdata is a Python package designed for efficient data handling and preprocessing for deep learning models. It provides tools to convert raw data into a format suitable for training, manage datasets, and feed data into training loops seamlessly, supporting both TensorFlow and PyTorch frameworks.

Table of Contents

• Features
• Installation
• Pipeline Overview
• Quick Start Guide
  • Defining a Custom TrainData Class
  • Running Data Conversion
  • Performing Training
    • Using TensorFlow
    • Using PyTorch
• Helper Scripts
• Documentation
• License

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Features

• Efficient Data Conversion: Convert raw data into a format optimized for training with deep learning frameworks.
• Flexible Data Management: Manage datasets through the DataCollection class, allowing splitting, shuffling, and batching.
• Support for Variable-Length Data: Handle datasets with variable-length sequences efficiently.
• Integration with TensorFlow and PyTorch: Seamlessly feed data into training loops for both frameworks.
• Multiprocessing Support: Utilize multiprocessing for faster data conversion and loading.

Installation

To install the latest version of djcdata from GitHub, run:

pip install git+https://github.com/jkiesele/djcdata

Note: The installation requires cmake version 3 or higher. On some systems (e.g., lxplus7), you might need to add cmake to your PATH:

export PATH=/cvmfs/sft.cern.ch/lcg/contrib/CMake/latest/Linux-x86_64/bin:$PATH

This adjustment is only needed during the installation process.

Pipeline Overview

The data processing pipeline in djcdata involves the following steps:

1. Define Conversion Logic: Create a custom TrainData class to define how raw data is converted.
2. Run Data Conversion: Use the provided scripts to convert raw data into the djcdata format.
3. Manage Datasets: Utilize DataCollection to manage and manipulate your dataset.
4. Perform Training: Use the data loaders to feed data into your training loop with TensorFlow or PyTorch.

Quick Start Guide

Defining a Custom TrainData Class

To convert your raw data, you need to define a custom class that inherits from TrainData and implements the convertFromSourceFile method. This method specifies how to read and process your raw data files.

from djcdata import TrainData
from djcdata import SimpleArray  # For handling variable-length data

class YourTrainDataClass(TrainData):
    def __init__(self):
        super(YourTrainDataClass, self).__init__()
        # Initialize any variables or parameters here

    def convertFromSourceFile(self, filename, weighterobjects, istraining):
        # Read your raw data from 'filename'
        import numpy as np

        # Example: Load data from a NumPy file
        data = np.load(filename)

        # Process and prepare your data
        # Split data into features, truth labels, and weights if applicable
        features = data['features']
        truths = data['truths']
        weights = data.get('weights', None)  # Optional

        # If using variable-length data, wrap arrays in SimpleArray
        features_array1 = SimpleArray(features, name="features1")
        features_array2 = SimpleArray(features, name="features2")
        truths_array = SimpleArray(truths, name="truths")

        # Return a tuple of (feature_arrays, truth_arrays, weight_arrays)
        return [features_array, features_array2], [truths_array], [weights] if weights is not None else []

• Features: Input data for your model.
• Truths: Ground truth labels or targets.
• Weights: Sample weights (optional).
• Note: For variable-length data (e.g., sequences of different lengths), use SimpleArray and also pass row splits to handle ragged tensors efficiently.

Running Data Conversion

Once you've defined your custom TrainData class, you can convert your raw data using the convertDJCFromSource.py script provided by djcdata. For this to work, YourTrainDataClass must to be part of a module calles datastructures.

Command Syntax:

convertDJCFromSource.py -i input_file_list.txt -o output_directory -c YourTrainDataClass

• -i: Path to a text file containing a list of your raw data files.
• -o: Output directory where the converted data will be stored.
• -c: The name of your custom TrainData class that handles data conversion.

Example:

convertDJCFromSource.py -i data/input_files.txt -o data/converted -c YourTrainDataClass

Additional Options:

• --gpu: Enable GPU usage for conversion (useful if conversion involves GPU operations).
• --nothreads: Use only a single process for conversion.
• --checkFiles: Enable file checking (requires fileIsValid method in TrainData to be defined).
• --testdata: Convert as test data (does not create weighter objects).
• --help: Display detailed help message with all available options.

Performing Training

After converting your data, you can use DataCollection to manage your dataset and feed data into your training loop.

from djcdata import DataCollection

# Load the data collection
train_data = DataCollection("data/converted/dataCollection.djcdc")

# Optionally split the data for validation
val_data = train_data.split(0.8)  # Use 80% for training and 20% of the data for validation

Using TensorFlow

For TensorFlow models, you can use the TrainDataGenerator to feed data into your training loop.

from djcdata import TrainDataGenerator

# Create generators
traingen = train_data.invokeGenerator()
valgen = val_data.invokeGenerator()

# Set batch size
batch_size = 32
traingen.setBatchSize(batch_size)
valgen.setBatchSize(batch_size)

# Training loop
model.fit(
    traingen.feedNumpyData(),
    steps_per_epoch=traingen.getNBatches(),
    validation_data=valgen.feedNumpyData(),
    validation_steps=valgen.getNBatches(),
    epochs=num_epochs
)

Using PyTorch

For PyTorch models, use the DJCDataLoader class to create data loaders compatible with PyTorch's training loop.

from djcdata import DJCDataLoader
import torch

# Device configuration
device = torch.device('cuda' if torch.cuda.is_available() else 'cpu')

# Initialize data loaders
train_loader = DJCDataLoader(
    data_path="data/converted/dataCollection.djcdc",
    batch_size=32,
    shuffle=True,
    device=device,
    dict_output=True  # Set to True if the output of the data loader should be dictionaries (convenience function)
)

# Split off validation data, here use 80% for training and 20% for validation. 
# Please note that the syntax is inverted w.r.t. the raw tensorflow interface in the previous example.
val_loader = train_loader.split(split_fraction=0.2)

# Training loop
for epoch in range(num_epochs):
    for batch_data in train_loader:
        # Unpack data
        x_batch, y_batch = batch_data[:2]
        # x_batch and y_batch are already on the device

        features1 = x_batch['features1']
        features2 = x_batch['features2']
        # The dictionary keys are the names defined for the SimpleArrays in the converFromSource function

        # Forward pass, loss computation, etc.
        # ...

    # Validation loop
    with torch.no_grad():
        for batch_data in val_loader:
            x_batch, y_batch = batch_data[:2]
            # Validation logic
            # ...

Key Points:

• Automatic Device Transfer: The DJCDataLoader automatically moves data to the specified device.
• Data Splitting: Use the split method to create validation data loaders.
• Custom Data Structures: For convenience, the output can also be given as a dictionary, for that to take effect, set dict_output=True. The dictionary keys will be the names of the SimpleArrays defined in the convertFromSource function.

Helper Scripts

djcdata provides several utility scripts to facilitate data conversion and management. All scripts support the --help option for detailed usage information.

• convertDJCFromSource.py: Converts raw data files into the djcdata format using your custom TrainData class.
• createDataCollectionFromTD.py: Creates a DataCollection wrapper from existing converted individual TrainData (.djctd) files.
• mergeOrSplitDJCFiles.py: Merges or splits individual a whole DataCollection into more fine or more coarsely grained individual TrainData files.
• validateDJCDataCollection.py: Validates the integrity of a DataCollection.
• validateDJCFiles.py: Validates a list (text file) of input files to convertFromSource.py (requires fileIsValid method in TrainData to be defined).

Usage:

For detailed usage of each script, run:

script_name.py --help

Example:

validateDJCDataCollection.py --help

Documentation

For more detailed documentation and advanced usage, please refer to the DeepJetCore documentation. djcdata is based on DeepJetCore and shares many of its concepts and functionalities.

Key Classes and Methods

• TrainData: Base class for defining how raw data is converted into the format used for training.
  • convertFromSourceFile: Method to be implemented for custom data conversion logic.
  • createWeighterObjects: (Optional) Create weighting objects for balancing datasets.
• DataCollection: Manages a collection of converted data samples.
  • createDataFromSource: Converts and collects data from source files.
  • split: Splits the data collection into training and validation sets.
  • invokeGenerator: Creates a data generator for feeding data into the training loop.
• TrainDataGenerator: Feeds data into the training loop for TensorFlow models.
• DJCDataLoader: Custom data loader compatible with PyTorch's DataLoader interface.
• SimpleArray: Handles variable-length data (ragged tensors) efficiently.

Handling Variable-Length Data

For datasets with variable-length sequences, wrap your data arrays in SimpleArray when returning them from convertFromSourceFile. This allows djcdata to manage ragged tensors without unnecessary padding.

Multiprocessing and Performance

djcdata utilizes multiprocessing to speed up data conversion and loading. The data generators and loaders handle shuffling, batching, and device transfers to optimize training performance.