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Understanding Custom Functions in DuckDB

By: angu10
16 January 2024 at 04:26

DuckDB's support for custom functions is a crucial feature that allows users to extend the database's capabilities by incorporating their logic and operations. Custom functions are user-defined functions (UDFs) that can be implemented in languages such as Python and then seamlessly integrated into DuckDB. This extensibility is invaluable when users encounter specific analytical challenges not addressed by the built-in functions. For instance, SQL often struggles to infer datetime formats, leading to the need for complex case-when statements. The parse_dates custom function showcased here, leveraging Pandas capabilities, becomes a powerful solution to overcome this limitation.

The parse_dates Function

The parse_dates function, in the provided Python code, is a practical example of a custom function designed to handle date parsing within DuckDB. This function leverages the popular Pandas library to parse dates based on user-defined formats. The flexibility of the function allows users to specify date formats and handles different scenarios gracefully, using Pandas' pd.to_datetime method.

def parse_dates(col, fmt):
    """
    Method to parse the dates based on the format provided,
    this will be created as a UDF in DuckDB
    """
    try:
        if fmt[0].lower() == "y":
            return pd.to_datetime(col, yearfirst=True, errors="coerce")
        if fmt[0].lower() == "m":
            return pd.to_datetime(col, dayfirst=True, errors="coerce")
    except (IndexError, ValueError):
        pass
    return None

This function is particularly useful in scenarios where the date formats in the dataset might vary, providing a flexible solution for date parsing within DuckDB.

Integrating parse_dates into DuckDB

The process of integrating the parse_dates function into DuckDB involves creating a corresponding function within the database. The create_function method checks whether the function already exists and, if not, registers it with DuckDB. The provided SQL query ensures that there are no duplicate entries before attempting to create the function.

def create_function(conn):
    """
    Create a function in DuckDB. Currently, it's hardcoded
    we can modify later based on the use case
    """
    function_check = """SELECT DISTINCT  function_name
                        FROM duckdb_functions()
                        WHERE lower(function_type) = 'scalar'
                        AND lower(function_name) in ('parse_dates')
                        ORDER BY function_name;"""

    function_check_output = conn.query(function_check)
    try:
        if not function_check_output:
            conn.create_function("parse_dates", parse_dates, [VARCHAR, VARCHAR], TIMESTAMP)
    except (duckdb.Error, ValueError) as error:
        raise ValueError(
            f"Failed to create function 'parse_dates': {str(error)}"
        ) from error

This step ensures that the custom function is available for use in DuckDB's SQL queries.

Unregistering the Custom Function

The unregister_function method allows users to remove the custom function from DuckDB. If, for any reason, users want to unregister the parse_dates function, this method facilitates the removal of the function from DuckDB.

def unregister_function(conn):
    """
    Unregister a function in DuckDB.
    """
    conn.remove_function("parse_dates")

This feature emphasizes the dynamic nature of DuckDB, allowing users to manage and tailor the set of available functions according to their evolving needs.

Conclusion

The integration of custom functions, such as the parse_dates example, exemplifies DuckDB's commitment to providing users with a customizable and extensible platform for data analysis. As users explore and create their custom functions, they gain the ability to enhance DuckDB's capabilities to address unique challenges in data analysis workflows. Custom functions not only open up new possibilities but also empower users to shape their analytical environment to suit their specific requirements, making DuckDB a versatile and user-friendly database for diverse analytical tasks.

Boosting Performance and Memory Efficiency with PyArrow and Pandas for Clinical Trial Data

By: angu10
29 August 2023 at 05:21

1. Introduction

In the world of data analysis and manipulation, efficiency and memory usage play crucial roles, especially when dealing with large datasets. Clinical trials generate vast amounts of data, making it imperative to employ tools that optimize both processing time and memory utilization. One such strategy involves combining the power of Pandas and PyArrow, two popular Python libraries for data manipulation and in-memory columnar storage, respectively.

In this blog, we'll delve into how PyArrow can be integrated with Pandas to enhance both processing speed and memory efficiency while analyzing a clinical trial dataset.

Create Dummy Clinical Dataset

Let's start by considering a sample clinical trial dataset, which consists of various attributes such as patient identifiers, demographic information, treatment details, medical measurements, and more. This dataset comprises meaningful columns that simulate the kind of data encountered in clinical trials. Here's how the dataset is generated using NumPy and Pandas:



import pandas as pd
import numpy as np

# Generating a sample dataset with 20 columns meaningful for clinical trials
np.random.seed(42)
num_rows = 100000
num_columns = 20

# Generating columns with meaningful names related to clinical trials
data = {
    'Patient_ID': np.arange(1, num_rows + 1),  # Unique identifier for each patient
    'Age': np.random.randint(18, 80, num_rows),  # Age of the patient
    'Sex': np.random.choice(['Male', 'Female'], num_rows),  # Gender of the patient
    'Treatment': np.random.choice(['Drug A', 'Drug B', 'Placebo'], num_rows),  # Treatment administered
    'Blood_Pressure': np.random.randint(80, 180, num_rows),  # Blood pressure reading
    'Cholesterol': np.random.randint(120, 300, num_rows),  # Cholesterol level
    'BMI': np.random.uniform(18, 40, num_rows),  # Body Mass Index
    'Heart_Rate': np.random.randint(60, 100, num_rows),  # Heart rate
    'Diabetes': np.random.choice(['Yes', 'No'], num_rows),  # Presence of diabetes
    'Smoker': np.random.choice(['Smoker', 'Non-Smoker'], num_rows),  # Smoking status
    'Family_History': np.random.choice(['Yes', 'No'], num_rows),  # Family history of conditions
    'Adverse_Event': np.random.choice(['Mild', 'Moderate', 'Severe', 'None'], num_rows),  # Adverse events experienced
    'Lab_Result_1': np.random.uniform(0, 10, num_rows),  # Laboratory result 1
    'Lab_Result_2': np.random.uniform(50, 150, num_rows),  # Laboratory result 2
    'Lab_Result_3': np.random.uniform(1, 20, num_rows),  # Laboratory result 3
    'Efficacy_Score': np.random.uniform(0, 100, num_rows),  # Efficacy score of treatment
    'Visit_1': np.random.choice(['Completed', 'Missed'], num_rows),  # Visit status
    'Visit_2': np.random.choice(['Completed', 'Missed'], num_rows),  # Visit status
    'Visit_3': np.random.choice(['Completed', 'Missed'], num_rows),  # Visit status
    'Follow_Up_Status': np.random.choice(['Ongoing', 'Completed'], num_rows)  # Follow-up status
}

df = pd.DataFrame(data)

# Display the first few rows of the DataFrame
df.head()



Integrating PyArrow with Pandas

To leverage the benefits of both Pandas and PyArrow, we'll first create a Pandas DataFrame from the clinical trial data, and then convert this DataFrame into a PyArrow Table. This step allows us to utilize the advanced memory layout optimization and columnar storage offered by PyArrow. Here's how it's done:



# Import required libraries
import pandas as pd
import pyarrow as pa

# Create pandas DataFrame from the clinical trial data
pandas_df = pd.DataFrame(df)

# Convert pandas DataFrame to pyarrow Table
pyarrow_table = pa.Table.from_pandas(pandas_df)


Measuring Memory Usage

One of the primary advantages of using PyArrow is its efficient memory utilization, particularly when working with large datasets. To visualize this benefit, we'll compare the memory usage of the Pandas DataFrame and the PyArrow Table:



# Calculate memory usage for Pandas DataFrame and PyArrow Table
pandas_memory_usage = pandas_df.memory_usage(deep=True).sum() / (1024 * 1024)
pyarrow_memory_usage = pyarrow_table.nbytes / (1024 * 1024)

# Create a memory usage comparison graph
plt.figure(figsize=(6, 4))
plt.bar(['Pandas', 'PyArrow'], [pandas_memory_usage, pyarrow_memory_usage], color=['blue', 'orange'])
plt.ylabel('Memory Usage (MB)')
plt.title('Memory Usage Comparison: Pandas vs. PyArrow')
plt.show()



Image description

The Benefits: Speed and Memory Efficiency

The integration of PyArrow with Pandas presents two significant benefits: improved processing speed and enhanced memory efficiency.

Processing Speed: PyArrow's columnar storage format optimizes data access and retrieval. This leads to faster query execution times, as the data of each column is stored together, reducing the amount of data read from memory. In scenarios like clinical trials, where complex analyses and querying are common, this acceleration in processing speed can significantly improve productivity.

Memory Efficiency: PyArrow employs highly efficient compression algorithms and storage techniques, which reduce the memory footprint of the dataset. This becomes increasingly crucial when working with large clinical trial datasets that might not fit entirely in memory. By minimizing memory usage, PyArrow allows for the manipulation of larger datasets without causing memory-related bottlenecks.

Conclusion

In this blog, I have explored how the integration of PyArrow with Pandas can lead to a substantial improvement in processing speed and memory efficiency when dealing with large clinical trial datasets. By capitalizing on PyArrow's columnar storage and advanced memory optimization techniques, analysts and researchers can perform complex analyses more swiftly and manage larger datasets without compromising memory limitations. The combined power of Pandas and PyArrow opens up new possibilities for insightful exploration and data-driven decision-making in the realm of clinical trials and beyond

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