tessl/pypi-tables

Hierarchical datasets for Python with HDF5 library for managing extremely large amounts of data

Overview

Eval results

Files

Groups and Navigation

Name: tessl/pypi-tables
Author: tessl

PyTables uses a hierarchical group structure similar to a filesystem for organizing data nodes. Groups serve as containers that can hold other groups and data nodes (tables, arrays), providing logical organization and namespace management for complex datasets.

Capabilities

Group Creation and Management

class Group:
    def __init__(self, parentnode, name, title="", new=False, filters=None):
        """Group constructor (typically called via File.create_group)."""
        
    def _f_walknodes(self, classname=None):
        """
        Walk all nodes in this group and its subgroups.
        
        Parameters:
        - classname (str): Filter by node class name
        
        Yields:
        Node: Each node in traversal order
        """
        
    def _f_list_nodes(self, classname=None):
        """
        List immediate child nodes.
        
        Parameters:
        - classname (str): Filter by node class name
        
        Returns:
        list: Child nodes of specified class
        """
        
    def __contains__(self, name):
        """
        Check if child node exists.
        
        Parameters:
        - name (str): Child node name
        
        Returns:
        bool: True if child exists
        """
        
    def __getitem__(self, name):
        """
        Get child node by name.
        
        Parameters:
        - name (str): Child node name
        
        Returns:
        Node: Child node object
        """
        
    def __iter__(self):
        """Iterate over immediate child nodes."""

Navigation and Path Operations

def get_node(file, where, name=None, classname=None):
    """
    Retrieve node by path.
    
    Parameters:
    - file (File): PyTables file object
    - where (str): Path to node or parent location
    - name (str): Node name if where is parent
    - classname (str): Expected class for validation
    
    Returns:
    Node: Retrieved node object
    """

def walk_nodes(file, where="/", classname=None):
    """
    Walk all nodes in hierarchy.
    
    Parameters:
    - file (File): PyTables file object
    - where (str): Starting location
    - classname (str): Filter by class name
    
    Yields:
    Node: Each node in traversal order
    """

Usage Examples

import tables as tb

with tb.open_file("hierarchy.h5", "w") as h5file:
    # Create nested group structure
    exp_group = h5file.create_group("/", "experiment", "Main Experiment")
    data_group = h5file.create_group(exp_group, "data", "Raw Data")
    analysis_group = h5file.create_group(exp_group, "analysis", "Analysis Results")
    
    # Create data in different groups
    raw_table = h5file.create_table(data_group, "measurements", MyDescription)
    results_array = h5file.create_array(analysis_group, "summary", [1, 2, 3])
    
    # Navigate hierarchy
    node = h5file.get_node("/experiment/data/measurements")
    
    # List children
    children = exp_group._f_list_nodes()
    
    # Walk entire tree
    for node in h5file.walk_nodes("/"):
        print(f"Found: {node._v_pathname}")

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