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HDF5 Integration

Note

For advanced users

Overview

A single whole-slide image may contain on the order of 1010 pixels, making it infeasible to process entire images in RAM. PathML supports efficient manipulation of large-scale imaging data via the h5path format, a hierarchical data structure which allows users to access small regions of the processed WSI without loading the entire image. This feature reduces the RAM required to run a PathML workflow (pipelines can be run on a consumer laptop), simplifies the reading and writing of processed WSIs, improves data exploration utilities, and enables fast reading for downstream tasks (e.g. PyTorch Dataloaders). Since slides are managed on disk, your drive must have sufficient storage. Performance will benefit from storage with fast read/write (SSD, NVMe).

How it Works

Each :class:`~pathml.core.SlideData` object is backed by an .h5path file on disk. All interaction with the .h5path file is handled automatically by the :class:`~pathml.core.h5managers.h5pathManager`. For example, when a user calls slidedata.tiles[tile_key], the :class:`~pathml.core.h5managers.h5pathManager` will retrieve the tile from disk and return it, without the user needing to worry about accessing the HDF5 file themself. As tiles are extracted and passed to a preprocessing pipeline, the :class:`~pathml.core.h5managers.h5pathManager` also handles aggregating the processed tiles into the .h5path file. At the conclusion of preprocessing, the h5py object can optionally be permanently written to disk in .h5path format via the :meth:`SlideData.write() <pathml.core.SlideData.write>` method.

About HDF5

The internals of PathML as well as the .h5path file format are based on the hierarchical data format HDF5, implemented by h5py.

HDF5 format consists of 3 types of elements:

Groups A "container," similar to a directory in a filesystem. Groups may contain Datasets, Attributes, or other Groups.
Datasets Rectangular collection of data elements. Wraps np.ndarray .
Attributes Small named metadata elements. Each attribute is attached to a Group or Dataset.

Groups are container-like and can be queried like dictionaries:

import h5py
root = h5py.File('path/to/file.h5path', 'r')
masks = root['masks']

Datasets can be treated like numpy.ndArray objects:

Important

To retrieve a numpy.ndArray object from h5py.Dataset you must slice the Dataset with NumPy fancy-indexing syntax: for example [...] to retrieve the full array, or [a:b, ...] to return the array with first dimension sliced to the interval [a, b].

import h5py
root = h5py.File('path/to/file.h5path', 'r')
im = root['tiles']['(0, 0)']['array'][...]
im_slice = root['tiles']['(0, 0)']['array'][0:100, 0:100, :]

Attributes are stored in a .attrs object which can be queried like a dictionary:

import h5py
root = h5py.File('path/to/file.h5path', 'r')
tile_shape = root['tiles'].attrs['tile_shape']

.h5path File Format

h5path utilizes a self-describing hierarchical file system similar to :class:`~pathml.core.SlideData`.

Here we examine the h5path file format in detail:

root/                           (Group)
├── fields/                     (Group)
│   ├── name                    (Attribute, str)
│   ├── shape                   (Attribute, tuple)
│   ├── labels                  (Group)
│   │   ├── label1              (Attribute, [str, int, float, array])
│   │   ├── label2              (Attribute, [str, int, float, array])
│   │   └── etc...
│   └── slide_type              (Group)
│       ├── stain               (Attribute, str)
│       ├── tma                 (Attribute, bool)
│       ├── rgb                 (Attribute, bool)
│       ├── volumetric          (Attribute, bool)
│       └── time_series         (Attribute, bool)
├── masks/                      (Group)
│   ├── mask1                   (Dataset, array)
│   ├── mask2                   (Dataset, array)
│   └── etc...
├── counts                      (Group)
│   └── `.h5ad` format
└── tiles/                      (Group)
    ├── tile_shape              (Attribute, tuple)
    ├── tile_stride             (Attribute, tuple)
    ├── tile_key1/              (Group)
    │   ├── array               (Dataset, array)
    │   ├── masks/              (Group)
    │   │   ├── mask1           (Dataset, array)
    │   │   ├── mask2           (Dataset, array)
    │   │   └── etc...
    │   ├── coords              (Attribute, tuple)
    │   ├── name                (Attribute, str)
    │   └── labels/             (Group)
    │       ├── label1          (Attribute, [str, int, float, array])
    │       ├── label2          (Attribute, [str, int, float, array])
    │       └── etc...
    ├── tile_key2/              (Group)
    │   └── etc...
    └── etc...

Slide-level metadata is stored in the fields/ group.

Slide-level counts matrix metadata is stored in the counts/ group.

The tiles/ group stores tile-level data. Each tile occupies its own group, and tile coordinates are used as keys for indexing tiles within the tiles/ group. Within each tile's group, the array dataset contains the tile image, the masks/ group contains tile-level masks, and other metadata including name, labels, and coords are stored as attributes. Slide-level metadata about tiling, including tile shape and stride, are stored as attributes in the tiles/ group.

Whole-slide masks are stored in the masks/ Group. All masks are enforced to be the same shape as the image array. However, when running a pipeline, these masks are moved to the tile-level and stored within the tile groups. The slide-level masks are therefore not saved when calling :meth:`SlideData.write() <pathml.core.SlideData.write>`.

By default, we use float16 as the data type for all Datasets and HDF5's ENUM type <https://docs.h5py.org/en/stable/special.html#enumerated-types> for masks, which are stored as 8-bit integers. Changing the dtype in the Slide constructor changes the data type used to store images.

Note

Be aware that the h5path format specification may change between major versions

Reading and Writing

:class:`~pathml.core.SlideData` objects are easily written to h5path format by calling :meth:`SlideData.write() <pathml.core.SlideData.write>`. All files with .h5 or .h5path extensions are loaded to :class:`~pathml.core.SlideData` objects automatically.