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webknossos.dataset

Dataset API

The high-level dataset API automatically reads and writes meta information for any dataset and updates them if necessary, such as the datasource-properties.json.

A dataset (webknossos.dataset.dataset.Dataset) is the entry-point for this API. The dataset stores the data on disk in .wkw-files (see webknossos-wrap (wkw)).

Each dataset consists of one or more layers (webknossos.dataset.layer.Layer), which themselves can comprise multiple magnifications (webknossos.dataset.mag_view.MagView).

Examples

Opening Datasets

from webknossos.dataset import Dataset

dataset = Dataset(<path_to_dataset>)
# Assuming that the dataset has a layer called 'color' and the layer has the magnification "1"
layer = dataset.get_layer("color")
mag1 = layer.get_mag("1")

Creating Datasets

from webknossos.dataset import Dataset
from webknossos.dataset import LayerCategories

dataset = Dataset.create(<path_to_new_dataset>, scale=(1, 1, 1))
layer = dataset.add_layer(
    layer_name="color",
    category=LayerCategories.COLOR_TYPE,
    dtype_per_channel="uint8",
    num_channels=3
)

mag1 = layer.add_mag("1")

Reading Datasets

from webknossos.dataset import Dataset

dataset = Dataset(<path_to_dataset>)
# Assuming that the dataset has a layer called 'color' and the layer has the magnification "1" and "2"
layer = dataset.get_layer("color")
mag1 = layer.get_mag("1")
mag2 = layer.get_mag("2")

data_in_mag1 = mag1.read()  # the offset and size from the properties are used
data_in_mag1_subset = mag1.read(offset=(10, 20, 30), size=(512, 512, 32))

data_in_mag2 = mag2.read()  # the offset and size from the properties are used
data_in_mag2_subset = mag2.read(offset=(5, 10, 15), size=(256, 256, 16))

Writing Datasets

from webknossos.dataset import Dataset

dataset = Dataset(<path_to_dataset>)
# Assuming that the dataset has a layer called 'color' and the layer has the magnification "1" and "2"
layer = dataset.get_layer("color")
mag1 = layer.get_mag("1")
mag2 = layer.get_mag("2")

# The properties are updated, if the written data exceeds the bounding box in the properties
mag1.write(
    offset=(10, 20, 30),
    data=(np.random.rand(3, 512, 512, 32) * 255).astype(np.uint8)  # assuming the layer has 3 channels
)

mag2.write(
    offset=(5, 10, 15),
    data=(np.random.rand(3, 256, 256, 16) * 255).astype(np.uint8)  # assuming the layer has 3 channels
)

Submodules

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