ecoscape-connectivity 0.0.5

EcoScape habitat connectivity computation.

EcoScape Connectivity Computation

This package implements the computation of connectivity and flow according to the EcoScape algorithm.

Authors

• Luca de Alfaro ([e-mail])
• Natalia Ocampo-Peñuela ([e-mail])
• Coen Adler ([e-mail])
• Artie Nazarov ([e-mail])
• Natalie Valett ([e-mail])
• Jasmine Tai ([e-mail])

Project home page

Usage

The package can be used both from the command line, and as a python module. For command line options, do:

ecoscape-connectivity --help

As a Python module, the main function is compute_connectivity:

from ecoscape_connectivity import compute_connectivity

def compute_connectivity(habitat_fn=None,
                         terrain_fn=None,
                         connectivity_fn=None,
                         flow_fn=None,
                         permeability_dict=None,
                         gap_crossing=2,
                         num_gaps=10,
                         num_simulations=400,
                         seed_density=4,
                         single_tile=False,
                         tile_size=1000,
                         tile_border=256,
                         minimum_habitat=1e-4,
                         in_memory=False,
                         generate_flow_memory=False)

The computation will be much faster if you run it with GPU support.

The output connectivity and flow are encoded in the output geotiffs as follows:

• For connectivity, the values from [0, 1] are linearly rescaled to the range 0..255 and encoded as integers, so that 0 corresponds to no connectivity, and 255 to maximum connectivity.
• For flow, the values of $f \in [0, \infty)$ are encoded in log-scale via $20 \cdot log_{10} (1 + f)$ (so that the flow is expressed in dB, like sound intensity), and clipped to integers in the 0..255 range.

Arguments:

• habitat_fn: name of habitat geotiff, or (if used as module) the GeoTiff object from habitat geotiff. This file must contain 0 = non habitat, and 1 = habitat.
• terrain_fn: name of the landscape matrix geotiff, or (if used as module) the GeoTiff object from landscape matrix geotiff. This file contains terrain categories that are translated via permeability_dict.
• connectivity_fn: output file name for connectivity.
• flow_fn: output file name for flow. If None, the flow is not computed, and the computation is faster.
• permeability_dict: Permeability dictionary. Gives the permeability of each terrain type, translating from the terrain codes, to the permeability in [0, 1]. If a terrain type is not found in the dictionary, it is assumed it has permeability 0.
• gap_crossing: size of gap crossing in pixels.
• num_gaps: number of gaps that can be crossed during dispersal.
• num_simulations: Number of simulations that are done.
• seed_density: density of seeds. There are this many seeds for every square with edge of dispersal distance.
• single_tile: if True, instead of iterating over small tiles, tries to read the input as a single large tile. This is faster, but might not fit into memory.
• tile_size: size of (square) tile in pixels.
• tile_border: size of tile border in pixels.
• minimum_habitat: if a tile has a fraction of habitat smaller than this, it is skipped. This saves time in countries where the habitat is only on a small portion.
• in_memory: whether the connectivity and flow should be saved in memory only. Because such files would be deleted on close, the open memory files will be returned as (repop_file, grad_file). Note that the parameters connectivity_fn and flow_fn are ignored if this is set to True, and at least connectivity will be returned. Flow is also generated only if generate_flow_memory is True. Only for use as module.
• generate_flow_memory: whether the flow should be generated in memory. Only used if in_memory is True. Only for use as module.

Example Notebooks

Here you can find a Colab Notebook that demonstrates connectivity computation.