EcoScape habitat connectivity computation.
Project description
EcoScape Connectivity Computation
This package implements the computation of connectivity and flow according to the EcoScape algorithm.
Authors
- Luca de Alfaro (luca@ucsc.edu)
- Natalia Ocampo-Peñuela (nocampop@ucsc.edu)
- Coen Adler (ctadler@ucsc.edu)
- Artie Nazarov (anazarov@ucsc.edu)
- Natalie Valett (nvalett@ucsc.edu)
- Jasmine Tai (cjtai@ucsc.edu)
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 parametersconnectivity_fn
andflow_fn
are ignored if this is set to True, and at least connectivity will be returned. Flow is also generated only ifgenerate_flow_memory
is True. Only for use as module.generate_flow_memory
: whether the flow should be generated in memory. Only used ifin_memory
is True. Only for use as module.
Example Notebooks
Here you can find a Colab Notebook that demonstrates connectivity computation.
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