pysilsub

A Python toolbox for performing the method of silent substitution

https://github.com/pysilentsubstitution/pysilsub

Science Score: 54.0%

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CITATION.cff file
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codemeta.json file
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Links to: zenodo.org
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Low similarity (9.8%) to scientific vocabulary

Keywords from Contributors

mesh sequences interactive hacking network-simulation

Last synced: 7 months ago · JSON representation ·

Repository

A Python toolbox for performing the method of silent substitution

Basic Info

Host: GitHub
Owner: PySilentSubstitution
License: mit
Language: Jupyter Notebook
Default Branch: main
Size: 142 MB

Statistics

Stars: 13
Watchers: 2
Forks: 2
Open Issues: 0
Releases: 4

Created over 4 years ago · Last pushed about 1 year ago

Metadata Files

Readme License Code of conduct Citation

Welcome to PySilentSubstitution!

PySilSub is a Python toolbox for performing the method of silent substitution in vision and nonvisual photoreception research.

Note: See also, PyPlr, a sister project offering a Python framework for researching the pupillary light reflex with the Pupil Core eye tracking platform.

With PySilSub, observer- and device-specific solutions to silent substitution problems are found with linear algebra or numerical optimisation via a configurable, intuitive interface.

```Python

Example 1 - Target melanopsin with 100% contrast (no background

specified), whilst ignoring rods and minimizing cone contrast,

for a 42-year-old observer and field size of 10 degrees. Solved

with numerical optimization.

from pysilsub import observers, problems

ssp = problems.SilentSubstitutionProblem.frompackagedata('STLAB1York') # Load example data ssp.observer = observers.ColorimetricObserver(age=42, fieldsize=10) # Assign custom observer model ssp.ignore = ['rh'] # Ignore rod photoreceptors ssp.silence = ['sc', 'mc', 'lc'] # Minimise cone contrast ssp.target = ['mel'] # Target melanopsin ssp.targetcontrast = 1.0 # With 100% contrast solution = ssp.optimsolve() # Solve with optimisation fig = ssp.plotsolution(solution.x) # Plot the solution ```

Example 1

Another example:

```Python

Example 2 - Target S-cones with 45% contrast against a specified

background spectrum (all primaries, half max) whilst ignoring rods

and minimizing contrast on L/M cones and melanopsin, assuming

32-year-old observer and 10-degree field size. Solved with linear

algebra.

from pysilsub import problems

ssp = problems.SilentSubstitutionProblem.frompackagedata('STLAB1York') # Load example data ssp.background = [.5] * ssp.nprimaries # Specify background spectrum ssp.ignore = ['rh'] # Ignore rod photoreceptors ssp.silence = ['mc', 'lc', 'mel'] # Silence L/M cones and melanopsin ssp.target = ['sc'] # Target S cones ssp.targetcontrast = .45 # With 45% contrast solution = ssp.linalgsolve() # Solve with linear algebra fig = ssp.plot_solution(solution) # Plot the solution ```

Example 2

Some features may serve a broader purpose in vision and circadian research. For example, computing and saving a full set of CIEPO06- and CIES026-compliant action spectra for a given observer age and field size.

```python from pysilsub.observers import ColorimetricObserver

ColorimetricObserver(age=32, fieldsize=10).saveaction_spectra() ```

For more information, check out the code, read the docs, and run pip install pysilsub to try out the examples above.

Citation (CITATION.cff)

cff-version: 0.1.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Martin"
  given-names: "Joel, T."
  orcid: "https://orcid.org/0000-0002-4475-3835"
- family-names: "Boynton"
  given-names: "Geoffrey, M."
  orcid: "https://orcid.org/0000-0001-6561-6920"
- family-names: "Baker"
  given-names: "Daniel, H."
  orcid: "https://orcid.org/0000-0002-0161-443X"
- family-names: "Wade"
  given-names: "Alex"
  orcid: "https://orcid.org/0000-0003-0656-2664"
- family-names: "Spitschan"
  given-names: "Manuel"
  orcid: "https://orcid.org/0000-0002-8572-9268"
title: "pysilsub"
version: 0.1.0
doi: 10.5281/zenodo.7776769 
date-released: 2023-03-31
url: "https://github.com/PySilentSubstitution/pysilsub"

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Total versions: 10
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pypi.org: pysilsub

Software for performing silent substitution in Python.

Homepage: https://github.com/PySilentSubstitution/pysilsub
Documentation: https://pysilentsubstitution.github.io/pysilsub/index.html
License: MIT
Latest release: 0.1.1
published over 2 years ago

Versions: 10
Dependent Packages: 0
Dependent Repositories: 1
Downloads: 10 Last month

Rankings

Dependent packages count: 7.3%

Stargazers count: 21.6%

Dependent repos count: 22.1%

Average: 24.6%

Forks count: 30.0%

Downloads: 42.1%

Maintainers (1)

jtmbeta

Last synced: 8 months ago

Dependencies

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setup.py pypi

colour-science *
importlib-resources *
matplotlib *
numpy *
pandas *
scipy *
seaborn *

pyproject.toml pypi

pysilsub

Science Score: 54.0%

Keywords from Contributors

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Metadata Files

README.md

Welcome to PySilentSubstitution!

Example 1 - Target melanopsin with 100% contrast (no background

specified), whilst ignoring rods and minimizing cone contrast,

for a 42-year-old observer and field size of 10 degrees. Solved

with numerical optimization.

Example 2 - Target S-cones with 45% contrast against a specified

background spectrum (all primaries, half max) whilst ignoring rods

and minimizing contrast on L/M cones and melanopsin, assuming

32-year-old observer and 10-degree field size. Solved with linear

algebra.

Citation (CITATION.cff)

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