def test_Simulation_set_optic_fiber_layer():
sim = p2p.Simulation(p2p.implants.ArgusI(), engine='serial')
# Invalid grid ranges
with pytest.raises(ValueError):
sim.set_optic_fiber_layer(x_range=[10, 0])
with pytest.raises(ValueError):
sim.set_optic_fiber_layer(x_range=[1, 2, 3])
with pytest.raises(ValueError):
sim.set_optic_fiber_layer(x_range='invalid')
with pytest.raises(ValueError):
sim.set_optic_fiber_layer(y_range=[10, 0])
with pytest.raises(ValueError):
sim.set_optic_fiber_layer(y_range=[1, 2, 3])
with pytest.raises(ValueError):
sim.set_optic_fiber_layer(y_range='invalid')
x_range = [-100, 100]
y_range = [0, 200]
sim.set_optic_fiber_layer(x_range=x_range,
y_range=y_range,
save_data=False)
npt.assert_equal(sim.ofl.gridx.min(), x_range[0])
npt.assert_equal(sim.ofl.gridx.max(), x_range[1])
npt.assert_equal(sim.ofl.gridy.min(), y_range[0])
npt.assert_equal(sim.ofl.gridy.max(), y_range[1])
npt.assert_equal(sim.ofl.range_x, np.diff(x_range))
npt.assert_equal(sim.ofl.range_x, np.diff(x_range))
# Smoke test
implant = p2p.implants.ElectrodeArray('epiretinal', 10, 0, 0, 0)
sim = p2p.Simulation(implant, engine='serial')
sim.set_optic_fiber_layer(x_range=0, y_range=0)
sim.set_optic_fiber_layer(x_range=[0, 0], y_range=[0, 0])
sim.set_optic_fiber_layer()
def test_brightness_movie():
logging.getLogger(__name__).info("test_brightness_movie()")
tsample = 0.075 / 1000
tsample_out = 1.0 / 30.0
s1 = p2p.stimuli.PulseTrain(freq=20,
dur=0.5,
pulse_dur=.075 / 1000.,
interphase_dur=.075 / 1000.,
delay=0.,
tsample=tsample,
amp=20,
pulsetype='cathodicfirst')
implant = p2p.implants.ElectrodeArray('epiretinal', [1, 1], [0, 1], [0, 1],
[0, 1])
# Smoke testing, feed the same stimulus through both electrodes:
sim = p2p.Simulation(implant, engine='serial')
sim.set_optic_fiber_layer(x_range=[-2, 2],
y_range=[-3, 3],
sampling=1,
save_data=False)
sim.set_ganglion_cell_layer('latest', tsample=tsample)
logging.getLogger(__name__).info(" - PulseTrain")
sim.pulse2percept([s1, s1], t_percept=tsample_out)
def test_Simulation_pulse2percept():
implant = p2p.implants.ElectrodeArray("epiretinal", 10, 0, 0, 0)
sim = p2p.Simulation(implant, engine='serial')
sim.set_optic_fiber_layer(x_range=[0, 0], y_range=[0, 0])
pt = p2p.stimuli.BiphasicPulse('cathodicfirst', 0.45 / 1000, 0.005 / 1000)
sim.pulse2percept(pt)
sim.pulse2percept(pt, layers=['GCL'])
sim.pulse2percept(pt, layers=['INL'])
# PulseTrain must have the same tsample as (implicitly set up) GCL
pt = p2p.stimuli.BiphasicPulse("cathodicfirst", 0.1, 0.001)
with pytest.raises(ValueError):
sim.pulse2percept(pt)
pt = p2p.stimuli.BiphasicPulse("cathodicfirst", 0.1, 0.005 / 1000)
with pytest.raises(ValueError):
sim.pulse2percept(pt, layers=['GCL', 'invalid'])
def test_Simulation_set_ganglion_cell_layer():
# A valid ganglion cell model
class Valid(p2p.retina.BaseModel):
def model_cascade(self, inval):
return inval
# Smoke test custom model
implant = p2p.implants.ElectrodeArray('epiretinal', 10, 0, 0, 0)
sim = p2p.Simulation(implant, engine='serial')
sim.set_optic_fiber_layer(x_range=0, y_range=0)
valid_model = Valid(tsample=0.2)
sim.set_ganglion_cell_layer(valid_model)
npt.assert_equal(isinstance(sim.gcl, p2p.retina.BaseModel), True)
npt.assert_equal(sim.gcl.tsample, 0.2)
# Smoke test latest model
for modelstr in ['latest', 'Latest', 'LATEST']:
sim.set_ganglion_cell_layer(modelstr, lweight=42)
npt.assert_equal(isinstance(sim.gcl, p2p.retina.TemporalModel), True)
npt.assert_equal(sim.gcl.lweight, 42)
sim.set_ganglion_cell_layer(modelstr, unknown_param=2) # smoke
# Smoke test Nanduri model
for modelstr in ['Nanduri2012', 'nanduri2012', 'NANDURI2012']:
sim.set_ganglion_cell_layer(modelstr, tau3=42)
npt.assert_equal(isinstance(sim.gcl, p2p.retina.Nanduri2012), True)
npt.assert_equal(sim.gcl.tau3, 42)
sim.set_ganglion_cell_layer(modelstr, unknown_param=2) # smoke
# Smoke test Horsager model
for modelstr in ['Horsager2009', 'horsager', 'HORSAGER2009']:
sim.set_ganglion_cell_layer(modelstr, tau3=42)
npt.assert_equal(isinstance(sim.gcl, p2p.retina.Horsager2009), True)
npt.assert_equal(sim.gcl.tau3, 42)
sim.set_ganglion_cell_layer(modelstr, unknown_param=2) # smoke
# Model unknown
with pytest.raises(ValueError):
sim.set_ganglion_cell_layer('unknown-model')
with pytest.raises(ValueError):
sim.set_ganglion_cell_layer(p2p.implants.ArgusII())
def img2percept(
infile,
implant_type='AlphaIMS',
engine_string='serial',
s_sample=25,
t_sample=0.005 / 1000,
dconst=0.01,
retinamodel='Nanduri2012',
naxons=501,
downsampling_input=None, # tuple of desired resolution, e.g. (104,104)
invert_input=False,
videobool=False,
tolerance=0.0):
"""
Run pulse2percept on an input image.
Parameters
----------
infile : str
path to input image file
implant_type : str
type of implant used for the simulation. Can be from ['AlphaIMS', 'ArgusI', 'ArgusII']
engine_string : str, default='serial'
parallelization engine used by p2p
s_sample
t_sample
dconst
retinamodel
naxons
downsampling_input
invert_input
videobool
tolerance
Returns
-------
"""
# TODO: Finish docstring
# choose implant type
implant = _import_implant(implant_type)
# configure simulation
sim = p2p.Simulation(implant,
engine=engine_string,
n_jobs=-1,
use_jit=False)
sim.set_optic_fiber_layer(sampling=s_sample,
sensitivity_rule='decay',
decay_const=dconst,
n_axons=naxons)
sim.set_ganglion_cell_layer(retinamodel, tsample=t_sample)
# load input image
if not videobool:
img_in = sio.imread(infile, as_gray=True)
if downsampling_input:
img_in = sit.resize(img_in, (104, 104))
if invert_input:
img_in = invert(img_in)
# generate pulsetrain
if videobool:
stim = p2p.stimuli.video2pulsetrain(infile, implant, tsample=t_sample)
else:
stim = p2p.stimuli.image2pulsetrain(img_in, implant, tsample=t_sample)
# choose retina layers to be included in simulation
simlayers = _choose_layers(retinamodel)
# generate percept from pulsetrain
percept = sim.pulse2percept(stim,
layers=simlayers,
t_percept=t_sample,
tol=tolerance)
return percept
import numpy as np
import pickle
import pulse2percept as p2p
videofile = '../data/kid-pool.avi'
stimfile = '../examples/notebooks/stim-kid-pool-amplitude.dat'
perceptfile = 'percept-kid-pool-amplitude'
# Place an Argus I array on the retina
argus = p2p.implants.ArgusII(x_center=0, y_center=0, h=100)
sim = p2p.Simulation(argus, engine='joblib', num_jobs=5)
# Set parameters of the optic fiber layer (OFL)
# In previous versions of the model, this used to be called the `Retina`
# object, which created a spatial grid and generated the axtron streak map.
sampling = 250 # spatial sampling of the retina (microns)
axon_lambda = 2 # constant that determines fall-off with axonal distance
sim.set_optic_fiber_layer(sampling=sampling,
axon_lambda=axon_lambda,
x_range=[-2800, 2800],
y_range=[-1700, 1700])
# Set parameters of the ganglion cell layer (GCL)
# In previous versions of the model, this used to be called `TemporalModel`.
t_gcl = 0.005 / 1000 # Sampling step (s) for the GCL computation
t_percept = 1.0 / 30.0 # Sampling step (s) for the perceptual output
sim.set_ganglion_cell_layer(tsample=t_gcl)
try:
stim = pickle.load(open(stimfile, "rb"))
def test_Simulation___init__():
implant = p2p.implants.Electrode("epiretinal", 10, 0, 0, 0)
with pytest.raises(TypeError):
p2p.Simulation(implant)
import numpy as np
import pickle
import pulse2percept as p2p
# Place an Argus I array on the retina
argus = p2p.implants.ArgusII(x_center=0, y_center=0, h=100)
sim = p2p.Simulation(argus)
# Set parameters of the optic fiber layer (OFL)
# In previous versions of the model, this used to be called the `Retina`
# object, which created a spatial grid and generated the axtron streak map.
sampling = 250 # spatial sampling of the retina (microns)
axon_lambda = 2 # constant that determines fall-off with axonal distance
sim.set_optic_fiber_layer(sampling=sampling,
axon_lambda=axon_lambda,
x_range=[-2800, 2800],
y_range=[-1700, 1700])
# Set parameters of the ganglion cell layer (GCL)
# In previous versions of the model, this used to be called `TemporalModel`.
t_gcl = 0.005 / 1000 # Sampling step (s) for the GCL computation
t_percept = 1.0 / 30.0 # Sampling step (s) for the perceptual output
sim.set_ganglion_cell_layer(tsample=t_gcl)
stim = p2p.stimuli.video2pulsetrain('../../data/boston-train.mp4',
argus,
framerate=30,
coding='amplitude',
valrange=[0, 60],
max_contrast=False,