def __init__(self, **params):
BaseStimulus.__init__(self, **params)
self._zoom_cache = {}
self.region_cache = {}
self.is_visible = True
self.transparent = True # And efficiency flag. It should be set to false by the stimulus if there are no transparent points in it.
# This will avoid all the code related to transparency which is very expensive.
self.region = VisualRegion(self.location_x, self.location_y,
self.size_x, self.size_y)
self.first_resolution_mismatch_display = True
def __init__(self, sim, num_threads, parameters):
Model.__init__(self, sim, num_threads, parameters)
# Load components
CortexExcL4 = load_component(self.parameters.l4_cortex_exc.component)
CortexInhL4 = load_component(self.parameters.l4_cortex_inh.component)
RetinaLGN = load_component(self.parameters.retina_lgn.component)
# Build and instrument the network
self.visual_field = VisualRegion(location_x=self.parameters.visual_field.centre[0],location_y=self.parameters.visual_field.centre[1],size_x=self.parameters.visual_field.size[0],size_y=self.parameters.visual_field.size[1])
self.input_layer = RetinaLGN(self, self.parameters.retina_lgn.params)
cortex_exc_l4 = CortexExcL4(self, self.parameters.l4_cortex_exc.params)
cortex_inh_l4 = CortexInhL4(self, self.parameters.l4_cortex_inh.params)
GaborConnector(self,self.input_layer.sheets['X_ON'],self.input_layer.sheets['X_OFF'],cortex_exc_l4,self.parameters.l4_cortex_exc.AfferentConnection,'V1AffConnection')
GaborConnector(self,self.input_layer.sheets['X_ON'],self.input_layer.sheets['X_OFF'],cortex_inh_l4,self.parameters.l4_cortex_inh.AfferentConnection,'V1AffInhConnection')
# initialize projections
ModularSingleWeightProbabilisticConnector(self,'V1L4ExcL4ExcConnectionRand',cortex_exc_l4,cortex_exc_l4,self.parameters.l4_cortex_exc.L4ExcL4ExcConnectionRand).connect()
ModularSingleWeightProbabilisticConnector(self,'V1L4ExcL4InhConnectionRand',cortex_exc_l4,cortex_inh_l4,self.parameters.l4_cortex_exc.L4ExcL4InhConnectionRand).connect()
ModularSingleWeightProbabilisticConnector(self,'V1L4InhL4ExcConnectionRand',cortex_inh_l4,cortex_exc_l4,self.parameters.l4_cortex_inh.L4InhL4ExcConnectionRand).connect()
ModularSingleWeightProbabilisticConnector(self,'V1L4InhL4InhConnectionRand',cortex_inh_l4,cortex_inh_l4,self.parameters.l4_cortex_inh.L4InhL4InhConnectionRand).connect()
# initialize projections
ModularSamplingProbabilisticConnector(self,'V1L4ExcL4ExcConnection',cortex_exc_l4,cortex_exc_l4,self.parameters.l4_cortex_exc.L4ExcL4ExcConnection).connect()
ModularSamplingProbabilisticConnector(self,'V1L4ExcL4InhConnection',cortex_exc_l4,cortex_inh_l4,self.parameters.l4_cortex_exc.L4ExcL4InhConnection).connect()
ModularSamplingProbabilisticConnector(self,'V1L4InhL4ExcConnection',cortex_inh_l4,cortex_exc_l4,self.parameters.l4_cortex_inh.L4InhL4ExcConnection).connect()
ModularSamplingProbabilisticConnector(self,'V1L4InhL4InhConnection',cortex_inh_l4,cortex_inh_l4,self.parameters.l4_cortex_inh.L4InhL4InhConnection).connect()
def __init__(self, sim, num_threads, parameters):
Model.__init__(self, sim, num_threads, parameters)
# Load components
RetinaLGN = load_component(self.parameters.retina_lgn.component)
PGN = load_component(self.parameters.pgn.component)
# Build and instrument the network
self.visual_field = VisualRegion(
location_x=self.parameters.visual_field.centre[0],
location_y=self.parameters.visual_field.centre[1],
size_x=self.parameters.visual_field.size[0],
size_y=self.parameters.visual_field.size[1])
# init layers
self.input_layer = RetinaLGN(self, self.parameters.retina_lgn.params)
pgn = PGN(self, self.parameters.pgn.params)
########################################################
# LGN-PGN
ModularSamplingProbabilisticConnector(
self,
'LGN_PGN_ConnectionOn', # name
self.input_layer.sheets['X_ON'], # source
pgn, # target
self.parameters.pgn.LGN_PGN_ConnectionOn # params
).connect()
ModularSamplingProbabilisticConnector(
self,
'LGN_PGN_ConnectionOff', # name
self.input_layer.sheets['X_OFF'], # source
pgn, # target
self.parameters.pgn.LGN_PGN_ConnectionOff # params
).connect()
ModularSamplingProbabilisticConnector(
self,
'PGN_PGN_Connection', # name
pgn, # source
pgn, # target
self.parameters.pgn.PGN_PGN_Connection # params
).connect()
ModularSamplingProbabilisticConnector(
self,
'PGN_LGN_ConnectionOn', # name
pgn, # source
self.input_layer.sheets['X_ON'], # target
self.parameters.pgn.PGN_LGN_ConnectionOn # params
).connect()
ModularSamplingProbabilisticConnector(
self,
'PGN_LGN_ConnectionOff', # name
pgn, # source
self.input_layer.sheets['X_OFF'], # target
self.parameters.pgn.PGN_LGN_ConnectionOff # params
).connect()
def __init__(self, **params):
BaseStimulus.__init__(self, **params)
self._zoom_cache = {}
self.region_cache = {}
self.is_visible = True
self.transparent = True # And efficiency flag. It should be set to false by the stimulus if there are no transparent points in it.
# This will avoid all the code related to transparency which is very expensive.
self.region = VisualRegion(self.location_x, self.location_y,
self.size_x, self.size_y)
self.first_resolution_mismatch_display=True
def __init__(self, sim, num_threads, parameters):
Model.__init__(self, sim, num_threads, parameters)
# Load components
RetinaLGN = load_component(self.parameters.sheets.retina_lgn.component)
# Build and instrument the network
self.visual_field = VisualRegion(
location_x=self.parameters.visual_field.centre[0],
location_y=self.parameters.visual_field.centre[1],
size_x=self.parameters.visual_field.size[0],
size_y=self.parameters.visual_field.size[1])
self.input_layer = RetinaLGN(self,
self.parameters.sheets.retina_lgn.params)
def _calculate_input_currents(self, visual_space, duration):
"""
Calculate the input currents for all cells.
"""
assert isinstance(visual_space, VisualSpace)
if duration is None:
duration = visual_space.get_maximum_duration()
# create population of CellWithReceptiveFields, setting the receptive
# field centres based on the size/location of self
logger.debug("Creating population of `CellWithReceptiveField`s")
input_cells = {}
#effective_visual_field_width, effective_visual_field_height = self.parameters.size
#x_values = numpy.linspace(-effective_visual_field_width/2.0, effective_visual_field_width/2.0, self.shape[0])
#y_values = numpy.linspace(-effective_visual_field_height/2.0, effective_visual_field_height/2.0, self.shape[1])
for rf_type in self.rf_types:
input_cells[rf_type] = []
for i in numpy.nonzero(self.sheets[rf_type].pop._mask_local)[0]:
#for i in xrange(0,len(self.sheets[rf_type].pop.positions[0])):
cell = CellWithReceptiveField(
self.sheets[rf_type].pop.positions[0][i],
self.sheets[rf_type].pop.positions[1][i], self.rf[rf_type],
self.parameters.gain, visual_space)
cell.initialize(visual_space.background_luminance, duration)
input_cells[rf_type].append(cell)
logger.debug("Processing frames")
t = 0
retinal_input = []
while t < duration:
t = visual_space.update()
for rf_type in self.rf_types:
for cell in input_cells[rf_type]:
cell.view()
visual_region = VisualRegion(location_x=0,
location_y=0,
size_x=self.parameters.size[0],
size_y=self.parameters.size[1])
im = visual_space.view(
visual_region, pixel_size=self.rf["X_ON"].spatial_resolution)
retinal_input.append(im)
input_currents = {}
for rf_type in self.rf_types:
input_currents[rf_type] = [
cell.response_current() for cell in input_cells[rf_type]
]
return (input_currents, retinal_input)
def __init__(self,simulator,num_threads,parameters):
Model.__init__(self,simulator,num_threads,parameters)
RetinaLGN = load_component(self.parameters.sheets.retina_lgn.component)
# Build and instrument the network
self.visual_field = VisualRegion(location_x=self.parameters.visual_field.centre[0],location_y=self.parameters.visual_field.centre[1],size_x=self.parameters.visual_field.size[0],size_y=self.parameters.visual_field.size[1])
self.input_layer = RetinaLGN(self, self.parameters.sheets.retina_lgn.params)
# which neurons to record
tr = {'spikes' : 'all',
'v' : numpy.arange(0,60,1),
'gsyn_exc' :numpy.arange(0,60,1),
'gsyn_inh' : numpy.arange(0,60,1),
}
self.input_layer.sheets['X_ON'].to_record = tr #'all'
self.input_layer.sheets['X_OFF'].to_record = tr #'all'
def __init__(self, x, y, receptive_field, gain_control,visual_space):
self.x = x # position in space
self.y = y #
self.visual_space = visual_space
assert isinstance(receptive_field, SpatioTemporalReceptiveField)
self.receptive_field = receptive_field
self.gain_control = gain_control # (nA.m²/cd) could imagine making this a function of
# the background luminance
self.i = 0
self.visual_region = VisualRegion(location_x=self.x,
location_y=self.y,
size_x=self.receptive_field.width,
size_y=self.receptive_field.height)
#logger.debug("view_array.shape = %s" % str(view_array.shape))
#logger.debug("receptive_field.kernel.shape = %s" % str(self.receptive_field.kernel.shape))
#logger.debug("response.shape = %s" % str(self.response.shape))
if visual_space.update_interval % self.receptive_field.temporal_resolution != 0:
errmsg = "The receptive field temporal resolution (%g ms) must be an integer multiple of the visual space update interval (%g ms)" % \
(self.receptive_field.temporal_resolution, visual_space.update_interval)
raise Exception(errmsg)
self.update_factor = int(visual_space.update_interval / self.receptive_field.temporal_resolution)
def __init__(self, sim, num_threads, parameters):
Model.__init__(self, sim, num_threads, parameters)
# Load components
CortexExcL4 = load_component(
self.parameters.sheets.l4_cortex_exc.component)
CortexInhL4 = load_component(
self.parameters.sheets.l4_cortex_inh.component)
if not self.parameters.only_afferent and self.parameters.l23:
CortexExcL23 = load_component(
self.parameters.sheets.l23_cortex_exc.component)
CortexInhL23 = load_component(
self.parameters.sheets.l23_cortex_inh.component)
RetinaLGN = load_component(self.parameters.sheets.retina_lgn.component)
# Build and instrument the network
self.visual_field = VisualRegion(
location_x=self.parameters.visual_field.centre[0],
location_y=self.parameters.visual_field.centre[1],
size_x=self.parameters.visual_field.size[0],
size_y=self.parameters.visual_field.size[1],
)
self.input_layer = RetinaLGN(self,
self.parameters.sheets.retina_lgn.params)
cortex_exc_l4 = CortexExcL4(
self, self.parameters.sheets.l4_cortex_exc.params)
cortex_inh_l4 = CortexInhL4(
self, self.parameters.sheets.l4_cortex_inh.params)
if not self.parameters.only_afferent and self.parameters.l23:
cortex_exc_l23 = CortexExcL23(
self, self.parameters.sheets.l23_cortex_exc.params)
cortex_inh_l23 = CortexInhL23(
self, self.parameters.sheets.l23_cortex_inh.params)
# initialize afferent layer 4 projections
GaborConnector(
self,
self.input_layer.sheets["X_ON"],
self.input_layer.sheets["X_OFF"],
cortex_exc_l4,
self.parameters.sheets.l4_cortex_exc.AfferentConnection,
"V1AffConnection",
)
GaborConnector(
self,
self.input_layer.sheets["X_ON"],
self.input_layer.sheets["X_OFF"],
cortex_inh_l4,
self.parameters.sheets.l4_cortex_inh.AfferentConnection,
"V1AffInhConnection",
)
# initialize lateral layer 4 projections
if not self.parameters.only_afferent:
ModularSamplingProbabilisticConnectorAnnotationSamplesCount(
self,
"V1L4ExcL4ExcConnection",
cortex_exc_l4,
cortex_exc_l4,
self.parameters.sheets.l4_cortex_exc.L4ExcL4ExcConnection,
).connect()
ModularSamplingProbabilisticConnectorAnnotationSamplesCount(
self,
"V1L4ExcL4InhConnection",
cortex_exc_l4,
cortex_inh_l4,
self.parameters.sheets.l4_cortex_exc.L4ExcL4InhConnection,
).connect()
ModularSamplingProbabilisticConnector(
self,
"V1L4InhL4ExcConnection",
cortex_inh_l4,
cortex_exc_l4,
self.parameters.sheets.l4_cortex_inh.L4InhL4ExcConnection,
).connect()
ModularSamplingProbabilisticConnector(
self,
"V1L4InhL4InhConnection",
cortex_inh_l4,
cortex_inh_l4,
self.parameters.sheets.l4_cortex_inh.L4InhL4InhConnection,
).connect()
if self.parameters.l23:
# initialize afferent layer 4 to layer 2/3 projection
ModularSamplingProbabilisticConnector(
self,
"V1L4ExcL23ExcConnection",
cortex_exc_l4,
cortex_exc_l23,
self.parameters.sheets.l23_cortex_exc.
L4ExcL23ExcConnection,
).connect()
ModularSamplingProbabilisticConnector(
self,
"V1L4ExcL23InhConnection",
cortex_exc_l4,
cortex_inh_l23,
self.parameters.sheets.l23_cortex_inh.
L4ExcL23InhConnection,
).connect()
ModularSamplingProbabilisticConnector(
self,
"V1L23ExcL23ExcConnection",
cortex_exc_l23,
cortex_exc_l23,
self.parameters.sheets.l23_cortex_exc.
L23ExcL23ExcConnection,
).connect()
ModularSamplingProbabilisticConnector(
self,
"V1L23ExcL23InhConnection",
cortex_exc_l23,
cortex_inh_l23,
self.parameters.sheets.l23_cortex_exc.
L23ExcL23InhConnection,
).connect()
ModularSamplingProbabilisticConnector(
self,
"V1L23InhL23ExcConnection",
cortex_inh_l23,
cortex_exc_l23,
self.parameters.sheets.l23_cortex_inh.
L23InhL23ExcConnection,
).connect()
ModularSamplingProbabilisticConnector(
self,
"V1L23InhL23InhConnection",
cortex_inh_l23,
cortex_inh_l23,
self.parameters.sheets.l23_cortex_inh.
L23InhL23InhConnection,
).connect()
if self.parameters.feedback:
ModularSamplingProbabilisticConnector(
self,
"V1L23ExcL4ExcConnection",
cortex_exc_l23,
cortex_exc_l4,
self.parameters.sheets.l23_cortex_exc.
L23ExcL4ExcConnection,
).connect()
ModularSamplingProbabilisticConnector(
self,
"V1L23ExcL4InhConnection",
cortex_exc_l23,
cortex_inh_l4,
self.parameters.sheets.l23_cortex_exc.
L23ExcL4InhConnection,
).connect()
def _calculate_input_currents(self, visual_space, duration):
"""
Calculate the input currents for all cells.
"""
assert isinstance(visual_space, VisualSpace)
if duration is None:
duration = visual_space.get_maximum_duration()
# create population of CellWithReceptiveFields, setting the receptive
# field centres based on the size/location of self
logger.debug("Creating population of `CellWithReceptiveField`s")
input_cells = OrderedDict()
#effective_visual_field_width, effective_visual_field_height = self.parameters.size
#x_values = numpy.linspace(-effective_visual_field_width/2.0, effective_visual_field_width/2.0, self.shape[0])
#y_values = numpy.linspace(-effective_visual_field_height/2.0, effective_visual_field_height/2.0, self.shape[1])
for rf_type in self.rf_types:
input_cells[rf_type] = []
for i in numpy.nonzero(self.sheets[rf_type].pop._mask_local)[0]:
#for i in range(0,len(self.sheets[rf_type].pop.positions[0])):
cell = CellWithReceptiveField(
self.sheets[rf_type].pop.positions[0][i],
self.sheets[rf_type].pop.positions[1][i], self.rf[rf_type],
self.parameters.gain_control, visual_space)
cell.initialize(visual_space.background_luminance, duration)
input_cells[rf_type].append(cell)
logger.debug("Processing frames")
t = 0
retinal_input = []
#import threading
#def view_cell(cell):
# cell.view()
if False:
while t < duration:
t = visual_space.update()
for rf_type in self.rf_types:
threads = []
for cell in input_cells[rf_type]:
thread = threading.Thread(target=cell.view())
thread.start()
threads.append(thread)
#cell.view()
for t in threads:
t.join()
while t < duration:
t = visual_space.update()
for rf_type in self.rf_types:
for cell in input_cells[rf_type]:
cell.view()
if self.model.parameters.store_stimuli == True:
visual_region = VisualRegion(
location_x=0,
location_y=0,
size_x=self.model.visual_field.size_x,
size_y=self.model.visual_field.size_y)
im = visual_space.view(
visual_region,
pixel_size=self.rf["X_ON"].spatial_resolution)
else:
im = None
retinal_input.append(im)
input_currents = OrderedDict()
for rf_type in self.rf_types:
input_currents[rf_type] = [
cell.response_current() for cell in input_cells[rf_type]
]
return (input_currents, retinal_input)
def __init__(self, sim, num_threads, parameters):
Model.__init__(self, sim, num_threads, parameters)
# Load components
LGN = load_component(self.parameters.lgn.component)
# Instance
self.input_layer = LGN(self, self.parameters.lgn.params)
# Build and instrument the network
self.visual_field = VisualRegion(
location_x=self.parameters.visual_field.centre[0],
location_y=self.parameters.visual_field.centre[1],
size_x=self.parameters.visual_field.size[0],
size_y=self.parameters.visual_field.size[1]
)
# PROJECTIONS
########################################################
# PGN
if withPGN:
# Load components
PGN = load_component( self.parameters.pgn.component )
# Instance
pgn = PGN(self, self.parameters.pgn.params)
# LGN-PGN
ModularSamplingProbabilisticConnector(
self,
'LGN_PGN_ConnectionOn', # name
self.input_layer.sheets['X_ON'], # source
pgn, # target
self.parameters.pgn.LGN_PGN_ConnectionOn # params
).connect()
ModularSamplingProbabilisticConnector(
self,
'LGN_PGN_ConnectionOff', # name
self.input_layer.sheets['X_OFF'], # source
pgn, # target
self.parameters.pgn.LGN_PGN_ConnectionOff # params
).connect()
ModularSamplingProbabilisticConnector(
self,
'PGN_PGN_Connection', # name
pgn, # source
pgn, # target
self.parameters.pgn.PGN_PGN_Connection # params
).connect()
ModularSamplingProbabilisticConnector(
self,
'PGN_LGN_ConnectionOn', # name
pgn, # source
self.input_layer.sheets['X_ON'], # target
self.parameters.pgn.PGN_LGN_ConnectionOn # params
).connect()
ModularSamplingProbabilisticConnector(
self,
'PGN_LGN_ConnectionOff', # name
pgn, # source
self.input_layer.sheets['X_OFF'], # target
self.parameters.pgn.PGN_LGN_ConnectionOff # params
).connect()
# V1
if withV1: # CTC
# Load components
CortexExcL4 = load_component(self.parameters.l4_cortex_exc.component)
CortexInhL4 = load_component(self.parameters.l4_cortex_inh.component)
# Instance
cortex_exc_l4 = CortexExcL4(self, self.parameters.l4_cortex_exc.params)
cortex_inh_l4 = CortexInhL4(self, self.parameters.l4_cortex_inh.params)
# ########################################################
# THALAMO-CORTICAL
# initialize afferent layer 4 projections
GaborConnector(
self,
self.input_layer.sheets['X_ON'],
self.input_layer.sheets['X_OFF'],
cortex_exc_l4, # target
self.parameters.l4_cortex_exc.AfferentConnection, # parameters
'V1AffConnection' # name
)
GaborConnector(
self,
self.input_layer.sheets['X_ON'],
self.input_layer.sheets['X_OFF'],
cortex_inh_l4,
self.parameters.l4_cortex_inh.AfferentConnection,
'V1AffInhConnection'
)
# ########################################################
# CORTICO-CORTICAL
# random lateral layer 4 projections
ModularSingleWeightProbabilisticConnector(
self,
'V1L4ExcL4ExcConnectionRand',
cortex_exc_l4,
cortex_exc_l4,
self.parameters.l4_cortex_exc.L4ExcL4ExcConnectionRand
).connect()
ModularSingleWeightProbabilisticConnector(
self,
'V1L4ExcL4InhConnectionRand',
cortex_exc_l4,
cortex_inh_l4,
self.parameters.l4_cortex_exc.L4ExcL4InhConnectionRand
).connect()
ModularSingleWeightProbabilisticConnector(
self,
'V1L4InhL4ExcConnectionRand',
cortex_inh_l4,
cortex_exc_l4,
self.parameters.l4_cortex_inh.L4InhL4ExcConnectionRand
).connect()
ModularSingleWeightProbabilisticConnector(
self,
'V1L4InhL4InhConnectionRand',
cortex_inh_l4,
cortex_inh_l4,
self.parameters.l4_cortex_inh.L4InhL4InhConnectionRand
).connect()
# lateral layer 4 projections
ModularSamplingProbabilisticConnector(
self,
'V1L4ExcL4ExcConnection',
cortex_exc_l4,
cortex_exc_l4,
self.parameters.l4_cortex_exc.L4ExcL4ExcConnection
).connect()
ModularSamplingProbabilisticConnector(
self,
'V1L4ExcL4InhConnection',
cortex_exc_l4,
cortex_inh_l4,
self.parameters.l4_cortex_exc.L4ExcL4InhConnection
).connect()
ModularSamplingProbabilisticConnector(
self,
'V1L4InhL4ExcConnection',
cortex_inh_l4,
cortex_exc_l4,
self.parameters.l4_cortex_inh.L4InhL4ExcConnection
).connect()
ModularSamplingProbabilisticConnector(
self,
'V1L4InhL4InhConnection',
cortex_inh_l4,
cortex_inh_l4,
self.parameters.l4_cortex_inh.L4InhL4InhConnection
).connect()
########################################################
# CORTICO-THALAMIC
if withFeedback_CxLGN:
ModularSamplingProbabilisticConnector(
self,
'V1EffConnectionOn',
cortex_exc_l4,
self.input_layer.sheets['X_ON'],
self.parameters.l4_cortex_exc.EfferentConnection_LGN
).connect()
ModularSamplingProbabilisticConnector(
self,
'V1EffConnectionOff',
cortex_exc_l4,
self.input_layer.sheets['X_OFF'],
self.parameters.l4_cortex_exc.EfferentConnection_LGN
).connect()
# GaborConnector(
# self,
# self.input_layer.sheets['X_ON'],
# self.input_layer.sheets['X_OFF'],
# cortex_exc_l4, # source
# self.parameters.l4_cortex_exc.EfferentConnection, # parameters
# 'V1EffConnection' # name
# )
if withFeedback_CxPGN and withPGN:
ModularSamplingProbabilisticConnector(
self,
'V1EffConnectionPGN',
cortex_exc_l4,
pgn,
self.parameters.l4_cortex_exc.EfferentConnection_PGN
).connect()
class VisualStimulus(BaseStimulus):
"""
Abstract base class for visual stimuli.
This class defines all parameters common to all visual stimuli.
This class implements all functions specified by the :class:`mozaik.stimuli.stimulus.BaseStimulus` interface.
The only function that remains to be implemented by the user whenever creating a new stimulus by subclassing
this class is the :func:`mozaik.stimuli.stimulus.BaseStimulus.frames` function.
This class also implements functions common to all visual stimuli that are required for it to be compatible
with the :class:`mozaik.space.VisualSpace` and class.
"""
background_luminance = SNumber(
lux,
doc=
"Background luminance. Maximum luminance of object allowed is 2*background_luminance"
)
density = SNumber(1 / (degrees),
doc="The density of stimulus - units per degree")
location_x = SNumber(degrees,
doc="x location of the center of visual region.")
location_y = SNumber(degrees,
doc="y location of the center of visual region.")
size_x = SNumber(degrees,
doc="The size of the region in degrees (asimuth).")
size_y = SNumber(degrees,
doc="The size of the region in degrees (elevation).")
def __init__(self, **params):
BaseStimulus.__init__(self, **params)
self._zoom_cache = {}
self.region_cache = {}
self.is_visible = True
self.transparent = True # And efficiency flag. It should be set to false by the stimulus if there are no transparent points in it.
# This will avoid all the code related to transparency which is very expensive.
self.region = VisualRegion(self.location_x, self.location_y,
self.size_x, self.size_y)
self.first_resolution_mismatch_display = True
def _calculate_zoom(self, actual_pixel_size, desired_pixel_size):
"""
Sometimes the interpolation procedure returns a new array that is too
small due to rounding error. This is a crude attempt to work around that.
"""
zoom = actual_pixel_size / desired_pixel_size
for i in self.img.shape:
if int(zoom * i) != round(zoom * i):
zoom *= (1 + 1e-15)
return zoom
def display(self, region, pixel_size):
assert isinstance(
region, VisualRegion
), "region must be a VisualRegion-descended object. Actually a %s" % type(
region)
size_in_pixels = numpy.ceil(
xy2ij((region.size_x, region.size_y)) /
float(pixel_size)).astype(int)
if self.transparent:
view = TRANSPARENT * numpy.ones(size_in_pixels)
else:
view = self.background_luminance * numpy.ones(size_in_pixels)
if region.overlaps(self.region):
if not self.region_cache.has_key(region):
intersection = region.intersection(self.region)
assert intersection == self.region.intersection(
region
) # just a consistency check. Could be removed if necessary for performance.
img_relative_left = (intersection.left -
self.region.left) / self.region.width
img_relative_width = intersection.width / self.region.width
img_relative_top = (intersection.top -
self.region.bottom) / self.region.height
#img_relative_bottom = (intersection.bottom - self.region.bottom) / self.region.height
img_relative_height = intersection.height / self.region.height
view_relative_left = (intersection.left -
region.left) / region.width
view_relative_width = intersection.width / region.width
view_relative_top = (intersection.top -
region.bottom) / region.height
#view_relative_bottom = (intersection.bottom - region.bottom) / region.height
view_relative_height = intersection.height / region.height
img_pixel_size = xy2ij(
(self.region.size_x, self.region.size_y
)) / self.img.shape # is self.size a tuple or an array?
assert img_pixel_size[0] == img_pixel_size[1]
# necessary instead of == comparison due to the floating math rounding errors
if abs(pixel_size - img_pixel_size[0]) < 0.0001:
img = self.img
else:
if self.first_resolution_mismatch_display:
logger.warning(
"Image pixel size does not match desired size (%g vs. %g) degrees. This is extremely inefficient!!!!!!!!!!!"
% (pixel_size, img_pixel_size[0]))
logger.warning("Image pixel size %g,%g" %
numpy.shape(self.img))
self.first_resolution_mismatch_display = False
# note that if the image is much larger than the view region, we might save some
# time by not rescaling the whole image, only the part within the view region.
zoom = self._calculate_zoom(
img_pixel_size[0],
pixel_size) # img_pixel_size[0]/pixel_size
#logger.debug("Image pixel size (%g deg) does not match desired size (%g deg). Zooming image by a factor %g" % (img_pixel_size[0], pixel_size, zoom))
if zoom in self._zoom_cache:
img = self._zoom_cache[zoom]
else:
img = interpolation.zoom(self.img, zoom)
self._zoom_cache[zoom] = img
j_start = numpy.round(img_relative_left *
img.shape[1]).astype(int)
delta_j = numpy.round(img_relative_width *
img.shape[1]).astype(int)
i_start = img.shape[0] - numpy.round(
img_relative_top * img.shape[0]).astype(int)
delta_i = numpy.round(img_relative_height *
img.shape[0]).astype(int)
l_start = numpy.round(view_relative_left *
size_in_pixels[1]).astype(int)
delta_l = numpy.round(view_relative_width *
size_in_pixels[1]).astype(int)
k_start = size_in_pixels[0] - numpy.round(
view_relative_top * size_in_pixels[0]).astype(int)
delta_k = numpy.round(view_relative_height *
size_in_pixels[0]).astype(int)
# unfortunatelly the above code can give inconsistent results even if the inputs are correct due to rounding errors
# therefore:
if abs(delta_j - delta_l) == 1:
delta_j = min(delta_j, delta_l)
delta_l = min(delta_j, delta_l)
if abs(delta_i - delta_k) == 1:
delta_i = min(delta_i, delta_k)
delta_k = min(delta_i, delta_k)
assert delta_j == delta_l, "delta_j = %g, delta_l = %g" % (
delta_j, delta_l)
assert delta_i == delta_k, "delta_i = %g, delta_k = %g" % (
delta_i, delta_k)
i_stop = i_start + delta_i
j_stop = j_start + delta_j
k_stop = k_start + delta_k
l_stop = l_start + delta_l
##logger.debug("i_start = %d, i_stop = %d, j_start = %d, j_stop = %d" % (i_start, i_stop, j_start, j_stop))
##logger.debug("k_start = %d, k_stop = %d, l_start = %d, l_stop = %d" % (k_start, k_stop, l_start, l_stop))
try:
self.region_cache[region] = ((k_start, k_start + delta_k,
l_start, l_start + delta_l),
(i_start, i_start + delta_i,
j_start, j_start + delta_j))
view[k_start:k_start + delta_k, l_start:l_start +
delta_l] = img[i_start:i_start + delta_i,
j_start:j_start + delta_j]
except ValueError:
logger.error(
"i_start = %d, i_stop = %d, j_start = %d, j_stop = %d"
% (i_start, i_stop, j_start, j_stop))
logger.error(
"k_start = %d, k_stop = %d, l_start = %d, l_stop = %d"
% (k_start, k_stop, l_start, l_stop))
logger.error("img.shape = %s, view.shape = %s" %
(img.shape, view.shape))
logger.error(
"img[i_start:i_stop, j_start:j_stop].shape = %s" %
str(img[i_start:i_stop, j_start:j_stop].shape))
logger.error(
"view[k_start:k_stop, l_start:l_stop].shape = %s" %
str(view[k_start:k_stop, l_start:l_stop].shape))
raise
else:
try:
((sx_min, sx_max, sy_min, sy_max),
(tx_min, tx_max, ty_min,
ty_max)) = self.region_cache[region]
view[sx_min:sx_max,
sy_min:sy_max] = self.img[tx_min:tx_max,
ty_min:ty_max]
except ValueError:
logger.error(
"i_start = %d, i_stop = %d, j_start = %d, j_stop = %d"
% (i_start, i_stop, j_start, j_stop))
logger.error(
"k_start = %d, k_stop = %d, l_start = %d, l_stop = %d"
% (k_start, k_stop, l_start, l_stop))
logger.error("img.shape = %s, view.shape = %s" %
(img.shape, view.shape))
logger.error(
"img[i_start:i_stop, j_start:j_stop].shape = %s" %
str(img[i_start:i_stop, j_start:j_stop].shape))
logger.error(
"view[k_start:k_stop, l_start:l_stop].shape = %s" %
str(view[k_start:k_stop, l_start:l_stop].shape))
raise
return view
def update(self):
"""
Sets the current frame to the next frame in the sequence.
"""
try:
self.img, self.variables = self._frames.next()
except StopIteration:
self.visible = False
else:
assert self.img.min() >= 0 or self.img.min(
) == TRANSPARENT, "frame minimum is less than zero: %g" % self.img.min(
)
assert self.img.max(
) <= 2 * self.background_luminance, "frame maximum (%g) is greater than the maximum luminance (%g)" % (
self.img.max(), 2 * self.background_luminance)
self._zoom_cache = {}
def reset(self):
"""
Reset to the first frame in the sequence.
"""
self.visible = True
self._frames = self.frames()
self.update()
def next_frame(self):
"""For creating movies"""
self.update()
return [self.img]
def __init__(self, sim, num_threads, parameters):
Model.__init__(self, sim, num_threads, parameters)
# Load components
CortexExcL4 = load_component(
self.parameters.sheets.l4_cortex_exc.component)
CortexInhL4 = load_component(
self.parameters.sheets.l4_cortex_inh.component)
if not self.parameters.only_afferent and self.parameters.l23:
CortexExcL23 = load_component(
self.parameters.sheets.l23_cortex_exc.component)
CortexInhL23 = load_component(
self.parameters.sheets.l23_cortex_inh.component)
RetinaLGN = load_component(self.parameters.sheets.retina_lgn.component)
# Build and instrument the network
self.visual_field = VisualRegion(
location_x=self.parameters.visual_field.centre[0],
location_y=self.parameters.visual_field.centre[1],
size_x=self.parameters.visual_field.size[0],
size_y=self.parameters.visual_field.size[1])
self.input_layer = RetinaLGN(
self, self.parameters.sheets.retina_lgn.params
) # 'pyNN.spiNNaker' has no attribute 'StepCurrentSource'
cortex_exc_l4 = CortexExcL4(
self, self.parameters.sheets.l4_cortex_exc.params
) # spiNNaker has no attribute EIF_cond_exp_isfa_ista ->Iz
cortex_inh_l4 = CortexInhL4(
self, self.parameters.sheets.l4_cortex_inh.params)
if not self.parameters.only_afferent and self.parameters.l23:
cortex_exc_l23 = CortexExcL23(
self, self.parameters.sheets.l23_cortex_exc.params)
cortex_inh_l23 = CortexInhL23(
self, self.parameters.sheets.l23_cortex_inh.params)
# initialize afferent layer 4 projections
GaborConnector(self, self.input_layer.sheets['X_ON'],
self.input_layer.sheets['X_OFF'], cortex_exc_l4,
self.parameters.sheets.l4_cortex_exc.AfferentConnection,
'V1AffConnection')
GaborConnector(self, self.input_layer.sheets['X_ON'],
self.input_layer.sheets['X_OFF'], cortex_inh_l4,
self.parameters.sheets.l4_cortex_inh.AfferentConnection,
'V1AffInhConnection')
# initialize lateral layer 4 projections
if not self.parameters.only_afferent:
ModularSamplingProbabilisticConnectorAnnotationSamplesCount(
self, 'V1L4ExcL4ExcConnection', cortex_exc_l4, cortex_exc_l4,
self.parameters.sheets.l4_cortex_exc.L4ExcL4ExcConnection
).connect()
ModularSamplingProbabilisticConnectorAnnotationSamplesCount(
self, 'V1L4ExcL4InhConnection', cortex_exc_l4, cortex_inh_l4,
self.parameters.sheets.l4_cortex_exc.L4ExcL4InhConnection
).connect()
ModularSamplingProbabilisticConnector(
self, 'V1L4InhL4ExcConnection', cortex_inh_l4, cortex_exc_l4,
self.parameters.sheets.l4_cortex_inh.L4InhL4ExcConnection
).connect()
ModularSamplingProbabilisticConnector(
self, 'V1L4InhL4InhConnection', cortex_inh_l4, cortex_inh_l4,
self.parameters.sheets.l4_cortex_inh.L4InhL4InhConnection
).connect()
if self.parameters.l23:
# if False:
# initialize afferent layer 4 to layer 2/3 projection
ModularSamplingProbabilisticConnector(
self, 'V1L4ExcL23ExcConnection', cortex_exc_l4,
cortex_exc_l23, self.parameters.sheets.l23_cortex_exc.
L4ExcL23ExcConnection).connect()
ModularSamplingProbabilisticConnector(
self, 'V1L4ExcL23InhConnection', cortex_exc_l4,
cortex_inh_l23, self.parameters.sheets.l23_cortex_inh.
L4ExcL23InhConnection).connect()
ModularSamplingProbabilisticConnector(
self, 'V1L23ExcL23ExcConnection', cortex_exc_l23,
cortex_exc_l23, self.parameters.sheets.l23_cortex_exc.
L23ExcL23ExcConnection).connect()
ModularSamplingProbabilisticConnector(
self, 'V1L23ExcL23InhConnection', cortex_exc_l23,
cortex_inh_l23, self.parameters.sheets.l23_cortex_exc.
L23ExcL23InhConnection).connect()
ModularSamplingProbabilisticConnector(
self, 'V1L23InhL23ExcConnection', cortex_inh_l23,
cortex_exc_l23, self.parameters.sheets.l23_cortex_inh.
L23InhL23ExcConnection).connect()
ModularSamplingProbabilisticConnector(
self, 'V1L23InhL23InhConnection', cortex_inh_l23,
cortex_inh_l23, self.parameters.sheets.l23_cortex_inh.
L23InhL23InhConnection).connect()
if self.parameters.feedback:
ModularSamplingProbabilisticConnector(
self, 'V1L23ExcL4ExcConnection', cortex_exc_l23,
cortex_exc_l4, self.parameters.sheets.l23_cortex_exc.
L23ExcL4ExcConnection).connect()
ModularSamplingProbabilisticConnector(
self, 'V1L23ExcL4InhConnection', cortex_exc_l23,
cortex_inh_l4, self.parameters.sheets.l23_cortex_exc.
L23ExcL4InhConnection).connect()
class VisualStimulus(BaseStimulus):
"""
Abstract base class for visual stimuli.
This class defines all parameters common to all visual stimuli.
This class implements all functions specified by the :class:`mozaik.stimuli.stimulus.BaseStimulus` interface.
The only function that remains to be implemented by the user whenever creating a new stimulus by subclassing
this class is the :func:`mozaik.stimuli.stimulus.BaseStimulus.frames` function.
This class also implements functions common to all visual stimuli that are required for it to be compatible
with the :class:`mozaik.space.VisualSpace` and class.
"""
background_luminance = SNumber(lux, doc="Background luminance. Maximum luminance of object allowed is 2*background_luminance")
density = SNumber(1/(degrees), doc="The density of stimulus - units per degree")
location_x = SNumber(degrees, doc="x location of the center of visual region.")
location_y = SNumber(degrees, doc="y location of the center of visual region.")
size_x = SNumber(degrees, doc="The size of the region in degrees (asimuth).")
size_y = SNumber(degrees, doc="The size of the region in degrees (elevation).")
def __init__(self, **params):
BaseStimulus.__init__(self, **params)
self._zoom_cache = {}
self.region_cache = {}
self.is_visible = True
self.transparent = True # And efficiency flag. It should be set to false by the stimulus if there are no transparent points in it.
# This will avoid all the code related to transparency which is very expensive.
self.region = VisualRegion(self.location_x, self.location_y,
self.size_x, self.size_y)
self.first_resolution_mismatch_display=True
def _calculate_zoom(self, actual_pixel_size, desired_pixel_size):
"""
Sometimes the interpolation procedure returns a new array that is too
small due to rounding error. This is a crude attempt to work around that.
"""
zoom = actual_pixel_size/desired_pixel_size
for i in self.img.shape:
if int(zoom*i) != round(zoom*i):
zoom *= (1 + 1e-15)
return zoom
def display(self, region, pixel_size):
assert isinstance(region, VisualRegion), "region must be a VisualRegion-descended object. Actually a %s" % type(region)
size_in_pixels = numpy.ceil(
xy2ij((region.size_x, region.size_y))
/float(pixel_size)).astype(int)
if self.transparent:
view = TRANSPARENT * numpy.ones(size_in_pixels)
else:
view = self.background_luminance * numpy.ones(size_in_pixels)
if region.overlaps(self.region):
if not self.region_cache.has_key(region):
intersection = region.intersection(self.region)
assert intersection == self.region.intersection(region) # just a consistency check. Could be removed if necessary for performance.
img_relative_left = (intersection.left - self.region.left) / self.region.width
img_relative_width = intersection.width/self.region.width
img_relative_top = (intersection.top - self.region.bottom) / self.region.height
#img_relative_bottom = (intersection.bottom - self.region.bottom) / self.region.height
img_relative_height = intersection.height / self.region.height
view_relative_left = (intersection.left - region.left) / region.width
view_relative_width = intersection.width / region.width
view_relative_top = (intersection.top - region.bottom) / region.height
#view_relative_bottom = (intersection.bottom - region.bottom) / region.height
view_relative_height = intersection.height / region.height
img_pixel_size = xy2ij((self.region.size_x, self.region.size_y)) / self.img.shape # is self.size a tuple or an array?
assert img_pixel_size[0] == img_pixel_size[1]
# necessary instead of == comparison due to the floating math rounding errors
if abs(pixel_size-img_pixel_size[0])<0.0001:
img = self.img
else:
if self.first_resolution_mismatch_display:
logger.warning("Image pixel size does not match desired size (%g vs. %g) degrees. This is extremely inefficient!!!!!!!!!!!" % (pixel_size,img_pixel_size[0]))
logger.warning("Image pixel size %g,%g" % numpy.shape(self.img))
self.first_resolution_mismatch_display = False
# note that if the image is much larger than the view region, we might save some
# time by not rescaling the whole image, only the part within the view region.
zoom = self._calculate_zoom(img_pixel_size[0], pixel_size) # img_pixel_size[0]/pixel_size
#logger.debug("Image pixel size (%g deg) does not match desired size (%g deg). Zooming image by a factor %g" % (img_pixel_size[0], pixel_size, zoom))
if zoom in self._zoom_cache:
img = self._zoom_cache[zoom]
else:
img = interpolation.zoom(self.img, zoom)
self._zoom_cache[zoom] = img
j_start = numpy.round(img_relative_left * img.shape[1]).astype(int)
delta_j = numpy.round(img_relative_width * img.shape[1]).astype(int)
i_start = img.shape[0] - numpy.round(img_relative_top * img.shape[0]).astype(int)
delta_i = numpy.round(img_relative_height * img.shape[0]).astype(int)
l_start = numpy.round(view_relative_left * size_in_pixels[1]).astype(int)
delta_l = numpy.round(view_relative_width * size_in_pixels[1]).astype(int)
k_start = size_in_pixels[0] - numpy.round(view_relative_top * size_in_pixels[0]).astype(int)
delta_k = numpy.round(view_relative_height * size_in_pixels[0]).astype(int)
# unfortunatelly the above code can give inconsistent results even if the inputs are correct due to rounding errors
# therefore:
if abs(delta_j-delta_l) == 1:
delta_j = min(delta_j,delta_l)
delta_l = min(delta_j,delta_l)
if abs(delta_i-delta_k) == 1:
delta_i = min(delta_i,delta_k)
delta_k = min(delta_i,delta_k)
assert delta_j == delta_l, "delta_j = %g, delta_l = %g" % (delta_j, delta_l)
assert delta_i == delta_k, "delta_i = %g, delta_k = %g" % (delta_i, delta_k)
i_stop = i_start + delta_i
j_stop = j_start + delta_j
k_stop = k_start + delta_k
l_stop = l_start + delta_l
##logger.debug("i_start = %d, i_stop = %d, j_start = %d, j_stop = %d" % (i_start, i_stop, j_start, j_stop))
##logger.debug("k_start = %d, k_stop = %d, l_start = %d, l_stop = %d" % (k_start, k_stop, l_start, l_stop))
try:
self.region_cache[region] = ((k_start,k_start+delta_k,l_start,l_start+delta_l),(i_start,i_start+delta_i, j_start,j_start+delta_j))
view[k_start:k_start+delta_k, l_start:l_start+delta_l] = img[i_start:i_start+delta_i, j_start:j_start+delta_j]
except ValueError:
logger.error("i_start = %d, i_stop = %d, j_start = %d, j_stop = %d" % (i_start, i_stop, j_start, j_stop))
logger.error("k_start = %d, k_stop = %d, l_start = %d, l_stop = %d" % (k_start, k_stop, l_start, l_stop))
logger.error("img.shape = %s, view.shape = %s" % (img.shape, view.shape))
logger.error("img[i_start:i_stop, j_start:j_stop].shape = %s" % str(img[i_start:i_stop, j_start:j_stop].shape))
logger.error("view[k_start:k_stop, l_start:l_stop].shape = %s" % str(view[k_start:k_stop, l_start:l_stop].shape))
raise
else:
try:
((sx_min,sx_max,sy_min,sy_max),(tx_min,tx_max,ty_min,ty_max)) = self.region_cache[region]
view[sx_min:sx_max,sy_min:sy_max] = self.img[tx_min:tx_max,ty_min:ty_max]
except ValueError:
logger.error("i_start = %d, i_stop = %d, j_start = %d, j_stop = %d" % (i_start, i_stop, j_start, j_stop))
logger.error("k_start = %d, k_stop = %d, l_start = %d, l_stop = %d" % (k_start, k_stop, l_start, l_stop))
logger.error("img.shape = %s, view.shape = %s" % (img.shape, view.shape))
logger.error("img[i_start:i_stop, j_start:j_stop].shape = %s" % str(img[i_start:i_stop, j_start:j_stop].shape))
logger.error("view[k_start:k_stop, l_start:l_stop].shape = %s" % str(view[k_start:k_stop, l_start:l_stop].shape))
raise
return view
def update(self):
"""
Sets the current frame to the next frame in the sequence.
"""
try:
self.img, self.variables = self._frames.next()
except StopIteration:
self.visible = False
else:
assert self.img.min() >= 0 or self.img.min() == TRANSPARENT, "frame minimum is less than zero: %g" % self.img.min()
assert self.img.max() <= 2*self.background_luminance, "frame maximum (%g) is greater than the maximum luminance (%g)" % (self.img.max(), 2*self.background_luminance)
self._zoom_cache = {}
def reset(self):
"""
Reset to the first frame in the sequence.
"""
self.visible = True
self._frames = self.frames()
self.update()
def next_frame(self):
"""For creating movies"""
self.update()
return [self.img]