def _setup_screen(self, config):
""" setup up screen generation or retrieval
This function setup stage of types of movies to be played
and can let self.get_screen_intensity_step to
generate video.
"""
self._image2d = image2Dfactory(self._input_type)(config)
# find the mappings of screen points to image
imagx, imagy = self.screen_to_image_map.map(self.grid[0],
self.grid[1])
# given the values on points of a rectangular grid, interpolator
# can find the values on any point of the plane by approximation
xmax, ymax = imagx.max(), imagy.max()
xmin, ymin = imagx.min(), imagy.min()
self._interpolator = ImageTransform(
self._image2d.get_grid(xmin, xmax, ymin, ymax), [imagx, imagy])
self.screen_write_step = config['Retina']['screen_write_step']
def get_intensities(self, file, config={}):
""" file: mat file is assumed but in case more file formats need to be
supported an additional field should be included in config
config: {'still_image': True(default)/False,
'steps':<simulation steps>,
'dt':<time step>, 'output_file':<filename>}
returns: numpy array with with height the number of simulation
steps and width the number of neurons.
The order of neurons is the same as that returned
in get_positions, with 'R1toR6' option for 'include'
configuration parameter
"""
try:
dt = config['dt']
except KeyError:
dt = 1e-4
try:
time_steps = config['steps']
except KeyError:
time_steps = 1000
try:
still_image = config['still_image']
except KeyError:
still_image = True
try:
# TODO
output_file = config['output_file']
except KeyError:
output_file = None
mat = loadmat(file)
try:
image = np.array(mat['im'])
except KeyError:
print('No variable "im" in given mat file')
print('Available variables (and meta-data): {}'.format(mat.keys()))
# photons were stored for 1ms
image *= (dt / 1e-3)
h_im, w_im = image.shape
transform = ImageTransform(image)
# screen positions
# should be much more than the number of photoreceptors
# shape (20, 3)*self._nrings
screenlat, screenlong = np.meshgrid(
np.linspace(0, PI / 2, 3 * self._nrings),
np.linspace(-PI, PI, 20 * self._nrings))
mapscreen = self.OMMATIDIUM_CLS.MAP_SCREEN
# plane positions
# shape (20, 3)*self._nrings
mx, my = mapscreen.map(screenlat, screenlong) # map from spherical
# grid to plane
# photoreceptor positions
photorlat, photorlong = self.get_positions({
'coord': 'spherical',
'include': 'R1toR6',
'add_dummy': False
})
if still_image:
mx = mx - mx.min() # start from 0
my = my - my.min()
mx *= h_im / mx.max() # scale to image size
my *= w_im / my.max()
# shape (20, 3)*self._nrings
transimage = transform.interpolate((mx, my))
intensities = self._get_intensities(transimage, photorlat,
photorlong, screenlat,
screenlong)
intensities = np.tile(intensities, (time_steps, 1))
else:
intensities = np.empty((time_steps, len(photorlat)),
dtype='float32')
mx = mx - mx.min() # start from 0
my = my - my.min()
for i in range(time_steps):
mx = mx + 2 * np.random.random() - 1 # move randomly
my = my + 2 * np.random.random() - 1 # between -1 and 1
mxi_max = mx.max()
if mxi_max > h_im:
mx = mx - 2 * (mxi_max - h_im)
mxi_min = mx.min()
if mxi_min < 0:
mx = mx - 2 * mxi_min
myi_max = my.max()
if myi_max > w_im:
my = my - 2 * (myi_max - w_im)
myi_min = my.min()
if myi_min < 0:
my = my - 2 * myi_min
transimage = transform.interpolate((mx, my))
intensities[i] = self._get_intensities(transimage, photorlat,
photorlong, screenlat,
screenlong)
# get interpolated image values on these positions
return intensities
def get_intensities(self, file, config={}):
""" file: mat file is assumed but in case more file formats need to be
supported an additional field should be included in config
config: {'still_image': True(default)/False,
'steps':<simulation steps>,
'dt':<time step>, 'output_file':<filename>}
returns: numpy array with with height the number of simulation
steps and width the number of neurons.
The order of neurons is the same as that returned
in get_positions, with 'R1toR6' option for 'include'
configuration parameter
"""
try:
dt = config["dt"]
except KeyError:
dt = 1e-4
try:
time_steps = config["steps"]
except KeyError:
time_steps = 1000
try:
still_image = config["still_image"]
except KeyError:
still_image = True
try:
# TODO
output_file = config["output_file"]
except KeyError:
output_file = None
mat = loadmat(file)
try:
image = np.array(mat["im"])
except KeyError:
print('No variable "im" in given mat file')
print("Available variables (and meta-data): {}".format(mat.keys()))
# photons were stored for 1ms
image *= dt / 1e-3
h_im, w_im = image.shape
transform = ImageTransform(image)
# screen positions
# should be much more than the number of photoreceptors
# shape (20, 3)*self._nrings
screenlat, screenlong = np.meshgrid(
np.linspace(0, PI / 2, 3 * self._nrings), np.linspace(-PI, PI, 20 * self._nrings)
)
mapscreen = self.OMMATIDIUM_CLS.MAP_SCREEN
# plane positions
# shape (20, 3)*self._nrings
mx, my = mapscreen.map(screenlat, screenlong) # map from spherical
# grid to plane
# photoreceptor positions
photorlat, photorlong = self.get_positions({"coord": "spherical", "include": "R1toR6", "add_dummy": False})
if still_image:
mx = mx - mx.min() # start from 0
my = my - my.min()
mx *= h_im / mx.max() # scale to image size
my *= w_im / my.max()
# shape (20, 3)*self._nrings
transimage = transform.interpolate((mx, my))
intensities = self._get_intensities(transimage, photorlat, photorlong, screenlat, screenlong)
intensities = np.tile(intensities, (time_steps, 1))
else:
intensities = np.empty((time_steps, len(photorlat)), dtype="float32")
mx = mx - mx.min() # start from 0
my = my - my.min()
for i in range(time_steps):
mx = mx + 2 * np.random.random() - 1 # move randomly
my = my + 2 * np.random.random() - 1 # between -1 and 1
mxi_max = mx.max()
if mxi_max > h_im:
mx = mx - 2 * (mxi_max - h_im)
mxi_min = mx.min()
if mxi_min < 0:
mx = mx - 2 * mxi_min
myi_max = my.max()
if myi_max > w_im:
my = my - 2 * (myi_max - w_im)
myi_min = my.min()
if myi_min < 0:
my = my - 2 * myi_min
transimage = transform.interpolate((mx, my))
intensities[i] = self._get_intensities(transimage, photorlat, photorlong, screenlat, screenlong)
# get interpolated image values on these positions
return intensities
def get_intensities(self, file, config={}):
""" file: input image file, mat file is assumed with a variable im in it
config: {'type': 'image'(default)/'video',
'steps':<simulation steps>,
'dt':<time step>,
'output_file':<filename>
'factors': list of factors for scaled image }
returns: numpy array with with height the number of simulation
steps and width the number of neurons.
The order of neurons is the same as that returned
in get_positions, with 'include'
configuration parameter set to 'R1toR6'
"""
# the order of ommatidia in output is the exact order of
# _ommatidia parameter
try:
dt = config['dt']
except KeyError:
dt = 1e-4
try:
time_steps = config['steps']
except KeyError:
time_steps = 1000
try:
type = config['type']
except KeyError:
type = 'image'
try:
output_file = config['output_file']
except KeyError:
output_file = None
try:
factors = config['factors']
except KeyError:
factors = [1]
mat = loadmat(file)
try:
image = np.array(mat['im'])
except KeyError:
print('No variable "im" in given mat file')
print('Available variables (and meta-data): {}'.format(mat.keys()))
# photons were stored for 1ms
image *= (dt/1e-3)
h_im, w_im = image.shape
transform = ImageTransform(image)
# screen positions
# should be much more than the number of photoreceptors
# shape (M, P)*self._nrings
screenlat, screenlong = np.meshgrid(np.linspace((PI/2)/self.PARALLELS,
PI/2, self.PARALLELS),
np.linspace(-PI, PI, self.MERIDIANS))
mapscreen = self.OMMATIDIUM_CLS.MAP_SCREEN
# plane positions
# shape (M, P)*self._nrings
mx, my = mapscreen.map(screenlat, screenlong) # map from spherical
# grid to plane
# photoreceptor positions
photorlat, photorlong = self.get_positions({'coord': 'spherical',
'include': 'R1toR6',
'add_dummy': False})
ind_weights = self._pre_get_intensities(mx.shape[0], mx.shape[1],
photorlat,photorlong,
screenlat,screenlong)
if type == 'image':
mx = mx - mx.min() # start from 0
my = my - my.min()
mx *= h_im/mx.max() # scale to image size
my *= w_im/my.max()
# shape (M, P)*self._nrings
transimage = transform.interpolate((mx, my))
intensities = self._get_intensities(transimage, ind_weights)
intensities = np.tile(intensities, (time_steps, 1))
# Equal or almost equal parts of the array equal with the
# factors are multiplied by the respective factor
ilen = len(intensities)
flen = len(factors)
for i, factor in enumerate(factors):
intensities[(i*ilen)//flen:((i+1)*ilen)//flen] *= factor
positions = None
elif type == 'video':
intensities = np.empty((time_steps, len(photorlat)),
dtype='float32')
positions = np.empty((time_steps, 4),
dtype='float32')
mx = mx - mx.min() # start from 0
my = my - my.min()
for i in range(time_steps):
scale = 0.1
mx = mx + scale*(2*np.random.random() - 1) # move randomly
my = my + scale*(2*np.random.random() - 1) # between -1 and 1
mxi_max = mx.max()
if mxi_max > h_im:
mx = mx - 2*(mxi_max-h_im)
mxi_min = mx.min()
if mxi_min < 0:
mx = mx - 2*mxi_min
myi_max = my.max()
if myi_max > w_im:
my = my - 2*(myi_max-w_im)
myi_min = my.min()
if myi_min < 0:
my = my - 2*myi_min
transimage = transform.interpolate((mx, my))
intensities[i] = self._get_intensities(transimage, ind_weights)
positions[i] = [mx.min(), mx.max(), my.min(), my.max()]
# get interpolated image values on these positions
if output_file:
with h5py.File(output_file, 'w') as f:
f.create_dataset('array', intensities.shape,
dtype=np.float64,
data=intensities)
InputConfig = namedtuple('InputConfig', 'image positions factors intensities')
self.input_config = InputConfig(image=image, positions=positions,
factors=factors,
intensities=intensities)
return intensities
class Screen(object):
""" Defines the geometry of screen and generates screen images """
__metaclass__ = ABCMeta
def __init__(self, config):
self._dtype = np.double
# config attributes
self._dt = config['General']['dt']
self._input_type = config['Retina']['intype']
if self._input_type is None:
raise ValueError('No input type specified')
# grid
self._setup_screen(config)
@abstractproperty
def screen_to_image_map(self):
pass
@abstractproperty
def grid(self):
""" :return: a meshgrid tuple e.g
[[x1, x2, x3],
[x1, x2, x3]],
[[y1, y1, y1],
[y2, y2, y2]]
"""
pass
def _setup_screen(self, config):
""" setup up screen generation or retrieval
This function setup stage of types of movies to be played
and can let self.get_screen_intensity_step to
generate video.
"""
self._image2d = image2Dfactory(self._input_type)(config)
# find the mappings of screen points to image
imagx, imagy = self.screen_to_image_map.map(self.grid[0],
self.grid[1])
# given the values on points of a rectangular grid, interpolator
# can find the values on any point of the plane by approximation
xmax, ymax = imagx.max(), imagy.max()
xmin, ymin = imagx.min(), imagy.min()
self._interpolator = ImageTransform(
self._image2d.get_grid(xmin, xmax, ymin, ymax), [imagx, imagy])
self.screen_write_step = config['Retina']['screen_write_step']
def setup_file(self, filename, read=False):
""" tell self to use filename instead of generating video """
self.file_open = False
self.filename = filename
if read:
self.store_to_file = False
self.read_from_file = True
self.file_position = 0
else:
self.store_to_file = True
self.read_from_file = False
self.skip_step = self.screen_write_step
self.step_count = 0
def get_screen_intensity_steps(self, num_steps):
""" generate or read the next num_steps of inputs """
if not self.file_open:
if self.read_from_file:
self.inputfile = h5py.File(self.filename, 'r')
self.inputarray = self.inputfile['/array']
else:
self.outputfile = h5py.File(self.filename, 'w')
self.outputfile.create_dataset(
'/array', (0, self._height, self._width),
dtype = self._dtype,
maxshape=(None, self._height, self._width),
compression = 9)
self.file_open = True
try:
if self.read_from_file:
screens = self.inputarray[self.file_position:self.file_position+num_steps]
self.file_position += num_steps
else:
# values on 2D
images = self._image2d.generate_2dimage(num_steps)
images = images[:,::-1,::-1]
# values on screen
screens = self._interpolator.interpolate(images)
if self.store_to_file:
if num_steps >= self.skip_step:
dataset_append(self.outputfile['/array'],
screens[(self.skip_step-self.step_count)%self.skip_step::self.skip_step])
self.step_count = (self.step_count+num_steps)%self.skip_step
else:
self.step_count %= self.skip_step
if self.step_count == 0:
dataset_append(self.outputfile['/array'], screens[[0]])
self.step_count += num_steps
if self.step_count > self.skip_step:
dataset_append(self.outputfile['/array'],
screens[[num_steps-(self.step_count-self.skip_step)]])
self.step_count -= self.skip_step
except AttributeError:
print('Function for file setup probably not called')
raise
return screens
@abstractmethod
def get_image2d_dim(self):
""" screen is supposed to map values from
(-x/2 to x/2) and (-y/2 to y/2)
where x, y are the values returned
from this function
"""
pass
@abstractmethod
def generate_video(self, data, coordinates, rng, videofile):
"""
data: values to be visualized
coordinates: coordinates of values on screen
a tuple of arrays
rng: range of values
videofile: the file where output will be written
"""
pass
def close_files(self):
try:
if self.store_to_file:
self.outputfile.close()
except AttributeError:
pass
try:
if self.read_from_file:
self.inputfile.close()
except AttributeError:
pass
