retinotopic_mapping.StimulusRoutines¶

This module define a base class Stim for visual stimulation. Each subclass of Stim defines a particular type of visual stimulus, i.e. UniformContrast or SparseNoise. When initiated, these subclasses take various parameter inputs to generate stimulus arrays and metadata dictionary which can be passed to the DisplayStimulus.DisplaySequence for displaying. Each subclass will have a method called generate_movie() or generate_movie_by_index() or both. Only when these methods are called, will heavy lifting calculation take place.

Stim¶

class retinotopic_mapping.StimulusRoutines.Stim(monitor, indicator, background=0.0, coordinate='degree', pregap_dur=2.0, postgap_dur=3.0)¶

generic class for visual stimulation. parent class for individual stimulus routines.

Parameters:

monitor : monitor object: the monitor used to display stimulus in the experiment
indicator : indicator object: the indicator used during stimulus
background : float, optional: background color of the monitor screen when stimulus is not being presented, takes values in [-1,1] and defaults to 0. (grey)
coordinate : str {‘degree’, ‘linear’}, optional: determines the representation of pixel coordinates on monitor, defaults to ‘degree’
pregap_dur : float, optional: duration of gap period before stimulus, measured in seconds, defaults to 2.
postgap_dur : float, optional: duration of gap period after stimulus, measured in seconds, defaults to 3.

Attributes:

postgap_frame_num
pregap_frame_num

Methods

`generate_frames`(self)	place holder of function “generate_frames” for each specific stimulus
`generate_movie`(self)	place holder of function ‘generate_movie’ for each specific stimulus
`generate_movie_by_index`(self)	place holder of function generate_movie_by_index() for each specific stimulus

clear
set_background
set_coordinate
set_indicator
set_monitor
set_postgap_dur
set_pregap_dur

UniformContrast¶

class retinotopic_mapping.StimulusRoutines.UniformContrast(monitor, indicator, duration, color=0.0, pregap_dur=2.0, postgap_dur=3.0, background=0.0, coordinate='degree')¶

Generate full field uniform luminance for recording spontaneous activity. Inherits from Stim.

The full field uniform luminance stimulus presents a fixed background color which is normally taken to be grey.

Parameters:

monitor : monitor object: contains display monitor information
indicator : indicator object: contains indicator information
coordinate : str from {‘degree’,’linear’}, optional: specifies coordinates, defaults to ‘degree’
background : float, optional: color of background. Takes values in [-1,1] where -1 is black and 1 is white
pregap_dur : float, optional: amount of time (in seconds) before the stimulus is presented, defaults to 2.
postgap_dur : float, optional: amount of time (in seconds) after the stimulus is presented, defaults to 3.
duration: float: number of seconds of the duration of the uniform luminance.
color : float, optional: the choice of color to display in the stimulus, defaults to 0. which is grey

Attributes:

postgap_frame_num
pregap_frame_num

Methods

`generate_frames`(self)	generate a tuple of parameters with information for each frame.
`generate_movie`(self)	generate movie for uniform contrast display frame by frame.
`generate_movie_by_index`(self)	compute the stimulus movie to be displayed by index.

clear
set_background
set_coordinate
set_indicator
set_monitor
set_postgap_dur
set_pregap_dur

generate_frames(self)¶

generate a tuple of parameters with information for each frame.

Information contained in each frame:

first element -: during display frames, value takes on 1 and value is 0 otherwise
second element - color of indicator: during display value is equal to 1 and during gaps value is equal to -1

generate_movie(self)¶

generate movie for uniform contrast display frame by frame.

Returns:	full_seq : nd array, uint8 3-d array of the stimulus to be displayed. full_dict : dict dictionary containing the information of the stimulus.

generate_movie_by_index(self)¶: compute the stimulus movie to be displayed by index.

FlashingCircle¶

class retinotopic_mapping.StimulusRoutines.FlashingCircle(monitor, indicator, coordinate='degree', center=(0.0, 60.0), radius=10.0, is_smooth_edge=False, smooth_width_ratio=0.2, smooth_func=<function blur_cos>, color=-1.0, flash_frame_num=3, pregap_dur=2.0, postgap_dur=3.0, background=0.0, midgap_dur=1.0, iteration=1)¶

Generate flashing circle stimulus.

Stimulus routine presents a circle centered at the position center with given radius.

Parameters:

monitor : monitor object

contains display monitor information

indicator : indicator object

contains indicator information

coordinate : str from {‘degree’,’linear’}, optional

specifies coordinates, defaults to ‘degree’

background : float, optional

color of background. Takes values in [-1,1] where -1 is black and 1 is white

pregap_dur : float, optional

amount of time (in seconds) before the stimulus is presented, defaults to 2.

postgap_dur : float, optional

amount of time (in seconds) after the stimulus is presented, defaults to 3.

center : 2-tuple, optional

center coordinate (altitude, azimuth) of the circle in degrees, defaults to (0.,60.).

radius : float, optional

radius of the circle, defaults to 10.

is_smooth_edge : bool

True, smooth circle edge with smooth_width_ratio and smooth_func False, do not smooth edge

smooth_width_ratio : float, should be smaller than 1.

the ratio between smooth band width and radius, circle edge is the middle of smooth band

smooth_func : function object

this function take to inputs: first, ndarray storing the distance from each pixel to smooth band center second, smooth band width

returns smoothed mask with same shape as input ndarray

color : float, optional

color of the circle, takes values in [-1,1], defaults to -1.

iteration : int, optional

total number of flashes, defaults to 1.

flash_frame : int, optional

number of frames that circle is displayed during each presentation of the stimulus, defaults to 3.

Attributes:

midgap_frame_num
postgap_frame_num
pregap_frame_num

Methods

`generate_frames`(self)	function to generate all the frames needed for the stimulation.
`generate_movie`(self)	generate movie frame by frame.
`generate_movie_by_index`(self)	compute the stimulus movie to be displayed by index.

clear
set_background
set_center
set_color
set_coordinate
set_flash_frame_num
set_indicator
set_monitor
set_postgap_dur
set_pregap_dur
set_radius

generate_frames(self)¶

function to generate all the frames needed for the stimulation.

Information contained in each frame:

first element :: during a gap, the value is equal to 0 and during display the value is equal to 1
second element :: corresponds to the color of indicator if indicator.is_sync is True, during stimulus the value is equal to 1., whereas during a gap the value isequal to -1.; if indicator.is_sync is False, indicator color will alternate between 1. and -1. at the frequency as indicator.freq

frames : list: list of information defining each frame.

generate_movie(self)¶: generate movie frame by frame.

generate_movie_by_index(self)¶: compute the stimulus movie to be displayed by index.

SparseNoise¶

class retinotopic_mapping.StimulusRoutines.SparseNoise(monitor, indicator, background=0.0, coordinate='degree', grid_space=(10.0, 10.0), probe_size=(10.0, 10.0), probe_orientation=0.0, probe_frame_num=6, subregion=None, sign='ON-OFF', iteration=1, pregap_dur=2.0, postgap_dur=3.0, is_include_edge=True)¶

generate sparse noise stimulus integrates flashing indicator for photodiode

This stimulus routine presents quasi-random noise in a specified region of the monitor. The background color can be customized but defaults to a grey value. Can specify the subregion of the monitor where the pixels will flash on and off (black and white respectively)

Parameters:

monitor : monitor object: contains display monitor information
indicator : indicator object: contains indicator information
coordinate : str from {‘degree’,’linear’}, optional: specifies coordinates, defaults to ‘degree’
background : float, optional: color of background. Takes values in [-1,1] where -1 is black and 1 is white
pregap_dur : float, optional: amount of time (in seconds) before the stimulus is presented, defaults to 2.
postgap_dur : float, optional: amount of time (in seconds) after the stimulus is presented, defaults to 3.
grid_space : 2-tuple of floats, optional: first coordinate is altitude, second coordinate is azimuth
probe_size : 2-tuple of floats, optional: size of flicker probes. First coordinate defines the width, and second coordinate defines the height
probe_orientation : float, optional: orientation of flicker probes
probe_frame_num : int, optional: number of frames for each square presentation
subregion : list or tuple: the region on the monitor that will display the sparse noise, list or tuple, [min_alt, max_alt, min_azi, max_azi]
sign : {‘ON-OFF’, ‘ON’, ‘OFF’}, optional: determines which pixels appear in the subregion, defaults to ‘ON-Off’ so that both on and off pixels appear. If ‘ON selected only on pixels (white) are displayed in the noise subregion while if `’OFF’ is selected only off (black) pixels are displayed in the noise
iteration : int, optional: number of times to present stimulus, defaults to 1
is_include_edge : bool, default True,: if True, the displayed probes will cover the edge case and ensure that the entire subregion is covered. If False, the displayed probes will exclude edge case and ensure that all the centers of displayed probes are within the subregion.

Attributes:

postgap_frame_num
pregap_frame_num

Methods

`generate_frames`(self)	function to generate all the frames needed for SparseNoise stimulus
`generate_movie`(self)	generate movie for display frame by frame
`generate_movie_by_index`(self)	compute the stimulus movie to be displayed by index.

clear
set_background
set_coordinate
set_indicator
set_monitor
set_postgap_dur
set_pregap_dur

generate_frames(self)¶

function to generate all the frames needed for SparseNoise stimulus

returns a list of information of all frames as a list of tuples

Information contained in each frame:

first element - int

when stimulus is displayed value is equal to 1, otherwise equal to 0,

second element - tuple,

retinotopic location of the center of current square,[alt, azi]

third element -

polarity of current square, 1 -> bright, -1-> dark

forth element - color of indicator

if synchronized : value equal to 0 when stimulus is not: begin displayed, and 1 for onset frame of stimulus for each square, -1 for the rest.
if non-synchronized: values alternate between -1 and 1: at defined frequency

for gap frames the second and third elements should be ‘None’

generate_movie(self)¶: generate movie for display frame by frame

generate_movie_by_index(self)¶: compute the stimulus movie to be displayed by index.

LocallySparseNoise¶

class retinotopic_mapping.StimulusRoutines.LocallySparseNoise(monitor, indicator, min_distance=20.0, background=0.0, coordinate='degree', grid_space=(10.0, 10.0), probe_size=(10.0, 10.0), probe_orientation=0.0, probe_frame_num=6, subregion=None, sign='ON-OFF', iteration=1, repeat=1, pregap_dur=2.0, postgap_dur=3.0, is_include_edge=True)¶

generate locally sparse noise stimulus integrates flashing indicator for photodiode

This stimulus routine presents quasi-random noise in a specified region of the monitor. The background color can be customized but defaults to a grey value. Can specify the subregion of the monitor where the pixels will flash on and off (black and white respectively)

Different from SparseNoise stimulus which presents only one probe at a time, the LocallySparseNoise presents multiple probes simultaneously to speed up the sampling frequency. The sparsity of probes is defined by minimum distance in visual degree: in any given frame, the centers of any pair of two probes will have distance larger than minimum distance in visual degrees. The method generate locally sparse noise here insures, for each iteration, all the locations in the subregion will be sampled once and only once.

Parameters:

monitor : monitor object: contains display monitor information
indicator : indicator object: contains indicator information
coordinate : str from {‘degree’,’linear’}, optional: specifies coordinates, defaults to ‘degree’
background : float, optional: color of background. Takes values in [-1,1] where -1 is black and 1 is white
pregap_dur : float, optional: amount of time (in seconds) before the stimulus is presented, defaults to 2.
postgap_dur : float, optional: amount of time (in seconds) after the stimulus is presented, defaults to 3.
min_distance : float, default 20.: the minimum distance in visual degree for any pair of probe centers in a given frame
grid_space : 2-tuple of floats, optional: first coordinate is altitude, second coordinate is azimuth
probe_size : 2-tuple of floats, optional: size of flicker probes. First coordinate defines the width, and second coordinate defines the height
probe_orientation : float, optional: orientation of flicker probes
probe_frame_num : int, optional: number of frames for each square presentation
subregion : list or tuple: the region on the monitor that will display the sparse noise, list or tuple, [min_alt, max_alt, min_azi, max_azi]
sign : {‘ON-OFF’, ‘ON’, ‘OFF’}, optional: determines which pixels appear in the subregion, defaults to ‘ON-Off’ so that both on and off pixels appear. If ‘ON selected only on pixels (white) are displayed in the noise subregion while if `’OFF’ is selected only off (black) pixels are displayed in the noise
iteration : int, optional: number of times to present stimulus with random order, the total number a paticular probe will be displayded will be iteration * repeat, defaults to 1
repeat : int, optional: number of repeat of whole sequence, the total number a paticular probe will be displayded will be iteration * repeat, defaults to 1
is_include_edge : bool, default True,: if True, the displayed probes will cover the edge case and ensure that the entire subregion is covered. If False, the displayed probes will exclude edge case and ensure that all the centers of displayed probes are within the subregion.

Attributes:

postgap_frame_num
pregap_frame_num

Methods

`generate_frames`(self)	place holder of function “generate_frames” for each specific stimulus
`generate_movie`(self)	place holder of function ‘generate_movie’ for each specific stimulus

clear
generate_movie_by_index
set_background
set_coordinate
set_indicator
set_monitor
set_postgap_dur
set_pregap_dur

generate_frames(self)¶: place holder of function “generate_frames” for each specific stimulus

generate_movie(self)¶: place holder of function ‘generate_movie’ for each specific stimulus

generate_movie_by_index(self)¶: place holder of function generate_movie_by_index() for each specific stimulus

DriftingGratingCircle¶

class retinotopic_mapping.StimulusRoutines.DriftingGratingCircle(monitor, indicator, background=0.0, coordinate='degree', center=(0.0, 60.0), sf_list=(0.08, ), tf_list=(4.0, ), dire_list=(0.0, ), con_list=(0.5, ), radius_list=(10.0, ), block_dur=2.0, midgap_dur=0.5, iteration=1, pregap_dur=2.0, postgap_dur=3.0, is_smooth_edge=False, smooth_width_ratio=0.2, smooth_func=<function blur_cos>, is_blank_block=True)¶

Generate drifting grating circle stimulus

Stimulus routine presents drifting grating stimulus inside of a circle centered at center. The drifting gratings are determined by spatial and temporal frequencies, directionality, contrast, and radius. The routine can generate several different gratings within one presentation by specifying multiple values of the parameters which characterize the stimulus.

Parameters:

monitor : monitor object: contains display monitor information
indicator : indicator object: contains indicator information
coordinate : str from {‘degree’,’linear’}, optional: specifies coordinates, defaults to ‘degree’
background : float, optional: color of background. Takes values in [-1,1] where -1 is black and 1 is white
pregap_dur : float, optional: amount of time (in seconds) before the stimulus is presented, defaults to 2.
postgap_dur : float, optional: amount of time (in seconds) after the stimulus is presented, defaults to 3.
center : 2-tuple of floats, optional: coordintes for center of the stimulus (altitude, azimuth)
sf_list : n-tuple, optional: list of spatial frequencies in cycles/unit, defaults to (0.08)
tf_list : n-tuple, optional: list of temportal frequencies in Hz, defaults to (4.)
dire_list : n-tuple, optional: list of directions in degrees, defaults to (0.)
con_list : n-tuple, optional: list of contrasts taking values in [0.,1.], defaults to (0.5)
radius_list : n-tuple: list of radii of circles, unit defined by self.coordinate, defaults to (10.)
block_dur : float, optional: duration of each condition in seconds, defaults to 2.
midgap_dur : float, optional: duration of gap between conditions, defaults to 0.5
iteration : int, optional: number of times the stimulus is displayed, defaults to 1
is_smooth_edge : bool: True, smooth circle edge with smooth_width_ratio and smooth_func False, do not smooth edge
smooth_width_ratio : float, should be smaller than 1.: the ratio between smooth band width and radius, circle edge is the middle of smooth band
smooth_func : function object: this function take two inputs: 1) ndarray storing the distance from each pixel to smooth band center; 2) smooth band width. returns smoothed mask with same shape as input ndarray
is_blank_block : bool: if True, one blank block (full screen background with the same duration of other blocks) will be displayed for each iteration. The frames of this condition will be: (1, 1, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1.0), the meaning of these numbers can be found in self.frame_config

Attributes:

block_frame_num
midgap_frame_num
postgap_frame_num
pregap_frame_num

Methods

`generate_frames`(self)	function to generate all the frames needed for DriftingGratingCircle returns a list of information of all frames as a list of tuples
`generate_movie`(self)	Generate movie frame by frame
`generate_movie_by_index`(self)	compute the stimulus movie to be displayed by index.

clear
set_background
set_coordinate
set_indicator
set_monitor
set_postgap_dur
set_pregap_dur

generate_frames(self)¶

function to generate all the frames needed for DriftingGratingCircle returns a list of information of all frames as a list of tuples

Information contained in each frame:

first element -: value equal to 1 during stimulus and 0 otherwise
second element -: on first frame in a cycle value takes on 1, and otherwise is equal to 0.
third element -: spatial frequency
forth element -: temporal frequency
fifth element -: direction, [0, 2*pi)
sixth element -: contrast, [-1., 1.]
seventh element -: size, float (radius of the circle in visual degree)
eighth element -: phase, [0, 2*pi)
ninth element -: indicator color [-1, 1]. Value is equal to 1 on the first frame of each cycle, -1 during gaps and otherwise 0.

during gap frames the second through the eighth elements should be ‘None’.

generate_movie(self)¶: Generate movie frame by frame

generate_movie_by_index(self)¶: compute the stimulus movie to be displayed by index.

StaticGratingCircle¶

class retinotopic_mapping.StimulusRoutines.StaticGratingCircle(monitor, indicator, background=0.0, coordinate='degree', center=(0.0, 60.0), sf_list=(0.08, ), ori_list=(0.0, 90.0), con_list=(0.5, ), radius_list=(10.0, ), phase_list=(0.0, 90.0, 180.0, 270.0), display_dur=0.25, midgap_dur=0.0, iteration=1, pregap_dur=2.0, postgap_dur=3.0, is_smooth_edge=False, smooth_width_ratio=0.2, smooth_func=<function blur_cos>, is_blank_block=True)¶

Generate static grating circle stimulus

Stimulus routine presents flashing static grating stimulus inside of a circle centered at center. The static gratings are determined by spatial frequencies, orientation, contrast, radius and phase. The routine can generate several different gratings within one presentation by specifying multiple values of the parameters which characterize the stimulus.

Parameters:

monitor : monitor object: contains display monitor information
indicator : indicator object: contains indicator information
coordinate : str from {‘degree’,’linear’}, optional: specifies coordinates, defaults to ‘degree’
background : float, optional: color of background. Takes values in [-1,1] where -1 is black and 1 is white
pregap_dur : float, optional: amount of time (in seconds) before the stimulus is presented, defaults to 2.
postgap_dur : float, optional: amount of time (in seconds) after the stimulus is presented, defaults to 3.
center : 2-tuple of floats, optional: coordintes for center of the stimulus (altitude, azimuth)
sf_list : n-tuple, optional: list of spatial frequencies in cycles/unit, defaults to (0.08)
ori_list : n-tuple, optional: list of directions in degrees, defaults to (0., 90.)
con_list : n-tuple, optional: list of contrasts taking values in [0.,1.], defaults to (0.5)
radius_list : n-tuple, optional: list of radii of circles, unit defined by self.coordinate, defaults to (10.)
phase_list : n-tuple, optional: list of phase of gratings in degrees, default (0., 90., 180., 270.)
display_dur : float, optional: duration of each condition in seconds, defaults to 0.25
midgap_dur, float, optional: duration of gap between conditions, defaults to 0.
iteration, int, optional: number of times the stimulus is displayed, defaults to 1
is_smooth_edge : bool: True, smooth circle edge with smooth_width_ratio and smooth_func False, do not smooth edge
smooth_width_ratio : float, should be smaller than 1.: the ratio between smooth band width and radius, circle edge is the middle of smooth band
smooth_func : function object: this function take two inputs: 1) ndarray storing the distance from each pixel to smooth band center; 2) smooth band width. returns smoothed mask with same shape as input ndarray
is_blank_block : bool, optional: if True, a full screen background will be displayed as an additional grating. The frames of this condition will be: (1, 0.0, 0.0, 0.0, 0.0, 0.0, 1.0 or 0.0), the meaning of these numbers can be found in self.frame_config

Attributes:

display_frame_num
midgap_frame_num
postgap_frame_num
pregap_frame_num

Methods

`generate_frames`(self)	place holder of function “generate_frames” for each specific stimulus
`generate_movie`(self)	place holder of function ‘generate_movie’ for each specific stimulus
`generate_movie_by_index`(self)	compute the stimulus movie to be displayed by index.

clear
set_background
set_coordinate
set_indicator
set_monitor
set_postgap_dur
set_pregap_dur

generate_frames(self)¶: place holder of function “generate_frames” for each specific stimulus

generate_movie(self)¶: place holder of function ‘generate_movie’ for each specific stimulus

generate_movie_by_index(self)¶: compute the stimulus movie to be displayed by index.

StaticImages¶

class retinotopic_mapping.StimulusRoutines.StaticImages(monitor, indicator, background=0.0, coordinate='degree', img_center=(0.0, 60.0), deg_per_pixel=(0.1, 0.1), display_dur=0.25, midgap_dur=0.0, iteration=1, pregap_dur=2.0, postgap_dur=3.0, is_blank_block=True)¶

Generate static images stimulus

Stimulus routine presents a sequence of static images in a random order. Currently the input image stack should be a tif file. The size of the image should be exactly same as the pixel dimension of downsized monitor pixel resolution. For example if self.monitor.resolution = (1200,1920) and self.monitor.downsample_rate = 10. The shape of input image stack should be n x 120 x 192. Value of the input image stack should be within the range of [-1., 1.]. The values out of this range will be handled by psychopy.visual.ImageStim() function. The reason of this seemingly stringent requirement is that, for visual physiological experiments, the parameters of visual stimuli should be very well controlled. Any imaging cropping, zooming, transformating etc. will affect luminance, contrast, spatial resolution etc. and produce unexpected effects.

This stimulus routing provides a method to generate such image stacks. StaticImages.wrap_images() takes a list of image files transform them into a desired spherically corrected and luminance normalized image stack into visual degree coordinates and save it as a tif file.

Parameters:

monitor : monitor object: contains display monitor information
indicator : indicator object: contains indicator information
coordinate : str from {‘degree’,’linear’}, optional: specifies coordinates, defaults to ‘degree’
background : float, optional: color of background. Takes values in [-1,1] where -1 is black and 1 is white
pregap_dur : float, optional: amount of time (in seconds) before the stimulus is presented, defaults to 2.
postgap_dur : float, optional: amount of time (in seconds) after the stimulus is presented, defaults to 3.
img_center : 2-tuple of floats, optional: coordintes for center of the images (altitude, azimuth)
deg_per_pixel: float, or list/tuple of two floats: pixel size in visual degrees of unwrapped image (altitude, azimuth), if float, assume sizes in altitude and azimuth are the same
display_dur : float, optional: duration of each condition in seconds, defaults to 0.25
midgap_dur : float, optional: duration of gap between conditions, defaults to 0.
iteration : int, optional: number of times the stimulus is displayed, defaults to 1
is_blank_block : bool, optional: if True, a full screen background will be displayed as an additional image. index of this image will be -1.

Attributes:

display_frame_num
midgap_frame_num
postgap_frame_num
pregap_frame_num

Methods

`generate_frames`(self)	place holder of function “generate_frames” for each specific stimulus
`generate_movie`(self)	place holder of function ‘generate_movie’ for each specific stimulus
`generate_movie_by_index`(self)	compute the stimulus movie to be displayed by index.
`set_imgs_from_hdf5`(self, imgs_file_path)	set 3d arrays from a hdf5 file for display.
`wrap_images`(self, work_dir)	look for the ‘images_original.tif’ in the work_dir, load the images, warp and luminance correct images, save wrapping results in an HDF5 file with name “wrapped_images_for_display.hdf5” in the work_dir

clear
set_background
set_coordinate
set_imgs_from_tif
set_indicator
set_monitor
set_postgap_dur
set_pregap_dur

generate_frames(self)¶: place holder of function “generate_frames” for each specific stimulus

generate_movie(self)¶: place holder of function ‘generate_movie’ for each specific stimulus

generate_movie_by_index(self)¶: compute the stimulus movie to be displayed by index.

set_imgs_from_hdf5(self, imgs_file_path)¶

set 3d arrays from a hdf5 file for display. Ideally the hdf5 file should be the result from self.wrap_images() method. Only designed to work with wrapped images

Parameters:	imgs_file_path : str system path ot the hdf5 file. It should have at least one dataset named ‘images_wrapped’ containing a 3d array of wrapped images to display

wrap_images(self, work_dir)¶: look for the ‘images_original.tif’ in the work_dir, load the images, warp and luminance correct images, save wrapping results in an HDF5 file with name “wrapped_images_for_display.hdf5” in the work_dir

StimulusSeparator¶

class retinotopic_mapping.StimulusRoutines.StimulusSeparator(monitor, indicator, coordinate='degree', background=0.0, indicator_on_frame_num=4, indicator_off_frame_num=4, cycle_num=10, pregap_dur=0.0, postgap_dur=0.0)¶

a quick flash of indicator to separate different visual stimuli when displayed in the same session

Parameters:

monitor : monitor object: contains display monitor information
indicator : indicator object: contains indicator information
coordinate : str from {‘degree’,’linear’}, optional: specifies coordinates, defaults to ‘degree’
background : float, optional: color of background. Takes values in [-1,1] where -1 is black and 1 is white
pregap_dur : float, optional: amount of time (in seconds) before the stimulus is presented, defaults to 2.
postgap_dur : float, optional: amount of time (in seconds) after the stimulus is presented, defaults to 3.
indicator_on_frame_num : int: number of frames the indicator is white, should be positive.
indicator_off_frame_num : int: number of frames the indicator is black, should be positive.
cycle_num : int: number of repeat of the indicator flash, should be positive.

Attributes:

postgap_frame_num
pregap_frame_num

Methods

`generate_frames`(self)	place holder of function “generate_frames” for each specific stimulus
`generate_movie`(self)	place holder of function ‘generate_movie’ for each specific stimulus

clear
generate_movie_by_index
set_background
set_coordinate
set_indicator
set_monitor
set_postgap_dur
set_pregap_dur

generate_frames(self)¶: place holder of function “generate_frames” for each specific stimulus

generate_movie(self)¶: place holder of function ‘generate_movie’ for each specific stimulus

generate_movie_by_index(self)¶: place holder of function generate_movie_by_index() for each specific stimulus

CombinedStimuli¶

class retinotopic_mapping.StimulusRoutines.CombinedStimuli(monitor, indicator, background=0.0, coordinate='degree', pregap_dur=2.0, postgap_dur=3.0)¶

the stimulus class that can combine different stimuli into one session.

example: >>> import retinotopic_mapping.StimulusRoutines as stim >>> from retinotopic_mapping.MonitorSetup import Monitor, Indicator >>> from retinotopic_mapping.DisplayStimulus import DisplaySequence >>> mon = Monitor(resolution=(1200, 1920), dis=15., mon_width_cm=52., mon_height_cm=32.) >>> ind = Indicator(mon) >>> uc = stim.UniformContrast(mon, ind, duration=10., color=-1.) >>> ss = stim.StimulusSeparator(mon, ind) >>> cs = stim.CombinedStimuli(mon, ind) >>> cs.set_stimuli([ss, uc, ss]) >>> ds = DisplaySequence(log_dir=’C:/data’) >>> ds.set_stim(cs) >>> ds.trigger_display()

Parameters:

monitor : monitor object: contains display monitor information
indicator : indicator object: contains indicator information
coordinate : str from {‘degree’,’linear’}, optional: specifies coordinates, defaults to ‘degree’
background : float, optional: color of background. Takes values in [-1,1] where -1 is black and 1 is white
pregap_dur : float, optional: amount of time (in seconds) before the stimulus is presented, defaults to 2.
postgap_dur : float, optional: amount of time (in seconds) after the stimulus is presented, defaults to 3.

Attributes:

postgap_frame_num
pregap_frame_num

Methods

generate_frames(self) place holder of function “generate_frames” for each specific stimulus

generate_movie(self) place holder of function ‘generate_movie’ for each specific stimulus

set_stimuli(self, stimuli[, static_images_path])

Parameters:

clear
generate_movie_by_index
set_background
set_coordinate
set_indicator
set_monitor
set_postgap_dur
set_pregap_dur

generate_movie_by_index(self)¶: place holder of function generate_movie_by_index() for each specific stimulus

set_stimuli(self, stimuli, static_images_path=None)¶

Parameters:	stimuli : list of above stimulus object static_images_path : str system path to the hdf5 file storing the wrapped images for display. If there is StaticImages stimulus in the stimuli list, it will try to load images and display

KSstim¶

class retinotopic_mapping.StimulusRoutines.KSstim(monitor, indicator, background=0.0, coordinate='degree', square_size=25.0, square_center=(0, 0), flicker_frame=10, sweep_width=20.0, step_width=0.15, direction='B2U', sweep_frame=1, iteration=1, pregap_dur=2.0, postgap_dur=3.0)¶

generate Kalatsky & Stryker stimulus

Kalatsky & Stryker (KS) stimulus routine presents checkerboard gratings that drift against a fixed background color.

Parameters:

monitor : monitor object: object storing experimental monitor setup information
indicator : indicator object: object storing photodiode indicator information
background : float, optional: background color of stimulus, takes values in [-1,1]. defaults to 0.
coordinate : str, optional: coordinate representation, either ‘degree’ or ‘linear’, defaults to ‘degree’
square_size : float, optional: size of flickering square, defaults to 25.
square_center: tuple, optional: coordinate of center point, defaults to (0,0)
flicker_frame : int, optional: number of frames in one flicker, defaults to 10
sweep_width : float, optional: width of sweeps measured in units cm or degs if coordinate value is ‘linear’ or ‘degree’ respectively. defaults to 20
step_width : float, optional: width of steps measured in units cm or degs if coordinate value is ‘linear’ or ‘degree’ respectively. defaults to 0.15
direction : {‘B2U’,’U2B’,’L2R’,’R2L’}, optional: the direction of sweep movement, defaults to ‘B2U’. ‘B2U’ means stim is presented from the bottom to the top of the screen, whereas ‘U2B’ is from the top to the bottom. ‘L2R’ is left to right and ‘R2L’ is right to left
sweep_frame : int, optional: roughly determines speed of the drifting grating, defaults to 1
iteration : int, optional: number of times that the stimulus will be repeated, defaults to 1
pregap_dur : float, optional: number of seconds before stimulus is presented, defaults to 2
postgap_dur : float, optional: number of seconds after stimulus is presented, defaults to 2

Attributes:

postgap_frame_num
pregap_frame_num

Methods

`generate_frames`(self)	function to generate all the frames needed for KS stimulation returnins a list of information of all frames as a list of tuples
`generate_movie`(self)	Function to Generate Kalatsky & Stryker visual stimulus frame by frame
`generate_movie_by_index`(self)	place holder of function generate_movie_by_index() for each specific stimulus
`generate_squares`(self)	generate checker board squares
`generate_sweeps`(self)	generate full screen sweep sequence
`plot_squares`(self)	plot checkerboard squares

clear
set_background
set_coordinate
set_direction
set_indicator
set_monitor
set_postgap_dur
set_pregap_dur
set_sweep_sigma
set_sweep_width

generate_frames(self)¶

function to generate all the frames needed for KS stimulation returnins a list of information of all frames as a list of tuples

Information contained in each frame:

first element -

during stimulus value is equal to 1 and 0 otherwise

second element -

square polarity, 1->not reversed; -1->reversed

third element:

sweeps, index in sweep table

forth element -

color of indicator

synchronized: gap->-1, sweep on -> 1 non-synchronized: alternating between -1 and 1 at defined frequency

for gap frames the second and third elements should be ‘None’

generate_movie(self)¶: Function to Generate Kalatsky & Stryker visual stimulus frame by frame

generate_movie_by_index(self)¶: place holder of function generate_movie_by_index() for each specific stimulus

generate_squares(self)¶: generate checker board squares

generate_sweeps(self)¶: generate full screen sweep sequence

plot_squares(self)¶: plot checkerboard squares

KSstimAllDir¶

class retinotopic_mapping.StimulusRoutines.KSstimAllDir(monitor, indicator, coordinate='degree', background=0.0, square_size=25, square_center=(0, 0), flicker_frame=6, sweep_width=20.0, step_width=0.15, sweep_frame=1, iteration=1, pregap_dur=2.0, postgap_dur=3.0)¶

generate Kalatsky & Stryker stimulation in all four direction contiuously

Generalizes the KS stimulus routine so that the drifting gratings can go in all four directions

Parameters:

monitor : monitor object: contains display monitor information
indicator : indicator object: contains indicator information
coordinate : str from {‘degree’,’linear’}, optional: specifies coordinates, defaults to ‘degree’
background : float, optional: color of background. Takes values in [-1,1] where -1 is black and 1 is white
square_size : int, optional: size of flickering square, defaults to 25.
square_center : tuple, optional: coordinate of center point of the square, defaults to (0,0)
flicker_frame : int, optional: number of frames per flicker while stimulus is being presented, defaults to 6
sweep_width : float, optional: width of sweeps. defaults to 20.
step_width : float, optional: width of steps. defaults to 0.15.
sweep_frame : int, optional: roughly determines speed of the drifting grating, defaults to 1
iteration : int, optional: number of times stimulus will be presented, defaults to 1
pregap_dur : float, optional: number of seconds before stimulus is presented, defaults to 2.
postgap_dur : float, optional: number of seconds after stimulus is presented, defaults to 3.

Methods

generate_movie(self) Generate stimulus movie frame by frame

generate_movie(self)¶: Generate stimulus movie frame by frame