def playsta(sta, frame_duration=None, cmap=None, centerzero=True, **kwargs):
"""
Create a looped animation for a single STA with 3 dimensions.
Parameters
---------
cmap:
Colormap to be used. Defaults to the specified colormap in the
config file.
centerzero:
Center the colormap around zero if True.
interval:
Frame rate for the animation in ms.
repeat_delay:
Time to wait before the animation is repeated in ms.
Note
----
The returned animation can be saved like so:
>>> ani = playsta(sta)
>>> ani.save('wheretosave/sta.gif', writer='imagemagick', fps=10)
"""
check_interactive_backend()
if cmap is None:
cmap = iof.config('colormap')
if centerzero:
vmax = asc.absmax(sta)
vmin = asc.absmin(sta)
else:
vmax, vmin = sta.max(), sta.min()
ims = []
fig = plt.figure()
ax = plt.gca()
for i in range(sta.shape[-1]):
im = ax.imshow(sta[:, :, i],
animated=True,
cmap=cmap,
vmin=vmin,
vmax=vmax)
ims.append([im]) # Needs to be a list of lists
ani = animation.ArtistAnimation(fig, ims, **kwargs)
return ani
def stashow(sta, ax=None, cbar=True, **kwargs):
"""
Plot STA in a nice way with proper colormap and colorbar.
STA can be single frame from checkerflicker or whole STA
from stripeflicker.
Following kwargs are available:
imshow
extent: Change the labels of the axes. [xmin, xmax, ymin, ymax]
aspect: Aspect ratio of the image. 'auto', 'equal'
cmap: Colormap to be used. Default is set in config
colorbar
size: Width of the colorbar as percentage of image dimension
Default is 2%
ticks: Where the ticks should be placed on the colorbar.
format: Format for the tick labels. Default is '%.2f'
Usage:
ax = plt.subplot(111)
stashow(sta, ax)
"""
vmax = asc.absmax(sta)
vmin = asc.absmin(sta)
# Make a dictionary for imshow and colorbar kwargs
imshowkw = {'cmap': iof.config('colormap'), 'vmin': vmin, 'vmax': vmax}
cbarkw = {'size': '2%', 'ticks': [vmin, vmax], 'format': '%.2f'}
for key, val in kwargs.items():
if key in ['extent', 'aspect', 'cmap']:
imshowkw.update({key: val})
elif key in ['size', 'ticks', 'format']:
cbarkw.update({key: val})
else:
raise ValueError(f'Unknown kwarg: {key}')
if ax is None:
ax = plt.gca()
im = ax.imshow(sta, **imshowkw)
spineless(ax)
if cbar:
colorbar(im, **cbarkw)
return im
ax.xaxis.set_ticklabels([])
elif row % nsubrows == 1:
ax.plot(motionfilt_r[mode_i, :], color='k')
if col == 0: ax.set_ylabel('Magnitude')
ax.set_ylim(motionfilt_r.min(), motionfilt_r.max())
ax.xaxis.set_ticklabels([])
elif row % nsubrows == 2:
ax.plot(motionfilt_theta[mode_i, :], color='r')
ax.yaxis.set_ticks([-np.pi, 0, np.pi])
ax.yaxis.set_ticklabels(['-π', 0, 'π'])
ax.xaxis.set_ticklabels([])
elif row % nsubrows == nsubrows - 1:
im = ax.imshow(cells[mode_i, :],
cmap='RdBu_r',
vmin=asc.absmin(cells),
vmax=asc.absmax(cells),
aspect='auto',
interpolation='nearest')
ax.set_xticks(np.array([0, .25, .5, .75, 1]) * cells.shape[-1])
ax.xaxis.set_ticklabels(
np.round((ax.get_xticks() * st.frame_duration), 1))
ax.set_xlabel('Time [s]')
if col == 0: ax.set_ylabel('Cells')
if mode_i == n_components - 1:
plf.colorbar(im)
# fig.tight_layout()
fig.subplots_adjust(wspace=0.3)
fig.savefig(
f'/Users/ycan/Downloads/2020-05-27_meeting/cca_DScells_shuffled.pdf')
plt.show()
stc2 = calc_stc(spikes, stimulus, filter_length)
fig, axes = plt.subplots(2, 1)
axes[0].plot(eigvals, 'o')
ax1 = axes[1]
ax1.plot(sta)
ax1.plot(eigvecs[:, 0])
ax1.plot(eigvecs[:, -1])
#%%
sp_mean = spikes.mean()
stim_covar = np.cov(rw, rowvar=False)
term1 = stc + (2 * (sta @ sta.T)) / sp_mean
bmel = np.linalg.inv(term1) @ sta
cmel = (np.linalg.inv(stim_covar) - sp_mean * np.linalg.inv(term1)) / 2
fig2, axes2 = plt.subplots(2, 2)
axes2 = axes2.flat
axes2[0].plot(bmel)
axes2[0].plot(sta, ls='dashed', color='grey', label='STA')
axes2[1].imshow(cmel,
cmap='seismic',
vmin=asc.absmin(cmel),
vmax=asc.absmax(cmel))
v, w = np.linalg.eigh(cmel)
eiginds = [0, -1]
axes2[2].plot(v, 'ko')
axes2[2].plot(v[eiginds[0]], 'o')
axes2[2].plot(v[eiginds[1]], 'o')
axes2[3].plot(w[:, eiginds])
def cca_omb_components(exp: str,
stim_nr: int,
n_components: int = 6,
regularization=None,
filter_length=None,
cca_solver: str = 'macke',
maxframes=None,
shufflespikes: bool = False,
exclude_allzero_spike_rows: bool = True,
savedir: str = None,
savefig: bool = True,
sort_by_nspikes: bool = True,
select_cells: list = None,
plot_first_ncells: int = None,
whiten: bool = False):
"""
Analyze OMB responses using cannonical correlation analysis and plot the results.
Parameters
---
n_components:
Number of components that will be requested from the CCA anaylsis. More numbers mean
the algortihm will stop at a later point. That means components of analyses with fewer
n_components are going to be identical to the first n components of the higher-number
component analyses.
regularization:
The regularization parameter to be passed onto rcca.CCA. Not relevant for macke
filter_length:
The length of the time window to be considered in the past for the stimulus and the responses.
Can be different for stimulus and response, if a tuple is given.
cca_solver:
Which CCA solver to use. Options are `rcca` and `macke`(default)
maxframes: int
Number of frames to load in the the experiment object. Used to avoid memory and performance
issues.
shufflespikes: bool
Whether to randomize the spikes, to validate the results
exclude_allzero_spike_rows:
Exclude all cells which have zero spikes for the duration of the stimulus.
savedir: str
Custom directory to save the figures and data files. If None, will be saved in the experiment
directory under appropritate path.
savefig: bool
Whether to save the figures.
sort_by_nspikes: bool
Wheter to sort the cell weights array by the number of spikes during the stimulus.
select_cells: list
A list of indexes for the subset of cells to perform the analysis for.
plot_first_ncells: int
Number of cells to plot in the cell plots.
"""
if regularization is None:
regularization = 0
st = OMB(exp, stim_nr, maxframes=maxframes)
if filter_length is None:
filter_length = st.filter_length
if type(filter_length) is int:
filter_length = (filter_length, filter_length)
if type(savedir) is str:
savedir = Path(savedir)
if savedir is None:
savedir = st.stim_dir / 'CCA'
savedir.mkdir(exist_ok=True, parents=True)
spikes = st.allspikes()
nonzerospikerows = ~np.isclose(spikes.sum(axis=1), 0)
# Set the mean to zero for spikes
spikes -= spikes.mean(axis=1)[:, None]
bgsteps = st.bgsteps
if select_cells is not None:
if type(select_cells) is not np.array:
select_cells = np.array(select_cells)
spikes = spikes[select_cells]
st.nclusters = len(select_cells)
# Convert to list for better string representation
# np.array is printed as "array([....])"
# with newline characters which is problematic in filenames
select_cells = list(select_cells)
# Exclude rows that have no spikes throughout
if exclude_allzero_spike_rows:
spikes = spikes[nonzerospikerows, :]
nspikes_percell = spikes.sum(axis=1)
if shufflespikes:
spikes = spikeshuffler.shufflebyrow(spikes)
figsavename = f'{n_components=}_{shufflespikes=}_{select_cells=}_{regularization=}_{filter_length=}_{whiten=}'
# If the file length gets too long due to the list of selected cells, summarize it.
if len(figsavename) > 200:
figsavename = f'{n_components=}_{shufflespikes=}_select_cells={len(select_cells)}cells-index{select_cells[0]}to{select_cells[-1]}_{regularization=}_{filter_length=}_{whiten=}'
#sp_train, sp_test, stim_train, stim_test = train_test_split(spikes, bgsteps)
stimulus = mft.packdims(st.bgsteps, filter_length[0])
spikes = mft.packdims(spikes, filter_length[1])
if cca_solver == 'rcca':
resp_comps, stim_comps, cancorrs = cca_rcca(spikes, stimulus,
filter_length,
n_components,
regularization, whiten)
# cells = np.swapaxes(spikes_res, 1, 0)
# cells = cells.reshape((n_components, st.nclusters, filter_length[1]))
# motionfilt_x = cca.ws[1][:filter_length[0]].T
# motionfilt_y = cca.ws[1][filter_length[0]:].T
elif cca_solver == 'macke':
resp_comps, stim_comps, cancorrs = cca_macke(spikes, stimulus,
filter_length,
n_components)
nsp_argsorted = np.argsort(nspikes_percell)
resp_comps_sorted_nsp = resp_comps[:, nsp_argsorted, :]
if sort_by_nspikes:
resp_comps_toplot = resp_comps_sorted_nsp
else:
resp_comps_toplot = resp_comps
if plot_first_ncells is not None:
resp_comps_toplot = resp_comps_toplot[:, :plot_first_ncells, ...]
motionfilt_r, motionfilt_theta = mft.cart2pol(stim_comps[:, 0, :],
stim_comps[:, 1, :])
#%%
nrows, ncols = plf.numsubplots(n_components)
fig_cells, axes_cells = plt.subplots(nrows, ncols, figsize=(10, 10))
for i in range(n_components):
ax = axes_cells.flat[i]
im = ax.imshow(resp_comps[i, :],
cmap='RdBu_r',
vmin=asc.absmin(resp_comps),
vmax=asc.absmax(resp_comps),
aspect='auto',
interpolation='nearest')
ax.set_title(f'{i}')
fig_cells.suptitle(f'Cells default order {shufflespikes=}')
if savefig:
fig_cells.savefig(savedir / f'{figsavename}_cells_default_order.pdf')
plt.close(fig_cells)
nsubplots = plf.numsubplots(n_components)
height_list = [1, 1, 1, 3] # ratios of the plots in each component
# Create a time vector for the stimulus plots
t_stim = -np.arange(0, filter_length[0] * st.frame_duration,
st.frame_duration)[::-1] * 1000
t_response = -np.arange(0, filter_length[1] * st.frame_duration,
st.frame_duration)[::-1] * 1000
xtick_loc_params = dict(nbins=4, steps=[2, 5, 10], integer=True)
nsubrows = len(height_list)
height_ratios = nsubplots[0] * height_list
fig, axes = plt.subplots(nrows=nsubplots[0] * nsubrows,
ncols=nsubplots[1],
gridspec_kw={'height_ratios': height_ratios},
figsize=(11, 10))
for row, ax_row in enumerate(axes):
for col, ax in enumerate(ax_row):
mode_i = int(row / nsubrows) * nsubplots[1] + col
# ax.text(0.5, 0.5, f'{mode_i}')
ax.set_yticks([])
# Plot motion filters
if row % nsubrows == 0:
ax.plot(t_stim,
stim_comps[mode_i, 0, :],
marker='o',
markersize=1)
ax.plot(t_stim,
stim_comps[mode_i, 1, :],
marker='o',
markersize=1)
if col == 0:
ax.set_ylabel('Motion',
rotation=0,
ha='right',
va='center')
ax.set_ylim(stim_comps.min(), stim_comps.max())
# Draw a horizontal line for zero and prevent rescaling of x-axis
xlims = ax.get_xlim()
ax.hlines(0,
*ax.get_xlim(),
colors='k',
linestyles='dashed',
alpha=0.3)
ax.set_xlim(*xlims)
# ax.set_title(f'Component {mode_i}', fontweight='bold')
ax.xaxis.set_major_locator(MaxNLocator(**xtick_loc_params))
if not mode_i == 0 or filter_length[0] == filter_length[1]:
ax.xaxis.set_ticklabels([])
else:
ax.tick_params(axis='x', labelsize=8)
# Plot magnitude of motion
elif row % nsubrows == 1:
ax.plot(t_stim,
motionfilt_r[mode_i, :],
color='k',
marker='o',
markersize=1)
if col == 0:
ax.set_ylabel('Magnitude',
rotation=0,
ha='right',
va='center')
ax.set_ylim(motionfilt_r.min(), motionfilt_r.max())
ax.xaxis.set_ticklabels([])
ax.xaxis.set_major_locator(MaxNLocator(**xtick_loc_params))
# Plot direction of motion
elif row % nsubrows == 2:
ax.plot(t_stim,
motionfilt_theta[mode_i, :],
color='r',
marker='o',
markersize=1)
if mode_i == 0:
ax.yaxis.set_ticks([-np.pi, 0, np.pi])
ax.yaxis.set_ticklabels(['-π', 0, 'π'])
ax.xaxis.set_ticklabels([])
ax.xaxis.set_major_locator(MaxNLocator(**xtick_loc_params))
# Plot cell weights
elif row % nsubrows == nsubrows - 1:
im = ax.imshow(resp_comps_toplot[mode_i, :],
cmap='RdBu_r',
vmin=asc.absmin(resp_comps),
vmax=asc.absmax(resp_comps),
aspect='auto',
interpolation='nearest',
extent=[
t_response[0], t_response[-1], 0,
resp_comps_toplot.shape[1]
])
ax.xaxis.set_major_locator(MaxNLocator(**xtick_loc_params))
if row == axes.shape[0] - 1:
ax.set_xlabel('Time before spike [ms]')
# ax.set_xticks(np.array([0, .25, .5, .75, 1]) * cells_toplot.shape[-1])
# ax.xaxis.set_ticklabels(-np.round((ax.get_xticks()*st.frame_duration), 2)[::-1])
else:
ax.xaxis.set_ticklabels([])
plf.integerticks(ax, 5, which='y')
if col == 0:
ax.set_ylabel(
f'Cells\n{"(sorted nsp)"*sort_by_nspikes}\n{("(first " + str(plot_first_ncells)+ " cells)")*(type(plot_first_ncells) is int) }',
rotation=0,
ha='right',
va='center')
else:
ax.yaxis.set_ticklabels([])
if mode_i == n_components - 1:
plf.colorbar(im)
# Add ticks on the right side of the plots
if col == nsubplots[1] - 1 and row % nsubrows != nsubrows - 1:
plf.integerticks(ax, 3, which='y')
ax.yaxis.tick_right()
fig.suptitle(
f'CCA components of {st.exp_foldername}\n{shufflespikes=} {n_components=}\n{sort_by_nspikes=}\n'
+ f'{select_cells=} {regularization=} {filter_length=}')
fig.subplots_adjust(wspace=0.1, hspace=0.3)
if savefig:
fig.savefig(savedir / f'{figsavename}_cellsandcomponents.pdf')
# plt.show()
plt.close(fig)
#%%
fig_corrs = plt.figure()
plt.plot(cancorrs, 'ko')
# plt.ylim([0.17, 0.24])
plt.xlabel('Component index')
plt.ylabel('Correlation')
plt.title(f'Cannonical correlations {shufflespikes=}')
if savefig:
fig_corrs.savefig(savedir / f'{figsavename}_correlation_coeffs.pdf')
# plt.show()
plt.close(fig_corrs)
fig_nlt, axes_nlt = plt.subplots(nrows, ncols, figsize=(10, 10))
stim_comps_flatter = stim_comps[:n_components].reshape(
(n_components, 2 * filter_length[0])).T
resp_comps_flatter = resp_comps[:n_components].reshape(
(n_components, resp_comps.shape[1] * filter_length[1])).T
# from IPython.core.debugger import Pdb; ipdb=Pdb(); ipdb.set_trace()
# Reshape to perform the convolution as a matrix multiplication
generator_stim = stimulus @ stim_comps_flatter
generator_resp = spikes @ resp_comps_flatter
for i, ax in enumerate(axes_nlt.flatten()):
nonlinearity, bins = nlt.calc_nonlin(generator_resp[:, i],
generator_stim[:, i])
# ax.scatter(generator_stim, generator_resp, s=1, alpha=0.5, facecolor='grey')
ax.plot(bins, nonlinearity, 'k')
if i == 0:
all_nonlinearities = np.empty((n_components, *nonlinearity.shape))
all_bins = np.empty((n_components, *bins.shape))
all_nonlinearities[i, ...] = nonlinearity
all_bins[i, ...] = bins
nlt_xlims = []
nlt_ylims = []
for i, ax in enumerate(axes_nlt.flatten()):
xlim = ax.get_xlim()
ylim = ax.get_ylim()
nlt_xlims.extend(xlim)
nlt_ylims.extend(ylim)
nlt_maxx, nlt_minx = max(nlt_xlims), min(nlt_xlims)
nlt_maxy, nlt_miny = max(nlt_ylims), min(nlt_ylims)
for i, ax in enumerate(axes_nlt.flatten()):
ax.set_xlim([nlt_minx, nlt_maxx])
ax.set_ylim([nlt_miny, nlt_maxy])
for i, axes_row in enumerate(axes_nlt):
for j, ax in enumerate(axes_row):
if i == nrows - 1:
ax.set_xlabel('Generator (motion)')
if j == 0:
ax.set_ylabel('Generator (cells)')
else:
ax.yaxis.set_ticklabels([])
ax.set_xlim([nlt_minx, nlt_maxx])
ax.set_ylim([nlt_miny, nlt_maxy])
fig_nlt.suptitle(f'Nonlinearities\n{figsavename}')
if savefig:
fig_nlt.savefig(savedir / f'{figsavename}_nonlinearity.png')
plt.close(fig_nlt)
keystosave = [
'n_components', 'resp_comps', 'stim_comps', 'motionfilt_r',
'motionfilt_theta', 'resp_comps_sorted_nsp', 'select_cells',
'regularization', 'filter_length', 'all_nonlinearities', 'all_bins',
'cca_solver'
]
datadict = dict()
for key in keystosave:
datadict[key] = locals()[key]
np.savez(savedir / figsavename, **datadict)
import matplotlib.pyplot as plt
cells = cca.x_weights_.T
motionfilt_x = cca.y_weights_[:filter_length].T
motionfilt_y = cca.y_weights_[filter_length:].T
fig, axes = plt.subplots(*plf.numsubplots(n_components))
for i, ax in enumerate(axes.flat):
ax.plot(motionfilt_x[i, :])
ax.plot(motionfilt_y[i, :])
ax.set_ylim(cca.y_weights_.min(), cca.y_weights_.max())
fig.suptitle('Stimulus components for each CCA filter')
plt.show()
im = plt.imshow(cells, cmap='RdBu_r', vmin=asc.absmin(cells), vmax=asc.absmax(cells))
plt.ylabel('Components')
plt.xlabel('Cells')
plf.colorbar(im)
plt.show()
plt.plot(cca.coef_[:, 0], cca.coef_[:, 1], 'ko')
plt.show()
offsets = np.arange(n_components)*.6
plt.plot(cca.y_weights_ + np.tile(offsets, (stimulus.shape[1], 1)), lw=0.5)
plt.hlines(offsets, 0, stimulus.shape[1], lw=.2)
ax.set_ylim(cca.y_weights_.min(), cca.y_weights_.max())
ax.set_title(f'Component {mode_i}', fontweight='bold')
ax.xaxis.set_ticklabels([])
elif row % nsubrows == 1:
ax.plot(motionfilt_r[mode_i, :], color='k')
if col==0: ax.set_ylabel('Magnitude')
ax.set_ylim(motionfilt_r.min(), motionfilt_r.max())
ax.xaxis.set_ticklabels([])
elif row % nsubrows == 2:
ax.plot(motionfilt_theta[mode_i, :], color='r')
ax.yaxis.set_ticks([-np.pi, 0, np.pi])
ax.yaxis.set_ticklabels(['-π', 0, 'π'])
ax.xaxis.set_ticklabels([])
elif row % nsubrows == nsubrows-1:
im = ax.imshow(cells[mode_i, :], cmap='RdBu_r',
vmin=asc.absmin(cells), vmax=asc.absmax(cells),
aspect='auto',
interpolation='nearest')
ax.set_xticks(np.array([0, .25, .5, .75, 1]) * cells.shape[-1])
ax.xaxis.set_ticklabels(np.round((ax.get_xticks()*st.frame_duration), 1))
ax.set_xlabel('Time [s]')
if col==0: ax.set_ylabel('Cells')
# fig.tight_layout()
fig.subplots_adjust(wspace=0.3)
selcels = '_'.join(map(str, selected_cells))
fig.savefig(f'/Users/ycan/Downloads/2020-05-27_meeting/{selcels}_shuffled{shuffle_spikes}.pdf')
plt.show()
#%%
def stabrowser(sta, frame_duration=None, cmap=None, centerzero=True, **kwargs):
"""
Returns an interactive plot to browse an spatiotemporal
STA. Requires an interactive matplotlib backend.
Parameters
--------
sta:
Numpy array containing the STA. Last dimension should index time.
frame_duration:
Time between each frame. (optional)
cmap:
Colormap to use.
centerzero:
Whether to center the colormap around zero for diverging colormaps.
Example
------
>>> print(sta.shape) # (xpixels, ypixels, time)
(75, 100, 40)
>>> fig, slider = stabrowser(sta, frame_duration=1/60)
Notes
-----
When calling the function, the slider is returned to prevent the reference
to it getting destroyed and to keep it interactive.
The dummy variable `_` can also be used.
"""
check_interactive_backend()
if cmap is None:
cmap = iof.config('colormap')
if centerzero:
vmax = asc.absmax(sta)
vmin = asc.absmin(sta)
else:
vmax, vmin = sta.max(), sta.min()
imshowkwargs = dict(cmap=cmap, vmax=vmax, vmin=vmin, **kwargs)
fig = plt.figure()
ax = fig.add_axes([0.1, 0.1, 0.8, 0.8])
initial_frame = 5
axsl = fig.add_axes([0.25, 0.05, 0.65, 0.03])
# For the slider to remain interactive, a reference to it should
# be kept, so it set to a variable and is returned by the function
slider_t = Slider(axsl,
'Frame before spike',
0,
sta.shape[-1] - 1,
valinit=initial_frame,
valstep=1,
valfmt='%2.0f')
def update(frame):
frame = int(frame)
im = ax.get_images()[0]
im.set_data(sta[..., frame])
if frame_duration is not None:
fig.suptitle(f'{frame*frame_duration*1000:4.0f} ms')
fig.canvas.draw_idle()
slider_t.on_changed(update)
ax.imshow(sta[..., initial_frame], **imshowkwargs)
ax.set_axis_off()
plt.tight_layout()
plt.subplots_adjust(wspace=.01, hspace=.01)
return fig, slider_t
def multistabrowser(stas,
frame_duration=None,
normalize=True,
cmap=None,
centerzero=True,
**kwargs):
"""
Returns an interactive plot to browse multiple spatiotemporal
STAs at the same time. Requires an interactive matplotlib backend.
Parameters
--------
stas:
Numpy array containing STAs. First dimension should index individual cells,
last dimension should index time.
Alternatively, this could be a list of numpy arrays.
frame_duration:
Time between each frame. (optional)
normalize:
Whether to normalize each STA
cmap:
Colormap to use.
centerzero:
Whether to center the colormap around zero for diverging colormaps.
Example
------
>>> print(stas.shape) # (nrcells, xpixels, ypixels, time)
(36, 75, 100, 40)
>>> fig, slider = stabrowser(stas, frame_duration=1/60)
Notes
-----
When calling the function, the slider is returned to prevent the reference
to it getting destroyed and to keep it interactive.
The dummy variable `_` can also be used.
"""
check_interactive_backend()
if isinstance(stas, list):
stas = np.array(stas)
if normalize:
stas = asc.normalize(stas)
if cmap is None:
cmap = iof.config('colormap')
if centerzero:
vmax = asc.absmax(stas)
vmin = asc.absmin(stas)
else:
vmax, vmin = stas.max(), stas.min()
imshowkwargs = dict(cmap=cmap, vmax=vmax, vmin=vmin, **kwargs)
rows, cols = numsubplots(stas.shape[0])
fig, axes = plt.subplots(rows, cols, sharex=True, sharey=True)
initial_frame = 5
axsl = fig.add_axes([0.25, 0.05, 0.65, 0.03])
# For the slider to remain interactive, a reference to it should
# be kept, so it set to a variable and is returned by the function
slider_t = Slider(axsl,
'Frame before spike',
0,
stas.shape[-1] - 1,
valinit=initial_frame,
valstep=1,
valfmt='%2.0f')
def update(frame):
frame = int(frame)
for i in range(rows):
for j in range(cols):
# Calculate the flattened index, equivalent to i*cols+j
flat_idx = np.ravel_multi_index([i, j], (rows, cols))
if flat_idx < stas.shape[0]:
im = axes[i, j].get_images()[0]
im.set_data(stas[flat_idx, ..., frame])
if frame_duration is not None:
fig.suptitle(f'{frame*frame_duration*1000:4.0f} ms')
fig.canvas.draw_idle()
slider_t.on_changed(update)
for i in range(rows):
for j in range(cols):
flat_idx = np.ravel_multi_index([i, j], (rows, cols))
ax = axes[i, j]
if flat_idx < stas.shape[0]:
ax.imshow(stas[i * cols + j, ..., initial_frame],
**imshowkwargs)
ax.set_axis_off()
plt.tight_layout()
plt.subplots_adjust(wspace=.01, hspace=.01)
return fig, slider_t
g = sns.jointplot(
'x',
'y',
sizes,
'scatter',
# shade_lowest = False,
# , xlim=[0, 6], ylim=[0, 6]
)
#%%
import plotfuncs as plf
plf.absmax() # stop the script
for i in range(len(stas)):
sta = stas[i]
plt.imshow(sta[..., max_inds[i][-1]],
cmap='RdBu_r',
vmax=asc.absmax(sta),
vmin=asc.absmin(sta))
drawellipse(all_pars[i])
plt.title(f'{i}')
plt.show()
#%%
fig, sl = plf.multistabrowser(stas)
for i in range(len(stas)):
ax = fig.axes[i]
drawellipse(all_pars[i], ax)