def smooth(x, isosbestic, calcium, **kwargs):
"""Function that smooths the raw data and displays it in a plot.
Args : x (arr) = The time data in X
isosbestic (arr) = The adjusted isosbestic signal (time fitted to the video)
calcium (arr) = The adjusted calcium signal (time fitted to the video)
kwargs (dict) = Dictionnary with the parameters
Returns : x (arr) = The new time data in X
isosbestic_smoothed (arr) = The smoothed isosbestic signal
calcium_smoothed (arr) = The smoothed calcium signal
"""
print("\nStarting smoothing for Isosbestic and Calcium signals !")
isosbestic_smoothed = smooth_signal(isosbestic, window_len=kwargs["smoothing_window"])[:-kwargs["smoothing_window"]+1]
calcium_smoothed = smooth_signal(calcium, window_len=kwargs["smoothing_window"])[:-kwargs["smoothing_window"]+1]
x_max = x[-1]
# print("Data length : {0}".format(ut.h_m_s(x_max, add_tags=True)))
if kwargs["photometry_pp"]["plots_to_display"]["smoothing"]:
xticks, xticklabels, unit = utils.generate_xticks_and_labels(x_max)
fig = plt.figure(figsize=(10, 5), dpi=200.)
ax0 = plt.subplot(211)
p, = ax0.plot(x, isosbestic_smoothed, alpha=0.8, c=kwargs["photometry_pp"]["purple_laser"], lw=kwargs["lw"])
ax0.set_xticks(xticks)
ax0.set_xticklabels(xticklabels, fontsize=kwargs["fsl"])
ax0.set_xlim(0, x_max)
y_min, y_max, round_factor = utils.generate_yticks(isosbestic_smoothed, 0.1)
ax0.set_yticks(np.arange(y_min, y_max+round_factor, round_factor))
ax0.set_yticklabels(["{:.0f}".format(i) for i in np.arange(y_min, y_max+round_factor, round_factor)*1000], fontsize=kwargs["fsl"])
ax0.set_ylim(y_min, y_max)
ax0.set_ylabel("mV", fontsize=kwargs["fsl"])
ax0.legend(handles=[p], labels=["isosbestic"], loc=2, fontsize=kwargs["fsl"])
ax0.set_title("Smoothed Isosbestic and Calcium signals", fontsize=kwargs["fst"])
ax0.tick_params(axis='both', which='major', labelsize=kwargs["fsl"])
ax1 = plt.subplot(212, sharex=ax0)
b, = ax1.plot(x, calcium_smoothed, alpha=0.8, c=kwargs["photometry_pp"]["blue_laser"], lw=kwargs["lw"])
ax1.set_xticks(xticks)
ax1.set_xticklabels(xticklabels, fontsize=kwargs["fsl"])
ax1.set_xlim(0, x_max)
y_min, y_max, round_factor = utils.generate_yticks(calcium_smoothed, 0.1)
ax1.set_yticks(np.arange(y_min, y_max+round_factor, round_factor))
ax1.set_yticklabels(["{:.0f}".format(i) for i in np.arange(y_min, y_max+round_factor, round_factor)*1000], fontsize=kwargs["fsl"])
ax1.set_ylim(y_min, y_max)
ax1.set_ylabel("mV", fontsize=kwargs["fsl"])
ax1.legend(handles=[b], labels=["calcium"], loc=2, fontsize=kwargs["fsl"])
ax1.set_xlabel("Time ({0})".format(unit), fontsize=kwargs["fsl"])
ax1.tick_params(axis='both', which='major', labelsize=kwargs["fsl"])
plt.tight_layout()
if kwargs["photometry_pp"]["multicursor"]:
multi = MultiCursor(fig.canvas, [ax0, ax1], color='r', lw=1, vertOn=[ax0, ax1]) # FIXME: unused
if kwargs["save"]:
plt.savefig(os.path.join(kwargs["save_dir"], "Smoothed_Signals.{0}".format(kwargs["extension"])), dpi=200.)
return x, isosbestic_smoothed, calcium_smoothed
def dFF(x, isosbestic, calcium, **kwargs):
"""Function that computes the dF/F of the fitted isosbestic and standardized (or not) calcium
signals and displays it in a plot.
Args : x (arr) = The time data in X
isosbestic (arr) = The fitted isosbestic signal
calcium (arr) = The standardized (or not) calcium signal
kwargs (dict) = Dictionnary with the parameters
Returns : dFF (arr) = Relative changes of fluorescence over time
"""
print("\nStarting the computation of dF/F !")
df_f = calcium - isosbestic # computing dF/F
max_x = x[-1]
# print("Data length : {0}".format(ut.h_m_s(max_x, add_tags=True)))
if kwargs["photometry_pp"]["plots_to_display"]["dFF"]:
xticks, xticklabels, unit = utils.generate_xticks_and_labels(max_x)
fig = plt.figure(figsize=(10, 3), dpi=200.)
ax0 = plt.subplot(111)
g, = ax0.plot(x, df_f, alpha=0.8, c="green", lw=kwargs["lw"])
ax0.plot((0, x[-1]), (0, 0), "--", color="black", lw=kwargs["lw"]) #Creates a horizontal dashed line at y = 0 to signal the baseline
ax0.set_xticks(xticks)
ax0.set_xticklabels(xticklabels, fontsize=kwargs["fsl"])
ax0.set_xlim(0, max_x)
ax0.set_xlabel("Time ({0})".format(unit), fontsize=kwargs["fsl"])
if kwargs["photometry_pp"]["standardize"]:
y_min, y_max, round_factor = utils.generate_yticks(df_f, 0.1)
ax0.set_yticks(np.arange(y_min, y_max+round_factor, round_factor))
ax0.set_yticklabels(["{:.0f}".format(i) for i in np.arange(y_min, y_max+round_factor, round_factor)], fontsize=kwargs["fsl"])
ax0.set_ylim(y_min, y_max)
ax0.set_ylabel(r"z-score $\Delta$F/F", fontsize=kwargs["fsl"])
ax0.legend(handles=[g], labels=[r"z-score $\Delta$F/F"], loc=2, fontsize=kwargs["fsl"])
ax0.set_title(r"z-score $\Delta$F/F", fontsize=kwargs["fst"])
else:
y_min, y_max, round_factor = utils.generate_yticks(df_f, 0.1)
ax0.set_yticks(np.arange(y_min, y_max+round_factor, round_factor))
ax0.set_yticklabels(["{:.0f}".format(i) for i in np.arange(y_min, y_max+round_factor, round_factor)*100], fontsize=kwargs["fsl"])
ax0.set_ylim(y_min, y_max)
ax0.set_ylabel(r"$\Delta$F/F", fontsize=kwargs["fsl"])
ax0.legend(handles=[g], labels=[r"$\Delta$F/F"], loc=2, fontsize=kwargs["fsl"])
ax0.set_title(r"$\Delta$F/F", fontsize=kwargs["fst"])
ax0.tick_params(axis='both', which='major', labelsize=kwargs["fsl"])
plt.tight_layout()
if kwargs["save"]:
plt.savefig(os.path.join(kwargs["save_dir"], "dFF.{0}".format(kwargs["extension"])), dpi=200.)
return df_f
def align_channels(x, isosbestic, calcium, **kwargs):
"""Function that performs the alignement of the fitted isosbestic and standardized (or not) calcium
signals and displays it in a plot.
Args : x (arr) = The time data in X
isosbestic (arr) = The fitted isosbestic signal
calcium (arr) = The standardized (or not) calcium signal
kwargs (dict) = Dictionnary with the parameters
"""
x_max = x[-1]
if kwargs["photometry_pp"]["plots_to_display"]["channel_alignement"]:
fig = plt.figure(figsize=(10, 3), dpi=200.) # FIXME: unused
ax0 = plt.subplot(111)
b, = ax0.plot(x, calcium, alpha=0.8, c=kwargs["photometry_pp"]["blue_laser"], lw=kwargs["lw"], zorder=0)
p, = ax0.plot(x, isosbestic, alpha=0.8, c=kwargs["photometry_pp"]["purple_laser"], lw=kwargs["lw"], zorder=1)
ax0.plot((0, x[-1]), (0, 0), "--", color="black", lw=kwargs["lw"]) #Creates a horizontal dashed line at y = 0 to signal the baseline
xticks, xticklabels, unit = utils.generate_xticks_and_labels(x_max)
ax0.set_xticks(xticks)
ax0.set_xticklabels(xticklabels, fontsize=kwargs["fsl"])
ax0.set_xlim(0, x_max)
ax0.set_xlabel("Time ({0})".format(unit), fontsize=kwargs["fsl"])
if kwargs["photometry_pp"]["standardize"]:
y_min, y_max, round_factor = utils.generate_yticks(np.concatenate((isosbestic, calcium)), 0.1)
ax0.set_yticks(np.arange(y_min, y_max+round_factor, round_factor))
ax0.set_yticklabels(["{:.0f}".format(i) for i in np.arange(y_min, y_max+round_factor, round_factor)], fontsize=kwargs["fsl"])
ax0.set_ylim(y_min, y_max)
ax0.set_ylabel("z-score", fontsize=kwargs["fsl"])
else:
y_min, y_max, round_factor = utils.generate_yticks(np.concatenate((isosbestic, calcium)), 0.1)
ax0.set_yticks(np.arange(y_min, y_max+round_factor, round_factor))
ax0.set_yticklabels(["{:.0f}".format(i) for i in np.arange(y_min, y_max+round_factor, round_factor)*100], fontsize=kwargs["fsl"])
ax0.set_ylim(y_min, y_max)
ax0.set_ylabel("Change in signal (%)", fontsize=kwargs["fsl"])
ax0.legend(handles=[p, b], labels=["isosbestic", "calcium"], loc=2, fontsize=kwargs["fsl"])
ax0.set_title("Alignement of Isosbestic and Calcium signals", fontsize=kwargs["fst"])
ax0.tick_params(axis='both', which='major', labelsize=kwargs["fsl"])
plt.tight_layout()
if kwargs["save"]:
plt.savefig(os.path.join(kwargs["save_dir"], "Alignement.{0}".format(kwargs["extension"])), dpi=200.)
def check_dF_with_behavior(position_bouts,
length_bouts,
color=("blue"),
name="dF_&_behavioral_overlay",
**kwargs):
"""Function that plots the pre-processed photometry data and overlays the
behavior data.
Args : position_bouts (arr) = list of start and end of each behavioral bout
length_bouts (list) = list of the length of each behavioral bout
color (list) = color(s) of the behavioral overlay(s)
kwargs (dict) = dictionnary with additional parameters
"""
fig = plt.figure(figsize=(10, 3), dpi=200.) # FIXME: unused
ax0 = plt.subplot(111)
n = 0
handles = []
if len(position_bouts) == 1:
labels = [kwargs["behavior_to_segment"]]
else:
labels = [kwargs["behavior_to_segment"], "Excluded"]
ax0.plot(kwargs["photometry_data"]["dFF"]["x"],
kwargs["photometry_data"]["dFF"]["dFF"],
color="green",
lw=kwargs["lw"])
ax0.plot(
0,
kwargs["video_end"] - kwargs["photometry_data"]["time_lost"], (0, 0),
"--",
color="blue",
lw=kwargs["lw"]
) #Creates a horizontal dashed line at y = 0 to signal the baseline
xticks, xticklabels, unit = utils.generate_xticks_and_labels(
kwargs["photometry_data"]["dFF"]["x"][-1])
ax0.set_xticks(xticks)
ax0.set_xticklabels(xticklabels, fontsize=kwargs["fsl"])
ax0.set_xlim(0, kwargs["photometry_data"]["dFF"]["x"][-1])
ax0.set_xlabel("Time ({0})".format(unit), fontsize=kwargs["fsl"])
y_min, y_max, round_factor = utils.generate_yticks(
kwargs["photometry_data"]["dFF"]["dFF"], 0.1)
ax0.set_yticks(np.arange(y_min, y_max + round_factor, round_factor))
ax0.set_ylim(y_min, y_max)
if kwargs["photometry_pp"]["standardize"]:
ax0.set_yticklabels([
"{:.0f}".format(i)
for i in np.arange(y_min, y_max + round_factor, round_factor)
],
fontsize=kwargs["fsl"])
else:
ax0.set_yticklabels([
"{:.0f}".format(i)
for i in np.arange(y_min, y_max + round_factor, round_factor) * 100
],
fontsize=kwargs["fsl"])
for P, L in zip(position_bouts, length_bouts):
patch = patches.Rectangle((0, 0),
1,
1,
alpha=0.3,
color=color[n],
lw=0,
edgecolor=None)
handles.append(patch)
for p, l in zip(P, L):
patch = patches.Rectangle(
(p[0], y_min + y_min * 0.1),
l, (y_max + y_max * 0.1) - (y_min + y_min * 0.1),
alpha=0.3,
color=color[n],
lw=0,
edgecolor=None)
ax0.add_patch(patch)
n += 1
ax0.legend(handles=handles, labels=labels, loc=2, fontsize=kwargs["fsl"])
plt.tight_layout()
if kwargs["save"]:
plt.savefig(os.path.join(kwargs["save_dir"],
"{0}.{1}".format(name, kwargs["extension"])),
dpi=200.)
def peri_event_plot(data_around_major_bouts,
length_major_bouts,
cmap="inferno",
**kwargs):
"""Function that plots the peri-event photometry data in two different formats.
First a line plot showing the average signal before and after initiation of the behavior,
Second a heatmap showing each individual signal traces before and after initiation of the behavior.
Args : data_around_major_bouts (arr) = list of the pre-processed photometry data
before and after initiation of the behavior
length_major_bouts (list) = list of the length of each behavioral bout
cmap (str) = colormap used for the heatmap
kwargs (dict) = dictionnary with additional parameters
"""
mean_data_around_bouts = np.mean(
data_around_major_bouts,
axis=0) # Computes the mean for the peri-event photometry data
std_data_around_bouts = np.std(
data_around_major_bouts, axis=0
) # Computes the standard deviation for the peri-event photometry data
fig = plt.figure(figsize=(5, 5), dpi=200.) # Creates a figure
# =============================================================================
# First Plot
# =============================================================================
ax0 = plt.subplot(2, 1, 1) # Creates a subplot for the first figure
x_range = np.linspace(0, len(mean_data_around_bouts),
len(mean_data_around_bouts))
ax0.plot(x_range,
mean_data_around_bouts,
color="green",
alpha=1.,
lw=kwargs["lw"] + 1,
zorder=1) # Plots the average signal
if kwargs["peri_event"][
"style"] == "individual": # If individual traces are to be displayed in the line plot
for l in data_around_major_bouts:
if kwargs["peri_event"]["individual_color"]:
ax0.plot(l, alpha=0.5, lw=kwargs["lw"],
zorder=0) # Plots individual traces
else:
ax0.plot(l, color="gray", alpha=0.5, lw=kwargs["lw"],
zorder=0) # Plots individual traces
ax0.plot(x_range,
mean_data_around_bouts + std_data_around_bouts,
color="green",
alpha=0.5,
lw=kwargs["lw"],
zorder=1)
ax0.plot(x_range,
mean_data_around_bouts - std_data_around_bouts,
color="green",
alpha=0.5,
lw=kwargs["lw"],
zorder=1)
ax0.fill_between(x_range,
mean_data_around_bouts,
(mean_data_around_bouts + std_data_around_bouts),
color="green",
alpha=0.1)
ax0.fill_between(x_range,
mean_data_around_bouts,
(mean_data_around_bouts - std_data_around_bouts),
color="green",
alpha=0.1)
y_min, y_max, round_factor = utils.generate_yticks(
data_around_major_bouts.flatten(), 0.2)
y_range = y_max - y_min
ax0.set_yticks(np.arange(y_min, y_max + round_factor, round_factor))
ax0.set_yticklabels([
"{:.0f}".format(i)
for i in np.arange(y_min, y_max + round_factor, round_factor)
],
fontsize=kwargs["fsl"])
ax0.set_ylim(y_min, y_max)
elif kwargs["peri_event"]["style"] == "average":
ax0.plot(x_range,
mean_data_around_bouts + std_data_around_bouts,
color="green",
alpha=0.3,
lw=kwargs["lw"])
ax0.plot(x_range,
mean_data_around_bouts - std_data_around_bouts,
color="green",
alpha=0.3,
lw=kwargs["lw"])
ax0.fill_between(x_range,
mean_data_around_bouts,
(mean_data_around_bouts + std_data_around_bouts),
color="green",
alpha=0.1)
ax0.fill_between(x_range,
mean_data_around_bouts,
(mean_data_around_bouts - std_data_around_bouts),
color="green",
alpha=0.1)
y_min, y_max, round_factor = utils.generate_yticks(
np.concatenate((mean_data_around_bouts + std_data_around_bouts,
mean_data_around_bouts - std_data_around_bouts)),
0.2)
y_range = y_max - y_min
ax0.set_yticks(np.arange(y_min, y_max + round_factor, round_factor))
ax0.set_yticklabels([
"{:.0f}".format(i)
for i in np.arange(y_min, y_max + round_factor, round_factor)
],
fontsize=kwargs["fsl"])
ax0.set_ylim(y_min, y_max)
# Creates a gray square on the line plot that represents the average length of a behavioral bout
patch = patches.Rectangle(
((kwargs["peri_event"]["graph_distance_pre"] + 0.5) *
kwargs["recording_sampling_rate"], -y_range * 0.1),
width=np.mean(length_major_bouts) * kwargs["recording_sampling_rate"],
height=y_range * 0.1,
color="gray",
lw=0,
alpha=0.7)
ax0.add_patch(patch) # Adds the patch to the plot
ax0.plot(
(0, len(mean_data_around_bouts)), (0, 0),
"--",
color="black",
lw=kwargs["lw"]
) # Creates a horizontal dashed line at y = 0 to signal the baseline
vline = ax0.axvline(
x=(kwargs["peri_event"]["graph_distance_pre"] + 0.5) *
kwargs["recording_sampling_rate"],
color='red',
linestyle='--',
lw=kwargs["lw"]
) # Creates a vertical dashed line at x = 0 to signal the begining of the behavioral bout
ax0.set_xticks(
np.linspace(0, ((kwargs["peri_event"]["graph_distance_pre"] +
kwargs["peri_event"]["graph_distance_post"] + 1) *
kwargs["recording_sampling_rate"]),
5)) #Generates ticks for the x axis
ax0.set_xticklabels(
np.linspace(-kwargs["peri_event"]["graph_distance_pre"],
kwargs["peri_event"]["graph_distance_post"], 5),
fontsize=kwargs["fsl"]) # Generates labels for the x axis
ax0.set_xlim(0,
len(mean_data_around_bouts)) # Sets the limits for the x axis
# ax0.set_xlabel("Time (s)", fontsize=kwargs["fsl"]) #Displays the label for the x axis
ax0.legend(
handles=[vline, patch],
labels=["Begining of bout", "Average behavioral bout length"],
loc=2,
fontsize=kwargs["fsl"]) # Displays the legend of the first figure
# =============================================================================
# Second Plot
# =============================================================================
ax1 = plt.subplot(2, 1, 2) # Creates a subplot for the second figure
if not kwargs["peri_event"]["normalize_heatmap"]:
heatmap = ax1.imshow(data_around_major_bouts,
cmap=cmap,
aspect="auto",
interpolation="none")
else:
heatmap = ax1.imshow(
data_around_major_bouts,
cmap=cmap,
aspect="auto",
norm=col.LogNorm(),
interpolation="none") # norm=matplotlib.colors.LogNorm()
ax1.axvline(x=(kwargs["peri_event"]["graph_distance_pre"] + 0.5) *
kwargs["recording_sampling_rate"],
color='red',
linestyle='--',
lw=kwargs["lw"])
ax1.set_xticks(
np.linspace(0, ((kwargs["peri_event"]["graph_distance_pre"] +
kwargs["peri_event"]["graph_distance_post"] + 1) *
kwargs["recording_sampling_rate"]),
5)) #Generates ticks for the x axis
ax1.set_xticklabels(
np.linspace(-kwargs["peri_event"]["graph_distance_pre"],
kwargs["peri_event"]["graph_distance_post"], 5),
fontsize=kwargs["fsl"]) #Generates labels for the x axis
ax1.set_xlim(0,
len(mean_data_around_bouts)) # Sets the limits for the x axis
ax1.set_xlabel("Time (s)",
fontsize=kwargs["fsl"]) # Displays the label for the x axis
ax1.set_yticks([])
ax1.set_ylim(-0.5, len(data_around_major_bouts) - 0.5)
ax1.set_ylabel("Duration of individual bouts (s)",
fontsize=kwargs["fsl"],
labelpad=20) # Displays the label for the x axis
for n, l in enumerate(length_major_bouts):
ax1.text(-len(mean_data_around_bouts) * 0.01,
n,
l,
ha="right",
va="center",
fontsize=kwargs["fsl"])
plt.gca().invert_yaxis()
cax = fig.add_axes([1, 0.1, 0.02, 0.35])
cb = plt.colorbar(heatmap, ax=ax1, cax=cax)
cb.ax.tick_params(labelsize=kwargs["fsl"])
cb.ax.get_yaxis().labelpad = 8
if kwargs["photometry_pp"]["standardize"]:
ax0.set_ylabel(
r"$\Delta$F/F (Z-Score)",
fontsize=kwargs["fsl"]) #Displays the label for the y axis
ax0.set_title(
r"$\Delta$F/F (Z-Score) in function of time before & after {0} initiation"
.format(kwargs["behavior_to_segment"]),
fontsize=kwargs["fst"]) #Displays the titel for the first figure
ax1.set_title(
r"Individual $\Delta$F/F (Z-Score) in function of time before & after {0} initiation"
.format(kwargs["behavior_to_segment"]),
fontsize=kwargs["fst"])
cb.ax.set_ylabel(r"$\Delta$F/F (Z-Score)",
rotation=270,
fontsize=kwargs["fsl"])
else:
ax0.set_ylabel(
r"$\Delta$F/F (%)",
fontsize=kwargs["fsl"]) #Displays the label for the y axis
ax0.set_title(
r"$\Delta$F/F (%) in function of time before & after {0} initiation"
.format(kwargs["behavior_to_segment"]),
fontsize=kwargs["fst"]) #Displays the titel for the first figure
ax1.set_title(
r"Individual $\Delta$F/F (%) in function of time before & after {0} initiation"
.format(kwargs["behavior_to_segment"]),
fontsize=kwargs["fst"])
cb.ax.set_ylabel(r"$\Delta$F/F (%)",
rotation=270,
fontsize=kwargs["fsl"])
plt.tight_layout()
if kwargs["save"]:
plt.savefig(os.path.join(
kwargs["save_dir"],
"Peri_Event_Plot.{0}".format(kwargs["extension"])),
dpi=200.,
bbox_inches='tight')
def standardization(x, isosbestic, calcium, **kwargs):
"""Function that performs the standardization of the corrected
signals and displays it in a plot.
Args : x (arr) = The time data in X
isosbestic (arr) = The baseline corrected isosbestic signal
calcium (arr) = The baseline corrected calcium signal
kwargs (dict) = Dictionnary with the parameters
Returns : isosbestic_standardized (arr) = The standardized isosbestic signal
calcium_standardized (arr) = The standardized calcium signal
"""
if kwargs["photometry_pp"]["standardize"]:
print("\nStarting standardization for Isosbestic and Calcium signals !")
isosbestic_standardized = (isosbestic - np.median(isosbestic)) / np.std(isosbestic) # standardization correction for isosbestic
calcium_standardized = (calcium - np.median(calcium)) / np.std(calcium) # standardization for calcium
x_max = x[-1]
if kwargs["photometry_pp"]["plots_to_display"]["standardization"]:
xticks, xticklabels, unit = utils.generate_xticks_and_labels(x_max)
fig = plt.figure(figsize=(10, 5), dpi=200.)
ax0 = plt.subplot(211)
p, = ax0.plot(x, isosbestic_standardized, alpha=0.8, c=kwargs["photometry_pp"]["purple_laser"], lw=kwargs["lw"])
ax0.plot((0, x[-1]), (0, 0), "--", color="black", lw=kwargs["lw"]) #Creates a horizontal dashed line at y = 0 to signal the baseline
ax0.set_xticks(xticks)
ax0.set_xticklabels(xticklabels, fontsize=kwargs["fsl"])
ax0.set_xlim(0, x_max)
y_min, y_max, round_factor = utils.generate_yticks(isosbestic_standardized, 0.1)
ax0.set_yticks(np.arange(y_min, y_max+round_factor, round_factor))
ax0.set_yticklabels(["{:.0f}".format(i) for i in np.arange(y_min, y_max+round_factor, round_factor)], fontsize=kwargs["fsl"])
ax0.set_ylim(y_min, y_max)
ax0.set_ylabel("z-score", fontsize=kwargs["fsl"])
ax0.legend(handles=[p], labels=["isosbestic"], loc=2, fontsize=kwargs["fsl"])
ax0.set_title("Standardization of Isosbestic and Calcium signals", fontsize=kwargs["fst"])
ax0.tick_params(axis='both', which='major', labelsize=kwargs["fsl"])
ax1 = plt.subplot(212, sharex=ax0)
b, = ax1.plot(x, calcium_standardized, alpha=0.8, c=kwargs["photometry_pp"]["blue_laser"], lw=kwargs["lw"])
ax1.plot((0, x[-1]), (0, 0), "--", color="black", lw=kwargs["lw"]) #Creates a horizontal dashed line at y = 0 to signal the baseline
ax1.set_xticks(xticks)
ax1.set_xticklabels(xticklabels, fontsize=kwargs["fsl"])
ax1.set_xlim(0, x_max)
y_min, y_max, round_factor = utils.generate_yticks(calcium_standardized, 0.1)
ax1.set_yticks(np.arange(y_min, y_max+round_factor, round_factor))
ax1.set_yticklabels(["{:.0f}".format(i) for i in np.arange(y_min, y_max+round_factor, round_factor)], fontsize=kwargs["fsl"])
ax1.set_ylim(y_min, y_max)
ax1.set_ylabel("z-score", fontsize=kwargs["fsl"])
ax1.legend(handles=[b], labels=["calcium"], loc=2, fontsize=kwargs["fsl"])
ax1.set_xlabel("Time ({0})".format(unit), fontsize=kwargs["fsl"])
ax1.tick_params(axis='both', which='major', labelsize=kwargs["fsl"])
plt.tight_layout()
if kwargs["photometry_pp"]["multicursor"]:
multi = MultiCursor(fig.canvas, [ax0, ax1], color='r', lw=1, vertOn=[ax0, ax1]) # FIXME: unused
if kwargs["save"]:
plt.savefig(os.path.join(kwargs["save_dir"], "Standardization.{0}".format(kwargs["extension"])), dpi=200.)
else:
utils.print_in_color("\nThe standardization step in skipped."
" Parameter plot_args['photometry_pp']['standardize'] == False", "RED")
isosbestic_standardized = isosbestic # standardization skipped
calcium_standardized = calcium # standardization skipped
return isosbestic_standardized, calcium_standardized
def find_baseline_and_crop(x, isosbestic, calcium, method="als", **kwargs):
"""Function that estimates the baseline of the smoothed signals and
displays it in a plot.
Args : x (arr) = The time data in X
isosbestic (arr) = The smoothed isosbestic signal (time fitted to the video)
calcium (arr) = The smoothed calcium signal (time fitted to the video)
kwargs (dict) = Dictionnary with the parameters
Returns : x (arr) = The time data in X
isosbestic (arr) = The cropped isosbestic signal
calcium (arr) = The cropped calcium signal
isosbestic_fc (arr) = The baseline for the isosbestic signal
calcium_fc (arr) = The baseline for the calcium signal
"""
print("\nStarting baseline computation for Isosbestic and Calcium signals !")
if method == "als":
x = crop_signal(x, int(kwargs["cropping_window"]))
x = x - x[0]
isosbestic = crop_signal(isosbestic, int(kwargs["cropping_window"]))
calcium = crop_signal(calcium, int(kwargs["cropping_window"]))
isosbestic_fc = baseline_asymmetric_least_squares_smoothing(isosbestic, kwargs["lambda"], kwargs["p"])
calcium_fc = baseline_asymmetric_least_squares_smoothing(calcium, kwargs["lambda"], kwargs["p"])
elif method == "ma":
x = crop_signal(x, int(kwargs["moving_average_window"]/2))
x = x - x[0]
isosbestic, isosbestic_fc = centered_moving_average(isosbestic, window=kwargs["moving_average_window"]) #moving average for isosbestic data
calcium, calcium_fc = centered_moving_average(calcium, window=kwargs["moving_average_window"]) #moving average for calcium data
x_max = x[-1]
# print("Data length : {0}".format(ut.h_m_s(x_max, add_tags=True)))
if kwargs["photometry_pp"]["plots_to_display"]["baseline_determination"]:
xticks, xticklabels, unit = utils.generate_xticks_and_labels(x_max)
fig = plt.figure(figsize=(10, 5), dpi=200.)
ax0 = plt.subplot(211)
p, = ax0.plot(x, isosbestic, alpha=0.8, c=kwargs["photometry_pp"]["purple_laser"], lw=kwargs["lw"])
ma, = ax0.plot(x, isosbestic_fc, alpha=0.8, c="orange", lw=2)
ax0.set_xticks(xticks)
ax0.set_xticklabels(xticklabels, fontsize=kwargs["fsl"])
ax0.set_xlim(0, x_max)
y_min, y_max, round_factor = utils.generate_yticks(isosbestic, 0.1)
ax0.set_yticks(np.arange(y_min, y_max+round_factor, round_factor))
ax0.set_yticklabels(["{:.0f}".format(i) for i in np.arange(y_min, y_max+round_factor, round_factor)*1000], fontsize=kwargs["fsl"])
ax0.set_ylim(y_min, y_max)
ax0.set_ylabel("mV", fontsize=kwargs["fsl"])
ax0.legend(handles=[p, ma], labels=["isosbestic", "baseline"], loc=2, fontsize=kwargs["fsl"])
ax0.set_title("Smoothed Isosbestic and Calcium signals with respective baselines", fontsize=kwargs["fst"])
ax0.tick_params(axis='both', which='major', labelsize=kwargs["fsl"])
ax1 = plt.subplot(212, sharex=ax0)
b, = ax1.plot(x, calcium, alpha=0.8, c=kwargs["photometry_pp"]["blue_laser"], lw=kwargs["lw"])
ma, = ax1.plot(x, calcium_fc, alpha=0.8, c="orange", lw=2)
ax1.set_xticks(xticks)
ax1.set_xticklabels(xticklabels, fontsize=kwargs["fsl"])
ax1.set_xlim(0, x_max)
y_min, y_max, round_factor = utils.generate_yticks(calcium, 0.1)
ax1.set_yticks(np.arange(y_min, y_max+round_factor, round_factor))
ax1.set_yticklabels(["{:.0f}".format(i) for i in np.arange(y_min, y_max+round_factor, round_factor)*1000], fontsize=kwargs["fsl"])
ax1.set_ylim(y_min, y_max)
ax1.set_ylabel("mV", fontsize=kwargs["fsl"])
ax1.legend(handles=[b, ma], labels=["calcium", "baseline"], loc=2, fontsize=kwargs["fsl"])
ax1.set_xlabel("Time ({0})".format(unit), fontsize=kwargs["fsl"])
ax1.tick_params(axis='both', which='major', labelsize=kwargs["fsl"])
plt.tight_layout()
if kwargs["photometry_pp"]["multicursor"]:
multi = MultiCursor(fig.canvas, [ax0, ax1], color='r', lw=1, vertOn=[ax0, ax1]) # FIXME: unused
if kwargs["save"]:
plt.savefig(os.path.join(kwargs["save_dir"], "Baseline_Determination.{0}"
.format(kwargs["extension"])), dpi=200.)
return x, isosbestic, calcium, isosbestic_fc, calcium_fc
def extract_raw_data(file, **kwargs):
"""Function that extracts the raw data from the csv file and displays it
in a plot.
Args : file (str) = The input photometry file for analysis
kwargs (dict) = Dictionnary with the parameters
Returns : x (arr) = The time data in X
isosbestic_adjusted (arr) = The adjusted isosbestic signal (time fitted to the video)
calcium_adjusted (arr) = The adjusted calcium signal (time fitted to the video)
"""
print("\nExtracting raw data for Isosbestic and Calcium recordings !")
photometry_data = np.load(file) # Load the NPY file
x = photometry_data[0] # time to be extracted
isosbestic_adjusted = photometry_data[1] # data compressed in time
calcium_adjusted = photometry_data[2] # data compressed in time
x_max = x[-1]
# print("Data length : {0}".format(ut.h_m_s(x_max, add_tags=True)))
if kwargs["photometry_pp"]["plots_to_display"]["raw_data"]:
xticks, xticklabels, unit = utils.generate_xticks_and_labels(x_max)
fig = plt.figure(figsize=(10, 5), dpi=200.)
ax0 = plt.subplot(211)
p, = ax0.plot(x, isosbestic_adjusted, alpha=0.8, c=kwargs["photometry_pp"]["purple_laser"], lw=kwargs["lw"])
ax0.set_xticks(xticks)
ax0.set_xticklabels(xticklabels, fontsize=kwargs["fsl"])
ax0.set_xlim(0, x_max)
y_min, y_max, round_factor = utils.generate_yticks(isosbestic_adjusted, 0.1)
ax0.set_yticks(np.arange(y_min, y_max+round_factor, round_factor))
ax0.set_yticklabels(["{:.0f}".format(i) for i in np.arange(y_min, y_max+round_factor, round_factor)*1000], fontsize=kwargs["fsl"])
ax0.set_ylim(y_min, y_max)
ax0.set_ylabel("mV", fontsize=kwargs["fsl"])
ax0.legend(handles=[p], labels=["isosbestic"], loc=2, fontsize=kwargs["fsl"])
ax0.set_title("Raw Isosbestic and Calcium signals", fontsize=kwargs["fst"])
ax0.tick_params(axis='both', which='major', labelsize=kwargs["fsl"])
ax1 = plt.subplot(212, sharex=ax0)
b, = ax1.plot(x, calcium_adjusted, alpha=0.8, c=kwargs["photometry_pp"]["blue_laser"], lw=kwargs["lw"])
ax1.set_xticks(xticks)
ax1.set_xticklabels(xticklabels, fontsize=kwargs["fsl"])
ax1.set_xlim(0, x_max)
y_min, y_max, round_factor = utils.generate_yticks(calcium_adjusted, 0.1)
ax1.set_yticks(np.arange(y_min, y_max+round_factor, round_factor))
ax1.set_yticklabels(["{:.0f}".format(i) for i in np.arange(y_min, y_max+round_factor, round_factor)*1000], fontsize=kwargs["fsl"])
ax1.set_ylim(y_min, y_max)
ax1.set_ylabel("mV", fontsize=kwargs["fsl"])
ax1.legend(handles=[b], labels=["calcium"], loc=2, fontsize=kwargs["fsl"])
ax1.set_xlabel("Time ({0})".format(unit), fontsize=kwargs["fsl"])
ax1.tick_params(axis='both', which='major', labelsize=kwargs["fsl"])
plt.tight_layout()
if kwargs["photometry_pp"]["multicursor"]:
multi = MultiCursor(fig.canvas, [ax0, ax1], color='r', lw=1, vertOn=[ax0, ax1]) # FIXME: unused
if kwargs["save"]:
plt.savefig(os.path.join(kwargs["save_dir"], "Raw_Signals.{0}".format(kwargs["extension"])), dpi=200.)
return x, isosbestic_adjusted, calcium_adjusted
def live_video_plot(video_clip, x_data, y_data, **kwargs):
def make_frame_mpl(t):
i = int(t)
if i < kwargs["video_photometry"]["display_threshold"]*kwargs["video_photometry"]["plot_acceleration"]:
try:
behavior_plot.set_data(x_data[0:i], y_data[0][0:i])
df_plot.set_data(x_data[0:i], y_data[1][0:i])
except :
print("Oups a problem occured")
last_frame = mplfig_to_npimage(live_figure)
return last_frame
else:
delta = (i/kwargs["video_photometry"]["plot_acceleration"]) - kwargs["video_photometry"]["display_threshold"]
live_ax0.set_xlim(x_data[0]+delta, x_data[0]+(i/kwargs["video_photometry"]["plot_acceleration"]))
live_ax1.set_xlim(x_data[0]+delta, x_data[0]+(i/kwargs["video_photometry"]["plot_acceleration"]))
try:
behavior_plot.set_data(x_data[0:i], y_data[0][0:i])
df_plot.set_data(x_data[0:i], y_data[1][0:i])
except:
print("Oups a problem occured")
last_frame = mplfig_to_npimage(live_figure)
return last_frame
number_subplots = len([x for x in y_data if x != []])
plt.style.use("dark_background")
live_figure = plt.figure(figsize=(10, 6), facecolor='black')
gs = live_figure.add_gridspec(nrows=number_subplots, ncols=1)
# =============================================================================
# First live axis
# =============================================================================
live_ax0 = live_figure.add_subplot(gs[0, :])
live_ax0.set_title("Behavior bouts : {0}".format(kwargs["behavior_to_segment"]), fontsize=10.)
live_ax0.set_xlim([x_data[0], x_data[0]+kwargs["video_photometry"]["display_threshold"]])
live_ax0.set_yticks([0, 1])
live_ax0.set_yticklabels(["Not behaving", "Behaving"], fontsize=10.)
live_ax0.set_ylim(-0.1, 1.1)
behavior_plot, = live_ax0.plot(x_data[0], y_data[0][0], '-', color="red", alpha=0.8, ms=1., lw=3.)
# =============================================================================
# Second live axis
# =============================================================================
live_ax1 = live_figure.add_subplot(gs[1, :])
live_ax1.set_title(r"$\Delta$F/F", fontsize=kwargs["fst"])
live_ax1.set_xlim([x_data[0], x_data[0]+kwargs["video_photometry"]["display_threshold"]])
live_ax1.set_xlabel("Time (s)", fontsize=10.)
y_min, y_max, round_factor = utils.generate_yticks(y_data[1], 0.1)
live_ax1.set_yticks(np.arange(y_min, y_max+round_factor, round_factor))
live_ax1.set_yticklabels(["{:.0f}".format(i) for i in np.arange(y_min, y_max+round_factor, round_factor)], fontsize=10.)
live_ax1.set_ylim(y_min, y_max)
df_plot, = live_ax1.plot(x_data[0], y_data[1][0], '-', color="green", alpha=1., ms=1., lw=3.)
plt.tight_layout()
animation = mpy.VideoClip(make_frame_mpl, duration=(kwargs["video_duration"] * kwargs["video_photometry"]["plot_acceleration"]))
clips = [clip.margin(2, color=[0, 0, 0]) for clip in [(video_clip.resize(kwargs["video_photometry"]["resize_video"]).speedx(kwargs["video_photometry"]["global_acceleration"])),\
animation.speedx(kwargs["video_photometry"]["global_acceleration"]).speedx(kwargs["video_photometry"]["plot_acceleration"])]]
final_clip = clips_array([[clips[0]],
[clips[1]]],
bg_color=[0, 0, 0])
final_clip.write_videofile(os.path.join(kwargs["save_dir"],"Live_Video_Plot.mp4"), fps=kwargs["video_photometry"]["live_plot_fps"])
# final_clip = final_clip.subclip(t_start=0, t_end=final_clip.duration-5)
# final_clip.write_gif(os.path.join(kwargs["save_dir"],"Live_Video_Plot.gif"), fps=kwargs["video_photometry"]["live_plot_fps"])
plt.style.use("default")