def run(self):
self.create_dir_in_workspace('reports')
frequency_plot_data = self.get_passed_object('frequency_plot')
centralized_frequency_plot_data = self.get_passed_object('centralized_frequency_plot')
frequency_region_plot_data = self.get_passed_object('frequency_region_plot')
frequency_frequency_plot_data = self.get_passed_object('frequency_frequency_plot')
low_freq_duration_plot_data = self.get_passed_object('low_freq_duration_plot')
high_freq_duration_plot_data = self.get_passed_object('high_freq_duration_plot')
low_freq_amplitude_plot_data = self.get_passed_object('low_freq_amplitude_plot')
high_freq_amplitude_plot_data = self.get_passed_object('high_freq_amplitude_plot')
# panel_plot = PanelPlot(xfigsize=11, yfigsize=11, i_max=1, j_max=1, title='', ytitle=self.params.output_title, ytitle_fontsize=16, wspace=0.3, hspace=0.3)
#
# panel_plot.add_plot_data_collection(0, 0, plot_data_collection=pdc)
#
# plot = panel_plot.generate_plot()
#
# plot_out_fname = self.get_path_to_resource_in_workspace('reports/ps_frequency_aggregate_plots.pdf')
#
# plot.savefig(plot_out_fname, dpi=300, bboxinches='tight')
pdc = PlotDataCollection(legend_on=True)
pdc.xlabel = 'Pulse Frequency (Hz)'
pdc.xlabel_fontsize = 16
for v,p in frequency_plot_data.iteritems():
p.xhline_pos=0.0
pdc.add_plot_data(p)
# panel_plot = PanelPlot(xfigsize=15, yfigsize=7.5, i_max=1, j_max=3, title='', ytitle=self.params.output_title, wspace=0.3, hspace=0.3)
panel_plot = PanelPlot(xfigsize=18.5, yfigsize=7.5, i_max=1, j_max=3, title='', ytitle=self.params.output_title, labelsize=20, ytitle_fontsize = 20)
min_y_list =[]
max_y_list =[]
r =pdc.get_yrange()
min_y_list.append(r[0])
max_y_list.append(r[1])
r =frequency_region_plot_data.get_yrange()
min_y_list.append(r[0])
max_y_list.append(r[1])
r =frequency_frequency_plot_data.get_yrange()
min_y_list.append(r[0])
max_y_list.append(r[1])
y_min = np.min(min_y_list)
y_max = np.max(max_y_list)
r = y_max - y_min
y_min -= 0.05*r
y_max += 0.15*r
pdc.ylim=[y_min,y_max]
frequency_region_plot_data.ylim=[y_min,y_max]
frequency_frequency_plot_data.ylim=[y_min,y_max]
pdc.xhline_pos = 0.0
frequency_region_plot_data.xhline_pos = 0.0
frequency_frequency_plot_data.xhline_pos = 0.0
# label fontsize
pdc.xlabel_fontsize = 20
pdc.ylabel_fontsize = 20
frequency_region_plot_data.xlabel_fontsize = 20
frequency_region_plot_data.ylabel_fontsize = 20
frequency_frequency_plot_data.xlabel_fontsize = 20
frequency_frequency_plot_data.ylabel_fontsize = 20
print '[y_min,y_max]=',[y_min,y_max]
panel_plot.add_plot_data_collection(0, 0, plot_data_collection=pdc)
panel_plot.add_plot_data(0, 1, plot_data=frequency_region_plot_data)
panel_plot.add_plot_data(0, 2, plot_data=frequency_frequency_plot_data)
plot = panel_plot.generate_plot()
plot_out_fname = self.get_path_to_resource_in_workspace('reports/ps_frequency_projection_plots.pdf')
plot.savefig(plot_out_fname, dpi=300, bboxinches='tight')
panel_plot = PanelPlot(i_max=1, j_max=1, title='', ytitle=self.params.output_title, ytitle_fontsize=24, wspace=0.3, hspace=0.3)
pdc = PlotDataCollection(legend_on=True)
pdc.xlabel = 'Duration (ms)'
pdc.xlabel_fontsize = 24
for v,p in low_freq_duration_plot_data.iteritems():
p.xhline_pos=0.0
pdc.add_plot_data(p)
panel_plot.add_plot_data_collection(0, 0, plot_data_collection=pdc)
plot = panel_plot.generate_plot()
plot_out_fname = self.get_path_to_resource_in_workspace('reports/ps_duration_low_aggregate_plots.pdf')
plot.savefig(plot_out_fname, dpi=300, bboxinches='tight')
panel_plot = PanelPlot(i_max=1, j_max=1, title='', ytitle=self.params.output_title, ytitle_fontsize=24, wspace=0.3, hspace=0.3)
pdc = PlotDataCollection(legend_on=True)
pdc.xlabel = 'Duration (ms)'
pdc.xlabel_fontsize = 24
for v,p in high_freq_duration_plot_data.iteritems():
p.xhline_pos=0.0
pdc.add_plot_data(p)
panel_plot.add_plot_data_collection(0, 0, plot_data_collection=pdc)
plot = panel_plot.generate_plot()
plot_out_fname = self.get_path_to_resource_in_workspace('reports/ps_duration_high_aggregate_plots.pdf')
plot.savefig(plot_out_fname, dpi=300, bboxinches='tight')
panel_plot = PanelPlot(i_max=1, j_max=1, title='', ytitle=self.params.output_title, ytitle_fontsize=24, wspace=0.3, hspace=0.3)
pdc = PlotDataCollection(legend_on=True)
pdc.xlabel = 'Amplitude (mA)'
pdc.xlabel_fontsize = 24
for v,p in low_freq_amplitude_plot_data.iteritems():
p.xhline_pos=0.0
pdc.add_plot_data(p)
panel_plot.add_plot_data_collection(0, 0, plot_data_collection=pdc)
plot = panel_plot.generate_plot()
plot_out_fname = self.get_path_to_resource_in_workspace('reports/ps_amplitude_low_aggregate_plots.pdf')
plot.savefig(plot_out_fname, dpi=300, bboxinches='tight')
panel_plot = PanelPlot(i_max=1, j_max=1, title='', ytitle=self.params.output_title, ytitle_fontsize=24, wspace=0.3, hspace=0.3)
pdc = PlotDataCollection(legend_on=True)
pdc.xlabel = 'Amplitude (mA)'
pdc.xlabel_fontsize = 24
for v,p in high_freq_amplitude_plot_data.iteritems():
p.xhline_pos=0.0
pdc.add_plot_data(p)
panel_plot.add_plot_data_collection(0, 0, plot_data_collection=pdc)
plot = panel_plot.generate_plot()
plot_out_fname = self.get_path_to_resource_in_workspace('reports/ps_amplitude_high_aggregate_plots.pdf')
plot.savefig(plot_out_fname, dpi=300, bboxinches='tight')
def run(self):
subject = self.pipeline.subject
task = self.pipeline.task
self.create_dir_in_workspace("reports")
session_summary_array = self.get_passed_object("session_summary_array")
serial_positions = np.arange(1, 13)
for session_summary in session_summary_array:
panel_plot = PanelPlot(
xfigsize=15, yfigsize=7.5, i_max=1, j_max=2, title="", wspace=0.3, hspace=0.3, labelsize=20
)
pd1 = PlotData(
x=serial_positions,
y=session_summary.prob_recall,
xlim=(0, 12),
ylim=(0.0, 1.0),
xlabel="Serial position\n(a)",
ylabel="Probability of recall",
)
pd1.xlabel_fontsize = 20
pd1.ylabel_fontsize = 20
pd2 = PlotData(
x=serial_positions,
y=session_summary.prob_first_recall,
xlim=(0, 12),
ylim=(0.0, 1.0),
xlabel="Serial position\n(b)",
ylabel="Probability of first recall",
)
pd2.xlabel_fontsize = 20
pd2.ylabel_fontsize = 20
# panel_plot.add_plot_data(0, 0, plot_data=pd1)
# panel_plot.add_plot_data(0, 1, plot_data=pd2)
#
# plot = panel_plot.generate_plot()
panel_plot.add_plot_data(0, 0, plot_data=pd1)
panel_plot.add_plot_data(0, 1, plot_data=pd2)
plot = panel_plot.generate_plot()
plot_out_fname = self.get_path_to_resource_in_workspace(
"reports/" + task + "-" + subject + "-prob_recall_plot_" + session_summary.name + ".pdf"
)
plot.savefig(plot_out_fname, dpi=300, bboxinches="tight")
if task == "RAM_CatFR1":
panel_plot = PanelPlot(xfigsize=6.0, yfigsize=6.0, i_max=1, j_max=1, title="", wspace=0.3, hspace=0.3)
pd = BarPlotData(
x=[0, 1],
y=[session_summary.irt_within_cat, session_summary.irt_between_cat],
ylabel="IRT (msec)",
x_tick_labels=["Within Cat", "Between Cat"],
barcolors=["grey", "grey"],
barwidth=0.5,
)
panel_plot.add_plot_data(0, 0, plot_data=pd)
plot = panel_plot.generate_plot()
plot_out_fname = self.get_path_to_resource_in_workspace(
"reports/" + task + "-" + subject + "-irt_plot_" + session_summary.name + ".pdf"
)
plot.savefig(plot_out_fname, dpi=300, bboxinches="tight")
panel_plot = PanelPlot(
xfigsize=10.0,
yfigsize=10.0,
i_max=1,
j_max=1,
title="",
xlabel="List",
ylabel="# of items",
labelsize=20,
)
pdc = PlotDataCollection()
# ----------------- FORMATTING
pdc.xlabel = "List number"
pdc.xlabel_fontsize = 20
pdc.ylabel = "# recalled words"
pdc.ylabel_fontsize = 20
n_lists = len(session_summary.n_stims_per_list)
print "Number of lists", n_lists
bpd_1 = BarPlotData(x=np.arange(n_lists), y=session_summary.n_stims_per_list, title="", alpha=0.1)
pd_1 = PlotData(
x=np.where(session_summary.is_stim_list)[0],
y=session_summary.n_recalls_per_list[session_summary.is_stim_list],
title="",
linestyle="",
color="red",
marker="o",
markersize=20,
)
pd_2 = PlotData(
x=np.where(~session_summary.is_stim_list)[0],
y=session_summary.n_recalls_per_list[~session_summary.is_stim_list],
title="",
linestyle="",
color="blue",
marker="o",
markersize=20,
)
print "np.where(session_summary.is_stim_list)[0]=", np.where(session_summary.is_stim_list)[0]
print "np.where(~session_summary.is_stim_list)[0]=", np.where(~session_summary.is_stim_list)[0]
pdc.add_plot_data(pd_1)
pdc.add_plot_data(pd_2)
pdc.add_plot_data(bpd_1)
panel_plot.add_plot_data_collection(0, 0, plot_data_collection=pdc)
plot = panel_plot.generate_plot()
plot_out_fname = self.get_path_to_resource_in_workspace(
"reports/" + task + "-" + subject + "-stim_and_recall_plot_" + session_summary.name + ".pdf"
)
plot.savefig(plot_out_fname, dpi=300, bboxinches="tight")
cumulative_summary = self.get_passed_object("cumulative_summary")
panel_plot = PanelPlot(xfigsize=15, yfigsize=7.5, i_max=1, j_max=2, title="", wspace=0.3, hspace=0.3)
pd1 = PlotData(
x=serial_positions,
y=cumulative_summary.prob_recall,
xlim=(0, 12),
ylim=(0.0, 1.0),
xlabel="Serial position\n(a)",
ylabel="Probability of recall",
)
pd2 = PlotData(
x=serial_positions,
y=cumulative_summary.prob_first_recall,
xlim=(0, 12),
ylim=(0.0, 1.0),
xlabel="Serial position\n(b)",
ylabel="Probability of first recall",
)
panel_plot.add_plot_data(0, 0, plot_data=pd1)
panel_plot.add_plot_data(0, 1, plot_data=pd2)
plot = panel_plot.generate_plot()
plot_out_fname = self.get_path_to_resource_in_workspace(
"reports/" + task + "-" + subject + "-prob_recall_plot_combined.pdf"
)
plot.savefig(plot_out_fname, dpi=300, bboxinches="tight")
if task == "RAM_CatFR1":
panel_plot = PanelPlot(xfigsize=6.0, yfigsize=6.0, i_max=1, j_max=1, title="", wspace=0.3, hspace=0.3)
pd = BarPlotData(
x=[0, 1],
y=[cumulative_summary.irt_within_cat, cumulative_summary.irt_between_cat],
ylabel="IRT (msec)",
x_tick_labels=["Within Cat", "Between Cat"],
barcolors=["grey", "grey"],
barwidth=0.5,
)
panel_plot.add_plot_data(0, 0, plot_data=pd)
plot = panel_plot.generate_plot()
plot_out_fname = self.get_path_to_resource_in_workspace(
"reports/" + task + "-" + subject + "-irt_plot_combined.pdf"
)
plot.savefig(plot_out_fname, dpi=300, bboxinches="tight")
def run(self):
subject = self.pipeline.subject
task = self.pipeline.task
self.create_dir_in_workspace('reports')
session_summary_array = self.get_passed_object('session_summary_array')
serial_positions = np.arange(1,13)
for session_summary in session_summary_array:
panel_plot = PanelPlot(xfigsize=15, yfigsize=7.5, i_max=1, j_max=2, title='', wspace=0.3, hspace=0.3, labelsize=20)
pd1 = PlotData(x=serial_positions, y=session_summary.prob_recall, xlim=(0,12), ylim=(0.0, 1.0), xlabel='Serial position\n(a)', ylabel='Probability of recall')
pd1.xlabel_fontsize = 20
pd1.ylabel_fontsize = 20
pd2 = PlotData(x=serial_positions, y=session_summary.prob_first_recall, xlim=(0,12), ylim=(0.0, 1.0), xlabel='Serial position\n(b)', ylabel='Probability of first recall')
pd2.xlabel_fontsize = 20
pd2.ylabel_fontsize = 20
# panel_plot.add_plot_data(0, 0, plot_data=pd1)
# panel_plot.add_plot_data(0, 1, plot_data=pd2)
#
# plot = panel_plot.generate_plot()
panel_plot.add_plot_data(0, 0, plot_data=pd1)
panel_plot.add_plot_data(0, 1, plot_data=pd2)
plot = panel_plot.generate_plot()
plot_out_fname = self.get_path_to_resource_in_workspace('reports/' + task + '-' + subject + '-prob_recall_plot_' + session_summary.name + '.pdf')
plot.savefig(plot_out_fname, dpi=300, bboxinches='tight')
if task == 'RAM_CatFR1':
panel_plot = PanelPlot(xfigsize=6.0, yfigsize=6.0, i_max=1, j_max=1, title='', wspace=0.3, hspace=0.3)
pd = BarPlotData(x=[0,1], y=[session_summary.irt_within_cat, session_summary.irt_between_cat], ylabel='IRT (msec)', x_tick_labels=['Within Cat', 'Between Cat'], barcolors=['grey','grey'], barwidth=0.5)
panel_plot.add_plot_data(0, 0, plot_data=pd)
plot = panel_plot.generate_plot()
plot_out_fname = self.get_path_to_resource_in_workspace('reports/' + task + '-' + subject + '-irt_plot_' + session_summary.name + '.pdf')
plot.savefig(plot_out_fname, dpi=300, bboxinches='tight')
panel_plot = PanelPlot(xfigsize=10.0, yfigsize=10.0, i_max=1, j_max=1, title='', xlabel='List', ylabel='# of items', labelsize=20)
pdc = PlotDataCollection()
#----------------- FORMATTING
pdc.xlabel = 'List number'
pdc.xlabel_fontsize = 20
pdc.ylabel ='# recalled words'
pdc.ylabel_fontsize = 20
n_lists = len(session_summary.n_stims_per_list)
print 'Number of lists', n_lists
bpd_1 = BarPlotData(x=np.arange(n_lists), y=session_summary.n_stims_per_list, title='', alpha=0.1)
pd_1 = PlotData(x=np.where(session_summary.is_stim_list)[0], y=session_summary.n_recalls_per_list[session_summary.is_stim_list],
title='', linestyle='', color='red', marker='o',markersize=20)
pd_2 = PlotData(x=np.where(~session_summary.is_stim_list)[0], y=session_summary.n_recalls_per_list[~session_summary.is_stim_list],
title='', linestyle='', color='blue', marker='o',markersize=20)
print 'np.where(session_summary.is_stim_list)[0]=',np.where(session_summary.is_stim_list)[0]
print 'np.where(~session_summary.is_stim_list)[0]=',np.where(~session_summary.is_stim_list)[0]
pdc.add_plot_data(pd_1)
pdc.add_plot_data(pd_2)
pdc.add_plot_data(bpd_1)
panel_plot.add_plot_data_collection(0, 0, plot_data_collection=pdc)
plot = panel_plot.generate_plot()
plot_out_fname = self.get_path_to_resource_in_workspace('reports/' + task + '-' + subject + '-stim_and_recall_plot_' + session_summary.name + '.pdf')
plot.savefig(plot_out_fname, dpi=300, bboxinches='tight')
cumulative_summary = self.get_passed_object('cumulative_summary')
panel_plot = PanelPlot(xfigsize=15, yfigsize=7.5, i_max=1, j_max=2, title='', wspace=0.3, hspace=0.3)
pd1 = PlotData(x=serial_positions, y=cumulative_summary.prob_recall, xlim=(0, 12), ylim=(0.0, 1.0), xlabel='Serial position\n(a)', ylabel='Probability of recall')
pd2 = PlotData(x=serial_positions, y=cumulative_summary.prob_first_recall, xlim=(0, 12), ylim=(0.0, 1.0), xlabel='Serial position\n(b)', ylabel='Probability of first recall')
panel_plot.add_plot_data(0, 0, plot_data=pd1)
panel_plot.add_plot_data(0, 1, plot_data=pd2)
plot = panel_plot.generate_plot()
plot_out_fname = self.get_path_to_resource_in_workspace('reports/' + task + '-' + subject + '-prob_recall_plot_combined.pdf')
plot.savefig(plot_out_fname, dpi=300, bboxinches='tight')
if task == 'RAM_CatFR1':
panel_plot = PanelPlot(xfigsize=6.0, yfigsize=6.0, i_max=1, j_max=1, title='', wspace=0.3, hspace=0.3)
pd = BarPlotData(x=[0,1], y=[cumulative_summary.irt_within_cat, cumulative_summary.irt_between_cat], ylabel='IRT (msec)', x_tick_labels=['Within Cat', 'Between Cat'], barcolors=['grey','grey'], barwidth=0.5)
panel_plot.add_plot_data(0, 0, plot_data=pd)
plot = panel_plot.generate_plot()
plot_out_fname = self.get_path_to_resource_in_workspace('reports/' + task + '-' + subject + '-irt_plot_combined.pdf')
plot.savefig(plot_out_fname, dpi=300, bboxinches='tight')