cooperative_channels_in_biological_neurons_via_dynamic_clamp/scripts/generate_report.py

import numpy
import pandas
from jinja2 import Environment, FileSystemLoader
from weasyprint import HTML

from tools.helper import get_filters
from tools.definitions import OUTPUT_FOLDER, HELPER_TABLE_FOLDER, STIMULATION_METADATA_FILTERED


def yes(bool_array):
    if numpy.isnan(bool_array.values[0]):
        return numpy.NaN
    else:
        return numpy.sum(bool_array.values.astype(numpy.int))


def no(bool_array):
    no_yes = yes(bool_array)
    if numpy.isnan(no_yes):
        return numpy.NaN
    else:
        return len(bool_array) - no_yes


# Prepare template
env = Environment(loader=FileSystemLoader('.'))
REPORT_HTML_TEMPLATE = "scripts/tools/report.html"
template = env.get_template(REPORT_HTML_TEMPLATE)

path_to_filtered_stimulus_file = OUTPUT_FOLDER+HELPER_TABLE_FOLDER+STIMULATION_METADATA_FILTERED
all_protocols = pandas.read_csv(path_to_filtered_stimulus_file, index_col="stimulation_id")

protocols_for_persistent_activity = all_protocols[get_filters(all_protocols) & (all_protocols["is_control"] == False)]
protocols_for_control = all_protocols[get_filters(all_protocols) & (all_protocols["is_control"] == True)]
protocols_filtered = all_protocols[get_filters(all_protocols)==False]

overview_protocols = pandas.DataFrame(protocols_for_persistent_activity.groupby(["protocol_type", "pulse_number"]).agg({
    "was_successful": [yes, no]}))

protocols = []
overview_plots=[]
for name, df in protocols_for_persistent_activity.groupby(["protocol_type", "pulse_number"]):
    protocol_dict = {
        "type": "{}-{}-success".format(name[0], name[1]),
        "stim_ids": df[df["was_successful"] == True].index.values,
    }
    protocols.append(protocol_dict)
    protocol_dict = {
        "type": "{}-{}-fail".format(name[0], name[1]),
        "stim_ids": df[df["was_successful"] == False].index.values,
    }
    protocols.append(protocol_dict)
    overview_plots.append("{}-{}".format(name[0], name[1]))


for name, df in protocols_for_control.groupby(["protocol_type", "pulse_number"]):
    protocol_dict = {
        "type": "{}-{}-control".format(name[0], name[1]),
        "stim_ids": df.index.values,
    }
    protocols.append(protocol_dict)

for name, df in protocols_filtered.groupby(["protocol_type", "pulse_number"]):
    protocol_dict = {
        "type": "{}-{}-reject".format(name[0], name[1]),
        "stim_ids": df.index.values,
    }
    protocols.append(protocol_dict)

template_vars = {
    "total_number_of_cells": len(all_protocols["cell_id"].unique()),
    "total_number_of_protocols": len(all_protocols),
    "number_of_analysed_protocols": len(protocols_for_persistent_activity)+len(protocols_for_control),
    "number_cooperative": len(protocols_for_persistent_activity),
    "number_independent": len(protocols_for_control),
    "number_of_filtered_protocols": len(protocols_filtered),

    "overview_table": overview_protocols.to_html(),
    "protocols": protocols,
    "overview_plots": overview_plots
}

html_out = template.render(template_vars)
path_to_report = OUTPUT_FOLDER+"report.pdf"
HTML(string=html_out, base_url='.').write_pdf(path_to_report, stylesheets=["scripts/tools/style.css"])