#!/usr/bin/env python3

import csv

import click
import matplotlib.pyplot as plt
import numpy as np
from sqlalchemy.orm import joinedload

from htsohm import load_config_file, db
from htsohm.db import Material

def limit_index(v, limits, sweep_points):
    if sweep_points == 1:
        return 0
    return int(round((sweep_points - 1) * (v - limits[0]) / (limits[1] - limits[0])))

@click.command()
@click.argument('config_path', type=click.Path())
@click.option('--csv-path', type=click.Path())
@click.option('--database-path', type=click.Path())
def bin_graph(config_path, csv_path=None, database_path=None):

    config = load_config_file(config_path)
    num_bins = config['number_of_convergence_bins']
    prop1range = [2.5, 5.0]
    prop2range = config['prop2range']

    if 'sweep_points' in config:
        lattice_sweep_points = sigma_sweep_points = epsilon_sweep_points = config['sweep_points']
    else:
        lattice_sweep_points = config['lattice_sweep_points']
        sigma_sweep_points = config['sigma_sweep_points']
        epsilon_sweep_points = config['epsilon_sweep_points']

    xticks = lattice_sweep_points - 1
    if xticks > 11:
        xticks = 11


    print("loading materials...")
    mats_by_lj = {}
    if csv_path:
        csvrows = np.loadtxt(csv_path, delimiter=',', skiprows=1)
        for m in csvrows:
            lj = (m[4], m[5]) # sigma, epsilon
            if lj not in mats_by_lj:
                mats_by_lj[lj] = []
            mats_by_lj[lj].append([m[1], m[7]]) # lattice a, abs volumetric loading

    else:
        db.init_database(db.get_sqlite_dbcs(database_path))
        session = db.get_session()
        mats = session.query(Material) \
            .options(joinedload("structure").joinedload("lennard_jones")) \
            .options(joinedload("gas_loading")).all()

        print("calculating material properties...")
        for m in mats:
            lj = (m.structure.lennard_jones[0].sigma, m.structure.lennard_jones[0].epsilon)
            if lj not in mats_by_lj:
                mats_by_lj[lj] = []
            print(m)
            mats_by_lj[lj].append([m.structure.a, m.gas_loading[0].absolute_volumetric_loading])

    print("plotting...")
    fig = plt.figure(figsize=(12,12), tight_layout=True)
    ax = fig.add_subplot(1, 1, 1)
    ax.set_xlim(prop1range[0], prop1range[1])
    ax.set_ylim(prop2range[0], prop2range[1])
    ax.set_xlabel("Lattice constant [Å]")
    ax.set_ylabel("Methane Loading (V [STP]/V)")
    ax.set_yticks(prop2range[1] * np.array([0.0, 0.25, 0.5, 0.75, 1.0]))
    ax.set_yticks(prop2range[1] * np.array(range(0,num_bins + 1))/num_bins, minor=True)

    ax.set_xticks(prop1range[0] + (prop1range[1] - prop1range[0]) * np.array(range(0,xticks))/(xticks - 1))
    ax.set_xticks(prop1range[0] + (prop1range[1] - prop1range[0]) * np.array(range(0,num_bins + 1))/num_bins, minor=True)

    # if show_grid:
    ax.grid(linestyle='-', color='0.8', zorder=0)


    absolute_limits_a = np.linspace(prop1range[0], prop1range[1],100)
    ml_atoms_a3_stp = 2.69e-5
    absolute_limits_ml = [ (1/a**3) / ml_atoms_a3_stp for a in absolute_limits_a]
    ax.plot(absolute_limits_a, absolute_limits_ml, lw=3, linestyle="--", color="black", zorder=15, label="all sites filled")

    for (sig, eps), a_ml in mats_by_lj.items():
        a_ml = np.array(a_ml)
        # sig_index = limit_index(sig, config['structure_parameters']['sigma_limits'], sigma_sweep_points)
        eps_index = limit_index(eps, config['structure_parameters']['epsilon_limits'], epsilon_sweep_points)
        # print(sig, eps, marker_index)


        alpha = (eps_index + 1) / epsilon_sweep_points
        if eps_index + 1 == epsilon_sweep_points:
            label = "sigma = %4.3f" % sig
        else:
            label = None

        ax.plot(a_ml[:,0], a_ml[:,1], lw=3, zorder=20, alpha=alpha, label=label)

    ax.legend()
    ax.set_title("Methane loading vs lattice constant. Lines colored by sigma. \nLine transparency shows epsilon (no transparency is highest epsilon value; highest transparency is lowest epsilon value)")

    fig.savefig("sig_eps_a_ml.png")
    plt.close(fig)


if __name__ == '__main__':
    bin_graph()

@@ -722,17 +722,64 @@
 e = 
-%5B2.5, 5.0
+config%5B'structure_parameters'%5D%5B'lattice_constant_limits'
 %5D%0A  

use lattice_constant limits for instead of hardcooded prop range