#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed May 20 13:32:14 2026

@author: jamesszalkie
"""
import numpy as np
import pandas as pd
from scipy.interpolate import interp1d
import uproot
import pycatima as catima
from scipy.integrate import cumulative_trapezoid
import matplotlib
matplotlib.use("Agg")
import matplotlib.pyplot as plt
import cmd
import shlex
import textwrap
import readline
import atexit
import os
import periodictable as pt
import re
from matplotlib.colors import PowerNorm

#Run program from terminal or IDE, and prompts will provide user steps

#histfile = os.path.expanduser("~/.uproot_shell_history")

#try:
#    readline.read_history_file(histfile)
#except FileNotFoundError:
#    pass

#atexit.register(readline.write_history_file, histfile)

#data = [z, mass_u, maximum MeV, name]
alpha_data = [2, 4.0026, 40, "alpha"]
proton_data = [1, 1.0078, 20, "proton"]
deuteron_data = [1, 2.014102, 30, "deuteron"]

dA = 3.2 #cm
dC = 4.2 #cm
dsx3 = 8.8 #cm

particles = {
    "alpha": alpha_data,
    "proton": proton_data,
    "deuteron": deuteron_data
}

interp_cache = {}

def make_E_vs_x(z, mass_u, emax_mev, label, npoints, P_TORR, TEMP_K):
    # GAS SETUP
    R = 8.3144
    P_TORR = 400
    TEMP_K = 293.15
    R = 8.3144

    # Gas density
    p_pa = P_TORR * 133.322
    molar_density = p_pa / (R * TEMP_K)

    m_he = 4.0026
    m_c  = 12.0000
    m_o  = 15.9949

    m_mix_avg = (0.96 * m_he) + (0.04 * (m_c + 2*m_o))

    rho_g_cm3 = (molar_density * m_mix_avg) / 1e6

    print(f"Gas density = {rho_g_cm3:.6e} g/cm^3")

    # MATERIAL
    material_def = [
        (m_he, 2, 0.96),
        (m_c,  6, 0.04),
        (m_o,  8, 0.08)
    ]

    gas_mix = catima.Material(material_def)
    gas_mix.density(rho_g_cm3)

    projectile = catima.Projectile(mass_u, z)

    # Energy grid
    E = np.linspace(0.01, emax_mev, npoints)

    # Stopping power array
    S_mass = np.zeros_like(E)

    for i, energy in enumerate(E):

        projectile.T(energy / mass_u)

        # MeV / (g/cm^2)
        S_mass[i] = catima.dedx(projectile, gas_mix)

    # Convert to MeV/cm
    S_linear = S_mass * rho_g_cm3

    # Sort descending energy
    sort_idx = np.argsort(E)[::-1]

    E = E[sort_idx]
    S_linear = S_linear[sort_idx]

    # Integrate dx/dE = 1/S(E)
    invS = 1.0 / S_linear

    x = cumulative_trapezoid(
        invS,
        E,
        initial=0
    )

    x = -x

    # Output table
    output = pd.DataFrame({
        "Distance_cm": x,
        "Energy_MeV": E
    })

    outfile = f"E_vs_x_{label}.dat"

    output.to_csv(
        outfile,
        sep='\t',
        index=False
    )

    print(f"Saved: {outfile}")

    return x, E

   #Generate energy loss tables from file
def load_table(filename):
    """
    Load table with columns:
        x(cm)   E(MeV)

    Returns:
        x_array, E_array
    """

    data = pd.read_csv(
        filename,
        sep=r'\s+',
        comment="#",
        header=None,
        skiprows=1
    )

    x = data.iloc[:, 0].to_numpy()
    E = data.iloc[:, 1].to_numpy()

    return x, E

def get_interpolators(particle):

    if particle in interp_cache:
        return interp_cache[particle]

    filename = f"E_vs_x_{particle}.dat"

    x, E = load_table(filename)

    E_of_x = interp1d(
        x,
        E,
        bounds_error=False,
        fill_value=0.0
    )

    x_of_E = interp1d(
        E[::-1],
        x[::-1],
        bounds_error=False,
        fill_value="extrapolate"
    )

    interp_cache[particle] = (E_of_x, x_of_E)

    return E_of_x, x_of_E

def energy_loss(particle, Ei, dl):

    E_of_x, x_of_E = get_interpolators(particle)

    xi = x_of_E(Ei)

    xf = xi + dl

    Ef = E_of_x(xf)

    return np.maximum(Ef, 0.0)

#def energy_loss_angular(particle, Ei, theta):
    
def energy_reconstruction(particle, Ef, dl):

    E_of_x, x_of_E = get_interpolators(particle)

    xf = x_of_E(Ef)

    xi = xf - dl

    Ei = E_of_x(xi)

    return np.maximum(Ei, 0.0)

def energy_distance(particle, Ei, Ef):

    _, x_of_E = get_interpolators(particle)

    xi = x_of_E(Ei)

    xf = x_of_E(Ef)

    return np.abs(xf - xi)


def resolve_particle(name):
    name = name.lower().strip().rstrip("s")
    if name in particles:
        return particles[name]
    match = re.match(r"([a-zA-Z]+)[-\s]?(\d+)", name)
    if match:
        element_symbol = match.group(1).capitalize()
        A = int(match.group(2))

        try:
            element = pt.elements.symbol(element_symbol)
            isotope = element[A]   # <-- THIS is the correct way

            return (
                isotope.number,   # Z
                isotope.mass,     # mass in u
                30.0,
                f"{element_symbol}-{A}"
            )
        except Exception:
            raise ValueError(f"Unknown isotope: {name}")
    try:
        elem = pt.elements.symbol(name.capitalize())
        return elem.number, elem.mass, 30.0, name
    except Exception:
        raise ValueError(f"Unknown particle/isotope: {name}")
    
    
def update_plot_data(name, values):
    for i, (existing_name, _) in enumerate(plot_data):
        if existing_name == name:
            plot_data[i] = (name, values)
            return
    plot_data.append((name, values))
    
def process_file(filename):

    tree = uproot.open(filename)["tree"]

    branches = ["Tb", "thetab", "sx3Z"]

    data = tree.arrays(branches, library="np")

    Ei = data["Tb"]
    theta = np.radians(data["thetab"])
    sx3Z = data["sx3Z"]

    mask = np.sin(theta) != 0

    Ei = Ei[mask]
    theta = theta[mask]
    sx3Z = sx3Z[mask]

    sin_theta = np.sin(theta)

    radii = np.array([3.2, 4.2, 6.6])

    dA = radii[0] / sin_theta
    dC = radii[1] / sin_theta
    dsx3 = radii[2] / sin_theta

    # Determine particle from filename
    lower = filename.lower()

    if "proton" in lower:
        particle = "proton"
    elif "alpha" in lower:
        particle = "alpha"
    else:
        particle = "proton"

    print(f"Computing energies for {particle}...")

    EA = energy_loss(particle, Ei, dA)
    EC = energy_loss(particle, Ei, dC)
    Esx3 = energy_loss(particle, Ei, dsx3)

    Elost = Ei - Esx3
    Eprop = EA - EC

    return {
        "particle": particle,
        "Ei": Ei,
        "sx3Z": sx3Z,
        "EA": EA,
        "EC": EC,
        "Esx3": Esx3,
        "Elost": Elost,
        "Eprop": Eprop
    }

class MyInteractiveApp(cmd.Cmd):
    def __init__(self):
        super().__init__()
        # Initial value set when the script starts
        self.buckets = 500
        self.T = 293.15
        self.P = 400
        self.temp_particle = [0, 0.0, 0.0, ""]
        self.rootFile = "SimAnasen1.root"
        self.file = None
        self.initialize_file()
        self.tree = None
        print("-" * 30)
        print("INTERACTIVE SHELL STARTED")
        self.print_params()
        print("Type 'help' for commands.")
        print("Type 'exit' to end program")
        print("-" * 30)
        
    def print_params(self):
        """Helper method to display current state"""
        print(f"Current Parameters: T={self.T} K, P={self.P} Torr")
        
    def initialize_file(self):
        """Load in default root file for anasen"""
        try:
            self.file = uproot.open(f"../Armory/{self.rootFile}")
        except:
            self.file = None
            print("\nATTENTION: Root file not found, continue without uproot functions or uproot file manually")

        
    #intro = "Interactive Shell Started. Type 'help' to see commands."
    prompt = ">> "
    
        
    def default(self, line):
        # Check if the command starts with our multi-word phrase
        if line.startswith("make table "):
            # Extract everything after "make table "
            args = line[len("make table "):].strip()
            self.do_make_table(args)
        elif line.startswith("set t") or line.startswith("Set T") or line.startswith("set T") or line.startswith("Set t"):
            args = line[len("set t "):].strip()
            self.do_set_T(args)
        elif line.startswith("set p") or line.startswith("Set P") or line.startswith("set P") or line.startswith("Set p"):
            args = line[len("set p "):].strip()
            self.do_set_P(args)
        elif line.startswith("set buckets") or line.startswith("Set Buckets") or line.startswith("set Buckets") or line.startswith("Set buckets"):
            args = line[len("set buckets "):].strip()
            self.do_set_Buckets(args)
        elif line.startswith("energy loss") or line.startswith("Energy Loss") or line.startswith("Energy loss"):
            args = line[len("energy loss "):].strip()
            self.do_energy_loss(args)
        elif line.startswith("energy reconstruction") or line.startswith("Energy Reconstruction") or line.startswith("Energy reconstruction"):
            args = line[len("energy reconstruction "):].strip()
            self.do_energy_reconstruction(args)
        elif line.startswith("energy distance") or line.startswith("Energy Distance") or line.startswith("Energy distance"):
            args = line[len("energy distance "):].strip()
            self.do_energy_distance(args)
        else:
            print(f"*** Unknown syntax: {line}")
            
    def do_T(self, arg):
        """Print value of T"""
        print(self.T)
        
    def do_Buckets(self, arg):
        """print number of histogram buckets and points"""
        print(self.buckets)
        
    def do_P(self, arg):
        """Print value of P (pressure)"""
        print(self.P)
        
    def do_make_particle(self, arg):
        """Enter parameters for new particle to be given to catyma system
        Ex: >> make_particle <z> <mass u> <maximum E value> <particle name>"""
        args = shlex.split(arg)
        z = int(args[0])
        mass_u = float(args[1])
        emax_mev = float(args[2]) 
        particle = args[3]
        self.temp_particle = [z, mass_u, emax_mev, particle]
        print(f"New particle '{particle}': z = {z}, mass_u = {mass_u}, emax_mev = {emax_mev}")  
            
    def do_set_T(self, arg):
        """Changes the value of T. Usage: set_t 300"""
        try:
            self.T = float(arg)
            print(f"T has been updated to {self.T}")
        except ValueError:
            print("Please enter a valid number for T.")
            
    def do_set_P(self, arg):
        """Changes the value of P in Torr. Usage: set_ 400"""
        try:
            self.P = float(arg)
            print(f"P has been updated to {self.P}")
        except ValueError:
            print("Please enter a valid number for P.")
            
    def do_set_Buckets(self, arg):
        """Changes the value of buckets"""
        try:
            self.buckets = int(arg)
            print(f"Number of buckets has been updated to {self.buckets}")
        except ValueError:
            print("Please enter a valid number of buckets.")

    def do_exit(self, arg):
        """Exits the application."""
        print("Closing application...")
        return True  # Returning True stops the cmdloop()
    
    def do_make_table(self, arg):
        """Create E vs X tables for particle, or isotopes
        Ex: >> make table proton <max energy (optional) >
        Ex: >> make table Co60 <max energy (optional) >
        Ex: >> make table N17 <max energy (optional) >"""
        try:
            args = shlex.split(arg)
    
            if not args:
                print("Please enter desired reaction particle")
                return
    
            name = args[0]
    
            if len(args) > 1:
                emax_mev = float(args[1])
            else:
                emax_mev = None
    
            z, mass_u, default_emax, label = resolve_particle(name)
    
            if emax_mev is None:
                emax_mev = default_emax
    
            x, E = make_E_vs_x(
                z,
                mass_u,
                emax_mev,
                label,
                self.buckets,
                self.P,
                self.T
            )
    
            plt.figure(figsize=(8,6))
            plt.plot(x, E)
            
            plt.xlabel("Distance (cm)")
            plt.ylabel("Energy (MeV)")
            plt.title(f"Energy Loss Curve {label.capitalize()}")
            plt.grid(True)
            textstr = f"T = {self.T:.2f} K\nP = {self.P:.2f} Torr"
            
            plt.gca().text(
                0.02, 0.02,
                textstr,
                transform=plt.gca().transAxes,
                fontsize=10,
                verticalalignment='bottom',
                bbox=dict(boxstyle="round", facecolor="white", alpha=0.7)
            )
            
            plt.tight_layout()
            filename = f"Energy_Loss_Curve_{label}.png"
            plt.savefig(filename, dpi=300, bbox_inches="tight")
            plt.close()
            
            print(f"Saved plot: {filename}")
    
        except Exception as e:
            print(f"Error in make_table: {e}")
    
    def load_table(self, arg):
        args = shlex.split(arg)
        particle = args[0]
        filename = f"E_vs_x_{particle}.dat"
        load_table(filename)
        print(f"Loaded table {filename}")
        
    def do_energy_loss(self, arg):
        """Find a final energy given an initial energy and distance travelled
        Ex: >> energy loss <particle> <initial energy MeV> <distance travelled cm>"""
        args = shlex.split(arg)
        try:
            particle = args[0]
            Ei = float(args[1])
            dl = float(args[2])
            Ei_offset = Ei * 1.1
            table_specs = f"{particle} {Ei_offset}"
            try:
                self.do_make_table(table_specs)
                Ef = energy_loss(particle, Ei, dl)
                print(f"\nFinal energy: {Ef:.6f} MeV\n")
            except:
                return
        except IndexError:
            print("Please input particle, initial energy, and distance travelled")
        
    def do_energy_reconstruction(self, arg):
        """Find a vertex energy given an final energy and distance travelled
        Ex: >> energy reconstruction <particle> <final energy MeV> <distance travelled cm>"""
        args = shlex.split(arg)
        try:
            particle = args[0]
            Ef = float(args[1])
            dl = float(args[2])
            try:
                Ei = energy_reconstruction(particle, Ef, dl)
                if Ei > 0:
                    print(f"\nInitial energy: {Ei:.6f} MeV\n")
                else:
                    print("Error: remake table with larger value, fallen off map")
            except:
                print("Particle energy table not made yet, please do so using 'make table'")
        except IndexError:
            print("Please input particle, final energy from detector, and distance travelled")
            
    def do_energy_distance(self, arg):
        """Find a distance travelled given an initial and final energy
        Ex: >> energy distance <particle> <initial energy> <final energy MeV>"""
        args = shlex.split(arg)
        try:
            particle = args[0]
            Ei = float(args[1])
            Ef = float(args[2])
            dE = Ei - Ef
            try:
                dl = energy_distance(particle, Ei, Ef)
                if dl > 0:
                    print(f"\nChange in energy: {dE:.6f} MeV")
                    print(f"Distance travelled: {dl:.6f} cm\n")
                else:
                    print("Error: remake table with larger value, fallen off map")
            except:
                print("Particle energy table not made yet, please do so using 'make table'")
        except IndexError:
            print("Please input particle, final energy from detector, and distance travelled")
            
    def do_uproot_file(self, arg):
        """Open a specific root file for inspection"""
    
        args = shlex.split(arg)
    
        if len(args) > 0:
            filename = args[0]
        else:
            filename = self.rootFile
    
        try:
            print(f"Opening {filename}")
    
            # Try Armory path first
            try:
                self.file = uproot.open(f"../Armory/{filename}")
            except FileNotFoundError:
                self.file = uproot.open(filename)
    
            print("File loaded successfully.")
            print("Keys:", self.file.keys())
    
        except Exception as e:
            print("Error opening file:", e)
    
    def do_print_file(self, arg):
        """Print contents of ROOT file"""
        args = shlex.split(arg)
        file = self.file
        if "keys" in args or len(args) == 0:
            print("Keys in file: ", file.keys())
        if "class_names" in args or len(args) == 0:
            print("Class names: ", file.classnames())
        
    def do_set_tree(self, arg):
    
        if self.file is None:
            print("No ROOT file loaded.")
            return
    
        keys = self.file.keys()
    
        print("Available trees:", keys)
    
        treeName = arg if len(arg) > 0 else "tree"
    
        try:
            # uproot automatically resolves ";1"
            self.tree = self.file[treeName]
    
            print(f"Tree loaded: {self.tree}")
            print("Branches:", self.tree.keys())
    
        except Exception as e:
            print("Error loading tree:", treeName)
            print("Exception:", e)

    def run_command_line(self):
        import readline
        import atexit
        import os
        import awkward as ak
        
        histfile = os.path.expanduser("~/.uproot_shell_history")
        
        try:
            readline.read_history_file(histfile)
        except FileNotFoundError:
            pass
        
        readline.set_history_length(1000)
        readline.parse_and_bind("tab: complete")
    
        atexit.register(readline.write_history_file, histfile)
    
        print("Custom Python CMD (type 'exit' to stop)")
        
        local_vars = {
            "file": self.file,
            "uproot": uproot,
            "np": np,
            #"ak": ak,
            "plt": plt,
            "self": self
        }
        
        startup_script = textwrap.dedent("""
        tree = file["tree"]
        """)
        
        exec(startup_script, globals(), local_vars)
        while True:
            try:
                entry = input(">>> ").strip()
                if entry.lower() in ["exit", "quit"]:
                    break
                if not entry:
                    continue
                try:
                    result = eval(entry, globals(), local_vars)
    
                    if result is not None:
                        print(result)
    
                except SyntaxError:
                    exec(entry, globals(), local_vars)
    
                if "tree" in local_vars:
                    self.tree = local_vars["tree"]
            except OverflowError():
                print("Arrays too large, causing crash")
            except Exception as e:
                print(f"Error: {e}")
        self.shell_vars = local_vars
    
    def do_uproot(self, arg):
        """Start up an in-program command line to use root tools with python, 
        look up 'uproot' for more details"""
        self.run_command_line()
        
    def do_energy_analysis(self, arg):
    
        args = shlex.split(arg)
    
        try:
            particle = args[0]
        except IndexError:
            print("Please indicate reactant for analysis")
            return
    
        try:
            max_events = int(args[1])
        except IndexError:
            max_events = None
    
        if self.tree is None:
            self.do_set_tree("")
            print(f"Using TTree: {self.tree}")
    
        branches = [
            "Tb",
            "thetab",
            "sx3Z"
        ]
    
        if max_events:
            n_events = max_events
        else:
            n_events = self.tree.num_entries
    
        print(f"Loading {n_events} events...")
    
        data = self.tree.arrays(
            branches,
            library="np",
            entry_stop=max_events
        )
        global Ei
        Ei = data["Tb"]
        global sx3Z
        sx3Z = data["sx3Z"]
    
        theta = np.radians(data["thetab"])
    
        # Remove theta = 0 events
        mask = np.sin(theta) != 0
    
        Ei = Ei[mask]
        theta = theta[mask]
    
        sin_theta = np.sin(theta)
    
        radii = np.array([3.2, 4.2, 6.6])
    
        dA = radii[0] / sin_theta
        dC = radii[1] / sin_theta
        dsx3 = radii[2] / sin_theta
    
        print("Calculating energy losses...")
        global EA
        EA = energy_loss(particle, Ei, dA)
        global EC
        EC = energy_loss(particle, Ei, dC)
        global Esx3
        Esx3 = energy_loss(particle, Ei, dsx3)
        global Eprop
        Eprop = EA - EC
        global Elost
        Elost = Ei - Esx3

        print("Analysis complete")

        print(f"Processed events: {len(Ei)}")

        print(f"Anode average energy: {np.mean(EA):.3f} MeV")

        print(f"Cathode average energy: {np.mean(EC):.3f} MeV")

        print(f"sx3 average energy: {np.mean(Esx3):.3f} MeV")

        print(f"Average total energy loss to sx3: {np.mean(Elost):.3f} MeV")

        print(f"Maximum total energy loss to sx3: {np.max(Elost):.3f} MeV")

        print(f"Minimum total energy loss to sx3: {np.min(Elost):.3f} MeV")

        print(f"Proportion counter average energy difference: {np.mean(Eprop):.3f} MeV")

        print(f"Maximum proportion counter energy difference: {np.max(Eprop):.3f} MeV")

        print(f"Minimum proportion counter energy difference: {np.min(Eprop):.3f} MeV")


        output_filename = "energy_analysis.root"

        print(f"Writing new tree to {output_filename}")

        # Load ALL original branches
        all_data = self.tree.arrays(
            library="np",
            entry_stop=max_events
        )

        # Create full-length arrays initialized to NaN
        n_total = len(data["Tb"])

        EA_full = np.full(n_total, np.nan)

        EC_full = np.full(n_total, np.nan)

        Esx3_full = np.full(n_total, np.nan)

        Eprop_full = np.full(n_total, np.nan)

        Elost_full = np.full(n_total, np.nan)

        # Put values back into valid entries
        EA_full[mask] = EA

        EC_full[mask] = EC

        Esx3_full[mask] = Esx3

        Eprop_full[mask] = Eprop

        Elost_full[mask] = Elost

        # Add new branches
        all_data["EA"] = EA_full

        all_data["EC"] = EC_full

        all_data["Esx3"] = Esx3_full

        all_data["Eprop"] = Eprop_full

        all_data["Elost"] = Elost_full

        # Write new ROOT file as a classic TTree
        with uproot.recreate(output_filename) as fout:

            branch_types = {
                name: array.dtype
                for name, array in all_data.items()
            }

            fout.mktree("tree", branch_types)

            fout["tree"].extend(all_data)

        print("Finished writing augmented ROOT file")   
        
    def do_make_plots(self, arg):
    
        import os
        
        global plot_data
        
        plot_data = []
    
        args = shlex.split(arg)
    
        particle = args[0] if len(args) > 0 else "proton"
        max_events = int(args[1]) if len(args) > 1 else None
    
        if self.tree is None:
            self.do_set_tree("")
            print(f"Using TTree: {self.tree}")
    
        branches = ["Tb", "thetab", "sx3Z"]
    
        data = self.tree.arrays(
            branches,
            library="np",
            entry_stop=max_events
        )
    
        Ei = data["Tb"]
        theta = np.radians(data["thetab"])
        sx3Z = data["sx3Z"]
    
        mask = np.sin(theta) != 0
    
        Ei = Ei[mask]
        theta = theta[mask]
        sx3Z = sx3Z[mask]
        
        update_plot_data(f"{particle}_Ei", Ei)
        update_plot_data(f"{particle}_sx3Z", sx3Z)
    
        sin_theta = np.sin(theta)
    
        radii = np.array([3.2, 4.2, 6.6])
    
        dA = radii[0] / sin_theta
        dC = radii[1] / sin_theta
        dsx3 = radii[2] / sin_theta
    
        print("Computing energies...")
    
        EA = energy_loss(particle, Ei, dA)
        EC = energy_loss(particle, Ei, dC)
        Esx3 = energy_loss(particle, Ei, dsx3)
    
        Elost = Ei - Esx3
        Eprop = EA - EC
        
        update_plot_data(f"{particle}_EA", EA)
        update_plot_data(f"{particle}_EC", EC)
        update_plot_data(f"{particle}_Esx3", Esx3)
        update_plot_data(f"{particle}_Elost", Elost)
        update_plot_data(f"{particle}_Eprop", Eprop)
    
        base = f"{particle}_plots"
        os.makedirs(base, exist_ok=True)
    
        print(f"Saving plots to folder: {base}")
    
        # 1. Histogram: energy loss
        plt.figure(figsize=(7,5))
        plt.hist(Elost, bins=200)
        plt.xlabel("Energy Loss (MeV)")
        plt.ylabel("Counts")
        plt.title(f"{particle} Total Energy Loss Distribution")
        plt.grid(True)
        plt.tight_layout()
        plt.savefig(f"{base}/Elost_hist.png", dpi=300)
        plt.close()
    
        #Histogram: sx3Z
        plt.figure(figsize=(7,5))
        plt.hist(sx3Z, bins=100)
        plt.xlabel("SX3 Z")
        plt.ylabel("Counts")
        plt.title(f"{particle} SX3 Position Distribution")
        plt.grid(True)
        plt.tight_layout()
        plt.savefig(f"{base}/sx3Z_hist.png", dpi=300)
        plt.close()
    
        #2D: Elost vs sx3Z
        plt.figure(figsize=(7,6))
        plt.hist2d(sx3Z, Elost, bins=200)
        plt.ylabel("Energy Loss (MeV)")
        plt.xlabel("SX3 Z")
        plt.title(f"{particle} Energy Loss vs SX3 Position")
        plt.colorbar(label="Counts")
        plt.tight_layout()
        plt.savefig(f"{base}/Elost_vs_sx3Z.png", dpi=300)
        plt.close()
    
        #Anode energy vs sx3 energy
        plt.figure(figsize=(7,6))
        plt.hist2d(EA, Esx3, bins=200)
        plt.xlabel("EA (MeV)")
        plt.ylabel("Esx3 (MeV)")
        plt.title(f"{particle} Anode vs SX3 Energy")
        plt.colorbar(label="Counts")
        plt.tight_layout()
        plt.savefig(f"{base}/EA_vs_Esx3.png", dpi=300)
        plt.close()
        
        #Prop counter energy loss
        plt.figure(figsize=(7,6))
        plt.hist2d(Eprop, sx3Z, bins=200)
        plt.xlabel("EA - EC (MeV)")
        plt.ylabel("SX3 Z")
        plt.title(f"{particle} Energy Propagation Difference vs Position")
        plt.colorbar(label="Counts")
        plt.tight_layout()
        plt.savefig(f"{base}/Eprop_vs_sx3Z.png", dpi=300)
        plt.close()
        
        plt.figure(figsize=(7,6))
        plt.hist2d(Esx3, Eprop, bins=200)
        plt.ylabel("PCEnergy")
        plt.xlabel("SX3 Energy (MeV)")
        plt.title(f"{particle} Energy Propagation Difference vs sx3 Energy")
        plt.colorbar(label="Counts")
        plt.xlim(0,30)
        plt.ylim(0,.45)
        plt.tight_layout()
        plt.savefig(f"{base}/Eprop_vs_Esx3.png", dpi=300)
        plt.close()
    
        print("Plotting complete.")
                
    def do_dual_plotter(self, arg):
        args = shlex.split(arg)
    
        if len(args) < 2:
            print("Usage: make dual plots proton_data.root alpha_data.root")
            return
    
        file1 = args[0]
        file2 = args[1]
    
        #Helper function

    
        #Process both files
        data1 = process_file(f"../Armory/{file1}")
        data2 = process_file(f"../Armory/{file2}")
    
        outdir = "dual_plots"
        os.makedirs(outdir, exist_ok=True)
    
        print(f"Saving plots to: {outdir}")
    
        #Overlay histogram: Elost
        plt.figure(figsize=(8,6))
    
        plt.hist(
            data1["Elost"],
            bins=200,
            histtype='step',
            linewidth=2,
            density=True,
            label=data1["particle"]
        )
    
        plt.hist(
            data2["Elost"],
            bins=200,
            histtype='step',
            linewidth=2,
            density=True,
            label=data2["particle"]
        )
    
        plt.xlabel("Energy Loss (MeV)")
        plt.ylabel("Normalized Counts")
        plt.title("Energy Loss Comparison")
        plt.legend()
        plt.grid(True)
        plt.tight_layout()
    
        plt.savefig(f"{outdir}/Elost_overlay.png", dpi=300)
        plt.close()
    
        #Overlay histogram: sx3Z
        plt.figure(figsize=(8,6))
    
        plt.hist(
            data1["sx3Z"],
            bins=150,
            histtype='step',
            linewidth=2,
            density=True,
            label=data1["particle"]
        )
    
        plt.hist(
            data2["sx3Z"],
            bins=150,
            histtype='step',
            linewidth=2,
            density=True,
            label=data2["particle"]
        )
    
        plt.xlabel("SX3 Z")
        plt.ylabel("Normalized Counts")
        plt.title("SX3 Position Comparison")
        plt.legend()
        plt.grid(True)
        plt.tight_layout()
    
        plt.savefig(f"{outdir}/sx3Z_overlay.png", dpi=300)
        plt.close()
    
        #Side-by-side 2D plots
        fig, axes = plt.subplots(1, 2, figsize=(14,6))
    
        h1 = axes[0].hist2d(
            data1["sx3Z"],
            data1["Elost"],
            bins=200
        )
    
        axes[0].set_title(f'{data1["particle"]} Elost vs SX3')
        axes[0].set_xlabel("SX3 Z")
        axes[0].set_ylabel("Energy Loss (MeV)")
    
        h2 = axes[1].hist2d(
            data2["sx3Z"],
            data2["Elost"],
            bins=200
        )
    
        axes[1].set_title(f'{data2["particle"]} Elost vs SX3')
        axes[1].set_xlabel("SX3 Z")
        axes[1].set_ylabel("Energy Loss (MeV)")
    
        fig.colorbar(h1[3], ax=axes[0], label="Counts")
        fig.colorbar(h2[3], ax=axes[1], label="Counts")
    
        plt.tight_layout()
    
        plt.savefig(f"{outdir}/Elost_vs_sx3_comparison.png", dpi=300)
        plt.close()
        
        #EA vs Esx3 overlay scatter
        plt.figure(figsize=(8,6))
    
        plt.scatter(
            data1["EA"],
            data1["Esx3"],
            s=1,
            alpha=0.3,
            label=data1["particle"]
        )
    
        plt.scatter(
            data2["EA"],
            data2["Esx3"],
            s=1,
            alpha=0.3,
            label=data2["particle"]
        )
    
        plt.xlabel("EA (MeV)")
        plt.ylabel("Esx3 (MeV)")
        plt.title("Anode vs SX3 Energy")
        plt.legend()
        plt.grid(True)
        plt.tight_layout()
    
        plt.savefig(f"{outdir}/EA_vs_Esx3_overlay.png", dpi=300)
        plt.close()
        
        #PCE vs SiE
        
        combined_Esx3 = np.concatenate([
            data1["Esx3"],
            data2["Esx3"]
        ])
        
        combined_Eprop = np.concatenate([
            data1["Eprop"],
            data2["Eprop"]
        ])
        
        plt.figure(figsize=(7,6))
        
        plt.hist2d(
            combined_Esx3,
            combined_Eprop,
            bins=100,
            range=[[0,30],[0,0.45]],
            cmap='viridis'   # same default matplotlib style
        )
        
        plt.ylabel("PCEnergy")
        plt.xlabel("SX3 Energy (MeV)")
        
        plt.title(
            f'{data1["particle"]} + {data2["particle"]} '
            'Energy Propagation Difference vs SX3 Energy'
        )
        
        plt.colorbar(label="Counts")
        
        plt.xlim(0,30)
        plt.ylim(0,0.45)
        
        plt.tight_layout()
        
        plt.savefig(f"{outdir}/Combined_Eprop_vs_Esx3.png", dpi=300)
        
        plt.close()
    
        print("Dual plotting complete.")
        
        
#exec(open("PCEnergyAnalysis.py").read())

if __name__ == "__main__":
    MyInteractiveApp().cmdloop()