Changes_up_to_March_7 #2

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Patchouligoo wants to merge 54 commits into apizzuto:master from Patchouligoo:master

Electron_detector_eff_analyzer.py

-Original file line number
+Diff line change
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+    import numpy as np
+    import pandas as pd
+    import matplotlib.pylab as plt
+    from matplotlib.colors import ListedColormap
+    import seaborn as sns
+    import os
+    plt.style.use("IceCube")
+    import matplotlib as mpl
+    import numpy as np
+    class DECOLeptonAnalyzer():
+        r'''This class is for making plots like the ones in the
+        notebook that read in a bunch of simulated files
+        and make analysis level plots'''
+        def __init__(self, pid, phi, thickness):
+            self.pid = pid
+            self.thichness = thickness
+            self.phi = phi
+        def read_hit_file(self, filename):
+            f = open(filename, 'r')
+            xhits, yhits, charge = [], [], []
+            # skip first 2 lines
+            f.readline()
+            f.readline()
+            x, y, c = [], [], []
+            flag = 1
+            while 1:
+                temp = f.readline().split()
+                if len(temp) < 1 or temp[0] == '#':
+                    break
+                if temp[0] == '===':
+                    continue
+                if temp[0] == '---':
+                    if flag == 1:
+                        flag = 0
+                    else:
+                        xhits.append(x)
+                        yhits.append(y)
+                        charge.append(c)
+                        x, y, c = [], [], []
+                else:
+                    x.append(float(temp[1][:-1]))
+                    y.append(float(temp[2][:-1]))
+                    c.append(float(temp[3][:-1]))
+            if len(x) > 0:
+                xhits.append(x)
+                yhits.append(y)
+                charge.append(c)
+            return xhits, yhits, charge
+        def get_E_deposited(self, en, ang, posz):
+            x, y, c = self.read_hit_file(
+                "./output/{}/{}_posz_{}_theta_{}_phi_{}_thickiness_{}_highstats.txt".format(self.pid, round(posz, 3), en, float(ang),
+                                                                                    float(self.phi), self.thichness))
+            dE_list = []
+            for i in range(len(c)):
+                dE_list.append(np.array(c[i]).sum() * 3.62)
+            dE_list = np.array(dE_list)
+            return dE_list.mean(), dE_list.std()
+    energy = "10keV"
+    theta = '90'
+    phi = '0'
+    particle_type = 'e-'
+    dep_thickness = 26.3
+    z_pos = np.linspace(-1 * dep_thickness/2, dep_thickness/2, 100)
+    a = DECOLeptonAnalyzer(particle_type, phi, dep_thickness)
+    E_list = []
+    err_list = []
+    for z in z_pos:
+        mean_val, std_val = a.get_E_deposited(energy, theta, z)
+        E_list.append(mean_val)
+        err_list.append(std_val)
+    f = plt.figure()
+    plt.errorbar(z_pos, E_list, yerr=err_list)
+    plt.xlabel("initial z position in um")
+    plt.ylabel("calibrated E in eV")
+    plt.show()

Electron_detector_eff_test.py

-Original file line number
+Diff line change
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+    r'''Class that handles various inputs and systematic parameters
+        and simulates muons'''
+    import os, sys
+    import subprocess
+    from pipes import quote
+    from math import *
+    import numpy as np
+    class DECOMuonSimulator():
+        r'''Simulator class for muons that uses allpix
+        and GEANT'''
+        def __init__(self, pid, energy, pos, theta, **kwargs):
+            self.pid = pid #Particle id, ie mu+, e-
+            self.pos = pos
+            self.energy = energy
+            self.theta = float(theta)
+            self.phi = float(kwargs.pop('phi', 0.))
+            self.depletion_thickness = float(kwargs.pop('depletion_thickness', 26.3))
+            #todo: NOTE: in unit of um !!!!!!!
+            # Set other possible systematics with kwargs, including
+            # electric fields, pixel size, etc.
+            self.path_to_root = os.getenv('DECO_ROOT_PATH')
+            self.path_to_geant = os.getenv('DECO_GEANT_PATH')
+            self.path_to_allpix = os.getenv('DECO_ALLPIX_PATH')
+            self.base_command = self.path_to_allpix + ' -c ./htc_wildfire/source_measurement.conf -o'
+        def write_source_file(self, n_events, want_plot):
+            with open('./htc_wildfire/source_measurement_replace.conf', 'r') as f:
+                data = f.readlines()
+            data[3] = data[3].format(n_events)
+            data[18] = data[18].format(str(self.pos[0]) + " " + str(self.pos[1]) + " " + str(self.pos[2]) + "um")
+            theta = pi - radians(self.theta)
+            phi = radians(self.phi)
+            dirx = 1*sin(theta)*cos(phi)
+            diry = 1*sin(theta)*sin(phi)
+            dirz = 1*cos(theta)
+            data[20] = data[20].format(str(dirx) + " " + str(diry) + " " + str(dirz))
+            if want_plot == 'true':
+                data[38] = data[38].format('true' + "\n" + "output_linegraphs = true \n output_plots_step = 100ps \n output_plots_align_pixels = true \n output_plots_use_pixel_units = true")
+            else:
+                data[38] = data[38].format("false")
+            with open('./htc_wildfire/source_measurement.conf', 'w') as wf:
+                wf.writelines(data)
+                wf.close()
+        """
+        def write_detector_file(self):
+            # USE THE PARAMETERS TO REWRITE DETECTOR FILE
+            with open('./htc_wildfire/detector_replace.conf', 'r') as f:
+                data = f.readlines()
+            data[-2] = data[-2].format(self.phi, self.theta, 0)
+            with open('./htc_wildfire/detector.conf', 'w') as wf:
+                wf.writelines(data)
+                wf.close()
+            with open('./htc_wildfire/htc_wildfire_shielded_replace.conf', 'r') as f:
+                data = f.readlines()
+            data[4] = data[4].format(self.depletion_thickness)
+            with open('./htc_wildfire/htc_wildfire_shielded.conf', 'w') as wf:
+                wf.writelines(data)
+                wf.close()
+        """
+        def set_output_file_name(self):
+            # write unique file name depending on parameters
+            if not os.path.exists("./output"):
+                os.system("mkdir ./output")
+            if not os.path.exists("./output/" + str(self.pid)):
+                os.system("mkdir ./output/" + str(self.pid))
+            self.outfile = str(self.pid) + "/" + "{}_posz_{}_theta_{:.1f}_phi_{:.1f}_thickiness_{:.1f}_highstats.txt".format(round(self.pos[2], 3), self.energy, self.theta, self.phi, self.depletion_thickness)
+            pass
+        def get_output_file_name(self):
+            try:
+                return self.outfile
+            except:
+                self.set_output_file_name()
+                return self.outfile
+        def run_simulation(self, n_events, want_charge_plot='false'):
+            self.source_local_env()
+            # Run the allpix simulation
+            output_file = self.get_output_file_name()
+            self.write_source_file(n_events, want_charge_plot)
+            my_command = self.base_command[:]
+            my_command += ' DepositionGeant4.particle_type="{}"'.format(self.pid)
+            my_command += ' -o DepositionGeant4.source_energy="{}"'.format(self.energy)
+            my_command += ' -o TextWriter.file_name="' + output_file + '"'
+            """check if simulated using file name"""
+            if self.check_if_simulated(output_file) is True:
+                print("has been simulated")
+                return
+            subprocess.call(my_command, shell=True)
+            return
+        def check_if_simulated(self, filename):
+            # Check to see if simulation has already been run for
+            # this set of parameters
+            if not os.path.exists("./output/" + filename):
+                return False
+            return True
+        def source_local_env(self):
+            geant = self.path_to_geant + "/bin/geant4.sh"
+            root = self.path_to_root + "/bin/thisroot.sh"
+            pass
+            # Run source scripts for ROOT and GEANT if the
+            # simulation doesn't work
+    dep_thickness = 26.3 #um
+    pos_list = []
+    z_pos = np.linspace(-1 * dep_thickness/2, dep_thickness/2, 100)
+    for i in range(len(z_pos)):
+        pos_list.append([0, 0, z_pos[i]])
+    #angles = ['0', '15', '30', '45', '60', '75']
+    #phis = ['0', '15', '30', '45', '60', '75', '90']
+    energy = ['10keV']
+    angles = ['90']
+    phis = ['0']
+    particle_type = 'e-'
+    want_charge_plot = "false"
+    for ene in energy:
+        for ang in angles:
+            for azi in phis:
+                for pos in pos_list:
+                    a = DECOMuonSimulator(particle_type, ene, pos, ang, phi=azi, depletion_thickness=str(dep_thickness))
+                    a.run_simulation(100, want_charge_plot)

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