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divergence_all_N_gaussian_fit_20190123.py
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divergence_all_N_gaussian_fit_20190123.py
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# -*- coding: utf-8 -*-
"""
Created on Tue Feb 19 16:54:54 2019
@author: similarities
"""
import matplotlib.pyplot as plt
import numpy as np
import os
import math
from lmfit.models import GaussianModel
class GaussianFitHighHarmonicDivergence:
def __init__(self, filename, lambda_fundamental, harmonic_selected):
self.filename = filename
# px size full picture * usually 0 - 2048
self.ymin = 0
self.ymax = 2048
# define Roi in x to avoid boarder effects
self.xmin = 150
self.xmax = 800
# integration ROI y for each HHG line
self.picture = np.empty([])
self.picture_background = np.empty([2048, 2048])
self.lambda_fundamental = lambda_fundamental
# calibration of picture in x [full angle], is given with offset here (0 in the middle)
self.full_divergence = 17.5
self.maximum_harmonic = 29
self.harmonic_selected = harmonic_selected
self.lineout_x = self.create_x_axis_in_mrad()
self.lineout_y = np.zeros([2048, 1])
self.filedescription = self.filename
# defines first harmonic N in pixels, note: the quadratic calibration is not valid for N<10
self.border_up, self.border_down = self.energy_range()
self.sigma_temp = float
self.amplitude_temp = float
self.center_temp = float
self.gaussian_result = np.zeros([self.maximum_harmonic, 5])
def create_x_axis_in_mrad(self):
c = self.full_divergence / 2048
return np.arange(self.xmin, self.xmax) * c
def open_file(self):
self.picture = plt.imread(self.filename)
return self.picture
def background(self):
back_mean = np.mean(self.picture[:, 1700:1800], axis=1)
for x in range(0, 2048):
self.picture_background[::, x] = self.picture[::, x] - back_mean[x]
self.background_x()
plt.figure(1)
plt.xlabel('[px]')
plt.ylabel('[px]')
plt.imshow(self.picture_background, label=self.filedescription)
return self.picture_background
def background_x(self):
back_mean = np.mean(self.picture[1950:2048, :], axis=0)
for x in range(0, 2048):
self.picture_background[x, ::] = self.picture[x, ::] - back_mean[x]
return self.picture_background
def nm_in_px(self, energy_nm):
# this function should be inverse of the grating function
self.px_boarder = int(4.71439193e-01 * energy_nm ** 2 - 1.06651902e+02 * energy_nm + 4.29603367e+03)
return self.px_boarder
def energy_range(self):
print(self.harmonic_selected)
previous_harmonic = self.lambda_fundamental / (self.harmonic_selected - 0.2)
next_harmonic = self.lambda_fundamental / (self.harmonic_selected + 0.2)
print(previous_harmonic, next_harmonic)
self.border_up = np.int(self.nm_in_px(previous_harmonic))
self.border_down = np.int(self.nm_in_px(next_harmonic))
print(self.border_up, self.border_down, "ROI in px")
self.pixel_range = np.int(self.border_down - self.border_up)
print(self.pixel_range, 'ROI in pixel range')
return self.border_up, self.border_down
def delta_energy(self):
lower = int(self.border_up)
upper = int(self.border_down)
delta = self.px_in_nm(lower) - self.px_in_nm(upper)
delta_vs_energy = delta / (self.lambda_fundamental / self.harmonic_selected)
return delta_vs_energy, delta
@staticmethod
def px_in_nm(px_number):
return 1.24679344e-06 * px_number ** 2 - 1.65566701e-02 * px_number + 5.22598053e+01
def create_sub_array_px_range(self):
border_up = int(self.border_up)
border_down = int(self.border_down)
self.print_h_lines()
return self.picture_background[border_up: border_down, self.xmin:self.xmax]
def print_h_lines(self):
plt.figure(1)
plt.hlines(self.border_up, xmin=0, xmax=2048, color="b", linewidth=0.3)
plt.hlines(self.border_down, xmin=0, xmax=2048, color="w", linewidth=0.3)
# plt.hlines(fundamental_in_px, xmin=0, xmax=2048, color='r', linewidth=0.1)
plt.vlines(self.xmin, ymin=0, ymax=2048, color="w", linewidth=0.5)
plt.vlines(self.xmax, ymin=0, ymax=2048, color="w", linewidth=0.5)
def check_fundamental(self):
sub_array = self.create_sub_array_px_range()
line_out_y = sub_array[::, 1200]
line_out_y_1 = np.arange(0, self.ymax)
self.plot_x_y(line_out_y_1, line_out_y, 'lineout_over_harmonic_y', 'px', 'counts', 4)
maximum_in_y = np.where(np.amax(sub_array[::, 1200]))
print('maximum px position: {0} in px-range {1}'.format(maximum_in_y, self.ymax))
def sum_over_pixel_range(self):
self.lineout_y = np.sum(self.create_sub_array_px_range(), axis=0)
return self.lineout_y
def set_to_zero_offest(self):
self.lineout_y[::] = self.lineout_y[::] - np.amin(self.lineout_y)
return self.lineout_y
def fit_gaussian(self):
self.sum_over_pixel_range()
self.set_to_zero_offest()
mod = GaussianModel()
pars = mod.guess(self.lineout_y, x=self.lineout_x)
out = mod.fit(self.lineout_y, pars, x=self.lineout_x)
self.sigma_temp = out.params['sigma'].value
self.amplitude_temp = out.params['amplitude'].value
self.center_temp = out.params['center'].value
# print('sigma: {0} for N:{1} = {2:8.2f}nm'
# .format(self.sigma_temp, self.harmonic_selected, self.lambda_fundamental / self.harmonic_selected))
self.plot_fit_function()
return self.sigma_temp, self.amplitude_temp, self.center_temp
def plot_x_y(self, x, y, name, x_label, y_label, plot_number):
plt.figure(plot_number)
plt.plot(x, y, label=name)
plt.xlabel(str(x_label))
plt.ylabel(str(y_label))
plt.legend()
def plot_scatter(self, x, y, name, x_label, y_label, plot_number):
plt.figure(plot_number)
plt.scatter(x, y, label=name)
plt.xlabel(str(x_label))
plt.ylabel(str(y_label))
plt.legend()
def plot_fit_function(self):
# IMPORTANT sigma corresponds to w(0) beamwaist = half beam aperture
c = self.full_divergence / 2048
xx = np.linspace(self.xmin * c, self.xmax * c, 1000)
yy = np.zeros([len(xx), 1])
for x in range(0, len(xx)):
yy[x] = (self.amplitude_temp / (self.sigma_temp * ((2 * math.pi) ** 0.5))) * math.exp(
(-(xx[x] - self.center_temp) ** 2) / (2 * self.sigma_temp ** 2))
self.plot_x_y(self.lineout_x, self.lineout_y, str(self.harmonic_selected), 'mrad', 'counts', 2)
self.plot_x_y(xx, yy, 'fit_' + str(self.harmonic_selected), 'mrad', 'counts', 2)
def batch_over_N(self):
for x in range(self.harmonic_selected, self.maximum_harmonic):
self.gaussian_result[x, 0] = x
self.harmonic_selected = x
self.border_up, self.border_down = self.energy_range()
self.fit_gaussian()
# self.plot_fit_function()
plt.figure(1)
plt.hlines(self.nm_in_px(self.lambda_fundamental / self.harmonic_selected), xmin=0, xmax=2048,
linewidth=0.5, alpha=0.1)
self.gaussian_result[x, 1] = self.sigma_temp
self.gaussian_result[x, 2] = np.sum(self.lineout_y[::])
self.gaussian_result[x, 4], self.gaussian_result[x, 3] = self.delta_energy()
# clean for empty entries
self.gaussian_result = np.delete(self.gaussian_result, np.where(~self.gaussian_result.any(axis=1))[0], axis=0)
self.plot_scatter(self.gaussian_result[::, 0], self.gaussian_result[::, 1], self.filedescription,
'harmonic number N', 'divergence in mrad', 3)
return self.gaussian_result
def prepare_header(self):
# insert header line and change index
header_names = (['harmonic number', 'mrad', 'integrated counts in delta E', 'harmonic in nm', 'delta E/E'])
parameter_info = (
['fundamental_nm:', str(self.lambda_fundamental), 'pixel_range:', str(self.ymax), 'xxxx'])
return np.vstack((header_names, self.gaussian_result, parameter_info))
def save_data(self):
result = self.prepare_header()
print('saved data')
np.savetxt(self.filedescription[31:42] + '_' + self.filedescription[-6:-4] + ".txt", result, delimiter=' ',
header='string', comments='',
fmt='%s')
def get_file_list(path_picture):
tif_files = []
counter = 0
for file in os.listdir(path_picture):
print(file)
try:
if file.endswith(".tif"):
tif_files.append(str(file))
counter = counter + 1
else:
print("only other files found")
except Exception as e:
raise e
return tif_files
def process_files(my_files, path):
for x in range(47, 49):
file = path + '/' + my_files[x]
ProcessImage = GaussianFitHighHarmonicDivergence(file, 795,
22)
ProcessImage.open_file()
ProcessImage.background()
ProcessImage.batch_over_N()
ProcessImage.save_data()
plt.show()
# insert the following ('filepath/picture_name.tif', fundamental frequency (float), harmonic number (int, first harmonic),
# "picture name for plot")
path_picture = 'rotated_20190123'
my_files = get_file_list(path_picture)
process_files(my_files, path_picture)