Source code for sas.sascalc.calculator.resolution_calculator

"""
This object is a small tool to allow user to quickly
determine the variance in q  from the
instrumental parameters.
"""
import sys
from math import pi, sqrt
import math
import logging

import numpy as np

from .instrument import Sample
from .instrument import Detector
from .instrument import TOF as Neutron
from .instrument import Aperture

logger = logging.getLogger(__name__)

#Plank's constant in cgs unit
_PLANK_H = 6.62606896E-27
#Gravitational acc. in cgs unit
_GRAVITY = 981.0


[docs]class ResolutionCalculator(object): """ compute resolution in 2D """ def __init__(self): # wavelength self.wave = Neutron() # sample self.sample = Sample() # aperture self.aperture = Aperture() # detector self.detector = Detector() # 2d image of the resolution self.image = [] self.image_lam = [] # resolutions # lamda in r-direction self.sigma_lamd = 0 # x-dir (no lamda) self.sigma_1 = 0 #y-dir (no lamda) self.sigma_2 = 0 # 1D total self.sigma_1d = 0 self.gravity_phi = None # q min and max self.qx_min = -0.3 self.qx_max = 0.3 self.qy_min = -0.3 self.qy_max = 0.3 # q min and max of the detector self.detector_qx_min = -0.3 self.detector_qx_max = 0.3 self.detector_qy_min = -0.3 self.detector_qy_max = 0.3 # possible max qrange self.qxmin_limit = 0 self.qxmax_limit = 0 self.qymin_limit = 0 self.qymax_limit = 0 # plots self.plot = None # instrumental params defaults self.mass = 0 self.intensity = 0 self.wavelength = 0 self.wavelength_spread = 0 self.source_aperture_size = [] self.source2sample_distance = [] self.sample2sample_distance = [] self.sample_aperture_size = [] self.sample2detector_distance = [] self.detector_pix_size = [] self.detector_size = [] self.get_all_instrument_params() # max q range for all lambdas self.qxrange = [] self.qyrange = []
[docs] def compute_and_plot(self, qx_value, qy_value, qx_min, qx_max, qy_min, qy_max, coord='cartesian'): """ Compute the resolution : qx_value: x component of q : qy_value: y component of q """ # make sure to update all the variables need. # except lambda, dlambda, and intensity self.get_all_instrument_params() # wavelength etc. lamda_list, dlamb_list = self.get_wave_list() intens_list = [] sig1_list = [] sig2_list = [] sigr_list = [] sigma1d_list = [] num_lamda = len(lamda_list) for num in range(num_lamda): lam = lamda_list[num] # wavelength spread dlam = dlamb_list[num] intens = self.setup_tof(lam, dlam) intens_list.append(intens) # cehck if tof if num_lamda > 1: tof = True else: tof = False # compute 2d resolution _, _, sigma_1, sigma_2, sigma_r, sigma1d = \ self.compute(lam, dlam, qx_value, qy_value, coord, tof) # make image image = self.get_image(qx_value, qy_value, sigma_1, sigma_2, sigma_r, qx_min, qx_max, qy_min, qy_max, coord, False) if qx_min > self.qx_min: qx_min = self.qx_min if qx_max < self.qx_max: qx_max = self.qx_max if qy_min > self.qy_min: qy_min = self.qy_min if qy_max < self.qy_max: qy_max = self.qy_max # set max qranges self.qxrange = [qx_min, qx_max] self.qyrange = [qy_min, qy_max] sig1_list.append(sigma_1) sig2_list.append(sigma_2) sigr_list.append(sigma_r) sigma1d_list.append(sigma1d) # redraw image in global 2d q-space. self.image_lam = [] total_intensity = 0 sigma_1 = 0 sigma_r = 0 sigma_2 = 0 sigma1d = 0 for ind in range(num_lamda): lam = lamda_list[ind] dlam = dlamb_list[ind] intens = self.setup_tof(lam, dlam) out = self.get_image(qx_value, qy_value, sig1_list[ind], sig2_list[ind], sigr_list[ind], qx_min, qx_max, qy_min, qy_max, coord) # this is the case of q being outside the detector #if numpy.all(out==0.0): # continue image = out # set variance as sigmas sigma_1 += sig1_list[ind] * sig1_list[ind] * self.intensity sigma_r += sigr_list[ind] * sigr_list[ind] * self.intensity sigma_2 += sig2_list[ind] * sig2_list[ind] * self.intensity sigma1d += sigma1d_list[ind] * sigma1d_list[ind] * self.intensity total_intensity += self.intensity if total_intensity != 0: # average variance image_out = image / total_intensity sigma_1 = sigma_1 / total_intensity sigma_r = sigma_r / total_intensity sigma_2 = sigma_2 / total_intensity sigma1d = sigma1d / total_intensity # set sigmas self.sigma_1 = sqrt(sigma_1) self.sigma_lamd = sqrt(sigma_r) self.sigma_2 = sqrt(sigma_2) self.sigma_1d = sqrt(sigma1d) # rescale max_im_val = 1 if max_im_val > 0: image_out /= max_im_val else: image_out = image * 0.0 # Don't calculate sigmas nor set self.sigmas! sigma_1 = 0 sigma_r = 0 sigma_2 = 0 sigma1d = 0 if len(self.image) > 0: self.image += image_out else: self.image = image_out # plot image return self.plot_image(self.image)
[docs] def setup_tof(self, wavelength, wavelength_spread): """ Setup all parameters in instrument : param ind: index of lambda, etc """ # set wave.wavelength self.set_wavelength(wavelength) self.set_wavelength_spread(wavelength_spread) self.intensity = self.wave.get_intensity() if wavelength == 0: msg = "Can't compute the resolution: the wavelength is zero..." raise RuntimeError(msg) return self.intensity
[docs] def compute(self, wavelength, wavelength_spread, qx_value, qy_value, coord='cartesian', tof=False): """ Compute the Q resoltuion in || and + direction of 2D : qx_value: x component of q : qy_value: y component of q """ coord = 'cartesian' lamb = wavelength lamb_spread = wavelength_spread # the shape of wavelength distribution if tof: # rectangular tof_factor = 2 else: # triangular tof_factor = 1 # Find polar values qr_value, phi = self._get_polar_value(qx_value, qy_value) # vacuum wave transfer knot = 2*pi/lamb # scattering angle theta; always true for plane detector # aligned vertically to the ko direction if qr_value > knot: theta = pi/2 else: theta = math.asin(qr_value/knot) # source aperture size rone = self.source_aperture_size # sample aperture size rtwo = self.sample_aperture_size # detector pixel size rthree = self.detector_pix_size # source to sample(aperture) distance l_ssa = self.source2sample_distance[0] # sample(aperture) to detector distance l_sad = self.sample2detector_distance[0] # sample (aperture) to sample distance l_sas = self.sample2sample_distance[0] # source to sample distance l_one = l_ssa + l_sas # sample to detector distance l_two = l_sad - l_sas # Sample offset correction for l_one and Lp on variance calculation l1_cor = (l_ssa * l_two) / (l_sas + l_two) lp_cor = (l_ssa * l_two) / (l_one + l_two) # the radial distance to the pixel from the center of the detector radius = math.tan(theta) * l_two #Lp = l_one*l_two/(l_one+l_two) # default polar coordinate comp1 = 'radial' comp2 = 'phi' # in the case of the cartesian coordinate if coord == 'cartesian': comp1 = 'x' comp2 = 'y' # sigma in the radial/x direction # for source aperture sigma_1 = self.get_variance(rone, l1_cor, phi, comp1) # for sample apperture sigma_1 += self.get_variance(rtwo, lp_cor, phi, comp1) # for detector pix sigma_1 += self.get_variance(rthree, l_two, phi, comp1) # for gravity term for 1d sigma_1grav1d = self.get_variance_gravity(l_ssa, l_sad, lamb, lamb_spread, phi, comp1, 'on') / tof_factor # for wavelength spread # reserve for 1d calculation A_value = self._cal_A_value(lamb, l_ssa, l_sad) sigma_wave_1, sigma_wave_1_1d = self.get_variance_wave(A_value, radius, l_two, lamb_spread, phi, 'radial', 'on') sigma_wave_1 /= tof_factor sigma_wave_1_1d /= tof_factor # for 1d variance_1d_1 = (sigma_1 + sigma_1grav1d) / 2 + sigma_wave_1_1d # normalize variance_1d_1 = knot * knot * variance_1d_1 / 12 # for 2d #sigma_1 += sigma_wave_1 # normalize sigma_1 = knot * sqrt(sigma_1 / 12) sigma_r = knot * sqrt(sigma_wave_1 / (tof_factor *12)) # sigma in the phi/y direction # for source apperture sigma_2 = self.get_variance(rone, l1_cor, phi, comp2) # for sample apperture sigma_2 += self.get_variance(rtwo, lp_cor, phi, comp2) # for detector pix sigma_2 += self.get_variance(rthree, l_two, phi, comp2) # for gravity term for 1d sigma_2grav1d = self.get_variance_gravity(l_ssa, l_sad, lamb, lamb_spread, phi, comp2, 'on') / tof_factor # for wavelength spread # reserve for 1d calculation sigma_wave_2, sigma_wave_2_1d = self.get_variance_wave(A_value, radius, l_two, lamb_spread, phi, 'phi', 'on') sigma_wave_2 /= tof_factor sigma_wave_2_1d /= tof_factor # for 1d variance_1d_2 = (sigma_2 + sigma_2grav1d) / 2 + sigma_wave_2_1d # normalize variance_1d_2 = knot * knot * variance_1d_2 / 12 # for 2d #sigma_2 = knot*sqrt(sigma_2/12) #sigma_2 += sigma_wave_2 # normalize sigma_2 = knot * sqrt(sigma_2 / 12) sigma1d = sqrt(variance_1d_1 + variance_1d_2) # set sigmas self.sigma_1 = sigma_1 self.sigma_lamd = sigma_r self.sigma_2 = sigma_2 self.sigma_1d = sigma1d return qr_value, phi, sigma_1, sigma_2, sigma_r, sigma1d
def _within_detector_range(self, qx_value, qy_value): """ check if qvalues are within detector range """ # detector range detector_qx_min = self.detector_qx_min detector_qx_max = self.detector_qx_max detector_qy_min = self.detector_qy_min detector_qy_max = self.detector_qy_max if self.qxmin_limit > detector_qx_min: self.qxmin_limit = detector_qx_min if self.qxmax_limit < detector_qx_max: self.qxmax_limit = detector_qx_max if self.qymin_limit > detector_qy_min: self.qymin_limit = detector_qy_min if self.qymax_limit < detector_qy_max: self.qymax_limit = detector_qy_max if qx_value < detector_qx_min or qx_value > detector_qx_max: return False if qy_value < detector_qy_min or qy_value > detector_qy_max: return False return True
[docs] def get_image(self, qx_value, qy_value, sigma_1, sigma_2, sigma_r, qx_min, qx_max, qy_min, qy_max, coord='cartesian', full_cal=True): """ Get the resolution in polar coordinate ready to plot : qx_value: qx_value value : qy_value: qy_value value : sigma_1: variance in r direction : sigma_2: variance in phi direction : coord: coordinate system of image, 'polar' or 'cartesian' """ # Get qx_max and qy_max... self._get_detector_qxqy_pixels() qr_value, phi = self._get_polar_value(qx_value, qy_value) # Check whether the q value is within the detector range if qx_min < self.qx_min: self.qx_min = qx_min #raise ValueError(msg) if qx_max > self.qx_max: self.qx_max = qx_max #raise ValueError(msg) if qy_min < self.qy_min: self.qy_min = qy_min #raise ValueError(msg) if qy_max > self.qy_max: self.qy_max = qy_max #raise ValueError(msg) if not full_cal: return None # Make an empty graph in the detector scale dx_size = (self.qx_max - self.qx_min) / (1000 - 1) dy_size = (self.qy_max - self.qy_min) / (1000 - 1) x_val = np.arange(self.qx_min, self.qx_max, dx_size) y_val = np.arange(self.qy_max, self.qy_min, -dy_size) q_1, q_2 = np.meshgrid(x_val, y_val) #q_phi = numpy.arctan(q_1,q_2) # check whether polar or cartesian if coord == 'polar': # Find polar values qr_value, phi = self._get_polar_value(qx_value, qy_value) q_1, q_2 = self._rotate_z(q_1, q_2, phi) qc_1 = qr_value qc_2 = 0.0 # Calculate the 2D Gaussian distribution image image = self._gaussian2d_polar(q_1, q_2, qc_1, qc_2, sigma_1, sigma_2, sigma_r) else: # catesian coordinate # qx_center qc_1 = qx_value # qy_center qc_2 = qy_value # Calculate the 2D Gaussian distribution image image = self._gaussian2d(q_1, q_2, qc_1, qc_2, sigma_1, sigma_2, sigma_r) # out side of detector if not self._within_detector_range(qx_value, qy_value): image *= 0.0 self.intensity = 0.0 #return self.image # Add it if there are more than one inputs. if len(self.image_lam) > 0: self.image_lam += image * self.intensity else: self.image_lam = image * self.intensity return self.image_lam
[docs] def plot_image(self, image): """ Plot image using pyplot : image: 2d resolution image : return plt: pylab object """ import matplotlib.pyplot as plt self.plot = plt plt.xlabel('$\\rm{Q}_{x} [A^{-1}]$') plt.ylabel('$\\rm{Q}_{y} [A^{-1}]$') # Max value of the image # max = numpy.max(image) qx_min, qx_max, qy_min, qy_max = self.get_detector_qrange() # Image im = plt.imshow(image, extent=[qx_min, qx_max, qy_min, qy_max]) # bilinear interpolation to make it smoother im.set_interpolation('bilinear') return plt
[docs] def reset_image(self): """ Reset image to default (=[]) """ self.image = []
[docs] def get_variance(self, size=[], distance=0, phi=0, comp='radial'): """ Get the variance when the slit/pinhole size is given : size: list that can be one(diameter for circular) or two components(lengths for rectangular) : distance: [z, x] where z along the incident beam, x // qx_value : comp: direction of the sigma; can be 'phi', 'y', 'x', and 'radial' : return variance: sigma^2 """ # check the length of size (list) len_size = len(size) # define sigma component direction if comp == 'radial': phi_x = math.cos(phi) phi_y = math.sin(phi) elif comp == 'phi': phi_x = math.sin(phi) phi_y = math.cos(phi) elif comp == 'x': phi_x = 1 phi_y = 0 elif comp == 'y': phi_x = 0 phi_y = 1 else: phi_x = 0 phi_y = 0 # calculate each component # for pinhole w/ radius = size[0]/2 if len_size == 1: x_comp = (0.5 * size[0]) * sqrt(3) y_comp = 0 # for rectangular slit elif len_size == 2: x_comp = size[0] * phi_x y_comp = size[1] * phi_y # otherwise else: raise ValueError(" Improper input...") # get them squared sigma = x_comp * x_comp sigma += y_comp * y_comp # normalize by distance sigma /= (distance * distance) return sigma
[docs] def get_variance_wave(self, A_value, radius, distance, spread, phi, comp='radial', switch='on'): """ Get the variance when the wavelength spread is given : radius: the radial distance from the beam center to the pix of q : distance: sample to detector distance : spread: wavelength spread (ratio) : comp: direction of the sigma; can be 'phi', 'y', 'x', and 'radial' : return variance: sigma^2 for 2d, sigma^2 for 1d [tuple] """ if switch.lower() == 'off': return 0, 0 # check the singular point if distance == 0 or comp == 'phi': return 0, 0 else: # calculate sigma^2 for 1d sigma1d = 2 * math.pow(radius/distance*spread, 2) if comp == 'x': sigma1d *= (math.cos(phi)*math.cos(phi)) elif comp == 'y': sigma1d *= (math.sin(phi)*math.sin(phi)) else: sigma1d *= 1 # sigma^2 for 2d # shift the coordinate due to the gravitational shift rad_x = radius * math.cos(phi) rad_y = A_value - radius * math.sin(phi) radius = math.sqrt(rad_x * rad_x + rad_y * rad_y) # new phi phi = math.atan2(-rad_y, rad_x) self.gravity_phi = phi # calculate sigma^2 sigma = 2 * math.pow(radius/distance*spread, 2) if comp == 'x': sigma *= (math.cos(phi)*math.cos(phi)) elif comp == 'y': sigma *= (math.sin(phi)*math.sin(phi)) else: sigma *= 1 return sigma, sigma1d
[docs] def get_variance_gravity(self, s_distance, d_distance, wavelength, spread, phi, comp='radial', switch='on'): """ Get the variance from gravity when the wavelength spread is given : s_distance: source to sample distance : d_distance: sample to detector distance : wavelength: wavelength : spread: wavelength spread (ratio) : comp: direction of the sigma; can be 'phi', 'y', 'x', and 'radial' : return variance: sigma^2 """ if switch.lower() == 'off': return 0 if self.mass == 0.0: return 0 # check the singular point if d_distance == 0 or comp == 'x': return 0 else: a_value = self._cal_A_value(None, s_distance, d_distance) # calculate sigma^2 sigma = math.pow(a_value / d_distance, 2) sigma *= math.pow(wavelength, 4) sigma *= math.pow(spread, 2) sigma *= 8 return sigma
def _cal_A_value(self, lamda, s_distance, d_distance): """ Calculate A value for gravity : s_distance: source to sample distance : d_distance: sample to detector distance """ # neutron mass in cgs unit self.mass = self.get_neutron_mass() # plank constant in cgs unit h_constant = _PLANK_H # gravity in cgs unit gravy = _GRAVITY # m/h m_over_h = self.mass / h_constant # A value a_value = d_distance * (s_distance + d_distance) a_value *= math.pow(m_over_h / 2, 2) a_value *= gravy # unit correction (1/cm to 1/A) for A and d_distance below a_value *= 1.0E-16 # if lamda is give (broad meanning of A) return 2* lamda^2 * A if lamda is not None: a_value *= (4 * lamda * lamda) return a_value
[docs] def get_intensity(self): """ Get intensity """ return self.wave.intensity
[docs] def get_wavelength(self): """ Get wavelength """ return self.wave.wavelength
[docs] def get_default_spectrum(self): """ Get default_spectrum """ return self.wave.get_default_spectrum()
[docs] def get_spectrum(self): """ Get _spectrum """ return self.wave.get_spectrum()
[docs] def get_wavelength_spread(self): """ Get wavelength spread """ return self.wave.wavelength_spread
[docs] def get_neutron_mass(self): """ Get Neutron mass """ return self.wave.mass
[docs] def get_source_aperture_size(self): """ Get source aperture size """ return self.aperture.source_size
[docs] def get_sample_aperture_size(self): """ Get sample aperture size """ return self.aperture.sample_size
[docs] def get_detector_pix_size(self): """ Get detector pixel size """ return self.detector.pix_size
[docs] def get_detector_size(self): """ Get detector size """ return self.detector.size
[docs] def get_source2sample_distance(self): """ Get detector source2sample_distance """ return self.aperture.sample_distance
[docs] def get_sample2sample_distance(self): """ Get detector sampleslitsample_distance """ return self.sample.distance
[docs] def get_sample2detector_distance(self): """ Get detector sample2detector_distance """ return self.detector.distance
[docs] def set_intensity(self, intensity): """ Set intensity """ self.wave.set_intensity(intensity)
[docs] def set_wave(self, wavelength): """ Set wavelength list or wavelength """ if wavelength.__class__.__name__ == 'list': self.wave.set_wave_list(wavelength) elif wavelength.__class__.__name__ == 'float': self.wave.set_wave_list([wavelength]) #self.set_wavelength(wavelength) else: raise TypeError("invalid wavlength---should be list or float")
[docs] def set_wave_spread(self, wavelength_spread): """ Set wavelength spread or wavelength spread """ if wavelength_spread.__class__.__name__ == 'list': self.wave.set_wave_spread_list(wavelength_spread) elif wavelength_spread.__class__.__name__ == 'float': self.wave.set_wave_spread_list([wavelength_spread]) else: raise TypeError("invalid wavelength spread---should be list or float")
[docs] def set_wavelength(self, wavelength): """ Set wavelength """ self.wavelength = wavelength self.wave.set_wavelength(wavelength)
[docs] def set_spectrum(self, spectrum): """ Set spectrum """ self.spectrum = spectrum self.wave.set_spectrum(spectrum)
[docs] def set_wavelength_spread(self, wavelength_spread): """ Set wavelength spread """ self.wavelength_spread = wavelength_spread self.wave.set_wavelength_spread(wavelength_spread)
[docs] def set_wave_list(self, wavelength_list, wavelengthspread_list): """ Set wavelength and its spread list """ self.wave.set_wave_list(wavelength_list) self.wave.set_wave_spread_list(wavelengthspread_list)
[docs] def get_wave_list(self): """ Set wavelength spread """ return self.wave.get_wave_list()
[docs] def get_intensity_list(self): """ Set wavelength spread """ return self.wave.get_intensity_list()
[docs] def set_source_aperture_size(self, size): """ Set source aperture size : param size: [dia_value] or [x_value, y_value] """ if len(size) < 1 or len(size) > 2: raise RuntimeError("The length of the size must be one or two.") self.aperture.set_source_size(size)
[docs] def set_neutron_mass(self, mass): """ Set Neutron mass """ self.wave.set_mass(mass) self.mass = mass
[docs] def set_sample_aperture_size(self, size): """ Set sample aperture size : param size: [dia_value] or [xheight_value, yheight_value] """ if len(size) < 1 or len(size) > 2: raise RuntimeError("The length of the size must be one or two.") self.aperture.set_sample_size(size)
[docs] def set_detector_pix_size(self, size): """ Set detector pixel size """ self.detector.set_pix_size(size)
[docs] def set_detector_size(self, size): """ Set detector size in number of pixels : param size: [pixel_nums] or [x_pix_num, yx_pix_num] """ self.detector.set_size(size)
[docs] def set_source2sample_distance(self, distance): """ Set detector source2sample_distance : param distance: [distance, x_offset] """ if len(distance) < 1 or len(distance) > 2: raise RuntimeError("The length of the size must be one or two.") self.aperture.set_sample_distance(distance)
[docs] def set_sample2sample_distance(self, distance): """ Set detector sample_slit2sample_distance : param distance: [distance, x_offset] """ if len(distance) < 1 or len(distance) > 2: raise RuntimeError("The length of the size must be one or two.") self.sample.set_distance(distance)
[docs] def set_sample2detector_distance(self, distance): """ Set detector sample2detector_distance : param distance: [distance, x_offset] """ if len(distance) < 1 or len(distance) > 2: raise RuntimeError("The length of the size must be one or two.") self.detector.set_distance(distance)
[docs] def get_all_instrument_params(self): """ Get all instrumental parameters """ self.mass = self.get_neutron_mass() self.spectrum = self.get_spectrum() self.source_aperture_size = self.get_source_aperture_size() self.sample_aperture_size = self.get_sample_aperture_size() self.detector_pix_size = self.get_detector_pix_size() self.detector_size = self.get_detector_size() self.source2sample_distance = self.get_source2sample_distance() self.sample2sample_distance = self.get_sample2sample_distance() self.sample2detector_distance = self.get_sample2detector_distance()
[docs] def get_detector_qrange(self): """ get max detector q ranges : return: qx_min, qx_max, qy_min, qy_max tuple """ if len(self.qxrange) != 2 or len(self.qyrange) != 2: return None qx_min = self.qxrange[0] qx_max = self.qxrange[1] qy_min = self.qyrange[0] qy_max = self.qyrange[1] return qx_min, qx_max, qy_min, qy_max
def _rotate_z(self, x_value, y_value, theta=0.0): """ Rotate x-y cordinate around z-axis by theta : x_value: numpy array of x values : y_value: numpy array of y values : theta: angle to rotate by in rad :return: x_prime, y-prime """ # rotate by theta x_prime = x_value * math.cos(theta) + y_value * math.sin(theta) y_prime = -x_value * math.sin(theta) + y_value * math.cos(theta) return x_prime, y_prime def _gaussian2d(self, x_val, y_val, x0_val, y0_val, sigma_x, sigma_y, sigma_r): """ Calculate 2D Gaussian distribution : x_val: x value : y_val: y value : x0_val: mean value in x-axis : y0_val: mean value in y-axis : sigma_x: variance in x-direction : sigma_y: variance in y-direction : return: gaussian (value) """ # phi values at each points (not at the center) x_value = x_val - x0_val y_value = y_val - y0_val phi_i = np.arctan2(y_val, x_val) # phi correction due to the gravity shift (in phi) phi_0 = math.atan2(y0_val, x0_val) phi_i = phi_i - phi_0 + self.gravity_phi sin_phi = np.sin(self.gravity_phi) cos_phi = np.cos(self.gravity_phi) x_p = x_value * cos_phi + y_value * sin_phi y_p = -x_value * sin_phi + y_value * cos_phi new_sig_x = sqrt(sigma_r * sigma_r / (sigma_x * sigma_x) + 1) new_sig_y = sqrt(sigma_r * sigma_r / (sigma_y * sigma_y) + 1) new_x = x_p * cos_phi / new_sig_x - y_p * sin_phi new_x /= sigma_x new_y = x_p * sin_phi / new_sig_y + y_p * cos_phi new_y /= sigma_y nu_value = -0.5 * (new_x * new_x + new_y * new_y) gaussian = np.exp(nu_value) # normalizing factor correction gaussian /= gaussian.sum() return gaussian def _gaussian2d_polar(self, x_val, y_val, x0_val, y0_val, sigma_x, sigma_y, sigma_r): """ Calculate 2D Gaussian distribution for polar coodinate : x_val: x value : y_val: y value : x0_val: mean value in x-axis : y0_val: mean value in y-axis : sigma_x: variance in r-direction : sigma_y: variance in phi-direction : sigma_r: wavelength variance in r-direction : return: gaussian (value) """ sigma_x = sqrt(sigma_x * sigma_x + sigma_r * sigma_r) # call gaussian1d gaussian = self._gaussian1d(x_val, x0_val, sigma_x) gaussian *= self._gaussian1d(y_val, y0_val, sigma_y) # normalizing factor correction if sigma_x != 0 and sigma_y != 0: gaussian *= sqrt(2 * pi) return gaussian def _gaussian1d(self, value, mean, sigma): """ Calculate 1D Gaussian distribution : value: value : mean: mean value : sigma: variance : return: gaussian (value) """ # default gaussian = 1.0 if sigma != 0: # get exponent nu_value = (value - mean) / sigma nu_value *= nu_value nu_value *= -0.5 gaussian *= np.exp(nu_value) gaussian /= sigma # normalize gaussian /= sqrt(2 * pi) return gaussian def _atan_phi(self, qy_value, qx_value): """ Find the angle phi of q on the detector plane for qx_value, qy_value given : qx_value: x component of q : qy_value: y component of q : return phi: the azimuthal angle of q on x-y plane """ phi = math.atan2(qy_value, qx_value) return phi def _get_detector_qxqy_pixels(self): """ Get the pixel positions of the detector in the qx_value-qy_value space """ # update all param values self.get_all_instrument_params() # wavelength wavelength = self.wave.wavelength # Gavity correction delta_y = self._get_beamcenter_drop() # in cm # detector_pix size detector_pix_size = self.detector_pix_size # Square or circular pixel if len(detector_pix_size) == 1: pix_x_size = detector_pix_size[0] pix_y_size = detector_pix_size[0] # rectangular pixel pixel elif len(detector_pix_size) == 2: pix_x_size = detector_pix_size[0] pix_y_size = detector_pix_size[1] else: raise ValueError(" Input value format error...") # Sample to detector distance = sample slit to detector # minus sample offset sample2detector_distance = self.sample2detector_distance[0] - \ self.sample2sample_distance[0] # detector offset in x-direction detector_offset = 0 try: detector_offset = self.sample2detector_distance[1] except: logger.error(sys.exc_value) # detector size in [no of pix_x,no of pix_y] detector_pix_nums_x = self.detector_size[0] # get pix_y if it exists, otherwse take it from [0] try: detector_pix_nums_y = self.detector_size[1] except: detector_pix_nums_y = self.detector_size[0] # detector offset in pix number offset_x = detector_offset / pix_x_size offset_y = delta_y / pix_y_size # beam center position in pix number (start from 0) center_x, center_y = self._get_beamcenter_position(detector_pix_nums_x, detector_pix_nums_y, offset_x, offset_y) # distance [cm] from the beam center on detector plane detector_ind_x = np.arange(detector_pix_nums_x) detector_ind_y = np.arange(detector_pix_nums_y) # shif 0.5 pixel so that pix position is at the center of the pixel detector_ind_x = detector_ind_x + 0.5 detector_ind_y = detector_ind_y + 0.5 # the relative postion from the beam center detector_ind_x = detector_ind_x - center_x detector_ind_y = detector_ind_y - center_y # unit correction in cm detector_ind_x = detector_ind_x * pix_x_size detector_ind_y = detector_ind_y * pix_y_size qx_value = np.zeros(len(detector_ind_x)) qy_value = np.zeros(len(detector_ind_y)) i = 0 for indx in detector_ind_x: qx_value[i] = self._get_qx(indx, sample2detector_distance, wavelength) i += 1 i = 0 for indy in detector_ind_y: qy_value[i] = self._get_qx(indy, sample2detector_distance, wavelength) i += 1 # qx_value and qy_value values in array qx_value = qx_value.repeat(detector_pix_nums_y) qx_value = qx_value.reshape(detector_pix_nums_x, detector_pix_nums_y) qy_value = qy_value.repeat(detector_pix_nums_x) qy_value = qy_value.reshape(detector_pix_nums_y, detector_pix_nums_x) qy_value = qy_value.transpose() # p min and max values among the center of pixels self.qx_min = np.min(qx_value) self.qx_max = np.max(qx_value) self.qy_min = np.min(qy_value) self.qy_max = np.max(qy_value) # Appr. min and max values of the detector display limits # i.e., edges of the last pixels. self.qy_min += self._get_qx(-0.5 * pix_y_size, sample2detector_distance, wavelength) self.qy_max += self._get_qx(0.5 * pix_y_size, sample2detector_distance, wavelength) #if self.qx_min == self.qx_max: self.qx_min += self._get_qx(-0.5 * pix_x_size, sample2detector_distance, wavelength) self.qx_max += self._get_qx(0.5 * pix_x_size, sample2detector_distance, wavelength) # min and max values of detecter self.detector_qx_min = self.qx_min self.detector_qx_max = self.qx_max self.detector_qy_min = self.qy_min self.detector_qy_max = self.qy_max # try to set it as a Data2D otherwise pass (not required for now) try: from sas.sascalc.dataloader.data_info import Data2D output = Data2D() inten = np.zeros_like(qx_value) output.data = inten output.qx_data = qx_value output.qy_data = qy_value except: logger.error(sys.exc_value) return output def _get_qx(self, dx_size, det_dist, wavelength): """ :param dx_size: x-distance from beam center [cm] :param det_dist: sample to detector distance [cm] :return: q-value at the given position """ # Distance from beam center in the plane of detector plane_dist = dx_size # full scattering angle on the x-axis theta = np.arctan(plane_dist / det_dist) qx_value = (2.0 * pi / wavelength) * np.sin(theta) return qx_value def _get_polar_value(self, qx_value, qy_value): """ Find qr_value and phi from qx_value and qy_value values : return qr_value, phi """ # find |q| on detector plane qr_value = sqrt(qx_value*qx_value + qy_value*qy_value) # find angle phi phi = self._atan_phi(qy_value, qx_value) return qr_value, phi def _get_beamcenter_position(self, num_x, num_y, offset_x, offset_y): """ :param num_x: number of pixel in x-direction :param num_y: number of pixel in y-direction :param offset: detector offset in x-direction in pix number :return: pix number; pos_x, pos_y in pix index """ # beam center position pos_x = num_x / 2 pos_y = num_y / 2 # correction for offset pos_x += offset_x # correction for gravity that is always negative pos_y -= offset_y return pos_x, pos_y def _get_beamcenter_drop(self): """ Get the beam center drop (delta y) in y diection due to gravity :return delta y: the beam center drop in cm """ # Check if mass == 0 (X-ray). if self.mass == 0: return 0 # Covert unit from A to cm unit_cm = 1e-08 # Velocity of neutron in horizontal direction (~ actual velocity) velocity = _PLANK_H / (self.mass * self.wave.wavelength * unit_cm) # Compute delta y delta_y = 0.5 delta_y *= _GRAVITY sampletodetector = self.sample2detector_distance[0] - \ self.sample2sample_distance[0] delta_y *= sampletodetector delta_y *= (self.source2sample_distance[0] + self.sample2detector_distance[0]) delta_y /= (velocity * velocity) return delta_y