apply black formating
Co-authored-by: Ivan Usov <ivan.a.usov@gmail.com>
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a287b78245
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@ -77,6 +77,7 @@ def update_image():
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image_glyph.color_mapper.low = im_min
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image_glyph.color_mapper.high = im_max
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def calculate_hkl(setup_type="nb_bi"):
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h = np.empty(shape=(IMAGE_H, IMAGE_W))
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k = np.empty(shape=(IMAGE_H, IMAGE_W))
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@ -435,6 +436,7 @@ def auto_toggle_callback(state):
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update_image()
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auto_toggle = Toggle(label="Auto Range", active=True, button_type="default")
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auto_toggle.on_click(auto_toggle_callback)
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@ -1,5 +1,6 @@
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import h5py
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def read_h5meta(filepath):
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"""Read and parse content of a h5meta file.
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@ -57,6 +58,7 @@ def read_detector_data(filepath):
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return det_data
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def open_h5meta(filepath):
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"""Open h5meta file like *.cami
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@ -4,6 +4,7 @@ from scipy.optimize import curve_fit
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from matplotlib import pyplot as plt
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import pyzebra
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def z4frgn(wave, ga, nu):
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"""CALCULATES DIFFRACTION VECTOR IN LAB SYSTEM FROM GA AND NU
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@ -18,13 +19,14 @@ def z4frgn(wave,ga,nu):
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pir = 180 / np.pi
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gar = ga / pir
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nur = nu / pir
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z4 = [0., 0., 0.]
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z4 = [0.0, 0.0, 0.0]
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z4[0] = (sin(gar) * cos(nur)) / wave
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z4[1]=( cos(gar)*cos(nur)-1. )/wave
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z4[1] = (cos(gar) * cos(nur) - 1.0) / wave
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z4[2] = (sin(nur)) / wave
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return z4
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def phimat(phi):
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"""BUSING AND LEVY CONVENTION ROTATION MATRIX FOR PHI OR OMEGA
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@ -48,6 +50,7 @@ def phimat(phi):
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return dum
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def z1frnb(wave, ga, nu, om):
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"""CALCULATE DIFFRACTION VECTOR Z1 FROM GA, OM, NU, ASSUMING CH=PH=0
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@ -65,6 +68,7 @@ def z1frnb(wave,ga,nu,om):
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return z3
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def chimat(chi):
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"""BUSING AND LEVY CONVENTION ROTATION MATRIX FOR CHI
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@ -88,6 +92,7 @@ def chimat(chi):
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return dum
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def z1frz3(z3, chi, phi):
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"""CALCULATE Z1 = [PHI]T.[CHI]T.Z3
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@ -108,6 +113,7 @@ def z1frz3(z3,chi,phi):
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return z1
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def z1frmd(wave, ga, om, chi, phi, nu):
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"""CALCULATE DIFFRACTION VECTOR Z1 FROM CH, PH, GA, OM, NU
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@ -122,6 +128,7 @@ def z1frmd(wave,ga,om,chi,phi,nu):
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return z1
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def det2pol(ddist, gammad, nud, x, y):
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"""CONVERTS FROM DETECTOR COORDINATES TO POLAR COORDINATES
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@ -150,6 +157,7 @@ def det2pol(ddist,gammad,nud,x,y):
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return gamma, nu
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def eqchph(z1):
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"""CALCULATE CHI, PHI TO PUT THE VECTOR Z1 IN THE EQUATORIAL PLANE
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@ -292,6 +300,7 @@ def fixdnu(wave,z1,ch2,ph2,nu):
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# for test run:
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# angtohkl(wave=1.18,ddist=616,gammad=48.66,om=-22.80,ch=0,ph=0,nud=0,x=128,y=64)
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def angtohkl(wave, ddist, gammad, om, ch, ph, nud, x, y):
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"""finds hkl-indices of a reflection from its position (x,y,angles) at the 2d-detector
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@ -305,16 +314,44 @@ def angtohkl(wave,ddist,gammad,om,ch,ph,nud,x,y):
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# define ub matrix if testing angtohkl(wave=1.18,ddist=616,gammad=48.66,om=-22.80,ch=0,ph=0,nud=0,x=128,y=64) against f90:
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# ub = np.array([-0.0178803,-0.0749231,0.0282804,-0.0070082,-0.0368001,-0.0577467,0.1609116,-0.0099281,0.0006274]).reshape(3,3)
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ub = np.array([0.04489,0.02045,-0.2334,-0.06447,0.00129,-0.16356,-0.00328,0.2542,0.0196]).reshape(3,3)
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print('The input values are: ga=', gammad, ', om=', om, ', ch=', ch, ', ph=', ph, ', nu=', nud, ', x=', x, ', y=', y)
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ub = np.array(
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[0.04489, 0.02045, -0.2334, -0.06447, 0.00129, -0.16356, -0.00328, 0.2542, 0.0196]
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).reshape(3, 3)
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print(
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"The input values are: ga=",
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gammad,
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", om=",
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om,
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", ch=",
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ch,
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", ph=",
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ph,
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", nu=",
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nud,
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", x=",
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x,
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", y=",
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y,
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)
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ga, nu = det2pol(ddist, gammad, nud, x, y)
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print('The calculated actual angles are: ga=', ga, ', om=', om, ', ch=', ch, ', ph=', ph, ', nu=', nu)
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print(
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"The calculated actual angles are: ga=",
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ga,
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", om=",
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om,
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", ch=",
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ch,
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", ph=",
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ph,
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", nu=",
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nu,
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)
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z1 = z1frmd(wave, ga, om, ch, ph, nu)
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print('The diffraction vector is:', z1[0],z1[1],z1[2])
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print("The diffraction vector is:", z1[0], z1[1], z1[2])
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ubinv = np.linalg.inv(ub)
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@ -322,12 +359,23 @@ def angtohkl(wave,ddist,gammad,om,ch,ph,nud,x,y):
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k = ubinv[1, 0] * z1[0] + ubinv[1, 1] * z1[1] + ubinv[1, 2] * z1[2]
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l = ubinv[2, 0] * z1[0] + ubinv[2, 1] * z1[1] + ubinv[2, 2] * z1[2]
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print('The Miller indexes are:', h,k,l)
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print("The Miller indexes are:", h, k, l)
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ch2, ph2 = eqchph(z1)
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ch, ph, ga, om = fixdnu(wave, z1, ch2, ph2, nu)
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print('Bisecting angles to put reflection into the detector center: ga=', ga, ', om=', om, ', ch=', ch, ', ph=', ph, ', nu=', nu)
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print(
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"Bisecting angles to put reflection into the detector center: ga=",
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ga,
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", om=",
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om,
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", ch=",
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ch,
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", ph=",
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ph,
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", nu=",
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nu,
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)
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def ang2hkl(wave, ddist, gammad, om, ch, ph, nud, ub, x, y):
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@ -340,6 +388,7 @@ def ang2hkl(wave, ddist, gammad, om, ch, ph, nud, ub, x, y):
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return hkl
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def gauss(x, *p):
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"""Defines Gaussian function
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@ -350,7 +399,8 @@ def gauss(x, *p):
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Gaussian function
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"""
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A, mu, sigma = p
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return A*np.exp(-(x-mu)**2/(2.*sigma**2))
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return A * np.exp(-((x - mu) ** 2) / (2.0 * sigma ** 2))
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def box_int(file, box):
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"""Calculates center of the peak in the NB-geometry angles and Intensity of the peak
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@ -376,7 +426,7 @@ def box_int(file,box):
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om = dat["rot_angle"][fr0:frN]
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cnts = np.sum(dat["data"][fr0:frN, j0:jN, i0:iN], axis=(1, 2))
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p0 = [1., 0., 1.]
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p0 = [1.0, 0.0, 1.0]
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coeff, var_matrix = curve_fit(gauss, range(len(cnts)), cnts, p0=p0)
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frC = fr0 + coeff[1]
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@ -393,16 +443,16 @@ def box_int(file,box):
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plt.subplot(131)
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plt.plot(range(len(cnts)), cnts)
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plt.plot(x_fit, y_fit)
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plt.ylabel('Intensity in the box')
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plt.xlabel('Frame N of the box')
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label='om'
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plt.ylabel("Intensity in the box")
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plt.xlabel("Frame N of the box")
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label = "om"
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# gamma fit
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sliceXY = dat["data"][fr0:frN, j0:jN, i0:iN]
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sliceXZ = np.sum(sliceXY, axis=1)
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sliceYZ = np.sum(sliceXY, axis=2)
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projX = np.sum(sliceXZ, axis=0)
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p0 = [1., 0., 1.]
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p0 = [1.0, 0.0, 1.0]
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coeff, var_matrix = curve_fit(gauss, range(len(projX)), projX, p0=p0)
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x = i0 + coeff[1]
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# gamma plot
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@ -411,12 +461,12 @@ def box_int(file,box):
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plt.subplot(132)
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plt.plot(range(len(projX)), projX)
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plt.plot(x_fit, y_fit)
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plt.ylabel('Intensity in the box')
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plt.xlabel('X-pixel of the box')
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plt.ylabel("Intensity in the box")
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plt.xlabel("X-pixel of the box")
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# nu fit
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projY = np.sum(sliceYZ, axis=0)
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p0 = [1., 0., 1.]
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p0 = [1.0, 0.0, 1.0]
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coeff, var_matrix = curve_fit(gauss, range(len(projY)), projY, p0=p0)
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y = j0 + coeff[1]
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# nu plot
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@ -425,9 +475,9 @@ def box_int(file,box):
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plt.subplot(133)
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plt.plot(range(len(projY)), projY)
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plt.plot(x_fit, y_fit)
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plt.ylabel('Intensity in the box')
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plt.xlabel('Y-pixel of the box')
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plt.ylabel("Intensity in the box")
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plt.xlabel("Y-pixel of the box")
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ga, nu = pyzebra.det2pol(ddist, sttC, nuC, x, y)
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return ga[0], omP, nu[0], Int # x0,y0,x0_fit,y0_fit,x1,y1,x1_fit,y1_fit,x2,y2,x2_fit,y2_fit
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return ga[0], omP, nu[0], Int
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