apply black formating

Co-authored-by: Ivan Usov <ivan.a.usov@gmail.com>

pyzebra/app.py

@@ -77,6 +77,7 @@ def update_image():
         image_glyph.color_mapper.low = im_min
         image_glyph.color_mapper.high = im_max
 
+
 def calculate_hkl(setup_type="nb_bi"):
     h = np.empty(shape=(IMAGE_H, IMAGE_W))
     k = np.empty(shape=(IMAGE_H, IMAGE_W))
@@ -435,6 +436,7 @@ def auto_toggle_callback(state):
 
     update_image()
 
+
 auto_toggle = Toggle(label="Auto Range", active=True, button_type="default")
 auto_toggle.on_click(auto_toggle_callback)
 

pyzebra/h5.py

@@ -1,5 +1,6 @@
 import h5py
 
+
 def read_h5meta(filepath):
     """Read and parse content of a h5meta file.
 
@@ -57,6 +58,7 @@ def read_detector_data(filepath):
 
     return det_data
 
+
 def open_h5meta(filepath):
     """Open h5meta file like *.cami
 

pyzebra/xtal.py

@@ -4,6 +4,7 @@ from scipy.optimize import curve_fit
 from matplotlib import pyplot as plt
 import pyzebra
 
+
 def z4frgn(wave, ga, nu):
     """CALCULATES DIFFRACTION VECTOR IN LAB SYSTEM FROM GA AND NU
 
@@ -18,13 +19,14 @@ def z4frgn(wave,ga,nu):
     pir = 180 / np.pi
     gar = ga / pir
     nur = nu / pir
-    z4 = [0., 0., 0.]
+    z4 = [0.0, 0.0, 0.0]
     z4[0] = (sin(gar) * cos(nur)) / wave
-    z4[1]=( cos(gar)*cos(nur)-1. )/wave
+    z4[1] = (cos(gar) * cos(nur) - 1.0) / wave
     z4[2] = (sin(nur)) / wave
 
     return z4
 
+
 def phimat(phi):
     """BUSING AND LEVY CONVENTION ROTATION MATRIX FOR PHI OR OMEGA
 
@@ -48,6 +50,7 @@ def phimat(phi):
 
     return dum
 
+
 def z1frnb(wave, ga, nu, om):
     """CALCULATE DIFFRACTION VECTOR Z1 FROM GA, OM, NU, ASSUMING CH=PH=0
 
@@ -65,6 +68,7 @@ def z1frnb(wave,ga,nu,om):
 
     return z3
 
+
 def chimat(chi):
     """BUSING AND LEVY CONVENTION ROTATION MATRIX FOR CHI
 
@@ -88,6 +92,7 @@ def chimat(chi):
 
     return dum
 
+
 def z1frz3(z3, chi, phi):
     """CALCULATE Z1 = [PHI]T.[CHI]T.Z3
 
@@ -108,6 +113,7 @@ def z1frz3(z3,chi,phi):
 
     return z1
 
+
 def z1frmd(wave, ga, om, chi, phi, nu):
     """CALCULATE DIFFRACTION VECTOR Z1 FROM CH, PH, GA, OM, NU
 
@@ -122,6 +128,7 @@ def z1frmd(wave,ga,om,chi,phi,nu):
 
     return z1
 
+
 def det2pol(ddist, gammad, nud, x, y):
     """CONVERTS FROM DETECTOR COORDINATES TO POLAR COORDINATES
 
@@ -150,6 +157,7 @@ def det2pol(ddist,gammad,nud,x,y):
 
     return gamma, nu
 
+
 def eqchph(z1):
     """CALCULATE CHI, PHI TO PUT THE VECTOR Z1 IN THE EQUATORIAL PLANE
 
@@ -292,6 +300,7 @@ def fixdnu(wave,z1,ch2,ph2,nu):
 # for test run:
 #   angtohkl(wave=1.18,ddist=616,gammad=48.66,om=-22.80,ch=0,ph=0,nud=0,x=128,y=64)
 
+
 def angtohkl(wave, ddist, gammad, om, ch, ph, nud, x, y):
     """finds hkl-indices of a reflection from its position (x,y,angles) at the 2d-detector
 
@@ -305,16 +314,44 @@ def angtohkl(wave,ddist,gammad,om,ch,ph,nud,x,y):
 
     # 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:
     #    ub = np.array([-0.0178803,-0.0749231,0.0282804,-0.0070082,-0.0368001,-0.0577467,0.1609116,-0.0099281,0.0006274]).reshape(3,3)
-    ub = np.array([0.04489,0.02045,-0.2334,-0.06447,0.00129,-0.16356,-0.00328,0.2542,0.0196]).reshape(3,3)    
+    ub = np.array(
-    print('The input values are: ga=', gammad, ', om=', om, ', ch=', ch, ', ph=', ph, ', nu=', nud, ', x=', x, ', y=', y)
+        [0.04489, 0.02045, -0.2334, -0.06447, 0.00129, -0.16356, -0.00328, 0.2542, 0.0196]
+    ).reshape(3, 3)
+    print(
+        "The input values are: ga=",
+        gammad,
+        ", om=",
+        om,
+        ", ch=",
+        ch,
+        ", ph=",
+        ph,
+        ", nu=",
+        nud,
+        ", x=",
+        x,
+        ", y=",
+        y,
+    )
 
     ga, nu = det2pol(ddist, gammad, nud, x, y)
 
-    print('The calculated actual angles are: ga=', ga, ', om=', om, ', ch=', ch, ', ph=', ph, ', nu=', nu)
+    print(
+        "The calculated actual angles are: ga=",
+        ga,
+        ", om=",
+        om,
+        ", ch=",
+        ch,
+        ", ph=",
+        ph,
+        ", nu=",
+        nu,
+    )
 
     z1 = z1frmd(wave, ga, om, ch, ph, nu)
 
-    print('The diffraction vector is:', z1[0],z1[1],z1[2])
+    print("The diffraction vector is:", z1[0], z1[1], z1[2])
 
     ubinv = np.linalg.inv(ub)
 
@@ -322,12 +359,23 @@ def angtohkl(wave,ddist,gammad,om,ch,ph,nud,x,y):
     k = ubinv[1, 0] * z1[0] + ubinv[1, 1] * z1[1] + ubinv[1, 2] * z1[2]
     l = ubinv[2, 0] * z1[0] + ubinv[2, 1] * z1[1] + ubinv[2, 2] * z1[2]
 
-    print('The Miller indexes are:', h,k,l)
+    print("The Miller indexes are:", h, k, l)
 
     ch2, ph2 = eqchph(z1)
     ch, ph, ga, om = fixdnu(wave, z1, ch2, ph2, nu)
 
-    print('Bisecting angles to put reflection into the detector center: ga=', ga, ', om=', om, ', ch=', ch, ', ph=', ph, ', nu=', nu)
+    print(
+        "Bisecting angles to put reflection into the detector center: ga=",
+        ga,
+        ", om=",
+        om,
+        ", ch=",
+        ch,
+        ", ph=",
+        ph,
+        ", nu=",
+        nu,
+    )
 
 
 def ang2hkl(wave, ddist, gammad, om, ch, ph, nud, ub, x, y):
@@ -340,6 +388,7 @@ def ang2hkl(wave, ddist, gammad, om, ch, ph, nud, ub, x, y):
 
     return hkl
 
+
 def gauss(x, *p):
     """Defines Gaussian function
 
@@ -350,7 +399,8 @@ def gauss(x, *p):
         Gaussian function
     """
     A, mu, sigma = p
-    return A*np.exp(-(x-mu)**2/(2.*sigma**2))
+    return A * np.exp(-((x - mu) ** 2) / (2.0 * sigma ** 2))
+
 
 def box_int(file, box):
     """Calculates center of the peak in the NB-geometry angles and Intensity of the peak
@@ -376,7 +426,7 @@ def box_int(file,box):
     om = dat["rot_angle"][fr0:frN]
     cnts = np.sum(dat["data"][fr0:frN, j0:jN, i0:iN], axis=(1, 2))
 
-    p0 = [1., 0., 1.]
+    p0 = [1.0, 0.0, 1.0]
     coeff, var_matrix = curve_fit(gauss, range(len(cnts)), cnts, p0=p0)
 
     frC = fr0 + coeff[1]
@@ -393,16 +443,16 @@ def box_int(file,box):
     plt.subplot(131)
     plt.plot(range(len(cnts)), cnts)
     plt.plot(x_fit, y_fit)
-    plt.ylabel('Intensity in the box')
+    plt.ylabel("Intensity in the box")
-    plt.xlabel('Frame N of the box')
+    plt.xlabel("Frame N of the box")
-    label='om'
+    label = "om"
     # gamma fit
     sliceXY = dat["data"][fr0:frN, j0:jN, i0:iN]
     sliceXZ = np.sum(sliceXY, axis=1)
     sliceYZ = np.sum(sliceXY, axis=2)
 
     projX = np.sum(sliceXZ, axis=0)
-    p0 = [1., 0., 1.]
+    p0 = [1.0, 0.0, 1.0]
     coeff, var_matrix = curve_fit(gauss, range(len(projX)), projX, p0=p0)
     x = i0 + coeff[1]
     # gamma plot
@@ -411,12 +461,12 @@ def box_int(file,box):
     plt.subplot(132)
     plt.plot(range(len(projX)), projX)
     plt.plot(x_fit, y_fit)
-    plt.ylabel('Intensity in the box')
+    plt.ylabel("Intensity in the box")
-    plt.xlabel('X-pixel of the box')
+    plt.xlabel("X-pixel of the box")
 
     # nu fit
     projY = np.sum(sliceYZ, axis=0)
-    p0 = [1., 0., 1.]
+    p0 = [1.0, 0.0, 1.0]
     coeff, var_matrix = curve_fit(gauss, range(len(projY)), projY, p0=p0)
     y = j0 + coeff[1]
     # nu plot
@@ -425,9 +475,9 @@ def box_int(file,box):
     plt.subplot(133)
     plt.plot(range(len(projY)), projY)
     plt.plot(x_fit, y_fit)
-    plt.ylabel('Intensity in the box')
+    plt.ylabel("Intensity in the box")
-    plt.xlabel('Y-pixel of the box')
+    plt.xlabel("Y-pixel of the box")
 
     ga, nu = pyzebra.det2pol(ddist, sttC, nuC, x, y)
 
-    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
+    return ga[0], omP, nu[0], Int