Code refactoring
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72fd54d268
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585d4b3f54
@ -351,10 +351,6 @@ def create():
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fwhm = np.sqrt(0.4639 * expr ** 2 - 0.4452 * expr + 0.1506) * res_mult # res in deg
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return fwhm
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def _bg(x, a, b):
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"""Linear background function """
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return a * x + b
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def plot_file_callback():
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orth_dir = list(map(float, hkl_normal.value.split()))
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cut_tol = hkl_delta.value
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@ -411,28 +407,26 @@ def create():
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# conversion matrix:
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M = np.array(
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[
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[1, 1 * np.cos(gamma_star), 1 * np.cos(beta_star)],
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[0, 1 * np.sin(gamma_star), -np.sin(beta_star) * np.cos(alpha)],
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[0, 0, 1 * np.sin(beta_star) * np.sin(alpha)],
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[1, np.cos(gamma_star), np.cos(beta_star)],
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[0, np.sin(gamma_star), -np.sin(beta_star) * np.cos(alpha)],
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[0, 0, np.sin(beta_star) * np.sin(alpha)],
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]
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)
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M_inv = np.linalg.inv(M)
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# Calculate in-plane y-direction
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x_c = np.matmul(M, x_dir)
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y_c = np.matmul(M, y_dir)
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o_c = np.matmul(M, orth_dir)
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x_c = M @ x_dir
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y_c = M @ y_dir
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o_c = M @ orth_dir
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# Normalize all directions
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y_c = y_c / np.linalg.norm(y_c)
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x_c = x_c / np.linalg.norm(x_c)
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o_c = o_c / np.linalg.norm(o_c)
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# Calculations
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# Read all data
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hkl_coord = []
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intensity_vec = []
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num_vec = []
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k_flag_vec = []
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file_flag_vec = []
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res_vec_x = []
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@ -449,19 +443,19 @@ def create():
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return
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# Loop throguh all data
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for i in range(len(file_data)):
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om = file_data[i]["omega"]
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gammad = file_data[i]["twotheta"]
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chi = file_data[i]["chi"]
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phi = file_data[i]["phi"]
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for scan in file_data:
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om = scan["omega"]
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gammad = scan["twotheta"]
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chi = scan["chi"]
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phi = scan["phi"]
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nud = 0 # 1d detector
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ub = file_data[i]["ub"]
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ddist = float(file_data[i]["detectorDistance"])
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counts = file_data[i]["counts"]
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mon = file_data[i]["monitor"]
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ub = scan["ub"]
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ddist = float(scan["detectorDistance"])
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counts = scan["counts"]
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mon = scan["monitor"]
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# Determine wavelength from mcvl value (is wavelength stored anywhere???)
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mcvl = file_data[i]["mcvl"]
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mcvl = scan["mcvl"]
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if mcvl == 2.2:
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wave = 1.178
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elif mcvl == 7.0:
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@ -471,20 +465,15 @@ def create():
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# Calculate resolution in degrees
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res = _res_fun(gammad, wave, res_mult)
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# convert to resolution in hkl along scan line
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ang2hkl_1d = pyzebra.ang2hkl_1d
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res_x = []
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res_y = []
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scan_om = np.linspace(om[0], om[-1], num=res_N)
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for i2 in range(res_N):
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expr1 = ang2hkl_1d(
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wave, ddist, gammad, scan_om[i2] + res / 2, chi, phi, nud, ub
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)
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expr2 = ang2hkl_1d(
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wave, ddist, gammad, scan_om[i2] - res / 2, chi, phi, nud, ub
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)
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hkl_temp = np.abs(expr1 - expr2) / 2
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hkl_temp = np.matmul(M, hkl_temp)
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for _om in np.linspace(om[0], om[-1], num=res_N):
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expr1 = ang2hkl_1d(wave, ddist, gammad, _om + res / 2, chi, phi, nud, ub)
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expr2 = ang2hkl_1d(wave, ddist, gammad, _om - res / 2, chi, phi, nud, ub)
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hkl_temp = M @ (np.abs(expr1 - expr2) / 2)
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res_x.append(hkl_temp[0])
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res_y.append(hkl_temp[1])
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@ -502,45 +491,20 @@ def create():
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x2 = om[-1]
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a = (y1 - y2) / (x1 - x2)
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b = y1 - a * x1
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intensity_exp = np.sum(counts - _bg(om, a, b))
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intensity_exp = np.sum(counts - (a * om + b))
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c = int(intensity_exp / mon * 10000)
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# Recognize k_flag_vec
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found = 0
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for j2 in range(len(k)):
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# Check if all three components match
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test1 = (
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np.abs(min(1 - np.mod(hkl_m[0], 1), np.mod(hkl_m[0], 1)) - k[j2][0]) < tol_k
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)
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test2 = (
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np.abs(min(1 - np.mod(hkl_m[1], 1), np.mod(hkl_m[1], 1)) - k[j2][1]) < tol_k
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)
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test3 = (
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np.abs(min(1 - np.mod(hkl_m[2], 1), np.mod(hkl_m[2], 1)) - k[j2][2]) < tol_k
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)
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if test1 and test2 and test3:
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found = 1
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min_hkl_m = np.minimum(1 - hkl_m % 1, hkl_m % 1)
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for j2, _k in enumerate(k):
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if all(np.abs(min_hkl_m - _k) < tol_k):
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k_flag_vec.append(j2)
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break
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if not found:
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else:
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k_flag_vec.append(len(k))
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# Save data
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hkl_list = [
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hkl1[0],
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hkl1[1],
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hkl1[2],
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hkl2[0],
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hkl2[1],
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hkl2[2],
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hkl_m[0],
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hkl_m[1],
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hkl_m[2],
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]
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hkl_coord.append(hkl_list)
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num_vec.append(i)
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hkl_coord.append([hkl1, hkl2, hkl_m])
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intensity_vec.append(c)
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file_flag_vec.append(j)
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res_vec_x.append(res_x)
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@ -555,29 +519,25 @@ def create():
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xs_minor, ys_minor = [], []
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if grid_flag:
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for yy in np.arange(min_grid_y, max_grid_y, 1):
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hkl1 = np.matmul(M, [0, yy, 0])
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xs.append([-5, 5])
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hkl1 = M @ [0, yy, 0]
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xs.append([min_grid_y, max_grid_y])
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ys.append([hkl1[1], hkl1[1]])
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for xx in np.arange(min_grid_x, max_grid_x, 1):
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hkl1 = [xx, min_grid_x, 0]
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hkl2 = [xx, max_grid_x, 0]
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hkl1 = np.matmul(M, hkl1)
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hkl2 = np.matmul(M, hkl2)
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hkl1 = M @ [xx, min_grid_x, 0]
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hkl2 = M @ [xx, max_grid_x, 0]
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xs.append([hkl1[0], hkl2[0]])
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ys.append([hkl1[1], hkl2[1]])
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if grid_minor_flag:
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for yy in np.arange(min_grid_y, max_grid_y, 1 / grid_div):
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hkl1 = np.matmul(M, [0, yy, 0])
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hkl1 = M @ [0, yy, 0]
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xs_minor.append([min_grid_y, max_grid_y])
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ys_minor.append([hkl1[1], hkl1[1]])
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for xx in np.arange(min_grid_x, max_grid_x, 1 / grid_div):
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hkl1 = [xx, min_grid_x, 0]
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hkl2 = [xx, max_grid_x, 0]
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hkl1 = np.matmul(M, hkl1)
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hkl2 = np.matmul(M, hkl2)
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hkl1 = M @ [xx, min_grid_x, 0]
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hkl2 = M @ [xx, max_grid_x, 0]
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xs_minor.append([hkl1[0], hkl2[0]])
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ys_minor.append([hkl1[1], hkl2[1]])
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@ -587,20 +547,17 @@ def create():
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el_x, el_y, el_w, el_h, el_c = [], [], [], [], []
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scan_xs, scan_ys, scan_x, scan_y = [], [], [], []
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scan_m, scan_s, scan_c, scan_l = [], [], [], []
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for j in range(len(num_vec)):
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for j in range(len(hkl_coord)):
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# Get middle hkl from list
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hklm = [x for x in hkl_coord[j][6:9]]
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hklm = np.matmul(M, hklm)
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hklm = M @ hkl_coord[j][2]
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# Decide if point is in the cut
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proj = np.dot(hklm, o_c)
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if abs(proj - cut_or) >= cut_tol:
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continue
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hkl1 = [x for x in hkl_coord[j][0:3]]
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hkl2 = [x for x in hkl_coord[j][3:6]]
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hkl1 = np.matmul(M, hkl1)
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hkl2 = np.matmul(M, hkl2)
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hkl1 = M @ hkl_coord[j][0]
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hkl2 = M @ hkl_coord[j][1]
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if intensity_flag:
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markersize = max(1, int(intensity_vec[j] / max(intensity_vec) * 20))
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