Add basic spind processing
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@ -1,18 +1,23 @@
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import json
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import math
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import os
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import subprocess
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import tempfile
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import numpy as np
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from bokeh.layouts import column, row
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from bokeh.models import (
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Button,
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Panel,
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Spinner,
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TextAreaInput,
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TextInput,
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)
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from bokeh.models import Button, Panel, Spinner, TextAreaInput, TextInput
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from scipy.optimize import curve_fit
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import pyzebra
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def create():
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path_prefix_textinput = TextInput(title="Path prefix:", value="")
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selection_list = TextAreaInput(title="ROIs:", rows=7)
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lattice_const_textinput = TextInput(title="Lattice constants:")
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lattice_const_textinput = TextInput(
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title="Lattice constants:", value="8.3211,8.3211,8.3211,90.00,90.00,90.00"
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)
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max_res_spinner = Spinner(title="max-res", value=2, step=0.01)
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seed_pool_size_spinner = Spinner(title="seed-pool-size", value=5, step=0.01)
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seed_len_tol_spinner = Spinner(title="seed-len-tol", value=0.02, step=0.01)
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@ -21,7 +26,55 @@ def create():
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def process_button_callback():
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with tempfile.TemporaryDirectory() as temp_dir:
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temp_file = temp_dir + "/temp.xml"
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temp_peak_list_dir = os.path.join(temp_dir, "peak_list")
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os.mkdir(temp_peak_list_dir)
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temp_event_file = os.path.join(temp_peak_list_dir, "event-0.txt")
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temp_hkl_file = os.path.join(temp_dir, "hkl.h5")
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roi_dict = json.loads(selection_list.value)
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subprocess.run(
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[
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"mpiexec",
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"-n",
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"2",
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"python",
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"spind/gen_hkl_table.py",
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lattice_const_textinput.value,
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"--max-res",
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str(max_res_spinner.value),
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"-o",
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temp_hkl_file,
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],
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check=True,
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)
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prepare_event_file(temp_event_file, roi_dict, path_prefix_textinput.value)
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subprocess.run(
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[
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"mpiexec",
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"-n",
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"2",
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"python",
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"spind/SPIND.py",
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temp_peak_list_dir,
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temp_hkl_file,
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"-o",
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"temp_dir",
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"--seed-pool-size",
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str(seed_pool_size_spinner.value),
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"--seed-len-tol",
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str(seed_len_tol_spinner.value),
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"--seed-angle-tol",
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str(seed_angle_tol_spinner.value),
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"--eval-hkl-tol",
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str(eval_hkl_tol_spinner.value),
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],
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check=True,
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)
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with open(os.path.join(temp_dir, "spind.txt")) as f_out:
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output_textarea.value = f_out.readlines()
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process_button = Button(label="Process", button_type="primary")
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process_button.on_click(process_button_callback)
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@ -30,6 +83,7 @@ def create():
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tab_layout = row(
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column(
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path_prefix_textinput,
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selection_list,
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lattice_const_textinput,
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max_res_spinner,
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@ -43,3 +97,69 @@ def create():
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)
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return Panel(child=tab_layout, title="spind")
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def gauss(x, *p):
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"""Defines Gaussian function
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Args:
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A - amplitude, mu - position of the center, sigma - width
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Returns:
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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) / (2.0 * sigma ** 2))
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def prepare_event_file(export_filename, roi_dict, path_prefix=""):
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p0 = [1.0, 0.0, 1.0]
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maxfev = 100000
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with open(export_filename, "w") as f:
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for file, rois in roi_dict.items():
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dat = pyzebra.read_detector_data(path_prefix + file)
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# here is assumed that only omega_angle can vary
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sttC = dat["pol_angle"][0]
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om = dat["rot_angle"]
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nuC = dat["tlt_angle"][0]
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ddist = dat["ddist"]
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for roi in rois:
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x0, xN, y0, yN, fr0, frN = roi
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data_roi = dat["data"][fr0:frN, y0:yN, x0:xN]
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# omega fit Here one should change to any rot_angle, i.e. phi
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cnts = np.sum(data_roi, axis=(1, 2))
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coeff, _ = curve_fit(gauss, range(len(cnts)), cnts, p0=p0, maxfev=maxfev)
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m = cnts.mean()
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sd = cnts.std()
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snr_cnts = np.where(sd == 0, 0, m / sd)
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frC = fr0 + coeff[1]
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omF = om[math.floor(frC)]
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omC = om[math.ceil(frC)]
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frStep = frC - math.floor(frC)
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omStep = omC - omF
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omP = omF + omStep * frStep
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Int = coeff[1] * abs(coeff[2] * omStep) * math.sqrt(2) * math.sqrt(np.pi)
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# gamma fit
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projX = np.sum(data_roi, axis=(0, 1))
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coeff, _ = curve_fit(gauss, range(len(projX)), projX, p0=p0, maxfev=maxfev)
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x = x0 + coeff[1]
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x_pos = x0 + round(coeff[1])
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# nu fit
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projY = np.sum(data_roi, axis=(0, 2))
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coeff, _ = curve_fit(gauss, range(len(projY)), projY, p0=p0, maxfev=maxfev)
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y = y0 + coeff[1]
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y_pos = y0 + round(coeff[1])
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ga, nu = pyzebra.det2pol(ddist, sttC, nuC, x, y)
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diff_vector = pyzebra.z1frmd(
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dat["wave"], ga, omP, dat["chi_angle"][0], dat["phi_angle"][0], nu[0]
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)
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d_spacing = float(pyzebra.dandth(dat["wave"], diff_vector)[0])
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dv1, dv2, dv3 = diff_vector.flatten() * 1e10
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f.write(f"{x_pos} {y_pos} {Int} {snr_cnts} {dv1} {dv2} {dv3} {d_spacing}\n")
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