parent
cf6527af13
commit
c2bd6c25f5
@ -36,7 +36,6 @@ from bokeh.models import (
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Spacer,
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Spinner,
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TableColumn,
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TextAreaInput,
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TextInput,
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Title,
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WheelZoomTool,
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@ -57,6 +56,8 @@ def create():
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det_data = {}
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cami_meta = {}
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num_formatter = NumberFormatter(format="0.00", nan_format="")
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def proposal_textinput_callback(_attr, _old, new):
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nonlocal cami_meta
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proposal = new.strip()
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@ -570,18 +571,46 @@ def create():
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h, k, l = calculate_hkl(det_data, index)
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image_source.data.update(h=[h], k=[k], l=[l])
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hkl_button = Button(label="Calculate hkl (slow)", width=210)
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hkl_button = Button(label="Calculate hkl (slow)", width=145)
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hkl_button.on_click(hkl_button_callback)
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def events_list_callback(_attr, _old, new):
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doc.events_list_spind.value = new
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events_data = dict(
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wave=[],
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ddist=[],
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frame=[],
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x_pos=[],
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y_pos=[],
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intensity=[],
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snr_cnts=[],
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gamma=[],
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omega=[],
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chi=[],
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phi=[],
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nu=[],
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)
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doc.events_data = events_data
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events_list = TextAreaInput(rows=7, width=830)
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events_list.on_change("value", events_list_callback)
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doc.events_list_hdf_viewer = events_list
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events_table_source = ColumnDataSource(events_data)
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events_table = DataTable(
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source=events_table_source,
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columns=[
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TableColumn(field="frame", title="Frame", formatter=num_formatter, width=70),
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TableColumn(field="x_pos", title="X", formatter=num_formatter, width=70),
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TableColumn(field="y_pos", title="Y", formatter=num_formatter, width=70),
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TableColumn(field="intensity", title="Intensity", formatter=num_formatter, width=70),
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TableColumn(field="gamma", title="Gamma", formatter=num_formatter, width=70),
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TableColumn(field="omega", title="Omega", formatter=num_formatter, width=70),
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TableColumn(field="chi", title="Chi", formatter=num_formatter, width=70),
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TableColumn(field="phi", title="Phi", formatter=num_formatter, width=70),
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TableColumn(field="nu", title="Nu", formatter=num_formatter, width=70),
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],
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height=150,
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width=630,
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autosize_mode="none",
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index_position=None,
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)
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def add_event_button_callback():
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diff_vec = []
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p0 = [1.0, 0.0, 1.0]
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maxfev = 100000
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@ -640,27 +669,36 @@ def create():
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coeff, _ = curve_fit(gauss, range(len(projY)), projY, p0=p0, maxfev=maxfev)
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y_pos = y0 + coeff[1]
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ga, nu = pyzebra.det2pol(ddist, gamma, nu, x_pos, y_pos)
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diff_vector = pyzebra.z1frmd(wave, ga, omega, chi, phi, nu)
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d_spacing = float(pyzebra.dandth(wave, diff_vector)[0])
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diff_vector = diff_vector.flatten() * 1e10
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dv1, dv2, dv3 = diff_vector
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events_data["wave"].append(wave)
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events_data["ddist"].append(ddist)
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events_data["frame"].append(frC)
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events_data["x_pos"].append(x_pos)
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events_data["y_pos"].append(y_pos)
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events_data["intensity"].append(intensity)
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events_data["snr_cnts"].append(snr_cnts)
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events_data["gamma"].append(gamma)
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events_data["omega"].append(omega)
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events_data["chi"].append(chi)
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events_data["phi"].append(phi)
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events_data["nu"].append(nu)
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diff_vec.append(diff_vector)
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events_table_source.data = events_data
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if events_list.value and not events_list.value.endswith("\n"):
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events_list.value = events_list.value + "\n"
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events_list.value = (
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events_list.value
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+ f"{x_pos} {y_pos} {intensity} {snr_cnts} {dv1} {dv2} {dv3} {d_spacing}"
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)
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add_event_button = Button(label="Add spind event")
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add_event_button = Button(label="Add spind event", width=145)
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add_event_button.on_click(add_event_button_callback)
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def remove_event_button_callback():
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ind2remove = events_table_source.selected.indices
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for value in events_data.values():
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for ind in reversed(ind2remove):
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del value[ind]
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events_table_source.data = events_data
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remove_event_button = Button(label="Remove spind event", width=145)
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remove_event_button.on_click(remove_event_button_callback)
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metadata_table_source = ColumnDataSource(dict(geom=[""], temp=[None], mf=[None]))
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num_formatter = NumberFormatter(format="0.00", nan_format="")
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metadata_table = DataTable(
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source=metadata_table_source,
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columns=[
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@ -687,8 +725,7 @@ def create():
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layout_controls = column(
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row(metadata_table, index_spinner, column(Spacer(height=25), index_slider)),
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row(add_event_button, hkl_button),
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row(events_list),
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row(column(add_event_button, remove_event_button), events_table),
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)
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layout_overview = column(
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@ -703,7 +740,7 @@ def create():
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tab_layout = row(
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column(import_layout, colormap_layout),
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column(layout_overview, layout_controls),
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column(roi_avg_plot, layout_image),
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column(roi_avg_plot, layout_image, hkl_button),
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)
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return Panel(child=tab_layout, title="hdf viewer")
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@ -16,17 +16,14 @@ from bokeh.models import (
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TextInput,
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)
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import pyzebra
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def create():
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doc = curdoc()
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events_data = doc.events_data
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def events_list_callback(_attr, _old, new):
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doc.events_list_hdf_viewer.value = new
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events_list = TextAreaInput(title="Spind events:", rows=7, width=1500)
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events_list.on_change("value", events_list_callback)
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doc.events_list_spind = events_list
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npeaks_spinner = Spinner(title="Number of peaks from hdf_view panel:", disabled=True)
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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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@ -74,9 +71,30 @@ def create():
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# prepare an event file
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diff_vec = []
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with open(temp_event_file, "w") as f:
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for event in events_list.value.splitlines():
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diff_vec.append(np.array(event.split()[4:7], dtype=float))
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f.write(event + "\n")
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npeaks = len(next(iter(doc.events_data.values())))
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for ind in range(npeaks):
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wave = events_data["wave"][ind]
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ddist = events_data["ddist"][ind]
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x_pos = events_data["x_pos"][ind]
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y_pos = events_data["y_pos"][ind]
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intensity = events_data["intensity"][ind]
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snr_cnts = events_data["snr_cnts"][ind]
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gamma = events_data["gamma"][ind]
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omega = events_data["omega"][ind]
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chi = events_data["chi"][ind]
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phi = events_data["phi"][ind]
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nu = events_data["nu"][ind]
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ga, nu = pyzebra.det2pol(ddist, gamma, nu, x_pos, y_pos)
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diff_vector = pyzebra.z1frmd(wave, ga, omega, chi, phi, nu)
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d_spacing = float(pyzebra.dandth(wave, diff_vector)[0])
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diff_vector = diff_vector.flatten() * 1e10
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dv1, dv2, dv3 = diff_vector
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diff_vec.append(diff_vector)
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f.write(
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f"{x_pos} {y_pos} {intensity} {snr_cnts} {dv1} {dv2} {dv3} {d_spacing}\n"
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)
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print(f"Content of {temp_event_file}:")
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with open(temp_event_file) as f:
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@ -183,18 +201,21 @@ def create():
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results_table_source.selected.on_change("indices", results_table_select_callback)
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tab_layout = column(
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events_list,
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row(
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column(
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lattice_const_textinput,
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row(max_res_spinner, seed_pool_size_spinner),
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row(seed_len_tol_spinner, seed_angle_tol_spinner),
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row(eval_hkl_tol_spinner),
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process_button,
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),
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column(results_table, row(ub_matrix_textareainput, hkl_textareainput)),
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tab_layout = row(
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column(
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npeaks_spinner,
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lattice_const_textinput,
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row(max_res_spinner, seed_pool_size_spinner),
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row(seed_len_tol_spinner, seed_angle_tol_spinner),
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row(eval_hkl_tol_spinner),
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process_button,
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),
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column(results_table, row(ub_matrix_textareainput, hkl_textareainput)),
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)
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async def update_npeaks_spinner():
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npeaks_spinner.value = len(next(iter(doc.events_data.values())))
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doc.add_periodic_callback(update_npeaks_spinner, 1000)
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return Panel(child=tab_layout, title="spind")
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