663 lines
23 KiB
Python
663 lines
23 KiB
Python
import base64
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import io
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import itertools
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import os
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import tempfile
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import types
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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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BasicTicker,
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Button,
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CheckboxEditor,
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ColumnDataSource,
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CustomJS,
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DataRange1d,
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DataTable,
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Div,
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Dropdown,
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FileInput,
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Grid,
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HoverTool,
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Legend,
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Line,
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LinearAxis,
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MultiLine,
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MultiSelect,
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NumberEditor,
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Panel,
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PanTool,
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Plot,
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RadioButtonGroup,
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ResetTool,
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Scatter,
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Select,
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Spacer,
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Span,
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Spinner,
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TableColumn,
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Tabs,
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TextAreaInput,
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TextInput,
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Toggle,
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WheelZoomTool,
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Whisker,
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)
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from bokeh.palettes import Category10, Turbo256
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from bokeh.transform import linear_cmap
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import pyzebra
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from pyzebra.ccl_io import AREA_METHODS
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javaScript = """
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for (let i = 0; i < js_data.data['fname'].length; i++) {
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if (js_data.data['content'][i] === "") continue;
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const blob = new Blob([js_data.data['content'][i]], {type: 'text/plain'})
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const link = document.createElement('a');
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document.body.appendChild(link);
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const url = window.URL.createObjectURL(blob);
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link.href = url;
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link.download = js_data.data['fname'][i];
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link.click();
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window.URL.revokeObjectURL(url);
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document.body.removeChild(link);
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}
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"""
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PROPOSAL_PATH = "/afs/psi.ch/project/sinqdata/2020/zebra/"
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def color_palette(n_colors):
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palette = itertools.cycle(Category10[10])
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return list(itertools.islice(palette, n_colors))
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def create():
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det_data = []
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fit_params = {}
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js_data = ColumnDataSource(data=dict(content=["", ""], fname=["", ""]))
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def proposal_textinput_callback(_attr, _old, new):
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full_proposal_path = os.path.join(PROPOSAL_PATH, new.strip())
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dat_file_list = []
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for file in os.listdir(full_proposal_path):
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if file.endswith(".dat"):
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dat_file_list.append((os.path.join(full_proposal_path, file), file))
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file_select.options = dat_file_list
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proposal_textinput = TextInput(title="Proposal number:", default_size=200)
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proposal_textinput.on_change("value", proposal_textinput_callback)
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def _init_datatable():
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scan_list = [s["idx"] for s in det_data]
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file_list = []
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for scan in det_data:
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file_list.append(os.path.basename(scan["original_filename"]))
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scan_table_source.data.update(
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file=file_list,
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scan=scan_list,
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param=[None] * len(scan_list),
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fit=[0] * len(scan_list),
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export=[True] * len(scan_list),
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)
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scan_table_source.selected.indices = []
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scan_table_source.selected.indices = [0]
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param_select.value = "user defined"
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def file_select_callback(_attr, _old, _new):
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pass
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file_select = MultiSelect(title="Available .dat files:", default_size=200, height=250)
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file_select.on_change("value", file_select_callback)
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def file_open_button_callback():
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nonlocal det_data
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det_data = []
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for f_name in file_select.value:
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with open(f_name) as file:
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base, ext = os.path.splitext(f_name)
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if det_data:
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append_data = pyzebra.parse_1D(file, ext)
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pyzebra.normalize_dataset(append_data, monitor_spinner.value)
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det_data.extend(append_data)
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else:
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det_data = pyzebra.parse_1D(file, ext)
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pyzebra.normalize_dataset(det_data, monitor_spinner.value)
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js_data.data.update(fname=[base + ".comm", base + ".incomm"])
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_init_datatable()
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_update_preview()
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file_open_button = Button(label="Open New", default_size=100)
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file_open_button.on_click(file_open_button_callback)
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def file_append_button_callback():
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for f_name in file_select.value:
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with open(f_name) as file:
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_, ext = os.path.splitext(f_name)
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append_data = pyzebra.parse_1D(file, ext)
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pyzebra.normalize_dataset(append_data, monitor_spinner.value)
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det_data.extend(append_data)
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_init_datatable()
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file_append_button = Button(label="Append", default_size=100)
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file_append_button.on_click(file_append_button_callback)
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def upload_button_callback(_attr, _old, new):
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nonlocal det_data
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det_data = []
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for f_str, f_name in zip(new, upload_button.filename):
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with io.StringIO(base64.b64decode(f_str).decode()) as file:
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base, ext = os.path.splitext(f_name)
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if det_data:
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append_data = pyzebra.parse_1D(file, ext)
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pyzebra.normalize_dataset(append_data, monitor_spinner.value)
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det_data.extend(append_data)
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else:
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det_data = pyzebra.parse_1D(file, ext)
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pyzebra.normalize_dataset(det_data, monitor_spinner.value)
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js_data.data.update(fname=[base + ".comm", base + ".incomm"])
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_init_datatable()
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_update_preview()
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upload_div = Div(text="or upload new .dat files:", margin=(5, 5, 0, 5))
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upload_button = FileInput(accept=".dat", multiple=True, default_size=200)
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upload_button.on_change("value", upload_button_callback)
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def append_upload_button_callback(_attr, _old, new):
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for f_str, f_name in zip(new, append_upload_button.filename):
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with io.StringIO(base64.b64decode(f_str).decode()) as file:
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_, ext = os.path.splitext(f_name)
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append_data = pyzebra.parse_1D(file, ext)
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pyzebra.normalize_dataset(append_data, monitor_spinner.value)
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det_data.extend(append_data)
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_init_datatable()
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append_upload_div = Div(text="append extra files:", margin=(5, 5, 0, 5))
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append_upload_button = FileInput(accept=".dat", multiple=True, default_size=200)
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append_upload_button.on_change("value", append_upload_button_callback)
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def monitor_spinner_callback(_attr, _old, new):
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if det_data:
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pyzebra.normalize_dataset(det_data, new)
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_update_plot()
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monitor_spinner = Spinner(title="Monitor:", mode="int", value=100_000, low=1, width=145)
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monitor_spinner.on_change("value", monitor_spinner_callback)
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def _update_table():
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fit_ok = [(1 if "fit" in scan else 0) for scan in det_data]
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scan_table_source.data.update(fit=fit_ok)
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def _update_plot():
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_update_single_scan_plot(_get_selected_scan())
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_update_overview()
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def _update_single_scan_plot(scan):
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scan_motor = scan["scan_motor"]
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y = scan["Counts"]
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x = scan[scan_motor]
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plot.axis[0].axis_label = scan_motor
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plot_scatter_source.data.update(x=x, y=y, y_upper=y + np.sqrt(y), y_lower=y - np.sqrt(y))
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fit = scan.get("fit")
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if fit is not None:
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x_fit = np.linspace(x[0], x[-1], 100)
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plot_fit_source.data.update(x=x_fit, y=fit.eval(x=x_fit))
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x_bkg = []
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y_bkg = []
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xs_peak = []
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ys_peak = []
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comps = fit.eval_components(x=x_fit)
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for i, model in enumerate(fit_params):
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if "linear" in model:
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x_bkg = x_fit
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y_bkg = comps[f"f{i}_"]
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elif any(val in model for val in ("gaussian", "voigt", "pvoigt")):
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xs_peak.append(x_fit)
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ys_peak.append(comps[f"f{i}_"])
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plot_bkg_source.data.update(x=x_bkg, y=y_bkg)
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plot_peak_source.data.update(xs=xs_peak, ys=ys_peak)
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fit_output_textinput.value = fit.fit_report()
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else:
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plot_fit_source.data.update(x=[], y=[])
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plot_bkg_source.data.update(x=[], y=[])
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plot_peak_source.data.update(xs=[], ys=[])
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fit_output_textinput.value = ""
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def _update_overview():
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xs = []
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ys = []
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param = []
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x = []
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y = []
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par = []
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for s, p in enumerate(scan_table_source.data["param"]):
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if p is not None:
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scan = det_data[s]
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scan_motor = scan["scan_motor"]
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xs.append(scan[scan_motor])
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x.extend(scan[scan_motor])
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ys.append(scan["Counts"])
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y.extend([float(p)] * len(scan[scan_motor]))
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param.append(float(p))
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par.extend(scan["Counts"])
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if det_data:
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scan_motor = det_data[0]["scan_motor"]
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ov_plot.axis[0].axis_label = scan_motor
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ov_param_plot.axis[0].axis_label = scan_motor
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ov_plot_mline_source.data.update(xs=xs, ys=ys, param=param, color=color_palette(len(xs)))
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if y:
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mapper["transform"].low = np.min([np.min(y) for y in ys])
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mapper["transform"].high = np.max([np.max(y) for y in ys])
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ov_param_plot_scatter_source.data.update(x=x, y=y, param=par)
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# Main plot
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plot = Plot(
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x_range=DataRange1d(),
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y_range=DataRange1d(only_visible=True),
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plot_height=450,
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plot_width=700,
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)
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plot.add_layout(LinearAxis(axis_label="Counts"), place="left")
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plot.add_layout(LinearAxis(axis_label="Scan motor"), place="below")
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plot.add_layout(Grid(dimension=0, ticker=BasicTicker()))
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plot.add_layout(Grid(dimension=1, ticker=BasicTicker()))
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plot_scatter_source = ColumnDataSource(dict(x=[0], y=[0], y_upper=[0], y_lower=[0]))
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plot_scatter = plot.add_glyph(
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plot_scatter_source, Scatter(x="x", y="y", line_color="steelblue")
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)
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plot.add_layout(Whisker(source=plot_scatter_source, base="x", upper="y_upper", lower="y_lower"))
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plot_fit_source = ColumnDataSource(dict(x=[0], y=[0]))
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plot_fit = plot.add_glyph(plot_fit_source, Line(x="x", y="y"))
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plot_bkg_source = ColumnDataSource(dict(x=[0], y=[0]))
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plot_bkg = plot.add_glyph(
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plot_bkg_source, Line(x="x", y="y", line_color="green", line_dash="dashed")
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)
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plot_peak_source = ColumnDataSource(dict(xs=[[0]], ys=[[0]]))
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plot_peak = plot.add_glyph(
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plot_peak_source, MultiLine(xs="xs", ys="ys", line_color="red", line_dash="dashed")
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)
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fit_from_span = Span(location=None, dimension="height", line_dash="dashed")
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plot.add_layout(fit_from_span)
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fit_to_span = Span(location=None, dimension="height", line_dash="dashed")
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plot.add_layout(fit_to_span)
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plot.add_layout(
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Legend(
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items=[
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("data", [plot_scatter]),
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("best fit", [plot_fit]),
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("peak", [plot_peak]),
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("linear", [plot_bkg]),
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],
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location="top_left",
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click_policy="hide",
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)
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)
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plot.add_tools(PanTool(), WheelZoomTool(), ResetTool())
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plot.toolbar.logo = None
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# Overview multilines plot
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ov_plot = Plot(x_range=DataRange1d(), y_range=DataRange1d(), plot_height=400, plot_width=700)
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ov_plot.add_layout(LinearAxis(axis_label="Counts"), place="left")
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ov_plot.add_layout(LinearAxis(axis_label="Scan motor"), place="below")
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ov_plot.add_layout(Grid(dimension=0, ticker=BasicTicker()))
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ov_plot.add_layout(Grid(dimension=1, ticker=BasicTicker()))
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ov_plot_mline_source = ColumnDataSource(dict(xs=[], ys=[], param=[], color=[]))
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ov_plot.add_glyph(ov_plot_mline_source, MultiLine(xs="xs", ys="ys", line_color="color"))
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hover_tool = HoverTool(tooltips=[("param", "@param")])
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ov_plot.add_tools(PanTool(), WheelZoomTool(), hover_tool, ResetTool())
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ov_plot.add_tools(PanTool(), WheelZoomTool(), ResetTool())
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ov_plot.toolbar.logo = None
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# Overview perams plot
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ov_param_plot = Plot(
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x_range=DataRange1d(), y_range=DataRange1d(), plot_height=400, plot_width=700
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)
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ov_param_plot.add_layout(LinearAxis(axis_label="Param"), place="left")
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ov_param_plot.add_layout(LinearAxis(axis_label="Scan motor"), place="below")
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ov_param_plot.add_layout(Grid(dimension=0, ticker=BasicTicker()))
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ov_param_plot.add_layout(Grid(dimension=1, ticker=BasicTicker()))
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ov_param_plot_scatter_source = ColumnDataSource(dict(x=[], y=[], param=[]))
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mapper = linear_cmap(field_name="param", palette=Turbo256, low=0, high=50)
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ov_param_plot.add_glyph(
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ov_param_plot_scatter_source,
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Scatter(x="x", y="y", line_color=mapper, fill_color=mapper, size=10),
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)
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ov_param_plot.add_tools(PanTool(), WheelZoomTool(), ResetTool())
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ov_param_plot.toolbar.logo = None
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# Plot tabs
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plots = Tabs(
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tabs=[
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Panel(child=plot, title="single scan"),
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Panel(child=ov_plot, title="overview"),
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Panel(child=ov_param_plot, title="overview map"),
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]
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)
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# Scan select
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def scan_table_select_callback(_attr, old, new):
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if not new:
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# skip empty selections
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return
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# Avoid selection of multiple indicies (via Shift+Click or Ctrl+Click)
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if len(new) > 1:
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# drop selection to the previous one
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scan_table_source.selected.indices = old
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return
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if len(old) > 1:
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# skip unnecessary update caused by selection drop
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return
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_update_plot()
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scan_table_source = ColumnDataSource(dict(file=[], scan=[], param=[], fit=[], export=[]))
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scan_table = DataTable(
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source=scan_table_source,
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columns=[
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TableColumn(field="file", title="file", width=150),
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TableColumn(field="scan", title="scan", width=50),
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TableColumn(field="param", title="param", editor=NumberEditor(), width=50),
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TableColumn(field="fit", title="Fit", width=50),
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TableColumn(field="export", title="Export", editor=CheckboxEditor(), width=50),
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],
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width=410, # +60 because of the index column
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editable=True,
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autosize_mode="none",
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)
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def scan_table_source_callback(_attr, _old, _new):
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if scan_table_source.selected.indices:
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_update_plot()
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scan_table_source.selected.on_change("indices", scan_table_select_callback)
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scan_table_source.on_change("data", scan_table_source_callback)
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def _get_selected_scan():
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return det_data[scan_table_source.selected.indices[0]]
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def param_select_callback(_attr, _old, new):
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if new == "user defined":
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param = [None] * len(det_data)
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else:
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param = [scan[new] for scan in det_data]
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scan_table_source.data["param"] = param
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param_select = Select(
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title="Parameter:",
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options=["user defined", "temp", "mf", "h", "k", "l"],
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value="user defined",
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default_size=145,
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)
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param_select.on_change("value", param_select_callback)
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def fit_from_spinner_callback(_attr, _old, new):
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fit_from_span.location = new
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fit_from_spinner = Spinner(title="Fit from:", default_size=145)
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fit_from_spinner.on_change("value", fit_from_spinner_callback)
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def fit_to_spinner_callback(_attr, _old, new):
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fit_to_span.location = new
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fit_to_spinner = Spinner(title="to:", default_size=145)
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fit_to_spinner.on_change("value", fit_to_spinner_callback)
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def fitparams_add_dropdown_callback(click):
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# bokeh requires (str, str) for MultiSelect options
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new_tag = f"{click.item}-{fitparams_select.tags[0]}"
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fitparams_select.options.append((new_tag, click.item))
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fit_params[new_tag] = fitparams_factory(click.item)
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fitparams_select.tags[0] += 1
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fitparams_add_dropdown = Dropdown(
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label="Add fit function",
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menu=[
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("Linear", "linear"),
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("Gaussian", "gaussian"),
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("Voigt", "voigt"),
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("Pseudo Voigt", "pvoigt"),
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# ("Pseudo Voigt1", "pseudovoigt1"),
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],
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default_size=145,
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)
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fitparams_add_dropdown.on_click(fitparams_add_dropdown_callback)
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def fitparams_select_callback(_attr, old, new):
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# Avoid selection of multiple indicies (via Shift+Click or Ctrl+Click)
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if len(new) > 1:
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# drop selection to the previous one
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fitparams_select.value = old
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return
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if len(old) > 1:
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# skip unnecessary update caused by selection drop
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return
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if new:
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fitparams_table_source.data.update(fit_params[new[0]])
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else:
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fitparams_table_source.data.update(dict(param=[], value=[], vary=[], min=[], max=[]))
|
|
|
|
fitparams_select = MultiSelect(options=[], height=120, default_size=145)
|
|
fitparams_select.tags = [0]
|
|
fitparams_select.on_change("value", fitparams_select_callback)
|
|
|
|
def fitparams_remove_button_callback():
|
|
if fitparams_select.value:
|
|
sel_tag = fitparams_select.value[0]
|
|
del fit_params[sel_tag]
|
|
for elem in fitparams_select.options:
|
|
if elem[0] == sel_tag:
|
|
fitparams_select.options.remove(elem)
|
|
break
|
|
|
|
fitparams_select.value = []
|
|
|
|
fitparams_remove_button = Button(label="Remove fit function", default_size=145)
|
|
fitparams_remove_button.on_click(fitparams_remove_button_callback)
|
|
|
|
def fitparams_factory(function):
|
|
if function == "linear":
|
|
params = ["slope", "intercept"]
|
|
elif function == "gaussian":
|
|
params = ["amplitude", "center", "sigma"]
|
|
elif function == "voigt":
|
|
params = ["amplitude", "center", "sigma", "gamma"]
|
|
elif function == "pvoigt":
|
|
params = ["amplitude", "center", "sigma", "fraction"]
|
|
elif function == "pseudovoigt1":
|
|
params = ["amplitude", "center", "g_sigma", "l_sigma", "fraction"]
|
|
else:
|
|
raise ValueError("Unknown fit function")
|
|
|
|
n = len(params)
|
|
fitparams = dict(
|
|
param=params, value=[None] * n, vary=[True] * n, min=[None] * n, max=[None] * n,
|
|
)
|
|
|
|
if function == "linear":
|
|
fitparams["value"] = [0, 0]
|
|
fitparams["vary"] = [False, False]
|
|
|
|
return fitparams
|
|
|
|
fitparams_table_source = ColumnDataSource(dict(param=[], value=[], vary=[], min=[], max=[]))
|
|
fitparams_table = DataTable(
|
|
source=fitparams_table_source,
|
|
columns=[
|
|
TableColumn(field="param", title="Parameter"),
|
|
TableColumn(field="value", title="Value", editor=NumberEditor()),
|
|
TableColumn(field="vary", title="Vary", editor=CheckboxEditor()),
|
|
TableColumn(field="min", title="Min", editor=NumberEditor()),
|
|
TableColumn(field="max", title="Max", editor=NumberEditor()),
|
|
],
|
|
height=200,
|
|
width=350,
|
|
index_position=None,
|
|
editable=True,
|
|
auto_edit=True,
|
|
)
|
|
|
|
# start with `background` and `gauss` fit functions added
|
|
fitparams_add_dropdown_callback(types.SimpleNamespace(item="linear"))
|
|
fitparams_add_dropdown_callback(types.SimpleNamespace(item="gaussian"))
|
|
fitparams_select.value = ["gaussian-1"] # add selection to gauss
|
|
|
|
fit_output_textinput = TextAreaInput(title="Fit results:", width=750, height=200)
|
|
|
|
def fit_all_button_callback():
|
|
for scan, export in zip(det_data, scan_table_source.data["export"]):
|
|
if export:
|
|
pyzebra.fit_scan(
|
|
scan, fit_params, fit_from=fit_from_spinner.value, fit_to=fit_to_spinner.value
|
|
)
|
|
|
|
_update_plot()
|
|
_update_table()
|
|
_update_preview()
|
|
|
|
fit_all_button = Button(label="Fit All", button_type="primary", default_size=145)
|
|
fit_all_button.on_click(fit_all_button_callback)
|
|
|
|
def fit_button_callback():
|
|
scan = _get_selected_scan()
|
|
pyzebra.fit_scan(
|
|
scan, fit_params, fit_from=fit_from_spinner.value, fit_to=fit_to_spinner.value
|
|
)
|
|
|
|
_update_plot()
|
|
_update_table()
|
|
_update_preview()
|
|
|
|
fit_button = Button(label="Fit Current", default_size=145)
|
|
fit_button.on_click(fit_button_callback)
|
|
|
|
def area_method_radiobutton_callback(_handler):
|
|
_update_preview()
|
|
|
|
area_method_radiobutton = RadioButtonGroup(
|
|
labels=["Fit area", "Int area"], active=0, default_size=145, disabled=True
|
|
)
|
|
area_method_radiobutton.on_click(area_method_radiobutton_callback)
|
|
|
|
bin_size_spinner = Spinner(
|
|
title="Bin size:", value=1, low=1, step=1, default_size=145, disabled=True
|
|
)
|
|
|
|
def lorentz_toggle_callback(_handler):
|
|
_update_preview()
|
|
|
|
lorentz_toggle = Toggle(label="Lorentz Correction", default_size=145)
|
|
lorentz_toggle.on_click(lorentz_toggle_callback)
|
|
|
|
export_preview_textinput = TextAreaInput(title="Export file preview:", width=450, height=400)
|
|
|
|
def _update_preview():
|
|
with tempfile.TemporaryDirectory() as temp_dir:
|
|
temp_file = temp_dir + "/temp"
|
|
export_data = []
|
|
for s, export in zip(det_data, scan_table_source.data["export"]):
|
|
if export:
|
|
export_data.append(s)
|
|
|
|
pyzebra.export_1D(
|
|
export_data,
|
|
temp_file,
|
|
area_method=AREA_METHODS[int(area_method_radiobutton.active)],
|
|
lorentz=lorentz_toggle.active,
|
|
)
|
|
|
|
exported_content = ""
|
|
file_content = []
|
|
for ext in (".comm", ".incomm"):
|
|
fname = temp_file + ext
|
|
if os.path.isfile(fname):
|
|
with open(fname) as f:
|
|
content = f.read()
|
|
exported_content += f"{ext} file:\n" + content
|
|
else:
|
|
content = ""
|
|
file_content.append(content)
|
|
|
|
js_data.data.update(content=file_content)
|
|
export_preview_textinput.value = exported_content
|
|
|
|
save_button = Button(label="Download File", button_type="success", default_size=220)
|
|
save_button.js_on_click(CustomJS(args={"js_data": js_data}, code=javaScript))
|
|
|
|
fitpeak_controls = row(
|
|
column(fitparams_add_dropdown, fitparams_select, fitparams_remove_button),
|
|
fitparams_table,
|
|
Spacer(width=20),
|
|
column(
|
|
row(fit_from_spinner, fit_to_spinner),
|
|
row(bin_size_spinner, column(Spacer(height=19), lorentz_toggle)),
|
|
row(area_method_radiobutton),
|
|
row(fit_button, fit_all_button),
|
|
),
|
|
)
|
|
|
|
scan_layout = column(scan_table, row(monitor_spinner, param_select))
|
|
|
|
import_layout = column(
|
|
proposal_textinput,
|
|
file_select,
|
|
row(file_open_button, file_append_button),
|
|
upload_div,
|
|
upload_button,
|
|
append_upload_div,
|
|
append_upload_button,
|
|
)
|
|
|
|
export_layout = column(export_preview_textinput, row(save_button))
|
|
|
|
tab_layout = column(
|
|
row(import_layout, scan_layout, plots, Spacer(width=30), export_layout),
|
|
row(fitpeak_controls, fit_output_textinput),
|
|
)
|
|
|
|
return Panel(child=tab_layout, title="param study")
|