parent
45a81aa632
commit
a299449209
@ -8,6 +8,7 @@ from bokeh.layouts import column, row
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from bokeh.models import Button, Panel, Tabs, TextAreaInput, TextInput
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from bokeh.models import Button, Panel, Tabs, TextAreaInput, TextInput
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import panel_ccl_integrate
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import panel_ccl_integrate
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import panel_ccl_compare
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import panel_hdf_anatric
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import panel_hdf_anatric
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import panel_hdf_param_study
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import panel_hdf_param_study
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import panel_hdf_viewer
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import panel_hdf_viewer
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@ -55,6 +56,7 @@ doc.add_root(
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panel_hdf_viewer.create(),
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panel_hdf_viewer.create(),
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panel_hdf_anatric.create(),
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panel_hdf_anatric.create(),
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panel_ccl_integrate.create(),
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panel_ccl_integrate.create(),
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panel_ccl_compare.create(),
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panel_param_study.create(),
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panel_param_study.create(),
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panel_hdf_param_study.create(),
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panel_hdf_param_study.create(),
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panel_spind.create(),
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panel_spind.create(),
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718
pyzebra/app/panel_ccl_compare.py
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718
pyzebra/app/panel_ccl_compare.py
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@ -0,0 +1,718 @@
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import base64
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import io
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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.io import curdoc
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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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CellEditor,
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CheckboxEditor,
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CheckboxGroup,
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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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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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RadioGroup,
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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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TextAreaInput,
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WheelZoomTool,
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Whisker,
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)
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import pyzebra
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from pyzebra.ccl_io import EXPORT_TARGETS
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from pyzebra.ccl_process import AREA_METHODS
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javaScript = """
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let j = 0;
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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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setTimeout(function() {
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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] + js_data.data['ext'][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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}, 100 * j)
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j++;
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}
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"""
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def create():
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doc = curdoc()
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det_data1 = []
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det_data2 = []
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fit_params = {}
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js_data = ColumnDataSource(data=dict(content=["", ""], fname=["", ""], ext=["", ""]))
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def file_select_update_for_proposal():
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proposal_path = proposal_textinput.name
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if proposal_path:
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file_list = []
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for file in os.listdir(proposal_path):
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if file.endswith((".ccl")):
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file_list.append((os.path.join(proposal_path, file), file))
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file_select.options = file_list
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file_open_button.disabled = False
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else:
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file_select.options = []
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file_open_button.disabled = True
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doc.add_periodic_callback(file_select_update_for_proposal, 5000)
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def proposal_textinput_callback(_attr, _old, _new):
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file_select_update_for_proposal()
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proposal_textinput = doc.proposal_textinput
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proposal_textinput.on_change("name", proposal_textinput_callback)
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def _init_datatable():
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# det_data2 should have the same metadata to det_data1
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scan_list = [s["idx"] for s in det_data1]
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hkl = [f'{s["h"]} {s["k"]} {s["l"]}' for s in det_data1]
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export = [s["export"] for s in det_data1]
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twotheta = [np.median(s["twotheta"]) if "twotheta" in s else None for s in det_data1]
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gamma = [np.median(s["gamma"]) if "gamma" in s else None for s in det_data1]
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omega = [np.median(s["omega"]) if "omega" in s else None for s in det_data1]
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chi = [np.median(s["chi"]) if "chi" in s else None for s in det_data1]
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phi = [np.median(s["phi"]) if "phi" in s else None for s in det_data1]
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nu = [np.median(s["nu"]) if "nu" in s else None for s in det_data1]
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scan_table_source.data.update(
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scan=scan_list,
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hkl=hkl,
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fit=[0] * len(scan_list),
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export=export,
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twotheta=twotheta,
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gamma=gamma,
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omega=omega,
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chi=chi,
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phi=phi,
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nu=nu,
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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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merge_options = [(str(i), f"{i} ({idx})") for i, idx in enumerate(scan_list)]
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merge_from_select.options = merge_options
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merge_from_select.value = merge_options[0][0]
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file_select = MultiSelect(title="Select 2 .ccl files:", width=210, height=250)
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def file_open_button_callback():
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if len(file_select.value) != 2:
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print("WARNING: Select exactly 2 .ccl files.")
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return
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new_data1 = []
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new_data2 = []
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for ind, f_path in enumerate(file_select.value):
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with open(f_path) as file:
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f_name = os.path.basename(f_path)
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base, ext = os.path.splitext(f_name)
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try:
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file_data = pyzebra.parse_1D(file, ext)
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except:
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print(f"Error loading {f_name}")
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return
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pyzebra.normalize_dataset(file_data, monitor_spinner.value)
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pyzebra.merge_duplicates(file_data)
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if ind == 0:
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js_data.data.update(fname=[base, base])
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new_data1 = file_data
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else: # ind = 1
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new_data2 = file_data
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# ignore extra scans at the end of the longest of the two files
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min_len = min(len(new_data1), len(new_data2))
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new_data1 = new_data1[:min_len]
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new_data2 = new_data2[:min_len]
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nonlocal det_data1, det_data2
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det_data1 = new_data1
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det_data2 = new_data2
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_init_datatable()
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file_open_button = Button(label="Open New", width=100, disabled=True)
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file_open_button.on_click(file_open_button_callback)
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def upload_button_callback(_attr, _old, _new):
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if len(upload_button.filename) != 2:
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print("WARNING: Upload exactly 2 .ccl files.")
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return
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new_data1 = []
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new_data2 = []
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for ind, f_str, f_name in enumerate(zip(upload_button.value, 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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try:
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file_data = pyzebra.parse_1D(file, ext)
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except:
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print(f"Error loading {f_name}")
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return
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pyzebra.normalize_dataset(file_data, monitor_spinner.value)
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pyzebra.merge_duplicates(file_data)
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if ind == 0:
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js_data.data.update(fname=[base, base])
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new_data1 = file_data
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else: # ind = 1
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new_data2 = file_data
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# ignore extra scans at the end of the longest of the two files
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min_len = min(len(new_data1), len(new_data2))
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new_data1 = new_data1[:min_len]
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new_data2 = new_data2[:min_len]
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nonlocal det_data1, det_data2
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det_data1 = new_data1
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det_data2 = new_data2
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_init_datatable()
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upload_div = Div(text="or upload 2 .ccl files:", margin=(5, 5, 0, 5))
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upload_button = FileInput(accept=".ccl", multiple=True, width=200)
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# for on_change("value", ...) or on_change("filename", ...),
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# see https://github.com/bokeh/bokeh/issues/11461
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upload_button.on_change("filename", upload_button_callback)
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def monitor_spinner_callback(_attr, old, new):
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if det_data1 and det_data2:
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pyzebra.normalize_dataset(det_data1, new)
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pyzebra.normalize_dataset(det_data2, 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_data1]
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export = [scan["export"] for scan in det_data1]
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scan_table_source.data.update(fit=fit_ok, export=export)
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def _update_plot():
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plot_scatter_source = [plot_scatter1_source, plot_scatter2_source]
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plot_fit_source = [plot_fit1_source, plot_fit2_source]
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plot_bkg_source = [plot_bkg1_source, plot_bkg2_source]
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plot_peak_source = [plot_peak1_source, plot_peak2_source]
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fit_output = ""
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for ind, scan in enumerate(_get_selected_scan()):
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scatter_source = plot_scatter_source[ind]
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fit_source = plot_fit_source[ind]
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bkg_source = plot_bkg_source[ind]
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peak_source = plot_peak_source[ind]
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scan_motor = scan["scan_motor"]
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y = scan["counts"]
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y_err = scan["counts_err"]
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x = scan[scan_motor]
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plot.axis[0].axis_label = scan_motor
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scatter_source.data.update(x=x, y=y, y_upper=y + y_err, y_lower=y - y_err)
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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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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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bkg_source.data.update(x=x_bkg, y=y_bkg)
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peak_source.data.update(xs=xs_peak, ys=ys_peak)
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if fit_output:
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fit_output = fit_output + "\n\n"
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fit_output = fit_output + fit.fit_report()
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else:
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fit_source.data.update(x=[], y=[])
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bkg_source.data.update(x=[], y=[])
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peak_source.data.update(xs=[], ys=[])
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fit_output_textinput.value = fit_output
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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=470,
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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_scatter1_source = ColumnDataSource(dict(x=[0], y=[0], y_upper=[0], y_lower=[0]))
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plot_scatter1 = plot.add_glyph(
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plot_scatter1_source, Scatter(x="x", y="y", line_color="steelblue")
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)
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plot.add_layout(
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Whisker(source=plot_scatter1_source, base="x", upper="y_upper", lower="y_lower")
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)
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plot_scatter2_source = ColumnDataSource(dict(x=[0], y=[0], y_upper=[0], y_lower=[0]))
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plot_scatter2 = plot.add_glyph(
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plot_scatter2_source, Scatter(x="x", y="y", line_color="firebrick")
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)
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plot.add_layout(
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Whisker(source=plot_scatter2_source, base="x", upper="y_upper", lower="y_lower")
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)
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plot_fit1_source = ColumnDataSource(dict(x=[0], y=[0]))
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plot_fit1 = plot.add_glyph(plot_fit1_source, Line(x="x", y="y"))
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plot_fit2_source = ColumnDataSource(dict(x=[0], y=[0]))
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plot_fit2 = plot.add_glyph(plot_fit2_source, Line(x="x", y="y"))
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plot_bkg1_source = ColumnDataSource(dict(x=[0], y=[0]))
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plot_bkg1 = plot.add_glyph(
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plot_bkg1_source, Line(x="x", y="y", line_color="steelblue", line_dash="dashed")
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)
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plot_bkg2_source = ColumnDataSource(dict(x=[0], y=[0]))
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plot_bkg2 = plot.add_glyph(
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plot_bkg2_source, Line(x="x", y="y", line_color="firebrick", line_dash="dashed")
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)
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plot_peak1_source = ColumnDataSource(dict(xs=[[0]], ys=[[0]]))
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plot_peak1 = plot.add_glyph(
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plot_peak1_source, MultiLine(xs="xs", ys="ys", line_color="steelblue", line_dash="dashed")
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)
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plot_peak2_source = ColumnDataSource(dict(xs=[[0]], ys=[[0]]))
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plot_peak2 = plot.add_glyph(
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plot_peak2_source, MultiLine(xs="xs", ys="ys", line_color="firebrick", 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")
|
||||||
|
plot.add_layout(fit_to_span)
|
||||||
|
|
||||||
|
plot.add_layout(
|
||||||
|
Legend(
|
||||||
|
items=[
|
||||||
|
("data 1", [plot_scatter1]),
|
||||||
|
("data 2", [plot_scatter2]),
|
||||||
|
("best fit 1", [plot_fit1]),
|
||||||
|
("best fit 2", [plot_fit2]),
|
||||||
|
("peak 1", [plot_peak1]),
|
||||||
|
("peak 2", [plot_peak2]),
|
||||||
|
("linear 1", [plot_bkg1]),
|
||||||
|
("linear 2", [plot_bkg2]),
|
||||||
|
],
|
||||||
|
location="top_left",
|
||||||
|
click_policy="hide",
|
||||||
|
)
|
||||||
|
)
|
||||||
|
|
||||||
|
plot.add_tools(PanTool(), WheelZoomTool(), ResetTool())
|
||||||
|
plot.toolbar.logo = None
|
||||||
|
|
||||||
|
# Scan select
|
||||||
|
def scan_table_select_callback(_attr, old, new):
|
||||||
|
if not new:
|
||||||
|
# skip empty selections
|
||||||
|
return
|
||||||
|
|
||||||
|
# Avoid selection of multiple indicies (via Shift+Click or Ctrl+Click)
|
||||||
|
if len(new) > 1:
|
||||||
|
# drop selection to the previous one
|
||||||
|
scan_table_source.selected.indices = old
|
||||||
|
return
|
||||||
|
|
||||||
|
if len(old) > 1:
|
||||||
|
# skip unnecessary update caused by selection drop
|
||||||
|
return
|
||||||
|
|
||||||
|
_update_plot()
|
||||||
|
|
||||||
|
def scan_table_source_callback(_attr, _old, new):
|
||||||
|
# unfortunately, we don't know if the change comes from data update or user input
|
||||||
|
# also `old` and `new` are the same for non-scalars
|
||||||
|
for scan1, scan2, export in zip(det_data1, det_data2, new["export"]):
|
||||||
|
scan1["export"] = export
|
||||||
|
scan2["export"] = export
|
||||||
|
_update_preview()
|
||||||
|
|
||||||
|
scan_table_source = ColumnDataSource(
|
||||||
|
dict(
|
||||||
|
scan=[],
|
||||||
|
hkl=[],
|
||||||
|
fit=[],
|
||||||
|
export=[],
|
||||||
|
twotheta=[],
|
||||||
|
gamma=[],
|
||||||
|
omega=[],
|
||||||
|
chi=[],
|
||||||
|
phi=[],
|
||||||
|
nu=[],
|
||||||
|
)
|
||||||
|
)
|
||||||
|
scan_table_source.on_change("data", scan_table_source_callback)
|
||||||
|
scan_table_source.selected.on_change("indices", scan_table_select_callback)
|
||||||
|
|
||||||
|
scan_table = DataTable(
|
||||||
|
source=scan_table_source,
|
||||||
|
columns=[
|
||||||
|
TableColumn(field="scan", title="Scan", editor=CellEditor(), width=50),
|
||||||
|
TableColumn(field="hkl", title="hkl", editor=CellEditor(), width=100),
|
||||||
|
TableColumn(field="fit", title="Fit", editor=CellEditor(), width=50),
|
||||||
|
TableColumn(field="export", title="Export", editor=CheckboxEditor(), width=50),
|
||||||
|
TableColumn(field="twotheta", title="2theta", editor=CellEditor(), width=50),
|
||||||
|
TableColumn(field="gamma", title="gamma", editor=CellEditor(), width=50),
|
||||||
|
TableColumn(field="omega", title="omega", editor=CellEditor(), width=50),
|
||||||
|
TableColumn(field="chi", title="chi", editor=CellEditor(), width=50),
|
||||||
|
TableColumn(field="phi", title="phi", editor=CellEditor(), width=50),
|
||||||
|
TableColumn(field="nu", title="nu", editor=CellEditor(), width=50),
|
||||||
|
],
|
||||||
|
width=310, # +60 because of the index column, but excluding twotheta onwards
|
||||||
|
height=350,
|
||||||
|
autosize_mode="none",
|
||||||
|
editable=True,
|
||||||
|
)
|
||||||
|
|
||||||
|
def _get_selected_scan():
|
||||||
|
ind = scan_table_source.selected.indices[0]
|
||||||
|
return det_data1[ind], det_data2[ind]
|
||||||
|
|
||||||
|
merge_from_select = Select(title="scan:", width=145)
|
||||||
|
|
||||||
|
def merge_button_callback():
|
||||||
|
scan_into1, scan_into2 = _get_selected_scan()
|
||||||
|
scan_from1 = det_data1[int(merge_from_select.value)]
|
||||||
|
scan_from2 = det_data2[int(merge_from_select.value)]
|
||||||
|
|
||||||
|
if scan_into1 is scan_from1:
|
||||||
|
print("WARNING: Selected scans for merging are identical")
|
||||||
|
return
|
||||||
|
|
||||||
|
pyzebra.merge_scans(scan_into1, scan_from1)
|
||||||
|
pyzebra.merge_scans(scan_into2, scan_from2)
|
||||||
|
_update_table()
|
||||||
|
_update_plot()
|
||||||
|
|
||||||
|
merge_button = Button(label="Merge into current", width=145)
|
||||||
|
merge_button.on_click(merge_button_callback)
|
||||||
|
|
||||||
|
def restore_button_callback():
|
||||||
|
scan1, scan2 = _get_selected_scan()
|
||||||
|
pyzebra.restore_scan(scan1)
|
||||||
|
pyzebra.restore_scan(scan2)
|
||||||
|
_update_table()
|
||||||
|
_update_plot()
|
||||||
|
|
||||||
|
restore_button = Button(label="Restore scan", width=145)
|
||||||
|
restore_button.on_click(restore_button_callback)
|
||||||
|
|
||||||
|
def fit_from_spinner_callback(_attr, _old, new):
|
||||||
|
fit_from_span.location = new
|
||||||
|
|
||||||
|
fit_from_spinner = Spinner(title="Fit from:", width=145)
|
||||||
|
fit_from_spinner.on_change("value", fit_from_spinner_callback)
|
||||||
|
|
||||||
|
def fit_to_spinner_callback(_attr, _old, new):
|
||||||
|
fit_to_span.location = new
|
||||||
|
|
||||||
|
fit_to_spinner = Spinner(title="to:", width=145)
|
||||||
|
fit_to_spinner.on_change("value", fit_to_spinner_callback)
|
||||||
|
|
||||||
|
def fitparams_add_dropdown_callback(click):
|
||||||
|
# bokeh requires (str, str) for MultiSelect options
|
||||||
|
new_tag = f"{click.item}-{fitparams_select.tags[0]}"
|
||||||
|
fitparams_select.options.append((new_tag, click.item))
|
||||||
|
fit_params[new_tag] = fitparams_factory(click.item)
|
||||||
|
fitparams_select.tags[0] += 1
|
||||||
|
|
||||||
|
fitparams_add_dropdown = Dropdown(
|
||||||
|
label="Add fit function",
|
||||||
|
menu=[
|
||||||
|
("Linear", "linear"),
|
||||||
|
("Gaussian", "gaussian"),
|
||||||
|
("Voigt", "voigt"),
|
||||||
|
("Pseudo Voigt", "pvoigt"),
|
||||||
|
# ("Pseudo Voigt1", "pseudovoigt1"),
|
||||||
|
],
|
||||||
|
width=145,
|
||||||
|
)
|
||||||
|
fitparams_add_dropdown.on_click(fitparams_add_dropdown_callback)
|
||||||
|
|
||||||
|
def fitparams_select_callback(_attr, old, new):
|
||||||
|
# Avoid selection of multiple indicies (via Shift+Click or Ctrl+Click)
|
||||||
|
if len(new) > 1:
|
||||||
|
# drop selection to the previous one
|
||||||
|
fitparams_select.value = old
|
||||||
|
return
|
||||||
|
|
||||||
|
if len(old) > 1:
|
||||||
|
# skip unnecessary update caused by selection drop
|
||||||
|
return
|
||||||
|
|
||||||
|
if new:
|
||||||
|
fitparams_table_source.data.update(fit_params[new[0]])
|
||||||
|
else:
|
||||||
|
fitparams_table_source.data.update(dict(param=[], value=[], vary=[], min=[], max=[]))
|
||||||
|
|
||||||
|
fitparams_select = MultiSelect(options=[], height=120, width=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", width=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, 1]
|
||||||
|
fitparams["vary"] = [False, True]
|
||||||
|
fitparams["min"] = [None, 0]
|
||||||
|
|
||||||
|
elif function == "gaussian":
|
||||||
|
fitparams["min"] = [0, None, None]
|
||||||
|
|
||||||
|
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", editor=CellEditor()),
|
||||||
|
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 proc_all_button_callback():
|
||||||
|
for scan in [*det_data1, *det_data2]:
|
||||||
|
if scan["export"]:
|
||||||
|
pyzebra.fit_scan(
|
||||||
|
scan, fit_params, fit_from=fit_from_spinner.value, fit_to=fit_to_spinner.value
|
||||||
|
)
|
||||||
|
pyzebra.get_area(
|
||||||
|
scan,
|
||||||
|
area_method=AREA_METHODS[area_method_radiobutton.active],
|
||||||
|
lorentz=lorentz_checkbox.active,
|
||||||
|
)
|
||||||
|
|
||||||
|
_update_plot()
|
||||||
|
_update_table()
|
||||||
|
|
||||||
|
proc_all_button = Button(label="Process All", button_type="primary", width=145)
|
||||||
|
proc_all_button.on_click(proc_all_button_callback)
|
||||||
|
|
||||||
|
def proc_button_callback():
|
||||||
|
for scan in _get_selected_scan():
|
||||||
|
pyzebra.fit_scan(
|
||||||
|
scan, fit_params, fit_from=fit_from_spinner.value, fit_to=fit_to_spinner.value
|
||||||
|
)
|
||||||
|
pyzebra.get_area(
|
||||||
|
scan,
|
||||||
|
area_method=AREA_METHODS[area_method_radiobutton.active],
|
||||||
|
lorentz=lorentz_checkbox.active,
|
||||||
|
)
|
||||||
|
|
||||||
|
_update_plot()
|
||||||
|
_update_table()
|
||||||
|
|
||||||
|
proc_button = Button(label="Process Current", width=145)
|
||||||
|
proc_button.on_click(proc_button_callback)
|
||||||
|
|
||||||
|
area_method_div = Div(text="Intensity:", margin=(5, 5, 0, 5))
|
||||||
|
area_method_radiobutton = RadioGroup(labels=["Function", "Area"], active=0, width=145)
|
||||||
|
|
||||||
|
intensity_diff_div = Div(text="Intensity diff:", margin=(5, 5, 0, 5))
|
||||||
|
intensity_diff_radiobutton = RadioGroup(
|
||||||
|
labels=["file1 - file2", "file2 - file1"], active=0, width=145
|
||||||
|
)
|
||||||
|
|
||||||
|
lorentz_checkbox = CheckboxGroup(labels=["Lorentz Correction"], width=145, margin=(13, 5, 5, 5))
|
||||||
|
|
||||||
|
export_preview_textinput = TextAreaInput(title="Export file(s) preview:", width=500, height=400)
|
||||||
|
|
||||||
|
def _update_preview():
|
||||||
|
with tempfile.TemporaryDirectory() as temp_dir:
|
||||||
|
temp_file = temp_dir + "/temp"
|
||||||
|
export_data1 = []
|
||||||
|
export_data2 = []
|
||||||
|
for scan1, scan2 in zip(det_data1, det_data2):
|
||||||
|
if scan1["export"]:
|
||||||
|
export_data1.append(scan1)
|
||||||
|
export_data2.append(scan2)
|
||||||
|
|
||||||
|
if intensity_diff_radiobutton.active:
|
||||||
|
export_data1, export_data2 = export_data2, export_data1
|
||||||
|
|
||||||
|
pyzebra.export_ccl_compare(
|
||||||
|
export_data1,
|
||||||
|
export_data2,
|
||||||
|
temp_file,
|
||||||
|
export_target_select.value,
|
||||||
|
hkl_precision=int(hkl_precision_select.value),
|
||||||
|
)
|
||||||
|
|
||||||
|
exported_content = ""
|
||||||
|
file_content = []
|
||||||
|
for ext in EXPORT_TARGETS[export_target_select.value]:
|
||||||
|
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
|
||||||
|
|
||||||
|
def export_target_select_callback(_attr, _old, new):
|
||||||
|
js_data.data.update(ext=EXPORT_TARGETS[new])
|
||||||
|
_update_preview()
|
||||||
|
|
||||||
|
export_target_select = Select(
|
||||||
|
title="Export target:", options=list(EXPORT_TARGETS.keys()), value="fullprof", width=80
|
||||||
|
)
|
||||||
|
export_target_select.on_change("value", export_target_select_callback)
|
||||||
|
js_data.data.update(ext=EXPORT_TARGETS[export_target_select.value])
|
||||||
|
|
||||||
|
def hkl_precision_select_callback(_attr, _old, _new):
|
||||||
|
_update_preview()
|
||||||
|
|
||||||
|
hkl_precision_select = Select(
|
||||||
|
title="hkl precision:", options=["2", "3", "4"], value="2", width=80
|
||||||
|
)
|
||||||
|
hkl_precision_select.on_change("value", hkl_precision_select_callback)
|
||||||
|
|
||||||
|
save_button = Button(label="Download File(s)", button_type="success", width=200)
|
||||||
|
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(
|
||||||
|
fit_from_spinner,
|
||||||
|
lorentz_checkbox,
|
||||||
|
area_method_div,
|
||||||
|
area_method_radiobutton,
|
||||||
|
intensity_diff_div,
|
||||||
|
intensity_diff_radiobutton,
|
||||||
|
),
|
||||||
|
column(fit_to_spinner, proc_button, proc_all_button),
|
||||||
|
)
|
||||||
|
|
||||||
|
scan_layout = column(
|
||||||
|
scan_table,
|
||||||
|
row(monitor_spinner, column(Spacer(height=19), restore_button)),
|
||||||
|
row(column(Spacer(height=19), merge_button), merge_from_select),
|
||||||
|
)
|
||||||
|
|
||||||
|
import_layout = column(file_select, file_open_button, upload_div, upload_button)
|
||||||
|
|
||||||
|
export_layout = column(
|
||||||
|
export_preview_textinput,
|
||||||
|
row(
|
||||||
|
export_target_select, hkl_precision_select, column(Spacer(height=19), row(save_button))
|
||||||
|
),
|
||||||
|
)
|
||||||
|
|
||||||
|
tab_layout = column(
|
||||||
|
row(import_layout, scan_layout, plot, Spacer(width=30), export_layout),
|
||||||
|
row(fitpeak_controls, fit_output_textinput),
|
||||||
|
)
|
||||||
|
|
||||||
|
return Panel(child=tab_layout, title="ccl compare")
|
||||||
@ -306,6 +306,63 @@ def export_1D(data, path, export_target, hkl_precision=2):
|
|||||||
out_file.writelines(content)
|
out_file.writelines(content)
|
||||||
|
|
||||||
|
|
||||||
|
def export_ccl_compare(data1, data2, path, export_target, hkl_precision=2):
|
||||||
|
"""Exports compare data in the .comm/.incomm format for fullprof or .col/.incol format for jana.
|
||||||
|
|
||||||
|
Scans with integer/real hkl values are saved in .comm/.incomm or .col/.incol files
|
||||||
|
correspondingly. If no scans are present for a particular output format, that file won't be
|
||||||
|
created.
|
||||||
|
"""
|
||||||
|
if export_target not in EXPORT_TARGETS:
|
||||||
|
raise ValueError(f"Unknown export target: {export_target}.")
|
||||||
|
|
||||||
|
zebra_mode = data1[0]["zebra_mode"]
|
||||||
|
exts = EXPORT_TARGETS[export_target]
|
||||||
|
file_content = {ext: [] for ext in exts}
|
||||||
|
|
||||||
|
for scan1, scan2 in zip(data1, data2):
|
||||||
|
if "fit" not in scan1:
|
||||||
|
continue
|
||||||
|
|
||||||
|
idx_str = f"{scan1['idx']:6}"
|
||||||
|
|
||||||
|
h, k, l = scan1["h"], scan1["k"], scan1["l"]
|
||||||
|
hkl_are_integers = isinstance(h, int) # if True, other indices are of type 'int' too
|
||||||
|
if hkl_are_integers:
|
||||||
|
hkl_str = f"{h:4}{k:4}{l:4}"
|
||||||
|
else:
|
||||||
|
hkl_str = f"{h:8.{hkl_precision}f}{k:8.{hkl_precision}f}{l:8.{hkl_precision}f}"
|
||||||
|
|
||||||
|
area_n1, area_s1 = scan1["area"]
|
||||||
|
area_n2, area_s2 = scan2["area"]
|
||||||
|
area_n = area_n1 - area_n2
|
||||||
|
area_s = np.sqrt(area_s1 ** 2 + area_s2 ** 2)
|
||||||
|
area_str = f"{area_n:10.2f}{area_s:10.2f}"
|
||||||
|
|
||||||
|
ang_str = ""
|
||||||
|
for angle, _ in CCL_ANGLES[zebra_mode]:
|
||||||
|
if angle == scan1["scan_motor"]:
|
||||||
|
angle_center = (np.min(scan1[angle]) + np.max(scan1[angle])) / 2
|
||||||
|
else:
|
||||||
|
angle_center = scan1[angle]
|
||||||
|
|
||||||
|
if angle == "twotheta" and export_target == "jana":
|
||||||
|
angle_center /= 2
|
||||||
|
|
||||||
|
ang_str = ang_str + f"{angle_center:8g}"
|
||||||
|
|
||||||
|
if export_target == "jana":
|
||||||
|
ang_str = ang_str + f"{scan1['temp']:8}" + f"{scan1['monitor']:8}"
|
||||||
|
|
||||||
|
ref = file_content[exts[0]] if hkl_are_integers else file_content[exts[1]]
|
||||||
|
ref.append(idx_str + hkl_str + area_str + ang_str + "\n")
|
||||||
|
|
||||||
|
for ext, content in file_content.items():
|
||||||
|
if content:
|
||||||
|
with open(path + ext, "w") as out_file:
|
||||||
|
out_file.writelines(content)
|
||||||
|
|
||||||
|
|
||||||
def export_param_study(data, param_data, path):
|
def export_param_study(data, param_data, path):
|
||||||
file_content = []
|
file_content = []
|
||||||
for scan, param in zip(data, param_data):
|
for scan, param in zip(data, param_data):
|
||||||
|
|||||||
Loading…
x
Reference in New Issue
Block a user