Rename panels
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207
pyzebra/app/panel_ccl_integrate.py
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207
pyzebra/app/panel_ccl_integrate.py
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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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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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Circle,
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ColumnDataSource,
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CustomJS,
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DataRange1d,
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Div,
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FileInput,
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Grid,
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Line,
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LinearAxis,
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Panel,
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Plot,
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Select,
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Spacer,
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TextAreaInput,
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TextInput,
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Toggle,
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)
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import pyzebra
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javaScript = """
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setTimeout(function() {
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const filename = 'output' + js_data.data['ext']
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const blob = new Blob([js_data.data['cont']], {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 = filename;
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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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}, 500);
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"""
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PROPOSAL_PATH = "/afs/psi.ch/project/sinqdata/2020/zebra/"
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def create():
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det_data = {}
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js_data = ColumnDataSource(data=dict(cont=[], ext=[]))
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def proposal_textinput_callback(_attr, _old, new):
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ccl_path = os.path.join(PROPOSAL_PATH, new)
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ccl_file_list = []
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for file in os.listdir(ccl_path):
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if file.endswith(".ccl"):
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ccl_file_list.append((os.path.join(ccl_path, file), file))
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ccl_file_select.options = ccl_file_list
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ccl_file_select.value = ccl_file_list[0][0]
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proposal_textinput = TextInput(title="Enter proposal number:")
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proposal_textinput.on_change("value", proposal_textinput_callback)
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def ccl_file_select_callback(_attr, _old, new):
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nonlocal det_data
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with open(new) as file:
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_, ext = os.path.splitext(new)
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det_data = pyzebra.parse_1D(file, ext)
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meas_list = list(det_data["Measurements"].keys())
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meas_select.options = meas_list
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meas_select.value = None
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meas_select.value = meas_list[0]
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ccl_file_select = Select(title="Available .ccl files")
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ccl_file_select.on_change("value", ccl_file_select_callback)
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def upload_button_callback(_attr, _old, new):
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nonlocal det_data
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with io.StringIO(base64.b64decode(new).decode()) as file:
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_, ext = os.path.splitext(upload_button.filename)
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det_data = pyzebra.parse_1D(file, ext)
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meas_list = list(det_data["Measurements"].keys())
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meas_select.options = meas_list
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meas_select.value = None
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meas_select.value = meas_list[0]
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upload_button = FileInput(accept=".ccl")
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upload_button.on_change("value", upload_button_callback)
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def _update_plot(ind):
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meas = det_data["Measurements"][ind]
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y = meas["Counts"]
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x = list(range(len(y)))
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plot_line_source.data.update(x=x, y=y)
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num_of_peaks = meas.get("num_of_peaks")
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if num_of_peaks is not None and num_of_peaks > 0:
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plot_circle_source.data.update(x=meas["peak_indexes"], y=meas["peak_heights"])
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else:
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plot_circle_source.data.update(x=[], y=[])
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fit = meas.get("fit")
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if fit is not None:
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plot_gauss_source.data.update(x=x, y=meas["fit"]["comps"]["gaussian"])
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plot_bkg_source.data.update(x=x, y=meas["fit"]["comps"]["background"])
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fit_output_textinput.value = str(fit["full_report"])
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else:
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plot_gauss_source.data.update(x=[], y=[])
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plot_bkg_source.data.update(x=[], y=[])
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fit_output_textinput.value = ""
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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(),
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plot_height=400,
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plot_width=700,
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toolbar_location=None,
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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(), 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_line_source = ColumnDataSource(dict(x=[0], y=[0]))
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plot.add_glyph(plot_line_source, Line(x="x", y="y", line_color="steelblue"))
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plot_gauss_source = ColumnDataSource(dict(x=[0], y=[0]))
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plot.add_glyph(plot_gauss_source, Line(x="x", y="y", line_color="red", line_dash="dashed"))
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plot_bkg_source = ColumnDataSource(dict(x=[0], y=[0]))
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plot.add_glyph(plot_bkg_source, Line(x="x", y="y", line_color="green", line_dash="dashed"))
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plot_circle_source = ColumnDataSource(dict(x=[], y=[]))
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plot.add_glyph(plot_circle_source, Circle(x="x", y="y"))
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# Measurement select
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def meas_select_callback(_attr, _old, new):
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if new is not None:
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_update_plot(new)
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meas_select = Select()
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meas_select.on_change("value", meas_select_callback)
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smooth_toggle = Toggle(label="Smooth curve")
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fit_output_textinput = TextAreaInput(title="Fit results:", width=600, height=400)
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def process_button_callback():
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nonlocal det_data
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for meas in det_data["Measurements"]:
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det_data = pyzebra.ccl_findpeaks(det_data, meas, smooth=smooth_toggle.active)
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num_of_peaks = det_data["Measurements"][meas].get("num_of_peaks")
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if num_of_peaks is not None and num_of_peaks == 1:
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det_data = pyzebra.fitccl(
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det_data,
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meas,
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guess=[None, None, None, None, None],
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vary=[True, True, True, True, True],
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constraints_min=[None, None, None, None, None],
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constraints_max=[None, None, None, None, None],
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)
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_update_plot(meas_select.value)
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process_button = Button(label="Process All", button_type="primary")
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process_button.on_click(process_button_callback)
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def export_results(det_data):
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if det_data["meta"]["indices"] == "hkl":
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ext = ".comm"
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elif det_data["meta"]["indices"] == "real":
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ext = ".incomm"
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with tempfile.TemporaryDirectory() as temp_dir:
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temp_file = temp_dir + "/temp"
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pyzebra.export_comm(det_data, temp_file)
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with open(f"{temp_file}{ext}") as f:
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output_content = f.read()
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return output_content, ext
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def save_button_callback():
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cont, ext = export_results(det_data)
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js_data.data.update(cont=[cont], ext=[ext])
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save_button = Button(label="Export to .comm/.incomm file:")
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save_button.on_click(save_button_callback)
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save_button.js_on_click(CustomJS(args={"js_data": js_data}, code=javaScript))
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upload_div = Div(text="Or upload .ccl file:")
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tab_layout = column(
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row(proposal_textinput, ccl_file_select),
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row(column(Spacer(height=5), upload_div), upload_button, meas_select),
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row(plot, Spacer(width=30), fit_output_textinput),
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row(column(smooth_toggle, process_button, save_button)),
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)
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return Panel(child=tab_layout, title="ccl integrate")
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