Initial implementation of hdf param study panel
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commit
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@ -4,12 +4,10 @@ import math
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import os
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import os
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import numpy as np
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import numpy as np
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from bokeh.events import MouseEnter
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from bokeh.io import curdoc
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from bokeh.io import curdoc
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from bokeh.layouts import column, gridplot, row
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from bokeh.layouts import column, gridplot, row
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from bokeh.models import (
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from bokeh.models import (
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BasicTicker,
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BasicTicker,
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BoxEditTool,
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BoxZoomTool,
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BoxZoomTool,
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Button,
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Button,
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CheckboxGroup,
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CheckboxGroup,
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@ -20,23 +18,21 @@ from bokeh.models import (
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FileInput,
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FileInput,
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Grid,
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Grid,
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MultiSelect,
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MultiSelect,
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NumberEditor,
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NumberFormatter,
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NumberFormatter,
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HoverTool,
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Image,
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Image,
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Line,
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LinearAxis,
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LinearAxis,
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LinearColorMapper,
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LinearColorMapper,
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Panel,
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Panel,
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PanTool,
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PanTool,
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Plot,
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Plot,
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Range1d,
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Range1d,
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Rect,
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ResetTool,
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ResetTool,
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Scatter,
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Select,
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Select,
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Slider,
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Spacer,
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Spinner,
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Spinner,
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TableColumn,
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TableColumn,
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Tabs,
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TextInput,
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TextInput,
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Title,
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Title,
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WheelZoomTool,
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WheelZoomTool,
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@ -54,6 +50,7 @@ IMAGE_PLOT_H = int(IMAGE_H * 2) + 27
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def create():
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def create():
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doc = curdoc()
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doc = curdoc()
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zebra_data = []
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det_data = {}
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det_data = {}
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cami_meta = {}
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cami_meta = {}
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@ -100,33 +97,133 @@ def create():
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upload_button = FileInput(accept=".cami", width=200)
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upload_button = FileInput(accept=".cami", width=200)
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upload_button.on_change("value", upload_button_callback)
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upload_button.on_change("value", upload_button_callback)
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file_select = MultiSelect(title="Available .hdf files:", width=210, height=320)
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def _init_datatable():
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file_list = []
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for scan in zebra_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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param=[None] * len(zebra_data),
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frame=[None] * len(zebra_data),
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x_pos=[None] * len(zebra_data),
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y_pos=[None] * len(zebra_data),
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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 _update_table():
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frame = []
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x_pos = []
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y_pos = []
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for scan in zebra_data:
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if "fit" in scan:
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framei = scan["fit"]["frame"]
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x_posi = scan["fit"]["x_pos"]
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y_posi = scan["fit"]["y_pos"]
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else:
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framei = x_posi = y_posi = None
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frame.append(framei)
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x_pos.append(x_posi)
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y_pos.append(y_posi)
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scan_table_source.data.update(frame=frame, x_pos=x_pos, y_pos=y_pos)
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def file_open_button_callback():
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nonlocal zebra_data
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zebra_data = []
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for f_name in file_select.value:
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zebra_data.append(pyzebra.read_detector_data(f_name))
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_init_datatable()
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file_open_button = Button(label="Open New", width=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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zebra_data.append(pyzebra.read_detector_data(f_name))
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_init_datatable()
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file_append_button = Button(label="Append", width=100)
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file_append_button.on_click(file_append_button_callback)
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# Scan select
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def scan_table_select_callback(_attr, old, new):
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nonlocal det_data
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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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det_data = zebra_data[new[0]]
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zebra_mode = det_data["zebra_mode"]
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if zebra_mode == "nb":
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metadata_table_source.data.update(geom=["normal beam"])
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else: # zebra_mode == "bi"
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metadata_table_source.data.update(geom=["bisecting"])
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update_image(0)
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update_overview_plot()
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def scan_table_source_callback(_attr, _old, _new):
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pass
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scan_table_source = ColumnDataSource(dict(file=[], param=[], frame=[], x_pos=[], y_pos=[]))
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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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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="param", title="param", editor=NumberEditor(), width=50),
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TableColumn(field="frame", title="Frame", width=70),
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TableColumn(field="x_pos", title="X", width=70),
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TableColumn(field="y_pos", title="Y", width=70),
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],
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width=470, # +60 because of the index column
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height=420,
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editable=True,
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autosize_mode="none",
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)
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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(zebra_data)
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else:
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# TODO: which value to take?
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param = [scan[new][0] for scan in zebra_data]
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scan_table_source.data["param"] = param
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_update_param_plot()
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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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width=145,
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)
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param_select.on_change("value", param_select_callback)
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def update_image(index=None):
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def update_image(index=None):
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if index is None:
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index = index_spinner.value
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current_image = det_data["data"][index]
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proj_v_line_source.data.update(
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x=np.arange(0, IMAGE_W) + 0.5, y=np.mean(current_image, axis=0)
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)
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proj_h_line_source.data.update(
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x=np.mean(current_image, axis=1), y=np.arange(0, IMAGE_H) + 0.5
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)
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image_source.data.update(
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h=[np.zeros((1, 1))], k=[np.zeros((1, 1))], l=[np.zeros((1, 1))],
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)
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image_source.data.update(image=[current_image])
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if main_auto_checkbox.active:
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im_min = np.min(current_image)
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im_max = np.max(current_image)
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display_min_spinner.value = im_min
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display_max_spinner.value = im_max
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image_glyph.color_mapper.low = im_min
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image_glyph.color_mapper.high = im_max
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if "mf" in det_data:
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if "mf" in det_data:
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metadata_table_source.data.update(mf=[det_data["mf"][index]])
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metadata_table_source.data.update(mf=[det_data["mf"][index]])
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else:
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else:
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@ -137,10 +234,6 @@ def create():
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else:
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else:
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metadata_table_source.data.update(temp=[None])
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metadata_table_source.data.update(temp=[None])
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gamma, nu = calculate_pol(det_data, index)
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omega = np.ones((IMAGE_H, IMAGE_W)) * det_data["omega"][index]
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image_source.data.update(gamma=[gamma], nu=[nu], omega=[omega])
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def update_overview_plot():
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def update_overview_plot():
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h5_data = det_data["data"]
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h5_data = det_data["data"]
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n_im, n_y, n_x = h5_data.shape
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n_im, n_y, n_x = h5_data.shape
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@ -182,191 +275,6 @@ def create():
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# handle both, ascending and descending sequences
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# handle both, ascending and descending sequences
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scanning_motor_range.bounds = (min(var_start, var_end), max(var_start, var_end))
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scanning_motor_range.bounds = (min(var_start, var_end), max(var_start, var_end))
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def file_select_callback(_attr, old, new):
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nonlocal det_data
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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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file_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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det_data = pyzebra.read_detector_data(new[0], cami_meta)
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index_spinner.value = 0
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index_spinner.high = det_data["data"].shape[0] - 1
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index_slider.end = det_data["data"].shape[0] - 1
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zebra_mode = det_data["zebra_mode"]
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if zebra_mode == "nb":
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metadata_table_source.data.update(geom=["normal beam"])
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else: # zebra_mode == "bi"
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metadata_table_source.data.update(geom=["bisecting"])
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update_image(0)
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update_overview_plot()
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file_select = MultiSelect(title="Available .hdf files:", width=210, height=250)
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file_select.on_change("value", file_select_callback)
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def index_callback(_attr, _old, new):
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update_image(new)
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index_slider = Slider(value=0, start=0, end=1, show_value=False, width=400)
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index_spinner = Spinner(title="Image index:", value=0, low=0, width=100)
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index_spinner.on_change("value", index_callback)
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index_slider.js_link("value_throttled", index_spinner, "value")
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index_spinner.js_link("value", index_slider, "value")
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plot = Plot(
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x_range=Range1d(0, IMAGE_W, bounds=(0, IMAGE_W)),
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y_range=Range1d(0, IMAGE_H, bounds=(0, IMAGE_H)),
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plot_height=IMAGE_PLOT_H,
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plot_width=IMAGE_PLOT_W,
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toolbar_location="left",
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)
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# ---- tools
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plot.toolbar.logo = None
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# ---- axes
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plot.add_layout(LinearAxis(), place="above")
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plot.add_layout(LinearAxis(major_label_orientation="vertical"), place="right")
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# ---- grid lines
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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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# ---- rgba image glyph
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image_source = ColumnDataSource(
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dict(
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image=[np.zeros((IMAGE_H, IMAGE_W), dtype="float32")],
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h=[np.zeros((1, 1))],
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k=[np.zeros((1, 1))],
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l=[np.zeros((1, 1))],
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gamma=[np.zeros((1, 1))],
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nu=[np.zeros((1, 1))],
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omega=[np.zeros((1, 1))],
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x=[0],
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y=[0],
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dw=[IMAGE_W],
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dh=[IMAGE_H],
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)
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)
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h_glyph = Image(image="h", x="x", y="y", dw="dw", dh="dh", global_alpha=0)
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k_glyph = Image(image="k", x="x", y="y", dw="dw", dh="dh", global_alpha=0)
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l_glyph = Image(image="l", x="x", y="y", dw="dw", dh="dh", global_alpha=0)
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gamma_glyph = Image(image="gamma", x="x", y="y", dw="dw", dh="dh", global_alpha=0)
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nu_glyph = Image(image="nu", x="x", y="y", dw="dw", dh="dh", global_alpha=0)
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omega_glyph = Image(image="omega", x="x", y="y", dw="dw", dh="dh", global_alpha=0)
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plot.add_glyph(image_source, h_glyph)
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plot.add_glyph(image_source, k_glyph)
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plot.add_glyph(image_source, l_glyph)
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plot.add_glyph(image_source, gamma_glyph)
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plot.add_glyph(image_source, nu_glyph)
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plot.add_glyph(image_source, omega_glyph)
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image_glyph = Image(image="image", x="x", y="y", dw="dw", dh="dh")
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plot.add_glyph(image_source, image_glyph, name="image_glyph")
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# calculate hkl-indices of first mouse entry
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def mouse_enter_callback(_event):
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if det_data and np.array_equal(image_source.data["h"][0], np.zeros((1, 1))):
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index = index_spinner.value
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h, k, l = calculate_hkl(det_data, index)
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image_source.data.update(h=[h], k=[k], l=[l])
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plot.on_event(MouseEnter, mouse_enter_callback)
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# ---- projections
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proj_v = Plot(
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x_range=plot.x_range,
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y_range=DataRange1d(),
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plot_height=150,
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plot_width=IMAGE_PLOT_W,
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toolbar_location=None,
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)
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proj_v.add_layout(LinearAxis(major_label_orientation="vertical"), place="right")
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proj_v.add_layout(LinearAxis(major_label_text_font_size="0pt"), place="below")
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proj_v.add_layout(Grid(dimension=0, ticker=BasicTicker()))
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proj_v.add_layout(Grid(dimension=1, ticker=BasicTicker()))
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proj_v_line_source = ColumnDataSource(dict(x=[], y=[]))
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proj_v.add_glyph(proj_v_line_source, Line(x="x", y="y", line_color="steelblue"))
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proj_h = Plot(
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x_range=DataRange1d(),
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y_range=plot.y_range,
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plot_height=IMAGE_PLOT_H,
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plot_width=150,
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toolbar_location=None,
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)
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proj_h.add_layout(LinearAxis(), place="above")
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proj_h.add_layout(LinearAxis(major_label_text_font_size="0pt"), place="left")
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proj_h.add_layout(Grid(dimension=0, ticker=BasicTicker()))
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|
||||||
proj_h.add_layout(Grid(dimension=1, ticker=BasicTicker()))
|
|
||||||
|
|
||||||
proj_h_line_source = ColumnDataSource(dict(x=[], y=[]))
|
|
||||||
proj_h.add_glyph(proj_h_line_source, Line(x="x", y="y", line_color="steelblue"))
|
|
||||||
|
|
||||||
# add tools
|
|
||||||
hovertool = HoverTool(
|
|
||||||
tooltips=[
|
|
||||||
("intensity", "@image"),
|
|
||||||
("gamma", "@gamma"),
|
|
||||||
("nu", "@nu"),
|
|
||||||
("omega", "@omega"),
|
|
||||||
("h", "@h"),
|
|
||||||
("k", "@k"),
|
|
||||||
("l", "@l"),
|
|
||||||
]
|
|
||||||
)
|
|
||||||
|
|
||||||
box_edit_source = ColumnDataSource(dict(x=[], y=[], width=[], height=[]))
|
|
||||||
box_edit_glyph = Rect(
|
|
||||||
x="x", y="y", width="width", height="height", fill_alpha=0, line_color="red"
|
|
||||||
)
|
|
||||||
box_edit_renderer = plot.add_glyph(box_edit_source, box_edit_glyph)
|
|
||||||
boxedittool = BoxEditTool(renderers=[box_edit_renderer], num_objects=1)
|
|
||||||
|
|
||||||
def box_edit_callback(_attr, _old, new):
|
|
||||||
if new["x"]:
|
|
||||||
h5_data = det_data["data"]
|
|
||||||
x_val = np.arange(h5_data.shape[0])
|
|
||||||
left = int(np.floor(new["x"][0]))
|
|
||||||
right = int(np.ceil(new["x"][0] + new["width"][0]))
|
|
||||||
bottom = int(np.floor(new["y"][0]))
|
|
||||||
top = int(np.ceil(new["y"][0] + new["height"][0]))
|
|
||||||
y_val = np.sum(h5_data[:, bottom:top, left:right], axis=(1, 2))
|
|
||||||
else:
|
|
||||||
x_val = []
|
|
||||||
y_val = []
|
|
||||||
|
|
||||||
roi_avg_plot_line_source.data.update(x=x_val, y=y_val)
|
|
||||||
|
|
||||||
box_edit_source.on_change("data", box_edit_callback)
|
|
||||||
|
|
||||||
wheelzoomtool = WheelZoomTool(maintain_focus=False)
|
|
||||||
plot.add_tools(
|
|
||||||
PanTool(), BoxZoomTool(), wheelzoomtool, ResetTool(), hovertool, boxedittool,
|
|
||||||
)
|
|
||||||
plot.toolbar.active_scroll = wheelzoomtool
|
|
||||||
|
|
||||||
# shared frame ranges
|
# shared frame ranges
|
||||||
frame_range = Range1d(0, 1, bounds=(0, 1))
|
frame_range = Range1d(0, 1, bounds=(0, 1))
|
||||||
scanning_motor_range = Range1d(0, 1, bounds=(0, 1))
|
scanning_motor_range = Range1d(0, 1, bounds=(0, 1))
|
||||||
@ -452,28 +360,6 @@ def create():
|
|||||||
overview_plot_y_image_source, overview_plot_y_image_glyph, name="image_glyph"
|
overview_plot_y_image_source, overview_plot_y_image_glyph, name="image_glyph"
|
||||||
)
|
)
|
||||||
|
|
||||||
roi_avg_plot = Plot(
|
|
||||||
x_range=DataRange1d(),
|
|
||||||
y_range=DataRange1d(),
|
|
||||||
plot_height=150,
|
|
||||||
plot_width=IMAGE_PLOT_W,
|
|
||||||
toolbar_location="left",
|
|
||||||
)
|
|
||||||
|
|
||||||
# ---- tools
|
|
||||||
roi_avg_plot.toolbar.logo = None
|
|
||||||
|
|
||||||
# ---- axes
|
|
||||||
roi_avg_plot.add_layout(LinearAxis(), place="below")
|
|
||||||
roi_avg_plot.add_layout(LinearAxis(major_label_orientation="vertical"), place="left")
|
|
||||||
|
|
||||||
# ---- grid lines
|
|
||||||
roi_avg_plot.add_layout(Grid(dimension=0, ticker=BasicTicker()))
|
|
||||||
roi_avg_plot.add_layout(Grid(dimension=1, ticker=BasicTicker()))
|
|
||||||
|
|
||||||
roi_avg_plot_line_source = ColumnDataSource(dict(x=[], y=[]))
|
|
||||||
roi_avg_plot.add_glyph(roi_avg_plot_line_source, Line(x="x", y="y", line_color="steelblue"))
|
|
||||||
|
|
||||||
cmap_dict = {
|
cmap_dict = {
|
||||||
"gray": Greys256,
|
"gray": Greys256,
|
||||||
"gray_reversed": Greys256[::-1],
|
"gray_reversed": Greys256[::-1],
|
||||||
@ -482,7 +368,6 @@ def create():
|
|||||||
}
|
}
|
||||||
|
|
||||||
def colormap_callback(_attr, _old, new):
|
def colormap_callback(_attr, _old, new):
|
||||||
image_glyph.color_mapper = LinearColorMapper(palette=cmap_dict[new])
|
|
||||||
overview_plot_x_image_glyph.color_mapper = LinearColorMapper(palette=cmap_dict[new])
|
overview_plot_x_image_glyph.color_mapper = LinearColorMapper(palette=cmap_dict[new])
|
||||||
overview_plot_y_image_glyph.color_mapper = LinearColorMapper(palette=cmap_dict[new])
|
overview_plot_y_image_glyph.color_mapper = LinearColorMapper(palette=cmap_dict[new])
|
||||||
|
|
||||||
@ -490,52 +375,6 @@ def create():
|
|||||||
colormap.on_change("value", colormap_callback)
|
colormap.on_change("value", colormap_callback)
|
||||||
colormap.value = "plasma"
|
colormap.value = "plasma"
|
||||||
|
|
||||||
STEP = 1
|
|
||||||
|
|
||||||
def main_auto_checkbox_callback(state):
|
|
||||||
if state:
|
|
||||||
display_min_spinner.disabled = True
|
|
||||||
display_max_spinner.disabled = True
|
|
||||||
else:
|
|
||||||
display_min_spinner.disabled = False
|
|
||||||
display_max_spinner.disabled = False
|
|
||||||
|
|
||||||
update_image()
|
|
||||||
|
|
||||||
main_auto_checkbox = CheckboxGroup(
|
|
||||||
labels=["Frame Intensity Range"], active=[0], width=145, margin=[10, 5, 0, 5]
|
|
||||||
)
|
|
||||||
main_auto_checkbox.on_click(main_auto_checkbox_callback)
|
|
||||||
|
|
||||||
def display_max_spinner_callback(_attr, _old_value, new_value):
|
|
||||||
display_min_spinner.high = new_value - STEP
|
|
||||||
image_glyph.color_mapper.high = new_value
|
|
||||||
|
|
||||||
display_max_spinner = Spinner(
|
|
||||||
low=0 + STEP,
|
|
||||||
value=1,
|
|
||||||
step=STEP,
|
|
||||||
disabled=bool(main_auto_checkbox.active),
|
|
||||||
width=100,
|
|
||||||
height=31,
|
|
||||||
)
|
|
||||||
display_max_spinner.on_change("value", display_max_spinner_callback)
|
|
||||||
|
|
||||||
def display_min_spinner_callback(_attr, _old_value, new_value):
|
|
||||||
display_max_spinner.low = new_value + STEP
|
|
||||||
image_glyph.color_mapper.low = new_value
|
|
||||||
|
|
||||||
display_min_spinner = Spinner(
|
|
||||||
low=0,
|
|
||||||
high=1 - STEP,
|
|
||||||
value=0,
|
|
||||||
step=STEP,
|
|
||||||
disabled=bool(main_auto_checkbox.active),
|
|
||||||
width=100,
|
|
||||||
height=31,
|
|
||||||
)
|
|
||||||
display_min_spinner.on_change("value", display_min_spinner_callback)
|
|
||||||
|
|
||||||
PROJ_STEP = 0.1
|
PROJ_STEP = 0.1
|
||||||
|
|
||||||
def proj_auto_checkbox_callback(state):
|
def proj_auto_checkbox_callback(state):
|
||||||
@ -584,59 +423,22 @@ def create():
|
|||||||
)
|
)
|
||||||
proj_display_min_spinner.on_change("value", proj_display_min_spinner_callback)
|
proj_display_min_spinner.on_change("value", proj_display_min_spinner_callback)
|
||||||
|
|
||||||
events_data = dict(
|
def fit_event(scan):
|
||||||
wave=[],
|
|
||||||
ddist=[],
|
|
||||||
cell=[],
|
|
||||||
frame=[],
|
|
||||||
x_pos=[],
|
|
||||||
y_pos=[],
|
|
||||||
intensity=[],
|
|
||||||
snr_cnts=[],
|
|
||||||
gamma=[],
|
|
||||||
omega=[],
|
|
||||||
chi=[],
|
|
||||||
phi=[],
|
|
||||||
nu=[],
|
|
||||||
)
|
|
||||||
doc.events_data = events_data
|
|
||||||
|
|
||||||
events_table_source = ColumnDataSource(events_data)
|
|
||||||
events_table = DataTable(
|
|
||||||
source=events_table_source,
|
|
||||||
columns=[
|
|
||||||
TableColumn(field="frame", title="Frame", formatter=num_formatter, width=70),
|
|
||||||
TableColumn(field="x_pos", title="X", formatter=num_formatter, width=70),
|
|
||||||
TableColumn(field="y_pos", title="Y", formatter=num_formatter, width=70),
|
|
||||||
TableColumn(field="intensity", title="Intensity", formatter=num_formatter, width=70),
|
|
||||||
TableColumn(field="gamma", title="Gamma", formatter=num_formatter, width=70),
|
|
||||||
TableColumn(field="omega", title="Omega", formatter=num_formatter, width=70),
|
|
||||||
TableColumn(field="chi", title="Chi", formatter=num_formatter, width=70),
|
|
||||||
TableColumn(field="phi", title="Phi", formatter=num_formatter, width=70),
|
|
||||||
TableColumn(field="nu", title="Nu", formatter=num_formatter, width=70),
|
|
||||||
],
|
|
||||||
height=150,
|
|
||||||
width=630,
|
|
||||||
autosize_mode="none",
|
|
||||||
index_position=None,
|
|
||||||
)
|
|
||||||
|
|
||||||
def add_event_button_callback():
|
|
||||||
p0 = [1.0, 0.0, 1.0]
|
p0 = [1.0, 0.0, 1.0]
|
||||||
maxfev = 100000
|
maxfev = 100000
|
||||||
|
|
||||||
wave = det_data["wave"]
|
# wave = scan["wave"]
|
||||||
ddist = det_data["ddist"]
|
# ddist = scan["ddist"]
|
||||||
cell = det_data["cell"]
|
# cell = scan["cell"]
|
||||||
|
|
||||||
gamma = det_data["gamma"][0]
|
# gamma = scan["gamma"][0]
|
||||||
omega = det_data["omega"][0]
|
# omega = scan["omega"][0]
|
||||||
nu = det_data["nu"][0]
|
# nu = scan["nu"][0]
|
||||||
chi = det_data["chi"][0]
|
# chi = scan["chi"][0]
|
||||||
phi = det_data["phi"][0]
|
# phi = scan["phi"][0]
|
||||||
|
|
||||||
scan_motor = det_data["scan_motor"]
|
scan_motor = scan["scan_motor"]
|
||||||
var_angle = det_data[scan_motor]
|
var_angle = scan[scan_motor]
|
||||||
|
|
||||||
x0 = int(np.floor(det_x_range.start))
|
x0 = int(np.floor(det_x_range.start))
|
||||||
xN = int(np.ceil(det_x_range.end))
|
xN = int(np.ceil(det_x_range.end))
|
||||||
@ -644,32 +446,32 @@ def create():
|
|||||||
yN = int(np.ceil(det_y_range.end))
|
yN = int(np.ceil(det_y_range.end))
|
||||||
fr0 = int(np.floor(frame_range.start))
|
fr0 = int(np.floor(frame_range.start))
|
||||||
frN = int(np.ceil(frame_range.end))
|
frN = int(np.ceil(frame_range.end))
|
||||||
data_roi = det_data["data"][fr0:frN, y0:yN, x0:xN]
|
data_roi = scan["data"][fr0:frN, y0:yN, x0:xN]
|
||||||
|
|
||||||
cnts = np.sum(data_roi, axis=(1, 2))
|
cnts = np.sum(data_roi, axis=(1, 2))
|
||||||
coeff, _ = curve_fit(gauss, range(len(cnts)), cnts, p0=p0, maxfev=maxfev)
|
coeff, _ = curve_fit(gauss, range(len(cnts)), cnts, p0=p0, maxfev=maxfev)
|
||||||
|
|
||||||
m = cnts.mean()
|
# m = cnts.mean()
|
||||||
sd = cnts.std()
|
# sd = cnts.std()
|
||||||
snr_cnts = np.where(sd == 0, 0, m / sd)
|
# snr_cnts = np.where(sd == 0, 0, m / sd)
|
||||||
|
|
||||||
frC = fr0 + coeff[1]
|
frC = fr0 + coeff[1]
|
||||||
var_F = var_angle[math.floor(frC)]
|
var_F = var_angle[math.floor(frC)]
|
||||||
var_C = var_angle[math.ceil(frC)]
|
var_C = var_angle[math.ceil(frC)]
|
||||||
frStep = frC - math.floor(frC)
|
# frStep = frC - math.floor(frC)
|
||||||
var_step = var_C - var_F
|
var_step = var_C - var_F
|
||||||
var_p = var_F + var_step * frStep
|
# var_p = var_F + var_step * frStep
|
||||||
|
|
||||||
if scan_motor == "gamma":
|
# if scan_motor == "gamma":
|
||||||
gamma = var_p
|
# gamma = var_p
|
||||||
elif scan_motor == "omega":
|
# elif scan_motor == "omega":
|
||||||
omega = var_p
|
# omega = var_p
|
||||||
elif scan_motor == "nu":
|
# elif scan_motor == "nu":
|
||||||
nu = var_p
|
# nu = var_p
|
||||||
elif scan_motor == "chi":
|
# elif scan_motor == "chi":
|
||||||
chi = var_p
|
# chi = var_p
|
||||||
elif scan_motor == "phi":
|
# elif scan_motor == "phi":
|
||||||
phi = var_p
|
# phi = var_p
|
||||||
|
|
||||||
intensity = coeff[1] * abs(coeff[2] * var_step) * math.sqrt(2) * math.sqrt(np.pi)
|
intensity = coeff[1] * abs(coeff[2] * var_step) * math.sqrt(2) * math.sqrt(np.pi)
|
||||||
|
|
||||||
@ -681,35 +483,7 @@ def create():
|
|||||||
coeff, _ = curve_fit(gauss, range(len(projY)), projY, p0=p0, maxfev=maxfev)
|
coeff, _ = curve_fit(gauss, range(len(projY)), projY, p0=p0, maxfev=maxfev)
|
||||||
y_pos = y0 + coeff[1]
|
y_pos = y0 + coeff[1]
|
||||||
|
|
||||||
events_data["wave"].append(wave)
|
scan["fit"] = {"frame": frC, "x_pos": x_pos, "y_pos": y_pos, "intensity": intensity}
|
||||||
events_data["ddist"].append(ddist)
|
|
||||||
events_data["cell"].append(cell)
|
|
||||||
events_data["frame"].append(frC)
|
|
||||||
events_data["x_pos"].append(x_pos)
|
|
||||||
events_data["y_pos"].append(y_pos)
|
|
||||||
events_data["intensity"].append(intensity)
|
|
||||||
events_data["snr_cnts"].append(snr_cnts)
|
|
||||||
events_data["gamma"].append(gamma)
|
|
||||||
events_data["omega"].append(omega)
|
|
||||||
events_data["chi"].append(chi)
|
|
||||||
events_data["phi"].append(phi)
|
|
||||||
events_data["nu"].append(nu)
|
|
||||||
|
|
||||||
events_table_source.data = events_data
|
|
||||||
|
|
||||||
add_event_button = Button(label="Add spind event", width=145)
|
|
||||||
add_event_button.on_click(add_event_button_callback)
|
|
||||||
|
|
||||||
def remove_event_button_callback():
|
|
||||||
ind2remove = events_table_source.selected.indices
|
|
||||||
for value in events_data.values():
|
|
||||||
for ind in reversed(ind2remove):
|
|
||||||
del value[ind]
|
|
||||||
|
|
||||||
events_table_source.data = events_data
|
|
||||||
|
|
||||||
remove_event_button = Button(label="Remove spind event", width=145)
|
|
||||||
remove_event_button.on_click(remove_event_button_callback)
|
|
||||||
|
|
||||||
metadata_table_source = ColumnDataSource(dict(geom=[""], temp=[None], mf=[None]))
|
metadata_table_source = ColumnDataSource(dict(geom=[""], temp=[None], mf=[None]))
|
||||||
metadata_table = DataTable(
|
metadata_table = DataTable(
|
||||||
@ -725,20 +499,78 @@ def create():
|
|||||||
index_position=None,
|
index_position=None,
|
||||||
)
|
)
|
||||||
|
|
||||||
# Final layout
|
def _update_param_plot():
|
||||||
import_layout = column(proposal_textinput, upload_div, upload_button, file_select)
|
x = []
|
||||||
layout_image = column(gridplot([[proj_v, None], [plot, proj_h]], merge_tools=False))
|
y = []
|
||||||
colormap_layout = column(
|
fit_param = fit_param_select.value
|
||||||
colormap,
|
for s, p in zip(zebra_data, scan_table_source.data["param"]):
|
||||||
main_auto_checkbox,
|
if "fit" in s and fit_param:
|
||||||
row(display_min_spinner, display_max_spinner),
|
x.append(p)
|
||||||
proj_auto_checkbox,
|
y.append(s["fit"][fit_param])
|
||||||
row(proj_display_min_spinner, proj_display_max_spinner),
|
print(x, y)
|
||||||
)
|
param_plot_scatter_source.data.update(x=x, y=y)
|
||||||
|
|
||||||
layout_controls = column(
|
# Parameter plot
|
||||||
row(metadata_table, index_spinner, column(Spacer(height=25), index_slider)),
|
param_plot = Plot(x_range=DataRange1d(), y_range=DataRange1d(), plot_height=400, plot_width=700)
|
||||||
row(column(add_event_button, remove_event_button), events_table),
|
|
||||||
|
param_plot.add_layout(LinearAxis(axis_label="Fit parameter"), place="left")
|
||||||
|
param_plot.add_layout(LinearAxis(axis_label="Parameter"), place="below")
|
||||||
|
|
||||||
|
param_plot.add_layout(Grid(dimension=0, ticker=BasicTicker()))
|
||||||
|
param_plot.add_layout(Grid(dimension=1, ticker=BasicTicker()))
|
||||||
|
|
||||||
|
param_plot_scatter_source = ColumnDataSource(dict(x=[], y=[]))
|
||||||
|
param_plot.add_glyph(param_plot_scatter_source, Scatter(x="x", y="y"))
|
||||||
|
|
||||||
|
param_plot.add_tools(PanTool(), WheelZoomTool(), ResetTool())
|
||||||
|
param_plot.toolbar.logo = None
|
||||||
|
|
||||||
|
def fit_param_select_callback(_attr, _old, _new):
|
||||||
|
_update_param_plot()
|
||||||
|
|
||||||
|
fit_param_select = Select(title="Fit parameter", options=[], width=145)
|
||||||
|
fit_param_select.on_change("value", fit_param_select_callback)
|
||||||
|
|
||||||
|
def proc_all_button_callback():
|
||||||
|
for scan in zebra_data:
|
||||||
|
fit_event(scan)
|
||||||
|
|
||||||
|
_update_table()
|
||||||
|
|
||||||
|
for scan in zebra_data:
|
||||||
|
if "fit" in scan:
|
||||||
|
options = list(scan["fit"].keys())
|
||||||
|
fit_param_select.options = options
|
||||||
|
fit_param_select.value = options[0]
|
||||||
|
break
|
||||||
|
|
||||||
|
_update_param_plot()
|
||||||
|
|
||||||
|
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():
|
||||||
|
fit_event(det_data)
|
||||||
|
|
||||||
|
_update_table()
|
||||||
|
|
||||||
|
for scan in zebra_data:
|
||||||
|
if "fit" in scan:
|
||||||
|
options = list(scan["fit"].keys())
|
||||||
|
fit_param_select.options = options
|
||||||
|
fit_param_select.value = options[0]
|
||||||
|
break
|
||||||
|
|
||||||
|
_update_param_plot()
|
||||||
|
|
||||||
|
proc_button = Button(label="Process Current", width=145)
|
||||||
|
proc_button.on_click(proc_button_callback)
|
||||||
|
|
||||||
|
layout_controls = row(
|
||||||
|
colormap,
|
||||||
|
column(proj_auto_checkbox, row(proj_display_min_spinner, proj_display_max_spinner)),
|
||||||
|
proc_button,
|
||||||
|
proc_all_button,
|
||||||
)
|
)
|
||||||
|
|
||||||
layout_overview = column(
|
layout_overview = column(
|
||||||
@ -748,14 +580,30 @@ def create():
|
|||||||
merge_tools=True,
|
merge_tools=True,
|
||||||
toolbar_location="left",
|
toolbar_location="left",
|
||||||
),
|
),
|
||||||
|
layout_controls,
|
||||||
)
|
)
|
||||||
|
|
||||||
tab_layout = row(
|
# Plot tabs
|
||||||
column(import_layout, colormap_layout),
|
plots = Tabs(
|
||||||
column(layout_overview, layout_controls),
|
tabs=[
|
||||||
column(roi_avg_plot, layout_image),
|
Panel(child=layout_overview, title="single scan"),
|
||||||
|
Panel(child=column(param_plot, row(fit_param_select)), title="parameter plot"),
|
||||||
|
]
|
||||||
)
|
)
|
||||||
|
|
||||||
|
# Final layout
|
||||||
|
import_layout = column(
|
||||||
|
proposal_textinput,
|
||||||
|
upload_div,
|
||||||
|
upload_button,
|
||||||
|
file_select,
|
||||||
|
row(file_open_button, file_append_button),
|
||||||
|
)
|
||||||
|
|
||||||
|
scan_layout = column(scan_table, row(param_select, metadata_table))
|
||||||
|
|
||||||
|
tab_layout = column(row(import_layout, scan_layout, plots))
|
||||||
|
|
||||||
return Panel(child=tab_layout, title="hdf param study")
|
return Panel(child=tab_layout, title="hdf param study")
|
||||||
|
|
||||||
|
|
||||||
@ -768,49 +616,3 @@ def gauss(x, *p):
|
|||||||
"""
|
"""
|
||||||
A, mu, sigma = p
|
A, mu, sigma = p
|
||||||
return A * np.exp(-((x - mu) ** 2) / (2.0 * sigma ** 2))
|
return A * np.exp(-((x - mu) ** 2) / (2.0 * sigma ** 2))
|
||||||
|
|
||||||
|
|
||||||
def calculate_hkl(det_data, index):
|
|
||||||
h = np.empty(shape=(IMAGE_H, IMAGE_W))
|
|
||||||
k = np.empty(shape=(IMAGE_H, IMAGE_W))
|
|
||||||
l = np.empty(shape=(IMAGE_H, IMAGE_W))
|
|
||||||
|
|
||||||
wave = det_data["wave"]
|
|
||||||
ddist = det_data["ddist"]
|
|
||||||
gammad = det_data["gamma"][index]
|
|
||||||
om = det_data["omega"][index]
|
|
||||||
nud = det_data["nu"]
|
|
||||||
ub = det_data["ub"]
|
|
||||||
geometry = det_data["zebra_mode"]
|
|
||||||
|
|
||||||
if geometry == "bi":
|
|
||||||
chi = det_data["chi"][index]
|
|
||||||
phi = det_data["phi"][index]
|
|
||||||
elif geometry == "nb":
|
|
||||||
chi = 0
|
|
||||||
phi = 0
|
|
||||||
else:
|
|
||||||
raise ValueError(f"Unknown geometry type '{geometry}'")
|
|
||||||
|
|
||||||
for xi in np.arange(IMAGE_W):
|
|
||||||
for yi in np.arange(IMAGE_H):
|
|
||||||
h[yi, xi], k[yi, xi], l[yi, xi] = pyzebra.ang2hkl(
|
|
||||||
wave, ddist, gammad, om, chi, phi, nud, ub, xi, yi
|
|
||||||
)
|
|
||||||
|
|
||||||
return h, k, l
|
|
||||||
|
|
||||||
|
|
||||||
def calculate_pol(det_data, index):
|
|
||||||
gamma = np.empty(shape=(IMAGE_H, IMAGE_W))
|
|
||||||
nu = np.empty(shape=(IMAGE_H, IMAGE_W))
|
|
||||||
|
|
||||||
ddist = det_data["ddist"]
|
|
||||||
gammad = det_data["gamma"][index]
|
|
||||||
nud = det_data["nu"]
|
|
||||||
|
|
||||||
for xi in np.arange(IMAGE_W):
|
|
||||||
for yi in np.arange(IMAGE_H):
|
|
||||||
gamma[yi, xi], nu[yi, xi] = pyzebra.det2pol(ddist, gammad, nud, xi, yi)
|
|
||||||
|
|
||||||
return gamma, nu
|
|
||||||
|
|||||||
@ -75,6 +75,7 @@ def read_detector_data(filepath, cami_meta=None):
|
|||||||
data = data.reshape(n, rows, cols)
|
data = data.reshape(n, rows, cols)
|
||||||
|
|
||||||
det_data = {"data": data}
|
det_data = {"data": data}
|
||||||
|
det_data["original_filename"] = filepath
|
||||||
|
|
||||||
if "/entry1/zebra_mode" in h5f:
|
if "/entry1/zebra_mode" in h5f:
|
||||||
det_data["zebra_mode"] = h5f["/entry1/zebra_mode"][0].decode()
|
det_data["zebra_mode"] = h5f["/entry1/zebra_mode"][0].decode()
|
||||||
|
|||||||
Loading…
x
Reference in New Issue
Block a user