Simplify plot creation in panel_hdf_param_study
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@ -6,37 +6,26 @@ import numpy as np
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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.models import (
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BasicTicker,
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BoxZoomTool,
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Button,
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CellEditor,
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CheckboxGroup,
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ColumnDataSource,
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DataRange1d,
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DataTable,
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Div,
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FileInput,
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Grid,
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Image,
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LinearAxis,
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LinearColorMapper,
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MultiSelect,
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NumberEditor,
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NumberFormatter,
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Panel,
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PanTool,
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Plot,
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Range1d,
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ResetTool,
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Scatter,
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Select,
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Spinner,
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TableColumn,
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Tabs,
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Title,
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WheelZoomTool,
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)
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from bokeh.palettes import Cividis256, Greys256, Plasma256 # pylint: disable=E0611
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from bokeh.palettes import Cividis256, Greys256, Plasma256
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from bokeh.plotting import figure
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import pyzebra
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@ -201,7 +190,7 @@ def create():
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else:
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metadata_table_source.data.update(temp=[None])
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update_overview_plot()
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_update_proj_plots()
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def scan_table_source_callback(_attr, _old, _new):
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pass
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@ -258,32 +247,32 @@ def create():
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)
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param_select.on_change("value", param_select_callback)
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def update_overview_plot():
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def _update_proj_plots():
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scan = _get_selected_scan()
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counts = scan["counts"]
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n_im, n_y, n_x = counts.shape
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overview_x = np.mean(counts, axis=1)
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overview_y = np.mean(counts, axis=2)
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im_proj_x = np.mean(counts, axis=1)
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im_proj_y = np.mean(counts, axis=2)
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# normalize for simpler colormapping
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overview_max_val = max(np.max(overview_x), np.max(overview_y))
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overview_x = 1000 * overview_x / overview_max_val
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overview_y = 1000 * overview_y / overview_max_val
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im_proj_max_val = max(np.max(im_proj_x), np.max(im_proj_y))
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im_proj_x = 1000 * im_proj_x / im_proj_max_val
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im_proj_y = 1000 * im_proj_y / im_proj_max_val
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overview_plot_x_image_source.data.update(image=[overview_x], dw=[n_x], dh=[n_im])
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overview_plot_y_image_source.data.update(image=[overview_y], dw=[n_y], dh=[n_im])
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proj_x_image_source.data.update(image=[im_proj_x], dw=[n_x], dh=[n_im])
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proj_y_image_source.data.update(image=[im_proj_y], dw=[n_y], dh=[n_im])
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if proj_auto_checkbox.active:
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im_min = min(np.min(overview_x), np.min(overview_y))
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im_max = max(np.max(overview_x), np.max(overview_y))
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im_min = min(np.min(im_proj_x), np.min(im_proj_y))
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im_max = max(np.max(im_proj_x), np.max(im_proj_y))
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proj_display_min_spinner.value = im_min
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proj_display_max_spinner.value = im_max
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overview_plot_x_image_glyph.color_mapper.low = im_min
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overview_plot_y_image_glyph.color_mapper.low = im_min
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overview_plot_x_image_glyph.color_mapper.high = im_max
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overview_plot_y_image_glyph.color_mapper.high = im_max
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proj_x_image_glyph.color_mapper.low = im_min
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proj_y_image_glyph.color_mapper.low = im_min
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proj_x_image_glyph.color_mapper.high = im_max
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proj_y_image_glyph.color_mapper.high = im_max
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frame_range.start = 0
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frame_range.end = n_im
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@ -292,7 +281,7 @@ def create():
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frame_range.bounds = (0, n_im)
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scan_motor = scan["scan_motor"]
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overview_plot_y.axis[1].axis_label = f"Scanning motor, {scan_motor}"
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proj_y_plot.axis[1].axis_label = f"Scanning motor, {scan_motor}"
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var = scan[scan_motor]
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var_start = var[0]
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@ -310,81 +299,52 @@ def create():
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scanning_motor_range = Range1d(0, 1, bounds=(0, 1))
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det_x_range = Range1d(0, IMAGE_W, bounds=(0, IMAGE_W))
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overview_plot_x = Plot(
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title=Title(text="Projections on X-axis"),
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proj_x_plot = figure(
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title="Projections on X-axis",
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x_axis_label="Coordinate X, pix",
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y_axis_label="Frame",
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x_range=det_x_range,
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y_range=frame_range,
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extra_y_ranges={"scanning_motor": scanning_motor_range},
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plot_height=400,
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plot_width=IMAGE_PLOT_W - 3,
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tools="pan,box_zoom,wheel_zoom,reset",
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active_scroll="wheel_zoom",
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)
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# ---- tools
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wheelzoomtool = WheelZoomTool(maintain_focus=False)
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overview_plot_x.toolbar.logo = None
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overview_plot_x.add_tools(PanTool(), BoxZoomTool(), wheelzoomtool, ResetTool())
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overview_plot_x.toolbar.active_scroll = wheelzoomtool
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proj_x_plot.yaxis.major_label_orientation = "vertical"
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proj_x_plot.toolbar.tools[2].maintain_focus = False
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# ---- axes
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overview_plot_x.add_layout(LinearAxis(axis_label="Coordinate X, pix"), place="below")
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overview_plot_x.add_layout(
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LinearAxis(axis_label="Frame", major_label_orientation="vertical"), place="left"
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)
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# ---- grid lines
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overview_plot_x.add_layout(Grid(dimension=0, ticker=BasicTicker()))
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overview_plot_x.add_layout(Grid(dimension=1, ticker=BasicTicker()))
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# ---- rgba image glyph
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overview_plot_x_image_source = ColumnDataSource(
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proj_x_image_source = ColumnDataSource(
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dict(image=[np.zeros((1, 1), dtype="float32")], x=[0], y=[0], dw=[IMAGE_W], dh=[1])
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)
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overview_plot_x_image_glyph = Image(image="image", x="x", y="y", dw="dw", dh="dh")
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overview_plot_x.add_glyph(
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overview_plot_x_image_source, overview_plot_x_image_glyph, name="image_glyph"
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)
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proj_x_image_glyph = proj_x_plot.image(source=proj_x_image_source).glyph
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det_y_range = Range1d(0, IMAGE_H, bounds=(0, IMAGE_H))
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overview_plot_y = Plot(
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title=Title(text="Projections on Y-axis"),
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proj_y_plot = figure(
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title="Projections on Y-axis",
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x_axis_label="Coordinate Y, pix",
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y_axis_label="Scanning motor",
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y_axis_location="right",
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x_range=det_y_range,
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y_range=frame_range,
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extra_y_ranges={"scanning_motor": scanning_motor_range},
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plot_height=400,
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plot_width=IMAGE_PLOT_H + 22,
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tools="pan,box_zoom,wheel_zoom,reset",
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active_scroll="wheel_zoom",
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)
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# ---- tools
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wheelzoomtool = WheelZoomTool(maintain_focus=False)
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overview_plot_y.toolbar.logo = None
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overview_plot_y.add_tools(PanTool(), BoxZoomTool(), wheelzoomtool, ResetTool())
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overview_plot_y.toolbar.active_scroll = wheelzoomtool
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proj_y_plot.yaxis.y_range_name = "scanning_motor"
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proj_y_plot.yaxis.major_label_orientation = "vertical"
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proj_y_plot.toolbar.tools[2].maintain_focus = False
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# ---- axes
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overview_plot_y.add_layout(LinearAxis(axis_label="Coordinate Y, pix"), place="below")
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overview_plot_y.add_layout(
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LinearAxis(
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y_range_name="scanning_motor",
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axis_label="Scanning motor",
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major_label_orientation="vertical",
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),
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place="right",
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)
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# ---- grid lines
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overview_plot_y.add_layout(Grid(dimension=0, ticker=BasicTicker()))
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overview_plot_y.add_layout(Grid(dimension=1, ticker=BasicTicker()))
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# ---- rgba image glyph
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overview_plot_y_image_source = ColumnDataSource(
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proj_y_image_source = ColumnDataSource(
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dict(image=[np.zeros((1, 1), dtype="float32")], x=[0], y=[0], dw=[IMAGE_H], dh=[1])
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)
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overview_plot_y_image_glyph = Image(image="image", x="x", y="y", dw="dw", dh="dh")
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overview_plot_y.add_glyph(
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overview_plot_y_image_source, overview_plot_y_image_glyph, name="image_glyph"
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)
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proj_y_image_glyph = proj_y_plot.image(source=proj_y_image_source).glyph
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cmap_dict = {
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"gray": Greys256,
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@ -394,8 +354,8 @@ def create():
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}
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def colormap_callback(_attr, _old, new):
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overview_plot_x_image_glyph.color_mapper = LinearColorMapper(palette=cmap_dict[new])
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overview_plot_y_image_glyph.color_mapper = LinearColorMapper(palette=cmap_dict[new])
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proj_x_image_glyph.color_mapper = LinearColorMapper(palette=cmap_dict[new])
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proj_y_image_glyph.color_mapper = LinearColorMapper(palette=cmap_dict[new])
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colormap = Select(title="Colormap:", options=list(cmap_dict.keys()), width=210)
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colormap.on_change("value", colormap_callback)
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@ -411,7 +371,7 @@ def create():
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proj_display_min_spinner.disabled = False
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proj_display_max_spinner.disabled = False
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update_overview_plot()
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_update_proj_plots()
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proj_auto_checkbox = CheckboxGroup(
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labels=["Projections Intensity Range"], active=[0], width=145, margin=[10, 5, 0, 5]
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@ -420,8 +380,8 @@ def create():
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def proj_display_max_spinner_callback(_attr, _old_value, new_value):
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proj_display_min_spinner.high = new_value - PROJ_STEP
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overview_plot_x_image_glyph.color_mapper.high = new_value
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overview_plot_y_image_glyph.color_mapper.high = new_value
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proj_x_image_glyph.color_mapper.high = new_value
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proj_y_image_glyph.color_mapper.high = new_value
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proj_display_max_spinner = Spinner(
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low=0 + PROJ_STEP,
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@ -435,8 +395,8 @@ def create():
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def proj_display_min_spinner_callback(_attr, _old_value, new_value):
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proj_display_max_spinner.low = new_value + PROJ_STEP
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overview_plot_x_image_glyph.color_mapper.low = new_value
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overview_plot_y_image_glyph.color_mapper.low = new_value
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proj_x_image_glyph.color_mapper.low = new_value
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proj_y_image_glyph.color_mapper.low = new_value
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proj_display_min_spinner = Spinner(
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low=0,
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@ -471,21 +431,20 @@ def create():
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if "fit" in s and fit_param:
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x.append(p)
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y.append(s["fit"][fit_param])
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param_plot_scatter_source.data.update(x=x, y=y)
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param_scatter_source.data.update(x=x, y=y)
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# Parameter plot
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param_plot = Plot(x_range=DataRange1d(), y_range=DataRange1d(), plot_height=400, plot_width=700)
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param_plot = figure(
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x_axis_label="Parameter",
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y_axis_label="Fit parameter",
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plot_height=400,
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plot_width=700,
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tools="pan,wheel_zoom,reset",
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)
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param_plot.add_layout(LinearAxis(axis_label="Fit parameter"), place="left")
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param_plot.add_layout(LinearAxis(axis_label="Parameter"), place="below")
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param_scatter_source = ColumnDataSource(dict(x=[], y=[]))
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param_plot.circle(source=param_scatter_source)
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param_plot.add_layout(Grid(dimension=0, ticker=BasicTicker()))
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param_plot.add_layout(Grid(dimension=1, ticker=BasicTicker()))
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param_plot_scatter_source = ColumnDataSource(dict(x=[], y=[]))
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param_plot.add_glyph(param_plot_scatter_source, Scatter(x="x", y="y"))
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param_plot.add_tools(PanTool(), WheelZoomTool(), ResetTool())
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param_plot.toolbar.logo = None
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def fit_param_select_callback(_attr, _old, _new):
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@ -553,12 +512,9 @@ def create():
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proc_all_button,
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)
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layout_overview = column(
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layout_proj = column(
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gridplot(
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[[overview_plot_x, overview_plot_y]],
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toolbar_options=dict(logo=None),
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merge_tools=True,
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toolbar_location="left",
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[[proj_x_plot, proj_y_plot]], toolbar_options={"logo": None}, toolbar_location="right"
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),
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layout_controls,
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)
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@ -566,7 +522,7 @@ def create():
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# Plot tabs
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plots = Tabs(
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tabs=[
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Panel(child=layout_overview, title="single scan"),
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Panel(child=layout_proj, title="single scan"),
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Panel(child=column(param_plot, row(fit_param_select)), title="parameter plot"),
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]
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)
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