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Simplify plot creation in panel_hdf_viewer

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This commit is contained in:
usov_i 2022-12-15 19:55:04 +01:00
parent 41f5157ba8
commit 7a7baadc8f
1 changed files with 93 additions and 181 deletions
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274
pyzebra/app/panel_hdf_viewer.py
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@ -7,41 +7,30 @@ from bokeh.events import MouseEnter
from bokeh.io import curdoc
from bokeh.layouts import column, gridplot, row
from bokeh.models import (
BasicTicker,
BoxEditTool,
BoxZoomTool,
Button,
CellEditor,
CheckboxGroup,
ColumnDataSource,
DataRange1d,
DataTable,
Div,
FileInput,
Grid,
HoverTool,
Image,
Line,
LinearAxis,
LinearColorMapper,
MultiSelect,
NumberFormatter,
Panel,
PanTool,
Plot,
Range1d,
Rect,
ResetTool,
Select,
Slider,
Spacer,
Spinner,
TableColumn,
Tabs,
Title,
WheelZoomTool,
)
from bokeh.palettes import Cividis256, Greys256, Plasma256 # pylint: disable=E0611
from bokeh.palettes import Cividis256, Greys256, Plasma256
from bokeh.plotting import figure
import pyzebra
@ -246,7 +235,7 @@ def create():
metadata_table_source.data.update(geom=["bisecting"])
_update_image()
_update_overview_plot()
_update_proj_plots()
def scan_table_source_callback(_attr, _old, new):
# unfortunately, we don't know if the change comes from data update or user input
@ -255,7 +244,7 @@ def create():
scan["export"] = export
scan_table_source = ColumnDataSource(
dict(scan=[], fit=[], export=[], twotheta=[], gamma=[], omega=[], chi=[], phi=[], nu=[],)
dict(scan=[], 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)
@ -290,7 +279,7 @@ def create():
if dataset:
pyzebra.normalize_dataset(dataset, new)
_update_image()
_update_overview_plot()
_update_proj_plots()
monitor_spinner = Spinner(title="Monitor:", mode="int", value=100_000, low=1, width=145)
monitor_spinner.on_change("value", monitor_spinner_callback)
@ -308,7 +297,7 @@ def create():
pyzebra.merge_h5_scans(scan_into, scan_from)
_update_table()
_update_image()
_update_overview_plot()
_update_proj_plots()
merge_button = Button(label="Merge into current", width=145)
merge_button.on_click(merge_button_callback)
@ -317,7 +306,7 @@ def create():
pyzebra.restore_scan(_get_selected_scan())
_update_table()
_update_image()
_update_overview_plot()
_update_proj_plots()
restore_button = Button(label="Restore scan", width=145)
restore_button.on_click(restore_button_callback)
@ -335,9 +324,7 @@ def create():
x=np.mean(current_image, axis=1), y=np.arange(0, IMAGE_H) + 0.5
)
image_source.data.update(
h=[np.zeros((1, 1))], k=[np.zeros((1, 1))], l=[np.zeros((1, 1))],
)
image_source.data.update(h=[np.zeros((1, 1))], k=[np.zeros((1, 1))], l=[np.zeros((1, 1))])
image_source.data.update(image=[current_image])
if main_auto_checkbox.active:
@ -389,35 +376,35 @@ def create():
)
detcenter_table_source.data.update(
gamma=[gamma_c], nu=[nu_c], omega=[omega_c], chi=[chi_c], phi=[phi_c],
gamma=[gamma_c], nu=[nu_c], omega=[omega_c], chi=[chi_c], phi=[phi_c]
)
def _update_overview_plot():
def _update_proj_plots():
scan = _get_selected_scan()
counts = scan["counts"]
n_im, n_y, n_x = counts.shape
overview_x = np.mean(counts, axis=1)
overview_y = np.mean(counts, axis=2)
im_proj_x = np.mean(counts, axis=1)
im_proj_y = np.mean(counts, axis=2)
# normalize for simpler colormapping
overview_max_val = max(np.max(overview_x), np.max(overview_y))
overview_x = 1000 * overview_x / overview_max_val
overview_y = 1000 * overview_y / overview_max_val
im_proj_max_val = max(np.max(im_proj_x), np.max(im_proj_y))
im_proj_x = 1000 * im_proj_x / im_proj_max_val
im_proj_y = 1000 * im_proj_y / im_proj_max_val
overview_plot_x_image_source.data.update(image=[overview_x], dw=[n_x], dh=[n_im])
overview_plot_y_image_source.data.update(image=[overview_y], dw=[n_y], dh=[n_im])
proj_x_image_source.data.update(image=[im_proj_x], dw=[n_x], dh=[n_im])
proj_y_image_source.data.update(image=[im_proj_y], dw=[n_y], dh=[n_im])
if proj_auto_checkbox.active:
im_min = min(np.min(overview_x), np.min(overview_y))
im_max = max(np.max(overview_x), np.max(overview_y))
im_min = min(np.min(im_proj_x), np.min(im_proj_y))
im_max = max(np.max(im_proj_x), np.max(im_proj_y))
proj_display_min_spinner.value = im_min
proj_display_max_spinner.value = im_max
overview_plot_x_image_glyph.color_mapper.low = im_min
overview_plot_y_image_glyph.color_mapper.low = im_min
overview_plot_x_image_glyph.color_mapper.high = im_max
overview_plot_y_image_glyph.color_mapper.high = im_max
proj_x_image_glyph.color_mapper.low = im_min
proj_y_image_glyph.color_mapper.low = im_min
proj_x_image_glyph.color_mapper.high = im_max
proj_y_image_glyph.color_mapper.high = im_max
frame_range.start = 0
frame_range.end = n_im
@ -426,7 +413,7 @@ def create():
frame_range.bounds = (0, n_im)
scan_motor = scan["scan_motor"]
overview_plot_y.axis[1].axis_label = f"Scanning motor, {scan_motor}"
proj_y_plot.axis[1].axis_label = f"Scanning motor, {scan_motor}"
var = scan[scan_motor]
var_start = var[0]
@ -472,26 +459,23 @@ def create():
index_slider.js_link("value_throttled", index_spinner, "value")
index_spinner.js_link("value", index_slider, "value")
plot = Plot(
# image viewer figure
plot = figure(
x_range=Range1d(0, IMAGE_W, bounds=(0, IMAGE_W)),
y_range=Range1d(0, IMAGE_H, bounds=(0, IMAGE_H)),
x_axis_location="above",
y_axis_location="right",
plot_height=IMAGE_PLOT_H,
plot_width=IMAGE_PLOT_W,
toolbar_location="left",
tools="pan,box_zoom,wheel_zoom,reset",
active_scroll="wheel_zoom",
)
# ---- tools
plot.yaxis.major_label_orientation = "vertical"
plot.toolbar.tools[2].maintain_focus = False
plot.toolbar.logo = None
# ---- axes
plot.add_layout(LinearAxis(), place="above")
plot.add_layout(LinearAxis(major_label_orientation="vertical"), place="right")
# ---- grid lines
plot.add_layout(Grid(dimension=0, ticker=BasicTicker()))
plot.add_layout(Grid(dimension=1, ticker=BasicTicker()))
# ---- rgba image glyph
image_source = ColumnDataSource(
dict(
image=[np.zeros((IMAGE_H, IMAGE_W), dtype="float32")],
@ -508,22 +492,13 @@ def create():
)
)
h_glyph = Image(image="h", x="x", y="y", dw="dw", dh="dh", global_alpha=0)
k_glyph = Image(image="k", x="x", y="y", dw="dw", dh="dh", global_alpha=0)
l_glyph = Image(image="l", x="x", y="y", dw="dw", dh="dh", global_alpha=0)
gamma_glyph = Image(image="gamma", x="x", y="y", dw="dw", dh="dh", global_alpha=0)
nu_glyph = Image(image="nu", x="x", y="y", dw="dw", dh="dh", global_alpha=0)
omega_glyph = Image(image="omega", x="x", y="y", dw="dw", dh="dh", global_alpha=0)
plot.add_glyph(image_source, h_glyph)
plot.add_glyph(image_source, k_glyph)
plot.add_glyph(image_source, l_glyph)
plot.add_glyph(image_source, gamma_glyph)
plot.add_glyph(image_source, nu_glyph)
plot.add_glyph(image_source, omega_glyph)
image_glyph = Image(image="image", x="x", y="y", dw="dw", dh="dh")
plot.add_glyph(image_source, image_glyph, name="image_glyph")
image_glyph = plot.image(source=image_source).glyph
plot.image(source=image_source, image="h", global_alpha=0)
plot.image(source=image_source, image="k", global_alpha=0)
plot.image(source=image_source, image="l", global_alpha=0)
plot.image(source=image_source, image="gamma", global_alpha=0)
plot.image(source=image_source, image="nu", global_alpha=0)
plot.image(source=image_source, image="omega", global_alpha=0)
# calculate hkl-indices of first mouse entry
def mouse_enter_callback(_event):
@ -535,42 +510,37 @@ def create():
plot.on_event(MouseEnter, mouse_enter_callback)
# ---- projections
proj_v = Plot(
# Single frame projection plots
proj_v = figure(
x_range=plot.x_range,
y_range=DataRange1d(),
y_axis_location="right",
plot_height=150,
plot_width=IMAGE_PLOT_W,
tools="",
toolbar_location=None,
)
proj_v.add_layout(LinearAxis(major_label_orientation="vertical"), place="right")
proj_v.add_layout(LinearAxis(major_label_text_font_size="0pt"), place="below")
proj_v.add_layout(Grid(dimension=0, ticker=BasicTicker()))
proj_v.add_layout(Grid(dimension=1, ticker=BasicTicker()))
proj_v.yaxis.major_label_orientation = "vertical"
proj_v.xaxis.major_label_text_font_size = "0pt"
proj_v_line_source = ColumnDataSource(dict(x=[], y=[]))
proj_v.add_glyph(proj_v_line_source, Line(x="x", y="y", line_color="steelblue"))
proj_v.line(source=proj_v_line_source, line_color="steelblue")
proj_h = Plot(
x_range=DataRange1d(),
proj_h = figure(
x_axis_location="above",
y_range=plot.y_range,
plot_height=IMAGE_PLOT_H,
plot_width=150,
tools="",
toolbar_location=None,
)
proj_h.add_layout(LinearAxis(), place="above")
proj_h.add_layout(LinearAxis(major_label_text_font_size="0pt"), place="left")
proj_h.add_layout(Grid(dimension=0, ticker=BasicTicker()))
proj_h.add_layout(Grid(dimension=1, ticker=BasicTicker()))
proj_h.yaxis.major_label_text_font_size = "0pt"
proj_h_line_source = ColumnDataSource(dict(x=[], y=[]))
proj_h.add_glyph(proj_h_line_source, Line(x="x", y="y", line_color="steelblue"))
proj_h.line(source=proj_h_line_source, line_color="steelblue")
# add tools
# extra tools
hovertool = HoverTool(
tooltips=[
("intensity", "@image"),
@ -584,10 +554,7 @@ def create():
)
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)
box_edit_renderer = plot.rect(source=box_edit_source, fill_alpha=0, line_color="red")
boxedittool = BoxEditTool(renderers=[box_edit_renderer], num_objects=1)
def box_edit_callback(_attr, _old, new):
@ -608,126 +575,74 @@ def create():
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
plot.add_tools(hovertool, boxedittool)
# Overview projection plots
# shared frame ranges
frame_range = Range1d(0, 1, bounds=(0, 1))
scanning_motor_range = Range1d(0, 1, bounds=(0, 1))
det_x_range = Range1d(0, IMAGE_W, bounds=(0, IMAGE_W))
gamma_range = Range1d(0, 1, bounds=(0, 1))
overview_plot_x = Plot(
title=Title(text="Projections on X-axis"),
proj_x_plot = figure(
title="Projections on X-axis",
x_axis_label="Coordinate X, pix",
y_axis_label="Frame",
x_range=det_x_range,
y_range=frame_range,
extra_x_ranges={"gamma": gamma_range},
extra_y_ranges={"scanning_motor": scanning_motor_range},
plot_height=450,
plot_width=IMAGE_PLOT_W - 3,
tools="pan,box_zoom,wheel_zoom,reset",
active_scroll="wheel_zoom",
)
# ---- tools
wheelzoomtool = WheelZoomTool(maintain_focus=False)
overview_plot_x.toolbar.logo = None
overview_plot_x.add_tools(
PanTool(), BoxZoomTool(), wheelzoomtool, ResetTool(),
)
overview_plot_x.toolbar.active_scroll = wheelzoomtool
proj_x_plot.yaxis.major_label_orientation = "vertical"
proj_x_plot.toolbar.tools[2].maintain_focus = False
# ---- axes
overview_plot_x.add_layout(LinearAxis(axis_label="Coordinate X, pix"), place="below")
overview_plot_x.add_layout(
LinearAxis(x_range_name="gamma", axis_label="Gamma, deg"), place="above"
)
overview_plot_x.add_layout(
LinearAxis(axis_label="Frame", major_label_orientation="vertical"), place="left"
)
proj_x_plot.add_layout(LinearAxis(x_range_name="gamma", axis_label="Gamma, deg"), place="above")
# ---- grid lines
overview_plot_x.add_layout(Grid(dimension=0, ticker=BasicTicker()))
overview_plot_x.add_layout(Grid(dimension=1, ticker=BasicTicker()))
# ---- rgba image glyph
overview_plot_x_image_source = ColumnDataSource(
proj_x_image_source = ColumnDataSource(
dict(image=[np.zeros((1, 1), dtype="float32")], x=[0], y=[0], dw=[IMAGE_W], dh=[1])
)
overview_plot_x_image_glyph = Image(image="image", x="x", y="y", dw="dw", dh="dh")
overview_plot_x.add_glyph(
overview_plot_x_image_source, overview_plot_x_image_glyph, name="image_glyph"
)
proj_x_image_glyph = proj_x_plot.image(source=proj_x_image_source).glyph
det_y_range = Range1d(0, IMAGE_H, bounds=(0, IMAGE_H))
nu_range = Range1d(0, 1, bounds=(0, 1))
overview_plot_y = Plot(
title=Title(text="Projections on Y-axis"),
proj_y_plot = figure(
title="Projections on Y-axis",
x_axis_label="Coordinate Y, pix",
y_axis_label="Scanning motor",
y_axis_location="right",
x_range=det_y_range,
y_range=frame_range,
extra_x_ranges={"nu": nu_range},
extra_y_ranges={"scanning_motor": scanning_motor_range},
plot_height=450,
plot_width=IMAGE_PLOT_H + 22,
tools="pan,box_zoom,wheel_zoom,reset",
active_scroll="wheel_zoom",
)
# ---- tools
wheelzoomtool = WheelZoomTool(maintain_focus=False)
overview_plot_y.toolbar.logo = None
overview_plot_y.add_tools(
PanTool(), BoxZoomTool(), wheelzoomtool, ResetTool(),
)
overview_plot_y.toolbar.active_scroll = wheelzoomtool
proj_y_plot.yaxis.y_range_name = "scanning_motor"
proj_y_plot.yaxis.major_label_orientation = "vertical"
proj_y_plot.toolbar.tools[2].maintain_focus = False
# ---- axes
overview_plot_y.add_layout(LinearAxis(axis_label="Coordinate Y, pix"), place="below")
overview_plot_y.add_layout(LinearAxis(x_range_name="nu", axis_label="Nu, deg"), place="above")
overview_plot_y.add_layout(
LinearAxis(
y_range_name="scanning_motor",
axis_label="Scanning motor",
major_label_orientation="vertical",
),
place="right",
)
proj_y_plot.add_layout(LinearAxis(x_range_name="nu", axis_label="Nu, deg"), place="above")
# ---- grid lines
overview_plot_y.add_layout(Grid(dimension=0, ticker=BasicTicker()))
overview_plot_y.add_layout(Grid(dimension=1, ticker=BasicTicker()))
# ---- rgba image glyph
overview_plot_y_image_source = ColumnDataSource(
proj_y_image_source = ColumnDataSource(
dict(image=[np.zeros((1, 1), dtype="float32")], x=[0], y=[0], dw=[IMAGE_H], dh=[1])
)
overview_plot_y_image_glyph = Image(image="image", x="x", y="y", dw="dw", dh="dh")
overview_plot_y.add_glyph(
overview_plot_y_image_source, overview_plot_y_image_glyph, name="image_glyph"
)
proj_y_image_glyph = proj_y_plot.image(source=proj_y_image_source).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 slice plot
roi_avg_plot = figure(plot_height=150, plot_width=IMAGE_PLOT_W, tools="", toolbar_location=None)
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"))
roi_avg_plot.line(source=roi_avg_plot_line_source, line_color="steelblue")
cmap_dict = {
"gray": Greys256,
@ -738,8 +653,8 @@ def create():
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_y_image_glyph.color_mapper = LinearColorMapper(palette=cmap_dict[new])
proj_x_image_glyph.color_mapper = LinearColorMapper(palette=cmap_dict[new])
proj_y_image_glyph.color_mapper = LinearColorMapper(palette=cmap_dict[new])
colormap = Select(title="Colormap:", options=list(cmap_dict.keys()), width=210)
colormap.on_change("value", colormap_callback)
@ -801,7 +716,7 @@ def create():
proj_display_min_spinner.disabled = False
proj_display_max_spinner.disabled = False
_update_overview_plot()
_update_proj_plots()
proj_auto_checkbox = CheckboxGroup(
labels=["Projections Intensity Range"], active=[0], width=145, margin=[10, 5, 0, 5]
@ -810,8 +725,8 @@ def create():
def proj_display_max_spinner_callback(_attr, _old_value, new_value):
proj_display_min_spinner.high = new_value - PROJ_STEP
overview_plot_x_image_glyph.color_mapper.high = new_value
overview_plot_y_image_glyph.color_mapper.high = new_value
proj_x_image_glyph.color_mapper.high = new_value
proj_y_image_glyph.color_mapper.high = new_value
proj_display_max_spinner = Spinner(
low=0 + PROJ_STEP,
@ -825,8 +740,8 @@ def create():
def proj_display_min_spinner_callback(_attr, _old_value, new_value):
proj_display_max_spinner.low = new_value + PROJ_STEP
overview_plot_x_image_glyph.color_mapper.low = new_value
overview_plot_y_image_glyph.color_mapper.low = new_value
proj_x_image_glyph.color_mapper.low = new_value
proj_y_image_glyph.color_mapper.low = new_value
proj_display_min_spinner = Spinner(
low=0,
@ -1021,13 +936,10 @@ def create():
row(column(add_event_button, remove_event_button), peak_tables),
)
layout_overview = column(
layout_proj = column(
gridplot(
[[overview_plot_x, overview_plot_y]],
toolbar_options=dict(logo=None),
merge_tools=True,
toolbar_location="left",
),
[[proj_x_plot, proj_y_plot]], toolbar_options={"logo": None}, toolbar_location="right"
)
)
scan_layout = column(
@ -1038,7 +950,7 @@ def create():
tab_layout = row(
column(import_layout, colormap_layout),
column(row(scan_layout, layout_overview), layout_controls),
column(row(scan_layout, layout_proj), layout_controls),
column(roi_avg_plot, layout_image),
)