Move data viewer into a separate panel
This commit is contained in:
@ -1,38 +1,9 @@
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import argparse
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import numpy as np
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from bokeh.io import curdoc
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from bokeh.layouts import column, gridplot, row
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from bokeh.models import (
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BasicTicker,
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BoxEditTool,
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BoxZoomTool,
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Button,
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ColumnDataSource,
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DataRange1d,
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Grid,
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HoverTool,
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Image,
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Line,
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LinearAxis,
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LinearColorMapper,
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PanTool,
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Plot,
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RadioButtonGroup,
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Range1d,
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Rect,
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ResetTool,
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Select,
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Spinner,
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TextAreaInput,
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TextInput,
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Title,
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Toggle,
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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.models import Tabs
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import pyzebra
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import panel_data_viewer
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parser = argparse.ArgumentParser(
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prog="pyzebra", formatter_class=argparse.ArgumentDefaultsHelpFormatter
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@ -44,487 +15,10 @@ parser.add_argument(
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args = parser.parse_args()
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IMAGE_W = 256
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IMAGE_H = 128
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doc = curdoc()
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doc.title = "pyzebra"
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global curent_h5_data, current_index, det_data
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roi_selection = {}
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def update_image():
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current_image = curent_h5_data[current_index]
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proj_v_line_source.data.update(x=np.arange(0, IMAGE_W) + 0.5, y=np.mean(current_image, axis=0))
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proj_h_line_source.data.update(x=np.mean(current_image, axis=1), y=np.arange(0, IMAGE_H) + 0.5)
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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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index_spinner.value = current_index
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if auto_toggle.active:
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im_max = int(np.max(current_image))
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im_min = int(np.min(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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def calculate_hkl(setup_type="nb_bi"):
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h = np.empty(shape=(IMAGE_H, IMAGE_W))
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k = np.empty(shape=(IMAGE_H, IMAGE_W))
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l = np.empty(shape=(IMAGE_H, IMAGE_W))
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wave = det_data["wave"]
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ddist = det_data["ddist"]
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gammad = det_data["pol_angle"][current_index]
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om = det_data["rot_angle"][current_index]
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nud = det_data["tlt_angle"]
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ub = det_data["UB"]
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if setup_type == "nb_bi":
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ch = det_data["chi_angle"][current_index]
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ph = det_data["phi_angle"][current_index]
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elif setup_type == "nb":
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ch = 0
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ph = 0
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else:
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raise ValueError(f"Unknown setup type '{setup_type}'")
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for xi in np.arange(IMAGE_W):
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for yi in np.arange(IMAGE_H):
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h[yi, xi], k[yi, xi], l[yi, xi] = pyzebra.ang2hkl(
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wave, ddist, gammad, om, ch, ph, nud, ub, xi, yi
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)
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return h, k, l
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def filelist_callback(_attr, _old, new):
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global curent_h5_data, current_index, det_data
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det_data = pyzebra.read_detector_data(new)
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data = det_data["data"]
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curent_h5_data = data
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current_index = 0
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update_image()
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# update overview plots
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overview_x = np.mean(data, axis=1)
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overview_y = np.mean(data, axis=2)
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overview_plot_x_image_source.data.update(
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image=[overview_x], dh=[overview_x.shape[0]], dw=[overview_x.shape[1]]
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)
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overview_plot_y_image_source.data.update(
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image=[overview_y], dh=[overview_y.shape[0]], dw=[overview_y.shape[1]]
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)
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filelist = Select()
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filelist.on_change("value", filelist_callback)
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def fileinput_callback(_attr, _old, new):
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h5meta_list = pyzebra.read_h5meta(new)
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file_list = h5meta_list["filelist"]
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filelist.options = file_list
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filelist.value = file_list[0]
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fileinput = TextInput()
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fileinput.on_change("value", fileinput_callback)
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def index_spinner_callback(_attr, _old, new):
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global current_index
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if 0 <= new < curent_h5_data.shape[0]:
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current_index = new
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update_image()
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index_spinner = Spinner(value=0)
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index_spinner.on_change("value", index_spinner_callback)
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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_H * 3,
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plot_width=IMAGE_W * 3,
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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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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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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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image_glyph = Image(image="image", x="x", y="y", dw="dw", dh="dh")
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image_renderer = plot.add_glyph(image_source, image_glyph, name="image_glyph")
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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=200,
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plot_width=IMAGE_W * 3,
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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_H * 3,
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plot_width=200,
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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()))
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proj_h_line_source = ColumnDataSource(dict(x=[], y=[]))
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proj_h.add_glyph(proj_h_line_source, Line(x="x", y="y", line_color="steelblue"))
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# add tools
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hovertool = HoverTool(tooltips=[("intensity", "@image"), ("h", "@h"), ("k", "@k"), ("l", "@l")])
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box_edit_source = ColumnDataSource(dict(x=[], y=[], width=[], height=[]))
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box_edit_glyph = Rect(x="x", y="y", width="width", height="height", fill_alpha=0, line_color="red")
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box_edit_renderer = plot.add_glyph(box_edit_source, box_edit_glyph)
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boxedittool = BoxEditTool(renderers=[box_edit_renderer], num_objects=1)
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def box_edit_callback(_attr, _old, new):
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if new["x"]:
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x_val = np.arange(curent_h5_data.shape[0])
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left = int(np.floor(new["x"][0]))
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right = int(np.ceil(new["x"][0] + new["width"][0]))
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bottom = int(np.floor(new["y"][0]))
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top = int(np.ceil(new["y"][0] + new["height"][0]))
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y_val = np.sum(curent_h5_data[:, bottom:top, left:right], axis=(1, 2))
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else:
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x_val = []
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y_val = []
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roi_avg_plot_line_source.data.update(x=x_val, y=y_val)
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box_edit_source.on_change("data", box_edit_callback)
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wheelzoomtool = WheelZoomTool(maintain_focus=False)
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plot.add_tools(
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PanTool(), BoxZoomTool(), wheelzoomtool, ResetTool(), hovertool, boxedittool,
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)
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plot.toolbar.active_scroll = wheelzoomtool
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# shared frame range
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frame_range = DataRange1d()
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det_x_range = DataRange1d()
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overview_plot_x = Plot(
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title=Title(text="Projections on X-axis"),
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x_range=det_x_range,
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y_range=frame_range,
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plot_height=400,
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plot_width=400,
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toolbar_location="left",
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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(
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PanTool(), BoxZoomTool(), wheelzoomtool, ResetTool(),
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)
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overview_plot_x.toolbar.active_scroll = wheelzoomtool
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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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dict(image=[np.zeros((1, 1), dtype="float32")], x=[0], y=[0], dw=[1], 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_image_renderer = 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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det_y_range = DataRange1d()
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overview_plot_y = Plot(
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title=Title(text="Projections on Y-axis"),
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x_range=det_y_range,
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y_range=frame_range,
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plot_height=400,
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plot_width=400,
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toolbar_location="left",
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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(
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PanTool(), BoxZoomTool(), wheelzoomtool, ResetTool(),
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)
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overview_plot_y.toolbar.active_scroll = wheelzoomtool
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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(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_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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dict(image=[np.zeros((1, 1), dtype="float32")], x=[0], y=[0], dw=[1], 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_image_renderer = 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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roi_avg_plot = Plot(
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x_range=DataRange1d(),
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y_range=DataRange1d(),
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plot_height=IMAGE_H * 3,
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plot_width=IMAGE_W * 3,
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toolbar_location="left",
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)
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# ---- tools
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roi_avg_plot.toolbar.logo = None
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# ---- axes
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roi_avg_plot.add_layout(LinearAxis(), place="below")
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roi_avg_plot.add_layout(LinearAxis(major_label_orientation="vertical"), place="left")
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# ---- grid lines
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roi_avg_plot.add_layout(Grid(dimension=0, ticker=BasicTicker()))
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roi_avg_plot.add_layout(Grid(dimension=1, ticker=BasicTicker()))
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roi_avg_plot_line_source = ColumnDataSource(dict(x=[], y=[]))
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roi_avg_plot.add_glyph(roi_avg_plot_line_source, Line(x="x", y="y", line_color="steelblue"))
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def prev_button_callback():
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global current_index
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if current_index > 0:
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current_index -= 1
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update_image()
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prev_button = Button(label="Previous")
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prev_button.on_click(prev_button_callback)
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def next_button_callback():
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global current_index
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if current_index < curent_h5_data.shape[0] - 1:
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current_index += 1
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update_image()
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next_button = Button(label="Next")
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next_button.on_click(next_button_callback)
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def animate():
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next_button_callback()
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def animate_toggle_callback(active):
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global cb
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if active:
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cb = doc.add_periodic_callback(animate, 300)
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else:
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doc.remove_periodic_callback(cb)
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animate_toggle = Toggle(label="Animate")
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animate_toggle.on_click(animate_toggle_callback)
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cmap_dict = {
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"gray": Greys256,
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"gray_reversed": Greys256[::-1],
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"plasma": Plasma256,
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"cividis": Cividis256,
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}
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def colormap_callback(_attr, _old, new):
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image_glyph.color_mapper = LinearColorMapper(palette=cmap_dict[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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colormap = Select(title="Colormap:", options=list(cmap_dict.keys()))
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colormap.on_change("value", colormap_callback)
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colormap.value = "plasma"
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radio_button_group = RadioButtonGroup(labels=["nb", "nb_bi"], active=0)
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STEP = 1
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# ---- colormap auto toggle button
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def auto_toggle_callback(state):
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if state:
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display_min_spinner.disabled = True
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display_max_spinner.disabled = True
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else:
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display_min_spinner.disabled = False
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display_max_spinner.disabled = False
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update_image()
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auto_toggle = Toggle(label="Auto Range", active=True, button_type="default")
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auto_toggle.on_click(auto_toggle_callback)
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# ---- colormap display max value
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def display_max_spinner_callback(_attr, _old_value, new_value):
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display_min_spinner.high = new_value - STEP
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image_glyph.color_mapper.high = new_value
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display_max_spinner = Spinner(
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title="Maximal Display Value:", low=0 + STEP, value=1, step=STEP, disabled=auto_toggle.active,
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)
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display_max_spinner.on_change("value", display_max_spinner_callback)
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# ---- colormap display min value
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def display_min_spinner_callback(_attr, _old_value, new_value):
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display_max_spinner.low = new_value + STEP
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image_glyph.color_mapper.low = new_value
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display_min_spinner = Spinner(
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title="Minimal Display Value:", high=1 - STEP, value=0, step=STEP, disabled=auto_toggle.active,
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)
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||||
display_min_spinner.on_change("value", display_min_spinner_callback)
|
||||
|
||||
|
||||
def hkl_button_callback():
|
||||
setup_type = "nb_bi" if radio_button_group.active else "nb"
|
||||
h, k, l = calculate_hkl(setup_type)
|
||||
image_source.data.update(h=[h], k=[k], l=[l])
|
||||
|
||||
|
||||
hkl_button = Button(label="Calculate hkl (slow)")
|
||||
hkl_button.on_click(hkl_button_callback)
|
||||
|
||||
|
||||
selection_list = TextAreaInput(rows=7)
|
||||
|
||||
|
||||
def selection_button_callback():
|
||||
global roi_selection
|
||||
selection = [
|
||||
int(np.floor(det_x_range.start)),
|
||||
int(np.ceil(det_x_range.end)),
|
||||
int(np.floor(det_y_range.start)),
|
||||
int(np.ceil(det_y_range.end)),
|
||||
int(np.floor(frame_range.start)),
|
||||
int(np.ceil(frame_range.end)),
|
||||
]
|
||||
|
||||
filename_id = filelist.value[-8:-4]
|
||||
if filename_id in roi_selection:
|
||||
roi_selection[f"{filename_id}"].append(selection)
|
||||
else:
|
||||
roi_selection[f"{filename_id}"] = [selection]
|
||||
|
||||
selection_list.value = str(roi_selection)
|
||||
|
||||
|
||||
selection_button = Button(label="Add selection")
|
||||
selection_button.on_click(selection_button_callback)
|
||||
|
||||
|
||||
# Final layout
|
||||
layout_image = gridplot([[proj_v, None], [plot, proj_h]], merge_tools=False)
|
||||
tab_main = panel_data_viewer.create(args.init_meta)
|
||||
|
||||
animate_layout = column(index_spinner, next_button, prev_button, animate_toggle)
|
||||
colormap_layout = column(colormap, auto_toggle, display_max_spinner, display_min_spinner)
|
||||
hkl_layout = column(radio_button_group, hkl_button)
|
||||
|
||||
layout_overview = gridplot(
|
||||
[[overview_plot_x, overview_plot_y]],
|
||||
toolbar_options=dict(logo=None),
|
||||
merge_tools=True,
|
||||
)
|
||||
|
||||
doc.add_root(
|
||||
row(
|
||||
column(fileinput, filelist, layout_image, row(colormap_layout, animate_layout, hkl_layout)),
|
||||
column(roi_avg_plot, layout_overview, row(selection_button, selection_list),),
|
||||
)
|
||||
)
|
||||
|
||||
# initiate fileinput
|
||||
if args.init_meta:
|
||||
fileinput.value = args.init_meta
|
||||
doc.add_root(Tabs(tabs=[tab_main]))
|
||||
|
||||
499
pyzebra/app/panel_data_viewer.py
Normal file
499
pyzebra/app/panel_data_viewer.py
Normal file
@ -0,0 +1,499 @@
|
||||
import numpy as np
|
||||
from bokeh.io import curdoc
|
||||
from bokeh.layouts import column, gridplot, row
|
||||
from bokeh.models import (
|
||||
BasicTicker,
|
||||
BoxEditTool,
|
||||
BoxZoomTool,
|
||||
Button,
|
||||
ColumnDataSource,
|
||||
DataRange1d,
|
||||
Grid,
|
||||
HoverTool,
|
||||
Image,
|
||||
Line,
|
||||
LinearAxis,
|
||||
LinearColorMapper,
|
||||
Panel,
|
||||
PanTool,
|
||||
Plot,
|
||||
RadioButtonGroup,
|
||||
Range1d,
|
||||
Rect,
|
||||
ResetTool,
|
||||
Select,
|
||||
Spinner,
|
||||
TextAreaInput,
|
||||
TextInput,
|
||||
Title,
|
||||
Toggle,
|
||||
WheelZoomTool,
|
||||
)
|
||||
from bokeh.palettes import Cividis256, Greys256, Plasma256 # pylint: disable=E0611
|
||||
|
||||
import pyzebra
|
||||
|
||||
IMAGE_W = 256
|
||||
IMAGE_H = 128
|
||||
|
||||
|
||||
def create(init_meta):
|
||||
doc = curdoc()
|
||||
|
||||
curent_h5_data = None
|
||||
current_index = None
|
||||
det_data = None
|
||||
roi_selection = {}
|
||||
|
||||
def update_image():
|
||||
current_image = curent_h5_data[current_index]
|
||||
proj_v_line_source.data.update(
|
||||
x=np.arange(0, IMAGE_W) + 0.5, y=np.mean(current_image, axis=0)
|
||||
)
|
||||
proj_h_line_source.data.update(
|
||||
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(image=[current_image])
|
||||
index_spinner.value = current_index
|
||||
|
||||
if auto_toggle.active:
|
||||
im_max = int(np.max(current_image))
|
||||
im_min = int(np.min(current_image))
|
||||
|
||||
display_min_spinner.value = im_min
|
||||
display_max_spinner.value = im_max
|
||||
|
||||
image_glyph.color_mapper.low = im_min
|
||||
image_glyph.color_mapper.high = im_max
|
||||
|
||||
def calculate_hkl(setup_type="nb_bi"):
|
||||
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["pol_angle"][current_index]
|
||||
om = det_data["rot_angle"][current_index]
|
||||
nud = det_data["tlt_angle"]
|
||||
ub = det_data["UB"]
|
||||
|
||||
if setup_type == "nb_bi":
|
||||
ch = det_data["chi_angle"][current_index]
|
||||
ph = det_data["phi_angle"][current_index]
|
||||
elif setup_type == "nb":
|
||||
ch = 0
|
||||
ph = 0
|
||||
else:
|
||||
raise ValueError(f"Unknown setup type '{setup_type}'")
|
||||
|
||||
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, ch, ph, nud, ub, xi, yi
|
||||
)
|
||||
|
||||
return h, k, l
|
||||
|
||||
def filelist_callback(_attr, _old, new):
|
||||
nonlocal curent_h5_data, current_index, det_data
|
||||
det_data = pyzebra.read_detector_data(new)
|
||||
data = det_data["data"]
|
||||
curent_h5_data = data
|
||||
current_index = 0
|
||||
update_image()
|
||||
|
||||
# update overview plots
|
||||
overview_x = np.mean(data, axis=1)
|
||||
overview_y = np.mean(data, axis=2)
|
||||
|
||||
overview_plot_x_image_source.data.update(
|
||||
image=[overview_x], dh=[overview_x.shape[0]], dw=[overview_x.shape[1]]
|
||||
)
|
||||
overview_plot_y_image_source.data.update(
|
||||
image=[overview_y], dh=[overview_y.shape[0]], dw=[overview_y.shape[1]]
|
||||
)
|
||||
|
||||
filelist = Select()
|
||||
filelist.on_change("value", filelist_callback)
|
||||
|
||||
def fileinput_callback(_attr, _old, new):
|
||||
h5meta_list = pyzebra.read_h5meta(new)
|
||||
file_list = h5meta_list["filelist"]
|
||||
filelist.options = file_list
|
||||
filelist.value = file_list[0]
|
||||
|
||||
fileinput = TextInput()
|
||||
fileinput.on_change("value", fileinput_callback)
|
||||
|
||||
def index_spinner_callback(_attr, _old, new):
|
||||
nonlocal current_index
|
||||
if 0 <= new < curent_h5_data.shape[0]:
|
||||
current_index = new
|
||||
update_image()
|
||||
|
||||
index_spinner = Spinner(value=0)
|
||||
index_spinner.on_change("value", index_spinner_callback)
|
||||
|
||||
plot = Plot(
|
||||
x_range=Range1d(0, IMAGE_W, bounds=(0, IMAGE_W)),
|
||||
y_range=Range1d(0, IMAGE_H, bounds=(0, IMAGE_H)),
|
||||
plot_height=IMAGE_H * 3,
|
||||
plot_width=IMAGE_W * 3,
|
||||
toolbar_location="left",
|
||||
)
|
||||
|
||||
# ---- tools
|
||||
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")],
|
||||
h=[np.zeros((1, 1))],
|
||||
k=[np.zeros((1, 1))],
|
||||
l=[np.zeros((1, 1))],
|
||||
x=[0],
|
||||
y=[0],
|
||||
dw=[IMAGE_W],
|
||||
dh=[IMAGE_H],
|
||||
)
|
||||
)
|
||||
|
||||
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)
|
||||
|
||||
plot.add_glyph(image_source, h_glyph)
|
||||
plot.add_glyph(image_source, k_glyph)
|
||||
plot.add_glyph(image_source, l_glyph)
|
||||
|
||||
image_glyph = Image(image="image", x="x", y="y", dw="dw", dh="dh")
|
||||
image_renderer = plot.add_glyph(image_source, image_glyph, name="image_glyph")
|
||||
|
||||
# ---- projections
|
||||
proj_v = Plot(
|
||||
x_range=plot.x_range,
|
||||
y_range=DataRange1d(),
|
||||
plot_height=200,
|
||||
plot_width=IMAGE_W * 3,
|
||||
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_line_source = ColumnDataSource(dict(x=[], y=[]))
|
||||
proj_v.add_glyph(proj_v_line_source, Line(x="x", y="y", line_color="steelblue"))
|
||||
|
||||
proj_h = Plot(
|
||||
x_range=DataRange1d(),
|
||||
y_range=plot.y_range,
|
||||
plot_height=IMAGE_H * 3,
|
||||
plot_width=200,
|
||||
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_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"), ("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"]:
|
||||
x_val = np.arange(curent_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(curent_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 range
|
||||
frame_range = DataRange1d()
|
||||
det_x_range = DataRange1d()
|
||||
overview_plot_x = Plot(
|
||||
title=Title(text="Projections on X-axis"),
|
||||
x_range=det_x_range,
|
||||
y_range=frame_range,
|
||||
plot_height=400,
|
||||
plot_width=400,
|
||||
toolbar_location="left",
|
||||
)
|
||||
|
||||
# ---- 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
|
||||
|
||||
# ---- axes
|
||||
overview_plot_x.add_layout(LinearAxis(axis_label="Coordinate X, pix"), place="below")
|
||||
overview_plot_x.add_layout(
|
||||
LinearAxis(axis_label="Frame", major_label_orientation="vertical"), place="left"
|
||||
)
|
||||
|
||||
# ---- 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(
|
||||
dict(image=[np.zeros((1, 1), dtype="float32")], x=[0], y=[0], dw=[1], dh=[1])
|
||||
)
|
||||
|
||||
overview_plot_x_image_glyph = Image(image="image", x="x", y="y", dw="dw", dh="dh")
|
||||
overview_plot_x_image_renderer = overview_plot_x.add_glyph(
|
||||
overview_plot_x_image_source, overview_plot_x_image_glyph, name="image_glyph"
|
||||
)
|
||||
|
||||
det_y_range = DataRange1d()
|
||||
overview_plot_y = Plot(
|
||||
title=Title(text="Projections on Y-axis"),
|
||||
x_range=det_y_range,
|
||||
y_range=frame_range,
|
||||
plot_height=400,
|
||||
plot_width=400,
|
||||
toolbar_location="left",
|
||||
)
|
||||
|
||||
# ---- 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
|
||||
|
||||
# ---- axes
|
||||
overview_plot_y.add_layout(LinearAxis(axis_label="Coordinate Y, pix"), place="below")
|
||||
overview_plot_y.add_layout(
|
||||
LinearAxis(axis_label="Frame", major_label_orientation="vertical"), place="left"
|
||||
)
|
||||
|
||||
# ---- 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(
|
||||
dict(image=[np.zeros((1, 1), dtype="float32")], x=[0], y=[0], dw=[1], dh=[1])
|
||||
)
|
||||
|
||||
overview_plot_y_image_glyph = Image(image="image", x="x", y="y", dw="dw", dh="dh")
|
||||
overview_plot_y_image_renderer = overview_plot_y.add_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=IMAGE_H * 3,
|
||||
plot_width=IMAGE_W * 3,
|
||||
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"))
|
||||
|
||||
def prev_button_callback():
|
||||
nonlocal current_index
|
||||
if current_index > 0:
|
||||
current_index -= 1
|
||||
update_image()
|
||||
|
||||
prev_button = Button(label="Previous")
|
||||
prev_button.on_click(prev_button_callback)
|
||||
|
||||
def next_button_callback():
|
||||
nonlocal current_index
|
||||
if current_index < curent_h5_data.shape[0] - 1:
|
||||
current_index += 1
|
||||
update_image()
|
||||
|
||||
next_button = Button(label="Next")
|
||||
next_button.on_click(next_button_callback)
|
||||
|
||||
def animate():
|
||||
next_button_callback()
|
||||
|
||||
cb = None
|
||||
def animate_toggle_callback(active):
|
||||
nonlocal cb
|
||||
if active:
|
||||
cb = doc.add_periodic_callback(animate, 300)
|
||||
else:
|
||||
doc.remove_periodic_callback(cb)
|
||||
|
||||
animate_toggle = Toggle(label="Animate")
|
||||
animate_toggle.on_click(animate_toggle_callback)
|
||||
|
||||
cmap_dict = {
|
||||
"gray": Greys256,
|
||||
"gray_reversed": Greys256[::-1],
|
||||
"plasma": Plasma256,
|
||||
"cividis": Cividis256,
|
||||
}
|
||||
|
||||
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])
|
||||
|
||||
colormap = Select(title="Colormap:", options=list(cmap_dict.keys()))
|
||||
colormap.on_change("value", colormap_callback)
|
||||
colormap.value = "plasma"
|
||||
|
||||
radio_button_group = RadioButtonGroup(labels=["nb", "nb_bi"], active=0)
|
||||
|
||||
STEP = 1
|
||||
|
||||
# ---- colormap auto toggle button
|
||||
def auto_toggle_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()
|
||||
|
||||
auto_toggle = Toggle(label="Auto Range", active=True, button_type="default")
|
||||
auto_toggle.on_click(auto_toggle_callback)
|
||||
|
||||
# ---- colormap display max value
|
||||
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(
|
||||
title="Maximal Display Value:",
|
||||
low=0 + STEP,
|
||||
value=1,
|
||||
step=STEP,
|
||||
disabled=auto_toggle.active,
|
||||
)
|
||||
display_max_spinner.on_change("value", display_max_spinner_callback)
|
||||
|
||||
# ---- colormap display min value
|
||||
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(
|
||||
title="Minimal Display Value:",
|
||||
high=1 - STEP,
|
||||
value=0,
|
||||
step=STEP,
|
||||
disabled=auto_toggle.active,
|
||||
)
|
||||
display_min_spinner.on_change("value", display_min_spinner_callback)
|
||||
|
||||
def hkl_button_callback():
|
||||
setup_type = "nb_bi" if radio_button_group.active else "nb"
|
||||
h, k, l = calculate_hkl(setup_type)
|
||||
image_source.data.update(h=[h], k=[k], l=[l])
|
||||
|
||||
hkl_button = Button(label="Calculate hkl (slow)")
|
||||
hkl_button.on_click(hkl_button_callback)
|
||||
|
||||
selection_list = TextAreaInput(rows=7)
|
||||
|
||||
def selection_button_callback():
|
||||
nonlocal roi_selection
|
||||
selection = [
|
||||
int(np.floor(det_x_range.start)),
|
||||
int(np.ceil(det_x_range.end)),
|
||||
int(np.floor(det_y_range.start)),
|
||||
int(np.ceil(det_y_range.end)),
|
||||
int(np.floor(frame_range.start)),
|
||||
int(np.ceil(frame_range.end)),
|
||||
]
|
||||
|
||||
filename_id = filelist.value[-8:-4]
|
||||
if filename_id in roi_selection:
|
||||
roi_selection[f"{filename_id}"].append(selection)
|
||||
else:
|
||||
roi_selection[f"{filename_id}"] = [selection]
|
||||
|
||||
selection_list.value = str(roi_selection)
|
||||
|
||||
selection_button = Button(label="Add selection")
|
||||
selection_button.on_click(selection_button_callback)
|
||||
|
||||
# Final layout
|
||||
layout_image = gridplot([[proj_v, None], [plot, proj_h]], merge_tools=False)
|
||||
|
||||
animate_layout = column(index_spinner, next_button, prev_button, animate_toggle)
|
||||
colormap_layout = column(colormap, auto_toggle, display_max_spinner, display_min_spinner)
|
||||
hkl_layout = column(radio_button_group, hkl_button)
|
||||
|
||||
layout_overview = gridplot(
|
||||
[[overview_plot_x, overview_plot_y]], toolbar_options=dict(logo=None), merge_tools=True,
|
||||
)
|
||||
|
||||
tab_layout = row(
|
||||
column(fileinput, filelist, layout_image, row(colormap_layout, animate_layout, hkl_layout)),
|
||||
column(roi_avg_plot, layout_overview, row(selection_button, selection_list),),
|
||||
)
|
||||
|
||||
# initiate fileinput
|
||||
if init_meta:
|
||||
fileinput.value = init_meta
|
||||
|
||||
return Panel(child=tab_layout, title="Data Viewer")
|
||||
Reference in New Issue
Block a user