368 lines
9.7 KiB
Python
368 lines
9.7 KiB
Python
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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Button,
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ColumnDataSource,
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DataRange1d,
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Dropdown,
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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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Range1d,
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Rect,
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ResetTool,
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SaveTool,
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Select,
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Spinner,
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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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import pyzebra
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parser = argparse.ArgumentParser(
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prog="pyzebra", formatter_class=argparse.ArgumentDefaultsHelpFormatter
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)
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parser.add_argument(
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"--init-meta",
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metavar="PATH",
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type=str,
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default="",
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help="initial path to .cami file",
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)
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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
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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(image=[current_image])
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index_spinner.value = current_index
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def filelist_callback(_attr, _old, new):
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global curent_h5_data, current_index
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data = pyzebra.read_detector_data(new)
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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 = Dropdown()
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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.menu = file_list
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fileinput = TextInput()
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fileinput.on_change("value", fileinput_callback)
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if args.init_meta:
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fileinput.value = args.init_meta
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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(image=[np.zeros((1, 1), dtype="float32")], x=[0], y=[0], dw=[IMAGE_W], dh=[IMAGE_H],)
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)
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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")], names=["image_glyph"])
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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])
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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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plot.add_tools(
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PanTool(), WheelZoomTool(maintain_focus=False), SaveTool(), ResetTool(), hovertool, boxedittool,
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)
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plot.toolbar.active_scroll = plot.tools[1]
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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=DataRange1d(),
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y_range=DataRange1d(),
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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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overview_plot_x.toolbar.logo = None
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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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overview_plot_y = Plot(
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title=Title(text="Projections on Y-axis"),
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x_range=DataRange1d(),
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y_range=DataRange1d(),
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plot_height=400,
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plot_width=400,
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toolbar_location="left",
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)
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# ---- tools
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overview_plot_y.toolbar.logo = None
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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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layout_image = gridplot([[proj_v, None], [plot, proj_h]], merge_tools=False)
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doc.add_root(
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row(
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column(
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fileinput,
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filelist,
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layout_image,
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row(prev_button, next_button),
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row(index_spinner, animate_toggle),
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row(colormap),
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),
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column(row(overview_plot_x, overview_plot_y), roi_avg_plot),
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)
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)
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