diff --git a/pyzebra/app/panel_hdf_viewer.py b/pyzebra/app/panel_hdf_viewer.py index 02f3b2d..c43a953 100644 --- a/pyzebra/app/panel_hdf_viewer.py +++ b/pyzebra/app/panel_hdf_viewer.py @@ -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), )