prototype edit and check panel

peakipy/cli/check_panel.py

@@ -75,8 +75,11 @@ def create_plotly_pane(cluster, plane):
 
 
 @app.command()
-def check_panel(
-    fits_path: Path, data_path: Path, config_path: Path = Path("./peakipy.config")
+def create_check_panel(
+    fits_path: Path,
+    data_path: Path,
+    config_path: Path = Path("./peakipy.config"),
+    edit_panel: bool = False,
 ):
     data = data_singleton()
     data.fits_path = fits_path
@@ -106,7 +109,10 @@ def check_panel(
         pn.Row(interactive_plotly_pane, interactive_cluster_pane),
         title="Peakipy check",
     )
-    check_pane.show()
+    if edit_panel:
+        return check_pane
+    else:
+        check_pane.show()
 
 
 if __name__ == "__main__":

peakipy/cli/edit.py

@@ -14,6 +14,9 @@
 from skimage.filters import threshold_otsu
 from rich import print
 
+
+import panel as pn
+
 from bokeh.io import curdoc
 from bokeh.events import ButtonClick, DoubleTap
 from bokeh.layouts import row, column, grid
@@ -39,6 +42,7 @@
 from bokeh.palettes import PuBuGn9, Category20, Viridis256, RdGy11, Reds256, YlOrRd9
 
 from peakipy.core import LoadData, read_config, StrucEl
+from check_panel import create_check_panel
 
 log_style = "overflow:scroll;"
 log_div = """<div style=%s>%s</div>"""
@@ -69,6 +73,7 @@ def __init__(self, peaklist_path: Path, data_path: Path):
         self.setup_initial_fit_threshold()
         self.setup_quit_button()
         self.setup_plot()
+        self.check_pane = ""
 
     def init(self, doc):
         """initialise the bokeh app"""
@@ -714,13 +719,19 @@ def fit_selected(self, event):
         if self.checkbox_group.active == []:
             fit_command = f"peakipy fit {self.TEMP_INPUT_CSV} {self.data_path} {self.TEMP_OUT_CSV} --lineshape {lineshape}{fix_command}{reference_planes_command}{initial_fit_threshold_command}{xy_bounds_command}"
             # plot_command = f"peakipy check {self.TEMP_OUT_CSV} {self.data_path} --label --individual --show --outname {self.TEMP_OUT_PLOT / Path('tmp.pdf')}"
-            plot_command = f"peakipy-check {self.TEMP_OUT_CSV} {self.data_path}"
+            self.check_pane = create_check_panel(
+                self.TEMP_OUT_CSV, self.data_path, edit_panel=True
+            )
+            # plot_command = f"peakipy-check {self.TEMP_OUT_CSV} {self.data_path}"
         else:
             plane_index = self.select_plane.value
             print(f"[yellow]Only fitting plane {plane_index}[/yellow]")
             fit_command = f"peakipy fit {self.TEMP_INPUT_CSV} {self.data_path} {self.TEMP_OUT_CSV} --lineshape {lineshape} --plane {plane_index}{fix_command}{reference_planes_command}{initial_fit_threshold_command}{xy_bounds_command}"
+            self.check_pane = create_check_panel(
+                self.TEMP_OUT_CSV, self.data_path, edit_panel=True
+            )
             # plot_command = f"peakipy check {self.TEMP_OUT_CSV} {self.data_path} --label --individual --outname {self.TEMP_OUT_PLOT / Path('tmp.pdf')} --plane {plane_index} --show"
-            plot_command = f"peakipy-check {self.TEMP_OUT_CSV} {self.data_path}"
+            # plot_command = f"peakipy-check {self.TEMP_OUT_CSV} {self.data_path}"
 
         print(f"[blue]{fit_command}[/blue]")
         self.fit_reports += fit_command + "<br>"
@@ -730,7 +741,7 @@ def fit_selected(self, event):
         self.fit_reports = self.fit_reports.replace("\n", "<br>")
         self.fit_reports_div.text = log_div % (log_style, self.fit_reports)
         # plot data
-        os.system(plot_command)
+        # os.system(plot_command)
 
     def save_peaks(self, event):
         if self.savefilename.value:

peakipy/cli/edit_panel.py

@@ -0,0 +1,38 @@
+from pathlib import Path
+import panel as pn
+
+from edit import BokehScript
+from check_panel import create_check_panel
+
+pn.extension("plotly")
+pn.config.theme = "dark"
+
+bs = BokehScript(
+    peaklist_path=Path("./edited_peaks.csv"), data_path=Path("./test1.ft2")
+)
+bokeh_pane = pn.pane.Bokeh(bs.p)
+table_pane = pn.pane.Bokeh(bs.data_table)
+spectrum_view_settings = pn.WidgetBox(
+    "# View settings", bs.pos_neg_contour_radiobutton, bs.contour_start
+)
+button = pn.widgets.Button(name="Click me", button_type="primary")
+fit_controls = pn.WidgetBox(
+    "# Fit controls", bs.select_lineshape_radiobuttons, bs.fit_button, button
+)
+
+
+def b(event):
+    check_app.loading = True
+    check_panel = create_check_panel(bs.TEMP_OUT_CSV, bs.data_path, edit_panel=True)
+    check_app.objects = check_panel.objects
+    check_app.loading = False
+
+
+button.on_click(b)
+fit_app = pn.Card(
+    pn.Column(bokeh_pane, fit_controls, spectrum_view_settings, table_pane),
+    title="Peakipy fit",
+)
+check_app = pn.Card(title="Peakipy check")
+app = pn.Column(fit_app, check_app)
+server = app.show(threaded=True)

peakipy/cli/main.py

@@ -85,7 +85,6 @@
     FitPeaksInput,
     FitPeaksArgs,
 )
-from .edit import BokehScript
 from .spec import yaml_file
 
 app = typer.Typer()
@@ -1475,15 +1474,15 @@ def check(
 
                 if ccpn_flag:
                     plt = PlotterWidget()
-                else:
-                    plt = matplotlib.pyplot
-                create_matplotlib_figure(
-                    plot_data, pdf, individual, label, ccpn_flag, show
-                )
                 # fig = create_plotly_figure(plot_data)
                 if plotly:
                     fig = create_plotly_figure(plot_data)
                     return fig
+                else:
+                    plt = matplotlib.pyplot
+                    create_matplotlib_figure(
+                        plot_data, pdf, individual, label, ccpn_flag, show
+                    )
                 # surf = pn.pane.plotly.Plotly(fig)
                 # app = pn.Column(surf)
                 # app.show(threaded=True)
@@ -1501,6 +1500,7 @@ def edit(
 ):
     from bokeh.util.browser import view
     from bokeh.server.server import Server
+    from .edit import BokehScript
 
     run_log()
     bs = BokehScript(peaklist_path=peaklist_path, data_path=data_path)