Gui cosmetics

doc/changes.rst

@@ -5,8 +5,12 @@ prospect's Change Log
 1.3.1 (unreleased)
 ------------------
 
+* Added a Text widget to enter a spectrum number by hand.
+* Added ``-colors`` option for the main plot's curves.
+* Handling the case of a missing spectrograph arm (PR `#95`_).
 * Don't use mask information when marking bad pixels in SDSS data (PR `#94`_).
 
+.. _`#95`: https://github.com/desihub/prospect/pull/95
 .. _`#94`: https://github.com/desihub/prospect/pull/94
 
 1.3.0 (2023-09-06)

py/prospect/js/update_plot.js

@@ -14,6 +14,13 @@ var nsmooth = smootherslider.value;
 // update VI widgets + infos for current spectrum
 //
 if (cb_obj == ispectrumslider) {
+    //
+    // Update ispec_input, avoiding recursive call
+    //
+    if (i_spectrum != parseInt(ispec_input.value)) {
+        ispec_input.value = String(i_spectrum);
+    }
+
     //
     // Update metadata using "shortcds" objects.
     //

py/prospect/scripts/prospect_pages.py

@@ -85,6 +85,7 @@ def _parse():
     parser.add_argument('--titlepage_prefix', help='Prefix for html page title', type=str, default='DESI_spectra')
     parser.add_argument('--top_metadata', help="""List of fibermap's metadata to be highlighted (display in the most visible table).
         Note: if fibermap contains FIRST/LAST/NUM_XX, then including XX in top_metadata will display all of FIRST/LAST/NUM_XX.""", nargs='+', type=str, default=None)
+    parser.add_argument('--colors', help="""Customize the curve's colors: 3 colors should be given, associated respectively to the coadded data, the model and the noise.""", nargs='+', type=str, default=None)
     parser.add_argument('--no_imaging', dest='with_imaging', help='Do not include thumb images from https://www.legacysurvey.org/viewer', action='store_false')
     parser.add_argument('--no_noise', dest='with_noise', help='Do not display noise vectors associated to spectra', action='store_false')
     parser.add_argument('--no_thumb_tab', dest='with_thumb_tab', help='Do not include a tab with spectra thumbnails', action='store_false')
@@ -296,6 +297,7 @@ def main():
         'with_full_2ndfit': False,
         'with_thumb_only_page': args.with_thumbnail_only_pages,
         'std_template_file': args.std_template_file,
+        'colors': args.colors,
         'with_imaging': args.with_imaging,
         'with_noise': args.with_noise,
         'with_thumb_tab': args.with_thumb_tab,

py/prospect/viewer/__init__.py

@@ -140,7 +140,7 @@ def create_model(spectra, zcat, archetype_fit=False, archetypes_dir=None, templa
 
 
 def plotspectra(spectra, zcatalog=None, redrock_cat=None, notebook=False, html_dir=None, title=None,
-                with_imaging=True, with_noise=True, with_thumb_tab=True, with_vi_widgets=True,
+                colors=None, with_imaging=True, with_noise=True, with_thumb_tab=True, with_vi_widgets=True,
                 top_metadata=None, vi_countdown=-1, with_thumb_only_page=False,
                 with_coaddcam=True, mask_type='DESI_TARGET',
                 model_from_zcat=True, model=None, num_approx_fits=None, with_full_2ndfit=True,
@@ -165,6 +165,9 @@ def plotspectra(spectra, zcatalog=None, redrock_cat=None, notebook=False, html_d
         Directory to store the HTML page if `notebook` is ``False``.
     title : :class:`str`, optional
         Title used to name the HTML page / the bokeh figure / the VI file.
+    colors : :class:`list`, optional
+        Customize the curve's colors: 3 colors should be given, associated respectively to
+        the coadded data, the model and the noise.
     with_imaging : :class:`bool`, optional
         If ``False``, don't include thumb image from https://www.legacysurvey.org/viewer.
     with_noise : :class:`bool`, optional
@@ -320,7 +323,7 @@ def plotspectra(spectra, zcatalog=None, redrock_cat=None, notebook=False, html_d
     #-- Graphical objects --
     #-------------------------
 
-    viewer_plots = ViewerPlots()
+    viewer_plots = ViewerPlots(colors=colors)
     viewer_plots.create_mainfig(spectra, title, viewer_cds, survey,
                                 with_noise=with_noise, with_coaddcam=with_coaddcam)
     viewer_plots.create_zoomfig(viewer_cds,

py/prospect/viewer/layouts.py

@@ -29,11 +29,13 @@ def __init__(self, plots, widgets, vi_widgets, with_vi_widgets=True):
         vi_widgets : :class:`ViewerVIWidgets`
         '''
 
-        #- Main 'navigator'
+        #- Main spectrum 'navigator'
         self.navigator = bl.row(
             bl.column(widgets.prev_button, width=widgets.navigation_button_width+15),
             bl.column(widgets.next_button, width=widgets.navigation_button_width+20),
-            bl.column(widgets.ispectrumslider, width=plots.plot_width+(plots.plot_height//2)-(60*len(vi_widgets.vi_quality_labels)+2*widgets.navigation_button_width+35))
+            bl.column(widgets.ispectrumslider, width=plots.plot_width+(plots.plot_height//2)-(60*len(vi_widgets.vi_quality_labels)+2*widgets.navigation_button_width+35+100)),
+            bl.column(widgets.ispec_input, width=100),
+            background='#ececf9'
         )
 
         #- Redshift widgets
@@ -70,9 +72,12 @@ def __init__(self, plots, widgets, vi_widgets, with_vi_widgets=True):
 
         #- VI widgets
         if with_vi_widgets :
-            self.navigator.children.insert(1, bl.column(vi_widgets.vi_quality_input, width=60*len(vi_widgets.vi_quality_labels)) )
+            self.navigator.children.insert(1, bl.column(
+                vi_widgets.vi_quality_input,
+                width=60*len(vi_widgets.vi_quality_labels)
+            ) )
             if vi_widgets.vi_countdown_toggle is None :
-                vi_header_block = bl.column( Div(text="VI optional indications :"), width=300 )
+                vi_header_block = bl.column( Div(text="VI optional indications:"), width=300 )
             else :
                 vi_header_block = bl.row(
                     bl.column( Div(text="VI optional indications :"), width=300 ),
@@ -124,14 +129,14 @@ def __init__(self, plots, widgets, vi_widgets, with_vi_widgets=True):
                                 bl.column(bl.Spacer(width=30)),
                                 bl.column(widgets.waveframe_buttons, width=120)
                               )
-        else :
+        else:
             waveframe_block = bl.column(widgets.waveframe_buttons, width=120)
         self.plot_widget_set.children.append(waveframe_block)
         if widgets.model_select is not None :
             self.plot_widget_set.children.insert(4, bl.column(widgets.model_select, width=200))
-        
+
         #- Assemble all widgets
-        if with_vi_widgets :
+        if with_vi_widgets:
             self.full_widget_set = bl.column(
                 bl.row(
                     self.vi_widget_set,
@@ -140,7 +145,12 @@ def __init__(self, plots, widgets, vi_widgets, with_vi_widgets=True):
                 ),
                 bl.column(vi_widgets.vi_guideline_div, width=2*widgets.plot_widget_width)
             )
-        else : self.full_widget_set = self.plot_widget_set
+        else:
+            N = len(self.plot_widget_set.children) // 2
+            self.full_widget_set = bl.row(
+                bl.column(self.plot_widget_set.children[0:N]),
+                bl.column(self.plot_widget_set.children[N:])
+            )
 
         self.main_bokehlayout = bl.column(
             bl.row(plots.fig, bl.column(plots.imfig, plots.zoomfig), bl.Spacer(width=20)),
@@ -153,6 +163,7 @@ def __init__(self, plots, widgets, vi_widgets, with_vi_widgets=True):
                 bl.column(widgets.oii_undo_button, width=50),
             ),
             self.navigator,
+            bl.column(bl.Spacer(height=10)),
             self.full_widget_set,
             sizing_mode='stretch_width'
         )

py/prospect/viewer/plots.py

@@ -89,7 +89,7 @@ class ViewerPlots(object):
     Encapsulates Bokeh plot-like objects that are part of prospect's GUI.
     """
 
-    def __init__(self):
+    def __init__(self, colors=None):
         # "Hardcoded" plotting parameters here:
         self.legend_outside_plot = True
         if (self.legend_outside_plot):
@@ -102,9 +102,15 @@ def __init__(self):
         self.plot_height=400
         self.colors = dict(b='#1f77b4', r='#d62728', z='maroon', coadd='#d62728', brz='#d62728')
         self.noise_colors = dict(b='greenyellow', r='green', z='forestgreen', coadd='green', brz='green')
+        self.model_color = 'black'
         ## overlap wavelengths are hardcoded, from 1907.10688 (Table 1)
         self.overlap_waves = [ [5660, 5930], [7470, 7720] ]
         self.alpha_overlapband = 0.03
+        if colors is not None:
+            assert len(colors)==3
+            self.colors['coadd'] = self.colors['brz'] = colors[0]
+            self.model_color = colors[1]
+            self.noise_colors['coadd'] = self.noise_colors['brz'] = colors[2]
 
         self.fig = None
         self.zoomfig = None
@@ -193,12 +199,16 @@ def create_mainfig(self, spectra, title, viewer_cds, survey, with_noise=True, wi
 
         self.model_lines = list()
         if viewer_cds.cds_model is not None:
-            lx = self.fig.line('plotwave', 'plotflux', source=viewer_cds.cds_model, line_color='black')
+            lx = self.fig.line('plotwave', 'plotflux',
+                               source=viewer_cds.cds_model,
+                               line_color=self.model_color)
             self.model_lines.append(lx)
 
         self.othermodel_lines = list()
         if viewer_cds.cds_othermodel is not None :
-            lx = self.fig.line('plotwave', 'plotflux', source=viewer_cds.cds_othermodel, line_color='black', line_dash='dashed')
+            lx = self.fig.line('plotwave', 'plotflux',
+                               source=viewer_cds.cds_othermodel,
+                               line_color=self.model_color, line_dash='dashed')
             self.othermodel_lines.append(lx)
 
         legend_items = [("data", self.data_lines[-1::-1])] #- reversed to get blue as lengend entry
@@ -244,9 +254,9 @@ def create_zoomfig(self, viewer_cds, with_noise=True, with_coaddcam=True):
                 self.zoom_noise_lines.append(lx)
 
         if viewer_cds.cds_model is not None:
-            lx = self.zoomfig.line('plotwave', 'plotflux', source=viewer_cds.cds_model, line_color='black')
+            lx = self.zoomfig.line('plotwave', 'plotflux', source=viewer_cds.cds_model, line_color=self.model_color)
         if viewer_cds.cds_othermodel is not None :
-            lx = self.zoomfig.line('plotwave', 'plotflux', source=viewer_cds.cds_othermodel, line_color='black', line_dash='dashed')
+            lx = self.zoomfig.line('plotwave', 'plotflux', source=viewer_cds.cds_othermodel, line_color=self.model_color, line_dash='dashed')
 
         #- Callback to update zoom window x-range
         self.zoom_callback = CustomJS(

py/prospect/viewer/widgets.py

@@ -77,7 +77,8 @@ def __init__(self, plots, nspec):
         # Ispectrumslider's value controls which spectrum is displayed
         # These two widgets call update_plot(), later defined
         slider_end = nspec-1 if nspec > 1 else 0.5 # Slider cannot have start=end
-        self.ispectrumslider = Slider(start=0, end=slider_end, value=0, step=1, title='Spectrum (0 to '+str(nspec-1)+')')
+        slidertitle = 'Spectrum number (0 to '+str(nspec-1)+')'
+        self.ispectrumslider = Slider(start=0, end=slider_end, value=0, step=1, title=slidertitle)
         self.smootherslider = Slider(start=0, end=26, value=0, step=1.0, title='Gaussian Sigma Smooth')
         self.coaddcam_buttons = None
         self.model_select = None
@@ -102,14 +103,28 @@ def add_navigation(self, nspec):
             }
             """)
         self.next_callback = CustomJS(
-            args=dict(ispectrumslider=self.ispectrumslider, nspec=nspec),
-            code="""
+            args = dict(ispectrumslider=self.ispectrumslider, nspec=nspec),
+            code = """
             if(ispectrumslider.value<nspec-1 && ispectrumslider.end>=1) {
                 ispectrumslider.value++
             }
             """)
         self.prev_button.js_on_event('button_click', self.prev_callback)
         self.next_button.js_on_event('button_click', self.next_callback)
+        #- Input spectrum number
+        self.ispec_input = TextInput(value=str(self.ispectrumslider.value), width=50)
+        self.ispec_input_callback = CustomJS(
+            args = dict(ispec_input=self.ispec_input, ispectrumslider=self.ispectrumslider, nspec=nspec),
+            code = """
+            var i_spec = parseInt(ispec_input.value) ;
+            if (Number.isInteger(i_spec) && i_spec>=0 && i_spec<nspec) {
+                // Avoid recursive call
+                if (i_spec != ispectrumslider.value) {
+                    ispectrumslider.value = i_spec ;
+                }
+            }
+            """)
+        self.ispec_input.js_on_change('value', self.ispec_input_callback)
 
     def add_resetrange(self, viewer_cds, plots):
         #-----
@@ -495,6 +510,7 @@ def add_update_plot_callback(self, viewer_cds, plots, vi_widgets):
                 shortcds_table_c = self.shortcds_table_c,
                 shortcds_table_d = self.shortcds_table_d,
                 ispectrumslider = self.ispectrumslider,
+                ispec_input = self.ispec_input,
                 smootherslider = self.smootherslider,
                 z_input = self.z_input,
                 widgetinfos = self.cds_widgetinfos,