Classes

doc/api.rst

@@ -5,6 +5,9 @@ prospect API
 .. automodule:: prospect
     :members:
 
+.. automodule:: prospect.grid_thumbs
+    :members:
+
 .. automodule:: prospect.mycoaddcam
     :members:
 
@@ -38,6 +41,9 @@ prospect API
 .. automodule:: prospect.scripts.specview_cmx_targets
     :members:
 
+.. automodule:: prospect.scripts.specview_per_expo
+    :members:
+
 .. automodule:: prospect.scripts.specview_per_night
     :members:
 
@@ -49,3 +55,21 @@ prospect API
 
 .. automodule:: prospect.utilities
     :members:
+
+.. automodule:: prospect.viewer
+    :members:
+
+.. automodule:: prospect.viewer_cds
+    :members:
+
+.. automodule:: prospect.viewer_plots
+    :members:
+
+.. automodule:: prospect.viewer_setup
+    :members:
+
+.. automodule:: prospect.viewer_widgets
+    :members:
+
+.. automodule:: prospect.viewer_vi_widgets
+    :members:

py/prospect/grid_thumbs.py

@@ -0,0 +1,66 @@
+# Licensed under a 3-clause BSD style license - see LICENSE.rst
+# -*- coding: utf-8 -*-
+"""
+====================
+prospect.grid_thumbs
+====================
+
+Grid of thumbnail plots displaying a set of spectra
+
+"""
+
+import numpy as np
+import astropy.convolution
+
+import bokeh.plotting as bk
+import bokeh.layouts as bl
+
+from .mycoaddcam import coaddcam_prospect
+
+# TODOS:
+# - structure: class??
+# - improve thumbs with infos, plot quality
+
+def grid_thumbs(spectra, thumb_width, x_range=(3400,10000), thumb_height=None, resamp_factor=15, ncols_grid=5, titles=None) :
+    '''
+    Create a bokeh gridplot of thumbnail pictures from spectra
+    - coadd arms
+    - smooth+resample to reduce size of embedded CDS, according to resamp_factor
+    - titles : optional list of titles for each thumb
+
+    TODO: Not tested on Spectrum1D objects.
+    '''
+
+    if thumb_height is None : thumb_height = thumb_width//2
+    if titles is not None : assert len(titles) == spectra.num_spectra()
+    thumb_wave, thumb_flux, dummy = coaddcam_prospect(spectra)
+    kernel = astropy.convolution.Gaussian1DKernel(stddev=resamp_factor)
+
+    thumb_plots = []
+    for i_spec in range(spectra.num_spectra()) :
+        x_vals = (thumb_wave[::resamp_factor])[resamp_factor:-resamp_factor]
+        # Use astropy convolution : handles NaNs
+        y_vals = astropy.convolution.convolve(thumb_flux[i_spec,:], kernel)
+        y_vals = (y_vals[::resamp_factor])[resamp_factor:-resamp_factor]
+        x_vals = x_vals[~np.isnan(y_vals)] # Needed to avoid 'ValueError: Out of range float values are not JSON compliant'
+        y_vals = y_vals[~np.isnan(y_vals)]
+        if len(x_vals)==0 : # All NaN ... this should not happen ...
+            ymin, ymax = -1, 1
+        else :
+            yampl = np.max(y_vals) - np.min(y_vals)
+            ymin = np.min(y_vals) - 0.1*yampl
+            ymax = np.max(y_vals) + 0.1*yampl
+        plot_title = None
+        if titles is not None : plot_title = titles[i_spec]
+        mini_plot = bk.figure(plot_width=thumb_width, plot_height=thumb_height, x_range=x_range, y_range=(ymin,ymax), title=plot_title)
+        if len(x_vals)!=0 : mini_plot.line(x_vals, y_vals, line_color='red')
+        mini_plot.xaxis.visible = False
+        mini_plot.yaxis.visible = False
+        mini_plot.min_border_left = 0
+        mini_plot.min_border_right = 0
+        mini_plot.min_border_top = 0
+        mini_plot.min_border_bottom = 0
+        thumb_plots.append(mini_plot)
+
+    return bl.gridplot(thumb_plots, ncols=ncols_grid, toolbar_location=None, sizing_mode='scale_width')
+

py/prospect/scripts/specview_cmx_coadds.py

@@ -18,7 +18,7 @@
 import desispec.spectra
 import desispec.frame
 
-from ..plotframes import plotspectra
+from ..viewer import plotspectra
 from ..myspecselect import myspecselect
 from ..myspecupdate import myspecupdate
 from ..utilities import specviewer_selection, match_redrock_zfit_to_spectra, match_zcat_to_spectra

py/prospect/scripts/specview_cmx_frames.py

@@ -21,7 +21,7 @@
 import desispec.spectra
 import desispec.frame
 
-from ..plotframes import plotspectra
+from ..viewer import plotspectra
 from ..myspecselect import myspecselect
 from ..myspecupdate import myspecupdate
 from ..utilities import frames2spectra, specviewer_selection, coadd_targets

py/prospect/scripts/specview_cmx_targets.py

@@ -15,7 +15,7 @@
 import desispec.io
 from desiutil.log import get_logger
 
-from ..plotframes import plotspectra
+from ..viewer import plotspectra
 from ..myspecselect import myspecselect
 from ..utilities import make_targetdict, load_spectra_zcat_from_targets  #, match_zcat_to_spectra
 

py/prospect/scripts/specview_per_night.py

@@ -22,7 +22,7 @@
 import desispec.frame
 
 from ..myspecselect import myspecselect # special (to be edited)
-from ..plotframes import plotspectra
+from ..viewer import plotspectra
 from ..utilities import match_zcat_to_spectra  #, match_vi_targets, miniplot_spectrum
 
 def _parse():
@@ -70,7 +70,7 @@ def main():
                 the_indices = sort_indices[(i_page-1)*args.nspecperfile:i_page*args.nspecperfile]
                 thespec = myspecselect(spectra, indices=the_indices)
                 thezb, kk = match_zcat_to_spectra(zbest,thespec)
-                model = plotframes.create_model(thespec, thezb)
+                #model = plotframes.create_model(thespec, thezb)
                 ### No VI results to display by default
                 # vifile = os.environ['HOME']+"/prospect/vilist_prototype.fits"
                 # vidata = match_vi_targets(vifile, thespec.fibermap["TARGETID"])
@@ -80,7 +80,7 @@ def main():
                     os.makedirs(html_dir)
                     os.mkdir(html_dir+"/vignettes")
 
-                plotframes.plotspectra(thespec, zcatalog=thezb, vidata=None, model=model, title=titlepage, html_dir=html_dir, is_coadded=False)
+                plotspectra(thespec, zcatalog=thezb, title=titlepage, html_dir=html_dir, is_coadded=False)
 #                 for i_spec in range(thespec.num_spectra()) :
 #                     saveplot = html_dir+"/vignettes/night"+thenight+"_"+file_label+"_"+str(i_page)+"_"+str(i_spec)+".png"
 #                     miniplot_spectrum(thespec, i_spec, model=model, saveplot=saveplot, smoothing = args.vignette_smoothing)

py/prospect/scripts/specview_per_pixel.py

@@ -24,8 +24,8 @@
 import desispec.frame
 
 from ..myspecselect import myspecselect  # special (to be edited)
-from ..plotframes import coadd_targets, create_model, plotspectra
-from ..utilities import specviewer_selection, match_zcat_to_spectra, match_vi_targets  #, miniplot_spectrum
+from ..viewer import plotspectra
+from ..utilities import coadd_targets, specviewer_selection, match_zcat_to_spectra, match_vi_targets  #, miniplot_spectrum
 
 
 def _parse():
@@ -108,13 +108,13 @@ def main():
                 titlepage = "chi2cut-"+str(args.chi2cut[0])+"-"+str(args.chi2cut[1])+"_"+titlepage
             if args.mask is not None :
                 titlepage = args.mask+"_"+titlepage
-            model = create_model(thespec, thezb)
+            #model = create_model(thespec, thezb)
             html_dir = os.path.join(webdir,"pix"+pixel)
             if not os.path.exists(html_dir) :
                 os.makedirs(html_dir)
                 os.mkdir(html_dir+"/vignettes")
 
-            plotspectra(thespec, zcatalog=zbest, model_from_zcat=True, vidata=None, model=None, title=titlepage, html_dir=html_dir, is_coadded=True, mask_type=args.mask_type)
+            plotspectra(thespec, zcatalog=zbest, model_from_zcat=True, model=None, title=titlepage, html_dir=html_dir, is_coadded=True, mask_type=args.mask_type)
 #             for i_spec in range(thespec.num_spectra()) :
 #                 saveplot = html_dir+"/vignettes/pix"+pixel+"_"+str(i_page)+"_"+str(i_spec)+".png"
 #                 miniplot_spectrum(thespec, i_spec, model=model, saveplot=saveplot, smoothing = args.vignette_smoothing)