Merge pull request #67 from desihub/classes

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.layouts
+    :members:
+
+.. automodule:: prospect.viewer.widgets
+    :members:
+
+.. automodule:: prospect.viewer.vi_widgets
+    :members:

doc/changes.rst

@@ -13,10 +13,12 @@ prospect's Change Log
 * Optional countdown widget (PR `#58`_).
 * Updated requests to legacysurvey (PR `#65`_)
 * Merge of DESI and specutils code in :mod:`prospect.viewer` (PR `#66`_).
+* Restructure :mod:`prospect.viewer` into classes (PR `#67`_).
 
 .. _`#58`: https://github.com/desihub/prospect/pull/58
 .. _`#65`: https://github.com/desihub/prospect/pull/65
 .. _`#66`: https://github.com/desihub/prospect/pull/66
+.. _`#67`: https://github.com/desihub/prospect/pull/67
 
 1.0.1 (2021-01-07)
 ------------------

doc/nb/Prospect_demo.ipynb

@@ -25,7 +25,7 @@
     "\n",
     "# Uncomment this line to use a specific version of prospect\n",
     "sys.path.insert(0,\"/global/homes/a/armengau/prospect/py\")\n",
-    "from prospect import utilities,plotframes"
+    "from prospect import viewer,plotframes"
    ]
   },
   {
@@ -43,6 +43,20 @@
    "execution_count": 3,
    "metadata": {},
    "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "INFO:spectra.py:253:read_spectra: iotime 0.991 sec to read coadd-3-70003-20200228.fits at 2021-02-09T12:44:03.833097\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "INFO:desiutil.log.dlm58.info:iotime 0.991 sec to read coadd-3-70003-20200228.fits at 2021-02-09T12:44:03.833097\n"
+     ]
+    },
     {
      "name": "stdout",
      "output_type": "stream",
@@ -96,48 +110,75 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Help on function plotspectra in module prospect.plotframes:\n",
+      "Help on function plotspectra in module prospect.viewer:\n",
       "\n",
-      "plotspectra(spectra, nspec=None, startspec=None, zcatalog=None, redrock_cat=None, num_approx_fits=None, with_full_2ndfit=True, model_from_zcat=True, model=None, notebook=False, is_coadded=True, title=None, html_dir=None, with_imaging=True, with_noise=True, with_coaddcam=True, mask_type='DESI_TARGET', with_thumb_tab=True, with_vi_widgets=True, with_thumb_only_page=False, template_dir=None, archetype_fit=False, archetypes_dir=None)\n",
+      "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, vi_countdown=-1, with_thumb_only_page=False, is_coadded=True, with_coaddcam=True, mask_type='DESI_TARGET', model_from_zcat=True, model=None, num_approx_fits=None, with_full_2ndfit=True, template_dir=None, archetype_fit=False, archetypes_dir=None)\n",
       "    Main prospect routine. From a set of spectra, creates a bokeh document\n",
       "    used for VI, to be displayed as an HTML page or within a Jupyter notebook.\n",
       "    \n",
       "    Parameters\n",
       "    ----------\n",
-      "    spectra: input spectra. Supported formats: 1) a 3-band DESI spectra object, with bands 'b', 'r', 'z'. 2) a single-band\n",
-      "        DESI spectra object, bandname 'brz'. 2) a list of 3 frames, associated to the b, r and z bands.\n",
-      "    zcatalog (default None): astropy Table, containing the 'ZBEST' output redrock. Currently supports redrock-PCA or archetype files. The entries in zcatalog must be matched one-by-one (in order) to spectra.\n",
-      "    redrock_cat (default None): astropy Table, containing Redrock output (as defined in utilities.match_redrock_zfit_to_spectra). Entries must be matched one-by-one (in order) to spectra.\n",
-      "    notebook (bool): if True, bokeh outputs the viewer to a notebook, else to a (static) HTML page\n",
-      "    html_dir (string): directory to store the HTML page if notebook is False\n",
-      "    title (string): title used to name the HTML page / the bokeh figure / the VI file\n",
-      "    mask_type : mask type to identify target categories from the fibermap. Available : DESI_TARGET,\n",
-      "        SV1_DESI_TARGET, CMX_TARGET. Default : DESI_TARGET.\n",
-      "    with_vi_widgets (bool): include widgets used to enter VI informations. Set it to False if you do not intend to\n",
-      "        record VI files.\n",
-      "    with_thumb_tab (bool): include a tab with thumbnails of spectra in bokeh viewer\n",
-      "    with_thumb_only_page (bool): when creating a static HTML (notebook==False), a light HTML page including only the thumb\n",
-      "        gallery will also be produced.\n",
-      "    nspec: select subsample of spectra, only for frame input\n",
-      "    startspec: if nspec is set, subsample selection will be [startspec:startspec+nspec]\n",
-      "    model_from_zcat: if True, model spectra will be computed from the input zcatalog\n",
-      "    model: if set, use this input set of model spectra (instead of computing it from zcat)\n",
-      "        model format (mwave, mflux); model must be entry-matched to zcatalog.\n",
-      "    is_coadded : set to True if spectra are coadds\n",
-      "    with_imaging : include thumb image from legacysurvey.org\n",
-      "    with_noise : include noise for each spectrum\n",
-      "    with_coaddcam : include camera-coaddition\n",
-      "    template_dir: Redrock template directory\n",
-      "    archetype_fit : if True, assume zbest derived from redrock --archetypes and plot model accordingly.\n",
-      "    archetypes_dir : directory path for archetypes if not $RR__ARCHETYPE_DIR.\n",
-      "    num_approx_fits (default None): nb of best fit models to display if redrock_cat is given. By default,\n",
-      "        num_approx_fits=(nb of best fits available in redrock_cat)\n",
+      "    spectra : :class:`~desispec.spectra.Spectra` or :class:`~specutils.Spectrum1D` or :class:`~specutils.SpectrumList` or list of :class:`~desispec.frame.Frame`\n",
+      "        Input spectra. :class:`~specutils.Spectrum1D` are assumed to be SDSS/BOSS/eBOSS.\n",
+      "        Otherwise DESI spectra or frames is assumed.\n",
+      "    zcatalog : :class:`~astropy.table.Table`, optional\n",
+      "        Redshift values, matched one-to-one with the input spectra.\n",
+      "    redrock_cat : :class:`~astropy.table.Table`, optional\n",
+      "        Redrock output (as defined in :func:`~prospect.utilities.match_redrock_zfit_to_spectra`).\n",
+      "        Entries must be matched one-by-one (in order) to spectra.\n",
+      "    notebook : :class:`bool`, optional\n",
+      "        If ``True``, bokeh outputs the viewer to a Jupyter notebook.\n",
+      "    html_dir : :class:`str`, optional\n",
+      "        Directory to store the HTML page if `notebook` is ``False``.\n",
+      "    title : :class:`str`, optional\n",
+      "        Title used to name the HTML page / the bokeh figure / the VI file.\n",
+      "    with_imaging : :class:`bool`, optional\n",
+      "        If ``False``, don't include thumb image from https://www.legacysurvey.org/viewer.\n",
+      "    with_noise : :class:`bool`, optional\n",
+      "        If ``False``, don't include uncertainty for each spectrum.\n",
+      "    with_thumb_tab : :class:`bool`, optional\n",
+      "        If ``False``, don't include a tab with spectra thumbnails.\n",
+      "    with_vi_widgets : :class:`bool`, optional\n",
+      "        Include widgets used to enter VI information. Set it to ``False`` if\n",
+      "        you do not intend to record VI files.\n",
+      "    vi_countdown : :class:`int`, optional\n",
+      "        If ``>0``, add a countdown widget in the VI panel, with a value in minutes given\n",
+      "        by `vi_countdown``.\n",
+      "    with_thumb_only_page : :class:`bool`, optional\n",
+      "        When creating a static HTML (`notebook` is ``False``), a light HTML\n",
+      "        page including only the thumb gallery will also be produced.\n",
+      "    is_coadded : :class:`bool`, optional\n",
+      "        Set to ``True`` if `spectra` are coadds.  This will always be assumed\n",
+      "        for SDSS-style inputs, but not for DESI inputs.\n",
+      "    with_coaddcam : :class:`bool`, optional\n",
+      "        Include camera-coaddition, only relevant for DESI.\n",
+      "    mask_type : :class:`str`, optional (default: DESI_TARGET)\n",
+      "        Bitmask type to identify target categories in the spectra. For DESI\n",
+      "        these could be: DESI_TARGET, SV1_DESI_TARGET, SV1_BGS_TARGET, CMX_TARGET.\n",
+      "    model_from_zcat : :class:`bool`, optional\n",
+      "        If ``True``, model spectra will be computed from the input `zcatalog`.\n",
+      "    model : :func:`tuple`, optional\n",
+      "        If set, use this input set of model spectra instead of computing it from `zcatalog`.\n",
+      "        model consists of (mwave, mflux); model must be entry-matched to `zcatalog`.\n",
+      "    num_approx_fits : :class:`int`, optional\n",
+      "        Number of best-fit models to display, if `redrock_cat` is provided.\n",
+      "        By default, all best-fit models available in `redrock_cat` are diplayed.\n",
+      "    with_full_2ndfit : :class:`bool`, optional\n",
+      "        If ``True``, the second best-fit model from `redrock_cat` will be displayed\n",
+      "        without approximation (no undersampling, full resolution).\n",
+      "    template_dir : :class:`str`, optional\n",
+      "        Redrock template directory.\n",
+      "    archetype_fit : :class:`bool`, optional\n",
+      "        If ``True``, assume `zcatalog` derived from :command:`redrock --archetypes`\n",
+      "        and plot model accordingly.\n",
+      "    archetypes_dir : :class:`str`, optional\n",
+      "        Directory path for archetypes if not :envvar:`RR_ARCHETYPE_DIR`.\n",
       "\n"
      ]
     }
    ],
    "source": [
-    "help(plotframes.plotspectra)"
+    "help(viewer.plotspectra)"
    ]
   },
   {
@@ -146,7 +187,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "plotframes.plotspectra(coadds_select, zcatalog=zbest_select, notebook=True, \n",
+    "viewer.plotspectra(coadds_select, zcatalog=zbest_select, notebook=True, \n",
     "                       title='Prospect_demo', \n",
     "                       mask_type='CMX_TARGET')"
    ]

doc/nb/Prospect_spectrum_service.ipynb

@@ -31,7 +31,7 @@
     "from astropy.table import Table\n",
     "from specutils import Spectrum1D, SpectrumCollection, SpectrumList\n",
     "from prospect.specutils import read_spPlate, read_spZbest\n",
-    "from prospect.plotspecutils import plotspectra"
+    "from prospect.viewer import plotspectra"
    ]
   },
   {
@@ -40,8 +40,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from dl import queryClient as qc, storeClient as sc\n",
-    "# import specClient as spec"
+    "from dl import queryClient as qc, storeClient as sc, specClient as spec"
    ]
   },
   {
@@ -569,7 +568,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.4"
+   "version": "3.7.6"
   }
  },
  "nbformat": 4,

doc/nb/Prospect_targetid.ipynb

@@ -23,7 +23,7 @@
     "# If not using the desiconda version of prospect: EDIT THIS to your path\n",
     "#sys.path.insert(0,\"/global/homes/X/XXXXX/prospect/py\") \n",
     "sys.path.insert(0,\"/global/homes/a/armengau/prospect/py\")\n",
-    "from prospect import plotframes, utilities\n",
+    "from prospect import viewer, utilities\n",
     "import desispec.io\n",
     "from astropy.table import Table, vstack\n",
     "import numpy as np\n",
@@ -63,7 +63,7 @@
     "spectra, zcat= utilities.load_spectra_zcat_from_targets(targets, tiledir, obs_db)\n",
     "\n",
     "# VI interface in notebook\n",
-    "plotframes.plotspectra(spectra, zcatalog=zcat, title='Target_select', notebook=True, mask_type='CMX_TARGET')"
+    "viewer.plotspectra(spectra, zcatalog=zcat, title='Target_select', notebook=True, mask_type='CMX_TARGET')"
    ]
   },
   {
@@ -96,7 +96,7 @@
     "spectra, zcat, rrtable = utilities.load_spectra_zcat_from_targets(targets, tiledir, obs_db, with_redrock=True)\n",
     "\n",
     "# VI interface in notebook\n",
-    "plotframes.plotspectra(spectra, zcatalog=zcat, redrock_cat=rrtable, title='Target_select', notebook=True, mask_type='CMX_TARGET')"
+    "viewer.plotspectra(spectra, zcatalog=zcat, redrock_cat=rrtable, title='Target_select', notebook=True, mask_type='CMX_TARGET')"
    ]
   }
  ],

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_expo.py

@@ -23,7 +23,7 @@
 
 from ..myspecselect import myspecselect  # special (to be edited)
 from ..plotframes import create_model, plotspectra
-from ..utilities import match_zbest_to_spectra, match_vi_targets  #, miniplot_spectrum
+from ..utilities import match_zcat_to_spectra, match_vi_targets  #, miniplot_spectrum
 
 def _parse():
     parser = argparse.ArgumentParser(description='Create html pages for the spectral viewer')

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)