Allow deployment of prospect without DESI software stack

doc/nb/Prospect_specutils.ipynb

@@ -16,6 +16,17 @@
    "outputs": [],
    "source": [
     "import os\n",
+    "import sys\n",
+    "sys.path.insert(0, os.path.join(os.environ['HOME'], 'Documents', 'Code', 'git', 'desihub', 'prospect', 'py'))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# import os\n",
     "import numpy as np\n",
     "from astropy.table import Table\n",
     "from specutils import Spectrum1D, SpectrumCollection, SpectrumList\n",
@@ -66,6 +77,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "os.environ['SPECTRO_REDUX'] = os.path.join(os.environ['HOME'], 'Documents', 'Data', 'sdss', 'dr16', 'sdss', 'spectro', 'redux')\n",
     "run2d = '26'\n",
     "plate = '2955'\n",
     "mjd = '54562'\n",
@@ -191,9 +203,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "DESI prospect",
+   "display_name": "Python 3",
    "language": "python",
-   "name": "desi-prospect"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
@@ -205,7 +217,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.9"
+   "version": "3.8.2"
   }
  },
  "nbformat": 4,

py/prospect/myspecselect.py

@@ -3,7 +3,11 @@
 # to include expid-based selection + indices-based selection
 # changes : fct name+args ; self=>thespec ; expid/indices-based selection + final selection
 
-import desispec.spectra
+_desispec_imported = True
+try:
+    import desispec.spectra
+except ImportError:
+    _desispec_imported = False
 
 def myspecselect(thespec, nights=None, bands=None, targets=None, fibers=None, expids=None, indices=None, invert=False, remove_scores=False, clean_fiberstatus=False, output_indices=False):
     """
@@ -15,21 +19,21 @@ def myspecselect(thespec, nights=None, bands=None, targets=None, fibers=None, ex
         bands (list): optional list of bands to select.
         targets (list): optional list of target IDs to select.
         fibers (list): list/array of fiber indices to select.
-        ADDED=> expids (list): list/array of individual exposures to select.      
-        ADDED =>indices (list) : list of raw (arbitrary) indices in the Spectra object to select. 
+        ADDED=> expids (list): list/array of individual exposures to select.
+        ADDED =>indices (list) : list of raw (arbitrary) indices in the Spectra object to select.
         invert (bool): after combining all criteria, invert selection.
         remove_scores (bool): probably tmp trick, TODO
         output_indices (bool): if True, also returns indices of kept spectra
     Returns (Spectra):
         a new Spectra object containing the selected data.
     """
-    
+
     keep_fiberstatus = None
     if clean_fiberstatus == False :
         keep_fiberstatus = [ True for x in range(thespec.num_spectra()) ]
     else :
         keep_fiberstatus = [ (x==0) for x in thespec.fibermap["FIBERSTATUS"] ]
-    
+
     keep_bands = None
     if bands is None:
         keep_bands = thespec.bands
@@ -47,7 +51,7 @@ def myspecselect(thespec, nights=None, bands=None, targets=None, fibers=None, ex
     if sum(keep_nights) == 0:
         print("myspecselect: no valid nights were selected.")
         return None
-    
+
     keep_targets = None
     if targets is None:
         keep_targets = [ True for x in range(thespec.num_spectra()) ]
@@ -56,7 +60,7 @@ def myspecselect(thespec, nights=None, bands=None, targets=None, fibers=None, ex
     if sum(keep_targets) == 0:
         print("myspecselect: no valid targets were selected.")
         return None
-    
+
     keep_fibers = None
     if fibers is None:
         keep_fibers = [ True for x in range(thespec.num_spectra()) ]
@@ -122,13 +126,13 @@ def myspecselect(thespec, nights=None, bands=None, targets=None, fibers=None, ex
     keep_scores = None
     if not remove_scores :
         if thespec.scores is not None : keep_scores = thespec.scores[keep]
-    
-    ret = desispec.spectra.Spectra(keep_bands, keep_wave, keep_flux, keep_ivar, 
-        mask=keep_mask, resolution_data=keep_res, 
+
+    ret = desispec.spectra.Spectra(keep_bands, keep_wave, keep_flux, keep_ivar,
+        mask=keep_mask, resolution_data=keep_res,
         fibermap=thespec.fibermap[keep], meta=thespec.meta, extra=keep_extra,
         single=thespec._single, scores=keep_scores)
 
     if output_indices :
         return (ret, keep)
-    
+
     return ret

py/prospect/myspecupdate.py

@@ -3,10 +3,19 @@
 # Reason : EXPID is not available in coadd spectra
 
 import numpy as np
-import desispec.spectra
-from desiutil.io import encode_table
-from desispec.maskbits import specmask
-from desispec.resolution import Resolution
+_desiutil_imported = True
+try:
+    from desiutil.io import encode_table
+except ImportError:
+    _desiutil_imported = False
+
+_desispec_imported = True
+try:
+    import desispec.spectra
+    from desispec.maskbits import specmask
+    from desispec.resolution import Resolution
+except ImportError:
+    _desispec_imported = False
 
 def myspecupdate(spectra_in, other) :
 
@@ -91,7 +100,7 @@ def myspecupdate(spectra_in, other) :
         or ("FIBER" not in spectra_in.fibermap.keys())
         or ("FIBER" not in other.fibermap.keys()) ) :
         check_exists = False
-    if check_exists : 
+    if check_exists :
         for r in range(nother):
             expid = other.fibermap[r]["EXPID"]
             fiber = other.fibermap[r]["FIBER"]
@@ -106,7 +115,7 @@ def myspecupdate(spectra_in, other) :
     indx_exists = np.where(exists == 1)[0]
     indx_new = np.where(exists == 0)[0]
 
-    # Make new data arrays of the correct size to hold both the old and 
+    # Make new data arrays of the correct size to hold both the old and
     # new data
 
     nupdate = len(indx_exists)