Update files based on recent changes in master branch.

README.rst

@@ -1,50 +1,13 @@
-===========
-fiberassign
-===========
-
-Introduction
-------------
-
-This repository provides code for DESI fiber assignment, *i.e.* assigning
-which fibers of which telescope pointings (tiles) should be assigned to
-observe which objects in a target catalog.
-
-Compiling
----------
-
-To compile the code, set ``$PLATFORM`` to one of the recipes in the
-``platforms/`` and then run ``make install``;  *e.g.* at NERSC::
-
-    make PLATFORM=nersc_desiconda install
 
-The version of fiberassign can be updated with::
-
-    make version
-
-or::
-
-    make TAG=1.2.3 version
-
-to set the version when tagging.
-
-Running
--------
+fiberassign
+==============
 
-The main executable ``fiberassign`` is a python wrapper around the
-C++ ``fiberassign_exec`` code.  Run ``fiberassign --help`` to see the
-full set of command line options.
+This repository contains code to plan the location of DESI fiber positioners.  Given information about the instrument, a list of pointings (tiles), and catalogs of prioritized targets, fiber assignment computes the best positioner locations for each tile.
 
-An example would be:: 
+For full documentation, please visit  `fiberassign on Read the Docs`_
 
-  fiberassign  \
-    --mtl targets/mtl.fits \
-    --stdstar targets/standards-dark.fits \
-    --sky targets/sky.fits \
-    --surveytiles fiberassign/dark-tiles.txt \
-    --fibstatusfile fiberstatus.ecsv \
-    --outdir $SCRATCH/temp/
+.. image:: https://readthedocs.org/projects/fiberassign/badge/?version=latest
+    :target: http://fiberassign.readthedocs.org/en/latest/
+    :alt: Documentation Status
 
-``doc/Guide_to_FiberAssignment.tex`` contains more details about underlying
-algorithms but is out of date for the details of running fiberassign.
-A pdf snapshot is available to DESI collaborators at
-https://desi.lbl.gov/DocDB/cgi-bin/private/ShowDocument?docid=2742 .
+.. _`fiberassign on Read the Docs`: http://fiberassign.readthedocs.org/en/latest/

bin/qa-fiberassign

@@ -28,7 +28,12 @@ fiberpos.sort('FIBER')
 fiber_locations = sorted(zip(fiberpos['FIBER'], fiberpos['LOCATION']))
 
 sky_mask = desi_mask.SKY
-std_mask = (desi_mask.STD_FSTAR | desi_mask.STD_BRIGHT | desi_mask.STD_WD)
+std_mask = 0
+for name in ['STD', 'STD_FSTAR', 'STD_WD',
+             'STD_FAINT', 'STD_FAINT_BEST',
+             'STD_BRIGHT', 'STD_BRIGHT_BEST']:
+    if name in desi_mask.names():
+        std_mask |= desi_mask[name]
 
 #- TODO: take hardcoded from src/global.h into config file
 stuck_mask = 2**1
@@ -42,8 +47,13 @@ for filename in args.tilefiles:
     fa = Table.read(filename, 'FIBERASSIGN')
     fa.sort('FIBER')
     assigned.append(fa)
-    tmp = Table.read(filename, 'POTENTIAL')['POTENTIALTARGETID']
-    covered.append(np.unique(tmp))
+    try:
+        potential = Table.read(filename, 'POTENTIAL_ASSIGNMENTS')
+    except KeyError:
+        potential = Table.read(filename, 'POTENTIAL')
+
+    covered.append(np.unique(potential['TARGETID']))
+
     errors = list()
 
     if len(np.unique(fa['FIBER'])) != 5000:
@@ -52,8 +62,21 @@ for filename in args.tilefiles:
     if len(np.unique(fa['LOCATION'])) != 5000:
         errors.append('Repeated location numbers')
 
-    is_stuck = ((fa['FIBERMASK'] & stuck_mask) != 0)
-    is_broken = ((fa['FIBERMASK'] & broken_mask) != 0)
+    #- There should be a faster way to do this
+    for fiber, targetid in zip(fa['FIBER'], fa['TARGETID']):
+        if targetid<0:
+            continue
+        ii = (potential['FIBER'] == fiber)
+        if targetid not in potential['TARGETID'][ii]:
+            errors.append('Assigned targets not in covered targets list')
+            break
+
+    num_no_desitarget = np.count_nonzero(fa['DESI_TARGET'] == 0)
+    if num_no_desitarget > 0:
+        errors.append('{} fibers with DESI_TARGET=0'.format(num_no_desitarget))
+
+    is_stuck = ((fa['FIBERSTATUS'] & stuck_mask) != 0)
+    is_broken = ((fa['FIBERSTATUS'] & broken_mask) != 0)
     is_unassigned = (fa['TARGETID'] < 0)
     n_good_unassigned = np.count_nonzero(is_unassigned & ~(is_stuck | is_broken))
     if n_good_unassigned > 0:
@@ -68,8 +91,8 @@ for filename in args.tilefiles:
         errors.append('fiber:location map incorrect')
 
     ii = fa['TARGETID'] >= 0
-    dx = (fa['XFOCAL_DESIGN'][ii] - fiberpos['X'][ii])
-    dy = (fa['YFOCAL_DESIGN'][ii] - fiberpos['Y'][ii])
+    dx = (fa['DESIGN_X'][ii] - fiberpos['X'][ii])
+    dy = (fa['DESIGN_Y'][ii] - fiberpos['Y'][ii])
     r = np.sqrt(dx**2 + dy**2)
     if np.max(r) > 6:
         errors.append('Fibers assigned to more than 6mm from positioner center')

doc/conf.py

@@ -88,6 +88,7 @@
 # General information about the project.
 project = 'fiberassign'
 copyright = '2014-2019, DESI Collaboration'
+author = 'Robert Cahn, Jaime E. Forero-Romero, Ted Kisner'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -249,7 +250,7 @@
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
   ('index', 'fiberassign.tex', 'fiberassign Documentation',
-   'DESI', 'manual'),
+   'DESI Collaboration', 'manual'),
 ]
 
 # The name of an image file (relative to this directory) to place at the top of
@@ -279,7 +280,7 @@
 # (source start file, name, description, authors, manual section).
 man_pages = [
     ('index', 'fiberassign', 'fiberassign Documentation',
-     ['DESI'], 1)
+     ['DESI Collaboration'], 1)
 ]
 
 # If true, show URL addresses after external links.
@@ -293,7 +294,7 @@
 #  dir menu entry, description, category)
 texinfo_documents = [
   ('index', 'fiberassign', 'fiberassign Documentation',
-   'DESI', 'fiberassign', 'One line description of project.',
+   'DESI Collaboration', 'fiberassign', 'One line description of project.',
    'Miscellaneous'),
 ]