Merge pull request #214 from desihub/fixtests

Fix test failures

.travis.yml

@@ -50,9 +50,9 @@ env:
         - DESISIM_TESTDATA_VERSION=0.3.3
         - SPECLITE_VERSION=0.5
         - SPECSIM_VERSION=v0.6
-        - SPECTER_VERSION=0.6.0
-        - DESISPEC_VERSION=0.12.0
-        - DESITARGET_VERSION=0.8.1
+        - SPECTER_VERSION=0.7.0
+        - DESISPEC_VERSION=0.13.1
+        - DESITARGET_VERSION=0.9.0
         # - DESIMODEL_VERSION=trunk
         - DESI_LOGLEVEL=DEBUG
         - MAIN_CMD='python setup.py'
@@ -63,7 +63,7 @@ env:
         # These packages will always be installed.
         - PIP_DEPENDENCIES=""
         # These packages will only be installed if we really need them.
-        - PIP_ALL_DEPENDENCIES="speclite==${SPECLITE_VERSION} coveralls"
+        - PIP_ALL_DEPENDENCIES="speclite==${SPECLITE_VERSION} coveralls fitsio"
         # These pip packages need to be installed in a certain order, so we
         # do that separately from the astropy/ci-helpers scripts.
         - DESIHUB_PIP_DEPENDENCIES="desiutil=${DESIUTIL_VERSION}"

py/desisim/io.py

@@ -107,8 +107,11 @@ def write_simspec(meta, truth, expid, night, header=None, outfile=None):
         outfile = '{}/simspec-{:08d}.fits'.format(outdir, expid)
 
     #- Primary HDU is just a header from the input
+    header = desispec.io.util.fitsheader(header)
+    if 'DOSVER' not in header:
+        header['DOSVER'] = 'SIM'
     hx = fits.HDUList()
-    hx.append(fits.PrimaryHDU(None, header=desispec.io.util.fitsheader(header)))
+    hx.append(fits.PrimaryHDU(None, header=header))
 
     #- Object flux HDU (might not exist, e.g. for an arc)
     if 'FLUX' in truth:
@@ -619,28 +622,29 @@ def read_basis_templates(objtype, subtype='', outwave=None, nspec=None,
     log.info('Reading {}'.format(infile))
 
     if objtype.upper() == 'QSO':
-        fx = fits.open(infile)
-        format_version = _qso_format_version(infile)
-        if format_version == 1:
-            flux = fx[0].data * 1E-17
-            hdr = fx[0].header
-            from desispec.io.util import header2wave
-            wave = header2wave(hdr)
-            meta = Table(fx[1].data)
-        elif format_version == 2:
-            flux = fx['SDSS_EIGEN'].data.copy()
-            wave = fx['SDSS_EIGEN_WAVE'].data.copy()
-            meta = Table([np.arange(flux.shape[0]),], names=['PCAVEC',])
-        else:
-            raise IOError('Unknown QSO basis template format version {}'.format(format_version))
-
-        fx.close()
+        with fits.open(infile) as fx:
+            format_version = _qso_format_version(infile)
+            if format_version == 1:
+                flux = fx[0].data * 1E-17
+                hdr = fx[0].header
+                from desispec.io.util import header2wave
+                wave = header2wave(hdr)
+                meta = Table(fx[1].data)
+            elif format_version == 2:
+                flux = fx['SDSS_EIGEN'].data.copy()
+                wave = fx['SDSS_EIGEN_WAVE'].data.copy()
+                meta = Table([np.arange(flux.shape[0]),], names=['PCAVEC',])
+            else:
+                raise IOError('Unknown QSO basis template format version {}'.format(format_version))
     else:
         flux, hdr = fits.getdata(infile, 0, header=True)
         meta = Table(fits.getdata(infile, 1))
         wave = fits.getdata(infile, 2)
 
         if (objtype.upper() == 'WD') and (subtype != ''):
+            if 'WDTYPE' not in meta.colnames:
+                raise RuntimeError('Please upgrade to basis_templates >=2.3 to get WDTYPE support')
+
             keep = np.where(meta['WDTYPE'] == subtype.upper())[0]
             if len(keep) == 0:
                 log.warning('Unrecognized white dwarf subtype {}!'.format(subtype))

py/desisim/lya_spectra.py

@@ -51,7 +51,7 @@ def get_spectra(lyafile, nqso=None, wave=None, templateid=None, normfilter='sdss
             nqso = len(h)-1
         templateid = np.arange(nqso)
     else:
-        templateid = np.array(templateid)
+        templateid = np.asarray(templateid)
         nqso = len(templateid)
 
     if rand is None:

py/desisim/pixsim.py

@@ -266,7 +266,7 @@ def xyslice2header(xyslice):
 
     if preproc:
         log.debug('Running preprocessing at {}'.format(asctime()))
-        image = desispec.preproc.preproc(rawpix, header)
+        image = desispec.preproc.preproc(rawpix, header, primary_header=simspec.header)
     else:
         log.debug('Skipping preprocessing')
         image = Image(np.zeros(rawpix.shape), np.zeros(rawpix.shape), meta=header)
@@ -346,6 +346,9 @@ def _project(args):
     try:
         psf, wave, phot, specmin = args
         nspec = phot.shape[0]
+        if phot.shape[-1] != wave.shape[-1]:
+            raise ValueError('phot.shape {} vs. wave.shape {} mismatch'.format(phot.shape, wave.shape))
+
         xyrange = psf.xyrange( [specmin, specmin+nspec], wave )
         img = psf.project(wave, phot, specmin=specmin, xyrange=xyrange)
         return (xyrange, img)
@@ -356,6 +359,7 @@ def _project(args):
             print('ERROR in _project', psf.wmin, psf.wmax, wave[0], wave[-1], phot.shape, specmin)
             traceback.print_exc()
             print('-'*60)
+
         raise e
 
 #- Move this into specter itself?

py/desisim/test/test_lya.py

@@ -34,6 +34,8 @@ def test_read_lya(self):
         self.assertEqual(flux.shape[0], self.nspec)
         self.assertEqual(wave.shape[0], flux.shape[1])
         self.assertEqual(len(meta), self.nspec)
+        templateid = [0,1,2]
+        nqso = len(templateid)
 
         flux, wave, meta = lya_spectra.get_spectra(self.infile, templateid=templateid,
                                                    wave=self.wave, seed=self.seed)