Move STIPS from PYSYNPHOT to synphot/stsynphot

.rtd-environment.yml

@@ -13,9 +13,10 @@ dependencies:
   # Docs
   - sphinx
   - docutils
+  - sphinx_rtd_theme
   - stsci_rtd_theme
 
   - pip:
     # Docs
     - astropy_helpers
-    - sphinx_astropy
+    - sphinx_astropy

.travis.yml

@@ -18,6 +18,9 @@ addons:
 
 env:
     global:
+        # Define Conda Version
+        - MINICONDA_VERSION=py37_4.8.3
+
         # The following versions are the 'default' for tests, unless
         # overridden underneath. They are defined here in order to save having
         # to repeat them for all configurations.
@@ -74,7 +77,7 @@ matrix:
         - name: "Doc Build Test"
           os: linux
           env: SETUP_CMD='build_docs -w'
-               CONDA_DEPENDENCIES=$CONDA_DEPENDENCIES_DOC
+               CONDA_ENVIRONMENT='.rtd-environment.yml'
 
         # Main test
         # ---------------------------
@@ -127,21 +130,23 @@ before_install:
     # download synphot data
     - mkdir $TEST_DATA_PATH/synphot
 
-    - wget -qO- http://ssb.stsci.edu/cdbs/tarfiles/synphot1.tar.gz -O $TEST_DATA_PATH/synphot1.tar.gz
-    - wget -qO- http://ssb.stsci.edu/cdbs/tarfiles/synphot2.tar.gz -O $TEST_DATA_PATH/synphot2.tar.gz
-    - wget -qO- http://ssb.stsci.edu/cdbs/tarfiles/synphot5.tar.gz -O $TEST_DATA_PATH/synphot5.tar.gz
+    - wget -qO- https://ssb.stsci.edu/trds/tarfiles/synphot1.tar.gz -O $TEST_DATA_PATH/synphot1.tar.gz
+    - wget -qO- https://ssb.stsci.edu/trds/tarfiles/synphot2.tar.gz -O $TEST_DATA_PATH/synphot2.tar.gz
+    - wget -qO- https://ssb.stsci.edu/trds/tarfiles/synphot5.tar.gz -O $TEST_DATA_PATH/synphot5.tar.gz
+    - wget -qO- https://ssb.stsci.edu/trds/tarfiles/synphot6.tar.gz -O $TEST_DATA_PATH/synphot6.tar.gz
 
     - tar -xzvf $TEST_DATA_PATH/synphot1.tar.gz -C $TEST_DATA_PATH/synphot/
     - tar -xzvf $TEST_DATA_PATH/synphot2.tar.gz -C $TEST_DATA_PATH/synphot/
     - tar -xzvf $TEST_DATA_PATH/synphot5.tar.gz -C $TEST_DATA_PATH/synphot/
+    - tar -xzvf $TEST_DATA_PATH/synphot6.tar.gz -C $TEST_DATA_PATH/synphot/
 
     - export PYSYN_CDBS=$TEST_DATA_PATH/synphot/grp/hst/cdbs
 
     # download pandeia_data data
-    - wget -qO- https://stsci.box.com/shared/static/5j506xzg9tem2l7ymaqzwqtxne7ts3sr.gz -O $TEST_DATA_PATH/pandeia_data-1.5_wfirst.gz
+    - wget -qO- https://stsci.box.com/shared/static/7voehzi5krrpml5wgyg8bo954ew7arh2.gz -O $TEST_DATA_PATH/pandeia_data-1.5.2rc2_roman.gz
 
-    - tar -xzvf $TEST_DATA_PATH/pandeia_data-1.5_wfirst.gz -C $TEST_DATA_PATH/
-    - export pandeia_refdata=$TEST_DATA_PATH/pandeia_data-1.5_wfirst
+    - tar -xzvf $TEST_DATA_PATH/pandeia_data-1.5.2rc2_roman.gz -C $TEST_DATA_PATH/
+    - export pandeia_refdata=$TEST_DATA_PATH/pandeia_data-1.5.2rc2_roman
 
     # download webbpsf data
     - wget -qO- https://stsci.box.com/shared/static/qcptcokkbx7fgi3c00w2732yezkxzb99.gz -O $TEST_DATA_PATH/webbpsf_data.gz

Dockerfile

@@ -59,14 +59,15 @@ RUN wget -qO- https://stsci.box.com/shared/static/iufbhsiu0lts16wmdsi12cun25888n
 ENV stips_data /opt/stips_data
 
 # Extract PySynphot reference data
-RUN wget -qO- http://ssb.stsci.edu/cdbs/tarfiles/synphot1.tar.gz | tar xvz
-RUN wget -qO- http://ssb.stsci.edu/cdbs/tarfiles/synphot2.tar.gz | tar xvz
-RUN wget -qO- http://ssb.stsci.edu/cdbs/tarfiles/synphot5.tar.gz | tar xvz
+RUN wget -qO- https://ssb.stsci.edu/trds/tarfiles/synphot1.tar.gz | tar xvz
+RUN wget -qO- https://ssb.stsci.edu/trds/tarfiles/synphot2.tar.gz | tar xvz
+RUN wget -qO- https://ssb.stsci.edu/trds/tarfiles/synphot5.tar.gz | tar xvz
+RUN wget -qO- https://ssb.stsci.edu/trds/tarfiles/synphot6.tar.gz | tar xvz
 ENV PYSYN_CDBS /opt/grp/hst/cdbs
 
 # Extract Pandeia reference data
-RUN wget -qO- https://stsci.box.com/shared/static/5j506xzg9tem2l7ymaqzwqtxne7ts3sr.gz | tar -xvz
-ENV pandeia_refdata /opt/pandeia_data-1.5_wfirst
+RUN wget -qO- https://stsci.box.com/shared/static/7voehzi5krrpml5wgyg8bo954ew7arh2.gz | tar -xvz
+ENV pandeia_refdata /opt/pandeia_data-1.5.2rc2_roman
 
 # Extract WebbPSF reference data
 # (note: version number env vars are declared close to where they are used

README.md

@@ -1,3 +1,5 @@
+|Travis Status| |PyPI Status|
+
 # STScI-STIPS
 
 For documentation and installation instructions please visit https://stsci-stips.readthedocs.io

docs/installation.rst

@@ -23,9 +23,9 @@ STIPS Requirements
 * `numpy`: STIPS uses numpy extensively for almost everything that it does.
 * `photutils`: STIPS uses photutils to determine the flux inside the half-light radius
   in generated Sersic profiles.
-* `pysynphot`: STIPS uses pysynphot to generate bandpasses, count rates, and
-  zero points. Note that pysynphot's data files (also known as the CDBS data tree) must also be
-  installed and available as indicated in pysynphot's documentation.
+* `synphot` and `stsynphot`: STIPS uses synphot and stsynphot to generate 
+  bandpasses, count rates, and zero points. Note that the reference data must
+  also be downloaded, as described below in "Doanloading Required Data".
 * `scipy`: STIPS uses scipy to manipulate its internal images (zoom and rotate).
 
 Finally, STIPS requires a set of data files whose location is marked by setting the environment
@@ -99,10 +99,11 @@ You will need to download the data and add them to your environmental path
 
 2. `cd` into a directory you would like to store the data in and run the following commands::
 
-    # PySynphot reference data
-    wget -qO- http://ssb.stsci.edu/cdbs/tarfiles/synphot1.tar.gz | tar xvz
-    wget -qO- http://ssb.stsci.edu/cdbs/tarfiles/synphot2.tar.gz | tar xvz
-    wget -qO- http://ssb.stsci.edu/cdbs/tarfiles/synphot5.tar.gz | tar xvz
+    # Synphot and STSynphot reference data
+    wget -qO- https://ssb.stsci.edu/trds/tarfiles/synphot1.tar.gz | tar xvz
+    wget -qO- https://ssb.stsci.edu/trds/tarfiles/synphot2.tar.gz | tar xvz
+    wget -qO- https://ssb.stsci.edu/trds/tarfiles/synphot5.tar.gz | tar xvz
+    wget -qO- https://ssb.stsci.edu/trds/tarfiles/synphot6.tar.gz | tar xvz
 
 
     # Pandeia reference data
@@ -115,9 +116,9 @@ You will need to download the data and add them to your environmental path
 
     export WEBBPSF_PATH=/<path_to_data_dir>/webbpsf-data
     export PYSYN_CDBS=/<path_to_data_dir>/grp/hst/cdbs
-    export pandeia_refdata=/<path_to_data_dir>/pandeia_data-x.x_wfirst
+    export pandeia_refdata=/<path_to_data_dir>/pandeia_data-x.x.x_roman
 
-Make sure that you have the correct version number for `pandeia_refdata` (replace the "x.x").
+Make sure that you have the correct version number for `pandeia_refdata` (replace the "x.x.x").
 
 .. note::
     The URL we provide in this section and the suggested pandeia reference data directory name

environment.yml

@@ -34,7 +34,8 @@ dependencies:
   - astropy
   - photutils
   - healpy
-  - pysynphot
+  - synphot
+  - stsynphot
   - esutil
 
   # Major modules
@@ -57,7 +58,7 @@ dependencies:
 
   - pip:
     # Major modules
-    - pandeia.engine==1.5
+    - pandeia.engine==1.5.2
     - jwst_backgrounds
 
     # Minor modules

stips/astro_image/astro_image.py

@@ -168,7 +168,7 @@ def __init__(self, **kwargs):
 
 
     def __del__(self):
-        if os.path.exists(self.fname):
+        if hasattr(self, 'fname') and os.path.exists(self.fname):
             os.remove(self.fname)
 
     def copy(self):

stips/data/CreatePhoenixGrid.py

@@ -17,31 +17,15 @@
 sys.path.append(os.path.abspath(os.path.join(os.getcwd(), "..", "..")))
 
 import numpy as np
-import pysynphot as ps
+import synphot as syn
+import stsynphot as stsyn
 from stips.utilities import InstrumentList
 from .. import __version__ as stips_version_info
 from astropy.io import fits as pyfits
+from astropy import units as u
 
 print("STIPS Version: {}".format(stips_version_info))
 
-COMPFILES =  sorted(glob.glob(os.path.join(os.environ["PYSYN_CDBS"],"mtab","*tmc.fits")))
-GRAPHFILES = sorted(glob.glob(os.path.join(os.environ["PYSYN_CDBS"],"mtab","*tmg.fits")))
-THERMFILES = sorted(glob.glob(os.path.join(os.environ["PYSYN_CDBS"],"mtab","*tmt.fits")))
-wfc3_refs = {
-                'comptable': COMPFILES[-1],
-                'graphtable': GRAPHFILES[-1],
-                'thermtable': THERMFILES[-1],
-                'area': 45238.93416,
-                'waveset': (500,26000,10000.,'log')
-            }
-
-area =  {
-            'nircamlong':   253260.0,
-            'nircamshort':  253260.0,
-            'miri':         253260.0,
-            'wfc3ir':       45238.93416,
-            'wfi':          45238.93416
-        }
 modes = {
             'nircamshort':  ['sw_imaging'],
             'nircamlong':   ['lw_imaging'],
@@ -66,6 +50,14 @@
                 'wfc3ir':       {'imaging':     "default"},
                 'wfi':          {'imaging':     "any"}
             }
+area =  {
+            'nircamlong':   253260.0,
+            'nircamshort':  253260.0,
+            'miri':         253260.0,
+            'wfc3ir':       45238.93416,
+            'wfi':          45238.93416
+        }
+
 
 def get_grid_points():
     grid_file = os.path.abspath(os.path.join(os.environ['PYSYN_CDBS'], "grid", "phoenix", "catalog.fits"))
@@ -81,7 +73,7 @@ def get_grid_points():
 
 
 if __name__ == '__main__':
-    norm_bandpass = ps.ObsBandpass('johnson,i')
+    norm_bandpass = syn.SpectralElement.from_filter('johnson_i')
     coords = get_grid_points()
     print(coords)
     bandpasses = {}
@@ -110,23 +102,23 @@ def get_grid_points():
             for k, teff in enumerate(coords[2]):
                 print("\t\t{}: Starting Teff = {}".format(time.ctime(), teff))
                 try:
-                    spec = ps.Icat('phoenix', teff, Z, logg)
+                    spec = stsyn.grid_to_spec('phoenix', teff, Z, logg)
                     counts = False
                     if sum(spec.flux) > 0:
                         counts = True
-                except ps.exceptions.ParameterOutOfBounds:
+                except syn.exceptions.ParameterOutOfBounds:
                     counts = False
                 for l, mag in enumerate(coords[3]):
                     print("\t\t\t{} of {}: {}: Starting Z = {}, log(g) = {}, Teff = {}, Mabs = {:>4}".format(n+1, total, time.ctime(), Z, logg, teff, mag), end='')
                     if counts:
-                        spec_norm = spec.renorm(mag, 'vegamag', norm_bandpass)
+                        norm_value = u.Magnitude(mag)
+                        spec_norm = spec.normalize(norm_value, norm_bandpass)
                     for instrument in instruments:
-                        ps.setref(area=area[instrument.lower()], waveset=(500, 260000, 10000., 'log'))
                         for mode in modes[instrument.lower()]:
                             for filter in filters[instrument.lower()][mode]:
                                 if counts:
-                                    obs = ps.Observation(spec_norm, bandpasses[instrument.lower()][filter], binset=spec_norm.wave)
-                                    result_arrays[instrument.lower()][filter][i,j,k,l] = obs.countrate()
+                                    obs = syn.Observation(spec_norm, bandpasses[instrument.lower()][filter], binset=spec_norm.waveset)
+                                    result_arrays[instrument.lower()][filter][i,j,k,l] = obs.countrate(area[mode])
                                     print(".", end='')
                                 else:
                                     result_arrays[instrument.lower()][filter][i,j,k,l] = 0.