Merge pull request #64 from hover2pi/master

awesimsoss v0.3.2

.travis.yml

@@ -3,9 +3,11 @@
 language: python
 python:
   - 3.6
-  - 3.5
 
 install:
+  - pip install git+https://github.com/astropy/astropy.git@763f069058cb1ee2038fa1cfa485452ec94b726e
+  - pip install git+https://github.com/spacetelescope/[email protected]
+  - pip install git+https://github.com/pypa/twine.git@68dc617bafbc8a32adbe41c12055efe6ba6d0e1e
   - pip install -r requirements_dev.txt
   - pip install -e .
   - pip install pytest pytest-cov coveralls

awesimsoss/awesim.py

@@ -319,8 +319,11 @@ def export(self, outfile, all_data=False):
         outfile: str
             The path of the output file
         """
+        if not outfile.endswith('_uncal.fits'):
+            raise ValueError("Filename must end with '_uncal.fits'")
+
         # Make a RampModel
-        data = self.tso
+        data = copy(self.tso)
         mod = RampModel(data=data, groupdq=np.zeros_like(data), pixeldq=np.zeros((self.nrows, self.ncols)), err=np.zeros_like(data))
         pix = utils.subarray_specs(self.subarray)
 
@@ -767,14 +770,17 @@ def plot_lightcurve(self, column, time_unit='s', resolution_mult=20, draw=True):
                 time = np.linspace(min(self.time), max(self.time), self.ngrps * self.nints * resolution_mult)
                 time = time * q.s.to('d')
 
+                # Generate transit model
                 tmodel = batman.TransitModel(self.tmodel, time)
                 tmodel.rp = self.rp[col]
                 theory = tmodel.light_curve(tmodel)
                 theory *= max(lightcurve) / max(theory)
 
-                time = time * q.d.to(time_unit)
+                # Convert time
+                time = time*q.d.to(time_unit)
 
-                lc.line(time, theory, legend=label + ' model', color=color, alpha=0.8)
+                # Add to figure
+                lc.line(time, theory, legend=label+' model', color=color, alpha=0.8)
 
             # Convert datatime
             data_time = self.time[self.ngrps - 1::self.ngrps].copy()
@@ -794,6 +800,8 @@ def plot_lightcurve(self, column, time_unit='s', resolution_mult=20, draw=True):
     @run_required
     def plot_spectrum(self, frame=0, order=None, noise=False, scale='log', draw=True):
         """
+        Plot a column sum of counts converted to flux density as a function of the mean column wavelength
+
         Parameters
         ----------
         frame: int
@@ -810,14 +818,14 @@ def plot_spectrum(self, frame=0, order=None, noise=False, scale='log', draw=True
         # Get the data cube
         tso = self._select_data(order, noise)
 
-        # Get extracted spectrum (Column sum for now)
+        # Get counts per wavelength (Column sum for now)
         wave = np.mean(self.wave[0], axis=0)
-        flux_out = np.sum(tso[frame].data, axis=0)
-        response = 1. / self.order1_response
+        counts = np.sum(tso[frame].data, axis=0)
+        response = self.order1_response
 
         # Convert response in [mJy/ADU/s] to [Flam/ADU/s] then invert so
         # that we can convert the flux at each wavelegth into [ADU/s]
-        flux_out *= response / self.time[np.mod(self.ngrps, frame)]
+        flux_out = (counts/response/(self.time[np.mod(self.ngrps, frame)]*q.s)).value
 
         # Trim wacky extracted edges
         flux_out[0] = flux_out[-1] = np.nan
@@ -897,9 +905,9 @@ def _reset_psfs(self):
 
                 # Convert response in [mJy/ADU/s] to [Flam/ADU/s] then invert so
                 # that we can convert the flux at each wavelegth into [ADU/s]
-                response = self.frame_time / (response * q.mJy * ac.c / (wave * q.um)**2).to(self.star[1].unit).value
-                flux = np.interp(self.avg_wave[order - 1], self.star[0], self.star[1], left=0, right=0) * response
-                cube = mt.SOSS_psf_cube(filt=self.filter, order=order, subarray=self.subarray) * flux[:, None, None]
+                response = self.frame_time/(response*q.mJy*ac.c/(wave*q.um)**2).to(self.star[1].unit)
+                flux = np.interp(wave, self.star[0].value, self.star[1].value, left=0, right=0)*self.star[1].unit*response
+                cube = mt.SOSS_psf_cube(filt=self.filter, order=order, subarray=self.subarray)*flux[:, None, None]
                 setattr(self, 'order{}_response'.format(order), response)
                 setattr(self, 'order{}_psfs'.format(order), cube)
 
@@ -923,12 +931,12 @@ def _select_data(self, order, noise, reshape=True):
             The selected data
         """
         if order in [1, 2]:
-            tso = getattr(self, 'tso_order{}_ideal'.format(order))
+            tso = copy(getattr(self, 'tso_order{}_ideal'.format(order)))
         else:
             if noise:
-                tso = self.tso
+                tso = copy(self.tso)
             else:
-                tso = self.tso_ideal
+                tso = copy(self.tso_ideal)
 
         # Reshape data
         if reshape:
@@ -1012,9 +1020,10 @@ def simulate(self, ld_coeffs=None, noise=True, model_grid=None, n_jobs=-1, **kwa
             # Set the radius at the given wavelength from the transmission
             # spectrum (Rp/R*)**2... or an array of ones
             if self.planet is not None:
-                tdepth = np.interp(wave, self.planet[0], self.planet[1])
+                tdepth = np.interp(wave, self.planet[0].to(q.um).value, self.planet[1])
             else:
                 tdepth = np.ones_like(wave)
+            tdepth[tdepth < 0] = np.nan
             self.rp = np.sqrt(tdepth)
 
             # Run multiprocessing to generate lightcurves

environment.yml

@@ -1,38 +1,60 @@
+name: awesimsoss
 channels:
   - conda-forge
   - http://ssb.stsci.edu/astroconda
   - defaults
 dependencies:
+  - anaconda-client=1.7.2=py_0
+  - astropy=4.0=py36h0b31af3_1
+  - astroquery=0.4=py_0
+  - bzip2=1.0.8=h01d97ff_1
   - ca-certificates=2019.6.16=hecc5488_0
   - certifi=2019.3.9=py36_0
+  - clyent=1.2.2=py_1
+  - conda=4.7.12=py36_0
+  - conda-build=3.18.11=py36_0
+  - conda-package-handling=1.6.0=py36h01d97ff_0
   - cryptography=2.7=py36h212c5bf_0
   - docutils=0.14=py36_1001
+  - glob2=0.7=py_0
   - healpy=1.11.0=py36_1
   - imageio=2.5.0=py36_0
   - libgcc=4.8.5=hdbeacc1_10
+  - liblief=0.9.0=h2a1bed3_1
   - libsodium=1.0.16=h470a237_1
+  - lz4-c=1.8.3=h6de7cb9_1001
+  - lzo=2.10=h1de35cc_1000
+  - mkl-service=2.3.0=py36h0b31af3_0
+  - mkl_fft=1.1.0=py36h3b54f70_1
+  - mkl_random=1.1.0=py36h86efe34_0
   - nbformat=4.4.0=py_1
   - nbsphinx=0.3.5=py_0
   - openssl=1.1.1b=h01d97ff_2
   - pandoc=2.3.1=0
   - pandocfilters=1.4.2=py_1
   - pip=19.1.1=py36_0
+  - pkginfo=1.5.0.1=py_0
+  - py-lief=0.9.0=py36h6d6d4d2_1
+  - pycosat=0.6.3=py36h0b31af3_1002
+  - python-libarchive-c=2.9=py36_0
+  - ripgrep=11.0.2=h01d97ff_3
+  - ruamel_yaml=0.15.71=py36h1de35cc_1000
   - snowballstemmer=1.2.1=py_1
   - tblib=1.4.0=py_0
   - tk=8.6.8=ha441bb4_0
+  - tqdm=4.36.1=py_0
   - webencodings=0.5.1=py_1
   - alabaster=0.7.12=py36_0
   - appnope=0.1.0=py36hf537a9a_0
   - asn1crypto=0.24.0=py36_0
-  - astropy=3.2.1=py36h1de35cc_0
   - atomicwrites=1.3.0=py36_1
   - attrs=19.1.0=py36_1
   - babel=2.7.0=py_0
   - backcall=0.1.0=py36_0
   - beautifulsoup4=4.7.1=py36_1
   - blas=1.0=mkl
   - bleach=3.1.0=py36_0
-  - bokeh=1.2.0=py36_0
+  - bokeh=1.3.4
   - cffi=1.12.3=py36hb5b8e2f_0
   - chardet=3.0.4=py36_1
   - click=7.0=py36_0
@@ -77,6 +99,7 @@ dependencies:
   - jupyter_core=4.4.0=py36_0
   - keyring=18.0.0=py36_0
   - kiwisolver=1.1.0=py36h0a44026_0
+  - libarchive=3.3.3=h786848e_5
   - libcxx=4.0.1=hcfea43d_1
   - libcxxabi=4.0.1=hcfea43d_1
   - libedit=3.1.20181209=hb402a30_0
@@ -95,18 +118,15 @@ dependencies:
   - matplotlib=3.1.0=py36h54f8f79_0
   - mistune=0.8.4=py36h1de35cc_0
   - mkl=2019.4=233
-  - mkl-service=2.0.2=py36h1de35cc_0
-  - mkl_fft=1.0.12=py36h5e564d8_0
-  - mkl_random=1.0.2=py36h27c97d8_0
   - more-itertools=7.0.0=py36_0
   - mpmath=1.1.0=py36_0
   - msgpack-python=0.6.1=py36h04f5b5a_1
   - nbconvert=5.5.0=py_0
   - ncurses=6.1=h0a44026_1
   - networkx=2.3=py_0
   - notebook=5.7.8=py36_0
-  - numpy=1.16.4=py36hacdab7b_0
-  - numpy-base=1.16.4=py36h6575580_0
+  - numpy=1.18.1=py36h7241aed_0
+  - numpy-base=1.18.1=py36h6575580_1
   - olefile=0.46=py36_0
   - packaging=19.0=py36_0
   - pandas=0.24.2=py36h0a44026_0
@@ -185,7 +205,6 @@ dependencies:
   - zlib=1.2.11=h1de35cc_3
   - zstd=1.3.7=h5bba6e5_0
   - asdf=2.3.3=py36_0
-  - astroquery=0.3.9=py36_0
   - cfitsio=3.440=1
   - crds=7.3.3=py36_0
   - drizzle=1.13=py36_0
@@ -203,30 +222,40 @@ dependencies:
   - stsci.tools=3.4.13=py36_1
   - verhawk=0.0.2=py36_1
   - webbpsf-data=0.8.0=0
+  - namedlist=1.7=py36_1
   - pip:
     - asteval==0.9.14
-    - bibtexparser==1.1.0
+    - awesimsoss==0.3.1
     - batman-package==2.4.6
+    - bibtexparser==1.1.0
+    - dustmaps==1.0.4
     - et-xmlfile==1.0.1
-    - exoctk==0.2.3
     - flask==1.0.3
     - future==0.17.1
+    - hotsoss==0.1.6
     - itsdangerous==1.1.0
     - jdcal==1.4
+    - jwst==0.13.8a0.dev37+g1f2237de
     - jwst-backgrounds==1.1.1
     - jwxml==0.3.0
+    - libarchive-c==2.9
+    - lief==0.9.0
+    - line-profiler==2.1.2
     - llvmlite==0.29.0
     - lmfit==0.9.13
+    - memory-profiler==0.55.0
     - msgpack==0.6.1
-    - namedlist==1.7
     - numba==0.44.1
     - numpydoc==0.8.0
     - openpyxl==2.5.8
     - poppy==0.7.0
+    - progressbar2==3.42.0
+    - pscript==0.7.1
     - pysiaf==0.2.4
+    - python-utils==2.3.0
     - relic==1.1.2
+    - sedkit==0.3.1
     - svo-filters==0.2.19
     - uncertainties==3.1.1
     - webbpsf==0.7.0
     - werkzeug==0.15.4
-    - git+https://github.com/spacetelescope/jwst@1f2237de#egg=jwst

requirements_dev.txt

@@ -6,19 +6,18 @@ flake8==3.6.0
 tox==3.5.3
 coverage==4.5.2
 Sphinx==1.8.2
-twine==1.12.1
+twine==3.1.1
 click==7.0
 
-astropy==3.0.3
+astropy==4.0
 numpy==1.16.1
-bokeh==1.0.4
-svo_filters==0.2.16
+bokeh==1.3.4
+svo_filters==0.2.19
 scipy==1.1.0
-astroquery==0.3.9
-hotsoss==0.1.5
-# webbpsf==0.7.0
+astroquery==0.4
+hotsoss==0.1.6
+webbpsf
 batman-package==2.4.6
-# exoctk
 
 pytest==4.0.0
 pytest-runner==4.2

setup.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.3.1
+current_version = 0.3.2
 commit = True
 tag = True
 

setup.py

@@ -25,9 +25,7 @@
         'Intended Audience :: Developers',
         'License :: OSI Approved :: MIT License',
         'Natural Language :: English',
-        'Programming Language :: Python :: 3.5',
-        'Programming Language :: Python :: 3.6',
-        'Programming Language :: Python :: 3.7',
+        'Programming Language :: Python :: 3.6'
     ],
     description="Advanced Webb Exposure SIMulator for SOSS",
     entry_points={
@@ -47,6 +45,6 @@
     test_suite='tests',
     tests_require=test_requirements,
     url='https://github.com/hover2pi/awesimsoss',
-    version='0.3.1',
+    version='0.3.2',
     zip_safe=False,
 )

tests/test_awesim.py

@@ -97,12 +97,13 @@ def test_add_lines(self):
     def test_export(self):
         """Test the export method"""
         # Make the TSO object and save
-        test_tso = TSO(ngrps=2, nints=2, star=self.star, subarray='SUBSTRIP256')
-        test_tso.simulate()
-        try:
-            test_tso.export('outfile.fits')
-        except NameError:
-            pass
+        test_tso = TestTSO(add_planet=True)
+
+        # Good filename
+        test_tso.export('outfile_uncal.fits')
+
+        # Bad filename (no '_uncal')
+        self.assertRaises(ValueError, test_tso.export, 'outfile.fits')
 
     def test_init(self):
         """Test that the TSO class is generated properly"""