Merge pull request #715 from kevin218/kbs

Update download script
kevin218 · Nov 6, 2024 · fde2b69 · fde2b69
2 parents 9de59a3 + 64a056d
commit fde2b69
Show file tree

Hide file tree

Showing 4 changed files with 7 additions and 16 deletions.
diff --git a/src/eureka/S3_data_reduction/nirspec.py b/src/eureka/S3_data_reduction/nirspec.py
@@ -7,7 +7,7 @@
 
 
 def read(filename, data, meta, log):
-    '''Reads single FITS file from JWST's NIRCam instrument.
+    '''Reads single FITS file from JWST's NIRSpec instrument.
 
     Parameters
     ----------
@@ -29,16 +29,6 @@ def read(filename, data, meta, log):
     log : logedit.Logedit
         The current log.
 
-    Notes
-    -----
-    History:
-
-    - November 2012 Kevin Stevenson
-        Initial version
-    - June 2021 Aarynn Carter/Eva-Maria Ahrer
-        Updated for NIRSpec
-    - Apr 22, 2022 Kevin Stevenson
-        Convert to using Xarray Dataset
     '''
     hdulist = fits.open(filename)
 

diff --git a/src/eureka/S3_data_reduction/optspex.py b/src/eureka/S3_data_reduction/optspex.py
@@ -593,9 +593,10 @@ def clean_median_flux(data, meta, log, m):
                     ~np.ma.getmaskarray(medflux[j])]
             goodrow = medflux[j][~np.ma.getmaskarray(outliers[j]) *
                                  ~np.ma.getmaskarray(medflux[j])]
-            f = spi.interp1d(x1, goodrow, 'linear', fill_value='extrapolate')
-            # f = spi.UnivariateSpline(x1, goodmed, k=1, s=None)
-            clean_med[j] = f(xx)
+            if len(goodrow) > 0:
+                f = spi.interp1d(x1, goodrow, 'linear', 
+                                 fill_value='extrapolate')
+                clean_med[j] = f(xx)
 
         # Assign cleaned median frame to data object
         data['medflux'] = (['y', 'x'], clean_med)

diff --git a/src/eureka/S6_planet_spectra/s6_spectra.py b/src/eureka/S6_planet_spectra/s6_spectra.py
@@ -123,7 +123,7 @@ def plot_spectra(eventlabel, ecf_path=None, s5_meta=None, input_meta=None):
             # Copy existing S5 log file and resume log
             meta.s6_logname = meta.outputdir+'S6_'+meta.eventlabel+'.log'
             log = logedit.Logedit(meta.s6_logname, read=meta.s5_logname)
-            log.writelog("\nStarting Stage 6: Light Curve Fitting\n")
+            log.writelog("\nStarting Stage 6: Plot Spectra\n")
             log.writelog(f"Eureka! Version: {meta.version}", mute=True)
             log.writelog(f"Input directory: {meta.inputdir}")
             log.writelog(f"Output directory: {meta.outputdir}")

diff --git a/src/eureka/lib/mastDownload.py b/src/eureka/lib/mastDownload.py
@@ -239,7 +239,7 @@ def filterJWST(proposal_id, observation, visit, calib_level, subgroup):
         calib_level = [calib_level]
     # Specify obsid using wildcards, obs_id can come in two flavours
     obsid = f'jw{proposal_id}{observation}{visit}_04*'
-    obsid2 = f'jw{proposal_id}-o{observation}_t{visit}*'
+    obsid2 = f'jw{proposal_id}-o{observation}_t*'
 
     # Query MAST for requested visit
     sci_table = Observations.query_criteria(proposal_id=proposal_id,