Merge pull request #705 from kevin218/tjb_working

Minor bug patches before v1.0

demos/JWST/S3_miri_photometry_template.ecf

@@ -26,7 +26,6 @@ interp_method   linear      # Interpolate bad pixels. Options: None (if no inter
 ctr_guess       [698, 516]  # Initial guess of centroid position. If None, will first perform centroiding on whole frame (can sometimes fail)
 ctr_cutout_size 10          # Cutoff size all around the centroid after the coarse centroid calculation or first centroid guess when using the mgmc method.
 centroid_method mgmc        # Method used for centroiding. Options: mgmc, fgc
-oneoverf_corr   None        # Options: None, meanerr, median
 skip_apphot_bg  False       # Skips the background subtraction during the aperture photometry step
 photap          5           # Size of photometry aperture in pixels
 skyin           12          # Inner sky annulus edge, in pixels

demos/JWST/S3_nircam_wfss_template.ecf

@@ -16,7 +16,8 @@ ywindow         [5,64]      # Vertical axis as seen in DS9
 xwindow         [100,1700]  # Horizontal axis as seen in DS9
 src_pos_type    gaussian    # Determine source position when not given in header (Options: header, gaussian, weighted, max, hst, or a numeric value)
 record_ypos     True        # Option to record the y position and width for each integration (only records if src_pos_type is gaussian)
-dqmask          False       # Mask pixels with an odd entry in the DQ array
+poly_wavelength	True		# Use an updated polynomial wavelength solution for NIRCam longwave spectroscopy instead of the linear wavelength solution currently assumed by STScI
+dqmask          True        # Mask pixels with an odd entry in the DQ array
 expand          1           # Super-sampling factor along cross-dispersion direction
 
 # Outlier rejection along time axis

environment.yml

@@ -37,7 +37,7 @@ dependencies:
     - pip:
         - astraeus@git+https://github.com/kevin218/Astraeus@main
         - celerite2 # Needed for GP
-        - crds
+        - crds<12 # Upper limit needed to avoid bugs with crds.get_context_name
         - exotic-ld==3.2.0 # Lower limit needed for updated JWST sensitivity files, upper limit needed for breaking changes
         - fleck
         - image_registration@git+https://github.com/keflavich/image_registration@master # Need GitHub version to avoid np.float issue

environment_pymc3.yml

@@ -40,7 +40,7 @@ dependencies:
         - arviz==0.12.1
         - astraeus@git+https://github.com/kevin218/Astraeus@main
         - celerite2 # Needed for GP
-        - crds
+        - crds<12 # Upper limit needed to avoid bugs with crds.get_context_name
         - exoplanet
         - exoplanet-core
         - exotic-ld==3.2.0 # Lower limit needed for updated JWST sensitivity files, upper limit needed for breaking changes

setup.cfg

@@ -32,7 +32,7 @@ install_requires =
     ccdproc
     celerite2 # Needed for GP
     corner
-    crds
+    crds<12 # Upper limit needed to avoid bugs with crds.get_context_name
     dynesty>1.0 # Lower limit needed for specific arguments
     emcee>3.0.0 # Lower limit needed for specific arguments
     exotic-ld==3.2.0 # Lower limit needed for updated JWST sensitivity files, upper limit needed for breaking changes

src/eureka/S1_detector_processing/group_level.py

@@ -185,8 +185,8 @@ def custom_ref_pixel(input_model, log, meta):
     for nint in range(all_data.shape[0]):
         for ngrp in range(all_data.shape[1]):
             intgrp_data = all_data[nint, ngrp, :, :]
-            dqmask = np.where((dq[nint, ngrp, :, :] % 2 == 1) |
-                              (dq[nint, ngrp, :, :] == 2))
+            dqmask = ((dq[nint, ngrp, :, :] % 2 == 1) |
+                      (dq[nint, ngrp, :, :] == 2))
             intgrp_data = np.ma.masked_where(dqmask, intgrp_data)
 
             if meta.masktrace:

src/eureka/S3_data_reduction/plots_s3.py

@@ -836,7 +836,7 @@ def phot_npix(data, meta):
         plt.pause(0.2)
 
 
-def phot_centroid_fgc(img, x, y, sx, sy, i, m, meta):
+def phot_centroid_fgc(img, mask, x, y, sx, sy, i, m, meta):
     """
     Plot of the gaussian fit to the centroid cutout. (Fig 3503)
 
@@ -845,6 +845,9 @@ def phot_centroid_fgc(img, x, y, sx, sy, i, m, meta):
     img : 2D numpy array
         Cutout of the center of the target which is used to determine the
         centroid position.
+    mask: 2D numpy array
+        A False indicates the corresponding element of Data is good, a
+        True indicates it is bad, same shape as data.
     x : float
         Centroid position in x direction.
     y : float
@@ -870,6 +873,9 @@ def phot_centroid_fgc(img, x, y, sx, sy, i, m, meta):
         Cleaned up plot &
         corrected plotting feature
     """
+    img = np.ma.copy(img)
+    img = np.ma.masked_where(mask, img)
+
     plt.figure(3503)
     plt.clf()
     fig, ax = plt.subplots(2, 2, num=3503, figsize=(8, 8))

src/eureka/S6_planet_spectra/s6_spectra.py

@@ -281,17 +281,18 @@ def plot_spectra(eventlabel, ecf_path=None, s5_meta=None, input_meta=None):
                         # Phase Curve Amplitude, first order
                         suffix = planetSuffix+channelSuffix
                         meta.y_label = 'Phase Curve Amplitude'+suffix
-                    elif meta.y_param_basic == 'pc_offset2':
-                        # Phase Curve Offset, second order
+                    elif meta.y_param_basic[:12] == 'offset_order':
+                        # Phase Curve Offset, nth order
                         suffix = planetSuffix+channelSuffix
-                        meta.y_label = 'Second Order Phase Curve Offset'+suffix
+                        meta.y_label = (f'Order {meta.y_param_basic[12:]}\n' +
+                                        'Phase Curve Offset' + suffix)
                         if meta.y_label_unit is None:
                             meta.y_label_unit = '($^{\\circ}$E)'
-                    elif meta.y_param_basic == 'pc_amp2':
-                        # Phase Curve Amplitude, second order
+                    elif meta.y_param_basic[:9] == 'amp_order':
+                        # Phase Curve Amplitude, nth order
                         suffix = planetSuffix+channelSuffix
-                        meta.y_label = ('Second Order Phase Curve Amplitude' +
-                                        suffix)
+                        meta.y_label = (f'Order {meta.y_param_basic[9:]}\n' +
+                                        'Phase Curve Amplitude' + suffix)
                     elif meta.y_param_basic in [f'u{i}' for i in range(1, 5)]:
                         # Limb darkening parameter
                         suffix = channelSuffix

src/eureka/lib/centerdriver.py

@@ -114,7 +114,7 @@ def centerdriver(method, data, guess, trim, radius, size, i, m, meta,
 
     # only plot when we do the second fit
     if (meta.isplots_S3 >= 5 and method[-4:] == '_sec' and i < meta.nplots):
-        plots_s3.phot_centroid_fgc(img, x, y, sx, sy, i, m, meta)
+        plots_s3.phot_centroid_fgc(img, msk, x, y, sx, sy, i, m, meta)
 
     # Make trimming correction and return
     return ((y, x) + cen - trim), extra, refrence_median_frame