Merge remote-tracking branch 'origin/main' into dev/kbs

.github/workflows/draft-pdf.yml

@@ -0,0 +1,24 @@
+name: "Build JOSS Paper Draft"
+on: [push]
+
+jobs:
+  paper:
+    runs-on: ubuntu-latest
+    name: Paper Draft
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+      - name: Build draft PDF
+        uses: openjournals/openjournals-draft-action@master
+        with:
+          journal: joss
+          # This should be the path to the paper within your repo.
+          paper-path: joss/paper.md
+      - name: Upload
+        uses: actions/upload-artifact@v1
+        with:
+          name: paper
+          # This is the output path where Pandoc will write the compiled
+          # PDF. Note, this should be the same directory as the input
+          # paper.md
+          path: joss/paper.pdf

demos/HST/S3_wfc3_template.ecf

@@ -62,8 +62,8 @@ save_output     True        # Save outputs for use in S4
 verbose         True        # If True, more details will be printed about steps
 
 # Project directory
-topdir          /home/User/
+topdir          /home/User/Data/TargetName/WFC3/
 
 # Directories relative to project dir
-inputdir        /Data/TargetName/WFC3/IMA # The folder containing the data files from HST
-outputdir       /Data/TargetName/WFC3/Stage3
+inputdir        IMA # The folder containing the data files from HST
+outputdir       Stage3

demos/HST/S4_wfc3_template.ecf

@@ -54,8 +54,8 @@ hide_plots      False   # If True, plots will automatically be closed rather tha
 verbose         False   # If True, more details will be printed about steps
 
 # Project directory
-topdir          /home/User
+topdir          /home/User/Data/TargetName/WFC3/
 
 # Directories relative to project dir
-inputdir        /Data/TargetName/WFC3/Stage3 # The folder containing the outputs from Eureka!'s S3 (will be overwritten if calling S3 and S4 sequentially)
-outputdir       /Data/TargetName/WFC3/Stage4
+inputdir        Stage3 # The folder containing the outputs from Eureka!'s S3 (will be overwritten if calling S3 and S4 sequentially)
+outputdir       Stage4

demos/HST/S5_wfc3_template.ecf

@@ -52,8 +52,8 @@ testing_model   False         # Boolean, set True to only inject a model source
 hide_plots      False         # If True, plots will automatically be closed rather than popping up
 
 # Project directory
-topdir          /home/User
+topdir          /home/User/Data/TargetName/WFC3/
 
 # Directories relative to project dir
-inputdir        /Data/TargetName/WFC3/Stage4    # The folder containing the outputs from Eureka!'s S4 pipeline (will be overwritten if calling S4 and S5 sequentially)
-outputdir       /Data/TargetName/WFC3/Stage5
+inputdir        Stage4    # The folder containing the outputs from Eureka!'s S4 pipeline (will be overwritten if calling S4 and S5 sequentially)
+outputdir       Stage5

demos/HST/S6_wfc3_template.ecf

@@ -29,7 +29,7 @@ testing_S6      False
 hide_plots      False # If True, plots will automatically be closed rather than popping up
 
 # Project directory
-topdir          /home/User/
+topdir          /home/User/Data/TargetName/WFC3/
 
 # Model to plot as well (path relative to project dir of a csv with col 1 as wavelength in microns, col 2 in the same units as the plotted spectrum, any headers preceded by a #)
 model_spectrum  None # Set to None if no model should be plotted
@@ -39,5 +39,5 @@ model_y_scalar  1 # Indicate whether model y-values have already been scaled (e.
 model_delimiter None #Delimiter between columns. Typical options: None (for space), ',' for comma
 
 # Directories relative to project dir
-inputdir        /Data/TargetName/WFC3/Stage5    # The folder containing the outputs from Eureka!'s S5 pipeline (will be overwritten if calling S5 and S6 sequentially)
-outputdir       /Data/TargetName/WFC3/Stage6
+inputdir        Stage5    # The folder containing the outputs from Eureka!'s S5 pipeline (will be overwritten if calling S5 and S6 sequentially)
+outputdir       Stage6

demos/HST/run_eureka_wfc3.py

@@ -1,6 +1,4 @@
-import sys
 import os
-sys.path.append(f'..{os.sep}..{os.sep}')
 import eureka.lib.plots
 import eureka.S3_data_reduction.s3_reduce as s3
 import eureka.S4_generate_lightcurves.s4_genLC as s4

demos/JWST/S1_miri_template.ecf

@@ -27,11 +27,11 @@ skip_gain_scale     False
 jump_rejection_threshold  4.0 #float, default is 4.0, CR sigma rejection threshold
 
 # Project directory
-topdir              /home/User
+topdir              /home/User/Data/JWST-Sim/MIRI/
 
 # Directories relative to topdir
-inputdir            /Data/JWST-Sim/MIRI/Uncalibrated
-outputdir           /Data/JWST-Sim/MIRI/Stage1
+inputdir            Uncalibrated
+outputdir           Stage1
 
 # Diagnostics
 testing_S1          False

demos/JWST/S1_nirx_template.ecf

@@ -26,11 +26,11 @@ skip_gain_scale     False
 jump_rejection_threshold  4.0 #float, default is 4.0, CR sigma rejection threshold
 
 # Project directory
-topdir              /home/User
+topdir              /home/User/Data/JWST-Sim/NIRSpec/
 
 # Directories relative to topdir
-inputdir            /Data/JWST-Sim/NIRSpec/Uncalibrated
-outputdir           /Data/JWST-Sim/NIRSpec/Stage1
+inputdir            Uncalibrated
+outputdir           Stage1
 
 # Diagnostics
 testing_S1          False

demos/JWST/S2_imaging_template.ecf

@@ -15,8 +15,8 @@ testing_S2          False
 hide_plots          False   # If True, plots will automatically be closed rather than popping up
 
 # Project directory
-topdir              /home/User/
+topdir              /home/User/Data/JWST-Sim/NIRCam/
 
 # Directories relative to topdir
-inputdir            /Data/JWST-Sim/MIRI/Stage1
-outputdir           /Data/JWST-Sim/MIRI/Stage2
+inputdir            Stage1
+outputdir           Stage2

demos/JWST/S2_miri_lrs_template.ecf

@@ -35,8 +35,8 @@ testing_S2              False
 hide_plots              False   # If True, plots will automatically be closed rather than popping up
 
 # Project directory
-topdir                  /home/User/
+topdir                  /home/User/Data/JWST-Sim/MIRI/
 
 # Directories relative to topdir
-inputdir                /Data/JWST-Sim/MIRI/Stage1
-outputdir               /Data/JWST-Sim/MIRI/Stage2
+inputdir                Stage1
+outputdir               Stage2

demos/JWST/S2_nircam_wfss_template.ecf

@@ -35,8 +35,8 @@ testing_S2              False
 hide_plots              False   # If True, plots will automatically be closed rather than popping up
 
 # Project directory
-topdir                  /home/User/
+topdir                  /home/User/Data/JWST-Sim/NIRCam/
 
 # Directories relative to topdir
-inputdir                /Data/JWST-Sim/NIRCam/Stage1
-outputdir               /Data/JWST-Sim/NIRCam/Stage2
+inputdir                Stage1
+outputdir               Stage2

demos/JWST/S2_nirspec_fs_template.ecf

@@ -35,8 +35,8 @@ testing_S2              False
 hide_plots              False   # If True, plots will automatically be closed rather than popping up
 
 # Project directory
-topdir                  /home/User/
+topdir                  /home/User/Data/JWST-Sim/NIRSpec/
 
 # Directories relative to topdir
-inputdir                /Data/JWST-Sim/NIRSpec/Stage1
-outputdir               /Data/JWST-Sim/NIRSpec/Stage2
+inputdir                Stage1
+outputdir               Stage2

demos/JWST/S3_miri_lrs_template.ecf

@@ -41,8 +41,8 @@ save_output     True        # Save outputs for use in S4
 verbose         True        # If True, more details will be printed about steps
 
 # Project directory
-topdir          /home/User/
+topdir          /home/User/Data/JWST-Sim/MIRI/
 
 # Directories relative to topdir
-inputdir        /Data/JWST-Sim/MIRI/Stage2/   # The folder containing the outputs from Eureka!'s S2 or JWST's S2 pipeline (will be overwritten if calling S2 and S3 sequentially)
-outputdir       /Data/JWST-Sim/MIRI/Stage3/
+inputdir        Stage2   # The folder containing the outputs from Eureka!'s S2 or JWST's S2 pipeline (will be overwritten if calling S2 and S3 sequentially)
+outputdir       Stage3

demos/JWST/S3_nircam_photometry_template.ecf

@@ -36,8 +36,8 @@ save_output     True        # Save outputs for use in S4
 verbose         True        # If True, more details will be printed about steps
 
 # Project directory
-topdir          /home/User/
+topdir          /home/User/Data/JWST-Sim/NIRCam/
 
 # Directories relative to topdir
-inputdir        /Data/JWST-Sim/NIRCam/Stage2/   # The folder containing the outputs from Eureka!'s S2 or JWST's S2 pipeline (will be overwritten if calling S2 and S3 sequentially)
-outputdir       /Data/JWST-Sim/NIRCam/Stage3/
+inputdir        Stage2   # The folder containing the outputs from Eureka!'s S2 or JWST's S2 pipeline (will be overwritten if calling S2 and S3 sequentially)
+outputdir       Stage3

demos/JWST/S3_nircam_wfss_template.ecf

@@ -40,8 +40,8 @@ save_output     True        # Save outputs for use in S4
 verbose         True        # If True, more details will be printed about steps
 
 # Project directory
-topdir          /home/User/
+topdir          /home/User/Data/JWST-Sim/NIRCam/
 
 # Directories relative to topdir
-inputdir        /Data/JWST-Sim/NIRCam/Stage2/   # The folder containing the outputs from Eureka!'s S2 or JWST's S2 pipeline (will be overwritten if calling S2 and S3 sequentially)
-outputdir       /Data/JWST-Sim/NIRCam/Stage3/
+inputdir        Stage2   # The folder containing the outputs from Eureka!'s S2 or JWST's S2 pipeline (will be overwritten if calling S2 and S3 sequentially)
+outputdir       Stage3

demos/JWST/S3_nirspec_fs_template.ecf

@@ -44,8 +44,8 @@ save_output     True        # Save outputs for use in S4
 verbose         True        # If True, more details will be printed about steps
 
 # Project directory
-topdir          /home/User/
+topdir          /home/User/Data/JWST-Sim/NIRSpec/
 
 # Directories relative to topdir
-inputdir        /Data/JWST-Sim/NIRSpec/Stage2/   # The folder containing the outputs from Eureka!'s S2 or JWST's S2 pipeline (will be overwritten if calling S2 and S3 sequentially)
-outputdir       /Data/JWST-Sim/NIRSpec/Stage3/
+inputdir        Stage2   # The folder containing the outputs from Eureka!'s S2 or JWST's S2 pipeline (will be overwritten if calling S2 and S3 sequentially)
+outputdir       Stage3

demos/JWST/S4_template.ecf

@@ -49,8 +49,8 @@ hide_plots      False   # If True, plots will automatically be closed rather tha
 verbose         True    # If True, more details will be printed about steps
 
 # Project directory
-topdir          /home/User
+topdir          /home/User/Data/JWST-Sim/NIRSpec/
 
 # Directories relative to topdir
-inputdir        /Data/JWST-Sim/NIRSpec/Stage3    # The folder containing the outputs from Eureka!'s S3 or JWST's S3 pipeline (will be overwritten if calling S3 and S4 sequentially)
-outputdir       /Data/JWST-Sim/NIRSpec/Stage4
+inputdir        Stage3    # The folder containing the outputs from Eureka!'s S3 or JWST's S3 pipeline (will be overwritten if calling S3 and S4 sequentially)
+outputdir       Stage4

demos/JWST/S5_template.ecf

@@ -57,8 +57,8 @@ testing_model   False   # Boolean, set True to only inject a model source of sys
 hide_plots      False   # If True, plots will automatically be closed rather than popping up
 
 # Project directory
-topdir          /home/User
+topdir          /home/User/Data/JWST-Sim/NIRSpec/
 
 # Directories relative to topdir
-inputdir        /Data/JWST-Sim/NIRSpec/Stage4/   # The folder containing the outputs from Eureka!'s S4 pipeline (will be overwritten if calling S4 and S5 sequentially)
-outputdir       /Data/JWST-Sim/NIRSpec/Stage5/
+inputdir        Stage4   # The folder containing the outputs from Eureka!'s S4 pipeline (will be overwritten if calling S4 and S5 sequentially)
+outputdir       Stage5

demos/JWST/S6_template.ecf

@@ -28,7 +28,7 @@ isplots_S6      5      # Generate few (1), some (3), or many (5) figures (Option
 hide_plots      False  # If True, plots will automatically be closed rather than popping up
 
 # Project directory
-topdir          /home/User/
+topdir          /home/User/Data/JWST-Sim/NIRSpec/
 
 # Model to plot underneath the fitted data points
 model_spectrum  None   # Path to the model spectrum relative to topdir. Set to None if no model should be plotted.
@@ -39,5 +39,5 @@ model_zorder    0      # The zorder of the model on the plot (0 for beneath the
 model_delimiter None   # Delimiter between columns. Typical options: None (for space), ',' for comma
 
 # Directories relative to topdir
-inputdir        /Data/JWST-Sim/NIRSpec/Stage5/   # The folder containing the outputs from Eureka!'s S5 pipeline (will be overwritten if calling S5 and S6 sequentially)
-outputdir       /Data/JWST-Sim/NIRSpec/Stage6/
+inputdir        Stage5   # The folder containing the outputs from Eureka!'s S5 pipeline (will be overwritten if calling S5 and S6 sequentially)
+outputdir       Stage6

demos/JWST/run_eureka.py

@@ -1,6 +1,4 @@
-import sys
 import os
-sys.path.insert(0, f'..{os.sep}..{os.sep}')
 import eureka.lib.plots
 import eureka.S1_detector_processing.s1_process as s1
 import eureka.S2_calibrations.s2_calibrate as s2

demos/README

@@ -0,0 +1,4 @@
+If you have come across this folder without first looking at the Eureka
+documentation or quickstart, please first visit
+https://eurekadocs.readthedocs.io/en/latest/quickstart.html for information on
+the files contained in this folder.

docs/media/S1_template.ecf

@@ -26,11 +26,11 @@ skip_gain_scale     False
 jump_rejection_threshold  4.0 #float, default is 4.0, CR sigma rejection threshold
 
 # Project directory
-topdir              /home/User
+topdir              /home/User/Data/JWST-Sim/NIRSpec/
 
 # Directories relative to topdir
-inputdir            /Data/JWST-Sim/NIRSpec/Uncalibrated
-outputdir           /Data/JWST-Sim/NIRSpec/Stage1
+inputdir            Uncalibrated
+outputdir           Stage1
 
 # Diagnostics
 testing_S1          False

docs/media/S2_template.ecf

@@ -35,8 +35,8 @@ testing_S2              False
 hide_plots              False   # If True, plots will automatically be closed rather than popping up
 
 # Project directory
-topdir                  /home/User/
+topdir                  /home/User/Data/JWST-Sim/NIRSpec/
 
 # Directories relative to topdir
-inputdir                /Data/JWST-Sim/NIRSpec/Stage1
-outputdir               /Data/JWST-Sim/NIRSpec/Stage2
+inputdir                Stage1
+outputdir               Stage2

docs/media/S3_template.ecf

@@ -44,8 +44,8 @@ save_output     True        # Save outputs for use in S4
 verbose         True        # If True, more details will be printed about steps
 
 # Project directory
-topdir          /home/User/
+topdir          /home/User/Data/JWST-Sim/NIRSpec/
 
 # Directories relative to topdir
-inputdir        /Data/JWST-Sim/NIRSpec/Stage2/   # The folder containing the outputs from Eureka!'s S2 or JWST's S2 pipeline (will be overwritten if calling S2 and S3 sequentially)
-outputdir       /Data/JWST-Sim/NIRSpec/Stage3/
+inputdir        Stage2   # The folder containing the outputs from Eureka!'s S2 or JWST's S2 pipeline (will be overwritten if calling S2 and S3 sequentially)
+outputdir       Stage3

docs/media/S4_template.ecf

@@ -49,8 +49,8 @@ hide_plots      False   # If True, plots will automatically be closed rather tha
 verbose         True    # If True, more details will be printed about steps
 
 # Project directory
-topdir          /home/User
+topdir          /home/User/Data/JWST-Sim/NIRSpec/
 
 # Directories relative to topdir
-inputdir        /Data/JWST-Sim/NIRSpec/Stage3    # The folder containing the outputs from Eureka!'s S3 or JWST's S3 pipeline (will be overwritten if calling S3 and S4 sequentially)
-outputdir       /Data/JWST-Sim/NIRSpec/Stage4
+inputdir        Stage3    # The folder containing the outputs from Eureka!'s S3 or JWST's S3 pipeline (will be overwritten if calling S3 and S4 sequentially)
+outputdir       Stage4

docs/media/S5_template.ecf

@@ -58,8 +58,8 @@ testing_model   False   # Boolean, set True to only inject a model source of sys
 hide_plots      False   # If True, plots will automatically be closed rather than popping up
 
 # Project directory
-topdir          /home/User
+topdir          /home/User/Data/JWST-Sim/NIRSpec/
 
 # Directories relative to topdir
-inputdir        /Data/JWST-Sim/NIRSpec/Stage4/   # The folder containing the outputs from Eureka!'s S4 pipeline (will be overwritten if calling S4 and S5 sequentially)
-outputdir       /Data/JWST-Sim/NIRSpec/Stage5/
+inputdir        Stage4   # The folder containing the outputs from Eureka!'s S4 pipeline (will be overwritten if calling S4 and S5 sequentially)
+outputdir       Stage5

docs/media/S6_template.ecf

@@ -28,7 +28,7 @@ isplots_S6      5      # Generate few (1), some (3), or many (5) figures (Option
 hide_plots      False  # If True, plots will automatically be closed rather than popping up
 
 # Project directory
-topdir          /home/User/
+topdir          /home/User/Data/JWST-Sim/NIRSpec/
 
 # Model to plot underneath the fitted data points
 model_spectrum  None   # Path to the model spectrum relative to topdir. Set to None if no model should be plotted.
@@ -39,5 +39,5 @@ model_zorder    0      # The zorder of the model on the plot (0 for beneath the
 model_delimiter None   # Delimiter between columns. Typical options: None (for space), ',' for comma
 
 # Directories relative to topdir
-inputdir        /Data/JWST-Sim/NIRSpec/Stage5/   # The folder containing the outputs from Eureka!'s S5 pipeline (will be overwritten if calling S5 and S6 sequentially)
-outputdir       /Data/JWST-Sim/NIRSpec/Stage6/
+inputdir        Stage5   # The folder containing the outputs from Eureka!'s S5 pipeline (will be overwritten if calling S5 and S6 sequentially)
+outputdir       Stage6

docs/source/ecf.rst

@@ -172,6 +172,10 @@ photometry
 ''''''''''
 Only used for photometry analyses. Set to True if the user wants to analyze a photometric dataset.
 
+poly_wavelength
+'''''''''''''''
+If True, use an updated polynomial wavelength solution for NIRCam longwave spectroscopy instead of the linear wavelength solution currently assumed by STScI.
+
 hst_cal
 '''''''
 Only used for HST analyses. The fully qualified path to the folder containing HST calibration files.
@@ -367,7 +371,7 @@ Sets how many plots should be saved when running Stage 3. A full description of
 
 nplots
 ''''''
-Sets how many integrations will be used for per-integration figures (Figs 3301, 3302, 3303, 3501). Useful for in-depth diagnoses of a few integrations without making thousands of figures. If set to None, a plot will be made for every integration.
+Sets how many integrations will be used for per-integration figures (Figs 3301, 3302, 3303, 3307, 3501, 3505). Useful for in-depth diagnoses of a few integrations without making thousands of figures. If set to None, a plot will be made for every integration.
 
 vmin
 ''''