Merge pull request #1818 from pypeit/staged

Merges develop into release (1.16.0 tag prep)
pypeit · Jun 11, 2024 · 8ec2351 · 8ec2351
2 parents c647d02 + e0737fe
commit 8ec2351
Show file tree

Hide file tree

Showing 384 changed files with 49,998 additions and 20,165 deletions.
diff --git a/.gitignore b/.gitignore
@@ -34,7 +34,6 @@ QA/
 # git has its own built in compression methods
 *.7z
 *.dmg
-*.gz
 *.iso
 *.jar
 *.rar

diff --git a/doc/Makefile b/doc/Makefile
@@ -70,6 +70,7 @@ apirst:
 	python ./scripts/build_bitmask_rst.py
 	python ./scripts/build_spectbl_rst.py
 	python ./scripts/make_example_files.py
+	python ./scripts/build_standardstbl_rst.py
 
 html:
 	make apirst

diff --git a/doc/api/pypeit.orderstack.rst b/doc/api/pypeit.orderstack.rst
@@ -0,0 +1,8 @@
+pypeit.orderstack module
+========================
+
+.. automodule:: pypeit.orderstack
+   :members:
+   :private-members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/doc/api/pypeit.rst b/doc/api/pypeit.rst
@@ -45,6 +45,7 @@ Submodules
    pypeit.manual_extract
    pypeit.metadata
    pypeit.onespec
+   pypeit.orderstack
    pypeit.pypeit
    pypeit.pypeitsetup
    pypeit.pypmsgs

diff --git a/doc/api/pypeit.scripts.compile_wvarxiv.rst b/doc/api/pypeit.scripts.compile_wvarxiv.rst
@@ -0,0 +1,8 @@
+pypeit.scripts.compile\_wvarxiv module
+======================================
+
+.. automodule:: pypeit.scripts.compile_wvarxiv
+   :members:
+   :private-members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/doc/api/pypeit.scripts.install_wvarxiv.rst b/doc/api/pypeit.scripts.install_wvarxiv.rst
@@ -0,0 +1,8 @@
+pypeit.scripts.install\_wvarxiv module
+======================================
+
+.. automodule:: pypeit.scripts.install_wvarxiv
+   :members:
+   :private-members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/doc/api/pypeit.scripts.rst b/doc/api/pypeit.scripts.rst
@@ -23,6 +23,7 @@ Submodules
    pypeit.scripts.coadd_datacube
    pypeit.scripts.collate_1d
    pypeit.scripts.compare_sky
+   pypeit.scripts.compile_wvarxiv
    pypeit.scripts.edge_inspector
    pypeit.scripts.flux_calib
    pypeit.scripts.flux_setup
@@ -31,6 +32,7 @@ Submodules
    pypeit.scripts.install_linelist
    pypeit.scripts.install_ql_calibs
    pypeit.scripts.install_telluric
+   pypeit.scripts.install_wvarxiv
    pypeit.scripts.lowrdx_skyspec
    pypeit.scripts.multislit_flexure
    pypeit.scripts.obslog

diff --git a/doc/calibrations/wave_calib.rst b/doc/calibrations/wave_calib.rst
@@ -352,8 +352,37 @@ basics
 Instructions on how to use this GUI are available by pressing
 the '?' key while hovering your mouse over the plotting window.
 You might find it helpful to specify the wavelength range of the
-linelist and the lamps to use using the ``pypeit_identify``
-command-line options.
+linelist and the lamps to use the ``pypeit_identify``
+command-line options.  The full list of identify operations is
+copied below:
+
+   .. code-block:: console
+
+      cursor : Select lines (LMB click)
+               Select regions (LMB drag = add, RMB drag = remove)
+               Navigate (LMB drag = pan, RMB drag = zoom)
+      left   : Advance the line list slider to the left by one
+      right  : Advance the line list slider to the right by one
+      p      : Toggle pan/zoom with the cursor
+      q      : Close Identify window and continue PypeIt reduction
+      a      : Automatically identify lines using current solution
+      c      : Clear automatically identified lines
+      d      : Delete all line identifications (start from scratch)
+      f      : Fit the wavelength solution
+      g      : Toggle ghost solution (show predicted line positions when wavelength is on the x-axis)
+      h      : Reset ghost parameters
+      i      : Include an undetected line to the detected line list
+               First select fitting pixels (LMB drag = add, RMB drag = remove)
+               Then press 'i' to perform a fit.         NOTE: ghost solution must be turned off to select fit regions.
+      l      : Load saved line IDs from file (waveids.ascii in local directory)
+      m      : Select a line
+      r      : Refit a line
+      s      : Save current line IDs to a file
+      w      : Toggle wavelength/pixels on the x-axis of the main panel
+      y      : Toggle the y-axis scale between logarithmic and linear
+      z      : Delete a single line identification
+      +/-    : Raise/Lower the order of the fitting polynomial
+
 
 Here is a standard sequence of moves once the GUI pops up:
 

diff --git a/doc/figures/nirspec/Arc_1dfit_A_0_DET01_S0060.png b/doc/figures/nirspec/Arc_1dfit_A_0_DET01_S0060.png
diff --git a/doc/figures/nirspec/Arc_2dfit_global_A_0_DET01.png b/doc/figures/nirspec/Arc_2dfit_global_A_0_DET01.png
diff --git a/doc/figures/nirspec/Arc_2dfit_orders_A_0_DET01.png b/doc/figures/nirspec/Arc_2dfit_orders_A_0_DET01.png
diff --git a/doc/figures/nirspec/Yband_debug_picketFence.png b/doc/figures/nirspec/Yband_debug_picketFence.png
diff --git a/doc/figures/nirspec/Yband_default_chkedges.png b/doc/figures/nirspec/Yband_default_chkedges.png
diff --git a/doc/figures/nirspec/pypeit_identify_gui.png b/doc/figures/nirspec/pypeit_identify_gui.png
diff --git a/doc/help/pypeit_cache_github_data.rst b/doc/help/pypeit_cache_github_data.rst
@@ -15,9 +15,10 @@
                       jwst_nirspec, keck_deimos, keck_esi, keck_hires, keck_kcrm,
                       keck_kcwi, keck_lris_blue, keck_lris_blue_orig, keck_lris_red,
                       keck_lris_red_mark4, keck_lris_red_orig, keck_mosfire,
-                      keck_nires, keck_nirspec_low, lbt_luci1, lbt_luci2,
-                      lbt_mods1b, lbt_mods1r, lbt_mods2b, lbt_mods2r, ldt_deveny,
-                      magellan_fire, magellan_fire_long, magellan_mage, mdm_modspec,
+                      keck_nires, keck_nirspec_high, keck_nirspec_high_old,
+                      keck_nirspec_low, lbt_luci1, lbt_luci2, lbt_mods1b,
+                      lbt_mods1r, lbt_mods2b, lbt_mods2r, ldt_deveny, magellan_fire,
+                      magellan_fire_long, magellan_mage, mdm_modspec,
                       mdm_osmos_mdm4k, mdm_osmos_r4k, mmt_binospec, mmt_bluechannel,
                       mmt_mmirs, not_alfosc, not_alfosc_vert, ntt_efosc2,
                       p200_dbsp_blue, p200_dbsp_red, p200_tspec, shane_kast_blue,

diff --git a/doc/help/pypeit_chk_for_calibs.rst b/doc/help/pypeit_chk_for_calibs.rst
@@ -22,12 +22,13 @@
                             keck_deimos, keck_esi, keck_hires, keck_kcrm, keck_kcwi,
                             keck_lris_blue, keck_lris_blue_orig, keck_lris_red,
                             keck_lris_red_mark4, keck_lris_red_orig, keck_mosfire,
-                            keck_nires, keck_nirspec_low, lbt_luci1, lbt_luci2,
-                            lbt_mods1b, lbt_mods1r, lbt_mods2b, lbt_mods2r,
-                            ldt_deveny, magellan_fire, magellan_fire_long,
-                            magellan_mage, mdm_modspec, mdm_osmos_mdm4k,
-                            mdm_osmos_r4k, mmt_binospec, mmt_bluechannel, mmt_mmirs,
-                            not_alfosc, not_alfosc_vert, ntt_efosc2, p200_dbsp_blue,
+                            keck_nires, keck_nirspec_high, keck_nirspec_high_old,
+                            keck_nirspec_low, lbt_luci1, lbt_luci2, lbt_mods1b,
+                            lbt_mods1r, lbt_mods2b, lbt_mods2r, ldt_deveny,
+                            magellan_fire, magellan_fire_long, magellan_mage,
+                            mdm_modspec, mdm_osmos_mdm4k, mdm_osmos_r4k,
+                            mmt_binospec, mmt_bluechannel, mmt_mmirs, not_alfosc,
+                            not_alfosc_vert, ntt_efosc2, p200_dbsp_blue,
                             p200_dbsp_red, p200_tspec, shane_kast_blue,
                             shane_kast_red, shane_kast_red_ret, soar_goodman_blue,
                             soar_goodman_red, tng_dolores, vlt_fors2, vlt_sinfoni,

diff --git a/doc/help/pypeit_compile_wvarxiv.rst b/doc/help/pypeit_compile_wvarxiv.rst
@@ -0,0 +1,19 @@
+.. code-block:: console
+
+    $ pypeit_compile_wvarxiv -h
+    usage: pypeit_compile_wvarxiv [-h] [--append] wvarxiv_folder instrument grating
+    
+    Read in a set of wxarxiv solutions from Identify and compile them into a single
+    fits file to be used with the reidentify method.
+    
+    positional arguments:
+      wvarxiv_folder  Location of the WVarxiv files
+      instrument      Name of instrument. e.g. keck_lris_blue, keck_deimos,
+                      gemini_gmos_south_ham
+      grating         Instrument grating name. E.g. b600, r400, 600_10000.
+    
+    options:
+      -h, --help      show this help message and exit
+      --append        Append to an existing file for this instrument. (default:
+                      False)
+    
diff --git a/doc/help/pypeit_identify.rst b/doc/help/pypeit_identify.rst
@@ -2,13 +2,13 @@
 
     $ pypeit_identify -h
     usage: pypeit_identify [-h] [--lamps LAMPS] [-s] [--wmin WMIN] [--wmax WMAX]
-                           [--slit SLIT] [--det DET] [--rmstol RMSTOL] [--fwhm FWHM]
-                           [--sigdetect SIGDETECT] [--pixtol PIXTOL] [--linear]
-                           [--force_save] [--rescale_resid] [-v VERBOSITY]
-                           [--try_old]
+                           [--slits SLITS] [-m] [-n] [--det DET] [--rmstol RMSTOL]
+                           [--fwhm FWHM] [--sigdetect SIGDETECT] [--pixtol PIXTOL]
+                           [--linear] [--force_save] [--rescale_resid]
+                           [-v VERBOSITY] [--try_old]
                            arc_file slits_file
     
-    Launch PypeIt identify tool, display extracted Arc, and load linelist.
+    Launch PypeIt pypeit_identify tool, display extracted Arc, and load linelist.
     
     positional arguments:
       arc_file              PypeIt Arc file
@@ -21,9 +21,15 @@
       -s, --solution        Load a wavelength solution from the arc_file (if it
                             exists) (default: False)
       --wmin WMIN           Minimum wavelength range (default: 3000.0)
-      --wmax WMAX           Maximum wavelength range (default: 26000.0)
-      --slit SLIT           Which slit to load for wavelength calibration (default:
-                            0)
+      --wmax WMAX           Maximum wavelength range (default: 50000.0)
+      --slits SLITS         Which slit to load for wavelength calibration. Format
+                            should be [0,1,...] for multiple slits, 0 for only one
+                            slit. If creating a new WaveCalib with the -n flag, this
+                            is not necessary. (default: 0)
+      -m, --multi           Set this flag to create wavelength solutions for muliple
+                            slits (default: False)
+      -n, --new_sol         Set this flag to construct a new WaveCalib file, rather
+                            than using the exising one (default: False)
       --det DET             Detector index (default: 1)
       --rmstol RMSTOL       RMS tolerance (default: 0.1)
       --fwhm FWHM           FWHM for line finding (default: 4.0)

diff --git a/doc/help/pypeit_install_wvarxiv.rst b/doc/help/pypeit_install_wvarxiv.rst
@@ -0,0 +1,14 @@
+.. code-block:: console
+
+    $ pypeit_install_wvarxiv -h
+    usage: pypeit_install_wvarxiv [-h] files [files ...]
+    
+    Script to install user-created wavelength templates
+    
+    positional arguments:
+      files       Filename(s) of the template files to be installed in the PypeIt
+                  cache
+    
+    options:
+      -h, --help  show this help message and exit
+    
diff --git a/doc/help/pypeit_obslog.rst b/doc/help/pypeit_obslog.rst
@@ -19,12 +19,13 @@
                             keck_deimos, keck_esi, keck_hires, keck_kcrm, keck_kcwi,
                             keck_lris_blue, keck_lris_blue_orig, keck_lris_red,
                             keck_lris_red_mark4, keck_lris_red_orig, keck_mosfire,
-                            keck_nires, keck_nirspec_low, lbt_luci1, lbt_luci2,
-                            lbt_mods1b, lbt_mods1r, lbt_mods2b, lbt_mods2r,
-                            ldt_deveny, magellan_fire, magellan_fire_long,
-                            magellan_mage, mdm_modspec, mdm_osmos_mdm4k,
-                            mdm_osmos_r4k, mmt_binospec, mmt_bluechannel, mmt_mmirs,
-                            not_alfosc, not_alfosc_vert, ntt_efosc2, p200_dbsp_blue,
+                            keck_nires, keck_nirspec_high, keck_nirspec_high_old,
+                            keck_nirspec_low, lbt_luci1, lbt_luci2, lbt_mods1b,
+                            lbt_mods1r, lbt_mods2b, lbt_mods2r, ldt_deveny,
+                            magellan_fire, magellan_fire_long, magellan_mage,
+                            mdm_modspec, mdm_osmos_mdm4k, mdm_osmos_r4k,
+                            mmt_binospec, mmt_bluechannel, mmt_mmirs, not_alfosc,
+                            not_alfosc_vert, ntt_efosc2, p200_dbsp_blue,
                             p200_dbsp_red, p200_tspec, shane_kast_blue,
                             shane_kast_red, shane_kast_red_ret, soar_goodman_blue,
                             soar_goodman_red, tng_dolores, vlt_fors2, vlt_sinfoni,

diff --git a/doc/help/pypeit_ql.rst b/doc/help/pypeit_ql.rst
@@ -26,12 +26,13 @@
                             keck_deimos, keck_esi, keck_hires, keck_kcrm, keck_kcwi,
                             keck_lris_blue, keck_lris_blue_orig, keck_lris_red,
                             keck_lris_red_mark4, keck_lris_red_orig, keck_mosfire,
-                            keck_nires, keck_nirspec_low, lbt_luci1, lbt_luci2,
-                            lbt_mods1b, lbt_mods1r, lbt_mods2b, lbt_mods2r,
-                            ldt_deveny, magellan_fire, magellan_fire_long,
-                            magellan_mage, mdm_modspec, mdm_osmos_mdm4k,
-                            mdm_osmos_r4k, mmt_binospec, mmt_bluechannel, mmt_mmirs,
-                            not_alfosc, not_alfosc_vert, ntt_efosc2, p200_dbsp_blue,
+                            keck_nires, keck_nirspec_high, keck_nirspec_high_old,
+                            keck_nirspec_low, lbt_luci1, lbt_luci2, lbt_mods1b,
+                            lbt_mods1r, lbt_mods2b, lbt_mods2r, ldt_deveny,
+                            magellan_fire, magellan_fire_long, magellan_mage,
+                            mdm_modspec, mdm_osmos_mdm4k, mdm_osmos_r4k,
+                            mmt_binospec, mmt_bluechannel, mmt_mmirs, not_alfosc,
+                            not_alfosc_vert, ntt_efosc2, p200_dbsp_blue,
                             p200_dbsp_red, p200_tspec, shane_kast_blue,
                             shane_kast_red, shane_kast_red_ret, soar_goodman_blue,
                             soar_goodman_red, tng_dolores, vlt_fors2, vlt_sinfoni,

diff --git a/doc/help/pypeit_setup.rst b/doc/help/pypeit_setup.rst
@@ -2,7 +2,7 @@
 
     $ pypeit_setup -h
     usage: pypeit_setup [-h] [-s SPECTROGRAPH] [-r ROOT [ROOT ...]] [-e EXTENSION]
-                        [-d OUTPUT_PATH] [-o] [-c CFG_SPLIT] [-b] [-m]
+                        [-d OUTPUT_PATH] [-o] [-c CFG_SPLIT] [-b] [-f] [-m]
                         [-v VERBOSITY] [-k] [-G]
     
     Parse data files to construct a pypeit file in preparation for reduction using
@@ -20,12 +20,13 @@
                             keck_deimos, keck_esi, keck_hires, keck_kcrm, keck_kcwi,
                             keck_lris_blue, keck_lris_blue_orig, keck_lris_red,
                             keck_lris_red_mark4, keck_lris_red_orig, keck_mosfire,
-                            keck_nires, keck_nirspec_low, lbt_luci1, lbt_luci2,
-                            lbt_mods1b, lbt_mods1r, lbt_mods2b, lbt_mods2r,
-                            ldt_deveny, magellan_fire, magellan_fire_long,
-                            magellan_mage, mdm_modspec, mdm_osmos_mdm4k,
-                            mdm_osmos_r4k, mmt_binospec, mmt_bluechannel, mmt_mmirs,
-                            not_alfosc, not_alfosc_vert, ntt_efosc2, p200_dbsp_blue,
+                            keck_nires, keck_nirspec_high, keck_nirspec_high_old,
+                            keck_nirspec_low, lbt_luci1, lbt_luci2, lbt_mods1b,
+                            lbt_mods1r, lbt_mods2b, lbt_mods2r, ldt_deveny,
+                            magellan_fire, magellan_fire_long, magellan_mage,
+                            mdm_modspec, mdm_osmos_mdm4k, mdm_osmos_r4k,
+                            mmt_binospec, mmt_bluechannel, mmt_mmirs, not_alfosc,
+                            not_alfosc_vert, ntt_efosc2, p200_dbsp_blue,
                             p200_dbsp_red, p200_tspec, shane_kast_blue,
                             shane_kast_red, shane_kast_red_ret, soar_goodman_blue,
                             soar_goodman_red, tng_dolores, vlt_fors2, vlt_sinfoni,
@@ -53,6 +54,8 @@
                             (default: None)
       -b, --background      Include the background-pair columns for the user to edit
                             (default: False)
+      -f, --flexure         Include the manual spatial shift (flexure) column for
+                            the user to edit (default: False)
       -m, --manual_extraction
                             Include the manual extraction column for the user to
                             edit (default: False)

diff --git a/doc/help/pypeit_trace_edges.rst b/doc/help/pypeit_trace_edges.rst
@@ -35,6 +35,7 @@
                             keck_hires, keck_kcrm, keck_kcwi, keck_lris_blue,
                             keck_lris_blue_orig, keck_lris_red, keck_lris_red_mark4,
                             keck_lris_red_orig, keck_mosfire, keck_nires,
+                            keck_nirspec_high, keck_nirspec_high_old,
                             keck_nirspec_low, lbt_luci1, lbt_luci2, lbt_mods1b,
                             lbt_mods1r, lbt_mods2b, lbt_mods2r, ldt_deveny,
                             magellan_fire, magellan_fire_long, magellan_mage,

diff --git a/doc/help/pypeit_view_fits.rst b/doc/help/pypeit_view_fits.rst
@@ -18,12 +18,13 @@
                            keck_deimos, keck_esi, keck_hires, keck_kcrm, keck_kcwi,
                            keck_lris_blue, keck_lris_blue_orig, keck_lris_red,
                            keck_lris_red_mark4, keck_lris_red_orig, keck_mosfire,
-                           keck_nires, keck_nirspec_low, lbt_luci1, lbt_luci2,
-                           lbt_mods1b, lbt_mods1r, lbt_mods2b, lbt_mods2r,
-                           ldt_deveny, magellan_fire, magellan_fire_long,
-                           magellan_mage, mdm_modspec, mdm_osmos_mdm4k,
-                           mdm_osmos_r4k, mmt_binospec, mmt_bluechannel, mmt_mmirs,
-                           not_alfosc, not_alfosc_vert, ntt_efosc2, p200_dbsp_blue,
+                           keck_nires, keck_nirspec_high, keck_nirspec_high_old,
+                           keck_nirspec_low, lbt_luci1, lbt_luci2, lbt_mods1b,
+                           lbt_mods1r, lbt_mods2b, lbt_mods2r, ldt_deveny,
+                           magellan_fire, magellan_fire_long, magellan_mage,
+                           mdm_modspec, mdm_osmos_mdm4k, mdm_osmos_r4k,
+                           mmt_binospec, mmt_bluechannel, mmt_mmirs, not_alfosc,
+                           not_alfosc_vert, ntt_efosc2, p200_dbsp_blue,
                            p200_dbsp_red, p200_tspec, shane_kast_blue,
                            shane_kast_red, shane_kast_red_ret, soar_goodman_blue,
                            soar_goodman_red, tng_dolores, vlt_fors2, vlt_sinfoni,

diff --git a/doc/help/run_pypeit.rst b/doc/help/run_pypeit.rst
@@ -4,7 +4,7 @@
     usage: run_pypeit [-h] [-v VERBOSITY] [-r REDUX_PATH] [-m] [-s] [-o] [-c]
                       pypeit_file
     
-    ##  [1;37;42mPypeIt : The Python Spectroscopic Data Reduction Pipeline v1.15.1.dev126+ga20cda141.d20240305[0m
+    ##  [1;37;42mPypeIt : The Python Spectroscopic Data Reduction Pipeline v1.15.1.dev151+g015ee23ce.d20240423[0m
     ##  
     ##  Available spectrographs include:
     ##   bok_bc, gemini_flamingos1, gemini_flamingos2, gemini_gmos_north_e2v,
@@ -14,15 +14,15 @@
     ##   keck_deimos, keck_esi, keck_hires, keck_kcrm, keck_kcwi,
     ##   keck_lris_blue, keck_lris_blue_orig, keck_lris_red,
     ##   keck_lris_red_mark4, keck_lris_red_orig, keck_mosfire, keck_nires,
-    ##   keck_nirspec_low, lbt_luci1, lbt_luci2, lbt_mods1b, lbt_mods1r,
-    ##   lbt_mods2b, lbt_mods2r, ldt_deveny, magellan_fire, magellan_fire_long,
-    ##   magellan_mage, mdm_modspec, mdm_osmos_mdm4k, mdm_osmos_r4k,
-    ##   mmt_binospec, mmt_bluechannel, mmt_mmirs, not_alfosc, not_alfosc_vert,
-    ##   ntt_efosc2, p200_dbsp_blue, p200_dbsp_red, p200_tspec,
-    ##   shane_kast_blue, shane_kast_red, shane_kast_red_ret,
-    ##   soar_goodman_blue, soar_goodman_red, tng_dolores, vlt_fors2,
-    ##   vlt_sinfoni, vlt_xshooter_nir, vlt_xshooter_uvb, vlt_xshooter_vis,
-    ##   wht_isis_blue, wht_isis_red
+    ##   keck_nirspec_high, keck_nirspec_high_old, keck_nirspec_low, lbt_luci1,
+    ##   lbt_luci2, lbt_mods1b, lbt_mods1r, lbt_mods2b, lbt_mods2r, ldt_deveny,
+    ##   magellan_fire, magellan_fire_long, magellan_mage, mdm_modspec,
+    ##   mdm_osmos_mdm4k, mdm_osmos_r4k, mmt_binospec, mmt_bluechannel,
+    ##   mmt_mmirs, not_alfosc, not_alfosc_vert, ntt_efosc2, p200_dbsp_blue,
+    ##   p200_dbsp_red, p200_tspec, shane_kast_blue, shane_kast_red,
+    ##   shane_kast_red_ret, soar_goodman_blue, soar_goodman_red, tng_dolores,
+    ##   vlt_fors2, vlt_sinfoni, vlt_xshooter_nir, vlt_xshooter_uvb,
+    ##   vlt_xshooter_vis, wht_isis_blue, wht_isis_red
     
     positional arguments:
       pypeit_file           PypeIt reduction file (must have .pypeit extension)