updated flexure docs

pypeit · Oct 2, 2024 · 77cf107 · 77cf107
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diff --git a/doc/calibrations/flexure.rst b/doc/calibrations/flexure.rst
@@ -26,12 +26,22 @@ Spatial Flexure
 The code has a simple yet relatively robust method to cross-correlate
 the slits against any input image to determine a rigid, spatial offset.
 This algorithm is performed for any frame type by setting
-``spat_flexure_correct = True`` in the ``process`` block
-of :ref:`processimagespar`.
+``spat_flexure_method = <method>`` in the ``process`` block
+of :ref:`processimagespar`, where you should replace ``<method>`` with one of the
+following valid methods:
+``skip`` - this will skip the spatial flexure correction
+``detector`` - this will calculate one spatial flexure value for all slits on the detector
+``slit`` - this will calculate the spatial flexure for each slit separately
+``edge`` - this will calculate the spatial flexure for each slit edge separately
 
 We have made our own determinations for which instruments to enable this as the
 default. Inspect the :ref:`instr_par` list to see if your instrument is included
-(search for the value of ``spat_flexure_correct``).
+(search for the value of ``spat_flexure_method``). We recommend that you use the
+``detector`` method for most instruments, unless you have good reason to believe
+that the spatial flexure is different for different slits or slit edges. Also note
+that some spectrographs post-process the spatial flexure values when using the ``slit``
+or ``edge`` methods (e.g. perform a linear fit to the spatial flexure values) to improve
+the result. Consult the documentation for your instrument to see if this is the case.
 
 Depending on what frame types you choose to correct, the
 code will behave somewhat differently.  Here we describe
@@ -49,11 +59,11 @@ add this to your PypeIt file:
 
     [scienceframe]
         [[process]]
-            spat_flexure_correct = True
+            spat_flexure_method = detector
     [calibrations]
         [[standardframe]]
             [[[process]]]
-                spat_flexure_correct = True
+                spat_flexure_method = detector
 
 This will:
 
@@ -75,7 +85,7 @@ following to your :doc:`../pypeit_file`:
     [calibrations]
         [[tiltframe]]
             [[[process]]]
-                spat_flexure_correct = True
+                spat_flexure_method = detector
 
 This will:
 

diff --git a/doc/calibrations/image_proc.rst b/doc/calibrations/image_proc.rst
@@ -288,8 +288,8 @@ Spatial Flexure Shift
 
 A spatial shift in the slit positions due to instrument flexure is calculated
 using :func:`~pypeit.core.flexure.spat_flexure_shift` if the
-``spat_flexure_correct`` parameter is true.  See :ref:`flexure` for additional
-discussion.
+``spat_flexure_method`` parameter is set to an option other than ``skip``.
+See :ref:`flexure` for additional discussion.
 
 Flat-fielding
 -------------

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 v1.16.1.dev468+g832ee84e4[0m
+    ##  [1;37;42mPypeIt : The Python Spectroscopic Data Reduction Pipeline v1.15.1.dev38+g075fdecaa.d20240212[0m
     ##  
     ##  Available spectrographs include:
     ##   aat_uhrf, bok_bc, gemini_flamingos1, gemini_flamingos2,

diff --git a/doc/include/class_datamodel_pypeitimage.rst b/doc/include/class_datamodel_pypeitimage.rst
@@ -1,5 +1,5 @@
 
-**Version**: 1.3.0
+**Version**: 1.3.1
 
 ================  ===================================================================================================  =================  ================================================================================================================================================================================================================================
 Attribute         Type                                                                                                 Array Type         Description                                                                                                                                                                                                                     

diff --git a/doc/include/datamodel_arcimage.rst b/doc/include/datamodel_arcimage.rst
@@ -1,5 +1,5 @@
 
-Version 1.3.0
+Version 1.3.1
 
 ================  ==============================  =========  ================================================================================================================================================
 HDU Name          HDU Type                        Data Type  Description                                                                                                                                     

diff --git a/doc/include/datamodel_biasimage.rst b/doc/include/datamodel_biasimage.rst
@@ -1,5 +1,5 @@
 
-Version 1.3.0
+Version 1.3.1
 
 =================  ==============================  =========  ================================================================================================================================================
 HDU Name           HDU Type                        Data Type  Description                                                                                                                                     

diff --git a/doc/include/datamodel_darkimage.rst b/doc/include/datamodel_darkimage.rst
@@ -1,5 +1,5 @@
 
-Version 1.3.0
+Version 1.3.1
 
 =================  ==============================  =========  ================================================================================================================================================
 HDU Name           HDU Type                        Data Type  Description                                                                                                                                     

diff --git a/doc/include/datamodel_tiltimage.rst b/doc/include/datamodel_tiltimage.rst
@@ -1,5 +1,5 @@
 
-Version 1.3.0
+Version 1.3.1
 
 =================  ==============================  =========  ================================================================================================================================================
 HDU Name           HDU Type                        Data Type  Description                                                                                                                                     

diff --git a/doc/include/gemini_gnirs_echelle_A.pypeit.rst b/doc/include/gemini_gnirs_echelle_A.pypeit.rst
@@ -1,7 +1,7 @@
 .. code-block:: console
 
-    # Auto-generated PypeIt input file using PypeIt version: 1.16.0
-    # UTC 2024-06-11T08:31:55
+    # Auto-generated PypeIt input file using PypeIt version: 1.15.1.dev38+g075fdecaa.d20240212
+    # UTC 2024-10-02T12:11:46.067+00:00
     
     # User-defined execution parameters
     [rdx]

diff --git a/doc/include/imgproc_defaults_table.rst b/doc/include/imgproc_defaults_table.rst
@@ -1,19 +1,19 @@
-========================  =========  =========  =========  =========  =========  =========  =========  =============  =============  ========  ============  ===========
-Parameter                 Default    ``bias``   ``dark``   ``trace``  ``arc``    ``tilt``   ``align``  ``pixelflat``  ``illumflat``  ``sky``   ``standard``  ``science``
-========================  =========  =========  =========  =========  =========  =========  =========  =============  =============  ========  ============  ===========
-``apply_gain``            ``True``                                                                                                                                      
-``use_pattern``           ``False``                                                                                                                                     
-``empirical_rn``          ``False``                                                                                                                                     
-``use_overscan``          ``True``                                                                                                                                      
-``trim``                  ``True``                                                                                                                                      
-``orient``                ``True``                                                                                                                                      
-``use_biasimage``         ``True``   ``False``                                                                                                                          
-``use_darkimage``         ``False``                                                                                                                                     
-``spat_flexure_correct``  ``none``                                                                                                                                      
-``use_pixelflat``         ``True``   ``False``  ``False``  ``False``  ``False``  ``False``  ``False``  ``False``      ``False``                                         
-``use_illumflat``         ``True``   ``False``  ``False``  ``False``  ``False``  ``False``  ``False``  ``False``      ``False``                                         
-``use_specillum``         ``False``                                                                                                                                     
-``shot_noise``            ``True``   ``False``                                                                                                                          
-``noise_floor``           ``0.0``                                                                                                    ``0.01``  ``0.01``      ``0.01``   
-``mask_cr``               ``False``             ``True``                                                                             ``True``  ``True``      ``True``   
-========================  =========  =========  =========  =========  =========  =========  =========  =============  =============  ========  ============  ===========
+=======================  =========  =========  =========  =========  =========  =========  =========  =============  =============  ========  ============  ===========
+Parameter                Default    ``bias``   ``dark``   ``trace``  ``arc``    ``tilt``   ``align``  ``pixelflat``  ``illumflat``  ``sky``   ``standard``  ``science``
+=======================  =========  =========  =========  =========  =========  =========  =========  =============  =============  ========  ============  ===========
+``apply_gain``           ``True``                                                                                                                                      
+``use_pattern``          ``False``                                                                                                                                     
+``empirical_rn``         ``False``                                                                                                                                     
+``use_overscan``         ``True``                                                                                                                                      
+``trim``                 ``True``                                                                                                                                      
+``orient``               ``True``                                                                                                                                      
+``use_biasimage``        ``True``   ``False``                                                                                                                          
+``use_darkimage``        ``False``                                                                                                                                     
+``spat_flexure_method``  ``skip``                                                                                                                                      
+``use_pixelflat``        ``True``   ``False``  ``False``  ``False``  ``False``  ``False``  ``False``  ``False``      ``False``                                         
+``use_illumflat``        ``True``   ``False``  ``False``  ``False``  ``False``  ``False``  ``False``  ``False``      ``False``                                         
+``use_specillum``        ``False``                                                                                                                                     
+``shot_noise``           ``True``   ``False``                                                                                                                          
+``noise_floor``          ``0.0``                                                                                                    ``0.01``  ``0.01``      ``0.01``   
+``mask_cr``              ``False``             ``True``                                                                             ``True``  ``True``      ``True``   
+=======================  =========  =========  =========  =========  =========  =========  =========  =============  =============  ========  ============  ===========
diff --git a/doc/include/keck_deimos.sorted.rst b/doc/include/keck_deimos.sorted.rst
@@ -14,13 +14,13 @@
         d0527_0030.fits.gz |                  arc,tilt |  57.99999999999999 |               45.0 | DOME PHLAT |     830G | LongMirr |     1,1 | 57900.077631 | 1.41291034 |     1.0 | 8099.98291016 | SINGLE:B |   OG550 | Kr Xe Ar Ne | 2017-05-27 | 01:51:53.87 |      30 |     0
         d0527_0031.fits.gz | pixelflat,illumflat,trace |  57.99999999999999 |               45.0 | DOME PHLAT |     830G | LongMirr |     1,1 |  57900.07851 | 1.41291034 |     4.0 | 8099.98291016 | SINGLE:B |   OG550 |          Qz | 2017-05-27 | 01:53:10.93 |      31 |     0
     DE.20170527.06790.fits | pixelflat,illumflat,trace |  57.99999999999999 |               45.0 | DOME PHLAT |     830G | LongMirr |     1,1 |  57900.07851 | 1.41291034 |     4.0 | 8099.98291016 | SINGLE:B |   OG550 |          Qz | 2017-05-27 | 01:53:10.93 |      31 |     0
-    DE.20170527.06864.fits | pixelflat,illumflat,trace |  57.99999999999999 |               45.0 | DOME PHLAT |     830G | LongMirr |     1,1 | 57900.079356 | 1.41291034 |     4.0 | 8099.98291016 | SINGLE:B |   OG550 |          Qz | 2017-05-27 | 01:54:24.03 |      32 |     0
         d0527_0032.fits.gz | pixelflat,illumflat,trace |  57.99999999999999 |               45.0 | DOME PHLAT |     830G | LongMirr |     1,1 | 57900.079356 | 1.41291034 |     4.0 | 8099.98291016 | SINGLE:B |   OG550 |          Qz | 2017-05-27 | 01:54:24.03 |      32 |     0
-        d0527_0033.fits.gz | pixelflat,illumflat,trace |  57.99999999999999 |               45.0 | DOME PHLAT |     830G | LongMirr |     1,1 | 57900.080211 | 1.41291034 |     4.0 | 8099.98291016 | SINGLE:B |   OG550 |          Qz | 2017-05-27 | 01:55:36.93 |      33 |     0
+    DE.20170527.06864.fits | pixelflat,illumflat,trace |  57.99999999999999 |               45.0 | DOME PHLAT |     830G | LongMirr |     1,1 | 57900.079356 | 1.41291034 |     4.0 | 8099.98291016 | SINGLE:B |   OG550 |          Qz | 2017-05-27 | 01:54:24.03 |      32 |     0
     DE.20170527.06936.fits | pixelflat,illumflat,trace |  57.99999999999999 |               45.0 | DOME PHLAT |     830G | LongMirr |     1,1 | 57900.080211 | 1.41291034 |     4.0 | 8099.98291016 | SINGLE:B |   OG550 |          Qz | 2017-05-27 | 01:55:36.93 |      33 |     0
+        d0527_0033.fits.gz | pixelflat,illumflat,trace |  57.99999999999999 |               45.0 | DOME PHLAT |     830G | LongMirr |     1,1 | 57900.080211 | 1.41291034 |     4.0 | 8099.98291016 | SINGLE:B |   OG550 |          Qz | 2017-05-27 | 01:55:36.93 |      33 |     0
     DE.20170527.37601.fits |                   science |  261.0363749999999 | 19.028166666666667 |   P261_OFF |     830G | LongMirr |     1,1 | 57900.435131 | 1.03078874 |  1200.0 | 8099.98291016 | SINGLE:B |   OG550 |         Off | 2017-05-27 | 10:26:41.61 |      80 |     0
-        d0527_0081.fits.gz |                   science |  261.0363749999999 | 19.028166666666667 |   P261_OFF |     830G | LongMirr |     1,1 | 57900.449842 | 1.01267696 |  1200.0 | 8099.98291016 | SINGLE:B |   OG550 |         Off | 2017-05-27 | 10:47:52.92 |      81 |     0
     DE.20170527.38872.fits |                   science |  261.0363749999999 | 19.028166666666667 |   P261_OFF |     830G | LongMirr |     1,1 | 57900.449842 | 1.01267696 |  1200.0 | 8099.98291016 | SINGLE:B |   OG550 |         Off | 2017-05-27 | 10:47:52.92 |      81 |     0
+        d0527_0081.fits.gz |                   science |  261.0363749999999 | 19.028166666666667 |   P261_OFF |     830G | LongMirr |     1,1 | 57900.449842 | 1.01267696 |  1200.0 | 8099.98291016 | SINGLE:B |   OG550 |         Off | 2017-05-27 | 10:47:52.92 |      81 |     0
     DE.20170527.41775.fits |                   science |  261.0362916666666 | 19.028888888888886 |   P261_OFF |     830G | LongMirr |     1,1 | 57900.483427 | 1.00093023 |  1200.0 | 8099.98291016 | SINGLE:B |   OG550 |         Off | 2017-05-27 | 11:36:15.35 |      83 |     0
         d0527_0083.fits.gz |                   science |  261.0362916666666 | 19.028888888888886 |   P261_OFF |     830G | LongMirr |     1,1 | 57900.483427 | 1.00093023 |  1200.0 | 8099.98291016 | SINGLE:B |   OG550 |         Off | 2017-05-27 | 11:36:15.35 |      83 |     0
     DE.20170527.43045.fits |                   science |  261.0362916666666 | 19.028888888888886 |   P261_OFF |     830G | LongMirr |     1,1 | 57900.498135 | 1.00838805 |  1200.0 | 8099.98291016 | SINGLE:B |   OG550 |         Off | 2017-05-27 | 11:57:25.35 |      84 |     0

diff --git a/doc/include/keck_deimos_A.pypeit.rst b/doc/include/keck_deimos_A.pypeit.rst
@@ -1,7 +1,7 @@
 .. code-block:: console
 
-    # Auto-generated PypeIt input file using PypeIt version: 1.16.0
-    # UTC 2024-06-11T08:31:55
+    # Auto-generated PypeIt input file using PypeIt version: 1.15.1.dev38+g075fdecaa.d20240212
+    # UTC 2024-10-02T12:11:45.568+00:00
     
     # User-defined execution parameters
     [rdx]

diff --git a/doc/include/keck_nires_A.pypeit.rst b/doc/include/keck_nires_A.pypeit.rst
@@ -1,7 +1,7 @@
 .. code-block:: console
 
-    # Auto-generated PypeIt input file using PypeIt version: 1.16.0
-    # UTC 2024-06-11T08:31:55
+    # Auto-generated PypeIt input file using PypeIt version: 1.15.1.dev38+g075fdecaa.d20240212
+    # UTC 2024-10-02T12:11:46.443+00:00
     
     # User-defined execution parameters
     [rdx]

diff --git a/doc/include/shane_kast_blue_A.pypeit.rst b/doc/include/shane_kast_blue_A.pypeit.rst
@@ -1,7 +1,7 @@
 .. code-block:: console
 
-    # Auto-generated PypeIt input file using PypeIt version: 1.16.0
-    # UTC 2024-06-11T08:31:55
+    # Auto-generated PypeIt input file using PypeIt version: 1.15.1.dev38+g075fdecaa.d20240212
+    # UTC 2024-10-02T12:11:39.981+00:00
     
     # User-defined execution parameters
     [rdx]