From 7d9463b13c6f80c00b947051fa83500d14885163 Mon Sep 17 00:00:00 2001 From: Christopher Montalban Date: Wed, 6 Mar 2024 12:00:02 -0300 Subject: [PATCH 1/2] Added help message to search.pattern --- goodman_pipeline/spectroscopy/redspec.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/goodman_pipeline/spectroscopy/redspec.py b/goodman_pipeline/spectroscopy/redspec.py index 5473846e..3afeaf6e 100755 --- a/goodman_pipeline/spectroscopy/redspec.py +++ b/goodman_pipeline/spectroscopy/redspec.py @@ -91,7 +91,7 @@ def get_args(arguments=None): type=str, metavar='', dest='pattern', - help="Pattern for matching the goodman's reduced data.") + help="Pattern for matching the goodman's reduced data. Default is cfzst*.") parser.add_argument('--output-prefix', action='store', From 4855003d7e4d8c657b736f11fd9716d19686ead1 Mon Sep 17 00:00:00 2001 From: Christopher Montalban Date: Mon, 11 Mar 2024 14:44:40 -0300 Subject: [PATCH 2/2] Add new section in documentation: Usage -> Common Issues --- docs/_common_issues.rst | 48 ++++++++++++++++++++ docs/_running_prepare_data_for_reduction.rst | 4 ++ docs/_running_redspec.rst | 9 ++-- docs/usage.rst | 3 +- 4 files changed, 59 insertions(+), 5 deletions(-) create mode 100644 docs/_common_issues.rst diff --git a/docs/_common_issues.rst b/docs/_common_issues.rst new file mode 100644 index 00000000..c5d5aac9 --- /dev/null +++ b/docs/_common_issues.rst @@ -0,0 +1,48 @@ +.. _common_issues: + +Common issues +************* + +No comparison lamps were found +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +The latest version may introduce changes to wavelength solutions. To +view the current list of available modes and lamps, please refer to the +`GitHub repository `_. + +If your lamp, filter, or mode is not included in the repository mentioned +above, ``redspec`` will not work as expected. This is particularly common +with custom modes of the |pipeline full name|. You may encounter the following +error after running ``redspec``: + +.. code-block:: console + + $ redspec + ፧ + [15:02:49][W]: No comparison lamps were provided for file ecfzst_0001_science.fits + +This error occurs because the |pipeline full name| relies on specific keywords to +extract spectra, such as: + +.. _`table lamp key`: + +.. table:: Keywords that are used to produce a wavelength solution. + + ========== ============================================================= + Keyword Purpose + ========== ============================================================= + LAMP_HGA Indicates if HgAr lamp is used. + LAMP_NE Indicates if Ne lamp is used. + LAMP_AR Indicates if Ar lamp is used. + LAMP_FE Indicates if Fe lamp is used. + LAMP_CU Indicates if Cu lamp is used. + WAVMODE Slit and mode configuration. + ========== ============================================================= + +Multiple spectra output +^^^^^^^^^^^^^^^^^^^^^^^^ + +When taking multiple ``ARC`` images during your observation run, they will be linked +with your science data. This means that if you capture several lamp files, +they will be processed alongside the science images, potentially resulting +in multiple outputs of the same spectrum. diff --git a/docs/_running_prepare_data_for_reduction.rst b/docs/_running_prepare_data_for_reduction.rst index 892d9810..060b0db8 100644 --- a/docs/_running_prepare_data_for_reduction.rst +++ b/docs/_running_prepare_data_for_reduction.rst @@ -25,6 +25,10 @@ need to change the following keywords. ``SYZY_400`` becomes ``400_SYZY``. - ``WAVMODE``: Replace whitespace with underscore and all letters are capitalized. For instance. ``400 m1`` becomes ``400_M1``. +- ``INSTRUME``: Instead of using the classical keywords 'Goodman Spectro' and + 'Goodman Imaging', the AEON standard keywords ``ghts_red`` and ``ghts_blue`` + will be used for spectroscopy, and ``ghts_red_imager`` and ``ghts_blue_imager`` + for imaging. This is an exception of the upper case rule. .. note:: diff --git a/docs/_running_redspec.rst b/docs/_running_redspec.rst index 222c6684..cd5d729a 100644 --- a/docs/_running_redspec.rst +++ b/docs/_running_redspec.rst @@ -27,13 +27,14 @@ behavior for every user or science case, we have implemented a set of is *current working directory*. - ``--proc-path `` Folder were processed data will be stored. Default is *current working directory*. -- ``--search-pattern `` Prefix for picking up files. Default - ``cfzst``. See :ref:`file-prefixes`. -- ``--output-prefix `` Prefix to be added to calibrated spectrum. +- ``--search-pattern `` Prefix for picking up files. Default is + ``cfzst-``. See :ref:`file-prefixes`. +- ``--output-prefix `` Prefix to be added to calibrated spectrum. Default is + ``w-``. See :ref:`file-prefixes`. - ``--extraction `` Select the :ref:`extraction-methods`. The only one implemented at the moment is ``fractional`` . - ``--fit-targets-with {moffat, gaussian}`` Model to fit peaks on spatial profile - while searching for spectroscopic targets. + while searching for spectroscopic targets. Default ``moffat``. - ``--target-min-width `` Minimum profile width for fitting the spatial axis of spectroscopic targets. If fitting a Moffat it will be reflected as the FWHM attribute of the fitted model and if fitting a Gaussian it will be reflected as the STDDEV attribute of the Gaussian model. diff --git a/docs/usage.rst b/docs/usage.rst index 446eb9fc..6e2733ce 100644 --- a/docs/usage.rst +++ b/docs/usage.rst @@ -34,9 +34,10 @@ Getting Help. .. include:: _extraction_methods.rst - .. include:: _file_prefixes.rst .. include:: _file_suffixes.rst .. include:: _shortcuts.rst + +.. include:: _common_issues.rst