Merge pull request #389 from Allonck/updateDCR

Update dcr

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 <https://github.com/soar-telescope/goodman_pipeline/tree/main/goodman_pipeline/data/ref_comp>`_.
+
+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.

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::
 

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 <path>`` Folder were processed data will be stored. Default
   is *current working directory*.
-- ``--search-pattern <pattern>`` Prefix for picking up files. Default
-  ``cfzst``. See :ref:`file-prefixes`.
-- ``--output-prefix <prefix>`` Prefix to be added to calibrated spectrum.
+- ``--search-pattern <pattern>`` Prefix for picking up files. Default is
+  ``cfzst-``. See :ref:`file-prefixes`.
+- ``--output-prefix <prefix>`` Prefix to be added to calibrated spectrum. Default is
+  ``w-``. See :ref:`file-prefixes`.
 - ``--extraction <method>`` 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 <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.

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

goodman_pipeline/core/core.py

@@ -323,6 +323,8 @@ def call_cosmic_rejection(ccd,
 
             _create(instrument=_instrument, binning=_binning, path=red_path)
 
+        #out_prefix = prefix + out_prefix #Move line here
+
         full_path = os.path.join(red_path, f"{out_prefix}_{image_name}")
 
         ccd.header.set('GSP_COSM',
@@ -919,24 +921,26 @@ def dcr_cosmicray_rejection(data_path, in_file, prefix,
     # define the name for the cosmic rays file
     cosmic_file = 'cosmic_' + '_'.join(in_file.split('_')[1:])
 
+    # get current working directory and goes to reduction folder
+    cwd = os.getcwd()
+    full_path_data = os.path.join(cwd, data_path)
+
     # define full path for all the files involved
-    full_path_in = os.path.join(data_path, in_file)
-    full_path_out = os.path.join(data_path, out_file)
-    full_path_cosmic = os.path.join(data_path, cosmic_file)
+    full_path_in = os.path.join(full_path_data, in_file)
+    full_path_out = os.path.join(full_path_data, out_file)
+    full_path_cosmic = os.path.join(full_path_data, cosmic_file)
 
     # this is the command for running dcr, all arguments are required
     command = 'dcr {:s} {:s} {:s}'.format(full_path_in,
                                           full_path_out,
                                           full_path_cosmic)
-
     log.debug('DCR command:')
     log.debug(command)
     # get the current working directory to go back to it later in case the
     # the pipeline has not been called from the same data directory.
-    cwd = os.getcwd()
 
     # move to the directory were the data is, dcr is expecting a file dcr.par
-    os.chdir(data_path)
+    os.chdir(full_path_data)
 
     # call dcr
     try:
@@ -969,7 +973,7 @@ def kill_process(process):  # pragma: no cover
     # wait for dcr to terminate
     # dcr.wait()
 
-    # go back to the original directory. Could be the same.
+    #go back to the original directory. Could be the same.
     os.chdir(cwd)
 
     # If no error stderr is an empty string
@@ -1012,7 +1016,6 @@ def kill_process(process):  # pragma: no cover
             os.unlink(full_path_out)
         return ccd
 
-
 def define_trim_section(sample_image, technique):
     """Get the initial trim section
 

goodman_pipeline/spectroscopy/redspec.py

@@ -91,7 +91,7 @@ def get_args(arguments=None):
                         type=str,
                         metavar='<Search Pattern>',
                         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',