Running a simple test recipe
============================

The following example describes how to employ the ``fridadrp-ifu_simulator``
script to generate a couple of simple exposures (target and sky) and execute a
very simple reduction recipe.

Initialize the file tree
------------------------

Download the following file `fridadrp_initial_tree_test1.tgz <https://guaix.fis.ucm.es/data/fridadrp/fridadrp_initial_tree_test1.tgz>`_

.. code-block:: console
   :class: no-copybutton

   (venv_frida) $ mkdir test1
   (venv_frida) $ cd test1

   # copy here the downloaded tgz file

   (venv_frida) $ tar zxvf fridadrp_initial_tree_test1.tgz
   ...
   ...
   (venv_frida) $ rm fridadrp_initial_tree_test1.tgz
   (venv_frida) $ tree

.. code-block::
   :class: my-special-block no-copybutton

   .
   ├── control.yaml
   ├── data
   │   ├── master_bpm_zeros.fits
   │   ├── master_dark_zeros.fits
   │   └── master_flat_ones.fits
   ├── scene_sky.yaml
   ├── scene_target.yaml
   └── test1.yaml

Execute the simulator
---------------------

Simulate the target exposure

.. code-block:: console

   (venv_frida) $ fridadrp-ifu_simulator \
    --scene scene_target.yaml \
    --grating medium-K \
    --scale fine \
    --prefix_intermediate_FITS target

.. code-block::
   :class: my-special-block no-copybutton

   ...
   ...
   Saving file: target_ifu_white2D_method0_os10.fits
   Saving file: target_ifu_white2D_method0_os1.fits
   Saving file: target_ifu_3D_method0.fits
   Saving file: target_rss_2D_method0.fits
   Saving file: target_detector_2D_method0.fits
   Saving file: target_rss_2D_method1.fits
   Saving file: target_ifu_3D_method1.fits

Copy the simulated detector image in the ``data/`` subdirectory

.. code-block:: console

   (venv_frida) $ cp target_detector_2D_method0.fits data 

.. numina-ximshow target_detector_2D_method0.fits --geometry 800,640,0,0 --cbar_orientation vertical --z1z2 "[0, 5]"
.. image:: test1/target_detector_2D_method0.png
   :width: 100%
   :alt: image target_detector_2D_method0.png

Simulate the sky exposure

.. code-block:: console

   (venv_frida) $ fridadrp-ifu_simulator \
     --scene scene_sky.yaml \
     --grating medium-K \
     --scale fine \
     --prefix_intermediate_FITS sky

.. code-block::
   :class: my-special-block no-copybutton

   ...
   ...
   Saving file: sky_ifu_white2D_method0_os10.fits
   Saving file: sky_ifu_white2D_method0_os1.fits
   Saving file: sky_ifu_3D_method0.fits
   Saving file: sky_rss_2D_method0.fits
   Saving file: sky_detector_2D_method0.fits
   Saving file: sky_rss_2D_method1.fits
   Saving file: sky_ifu_3D_method1.fits

Copy the simulated detector image in the ``data/`` subdirectory

.. code-block:: console

   (venv_frida) $ cp sky_detector_2D_method0.fits data 

.. numina-ximshow sky_detector_2D_method0.fits --geometry 800,640,0,0 --cbar_orientation vertical --z1z2 "[0, 5]"
.. image:: test1/sky_detector_2D_method0.png
   :width: 100%
   :alt: image sky_detector_2D_method0.png


Running the reduction recipe
----------------------------

.. note::

   Remember that the ``numina`` script is the interface with GTC pipelines. 
   In order to execute PyEmir recipes you should type something like:

   ::
   
      (venv_frida) $ numina run <observation_result_file.yaml> -r <requirements_file.yaml>

   where ``<observation_result_file.yaml>`` is an observation result file in 
   YAML format, and ``<requirements_files.yaml>`` is a requirements file, also 
   in YAML format.

   YAML is a human-readable data serialization language (for details see 
   `YAML Syntax
   <https://docs.ansible.com/ansible/latest/reference_appendices/YAMLSyntax.html>`_)

We are going to execute ``numina`` using the observation result file
``test1.yaml``.

.. code-block:: console

   (venv_frida) $ cat test1.yaml 

.. code-block::
   :class: my-special-block no-copybutton

   id: _test1
   instrument: FRIDA
   mode: test1
   frames:
     - target_detector_2D_method0.fits
     - sky_detector_2D_method0.fits
   enabled: True
   
.. code-block:: console

   (venv_frida) $ numina run test1.yaml -r control.yaml

.. code-block::
   :class: my-special-block no-copybutton

   ...
   ...

After the execution of the previous command, two subdirectories should have
appeared, with the syntax ``obsid<id>_<work/results>``. In this particular
example, these two subdirectories are ``obsid_test1_work`` and
``obsid_test1_result``. 

All the images (scientific and calibrations) involved in the reduction of a
particular block of the observation result file are copied into the ``...work``
subdirectories in order to preserve the original files. The results of the
execution of the reduction recipe are stored in the corresponding
``...results`` subdirectory.

.. code-block:: console

   (venv_frida) $ tree obsid_test1_*

.. code-block::
   :class: my-special-block no-copybutton

   obsid_test1_results
   ├── processing.log
   ├── reduced_image.fits
   ├── result.json
   └── task.json
   obsid_test1_work
   ├── index.pkl
   ├── sky_detector_2D_method0.fits -> /Users/cardiel/test1/data/sky_detector_2D_method0.fits
   └── target_detector_2D_method0.fits -> /Users/cardiel/test1/data/target_detector_2D_method0.fits

.. numina-ximshow obsid_test1_results/reduced_image.fits --geometry 800,640,0,0 --cbar_orientation vertical --z1z2 "[0, 5]"
.. image:: test1/reduced_image.png
   :width: 100%
   :alt: image reduced_image.png