Add the innitial version of dorothea's documentation

Author: bpalmeiro

docs/source/dorothea.rst

@@ -1,5 +1,205 @@
 Dorothea
-==========
+========
 
-.. caution::
-  This page is currently not created, we are working on it. If you would like to contribute on this documentation, reach `me <[email protected]>`_!
+*From ancient Greek, Δωροθέα: gift of God.*
+
+The purpose of *Dorothea* is to process the **PMaps** (outcome of *Irene*) and
+reconstruct point-like events. Therefore, all the information included in the S2 peaks
+is collapsed into a single x, y, and z deposition with a given E (the area under the S2 peak).
+Additionally, some parameters regarding the S1 and S2 peaks are provided as a tool for further selections.
+Last, it is worth noting that for events where more than S1 or S2 (or both) are
+present in the event, a point is reconstructed for each possible combination.
+
+
+.. _Dorothea input:
+
+Input
+-----
+
+* ``/Run/events``
+* ``/Run/runInfo``
+* ``/PMAPS/S1``
+* ``/PMAPS/S1Pmt``
+* ``/PMAPS/S2``
+* ``/PMAPS/S2Pmt``
+* ``/PMAPS/S2Si``
+
+.. _Dorothea output:
+
+Output
+------
+
+ * ``/DST/Events``: summary of the reconstructed events and their main properties. Each row represents one combination of an S1 and a S2 identified under the same ``event`` but with its corresponding  ``s1_peak`` and ``s2_peak`` identifier. The full list and description of the parameters in the table may be found later.
+ * ``/Filters/s12_selector``: flag for whether an event passed the S1 and S2 selections
+
+
+.. _Irene config:
+
+Config
+------
+
+Besides the :ref:`Common arguments to every city`, *Dorothea* has the following arguments:
+
+.. list-table::
+   :widths: 50 40 120
+   :header-rows: 1
+
+   * - **Parameter**
+     - **Type**
+     - **Description**
+
+   * - ``drift_v``
+     - ``float``
+     - Drift velocity of the secondary electrons towards the anode.
+
+   * - ``s1|s2_nmin|nmax``
+     - ``int``
+     - Lower/upper limits to the number of S1/S2 peaks per event.
+
+   * - ``s1|s2_emin|emax``
+     - ``float``
+     - Lower/upper limits to the energy (integral under the peak) of each S1/S2 peak (pes).
+
+   * - ``s1|s2_wmin|wmax``
+     - ``float``
+     - Lower/upper limits to the with (time over threshold) of each S1/S2 peak (ns).
+
+   * - ``s1|s2_hmin|hmax``
+     - ``float``
+     - Lower/upper limits to the height (maximum amplitude) of each S1/S2 peak (pes).
+
+   * - ``s1|s2_ethr``
+     - ``float``
+     - Threshold for each bin within each S1/S2 to be considered for the energy computation (pes).
+
+   * - ``s2_nsipmmin|nsipmminax``
+     - ``int``
+     - Lower/upper limits to the number of SiPM sensors with a recorded signal.
+
+   * - ``global_reco_params``
+     - ``dict``
+     - Set of parameters for the corona algorithm. Since the desired one is the barycenter reconstruction, the only mandatory elements in the dictionary are:
+
+        * ``Qthr``: charge threshold, ignore all SiPMs with less than Qthr pes.
+        * ``lm_radius=-1``: sets the algorithm to be the barycenter.
+
+
+.. _Dorothea workflow:
+
+Workflow
+--------
+
+The workflow for *Dorothea* is straightforward. After a filter removing all the peaks and events not satisfying the limits provided. Then, it proceeds to perform the point-like reconstruction. Basically, this algorithm collapses the whole S2 information into a single point:
+
+ * The *x* and *y* position are determined via a charge-weighted average. This makes use of the so-called ``corona`` `algorithm <https://github.com/next-exp/IC/blob/8be75c65aa2e452eae4ce2e51494a58eab18a0d4/invisible_cities/reco/xy_algorithms.py#L61>`_, with the proper configuration to apply the barycenter computation.
+ * The *z* coordinate is derived from the time difference between the maximum amplitude of the S1 and S2 considered, corrected by the drift velocity.
+ * The energy is the integral under the S2 of those bins above the threshold.
+
+ Besides, the reconstruction yields a set of useful values regarding the peaks that are also provided in the final table:
+
+ .. list-table::
+    :widths: 50 40 120
+    :header-rows: 1
+
+    * - **Parameter**
+      - **Type**
+      - **Description**
+
+    * - ``event``
+      - ``int``
+      - Event ID. As an event can have several S1 and S2 combinations, each one representing one row, this number identifies all the reconstructed points within the same original waveform.
+
+    * - ``time``
+      - ``float``
+      - Timestamp of the event.
+
+    * - ``s1_peak``
+      - ``int``
+      - S1 ID. It identifies the S1 within an event.
+
+    * - ``s2_peak``
+      - ``int``
+      - S2 ID. It identifies the S2 within an event.
+
+    * - ``nS1``
+      - ``int``
+      - Number of S1 present in the event.
+    * - ``nS2``
+      - ``int``
+      - Number of S2 present in the event.
+
+    * - ``S1w``
+      - ``float``
+      - S1 time over threshold (ns).
+
+    * - ``s1h``
+      - ``float``
+      - S1 maximum amplitude (pes).
+
+    * - ``S1e``
+      - ``float``
+      - S1 PMT- and time-summed amplitude over threshold (pes).
+
+    * - ``S1t``
+      - ``float``
+      -  Waveform time at maximum S1 amplitude (ns).
+
+    * - ``S2w``
+      - ``float``
+      - S2 time over threshold (ns).
+
+    * - ``s2h``
+      - ``float``
+      - S2 maximum amplitude (pes).
+
+    * - ``S2e``
+      - ``float``
+      - S2 PMT- and time-summed amplitude over threshold (pes).
+
+    * - ``S2t``
+      - ``float``
+      -  Waveform time at maximum S2 amplitude (ns).
+
+    * - ``S2q``
+      - ``float``
+      -  S2 SiPM- and time-summed amplitude over threshold (pes).
+
+    * - ``Nsipm``
+      - ``int``
+      - Number of SiPMs with signal over threshold.
+
+    * - ``DT``
+      - ``float``
+      - Drift Time —i.e., time difference between the corresponding S1 and S2— (:math:`\mu s`).
+
+    * - ``Z``
+      - ``float``
+      - Reconstructed z position coordinate —i.e., the DT times the drift velocity— (mm).
+
+    * - ``Zrms``
+      - ``float``
+      -  Standard deviation of the PMT  signal in the z coordinate (mm).
+
+    * - ``X``
+      - ``float``
+      - Reconstructed x position coordinate using the barycenter algorithm (mm).
+
+    * - ``Y``
+      - ``float``
+      - Reconstructed y position coordinate using the barycenter algorithm (mm).
+
+    * - ``R``
+      - ``float``
+      - Reconstructed radial coordinate, :math:`r^2=x^2+y^2` (mm).
+
+    * - ``Phi``
+      - ``float``
+      - Reconstructed azimuthal coordinate, :math:`\phi=\arctan(y/x)` (rad).
+
+    * - ``Xrms``
+      - ``float``
+      -  Standard deviation of the PMT  signal in the x coordinate (mm).
+
+    * - ``Yrms``
+      - ``float``
+      -  Standard deviation of the PMT  signal in the y coordinate (mm).