Add some documentation

Author: AntSimi

README.md

@@ -18,7 +18,7 @@ Method is used in :
 
 To avoid problems with installation, use of the virtualenv Python virtual environment is recommended.
 
-Then use pip to install all dependencies (numpy, scipy, matplotlib, netCDF4, cython, pyproj, Shapely, ...), e.g.:
+Then use pip to install all dependencies (numpy, scipy, matplotlib, netCDF4, pyproj, ...), e.g.:
 
 ```bash
 pip install numpy scipy netCDF4 matplotlib opencv-python pyyaml pyproj pint polygon3

doc/autodoc/observations.rst

@@ -1,7 +1,12 @@
 Observations
 ============
 
-.. automodule:: py_eddy_tracker.observations
+.. automodule:: py_eddy_tracker.observations.observation
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+.. automodule:: py_eddy_tracker.observations.tracking
     :members:
     :undoc-members:
     :show-inheritance:

doc/custom_tracking.rst

@@ -0,0 +1,3 @@
+==================
+Customize tracking
+==================

doc/grid_identification.rst

@@ -3,7 +3,32 @@ Eddy identification
 ===================
 
 Run the identification process for a single day
-***********************************************
+
+
+Shell/bash command
+******************
+
+Bash command will allow to process one grid, it will apply a filter and an identification.
+
+
+.. code-block:: bash
+
+    EddyId share/nrt_global_allsat_phy_l4_20190223_20190226.nc 20190223 \
+        adt ugos vgos longitude latitude \
+        out_directory -v DEBUG
+
+
+Filter could be modify with options *--cut_wavelength* and *--filter_order*. You could also defined height between two isolines with *--isoline_step*, which could
+improve speed profile quality and detect accurately tiny eddies. You could also use *--fit_errmax* to manage acceptable shape of eddies.
+
+An eddy identification will produce two files in the output directory, one for anticyclonic eddies and the other one for cyclonic.
+
+In regional area which are away from the equator, current could be deduce from height, juste write *None None* inplace of *ugos vgos*
+
+Python code
+***********
+
+If we want customize eddies identification, python module is here.
 
 Activate verbose
 

doc/index.rst

@@ -6,19 +6,30 @@
 Welcome to py-eddy-tracker's documentation!
 ===========================================
 
+
 .. toctree::
    :maxdepth: 2
    :caption: Installation
 
    installation
 
+
 .. toctree::
    :maxdepth: 2
    :caption: Grid manipulation
 
+   grid_identification
    grid_load_display
    spectrum
-   grid_identification
+
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Tracking
+
+   run_tracking
+   custom_tracking
+
 
 .. toctree::
    :maxdepth: 2

doc/run_tracking.rst

@@ -0,0 +1,33 @@
+========
+Tracking
+========
+
+To run a tracking just create an yaml file with minimal specification (*FILES_PATTERN* and *SAVE_DIR*).
+
+Example of yaml
+
+.. code-block:: yaml
+
+    PATHS:
+      # Files produces with EddyIdentification
+      FILES_PATTERN: MY/IDENTIFICATION_PATH/Anticyclonic*.nc
+      SAVE_DIR: MY_OUTPUT_PATH
+
+    # Number of timestep for missing detection
+    VIRTUAL_LENGTH_MAX: 3
+    # Minimal time to consider as a full track
+    TRACK_DURATION_MIN: 10
+
+To run:
+
+.. code-block:: bash
+
+    EddyTracking conf.yaml -v DEBUG
+
+
+It will produce 4 files by run:
+
+- A file of correspondances which will contains all the information to merge all identifications file
+- A file which will contains all the observations which are alone
+- A file which will contains all the short track which are shorter than TRACK_DURATION_MIN
+- A file which will contains all the long track which are longer than TRACK_DURATION_MIN

src/scripts/EddyId

@@ -24,7 +24,7 @@ def id_parser():
     parser.add_argument('--filter_order', default=3, type=int)
     parser.add_argument('--isoline_step', default=0.002, type=float,
                         help='Step between 2 isoline in m')
-    parser.add_argument('--fir_errmax', default=55, type=float,
+    parser.add_argument('--fit_errmax', default=55, type=float,
                         help='Error max accepted to fit circle in percent')
     parser.add_argument('--height_unit', default=None, type=str,
                         help='Force height unit')
@@ -49,7 +49,7 @@ if __name__ == '__main__':
     if args.cut_wavelength != 0:
         h.bessel_high_filter(args.h, args.cut_wavelength, order=args.filter_order)
     a, c = h.eddy_identification(args.h, u, v, date, args.isoline_step, pixel_limit=(5, 2000),
-                                 shape_error=args.fir_errmax, force_height_unit=args.height_unit,
+                                 shape_error=args.fit_errmax, force_height_unit=args.height_unit,
                                  force_speed_unit=args.speed_unit)
     if args.zarr:
         h = zarr.open(args.path_out + date.strftime('/Anticyclonic_%Y%m%d.zarr'), 'w')