merge

Author: adelepoulle

README.md

@@ -2,6 +2,18 @@
 
 # README #
 
+### Method ###
+
+Method was described in :
+
+[Mason, E., A. Pascual, and J. C. McWilliams, 2014: A new sea surface height–based code for oceanic mesoscale eddy tracking.](https://doi.org/10.1002/2016JC012611)
+
+### Use case ###
+
+Method is used in :
+ 
+[Mason, E., A. Pascual, P. Gaube, S.Ruiz, J. Pelegrí, A. Delepoulle, 2017: Subregional characterization of mesoscale eddies across the Brazil-Malvinas Confluence](https://doi.org/10.1002/2016JC012611)
+
 ### How do I get set up? ###
 
 To avoid problems with installation, use of the virtualenv Python virtual environment is recommended.
@@ -35,7 +47,3 @@ EddyTracking tracking.yaml
 for tracking.
 
 
-# Py Eddy Tracker module #
-
-### Grid manipulation ###
-

setup.py

@@ -7,15 +7,16 @@
     name="pyEddyTracker",
     version='3.0.0',
     description="Py-Eddy-Tracker libraries",
-    classifiers=['Development Status :: Alpha',
-                 'Topic :: Eddy',
+    classifiers=['Development Status :: 3 - Alpha',
+                 'Topic :: Scientific/Engineering :: Physics',
                  'Programming Language :: Python'],
     keywords='eddy science',
     author='emason',
     author_email='[email protected]',
     packages=find_packages('src'),
     package_dir={'': 'src'},
     scripts=[
+        'src/scripts/GridFiltering',
         'src/scripts/EddyId',
         'src/scripts/EddyIdentification',
         'src/scripts/EddyTracking',
@@ -33,13 +34,16 @@
     ext_modules=[Extension("py_eddy_tracker.tools",
                            ["src/py_eddy_tracker/tools.pyx"],
                            include_dirs=[numpy.get_include()])],
-    package_data={'py_eddy_tracker.featured_tracking': ['*.nc', ]},
+    package_data={
+        'py_eddy_tracker.featured_tracking': ['*.nc'],
+        'py_eddy_tracker': ['data/*.nc'],
+    },
     setup_requires=[
         'numpy>=1.14'],
     install_requires=[
         'numpy>=1.14',
         # Bug with 1.5.1 (slow memory leak)
-        'matplotlib>=2.0.0',
+        # 'matplotlib>=2.0.0',
         'scipy>=0.15.1',
         'netCDF4>=1.1.0',
         'opencv-python',

share/fig.py

@@ -0,0 +1,53 @@
+from matplotlib import pyplot as plt
+from py_eddy_tracker.dataset.grid import RegularGridDataset
+grid_name, lon_name, lat_name = 'nrt_global_allsat_phy_l4_20190223_20190226.nc', 'longitude', 'latitude'
+if False:
+
+    h = RegularGridDataset(grid_name, lon_name, lat_name)
+    
+    fig = plt.figure(figsize=(14, 12))
+    ax = fig.add_axes([.02, .51, .9, .45])
+    ax.set_title('ADT (m)')
+    ax.set_ylim(-75, 75)
+    ax.set_aspect('equal')
+    m = h.display(ax, name='adt', vmin=-1, vmax=1)
+    ax.grid(True)
+    plt.colorbar(m, cax=fig.add_axes([.94, .51, .01, .45]))
+    h = RegularGridDataset(grid_name, lon_name, lat_name)
+    h.bessel_high_filter('adt', 500, order=3)
+    ax = fig.add_axes([.02, .02, .9, .45])
+    ax.set_title('ADT Filtered (m)')
+    ax.set_aspect('equal')
+    ax.set_ylim(-75, 75)
+    m = h.display(ax, name='adt', vmin=-.1, vmax=.1)
+    ax.grid(True)
+    plt.colorbar(m, cax=fig.add_axes([.94, .02, .01, .45]))
+    fig.savefig('png/filter.png')
+
+if True:
+    import logging
+    logging.getLogger().setLevel('DEBUG') # Values: ERROR, WARNING, INFO, DEBUG
+    from datetime import datetime
+    h = RegularGridDataset(grid_name, lon_name, lat_name)
+    h.bessel_high_filter('adt', 500, order=3)
+    # h.bessel_high_filter('adt', 300, order=1)
+    date = datetime(2019, 2, 23)
+    a, c = h.eddy_identification(
+        'adt', 'ugos', 'vgos', # Variable to use for identification
+        date, # Date of identification
+        0.002, # step between two isolines of detection (m)
+        # 0.02, # step between two isolines of detection (m)
+        pixel_limit=(5, 2000), # Min and max of pixel can be include in contour
+        shape_error=55, # Error maximal of circle fitting over contour to be accepted
+        bbox_surface_min_degree=.125 ** 2, # degrees surface minimal to take in account contour
+        )
+    fig = plt.figure(figsize=(15,7))
+    ax = fig.add_axes([.03,.03,.94,.94])
+    ax.set_title('Eddies detected -- Cyclonic(red) and Anticyclonic(blue)')
+    ax.set_ylim(-75,75)
+    ax.set_xlim(0,360)
+    ax.set_aspect('equal')
+    a.display(ax, color='b', linewidth=.5)
+    c.display(ax, color='r', linewidth=.5)
+    ax.grid()
+    fig.savefig('png/eddies.png')