Add options to manage filename

Add some correction for numpy/python3

Author: adelepoulle

src/py_eddy_tracker/featured_tracking/old_tracker_reference.py

@@ -6,7 +6,7 @@
 
 
 class CheltonTracker(Model):
-    GROUND = GridDataset(path.join(path.dirname(__file__), 'mask_old.nc'), 'lon', 'lat')
+    GROUND = GridDataset(path.join(path.dirname(__file__), '/data/adelepoulle/Test/Test_eddy/20180220_high_res_mask/mask_1_60.nc'), 'lon', 'lat')
 
     @staticmethod
     def cost_function(records_in, records_out, distance):

src/py_eddy_tracker/grid/aviso.py

@@ -203,7 +203,7 @@ def set_mask(self, sla):
                 self.mask[:125, minus70] = True
 
                 # Mask all unwanted regions (Caspian Sea, etc)
-                self.labels = ndimage.label(-self.mask)[0]
+                self.labels = ndimage.label(~self.mask)[0]
 
                 # Set to known sea point
                 plus200 = argmin(abs(self.lonpad[0] - 200))

src/py_eddy_tracker/observations.py

@@ -37,6 +37,7 @@
 from shapely.geos import TopologicalError
 from . import VAR_DESCR, VAR_DESCR_inv
 import logging
+from datetime import datetime
 from scipy.interpolate  import RectBivariateSpline
 
 
@@ -781,7 +782,7 @@ def write_netcdf(self, path='./', filename='%(path)s/%(sign_type)s.nc'):
         """
         eddy_size = len(self.observations)
         sign_type = 'Cyclonic' if self.sign_type == -1 else 'Anticyclonic'
-        filename = filename % dict(path=path, sign_type=sign_type)
+        filename = filename % dict(path=path, sign_type=sign_type, prod_time=datetime.now().strftime('%Y%d%d'))
         logging.info('Store in %s', filename)
         with Dataset(filename, 'w', format='NETCDF4') as h_nc:
             logging.info('Create file %s', filename)

src/py_eddy_tracker/tracking.py

@@ -298,11 +298,12 @@ def load_state(self):
             flg_virtual = self.previous_correspondance.virtual
             with Dataset(self.filename_previous_correspondance) as general_handler:
                 self.current_id = general_handler.last_current_id
-                # Load last virtual obs
-                self.virtual_obs = VirtualEddiesObservations.from_netcdf(general_handler.groups['LastVirtualObs'])
-                # Load and last previous virtual obs to be merge with current => will be previous2_obs
-                self.current_obs = self.current_obs.merge(
-                    VirtualEddiesObservations.from_netcdf(general_handler.groups['LastPreviousVirtualObs']))
+                if flg_virtual:
+                    # Load last virtual obs
+                    self.virtual_obs = VirtualEddiesObservations.from_netcdf(general_handler.groups['LastVirtualObs'])
+                    # Load and last previous virtual obs to be merge with current => will be previous2_obs
+                    self.current_obs = self.current_obs.merge(
+                        VirtualEddiesObservations.from_netcdf(general_handler.groups['LastPreviousVirtualObs']))
             return first_dataset, flg_virtual
         return 1, False
 
@@ -406,8 +407,8 @@ def load_compatible(self, filename):
 
     @classmethod
     def load(cls, filename):
+        logging.info('Try load %s', filename)
         with Dataset(filename, 'r', format='NETCDF4') as h_nc:
-            logging.info('load %s', filename)
             datasets = list(h_nc.variables['FileIn'][:])
             datasets.append(h_nc.variables['FileOut'][-1])
 

src/scripts/EddyFinalTracking

@@ -24,6 +24,9 @@ def usage():
     parser.add_argument('--path_out',
                         default='./',
                         help='Path, where to write file')
+    parser.add_argument('--filename_model',
+                        default='%(path)s/%(sign_type)s.nc',
+                        help='Model to create file')
     parser.add_argument('--nb_obs_min',
                         type=int,
                         default=28,
@@ -61,4 +64,4 @@ if __name__ == '__main__':
     logging.info('%d tracks will be saved', len(unique(FINAL_EDDIES['track'])))
     logging.info('The mean length is %d observations after filtering', CORRESPONDANCES.nb_obs_by_tracks.mean())
 
-    FINAL_EDDIES.write_netcdf(path=CONFIG.path_out)
+    FINAL_EDDIES.write_netcdf(path=CONFIG.path_out, filename=CONFIG.filename_model)

src/scripts/EddyTracking

@@ -22,32 +22,43 @@ def usage():
         "Tool to use identification step to compute tracking")
     parser.add_argument('yaml_file',
                         help='Yaml file to configure py-eddy-tracker')
-    parser.add_argument('--filename',
+    parser.add_argument('--correspondance_in',
+                        help='Filename to save correspondance')
+    parser.add_argument('--correspondance_out',
                         help='Filename to save correspondance')
     parser.add_argument('--save_correspondance_and_stop',
                         action='store_true',
                         help='Stop tracking after correspondance computation,'
                              ' merging can be done with EddyFinalTracking')
+    parser.add_argument('--blank_period',
+                        type=int,
+                        default=0,
+                        help='Nb of detection which will not use at the end of the period')
     args = parser.parse_args()
 
     # Read yaml configuration file
     with open(args.yaml_file, 'r') as stream:
         config = yaml_load(stream)
-    return config, args.save_correspondance_and_stop, args.filename
+    if not exists(args.correspondance_in):
+        args.correspondance_in = None
+    return config, args.save_correspondance_and_stop, args.correspondance_in, args.correspondance_out, args.blank_period
 
 
 if __name__ == '__main__':
-    CONFIG, SAVE_STOP, CORRESPONDANCES_OUT = usage()
+    CONFIG, SAVE_STOP, CORRESPONDANCES_IN, CORRESPONDANCES_OUT, BLANK_PERIOD = usage()
 
     # Create output directory
     SAVE_DIR = CONFIG['PATHS'].get('SAVE_DIR', None)
     if SAVE_DIR is not None and not exists(SAVE_DIR):
         mkdir(SAVE_DIR)
 
+    YAML_CORRESPONDANCES_IN = CONFIG['PATHS'].get('CORRESPONDANCES_IN', None)
     YAML_CORRESPONDANCES_OUT = CONFIG['PATHS'].get('CORRESPONDANCES_OUT', None)
-    if CORRESPONDANCES_OUT is None and YAML_CORRESPONDANCES_OUT is not None:
+    if CORRESPONDANCES_IN is None:
+        CORRESPONDANCES_IN = YAML_CORRESPONDANCES_IN
+    if CORRESPONDANCES_OUT is None:
         CORRESPONDANCES_OUT = YAML_CORRESPONDANCES_OUT
-    else:
+    if YAML_CORRESPONDANCES_OUT is None and CORRESPONDANCES_OUT is None:
         CORRESPONDANCES_OUT = 'Correspondances.nc'
 
     if 'CLASS' in CONFIG:
@@ -68,14 +79,18 @@ if __name__ == '__main__':
         FILENAMES += glob(PATTERN)
     FILENAMES.sort()
 
+    if BLANK_PERIOD > 0:
+        FILENAMES = FILENAMES[:-BLANK_PERIOD]
+        logging.info('Last %d files will be pop', BLANK_PERIOD)
+
     START_TIME = dt.datetime.now()
     logging.info('Start tracking on %d files', len(FILENAMES))
 
     CORRESPONDANCES = Correspondances(
         datasets=FILENAMES,
         virtual=NB_VIRTUAL_OBS_MAX_BY_SEGMENT,
         class_method=CLASS,
-        previous_correspondance=CONFIG['PATHS'].get('CORRESPONDANCES_IN', None))
+        previous_correspondance=CORRESPONDANCES_IN)
 
     DATE_START, DATE_STOP = CORRESPONDANCES.period
     DICT_COMPLETION = dict(date_start=DATE_START, date_stop=DATE_STOP, date_prod=START_TIME)