bug fixes for too short profiles and duplicated profile samples

hyo/soundspeed/__init__.py

@@ -7,7 +7,7 @@
 log = logging.getLogger(__name__)
 log.addHandler(logging.NullHandler())
 
-__version__ = '2018.1.43'
+__version__ = '2018.1.44'
 __doc__ = "Sound Speed"
 __author__ = '[email protected]; [email protected]; [email protected]; ' \
  '[email protected]'

hyo/soundspeed/profile/ray_tracing/diff_tracedprofiles.py

@@ -75,6 +75,11 @@ def calc_diff(self):
 
  # logger.debug("end z: %s/%s" % (new_z[-1], old_z[-1]))
 
+ if (len(new_t) == 0) or (len(old_t) == 0):
+ self.new_rays.append(np.array([list(), list(), list()]))
+ self.old_rays.append(np.array([list(), list(), list()]))
+ return
+
  new_is_longer = False
  min_time = new_t[-1]
  if new_t[-1] > old_t[-1]:

hyo/soundspeed/profile/ray_tracing/tracedprofile.pyx

@@ -52,9 +52,10 @@ cdef class TracedProfile:
  break
 
  # remove extension value (if any)
- if (depths[-1] - depths[-2]) > 1000:
- logger.info("removed latest extension depth: %s" % depths[-1])
- del depths[-1]
+ if len(depths) > 3:
+ if (depths[-1] - depths[-2]) > 1000:
+ logger.info("removed latest extension depth: %s" % depths[-1])
+ del depths[-1]
 
  logger.info("profile timestamp: %s" % ssp.meta.utc_time)
  logger.debug("valid samples: %d" % (len(depths)), )
@@ -90,7 +91,8 @@ cdef class TracedProfile:
 
  if dz == 0: # if (dc == 0) and (dy == 0):
 
- logger.warning("skipping duplicated point: #%d" % idx)
+ # logger.debug("duplicated point: #%d" % idx)
+ beta.append(beta[idx]) # beta does not change
  continue
 
  # gradient = dc/dy
@@ -137,15 +139,27 @@ cdef class TracedProfile:
  # logger.debug("x:\n%s" % total_x)
  # logger.debug("t:\n%s" % total_t)
 
- harm_mean = (total_z[-1] - total_z[0]) / (total_t[-1] - total_t[0])
+ if len(depths) > 1:
+ harm_mean = (total_z[-1] - total_z[0]) / (total_t[-1] - total_t[0])
+ elif len(depths) == 1:
+ harm_mean = depths[0]
+ else:
+ raise RuntimeError("invalid profile with zero valid depth values")
  self.harmonic_means.append(harm_mean)
 
  # interpolate between 0 and 5000 meters with decimetric resolution
- interp_z = numpy.linspace(0, 5000, num=25001, endpoint=True)
- fx = interp1d(total_z, total_x, kind='cubic', bounds_error=False, fill_value=-1)
- interp_x = fx(interp_z)
- ft = interp1d(total_z, total_t, kind='cubic', bounds_error=False, fill_value=-1)
- interp_t = ft(interp_z)
+ if len(depths) > 1:
+ interp_z = numpy.linspace(0, 5000, num=25001, endpoint=True)
+ fx = interp1d(total_z, total_x, kind='cubic', bounds_error=False, fill_value=-1)
+ interp_x = fx(interp_z)
+ ft = interp1d(total_z, total_t, kind='cubic', bounds_error=False, fill_value=-1)
+ interp_t = ft(interp_z)
+
+ elif len(depths) == 1:
+ interp_z = total_z
+ interp_x = total_x
+ interp_t = total_t
+
  self.rays.append(numpy.array([interp_t, interp_x, interp_z]))
 
  logger.debug("rays: %d (%d samples per-ray)" % (len(self.rays), len(self.rays[0][0])))

hyo/soundspeedmanager/__init__.py

@@ -6,7 +6,7 @@
 logger = logging.getLogger(__name__)
 logger.addHandler(logging.NullHandler())
 
-__version__ = '2018.1.43'
+__version__ = '2018.1.44'
 __doc__ = "Sound Speed Manager"
 __author__ = '[email protected]; [email protected]; [email protected]; ' \
  '[email protected]'

hyo/soundspeedsettings/__init__.py

@@ -6,7 +6,7 @@
 logger = logging.getLogger(__name__)
 logger.addHandler(logging.NullHandler())
 
-__version__ = '2018.1.43'
+__version__ = '2018.1.44'
 __doc__ = "Sound Speed Settings"
 __author__ = '[email protected]; [email protected]; [email protected]; ' \
  '[email protected]'

setup.py

@@ -33,7 +33,7 @@ def txt_read(*paths):
 setup_args = dict()
 
 setup_args['name'] = 'hyo.soundspeed'
-setup_args['version'] = '2018.1.43'
+setup_args['version'] = '2018.1.44'
 setup_args['url'] = 'https://bitbucket.org/ccomjhc/hyo_soundspeed/'
 setup_args['license'] = 'LGPLv2.1 or CCOM-UNH Industrial Associate license'
 setup_args['author'] = 'Giuseppe Masetti(UNH,CCOM); Barry Gallagher(NOAA,OCS); ' \