minor fixes

examples/soundspeed/profile/ex_plot_bias_tracedprofile.py

@@ -3,14 +3,15 @@
 
 import numpy as np
 
+from hyo2.abc.lib.logging import set_logging
 from hyo2.soundspeed.profile.profile import Profile
 from hyo2.soundspeed.profile.profilelist import ProfileList
 from hyo2.soundspeed.profile.ray_tracing.tracedprofile import TracedProfile
 from hyo2.soundspeed.profile.ray_tracing.diff_tracedprofiles import DiffTracedProfiles
 from hyo2.soundspeed.profile.ray_tracing.plot_tracedprofiles import PlotTracedProfiles
 
-logging.basicConfig(level=logging.DEBUG)
 logger = logging.getLogger(__name__)
+set_logging(ns_list=["hyo2.soundspeed", ])
 
 
 # create an example profile for testing
@@ -52,3 +53,4 @@ def make_fake_ssp(bias=0.0):
 
 plot = PlotTracedProfiles(diff_tps=diff)
 plot.make_bias_plots()
+plot.make_comparison_plots()

examples/soundspeed/profile/ex_tracedprofile.py

@@ -17,46 +17,54 @@
 
 
 logger = logging.getLogger(__name__)
-set_logging()
+set_logging(ns_list=["hyo2.soundspeed", ])
 
 
 # create an example profile for testing
-def make_fake_ssp(bias=0.0):
+def make_fake_ssp(bias=0.0, nr_samples=100):
  p = Profile()
- d = np.arange(0.0, 100.0, 0.5)
- vs = np.arange(1450.0 + bias, 1550.0 + bias, 0.5)
- t = np.arange(0.0, 100.0, 0.5)
- s = np.arange(0.0, 100.0, 0.5)
+ d = np.linspace(0.0, 16.0, nr_samples)
+ vs_up = int(nr_samples / 4)
+ vs_down = nr_samples - 3 * vs_up
+ vs = np.concatenate([
+ np.linspace(1535.0 + bias, 1532.0 + bias, vs_up),
+ np.linspace(1532.0 + bias, 1528.0 + bias, vs_up),
+ np.linspace(1528.0 + bias, 1523.0 + bias, vs_up),
+ np.linspace(1523.0 + bias, 1500.0 + bias, vs_down)
+ ])
+ t = np.linspace(10.0, 20.0, nr_samples)
+ s = np.linspace(34.0, 35.0, nr_samples)
  p.init_proc(d.size)
  p.proc.depth = d
  p.proc.speed = vs
  p.proc.temp = t
  p.proc.sal = s
- p.proc.flag[40:50] = Dicts.flags['user']
- p.proc.flag[50:70] = Dicts.flags['filtered']
+ p.proc.flag[40:42] = Dicts.flags['user']
+ p.proc.flag[50:52] = Dicts.flags['filtered']
  p.meta.latitude = 43.13555
  p.meta.longitude = -70.9395
  p.meta.utc_time = datetime.utcnow()
  return p
 
 
-tss_depth = 5.0
-tss_value = 1500.0
-avg_depth = 1000.0
-half_swath_angle = 65.0
+tss_depth = 1.0
+tss_value = 1534.0
+avg_depth = 100.0
+half_swath_angle = 90.0
 ssp = make_fake_ssp(bias=0.0)
+# ssp.proc_debug_plot()
+# plt.show()
 ssp_list = ProfileList()
 ssp_list.append_profile(ssp)
-ssp_list.debug_plot()
-plt.show()
 
 start_time = datetime.now()
 profile = TracedProfile(tss_depth=tss_depth, tss_value=tss_value,
- avg_depth=avg_depth, # half_swath=half_swath_angle,
+ avg_depth=avg_depth, half_swath=half_swath_angle,
  ssp=ssp_list.cur)
 end_time = datetime.now()
 logger.debug("timing: %s" % (end_time - start_time))
 
 logger.debug("traced profile:\n%s" % profile)
-logger.debug("api:\n%s" % dir(profile))
-logger.debug("rays:\n%s" % profile.str_rays())
+# profile.debug_rays(ray_idx=45)
+profile.debug_plot(ray_idx=90)
+plt.show()

hyo2/soundspeed/profile/oceanography.py

@@ -352,18 +352,22 @@ def in_situ_temp(cls, s, t, p, pr):
  return t
 
  temp = t
- new_pot_t = cls.pot_temp(s=s, t=t, p=p, pr=pr)
+ new_pot_t = cls.pot_temp(s=s, t=temp, p=p, pr=pr)
+ # logger.debug("p: %s, pr: %s" % (p, pr))
  if new_pot_t < t:
  sign = 1
  else:
  sign = -1
 
- dt = new_pot_t - temp
+ dt = new_pot_t - t
+ new_dt = new_pot_t - t
 
- while np.abs(dt) > 0.001:
+ while abs(new_dt) > 0.001:
+ if abs(new_dt) > abs(dt):
+ sign = -sign
  temp += sign * 0.001
  new_pot_t = cls.pot_temp(s=s, t=temp, p=p, pr=pr)
- dt = new_pot_t - t
+ new_dt = new_pot_t - t
 
  return temp
 

hyo2/soundspeed/profile/ray_tracing/diff_tracedprofiles.py

@@ -50,9 +50,9 @@ def calc_diff(self):
  # first retrieve common areas for both profiles (and reset the 0 values)
  for idx in range(len(ray_new[0])):
 
- if ray_new[0][idx] == -1:
+ if np.isnan(ray_new[0][idx]):
  continue
- if ray_old[0][idx] == -1:
+ if np.isnan(ray_old[0][idx]):
  continue
 
  if not init_done:

hyo2/soundspeed/profile/ray_tracing/plot_tracedprofiles.py

@@ -84,23 +84,39 @@ def make_comparison_plots(self):
  svp_ax.grid(True)
 
  # calculate limits
- z_max = max(max(self._d.new_rays[-1][2]),
- max(self._d.old_rays[-1][2]))
+ t_idx_max = max(np.nanargmax(self._d.new_rays[-1][0]),
+ np.nanargmax(self._d.old_rays[-1][0]))
+ z_max = self._d.new_rays[-1][2][t_idx_max]
  x_max = max(max(self._d.new_rays[-1][1]),
  max(self._d.old_rays[-1][1]))
+ logger.debug("z max: %s, x max: %s" % (z_max, x_max))
 
- old_last_ray_x = self._d.old_rays[-1][1]
  new_last_ray_x = self._d.new_rays[-1][1]
- old_last_ray_z = self._d.old_rays[-1][2]
  new_last_ray_z = self._d.new_rays[-1][2]
- old_x_ends = [ray[1][-1] for ray in self._d.old_rays]
- new_x_ends = [ray[1][-1] for ray in self._d.new_rays]
- old_z_ends = [ray[2][-1] for ray in self._d.old_rays]
- new_z_ends = [ray[2][-1] for ray in self._d.new_rays]
- up_tol = [(ray[2][-1] - ray[2][-1] * self._d.variable_allowable_error - self._d.fixed_allowable_error)
- for ray in self._d.new_rays]
- down_tol = [(ray[2][-1] + ray[2][-1] * self._d.variable_allowable_error + self._d.fixed_allowable_error)
- for ray in self._d.new_rays]
+ new_t_max = np.nanmax(self._d.new_rays[-1][0])
+ old_t_idx_max = np.nanargmin(np.abs(self._d.old_rays[-1][0] - new_t_max))
+ old_last_ray_x = self._d.old_rays[-1][1][:old_t_idx_max]
+ old_last_ray_z = self._d.old_rays[-1][2][:old_t_idx_max]
+
+ new_x_ends = list()
+ new_z_ends = list()
+ old_x_ends = list()
+ old_z_ends = list()
+ up_tol = list()
+ down_tol = list()
+ for ray_idx, new_ray in enumerate(self._d.new_rays):
+ old_ray = self._d.old_rays[ray_idx]
+ new_t_idx_max = np.nanargmax(new_ray[0])
+ new_x_ends.append(new_ray[1][new_t_idx_max])
+ new_z_ends.append(new_ray[2][new_t_idx_max])
+ new_t_max = new_ray[0][new_t_idx_max]
+ old_t_idx_max = np.nanargmin(np.abs(old_ray[0] - new_t_max))
+ old_x_ends.append(old_ray[1][old_t_idx_max])
+ old_z_ends.append(old_ray[2][old_t_idx_max])
+ up_tol.append(new_ray[2][new_t_idx_max] - new_ray[2][new_t_idx_max] * self._d.variable_allowable_error -
+ self._d.fixed_allowable_error)
+ down_tol.append(new_ray[2][new_t_idx_max] + new_ray[2][new_t_idx_max] * self._d.variable_allowable_error +
+ self._d.fixed_allowable_error)
 
  # error plot axis
  err_ax = fig.add_subplot(1, 2, 2)
@@ -138,10 +154,12 @@ def make_bias_plots(self):
 
  start_time = datetime.now()
 
- z_max = max(max(self._d.new_rays[-1][2]),
- max(self._d.old_rays[-1][2]))
- x_max = max(max(self._d.new_rays[-1][1]),
- max(self._d.old_rays[-1][1]))
+ t_idx_max = max(np.nanargmax(self._d.new_rays[-1][0]),
+ np.nanargmax(self._d.old_rays[-1][0]))
+ z_max = self._d.new_rays[-1][2][t_idx_max]
+ x_max = max(np.nanmax(self._d.new_rays[-1][1]),
+ np.nanmax(self._d.old_rays[-1][1]))
+ logger.debug("z max: %s, x max: %s" % (z_max, x_max))
 
  xi, zi = np.mgrid[0:x_max:1000j, 0:z_max:1000j]
 
@@ -175,6 +193,11 @@ def make_bias_plots(self):
  logger.debug("skipping idx %s" % idx)
  continue
 
+ if np.isnan(ray[0][idx]) or np.isnan(ray[1][idx]):
+ continue
+ if np.isnan(self._d.old_rays[ang][0][idx]) or np.isnan(self._d.old_rays[ang][1][idx]):
+ continue
+
  t1 = np.append(t1, ray[0][idx])
  x1 = np.append(x1, ray[1][idx])
  z1 = np.append(z1, ray[2][idx])
@@ -190,10 +213,11 @@ def make_bias_plots(self):
  logger.debug("timing: %s" % (datetime.now() - start_time))
 
  # noinspection PyTypeChecker
- dxi = interpolate.griddata((x1, z1), dx, (xi, zi), method='linear')
+ dxi = interpolate.griddata((x1, z1), dx, (xi, zi), method='cubic')
  logger.debug("dxi: %s, min: %s, max: %s" % (dxi.shape, np.nanmin(dxi), np.nanmax(dxi)))
  # noinspection PyTypeChecker
- dzi = interpolate.griddata((x1, z1), dz, (xi, zi), method='linear')
+ dzi = interpolate.griddata((x1, z1), dz, (xi, zi), method='cubic')
+ logger.debug("dzi: %s, min: %s, max: %s" % (dzi.shape, np.nanmin(dzi), np.nanmax(dzi)))
 
  logger.debug("timing: %s" % (datetime.now() - start_time))
 

hyo2/soundspeed/profile/ray_tracing/tracedprofile.py

@@ -140,11 +140,12 @@ def __init__(self, ssp, half_swath=65, avg_depth=10000, tss_depth=None, tss_valu
  interp_x = fx(interp_z)
  ft = interp1d(total_z, total_t, kind='cubic', bounds_error=False, fill_value=np.nan)
  interp_t = ft(interp_z)
-
  elif len(depths) == 1:
  interp_z = total_z
  interp_x = total_x
  interp_t = total_t
+ else:
+ raise RuntimeError("invalid profile with zero valid depth values")
 
  self.rays.append(np.array([interp_t, interp_x, interp_z]))
 
@@ -166,7 +167,7 @@ def debug_rays(self, ray_idx=0):
  logger.debug("%10.4f %10.3f %10.2f"
  % (self.rays[ray_idx][0][idx], self.rays[ray_idx][1][idx], self.rays[ray_idx][2][idx]))
 
- def plot(self, ray_idx=0):
+ def debug_plot(self, ray_idx=0):
  nr_rays = len(self.rays)
  if (ray_idx < 0) or (ray_idx >= nr_rays):
  logger.warning("invalid ray index: %d (total rays: %d)" % (ray_idx, nr_rays))
@@ -176,7 +177,7 @@ def plot(self, ray_idx=0):
 
  plt.figure("Traced Profile", dpi=120)
 
- plt.subplot(131) # time
+ plt.subplot(131) # profile
  plt.plot(self.data[1], self.data[0])
  plt.gca().invert_yaxis()
  plt.grid(True)

setup.cfg

@@ -1,2 +1,2 @@
 [bdist_wheel]
-universal = 0
+universal = 1

setup.py

@@ -49,7 +49,6 @@ def find_version(*file_paths):
  setup_requires=[
  "setuptools",
  "wheel",
- "cython",
  ],
  install_requires=[
  "hyo2.abc",