removed Cythonized traced profile

examples/soundspeed/profile/ex_tracedprofile.py

@@ -7,50 +7,56 @@
 
 from datetime import datetime
 import numpy as np
+from matplotlib import pyplot as plt
 
+from hyo2.abc.lib.logging import set_logging
 from hyo2.soundspeed.profile.profile import Profile
 from hyo2.soundspeed.profile.dicts import Dicts
 from hyo2.soundspeed.profile.profilelist import ProfileList
 from hyo2.soundspeed.profile.ray_tracing.tracedprofile import TracedProfile
 
-logging.basicConfig(level=logging.DEBUG)
+
 logger = logging.getLogger(__name__)
+set_logging()
 
 
 # create an example profile for testing
 def make_fake_ssp(bias=0.0):
- ssp = Profile()
+ 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)
- ssp.init_proc(d.size)
- ssp.proc.depth = d
- ssp.proc.speed = vs
- ssp.proc.temp = t
- ssp.proc.sal = s
- ssp.proc.flag[40:50] = Dicts.flags['user']
- ssp.proc.flag[50:70] = Dicts.flags['filtered']
- ssp.meta.latitude = 43.13555
- ssp.meta.longitude = -70.9395
- ssp.meta.utc_time = datetime.utcnow()
- return ssp
+ 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.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 = 70.0
+half_swath_angle = 65.0
 ssp = make_fake_ssp(bias=0.0)
 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("api:\n%s" % dir(profile))
+logger.debug("rays:\n%s" % profile.str_rays())

hyo2/soundspeed/__init__.py

@@ -12,7 +12,7 @@
 logger.addHandler(logging.NullHandler())
 
 name = "Sound Speed"
-__version__ = '2019.2.1'
+__version__ = '2019.3.0'
 __copyright__ = 'Copyright 2019 University of New Hampshire, Center for Coastal and Ocean Mapping'
 
 lib_info = LibInfo()

hyo2/soundspeed/profile/ray_tracing/tracedprofile.pyx → hyo2/soundspeed/profile/ray_tracing/tracedprofile.py

@@ -1,37 +1,23 @@
-cimport numpy
-import numpy
-from scipy.interpolate import interp1d
+import numpy as np
 import math
-from cpython cimport datetime
 import logging
+from scipy.interpolate import interp1d
 
 logger = logging.getLogger(__name__)
 
-from hyo2.soundspeed.profile.dicts import Dicts
-
-
-cdef class TracedProfile:
 
- cpdef public double avg_depth
- cpdef public double half_swath
- cpdef public list rays
- cpdef public list harmonic_means
- cpdef public datetime.datetime date_time
- cpdef public double latitude
- cpdef public double longitude
- cpdef public list data
+class TracedProfile:
 
- def __init__(self, ssp, double half_swath=70, double avg_depth=10000, tss_depth=None, tss_value=None):
+ def __init__(self, ssp, half_swath=65, avg_depth=10000, tss_depth=None, tss_value=None):
  # PyDateTime_IMPORT
  self.avg_depth = avg_depth
  self.half_swath = half_swath
 
  # select samples for the ray tracing (must be deeper than the transducer depth)
  depths = list()
- if tss_depth is not None:
- depths.append(tss_depth)
  speeds = list()
- if tss_value is not None:
+ if (tss_depth is not None) and (tss_value is not None):
+ depths.append(tss_depth)
  speeds.append(tss_value)
 
  vi = ssp.proc_valid
@@ -66,7 +52,7 @@ def __init__(self, ssp, double half_swath=70, double avg_depth=10000, tss_depth=
  # ray-trace a few angles (ref: Lurton, An Introduction to UA, p.50-52)
  self.rays = list()
  self.harmonic_means = list()
- for angle in numpy.arange(0, int(math.ceil(self.half_swath + 1))):
+ for angle in np.arange(0, int(math.ceil(self.half_swath + 1))):
 
  # ray angles
  beta = list()
@@ -149,34 +135,64 @@ def __init__(self, ssp, double half_swath=70, double avg_depth=10000, tss_depth=
 
  # interpolate between 0 and 5000 meters with decimetric resolution
  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_z = np.linspace(0, 5000, num=25001, endpoint=True)
+ fx = interp1d(total_z, total_x, kind='cubic', bounds_error=False, fill_value=np.nan)
  interp_x = fx(interp_z)
- ft = interp1d(total_z, total_t, kind='cubic', bounds_error=False, fill_value=-1)
+ 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
 
- self.rays.append(numpy.array([interp_t, interp_x, interp_z]))
+ self.rays.append(np.array([interp_t, interp_x, interp_z]))
 
  logger.debug("rays: %d (%d samples per-ray)" % (len(self.rays), len(self.rays[0][0])))
  self.date_time = ssp.meta.utc_time
  self.latitude = ssp.meta.latitude
  self.longitude = ssp.meta.longitude
  self.data = [depths, speeds]
 
- def str_rays(self):
- msg = str()
- for ang in range(len(self.rays)):
- msg += "[%d]\n" % ang
-
- for idx in range(len(self.rays[ang][0])):
- msg += "%10.2f %10.2f %10.2f\n" \
- % (self.rays[ang][0][idx], self.rays[ang][1][idx], self.rays[ang][2][idx])
- return msg
+ def debug_rays(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))
+ return
+
+ logger.debug("[%d]" % ray_idx)
+ logger.debug("t | x | z |")
+ for idx in range(len(self.rays[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):
+ 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))
+ return
+
+ from matplotlib import pyplot as plt
+
+ plt.figure("Traced Profile", dpi=120)
+
+ plt.subplot(131) # time
+ plt.plot(self.data[1], self.data[0])
+ plt.gca().invert_yaxis()
+ plt.grid(True)
+ plt.title('profile')
+
+ plt.subplot(132) # time
+ plt.plot(self.rays[ray_idx][0], self.rays[ray_idx][2])
+ plt.gca().invert_yaxis()
+ plt.grid(True)
+ plt.title('z vs. time')
+
+ plt.subplot(133) # x
+ plt.plot(self.rays[ray_idx][1], self.rays[ray_idx][2])
+ plt.gca().invert_yaxis()
+ plt.grid(True)
+ plt.title('z vs. x')
 
  def __repr__(self):
  msg = "<%s>\n" % self.__class__.__name__
@@ -186,7 +202,7 @@ def __repr__(self):
  msg += " <longitude: %.7f>\n" % self.longitude
  msg += " <avg depth: %.3f>\n" % self.avg_depth
  msg += " <half swatch: %.1f>\n" % self.half_swath
- msg += " <profile valid samples: %d>" % len(self.data[0])
+ msg += " <profile valid samples: %d>\n" % len(self.data[0])
  msg += " <rays: %d>\n" % len(self.rays)
  msg += " <samples per ray: %d>\n" % len(self.rays[0][0])
 

hyo2/soundspeedmanager/__init__.py

@@ -11,7 +11,7 @@
 logger.addHandler(logging.NullHandler())
 
 name = "Sound Speed Manager"
-__version__ = "2019.2.1"
+__version__ = "2019.3.0"
 __copyright__ = "Copyright 2019 University of New Hampshire, Center for Coastal and Ocean Mapping"
 
 app_info = AppInfo()

hyo2/soundspeedsettings/__init__.py

@@ -11,7 +11,7 @@
 logger.addHandler(logging.NullHandler())
 
 name = "Sound Speed Settings"
-__version__ = '2019.2.1'
+__version__ = '2019.3.0'
 __copyright__ = 'Copyright 2019 University of New Hampshire, Center for Coastal and Ocean Mapping'
 
 app_info = AppInfo()

setup.py

@@ -1,11 +1,9 @@
 import codecs
 import os
 import re
-import numpy as np
 
 # Always prefer setuptools over distutils
-from setuptools import setup, find_packages, Extension
-from Cython.Build import cythonize
+from setuptools import setup, find_packages
 
 # ------------------------------------------------------------------
 # HELPER FUNCTIONS
@@ -62,18 +60,6 @@ def find_version(*file_paths):
  "scipy",
  "basemap" # you may also need: conda install -c conda-forge basemap-data-hires
  ],
- ext_modules=cythonize([
- Extension("hyo2.soundspeed.profile.ray_tracing.tracedprofile",
- sources=["hyo2/soundspeed/profile/ray_tracing/tracedprofile.pyx"],
- include_dirs=[np.get_include()],
- language='c++',
- # extra_compile_args=["-Zi", "/Od"],
- # extra_link_args=["-debug"],
- ),
- ],
- annotate=True,
- compiler_directives={'language_level': '3'}
- ),
  python_requires='>=3.5',
  entry_points={
  "gui_scripts": [