Some suggestions

.gitignore

@@ -1,6 +1,8 @@
 .venv
 .vscode
 
+.devcontainer/
+
 __pycache__
 
 build
@@ -18,4 +20,6 @@ work
 
 key.asc
 .~*
-VERSION*
+VERSION*
+
+test/test_data/*.xlsx

setup.py

@@ -52,12 +52,15 @@
 
 # if someone wants to output a requirements file
 # `python setup.py --list-all > requirements.txt`
-if '--list-all' in sys.argv:
- # will not include default requirements (numpy)
- print('\n'.join(requirements_all))
+if '--list-default' in sys.argv:
+ print('\n'.join(requirements_default))
+ exit()
+elif '--list-all' in sys.argv:
+ requirements = requirements_all.union(requirements_default)
+ print('\n'.join(requirements))
  exit()
 elif '--list-easy' in sys.argv:
- # again will not include numpy+setuptools
+ requirements = requirements_easy.union(requirements_default)
  print('\n'.join(requirements_easy))
  exit()
 

welleng/errors/tool_errors.py

@@ -1,12 +1,11 @@
+import os
+
 import numpy as np
-from numpy import sin, cos, tan, pi, sqrt
-from numpy.core.defchararray import index
 import yaml
-import os
+
 from collections import OrderedDict
-# import imp
+from numpy import sin, cos, tan, pi, sqrt
 
-# import welleng.error
 from ..utils import NEV_to_HLA
 
 # since this is running on different OS flavors

welleng/survey.py

@@ -49,11 +49,7 @@ def __init__(
  deg=True,
  depth_unit='meters',
  surface_unit='meters',
- mag_defaults={
- 'b_total': 50_000.,
- 'dip': 70.,
- 'declination': 0.,
- },
+ mag_defaults=None,
  **kwargs
  ):
  """
@@ -142,7 +138,11 @@ def __init__(
  self.G = G
  self.azi_reference = azi_reference
 
- self.mag_defaults = mag_defaults
+ self.mag_defaults = mag_defaults or {
+ 'b_total': 50_000.,
+ 'dip': 70.,
+ 'declination': 0.,
+ }
  self._get_mag_data(deg)
 
  def _get_mag_data(self, deg):
@@ -234,8 +234,8 @@ def __init__(
  cov_nev=None,
  cov_hla=None,
  error_model=None,
- start_xyz=[0., 0., 0.],
- start_nev=[0., 0., 0.],
+ start_xyz=None,
+ start_nev=None,
  start_cov_nev=None,
  deg=True,
  unit="meters",
@@ -325,8 +325,10 @@ def __init__(
  )
  self.unit = unit
  self.deg = deg
- self.start_xyz = start_xyz
- self.start_nev = start_nev
+
+ self.start_xyz = start_xyz or [0., 0., 0.]
+ self.start_nev = start_nev or [0., 0., 0.]
+
  self.md = np.array(md).astype('float64')
  self.start_cov_nev = start_cov_nev
 
@@ -384,6 +386,7 @@ def _process_azi_ref(self, inc, azi, deg):
  self.azi_true_deg - math.degrees(self.header.declination)
  )
  self._get_azi_mag_and_true_rad()
+
  elif self.header.azi_reference == 'true':
  if deg:
  self.azi_true_deg = np.array(azi).astype('float64')
@@ -400,6 +403,7 @@ def _process_azi_ref(self, inc, azi, deg):
  self._get_azi_mag_and_true_deg()
  azi_temp = self._get_azi_temp(deg)
  self._make_angles(inc, azi_temp, deg)
+
  else: # azi_reference is "magnetic"
  if deg:
  self.azi_mag_deg = np.array(azi).astype('float64')
@@ -444,8 +448,10 @@ def _get_azi_mag_and_true_deg(self):
  def _get_radius(self, radius=None):
  if radius is None:
  self.radius = np.full_like(self.md.astype(float), 0.3048)
+
  elif np.array([radius]).shape[-1] == 1:
  self.radius = np.full_like(self.md.astype(float), radius)
+
  else:
  assert len(radius) == len(self.md), "Check radius"
  self.radius = np.array(radius)
@@ -469,8 +475,10 @@ def _min_curve(self, vec):
  if self.x is None:
  # self.x, self.y, self.z = (mc.poss + self.start_xyz).T
  self.x, self.y, self.z = (mc.poss).T
+
  if self.n is None:
  self._get_nev()
+
  if vec is None:
  self.vec_xyz = get_vec(self.inc_rad, self.azi_grid_rad, deg=False)
  self.vec_nev = get_vec(
@@ -512,27 +520,29 @@ def get_error(self, error_model, return_error=False):
 
  if return_error:
  return self.err
- else:
-  return self
+
+ return self
 
  def _get_errors(self):
  """
  Initiate a welleng.error.ErrorModel object and calculate the
  covariance matrices with the specified error model.
  """
  if self.error_model:
- # if self.error_model == "iscwsa_mwd_rev4":
  self.err = ErrorModel(
  self,
  error_model=self.error_model
  )
  self.cov_hla = self.err.errors.cov_HLAs.T
  self.cov_nev = self.err.errors.cov_NEVs.T
+
  else:
  if self.cov_nev is not None and self.cov_hla is None:
  self.cov_hla = NEV_to_HLA(self.survey_rad, self.cov_nev.T).T
+
  elif self.cov_nev is None and self.cov_hla is not None:
  self.cov_nev = HLA_to_NEV(self.survey_rad, self.cov_hla.T).T
+
  else:
  pass
 
@@ -547,10 +557,7 @@ def _curvature_to_rate(self, curvature):
  with np.errstate(divide='ignore', invalid='ignore'):
  radius = 1 / curvature
  circumference = 2 * np.pi * radius
- if self.unit == 'meters':
- x = 30
- else:
- x = 100
+ x = 30 if self.unit == 'meters' else 100
  rate = np.absolute(np.degrees(2 * np.pi / circumference) * x)
 
  return rate
@@ -563,10 +570,7 @@ def _get_toolface_and_rates(self):
  # split the survey
  s = SplitSurvey(self)
 
- if self.unit == 'meters':
- x = 30
- else:
- x = 100
+ x = 30 if self.unit == 'meters' else 100
 
  # this is lazy I know, but I'm using this mostly for flags
  with np.errstate(divide='ignore', invalid='ignore'):
@@ -732,6 +736,7 @@ def project_to_bit(self, delta_md, dls=None, toolface=None):
  """
  if dls is None:
  dls = self.dls[-1]
+
  if toolface is None:
  toolface = self.toolface[-1]
 
@@ -817,10 +822,10 @@ def interpolate_md(survey, md):
  x = md - survey.md[idx]
  assert x >= 0
 
- return _interpolate_survey(survey, x=x, index=idx)
+ return _interpolate_survey(survey, md=x, index=idx)
 
 
-def _interpolate_survey(survey, x=0, index=0):
+def _interpolate_survey(survey, md=0, index=0):
  """
  Interpolates a point distance x between two survey stations
  using minimum curvature.
@@ -829,7 +834,7 @@ def _interpolate_survey(survey, x=0, index=0):
  ----------
  survey: welleng.Survey
  A survey object with at least two survey stations.
- x: float
+ md: float
  Length along well path from indexed survey station to
  perform the interpolate at. Must be less than length
  to the next survey station.
@@ -861,7 +866,7 @@ def _interpolate_survey(survey, x=0, index=0):
 
  total_dogleg = survey.dogleg[index + 1]
 
- dogleg = x * (total_dogleg / survey.delta_md[index + 1])
+ dogleg = md * (total_dogleg / survey.delta_md[index + 1])
 
  t = (
  (math.sin(total_dogleg - dogleg) / math.sin(total_dogleg)) * t1
@@ -876,7 +881,7 @@ def _interpolate_survey(survey, x=0, index=0):
  sh.azi_reference = 'grid'
 
  s = Survey(
- md=np.array([survey.md[index], survey.md[index] + x]),
+ md=np.array([survey.md[index], survey.md[index] + md]),
  inc=np.array([survey.inc_rad[index], inc]),
  azi=np.array([survey.azi_grid_rad[index], azi]),
  start_xyz=np.array([survey.x, survey.y, survey.z]).T[index],
@@ -885,8 +890,8 @@ def _interpolate_survey(survey, x=0, index=0):
  deg=False,
  )
  interpolated = False if any((
- x == 0,
- x == survey.md[index + 1] - survey.md[index]
+ md == 0,
+ md == survey.md[index + 1] - survey.md[index]
  )) else True
  s.interpolated = [False, interpolated]
 
@@ -932,7 +937,7 @@ def tidy_up_angle(d):
  dogleg = s_temp.dogleg[-1]
 
  if np.isnan(dogleg):
- return _interpolate_survey(survey, x=0, index=idx)
+ return _interpolate_survey(survey, md=0, index=idx)
 
  if dogleg == 0:
  x = (
@@ -989,7 +994,7 @@ def tidy_up_angle(d):
 
  assert x <= delta_md
 
- interpolated_survey = _interpolate_survey(survey, x=x, index=idx)
+ interpolated_survey = _interpolate_survey(survey, md=x, index=idx)
 
  interpolated = True if x > 0 else False
  node = get_node(interpolated_survey, 1, interpolated=interpolated)

welleng/utils.py

@@ -161,6 +161,7 @@ def get_vec(inc, azi, nev=False, r=1, deg=True):
  else:
  inc_rad = inc
  azi_rad = azi
+
  y = r * np.sin(inc_rad) * np.cos(azi_rad)
  x = r * np.sin(inc_rad) * np.sin(azi_rad)
  z = r * np.cos(inc_rad)
@@ -173,34 +174,35 @@ def get_vec(inc, azi, nev=False, r=1, deg=True):
  return vec / np.linalg.norm(vec, axis=-1).reshape(-1, 1)
 
 
-def get_nev(
- pos, start_xyz=np.array([0., 0., 0.]), start_nev=np.array([0., 0., 0.])
-):
+def get_nev(pos, start_xyz=None, start_nev=None):
  """
  Convert [x, y, z] coordinates to [n, e, tvd] coordinates.
 
  Params:
  pos: (n,3) array of floats
  Array of [x, y, z] coordinates
  start_xyz: (,3) array of floats
- The datum of the [x, y, z] cooardinates
+ The datum of the [x, y, z] coordinates
  start_nev: (,3) array of floats
  The datum of the [n, e, tvd] coordinates
 
  Returns:
  An (n,3) array of [n, e, tvd] coordinates.
  """
- # e, n, v = (
- # np.array([pos]).reshape(-1,3) - np.array([start_xyz])
- # ).T
+ start_xyz = start_xyz or np.array([0., 0., 0.])
+ start_nev = start_nev or np.array([0., 0., 0.])
+
  e, n, v = (
  np.array([pos]).reshape(-1, 3) - np.array([start_xyz])
  ).T
 
  return (np.array([n, e, v]).T + np.array([start_nev]))
 
 
-def get_xyz(pos, start_xyz=[0., 0., 0.], start_nev=[0., 0., 0.]):
+def get_xyz(pos, start_xyz=None, start_nev=None):
+ start_xyz = start_xyz or [0., 0., 0.]
+ start_nev = start_nev or [0., 0., 0.]
+
  y, x, z = (
  np.array([pos]).reshape(-1, 3) - np.array([start_nev])
  ).T
@@ -215,7 +217,6 @@ def _get_angles(vec):
 
  return np.stack((inc, azi), axis=1)
 
-
 if NUMBA:
  _get_angles = njit(_get_angles)
 
@@ -296,7 +297,7 @@ def NEV_to_HLA(survey, NEV, cov=True):
  The NEV coordinates or covariance matrices.
  cov: boolean
  If cov is True then a (3,3,d) array of covariance matrices
- is expecte, else a (d,3) array of coordinates.
+ is expected, else a (d,3) array of coordinates.
 
  Returns:
  Either a transformed (n,3) array of HLA coordinates or an