diff --git a/.gitignore b/.gitignore index 30d018a..7a144ba 100644 --- a/.gitignore +++ b/.gitignore @@ -1,6 +1,8 @@ .venv .vscode +.devcontainer/ + __pycache__ build @@ -18,4 +20,6 @@ work key.asc .~* -VERSION* \ No newline at end of file +VERSION* + +test/test_data/*.xlsx diff --git a/setup.py b/setup.py index febf115..9dc8a24 100644 --- a/setup.py +++ b/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() diff --git a/tests/test_data/error_mwdrev4_1_iscwsa_data.json b/tests/test_data/error_mwdrev4_1_iscwsa_data.json index dba9ffc..b6ac347 100644 --- a/tests/test_data/error_mwdrev4_1_iscwsa_data.json +++ b/tests/test_data/error_mwdrev4_1_iscwsa_data.json @@ -1 +1,1744 @@ -{"header": {"name": null, "latitude": 60, "longitude": 0.0098, "altitude": 0.0, "survey_date": "2020-12-30", "b_total": 50000, "dip": 1.2566370614359172, "convergence": 0.0, "declination": -0.06981317007977318, "vertical_inc_limit": 1.7453292519943296e-06, "depth_unit": "meters", "surface_unit": "meters", "G": 9.80665, "azi_reference": "true"}, "survey": {"md": [0, 30, 60, 90, 120, 150, 180, 210, 240, 270, 300, 330, 360, 390, 420, 450, 480, 510, 540, 570, 600, 630, 660, 690, 720, 750, 780, 810, 840, 870, 900, 930, 960, 990, 1020, 1050, 1080, 1110, 1140, 1170, 1200, 1230, 1260, 1290, 1320, 1350, 1380, 1410, 1440, 1470, 1500, 1530, 1560, 1590, 1620, 1650, 1680, 1710, 1740, 1770, 1800, 1830, 1860, 1890, 1920, 1950, 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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 diff --git a/welleng/survey.py b/welleng/survey.py index cb09071..5747f98 100644 --- a/welleng/survey.py +++ b/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( @@ -512,8 +520,8 @@ def get_error(self, error_model, return_error=False): if return_error: return self.err - else: - return self + + return self def _get_errors(self): """ @@ -521,18 +529,20 @@ def _get_errors(self): 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) diff --git a/welleng/utils.py b/welleng/utils.py index a6b8e69..edaa26d 100644 --- a/welleng/utils.py +++ b/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) @@ -173,9 +174,7 @@ 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. @@ -183,16 +182,16 @@ def get_nev( 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 @@ -200,7 +199,10 @@ def get_nev( 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