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Field alias - first try #146

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47d735a
first try at field alias
hyperiongeo Dec 22, 2020
a588392
unit testing and some cleanup
hyperiongeo Dec 22, 2020
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63,750 changes: 63,750 additions & 0 deletions tests/P-129_out_kb.LAS
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105 changes: 68 additions & 37 deletions welly/fields.py
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Expand Up @@ -5,52 +5,58 @@
:license: Apache 2.0
"""
from .crs import CRS
from .utils import lasio_get


las_sections = {'well', 'params'}
las_fields = {
'well': {
},
'header': {
'name': ('well', 'WELL'),
'field': ('well', 'FLD'),
'license': ('well', 'LIC'),
'uwi': ('well', 'UWI'),
'api': ('well', 'API'),
'company': ('well', 'COMP'),
'name': [{'section': 'well', "code": 'WELL'}],
'field': [{'section': 'well', "code": 'FLD'}],
'license': [{'section': 'well', "code": 'LIC'}],
'uwi': [{'section': 'well', "code": 'UWI'}],
'api': [{'section': 'well', "code": 'API'}],
'company': [{'section': 'well', "code": 'COMP'}],
},
'location': {
'location': ('well', 'LOC'),
'country': ('well', 'CTRY'),
'province': ('well', 'PROV'),
'state': ('well', 'STAT'),
'county': ('well', 'CNTY'),
'latitude': ('well', 'LATI'),
'longitude': ('well', 'LONG'),
'northing': ('well', 'NS'),
'easting': ('well', 'EW'),
'x': ('well', 'XCOORD'),
'y': ('well', 'YCOORD'),
'datum': ('well', 'GDAT'),
'section': ('well', 'SECT'),
'range': ('well', 'RANG'),
'township': ('well', 'TOWN'),
'api': ('well', 'API'),
'ekb': ('params', 'EKB'),
'egl': ('params', 'EGL'),
'kb': ('params', 'KB'),
'gl': ('params', 'GL'),
'td': ('params', 'TD'),
'tdd': ('params', 'TDD'),
'tdl': ('params', 'TDL'),
'location': [{'section': 'well', "code": 'LOC'}],
'country': [{'section': 'well', "code": 'CTRY'}],
'province': [{'section': 'well', "code": 'PROV'}],
'state': [{'section': 'well', "code": 'STAT'}],
'county': [{'section': 'well', "code": 'CNTY'}],
'latitude': [{'section': 'well', "code": 'LATI'}],
'longitude': [{'section': 'well', "code": 'LONG'}],
'northing': [{'section': 'well', "code": 'NS'},
{'section': 'well', "code": 'Y'}],
'easting': [{'section': 'well', "code": 'EW'},
{'section': 'well', "code": 'X'}],
'x': [{'section': 'well', "code": 'XCOORD'}],
'y': [{'section': 'well', "code": 'YCOORD'}],
'datum': [{'section': 'well', "code": 'GDAT'}],
'section': [{'section': 'well', "code": 'SECT'}],
'range': [{'section': 'well', "code": 'RANG'}],
'township': [{'section': 'well', "code": 'TOWN'}],
'api': [{'section': 'well', "code": 'API'}],
'kb': [{'section': 'params', "code": 'KB'},
{'section': 'params', "code": 'EKB'},
{'section': 'params', "code": 'EREF', "secondary_code": 'DREF', "secondary_desc": ["KB", "K.B.", "KELLY BUSHING"]}],
'gl': [{'section': 'params', "code": 'GL'},
{'section': 'params', "code": 'EGL'},
{'section': 'params', "code": 'EPD', "secondary_code": "PD", "secondary_desc": ["Ground Level", "G.L.", "GROUND LEVEL"]},
{'section': 'params', "code": 'Elevation', "secondary_code": "PermDatum", "secondary_desc": ["Ground Level", "G.L.", "GROUND LEVEL"]}],
'td': [{'section': 'params', "code": 'TD'}],
'tdd': [{'section': 'params', "code": 'TDD'}],
'tdl': [{'section': 'params', "code": 'TDL'}],
},
'data': {
'start': ('well', 'STRT'),
'stop': ('well', 'STOP'),
'step': ('well', 'STEP'),
'null': ('well', 'NULL'),
'run': ('params', 'RUN'),
'service_company': ('well', 'SRVC'),
'date': ('well', 'DATE')
'start': [{'section': 'well', "code": 'STRT'}],
'stop': [{'section': 'well', "code": 'STOP'}],
'step': [{'section': 'well', "code": 'STEP'}],
'null': [{'section': 'well', "code": 'NULL'}],
'run': [{'section': 'params', "code": 'RUN'}],
'service_company': [{'section': 'well', "code": 'SRVC'}],
'date': [{'section': 'well', "code": 'DATE'}],
}
}

Expand All @@ -61,3 +67,28 @@
'kb': (r"# WELL DATUM .+?: ([.0-9]+).+?", float),
'crs': (r"XYZ TRACE .+? \[\d+_(\d+)\] .+?", CRS.from_epsg),
}

def parse_fields(l, remap=None, funcs=None, initial_params=None,
field_alias=None, hdr_sect='header'):
params = {}
# print("parse_fields:", hdr_sect)
if initial_params is not None:
params = initial_params
fields = field_alias
if fields is None:
fields = las_fields[hdr_sect]
# print("____", fields)
for field, values in fields.items():
for val in values:
params[field] = lasio_get(l,
val,
# val['section'],
# val['code'],
# check=check,
remap=remap,
funcs=funcs)
# print("_______", val, field, params[field])
if params[field] is not None:
break

return params
10 changes: 2 additions & 8 deletions welly/header.py
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Expand Up @@ -6,7 +6,7 @@
"""
import csv

from .fields import las_fields
from .fields import las_fields, parse_fields
from . import utils


Expand Down Expand Up @@ -51,13 +51,7 @@ def from_lasio(cls, l, remap=None, funcs=None):
implementing a transform before loading. Can be a lambda.

"""
params = {}
for field, (sect, code) in las_fields['header'].items():
params[field] = utils.lasio_get(l,
sect,
code,
remap=remap,
funcs=funcs)
params = parse_fields(l, remap, funcs)
return cls(params)

@classmethod
Expand Down
19 changes: 8 additions & 11 deletions welly/location.py
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Expand Up @@ -15,7 +15,7 @@
import io

from . import utils
from .fields import las_fields
from .fields import las_fields, parse_fields, parse_fields
from .fields import dev_fields
from .crs import CRS
from .tools import compute_position_log
Expand Down Expand Up @@ -65,7 +65,7 @@ def __init__(self, params=None):
m = "The position log could not be computed. Consider "
m += "trying another setting for the 'method' argument."
warnings.warn(m)
dev_new, pos, dog = deviation, None, None
dev_new, pos, dog = self.deviation, None, None

self.position = pos
self.dogleg = dog
Expand Down Expand Up @@ -102,7 +102,7 @@ def crs_from_string(self, string):
return

@classmethod
def from_lasio(cls, l, remap=None, funcs=None):
def from_lasio(cls, l, remap=None, funcs=None, field_alias=None):
"""
Make a Location object from a lasio object. Assumes we're starting
with a lasio object, l.
Expand All @@ -112,19 +112,16 @@ def from_lasio(cls, l, remap=None, funcs=None):
remap (dict): Optional. A dict of 'old': 'new' LAS field names.
funcs (dict): Optional. A dict of 'las field': function() for
implementing a transform before loading. Can be a lambda.
field_alias ?????

Returns:
Location. An instance of this class.
"""
params = {}
funcs = funcs or {}
funcs['location'] = str
for field, (sect, code) in las_fields['location'].items():
params[field] = utils.lasio_get(l,
sect,
code,
remap=remap,
funcs=funcs)

params = parse_fields(l, remap, funcs, field_alias=field_alias,
hdr_sect='location')
return cls(params)

@classmethod
Expand Down Expand Up @@ -336,7 +333,7 @@ def trajectory(self, datum=None, elev=True, points=1000, **kwargs):

Returns:
ndarray. An array with shape (`points` x 3) representing the well
trajectory. Columns are (x, y, z).
trajectory. Columns are (x, y, z).
"""
pos = self.position.copy()

Expand Down
25 changes: 19 additions & 6 deletions welly/utils.py
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Expand Up @@ -57,7 +57,7 @@ def bbox(points):
def aspect(points):
"""
Aspect like 2:1 is shape like |___ (twice as wide as high).

This function returns the WIDTH per unit height.
"""
(minx, miny), (maxx, maxy) = bbox(points)
Expand Down Expand Up @@ -208,9 +208,10 @@ def list_and_add(a, b):


def lasio_get(l,
section,
# section,
item,
attrib='value',
# check=None,
default=None,
remap=None,
funcs=None):
Expand All @@ -231,18 +232,30 @@ def lasio_get(l,
The transformed item.
"""
remap = remap or {}
item_to_fetch = remap.get(item, item)
item_to_fetch = remap.get(item['code'], item['code'])
if item_to_fetch is None:
return None

try:
obj = getattr(l, section)
result = getattr(obj, item_to_fetch)[attrib]
obj = getattr(l, item['section'])
if 'secondary_code' in item:
result = default
for val in item['secondary_desc']:
# print(' ', val, val== getattr(obj, item['secondary_code'])[attrib])
if val == getattr(obj, item['secondary_code'])[attrib]:
# print("sdjnvkfjvbafkjvnafjlsvn lsajfv asfvasfv", item_to_fetch)
# print(getattr(obj, item_to_fetch)[attrib])
result = getattr(obj, item_to_fetch)[attrib]
# print("___******", result)
break
else:
result = getattr(obj, item_to_fetch)[attrib]

except:
return default

if funcs is not None:
f = funcs.get(item, null)
f = funcs.get(item['code'], null)
result = f(result)

return result
Expand Down
49 changes: 20 additions & 29 deletions welly/well.py
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Expand Up @@ -19,6 +19,7 @@

from . import utils
from .fields import las_fields as LAS_FIELDS
from .fields import parse_fields
from .curve import Curve
from .header import Header
from .location import Location
Expand Down Expand Up @@ -142,7 +143,7 @@ def _get_curve_mnemonics(self, keys=None, curves_only=True):
keys_ = []
else:
keys_ = utils.flatten_list(keys)

if curves_only:
keys = [k for k in keys_ if isinstance(self.data.get(k), Curve)]
else:
Expand All @@ -155,6 +156,7 @@ def from_lasio(cls,
l,
remap=None,
funcs=None,
field_alias=None,
data=True,
req=None,
alias=None,
Expand All @@ -170,6 +172,7 @@ def from_lasio(cls,
remap (dict): Optional. A dict of 'old': 'new' LAS field names.
funcs (dict): Optional. A dict of 'las field': function() for
implementing a transform before loading. Can be a lambda.
field_alias (dict): Optional. A dict of LAS param header mappings.
data (bool): Whether to load curves or not.
req (list): An alias list, giving all required curves.
alias (dict): An alias dictionary.
Expand Down Expand Up @@ -211,13 +214,7 @@ def from_lasio(cls,
l_index = getattr(l, index_attr)

# Build a dict of curves.
curve_params = {}
for field, (sect, code) in LAS_FIELDS['data'].items():
curve_params[field] = utils.lasio_get(l,
sect,
code,
remap=remap,
funcs=funcs)
curve_params = parse_fields(l, remap, funcs, hdr_sect='data')

# This is annoying, but I need the whole depth array to
# deal with edge cases, eg non-uniform sampling.
Expand Down Expand Up @@ -265,23 +262,20 @@ def from_lasio(cls,
# Build a dict of the other well data.
params = {'las': l,
'header': Header.from_lasio(l, remap=remap, funcs=funcs),
'location': Location.from_lasio(l, remap=remap, funcs=funcs),
'location': Location.from_lasio(l, field_alias=field_alias, remap=remap, funcs=funcs),
'data': curves,
'fname': fname}

for field, (sect, code) in LAS_FIELDS['well'].items():
params[field] = utils.lasio_get(l,
sect,
code,
remap=remap,
funcs=funcs)
params = parse_fields(l, remap, funcs, initial_params=params,
hdr_sect='well')
return cls(params)

@classmethod
def from_las(cls,
fname,
remap=None,
funcs=None,
field_alias=None,
data=True,
req=None,
alias=None,
Expand All @@ -298,6 +292,7 @@ def from_las(cls,
remap (dict): Optional. A dict of 'old': 'new' LAS field names.
funcs (dict): Optional. A dict of 'las field': function() for
implementing a transform before loading. Can be a lambda.
field_alias (dict): Optional. A dict of LAS param header mappings.
data (bool): Whether to load the data or only the header.
req (list): An alias list, giving all required curves.
alias (dict): An alias dictionary.
Expand Down Expand Up @@ -329,6 +324,7 @@ def from_las(cls,
return cls.from_lasio(las,
remap=remap,
funcs=funcs,
field_alias=field_alias,
data=data,
req=req,
alias=alias,
Expand Down Expand Up @@ -425,13 +421,14 @@ def to_lasio(self, keys=None, basis=None, null_value=-999.25):
for obj, dic in LAS_FIELDS.items():
if obj == 'data':
continue
for attr, (sect, item) in dic.items():
value = getattr(getattr(self, obj), attr, None)
try:
getattr(l, sect)[item].value = value
except:
h = lasio.HeaderItem(item, "", value, "")
getattr(l, sect)[item] = h
for attr, values in dic.items():
for val in values:
value = getattr(getattr(self, obj), attr, None)
try:
getattr(l, val['section'])[val['code']].value = value
except:
h = lasio.HeaderItem(val['code'], "", value, "")
getattr(l, val['section'])[val['code']] = h

# Clear curves from header portion.
l.header['Curves'] = []
Expand Down Expand Up @@ -547,13 +544,7 @@ def add_curves_from_lasio(self, l, remap=None, funcs=None):
Returns:
None. Works in place.
"""
params = {}
for field, (sect, code) in LAS_FIELDS['data'].items():
params[field] = utils.lasio_get(l,
sect,
code,
remap=remap,
funcs=funcs)
params = parse_fields(l, remap, funcs, hdr_sect='data')

curves = {c.mnemonic: Curve.from_lasio_curve(c, **params)
for c in l.curves}
Expand Down