def test_interval():
""" Test intervals.
"""
lexicon = Lexicon.default()
interval = Interval(20, 40, "Grey sandstone.", lexicon=lexicon)
assert interval.primary.lithology == 'sandstone'
fmt = "{colour} {lithology}"
answer = '20.00 m of grey sandstone'
assert interval.summary(fmt=fmt) == answer
interval_2 = Interval(40, 65, "Red sandstone.", lexicon=lexicon)
assert interval_2 != interval
assert interval_2 > interval
answer = '25.00 m of red sandstone'
assert max(interval, interval_2).summary(fmt=fmt) == answer
iv = interval_2 + interval
assert len(iv.components) == 2
assert iv.base - iv.top == 45.0
iv = interval + 5
assert iv.thickness == 25.0
rock = Component(r)
iv = interval + rock
assert len(iv.components) == 2
def test_error():
""" Test the IntervalError.
"""
lexicon = Lexicon.default()
interval = Interval(20, 40, "Grey sandstone.", lexicon=lexicon)
with pytest.raises(IntervalError):
interval + 'this will raise'
def test_histogram():
"""Test histogram. This example is from the tutorial.
"""
lexicon = Lexicon.default()
striplog = Striplog.from_las3(las3, lexicon=lexicon)
_, counts = striplog.histogram()
assert counts == (124, 6, 6, 5, 3)
def test_histogram():
"""Test histogram. This example is from the tutorial.
"""
lexicon = Lexicon.default()
striplog = Striplog.from_las3(las3, lexicon=lexicon)
_, counts = striplog.histogram()
assert counts == (124, 6, 6, 5, 3)
def test_from_csv():
lexicon = Lexicon.default()
csv_string = """ 200.000, 230.329, Anhydrite
230.329, 233.269, Grey vf-f sandstone
233.269, 234.700, Anhydrite
234.700, 236.596, Dolomite
236.596, 237.911, Red siltstone
237.911, 238.723, Anhydrite
238.723, 239.807, Grey vf-f sandstone
239.807, 240.774, Red siltstone
240.774, 241.122, Dolomite
241.122, 241.702, Grey siltstone
241.702, 243.095, Dolomite
243.095, 246.654, Grey vf-f sandstone
246.654, 247.234, Dolomite
247.234, 255.435, Grey vf-f sandstone
255.435, 258.723, Grey siltstone
258.723, 259.729, Dolomite
259.729, 260.967, Grey siltstone
260.967, 261.354, Dolomite
261.354, 267.041, Grey siltstone
267.041, 267.350, Dolomite
267.350, 274.004, Grey siltstone
274.004, 274.313, Dolomite
274.313, 294.816, Grey siltstone
294.816, 295.397, Dolomite
295.397, 296.286, Limestone
296.286, 300.000, Volcanic
"""
strip2 = Striplog.from_csv(csv_string, lexicon=lexicon)
assert len(strip2.top) == 7
def test_lexicon():
lexicon = Lexicon.default()
assert lexicon.find_synonym('Halite') == 'salt'
s = "lt gn ss w/ sp gy sh"
answer = 'lighter green sandstone with spotty gray shale'
assert lexicon.expand_abbreviations(s) == answer
def test_from_csv():
lexicon = Lexicon.default()
csv_string = """ 200.000, 230.329, Anhydrite
230.329, 233.269, Grey vf-f sandstone
233.269, 234.700, Anhydrite
234.700, 236.596, Dolomite
236.596, 237.911, Red siltstone
237.911, 238.723, Anhydrite
238.723, 239.807, Grey vf-f sandstone
239.807, 240.774, Red siltstone
240.774, 241.122, Dolomite
241.122, 241.702, Grey siltstone
241.702, 243.095, Dolomite
243.095, 246.654, Grey vf-f sandstone
246.654, 247.234, Dolomite
247.234, 255.435, Grey vf-f sandstone
255.435, 258.723, Grey siltstone
258.723, 259.729, Dolomite
259.729, 260.967, Grey siltstone
260.967, 261.354, Dolomite
261.354, 267.041, Grey siltstone
267.041, 267.350, Dolomite
267.350, 274.004, Grey siltstone
274.004, 274.313, Dolomite
274.313, 294.816, Grey siltstone
294.816, 295.397, Dolomite
295.397, 296.286, Limestone
296.286, 300.000, Volcanic
"""
strip2 = Striplog.from_csv(csv_string, lexicon=lexicon)
assert len(strip2.top) == 7
def test_error():
""" Test the IntervalError.
"""
lexicon = Lexicon.default()
interval = Interval(20, 40, "Grey sandstone.", lexicon=lexicon)
with pytest.raises(IntervalError):
interval + 'this will raise'
def test_interval():
""" Test intervals.
"""
lexicon = Lexicon.default()
interval = Interval(20, 40, "Grey sandstone.", lexicon=lexicon)
assert interval.primary.lithology == 'sandstone'
fmt = "{colour} {lithology}"
answer = '20.00 m of grey sandstone'
assert interval.summary(fmt=fmt) == answer
interval_2 = Interval(40, 65, "Red sandstone.", lexicon=lexicon)
assert interval_2 != interval
assert interval_2 > interval
answer = '25.00 m of red sandstone'
assert max(interval, interval_2).summary(fmt=fmt) == answer
iv = interval_2 + interval
assert len(iv.components) == 2
assert iv.base - iv.top == 45.0
iv = interval + 5
assert iv.thickness == 25.0
rock = Component(r)
iv = interval + rock
assert len(iv.components) == 2
def test_from_text():
rock3 = Component(r3)
lexicon = Lexicon.default()
s = 'Grey coarse sandstone.'
rock4 = Component.from_text(s, lexicon)
assert rock3 == rock4
rock5 = Component.from_text(s, lexicon, required='not there')
assert not rock5 # Should be None
def test_histogram():
"""Test histogram. This example is from the tutorial.
"""
lexicon = Lexicon.default()
striplog = Striplog.from_las3(las3, lexicon=lexicon)
thicks, *_ = striplog.histogram(plot=False) # See test_plots for plots.
t = [123.005, 7.919, 5.504, 4.022, 2.964]
assert np.allclose(t, thicks)
def test_from_text():
rock3 = Component(r3)
lexicon = Lexicon.default()
s = 'Grey coarse sandstone.'
rock4 = Component.from_text(s, lexicon)
assert rock3 == rock4
rock5 = Component.from_text(s, lexicon, required='not there')
assert not rock5 # Should be None
def test_lexicon():
"""All the tests...
"""
lexicon = Lexicon.default()
s = lexicon.__str__()
assert s is not ''
assert lexicon.__repr__() is not ''
assert lexicon.find_synonym('Halite') == 'salt'
assert len(lexicon.categories) == 4
s = "lt gn ss w/ sp gy sh"
answer = 'lighter green sandstone with spotty gray shale'
assert lexicon.expand_abbreviations(s) == answer
fname = "tutorial/lexicon.json"
l = Lexicon.from_json_file(fname)
assert l.__repr__() is not ''
def test_histogram():
"""Test histogram plot.
"""
fig, ax = plt.subplots()
lexicon = Lexicon.default()
striplog = Striplog.from_las3(las3, lexicon=lexicon)
*_, ax = striplog.histogram(ax=ax)
return fig
def __init__(self,
intervals=None,
components=None,
name='',
legend=None,
x_collar=0.,
y_collar=0.):
"""
build a Borehole3D object from Striplog.Intervals list
Parameters
-----------
intervals : list
list of Striplog.Interval object (default = None)
components :
(default = None)
name : str
legend : Striplog Legend object (default = None)
x_collar : float
X coordinate of the borehole (default = 0)
y_collar : float
Y coordinate of the borehole (default = 0)
"""
self.name = name
if legend is None or not isinstance(legend, Legend):
self.legend = Legend.default()
else:
self.legend = legend
self.x_collar = x_collar
self.y_collar = y_collar
self.omf_legend, self.omf_cmap = striplog_legend_to_omf_legend(
self.legend)
if intervals is None:
lexicon = Lexicon.default()
with open(ROOT_DIR + '/data/test.las', 'r') as las3:
default_intv = Striplog.from_las3(las3.read(), lexicon)
intervals = list(default_intv)
print("Pay attention that default intervals are actually used !\n")
self.intervals = intervals
self.geometry = []
# instantiation with supers properties
Striplog.__init__(self, list_of_Intervals=self.intervals)
# self.uid=uuid #get a unique for identification of borehole in the project
self.build_geometry()
def test_from_array():
lexicon = Lexicon.default()
a = [(100, 200, 'red sandstone'),
(200, 250, 'grey shale'),
(200, 250, 'red sandstone with shale stringers'),
]
s = Striplog.from_array(a, lexicon=lexicon)
assert s.__str__() != ''
def test_bar():
"""Test bar plot.
"""
fig, ax = plt.subplots()
lexicon = Lexicon.default()
striplog = Striplog.from_las3(las3, lexicon=lexicon)
legend = Legend.builtin('nagmdm__6_2')
ax = striplog.bar(sort=True, legend=legend, ax=ax, align='center')
return fig
def test_from_array():
lexicon = Lexicon.default()
a = [(100, 200, 'red sandstone'),
(200, 250, 'grey shale'),
(200, 250, 'red sandstone with shale stringers'),
]
s = Striplog._from_array(a, lexicon=lexicon)
assert s.__str__() != ''
def test_clean_lithology_descriptions():
lex = Lexicon.default()
descriptions = [
'Sand with qtz', 'Sand calc grey fg mg',
'Clay very sandy, grey greenish, pyritic', 'sandwithclay'
]
x = clean_lithology_descriptions(descriptions, lex)
assert x[0] == 'sand with quartz'
assert x[1] == 'sand calcitareous grey fg mg'
assert x[2] == 'clay very sandy, grey greenish, pyritic'
assert x[3] == 'sand with clay'
def update(self, transect):
"""
Updates the container data to a profile that intersect the
transect line.
Returns nothing. Sets attributes as a side effect.
Args:
transect (LineString): A transect line.
"""
Notice.info("Updating " + self.__class__.__name__)
# Preprocess
prepared = prep(transect.buffer(self.settings['buffer']))
# Get the intersecting points
points = filter(prepared.contains, self.lookup.keys())
self.reset_data()
self.names = []
for point in points:
name = self.lookup[point]
self.names.append(name)
print name,
pattern = "^" + name + "_out.las"
for fname in utils.walk(self.well_dir, pattern):
# This is a loop but there should only be one matching file.
well = Well(fname, null_subs=np.nan)
print well.curves.names
self.data.append(well)
self.log_lookup[name] = self.data[-1]
if not self.log_lookup.get(name):
print
self.data.append(None)
sl_name = getattr(self, 'striplog', None)
sl = None
if sl_name and (name == self.feature_well):
lexicon = Lexicon.default()
pattern = "^" + name + ".*striplog.las"
for fname in utils.walk(self.well_dir, pattern):
# Load the striplog.
sl = Well(fname, lexicon=lexicon, null_subs=np.nan)
# Add it to the well
self.log_lookup[name].add_striplog(sl.striplog[sl_name],
sl_name)
self.coords.append(transect.project(point))
def update(self, transect):
"""
Updates the container data to a profile that intersect the
transect line.
Returns nothing. Sets attributes as a side effect.
Args:
transect (LineString): A transect line.
"""
Notice.info("Updating " + self.__class__.__name__)
# Preprocess
prepared = prep(transect.buffer(self.settings['buffer']))
# Get the intersecting points
points = filter(prepared.contains, self.lookup.keys())
self.reset_data()
self.names = []
for point in points:
name = self.lookup[point]
self.names.append(name)
print name,
pattern = "^" + name + "_out.las"
for fname in utils.walk(self.well_dir, pattern):
# This is a loop but there should only be one matching file.
well = Well(fname, null_subs=np.nan)
print well.curves.names
self.data.append(well)
self.log_lookup[name] = self.data[-1]
if not self.log_lookup.get(name):
print
self.data.append(None)
sl_name = getattr(self, 'striplog', None)
sl = None
if sl_name and (name == self.feature_well):
lexicon = Lexicon.default()
pattern = "^" + name + ".*striplog.las"
for fname in utils.walk(self.well_dir, pattern):
# Load the striplog.
sl = Well(fname, lexicon=lexicon, null_subs=np.nan)
# Add it to the well
self.log_lookup[name].add_striplog(sl.striplog[sl_name],
sl_name)
self.coords.append(transect.project(point))
def test_from_array():
"""Test the array route.
Deprecated.
"""
lexicon = Lexicon.default()
a = [(100, 200, 'red sandstone'),
(200, 250, 'grey shale'),
(200, 250, 'red sandstone with shale stringers'),
]
with pytest.warns(DeprecationWarning):
s = Striplog._from_array(a, lexicon=lexicon)
assert s.__str__() != ''
def striplog_from_text(filename, lexicon=None):
""" creates a Striplog object from a las or flat text file
Parameters
----------
Lexicon : dict
A vocabulary for parsing lithologic or stratigraphic descriptions
(default set to Lexicon.default() if lexicon is None)
Returns
-------
strip: striplog object
"""
if lexicon is None:
lexicon = Lexicon.default()
if re.compile(r".+\.las").match(filename):
print(f"File {filename:s} OK! Creation of the striplog ...")
with open(filename, 'r') as las3:
strip = Striplog.from_las3(las3.read(), lexicon)
elif re.compile(r".+\.(csv|txt)").match(filename):
print(f"File {filename:s} OK! Creation of the striplog ...")
f = re.DOTALL | re.IGNORECASE
regex_data = r'start.+?\n(.+?)(?:\n\n+|\n*\#|\n*$)' # retrieve data of BH
pattern = re.compile(regex_data, flags=f)
with open(filename, 'r') as csv:
text = pattern.search(csv.read()).group(1)
text = re.sub(r'[\t]+', ';', re.sub(r'(\n+|\r\n|\r)', '\n', text.strip()))
strip = Striplog.from_descriptions(text, dlm=';', lexicon=lexicon)
else:
print("Error! Please check the file extension !")
raise
return strip
def test_from_csv():
"""Test the CSV route.
"""
lexicon = Lexicon.default()
strip2 = Striplog.from_csv(csv_intervals, lexicon=lexicon)
assert len(strip2.top) == 7
def test_from_csv():
lexicon = Lexicon.default()
strip2 = Striplog.from_csv(csv_string, lexicon=lexicon)
assert len(strip2.top) == 7
__author__ = 'kiruba' import numpy as np import matplotlib.pyplot as plt import pandas as pd import itertools from striplog import striplog, Legend, Lexicon legend = Legend.default() lexicon = Lexicon.default() csv_string = """ 200.000, 230.329, Anhydrite 230.329, 233.269, Grey vf-f sandstone 233.269, 234.700, Anhydrite 234.700, 236.596, Dolomite 236.596, 237.911, Red siltstone 237.911, 238.723, Anhydrite 238.723, 239.807, Grey vf-f sandstone 239.807, 240.774, Red siltstone 240.774, 241.122, Dolomite 241.122, 241.702, Grey siltstone 241.702, 243.095, Dolomite 243.095, 246.654, Grey vf-f sandstone 246.654, 247.234, Dolomite 247.234, 255.435, Grey vf-f sandstone 255.435, 258.723, Grey siltstone 258.723, 259.729, Dolomite 259.729, 260.967, Grey siltstone 260.967, 261.354, Dolomite 261.354, 267.041, Grey siltstone
def test_from_descriptions():
"""Test the CSV route.
"""
lexicon = Lexicon.default()
strip2 = Striplog.from_descriptions(text=csv_intervals, lexicon=lexicon)
assert len(strip2.top) == 7
def test_from_las3():
"""Test the LAS3 route.
"""
lexicon = Lexicon.default()
s = Striplog.from_las3(las3, lexicon=lexicon)
assert len(s) == 14
def test_from_array():
lexicon = Lexicon.default()
a = [(100, 200, "red sandstone"), (200, 250, "grey shale"), (200, 250, "red sandstone with shale stringers")]
s = Striplog._from_array(a, lexicon=lexicon)
assert s.__str__() != ""
def test_from_descriptions():
"""Test the CSV route.
"""
lexicon = Lexicon.default()
strip2 = Striplog.from_descriptions(text=csv_intervals, lexicon=lexicon)
assert len(strip2.unique) == 7
def test_histogram():
lexicon = Lexicon.default()
striplog = Striplog.from_las3(las3, lexicon=lexicon)
_, counts = striplog.histogram()
assert counts == (123, 6, 6, 5, 3)
def test_from_csv():
lexicon = Lexicon.default()
strip2 = Striplog.from_csv(csv_string, lexicon=lexicon)
assert len(strip2.top) == 7
__author__ = 'kiruba' import numpy as np import matplotlib.pyplot as plt import pandas as pd import itertools from striplog import striplog, Legend, Lexicon legend = Legend.default() lexicon = Lexicon.default() csv_string = """ 200.000, 230.329, Anhydrite 230.329, 233.269, Grey vf-f sandstone 233.269, 234.700, Anhydrite 234.700, 236.596, Dolomite 236.596, 237.911, Red siltstone 237.911, 238.723, Anhydrite 238.723, 239.807, Grey vf-f sandstone 239.807, 240.774, Red siltstone 240.774, 241.122, Dolomite 241.122, 241.702, Grey siltstone 241.702, 243.095, Dolomite 243.095, 246.654, Grey vf-f sandstone 246.654, 247.234, Dolomite 247.234, 255.435, Grey vf-f sandstone 255.435, 258.723, Grey siltstone 258.723, 259.729, Dolomite 259.729, 260.967, Grey siltstone 260.967, 261.354, Dolomite 261.354, 267.041, Grey siltstone 267.041, 267.350, Dolomite 267.350, 274.004, Grey siltstone
def test_histogram():
lexicon = Lexicon.default()
striplog = Striplog.from_las3(las3, lexicon=lexicon)
_, counts = striplog.histogram()
assert counts == (123, 6, 6, 5, 3)