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Merge pull request #25 from AlexanderJuestel/dev_pybore
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AddAttributes
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@AlexanderJuestel
AlexanderJuestel authored Mar 14, 2024
2 parents 6d7a1f8 + 59a1a70 commit 76c6138
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Showing 2 changed files with 141 additions and 34 deletions.
4 changes: 2 additions & 2 deletions pyborehole/borehole.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -1604,14 +1604,14 @@ def add_well_logs(self,
raise TypeError('path must be provided as str')

# Opening LAS file if provided
if path.endswith('.las'):
if path.endswith('.las') or path.endswith('.LAS'):

# Creating well logs from LAS file
self.logs = LASLogs(self,
path=path)

# Opening DLIS file if provided
elif path.endswith('.dlis'):
elif path.endswith('.dlis') or path.endswith('.DLIS'):

# Checking that the nodata value is of type int or float
if not isinstance(nodata, (int, float)):
Expand Down
171 changes: 139 additions & 32 deletions pyborehole/logs.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -380,7 +380,9 @@ def __init__(self,

def plot_well_logs(self,
tracks: Union[str, list],
depth_column: str = 'MD',
depth_column: str = 'DEPTH',
depth_min: Union[int, float] = None,
depth_max: Union[int, float] = None,
colors: Union[str, list] = None,
add_well_tops: bool = False,
add_well_design: bool = False,
Expand All @@ -393,8 +395,12 @@ def plot_well_logs(self,
tracks : Union[str, list]
Name/s of the logs to be plotted, e.g. ``tracks='SGR'`` or ``tracks=['SGR', 'K']``.
depth_column : str, default: ``'MD'``
Name of the column holding the depths, e.g. ``depth_column='MD'``.
depth_column : str, default: ``'DEPTH'``
Name of the column holding the depths, e.g. ``depth_column='DEPTH'``.
depth_min : Union[int, float]
Minimum depth to be plotted, e.g. ``depth_min=0``.
depth_max : Union[int, float]
Maximum depth to be plotted, e.g. ``depth_max=2000``.
colors : Union[str, list], default: ``None``
Colors of the logs, e.g. ``colors='black'`` or ``colors=['black', 'blue']``.
add_well_tops : bool, default: ``False``
Expand Down Expand Up @@ -460,6 +466,14 @@ def plot_well_logs(self,
if not {depth_column}.issubset(self.df):
raise ValueError('The depth_column is not part of the curves')

# Checking that depth_min is of type float or int
if not isinstance(depth_min, (int, float, type(None))):
raise ValueError('The minimum depth must be provided as int or float')

# Checking that depth_max is of type float or int
if not isinstance(depth_max, (int, float, type(None))):
raise ValueError('The maximum depth must be provided as int or float')

# Checking that the colors are provided as list or string
if not isinstance(colors, (list, str, type(None))):
raise TypeError('The track/s must bei either provided as str or a list of strings')
Expand Down Expand Up @@ -500,8 +514,14 @@ def plot_well_logs(self,
ax.plot(df[tracks], df[depth_column], color=colors)
ax.grid()
ax.invert_yaxis()
buffer = (max(df[depth_column]) - min(df[depth_column])) / 20
ax.set_ylim(max(df[depth_column]) + buffer, min(df[depth_column]) - buffer)
if not depth_min:
depth_min = min(df[depth_column])
if not depth_max:
depth_max = max(df[depth_column])

buffer = (depth_max - depth_min) / 20

ax.set_ylim(depth_max + buffer, depth_min - buffer)
ax.tick_params(top=True, labeltop=True, bottom=False, labelbottom=False)
ax.xaxis.set_label_position('top')
ax.set_xlabel(tracks + ' [%s]' %
Expand All @@ -510,7 +530,7 @@ def plot_well_logs(self,
ax.set_ylabel(depth_column + ' [m]')

# Fill between curve
if fill_between:
if fill_between is not None:
left_col_value = np.min(df[tracks].dropna().values)
right_col_value = np.max(df[tracks].dropna().values)
span = abs(left_col_value - right_col_value)
Expand Down Expand Up @@ -556,9 +576,12 @@ def plot_well_logs(self,
else:
for index, row in self.well_tops.df.iterrows():
ax[0 + k].axhline(row[self.well_tops.df.columns[1]], 0, 1, color='black')
ax[0 + k].text(0.05, row[self.well_tops.df.columns[1]] - 1, s=row[self.well_tops.df.columns[0]],
fontsize=6)
ax[0 + k].text(0.05, row[self.well_tops.df.columns[1]] - max(self.df[depth_column]) / 150,
s=row[self.well_tops.df.columns[0]],
fontsize=max(df[depth_column]) / 75)
ax[0 + k].grid()
ax[0 + k].xaxis.set_label_position('top')
ax[0 + k].set_xlabel('Well Tops')
ax[0 + k].axes.get_xaxis().set_ticks([])

# Adding well design
Expand Down Expand Up @@ -648,8 +671,14 @@ def plot_well_logs(self,
max_diam = np.max([elem.outer_diameter for key, elem in self.well_design.pipes.items()])

# Setting axes limits
buffer = (max(df[depth_column]) - min(df[depth_column])) / 20
ax[k].set_ylim(max(df[depth_column]) + buffer, min(df[depth_column]) - buffer)
if not depth_min:
depth_min = min(df[depth_column])
if not depth_max:
depth_max = max(df[depth_column])

buffer = (depth_max - depth_min) / 20

ax[k].set_ylim(depth_max + buffer, depth_min - buffer)
ax.set_xlim(-max_diam * 1, max_diam * 1)
# ax.invert_yaxis()

Expand All @@ -672,6 +701,15 @@ def plot_well_logs(self,
color='black' if isinstance(colors[i], type(None)) else colors[i])
ax[0].set_ylabel(depth_column + ' [m]')

if not depth_min:
depth_min = min(df[depth_column])
if not depth_max:
depth_max = max(df[depth_column])

buffer = (depth_max - depth_min) / 20

ax[0].set_ylim(depth_max + buffer, depth_min - buffer)

# Fill between curves
if fill_between is not None:
left_col_value = np.min(df[tracks[fill_between]].dropna().values)
Expand Down Expand Up @@ -720,7 +758,7 @@ def plot_well_logs(self,

def plot_well_log_along_path(self,
log: str,
depth_column: str = 'MD',
depth_column: str = 'DEPTH',
relative: bool = True,
spacing: Union[float, int] = 0.5,
radius_factor: Union[float, int] = 75):
Expand All @@ -730,8 +768,8 @@ def plot_well_log_along_path(self,
__________
log : str
Name of the log, e.g. ``log='GR'``.
depth_column : str, default: ``'MD'``
Name of the column holding the depths, e.g. ``depth_column='MD'``.
depth_column : str, default: ``'DEPTH'``
Name of the column holding the depths, e.g. ``depth_column='DEPTH'``.
relative : bool, default: ``True``
Boolean value to plot the tube with relative coordinates, e.g. ``relative=False``.
spacing : Union[float, int], default: ``0.5``
Expand Down Expand Up @@ -870,6 +908,7 @@ def plot_well_log_along_path(self,
def calculate_vshale(self,
method: str,
column: str,
column: str,
minz: Union[float, int] = None,
maxz: Union[float, int] = None,
depth_column: str = None) -> pd.DataFrame:
Expand All @@ -895,7 +934,7 @@ def calculate_vshale(self,
maxz : Union[float, int], default: ``None``
Maximum Z value, e.g. ``maxz=100``.
depth_column : str, default: ``None``
Name of the column holding the depths, e.g. ``depth_column='MD'``.
Name of the column holding the depths, e.g. ``depth_column='DEPTH'``.
Returns
_______
Expand Down Expand Up @@ -992,7 +1031,7 @@ def calculate_vshale_linear(self,
maxz : Union[float, int], default: ``None``
Maximum Z value, e.g. ``maxz=100``.
depth_column : str, default: ``None``
Name of the column holding the depths, e.g. ``depth_column='MD'``.
Name of the column holding the depths, e.g. ``depth_column='DEPTH'``.
Raises
______
Expand Down Expand Up @@ -1088,7 +1127,7 @@ def calculate_net_to_gross(self,
maxz : Union[float, int], default: ``None``
Maximum Z value, e.g. ``maxz=100``.
depth_column : str, default: ``None``
Name of the column holding the depths, e.g. ``depth_column='MD'``.
Name of the column holding the depths, e.g. ``depth_column='DEPTH'``.
Returns
_______
Expand Down Expand Up @@ -1246,7 +1285,7 @@ def despike_curve(self,
track: str,
window_length: int):

"""
"""Despike curve using a rolling window.
"""
Expand Down Expand Up @@ -1500,7 +1539,7 @@ def __init__(self,
>>> from pyborehole.borehole import Borehole
>>> borehole = Borehole(name='Weisweiler R1')
>>> borehole.init_properties(location=(6.313031, 50.835676), crs='EPSG:4326', altitude_above_sea_level=136)
>>> borehole.add_well_logs(path='Well_logs.las')
>>> borehole.add_well_logs(path='Well_logs.dlis')
>>> borehole.logs.df
======= ======= =========== ========= ========= ==========
Expand Down Expand Up @@ -1545,6 +1584,9 @@ def __init__(self,
# Getting Curves
curves = [channel.curves() for channel in dlis.channels]

# Getting Units
units = [channel.units for channel in dlis.channels]

# Creating DataFrame from curves
df = pd.DataFrame(curves).T

Expand All @@ -1557,9 +1599,49 @@ def __init__(self,
# Extracting DataFrame from DLIS file
self.df = df

# Changing the name of the depth column
self.df['DEPTH'] = self.df['DEPT']
self.df = self.df.drop('DEPT', axis=1)

# Creating Curves DataFrame
self.curves = pd.DataFrame(list(zip(columns, columns, columns, units)),
columns=['original_mnemonic',
'mnemonic',
'descr',
'unit'])

# Getting index of depth column
depth_column_index = columns.index('DEPT')

# Defining mnemonics
mnemonic = ['STRT', 'STOP', 'STEP', 'NULL']

# Defining units
units = [dlis.channels[depth_column_index].units,
dlis.channels[depth_column_index].units,
dlis.channels[depth_column_index].units,
'']

# Defining Values
value = [dlis.channels[depth_column_index].curves()[0],
dlis.channels[depth_column_index].curves()[-1],
dlis.channels[depth_column_index].frame.spacing,
-999]

# Defining Description
descr = ['', '', '', '']

self.well_header = pd.DataFrame(list(zip(mnemonic, units, value, descr)),
columns=['mnemonic',
'unit',
'value',
'descr'])

def plot_well_logs(self,
tracks: Union[str, list],
depth_column: str = 'MD',
depth_column: str = 'DEPTH',
depth_min: Union[int, float] = None,
depth_max: Union[int, float] = None,
colors: Union[str, list] = None,
add_well_tops: bool = False,
add_well_design: bool = False,
Expand All @@ -1572,8 +1654,12 @@ def plot_well_logs(self,
tracks : Union[str, list]
Name/s of the logs to be plotted, e.g. ``tracks='SGR'`` or ``tracks=['SGR', 'K']``.
depth_column : str, default: ``'MD'``
Name of the column holding the depths, e.g. ``depth_column='MD'``.
depth_column : str, default: ``'DEPTH'``
Name of the column holding the depths, e.g. ``depth_column='DEPTH'``.
depth_min : Union[int, float]
Minimum depth to be plotted, e.g. ``depth_min=0``.
depth_max : Union[int, float]
Maximum depth to be plotted, e.g. ``depth_max=2000``.
colors : Union[str, list], default: ``None``
Colors of the logs, e.g. ``colors='black'`` or ``colors=['black', 'blue']``.
add_well_tops : bool, default: ``False``
Expand Down Expand Up @@ -1635,6 +1721,14 @@ def plot_well_logs(self,
if not isinstance(depth_column, str):
raise TypeError('Depth_column must be provided as string')

# Checking that depth_min is of type float or int
if not isinstance(depth_min, (int, float, type(None))):
raise ValueError('The minimum depth must be provided as int or float')

# Checking that depth_max is of type float or int
if not isinstance(depth_max, (int, float, type(None))):
raise ValueError('The maximum depth must be provided as int or float')

# Checking that the depth column is in the DataFrame
if not {depth_column}.issubset(self.df):
raise ValueError('The depth_column is not part of the curves')
Expand Down Expand Up @@ -1670,8 +1764,15 @@ def plot_well_logs(self,
ax.plot(df[tracks], df[depth_column], color=colors)
ax.grid()
ax.invert_yaxis()
buffer = (max(df[depth_column]) - min(df[depth_column])) / 20
ax.set_ylim(max(df[depth_column]) + buffer, min(df[depth_column]) - buffer)

if not depth_min:
depth_min = min(df[depth_column])
if not depth_max:
depth_max = max(df[depth_column])

buffer = (depth_max - depth_min) / 20

ax.set_ylim(depth_max + buffer, depth_min - buffer)
ax.tick_params(top=True, labeltop=True, bottom=False, labelbottom=False)
ax.xaxis.set_label_position('top')
ax.set_xlabel(tracks + ' [%s]' %
Expand Down Expand Up @@ -1818,8 +1919,14 @@ def plot_well_logs(self,
max_diam = np.max([elem.outer_diameter for key, elem in self.well_design.pipes.items()])

# Setting axes limits
buffer = (max(df[depth_column]) - min(df[depth_column])) / 20
ax[k].set_ylim(max(df[depth_column]) + buffer, min(df[depth_column]) - buffer)
if not depth_min:
depth_min = min(df[depth_column])
if not depth_max:
depth_max = max(df[depth_column])

buffer = (depth_max - depth_min) / 20

ax[k].set_ylim(depth_max + buffer, depth_min - buffer)
ax.set_xlim(-max_diam * 1, max_diam * 1)
# ax.invert_yaxis()

Expand Down Expand Up @@ -1890,7 +1997,7 @@ def plot_well_logs(self,

def plot_well_log_along_path(self,
log: str,
depth_column: str = 'MD',
depth_column: str = 'DEPTH',
relative: bool = True,
spacing: Union[float, int] = 0.5,
radius_factor: Union[float, int] = 75):
Expand All @@ -1900,8 +2007,8 @@ def plot_well_log_along_path(self,
__________
log : str
Name of the log, e.g. ``log='GR'``.
depth_column : str, default: ``'MD'``
Name of the column holding the depths, e.g. ``depth_column='MD'``.
depth_column : str, default: ``'DEPTH'``
Name of the column holding the depths, e.g. ``depth_column='DEPTH'``.
relative : bool, default: ``True``
Boolean value to plot the tube with relative coordinates, e.g. ``relative=False``.
spacing : Union[float, int], default: ``0.5``
Expand Down Expand Up @@ -2066,7 +2173,7 @@ def calculate_vshale(self,
maxz : Union[float, int], default: ``None``
Maximum Z value, e.g. ``maxz=100``.
depth_column : str, default: ``None``
Name of the column holding the depths, e.g. ``depth_column='MD'``.
Name of the column holding the depths, e.g. ``depth_column='DEPTH'``.
Returns
_______
Expand Down Expand Up @@ -2163,7 +2270,7 @@ def calculate_vshale_linear(self,
maxz : Union[float, int], default: ``None``
Maximum Z value, e.g. ``maxz=100``.
depth_column : str, default: ``None``
Name of the column holding the depths, e.g. ``depth_column='MD'``.
Name of the column holding the depths, e.g. ``depth_column='DEPTH'``.
Raises
______
Expand Down Expand Up @@ -2259,7 +2366,7 @@ def calculate_net_to_gross(self,
maxz : Union[float, int], default: ``None``
Maximum Z value, e.g. ``maxz=100``.
depth_column : str, default: ``None``
Name of the column holding the depths, e.g. ``depth_column='MD'``.
Name of the column holding the depths, e.g. ``depth_column='DEPTH'``.
Returns
_______
Expand Down Expand Up @@ -2625,7 +2732,7 @@ def resample_log(log: Union[gpd.GeoDataFrame, LineString, pd.DataFrame],

# Creating gdf from values
if isinstance(log, pd.DataFrame):
log = gpd.GeoDataFrame(geometry=[LineString(log[[column_name, 'DEPTH']].values)])
log = gpd.GeoDataFrame(geometry=[LineString(log[[column_name, 'DEPTH']].dropna().values)])

# Extracting LineString from Value and assigning column name
if isinstance(log, gpd.GeoDataFrame):
Expand Down

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