(FEATURE) updated logging

lachlangrose · lachlangrose · commit 7fa8b7320086 · 2021-01-08T16:29:20.000+11:00
Now log to file or log to console and all loggers are
saved in a LoopStructural container.
You can log to file by using
log_to_file(filename,'info') and change console
logging level
log_to_console('info'/'debug'/'warning'/'error')
diff --git a/LoopStructural/__init__.py b/LoopStructural/__init__.py
@@ -19,15 +19,22 @@
 from logging.config import dictConfig
 import tempfile
 from pathlib import Path
-from .modelling.core.geological_model import GeologicalModel
-from .visualisation.model_visualisation import LavaVuModelViewer
-from .visualisation.map_viewer import MapView
-from .utils.utils import log_to_console, log_to_file
+
 
 #set up logging
 # temp_file = tempfile.mkdtemp()
 # if temp_file:
 #     # temp_file = tempfile.tempdir+Path('/default-loop-structural-logfile.log')
 #     log_to_file(temp_file)
-log_to_console()
+ch = logging.StreamHandler()
+formatter = logging.Formatter('%(asctime)s ~ %(name)-12s ~ %(levelname)-10s ~ %(message)s')
+ch.setFormatter(formatter)
+ch.setLevel(logging.WARNING)
+loggers = {}
 __version__ = '1.0.5'
+from .modelling.core.geological_model import GeologicalModel
+from .visualisation.model_visualisation import LavaVuModelViewer
+from .visualisation.map_viewer import MapView
+from .utils import log_to_console, log_to_file, getLogger
+logger = getLogger(__name__)
+logger.info("Imported LoopStructural")
diff --git a/LoopStructural/export/exporters.py b/LoopStructural/export/exporters.py
@@ -10,7 +10,8 @@
 from LoopStructural.export.file_formats import FileFormat
 
  
-logger = logging.getLogger(__name__)
+from LoopStructural.utils import getLogger
+logger = getLogger(__name__)
 
 
 def write_cubeface(model, file_name, data_label, nsteps, file_format):
diff --git a/LoopStructural/interpolators/discrete_fold_interpolator.py b/LoopStructural/interpolators/discrete_fold_interpolator.py
@@ -9,7 +9,8 @@
 from LoopStructural.interpolators.piecewiselinear_interpolator import \
     PiecewiseLinearInterpolator
 
-logger = logging.getLogger(__name__)
+from LoopStructural.utils import getLogger
+logger = getLogger(__name__)
 
 
 class DiscreteFoldInterpolator(PiecewiseLinearInterpolator):
diff --git a/LoopStructural/interpolators/discrete_interpolator.py b/LoopStructural/interpolators/discrete_interpolator.py
@@ -10,7 +10,8 @@
 from LoopStructural.interpolators.geological_interpolator import \
     GeologicalInterpolator
 
-logger = logging.getLogger(__name__)
+from LoopStructural.utils import getLogger
+logger = getLogger(__name__)
 
 
 class DiscreteInterpolator(GeologicalInterpolator):
diff --git a/LoopStructural/interpolators/finite_difference_interpolator.py b/LoopStructural/interpolators/finite_difference_interpolator.py
@@ -9,7 +9,8 @@
 from .discrete_interpolator import DiscreteInterpolator
 from .operator import Operator
 
-logger = logging.getLogger(__name__)
+from LoopStructural.utils import getLogger
+logger = getLogger(__name__)
 
 
 class FiniteDifferenceInterpolator(DiscreteInterpolator):
diff --git a/LoopStructural/interpolators/geological_interpolator.py b/LoopStructural/interpolators/geological_interpolator.py
@@ -5,7 +5,8 @@
 
 import numpy as np
 
-logger = logging.getLogger(__name__)
+from LoopStructural.utils import getLogger
+logger = getLogger(__name__)
 
 
 class GeologicalInterpolator:
diff --git a/LoopStructural/interpolators/operator.py b/LoopStructural/interpolators/operator.py
@@ -5,7 +5,8 @@
 
 import numpy as np
 
-logger = logging.getLogger(__name__)
+from LoopStructural.utils import getLogger
+logger = getLogger(__name__)
 
 
 class Operator(object):
diff --git a/LoopStructural/interpolators/piecewiselinear_interpolator.py b/LoopStructural/interpolators/piecewiselinear_interpolator.py
@@ -9,7 +9,8 @@
     DiscreteInterpolator
 from LoopStructural.utils.helper import get_vectors
 
-logger = logging.getLogger(__name__)
+from LoopStructural.utils import getLogger
+logger = getLogger(__name__)
 
 
 class PiecewiseLinearInterpolator(DiscreteInterpolator):
diff --git a/LoopStructural/interpolators/structured_grid.py b/LoopStructural/interpolators/structured_grid.py
@@ -6,7 +6,8 @@
 
 import numpy as np
 
-logger = logging.getLogger(__name__)
+from LoopStructural.utils import getLogger
+logger = getLogger(__name__)
 
 
 class StructuredGrid:
diff --git a/LoopStructural/interpolators/structured_tetra.py b/LoopStructural/interpolators/structured_tetra.py
@@ -6,7 +6,8 @@
 import numpy as np
 from LoopStructural.interpolators.cython.dsi_helper import cg, constant_norm, fold_cg
 
-logger = logging.getLogger(__name__)
+from LoopStructural.utils import getLogger
+logger = getLogger(__name__)
 
 class TetMesh:
     """
diff --git a/LoopStructural/interpolators/surfe_wrapper.py b/LoopStructural/interpolators/surfe_wrapper.py
@@ -9,7 +9,8 @@
 import logging
 import numpy as np
 
-logger = logging.getLogger(__name__)
+from LoopStructural.utils import getLogger
+logger = getLogger(__name__)
 
 import surfepy
 
diff --git a/LoopStructural/modelling/core/geological_model.py b/LoopStructural/modelling/core/geological_model.py
@@ -36,7 +36,8 @@
 from LoopStructural.utils.helper import (all_heading, gradient_vec_names,
                                          strike_dip_vector)
 
-logger = logging.getLogger(__name__)
+from LoopStructural.utils import getLogger
+logger = getLogger(__name__)
 if not surfe:
     logger.warning("Cannot import Surfe")
 
diff --git a/LoopStructural/modelling/fault/fault_function.py b/LoopStructural/modelling/fault/fault_function.py
@@ -2,7 +2,8 @@
 
 import numpy as np
 
-logger = logging.getLogger(__name__)
+from LoopStructural.utils import getLogger
+logger = getLogger(__name__)
 
 
 class CubicFunction:
diff --git a/LoopStructural/modelling/fault/fault_function_feature.py b/LoopStructural/modelling/fault/fault_function_feature.py
@@ -1,6 +1,7 @@
 import logging
 
-logger = logging.getLogger(__name__)
+from LoopStructural.utils import getLogger
+logger = getLogger(__name__)
 
 
 class FaultDisplacementFeature:
diff --git a/LoopStructural/modelling/fault/fault_segment.py b/LoopStructural/modelling/fault/fault_segment.py
@@ -2,7 +2,8 @@
 
 from LoopStructural.modelling.fault.fault_function_feature import FaultDisplacementFeature
 from LoopStructural.modelling.fault.fault_function import BaseFault
-logger = logging.getLogger(__name__)
+from LoopStructural.utils import getLogger
+logger = getLogger(__name__)
 from concurrent.futures import ThreadPoolExecutor
 import numpy as np
 
diff --git a/LoopStructural/modelling/features/cross_product_geological_feature.py b/LoopStructural/modelling/features/cross_product_geological_feature.py
@@ -7,7 +7,8 @@
 from LoopStructural.modelling.features.geological_feature import \
     GeologicalFeature
 
-logger = logging.getLogger(__name__)
+from LoopStructural.utils import getLogger
+logger = getLogger(__name__)
 
 
 class CrossProductGeologicalFeature(GeologicalFeature):
diff --git a/LoopStructural/modelling/features/geological_feature.py b/LoopStructural/modelling/features/geological_feature.py
@@ -5,7 +5,8 @@
 
 import numpy as np
 
-logger = logging.getLogger(__name__)
+from LoopStructural.utils import getLogger
+logger = getLogger(__name__)
 
 
 class GeologicalFeature:
diff --git a/LoopStructural/modelling/features/geological_feature_builder.py b/LoopStructural/modelling/features/geological_feature_builder.py
@@ -7,7 +7,8 @@
 import numpy as np
 import pandas as pd
 
-logger = logging.getLogger(__name__)
+from LoopStructural.utils import getLogger
+logger = getLogger(__name__)
 
 from LoopStructural.utils.helper import xyz_names, val_name, normal_vec_names, \
     weight_name, gradient_vec_names, tangent_vec_names, interface_name
diff --git a/LoopStructural/modelling/features/structural_frame.py b/LoopStructural/modelling/features/structural_frame.py
@@ -3,7 +3,8 @@
 """
 import logging
 import numpy as np
-logger = logging.getLogger(__name__)
+from LoopStructural.utils import getLogger
+logger = getLogger(__name__)
 
 
 class StructuralFrame:
diff --git a/LoopStructural/modelling/features/structural_frame_builder.py b/LoopStructural/modelling/features/structural_frame_builder.py
@@ -6,7 +6,8 @@
 
 import numpy as np
 
-logger = logging.getLogger(__name__)
+from LoopStructural.utils import getLogger
+logger = getLogger(__name__)
 
 from LoopStructural.modelling.features.cross_product_geological_feature \
     import \
diff --git a/LoopStructural/modelling/fold/fold.py b/LoopStructural/modelling/fold/fold.py
@@ -2,7 +2,8 @@
 
 import numpy as np
 
-logger = logging.getLogger(__name__)
+from LoopStructural.utils import getLogger
+logger = getLogger(__name__)
 
 
 class FoldEvent:
diff --git a/LoopStructural/modelling/fold/fold_rotation_angle.py b/LoopStructural/modelling/fold/fold_rotation_angle.py
@@ -7,7 +7,8 @@
     fourier_series
 from LoopStructural.modelling.fold import SVariogram
 
-logger = logging.getLogger(__name__)
+from LoopStructural.utils import getLogger
+logger = getLogger(__name__)
 
 
 class FoldRotationAngle:
diff --git a/LoopStructural/modelling/fold/fold_rotation_angle_feature.py b/LoopStructural/modelling/fold/fold_rotation_angle_feature.py
@@ -2,7 +2,8 @@
 
 import numpy as np
 
-logger = logging.getLogger(__name__)
+from LoopStructural.utils import getLogger
+logger = getLogger(__name__)
 
 
 class FoldRotationAngleFeature:
diff --git a/LoopStructural/modelling/fold/foldframe.py b/LoopStructural/modelling/fold/foldframe.py
@@ -4,7 +4,8 @@
 
 from LoopStructural.modelling.features.structural_frame import StructuralFrame
 
-logger = logging.getLogger(__name__)
+from LoopStructural.utils import getLogger
+logger = getLogger(__name__)
 
 
 class FoldFrame(StructuralFrame):
diff --git a/LoopStructural/modelling/fold/svariogram.py b/LoopStructural/modelling/fold/svariogram.py
@@ -2,7 +2,8 @@
 
 import numpy as np
 
-logger = logging.getLogger(__name__)
+from LoopStructural.utils import getLogger
+logger = getLogger(__name__)
 
 
 def find_peaks_and_troughs(x, y):
diff --git a/LoopStructural/utils/__init__.py b/LoopStructural/utils/__init__.py
@@ -11,4 +11,5 @@
     utils
 
 """
-from .map2loop import process_map2loop, build_model
+from .logging import getLogger, log_to_file, log_to_console
+from .map2loop import process_map2loop, build_model
diff --git a/LoopStructural/utils/exceptions.py b/LoopStructural/utils/exceptions.py
@@ -1,6 +1,7 @@
 import logging
 
-logger = logging.getLogger(__name__)
+from LoopStructural.utils import getLogger
+logger = getLogger(__name__)
 
 class LoopBaseException(Exception):
     """
diff --git a/LoopStructural/utils/helper.py b/LoopStructural/utils/helper.py
@@ -3,7 +3,8 @@
 import numpy as np
 from sklearn.decomposition import PCA
 
-logger = logging.getLogger(__name__)
+from LoopStructural.utils import getLogger
+logger = getLogger(__name__)
 
 
 def get_data_axis_aligned_bounding_box(xyz, buffer):
diff --git a/LoopStructural/utils/logging.py b/LoopStructural/utils/logging.py
@@ -0,0 +1,60 @@
+import logging
+import LoopStructural
+
+def get_levels():
+    """dict for converting to logger levels from string
+
+
+    Returns
+    -------
+    dict
+        contains all strings with corresponding logging levels.
+    """
+    return {'info':logging.INFO,'warning':logging.WARNING,'error':logging.ERROR,'debug':logging.DEBUG}
+
+def getLogger(name):
+    logger = logging.getLogger(name)
+    logger.addHandler(LoopStructural.ch)
+    LoopStructural.loggers[name] = logger
+    return logger
+
+def log_to_file(filename,level='info'):
+    """Set the logging parameters for log file
+
+
+    Parameters
+    ----------
+    filename : string
+        name of file or path to file
+    level : str, optional
+        'info', 'warning', 'error', 'debug' mapped to logging levels, by default 'info'
+    """
+    levels = get_levels()
+    level = levels.get(level,logging.WARNING)
+    fh = logging.FileHandler(filename)
+    fh.setFormatter(LoopStructural.formatter)
+    fh.setLevel(level)
+    for logger in LoopStructural.loggers.values():
+        for hdlr in logger.handlers[:]:  # remove the existing file handlers
+            if isinstance(hdlr,logging.FileHandler): #fixed two typos here
+                logger.removeHandler(hdlr)
+        logger.addHandler(fh) 
+        logger.setLevel(level)
+    
+
+def log_to_console(level='warning'):
+    """Set the level of logging to the console
+
+
+    Parameters
+    ----------
+    level : str, optional
+        'info', 'warning', 'error', 'debug' mapped to logging levels, by default 'info'
+    """
+    levels = get_levels()
+    level = levels.get(level,logging.WARNING)
+    for logger in LoopStructural.loggers.values():
+        for hdlr in logger.handlers:
+            # both stream and file are base stream, so check if not a filehandler
+            if not isinstance(hdlr,logging.FileHandler):
+                hdlr.setLevel(level)
diff --git a/LoopStructural/utils/map2loop.py b/LoopStructural/utils/map2loop.py
@@ -3,7 +3,8 @@
 import os
 import logging
 
-logger = logging.getLogger(__name__)
+from LoopStructural.utils import getLogger
+logger = getLogger(__name__)
 
 def process_map2loop(m2l_directory, flags={}):
     """
diff --git a/LoopStructural/utils/utils.py b/LoopStructural/utils/utils.py
diff --git a/LoopStructural/visualisation/map_viewer.py b/LoopStructural/visualisation/map_viewer.py
diff --git a/LoopStructural/visualisation/model_plotter.py b/LoopStructural/visualisation/model_plotter.py
diff --git a/LoopStructural/visualisation/model_visualisation.py b/LoopStructural/visualisation/model_visualisation.py
diff --git a/LoopStructural/visualisation/rotation_angle_plotter.py b/LoopStructural/visualisation/rotation_angle_plotter.py
