Merge pull request #66 from MTgeophysics/updates

Fix bug in MTData, added impedance units, updated simpeg 2d recipe.

Author: kujaku11

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 2.0.11
+current_version = 2.0.12
 files = setup.py mtpy/__init__.py README.md docs/source/conf.py
 commit = True
 tag = True

HISTORY.rst

@@ -58,4 +58,14 @@ History
 * Occam2d fixes by @alkirkby in https://github.com/MTgeophysics/mtpy-v2/pull/56
 * Updates by @kujaku11 in https://github.com/MTgeophysics/mtpy-v2/pull/61
 
-**Full Changelog**: https://github.com/MTgeophysics/mtpy-v2/compare/v2.0.10...v2.0.11
+**Full Changelog**: https://github.com/MTgeophysics/mtpy-v2/compare/v2.0.10...v2.0.11
+
+2.0.12 (2024-10-22)
+----------------------------
+
+* Fix rotations again by @kujaku11 in https://github.com/MTgeophysics/mtpy-v2/pull/57
+* Pin numpy versions <2.0 by @kkappler in https://github.com/MTgeophysics/mtpy-v2/pull/62
+* Occam2d fixes by @alkirkby in https://github.com/MTgeophysics/mtpy-v2/pull/56
+* Updates by @kujaku11 in https://github.com/MTgeophysics/mtpy-v2/pull/61
+
+**Full Changelog**: https://github.com/MTgeophysics/mtpy-v2/compare/v2.0.10...v2.0.12

README.md

@@ -7,7 +7,7 @@
 [![Documentation Status](https://readthedocs.org/projects/mtpy-v2/badge/?version=latest)](https://mtpy-v2.readthedocs.io/en/latest/?badge=latest)
 [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/MTgeophysics/mtpy-v2/main)
 
-## Version 2.0.11
+## Version 2.0.12
 
 # Description
 

docs/source/conf.py

@@ -67,9 +67,9 @@
 #
 
 # The short X.Y version.
-version = "2.0.11"
+version = "2.0.12"
 # The full version, including alpha/beta/rc tags.
-release = "2.0.11"
+release = "2.0.12"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

mtpy/__init__.py

@@ -18,7 +18,7 @@
 from mtpy.imaging.mtcolors import MT_CMAP_DICT, register_cmaps
 
 
-__version__ = "2.0.11"
+__version__ = "2.0.12"
 __all__ = ["MT", "MTData", "MTCollection"]
 
 # =============================================================================

mtpy/core/mt.py

@@ -14,7 +14,12 @@
 
 from mt_metadata.transfer_functions.core import TF
 
-from mtpy.core import Z, Tipper, COORDINATE_REFERENCE_FRAME_OPTIONS
+from mtpy.core.transfer_function import IMPEDANCE_UNITS
+from mtpy.core import (
+    Z,
+    Tipper,
+    COORDINATE_REFERENCE_FRAME_OPTIONS,
+)
 from mtpy.core.mt_location import MTLocation
 from mtpy.core.mt_dataframe import MTDataFrame
 from mtpy.utils.estimate_tf_quality_factor import EMTFStats
@@ -74,7 +79,7 @@ class MT(TF, MTLocation):
 
     """
 
-    def __init__(self, fn=None, **kwargs):
+    def __init__(self, fn=None, impedance_units="mt", **kwargs):
         tf_kwargs = {}
         for key in [
             "period",
@@ -113,6 +118,9 @@ def __init__(self, fn=None, **kwargs):
             self.station_metadata.transfer_function.sign_convention
         )
 
+        self._impedance_unit_factors = IMPEDANCE_UNITS
+        self.impedance_units = impedance_units
+
         for key, value in kwargs.items():
             setattr(self, key, value)
 
@@ -132,6 +140,7 @@ def clone_empty(self):
         new_mt_obj.model_elevation = self.model_elevation
         new_mt_obj._rotation_angle = self._rotation_angle
         new_mt_obj.profile_offset = self.profile_offset
+        new_mt_obj.impedance_units = self.impedance_units
 
         return new_mt_obj
 
@@ -211,6 +220,23 @@ def coordinate_reference_frame(self, value):
 
         self.station_metadata.transfer_function.sign_convention = value
 
+    @property
+    def impedance_units(self):
+        """impedance units"""
+        return self._impedance_units
+
+    @impedance_units.setter
+    def impedance_units(self, value):
+        """impedance units setter options are [ mt | ohm ]"""
+        if not isinstance(value, str):
+            raise TypeError("Units input must be a string.")
+        if value.lower() not in self._impedance_unit_factors.keys():
+            raise ValueError(
+                f"{value} is not an acceptable unit for impedance."
+            )
+
+        self._impedance_units = value
+
     @property
     def rotation_angle(self):
         """Rotation angle in degrees from north. In the coordinate reference frame"""
@@ -279,15 +305,17 @@ def rotate(self, theta_r, inplace=True):
 
     @property
     def Z(self):
-        r"""Mtpy.core.z.Z object to hold impedance tenso."""
+        r"""Mtpy.core.z.Z object to hold impedance tensor."""
 
         if self.has_impedance():
-            return Z(
+            z_object = Z(
                 z=self.impedance.to_numpy(),
                 z_error=self.impedance_error.to_numpy(),
                 frequency=self.frequency,
                 z_model_error=self.impedance_model_error.to_numpy(),
             )
+            z_object.units = self.impedance_units
+            return z_object
         return Z()
 
     @Z.setter
@@ -296,16 +324,24 @@ def Z(self, z_object):
 
         recalculate phase tensor and invariants, which shouldn't change except
         for strike angle.
+
+        Be sure to have appropriate units set
         """
+        # if a z object is given the underlying data is in mt units, even
+        # if the units are set to ohm.
+        self.impedance_units = z_object.units
         if not isinstance(z_object.frequency, type(None)):
             if self.frequency.size != z_object.frequency.size:
                 self.frequency = z_object.frequency
 
             elif not (self.frequency == z_object.frequency).all():
                 self.frequency = z_object.frequency
-        self.impedance = z_object.z
-        self.impedance_error = z_object.z_error
-        self.impedance_model_error = z_object.z_model_error
+        # set underlying data to units of mt
+        self.impedance = z_object._dataset.transfer_function.values
+        self.impedance_error = z_object._dataset.transfer_function_error.values
+        self.impedance_model_error = (
+            z_object._dataset.transfer_function_model_error.values
+        )
 
     @property
     def Tipper(self):
@@ -634,7 +670,7 @@ def plot_depth_of_penetration(self, **kwargs):
 
         return PlotPenetrationDepth1D(self, **kwargs)
 
-    def to_dataframe(self, utm_crs=None, cols=None):
+    def to_dataframe(self, utm_crs=None, cols=None, impedance_units="mt"):
         """Create a dataframe from the transfer function for use with plotting
         and modeling.
         :param cols:
@@ -644,6 +680,8 @@ def to_dataframe(self, utm_crs=None, cols=None):
         :param eter utm_crs: The utm zone to project station to, could be a
             name, pyproj.CRS, EPSG number, or anything that pyproj.CRS can intake.
         :type eter utm_crs: string, int, :class:`pyproj.CRS`
+        :param impedance_units: ["mt" [mV/km/nT] | "ohm" [Ohms] ]
+        :type impedance_units: str
         """
         if utm_crs is not None:
             self.utm_crs = utm_crs
@@ -667,19 +705,21 @@ def to_dataframe(self, utm_crs=None, cols=None):
 
         mt_df.dataframe.loc[:, "period"] = self.period
         if self.has_impedance():
-            mt_df.from_z_object(self.Z)
+            z_object = self.Z
+            z_object.units = impedance_units
+            mt_df.from_z_object(z_object)
         if self.has_tipper():
             mt_df.from_t_object(self.Tipper)
 
         return mt_df
 
-    def from_dataframe(self, mt_df):
+    def from_dataframe(self, mt_df, impedance_units="mt"):
         """Fill transfer function attributes from a dataframe for a single station.
         :param mt_df:
         :param df: DESCRIPTION.
         :type df: TYPE
-        :return: DESCRIPTION.
-        :rtype: TYPE
+        :param impedance_units: ["mt" [mV/km/nT] | "ohm" [Ohms] ]
+        :type impedance_units: str
         """
 
         if not isinstance(mt_df, MTDataFrame):
@@ -713,11 +753,9 @@ def from_dataframe(self, mt_df):
 
         self.tf_id = self.station
 
-        # self._transfer_function = self._initialize_transfer_function(
-        #     mt_df.period
-        # )
-
-        self.Z = mt_df.to_z_object()
+        z_obj = mt_df.to_z_object()
+        z_obj.units = impedance_units
+        self.Z = z_obj
         self.Tipper = mt_df.to_t_object()
 
     def compute_model_z_errors(
@@ -1072,9 +1110,7 @@ def add_white_noise(self, value, inplace=True):
             ] = self._transfer_function.transfer_function.real * (
                 noise_real
             ) + (
-                1j
-                * self._transfer_function.transfer_function.imag
-                * noise_imag
+                1j * self._transfer_function.transfer_function.imag * noise_imag
             )
 
             self._transfer_function["transfer_function_error"] = (
@@ -1088,9 +1124,7 @@ def add_white_noise(self, value, inplace=True):
             ] = self._transfer_function.transfer_function.real * (
                 noise_real
             ) + (
-                1j
-                * self._transfer_function.transfer_function.imag
-                * noise_imag
+                1j * self._transfer_function.transfer_function.imag * noise_imag
             )
 
             self._transfer_function["transfer_function_error"] = (