scikit-diveMove 0.3.2.post1__tar.gz → 0.3.3__tar.gz

{scikit-diveMove-0.3.2.post1/scikit_diveMove.egg-info → scikit-diveMove-0.3.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: scikit-diveMove
-Version: 0.3.2.post1
+Version: 0.3.3
 Summary: Python interface to R package diveMove
 Author-email: Sebastian Luque <spluque@gmail.com>
 License:                     GNU AFFERO GENERAL PUBLIC LICENSE

{scikit-diveMove-0.3.2.post1 → scikit-diveMove-0.3.3/scikit_diveMove.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: scikit-diveMove
-Version: 0.3.2.post1
+Version: 0.3.3
 Summary: Python interface to R package diveMove
 Author-email: Sebastian Luque <spluque@gmail.com>
 License:                     GNU AFFERO GENERAL PUBLIC LICENSE

{scikit-diveMove-0.3.2.post1 → scikit-diveMove-0.3.3}/skdiveMove/__init__.py

@@ -1,25 +1,48 @@
 """Top-level class for interacting with diveMove
 
 The :class:`TDR` class aims to be a comprehensive class to encapsulate the
-processing of `TDR` records from a data file.
+processing of `TDR` records from a NetCDF data file.
 
-This module instantiates an `R` session to interact with low-level
-functions and methods of package `diveMove`.
+Processing includes detection and quantification of periods of major
+activities in a TDR record, calibrating depth readings to generate
+summaries of diving behaviour. These procedures include wet/dry phase
+detection, zero-offset correction (ZOC) of depth, detection of dives, as
+well as proper labelling of the latter, among others utilities for the
+analysis of TDR records.
+
+All core procedures are encapsulated in :class:`TDR`, and are controlled by
+a set of user-defined variables in a configuration file, and systematically
+executed systematically by function :func:`calibrate`. This function can be
+used as a template for custom processing using different
+sequences. User-defined variables can also be directly specified as a
+dictionary, which is a class attribute. The standard approach follows the
+logical processing sequence described below:
+
+1. Zero-offset correction
+2. Detection of wet phases
+3. Detection of dives
+4. Detection of dive phases
+5. Speed calibration (if required)
+6. Calculation of statistics
+
+Class :class:`TDR` methods implement these steps. This module instantiates
+an `R` session to interact with low-level functions and methods of package
+`diveMove`.
 
 Calibration and phase detection
 -------------------------------
 
 .. autosummary::
 
-   TDR
+   TDR.read_netcdf
    TDR.zoc
    TDR.detect_wet
    TDR.detect_dives
    TDR.detect_dive_phases
    TDR.calibrate_speed
 
-Analyses
---------
+Analysis and summaries
+----------------------
 
 .. autosummary::
 
@@ -37,37 +60,26 @@ Plotting
    TDR.plot_phases
    TDR.plot_dive_model
 
-Functions
+Accessors
 ---------
 
 .. autosummary::
 
-   calibrate
-   dump_config_template
-
-
-Detect and quantify periods of major activities in a TDR record,
-calibrating depth readings to generate summaries of diving behaviour. These
-procedures include wet/dry phase detection, zero-offset correction (ZOC) of
-depth, detection of dives, as well as proper labelling of the latter, among
-others utilities for the analysis of TDR records.
+   TDR.extract_dives
+   TDR.get_depth
+   TDR.get_dive_deriv
+   TDR.get_dives_details
+   TDR.get_phases_params
+   TDR.get_speed
+   TDR.get_tdr
 
-All core procedures are encapsulated in :class:`TDR`, and are controlled by
-a set of user-defined variables in a configuration file, and systematically
-executed systematically by function :func:`calibrate`. This function can be
-used as a template for custom processing using different
-sequences. User-defined variables can also be directly specified as a
-dictionary, which is a class attribute. The standard approach follows the
-logical processing sequence described below:
+Functions
+---------
 
-1. Zero-offset correction
-2. Detection of wet phases
-3. Detection of dives
-4. Detection of dive phases
-5. Speed calibration (if required)
-6. Calculation of statistics
+.. autosummary::
 
-Class :class:`TDR` methods implement these steps.
+   calibrate
+   dump_config_template
 
 """
 
@@ -76,5 +88,5 @@ from skdiveMove.calibconfig import dump_config_template
 
 __author__ = "Sebastian Luque <spluque@gmail.com>"
 __license__ = "AGPLv3"
-__version__ = "0.3.2.post1"
+__version__ = "0.3.3"
 __all__ = ["TDR", "calibrate", "dump_config_template"]

{scikit-diveMove-0.3.2.post1 → scikit-diveMove-0.3.3}/skdiveMove/bouts/bouts.py

@@ -179,7 +179,7 @@ def _plot_bec(bec_x, bec_y, ax, xytext, horizontalalignment="left"):
         Argument passed to `matplotlib.annotate`; interpreted with
         textcoords="offset points".
     horizontalalignment : str
-        Argument passed to `matplotlib.annotate`.
+        Argument passed to :meth:`~matplotlib.axes.Axes.annotate`.
 
     """
     ylims = ax.get_ylim()
@@ -234,8 +234,6 @@ class Bouts(metaclass=ABCMeta):
             Method to use for calculating the frequencies: "standard"
             simply uses `x`, which "seq_diff" uses the sequential
             differences method.
-        **kwargs : optional keywords
-            Passed to histogram
 
         """
         self.x = x
@@ -273,7 +271,7 @@ class Bouts(metaclass=ABCMeta):
         return objcls + meth_str + lnfreq_str
 
     def init_pars(self, x_break, plot=True, ax=None, **kwargs):
-        """Find starting values for mixtures of random Poisson processes
+        r"""Find starting values for mixtures of random Poisson processes
 
         Starting values are calculated using the "broken stick" method.
 
@@ -281,15 +279,15 @@ class Bouts(metaclass=ABCMeta):
         ----------
         x_break : array_like
             One- or two-element array with values determining the break(s)
-            for broken stick model, such that x < x_break[0] is first
-            process, x >= x_break[1] & x < x_break[2] is second process,
-            and x >= x_break[2] is third one.
+            for broken stick model, such that :math:`x < x\_break_0` is
+            first process, :math:`x >= x\_break_1` & :math:`x < x\_break_2`
+            is second process, and :math:`x >= x\_break_2` is third one.
         plot : bool, optional
             Whether to plot the broken stick model.
         ax : matplotlib.Axes, optional
             An Axes instance to use as target.  Default is to create one.
         **kwargs : optional keyword arguments
-            Passed to plotting function.
+            Passed to plotting function. Ignored currently.
 
         Returns
         -------
@@ -365,8 +363,9 @@ class Bouts(metaclass=ABCMeta):
         ----------
         start : pandas.DataFrame
             DataFrame with coefficients for each process in columns.
-        **kwargs : optional keyword arguments
-            Passed to `scipy.optimize.curve_fit`.
+        **kwargs
+            Optional keyword arguments passed to
+            :func:`scipy.optimize.curve_fit`.
 
         Returns
         -------
@@ -411,7 +410,7 @@ class Bouts(metaclass=ABCMeta):
         -------
         out : numpy.ndarray, shape (n,)
             1-D array with BECs implied by `coefs`.  Length is
-            coefs.shape[1]
+            ``coefs.shape[1]``
 
         """
         # Find bec's per process by pairing columns

{scikit-diveMove-0.3.2.post1 → scikit-diveMove-0.3.3}/skdiveMove/bouts/boutsmle.py

@@ -330,8 +330,9 @@ class BoutsMLE(bouts.Bouts):
             with coefficients of the solution.
         ax : matplotlib.axes.Axes instance
             An Axes instance to use as target.
-        **kwargs : optional keyword arguments
-            Passed to `matplotlib.pyplot.gca`.
+        **kwargs
+            Optional keyword arguments passed to
+            :func:`matplotlib.pyplot.gca`.
 
         Returns
         -------

{scikit-diveMove-0.3.2.post1 → scikit-diveMove-0.3.3}/skdiveMove/bouts/boutsnls.py

@@ -66,8 +66,9 @@ class BoutsNLS(bouts.Bouts):
         ----------
         start : pandas.DataFrame
             DataFrame with coefficients for each process in columns.
-        **kwargs : optional keyword arguments
-            Passed to `scipy.optimize.curve_fit`.
+        **kwargs
+            Optional keyword arguments passed to
+            :func:`scipy.optimize.curve_fit`.
 
         Returns
         -------
@@ -93,7 +94,7 @@ class BoutsNLS(bouts.Bouts):
         -------
         out : numpy.ndarray, shape (n,)
             1-D array with BECs implied by `coefs`.  Length is
-            coefs.shape[1]
+            ``coefs.shape[1]``
 
         """
         # The metaclass implements this method
@@ -108,8 +109,9 @@ class BoutsNLS(bouts.Bouts):
             DataFrame with model coefficients in columns.
         ax : matplotlib.axes.Axes instance
             An Axes instance to use as target.
-        **kwargs : optional keyword arguments
-            Passed to `matplotlib.pyplot.gca`.
+        **kwargs
+            Optional keyword arguments passed to
+            :func:`matplotlib.pyplot.gca`.
 
         Returns
         -------

{scikit-diveMove-0.3.2.post1 → scikit-diveMove-0.3.3}/skdiveMove/calibspeed.py

@@ -43,7 +43,7 @@ def calibrate_speed(x, tau, contour_level, z=0, bad=[0, 0],
 
     Notes
     -----
-    See `skdiveMove.TDR.calibrate_speed` for details.
+    See :func:`~skdiveMove.TDR.calibrate_speed` for details.
 
     """
     # `gaussian_kde` expects variables in rows

{scikit-diveMove-0.3.2.post1 → scikit-diveMove-0.3.3}/skdiveMove/helpers.py

@@ -19,7 +19,7 @@ def _load_dataset(filename_or_obj, **kwargs):
     ----------
     filename_or_obj : str, Path or xarray.backends.*DataStore
         String indicating the file where the data comes from.
-    **kwargs :
+    **kwargs
         Keyword arguments passed to :func:`~xarray.load_dataset`.
 
     Returns
@@ -177,10 +177,9 @@ def _one_dive_stats(x, interval, has_speed=False):
         onames = onames_nospeed
 
     res_df = pd.DataFrame(res, columns=onames)
-    for tcol in range(3):
+    for tcol in onames[:3]:
         # This is per POSIXct convention in R
-        res_df.iloc[:, tcol] = pd.to_datetime(res_df.iloc[:, tcol],
-                                              unit="s")
+        res_df[tcol] = pd.to_datetime(res_df[tcol], unit="s")
 
     return res_df
 
@@ -252,7 +251,7 @@ def rle_key(x):
     2020-01-01 00:02:30+00:00    6
     2020-01-01 00:02:40+00:00    6
     2020-01-01 00:02:50+00:00    6
-    Freq: 10S, dtype: int64
+    Freq: 10s, dtype: int64
 
     """
     xout = x.ne(x.shift()).cumsum()

{scikit-diveMove-0.3.2.post1 → scikit-diveMove-0.3.3}/skdiveMove/imutools/allan.py

@@ -63,8 +63,8 @@ def _line_fun(t, alpha, tau_crit, adev_crit):
 def allan_coefs(taus, adevs):
     """Compute Allan deviation coefficients for each error type
 
-    Given averaging intervals ``taus`` and corresponding Allan deviation
-    ``adevs``, compute the Allan deviation coefficient for each error type:
+    Given averaging intervals `taus` and corresponding Allan deviation
+    `adevs`, compute the Allan deviation coefficient for each error type:
 
     - Quantization
     - (Angle, Velocity) Random Walk

{scikit-diveMove-0.3.2.post1 → scikit-diveMove-0.3.3}/skdiveMove/imutools/imu.py

@@ -47,7 +47,7 @@ class IMUBase:
     Examples
     --------
     This example illustrates some of the issues encountered while reading
-    data files in a real-world scenario.  ``scikit-diveMove`` includes a
+    data files in a real-world scenario.  `scikit-diveMove` includes a
     NetCDF file with IMU signals collected using a Samsung Galaxy S5 mobile
     phone.  Set up instance from NetCDF example data:
 
@@ -90,19 +90,22 @@ class IMUBase:
             Dataset containing IMU sensor DataArrays, and optionally other
             DataArrays.
         acceleration_name : str, optional
-            Name of the acceleration ``DataArray`` in the ``Dataset``.
+            Name of the acceleration :class:`~xarray.DataArray` in the
+            `dataset`.
         angular_velocity_name : str, optional
-            Name of the angular velocity ``DataArray`` in the ``Dataset``.
+            Name of the angular velocity :class:`~xarray.DataArray` in the
+            `dataset`.
         magnetic_density_name : str, optional
-            Name of the magnetic density ``DataArray`` in the ``Dataset``.
+            Name of the magnetic density :class:`~xarray.DataArray` in the
+            `dataset`.
         time_name : str, optional
-            Name of the time dimension in the dataset.
+            Name of the time dimension in the `dataset`.
         has_depth : bool, optional
             Whether input data include depth measurements.
         depth_name : str, optional
-            Name of the depth ``DataArray`` in the ``Dataset``.
+            Name of the depth :class:`~xarray.DataArray` in the `dataset`.
         imu_filename : str, optional
-            Name of the file from which ``dataset`` originated.
+            Name of the file from which `dataset` originated.
 
         """
         self.time_name = time_name
@@ -130,7 +133,7 @@ class IMUBase:
                     **kwargs):
         """Instantiate object by loading Dataset from NetCDF file
 
-        Provided all ``DataArray`` in the NetCDF file have the same
+        Provided all `DataArrays` in the NetCDF file have the same
         dimensions (N, 3), this is an efficient way to instantiate.
 
         Parameters
@@ -138,17 +141,19 @@ class IMUBase:
         imu_file : str
             As first argument for :func:`xarray.load_dataset`.
         acceleration_name : str, optional
-            Name of the acceleration ``DataArray`` in the ``Dataset``.
+            Name of the acceleration :class:`~xarray.DataArray` in the
+            :class:`~xarray.Dataset`.
         angular_velocity_name : str, optional
-            Name of the angular velocity ``DataArray`` in the ``Dataset``.
+            Name of the angular velocity :class:`~xarray.DataArray` in the
+            :class:`~xarray.Dataset`.
         magnetic_density_name : str, optional
-            Name of the magnetic density ``DataArray`` in the ``Dataset``.
-        dimension_names : list, optional
-            Names of the dimensions of the data in each of the sensors.
+            Name of the magnetic density :class:`~xarray.DataArray` in the
+            :class:`~xarray.Dataset`.
         has_depth : bool, optional
             Whether input data include depth measurements.
         depth_name : str, optional
-            Name of the depth ``DataArray`` in the ``Dataset``.
+            Name of the depth :class:`~xarray.DataArray` in the
+            :class:`~xarray.Dataset`.
         **kwargs
             Optional keyword arguments passed to
             :func:`xarray.load_dataset`.
@@ -185,7 +190,7 @@ class IMUBase:
         ----------
         sensor : str
             Attribute name of the sensor of interest
-        taus : float, str
+        taus : {float, str}
             Tau value, in seconds, for which to compute statistic.  Can be
             one of "octave" or "decade" for automatic generation of the
             value.
@@ -222,9 +227,9 @@ class IMUBase:
         This procedure implements the autonomous regression method for
         Allan variance described in [1]_.
 
-        Given averaging intervals ``taus`` and corresponding Allan
-        deviation ``adevs``, compute the Allan deviation coefficient for
-        each error type:
+        Given averaging intervals `taus` and corresponding Allan deviation
+        `adevs`, compute the Allan deviation coefficient for each error
+        type:
 
           - Quantization
           - (Angle, Velocity) Random Walk
@@ -236,7 +241,7 @@ class IMUBase:
         ----------
         sensor : str
             Attribute name of the sensor of interest
-        taus : float, str
+        taus : {float, str}
             Tau value, in seconds, for which to compute statistic.  Can be
             one of "octave" or "decade" for automatic generation of the
             value.
@@ -247,9 +252,9 @@ class IMUBase:
             Allan deviation coefficient and corresponding averaging time
             for each sensor axis and error type.
         adevs : pandas.DataFrame
-            `MultiIndex` DataFrame with Allan deviation, corresponding
-            averaging time, and fitted ARMAV model estimates of the
-            coefficients for each sensor axis and error type.
+            :class:`~pandas.MultiIndex` DataFrame with Allan deviation,
+            corresponding averaging time, and fitted ARMAV model estimates
+            of the coefficients for each sensor axis and error type.
 
         Notes
         -----
@@ -313,8 +318,8 @@ class IMUBase:
         ----------
         method : str, optional
             Name of the filtering method to use.
-        **kwargs : optional keyword arguments
-            Arguments passed to filtering method.
+        **kwargs
+            Optional keyword arguments passed to filtering method.
 
         """
         orienter_cls = getattr(filters, method)

{scikit-diveMove-0.3.2.post1 → scikit-diveMove-0.3.3}/skdiveMove/imutools/imu2body.py

@@ -71,7 +71,7 @@ def scatterIMU_svd(vectors, svd, R_ctr2i, normalize=False, center=False,
         vectors, sigma, right singular vectors).
     R_ctr2i : Rotation
         :class:`~scipy.spatial.transforms.Rotation` object describing the
-        rotation from the *centered* body frame to the ``IMU`` frame.
+        rotation from the *centered* body frame to the `IMU` frame.
     normalize : bool, optional
         Whether to normalize vectors.  Default assumes input is normalized.
     center : bool, optional
@@ -85,7 +85,7 @@ def scatterIMU_svd(vectors, svd, R_ctr2i, normalize=False, center=False,
         Output file for the animation.
     **kwargs
         Optional keyword arguments passed to
-        :func:`~matplotlib.pyplot.figure` (e.g. ``figsize``).
+        :func:`~matplotlib.pyplot.figure` (e.g. `figsize`).
 
     Returns
     -------
@@ -178,7 +178,7 @@ def _scatterIMU_svd(vectors, svd, R_b2i, normalize=False, title=None,
         Output file for the animation.
     **kwargs
         Optional keyword arguments passed to
-        :func:`~matplotlib.pyplot.figure` (e.g. ``figsize``).
+        :func:`~matplotlib.pyplot.figure` (e.g. `figsize`).
 
     Returns
     -------
@@ -266,7 +266,7 @@ def scatterIMU3D(vectors, col_vector, normalize=True, title=None,
         Title for the color bar.
     **kwargs
         Optional keyword arguments passed to
-        :func:`~matplotlib.pyplot.figure` (e.g. ``figsize``).
+        :func:`~matplotlib.pyplot.figure` (e.g. `figsize`).
 
     Returns
     -------
@@ -316,7 +316,7 @@ def tsplotIMU_depth(vectors, depth, time_name=_TIME_NAME, **kwargs):
         Array with depth measurements.
     **kwargs : optional keyword arguments
         Arguments passed to :func:`~matplotlib.pyplot.subplots`
-        (e.g. ``figsize``).
+        (e.g. `figsize`).
 
     Returns
     -------
@@ -377,7 +377,7 @@ class IMU2Body(IMUBase):
     covariance matrix, rather than the unscaled correlation (outer product)
     of acceleration as the input for Singular Value Decomposition.
 
-    In addition to attributes in :class:`IMUBase`, ``IMU2Body`` adds the
+    In addition to attributes in :class:`IMUBase`, `IMU2Body` adds the
     attributes listed below.
 
     Attributes
@@ -411,14 +411,14 @@ class IMU2Body(IMUBase):
     ...                                     savgol_parms=(99, 2))
     >>> print(imu)  # doctest: +ELLIPSIS
     IMU -- Class IMU2Body object
-    Source File          ...
-    IMU: <xarray.Dataset>
+    Source File           ...
+    IMU: <xarray.Dataset> ...
     Dimensions:           ...
     Coordinates:
       * timestamp         (timestamp) datetime64[ns] ...
-      * accelerometer     (accelerometer) object 'x' 'y' 'z'
-      * magnetometer      (magnetometer) object 'x' 'y' 'z'
-      * gyroscope         (gyroscope) object 'x' 'y' 'z'
+      * accelerometer     (accelerometer) <U1 12B 'x' 'y' 'z'
+      * magnetometer      (magnetometer) <U1 12B 'x' 'y' 'z'
+      * gyroscope         (gyroscope) <U1 12B 'x' 'y' 'z'
     Data variables:
         depth             (timestamp) float64 ...
         acceleration      (timestamp, accelerometer) float64 ...
@@ -466,7 +466,8 @@ class IMU2Body(IMUBase):
             diveMove's `diveStats` function.
         savgol_parms : tuple, optional
             A 2-element tuple with the window length and polynomial order
-            for the Savitzky-Golay filter to smooth acceleration.
+            for the Savitzky-Golay filter
+            (:func:`~scipy.signal.savgol_filter`) to smooth acceleration.
         **kwargs : optional keyword arguments
             Arguments passed to the `IMUBase.__init__` for instantiation,
             except `has_depth` because the input `Dataset` is assumed to
@@ -526,14 +527,15 @@ class IMU2Body(IMUBase):
             beginning of the next interval.
         savgol_parms : tuple, optional
             A 2-element tuple with the window length and polynomial order
-            for the Savitzky-Golay filter to smooth acceleration.
+            for the Savitzky-Golay filter
+            (:func:`~scipy.signal.savgol_filter`) to smooth acceleration.
         load_dataset_kwargs : dict, optional
             Dictionary of optional keyword arguments passed to
             :func:`xarray.load_dataset`.
-        **kwargs : optional keyword arguments
-            Additional arguments passed to :meth:`IMUBase.__init__` method,
-            except ``has_depth`` or ``imu_filename``.  The input
-            ``Dataset`` is assumed to have a depth ``DataArray``.
+        **kwargs
+            Optional keyword arguments passed to :meth:`IMUBase.__init__`
+            method, except `has_depth` or `imu_filename`.  The input
+            `Dataset` is assumed to have a depth `DataArray`.
 
         Returns
         -------
@@ -669,9 +671,9 @@ class IMU2Body(IMUBase):
             Index in surface details table to be analyzed.
         plot : bool, optional
             Whether to generate a plot of the estimate
-        **kwargs : optional keyword arguments
-            Arguments passed to :meth:`scatterIMU_svd`.  Only ``title`` and
-            ``animate`` are taken.
+        **kwargs
+            Optional keyword arguments passed to :meth:`scatterIMU_svd`.
+            Only `title` and `animate` are taken.
 
         Returns
         -------
@@ -749,7 +751,7 @@ class IMU2Body(IMUBase):
     def get_orientations(self):
         r"""Obtain orientation for all periods in surface details table
 
-        A quality index (``q``) for each estimate is calculated as:
+        A quality index (:math:`q`) for each estimate is calculated as:
 
         .. math::
 
@@ -814,8 +816,8 @@ class IMU2Body(IMUBase):
 
         Re-orient acceleration and magnetic density of IMU object relative
         to body frame, and return re-oriented IMU object.  Note that the
-        provided ``R_b2i`` must describe the rotation from the body frame
-        to the IMU frame.  The opposite rotation is applied to the
+        provided `R_b2i` must describe the rotation from the body frame to
+        the IMU frame.  The opposite rotation is applied to the
         acceleration and magnetic field vectors of the selected surface
         segment to orient the data in the body frame.
 
@@ -851,7 +853,7 @@ class IMU2Body(IMUBase):
     def orient_surfacings(self, R_all=None):
         """Apply orientation to all periods in surface details table
 
-        If the ``orientations`` attribute was filled, use it to build
+        If the `orientations` attribute was filled, use it to build
         multi-index dataframe, othewise, fill it.
 
         This method orients each segment independently, as opposed to a
@@ -871,7 +873,7 @@ class IMU2Body(IMUBase):
         Returns
         -------
         xarray.Dataset
-            Dataset with the re-oriented surface IMU objects.  If ``R_all``
+            Dataset with the re-oriented surface IMU objects.  If `R_all`
             was not provided, the Dataset contains an additional coordinate
             representing the surfacing period for each segment.
 
@@ -929,7 +931,7 @@ class IMU2Body(IMUBase):
         Returns
         -------
         xarray.Dataset
-            Dataset with the re-oriented IMU object.  If ``R_all`` was not
+            Dataset with the re-oriented IMU object.  If `R_all` was not
             provided, the Dataset contains an additional coordinate
             representing the surfacing period for each segment.
 
@@ -997,10 +999,10 @@ class IMU2Body(IMUBase):
         return imus
 
     def filter_surfacings(self, qual_thresh):
-        """Filter records from ``surface_details`` and ``orientations``
+        """Filter records from `surface_details` and `orientations`
 
-        Remove records from the ``surface_details`` and ``orientations``
-        attributes, based on ``quality`` and, optionally, duration of the
+        Remove records from the `surface_details` and `orientations`
+        attributes, based on `quality` and, optionally, duration of the
         surface period.  Records with quality higher than the specified
         value, and (optionally) duration lower than the specified number of
         seconds, are removed.
@@ -1082,7 +1084,7 @@ class IMU2Body(IMUBase):
             `vec_name="acceleration"`)
         **kwargs
             Optional keyword arguments passed to
-            :func:`~matplotlib.pyplot.subplots` (e.g. ``figsize``).
+            :func:`~matplotlib.pyplot.subplots` (e.g. `figsize`).
 
         Returns
         -------
@@ -1143,7 +1145,7 @@ class _TagTools(IMU2Body):
             Whether to generate a plot of the estimate
         **kwargs
             Optional keyword arguments passed to :meth:`scatterIMU_svd`.
-            Only ``title`` and ``animate`` are taken.
+            Only `title` and `animate` are taken.
 
         Returns
         -------