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Update DOLfYN API #77

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Dec 2, 2024
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Update DOLfYN API #77

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9909b6e
Update dolfyn api
jmcvey3 Sep 11, 2024
88d67aa
Update for current dolfyn PR
jmcvey3 Nov 14, 2024
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65 changes: 47 additions & 18 deletions docs/source/mhkit-python/api.dolfyn.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -30,8 +30,8 @@ import:
~mhkit.dolfyn.rotate.base.quaternion2orient
~mhkit.dolfyn.velocity.VelBinner

ADP Module
""""""""""
ADP Submodule
"""""""""""""
The other two ways are to import the instrument-specific
modules.
The ADP module contains routines for reading and working with
Expand All @@ -49,8 +49,8 @@ ADP/ADCP data and is imported using
~mhkit.dolfyn.velocity.VelBinner
~mhkit.dolfyn.adp.turbulence.ADPBinner

ADV Module
""""""""""
ADV Submodule
"""""""""""""
The ADV module contains routines for reading and working with
ADV data and is imported using
`from mhkit.dolfyn.adv import api`. It contains:
Expand All @@ -69,8 +69,8 @@ ADV data and is imported using
~mhkit.dolfyn.adv.turbulence.ADVBinner
~mhkit.dolfyn.adv.turbulence.turbulence_statistics

IO
""
IO Submodule
""""""""""""
The io submodule contains the following functions to read
binary Nortek (e.g., .VEC, .wpr, .ad2cp, etc.) or TRDI
(.000, .PD0, .ENX, etc.) data file.
Expand Down Expand Up @@ -110,8 +110,8 @@ binary Nortek (e.g., .VEC, .wpr, .ad2cp, etc.) or TRDI
:undoc-members:
:show-inheritance:

Rotate
""""""
Rotate Submodule
""""""""""""""""
The rotate submodule contains tools to rotate a dataset
to different coordinate systems. When a file is read into
dolfyn, the data will be stored in the same coordinate
Expand Down Expand Up @@ -159,9 +159,9 @@ ADP-specific functions:
:nosignatures:

~mhkit.dolfyn.adp.clean.set_range_offset
~mhkit.dolfyn.adp.clean.find_surface
~mhkit.dolfyn.adp.clean.find_surface_from_P
~mhkit.dolfyn.adp.clean.nan_beyond_surface
~mhkit.dolfyn.adp.clean.water_depth_from_amplitude
~mhkit.dolfyn.adp.clean.water_depth_from_pressure
~mhkit.dolfyn.adp.clean.remove_surface_interference
~mhkit.dolfyn.adp.clean.correlation_filter
~mhkit.dolfyn.adp.clean.medfilt_orient
~mhkit.dolfyn.adp.clean.val_exceeds_thresh
Expand Down Expand Up @@ -202,7 +202,7 @@ prior to collecting data.

~mhkit.dolfyn.adv.motion.correct_motion

.. automodule:: mhkit.dolfyn.adv.motion.correct_motion
.. automodule:: mhkit.dolfyn.adv.motion
:members:
:undoc-members:
:show-inheritance:
Expand All @@ -224,9 +224,10 @@ be called from `VelBinner`.
~mhkit.dolfyn.binned.TimeBinner.mean
~mhkit.dolfyn.binned.TimeBinner.variance
~mhkit.dolfyn.binned.TimeBinner.standard_deviation
~mhkit.dolfyn.binned.VelBinner.bin_average
~mhkit.dolfyn.binned.VelBinner.bin_variance
~mhkit.dolfyn.binned.VelBinner.autocovariance
~mhkit.dolfyn.velocity.VelBinner.bin_average
~mhkit.dolfyn.velocity.VelBinner.bin_variance
~mhkit.dolfyn.velocity.VelBinner.autocovariance
~mhkit.dolfyn.velocity.VelBinner.turbulence_intensity
~mhkit.dolfyn.velocity.VelBinner.turbulent_kinetic_energy
~mhkit.dolfyn.velocity.VelBinner.power_spectral_density

Expand All @@ -241,8 +242,8 @@ be called from `VelBinner`.
:show-inheritance:


Turbulence Analysis
"""""""""""""""""""
ADV Turbulence Analysis
"""""""""""""""""""""""
Functions for analyzing ADV data via the `ADVBinner` class,
beyond those described in `VelBinner`.

Expand All @@ -253,6 +254,8 @@ beyond those described in `VelBinner`.
~mhkit.dolfyn.adv.turbulence.turbulence_statistics
~mhkit.dolfyn.adv.turbulence.ADVBinner.reynolds_stress
~mhkit.dolfyn.adv.turbulence.ADVBinner.cross_spectral_density
~mhkit.dolfyn.adv.turbulence.ADVBinner.doppler_noise_level
~mhkit.dolfyn.adv.turbulence.ADVBinner.check_turbulence_cascade_slope
~mhkit.dolfyn.adv.turbulence.ADVBinner.dissipation_rate_LT83
~mhkit.dolfyn.adv.turbulence.ADVBinner.dissipation_rate_SF
~mhkit.dolfyn.adv.turbulence.ADVBinner.dissipation_rate_TE01
Expand All @@ -264,6 +267,33 @@ beyond those described in `VelBinner`.
:show-inheritance:


AD2CP Turbulence Analysis
"""""""""""""""""""""""""
Functions for analyzing turbulence from AD2CP measurements
via the `ADPBinner` class.

.. autosummary::
:nosignatures:

~mhkit.dolfyn.adv.turbulence.ADPBinner
~mhkit.dolfyn.adv.turbulence.ADPBinner.dudz
~mhkit.dolfyn.adv.turbulence.ADPBinner.dvdz
~mhkit.dolfyn.adv.turbulence.ADPBinner.dwdz
~mhkit.dolfyn.adv.turbulence.ADPBinner.shear_squared
~mhkit.dolfyn.adv.turbulence.ADPBinner.doppler_noise_level
~mhkit.dolfyn.adv.turbulence.ADPBinner.reynolds_stress_4beam
~mhkit.dolfyn.adv.turbulence.ADPBinner.stress_tensor_5beam
~mhkit.dolfyn.adv.turbulence.ADPBinner.check_turbulence_cascade_slope
~mhkit.dolfyn.adv.turbulence.ADPBinner.dissipation_rate_LT83
~mhkit.dolfyn.adv.turbulence.ADPBinner.dissipation_rate_SF
~mhkit.dolfyn.adv.turbulence.ADPBinner.friction_velocity

.. automodule:: mhkit.dolfyn.adp.turbulence
:members:
:undoc-members:
:show-inheritance:


Tools
"""""
Spectral analysis and miscellaneous DOLfYN functions are
Expand Down Expand Up @@ -326,4 +356,3 @@ of the stored time between a variety of time formats.
:members:
:undoc-members:
:show-inheritance: