CHANGELOG.rst

Changelog

3.1.0 (2024-09-13) ---

Added

• support for Python 3.12.

• AP sensing .tra support, as the reference temperature sensor data by this device in only logged in .tra and not in the .xml log files.

  added functions in io/apsensing.py to read .tra files if they are in the same directory as the .xml files.

• more test data from AP sensing device N4386B, which do also contain their .tra log files

Fixed

• device ID bug for APSensing. Device ID is N4386B instead of C320. C320 was an arbitrary name given for the wellbore by the user.

Changed

• the verify_timedeltas keyword argument is now optional when merging two single ended datasets.
• removed statsmodels as a dependency. It is now optional, and only used for testing the wls_sparse solver

3.0.3 (2024-04-18) ---

Fixed

• Improved error message when some variables cannot be shifted by the suggest_shift_double_ended function.

Changed:

• [dev] Moved to Ruff instead of isort for import sorting

3.0.2 (2024-04-13) ---

Fixed

• Bumpversion configuration was incorrect since v3.0.0. Therefore the 3.0.1 release failed. This is a re-release of 3.0.1:

3.0.1 (2024-04-13) ---

Fixed

• Oryx v4 double ended could have the backward measurements incorrectly cut off during loading.

3.0.0 (2023-11-05) ---

Added

• Calibration functions are now accessed via the .dts accessor in favor of the DataStore class.
• Improved the functionality of merge_double_ended, by adding a check that handles measurements missing in one channel while present in the other ([#171](#171))
• Support for Python 3.11
• matching_sections is now similarly implemented as sections.

Fixed

• Single-ended measurements with fix_alpha failed due to a bug introduced in v2.0.0 ([#173](#173)).
• Headers in example notebooks and their appearance in the docs are now at correct levels
• Big clean up of the documentation. The documentation is now more consistent and easier to read.

Changed

• Notebooks now reflect the new API with the .dts accessor.
• Calibration functions now return only calibration results instead of adding the results to the Dataset inplace.
• Standardized parameter names. Reduced the freedom in choosing parameter names and dimension names in favor of simplifying the code.
• Requiring netcdf4 >= 1.6.4
• Optional dependencies of xarray that improve performance are now required by default.
• variance_stokes_linear() does not default through zero anymore.
• Refactored calibration_single_ended and calibration_double_ended()
• Moved ParameterIndices classes to calibration_utils.py
• Flox included in requirements to speed up resampling via xarray ([Xarray #5734](pydata/xarray#5734)).

Removed

• Removed the DataStore module in favor of the dts accessor.
• Removed ds.resample_datastore() in favor of using xarray's resample function. See example notebook 2.
• Removed support for Python 3.8

Developer changes

• Added mypy to dev dependencies and CI.
• Using ruff for most of the formattting. Black is used for the notebooks. Isort is used for sorting the imports.
• Changed all import statements to be absolute instead of relative.
• Cleaned up old 'pylint: disable' comments

2.0.0 (2023-05-24)

• Faster approach on error propagation. As alternative to computational intensive Monte Carlo runs.
• Refractored some of the indexing logic of the calibration routines.
• Rewritten single-ended and double-ended example notebooks.
• Removed support for OLS calibration, as with minor extra efforts WLS could be used, which has significant benefits.

1.2.0 (2023-03-13)

Bug fixes

• Fixed deprecated np.float and np.int

Other

• Moved project build system & scripts to hatch.
• Project is now fully configured using pyproject.toml
• Linting is handled by Ruff.
• Notebooks are now rendered as part of the documentation.

Removed

• cli.py script (unused) has been removed.

New contributors: * Karl Lapo (@klapo)

1.1.2 (2022-09-25)

• Added support for Sensornet Sentinel v5 files.

1.1.1 (2022-09-25)

• Deprecated Python 3.7
• Fixed documention rendering
• Updated readme badges

1.1.0 (2022-09-25)

New features

• Added support for Python 3.9, 3.10.
• Silixa's xml version 8 is now supported

Bug fixes

• Loading in untested sensornet files will not give a UnboundLocalError error anymore
• Sensornet .ddf file version check is now more robust (commas are replaced to periods)
• Changed matplotlib's deprecated DivergingNorm to TwoSlopeNorm
• Updated the stokes_variance_linear docstring to remove incorrect and duplicate information
• Adjusted resample_datastore to avoid using deprecated 'base' kwarg, instead using the new arguments 'origin' and 'offset'. See http://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.resample.html

Others

• Notebook 04 on Stokes variance has been updated to explain the different estimation methods for the variance, and their importance.
• Notebook 07 and 08 have been updated to take into account the changes in ds.stokes_variance.
• Silenced xarray's __slots__ warning
• Deprecated Python 3.6
• CI has been moved to GitHub Actions. Travis-CI and AppVeyor have been removed.

1.0.2 (2020-05-04)

• Same as v1.0.1

1.0.1 (2020-05-04)

New features

• st_var can now be array-like. The array-like can vary in x or time, or both.
• When converting from a xr.Dataset to a DataStore object, the attributes arenow transfered over
• Added 'verbose' kwarg to shift_double_ended utility function to silence theconsole output

Bug fixes

• If the '_sections' attribute is missing from a DataStore object it is automagically re-added.
• Assert that stokes variances are passed when running a double-ended WLS calibration
• Added check for NaN/inf values in wls_sparse solver to avoid unclear error messages
• Before calibration, the values of the used reference temperatures are checked if they are valid (float dtype, no NaN/inf values, correct time dimension)

Others

• European Geosciences Union conference 2020 presentation added
• Updated documentation with content article
• Use YAPF formatting of the Python files
• Travis-CI.org integration in GitHub restored.

1.0.0 (2020-03-30)

• First major release
• Reduced flexibility in defining names under which the Stokes are stored
• 4 Averaging functions implemented, with uncertainty estimation. See notebook 16 for the various options
• Notebook about transient attenuation caused by for example connectors
• Bug in singel ended transient attenuation
• Check for consistent number of measurement locations across read files

0.9.2 (2020-03-17)

• Reduced flexibility in defining Stokes labels

0.9.1 (2020-03-17)

• Same as 0.9.2

0.9.0 (2020-03-16)

• Increased precision of least squares solver, as this was limiting theprecision of the parameter estimation
• The variance of the noise in the Stokes can change linear with the intensity
• Improved residuals plot function
• Reduced the number of equations for double ended calibration
• Support for transient attenuation due to connectors along fibers
• Matching sections

0.8.0 (2020-02-14)

• Valentine edition
• Added example for fixing parameters
• Bug fixed in routine for reading Sensornet files (Bor van der Scheer)
• Official support for Python 3.8
• When the datastore is printed to the screen, the mean and std of thereference temperature is plotted
• Integrated differential attenuation is reformulated. Starts integrating atthe first reference section location.
• Estimation of the variance of the Stokes that is linear dependent on theintensity (Poisson)
• Removed __slots__ attribute

0.7.4 (2020-01-26)

• Update automated zenodo reference requires to draft a new release

0.7.3 (2020-01-24)

• Solved xlim in subplots of plot_residuals_reference_sections funciton
• Solved YAML deprecation related problems
• Introduced new approach for double ended calibration, with a different Cfor the forward and backward channel
• First code added for time variant asymmetric attenuation, such as connectors.
• First code added for matching sections

0.7.2 (2019-11-22)

• Set alpha and or gamma to known value, with corresponding variance.
• Bug in computation of the weights for single and double-ended calibration
• Added notebook about merging two single ended measurements
• Added example notebook on how to create a custom datastore
• Added notebook examples for loading in data from the different manufa..
• Loading AP Sensing files and tests
• Loading Sensortran files

0.7.0 (2019-11-07)

• Ensure order of dimension upon initialization of DataStore. Resamplingwould lead to issues
• Bug in section definition (reported by Robert Law)
• Rewritten calibration solvers to align with article of this package
• Removed old calibration solvers
• New possibilities of saving and loading large DataStores saved to multiplenetCDF files

0.6.7 (2019-11-01)

• Use twine to check if the compiled package meets all the requirements of Pypi

0.6.6 (2019-11-01)

• Use twine to check if the compiled package meets all the requirements of Pypi

0.6.5 (2019-11-01)

• Major bug fix version.
• More flexibility in defining the time and space dimensions
• Fixed unsave yaml loading
• Added support for Silixa 7 files
• Start using __slots__ as it is something new
• xarray doesn't have the attribute ._initialized anymore. Rewritten teststo make more sense by checking the sum of the Stokes instead.
• Support for double ended Sensornet files and tests
• Bug fixing

0.6.4 (2019-04-09)

• More flexibility in defining the time dimension
• Cleanup of some plotting functions

0.6.3 (2019-04-03)

• Added reading support for zipped silixa files. Still rarely fails due to upstream bug.
• pretty __repr__
• Reworked double ended calibration procedure. Integrated differential attenuation outside of reference sections is now calculated seperately.
• New approach for estimation of Stokes variance. Not restricted to a decaying exponential
• Bug in averaging TMPF and TMPB to TMPW
• Modified residuals plot, especially useful for long fibers (Great work Bart!)
• Example notebooks updatred accordingly
• Bug in to_netcdf when passing encodings
• Better support for sections that are not related to a timeseries.

0.6.2 (2019-02-26)

• Double-ended weighted calibration procedure is rewritten so that the integrated differential attenuation outside of the reference sections is calculated seperately. Better memory usage and faster
• Other calibration routines cleaned up
• Official support for Python 3.7
• Coverage figures are now trustworthy
• String representation improved
• Include test for aligning double ended measurements
• Example for aligning double ended measurements

0.6.1 (2019-01-04)

• Many examples were shown in the documentation
• Fixed verbose settings of solvers
• Revised example notebooks
• Moved to 80 characters per line (PEP)
• More Python formatting using YAPF
• Use example of plot_residuals_reference_sections function in Stokes variance example notebook
• Support Python 3.7

0.6.0 (2018-12-08)

• Reworked the double-ended calibration routine and the routine for confidence intervals. The integrated differential attenuation is not zero at x=0 anymore.
• Verbose commands carpentry
• Bug fixed that would make the read_silixa routine crash if there are copies of the same file in the same folder
• Routine to read sensornet files. Only single-ended configurations supported for now. Anyone has double-ended measurements?
• Lazy calculation of the confidence intervals
• Bug solved. The x-coordinates where not calculated correctly. The bug only appeared for measurements along long cables.
• Example notebook of importing a timeseries. For example, importing measurments from an external temperature sensor for calibration.
• Updated documentation

0.5.3 (2018-10-26)

• No changes

0.5.2 (2018-10-26)

• New resample_datastore method (see basic usage notebook)
• New notebook on basic usage of DataStore
• Support for Silixa v4 (Windows xp based system) and Silixa v6 (Windows 7) measurement files
• The representation string now includes the sections
• Reorganized the IO related files
• CI: Add appveyor to continuesly test on Windows platform
• Auto load Silixa files to memory option, if size is small

0.5.1 (2018-10-19)

• Rewritten the routine that reads Silixa measurement files
• dts-calibration is now citable
• Refractored the MC confidence interval routine
• MC confidence interval routine speed up, with full dask support
• Link to mybinder.org to try the example notebooks online
• Added a few missing dependencies
• The routine to read the Silixa files is completely refractored. Faster, smarter. Supports both the path to a directory and a list of file paths.
• Changed imports from dtscalibration to be relative

0.4.0 (2018-09-06)

• Single ended calibration
• Confidence intervals for single ended calibration
• Example notebooks have figures embedded
• Several bugs squashed
• Reorganized DataStore functions

0.2.0 (2018-08-16)

• Double ended calibration
• Confidence intervals for double ended calibration

0.1.0 (2018-08-01)

• First release on PyPI.