Patches #321
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Patches #321
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- typo fix - add comment for where segment weights maybe added
- Update process_mth5 so check_if_fc_levels_already_exist is done before initializing mth5s - factor logic in TFKernel so that the actual check in the mth5 object is a standalone function - address old Note#3 in check_if_fc_levels_already_exist (ambiguity eliminated)
- test was packing data but not metadata - now metadata are being stored with the FCs - replace variable decimation_and_stft_config with fc_config
- add a property to TFK returns a boolean if all_fcs_already_exist - check all_fcs_already_exist at start of process_mth5 - if all_fcs_already_exist, do not build fc layers - move fc_level checking into TFK, out of process_mth5 - remove mode kwarg from tfk.initialize_mth5s(), get this info from tfk.get_mth5_file_open_mode() - kernel_dataset initializes "fc" column to None, rather than False - boolean state is set during check_if_fcs_already_exist
- kernel_dataset now has fc column of df initialized to None, rather than False - This means that asserting equality between dataframes must handle fc column carefully - Updated the test to respect this
- noted that the plotter for frq response not working in numpy 1.24, but OK in 1.25 - seems related to this: matplotlib/matplotlib#24106
- tidied up workflow in process_transfer_functions - created placeholders for segment weights - factored out some methods applied to X, Y, RR for readability
- add logger message as well
Add some placeholders for coherence sorting - frequency_band_helpers.py - add some placeholder methods - especially Spectrogram class -- a candidate to replace stft_obj in main flow - kernel_dataset.py: - Factor update_survey_metadata method into its own method for better readability - coherence_weights.py - experimental code for Jackkknife coherence weights - xarray_helpers.py - Deprecate unusued cast_3d_stft_to_2d_observations method from xarray_helpers - move notes from this method into stack_fcs()
- added a note on issue #119 about how jackknife may be better applied after simple and multiple coherences - misc notes/doc in coherence_weights and factoring - adjust_band_for_coherence_sorting added to frequency_band_helpers
- make logic depend on mth5 file version - re-add jupyter notebooks to tests to see if this has any effect there
- If fc_group already exists, get it instead of add it - If fc_decimation already exists, get it instead of add it - this reduces logging messages, but shouldn't change the behaviour
- have been experimenting with a few approaches to coherence sorting - have decided on a method using Spectrogram() class _crosspower method - most of what is in coherence sorting now is just messy, half tested, experimental muck - but it has a form of what I would like later, and there may be a few nuggets - so, against my better judgement I am committing it and tagging associated with issue #119
- rename df to less ambiguous frequency_increment - add solve_single_time_window to helper functions - add a test for solve_single_time_window - factor z-time-series calculation out of coherence into spectral features
- add temporary handling for issue #319 - add simple_solve and direct_solve tf helpers - add tests for helpersy
- some nomenclature tidying and add a bit more test coverage (fc_decimations=None case)
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A lot of housekeeping, some development on a jupyter notebook tour of EarthScope, and groundwork laid for coherence calculation via cross power feature.
This, plus a nearly ready manuscript for submission to JOSS (from joss branch) and much housekeeping of mth5 and mt_metadata say its time to merge into main and bump patch version.