Actual changes in echopype #971 #31

leewujung · 2023-03-10T16:20:52Z

No description provided.

…get_angle_complex/power_CW

…BB mode complex samples

…_params

…x_samples

…k80_complex.py

…_* and beamwidth_* in cal params construction

echopype/calibrate/cal_params.py

echopype/calibrate/ek80_complex.py

echopype/consolidate/api.py

echopype/consolidate/split_beam_angle.py

lsetiawan

Looks good overall. Again, minor changes to be made. 👍🏽

Co-authored-by: Don Setiawan <[email protected]>

leewujung · 2023-03-10T19:05:27Z

Thanks @lsetiawan ! I think I've addressed/committed all of your comments.

leewujung · 2023-03-10T19:08:07Z

Oops, some tests have failed. Let me look into that.

for more information, see https://pre-commit.ci

leewujung · 2023-03-10T19:14:22Z

Ok, fixed!

…to `max_mb` (OSOceanAcoustics#962) * Update `offload_to_zarr` to `use_swap` as well as `max_zarr_mb` to `max_mb` * Require raw_file and sonar_model * Fix linting error --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

echopype/calibrate/ek80_complex.py

echopype/consolidate/api.py

echopype/consolidate/split_beam_angle.py

lsetiawan

LGTM! Very minor docstring stuff, which you can do whatever you'd like 😄

* Update CITATION.cff * Add Brandon to software citation in CITATION.cff * docs: add citation section

…SOceanAcoustics#954) * Expand on validate_output_path docstring * Update docstring to vary examples * Remove plural 's' in combined_echodatas.zarr * Update combined_echodatas to combined_echodata * Update temp_output paths * Change run-test to use temp_ouput * Fix circular imports * Remove unused pathlib in core * Update text to `combine_echodata` Co-authored-by: Wu-Jung Lee <[email protected]> * Update api docstring Co-authored-by: Wu-Jung Lee <[email protected]> * Update docs/source/convert.rst Co-authored-by: Wu-Jung Lee <[email protected]> --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Wu-Jung Lee <[email protected]>

Co-authored-by: Don Setiawan <[email protected]>

…into fix-split-beam

Co-authored-by: Don Setiawan <[email protected]>

…into fix-split-beam

Co-authored-by: Don Setiawan <[email protected]>

…into fix-split-beam

* add some initial sketch on the changes * draft up cal_params.sanitize_user_cal_dict and param_dict2da * draft up get_cal_params_EK_new and _test_interp_da to handle all triage and interpolating of cal params * add test_get_interp_da and placeholder for other cal_param tests * add pre-commit fixes * add test for sanitize_user_cal_dict * tidy up comments * revise/rename param2da for organizing individual param, add test * add param2da use to sanitize_user_cal_dict, add corresponding tests * fix logic in get_cal_params_EK_new and clearly lay out alternative data type in _get_interp_da * revise default cal/env_params handling in CalibrateBase.__init__, still need to test these * change CalibrateEK80._cal_complex_samples to use params from self.cal_params; still need to do the same for CalibrateEK60 and CalibrateAZFP * add tests for only subset of channel needs to be interpolated * fix a few more things in _get_intep_da for EK80 CW mode data; note down new tests needed * minor tweak to use get_cal_params_EK_new for calibrating EK60 * remove the old get_cal_params_EK * completely remove old private functions in CalibrateEK80, run pre-commit * revise get_cal_params_AZFP to use sanitize_user_cal_dict * squeeze and drop beam dimension earlier in CalibrateAZFP._cal_power_samples * rename get_cal_params_EK_new to get_cal_params_EK * add test_get_cal_params_AZFP * add da name to individual param data in sanitize_user_cal_dict * allow coord combination (cal_channel_id, cal_frequency) in sanitize_user_cal_dict * add interp for user-input freq-dependent param values, add tests * add test_get_cal_params_EK60, change sanitize_user_cal_dict handling of EK types * move sequence of functions in cal_params.py * add test_get_vend_cal_params_power * add cal param intake integration test for EK80 BB complex * add cal param intake integration test for EK80 CW complex * add test_cal_params_intake_EK60 * fix bug re looping through params in PARAM_BEAM_NAME_MAP * add test_cal_params_intake_AZFP * fix bug in AZFP env param intake * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * remove else in param2da for readability * improve sonar_type typing * improve param2da p_val docstring * improve sanitize_user_cal_dict docstring * remove redundant else in sanitize_user_cal_dict * improve _get_interp_da docstring * change .data to .values * use self.waveform_mode in CalibrateEK60.__init__ * fix get_cal_params_AZFP docstring * improve get_cal_params_EK docstring * change default_dict to default_params, add Literal * use f-strings instead of % syntax in get_vend_filter_EK80 * add sonar_type as attribute for Calibrate* classes --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Don Setiawan <[email protected]>

…oustics#968) * reorder echo_range dimensions at azfp cal output * add test_range_dimensions for AZFP * add test_range_dimensions for EK60 * add test_range_dimensions for EK80 BB complex and CW complex * add test_range_dimensions for EK80 CW power * Define common dimension order global variable. Fix spelling error in test_range_integration.py --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Emilio Mayorga <[email protected]>

…e, keep beam dim removal in get_angle_power_sample

leewujung added 13 commits March 9, 2023 10:35

identify required changes, simplify docstring, move order of functions

08ee1e5

rename test_consolidate to test_consolidate_integration

a5a0404

fix bug in get_angle_complex_CW, add angle_params from source_Sv for …

a6dc4a1

…get_angle_complex/power_CW

rename and use the same routine get_angle_complex_samples for CW and …

b00e69d

…BB mode complex samples

add angle_sensitivity_* to CAL_PARAMS, fix bug in assembling in angle…

23b9c81

…_params

fix bug in passing in angle_params for all beam_type identical case

c82c5e8

fix bug re ping_time and range_sample dimensions in _get_angle_comple…

9b1e3fb

…x_samples

refactor get_filter_coeff() and get_vend_filter_EK80(), now both in e…

6061e8f

…k80_complex.py

change compress_pulse to output xr.DataArray instead of xr.Dataset

e49d984

add BB freq_center re frequency_nominal scaling for angle_sensitivity…

e990ccf

…_* and beamwidth_* in cal params construction

add pulse compression option to get_angle_complex_samples

df61885

add test for splitbeam processing for BB with pc

e2ebe19

run pre-commit

8fa4708

leewujung mentioned this pull request Mar 10, 2023

Refactor split-beam processing and add BB with pc option OSOceanAcoustics/echopype#971

Merged

remove TODO in docstring

9de0480

lsetiawan reviewed Mar 10, 2023

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leewujung and others added 2 commits March 10, 2023 10:00

change BB_fac to BB_factor

f14e0fe

improve get_vend_filter_EK80 docstring

963185a

Co-authored-by: Don Setiawan <[email protected]>

remove outdated NotImplementedError in get_angle_power_samples

7809ebc

leewujung and others added 2 commits March 10, 2023 11:09

add Literal to ek80_complex.py import

a8706ff

[pre-commit.ci] auto fixes from pre-commit.com hooks

66b1ac9

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lsetiawan approved these changes Mar 10, 2023

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emiliom and others added 17 commits March 11, 2023 08:27

Update CITATION.cff (OSOceanAcoustics#927)

6f88159

* Update CITATION.cff * Add Brandon to software citation in CITATION.cff * docs: add citation section

add TODO

8a923da

improve get_filter_coeff docstring

8ebed6d

Co-authored-by: Don Setiawan <[email protected]>

Merge branch 'fix-split-beam' of https://github.com/leewujung/echopype …

e1e353a

…into fix-split-beam

fix typo

97d5c7b

Co-authored-by: Don Setiawan <[email protected]>

improve get_angle_power_samples docstring

a635d28

Co-authored-by: Don Setiawan <[email protected]>

Merge branch 'fix-split-beam' of https://github.com/leewujung/echopype …

a899131

…into fix-split-beam

improve get_angle_complex_samples docstring

f9b1fad

Co-authored-by: Don Setiawan <[email protected]>

Merge branch 'fix-split-beam' of https://github.com/leewujung/echopype …

5cac799

…into fix-split-beam

add return to compress_pulse docstring

0a4e6be

Merge branch 'dev' into fix-split-beam

8557e7f

break long lines

235bc4c

remove beam dim checking for theta and phi in get_angle_complex_sampl…

00e35ab

…e, keep beam dim removal in get_angle_power_sample

add test placeholder for EK80 CW power angle

cfa31a5

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Actual changes in echopype #971 #31

Actual changes in echopype #971 #31

leewujung commented Mar 10, 2023

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leewujung commented Mar 10, 2023

leewujung commented Mar 10, 2023

leewujung commented Mar 10, 2023

lsetiawan left a comment

Actual changes in echopype #971 #31

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Actual changes in echopype #971 #31

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