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Merge pull request #41 from zxcvbnmike15/feature/area_correction
Feature/area correction
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| import logging | ||
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| from pathlib import Path | ||
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| from hyo2.openbst.lib.openbst import OpenBST | ||
| from hyo2.abc.lib.testing_paths import TestingPaths | ||
| from hyo2.openbst.lib.processing.process_methods.area_correction import AreaCorrectionEnum | ||
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| logger = logging.getLogger(__name__) | ||
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| testing = TestingPaths(root_folder=Path(__file__).parents[3].resolve()) | ||
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| bst = OpenBST(prj_name="test_area", force_new=True).prj | ||
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| raw_path = testing.download_data_folder().joinpath('raw_reson', '20190730_144835.s7k') | ||
| bst.add_raw(raw_path) | ||
| bst.check_health() | ||
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| # Test 1: Check we meet requirements = False | ||
| bst.area_correction() | ||
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| # Test 2: Method: Flat Seafloor assumption | ||
| bst.raw_decode() | ||
| bst.interpolation() | ||
| bst.raytrace() | ||
| bst.area_correction() |
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200 changes: 200 additions & 0 deletions
200
hyo2/openbst/lib/processing/process_methods/area_correction.py
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,200 @@ | ||
| import logging | ||
| import numpy as np | ||
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| from enum import Enum | ||
| from netCDF4 import Dataset, Group | ||
| from typing import Optional | ||
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| from hyo2.openbst.lib.nc_helper import NetCDFHelper | ||
| from hyo2.openbst.lib.processing.process_methods.raytracing import RayTraceParams | ||
| logger = logging.getLogger(__name__) | ||
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| # ## Area correction enum and dictionaries ## | ||
| class AreaCorrectionEnum(Enum): | ||
| flat_seafloor = 0 | ||
| local_slope = 1 | ||
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| area_correction_title = { | ||
| AreaCorrectionEnum.flat_seafloor: "Corrected Backscatter - Area Correction Using Flat Sealoor Assumption", | ||
| AreaCorrectionEnum.local_slope: "Corrected Backscatter - Area Correction Using Local Slope" | ||
| } | ||
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| # ## Area Correction Parameters Object ## | ||
| class AreaCorrectionParameters: | ||
| process_name = "area_correction" | ||
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| def __init__(self): | ||
| self.method_type = AreaCorrectionEnum.flat_seafloor | ||
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| def nc_write_parameters(self, grp_process: Group): | ||
| try: | ||
| grp_process.title = area_correction_title[self.method_type] | ||
| grp_process.method_type = self.method_type.name | ||
| return True | ||
| except TypeError: | ||
| return False | ||
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| def process_identifiers(self) -> list: | ||
| process_string = self.process_name | ||
| parameter_string = str() | ||
| for key, value in self.__dict__.items(): | ||
| parameter_string += key + str(value) | ||
| parameter_hash = NetCDFHelper.hash_string(input_str=parameter_string) | ||
| process_ids = [process_string, parameter_hash] | ||
| return process_ids | ||
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| # ## Area Compensation Class and Methods ## | ||
| class AreaCompensation: | ||
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| def __init__(self): | ||
| pass | ||
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| @classmethod | ||
| def area_correction(cls, ds_process: Dataset, ds_raw: Dataset, | ||
| parent: str, parameters: AreaCorrectionParameters): | ||
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| p_method_type = parameters.method_type | ||
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| grp_beam_geo = ds_raw.groups['beam_geometry'] | ||
| var_rx_bw_across = grp_beam_geo.variables['across_beamwidth'] | ||
| data_rx_bw_across = var_rx_bw_across[:] | ||
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| grp_runtime = ds_raw.groups['runtime_settings'] | ||
| var_tx_bw_along = grp_runtime.variables['tx_along_beam_width'] | ||
| data_tx_be_along = var_tx_bw_along[:] | ||
| var_sound_speed = grp_runtime.variables['sound_velocity'] | ||
| data_sound_speed = var_sound_speed[:] | ||
| var_pulse_length = grp_runtime.variables['tx_pulse_width'] | ||
| data_pulse_length = var_pulse_length[:] | ||
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| grp_raw = ds_raw.groups['raw_bathymetry_data'] | ||
| var_rx_angle = grp_raw.variables['rx_angle'] | ||
| data_rx_angle = var_rx_angle[:] | ||
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| data_backscatter = cls.find_bs_data(ds_process=ds_process, parent=parent) | ||
| data_raypath = cls.find_ray_data(ds_process=ds_process, parent=parent) | ||
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| if data_backscatter is None: | ||
| logger.error("Step not computed: Backscatter data not found") | ||
| return False | ||
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| if data_raypath is None: | ||
| logger.error("Step not computed: Raypath data not found") | ||
| return False | ||
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| if p_method_type is AreaCorrectionEnum.flat_seafloor: | ||
| data_out = cls.flat_seafloor(backscatter=data_backscatter, | ||
| rx_angle=data_rx_angle, raypath=data_raypath, | ||
| rx_beamwidth_across=data_rx_bw_across, | ||
| tx_beamwidth_along=data_tx_be_along[:, np.newaxis], | ||
| pulse_len=data_pulse_length[:, np.newaxis], | ||
| sound_speed=data_sound_speed[:, np.newaxis]) | ||
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| elif p_method_type is AreaCorrectionEnum.local_slope: | ||
| data_out = None | ||
| pass | ||
| else: | ||
| raise TypeError("Urecognized Method Type: %s" % p_method_type) | ||
| return data_out | ||
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| @classmethod | ||
| def write_data_to_nc(cls, data_dict: dict, grp_process: Group): | ||
| try: | ||
| grp_process.createDimension(dimname='ping', size=None) | ||
| grp_process.createDimension(dimname='beam', size=None) | ||
| grp_process.createDimension(dimname='angle', size=None) | ||
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| for data_name, data in data_dict.items(): | ||
| if data_name == 'backscatter_data': | ||
| var_bs_data = grp_process.createVariable(varname='backscatter_data', | ||
| datatype='f8', | ||
| dimensions=('ping', 'beam')) | ||
| var_bs_data[:] = data | ||
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| elif data_name == 'area_correction': | ||
| var_area_corr = grp_process.createVariable(varname='area_correction', | ||
| datatype='f8', | ||
| dimensions=('ping', 'beam')) | ||
| var_area_corr[:] = data | ||
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| elif data_name == 'area_corr_beam_limited': | ||
| var_area_bl = grp_process.createVariable(varname='beam_limited_area_correction', | ||
| datatype='f8', | ||
| dimensions=('ping', 'beam')) | ||
| var_area_bl[:] = data | ||
| elif data_name == 'area_corr_pulse_limited': | ||
| var_area_pl = grp_process.createVariable(varname='pulse_limited_area_correction', | ||
| datatype='f8', | ||
| dimensions=('ping', 'beam')) | ||
| var_area_pl[:] = data | ||
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| return True | ||
| except RuntimeError: | ||
| return False | ||
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| @classmethod | ||
| def flat_seafloor(cls, | ||
| backscatter: np.ma.MaskedArray, rx_angle: np.ma.MaskedArray, raypath: np.ma.MaskedArray, | ||
| rx_beamwidth_across: np.ndarray, tx_beamwidth_along: np.ndarray, | ||
| pulse_len: np.ndarray, sound_speed: np.ndarray): | ||
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| rx_beamwidth_across = np.deg2rad(rx_beamwidth_across) | ||
| tx_beamwidth_along = np.deg2rad(tx_beamwidth_along) | ||
| rx_angle = np.deg2rad(rx_angle) | ||
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| area_beam_lim = rx_beamwidth_across * tx_beamwidth_along * raypath ** 2 | ||
| area_pulse_lim = ((sound_speed * pulse_len) / (2 * np.sin(np.abs(rx_angle)))) * (tx_beamwidth_along * raypath) | ||
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| area_correction = 10 * np.ma.log10(np.minimum(area_beam_lim, area_pulse_lim)) | ||
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| bs_corrected = backscatter - area_correction | ||
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| data_out = { | ||
| 'backscatter_data': bs_corrected, | ||
| 'area_correction': area_correction, | ||
| 'area_corr_beam_limited': 10 * np.ma.log10(area_beam_lim), | ||
| 'area_corr_pulse_limited': 10 * np.ma.log10(area_pulse_lim) | ||
| } | ||
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| return data_out | ||
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| @classmethod | ||
| def local_slope(cls): | ||
| pass | ||
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| @classmethod | ||
| def find_bs_data(cls, ds_process: Dataset, parent: str): | ||
| grp_parent = ds_process.groups[parent] | ||
| try: | ||
| var_backscatter = grp_parent.variables['backscatter_data'] | ||
| data_backscatter = var_backscatter[:] | ||
| return data_backscatter | ||
| except KeyError: | ||
| parent = grp_parent.parent_process | ||
| if parent == 'ROOT': | ||
| return None | ||
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| data_backscatter = cls.find_bs_data(ds_process=ds_process, parent=parent) | ||
| return data_backscatter | ||
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| @classmethod | ||
| def find_ray_data(cls, ds_process: Dataset, parent: str): | ||
| grp_parent = ds_process.groups[parent] | ||
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| if RayTraceParams.process_name in parent: | ||
| var_ray_path = grp_parent.variables['path_length'] | ||
| data_ray_path = var_ray_path[:] | ||
| return data_ray_path | ||
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| elif grp_parent.parent_process == 'ROOT': | ||
| return None | ||
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| else: | ||
| parent = grp_parent.parent_process | ||
| data_ray_path = cls.find_ray_data(ds_process=ds_process, parent=parent) | ||
| return data_ray_path | ||
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