Refactored core

.github/workflows/unit-build.yml

@@ -2,9 +2,9 @@ name: unit tests
 
 on:
   push:
-    branches: [ main ]
+    branches: [ main, refactoring ]
   pull_request:
-    branches: [ main ]
+    branches: [ main, refactoring ]
 
 jobs:
   build:
@@ -13,7 +13,7 @@ jobs:
     timeout-minutes: 5
     strategy:
       matrix:
-        python-version: [ 3.8, 3.9]
+        python-version: [ "3.9", "3.10" ]
 
     steps:
     - uses: actions/checkout@v2
@@ -27,6 +27,9 @@ jobs:
         pip install pytest
         pip install -r requirements.txt
         pip install pytest-cov
+    - name: Run flake8 checks
+      run: |
+        flake8 gefest test --count --statistics
     - name: Test with pytest
       run: |
         pytest --cov=GEFEST -s test/

cases/breakwaters/main_arctic.py

@@ -0,0 +1,201 @@
+import pickle
+from functools import partial
+from gefest.core.algs.postproc.resolve_errors import Rules, apply_postprocess
+import numpy as np
+from hyperopt import hp
+from gefest.core.opt.operators.selections import tournament_selection,roulette_selection
+from gefest.core.algs.postproc.resolve_errors import Rules, postprocess
+from gefest.core.configs.optimization_params import OptimizationParams
+from gefest.core.configs.tuner_params import TunerParams
+from gefest.core.geometry import Structure
+from gefest.core.geometry.domain import Domain
+from gefest.core.geometry.geometry_2d import Geometry2D
+from gefest.core.geometry.utils import get_random_structure
+from gefest.core.opt.adapters.structure import StructureAdapter
+from gefest.core.opt.operators.crossovers import (
+    panmixis,
+    polygon_level_crossover,
+    structure_level_crossover,
+)
+from gefest.core.opt.operators.mutations import (
+    add_point,
+    add_poly,
+    drop_point,
+    drop_poly,
+    pos_change_point_mutation,
+    resize_poly,
+    rotate_poly,
+)
+import json
+from gefest.core.opt.tuning.tuner import GolemTuner
+from gefest.core.structure.prohibited import create_prohibited
+from gefest.core.viz.struct_vizualizer import GIFMaker
+from gefest.tools.estimators.simulators.sound_wave.sound_interface import (
+    SoundSimulator,
+    generate_map,
+)
+from gefest.tools.fitness import Fitness
+from gefest.tools.optimizers.GA.base_GA import BaseGA
+from pathlib import Path
+from gefest.tools.estimators.simulators.swan.swan_interface import Swan
+from shapely.geometry import shape
+# pre domain params
+root_path = Path(__file__).parent.parent.parent
+with open(f'{root_path}/cases/breakwaters/newdata/result_PwiOsA2HE2igZUel.geojson', 'r') as file:
+    res_list = json.load(file)
+with open(f'{root_path}/cases/breakwaters/newdata/border_PwiOsA2HE2igZUel.geojson', 'r') as file:
+    border_dict = json.load(file)
+border = shape(border_dict['features'][0]['geometry'])
+water = [i for i in res_list['features'] if i['properties']['type'] =='water']
+water_coord =[p['geometry']['coordinates'] for p in water]
+cargo_piers = [i for i in res_list['features'] if i['properties']['type'] =='cargo_pier']
+passenger_pier = [i for i in res_list['features'] if i['properties']['type'] =='passenger_pier']
+piers = [i for i in res_list['features'] if (i['properties']['type']=='passenger_pier') or (i['properties']['type'] =='cargo_pier')]
+piers_coords = [x[0] for x in [i['geometry']['coordinates'] for i in piers]]
+piers_line = [max(p,key=lambda i: i[1]) for p in piers_coords]
+unique_types = np.unique([i['properties']['type'] for i in res_list['features']])
+allow_water = [i for i in water_coord[0][0] if (i[0]>74.8) and (i[1]<67.942) and (i[1]>67.915)]
+###########
+allow_area = [[74.80,67.92],[74.80,67.94]]+allow_water +[[74.80,67.92]]
+grid_resolution_x = 17  # Number of points on x-axis
+grid_resolution_y = 31  # Number of points on y-axis
+coord_Y = np.linspace(min([p[1] for p in allow_area])*500, max([p[1] for p in allow_area])*500, grid_resolution_y + 1)  # X coordinate for spatial grid
+coord_X = np.linspace(min([p[0] for p in allow_area])*500, max([p[0] for p in allow_area])*500, grid_resolution_x + 1)
+grid = [grid_resolution_x, grid_resolution_y]  # points grid
+fixed_area = None
+targets = [[14,10],[16,10],[18,10]]
+
+
+def load_file_from_path(path: str):
+    with open(path, 'rb') as f:
+        file = pickle.load(f)
+        f.close()
+    return file
+
+
+if __name__ == '__main__':
+    # class SoundSimulator_(SoundSimulator):
+    #     def __init__(self, domain, obstacle_map=None):
+    #         super().__init__(domain, obstacle_map=None)
+    #         self.duration = 200
+    #         self.pressure_hist = np.zeros((self.duration, self.size_y, self.size_x))
+    #         if (
+    #                 obstacle_map is not None
+    #                 and (obstacle_map.shape[0], obstacle_map.shape[1]) == self.map_size
+    #         ):
+    #             print("** Map Accepted **")
+    #             self.obstacle_map = obstacle_map
+    #         elif obstacle_map is not None and obstacle_map.shape != self.map_size:
+    #             print("** Map size denied **")
+    #             self.obstacle_map = np.zeros((self.size_y, self.size_x))
+    #         else:
+    #             self.obstacle_map = np.zeros((self.size_y, self.size_x))
+
+    #  in the future all model can be loaded from configs
+
+    #  domain configuration
+    geometry = Geometry2D(is_closed=False, is_convex=True)
+    prohibited = create_prohibited(1, [], [], fixed_area=fixed_area)
+    domain = Domain(
+        allowed_area=[
+            (min(coord_X), min(coord_Y)),
+            (min(coord_X), max(coord_Y)),
+            (max(coord_X), max(coord_Y)),
+            (max(coord_X), min(coord_Y)),
+            (min(coord_X), min(coord_Y)),
+        ],
+        geometry=geometry,
+        max_poly_num=1,
+        min_poly_num=1,
+        max_points_num=10,
+        min_points_num=4,
+        prohibited_area=prohibited,
+    )
+
+    #  tuner config
+    tp = TunerParams(
+        tuner_type='sequential',
+        n_steps_tune=25,
+        sampling_variance=1,
+        hyperopt_dist=hp.uniform,
+    )
+    path_=f"{root_path}/cases/breakwaters/ob2/"
+    #Estimator
+    swan_estimator = Swan(
+        targets=targets,
+        domain=domain,
+        grid=grid,
+        path=path_,
+        hs_file_path='results/HSig_ob_example.dat'
+    )
+    #  fitness function
+    class SoundFieldFitness(Fitness):
+        def __init__(self, domain, estimator):
+            super().__init__(domain)
+            self.estimator=estimator
+        def fitness(self, ind: Structure):
+            fitness = self.estimator(ind)
+            return fitness
+
+    #  fitness estimator
+    estimator = SoundFieldFitness(
+        domain,
+        swan_estimator
+    )
+
+    #  optimization params config
+    opt_params = OptimizationParams(
+        crossovers=[
+            polygon_level_crossover,
+            structure_level_crossover,
+        ],
+        crossover_prob=0.3,
+        crossover_each_prob=[0.0, 1.0],
+        mutations=[
+            rotate_poly,
+            resize_poly,
+            add_point,
+            drop_point,
+            add_poly,
+            drop_poly,
+            pos_change_point_mutation,
+        ],
+        mutation_each_prob=[0.125, 0.125, 0.25, 0.25, 0.00, 0.00, 0.25],
+        pair_selector=panmixis,
+        postprocess_attempts=10,
+        domain=domain,
+        postprocessor=apply_postprocess,
+        estimator=estimator,
+        postprocess_rules=[
+            Rules.not_out_of_bounds.value,
+            Rules.not_closed_polygon.value,
+            Rules.not_self_intersects.value,
+            Rules.not_too_close_polygons.value,
+            # Rules.not_overlaps_prohibited.value,
+            Rules.not_too_close_points.value,
+        ],
+        extra=2,
+        n_jobs=0,
+        golem_adapter=StructureAdapter,
+        tuner_cfg=tp,
+        n_steps=5,
+        pop_size=6,
+        selector=roulette_selection
+    )
+
+    optimizer = BaseGA(opt_params)
+    optimized_pop = optimizer.optimize()
+
+    #  make mp4 of optimized pop here if need
+
+    # tuner = GolemTuner(opt_params)
+    # n_best_for_tune = 1
+    # tuned_individuals = tuner.tune(optimized_pop[0:n_best_for_tune])
+
+    #  make mp4 of tuned pop here if need
+
+    #  code to create mp4
+    ###
+    #  gm = GIFMaker(domain=domain)  # mp4 maker actually
+    #  gm.create_frame(_structure_, {'Optimized': _structure_.fitness}) #  make frames for each stucture you want
+    #  gm.make_gif('tuning', 500, ) #  save file

cases/breakwaters/ob2/INPUT

@@ -0,0 +1,54 @@
+$***********MODEL INPUT*********************************
+SET NAUTical
+MODE NONSTationary TWODimensional
+COORDinates spherical
+
+CGRID REGular xpc=74.70350703505787  ypc=67.88206697110601 alpc=0. &
+                  xlenc=0.128969 ylenc=0.086128 mxc=17 myc=31 &
+                  CIRCLE mdc=36 flow=0.05 fhigh=1. msc=25
+
+INPgrid BOTtom REGular xpinp=74.70350703505787  ypinp=67.88206697110601 & 
+                alpinp=0. mxinp=17 myinp=31 &
+                dxinp=0.0071370458 dyinp=0.0026897599 EXCeption -9
+READinp BOTtom fac=1 'data\bathy.bot' idla=1 0 FREE
+
+INPgrid WIND  REGular xpinp=74.70350703505787  ypinp=67.88206697110601 & 
+                alpinp=0. mxinp=17 myinp=31 &
+                dxinp=0.0071370458 dyinp=0.0026897599  &
+NONSTATIONARY 20180101.000000 6 HR 20180103.230000
+READinp WIND fac=1.21 SERIES 'data\wind_inventory.txt' 1 0 1 0 FREE
+
+BOUnd SHAPespec JONswap 3.3 PEAK DSPR DEGRees
+
+
+
+OBSTACLE TRANSM 0. REFL 0. LINE 74.810470, 67.930902, 74.806538, 67.930025, 74.803719, 67.928509, 74.809836, 67.923163, 74.810798, 67.922973, 74.811649, 67.926213, 74.811374, 67.929569
+$optline
+
+
+GEN3 ST6 6.5E-6 8.5E-5 4.0 4.0 UP HWANG VECTAU U10PROXY 35.0 AGROW 
+BREAKING
+FRiction JONswap CONstant 0.067
+TRIAD
+DIFFRACtion
+ PROP BSBT
+QUANTity  Per short='Tm-1,0' power=0.
+
+
+
+OUTPUT OPTIONS '%' TABLE 16 BLOCK 6 18
+
+BLOCK 'COMPGRID' NOHEAD 'results\HSig_ob_example.dat' LAYOUT 1 HSig OUT 20180102.000000 1. HR
+BLOCK 'COMPGRID' NOHEAD 'results\PDIR_ob_example.dat' LAYOUT 1 PDIR OUT 20180102.000000 1. HR
+BLOCK 'COMPGRID' NOHEAD 'results\RTP_ob_example.dat' LAYOUT 1 RTP OUT 20180102.000000 1. HR
+
+
+
+
+
+
+
+
+COMPUTE NONSTat 20180101.000000 10 MIN 20180103.230000
+
+STOP