Bathymetry generator

.gitignore

@@ -0,0 +1,152 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintainted in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/

bathymetry/.gitignore

@@ -0,0 +1,3 @@
+/1_scad
+/2_stl
+/3_pd

bathymetry/0_data/.ipynb_checkpoints/base-checkpoint.scad

@@ -0,0 +1,6 @@
+translate([150, 0, 0])
+mirror([1, 0, 0])
+rotate([90, 0, 0])
+translate([0, 0, -10])
+linear_extrude(20)
+polygon({});

bathymetry/0_data/artha_coords.csv

@@ -0,0 +1,2 @@
+lat,lon
+43.398489,-1.672400

bathymetry/0_data/base.scad

@@ -0,0 +1,4 @@
+rotate([90, 0, 0])
+translate([0, 0, -10])
+linear_extrude(20)
+polygon({});

bathymetry/0_data/bloc0.csv

@@ -0,0 +1,8 @@
+x,z
+-4,-0.5
+11.7,-0.5
+11.7,2.5
+9.25,8.2
+0,8.2
+0,2.5
+-4,2.5

bathymetry/0_data/bloc1.csv

@@ -0,0 +1,5 @@
+x,z
+9.25,-0.5
+9.25,4.75
+16.70,4.75
+16.6,-0.5

bathymetry/0_data/points.csv

@@ -0,0 +1,3 @@
+lat,lon
+43.398133,-1.672285
+43.400464,-1.67302

bathymetry/config.ini

@@ -0,0 +1,34 @@
+[main]
+logging = INFO
+plot = False
+N = 1024
+L0 = 120
+L1 = 30
+dir = 350
+bathy_max=-15
+
+[data]
+root = 0_data
+bathy = MNT_COTIER_BAIE_SJL_TANDEM_20m_WGS84_NM_ZNEG.glz
+artha = artha_coords.csv
+base_scad = base.scad
+points = points.csv
+blocs = bloc0.csv,bloc1.csv
+
+[scad]
+root = 1_scad
+bathy = bathy.scad
+bloc0 = bloc0.scad
+bloc1 = bloc1.scad
+rubble = rub.scad
+
+[stl]
+root = 2_stl
+bathy = bathy.stl
+bloc0 = bloc0.stl
+bloc1 = bloc1.stl
+rubble = rub.stl
+
+[pandas]
+root = 3_pd
+file = data.hdf

bathymetry/generate/__main__.py

@@ -0,0 +1,216 @@
+from pprint import pp
+import logging
+import configparser
+import pathlib
+import subprocess
+from time import time
+
+import pandas as pd
+import numpy as np
+from scipy.interpolate import griddata
+
+_t0 = time()
+config = configparser.ConfigParser()
+config.read('config.ini')
+
+if config['main']['plot'] == 'True': import matplotlib.pyplot as plt
+
+logging.basicConfig(level=config['main']['logging'])
+log = logging.getLogger('bathymetry')
+
+
+# --- Initialization
+log.info('Initialization')
+folders = {
+    'data': pathlib.Path(config['data']['root']),
+    'scad': pathlib.Path(config['scad']['root']),
+    'stl': pathlib.Path(config['stl']['root']),
+    'pandas': pathlib.Path(config['pandas']['root']),
+}
+for path in folders.values():
+    path.mkdir(exist_ok=True)
+
+bathy = pd.read_csv(
+    folders['data'].joinpath(config['data']['bathy']),
+    sep=' ',
+    names=('lon', 'lat', 'z'),
+)
+artha = pd.read_csv(
+    folders['data'].joinpath(config['data']['artha']),
+)
+
+earth_radius = 6371e3
+L0 = float(config['main']['L0'])
+L1 = float(config['main']['L1'])
+direction = float(config['main']['dir'])
+
+artha = artha.append(pd.DataFrame([
+    {
+        'lat': artha.lat.at[0] \
+            + np.cos(direction*np.pi/180) * L0/earth_radius * 180/np.pi,
+        'lon': artha.lon.at[0] \
+            + np.sin(direction*np.pi/180) * L0/earth_radius * 180/np.pi \
+                / np.cos(artha.lat.at[0] * np.pi/180),
+    },
+    {
+        'lat': artha.lat.at[0] \
+            - np.cos(direction*np.pi/180) * L1/earth_radius * 180/np.pi,
+        'lon': artha.lon.at[0] \
+            - np.sin(direction*np.pi/180) * L1/earth_radius * 180/np.pi \
+                / np.cos(artha.lat.at[0] * np.pi/180),
+    },
+], index=[-1, 1]))
+
+# --- Interpolation
+log.info('Interpolating data')
+N = int(config['main']['N'])
+line = pd.DataFrame({
+    'x': np.linspace(0, L0+L1, N),
+    'lat': np.linspace(artha.lat.at[-1], artha.lat.at[1], N),
+    'lon': np.linspace(artha.lon.at[-1], artha.lon.at[1], N),
+})
+line.set_index('x', inplace=True)
+
+line['z'] = griddata(
+    bathy[['lon','lat']],
+    bathy.z,
+    line[['lon','lat']],
+    method='linear',
+)
+
+# --- Adding blocs
+log.info('Adding blocs')
+b = config['data']['blocs'].split(',')
+blocs = pd.Series([
+    pd.read_csv(
+        folders['data'].joinpath(path),
+        index_col='x',
+    ) for path in b
+])
+for bloc in blocs:
+    bloc.index = L0 - bloc.index
+
+
+#line.z = all_blocs.z.fillna(line.z)
+
+lim = float(config['main']['bathy_max'])
+bathy_line = line.z.clip(upper=lim)
+rubble_line = line.z[line.z > lim]
+
+data_dict = {}
+for i in range(blocs.size):
+    data_dict[f'bloc{i}'] = blocs.iat[i].reset_index().values
+for name, data in (
+        ('bathy', bathy_line),
+        ('rubble', rubble_line),
+    ):
+    data_dict[name] = np.concatenate((
+        data.reset_index().values,
+        [[data.index.max(), data.min()],
+        [data.index.min(),data.min()]]
+    ))
+
+# --- Generating SCAD
+
+with open(folders['data'].joinpath(config['data']['base_scad'])) as bsf:
+    base_scad = bsf.read()
+for (name, data) in data_dict.items():
+    log.info(f'Generating {name}')
+    log.info('\tGenerating SCAD file')
+    scad_file = folders['scad'].joinpath(config['scad'][name])
+    with open(scad_file, 'w') as osf:
+        osf.write(base_scad.format(
+            np.array2string(
+                data,
+                threshold=np.inf,
+                separator=','
+            )
+        ))
+    log.info('\tGenerating STL file')
+    subprocess.run(('openscad', scad_file, '-o',
+        folders['stl'].joinpath(config['stl'][name])),
+        check=True,
+        capture_output=True)
+
+
+# --- Saving pandas
+log.info('Saving Pandas')
+
+with pd.HDFStore(
+        folders['pandas'].joinpath(config['pandas']['file']),
+        mode='w',
+        complib='blosc',
+    ) as hdf:
+    for name, data in (
+            ('bathy', bathy_line),
+            ('rubble', rubble_line),
+        ):
+        hdf.put(name, data)
+    for i, bloc in blocs.items():
+        hdf.put(f'bloc{i}', bloc)
+
+
+_t1 = time()
+log.info(f'Program ended successfully after {_t1-_t0:.2f}s')
+
+# --- Plotting
+
+if config['main']['plot'] == 'True':
+    log.info('Plotting data')
+    flt = (
+        ((bathy.lon-artha.lon.at[0]).abs() < 0.002) & \
+        ((bathy.lat-artha.lat.at[0]).abs() < 0.002)
+    )
+    
+    fig, ax = plt.subplots()
+    ax.scatter(
+        bathy.lon[flt],
+        bathy.lat[flt],
+        c=bathy.z[flt],
+        marker='1',
+        lw=1,
+    )
+    ax.scatter(
+        artha.lon,
+        artha.lat,
+        color='k',
+        marker='+',
+        lw=1,
+    )
+    ax.set(
+        aspect='equal',
+    )
+    
+    fig, ax = plt.subplots()
+    ax.plot(
+        bathy_line.index,
+        bathy_line,
+        color='k',
+        lw=1,
+        zorder=10,
+        label='Bathymetry',
+    )
+    ax.plot(
+        rubble_line.index,
+        rubble_line,
+        color='r',
+        lw=1,
+        zorder=11,
+        label='Rubble',
+    )
+    blocs.apply(lambda bloc: ax.fill_between(
+        bloc.index,
+        bloc.z,
+        color='k',
+        zorder=9,
+        alpha=.1,
+        label='Caisson',
+    ))
+    ax.set(
+        aspect='equal',
+        xlim=(bathy_line.index.min(), bathy_line.index.max()),
+    )
+    ax.grid()
+    fig.legend()
+    
+    plt.show(block=True)