From 56bc492c980a9b3a6044bfb0cf209ad3338a6e6f Mon Sep 17 00:00:00 2001 From: OuyangWenyu Date: Mon, 12 Feb 2024 16:21:21 +0800 Subject: [PATCH] rainfall_runoff_identify by Wang, Yang and bmi by Wang, Jingyi, but both have some bugs to be fixed * add some files * add wangjingyi's code * add requirements.txt * add dmca_esr.py and its test to util directory * fix mistake in test_session_division.py * fix mistake in test_session_division.py * change pypi distribute workflow * update workflow and add user * update workflow * update setup.py to add long_description * update setup.py to add long_description * Update setup.py change pypi project name * add bim package for env * delete xaj dir * refactor xajbim-related funcs, but not fully tested yet * delete some unused lines in xaj * add files from cookiecutter template * Create publish-to-pypi-token.yml * Update setup.py --------- Co-authored-by: forestbat --- .github/workflows/publish-to-pypi-token.yml | 37 + conf/config.yaml | 70 - environment-dev.yml | 9 + environment.yml | 3 +- hydromodel/calibrate/calibrate_ga_xaj_bmi.py | 1 - hydromodel/example/__init__.py | 0 hydromodel/example/division_flow.csv | 9132 ++++++++++++++++++ hydromodel/example/division_rain.csv | 9132 ++++++++++++++++++ hydromodel/models/xaj.py | 333 + setup.py | 67 +- test/test_data.py | 2 +- test/test_rr_event_iden.py | 4 +- 12 files changed, 18686 insertions(+), 104 deletions(-) create mode 100644 .github/workflows/publish-to-pypi-token.yml delete mode 100644 conf/config.yaml create mode 100644 hydromodel/example/__init__.py create mode 100644 hydromodel/example/division_flow.csv create mode 100644 hydromodel/example/division_rain.csv diff --git a/.github/workflows/publish-to-pypi-token.yml b/.github/workflows/publish-to-pypi-token.yml new file mode 100644 index 0000000..ef3c9e2 --- /dev/null +++ b/.github/workflows/publish-to-pypi-token.yml @@ -0,0 +1,37 @@ +name: Publish Python distributions to PyPI + +on: + push: + workflow_dispatch: + +jobs: + build-n-publish: + name: Build and publish Python distributions to PyPI + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@master + - name: Set up Python 3.9 + uses: actions/setup-python@v1 + with: + python-version: 3.9 + + - name: Install pypa/build + run: >- + python -m + pip install + build + --user + - name: Build a binary wheel and a source tarball + run: >- + python -m + build + --sdist + --wheel + --outdir dist/ + . + - name: Publish distribution to PyPI + uses: pypa/gh-action-pypi-publish@release/v1 + with: + user: __token__ + password: ${{ secrets.HYDRO_XAJ_TOKEN }} diff --git a/conf/config.yaml b/conf/config.yaml deleted file mode 100644 index 1faacd5..0000000 --- a/conf/config.yaml +++ /dev/null @@ -1,70 +0,0 @@ -model_params: - model_name: LSTMLinear - model_param: - input_size: 20 - hidden_size: 10 - output_size: 1 - num_layers: 2 - dropout_rate: 0.0 -data_params: - data_source_name: CAMELS - object_ids: ["01013500", "01022500"] - # closed interval - t_range_train: - - '1990-09-01' - - '2000-08-31' - t_range_valid: - - '2000-09-01' - - '2005-08-31' - t_range_test: - - '2005-09-01' - - '2010-08-31' - warmup_length: 0 - target_cols: - - usgsFlow - target_rm_nan: false - target_as_input: false - relevant_types: - - daymet - relevant_cols: - - dayl - - prcp - - srad - - tmax - - tmin - - vp - constant_cols: - - p_mean - - p_seasonality - - frac_snow - - aridity - - geol_porostiy - - geol_permeability - - soil_depth_statsgo - - soil_porosity - - soil_conductivity - - elev_mean - - slope_mean - - area_gages2 - - frac_forest - - lai_max - constant_only: false -training_params: - dataset: CamelsDataset - batch_first: true - seq_length: 100 - loss_func: MSELoss - optimizer: Adam - optim_params: - lr: 0.001 - train_epoch: 2 - batch_size: 32 - val_batch_size: 32 - random_seed: 1234 - device: - - 0 - num_workers: 0 -evaluate_params: - metrics: - - NSE - test_epoch: 2 \ No newline at end of file diff --git a/environment-dev.yml b/environment-dev.yml index e415a66..90bdb97 100644 --- a/environment-dev.yml +++ b/environment-dev.yml @@ -14,6 +14,9 @@ dependencies: - spotpy=1.5.14 - seaborn - tqdm + - yaml + - bmipy + # for dev - pyarrow - hydroerr - xarray @@ -25,8 +28,14 @@ dependencies: - sphinx - pytest - black + - flake8 + # pip - pip - pip: + - setuptools + - wheel + - twine + - bump2version - hydrodataset # config for deep learning - hydra-core diff --git a/environment.yml b/environment.yml index 02544ac..da831b9 100644 --- a/environment.yml +++ b/environment.yml @@ -13,7 +13,8 @@ dependencies: - spotpy=1.5.14 - seaborn - tqdm - - pytest + - yaml + - bmipy - pip - pip: - hydrodataset diff --git a/hydromodel/calibrate/calibrate_ga_xaj_bmi.py b/hydromodel/calibrate/calibrate_ga_xaj_bmi.py index b0e67d9..ab04e06 100644 --- a/hydromodel/calibrate/calibrate_ga_xaj_bmi.py +++ b/hydromodel/calibrate/calibrate_ga_xaj_bmi.py @@ -1,5 +1,4 @@ """Calibrate XAJ model using DEAP""" - import os import pickle import 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a/hydromodel/models/xaj.py b/hydromodel/models/xaj.py index 103286f..fb3daac 100644 --- a/hydromodel/models/xaj.py +++ b/hydromodel/models/xaj.py @@ -900,3 +900,336 @@ def xaj( if return_state: return q_sim, es, *w, s, fr, qi, qg return q_sim, es + + +def xaj_runoff( + p_and_e, + params_runoff: Union[np.array, list], + *w0, + s0, + fr0, + **kwargs, +) -> Union[tuple, np.array]: + model_name = kwargs.get("name", "xaj") + source_type = kwargs.get("source_type", "sources") + source_book = kwargs.get("source_book", "HF") + # params + param_ranges = MODEL_PARAM_DICT[model_name]["param_range"] + xaj_params = [ + (value[1] - value[0]) * params_runoff[:, i] + value[0] + for i, (key, value) in enumerate(param_ranges.items()) + ] + k = xaj_params[0] + b = xaj_params[1] + im = xaj_params[2] + um = xaj_params[3] + lm = xaj_params[4] + dm = xaj_params[5] + c = xaj_params[6] + sm = xaj_params[7] + ex = xaj_params[8] + ki_ = xaj_params[9] + kg_ = xaj_params[10] + # ki+kg should be smaller than 1; if not, we scale them + ki = np.where(ki_ + kg_ < 1.0, ki_, (1.0 - PRECISION) / (ki_ + kg_) * ki_) + kg = np.where(ki_ + kg_ < 1.0, kg_, (1.0 - PRECISION) / (ki_ + kg_) * kg_) + + # w0 = (0.5 * um, 0.5 * lm, 0.5 * dm) + inputs = p_and_e[:, :, :] + runoff_ims_ = np.full(inputs.shape[:2], 0.0) + rss_ = np.full(inputs.shape[:2], 0.0) + ris_ = np.full(inputs.shape[:2], 0.0) + rgs_ = np.full(inputs.shape[:2], 0.0) + es_ = np.full(inputs.shape[:2], 0.0) + for i in range(inputs.shape[0]): + if i == 0: + (r, rim, e, pe), w = generation( + inputs[i, :, :], k, b, im, um, lm, dm, c, *w0 + ) + if source_type == "sources": + (rs, ri, rg), (s, fr) = sources( + pe, r, sm, ex, ki, kg, s0, fr0, book=source_book + ) + elif source_type == "sources5mm": + (rs, ri, rg), (s, fr) = sources5mm( + pe, r, sm, ex, ki, kg, s0, fr0, book=source_book + ) + else: + raise NotImplementedError("No such divide-sources method") + else: + (r, rim, e, pe), w = generation( + inputs[i, :, :], k, b, im, um, lm, dm, c, *w + ) + if source_type == "sources": + (rs, ri, rg), (s, fr) = sources( + pe, r, sm, ex, ki, kg, s, fr, book=source_book + ) + elif source_type == "sources5mm": + (rs, ri, rg), (s, fr) = sources5mm( + pe, r, sm, ex, ki, kg, s, fr, book=source_book + ) + else: + raise NotImplementedError("No such divide-sources method") + # impevious part is pe * im + runoff_ims_[i, :] = rim + # so for non-imprvious part, the result should be corrected + rss_[i, :] = rs * (1 - im) + ris_[i, :] = ri * (1 - im) + rgs_[i, :] = rg * (1 - im) + es_[i, :] = e + # seq, batch, feature + runoff_im = np.expand_dims(runoff_ims_, axis=2) + rss = np.expand_dims(rss_, axis=2) + es = np.expand_dims(es_, axis=2) + return runoff_im, rss_, ris_, rgs_, es, rss + + +def xaj_route( + p_and_e, + params_route: Union[np.array, list], + ris_, + rgs_, + rss_, + rss, + runoff_im, + qi0, + qg0, + es, + **kwargs, +) -> Union[tuple, np.array]: + model_name = kwargs.get("name", "xaj") + # params + param_ranges = MODEL_PARAM_DICT[model_name]["param_range"] + if model_name == "xaj": + route_method = "CSL" + elif model_name == "xaj_mz": + route_method = "MZ" + else: + raise NotImplementedError( + "We don't provide this route method now! Please use 'CS' or 'MZ'!" + ) + xaj_params = [ + (value[1] - value[0]) * params_route[:, i] + value[0] + for i, (key, value) in enumerate(param_ranges.items()) + ] + if route_method == "CSL": + cs = xaj_params[11] + l = xaj_params[12] + + elif route_method == "MZ": + # we will use routing method from mizuRoute -- http://www.geosci-model-dev.net/9/2223/2016/ + a = xaj_params[11] + theta = xaj_params[12] + # make it as a parameter + kernel_size = int(xaj_params[15]) + else: + raise NotImplementedError( + "We don't provide this route method now! Please use 'CS' or 'MZ'!" + ) + ci = xaj_params[13] + cg = xaj_params[14] + + inputs = p_and_e[:, :, :] + qs = np.full(inputs.shape[:2], 0.0) + if route_method == "CSL": + qt = np.full(inputs.shape[:2], 0.0) + for i in range(inputs.shape[0]): + if i == 0: + qi = linear_reservoir(ris_[i], ci, qi0) + qg = linear_reservoir(rgs_[i], cg, qg0) + else: + qi = linear_reservoir(ris_[i], ci, qi) + qg = linear_reservoir(rgs_[i], cg, qg) + qs_ = rss_[i] + qt[i, :] = qs_ + qi + qg + + for j in range(len(l)): + lag = int(l[j]) + for i in range(lag): + qs[i, j] = qt[i, j] + if i == lag: + break + for i in range(lag, inputs.shape[0]): + qs[i, j] = cs[j] * qs[i - 1, j] + (1 - cs[j]) * qt[i - lag, j] + + elif route_method == "MZ": + rout_a = a.repeat(rss.shape[0]).reshape(rss.shape) + rout_b = theta.repeat(rss.shape[0]).reshape(rss.shape) + conv_uh = uh_gamma(rout_a, rout_b, kernel_size) + qs_ = uh_conv(runoff_im + rss, conv_uh) + for i in range(inputs.shape[0]): + if i == 0: + qi = linear_reservoir(ris_[i], ci, qi0) + qg = linear_reservoir(rgs_[i], cg, qg0) + else: + qi = linear_reservoir(ris_[i], ci, qi) + qg = linear_reservoir(rgs_[i], cg, qg) + qs[i, :] = qs_[i, :, 0] + qi + qg + else: + raise NotImplementedError( + "We don't provide this route method now! Please use 'CSL' or 'MZ'!" + ) + + # seq, batch, feature + q_sim = np.expand_dims(qs, axis=2) + return q_sim, es + + +def xaj_state( + p_and_e, + params: Union[np.array, list], + return_state=True, + warmup_length=365, + **kwargs, +) -> Union[tuple, np.array]: + # default values for some function parameters + model_name = kwargs["name"] if "name" in kwargs else "xaj" + source_type = kwargs["source_type"] if "source_type" in kwargs else "sources" + source_book = kwargs["source_book"] if "source_book" in kwargs else "HF" + # params + param_ranges = MODEL_PARAM_DICT[model_name]["param_range"] + if model_name == "xaj": + route_method = "CSL" + elif model_name == "xaj_mz": + route_method = "MZ" + else: + raise NotImplementedError( + "We don't provide this route method now! Please use 'CS' or 'MZ'!" + ) + xaj_params = [ + (value[1] - value[0]) * params[:, i] + value[0] + for i, (key, value) in enumerate(param_ranges.items()) + ] + k = xaj_params[0] + b = xaj_params[1] + im = xaj_params[2] + um = xaj_params[3] + lm = xaj_params[4] + dm = xaj_params[5] + c = xaj_params[6] + sm = xaj_params[7] + ex = xaj_params[8] + ki_ = xaj_params[9] + kg_ = xaj_params[10] + # ki+kg should be smaller than 1; if not, we scale them + ki = np.where(ki_ + kg_ < 1.0, ki_, (1.0 - PRECISION) / (ki_ + kg_) * ki_) + kg = np.where(ki_ + kg_ < 1.0, kg_, (1.0 - PRECISION) / (ki_ + kg_) * kg_) + if route_method == "CSL": + cs = xaj_params[11] + l = xaj_params[12] + + elif route_method == "MZ": + # we will use routing method from mizuRoute -- http://www.geosci-model-dev.net/9/2223/2016/ + a = xaj_params[11] + theta = xaj_params[12] + # make it as a parameter + kernel_size = int(xaj_params[15]) + else: + raise NotImplementedError( + "We don't provide this route method now! Please use 'CS' or 'MZ'!" + ) + ci = xaj_params[13] + cg = xaj_params[14] + + w0 = (0.5 * um, 0.5 * lm, 0.5 * dm) + s0 = 0.5 * sm + fr0 = np.full(ex.shape, 0.1) + qi0 = np.full(ci.shape, 0.1) + qg0 = np.full(cg.shape, 0.1) + + # state_variables + # inputs = p_and_e[warmup_length:, :, :] + inputs = p_and_e[:, :, :] + runoff_ims_ = np.full(inputs.shape[:2], 0.0) + rss_ = np.full(inputs.shape[:2], 0.0) + ris_ = np.full(inputs.shape[:2], 0.0) + rgs_ = np.full(inputs.shape[:2], 0.0) + es_ = np.full(inputs.shape[:2], 0.0) + for i in range(inputs.shape[0]): + if i == 0: + (r, rim, e, pe), w = generation( + inputs[i, :, :], k, b, im, um, lm, dm, c, *w0 + ) + if source_type == "sources": + (rs, ri, rg), (s, fr) = sources( + pe, r, sm, ex, ki, kg, s0, fr0, book=source_book + ) + elif source_type == "sources5mm": + (rs, ri, rg), (s, fr) = sources5mm( + pe, r, sm, ex, ki, kg, s0, fr0, book=source_book + ) + else: + raise NotImplementedError("No such divide-sources method") + else: + (r, rim, e, pe), w = generation( + inputs[i, :, :], k, b, im, um, lm, dm, c, *w + ) + if source_type == "sources": + (rs, ri, rg), (s, fr) = sources( + pe, r, sm, ex, ki, kg, s, fr, book=source_book + ) + elif source_type == "sources5mm": + (rs, ri, rg), (s, fr) = sources5mm( + pe, r, sm, ex, ki, kg, s, fr, book=source_book + ) + else: + raise NotImplementedError("No such divide-sources method") + # impevious part is pe * im + runoff_ims_[i, :] = rim + # so for non-imprvious part, the result should be corrected + rss_[i, :] = rs * (1 - im) + ris_[i, :] = ri * (1 - im) + rgs_[i, :] = rg * (1 - im) + es_[i, :] = e + # seq, batch, feature + runoff_im = np.expand_dims(runoff_ims_, axis=2) + rss = np.expand_dims(rss_, axis=2) + es = np.expand_dims(es_, axis=2) + + qs = np.full(inputs.shape[:2], 0.0) + + if route_method == "CSL": + qt = np.full(inputs.shape[:2], 0.0) + for i in range(inputs.shape[0]): + if i == 0: + qi = linear_reservoir(ris_[i], ci, qi0) + qg = linear_reservoir(rgs_[i], cg, qg0) + else: + qi = linear_reservoir(ris_[i], ci, qi) + qg = linear_reservoir(rgs_[i], cg, qg) + qs_ = rss_[i] + qt[i, :] = qs_ + qi + qg + + for j in range(len(l)): + # print(range(len(l))) + lag = int(l[j]) + for i in range(lag): + qs[i, j] = qt[i, j] + if i == lag: + break + for i in range(lag, inputs.shape[0]): + # print(inputs.shape[0]) + qs[i, j] = cs[j] * qs[i - 1, j] + (1 - cs[j]) * qt[i - lag, j] + + elif route_method == "MZ": + rout_a = a.repeat(rss.shape[0]).reshape(rss.shape) + rout_b = theta.repeat(rss.shape[0]).reshape(rss.shape) + conv_uh = uh_gamma(rout_a, rout_b, kernel_size) + qs_ = uh_conv(runoff_im + rss, conv_uh) + for i in range(inputs.shape[0]): + if i == 0: + qi = linear_reservoir(ris_[i], ci, qi0) + qg = linear_reservoir(rgs_[i], cg, qg0) + else: + qi = linear_reservoir(ris_[i], ci, qi) + qg = linear_reservoir(rgs_[i], cg, qg) + qs[i, :] = qs_[i, :, 0] + qi + qg + else: + raise NotImplementedError( + "We don't provide this route method now! Please use 'CSL' or 'MZ'!" + ) + + # seq, batch, feature + q_sim = np.expand_dims(qs, axis=2) + if return_state: + return q_sim, es, *w, s, fr, qi, qg diff --git a/setup.py b/setup.py index c50f827..a84d3bb 100644 --- a/setup.py +++ b/setup.py @@ -1,14 +1,19 @@ #!/usr/bin/env python - -"""The setup script.""" - +""" +Author: Wenyu Ouyang +Date: 2023-10-28 09:16:46 +LastEditTime: 2024-02-12 16:16:19 +LastEditors: Wenyu Ouyang +Description: The setup script +FilePath: \hydromodel\setup.py +Copyright (c) 2023-2024 Wenyu Ouyang. All rights reserved. +""" import io +import pathlib from os import path as op from setuptools import setup, find_packages -with open('README.md') as readme_file: - readme = readme_file.read() - +readme = pathlib.Path("README.md").read_text(encoding='utf-8') here = op.abspath(op.dirname(__file__)) # get the dependencies and installs @@ -18,45 +23,49 @@ install_requires = [x.strip() for x in all_reqs if "git+" not in x] dependency_links = [x.strip().replace("git+", "") for x in all_reqs if "git+" not in x] -requirements = [ ] +requirements = [] -setup_requirements = ['pytest-runner', ] +setup_requirements = [ + "pytest-runner", +] -test_requirements = ['pytest>=3', ] +test_requirements = [ + "pytest>=3", +] setup( author="Wenyu Ouyang", - author_email='wenyuouyang@outlook.com', - python_requires='>=3.8', + author_email="wenyuouyang@outlook.com", + python_requires=">=3.9", classifiers=[ - 'Intended Audience :: Developers', - 'License :: OSI Approved :: GNU General Public License v3 (GPLv3)', - 'Natural Language :: English', - 'Programming Language :: Python :: 3', - 'Programming Language :: Python :: 3.8', - 'Programming Language :: Python :: 3.9', - 'Programming Language :: Python :: 3.10', - 'Programming Language :: Python :: 3.11', + "Intended Audience :: Developers", + "License :: OSI Approved :: GNU General Public License v3 (GPLv3)", + "Natural Language :: English", + "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3.8", + "Programming Language :: Python :: 3.9", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", ], - description="Hydromodel is a python implementation for common hydrological models such as the XinAnJiang (XAJ) model, which is one of the most famous conceptual hydrological models, especially in Southern China.", + description="hydrological models starting from XinAnJiang", entry_points={ - 'console_scripts': [ - 'hydromodel=hydromodel.cli:main', + "console_scripts": [ + "hydromodel=hydromodel.cli:main", ], }, install_requires=install_requires, dependency_links=dependency_links, license="GNU General Public License v3", long_description=readme, - long_description_content_type='text/markdown', + long_description_content_type="text/markdown", include_package_data=True, - keywords='hydromodel', - name='hydromodel', - packages=find_packages(include=['hydromodel', 'hydromodel.*']), + keywords="hydromodel", + name="hydromodel", + packages=find_packages(include=["hydromodel", "hydromodel.*"]), setup_requires=setup_requirements, - test_suite='tests', + test_suite="tests", tests_require=test_requirements, - url='https://github.com/OuyangWenyu/hydromodel', - version='0.0.1', + url="https://github.com/iHeadWater/hydromodel", + version="0.0.2", zip_safe=False, ) diff --git a/test/test_data.py b/test/test_data.py index 6641bb0..af32d10 100644 --- a/test/test_data.py +++ b/test/test_data.py @@ -1,7 +1,7 @@ """ Author: Wenyu Ouyang Date: 2022-10-25 21:16:22 -LastEditTime: 2022-11-28 14:50:30 +LastEditTime: 2023-10-28 09:18:48 LastEditors: Wenyu Ouyang Description: Test for data preprocess FilePath: \hydro-model-xaj\test\test_data.py diff --git a/test/test_rr_event_iden.py b/test/test_rr_event_iden.py index 1107f06..bb5eb5e 100644 --- a/test/test_rr_event_iden.py +++ b/test/test_rr_event_iden.py @@ -1,10 +1,10 @@ """ Author: Wenyu Ouyang Date: 2023-10-28 09:23:22 -LastEditTime: 2024-02-11 23:53:20 +LastEditTime: 2024-02-12 16:17:26 LastEditors: Wenyu Ouyang Description: Test for rainfall-runoff event identification -FilePath: \hydro-model-xaj\test\test_rr_event_iden.py +FilePath: \hydromodel\test\test_rr_event_iden.py Copyright (c) 2023-2024 Wenyu Ouyang. All rights reserved. """