diff --git a/.github/workflows/docs_workflow.yml b/.github/workflows/docs_workflow.yml index 7002f96..0dddb26 100644 --- a/.github/workflows/docs_workflow.yml +++ b/.github/workflows/docs_workflow.yml @@ -15,7 +15,7 @@ on: jobs: docs_ubuntu: - runs-on: ubuntu-22.04 + runs-on: ubuntu-latest timeout-minutes: 90 @@ -43,7 +43,7 @@ jobs: NUMPY: '2.4' SCIPY: '1.17' PYYAML: '6.0.3' - JAX: '0.9' + JAX: '0.9.0' OPENMDAO: 'latest' DYMOS: 'latest' MPI4PY: '4.1' diff --git a/.github/workflows/tests_workflow.yml b/.github/workflows/tests_workflow.yml index e030e53..ec9a7dc 100644 --- a/.github/workflows/tests_workflow.yml +++ b/.github/workflows/tests_workflow.yml @@ -3,19 +3,27 @@ name: UQPCE Tests on: - # Trigger on push, pull request push: branches: [ main ] pull_request: branches: [ main, develop ] - # Trigger via workflow_dispatch event workflow_dispatch: + inputs: + uqpce_pixi: + type: boolean + description: "Run tests using uqpce's pixi environment" + required: false + default: true jobs: - test_ubuntu: - runs-on: ubuntu-22.04 + test_uqpce_pixi: + runs-on: ${{ matrix.runs-on }} + + defaults: + run: + shell: bash timeout-minutes: 90 @@ -23,155 +31,31 @@ jobs: fail-fast: false matrix: include: - # baseline versions except with pyoptsparse but no SNOPT - # build docs to verify those that use pyoptsparse do not use SNOPT - - NAME: baseline - PY: '3.11' - NUMPY: '2.0' - SCIPY: '1.13' - PYYAML: '6.0.2' - JAX: '0.6.1' - OPENMDAO: 'latest' - DYMOS: 'latest' - MPI4PY: '3.1.4' - OPTIONAL: '[docs]' - - # make sure the latest versions of things don't break the docs - - NAME: latest - PY: '3.14' - NUMPY: '2.4' - SCIPY: '1.17' - PYYAML: '6.0.3' - JAX: '0.9' - OPENMDAO: 'latest' - DYMOS: 'latest' - MPI4PY: '4.1' - OPTIONAL: '[docs]' + - pixi-env: default + runs-on: ubuntu-latest + - pixi-env: default + runs-on: macos-latest + - pixi-env: default + runs-on: windows-latest steps: - - name: Display run details - run: | - echo "=============================================================" - echo "Run #${GITHUB_RUN_NUMBER}" - echo "Run ID: ${GITHUB_RUN_ID}" - echo "Testing: ${GITHUB_REPOSITORY}" - echo "Triggered by: ${GITHUB_EVENT_NAME}" - echo "Initiated by: ${GITHUB_ACTOR}" - echo "=============================================================" - - name: Checkout code uses: actions/checkout@v4 - - name: Setup conda - uses: conda-incubator/setup-miniconda@v3 + - name: Install Pixi + uses: prefix-dev/setup-pixi@v0.9.6 with: - python-version: ${{ matrix.PY }} - channels: conda-forge - conda-remove-defaults: true - - - name: Install Numpy/Scipy - shell: bash -l {0} - run: | - echo "=============================================================" - echo "Install Numpy/Scipy" - echo "=============================================================" - conda install numpy=${{ matrix.NUMPY }} scipy=${{ matrix.SCIPY }} -q -y - - - name: Install OpenMDAO - if: matrix.OPENMDAO - shell: bash -l {0} - run: | - echo "=============================================================" - echo "Install OpenMDAO" - echo "=============================================================" - if [[ "${{ matrix.OPENMDAO }}" == "dev" ]]; then - pip install git+https://github.com/OpenMDAO/OpenMDAO - elif [[ "${{ matrix.OPENMDAO }}" == "latest" ]]; then - pip install openmdao - else - pip install openmdao==${{ matrix.OPENMDAO }} - fi - - - name: Install Dymos - if: matrix.DYMOS - shell: bash -l {0} - run: | - echo "=============================================================" - echo "Install Dymos" - echo "=============================================================" - if [[ "${{ matrix.DYMOS }}" == "dev" ]]; then - pip install git+https://github.com/OpenMDAO/dymos - elif [[ "${{ matrix.DYMOS }}" == "latest" ]]; then - pip install dymos - else - pip install dymos==${{ matrix.DYMOS }} - fi + environments: ${{ matrix.pixi-env }} - - name: Install PyYAML - if: matrix.PYYAML - shell: bash -l {0} - run: | - echo "=============================================================" - echo "Install PyYAML" - echo "=============================================================" - pip install PyYAML==${{ matrix.PYYAML }} - - - name: Install JAX - if: matrix.JAX - shell: bash -l {0} - run: | - echo "=============================================================" - echo "Install JAX" - echo "=============================================================" - pip install jax==${{ matrix.JAX }} - - - name: Install mpi4py - if: matrix.MPI4PY - shell: bash -l {0} - run: | - echo "=============================================================" - echo "Install mpi4py" - echo "=============================================================" - conda install mpi4py==${{ matrix.MPI4PY }} -q -y - - - name: Install UQPCE - shell: bash -l {0} - run: | - echo "=============================================================" - echo "Install UQPCE" - echo "=============================================================" - pip install .${{ matrix.OPTIONAL }} - - - name: Display environment info - id: env_info - shell: bash -l {0} + - name: Display run details run: | - conda info - conda list - echo "=============================================================" - echo "Check installed versions of Python, Numpy and Scipy" + echo "Run #${GITHUB_RUN_NUMBER}" + echo "Testing: ${GITHUB_REPOSITORY}" + echo "Pixi environment: ${{ matrix.pixi-env }}" + echo "OS: ${{ matrix.runs-on }}" echo "=============================================================" - python -c "import sys; assert str(sys.version).startswith(str(${{ matrix.PY }})), \ - f'Python version {sys.version} is not the requested version (${{ matrix.PY }})'" - - python -c "import numpy; assert str(numpy.__version__).startswith(str(${{ matrix.NUMPY }})), \ - f'Numpy version {numpy.__version__} is not the requested version (${{ matrix.NUMPY }})'" - - python -c "import scipy; assert str(scipy.__version__).startswith(str(${{ matrix.SCIPY }})), \ - f'Scipy version {scipy.__version__} is not the requested version (${{ matrix.SCIPY }})'" - - - name: Display dependency tree - if: failure() && steps.env_info.outcome == 'failure' - run: | - pip install pipdeptree - pipdeptree - name: Run tests - shell: bash -l {0} run: | - echo "=============================================================" - echo "Run Tests" - echo "=============================================================" - cd $HOME/work/UQPCE/UQPCE - python -m unittest discover uqpce "test*.py" \ No newline at end of file + pixi run -e ${{ matrix.pixi-env }} python -m unittest discover uqpce "test*.py" diff --git a/.gitignore b/.gitignore index 199893d..7ffdba9 100644 --- a/.gitignore +++ b/.gitignore @@ -103,4 +103,6 @@ venv.bak/ n2.html *SNOPT_print.out *SNOPT_summary.out -docs/_autosummary/* \ No newline at end of file +docs/_autosummary/*# pixi environments +.pixi/* +!.pixi/config.toml diff --git a/pixi.lock b/pixi.lock new file mode 100644 index 0000000..4233857 --- /dev/null +++ b/pixi.lock @@ -0,0 +1,5226 @@ +version: 7 +platforms: +- name: linux-64 +- name: osx-arm64 +- name: win-64 +environments: + all: + channels: + - url: https://conda.anaconda.org/conda-forge/ + indexes: + - 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cffi ; implementation_name == 'pypy' + requires_python: '>=3.8' +- pypi: https://files.pythonhosted.org/packages/fd/e1/3542a9cb596cadd76fcef413f19c79216e002623158befe6daa03dbfa88c/contourpy-1.3.3-cp314-cp314-macosx_11_0_arm64.whl + name: contourpy + version: 1.3.3 + sha256: cbedb772ed74ff5be440fa8eee9bd49f64f6e3fc09436d9c7d8f1c287b121d77 + requires_dist: + - numpy>=1.25 + - furo ; extra == 'docs' + - sphinx>=7.2 ; extra == 'docs' + - sphinx-copybutton ; extra == 'docs' + - bokeh ; extra == 'bokeh' + - selenium ; extra == 'bokeh' + - contourpy[bokeh,docs] ; extra == 'mypy' + - bokeh ; extra == 'mypy' + - docutils-stubs ; extra == 'mypy' + - mypy==1.17.0 ; extra == 'mypy' + - types-pillow ; extra == 'mypy' + - contourpy[test-no-images] ; extra == 'test' + - matplotlib ; extra == 'test' + - pillow ; extra == 'test' + - pytest ; extra == 'test-no-images' + - pytest-cov ; extra == 'test-no-images' + - pytest-rerunfailures ; extra == 'test-no-images' + - pytest-xdist ; extra == 'test-no-images' + - wurlitzer ; extra == 'test-no-images' + requires_python: '>=3.11' diff --git a/pyproject.toml b/pyproject.toml index 34a8a8b..dc8ad2c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -33,7 +33,7 @@ dependencies = [ "numpy>=2.0", "PyYAML", "matplotlib", - "scipy>=1.13", + "scipy>=1.13, <=1.17", "sympy", "openmdao>=3.43.0", "jax>=0.4.30", @@ -60,3 +60,22 @@ path = "uqpce/__init__.py" include = [ "uqpce", ] + +############################## +# pixi settings +############################## + +[tool.pixi.workspace] +channels = ["conda-forge"] +platforms = ["linux-64", "osx-arm64", "win-64"] +exclude-newer = "14d" + +[tool.pixi.pypi-dependencies] +uqpce = { path = ".", editable = true } + +[tool.pixi.environments] +default = { solve-group = "default" } +all = { features = ["all"], solve-group = "default" } +docs = { features = ["docs"], solve-group = "default" } + +[tool.pixi.tasks] diff --git a/uqpce/pce/model.py b/uqpce/pce/model.py index 41e6e4f..e414382 100644 --- a/uqpce/pce/model.py +++ b/uqpce/pce/model.py @@ -1,15 +1,15 @@ import copy -import numpy as np import matplotlib.pyplot as plt +import numpy as np from scipy import stats -from sympy import symbols, Matrix, factorial +from sympy import Matrix, factorial, symbols from sympy.utilities.lambdify import lambdify try: - from mpi4py.MPI import ( - DOUBLE as MPI_DOUBLE, COMM_WORLD as MPI_COMM_WORLD, SUM as MPI_SUM - ) + from mpi4py.MPI import COMM_WORLD as MPI_COMM_WORLD + from mpi4py.MPI import DOUBLE as MPI_DOUBLE + from mpi4py.MPI import SUM as MPI_SUM comm = MPI_COMM_WORLD rank = comm.rank @@ -24,22 +24,28 @@ from uqpce.pce._helpers import ( - evaluate_points, solve_coeffs, evaluate_points_verbose, - calc_difference, calc_mean_err, warn + calc_difference, + calc_mean_err, + evaluate_points, + evaluate_points_verbose, + solve_coeffs, + warn, ) from uqpce.pce.stats.statistics import ( - calc_term_count, calc_mean_sq_err, calc_hat_matrix + calc_hat_matrix, + calc_mean_sq_err, + calc_term_count, ) class MatrixSystem: """ - Inputs: responses- the array of responses from the results file + Inputs: responses- the array of responses from the results file (or from the user_function) var_list- the lsit of variables - - The matrix system built from the responses and input values. The - MatrixSystem is built and solved to acquire the matrix coefficients in + + The matrix system built from the responses and input values. The + MatrixSystem is built and solved to acquire the matrix coefficients in the systme of equations. """ @@ -73,7 +79,7 @@ def __init__(self, responses, var_list, verbose=False): def create_model_matrix(self): """ - Creates the model matrix to support an Nth order model. Supports + Creates the model matrix to support an Nth order model. Supports creating a model matrix with variables of varying orders. """ orders = np.array([var.order for var in self.var_list]) @@ -135,8 +141,8 @@ def create_model_matrix(self): def form_norm_sq(self, order): """ - Inputs: order- the order of polynomial expansion - + Inputs: order- the order of polynomial expansion + Creates the model matrix and the corresponding norm squared matrix. """ if ( @@ -184,7 +190,7 @@ def form_norm_sq(self, order): def build(self): """ - Builds the symbolic 'psi' matrix that represents the interactions + Builds the symbolic 'psi' matrix that represents the interactions of the variables. """ @@ -213,7 +219,7 @@ def build(self): var_basis_mat_symb = comm.allgather(var_basis_mat_symb_temp) var_basis_mat_symb = np.concatenate(var_basis_mat_symb, axis=1) else: - var_basis_mat_symb =var_basis_mat_symb_temp + var_basis_mat_symb =var_basis_mat_symb_temp for i in range(beg, end): curr_vect = 1 @@ -233,16 +239,19 @@ def build(self): else: self.var_basis_vect_symb = Matrix(var_basis_vect_symb_temp) + if self.var_basis_vect_symb.shape[0] == self.min_model_size: + self.var_basis_vect_symb = self.var_basis_vect_symb.T + self._var_basis_vect_symb = copy.copy(self.var_basis_vect_symb) return self.var_basis_vect_symb def evaluate(self, X): """ - Inputs: attribute- the attribute of variables used to calculate the + Inputs: attribute- the attribute of variables used to calculate the responses; this is almost always std_vals - - Fills the symbolic 'psi' variable basis system with the numbers that + + Fills the symbolic 'psi' variable basis system with the numbers that correspond to the variables in the matrix. """ @@ -253,7 +262,7 @@ def evaluate(self, X): self.var_basis_sys_eval = evaluate_points( var_basis_vect_func, X ) - + self._var_basis_sys_eval = np.copy(self.var_basis_sys_eval) return self.var_basis_sys_eval @@ -275,8 +284,8 @@ def _build_alt_model(self, responses, var_basis, norm_sq, idx): var_basis- the evaluated variable basis norm_sq- the norm squared idx- the index of the point that will be omitted - - Creates a model for the input combination; the mean, variance, and + + Creates a model for the input combination; the mean, variance, and errors are calculated and returned. """ incr_idx = idx + 1 @@ -316,7 +325,7 @@ def get_press_stats(self): for idx in range(self.act_model_size): temp = np.delete(self.var_basis_sys_eval, idx, axis=0) - responses = np.delete(self.responses, idx) + responses = np.delete(self.responses, idx, axis=0) matrix_coeffs = solve_coeffs(temp, responses) # create a model for each of the subsystems; check model error @@ -352,8 +361,8 @@ def get_press_stats(self): def update(self, combo): """ Inputs: combo- the combination used to update the attributes - - Updates the MatrixSystem attributes to reflect only the model terms + + Updates the MatrixSystem attributes to reflect only the model terms that correcpond to `combo`. """ combo = list(combo) @@ -371,12 +380,12 @@ def update(self, combo): class SurrogateModel: """ - Inputs: responses- the array of responses from the results file + Inputs: responses- the array of responses from the results file (or from the user_function) matrix_coeffs- the matrix coefficients solved for by MatrixSystem verbose- if statements should be printed by methods - - Gets the sobol indices of the varibles. Performs several calculations + + Gets the sobol indices of the varibles. Performs several calculations and checks on the model to check if it is a good representation. """ @@ -399,7 +408,7 @@ def __init__(self, responses=None, matrix_coeffs=None, verbose=False): def get_sobols(self, norm_sq): """ Inputs: norm_sq- the norm squared matrix - + Solves for the sobol sensitivities. """ tol = 1e-8 @@ -417,7 +426,7 @@ def get_sobols(self, norm_sq): def calc_var(self, norm_sq): """ Inputs: norm_sq- the norm squared matrix - + Calculates the mean and variance in the responses. """ @@ -442,11 +451,11 @@ def calc_var(self, norm_sq): def calc_error(self, var_basis): """ - Inputs: var_basis- the varibale basis matrix that consists of values + Inputs: var_basis- the varibale basis matrix that consists of values (not symbols) - - Solves for the calculated responses that the matrix coefficients and - variable basis ('alpha' and 'psi') result in as well as the difference + + Solves for the calculated responses that the matrix coefficients and + variable basis ('alpha' and 'psi') result in as well as the difference between these values and the actual values. """ prod = np.dot(var_basis, self.matrix_coeffs) @@ -459,11 +468,11 @@ def check_normality( self, var_basis_sys_eval, sig, graph_dir=None, sigfigs=5, plot=False ): """ - Inputs: var_basis_sys_eval- the variable basis system (not symbolic) + Inputs: var_basis_sys_eval- the variable basis system (not symbolic) matrix sig- the level of signif for the Shapiro-Wilks test graph_dir- the directory that the graphs are put into - + Ensures that the err follows a normal distribution. """ test_stat = np.zeros(self.model_cnt) @@ -532,10 +541,10 @@ def predict(self, var_basis_vect_symb, var_list_symb, X): verify_size- the size of the verification responses var_list_symb- the list of the variable string representations attr- the Variable attribute to be used for verification - beg_idx- the index at which to start using points from + beg_idx- the index at which to start using points from attribute `attr` - - Verifies the surrogate model by outputting the responses from + + Verifies the surrogate model by outputting the responses from verification input values put into the model. """ var_basis_vect_func = lambdify( diff --git a/uqpce/pce/pce.py b/uqpce/pce/pce.py index 6690b09..e5e4f37 100644 --- a/uqpce/pce/pce.py +++ b/uqpce/pce/pce.py @@ -1126,11 +1126,14 @@ def check_fit(self) -> str: shift = 5 spaces = self.sigfigs + shift + R_sq = np.atleast_1d(R_sq) + R_sq_adj = np.atleast_1d(R_sq_adj) + for m in range(self.model_cnt): self._stats_str[m] = (# formatting like this so 5 sig figs and aligned - f'PRESS statistic: {f"{float(press_stat[m]):.{self.sigfigs}}":{spaces}s}\n' - f'R\u00b2: {f"{float(R_sq[m]):.{self.sigfigs}}":{spaces}s}\n' - f'R\u00b2 adjusted: {f"{float(R_sq_adj[m]):.{self.sigfigs}}":{spaces}s}\n\n' + f'PRESS statistic: {f"{float(press_stat.flat[m]):.{self.sigfigs}}":{spaces}s}\n' + f'R\u00b2: {f"{float(R_sq.flat[m]):.{self.sigfigs}}":{spaces}s}\n' + f'R\u00b2 adjusted: {f"{float(R_sq_adj.flat[m]):.{self.sigfigs}}":{spaces}s}\n\n' ) return self._stats_str diff --git a/uqpce/pce/stats/statistics.py b/uqpce/pce/stats/statistics.py index e12e77c..b376881 100644 --- a/uqpce/pce/stats/statistics.py +++ b/uqpce/pce/stats/statistics.py @@ -1,10 +1,12 @@ import math + import numpy as np from numpy.linalg import inv from scipy.stats import t as t_stat try: - from mpi4py.MPI import DOUBLE as MPI_DOUBLE, COMM_WORLD as MPI_COMM_WORLD + from mpi4py.MPI import COMM_WORLD as MPI_COMM_WORLD + from mpi4py.MPI import DOUBLE as MPI_DOUBLE comm = MPI_COMM_WORLD rank = comm.rank size = comm.size @@ -39,14 +41,16 @@ def calc_R_sq(var_basis, matrix_coeffs, responses): R_sq = 1 - (err_sum_sq / tot_sum_sq) # equation for R^2 - if (R_sq > 1).any(): - if (R_sq > 1 + thresh).any(): - warn( - f'R squared value was {R_sq}. Check the variable basis and ' - 'responses.' - ) - - R_sq[(R_sq > 1.0) and (R_sq > 1 + thresh)] = 1.0 + R_sq = np.atleast_1d(R_sq) + bad = R_sq > 1 + thresh + if np.any(bad): + warn( + f'R squared value was {R_sq[bad]}. Check the variable basis and ' + 'responses.' + ) + R_sq = np.clip(R_sq, None, 1.0) + if R_sq.size == 1: + R_sq = float(R_sq[0]) return R_sq @@ -81,39 +85,23 @@ def calc_PRESS_res(var_basis, responses): Calculate the PRESS residual for a given model. """ - resp_count = len(responses) - err_ver_sq = np.zeros(resp_count) - - base = resp_count // size - rem = resp_count % size - beg = base * rank + (rank >= rem) * rem + (rank < rem) * rank - count = base + (rank < rem) - end = beg + count - - ranks = np.arange(0, size, dtype=int) - seq_count = (ranks < rem) + base - seq_disp = base * ranks + (ranks >= rem) * rem + (ranks < rem) * ranks - - err_ver_sq_temp = np.zeros(count) - - for idx in range(beg, end): + act_model_size = var_basis.shape[0] + responses = np.atleast_2d(responses) - temp_basis = np.delete(var_basis, idx, axis=0) - temp_resps = np.delete(responses, idx,) - matrix_coeffs = solve_coeffs(temp_basis, temp_resps) + if responses.shape[0] != act_model_size: + responses = responses.T - ver_pred = np.matmul(var_basis[idx], matrix_coeffs) - err_ver_sq_temp[idx - beg] = (responses[idx] - ver_pred) ** 2 + unq_resp_cnt = responses.shape[1] + press_res = np.zeros(unq_resp_cnt) - if comm: - comm.Allgatherv( - [err_ver_sq_temp, count, MPI_DOUBLE], - [err_ver_sq, seq_count, seq_disp, MPI_DOUBLE] - ) - else: - err_ver_sq = err_ver_sq_temp + for mod in range(unq_resp_cnt): + for idx in range(act_model_size): + temp_basis = np.delete(var_basis, idx, axis=0) + temp_resps = np.delete(responses[:, mod], idx) + matrix_coeffs = solve_coeffs(temp_basis, temp_resps) - press_res = np.sum(err_ver_sq) + ver_pred = np.matmul(var_basis[idx], matrix_coeffs) + press_res[mod] += (responses[idx, mod] - ver_pred) ** 2 return press_res @@ -135,6 +123,10 @@ def calc_pred_conf_int(var_basis, matrix_coeffs, responses, signif, var_basis_ve resp_count, term_count = var_basis.shape deg_of_free = resp_count - term_count + responses = responses.reshape(resp_count, -1) + matrix_coeffs = matrix_coeffs.reshape(term_count, -1) + num_diff_resps = responses.shape[1] + err_var = calc_error_variance(var_basis, matrix_coeffs, responses) basis_mat = np.matmul(var_basis.T, var_basis) # X'X @@ -144,15 +136,15 @@ def calc_pred_conf_int(var_basis, matrix_coeffs, responses, signif, var_basis_ve t_val = t_stat(deg_of_free).ppf(1 - signif / 2) # high CI bound resamp_size = len(var_basis_ver) - approx_conf = np.zeros(resamp_size) - conf_uncert = np.zeros(resamp_size) + approx_conf = np.zeros([resamp_size, num_diff_resps]) + conf_uncert = np.zeros([resamp_size, num_diff_resps]) for i in range(resamp_size): x_i = var_basis_ver[i] mult_matrices = np.matmul(np.matmul(x_i.T, inverse_mat), x_i) - approx_conf[i] = np.matmul(x_i, matrix_coeffs) # y_hat(x) - conf_uncert[i] = t_val * np.sqrt(err_var * (const + mult_matrices)) + approx_conf[i, :] = np.matmul(x_i, matrix_coeffs) # y_hat(x) + conf_uncert[i, :] = t_val * np.sqrt(err_var * (const + mult_matrices)) return approx_conf, conf_uncert @@ -175,6 +167,10 @@ def calc_mean_conf_int(var_basis, matrix_coeffs, responses, signif, var_basis_ve resp_count, term_count = var_basis.shape deg_of_free = resp_count - term_count + responses = responses.reshape(resp_count, -1) + matrix_coeffs = matrix_coeffs.reshape(term_count, -1) + num_diff_resps = matrix_coeffs.shape[1] + err_var = calc_error_variance(var_basis, matrix_coeffs, responses) basis_mat = np.matmul(var_basis.T, var_basis) # X'X @@ -184,15 +180,15 @@ def calc_mean_conf_int(var_basis, matrix_coeffs, responses, signif, var_basis_ve t_val = t_stat(deg_of_free).ppf(1 - signif / 2) # high CI bound resamp_size = len(var_basis_ver) - approx_mean = np.zeros([resamp_size, 1]) - pred_uncert = np.zeros([resamp_size, 1]) + approx_mean = np.zeros([resamp_size, num_diff_resps]) + pred_uncert = np.zeros([resamp_size, num_diff_resps]) for i in range(resamp_size): x_i = var_basis_ver[i] mult_matrices = np.matmul(np.matmul(x_i.T, inverse_mat), x_i) - approx_mean[i] = np.matmul(x_i, matrix_coeffs) # y_hat(x) - pred_uncert[i] = t_val * np.sqrt(err_var * mult_matrices) + approx_mean[i, :] = np.matmul(x_i, matrix_coeffs) # y_hat(x) + pred_uncert[i, :] = t_val * np.sqrt(err_var * mult_matrices) return approx_mean, pred_uncert @@ -208,9 +204,12 @@ def calc_coeff_conf_int(var_basis, matrix_coeffs, responses, signif): """ resp_count, term_count = var_basis.shape + responses = responses.reshape(resp_count, -1) + matrix_coeffs = matrix_coeffs.reshape(term_count, -1) + deg_of_free = resp_count - term_count - coeff_uncert = np.zeros(matrix_coeffs.shape) + coeff_uncert = np.zeros_like(matrix_coeffs) err_var = calc_error_variance(var_basis, matrix_coeffs, responses) @@ -221,7 +220,7 @@ def calc_coeff_conf_int(var_basis, matrix_coeffs, responses, signif): t_val = t_stat(deg_of_free).ppf(1 - signif / 2) # high CI bound for i in range(term_count): - coeff_uncert[i] = t_val * np.sqrt(err_var * inverse_mat[i, i]) + coeff_uncert[i, :] = t_val * np.sqrt(err_var * inverse_mat[i, i]) return coeff_uncert @@ -407,13 +406,15 @@ def calc_error_variance(var_basis, matrix_coeffs, responses): err_sum_sq = calc_error_sum_of_sq(var_basis, matrix_coeffs, responses) err_var = err_sum_sq / (resp_count - term_count) - if err_var < 0: + bad_idx = (err_var < 0) + + if (bad_idx).any(): if err_var >= high_err_thresh: warn( 'Error variance is small and negative. Taking the absolute ' 'value for use in calculations.' ) - err_var = np.abs(err_var) + err_var[bad_idx] = np.abs(err_var[bad_idx]) else: raise ValueError( f'The error variance for this model is {err_var} and should be ' @@ -433,10 +434,26 @@ def calc_error_sum_of_sq(var_basis, matrix_coeffs, responses): Design and Analysis of Experiments (8th) by Douglas Montgomery (pg. 453) """ - resp_mat = np.matmul(responses.T, responses) - coeff_dot_basis = np.matmul(matrix_coeffs.T, var_basis.T) + act_model_size, coeff_cnt = var_basis.shape + responses = np.atleast_2d(responses) + matrix_coeffs = np.atleast_2d(matrix_coeffs) + + if responses.shape[0] != act_model_size: + responses = responses.T + + if matrix_coeffs.shape[0] != coeff_cnt: + matrix_coeffs = matrix_coeffs.T - return resp_mat - np.matmul(coeff_dot_basis, responses) + unq_resp_cnt = responses.shape[1] + err_sum_sq = np.zeros(unq_resp_cnt) + + for i in range(unq_resp_cnt): + resp_mat = np.matmul(responses[:, i].T, responses[:, i]) + coeff_dot_basis = np.matmul(matrix_coeffs[:, i].T, var_basis.T) + + err_sum_sq[i] = resp_mat - np.matmul(coeff_dot_basis, responses[:, i]) + + return err_sum_sq def calc_total_sum_of_sq(var_basis, responses): @@ -449,9 +466,19 @@ def calc_total_sum_of_sq(var_basis, responses): Design and Analysis of Experiments (8th) by Douglas Montgomery (pg. 463) """ act_model_size = var_basis.shape[0] - resp_mat = np.matmul(responses.T, responses) + responses = np.atleast_2d(responses) + + if responses.shape[0] != act_model_size: + responses = responses.T + + unq_resp_cnt = responses.shape[1] + tot_sum_sq = np.zeros(unq_resp_cnt) - return resp_mat - (np.sum(responses) ** 2 / act_model_size) + for i in range(unq_resp_cnt): + resp_mat = np.matmul(responses[:, i].T, responses[:, i]) + tot_sum_sq[i] = resp_mat - (np.sum(responses[:, i]) ** 2 / act_model_size) + + return tot_sum_sq def calc_sum_sq_regr(matrix_coeffs, responses, var_basis): @@ -464,12 +491,24 @@ def calc_sum_sq_regr(matrix_coeffs, responses, var_basis): Design and Analysis of Experiments (8th) by Douglas Montgomery (pg. 463) """ - resp_cnt = len(responses) + act_model_size, coeff_cnt = var_basis.shape + responses = np.atleast_2d(responses) + matrix_coeffs = np.atleast_2d(matrix_coeffs) + + if responses.shape[0] != act_model_size: + responses = responses.T + + if matrix_coeffs.shape[0] != coeff_cnt: + matrix_coeffs = matrix_coeffs.T + + unq_resp_cnt = responses.shape[1] + regr_sum_sq = np.zeros(unq_resp_cnt) - regr_sum_sq = np.matmul( - np.matmul(np.transpose(matrix_coeffs), np.transpose(var_basis)), - responses - ) - (np.sum(responses) ** 2 / resp_cnt) + for i in range(unq_resp_cnt): + regr_sum_sq[i] = np.matmul( + np.matmul(np.transpose(matrix_coeffs[:, i]), np.transpose(var_basis)), + responses[:, i] + ) - (np.sum(responses[:, i]) ** 2 / act_model_size) return regr_sum_sq diff --git a/uqpce/test_suite/test_uqpce/test_pce.py b/uqpce/test_suite/test_uqpce/test_pce.py index 95a0ed5..dff47af 100644 --- a/uqpce/test_suite/test_uqpce/test_pce.py +++ b/uqpce/test_suite/test_uqpce/test_pce.py @@ -1,13 +1,15 @@ import unittest -from io import StringIO -import syslog + import numpy as np from uqpce import PCE from uqpce.pce.variables.continuous import ( - UniformVariable, NormalVariable, ContinuousVariable + ContinuousVariable, + NormalVariable, + UniformVariable, ) + class TestPCE(unittest.TestCase): def setUp(self): @@ -18,8 +20,8 @@ def setUp(self): ) self.var_dict = { - 'Variable 0':{'distribution':'uniform', 'interval_low':6, 'interval_high':7, 'type':'aleatory'}, - 'Variable 1':{'distribution':'normal', 'mean':2, 'stdev':7}, + 'Variable 0':{'distribution':'uniform', 'interval_low':6, 'interval_high':7, 'type':'aleatory'}, + 'Variable 1':{'distribution':'normal', 'mean':2, 'stdev':7}, 'Variable 2':{'distribution':'continuous', 'pdf':'x', 'interval_low':0, 'interval_high':1} } for key, value in self.var_dict.items(): @@ -39,9 +41,9 @@ def setUp(self): self.var_basis = np.array([ [1, -11, 0, 2+1/3, 181, 0, -25-2/3, -1, 0, 5.7], - [1, -5, 0.42857143, 5+1/3, 37, -2.14285714, -26-2/3, -0.81632653, + [1, -5, 0.42857143, 5+1/3, 37, -2.14285714, -26-2/3, -0.81632653, 2.28571429, 29.1], - [1, 1, 0.85714286, 8+1/3, 1, 0.85714286, 8+1/3, -0.26530612, + [1, 1, 0.85714286, 8+1/3, 1, 0.85714286, 8+1/3, -0.26530612, 7.14285714, 70.5] ]) @@ -113,11 +115,11 @@ def test_set_samples(self): self.pce.set_samples(self.X) self.assertTrue( - (self.pce._X == self.X).all(), + (self.pce._X == self.X).all(), msg='PCE set_samples is not correct' ) self.assertTrue( - (self.pce._X_stand == self.X_stand).all(), + (self.pce._X_stand == self.X_stand).all(), msg='PCE set_samples is not correct' ) @@ -126,14 +128,14 @@ def test_build_basis(self): self.pce.build_basis(order=2) self.assertTrue( - np.isclose(self.pce.var_basis, self.var_basis).all(), + np.isclose(self.pce.var_basis, self.var_basis).all(), msg='PCE build_basis is not correct' ) def test_fit(self): self.pce.fit(self.Xfull, self.yfull) self.assertTrue( - np.isclose(self.pce.matrix_coeffs, self.coeffs).all(), + np.isclose(self.pce.matrix_coeffs, self.coeffs).all(), msg='PCE fit is not correct' ) @@ -149,7 +151,7 @@ def test_predict(self): resp_pred = self.pce.predict(Xv) self.assertTrue( - np.isclose(resp_pred, self.yv).all(), + np.isclose(resp_pred, self.yv).all(), msg='PCE fit is not correct' ) @@ -158,7 +160,7 @@ def test_verification(self): err = self.pce.verification(self.Xfull, self.yfull) self.assertTrue( - (np.abs(err) < 1e-6).all(), + (np.abs(err) < 1e-6).all(), msg='PCE verification is not correct' ) @@ -167,7 +169,7 @@ def test_resample_surrogate(self): eval_resps = self.pce.resample_surrogate() self.assertTrue( - eval_resps.ravel().shape[0] == self.aleat_cnt, + eval_resps.ravel().shape[0] == self.aleat_cnt, msg='PCE resample_surrogate is not correct' ) diff --git a/uqpce/test_suite/test_uqpce/test_statistics.py b/uqpce/test_suite/test_uqpce/test_statistics.py index 1dbe38e..063b527 100644 --- a/uqpce/test_suite/test_uqpce/test_statistics.py +++ b/uqpce/test_suite/test_uqpce/test_statistics.py @@ -1,17 +1,29 @@ import unittest import numpy as np -from sympy import symbols, Matrix, lambdify +from sympy import Matrix, lambdify, symbols +from uqpce.pce._helpers import evaluate_points, solve_coeffs +from uqpce.pce.model import SurrogateModel from uqpce.pce.stats.statistics import ( - calc_error_variance, calc_coeff_conf_int, calc_pred_conf_int, - calc_R_sq_adj, calc_R_sq, calc_mean_conf_int, calc_term_count, - calc_min_responses, calc_partial_F, calc_mean_sq_err, calc_sum_sq_regr, - calc_error_sum_of_sq, calc_total_sum_of_sq, calc_PRESS_res, - calc_hat_matrix, get_sobol_bounds, calc_var_conf_int + calc_coeff_conf_int, + calc_error_sum_of_sq, + calc_error_variance, + calc_hat_matrix, + calc_mean_conf_int, + calc_mean_sq_err, + calc_min_responses, + calc_partial_F, + calc_pred_conf_int, + calc_PRESS_res, + calc_R_sq, + calc_R_sq_adj, + calc_sum_sq_regr, + calc_term_count, + calc_total_sum_of_sq, + calc_var_conf_int, + get_sobol_bounds, ) -from uqpce.pce.model import SurrogateModel -from uqpce.pce._helpers import solve_coeffs, evaluate_points from uqpce.pce.variables.continuous import UniformVariable @@ -56,7 +68,16 @@ def test_calc_R_sq(self): self.assertTrue( np.isclose(R_sq_calc, R_sq_act, rtol=0, atol=tol), - msg='calc_R_sq is not correct' + msg='calc_R_sq is not correct for 1D cases' + ) + + R_sq_calc_2D = calc_R_sq( + var_basis, np.vstack([matrix_coeffs, matrix_coeffs]), + np.vstack([responses, responses]) + ) + self.assertTrue( + np.isclose(R_sq_calc_2D, R_sq_act, rtol=0, atol=tol).all(), + msg='calc_R_sq is not correct for 2D cases' ) def test_calc_R_sq_adj(self): @@ -98,7 +119,16 @@ def test_calc_R_sq_adj(self): self.assertTrue( np.isclose(R_sq_adj_calc, R_sq_adj_act, rtol=0, atol=tol), - msg='statistics function calc_R_sq_adj is not correct' + msg='statistics function calc_R_sq_adj is not correct for 1D cases' + ) + + R_sq_calc_2D = calc_R_sq_adj( + var_basis, np.vstack([matrix_coeffs, matrix_coeffs]), + np.vstack([responses, responses]) + ) + self.assertTrue( + np.isclose(R_sq_calc_2D, R_sq_adj_act, rtol=0, atol=tol).all(), + msg='statistics function calc_R_sq_adj is not correct for 2D cases' ) def test_calc_PRESS_res(self): @@ -149,7 +179,14 @@ def test_calc_PRESS_res(self): self.assertAlmostEqual( true_press, press, delta=1e-1, - msg='statistics function calc_PRESS_res is not correct' + msg='statistics function calc_PRESS_res is not correct for 1D cases' + ) + + press_2D = calc_PRESS_res(new_basis, np.vstack([new_resps, new_resps])) + + self.assertTrue( + np.isclose(true_press, press_2D, rtol=1e-4, atol=1e-4).all(), + msg='statistics function calc_PRESS_res is not correct for 2D cases' ) def test_calc_pred_conf_int(self): @@ -197,7 +234,7 @@ def test_calc_pred_conf_int(self): def test_calc_mean_conf_int(self): """ - Applied Statistics and Probability for Engineers 4th Ed. (2007), + Applied Statistics and Probability for Engineers 4th Ed. (2007), (pg. 13, 440, 467) Douglas C. Montgomery & George C. Runger """ @@ -374,12 +411,12 @@ def test_get_sobol_bounds(self): First Tests: Design and Analysis of Experiments, 8th Ed. (pg 468) Douglas Montgomery - + Values compared to hand-calculated values from this data. - + Second Tests: - Calculates the smallest and largest of all possible Sobols- ensures - that the lowest corresponds to the low and the highest corresponds to + Calculates the smallest and largest of all possible Sobols- ensures + that the lowest corresponds to the low and the highest corresponds to the high. """ # Design and Analysis of Experiments 8th ed, pg 468 @@ -574,15 +611,20 @@ def test_calc_total_sum_of_sq(self): ]) SS_T_calc = calc_total_sum_of_sq(var_basis, responses) - self.assertAlmostEqual( SS_T_act, SS_T_calc, delta=tol, - msg='calc_total_sum_of_sq is not working correctly.' + msg='calc_total_sum_of_sq is not working correctly for the 1D case.' + ) + + SS_T_calc_2D = calc_total_sum_of_sq(var_basis, np.vstack([responses, responses])) + self.assertTrue( + np.isclose(SS_T_act, SS_T_calc_2D, rtol=tol, atol=tol).all(), + msg='calc_total_sum_of_sq is not working correctly for the 2D case.' ) def test_calc_sum_sq_regr(self): """ - Applied Statistics and Probability for Engineers 4th Ed. (2007), + Applied Statistics and Probability for Engineers 4th Ed. (2007), (pg. 462) Douglas C. Montgomery & George C. Runger """ SS_R_act = 5990.7712 @@ -627,7 +669,17 @@ def test_calc_sum_sq_regr(self): self.assertAlmostEqual( SS_R_act, SS_R_calc, delta=tol, - msg='calc_sum_sq_regr is not working correctly.' + msg='calc_sum_sq_regr is not working correctly for 1D cases.' + ) + + SS_R_calc_2D = calc_sum_sq_regr( + np.vstack([matrix_coeffs, matrix_coeffs]), + np.vstack([responses]), var_basis + ) + + self.assertTrue( + np.isclose(SS_R_act, SS_R_calc_2D, atol=tol, rtol=tol).all(), + msg='calc_sum_sq_regr is not working correctly for 2D cases.' ) def test_calc_mean_sq_err(self): diff --git a/uqpce/test_suite/test_uqpce/test_uqpce.py b/uqpce/test_suite/test_uqpce/test_uqpce.py index d08b04e..e277bbe 100644 --- a/uqpce/test_suite/test_uqpce/test_uqpce.py +++ b/uqpce/test_suite/test_uqpce/test_uqpce.py @@ -1,12 +1,15 @@ import unittest import numpy as np -from sympy import Matrix, symbols, Eq, N, expand, sympify +from sympy import Eq, Matrix, N, expand, symbols, sympify from uqpce.pce.model import MatrixSystem, SurrogateModel from uqpce.pce.variables.continuous import ( - UniformVariable, NormalVariable, BetaVariable, ExponentialVariable, - GammaVariable + BetaVariable, + ExponentialVariable, + GammaVariable, + NormalVariable, + UniformVariable, ) order = 2 @@ -155,10 +158,6 @@ sig_combo = np.array([0, 1, 2, 3, 4, 5, 7, 20]) -var_basis_vect_symb_upd, norm_sq_upd, model_matrix_upd, min_model_size_upd, var_basis_sys_eval_upd = ( - matrix.update(sig_combo) -) - class TestMatrixSystem(unittest.TestCase): @@ -185,6 +184,10 @@ def setUp(self): self.var = var self.press_stats = press_stats + var_basis_vect_symb_upd, norm_sq_upd, model_matrix_upd, min_model_size_upd, var_basis_sys_eval_upd = ( + matrix.update(sig_combo) + ) + self.var_basis_vect_symb_upd = var_basis_vect_symb_upd self.norm_sq_upd = norm_sq_upd self.model_matrix_upd = model_matrix_upd @@ -501,17 +504,17 @@ def test_update(self): ) self.assertTrue( - np.isclose(true_norm_sq, norm_sq_upd, rtol=0, atol=1e-6).all(), + np.isclose(true_norm_sq, self.norm_sq_upd, rtol=0, atol=1e-6).all(), msg='MatrixSystem update is not correct' ) self.assertTrue( - np.isclose(true_model_matrix, model_matrix_upd, rtol=0, atol=1e-6).all(), + np.isclose(true_model_matrix, self.model_matrix_upd, rtol=0, atol=1e-6).all(), msg='MatrixSystem update is not correct' ) self.assertEqual( - true_min_model_size, min_model_size_upd, + true_min_model_size, self.min_model_size_upd, msg='MatrixSystem update is not correct' )