From 55d1f7dfaba63b0b31e6dde10d318323cd5123ce Mon Sep 17 00:00:00 2001 From: Guillaume Bouvignies Date: Tue, 29 Aug 2023 17:57:09 +0200 Subject: [PATCH] Fix bug in grid search The parameters that are fitted when evaluating a grid point were not updated. In particular, after the grid search was done, the parameters to the best grid point were not returned. This is now fixed. --- .pre-commit-config.yaml | 2 +- chemex/optimize/gridding.py | 25 +- chemex/parameters/spin_system.py | 2 +- pdm.lock | 1091 ++++++++++++------------------ 4 files changed, 465 insertions(+), 655 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 139006bd..7015013f 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -17,7 +17,7 @@ repos: - repo: https://github.com/astral-sh/ruff-pre-commit # Ruff version. - rev: v0.0.277 + rev: v0.0.286 hooks: - id: ruff args: [--fix, --exit-non-zero-on-fix] diff --git a/chemex/optimize/gridding.py b/chemex/optimize/gridding.py index 7db47378..6ba2a4f8 100644 --- a/chemex/optimize/gridding.py +++ b/chemex/optimize/gridding.py @@ -62,10 +62,13 @@ def run_group_grid( shape = tuple(len(values) for values in group_grid.values()) grid_size = np.prod(shape) - basename = group.path if group.path != Path(".") else Path("grid") + basename = group.path if group.path != Path() else Path("grid") filename = path / "Grid" / f"{basename}.out" filename.parent.mkdir(parents=True, exist_ok=True) + best_chisqr = np.inf + best_params = group_params + with filename.open("w") as fileout: fileout.write(print_header(group_grid)) @@ -75,13 +78,19 @@ def run_group_grid( for values in track(grid_values, total=float(grid_size), description=" "): _set_param_values(group_params, grid_ids, values) - group_params = minimize(group.experiments, group_params, fitmethod) - stats = calculate_statistics(group.experiments, group_params) - chisqr_list.append(stats.get("chisqr")) - fileout.write(print_values(values, chisqr_list[-1])) + optimized_params = minimize(group.experiments, group_params, fitmethod) + stats = calculate_statistics(group.experiments, optimized_params) + chisqr: float = stats.get("chisqr", np.inf) + chisqr_list.append(chisqr) + fileout.write(print_values(values, chisqr)) fileout.flush() + if chisqr < best_chisqr: + best_chisqr = chisqr + best_params = optimized_params + chisqr_array = np.array(chisqr_list).reshape(shape) + database.update_from_parameters(best_params) return GridResult(group_grid, chisqr_array) @@ -142,7 +151,7 @@ def combine_grids( def set_params_from_grid(grids_1d: Iterable[GridResult]): par_values = {} for grid_result in grids_1d: - id_, values = list(grid_result.grid.items())[0] + id_, values = next(iter(grid_result.grid.items())) par_values[id_] = values[grid_result.chisqr.argmin()] database.set_param_values(par_values) @@ -239,7 +248,7 @@ def run_grid( groups = create_groups(experiments) - grid_results = [] + grid_results: list[GridResult] = [] for group in groups: if message := group.message: print_group_name(message) @@ -250,8 +259,6 @@ def run_grid( grids_1d = make_grids_nd(grid, grids_combined, 1) grids_2d = make_grids_nd(grid, grids_combined, 2) set_params_from_grid(grids_1d) - params = database.build_lmfit_params(experiments.param_ids) - database.update_from_parameters(params) plot_grid_1d(grids_1d, path / "Grid") plot_grid_2d(grids_2d, path / "Grid") diff --git a/chemex/parameters/spin_system.py b/chemex/parameters/spin_system.py index c070ed6d..d3e3c92f 100644 --- a/chemex/parameters/spin_system.py +++ b/chemex/parameters/spin_system.py @@ -134,7 +134,7 @@ def name(self) -> str: def match(self, other: Group) -> bool: symbol = other.symbol == self.symbol or not self.symbol - number = other.number == self.number or self.number == self.NO_NUMBER + number = self.number in (other.number, self.NO_NUMBER) suffix = other.suffix == self.suffix or not self.suffix return number and symbol and suffix diff --git a/pdm.lock b/pdm.lock index 444a3f14..d6669005 100644 --- a/pdm.lock +++ b/pdm.lock @@ -1,17 +1,32 @@ # This file is @generated by PDM. # It is not intended for manual editing. +[metadata] +groups = ["default", "linting"] +cross_platform = true +static_urls = false +lock_version = "4.3" +content_hash = "sha256:d85e84207b7cef870c53c519380c3f64e37cdfd01f4fc720977de3bab6cd7628" + [[package]] name = "annotated-types" version 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