diff --git a/.gitignore b/.gitignore index dc1b326..215cd98 100644 --- a/.gitignore +++ b/.gitignore @@ -1,6 +1,9 @@ ## General pieces to ignore during git pushing, so you can use git add . without adding everything. +*__pycache__ +*sbi-logs + # Distribution / packaging .Python build/ diff --git a/.gitmodules b/.gitmodules index 6790723..e69de29 100644 --- a/.gitmodules +++ b/.gitmodules @@ -1,3 +0,0 @@ -[submodule ".showyourwork"] - path = .showyourwork - url = https://github.com/showyourwork/showyourwork diff --git a/.showyourwork b/.showyourwork deleted file mode 160000 index bee25e5..0000000 --- a/.showyourwork +++ /dev/null @@ -1 +0,0 @@ -Subproject commit bee25e5e096fc9edaf9da7a447afdba464d5f198 diff --git a/environment.yml b/environment.yml deleted file mode 100644 index bdd8ef1..0000000 --- a/environment.yml +++ /dev/null @@ -1,10 +0,0 @@ -## THIS IS FOR SHOW YOUR WORK - DO NOT USE IT FOR YOUR PROJECT PLEASE -channels: - - defaults - - conda-forge -dependencies: - - numpy=1.19.2 - - pip=21.0.1 - - python=3.9 - - pip: - - matplotlib==3.4.3 diff --git a/plots/generative/mackelab_pairplot.pdf b/plots/generative/mackelab_pairplot.pdf new file mode 100644 index 0000000..351cae9 Binary files /dev/null and b/plots/generative/mackelab_pairplot.pdf differ diff --git a/plots/static/getdist_cornerplot.pdf b/plots/static/getdist_cornerplot.pdf new file mode 100644 index 0000000..d03e794 Binary files /dev/null and b/plots/static/getdist_cornerplot.pdf differ diff --git a/plots/static/mackelab_pairplot.pdf b/plots/static/mackelab_pairplot.pdf new file mode 100644 index 0000000..d6bcb45 Binary files /dev/null and b/plots/static/mackelab_pairplot.pdf differ diff --git a/poetry.lock b/poetry.lock index 0604d57..be36f89 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. 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(>=22.12)"] test = ["covdefaults (>=2.3)", "coverage (>=7.2.3)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23.1)", "pytest (>=7.3.1)", "pytest-env (>=0.8.1)", "pytest-freezegun (>=0.4.2)", "pytest-mock (>=3.10)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "setuptools (>=67.7.1)", "time-machine (>=2.9)"] -[[package]] -name = "wcwidth" -version = "0.2.13" -description = "Measures the displayed width of unicode strings in a terminal" -optional = false -python-versions = "*" -files = [ - {file = "wcwidth-0.2.13-py2.py3-none-any.whl", hash = "sha256:3da69048e4540d84af32131829ff948f1e022c1c6bdb8d6102117aac784f6859"}, - {file = "wcwidth-0.2.13.tar.gz", hash = "sha256:72ea0c06399eb286d978fdedb6923a9eb47e1c486ce63e9b4e64fc18303972b5"}, -] - -[[package]] -name = "webcolors" -version = "1.13" -description = "A library for working with the color formats defined by HTML and CSS." -optional = false -python-versions = ">=3.7" -files = [ - {file = "webcolors-1.13-py3-none-any.whl", hash = "sha256:29bc7e8752c0a1bd4a1f03c14d6e6a72e93d82193738fa860cbff59d0fcc11bf"}, - {file = "webcolors-1.13.tar.gz", hash = "sha256:c225b674c83fa923be93d235330ce0300373d02885cef23238813b0d5668304a"}, -] - -[package.extras] -docs = ["furo", "sphinx", "sphinx-copybutton", "sphinx-inline-tabs", "sphinx-notfound-page", "sphinxext-opengraph"] -tests = ["pytest", "pytest-cov"] - -[[package]] -name = "webencodings" -version = "0.5.1" -description = "Character encoding aliases for legacy web content" -optional = false -python-versions = "*" -files = [ - {file = "webencodings-0.5.1-py2.py3-none-any.whl", hash = "sha256:a0af1213f3c2226497a97e2b3aa01a7e4bee4f403f95be16fc9acd2947514a78"}, - {file = "webencodings-0.5.1.tar.gz", hash = "sha256:b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923"}, -] - -[[package]] -name = "websocket-client" -version = "1.7.0" -description = "WebSocket client for Python with low level API options" -optional = false -python-versions = ">=3.8" -files = [ - {file = "websocket-client-1.7.0.tar.gz", hash = "sha256:10e511ea3a8c744631d3bd77e61eb17ed09304c413ad42cf6ddfa4c7787e8fe6"}, - {file = "websocket_client-1.7.0-py3-none-any.whl", hash = "sha256:f4c3d22fec12a2461427a29957ff07d35098ee2d976d3ba244e688b8b4057588"}, -] - -[package.extras] -docs = ["Sphinx (>=6.0)", "sphinx-rtd-theme (>=1.1.0)"] -optional = ["python-socks", "wsaccel"] -test = ["websockets"] - [[package]] name = "werkzeug" version = "3.0.1" @@ -3936,17 +2366,6 @@ MarkupSafe = ">=2.1.1" [package.extras] watchdog = ["watchdog (>=2.3)"] -[[package]] -name = "widgetsnbextension" -version = "4.0.9" -description = "Jupyter interactive widgets for Jupyter Notebook" -optional = false -python-versions = ">=3.7" -files = [ - {file = "widgetsnbextension-4.0.9-py3-none-any.whl", hash = "sha256:91452ca8445beb805792f206e560c1769284267a30ceb1cec9f5bcc887d15175"}, - {file = "widgetsnbextension-4.0.9.tar.gz", hash = "sha256:3c1f5e46dc1166dfd40a42d685e6a51396fd34ff878742a3e47c6f0cc4a2a385"}, -] - [[package]] name = "xarray" version = "2024.1.1" @@ -4010,4 +2429,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p [metadata] lock-version = "2.0" python-versions = "^3.9" -content-hash = "ffff04f4488a8896218f2abba066c8c6a880a95dd1151f23dacaaa1c6bcbd45c" +content-hash = "ae2e5e776997e3e9eb45b0a4eb7c30bc4b807b8eb0006efb214fd1dd73d51550" diff --git a/pyproject.toml b/pyproject.toml index 0117976..bb84594 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -6,22 +6,25 @@ description = "a package for diagnosing posterior quality from inference methods authors = ["Becky Nevin "] license = "MIT" +[tool.poetry.scripts] +diagnose = "client.client:main" + [tool.poetry.dependencies] python = "^3.9" -jupyter = "^1.0.0" sbi = "^0.22.0" -flake8 = "^7.0.0" -black = "^24.1.1" pyarrow = "^15.0.0" getdist = "^1.4.7" h5py = "^3.10.0" +numpy = "^1.26.4" +matplotlib = "^3.8.3" -[tool.poetry.dev-dependencies] -pytest = "^7.3.2" [tool.poetry.group.dev.dependencies] pre-commit = "^3.3.2" pytest-cov = "^4.1.0" +flake8 = "^7.0.0" +pytest = "^7.3.2" +black = "^24.3.0" [build-system] requires = ["poetry-core>=1.0.0"] diff --git a/resources/saveddata/data_train.h5 b/resources/saveddata/data_train.h5 new file mode 100644 index 0000000..ce996c5 Binary files /dev/null and b/resources/saveddata/data_train.h5 differ diff --git a/resources/saveddata/data_validation.h5 b/resources/saveddata/data_validation.h5 new file mode 100644 index 0000000..d227c56 Binary files /dev/null and b/resources/saveddata/data_validation.h5 differ diff --git a/resources/savedmodels/sbi/sbi_linear_from_data.pkl b/resources/savedmodels/sbi/sbi_linear_from_data.pkl new file mode 100644 index 0000000..4b0b298 Binary files /dev/null and b/resources/savedmodels/sbi/sbi_linear_from_data.pkl differ diff --git a/resources/savedmodels/sbi/sbi_linear_generative.pkl b/resources/savedmodels/sbi/sbi_linear_generative.pkl new file mode 100644 index 0000000..667baf9 Binary files /dev/null and b/resources/savedmodels/sbi/sbi_linear_generative.pkl differ diff --git a/results/plots/generative/mackelab_pairplot.pdf b/results/plots/generative/mackelab_pairplot.pdf new file mode 100644 index 0000000..351cae9 Binary files /dev/null and b/results/plots/generative/mackelab_pairplot.pdf differ diff --git a/results/plots/static/getdist_cornerplot.pdf b/results/plots/static/getdist_cornerplot.pdf new file mode 100644 index 0000000..d03e794 Binary files /dev/null and b/results/plots/static/getdist_cornerplot.pdf differ diff --git a/results/plots/static/mackelab_pairplot.pdf b/results/plots/static/mackelab_pairplot.pdf new file mode 100644 index 0000000..d6bcb45 Binary files /dev/null and b/results/plots/static/mackelab_pairplot.pdf differ diff --git a/saveddata/data_train.h5 b/saveddata/data_train.h5 new file mode 100644 index 0000000..ce996c5 Binary files /dev/null and b/saveddata/data_train.h5 differ diff --git a/saveddata/data_validation.h5 b/saveddata/data_validation.h5 new file mode 100644 index 0000000..d227c56 Binary files /dev/null and b/saveddata/data_validation.h5 differ diff --git a/savedmodels/sbi/sbi_linear_from_data.pkl b/savedmodels/sbi/sbi_linear_from_data.pkl new file mode 100644 index 0000000..4b0b298 Binary files /dev/null and b/savedmodels/sbi/sbi_linear_from_data.pkl differ diff --git a/savedmodels/sbi/sbi_linear_generative.pkl b/savedmodels/sbi/sbi_linear_generative.pkl new file mode 100644 index 0000000..667baf9 Binary files /dev/null and b/savedmodels/sbi/sbi_linear_generative.pkl differ diff --git a/showyourwork.yml b/showyourwork.yml deleted file mode 100644 index 206454e..0000000 --- a/showyourwork.yml +++ /dev/null @@ -1,7 +0,0 @@ -version: 0.3.0 - -overleaf: - id: 62defbc43013ada57aa4c153 - push: - - src/tex/figures - - src/tex/output \ No newline at end of file diff --git a/Snakefile b/src/client/__init__.py similarity index 100% rename from Snakefile rename to src/client/__init__.py diff --git a/src/client/client.py b/src/client/client.py new file mode 100644 index 0000000..be486f1 --- /dev/null +++ b/src/client/client.py @@ -0,0 +1,79 @@ +import os +import yaml +from argparse import ArgumentParser + +from utils.config import Config +from utils.defaults import Defaults +from data import DataModules +from models import ModelModules +from metrics import Metrics +from plots import Plots + + +def parser(): + parser = ArgumentParser() + parser.add_argument("--config", '-c', default=None) + + # Model + parser.add_argument("--model_path", '-m', default=None) + parser.add_argument("--model_engine", '-e', default=Defaults['model']['model_engine'], choices=ModelModules.keys()) + + # Data + parser.add_argument("--data_path", '-d', default=None) + parser.add_argument("--data_engine", '-g', default=Defaults['data']['data_engine'], choices=DataModules.keys()) + parser.add_argument("--simulator", '-s', default=None) + # Common + parser.add_argument("--out_dir", default=Defaults['common']['out_dir']) + + # List of metrics (cannot supply specific kwargs) + parser.add_argument("--metrics", nargs='+', default=list(Defaults['metrics'].keys()), choices=Metrics.keys()) + + # List of plots + parser.add_argument("--plots", nargs='+', default=list(Defaults['plots'].keys()), choices=Plots.keys()) + + + args = parser.parse_args() + if args.config is not None: + config = Config(args.config) + + else: + temp_config = Defaults['common']['temp_config'] + os.makedirs(os.path.dirname(temp_config), exist_ok=True) + + input_yaml = { + "common": {"out_dir":args.out_dir}, + "model": {"model_path":args.model_path, "model_engine":args.model_engine}, + "data": {"data_path":args.data_path, "data_engine":args.data_engine, "simulator": args.simulator}, + "plots": {key: {} for key in args.plots}, + "metrics": {key: {} for key in args.metrics}, + } + + yaml.dump(input_yaml, open(temp_config, "w")) + config = Config(temp_config) + + return config + +def main(): + config = parser() + + model_path = config.get_item("model", "model_path") + model_engine = config.get_item("model", "model_engine", raise_exception=False) + model = ModelModules[model_engine](model_path) + + data_path = config.get_item("data", "data_path") + data_engine = config.get_item("data", "data_engine", raise_exception=False) + simulator_name = config.get_item("data", "simulator") + data = DataModules[data_engine](data_path, simulator_name) + + out_dir = config.get_item("common", "out_dir", raise_exception=False) + if not os.path.exists(os.path.dirname(out_dir)): + os.makedirs(os.path.dirname(out_dir)) + + metrics = config.get_section("metrics", raise_exception=False) + plots = config.get_section("plots", raise_exception=False) + + for metrics_name, metrics_args in metrics.items(): + Metrics[metrics_name](model, data, **metrics_args)() + + for plot_name, plot_args in plots.items(): + Plots[plot_name](model, data, save=True, show=False, out_dir=out_dir)(**plot_args) \ No newline at end of file diff --git a/src/data/__init__.py b/src/data/__init__.py new file mode 100644 index 0000000..4517898 --- /dev/null +++ b/src/data/__init__.py @@ -0,0 +1,9 @@ + +from data.h5_data import H5Data +from data.pickle_data import PickleData +from data.simulator import Simulator + +DataModules = { + "H5Data": H5Data, + "PickleData": PickleData +} \ No newline at end of file diff --git a/src/data/data.py b/src/data/data.py new file mode 100644 index 0000000..fbd87fb --- /dev/null +++ b/src/data/data.py @@ -0,0 +1,50 @@ +import importlib.util +import sys +import os + +from utils.config import get_item +from utils.defaults import Defaults + +class Data: + def __init__(self, path:str, simulator_name: str): + self.data = self._load(path) + self.simulator = self._load_simulator(simulator_name) + + def _load_simulator(self, name): + try: + simulator_path = os.environ[f"{Defaults['common']['sim_location']}:{name}"] + except KeyError as e: + raise RuntimeError(f"Simulator cannot be found using env var {e}. Hint: have you registed your simulation with utils.register_simulator?") + + new_class = os.path.dirname(simulator_path) + sys.path.insert(1, new_class) + + # TODO robust error checks + module_name = os.path.basename(simulator_path.rstrip('.py')) + m = importlib.import_module(module_name) + + simulator = getattr(m, name) + return simulator() + + def _load(self, path:str): + raise NotImplementedError + + def x_true(self): + # From Data + raise NotImplementedError + + def y_true(self): + return self.simulator(self.theta_true(), self.x_true()) + + def prior(self): + # From Data + raise NotImplementedError + + def theta_true(self): + return get_item("data", "theta_true") + + def sigma_true(self): + return get_item("data", "sigma_true") + + def save(self, data, path:str): + raise NotImplementedError \ No newline at end of file diff --git a/src/data/h5_data.py b/src/data/h5_data.py new file mode 100644 index 0000000..ffb4a78 --- /dev/null +++ b/src/data/h5_data.py @@ -0,0 +1,30 @@ +from typing import Any, Callable +import h5py +import numpy as np +import torch +import os + +from data.data import Data + +class H5Data(Data): + def __init__(self, path:str, simulator:Callable): + super().__init__(path, simulator) + + def _load(self, path): + assert path.split(".")[-1] == "h5", "File extension must be h5" + loaded_data = {} + with h5py.File(path, "r") as file: + for key in file.keys(): + loaded_data[key] = torch.Tensor(file[key][...]) + return loaded_data + + def save(self, data:dict[str, Any], path: str): # Todo typing for data dict + assert path.split(".")[-1] == "h5", "File extension must be h5" + if not os.path.exists(os.path.dirname(path)): + os.makedirs(os.path.dirname(path)) + + data_arrays = {key: np.asarray(value) for key, value in data.items()} + with h5py.File(path, "w") as file: + # Save each array as a dataset in the HDF5 file + for key, value in data_arrays.items(): + file.create_dataset(key, data=value) \ No newline at end of file diff --git a/src/data/pickle_data.py b/src/data/pickle_data.py new file mode 100644 index 0000000..ee7ef61 --- /dev/null +++ b/src/data/pickle_data.py @@ -0,0 +1,18 @@ +import pickle +from typing import Any, Callable +from data.data import Data + +class PickleData(Data): + def __init__(self, path:str, simulator:Callable): + super().__init__(path, simulator) + + def _load(self, path:str): + assert path.split('.')[-1] == 'pkl', "File extension must be 'pkl'" + with open(path, "rb") as file: + data = pickle.load(file) + return data + + def save(self, data:Any, path:str): + assert path.split('.')[-1] == 'pkl', "File extension must be 'pkl'" + with open(path, "wb") as file: + pickle.dump(data, file) \ No newline at end of file diff --git a/src/data/simulator.py b/src/data/simulator.py new file mode 100644 index 0000000..8fb269a --- /dev/null +++ b/src/data/simulator.py @@ -0,0 +1,10 @@ + +from typing import Any + +class Simulator: + def __init__(self) -> None: + pass + + def __call__(self, *args: Any, **kwds: Any) -> Any: + pass + diff --git a/src/metrics/__init__.py b/src/metrics/__init__.py new file mode 100644 index 0000000..d6206b0 --- /dev/null +++ b/src/metrics/__init__.py @@ -0,0 +1,3 @@ +Metrics = { + +} \ No newline at end of file diff --git a/src/metrics/metric.py b/src/metrics/metric.py new file mode 100644 index 0000000..7639ef5 --- /dev/null +++ b/src/metrics/metric.py @@ -0,0 +1,44 @@ +from typing import Any, Optional +import json +import os + +from data import data +from models import model + +class Metric: + def __init__(self, model:model, data:data, out_dir:Optional[str]=None) -> None: + self.model = model + self.data = data + + self.out_dir = out_dir + self.output = None + + def _collect_data_params(): + raise NotImplementedError + + def _run_model_inference(): + raise NotImplementedError + + def calculate(self): + raise NotImplementedError + + def _finish(self): + assert self.output is not None, "Calculation has not been completed, have you run Metric.calculate?" + + if self.out_dir is not None: + if not os.path.exists(os.path.dirname(self.out_dir)): + os.makedirs(os.path.dirname(self.out_dir)) + + with open(self.out_dir) as f: + data = json.load(f) + data.update(self.output) + json.dump(data, f, ensure_ascii=True) + f.close() + + def __call__(self, *args: Any, **kwds: Any) -> Any: + self._collect_data_params() + self._run_model_inference() + self.calculate() + self._finish() + + \ No newline at end of file diff --git a/src/models/__init__.py b/src/models/__init__.py new file mode 100644 index 0000000..b710af1 --- /dev/null +++ b/src/models/__init__.py @@ -0,0 +1,5 @@ +from models.sbi_model import SBIModel + +ModelModules = { + "SBIModel": SBIModel +} \ No newline at end of file diff --git a/src/models/model.py b/src/models/model.py new file mode 100644 index 0000000..5e75bf7 --- /dev/null +++ b/src/models/model.py @@ -0,0 +1,15 @@ +class Model: + def __init__(self, model_path:str) -> None: + self.model = self._load(model_path) + + def _load(self, path:str) -> None: + return NotImplementedError + + def sample_posterior(self): + return NotImplementedError + + def sample_simulation(self, data): + raise NotImplementedError + + def predict_posterior(self, data): + raise NotImplementedError diff --git a/src/models/sbi_model.py b/src/models/sbi_model.py new file mode 100644 index 0000000..866d95e --- /dev/null +++ b/src/models/sbi_model.py @@ -0,0 +1,24 @@ +import os +import pickle + +from models.model import Model + +class SBIModel(Model): + def __init__(self, model_path:str): + super().__init__(model_path) + + def _load(self, path:str) -> None: + assert os.path.exists(path), f"Cannot find model file at location {path}" + assert path.split(".")[-1] == 'pkl', "File extension must be 'pkl'" + + with open(path, "rb") as file: + posterior = pickle.load(file) + self.posterior = posterior + + def sample_posterior(self, n_samples:int, data): # TODO typing + return self.posterior.sample((n_samples,), x=data.y_true) + + def predict_posterior(self, data): + posterior_samples = self.sample_posterior(data.y_true) + posterior_predictive_samples = data.simulator(data.theta_true(), posterior_samples) + return posterior_predictive_samples \ No newline at end of file diff --git a/src/plots/__init__.py b/src/plots/__init__.py new file mode 100644 index 0000000..4810846 --- /dev/null +++ b/src/plots/__init__.py @@ -0,0 +1,7 @@ +from typing import TypeVar +from src.plots.plot import Display + +display = TypeVar("display", Display) +Plots = { + +} \ No newline at end of file diff --git a/src/plots/plot.py b/src/plots/plot.py new file mode 100644 index 0000000..ff385cb --- /dev/null +++ b/src/plots/plot.py @@ -0,0 +1,65 @@ +import os +from typing import Any, Optional +import matplotlib.pyplot as plt +from matplotlib import rcParams + +from src.data import data +from src.models import model + +from src.utils.config import get_item, get_section + +class Display: + def __init__(self, model:model, data:data, save:bool, show:bool, out_path:Optional[str]): + self.save = save + self.show = show + self.out_path = out_path.rstrip("/") + if self.save: + assert self.out_path is not None, "out_path required to save files." + + if not os.path.exists(os.path.dirname(out_path)): + os.makedirs(os.path.dirname(out_path)) + + self.model = model + self._data_setup(data) + self._common_settings() + self._plot_settings() + self.plot_name = self._plot_name() + + def _plot_name(self): + raise NotImplementedError + + def _data_setup(self, data): + # Set all the vars used for the plot + raise NotImplementedError + + def _plot_settings(self): + # TODO Pull fom a config for specific plots + raise NotImplementedError + + def _plot(self, **kwrgs): + # Make the plot object with plt. + raise NotImplementedError + + def _common_settings(self): + plot_common = get_section("plot_common", raise_exception=False) + rcParams["axes.spines.right"] = bool(plot_common['axis_spines']) + rcParams["axes.spines.top"] = bool(plot_common['axis_spines']) + + # Style + self.colorway = plot_common["colorway"] + tight_layout = bool(plot_common['tight_layout']) + if tight_layout: + plt.tight_layout() + plot_style = plot_common['plot_style'] + plt.style.use(plot_style) + + def _finish(self): + assert os.path.splitext(self.plot_name)[-1] != '', f"plot name, {self.plot_name}, is malformed. Please supply a name with an extension." + if self.save: + plt.savefig(f"{self.out_path}/{self.plot_name}") + if self.plot: + plt.show() + + def __call__(self, **kwargs) -> None: + self._plot(**kwargs) + self._finish() \ No newline at end of file diff --git a/src/scripts/evaluate.py b/src/scripts/evaluate.py index 5275656..5ef4553 100644 --- a/src/scripts/evaluate.py +++ b/src/scripts/evaluate.py @@ -34,7 +34,6 @@ def posterior_predictive( y_true = simulator(theta_true, x_true) # also go through and plot one sigma interval # plot the true values - plt.clf() xs_sim = np.linspace(0, 100, 101) ys_sim = np.array(posterior_predictive_samples) plt.fill_between( diff --git a/src/scripts/paths.py b/src/scripts/paths.py deleted file mode 100644 index 939c710..0000000 --- a/src/scripts/paths.py +++ /dev/null @@ -1,30 +0,0 @@ -""" -Exposes common paths useful for manipulating datasets and generating figures. - -""" -from pathlib import Path - -# Absolute path to the top level of the repository -root = Path(__file__).resolve().parents[2].absolute() - -# Absolute path to the `src` folder -src = root / "src" - -# Absolute path to the `src/data` folder (contains datasets) -data = src / "data" - -# Absolute path to the `src/static` folder (contains static images) -static = src / "static" - -# Absolute path to the `src/scripts` folder (contains figure/pipeline scripts) -scripts = src / "scripts" - -# Absolute path to the `src/tex` folder (contains the manuscript) -tex = src / "tex" - -# Absolute path to the `src/tex/figures` folder (contains figure output) -figures = tex / "figures" - -# Absolute path to the `src/tex/output` folder -# (contains other user-defined output) -output = tex / "output" diff --git a/src/scripts/train.py b/src/scripts/train.py deleted file mode 100644 index 3bba349..0000000 --- a/src/scripts/train.py +++ /dev/null @@ -1,47 +0,0 @@ -""" -Simple stubs to use for re-train of the final model -Can leave a default data source, or specify that 'load data' loads the dataset -used in the final version -""" - -import argparse - - -def architecture(): - """ - :return: compiled architecture of the model you want to have trained - """ - return 0 - - -def load_data(data_source): - """ - :return: data loader or full training data, split in val and train - """ - return 0, 0 - - -def train_model(data_source, n_epochs): - """ - :param data_source: - :param n_epochs: - :return: trained model, or simply None, but saved trained model - """ - data = load_data(data_source) - model = architecture() - - return data, model - - -if __name__ == "__main__": - parser = argparse.ArgumentParser() - parser.add_argument("--data_source", type=str, - help="Data used to train the model") - parser.add_argument( - "--n_epochs", type=int, - help="Integer number of epochs to train the model" - ) - - args = parser.parse_args() - - train_model(data_source=args.data_source, n_epochs=args.n_epochs) diff --git a/src/static/.gitignore b/src/static/.gitignore deleted file mode 100644 index e167a34..0000000 --- a/src/static/.gitignore +++ /dev/null @@ -1,2 +0,0 @@ -# Anything is game in this folder -!* diff --git a/src/tex/.gitignore b/src/tex/.gitignore deleted file mode 100644 index 841b7c7..0000000 --- a/src/tex/.gitignore +++ /dev/null @@ -1,2 +0,0 @@ -# Don't track TeX temporaries -*latexindent* \ No newline at end of file diff --git a/src/tex/bib.bib b/src/tex/bib.bib deleted file mode 100644 index 5ca6881..0000000 --- a/src/tex/bib.bib +++ /dev/null @@ -1,37 +0,0 @@ -@article{Hunter:2007, - Author = {Hunter, J. D.}, - Title = {Matplotlib: A 2D graphics environment}, - Journal = {Computing in Science \& Engineering}, - Volume = {9}, - Number = {3}, - Pages = {90--95}, - abstract = {Matplotlib is a 2D graphics package used for Python for - application development, interactive scripting, and publication-quality - image generation across user interfaces and operating systems.}, - publisher = {IEEE COMPUTER SOC}, - doi = {10.1109/MCSE.2007.55}, - year = 2007 - } - -@article{ harris2020array, - title = {Array programming with {NumPy}}, - author = {Charles R. Harris and K. Jarrod Millman and St{\'{e}}fan J. - van der Walt and Ralf Gommers and Pauli Virtanen and David - Cournapeau and Eric Wieser and Julian Taylor and Sebastian - Berg and Nathaniel J. Smith and Robert Kern and Matti Picus - and Stephan Hoyer and Marten H. van Kerkwijk and Matthew - Brett and Allan Haldane and Jaime Fern{\'{a}}ndez del - R{\'{i}}o and Mark Wiebe and Pearu Peterson and Pierre - G{\'{e}}rard-Marchant and Kevin Sheppard and Tyler Reddy and - Warren Weckesser and Hameer Abbasi and Christoph Gohlke and - Travis E. Oliphant}, - year = {2020}, - month = sep, - journal = {Nature}, - volume = {585}, - number = {7825}, - pages = {357--362}, - doi = {10.1038/s41586-020-2649-2}, - publisher = {Springer Science and Business Media {LLC}}, - url = {https://doi.org/10.1038/s41586-020-2649-2} -} \ No newline at end of file diff --git a/src/tex/figures/.gitignore b/src/tex/figures/.gitignore deleted file mode 100644 index 9d0f65c..0000000 --- a/src/tex/figures/.gitignore +++ /dev/null @@ -1,5 +0,0 @@ -# Nothing should be tracked in this folder... -* - -# Except the gitignore file itself! -!.gitignore \ No newline at end of file diff --git a/src/tex/ms.tex b/src/tex/ms.tex deleted file mode 100644 index ad2222b..0000000 --- a/src/tex/ms.tex +++ /dev/null @@ -1,254 +0,0 @@ - -\documentclass[twocolumn]{aastex631} - -% Import showyourwork magic -\usepackage{showyourwork} - -\usepackage[utf8]{inputenc} -\usepackage{amsmath} -\usepackage{unicode-math} - - -% Recommended, but optional, packages for figures and better typesetting: -\usepackage{microtype} -\usepackage{graphicx} -\usepackage{subfigure} -\usepackage{booktabs} % for professional tables -\usepackage{multirow} - -% hyperref makes hyperlinks in the resulting PDF. -% xurl can wrap the link if it spans a column (especially in citations). -\usepackage{hyperref} -\usepackage{xurl} - - -% This command creates a new command \editor{} that highlights any of the text in {} with a maroon color, so it can easily be spotted during internal review - -\usepackage[textsize=tiny]{todonotes} -\newcommand{\editor}[1]{{\color{purple} #1}} - -\begin{document} - -\title{DeepSkies - Template} % Define the title itself, so it may be used in headers - -\author{Author 1 \thanks{Corresponding Author, email@domain.com}} - - -\begin{abstract} - This document is meant to be used as a lose guide. - It includes useful and basic packages and formatting tips to keep you from hunting for formatting code while writing. - Please use this as a reference, and especially while writing without a specific journal already in mind. - This will not be the format all journals accept, so please use their defined style guides when work on your draft. - % Additionally, it's very nice to keep all your sentences on different lines. - % It makes editing a lot easier. -\end{abstract} - -\section{Basic Format and Style} - -\subsection{Format} - -The specific format of the paper if between you and your journal and your editors. -However, it is a good idea to include the basic sections of "Introduction, Methods, Conclusions". - -\subsection{Style} - -Names of coding packages denoted with: \texttt{Package}. - - - -\editor{Here is an quick comment that may appear, indicating an addition by an editor.} - -\subsubsection{Tables} - -Tables should act as summaries, and include error bars when applicable. Captions should draw attention to the main takeaway and can provide analysis, but not necessary give a full summary. -Please view sample table formats in the appendix ~\ref{tab:two_column} - - - - -\subsubsection{Plots and other graphics} - -When making graphics, please keep accessibility in mind. -All plots should be understandable in both black and white and color. -This requires things like using color blind friendly color packages (matplotlib's virdis for example), and changing line and marker styles for different elements of a graph. -Plots also must be clearly labeled and include legends where applicable. -Captions should both describe what the figure contains and its significance. - -When referencing a figure in the main text, please refer to it with \verb|~\ref{figure label}|. -Please view different figure layouts in the appendix ~\ref{fig:single_graphic_figure}. - - - -\subsubsection{Equations} - -Large equations should be numbered and included in an equation block such that -\begin{align} - E=mc^2 \label{eq:1} \\ - F=ma \label{eq:2} -\end{align} - - -Intermediate steps can not include numbers such that -\begin{align*} - A = \pi r^2 -\end{align*} - -Or by using: - -\begin{align} - A - &=B \label{eq:3}\\ - &=B \notag\\ - A - &=BCD \label{eq:4}\\ - &=B \notag -\end{align} - - -Labels are used so that they can be referenced later on using the command \verb|~\ref{eq:equation label}|. Singular symbols can be added into the middle of sentences using \verb|$\symbol$|, such that \verb|\pi| becomes $\pi$. - -\section {Acknowledgements} - -Make sure to cite \cite{harris2020array} all of your sources \cite{Hunter:2007}. - - -You can also optionally provide contributions by person: - -\paragraph{Author 1} -Author 1 contributed X Y and Z - -\paragraph{Author 2} -Author 2 contributed A B and C - -If you work with the DeepSkies research group; please include the following text: - -\emph{We acknowledge the Deep Skies Lab as a community of multi-domain experts and collaborators who’ve facilitated an environment of open discussion, idea-generation, and collaboration. This community was important for the development of this project.} - - -%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -% bibliography -%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% - - -% Style of the bib may change based on the publications requirements - -\bibliography{bib} - - - % Ending the multicol format before the appendix - -%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -% APPENDIX -%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -\newpage -\appendix -\section{Appendix} -You may include an appendix, it contains extra tables not required to understand the main body, but helpful references. - -\subsection{Figure References} -\begin{figure}[h] - \centering - \includegraphics[scale=.1] - {figures/frog.jpg} - \caption{ - This is a figure (containing a cute, although not colorblind friendly, frog) with a single graphic. - Because the original image is very large, it is resized with a smaller scale. - } - \label{fig:single_graphic_figure} -\end{figure} - - -\begin{figure}[h] - \begin{center} - \begin{minipage}{.35\linewidth} - \includegraphics[width=\linewidth]{figures/frog2.jpg} - - \caption{An example of using minipage to caption each image in a combined figure separately.} - \end{minipage}\hfill - - \begin{minipage}{.35\linewidth} - \includegraphics[width=\linewidth]{figures/frog3.jpg} - - \caption{This frog has it's own caption, so they can be referred to separately If you were heartless enough to separate them.} - \end{minipage} - \label{multifigAB} - - \end{center} - -\end{figure} - -% Todo Example of running show your work function within the tex to produce table - -\subsection{Table References} - -\begin{figure}[h] - \centering - \mbox{\subfigure{\includegraphics[width=.35\linewidth]{figures/frog2.jpg}}\quad - \subfigure{\includegraphics[width=.35\linewidth]{figures/frog3.jpg} }} - \caption{An example showing two images with a shared caption using subfigure. Now the frogs cannot be separated.} - \label{fig:multifigC} -\end{figure} - -\begin{table}[h] - \centering - \caption{Sample table with two columns and a header, with the caption placed on top.} - \label{tab:two_column} - \vspace{.2in} - \begin{tabular}{c | c} - \toprule - Header 1 & Header 2 \\ - \midrule - Entry 1 & 0 $\pm$ 0.001 \\ - Entry 2 & 1 $\pm$ 0.001 \\ - Entry 3 & 2 $\pm$ 0.001 \\ - \bottomrule - \end{tabular} -\end{table} - -\begin{table}[h] - \centering - \caption{A Table displaying multi-rows. Horizontal lines can be removed, but tend to lead to confusing tables.} - \vspace{.2in} - \label{tab:multirow} - \begin{tabular}{c|c|c} - - \toprule - Header 1 & Header 2 & Header 3 \\ - \midrule - - \multirow{2}*{Multi-Row} - & Row 1 & Row 1 \\ - \cline{2-3} % \cline{n_rows-n_columns} - & Row 2 & Row 2 \\ - - - \hline - Single-Row & Row 3 & Row 3\\ - \bottomrule - \end{tabular} - -\end{table} - -\begin{table}[h] - \centering - \caption{A Table with multiple columns.} - \label{tab:multicol} - \vspace{.2in} - - \begin{tabular}{c|c|c} - \toprule - \multicolumn{2}{c|}{Multi-Column} & Column 3 \\ - \midrule - Column 1 & Column 2 & Column 3 \\ - Column 1 & Column 2 & Column 3 \\ - \bottomrule - \end{tabular} -\end{table} - -% Todo: Show your work table drawing results from a function - -\end{document} diff --git a/src/tex/output/.gitignore b/src/tex/output/.gitignore deleted file mode 100644 index 9d0f65c..0000000 --- a/src/tex/output/.gitignore +++ /dev/null @@ -1,5 +0,0 @@ -# Nothing should be tracked in this folder... -* - -# Except the gitignore file itself! -!.gitignore \ No newline at end of file diff --git a/src/tex/showyourwork.sty b/src/tex/showyourwork.sty deleted file mode 100644 index 8432d72..0000000 --- a/src/tex/showyourwork.sty +++ /dev/null @@ -1,13 +0,0 @@ -\NeedsTeXFormat{LaTeX2e} -\ProvidesPackage{showyourwork}[2022/01/12 Open source science articles] - -\IfFileExists{./showyourwork.tex}{ - \input{showyourwork.tex} -}{ - \newcommand\GitHubURL{} - \newcommand\GitHubSHA{} - \newcommand\GitHubIcon{} - \newcommand\showyourwork{} - \newcommand\script[1]{} - \newcommand\variable[1]{} -} \ No newline at end of file diff --git a/src/utils/__init__.py b/src/utils/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/src/utils/config.py b/src/utils/config.py new file mode 100644 index 0000000..6a13cf3 --- /dev/null +++ b/src/utils/config.py @@ -0,0 +1,58 @@ + +from typing import Optional +import os +import yaml + +from utils.defaults import Defaults + +def get_item(section, item, raise_exception=True): + return Config().get_item(section, item, raise_exception) + +def get_section(section, raise_exception=True): + return Config().get_section(section, raise_exception) + + +class Config: + ENV_VAR_PATH = "DeepDiagnostics_Config" + def __init__(self, config_path:Optional[str]) -> None: + if config_path is not None: + # Add it to the env vars in case we need to get it later. + os.environ[self.ENV_VAR_PATH] = config_path + else: + # Get it from the env vars + try: + config_path = os.environ[self.ENV_VAR_PATH] + except KeyError: + assert False, "Cannot load config from enviroment. Hint: Have you set the config path by pasing a str path to Config?" + + self.config = self._read_config(config_path) + self._validate_config() + + def _validate_config(self): + # Validate common + # TODO + pass + + def _read_config(self, path): + assert os.path.exists(path), f"Config path at {path} does not exist." + with open(path, 'r') as f: + config = yaml.safe_load(f) + return config + + def get_item(self, section, item, raise_exception=True): + try: + return self.config[section][item] + except KeyError as e: + if raise_exception: + raise KeyError(f"Configuration File missing parameter {e}") + else: + return Defaults[section][item] + + def get_section(self, section, raise_exception=True): + try: + return self.config[section] + except KeyError as e: + if raise_exception: + raise KeyError(e) + else: + return Defaults[section] \ No newline at end of file diff --git a/src/utils/defaults.py b/src/utils/defaults.py new file mode 100644 index 0000000..e251dd8 --- /dev/null +++ b/src/utils/defaults.py @@ -0,0 +1,28 @@ +Defaults = { + "common":{ + "out_dir":"./DeepDiagonisticsResources/results/", + "temp_config": "./DeepDiagonisticsResources/temp/temp_config.yml", + "sim_location": "DeepDiagonisticsResources_Simulators" + }, + "model": { + "model_engine": "SBIModel" + }, + "data":{ + "data_engine": "H5Data" + }, + "plot_common": { + "axis_spines": False, + "tight_layout": True, + "colorway": "virdids", + "plot_style": "fast" + }, + "plots":{ + "type_of_plot":{"specific_kwargs"} + }, + "metric_common": { + + }, + "metrics":{ + "type_of_metrics":{"specific_kwargs"} + } +} \ No newline at end of file diff --git a/src/utils/register.py b/src/utils/register.py new file mode 100644 index 0000000..1800454 --- /dev/null +++ b/src/utils/register.py @@ -0,0 +1,10 @@ +import os +import inspect + +from utils.defaults import Defaults + +def register_simulator(simulator_name, simulator): + simulator_prefix = Defaults['common']['sim_location'] + env_var_name = f"{simulator_prefix}:{simulator_name}" + simulator_location = os.path.abspath(inspect.getfile(simulator)) + os.environ[env_var_name] = simulator_location \ No newline at end of file diff --git a/src/utils/variable_store.py b/src/utils/variable_store.py new file mode 100644 index 0000000..015edff --- /dev/null +++ b/src/utils/variable_store.py @@ -0,0 +1,12 @@ +class Vars: + def __init__(self, session="") -> None: + self.session = {} + + def add_variable(): + pass + + def read_variable(): + pass + + + \ No newline at end of file diff --git a/tests/conftest.py b/tests/conftest.py new file mode 100644 index 0000000..6c8278a --- /dev/null +++ b/tests/conftest.py @@ -0,0 +1,91 @@ +import pytest +import yaml + +from data import H5Data, Simulator +from models import SBIModel +from utils.register import register_simulator + + +class MockSimulator(Simulator): + def __init__(self): + pass + def __call__(self, thetas): + return thetas + + +@pytest.fixture +def model_path(): + return "resources/savedmodels/sbi/sbi_linear_from_data.pkl" + +@pytest.fixture +def data_path(): + return "resources/saveddata/data_validation.h5" + +@pytest.fixture +def simulator_name(): + name = MockSimulator.__name__ + register_simulator(name, MockSimulator) + return name + +@pytest.fixture +def mock_model(model_path): + return SBIModel(model_path) + +@pytest.fixture +def mock_data(data_path, simulator_name): + return H5Data(data_path, simulator_name) + +@pytest.fixture +def config_factory(): + def factory( + out_dir=None, + model_path=None, + model_engine=None, + data_path=None, + data_engine=None, + simulator=None, + plot_settings=None, + metrics_settings=None, + plots=None, + metrics=None +): + config = { "common": {}, "model": {}, "data":{}, "plot_common": {}, "plots":{}, "metric_common": {},"metrics":{}} + + # Single settings + if out_dir is not None: + config["common"]['out_dir'] = out_dir + if model_path is not None: + config['model']['model_path'] = model_path + if model_engine is not None: + config['model']['model_engine'] = model_engine + if data_path is not None: + config['data']['data_path'] = data_path + if data_engine is not None: + config['data']['data_engine'] = data_engine + if simulator is not None: + config['data']['simulator'] = simulator + + # Dict settings + if plot_settings is not None: + config['plot_common'] = plot_settings + if metrics_settings is not None: + config['metric_common'] = metrics_settings + + if metrics is not None: + if isinstance(metrics, dict): + config["metrics"] = metrics + if isinstance(metrics, list): + config["metrics"] = {metric: {} for metric in metrics} + + if plots is not None: + if isinstance(plots, dict): + config["plots"] = plots + if isinstance(metrics, list): + config["plots"] = {plot: {} for plot in plots} + + temp_outpath = "./temp_config.yml" + yaml.dump(config, open(temp_outpath, "w")) + + return temp_outpath + + return factory \ No newline at end of file diff --git a/tests/test_client.py b/tests/test_client.py new file mode 100644 index 0000000..03dfe54 --- /dev/null +++ b/tests/test_client.py @@ -0,0 +1,48 @@ +import pytest +import subprocess +import os + +def test_parser_args(model_path, data_path, simulator_name): + command = ["diagnose", + "--model_path", model_path, + "--data_path", data_path, + "--simulator", simulator_name] + process = subprocess.run(command) + exit_code = process.returncode + assert exit_code == 0 + print(process.stdout) + +def test_parser_config(config_factory, model_path, data_path, simulator_name): + config_path = config_factory(model_path=model_path, data_path=data_path, simulator=simulator_name) + command = ["diagnose", f"--config", config_path] + process = subprocess.run(command) + exit_code = process.returncode + assert exit_code == 0 + print(process.stdout) + +def test_main_no_methods(config_factory, model_path, data_path, simulator_name): + out_dir = "./test_out_dir/" + config_path = config_factory(model_path=model_path, data_path=data_path, simulator=simulator_name, plots=[], metrics=[], out_dir=out_dir) + command = ["diagnose", f"--config", config_path] + process = subprocess.run(command) + exit_code = process.returncode + assert exit_code == 0 + print(process.stdout) + + # There should be nothing at the outpath + assert os.listdir(out_dir) == [] + +def test_main_missing_config(): + config_path = "there_is_no_config_at_this_path.yml" + command = ["diagnose", f"--config", config_path] + process = subprocess.run(command) + exit_code = process.returncode + assert exit_code == 1 + print(process.stdout) + +def test_main_missing_args(model_path): + command = ["diagnose", "--model_path", model_path] + process = subprocess.run(command) + exit_code = process.returncode + assert exit_code == 1 + print(process.stdout)