diff --git a/Exareme-Docker/Dockerfile b/Exareme-Docker/Dockerfile index f36cd5db3..645702d45 100644 --- a/Exareme-Docker/Dockerfile +++ b/Exareme-Docker/Dockerfile @@ -34,6 +34,7 @@ RUN pip install pathlib RUN pip install tqdm RUN pip install colour RUN pip install tornado +RUN pip install statsmodels==0.10.2 # Installing R RUN apt install -y software-properties-common diff --git a/Exareme-Docker/src/mip-algorithms/ANOVA/properties.json b/Exareme-Docker/src/mip-algorithms/ANOVA/properties.json index 3d7fd140b..7dc79b5e1 100644 --- a/Exareme-Docker/src/mip-algorithms/ANOVA/properties.json +++ b/Exareme-Docker/src/mip-algorithms/ANOVA/properties.json @@ -1,7 +1,7 @@ { "name": "ANOVA", "desc": "Two-way analysis of variance (ANOVA)", - "label": "ANOVA", + "label": "Two-way ANOVA", "type": "iterative", "parameters": [{ "name": "x", diff --git a/Exareme-Docker/src/mip-algorithms/ANOVA_ONEWAY/__init__.py b/Exareme-Docker/src/mip-algorithms/ANOVA_ONEWAY/__init__.py new file mode 100644 index 000000000..2088f28a8 --- /dev/null +++ b/Exareme-Docker/src/mip-algorithms/ANOVA_ONEWAY/__init__.py @@ -0,0 +1,3 @@ +from .anova import Anova + +__all__ = ["Anova"] diff --git a/Exareme-Docker/src/mip-algorithms/ANOVA_ONEWAY/anova.py b/Exareme-Docker/src/mip-algorithms/ANOVA_ONEWAY/anova.py new file mode 100644 index 000000000..3d06a6121 --- /dev/null +++ b/Exareme-Docker/src/mip-algorithms/ANOVA_ONEWAY/anova.py @@ -0,0 +1,327 @@ +from __future__ import division +from __future__ import print_function +from __future__ import unicode_literals + +import itertools + +import numpy as np +import pandas as pd +import scipy.stats +from statsmodels.stats.libqsturng import psturng + +from mipframework import Algorithm +from mipframework import AlgorithmResult +from mipframework import TabularDataResource +from mipframework.highcharts import LineWithErrorbars +from utils.algorithm_utils import ExaremeError + + +class Anova(Algorithm): + def __init__(self, cli_args): + super(Anova, self).__init__(__file__, cli_args, intercept=False) + + def local_(self): + X = self.data.full + variable = self.parameters.y[0] + covariable = self.parameters.x[0] + var_label = self.metadata.label[variable] + covar_label = self.metadata.label[covariable] + covar_enums = self.metadata.enumerations[covariable] + + model = AdditiveAnovaModel(X, variable, covariable) + + self.push_and_add(model=model) + self.push_and_agree(var_label=var_label) + self.push_and_agree(covar_label=covar_label) + self.push_and_agree(covar_enums=covar_enums) + + def global_(self): + model = self.fetch("model") + var_label = self.fetch("var_label") + covar_label = self.fetch("covar_label") + covar_enums = self.fetch("covar_enums") + + if len(model.group_stats) < 2: + raise ExaremeError("Cannot perform Anova when there is only one level") + + res = model.get_anova_table() + + anova_table = TabularDataResource( + fields=["", "df", "sum sq", "mean sq", "F value", "Pr(>F)"], + data=[ + [ + covar_label, + res["df_explained"], + res["ss_explained"], + res["ms_explained"], + res["f_stat"], + res["p_value"], + ], + [ + "Residual", + res["df_residual"], + res["ss_residual"], + res["ms_residual"], + None, + None, + ], + ], + title="Anova Summary", + ) + + tukey_data = pairwise_tuckey(model, covar_enums) + tukey_hsd_table = TabularDataResource( + fields=list(tukey_data.columns), + data=list([list(row) for row in tukey_data.values]), + title="Tuckey Honest Significant Differences", + ) + tukey_dict = tukey_table_to_dict(tukey_data) + + mean_plot = create_mean_plot( + model.group_stats, var_label, covar_label, covar_enums + ) + + self.result = AlgorithmResult( + raw_data={"anova_table": res, "tukey_table": tukey_dict}, + tables=[anova_table, tukey_hsd_table], + highcharts=[mean_plot], + ) + + +class AdditiveAnovaModel(object): + def __init__(self, X=None, variable=None, covariable=None): + self._table = None + if X is not None and variable and covariable: + self.variable = variable + self.covariable = covariable + self.var_sq = variable + "_sq" + X[self.var_sq] = X[variable] ** 2 + + self.n_obs = X.shape[0] + + self.overall_stats = self.get_overall_stats(X) + + self.group_stats = self.get_group_stats(X) + + def __add__(self, other): + result = AdditiveAnovaModel() + + assert self.variable == other.variable, "variable names do not agree" + result.variable = self.variable + + assert self.covariable == other.covariable, "covariable names do not agree" + result.covariable = self.covariable + + result.n_obs = self.n_obs + other.n_obs + + result.overall_stats = self.overall_stats + other.overall_stats + + result.group_stats = self.group_stats.add(other.group_stats, fill_value=0) + + return result + + def get_overall_stats(self, X): + variable = self.variable + var_sq = self.var_sq + overall_stats = X[variable].agg(["count", "sum"]) + overall_ssq = X[var_sq].sum() + overall_stats = overall_stats.append( + pd.Series(data=overall_ssq, index=["sum_sq"]) + ) + return overall_stats + + def get_group_stats(self, X): + variable = self.variable + covar = self.covariable + var_sq = self.var_sq + group_stats = X[[variable, covar]].groupby(covar).agg(["count", "sum"]) + group_stats.columns = ["count", "sum"] + group_ssq = X[[var_sq, covar]].groupby(covar).sum() + group_ssq.columns = ["sum_sq"] + group_stats = group_stats.join(group_ssq) + return group_stats + + def get_df_explained(self): + return len(self.group_stats) - 1 + + def get_df_residual(self): + return self.n_obs - len(self.group_stats) + + def get_ss_residual(self): + overall_sum_sq = self.overall_stats["sum_sq"] + group_sum = self.group_stats["sum"] + group_count = self.group_stats["count"] + return overall_sum_sq - sum(group_sum ** 2 / group_count) + + def get_ss_total(self): + overall_sum_sq = self.overall_stats["sum_sq"] + overall_sum = self.overall_stats["sum"] + overall_count = self.overall_stats["count"] + return overall_sum_sq - (overall_sum ** 2 / overall_count) + + def get_ss_explained(self): + group_sum = self.group_stats["sum"] + group_count = self.group_stats["count"] + return sum((self.overall_mean - group_sum / group_count) ** 2 * group_count) + + def get_anova_table(self): + df_explained = self.get_df_explained() + df_residual = self.get_df_residual() + ss_explained = self.get_ss_explained() + ss_residual = self.get_ss_residual() + ms_explained = ss_explained / df_explained + ms_residual = ss_residual / df_residual + f_stat = ms_explained / ms_residual + p_value = 1 - scipy.stats.f.cdf(f_stat, df_explained, df_residual) + return dict( + df_explained=df_explained, + df_residual=df_residual, + ss_explained=ss_explained, + ss_residual=ss_residual, + ms_explained=ms_explained, + ms_residual=ms_residual, + f_stat=f_stat, + p_value=p_value, + ) + + @property + def table(self): + if self._table is None: + table = pd.DataFrame( + columns=["df", "sum_sq", "mean_sq", "F", "PR(>F)"], + index=[self.covariable, "Residual"], + ) + df_explained = self.get_df_explained() + df_residual = self.get_df_residual() + ss_explained = self.get_ss_explained() + ss_residual = self.get_ss_residual() + ms_explained = ss_explained / df_explained + ms_residual = ss_residual / df_residual + f_stat = ms_explained / ms_residual + p_value = 1 - scipy.stats.f.cdf(f_stat, df_explained, df_residual) + table.loc[self.covariable] = { + "df": df_explained, + "sum_sq": ss_explained, + "mean_sq": ms_explained, + "F": f_stat, + "PR(>F)": p_value, + } + table.loc["Residual"] = { + "df": df_residual, + "sum_sq": ss_residual, + "mean_sq": ms_residual, + "F": None, + "PR(>F)": None, + } + self._table = table + return table + + return self._table + + @property + def overall_mean(self): + return self.overall_stats["sum"] / self.overall_stats["count"] + + def to_dict(self): # useful for debugging + dd = { + "variable": self.variable, + "covariable": self.covariable, + "n_obs": self.n_obs, + "overall_stats": self.overall_stats.tolist(), + "group_stats": self.group_stats.values.tolist(), + } + return dd + + +def create_mean_plot(group_stats, variable, covariable, categories): + title = "Means plot: {v} ~ {c}".format(v=variable, c=covariable) + means = group_stats["sum"] / group_stats["count"] + variances = group_stats["sum_sq"] / group_stats["count"] - means ** 2 + sample_vars = (group_stats["count"] - 1) / group_stats["count"] * variances + sample_stds = np.sqrt(sample_vars) + + categories = [c for c in categories if c in group_stats.index] + means = [means[cat] for cat in categories] + sample_stds = [sample_stds[cat] for cat in categories] + data = [[m - s, m, m + s] for m, s in zip(means, sample_stds)] + return LineWithErrorbars( + title=title, + data=data, + categories=categories, + xname=covariable, + yname="95% CI: " + variable, + ) + + +def pairwise_tuckey(aov, categories): + categories = np.array(aov.group_stats.index) + n_groups = len(categories) + gnobs = aov.group_stats["count"].to_numpy() + gmeans = (aov.group_stats["sum"] / aov.group_stats["count"]).to_numpy() + gvar = aov.table.at["Residual", "mean_sq"] / gnobs + g1, g2 = np.array(list(itertools.combinations(np.arange(n_groups), 2))).T + mn = gmeans[g1] - gmeans[g2] + se = np.sqrt(gvar[g1] + gvar[g2]) + tval = mn / se + df = aov.table.at["Residual", "df"] + pval = psturng(np.sqrt(2) * np.abs(tval), n_groups, df) + thsd = pd.DataFrame( + columns=[ + "A", + "B", + "mean(A)", + "mean(B)", + "diff", + "Std.Err.", + "t value", + "Pr(>|t|)", + ], + index=range(n_groups * (n_groups - 1) // 2), + ) + thsd["A"] = categories[g1] + thsd["B"] = categories[g2] + thsd["mean(A)"] = gmeans[g1] + thsd["mean(B)"] = gmeans[g2] + thsd["diff"] = mn + thsd["Std.Err."] = se + thsd["t value"] = tval + thsd["Pr(>|t|)"] = pval + return thsd + + +def tukey_table_to_dict(table): + tukey_dict = [] + for _, row in table.iterrows(): + tukey_row = dict() + tukey_row["groupA"] = row["A"] + tukey_row["groupB"] = row["B"] + tukey_row["meanA"] = row["mean(A)"] + tukey_row["meanB"] = row["mean(B)"] + tukey_row["diff"] = row["diff"] + tukey_row["se"] = row["Std.Err."] + tukey_row["t_stat"] = row["t value"] + tukey_row["p_tukey"] = row["Pr(>|t|)"] + tukey_dict.append(tukey_row) + return tukey_dict + + +if __name__ == "__main__": + import time + from mipframework import create_runner + + algorithm_args = [ + "-y", + "rightmprgprecentralgyrusmedialsegment", + "-x", + "alzheimerbroadcategory", + "-pathology", + "dementia", + "-dataset", + "ppmi,adni", + "-filter", + "", + ] + runner = create_runner(Anova, algorithm_args=algorithm_args, num_workers=3,) + start = time.time() + runner.run() + end = time.time() diff --git a/Exareme-Docker/src/mip-algorithms/ANOVA_ONEWAY/generate_tescases_anova.py b/Exareme-Docker/src/mip-algorithms/ANOVA_ONEWAY/generate_tescases_anova.py new file mode 100644 index 000000000..a83c88ccc --- /dev/null +++ b/Exareme-Docker/src/mip-algorithms/ANOVA_ONEWAY/generate_tescases_anova.py @@ -0,0 +1,84 @@ +# XXX this module runs on python 3.9 because we need pingouin to calculate +# Tukey table. + +from pathlib import Path + +import numpy as np +from pingouin import pairwise_tukey +import statsmodels.api as sm +from statsmodels.formula.api import ols +from statsmodels.stats.libqsturng import psturng + +from mipframework.algorithmtest import AlgorithmTest +from mipframework.exceptions import PrivacyError +from utils.algorithm_utils import PRIVACY_MAGIC_NUMBER + + +class AnovaTest(AlgorithmTest): + def get_expected(self, alg_input): + # Get data and remove missing values + x_names = alg_input[0]["value"] + y_names = alg_input[1]["value"] + datasets = alg_input[3]["value"] + variables = y_names + if x_names != "": + variables += "," + x_names + try: + data = self.get_data(variables, datasets) + except PrivacyError: + return None + data = data.dropna() + n_obs = len(data) + n_groups = len(set(data[x_names])) + + # If n_obs < n_cols reject + if n_obs <= PRIVACY_MAGIC_NUMBER: + return None + if data[x_names].unique().shape[0] < 2: + return None + + # Anova + formula = "{y} ~ {x}".format(y=y_names, x=x_names) + lm = ols(formula, data=data).fit() + aov = sm.stats.anova_lm(lm) + result = aov.to_dict() + + # # Tukey test + tukey = pairwise_tukey(data=data, dv=y_names, between=x_names) + tukey_results = [] + for _, row in tukey.iterrows(): + tukey_result = dict() + tukey_result["groupA"] = row["A"] + tukey_result["groupB"] = row["B"] + tukey_result["meanA"] = row["mean(A)"] + tukey_result["meanB"] = row["mean(B)"] + tukey_result["diff"] = row["diff"] + tukey_result["se"] = row["se"] + tukey_result["t_stat"] = row["T"] + # computing pval because pingouin and statsmodels implementations + # of pstrung do not agree + pval = psturng( + np.sqrt(2) * np.abs(row["T"]), n_groups, result["df"]["Residual"] + ) + tukey_result["p_tukey"] = float(pval) + tukey_results.append(tukey_result) + + expected_out = dict() + expected_out["df_residual"] = result["df"]["Residual"] + expected_out["df_explained"] = result["df"][x_names] + expected_out["ss_residual"] = result["sum_sq"]["Residual"] + expected_out["ss_explained"] = result["sum_sq"][x_names] + expected_out["ms_residual"] = result["mean_sq"]["Residual"] + expected_out["ms_explained"] = result["mean_sq"][x_names] + expected_out["p_value"] = result["PR(>F)"][x_names] + expected_out["f_stat"] = result["F"][x_names] + expected_out["tukey_test"] = tukey_results + + return expected_out + + +if __name__ == "__main__": + prop_path = dbs_folder = Path(__file__).parent / "properties.json" + algtest = AnovaTest(prop_path.as_posix()) + algtest.generate_test_cases(num_tests=100) + algtest.to_json("anova_expected.json") diff --git a/Exareme-Docker/src/mip-algorithms/ANOVA_ONEWAY/global.py b/Exareme-Docker/src/mip-algorithms/ANOVA_ONEWAY/global.py new file mode 100644 index 000000000..e21a8753f --- /dev/null +++ b/Exareme-Docker/src/mip-algorithms/ANOVA_ONEWAY/global.py @@ -0,0 +1,10 @@ +import sys +from anova import Anova + + +def main(args): + Anova(args[1:]).global_() + + +if __name__ == "__main__": + Anova(sys.argv[1:]).global_() diff --git a/Exareme-Docker/src/mip-algorithms/ANOVA_ONEWAY/local.py b/Exareme-Docker/src/mip-algorithms/ANOVA_ONEWAY/local.py new file mode 100644 index 000000000..3bfefe58b --- /dev/null +++ b/Exareme-Docker/src/mip-algorithms/ANOVA_ONEWAY/local.py @@ -0,0 +1,10 @@ +import sys +from anova import Anova + + +def main(args): + Anova(args[1:]).local_() + + +if __name__ == "__main__": + Anova(sys.argv[1:]).local_() diff --git a/Exareme-Docker/src/mip-algorithms/ANOVA_ONEWAY/properties.json b/Exareme-Docker/src/mip-algorithms/ANOVA_ONEWAY/properties.json new file mode 100644 index 000000000..467517d20 --- /dev/null +++ b/Exareme-Docker/src/mip-algorithms/ANOVA_ONEWAY/properties.json @@ -0,0 +1,60 @@ +{ + "name": "ANOVA_ONEWAY", + "desc": "One-way analysis of variance (ANOVA)", + "label": "One-way ANOVA", + "type": "python_local_global", + "parameters": [{ + "name": "x", + "label": "x", + "desc": "A categorical variable on whose levels we perform the Anova.", + "type": "column", + "columnValuesSQLType": "", + "columnValuesIsCategorical": "true", + "columnValuesNumOfEnumerations": "", + "value": "ppmicategory", + "valueNotBlank": true, + "valueMultiple": false, + "valueType": "string" + }, { + "name": "y", + "label": "y", + "desc": "A numerical response variable.", + "type": "column", + "columnValuesSQLType": "real,integer", + "columnValuesIsCategorical": "false", + "columnValuesNumOfEnumerations": "", + "value": "lefthippocampus", + "valueNotBlank": true, + "valueMultiple": false, + "valueType": "string" + }, { + "name": "pathology", + "label": "pathology", + "desc": "The name of the pathology in which the dataset belongs to.", + "type": "pathology", + "value": "dementia", + "valueNotBlank": true, + "valueMultiple": false, + "valueType": "string" + }, { + "name": "dataset", + "label": "dataset", + "desc": "The names of one or more datasets, in which the algorithm will be executed.", + "type": "dataset", + "value": "ppmi", + "valueNotBlank": true, + "valueMultiple": true, + "valueType": "string" + }, { + "name": "filter", + "label": "filter", + "desc": "", + "type": "filter", + "value": "", + "valueNotBlank": false, + "valueMultiple": true, + "valueType": "string" + } + ] +} + diff --git a/Exareme-Docker/src/mip-algorithms/mipframework/hichart_server/app.py b/Exareme-Docker/src/mip-algorithms/mipframework/hichart_server/app.py index e34a24417..e571b5545 100644 --- a/Exareme-Docker/src/mip-algorithms/mipframework/hichart_server/app.py +++ b/Exareme-Docker/src/mip-algorithms/mipframework/hichart_server/app.py @@ -7,6 +7,7 @@ from LOGISTIC_REGRESSION import LogisticRegression from CALIBRATION_BELT import CalibrationBelt from KAPLAN_MEIER import KaplanMeier +from ANOVA_ONEWAY import Anova from NAIVE_BAYES import NaiveBayes app = Flask(__name__) @@ -35,6 +36,7 @@ "title": "Kaplan-Meier Survival Curves", "url": "kaplan_meier_survival", }, + "anova_errorbars": {"title": "Anova Mean Plot", "url": "anova_errorbars"}, "naive_bayes_confusion_matrix": { "title": "NaiveBayes CM", "url": "naive_bayes_confusion_matrix", @@ -51,6 +53,27 @@ def home(): ) +@app.route("/anova_errorbars") +def anova_errorbars(): + anova_args = [ + "-y", + "lefthippocampus", + "-x", + "alzheimerbroadcategory", + "-pathology", + "dementia", + "-dataset", + "adni", + "-filter", + "", + ] + result = get_algorithm_result(Anova, anova_args) + result = result["result"][3]["data"] + return render_template( + "highchart_layout.html", title="Anova Mean Plot", data=result + ) + + @app.route("/pca_scree_eigenvalues") def pca_scree_eigenvalues(): pca_args = [ diff --git a/Exareme-Docker/src/mip-algorithms/mipframework/highcharts/__init__.py b/Exareme-Docker/src/mip-algorithms/mipframework/highcharts/__init__.py index af010916f..8b4ef7ffa 100644 --- a/Exareme-Docker/src/mip-algorithms/mipframework/highcharts/__init__.py +++ b/Exareme-Docker/src/mip-algorithms/mipframework/highcharts/__init__.py @@ -5,6 +5,7 @@ ScreePlot, CalibrationBeltPlot, SurvivalCurves, + LineWithErrorbars, MultilabelConfisionMatrix, MulticlassROCCurve, ) @@ -16,6 +17,7 @@ "ScreePlot", "CalibrationBeltPlot", "SurvivalCurves", + "LineWithErrorbars", "MultilabelConfisionMatrix", "MulticlassROCCurve", ] diff --git a/Exareme-Docker/src/mip-algorithms/mipframework/highcharts/user_defined.py b/Exareme-Docker/src/mip-algorithms/mipframework/highcharts/user_defined.py index 97d4dc766..ebff1260d 100644 --- a/Exareme-Docker/src/mip-algorithms/mipframework/highcharts/user_defined.py +++ b/Exareme-Docker/src/mip-algorithms/mipframework/highcharts/user_defined.py @@ -1,7 +1,7 @@ from colour import Color -from .core import Heatmap_, Area_, Column_, Bubble_, Line_ +from .core import Heatmap_, Area_, Column_, Bubble_, Line_, Errorbar_ from .core import ( Title, Axis, @@ -494,6 +494,34 @@ def render(self): } +class LineWithErrorbars(HighchartTemplate): + def __init__(self, title, data, categories, xname, yname): + self.chart = ( + Errorbar_(title=Title(text=title)) + .set(xAxis=Axis(categories=categories, title=Title(text=xname))) + .set(yAxis=Axis(title=Title(text=yname))) + .set( + series=RenderableList( + [ + Series( + data=[[p[0], p[2]] for p in data], + type="errorbar", + pointWidth=200, + lineWidth=2, + ), + Series( + data=[p[1] for p in data], + type="line", + color="#0A1E6E", + name="", + ), + ] + ) + ) + .set(legend=Legend(enabled=False)) + ) + + colors_dark = [ "#7cb5ec", "#434348", diff --git a/Exareme-Docker/src/mip-algorithms/mipframework/runner/runner.py b/Exareme-Docker/src/mip-algorithms/mipframework/runner/runner.py index c29a403b4..d1fef37a6 100644 --- a/Exareme-Docker/src/mip-algorithms/mipframework/runner/runner.py +++ b/Exareme-Docker/src/mip-algorithms/mipframework/runner/runner.py @@ -20,6 +20,7 @@ "DescriptiveStats": "local-global", "KaplanMeier": "local-global", "ThreeC": "local", + "Anova": "local-global", "NaiveBayes": "multiple-local-global", "NaiveBayesTrain": "local-global", "GaussianNaiveBayesTrain": "local-global", diff --git a/Exareme-Docker/src/mip-algorithms/tests/algorithm_tests/expected/anova_expected.json b/Exareme-Docker/src/mip-algorithms/tests/algorithm_tests/expected/anova_expected.json new file mode 100644 index 000000000..6e4c3101b --- /dev/null +++ b/Exareme-Docker/src/mip-algorithms/tests/algorithm_tests/expected/anova_expected.json @@ -0,0 +1,6974 @@ +{ + "test_cases": [ + { + "input": [ + { + "name": "x", + "value": "alzheimerbroadcategory" + }, + { + "name": "y", + "value": "rightmprgprecentralgyrusmedialsegment" + }, + { + "name": "pathology", + "value": "dementia" + }, + { + "name": "dataset", + "value": "ppmi,adni" + }, + { + "name": "filter", + "value": "" + } + ], + "output": { + "df_residual": 1777.0, + "df_explained": 2.0, + "ss_residual": 198.9195428117932, + "ss_explained": 3.9913221690837792, + "ms_residual": 0.11194121711412111, + "ms_explained": 1.9956610845418896, + "p_value": 2.1585168508296565e-08, + "f_stat": 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1.5448460127681618, + "p_tukey": 0.27167490456882504 + }, + { + "groupA": "AD", + "groupB": "MCI", + "meanA": 2.0466812765957445, + "meanB": 2.02053552631579, + "diff": 0.026145750279954694, + "se": 0.07001461035947633, + "t_stat": 0.3734327756123251, + "p_tukey": 0.9 + }, + { + "groupA": "CN", + "groupB": "MCI", + "meanA": 1.9576682119205289, + "meanB": 2.02053552631579, + "diff": -0.06286731439526094, + "se": 0.06919788499106946, + "t_stat": -0.9085149698343304, + "p_tukey": 0.6243482531816258 + } + ] + } + } + ] +} \ No newline at end of file diff --git a/Exareme-Docker/src/mip-algorithms/tests/algorithm_tests/test_anova.py b/Exareme-Docker/src/mip-algorithms/tests/algorithm_tests/test_anova.py new file mode 100644 index 000000000..c00eed8e2 --- /dev/null +++ b/Exareme-Docker/src/mip-algorithms/tests/algorithm_tests/test_anova.py @@ -0,0 +1,46 @@ +import pytest +from pathlib import Path +import numpy as np + +from mipframework.testutils import get_test_params, get_algorithm_result +from ANOVA_ONEWAY import Anova + +expected_file = Path(__file__).parent / "expected" / "anova_expected.json" + + +@pytest.mark.parametrize( + "test_input, expected", get_test_params(expected_file, slice(80)) +) +def test_anova_algorithm_local(test_input, expected): + result = get_algorithm_result(Anova, test_input, num_workers=1) + aov = result["anova_table"] + tukey = result["tukey_table"] + e_aov = {k: v for k, v in expected.items() if k != "tukey_test"} + e_tukey = expected["tukey_test"] + assert set(e_aov) == set(aov.keys()) + for key, e_val in e_aov.items(): + r_val = aov[key] + assert np.isclose(e_val, r_val) + for et, rt in zip(e_tukey, tukey): + for key, e_val in et.items(): + r_val = rt[key] + assert e_val == r_val or np.isclose(e_val, r_val) + + +@pytest.mark.parametrize( + "test_input, expected", get_test_params(expected_file, slice(80, 95)) +) +def test_anova_algorithm_federated(test_input, expected): + result = get_algorithm_result(Anova, test_input, num_workers=10) + aov = result["anova_table"] + tukey = result["tukey_table"] + e_aov = {k: v for k, v in expected.items() if k != "tukey_test"} + e_tukey = expected["tukey_test"] + assert set(e_aov) == set(aov.keys()) + for key, e_val in e_aov.items(): + r_val = aov[key] + assert np.isclose(e_val, r_val) + for et, rt in zip(e_tukey, tukey): + for key, e_val in et.items(): + r_val = rt[key] + assert e_val == r_val or np.isclose(e_val, r_val) diff --git a/Exareme-Docker/src/mip-algorithms/tests/exareme_tests/test_privacy.py b/Exareme-Docker/src/mip-algorithms/tests/exareme_tests/test_privacy.py index 39f82f8e6..1872d3547 100644 --- a/Exareme-Docker/src/mip-algorithms/tests/exareme_tests/test_privacy.py +++ b/Exareme-Docker/src/mip-algorithms/tests/exareme_tests/test_privacy.py @@ -32,6 +32,7 @@ url_calibration = vm_url + "CALIBRATION_BELT" url_pearson = vm_url + "PEARSON_CORRELATION" url_logreg = vm_url + "LOGISTIC_REGRESSION" +url_anovaoneway = vm_url + "ANOVA_ONEWAY" def check_privacy_result(result): @@ -59,6 +60,22 @@ def test_ANOVA_Privacy(): check_privacy_result(r.text) +def test_ANOVA_ONEWAY_Privacy(): + logging.info("---------- TEST : Anova Oneway privacy test") + + data = [ + {"name": "x", "value": "alzheimerbroadcategory"}, + {"name": "y", "value": "rightmprgprecentralgyrusmedialsegment"}, + {"name": "pathology", "value": "dementia"}, + {"name": "dataset", "value": "adni_9rows"}, + {"name": "filter", "value": ""}, + ] + + headers = {"Content-type": "application/json", "Accept": "text/plain"} + r = requests.post(url_anovaoneway, data=json.dumps(data), headers=headers) + check_privacy_result(r.text) + + def test_Histogram_Privacy(): logging.info("---------- TEST : Algorithms for Privacy Error") data = [ diff --git a/Exareme-Docker/src/mip-algorithms/tests/integration_tests/test_exareme_integration_anova.py b/Exareme-Docker/src/mip-algorithms/tests/integration_tests/test_exareme_integration_anova.py new file mode 100644 index 000000000..63b052b4a --- /dev/null +++ b/Exareme-Docker/src/mip-algorithms/tests/integration_tests/test_exareme_integration_anova.py @@ -0,0 +1,33 @@ +import json + +import numpy as np +import pytest +import requests +from mipframework.testutils import get_test_params +from tests import vm_url +from tests.algorithm_tests.test_anova import expected_file + +headers = {"Content-type": "application/json", "Accept": "text/plain"} +url = vm_url + "ANOVA_ONEWAY" + + +@pytest.mark.parametrize( + "test_input, expected", get_test_params(expected_file, slice(95, 100)) +) +def test_anovaoneway_algorithm_exareme(test_input, expected): + result = requests.post(url, data=json.dumps(test_input), headers=headers) + result = json.loads(result.text) + result = result["result"][0]["data"] + + aov = result["anova_table"] + tukey = result["tukey_table"] + e_aov = {k: v for k, v in expected.items() if k != "tukey_test"} + e_tukey = expected["tukey_test"] + assert set(e_aov) == set(aov.keys()) + for key, e_val in e_aov.items(): + r_val = aov[key] + assert np.isclose(e_val, r_val) + for et, rt in zip(e_tukey, tukey): + for key, e_val in et.items(): + r_val = rt[key] + assert e_val == r_val or np.isclose(e_val, r_val) diff --git a/requirements.txt b/requirements.txt index 9d1beffb1..5709812ae 100644 --- a/requirements.txt +++ b/requirements.txt @@ -14,4 +14,4 @@ colour requests pytest pytest-xdist - +statsmodels==0.10.2