diff stacking_ensembles.py @ 26:ebf295f2faf6 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty

--- a/stacking_ensembles.py	Tue Jul 09 19:28:42 2019 -0400
+++ b/stacking_ensembles.py	Fri Aug 09 07:20:20 2019 -0400
@@ -1,26 +1,17 @@
 import argparse
+import ast
 import json
+import mlxtend.regressor
+import mlxtend.classifier
 import pandas as pd
 import pickle
-import xgboost
+import sklearn
+import sys
 import warnings
-from sklearn import (cluster, compose, decomposition, ensemble,
-                     feature_extraction, feature_selection,
-                     gaussian_process, kernel_approximation, metrics,
-                     model_selection, naive_bayes, neighbors,
-                     pipeline, preprocessing, svm, linear_model,
-                     tree, discriminant_analysis)
-from sklearn.model_selection._split import check_cv
-from feature_selectors import (DyRFE, DyRFECV,
-                               MyPipeline, MyimbPipeline)
-from iraps_classifier import (IRAPSCore, IRAPSClassifier,
-                              BinarizeTargetClassifier,
-                              BinarizeTargetRegressor)
-from preprocessors import Z_RandomOverSampler
-from utils import load_model, get_cv, get_estimator, get_search_params
+from sklearn import ensemble
 
-from mlxtend.regressor import StackingCVRegressor, StackingRegressor
-from mlxtend.classifier import StackingCVClassifier, StackingClassifier
+from galaxy_ml.utils import (load_model, get_cv, get_estimator,
+                          get_search_params)
 
 
 warnings.filterwarnings('ignore')
@@ -51,6 +42,8 @@
     with open(inputs_path, 'r') as param_handler:
         params = json.load(param_handler)
 
+    estimator_type = params['algo_selection']['estimator_type']
+    # get base estimators
     base_estimators = []
     for idx, base_file in enumerate(base_paths.split(',')):
         if base_file and base_file != 'None':
@@ -60,14 +53,23 @@
             estimator_json = (params['base_est_builder'][idx]
                               ['estimator_selector'])
             model = get_estimator(estimator_json)
-        base_estimators.append(model)
+
+        if estimator_type.startswith('sklearn'):
+            named = model.__class__.__name__.lower()
+            named = 'base_%d_%s' % (idx, named)
+            base_estimators.append((named, model))
+        else:
+            base_estimators.append(model)
 
-    if meta_path:
-        with open(meta_path, 'rb') as f:
-            meta_estimator = load_model(f)
-    else:
-        estimator_json = params['meta_estimator']['estimator_selector']
-        meta_estimator = get_estimator(estimator_json)
+    # get meta estimator, if applicable
+    if estimator_type.startswith('mlxtend'):
+        if meta_path:
+            with open(meta_path, 'rb') as f:
+                meta_estimator = load_model(f)
+        else:
+            estimator_json = (params['algo_selection']
+                              ['meta_estimator']['estimator_selector'])
+            meta_estimator = get_estimator(estimator_json)
 
     options = params['algo_selection']['options']
 
@@ -78,26 +80,26 @@
         # set n_jobs
         options['n_jobs'] = N_JOBS
 
-    if params['algo_selection']['estimator_type'] == 'StackingCVClassifier':
-        ensemble_estimator = StackingCVClassifier(
+    weights = options.pop('weights', None)
+    if weights:
+        options['weights'] = ast.literal_eval(weights)
+
+    mod_and_name = estimator_type.split('_')
+    mod = sys.modules[mod_and_name[0]]
+    klass = getattr(mod, mod_and_name[1])
+
+    if estimator_type.startswith('sklearn'):
+        options['n_jobs'] = N_JOBS
+        ensemble_estimator = klass(base_estimators, **options)
+
+    elif mod == mlxtend.classifier:
+        ensemble_estimator = klass(
             classifiers=base_estimators,
             meta_classifier=meta_estimator,
             **options)
 
-    elif params['algo_selection']['estimator_type'] == 'StackingClassifier':
-        ensemble_estimator = StackingClassifier(
-            classifiers=base_estimators,
-            meta_classifier=meta_estimator,
-            **options)
-
-    elif params['algo_selection']['estimator_type'] == 'StackingCVRegressor':
-        ensemble_estimator = StackingCVRegressor(
-            regressors=base_estimators,
-            meta_regressor=meta_estimator,
-            **options)
-
     else:
-        ensemble_estimator = StackingRegressor(
+        ensemble_estimator = klass(
             regressors=base_estimators,
             meta_regressor=meta_estimator,
             **options)