release v0.9.0

Resolve "release branch / CI on gpu"

Closes #58, #60, #71, #73, #76, #77, #78, #80, #81, #82, #85, #86, #87, #88, #90, #94, #95, #103, and #111

See merge request toar/machinelearningtools!89

.gitignore

@@ -45,9 +45,10 @@ Thumbs.db
 /data/
 /plots/
 
-# tmp folder #
-##############
+# tmp and logging folder #
+##########################
 /tmp/
+/logging/
 
 # test related data #
 #####################

.gitlab-ci.yml

@@ -23,13 +23,71 @@ version:
     paths:
       - badges/
 
+### Tests (from scratch) ###
+tests (from scratch):
+  tags:
+    - base
+    - zam347
+  stage: test
+  only:
+    - master
+    - /^release.*$/
+    - develop
+  variables:
+    FAILURE_THRESHOLD: 100
+    TEST_TYPE: "scratch"
+  before_script:
+    - chmod +x ./CI/update_badge.sh
+    - ./CI/update_badge.sh > /dev/null
+  script:
+    - zypper --non-interactive install binutils libproj-devel gdal-devel
+    - zypper --non-interactive install proj geos-devel
+    - pip install -r requirements.txt
+    - chmod +x ./CI/run_pytest.sh
+    - ./CI/run_pytest.sh
+  after_script:
+    - ./CI/update_badge.sh > /dev/null
+  artifacts:
+    name: pages
+    when: always
+    paths:
+      - badges/
+      - test_results/
+
+### Tests (on GPU) ###
+tests (on GPU):
+  tags:
+    - gpu
+    - zam347
+  stage: test
+  only:
+    - master
+    - /^release.*$/
+    - develop
+  variables:
+    FAILURE_THRESHOLD: 100
+    TEST_TYPE: "gpu"
+  before_script:
+    - chmod +x ./CI/update_badge.sh
+    - ./CI/update_badge.sh > /dev/null
+  script:
+    - pip install -r requirements.txt
+    - chmod +x ./CI/run_pytest.sh
+    - ./CI/run_pytest.sh
+  after_script:
+    - ./CI/update_badge.sh > /dev/null
+  artifacts:
+    name: pages
+    when: always
+    paths:
+      - badges/
+      - test_results/
+
 ### Tests ###
 tests:
   tags:
-    - leap
+    - machinelearningtools
     - zam347
-    - base
-    - django
   stage: test
   variables:
     FAILURE_THRESHOLD: 100
@@ -51,10 +109,8 @@ tests:
 
 coverage:
   tags:
-    - leap
+    - machinelearningtools
     - zam347
-    - base
-    - django
   stage: test
   variables:
     FAILURE_THRESHOLD: 50
@@ -79,7 +135,6 @@ coverage:
 pages:
   stage: pages
   tags:
-    - leap
     - zam347
     - base
   script:

CI/run_pytest.sh

 #!/bin/bash
 
 # run pytest for all run_modules
-python3 -m pytest --html=report.html --self-contained-html test/ | tee test_results.out
+python3.6 -m pytest --html=report.html --self-contained-html test/ | tee test_results.out
 
 IS_FAILED=$?
 
+if [ -z ${TEST_TYPE+x} ]; then
+    TEST_TYPE=""; else
+      TEST_TYPE="_"${TEST_TYPE};
+fi
+
 # move html test report
-mkdir test_results/
+TEST_RESULTS_DIR="test_results${TEST_TYPE}/"
+mkdir ${TEST_RESULTS_DIR}
 BRANCH_NAME=$( echo -e "${CI_COMMIT_REF_NAME////_}")
-mkdir test_results/${BRANCH_NAME}
-mkdir test_results/recent
-cp report.html test_results/${BRANCH_NAME}/.
-cp report.html test_results/recent/.
+mkdir "${TEST_RESULTS_DIR}/${BRANCH_NAME}"
+mkdir "${TEST_RESULTS_DIR}/recent"
+cp report.html "${TEST_RESULTS_DIR}/${BRANCH_NAME}/."
+cp report.html "${TEST_RESULTS_DIR}/recent/."
 if [[ "${CI_COMMIT_REF_NAME}" = "master" ]]; then
-    cp -r report.html test_results/.
+    cp -r report.html ${TEST_RESULTS_DIR}/.
 fi
 
 # exit 0 if no tests implemented
 RUN_NO_TESTS="$(grep -c 'no tests ran' test_results.out)"
-if [[ ${RUN_NO_TESTS} > 0 ]]; then
+if [[ ${RUN_NO_TESTS} -gt 0 ]]; then
     echo "no test available"
     echo "incomplete" > status.txt
     echo "no tests avail" > incomplete.txt
@@ -27,20 +33,19 @@ fi
 
 # extract if tests passed or not
 TEST_FAILED="$(grep -oP '(\d+\s{1}failed)' test_results.out)"
-TEST_FAILED="$(echo ${TEST_FAILED} | (grep -oP '\d*'))"
+TEST_FAILED="$(echo "${TEST_FAILED}" | (grep -oP '\d*'))"
 TEST_PASSED="$(grep -oP '\d+\s{1}passed' test_results.out)"
-TEST_PASSED="$(echo ${TEST_PASSED} | (grep -oP '\d*'))"
+TEST_PASSED="$(echo "${TEST_PASSED}" | (grep -oP '\d*'))"
 if [[ -z "$TEST_FAILED" ]]; then
     TEST_FAILED=0
 fi
-let "TEST_PASSED=${TEST_PASSED}-${TEST_FAILED}"
-
+(( TEST_PASSED=TEST_PASSED-TEST_FAILED ))
 # calculate metrics
-let "SUM=${TEST_FAILED}+${TEST_PASSED}"
-let "TEST_PASSED_RATIO=${TEST_PASSED}*100/${SUM}"
+(( SUM=TEST_FAILED+TEST_PASSED ))
+(( TEST_PASSED_RATIO=TEST_PASSED*100/SUM ))
 
 # report
-if [[ ${IS_FAILED} == 0 ]]; then
+if [[ ${IS_FAILED} -eq 0 ]]; then
     if [[ ${TEST_PASSED_RATIO} -lt 100 ]]; then
         echo "only ${TEST_PASSED_RATIO}% passed"
         echo "incomplete" > status.txt

CI/run_pytest_coverage.sh

 #!/usr/bin/env bash
 
 # run coverage twice, 1) for html deploy 2) for success evaluation
-python3 -m pytest --cov=src --cov-report html test/
-python3 -m pytest --cov=src --cov-report term test/ | tee coverage_results.out
+python3.6 -m pytest --cov=src --cov-report term  --cov-report html test/ | tee coverage_results.out
 
 IS_FAILED=$?
 
 # move html coverage report
 mkdir coverage/
 BRANCH_NAME=$( echo -e "${CI_COMMIT_REF_NAME////_}")
-mkdir coverage/${BRANCH_NAME}
-mkdir coverage/recent
-cp -r htmlcov/* coverage/${BRANCH_NAME}/.
+mkdir "coverage/${BRANCH_NAME}"
+mkdir "coverage/recent"
+cp -r htmlcov/* "coverage/${BRANCH_NAME}/."
 cp -r htmlcov/* coverage/recent/.
 if [[ "${CI_COMMIT_REF_NAME}" = "master" ]]; then
     cp -r htmlcov/* coverage/.
@@ -19,10 +18,10 @@ fi
 
 # extract coverage information
 COVERAGE_RATIO="$(grep -oP '\d+\%' coverage_results.out | tail -1)"
-COVERAGE_RATIO="$(echo ${COVERAGE_RATIO} | (grep -oP '\d*'))"
+COVERAGE_RATIO="$(echo "${COVERAGE_RATIO}" | (grep -oP '\d*'))"
 
 # report
-if [[ ${IS_FAILED} == 0 ]]; then
+if [[ ${IS_FAILED} -eq 0 ]]; then
     if [[ ${COVERAGE_RATIO} -lt ${COVERAGE_PASS_THRESHOLD} ]]; then
         echo "only ${COVERAGE_RATIO}% covered"
         echo "incomplete" > status.txt

German_background_stations.json

+["DENW094", "DEBW029", "DENI052", "DENI063", "DEBY109", "DEUB022", "DESN001", "DEUB013", "DETH016", "DEBY002", "DEBY005", "DEBY099", "DEUB038", "DEBE051", "DEBE056", "DEBE062", "DEBE032", "DEBE034", "DEBE010", "DEHE046", "DEST031", "DEBY122", "DERP022", "DEBY079", "DEBW102", "DEBW076", "DEBW045", "DESH016", "DESN004", "DEHE032", "DEBB050", "DEBW042", "DEBW046", "DENW067", "DESL019", "DEST014", "DENW062", "DEHE033", "DENW081", "DESH008", "DEBB055", "DENI011", "DEHB001", "DEHB004", "DEHB002", "DEHB003", "DEHB005", "DEST039", "DEUB003", "DEBW072", "DEST002", "DEBB001", "DEHE039", "DEBW035", "DESN005", "DEBW047", "DENW004", "DESN011", "DESN076", "DEBB064", "DEBB006", "DEHE001", "DESN012", "DEST030", "DESL003", "DEST104", "DENW050", "DENW008", "DETH026", "DESN085", "DESN014", "DESN092", "DENW071", "DEBW004", "DENI028", "DETH013", "DENI059", "DEBB007", "DEBW049", "DENI043", "DETH020", "DEBY017", "DEBY113", "DENW247", "DENW028", "DEBW025", "DEUB039", "DEBB009", "DEHE027", "DEBB042", "DEHE008", "DESN017", "DEBW084", "DEBW037", "DEHE058", "DEHE028", "DEBW112", "DEBY081", "DEBY082", "DEST032", "DETH009", "DEHE010", "DESN019", "DEHE023", "DETH036", "DETH040", "DEMV017", "DEBW028", "DENI042", "DEMV004", "DEMV019", "DEST044", "DEST050", "DEST072", "DEST022", "DEHH049", "DEHH047", "DEHH033", "DEHH050", "DEHH008", "DEHH021", "DENI054", "DEST070", "DEBB053", "DENW029", "DEBW050", "DEUB034", "DENW018", "DEST052", "DEBY020", "DENW063", "DESN050", "DETH061", "DERP014", "DETH024", "DEBW094", "DENI031", "DETH041", "DERP019", "DEBW081", "DEHE013", "DEBW021", "DEHE060", "DEBY031", "DESH021", "DESH033", "DEHE052", "DEBY004", "DESN024", "DEBW052", "DENW042", "DEBY032", "DENW053", "DENW059", "DEBB082", "DEBB031", "DEHE025", "DEBW053", "DEHE048", "DENW051", "DEBY034", "DEUB035", "DEUB032", "DESN028", "DESN059", "DEMV024", "DENW079", "DEHE044", "DEHE042", "DEBB043", "DEBB036", "DEBW024", "DERP001", "DEMV012", "DESH005", "DESH023", "DEUB031", "DENI062", "DENW006", "DEBB065", "DEST077", "DEST005", "DERP007", "DEBW006", "DEBW007", "DEHE030", "DENW015", "DEBY013", "DETH025", "DEUB033", "DEST025", "DEHE045", "DESN057", "DENW036", "DEBW044", "DEUB036", "DENW096", "DETH095", "DENW038", "DEBY089", "DEBY039", "DENW095", "DEBY047", "DEBB067", "DEBB040", "DEST078", "DENW065", "DENW066", "DEBY052", "DEUB030", "DETH027", "DEBB048", "DENW047", "DEBY049", "DERP021", "DEHE034", "DESN079", "DESL008", "DETH018", "DEBW103", "DEHE017", "DEBW111", "DENI016", "DENI038", "DENI058", "DENI029", "DEBY118", "DEBW032", "DEBW110", "DERP017", "DESN036", "DEBW026", "DETH042", "DEBB075", "DEBB052", "DEBB021", "DEBB038", "DESN051", "DEUB041", "DEBW020", "DEBW113", "DENW078", "DEHE018", "DEBW065", "DEBY062", "DEBW027", "DEBW041", "DEHE043", "DEMV007", "DEMV021", "DEBW054", "DETH005", "DESL012", "DESL011", "DEST069", "DEST071", "DEUB004", "DESH006", "DEUB029", "DEUB040", "DESN074", "DEBW031", "DENW013", "DENW179", "DEBW056", "DEBW087", "DEST061", "DEMV001", "DEBB024", "DEBW057", "DENW064", "DENW068", "DENW080", "DENI019", "DENI077", "DEHE026", "DEBB066", "DEBB083", "DEST063", "DEBW013", "DETH086", "DESL018", "DETH096", "DEBW059", "DEBY072", "DEBY088", "DEBW060", "DEBW107", "DEBW036", "DEUB026", "DEBW019", "DENW010", "DEST098", "DEHE019", "DEBW039", "DESL017", "DEBW034", "DEUB005", "DEBB051", "DEHE051", "DEBW023", "DEBY092", "DEBW008", "DEBW030", "DENI060", "DEST011", "DENW030", "DENI041", "DERP015", "DEUB001", "DERP016", "DERP028", "DERP013", "DEHE022", "DEUB021", "DEBW010", "DEST066", "DEBB063", "DEBB028", "DEHE024", "DENI020", "DENI051", "DERP025", "DEBY077", "DEMV018", "DEST089", "DEST028", "DETH060", "DEHE050", "DEUB028", "DESN045", "DEUB042"]

requirements.txt

@@ -43,17 +43,20 @@ pytest-cov==2.8.1
 pytest-html==2.0.1
 pytest-lazy-fixture==0.6.3
 pytest-metadata==1.8.0
+pytest-sugar
 python-dateutil==2.8.1
 pytz==2019.3
 PyYAML==5.3
 requests==2.23.0
 scipy==1.4.1
 seaborn==0.10.0
-Shapely==1.7.0
+--no-binary shapely Shapely==1.7.0
 six==1.11.0
 statsmodels==0.11.1
-tensorboard==1.12.2
-tensorflow==1.12.0
+tabulate
+tensorboard==1.13.1
+tensorflow-estimator==1.13.0
+tensorflow==1.13.1
 termcolor==1.1.0
 toolz==0.10.0
 urllib3==1.25.8

requirements_gpu.txt

+absl-py==0.9.0
+astor==0.8.1
+atomicwrites==1.3.0
+attrs==19.3.0
+Cartopy==0.17.0
+certifi==2019.11.28
+chardet==3.0.4
+cloudpickle==1.3.0
+coverage==5.0.3
+cycler==0.10.0
+Cython==0.29.15
+dask==2.11.0
+fsspec==0.6.2
+gast==0.3.3
+grpcio==1.27.2
+h5py==2.10.0
+idna==2.8
+importlib-metadata==1.5.0
+Keras==2.2.4
+Keras-Applications==1.0.8
+Keras-Preprocessing==1.1.0
+kiwisolver==1.1.0
+locket==0.2.0
+Markdown==3.2.1
+matplotlib==3.2.0
+mock==4.0.1
+more-itertools==8.2.0
+numpy==1.18.1
+packaging==20.3
+pandas==1.0.1
+partd==1.1.0
+patsy==0.5.1
+Pillow==7.0.0
+pluggy==0.13.1
+protobuf==3.11.3
+py==1.8.1
+pydot==1.4.1
+pyparsing==2.4.6
+pyproj==2.5.0
+pyshp==2.1.0
+pytest==5.3.5
+pytest-cov==2.8.1
+pytest-html==2.0.1
+pytest-lazy-fixture==0.6.3
+pytest-metadata==1.8.0
+pytest-sugar
+python-dateutil==2.8.1
+pytz==2019.3
+PyYAML==5.3
+requests==2.23.0
+scipy==1.4.1
+seaborn==0.10.0
+--no-binary shapely Shapely==1.7.0
+six==1.11.0
+statsmodels==0.11.1
+tabulate
+tensorboard==1.13.1
+tensorflow-estimator==1.13.0
+tensorflow-gpu==1.13.1
+termcolor==1.1.0
+toolz==0.10.0
+urllib3==1.25.8
+wcwidth==0.1.8
+Werkzeug==1.0.0
+xarray==0.15.0
+zipp==3.1.0

run.py

@@ -3,7 +3,6 @@ __date__ = '2019-11-14'
 
 
 import argparse
-import logging
 
 from src.run_modules.experiment_setup import ExperimentSetup
 from src.run_modules.model_setup import ModelSetup
@@ -17,7 +16,8 @@ def main(parser_args):
 
     with RunEnvironment():
         ExperimentSetup(parser_args, stations=['DEBW107', 'DEBY081', 'DEBW013', 'DEBW076', 'DEBW087', 'DEBW001'],
-                        station_type='background', trainable=False, create_new_model=False)
+                        station_type='background', trainable=False, create_new_model=False, window_history_size=6,
+                        create_new_bootstraps=True)
         PreProcessing()
 
         ModelSetup()
@@ -29,10 +29,6 @@ def main(parser_args):
 
 if __name__ == "__main__":
 
-    formatter = '%(asctime)s - %(levelname)s: %(message)s  [%(filename)s:%(funcName)s:%(lineno)s]'
-    logging.basicConfig(format=formatter, level=logging.INFO)
-    # logging.basicConfig(format=formatter, level=logging.DEBUG)
-
     parser = argparse.ArgumentParser()
     parser.add_argument('--experiment_date', metavar='--exp_date', type=str, default=None,
                         help="set experiment date as string")

run_hourly.py

@@ -29,10 +29,6 @@ def main(parser_args):
 
 if __name__ == "__main__":
 
-    formatter = '%(asctime)s - %(levelname)s: %(message)s  [%(filename)s:%(funcName)s:%(lineno)s]'
-    logging.basicConfig(format=formatter, level=logging.INFO)
-    # logging.basicConfig(format=formatter, level=logging.DEBUG)
-
     parser = argparse.ArgumentParser()
     parser.add_argument('--experiment_date', metavar='--exp_date', type=str, default=None,
                         help="set experiment date as string")

run_zam347.py

+__author__ = "Lukas Leufen"
+__date__ = '2019-11-14'
+
+
+import argparse
+import json
+import logging
+
+from src.run_modules.experiment_setup import ExperimentSetup
+from src.run_modules.model_setup import ModelSetup
+from src.run_modules.post_processing import PostProcessing
+from src.run_modules.pre_processing import PreProcessing
+from src.run_modules.run_environment import RunEnvironment
+from src.run_modules.training import Training
+
+
+def load_stations():
+
+    try:
+        filename = 'German_background_stations.json'
+        with open(filename, 'r') as jfile:
+            stations = json.load(jfile)
+            logging.info(f"load station IDs from file: {filename} ({len(stations)} stations)")
+            # stations.remove('DEUB042')
+    except FileNotFoundError:
+        stations = ['DEBW107', 'DEBY081', 'DEBW013', 'DEBW076', 'DEBW087', 'DEBW001']
+        # stations = ['DEBB050', 'DEBW107', 'DEBY081', 'DEBW013', 'DEBW076', 'DEBW087', 'DEBW001']
+        logging.info(f"Use stations from list: {stations}")
+
+    return stations
+
+
+def main(parser_args):
+
+    with RunEnvironment():
+
+        ExperimentSetup(parser_args, stations=load_stations(), station_type='background', trainable=False,
+                        create_new_model=True)
+        PreProcessing()
+
+        ModelSetup()
+
+        Training()
+
+        PostProcessing()
+
+
+if __name__ == "__main__":
+
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--experiment_date', metavar='--exp_date', type=str, default=None,
+                        help="set experiment date as string")
+    args = parser.parse_args(["--experiment_date", "testrun"])
+
+    main(args)

src/data_handling/bootstraps.py

@@ -2,152 +2,108 @@ __author__ = 'Felix Kleinert, Lukas Leufen'
 __date__ = '2020-02-07'
 
 
-from src.run_modules.run_environment import RunEnvironment
 from src.data_handling.data_generator import DataGenerator
 import numpy as np
 import logging
+import keras
 import dask.array as da
 import xarray as xr
 import os
 import re
 from src import helpers
+from typing import List, Union, Pattern, Tuple
 
 
-class BootStrapGenerator:
+class BootStrapGenerator(keras.utils.Sequence):
+    """
+    generator for bootstraps as keras sequence inheritance. Initialise with number of boots, the original history, the
+    shuffled data, all used variables and the current shuffled variable. While iterating over this generator, it returns
+    the bootstrapped history for given boot index (this is the iterator index) in the same format like the original
+    history ready to use. Note, that in some cases some samples can contain nan values (in these cases the entire data
+    row is null, not only single entries).
+    """
+    def __init__(self, number_of_boots: int, history: xr.DataArray, shuffled: xr.DataArray, variables: List[str],
+                 shuffled_variable: str):
+        self.number_of_boots = number_of_boots
+        self.variables = variables
+        self.history_orig = history
+        self.history = history.sel(variables=helpers.list_pop(self.variables, shuffled_variable))
+        self.shuffled = shuffled.sel(variables=shuffled_variable)
 
-    def __init__(self, orig_generator, boots, chunksize, bootstrap_path):
-        self.orig_generator: DataGenerator = orig_generator
-        self.stations = self.orig_generator.stations
-        self.variables = self.orig_generator.variables
-        self.boots = boots
-        self.chunksize = chunksize
-        self.bootstrap_path = bootstrap_path
-        self._iterator = 0
-        self.bootstrap_meta = []
-
-    def __len__(self):
-        """
-        display the number of stations
-        """
-        return len(self.orig_generator)*self.boots*len(self.variables)
-
-    def get_labels(self, key):
-        _, label = self.orig_generator[key]
-        for _ in range(self.boots):
-            yield label
-
-    def get_generator(self):
-        """
-        This is the implementation of the __next__ method of the iterator protocol. Get the data generator, and return
-        the history and label data of this generator.
-        :return:
-        """
-        while True:
-            for i, data in enumerate(self.orig_generator):
-                station = self.orig_generator.get_station_key(i)
-                logging.info(f"station: {station}")
-                hist, label = data
-                len_of_label = len(label)
-                shuffled_data = self.load_boot_data(station)
-                for var in self.variables:
-                    logging.info(f"  var: {var}")
-                    for boot in range(self.boots):
-                        logging.debug(f"boot: {boot}")
-                        boot_hist = hist.sel(variables=helpers.list_pop(self.variables, var))
-                        shuffled_var = shuffled_data.sel(variables=var, boots=boot).expand_dims("variables").drop("boots").transpose("datetime", "window", "Stations", "variables")
-                        boot_hist = boot_hist.combine_first(shuffled_var)
-                        boot_hist = boot_hist.sortby("variables")
-                        self.bootstrap_meta.extend([[var, station]]*len_of_label)
-                        yield boot_hist, label
-            return
-
-    def get_orig_prediction(self, path, file_name, prediction_name="CNN"):
-        file = os.path.join(path, file_name)
-        data = xr.open_dataarray(file)
-        for _ in range(self.boots):
-            yield data.sel(type=prediction_name).squeeze()
-
-    def load_boot_data(self, station):
-        files = os.listdir(self.bootstrap_path)
-        regex = re.compile(rf"{station}_\w*\.nc")
-        file_name = os.path.join(self.bootstrap_path, list(filter(regex.search, files))[0])
-        shuffled_data = xr.open_dataarray(file_name, chunks=100)
-        return shuffled_data
+    def __len__(self) -> int:
+        return self.number_of_boots
 
+    def __getitem__(self, index: int) -> xr.DataArray:
+        """
+        return bootstrapped history for given bootstrap index in same index structure like the original history object
+        :param index: boot index e [0, nboots-1]
+        :return: bootstrapped history ready to use
+        """
+        logging.debug(f"boot: {index}")
+        boot_hist = self.history.copy()
+        boot_hist = boot_hist.combine_first(self.__get_shuffled(index))
+        return boot_hist.reindex_like(self.history_orig)
 
-class BootStraps(RunEnvironment):
+    def __get_shuffled(self, index: int) -> xr.DataArray:
+        """
+        returns shuffled data for given boot index from shuffled attribute
+        :param index: boot index e [0, nboots-1]
+        :return: shuffled data
+        """
+        shuffled_var = self.shuffled.sel(boots=index).expand_dims("variables").drop("boots")
+        return shuffled_var.transpose("datetime", "window", "Stations", "variables")
 
-    def __init__(self, data, bootstrap_path, number_bootstraps=10):
 
-        super().__init__()
-        self.data: DataGenerator = data
-        self.number_bootstraps = number_bootstraps
+class CreateShuffledData:
+    """
+    Verify and create shuffled data for all data contained in given data generator class. Starts automatically on
+    initialisation, no further calls are required. Check and new creations are all performed inside bootstrap_path.
+    """
+    def __init__(self, data: DataGenerator, number_of_bootstraps: int, bootstrap_path: str):
+        self.data = data
+        self.number_of_bootstraps = number_of_bootstraps
         self.bootstrap_path = bootstrap_path
-        self.chunks = self.get_chunk_size()
         self.create_shuffled_data()
-        self._boot_strap_generator = BootStrapGenerator(self.data, self.number_bootstraps, self.chunks, self.bootstrap_path)
-
-    def get_boot_strap_meta(self):
-        return self._boot_strap_generator.bootstrap_meta
-
-    def boot_strap_generator(self):
-        return self._boot_strap_generator.get_generator()
-
-    def get_boot_strap_generator_length(self):
-        return self._boot_strap_generator.__len__()
-
-    def get_labels(self, key):
-        labels_list = []
-        chunks = None
-        for labels in self._boot_strap_generator.get_labels(key):
-            if len(labels_list) == 0:
-                chunks = (100, labels.data.shape[1])
-            labels_list.append(da.from_array(labels.data, chunks=chunks))
-        labels_out = da.concatenate(labels_list, axis=0)
-        return labels_out.compute()
-
-    def get_orig_prediction(self, path, name):
-        labels_list = []
-        chunks = None
-        for labels in self._boot_strap_generator.get_orig_prediction(path, name):
-            if len(labels_list) == 0:
-                chunks = (100, labels.data.shape[1])
-            labels_list.append(da.from_array(labels.data, chunks=chunks))
-        labels_out = da.concatenate(labels_list, axis=0)
-        labels_out = labels_out.compute()
-        return labels_out[~np.isnan(labels_out).any(axis=1), :]
-
-    def get_chunk_size(self):
-        hist, _ = self.data[0]
-        return (100, *hist.shape[1:], self.number_bootstraps)
-
-    def create_shuffled_data(self):
+
+    def create_shuffled_data(self) -> None:
         """
         Create shuffled data. Use original test data, add dimension 'boots' with length number of bootstraps and insert
         randomly selected variables. If there is a suitable local file for requested window size and number of
         bootstraps, no additional file will be created inside this function.
         """
-        logging.info("create shuffled bootstrap data")
+        logging.info("create / check shuffled bootstrap data")
         variables_str = '_'.join(sorted(self.data.variables))
         window = self.data.window_history_size
         for station in self.data.stations:
             valid, nboot = self.valid_bootstrap_file(station, variables_str, window)
             if not valid:
                 logging.info(f'create bootstap data for {station}')
-                hist, _ = self.data[station]
-                data = hist.copy()
-                file_name = f"{station}_{variables_str}_hist{window}_nboots{nboot}_shuffled.nc"
-                file_path = os.path.join(self.bootstrap_path, file_name)
-                data = data.expand_dims({'boots': range(nboot)}, axis=-1)
+                hist = self.data.get_data_generator(station).get_transposed_history()
+                file_path = self._set_file_path(station, variables_str, window, nboot)
+                hist = hist.expand_dims({'boots': range(nboot)}, axis=-1)
                 shuffled_variable = []
-                for i, var in enumerate(data.coords['variables']):
-                    single_variable = data.sel(variables=var).values
-                    shuffled_variable.append(self.shuffle_single_variable(single_variable, chunks=(100, *data.shape[1:3], data.shape[-1])))
-                shuffled_variable_da = da.stack(shuffled_variable, axis=-2, ).rechunk("auto")
-                shuffled_data = xr.DataArray(shuffled_variable_da, coords=data.coords, dims=data.dims)
+                chunks = (100, *hist.shape[1:3], hist.shape[-1])
+                for i, var in enumerate(hist.coords['variables']):
+                    single_variable = hist.sel(variables=var).values
+                    shuffled_variable.append(self.shuffle(single_variable, chunks=chunks))
+                shuffled_variable_da = da.stack(shuffled_variable, axis=-2).rechunk("auto")
+                shuffled_data = xr.DataArray(shuffled_variable_da, coords=hist.coords, dims=hist.dims)
                 shuffled_data.to_netcdf(file_path)
 
-    def valid_bootstrap_file(self, station, variables, window):
+    def _set_file_path(self, station: str, variables: str, window: int, nboots: int) -> str:
+        """
+        Set file name following naming convention <station>_<var1>_<var2>_..._hist<window>_nboots<nboots>_shuffled.nc