timewise 0.5.3__py3-none-any.whl → 1.0.0a1__py3-none-any.whl

timewise/wise_bigdata_desy_cluster.py

@@ -1,1407 +0,0 @@
-import getpass
-import os
-import json
-import subprocess
-import math
-import pickle
-import queue
-import threading
-import argparse
-import time
-import seaborn as sns
-import backoff
-import shutil
-import gc
-import tqdm
-import sys
-from pathlib import Path
-
-from functools import cache
-from scipy.stats import chi2, f
-import matplotlib.pyplot as plt
-import numpy as np
-import pandas as pd
-import pyvo as vo
-import traceback as tb
-import gzip
-import logging
-
-from typing import List
-
-from timewise.general import get_directories, backoff_hndlr
-from timewise.wise_data_by_visit import WiseDataByVisit
-from timewise.utils import StableAsyncTAPJob, ErrorQueue, ExceptionSafeThread
-
-
-logger = logging.getLogger(__name__)
-
-
-class WISEDataDESYCluster(WiseDataByVisit):
-    """
-    A class to download WISE data with multiple threads and do the binning on the DESY cluster.
-    In addition to the attributes of `WiseDataByVisit` this class has the following attributes:
-
-    :param executable_filename: the filename of the executable that will be submitted to the cluster
-    :type executable_filename: Path
-    :param submit_file_filename: the filename of the submit file that will be submitted to the cluster
-    :type submit_file_filename: Path
-    :param job_id: the job id of the submitted job
-    :type job_id: str
-    :param cluster_jobID_map: a dictionary mapping the chunk number to the cluster job id
-    :type cluster_jobID_map: dict
-    :param clusterJob_chunk_map: a dictionary mapping the cluster job id to the chunk number
-    :type clusterJob_chunk_map: dict
-    :param cluster_info_file: the filename of the file that stores the cluster info, loaded by the cluster jobs
-    :type cluster_info_file: Path
-    :param start_time: the time when the download started
-    :type start_time: float
-    """
-    status_cmd = f'qstat -u {getpass.getuser()}'
-    # finding the file that contains the setup function
-    if (env_file := os.getenv('TIMEWISE_DESY_CLUSTER_BASHFILE')) is not None:
-        BASHFILE = Path(env_file)
-    else:
-        BASHFILE = Path("~/.bashrc").expanduser()
-
-    def __init__(
-            self,
-            base_name,
-            parent_sample_class,
-            min_sep_arcsec,
-            n_chunks,
-            clean_outliers_when_binning=True,
-            multiply_flux_error=True
-    ):
-        """
-        Constructor of the class.
-
-        :param base_name: the base name of the data directory
-        :type base_name: str
-        :param parent_sample_class: the parent sample class
-        :type parent_sample_class: ParentSampleBase
-        :param min_sep_arcsec: query region around source for positional query
-        :type min_sep_arcsec: float
-        :param n_chunks: number of chunks to split the sample into
-        :type n_chunks: int
-        :param clean_outliers_when_binning: if True, clean outliers when binning
-        :type clean_outliers_when_binning: bool
-        """
-
-        super().__init__(base_name=base_name, parent_sample_class=parent_sample_class, min_sep_arcsec=min_sep_arcsec,
-                         n_chunks=n_chunks, clean_outliers_when_binning=clean_outliers_when_binning,
-                         multiply_flux_error=multiply_flux_error)
-
-        # set up cluster stuff
-        self._status_output = None
-        directories = get_directories()
-        self.executable_filename = self.cluster_dir / "run_timewise.sh"
-        self.submit_file_filename = self.cluster_dir / "submit_file.submit"
-        self.job_id = None
-
-        self.cluster_jobID_map = None
-        self.clusterJob_chunk_map = None
-        self.cluster_info_file = self.cluster_dir / 'cluster_info.pkl'
-        self._overwrite = True
-
-        # these attributes will be set later and are used to pass them to the threads
-        self._n_cluster_jobs_per_chunk = None
-        self._storage_dir = None
-
-        # status attributes
-        self.start_time = None
-        self._total_tasks = None
-        self._done_tasks = None
-
-        self._tap_queue = None
-        self._cluster_queue = None
-        self._io_queue = None
-        self._io_queue_done = None
-        self._combining_queue = None
-
-    # ---------------------------------------------------------------------------------- #
-    # START using gzip to compress the data when saving     #
-    # ----------------------------------------------------- #
-
-    def _data_product_filename(self, service, chunk_number=None, jobID=None, use_bigdata_dir=False):
-        fn = super(WISEDataDESYCluster, self)._data_product_filename(service, chunk_number=chunk_number, jobID=jobID)
-
-        if use_bigdata_dir:
-            d = get_directories()
-            fn = str(fn).replace(str(d["data_dir"]), str(d["bigdata_dir"]))
-
-        return Path(str(fn) + ".gz")
-
-    def load_data_product(
-            self,
-            service,
-            chunk_number=None,
-            jobID=None,
-            return_filename=False,
-            use_bigdata_dir=False,
-            verify_contains_lightcurves=False
-    ):
-        fn = self._data_product_filename(
-            service,
-            chunk_number,
-            jobID,
-            use_bigdata_dir=use_bigdata_dir
-        )
-
-        logger.debug(f"loading {fn}")
-        try:
-            with gzip.open(fn, 'rt', encoding="utf-8") as fzip:
-                data_product = json.load(fzip)
-
-            if verify_contains_lightcurves:
-                try:
-                    self._verify_contains_lightcurves(data_product)
-                except KeyError as e:
-                    raise KeyError(f"{fn}: {e}")
-
-            if return_filename:
-                return data_product, fn
-            return data_product
-        except FileNotFoundError:
-            logger.warning(f"No file {fn}")
-
-    def _save_data_product(
-            self,
-            data_product,
-            service,
-            chunk_number=None,
-            jobID=None,
-            overwrite=False,
-            use_bigdata_dir=False
-    ):
-        fn = self._data_product_filename(
-            service,
-            chunk_number,
-            jobID,
-            use_bigdata_dir=use_bigdata_dir
-        )
-        logger.debug(f"saving {len(data_product)} new objects to {fn}")
-
-        if fn == self._data_product_filename(service):
-            self._cached_final_products['lightcurves'][service] = data_product
-
-        if not overwrite:
-            try:
-                old_data_product = self.load_data_product(service=service, chunk_number=chunk_number, jobID=jobID)
-
-                if old_data_product is not None:
-                    logger.debug(f"Found {len(old_data_product)}. Combining")
-                    data_product = data_product.update(old_data_product)
-
-            except FileNotFoundError as e:
-                logger.info(f"FileNotFoundError: {e}. Making new binned lightcurves.")
-
-        with gzip.open(fn, 'wt', encoding="utf-8") as fzip:
-            json.dump(data_product, fzip)
-
-    # ----------------------------------------------------- #
-    # END using gzip to compress the data when saving       #
-    # ---------------------------------------------------------------------------------- #
-
-    def get_sample_photometric_data(self, max_nTAPjobs=8, perc=1, tables=None, chunks=None,
-                                    cluster_jobs_per_chunk=100, wait=5, remove_chunks=False,
-                                    query_type='positional', overwrite=True,
-                                    storage_directory=None,
-                                    node_memory='8G',
-                                    skip_download=False,
-                                    skip_input=False,
-                                    mask_by_position=False):
-        """
-        An alternative to `get_photometric_data()` that uses the DESY cluster and is optimised for large datasets.
-
-        :param max_nTAPjobs: The maximum number of TAP jobs active at the same time.
-        :type max_nTAPjobs: int
-        :param perc: The percentage of chunks to download
-        :type perc: float
-        :param tables: The tables to query
-        :type tables: str or list-like
-        :param chunks: chunks to download, default is all of the chunks
-        :type chunks: list-like
-        :param cluster_jobs_per_chunk: number of cluster jobs per chunk
-        :type cluster_jobs_per_chunk: int
-        :param wait: time in hours to wait after submitting TAP jobs
-        :type wait: float
-        :param remove_chunks: remove single chunk files after binning
-        :type remove_chunks: bool
-        :param query_type: 'positional': query photometry based on distance from object, 'by_allwise_id': select all photometry points within a radius of 50 arcsec with the corresponding AllWISE ID
-        :type query_type: str
-        :param overwrite: overwrite already existing lightcurves and metadata
-        :type overwrite: bool
-        :param storage_directory: move binned files and raw data here after work is done, defaults to TIMEWISE_BIGDATA_DIR
-        :type storage_directory: str | Path
-        :param node_memory: memory per node on the cluster, default is 8G
-        :type node_memory: str
-        :param skip_download: if True, assume data is already downloaded, only do binning in that case
-        :type skip_download: bool
-        :param skip_input: if True do not ask if data is correct before download
-        :type skip_input: bool
-        :param mask_by_position: if `True` mask single exposures that are too far away from the bulk
-        :type mask_by_position: bool
-        """
-
-        # --------------------- set defaults --------------------------- #
-
-        mag = True
-        flux = True
-
-        if tables is None:
-            tables = [
-                'AllWISE Multiepoch Photometry Table',
-                'NEOWISE-R Single Exposure (L1b) Source Table'
-            ]
-        tables = np.atleast_1d(tables)
-
-        if chunks is None:
-            chunks = list(range(round(int(self.n_chunks * perc))))
-        else:
-            cm = [c not in self.chunk_map for c in chunks]
-            if np.any(cm):
-                raise ValueError(f"Chunks {np.array(chunks)[cm]} are not in chunk map. "
-                                 f"Probably they are larger than the set chunk number of {self._n_chunks}")
-
-        if remove_chunks:
-            raise NotImplementedError("Removing chunks is not implemented yet!")
-
-        if query_type not in self.query_types:
-            raise ValueError(f"Unknown query type {query_type}! Choose one of {self.query_types}")
-
-        service = 'tap'
-
-        # set up dictionary to store jobs in
-        self.tap_jobs = {t: dict() for t in tables}
-
-        logger.debug(f"Getting {perc * 100:.2f}% of lightcurve chunks ({len(chunks)}) via {service} "
-                     f"in {'magnitude' if mag else ''} {'flux' if flux else ''} "
-                     f"from {tables}\nskipping download: {skip_download}")
-
-        if not skip_input:
-            input('Correct? [hit enter] ')
-
-        # --------------------------- set up cluster info --------------------------- #
-
-        self.n_cluster_jobs_per_chunk = cluster_jobs_per_chunk
-        self.clear_cluster_log_dir()
-        self._save_cluster_info()
-        self._overwrite = overwrite
-        self._storage_dir = get_directories()['bigdata_dir'] if storage_directory is None else Path(storage_directory)
-
-        # --------------------------- set up queues --------------------------- #
-
-        self.queue = queue.Queue()
-        self._tap_queue = ErrorQueue()
-        self._cluster_queue = ErrorQueue()
-        self._io_queue = queue.PriorityQueue()
-        self._io_queue_done = queue.Queue()
-        self._combining_queue = ErrorQueue()
-
-        # --------------------------- starting threads --------------------------- #
-
-        tap_threads = [
-            ExceptionSafeThread(error_queue=self._tap_queue, target=self._tap_thread, daemon=True, name=f"TAPThread{_}")
-            for _ in range(max_nTAPjobs)
-        ]
-        cluster_threads = [
-            ExceptionSafeThread(error_queue=self._cluster_queue, target=self._cluster_thread, daemon=True, name=f"ClusterThread{_}")
-            for _ in range(max_nTAPjobs)
-        ]
-        io_thread = threading.Thread(target=self._io_thread, daemon=True, name="IOThread")
-        combining_thread = ExceptionSafeThread(error_queue=self._combining_queue, target=self._combining_thread, daemon=True, name="CombiningThread")
-        status_thread = threading.Thread(target=self._status_thread, daemon=True, name='StatusThread')
-
-        for t in tap_threads + cluster_threads + [io_thread, combining_thread]:
-            logger.debug('starting thread')
-            t.start()
-
-        logger.debug(f'started {len(tap_threads)} TAP threads and {len(cluster_threads)} cluster threads.')
-
-        # --------------------------- filling queue with tasks --------------------------- #
-
-        self.start_time = time.time()
-        self._total_tasks = len(chunks)
-        self._done_tasks = 0
-
-        for c in chunks:
-            if not skip_download:
-                self._tap_queue.put((tables, c, wait, mag, flux, node_memory, query_type, mask_by_position))
-            else:
-                self._cluster_queue.put((node_memory, c, mask_by_position))
-
-        status_thread.start()
-
-        # --------------------------- wait for completion --------------------------- #
-
-        logger.debug(f'added {self._tap_queue.qsize()} tasks to tap queue')
-        self._tap_queue.join()
-        logger.debug('TAP done')
-        self._cluster_queue.join()
-        logger.debug('cluster done')
-        self._combining_queue.join()
-        logger.debug('combining done')
-
-        # unset queues
-        self.queue = None
-        self._tap_queue = None
-        self._cluster_queue = None
-        self._io_queue = None
-        self._io_queue_done = None
-        self._combining_queue = None
-
-    @backoff.on_exception(
-        backoff.expo,
-        vo.dal.exceptions.DALServiceError,
-        giveup=WiseDataByVisit._give_up_tap,
-        max_tries=50,
-        on_backoff=backoff_hndlr
-    )
-    def _wait_for_job(self, t, i):
-        logger.info(f"Waiting on {i}th query of {t} ........")
-        _job = StableAsyncTAPJob(url=self.tap_jobs[t][i])
-        _job.wait()
-        logger.info(f'{i}th query of {t}: Done!')
-
-    def _get_results_from_job(self, t, i):
-        logger.debug(f"getting results for {i}th query of {t} .........")
-        _job = StableAsyncTAPJob(url=self.tap_jobs[t][i])
-        lightcurve = _job.fetch_result().to_table().to_pandas()
-        fn = self._chunk_photometry_cache_filename(t, i)
-        table_nice_name = self.get_db_name(t, nice=True)
-        logger.debug(f"{i}th query of {table_nice_name}: saving under {fn}")
-        cols = dict(self.photometry_table_keymap[table_nice_name]['mag'])
-        cols.update(self.photometry_table_keymap[table_nice_name]['flux'])
-
-        if 'allwise' in t:
-            cols['cntr_mf'] = 'allwise_cntr'
-
-        lightcurve.rename(columns=cols).to_csv(fn)
-        return
-
-    def _io_queue_hash(self, method_name, args):
-        return f"{method_name}_{args}"
-
-    def _wait_for_io_task(self, method_name, args):
-        h = self._io_queue_hash(method_name, args)
-        logger.debug(f"waiting on io-task {h}")
-
-        while True:
-            _io_queue_done = list(self._io_queue_done.queue)
-            if h in _io_queue_done:
-                break
-
-            time.sleep(30)
-
-        logger.debug(f"{h} done!")
-
-    def _io_thread(self):
-        logger.debug("started in-out thread")
-        while True:
-            priority, method_name, args = self._io_queue.get(block=True)
-            logger.debug(f"executing {method_name} with arguments {args} (priority {priority})")
-
-            try:
-                self.__getattribute__(method_name)(*args)
-                self._io_queue_done.put(self._io_queue_hash(method_name, args))
-            except Exception as e:
-                msg = (
-                    f"#################################################################\n"
-                    f"                !!!     ATTENTION     !!!                 \n"
-                    f" ----------------- {method_name}({args}) ---------------- \n"
-                    f"                      AN ERROR OCCURED                    \n"
-                    f"\n{''.join(tb.format_exception(None, e, e.__traceback__))}\n\n"
-                    f"putting {method_name}({args}) back into IO-queue\n"
-                    f"#################################################################\n"
-                )
-                logger.error(msg)
-                self._io_queue.put((priority, method_name, args))
-            finally:
-                self._io_queue.task_done()
-                gc.collect()
-
-    def _tap_thread(self):
-        logger.debug(f'started tap thread')
-        while True:
-            tables, chunk, wait, mag, flux, node_memory, query_type, mask_by_position = self._tap_queue.get(block=True)
-            logger.debug(f'querying IRSA for chunk {chunk}')
-
-            submit_to_cluster = True
-
-            for i in range(len(tables) + 1):
-
-                # -----------   submit jobs for chunk i via the IRSA TAP  ---------- #
-                if i < len(tables):
-                    t = tables[i]
-                    submit_method = "_submit_job_to_TAP"
-                    submit_args = [chunk, t, mag, flux, query_type]
-                    self._io_queue.put((1, submit_method, submit_args))
-                    self._wait_for_io_task(submit_method, submit_args)
-
-                # --------------  get results of TAP job for chunk i-1 ------------- #
-                if i > 0:
-                    t_before = tables[i - 1]
-                    phase = StableAsyncTAPJob(url=self.tap_jobs[t_before][chunk]).phase
-                    if phase == "COMPLETED":
-                        result_method = "_get_results_from_job"
-                        result_args = [t_before, chunk]
-                        self._io_queue.put((2, result_method, result_args))
-                        self._wait_for_io_task(result_method, result_args)
-
-                    else:
-                        logger.warning(
-                            f"No completion for {chunk}th query of {t_before}! "
-                            f"Phase is {phase}!"
-                        )
-                        submit_to_cluster = False
-
-                # ---------------   wait for the TAP job of chunk i  -------------- #
-                if i < len(tables):
-                    t = tables[i]
-                    logger.info(f'waiting for {wait} hours')
-                    time.sleep(wait * 3600)
-
-                    try:
-                        self._wait_for_job(t, chunk)
-                    except vo.dal.exceptions.DALServiceError:
-                        logger.warning(f"could not wait for {chunk}th query of {t}! Not submitting to cluster.")
-                        # mark task as done and move on without submission to cluster
-                        submit_to_cluster = False
-                        continue
-
-            self._tap_queue.task_done()
-            if submit_to_cluster:
-                self._cluster_queue.put((node_memory, chunk, mask_by_position))
-
-            gc.collect()
-
-    def _move_file_to_storage(self, filename):
-        data_dir = str(get_directories()['data_dir'])
-        dst_fn = Path(str(filename).replace(str(data_dir), str(self._storage_dir)))
-        dst_fn.parent.mkdir(parents=True, exist_ok=True)
-
-        logger.debug(f"copy {filename} to {dst_fn}")
-
-        try:
-            shutil.copy2(filename, dst_fn)
-
-            if Path(filename).stat().st_size == dst_fn.stat().st_size:
-                logger.debug(f"copy successful, removing {filename}")
-                os.remove(filename)
-            else:
-                logger.warning(f"copy from {filename} to {dst_fn} gone wrong! Not removing source.")
-
-        except FileNotFoundError as e:
-            logger.warning(f"FileNotFoundError: {e}!")
-
-    def _cluster_thread(self):
-        logger.debug(f'started cluster thread')
-        while True:
-            node_memory, chunk, mask_by_position = self._cluster_queue.get(block=True)
-
-            logger.info(f'got all TAP results for chunk {chunk}. submitting to cluster')
-            job_id = self.submit_to_cluster(
-                node_memory=node_memory,
-                single_chunk=chunk,
-                mask_by_position=mask_by_position
-            )
-
-            if not job_id:
-                logger.warning(f"could not submit {chunk} to cluster! Try later")
-                self._cluster_queue.put((node_memory, chunk, mask_by_position))
-                self._cluster_queue.task_done()
-
-            else:
-                logger.debug(f'waiting for chunk {chunk} (Cluster job {job_id})')
-                self.wait_for_job(job_id)
-                logger.debug(f'cluster done for chunk {chunk} (Cluster job {job_id}).')
-
-                log_files = Path("./").glob(f"{job_id}_*")
-                log_files_abs = [p.absolute() for p in log_files]
-                logger.debug(f"moving {len(log_files_abs)} log files to {self.cluster_log_dir}")
-                for f in log_files_abs:
-                    shutil.move(f, self.cluster_log_dir)
-
-                gc.collect()
-
-                logger.debug(f"cluster thread done for chunk {chunk} (Cluster job {job_id}). "
-                             f"Submitting to combining queue")
-                self._combining_queue.put(chunk)
-                self._cluster_queue.task_done()
-
-    def _combining_thread(self):
-        logger.debug(f'started combining thread')
-        while True:
-
-            try:
-                chunk = self._combining_queue.get(block=True)
-            except AttributeError:  # when self._combining_queue is None, meaning it was reset in main thread
-                break
-            logger.debug(f"combining chunk {chunk}")
-
-            try:
-                success = self._combine_data_products('tap', chunk_number=chunk, remove=True, overwrite=self._overwrite)
-
-                if success:
-                    if self._storage_dir:
-                        filenames_to_move = [
-                            self._data_product_filename(service='tap', chunk_number=chunk),
-                        ]
-
-                        for t in self.photometry_table_keymap.keys():
-                            filenames_to_move.append(self._chunk_photometry_cache_filename(t, chunk))
-    
-                        for fn in filenames_to_move:
-                            try:
-                                self._move_file_to_storage(fn)
-                            except shutil.SameFileError as e:
-                                logger.error(f"{e}. Not moving.")
-
-                else:
-                    msg = f"Chunk {chunk}: Combining data products not successfully!"
-                    if self._storage_dir:
-                        msg += " Not moving files to storage."
-                    logger.warning(msg)
-
-            finally:
-                self._combining_queue.task_done()
-                self._done_tasks += 1
-                gc.collect()
-
-    def _status_thread(self):
-        logger.debug('started status thread')
-        while True:
-            n_tap_tasks_queued = self._tap_queue.qsize()
-            n_cluster_tasks_queued = self._cluster_queue.qsize()
-            n_remaining = self._total_tasks - self._done_tasks
-            elapsed_time = time.time() - self.start_time
-            time_per_task = elapsed_time / self._done_tasks if self._done_tasks > 0 else np.nan
-            remaining_time = n_remaining * time_per_task
-
-            msg = f"\n-----------------     STATUS     -----------------\n" \
-                  f"\ttasks in TAP queue:_______{n_tap_tasks_queued}\n" \
-                  f"\ttasks in cluster queue:___{n_cluster_tasks_queued}\n" \
-                  f"\tperformed io tasks:_______{len(list(self._io_queue_done.queue))}\n" \
-                  f"\tdone total:_______________{self._done_tasks}/{self._total_tasks}\n" \
-                  f"\truntime:__________________{elapsed_time/3600:.2f} hours\n" \
-                  f"\tremaining:________________{remaining_time/3600:.2f} hours"
-
-            logger.info(msg)
-            time.sleep(5*3600)
-
-    # ----------------------------------------------------------------------------------- #
-    # START using cluster for downloading and binning      #
-    # ---------------------------------------------------- #
-
-    @staticmethod
-    @backoff.on_exception(
-        backoff.expo,
-        OSError,
-        max_time=2*3600,
-        on_backoff=backoff_hndlr,
-        jitter=backoff.full_jitter,
-    )
-    def _execute_bash_command(cmd):
-        with subprocess.Popen(cmd, stdout=subprocess.PIPE, shell=True) as process:
-            msg = process.stdout.read().decode()
-            process.terminate()
-        return msg
-
-    @staticmethod
-    def get_condor_status():
-        """
-        Queries condor to get cluster status.
-        :return: str, output of query command
-        """
-        cmd = "condor_q"
-        return WISEDataDESYCluster._execute_bash_command(cmd)
-
-    def collect_condor_status(self):
-        """Gets the condor status and saves it to private attribute"""
-        self._status_output = self.get_condor_status()
-
-    def condor_status(self, job_id):
-        """
-        Get the status of jobs running on condor.
-        :return: number of jobs that are done, running, waiting, total, held
-        """
-        status_list = [
-            [y for y in ii.split(" ") if y]
-            for ii in self._status_output.split("\n")[4:-6]
-        ]
-        done = running = waiting = total = held = None
-
-        for li in status_list:
-            if li[2] == job_id:
-                done, running, waiting = li[5:8]
-                held = 0 if len(li) == 10 else li[8]
-                total = li[-2]
-
-        return done, running, waiting, total, held
-
-    def wait_for_job(self, job_id=None):
-        """
-        Wait until the cluster job is done
-        """
-
-        _job_id = job_id or self.job_id
-
-        if _job_id:
-            logger.info("waiting for job with ID " + str(_job_id))
-            time.sleep(5)
-
-            self.collect_condor_status()
-            j = 0
-            while not np.all(np.array(self.condor_status(_job_id)) == None):
-                d, r, w, t, h = self.condor_status(_job_id)
-                logger.info(
-                    f"{time.asctime(time.localtime())} - Job{_job_id}: "
-                    f"{d} done, {r} running, {w} waiting, {h} held of total {t}"
-                )
-                j += 1
-                if j > 7:
-                    logger.info(self._status_output)
-                    j = 0
-                time.sleep(90)
-                self.collect_condor_status()
-
-            logger.info("Done waiting for job with ID " + str(_job_id))
-
-        else:
-            logger.info(f"No Job ID!")
-
-    @property
-    def n_cluster_jobs_per_chunk(self):
-        return self._n_cluster_jobs_per_chunk
-
-    @n_cluster_jobs_per_chunk.setter
-    def n_cluster_jobs_per_chunk(self, value):
-        self._n_cluster_jobs_per_chunk = value
-
-        if value:
-            n_jobs = self.n_chunks * int(value)
-            logger.debug(f'setting {n_jobs} jobs.')
-            self.cluster_jobID_map = np.zeros(len(self.parent_sample.df), dtype=int)
-            self.clusterJob_chunk_map = pd.DataFrame(columns=['chunk_number'])
-
-            for chunk_number in range(self.n_chunks):
-                indices = np.where(self.chunk_map == chunk_number)[0]
-                N_inds_per_job = int(math.ceil(len(indices) / self._n_cluster_jobs_per_chunk))
-                for j in range(self._n_cluster_jobs_per_chunk):
-                    job_nr = chunk_number*self._n_cluster_jobs_per_chunk + j + 1
-                    self.clusterJob_chunk_map.loc[job_nr] = [chunk_number]
-                    start_ind = j * N_inds_per_job
-                    end_ind = start_ind + N_inds_per_job
-                    self.cluster_jobID_map[indices[start_ind:end_ind]] = job_nr
-
-        else:
-            logger.warning(f'Invalid value for n_cluster_jobs_per_chunk: {value}')
-
-    def _get_chunk_number_for_job(self, jobID):
-        chunk_number = self.clusterJob_chunk_map.loc[jobID, 'chunk_number']
-        return chunk_number
-
-    def _save_cluster_info(self):
-        logger.debug(f"writing cluster info to {self.cluster_info_file}")
-        with open(self.cluster_info_file, "wb") as f:
-            pickle.dump((self.cluster_jobID_map, self.clusterJob_chunk_map, self.clean_outliers_when_binning), f)
-
-    def _load_cluster_info(self):
-        logger.debug(f"loading cluster info from {self.cluster_info_file}")
-        with open(self.cluster_info_file, "rb") as f:
-            self.cluster_jobID_map, self.clusterJob_chunk_map, self.clean_outliers_when_binning = pickle.load(f)
-
-    def clear_cluster_log_dir(self):
-        """
-        Clears the directory where cluster logs are stored
-        """
-        fns = self.cluster_log_dir.glob("*")
-        for fn in fns:
-            (self.cluster_log_dir / fn).unlink()
-
-    def make_executable_file(self):
-        """
-        Produces the executable that will be submitted to the NPX cluster.
-        """
-        logging_level = logger.getEffectiveLevel()
-        script_fn = os.path.realpath(__file__)
-
-        txt = (
-            f'{sys.executable} {script_fn} '
-            f'--logging_level {logging_level} '
-            f'--base_name {self.base_name} '
-            f'--min_sep_arcsec {self.min_sep.to("arcsec").value} '
-            f'--n_chunks {self._n_chunks} '
-            f'--job_id $1 '
-            f'--mask_by_position $2'
-        )
-
-        logger.debug("writing executable to " + str(self.executable_filename))
-        with self.executable_filename.open("w") as f:
-            f.write(txt)
-
-    def get_submit_file_filename(self, ids):
-        """
-        Get the filename of the submit file for given job ids
-
-        :param ids: list of job ids
-        :type ids: list
-        :return: filename
-        :rtype: str
-        """
-        ids = np.atleast_1d(ids)
-        ids_string = f"{min(ids)}-{max(ids)}"
-        return self.cluster_dir / f"ids{ids_string}.submit"
-
-    def make_submit_file(
-            self,
-            job_ids: (int, List[int]),
-            node_memory: str = '8G',
-            mask_by_position: bool = False
-    ):
-        """
-        Produces the submit file that will be submitted to the NPX cluster.
-
-        :param job_ids: The job ID or list of job IDs to submit
-        :type job_ids: int or list of ints
-        :param node_memory: The amount of memory to request for each node
-        :type node_memory: str
-        :param mask_by_position: if `True` mask single exposures that are too far away from the bulk
-        :type mask_by_position: bool
-        """
-
-        q = "1 job_id in " + ", ".join(np.atleast_1d(job_ids).astype(str))
-        d = get_directories()
-        data_dir = str(d['data_dir'])
-        bigdata_dir = str(d['bigdata_dir'])
-
-        text = (
-            f"executable = {self.executable_filename} \n"
-            f"environment = \"TIMEWISE_DATA={data_dir} TIMEWISE_BIGDATA={bigdata_dir}\" \n"
-            f"log = $(cluster)_$(process)job.log \n"
-            f"output = $(cluster)_$(process)job.out \n"
-            f"error = $(cluster)_$(process)job.err \n"
-            f"should_transfer_files   = YES \n"
-            f"when_to_transfer_output = ON_EXIT \n"
-            f"arguments = $(job_id) {mask_by_position}\n"
-            f"RequestMemory = {node_memory} \n"
-            f"\n"
-            f"queue {q}"
-        )
-
-        fn = self.get_submit_file_filename(job_ids)
-        logger.debug("writing submitfile at " + fn)
-        with open(fn, "w") as f:
-            f.write(text)
-
-    def submit_to_cluster(self, node_memory, single_chunk=None, mask_by_position=False):
-        """
-        Submit jobs to cluster
-
-        :param node_memory: memory per node
-        :type node_memory: str
-        :param single_chunk: number of single chunk to run on the cluster
-        :type single_chunk: int
-        :param mask_by_position: if `True` mask single exposures that are too far away from the bulk
-        :type mask_by_position: bool
-        :return: ID of the cluster job
-        :rtype: int
-        """
-
-        if isinstance(single_chunk, type(None)):
-            _start_id = 1
-            _end_id = int(self.n_chunks*self.n_cluster_jobs_per_chunk)
-        else:
-            _start_id = int(single_chunk*self.n_cluster_jobs_per_chunk) + 1
-            _end_id = int(_start_id + self.n_cluster_jobs_per_chunk) - 1
-
-        job_ids = list(range(_start_id, _end_id + 1))
-
-        # make data_product files, storing essential info from parent_sample
-        for jobID in job_ids:
-            indices = self.parent_sample.df.index[self.cluster_jobID_map == jobID]
-            logger.debug(f"starting data_product for {len(indices)} objects.")
-            data_product = self._start_data_product(parent_sample_indices=indices)
-            chunk_number = self._get_chunk_number_for_job(jobID)
-            self._save_data_product(data_product, service="tap", chunk_number=chunk_number, jobID=jobID)
-
-        # make position mask files
-        if mask_by_position:
-            if single_chunk:
-                chunk_numbers = [single_chunk]
-            else:
-                chunk_numbers = list(range(self.n_chunks))
-            for c in chunk_numbers:
-                self.get_position_mask(service="tap", chunk_number=c)
-
-        self.make_executable_file()
-        self.make_submit_file(job_ids=job_ids, node_memory=node_memory, mask_by_position=mask_by_position)
-
-        submit_cmd = 'condor_submit ' + self.get_submit_file_filename(job_ids)
-        logger.info(f"{time.asctime(time.localtime())}: {submit_cmd}")
-
-        try:
-            msg = self._execute_bash_command(submit_cmd)
-            logger.info(str(msg))
-            job_id = str(msg).split("cluster ")[-1].split(".")[0]
-            logger.info(f"Running on cluster with ID {job_id}")
-            self.job_id = job_id
-            return job_id
-
-        except OSError:
-            return
-
-    def run_cluster(self, node_memory, service):
-        """
-        Run the DESY cluster
-
-        :param node_memory: memory per node
-        :type node_memory: str
-        :param service: service to use for querying the data
-        :type service: str
-        """
-
-        self.clear_cluster_log_dir()
-        self._save_cluster_info()
-        self.submit_to_cluster(node_memory)
-        self.wait_for_job()
-        for c in range(self.n_chunks):
-            self._combine_data_products(service, chunk_number=c, remove=True, overwrite=True)
-
-    # ---------------------------------------------------- #
-    # END using cluster for downloading and binning        #
-    # ----------------------------------------------------------------------------------- #
-
-    ###########################################################################################################
-    # START MAKE PLOTTING FUNCTIONS     #
-    #####################################
-
-    def plot_lc(
-            self,
-            parent_sample_idx,
-            service='tap',
-            plot_unbinned=False,
-            plot_binned=True,
-            interactive=False,
-            fn=None,
-            ax=None,
-            save=True,
-            lum_key='flux_density',
-            load_from_bigdata_dir=False,
-            **kwargs
-    ):
-        """Make a pretty plot of a lightcurve
-
-        :param parent_sample_idx: The index in the parent sample of the lightcurve
-        :type parent_sample_idx: int or str
-        :param service: the service with which the lightcurves were downloaded
-        :type service: str
-        :param plot_unbinned: plot unbinned data
-        :type plot_unbinned: bool
-        :param plot_binned: plot binned lightcurve
-        :type plot_binned: bool
-        :param interactive: interactive mode
-        :type interactive: bool
-        :param fn: filename, defaults to </path/to/timewise/data/dir>/output/plots/<base_name>/<parent_sample_index>_<lum_key>.pdf
-        :type fn: str
-        :param ax: pre-existing matplotlib.Axis
-        :param save: save the plot
-        :type save: bool
-        :param lum_key: the unit of luminosity to use in the plot, either of 'mag', 'flux_density' or 'luminosity'
-        :type lum_key: str
-        :param load_from_bigdata_dir: load from the the big data storage directory
-        :type load_from_bigdata_dir: bool
-        :param kwargs: any additional kwargs will be passed on to `matplotlib.pyplot.subplots()`
-        :return: the matplotlib.Figure and matplotlib.Axes if `interactive=True`
-        """
-
-        logger.debug(f"loading binned lightcurves")
-
-        _get_unbinned_lcs_fct = self.get_unbinned_lightcurves \
-            if service == 'tap' else self._get_unbinned_lightcurves_gator
-
-        wise_id = self.parent_sample.df.loc[int(parent_sample_idx), self.parent_wise_source_id_key]
-        if isinstance(wise_id, float) and not np.isnan(wise_id):
-            wise_id = int(wise_id)
-        logger.debug(f"{wise_id} for {parent_sample_idx}")
-
-        _chunk_number = self._get_chunk_number(parent_sample_index=parent_sample_idx)
-        data_product = self.load_data_product(
-            service,
-            chunk_number=_chunk_number,
-            use_bigdata_dir=load_from_bigdata_dir
-        )
-        lc = pd.DataFrame.from_dict(data_product[parent_sample_idx]["timewise_lightcurve"])
-
-        if plot_unbinned:
-
-            if service == 'tap':
-                unbinned_lcs = self.get_unbinned_lightcurves(_chunk_number)
-
-            else:
-                unbinned_lcs = self._get_unbinned_lightcurves_gator(_chunk_number)
-
-            unbinned_lc = unbinned_lcs[unbinned_lcs[self._tap_orig_id_key] == int(parent_sample_idx)]
-
-        else:
-            unbinned_lc = None
-
-        _lc = lc if plot_binned else None
-
-        if not fn:
-            fn = self.plots_dir / f"{parent_sample_idx}_{lum_key}.pdf"
-
-        return self._plot_lc(lightcurve=_lc, unbinned_lc=unbinned_lc, interactive=interactive, fn=fn, ax=ax,
-                             save=save, lum_key=lum_key, **kwargs)
-
-    # --------------------------------------------------------------------------------------
-    #             START Chi2 plots
-    # -------------------------------------------
-
-    @cache
-    def get_red_chi2(self, chunk, lum_key, use_bigdata_dir=False):
-        """
-        Get the reduced chi2 for a given chunk or multiple chunks
-
-        :param chunk: the chunk number or list of chunk numbers
-        :type chunk: int or list
-        :param lum_key: the unit of luminosity to use in the plot, either of 'mag', 'flux' or 'flux_density'
-        :type lum_key: str
-        :param use_bigdata_dir: load from the big data storage directory, default is False
-        :type use_bigdata_dir: bool, optional
-        :return: the reduced chi2 for each band, the DataFrame will have columns `chi2`, `med_lum` and `N_datapoints`
-        :rtype: dict[str, pd.DataFrame]
-        """
-
-        logger.info(f"getting reduced chi2 for chunk {chunk}")
-        data_product = self.load_data_product(service="tap", chunk_number=chunk, use_bigdata_dir=use_bigdata_dir)
-
-        chi2_val = {b: dict() for b in self.bands}
-
-        for b in self.bands:
-            key1 = f"{b}_chi2_to_med{lum_key}"
-            key2 = f"{b}_N_datapoints{lum_key}"
-            key3 = f"{b}_median{lum_key}"
-            logger.debug(f"{key1}, {key2}")
-
-            for i, idata_product in tqdm.tqdm(
-                    data_product.items(),
-                    total=len(data_product),
-                    desc="collecting chi2 values"
-            ):
-                if "timewise_metadata" in idata_product:
-                    imetadata = idata_product["timewise_metadata"]
-
-                    if (key1 in imetadata) and (key2 in imetadata):
-                        ndof = (imetadata[key2] - 1)
-                        v = {
-                            "chi2": imetadata[key1] / ndof if ndof > 0 else np.nan,
-                            "med_lum": imetadata[key3],
-                            "N_datapoints": imetadata[key2]
-                        }
-                        chi2_val[b][i] = v
-
-        return {b: pd.DataFrame.from_dict(chi2_val[b], orient='index') for b in self.bands}
-
-    def make_chi2_plot(
-            self,
-            index_mask=None,
-            chunks=None,
-            load_from_bigdata_dir=False,
-            lum_key="_flux_density",
-            interactive=False,
-            save=False,
-            nbins=100,
-            cumulative=True,
-            upper_bound=4
-    ):
-        """
-        Make a plot of the reduced chi2 distribution for a given chunk or multiple chunks
-
-        :param index_mask: a mask to apply to the parent sample, eg {'AGNs': agn_mask}
-        :type index_mask: dict
-        :param chunks: the chunk number or list of chunk numbers
-        :type chunks: int or list
-        :param load_from_bigdata_dir: load from the big data storage directory, default is False
-        :type load_from_bigdata_dir: bool, optional
-        :param lum_key: the unit of luminosity to use in the plot, either of 'mag', 'flux' or 'flux_density'
-        :type lum_key: str
-        :param interactive: return the figure and axes if True, default is False
-        :type interactive: bool
-        :param save: save the plot, default is False
-        :type save: bool
-        :param nbins: the number of bins to use in the histogram, default is 100
-        :type nbins: int
-        :param cumulative: plot the cumulative distribution, default is True
-        :type cumulative: bool
-        :param upper_bound: the upper bound of the x-axis, default is 4
-        :type upper_bound: float
-        :return: the matplotlib.Figure and matplotlib.Axes if `interactive=True`
-        :rtype: tuple[mpl.Figure, mpl.Axes]
-        """
-
-        if chunks is None:
-            chunks = list(range(self.n_chunks))
-
-        chi2_data_list = [self.get_red_chi2(chunk, lum_key, load_from_bigdata_dir) for chunk in chunks]
-        chi2_data = {b: pd.concat([d[b] for d in chi2_data_list]) for b in self.bands}
-
-        N_datapoints = set.intersection(*[set(df["N_datapoints"].unique()) for b, df in chi2_data.items()])
-
-        res = list()
-
-        for n in N_datapoints:
-
-            if n == 1:
-                continue
-
-            chi2_df_sel = {b: df[df["N_datapoints"] == n]["chi2"] for b, df in chi2_data.items()}
-
-            logger.info(f"making chi2 histogram for lightcurves with {n} datapoints")
-
-            fig, axs = plt.subplots(
-                ncols=len(self.bands),
-                figsize=(10, 5),
-                sharey="all",
-                sharex="all"
-            )
-
-            index_colors = (
-                {k: f"C{(i+1)*2}"
-                 for i, k in enumerate(index_mask.keys())}
-                if index_mask is not None else None
-            )
-
-            x = np.linspace(0, upper_bound, nbins)
-            x = np.concatenate([x, [1e6]])
-
-            for ax, band in zip(axs, self.bands):
-                h, b, _ = ax.hist(
-                    chi2_df_sel[band].values.flatten(),
-                    label="all",
-                    density=True,
-                    cumulative=cumulative,
-                    color="k",
-                    bins=x,
-                    lw=3,
-                    histtype="step",
-                    zorder=20,
-                )
-                bmids = (b[1:] + b[:-1]) / 2
-
-                # if cumulative then also calculate the histogram of the PDF
-                # this will be used later to calculate the goodness of fit to the F- and Chi2-distribution
-                hpdf = h if not cumulative else \
-                    np.histogram(chi2_df_sel[band].values.flatten(), bins=x, density=True)[0]
-                nonzero_m = hpdf > 0
-
-                # we need the absolute histogram numbers to calculate the uncsertainties of the density bins
-                # The uncertainty of the density bin d_i is
-                #
-                #       u_di = u_ci * sum_{j not i}(c_j) / [(sum_{j}c_j)^2 * (b_{i+1} - b_{i})]
-                #
-                # where u_ci = sqrt(c_i) is the uncertainty of the counts bin c_i
-                #
-                h_abs = np.histogram(chi2_df_sel[band].values.flatten(), bins=x, density=False)[0][nonzero_m]
-                h_abs_sum = np.sum(h_abs)
-                h_sum_not_i = h_abs_sum - h_abs
-                u_density = np.sqrt(h_abs) * h_sum_not_i / (h_abs_sum ** 2 * (np.diff(x))[nonzero_m])
-
-                if index_mask is not None:
-                    for i, (label, indices) in enumerate(index_mask.items()):
-                        _indices = chi2_df_sel[band].index.intersection(indices)
-                        kwargs = (
-                            dict()
-                            if cumulative else
-                            {"edgecolor": "k"}
-                        )
-
-                        sns.histplot(
-                            chi2_df_sel[band].loc[_indices].values.flatten(),
-                            label=label,
-                            stat="density",
-                            bins=b,
-                            ax=ax,
-                            color=index_colors[label],
-                            element="step" if cumulative else "bars",
-                            alpha=0.7,
-                            fill=not cumulative,
-                            zorder=10,
-                            lw=3 if cumulative else 1,
-                            cumulative=cumulative,
-                            **kwargs
-                        )
-
-                # select non-NaN's and values below `upper_bound`
-                x_dense = np.linspace(min(x), upper_bound, 1000)
-                sel = chi2_df_sel[band][(~chi2_df_sel[band].isna()) & (chi2_df_sel[band] < upper_bound)]
-                if len(sel) > 0:
-
-                    # fit an F-distribution
-                    fpars = f.fit(sel, n-1, 1e5, f0=n-1, floc=0)
-                    frozenf = f(*fpars)
-                    fpdf = frozenf.pdf
-
-                    # if cumulative then draw the CDF instead of the PDF
-                    ffunc = frozenf.cdf if cumulative else fpdf
-
-                    # To see how well the distribution fits the data we'll calculate the chi2
-                    # to the PDF (not to the CDF because the bins in CDF are correlated)
-                    ndof_fit = len(bmids[nonzero_m]) - 2
-                    F_chi2fit = sum((hpdf[nonzero_m] - fpdf(bmids[nonzero_m])) ** 2 / u_density**2) / ndof_fit
-
-                    # plot the fitted distribution
-                    ax.plot(x_dense, ffunc(x_dense), color='deepskyblue', ls="--", lw=3,
-                            label=(
-                                rf"F-distribution" + "\n" +
-                                rf"$\nu_1$={fpars[0]:.0f}, $\nu_2$={fpars[1]:.2f}, scale={fpars[-1]:.2f}"
-                            ),
-                            zorder=30
-                            )
-
-                # we will also show the expected chi2 distribution
-                pars_expected = (n - 1, 0, 1 / (n - 1))
-                chi2_expected = chi2(*pars_expected)
-                r = chi2_expected.cdf(x_dense) if cumulative else chi2_expected.pdf(x_dense)
-                chi2_fitchi2 = sum((hpdf[nonzero_m] - chi2_expected.pdf(bmids[nonzero_m])) ** 2 / hpdf[nonzero_m])
-                ax.plot(x_dense, r, color="deepskyblue", ls=":", lw=3,
-                        label=rf"$\chi^2$-distribution" + "\n" + rf"$\nu$: {n - 1:.0f}",
-                        zorder=30)
-
-                ax.legend()
-                ax.set_xlabel(r"$\chi^2_{" + band + "} / N_{visits," + band + "}$")
-                ax.set_xlim(0, upper_bound)
-
-                for loc in ["top", "right"]:
-                    ax.spines[loc].set_visible(False)
-
-            fig.suptitle(f"{n} datapoints")
-            fig.tight_layout()
-
-            if save:
-                kind = "cdf" if cumulative else "pdf"
-                chunk_str = "chunks_" + "_".join([str(c) for c in chunks]) \
-                    if len(chunks) != self.n_chunks \
-                    else "all_chunks"
-                fn = self.plots_dir / f"chi2_plots" / lum_key / f"{n}_datapoints_{kind}_{chunk_str}.pdf"
-                fn.parent.mkdir(parents=True, exist_ok=True)
-                logger.debug(f"saving under {fn}")
-                fig.savefig(fn)
-
-            if interactive:
-                res.append((fig, axs))
-            else:
-                plt.close()
-
-        if interactive:
-            return res
-
-    # -------------------------------------------
-    #             END Chi2 plots
-    # --------------------------------------------------------------------------------------
-
-    # --------------------------------------------------------------------------------------
-    #             START coverage plots
-    # -------------------------------------------
-
-    @cache
-    def get_coverage(self, chunk, lum_key, load_from_bigdata_dir=False):
-        """
-        Get the coverage of the MEASURED median for a given chunk and lum_key
-
-        :param chunk: chunk number
-        :type chunk: int, list[int]]
-        :param lum_key: luminosity key
-        :type lum_key: str
-        :param load_from_bigdata_dir: if True, load the coverage from the bigdata directory
-        :type load_from_bigdata_dir: bool, optional
-        """
-        logger.info(f"getting coverage for chunk {chunk}")
-        data_product = self.load_data_product(service="tap", chunk_number=chunk, use_bigdata_dir=load_from_bigdata_dir)
-
-        coverage_val = {b: dict() for b in self.bands}
-
-        for b in self.bands:
-            key1 = f"{b}_coverage_of_median{lum_key}"
-            for i, idata_product in tqdm.tqdm(
-                    data_product.items(),
-                    total=len(data_product),
-                    desc="collecting coverage values"
-            ):
-                if "timewise_metadata" in idata_product:
-                    imetadata = idata_product["timewise_metadata"]
-
-                    if key1 in imetadata:
-                        v = {
-                            "coverage": imetadata[key1]
-                        }
-                        coverage_val[b][i] = v
-
-        return {b: pd.DataFrame.from_dict(coverage_val[b], orient='index') for b in self.bands}
-
-    @staticmethod
-    def get_quantiles_label(df, cl=0.68):
-        """
-        Get the quantiles label for a given coverage level
-        """
-        med = np.nanmedian(df)
-        ic = np.nanpercentile(df, [50 - cl / 2 * 100, 50 + cl / 2 * 100]) - med
-        label = rf"$ {med:.2f} ^{{ +{ic[1]:.2f} }} _{{ {ic[0]:.2f} }}$"
-        return label
-
-    def make_coverage_plots(
-            self,
-            index_mask=None,
-            chunks=None,
-            load_from_bigdata_dir=False,
-            lum_key="_flux_density",
-            interactive=False,
-            save=False,
-            nbins=100,
-    ):
-        """
-        Make the coverage plots for the measured median of the specified luminosity unit
-
-        :param index_mask: index mask to apply to the data, e.g. {"AGNs": agn_mask}
-        :type index_mask: dict, optional
-        :param chunks: chunks to use, if None use all chunks
-        :type chunks: list[int], int, optional
-        :param load_from_bigdata_dir: if True, load the coverage from the bigdata directory
-        :type load_from_bigdata_dir: bool, optional
-        :param lum_key: luminosity key, either of "_flux_density" or "_mag", default is "_flux_density"
-        :type lum_key: str, optional
-        :param interactive: if True, return the figures and axes, otherwise close them
-        :type interactive: bool, optional
-        :param save: if True, save the figures
-        :type save: bool, optional
-        :param nbins: number of bins for the histograms
-        :type nbins: int, optional
-        :return: if interactive, return the figures and axes, otherwise close them
-        :rtype: list[tuple[matplotlib.figure.Figure, matplotlib.axes.Axes]]
-        """
-
-        if chunks is None:
-            chunks = list(range(self.n_chunks))
-
-        coverages = [self.get_coverage(chunk, lum_key, load_from_bigdata_dir=load_from_bigdata_dir) for chunk in chunks]
-        coverages_df = {b: pd.concat([c[b] for c in coverages]) for b in self.bands}
-
-        fig, axs = plt.subplots(
-            1, len(self.bands),
-            figsize=(len(self.bands) * 4, 4),
-            sharey="all",
-            sharex="all"
-        )
-
-        for ax, band in zip(axs, self.bands):
-            _coverages = coverages_df[band].values.flatten()
-            label = "all\n" + self.get_quantiles_label(_coverages)
-
-            sns.histplot(
-                _coverages,
-                label=label,
-                stat="density",
-                bins=nbins,
-                ax=ax,
-                element="step",
-                fill=False,
-                lw=3,
-                color="k",
-                zorder=20,
-            )
-
-            ax.set_xlabel("coverage " + band)
-            ax.set_xlim(0, 1)
-            fig.suptitle(f"coverage of median")
-            fig.tight_layout()
-
-            if index_mask is not None:
-                for i, (label, indices) in enumerate(index_mask.items()):
-                    _indices = coverages_df[band].index.intersection(indices)
-                    _coverages = coverages_df[band].loc[_indices].values.flatten()
-                    _label = label + "\n" + self.get_quantiles_label(_coverages)
-                    sns.histplot(
-                        _coverages,
-                        label=_label,
-                        stat="density",
-                        bins=nbins,
-                        ax=ax,
-                        color=f"C{(i+1)*2}",
-                        element="bars",
-                        alpha=0.7,
-                        fill=True,
-                        zorder=10
-                    )
-
-            ax.legend()
-            for loc in ["top", "right"]:
-                ax.spines[loc].set_visible(False)
-
-            ax.grid("on", axis="y", ls=":", lw=0.5, color="k", alpha=0.5, zorder=0)
-
-        axs[0].set_ylabel("density")
-
-        if save:
-            chunk_str = "chunks_" + "_".join([str(c) for c in chunks]) \
-                if len(chunks) != self.n_chunks \
-                else "all_chunks"
-            fn = self.plots_dir / f"coverage_plots" / lum_key / f"{chunk_str}.pdf"
-            fn.parent.mkdir(parents=True, exist_ok=True)
-            logger.debug(f"saving under {fn}")
-            fig.savefig(fn)
-
-        if interactive:
-            return fig, axs
-        else:
-            plt.close()
-
-    # -------------------------------------------
-    #             END coverage plots
-    # --------------------------------------------------------------------------------------
-
-    #####################################
-    # END MAKE PLOTTING FUNCTIONS       #
-    ###########################################################################################################
-
-
-if __name__ == '__main__':
-    parser = argparse.ArgumentParser()
-    parser.add_argument('--job_id', type=int)
-    parser.add_argument('--base_name', type=str)
-    parser.add_argument('--min_sep_arcsec', type=float)
-    parser.add_argument('--n_chunks', type=int)
-    parser.add_argument('--mask_by_position', type=str, default=False)
-    parser.add_argument('--logging_level', type=str, default='INFO')
-    cfg = parser.parse_args()
-
-    try:
-        logging_level = int(cfg.logging_level)
-    except ValueError:
-        logging_level = cfg.logging_level.upper()
-
-    logging.getLogger("timewise").setLevel(logging_level)
-    logger = logging.getLogger("timewise.main")
-    logger.info(json.dumps(vars(cfg), indent=4))
-
-    wd = WISEDataDESYCluster(base_name=cfg.base_name,
-                             min_sep_arcsec=cfg.min_sep_arcsec,
-                             n_chunks=cfg.n_chunks,
-                             parent_sample_class=None)
-    wd._load_cluster_info()
-    chunk_number = wd._get_chunk_number_for_job(cfg.job_id)
-
-    match cfg.mask_by_position:
-        case "True":
-            mask_by_position = True
-        case "False":
-            mask_by_position = False
-        case other:
-            raise ValueError(f"mask_by_position has to be either of 'True' or 'False', not {cfg.mask_by_position}")
-
-    wd._subprocess_select_and_bin(
-        service='tap',
-        chunk_number=chunk_number,
-        jobID=cfg.job_id,
-        mask_by_position=mask_by_position
-    )
-    wd.calculate_metadata(service='tap', chunk_number=chunk_number, jobID=cfg.job_id)