From 66d1c7c983b198e04745cff69ca8b50c3c5e39e2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Alberto=20Us=C3=B3n=20Andr=C3=A9s?= <ausonandres@gmail.com>
Date: Wed, 11 Mar 2020 17:28:16 +0100
Subject: [PATCH 01/15] Add function to save histograms as pdf files during map
 creation.

---
 krcal/core/io_functions.py | 45 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 45 insertions(+)

diff --git a/krcal/core/io_functions.py b/krcal/core/io_functions.py
index c3d2ca38..2187a761 100644
--- a/krcal/core/io_functions.py
+++ b/krcal/core/io_functions.py
@@ -1,5 +1,6 @@
 import numpy  as np
 import pandas as pd
+import matplotlib.pyplot as plt
 from   invisible_cities.core.core_functions import shift_to_bin_centers
 from   typing         import Tuple
 from . kr_types       import ASectorMap
@@ -50,3 +51,47 @@ def compute_and_save_hist_as_pd(values     : np.array           ,
     out_file.put(hist_name, table, format='table', data_columns=True)
 
     return
+
+
+
+def compute_and_save_hist_as_pdf(values     : np.array           ,
+                                 out_file   : str                ,
+                                 n_bins     : int                ,
+                                 range_hist : Tuple[float, float],
+                                 title      : str                ,
+                                 x_label    : str                ,
+                                 y_range    : Tuple[float, float],
+                                 norm       : bool = False       )->None:
+    """
+    Computes 1d-histogram and saves it as a pdf image.
+    Parameters
+    ----------
+    values : np.array
+        Array with values to be plotted.
+    out_file: string
+        File where histogram will be saved.
+    n_bins: int
+        Number of bins to make the histogram.
+    range_hist: length-2 tuple (optional)
+        Range of the histogram.
+    title: str
+        Title for the plot.
+    x_label: str
+        Label for X-axis.
+    y_range: length-2 tuple
+        Limit fot Y-axis.
+    norm: bool
+        If True, histogram will be normalized.
+    """
+    fig = plt.figure();
+    plt.hist(values, bins = n_bins,
+             range = range_hist, density = norm,
+             histtype='step', linewidth=2);
+    plt.ylabel('Entries');
+    plt.xlabel(x_label);
+    plt.title(title);
+    plt.ylim(y_range);
+    plt.grid(True, alpha=0.5, color='k', linestyle=':');
+    fig.savefig(out_file.format(title).replace(" ", ""), bbox_inches='tight')
+
+    return

From 90fc3db5081974f64345eb4ca7880d9f9875ad92 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Alberto=20Us=C3=B3n=20Andr=C3=A9s?= <ausonandres@gmail.com>
Date: Wed, 11 Mar 2020 17:30:52 +0100
Subject: [PATCH 02/15] Add function to plot and save as pdf evolution for a
 given parameter

---
 krcal/core/io_functions.py | 50 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 50 insertions(+)

diff --git a/krcal/core/io_functions.py b/krcal/core/io_functions.py
index 2187a761..cf7d37a6 100644
--- a/krcal/core/io_functions.py
+++ b/krcal/core/io_functions.py
@@ -1,6 +1,7 @@
 import numpy  as np
 import pandas as pd
 import matplotlib.pyplot as plt
+import matplotlib.dates  as md
 from   invisible_cities.core.core_functions import shift_to_bin_centers
 from   typing         import Tuple
 from . kr_types       import ASectorMap
@@ -95,3 +96,52 @@ def compute_and_save_hist_as_pdf(values     : np.array           ,
     fig.savefig(out_file.format(title).replace(" ", ""), bbox_inches='tight')
 
     return
+
+
+def plot_and_save_evolution_figure(time        : np.array   ,
+                                   param_name  : str        ,
+                                   param       : np.array   ,
+                                   param_u     : np.array   ,
+                                   units       : str        ,
+                                   file_name   : str        ,
+                                   n_sigmas_lim: int     = 1):
+    """
+    Plot and save evolution of a given parameter vs time.
+    Parameters
+    ----------
+    time : np.array
+        Array with the centers of each time interval (X-values).
+    param_name : string
+        Name of the parameter to plot.
+    param : np.array
+        Array with the magnitude to plot (Y-values).
+    param_u : np.array
+        Array with uncertainty values.
+    units : string
+        Units to be shown in x-label.
+
+    Returns
+    ----------
+    Nothing
+    """
+    fig = plt.figure()
+    plt.errorbar(time, param, param_u, fmt='.')
+    plt.xlabel('Date')
+    plt.ylabel('{0} ({1})'.format(param_name, units));
+    plt.title('{0}'.format(param_name))
+    mean = np.mean(param)
+    std  = np.std(param)
+    plt.ylim(param.min()-std*n_sigmas_lim,
+             param.max()+std*n_sigmas_lim)
+    plt.grid(True, alpha=0.5, color='k', linestyle=':')
+    ax = plt.gca()
+    xfmt = md.DateFormatter('%d-%m %H:%M')
+    ax.xaxis.set_major_formatter(xfmt)
+    plt.xticks( rotation=25 )
+    plt.text(0.03,0.9,
+             'Mean= {0} \n Std= {1}'.format(np.round(mean,4), np.round(std,4)),
+             fontsize=10, transform=ax.transAxes,
+             bbox={'facecolor': 'white', 'alpha': 1, 'pad': 5})
+    fig.savefig(file_name.format(param_name), bbox_inches='tight')
+
+    return

From a2c490f327b5c7c37d6503a368784adfd7874f24 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Alberto=20Us=C3=B3n=20Andr=C3=A9s?= <ausonandres@gmail.com>
Date: Wed, 11 Mar 2020 17:51:35 +0100
Subject: [PATCH 03/15] Add function to select parameter of temp_evol table to
 plot it

---
 krcal/core/plot_utils.py | 42 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 42 insertions(+)
 create mode 100644 krcal/core/plot_utils.py

diff --git a/krcal/core/plot_utils.py b/krcal/core/plot_utils.py
new file mode 100644
index 00000000..473cb325
--- /dev/null
+++ b/krcal/core/plot_utils.py
@@ -0,0 +1,42 @@
+import pandas as pd
+import numpy  as np
+import datetime
+from . io_functions import plot_and_save_evolution_figure
+
+def par_selection_to_plot_vs_time(evol_table: pd.DataFrame,
+                                  file_name : str         ):
+    """
+    Selects parameters in time_evolution map table and
+    applies over them a function to plot all of them
+    Parameters
+    ----------
+    evol_table : pd.DataFrame
+        Table with temporal evolution information.
+    file_name : string
+        Standard name for saved files.
+
+    Returns
+    ----------
+    Nothing
+    """
+    time_ = list(map(datetime.datetime.fromtimestamp, evol_table.ts))
+    units_vect = ['pes', 'mus', 'mm/mus', '%', 'ns', 'pes',
+                  'pes', 'mus', 'pes', 'pes', 'pes', '# SiPM']
+
+    for idx, par in enumerate(evol_table.columns[1:-7:2]):
+        plot_and_save_evolution_figure(time         = time_              ,
+                                       param_name   = par                ,
+                                       param        = evol_table[par]    ,
+                                       param_u      = evol_table[par+'u'],
+                                       units        = units_vect[idx]    ,
+                                       file_name    = file_name          ,
+                                       n_sigmas_lim = 5             )
+    for idx, par in enumerate(evol_table.columns[-3:]):
+        plot_and_save_evolution_figure(time         = time_          ,
+                                       param_name   = par            ,
+                                       param        = evol_table[par],
+                                       param_u      = 0              ,
+                                       units        = '%'            ,
+                                       file_name    = file_name      ,
+                                       n_sigmas_lim = 10             )
+    return

From e99e9826f46d12cb985adf59a023c5439ce76a43 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Alberto=20Us=C3=B3n=20Andr=C3=A9s?= <ausonandres@gmail.com>
Date: Wed, 11 Mar 2020 18:07:40 +0100
Subject: [PATCH 04/15] Change checking function to save histogram files
 separately as pdf

---
 krcal/map_builder/map_builder_functions.py | 34 ++++++++++++++++++++++
 1 file changed, 34 insertions(+)

diff --git a/krcal/map_builder/map_builder_functions.py b/krcal/map_builder/map_builder_functions.py
index 2c43771e..6f4b2b45 100644
--- a/krcal/map_builder/map_builder_functions.py
+++ b/krcal/map_builder/map_builder_functions.py
@@ -26,6 +26,7 @@
 from .. core.kr_parevol_functions          import get_number_of_time_bins
 from .. core.io_functions                  import write_complete_maps
 from .. core.io_functions                  import compute_and_save_hist_as_pd
+from .. core.io_functions                  import compute_and_save_hist_as_pdf
 from .. core.histo_functions               import compute_similar_histo
 from .. core.histo_functions               import normalize_histo_and_poisson_error
 from .. core.histo_functions               import ref_hist
@@ -121,6 +122,7 @@ def selection_nS_mask_and_checking(dst        : pd.DataFrame                ,
                                    column     : type_of_signal              ,
                                    interval   : Tuple[float, float]         ,
                                    output_f   : pd.HDFStore                 ,
+                                   monitoring : str                 = None  ,
                                    input_mask : np.array            = None  ,
                                    nbins_hist : int                 = 10    ,
                                    range_hist : Tuple[float, float] = (0,10),
@@ -141,6 +143,8 @@ def selection_nS_mask_and_checking(dst        : pd.DataFrame                ,
         (given by the config file) the map production will abort.
     output_f: pd.HDFStore
         File where histogram will be saved.
+    monitoring: str (optional)
+        If specified (with a file name) a histogram will be save with that name.
     input_mask: np.array (Optional)
         Selection mask of the previous cut. If this is the first selection
         cut, input_mask is set to be an all True array.
@@ -172,6 +176,17 @@ def selection_nS_mask_and_checking(dst        : pd.DataFrame                ,
                                 range_hist = range_hist,
                                 norm       = norm)
 
+    if monitoring:
+        compute_and_save_hist_as_pdf(values     = getattr(mod_dst,
+                                                          column.value),
+                                     out_file   = monitoring,
+                                     n_bins     = nbins_hist,
+                                     range_hist = range_hist,
+                                     title      = column.value,
+                                     x_label    = column.value,
+                                     y_range    = (0,1),
+                                     norm       = norm)
+
     message  = "Selection efficiency of "
     message += column.value
     message += "==1 ({0}) out of range ".format(np.round(eff, 3))
@@ -220,6 +235,8 @@ def check_Z_dst(Z_vect   : np.array     ,
 def check_rate_and_hist(times      : np.array           ,
                         output_f   : pd.HDFStore        ,
                         name_table : str                ,
+                        hist_title : str                ,
+                        monitoring : str         = None ,
                         n_dev      : float       = 5    ,
                         bin_size   : int         = 180  ,
                         normed     : bool        = False)->None:
@@ -234,6 +251,10 @@ def check_rate_and_hist(times      : np.array           ,
         File where histogram will be saved.
     name_table: string
         Name for the histogram table inside file.
+    hist_title: sting
+        Name for the histogram title.
+    monitoring: str (optional)
+        If specified, histogram plots will be save with given name.
     n_dev: float
         Relative standard deviation to judge if
         distribution is correct.
@@ -260,6 +281,16 @@ def check_rate_and_hist(times      : np.array           ,
                                 range_hist= (min_time  ,
                                              max_time) ,
                                 norm      = normed     )
+    if monitoring:
+        compute_and_save_hist_as_pdf(values     = times,
+                                     out_file   = monitoring,
+                                     n_bins     = ntimebins,
+                                     range_hist = (min_time  ,
+                                                   max_time),
+                                     title      = hist_title,
+                                     x_label    = 'Time (s)',
+                                     y_range    = (0,6000),
+                                     norm       = normed)
 
     n, _     = np.histogram(times, bins=ntimebins,
                             range = (min_time, max_time))
@@ -628,12 +659,14 @@ def apply_cuts(dst              : pd.DataFrame       ,
                nsigmas_Zdst     : float              ,
                bootstrapmap     : ASectorMap         ,
                band_sel_params  : dict               ,
+               monitoring       : str                ,
                ) -> pd.DataFrame:
     n0    = dst.event.nunique()
     mask1 = selection_nS_mask_and_checking(dst = dst                  ,
                                            column = S1_signal         ,
                                            interval = nS1_eff_interval,
                                            output_f = store_hist_s1   ,
+                                           monitoring = monitoring    ,
                                            **ns1_histo_params         )
     nS1   = dst[mask1].event.nunique()
     print("    1 S1 cut efficiency within the expectations ({0:2.2f}%)".format(nS1/n0*100))
@@ -641,6 +674,7 @@ def apply_cuts(dst              : pd.DataFrame       ,
                                            column = S2_signal         ,
                                            interval = nS2_eff_interval,
                                            output_f = store_hist_s2   ,
+                                           monitoring = monitoring    ,
                                            input_mask = mask1         ,
                                            **ns2_histo_params         )
     nS2   = dst[mask2].event.nunique()

From 8d325f01aa2e176a354db0704ac2b5bdda46278d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Alberto=20Us=C3=B3n=20Andr=C3=A9s?= <ausonandres@gmail.com>
Date: Wed, 11 Mar 2020 18:10:17 +0100
Subject: [PATCH 05/15] Change code to not save histograms as DataFrame in one
 file

---
 krcal/map_builder/map_builder_functions.py | 104 ++++++++-------------
 1 file changed, 39 insertions(+), 65 deletions(-)

diff --git a/krcal/map_builder/map_builder_functions.py b/krcal/map_builder/map_builder_functions.py
index 6f4b2b45..435e6a26 100644
--- a/krcal/map_builder/map_builder_functions.py
+++ b/krcal/map_builder/map_builder_functions.py
@@ -25,7 +25,6 @@
 from .. core.kr_parevol_functions          import cut_time_evolution
 from .. core.kr_parevol_functions          import get_number_of_time_bins
 from .. core.io_functions                  import write_complete_maps
-from .. core.io_functions                  import compute_and_save_hist_as_pd
 from .. core.io_functions                  import compute_and_save_hist_as_pdf
 from .. core.histo_functions               import compute_similar_histo
 from .. core.histo_functions               import normalize_histo_and_poisson_error
@@ -121,7 +120,6 @@ def load_data(input_path         : str ,
 def selection_nS_mask_and_checking(dst        : pd.DataFrame                ,
                                    column     : type_of_signal              ,
                                    interval   : Tuple[float, float]         ,
-                                   output_f   : pd.HDFStore                 ,
                                    monitoring : str                 = None  ,
                                    input_mask : np.array            = None  ,
                                    nbins_hist : int                 = 10    ,
@@ -141,8 +139,6 @@ def selection_nS_mask_and_checking(dst        : pd.DataFrame                ,
     interval: length-2 tuple
         If the selection efficiency is out of this interval
         (given by the config file) the map production will abort.
-    output_f: pd.HDFStore
-        File where histogram will be saved.
     monitoring: str (optional)
         If specified (with a file name) a histogram will be save with that name.
     input_mask: np.array (Optional)
@@ -168,13 +164,6 @@ def selection_nS_mask_and_checking(dst        : pd.DataFrame                ,
     eff              = nevts_after / nevts_before
 
     mod_dst = dst[['event', column.value]].drop_duplicates()
-    compute_and_save_hist_as_pd(values     = getattr(mod_dst,
-                                                     column.value),
-                                out_file   = output_f,
-                                hist_name  = column.value,
-                                n_bins     = nbins_hist,
-                                range_hist = range_hist,
-                                norm       = norm)
 
     if monitoring:
         compute_and_save_hist_as_pdf(values     = getattr(mod_dst,
@@ -233,8 +222,6 @@ def check_Z_dst(Z_vect   : np.array     ,
     return;
 
 def check_rate_and_hist(times      : np.array           ,
-                        output_f   : pd.HDFStore        ,
-                        name_table : str                ,
                         hist_title : str                ,
                         monitoring : str         = None ,
                         n_dev      : float       = 5    ,
@@ -247,10 +234,6 @@ def check_rate_and_hist(times      : np.array           ,
     ----------
     times: np.array
         Time of the events.
-    output_f: pd.HDFStore
-        File where histogram will be saved.
-    name_table: string
-        Name for the histogram table inside file.
     hist_title: sting
         Name for the histogram title.
     monitoring: str (optional)
@@ -274,13 +257,6 @@ def check_rate_and_hist(times      : np.array           ,
                                          min_time,
                                          max_time)
 
-    compute_and_save_hist_as_pd(values    = times      ,
-                                out_file  = output_f   ,
-                                hist_name = name_table ,
-                                n_bins    = ntimebins  ,
-                                range_hist= (min_time  ,
-                                             max_time) ,
-                                norm      = normed     )
     if monitoring:
         compute_and_save_hist_as_pdf(values     = times,
                                      out_file   = monitoring,
@@ -649,11 +625,9 @@ def compute_map(dst          : pd.DataFrame,
 def apply_cuts(dst              : pd.DataFrame       ,
                S1_signal        : type_of_signal     ,
                nS1_eff_interval : Tuple[float, float],
-               store_hist_s1    : pd.HDFStore        ,
                ns1_histo_params : dict               ,
                S2_signal        : type_of_signal     ,
                nS2_eff_interval : Tuple[float, float],
-               store_hist_s2    : pd.HDFStore        ,
                ns2_histo_params : dict               ,
                ref_Z_histo      : pd.DataFrame       ,
                nsigmas_Zdst     : float              ,
@@ -665,7 +639,6 @@ def apply_cuts(dst              : pd.DataFrame       ,
     mask1 = selection_nS_mask_and_checking(dst = dst                  ,
                                            column = S1_signal         ,
                                            interval = nS1_eff_interval,
-                                           output_f = store_hist_s1   ,
                                            monitoring = monitoring    ,
                                            **ns1_histo_params         )
     nS1   = dst[mask1].event.nunique()
@@ -673,7 +646,6 @@ def apply_cuts(dst              : pd.DataFrame       ,
     mask2 = selection_nS_mask_and_checking(dst = dst                  ,
                                            column = S2_signal         ,
                                            interval = nS2_eff_interval,
-                                           output_f = store_hist_s2   ,
                                            monitoring = monitoring    ,
                                            input_mask = mask1         ,
                                            **ns2_histo_params         )
@@ -710,43 +682,45 @@ def map_builder(config):
                                                quality_ranges     = config.quality_ranges    ,
                                                **config.ref_Z_histogram                      )
 
-    with pd.HDFStore(config.file_out_hists, "w", complib=str("zlib"), complevel=4) as store_hist:
-        print("Checking the dst and appling 1S1, 1S2 and z-band selections:")
-
-        nev_before = dst.event.nunique()
-        print("    Number of events before any selection: {0}".format(nev_before))
-        check_rate_and_hist(times      = dst.time         ,
-                            output_f   = store_hist       ,
-                            name_table = "rate_before_sel",
-                            n_dev      = config.n_dev_rate,
-                            **config.rate_histo_params    )
-
-        dst_passed_cut, masks = apply_cuts(dst       = dst                    ,
-                                    S1_signal        = type_of_signal.nS1     ,
-                                    nS1_eff_interval = (config.nS1_eff_min    ,
-                                                        config.nS1_eff_max)   ,
-                                    store_hist_s1    = store_hist             ,
-                                    ns1_histo_params = config.ns1_histo_params,
-                                    S2_signal        = type_of_signal.nS2     ,
-                                    nS2_eff_interval = (config.nS2_eff_min    ,
-                                                        config.nS2_eff_max)   ,
-                                    store_hist_s2    = store_hist             ,
-                                    ns2_histo_params = config.ns2_histo_params,
-                                    nsigmas_Zdst     = config.nsigmas_Zdst    ,
-                                    ref_Z_histo      = ref_histos.
-                                                           Z_dist_hist,
-                                    bootstrapmap     = bootstrapmap           ,
-                                    band_sel_params  = config.band_sel_params )
-
-        check_rate_and_hist(times      = dst_passed_cut.time,
-                            output_f   = store_hist         ,
-                            name_table = "rate_after_sel"   ,
-                            n_dev      = config.n_dev_rate  ,
-                            **config.rate_histo_params      )
-
-        nev_after = dst_passed_cut.event.nunique()
-        ratio     = nev_after/nev_before*100
-        print("    Number of events passing the cuts: {0} ({1:2.2f}%)".format(nev_after, ratio))
+    monitoring = config.monitoring_path
+    if monitoring:
+        monitoring = monitoring + 'Run{0}_{{0}}_plot.pdf'.format(config.run_number)
+
+    print("Checking the dst and appling 1S1, 1S2 and z-band selections:")
+
+    nev_before = dst.event.nunique()
+    print("    Number of events before any selection: {0}".format(nev_before))
+    check_rate_and_hist(times      = dst.time         ,
+                        hist_title = "Rate Before Selection",
+                        monitoring = monitoring,
+                        n_dev      = config.n_dev_rate,
+                        **config.rate_histo_params    )
+
+    dst_passed_cut, masks = apply_cuts(dst       = dst                    ,
+                                S1_signal        = type_of_signal.nS1     ,
+                                nS1_eff_interval = (config.nS1_eff_min    ,
+                                                    config.nS1_eff_max)   ,
+                                ns1_histo_params = config.ns1_histo_params,
+                                S2_signal        = type_of_signal.nS2     ,
+                                nS2_eff_interval = (config.nS2_eff_min    ,
+                                                    config.nS2_eff_max)   ,
+                                ns2_histo_params = config.ns2_histo_params,
+                                nsigmas_Zdst     = config.nsigmas_Zdst    ,
+                                ref_Z_histo      = ref_histos.
+                                                       Z_dist_hist        ,
+                                bootstrapmap     = bootstrapmap           ,
+                                band_sel_params  = config.band_sel_params ,
+                                monitoring       = monitoring             )
+
+    check_rate_and_hist(times      = dst_passed_cut.time         ,
+                        hist_title = "Rate After Selection",
+                        monitoring = monitoring,
+                        n_dev      = config.n_dev_rate,
+                        **config.rate_histo_params    )
+
+    nev_after = dst_passed_cut.event.nunique()
+    ratio     = nev_after/nev_before*100
+    print("    Number of events passing the cuts: {0} ({1:2.2f}%)".format(nev_after, ratio))
 
 
     print("Map computation:")

From 11e8dd358a128aeeb425515231d1ea13186d52c6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Alberto=20Us=C3=B3n=20Andr=C3=A9s?= <ausonandres@gmail.com>
Date: Wed, 11 Mar 2020 18:11:25 +0100
Subject: [PATCH 06/15] Add functionality to plot and save evolution of krypton
 parameters

---
 krcal/map_builder/map_builder_functions.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/krcal/map_builder/map_builder_functions.py b/krcal/map_builder/map_builder_functions.py
index 435e6a26..39303867 100644
--- a/krcal/map_builder/map_builder_functions.py
+++ b/krcal/map_builder/map_builder_functions.py
@@ -29,6 +29,7 @@
 from .. core.histo_functions               import compute_similar_histo
 from .. core.histo_functions               import normalize_histo_and_poisson_error
 from .. core.histo_functions               import ref_hist
+from .. core.plot_utils                    import par_selection_to_plot_vs_time
 
 from . checking_functions                  import check_if_values_in_interval
 from . checking_functions                  import check_failed_fits
@@ -746,4 +747,8 @@ def map_builder(config):
     write_complete_maps(asm      = final_map          ,
                         filename = config.file_out_map)
     print("Map successfully computed and saved in : {0}".format(config.file_out_map))
-    print("Control histograms saved in            : {0}".format(config.file_out_hists))
+    if monitoring:
+        par_selection_to_plot_vs_time(evol_table = final_map.t_evol,
+                                      file_name  = monitoring              )
+        print("Control histograms saved in            : {0}".format(monitoring.
+                    replace(monitoring.split('/', -1)[-1], '')))

From ed36e665617c9aaa2f074f51dd5a256546406a61 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Alberto=20Us=C3=B3n=20Andr=C3=A9s?= <ausonandres@gmail.com>
Date: Wed, 11 Mar 2020 19:14:06 +0100
Subject: [PATCH 07/15] Adapt config. files to new feature

---
 krcal/map_builder/config_HEcal.conf            | 2 +-
 krcal/map_builder/config_HEcal_HighKrRate.conf | 2 +-
 krcal/map_builder/config_LBphys.conf           | 2 +-
 krcal/map_builder/config_LBphys_run4.conf      | 2 +-
 krcal/map_builder/config_NoChecks.conf         | 2 +-
 5 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/krcal/map_builder/config_HEcal.conf b/krcal/map_builder/config_HEcal.conf
index b67cca60..34bf0b9a 100644
--- a/krcal/map_builder/config_HEcal.conf
+++ b/krcal/map_builder/config_HEcal.conf
@@ -2,7 +2,7 @@ folder             = '{folderin}'
 file_in            = '{filein}'
 file_bootstrap_map = '$ICDIR/database/test_data/kr_emap_xy_100_100_r_6573_time.h5'
 file_out_map       = '{fileoutmap}'
-file_out_hists     = '{fileouthist}'
+monitoring_path    = '{folderouthists}'
 
 # High Energy Configuration File:
 ref_Z_histogram    = dict(
diff --git a/krcal/map_builder/config_HEcal_HighKrRate.conf b/krcal/map_builder/config_HEcal_HighKrRate.conf
index 24d46f88..385948bc 100644
--- a/krcal/map_builder/config_HEcal_HighKrRate.conf
+++ b/krcal/map_builder/config_HEcal_HighKrRate.conf
@@ -2,7 +2,7 @@ folder             = '{folderin}'
 file_in            = '{filein}'
 file_bootstrap_map = '$ICDIR/database/test_data/kr_emap_xy_100_100_r_6573_time.h5'
 file_out_map       = '{fileoutmap}'
-file_out_hists     = '{fileouthist}'
+monitoring_path    = '{folderouthists}'
 
 # High Energy Configuration File:
 ref_Z_histogram    = dict(
diff --git a/krcal/map_builder/config_LBphys.conf b/krcal/map_builder/config_LBphys.conf
index 776ee2f6..e78caefa 100644
--- a/krcal/map_builder/config_LBphys.conf
+++ b/krcal/map_builder/config_LBphys.conf
@@ -2,7 +2,7 @@ folder             = '{folderin}'
 file_in            = '{filein}'
 file_bootstrap_map = '$ICDIR/database/test_data/kr_emap_xy_100_100_r_6573_time.h5'
 file_out_map       = '{fileoutmap}'
-file_out_hists     = '{fileouthist}'
+monitoring_path    = '{folderouthists}'
 
 # Low Background Configuration File:
 ref_Z_histogram    = dict(
diff --git a/krcal/map_builder/config_LBphys_run4.conf b/krcal/map_builder/config_LBphys_run4.conf
index 6b13710c..960580a0 100644
--- a/krcal/map_builder/config_LBphys_run4.conf
+++ b/krcal/map_builder/config_LBphys_run4.conf
@@ -2,7 +2,7 @@ folder             = '{folderin}'
 file_in            = '{filein}'
 file_bootstrap_map = '$ICDIR/database/test_data/kr_emap_xy_100_100_r_6573_time.h5'
 file_out_map       = '{fileoutmap}'
-file_out_hists     = '{fileouthist}'
+monitoring_path    = '{folderouthists}'
 
 # Low Background Configuration File:
 ref_Z_histogram    = dict(
diff --git a/krcal/map_builder/config_NoChecks.conf b/krcal/map_builder/config_NoChecks.conf
index 169cd9ac..27382dcc 100644
--- a/krcal/map_builder/config_NoChecks.conf
+++ b/krcal/map_builder/config_NoChecks.conf
@@ -2,7 +2,7 @@ folder             = '{folderin}'
 file_in            = '{filein}'
 file_bootstrap_map = '$ICDIR/database/test_data/kr_emap_xy_100_100_r_6573_time.h5'
 file_out_map       = '{fileoutmap}'
-file_out_hists     = '{fileouthist}'
+monitoring_path    = '{folderouthists}'
 
 # High Energy Configuration File:
 ref_Z_histogram    = dict(

From f8c7355e224e9e629ad9ee9a478f2175b2aee2be Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Alberto=20Us=C3=B3n=20Andr=C3=A9s?= <ausonandres@gmail.com>
Date: Thu, 12 Mar 2020 09:13:31 +0100
Subject: [PATCH 08/15] Change test functions to fit new functionality

---
 .../map_builder/map_builder_functions_test.py | 92 +++++++++----------
 1 file changed, 46 insertions(+), 46 deletions(-)

diff --git a/krcal/map_builder/map_builder_functions_test.py b/krcal/map_builder/map_builder_functions_test.py
index 75a261a2..6c3b1e38 100644
--- a/krcal/map_builder/map_builder_functions_test.py
+++ b/krcal/map_builder/map_builder_functions_test.py
@@ -44,10 +44,10 @@ def test_scrip_runs_and_produces_correct_outputs(folder_test_dst  ,
     """
     Run map creation script and check if an ASectormap is the output.
     """
-    map_file_out   = os.path.join(output_maps_tmdir, 'test_out_map.h5')
-    histo_file_out = os.path.join(output_maps_tmdir, 'test_out_histo.h5')
-    default_n_bins = 15
-    run_number     = 7517
+    map_file_out    = os.path.join(output_maps_tmdir, 'test_out_map.h5')
+    monitoring_path = None
+    default_n_bins  = 15
+    run_number      = 7517
     config = configure('maps $ICARO/krcal/map_builder/config_LBphys.conf'.split())
     map_params_new = copy.copy(config.as_namespace.map_params)
     map_params_new['nmin']          = 100
@@ -149,7 +149,7 @@ def test_correct_map_with_unsorted_dst(folder_test_dst  ,
     """
     map_file_sort   = os.path.join(output_maps_tmdir, 'test_out_map.h5')
     map_file_unsort = os.path.join(output_maps_tmdir, 'test_out_unsort.h5')
-    histo_file_out = os.path.join(output_maps_tmdir, 'test_out_histo.h5')
+    monitoring_path = None
 
     dst = load_dst(folder_test_dst+test_dst_file, 'DST', 'Events')
     if "index" in dst:del dst["index"]
@@ -190,18 +190,18 @@ def test_exception_s1(folder_test_dst, test_dst_file, output_maps_tmdir):
     This test checks if exception raises when ns1=1 efficiency is out of range.
     """
     conf = configure('maps $ICARO/krcal/map_builder/config_LBphys.conf'.split())
-    map_file_out   = os.path.join(output_maps_tmdir, 'test_out_map_s1.h5'  )
-    histo_file_out = os.path.join(output_maps_tmdir, 'test_out_histo_s1.h5')
+    map_file_out    = os.path.join(output_maps_tmdir, 'test_out_map_s1.h5'  )
+    monitoring_path = None
     min_eff_test = 0.
     max_eff_test = 0.8
     run_number   = 7517
-    conf.update(dict(folder         = folder_test_dst,
-                     file_in        = test_dst_file  ,
-                     file_out_map   = map_file_out   ,
-                     file_out_hists = histo_file_out ,
-                     nS1_eff_min    = min_eff_test   ,
-                     nS1_eff_max    = max_eff_test   ,
-                     run_number     = run_number     ))
+    conf.update(dict(folder          = folder_test_dst,
+                     file_in         = test_dst_file  ,
+                     file_out_map    = map_file_out   ,
+                     monitoring_path = monitoring_path,
+                     nS1_eff_min     = min_eff_test   ,
+                     nS1_eff_max     = max_eff_test   ,
+                     run_number      = run_number     ))
 
     assert_raises(AbortingMapCreation,
                   map_builder        ,
@@ -212,18 +212,18 @@ def test_exception_s2(folder_test_dst, test_dst_file, output_maps_tmdir):
     This test checks if exception raises when nS2=1 efficiency is out of range.
     """
     conf = configure('maps $ICARO/krcal/map_builder/config_LBphys.conf'.split())
-    map_file_out   = os.path.join(output_maps_tmdir, 'test_out_map_s2.h5'  )
-    histo_file_out = os.path.join(output_maps_tmdir, 'test_out_histo_s2.h5')
+    map_file_out    = os.path.join(output_maps_tmdir, 'test_out_map_s2.h5'  )
+    monitoring_path = None
     min_eff_test = 0.
     max_eff_test = 0.9
     run_number   = 7517
-    conf.update(dict(folder         = folder_test_dst,
-                     file_in        = test_dst_file  ,
-                     file_out_map   = map_file_out   ,
-                     file_out_hists = histo_file_out ,
-                     nS2_eff_min    = min_eff_test   ,
-                     nS2_eff_max    = max_eff_test   ,
-                     run_number     = run_number     ))
+    conf.update(dict(folder          = folder_test_dst ,
+                     file_in         = test_dst_file   ,
+                     file_out_map    = map_file_out    ,
+                     monitoring_path = monitoring_path ,
+                     nS2_eff_min     = min_eff_test    ,
+                     nS2_eff_max     = max_eff_test    ,
+                     run_number      = run_number      ))
 
     assert_raises(AbortingMapCreation,
                   map_builder        ,
@@ -234,16 +234,16 @@ def test_exception_rate(folder_test_dst, test_dst_file, output_maps_tmdir):
     This test checks if exception raises when rate distribution is not flat enough.
     """
     conf = configure('maps $ICARO/krcal/map_builder/config_LBphys.conf'.split())
-    map_file_out   = os.path.join(output_maps_tmdir, 'test_out_map_rate.h5'  )
-    histo_file_out = os.path.join(output_maps_tmdir, 'test_out_histo_rate.h5')
+    map_file_out    = os.path.join(output_maps_tmdir, 'test_out_map_rate.h5'  )
+    monitoring_path = None
     n_dev_rate = 0.5
     run_number   = 7517
-    conf.update(dict(folder         = folder_test_dst,
-                     file_in        = test_dst_file  ,
-                     file_out_map   = map_file_out   ,
-                     file_out_hists = histo_file_out ,
-                     n_dev_rate     = n_dev_rate     ,
-                     run_number     = run_number     ))
+    conf.update(dict(folder          = folder_test_dst,
+                     file_in         = test_dst_file  ,
+                     file_out_map    = map_file_out   ,
+                     monitoring_path = monitoring_path,
+                     n_dev_rate      = n_dev_rate     ,
+                     run_number      = run_number     ))
 
     assert_raises(AbortingMapCreation,
                   map_builder        ,
@@ -255,16 +255,16 @@ def test_exception_Zdst(folder_test_dst, test_dst_file, output_maps_tmdir):
     similar enough to the reference one.
     """
     conf = configure('maps $ICARO/krcal/map_builder/config_LBphys.conf'.split())
-    map_file_out   = os.path.join(output_maps_tmdir, 'test_out_map_Z.h5'  )
-    histo_file_out = os.path.join(output_maps_tmdir, 'test_out_histo_Z.h5')
+    map_file_out    = os.path.join(output_maps_tmdir, 'test_out_map_Z.h5'  )
+    monitoring_path = None
     nsigmas_Zdst = 0.5
     run_number   = 7517
-    conf.update(dict(folder         = folder_test_dst,
-                     file_in        = test_dst_file  ,
-                     file_out_map   = map_file_out   ,
-                     file_out_hists = histo_file_out ,
-                     nsigmas_Zdst   = nsigmas_Zdst   ,
-                     run_number     = run_number     ))
+    conf.update(dict(folder          = folder_test_dst,
+                     file_in         = test_dst_file  ,
+                     file_out_map    = map_file_out   ,
+                     monitoring_path = monitoring_path,
+                     nsigmas_Zdst    = nsigmas_Zdst   ,
+                     run_number      = run_number     ))
 
     assert_raises(AbortingMapCreation,
                   map_builder        ,
@@ -276,18 +276,18 @@ def test_exception_bandsel(folder_test_dst, test_dst_file, output_maps_tmdir):
     out of a given range.
     """
     conf = configure('maps $ICARO/krcal/map_builder/config_LBphys.conf'.split())
-    map_file_out   = os.path.join(output_maps_tmdir, 'test_out_map_bandsel.h5'  )
-    histo_file_out = os.path.join(output_maps_tmdir, 'test_out_histo_bandsel.h5')
+    map_file_out    = os.path.join(output_maps_tmdir, 'test_out_map_bandsel.h5'  )
+    monitoring_path = None
     band_sel_params_new = copy.copy(conf.as_namespace.band_sel_params)
     band_sel_params_new['eff_min'] = 0.
     band_sel_params_new['eff_max'] = 0.89
     run_number = 7517
-    conf.update(dict(folder         = folder_test_dst,
-                     file_in        = test_dst_file  ,
-                     file_out_map   = map_file_out   ,
-                     file_out_hists = histo_file_out ,
+    conf.update(dict(folder          = folder_test_dst    ,
+                     file_in         = test_dst_file      ,
+                     file_out_map    = map_file_out       ,
+                     monitoring_path = monitoring_path    ,
                      band_sel_params = band_sel_params_new,
-                     run_number     = run_number     ))
+                     run_number      = run_number         ))
     assert_raises(AbortingMapCreation,
                   map_builder        ,
                   conf.as_namespace  )

From 2b33dcc3a2229a6922d199dd41e92d5c0e7c8a8e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Alberto=20Us=C3=B3n=20Andr=C3=A9s?= <ausonandres@gmail.com>
Date: Thu, 12 Mar 2020 10:18:07 +0100
Subject: [PATCH 09/15] Add test to check that plots have been saved
 successfully

---
 .../map_builder/map_builder_functions_test.py | 24 +++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/krcal/map_builder/map_builder_functions_test.py b/krcal/map_builder/map_builder_functions_test.py
index 6c3b1e38..9e1e4494 100644
--- a/krcal/map_builder/map_builder_functions_test.py
+++ b/krcal/map_builder/map_builder_functions_test.py
@@ -291,3 +291,27 @@ def test_exception_bandsel(folder_test_dst, test_dst_file, output_maps_tmdir):
     assert_raises(AbortingMapCreation,
                   map_builder        ,
                   conf.as_namespace  )
+
+
+def test_monitoring_plots_are_created(folder_test_dst, test_dst_file, output_maps_tmdir):
+    """
+    This test checks that monitoring plots are created if a
+    folder to store them is provided.
+    """
+    conf = configure('maps $ICARO/krcal/map_builder/config_LBphys.conf'.split())
+    map_file_out    = os.path.join(output_maps_tmdir, 'test_out_map.h5'  )
+    monitoring_path = output_maps_tmdir
+    default_n_bins  = 15
+    run_number      = 7517
+    conf.update(dict(folder          = folder_test_dst,
+                     file_in         = test_dst_file  ,
+                     file_out_map    = map_file_out   ,
+                     monitoring_path = monitoring_path,
+                     default_n_bins  = default_n_bins ,
+                     run_number      = run_number     ))
+    emaps = read_maps(map_file_out)
+    pars = emaps.t_evol.columns[1:-7:2].tolist()
+    pars = pars + emaps.t_evol.columns[-3:].tolist()
+    for par in pars:
+        plot_fname = output_maps_tmdir + 'Run{0}_{1}_plot.pdf'.format(run_number, par)
+        assert os.path.exists(output_maps_tmdir)

From cd7c27a3aff970a0a6abfc56dc903a7d8ce58bdc Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Alberto=20Us=C3=B3n=20Andr=C3=A9s?= <ausonandres@gmail.com>
Date: Thu, 12 Mar 2020 12:31:24 +0100
Subject: [PATCH 10/15] Cosmetics

---
 krcal/core/io_functions.py                    | 32 +++++++++++--------
 krcal/core/plot_utils.py                      |  2 +-
 krcal/map_builder/config_HEcal.conf           |  2 +-
 .../map_builder/config_HEcal_HighKrRate.conf  |  2 +-
 krcal/map_builder/config_LBphys.conf          |  2 +-
 krcal/map_builder/config_LBphys_run4.conf     |  2 +-
 krcal/map_builder/config_NoChecks.conf        |  2 +-
 krcal/map_builder/map_builder_functions.py    | 14 ++++----
 .../map_builder/map_builder_functions_test.py | 20 ++++++------
 9 files changed, 41 insertions(+), 37 deletions(-)

diff --git a/krcal/core/io_functions.py b/krcal/core/io_functions.py
index cf7d37a6..089c911c 100644
--- a/krcal/core/io_functions.py
+++ b/krcal/core/io_functions.py
@@ -84,15 +84,18 @@ def compute_and_save_hist_as_pdf(values     : np.array           ,
     norm: bool
         If True, histogram will be normalized.
     """
-    fig = plt.figure();
-    plt.hist(values, bins = n_bins,
-             range = range_hist, density = norm,
-             histtype='step', linewidth=2);
-    plt.ylabel('Entries');
-    plt.xlabel(x_label);
-    plt.title(title);
-    plt.ylim(y_range);
-    plt.grid(True, alpha=0.5, color='k', linestyle=':');
+    fig = plt.figure()
+    plt.hist(values                ,
+             bins      = n_bins    ,
+             range     = range_hist,
+             density   = norm      ,
+             histtype  = 'step'    ,
+             linewidth = 2         );
+    plt.ylabel('Entries')
+    plt.xlabel(x_label)
+    plt.title(title)
+    plt.ylim(y_range)
+    plt.grid(True, alpha=0.5, color='k', linestyle=':')
     fig.savefig(out_file.format(title).replace(" ", ""), bbox_inches='tight')
 
     return
@@ -127,21 +130,22 @@ def plot_and_save_evolution_figure(time        : np.array   ,
     fig = plt.figure()
     plt.errorbar(time, param, param_u, fmt='.')
     plt.xlabel('Date')
-    plt.ylabel('{0} ({1})'.format(param_name, units));
+    plt.ylabel('{0} ({1})'.format(param_name, units))
     plt.title('{0}'.format(param_name))
     mean = np.mean(param)
     std  = np.std(param)
     plt.ylim(param.min()-std*n_sigmas_lim,
              param.max()+std*n_sigmas_lim)
     plt.grid(True, alpha=0.5, color='k', linestyle=':')
-    ax = plt.gca()
+    ax   = plt.gca()
     xfmt = md.DateFormatter('%d-%m %H:%M')
     ax.xaxis.set_major_formatter(xfmt)
     plt.xticks( rotation=25 )
-    plt.text(0.03,0.9,
+    plt.text(0.03, 0.9,
              'Mean= {0} \n Std= {1}'.format(np.round(mean,4), np.round(std,4)),
-             fontsize=10, transform=ax.transAxes,
-             bbox={'facecolor': 'white', 'alpha': 1, 'pad': 5})
+             fontsize  = 10,
+             transform = ax.transAxes,
+             bbox      = {'facecolor': 'white', 'alpha': 1, 'pad': 5})
     fig.savefig(file_name.format(param_name), bbox_inches='tight')
 
     return
diff --git a/krcal/core/plot_utils.py b/krcal/core/plot_utils.py
index 473cb325..6d7454ff 100644
--- a/krcal/core/plot_utils.py
+++ b/krcal/core/plot_utils.py
@@ -19,7 +19,7 @@ def par_selection_to_plot_vs_time(evol_table: pd.DataFrame,
     ----------
     Nothing
     """
-    time_ = list(map(datetime.datetime.fromtimestamp, evol_table.ts))
+    time_      = list(map(datetime.datetime.fromtimestamp, evol_table.ts))
     units_vect = ['pes', 'mus', 'mm/mus', '%', 'ns', 'pes',
                   'pes', 'mus', 'pes', 'pes', 'pes', '# SiPM']
 
diff --git a/krcal/map_builder/config_HEcal.conf b/krcal/map_builder/config_HEcal.conf
index 34bf0b9a..a8c0c36a 100644
--- a/krcal/map_builder/config_HEcal.conf
+++ b/krcal/map_builder/config_HEcal.conf
@@ -2,7 +2,7 @@ folder             = '{folderin}'
 file_in            = '{filein}'
 file_bootstrap_map = '$ICDIR/database/test_data/kr_emap_xy_100_100_r_6573_time.h5'
 file_out_map       = '{fileoutmap}'
-monitoring_path    = '{folderouthists}'
+monitoring_path    = '{folderoutmonitorplots}'
 
 # High Energy Configuration File:
 ref_Z_histogram    = dict(
diff --git a/krcal/map_builder/config_HEcal_HighKrRate.conf b/krcal/map_builder/config_HEcal_HighKrRate.conf
index 385948bc..84a21950 100644
--- a/krcal/map_builder/config_HEcal_HighKrRate.conf
+++ b/krcal/map_builder/config_HEcal_HighKrRate.conf
@@ -2,7 +2,7 @@ folder             = '{folderin}'
 file_in            = '{filein}'
 file_bootstrap_map = '$ICDIR/database/test_data/kr_emap_xy_100_100_r_6573_time.h5'
 file_out_map       = '{fileoutmap}'
-monitoring_path    = '{folderouthists}'
+monitoring_path    = '{folderoutmonitorplots}'
 
 # High Energy Configuration File:
 ref_Z_histogram    = dict(
diff --git a/krcal/map_builder/config_LBphys.conf b/krcal/map_builder/config_LBphys.conf
index e78caefa..64da92a9 100644
--- a/krcal/map_builder/config_LBphys.conf
+++ b/krcal/map_builder/config_LBphys.conf
@@ -2,7 +2,7 @@ folder             = '{folderin}'
 file_in            = '{filein}'
 file_bootstrap_map = '$ICDIR/database/test_data/kr_emap_xy_100_100_r_6573_time.h5'
 file_out_map       = '{fileoutmap}'
-monitoring_path    = '{folderouthists}'
+monitoring_path    = '{folderoutmonitorplots}'
 
 # Low Background Configuration File:
 ref_Z_histogram    = dict(
diff --git a/krcal/map_builder/config_LBphys_run4.conf b/krcal/map_builder/config_LBphys_run4.conf
index 960580a0..0c373fc2 100644
--- a/krcal/map_builder/config_LBphys_run4.conf
+++ b/krcal/map_builder/config_LBphys_run4.conf
@@ -2,7 +2,7 @@ folder             = '{folderin}'
 file_in            = '{filein}'
 file_bootstrap_map = '$ICDIR/database/test_data/kr_emap_xy_100_100_r_6573_time.h5'
 file_out_map       = '{fileoutmap}'
-monitoring_path    = '{folderouthists}'
+monitoring_path    = '{folderoutmonitorplots}'
 
 # Low Background Configuration File:
 ref_Z_histogram    = dict(
diff --git a/krcal/map_builder/config_NoChecks.conf b/krcal/map_builder/config_NoChecks.conf
index 27382dcc..47c15c18 100644
--- a/krcal/map_builder/config_NoChecks.conf
+++ b/krcal/map_builder/config_NoChecks.conf
@@ -2,7 +2,7 @@ folder             = '{folderin}'
 file_in            = '{filein}'
 file_bootstrap_map = '$ICDIR/database/test_data/kr_emap_xy_100_100_r_6573_time.h5'
 file_out_map       = '{fileoutmap}'
-monitoring_path    = '{folderouthists}'
+monitoring_path    = '{folderoutmonitorplots}'
 
 # High Energy Configuration File:
 ref_Z_histogram    = dict(
diff --git a/krcal/map_builder/map_builder_functions.py b/krcal/map_builder/map_builder_functions.py
index 39303867..77252003 100644
--- a/krcal/map_builder/map_builder_functions.py
+++ b/krcal/map_builder/map_builder_functions.py
@@ -167,7 +167,7 @@ def selection_nS_mask_and_checking(dst        : pd.DataFrame                ,
     mod_dst = dst[['event', column.value]].drop_duplicates()
 
     if monitoring:
-        compute_and_save_hist_as_pdf(values     = getattr(mod_dst,
+        compute_and_save_hist_as_pdf(values     = getattr(mod_dst      ,
                                                           column.value),
                                      out_file   = monitoring,
                                      n_bins     = nbins_hist,
@@ -259,15 +259,15 @@ def check_rate_and_hist(times      : np.array           ,
                                          max_time)
 
     if monitoring:
-        compute_and_save_hist_as_pdf(values     = times,
+        compute_and_save_hist_as_pdf(values     = times     ,
                                      out_file   = monitoring,
-                                     n_bins     = ntimebins,
-                                     range_hist = (min_time  ,
+                                     n_bins     = ntimebins ,
+                                     range_hist = (min_time,
                                                    max_time),
                                      title      = hist_title,
                                      x_label    = 'Time (s)',
-                                     y_range    = (0,6000),
-                                     norm       = normed)
+                                     y_range    = (0, 6000) ,
+                                     norm       = normed    )
 
     n, _     = np.histogram(times, bins=ntimebins,
                             range = (min_time, max_time))
@@ -749,6 +749,6 @@ def map_builder(config):
     print("Map successfully computed and saved in : {0}".format(config.file_out_map))
     if monitoring:
         par_selection_to_plot_vs_time(evol_table = final_map.t_evol,
-                                      file_name  = monitoring              )
+                                      file_name  = monitoring      )
         print("Control histograms saved in            : {0}".format(monitoring.
                     replace(monitoring.split('/', -1)[-1], '')))
diff --git a/krcal/map_builder/map_builder_functions_test.py b/krcal/map_builder/map_builder_functions_test.py
index 9e1e4494..e60fd3c3 100644
--- a/krcal/map_builder/map_builder_functions_test.py
+++ b/krcal/map_builder/map_builder_functions_test.py
@@ -192,9 +192,9 @@ def test_exception_s1(folder_test_dst, test_dst_file, output_maps_tmdir):
     conf = configure('maps $ICARO/krcal/map_builder/config_LBphys.conf'.split())
     map_file_out    = os.path.join(output_maps_tmdir, 'test_out_map_s1.h5'  )
     monitoring_path = None
-    min_eff_test = 0.
-    max_eff_test = 0.8
-    run_number   = 7517
+    min_eff_test    = 0.
+    max_eff_test    = 0.8
+    run_number      = 7517
     conf.update(dict(folder          = folder_test_dst,
                      file_in         = test_dst_file  ,
                      file_out_map    = map_file_out   ,
@@ -214,9 +214,9 @@ def test_exception_s2(folder_test_dst, test_dst_file, output_maps_tmdir):
     conf = configure('maps $ICARO/krcal/map_builder/config_LBphys.conf'.split())
     map_file_out    = os.path.join(output_maps_tmdir, 'test_out_map_s2.h5'  )
     monitoring_path = None
-    min_eff_test = 0.
-    max_eff_test = 0.9
-    run_number   = 7517
+    min_eff_test    = 0.
+    max_eff_test    = 0.9
+    run_number      = 7517
     conf.update(dict(folder          = folder_test_dst ,
                      file_in         = test_dst_file   ,
                      file_out_map    = map_file_out    ,
@@ -236,8 +236,8 @@ def test_exception_rate(folder_test_dst, test_dst_file, output_maps_tmdir):
     conf = configure('maps $ICARO/krcal/map_builder/config_LBphys.conf'.split())
     map_file_out    = os.path.join(output_maps_tmdir, 'test_out_map_rate.h5'  )
     monitoring_path = None
-    n_dev_rate = 0.5
-    run_number   = 7517
+    n_dev_rate      = 0.5
+    run_number      = 7517
     conf.update(dict(folder          = folder_test_dst,
                      file_in         = test_dst_file  ,
                      file_out_map    = map_file_out   ,
@@ -257,8 +257,8 @@ def test_exception_Zdst(folder_test_dst, test_dst_file, output_maps_tmdir):
     conf = configure('maps $ICARO/krcal/map_builder/config_LBphys.conf'.split())
     map_file_out    = os.path.join(output_maps_tmdir, 'test_out_map_Z.h5'  )
     monitoring_path = None
-    nsigmas_Zdst = 0.5
-    run_number   = 7517
+    nsigmas_Zdst    = 0.5
+    run_number      = 7517
     conf.update(dict(folder          = folder_test_dst,
                      file_in         = test_dst_file  ,
                      file_out_map    = map_file_out   ,

From 3869b6ce1caee61fee0d306f7ffc9854b0d893d0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Alberto=20Us=C3=B3n=20Andr=C3=A9s?= <ausonandres@gmail.com>
Date: Thu, 12 Mar 2020 12:43:10 +0100
Subject: [PATCH 11/15] Change message when saving monitoring plots

---
 krcal/map_builder/map_builder_functions.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/krcal/map_builder/map_builder_functions.py b/krcal/map_builder/map_builder_functions.py
index 77252003..0e5df271 100644
--- a/krcal/map_builder/map_builder_functions.py
+++ b/krcal/map_builder/map_builder_functions.py
@@ -750,5 +750,4 @@ def map_builder(config):
     if monitoring:
         par_selection_to_plot_vs_time(evol_table = final_map.t_evol,
                                       file_name  = monitoring      )
-        print("Control histograms saved in            : {0}".format(monitoring.
-                    replace(monitoring.split('/', -1)[-1], '')))
+        print("Control plots saved in folder          : {0}".format(config.monitoring_path))

From 83095182a6d64e12a42d19d9cb58f33b291caa5e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Alberto=20Us=C3=B3n=20Andr=C3=A9s?= <ausonandres@gmail.com>
Date: Thu, 12 Mar 2020 12:50:49 +0100
Subject: [PATCH 12/15] Correct Docstrings

---
 krcal/core/io_functions.py                 | 5 +++++
 krcal/map_builder/map_builder_functions.py | 2 +-
 2 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/krcal/core/io_functions.py b/krcal/core/io_functions.py
index 089c911c..6000b5c0 100644
--- a/krcal/core/io_functions.py
+++ b/krcal/core/io_functions.py
@@ -122,6 +122,11 @@ def plot_and_save_evolution_figure(time        : np.array   ,
         Array with uncertainty values.
     units : string
         Units to be shown in x-label.
+    file_name : string
+        Name of file for plots. It must contain '{0}' to be name after
+        the plotted parameter.
+    n_sigmas_lim : int (optional)
+        Number of sigmas to set the Y-axis limits in plots.
 
     Returns
     ----------
diff --git a/krcal/map_builder/map_builder_functions.py b/krcal/map_builder/map_builder_functions.py
index 0e5df271..83e0cb01 100644
--- a/krcal/map_builder/map_builder_functions.py
+++ b/krcal/map_builder/map_builder_functions.py
@@ -235,7 +235,7 @@ def check_rate_and_hist(times      : np.array           ,
     ----------
     times: np.array
         Time of the events.
-    hist_title: sting
+    hist_title: string
         Name for the histogram title.
     monitoring: str (optional)
         If specified, histogram plots will be save with given name.

From 933dfd77ec424e8ed446738f504ed514abfde228 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Alberto=20Us=C3=B3n=20Andr=C3=A9s?= <ausonandres@gmail.com>
Date: Thu, 12 Mar 2020 14:01:34 +0100
Subject: [PATCH 13/15] Change type hints from np.array to np.ndarray

---
 krcal/core/io_functions.py | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/krcal/core/io_functions.py b/krcal/core/io_functions.py
index 6000b5c0..7dfa9c05 100644
--- a/krcal/core/io_functions.py
+++ b/krcal/core/io_functions.py
@@ -55,7 +55,7 @@ def compute_and_save_hist_as_pd(values     : np.array           ,
 
 
 
-def compute_and_save_hist_as_pdf(values     : np.array           ,
+def compute_and_save_hist_as_pdf(values     : np.ndarray          ,
                                  out_file   : str                ,
                                  n_bins     : int                ,
                                  range_hist : Tuple[float, float],
@@ -67,7 +67,7 @@ def compute_and_save_hist_as_pdf(values     : np.array           ,
     Computes 1d-histogram and saves it as a pdf image.
     Parameters
     ----------
-    values : np.array
+    values : np.ndarray
         Array with values to be plotted.
     out_file: string
         File where histogram will be saved.
@@ -101,10 +101,10 @@ def compute_and_save_hist_as_pdf(values     : np.array           ,
     return
 
 
-def plot_and_save_evolution_figure(time        : np.array   ,
+def plot_and_save_evolution_figure(time        : np.ndarray  ,
                                    param_name  : str        ,
-                                   param       : np.array   ,
-                                   param_u     : np.array   ,
+                                   param       : np.ndarray  ,
+                                   param_u     : np.ndarray  ,
                                    units       : str        ,
                                    file_name   : str        ,
                                    n_sigmas_lim: int     = 1):
@@ -112,13 +112,13 @@ def plot_and_save_evolution_figure(time        : np.array   ,
     Plot and save evolution of a given parameter vs time.
     Parameters
     ----------
-    time : np.array
+    time : np.ndarray
         Array with the centers of each time interval (X-values).
     param_name : string
         Name of the parameter to plot.
-    param : np.array
+    param : np.ndarray
         Array with the magnitude to plot (Y-values).
-    param_u : np.array
+    param_u : np.ndarray
         Array with uncertainty values.
     units : string
         Units to be shown in x-label.

From e99d3bc0d33aa1b4ef493e6e9fe159018ac93990 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Alberto=20Us=C3=B3n=20Andr=C3=A9s?= <ausonandres@gmail.com>
Date: Thu, 12 Mar 2020 14:51:09 +0100
Subject: [PATCH 14/15] Change syntax to use f-string instead of format along
 map creation

---
 krcal/map_builder/checking_functions.py    |  6 ++--
 krcal/map_builder/map_builder_functions.py | 40 +++++++++++-----------
 2 files changed, 23 insertions(+), 23 deletions(-)

diff --git a/krcal/map_builder/checking_functions.py b/krcal/map_builder/checking_functions.py
index 8b46e4ab..f6080029 100644
--- a/krcal/map_builder/checking_functions.py
+++ b/krcal/map_builder/checking_functions.py
@@ -52,9 +52,9 @@ def check_failed_fits(maps      : ASectorMap,
     map_values_in_core = maps.lt.values[inner_core_mask]
     numFailed = np.count_nonzero(np.isnan(map_values_in_core))
     if numFailed > maxFailed:
-        message = "Number of failed fits ({0}) ".format(numFailed)
-        message += "exceeds max. allowed ({0}).".format(maxFailed)
+        message = f"Number of failed fits ({numFailed}) "
+        message += f"exceeds max. allowed ({maxFailed})."
         raise AbortingMapCreation(message)
     else:
-        print("    Number of failing fits: {0}".format(numFailed))
+        print(f"    Number of failing fits: {numFailed}")
         return
diff --git a/krcal/map_builder/map_builder_functions.py b/krcal/map_builder/map_builder_functions.py
index 83e0cb01..a08485ed 100644
--- a/krcal/map_builder/map_builder_functions.py
+++ b/krcal/map_builder/map_builder_functions.py
@@ -179,8 +179,8 @@ def selection_nS_mask_and_checking(dst        : pd.DataFrame                ,
 
     message  = "Selection efficiency of "
     message += column.value
-    message += "==1 ({0}) out of range ".format(np.round(eff, 3))
-    message += "({0} - {1}).".format(interval[0], interval[1])
+    message += f"==1 ({eff:.3f}) out of range "
+    message += f"({interval[0]} - {interval[1]})."
     check_if_values_in_interval(values          = np.array(eff),
                                 low_lim         = interval[0]  ,
                                 up_lim          = interval[1]  ,
@@ -215,7 +215,7 @@ def check_Z_dst(Z_vect   : np.array     ,
     diff_sig   = diff / np.sqrt(err_N**2+ref_hist.err_bin_entries**2)
 
     message    = "Z distribution very different to reference one. "
-    message   += "At least 1 point out of {0} sigmas region. ".format(n_sigmas)
+    message   += f"At least 1 point out of {n_sigmas} sigmas region. "
     check_if_values_in_interval(values          = diff_sig ,
                                 low_lim         = -n_sigmas,
                                 up_lim          = n_sigmas ,
@@ -275,8 +275,8 @@ def check_rate_and_hist(times      : np.array           ,
     dev      = np.std(n, ddof = 1)
     rel_dev  = dev / mean * 100
 
-    message  = "Relative deviation ({0}) greater ".format(rel_dev)
-    message += "than the allowed one ({0}).".format(n_dev)
+    message  = f"Relative deviation ({rel_dev}) greater "
+    message += f"than the allowed one ({n_dev})."
     check_if_values_in_interval(values          = np.array(rel_dev),
                                 low_lim         = 0                ,
                                 up_lim          = n_dev            ,
@@ -348,8 +348,8 @@ def band_selector_and_check(dst       : pd.DataFrame,
                                                            nsigma  = nsigma_sel)
 
     effsel   = dst[sel_krband].event.nunique()/dst[input_mask].event.nunique()
-    message  = "Band selection efficiency {0} ".format(np.round(effsel, 3))
-    message += "out of range: ({0} - {1}).".format(eff_min, eff_max)
+    message  = f"Band selection efficiency {effsel:.3f} "
+    message += f"out of range: ({eff_min} - {eff_max})."
     check_if_values_in_interval(values          = np.array(effsel),
                                 low_lim         = eff_min         ,
                                 up_lim          = eff_max         ,
@@ -563,8 +563,8 @@ def add_krevol(maps         : ASectorMap,
 
     e0par       = np.array([pars['e0'].mean(), pars['e0'].var()**0.5])
     ltpar       = np.array([pars['lt'].mean(), pars['lt'].var()**0.5])
-    print("    Mean core E0: {0:.1f}+-{1:.1f} pes".format(*e0par))
-    print("    Mean core Lt: {0:.1f}+-{1:.1f} mus".format(*ltpar))
+    print(f"    Mean core E0: {e0par[0]:.1f}+-{e0par[1]:.1f} pes")
+    print(f"    Mean core Lt: {ltpar[0]:.1f}+-{ltpar[1]:.1f} mus")
 
 
     maps.t_evol = pars_ec
@@ -643,7 +643,7 @@ def apply_cuts(dst              : pd.DataFrame       ,
                                            monitoring = monitoring    ,
                                            **ns1_histo_params         )
     nS1   = dst[mask1].event.nunique()
-    print("    1 S1 cut efficiency within the expectations ({0:2.2f}%)".format(nS1/n0*100))
+    print(f"    1 S1 cut efficiency within the expectations ({nS1/n0*100:2.2f}%)")
     mask2 = selection_nS_mask_and_checking(dst = dst                  ,
                                            column = S2_signal         ,
                                            interval = nS2_eff_interval,
@@ -651,7 +651,7 @@ def apply_cuts(dst              : pd.DataFrame       ,
                                            input_mask = mask1         ,
                                            **ns2_histo_params         )
     nS2   = dst[mask2].event.nunique()
-    print("    1 S2 cut efficiency within the expectations ({0:2.2f}%)".format(nS2/nS1*100))
+    print(f"    1 S2 cut efficiency within the expectations ({nS2/nS1*100:2.2f}%)")
     check_Z_dst(Z_vect   = dst[mask2].Z,
                 ref_hist = ref_Z_histo ,
                 n_sigmas = nsigmas_Zdst)
@@ -661,7 +661,7 @@ def apply_cuts(dst              : pd.DataFrame       ,
                                     input_mask = mask2       ,
                                     **band_sel_params        )
     nZb   = dst[mask3].event.nunique()
-    print("    Z band cut efficiency within the expectations ({0:2.2f}%)".format(nZb/nS2*100))
+    print(f"    Z band cut efficiency within the expectations ({nZb/nS2*100:2.2f}%)")
 
     masks = masks_container(s1   = mask1,
                             s2   = mask2,
@@ -672,9 +672,9 @@ def map_builder(config):
 
     print("Map builder starting...")
     print("Reading input files:")
-    print("    Input dst folder   : {}".format(config.folder))
-    print("    Input boostrap map : {}".format(config.file_bootstrap_map))
-    print("    Input histogram map: {}".format(config.ref_Z_histogram['ref_histo_file']))
+    print(f"    Input dst folder   : {config.folder}")
+    print(f"    Input boostrap map : {config.file_bootstrap_map}")
+    print(f"    Input histogram map: {config.ref_Z_histogram['ref_histo_file']}")
 
 
     dst, bootstrapmap, ref_histos  = load_data(input_path         = config.folder            ,
@@ -685,7 +685,7 @@ def map_builder(config):
 
     monitoring = config.monitoring_path
     if monitoring:
-        monitoring = monitoring + 'Run{0}_{{0}}_plot.pdf'.format(config.run_number)
+        monitoring = monitoring + f'Run{config.run_number}_{{0}}_plot.pdf'
 
     print("Checking the dst and appling 1S1, 1S2 and z-band selections:")
 
@@ -721,7 +721,7 @@ def map_builder(config):
 
     nev_after = dst_passed_cut.event.nunique()
     ratio     = nev_after/nev_before*100
-    print("    Number of events passing the cuts: {0} ({1:2.2f}%)".format(nev_after, ratio))
+    print(f"    Number of events passing the cuts: {nev_after} ({ratio:2.2f}%)")
 
 
     print("Map computation:")
@@ -729,7 +729,7 @@ def map_builder(config):
                                       thr_events_for_map_bins = config.thr_evts_for_sel_map_bins,
                                       n_bins                  = config.default_n_bins           )
 
-    print("    Number of bins: {0}x{0}".format(number_of_bins))
+    print(f"    Number of bins: {number_of_bins}x{number_of_bins}")
 
     final_map      = compute_map(dst        = dst_passed_cut   ,
                                  run_number = config.run_number,
@@ -746,8 +746,8 @@ def map_builder(config):
 
     write_complete_maps(asm      = final_map          ,
                         filename = config.file_out_map)
-    print("Map successfully computed and saved in : {0}".format(config.file_out_map))
+    print(f"Map successfully computed and saved in : {config.file_out_map}")
     if monitoring:
         par_selection_to_plot_vs_time(evol_table = final_map.t_evol,
                                       file_name  = monitoring      )
-        print("Control plots saved in folder          : {0}".format(config.monitoring_path))
+        print(f"Control plots saved in folder          : {config.monitoring_path}")

From cd2e97f34d4424b44b5461f76b3642789592b21e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Alberto=20Us=C3=B3n=20Andr=C3=A9s?= <ausonandres@gmail.com>
Date: Thu, 12 Mar 2020 17:21:58 +0100
Subject: [PATCH 15/15] Add comment in config to show how to run without
 monitoring plots

---
 krcal/map_builder/config_HEcal.conf            | 2 +-
 krcal/map_builder/config_HEcal_HighKrRate.conf | 2 +-
 krcal/map_builder/config_LBphys.conf           | 2 +-
 krcal/map_builder/config_LBphys_run4.conf      | 2 +-
 krcal/map_builder/config_NoChecks.conf         | 2 +-
 5 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/krcal/map_builder/config_HEcal.conf b/krcal/map_builder/config_HEcal.conf
index a8c0c36a..d9d45d7b 100644
--- a/krcal/map_builder/config_HEcal.conf
+++ b/krcal/map_builder/config_HEcal.conf
@@ -2,7 +2,7 @@ folder             = '{folderin}'
 file_in            = '{filein}'
 file_bootstrap_map = '$ICDIR/database/test_data/kr_emap_xy_100_100_r_6573_time.h5'
 file_out_map       = '{fileoutmap}'
-monitoring_path    = '{folderoutmonitorplots}'
+monitoring_path    = '{folderoutmonitorplots}'    #if monitoring_path = None, no monitoring plots produced
 
 # High Energy Configuration File:
 ref_Z_histogram    = dict(
diff --git a/krcal/map_builder/config_HEcal_HighKrRate.conf b/krcal/map_builder/config_HEcal_HighKrRate.conf
index 84a21950..0b7158f2 100644
--- a/krcal/map_builder/config_HEcal_HighKrRate.conf
+++ b/krcal/map_builder/config_HEcal_HighKrRate.conf
@@ -2,7 +2,7 @@ folder             = '{folderin}'
 file_in            = '{filein}'
 file_bootstrap_map = '$ICDIR/database/test_data/kr_emap_xy_100_100_r_6573_time.h5'
 file_out_map       = '{fileoutmap}'
-monitoring_path    = '{folderoutmonitorplots}'
+monitoring_path    = '{folderoutmonitorplots}'    #if monitoring_path = None, no monitoring plots produced
 
 # High Energy Configuration File:
 ref_Z_histogram    = dict(
diff --git a/krcal/map_builder/config_LBphys.conf b/krcal/map_builder/config_LBphys.conf
index 64da92a9..f817dc0a 100644
--- a/krcal/map_builder/config_LBphys.conf
+++ b/krcal/map_builder/config_LBphys.conf
@@ -2,7 +2,7 @@ folder             = '{folderin}'
 file_in            = '{filein}'
 file_bootstrap_map = '$ICDIR/database/test_data/kr_emap_xy_100_100_r_6573_time.h5'
 file_out_map       = '{fileoutmap}'
-monitoring_path    = '{folderoutmonitorplots}'
+monitoring_path    = '{folderoutmonitorplots}'    #if monitoring_path = None, no monitoring plots produced
 
 # Low Background Configuration File:
 ref_Z_histogram    = dict(
diff --git a/krcal/map_builder/config_LBphys_run4.conf b/krcal/map_builder/config_LBphys_run4.conf
index 0c373fc2..a5b52d98 100644
--- a/krcal/map_builder/config_LBphys_run4.conf
+++ b/krcal/map_builder/config_LBphys_run4.conf
@@ -2,7 +2,7 @@ folder             = '{folderin}'
 file_in            = '{filein}'
 file_bootstrap_map = '$ICDIR/database/test_data/kr_emap_xy_100_100_r_6573_time.h5'
 file_out_map       = '{fileoutmap}'
-monitoring_path    = '{folderoutmonitorplots}'
+monitoring_path    = '{folderoutmonitorplots}'    #if monitoring_path = None, no monitoring plots produced
 
 # Low Background Configuration File:
 ref_Z_histogram    = dict(
diff --git a/krcal/map_builder/config_NoChecks.conf b/krcal/map_builder/config_NoChecks.conf
index 47c15c18..7d345822 100644
--- a/krcal/map_builder/config_NoChecks.conf
+++ b/krcal/map_builder/config_NoChecks.conf
@@ -2,7 +2,7 @@ folder             = '{folderin}'
 file_in            = '{filein}'
 file_bootstrap_map = '$ICDIR/database/test_data/kr_emap_xy_100_100_r_6573_time.h5'
 file_out_map       = '{fileoutmap}'
-monitoring_path    = '{folderoutmonitorplots}'
+monitoring_path    = '{folderoutmonitorplots}'    #if monitoring_path = None, no monitoring plots produced
 
 # High Energy Configuration File:
 ref_Z_histogram    = dict(