Merge branch 'release0.2'

# Conflicts:
#	utils.py

.gitignore

@@ -211,3 +211,5 @@ flycheck_*.el
 /network-security.data
 
 
+/__simulate_fail.json
+/mailing_list.yaml

README.md

@@ -1,6 +1,6 @@
 # survBot
 
-version: 0.1
+version: 0.2
 
 survBot is a small program used to track station quality channels of DSEBRA stations via PowBox output over SOH channels
  by analysing contents of a Seiscomp3 datapath.
@@ -40,8 +40,16 @@ The GUI can be loaded via
 python survBotGui.py
 ```
 
+## Version Changes
+- surveillance of mass, clock and gaps
+- individual mailing lists for different stations
+- html mail with recent status information
+- updated web page design
+- restructured parameter file
+- recognize if PBox is disconnected
+
 ## Staff
 
 Original author: M.Paffrath (marcel.paffrath@rub.de)
 
-November 2022
+June 2023

__init__.py

@@ -0,0 +1,3 @@
+# survBot is a small program used to track station quality channels of DSEBRA stations via PowBox output
+# over SOH channels by analysing contents of a Seiscomp3 datapath.
+__version__ = "0.2"

mailing_list.yaml

@@ -0,0 +1,9 @@
+# specify mail addresses and station network ids for which information mails shall be sent, e.g.:
+# "mail.address@provider.com, mail.address2@provider2.com":
+#   - 1Y.GR01
+#   - 1Y.GR02
+# "mail.address3@provder.com":
+#   - 1Y.GR03
+
+#"kasper.fischer@rub.de":
+#    - 1Y.GR01

parameters.yaml

@@ -1,17 +1,17 @@
 # Parameters file for Surveillance Bot
 datapath: "/data/SDS/"                    # SC3 Datapath
-networks: ["1Y", "HA"]                    # select networks, list or str
+networks: ["1Y", "HA", "MK"]              # select networks, list or str
 stations: "*"                             # select stations, list or str
 locations: "*"                            # select locations, list or str
-stations_blacklist: ["TEST", "EREA"]      # exclude these stations
+stations_blacklist: ["TEST", "EREA", "DOMV"]      # exclude these stations
 networks_blacklist: []                    # exclude these networks
 interval: 60               # Perform checks every x seconds
-n_track: 300               # wait n_track * intervals before performing an action (i.e. send mail/end highlight status)
-timespan: 7                # Check data of the recent x days
+n_track: 360               # wait n_track * intervals before performing an action (i.e. send mail/end highlight status)
+timespan: 3                # Check data of the recent x days
 verbosity: 0               # verbosity flag
 track_changes: True        # tracks all changes since GUI startup by text highlighting (GUI only)
-warn_count: False           # show number of warnings and errors in table
-min_sample: 3              # minimum samples for raising Warn/FAIL
+warn_count: False          # show number of warnings and errors in table
+min_sample: 5              # minimum samples for raising Warn/FAIL
 dt_thresh: [300, 1800]     # threshold (s) for timing delay colourisation (yellow/red)
 html_figures: True         # Create html figure directory and links
 reread_parameters: True    # reread parameters file (change parameters on runtime, not for itself/GUI refresh/datapath)
@@ -44,8 +44,9 @@ THRESHOLDS:
   unclassified: 5              # min voltage samples not classified for warning
   max_vm_warn: 1.5             # threshold for mass offset (warn), fail)
   max_vm_fail: 2.5             # threshold for mass offset (warn), fail)
-  clockquality_warn: 90        # clock quality ranges from 0 % to 100 % with 100 % being the best level
-  clockquality_fail: 70
+  clockquality_warn: 90        # warn level - clock quality ranges from 0 % to 100 % with 100 % being the best level
+  clockquality_fail: 70        # fail level
+  min_gap: 0.1                 # minimum for gap declaration, should be > 0 [s]
 
 
 # ---------------------------------- Specification of input channels ---------------------------------------------------
@@ -62,7 +63,7 @@ THRESHOLDS:
 CHANNELS:
   EX1:
     unit: 1e-6
-    name: "Temperature (°C)"
+    name: "PowBox Temperature (°C)"
     ticks: [-10, 50, 10]
     transform:
       - ["*", 20]
@@ -70,44 +71,47 @@ CHANNELS:
     warn: "max_temp"
   EX2:
     unit: 1e-6
-    name: "230V/12V (V)"
-    ticks: [1, 5, 1]
+    name: "PowBox 230V/12V (V)"
+    ticks: [0, 5, 1]
     warn: [2, 3, 4, 4.5, 5]
   EX3:
     unit: 1e-6
-    name: "Rout/Charge (V)"
-    ticks: [1, 5, 1]
+    name: "PowBox Router/Charger (V)"
+    ticks: [0, 5, 1]
     warn: [2, 2.5, 3, 4, 5]
   VEI:
     unit: 1e-3
-    name: "Logger (V)"
+    name: "Datalogger (V)"
     ticks: [9, 15, 1]
     warn: ["low_volt", "high_volt"]
     fail: 10.5
   VM1:
     unit: 1e-6
-    name: "Mass 1 (V)"
+    name: "Mass position W (V)"
     ticks: [-2.5, 2.5, 1]
     warn: [-1.5, 1.5]
     fail: [-2.5, 2.5]
   VM2:
     unit: 1e-6
-    name: "Mass 2 (V)"
+    name: "Mass position V (V)"
     ticks: [-2.5, 2.5, 1]
     warn: [-1.5, 1.5]
     fail: [-2.5, 2.5]
   VM3:
     unit: 1e-6
-    name: "Mass 3 (V)"
+    name: "Mass position U (V)"
     ticks: [-2.5, 2.5, 1]
     warn: [-1.5, 1.5]
     fail: [-2.5, 2.5]
   LCQ:
-    name: "Clock Q (%)"
+    name: "Clock quality (%)"
     ticks: [0, 100, 20]
     warn: "clockquality_warn"
     fail: "clockquality_fail"
 
+# specify data channels (can be additional to the above). From these channels only headers will be read
+data_channels: ["HHZ", "HHN", "HHE"]
+
 
 # ---------------------------------------- OPTIONAL PARAMETERS ---------------------------------------------------------
 
@@ -118,6 +122,15 @@ add_links:
   slmon: {"URL": "../slmon/{nw}_{st}.html", "text": "show"}
   24h-plot: {"URL": "../scheli/{nw}/{st}.png", "text": "plot"}
 
+# add station-independent links below html table (list items separated with -)
+add_global_links:
+  # for example: - {"text": "our homepage", "URL": "https://www.rub.de"}
+  - {"text": "show recent events on map",
+     "URL": "https://fdsnws.geophysik.ruhr-uni-bochum.de/map/?lat=39.5&lon=21&zoom=7&baselayer=mapnik"}
+
+# html logo at page bottom (path relative to html directory)
+html_logo: "figures/Logo_RUB_BLAU_rgb.png"
+
 # E-mail notifications
 EMAIL:
   mailserver: "localhost"
@@ -125,3 +138,5 @@ EMAIL:
   sender: "webmaster@geophysik.ruhr-uni-bochum.de" # mail sender
   stations_blacklist: ['GR33']                     # do not send emails for specific stations
   networks_blacklist: []                           # do not send emails for specific network
+  # specify recipients for single stations in a yaml: key = email-address, val = station list (e.g. [1Y.GR01, 1Y.GR02])
+  external_mail_list: "mailing_list.yaml"

stylesheets/desktop.css

@@ -2,26 +2,36 @@ body {
     background-color: #ffffff;
     place-items: center;
     text-align: center;
+    padding-bottom: 30px;
+    font-family: "Helvetica", "sans-serif";
+}
+
+table {
+    position: relative
 }
 
 td {
-    border-radius: 4px;
+    border-radius: 2px;
     padding: 0px;
+    white-space: nowrap;
 }
 
 th {
     background-color: #999;
-    border-radius: 4px;
+    color: #fff;
+    border-radius: 2px;
     padding: 3px 1px;
+    position: sticky;
+    top: 0;
 }
 
 a:link, a:visited {
-    background-color: #ccc;
+    background-color: #e8e8e8;
     color: #000;
     text-decoration: none;
     display: block;
     border-radius: 4px;
-    border: 1px solid #bbb;
+    border: 1px solid #ccc;
 }
 
 a:hover {
@@ -37,3 +47,12 @@ a:hover {
     50%		{ background-color: #ff3200;}
     100%	{ background-color: #ffcc00;}
 }
+
+.footer {
+   position: fixed;
+   left: 0;
+   bottom: 0;
+   width: 100%;
+   height: 50px;
+   text-align: center;
+}

stylesheets/mobile.css

@@ -2,26 +2,36 @@ body {
     background-color: #ffffff;
     place-items: center;
     text-align: center;
+    padding-bottom: 30px;
+    font-family: "Helvetica", "sans-serif";
+}
+
+table {
+    position: relative
 }
 
 td {
-    border-radius: 4px;
+    border-radius: 3px;
     padding: 10px 2px;
+    white-space: nowrap;
 }
 
 th {
     background-color: #999;
-    border-radius: 4px;
+    color: #fff;
+    border-radius: 3px;
     padding: 10px, 2px;
+    position: sticky;
+    top: 0;
 }
 
-a:link {
-    background-color: #ccc;
+a:link, a:visited {
+    background-color: #e8e8e8;
     color: #000;
     text-decoration: none;
     display: block;
-    border-radius: 4px;
-    border: 1px solid #bbb;
+    border-radius: 6px;
+    border: 1px solid #ccc;
 }
 
 a:hover {
@@ -37,7 +47,16 @@ a:hover {
     animation: blinkingBackground 2s infinite;
 }
 @keyframes blinkingBackground{
-    0%		{ background-color: #ffee00;}
+    0%		{ background-color: #ffcc00;}
     50%		{ background-color: #ff3200;}
-    100%	{ background-color: #ffee00;}
+    100%	{ background-color: #ffcc00;}
+}
+
+.footer {
+   position: fixed;
+   left: 0;
+   bottom: 0;
+   width: 100%;
+   height: 50px;
+   text-align: center;
 }

survBot.py

@@ -5,9 +5,12 @@ __version__ = '0.1'
 __author__ = 'Marcel Paffrath'
 
 import os
+import io
+import copy
 import traceback
 import yaml
 import argparse
+import json
 
 import time
 from datetime import timedelta
@@ -17,13 +20,14 @@ import matplotlib.pyplot as plt
 from obspy import read, UTCDateTime, Stream
 from obspy.clients.filesystem.sds import Client
 
-from write_utils import write_html_text, write_html_row, write_html_footer, write_html_header, get_print_title_str, \
-    init_html_table, finish_html_table
-from utils import get_bg_color, modify_stream_for_plot, trace_yticks, trace_thresholds
+from write_utils import get_html_text, get_html_link, get_html_row, html_footer, get_html_header, get_print_title_str, \
+    init_html_table, finish_html_table, get_mail_html_header, add_html_image
+from utils import get_bg_color, get_font_color, modify_stream_for_plot, set_axis_yticks, set_axis_color, plot_axis_thresholds
 
 try:
     import smtplib
-    from email.mime.text import MIMEText
+    from email.message import EmailMessage
+    from email.utils import make_msgid
 
     mail_functionality = True
 except ImportError:
@@ -49,17 +53,23 @@ def read_yaml(file_path, n_read=3):
 
 
 def nsl_from_id(nwst_id):
+    nwst_id = get_full_seed_id(nwst_id)
     network, station, location = nwst_id.split('.')
     return dict(network=network, station=station, location=location)
 
 
+def get_full_seed_id(nwst_id):
+    seed_id = '{}.{}.{}'.format(*nwst_id.split('.'), '')
+    return seed_id
+
+
 def get_nwst_id(trace):
     stats = trace.stats
     return f'{stats.network}.{stats.station}.'  # {stats.location}'
 
 
 def fancy_timestr(dt, thresh=600, modif='+'):
-    if dt > timedelta(seconds=thresh):
+    if isinstance(dt, timedelta) and dt > timedelta(seconds=thresh):
         value = f'{modif} ' + str(dt) + f' {modif}'
     else:
         value = str(dt)
@@ -68,7 +78,8 @@ def fancy_timestr(dt, thresh=600, modif='+'):
 
 class SurveillanceBot(object):
     def __init__(self, parameter_path, outpath_html=None):
-        self.keys = ['last active', '230V', '12V', 'router', 'charger', 'voltage', 'mass', 'temp', 'other']
+        self.keys = ['last active', '230V', '12V', 'router', 'charger', 'voltage', 'mass', 'clock', 'gaps', 'temp',
+                     'other']
         self.parameter_path = parameter_path
         self.update_parameters()
         self.starttime = UTCDateTime()
@@ -76,24 +87,32 @@ class SurveillanceBot(object):
         self.current_day = self.starttime.julday
         self.outpath_html = outpath_html
         self.filenames = []
-        self.filenames_read = []
+        self.filenames_wf_data = []
+        self.filenames_read_last_modif = {}
         self.station_list = []
         self.analysis_print_list = []
         self.analysis_results = {}
         self.status_track = {}
         self.dataStream = Stream()
         self.data = {}
+        self.gaps = []
         self.print_count = 0
         self.status_message = ''
         self.html_fig_dir = 'figures'
 
+        self.active_figures = {}
+
         self.cl = Client(self.parameters.get('datapath'))  # TODO: Check if this has to be loaded again on update
         self.get_stations()
 
     def update_parameters(self):
         self.parameters = read_yaml(self.parameter_path)
-        # add channels to list in parameters dicitonary
-        self.parameters['channels'] = list(self.parameters.get('CHANNELS').keys())
+        # add channels to list in parameters dictionary, also add data channels
+        channels = list(self.parameters.get('CHANNELS').keys())
+        for channel in self.parameters.get('data_channels'):
+            if not channel in channels:
+                channels.append(channel)
+        self.parameters['channels'] = channels
         self.reread_parameters = self.parameters.get('reread_parameters')
         self.dt_thresh = [int(val) for val in self.parameters.get('dt_thresh')]
         self.verbosity = self.parameters.get('verbosity')
@@ -101,9 +120,16 @@ class SurveillanceBot(object):
         self.networks_blacklist = self.parameters.get('networks_blacklist')
         self.refresh_period = self.parameters.get('interval')
         self.transform_parameters()
+
         add_links = self.parameters.get('add_links')
         self.add_links = add_links if add_links else {}
 
+        add_global_links = self.parameters.get('add_global_links')
+        # in case user forgets "-" in parameters file
+        if isinstance(add_global_links, dict):
+            add_global_links = [add_global_links]
+        self.add_global_links = add_global_links if add_global_links else []
+
     def transform_parameters(self):
         for key in ['networks', 'stations', 'locations', 'channels']:
             parameter = self.parameters.get(key)
@@ -129,25 +155,31 @@ class SurveillanceBot(object):
 
     def get_filenames(self):
         self.filenames = []
+        self.filenames_wf_data = []
         time_now = UTCDateTime()
         t1 = time_now - self.parameters.get('timespan') * 24 * 3600
         networks = self.parameters.get('networks')
         stations = self.parameters.get('stations')
         locations = self.parameters.get('locations')
         channels = self.parameters.get('channels')
+        channels_wf_data = self.parameters.get('data_channels')
         for network in networks:
             for station in stations:
                 for location in locations:
                     for channel in channels:
-                        self.filenames += list(self.cl._get_filenames(network, station, location, channel,
-                                                                      starttime=t1, endtime=time_now))
+                        fnames = list(self.cl._get_filenames(network, station, location, channel,
+                                                             starttime=t1, endtime=time_now))
+                        self.filenames += fnames
 
-    def read_data(self, re_read_at_hour=1, daily_overlap=2):
+                        # keep track of filenames with wf data (only read headers later)
+                        if channel in channels_wf_data:
+                            self.filenames_wf_data += fnames
+
+    def read_data(self, re_read_at_hour=1):
         '''
         read data method reads new data into self.stream
 
         :param re_read_at_hour: update archive at specified hour each day (hours up to 24)
-        :param daily_overlap: re-read data of previous day until specified hour (hours up to 24)
         '''
         self.data = {}
 
@@ -155,28 +187,31 @@ class SurveillanceBot(object):
         curr_time = UTCDateTime()
         current_day = curr_time.julday
         current_hour = curr_time.hour
-        yesterday = (curr_time - 24. * 3600.).julday
         if re_read_at_hour is not False and current_day != self.current_day and current_hour == re_read_at_hour:
-            self.filenames_read = []
+            self.filenames_read_last_modif = {}
             self.dataStream = Stream()
             self.current_day = current_day
 
         # add all data to current stream
         for filename in self.filenames:
-            if filename in self.filenames_read:
+            # if file already read and last modification time is the same as of last read operation: continue
+            if self.filenames_read_last_modif.get(filename) == os.path.getmtime(filename):
+                if self.verbosity > 0:
+                    print('Continue on file', filename)
                 continue
             try:
-                st_new = read(filename, dtype=float)
-                # add file to read filenames to prevent re-reading in case it is not the current day (or end of
-                # previous day)
-                if not filename.endswith(f'{current_day:03}') and not (
-                        filename.endswith(f'{yesterday:03}') and current_hour <= daily_overlap):
-                    self.filenames_read.append(filename)
+                # read only header of wf_data
+                if filename in self.filenames_wf_data:
+                    st_new = read(filename, headonly=True)
+                else:
+                    st_new = read(filename, dtype=float)
+                self.filenames_read_last_modif[filename] = os.path.getmtime(filename)
             except Exception as e:
                 print(f'Could not read file {filename}:', e)
                 continue
             self.dataStream += st_new
-        self.dataStream.merge(fill_value=np.nan)
+        self.gaps = self.dataStream.get_gaps(min_gap=self.parameters['THRESHOLDS'].get('min_gap'))
+        self.dataStream.merge()
 
         # organise data in dictionary with key for each station
         for trace in self.dataStream:
@@ -251,7 +286,7 @@ class SurveillanceBot(object):
     def get_station_delay(self, nwst_id):
         """ try to get station delay from SDS archive using client"""
         locations = ['', '0', '00']
-        channels = ['HHZ', 'HHE', 'HHN'] + self.parameters.get('channels')
+        channels = self.parameters.get('channels') + self.parameters.get('data_channels')
         network, station = nwst_id.split('.')[:2]
 
         times = []
@@ -338,21 +373,25 @@ class SurveillanceBot(object):
         for nwst_id in self.station_list:
             self.write_html_figure(nwst_id)
 
-    def write_html_figure(self, nwst_id):
+    def write_html_figure(self, nwst_id, save_bytes=False):
         """ Write figure for html for specified station """
         self.check_fig_dir()
 
         fig = plt.figure(figsize=(16, 9))
-        fnout = self.get_fig_path_abs(nwst_id)
-        st = self.data.get(nwst_id)
+        fnames_out = [self.get_fig_path_abs(nwst_id), io.BytesIO()]
+        st = self.data.get(get_full_seed_id(nwst_id))
         if st:
-            # TODO: this section might fail, adding try-except block for analysis and to prevent program from crashing
+            # TODO: this section failed once, adding try-except block for analysis and to prevent program from crashing
             try:
+                endtime = UTCDateTime()
+                starttime = endtime - self.parameters.get('timespan') * 24 * 3600
                 st = modify_stream_for_plot(st, parameters=self.parameters)
-                st.plot(fig=fig, show=False, draw=False, block=False, equal_scale=False, method='full')
-                # trace_ylabels(fig, self.parameters, self.verbosity)
-                trace_yticks(fig, self.parameters, self.verbosity)
-                trace_thresholds(fig, self.parameters, self.verbosity)
+                st.plot(fig=fig, show=False, draw=False, block=False, equal_scale=False, method='full',
+                        starttime=starttime, endtime=endtime)
+                # set_axis_ylabels(fig, self.parameters, self.verbosity)
+                set_axis_yticks(fig, self.parameters, self.verbosity)
+                set_axis_color(fig)
+                plot_axis_thresholds(fig, self.parameters, self.verbosity)
             except Exception as e:
                 print(f'Could not generate plot for {nwst_id}:')
                 print(traceback.format_exc())
@@ -362,84 +401,125 @@ class SurveillanceBot(object):
                              f'Refreshed hourly or on FAIL status.')
                 for ax in fig.axes:
                     ax.grid(True, alpha=0.1)
-                fig.savefig(fnout, dpi=150., bbox_inches='tight')
+                for fnout in fnames_out:
+                    fig.savefig(fnout, dpi=150., bbox_inches='tight')
+                # if needed save figure as virtual object (e.g. for mailing)
+                if save_bytes:
+                    fnames_out[-1].seek(0)
+                    self.active_figures[nwst_id] = fnames_out[-1]
         plt.close(fig)
 
-    def write_html_table(self, default_color='#e6e6e6', default_header_color='#999', hide_keys_mobile=('other')):
+    def get_html_class(self, hide_keys_mobile=None, status=None, check_key=None):
+        """ helper function for html class if a certain condition is fulfilled """
+        html_class = None
+        if status and status.is_active:
+            html_class = 'blink-bg'
+        if hide_keys_mobile and check_key in hide_keys_mobile:
+            html_class = 'hidden-mobile'
+        return html_class
 
-        def get_html_class(status=None, check_key=None):
-            """ helper function for html class if a certain condition is fulfilled """
-            html_class = None
-            if status and status.is_active:
-                html_class = 'blink-bg'
-            if check_key in hide_keys_mobile:
-                html_class = 'hidden-mobile'
-            return html_class
+    def make_html_table_header(self, default_header_color, hide_keys_mobile=None, add_links=True):
+        # First write header items
+        header = self.keys.copy()
+        # add columns for additional links
+        if add_links:
+            for key in self.add_links:
+                header.insert(-1, key)
 
+        header_items = [dict(text='Station', color=default_header_color)]
+        for check_key in header:
+            html_class = self.get_html_class(hide_keys_mobile, check_key=check_key)
+            item = dict(text=check_key, color=default_header_color, html_class=html_class)
+            header_items.append(item)
+
+        return header, header_items
+
+    def get_html_row_items(self, status_dict, nwst_id, header, default_color, hide_keys_mobile=None,
+                           hyperlinks=True):
+        ''' create a html table row for the different keys '''
+
+        fig_name = self.get_fig_path_rel(nwst_id)
+        nwst_id_str = nwst_id.rstrip('.')
+        col_items = [dict(text=nwst_id_str, color=default_color, hyperlink=fig_name if hyperlinks else None,
+                          bold=True, tooltip=f'Show plot of {nwst_id_str}', font_color='#000000')]
+
+        for check_key in header:
+            if check_key in self.keys:
+                status = status_dict.get(check_key)
+                message, detailed_message = status.get_status_str()
+
+                # get background color
+                dt_thresh = [timedelta(seconds=sec) for sec in self.dt_thresh]
+                bg_color = get_bg_color(check_key, status, dt_thresh, hex=True)
+                if not bg_color:
+                    bg_color = default_color
+                font_color = get_font_color(bg_color, hex=True)
+
+                # add degree sign for temp
+                if check_key == 'temp':
+                    if not type(message) in [str]:
+                        message = str(message) + deg_str
+
+                html_class = self.get_html_class(hide_keys_mobile, status=status, check_key=check_key)
+                item = dict(text=str(message), tooltip=str(detailed_message), color=bg_color,
+                            html_class=html_class, font_color=font_color)
+            elif check_key in self.add_links:
+                value = self.add_links.get(check_key).get('URL')
+                link_text = self.add_links.get(check_key).get('text')
+                if not value:
+                    continue
+                nw, st = nwst_id.split('.')[:2]
+                hyperlink_dict = dict(nw=nw, st=st, nwst_id=nwst_id)
+                link = value.format(**hyperlink_dict)
+                item = dict(text=link_text, tooltip=link, hyperlink=link if hyperlinks else None, color=default_color)
+            else:
+                item = dict(text='', tooltip='')
+            col_items.append(item)
+
+        return col_items
+
+    def write_html_table(self, default_color='#e6e6e6', default_header_color='#999999', hide_keys_mobile=('other',)):
         self.check_html_dir()
         fnout = pjoin(self.outpath_html, 'survBot_out.html')
         if not fnout:
             return
         try:
             with open(fnout, 'w') as outfile:
-                write_html_header(outfile, self.refresh_period)
-                # write_html_table_title(outfile, self.parameters)
-                init_html_table(outfile)
+                outfile.write(get_html_header(self.refresh_period))
 
-                # First write header items
-                header = self.keys.copy()
-                # add columns for additional links
-                for key in self.add_links:
-                    header.insert(-1, key)
-                header_items = [dict(text='Station', color=default_header_color)]
-                for check_key in header:
-                    html_class = get_html_class(check_key=check_key)
-                    item = dict(text=check_key, color=default_header_color, html_class=html_class)
-                    header_items.append(item)
-                write_html_row(outfile, header_items, html_key='th')
+                # write_html_table_title(self.parameters)
+                outfile.write(init_html_table())
 
-                # Write all cells
+                # write html header row
+                header, header_items = self.make_html_table_header(default_header_color, hide_keys_mobile)
+                html_row = get_html_row(header_items, html_key='th')
+                outfile.write(html_row)
+
+                # Write all cells (row after row)
                 for nwst_id in self.station_list:
-                    fig_name = self.get_fig_path_rel(nwst_id)
-                    nwst_id_str = nwst_id.rstrip('.')
-                    col_items = [dict(text=nwst_id_str, color=default_color, hyperlink=fig_name,
-                                      bold=True, tooltip=f'Show plot of {nwst_id_str}')]
-                    for check_key in header:
-                        if check_key in self.keys:
-                            status_dict = self.analysis_results.get(nwst_id)
-                            status = status_dict.get(check_key)
-                            message, detailed_message = status.get_status_str()
+                    # get list with column-wise items to write as a html row
+                    status_dict = self.analysis_results.get(nwst_id)
+                    col_items = self.get_html_row_items(status_dict, nwst_id, header, default_color, hide_keys_mobile)
+                    outfile.write(get_html_row(col_items))
 
-                            # get background color
-                            dt_thresh = [timedelta(seconds=sec) for sec in self.dt_thresh]
-                            bg_color = get_bg_color(check_key, status, dt_thresh, hex=True)
-                            if not bg_color:
-                                bg_color = default_color
+                outfile.write(finish_html_table())
 
-                            # add degree sign for temp
-                            if check_key == 'temp':
-                                if not type(message) in [str]:
-                                    message = str(message) + deg_str
+                # add optional links below html table
+                for dct in self.add_global_links:
+                    link_str = get_html_link(dct.get('text'), dct.get('URL'))
+                    outfile.write(get_html_text(link_str))
 
-                            html_class = get_html_class(status=status, check_key=check_key)
-                            item = dict(text=str(message), tooltip=str(detailed_message), color=bg_color,
-                                        html_class=html_class)
-                        elif check_key in self.add_links:
-                            value = self.add_links.get(check_key).get('URL')
-                            link_text = self.add_links.get(check_key).get('text')
-                            if not value:
-                                continue
-                            nw, st = nwst_id.split('.')[:2]
-                            hyperlink_dict = dict(nw=nw, st=st, nwst_id=nwst_id)
-                            link = value.format(**hyperlink_dict)
-                            item = dict(text=link_text, tooltip=link, hyperlink=link, color=default_color)
-                        col_items.append(item)
+                # add status message
+                outfile.write(get_html_text(self.status_message))
 
-                    write_html_row(outfile, col_items)
+                # write footer with optional logo
+                logo_file = self.parameters.get('html_logo')
+                if not os.path.isfile(pjoin(self.outpath_html, logo_file)):
+                    print(f'Specified file {logo_file} not found.')
+                    logo_file = None
+
+                outfile.write(html_footer(footer_logo=logo_file))
 
-                finish_html_table(outfile)
-                write_html_text(outfile, self.status_message)
-                write_html_footer(outfile)
         except Exception as e:
             print(f'Could not write HTML table to {fnout}:')
             print(traceback.format_exc())
@@ -468,19 +548,22 @@ class SurveillanceBot(object):
 
 
 class StationQC(object):
-    def __init__(self, parent, stream, nsl, parameters, keys, starttime, verbosity, print_func, status_track={}):
+    def __init__(self, parent, stream, nsl, parameters, keys, starttime, verbosity, print_func, status_track=None):
         """
         Station Quality Check class.
         :param nsl: dictionary containing network, station and location (key: str)
         :param parameters: parameters dictionary from parameters.yaml file
         """
+        if status_track is None:
+            status_track = {}
         self.parent = parent
         self.stream = stream
         self.nsl = nsl
         self.network = nsl.get('network')
         self.station = nsl.get('station')
         self.location = nsl.get('location')
-        self.parameters = parameters
+        # make a copy of parameters object to prevent accidental changes
+        self.parameters = copy.deepcopy(parameters)
         self.program_starttime = starttime
         self.verbosity = verbosity
         self.last_active = False
@@ -541,29 +624,35 @@ class StationQC(object):
         # current_status_message = '' if current_status_message in [None, 'OK', '-'] else current_status_message + ' | '
         # self.status_dict[key] = current_status_message + status_message
 
-    def error(self, key, detailed_message, last_occurrence=None, count=1):
+    def error(self, key, detailed_message, last_occurrence=None, count=1, disc=False):
+        send_mail = False
         new_error = StatusError(count=count, show_count=self.parameters.get('warn_count'))
+        if disc:
+            new_error.set_disconnected()
         current_status = self.status_dict.get(key)
         if current_status.is_error:
             current_status.count += count
         else:
             current_status = new_error
             # if error is new and not on program-startup set active and refresh plot (using parent class)
-            if self.search_previous_errors(key, n_errors=1) is True:
-                self.parent.write_html_figure(self.nwst_id)
+            if self.status_track.get(key) and not self.status_track.get(key)[-1]:
+                self.parent.write_html_figure(self.nwst_id, save_bytes=True)
 
         if self.verbosity:
             self.print(f'{UTCDateTime()}: {detailed_message}', flush=False)
 
         # do not send error mail if this is the first run (e.g. program startup) or state was already error (unchanged)
         if self.search_previous_errors(key) is True:
-            self.send_mail(key, status_type='FAIL', additional_message=detailed_message)
-            # set status to "inactive" after sending info mail
+            send_mail = True
+            # set status to "inactive" when info mail is sent
             current_status.is_active = False
         elif self.search_previous_errors(key) == 'active':
             current_status.is_active = True
 
+        # first update status, then send mail
         self._update_status(key, current_status, detailed_message, last_occurrence)
+        if send_mail:
+            self.send_mail(key, status_type='FAIL', additional_message=detailed_message)
 
     def search_previous_errors(self, key, n_errors=None):
         """
@@ -574,8 +663,16 @@ class StationQC(object):
         In all other cases return False.
         This also prevents sending status (e.g. mail) in case of program startup
         """
-        if n_errors is not None:
-            n_errors = self.parameters.get('n_track') + 1
+        if n_errors is None:
+            n_errors = self.parameters.get('n_track')
+
+        # +1 to check whether n_errors + 1 was no error (error is new)
+        n_errors += 1
+
+        # simulate an error specified in json file (dictionary: {nwst_id: key} )
+        if self._simulated_error_check(key) is True:
+            print(f'Simulating Error on {self.nwst_id}, {key}')
+            return True
 
         previous_errors = self.status_track.get(key)
         # only if error list is filled n_track times
@@ -583,11 +680,19 @@ class StationQC(object):
             # if first entry was no error but all others are, return True (-> new Fail n_track times)
             if not previous_errors[0] and all(previous_errors[1:]):
                 return True
-        # in case previous_errors exists, last item is error but not all items are error, error still active
-        elif previous_errors and previous_errors[-1] and not all(previous_errors):
+        # in case previous_errors exist, last item is error but not all items are error, error still active
+        if previous_errors and previous_errors[-1] and not all(previous_errors):
             return 'active'
         return False
 
+    def _simulated_error_check(self, key, fname='simulate_fail.json'):
+        if not os.path.isfile(fname):
+            return
+        with open(fname) as fid:
+            d = json.load(fid)
+        if d.get(self.nwst_id) == key:
+            return True
+
     def send_mail(self, key, status_type, additional_message=''):
         """ Send info mail using parameters specified in parameters file """
         if not mail_functionality:
@@ -615,23 +720,93 @@ class StationQC(object):
 
         sender = mail_params.get('sender')
         addresses = mail_params.get('addresses')
+        add_addresses = self.get_additional_mail_recipients(mail_params)
+        if add_addresses:
+            # create copy of addresses ( [:] ) to prevent changing original, general list with addresses
+            addresses = addresses[:] + list(add_addresses)
         server = mail_params.get('mailserver')
         if not sender or not addresses:
             if self.verbosity:
-                print('Mail sender or addresses not correctly defined. Return')
+                print('Mail sender or addresses not (correctly) defined. Return')
             return
         dt = self.get_dt_for_action()
         text = f'{key}: Status {status_type} longer than {dt}: ' + additional_message
-        msg = MIMEText(text)
+
+        msg = EmailMessage()
+
         msg['Subject'] = f'new message on station {self.nwst_id}'
         msg['From'] = sender
         msg['To'] = ', '.join(addresses)
 
+        msg.set_content(text)
+
+        # html mail version
+        html_str = self.add_html_mail_body(text)
+        msg.add_alternative(html_str, subtype='html')
+
         # send message via SMTP server
         s = smtplib.SMTP(server)
-        s.sendmail(sender, addresses, msg.as_string())
+        s.send_message(msg)
         s.quit()
 
+    def add_html_mail_body(self, text, default_color='#e6e6e6'):
+        parent = self.parent
+
+        header, header_items = parent.make_html_table_header('#999999', add_links=False)
+        col_items = parent.get_html_row_items(self.status_dict, self.nwst_id, header, default_color, hyperlinks=False)
+
+        # set general status text
+        html_str = get_html_text(text)
+
+        # init html header and table
+        html_str += get_mail_html_header()
+        html_str += init_html_table()
+
+        # add table header and row of current station
+        html_str += get_html_row(header_items, html_key='th')
+        html_str += get_html_row(col_items)
+
+        html_str += finish_html_table()
+
+        if self.nwst_id in self.parent.active_figures.keys():
+            fid = self.parent.active_figures.pop(self.nwst_id)
+            html_str += add_html_image(img_data=fid.read())
+
+        html_str += html_footer()
+
+        return html_str
+
+    def get_additional_mail_recipients(self, mail_params):
+        """ return additional recipients from external mail list if this station (self.nwst_id) is specified """
+        eml_filename = mail_params.get('external_mail_list')
+        if eml_filename:
+            # try to open file
+            try:
+                with open(eml_filename, 'r') as fid:
+                    address_dict = yaml.safe_load(fid)
+
+                for address, nwst_ids in address_dict.items():
+                    if self.nwst_id in nwst_ids:
+                        yield address
+            # file not existing
+            except FileNotFoundError as e:
+                if self.verbosity:
+                    print(e)
+            # no dictionary
+            except AttributeError as e:
+                if self.verbosity:
+                    print(f'Could not read dictionary from file {eml_filename}: {e}')
+            # other exceptions
+            except Exception as e:
+                if self.verbosity:
+                    print(f'Could not open file {eml_filename}: {e}')
+        # no file specified
+        else:
+            if self.verbosity:
+                print('No external mail list set.')
+
+        return []
+
     def get_dt_for_action(self):
         n_track = self.parameters.get('n_track')
         interval = self.parameters.get('interval')
@@ -677,10 +852,23 @@ class StationQC(object):
             return max(endtimes)
 
     def check_for_inactive_message(self, key, dt_active):
+        """ send mail if station is inactive longer than dt_action and no FAIL status is present """
+
+        # check if any error is present in status_dict and not disconnected (in that case an email is sent already)
+        if self.check_for_any_error_no_dcn():
+            return
+
         dt_action = self.get_dt_for_action()
         interval = self.parameters.get('interval')
+
         if dt_action <= dt_active < dt_action + timedelta(seconds=interval):
-            self.send_mail(key, status_type='Inactive')
+            detailed_message = f'\n{self.nwst_id}\n\n'
+            for key, status in self.status_dict.items():
+                detailed_message += f'{key}: {status.message}\n'
+            self.send_mail(key, status_type='Inactive', additional_message=detailed_message)
+
+    def check_for_any_error_no_dcn(self):
+        return any([status.is_error and not status.connection_error for status in self.status_dict.values()])
 
     def start(self):
         self.analyse_channels()
@@ -693,13 +881,23 @@ class StationQC(object):
             self.print(150 * '#')
             self.print('This is StationQT. Calculating quality for station'
                        ' {network}.{station}.{location}'.format(**self.nsl))
-        self.activity_check()
         self.voltage_analysis()
         self.pb_temp_analysis()
         self.pb_power_analysis()
         self.pb_rout_charge_analysis()
         self.mass_analysis()
-        #self.clock_quality_analysis()
+        self.clock_quality_analysis()
+        self.gaps_analysis()
+
+        # activity check should be done last for useful status output (e.g. email)
+        self.activity_check()
+
+        self._simulate_error()
+
+    def _simulate_error(self):
+        for key in self.keys:
+            if self._simulated_error_check(key):
+                self.error(key, 'SIMULATED ERROR')
 
     def return_print_analysis(self):
         items = [self.nwst_id]
@@ -717,6 +915,15 @@ class StationQC(object):
     def return_analysis(self):
         return self.status_dict
 
+    def get_unit_factor(self, channel):
+        """ Get channel multiplier for unit from parameters. If none is specified return 1 """
+        channel_params = self.parameters.get('CHANNELS').get(channel)
+        if channel_params:
+            multiplier = channel_params.get('unit')
+            if multiplier:
+                return float(multiplier)
+        return 1
+
     def get_last_occurrence_timestring(self, trace, indices):
         """ returns a nicely formatted string of the timedelta since program starttime and occurrence and abs time"""
         last_occur = self.get_last_occurrence(trace, indices)
@@ -728,44 +935,52 @@ class StationQC(object):
     def get_last_occurrence(self, trace, indices):
         return self.get_time(trace, indices[-1])
 
-    def clock_quality_analysis(self, channel='LCQ'):
+    def clock_quality_analysis(self, channel='LCQ', n_sample_average=10):
         """ Analyse clock quality """
         key = 'clock'
         st = self.stream.select(channel=channel)
         trace = self.get_trace(st, key)
-        if not trace: return
-        clockQuality = trace.data
-        clockQuality_warn_level = self.parameters.get('THRESHOLDS').get('clockquality_warn')
-        clockQuality_fail_level = self.parameters.get('THRESHOLDS').get('clockquality_fail')
+        if not trace:
+            return
+        clock_quality = trace.data
+        clock_quality_warn_level = self.parameters.get('THRESHOLDS').get('clockquality_warn')
+        clock_quality_fail_level = self.parameters.get('THRESHOLDS').get('clockquality_fail')
 
         if self.verbosity > 1:
             self.print(40 * '-')
             self.print('Performing Clock Quality check', flush=False)
 
-        clockQuality_warn = np.where(clockQuality < clockQuality_warn_level)[0]
-        clockQuality_fail = np.where(clockQuality < clockQuality_fail_level)[0]
+        clockQuality_warn = np.where(clock_quality < clock_quality_warn_level)[0]
+        clockQuality_fail = np.where(clock_quality < clock_quality_fail_level)[0]
 
         if len(clockQuality_warn) == 0 and len(clockQuality_fail) == 0:
-            self.status_ok(key, detailed_message=f'ClockQuality={(clockQuality[-1])}')
+            self.status_ok(key, detailed_message=f'ClockQuality={(clock_quality[-1])}')
             return
 
+        last_val_average = np.nanmean(clock_quality[-n_sample_average:])
+
+        # keep OK status if there are only minor warnings (lower warn level)
         warn_message = f'Trace {trace.get_id()}:'
         if len(clockQuality_warn) > 0:
             # try calculate number of warn peaks from gaps between indices
             n_qc_warn = self.calc_occurrences(clockQuality_warn)
-            detailed_message = warn_message + f' {n_qc_warn}x Qlock Quality less then {clockQuality_warn_level}%' \
+            detailed_message = warn_message + f' {n_qc_warn}x Clock quality less then {clock_quality_warn_level}%' \
                                + self.get_last_occurrence_timestring(trace, clockQuality_warn)
-            self.warn(key, detailed_message=detailed_message, count=n_qc_warn,
-                      last_occurrence=self.get_last_occurrence(trace, clockQuality_warn))
+            self.status_ok(key, detailed_message=detailed_message)
 
+        # set WARN status for severe warnings in the past
         if len(clockQuality_fail) > 0:
             # try calculate number of fail peaks from gaps between indices
             n_qc_fail = self.calc_occurrences(clockQuality_fail)
-            detailed_message = warn_message + f' {n_qc_fail}x Qlock Quality less then {clockQuality_fail_level}%' \
+            detailed_message = warn_message + f' {n_qc_fail}x Clock quality less then {clock_quality_fail_level}%' \
                                + self.get_last_occurrence_timestring(trace, clockQuality_fail)
-            self.error(key, detailed_message=detailed_message, count=n_qc_fail,
+            self.warn(key, detailed_message=detailed_message, count=n_qc_fail,
                       last_occurrence=self.get_last_occurrence(trace, clockQuality_fail))
 
+        # set FAIL state if last value is less than fail level
+        if last_val_average < clock_quality_fail_level:
+            self.error(key, detailed_message=f'ClockQuality={(clock_quality[-1])}')
+
     def voltage_analysis(self, channel='VEI'):
         """ Analyse voltage channel for over/undervoltage """
         key = 'voltage'
@@ -773,7 +988,7 @@ class StationQC(object):
         trace = self.get_trace(st, key)
         if not trace:
             return
-        voltage = trace.data * 1e-3
+        voltage = trace.data * self.get_unit_factor(channel)
         low_volt = self.parameters.get('THRESHOLDS').get('low_volt')
         high_volt = self.parameters.get('THRESHOLDS').get('high_volt')
 
@@ -812,7 +1027,7 @@ class StationQC(object):
         trace = self.get_trace(st, key)
         if not trace:
             return
-        voltage = trace.data * 1e-6
+        voltage = trace.data * self.get_unit_factor(channel)
         thresholds = self.parameters.get('THRESHOLDS')
         temp = 20. * voltage - 20
         # average temp
@@ -858,7 +1073,7 @@ class StationQC(object):
 
         # correct for channel unit
         for trace in st:
-            trace.data = trace.data * 1e-6  # hardcoded, change this?
+            trace.data = trace.data * self.get_unit_factor(trace.stats.channel)
 
         # calculate average of absolute maximum of mass offset of last n_samp_mean
         last_values = np.array([trace.data[-n_samp_mean:] for trace in st])
@@ -878,10 +1093,10 @@ class StationQC(object):
             self.status_ok(key, detailed_message=f'{common_highest_val}V')
         elif max_vm_warn <= common_highest_val < max_vm_fail:
             self.warn(key=key,
-                      detailed_message=f'Warning raised for mass centering. Highest val {common_highest_val}V', )
+                      detailed_message=f'Warning raised for mass centering. Highest val (abs) {common_highest_val}V', )
         else:
             self.error(key=key,
-                      detailed_message=f'Fail status for mass centering. Highest val {common_highest_val}V',)
+                      detailed_message=f'Fail status for mass centering. Highest val (abs) {common_highest_val}V',)
 
         if self.verbosity > 1:
             self.print(40 * '-')
@@ -896,7 +1111,7 @@ class StationQC(object):
         if not trace:
             return
 
-        voltage = trace.data * 1e-6
+        voltage = trace.data * self.get_unit_factor(channel)
         if self.verbosity > 1:
             self.print(40 * '-')
             self.print('Performing PowBox 12V/230V check (EX2)', flush=False)
@@ -919,7 +1134,7 @@ class StationQC(object):
         if not trace:
             return
 
-        voltage = trace.data * 1e-6
+        voltage = trace.data * self.get_unit_factor(channel)
         if self.verbosity > 1:
             self.print(40 * '-')
             self.print('Performing PowBox Router/Charger check (EX3)', flush=False)
@@ -946,7 +1161,7 @@ class StationQC(object):
                     if message == 'OK':
                         self.status_ok(key)
                         continue
-                    if volt_lvl > 1:
+                    if volt_lvl != 1:
                         n_occurrences = self.calc_occurrences(ind_array)
                         self.warn(key=key,
                                   detailed_message=f'Trace {trace.get_id()}: '
@@ -955,8 +1170,30 @@ class StationQC(object):
                                   count=n_occurrences,
                                   last_occurrence=self.get_last_occurrence(trace, ind_array))
                     # if last_val == current voltage (which is not 1) -> FAIL or last_val < 1: PBox no data
-                    if volt_lvl == last_val or (volt_lvl == -1 and last_val < 1):
+                    if volt_lvl == last_val:
                         self.error(key, detailed_message=f'Last PowBox voltage state {last_val}V: {message}')
+                    elif volt_lvl == -1 and last_val < 1:
+                        self.error(key, detailed_message=f'PowBox under 1V - connection error', disc=True)
+
+    def gaps_analysis(self, key='gaps'):
+        """ return gaps of a given nwst_id """
+
+        gaps = []
+        for gap_list in self.parent.gaps:
+            nw_gap, st_gap = gap_list[:2]
+            if nw_gap == self.network and st_gap == self.station:
+                gaps.append(gap_list)
+
+        if not gaps:
+            self.status_ok(key=key)
+            return
+
+        detailed_message = ''
+        for gap_list in gaps:
+            text = '{}.{}.{}.{}: last sample - {}, next sample - {}, delta {}, samples {}\n'.format(*gap_list)
+            detailed_message += text
+
+        self.warn(key=key, detailed_message=detailed_message, count=len(gaps))
 
     def calc_occurrences(self, ind_array):
         # try calculate number of voltage peaks/plateaus from gaps between indices
@@ -1070,19 +1307,23 @@ class StationQC(object):
 
 
 class Status(object):
+    """ Basic Status class. All status classes are derived from this class."""
     def __init__(self, message=None, detailed_messages=None, count: int = 0, last_occurrence=None, show_count=True):
         if message is None:
             message = '-'
         if detailed_messages is None:
             detailed_messages = []
+
         self.show_count = show_count
         self.message = message
         self.messages = [message]
         self.detailed_messages = detailed_messages
         self.count = count
         self.last_occurrence = last_occurrence
+
         self.is_warn = None
         self.is_error = None
+        self.connection_error = None
         self.is_other = False
         self.is_active = False
 
@@ -1129,6 +1370,15 @@ class StatusError(Status):
         super(StatusError, self).__init__(message=message, count=count, last_occurrence=last_occurence,
                                           detailed_messages=detailed_messages, show_count=show_count)
         self.set_error()
+        self.default_message = message
+
+    def set_disconnected(self, message='DCN'):
+        self.connection_error = True
+        self.message = message
+
+    def set_connected(self):
+        self.connection_error = False
+        self.message = self.default_message
 
 
 class StatusOther(Status):
@@ -1162,7 +1412,9 @@ class StatusOther(Status):
 if __name__ == '__main__':
     parser = argparse.ArgumentParser(description='Call survBot')
     parser.add_argument('-html', dest='html_path', default=None, help='filepath for HTML output')
+    parser.add_argument('-parfile', dest='parfile', default='parameters.yaml',
+                        help='parameter file (default: parameters.yaml)')
     args = parser.parse_args()
 
-    survBot = SurveillanceBot(parameter_path='parameters.yaml', outpath_html=args.html_path)
+    survBot = SurveillanceBot(parameter_path=args.parfile, outpath_html=args.html_path)
     survBot.start()

survBotGUI.py

@@ -34,7 +34,7 @@ from obspy import UTCDateTime
 
 from survBot import SurveillanceBot
 from write_utils import *
-from utils import get_bg_color, modify_stream_for_plot, trace_yticks, trace_thresholds
+from utils import get_bg_color, modify_stream_for_plot, set_axis_yticks, set_axis_color, plot_axis_thresholds
 
 try:
     from rest_api.utils import get_station_iccid
@@ -316,9 +316,10 @@ class MainWindow(QtWidgets.QMainWindow):
             self.plot_widget.setWindowTitle(nwst_id)
             st = modify_stream_for_plot(st, parameters=self.parameters)
             st.plot(equal_scale=False, method='full', block=False, fig=self.plot_widget.canvas.fig)
-            # trace_ylabels(fig=self.plot_widget.canvas.fig, parameters=self.parameters)
-            trace_yticks(fig=self.plot_widget.canvas.fig, parameters=self.parameters)
-            trace_thresholds(fig=self.plot_widget.canvas.fig, parameters=self.parameters)
+            # set_axis_ylabels(fig=self.plot_widget.canvas.fig, parameters=self.parameters)
+            set_axis_yticks(fig=self.plot_widget.canvas.fig, parameters=self.parameters)
+            set_axis_color(fig=self.plot_widget.canvas.fig)
+            plot_axis_thresholds(fig=self.plot_widget.canvas.fig, parameters=self.parameters)
             self.plot_widget.show()
 
     def notification(self, text):

utils.py

@@ -19,7 +19,10 @@ def get_bg_color(check_key, status, dt_thresh=None, hex=False):
         if status.is_warn:
             bg_color = get_warn_color(status.count)
         elif status.is_error:
-            bg_color = get_color('FAIL')
+            if status.connection_error:
+                bg_color = get_color('disc')
+            else:
+                bg_color = get_color('FAIL')
         else:
             bg_color = get_color(message)
     if not bg_color:
@@ -31,12 +34,19 @@ def get_bg_color(check_key, status, dt_thresh=None, hex=False):
 
 
 def get_color(key):
-    # some GUI default colors
-    colors_dict = {'FAIL': (255, 50, 0, 255),
+    # some old GUI default colors
+    # colors_dict = {'FAIL': (255, 85, 50, 255),
+    #                'NO DATA': (255, 255, 125, 255),
+    #                'WARN': (255, 255, 80, 255),
+    #                'OK': (173, 255, 133, 255),
+    #                'undefined': (230, 230, 230, 255),
+    #                'disc': (255, 160, 40, 255),}
+    colors_dict = {'FAIL': (195, 29, 14, 255),
                    'NO DATA': (255, 255, 125, 255),
-                   'WARN': (255, 255, 80, 255),
-                   'OK': (125, 255, 125, 255),
-                   'undefined': (230, 230, 230, 255)}
+                   'WARN': (250, 192, 63, 255),
+                   'OK': (185, 245, 145, 255),
+                   'undefined': (240, 240, 240, 255),
+                   'disc': (126, 127, 131, 255), }
     return colors_dict.get(key)
 
 
@@ -47,16 +57,19 @@ def get_color_mpl(key):
 
 def get_time_delay_color(dt, dt_thresh):
     """ Set color of time delay after thresholds specified in self.dt_thresh """
-    if dt < dt_thresh[0]:
-        return get_color('OK')
-    elif dt_thresh[0] <= dt < dt_thresh[1]:
-        return get_color('WARN')
+    if isinstance(dt, type(dt_thresh[0])):
+        if dt < dt_thresh[0]:
+            return get_color('OK')
+        elif dt_thresh[0] <= dt < dt_thresh[1]:
+            return get_color('WARN')
     return get_color('FAIL')
 
 
-def get_warn_color(count):
-    color = (min([255, 200 + count ** 2]), 255, 80, 255)
-    return color
+def get_warn_color(count, n_colors=20):
+    if count >= n_colors:
+        count = -1
+    gradient = np.linspace((240, 245, 110, 255), (250, 192, 63, 255), n_colors, dtype=int)
+    return tuple(gradient[count])
 
 
 def get_mass_color(message):
@@ -76,6 +89,24 @@ def get_temp_color(temp, vmin=-10, vmax=60, cmap='coolwarm'):
     return rgba
 
 
+def get_font_color(bg_color, hex=False):
+    if hex:
+        bg_color = matplotlib.colors.to_rgb(bg_color)
+    bg_color_hsv = matplotlib.colors.rgb_to_hsv(bg_color)
+    bg_color_hsl = hsv_to_hsl(bg_color_hsv)
+    font_color = (255, 255, 255, 255) if bg_color_hsl[2] < 0.6 else (0, 0, 0, 255)
+    if hex:
+        font_color = '#{:02x}{:02x}{:02x}'.format(*font_color[:3])
+    return font_color
+
+
+def hsv_to_hsl(hsv):
+    hue, saturation, value = hsv
+    lightness = value * (1 - saturation / 2)
+    saturation = 0 if lightness in (0, 1) else (value - lightness) / min(lightness, 1 - lightness)
+    return hue, saturation, lightness
+
+
 def modify_stream_for_plot(input_stream, parameters):
     """ copy (if necessary) and modify stream for plotting """
 
@@ -110,7 +141,7 @@ def modify_stream_for_plot(input_stream, parameters):
 
         # modify trace id to maintain plotting order
         name = channel_dict.get('name')
-        tr.id = f'trace {index + 1}: {name} - {tr.id}'
+        tr.id = f'{index + 1}: {name} - {tr.id}'
 
         st.append(tr)
 
@@ -139,7 +170,7 @@ def transform_trace(data, transf):
     return data
 
 
-def trace_ylabels(fig, parameters, verbosity=0):
+def set_axis_ylabels(fig, parameters, verbosity=0):
     """
     Adds channel names to y-axis if defined in parameters.
     """
@@ -155,7 +186,16 @@ def trace_ylabels(fig, parameters, verbosity=0):
             ax.set_ylabel(channel_name)
 
 
-def trace_yticks(fig, parameters, verbosity=0):
+def set_axis_color(fig, color='0.8'):
+    """
+    Set all axes of figure to specific color
+    """
+    for ax in fig.axes:
+        for key in ['bottom', 'top', 'right', 'left']:
+            ax.spines[key].set_color(color)
+
+
+def set_axis_yticks(fig, parameters, verbosity=0):
     """
     Adds channel names to y-axis if defined in parameters.
     """
@@ -176,7 +216,7 @@ def trace_yticks(fig, parameters, verbosity=0):
         ax.set_ylim(ymin - 0.33 * step, ymax + 0.33 * step)
 
 
-def trace_thresholds(fig, parameters, verbosity=0):
+def plot_axis_thresholds(fig, parameters, verbosity=0):
     """
     Adds channel thresholds (warn, fail) to y-axis if defined in parameters.
     """
@@ -205,4 +245,4 @@ def plot_threshold_lines(fig, channel_threshold_list, parameters, **kwargs):
             if isinstance(warn_thresh, str):
                 warn_thresh = parameters.get('THRESHOLDS').get(warn_thresh)
             if type(warn_thresh in (float, int)):
-                ax.axhline(warn_thresh, **kwargs)
+                ax.axhline(warn_thresh, **kwargs)

write_utils.py

@@ -1,16 +1,21 @@
+from base64 import b64encode
 from datetime import timedelta
 
 
-def write_html_table_title(fobj, parameters):
+def _convert_to_textstring(lst):
+    return '\n'.join(lst)
+
+
+def get_html_table_title(parameters):
     title = get_print_title_str(parameters)
-    fobj.write(f'<h3>{title}</h3>\n')
+    return f'<h3>{title}</h3>\n'
 
 
-def write_html_text(fobj, text):
-    fobj.write(f'<p>{text}</p>\n')
+def get_html_text(text):
+    return f'<p>{text}</p>\n'
 
 
-def write_html_header(fobj, refresh_rate=10):
+def get_html_header(refresh_rate=10):
     header = ['<!DOCTYPE html>',
               '<html>',
               '<head>',
@@ -21,28 +26,52 @@ def write_html_header(fobj, refresh_rate=10):
               '<meta charset="utf-8">',
               '<meta name="viewport" content="width=device-width, initial-scale=1">',
               '<body>']
-    for item in header:
-        fobj.write(item + '\n')
+    header = _convert_to_textstring(header)
+    return header
 
 
-def init_html_table(fobj):
-    fobj.write('<table style="width:100%">\n')
+def get_mail_html_header():
+    header = ['<html>',
+              '<head>',
+              '</head>',
+              '<body>']
+    header = _convert_to_textstring(header)
+    return header
 
 
-def finish_html_table(fobj):
-    fobj.write('</table>\n')
+def init_html_table():
+    return '<table style="width:100%">\n'
 
 
-def write_html_footer(fobj):
-    footer = ['</body>',
-              '</html>']
-    for item in footer:
-        fobj.write(item + '\n')
+def finish_html_table():
+    return '</table>\n'
 
 
-def write_html_row(fobj, items, html_key='td'):
+def html_footer(footer_logo=None):
+    footer = ['</body>']
+    if footer_logo:
+        logo_items = [f'<div class="footer">',
+                      f'  <img style="float: right; padding: 10px;" src="{footer_logo}" height=30px>',
+                      f'</div>']
+        footer += logo_items
+    footer.append('</html>\n')
+
+    footer = _convert_to_textstring(footer)
+    return footer
+
+
+def add_html_image(img_data, img_format='png'):
+    return f"""<br>\n<img width="100%" src="data:image/{img_format};base64, {b64encode(img_data).decode('ascii')}">"""
+
+
+def get_html_link(text, link):
+    return f'<a href="{link}"> {text} </a>'
+
+
+def get_html_row(items, html_key='td'):
+    row_string = ''
     default_space = '  '
-    fobj.write(default_space + '<tr>\n')
+    row_string += default_space + '<tr>\n'
     for item in items:
         text = item.get('text')
         if item.get('bold'):
@@ -50,16 +79,16 @@ def write_html_row(fobj, items, html_key='td'):
         if item.get('italic'):
             text = '<i>' + text + '</i>'
         tooltip = item.get('tooltip')
-        color = item.get('color')
-        # check for black background of headers (shouldnt happen anymore)
-        color = '#e6e6e6' if color == '#000000' else color
+        font_color = item.get('font_color')
         hyperlink = item.get('hyperlink')
-        image_str = f'<a href="{hyperlink}">' if hyperlink else ''
+        color = 'transparent' if hyperlink else item.get('color')
+        text_str = get_html_link(text, hyperlink) if hyperlink else text
         html_class = item.get('html_class')
         class_str = f' class="{html_class}"' if html_class else ''
-        fobj.write(2 * default_space + f'<{html_key}{class_str} bgcolor="{color}" title="{tooltip}"> {image_str}'
-                   + text + f'</{html_key}>\n')
-    fobj.write(default_space + '</tr>\n')
+        row_string += 2 * default_space + f'<{html_key}{class_str} bgcolor="{color}" title="{tooltip}"' \
+                      + f'style="color:{font_color}"> {text_str}</{html_key}>\n'
+    row_string += default_space + '</tr>\n'
+    return row_string
 
 
 def get_print_title_str(parameters):