Merge branch 'release0.2'

.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

@@ -1,18 +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
-channels: ["EX1", "EX2", "EX3", "VEI"]    # Specify SOH channels, currently supported EX[1-3] and VEI
+stations_blacklist: ["TEST", "EREA", "DOMV"]      # exclude these stations
-stations_blacklist: ["TEST", "EREA"]      # 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)
+n_track: 360               # wait n_track * intervals before performing an action (i.e. send mail/end highlight status)
-timespan: 7                # Check data of the recent x days
+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
+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)
@@ -43,6 +42,76 @@ THRESHOLDS:
   low_volt: 12                 # min voltage for low voltage warning
   high_volt: 14.8              # max voltage for over voltage warning
   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        # 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 ---------------------------------------------------
+# Currently supported: EX[1-3], VEI, VM[1-3], LCQ
+#
+# For each channel a factor 'unit' for unit conversion (e.g. to SI) can be provided, as well as a 'name'
+# and 'ticks' [ymin, ymax, ystep] for plotting.
+# 'warn' and 'fail' plot horizontal lines in corresponding colors (can be str in TRESHOLDS, int/float or iterable)
+#
+# 'transform' can be provided for plotting to perform arithmetic operations in given order, e.g.:
+#  transform: - ["*", 20]
+#             - ["-", 20]
+#  --> PBox EX1 V to deg C: 20 * x -20
+CHANNELS:
+  EX1:
+    unit: 1e-6
+    name: "PowBox Temperature (°C)"
+    ticks: [-10, 50, 10]
+    transform:
+      - ["*", 20]
+      - ["-", 20]
+    warn: "max_temp"
+  EX2:
+    unit: 1e-6
+    name: "PowBox 230V/12V (V)"
+    ticks: [0, 5, 1]
+    warn: [2, 3, 4, 4.5, 5]
+  EX3:
+    unit: 1e-6
+    name: "PowBox Router/Charger (V)"
+    ticks: [0, 5, 1]
+    warn: [2, 2.5, 3, 4, 5]
+  VEI:
+    unit: 1e-3
+    name: "Datalogger (V)"
+    ticks: [9, 15, 1]
+    warn: ["low_volt", "high_volt"]
+    fail: 10.5
+  VM1:
+    unit: 1e-6
+    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 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 position U (V)"
+    ticks: [-2.5, 2.5, 1]
+    warn: [-1.5, 1.5]
+    fail: [-2.5, 2.5]
+  LCQ:
+    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 ---------------------------------------------------------
 
@@ -53,6 +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"
@@ -60,25 +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])
-# names for plotting of the above defined parameter "channels" in the same order
+  external_mail_list: "mailing_list.yaml"
-channel_names: ["Temperature (°C)", "230V/12V Status (V)", "Router/Charger State (V)", "Logger Voltage (V)"]
-# specify y-ticks (and ylims) giving, (ymin, ymax, step) for each of the above channels (0: default)
-CHANNEL_TICKS:
-  - [-10, 50, 10]
-  - [1, 5, 1]
-  - [1, 5, 1]
-  - [9, 15, 1]
-
-# Factor for channel to SI-units (for plotting)
-CHANNEL_UNITS:
-  EX1: 1e-6
-  EX2: 1e-6
-  EX3: 1e-6
-  VEI: 1e-3
-
-# Transform channel for plotting, perform arithmetic operations in given order, e.g.: PBox EX1 V to deg C: 20 * x -20
-CHANNEL_TRANSFORM:
-  EX1:
-    - ["*", 20]
-    - ["-", 20]

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 {
+a:link, a:visited {
-    background-color: #ccc;
+    background-color: #e8e8e8;
     color: #000;
     text-decoration: none;
     display: block;
-    border-radius: 4px;
+    border-radius: 6px;
-    border: 1px solid #bbb;
+    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, \
+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
+    init_html_table, finish_html_table, get_mail_html_header, add_html_image
-from utils import get_bg_color, modify_stream_for_plot, trace_ylabels, trace_yticks
+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:
@@ -36,23 +40,36 @@ CLR = "\x1B[0K"
 deg_str = '\N{DEGREE SIGN}C'
 
 
-def read_yaml(file_path):
+def read_yaml(file_path, n_read=3):
+    for index in range(n_read):
+        try:
             with open(file_path, "r") as f:
-        return yaml.safe_load(f)
+                params = yaml.safe_load(f)
+        except Exception as e:
+            print(f'Could not read parameters file: {e}.\nWill try again {n_read - index - 1} time(s).')
+            time.sleep(10)
+            continue
+        return params
 
 
 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)
@@ -61,7 +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', '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()
@@ -69,22 +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 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')
@@ -92,9 +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)
@@ -120,25 +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,
+                        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 = {}
 
@@ -146,28 +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:
+                # 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)
-                # add file to read filenames to prevent re-reading in case it is not the current day (or end of
+                self.filenames_read_last_modif[filename] = os.path.getmtime(filename)
-                # 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)
             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:
@@ -242,7 +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', 'VEI', 'EX1', 'EX2', 'EX3']
+        channels = self.parameters.get('channels') + self.parameters.get('data_channels')
         network, station = nwst_id.split('.')[:2]
 
         times = []
@@ -329,20 +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)
+        fnames_out = [self.get_fig_path_abs(nwst_id), io.BytesIO()]
-        st = self.data.get(nwst_id)
+        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')
+                st.plot(fig=fig, show=False, draw=False, block=False, equal_scale=False, method='full',
-                trace_ylabels(fig, self.parameters, self.verbosity)
+                        starttime=starttime, endtime=endtime)
-                trace_yticks(fig, self.parameters, self.verbosity)
+                # 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())
@@ -352,51 +401,50 @@ class SurveillanceBot(object):
                              f'Refreshed hourly or on FAIL status.')
                 for ax in fig.axes:
                     ax.grid(True, alpha=0.1)
+                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):
-
-        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:
+        if hide_keys_mobile and check_key in hide_keys_mobile:
             html_class = 'hidden-mobile'
         return html_class
 
-        self.check_html_dir()
+    def make_html_table_header(self, default_header_color, hide_keys_mobile=None, add_links=True):
-        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)
-
         # 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 = get_html_class(check_key=check_key)
+            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)
-                write_html_row(outfile, header_items, html_key='th')
 
-                # Write all cells
+        return header, header_items
-                for nwst_id in self.station_list:
+
+    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,
+        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}')]
+                          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_dict = self.analysis_results.get(nwst_id)
                 status = status_dict.get(check_key)
                 message, detailed_message = status.get_status_str()
 
@@ -405,15 +453,16 @@ class SurveillanceBot(object):
                 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 = get_html_class(status=status, check_key=check_key)
+                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)
+                            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')
@@ -422,18 +471,62 @@ class SurveillanceBot(object):
                 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)
+                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)
 
-                    write_html_row(outfile, col_items)
+        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:
+                outfile.write(get_html_header(self.refresh_period))
+
+                # write_html_table_title(self.parameters)
+                outfile.write(init_html_table())
+
+                # 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:
+                    # 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))
+
+                outfile.write(finish_html_table())
+
+                # 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))
+
+                # add status message
+                outfile.write(get_html_text(self.status_message))
+
+                # 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())
 
+        if self.verbosity:
+            print(f'Wrote html table to {fnout}')
+
     def update_status_message(self):
         timespan = timedelta(seconds=int(self.parameters.get('timespan') * 24 * 3600))
         self.status_message = f'Program starttime (UTC) {self.starttime.strftime("%Y-%m-%d %H:%M:%S")} | ' \
@@ -455,19 +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
@@ -528,29 +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:
+            if self.status_track.get(key) and not self.status_track.get(key)[-1]:
-                self.parent.write_html_figure(self.nwst_id)
+                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)
+            send_mail = True
-            # set status to "inactive" after sending info mail
+            # 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):
         """
@@ -561,8 +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:
+        if n_errors is None:
-            n_errors = self.parameters.get('n_track') + 1
+            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
@@ -570,11 +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
+        # in case previous_errors exist, 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):
+        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:
@@ -602,23 +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')
@@ -664,10 +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()
@@ -680,11 +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.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]
@@ -702,6 +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)
@@ -713,13 +935,60 @@ class StationQC(object):
     def get_last_occurrence(self, trace, indices):
         return self.get_time(trace, indices[-1])
 
+    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
+        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(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={(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 Clock quality less then {clock_quality_warn_level}%' \
+                               + self.get_last_occurrence_timestring(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 Clock quality less then {clock_quality_fail_level}%' \
+                               + self.get_last_occurrence_timestring(trace, clockQuality_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'
         st = self.stream.select(channel=channel)
         trace = self.get_trace(st, key)
-        if not trace: return
+        if not trace:
-        voltage = trace.data * 1e-3
+            return
+        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')
 
@@ -756,14 +1025,15 @@ class StationQC(object):
         key = 'temp'
         st = self.stream.select(channel=channel)
         trace = self.get_trace(st, key)
-        if not trace: return
+        if not trace:
-        voltage = trace.data * 1e-6
+            return
+        voltage = trace.data * self.get_unit_factor(channel)
         thresholds = self.parameters.get('THRESHOLDS')
         temp = 20. * voltage - 20
         # average temp
         timespan = min([self.parameters.get('timespan') * 24 * 3600, int(len(temp) / trace.stats.sampling_rate)])
         nsamp_av = int(trace.stats.sampling_rate) * timespan
-        av_temp_str = str(round(np.mean(temp[-nsamp_av:]), 1)) + deg_str
+        av_temp_str = str(round(np.nanmean(temp[-nsamp_av:]), 1)) + deg_str
         # dt of average
         dt_t_str = str(timedelta(seconds=int(timespan))).replace(', 0:00:00', '')
         # current temp
@@ -771,7 +1041,7 @@ class StationQC(object):
         if self.verbosity > 1:
             self.print(40 * '-')
             self.print('Performing PowBox temperature check (EX1)', flush=False)
-            self.print(f'Average temperature at {np.mean(temp)}\N{DEGREE SIGN}', flush=False)
+            self.print(f'Average temperature at {np.nanmean(temp)}\N{DEGREE SIGN}', flush=False)
             self.print(f'Peak temperature at {max(temp)}\N{DEGREE SIGN}', flush=False)
             self.print(f'Min temperature at {min(temp)}\N{DEGREE SIGN}', flush=False)
         max_temp = thresholds.get('max_temp')
@@ -787,6 +1057,52 @@ class StationQC(object):
                            status_message=cur_temp,
                            detailed_message=f'Average temperature of last {dt_t_str}: {av_temp_str}')
 
+    def mass_analysis(self, channels=('VM1', 'VM2', 'VM3'), n_samp_mean=10):
+        """ Analyse datalogger mass channels. """
+        key = 'mass'
+
+        # build stream with all channels
+        st = Stream()
+        for channel in channels:
+            st += self.stream.select(channel=channel).copy()
+        st.merge()
+
+        # return if there are no three components
+        if not len(st) == 3:
+            return
+
+        # correct for channel unit
+        for trace in st:
+            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])
+        last_val_mean = np.nanmean(last_values, axis=1)
+        common_highest_val = np.nanmax(abs(last_val_mean))
+        common_highest_val = round(common_highest_val, 1)
+
+        # get thresholds for WARN (max_vm_warn) and FAIL (max_vm_fail)
+        thresholds = self.parameters.get('THRESHOLDS')
+        max_vm_warn = thresholds.get('max_vm_warn')
+        max_vm_fail = thresholds.get('max_vm_fail')
+        if not max_vm_warn or not max_vm_fail:
+            return
+
+        # change status depending on common_highest_val
+        if common_highest_val < max_vm_warn:
+            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 (abs) {common_highest_val}V', )
+        else:
+            self.error(key=key,
+                      detailed_message=f'Fail status for mass centering. Highest val (abs) {common_highest_val}V',)
+
+        if self.verbosity > 1:
+            self.print(40 * '-')
+            self.print('Performing mass position check', flush=False)
+            self.print(f'Average mass position at {common_highest_val}', flush=False)
+
     def pb_power_analysis(self, channel='EX2', pb_dict_key='pb_SOH2'):
         """ Analyse EX2 channel of PowBox """
         keys = ['230V', '12V']
@@ -795,7 +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)
@@ -818,7 +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)
@@ -845,7 +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()}: '
@@ -854,8 +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
@@ -969,19 +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
 
@@ -1028,6 +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):
@@ -1061,7 +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_ylabels, trace_yticks
+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
@@ -316,8 +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)
+            # set_axis_ylabels(fig=self.plot_widget.canvas.fig, parameters=self.parameters)
-            trace_yticks(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

@@ -2,6 +2,9 @@
 # -*- coding: utf-8 -*-
 
 import matplotlib
+import numpy as np
+
+from obspy import Stream
 
 
 def get_bg_color(check_key, status, dt_thresh=None, hex=False):
@@ -10,10 +13,15 @@ def get_bg_color(check_key, status, dt_thresh=None, hex=False):
         bg_color = get_time_delay_color(message, dt_thresh)
     elif check_key == 'temp':
         bg_color = get_temp_color(message)
+    elif check_key == 'mass':
+        bg_color = get_mass_color(message)
     else:
         if status.is_warn:
-            bg_color = get_color('WARNX')(status.count)
+            bg_color = get_warn_color(status.count)
         elif status.is_error:
+            if status.connection_error:
+                bg_color = get_color('disc')
+            else:
                 bg_color = get_color('FAIL')
         else:
             bg_color = get_color(message)
@@ -26,18 +34,30 @@ def get_bg_color(check_key, status, dt_thresh=None, hex=False):
 
 
 def get_color(key):
-    # some GUI default colors
+    # some old GUI default colors
-    colors_dict = {'FAIL': (255, 50, 0, 255),
+    # 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),
+                   'WARN': (250, 192, 63, 255),
-                   'WARNX': lambda x: (min([255, 200 + x ** 2]), 255, 80, 255),
+                   'OK': (185, 245, 145, 255),
-                   'OK': (125, 255, 125, 255),
+                   'undefined': (240, 240, 240, 255),
-                   'undefined': (230, 230, 230, 255)}
+                   'disc': (126, 127, 131, 255), }
     return colors_dict.get(key)
 
 
+def get_color_mpl(key):
+    color_tup = get_color(key)
+    return np.array([color/255. for color in color_tup])
+
+
 def get_time_delay_color(dt, dt_thresh):
     """ Set color of time delay after thresholds specified in self.dt_thresh """
+    if isinstance(dt, type(dt_thresh[0])):
         if dt < dt_thresh[0]:
             return get_color('OK')
         elif dt_thresh[0] <= dt < dt_thresh[1]:
@@ -45,6 +65,20 @@ def get_time_delay_color(dt, dt_thresh):
     return get_color('FAIL')
 
 
+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):
+    # can change this to something else if wanted. This way it always returns get_color (without warn count)
+    if isinstance(message, (float, int)):
+        return get_color('OK')
+    return get_color(message)
+
+
 def get_temp_color(temp, vmin=-10, vmax=60, cmap='coolwarm'):
     """ Get an rgba temperature value back from specified cmap, linearly interpolated between vmin and vmax. """
     if type(temp) in [str]:
@@ -55,29 +89,61 @@ def get_temp_color(temp, vmin=-10, vmax=60, cmap='coolwarm'):
     return rgba
 
 
-def modify_stream_for_plot(st, parameters):
+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 """
-    ch_units = parameters.get('CHANNEL_UNITS')
-    ch_transf = parameters.get('CHANNEL_TRANSFORM')
 
-    # if either of both are defined make copy
+    # make a copy
-    if ch_units or ch_transf:
+    st = Stream()
-        st = st.copy()
 
-    # modify trace for plotting by multiplying unit factor (e.g. 1e-3 mV to V)
+    channels_dict = parameters.get('CHANNELS')
-    if ch_units:
+
-        for tr in st:
+    # iterate over all channels and put them to new stream in order
-            channel = tr.stats.channel
+    for index, ch_tup in enumerate(channels_dict.items()):
-            unit_factor = ch_units.get(channel)
+        # unpack tuple from items
+        channel, channel_dict = ch_tup
+
+        # get correct channel from stream
+        st_sel = input_stream.select(channel=channel)
+        # in case there are != 1 there is ambiguity
+        if not len(st_sel) == 1:
+            continue
+
+        # make a copy to not modify original stream!
+        tr = st_sel[0].copy()
+
+        # multiply with conversion factor for unit
+        unit_factor = channel_dict.get('unit')
         if unit_factor:
             tr.data = tr.data * float(unit_factor)
-    # modify trace for plotting by other arithmetic expressions
+
-    if ch_transf:
+        # apply transformations if provided
-        for tr in st:
+        transform = channel_dict.get('transform')
-            channel = tr.stats.channel
+        if transform:
-            transf = ch_transf.get(channel)
+            tr.data = transform_trace(tr.data, transform)
-            if transf:
+
-                tr.data = transform_trace(tr.data, transf)
+        # modify trace id to maintain plotting order
+        name = channel_dict.get('name')
+        tr.id = f'{index + 1}: {name} - {tr.id}'
+
+        st.append(tr)
 
     return st
 
@@ -104,13 +170,11 @@ 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.
-    Can get mixed up if channel order in stream and channel names defined in parameters.yaml differ, but it is
-    difficult to assess the correct order from Obspy plotting routing.
     """
-    names = parameters.get('channel_names')
+    names = [channel.get('name') for channel in parameters.get('CHANNELS').values()]
     if not names: # or not len(st.traces):
         return
     if not len(names) == len(fig.axes):
@@ -122,13 +186,20 @@ 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.
-    Can get mixed up if channel order in stream and channel names defined in parameters.yaml differ, but it is
-    difficult to assess the correct order from Obspy plotting routing.
     """
-    ticks = parameters.get('CHANNEL_TICKS')
+    ticks = [channel.get('ticks') for channel in parameters.get('CHANNELS').values()]
     if not ticks:
         return
     if not len(ticks) == len(fig.axes):
@@ -140,6 +211,38 @@ def trace_yticks(fig, parameters, verbosity=0):
             continue
         ymin, ymax, step = ytick_tripple
 
-        yticks = list(range(ymin, ymax + step, step))
+        yticks = list(np.arange(ymin, ymax + step, step))
         ax.set_yticks(yticks)
-        ax.set_ylim(ymin - step, ymax + step)
+        ax.set_ylim(ymin - 0.33 * step, ymax + 0.33 * step)
+
+
+def plot_axis_thresholds(fig, parameters, verbosity=0):
+    """
+    Adds channel thresholds (warn, fail) to y-axis if defined in parameters.
+    """
+    if verbosity > 0:
+        print('Plotting trace thresholds')
+
+    keys_colors = {'warn': dict(color=0.8 * get_color_mpl('WARN'), linestyle=(0, (5, 10)), alpha=0.5, linewidth=0.7),
+                   'fail': dict(color=0.8 * get_color_mpl('FAIL'), linestyle='solid', alpha=0.5, linewidth=0.7)}
+
+    for key, kwargs in keys_colors.items():
+        channel_threshold_list = [channel.get(key) for channel in parameters.get('CHANNELS').values()]
+        if not channel_threshold_list:
+            continue
+        plot_threshold_lines(fig, channel_threshold_list, parameters, **kwargs)
+
+
+def plot_threshold_lines(fig, channel_threshold_list, parameters, **kwargs):
+    for channel_thresholds, ax in zip(channel_threshold_list, fig.axes):
+        if not channel_thresholds:
+            continue
+
+        if not isinstance(channel_thresholds, (list, tuple)):
+            channel_thresholds = [channel_thresholds]
+
+        for warn_thresh in channel_thresholds:
+            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)

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):
+def get_html_text(text):
-    fobj.write(f'<p>{text}</p>\n')
+    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:
+    header = _convert_to_textstring(header)
-        fobj.write(item + '\n')
+    return header
 
 
-def init_html_table(fobj):
+def get_mail_html_header():
-    fobj.write('<table style="width:100%">\n')
+    header = ['<html>',
+              '<head>',
+              '</head>',
+              '<body>']
+    header = _convert_to_textstring(header)
+    return header
 
 
-def finish_html_table(fobj):
+def init_html_table():
-    fobj.write('</table>\n')
+    return '<table style="width:100%">\n'
 
 
-def write_html_footer(fobj):
+def finish_html_table():
-    footer = ['</body>',
+    return '</table>\n'
-              '</html>']
-    for item in footer:
-        fobj.write(item + '\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')
+        font_color = item.get('font_color')
-        # check for black background of headers (shouldnt happen anymore)
-        color = '#e6e6e6' if color == '#000000' else 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}'
+        row_string += 2 * default_space + f'<{html_key}{class_str} bgcolor="{color}" title="{tooltip}"' \
-                   + text + f'</{html_key}>\n')
+                      + f'style="color:{font_color}"> {text_str}</{html_key}>\n'
-    fobj.write(default_space + '</tr>\n')
+    row_string += default_space + '</tr>\n'
+    return row_string
 
 
 def get_print_title_str(parameters):