Merge remote-tracking branch 'origin/issue/1' into issue/1

Reviewed-on: #3

README.md

@@ -32,6 +32,8 @@ The main program with html output is executed by entering
 python survBot.py -html path_for_html_output
 ```
 
+There are example stylesheets in the folder *stylesheets* that can be copied into the path_for_html_output if desired.
+
 The GUI can be loaded via
 
 ```shell script

parameters.yaml

@@ -1,24 +1,27 @@
 # Parameters file for Surveillance Bot
-datapath: '/data/SDS/'      # SC3 Datapath
-networks: ['1Y', 'HA']
-stations: '*'
-locations: '*'
-channels: ['EX1', 'EX2', 'EX3', 'VEI']    # Specify SOH channels, currently supported EX[1-3] and VEI
-stations_blacklist: ['TEST', 'EREA']
-networks_blacklist: []
+datapath: "/data/SDS/"                    # SC3 Datapath
+networks: ["1Y", "HA"]                    # select networks, list or str
+stations: "*"                             # select stations, list or str
+locations: "*"                            # select locations, list or str
+channels: ["EX1", "EX2", "EX3", "VEI", "LCQ"]    # Specify SOH channels, currently supported EX[1-3], VEI and LCQ
+stations_blacklist: ["TEST", "EREA"]      # exclude these stations
+networks_blacklist: []                    # exclude these networks
 interval: 60               # Perform checks every x seconds
-timespan: 3                # Check data of the recent x days
-verbosity: 0
-reread_parameters: True    # reread parameters file (change parameters on runtime, not for itself/GUI refresh/datapath)
+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
+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
 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)
 
 POWBOX:
   pb_ok: 1  # Voltage for PowBox OK
   pb_SOH2: # PowBox channel 2 voltage translations
     -1: {"230V": "PBox under 1V", "12V": "PBox under 1V"}
-    1: {"230V": 'OK', "12V": "OK"}
+    1: {"230V": "OK", "12V": "OK"}
     2: {"230V": "OFF", "12V": "OK"}
     3: {"230V": "OK", "12V": "overvoltage"}
     4: {"230V": "OK", "12V": "undervoltage"}
@@ -33,10 +36,52 @@ POWBOX:
     4: {"router": "FAIL", "charger": "0 < resets < 3"}
     5: {"router": "FAIL", "charger": "locked"}
 
-
+# Thresholds for program warnings/voltage classifications
 THRESHOLDS:
   pb_thresh: 0.2               # Threshold for PowBox Voltage check +/- (V)
   max_temp: 50                 # max temperature for temperature warning
   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
+  clockquality_warn: 90        # clock quality ranges from 0 % to 100 % with 100 % being the best level
+  clockquality_fail: 70
+
+# ---------------------------------------- OPTIONAL PARAMETERS ---------------------------------------------------------
+
+# add links to html table with specified key as column and value as relative link, interpretable string parameters:
+# nw (e.g. 1Y), st (e.g. GR01A), nwst_id (e.g. 1Y.GR01A)
+add_links:
+  # for example: slmon: {"URL": "path/{nw}_{st}.html", "text": "link"}
+  slmon: {"URL": "../slmon/{nw}_{st}.html", "text": "show"}
+  24h-plot: {"URL": "../scheli/{nw}/{st}.png", "text": "plot"}
+
+# E-mail notifications
+EMAIL:
+  mailserver: "localhost"
+  addresses: ["marcel.paffrath@rub.de", "kasper.fischer@rub.de"]  # list of mail addresses for info mails
+  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
+
+# names for plotting of the above defined parameter "channels" in the same order
+channel_names: ["Clock Quality (%)", "Temperature (°C)", "230V/12V Status (V)", "Router/Charger State (V)", "Logger Voltage (V)"] # names for plotting (optional)
+# specify y-ticks (and ylims) giving, (ymin, ymax, step) for each of the above channels (0: default)
+CHANNEL_TICKS:
+  - [0, 100, 20]
+  - [-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

@@ -0,0 +1,39 @@
+body {
+    background-color: #ffffff;
+    place-items: center;
+    text-align: center;
+}
+
+td {
+    border-radius: 4px;
+    padding: 0px;
+}
+
+th {
+    background-color: #999;
+    border-radius: 4px;
+    padding: 3px 1px;
+}
+
+a:link, a:visited {
+    background-color: #ccc;
+    color: #000;
+    text-decoration: none;
+    display: block;
+    border-radius: 4px;
+    border: 1px solid #bbb;
+}
+
+a:hover {
+    background-color: #aaa;
+    display: block;			  
+}
+
+.blink-bg {
+    animation: blinkingBackground 2s infinite;
+}
+@keyframes blinkingBackground{
+    0%		{ background-color: #ffcc00;}
+    50%		{ background-color: #ff3200;}
+    100%	{ background-color: #ffcc00;}
+}

stylesheets/mobile.css

@@ -0,0 +1,43 @@
+body {
+    background-color: #ffffff;
+    place-items: center;
+    text-align: center;
+}
+
+td {
+    border-radius: 4px;
+    padding: 10px 2px;
+}
+
+th {
+    background-color: #999;
+    border-radius: 4px;
+    padding: 10px, 2px;
+}
+
+a:link {
+    background-color: #ccc;
+    color: #000;
+    text-decoration: none;
+    display: block;
+    border-radius: 4px;
+    border: 1px solid #bbb;
+}
+
+a:hover {
+    background-color: #aaa;
+    display: block;			  
+}
+
+.hidden-mobile {
+    display: none;
+}
+
+.blink-bg {
+    animation: blinkingBackground 2s infinite;
+}
+@keyframes blinkingBackground{
+    0%		{ background-color: #ffee00;}
+    50%		{ background-color: #ff3200;}
+    100%	{ background-color: #ffee00;}
+}

survBot.py

@@ -17,9 +17,18 @@ 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 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
+from utils import get_bg_color, modify_stream_for_plot, trace_ylabels, trace_yticks
+
+try:
+    import smtplib
+    from email.mime.text import MIMEText
+
+    mail_functionality = True
+except ImportError:
+    print('Could not import smtplib or mail. Disabled sending mails.')
+    mail_functionality = False
 
 pjoin = os.path.join
 UP = "\x1B[{length}A"
@@ -32,12 +41,12 @@ def read_yaml(file_path):
         return yaml.safe_load(f)
 
 
-def nsl_from_id(st_id):
-    network, station, location = st_id.split('.')
+def nsl_from_id(nwst_id):
+    network, station, location = nwst_id.split('.')
     return dict(network=network, station=station, location=location)
 
 
-def get_st_id(trace):
+def get_nwst_id(trace):
     stats = trace.stats
     return f'{stats.network}.{stats.station}.'  # {stats.location}'
 
@@ -52,7 +61,7 @@ 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', 'clock', 'temp', 'other']
         self.parameter_path = parameter_path
         self.update_parameters()
         self.starttime = UTCDateTime()
@@ -64,6 +73,7 @@ class SurveillanceBot(object):
         self.station_list = []
         self.analysis_print_list = []
         self.analysis_results = {}
+        self.status_track = {}
         self.dataStream = Stream()
         self.data = {}
         self.print_count = 0
@@ -82,6 +92,8 @@ 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 {}
 
     def transform_parameters(self):
         for key in ['networks', 'stations', 'locations', 'channels']:
@@ -103,8 +115,8 @@ class SurveillanceBot(object):
             if self.networks_blacklist and nw in self.networks_blacklist:
                 continue
             if (networks == ['*'] or nw in networks) and (stations == ['*'] or st in stations):
-                st_id = f'{nw}.{st}.'
-                self.station_list.append(st_id)
+                nwst_id = f'{nw}.{st}.'
+                self.station_list.append(nwst_id)
 
     def get_filenames(self):
         self.filenames = []
@@ -145,7 +157,7 @@ class SurveillanceBot(object):
             if filename in self.filenames_read:
                 continue
             try:
-                st_new = read(filename)
+                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 (
@@ -155,14 +167,14 @@ class SurveillanceBot(object):
                 print(f'Could not read file {filename}:', e)
                 continue
             self.dataStream += st_new
-        self.dataStream.merge()
+        self.dataStream.merge(fill_value=np.nan)
 
         # organise data in dictionary with key for each station
         for trace in self.dataStream:
-            st_id = get_st_id(trace)
-            if not st_id in self.data.keys():
-                self.data[st_id] = Stream()
-            self.data[st_id].append(trace)
+            nwst_id = get_nwst_id(trace)
+            if not nwst_id in self.data.keys():
+                self.data[nwst_id] = Stream()
+            self.data[nwst_id].append(trace)
 
     def execute_qc(self):
         if self.reread_parameters:
@@ -173,47 +185,65 @@ class SurveillanceBot(object):
 
         self.analysis_print_list = []
         self.analysis_results = {}
-        for st_id in sorted(self.station_list):
-            stream = self.data.get(st_id)
+        for nwst_id in sorted(self.station_list):
+            stream = self.data.get(nwst_id)
             if stream:
-                nsl = nsl_from_id(st_id)
-                station_qc = StationQC(stream, nsl, self.parameters, self.keys, qc_starttime, self.verbosity,
-                                       print_func=self.print)
+                nsl = nsl_from_id(nwst_id)
+                station_qc = StationQC(self, stream, nsl, self.parameters, self.keys, qc_starttime,
+                                       self.verbosity, print_func=self.print,
+                                       status_track=self.status_track.get(nwst_id))
                 analysis_print_result = station_qc.return_print_analysis()
-                station_dict, warn_dict = station_qc.return_analysis()
+                station_dict = station_qc.return_analysis()
             else:
-                analysis_print_result = self.get_no_data_station(st_id, to_print=True)
-                station_dict, warn_dict = self.get_no_data_station(st_id)
+                analysis_print_result = self.get_no_data_station(nwst_id, to_print=True)
+                station_dict = self.get_no_data_station(nwst_id)
             self.analysis_print_list.append(analysis_print_result)
-            self.analysis_results[st_id] = (station_dict, warn_dict)
+            self.analysis_results[nwst_id] = station_dict
+        self.track_status()
 
         self.update_status_message()
         return 'ok'
 
-    def get_no_data_station(self, st_id, no_data='-', to_print=False):
-        delay = self.get_station_delay(st_id)
+    def track_status(self):
+        """
+        tracks error status of the last n_track + 1 errors.
+        """
+        n_track = self.parameters.get('n_track')
+        if not n_track or n_track < 1:
+            return
+        for nwst_id, analysis_dict in self.analysis_results.items():
+            if not nwst_id in self.status_track.keys():
+                self.status_track[nwst_id] = {}
+            for key, status in analysis_dict.items():
+                if not key in self.status_track[nwst_id].keys():
+                    self.status_track[nwst_id][key] = []
+                track_lst = self.status_track[nwst_id][key]
+                # pop list until length is n_track + 1
+                while len(track_lst) > n_track:
+                    track_lst.pop(0)
+                track_lst.append(status.is_error)
+
+    def get_no_data_station(self, nwst_id, no_data='-', to_print=False):
+        delay = self.get_station_delay(nwst_id)
         if not to_print:
             status_dict = {}
-            warn_dict = {}
             for key in self.keys:
                 if key == 'last active':
-                    status_dict[key] = timedelta(seconds=int(delay))
-                    warn_dict[key] = 'No data within set timespan'
+                    status_dict[key] = Status(message=timedelta(seconds=int(delay)), detailed_messages=['No data'])
                 else:
-                    status_dict[key] = no_data
-                    warn_dict[key] = 'No data'
-            return status_dict, warn_dict
+                    status_dict[key] = Status(message=no_data, detailed_messages=['No data'])
+            return status_dict
         else:
-            items = [st_id.rstrip('.')] + [fancy_timestr(timedelta(seconds=int(delay)))]
+            items = [nwst_id.rstrip('.')] + [fancy_timestr(timedelta(seconds=int(delay)))]
             for _ in range(len(self.keys) - 1):
                 items.append(no_data)
             return items
 
-    def get_station_delay(self, st_id):
+    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']
-        network, station = st_id.split('.')[:2]
+        network, station = nwst_id.split('.')[:2]
 
         times = []
         for channel in channels:
@@ -248,7 +278,7 @@ class SurveillanceBot(object):
             if self.outpath_html:
                 self.write_html_table()
                 if self.parameters.get('html_figures'):
-                    self.write_html_figures(check_plot_time=not(first_exec))
+                    self.write_html_figures(check_plot_time=not (first_exec))
             else:
                 self.print_analysis()
             time.sleep(self.refresh_period)
@@ -276,11 +306,11 @@ class SurveillanceBot(object):
             self.plot_hour += 1
         return True
 
-    def get_fig_path_abs(self, st_id):
-        return pjoin(self.outpath_html, self.get_fig_path_rel(st_id))
+    def get_fig_path_abs(self, nwst_id):
+        return pjoin(self.outpath_html, self.get_fig_path_rel(nwst_id))
 
-    def get_fig_path_rel(self, st_id, fig_format='png'):
-        return os.path.join(self.html_fig_dir, f'{st_id.rstrip(".")}.{fig_format}')
+    def get_fig_path_rel(self, nwst_id, fig_format='png'):
+        return os.path.join(self.html_fig_dir, f'{nwst_id.rstrip(".")}.{fig_format}')
 
     def check_fig_dir(self):
         fdir = pjoin(self.outpath_html, self.html_fig_dir)
@@ -292,23 +322,50 @@ class SurveillanceBot(object):
             os.mkdir(self.outpath_html)
 
     def write_html_figures(self, check_plot_time=True):
-        """ Write figures for html, right now hardcoded hourly """
+        """ Write figures for html (e.g. hourly) """
         if check_plot_time and not self.check_plot_hour():
             return
+
+        for nwst_id in self.station_list:
+            self.write_html_figure(nwst_id)
+
+    def write_html_figure(self, nwst_id):
+        """ Write figure for html for specified station """
         self.check_fig_dir()
 
-        for st_id in self.station_list:
         fig = plt.figure(figsize=(16, 9))
-            fnout = self.get_fig_path_abs(st_id)
-            st = self.data.get(st_id)
+        fnout = self.get_fig_path_abs(nwst_id)
+        st = self.data.get(nwst_id)
         if st:
+            # TODO: this section might fail, adding try-except block for analysis and to prevent program from crashing
+            try:
+                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)
+            except Exception as e:
+                print(f'Could not generate plot for {nwst_id}:')
+                print(traceback.format_exc())
+            if len(fig.axes) > 0:
                 ax = fig.axes[0]
-                ax.set_title(f'Hourly refreshed plot at (UTC) {UTCDateTime.now().strftime("%Y-%m-%d %H:%M:%S")}')
+                ax.set_title(f'Plot refreshed at (UTC) {UTCDateTime.now().strftime("%Y-%m-%d %H:%M:%S")}. '
+                             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')
         plt.close(fig)
 
-    def write_html_table(self, default_color='#e6e6e6'):
+    def write_html_table(self, default_color='#e6e6e6', default_header_color='#999', hide_keys_mobile=('other')):
+
+        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
+
         self.check_html_dir()
         fnout = pjoin(self.outpath_html, 'survBot_out.html')
         if not fnout:
@@ -316,23 +373,32 @@ class SurveillanceBot(object):
         try:
             with open(fnout, 'w') as outfile:
                 write_html_header(outfile, self.refresh_period)
-                #write_html_table_title(outfile, self.parameters)
+                # write_html_table_title(outfile, self.parameters)
                 init_html_table(outfile)
 
                 # First write header items
-                header_items = [dict(text='Station', color=default_color)]
-                for check_key in self.keys:
-                    item = dict(text=check_key, color=default_color)
+                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 all cells
-                for st_id in self.station_list:
-                    fig_name = self.get_fig_path_rel(st_id)
-                    col_items = [dict(text=st_id.rstrip('.'), color=default_color, image_src=fig_name)]
-                    for check_key in self.keys:
-                        status_dict, detailed_dict = self.analysis_results.get(st_id)
+                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 background color
                             dt_thresh = [timedelta(seconds=sec) for sec in self.dt_thresh]
@@ -342,12 +408,23 @@ class SurveillanceBot(object):
 
                             # add degree sign for temp
                             if check_key == 'temp':
-                            if not type(status) in [str]:
-                                status = str(status) + deg_str
+                                if not type(message) in [str]:
+                                    message = str(message) + deg_str
 
-                        item = dict(text=str(status), tooltip=str(detailed_dict.get(check_key)),
-                                    color=bg_color)
+                            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)
+
                     write_html_row(outfile, col_items)
 
                 finish_html_table(outfile)
@@ -361,7 +438,7 @@ class SurveillanceBot(object):
         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")} | ' \
                               f'Current time (UTC) {UTCDateTime().strftime("%Y-%m-%d %H:%M:%S")} | ' \
-                              f'Refresh period: {self.refresh_period}s | '\
+                              f'Refresh period: {self.refresh_period}s | ' \
                               f'Showing data of last {timespan}'
 
     def print(self, string, **kwargs):
@@ -378,12 +455,13 @@ class SurveillanceBot(object):
 
 
 class StationQC(object):
-    def __init__(self, stream, nsl, parameters, keys, starttime, verbosity, print_func):
+    def __init__(self, parent, stream, nsl, parameters, keys, starttime, verbosity, print_func, status_track={}):
         """
         Station Quality Check class.
         :param nsl: dictionary containing network, station and location (key: str)
         :param parameters: parameters dictionary from parameters.yaml file
         """
+        self.parent = parent
         self.stream = stream
         self.nsl = nsl
         self.network = nsl.get('network')
@@ -395,51 +473,186 @@ class StationQC(object):
         self.last_active = False
         self.print = print_func
 
-        timespan = self.parameters.get('timespan') * 24 * 3600
-        self.analysis_starttime = self.program_starttime - timespan
-
         self.keys = keys
-        self.detailed_status_dict = {key: None for key in self.keys}
-        self.status_dict = {key: '-' for key in self.keys}
-        self.activity_check()
+        self.status_dict = {key: Status() for key in self.keys}
 
-        self.analyse_channels()
+        if not status_track:
+            status_track = {}
+        self.status_track = status_track
 
-    def status_ok(self, key, message=None, status_message='OK'):
-        self.status_dict[key] = status_message
-        self.detailed_status_dict[key] = message
+        self.start()
 
-    def warn(self, key, detailed_message, status_message='WARN'):
-        # update detailed status if already existing
-        current_message = self.detailed_status_dict.get(key)
-        current_message = '' if current_message in [None, '-'] else current_message + ' | '
-        self.detailed_status_dict[key] = current_message + detailed_message
+    @property
+    def nwst_id(self):
+        return f'{self.network}.{self.station}'
 
-        # this is becoming a little bit too complicated (adding warnings to existing)
-        current_status_message = self.status_dict.get(key)
-        current_status_message = '' if current_status_message in [None, 'OK', '-'] else current_status_message + ' | '
-        self.status_dict[key] = current_status_message + status_message
+    def status_ok(self, key, detailed_message="Everything OK", status_message='OK', overwrite=False):
+        current_status = self.status_dict.get(key)
+        # do not overwrite existing warnings or errors
+        if not overwrite and (current_status.is_warn or current_status.is_error):
+            return
+        self.status_dict[key] = StatusOK(message=status_message, detailed_messages=[detailed_message])
+
+    def warn(self, key, detailed_message, last_occurrence=None, count=1):
+        if key == 'other':
+            self.status_other(detailed_message, last_occurrence, count)
+
+        new_warn = StatusWarn(count=count, show_count=self.parameters.get('warn_count'))
+
+        current_status = self.status_dict.get(key)
 
         # change this to something more useful, SMS/EMAIL/PUSH
         if self.verbosity:
             self.print(f'{UTCDateTime()}: {detailed_message}', flush=False)
+
+        # if error, do not overwrite with warning
+        if current_status.is_error:
+            return
+
+        if current_status.is_warn:
+            current_status.count += count
+        else:
+            current_status = new_warn
+
+        self._update_status(key, current_status, detailed_message, last_occurrence)
+
         # warnings.warn(message)
 
-    def error(self, key, message):
-        self.detailed_status_dict[key] = message
-        self.status_dict[key] = 'FAIL'
-        # change this to something more useful, SMS/EMAIL/PUSH
+        # # update detailed status if already existing
+        # current_message = self.detailed_status_dict.get(key)
+        # current_message = '' if current_message in [None, '-'] else current_message + ' | '
+        # self.detailed_status_dict[key] = current_message + detailed_message
+        #
+        # # this is becoming a little bit too complicated (adding warnings to existing)
+        # current_status_message = self.status_dict.get(key)
+        # 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):
+        new_error = StatusError(count=count, show_count=self.parameters.get('warn_count'))
+        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.verbosity:
-            self.print(f'{UTCDateTime()}: {message}', flush=False)
-        # warnings.warn(message)
+            self.print(f'{UTCDateTime()}: {detailed_message}', flush=False)
 
-    def activity_check(self):
+        # 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
+            current_status.is_active = False
+        elif self.search_previous_errors(key) == 'active':
+            current_status.is_active = True
+
+        self._update_status(key, current_status, detailed_message, last_occurrence)
+
+    def search_previous_errors(self, key, n_errors=None):
+        """
+        Check n_track + 1 previous statuses for errors.
+        If first item in list is no error but all others are return True
+        (first time n_track errors appeared if ALL n_track + 1 are error: error is old)
+        If last item is error but not all items are error yet return keyword 'active' -> error active, no message sent
+        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
+
+        previous_errors = self.status_track.get(key)
+        # only if error list is filled n_track times
+        if previous_errors and len(previous_errors) == n_errors:
+            # 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):
+            return 'active'
+        return False
+
+    def send_mail(self, key, status_type, additional_message=''):
+        """ Send info mail using parameters specified in parameters file """
+        if not mail_functionality:
+            if self.verbosity:
+                print('Mail functionality disabled. Return')
+            return
+
+        mail_params = self.parameters.get('EMAIL')
+        if not mail_params:
+            if self.verbosity:
+                print('parameter "EMAIL" not set in parameter file. Return')
+            return
+
+        stations_blacklist = mail_params.get('stations_blacklist')
+        if stations_blacklist and self.station in stations_blacklist:
+            if self.verbosity:
+                print(f'Station {self.station} listed in blacklist. Return')
+            return
+
+        networks_blacklist = mail_params.get('networks_blacklist')
+        if networks_blacklist and self.network in networks_blacklist:
+            if self.verbosity:
+                print(f'Station {self.station} of network {self.network} listed in blacklist. Return')
+            return
+
+        sender = mail_params.get('sender')
+        addresses = mail_params.get('addresses')
+        server = mail_params.get('mailserver')
+        if not sender or not addresses:
+            if self.verbosity:
+                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['Subject'] = f'new message on station {self.nwst_id}'
+        msg['From'] = sender
+        msg['To'] = ', '.join(addresses)
+
+        # send message via SMTP server
+        s = smtplib.SMTP(server)
+        s.sendmail(sender, addresses, msg.as_string())
+        s.quit()
+
+    def get_dt_for_action(self):
+        n_track = self.parameters.get('n_track')
+        interval = self.parameters.get('interval')
+        dt = timedelta(seconds=n_track * interval)
+        return dt
+
+    def status_other(self, detailed_message, status_message, last_occurrence=None, count=1):
+        key = 'other'
+        new_status = StatusOther(count=count, messages=[status_message])
+        current_status = self.status_dict.get(key)
+        if current_status.is_other:
+            current_status.count += count
+            current_status.messages.append(status_message)
+        else:
+            current_status = new_status
+
+        self._update_status(key, current_status, detailed_message, last_occurrence)
+
+    def _update_status(self, key, current_status, detailed_message, last_occurrence):
+        current_status.detailed_messages.append(detailed_message)
+        current_status.last_occurrence = last_occurrence
+
+        self.status_dict[key] = current_status
+
+    def activity_check(self, key='last_active'):
         self.last_active = self.last_activity()
         if not self.last_active:
-            message = 'FAIL'
+            status = StatusError()
         else:
-            message = timedelta(seconds=int(self.program_starttime - self.last_active))
-        self.status_dict['last active'] = message
+            dt_active = timedelta(seconds=int(self.program_starttime - self.last_active))
+            status = Status(message=dt_active)
+            self.check_for_inactive_message(key, dt_active)
+
+        self.status_dict['last active'] = status
 
     def last_activity(self):
         if not self.stream:
@@ -450,39 +663,95 @@ class StationQC(object):
         if len(endtimes) > 0:
             return max(endtimes)
 
+    def check_for_inactive_message(self, key, dt_active):
+        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')
+
+    def start(self):
+        self.analyse_channels()
+
     def analyse_channels(self):
+        timespan = self.parameters.get('timespan') * 24 * 3600
+        self.analysis_starttime = self.program_starttime - timespan
+
         if self.verbosity > 0:
             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.clock_quality_analysis()
 
     def return_print_analysis(self):
-        items = [f'{self.network}.{self.station}']
+        items = [self.nwst_id]
         for key in self.keys:
-            item = self.status_dict[key]
+            status = self.status_dict[key]
+            message = status.message
             if key == 'last active':
-                items.append(fancy_timestr(item))
+                items.append(fancy_timestr(message))
             elif key == 'temp':
-                items.append(str(item) + deg_str)
+                items.append(str(message) + deg_str)
             else:
-                items.append(str(item))
+                items.append(str(message))
         return items
 
     def return_analysis(self):
-        return self.status_dict, self.detailed_status_dict
+        return self.status_dict
 
     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_time(trace, indices[-1])
+        last_occur = self.get_last_occurrence(trace, indices)
         if not last_occur:
             return ''
         last_occur_dt = timedelta(seconds=int(self.program_starttime - last_occur))
         return f', Last occurrence: {last_occur_dt} ({last_occur.strftime("%Y-%m-%d %H:%M:%S")})'
 
+    def get_last_occurrence(self, trace, indices):
+        return self.get_time(trace, indices[-1])
+
+    def clock_quality_analysis(self, channel='LCQ'):
+        """ 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 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]
+
+        if len(clockQuality_warn) == 0 and len(clockQuality_fail) == 0:
+            self.status_ok(key, detailed_message=f'ClockQuality={(clockQuality[-1])}')
+            return
+ 
+        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}' \
+                               + 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))
+
+        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}V ' \
+                               + self.get_last_occurrence_timestring(trace, clockQuality_fail)
+            self.error(key, detailed_message=detailed_message, count=n_qc_fail,
+                      last_occurrence=self.get_last_occurrence(trace, clockQuality_fail))
+
     def voltage_analysis(self, channel='VEI'):
         """ Analyse voltage channel for over/undervoltage """
         key = 'voltage'
@@ -501,24 +770,25 @@ class StationQC(object):
         undervolt = np.where(voltage < low_volt)[0]
 
         if len(overvolt) == 0 and len(undervolt) == 0:
-            self.status_ok(key, message=f'U={(voltage[-1])}V')
+            self.status_ok(key, detailed_message=f'U={(voltage[-1])}V')
             return
 
-        n_overvolt = 0
-        n_undervolt = 0
-
         warn_message = f'Trace {trace.get_id()}:'
         if len(overvolt) > 0:
             # try calculate number of voltage peaks from gaps between indices
             n_overvolt = len(np.where(np.diff(overvolt) > 1)[0]) + 1
-            warn_message += f' {n_overvolt}x Voltage over {high_volt}V' \
+            detailed_message = warn_message + f' {n_overvolt}x Voltage over {high_volt}V' \
                                + self.get_last_occurrence_timestring(trace, overvolt)
+            self.warn(key, detailed_message=detailed_message, count=n_overvolt,
+                      last_occurrence=self.get_last_occurrence(trace, overvolt))
+
         if len(undervolt) > 0:
             # try calculate number of voltage peaks from gaps between indices
             n_undervolt = len(np.where(np.diff(undervolt) > 1)[0]) + 1
-            warn_message += f' {n_undervolt}x Voltage under {low_volt}V ' \
+            detailed_message = warn_message + f' {n_undervolt}x Voltage under {low_volt}V ' \
                                + self.get_last_occurrence_timestring(trace, undervolt)
-        self.warn(key, detailed_message=warn_message, status_message='WARN ({})'.format(n_overvolt + n_undervolt))
+            self.warn(key, detailed_message=detailed_message, count=n_undervolt,
+                      last_occurrence=self.get_last_occurrence(trace, undervolt))
 
     def pb_temp_analysis(self, channel='EX1'):
         """ Analyse PowBox temperature output. """
@@ -534,7 +804,7 @@ class StationQC(object):
         nsamp_av = int(trace.stats.sampling_rate) * timespan
         av_temp_str = str(round(np.mean(temp[-nsamp_av:]), 1)) + deg_str
         # dt of average
-        dt_t_str = str(timedelta(seconds=int(timespan)))
+        dt_t_str = str(timedelta(seconds=int(timespan))).replace(', 0:00:00', '')
         # current temp
         cur_temp = round(temp[-1], 1)
         if self.verbosity > 1:
@@ -547,14 +817,14 @@ class StationQC(object):
         t_check = np.where(temp > max_temp)[0]
         if len(t_check) > 0:
             self.warn(key=key,
-                      status_message=cur_temp,
                       detailed_message=f'Trace {trace.get_id()}: '
                                        f'Temperature over {max_temp}\N{DEGREE SIGN} at {trace.get_id()}!'
-                                       + self.get_last_occurrence_timestring(trace, t_check))
+                                       + self.get_last_occurrence_timestring(trace, t_check),
+                      last_occurrence=self.get_last_occurrence(trace, t_check))
         else:
             self.status_ok(key,
                            status_message=cur_temp,
-                           message=f'Average temperature of last {dt_t_str}: {av_temp_str}')
+                           detailed_message=f'Average temperature of last {dt_t_str}: {av_temp_str}')
 
     def pb_power_analysis(self, channel='EX2', pb_dict_key='pb_SOH2'):
         """ Analyse EX2 channel of PowBox """
@@ -604,22 +874,53 @@ class StationQC(object):
     def in_depth_voltage_check(self, trace, voltage_dict, soh_params, last_val):
         """ Associate values in voltage_dict to error messages specified in SOH_params and warn."""
         for volt_lvl, ind_array in voltage_dict.items():
-            if volt_lvl == 1: continue  # No need to do anything here
+            if volt_lvl == 1:
+                continue  # No need to do anything here
             if len(ind_array) > 0:
+                # get result from parameter dictionary for voltage level
                 result = soh_params.get(volt_lvl)
                 for key, message in result.items():
+                    # if result is OK, continue with next voltage level
                     if message == 'OK':
                         self.status_ok(key)
                         continue
-                    # try calculate number of voltage peaks from gaps between indices
-                    n_occurrences = len(np.where(np.diff(ind_array) > 1)[0]) + 1
+                    if volt_lvl > 1:
+                        n_occurrences = self.calc_occurrences(ind_array)
                         self.warn(key=key,
                                   detailed_message=f'Trace {trace.get_id()}: '
                                                    f'Found {n_occurrences} occurrence(s) of {volt_lvl}V: {key}: {message}'
                                                    + self.get_last_occurrence_timestring(trace, ind_array),
-                              status_message='WARN ({})'.format(n_occurrences))
-                    if last_val != 1:
-                        self.error(key, message=f'Last PowBox voltage state {last_val}V: {message}')
+                                  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):
+                        self.error(key, detailed_message=f'Last PowBox voltage state {last_val}V: {message}')
+
+    def calc_occurrences(self, ind_array):
+        # try calculate number of voltage peaks/plateaus from gaps between indices
+        if len(ind_array) == 0:
+            return 0
+        else:
+            # start index at 1 if there are gaps (n_peaks = n_gaps + 1)
+            n_occurrences = 1
+
+        min_samples = self.parameters.get('min_sample')
+        if not min_samples:
+            min_samples = 1
+
+        # calculated differences in index array, diff > 1: gap, diff == 1: within peak/plateau
+        diffs = np.diff(ind_array)
+        gap_start_inds = np.where(np.diff(ind_array) > 1)[0]
+        # iterate over all gaps and check "min_samples" before the gap
+        for gsi in gap_start_inds:
+            # right boundary index of peak (gap index - 1)
+            peak_rb_ind = gsi - 1
+            # left boundary index of peak
+            peak_lb_ind = max([0, peak_rb_ind - min_samples])
+            if all(diffs[peak_lb_ind: peak_rb_ind] == 1):
+                n_occurrences += 1
+
+        return n_occurrences
 
     def get_trace(self, stream, keys):
         if not type(keys) == list:
@@ -673,8 +974,7 @@ class StationQC(object):
             # try calculate number of occurences from gaps between indices
             n_occurrences = len(np.where(np.diff(under) > 1)[0]) + 1
             voltage_dict[-1] = under
-            self.warn(key='other',
-                      detailed_message=f'Trace {trace.get_id()}: '
+            self.status_other(detailed_message=f'Trace {trace.get_id()}: '
                                                f'Voltage below {pb_ok}V in {len(under)} samples, {n_occurrences} time(s). '
                                                f'Mean voltage: {np.mean(voltage):.2}'
                                                + self.get_last_occurrence_timestring(trace, under),
@@ -695,7 +995,7 @@ class StationQC(object):
             n_unclassified = len(unclassified_indices)
             max_uncl = self.parameters.get('THRESHOLDS').get('unclassified')
             if max_uncl and n_unclassified > max_uncl:
-                self.warn(key='other', detailed_message=f'Trace {trace.get_id()}: '
+                self.status_other(detailed_message=f'Trace {trace.get_id()}: '
                                                    f'{n_unclassified}/{len(all_indices)} '
                                                    f'unclassified voltage values in channel {trace.get_id()}',
                                   status_message=f'{channel}: {n_unclassified} uncl.')
@@ -707,6 +1007,96 @@ class StationQC(object):
         return trace.stats.starttime + trace.stats.delta * index
 
 
+class Status(object):
+    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.is_other = False
+        self.is_active = False
+
+    def set_warn(self):
+        self.is_warn = True
+
+    def set_error(self):
+        self.is_warn = False
+        self.is_error = True
+
+    def set_ok(self):
+        self.is_warn = False
+        self.is_error = False
+
+    def get_status_str(self):
+        message = self.message
+        if self.count > 1 and self.show_count:
+            message += f' ({self.count})'
+        detailed_message = ''
+
+        for index, dm in enumerate(self.detailed_messages):
+            if index > 0:
+                detailed_message += ' | '
+            detailed_message += dm
+
+        return message, detailed_message
+
+
+class StatusOK(Status):
+    def __init__(self, message='OK', detailed_messages=None):
+        super(StatusOK, self).__init__(message=message, detailed_messages=detailed_messages)
+        self.set_ok()
+
+
+class StatusWarn(Status):
+    def __init__(self, message='WARN', count=1, last_occurence=None, detailed_messages=None, show_count=False):
+        super(StatusWarn, self).__init__(message=message, count=count, last_occurrence=last_occurence,
+                                         detailed_messages=detailed_messages, show_count=show_count)
+        self.set_warn()
+
+
+class StatusError(Status):
+    def __init__(self, message='FAIL', count=1, last_occurence=None, detailed_messages=None, show_count=False):
+        super(StatusError, self).__init__(message=message, count=count, last_occurrence=last_occurence,
+                                          detailed_messages=detailed_messages, show_count=show_count)
+        self.set_error()
+
+
+class StatusOther(Status):
+    def __init__(self, messages=None, count=1, last_occurence=None, detailed_messages=None):
+        super(StatusOther, self).__init__(count=count, last_occurrence=last_occurence,
+                                          detailed_messages=detailed_messages)
+        if messages is None:
+            messages = []
+        self.messages = messages
+        self.is_other = True
+
+    def get_status_str(self):
+        if self.messages == []:
+            return '-'
+
+        message = ''
+        for index, mes in enumerate(self.messages):
+            if index > 0:
+                message += ' | '
+            message += mes
+
+        detailed_message = ''
+        for index, dm in enumerate(self.detailed_messages):
+            if index > 0:
+                detailed_message += ' | '
+            detailed_message += dm
+
+        return message, detailed_message
+
+
 if __name__ == '__main__':
     parser = argparse.ArgumentParser(description='Call survBot')
     parser.add_argument('-html', dest='html_path', default=None, help='filepath for HTML output')

survBotGUI.py

@@ -22,7 +22,6 @@ except ImportError:
         except ImportError:
             raise ImportError('Could import neither of PySide2, PySide6 or PyQt5')
 
-import matplotlib
 from matplotlib.figure import Figure
 
 if QtGui.__package__ in ['PySide2', 'PyQt5', 'PySide6']:
@@ -35,7 +34,7 @@ from obspy import UTCDateTime
 
 from survBot import SurveillanceBot
 from write_utils import *
-from utils import get_bg_color
+from utils import get_bg_color, modify_stream_for_plot, trace_ylabels, trace_yticks
 
 try:
     from rest_api.utils import get_station_iccid
@@ -130,10 +129,10 @@ class MainWindow(QtWidgets.QMainWindow):
         self.table.setRowCount(len(station_list))
         self.table.setHorizontalHeaderLabels(keys)
 
-        for index, st_id in enumerate(station_list):
+        for index, nwst_id in enumerate(station_list):
             item = QtWidgets.QTableWidgetItem()
-            item.setText(str(st_id.rstrip('.')))
-            item.setData(QtCore.Qt.UserRole, st_id)
+            item.setText(str(nwst_id.rstrip('.')))
+            item.setData(QtCore.Qt.UserRole, nwst_id)
             self.table.setVerticalHeaderItem(index, item)
 
         self.main_layout.addWidget(self.table)
@@ -180,38 +179,38 @@ class MainWindow(QtWidgets.QMainWindow):
         header_item = self.table.verticalHeaderItem(row_ind)
         if not header_item:
            return
-        st_id = header_item.data(QtCore.Qt.UserRole)
+        nwst_id = header_item.data(QtCore.Qt.UserRole)
 
         context_menu = QtWidgets.QMenu()
         read_sms = context_menu.addAction('Get last SMS')
         send_sms = context_menu.addAction('Send SMS')
         action = context_menu.exec_(self.mapToGlobal(self.last_mouse_loc))
         if action == read_sms:
-           self.read_sms(st_id)
+           self.read_sms(nwst_id)
         elif action == send_sms:
-           self.send_sms(st_id)
+           self.send_sms(nwst_id)
 
-    def read_sms(self, st_id):
+    def read_sms(self, nwst_id):
         """ Read recent SMS over rest_api using whereversim portal """
-        station = st_id.split('.')[1]
+        station = nwst_id.split('.')[1]
         iccid = get_station_iccid(station)
         if not iccid:
-            print('Could not find iccid for station', st_id)
+            print('Could not find iccid for station', nwst_id)
             return
         sms_widget = ReadSMSWidget(parent=self, iccid=iccid)
-        sms_widget.setWindowTitle(f'Recent SMS of station: {st_id}')
+        sms_widget.setWindowTitle(f'Recent SMS of station: {nwst_id}')
         if sms_widget.data:
             sms_widget.show()
         else:
             self.notification('No recent messages found.')
 
-    def send_sms(self, st_id):
+    def send_sms(self, nwst_id):
         """ Send SMS over rest_api using whereversim portal """
-        station = st_id.split('.')[1]
+        station = nwst_id.split('.')[1]
         iccid = get_station_iccid(station)
 
         sms_widget = SendSMSWidget(parent=self, iccid=iccid)
-        sms_widget.setWindowTitle(f'Send SMS to station: {st_id}')
+        sms_widget.setWindowTitle(f'Send SMS to station: {nwst_id}')
         sms_widget.show()
 
     def set_clear_on_refresh(self):
@@ -230,19 +229,19 @@ class MainWindow(QtWidgets.QMainWindow):
         self.fill_status_bar()
 
         for col_ind, check_key in enumerate(self.survBot.keys):
-            for row_ind, st_id in enumerate(self.survBot.station_list):
-                status_dict, detailed_dict = self.survBot.analysis_results.get(st_id)
+            for row_ind, nwst_id in enumerate(self.survBot.station_list):
+                status_dict = self.survBot.analysis_results.get(nwst_id)
                 status = status_dict.get(check_key)
-                detailed_message = detailed_dict.get(check_key)
+                message, detailed_message = status.get_status_str()
 
                 dt_thresh = [timedelta(seconds=sec) for sec in self.dt_thresh]
                 bg_color = get_bg_color(check_key, status, dt_thresh)
                 if check_key == 'temp':
-                    if not type(status) in [str]:
-                        status = str(status) + deg_str
+                    if not type(message) in [str]:
+                        message = str(message) + deg_str
 
                 # Continue if nothing changed
-                text = str(status)
+                text = str(message)
                 cur_item = self.table.item(row_ind, col_ind)
                 if cur_item and text == cur_item.text():
                     if not self.parameters.get('track_changes') or self.clear_on_refresh:
@@ -253,9 +252,9 @@ class MainWindow(QtWidgets.QMainWindow):
 
                 # Create new data item
                 item = QtWidgets.QTableWidgetItem()
-                item.setText(str(status))
+                item.setText(str(message))
                 item.setTextAlignment(QtCore.Qt.AlignCenter)
-                item.setData(QtCore.Qt.UserRole, (st_id, check_key))
+                item.setData(QtCore.Qt.UserRole, (nwst_id, check_key))
 
                 # if text changed (known from above) set highlight color/font else (new init) set to default
                 cur_item = self.table.item(row_ind, col_ind)
@@ -310,12 +309,15 @@ class MainWindow(QtWidgets.QMainWindow):
             vheader.setSectionResizeMode(index, QtWidgets.QHeaderView.Stretch)
 
     def plot_stream(self, item):
-        st_id, check = item.data(QtCore.Qt.UserRole)
-        st = self.survBot.data.get(st_id)
+        nwst_id, check = item.data(QtCore.Qt.UserRole)
+        st = self.survBot.data.get(nwst_id)
         if st:
             self.plot_widget = PlotWidget(self)
-            self.plot_widget.setWindowTitle(st_id)
+            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)
             self.plot_widget.show()
 
     def notification(self, text):

utils.py

@@ -3,18 +3,20 @@
 
 import matplotlib
 
+
 def get_bg_color(check_key, status, dt_thresh=None, hex=False):
+    message = status.message
     if check_key == 'last active':
-        bg_color = get_time_delay_color(status, dt_thresh)
+        bg_color = get_time_delay_color(message, dt_thresh)
     elif check_key == 'temp':
-        bg_color = get_temp_color(status)
+        bg_color = get_temp_color(message)
     else:
-        statussplit = status.split(' ')
-        if len(statussplit) > 1 and statussplit[0] == 'WARN':
-            x = int(status.split(' ')[-1].lstrip('(').rstrip(')'))
-            bg_color = get_color('WARNX')(x)
+        if status.is_warn:
+            bg_color = get_color('WARNX')(status.count)
+        elif status.is_error:
+            bg_color = get_color('FAIL')
         else:
-            bg_color = get_color(status)
+            bg_color = get_color(message)
     if not bg_color:
         bg_color = get_color('undefined')
 
@@ -22,16 +24,18 @@ def get_bg_color(check_key, status, dt_thresh=None, hex=False):
         bg_color = '#{:02x}{:02x}{:02x}'.format(*bg_color[:3])
     return bg_color
 
+
 def get_color(key):
     # some GUI default colors
     colors_dict = {'FAIL': (255, 50, 0, 255),
                    'NO DATA': (255, 255, 125, 255),
-                   'WARN': (255, 255, 125, 255),
-                   'WARNX': lambda x: (min([255, 200 + x ** 2]), 255, 125, 255),
+                   'WARN': (255, 255, 80, 255),
+                   'WARNX': lambda x: (min([255, 200 + x ** 2]), 255, 80, 255),
                    'OK': (125, 255, 125, 255),
                    'undefined': (230, 230, 230, 255)}
     return colors_dict.get(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]:
@@ -40,6 +44,7 @@ def get_time_delay_color(dt, dt_thresh):
         return get_color('WARN')
     return get_color('FAIL')
 
+
 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]:
@@ -49,3 +54,92 @@ def get_temp_color(temp, vmin=-10, vmax=60, cmap='coolwarm'):
     rgba = [int(255 * c) for c in cmap(val)]
     return rgba
 
+
+def modify_stream_for_plot(st, 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
+    if ch_units or ch_transf:
+        st = st.copy()
+
+    # modify trace for plotting by multiplying unit factor (e.g. 1e-3 mV to V)
+    if ch_units:
+        for tr in st:
+            channel = tr.stats.channel
+            unit_factor = ch_units.get(channel)
+            if unit_factor:
+                tr.data = tr.data * float(unit_factor)
+    # modify trace for plotting by other arithmetic expressions
+    if ch_transf:
+        for tr in st:
+            channel = tr.stats.channel
+            transf = ch_transf.get(channel)
+            if transf:
+                tr.data = transform_trace(tr.data, transf)
+
+    return st
+
+
+def transform_trace(data, transf):
+    """
+    Transform trace with arithmetic operations in order, specified in transf
+    @param data: numpy array
+    @param transf: list of lists with arithmetic operations (e.g. [['*', '20'], ] -> multiply data by 20
+    """
+    # This looks a little bit hardcoded, however it is safer than using e.g. "eval"
+    for operator_str, val in transf:
+        if operator_str == '+':
+            data = data + val
+        elif operator_str == '-':
+            data = data - val
+        elif operator_str == '*':
+            data = data * val
+        elif operator_str == '/':
+            data = data / val
+        else:
+            raise IOError(f'Unknown arithmethic operator string: {operator_str}')
+
+    return data
+
+
+def trace_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')
+    if not names: # or not len(st.traces):
+        return
+    if not len(names) == len(fig.axes):
+        if verbosity:
+            print('Mismatch in axis and label lengths. Not adding plot labels')
+        return
+    for channel_name, ax in zip(names, fig.axes):
+        if channel_name:
+            ax.set_ylabel(channel_name)
+
+
+def trace_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')
+    if not ticks:
+        return
+    if not len(ticks) == len(fig.axes):
+        if verbosity:
+            print('Mismatch in axis tick and label lengths. Not changing plot ticks.')
+        return
+    for ytick_tripple, ax in zip(ticks, fig.axes):
+        if not ytick_tripple:
+            continue
+        ymin, ymax, step = ytick_tripple
+
+        yticks = list(range(ymin, ymax + step, step))
+        ax.set_yticks(yticks)
+        ax.set_ylim(ymin - step, ymax + step)

write_utils.py

@@ -1,55 +1,68 @@
 from datetime import timedelta
 
+
 def write_html_table_title(fobj, parameters):
     title = get_print_title_str(parameters)
     fobj.write(f'<h3>{title}</h3>\n')
 
+
 def write_html_text(fobj, text):
     fobj.write(f'<p>{text}</p>\n')
 
+
 def write_html_header(fobj, refresh_rate=10):
     header = ['<!DOCTYPE html>',
               '<html>',
+              '<head>',
+              '  <link rel="stylesheet" media="only screen and (max-width: 400px)" href="mobile.css" />',
+              '  <link rel="stylesheet" media="only screen and (min-width: 401px)" href="desktop.css" />',
+              '</head>',
               f'<meta http-equiv="refresh" content="{refresh_rate}" >',
               '<meta charset="utf-8">',
+              '<meta name="viewport" content="width=device-width, initial-scale=1">',
               '<body>']
-    # style = ['<style>',
-    #           'table, th, td {',
-    #           'border:1px solid black;',
-    #           '}',
-    #           '</style>',]
     for item in header:
         fobj.write(item + '\n')
 
+
 def init_html_table(fobj):
     fobj.write('<table style="width:100%">\n')
 
+
 def finish_html_table(fobj):
     fobj.write('</table>\n')
 
+
 def write_html_footer(fobj):
     footer = ['</body>',
               '</html>']
     for item in footer:
         fobj.write(item + '\n')
 
+
 def write_html_row(fobj, items, html_key='td'):
     default_space = '  '
     fobj.write(default_space + '<tr>\n')
     for item in items:
         text = item.get('text')
+        if item.get('bold'):
+            text = '<b>' + text + '</b>'
+        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
-        image_src = item.get('image_src')
-        image_str = f'<a href="{image_src}">' if image_src else ''
-        fobj.write(2 * default_space + f'<{html_key} bgcolor="{color}" title="{tooltip}"> {image_str}'
+        hyperlink = item.get('hyperlink')
+        image_str = f'<a href="{hyperlink}">' if hyperlink else ''
+        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')
 
+
 def get_print_title_str(parameters):
     timespan = parameters.get('timespan') * 24 * 3600
-    tdelta_str = str(timedelta(seconds=int(timespan)))
+    tdelta_str = str(timedelta(seconds=int(timespan))).replace(', 0:00:00', '')
     return f'Analysis table of router quality within the last {tdelta_str}'
-