Merge remote-tracking branch 'origin/develop' into develop

# Conflicts:
#	parameters.yaml
#	survBot.py

parameters.yaml

@@ -4,7 +4,7 @@ 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",
-           "VM1", "VM2", "VM3"]    # Specify SOH channels, currently supported EX[1-3], VEI and VM[1-3]
+           "VM1", "VM2", "VM3", "LCQ"]    # Specify SOH channels, currently supported EX[1-3], VEI and VM[1-3]
 stations_blacklist: ["TEST", "EREA"]      # exclude these stations
 networks_blacklist: []                    # exclude these networks
 interval: 60               # Perform checks every x seconds
@@ -45,6 +45,8 @@ THRESHOLDS:
   high_volt: 14.8              # max voltage for over voltage warning
   unclassified: 5              # min voltage samples not classified for warning
   max_vm: [1.5, 2.5]           # thresholds for mass offset (warn, fail)
+  clockquality_warn: 90        # clock quality ranges from 0 % to 100 % with 100 % being the best level
+  clockquality_fail: 70
 
 # ---------------------------------------- OPTIONAL PARAMETERS ---------------------------------------------------------
 
@@ -70,7 +72,8 @@ channel_names: ["Temperature (°C)",
                 "Logger (V)",
                 "Mass 1 (V)",
                 "Mass 2 (V)",
-                "Mass 3 (V)"]
+                "Mass 3 (V)",
+                "Clock Q (%)"]
 
 # specify y-ticks (and ylims) giving, (ymin, ymax, step) for each of the above channels (0: default)
 CHANNEL_TICKS:
@@ -81,6 +84,7 @@ CHANNEL_TICKS:
   - [-2, 2, 1]
   - [-2, 2, 1]
   - [-2, 2, 1]
+  - [0, 100, 20]
 
 # Factor for channel to SI-units (for plotting)
 CHANNEL_UNITS:

survBot.py

@@ -61,7 +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', 'mass', 'temp', 'other']
+        self.keys = ['last active', '230V', '12V', 'router', 'charger', 'voltage', 'mass', 'clock', 'temp', 'other']
         self.parameter_path = parameter_path
         self.update_parameters()
         self.starttime = UTCDateTime()
@@ -686,6 +686,7 @@ class StationQC(object):
         self.pb_power_analysis()
         self.pb_rout_charge_analysis()
         self.mass_analysis()
+        self.clock_quality_analysis()
 
     def return_print_analysis(self):
         items = [self.nwst_id]
@@ -714,6 +715,44 @@ class StationQC(object):
     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}%' \
+                               + 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'
@@ -1107,23 +1146,6 @@ class StatusOther(Status):
         return message, detailed_message
 
 
-def common_mass_trace(st):
-    traces = st.traces
-    if not len(traces) == 3:
-        return
-    check_keys = ['sampling_rate', 'starttime', 'endtime', 'npts']
-    # check if values of the above keys are identical for all traces
-    for c_key in check_keys:
-        if not traces[0].stats.get(c_key) == traces[1].stats.get(c_key) == traces[2].stats.get(c_key):
-            return
-    max_1_2 = np.fmax(abs(traces[0]), abs(traces[1]))
-    abs_max = np.fmax(max_1_2, abs(traces[2]))
-    return_trace = traces[0].copy()
-    return_trace.data = abs_max
-    return return_trace
-
-
-
 if __name__ == '__main__':
     parser = argparse.ArgumentParser(description='Call survBot')
     parser.add_argument('-html', dest='html_path', default=None, help='filepath for HTML output')