Custom dates plot ccftime & start of brand new test suite for api.py

msnoise/api.py

@@ -193,7 +193,7 @@ def update_config(session, name, value):
     """
 
     config = session.query(Config).filter(Config.name == name).first()
-    if "NULL" in value: 
+    if "NULL" in value:
         config.value = None
     else:
         config.value = value
@@ -996,7 +996,7 @@ def export_mseed(db, filename, pair, components, filterid, corr, ncorr=0,
     except:
         pass
     filename += ".MSEED"
-    
+
     if maxlag is None:
         maxlag = float(get_config(db, "maxlag"))
     if cc_sampling_rate is None:
@@ -1187,7 +1187,7 @@ def build_ref_datelist(session):
     return start, end, datelist.tolist()
 
 
-def build_movstack_datelist(session):
+def build_movstack_datelist(session, startdate=None, enddate=None):
     """
     Creates a date array for the analyse period.
     The returned tuple contains a start and an end date, and a list of
@@ -1196,12 +1196,19 @@ def build_movstack_datelist(session):
     :type session: :class:`sqlalchemy.orm.session.Session`
     :param session: A :class:`~sqlalchemy.orm.session.Session` object, as
         obtained by :func:`connect`
-
-    :rtype: tuple
-    :returns: (start, end, datelist)
-    """
-    begin = get_config(session, "startdate")
-    end = get_config(session, "enddate")
+    :type startdate: str
+    :param startdate: a startdate for which method should create a date array.
+        Defaults to None, in this case method gets the value from database.
+    :type enddate: str
+    :param enddate: a enddate for which method should create a date array.
+        Defaults to None, in this case method gets the value from database.
+
+    :rtype: (datetime.date, datetime.date, list of datetime.date)
+    :returns: Returns startdate, enddate and a list of all days between those.
+    """
+    begin = startdate if startdate is not None else get_config(session,
+                                                               "startdate")
+    end = enddate if enddate is not None else get_config(session, "enddate")
     if begin[0] == '-':
         start = datetime.date.today() + datetime.timedelta(days=int(begin))
         end = datetime.date.today() + datetime.timedelta(days=int(end))
@@ -1433,7 +1440,7 @@ def make_same_length(st):
     # apply the mask to all traces
     for tr in st:
         tr.data.mask = mask
-    
+
     # remove the masks from the stream 
     st = st.split()
     return st

msnoise/msnoise_admin.py

@@ -182,23 +182,23 @@ def mwcs_step(form, field):
         if field.data > form.data['mwcs_wlen']:
             raise ValidationError("'mwcs_step' should be smaller or equal to"
                                   " 'mwcs_wlen'")
-    
+
     form_args = dict(
         mwcs_low=dict(validators=[mwcs_low]),
         mwcs_high=dict(validators=[mwcs_high]),
         high=dict(validators=[high]),
         mwcs_step=dict(validators=[mwcs_step]),
     )
-    
+
     column_list = ('ref', 'low', 'mwcs_low', 'mwcs_high', 'high',
                    'rms_threshold', 'mwcs_wlen', 'mwcs_step', 'used')
     form_columns = ('low', 'mwcs_low', 'mwcs_high', 'high',
                     'rms_threshold', 'mwcs_wlen', 'mwcs_step', 'used')
-    
+
     def __init__(self, session, **kwargs):
         # You can pass name and other parameters if you want to
         super(FilterView, self).__init__(Filter, session, **kwargs)
-        
+
     @action('used',
             lazy_gettext('Toggle Used'),
             lazy_gettext('Are you sure you want to update selected models?'))
@@ -211,7 +211,7 @@ def used(self, ids):
             else:
                 s.used = True
         self.session.commit()
-        return  
+        return
 
 
 MY_DEFAULT_FORMATTERS = dict(typefmt.BASE_FORMATTERS)
@@ -224,10 +224,10 @@ class StationView(ModelView):
     view_title = "Station Configuration"
     column_filters = ('net', 'used')
     column_type_formatters = MY_DEFAULT_FORMATTERS
-    
+
     def __init__(self, session, **kwargs):
         super(StationView, self).__init__(Station, session, **kwargs)
-    
+
     @action('used',
             lazy_gettext('Toggle Used'),
             lazy_gettext('Are you sure you want to update selected models?'))
@@ -240,7 +240,7 @@ def used(self, ids):
             else:
                 s.used = True
         self.session.commit()
-        return  
+        return
 
 
 class DataAvailabilityView(ModelView):
@@ -255,7 +255,7 @@ class DataAvailabilityView(ModelView):
     def __init__(self, session, **kwargs):
         super(DataAvailabilityView, self).__init__(DataAvailability, session,
                                                    **kwargs)
-    
+
     @action('modified',
             lazy_gettext('Mark as (M)odified'),
             lazy_gettext('Are you sure you want to update selected models?'))
@@ -271,7 +271,7 @@ def modified(self, ids):
                        '%(count)s models were successfully flagged (M)odified.',
               count, count=count))
         return
-    
+
 
 class JobView(ModelView):
     view_title = "Jobs"
@@ -284,7 +284,7 @@ class JobView(ModelView):
 
     def __init__(self, session, **kwargs):
         super(JobView, self).__init__(Job, session, **kwargs)
-    
+
     @action('todo',
             lazy_gettext('Mark as (T)odo'),
             lazy_gettext('Are you sure you want to update selected models?'))
@@ -295,7 +295,7 @@ def todo(self, ids):
             s.flag = 'T'
         self.session.commit()
         return
-    
+
     @action('done',
             lazy_gettext('Mark as (D)one'),
             lazy_gettext('Are you sure you want to update selected models?'))
@@ -306,7 +306,7 @@ def done(self, ids):
             s.flag = 'D'
         self.session.commit()
         return
-    
+
     @action('deletetype',
             lazy_gettext('Delete all Jobs of the same "Type"'),
             lazy_gettext('Are you sure you want to delete all those models?'))
@@ -318,7 +318,7 @@ def deletetype(self, ids):
         self.get_query().filter(Job.jobtype == type_to_delete).delete()
         self.session.commit()
         return
-    
+
     @action('massTodo',
             lazy_gettext('Mark all Jobs of the same Type as (T)odo'),
             lazy_gettext('Are you sure you want to update all those models?'))
@@ -327,7 +327,7 @@ def massTodo(self, ids):
         query = self.get_query().filter(model_pk.in_(ids))
         for s in query.all():
             type_to_delete = s.jobtype
-        
+
         for s in self.get_query().filter(Job.jobtype == type_to_delete).all():
             s.flag = 'T'
         self.session.commit()
@@ -564,7 +564,7 @@ def allresults():
     start, end, dates = build_ref_datelist(db)
     i, result = get_results(db,station1, station2, filterid, components, dates,
                             format=format)
-    
+
     data = {}
     if format == 'stack':
         if i != 0:
@@ -603,7 +603,7 @@ def new_jobsTRIG():
     o['count'] = count
     o = json.dumps(o)
     return flask.Response(o, mimetype='application/json')
-    
+
 
 @app.route('/admin/jobs_list.json')
 def joblists():
@@ -666,7 +666,7 @@ def main(port=5000):
     db.close()
 
     admin = Admin(app, template_mode='bootstrap2')
-    
+
     if "msnoise_brand" in os.environ:
         tmp = eval(os.environ["msnoise_brand"])
         name, logo = tmp.split("|")

msnoise/plots/ccftime.py

@@ -4,7 +4,9 @@
 selectable too. The ``--ampli`` argument allows to increase the vertical scale
 of the CCFs. The ``--seismic`` shows the up-going wiggles with a black-filled
 background (very heavy !). Passing ``--refilter`` allows to bandpass filter
-CCFs before plotting (new in 1.5).
+CCFs before plotting (new in 1.5). Passing ``--startdate`` and ``--enddate``
+parameters allows to specify which period of data should be plotted. By default
+the plot uses dates determined in database.
 
 .. include:: clickhelp/msnoise-plot-ccftime.rst
 
@@ -17,22 +19,26 @@
 """
 # plot interferogram
 
+import datetime
+
 import matplotlib.dates as mdates
 import matplotlib.pyplot as plt
+import numpy as np
 from matplotlib.widgets import Cursor
-
-from obspy.signal.filter import envelope as obspy_envelope
 from obspy.signal.filter import bandpass
-from ..api import *
+from obspy.signal.filter import envelope as obspy_envelope
+
+from msnoise.api import connect, get_config, get_maxlag_samples, \
+    build_movstack_datelist, get_filters, get_results
 
 
 def main(sta1, sta2, filterid, components, mov_stack=1, ampli=5, seismic=False,
-         show=False, outfile=None, envelope=False, refilter=None):
+         show=False, outfile=None, envelope=False, refilter=None,  startdate=None, enddate=None):
     db = connect()
     maxlag = float(get_config(db, 'maxlag'))
     samples = get_maxlag_samples(db)
     cc_sampling_rate = float(get_config(db, 'cc_sampling_rate'))
-    start, end, datelist = build_movstack_datelist(db)
+    start, end, datelist = build_movstack_datelist(db, startdate, enddate)
     base = mdates.date2num(start) 
     plt.figure(figsize=(12, 9))
     sta1 = sta1.replace('.', '_')

msnoise/s000installer.py

@@ -30,7 +30,6 @@
     directory. It's not very safe, but until now we haven't thought of another
     solution.
 """
-import argparse
 import sys
 from getpass import getpass
 

msnoise/scripts/msnoise.py

@@ -562,17 +562,21 @@ def interferogram(ctx, sta1, sta2, filterid, comp, mov_stack, show, outfile,
 @click.option('-r', '--refilter', default=None,
               help='Refilter CCFs before plotting (e.g. 4:8 for filtering CCFs '
                    'between 4.0 and 8.0 Hz. This will update the plot title.')
+@click.option('--startdate', help='Change startdate',
+              default=None, type=str)
+@click.option('--enddate', help='Change enddate',
+              default=None, type=str)
 @click.pass_context
 def ccftime(ctx, sta1, sta2, filterid, comp, mov_stack,
-            ampli, seismic, show, outfile, envelope, refilter):
+            ampli, seismic, show, outfile, envelope, refilter, startdate, enddate):
     """Plots the ccf vs time between sta1 and sta2 (parses the dt/t results)\n
     STA1 and STA2 must be provided with this format: NET.STA !"""
     if ctx.obj['MSNOISE_custom']:
         from ccftime import main
     else:
         from ..plots.ccftime import main
     main(sta1, sta2, filterid, comp, mov_stack, ampli, seismic, show, outfile,
-         envelope, refilter)
+         envelope, refilter, startdate, enddate)
 
 
 @click.command()