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schainpy/model/graphics/jroplot_base.py +5 -3

             # Copyright (c) 2012-2020 Jicamarca Radio Observatory
             # All rights reserved.
             #
             # Distributed under the terms of the BSD 3-clause license.
             """Base class to create plot operations
             """
             import os
             import sys
             import zmq
             import time
             import numpy
             import datetime
             from collections import deque
             from functools import wraps
             from threading import Thread
             import matplotlib
             if 'BACKEND' in os.environ:
                 matplotlib.use(os.environ['BACKEND'])
             elif 'linux' in sys.platform:
                 matplotlib.use("TkAgg")
             elif 'darwin' in sys.platform:
                 matplotlib.use('MacOSX')
             else:
                 from schainpy.utils import log
                 log.warning('Using default Backend="Agg"', 'INFO')
                 matplotlib.use('Agg')
             import matplotlib.pyplot as plt
             from matplotlib.patches import Polygon
             from mpl_toolkits.axes_grid1 import make_axes_locatable
             from matplotlib.ticker import FuncFormatter, LinearLocator, MultipleLocator
             from schainpy.model.data.jrodata import PlotterData
             from schainpy.model.proc.jroproc_base import ProcessingUnit, Operation, MPDecorator
             from schainpy.utils import log
             jet_values = matplotlib.pyplot.get_cmap('jet', 100)(numpy.arange(100))[10:90]
             blu_values = matplotlib.pyplot.get_cmap(
                 'seismic_r', 20)(numpy.arange(20))[10:15]
             ncmap = matplotlib.colors.LinearSegmentedColormap.from_list(
                 'jro', numpy.vstack((blu_values, jet_values)))
             matplotlib.pyplot.register_cmap(cmap=ncmap)
             CMAPS = [plt.get_cmap(s) for s in ('jro', 'jet', 'viridis',
                                                'plasma', 'inferno', 'Greys', 'seismic', 'bwr', 'coolwarm')]
             EARTH_RADIUS = 6.3710e3
             def ll2xy(lat1, lon1, lat2, lon2):
                 p = 0.017453292519943295
                 a = 0.5 - numpy.cos((lat2 - lat1) * p)/2 + numpy.cos(lat1 * p) * \
                     numpy.cos(lat2 * p) * (1 - numpy.cos((lon2 - lon1) * p)) / 2
                 r = 12742 * numpy.arcsin(numpy.sqrt(a))
                 theta = numpy.arctan2(numpy.sin((lon2-lon1)*p)*numpy.cos(lat2*p), numpy.cos(lat1*p)
                                       * numpy.sin(lat2*p)-numpy.sin(lat1*p)*numpy.cos(lat2*p)*numpy.cos((lon2-lon1)*p))
                 theta = -theta + numpy.pi/2
                 return r*numpy.cos(theta), r*numpy.sin(theta)
             def km2deg(km):
                 '''
                 Convert distance in km to degrees
                 '''
                 return numpy.rad2deg(km/EARTH_RADIUS)
             def figpause(interval):
                 backend = plt.rcParams['backend']
                 if backend in matplotlib.rcsetup.interactive_bk:
                     figManager = matplotlib._pylab_helpers.Gcf.get_active()
                     if figManager is not None:
                         canvas = figManager.canvas
                         if canvas.figure.stale:
                             canvas.draw()
                         try:
                             canvas.start_event_loop(interval)
                         except:
                             pass
                         return
             def popup(message):
                 '''
                 '''
                 fig = plt.figure(figsize=(12, 8), facecolor='r')
                 text = '\n'.join([s.strip() for s in message.split(':')])
                 fig.text(0.01, 0.5, text, ha='left', va='center',
                          size='20', weight='heavy', color='w')
                 fig.show()
                 figpause(1000)
             class Throttle(object):
                 '''
                 Decorator that prevents a function from being called more than once every
                 time period.
                 To create a function that cannot be called more than once a minute, but
                 will sleep until it can be called:
                 @Throttle(minutes=1)
                 def foo():
                   pass
                 for i in range(10):
                   foo()
                   print "This function has run %s times." % i
                 '''
                 def __init__(self, seconds=0, minutes=0, hours=0):
                     self.throttle_period = datetime.timedelta(
                         seconds=seconds, minutes=minutes, hours=hours
                     )
                     self.time_of_last_call = datetime.datetime.min
                 def __call__(self, fn):
                     @wraps(fn)
                     def wrapper(*args, **kwargs):
                         coerce = kwargs.pop('coerce', None)
                         if coerce:
                             self.time_of_last_call = datetime.datetime.now()
                             return fn(*args, **kwargs)
                         else:
                             now = datetime.datetime.now()
                             time_since_last_call = now - self.time_of_last_call
                             time_left = self.throttle_period - time_since_last_call
                             if time_left > datetime.timedelta(seconds=0):
                                 return
                         self.time_of_last_call = datetime.datetime.now()
                         return fn(*args, **kwargs)
                     return wrapper
             def apply_throttle(value):
                 @Throttle(seconds=value)
                 def fnThrottled(fn):
                     fn()
                 return fnThrottled
             @MPDecorator
             class Plot(Operation):
                 """Base class for Schain plotting operations
                 This class should never be use directtly you must subclass a new operation,
                 children classes must be defined as follow:
                 ExamplePlot(Plot):
                     CODE = 'code'
                     colormap = 'jet'
                     plot_type = 'pcolor' # options are ('pcolor', 'pcolorbuffer', 'scatter', 'scatterbuffer')
                     def setup(self):
                         pass
                     def plot(self):
                         pass
                 """
                 CODE = 'Figure'
                 colormap = 'jet'
                 bgcolor = 'white'
                 buffering = True
                 __missing = 1E30
                 __attrs__ = ['show', 'save', 'ymin', 'ymax', 'zmin', 'zmax', 'title',
                              'showprofile']
                 def __init__(self):
                     Operation.__init__(self)
                     self.isConfig = False
                     self.isPlotConfig = False
                     self.save_time = 0
                     self.sender_time = 0
                     self.data = None
                     self.firsttime = True
                     self.sender_queue = deque(maxlen=10)
                     self.plots_adjust = {'left': 0.125, 'right': 0.9, 'bottom': 0.15, 'top': 0.9, 'wspace': 0.2, 'hspace': 0.2}
                 def __fmtTime(self, x, pos):
                     '''
                     '''
                     return '{}'.format(self.getDateTime(x).strftime('%H:%M'))
                 def __setup(self, **kwargs):
                     '''
                     Initialize variables
                     '''
                     self.figures = []
                     self.axes = []
                     self.cb_axes = []
                     self.localtime = kwargs.pop('localtime', True)
                     self.show = kwargs.get('show', True)
                     self.save = kwargs.get('save', False)
                     self.save_period = kwargs.get('save_period', 0)
                     self.colormap = kwargs.get('colormap', self.colormap)
                     self.colormap_coh = kwargs.get('colormap_coh', 'jet')
                     self.colormap_phase = kwargs.get('colormap_phase', 'RdBu_r')
                     self.colormaps = kwargs.get('colormaps', None)
                     self.bgcolor = kwargs.get('bgcolor', self.bgcolor)
                     self.showprofile = kwargs.get('showprofile', False)
                     self.title = kwargs.get('wintitle', self.CODE.upper())
                     self.cb_label = kwargs.get('cb_label', None)
                     self.cb_labels = kwargs.get('cb_labels', None)
                     self.labels = kwargs.get('labels', None)
                     self.xaxis = kwargs.get('xaxis', 'frequency')
                     self.zmin = kwargs.get('zmin', None)
                     self.zmax = kwargs.get('zmax', None)
                     self.zlimits = kwargs.get('zlimits', None)
                     self.xlimits = kwargs.get('xlimits', None)
                     self.xstep_given = kwargs.get('xstep_given', None)
                     self.ystep_given = kwargs.get('ystep_given', None)
                     self.autoxticks = kwargs.get('autoxticks', True)
                     self.xmin = kwargs.get('xmin', None)
                     self.xmax = kwargs.get('xmax', None)
                     self.xrange = kwargs.get('xrange', 12)
                     self.xscale = kwargs.get('xscale', None)
                     self.ymin = kwargs.get('ymin', None)
                     self.ymax = kwargs.get('ymax', None)
                     self.yscale = kwargs.get('yscale', None)
                     self.xlabel = kwargs.get('xlabel', None)
                     self.attr_time = kwargs.get('attr_time', 'utctime')
                     self.attr_data = kwargs.get('attr_data', 'data_param')
                     self.decimation = kwargs.get('decimation', None)
                     self.oneFigure = kwargs.get('oneFigure', True)
                     self.width = kwargs.get('width', None)
                     self.height = kwargs.get('height', None)
                     self.colorbar = kwargs.get('colorbar', True)
                     self.factors = kwargs.get('factors', [1, 1, 1, 1, 1, 1, 1, 1])
                     self.channels = kwargs.get('channels', None)
                     self.titles = kwargs.get('titles', [])
                     self.polar = False
                     self.type = kwargs.get('type', 'iq')
                     self.grid = kwargs.get('grid', False)
                     self.pause = kwargs.get('pause', False)
                     self.save_code = kwargs.get('save_code', self.CODE)
                     self.throttle = kwargs.get('throttle', 0)
                     self.exp_code = kwargs.get('exp_code', None)
                     self.server = kwargs.get('server', False)
                     self.sender_period = kwargs.get('sender_period', 60)
                     self.tag = kwargs.get('tag', '')
                     self.height_index = kwargs.get('height_index', None)
                     self.__throttle_plot = apply_throttle(self.throttle)
                     code = self.attr_data if self.attr_data else self.CODE
                     self.data = PlotterData(self.CODE, self.exp_code, self.localtime)
                     #self.EEJtype = kwargs.get('EEJtype', 2)
                     if self.server:
                         if not self.server.startswith('tcp://'):
                             self.server = 'tcp://{}'.format(self.server)
                         log.success(
                             'Sending to server: {}'.format(self.server),
                             self.name
                         )
                     if isinstance(self.attr_data, str):
                         self.attr_data = [self.attr_data]
                 def __setup_plot(self):
                     '''
                     Common setup for all figures, here figures and axes are created
                     '''
                     self.setup()
                     self.time_label = 'LT' if self.localtime else 'UTC'
                     if self.width is None:
                         self.width = 8
                     self.figures = []
                     self.axes = []
                     self.cb_axes = []
                     self.pf_axes = []
                     self.cmaps = []
                     size = '15%' if self.ncols == 1 else '30%'
                     pad = '4%' if self.ncols == 1 else '8%'
                     if self.oneFigure:
                         if self.height is None:
                             self.height = 1.4 * self.nrows + 1
                         fig = plt.figure(figsize=(self.width, self.height),
                                          edgecolor='k',
                                          facecolor='w')
                         self.figures.append(fig)
                         for n in range(self.nplots):
                             ax = fig.add_subplot(self.nrows, self.ncols,
                                                  n + 1, polar=self.polar)
                             ax.tick_params(labelsize=8)
                             ax.firsttime = True
                             ax.index = 0
                             ax.press = None
                             self.axes.append(ax)
                             if self.showprofile:
                                 cax = self.__add_axes(ax, size=size, pad=pad)
                                 cax.tick_params(labelsize=8)
                                 self.pf_axes.append(cax)
                     else:
                         if self.height is None:
                             self.height = 3
                         for n in range(self.nplots):
                             fig = plt.figure(figsize=(self.width, self.height),
                                              edgecolor='k',
                                              facecolor='w')
                             ax = fig.add_subplot(1, 1, 1, polar=self.polar)
                             ax.tick_params(labelsize=8)
                             ax.firsttime = True
                             ax.index = 0
                             ax.press = None
                             self.figures.append(fig)
                             self.axes.append(ax)
                             if self.showprofile:
                                 cax = self.__add_axes(ax, size=size, pad=pad)
                                 cax.tick_params(labelsize=8)
                                 self.pf_axes.append(cax)
                     for n in range(self.nrows):
                         if self.colormaps is not None:
                             cmap = plt.get_cmap(self.colormaps[n])
                         else:
                             cmap = plt.get_cmap(self.colormap)
                         cmap.set_bad(self.bgcolor, 1.)
                         self.cmaps.append(cmap)
                 def __add_axes(self, ax, size='30%', pad='8%'):
                     '''
                     Add new axes to the given figure
                     '''
                     divider = make_axes_locatable(ax)
                     nax = divider.new_horizontal(size=size, pad=pad)
                     ax.figure.add_axes(nax)
                     return nax
                 def fill_gaps(self, x_buffer, y_buffer, z_buffer):
                     '''
                     Create a masked array for missing data
                     '''
                     if x_buffer.shape[0] < 2:
                         return x_buffer, y_buffer, z_buffer
                     deltas = x_buffer[1:] - x_buffer[0:-1]
                     x_median = numpy.median(deltas)
                     index = numpy.where(deltas > 5 * x_median)
                     if len(index[0]) != 0:
                         z_buffer[::, index[0], ::] = self.__missing
                         z_buffer = numpy.ma.masked_inside(z_buffer,
 .99 * self.__missing,
 .01 * self.__missing)
                     return x_buffer, y_buffer, z_buffer
                 def decimate(self):
                     # dx = int(len(self.x)/self.__MAXNUMX) + 1
                     dy = int(len(self.y) / self.decimation) + 1
                     # x = self.x[::dx]
                     x = self.x
                     y = self.y[::dy]
                     z = self.z[::, ::, ::dy]
                     return x, y, z
                 def format(self):
                     '''
                     Set min and max values, labels, ticks and titles
                     '''
                     for n, ax in enumerate(self.axes):
                         if ax.firsttime:
                             if self.xaxis != 'time':
                                 xmin = self.xmin
                                 xmax = self.xmax
                             else:
                                 xmin = self.tmin
                                 xmax = self.tmin + self.xrange*60*60
                                 ax.xaxis.set_major_formatter(FuncFormatter(self.__fmtTime))
                                 ax.xaxis.set_major_locator(LinearLocator(9))
                             ymin = self.ymin if self.ymin is not None else numpy.nanmin(self.y[numpy.isfinite(self.y)])
                             ymax = self.ymax if self.ymax is not None else numpy.nanmax(self.y[numpy.isfinite(self.y)])
                             ax.set_facecolor(self.bgcolor)
                             if self.xscale:
                                 ax.xaxis.set_major_formatter(FuncFormatter(
                                     lambda x, pos: '{0:g}'.format(x*self.xscale)))
                             if self.yscale:
                                 ax.yaxis.set_major_formatter(FuncFormatter(
                                     lambda x, pos: '{0:g}'.format(x*self.yscale)))
                             if self.xlabel is not None:
                                 ax.set_xlabel(self.xlabel)
                             if self.ylabel is not None:
                                 ax.set_ylabel(self.ylabel)
                             if self.showprofile:
                                 if self.zlimits is not None:
                                     self.zmin, self.zmax = self.zlimits[n]
                                 self.pf_axes[n].set_ylim(ymin, ymax)
                                 self.pf_axes[n].set_xlim(self.zmin, self.zmax)
                                 self.pf_axes[n].set_xlabel('dB')
                                 self.pf_axes[n].grid(b=True, axis='x')
                                 [tick.set_visible(False)
                                  for tick in self.pf_axes[n].get_yticklabels()]
                             if self.colorbar:
                                 ax.cbar = plt.colorbar(
                                     ax.plt, ax=ax, fraction=0.05, pad=0.02, aspect=10)
                                 ax.cbar.ax.tick_params(labelsize=8)
                                 ax.cbar.ax.press = None
                                 if self.cb_label:
                                     ax.cbar.set_label(self.cb_label, size=8)
                                 elif self.cb_labels:
                                     ax.cbar.set_label(self.cb_labels[n], size=8)
                             else:
                                 ax.cbar = None
                             ax.set_xlim(xmin, xmax)
                             ax.set_ylim(ymin, ymax)
                             ax.firsttime = False
                             if self.grid:
                                 ax.grid(True)
                         if not self.polar:
                             ax.set_title('{} {} {}'.format(
                                 self.titles[n],
                                 self.getDateTime(self.data.max_time).strftime(
                                     '%Y-%m-%d %H:%M:%S'),
                                 self.time_label),
                                 size=8)
                         else:
                             ax.set_title('{}'.format(self.titles[n]), size=8)
                             ax.set_ylim(0, 90)
                             ax.set_yticks(numpy.arange(0, 90, 20))
                             ax.yaxis.labelpad = 40
                     if self.firsttime:
                         for n, fig in enumerate(self.figures):
                             fig.subplots_adjust(**self.plots_adjust)
                         self.firsttime = False
                 def clear_figures(self):
                     '''
                     Reset axes for redraw plots
                     '''
                     for ax in self.axes+self.pf_axes+self.cb_axes:
                         ax.clear()
                         ax.firsttime = True
                         if hasattr(ax, 'cbar') and ax.cbar:
                             ax.cbar.remove()
                 def __plot(self):
                     '''
                     Main function to plot, format and save figures
                     '''
                     self.plot()
                     self.format()
                     for n, fig in enumerate(self.figures):
                         if self.nrows == 0 or self.nplots == 0:
                             log.warning('No data', self.name)
                             fig.text(0.5, 0.5, 'No Data', fontsize='large', ha='center')
                             fig.canvas.manager.set_window_title(self.CODE)
                             continue
                         fig.canvas.manager.set_window_title('{} - {}'.format(self.title,
                                                                              self.getDateTime(self.data.max_time).strftime('%Y/%m/%d')))
                         fig.canvas.draw()
                         if self.show:
                             fig.show()
                             figpause(0.01)
                         if self.save:
                             self.save_figure(n)
                     if self.server:
                         self.send_to_server()
                 def __update(self, dataOut, timestamp):
                     '''
                     '''
                     metadata = {
                         'yrange': dataOut.heightList,
                         'interval': dataOut.timeInterval,
                         'channels': dataOut.channelList
                     }
                     data, meta = self.update(dataOut)
                     metadata.update(meta)
                     self.data.update(data, timestamp, metadata)
                 def save_figure(self, n):
                     '''
                     '''
                     if (self.data.max_time - self.save_time) <= self.save_period:
                         return
                     self.save_time = self.data.max_time
                     fig = self.figures[n]
                     if self.throttle == 0:
                         figname = os.path.join(
                             self.save,
                             self.save_code,
                             '{}_{}.png'.format(
                                 self.save_code,
                                 self.getDateTime(self.data.max_time).strftime(
                                     '%Y%m%d_%H%M%S'
                                     ),
                                 )
                             )
                         log.log('Saving figure: {}'.format(figname), self.name)
                         if not os.path.isdir(os.path.dirname(figname)):
                             os.makedirs(os.path.dirname(figname))
                         fig.savefig(figname)
                     figname = os.path.join(
                         self.save,
                         #self.save_code,
                         '{}_{}.png'.format(
                             self.save_code,
                             self.getDateTime(self.data.min_time).strftime(
                                 '%Y%m%d'
                                 ),
                             )
                         )
                     log.log('Saving figure: {}'.format(figname), self.name)
                     if not os.path.isdir(os.path.dirname(figname)):
                         os.makedirs(os.path.dirname(figname))
                     fig.savefig(figname)
                 def send_to_server(self):
                     '''
                     '''
                     if self.exp_code == None:
                         log.warning('Missing `exp_code` skipping sending to server...')
                     last_time = self.data.max_time
                     interval = last_time - self.sender_time
                     if interval < self.sender_period:
                         return
                     self.sender_time = last_time
-                    attrs = ['titles', 'zmin', 'zmax', 'tag', 'ymin', 'ymax']
+                    attrs = ['titles', 'zmin', 'zmax', 'tag', 'ymin', 'ymax', 'zlimits']
                     for attr in attrs:
                         value = getattr(self, attr)
                         if value:
                             if isinstance(value, (numpy.float32, numpy.float64)):
                                 value = round(float(value), 2)
                             self.data.meta[attr] = value
                     if self.colormap == 'jet':
                         self.data.meta['colormap'] = 'Jet'
                     elif 'RdBu' in self.colormap:
                         self.data.meta['colormap'] = 'RdBu'
                     else:
                         self.data.meta['colormap'] = 'Viridis'
                     self.data.meta['interval'] = int(interval)
                     #print(last_time)
                     #print(time.time())
                     #exit(1)
                     self.sender_queue.append(last_time)
                     while True:
                         try:
                             tm = self.sender_queue.popleft()
                         except IndexError:
                             break
                         msg = self.data.jsonify(tm, self.save_code, self.plot_type)
                         self.socket.send_string(msg)
                         socks = dict(self.poll.poll(2000))
                         if socks.get(self.socket) == zmq.POLLIN:
                             reply = self.socket.recv_string()
                             if reply == 'ok':
                                 log.log("Response from server ok", self.name)
                                 time.sleep(0.1)
                                 continue
                             else:
                                 log.warning(
                                     "Malformed reply from server: {}".format(reply), self.name)
                         else:
                             log.warning(
                                 "No response from server, retrying...", self.name)
                         self.sender_queue.appendleft(tm)
                         self.socket.setsockopt(zmq.LINGER, 0)
                         self.socket.close()
                         self.poll.unregister(self.socket)
                         self.socket = self.context.socket(zmq.REQ)
                         self.socket.connect(self.server)
                         self.poll.register(self.socket, zmq.POLLIN)
                         break
                 def setup(self):
                     '''
                     This method should be implemented in the child class, the following
                     attributes should be set:
                     self.nrows: number of rows
                     self.ncols: number of cols
                     self.nplots: number of plots (channels or pairs)
                     self.ylabel: label for Y axes
                     self.titles: list of axes title
                     '''
                     raise NotImplementedError
                 def plot(self):
                     '''
                     Must be defined in the child class, the actual plotting method
                     '''
                     raise NotImplementedError
                 def update(self, dataOut):
                     '''
                     Must be defined in the child class, update self.data with new data
                     '''
                     data = {
                         self.CODE: getattr(dataOut, 'data_{}'.format(self.CODE))
                     }
                     meta = {}
                     return data, meta
                 def run(self, dataOut, **kwargs):
                     '''
                     Main plotting routine
                     '''
                     if self.isConfig is False:
                         self.__setup(**kwargs)
                         if self.localtime:
                             self.getDateTime = datetime.datetime.fromtimestamp
                         else:
                             self.getDateTime = datetime.datetime.utcfromtimestamp
                         self.data.setup()
                         self.isConfig = True
                         if self.server:
                             self.context = zmq.Context()
                             self.socket = self.context.socket(zmq.REQ)
                             self.socket.connect(self.server)
                             self.poll = zmq.Poller()
                             self.poll.register(self.socket, zmq.POLLIN)
                     tm = getattr(dataOut, self.attr_time)
                     if self.data and 'time' in self.xaxis and (tm - self.tmin) >= self.xrange*60*60:
                         self.save_time = tm
                         self.__plot()
-                        self.tmin += self.xrange*60*60
+                        #self.tmin += self.xrange*60*60 #Modified by R. Flores
+                        self.tmin += 24*60*60 #Modified by R. Flores
                         self.data.setup()
                         self.clear_figures()
                     self.__update(dataOut, tm)
                     if self.isPlotConfig is False:
                         self.__setup_plot()
                         self.isPlotConfig = True
                         if self.xaxis == 'time':
                             dt = self.getDateTime(tm)
                             if self.xmin is None:
                                 self.tmin = tm
                                 self.xmin = dt.hour
                             minutes = (self.xmin-int(self.xmin)) * 60
                             seconds = (minutes - int(minutes)) * 60
                             self.tmin = (dt.replace(hour=int(self.xmin), minute=int(minutes), second=int(seconds)) -
                                     datetime.datetime(1970, 1, 1)).total_seconds()
                             if self.localtime:
                                 self.tmin += time.timezone
                             if self.xmin is not None and self.xmax is not None:
                                 self.xrange = self.xmax - self.xmin
                     if self.throttle == 0:
                         self.__plot()
                     else:
                         self.__throttle_plot(self.__plot)#, coerce=coerce)
                 def close(self):
                     if self.data and not self.data.flagNoData:
                         self.save_time = 0
                         self.__plot()
                     if self.data and not self.data.flagNoData and self.pause:
                         figpause(10)

schainpy/model/graphics/jroplot_spectra.py +7 -1

             # Copyright (c) 2012-2021 Jicamarca Radio Observatory
             # All rights reserved.
             #
             # Distributed under the terms of the BSD 3-clause license.
             """Classes to plot Spectra data
             """
             import os
             import numpy
-            import collections.abc
+            #import collections.abc
             from schainpy.model.graphics.jroplot_base import Plot, plt, log
             class SpectraPlot(Plot):
                 '''
                 Plot for Spectra data
                 '''
                 CODE = 'spc'
                 colormap = 'jet'
                 plot_type = 'pcolor'
                 buffering = False
                 def setup(self):
                     self.nplots = len(self.data.channels)
                     self.ncols = int(numpy.sqrt(self.nplots) + 0.9)
                     self.nrows = int((1.0 * self.nplots / self.ncols) + 0.9)
                     self.height = 2.6 * self.nrows
                     self.cb_label = 'dB'
                     if self.showprofile:
                         self.width = 4 * self.ncols
                     else:
                         self.width = 3.5 * self.ncols
                     self.plots_adjust.update({'wspace': 0.8, 'hspace':0.2, 'left': 0.2, 'right': 0.9, 'bottom': 0.18})
                     self.ylabel = 'Range [km]'
                 def update(self, dataOut):
                     data = {}
                     meta = {}
                     spc = 10*numpy.log10(dataOut.data_spc/dataOut.normFactor)
                     #print("Spc: ",spc[0])
                     #exit(1)
                     data['spc'] = spc
                     data['rti'] = dataOut.getPower()
                     #print(data['rti'][0])
                     #exit(1)
                     #print("NormFactor: ",dataOut.normFactor)
                     #data['noise'] = 10*numpy.log10(dataOut.getNoise()/dataOut.normFactor)
                     if hasattr(dataOut, 'LagPlot'): #Double Pulse
                         max_hei_id = dataOut.nHeights - 2*dataOut.LagPlot
                         #data['noise'] = 10*numpy.log10(dataOut.getNoise(ymin_index=46,ymax_index=max_hei_id)/dataOut.normFactor)
                         #data['noise'] = 10*numpy.log10(dataOut.getNoise(ymin_index=40,ymax_index=max_hei_id)/dataOut.normFactor)
                         data['noise'] = 10*numpy.log10(dataOut.getNoise(ymin_index=53,ymax_index=max_hei_id)/dataOut.normFactor)
                         data['noise'][0] = 10*numpy.log10(dataOut.getNoise(ymin_index=53)[0]/dataOut.normFactor)
                         #data['noise'][1] = 22.035507
                     else:
                         data['noise'] = 10*numpy.log10(dataOut.getNoise()/dataOut.normFactor)
                     #data['noise'] = 10*numpy.log10(dataOut.getNoise(ymin_index=26,ymax_index=44)/dataOut.normFactor)
                     meta['xrange'] = (dataOut.getFreqRange(1)/1000., dataOut.getAcfRange(1), dataOut.getVelRange(1))
                     if self.CODE == 'spc_moments':
                         data['moments'] = dataOut.moments
                     if self.CODE == 'gaussian_fit':
                         data['gaussfit'] = dataOut.DGauFitParams
                     return data, meta
                 def plot(self):
                     if self.xaxis == "frequency":
                         x = self.data.xrange[0]
                         self.xlabel = "Frequency (kHz)"
                     elif self.xaxis == "time":
                         x = self.data.xrange[1]
                         self.xlabel = "Time (ms)"
                     else:
                         x = self.data.xrange[2]
                         self.xlabel = "Velocity (m/s)"
                     if (self.CODE == 'spc_moments') | (self.CODE == 'gaussian_fit'):
                         x = self.data.xrange[2]
                         self.xlabel = "Velocity (m/s)"
                     self.titles = []
                     y = self.data.yrange
                     self.y = y
                     data = self.data[-1]
                     z = data['spc']
                     self.CODE2 = 'spc_oblique'
                     for n, ax in enumerate(self.axes):
                         noise = data['noise'][n]
                         if self.CODE == 'spc_moments':
                             mean = data['moments'][n, 1]
                         if self.CODE == 'gaussian_fit':
                             gau0 = data['gaussfit'][n][2,:,0]
                             gau1 = data['gaussfit'][n][2,:,1]
                         if ax.firsttime:
                             self.xmax = self.xmax if self.xmax else numpy.nanmax(x)
                             self.xmin = self.xmin if self.xmin else numpy.nanmin(x)#-self.xmax
                             #self.zmin = self.zmin if self.zmin else numpy.nanmin(z)
                             #self.zmax = self.zmax if self.zmax else numpy.nanmax(z)
                             if self.zlimits is not None:
                                 self.zmin, self.zmax = self.zlimits[n]
                             ax.plt = ax.pcolormesh(x, y, z[n].T,
                                                    vmin=self.zmin,
                                                    vmax=self.zmax,
                                                    cmap=plt.get_cmap(self.colormap),
                                                    )
                             if self.showprofile:
                                 ax.plt_profile = self.pf_axes[n].plot(
                                     data['rti'][n], y)[0]
                                 ax.plt_noise = self.pf_axes[n].plot(numpy.repeat(noise, len(y)), y,
                                                                     color="k", linestyle="dashed", lw=1)[0]
                             if self.CODE == 'spc_moments':
                                 ax.plt_mean = ax.plot(mean, y, color='k', lw=1)[0]
                             if self.CODE == 'gaussian_fit':
                                 ax.plt_gau0 = ax.plot(gau0, y, color='r', lw=1)[0]
                                 ax.plt_gau1 = ax.plot(gau1, y, color='y', lw=1)[0]
                         else:
                             if self.zlimits is not None:
                                 self.zmin, self.zmax = self.zlimits[n]
                             ax.plt.set_array(z[n].T.ravel())
                             if self.showprofile:
                                 ax.plt_profile.set_data(data['rti'][n], y)
                                 ax.plt_noise.set_data(numpy.repeat(noise, len(y)), y)
                             if self.CODE == 'spc_moments':
                                 ax.plt_mean.set_data(mean, y)
                             if self.CODE == 'gaussian_fit':
                                 ax.plt_gau0.set_data(gau0, y)
                                 ax.plt_gau1.set_data(gau1, y)
                         self.titles.append('CH {}: {:3.2f}dB'.format(n, noise))
             class SpectraObliquePlot(Plot):
                 '''
                 Plot for Spectra data
                 '''
                 CODE = 'spc_oblique'
                 colormap = 'jet'
                 plot_type = 'pcolor'
                 def setup(self):
                     self.xaxis = "oblique"
                     self.nplots = len(self.data.channels)
                     self.ncols = int(numpy.sqrt(self.nplots) + 0.9)
                     self.nrows = int((1.0 * self.nplots / self.ncols) + 0.9)
                     self.height = 2.6 * self.nrows
                     self.cb_label = 'dB'
                     if self.showprofile:
                         self.width = 4 * self.ncols
                     else:
                         self.width = 3.5 * self.ncols
                     self.plots_adjust.update({'wspace': 0.8, 'hspace':0.2, 'left': 0.2, 'right': 0.9, 'bottom': 0.18})
                     self.ylabel = 'Range [km]'
                 def update(self, dataOut):
                     data = {}
                     meta = {}
                     spc = 10*numpy.log10(dataOut.data_spc/dataOut.normFactor)
                     data['spc'] = spc
                     data['rti'] = dataOut.getPower()
                     data['noise'] = 10*numpy.log10(dataOut.getNoise()/dataOut.normFactor)
                     meta['xrange'] = (dataOut.getFreqRange(1)/1000., dataOut.getAcfRange(1), dataOut.getVelRange(1))
                     '''
                     data['shift1'] = dataOut.Oblique_params[0,-2,:]
                     data['shift2'] = dataOut.Oblique_params[0,-1,:]
                     data['shift1_error'] = dataOut.Oblique_param_errors[0,-2,:]
                     data['shift2_error'] = dataOut.Oblique_param_errors[0,-1,:]
                     '''
                     '''
                     data['shift1'] = dataOut.Oblique_params[0,1,:]
                     data['shift2'] = dataOut.Oblique_params[0,4,:]
                     data['shift1_error'] = dataOut.Oblique_param_errors[0,1,:]
                     data['shift2_error'] = dataOut.Oblique_param_errors[0,4,:]
                     '''
                     data['shift1'] = dataOut.Dop_EEJ_T1[0]
                     data['shift2'] = dataOut.Dop_EEJ_T2[0]
+                    data['max_val_2'] = dataOut.Oblique_params[0,-1,:]
                     data['shift1_error'] = dataOut.Err_Dop_EEJ_T1[0]
                     data['shift2_error'] = dataOut.Err_Dop_EEJ_T2[0]
                     return data, meta
                 def plot(self):
                     if self.xaxis == "frequency":
                         x = self.data.xrange[0]
                         self.xlabel = "Frequency (kHz)"
                     elif self.xaxis == "time":
                         x = self.data.xrange[1]
                         self.xlabel = "Time (ms)"
                     else:
                         x = self.data.xrange[2]
                         self.xlabel = "Velocity (m/s)"
                     self.titles = []
                     y = self.data.yrange
                     self.y = y
                     data = self.data[-1]
                     z = data['spc']
                     for n, ax in enumerate(self.axes):
                         noise = self.data['noise'][n][-1]
                         shift1 = data['shift1']
                         #print(shift1)
                         shift2 = data['shift2']
+                        max_val_2 = data['max_val_2']
                         err1 = data['shift1_error']
                         err2 = data['shift2_error']
                         if ax.firsttime:
                             self.xmax = self.xmax if self.xmax else numpy.nanmax(x)
                             self.xmin = self.xmin if self.xmin else -self.xmax
                             self.zmin = self.zmin if self.zmin else numpy.nanmin(z)
                             self.zmax = self.zmax if self.zmax else numpy.nanmax(z)
                             ax.plt = ax.pcolormesh(x, y, z[n].T,
                                                    vmin=self.zmin,
                                                    vmax=self.zmax,
                                                    cmap=plt.get_cmap(self.colormap)
                                                    )
                             if self.showprofile:
                                 ax.plt_profile = self.pf_axes[n].plot(
                                     self.data['rti'][n][-1], y)[0]
                                 ax.plt_noise = self.pf_axes[n].plot(numpy.repeat(noise, len(y)), y,
                                                                     color="k", linestyle="dashed", lw=1)[0]
                             self.ploterr1 = ax.errorbar(shift1, y, xerr=err1, fmt='k^', elinewidth=2.2, marker='o', linestyle='None',markersize=2.5,capsize=0.3,markeredgewidth=0.2)
                             self.ploterr2 = ax.errorbar(shift2, y, xerr=err2, fmt='m^',elinewidth=2.2,marker='o',linestyle='None',markersize=2.5,capsize=0.3,markeredgewidth=0.2)
+                            self.ploterr3 = ax.errorbar(max_val_2, y, xerr=0, fmt='g^',elinewidth=2.2,marker='o',linestyle='None',markersize=2.5,capsize=0.3,markeredgewidth=0.2)
                             #print("plotter1: ", self.ploterr1,shift1)
                         else:
                             #print("else plotter1: ", self.ploterr1,shift1)
                             self.ploterr1.remove()
                             self.ploterr2.remove()
+                            self.ploterr3.remove()
                             ax.plt.set_array(z[n].T.ravel())
                             if self.showprofile:
                                 ax.plt_profile.set_data(self.data['rti'][n][-1], y)
                                 ax.plt_noise.set_data(numpy.repeat(noise, len(y)), y)
                             self.ploterr1 = ax.errorbar(shift1, y, xerr=err1, fmt='k^', elinewidth=2.2, marker='o', linestyle='None',markersize=2.5,capsize=0.3,markeredgewidth=0.2)
                             self.ploterr2 = ax.errorbar(shift2, y, xerr=err2, fmt='m^',elinewidth=2.2,marker='o',linestyle='None',markersize=2.5,capsize=0.3,markeredgewidth=0.2)
+                            self.ploterr3 = ax.errorbar(max_val_2, y, xerr=0, fmt='g^',elinewidth=2.2,marker='o',linestyle='None',markersize=2.5,capsize=0.3,markeredgewidth=0.2)
                         self.titles.append('CH {}: {:3.2f}dB'.format(n, noise))
             class CrossSpectraPlot(Plot):
                 CODE = 'cspc'
                 colormap = 'jet'
                 plot_type = 'pcolor'
                 zmin_coh = None
                 zmax_coh = None
                 zmin_phase = None
                 zmax_phase = None
                 def setup(self):
                     self.ncols = 4
                     self.nplots = len(self.data.pairs) * 2
                     self.nrows = int((1.0 * self.nplots / self.ncols) + 0.9)
                     self.width = 3.1 * self.ncols
                     self.height = 5 * self.nrows
                     self.ylabel = 'Range [km]'
                     self.showprofile = False
                     self.plots_adjust.update({'left': 0.08, 'right': 0.92, 'wspace': 0.5, 'hspace':0.4, 'top':0.95, 'bottom': 0.08})
                 def update(self, dataOut):
                     data = {}
                     meta = {}
                     spc = dataOut.data_spc
                     cspc = dataOut.data_cspc
                     meta['xrange'] = (dataOut.getFreqRange(1)/1000., dataOut.getAcfRange(1), dataOut.getVelRange(1))
                     meta['pairs'] = dataOut.pairsList
                     tmp = []
                     for n, pair in enumerate(meta['pairs']):
                         out = cspc[n] / numpy.sqrt(spc[pair[0]] * spc[pair[1]])
                         coh = numpy.abs(out)
                         phase = numpy.arctan2(out.imag, out.real) * 180 / numpy.pi
                         tmp.append(coh)
                         tmp.append(phase)
                     data['cspc'] = numpy.array(tmp)
                     return data, meta
                 def plot(self):
                     if self.xaxis == "frequency":
                         x = self.data.xrange[0]
                         self.xlabel = "Frequency (kHz)"
                     elif self.xaxis == "time":
                         x = self.data.xrange[1]
                         self.xlabel = "Time (ms)"
                     else:
                         x = self.data.xrange[2]
                         self.xlabel = "Velocity (m/s)"
                     self.titles = []
                     y = self.data.yrange
                     self.y = y
                     data = self.data[-1]
                     cspc = data['cspc']
                     for n in range(len(self.data.pairs)):
                         pair = self.data.pairs[n]
                         coh = cspc[n*2]
                         phase = cspc[n*2+1]
                         ax = self.axes[2 * n]
                         if ax.firsttime:
                             ax.plt = ax.pcolormesh(x, y, coh.T,
                                                    vmin=0,
                                                    vmax=1,
                                                    cmap=plt.get_cmap(self.colormap_coh)
                                                    )
                         else:
                             ax.plt.set_array(coh.T.ravel())
                         self.titles.append(
                             'Coherence Ch{} * Ch{}'.format(pair[0], pair[1]))
                         ax = self.axes[2 * n + 1]
                         if ax.firsttime:
                             ax.plt = ax.pcolormesh(x, y, phase.T,
                                                    vmin=-180,
                                                    vmax=180,
                                                    cmap=plt.get_cmap(self.colormap_phase)
                                                    )
                         else:
                             ax.plt.set_array(phase.T.ravel())
                         self.titles.append('Phase CH{} * CH{}'.format(pair[0], pair[1]))
             class CrossSpectra4Plot(Plot):
                 CODE = 'cspc'
                 colormap = 'jet'
                 plot_type = 'pcolor'
                 zmin_coh = None
                 zmax_coh = None
                 zmin_phase = None
                 zmax_phase = None
                 def setup(self):
                     self.ncols = 4
                     self.nrows = len(self.data.pairs)
                     self.nplots = self.nrows * 4
                     self.width = 3.1 * self.ncols
                     self.height = 5 * self.nrows
                     self.ylabel = 'Range [km]'
                     self.showprofile = False
                     self.plots_adjust.update({'left': 0.08, 'right': 0.92, 'wspace': 0.5, 'hspace':0.4, 'top':0.95, 'bottom': 0.08})
                 def plot(self):
                     if self.xaxis == "frequency":
                         x = self.data.xrange[0]
                         self.xlabel = "Frequency (kHz)"
                     elif self.xaxis == "time":
                         x = self.data.xrange[1]
                         self.xlabel = "Time (ms)"
                     else:
                         x = self.data.xrange[2]
                         self.xlabel = "Velocity (m/s)"
                     self.titles = []
                     y = self.data.heights
                     self.y = y
                     nspc = self.data['spc']
                     #print(numpy.shape(self.data['spc']))
                     spc = self.data['cspc'][0]
                     #print(numpy.shape(nspc))
                     #exit()
                     #nspc[1,:,:] = numpy.flip(nspc[1,:,:],axis=0)
                     #print(numpy.shape(spc))
                     #exit()
                     cspc = self.data['cspc'][1]
                     #xflip=numpy.flip(x)
                     #print(numpy.shape(cspc))
                     #exit()
                     for n in range(self.nrows):
                         noise = self.data['noise'][:,-1]
                         pair = self.data.pairs[n]
                         #print(pair)
                         #exit()
                         ax = self.axes[4 * n]
                         if ax.firsttime:
                             self.xmax = self.xmax if self.xmax else numpy.nanmax(x)
                             self.xmin = self.xmin if self.xmin else -self.xmax
                             self.zmin = self.zmin if self.zmin else numpy.nanmin(nspc)
                             self.zmax = self.zmax if self.zmax else numpy.nanmax(nspc)
                             ax.plt = ax.pcolormesh(x , y , nspc[pair[0]].T,
                                                    vmin=self.zmin,
                                                    vmax=self.zmax,
                                                    cmap=plt.get_cmap(self.colormap)
                                                    )
                         else:
                             #print(numpy.shape(nspc[pair[0]].T))
                             #exit()
                             ax.plt.set_array(nspc[pair[0]].T.ravel())
                         self.titles.append('CH {}: {:3.2f}dB'.format(pair[0], noise[pair[0]]))
                         ax = self.axes[4 * n + 1]
                         if ax.firsttime:
                             ax.plt = ax.pcolormesh(x , y, numpy.flip(nspc[pair[1]],axis=0).T,
                                                    vmin=self.zmin,
                                                    vmax=self.zmax,
                                                    cmap=plt.get_cmap(self.colormap)
                                                    )
                         else:
                             ax.plt.set_array(numpy.flip(nspc[pair[1]],axis=0).T.ravel())
                         self.titles.append('CH {}: {:3.2f}dB'.format(pair[1], noise[pair[1]]))
                         out = cspc[n] / numpy.sqrt(spc[pair[0]] * spc[pair[1]])
                         coh = numpy.abs(out)
                         phase = numpy.arctan2(out.imag, out.real) * 180 / numpy.pi
                         ax = self.axes[4 * n + 2]
                         if ax.firsttime:
                             ax.plt = ax.pcolormesh(x, y, numpy.flip(coh,axis=0).T,
                                                    vmin=0,
                                                    vmax=1,
                                                    cmap=plt.get_cmap(self.colormap_coh)
                                                    )
                         else:
                             ax.plt.set_array(numpy.flip(coh,axis=0).T.ravel())
                         self.titles.append(
                             'Coherence Ch{} * Ch{}'.format(pair[0], pair[1]))
                         ax = self.axes[4 * n + 3]
                         if ax.firsttime:
                             ax.plt = ax.pcolormesh(x, y, numpy.flip(phase,axis=0).T,
                                                    vmin=-180,
                                                    vmax=180,
                                                    cmap=plt.get_cmap(self.colormap_phase)
                                                    )
                         else:
                             ax.plt.set_array(numpy.flip(phase,axis=0).T.ravel())
                         self.titles.append('Phase CH{} * CH{}'.format(pair[0], pair[1]))
             class CrossSpectra2Plot(Plot):
                 CODE = 'cspc'
                 colormap = 'jet'
                 plot_type = 'pcolor'
                 zmin_coh = None
                 zmax_coh = None
                 zmin_phase = None
                 zmax_phase = None
                 def setup(self):
                     self.ncols = 1
                     self.nrows = len(self.data.pairs)
                     self.nplots = self.nrows * 1
                     self.width = 3.1 * self.ncols
                     self.height = 5 * self.nrows
                     self.ylabel = 'Range [km]'
                     self.showprofile = False
                     self.plots_adjust.update({'left': 0.22, 'right': .90, 'wspace': 0.5, 'hspace':0.4, 'top':0.95, 'bottom': 0.08})
                 def plot(self):
                     if self.xaxis == "frequency":
                         x = self.data.xrange[0]
                         self.xlabel = "Frequency (kHz)"
                     elif self.xaxis == "time":
                         x = self.data.xrange[1]
                         self.xlabel = "Time (ms)"
                     else:
                         x = self.data.xrange[2]
                         self.xlabel = "Velocity (m/s)"
                     self.titles = []
                     y = self.data.heights
                     self.y = y
                     #nspc = self.data['spc']
                     #print(numpy.shape(self.data['spc']))
                     #spc = self.data['cspc'][0]
                     #print(numpy.shape(spc))
                     #exit()
                     cspc = self.data['cspc'][1]
                     #print(numpy.shape(cspc))
                     #exit()
                     for n in range(self.nrows):
                         noise = self.data['noise'][:,-1]
                         pair = self.data.pairs[n]
                         #print(pair)            #exit()
                         out = cspc[n]# / numpy.sqrt(spc[pair[0]] * spc[pair[1]])
                         #print(out[:,53])
                         #exit()
                         cross = numpy.abs(out)
                         z = cross/self.data.nFactor
                         #print("here")
                         #print(dataOut.data_spc[0,0,0])
                         #exit()
                         cross = 10*numpy.log10(z)
                         #print(numpy.shape(cross))
                         #print(cross[0,:])
                         #print(self.data.nFactor)
                         #exit()
                         #phase = numpy.arctan2(out.imag, out.real) * 180 / numpy.pi
                         ax = self.axes[1 * n]
                         if ax.firsttime:
                             self.xmax = self.xmax if self.xmax else numpy.nanmax(x)
                             self.xmin = self.xmin if self.xmin else -self.xmax
                             self.zmin = self.zmin if self.zmin else numpy.nanmin(cross)
                             self.zmax = self.zmax if self.zmax else numpy.nanmax(cross)
                             ax.plt = ax.pcolormesh(x, y, cross.T,
                                                    vmin=self.zmin,
                                                    vmax=self.zmax,
                                                    cmap=plt.get_cmap(self.colormap)
                                                    )
                         else:
                             ax.plt.set_array(cross.T.ravel())
                         self.titles.append(
                             'Cross Spectra Power Ch{} * Ch{}'.format(pair[0], pair[1]))
             class CrossSpectra3Plot(Plot):
                 CODE = 'cspc'
                 colormap = 'jet'
                 plot_type = 'pcolor'
                 zmin_coh = None
                 zmax_coh = None
                 zmin_phase = None
                 zmax_phase = None
                 def setup(self):
                     self.ncols = 3
                     self.nrows = len(self.data.pairs)
                     self.nplots = self.nrows * 3
                     self.width = 3.1 * self.ncols
                     self.height = 5 * self.nrows
                     self.ylabel = 'Range [km]'
                     self.showprofile = False
                     self.plots_adjust.update({'left': 0.22, 'right': .90, 'wspace': 0.5, 'hspace':0.4, 'top':0.95, 'bottom': 0.08})
                 def plot(self):
                     if self.xaxis == "frequency":
                         x = self.data.xrange[0]
                         self.xlabel = "Frequency (kHz)"
                     elif self.xaxis == "time":
                         x = self.data.xrange[1]
                         self.xlabel = "Time (ms)"
                     else:
                         x = self.data.xrange[2]
                         self.xlabel = "Velocity (m/s)"
                     self.titles = []
                     y = self.data.heights
                     self.y = y
                     #nspc = self.data['spc']
                     #print(numpy.shape(self.data['spc']))
                     #spc = self.data['cspc'][0]
                     #print(numpy.shape(spc))
                     #exit()
                     cspc = self.data['cspc'][1]
                     #print(numpy.shape(cspc))
                     #exit()
                     for n in range(self.nrows):
                         noise = self.data['noise'][:,-1]
                         pair = self.data.pairs[n]
                         #print(pair)            #exit()
                         out = cspc[n]# / numpy.sqrt(spc[pair[0]] * spc[pair[1]])
                         #print(out[:,53])
                         #exit()
                         cross = numpy.abs(out)
                         z = cross/self.data.nFactor
                         cross = 10*numpy.log10(z)
                         out_r= out.real/self.data.nFactor
                         #out_r = 10*numpy.log10(out_r)
                         out_i= out.imag/self.data.nFactor
                         #out_i = 10*numpy.log10(out_i)
                         #print(numpy.shape(cross))
                         #print(cross[0,:])
                         #print(self.data.nFactor)
                         #exit()
                         #phase = numpy.arctan2(out.imag, out.real) * 180 / numpy.pi
                         ax = self.axes[3 * n]
                         if ax.firsttime:
                             self.xmax = self.xmax if self.xmax else numpy.nanmax(x)
                             self.xmin = self.xmin if self.xmin else -self.xmax
                             self.zmin = self.zmin if self.zmin else numpy.nanmin(cross)
                             self.zmax = self.zmax if self.zmax else numpy.nanmax(cross)
                             ax.plt = ax.pcolormesh(x, y, cross.T,
                                                    vmin=self.zmin,
                                                    vmax=self.zmax,
                                                    cmap=plt.get_cmap(self.colormap)
                                                    )
                         else:
                             ax.plt.set_array(cross.T.ravel())
                         self.titles.append(
                             'Cross Spectra Power Ch{} * Ch{}'.format(pair[0], pair[1]))
                         ax = self.axes[3 * n + 1]
                         if ax.firsttime:
                             self.xmax = self.xmax if self.xmax else numpy.nanmax(x)
                             self.xmin = self.xmin if self.xmin else -self.xmax
                             self.zmin = self.zmin if self.zmin else numpy.nanmin(cross)
                             self.zmax = self.zmax if self.zmax else numpy.nanmax(cross)
                             ax.plt = ax.pcolormesh(x, y, out_r.T,
                                                    vmin=-1.e6,
                                                    vmax=0,
                                                    cmap=plt.get_cmap(self.colormap)
                                                    )
                         else:
                             ax.plt.set_array(out_r.T.ravel())
                         self.titles.append(
                             'Cross Spectra Real Ch{} * Ch{}'.format(pair[0], pair[1]))
                         ax = self.axes[3 * n + 2]
                         if ax.firsttime:
                             self.xmax = self.xmax if self.xmax else numpy.nanmax(x)
                             self.xmin = self.xmin if self.xmin else -self.xmax
                             self.zmin = self.zmin if self.zmin else numpy.nanmin(cross)
                             self.zmax = self.zmax if self.zmax else numpy.nanmax(cross)
                             ax.plt = ax.pcolormesh(x, y, out_i.T,
                                                    vmin=-1.e6,
                                                    vmax=1.e6,
                                                    cmap=plt.get_cmap(self.colormap)
                                                    )
                         else:
                             ax.plt.set_array(out_i.T.ravel())
                         self.titles.append(
                             'Cross Spectra Imag Ch{} * Ch{}'.format(pair[0], pair[1]))
             class RTIPlot(Plot):
                 '''
                 Plot for RTI data
                 '''
                 CODE = 'rti'
                 colormap = 'jet'
                 plot_type = 'pcolorbuffer'
                 def setup(self):
                     self.xaxis = 'time'
                     self.ncols = 1
                     self.nrows = len(self.data.channels)
                     self.nplots = len(self.data.channels)
                     self.ylabel = 'Range [km]'
                     self.xlabel = 'Time'
                     self.cb_label = 'dB'
                     self.plots_adjust.update({'hspace':0.8, 'left': 0.1, 'bottom': 0.1, 'right':0.95})
                     self.titles = ['{} Channel {}'.format(
                         self.CODE.upper(), x) for x in range(self.nrows)]
                 def update(self, dataOut):
                     data = {}
                     meta = {}
                     data['rti'] = dataOut.getPower()
                     #print(numpy.shape(data['rti']))
                     data['noise'] = 10*numpy.log10(dataOut.getNoise()/dataOut.normFactor)
                     return data, meta
                 def plot(self):
                     self.x = self.data.times
                     self.y = self.data.yrange
                     self.z = self.data[self.CODE]
                     self.z = numpy.ma.masked_invalid(self.z)
                     if self.decimation is None:
                         x, y, z = self.fill_gaps(self.x, self.y, self.z)
                     else:
                         x, y, z = self.fill_gaps(*self.decimate())
                     '''
                     if not isinstance(self.zmin, collections.abc.Sequence):
                         if not self.zmin:
                             self.zmin = [numpy.min(self.z)]*len(self.axes)
                         else:
                             self.zmin = [self.zmin]*len(self.axes)
                     if not isinstance(self.zmax, collections.abc.Sequence):
                         if not self.zmax:
                             self.zmax = [numpy.max(self.z)]*len(self.axes)
                         else:
                             self.zmax = [self.zmax]*len(self.axes)
                             '''
                     for n, ax in enumerate(self.axes):
                         self.zmin = self.zmin if self.zmin else numpy.min(self.z)
                         self.zmax = self.zmax if self.zmax else numpy.max(self.z)
                         if ax.firsttime:
                             if self.zlimits is not None:
                                 self.zmin, self.zmax = self.zlimits[n]
                             ax.plt = ax.pcolormesh(x, y, z[n].T,
                                                    vmin=self.zmin,
                                                    vmax=self.zmax,
                                                    cmap=plt.get_cmap(self.colormap)
                                                    )
                             if self.showprofile:
                                 ax.plot_profile = self.pf_axes[n].plot(
                                     self.data['rti'][n][-1], self.y)[0]
                                 ax.plot_noise = self.pf_axes[n].plot(numpy.repeat(self.data['noise'][n][-1], len(self.y)), self.y,
                                                                      color="k", linestyle="dashed", lw=1)[0]
                         else:
                             if self.zlimits is not None:
                                 self.zmin, self.zmax = self.zlimits[n]
                             ax.collections.remove(ax.collections[0])
                             ax.plt = ax.pcolormesh(x, y, z[n].T,
                                                    vmin=self.zmin,
                                                    vmax=self.zmax,
                                                    cmap=plt.get_cmap(self.colormap)
                                                    )
                             if self.showprofile:
                                 ax.plot_profile.set_data(self.data['rti'][n][-1], self.y)
                                 ax.plot_noise.set_data(numpy.repeat(
                                     self.data['noise'][n][-1], len(self.y)), self.y)
             class SpectrogramPlot(Plot):
                 '''
                 Plot for Spectrogram data
                 '''
                 CODE = 'Spectrogram_Profile'
                 colormap = 'binary'
                 plot_type = 'pcolorbuffer'
                 def setup(self):
                     self.xaxis = 'time'
                     self.ncols = 1
                     self.nrows = len(self.data.channels)
                     self.nplots = len(self.data.channels)
                     self.xlabel = 'Time'
                     #self.cb_label = 'dB'
                     self.plots_adjust.update({'hspace':1.2, 'left': 0.1, 'bottom': 0.12, 'right':0.95})
                     self.titles = []
                     #self.titles = ['{} Channel {} \n H = {} km ({} - {})'.format(
                         #self.CODE.upper(), x, self.data.heightList[self.data.hei], self.data.heightList[self.data.hei],self.data.heightList[self.data.hei]+(self.data.DH*self.data.nProfiles)) for x in range(self.nrows)]
                     self.titles = ['{} Channel {}'.format(
                         self.CODE.upper(), x) for x in range(self.nrows)]
                 def update(self, dataOut):
                     data = {}
                     meta = {}
                     maxHei = 1620#+12000
                     indb = numpy.where(dataOut.heightList <= maxHei)
                     hei = indb[0][-1]
                     #print(dataOut.heightList)
                     factor = dataOut.nIncohInt
                     z = dataOut.data_spc[:,:,hei] / factor
                     z = numpy.where(numpy.isfinite(z), z, numpy.NAN)
                     #buffer = 10 * numpy.log10(z)
                     meta['xrange'] = (dataOut.getFreqRange(1)/1000., dataOut.getAcfRange(1), dataOut.getVelRange(1))
                     #self.hei = hei
                     #self.heightList = dataOut.heightList
                     #self.DH = (dataOut.heightList[1] - dataOut.heightList[0])/dataOut.step
                     #self.nProfiles = dataOut.nProfiles
                     data['Spectrogram_Profile'] = 10 * numpy.log10(z)
                     data['hei'] = hei
                     data['DH'] = (dataOut.heightList[1] - dataOut.heightList[0])/dataOut.step
                     data['nProfiles'] = dataOut.nProfiles
                     #meta['yrange'] = dataOut.heightList[0:dataOut.NSHTS]
                     '''
                     import matplotlib.pyplot as plt
                     plt.plot(10 * numpy.log10(z[0,:]))
                     plt.show()
                     from time import sleep
                     sleep(10)
                     '''
                     return data, meta
                 def plot(self):
                     self.x = self.data.times
                     self.z = self.data[self.CODE]
                     self.y = self.data.xrange[0]
                     hei = self.data['hei'][-1]
                     DH = self.data['DH'][-1]
                     nProfiles = self.data['nProfiles'][-1]
                     self.ylabel = "Frequency (kHz)"
                     self.z = numpy.ma.masked_invalid(self.z)
                     if self.decimation is None:
                         x, y, z = self.fill_gaps(self.x, self.y, self.z)
                     else:
                         x, y, z = self.fill_gaps(*self.decimate())
                     for n, ax in enumerate(self.axes):
                         self.zmin = self.zmin if self.zmin else numpy.min(self.z)
                         self.zmax = self.zmax if self.zmax else numpy.max(self.z)
                         data = self.data[-1]
                         if ax.firsttime:
                             ax.plt = ax.pcolormesh(x, y, z[n].T,
                                                    vmin=self.zmin,
                                                    vmax=self.zmax,
                                                    cmap=plt.get_cmap(self.colormap)
                                                    )
                         else:
                             ax.collections.remove(ax.collections[0])
                             ax.plt = ax.pcolormesh(x, y, z[n].T,
                                                    vmin=self.zmin,
                                                    vmax=self.zmax,
                                                    cmap=plt.get_cmap(self.colormap)
                                                    )
                     #self.titles.append('Spectrogram')
                     #self.titles.append('{} Channel {} \n H = {} km ({} - {})'.format(
                         #self.CODE.upper(), x, y[hei], y[hei],y[hei]+(DH*nProfiles)))
             class CoherencePlot(RTIPlot):
                 '''
                 Plot for Coherence data
                 '''
                 CODE = 'coh'
                 def setup(self):
                     self.xaxis = 'time'
                     self.ncols = 1
                     self.nrows = len(self.data.pairs)
                     self.nplots = len(self.data.pairs)
                     self.ylabel = 'Range [km]'
                     self.xlabel = 'Time'
                     self.plots_adjust.update({'hspace':0.6, 'left': 0.1, 'bottom': 0.1,'right':0.95})
                     if self.CODE == 'coh':
                         self.cb_label = ''
                         self.titles = [
                             'Coherence Map Ch{} * Ch{}'.format(x[0], x[1]) for x in self.data.pairs]
                     else:
                         self.cb_label = 'Degrees'
                         self.titles = [
                             'Phase Map Ch{} * Ch{}'.format(x[0], x[1]) for x in self.data.pairs]
                 def update(self, dataOut):
                     data = {}
                     meta = {}
                     data['coh'] = dataOut.getCoherence()
                     meta['pairs'] = dataOut.pairsList
                     return data, meta
             class PhasePlot(CoherencePlot):
                 '''
                 Plot for Phase map data
                 '''
                 CODE = 'phase'
                 colormap = 'seismic'
                 def update(self, dataOut):
                     data = {}
                     meta = {}
                     data['phase'] = dataOut.getCoherence(phase=True)
                     meta['pairs'] = dataOut.pairsList
                     return data, meta
             class NoisePlot(Plot):
                 '''
                 Plot for noise
                 '''
                 CODE = 'noise'
                 plot_type = 'scatterbuffer'
                 def setup(self):
                     self.xaxis = 'time'
                     self.ncols = 1
                     self.nrows = 1
                     self.nplots = 1
                     self.ylabel = 'Intensity [dB]'
                     self.xlabel = 'Time'
                     self.titles = ['Noise']
                     self.colorbar = False
                     self.plots_adjust.update({'right': 0.85 })
                 def update(self, dataOut):
                     data = {}
                     meta = {}
                     data['noise'] = 10*numpy.log10(dataOut.getNoise()/dataOut.normFactor).reshape(dataOut.nChannels, 1)
                     meta['yrange'] = numpy.array([])
                     return data, meta
                 def plot(self):
                     x = self.data.times
                     xmin = self.data.min_time
                     xmax = xmin + self.xrange * 60 * 60
                     Y = self.data['noise']
                     if self.axes[0].firsttime:
                         self.ymin = numpy.nanmin(Y) - 5
                         self.ymax = numpy.nanmax(Y) + 5
                         for ch in self.data.channels:
                             y = Y[ch]
                             self.axes[0].plot(x, y, lw=1, label='Ch{}'.format(ch))
                         plt.legend(bbox_to_anchor=(1.18, 1.0))
                     else:
                         for ch in self.data.channels:
                             y = Y[ch]
                             self.axes[0].lines[ch].set_data(x, y)
                     self.ymin = numpy.nanmin(Y) - 5
                     self.ymax = numpy.nanmax(Y) + 10
             class PowerProfilePlot(Plot):
                 CODE = 'pow_profile'
                 plot_type = 'scatter'
                 def setup(self):
                     self.ncols = 1
                     self.nrows = 1
                     self.nplots = 1
                     self.height = 4
                     self.width = 3
                     self.ylabel = 'Range [km]'
                     self.xlabel = 'Intensity [dB]'
                     self.titles = ['Power Profile']
                     self.colorbar = False
                 def update(self, dataOut):
                     data = {}
                     meta = {}
                     data[self.CODE] = dataOut.getPower()
                     return data, meta
                 def plot(self):
                     y = self.data.yrange
                     self.y = y
                     x = self.data[-1][self.CODE]
                     if self.xmin is None: self.xmin = numpy.nanmin(x)*0.9
                     if self.xmax is None: self.xmax = numpy.nanmax(x)*1.1
                     if self.axes[0].firsttime:
                         for ch in self.data.channels:
                             self.axes[0].plot(x[ch], y, lw=1, label='Ch{}'.format(ch))
                         plt.legend()
                     else:
                         for ch in self.data.channels:
                             self.axes[0].lines[ch].set_data(x[ch], y)
             class SpectraCutPlot(Plot):
                 CODE = 'spc_cut'
                 plot_type = 'scatter'
                 buffering = False
                 def setup(self):
                     self.nplots = len(self.data.channels)
                     self.ncols = int(numpy.sqrt(self.nplots) + 0.9)
                     self.nrows = int((1.0 * self.nplots / self.ncols) + 0.9)
                     self.width = 3.4 * self.ncols + 1.5
                     self.height = 3 * self.nrows
                     self.ylabel = 'Power [dB]'
                     self.colorbar = False
                     self.plots_adjust.update({'left':0.1, 'hspace':0.3, 'right': 0.75, 'bottom':0.08})
                 def update(self, dataOut):
                     data = {}
                     meta = {}
                     spc = 10*numpy.log10(dataOut.data_spc/dataOut.normFactor)
                     data['spc'] = spc
                     meta['xrange'] = (dataOut.getFreqRange(1)/1000., dataOut.getAcfRange(1), dataOut.getVelRange(1))
                     if self.CODE == 'cut_gaussian_fit':
                         data['gauss_fit0'] = 10*numpy.log10(dataOut.GaussFit0/dataOut.normFactor)
                         data['gauss_fit1'] = 10*numpy.log10(dataOut.GaussFit1/dataOut.normFactor)
                     return data, meta
                 def plot(self):
                     if self.xaxis == "frequency":
                         x = self.data.xrange[0][1:]
                         self.xlabel = "Frequency (kHz)"
                     elif self.xaxis == "time":
                         x = self.data.xrange[1]
                         self.xlabel = "Time (ms)"
                     else:
                         x = self.data.xrange[2][:-1]
                         self.xlabel = "Velocity (m/s)"
                     if self.CODE == 'cut_gaussian_fit':
                         x = self.data.xrange[2][:-1]
                         self.xlabel = "Velocity (m/s)"
                     self.titles = []
                     y = self.data.yrange
                     data = self.data[-1]
                     z = data['spc']
                     if self.height_index:
                         index = numpy.array(self.height_index)
                     else:
                         index = numpy.arange(0, len(y), int((len(y))/9))
                     for n, ax in enumerate(self.axes):
                         if self.CODE == 'cut_gaussian_fit':
                             gau0 = data['gauss_fit0']
                             gau1 = data['gauss_fit1']
                         if ax.firsttime:
                             self.xmax = self.xmax if self.xmax else numpy.nanmax(x)
                             self.xmin = self.xmin if self.xmin else -self.xmax
                             self.ymin = self.ymin if self.ymin else numpy.nanmin(z[:,:,index])
                             self.ymax = self.ymax if self.ymax else numpy.nanmax(z[:,:,index])
                             #print(self.ymax)
                             #print(z[n, :, index])
                             ax.plt = ax.plot(x, z[n, :, index].T, lw=0.25)
                             if self.CODE == 'cut_gaussian_fit':
                                 ax.plt_gau0 = ax.plot(x, gau0[n, :, index].T, lw=1, linestyle='-.')
                                 for i, line in enumerate(ax.plt_gau0):
                                     line.set_color(ax.plt[i].get_color())
                                 ax.plt_gau1 = ax.plot(x, gau1[n, :, index].T, lw=1, linestyle='--')
                                 for i, line in enumerate(ax.plt_gau1):
                                     line.set_color(ax.plt[i].get_color())
                             labels = ['Range = {:2.1f}km'.format(y[i]) for i in index]
                             self.figures[0].legend(ax.plt, labels, loc='center right')
                         else:
                             for i, line in enumerate(ax.plt):
                                 line.set_data(x, z[n, :, index[i]].T)
                             for i, line in enumerate(ax.plt_gau0):
                                 line.set_data(x, gau0[n, :, index[i]].T)
                                 line.set_color(ax.plt[i].get_color())
                             for i, line in enumerate(ax.plt_gau1):
                                 line.set_data(x, gau1[n, :, index[i]].T)
                                 line.set_color(ax.plt[i].get_color())
                         self.titles.append('CH {}'.format(n))
             class BeaconPhase(Plot):
                 __isConfig = None
                 __nsubplots = None
                 PREFIX = 'beacon_phase'
                 def __init__(self):
                     Plot.__init__(self)
                     self.timerange = 24*60*60
                     self.isConfig = False
                     self.__nsubplots = 1
                     self.counter_imagwr = 0
                     self.WIDTH = 800
                     self.HEIGHT = 400
                     self.WIDTHPROF = 120
                     self.HEIGHTPROF = 0
                     self.xdata = None
                     self.ydata = None
                     self.PLOT_CODE = BEACON_CODE
                     self.FTP_WEI = None
                     self.EXP_CODE = None
                     self.SUB_EXP_CODE = None
                     self.PLOT_POS = None
                     self.filename_phase = None
                     self.figfile = None
                     self.xmin = None
                     self.xmax = None
                 def getSubplots(self):
                     ncol = 1
                     nrow = 1
                     return nrow, ncol
                 def setup(self, id, nplots, wintitle, showprofile=True, show=True):
                     self.__showprofile = showprofile
                     self.nplots = nplots
                     ncolspan = 7
                     colspan = 6
                     self.__nsubplots = 2
                     self.createFigure(id = id,
                                       wintitle = wintitle,
                                       widthplot = self.WIDTH+self.WIDTHPROF,
                                       heightplot = self.HEIGHT+self.HEIGHTPROF,
                                       show=show)
                     nrow, ncol = self.getSubplots()
                     self.addAxes(nrow, ncol*ncolspan, 0, 0, colspan, 1)
                 def save_phase(self, filename_phase):
                     f = open(filename_phase,'w+')
                     f.write('\n\n')
                     f.write('JICAMARCA RADIO OBSERVATORY - Beacon Phase \n')
                     f.write('DD MM YYYY  HH MM SS   pair(2,0) pair(2,1) pair(2,3) pair(2,4)\n\n' )
                     f.close()
                 def save_data(self, filename_phase, data, data_datetime):
                     f=open(filename_phase,'a')
                     timetuple_data = data_datetime.timetuple()
                     day = str(timetuple_data.tm_mday)
                     month = str(timetuple_data.tm_mon)
                     year = str(timetuple_data.tm_year)
                     hour = str(timetuple_data.tm_hour)
                     minute = str(timetuple_data.tm_min)
                     second = str(timetuple_data.tm_sec)
                     f.write(day+' '+month+' '+year+'  '+hour+' '+minute+' '+second+'   '+str(data[0])+'   '+str(data[1])+'   '+str(data[2])+'   '+str(data[3])+'\n')
                     f.close()
                 def plot(self):
                     log.warning('TODO: Not yet implemented...')
                 def run(self, dataOut, id, wintitle="", pairsList=None, showprofile='True',
                         xmin=None, xmax=None, ymin=None, ymax=None, hmin=None, hmax=None,
                         timerange=None,
                         save=False, figpath='./', figfile=None, show=True, ftp=False, wr_period=1,
                         server=None, folder=None, username=None, password=None,
                         ftp_wei=0, exp_code=0, sub_exp_code=0, plot_pos=0):
                     if dataOut.flagNoData:
                         return dataOut
                     if not isTimeInHourRange(dataOut.datatime, xmin, xmax):
                         return
                     if pairsList == None:
                         pairsIndexList = dataOut.pairsIndexList[:10]
                     else:
                         pairsIndexList = []
                         for pair in pairsList:
                             if pair not in dataOut.pairsList:
                                 raise ValueError("Pair %s is not in dataOut.pairsList" %(pair))
                             pairsIndexList.append(dataOut.pairsList.index(pair))
                     if pairsIndexList == []:
                         return
              #         if len(pairsIndexList) > 4:
              #             pairsIndexList = pairsIndexList[0:4]
                     hmin_index = None
                     hmax_index = None
                     if hmin != None and hmax != None:
                         indexes = numpy.arange(dataOut.nHeights)
                         hmin_list = indexes[dataOut.heightList >= hmin]
                         hmax_list = indexes[dataOut.heightList <= hmax]
                         if hmin_list.any():
                             hmin_index = hmin_list[0]
                         if hmax_list.any():
                             hmax_index = hmax_list[-1]+1
                     x = dataOut.getTimeRange()
                     thisDatetime = dataOut.datatime
                     title = wintitle + " Signal Phase" # : %s" %(thisDatetime.strftime("%d-%b-%Y"))
                     xlabel = "Local Time"
                     ylabel = "Phase (degrees)"
                     update_figfile = False
                     nplots = len(pairsIndexList)
                     #phase = numpy.zeros((len(pairsIndexList),len(dataOut.beacon_heiIndexList)))
                     phase_beacon = numpy.zeros(len(pairsIndexList))
                     for i in range(nplots):
                         pair = dataOut.pairsList[pairsIndexList[i]]
                         ccf = numpy.average(dataOut.data_cspc[pairsIndexList[i], :, hmin_index:hmax_index], axis=0)
                         powa = numpy.average(dataOut.data_spc[pair[0], :, hmin_index:hmax_index], axis=0)
                         powb = numpy.average(dataOut.data_spc[pair[1], :, hmin_index:hmax_index], axis=0)
                         avgcoherenceComplex = ccf/numpy.sqrt(powa*powb)
                         phase = numpy.arctan2(avgcoherenceComplex.imag, avgcoherenceComplex.real)*180/numpy.pi
                         if dataOut.beacon_heiIndexList:
                             phase_beacon[i] = numpy.average(phase[dataOut.beacon_heiIndexList])
                         else:
                             phase_beacon[i] = numpy.average(phase)
                     if not self.isConfig:
                         nplots = len(pairsIndexList)
                         self.setup(id=id,
                                    nplots=nplots,
                                    wintitle=wintitle,
                                    showprofile=showprofile,
                                    show=show)
                         if timerange != None:
                             self.timerange = timerange
                         self.xmin, self.xmax = self.getTimeLim(x, xmin, xmax, timerange)
                         if ymin == None: ymin = 0
                         if ymax == None: ymax = 360
                         self.FTP_WEI = ftp_wei
                         self.EXP_CODE = exp_code
                         self.SUB_EXP_CODE = sub_exp_code
                         self.PLOT_POS = plot_pos
                         self.name = thisDatetime.strftime("%Y%m%d_%H%M%S")
                         self.isConfig = True
                         self.figfile = figfile
                         self.xdata = numpy.array([])
                         self.ydata = numpy.array([])
                         update_figfile = True
                         #open file beacon phase
                         path = '%s%03d' %(self.PREFIX, self.id)
                         beacon_file = os.path.join(path,'%s.txt'%self.name)
                         self.filename_phase = os.path.join(figpath,beacon_file)
                         #self.save_phase(self.filename_phase)
                     #store data beacon phase
                     #self.save_data(self.filename_phase, phase_beacon, thisDatetime)
                     self.setWinTitle(title)
                     title = "Phase Plot %s" %(thisDatetime.strftime("%Y/%m/%d %H:%M:%S"))
                     legendlabels = ["Pair (%d,%d)"%(pair[0], pair[1]) for pair in dataOut.pairsList]
                     axes = self.axesList[0]
                     self.xdata = numpy.hstack((self.xdata, x[0:1]))
                     if len(self.ydata)==0:
                         self.ydata = phase_beacon.reshape(-1,1)
                     else:
                         self.ydata = numpy.hstack((self.ydata, phase_beacon.reshape(-1,1)))
                     axes.pmultilineyaxis(x=self.xdata, y=self.ydata,
                                 xmin=self.xmin, xmax=self.xmax, ymin=ymin, ymax=ymax,
                                 xlabel=xlabel, ylabel=ylabel, title=title, legendlabels=legendlabels, marker='x', markersize=8, linestyle="solid",
                                 XAxisAsTime=True, grid='both'
                                 )
                     self.draw()
                     if dataOut.ltctime >= self.xmax:
                         self.counter_imagwr = wr_period
                         self.isConfig = False
                         update_figfile = True
                     self.save(figpath=figpath,
                               figfile=figfile,
                               save=save,
                               ftp=ftp,
                               wr_period=wr_period,
                               thisDatetime=thisDatetime,
                               update_figfile=update_figfile)
                     return dataOut

schainpy/model/graphics/jroplot_voltage_lags.py +4 -4

             import os
             import time
             import math
             import datetime
             import numpy
-            import collections.abc
             from schainpy.model.proc.jroproc_base import ProcessingUnit, Operation, MPDecorator  #YONG
             from .jroplot_spectra import RTIPlot, NoisePlot
             from schainpy.utils import log
             from .plotting_codes import *
             from schainpy.model.graphics.jroplot_base import Plot, plt
             import matplotlib.pyplot as plt
             import matplotlib.colors as colors
             from matplotlib.ticker import MultipleLocator
             class RTIDPPlot(RTIPlot):
                 '''Plot for RTI Double Pulse Experiment
                 '''
                 CODE = 'RTIDP'
                 colormap = 'jet'
                 plot_name = 'RTI'
                 plot_type = 'pcolorbuffer'
                 def setup(self):
                     self.xaxis = 'time'
                     self.ncols = 1
                     self.nrows = 3
                     self.nplots = self.nrows
                     self.ylabel = 'Range [km]'
                     self.xlabel = 'Time (LT)'
                     self.cb_label = 'Intensity (dB)'
                     self.plots_adjust.update({'hspace':0.8, 'left': 0.1, 'bottom': 0.1, 'right':0.95})
                     self.titles = ['{} Channel {}'.format(
                         self.plot_name.upper(), '0x1'),'{} Channel {}'.format(
                             self.plot_name.upper(), '0'),'{} Channel {}'.format(
                                 self.plot_name.upper(), '1')]
                 def update(self, dataOut):
                     data = {}
                     meta = {}
                     data['rti'] = dataOut.data_for_RTI_DP
                     data['NDP'] = dataOut.NDP
                     return data, meta
                 def plot(self):
                     NDP = self.data['NDP'][-1]
                     self.x = self.data.times
                     self.y = self.data.yrange[0:NDP]
                     self.z = self.data['rti']
                     self.z = numpy.ma.masked_invalid(self.z)
                     if self.decimation is None:
                         x, y, z = self.fill_gaps(self.x, self.y, self.z)
                     else:
                         x, y, z = self.fill_gaps(*self.decimate())
                     for n, ax in enumerate(self.axes):
                         self.zmax = self.zmax if self.zmax is not None else numpy.max(
                             self.z[1][0,12:40])
                         self.zmin = self.zmin if self.zmin is not None else numpy.min(
                             self.z[1][0,12:40])
                         if ax.firsttime:
                             if self.zlimits is not None:
                                 self.zmin, self.zmax = self.zlimits[n]
                             ax.plt = ax.pcolormesh(x, y, z[n].T,
                                                    vmin=self.zmin,
                                                    vmax=self.zmax,
                                                    cmap=plt.get_cmap(self.colormap)
                                                    )
                         else:
                             #if self.zlimits is not None:
                                 #self.zmin, self.zmax = self.zlimits[n]
                             ax.collections.remove(ax.collections[0])
                             ax.plt = ax.pcolormesh(x, y, z[n].T,
                                                    vmin=self.zmin,
                                                    vmax=self.zmax,
                                                    cmap=plt.get_cmap(self.colormap)
                                                    )
             class RTILPPlot(RTIPlot):
                 '''
                    Plot for RTI Long Pulse
                 '''
                 CODE = 'RTILP'
                 colormap = 'jet'
                 plot_name = 'RTI LP'
                 plot_type = 'pcolorbuffer'
                 def setup(self):
                     self.xaxis = 'time'
                     self.ncols = 1
                     self.nrows = 2
                     self.nplots = self.nrows
                     self.ylabel = 'Range [km]'
                     self.xlabel = 'Time (LT)'
                     self.cb_label = 'Intensity (dB)'
                     self.plots_adjust.update({'hspace':0.8, 'left': 0.1, 'bottom': 0.1, 'right':0.95})
                     self.titles = ['{} Channel {}'.format(
                         self.plot_name.upper(), '0'),'{} Channel {}'.format(
                             self.plot_name.upper(), '1'),'{} Channel {}'.format(
                                 self.plot_name.upper(), '2'),'{} Channel {}'.format(
                                     self.plot_name.upper(), '3')]
                 def update(self, dataOut):
                     data = {}
                     meta = {}
                     data['rti'] = dataOut.data_for_RTI_LP
                     data['NRANGE'] = dataOut.NRANGE
                     return data, meta
                 def plot(self):
                     NRANGE = self.data['NRANGE'][-1]
                     self.x = self.data.times
                     self.y = self.data.yrange[0:NRANGE]
                     self.z = self.data['rti']
                     self.z = numpy.ma.masked_invalid(self.z)
                     if self.decimation is None:
                         x, y, z = self.fill_gaps(self.x, self.y, self.z)
                     else:
                         x, y, z = self.fill_gaps(*self.decimate())
                     for n, ax in enumerate(self.axes):
                         self.zmax = self.zmax if self.zmax is not None else numpy.max(
                             self.z[1][0,12:40])
                         self.zmin = self.zmin if self.zmin is not None else numpy.min(
                             self.z[1][0,12:40])
                         if ax.firsttime:
                             if self.zlimits is not None:
                                 self.zmin, self.zmax = self.zlimits[n]
                             ax.plt = ax.pcolormesh(x, y, z[n].T,
                                                    vmin=self.zmin,
                                                    vmax=self.zmax,
                                                    cmap=plt.get_cmap(self.colormap)
                                                    )
                         else:
                             if self.zlimits is not None:
                                 self.zmin, self.zmax = self.zlimits[n]
                             ax.collections.remove(ax.collections[0])
                             ax.plt = ax.pcolormesh(x, y, z[n].T,
                                                    vmin=self.zmin,
                                                    vmax=self.zmax,
                                                    cmap=plt.get_cmap(self.colormap)
                                                    )
             class DenRTIPlot(RTIPlot):
                 '''
                    Plot for Den
                 '''
                 CODE = 'denrti'
                 colormap = 'jet'
                 def setup(self):
                     self.xaxis = 'time'
                     self.ncols = 1
                     self.nrows = self.data.shape(self.CODE)[0]
                     self.nplots = self.nrows
                     self.ylabel = 'Range [km]'
                     self.xlabel = 'Time (LT)'
                     self.plots_adjust.update({'wspace': 0.8, 'hspace':0.2, 'left': 0.2, 'right': 0.9, 'bottom': 0.18})
                     if self.CODE == 'denrti':
                         self.cb_label = r'$\mathrm{N_e}$ Electron Density ($\mathrm{1/cm^3}$)'
                     self.titles = ['Electron Density RTI']
                 def update(self, dataOut):
                     data = {}
                     meta = {}
                     data['denrti'] = dataOut.DensityFinal*1.e-6 #To Plot in cm^-3
                     return data, meta
                 def plot(self):
                     self.x = self.data.times
                     self.y = self.data.yrange
                     self.z = self.data[self.CODE]
                     self.z = numpy.ma.masked_invalid(self.z)
                     if self.decimation is None:
                         x, y, z = self.fill_gaps(self.x, self.y, self.z)
                     else:
                         x, y, z = self.fill_gaps(*self.decimate())
                     for n, ax in enumerate(self.axes):
                         self.zmax = self.zmax if self.zmax is not None else numpy.max(
                             self.z[n])
                         self.zmin = self.zmin if self.zmin is not None else numpy.min(
                             self.z[n])
                         if ax.firsttime:
                             if self.zlimits is not None:
                                 self.zmin, self.zmax = self.zlimits[n]
                             if numpy.log10(self.zmin)<0:
                                 self.zmin=1
                             ax.plt = ax.pcolormesh(x, y, z[n].T * self.factors[n],
                                                    vmin=self.zmin,
                                                    vmax=self.zmax,
                                                    cmap=self.cmaps[n],
                                                    norm=colors.LogNorm()
                                                    )
                         else:
                             if self.zlimits is not None:
                                 self.zmin, self.zmax = self.zlimits[n]
                             ax.collections.remove(ax.collections[0])
                             ax.plt = ax.pcolormesh(x, y, z[n].T * self.factors[n],
                                                    vmin=self.zmin,
                                                    vmax=self.zmax,
                                                    cmap=self.cmaps[n],
                                                    norm=colors.LogNorm()
                                                    )
             class ETempRTIPlot(RTIPlot):
                 '''
                    Plot for Electron Temperature
                 '''
                 CODE = 'ETemp'
                 colormap = 'jet'
                 def setup(self):
                     self.xaxis = 'time'
                     self.ncols = 1
                     self.nrows = self.data.shape(self.CODE)[0]
                     self.nplots = self.nrows
                     self.ylabel = 'Range [km]'
                     self.xlabel = 'Time (LT)'
                     self.plots_adjust.update({'wspace': 0.8, 'hspace':0.2, 'left': 0.2, 'right': 0.9, 'bottom': 0.18})
                     if self.CODE == 'ETemp':
                         self.cb_label = 'Electron Temperature (K)'
                         self.titles = ['Electron Temperature RTI']
                     if self.CODE == 'ITemp':
                         self.cb_label = 'Ion Temperature (K)'
                         self.titles = ['Ion Temperature RTI']
                     if self.CODE == 'HeFracLP':
                         self.cb_label='He+ Fraction'
                         self.titles = ['He+ Fraction RTI']
                         self.zmax=0.16
                     if self.CODE== 'HFracLP':
                         self.cb_label='H+ Fraction'
                         self.titles = ['H+ Fraction RTI']
                 def update(self, dataOut):
                     data = {}
                     meta = {}
                     data['ETemp'] = dataOut.ElecTempFinal
                     return data, meta
                 def plot(self):
                     self.x = self.data.times
                     self.y = self.data.yrange
                     self.z = self.data[self.CODE]
                     self.z = numpy.ma.masked_invalid(self.z)
                     if self.decimation is None:
                         x, y, z = self.fill_gaps(self.x, self.y, self.z)
                     else:
                         x, y, z = self.fill_gaps(*self.decimate())
                     for n, ax in enumerate(self.axes):
                         self.zmax = self.zmax if self.zmax is not None else numpy.max(
                             self.z[n])
                         self.zmin = self.zmin if self.zmin is not None else numpy.min(
                             self.z[n])
                         if ax.firsttime:
                             if self.zlimits is not None:
                                 self.zmin, self.zmax = self.zlimits[n]
                             ax.plt = ax.pcolormesh(x, y, z[n].T * self.factors[n],
                                                    vmin=self.zmin,
                                                    vmax=self.zmax,
                                                    cmap=self.cmaps[n]
                                                    )
                             #plt.tight_layout()
                         else:
                             if self.zlimits is not None:
                                 self.zmin, self.zmax = self.zlimits[n]
                             ax.collections.remove(ax.collections[0])
                             ax.plt = ax.pcolormesh(x, y, z[n].T * self.factors[n],
                                                    vmin=self.zmin,
                                                    vmax=self.zmax,
                                                    cmap=self.cmaps[n]
                                                    )
             class ITempRTIPlot(ETempRTIPlot):
                 '''
                    Plot for Ion Temperature
                 '''
                 CODE = 'ITemp'
                 colormap = 'jet'
                 plot_name = 'Ion Temperature'
                 def update(self, dataOut):
                     data = {}
                     meta = {}
                     data['ITemp'] = dataOut.IonTempFinal
                     return data, meta
             class HFracRTIPlot(ETempRTIPlot):
                 '''
                    Plot for H+ LP
                 '''
                 CODE = 'HFracLP'
                 colormap = 'jet'
                 plot_name = 'H+ Frac'
                 def update(self, dataOut):
                     data = {}
                     meta = {}
                     data['HFracLP'] = dataOut.PhyFinal
                     return data, meta
             class HeFracRTIPlot(ETempRTIPlot):
                 '''
                    Plot for He+ LP
                 '''
                 CODE = 'HeFracLP'
                 colormap = 'jet'
                 plot_name = 'He+ Frac'
                 def update(self, dataOut):
                     data = {}
                     meta = {}
                     data['HeFracLP'] = dataOut.PheFinal
                     return data, meta
             class TempsDPPlot(Plot):
                 '''
                 Plot for Electron - Ion Temperatures
                 '''
                 CODE = 'tempsDP'
                 #plot_name = 'Temperatures'
                 plot_type = 'scatterbuffer'
                 def setup(self):
                     self.ncols = 1
                     self.nrows = 1
                     self.nplots = 1
                     self.ylabel = 'Range [km]'
                     self.xlabel = 'Temperature (K)'
                     self.titles = ['Electron/Ion Temperatures']
                     self.width = 3.5
                     self.height = 5.5
                     self.colorbar = False
                     self.plots_adjust.update({'left': 0.17, 'right': 0.88, 'bottom': 0.1})
                 def update(self, dataOut):
                     data = {}
                     meta = {}
                     data['Te'] = dataOut.te2
                     data['Ti'] = dataOut.ti2
                     data['Te_error'] = dataOut.ete2
                     data['Ti_error'] = dataOut.eti2
                     meta['yrange'] = dataOut.heightList[0:dataOut.NSHTS]
                     return data, meta
                 def plot(self):
                     y = self.data.yrange
                     self.xmin = -100
                     self.xmax = 5000
                     ax = self.axes[0]
                     data = self.data[-1]
                     Te = data['Te']
                     Ti = data['Ti']
                     errTe = data['Te_error']
                     errTi = data['Ti_error']
                     if ax.firsttime:
                         ax.errorbar(Te, y, xerr=errTe, fmt='r^',elinewidth=1.0,color='b',linewidth=2.0, label='Te')
                         ax.errorbar(Ti, y, fmt='k^', xerr=errTi,elinewidth=1.0,color='b',linewidth=2.0, label='Ti')
                         plt.legend(loc='lower right')
                         self.ystep_given = 50
                         ax.yaxis.set_minor_locator(MultipleLocator(15))
                         ax.grid(which='minor')
                     else:
                         self.clear_figures()
                         ax.errorbar(Te, y, xerr=errTe, fmt='r^',elinewidth=1.0,color='b',linewidth=2.0, label='Te')
                         ax.errorbar(Ti, y, fmt='k^', xerr=errTi,elinewidth=1.0,color='b',linewidth=2.0, label='Ti')
                         plt.legend(loc='lower right')
                         ax.yaxis.set_minor_locator(MultipleLocator(15))
             class TempsHPPlot(Plot):
                 '''
                 Plot for Temperatures Hybrid Experiment
                 '''
                 CODE = 'temps_LP'
                 #plot_name = 'Temperatures'
                 plot_type = 'scatterbuffer'
                 def setup(self):
                     self.ncols = 1
                     self.nrows = 1
                     self.nplots = 1
                     self.ylabel = 'Range [km]'
                     self.xlabel = 'Temperature (K)'
                     self.titles = ['Electron/Ion Temperatures']
                     self.width = 3.5
                     self.height = 6.5
                     self.colorbar = False
                     self.plots_adjust.update({'left': 0.17, 'right': 0.88, 'bottom': 0.1})
                 def update(self, dataOut):
                     data = {}
                     meta = {}
                     data['Te'] = numpy.concatenate((dataOut.te2[:dataOut.cut],dataOut.te[dataOut.cut:]))
                     data['Ti'] = numpy.concatenate((dataOut.ti2[:dataOut.cut],dataOut.ti[dataOut.cut:]))
                     data['Te_error'] = numpy.concatenate((dataOut.ete2[:dataOut.cut],dataOut.ete[dataOut.cut:]))
                     data['Ti_error'] = numpy.concatenate((dataOut.eti2[:dataOut.cut],dataOut.eti[dataOut.cut:]))
                     meta['yrange'] = dataOut.heightList[0:dataOut.NACF]
                     return data, meta
                 def plot(self):
                     self.y = self.data.yrange
                     self.xmin = -100
                     self.xmax = 4500
                     ax = self.axes[0]
                     data = self.data[-1]
                     Te = data['Te']
                     Ti = data['Ti']
                     errTe = data['Te_error']
                     errTi = data['Ti_error']
                     if ax.firsttime:
                         ax.errorbar(Te, self.y, xerr=errTe, fmt='r^',elinewidth=1.0,color='b',linewidth=2.0, label='Te')
                         ax.errorbar(Ti, self.y, fmt='k^', xerr=errTi,elinewidth=1.0,color='b',linewidth=2.0, label='Ti')
                         plt.legend(loc='lower right')
                         self.ystep_given = 200
                         ax.yaxis.set_minor_locator(MultipleLocator(15))
                         ax.grid(which='minor')
                     else:
                         self.clear_figures()
                         ax.errorbar(Te, self.y, xerr=errTe, fmt='r^',elinewidth=1.0,color='b',linewidth=2.0, label='Te')
                         ax.errorbar(Ti, self.y, fmt='k^', xerr=errTi,elinewidth=1.0,color='b',linewidth=2.0, label='Ti')
                         plt.legend(loc='lower right')
                         ax.yaxis.set_minor_locator(MultipleLocator(15))
                         ax.grid(which='minor')
             class FracsHPPlot(Plot):
                 '''
                 Plot for Composition LP
                 '''
                 CODE = 'fracs_LP'
                 plot_type = 'scatterbuffer'
                 def setup(self):
                     self.ncols = 1
                     self.nrows = 1
                     self.nplots = 1
                     self.ylabel = 'Range [km]'
                     self.xlabel = 'Frac'
                     self.titles = ['Composition']
                     self.width = 3.5
                     self.height = 6.5
                     self.colorbar = False
                     self.plots_adjust.update({'left': 0.17, 'right': 0.88, 'bottom': 0.1})
                 def update(self, dataOut):
                     data = {}
                     meta = {}
                     #aux_nan=numpy.zeros(dataOut.cut,'float32')
                     #aux_nan[:]=numpy.nan
                     #data['ph'] = numpy.concatenate((aux_nan,dataOut.ph[dataOut.cut:]))
                     #data['eph'] = numpy.concatenate((aux_nan,dataOut.eph[dataOut.cut:]))
                     data['ph'] = dataOut.ph[dataOut.cut:]
                     data['eph'] = dataOut.eph[dataOut.cut:]
                     data['phe'] = dataOut.phe[dataOut.cut:]
                     data['ephe'] = dataOut.ephe[dataOut.cut:]
                     data['cut'] = dataOut.cut
                     meta['yrange'] = dataOut.heightList[0:dataOut.NACF]
                     return data, meta
                 def plot(self):
                     data = self.data[-1]
                     ph = data['ph']
                     eph = data['eph']
                     phe = data['phe']
                     ephe = data['ephe']
                     cut = data['cut']
                     self.y = self.data.yrange
                     self.xmin = 0
                     self.xmax = 1
                     ax = self.axes[0]
                     if ax.firsttime:
                         ax.errorbar(ph, self.y[cut:], xerr=eph, fmt='r^',elinewidth=1.0,color='b',linewidth=2.0, label='H+')
                         ax.errorbar(phe, self.y[cut:], fmt='k^', xerr=ephe,elinewidth=1.0,color='b',linewidth=2.0, label='He+')
                         plt.legend(loc='lower right')
                         self.xstep_given = 0.2
                         self.ystep_given = 200
                         ax.yaxis.set_minor_locator(MultipleLocator(15))
                         ax.grid(which='minor')
                     else:
                         self.clear_figures()
                         ax.errorbar(ph, self.y[cut:], xerr=eph, fmt='r^',elinewidth=1.0,color='b',linewidth=2.0, label='H+')
                         ax.errorbar(phe, self.y[cut:], fmt='k^', xerr=ephe,elinewidth=1.0,color='b',linewidth=2.0, label='He+')
                         plt.legend(loc='lower right')
                         ax.yaxis.set_minor_locator(MultipleLocator(15))
                         ax.grid(which='minor')
             class EDensityPlot(Plot):
                 '''
                 Plot for electron density
                 '''
                 CODE = 'den'
                 #plot_name = 'Electron Density'
                 plot_type = 'scatterbuffer'
                 def setup(self):
                     self.ncols = 1
                     self.nrows = 1
                     self.nplots = 1
                     self.ylabel = 'Range [km]'
                     self.xlabel = r'$\mathrm{N_e}$ Electron Density ($\mathrm{1/cm^3}$)'
                     self.titles = ['Electron Density']
                     self.width = 3.5
                     self.height = 5.5
                     self.colorbar = False
                     self.plots_adjust.update({'left': 0.17, 'right': 0.88, 'bottom': 0.1})
                 def update(self, dataOut):
                     data = {}
                     meta = {}
                     data['den_power'] = dataOut.ph2[:dataOut.NSHTS]
                     data['den_Faraday'] = dataOut.dphi[:dataOut.NSHTS]
                     data['den_error'] = dataOut.sdp2[:dataOut.NSHTS]
                     #data['err_Faraday'] = dataOut.sdn1[:dataOut.NSHTS]
                     data['NSHTS'] = dataOut.NSHTS
                     meta['yrange'] = dataOut.heightList[0:dataOut.NSHTS]
                     return data, meta
                 def plot(self):
                     y = self.data.yrange
                     self.xmin = 1e3
                     self.xmax = 1e7
                     ax = self.axes[0]
                     data = self.data[-1]
                     DenPow = data['den_power']
                     DenFar = data['den_Faraday']
                     errDenPow = data['den_error']
                     #errFaraday = data['err_Faraday']
                     NSHTS = data['NSHTS']
                     if self.CODE == 'denLP':
                         DenPowLP = data['den_LP']
                         errDenPowLP = data['den_LP_error']
                         cut = data['cut']
                     if ax.firsttime:
                         self.autoxticks=False
                         #ax.errorbar(DenFar, y[:NSHTS], xerr=1, fmt='h-',elinewidth=1.0,color='g',linewidth=1.0, label='Faraday Profile',markersize=2)
                         ax.errorbar(DenFar, y[:NSHTS], xerr=1, fmt='h-',elinewidth=1.0,color='g',linewidth=1.0, label='Faraday',markersize=2)
                         #ax.errorbar(DenPow, y[:NSHTS], fmt='k^-', xerr=errDenPow,elinewidth=1.0,color='b',linewidth=1.0, label='Power Profile',markersize=2)
                         ax.errorbar(DenPow, y[:NSHTS], fmt='k^-', xerr=errDenPow,elinewidth=1.0,color='b',linewidth=1.0, label='Power',markersize=2)
                         if self.CODE=='denLP':
                             ax.errorbar(DenPowLP[cut:], y[cut:], xerr=errDenPowLP[cut:], fmt='r^-',elinewidth=1.0,color='r',linewidth=1.0, label='LP Profile',markersize=2)
                         plt.legend(loc='upper left',fontsize=8.5)
                         #plt.legend(loc='lower left',fontsize=8.5)
                         ax.set_xscale("log", nonposx='clip')
                         grid_y_ticks=numpy.arange(numpy.nanmin(y),numpy.nanmax(y),50)
                         self.ystep_given=100
                         if self.CODE=='denLP':
                             self.ystep_given=200
                         ax.set_yticks(grid_y_ticks,minor=True)
                         ax.grid(which='minor')
                     else:
                         dataBefore = self.data[-2]
                         DenPowBefore = dataBefore['den_power']
                         self.clear_figures()
                         #ax.errorbar(DenFar, y[:NSHTS], xerr=1, fmt='h-',elinewidth=1.0,color='g',linewidth=1.0, label='Faraday Profile',markersize=2)
                         ax.errorbar(DenFar, y[:NSHTS], xerr=1, fmt='h-',elinewidth=1.0,color='g',linewidth=1.0, label='Faraday',markersize=2)
                         #ax.errorbar(DenPow, y[:NSHTS], fmt='k^-', xerr=errDenPow,elinewidth=1.0,color='b',linewidth=1.0, label='Power Profile',markersize=2)
                         ax.errorbar(DenPow, y[:NSHTS], fmt='k^-', xerr=errDenPow,elinewidth=1.0,color='b',linewidth=1.0, label='Power',markersize=2)
                         ax.errorbar(DenPowBefore, y[:NSHTS], elinewidth=1.0,color='r',linewidth=0.5,linestyle="dashed")
                         if self.CODE=='denLP':
                             ax.errorbar(DenPowLP[cut:], y[cut:], fmt='r^-', xerr=errDenPowLP[cut:],elinewidth=1.0,color='r',linewidth=1.0, label='LP Profile',markersize=2)
                         ax.set_xscale("log", nonposx='clip')
                         grid_y_ticks=numpy.arange(numpy.nanmin(y),numpy.nanmax(y),50)
                         ax.set_yticks(grid_y_ticks,minor=True)
                         ax.grid(which='minor')
                         plt.legend(loc='upper left',fontsize=8.5)
                         #plt.legend(loc='lower left',fontsize=8.5)
             class FaradayAnglePlot(Plot):
                 '''
                 Plot for electron density
                 '''
                 CODE = 'angle'
                 plot_name = 'Faraday Angle'
                 plot_type = 'scatterbuffer'
                 def setup(self):
                     self.ncols = 1
                     self.nrows = 1
                     self.nplots = 1
                     self.ylabel = 'Range [km]'
                     self.xlabel = 'Faraday Angle (º)'
                     self.titles = ['Electron Density']
                     self.width = 3.5
                     self.height = 5.5
                     self.colorbar = False
                     self.plots_adjust.update({'left': 0.17, 'right': 0.88, 'bottom': 0.1})
                 def update(self, dataOut):
                     data = {}
                     meta = {}
                     data['angle'] = numpy.degrees(dataOut.phi)
                     #'''
-                    print(dataOut.phi_uwrp)
+                    #print(dataOut.phi_uwrp)
-                    print(data['angle'])
+                    #print(data['angle'])
-                    exit(1)
+                    #exit(1)
                     #'''
                     data['dphi'] = dataOut.dphi_uc*10
                     #print(dataOut.dphi)
                     #data['NSHTS'] = dataOut.NSHTS
                     #meta['yrange'] = dataOut.heightList[0:dataOut.NSHTS]
                     return data, meta
                 def plot(self):
                     data = self.data[-1]
                     self.x = data[self.CODE]
                     dphi = data['dphi']
                     self.y = self.data.yrange
                     self.xmin = -360#-180
                     self.xmax = 360#180
                     ax = self.axes[0]
                     if ax.firsttime:
                         self.autoxticks=False
                         #if self.CODE=='den':
                         ax.plot(self.x, self.y,marker='o',color='g',linewidth=1.0,markersize=2)
                         ax.plot(dphi, self.y,marker='o',color='blue',linewidth=1.0,markersize=2)
                         grid_y_ticks=numpy.arange(numpy.nanmin(self.y),numpy.nanmax(self.y),50)
                         self.ystep_given=100
                         if self.CODE=='denLP':
                             self.ystep_given=200
                         ax.set_yticks(grid_y_ticks,minor=True)
                         ax.grid(which='minor')
                         #plt.tight_layout()
                     else:
                         self.clear_figures()
                         #if self.CODE=='den':
                         #print(numpy.shape(self.x))
                         ax.plot(self.x, self.y, marker='o',color='g',linewidth=1.0, markersize=2)
                         ax.plot(dphi, self.y,marker='o',color='blue',linewidth=1.0,markersize=2)
                         grid_y_ticks=numpy.arange(numpy.nanmin(self.y),numpy.nanmax(self.y),50)
                         ax.set_yticks(grid_y_ticks,minor=True)
                         ax.grid(which='minor')
             class EDensityHPPlot(EDensityPlot):
                 '''
                    Plot for Electron Density Hybrid Experiment
                 '''
                 CODE = 'denLP'
                 plot_name = 'Electron Density'
                 plot_type = 'scatterbuffer'
                 def update(self, dataOut):
                     data = {}
                     meta = {}
                     data['den_power'] = dataOut.ph2[:dataOut.NSHTS]
                     data['den_Faraday']=dataOut.dphi[:dataOut.NSHTS]
                     data['den_error']=dataOut.sdp2[:dataOut.NSHTS]
                     data['den_LP']=dataOut.ne[:dataOut.NACF]
                     data['den_LP_error']=dataOut.ene[:dataOut.NACF]*dataOut.ne[:dataOut.NACF]*0.434
                     #self.ene=10**dataOut.ene[:dataOut.NACF]
                     data['NSHTS']=dataOut.NSHTS
                     data['cut']=dataOut.cut
                     return data, meta
             class ACFsPlot(Plot):
                 '''
                 Plot for ACFs Double Pulse Experiment
                 '''
                 CODE = 'acfs'
                 #plot_name = 'ACF'
                 plot_type = 'scatterbuffer'
                 def setup(self):
                     self.ncols = 1
                     self.nrows = 1
                     self.nplots = 1
                     self.ylabel = 'Range [km]'
                     self.xlabel = 'Lag (ms)'
                     self.titles = ['ACFs']
                     self.width = 3.5
                     self.height = 5.5
                     self.colorbar = False
                     self.plots_adjust.update({'left': 0.17, 'right': 0.88, 'bottom': 0.1})
                 def update(self, dataOut):
                     data = {}
                     meta = {}
                     data['ACFs'] = dataOut.acfs_to_plot
                     data['ACFs_error'] = dataOut.acfs_error_to_plot
                     data['lags'] = dataOut.lags_to_plot
                     data['Lag_contaminated_1'] = dataOut.x_igcej_to_plot
                     data['Lag_contaminated_2'] = dataOut.x_ibad_to_plot
                     data['Height_contaminated_1'] = dataOut.y_igcej_to_plot
                     data['Height_contaminated_2'] = dataOut.y_ibad_to_plot
                     meta['yrange'] = numpy.array([])
                     #meta['NSHTS'] = dataOut.NSHTS
                     #meta['DPL'] = dataOut.DPL
                     data['NSHTS'] = dataOut.NSHTS #This is metadata
                     data['DPL'] = dataOut.DPL #This is metadata
                     return data, meta
                 def plot(self):
                     data = self.data[-1]
                     #NSHTS = self.meta['NSHTS']
                     #DPL = self.meta['DPL']
                     NSHTS = data['NSHTS'] #This is metadata
                     DPL = data['DPL'] #This is metadata
                     lags = data['lags']
                     ACFs = data['ACFs']
                     errACFs = data['ACFs_error']
                     BadLag1 = data['Lag_contaminated_1']
                     BadLag2 = data['Lag_contaminated_2']
                     BadHei1 = data['Height_contaminated_1']
                     BadHei2 = data['Height_contaminated_2']
                     self.xmin = 0.0
                     self.xmax = 2.0
                     self.y = ACFs
                     ax = self.axes[0]
                     if ax.firsttime:
                         for i in range(NSHTS):
                             x_aux = numpy.isfinite(lags[i,:])
                             y_aux = numpy.isfinite(ACFs[i,:])
                             yerr_aux = numpy.isfinite(errACFs[i,:])
                             x_igcej_aux = numpy.isfinite(BadLag1[i,:])
                             y_igcej_aux = numpy.isfinite(BadHei1[i,:])
                             x_ibad_aux = numpy.isfinite(BadLag2[i,:])
                             y_ibad_aux = numpy.isfinite(BadHei2[i,:])
                             if lags[i,:][~numpy.isnan(lags[i,:])].shape[0]>2:
                                 ax.errorbar(lags[i,x_aux], ACFs[i,y_aux], yerr=errACFs[i,x_aux],color='b',marker='o',linewidth=1.0,markersize=2)
                             ax.plot(BadLag1[i,x_igcej_aux],BadHei1[i,y_igcej_aux],'x',color='red',markersize=2)
                             ax.plot(BadLag2[i,x_ibad_aux],BadHei2[i,y_ibad_aux],'X',color='red',markersize=2)
                         self.xstep_given = (self.xmax-self.xmin)/(DPL-1)
                         self.ystep_given = 50
                         ax.yaxis.set_minor_locator(MultipleLocator(15))
                         ax.grid(which='minor')
                     else:
                         self.clear_figures()
                         for i in range(NSHTS):
                             x_aux = numpy.isfinite(lags[i,:])
                             y_aux = numpy.isfinite(ACFs[i,:])
                             yerr_aux = numpy.isfinite(errACFs[i,:])
                             x_igcej_aux = numpy.isfinite(BadLag1[i,:])
                             y_igcej_aux = numpy.isfinite(BadHei1[i,:])
                             x_ibad_aux = numpy.isfinite(BadLag2[i,:])
                             y_ibad_aux = numpy.isfinite(BadHei2[i,:])
                             if lags[i,:][~numpy.isnan(lags[i,:])].shape[0]>2:
                                 ax.errorbar(lags[i,x_aux], ACFs[i,y_aux], yerr=errACFs[i,x_aux],linewidth=1.0,markersize=2,color='b',marker='o')
                             ax.plot(BadLag1[i,x_igcej_aux],BadHei1[i,y_igcej_aux],'x',color='red',markersize=2)
                             ax.plot(BadLag2[i,x_ibad_aux],BadHei2[i,y_ibad_aux],'X',color='red',markersize=2)
                         ax.yaxis.set_minor_locator(MultipleLocator(15))
             class ACFsLPPlot(Plot):
                 '''
                 Plot for ACFs Double Pulse Experiment
                 '''
                 CODE = 'acfs_LP'
                 #plot_name = 'ACF'
                 plot_type = 'scatterbuffer'
                 def setup(self):
                     self.ncols = 1
                     self.nrows = 1
                     self.nplots = 1
                     self.ylabel = 'Range [km]'
                     self.xlabel = 'Lag (ms)'
                     self.titles = ['ACFs']
                     self.width = 3.5
                     self.height = 5.5
                     self.colorbar = False
                     self.plots_adjust.update({'left': 0.17, 'right': 0.88, 'bottom': 0.1})
                 def update(self, dataOut):
                     data = {}
                     meta = {}
                     aux=numpy.zeros((dataOut.NACF,dataOut.IBITS),'float32')
                     errors=numpy.zeros((dataOut.NACF,dataOut.IBITS),'float32')
                     lags_LP_to_plot=numpy.zeros((dataOut.NACF,dataOut.IBITS),'float32')
                     for i in range(dataOut.NACF):
                         for j in range(dataOut.IBITS):
                             if numpy.abs(dataOut.errors[j,i]/dataOut.output_LP_integrated.real[0,i,0])<1.0:
                                 aux[i,j]=dataOut.output_LP_integrated.real[j,i,0]/dataOut.output_LP_integrated.real[0,i,0]
                                 aux[i,j]=max(min(aux[i,j],1.0),-1.0)*dataOut.DH+dataOut.heightList[i]
                                 lags_LP_to_plot[i,j]=dataOut.lags_LP[j]
                                 errors[i,j]=dataOut.errors[j,i]/dataOut.output_LP_integrated.real[0,i,0]*dataOut.DH
                             else:
                                 aux[i,j]=numpy.nan
                                 lags_LP_to_plot[i,j]=numpy.nan
                                 errors[i,j]=numpy.nan
                     data['ACFs'] = aux
                     data['ACFs_error'] = errors
                     data['lags'] = lags_LP_to_plot
                     meta['yrange'] = numpy.array([])
                     #meta['NACF'] = dataOut.NACF
                     #meta['NLAG'] = dataOut.NLAG
                     data['NACF'] = dataOut.NACF #This is metadata
                     data['NLAG'] = dataOut.NLAG #This is metadata
                     return data, meta
                 def plot(self):
                     data = self.data[-1]
                     #NACF = self.meta['NACF']
                     #NLAG = self.meta['NLAG']
                     NACF = data['NACF'] #This is metadata
                     NLAG = data['NLAG'] #This is metadata
                     lags = data['lags']
                     ACFs = data['ACFs']
                     errACFs = data['ACFs_error']
                     self.xmin = 0.0
                     self.xmax = 1.5
                     self.y = ACFs
                     ax = self.axes[0]
                     if ax.firsttime:
                         for i in range(NACF):
                             x_aux = numpy.isfinite(lags[i,:])
                             y_aux = numpy.isfinite(ACFs[i,:])
                             yerr_aux = numpy.isfinite(errACFs[i,:])
                             if lags[i,:][~numpy.isnan(lags[i,:])].shape[0]>2:
                                 ax.errorbar(lags[i,x_aux], ACFs[i,y_aux], yerr=errACFs[i,x_aux],color='b',linewidth=1.0,markersize=2,ecolor='r')
                         #self.xstep_given = (self.xmax-self.xmin)/(self.data.NLAG-1)
                         self.xstep_given=0.3
                         self.ystep_given = 200
                         ax.yaxis.set_minor_locator(MultipleLocator(15))
                         ax.grid(which='minor')
                     else:
                         self.clear_figures()
                         for i in range(NACF):
                             x_aux = numpy.isfinite(lags[i,:])
                             y_aux = numpy.isfinite(ACFs[i,:])
                             yerr_aux = numpy.isfinite(errACFs[i,:])
                             if lags[i,:][~numpy.isnan(lags[i,:])].shape[0]>2:
                                 ax.errorbar(lags[i,x_aux], ACFs[i,y_aux], yerr=errACFs[i,x_aux],color='b',linewidth=1.0,markersize=2,ecolor='r')
                         ax.yaxis.set_minor_locator(MultipleLocator(15))
             class CrossProductsPlot(Plot):
                 '''
                 Plot for cross products
                 '''
                 CODE = 'crossprod'
                 plot_name = 'Cross Products'
                 plot_type = 'scatterbuffer'
                 def setup(self):
                     self.ncols = 3
                     self.nrows = 1
                     self.nplots = 3
                     self.ylabel = 'Range [km]'
                     self.titles = []
                     self.width = 3.5*self.nplots
                     self.height = 5.5
                     self.colorbar = False
                     self.plots_adjust.update({'wspace':.3, 'left': 0.12, 'right': 0.92, 'bottom': 0.1})
                 def update(self, dataOut):
                     data = {}
                     meta = {}
                     data['crossprod'] = dataOut.crossprods
                     data['NDP'] = dataOut.NDP
                     return data, meta
                 def plot(self):
                     NDP = self.data['NDP'][-1]
                     x = self.data['crossprod'][:,-1,:,:,:,:]
                     y = self.data.yrange[0:NDP]
                     for n, ax in enumerate(self.axes):
                         self.xmin=numpy.min(numpy.concatenate((x[n][0,20:30,0,0],x[n][1,20:30,0,0],x[n][2,20:30,0,0],x[n][3,20:30,0,0])))
                         self.xmax=numpy.max(numpy.concatenate((x[n][0,20:30,0,0],x[n][1,20:30,0,0],x[n][2,20:30,0,0],x[n][3,20:30,0,0])))
                         if ax.firsttime:
                             self.autoxticks=False
                             if n==0:
                                 label1='kax'
                                 label2='kay'
                                 label3='kbx'
                                 label4='kby'
                                 self.xlimits=[(self.xmin,self.xmax)]
                             elif n==1:
                                 label1='kax2'
                                 label2='kay2'
                                 label3='kbx2'
                                 label4='kby2'
                                 self.xlimits.append((self.xmin,self.xmax))
                             elif n==2:
                                 label1='kaxay'
                                 label2='kbxby'
                                 label3='kaxbx'
                                 label4='kaxby'
                                 self.xlimits.append((self.xmin,self.xmax))
                             ax.plotline1 = ax.plot(x[n][0,:,0,0], y, color='r',linewidth=2.0, label=label1)
                             ax.plotline2 = ax.plot(x[n][1,:,0,0], y, color='k',linewidth=2.0, label=label2)
                             ax.plotline3 = ax.plot(x[n][2,:,0,0], y, color='b',linewidth=2.0, label=label3)
                             ax.plotline4 = ax.plot(x[n][3,:,0,0], y, color='m',linewidth=2.0, label=label4)
                             ax.legend(loc='upper right')
                             ax.set_xlim(self.xmin, self.xmax)
                             self.titles.append('{}'.format(self.plot_name.upper()))
                         else:
                             if n==0:
                                 self.xlimits=[(self.xmin,self.xmax)]
                             else:
                                 self.xlimits.append((self.xmin,self.xmax))
                             ax.set_xlim(self.xmin, self.xmax)
                             ax.plotline1[0].set_data(x[n][0,:,0,0],y)
                             ax.plotline2[0].set_data(x[n][1,:,0,0],y)
                             ax.plotline3[0].set_data(x[n][2,:,0,0],y)
                             ax.plotline4[0].set_data(x[n][3,:,0,0],y)
                             self.titles.append('{}'.format(self.plot_name.upper()))
             class CrossProductsLPPlot(Plot):
                 '''
                 Plot for cross products LP
                 '''
                 CODE = 'crossprodslp'
                 plot_name = 'Cross Products LP'
                 plot_type = 'scatterbuffer'
                 def setup(self):
                     self.ncols = 2
                     self.nrows = 1
                     self.nplots = 2
                     self.ylabel = 'Range [km]'
                     self.xlabel = 'dB'
                     self.width = 3.5*self.nplots
                     self.height = 5.5
                     self.colorbar = False
                     self.titles = []
                     self.plots_adjust.update({'wspace': .8 ,'left': 0.17, 'right': 0.88, 'bottom': 0.1})
                 def update(self, dataOut):
                     data = {}
                     meta = {}
                     data['crossprodslp'] = 10*numpy.log10(numpy.abs(dataOut.output_LP))
                     data['NRANGE'] = dataOut.NRANGE #This is metadata
                     data['NLAG'] = dataOut.NLAG #This is metadata
                     return data, meta
                 def plot(self):
                     NRANGE = self.data['NRANGE'][-1]
                     NLAG = self.data['NLAG'][-1]
                     x = self.data[self.CODE][:,-1,:,:]
                     self.y = self.data.yrange[0:NRANGE]
                     label_array=numpy.array(['lag '+ str(x) for x in range(NLAG)])
                     color_array=['r','k','g','b','c','m','y','orange','steelblue','purple','peru','darksalmon','grey','limegreen','olive','midnightblue']
                     for n, ax in enumerate(self.axes):
                         self.xmin=28#30
                         self.xmax=70#70
                         #self.xmin=numpy.min(numpy.concatenate((self.x[0,:,n],self.x[1,:,n])))
                         #self.xmax=numpy.max(numpy.concatenate((self.x[0,:,n],self.x[1,:,n])))
                         if ax.firsttime:
                             self.autoxticks=False
                             if n == 0:
                                 self.plotline_array=numpy.zeros((2,NLAG),dtype=object)
                             for i in range(NLAG):
                                 self.plotline_array[n,i], = ax.plot(x[i,:,n], self.y, color=color_array[i],linewidth=1.0, label=label_array[i])
                             ax.legend(loc='upper right')
                             ax.set_xlim(self.xmin, self.xmax)
                             if n==0:
                                 self.titles.append('{} CH0'.format(self.plot_name.upper()))
                             if n==1:
                                 self.titles.append('{} CH1'.format(self.plot_name.upper()))
                         else:
                             for i in range(NLAG):
                                 self.plotline_array[n,i].set_data(x[i,:,n],self.y)
                             if n==0:
                                 self.titles.append('{} CH0'.format(self.plot_name.upper()))
                             if n==1:
                                 self.titles.append('{} CH1'.format(self.plot_name.upper()))
             class NoiseDPPlot(NoisePlot):
                 '''
                 Plot for noise Double Pulse
                 '''
                 CODE = 'noise'
                 #plot_name = 'Noise'
                 #plot_type = 'scatterbuffer'
                 def update(self, dataOut):
                     data = {}
                     meta = {}
                     data['noise'] = 10*numpy.log10(dataOut.noise_final)
                     return data, meta
             class XmitWaveformPlot(Plot):
                 '''
                 Plot for xmit waveform
                 '''
                 CODE = 'xmit'
                 plot_name = 'Xmit Waveform'
                 plot_type = 'scatterbuffer'
                 def setup(self):
                     self.ncols = 1
                     self.nrows = 1
                     self.nplots = 1
                     self.ylabel = ''
                     self.xlabel = 'Number of Lag'
                     self.width = 5.5
                     self.height = 3.5
                     self.colorbar = False
                     self.plots_adjust.update({'right': 0.85 })
                     self.titles = [self.plot_name]
                     #self.plots_adjust.update({'left': 0.17, 'right': 0.88, 'bottom': 0.1})
                     #if not self.titles:
                         #self.titles = self.data.parameters \
                             #if self.data.parameters else ['{}'.format(self.plot_name.upper())]
                 def update(self, dataOut):
                     data = {}
                     meta = {}
                     y_1=numpy.arctan2(dataOut.output_LP[:,0,2].imag,dataOut.output_LP[:,0,2].real)* 180 / (numpy.pi*10)
                     y_2=numpy.abs(dataOut.output_LP[:,0,2])
                     norm=numpy.max(y_2)
                     norm=max(norm,0.1)
                     y_2=y_2/norm
                     meta['yrange'] = numpy.array([])
                     data['xmit'] = numpy.vstack((y_1,y_2))
                     data['NLAG'] = dataOut.NLAG
                     return data, meta
                 def plot(self):
                     data = self.data[-1]
                     NLAG = data['NLAG']
                     x = numpy.arange(0,NLAG,1,'float32')
                     y = data['xmit']
                     self.xmin = 0
                     self.xmax = NLAG-1
                     self.ymin = -1.0
                     self.ymax = 1.0
                     ax = self.axes[0]
                     if ax.firsttime:
                         ax.plotline0=ax.plot(x,y[0,:],color='blue')
                         ax.plotline1=ax.plot(x,y[1,:],color='red')
                         secax=ax.secondary_xaxis(location=0.5)
                         secax.xaxis.tick_bottom()
                         secax.tick_params( labelleft=False, labeltop=False,
                                   labelright=False, labelbottom=False)
                         self.xstep_given = 3
                         self.ystep_given = .25
                         secax.set_xticks(numpy.linspace(self.xmin, self.xmax, 6)) #only works on matplotlib.version>3.2
                     else:
                         ax.plotline0[0].set_data(x,y[0,:])
                         ax.plotline1[0].set_data(x,y[1,:])

schainpy/model/io/jroIO_base.py +2 -3

             """
             Created on Jul 2, 2014
             @author: roj-idl71
             """
             import os
             import sys
             import glob
             import time
             import numpy
             import fnmatch
             import inspect
             import time
             import datetime
             import zmq
             from schainpy.model.proc.jroproc_base import Operation, MPDecorator
             from schainpy.model.data.jroheaderIO import PROCFLAG, BasicHeader, SystemHeader, RadarControllerHeader, ProcessingHeader
             from schainpy.model.data.jroheaderIO import get_dtype_index, get_numpy_dtype, get_procflag_dtype, get_dtype_width
             from schainpy.utils import log
             import schainpy.admin
             LOCALTIME = True
             DT_DIRECTIVES = {
                 '%Y': 4,
                 '%y': 2,
                 '%m': 2,
                 '%d': 2,
                 '%j': 3,
                 '%H': 2,
                 '%M': 2,
                 '%S': 2,
                 '%f': 6
             }
             def isNumber(cad):
                 """
                 Chequea si el conjunto de caracteres que componen un string puede ser convertidos a un numero.
                 Excepciones:
                     Si un determinado string no puede ser convertido a numero
                 Input:
                     str, string al cual se le analiza para determinar si convertible a un numero o no
                 Return:
                     True    :    si el string es uno numerico
                     False   :    no es un string numerico
                 """
                 try:
                     float(cad)
                     return True
                 except:
                     return False
             def isFileInEpoch(filename, startUTSeconds, endUTSeconds):
                 """
                 Esta funcion determina si un archivo de datos se encuentra o no dentro del rango de fecha especificado.
                 Inputs:
                     filename            :    nombre completo del archivo de datos en formato Jicamarca (.r)
                     startUTSeconds      :    fecha inicial del rango seleccionado. La fecha esta dada en
                                              segundos contados desde 01/01/1970.
                     endUTSeconds        :    fecha final del rango seleccionado. La fecha esta dada en
                                              segundos contados desde 01/01/1970.
                 Return:
                     Boolean    :    Retorna True si el archivo de datos contiene datos en el rango de
                                     fecha especificado, de lo contrario retorna False.
                 Excepciones:
                     Si el archivo no existe o no puede ser abierto
                     Si la cabecera no puede ser leida.
                 """
                 basicHeaderObj = BasicHeader(LOCALTIME)
                 try:
                     fp = open(filename, 'rb')
                 except IOError:
                     print("The file %s can't be opened" % (filename))
                     return 0
                 sts = basicHeaderObj.read(fp)
                 fp.close()
                 if not(sts):
                     print("Skipping the file %s because it has not a valid header" % (filename))
                     return 0
                 if not ((startUTSeconds <= basicHeaderObj.utc) and (endUTSeconds > basicHeaderObj.utc)):
                     return 0
                 return 1
             def isTimeInRange(thisTime, startTime, endTime):
                 if endTime >= startTime:
                     if (thisTime < startTime) or (thisTime > endTime):
                         return 0
                     return 1
                 else:
                     if (thisTime < startTime) and (thisTime > endTime):
                         return 0
                     return 1
             def isFileInTimeRange(filename, startDate, endDate, startTime, endTime):
                 """
                 Retorna 1 si el archivo de datos se encuentra dentro del rango de horas especificado.
                 Inputs:
                     filename            :    nombre completo del archivo de datos en formato Jicamarca (.r)
                     startDate          :    fecha inicial del rango seleccionado en formato datetime.date
                     endDate            :    fecha final del rango seleccionado en formato datetime.date
                     startTime          :    tiempo inicial del rango seleccionado en formato datetime.time
                     endTime            :    tiempo final del rango seleccionado en formato datetime.time
                 Return:
                     Boolean    :    Retorna True si el archivo de datos contiene datos en el rango de
                                     fecha especificado, de lo contrario retorna False.
                 Excepciones:
                     Si el archivo no existe o no puede ser abierto
                     Si la cabecera no puede ser leida.
                 """
                 try:
                     fp = open(filename, 'rb')
                 except IOError:
                     print("The file %s can't be opened" % (filename))
                     return None
                 firstBasicHeaderObj = BasicHeader(LOCALTIME)
                 systemHeaderObj = SystemHeader()
                 radarControllerHeaderObj = RadarControllerHeader()
                 processingHeaderObj = ProcessingHeader()
                 lastBasicHeaderObj = BasicHeader(LOCALTIME)
                 sts = firstBasicHeaderObj.read(fp)
                 if not(sts):
                     print("[Reading] Skipping the file %s because it has not a valid header" % (filename))
                     return None
                 if not systemHeaderObj.read(fp):
                     return None
                 if not radarControllerHeaderObj.read(fp):
                     return None
                 if not processingHeaderObj.read(fp):
                     return None
                 filesize = os.path.getsize(filename)
                 offset = processingHeaderObj.blockSize + 24  # header size
                 if filesize <= offset:
                     print("[Reading] %s: This file has not enough data" % filename)
                     return None
                 fp.seek(-offset, 2)
                 sts = lastBasicHeaderObj.read(fp)
                 fp.close()
                 thisDatetime = lastBasicHeaderObj.datatime
                 thisTime_last_block = thisDatetime.time()
                 thisDatetime = firstBasicHeaderObj.datatime
                 thisDate = thisDatetime.date()
                 thisTime_first_block = thisDatetime.time()
                 # General case
                 #           o>>>>>>>>>>>>>><<<<<<<<<<<<<<o
                 #-----------o----------------------------o-----------
                 #       startTime                     endTime
                 if endTime >= startTime:
                     if (thisTime_last_block < startTime) or (thisTime_first_block > endTime):
                         return None
                     return thisDatetime
                 # If endTime < startTime then endTime belongs to the next day
                 #<<<<<<<<<<<o                            o>>>>>>>>>>>
                 #-----------o----------------------------o-----------
                 #        endTime                    startTime
                 if (thisDate == startDate) and (thisTime_last_block < startTime):
                     return None
                 if (thisDate == endDate) and (thisTime_first_block > endTime):
                     return None
                 if (thisTime_last_block < startTime) and (thisTime_first_block > endTime):
                     return None
                 return thisDatetime
             def isFolderInDateRange(folder, startDate=None, endDate=None):
                 """
                 Retorna 1 si el archivo de datos se encuentra dentro del rango de horas especificado.
                 Inputs:
                     folder            :    nombre completo del directorio.
                                            Su formato deberia ser "/path_root/?YYYYDDD"
                                             siendo:
                                                 YYYY    :    Anio         (ejemplo 2015)
                                                 DDD     :    Dia del anio (ejemplo 305)
                     startDate          :    fecha inicial del rango seleccionado en formato datetime.date
                     endDate            :    fecha final del rango seleccionado en formato datetime.date
                 Return:
                     Boolean    :    Retorna True si el archivo de datos contiene datos en el rango de
                                     fecha especificado, de lo contrario retorna False.
                 Excepciones:
                     Si el directorio no tiene el formato adecuado
                 """
                 basename = os.path.basename(folder)
                 if not isRadarFolder(basename):
                     print("The folder %s has not the rigth format" % folder)
                     return 0
                 if startDate and endDate:
                     thisDate = getDateFromRadarFolder(basename)
                     if thisDate < startDate:
                         return 0
                     if thisDate > endDate:
                         return 0
                 return 1
             def isFileInDateRange(filename, startDate=None, endDate=None):
                 """
                 Retorna 1 si el archivo de datos se encuentra dentro del rango de horas especificado.
                 Inputs:
                     filename            :    nombre completo del archivo de datos en formato Jicamarca (.r)
                                            Su formato deberia ser "?YYYYDDDsss"
                                             siendo:
                                                 YYYY    :    Anio         (ejemplo 2015)
                                                 DDD     :    Dia del anio (ejemplo 305)
                                                 sss     :    set
                     startDate          :    fecha inicial del rango seleccionado en formato datetime.date
                     endDate            :    fecha final del rango seleccionado en formato datetime.date
                 Return:
                     Boolean    :    Retorna True si el archivo de datos contiene datos en el rango de
                                     fecha especificado, de lo contrario retorna False.
                 Excepciones:
                     Si el archivo no tiene el formato adecuado
                 """
                 basename = os.path.basename(filename)
                 if not isRadarFile(basename):
                     print("The filename %s has not the rigth format" % filename)
                     return 0
                 if startDate and endDate:
                     thisDate = getDateFromRadarFile(basename)
                     if thisDate < startDate:
                         return 0
                     if thisDate > endDate:
                         return 0
                 return 1
             def getFileFromSet(path, ext, set):
                 validFilelist = []
                 fileList = os.listdir(path)
                 # 0 1234 567 89A BCDE
                 # H YYYY DDD SSS .ext
                 for thisFile in fileList:
                     try:
                         year = int(thisFile[1:5])
                         doy = int(thisFile[5:8])
                     except:
                         continue
                     if (os.path.splitext(thisFile)[-1].lower() != ext.lower()):
                         continue
                     validFilelist.append(thisFile)
                 myfile = fnmatch.filter(
                     validFilelist, '*%4.4d%3.3d%3.3d*' % (year, doy, set))
                 if len(myfile) != 0:
                     return myfile[0]
                 else:
                     filename = '*%4.4d%3.3d%3.3d%s' % (year, doy, set, ext.lower())
                     print('the filename %s does not exist' % filename)
                     print('...going to the last file: ')
                 if validFilelist:
                     validFilelist = sorted(validFilelist, key=str.lower)
                     return validFilelist[-1]
                 return None
             def getlastFileFromPath(path, ext):
                 """
                 Depura el fileList dejando solo los que cumplan el formato de "PYYYYDDDSSS.ext"
                 al final de la depuracion devuelve el ultimo file de la lista que quedo.
                 Input:
                     fileList    :    lista conteniendo todos los files (sin path) que componen una determinada carpeta
                     ext         :    extension de los files contenidos en una carpeta
                 Return:
                     El ultimo file de una determinada carpeta, no se considera el path.
                 """
                 validFilelist = []
                 fileList = os.listdir(path)
                 # 0 1234 567 89A BCDE
                 # H YYYY DDD SSS .ext
                 for thisFile in fileList:
                     year = thisFile[1:5]
                     if not isNumber(year):
                         continue
                     doy = thisFile[5:8]
                     if not isNumber(doy):
                         continue
                     year = int(year)
                     doy = int(doy)
                     if (os.path.splitext(thisFile)[-1].lower() != ext.lower()):
                         continue
                     validFilelist.append(thisFile)
                 if validFilelist:
                     validFilelist = sorted(validFilelist, key=str.lower)
                     return validFilelist[-1]
                 return None
             def isRadarFolder(folder):
                 try:
                     year = int(folder[1:5])
                     doy = int(folder[5:8])
                 except:
                     return 0
                 return 1
             def isRadarFile(file):
                 try:
                     year = int(file[1:5])
                     doy = int(file[5:8])
                     set = int(file[8:11])
                 except:
                     return 0
                 return 1
             def getDateFromRadarFile(file):
                 try:
                     year = int(file[1:5])
                     doy = int(file[5:8])
                     set = int(file[8:11])
                 except:
                     return None
                 thisDate = datetime.date(year, 1, 1) + datetime.timedelta(doy - 1)
                 return thisDate
             def getDateFromRadarFolder(folder):
                 try:
                     year = int(folder[1:5])
                     doy = int(folder[5:8])
                 except:
                     return None
                 thisDate = datetime.date(year, 1, 1) + datetime.timedelta(doy - 1)
                 return thisDate
             def parse_format(s, fmt):
                 for i in range(fmt.count('%')):
                     x = fmt.index('%')
                     d = DT_DIRECTIVES[fmt[x:x+2]]
                     fmt = fmt.replace(fmt[x:x+2], s[x:x+d])
                 return fmt
             class Reader(object):
                 c = 3E8
                 isConfig = False
                 dtype = None
                 pathList = []
                 filenameList = []
                 datetimeList = []
                 filename = None
                 ext = None
                 flagIsNewFile = 1
                 flagDiscontinuousBlock = 0
                 flagIsNewBlock = 0
                 flagNoMoreFiles = 0
                 fp = None
                 firstHeaderSize = 0
                 basicHeaderSize = 24
                 versionFile = 1103
                 fileSize = None
                 fileSizeByHeader = None
                 fileIndex = -1
                 profileIndex = None
                 blockIndex = 0
                 nTotalBlocks = 0
                 maxTimeStep = 30
                 lastUTTime = None
                 datablock = None
                 dataOut = None
                 getByBlock = False
                 path = None
                 startDate = None
                 endDate = None
                 startTime = datetime.time(0, 0, 0)
                 endTime = datetime.time(23, 59, 59)
                 set = None
                 expLabel = ""
                 online = False
                 delay = 60
                 nTries = 3  # quantity tries
                 nFiles = 3  # number of files for searching
                 walk = True
                 getblock = False
                 nTxs = 1
                 realtime = False
                 blocksize = 0
                 blocktime = None
                 warnings = True
                 verbose = True
                 server = None
                 format = None
                 oneDDict = None
                 twoDDict = None
                 independentParam = None
                 filefmt = None
                 folderfmt = None
                 open_file = open
                 open_mode = 'rb'
                 def run(self):
                     raise NotImplementedError
                 def getAllowedArgs(self):
                     if hasattr(self, '__attrs__'):
                         return self.__attrs__
                     else:
                         return inspect.getargspec(self.run).args
                 def set_kwargs(self, **kwargs):
                     for key, value in kwargs.items():
                         setattr(self, key, value)
                 def find_folders(self, path, startDate, endDate, folderfmt, last=False):
                     folders = [x for f in path.split(',')
                                for x in os.listdir(f) if os.path.isdir(os.path.join(f, x))]
                     folders.sort()
                     if last:
                         folders = [folders[-1]]
                     for folder in folders:
                         try:
                             dt = datetime.datetime.strptime(parse_format(folder, folderfmt), folderfmt).date()
                             if dt >= startDate and dt <= endDate:
                                 yield os.path.join(path, folder)
                             else:
                                 log.log('Skiping folder {}'.format(folder), self.name)
                         except Exception as e:
                             log.log('Skiping folder {}'.format(folder), self.name)
                             continue
                     return
                 def find_files(self, folders, ext, filefmt, startDate=None, endDate=None,
                                expLabel='', last=False):
                     for path in folders:
-                        files = glob.glob1(path, '*{}'.format(ext))
+                        files = glob.glob1(path+'/'+expLabel, '*{}'.format(ext))
                         files.sort()
                         if last:
                             if files:
                                 fo = files[-1]
                                 try:
                                     dt = datetime.datetime.strptime(parse_format(fo, filefmt), filefmt).date()
                                     yield os.path.join(path, expLabel, fo)
                                 except Exception as e:
                                     pass
                                 return
                             else:
                                 return
                         for fo in files:
                             try:
                                 dt = datetime.datetime.strptime(parse_format(fo, filefmt), filefmt).date()
                                 #print(dt)
                                 #print(startDate)
                                 #print(endDate)
                                 if dt >= startDate and dt <= endDate:
                                     yield os.path.join(path, expLabel, fo)
                                 else:
                                     log.log('Skiping file {}'.format(fo), self.name)
                             except Exception as e:
                                 log.log('Skiping file {}'.format(fo), self.name)
                                 continue
                 def searchFilesOffLine(self, path, startDate, endDate,
                                        expLabel, ext, walk,
                                        filefmt, folderfmt):
                     """Search files in offline mode for the given arguments
                     Return:
                         Generator of files
                     """
                     if walk:
                         folders = self.find_folders(
                             path, startDate, endDate, folderfmt)
+                        #print("folders: ", folders)
                     else:
                         folders = path.split(',')
                     return self.find_files(
                         folders, ext, filefmt, startDate, endDate, expLabel)
                 def searchFilesOnLine(self, path, startDate, endDate,
                                       expLabel, ext, walk,
                                       filefmt, folderfmt):
                     """Search for the last file of the last folder
                     Arguments:
                         path        :    carpeta donde estan contenidos los files que contiene data
                         expLabel    :    Nombre del subexperimento (subfolder)
                         ext         :    extension de los files
                         walk        :    Si es habilitado no realiza busquedas dentro de los ubdirectorios (doypath)
                     Return:
                         generator with the full path of last filename
                     """
                     if walk:
                         folders = self.find_folders(
                             path, startDate, endDate, folderfmt, last=True)
                     else:
                         folders = path.split(',')
                     return self.find_files(
                         folders, ext, filefmt, startDate, endDate, expLabel, last=True)
                 def setNextFile(self):
                     """Set the next file to be readed open it and parse de file header"""
                     #print("fp: ",self.fp)
                     while True:
                         #print(self.fp)
                         if self.fp != None:
                             self.fp.close()
                             #print("setNextFile")
                             #print("BEFORE OPENING",self.filename)
                         if self.online:
                             newFile = self.setNextFileOnline()
                         else:
                             newFile = self.setNextFileOffline()
                             #print("newFile: ",newFile)
                         if not(newFile):
                             if self.online:
                                 raise schainpy.admin.SchainError('Time to wait for new files reach')
                             else:
                                 if self.fileIndex == -1:
                                     #print("OKK")
                                     raise schainpy.admin.SchainWarning('No files found in the given path')
                                 else:
                                     raise schainpy.admin.SchainWarning('No more files to read')
                         if self.verifyFile(self.filename):
                             break
                     ##print("BEFORE OPENING",self.filename)
                     log.log('Opening file: %s' % self.filename, self.name)
                     self.readFirstHeader()
                     self.nReadBlocks = 0
                 def setNextFileOnline(self):
                     """Check for the next file to be readed in online mode.
                     Set:
                         self.filename
                         self.fp
                         self.filesize
                     Return:
                         boolean
                     """
                     nextFile = True
                     nextDay = False
                     for nFiles in range(self.nFiles+1):
                         for nTries in range(self.nTries):
                             fullfilename, filename = self.checkForRealPath(nextFile, nextDay)
                             if fullfilename is not None:
                                 break
                             log.warning(
                                 "Waiting %0.2f sec for the next file: \"%s\" , try %02d ..." % (self.delay, filename, nTries + 1),
                                 self.name)
                             time.sleep(self.delay)
                             nextFile = False
                             continue
                         if fullfilename is not None:
                             break
                         #self.nTries = 1
                         nextFile = True
                         if nFiles == (self.nFiles - 1):
                             log.log('Trying with next day...', self.name)
                             nextDay = True
                             self.nTries = 3
                     if fullfilename:
                         self.fileSize = os.path.getsize(fullfilename)
                         self.filename = fullfilename
                         self.flagIsNewFile = 1
                         if self.fp != None:
                             self.fp.close()
                         #print(fullfilename)
                         self.fp = self.open_file(fullfilename, self.open_mode)
                         self.flagNoMoreFiles = 0
                         self.fileIndex += 1
                         return 1
                     else:
                         return 0
                 def setNextFileOffline(self):
                     """Open the next file to be readed in offline mode"""
                     try:
                         filename = next(self.filenameList)
                         self.fileIndex +=1
                     except StopIteration:
                         self.flagNoMoreFiles = 1
                         return 0
                     #print(self.fileIndex)
                     #print(filename)
                     self.filename = filename
                     self.fileSize = os.path.getsize(filename)
                     self.fp = self.open_file(filename, self.open_mode)
                     self.flagIsNewFile = 1
                     return 1
                 @staticmethod
                 def isDateTimeInRange(dt, startDate, endDate, startTime, endTime):
                     """Check if the given datetime is in range"""
                     if startDate <= dt.date() <= endDate:
                         if startTime <= dt.time() <= endTime:
                             return True
                     return False
                 def verifyFile(self, filename):
                     """Check for a valid file
                     Arguments:
                         filename -- full path filename
                     Return:
                         boolean
                     """
                     return True
                 def checkForRealPath(self, nextFile, nextDay):
                     """Check if the next file to be readed exists"""
                     raise NotImplementedError
                 def readFirstHeader(self):
                     """Parse the file header"""
                     pass
                 def waitDataBlock(self, pointer_location, blocksize=None):
                     """
                     """
                     currentPointer = pointer_location
                     if blocksize is None:
                         neededSize = self.processingHeaderObj.blockSize  # + self.basicHeaderSize
                     else:
                         neededSize = blocksize
                     for nTries in range(self.nTries):
                         self.fp.close()
                         self.fp = open(self.filename, 'rb')
                         self.fp.seek(currentPointer)
                         self.fileSize = os.path.getsize(self.filename)
                         currentSize = self.fileSize - currentPointer
                         if (currentSize >= neededSize):
                             return 1
                         log.warning(
                             "Waiting %0.2f seconds for the next block, try %03d ..." % (self.delay, nTries + 1),
                             self.name
                             )
                         time.sleep(self.delay)
                     return 0
             class JRODataReader(Reader):
                 utc = 0
                 nReadBlocks = 0
                 foldercounter = 0
                 firstHeaderSize = 0
                 basicHeaderSize = 24
                 __isFirstTimeOnline = 1
                 filefmt = "*%Y%j***"
                 folderfmt = "*%Y%j"
                 __attrs__ = ['path', 'startDate', 'endDate', 'startTime', 'endTime', 'online', 'delay', 'walk']
                 def getDtypeWidth(self):
                     dtype_index = get_dtype_index(self.dtype)
                     dtype_width = get_dtype_width(dtype_index)
                     return dtype_width
                 def checkForRealPath(self, nextFile, nextDay):
                     """Check if the next file to be readed exists.
                     Example    :
                         nombre correcto del file es  .../.../D2009307/P2009307367.ext
                         Entonces la funcion prueba con las siguientes combinaciones
                             .../.../y2009307367.ext
                             .../.../Y2009307367.ext
                             .../.../x2009307/y2009307367.ext
                             .../.../x2009307/Y2009307367.ext
                             .../.../X2009307/y2009307367.ext
                             .../.../X2009307/Y2009307367.ext
                         siendo para este caso, la ultima combinacion de letras, identica al file buscado
                     Return:
                         str -- fullpath of the file
                     """
                     if nextFile:
                         self.set += 1
                     if nextDay:
                         self.set = 0
                         self.doy += 1
                     foldercounter = 0
                     prefixDirList = [None, 'd', 'D']
                     if self.ext.lower() == ".r":  # voltage
                         prefixFileList = ['d', 'D']
                     elif self.ext.lower() == ".pdata":  # spectra
                         prefixFileList = ['p', 'P']
                     ##############DP##############
                     elif self.ext.lower() == ".dat":  # dat
                         prefixFileList = ['z', 'Z']
                     ##############DP##############
                     # barrido por las combinaciones posibles
                     for prefixDir in prefixDirList:
                         thispath = self.path
                         if prefixDir != None:
                             # formo el nombre del directorio xYYYYDDD (x=d o x=D)
                             if foldercounter == 0:
                                 thispath = os.path.join(self.path, "%s%04d%03d" %
                                                         (prefixDir, self.year, self.doy))
                             else:
                                 thispath = os.path.join(self.path, "%s%04d%03d_%02d" % (
                                     prefixDir, self.year, self.doy, foldercounter))
                         for prefixFile in prefixFileList:  # barrido por las dos combinaciones posibles de "D"
                             # formo el nombre del file xYYYYDDDSSS.ext
                             filename = "%s%04d%03d%03d%s" % (prefixFile, self.year, self.doy, self.set, self.ext)
                             fullfilename = os.path.join(
                                 thispath, filename)
                             if os.path.exists(fullfilename):
                                 return fullfilename, filename
                     return None, filename
                 def __waitNewBlock(self):
                     """
                     Return 1 si se encontro un nuevo bloque de datos, 0 de otra forma.
                     Si el modo de lectura es OffLine siempre retorn 0
                     """
                     if not self.online:
                         return 0
                     if (self.nReadBlocks >= self.processingHeaderObj.dataBlocksPerFile):
                         return 0
                     currentPointer = self.fp.tell()
                     neededSize = self.processingHeaderObj.blockSize + self.basicHeaderSize
                     for nTries in range(self.nTries):
                         self.fp.close()
                         self.fp = open(self.filename, 'rb')
                         self.fp.seek(currentPointer)
                         self.fileSize = os.path.getsize(self.filename)
                         currentSize = self.fileSize - currentPointer
                         if (currentSize >= neededSize):
                             self.basicHeaderObj.read(self.fp)
                             return 1
                         if self.fileSize == self.fileSizeByHeader:
                             #                self.flagEoF = True
                             return 0
                         print("[Reading] Waiting %0.2f seconds for the next block, try %03d ..." % (self.delay, nTries + 1))
                         #print(self.filename)
                         time.sleep(self.delay)
                     return 0
                 def __setNewBlock(self):
                     if self.fp == None:
                         return 0
                     if self.flagIsNewFile:
                         self.lastUTTime = self.basicHeaderObj.utc
                         return 1
                     if self.realtime:
                         self.flagDiscontinuousBlock = 1
                         if not(self.setNextFile()):
                             return 0
                         else:
                             return 1
                     currentSize = self.fileSize - self.fp.tell()
                     neededSize = self.processingHeaderObj.blockSize + self.basicHeaderSize
                     if (currentSize >= neededSize):
                         self.basicHeaderObj.read(self.fp)
                         self.lastUTTime = self.basicHeaderObj.utc
                         return 1
                     if self.__waitNewBlock():
                         self.lastUTTime = self.basicHeaderObj.utc
                         return 1
                     if not(self.setNextFile()):
                         return 0
                     deltaTime = self.basicHeaderObj.utc - self.lastUTTime
                     self.lastUTTime = self.basicHeaderObj.utc
                     self.flagDiscontinuousBlock = 0
                     if deltaTime > self.maxTimeStep:
                         self.flagDiscontinuousBlock = 1
                     return 1
                 def readNextBlock(self):
                     while True:
                         if not(self.__setNewBlock()):
                             continue
                         if not(self.readBlock()):
                             return 0
                         self.getBasicHeader()
                         if not self.isDateTimeInRange(self.dataOut.datatime, self.startDate, self.endDate, self.startTime, self.endTime):
                             print("[Reading] Block No. %d/%d -> %s [Skipping]" % (self.nReadBlocks,
                                                                                   self.processingHeaderObj.dataBlocksPerFile,
                                                                                   self.dataOut.datatime.ctime()))
                             continue
                         break
                     if self.verbose:
                         print("[Reading] Block No. %d/%d -> %s" % (self.nReadBlocks,
                                                                    self.processingHeaderObj.dataBlocksPerFile,
                                                                    self.dataOut.datatime.ctime()))
                         #################DP#################
                         self.dataOut.TimeBlockDate=self.dataOut.datatime.ctime()
                         self.dataOut.TimeBlockSeconds=time.mktime(time.strptime(self.dataOut.datatime.ctime()))
                         #################DP#################
                     return 1
                 def readFirstHeader(self):
                     self.basicHeaderObj.read(self.fp)
                     self.systemHeaderObj.read(self.fp)
                     self.radarControllerHeaderObj.read(self.fp)
                     self.processingHeaderObj.read(self.fp)
                     self.firstHeaderSize = self.basicHeaderObj.size
                     datatype = int(numpy.log2((self.processingHeaderObj.processFlags &
                                                PROCFLAG.DATATYPE_MASK)) - numpy.log2(PROCFLAG.DATATYPE_CHAR))
                     if datatype == 0:
                         datatype_str = numpy.dtype([('real', '<i1'), ('imag', '<i1')])
                     elif datatype == 1:
                         datatype_str = numpy.dtype([('real', '<i2'), ('imag', '<i2')])
                     elif datatype == 2:
                         datatype_str = numpy.dtype([('real', '<i4'), ('imag', '<i4')])
                     elif datatype == 3:
                         datatype_str = numpy.dtype([('real', '<i8'), ('imag', '<i8')])
                     elif datatype == 4:
                         datatype_str = numpy.dtype([('real', '<f4'), ('imag', '<f4')])
                     elif datatype == 5:
                         datatype_str = numpy.dtype([('real', '<f8'), ('imag', '<f8')])
                     else:
                         raise ValueError('Data type was not defined')
                     self.dtype = datatype_str
                     #self.ippSeconds = 2 * 1000 * self.radarControllerHeaderObj.ipp / self.c
                     self.fileSizeByHeader = self.processingHeaderObj.dataBlocksPerFile * self.processingHeaderObj.blockSize + \
                         self.firstHeaderSize + self.basicHeaderSize * \
                         (self.processingHeaderObj.dataBlocksPerFile - 1)
                     #        self.dataOut.channelList = numpy.arange(self.systemHeaderObj.numChannels)
                     #        self.dataOut.channelIndexList = numpy.arange(self.systemHeaderObj.numChannels)
                     self.getBlockDimension()
                 def verifyFile(self, filename):
                     flag = True
                     try:
                         fp = open(filename, 'rb')
                     except IOError:
                         log.error("File {} can't be opened".format(filename), self.name)
                         return False
                     if self.online and self.waitDataBlock(0):
                         pass
                     basicHeaderObj = BasicHeader(LOCALTIME)
                     systemHeaderObj = SystemHeader()
                     radarControllerHeaderObj = RadarControllerHeader()
                     processingHeaderObj = ProcessingHeader()
                     if not(basicHeaderObj.read(fp)):
                         flag = False
                     if not(systemHeaderObj.read(fp)):
                         flag = False
                     if not(radarControllerHeaderObj.read(fp)):
                         flag = False
                     if not(processingHeaderObj.read(fp)):
                         flag = False
                     if not self.online:
                         dt1 = basicHeaderObj.datatime
                         pos = self.fileSize-processingHeaderObj.blockSize-24
                         if pos<0:
                             flag = False
                             log.error('Invalid size for file: {}'.format(self.filename), self.name)
                         else:
                             fp.seek(pos)
                             if not(basicHeaderObj.read(fp)):
                                 flag = False
                         dt2 = basicHeaderObj.datatime
                         if not self.isDateTimeInRange(dt1, self.startDate, self.endDate, self.startTime, self.endTime) and not \
                                 self.isDateTimeInRange(dt2, self.startDate, self.endDate, self.startTime, self.endTime):
                             flag = False
                     fp.close()
                     return flag
                 def findDatafiles(self, path, startDate=None, endDate=None, expLabel='', ext='.r', walk=True, include_path=False):
                     path_empty = True
                     dateList = []
                     pathList = []
                     multi_path = path.split(',')
                     if not walk:
                         for single_path in multi_path:
                             if not os.path.isdir(single_path):
                                 continue
                             fileList = glob.glob1(single_path, "*" + ext)
                             if not fileList:
                                 continue
                             path_empty = False
                             fileList.sort()
                             for thisFile in fileList:
                                 if not os.path.isfile(os.path.join(single_path, thisFile)):
                                     continue
                                 if not isRadarFile(thisFile):
                                     continue
                                 if not isFileInDateRange(thisFile, startDate, endDate):
                                     continue
                                 thisDate = getDateFromRadarFile(thisFile)
                                 if thisDate in dateList or single_path in pathList:
                                     continue
                                 dateList.append(thisDate)
                                 pathList.append(single_path)
                     else:
                         for single_path in multi_path:
                             if not os.path.isdir(single_path):
                                 continue
                             dirList = []
                             for thisPath in os.listdir(single_path):
                                 if not os.path.isdir(os.path.join(single_path, thisPath)):
                                     continue
                                 if not isRadarFolder(thisPath):
                                     continue
                                 if not isFolderInDateRange(thisPath, startDate, endDate):
                                     continue
                                 dirList.append(thisPath)
                             if not dirList:
                                 continue
                             dirList.sort()
                             for thisDir in dirList:
                                 datapath = os.path.join(single_path, thisDir, expLabel)
                                 fileList = glob.glob1(datapath, "*" + ext)
                                 if not fileList:
                                     continue
                                 path_empty = False
                                 thisDate = getDateFromRadarFolder(thisDir)
                                 pathList.append(datapath)
                                 dateList.append(thisDate)
                     dateList.sort()
                     if walk:
                         pattern_path = os.path.join(multi_path[0], "[dYYYYDDD]", expLabel)
                     else:
                         pattern_path = multi_path[0]
                     if path_empty:
                         raise schainpy.admin.SchainError("[Reading] No *%s files in %s for %s to %s" % (ext, pattern_path, startDate, endDate))
                     else:
                         if not dateList:
                             raise schainpy.admin.SchainError("[Reading] Date range selected invalid [%s - %s]: No *%s files in %s)" % (startDate, endDate, ext, path))
                     if include_path:
                         return dateList, pathList
                     return dateList
                 def setup(self, **kwargs):
                     self.set_kwargs(**kwargs)
                     if not self.ext.startswith('.'):
                         self.ext = '.{}'.format(self.ext)
                     if self.server is not None:
                         if 'tcp://' in self.server:
                             address = server
                         else:
                             address = 'ipc:///tmp/%s' % self.server
                         self.server = address
                         self.context = zmq.Context()
                         self.receiver = self.context.socket(zmq.PULL)
                         self.receiver.connect(self.server)
                         time.sleep(0.5)
                         print('[Starting] ReceiverData from {}'.format(self.server))
                     else:
                         self.server = None
                         if self.path == None:
                             raise ValueError("[Reading] The path is not valid")
                         if self.online:
                             log.log("[Reading] Searching files in online mode...", self.name)
                             for nTries in range(self.nTries):
                                 fullpath = self.searchFilesOnLine(self.path, self.startDate,
                                     self.endDate, self.expLabel, self.ext, self.walk,
                                     self.filefmt, self.folderfmt)
                                 try:
                                     fullpath = next(fullpath)
                                 except:
                                     fullpath = None
                                 if fullpath:
                                     break
                                 log.warning(
                                     'Waiting {} sec for a valid file in {}: try {} ...'.format(
                                         self.delay, self.path, nTries + 1),
                                     self.name)
                                 time.sleep(self.delay)
                             if not(fullpath):
                                 raise schainpy.admin.SchainError(
                                     'There isn\'t any valid file in {}'.format(self.path))
                             pathname, filename = os.path.split(fullpath)
                             self.year = int(filename[1:5])
                             self.doy = int(filename[5:8])
                             self.set = int(filename[8:11]) - 1
                         else:
                             log.log("Searching files in {}".format(self.path), self.name)
                             self.filenameList = self.searchFilesOffLine(self.path, self.startDate,
                                 self.endDate, self.expLabel, self.ext, self.walk, self.filefmt, self.folderfmt)
                         self.setNextFile()
                     return
                 def getBasicHeader(self):
                     self.dataOut.utctime = self.basicHeaderObj.utc + self.basicHeaderObj.miliSecond / \
 . + self.profileIndex * self.radarControllerHeaderObj.ippSeconds
                     self.dataOut.flagDiscontinuousBlock = self.flagDiscontinuousBlock
                     self.dataOut.timeZone = self.basicHeaderObj.timeZone
                     self.dataOut.dstFlag = self.basicHeaderObj.dstFlag
                     self.dataOut.errorCount = self.basicHeaderObj.errorCount
                     self.dataOut.useLocalTime = self.basicHeaderObj.useLocalTime
                     self.dataOut.ippSeconds = self.radarControllerHeaderObj.ippSeconds / self.nTxs
                 def getFirstHeader(self):
                     raise NotImplementedError
                 def getData(self):
                     raise NotImplementedError
                 def hasNotDataInBuffer(self):
                     raise NotImplementedError
                 def readBlock(self):
                     raise NotImplementedError
                 def isEndProcess(self):
                     return self.flagNoMoreFiles
                 def printReadBlocks(self):
                     print("[Reading] Number of read blocks per file %04d" % self.nReadBlocks)
                 def printTotalBlocks(self):
                     print("[Reading] Number of read blocks %04d" % self.nTotalBlocks)
                 def run(self, **kwargs):
                     """
                     Arguments:
                         path        :
                         startDate   :
                         endDate     :
                         startTime   :
                         endTime     :
                         set         :
                         expLabel    :
                         ext         :
                         online      :
                         delay       :
                         walk        :
                         getblock    :
                         nTxs        :
                         realtime    :
                         blocksize   :
                         blocktime   :
                         skip        :
                         cursor      :
                         warnings    :
                         server      :
                         verbose     :
                         format      :
                         oneDDict    :
                         twoDDict    :
                         independentParam    :
                     """
                     if not(self.isConfig):
                         self.setup(**kwargs)
                         self.isConfig = True
                     if self.server is None:
                         self.getData()
                     else:
                         self.getFromServer()
             class JRODataWriter(Reader):
                 """
                 Esta clase permite escribir datos a archivos procesados (.r o ,pdata). La escritura
                 de los datos siempre se realiza por bloques.
                 """
                 setFile = None
                 profilesPerBlock = None
                 blocksPerFile = None
                 nWriteBlocks = 0
                 fileDate = None
                 def __init__(self, dataOut=None):
                     raise NotImplementedError
                 def hasAllDataInBuffer(self):
                     raise NotImplementedError
                 def setBlockDimension(self):
                     raise NotImplementedError
                 def writeBlock(self):
                     raise NotImplementedError
                 def putData(self):
                     raise NotImplementedError
                 def getDtypeWidth(self):
                     dtype_index = get_dtype_index(self.dtype)
                     dtype_width = get_dtype_width(dtype_index)
                     return dtype_width
                 def getProcessFlags(self):
                     processFlags = 0
                     dtype_index = get_dtype_index(self.dtype)
                     procflag_dtype = get_procflag_dtype(dtype_index)
                     processFlags += procflag_dtype
                     if self.dataOut.flagDecodeData:
                         processFlags += PROCFLAG.DECODE_DATA
                     if self.dataOut.flagDeflipData:
                         processFlags += PROCFLAG.DEFLIP_DATA
                     if self.dataOut.code is not None:
                         processFlags += PROCFLAG.DEFINE_PROCESS_CODE
                     if self.dataOut.nCohInt > 1:
                         processFlags += PROCFLAG.COHERENT_INTEGRATION
                     if self.dataOut.type == "Spectra":
                         if self.dataOut.nIncohInt > 1:
                             processFlags += PROCFLAG.INCOHERENT_INTEGRATION
                         if self.dataOut.data_dc is not None:
                             processFlags += PROCFLAG.SAVE_CHANNELS_DC
                         if self.dataOut.flagShiftFFT:
                             processFlags += PROCFLAG.SHIFT_FFT_DATA
                     return processFlags
                 def setBasicHeader(self):
                     self.basicHeaderObj.size = self.basicHeaderSize  # bytes
                     self.basicHeaderObj.version = self.versionFile
                     self.basicHeaderObj.dataBlock = self.nTotalBlocks
                     utc = numpy.floor(self.dataOut.utctime)
                     milisecond = (self.dataOut.utctime - utc) * 1000.0
                     self.basicHeaderObj.utc = utc
                     self.basicHeaderObj.miliSecond = milisecond
                     self.basicHeaderObj.timeZone = self.dataOut.timeZone
                     self.basicHeaderObj.dstFlag = self.dataOut.dstFlag
                     self.basicHeaderObj.errorCount = self.dataOut.errorCount
                 def setFirstHeader(self):
                     """
                     Obtiene una copia del First Header
                     Affected:
                         self.basicHeaderObj
                         self.systemHeaderObj
                         self.radarControllerHeaderObj
                         self.processingHeaderObj self.
                     Return:
                         None
                     """
                     raise NotImplementedError
                 def __writeFirstHeader(self):
                     """
                     Escribe el primer header del file es decir el Basic header y el Long header (SystemHeader, RadarControllerHeader, ProcessingHeader)
                     Affected:
                         __dataType
                     Return:
                         None
                     """
             #        CALCULAR PARAMETROS
                     sizeLongHeader = self.systemHeaderObj.size + \
                         self.radarControllerHeaderObj.size + self.processingHeaderObj.size
                     self.basicHeaderObj.size = self.basicHeaderSize + sizeLongHeader
                     self.basicHeaderObj.write(self.fp)
                     self.systemHeaderObj.write(self.fp)
                     self.radarControllerHeaderObj.write(self.fp)
                     self.processingHeaderObj.write(self.fp)
                 def __setNewBlock(self):
                     """
                     Si es un nuevo file escribe el First Header caso contrario escribe solo el Basic Header
                     Return:
 :    si no pudo escribir nada
 :    Si escribio el Basic el First Header
                     """
                     if self.fp == None:
                         self.setNextFile()
                     if self.flagIsNewFile:
                         return 1
                     if self.blockIndex < self.processingHeaderObj.dataBlocksPerFile:
                         self.basicHeaderObj.write(self.fp)
                         return 1
                     if not(self.setNextFile()):
                         return 0
                     return 1
                 def writeNextBlock(self):
                     """
                     Selecciona el bloque siguiente de datos y los escribe en un file
                     Return:
 :    Si no hizo pudo escribir el bloque de datos
 :    Si no pudo escribir el bloque de datos
                     """
                     if not(self.__setNewBlock()):
                         return 0
                     self.writeBlock()
                     print("[Writing] Block No. %d/%d" % (self.blockIndex,
                                                          self.processingHeaderObj.dataBlocksPerFile))
                     return 1
                 def setNextFile(self):
                     """Determina el siguiente file que sera escrito
                     Affected:
                         self.filename
                         self.subfolder
                         self.fp
                         self.setFile
                         self.flagIsNewFile
                     Return:
 :    Si el archivo no puede ser escrito
 :    Si el archivo esta listo para ser escrito
                     """
                     ext = self.ext
                     path = self.path
                     if self.fp != None:
                         self.fp.close()
                     if not os.path.exists(path):
                         os.mkdir(path)
                     timeTuple = time.localtime(self.dataOut.utctime)
                     subfolder = 'd%4.4d%3.3d' % (timeTuple.tm_year, timeTuple.tm_yday)
                     fullpath = os.path.join(path, subfolder)
                     setFile = self.setFile
                     if not(os.path.exists(fullpath)):
                         os.mkdir(fullpath)
                         setFile = -1  # inicializo mi contador de seteo
                     else:
                         filesList = os.listdir(fullpath)
                         if len(filesList) > 0:
                             filesList = sorted(filesList, key=str.lower)
                             filen = filesList[-1]
                             # el filename debera tener el siguiente formato
                             # 0 1234 567 89A BCDE (hex)
                             # x YYYY DDD SSS .ext
                             if isNumber(filen[8:11]):
                                 # inicializo mi contador de seteo al seteo del ultimo file
                                 setFile = int(filen[8:11])
                             else:
                                 setFile = -1
                         else:
                             setFile = -1  # inicializo mi contador de seteo
                     setFile += 1
                     # If this is a new day it resets some values
                     if self.dataOut.datatime.date() > self.fileDate:
                         setFile = 0
                         self.nTotalBlocks = 0
                     filen = '{}{:04d}{:03d}{:03d}{}'.format(
                             self.optchar, timeTuple.tm_year, timeTuple.tm_yday, setFile, ext)
                     filename = os.path.join(path, subfolder, filen)
                     fp = open(filename, 'wb')
                     self.blockIndex = 0
                     self.filename = filename
                     self.subfolder = subfolder
                     self.fp = fp
                     self.setFile = setFile
                     self.flagIsNewFile = 1
                     self.fileDate = self.dataOut.datatime.date()
                     self.setFirstHeader()
                     print('[Writing] Opening file: %s' % self.filename)
                     self.__writeFirstHeader()
                     return 1
                 def setup(self, dataOut, path, blocksPerFile, profilesPerBlock=64, set=None, ext=None, datatype=4):
                     """
                     Setea el tipo de formato en la cual sera guardada la data y escribe el First Header
                     Inputs:
                         path                :    directory where data will be saved
                         profilesPerBlock    :    number of profiles per block
                         set                 :    initial file set
                         datatype            :    An integer number that defines data type:
 : int8  (1 byte)
 : int16 (2 bytes)
 : int32 (4 bytes)
 : int64 (8 bytes)
 : float32 (4 bytes)
 : double64 (8 bytes)
                     Return:
 :    Si no realizo un buen seteo
 :    Si realizo un buen seteo
                     """
                     if ext == None:
                         ext = self.ext
                     self.ext = ext.lower()
                     self.path = path
                     if set is None:
                         self.setFile = -1
                     else:
                         self.setFile = set - 1
                     self.blocksPerFile = blocksPerFile
                     self.profilesPerBlock = profilesPerBlock
                     self.dataOut = dataOut
                     self.fileDate = self.dataOut.datatime.date()
                     self.dtype = self.dataOut.dtype
                     if datatype is not None:
                         self.dtype = get_numpy_dtype(datatype)
                     if not(self.setNextFile()):
                         print("[Writing] There isn't a next file")
                         return 0
                     self.setBlockDimension()
                     return 1
                 def run(self, dataOut, path, blocksPerFile=100, profilesPerBlock=64, set=None, ext=None, datatype=4, **kwargs):
                     if not(self.isConfig):
                         self.setup(dataOut, path, blocksPerFile, profilesPerBlock=profilesPerBlock,
                                    set=set, ext=ext, datatype=datatype, **kwargs)
                         self.isConfig = True
                     self.dataOut = dataOut
                     self.putData()
                     return self.dataOut
             @MPDecorator
             class printInfo(Operation):
                 def __init__(self):
                     Operation.__init__(self)
                     self.__printInfo = True
                 def run(self, dataOut, headers = ['systemHeaderObj', 'radarControllerHeaderObj', 'processingHeaderObj']):
                     if self.__printInfo == False:
                         return
                     for header in headers:
                         if hasattr(dataOut, header):
                             obj = getattr(dataOut, header)
                             if hasattr(obj, 'printInfo'):
                                 obj.printInfo()
                             else:
                                 print(obj)
                         else:
                             log.warning('Header {} Not found in object'.format(header))
                     self.__printInfo = False

schainpy/model/io/jroIO_madrigal.py +19 -1

             '''
             Created on Aug 1, 2017
             @author: Juan C. Espinoza
             '''
             import os
             import sys
             import time
             import json
             import glob
             import datetime
             import numpy
             import h5py
             import schainpy.admin
             from schainpy.model.io.jroIO_base import LOCALTIME, Reader
             from schainpy.model.proc.jroproc_base import ProcessingUnit, Operation, MPDecorator
             from schainpy.model.data.jrodata import Parameters
             from schainpy.utils import log
             try:
                 import madrigal.cedar
             except:
                 pass
             try:
                 basestring
             except:
                 basestring = str
             DEF_CATALOG = {
                 'principleInvestigator': 'Marco Milla',
                 'expPurpose': '',
                 'cycleTime': '',
                 'correlativeExp': '',
                 'sciRemarks': '',
                 'instRemarks': ''
                 }
             DEF_HEADER = {
                 'kindatDesc': '',
                 'analyst': 'Jicamarca User',
                 'comments': '',
                 'history': ''
                 }
             MNEMONICS = {
 : 'jro',
 : 'jbr',
 : 'jul',
 : 'jas',
 : 'pbr',
 : 'hbr',
 : 'obr',
 : 'clr'
             }
             UT1970 = datetime.datetime(1970, 1, 1) - datetime.timedelta(seconds=time.timezone)
             def load_json(obj):
                 '''
                 Parse json as string instead of unicode
                 '''
                 if isinstance(obj, str):
                     iterable = json.loads(obj)
                 else:
                     iterable = obj
                 if isinstance(iterable, dict):
                     return {str(k): load_json(v) if isinstance(v, dict) else str(v) if isinstance(v, basestring) else v
                         for k, v in list(iterable.items())}
                 elif isinstance(iterable, (list, tuple)):
                     return [str(v) if isinstance(v, basestring) else v for v in iterable]
                 return iterable
             class MADReader(Reader, ProcessingUnit):
                 def __init__(self):
                     ProcessingUnit.__init__(self)
                     self.dataOut = Parameters()
                     self.counter_records = 0
                     self.nrecords = None
                     self.flagNoMoreFiles = 0
                     self.filename = None
                     self.intervals = set()
                     self.datatime = datetime.datetime(1900,1,1)
                     self.format = None
                     self.filefmt = "***%Y%m%d*******"
                 def setup(self, **kwargs):
                     self.set_kwargs(**kwargs)
                     self.oneDDict = load_json(self.oneDDict)
                     self.twoDDict = load_json(self.twoDDict)
                     self.ind2DList = load_json(self.ind2DList)
                     self.independentParam = self.ind2DList[0]
                     if self.path is None:
                         raise ValueError('The path is not valid')
                     self.open_file = open
                     self.open_mode = 'rb'
                     if self.format is None:
                         raise ValueError('The format is not valid choose simple or hdf5')
                     elif self.format.lower() in ('simple', 'txt'):
                         self.ext = '.txt'
                     elif self.format.lower() in ('cedar',):
                         self.ext = '.001'
                     else:
                         self.ext = '.hdf5'
                         self.open_file = h5py.File
                         self.open_mode = 'r'
                     if self.online:
                         log.log("Searching files in online mode...", self.name)
                         for nTries in range(self.nTries):
                             fullpath = self.searchFilesOnLine(self.path, self.startDate,
                                 self.endDate, self.expLabel, self.ext, self.walk,
                                 self.filefmt, self.folderfmt)
                             try:
                                 fullpath = next(fullpath)
                             except:
                                 fullpath = None
                             if fullpath:
                                 break
                             log.warning(
                                 'Waiting {} sec for a valid file in {}: try {} ...'.format(
                                     self.delay, self.path, nTries + 1),
                                 self.name)
                             time.sleep(self.delay)
                         if not(fullpath):
                             raise schainpy.admin.SchainError(
                                 'There isn\'t any valid file in {}'.format(self.path))
                     else:
                         log.log("Searching files in {}".format(self.path), self.name)
                         self.filenameList = self.searchFilesOffLine(self.path, self.startDate,
                             self.endDate, self.expLabel, self.ext, self.walk, self.filefmt, self.folderfmt)
                     self.setNextFile()
                 def readFirstHeader(self):
                     '''Read header and data'''
                     self.parseHeader()
                     self.parseData()
                     self.blockIndex = 0
                     return
                 def parseHeader(self):
                     '''
                     '''
                     self.output = {}
                     self.version = '2'
                     s_parameters = None
                     if self.ext == '.txt':
                         self.parameters = [s.strip().lower() for s in self.fp.readline().decode().strip().split(' ') if s]
                     elif self.ext == '.hdf5':
                         self.metadata = self.fp['Metadata']
                         if '_record_layout' in self.metadata:
                             s_parameters = [s[0].lower().decode() for s in self.metadata['Independent Spatial Parameters']]
                             self.version = '3'
                         self.parameters = [s[0].lower().decode() for s in self.metadata['Data Parameters']]
                     log.success('Parameters found: {}'.format(self.parameters),
                                 'MADReader')
                     if s_parameters:
                         log.success('Spatial parameters found: {}'.format(s_parameters),
                                     'MADReader')
                     for param in list(self.oneDDict.keys()):
                         if param.lower() not in self.parameters:
                             log.warning(
                                 'Parameter {} not found will be ignored'.format(
                                     param),
                                 'MADReader')
                             self.oneDDict.pop(param, None)
                     for param, value in list(self.twoDDict.items()):
                         if param.lower() not in self.parameters:
                             log.warning(
                                 'Parameter {} not found, it will be ignored'.format(
                                     param),
                                 'MADReader')
                             self.twoDDict.pop(param, None)
                             continue
                         if isinstance(value, list):
                             if value[0] not in self.output:
                                 self.output[value[0]] = []
                             self.output[value[0]].append([])
                 def parseData(self):
                     '''
                     '''
                     if self.ext == '.txt':
                         self.data = numpy.genfromtxt(self.fp, missing_values=('missing'))
                         self.nrecords = self.data.shape[0]
                         self.ranges = numpy.unique(self.data[:,self.parameters.index(self.independentParam.lower())])
                         self.counter_records = 0
                     elif self.ext == '.hdf5':
                         self.data = self.fp['Data']
                         self.ranges = numpy.unique(self.data['Table Layout'][self.independentParam.lower()])
                         self.times = numpy.unique(self.data['Table Layout']['ut1_unix'])
                         self.counter_records = int(self.data['Table Layout']['recno'][0])
                         self.nrecords = int(self.data['Table Layout']['recno'][-1])
                 def readNextBlock(self):
                     while True:
                         self.flagDiscontinuousBlock = 0
                         if self.counter_records == self.nrecords:
                             self.setNextFile()
                         self.readBlock()
                         if (self.datatime < datetime.datetime.combine(self.startDate, self.startTime)) or \
                            (self.datatime > datetime.datetime.combine(self.endDate, self.endTime)):
                             log.warning(
                                 'Reading Record No. {}/{} -> {} [Skipping]'.format(
                                     self.counter_records,
                                     self.nrecords,
                                     self.datatime.ctime()),
                                 'MADReader')
                             continue
                         break
                     log.log(
                         'Reading Record No. {}/{} -> {}'.format(
                             self.counter_records,
                             self.nrecords,
                             self.datatime.ctime()),
                         'MADReader')
                     return 1
                 def readBlock(self):
                     '''
                     '''
                     dum = []
                     if self.ext == '.txt':
                         dt = self.data[self.counter_records][:6].astype(int)
                         if datetime.datetime(dt[0], dt[1], dt[2], dt[3], dt[4], dt[5]).date() > self.datatime.date():
                             self.flagDiscontinuousBlock = 1
                         self.datatime = datetime.datetime(dt[0], dt[1], dt[2], dt[3], dt[4], dt[5])
                         while True:
                             dt = self.data[self.counter_records][:6].astype(int)
                             datatime = datetime.datetime(dt[0], dt[1], dt[2], dt[3], dt[4], dt[5])
                             if datatime == self.datatime:
                                 dum.append(self.data[self.counter_records])
                                 self.counter_records += 1
                                 if self.counter_records == self.nrecords:
                                     break
                                 continue
                             self.intervals.add((datatime-self.datatime).seconds)
                             break
                     elif self.ext == '.hdf5':
                         datatime = datetime.datetime.utcfromtimestamp(
                             self.times[self.counter_records])
                         dum = self.data['Table Layout'][self.data['Table Layout']['recno']==self.counter_records]
                         self.intervals.add((datatime-self.datatime).seconds)
                         if datatime.date()>self.datatime.date():
                             self.flagDiscontinuousBlock = 1
                         self.datatime = datatime
                         self.counter_records += 1
                     self.buffer = numpy.array(dum)
                     return
                 def set_output(self):
                     '''
                     Storing data from buffer to dataOut object
                     '''
                     parameters = [None for __ in self.parameters]
                     for param, attr in list(self.oneDDict.items()):
                         x = self.parameters.index(param.lower())
                         setattr(self.dataOut, attr, self.buffer[0][x])
                     for param, value in list(self.twoDDict.items()):
                         dummy = numpy.zeros(self.ranges.shape) + numpy.nan
                         if self.ext == '.txt':
                             x = self.parameters.index(param.lower())
                             y = self.parameters.index(self.independentParam.lower())
                             ranges = self.buffer[:,y]
                             #if self.ranges.size == ranges.size:
                             #    continue
                             index = numpy.where(numpy.in1d(self.ranges, ranges))[0]
                             dummy[index] = self.buffer[:,x]
                         else:
                             ranges = self.buffer[self.independentParam.lower()]
                             index = numpy.where(numpy.in1d(self.ranges, ranges))[0]
                             dummy[index] = self.buffer[param.lower()]
                         if isinstance(value, str):
                             if value not in self.independentParam:
                                 setattr(self.dataOut, value, dummy.reshape(1,-1))
                         elif isinstance(value, list):
                             self.output[value[0]][value[1]] = dummy
                             parameters[value[1]] = param
                     for key, value in list(self.output.items()):
                         setattr(self.dataOut, key, numpy.array(value))
                     self.dataOut.parameters = [s for s in parameters if s]
                     self.dataOut.heightList = self.ranges
                     self.dataOut.utctime = (self.datatime - datetime.datetime(1970, 1, 1)).total_seconds()
                     self.dataOut.utctimeInit = self.dataOut.utctime
                     self.dataOut.paramInterval = min(self.intervals)
                     self.dataOut.useLocalTime = False
                     self.dataOut.flagNoData = False
                     self.dataOut.nrecords = self.nrecords
                     self.dataOut.flagDiscontinuousBlock = self.flagDiscontinuousBlock
                 def getData(self):
                     '''
                     Storing data from databuffer to dataOut object
                     '''
                     if not  self.readNextBlock():
                         self.dataOut.flagNoData = True
                         return 0
                     self.set_output()
                     return 1
                 def run(self, **kwargs):
                     if not(self.isConfig):
                         self.setup(**kwargs)
                         self.isConfig = True
                     self.getData()
                     return
             @MPDecorator
             class MADWriter(Operation):
                 '''Writing module for Madrigal files
             type: external
             Inputs:
                         path        path where files will be created
                         oneDDict    json of one-dimensional parameters in record where keys
                                     are Madrigal codes (integers or mnemonics) and values the corresponding
                                     dataOut attribute e.g: {
                                         'gdlatr': 'lat',
                                         'gdlonr': 'lon',
                                         'gdlat2':'lat',
                                         'glon2':'lon'}
                         ind2DList   list of independent spatial two-dimensional parameters e.g:
                                     ['heigthList']
                         twoDDict    json of two-dimensional parameters in record where keys
                                     are Madrigal codes (integers or mnemonics) and values the corresponding
                                     dataOut attribute if multidimensional array specify as tupple
                                     ('attr', pos) e.g: {
                                         'gdalt': 'heightList',
                                         'vn1p2': ('data_output', 0),
                                         'vn2p2': ('data_output', 1),
                                         'vn3': ('data_output', 2),
                                         'snl': ('data_SNR', 'db')
                                         }
                         metadata    json of madrigal metadata (kinst, kindat, catalog and header)
                         format      hdf5, cedar
                         blocks      number of blocks per file'''
                 __attrs__ = ['path', 'oneDDict', 'ind2DList', 'twoDDict','metadata', 'format', 'blocks']
                 missing = -32767
+                currentDay = None
                 def __init__(self):
                     Operation.__init__(self)
                     self.dataOut = Parameters()
                     self.counter = 0
                     self.path = None
                     self.fp = None
                 def run(self, dataOut, path, oneDDict, ind2DList='[]', twoDDict='{}',
                         metadata='{}', format='cedar', **kwargs):
                     #if dataOut.AUX==1: #Modified
                     if not self.isConfig:
                         self.setup(path, oneDDict, ind2DList, twoDDict, metadata, format, **kwargs)
                         self.isConfig = True
                     self.dataOut = dataOut
                     self.putData()
                     return 1
                 def setup(self, path, oneDDict, ind2DList, twoDDict, metadata, format, **kwargs):
                     '''
                     Configure Operation
                     '''
                     self.path = path
                     self.blocks = kwargs.get('blocks', None)
                     self.counter = 0
                     self.oneDDict = load_json(oneDDict)
                     self.twoDDict = load_json(twoDDict)
                     self.ind2DList = load_json(ind2DList)
                     meta = load_json(metadata)
                     self.kinst = meta.get('kinst')
                     self.kindat = meta.get('kindat')
                     self.catalog = meta.get('catalog', DEF_CATALOG)
                     self.header = meta.get('header', DEF_HEADER)
                     if format == 'cedar':
                         self.ext = '.dat'
                         self.extra_args = {}
                     elif format == 'hdf5':
                         self.ext = '.hdf5'
                         self.extra_args = {'ind2DList': self.ind2DList}
                     self.keys = [k.lower() for k in self.twoDDict]
                     if 'range' in self.keys:
                         self.keys.remove('range')
                     if 'gdalt' in self.keys:
                         self.keys.remove('gdalt')
                 def setFile(self):
                     '''
                     Create new cedar file object
                     '''
                     self.mnemonic = MNEMONICS[self.kinst]   #TODO get mnemonic from madrigal
                     date = datetime.datetime.utcfromtimestamp(self.dataOut.utctime)
                     #if self.dataOut.input_dat_type:
                         #date=datetime.datetime.fromtimestamp(self.dataOut.TimeBlockSeconds_for_dp_power)
                     #print("date",date)
                     filename = '{}{}{}'.format(self.mnemonic,
                                                date.strftime('%Y%m%d_%H%M%S'),
                                                self.ext)
                     self.fullname = os.path.join(self.path, filename)
                     if os.path.isfile(self.fullname) :
                         log.warning(
                             'Destination file {} already exists, previous file deleted.'.format(
                                 self.fullname),
                             'MADWriter')
                         os.remove(self.fullname)
                     try:
                         log.success(
                             'Creating file: {}'.format(self.fullname),
                             'MADWriter')
                         if not os.path.exists(self.path):
                             os.makedirs(self.path)
                         self.fp = madrigal.cedar.MadrigalCedarFile(self.fullname, True)
                     except ValueError as e:
                         log.error(
                             'Impossible to create a cedar object with "madrigal.cedar.MadrigalCedarFile"',
                             'MADWriter')
                         return
                     return 1
                 def writeBlock(self):
                     '''
                     Add data records to cedar file taking data from oneDDict and twoDDict
                     attributes.
                     Allowed parameters in: parcodes.tab
                     '''
                     #self.dataOut.paramInterval=2
                     startTime = datetime.datetime.utcfromtimestamp(self.dataOut.utctime)
                     endTime = startTime + datetime.timedelta(seconds=self.dataOut.paramInterval)
                     #if self.dataOut.input_dat_type:
                     #if self.dataOut.experiment=="DP":
                         #startTime=datetime.datetime.fromtimestamp(self.dataOut.TimeBlockSeconds_for_dp_power)
                         #endTime = startTime + datetime.timedelta(seconds=self.dataOut.paramInterval)
                     #print("2: ",startTime)
                     #print(endTime)
                     heights = self.dataOut.heightList
                     #print(heights)
                     #exit(1)
                     #print(self.blocks)
                     #print(startTime)
                     #print(endTime)
                     #print(heights)
                     #input()
                     if self.ext == '.dat':
                         for key, value in list(self.twoDDict.items()):
                             if isinstance(value, str):
                                 data = getattr(self.dataOut, value)
                                 invalid = numpy.isnan(data)
                                 data[invalid] = self.missing
                             elif isinstance(value, (tuple, list)):
                                 attr, key = value
                                 data = getattr(self.dataOut, attr)
                                 invalid = numpy.isnan(data)
                                 data[invalid] = self.missing
                     out = {}
                     for key, value in list(self.twoDDict.items()):
                         key = key.lower()
                         if isinstance(value, str):
                             if 'db' in value.lower():
                                 tmp = getattr(self.dataOut, value.replace('_db', ''))
                                 SNRavg = numpy.average(tmp, axis=0)
                                 tmp = 10*numpy.log10(SNRavg)
                             else:
                                 tmp = getattr(self.dataOut, value)
                             out[key] = tmp.flatten()[:len(heights)]
                         elif isinstance(value, (tuple, list)):
                             attr, x = value
                             data = getattr(self.dataOut, attr)
                             #print(x)
                             #print(len(heights))
                             #print(data[int(x)][:len(heights)])
                             #print(numpy.shape(out))
                             #print(numpy.shape(data))
                             out[key] = data[int(x)][:len(heights)]
                     a = numpy.array([out[k] for k in self.keys])
                     #print(a)
                     nrows = numpy.array([numpy.isnan(a[:, x]).all() for x in range(len(heights))])
                     index = numpy.where(nrows == False)[0]
                     #print(startTime.minute)
                     rec = madrigal.cedar.MadrigalDataRecord(
                         self.kinst,
                         self.kindat,
                         startTime.year,
                         startTime.month,
                         startTime.day,
                         startTime.hour,
                         startTime.minute,
                         startTime.second,
                         startTime.microsecond/10000,
                         endTime.year,
                         endTime.month,
                         endTime.day,
                         endTime.hour,
                         endTime.minute,
                         endTime.second,
                         endTime.microsecond/10000,
                         list(self.oneDDict.keys()),
                         list(self.twoDDict.keys()),
                         len(index),
                         **self.extra_args
                     )
                     #print("rec",rec)
                     # Setting 1d values
                     for key in self.oneDDict:
                         rec.set1D(key, getattr(self.dataOut, self.oneDDict[key]))
                     # Setting 2d values
                     nrec = 0
                     for n in index:
                         for key in out:
                             rec.set2D(key, nrec, out[key][n])
                         nrec += 1
                     self.fp.append(rec)
                     if self.ext == '.hdf5' and self.counter %2 == 0 and self.counter > 0:
                         #print("here")
                         self.fp.dump()
                     if self.counter % 20 == 0 and self.counter > 0:
                         #self.fp.write()
                         log.log(
                             'Writing {} records'.format(
                                 self.counter),
                             'MADWriter')
                 def setHeader(self):
                     '''
                     Create an add catalog and header to cedar file
                     '''
                     log.success('Closing file {}'.format(self.fullname), 'MADWriter')
                     if self.ext == '.dat':
                         self.fp.write()
                     else:
                         self.fp.dump()
                         self.fp.close()
                     header = madrigal.cedar.CatalogHeaderCreator(self.fullname)
                     header.createCatalog(**self.catalog)
                     header.createHeader(**self.header)
                     header.write()
+                def timeFlag(self):
+                    currentTime = self.dataOut.utctime
+                    timeTuple = time.localtime(currentTime)
+                    dataDay = timeTuple.tm_yday
+                    if self.currentDay is None:
+                        self.currentDay = dataDay
+                        return False
+                    #Si el dia es diferente
+                    if dataDay != self.currentDay:
+                        self.currentDay = dataDay
+                        return True
+                    else:
+                        return False
                 def putData(self):
                     if self.dataOut.flagNoData:
                         return 0
-                    if self.dataOut.flagDiscontinuousBlock or self.counter == self.blocks:
+                    if self.dataOut.flagDiscontinuousBlock or self.counter == self.blocks or self.timeFlag():
                         if self.counter > 0:
                             self.setHeader()
                         self.counter = 0
                     if self.counter == 0:
                         self.setFile()
                     self.writeBlock()
                     self.counter += 1
                 def close(self):
                     if self.counter > 0:
                         self.setHeader()

schainpy/model/io/jroIO_spectra.py 0 0

NO CONTENT: modified file

schainpy/model/proc/jroproc_parameters.py 0 0

	1	NO CONTENT: modified file			NO CONTENT: modified file
The requested commit or file is too big and content was truncated. Show full diff

schainpy/model/proc/jroproc_spectra_acf.py 0 0

	1	NO CONTENT: modified file			NO CONTENT: modified file
The requested commit or file is too big and content was truncated. Show full diff

schainpy/model/proc/jroproc_spectra_lags_faraday.py 0 0

	1	NO CONTENT: modified file			NO CONTENT: modified file
The requested commit or file is too big and content was truncated. Show full diff

schainpy/model/proc/jroproc_voltage.py 0 0

	1	NO CONTENT: modified file			NO CONTENT: modified file
The requested commit or file is too big and content was truncated. Show full diff

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