Source code for spacepy.ae9ap9

#!/usr/bin/env python
# -*- coding: utf-8 -*-
Module for reading and dealing with AE9AP9 data files.

See to download the model.
This is not a AE9AP9 runner.

Authors: Brian Larsen, Steve Morley
Institution: Los Alamos National Laboratory

Copyright 2015 Los Alamos National Security, LLC.

This module provides a convenient class for handling data from
AE9/AP9 (and legacy models provided by the software).

.. rubric:: Class
.. autosummary::
    :template: clean_class.rst
    :toctree: autosummary


Though the class is derived from SpacePy's SpaceData, the class also provides several methods
targeted at the AE9/AP9 output. Additional functions for working with the data are provided.

.. rubric:: Functions
.. autosummary::
    :template: clean_function.rst
    :toctree: autosummary



import datetime as dt
import gzip
import os
import re
import warnings

from dateutil import relativedelta
import numpy as np

import spacepy.coordinates as spc
import spacepy.datamodel as dm
import spacepy.plot as splot
import spacepy.time as spt
import spacepy.toolbox as tb

__contact__ = 'Brian Larsen,'

[docs]class Ae9Data(dm.SpaceData): """Dictionary-like container for AE9/AP9/SPM data, derived from SpacePy's datamodel To inspect the variables within this class, use the tree method. To export the data to a CDF, HDF5 or JSON-headed ASCII file use the relevant "to" method (toCDF, toHDF5, toJSONheadedASCII). .. autosummary:: ~Ae9Data.getLm ~Ae9Data.plotOrbit ~Ae9Data.plotSummary ~Ae9Data.plotSpectrogram ~Ae9Data.setUnits .. automethod:: getLm .. automethod:: plotOrbit .. automethod:: plotSummary .. automethod:: plotSpectrogram .. automethod:: setUnits """
[docs] def setUnits(self, per=None): """Set units of energy and flux/fluence If keyword 'per' is set to None, this method reports the units currently set. To set energy in MeV and flux/fluence in 'per MeV', set 'per=MeV'. Valid options are 'eV', 'keV', 'Mev' and 'GeV'. Other Parameters ---------------- per : string (optional) Energy units for both energy and flux/fluence """ curr = self['Energy'].attrs['UNITS'] particle_var = self.attrs['varname'] if not per: print('Energy units: {0}'.format(curr)) print('{0} units: {1}'.format(particle_var, self[particle_var].attrs['UNITS'])) return unitlist = ['eV', 'keV', 'MeV', 'GeV'] faclist = [1, 1e3, 1e6, 1e9] if per not in unitlist: raise ValueError("Units of {0} are not supported: Valid options are {1}".format(per, unitlist)) else: if per == curr: return unitidx_from = unitlist.index(curr) unitidx_to = unitlist.index(per) self[particle_var] /= faclist[unitidx_from] # convert to eV self[particle_var] *= faclist[unitidx_to] # convert to target units self[particle_var].attrs['UNITS'] = self[particle_var].attrs['UNITS'].replace(curr, per) self['Energy'] *= faclist[unitidx_from] # convert to eV self['Energy'] /= faclist[unitidx_to] # convert to target units self['Energy'].attrs['UNITS'] = self['Energy'].attrs['UNITS'].replace(curr, per)
[docs] def getLm(self, alpha=[90], model='T89'): """Calculate McIlwain L for the imported AE9/AP9 run and add to object """ import spacepy.irbempy as ib ticks = spt.Ticktock(self['Epoch']) loci = spc.Coords(self['Coords'], self['Coords'].attrs['COORD_SYS'], 'car') loci.ticks = ticks retvals = ib.get_Lm(ticks, loci, alpha, extMag=model) self['Lm'] = dm.dmarray(retvals['Lm'].squeeze(), attrs={ 'MODEL': model })
def _makeOrbitAxis(self, ser1, ser2, ax_target): """Helper function. Not intended for direct use. cx is the set of coordinates for plotting, ax_target is an axes object""" l1 = ax_target.plot(ser1, ser2) if np.abs((ax_target.get_xlim()[1] - ax_target.get_xlim()[0])) < 1: refpt = np.abs(np.max(ax_target.get_xlim())) ax_target.set_xlim([-1.25 * refpt, 1.25 * refpt]) ax_target.set_ylim(ax_target.get_xlim()) l1[0].set_marker('o') c1 = splot.plt.Circle([0, 0], radius=1.0, fc='none', ec='k') ax_target.add_artist(c1) else: splot.dual_half_circle(ax=ax_target) return ax_target
[docs] def plotSummary(self, timerange=None, coord_sys=None, fig_target=None, spec=False, orbit_params=(False, True), **kwargs): """Generate summary plot of AE9/AP9/SPM data loaded spec : if True, plot spectrogram instead of flux/fluence lineplot, requires 'ecol' keyword """ if timerange: if isinstance(timerange, spt.Ticktock): t1 = timerange.UTC[0] t2 = timerange.UTC[-1] elif isinstance(timerange[0], dt.datetime): t1 = timerange[0] t2 = timerange[-1] else: raise TypeError('Incorrect data type provided for timerange') # now select subset i_use = tb.tOverlapHalf([t1, t2], self['Epoch']) t_use = self['Epoch'][i_use] c_use = self['Coords'][i_use] f_use = self[self.attrs['varname']][i_use, ...] else: t_use = self['Epoch'] c_use = self['Coords'] f_use = self[self.attrs['varname']] if coord_sys and (coord_sys.upper() != c_use.attrs['COORD_SYS']): # TODO: We assume cartesian, make flexible so can take spherical cx = spc.Coords(c_use, c_use.attrs['COORD_SYS'], 'car') cx.ticks = spt.Ticktock(t_use) cx = cx.convert(coord_sys.upper(), 'car').data else: coord_sys = c_use.attrs['COORD_SYS'] cx = c_use sys_subs = r'$_{' + coord_sys + r'}$''spacepy') if orbit_params[0]: landscape = orbit_params[1] locs = [121, 122] if landscape else [211, 212] else: locs = [223, 224] landscape = True if fig_target: fig, ax1 = splot.set_target(fig_target, loc=locs[0]) else: fig, ax1 = splot.set_target(fig_target, figsize=(8, 8), loc=locs[0]) fig, ax2 = splot.set_target(fig, loc=locs[1]) ax1 = self._makeOrbitAxis(cx[:, 0], cx[:, 1], ax1) ax2 = self._makeOrbitAxis(cx[:, 0], cx[:, 2], ax2) if landscape: ax1.set_xlabel('X{0} [{1}]'.format(sys_subs, self['Coords'].attrs['UNITS'])) ax2.set_xlabel('X{0} [{1}]'.format(sys_subs, self['Coords'].attrs['UNITS'])) ax1.set_ylabel('Y{0} [{1}]'.format(sys_subs, self['Coords'].attrs['UNITS'])) ax2.set_ylabel('Z{0} [{1}]'.format(sys_subs, self['Coords'].attrs['UNITS'])) ax1xl, ax1yl, ax2xl, ax2yl = ax1.get_xlim(), ax1.get_ylim(), ax2.get_xlim(), ax2.get_ylim() maxabslim = np.max(np.abs([ax1xl, ax1yl, ax2xl, ax2yl])) if np.abs((ax1.get_xlim()[1] - ax1.get_xlim()[0])) < 1: refpt = maxabslim ax1.set_xlim([-1.25 * refpt, 1.25 * refpt]) ax1.set_ylim(ax1.get_xlim()) refpt = ax2.get_xlim()[0] ax2.set_xlim([-1.25 * refpt, 1.25 * refpt]) ax2.set_ylim(ax1.get_xlim()) else: ax1.set_xlim([-maxabslim, maxabslim]) ax1.set_ylim([-maxabslim, maxabslim]) ax2.set_xlim([-maxabslim, maxabslim]) ax2.set_ylim(ax2.get_xlim()) ax1.invert_yaxis() ax1.invert_xaxis() ax2.invert_xaxis() ax1.set_aspect('equal') ax2.set_aspect('equal') if not orbit_params[0]: ax3 = splot.plt.subplot2grid((2, 2), (0, 0), colspan=2) if not spec: l3 = ax3.semilogy(t_use, f_use) ylab = '{0} ['.format(self.attrs['varname']) + re.sub('(\^[\d|-]*)+', _grp2mathmode, self[self.attrs['varname']].attrs['UNITS']) + ']' ax3.set_ylabel(ylab) for ll, nn in zip(l3, self['Energy']): ll.set_label('{0} {1}'.format(nn, self['Energy'].attrs['UNITS'])) ncol = len(self['Energy']) // 2 if len(self['Energy']) <= 6 else 3 leg = ax3.legend(loc='center', bbox_to_anchor=(0.5, 1), ncol=ncol, frameon=True, framealpha=0.5) lims3 = ax3.get_ylim() newupper = 10 ** (np.log10(lims3[0]) + (np.log10(lims3[1] / lims3[0]) * 1.125)) ax3.set_ylim([lims3[0], newupper]) splot.applySmartTimeTicks(ax3, t_use) fig.tight_layout() pos3 = ax3.get_position() ax3.set_position([pos3.x0, pos3.y0, pos3.width, pos3.height * 0.8]) # fig.suptitle('{model_type}\n'.format(**self.attrs) + # '{0} - {1}'.format(t_use[0].isoformat()[:19], t_use[-1].isoformat()[:19])) else: if timerange: raise NotImplementedError('Time range selection not yet implemented for spectrograms') pos3 = ax3.get_position() ax3.set_position([pos3.x0, pos3.y0, pos3.width, pos3.height * 0.9]) ecol = kwargs['ecol'] if 'ecol' in kwargs else 0 ax3 = self.plotSpectrogram(target=ax3, ecol=ecol) splot.plt.subplots_adjust(wspace=0.3) pos1 = ax1.get_position() ax1.set_position([pos3.x0, pos1.y0, pos1.width, pos1.height]) splot.revert_style() return fig
[docs] def plotOrbit(self, timerange=None, coord_sys=None, landscape=True, fig_target=None): """ Plot X-Y and X-Z projections of satellite orbit in requested coordinate system """ fig = self.plotSummary(timerange=timerange, coord_sys=coord_sys, fig_target=fig_target, orbit_params=(True, landscape)) return fig
[docs] def plotSpectrogram(self, ecol=0, pvars=None, **kwargs): ''' Plot a spectrogram of the flux along the requested orbit, as a function of Lm and time Other Parameters ---------------- zlim : list 2-element list with upper and lower bounds for color scale colorbar_label : string text to appear next to colorbar (default is 'Flux' plus the units) ylabel : string text to label y-axis (default is 'Lm' plus the field model name) title : string text to appear above spectrogram (default is climatology model name, data type and energy) pvars : list list of plotting variable names in order [Epoch-like (X axis), Flux-like (Z axis), Energy (Index var for Flux-like)] ylim : list 2-element list with upper and lower bounds for y axis ''' import spacepy.plot as splot if 'Lm' not in self: self.getLm() sd = dm.SpaceData() if pvars is None: varname = self.attrs['varname'] enname = 'Energy' epvar = 'Epoch' else: epvar = pvars[0] varname = pvars[1] enname = pvars[2] if len(self['Lm']) != len(self[epvar]): #Lm needs interpolating to new timebase import matplotlib.dates as mpd tmptimetarg, tmptimesrc = mpd.date2num(self[epvar]), mpd.date2num(self['Epoch']) sd['Lm'] = dm.dmarray(np.interp(tmptimetarg, tmptimesrc, self['Lm'], left=np.nan, right=np.nan)) else: sd['Lm'] = self['Lm'] #filter any bad Lm goodidx = sd['Lm']>1 sd['Lm'] = sd['Lm'][goodidx] if 'ylim' in kwargs: Lm_lim = kwargs['ylim'] del kwargs['ylim'] else: Lm_lim = [2.0,8.0] #TODO: allow user-definition of bins in time and Lm sd['Epoch'] = dm.dmcopy(self[epvar])[goodidx] #TODO: assumes 1 pitch angle, generalize try: sd['1D_dataset'] = self[varname][goodidx,ecol] #TODO: assumes 1 pitch angle, generalize except IndexError: #1-D sd['1D_dataset'] = self[varname][goodidx] bins = [[],[]] if 'tbins' not in kwargs: bins[0] = spt.tickrange(self[epvar][0], self[epvar][-1], 3/24.).UTC else: bins[0] = kwargs['tbins'] del kwargs['tbins'] if 'Lbins' not in kwargs: bins[1] = np.arange(Lm_lim[0], Lm_lim[1], 1./4.) else: bins[1] = kwargs['Lbins'] del kwargs['Lbins'] spec = splot.spectrogram(sd, variables=['Epoch', 'Lm', '1D_dataset'], ylim=Lm_lim, bins=bins) if 'zlim' not in kwargs: zmax = 10 ** (int(np.log10(max(sd['1D_dataset']))) + 1) idx = np.logical_and(sd['1D_dataset'] > 0, sd['Lm'] > Lm_lim[0]) idx = np.logical_and(idx, sd['Lm'] <= Lm_lim[1]) zmin = 10 ** int(np.log10(min(sd['1D_dataset'][idx]))) kwargs['zlim'] = [zmin, zmax] if 'colorbar_label' not in kwargs: flux_units = self[varname].attrs['UNITS'] kwargs['colorbar_label'] = '{0} ['.format(varname) + re.sub('(\^[\d|-]*)+', _grp2mathmode, flux_units) + ']' if 'ylabel' not in kwargs: kwargs['ylabel'] = 'L$_M$' + ' ' + '[{0}]'.format(self['Lm'].attrs['MODEL']) if 'title' not in kwargs: kwargs['title'] = '{model_type} {varname}: '.format(**self.attrs) + \ '{0:5.2f} {1}'.format(self[enname][ecol], self[enname].attrs['UNITS']) reset_shrink = splot.mpl.mathtext.SHRINK_FACTOR splot.mpl.mathtext.SHRINK_FACTOR = 0.85 splot.mpl.mathtext.GROW_FACTOR = 1 / 0.85 ax = spec.plot(cmap='plasma', **kwargs) splot.mpl.mathtext.SHRINK_FACTOR = reset_shrink splot.mpl.mathtext.GROW_FACTOR = 1 / reset_shrink return ax
[docs]def readFile(fname, comments='#'): """ read a model generated file into a datamodel.SpaceData object Parameters ========== fname : str filename of the file Other Parameters ================ comments : str (optional) String that is the comments in the data file Returns ======= out : :mod:`~spacepy.datamodel.SpaceData` Data contained in the file Examples ======== >>> from spacepy import ae9ap9 >>> ae9ap9.readFile('ephem_sat.dat').tree(verbose=1) + |____Epoch (spacepy.datamodel.dmarray (121,)) |____Coords (spacepy.datamodel.dmarray (121, 3)) |____MJD (spacepy.datamodel.dmarray (121,)) |____posComp (spacepy.datamodel.dmarray (3,)) """ if not os.path.isfile(fname): raise (ValueError("File {0} not found".format(fname))) # get the header information first header = parseHeader(fname) # and read in all the data data = np.loadtxt(fname, delimiter=header['delimiter'], comments=comments) # now parse the data ans = Ae9Data() # parse the datetime if it is there (it is always first) if 'datetime' in header['columns'][0]: if header['time_format'] == 'eDOY': # have to massage the data first year = data[:, 0].astype(int) frac = data[:, 1] time = spt.Ticktock([dt.datetime(y, 1, 1) + relativedelta.relativedelta(days=v) for y, v in zip(year, frac)], 'UTC') ans[header['time_format']] = dm.dmarray(data[:, 0:2]) ans[header['time_format']].attrs['VAR_TYPE'] = 'support_data' ans[header['time_format']].attrs['LABL_PTR_1'] = 'timeComp' ans['timeComp'] = dm.dmarray(['Year', 'eDOY']) ans['timeComp'].attrs['VAR_TYPE'] = 'metadata' del header['columns'][0:2] data = data[:, 2:] elif header['time_format'] == 'UTC': # have to massage the data first tm = data[:, 0:6].astype(int) time = spt.Ticktock([dt.datetime(*v) for v in tm], 'UTC') ans[header['time_format']] = dm.dmarray(data[:, 0:6]) ans[header['time_format']].attrs['VAR_TYPE'] = 'support_data' ans[header['time_format']].attrs['LABL_PTR_1'] = 'timeComp' ans['timeComp'] = dm.dmarray(['Year', 'Month', 'Day', 'Hour', 'Minute', 'Second']) ans['timeComp'].attrs['VAR_TYPE'] = 'metadata' del header['columns'][0:6] data = data[:, 6:] else: time = spt.Ticktock(data[:, 0], header['time_format']) ans[header['time_format']] = dm.dmarray(data[:, 0]) ans[header['time_format']].attrs['VAR_TYPE'] = 'support_data' del header['columns'][0] data = data[:, 1:] ans['Epoch'] = dm.dmarray(time.UTC) ans['Epoch'].attrs['VAR_TYPE'] = 'support_data' # parse the position, it is always next if 'posx' in header['columns'][0]: varname = 'Coords' pos = dm.dmarray(data[:, 0:3]) ans[varname] = pos ans[varname].attrs['UNITS'] = header['coord_system'][1] ans[varname].attrs['FIELDNAM'] = varname ans[varname].attrs['LABLAXIS'] = 'Position' ans[varname].attrs['DEPEND_0'] = 'Epoch' ans[varname].attrs['LABL_PTR_1'] = 'posComp' ans[varname].attrs['VAR_TYPE'] = 'data' ans[varname].attrs['COORD_SYS'] = header['coord_system'][0] ans['posComp'] = dm.dmarray(['X', 'Y', 'Z']) ans['posComp'].attrs['VAR_TYPE'] = 'metadata' del header['columns'][0:3] data = data[:, 3:] # if there are PA they are now if header['columns'] and ('pitch' in header['columns'][0]): raise (NotImplementedError("Sorry have not implemented pitch angle resolved files yet")) ## This is an issue and the files have repeadedlines at the same time for each pitch ## angle. They would all need to be read in them combines into a multi-d array # now parse fluence, flux, or doserate # do all the rest of the column headers match? col_arr = np.asarray(header['columns']) if header['columns'] and (col_arr == col_arr[0]).all(): varname = col_arr[0][0].title() ans[varname] = dm.dmarray(data) ans[varname].attrs['UNITS'] = str(col_arr[0][1]) ans[varname].attrs['FIELDNAM'] = varname ans[varname].attrs['LABLAXIS'] = varname ans[varname].attrs['VAR_TYPE'] = 'data' ans[varname].attrs['SCALETYP'] = 'log' header['varname'] = varname ans[varname].attrs[ 'Description'] = '{flux_direction} {varname} based on {flux_type} from the {model_type} model'.format( **header) ans[varname].attrs['DEPEND_0'] = 'Epoch' if ans[varname].shape[1] == header['energy'][0].shape[0]: ans[varname].attrs['DEPEND_1'] = 'Energy' if 'percentile' in header: ans[varname].attrs['TITLE'] = '{0} percentile'.format(header['percentile']) # create the energy variable if 'energy' in header: ans['Energy'] = dm.dmarray(header['energy'][0]) ans['Energy'].attrs['UNITS'] = header['energy'][1] ans['Energy'].attrs['FIELDNAM'] = 'Energy' ans['Energy'].attrs['LABLAXIS'] = 'Energy' ans['Energy'].attrs['VAR_TYPE'] = 'data' ans['Energy'].attrs['SCALETYP'] = 'log' ans['Energy'].attrs['VAR_TYPE'] = 'support_data' skip_header = ['columns', 'coord_system', 'delimiter', 'energy', 'flux_direction'] for k in header: if k not in skip_header: ans.attrs[k] = header[k] return ans
def _parseInfo(header): """ given a header parse and return the common information in all headers # Time format: Modified Julian Date # Coordinate system: GEI (Geocentric Equatorial Inertial) Cartesian in Earth radii # Data Delimiter: comma """ # get the time format, it is in all the files ans = { } for ind, val in enumerate(header): if "Time format:" in val: if "Modified Julian Date" in val: ans['time_format'] = 'MJD' elif "Year, day_of_year.frac" in val: ans['time_format'] = 'eDOY' elif "Year, Month, Day, Hour, Minute, Seconds" in val: ans['time_format'] = 'UTC' else: raise (NotImplementedError("Sorry can't read that time format yet: {0}".format(val))) elif "Coordinate system:" in val: coord_sys = val.split(':')[1].strip().split()[0] if "in Earth radii" in val: ans['coord_system'] = (coord_sys, 'Re') else: ans['coord_system'] = (coord_sys, '') elif "Data Delimiter:" in val: if "comma" in val: ans['delimiter'] = ',' else: raise (NotImplementedError("Sorry can't read that delimiter yet")) elif "Ae9Ap9 Software Version:" in val: match = re.match(r'^Ae9Ap9 Software Version:.*(\d\.\d\d\.\d\d\d)$', val) version = ans['software_version'] = version elif "Model type:" in val: match = re.match(r'^Model type:(.*)$', val) mtype = ans['model_type'] = mtype elif "CRRESELE Software Version:" in val: match = re.match(r'^CRRESELE Software Version:.*(\d\.\d\d\.\d\d\d)$', val) version = ans['software_version'] = version ans['model_type'] = 'CRRESELE/PRO' elif "Flux type:" in val: match = re.match(r'^Flux type:(.*)$', val) ftype = ans['flux_type'] = ftype elif "Flux direction:" in val: if '=' not in val: match = re.match(r'^Flux direction:(.*)$', val) fdir = else: pa = val.split('=')[1].strip() fdir = np.asarray(pa.split()) ans['flux_direction'] = fdir elif "Energy levels" in val: match = re.match(r'^Energy levels.*\((.*)\):(.*)$', val) ans['energy'] = (np.asarray(, # Get the orbital element propagator, two versions based on AE9 model changes # new format data file elif "Propagator" in val: # New format match ='Propagator:\ (.*)$', val) ans['propagator'] = elif "generated from specified elements" in val: # In both old and new match ='^generated from specified elements.*:\ (.*)$', val) if match: # But old has propagator on this line; process and warn warnings.warn( "Support for orbit files from AE9AP9 model <1.5 is deprecated; please update to model 1.5 or later.", DeprecationWarning) ans['propagator'] = return ans def _readHeader(fname): """ read only the header from a Ae9Ap9 file """ dat = [] if fname.endswith('.gz'): try: fp =, 'rt') except ValueError: #Python 2.7 (Windows) compatibility fp = else: fp = open(fname, 'rt') while True: tmp = fp.readline() if tmp[0] not in ('#', 35): break dat.append(tmp.strip()) dat = [v[1:].strip() for v in dat] fp.close() return dat
[docs]def parseHeader(fname): """ given an AE9AP9 output test file parse the header and return the information in a dictionary .. versionchanged:: 0.3.0 The underlying AE9AP9 model changed the ephem file format and this reader was updated to match. Reading the old format will issue DeprecationWarning. Parameters ========== fname : str filename of the file Returns ======= out : dict Dictionary of the header information in the file """ ans = { } ans['filename'] = os.path.abspath(fname) header = _readHeader(fname) # get the information ans.update(_parseInfo(header)) columns = header[-1].split(ans['delimiter']) columns_unq = _unique_elements_order(columns) len_columns_unq = len(columns) # pull the units off the column headings cols = [] while columns_unq: tmp = columns_unq.pop(0) umatch = re.match(r'(.*)\((.*)\).*', tmp) if umatch: cols.append((, else: cols.append(tmp) # now go through and see if any non-tuple entry has the same name as a tuple entry to_remove = [] for ii, c1 in enumerate(cols): if not isinstance(c1, tuple): for jj, c2 in enumerate(cols[ii:]): if c2[0] == c1: to_remove.append(ii) if to_remove: for v in to_remove: del cols[v] # and now replicate the last entry enough times to make it the right length cols.extend([cols[-1]] * (len_columns_unq - len(cols))) ans['columns'] = cols if 'pctile' in os.path.basename(fname): # capture the percentile match = re.match(r'.*_(\d\d).txt', os.path.basename(fname)) ans['percentile'] = float( return ans
def _unique_elements_order(seq): """ see """ seen = set() seen_add = seen.add return [x for x in seq if not (x in seen or seen_add(x))] def combinePercentiles(files, timeframe='all', verbose=True): """ combine files at different percentiles into one file with the spectra at different percentiles for easy plotting and analysis NOTE: Requires pandas for any timeframe other than 'all' Parameters ========== files : str Filenames of the percentile files Other Parameters ================ timeframe : str Timeframe to average the input spectra over (either 'all' or a pandas understoop resample() time verbose : boolean Print out information while reading the files Returns ======= out : :mod:`~spacepy.datamodel.SpaceData` Combined output spectra of the file """ if not files: raise (ValueError("Must input files")) data = { } for fname in files: if verbose: print("Reading: {0}".format(fname)) tmp = readFile(fname) if 'percentile' not in tmp.attrs: raise (ValueError("File {0} does not have a percentile key".format(fname))) data[tmp.attrs['percentile']] = tmp varnames = ['Flux', 'Fluence', 'Dose', None] for varname in varnames: if varname in data[list(data.keys())[0]]: break # this leaves it where it was found if varname is None: raise (ValueError("Did not understand file type could not find one of {0}".format(varnames))) # now that they are all read in, we collapse them down to different time bases if timeframe == 'all': # this is just a full collapse # find the var to collapse d_comp = np.asarray([]) ps = sorted(data.keys())[::-1] for p in ps: if data[p][varname].attrs['DEPEND_0'] == 'Epoch': d_comp = np.concatenate((d_comp, data[p][varname].mean(axis=0))) # full time collapse else: d_comp = np.concatenate((d_comp, data[p][varname])) # full time collapse d_comp = d_comp.reshape(len(ps), -1).T else: try: import pandas as pd except ImportError: raise (ImportError("panads is required for timeframe other than 'all'")) raise (NotImplementedError("Timeframes other than 'all' not yet implemented")) # make a dataframe # resample to timeframe # join everything # meet up at same place for output # now that we have all the data prep it to a spacedata ans = dm.SpaceData() ans[varname] = dm.dmarray(d_comp) if timeframe == 'all': ans[varname].attrs['DEPEND_0'] = 'Energy' ans[varname].attrs['DEPEND_1'] = 'Percentile' ans[varname].attrs['DISPLAY_TYPE'] = 'time_series' for k in data[p][varname].attrs: if 'DEPEND' in k: continue else: ans[varname].attrs[k] = data[p][varname].attrs[k] ans['Energy'] = data[p]['Energy'] ans['Percentile'] = dm.dmarray(ps) ans['Percentile'].attrs['FIELDNAM'] = 'Percentile' ans['Percentile'].attrs['LABLAXIS'] = 'Percentile' ans['Percentile'].attrs['VALIDMIN'] = 0.0 ans['Percentile'].attrs['VALIDMAX'] = 100.0 ans['Percentile'].attrs['SCALETYP'] = 'support_data' return ans def _getData(fnames): """ helper routine for dm.toCDF and dm.toHDF5 and dm.toJSONheadedASCII since the data prep is all the same """ if hasattr(fnames, 'strip'): # it is a string return readFile(fnames) else: return combinePercentiles(fnames) def _grp2mathmode(matchobj): """Helper function to latex-ify the units for plotting""" unitstr = unitstr = unitstr[0] + '{' + unitstr[1:] return '$' + unitstr + '}$'