Source Code for Module kenozooid.rglue

  1  # Kenozooid - dive planning and analysis toolbox. 
  2  # 
  3  # Copyright (C) 2009-2019 by Artur Wroblewski <wrobell@riseup.net> 
  4  # 
  5  # This program is free software: you can redistribute it and/or modify 
  6  # it under the terms of the GNU General Public License as published by 
  7  # the Free Software Foundation, either version 3 of the License, or 
  8  # (at your option) any later version. 
  9  # 
 10  # This program is distributed in the hope that it will be useful, 
 11  # but WITHOUT ANY WARRANTY; without even the implied warranty of 
 12  # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the 
 13  # GNU General Public License for more details. 
 14  # 
 15  # You should have received a copy of the GNU General Public License 
 16  # along with this program.  If not, see <http://www.gnu.org/licenses/>. 
 17  # 
 18   
 19  """ 
 20  rpy integration functions. 
 21  """ 
 22   
 23  from functools import partial 
 24  import itertools 
 25   
 26  import rpy2.robjects as ro 
 27  R = ro.r 
 28   
 29  import kenozooid 
 30  import kenozooid.calc as kcc 
 31   
 32 -def _vec(c, na, data): 
 33      """ 
 34      Create vector for given type using rpy interface. 
 35   
 36      :Parameters: 
 37       c 
 38          Vector class, i.e. BoolVector, FloatVector. 
 39       na 
 40          NA value, which should be used for None values. 
 41       data 
 42          Iterable, the source of vector data. 
 43      """ 
 44      return c([na if v is None else v for v in data]) 
 45   
 46   
 47 -def df(cols, vf, data): 
 48      """ 
 49      Create R data frame using rpy interface. 
 50   
 51      :Parameters: 
 52       cols 
 53          Column names. 
 54       vf 
 55          Vector constructors. 
 56       data 
 57          Iterable of data frame rows (not columns). 
 58      """ 
 59      od = {n: f(d) for n, f, d in zip(cols, vf, zip(*data))} 
 60      return ro.DataFrame(od) 
 61   
 62   
 63 -def dives_df(dives): 
 64      """ 
 65      Create R data frame for dives using rpy interface. 
 66      """ 
 67      cols = 'number', 'datetime', 'depth', 'duration', 'temp', 'avg_depth' 
 68      vf = int_vec, dt_vec, float_vec, float_vec, float_vec, float_vec 
 69      return df(cols, vf, dives) 
 70   
 71   
 72 -def dive_profiles_df(dives): 
 73      """ 
 74      Create R data frame for dive profiles using rpy interface. 
 75      """ 
 76      cols = ('dive', 'depth', 'time', 'temp', 'setpoint',  
 77          'deco_time', 'deco_depth', 'deco_alarm', 
 78          'gas_name', 'gas_o2', 'gas_he', 'mod_low', 'mod_high') 
 79      vf = (int_vec, ) + (float_vec, ) * 6 + (bool_vec, str_vec, int_vec, 
 80              int_vec, float_vec, float_vec) 
 81      p = ((k, s.depth, s.time, s.temp, s.setpoint, s.deco_time, s.deco_depth, s.alarm, 
 82            None if s.gas is None else s.gas.name, 
 83            None if s.gas is None else s.gas.o2, 
 84            None if s.gas is None else s.gas.he, 
 85            None if s.gas is None else kcc.mod(s.gas.o2, 1.4), 
 86            None if s.gas is None else kcc.mod(s.gas.o2, 1.6), 
 87           ) for k, dive in enumerate(dives, 1) for s in dive.profile) 
 88      return df(cols, vf, p) 
 89   
 90   
 91 -def inject_dive_data(dives): 
 92      """ 
 93      Inject dive data into R space. Two variables are created 
 94   
 95      kz.dives 
 96          Data frame of dives. 
 97   
 98      kz.profiles 
 99          Data frame of dive profiles 
100   
101      :Parameters: 
102       dives 
103          Collection of dive data. 
104      """ 
105      d1, d2 = itertools.tee(dives, 2) 
106      d_df = dives_df(d1) 
107      p_df = dive_profiles_df(d2) 
108   
109      ro.globalenv['kz.dives'] = d_df 
110      ro.globalenv['kz.profiles'] = p_df 
111      ro.globalenv['kz.version'] = kenozooid.__version__ 
112      R('kz.dives$datetime = as.POSIXct(kz.dives$datetime)') 
113   
114   
115  bool_vec = partial(_vec, ro.BoolVector, ro.NA_Logical) 
116  float_vec = partial(_vec, ro.FloatVector, ro.NA_Real) 
117  int_vec = partial(_vec, ro.IntVector, ro.NA_Integer) 
118  str_vec = partial(_vec, ro.StrVector, ro.NA_Character) 
119  dt_vec = partial(_vec, ro.POSIXct.sexp_from_datetime, ro.NULL) 
120   
121  # vim: sw=4:et:ai 
122