diff --git a/boxmox/data.py b/boxmox/data.py
index 46a7f879aed3018824c5540e5a09697381cb29be..45c744f38890af382e7f0583ddf84a109ada88a6 100644
--- a/boxmox/data.py
+++ b/boxmox/data.py
@@ -3,18 +3,36 @@ import sys
import shutil
import StringIO
import csv
-import warnings
import numpy as np
+def _mygenfromtxt2(f):
+ curpos = f.tell()
+ try:
+ dialect = csv.Sniffer().sniff(f.read(1048576), delimiters=";, ")
+ dialect.skipinitialspace = True
+ f.seek(curpos)
+ spamreader = csv.reader(f, dialect)
+ except:
+ # could not determine dialect, falling back to default.
+ f.seek(curpos)
+ spamreader = csv.reader(f, skipinitialspace = True, delimiter=" ")
+ # twice as fast as np.genfromtxt(..., names=True)
+ hdr = spamreader.next()
+ dat = []
+ for row in spamreader:
+ dat.append( tuple(map(float, row)) )
+ return dat, hdr
+
def _mygenfromtxt(f):
curpos = f.tell()
try:
dialect = csv.Sniffer().sniff(f.read(1048576), delimiters=";, ")
+ dialect.skipinitialspace = True
f.seek(curpos)
spamreader = csv.reader(f, dialect)
except:
- warnings.warn('Could not determine dialect, falling back to default.')
+ # could not determine dialect, falling back to default.
f.seek(curpos)
spamreader = csv.reader(f, skipinitialspace = True, delimiter=" ")
# twice as fast as np.genfromtxt(..., names=True)
@@ -24,9 +42,132 @@ def _mygenfromtxt(f):
dat.append( tuple(map(float, row)) )
return np.array(dat, dtype=[(_, float) for _ in hdr])
-class InputFile:
+def InputFile(fpath=None, version=1.0):
+ if not fpath is None:
+ # file format discovery: 3 lines with numbers ==> 1.7
+ with open(fpath, 'rb') as f:
+ one = f.readline()
+ two = f.readline()
+ tre = f.readline()
+ try:
+ test = int(tre)
+ version = 1.7
+ except:
+ version = 1.0
+ pass
+
+ if version >= 1.7:
+ return InputFile17(fpath=fpath, version=version)
+ else:
+ return InputFileOrig(fpath=fpath)
+
+class InputFile17:
'''
- A generic BOXMOX input file. Getting and setting of values
+ A generic BOXMOX input file (>= v 1.7). Getting and setting of values
+ works like a dictionary::
+
+ print(inp['O3'])
+ inp['O3'] = 0.040
+
+ '''
+ @property
+ def nvar(self):
+ '''
+ Number of variables.
+ '''
+ return len( [ x for x in self.keys() ] )
+ @property
+ def nanc(self):
+ '''
+ Number of ancillary variables.
+ '''
+ return len( [ x for x in self.anc.keys() ] )
+ def __getitem__(self, item):
+ return [ self.__data[i] for i in item ] if isinstance(item, list) else self.__data[item]
+ def __setitem__(self, item, values):
+ if isinstance(item, list):
+ for i, v in zip(item, values):
+ self.__data[i] = v
+ else:
+ self.__data[item] = values
+ def keys(self):
+ return self.__data.keys()
+
+ def read(self, fpath):
+ '''
+ Read input file from path.
+ '''
+ with open(fpath, 'rb') as f:
+ nvar = int(f.readline().replace(',', ''))
+ nanc = int(f.readline().replace(',', ''))
+ self.timeFormat = int(f.readline().replace(',', ''))
+ dmp, hdr = _mygenfromtxt2(f)
+
+ ntime = 0
+ if not self.timeFormat == 0:
+ self.timeVar = hdr[0]
+ self.time = [ x[0] for x in dmp ]
+ ntime = 1
+ self.anc = { hdr[i]: [ x[i] for x in dmp ] for i in range(ntime, ntime+nanc) }
+ self.__data = { hdr[i]: [ x[i] for x in dmp ] for i in range(ntime+nanc, len(dmp[0])) }
+
+ def __str__(self):
+ f = StringIO.StringIO()
+ self.write(f)
+ return(f.getvalue())
+
+ def write(self, f=sys.stdout, version=1.7):
+ '''
+ Write to <f>. <f> can be file handle or other connection. Defaults to sys.stdout.
+ '''
+ # possibility to create old version output from new version data
+ if version >= 1.7:
+ f.write('{0:1d}'.format(self.nvar) +'\n')
+ f.write('{0:1d}'.format(self.nanc) +'\n')
+ else:
+ f.write('{0:1d}'.format(self.nanc+self.nvar) +'\n')
+ f.write('{0:1d}'.format(self.timeFormat) +'\n')
+
+ data_names = [ key for key in self.keys() ]
+ anc_names = [ key for key in self.anc.keys() ]
+ hdr_line = '{0:s}\n' .format(' '.join(anc_names + data_names))
+ if str(self.timeFormat) != "0" :
+ hdr_line = self.timeVar + ' ' + hdr_line
+ f.write(hdr_line)
+
+ if isinstance(self.time, list):
+ for itime, xtime in enumerate(self.time):
+ line = [ xtime ] + [ self.anc[key][itime] for key in anc_names ] + [ self.__data[key][itime] for key in data_names ]
+ f.write(' '.join('{0:e}'.format(x) for x in line) + '\n')
+ else:
+ data_line = ' '.join( '{0:e}'.format(float(self.anc[x])) for x in self.anc.keys() ) + ' ' + ' '.join( '{0:e}'.format(float(self.__data[x])) for x in self.keys() ) + '\n'
+ if not self.time is None:
+ data_line = '{0:e}'.format(float(self.time)) + ' ' + data_line
+ f.write(data_line)
+
+ def __init__(self, fpath=None, version=1.7):
+ #: Time format (0: constant, 1: seconds since start, 2: hour of diurnal cycle)
+ self.timeFormat = 0
+ self.timeVar = 'time'
+ self.time = None
+
+ self.anc = {}
+
+ self.__data = {}
+
+ self.version = version
+
+ #: File path of the underlying file (if it exists (yet))
+ self.fpath = fpath
+ if not self.fpath is None:
+ try:
+ self.read(self.fpath)
+ except Exception as e:
+ print("Reading input file {:s} failed: {:s}".format(self.fpath, str(e)))
+
+class InputFileOrig:
+ '''
+ A generic BOXMOX input file (< 1.7). Getting and setting of values
works like a dictionary::
print(inp['O3'])
@@ -49,6 +190,7 @@ class InputFile:
self.__data[item] = values
def keys(self):
return self.__data.keys()
+
def read(self, fpath):
'''
Read input file from path.
@@ -67,11 +209,13 @@ class InputFile:
self.write(f)
return(f.getvalue())
- def write(self, f=sys.stdout):
+ def write(self, f=sys.stdout, version=1.0):
'''
Write to <f>. <f> can be file handle or other connection. Defaults to sys.stdout.
'''
f.write('{0:1d}'.format(self.nvar) +'\n')
+ if version >= 1.7:
+ f.write('{0:1d}'.format(0) +'\n')
f.write('{0:1d}'.format(self.timeFormat) +'\n')
column_names = [ key for key in self.keys() if key != self.__timeVar ]
@@ -91,6 +235,8 @@ class InputFile:
self.__timeVar = 'time'
self.__data = {}
+ self.version = 0.0
+
#: File path of the underlying file (if it exists (yet))
self.fpath = fpath
if not self.fpath is None:
diff --git a/boxmox/experiment.py b/boxmox/experiment.py
index 48a3a815e22784564075da6f114a1cce32712aa7..0f8a89e0ebbd543e427f6dd3cd874d8862881b7c 100644
--- a/boxmox/experiment.py
+++ b/boxmox/experiment.py
@@ -113,6 +113,25 @@ class Experiment:
#: Namelist
self.namelist = Namelist(os.path.join(self.path, 'BOXMOX.nml'))
+ self.version = self._determineVersion(self.path)
+
+ def _determineVersion(self, path):
+ version = 1.0
+ versionFile = os.path.join(path, 'VERSION')
+ if os.path.exists(versionFile):
+ try:
+ with open(versionFile, 'rb') as f:
+ line = f.readline().rstrip()
+ line = ".".join(line.split(".")[0:min(2, len(line.split(".")))])
+ # for development only:
+ if line == "__BOXMOX_VERSION__":
+ line = 1.7
+ version = float(line)
+ except:
+ version = 1.0
+ pass
+ return version
+
def _populateInput(self):
inputFileNames = [f for f in os.listdir(self.path) if f.endswith('.csv')]
self.input = { x.replace('.csv', '') : InputFile(os.path.join(self.path, x)) for x in inputFileNames }
@@ -120,7 +139,6 @@ class Experiment:
def __new(self):
try:
s.call(["new_BOXMOX_experiment", self.mechanism, self.path])
-# s.check_output(["new_BOXMOX_experiment", "-f", self.mechanism, self.path], stderr=s.STDOUT)
self._populateInput()
except s.CalledProcessError as e:
@@ -172,7 +190,7 @@ class Experiment:
for type in self.input:
with open( os.path.join(self.path, type + '.csv'), 'wb') as f:
- self.input[type].write(f)
+ self.input[type].write(f, version=self.version)
pwd = os.getcwd()
os.chdir(self.path)