def build_timespectra(self):
""" Attempts to build timespectra form picklefile, legacy and finally
from the raw datafiles."""
# Files in working directory, ignore certain extensions; ignore directories
infiles = get_files_in_dir(self.inpath, sort=True)
infiles = [f for f in infiles if not ext(f) in self.img_ignore]
if not infiles:
raise IOError("No valid files found in %s" % self.infolder)
# Try get timespectra from picklefiles
ts_full = self._ts_from_picklefiles(infiles)
if ts_full:
return ts_full
# Try get timespectra from timefile/datafile (legacy)
ts_full = self._ts_from_legacy(infiles)
if ts_full:
return ts_full
# Import from raw specfiles (overwrite if data < 1s apart)
logger.info('Loading contents of %s multiple raw spectral '
'files %s.' % (self.infolder, len(infiles)))
try:
return from_spec_files(infiles, name=self.infolder,
check_for_overlapping_time=False)
except Exception as exc:
logger.critical('Could not import files from pickle, legacy or'
' from_spec_files()')
raise
def build_timespectra(self):
""" Attempts to build timespectra form picklefile, legacy and finally
from the raw datafiles."""
# Files in working directory, ignore certain extensions; ignore directories
infiles = get_files_in_dir(self.inpath, sort=True)
infiles = [f for f in infiles if not ext(f) in self.img_ignore]
if not infiles:
raise IOError("No valid files found in %s" % self.infolder)
# Try get timespectra from picklefiles
ts_full = self._ts_from_picklefiles(infiles)
if ts_full:
return ts_full
# Try get timespectra from timefile/datafile (legacy)
ts_full = self._ts_from_legacy(infiles)
if ts_full:
return ts_full
# Import from raw specfiles (overwrite if data < 1s apart)
logger.info('Loading contents of %s multiple raw spectral '
'files %s.' % (self.infolder, len(infiles)))
try:
return from_spec_files(infiles,
name=self.infolder,
check_for_overlapping_time=False)
except Exception as exc:
logger.critical('Could not import files from pickle, legacy or'
' from_spec_files()')
raise
def from_oceanoptics(directory, sample_by=None, sort=True, **from_spec_files_kwds):
''' Wrapper to from_spec_files to both generate a file list from a directory and read files into time spectra.
Parameters:
-----------
directory: directory with raw spectral files.
sample_by: Sample every X files. (Useful for reducing large datsets prior to readin)
**from_spec_files_kwds: All kwds passed to from_spec_files().
Notes:
------
Slice works by taking the 0 file every time and counting from there. So if you enter sample_by=3,
expect to get files 0, 3, 6 etc... but if sample_by_10, you get files 0,10,20
'''
files=get_files_in_dir(directory, sort=sort)
if sample_by:
files=files[0::sample_by] #Slice already takes cares of most errors
return from_spec_files(files, **from_spec_files_kwds)
files=get_files_in_dir(directory, sort=sort)
if sample_by:
files=files[0::sample_by] #Slice already takes cares of most errors
return from_spec_files(files, **from_spec_files_kwds)
if __name__=='__main__':
# Assumes datapath is ../data/gwuspecdata...
### Test of raw fiber spectral data
ts=from_oceanoptics('../data/gwuspecdata/fiber1', sample_by=10, sort=True, name='oceanopticstest')
files=get_files_in_dir('../data/gwuspecdata/fiber1')
ts=from_spec_files(files, name='Test Spectra')
#print ts, type(ts)
### Test of timefile/datafile
#dfile='../data/gwuspecdata/ex_tf_df/11_data.txt'
#tfile='../data/gwuspecdata/ex_tf_df/11_tfile.txt'
#ts2=from_timefile_datafile(dfile, tfile, extract_dark=True, name='Test Spec 2')
#print ts2, type(ts2)
### Test of chem UVVIS data
files=get_files_in_dir('../data/gwuspecdata/IRData')
ts3=from_gwu_chem_UVVIS(files, name='IR Spec')
print ts3, type(ts3), ts3[ts3.columns[0]]
### ADD CHEM IR DATA (Did it in a notebook at one point actually)
