def OpenG2M1s(froot, expt_idx=None, roi_idx=None):
res = []
filter_str = ''
if roi_idx is not None:
filter_str += '_' + ROI_PREFIX + str(roi_idx).zfill(ROI_IDXLEN)
if expt_idx is not None:
filter_str += '_' + EXP_PREFIX + +str(expt_idx).zfill(EXP_IDXLEN)
fnames_list = sf.FindFileNames(froot,
Prefix=G2M1_PREFIX,
Ext='.dat',
FilterString=filter_str,
Sort='ASC')
ROI_list = [sf.FirstIntInStr(name) for name in fnames_list]
exptime_list = [sf.LastIntInStr(name) for name in fnames_list]
lagtimes = []
imgtimes = []
for i, fname in enumerate(fnames_list):
res_g2m1, res_hdr = sf.LoadResFile(os.path.join(froot, fname),
delimiter=TXT_DELIMITER,
comments=TXT_COMMENT,
readHeader=True,
isolateFirst=0)
res.append(res_g2m1[:, 1::2].T)
lagtimes.append(res_g2m1[:, ::2].T)
imgtimes.append(
np.asarray([
sf.FirstFloatInStr(res_hdr[j])
for j in range(1, len(res_hdr), 2)
]))
return res, lagtimes, imgtimes, ROI_list, exptime_list
def ReadCIfile(self, fname):
roi_idx = sf.FirstIntInStr(fname)
exp_idx = sf.LastIntInStr(fname)
cur_cI = np.loadtxt(os.path.join(self.outFolder, fname),
**self.loadtxt_kwargs)
cur_times = cur_cI[:, 0]
cur_cI = cur_cI[:, 1:] # skip first row with image times
if (cur_cI.shape != (self.NumTimes(), self.NumLagtimes())):
logging.warning(
'cI result file {0} potentially corrupted: shape {1} does not match expected {2}'
.format(fname, cur_cI.shape,
(self.NumTimes(), self.NumLagtimes())))
return cur_cI, cur_times, roi_idx, exp_idx
def OpenCIs(froot):
res = []
fnames_list = sf.FindFileNames(froot,
Prefix=CI_PREFIX + '_',
Ext='.dat',
Sort='ASC')
ROI_list = [sf.FirstIntInStr(name) for name in fnames_list]
exptime_list = [sf.LastIntInStr(name) for name in fnames_list]
lagtimes = []
imgtimes = []
for i, fname in enumerate(fnames_list):
res_cI, res_hdr, col_times = sf.LoadResFile(os.path.join(froot, fname),
delimiter=TXT_DELIMITER,
comments=TXT_COMMENT,
readHeader=True,
isolateFirst=1)
res.append(res_cI)
lagtimes.append(np.asarray([sf.FirstIntInStr(hdr) for hdr in res_hdr]))
imgtimes.append(col_times)
return res, imgtimes, lagtimes, ROI_list, exptime_list
def LoadFiles(self,
mi_fnames,
metadata_section='MIfile',
open_mifiles=True,
replace_previous=False):
"""Load list of filenames
Parameters
----------
mi_fnames : list of filenames (full path, str)
open_mifiles : if True, open each MIfile for reading
replace_previous : if True, replace eventual preexisting list of MIfile
"""
if (replace_previous or self.MIfiles is None):
self.MIfiles = []
self.IdxList = []
for i in range(len(mi_fnames)):
self.IdxList.append(sf.LastIntInStr(mi_fnames[i]))
self.MIfiles.append(
MI.MIfile(mi_fnames[i],
self.MetaData.ToDict(section=metadata_section)))
if open_mifiles:
self.MIfiles[-1].OpenForReading()
self._loaded = True
def GetCorrMaps(self,
openMIfiles=True,
getAutocorr=True,
check_lagtimes=False):
"""Searches for MIfile correlation maps
Parameters
----------
openMIfiles: if true, it opens all MIfiles for reading.
getAutocorr: if True, returns d0 in the list of correlation maps
otherwise, returns None instead of the autocorrelation map
check_lagtimes: if true, checks that the lagtimes extracted from the filenames match with self.lagList
Returns
-------
corr_config: configuration file for correlation maps
corr_mifiles: list of correlation maps, one per time delay
lag_list: list of lagtimes
"""
if not self._corrmaps_loaded:
assert os.path.isdir(
self.outFolder), 'Correlation map folder ' + str(
self.outFolder) + ' not found.'
config_fname = os.path.join(self.outFolder, 'CorrMapsConfig.ini')
assert os.path.isfile(config_fname), 'Configuration file ' + str(
config_fname) + ' not found'
self.conf_cmaps = cf.Config(config_fname)
all_cmap_fnames = sf.FindFileNames(self.outFolder,
Prefix='CorrMap_d',
Ext='.dat',
Sort='ASC',
AppendFolder=True)
self.cmap_mifiles = []
self.all_lagtimes = []
for i in range(len(all_cmap_fnames)):
cur_lag = sf.LastIntInStr(all_cmap_fnames[i])
self.all_lagtimes.append(cur_lag)
self.cmap_mifiles.append(
MI.MIfile(
all_cmap_fnames[i],
self.conf_cmaps.ToDict(section='corrmap_metadata')))
self.cmap_mifiles[-1].OpenForReading()
# Check lagtimes for consistency
if (check_lagtimes):
print(
'These are all lagtimes. They should be already sorted and not contain 0:'
)
print(self.all_lagtimes)
for cur_lag in self.lagList:
if (cur_lag not in self.all_lagtimes):
print(
'WARNING: no correlation map found for lagtime ' +
str(cur_lag))
self._corrmaps_loaded = True
if (self.all_lagtimes[0] == 0 and getAutocorr == False):
return self.conf_cmaps, [
None
] + self.cmap_mifiles[1:], self.all_lagtimes
else:
return self.conf_cmaps, self.cmap_mifiles, self.all_lagtimes