def LoadFromConfig(ConfigFile, input_sect='input', outFolder=None):
"""Loads a SALS object from a config file like the one exported with VelMaps.ExportConfig()
Parameters
----------
ConfigFile : full path of the config file to read
outFolder : folder containing velocity and correlation maps.
if None, the value from the config file will be used
if not None, the value from the config file will be discarded
Returns
-------
a SALS object, eventually with an "empty" image MIfile (containing metadata but no actual image data)
"""
config = cf.Config(ConfigFile)
froot = config.Get('global', 'root', '', str)
miin_fname = config.Get(input_sect, 'mi_file', None, str)
miin_meta_fname = config.Get(input_sect, 'meta_file', None, str)
input_stack = False
if (miin_fname is not None):
# if miin_fname is a string, let's use a single MIfile as input.
# otherwise, it can be a list: in that case, let's use a MIstack as input
if (isinstance(miin_fname, str)):
miin_fname = os.path.join(froot, miin_fname)
else:
input_stack = True
for i in range(len(miin_fname)):
miin_fname[i] = os.path.join(froot, miin_fname[i])
if (miin_meta_fname is not None):
miin_meta_fname = os.path.join(froot, miin_meta_fname)
elif input_stack:
logging.error(
'SALS.LoadFromConfig ERROR: medatada filename must be specified when loading a MIstack'
)
return None
if input_stack:
MIin = MIs.MIstack(miin_fname,
miin_meta_fname,
Load=True,
StackType='t')
else:
MIin = MI.MIfile(miin_fname, miin_meta_fname)
ctrPos = config.Get('SALS_parameters', 'center_pos', None, float)
if (ctrPos is None):
logging.error(
'SALS.LoadFromConfig ERROR: no SALS_parameters.center_pos parameter found in config file '
+ str(ConfigFile))
return None
else:
r_max = ppf.MaxRadius(MIin.ImageShape(), ctrPos)
radRange = sf.ValidateRange(config.Get('SALS_parameters', 'r_range',
None, float),
r_max,
MinVal=1,
replaceNone=True)
angRange = sf.ValidateRange(config.Get('SALS_parameters', 'a_range',
None, float),
2 * np.pi,
replaceNone=True)
rSlices = np.geomspace(radRange[0],
radRange[1],
int(radRange[2]) + 1,
endpoint=True)
aSlices = np.linspace(angRange[0],
angRange[1],
int(angRange[2]) + 1,
endpoint=True)
if (outFolder is None):
outFolder = config.Get(input_sect, 'out_folder', None, str)
if (outFolder is not None):
outFolder = os.path.join(config.Get('global', 'root', '', str),
outFolder)
mask = config.Get('SALS_parameters', 'px_mask', None, str)
mask = MI.ReadBinary(
sf.PathJoinOrNone(froot,
config.Get(input_sect, 'px_mask', mask, str)),
MIin.ImageShape(), MIin.DataFormat(), 0)
dark = MI.ReadBinary(
sf.PathJoinOrNone(froot,
config.Get(input_sect, 'dark_bkg', None, str)),
MIin.ImageShape(), MIin.DataFormat(), 0)
opt = MI.ReadBinary(
sf.PathJoinOrNone(froot,
config.Get(input_sect, 'opt_bkg', None, str)),
MIin.ImageShape(), MIin.DataFormat(), 0)
PD_data = sf.PathJoinOrNone(
froot, config.Get(input_sect, 'pd_file', None, str))
if (PD_data is not None):
PD_data = np.loadtxt(PD_data, dtype=float)
img_times = config.Get(input_sect, 'img_times', None, str)
if img_times is not None:
# if miin_fname is a string, let's use a single text file as input.
# otherwise, it can be a list: in that case, let's open each text file and append all results
if (isinstance(img_times, str)):
img_times = np.loadtxt(os.path.join(froot, img_times),
dtype=float,
usecols=config.Get(
'format', 'img_times_colidx', 0,
int),
skiprows=1)
else:
tmp_times = np.empty(shape=(0, ), dtype=float)
for cur_f in img_times:
tmp_times = np.append(
tmp_times,
np.loadtxt(os.path.join(froot, cur_f),
dtype=float,
usecols=config.Get('format',
'img_times_colidx', 0,
int),
skiprows=1))
img_times = tmp_times
exp_times = sf.PathJoinOrNone(
froot, config.Get(input_sect, 'exp_times', None, str))
if (exp_times is not None):
exp_times = np.unique(
np.loadtxt(exp_times,
dtype=float,
usecols=config.Get('format', 'exp_times_colidx', 0,
int)))
dlsLags = config.Get('SALS_parameters', 'dls_lags', None, int)
tavgT = config.Get('SALS_parameters', 'timeavg_T', None, int)
return SALS(MIin, outFolder, ctrPos, [rSlices, aSlices], mask,
[dark, opt, PD_data], exp_times, dlsLags, img_times, tavgT)
def Validate_zRange(zRange, zSize, replaceNone=True):
return sf.ValidateRange(zRange, zSize, MinVal=0, replaceNone=replaceNone)