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Commit e0c6d930 authored by ssomnath's avatar ssomnath
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get_parms_from_old_mat now has verbose mode

parent 6c4ed5fc
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pycroscopy/io/translators/be_odf.py
View file @ e0c6d930
......@@ -114,7 +114,8 @@ class BEodfTranslator(Translator):
else:
return None
def translate(self, file_path, show_plots=True, save_plots=True, do_histogram=False, verbose=False):
def translate(self, file_path, show_plots=True, save_plots=True,
do_histogram=False, verbose=False):
"""
Translates .dat data file(s) to a single .h5 file
......@@ -152,7 +153,7 @@ class BEodfTranslator(Translator):
elif 'old_mat_parms' in path_dict.keys():
if verbose:
print('\treading parameters from old mat file')
parm_dict = self.__get_parms_from_old_mat(path_dict['old_mat_parms'])
parm_dict = self.__get_parms_from_old_mat(path_dict['old_mat_parms'], verbose=verbose)
if parm_dict['VS_steps_per_full_cycle'] == 0:
isBEPS=False
else:
......@@ -367,6 +368,10 @@ class BEodfTranslator(Translator):
parm_dict,
UDVS_labs,
UDVS_units)
if verbose:
print('\t\tspec_vals_labs_names: {}'.format(spec_vals_labs_names))
# Not sure what is happening here but this should work.
spec_dim_dict = dict()
for entry in spec_vals_labs_names:
......@@ -972,7 +977,7 @@ class BEodfTranslator(Translator):
return 0, 0
@staticmethod
def __get_parms_from_old_mat(file_path):
def __get_parms_from_old_mat(file_path, verbose=False):
"""
Formats parameters found in the old parameters .mat file into a dictionary
as though the dataset had a parms.txt describing it
......@@ -981,6 +986,8 @@ class BEodfTranslator(Translator):
--------------------
file_path : Unicode / String
absolute filepath of the .mat file containing the parameters
verbose : bool, optional, default = False
Whether or not to print statemetns for debugging purposes
Returns
--------------------
......@@ -1009,7 +1016,11 @@ class BEodfTranslator(Translator):
try:
BE_parm_vec_2 = matread['BE_parm_vec_2']
except KeyError:
BE_parm_vec_2 = 'None'
BE_parm_vec_2 = None
if verbose:
print('\t\tBE_parm_vec_1: {}'.format(BE_parm_vec_1))
print('\t\tBE_parm_vec_2: {}'.format(BE_parm_vec_2))
# Not required for translation but necessary to have
if BE_parm_vec_1[0] == 3 or BE_parm_vec_2[0] == 3:
......@@ -1031,6 +1042,8 @@ class BEodfTranslator(Translator):
parm_dict['BE_bins_per_read'] = len(matread['bin_w'])
assembly_parm_vec = matread['assembly_parm_vec']
if verbose:
print('\t\tassembly_parm_vec: {}'.format(assembly_parm_vec))
if assembly_parm_vec[2] == 0:
parm_dict['VS_measure_in_field_loops'] = 'out-of-field'
......@@ -1051,6 +1064,10 @@ class BEodfTranslator(Translator):
VS_parms = matread['SS_parm_vec']
dc_amp_vec_full = matread['dc_amp_vec_full']
if verbose:
print('\t\tVS_parms: {}'.format(VS_parms))
print('\t\tdc_amp_vec_full: {}'.format(dc_amp_vec_full))
VS_start_V = VS_parms[4]
VS_start_loop_amp = VS_parms[5]
VS_final_loop_amp = VS_parms[6]
......@@ -1072,15 +1089,20 @@ class BEodfTranslator(Translator):
parm_dict['FORC_V_low2_[V]'] = -10
if VS_parms[0] == 0 or VS_parms[0] == 9:
if verbose:
print('\t\tDC modulation or current mode based on VS parms[0]')
parm_dict['VS_mode'] = 'DC modulation mode'
if VS_parms[0] == 9:
if verbose:
print('\t\tcurrent mode based on VS parms[0]')
parm_dict['VS_mode'] = 'current mode'
parm_dict['VS_amplitude_[V]'] = 0.5 * (max(dc_amp_vec_full) - np.min(dc_amp_vec_full)) # SS_max_offset_amplitude
parm_dict['VS_offset_[V]'] = np.max(dc_amp_vec_full) + np.min(
dc_amp_vec_full)
elif VS_parms[0] == 1 or VS_parms[0] == 6 or VS_parms[0] == 7:
# FORC
if verbose:
print('\t\tFORC, based on VS parms[0]')
# Could not tell difference between mode = 1 or 6
# mode 7 = multiple FORC cycles
parm_dict['VS_mode'] = 'DC modulation mode'
......@@ -1088,12 +1110,18 @@ class BEodfTranslator(Translator):
'VS_amplitude_[V]'] = 1 # VS_parms[1] # SS_max_offset_amplitude
parm_dict['VS_offset_[V]'] = 0
if VS_parms[0] == 7:
if verbose:
print('\t\t\tFORC with 2 cycles')
parm_dict['VS_number_of_cycles'] = 2
parm_dict['FORC_num_of_FORC_cycles'] = VS_parms[2] // 2
else:
if verbose:
print('\t\t\tFORC with 1 cycle')
parm_dict['VS_number_of_cycles'] = 1
parm_dict['FORC_num_of_FORC_cycles'] = VS_parms[2]
if True:
if verbose:
print('\t\t\tMeasuring FORC high and low vals from DC vec')
# Grabbing hi lo values directly from the vec
left = dc_amp_vec_full[:parm_dict['VS_steps_per_full_cycle']]
right = dc_amp_vec_full[
......@@ -1103,6 +1131,8 @@ class BEodfTranslator(Translator):
parm_dict['FORC_V_low1_[V]'] = np.min(left)
parm_dict['FORC_V_low2_[V]'] = np.min(right)
else:
if verbose:
print('\t\t\tGrabbing FORC high and low vals from parms')
# Not getting correct values with prescribed method
parm_dict['FORC_V_high1_[V]'] = VS_start_V
parm_dict['FORC_V_high2_[V]'] = VS_start_V
......@@ -1110,7 +1140,8 @@ class BEodfTranslator(Translator):
parm_dict['FORC_V_low2_[V]'] = VS_start_V - VS_final_loop_amp
elif VS_parms[0] == 2 or VS_parms[0] == 3:
# AC mode
if verbose:
print('\t\tAC Spectroscopy with time reversal, based on VS parms')
if VS_parms[0] == 3:
# These numbers seemed to match with the v_dc vector
parm_dict['VS_number_of_cycles'] = int(VS_parms[2]) * 2
......@@ -1120,29 +1151,42 @@ class BEodfTranslator(Translator):
parm_dict['VS_amplitude_[V]'] = 0.5 * VS_final_loop_amp
parm_dict[
'VS_offset_[V]'] = 0 # this is not correct. Fix manually when it comes to UDVS generation?
# print('---We have AC Modulation mode file here---')
else:
# Did not see any examples of this...
parm_dict['VS_mode'] = 'Custom'
# Assigning the phase and fraction for bi-polar triangular waveforms
if VS_parms[0] not in [2, 3]:
if verbose:
print('\t\tEstimating phase and fraction based on slopes of first cycle')
slopes = []
for ind in range(4):
subsection = dc_amp_vec_full[ind * parm_dict['VS_steps_per_full_cycle'] // 4: (ind + 1) * parm_dict['VS_steps_per_full_cycle'] // 4]
slopes.append(np.mean(np.diff(subsection)))
if verbose:
print('\t\t\tslopes for quarters: {}'.format(slopes))
frac, phas = BEodfTranslator.__infer_frac_phase(slopes)
if verbose:
print('\t\t\tCycle fraction: {}, Phase: {}'.format(frac, phas))
for str_val, num_val in zip(['full', '1/2', '1/4', '3/4'],
[1., 0.5, 0.25, 0.75]):
if frac == num_val:
parm_dict['VS_cycle_fraction'] = str_val
break
for str_val, num_val in zip(['1/4', '1/2', '3/4'],
[0.25, 0.5, 0.75]):
if phas == num_val:
parm_dict['VS_cycle_phase_shift'] = str_val
break
if verbose:
print('\t\t\tCycle fraction: {}, Phase: {}'
''.format(parm_dict['VS_cycle_fraction'],
parm_dict['VS_cycle_phase_shift']))
if verbose:
print('\t\tEstimating File params from path: {}'.format(file_path))
parent, _ = path.split(file_path)
parent, expt_name = path.split(parent)
if expt_name.endswith('_c'):
......@@ -1163,6 +1207,9 @@ class BEodfTranslator(Translator):
parm_dict['File_file_suffix'] = suffix
header = matread['__header__'].decode("utf-8")
if verbose:
print('\t\tEstimating experiment date and time from .mat file '
'header: {} '.format(header))
targ_str = 'Created on: '
try:
ind = header.index(targ_str)
......
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