Commit c33f1ee5 authored by Rama Vasudevan's avatar Rama Vasudevan
Browse files

Changes to BEODF translator and BELoopFitter

Small change to BELoopFitter to allow it to work on FORC datasets, and a major update of the BE ODF translator to enable multiple channel translation (limited now to just one auxiliary channel).
parent c66552c8
......@@ -320,7 +320,7 @@ class BELoopFitter(Fitter):
if solver_options is None:
solver_options = {'jac': '2-point'}
Set the number of processors and the ammount of RAM to use in the fit
Set the number of processors and the amount of RAM to use in the fit
if processors is None:
processors = self._maxCpus
......@@ -378,7 +378,6 @@ class BELoopFitter(Fitter):
Do the fit
results = list()
legit_solver = solver_type in scipy.optimize.__dict__.keys()
legit_obj_func = obj_func['obj_func'] in BE_Fit_Methods().methods
if legit_solver and legit_obj_func:
......@@ -390,12 +389,9 @@ class BELoopFitter(Fitter):
obj_func={'class': 'BE_Fit_Methods', 'obj_func': 'BE_LOOP', 'xvals': vdc_shifted})
# TODO: need a different .reformatResults to process fitting results
temp = self._reformat_results(temp, obj_func['obj_func'])
temp = self._reshape_results_for_h5(temp, nd_mat_shape_dc_first)
results = self._reshape_results_for_h5(temp, nd_mat_shape_dc_first)
results.append(temp) = np.hstack(tuple(results))
self.h5_fit[self._start_pos:self._end_pos, self._current_met_spec_slice] = results
self._start_pos = self._end_pos
......@@ -18,8 +18,10 @@ from .df_utils.be_utils import trimUDVS, getSpectroscopicParmLabel, parmsToDict,
from import Translator, generate_dummy_main_parms
from import INDICES_DTYPE, VALUES_DTYPE, Dimension, calc_chunks
from import write_ind_val_dsets, write_main_dataset, write_region_references, \
create_indexed_group, write_simple_attrs, write_book_keeping_attrs
create_indexed_group, write_simple_attrs, write_book_keeping_attrs, copy_attributes,\
from import USIDataset
from import get_available_memory
class BEodfTranslator(Translator):
......@@ -115,6 +117,18 @@ class BEodfTranslator(Translator):
if real_size != imag_size:
raise ValueError("Real and imaginary file sizes DON'T match!. Ending")
#Check here if a second channel for current is present
# Look for the file containing the current data
file_names = listdir(folder_path)
aux_files = []
for fname in file_names:
if 'AI2' in fname:
if 'write' in fname:
current_file = path.join(folder_path, fname)
aux_files.append(path.join(folder_path, fname))
add_pix = False
num_rows = int(parm_dict['grid_num_rows'])
num_cols = int(parm_dict['grid_num_cols'])
......@@ -336,10 +350,16 @@ class BEodfTranslator(Translator):
spec_label=spec_label, show_plots=show_plots, save_plots=save_plots,
do_histogram=do_histogram, debug=verbose)
self.h5_raw = USIDataset(self.h5_raw)
#Go ahead and read the current data in the second (current) channel
if current_data_exists: #If a .dat file matches
self._read_secondary_channel(h5_meas_group, aux_files)
return h5_path
def _read_data(self, UDVS_mat, parm_dict, path_dict, real_size, isBEPS, add_pix):
Checks if the data is BEPS or BELine and calls the correct function to read the data from
......@@ -572,6 +592,107 @@ class BEodfTranslator(Translator):
return basename, path_dict
def _read_secondary_channel(self, h5_meas_group, aux_file_path):
Reads secondary channel stored in AI .mat file
Currently works for in-field measurements only, but should be updated to
include both in and out of field measurements
h5_meas_group : h5 group
Reference to the Measurement group
aux_file_path : String / Unicode
Absolute file path of the secondary channel file.
print('---- Reading Secondary Channel ----------')
if len(aux_file_path)>1:
print('Detected multiple files, assuming in and out of field')
aux_file_paths = aux_file_path
aux_file_paths = list(aux_file_path)
freq_index = self.h5_raw.spec_dim_labels.index('Frequency')
num_pix = self.h5_raw.shape[0]
spectral_len = 1
for i in range(len(self.h5_raw.spec_dim_sizes)):
if i == freq_index:
spectral_len = spectral_len * self.h5_raw.spec_dim_sizes[i]
#num_forc_cycles = self.h5_raw.spec_dim_sizes[self.h5_raw.spec_dim_labels.index("FORC")]
#num_dc_steps = self.h5_raw.spec_dim_sizes[self.h5_raw.spec_dim_labels.index("DC_Offset")]
# create a new channel
h5_current_channel_group = create_indexed_group(h5_meas_group, 'Channel')
# Copy attributes from the main channel
copy_attributes(self.h5_raw.parent, h5_current_channel_group)
# Modify attributes that are different
write_simple_attrs(h5_current_channel_group, {'Channel_Input': 'IO_Analog_Input_2',
'channel_type': 'Current'}, verbose=True)
#Get the reduced dimensions
h5_current_spec_inds, h5_current_spec_values = write_reduced_spec_dsets(h5_current_channel_group,
self.h5_raw.h5_spec_vals, 'Frequency')
h5_current_main = write_main_dataset(h5_current_channel_group, # parent HDF5 group
(num_pix, spectral_len), # shape of Main dataset
'Raw_Data', # Name of main dataset
'Current', # Physical quantity contained in Main dataset
'nA', # Units for the physical quantity
None, # Position dimensions
None, # Spectroscopic dimensions
dtype=np.float32, # data type / precision
main_dset_attrs={'IO_rate': 4E+6, 'Amplifier_Gain': 9})
# Now calculate the number of positions that can be stored in memory in one go.
b_per_position = np.float32(0).itemsize * spectral_len
max_pos_per_read = int(np.floor((get_available_memory()) / b_per_position))
# if self._verbose:
print('Allowed to read {} pixels per chunk'.format(max_pos_per_read))
#Open the read and write files and write them to the hdf5 file
for aux_file in aux_file_paths:
if 'write' in aux_file:
infield = True
cur_file = open(aux_file, "rb")
start_pix = 0
while start_pix < num_pix:
end_pix = min(num_pix, start_pix + max_pos_per_read)
# TODO: Fix for when it won't fit in memory.
#if max_pos_per_read * b_per_position > num_pix * b_per_position:
cur_data = np.frombuffer(, dtype='f')
#cur_data = np.frombuffer( * b_per_position), dtype='f')
cur_data = cur_data.reshape(end_pix - start_pix, spectral_len//2)
# Write to h5
if infield:
h5_current_main[start_pix:end_pix, ::2] = cur_data
h5_current_main[start_pix:end_pix, 1::2] = cur_data
start_pix = end_pix
def __read_old_mat_be_vecs(file_path):
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