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Commit 8a5734de authored by ssomnath's avatar ssomnath
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Added verbose statements to Q factor checking

parent cc6a0c96
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pycroscopy/io/translators/be_odf.py
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......@@ -577,22 +577,36 @@ class BEodfTranslator(Translator):
# Do this for all BE-Line (always small enough to read in one shot)
if verbose:
print('\t\tReading all raw data for BE-Line in one shot')
self._quick_read_data(path_dict['read_real'], path_dict['read_imag'], parm_dict['num_udvs_steps'])
elif real_size < self.max_ram and parm_dict['VS_measure_in_field_loops'] == 'out-of-field':
self._quick_read_data(path_dict['read_real'],
path_dict['read_imag'],
parm_dict['num_udvs_steps'],
verbose=verbose)
elif real_size < self.max_ram and \
parm_dict['VS_measure_in_field_loops'] == 'out-of-field':
# Do this for out-of-field BEPS ONLY that is also small (256 MB)
if verbose:
print('\t\tReading all raw BEPS (out-of-field) data in one shot')
self._quick_read_data(path_dict['read_real'], path_dict['read_imag'], parm_dict['num_udvs_steps'])
elif real_size < self.max_ram and parm_dict['VS_measure_in_field_loops'] == 'in-field':
print('\t\tReading all raw BEPS (out-of-field) data at once')
self._quick_read_data(path_dict['read_real'],
path_dict['read_imag'],
parm_dict['num_udvs_steps'],
verbose=verbose)
elif real_size < self.max_ram and \
parm_dict['VS_measure_in_field_loops'] == 'in-field':
# Do this for in-field only
if verbose:
print('\t\tReading all raw BEPS (in-field only) data in one shot')
self._quick_read_data(path_dict['write_real'], path_dict['write_imag'], parm_dict['num_udvs_steps'])
print('\t\tReading all raw BEPS (in-field only) data at once')
self._quick_read_data(path_dict['write_real'],
path_dict['write_imag'],
parm_dict['num_udvs_steps'],
verbose=verbose)
else:
# Large BEPS datasets OR those with in-and-out of field
if verbose:
print('\t\tReading all raw data for in and out of filed OR very large file')
self._read_beps_data(path_dict, UDVS_mat.shape[0], parm_dict['VS_measure_in_field_loops'], add_pix)
print('\t\tReading all raw data for in-and-out-of-field OR '
'very large file one pixel at a time')
self._read_beps_data(path_dict, UDVS_mat.shape[0],
parm_dict['VS_measure_in_field_loops'],
add_pix)
self.h5_raw.file.flush()
def _read_beps_data(self, path_dict, udvs_steps, mode, add_pixel=False):
......@@ -698,7 +712,8 @@ class BEodfTranslator(Translator):
print('---- Finished reading files -----')
def _quick_read_data(self, real_path, imag_path, udvs_steps):
def _quick_read_data(self, real_path, imag_path, udvs_steps,
verbose=False):
"""
Returns information about the excitation BE waveform present in the .mat file
......@@ -710,18 +725,25 @@ class BEodfTranslator(Translator):
Absolute file path of the real data file
udvs_steps : unsigned int
Number of UDVS steps
verbose : bool, optional. Defdault = False
Whether or not to print debugging logs
"""
print('---- reading all data at once ----------')
parser = BEodfParser(real_path, imag_path, self.h5_raw.shape[0], self.h5_raw.shape[1] * 4)
parser = BEodfParser(real_path, imag_path, self.h5_raw.shape[0],
self.h5_raw.shape[1] * 4)
step_size = self.h5_raw.shape[1] / udvs_steps
rand_spectra = self._get_random_spectra([parser], self.h5_raw.shape[0], udvs_steps, step_size,
num_spectra=self.num_rand_spectra)
rand_spectra = self._get_random_spectra([parser],
self.h5_raw.shape[0],
udvs_steps, step_size,
num_spectra=self.num_rand_spectra,
verbose=verbose)
if verbose:
print('\t\t\tChecking if conjugate is required')
take_conjugate = requires_conjugate(rand_spectra, cores=self._cores)
raw_vec = parser.read_all_data()
if take_conjugate:
print('Taking conjugate to ensure positive Quality factors')
if verbose:
print('\t'*4 + 'Taking conjugate for positive quality factors')
raw_vec = np.conjugate(raw_vec)
if raw_vec.shape != np.prod(self.h5_raw.shape):
......@@ -736,7 +758,6 @@ class BEodfTranslator(Translator):
else:
raw_mat = raw_vec.reshape(self.h5_raw.shape[0], self.h5_raw.shape[1])
# Write to the h5 dataset:
self.mean_resp = np.mean(raw_mat, axis=0)
self.max_resp = np.amax(np.abs(raw_mat), axis=0)
......@@ -1426,7 +1447,8 @@ class BEodfTranslator(Translator):
return UD_VS_table_label, UD_VS_table_unit, udvs_table
@staticmethod
def _get_random_spectra(parsers, num_pixels, num_udvs_steps, num_bins, num_spectra=100, verbose=False):
def _get_random_spectra(parsers, num_pixels, num_udvs_steps, num_bins,
num_spectra=100, verbose=False):
"""
Parameters
----------
......@@ -1448,6 +1470,11 @@ class BEodfTranslator(Translator):
chosen_spectra : 2D complex numpy array
spectrogram or spectra arranged as [instance, spectrum]
"""
if verbose:
print('\t' * 4 + 'Getting random spectra for Q factor testing')
print('\t' * 4 + 'num_pixels: {} num_udvs_steps: {}, num_bins: {},'
' num_spectra: {}'.format(num_pixels, num_udvs_steps,
num_bins, num_spectra))
num_pixels = int(num_pixels)
num_udvs_steps = int(num_udvs_steps)
num_bins = int(num_bins)
......@@ -1458,7 +1485,17 @@ class BEodfTranslator(Translator):
selected_parsers = np.random.randint(0, len(parsers), size=num_spectra)
if verbose:
print('Selecting the following random pixels, UDVS steps, parsers')
print('\t' * 4 + 'num_spectra: {}'.format(num_spectra))
print('\t' * 4 + 'selected_pixels:\n' + '\t' * 5 +
'{}'.format(selected_pixels))
print('\t' * 4 + 'selected_steps:\n' + '\t' * 5 +
'{}'.format(selected_steps))
print('\t' * 4 + 'selected_parsers:\n' + '\t' * 5 +
'{}'.format(selected_parsers))
if verbose:
print('\t' * 4 + 'Selecting the following random pixels, '
'UDVS steps, parsers')
print(np.vstack((selected_pixels, selected_steps, selected_parsers)))
chosen_spectra = np.zeros(shape=(num_spectra, num_bins), dtype=np.complex64)
......
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