Unverified Commit 99c7a05f authored by Suhas Somnath's avatar Suhas Somnath Committed by GitHub
Browse files

Merge pull request #200 from pycroscopy/Rama-Dev

Rama dev merging for TRKPFM Translator Update
parents 6fb6b02e 941bd95c
......@@ -10,13 +10,12 @@ from __future__ import division, print_function, absolute_import, unicode_litera
from os import path, remove, listdir # File Path formatting
import numpy as np # For array operations
import h5py
from scipy.io import loadmat
from pyUSID.io.translator import Translator, generate_dummy_main_parms
from pyUSID.io.write_utils import Dimension
from pyUSID.io.hdf_utils import get_h5_obj_refs, link_h5_objects_as_attrs
from ..hdf_writer import HDFwriter # Now the translator is responsible for writing the data.
from ..virtual_data import VirtualGroup, VirtualDataset
from ..write_utils import build_ind_val_dsets
from pyUSID.io.hdf_utils import get_h5_obj_refs, link_h5_objects_as_attrs, \
write_simple_attrs, write_main_dataset, create_indexed_group
class TRKPFMTranslator(Translator):
......@@ -67,7 +66,7 @@ class TRKPFMTranslator(Translator):
data_lengths = []
while cont_cond:
print(count, f.tell())
#print(count, f.tell())
count += 1
data_length = np.fromfile(f, dtype=np.float32, count=1)
......@@ -108,6 +107,7 @@ class TRKPFMTranslator(Translator):
f = open(self.file_list[0], 'rb')
spectrogram_size, count_vals = self._parse_spectrogram_size(f)
print("Excitation waveform shape: ", excit_wfm.shape)
print("spectrogram size:", spectrogram_size)
num_pixels = parm_dict['grid_num_rows'] * parm_dict['grid_num_cols']
print('Number of pixels: ', num_pixels)
......@@ -115,65 +115,76 @@ class TRKPFMTranslator(Translator):
if (num_pixels + 1) != count_vals:
print("Data size does not match number of pixels expected. Cannot continue")
#Find how many channels we have to make
num_ai_chans = num_dat_files // 2 # Division by 2 due to real/imaginary
# Now start creating datasets and populating:
#Start with getting an h5 file
h5_file = h5py.File(self.h5_path)
ds_spec_inds, ds_spec_vals = build_ind_val_dsets(Dimension('Bias', 'V', excit_wfm), is_spectral=True,
#First create a measurement group
h5_meas_group = create_indexed_group(h5_file, 'Measurement')
ds_spec_vals.data = np.atleast_2d(excit_wfm) # The data generated above varies linearly. Override.
#Set up some parameters that will be written as attributes to this Measurement group
global_parms = generate_dummy_main_parms()
global_parms['data_type'] = 'trKPFM'
global_parms['translator'] = 'trKPFM'
write_simple_attrs(h5_meas_group, global_parms)
write_simple_attrs(h5_meas_group, parm_dict)
pos_desc = [Dimension('X', 'a.u.', np.arange(parm_dict['grid_num_cols'])),
Dimension('Y', 'a.u.', np.arange(parm_dict['grid_num_rows']))]
#Now start building the position and spectroscopic dimension containers
#There's only one spectroscpoic dimension and two position dimensions
ds_pos_ind, ds_pos_val = build_ind_val_dsets(pos_desc, is_spectral=False, verbose=False)
#The excit_wfm only has the DC values without any information on cycles, time, etc.
#What we really need is to add the time component. For every DC step there are some time steps.
ds_raw_data = VirtualDataset('Raw_Data', data=[],
maxshape=(ds_pos_ind.shape[0], spectrogram_size - 5),
dtype=np.complex64, chunking=(1, spectrogram_size - 5), compression='gzip')
ds_raw_data.attrs['quantity'] = ['Complex']
num_time_steps = (spectrogram_size-5) //excit_wfm.size
aux_ds_names = ['Position_Indices', 'Position_Values',
'Spectroscopic_Indices', 'Spectroscopic_Values']
#Let's repeat the excitation so that we get the full vector of same size as the spectrogram
#TODO: Check if this is the norm for this type of dataset
num_ai_chans = np.int(num_dat_files / 2) # Division by 2 due to real/imaginary
full_spect_val = np.copy(excit_wfm).repeat(num_time_steps)
# technically should change the date, etc.
spm_data = VirtualGroup('')
global_parms = generate_dummy_main_parms()
global_parms['data_type'] = 'trKPFM'
global_parms['translator'] = 'trKPFM'
spm_data.attrs = global_parms
meas_grp = VirtualGroup('Measurement_000')
meas_grp.attrs = parm_dict
spec_dims = Dimension('Bias', 'V', full_spect_val)
pos_dims = [Dimension('Cols', 'nm', parm_dict['grid_num_cols']),
Dimension('Rows', 'um', parm_dict['grid_num_rows'])]
hdf = HDFwriter(self.h5_path)
# spm_data.showTree()
hdf.write(spm_data, print_log=False)
self.raw_datasets = list()
for chan_index in range(num_ai_chans):
chan_grp = VirtualGroup('{:s}{:03d}'.format('Channel_', chan_index), '/Measurement_000/')
chan_grp = create_indexed_group(h5_meas_group,'Channel')
if chan_index == 0:
chan_grp.attrs = {'Harmonic': 1}
write_simple_attrs(chan_grp,{'Harmonic': 1})
chan_grp.attrs = {'Harmonic': 2}
chan_grp.add_children([ds_pos_ind, ds_pos_val, ds_spec_inds, ds_spec_vals,
h5_refs = hdf.write(chan_grp, print_log=False)
h5_raw = get_h5_obj_refs(['Raw_Data'], h5_refs)[0]
link_h5_objects_as_attrs(h5_raw, get_h5_obj_refs(aux_ds_names, h5_refs))
write_simple_attrs(chan_grp,{'Harmonic': 2})
h5_raw = write_main_dataset(chan_grp, # parent HDF5 group
(num_pixels, spectrogram_size - 5),
# shape of Main dataset
'Raw_Data', # Name of main dataset
'Deflection', # Physical quantity contained in Main dataset
'V', # Units for the physical quantity
pos_dims, # Position dimensions
spec_dims, # Spectroscopic dimensions
dtype=np.complex64, # data type / precision
chunks=(1, spectrogram_size - 5),
main_dset_attrs={'quantity': 'Complex'})
#h5_refs = hdf.write(chan_grp, print_log=False)
#h5_raw = get_h5_obj_refs(['Raw_Data'], h5_refs)[0]
#link_h5_objects_as_attrs(h5_raw, get_h5_obj_refs(aux_ds_names, h5_refs))
# Now that the N channels have been made, populate them with the actual data....
self._read_data(parm_dict, parm_path, spectrogram_size)
return self.h5_path
def _read_data(self, parm_dict, parm_path, data_length):
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