Commit 11d8e24b authored by Chris Smith's avatar Chris Smith
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Update uiGetFile call in notebook

parent b0b1cfc3
%% Cell type:markdown id: tags:
# Band Excitation data procesing using pycroscopy
### Suhas Somnath, Chris R. Smith, Stephen Jesse
The Center for Nanophase Materials Science and The Institute for Functional Imaging for Materials <br>
Oak Ridge National Laboratory<br>
%% Cell type:markdown id: tags:
## Configure the notebook
%% Cell type:code id: tags:
``` python
!pip install -U numpy matplotlib Ipython ipywidgets pycroscopy
# Ensure python 3 compatibility
from __future__ import division, print_function, absolute_import
# Import necessary libraries:
# General utilities:
import sys
import os
# Computation:
import numpy as np
import h5py
# Visualization:
import matplotlib.pyplot as plt
from IPython.display import display
import ipywidgets as widgets
# Finally, pycroscopy itself
import pycroscopy as px
# set up notebook to show plots within the notebook
% matplotlib inline
%% Cell type:markdown id: tags:
## Set some basic parameters for computation
This notebook performs some functional fitting whose duration can be substantially decreased by using more memory and CPU cores. We have provided default values below but you may choose to change them if necessary.
%% Cell type:code id: tags:
``` python
max_mem = 1024*8 # Maximum memory to use, in Mbs. Default = 1024
max_cores = None # Number of logical cores to use in fitting. None uses all but 2 available cores.
%% Cell type:markdown id: tags:
## Make the data pycroscopy compatible
Converting the raw data into a pycroscopy compatible hierarchical data format (HDF or .h5) file gives you access to the fast fitting algorithms and powerful analysis functions within pycroscopy
#### H5 files:
* are like smart containers that can store matrices with data, folders to organize these datasets, images, metadata like experimental parameters, links or shortcuts to datasets, etc.
* are readily compatible with high-performance computing facilities
* scale very efficiently from few kilobytes to several terabytes
* can be read and modified using any language including Python, Matlab, C/C++, Java, Fortran, Igor Pro, etc.
#### You can load either of the following:
* Any .mat or .txt parameter file from the original experiment
* A .h5 file generated from the raw data using pycroscopy - skips translation
You can select desired file type by choosing the second option in the pull down menu on the bottom right of the file window
%% Cell type:code id: tags:
``` python
input_file_path = px.io_utils.uiGetFile(caption='Select translated .h5 file or raw experiment data',
filter='Parameters for raw BE data (*.txt *.mat *xls *.xlsx);; \
file_filter='Parameters for raw BE data (*.txt *.mat *xls *.xlsx);; \
Translated file (*.h5)')
(data_dir, data_name) = os.path.split(input_file_path)
if input_file_path.endswith('.h5'):
# No translation here
h5_path = input_file_path
force = False # Set this to true to force patching of the datafile.
tl = px.LabViewH5Patcher()
hdf = tl.translate(h5_path, force_patch=force)
# Set the data to be translated
data_path = input_file_path
(junk, base_name) = os.path.split(data_dir)
# Check if the data is in the new or old format. Initialize the correct translator for the format.
if base_name == 'newdataformat':
(junk, base_name) = os.path.split(junk)
translator = px.BEPSndfTranslator(max_mem_mb=max_mem)
translator = px.BEodfTranslator(max_mem_mb=max_mem)
if base_name.endswith('_d'):
base_name = base_name[:-2]
# Translate the data
h5_path = translator.translate(data_path, show_plots=True, save_plots=False)
hdf = px.ioHDF5(h5_path)
print('Working on:\n' + h5_path)
h5_main = px.hdf_utils.getDataSet(hdf.file, 'Raw_Data')[0]
%% Cell type:markdown id: tags:
##### Inspect the contents of this h5 data file
The file contents are stored in a tree structure, just like files on a conventional computer.
The data is stored as a 2D matrix (position, spectroscopic value) regardless of the dimensionality of the data. Thus, the positions will be arranged as row0-col0, row0-col1.... row0-colN, row1-col0.... and the data for each position is stored as it was chronologically collected
The main dataset is always accompanied by four ancillary datasets that explain the position and spectroscopic value of any given element in the dataset.
%% Cell type:code id: tags:
``` python
print('Datasets and datagroups within the file:\n------------------------------------')
print('\nThe main dataset:\n------------------------------------')
print('\nThe ancillary datasets:\n------------------------------------')
print('\nMetadata or attributes in a datagroup\n------------------------------------')
for key in hdf.file['/Measurement_000'].attrs:
print('{} : {}'.format(key, hdf.file['/Measurement_000'].attrs[key]))
%% Cell type:markdown id: tags:
## Get some basic parameters from the H5 file
This information will be vital for futher analysis and visualization of the data
%% Cell type:code id: tags:
``` python
h5_pos_inds = px.hdf_utils.getAuxData(h5_main, auxDataName='Position_Indices')[-1]
pos_sort = px.hdf_utils.get_sort_order(np.transpose(h5_pos_inds))
pos_dims = px.hdf_utils.get_dimensionality(np.transpose(h5_pos_inds), pos_sort)
pos_labels = np.array(px.hdf_utils.get_attr(h5_pos_inds, 'labels'))[pos_sort]
print(pos_labels, pos_dims)
parm_dict = hdf.file['/Measurement_000'].attrs
is_ckpfm = hdf.file.attrs['data_type'] == 'cKPFMData'
if is_ckpfm:
num_write_steps = parm_dict['VS_num_DC_write_steps']
num_read_steps = parm_dict['VS_num_read_steps']
num_fields = 2
%% Cell type:markdown id: tags:
## Visualize the raw data
Use the sliders below to visualize spatial maps (2D only for now), and spectrograms.
For simplicity, all the spectroscopic dimensions such as frequency, excitation bias, cycle, field, etc. have been collapsed to a single slider.
%% Cell type:code id: tags:
``` python
%% Cell type:markdown id: tags:
## Fit the Band Excitation (BE) spectra
Fit each of the acquired spectra to a simple harmonic oscillator (SHO) model to extract the following information regarding the response:
* Oscillation amplitude
* Phase
* Resonance frequency
* Quality factor
By default, the cell below will take any previous result instead of re-computing the SHO fit
%% Cell type:code id: tags:
``` python
sho_fit_points = 5 # The number of data points at each step to use when fitting
h5_sho_group = px.hdf_utils.findH5group(h5_main, 'SHO_Fit')
sho_fitter = px.BESHOmodel(h5_main, parallel=True)
if len(h5_sho_group) == 0:
print('No SHO fit found. Doing SHO Fitting now')
h5_sho_guess = sho_fitter.do_guess(strategy='complex_gaussian', processors=max_cores, options={'num_points':sho_fit_points})
h5_sho_fit = sho_fitter.do_fit(processors=max_cores)
print('Taking previous SHO results already present in file')
h5_sho_guess = h5_sho_group[-1]['Guess']
h5_sho_fit = h5_sho_group[-1]['Fit']
except KeyError:
print('Previously computed guess found. Now computing fit')
h5_sho_fit = sho_fitter.do_fit(processors=max_cores, h5_guess=h5_sho_guess)
%% Cell type:markdown id: tags:
## Visualize the SHO results
Here, we visualize the parameters for the SHO fits. BE-line (3D) data is visualized via simple spatial maps of the SHO parameters while more complex BEPS datasets (4+ dimensions) can be visualized using a simple interactive visualizer below.
You can choose to visualize the guesses for SHO function or the final fit values from the first line of the cell below.
Use the sliders below to inspect the BE response at any given location.
%% Cell type:code id: tags:
``` python
h5_sho_spec_inds = px.hdf_utils.getAuxData(h5_sho_fit, auxDataName='Spectroscopic_Indices')[0]
sho_spec_labels =,'labels')
if is_ckpfm:
# It turns out that the read voltage index starts from 1 instead of 0
# Also the VDC indices are NOT repeating. They are just rising monotonically
write_volt_index = np.argwhere(sho_spec_labels == 'write_bias')[0][0]
read_volt_index = np.argwhere(sho_spec_labels == 'read_bias')[0][0]
h5_sho_spec_inds[read_volt_index, :] -= 1
h5_sho_spec_inds[write_volt_index, :] = np.tile(np.repeat(np.arange(num_write_steps), num_fields), num_read_steps)
(Nd_mat, success, nd_labels) =, get_labels=True)
print('Reshape Success: ' + str(success))
%% Cell type:code id: tags:
``` python
use_sho_guess = False
use_static_viz_func = False
if use_sho_guess:
sho_dset = h5_sho_guess
sho_dset = h5_sho_fit
data_type =, 'data_type')
if data_type == 'BELineData' or len(pos_dims) != 2:
use_static_viz_func = True
step_chan = None
vs_mode =, 'VS_mode')
if vs_mode not in ['AC modulation mode with time reversal',
'DC modulation mode']:
use_static_viz_func = True
if vs_mode == 'DC modulation mode':
step_chan = 'DC_Offset'
step_chan = 'AC_Amplitude'
if not use_static_viz_func:
# use interactive visualization
px.be_viz_utils.jupyter_visualize_beps_sho(sho_dset, step_chan)
print('There was a problem with the interactive visualizer')
use_static_viz_func = True
if use_static_viz_func:
# show plots of SHO results vs. applied bias
px.be_viz_utils.visualize_sho_results(sho_dset, show_plots=True,
%% Cell type:markdown id: tags:
## Fit loops to a function
This is applicable only to DC voltage spectroscopy datasets from BEPS. The PFM hysteresis loops in this dataset will be projected to maximize the loop area and then fitted to a function.
Note: This computation generally takes a while for reasonably sized datasets.
%% Cell type:code id: tags:
``` python
# Do the Loop Fitting on the SHO Fit dataset
loop_success = False
h5_loop_group = px.hdf_utils.findH5group(h5_sho_fit, 'Loop_Fit')
if len(h5_loop_group) == 0:
loop_fitter = px.BELoopModel(h5_sho_fit, parallel=True)
print('No loop fits found. Fitting now....')
h5_loop_guess = loop_fitter.do_guess(processors=max_cores, max_mem=max_mem)
h5_loop_fit = loop_fitter.do_fit(processors=max_cores, max_mem=max_mem)
loop_success = True
except ValueError:
print('Loop fitting is applicable only to DC spectroscopy datasets!')
loop_success = True
print('Taking previously computed loop fits')
h5_loop_guess = h5_loop_group[-1]['Guess']
h5_loop_fit = h5_loop_group[-1]['Fit']
%% Cell type:markdown id: tags:
## Prepare datasets for visualization
%% Cell type:code id: tags:
``` python
# Prepare some variables for plotting loops fits and guesses
# Plot the Loop Guess and Fit Results
if loop_success:
h5_projected_loops = h5_loop_guess.parent['Projected_Loops']
h5_proj_spec_inds = px.hdf_utils.getAuxData(h5_projected_loops,
h5_proj_spec_vals = px.hdf_utils.getAuxData(h5_projected_loops,
# reshape the vdc_vec into DC_step by Loop
sort_order = px.hdf_utils.get_sort_order(h5_proj_spec_inds)
dims = px.hdf_utils.get_dimensionality(h5_proj_spec_inds[()],
vdc_vec = np.reshape(h5_proj_spec_vals[h5_proj_spec_vals.attrs['DC_Offset']], dims).T
#Also reshape the projected loops to Positions-DC_Step-Loop
# Also reshape the projected loops to Positions-DC_Step-Loop
proj_nd, _ = px.hdf_utils.reshape_to_Ndims(h5_projected_loops)
proj_3d = np.reshape(proj_nd, [h5_projected_loops.shape[0],
proj_nd.shape[2], -1])
%% Cell type:markdown id: tags:
## Visualize Loop fits
%% Cell type:code id: tags:
``` python
use_static_plots = False
if loop_success:
if not use_static_plots:
px.be_viz_utils.jupyter_visualize_beps_loops(h5_projected_loops, h5_loop_guess, h5_loop_fit)
print('There was a problem with the interactive visualizer')
use_static_plots = True
if use_static_plots:
for iloop in range(h5_loop_guess.shape[1]):
fig, ax = px.be_viz_utils.plot_loop_guess_fit(vdc_vec[:, iloop], proj_3d[:, :, iloop],
h5_loop_guess[:, iloop], h5_loop_fit[:, iloop],
title='Loop {} - All Positions'.format(iloop))
%% Cell type:markdown id: tags:
## Save and close
* Save the .h5 file that we are working on by closing it. <br>
* Also, consider exporting this notebook as a notebook or an html file. <br> To do this, go to File >> Download as >> HTML
* Finally consider saving this notebook if necessary
%% Cell type:code id: tags:
``` python
# hdf.close()
%% Cell type:code id: tags:
``` python
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