Commit 9bff0fee authored by Unknown's avatar Unknown
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BE processing notebook update

parent 9d6383a4
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
# Band Excitation data procesing using pycroscopy # Band Excitation data procesing using pycroscopy
### Suhas Somnath, Chris R. Smith, Stephen Jesse ### Suhas Somnath, Chris R. Smith, Stephen Jesse
The Center for Nanophase Materials Science and The Institute for Functional Imaging for Materials <br> The Center for Nanophase Materials Science and The Institute for Functional Imaging for Materials <br>
Oak Ridge National Laboratory<br> Oak Ridge National Laboratory<br>
2/10/2017 2/10/2017
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
## Configure the notebook ## Configure the notebook
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
!pip install -U numpy matplotlib Ipython ipywidgets pycroscopy !pip install -U numpy matplotlib Ipython ipywidgets pycroscopy
# Ensure python 3 compatibility # Ensure python 3 compatibility
from __future__ import division, print_function, absolute_import from __future__ import division, print_function, absolute_import
# Import necessary libraries: # Import necessary libraries:
# General utilities: # General utilities:
import sys import sys
import os import os
import shutil import shutil
# Computation: # Computation:
import numpy as np import numpy as np
import h5py import h5py
# Visualization: # Visualization:
# import ipympl # import ipympl
import matplotlib.pyplot as plt import matplotlib.pyplot as plt
import matplotlib.widgets as mpw import matplotlib.widgets as mpw
from IPython.display import display, clear_output, HTML from IPython.display import display, clear_output, HTML
import ipywidgets as widgets import ipywidgets as widgets
# Finally, pycroscopy itself # Finally, pycroscopy itself
sys.path.append('..') sys.path.append('..')
import pycroscopy as px import pycroscopy as px
# set up notebook to show plots within the notebook # set up notebook to show plots within the notebook
% matplotlib notebook % matplotlib notebook
# Make Notebook take up most of page width # Make Notebook take up most of page width
display(HTML(data=""" display(HTML(data="""
<style> <style>
div#notebook-container { width: 95%; } div#notebook-container { width: 95%; }
div#menubar-container { width: 65%; } div#menubar-container { width: 65%; }
div#maintoolbar-container { width: 99%; } div#maintoolbar-container { width: 99%; }
</style> </style>
""")) """))
``` ```
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
## Set some basic parameters for computation ## 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. 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: %% Cell type:code id: tags:
``` python ``` python
max_mem = 1024*2 # Maximum memory to use, in Mbs. Default = 1024 max_mem = 1024*8 # Maximum memory to use, in Mbs. Default = 1024
max_cores = 2 # Number of logical cores to use in fitting. None uses all but 2 available cores. max_cores = None # Number of logical cores to use in fitting. None uses all but 2 available cores.
``` ```
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
## Make the data pycroscopy compatible ## 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 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: #### 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 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 * are readily compatible with high-performance computing facilities
* scale very efficiently from few kilobytes to several terabytes * 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. * 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: #### You can load either of the following:
* Any .mat or .txt parameter file from the original experiment * Any .mat or .txt parameter file from the original experiment
* A .h5 file generated from the raw data using pycroscopy - skips translation * 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 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: %% Cell type:code id: tags:
``` python ``` python
input_file_path = px.io_utils.uiGetFile(caption='Select translated .h5 file or raw experiment data', input_file_path = px.io_utils.uiGetFile(caption='Select translated .h5 file or raw experiment data',
file_filter='Parameters for raw BE data (*.txt *.mat *xls *.xlsx);; \ file_filter='Parameters for raw BE data (*.txt *.mat *xls *.xlsx);; \
Translated file (*.h5)') Translated file (*.h5)')
(data_dir, filename) = os.path.split(input_file_path) (data_dir, filename) = os.path.split(input_file_path)
if copy_input_file:
_, ext = os.path.splitext(filename)
temp_path = os.path.join(data_dir, 'temp_file'+ext)
if os.path.exists(temp_path):
os.remove(temp_path)
shutil.copy2(input_file_path, temp_path)
input_file_path = temp_path
if input_file_path.endswith('.h5'): if input_file_path.endswith('.h5'):
# No translation here # No translation here
h5_path = input_file_path h5_path = input_file_path
force = False # Set this to true to force patching of the datafile. force = False # Set this to true to force patching of the datafile.
tl = px.LabViewH5Patcher() tl = px.LabViewH5Patcher()
hdf = tl.translate(h5_path, force_patch=force) hdf = tl.translate(h5_path, force_patch=force)
else: else:
# Set the data to be translated # Set the data to be translated
data_path = input_file_path data_path = input_file_path
(junk, base_name) = os.path.split(data_dir) (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. # Check if the data is in the new or old format. Initialize the correct translator for the format.
if base_name == 'newdataformat': if base_name == 'newdataformat':
(junk, base_name) = os.path.split(junk) (junk, base_name) = os.path.split(junk)
translator = px.BEPSndfTranslator(max_mem_mb=max_mem) translator = px.BEPSndfTranslator(max_mem_mb=max_mem)
else: else:
translator = px.BEodfTranslator(max_mem_mb=max_mem) translator = px.BEodfTranslator(max_mem_mb=max_mem)
if base_name.endswith('_d'): if base_name.endswith('_d'):
base_name = base_name[:-2] base_name = base_name[:-2]
# Translate the data # Translate the data
h5_path = translator.translate(data_path, show_plots=True, save_plots=False) h5_path = translator.translate(data_path, show_plots=True, save_plots=False)
hdf = px.ioHDF5(h5_path) hdf = px.ioHDF5(h5_path)
print('Working on:\n' + h5_path) print('Working on:\n' + h5_path)
h5_main = px.hdf_utils.getDataSet(hdf.file, 'Raw_Data')[0] h5_main = px.hdf_utils.getDataSet(hdf.file, 'Raw_Data')[0]
``` ```
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
##### Inspect the contents of this h5 data file ##### 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 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 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. 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: %% Cell type:code id: tags:
``` python ``` python
print('Datasets and datagroups within the file:\n------------------------------------') print('Datasets and datagroups within the file:\n------------------------------------')
px.io.hdf_utils.print_tree(hdf.file) px.io.hdf_utils.print_tree(hdf.file)
print('\nThe main dataset:\n------------------------------------') print('\nThe main dataset:\n------------------------------------')
print(h5_main) print(h5_main)
print('\nThe ancillary datasets:\n------------------------------------') print('\nThe ancillary datasets:\n------------------------------------')
print(hdf.file['/Measurement_000/Channel_000/Position_Indices']) print(hdf.file['/Measurement_000/Channel_000/Position_Indices'])
print(hdf.file['/Measurement_000/Channel_000/Position_Values']) print(hdf.file['/Measurement_000/Channel_000/Position_Values'])
print(hdf.file['/Measurement_000/Channel_000/Spectroscopic_Indices']) print(hdf.file['/Measurement_000/Channel_000/Spectroscopic_Indices'])
print(hdf.file['/Measurement_000/Channel_000/Spectroscopic_Values']) print(hdf.file['/Measurement_000/Channel_000/Spectroscopic_Values'])
print('\nMetadata or attributes in a datagroup\n------------------------------------') print('\nMetadata or attributes in a datagroup\n------------------------------------')
for key in hdf.file['/Measurement_000'].attrs: for key in hdf.file['/Measurement_000'].attrs:
print('{} : {}'.format(key, hdf.file['/Measurement_000'].attrs[key])) print('{} : {}'.format(key, hdf.file['/Measurement_000'].attrs[key]))
``` ```
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
## Get some basic parameters from the H5 file ## Get some basic parameters from the H5 file
This information will be vital for futher analysis and visualization of the data This information will be vital for futher analysis and visualization of the data
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
h5_pos_inds = px.hdf_utils.getAuxData(h5_main, auxDataName='Position_Indices')[-1] 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_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_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] pos_labels = np.array(px.hdf_utils.get_attr(h5_pos_inds, 'labels'))[pos_sort]
print(pos_labels, pos_dims) print(pos_labels, pos_dims)
parm_dict = hdf.file['/Measurement_000'].attrs parm_dict = hdf.file['/Measurement_000'].attrs
is_ckpfm = hdf.file.attrs['data_type'] == 'cKPFMData' is_ckpfm = hdf.file.attrs['data_type'] == 'cKPFMData'
if is_ckpfm: if is_ckpfm:
num_write_steps = parm_dict['VS_num_DC_write_steps'] num_write_steps = parm_dict['VS_num_DC_write_steps']
num_read_steps = parm_dict['VS_num_read_steps'] num_read_steps = parm_dict['VS_num_read_steps']
num_fields = 2 num_fields = 2
``` ```
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
## Visualize the raw data ## Visualize the raw data
Use the sliders below to visualize spatial maps (2D only for now), and spectrograms. 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. 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: %% Cell type:code id: tags:
``` python ``` python
px.be_viz_utils.jupyter_visualize_be_spectrograms(h5_main) px.be_viz_utils.jupyter_visualize_be_spectrograms(h5_main)
``` ```
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
sho_fit_points = 5 # The number of data points at each step to use when fitting 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') h5_sho_group = px.hdf_utils.findH5group(h5_main, 'SHO_Fit')
sho_fitter = px.BESHOmodel(h5_main, parallel=True) sho_fitter = px.BESHOmodel(h5_main, parallel=True)
if len(h5_sho_group) == 0: if len(h5_sho_group) == 0:
print('No SHO fit found. Doing SHO Fitting now') 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_guess = sho_fitter.do_guess(strategy='complex_gaussian', processors=max_cores, max_mem=max_mem, options={'num_points':sho_fit_points})
h5_sho_fit = sho_fitter.do_fit(processors=max_cores) h5_sho_fit = sho_fitter.do_fit(processors=max_cores, max_mem=max_mem)
else: else:
print('Taking previous SHO results already present in file') print('Taking previous SHO results already present in file')
h5_sho_guess = h5_sho_group[-1]['Guess'] h5_sho_guess = h5_sho_group[-1]['Guess']
try: try:
h5_sho_fit = h5_sho_group[-1]['Fit'] h5_sho_fit = h5_sho_group[-1]['Fit']
except KeyError: except KeyError:
print('Previously computed guess found. Now computing fit') print('Previously computed guess found. Now computing fit')
h5_sho_fit = sho_fitter.do_fit(processors=max_cores, h5_guess=h5_sho_guess) h5_sho_fit = sho_fitter.do_fit(processors=max_cores, max_mem=max_mem, h5_guess=h5_sho_guess)
``` ```
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
## Visualize the SHO results ## 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. 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. 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. Use the sliders below to inspect the BE response at any given location.
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
h5_sho_spec_inds = px.hdf_utils.getAuxData(h5_sho_fit, auxDataName='Spectroscopic_Indices')[0] h5_sho_spec_inds = px.hdf_utils.getAuxData(h5_sho_fit, auxDataName='Spectroscopic_Indices')[0]
sho_spec_labels = px.io.hdf_utils.get_attr(h5_sho_spec_inds,'labels') sho_spec_labels = px.io.hdf_utils.get_attr(h5_sho_spec_inds,'labels')
if is_ckpfm: if is_ckpfm:
# It turns out that the read voltage index starts from 1 instead of 0 # 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 # Also the VDC indices are NOT repeating. They are just rising monotonically
write_volt_index = np.argwhere(sho_spec_labels == 'write_bias')[0][0] write_volt_index = np.argwhere(sho_spec_labels == 'write_bias')[0][0]
read_volt_index = np.argwhere(sho_spec_labels == 'read_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[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) 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) = px.io.hdf_utils.reshape_to_Ndims(h5_sho_fit, get_labels=True) (Nd_mat, success, nd_labels) = px.io.hdf_utils.reshape_to_Ndims(h5_sho_fit, get_labels=True)
print('Reshape Success: ' + str(success)) print('Reshape Success: ' + str(success))
print(nd_labels) print(nd_labels)
print(Nd_mat.shape) print(Nd_mat.shape)
``` ```
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
use_sho_guess = False use_sho_guess = False
use_static_viz_func = False use_static_viz_func = False
if use_sho_guess: if use_sho_guess:
sho_dset = h5_sho_guess sho_dset = h5_sho_guess
else: else:
sho_dset = h5_sho_fit sho_dset = h5_sho_fit
data_type = px.io.hdf_utils.get_attr(hdf.file, 'data_type') data_type = px.io.hdf_utils.get_attr(hdf.file, 'data_type')
if data_type == 'BELineData' or len(pos_dims) != 2: if data_type == 'BELineData' or len(pos_dims) != 2:
use_static_viz_func = True use_static_viz_func = True
step_chan = None step_chan = None
else: else:
vs_mode = px.io.hdf_utils.get_attr(h5_main.parent.parent, 'VS_mode') vs_mode = px.io.hdf_utils.get_attr(h5_main.parent.parent, 'VS_mode')
if vs_mode not in ['AC modulation mode with time reversal', if vs_mode not in ['AC modulation mode with time reversal',
'DC modulation mode']: 'DC modulation mode']:
use_static_viz_func = True use_static_viz_func = True
else: else:
if vs_mode == 'DC modulation mode': if vs_mode == 'DC modulation mode':
step_chan = 'DC_Offset' step_chan = 'DC_Offset'
else: else:
step_chan = 'AC_Amplitude' step_chan = 'AC_Amplitude'
if not use_static_viz_func: if not use_static_viz_func:
try: try:
# use interactive visualization # use interactive visualization
px.be_viz_utils.jupyter_visualize_beps_sho(sho_dset, step_chan) px.be_viz_utils.jupyter_visualize_beps_sho(sho_dset, step_chan)
except: except:
raise raise
print('There was a problem with the interactive visualizer') print('There was a problem with the interactive visualizer')
use_static_viz_func = True use_static_viz_func = True
else: else:
# show plots of SHO results vs. applied bias # show plots of SHO results vs. applied bias
px.be_viz_utils.visualize_sho_results(sho_dset, show_plots=True, px.be_viz_utils.visualize_sho_results(sho_dset, show_plots=True,
save_plots=False) save_plots=False)
``` ```
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
## Fit loops to a function ## 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. 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. Note: This computation generally takes a while for reasonably sized datasets.
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
# Do the Loop Fitting on the SHO Fit dataset # Do the Loop Fitting on the SHO Fit dataset
loop_success = False loop_success = False
h5_loop_group = px.hdf_utils.findH5group(h5_sho_fit, 'Loop_Fit') h5_loop_group = px.hdf_utils.findH5group(h5_sho_fit, 'Loop_Fit')
if len(h5_loop_group) == 0: if len(h5_loop_group) == 0:
try: try:
loop_fitter = px.BELoopModel(h5_sho_fit, parallel=True) loop_fitter = px.BELoopModel(h5_sho_fit, parallel=True)
print('No loop fits found. Fitting now....') print('No loop fits found. Fitting now....')
h5_loop_guess = loop_fitter.do_guess(processors=max_cores, max_mem=max_mem) 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) h5_loop_fit = loop_fitter.do_fit(processors=max_cores, max_mem=max_mem)
loop_success = True loop_success = True
except ValueError: except ValueError:
print('Loop fitting is applicable only to DC spectroscopy datasets!') print('Loop fitting is applicable only to DC spectroscopy datasets!')
else: else:
loop_success = True loop_success = True
print('Taking previously computed loop fits') print('Taking previously computed loop fits')
h5_loop_guess = h5_loop_group[-1]['Guess'] h5_loop_guess = h5_loop_group[-1]['Guess']
h5_loop_fit = h5_loop_group[-1]['Fit'] h5_loop_fit = h5_loop_group[-1]['Fit']
h5_loop_group = h5_loop_fit.parent h5_loop_group = h5_loop_fit.parent
``` ```
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
## Prepare datasets for visualization ## Prepare datasets for visualization
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
# Prepare some variables for plotting loops fits and guesses # Prepare some variables for plotting loops fits and guesses
# Plot the Loop Guess and Fit Results # Plot the Loop Guess and Fit Results
if loop_success: if loop_success:
h5_projected_loops = h5_loop_guess.parent['Projected_Loops'] h5_projected_loops = h5_loop_guess.parent['Projected_Loops']
h5_proj_spec_inds = px.hdf_utils.getAuxData(h5_projected_loops, h5_proj_spec_inds = px.hdf_utils.getAuxData(h5_projected_loops,
auxDataName='Spectroscopic_Indices')[-1] auxDataName='Spectroscopic_Indices')[-1]
h5_proj_spec_vals = px.hdf_utils.getAuxData(h5_projected_loops, h5_proj_spec_vals = px.hdf_utils.getAuxData(h5_projected_loops,
auxDataName='Spectroscopic_Values')[-1] auxDataName='Spectroscopic_Values')[-1]
# reshape the vdc_vec into DC_step by Loop # reshape the vdc_vec into DC_step by Loop
sort_order = px.hdf_utils.get_sort_order(h5_proj_spec_inds) sort_order = px.hdf_utils.get_sort_order(h5_proj_spec_inds)
dims = px.hdf_utils.get_dimensionality(h5_proj_spec_inds[()], dims = px.hdf_utils.get_dimensionality(h5_proj_spec_inds[()],
sort_order[::-1]) sort_order[::-1])
vdc_vec = np.reshape(h5_proj_spec_vals[h5_proj_spec_vals.attrs['DC_Offset']], dims).T 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
# 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_nd, _ = px.hdf_utils.reshape_to_Ndims(h5_projected_loops)
proj_3d = np.reshape(proj_nd, [h5_projected_loops.shape[0], proj_3d = np.reshape(proj_nd, [h5_projected_loops.shape[0],
proj_nd.shape[2], -1]) proj_nd.shape[2], -1])
``` ```
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
## Visualize Loop fits ## Visualize Loop fits
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
use_static_plots = False use_static_plots = False
if loop_success: if loop_success:
if not use_static_plots: if not use_static_plots:
try: try:
px.be_viz_utils.jupyter_visualize_beps_loops(h5_projected_loops, h5_loop_guess, h5_loop_fit) px.be_viz_utils.jupyter_visualize_beps_loops(h5_projected_loops, h5_loop_guess, h5_loop_fit)
except: except:
print('There was a problem with the interactive visualizer') print('There was a problem with the interactive visualizer')
use_static_plots = True use_static_plots = True
if use_static_plots: if use_static_plots:
for iloop in range(h5_loop_guess.shape[1]): 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], fig, ax = px.be_viz_utils.plot_loop_guess_fit(vdc_vec[:, iloop], proj_3d[:, :, iloop],
h5_loop_guess[:, iloop], h5_loop_fit[:, iloop], h5_loop_guess[:, iloop], h5_loop_fit[:, iloop],
title='Loop {} - All Positions'.format(iloop)) title='Loop {} - All Positions'.format(iloop))
``` ```
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
## Loop Parameters ## Loop Parameters
We will now load the loop parameters caluculated from the fit and plot them. We will now load the loop parameters caluculated from the fit and plot them.
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
h5_loop_parameters = h5_loop_group['Fit_Loop_Parameters'] h5_loop_parameters = h5_loop_group['Fit_Loop_Parameters']
px.viz.be_viz_utils.jupyter_visualize_parameter_maps(h5_loop_parameters) px.viz.be_viz_utils.jupyter_visualize_parameter_maps(h5_loop_parameters)
``` ```
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
map_parm = 'Work of Switching' map_parm = 'Work of Switching'
plot_cycle = 0 plot_cycle = 0
plot_position = (int(pos_dims[0]/2), int(pos_dims[1]/2)) plot_position = (int(pos_dims[0]/2), int(pos_dims[1]/2))
plot_bias_step = 0 plot_bias_step = 0
h5_main.pos_dim_sizes
px.viz.be_viz_utils.plot_loop_sho_raw_comparison(h5_loop_parameters, map_parm, plot_cycle, plot_position, plot_bias_step) px.viz.be_viz_utils.plot_loop_sho_raw_comparison(h5_loop_parameters, map_parm, plot_cycle, plot_position, plot_bias_step)
``` ```
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
## Save and close ## Save and close
* Save the .h5 file that we are working on by closing it. <br> * 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 * 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 * Finally consider saving this notebook if necessary
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
hdf.close() # hdf.close()
``` ```
......
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