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Commit 7912e34a authored by ssomnath's avatar ssomnath
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Removed BE QT visualizers

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pycroscopy/viz/be_visualizers/io_funcs.py deleted 100644 → 0
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"""
Created on Apr 20, 2016
@author: Chris Smith -- csmith55@utk.edu
"""
import sys
import numpy as np
import h5py
sys.path.append('../')
from scipy.io import loadmat
def loadDataFunc(filePath, **kwargs):
"""
Function to load the N-D data from a .mat file
Output: N-D numpy data array, Nx2 x-vector array
array indices are (Step, #rows, #cols, cycle#)
"""
data = loadmat(filePath)
data_mat = data['loop_mat']
data_mat = data_mat[:, :, :, :]
data_mat[np.where(data_mat > 1E-1)] = 0 # Presumably, this will not be requried.
data_mat[np.where(data_mat < -1E-1)] = 0 # Otherwise we will have to write smoothing/cleaning functions
data_mat = np.transpose(data_mat, (3, 0, 1, 2))
xvec = data['VV'].ravel()
return data_mat, xvec
def readData(h5_path, dset_name='SHO_Fit_Guess'):
"""
Reads the hdf5 data file and calls appropriate reader based on data type
Input:
h5_path -- the absolute file path to the hdf5 file to be read in.
dset_name -- the name of the main dataset
Outputs:
data_mat -- the transformed data read to be plotted
xvec -- numpy array containing the possible plot data of the slice viewer
xvec_labs -- numpy array of labels and units for the xvec array
"""
h5_file = h5py.File(h5_path, 'r')
exp_type = h5_file.attrs['data_type']
h5_group = h5_file['Measurement_000']
data_type = h5_group.attrs['VS_mode']
if data_type == 'DC modulation mode':
return readDCData(h5_group)
elif data_type == 'AC modulation mode with time reversal':
return readACData(h5_group)
# return readDataGen(h5_group['SHO_Fit_Results'])
def readDCData(h5_group):
"""
Reads the data for DC modulation experiments
Inputs:
h5_group -- hdf5 group holding the SHO_Fit Data for the chosen
Measurement group
Outputs:
data_guess -- the transformed data to be plotted
xvec -- numpy array containing the possible plot data of the slice viewer
xvec_labs -- numpy array of labels and units for the xvec array
"""
h5_chan = h5_group['Channel_000']
h5_main = h5_chan['Raw_Data']
h5_file = h5_main.file
h5_specv = h5_file[h5_main.attrs['Spectroscopic_Values']]
h5_bins = h5_file[h5_main.attrs['Bin_Frequencies']]
h5_shogroup = h5_chan['Raw_Data-SHO_Fit_000']
h5_guess = h5_shogroup['Guess']
h5_data_labels = h5_specv.attrs['labels']
h5_sho_specv = h5_file[h5_guess.attrs['Spectroscopic_Values']]
h5_indices = h5_file[h5_guess.attrs['Spectroscopic_Indices']]
h5_pos = h5_file[h5_main.attrs['Position_Indices']]
num_rows, num_cols = __getPos(h5_pos)
num_pos = num_rows * num_cols
ndims = len(np.where(np.array(h5_pos.shape) > 1)[0])
num_cycles = h5_group.attrs['VS_number_of_cycles']
num_steps = len(np.unique(h5_indices[:, 1]))
num_bins = len(np.unique(h5_bins))
data_xvec = h5_sho_specv[h5_sho_specv.attrs['DC_Offset']].flatten()
field_type = h5_group.attrs['VS_measure_in_field_loops']
'''
Separate data into cycles
'''
data_guess = np.reshape(h5_guess, [num_pos, num_cycles, -1])
data_guess = np.transpose(data_guess, [1, 2, 0])
data_xvec = np.reshape(data_xvec, [num_cycles, -1])
data_main = np.reshape(h5_main, [num_pos, num_cycles, -1])
data_main = np.transpose(data_main, [1, 2, 0])
pt_xvec = np.tile(np.arange(data_xvec.shape[1]), [num_cycles, 1])
if field_type == 'in and out-of-field':
'''
Seperate out in-field and out-of-field values
'''
data_guess = np.array([data_guess[:, slice(0, None, 2), :], data_guess[:, slice(1, None, 2), :]])
data_guess = np.reshape(data_guess, (2, num_cycles, -1, num_rows, num_cols))
data_xvec = np.array([data_xvec[:, slice(0, None, 2)], data_xvec[:, slice(1, None, 2)]])
pt_xvec = np.array([pt_xvec[:, slice(0, None, 2)], pt_xvec[:, slice(1, None, 2)]])
data_main = np.reshape(data_main, (num_cycles, -1, num_bins, num_rows, num_cols))
data_main = np.array([data_main[:, slice(0, None, 2), :, :, :], data_main[:, slice(1, None, 2), :, :, :]])
data_parts = ['In-field', 'Out-of-field']
elif field_type == 'in-field':
data_guess = np.reshape(data_guess, (1, num_cycles, -1, num_rows, num_cols))
data_xvec = data_xvec.reshape(1, num_cycles, -1)
pt_xvec = pt_xvec.reshape(1, num_cycles, -1)
data_main = np.reshape(data_main, (1, num_cycles, -1, num_bins, num_rows, num_cols))
data_parts = ['In-field']
elif field_type == 'out-of-field':
data_guess = np.reshape(data_guess, (1, num_cycles, -1, num_rows, num_cols))
data_xvec = data_xvec.reshape(1, num_cycles, -1)
pt_xvec = pt_xvec.reshape(1, num_cycles, -1)
data_main = np.reshape(data_main, (1, num_cycles, -1, num_bins, num_rows, num_cols))
data_parts = ['Out-of-field']
else:
raise ValueError('Unknown field type in data. Cannot parse')
'''
Repeat steps for reading guess on the results if present
'''
try:
h5_results = h5_shogroup['Fit']
data_results = np.reshape(h5_results, [num_pos, num_cycles, -1])
data_results = np.transpose(data_results, [1, 2, 0])
if field_type == 'in and out-of-field':
data_results = np.array([data_results[:, slice(0, None, 2), :],
data_results[:, slice(1, None, 2), :]])
data_results = np.reshape(data_results, (2, num_cycles, -1, num_rows, num_cols))
elif field_type == 'in-field':
data_results = np.reshape(data_results, (1, num_cycles, -1, num_rows, num_cols))
elif field_type == 'out-of-field':
data_results = np.reshape(data_results, (1, num_cycles, -1, num_rows, num_cols))
except KeyError:
data_results = None
xvec = np.array([data_xvec, pt_xvec])
xvec_labs = np.array([['Voltage', 'V'], ['UDVS Step', '']])
data_labs = h5_data_labels
data_units = list()
for label in data_labs:
if label == 'Amplitude':
data_units.append('V')
elif label == 'Frequency':
data_units.append('Hz')
elif label == 'Quality Factor':
data_units.append('')
elif label == 'Phase':
data_units.append('rad')
# xaxis = {'XData':data_xvec,
# 'XData Name':'Voltage',
# 'XData Unit':'V',
# 'XStep':pt_xvec,
# 'XStep Name':'UDVS Step',
# 'XStep Unit':''}
# yaxis = dict([(data_labs[i],data_units[i]) for i in xrange(4)])
# elements = {'Field':data_parts,
# 'Parameters':yaxis,
# 'Cycles':num_cycles,
# 'Steps':num_steps,
# 'X positions':num_rows,
# 'Y positions':num_cols}
#
# data_pack = {'Guess':data_guess,
# 'Fit':data_results,
# 'Raw':data_main,
# 'Data Elements':elements,
# 'X-axis':xaxis,
# 'Y-axis':yaxis,
# 'Num Cycles':num_cycles,
# 'Groups':data_parts,
# 'Dims':ndims,
# 'Bins':h5_bins.value}
return data_guess, data_results, xvec, xvec_labs, data_parts, ndims, data_main, np.unique(h5_bins.value)
def readACData(h5_group):
"""
Reads the data for AC modulation experiments
Inputs:
h5_group -- hdf5 group holding the SHO_Fit Data for the chosen
Measurement group
Outputs:
data_guess -- the transformed data to be plotted
xvec -- numpy array containing the possible plot data of the slice viewer
xvec_labs -- numpy array of labels and units for the xvec array
"""
h5_chan = h5_group['Channel_000']
h5_main = h5_chan['Raw_Data']
h5_specv = h5_chan['Spectroscopic_Values']
h5_bins = h5_chan['Bin_Frequencies']
h5_shogroup = h5_chan['Raw_Data-SHO_Fit_000']
h5_guess = h5_shogroup['Guess']
h5_data_labels = h5_specv.attrs['labels']
h5_sho_specv = h5_shogroup['Spectroscopic_Values']
h5_indices = h5_shogroup['Spectroscopic_Indices']
h5_pos = h5_chan['Position_Indices']
num_rows, num_cols = __getPos(h5_pos)
num_pos = num_rows * num_cols
ndims = len(np.where(np.array(h5_pos.shape) > 1)[0])
num_cycles = h5_group.attrs['VS_number_of_cycles']
num_steps = len(np.unique(h5_indices[:, 1]))
num_bins = len(np.unique(h5_bins))
data_xvec = h5_sho_specv[h5_sho_specv.attrs['AC_Amplitude']].flatten()
direction = h5_specv[h5_specv.attrs['Direction']].flatten()
direction = h5_sho_specv[h5_sho_specv.attrs['Direction']].flatten()
'''
Separate data into cycles
'''
data_guess = np.reshape(h5_guess, [num_pos, num_cycles, -1])
data_guess = np.transpose(data_guess, [1, 2, 0])
data_xvec = np.reshape(data_xvec, [num_cycles, -1])
data_main = np.reshape(h5_main, [num_pos, num_cycles, -1])
data_main = np.transpose(data_main, [1, 2, 0])
pt_xvec = np.tile(np.arange(data_xvec.shape[1]), [num_cycles, 1])
'''
Seperate out forward and reverse values
'''
for_dir = np.where(direction == 1.0)[0]
rev_dir = np.where(direction == -1.0)[0]
data_guess = np.array([data_guess[:, for_dir, :], data_guess[:, rev_dir, :]])
data_guess = np.reshape(data_guess, (2, num_cycles, -1, num_rows, num_cols))
data_main = np.reshape(data_main, (num_cycles, -1, num_bins, num_rows, num_cols))
data_main = np.array([data_main[:, for_dir, :, :, :], data_main[:, rev_dir, :, :, :]])
data_xvec = np.array([data_xvec[:, for_dir], data_xvec[:, rev_dir]])
pt_xvec = np.array([pt_xvec[:, for_dir], pt_xvec[:, rev_dir]])
data_parts = ['Forward', 'Reverse']
# '''
# Get the mean and standard deviation of each variable
# Then use these to set upper and lower bounds
# '''
# for var in xrange(data_guess.shape[0]):
# for cycle in xrange(data_guess.shape[1]):
# mean_data, std_data = getGoodLims(data_guess[var,cycle,:,:])
# max_data = mean_data+3*std_data
# min_data = mean_data-3*std_data
# np.clip(data_guess[var,cycle,:,:],min_data,max_data,data_guess[var,cycle,:,:])
xvec = np.array([data_xvec, pt_xvec])
xvec_labs = np.array([['AC Current', 'A'], ['UDVS Step', '']])
'''
Repeat steps for reading guess on the results if present
'''
try:
h5_results = h5_shogroup['Fit']
data_results = np.reshape(h5_results, [num_pos, num_cycles, -1])
data_results = np.transpose(data_results, [1, 2, 0])
data_results = np.array([data_results[:, for_dir, :], data_results[:, rev_dir, :]])
data_results = np.reshape(data_results, (2, num_cycles, -1, num_rows, num_cols))
except KeyError:
data_results = None
except:
raise
data_labs = h5_data_labels
data_units = list()
for label in data_labs:
if label == 'Amplitude':
data_units.append('V')
elif label == 'Frequency':
data_units.append('Hz')
elif label == 'Quality Factor':
data_units.append('')
elif label == 'Phase':
data_units.append('rad')
# xaxis = {'XData':data_xvec,
# 'XData Name':'Voltage',
# 'XData Unit':'V',
# 'XStep':pt_xvec,
# 'XStep Name':'UDVS Step',
# 'XStep Unit':''}
# yaxis = dict([(data_labs[i],data_units[i]) for i in xrange(4)])
# elements = {'Field':data_parts,
# 'Parameters':yaxis,
# 'Cycles':num_cycles,
# 'Steps':num_steps,
# 'X positions':num_rows,
# 'Y positions':num_cols}
#
# data_pack = {'Guess':data_guess,
# 'Fit':data_results,
# 'Raw':data_main,
# 'Data Elements':elements,
# 'X-axis':xaxis,
# 'Y-axis':yaxis,
# 'Num Cycles':num_cycles,
# 'Groups':data_parts,
# 'Dims':ndims,
# 'Bins':h5_bins.value}
return data_guess, data_results, xvec, xvec_labs, data_parts, ndims, data_main, np.unique(h5_bins.value)
def getSpectralData(point, data_mat):
"""
This function accepts a tuple (x,y) and extracts the spectra
from matrix (data) at that point, and returns an Nx2 vector
Inputs:
point -- (x,y) position to be retrieved from data_mat
data_mat -- matrix to retrieve data from
Outputs:
"""
spec_ydata = data_mat[:, int(np.round(point[0])), int(np.round(point[1]))]
return spec_ydata.ravel()
def __getPos(h5_pos):
"""
Return the number of rows and columns in the dataset
"""
num_rows = len(np.unique(h5_pos[:, 0]))
try:
num_cols = len(np.unique(h5_pos[:, 1]))
except ValueError:
num_cols = 1
return num_rows, num_cols
def __findDataset(h5_file, ds_name):
"""
Uses visit() to find all datasets with the desired name
"""
print('Finding all instances of', ds_name)
ds = []
def __findName(name, obj):
if name.split('/')[-1] == ds_name and isinstance(obj, h5py.Dataset):
ds.append([name, obj])
return
h5_file.visititems(__findName)
return ds
pycroscopy/viz/be_visualizers/plot_functions.py deleted 100644 → 0
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pycroscopy/viz/be_visualizers/sho_master.py deleted 100644 → 0
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# -*- coding: utf-8 -*-
# -*- coding: utf-8 -*-
"""
Spyder Editor
Test some different plotting functionalities
Loads data and views them using functions written with PyQtGraph
"""
import sys
from .plot_functions import BEPSwindow
import pyqtgraph as pg
if __name__ == '__main__':
'''
Need to load the file from PySPM that should be visualized.
Then need to extract the parameters from the file, such as the type
of measurement, number of cycles and the Vdc vector.
We then need to feed all of this to the visualizer
We also need to add another selection bar, that determines what we are
plotting i.e. A, phi, omega, or Q.
'''
app = pg.QtGui.QApplication([])
h5_path = None
'''
Make window, cross-hairs, widgets, ROI, etc.
'''
win = BEPSwindow()
win.setup(h5_path)
win.showMaximized()
win.setSignals()
sys.exit(app.exec_())
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