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Commit 01d5d5d8 authored by Somnath, Suhas's avatar Somnath, Suhas
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clean up of plot_utils. PEP8 cleaning. Cleared confusion regarding the names... 

clean up of plot_utils. PEP8 cleaning. Cleared confusion regarding the names of the clustering plotting functions
parent e531a7ba
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pycroscopy/io/translators/be_utils.py
View file @ 01d5d5d8
......@@ -20,7 +20,7 @@ from ..io_utils import getAvailableMem, recommendCores
from ..microdata import MicroDataset, MicroDataGroup
from ...analysis.optimize import Optimize
from ...processing.proc_utils import buildHistogram
from ...viz.plot_utils import plot1DSpectrum, plot2DSpectrogram, plotHistgrams
from ...viz.plot_utils import plot_1d_spectrum, plot_2d_spectrogram, plot_histgrams
def parmsToDict(filepath, parms_to_remove=[]):
......@@ -479,10 +479,10 @@ def generatePlotGroups(h5_main, hdf, mean_resp, folder_path, basename, max_resp=
path_1d = path.join(folder_path, basename + '_Step_Avg_' + fig_title + '.png')
path_2d = path.join(folder_path, basename + '_Mean_Spec_' + fig_title + '.png')
path_hist = path.join(folder_path, basename + '_Histograms_' + fig_title + '.png')
plot1DSpectrum(step_averaged_vec, freq_vec, fig_title, figure_path=path_1d)
plot2DSpectrogram(mean_spec, freq_vec, fig_title, figure_path=path_2d)
plot_1d_spectrum(step_averaged_vec, freq_vec, fig_title, figure_path=path_1d)
plot_2d_spectrogram(mean_spec, freq_vec, fig_title, figure_path=path_2d)
if do_histogram:
plotHistgrams(hist_mat, hist_indices, grp.name, figure_path=path_hist)
plot_histgrams(hist_mat, hist_indices, grp.name, figure_path=path_hist)
if show_plots:
plt.show()
......@@ -545,13 +545,13 @@ def visualize_plot_groups(h5_filepath):
plt_grp = grp[plt_grp_name]
if expt_type == 'BEPSData':
spect_data = plt_grp['Mean_Spectrogram'].value
plot2DSpectrogram(spect_data, plt_grp['Bin_Frequencies'].value, plt_grp.attrs['Name'])
plot_2d_spectrogram(spect_data, plt_grp['Bin_Frequencies'].value, plt_grp.attrs['Name'])
step_avg_data = plt_grp['Step_Averaged_Response']
plot1DSpectrum(step_avg_data, plt_grp['Bin_Frequencies'].value, plt_grp.attrs['Name'])
plot_1d_spectrum(step_avg_data, plt_grp['Bin_Frequencies'].value, plt_grp.attrs['Name'])
try:
hist_data = plt_grp['Histograms']
hist_bins = plt_grp['Histograms_Indicies']
plotHistgrams(hist_data, hist_bins, plt_grp.attrs['Name'])
plot_histgrams(hist_data, hist_bins, plt_grp.attrs['Name'])
except:
pass
......@@ -1302,7 +1302,7 @@ class BEHistogram():
if save_plot:
basename,junk = path.splitext(h5_path)
plotfile = '{}_MG{}_PG{}_Histograms.png'.format(basename,im,ip)
plotHistgrams(hist_mat, hist_indices, p_group, plotfile)
plot_histgrams(hist_mat, hist_indices, p_group, plotfile)
if show_plot:
plt.show()
......
pycroscopy/processing/scripts/ImageWindowing.py
View file @ 01d5d5d8
......@@ -15,7 +15,7 @@ from pycroscopy import ImageTranslator
from pycroscopy.processing.image_processing import ImageWindow
from pycroscopy.processing.svd_utils import doSVD
from pycroscopy import Cluster
from pycroscopy.viz.plot_utils import plotScree, plot_map_stack, plotSpectrograms, plotClusterResults
from pycroscopy.viz.plot_utils import plotScree, plot_map_stack, plotSpectrograms, plot_cluster_results_together
from pycroscopy.io.io_utils import uiGetFile
if __name__ == '__main__':
......@@ -205,7 +205,7 @@ if __name__ == '__main__':
h5_centroids_raw = h5_kmeans_raw['Mean_Response']
h5_km_spec_raw = h5_file[h5_centroids_raw.attrs['Spectroscopic_Values']][1]
fig601, ax601 = plotClusterResults(h5_labels_raw, h5_centroids_raw, spec_val=h5_km_spec_raw)
fig601, ax601 = plot_cluster_results_together(h5_labels_raw, h5_centroids_raw, spec_val=h5_km_spec_raw)
fig601.savefig(os.path.join(folder, km_name + '_KMeans.png'), format='png', dpi=300)
plt.close('all')
......@@ -231,7 +231,7 @@ if __name__ == '__main__':
h5_centroids_U = h5_kmeans_U['Mean_Response']
h5_km_spec_U = h5_file[h5_centroids_U.attrs['Spectroscopic_Values']]
fig601, ax601 = plotClusterResults(h5_labels_U, h5_centroids_U, spec_val=h5_km_spec_U)
fig601, ax601 = plot_cluster_results_together(h5_labels_U, h5_centroids_U, spec_val=h5_km_spec_U)
fig601.savefig(os.path.join(folder, km_name + '_KMeans.png'), format='png', dpi=300)
del fig601, ax601
plt.close('all')
......
pycroscopy/viz/plot_utils.py
View file @ 01d5d5d8
......@@ -545,10 +545,9 @@ def plot_map_stack(map_stack, num_comps=9, stdevs=2, color_bar_mode=None, evenly
return fig202, axes202
# TODO: The label and units for the main dataset itself are missing in most cases! - ie. I don't know that the data is 'Current' and 'nA'
def plot_cluster_results(h5_group, y_spec_label):
def plot_cluster_h5_group(h5_group, y_spec_label):
# TODO: The label and units for the main dataset itself are missing in most cases! - ie. I don't know that the data is 'Current' and 'nA'
h5_labels = h5_group['Labels']
try:
h5_mean_resp = h5_group['Mean_Response']
......@@ -583,16 +582,16 @@ def plot_cluster_results(h5_group, y_spec_label):
# Figure out the correct axes labels for label map:
pos_labels = get_formatted_labels(h5_pos_vals)
plotClusterResults(label_mat, mean_response, spec_val=np.squeeze(h5_spec_vals[0]),
spec_label=x_spec_label, resp_label=y_spec_label,
pos_labels=pos_labels, pos_ticks=pos_ticks)
plot_cluster_results_together(label_mat, mean_response, spec_val=np.squeeze(h5_spec_vals[0]),
spec_label=x_spec_label, resp_label=y_spec_label,
pos_labels=pos_labels, pos_ticks=pos_ticks)
###############################################################################
def plotClusterResults(label_mat, mean_response, spec_val=None, cmap=plt.cm.jet,
spec_label='Spectroscopic Value', resp_label='Response',
pos_labels=('X', 'Y'), pos_ticks=None):
def plot_cluster_results_together(label_mat, mean_response, spec_val=None, cmap=plt.cm.jet,
spec_label='Spectroscopic Value', resp_label='Response',
pos_labels=('X', 'Y'), pos_ticks=None):
"""
Plot the cluster labels and mean response for each cluster in separate plots
......@@ -600,10 +599,10 @@ def plotClusterResults(label_mat, mean_response, spec_val=None, cmap=plt.cm.jet,
----------
label_mat : 2D ndarray or h5py.Dataset of ints
Spatial map of cluster labels structured as [rows, cols]
mean_response : 2D ndarray or h5py.Dataset
mean_response : 2D array or h5py.Dataset
Mean value of each cluster over all samples
arranged as [cluster number, features]
spec_val : 1D ndarray or h5py.Dataset of floats, optional
spec_val : 1D array or h5py.Dataset of floats, optional
X axis to plot the centroids against
If no value is specified, the data is plotted against the index
cmap : plt.cm object or str, optional
......@@ -629,7 +628,7 @@ def plotClusterResults(label_mat, mean_response, spec_val=None, cmap=plt.cm.jet,
Axes of the individual plots within `fig`
"""
def __plotCentroids(centroids, ax, spec_val, spec_label, y_label, cmap, title=None):
def __plot_centroids(centroids, ax, spec_val, spec_label, y_label, cmap, title=None):
plot_line_family(ax, spec_val, centroids, label_prefix='Cluster', cmap=cmap)
ax.set_ylabel(y_label)
# ax.legend(loc='best')
......@@ -647,9 +646,9 @@ def plotClusterResults(label_mat, mean_response, spec_val=None, cmap=plt.cm.jet,
ax_phase = plt.subplot2grid((2, 12), (1, 6), colspan=4)
axes = [ax_map, ax_amp, ax_phase]
__plotCentroids(np.abs(mean_response), ax_amp, spec_val, spec_label,
__plot_centroids(np.abs(mean_response), ax_amp, spec_val, spec_label,
resp_label + ' - Amplitude', cmap, 'Mean Response')
__plotCentroids(np.angle(mean_response), ax_phase, spec_val, spec_label,
__plot_centroids(np.angle(mean_response), ax_phase, spec_val, spec_label,
resp_label + ' - Phase', cmap)
plot_handles, plot_labels = ax_amp.get_legend_handles_labels()
......@@ -658,7 +657,7 @@ def plotClusterResults(label_mat, mean_response, spec_val=None, cmap=plt.cm.jet,
ax_map = plt.subplot2grid((1, 12), (0, 0), colspan=6)
ax_resp = plt.subplot2grid((1, 12), (0, 6), colspan=4)
axes = [ax_map, ax_resp]
__plotCentroids(mean_response, ax_resp, spec_val, spec_label,
__plot_centroids(mean_response, ax_resp, spec_val, spec_label,
resp_label, cmap, 'Mean Response')
plot_handles, plot_labels = ax_resp.get_legend_handles_labels()
......@@ -706,8 +705,8 @@ def plotClusterResults(label_mat, mean_response, spec_val=None, cmap=plt.cm.jet,
###############################################################################
def plotKMeansClusters(label_mat, cluster_centroids, max_centroids=4,
spec_val=None, x_label='Excitation (a.u.)', y_label='Response (a.u.)'):
def plot_cluster_results_separate(label_mat, cluster_centroids, max_centroids=4,
spec_val=None, x_label='Excitation (a.u.)', y_label='Response (a.u.)'):
"""
Plots the provided labels mat and centroids from clustering
......@@ -795,8 +794,8 @@ def plotKMeansClusters(label_mat, cluster_centroids, max_centroids=4,
###############################################################################
def plotClusterDendrograms(label_mat, e_vals, num_comp, num_cluster, mode='Full', last=None,
sort_type='distance', sort_mode=True):
def plot_cluster_dendrogram(label_mat, e_vals, num_comp, num_cluster, mode='Full', last=None,
sort_type='distance', sort_mode=True):
"""
Creates and plots the dendrograms for the given label_mat and
eigenvalues
......@@ -807,7 +806,7 @@ def plotClusterDendrograms(label_mat, e_vals, num_comp, num_cluster, mode='Full'
structured as [rows, cols], from KMeans clustering
e_vals: 3D real numpy array of eigenvalues
structured as [component, rows, cols]
num_comps : int
num_comp : int
Number of components used to make eigenvalues
num_cluster : int
Number of cluster used to make the label_mat
......@@ -846,7 +845,6 @@ def plotClusterDendrograms(label_mat, e_vals, num_comp, num_cluster, mode='Full'
elif mode == 'Truncated':
print 'Creating truncated dendrogram from clusters. Will stop at {}.'.format(last)
mode = 'lastp'
show_contracted = True
else:
raise ValueError('Error: Unknown mode requested for plotting dendrograms. mode={}'.format(mode))
......@@ -868,8 +866,7 @@ def plotClusterDendrograms(label_mat, e_vals, num_comp, num_cluster, mode='Full'
centroid_mat[k1, :] = np.mean(u_stack, 0)
# Get the distrance between cluster means
# Get the distrance between cluster means
distance_mat = scipy.spatial.distance.pdist(centroid_mat)
# get hierachical pairings of clusters
......@@ -888,7 +885,7 @@ def plotClusterDendrograms(label_mat, e_vals, num_comp, num_cluster, mode='Full'
return fig
def plot1DSpectrum(data_vec, freq, title, figure_path=None):
def plot_1d_spectrum(data_vec, freq, title, figure_path=None):
"""
Plots the Step averaged BE response
......@@ -911,26 +908,25 @@ def plot1DSpectrum(data_vec, freq, title, figure_path=None):
Axis handle
"""
if len(data_vec) != len(freq):
# print '1D:',data_vec.shape, freq.shape
warn('plot2DSpectrogram: Incompatible data sizes!!!!')
warn('plot_1d_spectrum: Incompatible data sizes!!!!')
print('1D:', data_vec.shape, freq.shape)
return
freq = freq * 1E-3 # to kHz
fig, ax = plt.subplots(nrows=2, ncols=1, sharex=True);
freq *= 1E-3 # to kHz
fig, ax = plt.subplots(nrows=2, ncols=1, sharex=True)
ax[0].plot(freq, np.abs(data_vec) * 1E+3)
ax[0].set_title('Amplitude (mV)')
# ax[0].set_xlabel('Frequency (kHz)')
ax[1].plot(freq, np.angle(data_vec) * 180 / np.pi)
ax[1].set_title('Phase (deg)')
ax[1].set_xlabel('Frequency (kHz)')
fig.suptitle(title + ': mean UDVS, mean spatial response')
if figure_path:
plt.savefig(figure_path, format='png', dpi=300)
return (fig, ax)
return fig, ax
###############################################################################
def plot2DSpectrogram(mean_spectrogram, freq, title, figure_path=None):
def plot_2d_spectrogram(mean_spectrogram, freq, title, figure_path=None):
"""
Plots the position averaged spectrogram
......@@ -953,11 +949,11 @@ def plot2DSpectrogram(mean_spectrogram, freq, title, figure_path=None):
Axis handle
"""
if mean_spectrogram.shape[1] != len(freq):
# print '2D:',mean_spectrogram.shape, freq.shape
warn('plot2DSpectrogram: Incompatible data sizes!!!!')
warn('plot_2d_spectrogram: Incompatible data sizes!!!!')
print('2D:', mean_spectrogram.shape, freq.shape)
return
freq = freq * 1E-3 # to kHz
fig, ax = plt.subplots(nrows=2, ncols=1, sharex=True);
freq *= 1E-3 # to kHz
fig, ax = plt.subplots(nrows=2, ncols=1, sharex=True)
# print mean_spectrogram.shape
# print freq.shape
ax[0].imshow(np.abs(mean_spectrogram), interpolation='nearest',
......@@ -975,12 +971,12 @@ def plot2DSpectrogram(mean_spectrogram, freq, title, figure_path=None):
fig.suptitle(title)
if figure_path:
plt.savefig(figure_path, format='png', dpi=300)
return (fig, ax)
return fig, ax
###############################################################################
def plotHistgrams(p_hist, p_hbins, title, figure_path=None):
def plot_histgrams(p_hist, p_hbins, title, figure_path=None):
"""
Plots the position averaged spectrogram
......@@ -1047,7 +1043,7 @@ def plotHistgrams(p_hist, p_hbins, title, figure_path=None):
return fig
def visualizeSHOResults(h5_main, save_plots=True, show_plots=True):
def visualize_sho_results(h5_main, save_plots=True, show_plots=True):
"""
Plots some loops, amplitude, phase maps for BE-Line and BEPS datasets.\n
Note: The file MUST contain SHO fit gusses at the very least
......
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