Commit 17df1f4e authored by Somnath, Suhas's avatar Somnath, Suhas
Browse files

Using the new formulation of the Cluster and SVD classes

parent 5b24d814
......@@ -25,10 +25,12 @@
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.patches as patches
from IPython.display import display, HTML
import ipywidgets as widgets
from sklearn.cluster import KMeans
import pycroscopy as px
# set up notebook to show plots within the notebook
% matplotlib notebook
......@@ -167,18 +169,19 @@
Here, SVD essentially compares every single ronchigram with every other ronchigram to find statistically significant trends in the dataset. Such correlation would be infeasible if the ronchigrams were averaged to bright-field and dark-field scalar values.
%% Cell type:code id: tags:
``` python
proc = px.SVD(h5_main, num_comps=256)
# First check if SVD was already computed on this dataset:
h5_svd_group = px.hdf_utils.findH5group(h5_main, 'SVD')
if len(h5_svd_group) == 0:
if proc.duplicate_h5_groups is None:
print('No prior SVD results found - doing SVD now')
h5_svd_group = px.doSVD(h5_main, num_comps=256)
h5_svd_group = proc.compute()
print('Taking previous SVD results already present in file')
h5_svd_group = h5_svd_group[-1]
h5_svd_group = proc.duplicate_h5_groups[-1]
h5_u = h5_svd_group['U']
h5_v = h5_svd_group['V']
h5_s = h5_svd_group['S']
num_comps = 16
......@@ -241,20 +244,22 @@
%% Cell type:code id: tags:
``` python
# Attempt to find any previous computation
h5_kmeans_group = px.hdf_utils.findH5group(h5_u, 'Cluster')
if len(h5_kmeans_group) == 0:
num_clusters = 32
spectral_components = 128
estimator = KMeans(n_clusters=num_clusters)
proc = px.Cluster(h5_u, estimator, num_comps=spectral_components)
if proc.duplicate_h5_groups is None:
print('No k-Means computation found. Doing K-Means now')
num_clusters = 32
num_comps_for_clustering = 128
estimator = px.Cluster(h5_u, 'KMeans', num_comps=num_comps_for_clustering, n_clusters=num_clusters)
h5_kmeans_group = estimator.do_cluster()
h5_kmeans_group = proc.compute()
print('Taking existing results of previous K-Means computation')
h5_kmeans_group = h5_kmeans_group[-1]
h5_kmeans_group = proc.duplicate_h5_groups[-1]
h5_labels = h5_kmeans_group['Labels']
h5_centroids = h5_kmeans_group['Mean_Response']
# In case we take existing results, we need to get these parameters
......@@ -281,11 +286,11 @@
The vertical length of the branches indicates the relative separation between neighboring clusters.
%% Cell type:code id: tags:
``` python
e_vals = np.reshape(h5_u[:, :num_comps_for_clustering],
e_vals = np.reshape(h5_u[:, :spectral_components],
(num_rows, num_cols, -1))
fig = px.plot_utils.plot_cluster_dendrogram(label_mat, e_vals,
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