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Add NMF option to decomposition menu and toolbar #166

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Add NMF option to decomposition menu and toolbar #166

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62 changes: 62 additions & 0 deletions hyperspyui/images/nmf.svg
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43 changes: 43 additions & 0 deletions hyperspyui/plugins/mva.py
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Original file line number Diff line number Diff line change
Expand Up @@ -116,6 +116,10 @@ def create_actions(self):
icon='bss.svg',
tip=tr("Run Blind Source Separation"),
selection_callback=self.selection_rules)
self.add_action('nmf', tr("NMF"), self.nmf,
icon='nmf.svg',
tip=tr("Run Non-negative Matrix Factorization"),
selection_callback=self.selection_rules)
self.add_action('bss_model', tr("BSS model"), self.bss_model,
icon='bss.svg',
tip=tr("Create a Blind Source Separation "
Expand All @@ -130,12 +134,14 @@ def create_menu(self):
self.ui.actions['plot_decomposition_results'])
self.add_menuitem('Decomposition', self.ui.actions['pca'])
self.add_menuitem('Decomposition', self.ui.actions['bss'])
self.add_menuitem('Decomposition', self.ui.actions['nmf'])
self.add_menuitem('Decomposition', self.ui.actions['bss_model'])
self.add_menuitem('Decomposition', self.ui.actions['clear'])

def create_toolbars(self):
self.add_toolbar_button("Decomposition", self.ui.actions['pca'])
self.add_toolbar_button("Decomposition", self.ui.actions['bss'])
self.add_toolbar_button("Decomposition", self.ui.actions['nmf'])

def selection_rules(self, win, action):
"""
Expand Down Expand Up @@ -200,12 +206,25 @@ def _do_bss(self, s, n_components, algorithm=None):
else:
s.blind_source_separation(n_components)

def _do_nmf(self, s, n_components, algorithm=None):
"""
Perform NMF decomposition
"""
s.decomposition(algorithm=algorithm, output_dimension=n_components)


def get_bss_results(self, signal):
factors = signal.get_bss_factors()
loadings = signal.get_bss_loadings()
factors.axes_manager._axes[0] = loadings.axes_manager._axes[0]
return loadings, factors

def get_decomposition_results(self, signal):
factors = signal.get_decomposition_factors()
loadings = signal.get_decomposition_loadings()
factors.axes_manager._axes[0] = loadings.axes_manager._axes[0]
return loadings, factors

def _record(self, autosig, model, signal, n_components):
if autosig:
self.record_code(r"<p>.{0}(n_components={1})".format(
Expand Down Expand Up @@ -255,6 +274,14 @@ def _perform_model(self, ns, n_components):
o.metadata.General.title = ns.signal.name + "[BSS-Loadings]"
f.plot()
o.plot()
elif ns.model == 'nmf':
self._do_nmf(ns.s, n_components=n_components, algorithm='nmf')
f, o = self.get_decomposition_results(ns.s)
o.metadata.add_dictionary(ns.s.metadata.as_dictionary())
f.metadata.General.title = ns.signal.name + "[NMF-Factors]"
o.metadata.General.title = ns.signal.name + "[NMF-Loadings]"
f.plot()
o.plot()
elif ns.model == 'bss_model':
# Here we have to assume the user has actually performed the BSS
# decomposition first!
Expand Down Expand Up @@ -365,6 +392,22 @@ def bss(self, signal=None, n_components=None, advanced=False):
else:
self.do_after_scree('bss', signal, n_components)

def nmf(self, signal=None, n_components=None, advanced=False):
"""
Performs decomposition if neccessary, then plots the scree for the user
to select the number of components to use for a non-negative matrix
factorization. The selection is made by clicking on the scree, which
closes the scree and proceeds with the factorization.
"""
if advanced:
diag = make_advanced_dialog(self.ui)
dr = diag.exec_()
if dr == QDialog.Accepted:
self.do_after_scree(
'nmf', signal, n_components=diag.components())
else:
self.do_after_scree('nmf', signal, n_components)

def bss_model(self, signal=None, n_components=None, advanced=False):
"""
Performs decomposition if neccessary, then plots the scree for the user
Expand Down