def cluster_analysis(self):
from xia2.Modules.MultiCrystal import multi_crystal_analysis
labels = self._data_manager.experiments.identifiers()
mca = multi_crystal_analysis(self._intensities_separate[0],
labels=labels,
prefix=None)
self._cc_cluster_json = mca.to_plotly_json(mca.cc_matrix,
mca.cc_linkage_matrix,
labels=labels)
self._cc_cluster_table = mca.as_table(mca.cc_clusters)
self._cos_angle_cluster_json = mca.to_plotly_json(
mca.cos_angle_matrix,
mca.cos_angle_linkage_matrix,
labels=labels,
matrix_type="cos_angle",
)
self._cos_angle_cluster_table = mca.as_table(mca.cos_angle_clusters)
self._cosym_graphs = OrderedDict()
self._cosym_graphs.update(
plot_rij_histogram(mca.cosym.target.rij_matrix,
key="cosym_rij_histogram_sg"))
self._cosym_graphs.update(
plot_coords(mca.cosym.coords,
mca.cosym.cluster_labels,
key="cosym_coordinates_sg"))
self._cluster_analysis = mca
return self._cluster_analysis
def make_plots(self):
"""Generate cosym cluster analysis plot data."""
d = OrderedDict()
d.update(plot_rij_histogram(self.data["rij_matrix"]))
d.update(plot_coords(self.data["coordinates"], self.data["labels"]))
graphs = {"cosym_graphs": d}
return graphs
def test_plot_coords():
coords = flex.double([0, 1, 0, 1, 1, 0, 1, 0])
coords.reshape(flex.grid((4, 2)))
labels = flex.int([0, 0, 1, 1])
d = plots.plot_coords(coords, labels=labels)
assert "cosym_coordinates" in d
assert set(d["cosym_coordinates"]) == {"layout", "data"}
assert d["cosym_coordinates"]["data"][0]["x"] == [0.0, 0.0]
assert d["cosym_coordinates"]["data"][0]["y"] == [1.0, 1.0]
assert d["cosym_coordinates"]["data"][1]["x"] == [1.0, 1.0]
assert d["cosym_coordinates"]["data"][1]["y"] == [0.0, 0.0]
def test_plot_coords():
coords = np.array([0.5, 0.5, 0, 1, 0, 1, 1, 0, 1, 0]).reshape(5, 2)
labels = np.array([-1, 0, 0, 1, 1])
d = plots.plot_coords(coords, labels=labels)
assert "cosym_coordinates" in d
assert set(d["cosym_coordinates"]) == {"data", "help", "layout"}
assert (d["cosym_coordinates"]["data"][0]["marker"]["color"] ==
"rgb(0.000000,0.000000,0.000000)")
assert d["cosym_coordinates"]["data"][0]["x"] == [0.5]
assert d["cosym_coordinates"]["data"][0]["y"] == [0.5]
assert d["cosym_coordinates"]["data"][1]["x"] == [0.0, 0.0]
assert d["cosym_coordinates"]["data"][1]["y"] == [1.0, 1.0]
assert d["cosym_coordinates"]["data"][2]["x"] == [1.0, 1.0]
assert d["cosym_coordinates"]["data"][2]["y"] == [0.0, 0.0]
