def run(_args):
if _args < 2:
raise IOError("Must give at least one path to folder of pickles")
ucs = Cluster.from_directories(_args.folders,
"cxi_targt_uc",
n_images=args.n)
if not _args.noplot:
clusters, _ = ucs.ab_cluster(_args.t,
log=_args.log,
write_file_lists=_args.nofiles,
schnell=_args.schnell,
doplot=_args.noplot)
else:
plt.figure("Andrews-Bernstein distance dendogram", figsize=(12, 8))
ax = plt.gca()
clusters, cluster_axes = ucs.ab_cluster(_args.t,
log=_args.log,
ax=ax,
write_file_lists=_args.nofiles,
schnell=_args.schnell,
doplot=_args.noplot)
plt.tight_layout()
plt.show()
print unit_cell_info(clusters)
def run(_args):
if _args < 2:
raise IOError("Must give at least one path to folder of pickles")
ucs = Cluster.from_directories(_args.folders, "cluster_42")
logging.info("Data imported.")
# Set up mega-plot
plt.figure(figsize=(22, 15))
gs = gridspec.GridSpec(3, 3, height_ratios=[1, 1, 3])
orr_axes = [plt.subplot(gs[0, 0]), plt.subplot(gs[0, 1]), plt.subplot(gs[0, 2])]
inten_axes = [plt.subplot(gs[1, 0]), plt.subplot(gs[1, 1]), plt.subplot(gs[1, 2])]
clust_ax = plt.subplot(gs[2, :])
orr_axes = ucs.visualise_orientational_distribution(orr_axes, cbar=True)
inten_axes = ucs.intensity_statistics(inten_axes)
clusters, cluster_ax = ucs.ab_cluster(
_args.t, log=_args.log, ax=clust_ax, schnell=_args.fast, write_file_lists=False
)
# plt.text("cluster.42 Plot Everything!")
plt.tight_layout()
print unit_cell_info(clusters)
plt.show()
def run(_args):
if _args < 2:
raise IOError("Must give at least one path to folder of pickles")
ucs = Cluster.from_directories(_args.folders, "cluster_42")
logging.info("Data imported.")
# Set up mega-plot
plt.figure(figsize=(22, 15))
gs = gridspec.GridSpec(3, 3, height_ratios=[1, 1, 3])
orr_axes = [plt.subplot(gs[0, 0]),
plt.subplot(gs[0, 1]),
plt.subplot(gs[0, 2])]
inten_axes = [plt.subplot(gs[1, 0]),
plt.subplot(gs[1, 1]),
plt.subplot(gs[1, 2])]
clust_ax = plt.subplot(gs[2, :])
orr_axes = ucs.visualise_orientational_distribution(orr_axes, cbar=True)
inten_axes = ucs.intensity_statistics(inten_axes)
clusters, cluster_ax = ucs.ab_cluster(_args.t, log=_args.log, ax=clust_ax,
schnell=_args.fast, write_file_lists=False)
#plt.text("cluster.42 Plot Everything!")
plt.tight_layout()
print(unit_cell_info(clusters))
plt.show()
def run(_args):
if _args < 2:
raise IOError("Must provide location(s) of pickles")
if _args.paths:
ucs = Cluster.from_files(raw_input=_args.dirs,
n_images=_args.n,
dials=_args.dials)
else:
ucs = Cluster.from_directories(_args.dirs,
n_images=_args.n,
dials=_args.dials)
if not _args.noplot:
clusters, _ = ucs.ab_cluster(_args.t,
log=_args.log,
write_file_lists=_args.nofiles,
schnell=_args.schnell,
doplot=_args.noplot)
print unit_cell_info(clusters)
else:
plt.figure("Andrews-Bernstein distance dendogram", figsize=(12, 8))
ax = plt.gca()
clusters, cluster_axes = ucs.ab_cluster(_args.t,
log=_args.log,
ax=ax,
write_file_lists=_args.nofiles,
schnell=_args.schnell,
doplot=_args.noplot)
print unit_cell_info(clusters)
plt.tight_layout()
plt.show()
def run(_args):
if _args < 2:
raise IOError("Must give at least one path to folder of pickles")
import logging
from xfel.clustering.cluster import Cluster
FORMAT = '%(levelname)s %(module)s.%(funcName)s: %(message)s'
logging.basicConfig(level=logging.WARNING, format=FORMAT)
cluster = Cluster.from_directories(_args.folders,
'Command line visualisation')
logging.info("data imported")
cluster.visualise_orientational_distribution()
def run(_args):
if _args < 2:
raise IOError("Must give at least one path to folder of pickles")
import logging
from xfel.clustering.cluster import Cluster
FORMAT = '%(levelname)s %(module)s.%(funcName)s: %(message)s'
logging.basicConfig(level=logging.WARNING, format=FORMAT)
cluster = Cluster.from_directories(_args.folders,
'Command line visualisation')
logging.info("data imported")
cluster.visualise_orientational_distribution()
def run(_args):
if _args < 2:
raise IOError("Must give at least one path to folder of pickles")
ucs = Cluster.from_directories(_args.folders, "Per-frame-Wilson")
logging.info("Data imported.")
fig = plt.figure(figsize=(10, 10))
ax = plt.gca()
ucs.members[0].plot_wilson(ax=ax)
browser = Key_event(ax, ucs.members, fig)
fig.canvas.mpl_connect('key_press_event', browser.key_event)
plt.show()
def run(_args):
if _args < 2:
raise IOError("Must give at least one path to folder of pickles")
ucs = Cluster.from_directories(_args.folders, "Per-frame-Wilson")
logging.info("Data imported.")
fig = plt.figure(figsize=(10,10))
ax = plt.gca()
ucs.members[0].plot_wilson(ax=ax)
browser = Key_event(ax, ucs.members, fig)
fig.canvas.mpl_connect('key_press_event', browser.key_event)
plt.show()
def run(_args):
if _args < 2:
raise IOError("Must give at least one path to folder of pickles")
ucs = Cluster.from_directories(_args.folders, "cluster_intensity_stats")
logging.info("Data imported.")
plt.figure(figsize=(20,10))
gs = gridspec.GridSpec(3, 2, width_ratios=[1, 3])
inten_axes = [plt.subplot(gs[0,0]),
plt.subplot(gs[1,0]),
plt.subplot(gs[2,0])]
big_axes = plt.subplot(gs[:,1])
ucs.intensity_statistics(ax=inten_axes)
ucs.all_frames_intensity_stats(ax=big_axes)
plt.tight_layout()
plt.show()
def run(_args):
if _args < 2:
raise IOError("Must give at least one path to folder of pickles")
ucs = Cluster.from_directories(_args.folders, "cluster_intensity_stats")
logging.info("Data imported.")
plt.figure(figsize=(20,10))
gs = gridspec.GridSpec(3, 2, width_ratios=[1, 3])
inten_axes = [plt.subplot(gs[0,0]),
plt.subplot(gs[1,0]),
plt.subplot(gs[2,0])]
big_axes = plt.subplot(gs[:,1])
ucs.intensity_statistics(ax=inten_axes)
ucs.all_frames_intensity_stats(ax=big_axes)
plt.tight_layout()
plt.show()
def run(_args):
if _args < 2:
raise IOError("Must give at least one path to folder of pickles")
ucs = Cluster.from_directories(_args.folders, "cxi_targt_uc")
if not _args.noplot:
clusters, _ = ucs.ab_cluster(_args.t, log=_args.log,
write_file_lists=_args.nofiles,
schnell=_args.schnell,
doplot=_args.noplot)
else:
plt.figure("Andrews-Bernstein distance dendogram", figsize=(12, 8))
ax = plt.gca()
clusters, cluster_axes = ucs.ab_cluster(_args.t, log=_args.log, ax=ax,
write_file_lists=_args.nofiles,
schnell=_args.schnell,
doplot=_args.noplot)
plt.tight_layout()
plt.show()
print unit_cell_info(clusters)
