def create_particles_plot_map(
stack_file_path,
indices,
values=None,
vmin=None,
vmax=None,
colmap="viridis",
title=None,
colorlabel=None,
plotpos=(),
):
"""Multiline Comment0"""
x_coordinates = []
y_coordinates = []
value_for_coloring = []
for value_index, particle_index in enumerate(indices):
particle = sp_ctf_refine_io.read_particle(stack_file_path,
particle_index,
header_only=True)
particle_coord = particle.get_attr("ptcl_source_coord")
x_coordinates.append(particle_coord[0])
y_coordinates.append(particle_coord[1])
if values is None:
particle_ctf = particle.get_attr("ctf")
value_for_coloring.append(particle_ctf.defocus)
else:
val_for_col = values[value_index]
value_for_coloring.append(val_for_col)
axis = matplotlib.pyplot.subplot(*plotpos)
scatter = axis.scatter(
x_coordinates,
y_coordinates,
c=value_for_coloring,
vmin=vmin,
vmax=vmax,
marker="o",
cmap=colmap,
s=50,
lw=0,
)
matplotlib.pyplot.xlabel("Image dimension x")
matplotlib.pyplot.ylabel("Image dimension y")
cbar = matplotlib.pyplot.colorbar(scatter)
if colorlabel:
cbar.set_label(colorlabel, rotation=270)
if title:
axis.set_title(title, fontsize=7)
if vmin != None or vmax != None:
ticks = [t.get_text() for t in cbar.ax.get_yticklabels()]
ticks[0] = "<" + ticks[0]
ticks[-1] = ">" + ticks[-1]
cbar.ax.set_yticklabels(ticks)
matplotlib.pyplot.setp(axis.get_xticklabels(),
rotation=30,
horizontalalignment="right")
return axis
def _main_():
argparser = setup_argparser()
args = argparser.parse_args()
path_to_resultsfile = args.resultsfile
mode = args.mode
lower_then = args.lower_then
greater_then = args.greater_then
path_output = args.output
path_stack = args.stack
field = args.field
field_index_error = 1
field_index_dr_ratio = 3
if field == "ERROR":
field = field_index_error
elif field == "DR_RATIO":
field = field_index_dr_ratio
# Read in error file
results = np.loadtxt(path_to_resultsfile, delimiter=",")
# Identify relevant particles
relevant_selection = [
a and b for a, b in zip(results[:, field] <= lower_then,
results[:, field] >= greater_then)
]
# Write stack
number_of_particles = EMAN2.EMUtil.get_image_count(path_stack)
local_bdb_stack = EMAN2db.db_open_dict(path_output)
sp_global_def.write_command(EMAN2db.db_parse_path(path_output)[0])
num_particles_relevant = 0
for particle_index in range(number_of_particles):
particle = sp_ctf_refine_io.read_particle(path_stack,
particle_index,
header_only=True)
particle_header = particle.get_attr_dict()
if relevant_selection[particle_index]:
pctf = particle_header["ctf"]
pctf.defocus = results[particle_index, 2]
particle_header["ctf"] = pctf
num_particles_relevant = num_particles_relevant + 1
if mode == "UPDATE":
local_bdb_stack[particle_index] = particle_header
elif mode == "EXTRACT" and relevant_selection[particle_index]:
local_bdb_stack[num_particles_relevant - 1] = particle_header
EMAN2db.db_close_dict(local_bdb_stack)
sp_global_def.sxprint("Particles updated/extracted",
num_particles_relevant)
def refine_set(particle_indices):
"""
Runs the defocus refinement for a set of particles.
:param particle_indices: Indicies of the particles inside the stack
:return: List of refined CTFs.
"""
try:
refined_ctfs = []
particle_micrographs = {}
for particle_index in particle_indices:
particle = sp_ctf_refine_io.read_particle(STACK_FILE_PATH, particle_index)
# particle.write_image("/home/twagner/temp/refine/"+str(particle_index)+"particle.hdf")
if RESOLUTION is not None and PIXEL_SIZE is not None:
particle = particle.process(
"filter.lowpass.gauss",
{"cutoff_freq": 1.0 / RESOLUTION, "apix": PIXEL_SIZE},
)
# In case of phase plate a high pass might be necessary
# if PARTICLE_DIAMETER is not None
# particle = particle.process("filter.highpass.gauss",{"cutoff_freq":1.0/160})
particle_projection_params = PROJECTION_PARAMETERS[particle_index].tolist()
# As i shift the volume and not the particle, multiply by -1
particle_projection_params[3] = -1 * particle_projection_params[3]
particle_projection_params[4] = -1 * particle_projection_params[4]
# particle_projection_params[3] = add_proj_error(particle_projection_params, 3, 2)
# particle_projection_params[4] = add_proj_error(particle_projection_params, 4, 2)
# particle_projection_params[2] = add_proj_error(particle_projection_params, 2, 2)
particle_ctf = particle.get_attr("ctf")
volume = VOLUME1
if HALF_MAP_ASSIGNEMENTS is not None:
if HALF_MAP_ASSIGNEMENTS[particle_index] != 0:
volume = VOLUME2
best_ctf, error, drratio = refine_defocus_with_error_est(
particle_volume=volume,
particle_image=particle,
projection_angle_and_shift=particle_projection_params,
current_ctf=particle_ctf,
def_search_range=DEFOCUS_SEARCH_RANGE,
def_step_size=DEFOCUS_STEP_SIZE,
)
particle_micrograph_filename = particle.get_attr("ptcl_source_image")
if particle_micrograph_filename in particle_micrographs:
particle_micrographs[particle_micrograph_filename]["indices"].append(
particle_index
)
particle_micrographs[particle_micrograph_filename]["defocus"].append(
best_ctf.defocus
)
particle_micrographs[particle_micrograph_filename]["diff"].append(
particle_ctf.defocus - best_ctf.defocus
)
particle_micrographs[particle_micrograph_filename]["error"].append(
error
)
particle_micrographs[particle_micrograph_filename]["drratio"].append(
drratio
)
else:
particle_micrographs[particle_micrograph_filename] = {
"indices": [particle_index],
"diff": [particle_ctf.defocus - best_ctf.defocus],
"error": [error],
"defocus": [best_ctf.defocus],
"drratio": [drratio],
}
refined_ctfs.append(best_ctf)
del particle_projection_params
del volume
del particle_ctf
del particle
except Exception as err:
import traceback
sp_global_def.sxprint(
"Exception happend for particles in range ",
np.min(particle_indices),
"-",
np.max(particle_indices),
)
traceback.print_exc()
raise err
return refined_ctfs, particle_micrographs