def simple():
"""
Simulate the image
"""
# Get the start time
start_time = time.time()
# Create the argument parser
parser = argparse.ArgumentParser(description="Simulate the image")
# Add some command line arguments
parser.add_argument(
"-c",
"--config",
type=str,
default=None,
dest="config",
help="The yaml file to configure the simulation",
)
parser.add_argument(
"-o",
"--output",
type=str,
default="output.h5",
dest="output",
help="The filename for the output",
)
parser.add_argument(
"atoms",
type=str,
default=None,
nargs="?",
help="The filename for the input atoms",
)
# Parse the arguments
args = parser.parse_args()
# Configure some basic logging
parakeet.command_line.configure_logging()
# Load the full configuration
config = parakeet.config.load(args.config)
# Print some options
parakeet.config.show(config)
# Create the microscope
microscope = parakeet.microscope.new(**config["microscope"])
# Create the exit wave data
logger.info(f"Loading sample from {args.atoms}")
atoms = parakeet.sample.AtomData.from_text_file(args.atoms)
# Create the simulation
simulation = parakeet.simulation.simple(
microscope=microscope,
atoms=atoms,
device=config["device"],
simulation=config["simulation"],
)
# Create the writer
logger.info(f"Opening file: {args.output}")
writer = parakeet.io.new(
args.output,
shape=simulation.shape,
pixel_size=simulation.pixel_size,
dtype=numpy.complex64,
)
# Run the simulation
simulation.run(writer)
# Write some timing stats
logger.info("Time taken: %.2f seconds" % (time.time() - start_time))
def image(args=None):
"""
Simulate the image with noise
"""
# Get the start time
start_time = time.time()
# Create the argument parser
parser = argparse.ArgumentParser(description="Simulate the image")
# Add some command line arguments
parser.add_argument(
"-c",
"--config",
type=str,
default=None,
dest="config",
help="The yaml file to configure the simulation",
)
parser.add_argument(
"-o",
"--optics",
type=str,
default="optics.h5",
dest="optics",
help="The filename for the optics",
)
parser.add_argument(
"-i",
"--image",
type=str,
default="image.h5",
dest="image",
help="The filename for the image",
)
# Parse the arguments
args = parser.parse_args(args=args)
# Configure some basic logging
parakeet.command_line.configure_logging()
# Load the full configuration
config = parakeet.config.load(args.config)
# Print some options
parakeet.config.show(config)
# Create the microscope
microscope = parakeet.microscope.new(**config["microscope"])
# Create the exit wave data
logger.info(f"Loading sample from {args.optics}")
optics = parakeet.io.open(args.optics)
# Create the scan
config["scan"]["angles"] = optics.angle
config["scan"]["positions"] = optics.position[:, 1]
scan = parakeet.scan.new(**config["scan"])
# Create the simulation
simulation = parakeet.simulation.image(
microscope=microscope,
optics=optics,
scan=scan,
device=config["device"],
simulation=config["simulation"],
cluster=config["cluster"],
)
# Create the writer
logger.info(f"Opening file: {args.image}")
writer = parakeet.io.new(
args.image,
shape=simulation.shape,
pixel_size=simulation.pixel_size,
dtype=numpy.float32,
)
# Run the simulation
simulation.run(writer)
# Write some timing stats
logger.info("Time taken: %.2f seconds" % (time.time() - start_time))
def projected_potential(args=None):
"""
Simulate the projected potential from the sample
"""
# Get the start time
start_time = time.time()
# Create the argument parser
parser = argparse.ArgumentParser(
description="Simulate the exit wave from the sample")
# Add some command line arguments
parser.add_argument(
"-c",
"--config",
type=str,
default=None,
dest="config",
help="The yaml file to configure the simulation",
)
parser.add_argument(
"-d",
"--device",
choices=["cpu", "gpu"],
default=None,
dest="device",
help="Choose the device to use",
)
parser.add_argument(
"--cluster.max_workers",
type=int,
default=None,
dest="cluster_max_workers",
help="The maximum number of worker processes",
)
parser.add_argument(
"--cluster.method",
type=str,
choices=["sge"],
default=None,
dest="cluster_method",
help="The cluster method to use",
)
parser.add_argument(
"-s",
"--sample",
type=str,
default="sample.h5",
dest="sample",
help="The filename for the sample",
)
# Parse the arguments
args = parser.parse_args(args=args)
# Configure some basic logging
parakeet.command_line.configure_logging()
# Set the command line args in a dict
command_line = {}
if args.device is not None:
command_line["device"] = args.device
if args.cluster_max_workers is not None or args.cluster_method is not None:
command_line["cluster"] = {}
if args.cluster_max_workers is not None:
command_line["cluster"]["max_workers"] = args.cluster_max_workers
if args.cluster_method is not None:
command_line["cluster"]["method"] = args.cluster_method
# Load the full configuration
config = parakeet.config.load(args.config, command_line)
# Print some options
parakeet.config.show(config)
# Create the microscope
microscope = parakeet.microscope.new(**config["microscope"])
# Create the sample
logger.info(f"Loading sample from {args.sample}")
sample = parakeet.sample.load(args.sample)
# Create the scan
if config["scan"]["step_pos"] == "auto":
radius = sample.shape_radius
config["scan"][
"step_pos"] = config["scan"]["step_angle"] * radius * pi / 180.0
scan = parakeet.scan.new(**config["scan"])
if scan.positions[-1] > sample.containing_box[1][0]:
raise RuntimeError("Scan goes beyond sample containing box")
# Create the simulation
simulation = parakeet.simulation.projected_potential(
microscope=microscope,
sample=sample,
scan=scan,
device=config["device"],
simulation=config["simulation"],
cluster=config["cluster"],
)
# Run the simulation
simulation.run()
# Write some timing stats
logger.info("Time taken: %.2f seconds" % (time.time() - start_time))
def ctf(args=None):
"""
Simulate the ctf
"""
# Get the start time
start_time = time.time()
# Create the argument parser
parser = argparse.ArgumentParser(description="Simulate the ctf")
# Add some command line arguments
parser.add_argument(
"-c",
"--config",
type=str,
default=None,
dest="config",
help="The yaml file to configure the simulation",
)
parser.add_argument(
"-o",
type=str,
default="ctf.h5",
dest="output",
help="The filename for the output",
)
# Parse the arguments
args = parser.parse_args(args=args)
# Configure some basic logging
parakeet.command_line.configure_logging()
# Load the full configuration
config = parakeet.config.load(args.config)
# Print some options
parakeet.config.show(config)
# Create the microscope
microscope = parakeet.microscope.new(**config["microscope"])
# Create the simulation
simulation = parakeet.simulation.ctf(microscope=microscope,
simulation=config["simulation"])
# Create the writer
logger.info(f"Opening file: {args.output}")
writer = parakeet.io.new(
args.output,
shape=simulation.shape,
pixel_size=simulation.pixel_size,
dtype=numpy.complex64,
)
# Run the simulation
simulation.run(writer)
# Write some timing stats
logger.info("Time taken: %.2f seconds" % (time.time() - start_time))
def optics(args=None):
"""
Simulate the optics
"""
# Get the start time
start_time = time.time()
# Create the argument parser
parser = argparse.ArgumentParser(description="Simulate the optics")
# Add some command line arguments
parser.add_argument(
"-c",
"--config",
type=str,
default=None,
dest="config",
help="The yaml file to configure the simulation",
)
parser.add_argument(
"-d",
"--device",
choices=["cpu", "gpu"],
default=None,
dest="device",
help="Choose the device to use",
)
parser.add_argument(
"--cluster.max_workers",
type=int,
default=None,
dest="cluster_max_workers",
help="The maximum number of worker processes",
)
parser.add_argument(
"--cluster.method",
type=str,
choices=["sge"],
default=None,
dest="cluster_method",
help="The cluster method to use",
)
parser.add_argument(
"-e",
"--exit_wave",
type=str,
default="exit_wave.h5",
dest="exit_wave",
help="The filename for the exit wave",
)
parser.add_argument(
"-o",
"--optics",
type=str,
default="optics.h5",
dest="optics",
help="The filename for the optics",
)
# Parse the arguments
args = parser.parse_args(args=args)
# Configure some basic logging
parakeet.command_line.configure_logging()
# Set the command line args in a dict
command_line = {}
if args.device is not None:
command_line["device"] = args.device
if args.cluster_max_workers is not None or args.cluster_method is not None:
command_line["cluster"] = {}
if args.cluster_max_workers is not None:
command_line["cluster"]["max_workers"] = args.cluster_max_workers
if args.cluster_method is not None:
command_line["cluster"]["method"] = args.cluster_method
# Load the full configuration
config = parakeet.config.load(args.config, command_line)
# Print some options
parakeet.config.show(config)
# Create the microscope
microscope = parakeet.microscope.new(**config["microscope"])
# Create the exit wave data
logger.info(f"Loading sample from {args.exit_wave}")
exit_wave = parakeet.io.open(args.exit_wave)
# Create the scan
config["scan"]["angles"] = exit_wave.angle
config["scan"]["positions"] = exit_wave.position[:, 1]
scan = parakeet.scan.new(**config["scan"])
# Create the simulation
simulation = parakeet.simulation.optics(
microscope=microscope,
exit_wave=exit_wave,
scan=scan,
device=config["device"],
simulation=config["simulation"],
sample=config["sample"],
cluster=config["cluster"],
)
# Create the writer
logger.info(f"Opening file: {args.optics}")
writer = parakeet.io.new(
args.optics,
shape=simulation.shape,
pixel_size=simulation.pixel_size,
dtype=numpy.float32,
)
# Run the simulation
simulation.run(writer)
# Write some timing stats
logger.info("Time taken: %.2f seconds" % (time.time() - start_time))