Command line programs

Config file manipulation programs

parakeet.config.new

Generate a new config file

usage: parakeet.config.new [-h] [-c CONFIG] [-f FULL]

Named Arguments

-c, --config

The yaml file to configure the simulation

Default: “config.yaml”

-f, --full

Generate a file with the full configuration specification

Default: False

parakeet.config.show

Show the configuration

usage: parakeet.config.show [-h] [-c CONFIG] [-s SCHEMA]

Named Arguments

-c, --config: The yaml file to configure the simulation
-s, --schema: Show the config schema. To show full scheme type ‘-s .’. To show the schema for a specific section type e.g. ‘-s /definitions/Simulation’

parakeet.config.edit

Edit the configuration

usage: parakeet.config.edit [-h] -i INPUT -o OUTPUT -s CONFIG

Named Arguments

-i, --input

The input yaml file to configure the simulation

-o, --output

The output yaml file to configure the simulation

-s

The configuration string

Default: “”

Sample manipulation programs

parakeet.sample.new

Create a new sample model

usage: parakeet.sample.new [-h] -c CONFIG [-s SAMPLE]

Named Arguments

-c, --config

The yaml file to configure the simulation

-s, --sample

The filename for the sample file

Default: “sample.h5”

parakeet.sample.add_molecules

Add molecules to the sample model

usage: parakeet.sample.add_molecules [-h] -c CONFIG [-s SAMPLE]

Named Arguments

-c, --config

The yaml file to configure the simulation

-s, --sample

The filename for the sample file

Default: “sample.h5”

parakeet.sample.mill

Mill the sample

usage: parakeet.sample.mill [-h] -c CONFIG [-s SAMPLE]

Named Arguments

-c, --config

The yaml file to configure the simulation

-s, --sample

The filename for the sample file

Default: “sample.h5”

parakeet.sample.sputter

Sputter the sample

usage: parakeet.sample.sputter [-h] -c CONFIG [-s SAMPLE]

Named Arguments

-c, --config

The yaml file to configure the simulation

-s, --sample

The filename for the sample file

Default: “sample.h5”

parakeet.sample.show

Print details about the sample model

usage: parakeet.sample.show [-h] [-s SAMPLE]

Named Arguments

-s, --sample

The filename for the sample file

Default: “sample.h5”

Image Simulation programs

parakeet.simulate.potential

Simulate the projected potential from the sample

usage: parakeet.simulate.potential [-h] -c CONFIG [-s SAMPLE] [-p POTENTIAL]
                                   [-d {cpu,gpu}] [--nproc NPROC]
                                   [--gpu_id GPU_ID]

Named Arguments

-c, --config

The yaml file to configure the simulation

-s, --sample

The filename for the sample

Default: “sample.h5”

-p, --potential

The prefix for the filename for the potential

Default: “potential”

-d, --device

Possible choices: cpu, gpu

Choose the device to use

--nproc

The number of processes to use

--gpu_id

The GPU ids (must match number of processors)

parakeet.simulate.exit_wave

Simulate the exit wave from the sample

usage: parakeet.simulate.exit_wave [-h] -c CONFIG [-s SAMPLE] [-e EXIT_WAVE]
                                   [-d {cpu,gpu}] [--nproc NPROC]
                                   [--gpu_id GPU_ID]

Named Arguments

-c, --config

The yaml file to configure the simulation

-s, --sample

The filename for the sample

Default: “sample.h5”

-e, --exit_wave

The filename for the exit wave

Default: “exit_wave.h5”

-d, --device

Possible choices: cpu, gpu

Choose the device to use

--nproc

The number of processes to use

--gpu_id

The GPU ids (must match number of processors)

parakeet.simulate.optics

Simulate the optics and infinite dose image

usage: parakeet.simulate.optics [-h] -c CONFIG [-d {cpu,gpu}] [--nproc NPROC]
                                [--gpu_id GPU_ID] [-e EXIT_WAVE] [-o OPTICS]

Named Arguments

-c, --config

The yaml file to configure the simulation

-d, --device

Possible choices: cpu, gpu

Choose the device to use

--nproc

The number of processes to use

--gpu_id

The GPU ids (must match number of processors)

-e, --exit_wave

The filename for the exit wave

Default: “exit_wave.h5”

-o, --optics

The filename for the optics

Default: “optics.h5”

parakeet.simulate.ctf

Simulate the ctf

usage: parakeet.simulate.ctf [-h] -c CONFIG [-o OUTPUT]

Named Arguments

-c, --config

The yaml file to configure the simulation

-o

The filename for the output

Default: “ctf.h5”

parakeet.simulate.image

Simulate the noisy detector image

usage: parakeet.simulate.image [-h] -c CONFIG [-o OPTICS] [-i IMAGE]

Named Arguments

-c, --config

The yaml file to configure the simulation

-o, --optics

The filename for the optics

Default: “optics.h5”

-i, --image

The filename for the image

Default: “image.h5”

parakeet.simulate.simple

Simulate the whole process

usage: parakeet.simulate.simple [-h] -c CONFIG [-o OUTPUT] [atoms]

Positional Arguments

atoms: The filename for the input atoms

Named Arguments

-c, --config

The yaml file to configure the simulation

-o, --output

The filename for the output

Default: “output.h5”

Analysis programs

parakeet.analyse.reconstruct

Reconstruct the volume

usage: parakeet.analyse.reconstruct [-h] -c CONFIG [-d {cpu,gpu}] [-i IMAGE]
                                    [-r REC]

Named Arguments

-c, --config

The yaml file to configure the simulation

-d, --device

Possible choices: cpu, gpu

Choose the device to use

-i, --image

The filename for the image

Default: “image.mrc”

-r, --rec

The filename for the reconstruction

Default: “rec.mrc”

parakeet.analyse.correct

3D CTF correction of the images

usage: parakeet.analyse.correct [-h] -c CONFIG [-i IMAGE] [-cr CORRECTED]
                                [-ndf NUM_DEFOCUS] [-d {cpu,gpu}]

Named Arguments

-c, --config

The yaml file to configure the simulation

-i, --image

The filename for the image

Default: “image.mrc”

-cr, --corrected

The filename for the corrected image

Default: “corrected_image.mrc”

-ndf, --num-defocus

Number of defoci that correspond to different depths through for which the sample will be 3D CTF corrected

-d, --device

Possible choices: cpu, gpu

Choose the device to use

parakeet.analyse.average_particles

Perform sub tomogram averaging

usage: parakeet.analyse.average_particles [-h] -c CONFIG [-s SAMPLE] [-r REC]
                                          [-h1 HALF1] [-h2 HALF2]
                                          [-psz PARTICLE_SIZE]
                                          [-n NUM_PARTICLES]

Named Arguments

-c, --config

The yaml file to configure the simulation

-s, --sample

The filename for the sample

Default: “sample.h5”

-r, --rec

The filename for the reconstruction

Default: “rec.mrc”

-h1, --half1

The filename for the particle average

Default: “half1.mrc”

-h2, --half2

The filename for the particle average

Default: “half2.mrc”

-psz, --particle_size

The size of the particles extracted (px)

Default: 0

-n, --num_particles

The number of particles to use

Default: 0

parakeet.analyse.average_all_particles

Perform sub tomogram averaging

usage: parakeet.analyse.average_all_particles [-h] -c CONFIG [-s SAMPLE]
                                              [-r REC] [-avm AVERAGE]
                                              [-psz PARTICLE_SIZE]
                                              [-n NUM_PARTICLES]

Named Arguments

-c, --config

The yaml file to configure the simulation

-s, --sample

The filename for the sample

Default: “sample.h5”

-r, --rec

The filename for the reconstruction

Default: “rec.mrc”

-avm, --average_map

The filename for the particle average

Default: “average_map.mrc”

-psz, --particle_size

The size of the particles extracted (px)

Default: 0

-n, --num_particles

The number of particles to use

Default: 0

parakeet.analyse.extract

Perform sub tomogram extraction

usage: parakeet.analyse.extract [-h] -c CONFIG [-s SAMPLE] [-r REC]
                                [-pm PARTICLES] [-psz PARTICLE_SIZE]
                                [-psm PARTICLE_SAMPLING]

Named Arguments

-c, --config

The yaml file to configure the simulation

-s, --sample

The filename for the sample

Default: “sample.h5”

-r, --rec

The filename for the reconstruction

Default: “rec.mrc”

-pm, --particle_map

The filename for the particle average

Default: “particle_map.h5”

-psz, --particle_size

The size of the particles extracted (px)

Default: 0

-psm, --particle_sampling

The sampling of the particle volume (factor of 2)

Default: 1

parakeet.analyse.refine

Refine map and model

usage: parakeet.analyse.refine [-h] -c CONFIG [-s SAMPLE] [-r REC]

Named Arguments

-c, --config

The yaml file to configure the simulation

-s, --sample

The filename for the sample

Default: “sample.h5”

-r, --rec

The filename for the reconstruction

Default: “half1.mrc”

PDB file programs

parakeet.pdb.read

Read a PDB file

usage: parakeet.pdb.read [-h] filename

Positional Arguments

filename: The path to the PDB file

parakeet.pdb.get

Get a PDB file

usage: parakeet.pdb.get [-h] [-d DIRECTORY] id

Positional Arguments

id: The PDB ID

Named Arguments

-d, --directory

The directory to save to

Default: “.”

Other programs

parakeet.export

Export images to a different format

usage: parakeet.export [-h] -o OUTPUT [--rot90 ROT90]
                       [--rotation_range ROTATION_RANGE | --select_images SELECT_IMAGES]
                       [--roi ROI]
                       [--complex_mode {complex,real,imaginary,amplitude,phase,phase_unwrap,square,imaginary_square}]
                       [--interlace INTERLACE] [--rebin REBIN]
                       [--filter_resolution FILTER_RESOLUTION]
                       [--filter_shape {square,gaussian}] [--vmin VMIN]
                       [--vmax VMAX] [--sort {angle}]
                       filename

Positional Arguments

filename: The input filename

Named Arguments

-o, --output

The output filename

--rot90

Rotate the image 90deg counter clockwise

Default: False

--rotation_range

Select a rotation range (deg).

Multiple rotation ranges can be specified as: –rotation_range=start1,stop1;start2,stop2

--select_images

Select a range of images (start,stop,step)

--roi

Select a region of interest (–roi=x0,y0,x1,y1)

--complex_mode

Possible choices: complex, real, imaginary, amplitude, phase, phase_unwrap, square, imaginary_square

How to treat complex numbers

Default: “complex”

--interlace

Interlace the scan. If the value <= 1 then the images are kept in the same order, otherwise, the images are reordered by skipping images. For example, if –interlace=2 is set then the images will be written out as [1, 3, 5, … , 2, 4, 6, …]

--rebin

The rebinned factor. The shape of the output images will be original_shape / rebin

Default: 1

--filter_resolution

The resolution of the filter (A)

--filter_shape

Possible choices: square, gaussian

The shape of the filter

--vmin

The minimum pixel value when exporting to an image

--vmax

The maximum pixel value when exporting to an image

--sort

Possible choices: angle

Sort the images

parakeet.run

Run full simulation experiment

usage: parakeet.run [-h] -c CONFIG [-s SAMPLE] [-e EXIT_WAVE] [-o OPTICS]
                    [-i IMAGE] [-d {cpu,gpu}] [--nproc NPROC]
                    [--gpu_id GPU_ID]
                    [--steps {all,sample,sample.new,sample.add_molecules,simulate,simulate.exit_wave,simulate.optics,simulate.image} [{all,sample,sample.new,sample.add_molecules,simulate,simulate.exit_wave,simulate.optics,simulate.image} ...]]

Named Arguments

-c, --config

The yaml file to configure the simulation

-s, --sample

The filename for the sample

Default: “sample.h5”

-e, --exit_wave

The filename for the exit wave

Default: “exit_wave.h5”

-o, --optics

The filename for the optics

Default: “optics.h5”

-i, --image

The filename for the image

Default: “image.h5”

-d, --device

Possible choices: cpu, gpu

Choose the device to use

--nproc

The number of processes to use

--gpu_id

The GPU ids (must match number of processors)

--steps

Possible choices: all, sample, sample.new, sample.add_molecules, simulate, simulate.exit_wave, simulate.optics, simulate.image

Which simulation steps to run

parakeet

Parakeet: simulate some TEM images!

usage: parakeet [-h]
                {config,sample,simulate,analyse,metadata,pdb,export,run} ...

Positional Arguments

command

Possible choices: config, sample, simulate, analyse, metadata, pdb, export, run

The parakeet sub commands

Sub-commands

config

Commands to manipulate configuration files

parakeet config [-h] {new,edit,show} ...

Positional Arguments

config_command

Possible choices: new, edit, show

The parakeet config sub commands

Sub-commands

new

Generate a new config file

parakeet config new [-h] [-c CONFIG] [-f FULL]

Named Arguments

-c, --config

The yaml file to configure the simulation

Default: “config.yaml”

-f, --full

Generate a file with the full configuration specification

Default: False

edit

Edit the configuration

parakeet config edit [-h] -i INPUT -o OUTPUT -s CONFIG

Named Arguments

-i, --input

The input yaml file to configure the simulation

-o, --output

The output yaml file to configure the simulation

-s

The configuration string

Default: “”

show

Show the configuration

parakeet config show [-h] [-c CONFIG] [-s SCHEMA]

Named Arguments

-c, --config: The yaml file to configure the simulation
-s, --schema: Show the config schema. To show full scheme type ‘-s .’. To show the schema for a specific section type e.g. ‘-s /definitions/Simulation’

sample

Commands to manipulate the sample files

parakeet sample [-h] {new,add_molecules,mill,sputter,show} ...

Positional Arguments

sample_command

Possible choices: new, add_molecules, mill, sputter, show

The parakeet sample sub commands

Sub-commands

new

Create a new sample model

parakeet sample new [-h] -c CONFIG [-s SAMPLE]

Named Arguments

-c, --config

The yaml file to configure the simulation

-s, --sample

The filename for the sample file

Default: “sample.h5”

add_molecules

Add molecules to the sample model

parakeet sample add_molecules [-h] -c CONFIG [-s SAMPLE]

Named Arguments

-c, --config

The yaml file to configure the simulation

-s, --sample

The filename for the sample file

Default: “sample.h5”

mill

Mill the sample

parakeet sample mill [-h] -c CONFIG [-s SAMPLE]

Named Arguments

-c, --config

The yaml file to configure the simulation

-s, --sample

The filename for the sample file

Default: “sample.h5”

sputter

Sputter the sample

parakeet sample sputter [-h] -c CONFIG [-s SAMPLE]

Named Arguments

-c, --config

The yaml file to configure the simulation

-s, --sample

The filename for the sample file

Default: “sample.h5”

show

Print details about the sample model

parakeet sample show [-h] [-s SAMPLE]

Named Arguments

-s, --sample

The filename for the sample file

Default: “sample.h5”

simulate

Commands to simulate the TEM images

parakeet simulate [-h] {potential,exit_wave,optics,image,ctf} ...

Positional Arguments

simulate_command

Possible choices: potential, exit_wave, optics, image, ctf

The parakeet simulate sub commands

Sub-commands

potential

Simulate the projected potential from the sample

parakeet simulate potential [-h] -c CONFIG [-s SAMPLE] [-p POTENTIAL]
                            [-d {cpu,gpu}] [--nproc NPROC] [--gpu_id GPU_ID]

Named Arguments

-c, --config

The yaml file to configure the simulation

-s, --sample

The filename for the sample

Default: “sample.h5”

-p, --potential

The prefix for the filename for the potential

Default: “potential”

-d, --device

Possible choices: cpu, gpu

Choose the device to use

--nproc

The number of processes to use

--gpu_id

The GPU ids (must match number of processors)

exit_wave

Simulate the exit wave from the sample

parakeet simulate exit_wave [-h] -c CONFIG [-s SAMPLE] [-e EXIT_WAVE]
                            [-d {cpu,gpu}] [--nproc NPROC] [--gpu_id GPU_ID]

Named Arguments

-c, --config

The yaml file to configure the simulation

-s, --sample

The filename for the sample

Default: “sample.h5”

-e, --exit_wave

The filename for the exit wave

Default: “exit_wave.h5”

-d, --device

Possible choices: cpu, gpu

Choose the device to use

--nproc

The number of processes to use

--gpu_id

The GPU ids (must match number of processors)

optics

Simulate the optics and infinite dose image

parakeet simulate optics [-h] -c CONFIG [-d {cpu,gpu}] [--nproc NPROC]
                         [--gpu_id GPU_ID] [-e EXIT_WAVE] [-o OPTICS]

Named Arguments

-c, --config

The yaml file to configure the simulation

-d, --device

Possible choices: cpu, gpu

Choose the device to use

--nproc

The number of processes to use

--gpu_id

The GPU ids (must match number of processors)

-e, --exit_wave

The filename for the exit wave

Default: “exit_wave.h5”

-o, --optics

The filename for the optics

Default: “optics.h5”

image

Simulate the noisy detector image

parakeet simulate image [-h] -c CONFIG [-o OPTICS] [-i IMAGE]

Named Arguments

-c, --config

The yaml file to configure the simulation

-o, --optics

The filename for the optics

Default: “optics.h5”

-i, --image

The filename for the image

Default: “image.h5”

ctf

Simulate the ctf

parakeet simulate ctf [-h] -c CONFIG [-o OUTPUT]

Named Arguments

-c, --config

The yaml file to configure the simulation

-o

The filename for the output

Default: “ctf.h5”

analyse

Commands to analyse the simulated data

parakeet analyse [-h]
                 {reconstruct,correct,average_particles,average_all_particles,extract,refine}
                 ...

Positional Arguments

analyse_command

Possible choices: reconstruct, correct, average_particles, average_all_particles, extract, refine

The parakeet analyse sub commands

Sub-commands

reconstruct

Reconstruct the volume

parakeet analyse reconstruct [-h] -c CONFIG [-d {cpu,gpu}] [-i IMAGE] [-r REC]

Named Arguments

-c, --config

The yaml file to configure the simulation

-d, --device

Possible choices: cpu, gpu

Choose the device to use

-i, --image

The filename for the image

Default: “image.mrc”

-r, --rec

The filename for the reconstruction

Default: “rec.mrc”

correct

3D CTF correction of the images

parakeet analyse correct [-h] -c CONFIG [-i IMAGE] [-cr CORRECTED]
                         [-ndf NUM_DEFOCUS] [-d {cpu,gpu}]

Named Arguments

-c, --config

The yaml file to configure the simulation

-i, --image

The filename for the image

Default: “image.mrc”

-cr, --corrected

The filename for the corrected image

Default: “corrected_image.mrc”

-ndf, --num-defocus

Number of defoci that correspond to different depths through for which the sample will be 3D CTF corrected

-d, --device

Possible choices: cpu, gpu

Choose the device to use

average_particles

Perform sub tomogram averaging

parakeet analyse average_particles [-h] -c CONFIG [-s SAMPLE] [-r REC]
                                   [-h1 HALF1] [-h2 HALF2]
                                   [-psz PARTICLE_SIZE] [-n NUM_PARTICLES]

Named Arguments

-c, --config

The yaml file to configure the simulation

-s, --sample

The filename for the sample

Default: “sample.h5”

-r, --rec

The filename for the reconstruction

Default: “rec.mrc”

-h1, --half1

The filename for the particle average

Default: “half1.mrc”

-h2, --half2

The filename for the particle average

Default: “half2.mrc”

-psz, --particle_size

The size of the particles extracted (px)

Default: 0

-n, --num_particles

The number of particles to use

Default: 0

average_all_particles

Perform sub tomogram averaging

parakeet analyse average_all_particles [-h] -c CONFIG [-s SAMPLE] [-r REC]
                                       [-avm AVERAGE] [-psz PARTICLE_SIZE]
                                       [-n NUM_PARTICLES]

Named Arguments

-c, --config

The yaml file to configure the simulation

-s, --sample

The filename for the sample

Default: “sample.h5”

-r, --rec

The filename for the reconstruction

Default: “rec.mrc”

-avm, --average_map

The filename for the particle average

Default: “average_map.mrc”

-psz, --particle_size

The size of the particles extracted (px)

Default: 0

-n, --num_particles

The number of particles to use

Default: 0

extract

Perform sub tomogram extraction

parakeet analyse extract [-h] -c CONFIG [-s SAMPLE] [-r REC] [-pm PARTICLES]
                         [-psz PARTICLE_SIZE] [-psm PARTICLE_SAMPLING]

Named Arguments

-c, --config

The yaml file to configure the simulation

-s, --sample

The filename for the sample

Default: “sample.h5”

-r, --rec

The filename for the reconstruction

Default: “rec.mrc”

-pm, --particle_map

The filename for the particle average

Default: “particle_map.h5”

-psz, --particle_size

The size of the particles extracted (px)

Default: 0

-psm, --particle_sampling

The sampling of the particle volume (factor of 2)

Default: 1

refine

Refine map and model

parakeet analyse refine [-h] -c CONFIG [-s SAMPLE] [-r REC]

Named Arguments

-c, --config

The yaml file to configure the simulation

-s, --sample

The filename for the sample

Default: “sample.h5”

-r, --rec

The filename for the reconstruction

Default: “half1.mrc”

metadata

Commands to manipulate metadata

parakeet metadata [-h] {export} ...

Positional Arguments

metadata_command

Possible choices: export

The parakeet metadata sub commands

Sub-commands

export

Export the metadata to star files for downstream processing

parakeet metadata export [-h] [-c CONFIG] [-s SAMPLE] [-i IMAGE]
                         [--directory DIRECTORY] [--relion RELION]

Named Arguments

-c, --config

The yaml file to configure the simulation

Default: “config.yaml”

-s, --sample

The filename for the sample file

Default: “sample.h5”

-i, --image

The filename for the image file

Default: “image.h5”

--directory

The directory to export to

Default: “.”

--relion

Export the relion metadata

Default: True

pdb

Commands to operate on pdb files

parakeet pdb [-h] {get,read} ...

Positional Arguments

pdb_command

Possible choices: get, read

The parakeet pdb sub commands

Sub-commands

get

Get a PDB file

parakeet pdb get [-h] [-d DIRECTORY] id

Positional Arguments

id: The PDB ID

Named Arguments

-d, --directory

The directory to save to

Default: “.”

read

Read a PDB file

parakeet pdb read [-h] filename

Positional Arguments

filename: The path to the PDB file

export

Export images to a different format

parakeet export [-h] -o OUTPUT [--rot90 ROT90]
                [--rotation_range ROTATION_RANGE | --select_images SELECT_IMAGES]
                [--roi ROI]
                [--complex_mode {complex,real,imaginary,amplitude,phase,phase_unwrap,square,imaginary_square}]
                [--interlace INTERLACE] [--rebin REBIN]
                [--filter_resolution FILTER_RESOLUTION]
                [--filter_shape {square,gaussian}] [--vmin VMIN] [--vmax VMAX]
                [--sort {angle}]
                filename

Positional Arguments

filename: The input filename

Named Arguments

-o, --output

The output filename

--rot90

Rotate the image 90deg counter clockwise

Default: False

--rotation_range

Select a rotation range (deg).

Multiple rotation ranges can be specified as: –rotation_range=start1,stop1;start2,stop2

--select_images

Select a range of images (start,stop,step)

--roi

Select a region of interest (–roi=x0,y0,x1,y1)

--complex_mode

Possible choices: complex, real, imaginary, amplitude, phase, phase_unwrap, square, imaginary_square

How to treat complex numbers

Default: “complex”

--interlace

Interlace the scan. If the value <= 1 then the images are kept in the same order, otherwise, the images are reordered by skipping images. For example, if –interlace=2 is set then the images will be written out as [1, 3, 5, … , 2, 4, 6, …]

--rebin

The rebinned factor. The shape of the output images will be original_shape / rebin

Default: 1

--filter_resolution

The resolution of the filter (A)

--filter_shape

Possible choices: square, gaussian

The shape of the filter

--vmin

The minimum pixel value when exporting to an image

--vmax

The maximum pixel value when exporting to an image

--sort

Possible choices: angle

Sort the images

run

Run full simulation experiment

parakeet run [-h] -c CONFIG [-s SAMPLE] [-e EXIT_WAVE] [-o OPTICS] [-i IMAGE]
             [-d {cpu,gpu}] [--nproc NPROC] [--gpu_id GPU_ID]
             [--steps {all,sample,sample.new,sample.add_molecules,simulate,simulate.exit_wave,simulate.optics,simulate.image} [{all,sample,sample.new,sample.add_molecules,simulate,simulate.exit_wave,simulate.optics,simulate.image} ...]]

Named Arguments

-c, --config

The yaml file to configure the simulation

-s, --sample

The filename for the sample

Default: “sample.h5”

-e, --exit_wave

The filename for the exit wave

Default: “exit_wave.h5”

-o, --optics

The filename for the optics

Default: “optics.h5”

-i, --image

The filename for the image

Default: “image.h5”

-d, --device

Possible choices: cpu, gpu

Choose the device to use

--nproc

The number of processes to use

--gpu_id

The GPU ids (must match number of processors)

--steps

Possible choices: all, sample, sample.new, sample.add_molecules, simulate, simulate.exit_wave, simulate.optics, simulate.image

Which simulation steps to run