Frame Series
CTF specimen-thickness fitting is disabled by default. Use --fit_thickness with
fs_ctf, or --c_fit_thickness with fs_motion_and_ctf, to enable it. Without
these flags, thickness is fixed to zero and saved as zero; defocus, astigmatism,
and the spatial defocus grid are still fitted. The choice is saved in
OptionsCTF.FitThickness. Enable thickness only when the fitted frequency range
contains enough thickness-dependent signal to distinguish it from the envelope.
The requested window is a minimum extraction size. At small pixel sizes or large defocus, the fitter enlarges the physical aperture to retain signal in the low-frequency support band (through 10 Å, or the requested coarser limit). Fourier padding alone cannot provide this support. The actual aperture is logged, while spectrum display dimensions retain the requested window size. Adequate requested apertures stay unchanged to preserve spatial sampling. The spatial defocus grid also models the defocus change across each aperture. Movie initialization pools all patch spectra before releasing the spatial grid.
fs_motion_and_ctf
WarpTools - a collection of tools for EM data pre-processing
Version 2.0.0
Showing all available options for command fs_motion_and_ctf:
------------------------------Data import settings------------------------------
--settings REQUIRED Path to Warp's .settings file, typically loca
ted in the processing folder. Default file name is 'pr
evious.settings'.
--------------------------------------------------------------------------------
--m_range_min Default: 500. Minimum resolution in Angstrom to consid
er in fit
--m_range_max Default: 10. Maximum resolution in Angstrom to conside
r in fit
--m_bfac Default: -500. Downweight higher spatial frequencies u
sing a B-factor, in Angstrom^2
--m_grid Resolution of the motion model grid in X, Y, and tempo
ral dimensions, separated by 'x': e.g. 5x5x40; empty =
auto
--c_window Default: 512. Patch size for CTF estimation in binned
pixels
--c_range_min Default: 30. Minimum resolution in Angstrom to conside
r in fit
--c_range_max Default: 4. Maximum resolution in Angstrom to consider
in fit
--c_defocus_min Default: 0.5. Minimum defocus value in um to explore d
uring fitting
--c_defocus_max Default: 5. Maximum defocus value in um to explore dur
ing fitting
--c_voltage Default: 300. Acceleration voltage of the microscope i
n kV
--c_cs Default: 2.7. Spherical aberration of the microscope i
n mm
--c_amplitude Default: 0.07. Amplitude contrast of the sample, usual
ly 0.07-0.10 for cryo
--c_fit_phase Fit the phase shift of a phase plate
--c_fit_thickness Fit specimen thickness (disabled by default)
--c_use_sum Use the movie average spectrum instead of the average
of individual frames' spectra. Can help in the absence
of an energy filter, or when signal is low.
--c_grid Resolution of the spatial defocus grid in X and Y,
separated by 'x': e.g. 6x6; empty = auto
--out_averages Export aligned averages
--out_average_halves Export aligned averages of odd and even frames separat
ely, e.g. for denoiser training
--out_skip_first Default: 0. Skip first N frames when exporting average
s
--out_skip_last Default: 0. Skip last N frames when exporting averages
-------------------------------Work distribution--------------------------------
--device_list Space-separated list of GPU IDs to use for processing.
Default: all GPUs in the system
--perdevice Default: 1. Number of processes per GPU
----------------------Advanced data import & flow options-----------------------
--input_data Overrides the list of input files specified in the .se
ttings file. Accepts a space-separated list of files,
wildcard patterns, or .txt files with one file name pe
r line.
--input_data_recursive Enables recursive search for files matching the wildca
rd pattern specified in --input_data. Only applicable
when processing and directories are separate. All file
names must be unique.
--input_processing Specifies an alternative directory containing pre-proc
essed results. Overrides the processing directory in t
he .settings file.
--output_processing Specifies an alternative directory to save processing
results. Overrides the processing directory in the .se
ttings file.
--input_norawdata Ignore the existence of raw data and look for XML meta
data in the processing directory instead.
-----------------------Advanced remote work distribution------------------------
--workers List of remote workers to be used instead of locally s
pawned processes. Formatted as hostname:port, separate
d by spaces
fs_motion
WarpTools - a collection of tools for EM data pre-processing
Version 2.0.0
Showing all available options for command fs_motion:
------------------------------Data import settings------------------------------
--settings REQUIRED Path to Warp's .settings file, typically loca
ted in the processing folder. Default file name is 'pr
evious.settings'.
--------------------------------------------------------------------------------
--range_min Default: 500. Minimum resolution in Angstrom to consid
er in fit
--range_max Default: 10. Maximum resolution in Angstrom to conside
r in fit
--bfac Default: -500. Downweight higher spatial frequencies u
sing a B-factor, in Angstrom^2
--grid Resolution of the motion model grid in X, Y, and tempo
ral dimensions, separated by 'x': e.g. 5x5x40; empty =
auto
--averages Export aligned averages
--average_halves Export aligned averages of odd and even frames separat
ely, e.g. for denoiser training
--skip_first Default: 0. Skip first N frames when exporting average
s
--skip_last Default: 0. Skip last N frames when exporting averages
-------------------------------Work distribution--------------------------------
--device_list Space-separated list of GPU IDs to use for processing.
Default: all GPUs in the system
--perdevice Default: 1. Number of processes per GPU
----------------------Advanced data import & flow options-----------------------
--input_data Overrides the list of input files specified in the .se
ttings file. Accepts a space-separated list of files,
wildcard patterns, or .txt files with one file name pe
r line.
--input_data_recursive Enables recursive search for files matching the wildca
rd pattern specified in --input_data. Only applicable
when processing and directories are separate. All file
names must be unique.
--input_processing Specifies an alternative directory containing pre-proc
essed results. Overrides the processing directory in t
he .settings file.
--output_processing Specifies an alternative directory to save processing
results. Overrides the processing directory in the .se
ttings file.
--input_norawdata Ignore the existence of raw data and look for XML meta
data in the processing directory instead.
-----------------------Advanced remote work distribution------------------------
--workers List of remote workers to be used instead of locally s
pawned processes. Formatted as hostname:port, separate
d by spaces
fs_ctf
WarpTools - a collection of tools for EM data pre-processing
Version 2.0.0
Showing all available options for command fs_ctf:
------------------------------Data import settings------------------------------
--settings REQUIRED Path to Warp's .settings file, typically loca
ted in the processing folder. Default file name is 'pr
evious.settings'.
--------------------------------------------------------------------------------
--window Default: 512. Patch size for CTF estimation in binned
pixels
--range_min Default: 30. Minimum resolution in Angstrom to conside
r in fit
--range_max Default: 4. Maximum resolution in Angstrom to consider
in fit
--defocus_min Default: 0.5. Minimum defocus value in um to explore d
uring fitting
--defocus_max Default: 5. Maximum defocus value in um to explore dur
ing fitting
--voltage Default: 300. Acceleration voltage of the microscope i
n kV
--cs Default: 2.7. Spherical aberration of the microscope i
n mm
--amplitude Default: 0.07. Amplitude contrast of the sample, usual
ly 0.07-0.10 for cryo
--fit_phase Fit the phase shift of a phase plate
--use_sum Use the movie average spectrum instead of the average
of individual frames' spectra. Can help in the absence
of an energy filter, or when signal is low.
--grid Resolution of the spatial defocus grid in X and Y,
separated by 'x': e.g. 6x6; empty = auto
-------------------------------Work distribution--------------------------------
--device_list Space-separated list of GPU IDs to use for processing.
Default: all GPUs in the system
--perdevice Default: 1. Number of processes per GPU
----------------------Advanced data import & flow options-----------------------
--input_data Overrides the list of input files specified in the .se
ttings file. Accepts a space-separated list of files,
wildcard patterns, or .txt files with one file name pe
r line.
--input_data_recursive Enables recursive search for files matching the wildca
rd pattern specified in --input_data. Only applicable
when processing and directories are separate. All file
names must be unique.
--input_processing Specifies an alternative directory containing pre-proc
essed results. Overrides the processing directory in t
he .settings file.
--output_processing Specifies an alternative directory to save processing
results. Overrides the processing directory in the .se
ttings file.
--input_norawdata Ignore the existence of raw data and look for XML meta
data in the processing directory instead.
-----------------------Advanced remote work distribution------------------------
--workers List of remote workers to be used instead of locally s
pawned processes. Formatted as hostname:port, separate
d by spaces
fs_boxnet_infer
WarpTools - a collection of tools for EM data pre-processing
Version 2.0.0
Showing all available options for command fs_boxnet_infer:
------------------------------Data import settings------------------------------
--settings REQUIRED Path to Warp's .settings file, typically loca
ted in the processing folder. Default file name is 'pr
evious.settings'.
--------------------------------------------------------------------------------
--model REQUIRED Path to the .pt file containing the model wei
ghts
--perprocess Default: 4. Number of threads per process; the model i
s loaded only once per process and oversubscription ca
n save memory
--diameter Default: 100. Approximate particle diameter in Angstro
m
--threshold Default: 0.5. Picking score threshold, between 0.0 and
1.0
--distance Default: 0. Minimum distance in Angstrom to maintain b
etween picked positions and masked pixels
--negative Expect negative stain-like contrast (mass = bright)
--suffix_star Override the suffix added to the particle STAR file; l
eave empty to use model name
--patchsize Default: 512. Size of the BoxNet input window that the
model was trained with, a multiple of 256; the defaul
t for models shipped with Warp is 512
-------------------------------Work distribution--------------------------------
--device_list Space-separated list of GPU IDs to use for processing.
Default: all GPUs in the system
--perdevice Default: 1. Number of processes per GPU
----------------------Advanced data import & flow options-----------------------
--input_data Overrides the list of input files specified in the .se
ttings file. Accepts a space-separated list of files,
wildcard patterns, or .txt files with one file name pe
r line.
--input_data_recursive Enables recursive search for files matching the wildca
rd pattern specified in --input_data. Only applicable
when processing and directories are separate. All file
names must be unique.
--input_processing Specifies an alternative directory containing pre-proc
essed results. Overrides the processing directory in t
he .settings file.
--output_processing Specifies an alternative directory to save processing
results. Overrides the processing directory in the .se
ttings file.
--input_norawdata Ignore the existence of raw data and look for XML meta
data in the processing directory instead.
-----------------------Advanced remote work distribution------------------------
--workers List of remote workers to be used instead of locally s
pawned processes. Formatted as hostname:port, separate
d by spaces
fs_boxnet_train
WarpTools - a collection of tools for EM data pre-processing
Version 2.0.0
Showing all available options for command fs_boxnet_train:
--------------------------------------------------------------------------------
--model_in Path to the .pt file containing the old model weights; mod
el will be initialized from scratch if this is left empty
--model_out REQUIRED Path to the .pt file where the new model weights
will be saved
--examples REQUIRED Path to a folder containing TIFF files with examp
les prepared with boxnet_examples_frameseries
--examples_general Path to a folder containing TIFF files with examples used
to train a more general model, which will be mixed 1:1 wit
h new examples to reduce overfitting
--no_mask Don't consider mask labels in training; they will be conve
rted to background labels
--patchsize Default: 512. Size of the BoxNet input window, a multiple
of 256; remember to use the same window with boxnet_infer_
frameseries
--batchsize Default: 8. Size of the minibatches used in training; larg
er batches require more GPU memory; must be divisible by n
umber of devices
--lr_start Default: 5E-05. Learning rate at training start
--lr_end Default: 1E-05. Learning rate at training end, with linear
interpolation in-between
--epochs Default: 100. Number of training epochs
--checkpoints Default: 0. Save checkpoints every N minutes; set to 0 to
disable
--devices Space-separated list of GPU IDs to be used for training
fs_export_micrographs
WarpTools - a collection of tools for EM data pre-processing
Version 2.0.0
Showing all available options for command fs_export_micrographs:
------------------------------Data import settings------------------------------
--settings REQUIRED Path to Warp's .settings file, typically loca
ted in the processing folder. Default file name is 'pr
evious.settings'.
--------------------------------------------------------------------------------
--averages Export aligned averages
--average_halves Export aligned averages of odd and even frames separat
ely, e.g. for denoiser training
--skip_first Default: 0. Skip first N frames when exporting average
s
--skip_last Default: 0. Skip last N frames when exporting averages
-------------------------------Work distribution--------------------------------
--device_list Space-separated list of GPU IDs to use for processing.
Default: all GPUs in the system
--perdevice Default: 1. Number of processes per GPU
----------------------Advanced data import & flow options-----------------------
--input_data Overrides the list of input files specified in the .se
ttings file. Accepts a space-separated list of files,
wildcard patterns, or .txt files with one file name pe
r line.
--input_data_recursive Enables recursive search for files matching the wildca
rd pattern specified in --input_data. Only applicable
when processing and directories are separate. All file
names must be unique.
--input_processing Specifies an alternative directory containing pre-proc
essed results. Overrides the processing directory in t
he .settings file.
--output_processing Specifies an alternative directory to save processing
results. Overrides the processing directory in the .se
ttings file.
--input_norawdata Ignore the existence of raw data and look for XML meta
data in the processing directory instead.
-----------------------Advanced remote work distribution------------------------
--workers List of remote workers to be used instead of locally s
pawned processes. Formatted as hostname:port, separate
d by spaces
fs_export_particles
WarpTools - a collection of tools for EM data pre-processing
Version 2.0.0
Showing all available options for command fs_export_particles:
------------------------------Data import settings------------------------------
--settings REQUIRED Path to Warp's .settings file, typically loc
ated in the processing folder. Default file name is '
previous.settings'.
----------------------STAR files with particle coordinates----------------------
-i, --input REQUIRED Path to folder containing the STAR files; or
path to a single STAR file
--patterns Space-separated list of file name search patterns or
STAR file names when --star is a folder
-------------------------------------Output-------------------------------------
-o, --output REQUIRED Where to write the STAR file containing info
rmation about the exported particles
--suffix_out Default: . Suffix to add at the end of each stack's n
ame; the full name will be [movie name][--suffix_out]
.mrcs
--angpix_out Pixel size the extracted particles will be scaled to;
leave out to use binned pixel size from input settin
gs
--box REQUIRED Particle box size in pixels
--diameter REQUIRED Particle diameter in Angstrom
--relative_output_paths Make paths in output STAR file relative to the locati
on of the STAR file. They will be relative to the wor
king directory otherwise.
-------------------Export type (REQUIRED, mutually exclusive)-------------------
--averages Export particle averages; mutually exclusive with oth
er export types
--halves Export particle half-averages e.g. for denoising; mut
ually exclusive with other export types
--only_star Don't export, only write out STAR table; mutually exc
lusive with other export types
-------------------------------Coordinate scaling-------------------------------
--angpix_coords REQUIRED Pixel size for the input coordinates
--angpix_shifts Pixel size for refined shifts if not given in Angstro
m (when using rlnOriginX instead of rlnOriginXAngst)
---------------------------------Expert options---------------------------------
--dont_invert Don't invert contrast, e.g. for negative stain data
--dont_normalize Don't normalize background (RELION will complain!)
--dont_center Don't re-center particles based on refined shifts
--flip_phases Pre-flip phases in bigger box to avoid signal loss du
e to delocalization
--keep_ctf Keep CTF information from STAR inputs
--skip_first_frames Default: 0. Skip first N frames
--skip_last_frames Default: 0. Skip last N frames
-------------------------------Work distribution--------------------------------
--device_list Space-separated list of GPU IDs to use for processing
. Default: all GPUs in the system
--perdevice Default: 1. Number of processes per GPU
----------------------Advanced data import & flow options-----------------------
--input_data Overrides the list of input files specified in the .s
ettings file. Accepts a space-separated list of files
, wildcard patterns, or .txt files with one file name
per line.
--input_data_recursive Enables recursive search for files matching the wildc
ard pattern specified in --input_data. Only applicabl
e when processing and directories are separate. All f
ile names must be unique.
--input_processing Specifies an alternative directory containing pre-pro
cessed results. Overrides the processing directory in
the .settings file.
--output_processing Specifies an alternative directory to save processing
results. Overrides the processing directory in the .
settings file.
--input_norawdata Ignore the existence of raw data and look for XML met
adata in the processing directory instead.
-----------------------Advanced remote work distribution------------------------
--workers List of remote workers to be used instead of locally
spawned processes. Formatted as hostname:port, separa
ted by spaces