Frame Series
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_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 defocus model grid in X, Y, and temp
oral dimensions, separated by 'x': e.g. 5x5x40; empty
= auto; Z > 1 is purely experimental
--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.
-----------------------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.
-----------------------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_ctffs_boxnet_infer
WarpTools - a collection of tools for EM data pre-processing
Version 2.0.0
Unknown command, showing all available commands:
------------------------------------General-------------------------------------
change_selection Change the manual selection status (selected | deselect
ed | null) for every item
create_settings Create data import settings
filter_quality Filter frame/tilt series by various quality metrics, or
just print out histograms
move_data Changes the location of raw data in XML metadata; use i
t when the raw data moves, or you switch between Window
s and Linux
threshold_picks Apply a score threshold to particles picked through tem
plate-matching from tilt or frame series
----------------------------------Frame series----------------------------------
fs_motion_and_ctf Estimate motion in frame series, produce aligned averag
es, estimate CTF – all in one go!
fs_motion Estimate motion in frame series, produce aligned averag
es
fs_boxnet_infer Run a trained BoxNet model on frameseries averages, pro
ducing particle positions and masks
fs_boxnet_train (Re)train a BoxNet model on image/label pairs, producin
g a new model
fs_ctf Estimate CTF parameters in frame series
fs_export_micrographs Create aligned averages or half-averages from frame ser
ies with previously estimated motion
fs_export_particles Extract particles from tilt series
--------------------------------------Help--------------------------------------
helpgpt Get help from ChatGPT; requires an OpenAI API key store
d in ~/openai.key
----------------------------------Tilt series-----------------------------------
ts_aretomo Create tilt series stacks and run AreTomo2 to obtain ti
lt series alignments
ts_ctf Estimate CTF parameters in frame series
ts_defocus_hand Check and/or set defocus handedness for all tilt series
ts_etomo_fiducials Create tilt series stacks and run Etomo fiducial tracki
ng to obtain tilt series alignments
ts_etomo_patches Create tilt series stacks and run Etomo patch tracking
to obtain tilt series alignments
ts_eval_model Map 3D positions to sets of 2D image coordinates consid
ering a tilt series' deformation model
ts_export_particles Export particles as 3D volumes or 2D image series.
ts_import_alignments Import tilt series alignments from IMOD or AreTomo
ts_import Create .tomostar files based on a combination of MDOC f
iles, aligned frame series, and optional tilt series al
ignments from IMOD or AreTomo
ts_reconstruct Reconstruct tomograms for various tasks and, optionally
, half-tomograms for denoiser training
ts_stack Create tilt series stacks, i.e. put all of a series' ti
lt images in one .st file, to be used with IMOD, AreTom
o etc.
ts_template_match Match previously reconstructed tomograms against a 3D t
emplate, producing a list of the highest-scoring matche
s
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.
-----------------------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.
-----------------------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