Scripts and Tools for Electron Microscopy Analysis.
Project description
STEMIA
Scripts and Tools for Electron Microscopy Image Analysis.
This is a simple personal collection of (sometimes...) useful scripts and tools for cryoem/cryoet.
Installation
pip install stemia
Tools
Everything is accessible through the main command line interface stemia
. Try stemia -h
.
stemia aretomo aln2xf
Usage: stemia aretomo aln2xf [OPTIONS] ALN_FILE
Convert AreTomo `aln` file to imod `xf` format.
Options:
-f, --overwrite overwrite existing output
--help Show this message and exit.
stemia aretomo batch_warp
Usage: stemia aretomo batch_warp [OPTIONS] WARP_DIR
Run aretomo in batch on data preprocessed in warp.
Needs to be ran after imod stacks were generated. Requires ccderaser and
AreTomo>=1.3.0. Assumes the default Warp directory structure with generated
imod stacks.
Options:
-m, --mdoc-dir PATH
-o, --output-dir PATH output directory for all the processing. If
None, defined as warp_dir/aretomo
-d, --dry-run only print some info, without running the
commands.
-v, --verbose print individual commands
-j, --just TEXT reconstruct just these tomograms
-e, --exclude TEXT exclude these tomograms from the run
-t, --sample-thickness INTEGER unbinned thickness of the SAMPLE (ice or
lamella) used for alignment
-z, --z-thickness INTEGER unbinned thickness of the RECONSTRUCTION.
-b, --binning INTEGER binning for aretomo reconstruction (relative
to warp binning)
-a, --tilt-axis FLOAT starting tilt axis for AreTomo, if any
-p, --patches INTEGER number of patches for local alignment in
aretomo (NxN), if any
-r, --roi-dir PATH directory containing ROI files. Extension
does not matter, but names should be same as
TS.
-f, --overwrite overwrite any previous existing run
--train whether to train a new denosing model
--topaz-patch-size INTEGER patch size for denoising in topaz.
--start-from [fix|align|tilt_mdocs|reconstruct|stack_halves|reconstruct_halves|denoise]
use outputs from a previous run, starting
processing at this step
--stop-at [fix|align|tilt_mdocs|reconstruct|stack_halves|reconstruct_halves|denoise]
terminate processing after this step
--ccderaser TEXT command for ccderaser
--aretomo TEXT command for aretomo
--gpus TEXT Comma separated list of gpus to use for
aretomo. Default to all.
--tiltcorr / --no-tiltcorr do not correct sample tilt
--help Show this message and exit.
stemia aretomo batch
Usage: stemia aretomo batch [OPTIONS]
Run AreTomo on a full directory.
Options:
--help Show this message and exit.
stemia cryosparc csplot
Usage: stemia cryosparc csplot [OPTIONS] JOB_DIR
Read a cryosparc job directory and plot interactively any column.
All the related data from parent jobs will also be loaded. An interactive
ipython shell will be opened with data loaded into a pandas dataframe.
JOB_DIR: a cryosparc job directory.
Options:
--drop-na drop rows that contain NaN values (e.g: micrographs with
no particles)
--no-particles do not read particles data
--no-micrographs do not read micrographs data
--help Show this message and exit.
stemia cryosparc fix_filament_ids
Usage: stemia cryosparc fix_filament_ids [OPTIONS] STAR_FILE
Replace cryosparc filament ids with small unique integers.
Relion will fail with cryosparc IDs because of overflows.
Options:
-o, --star-output FILE where to put the updated version of the star file
[default: <STAR_FILE>_fixed_id.star]
-f, --overwrite overwrite output if exists
--help Show this message and exit.
stemia cryosparc generate_tilt_angles
Usage: stemia cryosparc generate_tilt_angles [OPTIONS] STAR_FILE TILT_ANGLE
TILT_AXIS
Generate angle priors for a tilted dataset.
Read a Relion STAR_FILE with in-plane angles and generate priors for rot and
tilt angles based on a TILT_ANGLE around a TILT_AXIS.
Options:
-r, --radians Provide angles in radians instead of degrees
-o, --star-output FILE where to put the updated version of the star file
[default: <STAR_FILE>_tilted.star]
-f, --overwrite overwrite output if exists
--help Show this message and exit.
stemia cryosparc merge_defects_gainref
Usage: stemia cryosparc merge_defects_gainref [OPTIONS] DEFECTS GAINREF
Merge serialEM defects and gainref for cryosparc usage.
requires active sbrgrid.
Options:
-d, --output-defects FILE
-o, --output-gainref FILE
-f, --overwrite overwrite output if exists
--help Show this message and exit.
stemia image center_filament
Usage: stemia image center_filament [OPTIONS] INPUT [OUTPUT]
Center an mrc image (stack) containing filament(s).
Can update particles in a RELION .star file accordingly. If OUTPUT is not
given, default to INPUT_centered.mrc
Options:
-s, --update-star FILE a RELION .star file to update with new
particle positions
-o, --star-output FILE where to put the updated version of the star
file. Only used if -s is passed [default:
STARFILE_centered.star]
--update-by [class|particle] whether to update particle positions by
classes or 1 by 1. Only used if -s is passed
[default: class]
-f, --overwrite overwrite output if exists
-n, --n-filaments INTEGER number of filaments on the image [default: 2]
-p, --percentile INTEGER percentile for binarisation [default: 85]
--help Show this message and exit.
stemia image create_mask
Usage: stemia image create_mask [OPTIONS] INPUT OUTPUT
Create a mask for INPUT.
Axis order is zyx!
Options:
-t, --mask-type [sphere|cylinder|threshold]
-c, --center FLOAT center of the mask
-a, --axis INTEGER main symmetry axis (for cylinder)
-r, --radius FLOAT radius of the mask. If thresholding,
equivalent to "hard padding" [required]
-i, --inner-radius FLOAT inner radius of the mask (if any)
-p, --padding FLOAT smooth padding
--ang / --px whether the radius and padding are in
angstrom or pixels
--threshold FLOAT threshold for binarization of the input map
-f, --overwrite overwrite output if exists
--help Show this message and exit.
stemia image extract_z_snapshots
Usage: stemia image extract_z_snapshots [OPTIONS] [INPUTS]...
Grab z slices at regular intervals from a tomogram as jpg images.
INPUTS: any number of paths of volume images
Options:
-o, --output-dir PATH
-n, --n-slices INTEGER number of equidistant slices to extract
--keep-extrema whether to keep slices at z=0 and z=-1 (if false,
slices is reduced by 2)
-a, --average INTEGER number of slices to average over
-s, --size TEXT size of final image (X,Y)
-r, --range TEXT range of slices to image (A,B)
--axis INTEGER axis along which to do the slicing
--help Show this message and exit.
stemia image flip_z
Usage: stemia image flip_z [OPTIONS] STAR_PATH
Flip the z axis for particles in a RELION star file.
STAR_PATH: star file to flip along z
Assumes all tomograms have the same shape.
Options:
-o, --output FILE
-m, --mrc_path FILE
--star_pixel_size FLOAT
--mrc_pixel_size FLOAT
--z_shape INTEGER
--help Show this message and exit.
stemia image fourier_crop
Usage: stemia image fourier_crop [OPTIONS] [INPUTS]...
Bin mrc images to the specified pixel size using fourier cropping.
Options:
-b, --binning FLOAT binning amount [required]
-f, --overwrite overwrite output if exists
--help Show this message and exit.
stemia image rescale
Usage: stemia image rescale [OPTIONS] INPUT OUTPUT TARGET_PIXEL_SIZE
Rescale an mrc image to the specified pixel size.
TARGET_PIXEL_SIZE: target pixel size in Angstrom
Options:
--input-pixel-size FLOAT force input pizel size and ignore mrc header
-f, --overwrite overwrite output if exists
--help Show this message and exit.
stemia imod find_NAD_params
Usage: stemia imod find_NAD_params [OPTIONS] INPUT
Test a range of k and iteration values for nad_eed_3d
Options:
-k, --k-values TEXT
-i, --iterations TEXT
-s, --std TEXT
--help Show this message and exit.
stemia relion align_filament_particles
Usage: stemia relion align_filament_particles [OPTIONS] STAR_FILE
Fix filament PsiPriors so they are consistent within a filament.
Read a Relion STAR_FILE with in-plane angles and filament info and flip any
particle that's not consistent with the rest of the filament.
If a consensus cannot be reached, or the filament has too few particles,
discard the whole filament.
Options:
-o, --star-output FILE where to put the updated version of the star
file [default: <STAR_FILE>_aligned.star]
-t, --tolerance FLOAT angle in degrees within which neighbouring
particles are considered aligned
-c, --consensus-threshold FLOAT
require an angle consensus at least higher
than this to use a filament.
-d, --drop-below INTEGER drop filaments if they have fewer than this
number of particles
-r, --rotate-bad-particles rotate bad particles to match the rest of
the filament
-f, --overwrite overwrite output if exists
--help Show this message and exit.
stemia warp fix_mdoc
Usage: stemia warp fix_mdoc [OPTIONS] MDOC_DIR
Fix mdoc files to point to the right data.
Options:
-d, --data-dir PATH
--help Show this message and exit.
stemia warp merge_star
Usage: stemia warp merge_star [OPTIONS] [STAR_FILES]...
Merge star files ignoring optic groups and ensuring columns for warp.
Options:
-o, --star-output FILE where to put the merged star file [required]
-f, --overwrite overwrite output if exists
--help Show this message and exit.
stemia warp offset_angle
Usage: stemia warp offset_angle [OPTIONS] [WARP_DIR]
Offset tilt angles in warp xml files.
Options:
--help Show this message and exit.
stemia warp parse_xml
Usage: stemia warp parse_xml [OPTIONS] XML_FILE
Parse a warp xml file and print its content.
Options:
--help Show this message and exit.
stemia warp prepare_isonet
Usage: stemia warp prepare_isonet [OPTIONS] WARP_DIR ISO_STAR
Update an isonet starfile with preprocessing data from warp.
Options:
--help Show this message and exit.
stemia warp spoof_mdoc
Usage: stemia warp spoof_mdoc [OPTIONS] [RAWTLT_FILES]...
Create dummy mdocs for warp.
RAWTLT_FILES: simple file with one tilt angle per line. Order should match
sorted filenames.
Options:
-d, --dose-per-image FLOAT electron dose per tilt image (or per frame if
inputs are movies) [required]
-p, --pixel-size FLOAT
-e, --extension [tif|mrc]
-f, --overwrite
--help Show this message and exit.
stemia warp summarize
Usage: stemia warp summarize [OPTIONS] [WARP_DIR]
Summarize the state of a Warp project.
Reports for each tilt series: - discarded: number of discarded tilts -
total: total number oftilts in raw data - stacked: number of image slices in
imod output directory - mismatch: whether stacked != (total - discarded) -
resolution: estimated resolution if processed
Options:
--help Show this message and exit.
stemia warp preprocess_serialem
Usage: stemia warp preprocess_serialem [OPTIONS] RAW_DATA_DIR
Prepare and unpack data from sterialEM for Warp.
You must be in a new directory for this to work; new files will be placed
there with the same name as the original tifs.
RAW_DATA_DIR: the directory containing the raw data
Options:
--help Show this message and exit.
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