diff --git a/README.md b/README.md deleted file mode 100644 index c2c0a22..0000000 --- a/README.md +++ /dev/null @@ -1,227 +0,0 @@ -# PySIMRecon - -Easy to use wrapper for pyCUDAsirecon, allowing the use of DV (DeltaVision) files without IVE/Priism (UCSF library with MRC/DV support). - -This is built for easy use from the command line or as part of an auto-processing pipeline, allowing parameters to be pre-configured or defined at runtime. - -### Goal - -To reconstruct the SIM data and create OTFs from PSFs from the cryoSIM at B24, Diamond from the .dv files created by Cockpit. Requirements are: - -- Easy to use -- Open source -- Reproducable results -- Can be used as part of an automatic processing pipeline - -### Current state - -Under development - -{{ SECTIONCONFIGURATION_MD }} - -### CLI - -##### sim-otf - -``` -usage: sim-otf [-c CONFIG_PATH] [-p PSF_PATHS [PSF_PATHS ...]] - [-o OUTPUT_DIRECTORY] [--overwrite] [--no-cleanup] - [--shape XY_SHAPE XY_SHAPE] [-v] [--no-progress] - [--nphases NPHASES] [--ls LS] [--na NA] [--nimm NIMM] - [--background BACKGROUND] [--beaddiam BEADDIAM] [--angle ANGLE] - [--nocompen NOCOMPEN] [--fixorigin FIXORIGIN FIXORIGIN] - [--leavekz LEAVEKZ LEAVEKZ LEAVEKZ] [-h] - -SIM PSFs to OTFs - -options: - -c CONFIG_PATH, --config-path CONFIG_PATH - Path to the root config that specifies the paths to - the OTFs and the other configs - -p PSF_PATHS [PSF_PATHS ...], --psf PSF_PATHS [PSF_PATHS ...] - Paths to PSF files to be reconstructed (multiple paths - can be given) - -o OUTPUT_DIRECTORY, --output-directory OUTPUT_DIRECTORY - If specified, the output directory that the OTFs will - be saved in, otherwise each OTF will be saved in the - same directory as its PSF - --overwrite If specified, files will be overwritten if they - already exist (unique filenames will be used - otherwise) - --no-cleanup If specified, files created during the OTF creation - process will not be cleaned up - --shape XY_SHAPE XY_SHAPE - Takes 2 integers (X Y), specifying the shape to crop - PSFs to before converting (powers of 2 are fastest) - -v, --verbose Show more logging - --no-progress turn off progress bars (only has an effect if tqdm is - installed) - -h, --help show this help message and exit - -Overrides: - Arguments that override configured values. Defaults stated are only used - if no value is given or configured. - - --nphases NPHASES Number of pattern phases per SIM direction - --ls LS Line spacing of SIM pattern in microns - --na NA Detection objective's numerical aperture - --nimm NIMM Refractive index of immersion medium - --background BACKGROUND - Camera readout background - --beaddiam BEADDIAM The diameter of the bead in microns, by default 0.12 - --angle ANGLE The k0 vector angle with which the PSF is taken, by - default 0 - --nocompen NOCOMPEN Do not perform bead size compensation, default False - (do perform) - --fixorigin FIXORIGIN FIXORIGIN - The starting and end pixel for interpolation along kr - axis, by default (2, 9) - --leavekz LEAVEKZ LEAVEKZ LEAVEKZ - Pixels to be retained on kz axis, by default (0, 0, 0) -``` - -##### sim-recon - -``` -usage: sim-recon [-c CONFIG_PATH] [-d SIM_DATA_PATHS [SIM_DATA_PATHS ...]] - [-o OUTPUT_DIRECTORY] [--overwrite] [--no-cleanup] - [--keep-split] [--parallel] [-v] [--no-progress] - [--ndirs NDIRS] [--nphases NPHASES] [--nordersout NORDERSOUT] - [--angle0 ANGLE0] [--ls LS] [--na NA] [--nimm NIMM] - [--wiener WIENER] [--zoomfact ZOOMFACT] [--zzoom ZZOOM] - [--background BACKGROUND] [--usecorr USECORR] - [--k0angles K0ANGLES K0ANGLES K0ANGLES] [--otfRA OTFRA] - [--otfPerAngle OTFPERANGLE] [--fastSI FASTSI] - [--k0searchAll K0SEARCHALL] [--norescale NORESCALE] - [--equalizez EQUALIZEZ] [--equalizet EQUALIZET] - [--dampenOrder0 DAMPENORDER0] [--nosuppress NOSUPPRESS] - [--nokz0 NOKZ0] [--gammaApo GAMMAAPO] - [--explodefact EXPLODEFACT] [--nofilterovlps NOFILTEROVLPS] - [--deskew DESKEW] [--deskewshift DESKEWSHIFT] - [--noRecon NORECON] [--cropXY CROPXY] [--xyres XYRES] - [--zres ZRES] [--zresPSF ZRESPSF] [--wavelength WAVELENGTH] - [-h] - -Reconstruct SIM data - -options: - -c CONFIG_PATH, --config-path CONFIG_PATH - Path to the root config that specifies the paths to - the OTFs and the other configs - -d SIM_DATA_PATHS [SIM_DATA_PATHS ...], --data SIM_DATA_PATHS [SIM_DATA_PATHS ...] - Paths to SIM data files to be reconstructed (multiple - paths can be given) - -o OUTPUT_DIRECTORY, --output-directory OUTPUT_DIRECTORY - The output directory to save reconstructed files in - --overwrite If specified, files will be overwritten if they - already exist (unique filenames will be used - otherwise) - --no-cleanup If specified, files created during the reconstruction - process will not be cleaned up - --keep-split If specified, channels will not be stitched back - together after reconstruction - --parallel If specified, up to 2 processes will be run at a time - -v, --verbose Show more logging - --no-progress turn off progress bars (only has an effect if tqdm is - installed) - -h, --help show this help message and exit - -Overrides: - Arguments that override configured values. Defaults stated are only used - if no value is given or configured. - - --ndirs NDIRS Number of SIM directions - --nphases NPHASES Number of pattern phases per SIM direction - --nordersout NORDERSOUT - Number of output SIM orders (must be <= nphases//2; - safe to ignore usually) - --angle0 ANGLE0 Angle of the first SIM angle in radians - --ls LS Line spacing of SIM pattern in microns - --na NA Detection objective's numerical aperture - --nimm NIMM Refractive index of immersion medium - --wiener WIENER Wiener constant; lower value leads to higher - resolution and noise; playing with it extensively is - strongly encouraged - --zoomfact ZOOMFACT Lateral zoom factor in the output over the input - images; leaving it at 2 should be fine in most cases - --zzoom ZZOOM Axial zoom factor; almost never needed - --background BACKGROUND - Camera readout background - --usecorr USECORR Use a flat-field correction file if provided - --k0angles K0ANGLES K0ANGLES K0ANGLES - Use these pattern vector k0 angles for all directions - (instead of inferring the rest angles from angle0) - --otfRA OTFRA Use rotationally averaged OTF; otherwise uses 3/2D OTF - for 3/2D raw data - --otfPerAngle OTFPERANGLE - Use one OTF per SIM angle; otherwise one OTF is used - for all angles, which is how it's been done - traditionally - --fastSI FASTSI SIM image is organized in Z->Angle->Phase order; - otherwise assuming Angle->Z->Phase image order - --k0searchAll K0SEARCHALL - Search for k0 at all time points - --norescale NORESCALE - No bleach correction - --equalizez EQUALIZEZ - Bleach correction for z - --equalizet EQUALIZET - Bleach correction for time - --dampenOrder0 DAMPENORDER0 - Dampen order-0 in final assembly; do not use for 2D - SIM; good choice for high-background images - --nosuppress NOSUPPRESS - Do not suppress DC singularity in the result (good - choice for 2D/TIRF data) - --nokz0 NOKZ0 Do not use kz=0 plane of the 0th order in the final - assembly (mostly for debug) - --gammaApo GAMMAAPO Output apodization gamma; 1.0 means triangular apo; - lower value means less dampening of high-resolution - info at the trade-off of higher noise - --explodefact EXPLODEFACT - Artificially exploding the reciprocal-space distance - between orders by this factor (for debug) - --nofilterovlps NOFILTEROVLPS - --deskew DESKEW Deskew angle; if not 0.0 then perform deskewing before - processing - --deskewshift DESKEWSHIFT - If deskewed, the output image's extra shift in X - (positive->left) - --noRecon NORECON No reconstruction will be performed; useful when - combined with "deskew": - --cropXY CROPXY Crop the X-Y dimension to this number; 0 means no - cropping - --xyres XYRES X-Y pixel size (only used for TIFF files) - --zres ZRES Z pixel size (only used for TIFF files) - --zresPSF ZRESPSF Z pixel size (used in PSF TIFF files) - --wavelength WAVELENGTH - Emission wavelength in nm (only used for TIFF files) -``` - -##### otf-view - -``` -usage: otf-view [-h] [--show] [--show-only] [-o OUTPUT_DIRECTORY] [-v] - [--no-progress] - otf_paths [otf_paths ...] - -Create OTF views - -positional arguments: - otf_paths OTF file paths - -options: - -h, --help show this help message and exit - --show Display the plots while running - --show-only Show plots without saving - -o OUTPUT_DIRECTORY, --output-directory OUTPUT_DIRECTORY - Save to this directory if saving plots, otherwise each - plot will be saved with its input file - -v, --verbose Show more logging - --no-progress turn off progress bars (only has an effect if tqdm is - installed) -``` - -##### dv2tiff - -Accepts a list of DV files to be converted to TIFFs (with some OME metadata). diff --git a/docs/help/otf_view.txt b/docs/help/otf_view.txt index 6c750bd..372985e 100644 --- a/docs/help/otf_view.txt +++ b/docs/help/otf_view.txt @@ -17,3 +17,4 @@ options: -v, --verbose Show more logging --no-progress turn off progress bars (only has an effect if tqdm is installed) +sdfsdf diff --git a/docs/help/sim_otf.txt b/docs/help/sim_otf.txt index fa92dc1..95382de 100644 --- a/docs/help/sim_otf.txt +++ b/docs/help/sim_otf.txt @@ -52,3 +52,4 @@ Overrides: axis, by default (2, 9) --leavekz LEAVEKZ LEAVEKZ LEAVEKZ Pixels to be retained on kz axis, by default (0, 0, 0) +sad diff --git a/docs/help/sim_recon.txt b/docs/help/sim_recon.txt index 5a546a1..5630e53 100644 --- a/docs/help/sim_recon.txt +++ b/docs/help/sim_recon.txt @@ -111,3 +111,4 @@ Overrides: --zresPSF ZRESPSF Z pixel size (used in PSF TIFF files) --wavelength WAVELENGTH Emission wavelength in nm (only used for TIFF files) + safas