cryodrgn abinit command API

A full list of parameters that can be used to control the behavior of the drgnai abinit command

Required Arguments

particles The input particle stack (.mrcs, .star, .cs, or .txt).

--outdir/-o The directory where model outputs will be saved.

--ctf Path to CTF parameters (.pkl). Must be the size of the full dataset.

Other input parameters

--ind Path to indices (.pkl) or number of images to keep (first images kept). Default is to use full dataset if not given.

--datadir When using a .star or .cs file with relative paths, path to the directory containing the .mrcs files.

--relion31 Flag for RELION3.1 .star file format.

--uninvert-data Flag for not inverting input data (e.g. for EMPIAR-10076).

--load Path to a checkpoint (weights.<epoch>.pkl) to load.

--load-poses Path to a pose file (pose.<epoch>.pkl) to load.

--lazy Flag for lazy data loading, which uses less GPU memory.

--max-threads Number of threads to use for data loading.

--no-trans Flag for indicating that the dataset does not contain translations.

--norm Override the default method for normalizing the images stack using two values (mean, std).

Training scheduling

--num-epochs Number of total epochs to train for.

--epochs-sgd Number of epochs to train for SGD.

--epochs-pose-search Number of epochs for hierarchical pose search.

--n-imgs-pose-search Alternatively, the number of images to use for hierarchical pose search instead of specifying in epochs.

Loss

--beta-conf [string, default = 0.0] Beta term penalizing the KL divergence of the posterior distribution of conformations. Only used in variational mode.

--trans-l1-regularizer [string, default = 0.0] Strength of the L1 regularizer applied on estimated translations.

--l2-smoothness-regularizer [string, default = 0.0] Strength of the L2 smoothness regularization (penalization of strong gradients).

Optimizers

--hypervolume-optimizer-type [string, default = “adam”] Optimizer type for the hypervolume (choice: “adam”).

--pose-table-optimizer-type [string, default = “adam”] Optimizer for the pose table (choice: “adam”, “lbfgs”).

--conf-table-optimizer-type [string, default = “adam”] Optimizer for the conformation table (choice: “adam”).

--conf-encoder-optimizer-type [string, default = “adam”] Optimizer for the conformation encoder.

--lr [float, default = 1e-4] Learning rate of the hypervolume.

--lr-pose_table [float, default = 1e-3] Learning rate of the pose table.

--lr-conf-table [float, default = 1e-2] Learning rate fo the conformation table.

--lr-conf-encoder [float, default = 1e-4] Learning rate of the conformation encoder.

--wd [float, default = 0.0] Weight decay used by Adam optimizers.

Masking

--output-mask [string, default = “circ”] Type of output mask (choice: "circ", “frequency_marching”)

--add-one-frequency-every [int, default = 100,000] Frequency for adding new frequencies in the output mask, during HPS (in images).

--n-frequencies-per-epoch [int, default = 10] Number of frequencies to add in the output mask at each epoch, during SGD.

--max-freq [int, default = None] Highest frequency to use in the loss. Use all frequencies if None.

--window-radius-gt-real [float, default = 0.85] Radius of the circular mask applied on images in real space (maximum radius is 1).

--l-start-fm [int, default = 12] Starting size for the output mask when using frequency marching.

Conformations

--variational-het [bool, default = False] Flag activating the variational mode of conformation estimation.

--zdim [int, default = 4] Dimension of conformations.

--std-z-init [float, default = 0.1] Standard deviation of the initial conformations (i.i.d. with a centered Gaussian distribution).

--use-conf-encoder [bool, default = False] Flag for using an encoder to predict conformations.

--depth-cnn [int, default = 5] Depth of the encoder.

--channels-cnn [int, default = 32] Number of channels in the encoder.

--kernel-size-cnn [int, default = 3] Size of the kernels in the encoder.

--resolution-encoder [int, default = None] Resolution of images given to the encoder. Images are nto downsampled if None.

Hypervolume

--explicit-volume [bool, default = False] Flag for using an explicit volume (voxel array).

--layers [int, default = 3] Number of hidden layers in the hypervolume.

--dim [int, default = 256] Dimension of hidden layers in the hypervolume.

--pe-type [string, default = “gaussian”] Type of positional encoding for Fourier coordinates (choice: “gaussian”).

--pe-dim [int, default = 64] Number of frequencies used for positional encoding.

--feat-sigma [float, default = 0.5] Standard deviation of encoding frquencies.

--hypervolume-domain [string, default = “hartley”] Domain of the hypervolume (choice: “hartley”).

--pe-type-conf [string, default = None] Type of positional encoding for conformations (choice: None, “geom”).

Pre-training

--n-imgs-pretrain [int, default = 10,000] Number of images used for pre-training.

--pretrain-with-gt-poses [bool, default = False] Flag for using ground truth poses at pre-training time.

Pose Search

--l-start [int, default = 12] Number of frequencies used during the first pose search step.

--l-end [int, default = 32] Number of frequencies used during the last pose search step.

--niter [int, default = 4] Number of pose search iterations.

--t-extent [float, default = 20.0] Extent of the translation seach grid, in pixels.

--t-ngrid [int, default = 7] Number of point per dimension in the translation search grid.

--t-xshift [float, default = 0.0] X-axis shift of the translation search grid.

--t-yshift [float, default = 0.0] Y-axis shift of the translation search grid.

--no-trans-search-at-pose-search [bool, default = False] Flag for by-passing the translation search.

--nkeptposes [int, default = 8] Number of poses kept per image.

--base-healpy: [int, default = 2] Base healpy index.

Others

--color-palette [string, default = None] Type of palette used to visualize the predicted conformations (choice: None, “rainbow”, “linear”).

--no-amp Flag for disabling torch.cuda.amp Automatic Mixed Precision.

--test-installation [bool, default = False] Flag for testing the installation.

--seed [int, default = -1] Random seed. Randomly chosen if negative.

--verbose [bool, default = False] Flag for more verbose model logging.

--multigpu [bool, default = False] Flag for activating multi-GPU mode if more than one GPU is available.

--checkpoint [int, default = 5] Outputs from every nth epoch will saved, along with every pose search epoch.

--log-interval [int, default=10000] Logging interval in number of images.