SIMPLE

Use when working in SIMPLE's src/main/nano subsystem, including nanoparticle and molecule data structures, graphene and time-series helpers, and the SINGLE-specific domain logic that supports liquid-cell and nanoparticle workflows.

Use when working on SIMPLE's abinitio2D workflow and its cluster2D stages, including 2D search strategies, probabilistic 2D sampling, class-average restoration, distributed partial class-average assembly, online matcher particle I/O, project updates, and streaming/rejection helpers.

Use when working on SIMPLE's model_cavgs_rejection application, simple_cavg_quality feature-space selector, class-average quality selection, quality_mode=analyze outputs, cavgs_quality feature/reference tables, chunk vs pool rejection tuning, or microchunk quality-vector integration.

Use when studying, explaining, or modifying SIMPLE's fractional-update and trailing-reconstruction workflow, including update_frac sampling, sampled/updatecnt bookkeeping, matcher reconstruction I/O, partial even/odd reconstruction handoff, rec3D/volassemble ownership, downsampling compatibility, obsfield mirrors, and stage-to-stage previous-reference contracts.

Use when working in SIMPLE's src/main/stream subsystem, including online/mini-stream orchestration, chunk and microchunk processing, staged pipeline steps, watchers, queue/message definitions, and streaming variants of preprocessing and cluster2D workflows.

Use when working on SIMPLE's streaming microchunk class-average rejection, simple_microchunked2D lifecycle sentinels, pass-1/pass-2/refchunk/match generation, skip_pass_2 behavior, simple_cluster2D_rejector criteria, or boundaries with model_cavgs_rejection.

Use when working on SIMPLE's refine3D workflow, including CLI/UI entrypoints, commanders, probabilistic pre-alignment, 3D search and matcher strategies, online partial reconstruction, volassemble, automasking, nonuniform filtering, multi-state behavior, distributed execution, and related abinitio3D refinement code paths.

Use when working on SIMPLE abinitio3D sampling policy, update_frac or nsample behavior, prob_align/prob_tab sampling reuse, sampled/updatecnt bookkeeping, online matcher reconstruction I/O, or volassemble trailing-update weighting.

Use when working anywhere in the SIMPLE repository and you need a high-level architectural map of the cryo-EM platform, including the relationship between production executables, the src core library, src/main subsystems, tests, scripts, docs, and the NICE layer.

Use when working in SIMPLE's src/main/nu_filt subsystem, including simple_nu_filter, candidate-bank setup, mask-packed objective costs, ordered-label Potts smoothing, high-resolution shell extension, NU local-resolution output, and cleanup of module-level filter state.

Use when working in SIMPLE's src/main/params subsystem, including the parameters type, command-line parameter binding, typed parsing, derived parameter phases, dynamic defaults, filt_mode flags, and validation of parsed workflow state.

Use when working in SIMPLE's src/main/pca subsystem, including PCA, PPCA, complex PPCA, kernel PCA, diffusion maps, and SVD-backed dimensionality-reduction code used in analysis and denoising workflows.

Use when working with the root modules directly under SIMPLE's src/main directory, especially orchestration modules like builder, command-line parsing, convergence, ab initio controllers, probability tables, simulation, symmetry, and other cross-subsystem foundation code.

Use when working in SIMPLE's src/main/volume subsystem, including reconstruction objects, even/odd reconstruction handling, volume analysis, docking, interpolation, polar-Fourier volume correlation, and postprocessing policy such as automasking and nonuniform filtering.

Use when editing SIMPLE's Fortran code and you need repo-specific guidance on the modern Fortran style used here, including modules, submodules, type-bound procedures, abstract command interfaces, generated sources, OpenMP-aware code, and common patterns for extending the code safely.

Use when working on SIMPLE's nonuniform filtering and volume-domain regularization path, including filt_mode=nonuniform or nonuniform_lpset, nu_refine, simple_nu_filter, nonuniform mask selection, _nu_filt/_nu_locres outputs, ML-regularized auxiliary replacement coupling, or volassemble postprocessing.

Use when working in SIMPLE's src/main/apis subsystem, including public API aggregator modules that bundle imports for executables, commanders, core helpers, GUI metadata, orientation APIs, polar Fourier APIs, and stream/test entrypoints.

Use when working in SIMPLE's src/main/class subsystem, including class averaging, class FRCs, restore paths, and 2D class-product generation used by cluster2D and related workflows.

Use when working in SIMPLE's src/main/commanders subsystem, including abstract command interfaces plus the SIMPLE, SINGLE, and test commander families that own high-level workflow behavior for most CLI programs.

Use when working in SIMPLE's src/main/ctf subsystem, including microscope contrast transfer function models, anisotropic/patched CTF estimation, fitting cost functions, and iterative estimation workflows.

Use when working in SIMPLE's src/main/exec subsystem, including the execution-router modules that dispatch program names to commander objects for SIMPLE, SINGLE, and test workflows.

Use when working in SIMPLE's src/main/image subsystem, including the core image type, FFT and Fourier-space operations, geometry, filtering, masks, I/O, projector classes, and related image-processing infrastructure.

Use when working in SIMPLE's src/main/interp subsystem, including gridding, Kaiser-Bessel interpolation, edge/window functions, and interpolation support used by reconstruction and Fourier-domain workflows.

Use when working in SIMPLE's src/main/motion subsystem, including hybrid global/local motion correction, patched alignment, iterative correction, nano-specific motion paths, and helper utilities for movie alignment workflows.

Use when working in SIMPLE's src/main/opt subsystem, including optimizer abstractions, BFGS, L-BFGS-B, simplex, particle swarm, differential evolution, conjugate-gradient variants, and optimization factories/specs used throughout the platform.

Use when working in SIMPLE's src/main/ori subsystem, including orientation records, orientation collections, sampling, transforms, I/O, statistics, neighborhood relations, and weighting logic used by 2D and 3D search workflows.

Use when working in SIMPLE's src/main/pftc subsystem, including polar Fourier transform calculation, correlation, geometry, memoization, CTF-aware paths, restore/state operations, and search support for alignment workflows.

Use when working in SIMPLE's src/main/pick subsystem, including segmentation-based picking, picking references, iterative picking helpers, and picker utilities used by particle-extraction workflows.

Use when working in SIMPLE's src/main/project subsystem, including the sp_project type, segment ownership for mic/stk/ptcl/cls/out/optics data, binary project I/O, and project-level metadata and artifact management.

Use when working in SIMPLE's src/main/star subsystem, including STAR file parsing/wrapping, Relion interoperability, starproject import/export utilities, and stream-aware STAR project handling.

Use when working in SIMPLE's src/main/strategies subsystem, including parallelization strategies, 2D and 3D search strategies, matchers, batching, reconstruction helpers, and the execution-policy layer between commanders and low-level scientific objects.

Use when working in SIMPLE's src/main/ui subsystem, including program registration, parameter metadata, CLI-visible program definitions, test UI groups, SINGLE/simple/stream UI groups, and JSON metadata generation for NICE and other interfaces.