Markdown Documentation Index¶

This file is automatically generated by scripts/generate_md_index.py. It provides a complete index of all Markdown documentation available in the repository.

Documentation files will link to this website, other files will link directly to Github.

.github¶

• Copilot Code Review Instructions for milk (copilot-code-review-instructions.md)
• Copilot Instructions — milk (copilot-instructions.md)
• pull_request_template.md

.github/ISSUE_TEMPLATE¶

• documentation.md

Root¶

• Agent Onboarding — milk (AGENTS.md)
• Project: milk (CLAUDE.md)
• Contributing to milk (CONTRIBUTING.md)
• Milk (README.md)

docs¶

• MILK & CACAO (index.md)
• Notes for Future Reference (notes_for_future.md)
• Tags (tags.md)
• What's New (whatsnew.md)

docs/arch¶

• FPS Standalone and CMD Modes (FPS_Standalone_CMD_Modes.md)
• Software Architecture (architecture.md)
• Dependency Graph (dependency_graph.md)
• Programmer's Guide to milk (programmers_guide.md)

docs/developer¶

• Working with the documentation (DocumentingCode.md)
• Loading, Creating Additional Modules (LoadingModules.md)
• Module Files (ModuleFiles.md)
• Template Source Code (TemplateSourceCode.md)
• Working with git (WorkingWithGit.md)
• Code Assist Tools (code_assist.md)
• Coding Standards (coding_standards.md)
• Dependency System: managing extra dependencies (dependency_system.md)
• Adding a Plugin to Milk (plugins.md)
• Developer tooling (tooling.md)
• Developer Tutorial: Writing Your First Milk Module (tutorial.md)

docs/guide¶

• Command Line Interface Syntax (CLIcore.md)
• FIFO Command Input (fifo.md)
• Function Processing System (FPS) (fps.md)
• fpsCTRL Reference (fpsCTRL_reference.md)
• Readline Keyboard Shortcuts (helpreadline.md)
• Process Info (procinfo) (procinfo.md)
• Python API (python.md)
• Scripting (scripting.md)
• Scripts Reference (scripts.md)
• FPS Sequencer (milk-seq) (sequencer.md)
• Stream Slicing (slicing.md)
• Shared Memory Streams (ImageStreamIO) (streams.md)
• Valkey Integration (valkey.md)

docs/includes¶

• abbreviations.md

docs/maintenance¶

• Project management operations (pm_operations.md)

docs/operations¶

• Debugging (debugging.md)
• Performance Tuning (performance.md)
• Profile-Guided Optimization (PGO) & Link-Time Optimization (LTO) (pgo.md)

docs/quickstart¶

• CLI Overview (CLI_Overview.md)
• Build Tiers (build_tiers.md)
• Installation (compile.md)
• FAQ & Troubleshooting (faq.md)

milk-examples¶

• Milk Examples (README.md)

milk-examples/example01_ImageStreamIO¶

• Example 01: ImageStreamIO (README.md)

milk-examples/example02_processinfo¶

• Example 02: ImageStreamIO + ProcessInfo (README.md)

milk-examples/example03_fps¶

• Example 03: ImageStreamIO + ProcessInfo + FPS (README.md)

plugins/cacao-src¶

• Project: cacao (GEMINI.md)
• cacao : Compute And Control for Adaptive Optics (README.md)

plugins/cacao-src/AOloopControl¶

• Module: AOloopControl (README.md)

plugins/cacao-src/AOloopControl/doc¶

• Module AOloopControl {#page_module_AOloopControl} (AOloopControl.md)
• cacao Control: Setup and Overview {#page_cacao_Control_Setup_Overview} (cacao_Control_Setup_Overview.md)
• cacao Hardware Simulation {#page_cacao_Hardware_Simulation} (cacao_Hardware_Simulation.md)
• cacao Initial Setup {#page_cacao_Initial_Setup} (cacao_Initial_Setup.md)
• cacao Software Overview {#page_cacao_Software_Overview} (cacao_Software_Overview.md)
• Auxiliary processes {#page_cacao_aux_processes} (cacao_aux_processes.md)
• Building control matrix {#page_cacao_building_control_matrix} (cacao_building_control_matrix.md)
• Calibration {#page_cacao_calibration} (cacao_calibration.md)
• CONF DIRECTORY CONTENT {#page_cacao_conf_directory} (cacao_conf_directory.md)
• MANAGING MULTIPLE PROCESSES {#page_cacao_managing_processes} (cacao_managing_processes.md)
• Offsetting {#page_cacao_offsetting} (cacao_offsetting.md)
• Predictive control {#page_cacao_predictive_control} (cacao_predictive_control.md)
• Running the loop: setting mode (CPU/GPU) {#page_cacao_running_loop_mode} (cacao_running_loop_mode.md)
• Setting up hardware interfaces {#page_cacao_setting_up_hardware_interfaces} (cacao_setting_up_hardware_interfaces.md)
• APPENDIX A: SHARED MEMORY STREAMS {#page_cacao_sharedmem_streams} (cacao_sharedmem_streams.md)
• STEP-BY-STEP EXAMPLE {#page_cacao_stepbystep_example} (cacao_stepbystep_example.md)
• Configuring and Running cacao {#page_cacao_top_guide} (cacao_top_guide.md)

plugins/cacao-src/AOloopControl/docdir¶

• Initial Setup (AOloopControl.md)
• Processes (AOloopControl_ProgGuide.md)
• Making AO control modes (aolmkmodes.md)
• List of shared memory streams and semaphores {#streams_semaphores} (sharedmemstreams.md)

plugins/cacao-src/AOloopControl/examples¶

• List of examples (README.md)

plugins/cacao-src/AOloopControl/examples/KalAO-dmloop-conf¶

• Overview (README.md)

plugins/cacao-src/AOloopControl/examples/KalAO-ttmloop-conf¶

• Overview (README.md)

plugins/cacao-src/AOloopControl/examples/MAPS-vispyr-conf¶

• Observing Run Notes: (ObsRunNotes.md)
• Overview (README.md)
• Startup Simple (SimpleStartup.md)

plugins/cacao-src/AOloopControl/examples/ao3k-apd188-conf¶

• Overview (README.md)

plugins/cacao-src/AOloopControl/examples/ao3k-apd3k-conf¶

• README.md

plugins/cacao-src/AOloopControl/examples/ao3k-bimdm3kpt-conf¶

• Overview (README.md)

plugins/cacao-src/AOloopControl/examples/ao3k-lowfs188-conf¶

• Overview (README.md)

plugins/cacao-src/AOloopControl/examples/ao3k-lowfs3k-conf¶

• README.md

plugins/cacao-src/AOloopControl/examples/ao3k-nirpyr188-conf¶

• Overview (README.md)

plugins/cacao-src/AOloopControl/examples/ao3k-nirpyr3k-conf¶

• Overview (README.md)

plugins/cacao-src/AOloopControl/examples/ao3k-ttoff188-conf¶

• Overview (README.md)

plugins/cacao-src/AOloopControl/examples/ao3k-ttoff3k-conf¶

• Overview (README.md)

plugins/cacao-src/AOloopControl/examples/archieved-old-donotuse¶

• Overview (README.md)

plugins/cacao-src/AOloopControl/examples/scexao-LDFC-conf¶

• Overview (README.md)

plugins/cacao-src/AOloopControl/examples/scexao-NIRPL-conf¶

• Overview (README.md)

plugins/cacao-src/AOloopControl/examples/scexao-vispyr-bin1-conf¶

• Overview (README.md)

plugins/cacao-src/AOloopControl/examples/scexao-vispyr-bin2-conf¶

• Overview (README.md)

plugins/cacao-src/AOloopControl_DM¶

• Module: AOloopControl_DM (README.md)

plugins/cacao-src/AOloopControl_DM/doc¶

• AOloopControl_DM {#page_module_AOloopControl_DM} (AOloopControl_DM.md)

plugins/cacao-src/AOloopControl_IOtools¶

• Module: AOloopControl_IOtools (README.md)

plugins/cacao-src/AOloopControl_PredictiveControl¶

• AOloopControl_PredictiveControl (README.md)

plugins/cacao-src/AOloopControl_PredictiveControl/doc¶

• AOloopControl PredictiveControl {#page_module_AOloopControl_PredictiveControl} (AOloopControl_PredictiveControl.md)

plugins/cacao-src/AOloopControl_acquireCalib¶

• Module: AOloopControl_acquireCalib (README.md)

plugins/cacao-src/AOloopControl_compTools¶

• AOloopControl_compTools (README.md)

plugins/cacao-src/AOloopControl_compTools/doc¶

• AOloopControl_compTools {#page_module_AOloopControl_compTools} (AOloopControl_compTools.md)

plugins/cacao-src/AOloopControl_perfTest¶

• Module: AOloopControl_perfTest (README.md)

plugins/cacao-src/AOloopControl_perfTest/doc¶

• AOloopControl_perfTest {#page_module_AOloopControl_perfTest} (AOloopControl_perfTest.md)

plugins/cacao-src/computeCalib¶

• Module: computeCalib (README.md)

plugins/cacao-src/computeCalib/doc¶

• AOloopControl computeCalib {#page_module_AOloopControl_computeCalib} (AOloopControl_computeCalib.md)

plugins/cacao-src/docs¶

• CACAO Documentation (index.md)

plugins/cacao-src/pyramidWFStools¶

• Module: pyramidWFStools (README.md)

plugins/milk-extra-src/ZernikePolyn¶

• Module: ZernikePolyn (README.md)

plugins/milk-extra-src/clustering¶

• Module: clustering (README.md)

plugins/milk-extra-src/fft¶

• Module: fft (README.md)

plugins/milk-extra-src/image_basic¶

• Module: image_basic (README.md)

plugins/milk-extra-src/image_filter¶

• Module: image_filter (README.md)

plugins/milk-extra-src/image_format¶

• Module: image_format (README.md)

plugins/milk-extra-src/image_gen¶

• Module: image_gen (README.md)

plugins/milk-extra-src/img_reduce¶

• Module: img_reduce (README.md)

plugins/milk-extra-src/info¶

• Module: info (README.md)

plugins/milk-extra-src/kdtree¶

• Module: kdtree (README.md)

plugins/milk-extra-src/linARfilterPred¶

• Module: linARfilterPred (README.md)

plugins/milk-extra-src/linalgebra¶

• Module: linalgebra (README.md)

plugins/milk-extra-src/linopt_imtools¶

• Module: linopt_imtools (README.md)

plugins/milk-extra-src/psf¶

• Module: psf (README.md)

plugins/milk-extra-src/statistic¶

• Module: statistic (README.md)

plugins/test-src/compilertest¶

• For compilation testing. (README.md)

python¶

• README.md

python/tests/conftestaux/gpu_monitor¶

• tests/gpu_monitor (README.md)

python/tests/resources/aolinearsimulator-conf/data¶

• Note on data (note.md)

python_module¶

• CacaoProcessTools (README.md)

src/cli/CLIcore¶

• CommandLineInterface Change Log {#page_CommandLineInterface_ChangeLog} (CHANGELOG.md)
• CLIcore (README.md)

src/cli/libenginecli¶

• libenginecli (README.md)

src/cli/libmilkscript¶

• libmilkscript (README.md)

src/cli/overview¶

• overview (milk-CTRL) (README.md)

src/cli/streamCTRL¶

• streamCTRL (README.md)

src/coremods/COREMOD_arith¶

• Module: COREMOD_arith (README.md)

src/coremods/COREMOD_iofits¶

• Module: COREMOD_iofits (README.md)

src/coremods/COREMOD_memory¶

• Module: COREMOD_memory (README.md)

src/coremods/COREMOD_tools¶

• Module: COREMOD_tools (README.md)

src/engine/ImageStreamIO¶

• Change Log (CHANGELOG.md)
• Module ImageStreamIO {#page_module_ImageStreamIO} (README.md)

src/engine/ImageStreamIO/python_module¶

• ImageStreamIOWrap (README.md)

src/engine/libfps¶

• Module: libfps (README.md)

src/engine/libfpsseq¶

• libfpsseq (README.md)

src/engine/libmilkcommon¶

• libmilkcommon (README.md)

src/engine/libmilkdata¶

• Module: libmilkdata (README.md)

src/engine/libprocessinfo¶

• libprocessinfo: MILK Process Management Library (README.md)

src/fpsvalkey¶

• milk-fps-valkey — FPS Parameter Sync to Valkey (README.md)

src/isio-tools¶

• isio-tools (README.md)

src/milk_module_example¶

• Module: milk_module_example (README.md)

tree-sitter-milkcli¶

• tree-sitter-milkcli (README.md)