@brainpilot/skills 0.0.6 → 0.0.7
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/package.json +2 -2
- package/skills/01_Meta-Skills/academic-research-hub/SKILL.md +108 -0
- package/skills/01_Meta-Skills/academic-research-hub/scripts/requirements.txt +17 -0
- package/skills/01_Meta-Skills/academic-research-hub/scripts/research.py +781 -0
- package/skills/01_Meta-Skills/beautiful-log/SKILL.md +64 -0
- package/skills/01_Meta-Skills/beautiful-log/scripts/beautiful_log.py +274 -0
- package/skills/01_Meta-Skills/ethoclaw-daily-paper/SKILL.md +130 -0
- package/skills/01_Meta-Skills/ethoclaw-daily-paper/assets/config.template.yaml +54 -0
- package/skills/01_Meta-Skills/ethoclaw-daily-paper/assets/top5_digest_template.md +5 -0
- package/skills/01_Meta-Skills/ethoclaw-daily-paper/scripts/build_top5_digest.py +300 -0
- package/skills/01_Meta-Skills/ethoclaw-daily-paper/scripts/common.py +137 -0
- package/skills/01_Meta-Skills/ethoclaw-daily-paper/scripts/merge_results.py +106 -0
- package/skills/01_Meta-Skills/ethoclaw-daily-paper/scripts/run_pipeline.py +177 -0
- package/skills/01_Meta-Skills/ethoclaw-daily-paper/scripts/search_arxiv.py +162 -0
- package/skills/01_Meta-Skills/ethoclaw-daily-paper/scripts/search_pubmed.py +202 -0
- package/skills/01_Meta-Skills/ethoclaw-normalize-tabular/SKILL.md +173 -0
- package/skills/01_Meta-Skills/ethoclaw-normalize-tabular/scripts/normalize_data.py +874 -0
- package/skills/01_Meta-Skills/ethoclaw-pdf-research/SKILL.md +134 -0
- package/skills/01_Meta-Skills/ethoclaw-pdf-research/references/confirmation-prompts.md +31 -0
- package/skills/01_Meta-Skills/ethoclaw-pdf-research/references/output-patterns.md +45 -0
- package/skills/01_Meta-Skills/ethoclaw-pdf-research/scripts/build_markdown_deliverables.py +41 -0
- package/skills/01_Meta-Skills/ethoclaw-pdf-research/scripts/build_research_log.py +84 -0
- package/skills/01_Meta-Skills/ethoclaw-pdf-research/scripts/build_summary_md.py +63 -0
- package/skills/01_Meta-Skills/ethoclaw-pdf-research/scripts/extract_pdf_bundle.py +140 -0
- package/skills/01_Meta-Skills/experiment-controller/SKILL.md +140 -0
- package/skills/01_Meta-Skills/knowledge-graph-builder/SKILL.md +366 -0
- package/skills/01_Meta-Skills/knowledge-graph-builder/scripts/entity_resolution.py +120 -0
- package/skills/01_Meta-Skills/knowledge-graph-builder/scripts/extraction_prompt_template.txt +19 -0
- package/skills/01_Meta-Skills/knowledge-graph-builder/scripts/graph_query.py +106 -0
- package/skills/01_Meta-Skills/knowledge-graph-builder/scripts/hypothesis_cli_reference.py +42 -0
- package/skills/01_Meta-Skills/knowledge-graph-builder/scripts/new_data_source_template.py +116 -0
- package/skills/01_Meta-Skills/knowledge-graph-builder/scripts/requirements.txt +15 -0
- package/skills/01_Meta-Skills/method-design/SKILL.md +61 -0
- package/skills/01_Meta-Skills/multi-search-engine/SKILL.md +119 -0
- package/skills/01_Meta-Skills/research-idea/SKILL.md +65 -0
- package/skills/05_EEG_ERP/eeg-skill/SKILL.md +197 -0
- package/skills/05_EEG_ERP/meg-skill/SKILL.md +188 -0
- package/skills/05_EEG_ERP/meg-skill/scripts/time_frequency.py +223 -0
- package/skills/05_EEG_ERP/mne-eeg-tool/SKILL.md +165 -0
- package/skills/05_EEG_ERP/mne-eeg-tool/scripts/eeg_pipeline_reference.py +231 -0
- package/skills/05_EEG_ERP/seed-iv-skill/SKILL.md +184 -0
- package/skills/05_EEG_ERP/seed-iv-skill/scripts/classify_seed_iv.py +154 -0
- package/skills/05_EEG_ERP/seed-iv-skill/scripts/extract_seed_iv_features.py +190 -0
- package/skills/05_EEG_ERP/seed-iv-skill/scripts/validate_seed_iv.py +102 -0
- package/skills/05_EEG_ERP/seed-vig-skill/SKILL.md +182 -0
- package/skills/05_EEG_ERP/seed-vig-skill/scripts/classify_seed_vig.py +165 -0
- package/skills/05_EEG_ERP/seed-vig-skill/scripts/extract_seed_vig_features.py +185 -0
- package/skills/05_EEG_ERP/seed-vig-skill/scripts/validate_seed_vig.py +88 -0
- package/skills/06_fMRI_Neuroimaging/abcd-skill/SKILL.md +308 -0
- package/skills/06_fMRI_Neuroimaging/abcd-skill/scripts/abcd_qc_summary.py +449 -0
- package/skills/06_fMRI_Neuroimaging/abcd-skill/scripts/extract_abcd_phenotype.py +292 -0
- package/skills/06_fMRI_Neuroimaging/abcd-skill/scripts/reorganize_abcd.py +387 -0
- package/skills/06_fMRI_Neuroimaging/abide-skill/SKILL.md +302 -0
- package/skills/06_fMRI_Neuroimaging/abide-skill/scripts/abide_qc_summary.py +317 -0
- package/skills/06_fMRI_Neuroimaging/abide-skill/scripts/extract_abide_phenotype.py +267 -0
- package/skills/06_fMRI_Neuroimaging/abide-skill/scripts/reorganize_abide.py +387 -0
- package/skills/06_fMRI_Neuroimaging/adhd200-skill/SKILL.md +244 -0
- package/skills/06_fMRI_Neuroimaging/adhd200-skill/scripts/adhd200_qc_summary.py +98 -0
- package/skills/06_fMRI_Neuroimaging/adhd200-skill/scripts/extract_adhd200_phenotype.py +134 -0
- package/skills/06_fMRI_Neuroimaging/adhd200-skill/scripts/reorganize_adhd200.py +206 -0
- package/skills/06_fMRI_Neuroimaging/adni-skill/SKILL.md +358 -0
- package/skills/06_fMRI_Neuroimaging/adni-skill/scripts/generate_adni_task_files.py +1305 -0
- package/skills/06_fMRI_Neuroimaging/adni-skill/scripts/generate_vqa_from_tasks.py +766 -0
- package/skills/06_fMRI_Neuroimaging/adni-skill/scripts/reorganize_adni.py +491 -0
- package/skills/06_fMRI_Neuroimaging/aibl-skill/SKILL.md +295 -0
- package/skills/06_fMRI_Neuroimaging/aibl-skill/scripts/aibl_qc_summary.py +260 -0
- package/skills/06_fMRI_Neuroimaging/aibl-skill/scripts/extract_aibl_phenotype.py +365 -0
- package/skills/06_fMRI_Neuroimaging/aibl-skill/scripts/reorganize_aibl.py +394 -0
- package/skills/06_fMRI_Neuroimaging/aomic-skill/SKILL.md +292 -0
- package/skills/06_fMRI_Neuroimaging/aomic-skill/scripts/aomic_qc_summary.py +258 -0
- package/skills/06_fMRI_Neuroimaging/aomic-skill/scripts/extract_aomic_phenotype.py +284 -0
- package/skills/06_fMRI_Neuroimaging/aomic-skill/scripts/reorganize_aomic.py +322 -0
- package/skills/06_fMRI_Neuroimaging/asl-skill/SKILL.md +168 -0
- package/skills/06_fMRI_Neuroimaging/asl-skill/scripts/compute_cbf.py +224 -0
- package/skills/06_fMRI_Neuroimaging/bids-organizer/SKILL.md +241 -0
- package/skills/06_fMRI_Neuroimaging/bold5000-skill/SKILL.md +186 -0
- package/skills/06_fMRI_Neuroimaging/bold5000-skill/scripts/bold5000_qc_summary.py +96 -0
- package/skills/06_fMRI_Neuroimaging/bold5000-skill/scripts/extract_bold5000_stimulus.py +125 -0
- package/skills/06_fMRI_Neuroimaging/bold5000-skill/scripts/reorganize_bold5000.py +102 -0
- package/skills/06_fMRI_Neuroimaging/camcan-skill/SKILL.md +213 -0
- package/skills/06_fMRI_Neuroimaging/camcan-skill/scripts/camcan_qc_summary.py +131 -0
- package/skills/06_fMRI_Neuroimaging/camcan-skill/scripts/extract_camcan_phenotype.py +145 -0
- package/skills/06_fMRI_Neuroimaging/camcan-skill/scripts/validate_camcan.py +141 -0
- package/skills/06_fMRI_Neuroimaging/cobre-skill/SKILL.md +201 -0
- package/skills/06_fMRI_Neuroimaging/cobre-skill/scripts/cobre_qc_summary.py +95 -0
- package/skills/06_fMRI_Neuroimaging/cobre-skill/scripts/extract_cobre_phenotype.py +104 -0
- package/skills/06_fMRI_Neuroimaging/cobre-skill/scripts/reorganize_cobre.py +140 -0
- package/skills/06_fMRI_Neuroimaging/conn-tool/SKILL.md +180 -0
- package/skills/06_fMRI_Neuroimaging/dcm2nii/SKILL.md +189 -0
- package/skills/06_fMRI_Neuroimaging/dmt-har-med-skill/SKILL.md +183 -0
- package/skills/06_fMRI_Neuroimaging/dmt-har-med-skill/scripts/dmt_har_med_qc_summary.py +96 -0
- package/skills/06_fMRI_Neuroimaging/dmt-har-med-skill/scripts/extract_dmt_har_med_phenotype.py +121 -0
- package/skills/06_fMRI_Neuroimaging/dmt-har-med-skill/scripts/reorganize_dmt_har_med.py +125 -0
- package/skills/06_fMRI_Neuroimaging/dwi-skill/SKILL.md +359 -0
- package/skills/06_fMRI_Neuroimaging/fmri-skill/SKILL.md +371 -0
- package/skills/06_fMRI_Neuroimaging/fmriprep-tool/SKILL.md +228 -0
- package/skills/06_fMRI_Neuroimaging/freesurfer-tool/SKILL.md +286 -0
- package/skills/06_fMRI_Neuroimaging/freesurfer-tool/scripts/freesurfer_processor.py +145 -0
- package/skills/06_fMRI_Neuroimaging/fsl-tool/SKILL.md +208 -0
- package/skills/06_fMRI_Neuroimaging/hbn-skill/SKILL.md +271 -0
- package/skills/06_fMRI_Neuroimaging/hbn-skill/scripts/extract_hbn_phenotype.py +107 -0
- package/skills/06_fMRI_Neuroimaging/hbn-skill/scripts/hbn_qc_summary.py +96 -0
- package/skills/06_fMRI_Neuroimaging/hbn-skill/scripts/reorganize_hbn.py +150 -0
- package/skills/06_fMRI_Neuroimaging/hcpa-skill/SKILL.md +210 -0
- package/skills/06_fMRI_Neuroimaging/hcpa-skill/scripts/extract_hcpa_phenotype.py +146 -0
- package/skills/06_fMRI_Neuroimaging/hcpa-skill/scripts/hcpa_qc_summary.py +120 -0
- package/skills/06_fMRI_Neuroimaging/hcpa-skill/scripts/reorganize_hcpa.py +155 -0
- package/skills/06_fMRI_Neuroimaging/hcpd-skill/SKILL.md +210 -0
- package/skills/06_fMRI_Neuroimaging/hcpd-skill/scripts/extract_hcpd_phenotype.py +148 -0
- package/skills/06_fMRI_Neuroimaging/hcpd-skill/scripts/hcpd_qc_summary.py +125 -0
- package/skills/06_fMRI_Neuroimaging/hcpd-skill/scripts/reorganize_hcpd.py +146 -0
- package/skills/06_fMRI_Neuroimaging/hcpep-skill/SKILL.md +215 -0
- package/skills/06_fMRI_Neuroimaging/hcpep-skill/scripts/extract_hcpep_phenotype.py +157 -0
- package/skills/06_fMRI_Neuroimaging/hcpep-skill/scripts/hcpep_qc_summary.py +143 -0
- package/skills/06_fMRI_Neuroimaging/hcpep-skill/scripts/reorganize_hcpep.py +146 -0
- package/skills/06_fMRI_Neuroimaging/hcppipeline-tool/SKILL.md +217 -0
- package/skills/06_fMRI_Neuroimaging/hcpya-skill/SKILL.md +214 -0
- package/skills/06_fMRI_Neuroimaging/hcpya-skill/scripts/extract_hcpya_phenotype.py +190 -0
- package/skills/06_fMRI_Neuroimaging/hcpya-skill/scripts/hcpya_qc_summary.py +152 -0
- package/skills/06_fMRI_Neuroimaging/hcpya-skill/scripts/reorganize_hcpya.py +203 -0
- package/skills/06_fMRI_Neuroimaging/ixi-skill/SKILL.md +198 -0
- package/skills/06_fMRI_Neuroimaging/ixi-skill/scripts/ixi_qc_summary.py +137 -0
- package/skills/06_fMRI_Neuroimaging/ixi-skill/scripts/reorganize_ixi.py +190 -0
- package/skills/06_fMRI_Neuroimaging/mnd-skill/SKILL.md +191 -0
- package/skills/06_fMRI_Neuroimaging/mnd-skill/scripts/extract_mnd_phenotype.py +143 -0
- package/skills/06_fMRI_Neuroimaging/mnd-skill/scripts/mnd_qc_summary.py +120 -0
- package/skills/06_fMRI_Neuroimaging/mnd-skill/scripts/validate_mnd.py +107 -0
- package/skills/06_fMRI_Neuroimaging/mschallenge-skill/SKILL.md +203 -0
- package/skills/06_fMRI_Neuroimaging/mschallenge-skill/scripts/analyze_lesions.py +119 -0
- package/skills/06_fMRI_Neuroimaging/mschallenge-skill/scripts/longitudinal_lesion.py +148 -0
- package/skills/06_fMRI_Neuroimaging/mschallenge-skill/scripts/mschallenge_qc_summary.py +132 -0
- package/skills/06_fMRI_Neuroimaging/mschallenge-skill/scripts/validate_mschallenge.py +116 -0
- package/skills/06_fMRI_Neuroimaging/nibabel-skill/SKILL.md +184 -0
- package/skills/06_fMRI_Neuroimaging/nibabel-skill/scripts/atlas_coordinate_reference.py +61 -0
- package/skills/06_fMRI_Neuroimaging/nibabel-skill/scripts/freesurfer_io_reference.py +34 -0
- package/skills/06_fMRI_Neuroimaging/nibabel-skill/scripts/nifti_inspection_reference.py +35 -0
- package/skills/06_fMRI_Neuroimaging/nifd-skill/SKILL.md +205 -0
- package/skills/06_fMRI_Neuroimaging/nifd-skill/scripts/extract_nifd_phenotype.py +132 -0
- package/skills/06_fMRI_Neuroimaging/nifd-skill/scripts/nifd_qc_summary.py +111 -0
- package/skills/06_fMRI_Neuroimaging/nifd-skill/scripts/validate_nifd.py +111 -0
- package/skills/06_fMRI_Neuroimaging/nii2dcm/SKILL.md +143 -0
- package/skills/06_fMRI_Neuroimaging/nilearn-tool/SKILL.md +266 -0
- package/skills/06_fMRI_Neuroimaging/nilearn-tool/scripts/connectome_reference.py +65 -0
- package/skills/06_fMRI_Neuroimaging/nilearn-tool/scripts/denoise_timeseries_reference.py +58 -0
- package/skills/06_fMRI_Neuroimaging/nilearn-tool/scripts/hierarchical_parcellation_reference.py +53 -0
- package/skills/06_fMRI_Neuroimaging/nilearn-tool/scripts/kmeans_parcellation_reference.py +53 -0
- package/skills/06_fMRI_Neuroimaging/nilearn-tool/scripts/preprocess_bold_reference.py +76 -0
- package/skills/06_fMRI_Neuroimaging/nilearn-tool/scripts/rest_dictlearning_reference.py +56 -0
- package/skills/06_fMRI_Neuroimaging/nilearn-tool/scripts/rest_ica_reference.py +59 -0
- package/skills/06_fMRI_Neuroimaging/nilearn-tool/scripts/second_level_glm_reference.py +58 -0
- package/skills/06_fMRI_Neuroimaging/nilearn-tool/scripts/spacenet_classifier_reference.py +59 -0
- package/skills/06_fMRI_Neuroimaging/nilearn-tool/scripts/svm_classifier_reference.py +60 -0
- package/skills/06_fMRI_Neuroimaging/nilearn-tool/scripts/task_glm_reference.py +63 -0
- package/skills/06_fMRI_Neuroimaging/nilearn-tool/scripts/zalff_summary_reference.py +109 -0
- package/skills/06_fMRI_Neuroimaging/nsd-skill/SKILL.md +210 -0
- package/skills/06_fMRI_Neuroimaging/nsd-skill/scripts/extract_nsd_stimulus.py +171 -0
- package/skills/06_fMRI_Neuroimaging/nsd-skill/scripts/nsd_qc_summary.py +142 -0
- package/skills/06_fMRI_Neuroimaging/nsd-skill/scripts/validate_nsd.py +142 -0
- package/skills/06_fMRI_Neuroimaging/oasis-skill/SKILL.md +205 -0
- package/skills/06_fMRI_Neuroimaging/oasis-skill/scripts/extract_oasis_phenotype.py +126 -0
- package/skills/06_fMRI_Neuroimaging/oasis-skill/scripts/oasis_qc_summary.py +115 -0
- package/skills/06_fMRI_Neuroimaging/oasis-skill/scripts/validate_oasis.py +119 -0
- package/skills/06_fMRI_Neuroimaging/pet-skill/SKILL.md +173 -0
- package/skills/06_fMRI_Neuroimaging/pet-skill/scripts/compute_suvr.py +202 -0
- package/skills/06_fMRI_Neuroimaging/pnc-skill/SKILL.md +206 -0
- package/skills/06_fMRI_Neuroimaging/pnc-skill/scripts/extract_pnc_phenotype.py +136 -0
- package/skills/06_fMRI_Neuroimaging/pnc-skill/scripts/pnc_qc_summary.py +116 -0
- package/skills/06_fMRI_Neuroimaging/pnc-skill/scripts/validate_pnc.py +120 -0
- package/skills/06_fMRI_Neuroimaging/ppmi-skill/SKILL.md +209 -0
- package/skills/06_fMRI_Neuroimaging/ppmi-skill/scripts/extract_ppmi_phenotype.py +138 -0
- package/skills/06_fMRI_Neuroimaging/ppmi-skill/scripts/ppmi_qc_summary.py +111 -0
- package/skills/06_fMRI_Neuroimaging/ppmi-skill/scripts/validate_ppmi.py +117 -0
- package/skills/06_fMRI_Neuroimaging/qsiprep-tool/SKILL.md +320 -0
- package/skills/06_fMRI_Neuroimaging/rest-mneta-mdd-skill/SKILL.md +215 -0
- package/skills/06_fMRI_Neuroimaging/rest-mneta-mdd-skill/scripts/extract_rest_mdd_phenotype.py +132 -0
- package/skills/06_fMRI_Neuroimaging/rest-mneta-mdd-skill/scripts/harmonize_sites.py +152 -0
- package/skills/06_fMRI_Neuroimaging/rest-mneta-mdd-skill/scripts/rest_mdd_qc_summary.py +124 -0
- package/skills/06_fMRI_Neuroimaging/rest-mneta-mdd-skill/scripts/validate_rest_mdd.py +103 -0
- package/skills/06_fMRI_Neuroimaging/smri-skill/SKILL.md +302 -0
- package/skills/06_fMRI_Neuroimaging/tcp-skill/SKILL.md +204 -0
- package/skills/06_fMRI_Neuroimaging/tcp-skill/scripts/extract_tcp_phenotype.py +139 -0
- package/skills/06_fMRI_Neuroimaging/tcp-skill/scripts/tcp_qc_summary.py +111 -0
- package/skills/06_fMRI_Neuroimaging/tcp-skill/scripts/validate_tcp.py +99 -0
- package/skills/06_fMRI_Neuroimaging/ucla-cnp-skill/SKILL.md +217 -0
- package/skills/06_fMRI_Neuroimaging/ucla-cnp-skill/scripts/extract_ucla_cnp_phenotype.py +145 -0
- package/skills/06_fMRI_Neuroimaging/ucla-cnp-skill/scripts/ucla_cnp_qc_summary.py +111 -0
- package/skills/06_fMRI_Neuroimaging/ucla-cnp-skill/scripts/validate_ucla_cnp.py +113 -0
- package/skills/06_fMRI_Neuroimaging/ukb-skill/SKILL.md +310 -0
- package/skills/06_fMRI_Neuroimaging/ukb-skill/scripts/build_ukb_survival.py +210 -0
- package/skills/06_fMRI_Neuroimaging/ukb-skill/scripts/extract_ukb_cases.py +308 -0
- package/skills/06_fMRI_Neuroimaging/ukb-skill/scripts/extract_ukb_phenotype.py +232 -0
- package/skills/06_fMRI_Neuroimaging/ukb-skill/scripts/ukb_qc_summary.py +158 -0
- package/skills/06_fMRI_Neuroimaging/wmh-segmentation/SKILL.md +133 -0
- package/skills/07_Computational_Modeling/detrending/SKILL.md +118 -0
- package/skills/07_Computational_Modeling/dictlearning/SKILL.md +122 -0
- package/skills/07_Computational_Modeling/filtering/SKILL.md +121 -0
- package/skills/07_Computational_Modeling/glm/SKILL.md +153 -0
- package/skills/07_Computational_Modeling/hierarchical/SKILL.md +121 -0
- package/skills/07_Computational_Modeling/ica/SKILL.md +122 -0
- package/skills/07_Computational_Modeling/kmeans/SKILL.md +119 -0
- package/skills/07_Computational_Modeling/run_models/SKILL.md +427 -0
- package/skills/07_Computational_Modeling/spacenet/SKILL.md +122 -0
- package/skills/07_Computational_Modeling/svm/SKILL.md +120 -0
- package/skills/08_Computational_Neuroscience/brain_gnn/SKILL.md +183 -0
- package/skills/08_Computational_Neuroscience/dipy-tool/SKILL.md +239 -0
- package/skills/08_Computational_Neuroscience/dipy-tool/scripts/dti_metrics_reference.py +70 -0
- package/skills/08_Computational_Neuroscience/dipy-tool/scripts/load_and_mask_reference.py +76 -0
- package/skills/08_Computational_Neuroscience/dipy-tool/scripts/roi_stats_reference.py +59 -0
- package/skills/08_Computational_Neuroscience/fm_app/SKILL.md +195 -0
- package/skills/08_Computational_Neuroscience/neurostorm/SKILL.md +151 -0
- package/skills/13_Visualization/brain-visualization/SKILL.md +191 -0
- package/skills/13_Visualization/brain-visualization/scripts/connectome_reference.py +108 -0
- package/skills/13_Visualization/brain-visualization/scripts/freesurfer_ply_reference.py +54 -0
- package/skills/13_Visualization/brain-visualization/scripts/zalff_summary_reference.py +116 -0
- package/skills/13_Visualization/ethoclaw-paper-figure-layout/SKILL.md +78 -0
- package/skills/13_Visualization/ethoclaw-paper-figure-layout/assets/naturecomm_figures.tex +74 -0
- package/skills/13_Visualization/ethoclaw-paper-figure-layout/scripts/layout_results_foldered.py +579 -0
- package/skills/14_Writing/overleaf-skill/SKILL.md +184 -0
- package/skills/14_Writing/overleaf-skill/scripts/install.sh +30 -0
- package/skills/14_Writing/paper-writing/SKILL.md +146 -0
- package/skills/14_Writing/paper-writing/scripts/data_statement_templates.py +164 -0
- package/skills/14_Writing/paper-writing/scripts/figure_templates.py +315 -0
- package/skills/14_Writing/paper-writing/scripts/nature_figure_style.py +214 -0
- package/skills/14_Writing/paper-writing/scripts/section_phrasebank.py +246 -0
- package/skills/16_Animal_Behavior/deeplabcut/SKILL.md +154 -0
- package/skills/16_Animal_Behavior/deeplabcut/references/3d-pose.md +89 -0
- package/skills/16_Animal_Behavior/deeplabcut/references/maDLC.md +123 -0
- package/skills/16_Animal_Behavior/deeplabcut/references/modelzoo.md +98 -0
- package/skills/16_Animal_Behavior/deeplabcut/references/standard-pipeline.md +165 -0
- package/skills/16_Animal_Behavior/deeplabcut/references/utilities.md +146 -0
- package/skills/16_Animal_Behavior/ethoclaw-analysis-report/SKILL.md +274 -0
- package/skills/16_Animal_Behavior/ethoclaw-analysis-report/assets/report_template_en.html +112 -0
- package/skills/16_Animal_Behavior/ethoclaw-analysis-report/assets/report_template_en.md +21 -0
- package/skills/16_Animal_Behavior/ethoclaw-analysis-report/assets/section_templates/cluster-section.md +5 -0
- package/skills/16_Animal_Behavior/ethoclaw-analysis-report/assets/section_templates/heatmap-section.md +5 -0
- package/skills/16_Animal_Behavior/ethoclaw-analysis-report/assets/section_templates/integrated-interpretation.md +3 -0
- package/skills/16_Animal_Behavior/ethoclaw-analysis-report/assets/section_templates/overview.md +3 -0
- package/skills/16_Animal_Behavior/ethoclaw-analysis-report/assets/section_templates/project-summary.md +3 -0
- package/skills/16_Animal_Behavior/ethoclaw-analysis-report/assets/section_templates/radar-section.md +5 -0
- package/skills/16_Animal_Behavior/ethoclaw-analysis-report/assets/section_templates/raw-trajectory.md +3 -0
- package/skills/16_Animal_Behavior/ethoclaw-analysis-report/assets/section_templates/sample-check.md +3 -0
- package/skills/16_Animal_Behavior/ethoclaw-analysis-report/assets/section_templates/single-subject-section.md +3 -0
- package/skills/16_Animal_Behavior/ethoclaw-analysis-report/assets/section_templates/stats-section.md +5 -0
- package/skills/16_Animal_Behavior/ethoclaw-analysis-report/references/experiment-types/epm.md +52 -0
- package/skills/16_Animal_Behavior/ethoclaw-analysis-report/references/experiment-types/fst.md +37 -0
- package/skills/16_Animal_Behavior/ethoclaw-analysis-report/references/experiment-types/nor.md +39 -0
- package/skills/16_Animal_Behavior/ethoclaw-analysis-report/references/experiment-types/oft.md +43 -0
- package/skills/16_Animal_Behavior/ethoclaw-analysis-report/references/experiment-types/tcst.md +45 -0
- package/skills/16_Animal_Behavior/ethoclaw-analysis-report/references/experiment-types/tst.md +36 -0
- package/skills/16_Animal_Behavior/ethoclaw-analysis-report/references/input-types.md +59 -0
- package/skills/16_Animal_Behavior/ethoclaw-analysis-report/references/interpretation-guardrails.md +45 -0
- package/skills/16_Animal_Behavior/ethoclaw-analysis-report/references/metadata-schema.md +57 -0
- package/skills/16_Animal_Behavior/ethoclaw-analysis-report/references/report-sections.md +86 -0
- package/skills/16_Animal_Behavior/ethoclaw-analysis-report/references/section-selection-rules.md +169 -0
- package/skills/16_Animal_Behavior/ethoclaw-analysis-report/scripts/build_report_manifest.py +27 -0
- package/skills/16_Animal_Behavior/ethoclaw-analysis-report/scripts/render_report.py +34 -0
- package/skills/16_Animal_Behavior/ethoclaw-analysis-report/scripts/report_utils.py +1121 -0
- package/skills/16_Animal_Behavior/ethoclaw-animal-grounding/SKILL.md +390 -0
- package/skills/16_Animal_Behavior/ethoclaw-animal-grounding/reference_code.py +98 -0
- package/skills/16_Animal_Behavior/ethoclaw-animal-pose-estimation/SKILL.md +336 -0
- package/skills/16_Animal_Behavior/ethoclaw-kinematic-parameter-generator/README.md +21 -0
- package/skills/16_Animal_Behavior/ethoclaw-kinematic-parameter-generator/SKILL.md +41 -0
- package/skills/16_Animal_Behavior/ethoclaw-kinematic-parameter-generator/batch_kinematic_generator.py +663 -0
- package/skills/16_Animal_Behavior/ethoclaw-kinematic-parameter-generator/config.json +19 -0
- package/skills/16_Animal_Behavior/ethoclaw-kinematic-parameter-generator/generate_kinematic_parameter.py +401 -0
- package/skills/16_Animal_Behavior/ethoclaw-kinematic-parameter-generator/kinematic_generator.py +265 -0
- package/skills/16_Animal_Behavior/ethoclaw-multiparameter-clustermap-generate/SKILL.md +72 -0
- package/skills/16_Animal_Behavior/ethoclaw-multiparameter-clustermap-generate/references/config.example.toml +56 -0
- package/skills/16_Animal_Behavior/ethoclaw-multiparameter-clustermap-generate/scripts/cluster_all_params.py +232 -0
- package/skills/16_Animal_Behavior/ethoclaw-multiparameter-clustermap-generate/scripts/cluster_all_params_from_config.py +236 -0
- package/skills/16_Animal_Behavior/ethoclaw-multiparameter-radar-generate/SKILL.md +68 -0
- package/skills/16_Animal_Behavior/ethoclaw-multiparameter-radar-generate/references/notes.md +5 -0
- package/skills/16_Animal_Behavior/ethoclaw-multiparameter-radar-generate/scripts/plot_h5_radar.py +513 -0
- package/skills/16_Animal_Behavior/ethoclaw-multiparameter-violin-stats-generate/SKILL.md +52 -0
- package/skills/16_Animal_Behavior/ethoclaw-multiparameter-violin-stats-generate/config.toml +81 -0
- package/skills/16_Animal_Behavior/ethoclaw-multiparameter-violin-stats-generate/references/stats-rule.md +18 -0
- package/skills/16_Animal_Behavior/ethoclaw-multiparameter-violin-stats-generate/scripts/h5_inspect.py +79 -0
- package/skills/16_Animal_Behavior/ethoclaw-multiparameter-violin-stats-generate/scripts/h5_violin_batch.py +624 -0
- package/skills/16_Animal_Behavior/ethoclaw-multiparameter-violin-stats-generate/scripts/h5_violin_stats.py +438 -0
- package/skills/16_Animal_Behavior/ethoclaw-trajectory-velocity-heatmap-generate/SKILL.md +280 -0
- package/skills/16_Animal_Behavior/ethoclaw-trajectory-velocity-heatmap-generate/core_scripts/heatmap_trajectory.py +790 -0
- package/skills/16_Animal_Behavior/ethoclaw-trajectory-velocity-heatmap-generate/core_scripts/heatmap_velocity.py +855 -0
- package/skills/16_Animal_Behavior/ethoclaw-trajectory-velocity-heatmap-generate/reference_data/reference_2d.csv +101 -0
- package/skills/16_Animal_Behavior/ethoclaw-trajectory-velocity-heatmap-generate/reference_data/reference_2d.h5 +0 -0
- package/skills/16_Animal_Behavior/ethoclaw-trajectory-velocity-heatmap-generate/reference_data/reference_data_readme.md +126 -0
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---
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name: ethoclaw-normalize-tabular
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description: Check environment, inspect, and normalize local CSV, Excel, and HDF5 files into analysis-ready tabular outputs.
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metadata: { "openclaw": { "emoji": "🧾", "requires": { "bins": ["python3"] } } }
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---
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# Normalize Tabular
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Use this skill when the user wants to inspect, clean, standardize, or convert local `.csv`, `.xlsx`, `.xls`, `.h5`, or `.hdf5` files into a more analysis-friendly tabular format.
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Prefer deterministic local conversion through the bundled script instead of doing large manual transformations in-model.
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## Bundled Tool
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This skill expects the following helper script to exist:
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- `scripts/normalize_data.py`
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The script supports three commands:
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- `check-env`
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- `inspect`
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- `convert`
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Examples:
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```bash
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python3 "{baseDir}/scripts/normalize_data.py" check-env
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python3 "{baseDir}/scripts/normalize_data.py" inspect "/path/to/data.csv"
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python3 "{baseDir}/scripts/normalize_data.py" convert "/path/to/data.csv" --out "/path/to/out"
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python3 "{baseDir}/scripts/normalize_data.py" convert "/path/to/data.xlsx" --sheet "Sheet1" --out "/path/to/out"
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python3 "{baseDir}/scripts/normalize_data.py" convert "/path/to/data.h5" --dataset "pose" --out "/path/to/out"
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```
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## Default Workflow
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Follow this sequence unless the user explicitly wants only an environment check.
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### 1. Check Environment First
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Run:
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```bash
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python3 "{baseDir}/scripts/normalize_data.py" check-env
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```
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If required Python packages are missing, stop before conversion and explain the missing dependencies and install hint.
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### 2. Validate The Input Path
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Confirm the referenced local file exists.
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### 3. Inspect First
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Run:
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```bash
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python3 "{baseDir}/scripts/normalize_data.py" inspect "<input>"
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```
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Summarize the result for the user:
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- detected source format
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- rows and columns for CSV and Excel when available
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- sheet names for Excel
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- dataset names and shapes for HDF5
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### 4. Decide Whether Conversion Is Safe
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Convert immediately only when the source is unambiguous.
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Unambiguous means:
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- CSV: directly convertible
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- Excel: only one sheet, or the user explicitly named the sheet
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- HDF5: only one usable dataset, or the user explicitly named the dataset
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### 5. Convert
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When safe, run:
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```bash
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python3 "{baseDir}/scripts/normalize_data.py" convert "<input>" --out "<out_dir>"
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```
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If needed, include:
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```bash
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--sheet "<sheet_name>"
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--dataset "<dataset_name>"
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```
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### 6. Report The Result
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Always return:
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- environment status
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- what was detected
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- what was converted
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- output file paths
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- notable layout or schema details
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- warnings, fallbacks, or unsupported structures
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## Ambiguity Rules
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Do not guess silently when structure is ambiguous.
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### Excel
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- do not silently pick one
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- list available sheets
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- recommend the most likely rectangular data sheet if there is a clear candidate
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- ask one focused follow-up only if needed
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### HDF5
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- do not silently pick one
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- list available datasets and shapes
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- recommend the most likely tabular or pose dataset if there is a clear candidate
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- ask one focused follow-up only if needed
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## HDF5 Rules
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Never assume all HDF5 files are plain tables.
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Possible structures include:
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- 1D vectors
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- 2D tables
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- structured arrays
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- pose tensors such as `(frame, point, 2)` or `(frame, point, 3)`
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- higher-dimensional non-tabular arrays
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Rules:
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- only convert automatically when the script supports the detected structure safely
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- never silently flatten unsupported higher-dimensional arrays
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- report unsupported structures clearly
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## Output Contract
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Prefer this output package:
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```text
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<out_dir>/
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normalized/
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<name>.parquet
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schemas/
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reports/
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<name>.report.json
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```
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If parquet writing fails, a CSV fallback is acceptable.
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## Dependencies
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Typical Python packages:
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```bash
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python3 -m pip install pandas openpyxl pyarrow h5py
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```
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## OpenClaw Compatibility Notes
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- Keep this skill self-contained
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- Prefer the bundled script over ad hoc in-model table rewriting
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- Keep YAML frontmatter minimal for compatibility
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- If `{baseDir}` is not expanded by your runtime, replace it with the absolute path to this skill folder
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