medsci-skills 4.1.0
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/LICENSE +50 -0
- package/README.md +602 -0
- package/README_FIRST.md +27 -0
- package/bin/medsci-skills.js +159 -0
- package/installers/install-macos.command +19 -0
- package/installers/install-windows.cmd +26 -0
- package/installers/install-windows.ps1 +17 -0
- package/installers/install.py +218 -0
- package/metadata/skills_catalog.json +452 -0
- package/package.json +48 -0
- package/skills/academic-aio/SKILL.md +408 -0
- package/skills/academic-aio/references/case_studies/kjr_mllm_2025.md +82 -0
- package/skills/academic-aio/references/checklists/AIO_GENERAL.md +354 -0
- package/skills/academic-aio/references/journal_summarybox_templates.yaml +126 -0
- package/skills/academic-aio/references/oac_funding_checklist.yaml +129 -0
- package/skills/academic-aio/references/reporting_guideline_mapping.md +39 -0
- package/skills/academic-aio/references/schema_markup_templates/CodeRepository.jsonld +32 -0
- package/skills/academic-aio/references/schema_markup_templates/Dataset.jsonld +36 -0
- package/skills/academic-aio/references/schema_markup_templates/Person.jsonld +30 -0
- package/skills/academic-aio/references/schema_markup_templates/README.md +43 -0
- package/skills/academic-aio/references/schema_markup_templates/ScholarlyArticle.jsonld +55 -0
- package/skills/academic-aio/scripts/batch_metadata_audit.py +169 -0
- package/skills/academic-aio/scripts/validate_schema.py +118 -0
- package/skills/academic-aio/skill.yml +36 -0
- package/skills/academic-aio/templates/aio_audit_checklist.md.j2 +108 -0
- package/skills/add-journal/SKILL.md +482 -0
- package/skills/add-journal/skill.yml +33 -0
- package/skills/analyze-stats/SKILL.md +598 -0
- package/skills/analyze-stats/references/analysis_guides/missing_data.md +109 -0
- package/skills/analyze-stats/references/analysis_guides/nhis_icd10_mapping.md +247 -0
- package/skills/analyze-stats/references/analysis_guides/propensity_score.md +132 -0
- package/skills/analyze-stats/references/analysis_guides/regression.md +115 -0
- package/skills/analyze-stats/references/analysis_guides/repeated_measures.md +160 -0
- package/skills/analyze-stats/references/analysis_guides/survey_weighted.md +366 -0
- package/skills/analyze-stats/references/analysis_guides/test_selection.md +86 -0
- package/skills/analyze-stats/references/style/figure_style.mplstyle +69 -0
- package/skills/analyze-stats/references/style/theme_publication.R +147 -0
- package/skills/analyze-stats/references/table-standards/journal-profiles/ajr.yaml +51 -0
- package/skills/analyze-stats/references/table-standards/journal-profiles/european_radiology.yaml +55 -0
- package/skills/analyze-stats/references/table-standards/journal-profiles/jama.yaml +66 -0
- package/skills/analyze-stats/references/table-standards/journal-profiles/lancet.yaml +57 -0
- package/skills/analyze-stats/references/table-standards/journal-profiles/nejm.yaml +51 -0
- package/skills/analyze-stats/references/table-standards/journal-profiles/radiology.yaml +66 -0
- package/skills/analyze-stats/references/table-standards/table-standards.md +287 -0
- package/skills/analyze-stats/references/table-standards/table-types/diagnostic_accuracy.md +36 -0
- package/skills/analyze-stats/references/table-standards/table-types/meta_analysis.md +58 -0
- package/skills/analyze-stats/references/table-standards/table-types/model_comparison.md +36 -0
- package/skills/analyze-stats/references/table-standards/table-types/regression_results.md +50 -0
- package/skills/analyze-stats/references/table-standards/table-types/table1_demographics.md +51 -0
- package/skills/analyze-stats/references/table-standards/tool-comparison.md +79 -0
- package/skills/analyze-stats/references/templates/agreement_analysis.py +436 -0
- package/skills/analyze-stats/references/templates/dca_plot.R +237 -0
- package/skills/analyze-stats/references/templates/diagnostic_accuracy.py +401 -0
- package/skills/analyze-stats/references/templates/dta_meta_analysis.R +384 -0
- package/skills/analyze-stats/references/templates/forest_plot.py +412 -0
- package/skills/analyze-stats/references/templates/likert_summary.py +356 -0
- package/skills/analyze-stats/references/templates/meta_analysis.R +365 -0
- package/skills/analyze-stats/references/templates/propensity_score.py +478 -0
- package/skills/analyze-stats/references/templates/regression.py +425 -0
- package/skills/analyze-stats/references/templates/repeated_measures.py +434 -0
- package/skills/analyze-stats/references/templates/sample_size.R +382 -0
- package/skills/analyze-stats/references/templates/survey_weighted_analysis.py +411 -0
- package/skills/analyze-stats/references/templates/survival_analysis.py +325 -0
- package/skills/analyze-stats/references/templates/table1_demographics.py +287 -0
- package/skills/analyze-stats/scripts/check_generated_code.py +335 -0
- package/skills/analyze-stats/skill.yml +38 -0
- package/skills/analyze-stats/tests/fixtures/gen_bad.R +16 -0
- package/skills/analyze-stats/tests/fixtures/gen_bad.py +24 -0
- package/skills/analyze-stats/tests/fixtures/gen_clean.py +21 -0
- package/skills/analyze-stats/tests/test_generated_code.sh +59 -0
- package/skills/analyze-stats/tests/test_survival_template.sh +53 -0
- package/skills/author-strategy/SKILL.md +117 -0
- package/skills/author-strategy/analyze_patterns.py +303 -0
- package/skills/author-strategy/fetch_pubmed.py +374 -0
- package/skills/author-strategy/skill.yml +34 -0
- package/skills/batch-cohort/SKILL.md +223 -0
- package/skills/batch-cohort/references/base_template_knhanes.R +210 -0
- package/skills/batch-cohort/references/batch_template_generator.R +222 -0
- package/skills/batch-cohort/references/variable_coding_registry.md +136 -0
- package/skills/batch-cohort/skill.yml +35 -0
- package/skills/calc-sample-size/SKILL.md +491 -0
- package/skills/calc-sample-size/references/formulas.md +655 -0
- package/skills/calc-sample-size/references/observational_cohort.md +49 -0
- package/skills/calc-sample-size/skill.yml +51 -0
- package/skills/check-reporting/SKILL.md +534 -0
- package/skills/check-reporting/references/LICENSES.md +41 -0
- package/skills/check-reporting/references/checklists/AMSTAR2.md +54 -0
- package/skills/check-reporting/references/checklists/ARRIVE_2.md +234 -0
- package/skills/check-reporting/references/checklists/CARE.md +102 -0
- package/skills/check-reporting/references/checklists/CLAIM_2024.md +128 -0
- package/skills/check-reporting/references/checklists/CLEAR.md +113 -0
- package/skills/check-reporting/references/checklists/CONSORT.md +86 -0
- package/skills/check-reporting/references/checklists/COSMIN_RoB.md +136 -0
- package/skills/check-reporting/references/checklists/GRRAS.md +61 -0
- package/skills/check-reporting/references/checklists/MI_CLEAR_LLM.md +167 -0
- package/skills/check-reporting/references/checklists/MOOSE.md +85 -0
- package/skills/check-reporting/references/checklists/NOS.md +88 -0
- package/skills/check-reporting/references/checklists/PRISMA_2020.md +135 -0
- package/skills/check-reporting/references/checklists/PRISMA_DTA.md +36 -0
- package/skills/check-reporting/references/checklists/PRISMA_P.md +56 -0
- package/skills/check-reporting/references/checklists/PROBAST.md +75 -0
- package/skills/check-reporting/references/checklists/PROBAST_AI.md +130 -0
- package/skills/check-reporting/references/checklists/QUADAS2.md +77 -0
- package/skills/check-reporting/references/checklists/QUADAS_C.md +131 -0
- package/skills/check-reporting/references/checklists/ROBINS_E.md +179 -0
- package/skills/check-reporting/references/checklists/ROBINS_I.md +87 -0
- package/skills/check-reporting/references/checklists/ROBIS.md +114 -0
- package/skills/check-reporting/references/checklists/ROB_ME.md +126 -0
- package/skills/check-reporting/references/checklists/RoB2.md +79 -0
- package/skills/check-reporting/references/checklists/RoB_NMA.md +96 -0
- package/skills/check-reporting/references/checklists/SPIRIT.md +112 -0
- package/skills/check-reporting/references/checklists/SQUIRE_2.md +68 -0
- package/skills/check-reporting/references/checklists/STARD.md +129 -0
- package/skills/check-reporting/references/checklists/STARD_AI.md +211 -0
- package/skills/check-reporting/references/checklists/STROBE.md +80 -0
- package/skills/check-reporting/references/checklists/SWiM.md +33 -0
- package/skills/check-reporting/references/checklists/TRIPOD.md +157 -0
- package/skills/check-reporting/references/checklists/TRIPOD_AI.md +140 -0
- package/skills/check-reporting/references/step4c_registration_timing.md +93 -0
- package/skills/check-reporting/references/step4d_prisma_figure_audit.md +137 -0
- package/skills/check-reporting/scripts/check_checklist_exists.py +183 -0
- package/skills/check-reporting/scripts/check_checklist_version.py +168 -0
- package/skills/check-reporting/scripts/check_framework_naming.py +206 -0
- package/skills/check-reporting/scripts/check_prisma_figure.py +209 -0
- package/skills/check-reporting/scripts/prisma_cascade_check.py +274 -0
- package/skills/check-reporting/skill.yml +41 -0
- package/skills/check-reporting/tests/fixtures/framework_bad.md +8 -0
- package/skills/check-reporting/tests/fixtures/framework_clean.md +7 -0
- package/skills/check-reporting/tests/test_checklist_fail_fast.sh +77 -0
- package/skills/check-reporting/tests/test_checklist_version.sh +72 -0
- package/skills/check-reporting/tests/test_framework_naming.sh +45 -0
- package/skills/check-reporting/tests/test_prisma_cascade.sh +104 -0
- package/skills/clean-data/SKILL.md +180 -0
- package/skills/clean-data/references/cleaning_patterns.md +299 -0
- package/skills/clean-data/references/profiling_template.py +304 -0
- package/skills/clean-data/scripts/check_structural_zero.py +174 -0
- package/skills/clean-data/skill.yml +35 -0
- package/skills/clean-data/tests/fixtures/smoking.csv +8 -0
- package/skills/clean-data/tests/test_structural_zero.sh +49 -0
- package/skills/cross-national/SKILL.md +264 -0
- package/skills/cross-national/skill.yml +37 -0
- package/skills/define-variables/SKILL.md +146 -0
- package/skills/define-variables/references/common_definitions.md +190 -0
- package/skills/define-variables/skill.yml +34 -0
- package/skills/define-variables/templates/variable_operationalization.md +64 -0
- package/skills/deidentify/SKILL.md +203 -0
- package/skills/deidentify/deidentify.py +1224 -0
- package/skills/deidentify/locales/_template.json +45 -0
- package/skills/deidentify/locales/au.json +43 -0
- package/skills/deidentify/locales/ca.json +44 -0
- package/skills/deidentify/locales/cn.json +47 -0
- package/skills/deidentify/locales/de.json +48 -0
- package/skills/deidentify/locales/fr.json +48 -0
- package/skills/deidentify/locales/in.json +48 -0
- package/skills/deidentify/locales/jp.json +48 -0
- package/skills/deidentify/locales/kr.json +48 -0
- package/skills/deidentify/locales/uk.json +45 -0
- package/skills/deidentify/locales/us.json +43 -0
- package/skills/deidentify/references/date_shift_guide.md +82 -0
- package/skills/deidentify/references/hipaa_18_identifiers.md +48 -0
- package/skills/deidentify/references/korean_phi_patterns.md +135 -0
- package/skills/deidentify/skill.yml +43 -0
- package/skills/deidentify/tests/README.md +26 -0
- package/skills/deidentify/tests/test_clean.csv +16 -0
- package/skills/deidentify/tests/test_edge_cases.csv +11 -0
- package/skills/deidentify/tests/test_phi_korean.csv +11 -0
- package/skills/design-ai-benchmarking/SKILL.md +214 -0
- package/skills/design-ai-benchmarking/references/benchmark_export_schema.json +69 -0
- package/skills/design-ai-benchmarking/references/elicitation_rubric_template.md +37 -0
- package/skills/design-ai-benchmarking/skill.yml +38 -0
- package/skills/design-study/SKILL.md +298 -0
- package/skills/design-study/skill.yml +33 -0
- package/skills/fill-icmje-coi/SKILL.md +216 -0
- package/skills/fill-icmje-coi/scripts/fill_icmje_coi.py +140 -0
- package/skills/fill-icmje-coi/skill.yml +35 -0
- package/skills/fill-icmje-coi/templates/icmje_coi_seed_synthetic.docx +0 -0
- package/skills/fill-protocol/SKILL.md +248 -0
- package/skills/fill-protocol/examples/example_irb_template.yaml +53 -0
- package/skills/fill-protocol/references/best_practices.md +121 -0
- package/skills/fill-protocol/scripts/doc_to_docx.py +111 -0
- package/skills/fill-protocol/scripts/fill_form.py +611 -0
- package/skills/fill-protocol/scripts/inspect_template.py +61 -0
- package/skills/fill-protocol/setup.sh +162 -0
- package/skills/fill-protocol/skill.yml +37 -0
- package/skills/find-cohort-gap/SKILL.md +309 -0
- package/skills/find-cohort-gap/references/cohort_profile_template.md +93 -0
- package/skills/find-cohort-gap/references/onepager_template.md +84 -0
- package/skills/find-cohort-gap/references/pattern_scoring_rubric.md +169 -0
- package/skills/find-cohort-gap/references/saturation_query_templates.md +143 -0
- package/skills/find-cohort-gap/skill.yml +35 -0
- package/skills/find-journal/POLICY.md +87 -0
- package/skills/find-journal/SKILL.md +340 -0
- package/skills/find-journal/references/journal_profiles/AJNR.md +29 -0
- package/skills/find-journal/references/journal_profiles/AJR.md +30 -0
- package/skills/find-journal/references/journal_profiles/Abdominal_Radiology.md +30 -0
- package/skills/find-journal/references/journal_profiles/Academic_Radiology.md +30 -0
- package/skills/find-journal/references/journal_profiles/Annals_of_Internal_Medicine.md +33 -0
- package/skills/find-journal/references/journal_profiles/Artificial_Intelligence_in_Medicine.md +28 -0
- package/skills/find-journal/references/journal_profiles/BMC_Medicine.md +31 -0
- package/skills/find-journal/references/journal_profiles/British_Journal_of_Radiology.md +39 -0
- package/skills/find-journal/references/journal_profiles/CVIR.md +30 -0
- package/skills/find-journal/references/journal_profiles/Chest.md +39 -0
- package/skills/find-journal/references/journal_profiles/Clinical_Radiology.md +30 -0
- package/skills/find-journal/references/journal_profiles/Clinical_and_Molecular_Hepatology.md +32 -0
- package/skills/find-journal/references/journal_profiles/Diabetes_Metabolism_Journal.md +36 -0
- package/skills/find-journal/references/journal_profiles/Diagnostic_and_Interventional_Radiology.md +32 -0
- package/skills/find-journal/references/journal_profiles/Endocrinology_and_Metabolism.md +37 -0
- package/skills/find-journal/references/journal_profiles/European_Journal_of_Preventive_Cardiology.md +39 -0
- package/skills/find-journal/references/journal_profiles/European_Radiology.md +29 -0
- package/skills/find-journal/references/journal_profiles/Hepatology_Communications.md +40 -0
- package/skills/find-journal/references/journal_profiles/Hepatology_International.md +37 -0
- package/skills/find-journal/references/journal_profiles/IEEE_JBHI.md +28 -0
- package/skills/find-journal/references/journal_profiles/IEEE_TMI.md +28 -0
- package/skills/find-journal/references/journal_profiles/INSI.md +29 -0
- package/skills/find-journal/references/journal_profiles/Investigative_Radiology.md +25 -0
- package/skills/find-journal/references/journal_profiles/JACC_Advances.md +41 -0
- package/skills/find-journal/references/journal_profiles/JACC_Asia.md +30 -0
- package/skills/find-journal/references/journal_profiles/JACR.md +28 -0
- package/skills/find-journal/references/journal_profiles/JAMA.md +40 -0
- package/skills/find-journal/references/journal_profiles/JAMA_Network_Open.md +30 -0
- package/skills/find-journal/references/journal_profiles/JCSM.md +39 -0
- package/skills/find-journal/references/journal_profiles/JKMS.md +32 -0
- package/skills/find-journal/references/journal_profiles/JMIR.md +29 -0
- package/skills/find-journal/references/journal_profiles/JMIR_Medical_Education.md +29 -0
- package/skills/find-journal/references/journal_profiles/JNIS.md +35 -0
- package/skills/find-journal/references/journal_profiles/JVIR.md +31 -0
- package/skills/find-journal/references/journal_profiles/Journal_of_Biomedical_Informatics.md +29 -0
- package/skills/find-journal/references/journal_profiles/Journal_of_Clinical_Endocrinology_and_Metabolism.md +40 -0
- package/skills/find-journal/references/journal_profiles/Journal_of_Magnetic_Resonance_Imaging.md +30 -0
- package/skills/find-journal/references/journal_profiles/Journal_of_Nuclear_Medicine.md +31 -0
- package/skills/find-journal/references/journal_profiles/Journal_of_Stroke.md +32 -0
- package/skills/find-journal/references/journal_profiles/KJR.md +38 -0
- package/skills/find-journal/references/journal_profiles/Korean_Circulation_Journal.md +38 -0
- package/skills/find-journal/references/journal_profiles/Korean_Journal_of_Internal_Medicine.md +36 -0
- package/skills/find-journal/references/journal_profiles/Lancet_Diabetes_and_Endocrinology.md +40 -0
- package/skills/find-journal/references/journal_profiles/Lancet_Gastroenterology_and_Hepatology.md +49 -0
- package/skills/find-journal/references/journal_profiles/Lancet_Infectious_Diseases.md +38 -0
- package/skills/find-journal/references/journal_profiles/Lancet_Neurology.md +39 -0
- package/skills/find-journal/references/journal_profiles/Lancet_Oncology.md +40 -0
- package/skills/find-journal/references/journal_profiles/Lancet_Psychiatry.md +38 -0
- package/skills/find-journal/references/journal_profiles/Lancet_Public_Health.md +30 -0
- package/skills/find-journal/references/journal_profiles/Lancet_Respiratory_Medicine.md +39 -0
- package/skills/find-journal/references/journal_profiles/Liver_International.md +33 -0
- package/skills/find-journal/references/journal_profiles/Medical_Image_Analysis.md +28 -0
- package/skills/find-journal/references/journal_profiles/NEJM.md +33 -0
- package/skills/find-journal/references/journal_profiles/Nature_Machine_Intelligence.md +31 -0
- package/skills/find-journal/references/journal_profiles/Nature_Medicine.md +39 -0
- package/skills/find-journal/references/journal_profiles/Neuroradiology.md +31 -0
- package/skills/find-journal/references/journal_profiles/Nutrition_Metabolism_and_Cardiovascular_Diseases.md +39 -0
- package/skills/find-journal/references/journal_profiles/PLOS_Medicine.md +32 -0
- package/skills/find-journal/references/journal_profiles/RYAI.md +28 -0
- package/skills/find-journal/references/journal_profiles/Radiology.md +29 -0
- package/skills/find-journal/references/journal_profiles/Skeletal_Radiology.md +31 -0
- package/skills/find-journal/references/journal_profiles/Stroke.md +37 -0
- package/skills/find-journal/references/journal_profiles/The_BMJ.md +31 -0
- package/skills/find-journal/references/journal_profiles/The_Lancet.md +31 -0
- package/skills/find-journal/references/journal_profiles/The_Lancet_Digital_Health.md +29 -0
- package/skills/find-journal/references/journal_profiles/World_Journal_of_Hepatology.md +53 -0
- package/skills/find-journal/references/journal_profiles/npj_Digital_Medicine.md +29 -0
- package/skills/find-journal/skill.yml +34 -0
- package/skills/fulltext-retrieval/SKILL.md +174 -0
- package/skills/fulltext-retrieval/fetch_oa.py +433 -0
- package/skills/fulltext-retrieval/pdf_to_md.py +160 -0
- package/skills/fulltext-retrieval/skill.yml +41 -0
- package/skills/generate-codebook/SKILL.md +155 -0
- package/skills/generate-codebook/references/codebook_schema.md +76 -0
- package/skills/generate-codebook/scripts/generate_codebook.py +278 -0
- package/skills/generate-codebook/skill.yml +35 -0
- package/skills/generate-codebook/tests/test_generate_codebook.sh +76 -0
- package/skills/grant-builder/SKILL.md +251 -0
- package/skills/grant-builder/skill.yml +34 -0
- package/skills/humanize/SKILL.md +251 -0
- package/skills/humanize/references/ai_patterns.md +571 -0
- package/skills/humanize/skill.yml +33 -0
- package/skills/intake-project/SKILL.md +264 -0
- package/skills/intake-project/skill.yml +34 -0
- package/skills/lit-sync/SKILL.md +448 -0
- package/skills/lit-sync/references/locale/ko/note_templates.md +110 -0
- package/skills/lit-sync/skill.yml +52 -0
- package/skills/lit-sync/tests/test_poll_logic.sh +92 -0
- package/skills/ma-scout/SKILL.md +640 -0
- package/skills/ma-scout/references/project_readme_template.md +95 -0
- package/skills/ma-scout/references/project_readme_template_ko.md +82 -0
- package/skills/ma-scout/skill.yml +33 -0
- package/skills/make-figures/SKILL.md +957 -0
- package/skills/make-figures/references/critic_rubrics/data_plot.md +166 -0
- package/skills/make-figures/references/critic_rubrics/flow_diagram.md +169 -0
- package/skills/make-figures/references/design_principles.md +181 -0
- package/skills/make-figures/references/exemplar_diagrams/README.md +65 -0
- package/skills/make-figures/references/exemplar_diagrams/consort/README.md +15 -0
- package/skills/make-figures/references/exemplar_diagrams/consort/template_input.yaml +37 -0
- package/skills/make-figures/references/exemplar_diagrams/consort/template_output.pdf +0 -0
- package/skills/make-figures/references/exemplar_diagrams/consort/template_output.png +0 -0
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- package/skills/self-review/tests/test_confounding_completeness.sh +66 -0
- package/skills/self-review/tests/test_panel_diversity.sh +55 -0
- package/skills/self-review/tests/test_panel_mode.sh +69 -0
- package/skills/self-review/tests/test_reference_adequacy.sh +68 -0
- package/skills/self-review/tests/test_reviewer_team_consistency.sh +138 -0
- package/skills/self-review/tests/test_scope_coherence.sh +46 -0
- package/skills/setup-medsci/SKILL.md +110 -0
- package/skills/setup-medsci/references/setup-checklist.md +51 -0
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- package/skills/sync-submission/SKILL.md +382 -0
- package/skills/sync-submission/scripts/author_registry_example.yaml +36 -0
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- package/skills/sync-submission/scripts/check_asset_anonymization.py +300 -0
- package/skills/sync-submission/scripts/check_cross_artifact_stale.py +211 -0
- package/skills/sync-submission/scripts/cover_letter_drift_check.py +451 -0
- package/skills/sync-submission/scripts/cross_document_n_check.py +486 -0
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- package/skills/sync-submission/scripts/preflight_gate.py +458 -0
- package/skills/sync-submission/scripts/scope_drift_check.py +362 -0
- package/skills/sync-submission/scripts/sync_submission.py +169 -0
- package/skills/sync-submission/skill.yml +43 -0
- package/skills/sync-submission/tests/fixtures/copy_ok.md +5 -0
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- package/skills/sync-submission/tests/fixtures/ssot.md +5 -0
- package/skills/sync-submission/tests/test_asset_anonymization.sh +99 -0
- package/skills/sync-submission/tests/test_copy_divergence.sh +44 -0
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- package/skills/verify-refs/SKILL.md +177 -0
- package/skills/verify-refs/references/manual_checkpoint_guide.md +100 -0
- package/skills/verify-refs/scripts/verify_cli.sh +62 -0
- package/skills/verify-refs/scripts/verify_refs.py +782 -0
- package/skills/verify-refs/skill.yml +44 -0
- package/skills/verify-refs/tests/fixtures/pagination_placeholder.bib +17 -0
- package/skills/verify-refs/tests/test_pagination_placeholder.sh +42 -0
- package/skills/version-dataset/SKILL.md +143 -0
- package/skills/version-dataset/references/manifest_schema.md +72 -0
- package/skills/version-dataset/scripts/version_dataset.py +242 -0
- package/skills/version-dataset/skill.yml +35 -0
- package/skills/version-dataset/tests/test_version_dataset.sh +52 -0
- package/skills/write-paper/SKILL.md +1148 -0
- package/skills/write-paper/references/exemplar_methods/README.md +38 -0
- package/skills/write-paper/references/exemplar_methods/ai_validation_tripod_claim.md +47 -0
- package/skills/write-paper/references/exemplar_methods/diagnostic_accuracy_stard.md +50 -0
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#!/usr/bin/env python3
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"""Reference template library for editable academic PPTX generation.
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Design tokens (NAVY/TEAL/ORANGE/GRAY, Apple SD Gothic Neo) and 16:9 fixed
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coordinate zones are defaults — adapt to journal/institution conventions
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as needed. NO markdown parsing, NO `cur_top` cumulative tracking (both
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produce drift artifacts).
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Each slide is defined as structured data → rendered by a type-specific
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template function (T_lead / T_text / T_table / T_image_right / T_two_col
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/ T_quote_slide / T_highlight_slide / T_metaphor_body / T_two_col_with_box
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/ T_table_two_col).
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`build_demo_slides()` at the bottom demonstrates every template with
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generic academic placeholder content; copy and replace with your own
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content function for a real deck.
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Speaker-note injection: `parse_notes()` reads a markdown script with
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`## Slide N:` headers and maps sections back to slide indices. For an
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existing deck where you only want to add notes (no design regeneration),
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use the sibling `inject_speaker_notes.py` instead.
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Mac PowerPoint compatibility — verify before delivery:
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1. TIFF images: `find ppt/media -iname '*.tif*'` → convert to PNG
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2. `<a:sp3d>` 3D bevels in rPr render as red outlines on Mac → strip
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match actual slide count
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See `references/workflow-checklist.md` and the user-level rule
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`~/.claude/rules/pptx-mac-compatibility.md` for the full checklist.
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"""
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import os
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import re
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from pptx import Presentation
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from pptx.util import Inches, Pt, Emu
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from pptx.dml.color import RGBColor
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from pptx.enum.text import PP_ALIGN, MSO_ANCHOR, MSO_AUTO_SIZE
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from pptx.enum.shapes import MSO_SHAPE
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from pptx.oxml.ns import qn
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# ── Design tokens ──────────────────────────────────────────────
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NAVY = RGBColor(0x1B, 0x2A, 0x4A)
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TEAL = RGBColor(0x00, 0x72, 0xB2)
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ORANGE = RGBColor(0xD5, 0x5E, 0x00)
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GRAY = RGBColor(0x33, 0x33, 0x33)
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WHITE = RGBColor(0xFF, 0xFF, 0xFF)
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LGRAY = RGBColor(0x99, 0x99, 0x99)
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BG_BLUE = RGBColor(0xF0, 0xF7, 0xFF)
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BG_YELLOW = RGBColor(0xFF, 0xF8, 0xE1)
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SUB_BLUE = RGBColor(0x7B, 0xB8, 0xE0)
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FONT = 'Apple SD Gothic Neo'
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SW = Inches(13.333) # slide width
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SH = Inches(7.5) # slide height
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MR = Inches(0.8) # margin right
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SUB_Y = TITLE_Y + TITLE_H
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SUB_H = Inches(0.5)
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def _bg(slide, color):
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p = tf.paragraphs[0]
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return tb
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parts = re.split(r'(\*\*.*?\*\*)', txt)
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def _multiline(slide, x, y, w, h, lines, sz=20, color=GRAY, auto_fit=True):
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if first:
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p = tf.add_paragraph()
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p.space_before = Pt(6)
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is_bullet = line.startswith('- ') or line.startswith('✓ ')
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def _title_block(slide, title, subtitle=None, width=None):
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w = width or CW
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bar = slide.shapes.add_shape(MSO_SHAPE.RECTANGLE,
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ML, TITLE_Y + Inches(0.7), w, Inches(0.05))
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bar.fill.solid()
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if subtitle:
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nr = len(rows) + 1
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return
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shape = slide.shapes.add_table(nr, nc, x, y, w, row_h * nr)
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tbl = shape.table
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163
|
+
|
|
164
|
+
for i, row in enumerate(rows):
|
|
165
|
+
for j, val in enumerate(row):
|
|
166
|
+
if j >= nc:
|
|
167
|
+
break
|
|
168
|
+
c = tbl.cell(i + 1, j)
|
|
169
|
+
c.text = val.strip('*')
|
|
170
|
+
bg = RGBColor(0xF5, 0xF5, 0xF5) if i % 2 == 0 else WHITE
|
|
171
|
+
bld = val.strip().startswith('**')
|
|
172
|
+
_cell_style(c, 14, GRAY, bld, bg)
|
|
173
|
+
|
|
174
|
+
def _cell_style(cell, sz, color, bold, bg):
|
|
175
|
+
for p in cell.text_frame.paragraphs:
|
|
176
|
+
for r in p.runs:
|
|
177
|
+
r.font.size = Pt(sz)
|
|
178
|
+
r.font.color.rgb = color
|
|
179
|
+
r.font.bold = bold
|
|
180
|
+
r.font.name = FONT
|
|
181
|
+
cell.vertical_anchor = MSO_ANCHOR.MIDDLE
|
|
182
|
+
tcPr = cell._tc.get_or_add_tcPr()
|
|
183
|
+
sf = tcPr.makeelement(qn('a:solidFill'), {})
|
|
184
|
+
sf.append(sf.makeelement(qn('a:srgbClr'), {'val': str(bg)}))
|
|
185
|
+
tcPr.append(sf)
|
|
186
|
+
|
|
187
|
+
def _quote(slide, txt, x, y, w, h, sz=20):
|
|
188
|
+
"""Blockquote with teal left bar + blue background."""
|
|
189
|
+
# Bar
|
|
190
|
+
bar = slide.shapes.add_shape(MSO_SHAPE.RECTANGLE, x, y, Inches(0.08), h)
|
|
191
|
+
bar.fill.solid(); bar.fill.fore_color.rgb = TEAL
|
|
192
|
+
bar.line.fill.background()
|
|
193
|
+
# Background
|
|
194
|
+
bg = slide.shapes.add_shape(MSO_SHAPE.RECTANGLE,
|
|
195
|
+
x + Inches(0.08), y, w - Inches(0.08), h)
|
|
196
|
+
bg.fill.solid(); bg.fill.fore_color.rgb = BG_BLUE
|
|
197
|
+
bg.line.fill.background()
|
|
198
|
+
# Text
|
|
199
|
+
_text(slide, x + Inches(0.3), y + Inches(0.1),
|
|
200
|
+
w - Inches(0.5), h - Inches(0.2), txt, sz=sz, auto_fit=True)
|
|
201
|
+
|
|
202
|
+
def _highlight(slide, lines, x, y, w, h):
|
|
203
|
+
"""Yellow highlight box with orange border."""
|
|
204
|
+
box = slide.shapes.add_shape(MSO_SHAPE.ROUNDED_RECTANGLE, x, y, w, h)
|
|
205
|
+
box.fill.solid(); box.fill.fore_color.rgb = BG_YELLOW
|
|
206
|
+
box.line.color.rgb = ORANGE; box.line.width = Pt(2)
|
|
207
|
+
_multiline(slide, x + Inches(0.3), y + Inches(0.2),
|
|
208
|
+
w - Inches(0.6), h - Inches(0.4), lines, sz=18, auto_fit=True)
|
|
209
|
+
|
|
210
|
+
def _metaphor(slide, lines, x, y, w, h):
|
|
211
|
+
"""Light-blue metaphor box with teal left bar."""
|
|
212
|
+
bar = slide.shapes.add_shape(MSO_SHAPE.RECTANGLE, x, y, Inches(0.08), h)
|
|
213
|
+
bar.fill.solid(); bar.fill.fore_color.rgb = TEAL
|
|
214
|
+
bar.line.fill.background()
|
|
215
|
+
bg = slide.shapes.add_shape(MSO_SHAPE.RECTANGLE,
|
|
216
|
+
x + Inches(0.08), y, w - Inches(0.08), h)
|
|
217
|
+
bg.fill.solid(); bg.fill.fore_color.rgb = BG_BLUE
|
|
218
|
+
bg.line.fill.background()
|
|
219
|
+
_multiline(slide, x + Inches(0.3), y + Inches(0.15),
|
|
220
|
+
w - Inches(0.6), h - Inches(0.3), lines, sz=17, auto_fit=True)
|
|
221
|
+
|
|
222
|
+
def _image(slide, path, x, y, w, h):
|
|
223
|
+
"""Add image preserving aspect ratio, centered in box."""
|
|
224
|
+
if not os.path.exists(path):
|
|
225
|
+
print(f' WARNING: {path} not found')
|
|
226
|
+
return
|
|
227
|
+
from PIL import Image as PILImage
|
|
228
|
+
with PILImage.open(path) as img:
|
|
229
|
+
iw, ih = img.size
|
|
230
|
+
aspect = iw / ih
|
|
231
|
+
tw, th = int(w), int(h)
|
|
232
|
+
if tw / th > aspect:
|
|
233
|
+
fw, fh = int(th * aspect), th
|
|
234
|
+
else:
|
|
235
|
+
fw, fh = tw, int(tw / aspect)
|
|
236
|
+
ax = x + (tw - fw) // 2
|
|
237
|
+
ay = y + (th - fh) // 2
|
|
238
|
+
slide.shapes.add_picture(path, ax, ay, fw, fh)
|
|
239
|
+
|
|
240
|
+
def _slidenum(slide, n, total):
|
|
241
|
+
_text(slide, SW - Inches(1.2), SH - Inches(0.45), Inches(1.0), Inches(0.3),
|
|
242
|
+
f'{n} / {total}', sz=10, color=LGRAY, align=PP_ALIGN.RIGHT)
|
|
243
|
+
|
|
244
|
+
|
|
245
|
+
# ── Slide type templates ───────────────────────────────────────
|
|
246
|
+
def T_lead(prs, title, subtitle='', extra=''):
|
|
247
|
+
"""Section divider: navy bg, centered white text."""
|
|
248
|
+
s = prs.slides.add_slide(prs.slide_layouts[6])
|
|
249
|
+
_bg(s, NAVY)
|
|
250
|
+
_text(s, ML, Inches(2.2), CW, Inches(1.2), title,
|
|
251
|
+
sz=40, color=WHITE, bold=True, align=PP_ALIGN.CENTER)
|
|
252
|
+
if subtitle:
|
|
253
|
+
_text(s, ML, Inches(3.6), CW, Inches(0.8), subtitle,
|
|
254
|
+
sz=24, color=SUB_BLUE, align=PP_ALIGN.CENTER)
|
|
255
|
+
if extra:
|
|
256
|
+
_text(s, ML, Inches(4.6), CW, Inches(1.0), extra,
|
|
257
|
+
sz=18, color=LGRAY, align=PP_ALIGN.CENTER)
|
|
258
|
+
return s
|
|
259
|
+
|
|
260
|
+
def T_text(prs, title, body_lines, subtitle=None):
|
|
261
|
+
"""Title + bullet/text body. Most common type."""
|
|
262
|
+
s = prs.slides.add_slide(prs.slide_layouts[6])
|
|
263
|
+
_title_block(s, title, subtitle)
|
|
264
|
+
_multiline(s, ML, BODY_Y, CW, BODY_H, body_lines, sz=20)
|
|
265
|
+
return s
|
|
266
|
+
|
|
267
|
+
def T_table(prs, title, headers, rows, subtitle=None, body_before=None):
|
|
268
|
+
"""Title + optional body text + table."""
|
|
269
|
+
s = prs.slides.add_slide(prs.slide_layouts[6])
|
|
270
|
+
_title_block(s, title, subtitle)
|
|
271
|
+
tbl_y = BODY_Y
|
|
272
|
+
if body_before:
|
|
273
|
+
_multiline(s, ML, BODY_Y, CW, Inches(1.5), body_before, sz=20)
|
|
274
|
+
tbl_y = BODY_Y + Inches(1.6)
|
|
275
|
+
_table(s, headers, rows, ML, tbl_y, CW)
|
|
276
|
+
return s
|
|
277
|
+
|
|
278
|
+
def T_image_right(prs, title, body_lines, img_path, img_pct=30, subtitle=None):
|
|
279
|
+
"""Title + body on left, image on right."""
|
|
280
|
+
s = prs.slides.add_slide(prs.slide_layouts[6])
|
|
281
|
+
frac = img_pct / 100
|
|
282
|
+
tw = int(SW * (1 - frac) - ML - Inches(0.3))
|
|
283
|
+
iw = int(SW * frac)
|
|
284
|
+
ix = SW - iw
|
|
285
|
+
|
|
286
|
+
_title_block(s, title, subtitle, width=tw)
|
|
287
|
+
_multiline(s, ML, BODY_Y, tw, BODY_H, body_lines, sz=20)
|
|
288
|
+
_image(s, img_path, ix, Inches(0.2), iw, SH - Inches(0.4))
|
|
289
|
+
return s
|
|
290
|
+
|
|
291
|
+
def T_quote_slide(prs, title, quotes, body_after=None, img_path=None,
|
|
292
|
+
img_pct=30, subtitle=None):
|
|
293
|
+
"""Title + blockquote(s). Optionally with image."""
|
|
294
|
+
s = prs.slides.add_slide(prs.slide_layouts[6])
|
|
295
|
+
|
|
296
|
+
if img_path:
|
|
297
|
+
frac = img_pct / 100
|
|
298
|
+
tw = int(SW * (1 - frac) - ML - Inches(0.3))
|
|
299
|
+
iw = int(SW * frac)
|
|
300
|
+
ix = SW - iw
|
|
301
|
+
_title_block(s, title, subtitle, width=tw)
|
|
302
|
+
_image(s, img_path, ix, Inches(0.2), iw, SH - Inches(0.4))
|
|
303
|
+
else:
|
|
304
|
+
tw = CW
|
|
305
|
+
_title_block(s, title, subtitle)
|
|
306
|
+
|
|
307
|
+
# Distribute quotes evenly in body area
|
|
308
|
+
n = len(quotes)
|
|
309
|
+
gap = Inches(0.15)
|
|
310
|
+
q_h = int((BODY_H - gap * (n - 1)) / n) if n else BODY_H
|
|
311
|
+
|
|
312
|
+
for i, q in enumerate(quotes):
|
|
313
|
+
qy = BODY_Y + (q_h + gap) * i
|
|
314
|
+
_quote(s, q, ML, qy, tw, q_h, sz=18)
|
|
315
|
+
|
|
316
|
+
if body_after:
|
|
317
|
+
_text(s, ML, SH - Inches(1.2), tw, Inches(0.6),
|
|
318
|
+
body_after, sz=16, color=GRAY)
|
|
319
|
+
return s
|
|
320
|
+
|
|
321
|
+
def T_two_col(prs, title, left_lines, right_lines, subtitle=None):
|
|
322
|
+
"""Two-column layout."""
|
|
323
|
+
s = prs.slides.add_slide(prs.slide_layouts[6])
|
|
324
|
+
_title_block(s, title, subtitle)
|
|
325
|
+
cw = int((CW - Inches(0.5)) / 2)
|
|
326
|
+
gap = Inches(0.5)
|
|
327
|
+
_multiline(s, ML, BODY_Y, cw, BODY_H, left_lines, sz=18)
|
|
328
|
+
_multiline(s, ML + cw + gap, BODY_Y, cw, BODY_H, right_lines, sz=18)
|
|
329
|
+
return s
|
|
330
|
+
|
|
331
|
+
def T_two_col_with_box(prs, title, left_lines, right_lines, subtitle=None,
|
|
332
|
+
metaphor_col=None, metaphor_lines=None):
|
|
333
|
+
"""Two-column with metaphor/highlight box in one column."""
|
|
334
|
+
s = prs.slides.add_slide(prs.slide_layouts[6])
|
|
335
|
+
_title_block(s, title, subtitle)
|
|
336
|
+
cw = int((CW - Inches(0.5)) / 2)
|
|
337
|
+
gap = Inches(0.5)
|
|
338
|
+
|
|
339
|
+
# Left column
|
|
340
|
+
if metaphor_col == 'left' and metaphor_lines:
|
|
341
|
+
_metaphor(s, metaphor_lines, ML, BODY_Y, cw, Inches(2.5))
|
|
342
|
+
_multiline(s, ML, BODY_Y + Inches(2.7), cw, BODY_H - Inches(2.7),
|
|
343
|
+
left_lines, sz=18)
|
|
344
|
+
else:
|
|
345
|
+
_multiline(s, ML, BODY_Y, cw, BODY_H, left_lines, sz=18)
|
|
346
|
+
|
|
347
|
+
# Right column
|
|
348
|
+
rx = ML + cw + gap
|
|
349
|
+
if metaphor_col == 'right' and metaphor_lines:
|
|
350
|
+
_metaphor(s, metaphor_lines, rx, BODY_Y, cw, Inches(2.5))
|
|
351
|
+
_multiline(s, rx, BODY_Y + Inches(2.7), cw, BODY_H - Inches(2.7),
|
|
352
|
+
right_lines, sz=18)
|
|
353
|
+
else:
|
|
354
|
+
_multiline(s, rx, BODY_Y, cw, BODY_H, right_lines, sz=18)
|
|
355
|
+
return s
|
|
356
|
+
|
|
357
|
+
def T_highlight_slide(prs, title, highlight_lines, subtitle=None,
|
|
358
|
+
body_before=None):
|
|
359
|
+
"""Slide with prominent highlight box."""
|
|
360
|
+
s = prs.slides.add_slide(prs.slide_layouts[6])
|
|
361
|
+
_title_block(s, title, subtitle)
|
|
362
|
+
hy = BODY_Y
|
|
363
|
+
if body_before:
|
|
364
|
+
_multiline(s, ML, BODY_Y, CW, Inches(1.0), body_before, sz=20)
|
|
365
|
+
hy = BODY_Y + Inches(1.2)
|
|
366
|
+
_highlight(s, highlight_lines, ML, hy, CW, SH - hy - Inches(0.5))
|
|
367
|
+
return s
|
|
368
|
+
|
|
369
|
+
def T_metaphor_body(prs, title, body_lines, metaphor_lines, subtitle=None):
|
|
370
|
+
"""Body text + metaphor box below."""
|
|
371
|
+
s = prs.slides.add_slide(prs.slide_layouts[6])
|
|
372
|
+
_title_block(s, title, subtitle)
|
|
373
|
+
mid = BODY_Y + BODY_H * 0.55
|
|
374
|
+
_multiline(s, ML, BODY_Y, CW, mid - BODY_Y - Inches(0.1),
|
|
375
|
+
body_lines, sz=20)
|
|
376
|
+
_metaphor(s, metaphor_lines, ML, mid, CW, SH - mid - Inches(0.5))
|
|
377
|
+
return s
|
|
378
|
+
|
|
379
|
+
def T_table_two_col(prs, title, left_lines, headers, rows, subtitle=None):
|
|
380
|
+
"""Left text + right table."""
|
|
381
|
+
s = prs.slides.add_slide(prs.slide_layouts[6])
|
|
382
|
+
_title_block(s, title, subtitle)
|
|
383
|
+
cw = int((CW - Inches(0.5)) / 2)
|
|
384
|
+
gap = Inches(0.5)
|
|
385
|
+
_multiline(s, ML, BODY_Y, cw, BODY_H, left_lines, sz=18)
|
|
386
|
+
_table(s, headers, rows, ML + cw + gap, BODY_Y, cw)
|
|
387
|
+
return s
|
|
388
|
+
|
|
389
|
+
|
|
390
|
+
# ── Speaker notes ──────────────────────────────────────────────
|
|
391
|
+
def parse_notes(path):
|
|
392
|
+
with open(path, 'r', encoding='utf-8') as f:
|
|
393
|
+
content = f.read()
|
|
394
|
+
# Match either `## Slide N:` (English) or legacy `--- 슬라이드 N: ... ---`
|
|
395
|
+
pattern = r'(?:^##\s*Slide\s+(\d+)\s*:|---\s*슬라이드\s*(\d+)\s*:.*?---)'
|
|
396
|
+
matches = list(re.finditer(pattern, content, flags=re.MULTILINE))
|
|
397
|
+
notes = {}
|
|
398
|
+
for i, m in enumerate(matches):
|
|
399
|
+
num = int(m.group(1) or m.group(2))
|
|
400
|
+
start = m.end()
|
|
401
|
+
end = matches[i + 1].start() if i + 1 < len(matches) else len(content)
|
|
402
|
+
raw = content[start:end].strip()
|
|
403
|
+
# Clean
|
|
404
|
+
lines = []
|
|
405
|
+
for line in raw.split('\n'):
|
|
406
|
+
s = line.strip()
|
|
407
|
+
if s.startswith('## Part ') or s == '---' or s.startswith('```'):
|
|
408
|
+
continue
|
|
409
|
+
if s.startswith('*(') and s.endswith(')*'):
|
|
410
|
+
lines.append(f'[{s[2:-2].strip()}]')
|
|
411
|
+
else:
|
|
412
|
+
lines.append(s.replace('**', '').replace('*', ''))
|
|
413
|
+
text = re.sub(r'\n{3,}', '\n\n', '\n'.join(lines).strip())
|
|
414
|
+
if text:
|
|
415
|
+
notes[num] = text
|
|
416
|
+
return notes
|
|
417
|
+
|
|
418
|
+
|
|
419
|
+
# ── Demo: showcase every template ───────────────────────────────
|
|
420
|
+
def build_demo_slides(prs):
|
|
421
|
+
"""Generic academic demo — one slide per template type.
|
|
422
|
+
|
|
423
|
+
Replace this function with your own content builder. Keep all content
|
|
424
|
+
as inline structured data (lists, dicts) — never parse markdown.
|
|
425
|
+
"""
|
|
426
|
+
slides = []
|
|
427
|
+
|
|
428
|
+
# 1. Title (T_lead)
|
|
429
|
+
slides.append(T_lead(
|
|
430
|
+
prs,
|
|
431
|
+
'Editable Academic PPTX — Template Showcase',
|
|
432
|
+
'A python-pptx reference deck',
|
|
433
|
+
'Speaker · Affiliation · Date'))
|
|
434
|
+
|
|
435
|
+
# 2. Section divider (T_lead)
|
|
436
|
+
slides.append(T_lead(
|
|
437
|
+
prs,
|
|
438
|
+
'Section 1: Background',
|
|
439
|
+
'Setting up the question'))
|
|
440
|
+
|
|
441
|
+
# 3. Bullet body (T_text)
|
|
442
|
+
slides.append(T_text(
|
|
443
|
+
prs,
|
|
444
|
+
'Background',
|
|
445
|
+
['- Disease X affects an estimated **N patients** worldwide.',
|
|
446
|
+
'- Standard imaging modality: **modality Y**.',
|
|
447
|
+
'- Existing limitations:',
|
|
448
|
+
' - Inter-reader variability',
|
|
449
|
+
' - Long acquisition time',
|
|
450
|
+
' - Reader fatigue on volume studies'],
|
|
451
|
+
subtitle='Why this study matters'))
|
|
452
|
+
|
|
453
|
+
# 4. Two-column compare (T_two_col)
|
|
454
|
+
slides.append(T_two_col(
|
|
455
|
+
prs,
|
|
456
|
+
'Conventional vs. Proposed Approach',
|
|
457
|
+
['### Conventional',
|
|
458
|
+
'- Manual segmentation',
|
|
459
|
+
'- ~30 min per case',
|
|
460
|
+
'- Reader-dependent'],
|
|
461
|
+
['### Proposed',
|
|
462
|
+
'- Deep-learning assisted',
|
|
463
|
+
'- ~3 min per case',
|
|
464
|
+
'- Standardized output'],
|
|
465
|
+
subtitle='Workflow comparison'))
|
|
466
|
+
|
|
467
|
+
# 5. Quote slide (T_quote_slide)
|
|
468
|
+
slides.append(T_quote_slide(
|
|
469
|
+
prs,
|
|
470
|
+
'Prior Evidence',
|
|
471
|
+
['"AI-assisted reading reduced inter-reader variability '
|
|
472
|
+
'by 40% in a multi-center study." — Author et al., Journal Y, 2024',
|
|
473
|
+
'"External validation remains the principal gap in clinical '
|
|
474
|
+
'translation of imaging AI." — Reviewer A, 2025']))
|
|
475
|
+
|
|
476
|
+
# 6. Table (T_table)
|
|
477
|
+
slides.append(T_table(
|
|
478
|
+
prs,
|
|
479
|
+
'Cohort Characteristics',
|
|
480
|
+
['Variable', 'Training (n=800)', 'Internal test (n=200)', 'External (n=300)'],
|
|
481
|
+
[['Age, mean (SD)', '62 (11)', '63 (10)', '60 (12)'],
|
|
482
|
+
['Female, n (%)', '420 (52.5)', '105 (52.5)', '160 (53.3)'],
|
|
483
|
+
['Disease prevalence', '38%', '40%', '35%'],
|
|
484
|
+
['**Imaging vendor mix**', 'A/B/C', 'A/B/C', 'D/E']],
|
|
485
|
+
subtitle='Demographics across splits'))
|
|
486
|
+
|
|
487
|
+
# 7. Image-right (T_image_right) — pass empty path to skip image safely
|
|
488
|
+
slides.append(T_image_right(
|
|
489
|
+
prs,
|
|
490
|
+
'Methods Pipeline',
|
|
491
|
+
['- DICOM ingest with anonymization',
|
|
492
|
+
'- Preprocessing: resampling, normalization',
|
|
493
|
+
'- Model: 3D U-Net (or transformer variant)',
|
|
494
|
+
'- Output: probability map + binary mask',
|
|
495
|
+
'- QA: radiologist override loop'],
|
|
496
|
+
img_path='figures/pipeline.png', # replace with real asset
|
|
497
|
+
img_pct=35,
|
|
498
|
+
subtitle='From DICOM to decision'))
|
|
499
|
+
|
|
500
|
+
# 8. Highlight slide (T_highlight_slide)
|
|
501
|
+
slides.append(T_highlight_slide(
|
|
502
|
+
prs,
|
|
503
|
+
'Primary Result',
|
|
504
|
+
['**AUC = 0.92 (95% CI 0.89–0.95)** on external test set',
|
|
505
|
+
'Sensitivity 0.88 · Specificity 0.91',
|
|
506
|
+
'Non-inferior to senior reader (Δ AUC = 0.01, p = 0.78)'],
|
|
507
|
+
subtitle='Diagnostic performance',
|
|
508
|
+
body_before=['On the prospectively collected external cohort '
|
|
509
|
+
'(n = 300, 5 sites):']))
|
|
510
|
+
|
|
511
|
+
# 9. Metaphor body (T_metaphor_body)
|
|
512
|
+
slides.append(T_metaphor_body(
|
|
513
|
+
prs,
|
|
514
|
+
'Interpretation',
|
|
515
|
+
['- Performance preserved across vendor and protocol shifts.',
|
|
516
|
+
'- Calibration check: ECE = 0.04 → clinically usable.',
|
|
517
|
+
'- Failure modes concentrated in motion-degraded studies.'],
|
|
518
|
+
['Think of the model as a **second reader** — fast, consistent, '
|
|
519
|
+
'never tired — but still requiring a final human sign-off on '
|
|
520
|
+
'edge cases.'],
|
|
521
|
+
subtitle='What it means in practice'))
|
|
522
|
+
|
|
523
|
+
# 10. Two-col with metaphor box (T_two_col_with_box)
|
|
524
|
+
slides.append(T_two_col_with_box(
|
|
525
|
+
prs,
|
|
526
|
+
'Limitations and Mitigations',
|
|
527
|
+
['### Limitations',
|
|
528
|
+
'- Single-modality input',
|
|
529
|
+
'- Retrospective external set',
|
|
530
|
+
'- No outcome data yet'],
|
|
531
|
+
['### Planned next steps',
|
|
532
|
+
'- Multi-modal fusion',
|
|
533
|
+
'- Prospective registration',
|
|
534
|
+
'- 12-month outcome follow-up'],
|
|
535
|
+
metaphor_col='right',
|
|
536
|
+
metaphor_lines=['**Open question** — is diagnostic accuracy a '
|
|
537
|
+
'sufficient endpoint, or do we need clinical '
|
|
538
|
+
'utility evidence?'],
|
|
539
|
+
subtitle='Honest accounting'))
|
|
540
|
+
|
|
541
|
+
# 11. Table-two-col (T_table_two_col)
|
|
542
|
+
slides.append(T_table_two_col(
|
|
543
|
+
prs,
|
|
544
|
+
'Comparison with Published Models',
|
|
545
|
+
['### Take-aways',
|
|
546
|
+
'- Comparable AUC at lower compute',
|
|
547
|
+
'- Better calibration on minority subgroup',
|
|
548
|
+
'- Released checkpoint + DICOM-SR exporter'],
|
|
549
|
+
['Model', 'AUC', 'Params'],
|
|
550
|
+
[['Baseline', '0.85', '11M'],
|
|
551
|
+
['Prior SOTA', '0.91', '78M'],
|
|
552
|
+
['**Ours**', '**0.92**', '**24M**']],
|
|
553
|
+
subtitle='Where this work sits'))
|
|
554
|
+
|
|
555
|
+
# 12. Take-home (T_text)
|
|
556
|
+
slides.append(T_text(
|
|
557
|
+
prs,
|
|
558
|
+
'Take-Home Messages',
|
|
559
|
+
['1. The model generalized to a **5-site external cohort** '
|
|
560
|
+
'(AUC 0.92).',
|
|
561
|
+
'2. Performance was **non-inferior to a senior reader**.',
|
|
562
|
+
'3. **Calibration and failure-mode transparency** were the '
|
|
563
|
+
'features that earned clinician trust — not raw AUC.',
|
|
564
|
+
'4. Next: prospective validation tied to clinical outcomes.'],
|
|
565
|
+
subtitle='Three points to remember'))
|
|
566
|
+
|
|
567
|
+
return slides
|
|
568
|
+
|
|
569
|
+
|
|
570
|
+
# ── Main ────────────────────────────────────────────────────────
|
|
571
|
+
def main():
|
|
572
|
+
prs = Presentation()
|
|
573
|
+
prs.slide_width = SW
|
|
574
|
+
prs.slide_height = SH
|
|
575
|
+
|
|
576
|
+
print('Building demo slides...')
|
|
577
|
+
slides = build_demo_slides(prs)
|
|
578
|
+
total = len(slides)
|
|
579
|
+
print(f' {total} slides created')
|
|
580
|
+
|
|
581
|
+
# Slide numbers (skip lead/section-divider slides with solid bg)
|
|
582
|
+
for i, slide in enumerate(slides):
|
|
583
|
+
bg_type = slide.background.fill.type
|
|
584
|
+
is_lead = bg_type is not None and 'SOLID' in str(bg_type)
|
|
585
|
+
if not is_lead:
|
|
586
|
+
_slidenum(slide, i + 1, total)
|
|
587
|
+
|
|
588
|
+
# Optional speaker-note injection — uncomment if a script file exists
|
|
589
|
+
# notes = parse_notes('speaker_script.md')
|
|
590
|
+
# for i, slide in enumerate(slides):
|
|
591
|
+
# num = i + 1
|
|
592
|
+
# if num in notes:
|
|
593
|
+
# slide.notes_slide.notes_text_frame.text = notes[num]
|
|
594
|
+
|
|
595
|
+
out = 'demo_slide_deck.pptx'
|
|
596
|
+
prs.save(out)
|
|
597
|
+
sz = os.path.getsize(out) / 1024
|
|
598
|
+
print(f'\nDone: {out}')
|
|
599
|
+
print(f' Slides: {total}')
|
|
600
|
+
print(f' Size: {sz:.0f} KB, Editable: YES')
|
|
601
|
+
|
|
602
|
+
|
|
603
|
+
if __name__ == '__main__':
|
|
604
|
+
main()
|