first implementation - image/drawing integration
This commit is contained in:
Adrien
@@ -0,0 +1,47 @@
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package com.aiteacher.document;
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import jakarta.persistence.*;
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import java.time.Instant;
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import java.util.UUID;
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@Entity
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@Table(name = "chapter")
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public class ChapterEntity {
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@Id
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@Column(name = "id", length = 200)
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private String id;
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@Column(name = "book_id", nullable = false)
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private UUID bookId;
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@Column(name = "number", nullable = false)
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private int number;
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@Column(name = "title", length = 500)
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private String title;
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@Column(name = "page_start")
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private Integer pageStart;
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@Column(name = "created_at", nullable = false)
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private Instant createdAt;
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public ChapterEntity() {}
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public ChapterEntity(String id, UUID bookId, int number, String title, Integer pageStart) {
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this.id = id;
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this.bookId = bookId;
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this.number = number;
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this.title = title;
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this.pageStart = pageStart;
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this.createdAt = Instant.now();
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}
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public String getId() { return id; }
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public UUID getBookId() { return bookId; }
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public int getNumber() { return number; }
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public String getTitle() { return title; }
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public Integer getPageStart() { return pageStart; }
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public Instant getCreatedAt() { return createdAt; }
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}
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@@ -0,0 +1,9 @@
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package com.aiteacher.document;
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import org.springframework.data.jpa.repository.JpaRepository;
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import java.util.UUID;
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public interface ChapterRepository extends JpaRepository<ChapterEntity, String> {
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void deleteAllByBookId(UUID bookId);
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}
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@@ -0,0 +1,58 @@
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package com.aiteacher.document;
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import jakarta.persistence.*;
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import java.io.Serializable;
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import java.util.Objects;
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import java.util.UUID;
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@Entity
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@Table(name = "chunk_figure_ref")
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@IdClass(ChunkFigureRefEntity.PK.class)
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public class ChunkFigureRefEntity {
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@Id
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@Column(name = "chunk_id", nullable = false)
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private UUID chunkId;
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@Id
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@Column(name = "figure_id", nullable = false, length = 200)
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private String figureId;
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@Column(name = "mention_page")
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private Integer mentionPage;
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public ChunkFigureRefEntity() {}
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public ChunkFigureRefEntity(UUID chunkId, String figureId, Integer mentionPage) {
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this.chunkId = chunkId;
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this.figureId = figureId;
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this.mentionPage = mentionPage;
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}
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public UUID getChunkId() { return chunkId; }
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public String getFigureId() { return figureId; }
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public Integer getMentionPage() { return mentionPage; }
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public static class PK implements Serializable {
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private UUID chunkId;
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private String figureId;
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public PK() {}
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public PK(UUID chunkId, String figureId) {
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this.chunkId = chunkId;
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this.figureId = figureId;
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}
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@Override
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public boolean equals(Object o) {
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if (this == o) return true;
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if (!(o instanceof PK pk)) return false;
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return Objects.equals(chunkId, pk.chunkId) && Objects.equals(figureId, pk.figureId);
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}
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@Override
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public int hashCode() {
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return Objects.hash(chunkId, figureId);
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}
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}
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}
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@@ -0,0 +1,18 @@
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package com.aiteacher.document;
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import org.springframework.data.jpa.repository.JpaRepository;
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import org.springframework.data.jpa.repository.Query;
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import org.springframework.data.repository.query.Param;
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import java.util.List;
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import java.util.UUID;
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public interface ChunkFigureRefRepository extends JpaRepository<ChunkFigureRefEntity, ChunkFigureRefEntity.PK> {
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@Query("SELECT r FROM ChunkFigureRefEntity r WHERE r.chunkId IN :chunkIds")
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List<ChunkFigureRefEntity> findByChunkIdIn(@Param("chunkIds") List<UUID> chunkIds);
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@Query("DELETE FROM ChunkFigureRefEntity r WHERE r.figureId IN :figureIds")
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@org.springframework.data.jpa.repository.Modifying
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void deleteByFigureIdIn(@Param("figureIds") List<String> figureIds);
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}
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@@ -0,0 +1,62 @@
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package com.aiteacher.document;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import org.springframework.ai.document.Document;
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import org.springframework.stereotype.Service;
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import java.util.List;
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import java.util.UUID;
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import java.util.regex.Matcher;
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import java.util.regex.Pattern;
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/**
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* Scans chunk text for "Fig. X" and "Figure X" references and persists
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* ChunkFigureRefEntity rows linking that chunk to its referenced figures.
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*/
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@Service
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public class ChunkFigureRefService {
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private static final Logger log = LoggerFactory.getLogger(ChunkFigureRefService.class);
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// Matches: "Fig. 12-4", "Fig. 12.4", "Fig 12", "Figure 12-4", etc.
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private static final Pattern REF_PATTERN =
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Pattern.compile("(?i)\\b(Fig\\.?|Figure)\\s+(\\d+[\\-.\\d]*)");
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private final ChunkFigureRefRepository refRepository;
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public ChunkFigureRefService(ChunkFigureRefRepository refRepository) {
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this.refRepository = refRepository;
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}
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/**
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* For each text chunk, finds figure references and persists ChunkFigureRefEntity rows.
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*/
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public void linkChunksToFigures(List<Document> chunks, List<FigureEntity> bookFigures,
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int pageNum) {
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if (bookFigures.isEmpty()) return;
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for (Document chunk : chunks) {
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String chunkIdStr = chunk.getId();
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UUID chunkId;
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try {
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chunkId = UUID.fromString(chunkIdStr);
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} catch (IllegalArgumentException ex) {
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log.warn("Chunk has non-UUID id: {}", chunkIdStr);
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continue;
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}
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Matcher m = REF_PATTERN.matcher(chunk.getText());
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while (m.find()) {
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String refNum = m.group(2).trim();
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// Find matching figure by label suffix
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for (FigureEntity figure : bookFigures) {
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if (figure.getLabel() != null && figure.getLabel().endsWith(refNum)) {
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refRepository.save(new ChunkFigureRefEntity(chunkId, figure.getId(), pageNum));
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break;
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}
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}
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}
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}
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}
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}
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@@ -0,0 +1,82 @@
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package com.aiteacher.document;
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import jakarta.persistence.*;
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import java.time.Instant;
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import java.util.UUID;
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@Entity
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@Table(name = "figure")
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public class FigureEntity {
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@Id
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@Column(name = "id", length = 200)
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private String id;
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@Column(name = "book_id", nullable = false)
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private UUID bookId;
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@Column(name = "section_id", length = 200)
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private String sectionId;
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@Column(name = "chapter_id", length = 200)
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private String chapterId;
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@Column(name = "label", length = 100)
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private String label;
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@Column(name = "caption", columnDefinition = "TEXT")
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private String caption;
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@Enumerated(EnumType.STRING)
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@Column(name = "figure_type", nullable = false, length = 50)
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private FigureType figureType;
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@Column(name = "page", nullable = false)
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private int page;
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@Column(name = "image_path", nullable = false, length = 1000)
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private String imagePath;
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@Column(name = "caption_embedding_id")
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private UUID captionEmbeddingId;
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@Column(name = "created_at", nullable = false)
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private Instant createdAt;
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public FigureEntity() {}
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public FigureEntity(String id, UUID bookId, String sectionId, String chapterId,
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String label, String caption, FigureType figureType,
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int page, String imagePath) {
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this.id = id;
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this.bookId = bookId;
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this.sectionId = sectionId;
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this.chapterId = chapterId;
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this.label = label;
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this.caption = caption;
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this.figureType = figureType;
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this.page = page;
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this.imagePath = imagePath;
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this.createdAt = Instant.now();
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}
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public String getId() { return id; }
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public UUID getBookId() { return bookId; }
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public String getSectionId() { return sectionId; }
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public String getChapterId() { return chapterId; }
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public String getLabel() { return label; }
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public String getCaption() { return caption; }
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public FigureType getFigureType() { return figureType; }
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public int getPage() { return page; }
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public String getImagePath() { return imagePath; }
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public UUID getCaptionEmbeddingId() { return captionEmbeddingId; }
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public Instant getCreatedAt() { return createdAt; }
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public void setCaptionEmbeddingId(UUID captionEmbeddingId) {
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this.captionEmbeddingId = captionEmbeddingId;
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}
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public void setCaption(String caption) {
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this.caption = caption;
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}
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}
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@@ -0,0 +1,135 @@
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package com.aiteacher.document;
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import com.aiteacher.figure.FigureStorageService;
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import org.apache.pdfbox.Loader;
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import org.apache.pdfbox.cos.COSName;
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import org.apache.pdfbox.pdmodel.PDDocument;
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import org.apache.pdfbox.pdmodel.PDPage;
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import org.apache.pdfbox.pdmodel.graphics.PDXObject;
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import org.apache.pdfbox.pdmodel.graphics.image.PDImageXObject;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import org.springframework.beans.factory.annotation.Value;
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import org.springframework.stereotype.Service;
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import java.awt.image.BufferedImage;
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import java.io.IOException;
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import java.nio.file.Path;
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import java.util.ArrayList;
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import java.util.List;
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import java.util.UUID;
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import java.util.regex.Matcher;
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import java.util.regex.Pattern;
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/**
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* Extracts images from each PDF page using PDFBox.
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* Images below the configured minimum size are skipped.
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* Caption is detected by the "Fig." pattern in page text.
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*/
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@Service
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public class FigureExtractionService {
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private static final Logger log = LoggerFactory.getLogger(FigureExtractionService.class);
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// Caption: line starting with "Fig." or "Figure" followed by a number
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private static final Pattern CAPTION_PATTERN =
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Pattern.compile("(?m)^(Fig\\.?\\s*\\d+[\\-.]?\\d*[^\\n]*)", Pattern.CASE_INSENSITIVE);
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// Figure label: "Fig. 12-4" or "Fig. 12.4"
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private static final Pattern LABEL_PATTERN =
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Pattern.compile("(?i)Fig\\.?\\s*(\\d+[\\-.\\d]*)");
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private final FigureStorageService storageService;
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private final FigureRepository figureRepository;
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private final int minImageSizePx;
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public FigureExtractionService(
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FigureStorageService storageService,
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FigureRepository figureRepository,
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@Value("${app.figure-storage.min-image-size-px:100}") int minImageSizePx) {
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this.storageService = storageService;
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this.figureRepository = figureRepository;
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this.minImageSizePx = minImageSizePx;
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}
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/**
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* Extracts all qualifying images from the PDF for the given book.
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* Returns persisted FigureEntity list (without vision descriptions — set later).
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*/
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public List<FigureEntity> extract(UUID bookId, String chapterId,
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List<SectionEntity> sections, Path pdfPath) {
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List<FigureEntity> figures = new ArrayList<>();
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int figureCounter = 0;
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try (PDDocument doc = Loader.loadPDF(pdfPath.toFile())) {
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for (SectionEntity section : sections) {
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int pageIndex = section.getPageStart() - 1; // 0-based
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if (pageIndex < 0 || pageIndex >= doc.getNumberOfPages()) continue;
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PDPage page = doc.getPage(pageIndex);
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String pageText = section.getFullText();
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try {
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for (COSName name : page.getResources().getXObjectNames()) {
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PDXObject xObject = page.getResources().getXObject(name);
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if (!(xObject instanceof PDImageXObject image)) continue;
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BufferedImage bufferedImage = image.getImage();
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if (bufferedImage.getWidth() < minImageSizePx
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|| bufferedImage.getHeight() < minImageSizePx) {
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continue; // skip decorative images
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}
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figureCounter++;
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String figureId = bookId + "-fig-" + pageIndex + "-" + figureCounter;
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String caption = detectCaption(pageText);
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String label = detectLabel(caption, figureCounter);
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FigureType type = classifyType(caption, pageText);
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String imagePath = storageService.save(bookId, figureId, bufferedImage);
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FigureEntity figure = new FigureEntity(
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figureId, bookId, section.getId(), chapterId,
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label, caption, type, section.getPageStart(), imagePath
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);
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figures.add(figureRepository.save(figure));
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}
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} catch (IOException ex) {
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log.warn("Failed to extract images from page {} of book {}: {}",
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section.getPageStart(), bookId, ex.getMessage());
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}
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}
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} catch (IOException ex) {
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log.error("Could not open PDF for image extraction, book {}", bookId, ex);
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}
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log.info("Extracted {} figures for book {}", figures.size(), bookId);
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return figures;
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}
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private String detectCaption(String pageText) {
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if (pageText == null) return null;
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Matcher m = CAPTION_PATTERN.matcher(pageText);
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return m.find() ? m.group(1).trim() : null;
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}
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private String detectLabel(String caption, int counter) {
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if (caption != null) {
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Matcher m = LABEL_PATTERN.matcher(caption);
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if (m.find()) return "Fig. " + m.group(1).trim();
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}
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return "Fig. " + counter;
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}
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private FigureType classifyType(String caption, String pageText) {
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String combined = ((caption != null ? caption : "") + " " + (pageText != null ? pageText : "")).toLowerCase();
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if (combined.contains("mri") || combined.contains("ct ") || combined.contains("magnetic")
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|| combined.contains("tomography")) return FigureType.MRI_CT_SCAN;
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if (combined.contains("intraoperative") || combined.contains("intra-op")) return FigureType.INTRAOPERATIVE_IMAGE;
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if (caption != null && caption.toLowerCase().startsWith("table")) return FigureType.TABLE;
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if (combined.contains("chart") || combined.contains("histogram") || combined.contains("graph"))
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return FigureType.CHART;
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if (combined.contains("photograph") || combined.contains("photo")) return FigureType.SURGICAL_PHOTOGRAPH;
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return FigureType.ANATOMICAL_DIAGRAM;
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}
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}
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@@ -0,0 +1,11 @@
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package com.aiteacher.document;
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import org.springframework.data.jpa.repository.JpaRepository;
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import java.util.List;
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import java.util.UUID;
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public interface FigureRepository extends JpaRepository<FigureEntity, String> {
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List<FigureEntity> findAllByBookId(UUID bookId);
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void deleteAllByBookId(UUID bookId);
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}
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@@ -0,0 +1,10 @@
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package com.aiteacher.document;
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public enum FigureType {
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ANATOMICAL_DIAGRAM,
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SURGICAL_PHOTOGRAPH,
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MRI_CT_SCAN,
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TABLE,
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CHART,
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INTRAOPERATIVE_IMAGE
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}
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@@ -0,0 +1,71 @@
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package com.aiteacher.document;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import org.springframework.ai.reader.pdf.PagePdfDocumentReader;
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import org.springframework.ai.reader.pdf.config.PdfDocumentReaderConfig;
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import org.springframework.core.io.FileSystemResource;
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import org.springframework.stereotype.Service;
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import org.springframework.transaction.annotation.Transactional;
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import java.nio.file.Path;
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import java.util.ArrayList;
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import java.util.List;
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import java.util.UUID;
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/**
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* Parses a PDF into page-level SectionEntity records stored in Postgres.
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* Each page becomes one section, grouped under a single chapter per book.
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*/
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@Service
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public class PdfStructureParser {
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private static final Logger log = LoggerFactory.getLogger(PdfStructureParser.class);
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private final ChapterRepository chapterRepository;
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private final SectionRepository sectionRepository;
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public PdfStructureParser(ChapterRepository chapterRepository,
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SectionRepository sectionRepository) {
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this.chapterRepository = chapterRepository;
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this.sectionRepository = sectionRepository;
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}
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@Transactional
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public List<SectionEntity> parse(UUID bookId, String bookTitle, Path pdfPath) {
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log.info("Parsing PDF structure for book {}", bookId);
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// One chapter per book
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String chapterId = bookId + "-ch1";
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ChapterEntity chapter = new ChapterEntity(chapterId, bookId, 1, bookTitle, 1);
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chapterRepository.save(chapter);
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// One section per page
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PagePdfDocumentReader reader = new PagePdfDocumentReader(
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new FileSystemResource(pdfPath.toFile()),
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PdfDocumentReaderConfig.builder().withPagesPerDocument(1).build()
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);
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List<org.springframework.ai.document.Document> pages = reader.get();
|
||||
List<SectionEntity> sections = new ArrayList<>();
|
||||
|
||||
for (int i = 0; i < pages.size(); i++) {
|
||||
int pageNum = i + 1;
|
||||
String text = pages.get(i).getText();
|
||||
if (text == null || text.isBlank()) continue;
|
||||
|
||||
String sectionId = bookId + "-p" + pageNum;
|
||||
SectionEntity section = new SectionEntity(
|
||||
sectionId, chapterId, bookId,
|
||||
String.valueOf(pageNum),
|
||||
"Page " + pageNum,
|
||||
pageNum, pageNum,
|
||||
text
|
||||
);
|
||||
sections.add(sectionRepository.save(section));
|
||||
}
|
||||
|
||||
log.info("Parsed {} sections for book {}", sections.size(), bookId);
|
||||
return sections;
|
||||
}
|
||||
}
|
||||
@@ -0,0 +1,63 @@
|
||||
package com.aiteacher.document;
|
||||
|
||||
import jakarta.persistence.*;
|
||||
import java.time.Instant;
|
||||
import java.util.UUID;
|
||||
|
||||
@Entity
|
||||
@Table(name = "section")
|
||||
public class SectionEntity {
|
||||
|
||||
@Id
|
||||
@Column(name = "id", length = 200)
|
||||
private String id;
|
||||
|
||||
@Column(name = "chapter_id", nullable = false, length = 200)
|
||||
private String chapterId;
|
||||
|
||||
@Column(name = "book_id", nullable = false)
|
||||
private UUID bookId;
|
||||
|
||||
@Column(name = "number", length = 50)
|
||||
private String number;
|
||||
|
||||
@Column(name = "title", length = 500)
|
||||
private String title;
|
||||
|
||||
@Column(name = "page_start", nullable = false)
|
||||
private int pageStart;
|
||||
|
||||
@Column(name = "page_end", nullable = false)
|
||||
private int pageEnd;
|
||||
|
||||
@Column(name = "full_text", nullable = false, columnDefinition = "TEXT")
|
||||
private String fullText;
|
||||
|
||||
@Column(name = "created_at", nullable = false)
|
||||
private Instant createdAt;
|
||||
|
||||
public SectionEntity() {}
|
||||
|
||||
public SectionEntity(String id, String chapterId, UUID bookId, String number,
|
||||
String title, int pageStart, int pageEnd, String fullText) {
|
||||
this.id = id;
|
||||
this.chapterId = chapterId;
|
||||
this.bookId = bookId;
|
||||
this.number = number;
|
||||
this.title = title;
|
||||
this.pageStart = pageStart;
|
||||
this.pageEnd = pageEnd;
|
||||
this.fullText = fullText;
|
||||
this.createdAt = Instant.now();
|
||||
}
|
||||
|
||||
public String getId() { return id; }
|
||||
public String getChapterId() { return chapterId; }
|
||||
public UUID getBookId() { return bookId; }
|
||||
public String getNumber() { return number; }
|
||||
public String getTitle() { return title; }
|
||||
public int getPageStart() { return pageStart; }
|
||||
public int getPageEnd() { return pageEnd; }
|
||||
public String getFullText() { return fullText; }
|
||||
public Instant getCreatedAt() { return createdAt; }
|
||||
}
|
||||
@@ -0,0 +1,11 @@
|
||||
package com.aiteacher.document;
|
||||
|
||||
import org.springframework.data.jpa.repository.JpaRepository;
|
||||
|
||||
import java.util.List;
|
||||
import java.util.UUID;
|
||||
|
||||
public interface SectionRepository extends JpaRepository<SectionEntity, String> {
|
||||
List<SectionEntity> findAllByBookId(UUID bookId);
|
||||
void deleteAllByBookId(UUID bookId);
|
||||
}
|
||||
@@ -0,0 +1,65 @@
|
||||
package com.aiteacher.document;
|
||||
|
||||
import org.springframework.ai.document.Document;
|
||||
import org.springframework.stereotype.Service;
|
||||
|
||||
import java.util.ArrayList;
|
||||
import java.util.HashMap;
|
||||
import java.util.List;
|
||||
import java.util.Map;
|
||||
import java.util.UUID;
|
||||
|
||||
/**
|
||||
* Splits a SectionEntity's full text into overlapping chunks for vector embedding.
|
||||
* Target size: ~1800 characters (~450 tokens); overlap: 200 characters.
|
||||
*/
|
||||
@Service
|
||||
public class TextChunkingService {
|
||||
|
||||
private static final int TARGET_CHARS = 1800;
|
||||
private static final int OVERLAP_CHARS = 200;
|
||||
|
||||
public List<Document> chunk(SectionEntity section, String bookTitle) {
|
||||
String text = section.getFullText();
|
||||
if (text == null || text.isBlank()) return List.of();
|
||||
|
||||
List<String> windows = split(text);
|
||||
List<Document> documents = new ArrayList<>();
|
||||
|
||||
for (int i = 0; i < windows.size(); i++) {
|
||||
String chunkId = UUID.randomUUID().toString();
|
||||
Map<String, Object> metadata = buildMetadata(section, bookTitle, i, windows.size(), chunkId);
|
||||
documents.add(new Document(chunkId, windows.get(i), metadata));
|
||||
}
|
||||
return documents;
|
||||
}
|
||||
|
||||
private List<String> split(String text) {
|
||||
List<String> windows = new ArrayList<>();
|
||||
int start = 0;
|
||||
while (start < text.length()) {
|
||||
int end = Math.min(start + TARGET_CHARS, text.length());
|
||||
windows.add(text.substring(start, end));
|
||||
if (end == text.length()) break;
|
||||
start = end - OVERLAP_CHARS;
|
||||
}
|
||||
return windows;
|
||||
}
|
||||
|
||||
private Map<String, Object> buildMetadata(SectionEntity section, String bookTitle,
|
||||
int index, int total, String chunkId) {
|
||||
Map<String, Object> m = new HashMap<>();
|
||||
m.put("type", "TEXT");
|
||||
m.put("book_id", section.getBookId().toString());
|
||||
m.put("book_title", bookTitle);
|
||||
m.put("chapter_id", section.getChapterId());
|
||||
m.put("section_id", section.getId());
|
||||
m.put("section_title", section.getTitle() != null ? section.getTitle() : "");
|
||||
m.put("page_start", section.getPageStart());
|
||||
m.put("page_end", section.getPageEnd());
|
||||
m.put("chunk_index", index);
|
||||
m.put("total_chunks", total);
|
||||
m.put("chunk_id", chunkId);
|
||||
return m;
|
||||
}
|
||||
}
|
||||
@@ -0,0 +1,49 @@
|
||||
package com.aiteacher.document;
|
||||
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
import org.springframework.ai.chat.client.ChatClient;
|
||||
import org.springframework.core.io.FileSystemResource;
|
||||
import org.springframework.stereotype.Service;
|
||||
import org.springframework.util.MimeTypeUtils;
|
||||
|
||||
import java.nio.file.Path;
|
||||
|
||||
/**
|
||||
* Generates a clinical text description for an extracted figure image
|
||||
* using the OpenAI vision model via Spring AI ChatClient.
|
||||
*/
|
||||
@Service
|
||||
public class VisionDescriptionService {
|
||||
|
||||
private static final Logger log = LoggerFactory.getLogger(VisionDescriptionService.class);
|
||||
|
||||
private static final String PROMPT =
|
||||
"You are a neurosurgery educator. Provide a brief 2-3 sentence clinical description of " +
|
||||
"this image. Focus on anatomical structures, surgical landmarks, labels, and clinical " +
|
||||
"significance. If text or labels are visible, include them verbatim.";
|
||||
|
||||
private final ChatClient chatClient;
|
||||
|
||||
public VisionDescriptionService(ChatClient chatClient) {
|
||||
this.chatClient = chatClient;
|
||||
}
|
||||
|
||||
/**
|
||||
* Returns a description string. Falls back to the provided caption if vision fails.
|
||||
*/
|
||||
public String describe(Path imagePath, String captionFallback) {
|
||||
try {
|
||||
return chatClient.prompt()
|
||||
.user(u -> u
|
||||
.text(PROMPT)
|
||||
.media(MimeTypeUtils.IMAGE_PNG, new FileSystemResource(imagePath.toFile())))
|
||||
.call()
|
||||
.content();
|
||||
} catch (Exception ex) {
|
||||
log.warn("Vision description failed for {}: {} — using caption as fallback",
|
||||
imagePath.getFileName(), ex.getMessage());
|
||||
return captionFallback != null ? captionFallback : "Figure";
|
||||
}
|
||||
}
|
||||
}
|
||||
Reference in New Issue
Block a user