Adding vectorization

.devcontainer/devcontainer.json

@@ -20,7 +20,7 @@
         "editor.formatOnSave": true,
         "editor.tabSize": 2,
         "python.analysis.typeCheckingMode": "standard",
-        "python.formatting.blackArgs": [
+        "python.formatting.blackArgs": [do
           "--line-length=88"
         ],
         "python.formatting.provider": "black"
@@ -41,7 +41,8 @@
   "mounts": [
     "source=${localEnv:HOME}${localEnv:USERPROFILE}/.ssh,target=/home/vscode/.ssh,type=bind,consistency=cached"
   ],
-  "postCreateCommand": "sudo apt-get install -y inotify-tools && (grep -q 'IgnoreUnknown UseKeychain' ~/.ssh/config 2>/dev/null || sed -i '/UseKeychain/i IgnoreUnknown UseKeychain' ~/.ssh/config 2>/dev/null) && git config core.editor '/usr/bin/vim' && git config pull.rebase false && sudo curl -fsSL https://gist.githubusercontent.com/pmalacho-mit/d64caa8e16b0b0fdd5e58cc37a0ce242/raw/8f0f620d4a65f6f3d930ea14e7c2fdf382ef1bf1/codeblockify.sh -o /usr/local/bin/codeblockify && sudo chmod +x /usr/local/bin/codeblockify && curl -fsSL https://raw.githubusercontent.com/pmalacho-mit/devcontainers/refs/heads/main/src/difftastic/install.sh | sudo install -m 0755 /dev/stdin /usr/local/bin/difftastic && git config diff.external difftastic",
+  "postCreateCommand": "sudo apt-get install -y inotify-tools && sudo apt-get update && sudo apt-get install -y libasound-dev libportaudio2 libportaudiocpp0 portaudio19-dev && sudo apt-get install -y gcc && (grep -q 'IgnoreUnknown UseKeychain' ~/.ssh/config 2>/dev/null || sed -i '/UseKeychain/i IgnoreUnknown UseKeychain' ~/.ssh/config 2>/dev/null) && git config core.editor '/usr/bin/vim' && git config pull.rebase false && sudo curl -fsSL https://gist.githubusercontent.com/pmalacho-mit/d64caa8e16b0b0fdd5e58cc37a0ce242/raw/8f0f620d4a65f6f3d930ea14e7c2fdf382ef1bf1/codeblockify.sh -o /usr/local/bin/codeblockify && sudo chmod +x /usr/local/bin/codeblockify && curl -fsSL https://raw.githubusercontent.com/pmalacho-mit/devcontainers/refs/heads/main/src/difftastic/install.sh | sudo install -m 0755 /dev/stdin /usr/local/bin/difftastic && git config diff.external difftastic",
   "workspaceFolder": "${localWorkspaceFolder}",
-  "workspaceMount": "source=${localWorkspaceFolder},target=${localWorkspaceFolder},type=bind"
-}
+  "workspaceMount": "source=${localWorkspaceFolder},target=${localWorkspaceFolder},type=bind",
+  "postStartCommand": "pip install --upgrade -r requirements.txt"
+}

arc_line_vectorization_suede/.dependencies/requirements.txt

@@ -0,0 +1,5 @@
+networkx==3.6.1
+numpy==2.4.4
+pillow==12.2.0
+scikit-image==0.26.0
+scipy==1.17.1

arc_line_vectorization_suede/.github/workflows/subrepo-pull-into-main.yml

@@ -0,0 +1,184 @@
+name: subrepo-pull-into-main
+on:
+  push:
+    branches: [release]
+
+permissions:
+  contents: write
+  pull-requests: write
+
+jobs:
+  pull-to-main:
+    if: ${{ github.run_number > 1 }}
+    runs-on: ubuntu-latest
+    steps:
+      - name: Set up Git user
+        run: |
+          git config --global user.email "action@github.com"
+          git config --global user.name "GitHub Action"
+
+      - name: Install git-subrepo
+        run: |
+          git clone https://github.com/ingydotnet/git-subrepo ~/.git-subrepo
+          source ~/.git-subrepo/.rc
+          git subrepo --version
+
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          ref: release
+
+      - name: Revert (non-merge) commits from this push
+        id: revert-release
+        run: |
+          set -e
+
+          # Commit at the tip of release when this workflow runs (i.e., AFTER)
+          TRIGGER_COMMIT=$(git rev-parse HEAD)
+          echo "Trigger commit: $TRIGGER_COMMIT"
+          echo "trigger-commit=$TRIGGER_COMMIT" >> "$GITHUB_OUTPUT"
+
+          # Get BEFORE and AFTER from the push event
+          BEFORE="${{ github.event.before }}"
+          AFTER="${{ github.sha }}"
+          echo "Before: $BEFORE"
+          echo "After:  $AFTER"
+
+          # List non-merge commits introduced by this push (newest-first)
+          COMMITS=$(git rev-list --no-merges "$BEFORE..$AFTER" || true)
+
+          if [ -z "$COMMITS" ]; then
+            echo "No non-merge commits to revert between $BEFORE and $AFTER."
+          fi
+
+          echo "Non-merge commits found:"
+          echo "$COMMITS"
+
+          # ---- Collect all commit messages (newest → oldest) ----
+          ALL_MSGS=""
+          for c in $COMMITS; do
+            MSG=$(git log -1 --format=%B "$c")
+            ALL_MSGS="$ALL_MSGS
+
+            ---
+            Commit: $c
+            $MSG
+            "
+          done
+
+          echo "all-commit-messages<<EOF" >> "$GITHUB_OUTPUT"
+          echo "$ALL_MSGS" >> "$GITHUB_OUTPUT"
+          echo "EOF" >> "$GITHUB_OUTPUT"
+
+          # ---- Revert the commits (newest-first) ----
+          for c in $COMMITS; do
+            echo "Reverting $c"
+            git revert --no-edit "$c"
+          done
+
+          # Capture the commit that represents the final revert state
+          REVERT_COMMIT=$(git rev-parse HEAD)
+          echo "revert-commit=$REVERT_COMMIT" >> "$GITHUB_OUTPUT"
+
+          # Push the revert(s) back to release
+          git push origin release
+
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          ref: main
+
+      - name: Check for release/ folder
+        run: |
+          if [ ! -d "release" ]; then
+            echo "release/ folder not found on main branch. Exiting early."
+            exit 0
+          fi
+
+      - name: Update ./release to latest
+        run: |
+          set -e
+          source ~/.git-subrepo/.rc
+          git subrepo pull ./release
+
+      - name: Capture .gitrepo content
+        id: capture-gitrepo
+        run: |
+          set -e
+          # Save the current .gitrepo content
+          GITREPO_CONTENT=$(cat ./release/.gitrepo)
+          echo "gitrepo-content<<EOF" >> $GITHUB_OUTPUT
+          echo "$GITREPO_CONTENT" >> $GITHUB_OUTPUT
+          echo "EOF" >> $GITHUB_OUTPUT
+
+      - name: Determine repository owner and name
+        id: repo-info
+        run: |
+          set -e
+          OWNER="${{ github.repository_owner }}"
+          NAME="${{ github.event.repository.name }}"
+          echo "owner=$OWNER" >> $GITHUB_OUTPUT
+          echo "name=$NAME" >> $GITHUB_OUTPUT
+          echo "Repository: $OWNER/$NAME"
+
+      - name: Delete release folder
+        run: |
+          rm -rf ./release
+          echo "Deleted release/ folder"
+
+      - name: Install trigger commit using degit.sh
+        run: |
+          set -e
+          # Download and execute degit.sh to install the trigger commit
+          bash <(curl -fsSL https://raw.githubusercontent.com/pmalacho-mit/suede/refs/heads/main/scripts/utils/degit.sh) \
+            --repo "${{ steps.repo-info.outputs.owner }}/${{ steps.repo-info.outputs.name }}" \
+            --commit "${{ steps.revert-release.outputs.trigger-commit }}" \
+            --destination release
+          echo "Installed trigger commit into release/ folder"
+
+      - name: Recreate .gitrepo file
+        run: |
+          set -e
+          # Write the original .gitrepo content
+          cat > ./release/.gitrepo << 'EOF'
+          ${{ steps.capture-gitrepo.outputs.gitrepo-content }}
+          EOF
+
+          echo "Updated .gitrepo file:"
+          cat ./release/.gitrepo
+
+      - name: Generate branch name
+        id: generate-branch-name
+        run: |
+          TIMESTAMP=$(date +%Y_%m_%d-%H_%M_%S_%Z)
+          BRANCH_NAME="chore/update-release-${TIMESTAMP}"
+          echo "branch-name=$BRANCH_NAME" >> $GITHUB_OUTPUT
+          echo "Using branch name: $BRANCH_NAME"
+
+      - name: Commit and push changes
+        run: |
+          set -e
+          git switch -c "${{ steps.generate-branch-name.outputs.branch-name }}"
+          git add release/
+          git commit -m "chore(suede): update release to trigger commits:\n ${{ steps.revert-release.outputs.trigger-commit }}
+
+          Original commit messages:
+          ${{ steps.revert-release.outputs.all-commit-messages }}"
+          git push -u origin HEAD
+
+      - name: Create PR
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          gh pr create \
+            --base main \
+            --head "${{ steps.generate-branch-name.outputs.branch-name }}" \
+            --title "chore(suede): pull latest upstream release into main" \
+            --body "Automated subrepo pull of origin:release into ./release
+
+          **Trigger commit:** ${{ steps.revert-release.outputs.trigger-commit }}
+
+          **Original commit messages:**
+          \`\`\`
+          ${{ steps.revert-release.outputs.all-commit-messages }}
+          \`\`\`"

arc_line_vectorization_suede/.gitignore

@@ -0,0 +1,4 @@
+.dependencies/*
+!.dependencies/*.gitrepo
+!.dependencies/package.json
+!.dependencies/requirements.txt

arc_line_vectorization_suede/.gitrepo

@@ -0,0 +1,12 @@
+; DO NOT EDIT (unless you know what you are doing)
+;
+; This subdirectory is a git "subrepo", and this file is maintained by the
+; git-subrepo command. See https://github.com/ingydotnet/git-subrepo#readme
+;
+[subrepo]
+	remote = https://github.com/mitmedialab/arc-line-vectorization-suede
+	branch = release
+	commit = dbd7ae57777451681797fc9822edc669973ac572
+	parent = 4e366f127ad247aca176d1e87cf68225e0bb7e34
+	method = merge
+	cmdver = 0.4.9

arc_line_vectorization_suede/__init__.py

@@ -0,0 +1,116 @@
+from .skeletonize import Skeletonize, ImageSource
+from .segment import Segment
+from .graph import StrokeGraph
+from .vectorize.low_geometry import Vectorize as LowGeometryVectorize
+from .vectorize.high_geometry import Vectorize as HighGeometryVectorize
+from .commands import DrawingCommand
+
+import numpy as np
+
+
+def default_pipeline(source: ImageSource):
+    skeleton = Skeletonize(
+        source,
+        Skeletonize.Config.Binarize(threshold=0.5),
+        Skeletonize.Config.Skeletonize(method="zhang"),
+        Skeletonize.Config.Collapse(
+            skeletonize_method="lee",
+            max_hole_area=10,
+            max_thin_thickness=3.0,
+            reskeletonize=True,
+        ),
+        detect_config={
+            "local_tau_radius": 40,
+            "fat_ratio": 1.3,
+            "min_fat_area": 8,
+            "group_dilate": 15,
+            "skel_ring_dilate": 5,
+            "pairing_tangent_steps": 8,
+            "pairing_threshold": 1.2,
+            "min_chromosome_skel_length": 15,
+        },
+    )
+
+    junction_tol = 2.5
+    tangent_sample = 10
+
+    segment = Segment(
+        skeleton.uncrossed,
+        skeleton.binary,
+        Segment.Config.Segment(min_length=10.0),
+        Segment.Config.Fuse(
+            max_path_length=20,
+            lookback=10,
+            min_tangent_score=0.5,
+            gap_penalty=0.05,
+            curvature_penalty=3.0,
+        ),
+        Segment.Config.Repair(
+            junction_tol=junction_tol,
+            stable_skip=2,
+            stable_sample=6,
+            max_junction_region_length=20,
+            min_output_polyline_length=2,
+            min_tangent_spread_deg=15.0,
+            interp_max_spacing=1.0,
+            min_curvature_spike_ratio=2.0,
+            curvature_context_window=8,
+        ),
+        Segment.Config.PostRepairFuse(
+            junction_tol=junction_tol,
+            tangent_skip=2,
+            tangent_sample=tangent_sample,
+            min_tangent_score=0.6,
+            curvature_penalty=1.0,
+        ),
+    )
+
+    graph = StrokeGraph(
+        segment.fused_post_repair,
+        StrokeGraph.Config.Build(
+            junction_tol=junction_tol,  # match Repair.junction_tol
+            terminal_tangent_window=10,  # should match fuse.lookback
+            crossing_tangent_skip=2,  # baseline; dynamic walk handles arbitrary bridges
+            crossing_tangent_half_window=6,
+            cusp_angle_threshold_deg=50.0,  # raise to ~50 to handle bikelove's cusp-like junction
+            cluster_merge_centroid_distance=10.0,
+            cluster_merge_index_gap=10,
+        ),
+    )
+
+    start_pos = np.array([0.0, 0.0])
+    start_heading = 0.0
+    low_geometry = LowGeometryVectorize(
+        graph,
+        start_pos=start_pos,
+        start_heading=start_heading,
+    )
+    high_geometry = HighGeometryVectorize(
+        segment.fused_post_repair,
+        start_pos=start_pos,
+        start_heading=start_heading,
+        commands=HighGeometryVectorize.Config.ToCommands(
+            sigma=2.0,
+            corner_threshold=0.25,
+            max_fit_residual=5.0,
+        ),
+        consolidate=HighGeometryVectorize.Config.Consolidate(
+            center_tol_rel=0.25,
+            radius_tol_rel=0.25,
+            center_tol_abs=3.0,
+            radius_tol_abs=3.0,
+            max_endpoint_snap_rel=0.15,
+            max_endpoint_snap_abs=6.0,
+            proximity_min_radius_ratio=0.4,
+            line_angle_tol_deg=6.0,
+            line_offset_tol_abs=5.0,
+            min_line_length=5.0,
+            max_line_endpoint_snap_abs=5.0,
+            junction_epsilon=3.0,
+            merge_arcs=True,
+            merge_lines=True,
+            return_report=False,
+        ),
+    )
+
+    return skeleton, segment, graph, low_geometry, high_geometry