docs: add todays status update presentation

Author: 404Simon

docs/update_06_23.pdf

@@ -0,0 +1,256 @@
+#set page(
+  width: 28.8cm,
+  height: 16.2cm,
+  margin: (top: 1.4cm, bottom: 1cm, left: 1.8cm, right: 1.8cm),
+  fill: white,
+  numbering: "1",
+  number-align: right,
+)
+
+#set text(font: "New Computer Modern", size: 16pt)
+#set par(justify: true, leading: 0.65em)
+
+#let accent = rgb("#1d4ed8")
+#let accent-light = rgb("#eff6ff")
+#let accent-mid = rgb("#93c5fd")
+#let muted = rgb("#6b7280")
+#let dark = rgb("#111827")
+#let green-bg = rgb("#f0fdf4")
+#let green-border = rgb("#bbf7d0")
+#let green-text = rgb("#166534")
+
+#let slide(title, body) = {
+  pagebreak()
+  block(
+    width: 100%,
+    inset: (top: 8pt, bottom: 10pt, left: 0pt, right: 0pt),
+    stroke: (bottom: 2.5pt + accent),
+  )[
+    #text(size: 24pt, fill: accent, weight: "bold")[#title]
+  ]
+  v(0.5cm)
+  body
+}
+
+#let highlight(body) = {
+  block(
+    width: 100%,
+    fill: accent-light,
+    inset: 14pt,
+    radius: 6pt,
+    stroke: 1pt + accent-mid,
+  )[
+    #body
+  ]
+}
+
+#let proofbox(body) = {
+  block(
+    width: 100%,
+    fill: green-bg,
+    inset: 14pt,
+    radius: 6pt,
+    stroke: 1pt + green-border,
+  )[
+    #body
+  ]
+}
+
+#let color-cell(c, label) = {
+  block(
+    width: 1.2em,
+    height: 1.2em,
+    fill: c,
+    inset: 0pt,
+    align(center + horizon, text(size: 0.55em, weight: "bold", fill: if label == "D" { black } else { white }, label)),
+  )
+}
+
+#let color-row(colors, labels, sz: 1.2em) = {
+  let cells = ()
+  for i in range(colors.len()) {
+    cells.push(block(width: sz, height: sz, fill: colors.at(i), inset: 0pt))
+  }
+  grid(columns: (sz,) * colors.len(), rows: (sz,), gutter: 0pt, ..cells)
+}
+
+#align(center + horizon)[
+  #block(width: 80%)[
+    #align(center)[
+      #text(size: 34pt, fill: accent, weight: "bold")[
+        VesSkel\
+      ]
+      #v(1.0cm)
+      #text(size: 20pt, fill: dark)[
+        Vessel Skeletonization and Graph-Based\
+        Phenotype Analysis in Retinal Fundus Images
+      ]
+      #v(1.2cm)
+      #line(length: 40%, stroke: 1.5pt + accent)
+      #v(0.8cm)
+      #text(size: 16pt, fill: muted)[
+        Simon Wittmann
+
+        Supervisor: Anna Möller
+      ]
+      #v(0.3cm)
+      #text(size: 14pt, fill: muted)[
+        23. Juni 2026
+      ]
+    ]
+  ]
+]
+
+#slide("Implementation Progress")[
+  #v(-0.3cm)
+  + preprocessing: binary closing & hole filling
+  + new features & updated Feature Comparison Table
+  + 3D thinning performance (#sym.arrow parallel scanning, epoch removal tracking)
+  + benchmark results (2D + 3D vs skimage & VesselVio)
+  + nicer CLI UX (shorter subcommands, worker feedback)
+  + paper draft started
+  + prediction notebook refactored
+]
+
+#slide("Preprocessing: Binary Closing & Hole Filling")[
+  *Binary closing* bridges small gaps in segmented vessels before thinning
+
+  *Hole filling* fills enclosed background regions inside vessels
+
+  #v(0.3cm)
+  #table(
+    columns: (auto, auto, 1fr),
+    stroke: 0.5pt + rgb("#e5e7eb"),
+    inset: 7pt,
+    fill: (x, y) => if y == 0 { accent-light } else if calc.odd(y) { rgb("#f9fafb") },
+    [*Config Key*], [*Default*], [*Description*],
+    [`closing_iterations`], [`0`], [binary closing iterations (0 = off)],
+    [`fill_holes`], [`false`], [fill enclosed background regions],
+    [`max_hole_size`], [`0`], [max filled hole area (0 = unlimited)],
+    [`show_preprocessed`], [`false`], [show preprocessed binary in napari],
+  )
+
+  #v(0.3cm)
+  #highlight[
+    Supporting tests: in `test_preprocessing.py` covering closing, hole filling, size thresholding.
+  ]
+]
+
+#slide("New Features")[
+  *Key additions since last update:*
+  + Mean segment volume ($V = pi sum r_i^2$ for each segment)
+  + Mean segment surface area ($A = 2 pi sum r_i$)
+  + Added to `per_segment_radii` output and summary features
+  + Used in downstream classification
+
+  #v(0.3cm)
+  *Feature Table Update:*
+  + Re-mapped which features are feasible (many marked "nope")
+  + only TODO left: per-node metrics
+
+  SHOW TABLE
+]
+
+#slide("3D Thinning Performance Improvements")[
+  #columns(2, gutter: 1.5em)[
+    *Epoch-Based Removal Tracking*
+
+    Problem: vanilla Lee94 re-checks simplicity (DFS on 26-neighbor graph) for *every* candidate before removal
+
+    Insight: `_mark_removable_candidates` already verified all candidates before any removals in this batch. If none of a candidate's 26 neighbors have been removed yet, the old verdict is still valid - skip the DFS.
+
+
+    #colbreak()
+    Mechanism:
+    + `epoch` increments per batch; stamped at each removed voxel
+    + Scan 26 neighbors for stamp == current epoch (cheap, 26 int comparisons)
+    + If no neighbor stamped → remove immediately
+    + If neighbor stamped → re-run DFS to verify still simple
+    + Never reset; monotonically increasing epoch makes old stamps invisible
+  ]
+]
+
+#slide("Benchmark Results")[
+  #v(-0.3cm)
+  #columns(2, gutter: 1.5em)[
+
+    *2D (HRF dataset, 45 images)*
+    #table(
+      columns: (auto, auto, auto),
+      stroke: 0.5pt + rgb("#e5e7eb"),
+      inset: 5pt,
+      fill: (x, y) => if y == 0 { accent-light } else if calc.odd(y) { rgb("#f9fafb") },
+      [], [*Mean (s)*], [*vs vesskel*],
+      [vesskel], [0.084], [-],
+      [skimage Zhang], [0.157], [1.87x slower],
+      [skimage Lee], [0.438], [5.21x slower],
+      [VesselVio Lee], [0.796], [9.46x slower],
+    )
+
+    #colbreak()
+    *3D (vessap test volume)*
+    #table(
+      columns: (auto, auto, auto),
+      stroke: 0.5pt + rgb("#e5e7eb"),
+      inset: 5pt,
+      fill: (x, y) => if y == 0 { accent-light } else if calc.odd(y) { rgb("#f9fafb") },
+      [], [*Mean (s)*], [*vs vesskel*],
+      [vesskel], [0.730], [-],
+      [skimage Lee], [1.024], [1.4x slower],
+      [VesselVio Lee], [0.804], [1.10x slower],
+    )
+  ]
+
+  *Key Takeaways*
+  #highlight[
+    + 2D is highly optimized via LUT-based simplicity check
+    + 3D competitive with skimage and VesselVio
+    + Pure Python + Numba - no Cython, no compiled extensions
+  ]
+]
+
+#slide("CLI Improvements")[
+  *Shorter Subcommands*
+  - `vesskel init config.json` instead of `vesskel config-init --out config.json`
+  - `vesskel validate config.json` instead of `vesskel validate-config --config config.json`
+
+  *Instant Worker Feedback*
+  - `vesskel run (-j N)` now prints: `Spawning N worker processes...`
+
+  *Default Config Changed*
+  - `branches`, `branch_text`, `summary` now default `false`
+]
+
+#slide("Paper Draft")[
+  *First Table of Content draft started*
+
+  #v(0.3cm)
+  *also: Prediction Notebook Refactored*
+  + `analysis/HRF_Prediction.ipynb` restructured
+  + Pipeline runs within the notebook
+  + Cleaner separation between analysis and reporting
+  + No notable Performance improvements, even though cleanup ran and more features available #sym.arrow more investigation needed
+]
+
+#slide("Summary & Next Steps")[
+  #columns(2, gutter: 1.5em)[
+    *What I did:*
+    + Preprocessing (closing, hole filling)
+    + Per-segment volume & surface area
+    + 3D thinning speedups (parallel scanning, epoch tracking)
+    + Benchmark scripts (2D + 3D)
+    + CLI polish (shorter cmds, worker feedback)
+    + Table of Content draft
+    + Feature table finalized
+    + Prediction notebook refactored
+
+    #colbreak()
+
+    *Next steps:*
+    + per_node features finalization
+    + finalize Phenotype Prediction
+    + nice documentation
+    + Write the paper
+    + (optional) more tests
+  ]
+]