diff --git a/README.md b/README.md
index 1930a81..ab43559 100644
--- a/README.md
+++ b/README.md
@@ -56,12 +56,8 @@ Group website: https://murphy-group.chemistry.illinois.edu/
## Notes:
- DO NOT double-click on RodSizer_CLEANER_MacOS.command unless you are sure that you want to clean ALL local history of data and reports.
-- First-time launching may take some time, like 5-10 mins. Most of that is
- installing the deep-learning packages (`tensorflow` + `stardist`, ~1 GB). These
- are kept for possible future ML-based detection but are **not used** by the
- current pipeline (K-means + watershed), so the wait is one-time setup only —
- later launches are fast. See `backend/requirements.txt` to remove them if you
- want a leaner install.
+- First-time launching takes a few minutes (typically 2-3) while Python
+ packages are installed. This is one-time setup only — later launches are fast.
- Try ask a coding agent if there's an issue with environment setup.
- MacOS is more recommended.
- (Windows) If Windows Defender asks, click `More Info` -> `Run Anyway`.
@@ -88,4 +84,4 @@ Group website: https://murphy-group.chemistry.illinois.edu/
## Requirements
- macOS or Windows
-- Python 3 installed (standard on most Macs, or downloadable from `python.org`)
+- Python 3.10-3.12 (the Mac launcher installs it automatically if missing; on Windows download from `python.org`)
diff --git a/RodSizer_DEBUG_Windows.bat b/RodSizer_DEBUG_Windows.bat
index 5f13165..e55bd80 100644
--- a/RodSizer_DEBUG_Windows.bat
+++ b/RodSizer_DEBUG_Windows.bat
@@ -32,9 +32,11 @@ REM Auto-Detect
if exist "C:\Python39\python.exe" set "PY_EXE=C:\Python39\python.exe" & goto FOUND_PYTHON
if exist "C:\Python310\python.exe" set "PY_EXE=C:\Python310\python.exe" & goto FOUND_PYTHON
if exist "C:\Python311\python.exe" set "PY_EXE=C:\Python311\python.exe" & goto FOUND_PYTHON
+if exist "C:\Python312\python.exe" set "PY_EXE=C:\Python312\python.exe" & goto FOUND_PYTHON
if exist "C:\Program Files\Python39\python.exe" set "PY_EXE=C:\Program Files\Python39\python.exe" & goto FOUND_PYTHON
if exist "C:\Program Files\Python310\python.exe" set "PY_EXE=C:\Program Files\Python310\python.exe" & goto FOUND_PYTHON
if exist "C:\Program Files\Python311\python.exe" set "PY_EXE=C:\Program Files\Python311\python.exe" & goto FOUND_PYTHON
+if exist "C:\Program Files\Python312\python.exe" set "PY_EXE=C:\Program Files\Python312\python.exe" & goto FOUND_PYTHON
:ASK_USER
echo.
diff --git a/RodSizer_Launcher_MacOS.command b/RodSizer_Launcher_MacOS.command
index b33ea75..b5aa3e0 100755
--- a/RodSizer_Launcher_MacOS.command
+++ b/RodSizer_Launcher_MacOS.command
@@ -74,65 +74,47 @@ if command -v tesseract &>/dev/null; then
fi
# =============================================================================
-# STEP 2 — Python 3.11
-#
-# TensorFlow 2.x officially supports Python 3.8–3.11.
-# Python 3.12+ does NOT have stable TensorFlow wheels yet.
-# We therefore require Python 3.11 specifically.
+# STEP 2 — Python 3.10-3.12
+# (the pinned dependency set in backend/requirements.txt targets these
+# versions; 3.13+ lacks wheels for the pinned numpy)
# =============================================================================
-step "Step 2/4: Checking Python 3.11"
+step "Step 2/4: Checking Python"
PYTHON_CMD=""
-# Helper: find python3.11 by checking all known locations
-find_python311() {
- # 1. Homebrew-managed path (most reliable — works regardless of PATH)
- local brew_prefix
- brew_prefix="$(brew --prefix python@3.11 2>/dev/null)"
- if [ -n "$brew_prefix" ] && [ -x "$brew_prefix/bin/python3.11" ]; then
- echo "$brew_prefix/bin/python3.11"; return
- fi
-
- # 2. Direct binary in PATH
- if command -v python3.11 &>/dev/null; then
- command -v python3.11; return
- fi
-
- # 3. Common Homebrew Cellar fallback (Apple Silicon)
- local cellar_py
- cellar_py=$(ls /opt/homebrew/Cellar/python@3.11/*/bin/python3.11 2>/dev/null | sort -V | tail -1)
- if [ -x "$cellar_py" ]; then
- echo "$cellar_py"; return
- fi
- # Intel
- cellar_py=$(ls /usr/local/Cellar/python@3.11/*/bin/python3.11 2>/dev/null | sort -V | tail -1)
- if [ -x "$cellar_py" ]; then
- echo "$cellar_py"; return
- fi
-
- # 4. pyenv
- if command -v pyenv &>/dev/null; then
- local pyenv_ver
- pyenv_ver=$(pyenv versions --bare 2>/dev/null | grep "^3\.11\." | sort -V | tail -1)
- if [ -n "$pyenv_ver" ]; then
- local pyenv_py="$(pyenv root)/versions/$pyenv_ver/bin/python3.11"
- [ -x "$pyenv_py" ] && echo "$pyenv_py"; return
+# Helper: find a suitable Python (3.10-3.12), preferring newer versions
+find_python() {
+ local candidate
+ for candidate in python3.12 python3.11 python3.10 python3; do
+ if command -v "$candidate" &>/dev/null; then
+ if "$candidate" -c 'import sys; sys.exit(0 if (3, 10) <= sys.version_info[:2] <= (3, 12) else 1)' &>/dev/null; then
+ command -v "$candidate"; return
+ fi
fi
- fi
+ done
+
+ # Homebrew-managed fallback (works regardless of PATH)
+ local brew_prefix ver
+ for ver in 3.12 3.11 3.10; do
+ brew_prefix="$(brew --prefix python@$ver 2>/dev/null)"
+ if [ -n "$brew_prefix" ] && [ -x "$brew_prefix/bin/python$ver" ]; then
+ echo "$brew_prefix/bin/python$ver"; return
+ fi
+ done
}
-PYTHON_CMD="$(find_python311)"
+PYTHON_CMD="$(find_python)"
# If still not found, install via Homebrew then retry
if [ -z "$PYTHON_CMD" ]; then
- warn "Python 3.11 not found. Installing via Homebrew (needed for TensorFlow)..."
- brew install python@3.11
- PYTHON_CMD="$(find_python311)"
+ warn "Python 3.10-3.12 not found. Installing 3.12 via Homebrew..."
+ brew install python@3.12
+ PYTHON_CMD="$(find_python)"
fi
if [ -z "$PYTHON_CMD" ] || [ ! -x "$PYTHON_CMD" ]; then
- error "Could not find or install Python 3.11."
- error "Please install it manually: brew install python@3.11"
+ error "Could not find or install Python."
+ error "Please install it manually: brew install python@3.12"
echo "Press Enter to close..."; read -r; exit 1
fi
@@ -170,84 +152,21 @@ needs_python_packages() {
"$VENV_PYTHON" - <<'PY' &>/dev/null
import importlib
-for name in ("fastapi", "uvicorn", "tensorflow", "numpy", "cv2", "stardist"):
+for name in ("fastapi", "uvicorn", "numpy", "cv2", "skimage", "tifffile", "h5py"):
importlib.import_module(name)
PY
}
-install_tensorflow_with_fallback() {
- local tf_spec="tensorflow==2.21.0"
-
- info "Installing TensorFlow..."
- if "$VENV_PYTHON" -m pip install "$tf_spec"; then
- return 0
- fi
-
- warn "pip could not resolve tensorflow from the package index."
- warn "Retrying TensorFlow install directly from PyPI..."
- PIP_CONFIG_FILE=/dev/null "$VENV_PYTHON" -m pip install --index-url https://pypi.org/simple "$tf_spec" && return 0
-
- return 1
-}
-
# Check whether a first-time install is needed
if ! needs_python_packages; then
- info "Installing Python packages — this may take 5–10 minutes on first run."
+ info "Installing Python packages — this may take 2–3 minutes on first run."
info "Please do NOT close this window."
# Upgrade pip / setuptools silently
"$VENV_PYTHON" -m pip install --upgrade pip setuptools wheel --quiet
- # ── TensorFlow first (sets numpy version constraint everything else must follow) ──
- #
- # tensorflow-macos was deprecated at 2.13 and forces numpy<2, which conflicts
- # with opencv-python-headless >=4.9 and ncempy >=1.15 (both require numpy>=2).
- #
- # tensorflow >= 2.16 ships a universal wheel that runs natively on Apple
- # Silicon (M-series) without a separate macos fork, and is compatible with
- # numpy 2.x. tensorflow-metal is still the GPU-acceleration plugin for M-chips.
- if ! install_tensorflow_with_fallback; then
- error "TensorFlow installation failed."
- error "This is usually a package-index or network issue, not a RodSizer code issue."
- if [ "$IS_APPLE_SILICON" = true ]; then
- error "If needed, try this manually inside backend/.venv:"
- error " python -m pip install --index-url https://pypi.org/simple tensorflow==2.21.0"
- else
- error "Try rerunning later, or install TensorFlow manually inside backend/.venv."
- fi
- echo "Press Enter to close..."; read -r; exit 1
- fi
-
- # Note: tensorflow-metal is NOT installed because v1.2.0 is incompatible
- # with tensorflow >=2.16 (dlopen fails on _pywrap_tensorflow_internal.so).
- # Modern TensorFlow already runs natively on Apple Silicon without it.
-
- if ! "$VENV_PYTHON" -c "import tensorflow" &>/dev/null 2>&1; then
- error "TensorFlow import failed after installation."
- error "Try deleting backend/.venv and relaunching, or check network connectivity."
- echo "Press Enter to close..."; read -r; exit 1
- fi
-
- # ── Remaining packages (numpy version is now fixed by TF above) ─────────────
- TMP_REQ=$(mktemp /tmp/rodsizer_req_XXXX.txt)
- grep -v "^tensorflow" "$BACKEND_DIR/requirements.txt" > "$TMP_REQ"
-
- if ! "$VENV_PYTHON" -m pip install -r "$TMP_REQ" --quiet; then
+ if ! "$VENV_PYTHON" -m pip install -r "$BACKEND_DIR/requirements.txt" --quiet; then
error "Failed to install some packages. Check the output above."
- rm -f "$TMP_REQ"
- echo "Press Enter to close..."; read -r; exit 1
- fi
- rm -f "$TMP_REQ"
-
- # ── Verify tensorflow is importable ───────────────────────────────────────
- if ! "$VENV_PYTHON" -c "import tensorflow" &>/dev/null 2>&1; then
- error "TensorFlow installation failed."
- error "Try running this manually inside the venv:"
- if [ "$IS_APPLE_SILICON" = true ]; then
- error " python -m pip install --index-url https://pypi.org/simple tensorflow==2.21.0"
- else
- error " python -m pip install tensorflow==2.21.0"
- fi
echo "Press Enter to close..."; read -r; exit 1
fi
diff --git a/RodSizer_Launcher_Windows.bat b/RodSizer_Launcher_Windows.bat
index 1273e89..8a5b50e 100644
--- a/RodSizer_Launcher_Windows.bat
+++ b/RodSizer_Launcher_Windows.bat
@@ -29,9 +29,11 @@ REM --- 3. Try Auto-Detect Common Paths ---
if exist "C:\Python39\python.exe" set "PY_EXE=C:\Python39\python.exe" & goto FOUND_PYTHON
if exist "C:\Python310\python.exe" set "PY_EXE=C:\Python310\python.exe" & goto FOUND_PYTHON
if exist "C:\Python311\python.exe" set "PY_EXE=C:\Python311\python.exe" & goto FOUND_PYTHON
+if exist "C:\Python312\python.exe" set "PY_EXE=C:\Python312\python.exe" & goto FOUND_PYTHON
if exist "C:\Program Files\Python39\python.exe" set "PY_EXE=C:\Program Files\Python39\python.exe" & goto FOUND_PYTHON
if exist "C:\Program Files\Python310\python.exe" set "PY_EXE=C:\Program Files\Python310\python.exe" & goto FOUND_PYTHON
if exist "C:\Program Files\Python311\python.exe" set "PY_EXE=C:\Program Files\Python311\python.exe" & goto FOUND_PYTHON
+if exist "C:\Program Files\Python312\python.exe" set "PY_EXE=C:\Program Files\Python312\python.exe" & goto FOUND_PYTHON
REM --- 4. User Input Fallback ---
:ASK_USER
diff --git a/backend/requirements.txt b/backend/requirements.txt
index ee2d12c..1c30e9a 100644
--- a/backend/requirements.txt
+++ b/backend/requirements.txt
@@ -1,24 +1,24 @@
-fastapi
-uvicorn
-python-multipart
-numpy
-opencv-python-headless
-scikit-image
-ncempy
-matplotlib
-pandas
-Pillow
-pytesseract
-tifffile
-openpyxl
-h5py
+# Pinned, known-good dependency set (tested on Python 3.12, July 2026).
+# Pinning exact versions keeps every computer running identical code —
+# unpinned installs were a major source of "works here, not there" bugs.
+# Python 3.10-3.12 required (numpy 1.26 has no wheels for 3.13+).
+fastapi==0.122.0
+uvicorn==0.38.0
+python-multipart==0.0.20
+numpy==1.26.4
+opencv-python-headless==4.12.0.88
+scikit-image==0.25.2
+ncempy==1.14
+matplotlib==3.10.7
+pandas==2.3.3
+Pillow==12.0.0
+pytesseract==0.3.13
+tifffile==2025.10.16
+openpyxl==3.1.5
+h5py==3.15.1
-# --- Heavy deps kept for possible future ML detection (NOT used right now) ---
-# stardist + tensorflow are the main reason the FIRST-TIME setup is slow (~5-10
-# min) and large (~1 GB+): they pull in a full TensorFlow build. The current
-# detection pipeline is K-means + distance-transform watershed and does NOT use
-# them (they are imported nowhere in the hot path). They are kept on purpose in
-# case StarDist-based detection is added later. Remove these two lines if you
-# want a much faster, smaller install and don't plan to use StarDist.
-stardist
-tensorflow
+# NOTE: stardist + tensorflow were removed (July 2026). Nothing in the current
+# pipeline (K-means + distance-transform watershed) uses them, and they were the
+# main reason first-time setup was slow (~5-10 min, ~1 GB) and failed on some
+# machines (no TensorFlow wheels for newer Python versions). If StarDist-based
+# detection is ever added, re-add: stardist and tensorflow
diff --git a/frontend/folder_analysis.html b/frontend/folder_analysis.html
index d383a03..2c019ae 100644
--- a/frontend/folder_analysis.html
+++ b/frontend/folder_analysis.html
@@ -278,11 +278,11 @@ Batch Ledger
- | Source Image |
- ID |
- L (nm) |
- W (nm) |
- AR |
+ Source Image |
+ ID |
+ L (nm) |
+ W (nm) |
+ AR |
@@ -308,6 +308,8 @@ Batch Ledger
dlBtn.href = `/folders/${encodeURIComponent(folderName)}/export_aggregate`;
let lengthChart, widthChart;
+ let currentData = [];
+ let currentSort = { column: null, direction: 'asc' };
async function loadAggregateData() {
try {
@@ -338,14 +340,41 @@ Batch Ledger
document.getElementById('meanAR').textContent = data.stats.mean_ar || "-";
// Charts
- const items = data.data;
+ currentData = data.data || [];
+ const items = currentData;
const lengths = items.map(d => d.length_nm);
const widths = items.map(d => d.width_nm);
lengthChart = createHistogram('lengthChart', 'Length Distribution', lengths);
widthChart = createHistogram('widthChart', 'Width Distribution', widths);
- // Table
+ renderTable();
+ }
+
+ function renderTable() {
+ let items = currentData.slice();
+
+ if (currentSort.column) {
+ const col = currentSort.column;
+ const dir = currentSort.direction === 'asc' ? 1 : -1;
+ items.sort((a, b) => {
+ const va = a[col], vb = b[col];
+ if (typeof va === 'string' || typeof vb === 'string') {
+ return String(va ?? '').localeCompare(String(vb ?? '')) * dir;
+ }
+ return ((va ?? 0) - (vb ?? 0)) * dir;
+ });
+ }
+
+ // Update header arrows
+ document.querySelectorAll('#dataTable .sort-arrow').forEach(span => {
+ if (span.dataset.col === currentSort.column) {
+ span.textContent = currentSort.direction === 'asc' ? '▲' : '▼';
+ } else {
+ span.textContent = '';
+ }
+ });
+
const tbody = document.querySelector('#dataTable tbody');
tbody.innerHTML = '';
items.forEach(item => {
@@ -366,6 +395,16 @@ Batch Ledger
});
}
+ function sortTable(column) {
+ if (currentSort.column === column) {
+ currentSort.direction = currentSort.direction === 'asc' ? 'desc' : 'asc';
+ } else {
+ currentSort.column = column;
+ currentSort.direction = 'asc';
+ }
+ renderTable();
+ }
+
function createHistogram(canvasId, label, data) {
const ctx = document.getElementById(canvasId).getContext('2d');
if (!data.length) return;