wellcrop 0.1.0__tar.gz

wellcrop-0.1.0/.gitignore

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wellcrop-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2026 Arseni
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

wellcrop-0.1.0/PKG-INFO

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+Metadata-Version: 2.5
+Name: wellcrop
+Version: 0.1.0
+Summary: A computer vision utility for automated detection, alignment, and extraction of wells from multi-well plate scans.
+Author: Districtfine
+License-Expression: MIT
+License-File: LICENSE
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Image Processing
+Requires-Python: >=3.9
+Requires-Dist: numpy>=1.22.0
+Requires-Dist: opencv-python>=4.5.0
+Requires-Dist: scipy>=1.9.0
+Provides-Extra: dev
+Requires-Dist: matplotlib>=3.5.0; extra == 'dev'
+Requires-Dist: pytest>=7.0.0; extra == 'dev'
+Requires-Dist: tifffile>=2023.1.0; extra == 'dev'
+Provides-Extra: viz
+Requires-Dist: matplotlib>=3.5.0; extra == 'viz'
+Description-Content-Type: text/markdown
+
+# wellcrop
+
+A lightweight computer vision utility for automated detection, alignment, and extraction of individual wells from multi-well plate scans.
+
+---
+
+## Highlights
+
+* 🔍 **Shift & Skew Tolerant:** Accommodates hand-placed plates on flatbed scanners via directional gradient edge snapping and 2D affine grid estimation.
+* 🎯 **Hough Ring Locking:** Snaps analytic well centers to physical plastic rims via localized Hough circle transforms.
+* ✂️ **Automatic Masking:** Crops and isolates pure circular wells, shaving off outer plastic rims and blacking out corners.
+* 🪶 **Zero Heavy AI Dependencies:** No PyTorch, CUDA, or model weights required. Built purely on `numpy`, `opencv-python`, and `scipy`.
+
+---
+
+## Installation
+
+```bash
+pip install wellcrop
+```
+
+---
+
+## Quickstart
+
+```python
+import tifffile as tifi
+import wellcrop
+
+# 1. Load scan image
+image = tifi.imread("plate_scan.tif")
+
+# 2. Define ROI hints (fractions in [0, 1] drawn once on a reference scan)
+roi_hints = [
+    {"x": 0.05, "y": 0.08, "w": 0.40, "h": 0.84, "rows": 3, "cols": 2, "letter": "A"}
+]
+
+# 3. Detect & extract well crops
+detector = wellcrop.PlateDetector(margin_frac=0.20)
+wells = detector.crop(image, roi_hints=roi_hints)
+
+# 4. Access individual well crops and metadata
+for well in wells:
+    print(f"Well {well.label}: center=({well.x}, {well.y}), radius={well.radius}px")
+    # well.image is a circular-masked NumPy RGB array
+    well.save(f"output/{well.label}.png")
+```
+
+---
+
+## Visual QA Overlay
+
+Generate diagnostic overlays (showing padded search boxes, detected plate boxes, and snapped well rings):
+
+```python
+import cv2
+
+# Draw overlay directly onto the scan
+overlay = wellcrop.draw_overlay(image, wells, roi_hints=roi_hints)
+cv2.imwrite("grid_preview.png", cv2.cvtColor(overlay, cv2.COLOR_RGB2BGR))
+```
+
+---
+
+## How it Works
+
+1. **ROI-Scoped Search:** Expands the user's initial approximate plate bounding box by `margin_frac` to absorb scanner placement shift.
+2. **Directional Edge Snapping:** Projects Sobel gradients along vertical and horizontal axes to find true plate walls, reconciling them under rigid geometry constraints.
+3. **Stacked Plate Reconciliation:** Identifies shared dividing ribs for multi-tray formats so vertically stacked plates never overlap.
+4. **Grid Estimation & Ring Snapping:** Computes analytic well centers, locks physical rims with local Hough circle searches, and fits a 2D affine transform to absorb plate rotation.
+5. **Rim Trimming & Masking:** Shaves outer plastic rims and masks corners so downstream analyzers only see pure well contents.
+
+---
+
+## License
+
+MIT License. See [LICENSE](LICENSE) for details.

wellcrop-0.1.0/README.md

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+# wellcrop
+
+A lightweight computer vision utility for automated detection, alignment, and extraction of individual wells from multi-well plate scans.
+
+---
+
+## Highlights
+
+* 🔍 **Shift & Skew Tolerant:** Accommodates hand-placed plates on flatbed scanners via directional gradient edge snapping and 2D affine grid estimation.
+* 🎯 **Hough Ring Locking:** Snaps analytic well centers to physical plastic rims via localized Hough circle transforms.
+* ✂️ **Automatic Masking:** Crops and isolates pure circular wells, shaving off outer plastic rims and blacking out corners.
+* 🪶 **Zero Heavy AI Dependencies:** No PyTorch, CUDA, or model weights required. Built purely on `numpy`, `opencv-python`, and `scipy`.
+
+---
+
+## Installation
+
+```bash
+pip install wellcrop
+```
+
+---
+
+## Quickstart
+
+```python
+import tifffile as tifi
+import wellcrop
+
+# 1. Load scan image
+image = tifi.imread("plate_scan.tif")
+
+# 2. Define ROI hints (fractions in [0, 1] drawn once on a reference scan)
+roi_hints = [
+    {"x": 0.05, "y": 0.08, "w": 0.40, "h": 0.84, "rows": 3, "cols": 2, "letter": "A"}
+]
+
+# 3. Detect & extract well crops
+detector = wellcrop.PlateDetector(margin_frac=0.20)
+wells = detector.crop(image, roi_hints=roi_hints)
+
+# 4. Access individual well crops and metadata
+for well in wells:
+    print(f"Well {well.label}: center=({well.x}, {well.y}), radius={well.radius}px")
+    # well.image is a circular-masked NumPy RGB array
+    well.save(f"output/{well.label}.png")
+```
+
+---
+
+## Visual QA Overlay
+
+Generate diagnostic overlays (showing padded search boxes, detected plate boxes, and snapped well rings):
+
+```python
+import cv2
+
+# Draw overlay directly onto the scan
+overlay = wellcrop.draw_overlay(image, wells, roi_hints=roi_hints)
+cv2.imwrite("grid_preview.png", cv2.cvtColor(overlay, cv2.COLOR_RGB2BGR))
+```
+
+---
+
+## How it Works
+
+1. **ROI-Scoped Search:** Expands the user's initial approximate plate bounding box by `margin_frac` to absorb scanner placement shift.
+2. **Directional Edge Snapping:** Projects Sobel gradients along vertical and horizontal axes to find true plate walls, reconciling them under rigid geometry constraints.
+3. **Stacked Plate Reconciliation:** Identifies shared dividing ribs for multi-tray formats so vertically stacked plates never overlap.
+4. **Grid Estimation & Ring Snapping:** Computes analytic well centers, locks physical rims with local Hough circle searches, and fits a 2D affine transform to absorb plate rotation.
+5. **Rim Trimming & Masking:** Shaves outer plastic rims and masks corners so downstream analyzers only see pure well contents.
+
+---
+
+## License
+
+MIT License. See [LICENSE](LICENSE) for details.

wellcrop-0.1.0/pyproject.toml

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+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[project]
+name = "wellcrop"
+version = "0.1.0"
+description = "A computer vision utility for automated detection, alignment, and extraction of wells from multi-well plate scans."
+readme = "README.md"
+license = "MIT"
+requires-python = ">=3.9"
+authors = [
+    { name = "Districtfine" }
+]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "Topic :: Scientific/Engineering :: Image Processing",
+    "License :: OSI Approved :: MIT License",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+]
+dependencies = [
+    "numpy>=1.22.0",
+    "opencv-python>=4.5.0",
+    "scipy>=1.9.0",
+]
+
+[project.optional-dependencies]
+dev = [
+    "pytest>=7.0.0",
+    "tifffile>=2023.1.0",
+    "matplotlib>=3.5.0",
+]
+viz = [
+    "matplotlib>=3.5.0",
+]
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/wellcrop"]

wellcrop-0.1.0/src/wellcrop/__init__.py

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+"""wellcrop: A computer vision utility for automated detection, alignment, and extraction of wells from multi-well plate scans."""
+
+from .detector import PlateDetector, detect_wells_from_rois
+from .edges import (
+    detect_plate_rect_edges,
+    reconcile_vertical_borders,
+    resolve_axis,
+    snap_edge,
+)
+from .geometry import pad_box, roi_frac_to_px, well_grid_fracs
+from .grid import fit_grid_axis, fit_grid_transform, place_wells
+from .refine import refine_well
+from .visualization import draw_overlay, render_overlay_matplotlib
+from .well import Well
+
+__version__ = "0.1.0"
+
+__all__ = [
+    "PlateDetector",
+    "Well",
+    "detect_wells_from_rois",
+    "draw_overlay",
+    "render_overlay_matplotlib",
+    "refine_well",
+    "place_wells",
+    "fit_grid_axis",
+    "fit_grid_transform",
+    "detect_plate_rect_edges",
+    "snap_edge",
+    "resolve_axis",
+    "reconcile_vertical_borders",
+    "roi_frac_to_px",
+    "pad_box",
+    "well_grid_fracs",
+]