diffusion-cartogram 0.2.0__tar.gz → 0.2.2__tar.gz

diffusion_cartogram-0.2.2/CHANGELOG.md

@@ -0,0 +1,80 @@
+# Changelog
+
+## [0.2.2] - 2026-08-31
+
+### New: Additional reconstruction options
+
+- **Added** `load_mesh_topology(mesh_path)`: loads a mesh's own vertices,
+  faces, and per-vertex normals with **no resampling**. This is the new
+  default entry point for the deformation pipeline (replaces `create_pcd` as
+  the "get me surface points" call for most users; `create_pcd` still exists
+  unchanged for anyone who wants a lighter/resampled point cloud, or as the
+  Poisson fallback's input).
+- **Modified** `export_mesh_file(filename, deformed_pcd, ...)`:
+  - New parameters: `method='none'` (new default), `original_faces=None`.
+  - `method='none'`: requires `original_faces`; if given, saves
+    `(deformed_pcd, original_faces)` directly via
+    `pymeshlab.Mesh(vertex_matrix=..., face_matrix=...)` -- no reconstruction. 
+  - If `method='none'` but `original_faces` is `None`: emits a
+    `RuntimeWarning` and **falls back to `method='poisson'`** (the prior,
+    only, behavior) automatically.
+  - `method='poisson'`: unchanged prior behavior (screened Poisson
+    reconstruction with estimated normals), reachable explicitly or via the
+    automatic fallback above.
+  - Added `method='ball_pivoting'` and `method='alpha_shape'` alongside `'none'`/  `'poisson'`. New parameters, all with defaults matching pymeshlab's own except `alpha_filtering`. `ball_radius=0.0` (0% = auto-estimated), `ball_clustering=20.0`, `ball_creasethr=90.0`, `ball_deletefaces=False`, `alpha=1.0`, `alpha_filtering='Alpha Shape'` (pymeshlab's own filter default is `'Alpha Complex'`, deliberately overridden -- `'Alpha Complex'` retains interior simplicial-complex faces, not just the outer boundary).
+  - Backward compatible: existing callers that only ever passed
+    `(filename, deformed_pcd)` keep working exactly as before, just now with
+    a printed warning nudging them toward the no-reconstruction path.
+  
+
+## [0.2.1] - 2026-07-31
+
+### New: Post hoc animation 
+- **`animate_surface_posthoc`** - Interpolate the final displacement field and densities to create an animation for display purposes. Faster than running with tracking but not guaranteed to be accurate at intermediate steps
+- **`animate_map_posthoc`** - Same function implemented for 2D maps
+
+## [0.2.0] - 2026-04-29
+
+### New: 2D VDERM Pipeline
+
+- **`VDERMGrid2D`** — 2-D Lagrangian-Eulerian grid; same physics as `VDERMGrid` (diffusion + gradient advection) with one dimension removed. Compatible with the existing `run_VDERM()` function.
+- **`run_VDERM_2d_with_tracking()`** — tracking run with grid and map-point exports (CSV format: `x y v_x v_y rho` for grid, `x y rho` for map points).
+- **`make_initial_grid_2d()`** / **`compute_grid_dimensions_2d()`** / **`print_grid_info_2d()`** — 2-D grid utilities mirroring the 3-D equivalents.
+- **`interpolate_to_map_2d()`** / **`interpolate_densities_2d()`** / **`interpolate_velocities_2d()`** — 2-D interpolation from grid to arbitrary point sets.
+
+### New: Geographic I/O (`pip install diffusion-cartogram[2D]`)
+
+- **`read_geojson(filepath)`** — extract 2-D point array from GeoJSON (polygon boundaries, point features, line features).
+- **`read_shapefile(filepath)`** — same for Shapefiles.
+- **`read_geotiff(filepath, band=1)`** — read a raster band plus coordinate arrays.
+- **`density_from_geotiff(grid_2d, filepath)`** — sample a GeoTIFF raster onto a `VDERMGrid2D` density field with bilinear interpolation; handles north-up rasters and nodata automatically.
+- **`write_csv_2d()`** / **`read_csv_2d()`** — simple 2-column / 3-column CSV I/O for 2-D point sets.
+
+### New: 2D Visualization
+
+- **`plot_map_2d()`** — scatter plot of 2-D points with optional density colouring.
+- **`plot_density_field_2d()`** — heatmap of the `VDERMGrid2D` density field.
+- **`plot_map_before_after()`** — side-by-side comparison of original and deformed map.
+- **`animate_map_deformation_2d()`** — GIF / MP4 animation from `vderm_map/` CSV exports.
+- **`animate_grid_deformation_2d()`** — GIF / MP4 animation from `vderm_grid/` CSV exports.
+- **`plot_density_evolution_2d()`** — density statistics over iterations.
+
+### Packaging
+
+- Version bumped to **0.2.0**.
+- New optional dependency group **`[2D]`**: geopandas, rasterio, shapely.
+- New optional dependency group **`[3D]`**: pymeshlab.
+- New optional dependency group **`[all]`**: `[2D]` + `[3D]`.
+- `pyproject.toml` now points `readme` at `README_pypi.md` (no embedded GIF) for PyPI; `README.md` remains the full GitHub README.
+
+## [0.1.0] - 2026-02-09
+
+### Initial Release
+
+- Core VDERM algorithm implementation
+- Flexible XYZ file I/O
+- Optional mesh support via PyMeshLab
+- Visualization and animation tools
+- Tracking with intermediate exports
+- ParaView export capabilities
+- Comprehensive example notebooks

diffusion_cartogram-0.2.2/MANIFEST.in

@@ -0,0 +1,23 @@
+# Include essential files
+include README.md
+include LICENSE
+include CHANGELOG.md
+
+# Include package code
+recursive-include diffusion_cartogram *.py
+
+# Exclude examples, tests, and large files
+prune examples
+prune tests
+global-exclude *.stl
+global-exclude *.obj
+global-exclude *.ply
+global-exclude *.xyz
+global-exclude *.gif
+global-exclude *.mp4
+global-exclude *.png
+global-exclude *.jpg
+global-exclude .git*
+global-exclude __pycache__
+global-exclude *.pyc
+global-exclude .DS_Store

{diffusion_cartogram-0.2.0/diffusion_cartogram.egg-info → diffusion_cartogram-0.2.2}/PKG-INFO

@@ -1,9 +1,29 @@
 Metadata-Version: 2.4
 Name: diffusion-cartogram
-Version: 0.2.0
+Version: 0.2.2
 Summary: Volumetric Density-Equalizing Reference Map — 3D shape deformation and 2D cartogram generation
 Author-email: Jonah Spector <spector.jo@northeastern.edu>
-License-Expression: MIT
+License: MIT License
+        
+        Copyright (c) 2026 Jonah Spector
+        
+        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.
 Project-URL: Homepage, https://github.com/jspector792/diffusion-cartogram
 Project-URL: Repository, https://github.com/jspector792/diffusion-cartogram
 Project-URL: Issues, https://github.com/jspector792/diffusion-cartogram/issues

{diffusion_cartogram-0.2.0 → diffusion_cartogram-0.2.2}/README.md

@@ -253,8 +253,8 @@ If you use this package in academic work, please cite the appropriate original p
 And optionally, this implementation:
 ```bibtex
 @software{vderm2026,
-  title={diffusion-cartogram: A Python implementation of Volumetric Density-Equalizing Reference Map},
-  author={Jonah Spector},
+  title={diffusion-cartogram: A Python package for diffusion deformations in 2 and 3 dimensions},
+  author={Jonah Spector and Albert-László Barabási},
   year={2026},
   url={https://github.com/jspector792/diffusion-cartogram}
 }

{diffusion_cartogram-0.2.0 → diffusion_cartogram-0.2.2}/diffusion_cartogram/__init__.py

@@ -29,13 +29,14 @@ cartogram deformation from GeoJSON / Shapefile inputs.
 >>> vd.plot_map_2d(deformed, title='Population Cartogram')
 """
 
-__version__ = '0.2.0'
+__version__ = '0.2.2'
 
 # Core VDERM classes and algorithms
 from .core import (
     VDERMGrid,
     run_VDERM,
     run_VDERM_with_tracking,
+    animate_surface_posthoc,
 )
 
 # I/O functions
@@ -43,6 +44,7 @@ from .core import (
     write_xyz,
     read_xyz,
     create_pcd,
+    load_mesh_topology,
     export_mesh_file,
     export_mesh_vtk,
 )
@@ -85,11 +87,13 @@ __all__ = [
     'VDERMGrid',
     'run_VDERM',
     'run_VDERM_with_tracking',
-    
+    'animate_surface_posthoc',
+
     # I/O
     'write_xyz',
     'read_xyz',
     'create_pcd',
+    'load_mesh_topology',
     'export_mesh_file',
     'export_mesh_vtk',
     
@@ -126,6 +130,7 @@ if _has_visualization:
 from .core_2d import (
     VDERMGrid2D,
     run_VDERM_2d_with_tracking,
+    animate_map_posthoc,
 )
 
 # 2-D grid utilities
@@ -172,7 +177,8 @@ __all__ += [
     # 2-D classes and algorithms
     'VDERMGrid2D',
     'run_VDERM_2d_with_tracking',
-    # 2-D grid utilities
+    'animate_map_posthoc',
+# 2-D grid utilities
     'compute_grid_dimensions_2d',
     'make_initial_grid_2d',
     'print_grid_info_2d',