Raster reconstruction changes (#65)

* Partial rewrite of reconstruct_grid `gplately.grids.reconstruct_grid` now uses `scipy.spatial.transform.Rotation` to perform rotations and `scipy.spatial.cKDTree` for nearest-neighbour interpolation after rotation. * Raster reconstruction tweaks Minor changes to raster reconstruction, including: * Add `inplace` argument to `Raster.reconstruct` * Allow matplotlib colour strings for `fill_value` * For 3D colour images, check values are within valid ranges * Add _parse_extent_origin function Extract `extent` and `origin` parameter handling for several functions and methods to a new `_parse_extent_origin` function. * Update raster documentation and notebook Update documentation for `Raster` and `reconstruct_grid`, and edit and re-run `06-Rasters.ipynb`. * Update Raster time when reconstructing in-place * Update raster tests Add `test_reverse_reconstruct` to check that reverse reconstruction is working well, and make sure that plate models other than Muller2019 are available. * Update Raster signatures Switch calls to `Raster` from `array` or `filename` to `data`. Also re-run affected notebooks.
GPlates · Feb 23, 2023 · d7e90db · d7e90db
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diff --git a/.gitignore b/.gitignore
@@ -2,3 +2,4 @@
 gplately.egg-info
 build
 __pycache__
+.ipynb_checkpoints
diff --git a/Notebooks/01-GettingStarted.ipynb b/Notebooks/01-GettingStarted.ipynb
diff --git a/Notebooks/04-VelocityBasics.ipynb b/Notebooks/04-VelocityBasics.ipynb
diff --git a/Notebooks/06-Rasters.ipynb b/Notebooks/06-Rasters.ipynb
diff --git a/Notebooks/08-PredictingSlabDip.ipynb b/Notebooks/08-PredictingSlabDip.ipynb
diff --git a/Notebooks/NotebookFiles/.gitignore b/Notebooks/NotebookFiles/.gitignore
@@ -1 +1,4 @@
 reconstructed_etopo.nc
+GlobalAveragePlateVelocities.csv
+average_plate_velocity.pdf
+India_collision.pdf
diff --git a/README.md b/README.md
@@ -151,7 +151,7 @@ relief rasters. You can also reconstruct raster data back through geological tim
 ```python
 time = 0
 agegrid = gdownload.get_age_grid(time)
-graster = gplately.Raster(model, array=agegrid, extent=[-180,180,-90,90])
+graster = gplately.Raster(model, data=agegrid, extent=[-180,180,-90,90])
 ```
 
 Below is a plot of the original Müller et al. (2019) age grid (L) and an age-grid resampled with the `Raster` object (R):

diff --git a/gplately/download.py b/gplately/download.py
@@ -1315,7 +1315,7 @@ def get_raster(self, raster_id_string=None):
         else:
             # If the downloaded raster is a grid, process it with the gplately.Raster object
             if any(grid_extension in raster_filenames for grid_extension in grid_extensions):
-                raster_matrix = _gplately.grids.Raster(filename=raster_filenames).data
+                raster_matrix = _gplately.grids.Raster(data=raster_filenames).data
 
             # Otherwise, the raster is an image; use imread to process
             else: