From ccfe276ae1283a2806b0b1dd9ad08119d7371b7e Mon Sep 17 00:00:00 2001
From: Philip Eisenlohr <eisenlohr@egr.msu.edu>
Date: Tue, 2 Nov 2021 14:28:54 -0400
Subject: [PATCH] fixed type hinting for seeds.py and grid_filters.py

---
 python/damask/grid_filters.py | 56 ++++++++++++++++++++---------------
 python/damask/seeds.py        |  4 +--
 2 files changed, 34 insertions(+), 26 deletions(-)

diff --git a/python/damask/grid_filters.py b/python/damask/grid_filters.py
index 816c727cd..cb6388f41 100644
--- a/python/damask/grid_filters.py
+++ b/python/damask/grid_filters.py
@@ -12,9 +12,11 @@ the following operations are required for tensorial data:
 
 """
 from scipy import spatial as _spatial
+from typing import Sequence, Tuple, Union
+
 import numpy as _np
 
-def _ks(size,cells,first_order=False):
+def _ks(size: _np.ndarray, cells: Union[_np.ndarray,Sequence[int]], first_order: bool = False) -> _np.ndarray:
     """
     Get wave numbers operator.
 
@@ -41,7 +43,7 @@ def _ks(size,cells,first_order=False):
     return _np.stack(_np.meshgrid(k_sk,k_sj,k_si,indexing = 'ij'), axis=-1)
 
 
-def curl(size,f):
+def curl(size: _np.ndarray, f: _np.ndarray) -> _np.ndarray:
     u"""
     Calculate curl of a vector or tensor field in Fourier space.
 
@@ -72,7 +74,7 @@ def curl(size,f):
     return _np.fft.irfftn(curl_,axes=(0,1,2),s=f.shape[:3])
 
 
-def divergence(size,f):
+def divergence(size: _np.ndarray, f: _np.ndarray) -> _np.ndarray:
     u"""
     Calculate divergence of a vector or tensor field in Fourier space.
 
@@ -99,7 +101,7 @@ def divergence(size,f):
     return _np.fft.irfftn(div_,axes=(0,1,2),s=f.shape[:3])
 
 
-def gradient(size,f):
+def gradient(size: _np.ndarray, f: _np.ndarray) -> _np.ndarray:
     u"""
     Calculate gradient of a scalar or vector fieldin Fourier space.
 
@@ -126,7 +128,9 @@ def gradient(size,f):
     return _np.fft.irfftn(grad_,axes=(0,1,2),s=f.shape[:3])
 
 
-def coordinates0_point(cells,size,origin=_np.zeros(3)):
+def coordinates0_point(cells: Union[ _np.ndarray,Sequence[int]],
+                       size: _np.ndarray,
+                       origin: _np.ndarray = _np.zeros(3)) -> _np.ndarray:
     """
     Cell center positions (undeformed).
 
@@ -145,8 +149,8 @@ def coordinates0_point(cells,size,origin=_np.zeros(3)):
         Undeformed cell center coordinates.
 
     """
-    start = origin        + size/cells*.5
-    end   = origin + size - size/cells*.5
+    start = origin        + size/_np.array(cells)*.5
+    end   = origin + size - size/_np.array(cells)*.5
 
     return _np.stack(_np.meshgrid(_np.linspace(start[0],end[0],cells[0]),
                                   _np.linspace(start[1],end[1],cells[1]),
@@ -154,7 +158,7 @@ def coordinates0_point(cells,size,origin=_np.zeros(3)):
                      axis = -1)
 
 
-def displacement_fluct_point(size,F):
+def displacement_fluct_point(size: _np.ndarray, F: _np.ndarray) -> _np.ndarray:
     """
     Cell center displacement field from fluctuation part of the deformation gradient field.
 
@@ -186,7 +190,7 @@ def displacement_fluct_point(size,F):
     return _np.fft.irfftn(displacement,axes=(0,1,2),s=F.shape[:3])
 
 
-def displacement_avg_point(size,F):
+def displacement_avg_point(size: _np.ndarray, F: _np.ndarray) -> _np.ndarray:
     """
     Cell center displacement field from average part of the deformation gradient field.
 
@@ -207,7 +211,7 @@ def displacement_avg_point(size,F):
     return _np.einsum('ml,ijkl->ijkm',F_avg - _np.eye(3),coordinates0_point(F.shape[:3],size))
 
 
-def displacement_point(size,F):
+def displacement_point(size: _np.ndarray, F: _np.ndarray) -> _np.ndarray:
     """
     Cell center displacement field from deformation gradient field.
 
@@ -227,7 +231,7 @@ def displacement_point(size,F):
     return displacement_avg_point(size,F) + displacement_fluct_point(size,F)
 
 
-def coordinates_point(size,F,origin=_np.zeros(3)):
+def coordinates_point(size: _np.ndarray, F: _np.ndarray, origin: _np.ndarray = _np.zeros(3)) -> _np.ndarray:
     """
     Cell center positions.
 
@@ -249,7 +253,8 @@ def coordinates_point(size,F,origin=_np.zeros(3)):
     return coordinates0_point(F.shape[:3],size,origin) + displacement_point(size,F)
 
 
-def cellsSizeOrigin_coordinates0_point(coordinates0,ordered=True):
+def cellsSizeOrigin_coordinates0_point(coordinates0: _np.ndarray,
+                                       ordered: bool = True) -> Tuple[_np.ndarray,_np.ndarray,_np.ndarray]:
     """
     Return grid 'DNA', i.e. cells, size, and origin from 1D array of point positions.
 
@@ -292,13 +297,15 @@ def cellsSizeOrigin_coordinates0_point(coordinates0,ordered=True):
         raise ValueError('Regular cell spacing violated.')
 
     if ordered and not _np.allclose(coordinates0.reshape(tuple(cells)+(3,),order='F'),
-                                    coordinates0_point(cells,size,origin),atol=atol):
+                                    coordinates0_point(list(cells),size,origin),atol=atol):
         raise ValueError('Input data is not ordered (x fast, z slow).')
 
     return (cells,size,origin)
 
 
-def coordinates0_node(cells,size,origin=_np.zeros(3)):
+def coordinates0_node(cells: Union[_np.ndarray,Sequence[int]],
+                      size: _np.ndarray,
+                      origin: _np.ndarray = _np.zeros(3)) -> _np.ndarray:
     """
     Nodal positions (undeformed).
 
@@ -323,7 +330,7 @@ def coordinates0_node(cells,size,origin=_np.zeros(3)):
                      axis = -1)
 
 
-def displacement_fluct_node(size,F):
+def displacement_fluct_node(size: _np.ndarray, F: _np.ndarray) -> _np.ndarray:
     """
     Nodal displacement field from fluctuation part of the deformation gradient field.
 
@@ -343,7 +350,7 @@ def displacement_fluct_node(size,F):
     return point_to_node(displacement_fluct_point(size,F))
 
 
-def displacement_avg_node(size,F):
+def displacement_avg_node(size: _np.ndarray, F: _np.ndarray) -> _np.ndarray:
     """
     Nodal displacement field from average part of the deformation gradient field.
 
@@ -364,7 +371,7 @@ def displacement_avg_node(size,F):
     return _np.einsum('ml,ijkl->ijkm',F_avg - _np.eye(3),coordinates0_node(F.shape[:3],size))
 
 
-def displacement_node(size,F):
+def displacement_node(size: _np.ndarray, F: _np.ndarray) -> _np.ndarray:
     """
     Nodal displacement field from deformation gradient field.
 
@@ -384,7 +391,7 @@ def displacement_node(size,F):
     return displacement_avg_node(size,F) + displacement_fluct_node(size,F)
 
 
-def coordinates_node(size,F,origin=_np.zeros(3)):
+def coordinates_node(size: _np.ndarray, F: _np.ndarray, origin: _np.ndarray = _np.zeros(3)) -> _np.ndarray:
     """
     Nodal positions.
 
@@ -406,7 +413,8 @@ def coordinates_node(size,F,origin=_np.zeros(3)):
     return coordinates0_node(F.shape[:3],size,origin) + displacement_node(size,F)
 
 
-def cellsSizeOrigin_coordinates0_node(coordinates0,ordered=True):
+def cellsSizeOrigin_coordinates0_node(coordinates0: _np.ndarray,
+                                      ordered: bool = True) -> Tuple[_np.ndarray,_np.ndarray,_np.ndarray]:
     """
     Return grid 'DNA', i.e. cells, size, and origin from 1D array of nodal positions.
 
@@ -441,13 +449,13 @@ def cellsSizeOrigin_coordinates0_node(coordinates0,ordered=True):
         raise ValueError('Regular cell spacing violated.')
 
     if ordered and not _np.allclose(coordinates0.reshape(tuple(cells+1)+(3,),order='F'),
-                                    coordinates0_node(cells,size,origin),atol=atol):
+                                    coordinates0_node(list(cells),size,origin),atol=atol):
         raise ValueError('Input data is not ordered (x fast, z slow).')
 
     return (cells,size,origin)
 
 
-def point_to_node(cell_data):
+def point_to_node(cell_data: _np.ndarray) -> _np.ndarray:
     """
     Interpolate periodic point data to nodal data.
 
@@ -469,7 +477,7 @@ def point_to_node(cell_data):
     return _np.pad(n,((0,1),(0,1),(0,1))+((0,0),)*len(cell_data.shape[3:]),mode='wrap')
 
 
-def node_to_point(node_data):
+def node_to_point(node_data: _np.ndarray) -> _np.ndarray:
     """
     Interpolate periodic nodal data to point data.
 
@@ -491,7 +499,7 @@ def node_to_point(node_data):
     return c[1:,1:,1:]
 
 
-def coordinates0_valid(coordinates0):
+def coordinates0_valid(coordinates0: _np.ndarray) -> bool:
     """
     Check whether coordinates form a regular grid.
 
@@ -513,7 +521,7 @@ def coordinates0_valid(coordinates0):
         return False
 
 
-def regrid(size,F,cells):
+def regrid(size: _np.ndarray, F: _np.ndarray, cells: Union[_np.ndarray,Sequence[int]]) -> _np.ndarray:
     """
     Return mapping from coordinates in deformed configuration to a regular grid.
 
diff --git a/python/damask/seeds.py b/python/damask/seeds.py
index 85b28850b..1d7dfc58e 100644
--- a/python/damask/seeds.py
+++ b/python/damask/seeds.py
@@ -1,7 +1,7 @@
 """Functionality for generation of seed points for Voronoi or Laguerre tessellation."""
 
 from scipy import spatial as _spatial
-from typing import Sequence
+from typing import Sequence,Tuple
 
 import numpy as _np
 
@@ -97,7 +97,7 @@ def from_Poisson_disc(size: _np.ndarray, N_seeds: int, N_candidates: int, distan
 
 
 def from_grid(grid, selection: Sequence[int] = None,
-              invert: bool = False, average: bool = False, periodic: bool = True) -> tuple[_np.ndarray, _np.ndarray]:
+              invert: bool = False, average: bool = False, periodic: bool = True) -> Tuple[_np.ndarray, _np.ndarray]:
     """
     Create seeds from grid description.