Correctly reserve the grid data dtype by converting ctypes array to numpy array with np.ctypeslib.as_array (#3446)

Author: seisman

pygmt/datatypes/grid.py

@@ -40,16 +40,15 @@ class _GMT_GRID(ctp.Structure):  # noqa: N801
     ...         print(header.pad[:])
     ...         print(header.mem_layout, header.nan_value, header.xy_off)
     ...         # The x and y coordinates
-    ...         print(grid.x[: header.n_columns])
-    ...         print(grid.y[: header.n_rows])
+    ...         x = np.ctypeslib.as_array(grid.x, shape=(header.n_columns,)).copy()
+    ...         y = np.ctypeslib.as_array(grid.y, shape=(header.n_rows,)).copy()
     ...         # The data array (with paddings)
-    ...         data = np.reshape(
-    ...             grid.data[: header.mx * header.my], (header.my, header.mx)
-    ...         )
+    ...         data = np.ctypeslib.as_array(
+    ...             grid.data, shape=(header.my, header.mx)
+    ...         ).copy()
     ...         # The data array (without paddings)
     ...         pad = header.pad[:]
     ...         data = data[pad[2] : header.my - pad[3], pad[0] : header.mx - pad[1]]
-    ...         print(data)
     14 8 1
     [-55.0, -47.0, -24.0, -10.0] 190.0 981.0 [1.0, 1.0]
     1.0 0.0
@@ -61,22 +60,26 @@ class _GMT_GRID(ctp.Structure):  # noqa: N801
     18 1 12 18
     [2, 2, 2, 2]
     b'' nan 0.5
-    [-54.5, -53.5, -52.5, -51.5, -50.5, -49.5, -48.5, -47.5]
-    [-10.5, -11.5, -12.5, -13.5, -14.5, -15.5, ..., -22.5, -23.5]
-    [[347.5 331.5 309.  282.  190.  208.  299.5 348. ]
-    [349.  313.  325.5 247.  191.  225.  260.  452.5]
-    [345.5 320.  335.  292.  207.5 247.  325.  346.5]
-    [450.5 395.5 366.  248.  250.  354.5 550.  797.5]
-    [494.5 488.5 357.  254.5 286.  484.5 653.5 930. ]
-    [601.  526.5 535.  299.  398.5 645.  797.5 964. ]
-    [308.  595.5 555.5 556.  580.  770.  927.  920. ]
-    [521.5 682.5 796.  886.  571.5 638.5 739.5 881.5]
-    [310.  521.5 757.  570.5 538.5 524.  686.5 794. ]
-    [561.5 539.  446.5 481.5 439.5 553.  726.5 981. ]
-    [557.  435.  385.5 345.5 413.5 496.  519.5 833.5]
-    [373.  367.5 349.  352.5 419.5 428.  570.  667.5]
-    [383.  284.5 344.5 394.  491.  556.5 578.5 618.5]
-    [347.5 344.5 386.  640.5 617.  579.  646.5 671. ]]
+    >>> x
+    array([-54.5, -53.5, -52.5, -51.5, -50.5, -49.5, -48.5, -47.5])
+    >>> y
+    array([-10.5, -11.5, -12.5, -13.5, ..., -20.5, -21.5, -22.5, -23.5])
+    >>> data
+    array([[347.5, 331.5, 309. , 282. , 190. , 208. , 299.5, 348. ],
+           [349. , 313. , 325.5, 247. , 191. , 225. , 260. , 452.5],
+           [345.5, 320. , 335. , 292. , 207.5, 247. , 325. , 346.5],
+           [450.5, 395.5, 366. , 248. , 250. , 354.5, 550. , 797.5],
+           [494.5, 488.5, 357. , 254.5, 286. , 484.5, 653.5, 930. ],
+           [601. , 526.5, 535. , 299. , 398.5, 645. , 797.5, 964. ],
+           [308. , 595.5, 555.5, 556. , 580. , 770. , 927. , 920. ],
+           [521.5, 682.5, 796. , 886. , 571.5, 638.5, 739.5, 881.5],
+           [310. , 521.5, 757. , 570.5, 538.5, 524. , 686.5, 794. ],
+           [561.5, 539. , 446.5, 481.5, 439.5, 553. , 726.5, 981. ],
+           [557. , 435. , 385.5, 345.5, 413.5, 496. , 519.5, 833.5],
+           [373. , 367.5, 349. , 352.5, 419.5, 428. , 570. , 667.5],
+           [383. , 284.5, 344.5, 394. , 491. , 556.5, 578.5, 618.5],
+           [347.5, 344.5, 386. , 640.5, 617. , 579. , 646.5, 671. ]],
+          dtype=float32)
     """
 
     _fields_: ClassVar = [
@@ -126,7 +129,8 @@ def to_dataarray(self) -> xr.DataArray:
                [450.5, 395.5, 366. , 248. , 250. , 354.5, 550. , 797.5],
                [345.5, 320. , 335. , 292. , 207.5, 247. , 325. , 346.5],
                [349. , 313. , 325.5, 247. , 191. , 225. , 260. , 452.5],
-               [347.5, 331.5, 309. , 282. , 190. , 208. , 299.5, 348. ]])
+               [347.5, 331.5, 309. , 282. , 190. , 208. , 299.5, 348. ]],
+              dtype=float32)
         Coordinates:
           * lat      (lat) float64... -23.5 -22.5 -21.5 -20.5 ... -12.5 -11.5 -10.5
           * lon      (lon) float64... -54.5 -53.5 -52.5 -51.5 -50.5 -49.5 -48.5 -47.5
@@ -169,16 +173,14 @@ def to_dataarray(self) -> xr.DataArray:
         # Get dimensions and their attributes from the header.
         dims, dim_attrs = header.dims, header.dim_attrs
         # The coordinates, given as a tuple of the form (dims, data, attrs)
-        coords = [
-            (dims[0], self.y[: header.n_rows], dim_attrs[0]),
-            (dims[1], self.x[: header.n_columns], dim_attrs[1]),
-        ]
+        x = np.ctypeslib.as_array(self.x, shape=(header.n_columns,)).copy()
+        y = np.ctypeslib.as_array(self.y, shape=(header.n_rows,)).copy()
+        coords = [(dims[0], y, dim_attrs[0]), (dims[1], x, dim_attrs[1])]
 
         # The data array without paddings
+        data = np.ctypeslib.as_array(self.data, shape=(header.my, header.mx)).copy()
         pad = header.pad[:]
-        data = np.reshape(self.data[: header.mx * header.my], (header.my, header.mx))[
-            pad[2] : header.my - pad[3], pad[0] : header.mx - pad[1]
-        ]
+        data = data[pad[2] : header.my - pad[3], pad[0] : header.mx - pad[1]]
 
         # Create the xarray.DataArray object
         grid = xr.DataArray(

pygmt/datatypes/image.py

@@ -38,13 +38,12 @@ class _GMT_IMAGE(ctp.Structure):  # noqa: N801
     ...         # Image-specific attributes.
     ...         print(image.type, image.n_indexed_colors)
     ...         # The x and y coordinates
-    ...         x = image.x[: header.n_columns]
-    ...         y = image.y[: header.n_rows]
+    ...         x = np.ctypeslib.as_array(image.x, shape=(header.n_columns,)).copy()
+    ...         y = np.ctypeslib.as_array(image.y, shape=(header.n_rows,)).copy()
     ...         # The data array (with paddings)
-    ...         data = np.reshape(
-    ...             image.data[: header.n_bands * header.mx * header.my],
-    ...             (header.my, header.mx, header.n_bands),
-    ...         )
+    ...         data = np.ctypeslib.as_array(
+    ...             image.data, shape=(header.my, header.mx, header.n_bands)
+    ...         ).copy()
     ...         # The data array (without paddings)
     ...         pad = header.pad[:]
     ...         data = data[pad[2] : header.my - pad[3], pad[0] : header.mx - pad[1], :]
@@ -60,10 +59,10 @@ class _GMT_IMAGE(ctp.Structure):  # noqa: N801
     [2, 2, 2, 2]
     b'BRPa' 0.5
     1 0
-    >>> x
-    [-179.5, -178.5, ..., 178.5, 179.5]
-    >>> y
-    [89.5, 88.5, ..., -88.5, -89.5]
+    >>> x  # doctest: +NORMALIZE_WHITESPACE, +ELLIPSIS
+    array([-179.5, -178.5, ..., 178.5, 179.5])
+    >>> y  # doctest: +NORMALIZE_WHITESPACE, +ELLIPSIS
+    array([ 89.5,  88.5, ..., -88.5, -89.5])
     >>> data.shape
     (180, 360, 3)
     >>> data.min(), data.max()

pygmt/tests/test_sphinterpolate.py

@@ -41,4 +41,4 @@ def test_sphinterpolate_no_outgrid(mars):
     npt.assert_allclose(temp_grid.max(), 14628.144)
     npt.assert_allclose(temp_grid.min(), -6908.1987)
     npt.assert_allclose(temp_grid.median(), 118.96849)
-    npt.assert_allclose(temp_grid.mean(), 272.60578)
+    npt.assert_allclose(temp_grid.mean(), 272.60593)