Add read_subarray and write_subarray methods to arrays (#1824)

Add read_subarray and write_subarray methods to arrays

Author: jp-dark

tiledb/cc/subarray.cc

@@ -632,6 +632,11 @@ void init_subarray(py::module &m) {
            })
 #endif
 
+      .def("_has_label_range",
+           [](Subarray &subarray, const Context &ctx, uint32_t dim_idx) {
+             return has_label_range(ctx, subarray, dim_idx);
+           })
+
       .def("copy_ranges",
            [](Subarray &subarray, Subarray &original, py::iterable dims) {
              for (auto dim_idx : dims) {
@@ -671,10 +676,6 @@ void init_subarray(py::module &m) {
                  static_cast<py::ssize_t *>(shape_result.ptr);
              // Set size for each dimension.
              for (uint32_t dim_idx{0}; dim_idx < ndim; ++dim_idx) {
-               if (has_label_range(ctx, subarray, dim_idx)) {
-                 throw TileDBPyError(
-                     "Cannot get the shape of a subarray with label ranges.");
-               }
                shape_ptr[dim_idx] = length_ranges(subarray, dim_idx);
              }
              return shape;

tiledb/indexing.pyx

@@ -32,7 +32,7 @@ cdef class DomainIndexer(object):
         self.array_ref = weakref.ref(array)
         self.schema = array.schema
         self.query = query
-    
+
     @property
     def schema(self):
         return self.array.array_ref().schema
@@ -44,6 +44,7 @@ cdef class DomainIndexer(object):
         return self.array_ref()
 
     def __getitem__(self, object idx):
+        from .subarray import Subarray # prevent circular import
         # implements domain-based indexing: slice by domain coordinates, not 0-based python indexing
 
         schema = self.array.schema
@@ -68,11 +69,13 @@ cdef class DomainIndexer(object):
             else:
                 new_idx.append(dim_idx)
 
-        subarray = list()
+        dim_ranges = list()
 
         for i, subidx in enumerate(new_idx):
             assert isinstance(subidx, slice)
-            subarray.append((subidx.start, subidx.stop))
+            dim_ranges.append((subidx.start, subidx.stop))
+        subarray = Subarray(self.array)
+        subarray.add_ranges([list([x]) for x in dim_ranges])
 
         attr_names = list(schema.attr(i).name for i in range(schema.nattr))
         attr_cond = None

tiledb/libtiledb.pxd

@@ -1198,10 +1198,10 @@ cdef class Array(object):
     cdef _ndarray_is_varlen(self, np.ndarray array)
 
 cdef class SparseArrayImpl(Array):
-    cdef _read_sparse_subarray(self, list subarray, list attr_names, object cond, tiledb_layout_t layout)
+    cdef _read_sparse_subarray(self, object subarray, list attr_names, object cond, tiledb_layout_t layout)
 
 cdef class DenseArrayImpl(Array):
-    cdef _read_dense_subarray(self, list subarray, list attr_names, object cond, tiledb_layout_t layout, bint include_coords)
+    cdef _read_dense_subarray(self, object subarray, list attr_names, object cond, tiledb_layout_t layout, bint include_coords)
 
 cdef class Query(object):
     cdef Array array