Cache named vectors/matrices, generalize relayout.

tanaylab · Mar 29, 2024 · d76945c · d76945c
1 parent 744bf6c
commit d76945c
Show file tree

Hide file tree

Showing 6 changed files with 86 additions and 82 deletions.
diff --git a/docs/v0.1.0/.documenter-siteinfo.json b/docs/v0.1.0/.documenter-siteinfo.json
@@ -1 +1 @@
-{"documenter":{"julia_version":"1.10.2","generation_timestamp":"2024-03-29T21:22:31","documenter_version":"1.3.0"}}
+{"documenter":{"julia_version":"1.10.2","generation_timestamp":"2024-03-29T23:41:20","documenter_version":"1.3.0"}}
diff --git a/src/data.jl b/src/data.jl
@@ -83,6 +83,9 @@ using NamedArrays
 using SparseArrays
 
 import Daf.Formats
+import Daf.Formats.as_named_matrix
+import Daf.Formats.as_named_vector
+import Daf.Formats.as_read_only_array
 import Daf.Formats.CacheEntry
 import Daf.Formats.FormatReader
 import Daf.Formats.FormatWriter
@@ -1509,7 +1512,10 @@ function get_matrix(
                         Formats.store_cached_dependency_key!(daf, cache_key, Formats.axis_cache_key(rows_axis))
                         Formats.store_cached_dependency_key!(daf, cache_key, Formats.axis_cache_key(columns_axis))
                         flipped_matrix = Formats.get_matrix_through_cache(daf, columns_axis, rows_axis, name)
-                        return CacheEntry(MemoryData, transpose(relayout!(flipped_matrix)))
+                        return CacheEntry(
+                            MemoryData,
+                            as_named_matrix(daf, rows_axis, columns_axis, transpose(relayout!(flipped_matrix))),
+                        )
                     end
                     matrix = cache_entry.data
                 end
@@ -1613,22 +1619,6 @@ function require_not_name(daf::DafReader, axis::AbstractString, name::AbstractSt
     return nothing
 end
 
-function as_read_only_array(array::SparseArrays.ReadOnly)::SparseArrays.ReadOnly
-    return array
-end
-
-function as_read_only_array(array::NamedArray)::NamedArray
-    if array.array isa SparseArrays.ReadOnly
-        return array  # untested
-    else
-        return NamedArray(as_read_only_array(array.array), array.dicts, array.dimnames)
-    end
-end
-
-function as_read_only_array(array::AbstractArray)::SparseArrays.ReadOnly
-    return SparseArrays.ReadOnly(array)
-end
-
 function require_dim_name(
     daf::DafReader,
     axis::AbstractString,
@@ -1657,54 +1647,6 @@ function require_axis_names(
     end
 end
 
-function as_named_vector(daf::DafReader, axis::AbstractString, vector::NamedVector)::NamedArray
-    return vector
-end
-
-function as_named_vector(daf::DafReader, axis::AbstractString, vector::AbstractVector)::NamedArray
-    axis_names_dict = get(daf.internal.axes, axis, nothing)
-    if axis_names_dict == nothing
-        named_array = NamedArray(vector; names = (get_axis(daf, axis),), dimnames = (axis,))
-        daf.internal.axes[axis] = named_array.dicts[1]
-        return named_array
-
-    else
-        return NamedArray(vector, (axis_names_dict,), (axis,))
-    end
-end
-
-function as_named_matrix(
-    daf::DafReader,
-    rows_axis::AbstractString,
-    columns_axis::AbstractString,
-    matrix::NamedMatrix,
-)::NamedArray
-    return matrix
-end
-
-function as_named_matrix(
-    daf::DafReader,
-    rows_axis::AbstractString,
-    columns_axis::AbstractString,
-    matrix::AbstractMatrix,
-)::NamedArray
-    rows_axis_names_dict = get(daf.internal.axes, rows_axis, nothing)
-    columns_axis_names_dict = get(daf.internal.axes, columns_axis, nothing)
-    if rows_axis_names_dict == nothing || columns_axis_names_dict == nothing
-        named_array = NamedArray(
-            matrix;
-            names = (get_axis(daf, rows_axis), get_axis(daf, columns_axis)),
-            dimnames = (rows_axis, columns_axis),
-        )
-        daf.internal.axes[rows_axis] = named_array.dicts[1]
-        daf.internal.axes[columns_axis] = named_array.dicts[2]
-        return named_array
-
-    else
-        return NamedArray(matrix, (rows_axis_names_dict, columns_axis_names_dict), (rows_axis, columns_axis))
-    end
-end
-
 function base_array(array::AbstractArray)::AbstractArray
     return array
 end

diff --git a/src/formats.jl b/src/formats.jl
@@ -49,6 +49,7 @@ using Daf.MatrixLayouts
 using Daf.Messages
 using Daf.StorageTypes
 using Daf.Tokens
+using NamedArrays
 using OrderedCollections
 using SparseArrays
 
@@ -94,7 +95,7 @@ If too much data has been cached, call `empty_cache!` to release it.
 
 struct CacheEntry
     cache_type::CacheType
-    data::Union{AbstractStringSet, StorageScalar, StorageVector, StorageMatrix}
+    data::Union{AbstractStringSet, AbstractStringVector, StorageScalar, NamedArray}
 end
 
 """
@@ -687,7 +688,7 @@ end
 function cache_data!(
     format::FormatReader,
     cache_key::AbstractString,
-    data::Union{AbstractStringSet, StorageScalar, StorageVector, StorageMatrix},
+    data::Union{AbstractStringSet, AbstractStringVector, StorageScalar, NamedArray},
     cache_type::CacheType,
 )::Nothing
     @assert format.internal.writer_thread[1] == threadid()
@@ -756,7 +757,8 @@ function cache_vector!(
     cache_type::CacheType,
 )::Nothing
     cache_key = vector_cache_key(axis, name)
-    cache_data!(format, cache_key, vector, cache_type)
+    named_vector = as_named_vector(format, axis, vector)
+    cache_data!(format, cache_key, named_vector, cache_type)
     store_cached_dependency_key!(format, cache_key, axis_cache_key(axis))
     return nothing
 end
@@ -770,12 +772,76 @@ function cache_matrix!(
     cache_type::CacheType,
 )::Nothing
     cache_key = matrix_cache_key(rows_axis, columns_axis, name)
-    cache_data!(format, cache_key, matrix, cache_type)
+    named_matrix = as_named_matrix(format, rows_axis, columns_axis, matrix)
+    cache_data!(format, cache_key, named_matrix, cache_type)
     store_cached_dependency_key!(format, cache_key, axis_cache_key(rows_axis))
     store_cached_dependency_key!(format, cache_key, axis_cache_key(columns_axis))
     return nothing
 end
 
+function as_named_vector(format::FormatReader, axis::AbstractString, vector::NamedVector)::NamedArray
+    return vector
+end
+
+function as_named_vector(format::FormatReader, axis::AbstractString, vector::AbstractVector)::NamedArray
+    axis_names_dict = get(format.internal.axes, axis, nothing)
+    if axis_names_dict == nothing
+        names = as_read_only_array(Formats.get_axis_through_cache(format, axis))
+        named_array = NamedArray(vector; names = (names,), dimnames = (axis,))
+        format.internal.axes[axis] = named_array.dicts[1]
+        return named_array
+
+    else
+        return NamedArray(vector, (axis_names_dict,), (axis,))
+    end
+end
+
+function as_named_matrix(
+    format::FormatReader,
+    rows_axis::AbstractString,
+    columns_axis::AbstractString,
+    matrix::NamedMatrix,
+)::NamedArray
+    return matrix
+end
+
+function as_named_matrix(
+    format::FormatReader,
+    rows_axis::AbstractString,
+    columns_axis::AbstractString,
+    matrix::AbstractMatrix,
+)::NamedArray
+    rows_axis_names_dict = get(format.internal.axes, rows_axis, nothing)
+    columns_axis_names_dict = get(format.internal.axes, columns_axis, nothing)
+    if rows_axis_names_dict == nothing || columns_axis_names_dict == nothing
+        rows_names = as_read_only_array(Formats.get_axis_through_cache(format, rows_axis))
+        columns_names = as_read_only_array(Formats.get_axis_through_cache(format, columns_axis))
+        named_array = NamedArray(matrix; names = (rows_names, columns_names), dimnames = (rows_axis, columns_axis))
+        format.internal.axes[rows_axis] = named_array.dicts[1]
+        format.internal.axes[columns_axis] = named_array.dicts[2]
+        return named_array
+
+    else
+        return NamedArray(matrix, (rows_axis_names_dict, columns_axis_names_dict), (rows_axis, columns_axis))
+    end
+end
+
+function as_read_only_array(array::SparseArrays.ReadOnly)::SparseArrays.ReadOnly
+    return array
+end
+
+function as_read_only_array(array::NamedArray)::NamedArray
+    if array.array isa SparseArrays.ReadOnly
+        return array  # untested
+    else
+        return NamedArray(as_read_only_array(array.array), array.dicts, array.dimnames)
+    end
+end
+
+function as_read_only_array(array::AbstractArray)::SparseArrays.ReadOnly
+    return SparseArrays.ReadOnly(array)
+end
+
 function scalar_names_cache_key()::String
     return "? scalars"
 end

diff --git a/src/matrix_layouts.jl b/src/matrix_layouts.jl
@@ -326,9 +326,11 @@ function relayout!(destination::DenseMatrix, source::AbstractMatrix)::DenseMatri
         error("relayout destination size: $(size(destination))\nis different from source size: $(size(source))")
     end
     if issparse(source)
-        error("relayout dense destination: $(typeof(destination))\nand sparse source: $(typeof(source))")
+        destination .= source
+    else
+        transpose!(destination, transpose(source))
     end
-    return transpose!(destination, transpose(source))
+    return destination
 end
 
 function relayout!(destination::AbstractMatrix, source::AbstractMatrix)::AbstractMatrix  # untested

diff --git a/test/matrix_layouts.jl b/test/matrix_layouts.jl
@@ -272,11 +272,10 @@ nested_test("matrix_layouts") do
                 end
 
                 nested_test("destination_dense") do
-                    destination = rand(4, 6)
-                    @test_throws dedent("""
-                        relayout dense destination: Matrix{Float64}
-                        and sparse source: SparseMatrixCSC{Float64, Int64}
-                    """) relayout!(destination, source)
+                    destination = transpose(rand(6, 4))
+                    relayout!(destination, source)
+                    @test major_axis(destination) == Rows
+                    @test destination == source
                 end
 
                 nested_test("read_only") do

diff --git a/test/runtests.jl b/test/runtests.jl
@@ -59,11 +59,6 @@ function with_unwrapping_exceptions(action::Function)::Any
     end
 end
 
-#function test_similar(left::Any, right::Any)::Nothing
-#    @test "$(left)" == "$(right)"
-#    return nothing
-#end
-
 include("matrix_layouts.jl")
 include("messages.jl")
 include("data.jl")