From 02afdcd4b7ab56df868eed21644488a379d07a2a Mon Sep 17 00:00:00 2001
From: jingpengw <jingpeng.wu@gmail.com>
Date: Wed, 26 Dec 2018 04:02:14 -0500
Subject: [PATCH] make raw encoding really not doing anything; fix a bug of
 creating temp layer; fix a bug of reinterpret

---
 src/Codings.jl           |  5 ++---
 src/Infos.jl             | 17 +++++++++++++----
 src/backends/BinDicts.jl |  7 ++++---
 src/modes/sequential.jl  |  3 ++-
 src/type.jl              |  5 +++--
 5 files changed, 24 insertions(+), 13 deletions(-)

diff --git a/src/Codings.jl b/src/Codings.jl
index 27a5c86..c29b39b 100644
--- a/src/Codings.jl
+++ b/src/Codings.jl
@@ -31,10 +31,10 @@ struct BlosclzCoding <: AbstractBigArrayCoding end
 struct GzipCoding    <: AbstractBigArrayCoding end
 struct ZstdCoding    <: AbstractBigArrayCoding end 
 
-const DEFAULT_CODING = RawCoding
+const DEFAULT_CODING = GzipCoding
 
 function encode(data::Array, coding::Type{RawCoding})
-    reinterpret(UInt8, data[:])
+    reinterpret(UInt8, data[:]) |> Vector
 end
 
 function decode(data::Vector{UInt8}, coding::Type{RawCoding})
@@ -42,7 +42,6 @@ function decode(data::Vector{UInt8}, coding::Type{RawCoding})
 end
 
 function encode(data::Array, coding::Type{ZstdCoding})
-    #Libz.deflate(reinterpret(UInt8, data[:]))
     transcode(ZstdCompressor, reinterpret(UInt8, vec(data)) |> Vector)
 end
 
diff --git a/src/Infos.jl b/src/Infos.jl
index 2052b0a..eb79369 100644
--- a/src/Infos.jl
+++ b/src/Infos.jl
@@ -22,7 +22,7 @@ export InfoScale
 
 const ENCODING_MAP = Dict{String,Any}(
     # note that the raw encoding in cloud storage will be automatically gzip encoded!
-    "raw"       => GzipCoding,
+    "raw"       => RawCoding,
     "jpeg"      => JPEGCoding,
     "blosclz"   => BlosclzCoding,
     "gzip"      => GzipCoding, 
@@ -89,7 +89,7 @@ function Base.Dict(self::InfoScale)
         end 
     end
     d[:size] = [get_volume_size(self)...]
-    d[:voxelOffset] = [Tuple(get_voxel_offset(self))...]
+    d[:voxel_offset] = [Tuple(get_voxel_offset(self))...]
     return d
 end
 
@@ -120,8 +120,17 @@ end
 end 
 
 @inline function get_encoding(self::InfoScale) self.encoding end
+@inline function set_encoding!(self::InfoScale, encoding::DataType) 
+    self.encoding = encoding 
+end
+
+"""
+    set_encoding!(self::InfoScale, encoding::Symbol)
 
-@inline function set_encoding!(self::InfoScale, encoding::Symbol)
+the encoding map is: 
+$(ENCODING_MAP)
+"""
+@inline function set_encoding!(self::InfoScale, encoding::String)
     self.encoding = ENCODING_MAP[encoding]
 end 
 
@@ -328,7 +337,7 @@ end
 @inline function get_encoding(self::Info, mip::Integer=1)
     InfoScales.get_encoding( get_scales(self)[mip] )
 end 
-@inline function set_encoding!(self::Info, encoding::DataType)
+@inline function set_encoding!(self::Info, encoding::Union{String, DataType})
     for scale in get_scales(self)
         InfoScales.set_encoding!(scale, encoding)
     end 
diff --git a/src/backends/BinDicts.jl b/src/backends/BinDicts.jl
index 3efd2bd..eb3cd4a 100644
--- a/src/backends/BinDicts.jl
+++ b/src/backends/BinDicts.jl
@@ -18,8 +18,8 @@ struct BinDict <: AbstractBigArrayBackend
     end 
 end 
 
-@inline function Base.show(self::BinDict)
-    println("BinDict in ", get_path(self))
+@inline function Base.show(io::IO, self::BinDict)
+    write(io, "BinDict in " * get_path(self))
 end 
 
 @inline function get_path(self::BinDict)
@@ -42,7 +42,7 @@ end
 end 
 
 @inline function Base.setindex!( self::BinDict, value::Array, key::AbstractString )
-    data = reinterpret(UInt8, value[:])
+    data = reinterpret(UInt8, value[:]) |> Vector
     fileName = joinpath( get_path(self), key )
     write(fileName, data)
 end
@@ -63,3 +63,4 @@ end
 
 
 end # module
+
diff --git a/src/modes/sequential.jl b/src/modes/sequential.jl
index b902f64..4417fea 100644
--- a/src/modes/sequential.jl
+++ b/src/modes/sequential.jl
@@ -11,7 +11,8 @@ function setindex_sequential!( ba::BigArray{D,T,N}, buf::Array{T,N},
         chunkGlobalRange, globalRange, rangeInChunk, rangeInBuffer = adjust_volume_boundary(ba, 
                                     chunkGlobalRange, globalRange, rangeInChunk, rangeInBuffer)
         @inbounds chk = buf[rangeInBuffer]
-        ba.kvStore[ joinpath(mipLevelName, cartesian_range2string(chunkGlobalRange)) ] = encode( chk, C)
+        ba.kvStore[ joinpath(mipLevelName, cartesian_range2string(chunkGlobalRange)) ] = 
+                                                                            encode( chk, C)
     end
 end 
 
diff --git a/src/type.jl b/src/type.jl
index 62bd8f4..0c4d902 100644
--- a/src/type.jl
+++ b/src/type.jl
@@ -21,6 +21,7 @@ end
 function BigArray(layerPath::AbstractString; mip::Int=1, fillMissing::Bool=DEFAULT_FILL_MISSING, 
                   mode::Symbol=DEFAULT_MODE)
     if isdir(layerPath) || startswith(layerPath, "file://")
+        layerPath = replace(layerPath, "file://"=>"/", count=1)
         d = BinDict(layerPath)
     elseif startswith(layerPath, "gs://")
         d = GSDict(layerPath)
@@ -35,7 +36,7 @@ end
 @inline function BigArray(d::AbstractBigArrayBackend; mip::Int=1, 
                           fillMissing::Bool=DEFAULT_FILL_MISSING, 
                           mode::Symbol=DEFAULT_MODE)  
-    info = d["info"] |> Info 
+    info = d["info"] |> Info
     return BigArray(d, info, mip, fillMissing, mode)
 end
 
@@ -93,7 +94,7 @@ function BigArray(info::Info{T,N}; mip::Integer=1,
     datasetDir = joinpath(layerDir, string(Infos.get_key(info, 1))) 
     mkdir(layerDir)
     mkdir(datasetDir)
-    d = BinDict(datasetDir)
+    d = BinDict(layerDir)
     
     # write the info as file 
     write(joinpath(layerDir, "info"), JSON.json(Dict(info)))