Merge pull request #13 from slimgroup/misc-bugs

Fix undef access

Project.toml

@@ -1,7 +1,7 @@
 name = "SegyIO"
 uuid = "157a0f19-4d44-4de5-a0d0-07e2f0ac4dfa"
 authors = ["Henryk Modzelewski <henryk_modzelewski@mac.com>"]
-version = "0.8.2"
+version = "0.8.3"
 
 [deps]
 Distributed = "8ba89e20-285c-5b6f-9357-94700520ee1b"

src/read/extract_con_headers.jl

@@ -31,7 +31,7 @@ function extractor(con, keys, block)
     headers = read_con_headers(con, copy(keys), block, prealloc_traces = 10000000)
     ntraces = length(headers)
     nkeys = length(keys)  
-    header_array = Array{Int32,2}(undef, ntraces, nkeys)
+    header_array = Array{Int32, 2}(undef, ntraces, nkeys)
 
     for cur_key in 1:nkeys
         header_array[:,cur_key] = get_header(headers, Symbol(keys[cur_key]), scale=false)

src/read/read_block_headers.jl

@@ -8,7 +8,8 @@ function read_block_headers!(b::BlockScan, keys::Array{String, 1}, ns::Int, dsf:
     s = IOBuffer(read(f, brange))
     ntraces = Int((brange)/(240 + ns*4))
     fh = FileHeader()
-    fh.bfh.ns = ns; fh.bfh.DataSampleFormat = dsf
+    fh.bfh.ns = ns
+    fh.bfh.DataSampleFormat = dsf
 
     # Check dsf
     datatype = Float32
@@ -19,9 +20,10 @@ function read_block_headers!(b::BlockScan, keys::Array{String, 1}, ns::Int, dsf:
     end
 
     th_b2s = th_byte2sample()
+    tmph = zeros(UInt8, 240)
     # Read each traceheader
     for trace in 1:ntraces
-        read_traceheader!(s, keys, th_b2s, headers[trace])
+        read_traceheader!(s, keys, th_b2s, headers[trace]; th=tmph)
         skip(s, ns*4)
     end
 

src/read/read_con.jl

@@ -24,8 +24,9 @@ function read_con(con::SeisCon, blocks::Array{Int,1};
 
     # Pre-allocate
     data = Array{datatype,2}(undef, con.ns, prealloc_traces) 
-    headers = [BinaryTraceHeader() for _=1:prealloc_traces]
-    fh = FileHeader(); set_fileheader!(fh.bfh, :ns, con.ns)
+    headers = zeros(BinaryTraceHeader, prealloc_traces)
+    fh = FileHeader()
+    set_fileheader!(fh.bfh, :ns, con.ns)
     set_fileheader!(fh.bfh, :DataSampleFormat, con.dsf)
 
     trace_count = 0
@@ -42,7 +43,7 @@ function read_con(con::SeisCon, blocks::Array{Int,1};
             println("Expanding preallocated memory")
             prealloc_traces *= 2
             data = hcat(data, Array{datatype,2}(undef, con.ns, ntraces+prealloc_traces))
-            append!(headers, Array{BinaryTraceHeader,1}(undef, ntraces+prealloc_traces))
+            append!(headers, zeros(BinaryTraceHeader, ntraces+prealloc_traces))
         end
         tmp_data = view(data, :,(trace_count+1):(trace_count+ntraces))
         tmp_headers = view(headers, (trace_count+1):(trace_count+ntraces)) 
@@ -73,7 +74,7 @@ function read_con(con::SeisCon, keys::Array{String,1}, blocks::Array{Int,1};
 
     # Pre-allocate
     data = Array{datatype,2}(undef, con.ns, prealloc_traces) 
-    headers = [BinaryTraceHeader() for _=1:prealloc_traces]
+    headers = zeros(BinaryTraceHeader, prealloc_traces)
     fh = FileHeader(); set_fileheader!(fh.bfh, :ns, con.ns)
     set_fileheader!(fh.bfh, :DataSampleFormat, con.dsf)
 
@@ -90,7 +91,7 @@ function read_con(con::SeisCon, keys::Array{String,1}, blocks::Array{Int,1};
         if ~isroom
             println("Expanding preallocated memory")
             data = hcat(data, Array{datatype,2}(undef, con.ns, ntraces+prealloc_traces))
-            append!(headers, Array{BinaryTraceHeader,1}(undef, ntraces+prealloc_traces))
+            append!(headers, zeros(BinaryTraceHeader, ntraces+prealloc_traces))
             prealloc_traces *= 2
         end
         tmp_data = view(data, :,(trace_count+1):(trace_count+ntraces))

src/read/read_con_headers.jl

@@ -27,8 +27,9 @@ function read_con_headers(con::SeisCon, keys::Array{String,1}, blocks::Array{Int
     in("ElevationScalar", keys) ? nothing : push!(keys, "ElevationScalar")
 
     # Pre-allocate
-    headers = Array{BinaryTraceHeader,1}(undef, prealloc_traces) 
-    fh = FileHeader(); set_fileheader!(fh.bfh, :ns, con.ns)
+    headers = zeros(BinaryTraceHeader, prealloc_traces)
+    fh = FileHeader()
+    set_fileheader!(fh.bfh, :ns, con.ns)
     set_fileheader!(fh.bfh, :DataSampleFormat, con.dsf)
 
     # Read all blocks
@@ -45,7 +46,8 @@ function read_con_headers(con::SeisCon, keys::Array{String,1}, blocks::Array{Int
             println("Expanding preallocated memory")
             prealloc_traces *= 2
             prealloc_traces += ntraces
-            append!(headers, Array{BinaryTraceHeader,1}(undef, ntraces+prealloc_traces))
+            prealloc_headers = zeros(BinaryTraceHeader, ntraces+prealloc_traces)
+            append!(headers, prealloc_headers)
         end
         tmp_headers = view(headers, (trace_count+1):(trace_count+ntraces)) 
 

src/read/read_file.jl

@@ -42,7 +42,7 @@ function read_file(s::IO, keys::Array{String, 1}, warn_user::Bool;
     ntraces = Int((end_byte - start_byte)/trace_size)
 
     # Preallocate memory
-    headers = [BinaryTraceHeader() for _ = 1:ntraces]
+    headers = zeros(BinaryTraceHeader, ntraces)
     data = Array{datatype, 2}(undef, fh.bfh.ns, ntraces)
     th_b2s = th_byte2sample()
 

src/scan/scan_block.jl

@@ -6,7 +6,7 @@ function scan_block(buf::IO, mem_block::Int, mem_trace::Int, keys::Array{String,
     # Calc info about this block
     startbyte = position(buf) + chunk_start
     ntraces_block = Int(mem_block/mem_trace)
-    headers = [BinaryTraceHeader() for _ = 1:ntraces_block]
+    headers = zeros(BinaryTraceHeader, ntraces_block)
     count = 0    
 
     # Read all headers and record end byte

src/scan/scan_shots.jl

@@ -9,7 +9,7 @@ function scan_shots!(s::IO, mem_chunk::Int, mem_trace::Int,
     eof(s) ? (fl_eof=true) : nothing
     buf_size = position(seekend(buf)); seekstart(buf)
     ntraces = Int(floor(buf_size/mem_trace))
-    headers = [BinaryTraceHeader() for _ = 1:ntraces]
+    headers = zeros(BinaryTraceHeader, ntraces)
 
     # Get headers from chunk
     th = zeros(UInt8, 240)
@@ -31,6 +31,7 @@ function scan_shots!(s::IO, mem_chunk::Int, mem_trace::Int,
     #combo = [[view(sx,i) view(sy,i)] for i in 1:ntraces]
     combo = [[sx[i] sy[i]] for i in 1:ntraces]
     part = delim_vector(combo, 1)
+
     fl_eof ? push!(part, length(combo) + 1) : push!(part, ntraces + 1)
 
     # Summarise each shot

src/types/BinaryTraceHeader.jl

@@ -204,6 +204,8 @@ function BinaryTraceHeader()
     0,0,0,0,0,0,0,0,0,0,0)
 end
 
+Base.zeros(::Type{BinaryTraceHeader}, n::Integer) = [BinaryTraceHeader() for _=1:n]
+
 function show(io::IO, bth::BinaryTraceHeader)
 
     println("BinaryTraceHeader:")

src/types/SeisBlock.jl

@@ -20,7 +20,7 @@ function SeisBlock(data::Matrix{DT}) where {DT<:Union{Float32, IBMFloat32}}
     DT==Float32 ? fh.bfh.DataSampleFormat=5 : fh.bfh.DataSampleFormat=1
 
     # Construct TraceHeaders
-    traceheaders = [BinaryTraceHeader() for i in 1:ntraces]
+    traceheaders = zeros(BinaryTraceHeader, ntraces)
     set_traceheader!(traceheaders, :ns, ns*ones(Int16, ntraces))
 
     # Construct Block