Fix bug and add consistency tests. (#20)

* Fix "bytesize not defined" and add tests.

* Format the codes.

* Add consistency tests and fix bugs.

* Format the codes.

* Move PyCall to [extras]

* Using Conda to install packages for tests.

* Using conda.

* Using CondPkg and PythonCall.

* Update Project.toml

Co-authored-by: Seth Axen <[email protected]>

* Update Project.toml

Co-authored-by: Seth Axen <[email protected]>

* Update test/consistency.jl

Co-authored-by: Seth Axen <[email protected]>

* Update test/runtests.jl

Co-authored-by: Seth Axen <[email protected]>

* Update consistency.jl

* Update CondaPkg.toml.

---------

Co-authored-by: Seth Axen <[email protected]>

.gitignore

@@ -2,4 +2,5 @@
 *.jl.cov
 *.jl.mem
 /docs/build/
-Manifest.toml
+Manifest.toml
+/.CondaPkg

CondaPkg.toml

@@ -0,0 +1,3 @@
+[deps]
+mrcfile = ">=1.2,<2.0"
+numpy = ">=1.1,<2.0"

Project.toml

@@ -1,7 +1,7 @@
 name = "MRCFile"
 uuid = "c18c01d3-0ab9-49c3-bd2d-8f2e64a2b7a5"
 authors = ["Seth Axen <[email protected]>"]
-version = "0.1.1"
+version = "0.1.2"
 
 [deps]
 CodecBzip2 = "523fee87-0ab8-5b00-afb7-3ecf72e48cfd"
@@ -20,7 +20,9 @@ TranscodingStreams = "0.9"
 julia = "^1"
 
 [extras]
+CondaPkg = "992eb4ea-22a4-4c89-a5bb-47a3300528ab"
+PythonCall = "6099a3de-0909-46bc-b1f4-468b9a2dfc0d"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["Test"]
+test = ["CondaPkg", "PythonCall", "Test"]

src/header.jl

@@ -111,7 +111,7 @@ function sizeoffield(name, type)
 end
 
 function bytestoentry(name, type, pointer)
-    name === :exttyp && return _unsafe_string(pointer, 4)
+    name === :exttyp && return unsafe_string(convert(Ptr{UInt8}, pointer), 4)
     name === :map && return _unsafe_string(pointer, 4)
     name === :label && return ntuple(Val(10)) do i
         return strip(_unsafe_string(pointer + (i - 1) * 80, 80), ' ')

src/io.jl

@@ -63,7 +63,7 @@ Read MRC file or stream, using a memory-mapped array to access the data.
 function read_mmap(io::IO, ::Type{MRCData})
     head = read(io, MRCHeader)
     exthead = read(io, MRCExtendedHeader; header=head)
-    arraytype = Array{MRC.datatype(head),ndims(head)}
+    arraytype = Array{datatype(head),ndims(head)}
     data = Mmap.mmap(io, arraytype, size(head)[1:ndims(head)])
     return MRCData(head, exthead, data)
 end

test/consistency.jl

@@ -0,0 +1,97 @@
+using Test
+using CondaPkg
+using PythonCall
+
+# Load the Python module/package
+numpy = pyimport("numpy")
+mrcfile = pyimport("mrcfile")
+
+function compare_map(map_jl::Array{Float32,3}, map_py::Array{Float32,3})
+    # dimensions permuted due to row-major storage in Python and col-major in Julia
+    # see https://github.com/sethaxen/MRCFile.jl/issues/10
+    @test_broken map_jl == map_py
+    permuted_py = permutedims(map_py, (3, 2, 1))
+    @test map_jl == permuted_py
+end
+
+function compare_header(header_jl::MRCHeader, header_py::Py)
+    @test Bool(header_jl.nx == header_py.nx)
+    @test Bool(header_jl.ny == header_py.ny)
+    @test Bool(header_jl.nz == header_py.nz)
+    @test Bool(header_jl.mode == header_py.mode)
+    @test Bool(header_jl.nxstart == header_py.nxstart)
+    @test Bool(header_jl.nystart == header_py.nystart)
+    @test Bool(header_jl.nzstart == header_py.nzstart)
+    @test Bool(header_jl.mx == header_py.mx)
+    @test Bool(header_jl.my == header_py.my)
+    @test Bool(header_jl.mz == header_py.mz)
+    @test Bool(header_jl.cella_x == header_py.cella.x)
+    @test Bool(header_jl.cella_y == header_py.cella.y)
+    @test Bool(header_jl.cella_z == header_py.cella.z)
+    @test Bool(header_jl.cellb_alpha == header_py.cellb.alpha)
+    @test Bool(header_jl.cellb_beta == header_py.cellb.beta)
+    @test Bool(header_jl.cellb_gamma == header_py.cellb.gamma)
+    @test Bool(header_jl.mapc == header_py.mapc)
+    @test Bool(header_jl.mapr == header_py.mapr)
+    @test Bool(header_jl.maps == header_py.maps)
+    @test Bool(header_jl.dmin == header_py.dmin)
+    @test Bool(header_jl.dmax == header_py.dmax)
+    @test Bool(header_jl.dmean == header_py.dmean)
+    @test Bool(header_jl.ispg == header_py.ispg)
+    @test Bool(header_jl.nsymbt == header_py.nsymbt)
+    @test [UInt8(b) for b in header_jl.extra1] == pyconvert(Vector{UInt8}, header_py.extra1.tobytes())
+    @test [UInt8(b) for b in header_jl.exttyp] == pyconvert(Vector{UInt8}, header_py.exttyp.tobytes())
+    @test Bool(header_jl.nversion == header_py.nversion)
+    @test ([UInt8(b) for b in header_jl.extra2]) == pyconvert(Vector{UInt8}, header_py.extra2.tobytes())
+    @test Bool(header_jl.origin_x == header_py.origin.x)
+    @test Bool(header_jl.origin_y == header_py.origin.y)
+    @test Bool(header_jl.origin_z == header_py.origin.z)
+    @test [UInt8(b) for b in header_jl.map] == pyconvert(Vector{UInt8}, header_py.map.tobytes())
+    @test [UInt8(b) for b in header_jl.machst] == pyconvert(Vector{UInt8}, header_py.machst.tobytes())
+    @test Bool(header_jl.rms == header_py.rms)
+    @test Bool(header_jl.nlabl == header_py.nlabl)
+    @test join(header_jl.label) ==
+        pyconvert(String, header_py.label.tostring().decode().strip())
+end
+
+function compare_extendedheader(exh_jl::MRCExtendedHeader, exh_py::Py)
+    @test [UInt8(b) for b in exh_jl.data] == pyconvert(Vector{UInt8}, exh_py.tobytes())
+end
+
+function compare_mrcfile(map_path::String)
+    emd_jl = read(map_path, MRCData)
+    map_jl = emd_jl.data
+    header_jl = header(emd_jl)
+    exh_jl = extendedheader(emd_jl)
+
+    emd_py = mrcfile.open(map_path; mode="r")
+    data_copy = numpy.copy(emd_py.data)  # Create a copy of the data
+    map_py = pyconvert(Array{Float32,3}, data_copy)
+    header_py = emd_py.header
+    exh_py = emd_py.extended_header
+    emd_py.close()  # Make sure the file is closed even if an error occurs
+
+    @testset "map" begin
+        compare_map(map_jl, map_py)
+    end
+
+    @testset "header" begin
+        compare_header(header_jl, header_py)
+    end
+
+    @testset "extendedheader" begin
+        compare_extendedheader(exh_jl, exh_py)
+    end
+end
+
+@testset "Consistency Test" begin
+    @testset "emd_3001.map" begin
+        emd3001_path = "$(@__DIR__)/testdata/emd_3001.map"
+        compare_mrcfile(emd3001_path)
+    end
+
+    @testset "emd_3197" begin
+        emd3197_path = "$(@__DIR__)/testdata/emd_3197.map"
+        compare_mrcfile(emd3197_path)
+    end
+end

test/io.jl

@@ -33,7 +33,7 @@
             @test h.ispg === Int32(4)
             @test h.nsymbt == sizeof(eh) == Int32(160)
             @test h.extra1 === Tuple(zeros(UInt8, 8))
-            @test h.exttyp === ""
+            @test h.exttyp === "\0\0\0\0"
             @test h.nversion === Int32(0)
             @test h.extra2 === Tuple(zeros(UInt8, 84))
             @test h.origin_x === Float32(0)
@@ -80,7 +80,7 @@
             @test h.ispg === Int32(1)
             @test h.nsymbt == sizeof(eh) == Int32(0)
             @test h.extra1 === Tuple(zeros(UInt8, 8))
-            @test h.exttyp === ""
+            @test h.exttyp === "\0\0\0\0"
             @test h.nversion === Int32(0)
             @test h.extra2 === Tuple(zeros(UInt8, 84))
             @test h.origin_x === Float32(0)
@@ -96,6 +96,12 @@
     end
 end
 
+@testset "read_mmap" begin
+    emd3001 = read("$(@__DIR__)/testdata/emd_3001.map", MRCData)
+    emd3001mmap = read_mmap("$(@__DIR__)/testdata/emd_3001.map", MRCData)
+    @test emd3001 == emd3001mmap
+end
+
 @testset "write" begin
     @testset "buffer size has no effect on data" begin
         emd3001 = read("$(@__DIR__)/testdata/emd_3001.map", MRCData)

test/runtests.jl

@@ -6,4 +6,5 @@ using Test
     include("header.jl")
     include("io.jl")
     include("data.jl")
+    VERSION >= v"1.6" && include("consistency.jl")
 end