Merge pull request #13 from tlnagy/tn/position-as-axis

add prelim support for position as an additional axis

Author: tlnagy

src/loader.jl

@@ -18,15 +18,45 @@ function load(io::Stream{format"OMETIFF"})
     images = find(omexml, "/ns:OME/ns:Image",["ns"=>namespace(omexml)])
     results = Array{AxisArray}(length(images))
 
-    for (idx, image) in enumerate(images)
-        files = Dict{String, TiffFile}()
+    pos_names = nodecontent.(find(omexml, "/ns:OME/ns:Image/ns:StageLabel[@Name]/@Name",["ns"=>namespace(omexml)]))
+    # if all position names aren't unique then substitute names
+    if length(pos_names) == 0 || !allunique(pos_names)
+        pos_names = ["Pos$i" for i in 1:length(images)]
+    end
 
+    pixels = []
+    master_rawtype = Nullable{DataType}()
+    mappedtype = Int64
+    master_dims = []
+    axes_dims = Nullable{Vector{AxisArrays.Axis}}()
+    for (idx, image) in enumerate(images)
         pixel = findfirst(image, "./ns:Pixels", ["ns"=>namespace(omexml)])
-        tiffdatas = find(pixel, "./ns:TiffData", ["ns"=>namespace(omexml)])
-
+        dims, axes_info = build_axes(pixel)
         rawtype, mappedtype = type_mapping[pixel["Type"]]
 
-        dims, axes_info = build_axes(pixel)
+        if isnull(master_rawtype)
+            master_rawtype = Nullable(rawtype)
+        elseif get(master_rawtype) != rawtype
+            throw(FileIO.LoaderError("OMETIFF", "Multiple different storage types not supported in a multi position image"))
+        end
+
+        if isnull(axes_dims)
+            axes_dims = Nullable(axes_info)
+            master_dims = dims
+        elseif get(axes_dims) != axes_info
+            throw(FileIO.LoaderError("OMETIFF", "Axes changing between multiple imaging positions is not supported yet"))
+        end
+        push!(pixels, pixel)
+    end
+    push!(get(axes_dims), Axis{:position}(Symbol.(pos_names)))
+    push!(master_dims, length(pos_names))
+
+    data = Array{get(master_rawtype), length(master_dims)}(master_dims...)
+
+    for (pos_idx, pixel) in enumerate(pixels)
+        files = Dict{String, TiffFile}()
+
+        tiffdatas = find(pixel, "./ns:TiffData", ["ns"=>namespace(omexml)])
 
         # TODO: Only the IFDs with a corresponding slice should be loaded.
         slices = DefaultDict{String, Dict{Int, ImageSlice}}(Dict{Int, ImageSlice}())
@@ -35,8 +65,7 @@ function load(io::Stream{format"OMETIFF"})
             slices[slice.file.filepath][slice.ifd_idx] = slice
         end
 
-        data = Array{rawtype, length(dims)}(dims...)
-        height, width = dims[1:2]
+        height, width = master_dims[1:2]
 
         for (filepath, ifds) in slices
             file = files[filepath]
@@ -49,26 +78,25 @@ function load(io::Stream{format"OMETIFF"})
                 read_dims = n_strips > 1 ? (strip_len) : (height, width)
 
                 # TODO: This shouldn't be allocated for each ifd
-                tmp = Array{rawtype}(read_dims...)
+                tmp = Array{get(master_rawtype)}(read_dims...)
                 for j in 1:n_strips
                     seek(file.io, strip_offsets[j])
                     read!(file.io, tmp)
                     tmp = file.need_bswap ? bswap.(tmp) : tmp
                     if n_strips > 1
-                        data[j, :, ifd.z_idx, ifd.c_idx, ifd.t_idx]= tmp
+                        data[j, :, ifd.z_idx, ifd.c_idx, ifd.t_idx, pos_idx]= tmp
                     else
-                        data[:, :, ifd.z_idx, ifd.c_idx, ifd.t_idx] = tmp
+                        data[:, :, ifd.z_idx, ifd.c_idx, ifd.t_idx, pos_idx] = tmp
                     end
                 end
             end
         end
 
         # drop unnecessary axes
         # TODO: Reduce the number of allocations here
-        squeezed_data = squeeze(Gray.(reinterpret(mappedtype, data)), (find(dims .== 1)...))
-        results[idx] = AxisArray(squeezed_data, axes_info[dims .> 1]...)
     end
-    length(results) == 1 ? results[1] : results
+    squeezed_data = squeeze(Gray.(reinterpret(mappedtype, data)), (find(master_dims .== 1)...))
+    AxisArray(squeezed_data, get(axes_dims)[master_dims .> 1]...)
 end
 
 """Corresponding Julian types for OME-XML types"""

test/runtests.jl

@@ -42,6 +42,15 @@ using Base.Test
             @test size(img[Axis{:z}(1)]) == (167, 439, 3)
         end
     end
+    @testset "Multi position OME-TIFF" begin
+        open("testdata/singles/background_1_MMStack.ome.tif") do f
+            s = Stream(format"OMETIFF", f, OMETIFF.extract_filename(f))
+            img = OMETIFF.load(s)
+            @test size(img) == (1024, 1024, 9)
+            # check position indexing
+            @test size(img[Axis{:position}(:Pos1)]) == (1024, 1024)
+        end
+    end
 end
 @testset "Multi file OME-TIFFs" begin
     @testset "Multi file Z stack with master file" begin