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fix some depecations
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@tknopp
tknopp committed Jun 27, 2020
1 parent 5346093 commit da9cef5
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Showing 6 changed files with 114 additions and 117 deletions.
164 changes: 81 additions & 83 deletions src/AnalyzeNifti.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -34,48 +34,48 @@ end
function savedata_analyze(filename::AbstractString, im::ImageMeta; verbose = false, saveas16bit=false, perm=nothing, permRGBData=false)
filenamebase, ext = splitext(filename)

im["permRGBData"] = permRGBData
im[:permRGBData] = permRGBData

if get(im,"dim",3) < 3
warn("voxel size will be wrong for 1D/2D data")
end
T = eltype(im)
if T <: AbstractFloat
c = data(im)
im["cmin"] = minimum(c)
im["cmax"] = maximum(c)
c = arraydata(im)
im[:cmin] = minimum(c)
im[:cmax] = maximum(c)
if saveas16bit
im["scalingFactor"] = 2^14 / maximum(c)
c *= im["scalingFactor"]
im[:scalingFactor] = 2^14 / maximum(c)
c *= im[:scalingFactor]
c = round(Int16,c)
im["datatype"] = ElementType.INT16
im[:datatype] = ElementType.INT16
else
im["scalingFactor"] = 1
im[:scalingFactor] = 1
if eltype(c) != Float32
#c = map(Float32,c) #this does not work for franzi
c = AxisArray(map(f, c.data), c.axes...)
end
im["datatype"] = ElementType.FLOAT32
im[:datatype] = ElementType.FLOAT32
end
im["size"] = [size(c,i) for i=1:4]
im["ndims"] = ndims(c)
im[:size] = [size(c,i) for i=1:4]
im[:ndims] = ndims(c)
else
c = data(im).data
im["cmin"] = 0
im["cmax"] = 1
im["scalingFactor"] = 1
c = arraydata(im).data
im[:cmin] = 0
im[:cmax] = 1
im[:scalingFactor] = 1
if T <: RGB
# This is what is returned by colorize or blend
im["datatype"] = ElementType.RGB
im["size"] = [size(c,i) for i=1:4]
im["ndims"] = ndims(c)
im[:datatype] = ElementType.RGB
im[:size] = [size(c,i) for i=1:4]
im[:ndims] = ndims(c)

elseif T == UInt8
# This is what is returned by fusedVolumes
im["datatype"] = ElementType.RGB
im[:datatype] = ElementType.RGB
c = reorderColor(c)
im["size"] = [size(c,i) for i=1:4]
im["ndims"] = ndims(c)
im[:size] = [size(c,i) for i=1:4]
im[:ndims] = ndims(c)

else
error("Colored data has to be passed as ...")
Expand All @@ -93,22 +93,22 @@ function savedata_analyze(filename::AbstractString, im::ImageMeta; verbose = fal
end

header = properties(im)
header["pixelspacing"] = collect(ustrip.(pixelspacing(im)))
header["offset"] = collect(imcenter(im))
header[:pixelspacing] = collect(ustrip.(pixelspacing(im)))
header[:offset] = collect(imcenter(im))


if ext == ".nii"
im["nii_file"] = true
im["vox_offset"] = 352
im[:nii_file] = true
im[:vox_offset] = 352

open(filenamebase*".nii","w") do fd
write_analyze_hdr(fd, header)
write(fd, Int32(0))
write(fd, c)
end
else
im["nii_file"] = false
im["vox_offset"] = 0
im[:nii_file] = false
im[:vox_offset] = 0
# write data
open(filenamebase*".img","w") do fd
write(fd, c)
Expand Down Expand Up @@ -144,11 +144,11 @@ function loaddata_analyze(filename::AbstractString)
end
end

pixspacing = header["pixelspacing"]*1000u"mm"
offset = header["offset"]*1000u"mm" .- 0.5.*pixspacing.*header["size"][1:3] .+ 0.5.*pixspacing
pixspacing = header[:pixelspacing]*1000u"mm"
offset = header[:offset]*1000u"mm" .- 0.5.*pixspacing.*header[:size][1:3] .+ 0.5.*pixspacing
if ndims(c) == 4
im = AxisArray(c, (:x,:y,:z,:time), tuple(pixspacing...,one(typeof(header["pixelspacing"][1]))*u"s"),
tuple(offset..., zero(typeof(header["offset"][1]))*u"s"))
im = AxisArray(c, (:x,:y,:z,:time), tuple(pixspacing...,one(typeof(header[:pixelspacing][1]))*u"s"),
tuple(offset..., zero(typeof(header[:offset][1]))*u"s"))
else
im = AxisArray(c, (:x,:y,:z), tuple(pixspacing...), tuple(offset... ))
end
Expand All @@ -162,13 +162,13 @@ function loaddata_analyze(filename::AbstractString)
end

function read_analyze_data(fd,header)
if header["datatype"] == ElementType.RGB
if header[:datatype] == ElementType.RGB
# colored data
s = header["size"]
if header["permRGBData"] == false
c = read!(fd, Array{RGB{N0f8}}(undef, header["size"]...))
s = header[:size]
if header[:permRGBData] == false
c = read!(fd, Array{RGB{N0f8}}(undef, header[:size]...))
else
if header["dim"] == 3
if header[:dim] == 3
@info "3D data"
c = read!(fd, Array{Int8}(undef, s[1], s[2], 3, s[3]))
#c = read(fd, UInt8, s[1], s[2], 3, s[3])
Expand All @@ -183,22 +183,22 @@ function read_analyze_data(fd,header)
end
end
else
if header["datatype"] == ElementType.FLOAT32
c = read!(fd, Array{Float32}(undef, header["size"]...))
if header[:datatype] == ElementType.FLOAT32
c = read!(fd, Array{Float32}(undef, header[:size]...))
else
c = map(Float32, read!(fd, Array{Int16}(undef, header["size"]...)) )
c = map(Float32, read!(fd, Array{Int16}(undef, header[:size]...)) )
end

if header["scalingFactor"] > 0
c *= (1/header["scalingFactor"])
if header[:scalingFactor] > 0
c *= (1/header[:scalingFactor])
end
end
return c
end

function write_analyze_hdr(fd, header)

s = header["pixelspacing"].*1000
s = header[:pixelspacing].*1000

write(fd, Int32(348)) #sizeof_hdr::Int32

Expand All @@ -212,11 +212,11 @@ function write_analyze_hdr(fd, header)
write(fd, 'r') #char regular;
write(fd, '0') #char hkey_un0;

write(fd, Int16(header["ndims"])) #short int dim[8];
write(fd, Int16(header["size"][1]))
write(fd, Int16(header["size"][2]))
write(fd, Int16(header["size"][3]))
write(fd, Int16(header["size"][4]))
write(fd, Int16(header[:ndims])) #short int dim[8];
write(fd, Int16(header[:size][1]))
write(fd, Int16(header[:size][2]))
write(fd, Int16(header[:size][3]))
write(fd, Int16(header[:size][4]))
write(fd, ones(Int16,3))


Expand All @@ -227,8 +227,8 @@ function write_analyze_hdr(fd, header)
write(fd, zeros(Int16,1)) # unused1 Int16


write(fd, Int16(header["datatype"])) #short int datatype; -> Float32
write(fd, Int16(_bitpix(header["datatype"]))) #short int bitpix;
write(fd, Int16(header[:datatype])) #short int datatype; -> Float32
write(fd, Int16(_bitpix(header[:datatype]))) #short int bitpix;
write(fd, Int16(0)) #short int dim_un0;

write(fd, Float32(0)) # number of spatial dims
Expand All @@ -238,24 +238,24 @@ function write_analyze_hdr(fd, header)
write(fd, zeros(Float32,4)) # float pixdim[8];


write(fd, Float32(header["vox_offset"])) #float vox_offset;
write(fd, Float32(header[:vox_offset])) #float vox_offset;
#float funused1;
#float funused2;

off = ustrip.(uconvert.(Unitful.mm,header["offset"]))
off = ustrip.(uconvert.(Unitful.mm,header[:offset]))
write(fd, Float32(off[1]))
write(fd, Float32(off[2]))
write(fd, Float32(off[3])) #float funused3;
write(fd, Float32(header["scalingFactor"])) #float cal_max; HERE WE STORE THE SCALING FACTOR!
write(fd, Float32(header[:scalingFactor])) #float cal_max; HERE WE STORE THE SCALING FACTOR!
write(fd, Float32(0)) #float cal_min;
write(fd, Float32(header["permRGBData"])) #float compressed;
write(fd, Float32(header[:permRGBData])) #float compressed;
write(fd, Float32(0)) #float verified;
#write(fd, round(Int32,header["cmin"]))
#write(fd, round(Int32,header["cmax"]))#int glmax,glmin;
#write(fd, round(Int32,header[:cmin]))
#write(fd, round(Int32,header[:cmax]))#int glmax,glmin;
write(fd, zero(Int32))
write(fd, Int32(typemax(Int32)))#int glmax,glmin;

description = Vector{UInt8}(header["experimentDescription"])
description = Vector{UInt8}(header[:experimentDescription])
description = length(description) > 9 ? description[1:9] : description
@debug "" description
write(fd, description)
Expand All @@ -266,20 +266,20 @@ function write_analyze_hdr(fd, header)
write(fd, zeros(Int8,10)) #char originator[10];
write(fd, zeros(Int8,10)) #char generated[10];

scannum = Vector{UInt8}(string(header["experimentNumber"]))
scannum = Vector{UInt8}(string(header[:experimentNumber]))
scannum = length(scannum) > 9 ? scannum[1:9] : scannum
@debug "" scannum
write(fd, scannum)
write(fd, zeros(Int8,10-length(scannum))) #char scannum[10];


subjName = Vector{UInt8}(header["experimentSubject"])
subjName = Vector{UInt8}(header[:experimentSubject])
subjName = length(subjName) > 9 ? subjName[1:9] : subjName
@debug "" subjName
write(fd, subjName)
write(fd, zeros(Int8,10-length(subjName))) #char patient_id[10];

dateStr, timeStr = split("$(header["acqStartTime"])","T")
dateStr, timeStr = split("$(header[:acqStartTime])","T")
dateStr = prod(split(dateStr,"-"))
timeStr = split(timeStr,".")[1]
timeStr = prod(split(timeStr,":"))
Expand All @@ -302,20 +302,20 @@ function write_analyze_hdr(fd, header)
write(fd, Int32(0))
write(fd, Int32(0)) # int omax, omin;
write(fd, Int32(0)) # int smax, smin;
if !header["nii_file"]
if !header[:nii_file]
write(fd, UInt32(0x6E693100))
else
write(fd, UInt32(0x6E2B3100))
end
end

function read_analyze_hdr(fd)
header = Dict{String,Any}()
header = Dict{Symbol,Any}()

read(fd, Int32) #sizeof_hdr::Int32

data_type = String( read!(fd, Array{UInt8}(undef, 10)) ) #char data_type[10];
header["data_type"] = data_type
header[:data_type] = data_type

read!(fd, Array{Int8}(undef, 18)) #char db_name[18];
read(fd, Int32) # int extents;
Expand All @@ -324,66 +324,66 @@ function read_analyze_hdr(fd)
read(fd, Int8) #char hkey_un0;

dim = read(fd, Int16)
header["dim"] = dim
header[:dim] = dim
sizes = read!(fd, Array{Int16}(undef, 7)) #short int dim[8];
header["size"] = sizes[1:dim]
header[:size] = sizes[1:dim]

read!(fd, Array{Int8}(undef, 4)) #vox_units uchar[4] spatial units of measure for a voxel
read!(fd, Array{Int8}(undef, 8)) # cal_units uchar[8] name of the calibration unit


read(fd, Int16) # unused1 Int16

header["datatype"] = read(fd, Int16) #short int datatype; -> Float32
header[:datatype] = read(fd, Int16) #short int datatype; -> Float32
read(fd, Int16) #short int bitpix;
read(fd, Int16) #short int dim_un0;

read(fd, Float32)
voxelSize = read!(fd, Array{Float32}(undef, 7)) # float pixdim[8];
header["pixelspacing"] = voxelSize[1:3] ./ 1000 # this is restricted to 3D...
header[:pixelspacing] = voxelSize[1:3] ./ 1000 # this is restricted to 3D...

if header["dim"] == 4
header["timedim"] = 4
if header[:dim] == 4
header[:timedim] = 4
else
header["timedim"] = 0 #This is likely not always correct
header[:timedim] = 0 #This is likely not always correct
end

read(fd, Float32) #float vox_offset;
#float funused1;
#float funused2;
off = read!(fd, Array{Float32}(undef,3)) #float funused3;
header["offset"] = off
if header["data_type"][1:3]!="MPI"
header["offset"][:] .= 0.0
header[:offset] = off
if header[:data_type][1:3]!="MPI"
header[:offset][:] .= 0.0
end
header["scalingFactor"] = read(fd, Float32) #float cal_max; #HERE WE READ THE SCALING FACTOR
header[:scalingFactor] = read(fd, Float32) #float cal_max; #HERE WE READ THE SCALING FACTOR
read(fd, Float32) #float cal_min;
header["permRGBData"] = (read(fd, Float32) != 0.0) #float compressed;
header[:permRGBData] = (read(fd, Float32) != 0.0) #float compressed;
read(fd, Float32) #float verified;
cmin = read(fd, Int32)
header["cmin"] = cmin
header[:cmin] = cmin
cmax = read(fd, Int32)
header["cmax"] = cmax #int glmax,glmin;
header[:cmax] = cmax #int glmax,glmin;

descr = String( read!(fd, Array{UInt8}(undef, 80)) ) #char descrip[80];
header["experimentDescription"] = descr
header[:experimentDescription] = descr

read!(fd, Array{UInt8}(undef, 24)) #char aux_file[24];
read(fd, UInt8) #char orient;
read!(fd, Array{UInt8}(undef, 10)) #char originator[10];
read!(fd, Array{UInt8}(undef, 10)) #char generated[10];

scannum = String( read!(fd, Array{UInt8}(undef, 10)) ) #char scannum[10];
header["experimentNumber"] = scannum
header[:experimentNumber] = scannum

patient_id = String( read!(fd, Array{UInt8}(undef, 10)) ) #char patient_id[10];
header["experimentSubject"] = patient_id
header[:experimentSubject] = patient_id

exp_date = String( read!(fd, Array{UInt8}(undef, 10)) ) #char exp_date[10];
header["date"] = exp_date
header[:date] = exp_date

exp_time = String( read!(fd, Array{UInt8}(undef, 10)) ) #char exp_time[10];
header["time"] = exp_time
header[:time] = exp_time


read!(fd, Array{UInt8}(undef, 3)) #char hist_un0[3];
Expand All @@ -398,5 +398,3 @@ function read_analyze_hdr(fd)

return header
end


5 changes: 2 additions & 3 deletions src/Arrays.jl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -3,9 +3,9 @@ export makeAxisArray, converttometer, imcenter
converttometer(x::NTuple{D,T}) where {D,T<:Quantity} = ustrip.(uconvert.(u"m",x))
converttometer(x::NTuple{D,T}) where {D,T<:AbstractFloat} = x

imcenter(img::AxisArray) = map(x->(0.5*(last(x)+first(x))),
imcenter(img::AxisArray) = map(x->(0.5*(last(x)+first(x))),
ImageAxes.filter_space_axes(AxisArrays.axes(img), axisvalues(img)))
imcenter(img::ImageMeta) = imcenter(data(img))
imcenter(img::ImageMeta) = imcenter(arraydata(img))

function makeAxisArray(array::Array{T,5}, pixelspacing, offset, dt) where T
N = size(array)
Expand Down Expand Up @@ -34,4 +34,3 @@ function makeAxisArray(array::Array{T,3}, pixelspacing, offset) where T
Axis{:z}(range(offset[3],step=pixelspacing[3],length=N[3])))
return im
end

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