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correct space error
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@aTrotier
aTrotier committed Oct 10, 2022
1 parent 91f4df0 commit 3d234a1
Showing 1 changed file with 206 additions and 15 deletions.
221 changes: 206 additions & 15 deletions RECO_a_MP2RAGE_CS/RECO_JULIA_A_MP2RAGE_CS/macro/utils_write_bruker.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@ using MRIReco
const BrukerWordType = ["_32BIT_SGN_INT","_16BIT_SGN_INT","_32BIT_FLOAT","_8BIT_UNSGN_INT"]


function my_bruker_write_in_REAL(image_4D::Array{Float32,4},dirname::String;calcOffsetSlope=true)
function my_bruker_write_in_REAL(image_4D::Array{Float32,4},dirname::String;calcOffsetSlope=true)
VisuCoreWordType = "_32BIT_FLOAT";
VisuCoreByteOrder = "littleEndian";
VisuCoreDataSlope = ones(size(image_4D,4));
Expand Down Expand Up @@ -37,7 +37,7 @@ function my_bruker_write_in_REAL(image_4D::Array{Float32,4},dirname::String;calc
allowed_max=255 -1;
else
@error "Data-Format not correct specified! VisuCoreWordType should be equal to : \n
[\"_32BIT_SGN_INT\",\"_16BIT_SGN_INT\",\"_32BIT_FLOAT\",\"_8BIT_UNSGN_INT\"]"
[\"_32BIT_SGN_INT\",\"_16BIT_SGN_INT\",\"_32BIT_FLOAT\",\"_8BIT_UNSGN_INT\"]"
end

nframes = size(image_4D,4)
Expand All @@ -48,10 +48,10 @@ function my_bruker_write_in_REAL(image_4D::Array{Float32,4},dirname::String;calc
for i = 1:nframes
minVal = minimum(filter(!isnan,image_4D[:,:,:,i]))
maxVal = maximum(filter(!isnan,image_4D[:,:,:,i]))

(minVal < allowed_min) ? println("Some value of the image are inferior to the minimum allowed value") : 1
(maxVal > allowed_max) ? println("Some value of the image are superior to the minimum allowed value") : 1

image_4D = Float32.(image_4D)
push!(VisuCoreDataMin,minVal)
push!(VisuCoreDataMax,maxVal)
Expand All @@ -61,7 +61,7 @@ function my_bruker_write_in_REAL(image_4D::Array{Float32,4},dirname::String;calc
write(twodseq,image_4D)
close(twodseq);


f = open(dirname*"/visu_pars")
lines = readlines(f)
close(f)
Expand All @@ -70,29 +70,29 @@ function my_bruker_write_in_REAL(image_4D::Array{Float32,4},dirname::String;calc
for i = 1:length(lines)
if contains(lines[i],"##\$VisuCoreFrameCount=") lines2[i]="##\$VisuCoreFrameCount=$nframes" end

if contains(lines[i],"##\$VisuCoreDataMin=")
lines2[i]="##\$VisuCoreDataMin= ( $nframes )"
if contains(lines[i],"##\$VisuCoreDataMin=")
lines2[i]="##\$VisuCoreDataMin=( $nframes )"
str = prod([string(VisuCoreDataMin[i]) * " " for i=1:nframes])
str = str[1:end-1]
lines2[i+1]="$str"
end

if contains(lines[i],"##\$VisuCoreDataMax=")
lines2[i]="##\$VisuCoreDataMax= ( $nframes )"
if contains(lines[i],"##\$VisuCoreDataMax=")
lines2[i]="##\$VisuCoreDataMax=( $nframes )"
str = prod([string(VisuCoreDataMax[i]) * " " for i=1:nframes])
str = str[1:end-1]
lines2[i+1]="$str"
end

if contains(lines[i],"##\$VisuCoreDataOffs=")
lines2[i]="##\$VisuCoreDataOffs= ( $nframes )"
if contains(lines[i],"##\$VisuCoreDataOffs=")
lines2[i]="##\$VisuCoreDataOffs=( $nframes )"
str = prod([string(VisuCoreDataOffs[i]) * " " for i=1:nframes])
str = str[1:end-1]
lines2[i+1]="$str"
end

if contains(lines[i],"##\$VisuCoreDataSlope=")
lines2[i]="##\$VisuCoreDataSlope= ( $nframes )"
if contains(lines[i],"##\$VisuCoreDataSlope=")
lines2[i]="##\$VisuCoreDataSlope=( $nframes )"
str = prod([string(VisuCoreDataSlope[i]) * " " for i=1:nframes])
str = str[1:end-1]
lines2[i+1]="$str"
Expand All @@ -102,11 +102,11 @@ function my_bruker_write_in_REAL(image_4D::Array{Float32,4},dirname::String;calc

if contains(lines[i],"##\$VisuCoreWordType=") lines2[i]="##\$VisuCoreWordType=$VisuCoreWordType" end

if contains(lines[i],"##\$VisuFGOrderDesc=")
if contains(lines[i],"##\$VisuFGOrderDesc=")
lines2[i+1]="($nframes, <FG_CYCLE>, <>, 0, 0)"
end

if contains(lines[i],"##\$VisuGroupDepVals=")
if contains(lines[i],"##\$VisuGroupDepVals=")
lines2[i+1]="(<>, 0)"
end
end
Expand All @@ -120,3 +120,194 @@ function my_bruker_write_in_REAL(image_4D::Array{Float32,4},dirname::String;calc
end
close(f)
end





"""
[VisuCoreDataSlope, VisuCoreDataOffs, VisuCoreDataMin, VisuCoreDataMax]=bruker_genSlopeOffsMinMax(VisuCoreWordType, data, VisuCoreDataSlope, VisuCoreDataOffs)
Implementation in Julia of the function from bruker pv_matlab
# TODO :
1) vérifier complex et matrix > 5 dims
% generates some important visu-parameters from a dataset, dependends on
% the target word-type.
% There are 2 modi:
% - insert VisuCoreWordType, data, VisuCoreDataSlope=1 and VisuCoreDataOffs=0 -> will calculate all output
% variables
% - insert a different Slope or Offset -> will calculate only the VisuCoreDataMin,
% VisuCoreDataMax based on data, VisuCoreDataSlope and VisuCoreDataOffs
%
% Note: VisuCoreWordType _32BIT_SGN_INT _16BIT_SGN_INT and _32BIT_FLOAT
% and if you calculate all parameters, it will leave the zero-value by the zero-value, that means:
% it's possible that not the complete range is used.
%
% IN: some Parameter of visu_pars, and the data-matrix with (dim1, dim2, dim3, dim4, NumberFrames)
% Out: some visu_pars parameter which are necessary for writing a PV-dataset
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Copyright (c) 2012
% Bruker BioSpin MRI GmbH
% D-76275 Ettlingen, Germany
%
% All Rights Reserved
%
% bruker_genSlopeOffsMinMax.m,v 1.1 2012/09/11 14:22:10 pfre Exp
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
"""
function bruker_genSlopeOffsMinMax(VisuCoreWordType::String, data::Array, VisuCoreDataSlope=[1], VisuCoreDataOffs=[0])

if(VisuCoreWordType == "_32BIT_SGN_INT")
allowed_min=-2147483648 +1;
allowed_max= 2147483647 -1;
keepimagezero=true;
calcOffsetSlope=true;
elseif (VisuCoreWordType == "_16BIT_SGN_INT")
allowed_min=-32768 +1;
allowed_max=32767 -1;
keepimagezero=true;
calcOffsetSlope=true;
elseif (VisuCoreWordType == "_32BIT_FLOAT")
allowed_min=-prevfloat(Inf32) +1;
allowed_max=prevfloat(Inf32) -1;
keepimagezero=true;
calcOffsetSlope=false;
elseif (VisuCoreWordType == "_8BIT_UNSGN_INT")
allowed_min=0 +1;
allowed_max=255 -1;
keepimagezero=false;
calcOffsetSlope=true;
else
@error "Data-Format not correct specified! VisuCoreWordType should be equal to : \n
[\"_32BIT_SGN_INT\",\"_16BIT_SGN_INT\",\"_32BIT_FLOAT\",\"_8BIT_UNSGN_INT\"]"
end

# Read Mins and Maxs
dims = size(dataB)

if length(dims)<=5 && isreal(dataB[1])
maxpos=zeros(size(dataB,5),1)
maxneg=zeros(size(dataB,5),1)

for i=1:size(data,5)
maxpos[i]=maximum(dataB[:,:,:,:,i])
maxneg[i]=minimum(dataB[:,:,:,:,i])
end

elseif isreal(dataB[1])
@warn "dims > 5 is not tested"
frameCount = prod(dims[5:end])
maxpos=zeros(frameCount,1);
maxneg=zeros(frameCount,1);
dimlist=dims[5:end];

# generate mapping-table1:
dimmatrix_tmp=zeros(prod(dimlist),length(dimlist));
for i1=1:prod(dimlist)
modulus=mod(i1-1,dimlist[end]);
reminder=fix((i1-1)/dimlist[end]);
dimmatrix_tmp[i1,length(dimlist)]=modulus+1;
for i2=length(dimlist)-1:-1:1
modulus=mod(reminder,dimlist[i2]);
reminder=fix(reminder/dimlist[i2]);
dimmatrix_tmp[i1,i2]=modulus+1;
end
end
# convert to 10 Dims:
dimmatrix=ones(size(dimmatrix_tmp,1),10);
dimmatrix[:,1:size(dimmatrix_tmp,2)]=dimmatrix_tmp;
dimmatrix_tmp = nothing

# generate mapping-table2:
map=reshape(1:frameCount, dimlist);

for i=1:size(dimmatrix,1)
counter=map[dimmatrix[i,1], dimmatrix[i,2], dimmatrix[i,3], dimmatrix[i,4], dimmatrix[i,5], dimmatrix[i,6], dimmatrix[i,7], dimmatrix[i,8], dimmatrix[i,9], dimmatrix[i,10]];
maxpos[counter]=maximum(data[:,:,:,:,dimmatrix[i,1], dimmatrix[i,2], dimmatrix[i,3], dimmatrix[i,4], dimmatrix[i,5], dimmatrix[i,6], dimmatrix[i,7], dimmatrix[i,8], dimmatrix[i,9], dimmatrix[i,10]]);
maxneg[counter]=minimum(data[:,:,:,:,dimmatrix[i,1], dimmatrix[i,2], dimmatrix[i,3], dimmatrix[i,4], dimmatrix[i,5], dimmatrix[i,6], dimmatrix[i,7], dimmatrix[i,8], dimmatrix[i,9], dimmatrix[i,10]]);
end

elseif ~isreal(dataB[1])
@warn "dims > 5 is not tested"
frameCount=prod(dims[5:end]);
maxpos=zeros(2*frameCount,1);
maxneg=zeros(2*frameCount,1);
dimlist=dims[5:end];

# generate mapping-table1:
dimmatrix_tmp=zeros(prod(dimlist),length(dimlist));
for i1=1:prod(dimlist)
modulus=mod(i1-1,dimlist[end]);
reminder=fix((i1-1)/dimlist[end]);
dimmatrix_tmp[i1,length(dimlist)]=modulus+1;
for i2=length(dimlist)-1:-1:1
modulus=mod(reminder,dimlist[i2]);
reminder=fix(reminder/dimlist[i2]);
dimmatrix_tmp[i1,i2]=modulus+1;
end
end
# convert to 10 Dims:
dimmatrix=ones(size(dimmatrix_tmp,1),10);
dimmatrix[:,1:size(dimmatrix_tmp,2)]=dimmatrix_tmp;
dimmatrix_tmp = nothing

# generate mapping-table2:
map=reshape(1:frameCount, [dimlist,1]);

for i=1:size(dimmatrix,1)
counter=map[dimmatrix[i,1], dimmatrix[i,2], dimmatrix[i,3], dimmatrix[i,4], dimmatrix[i,5], dimmatrix[i,6], dimmatrix[i,7], dimmatrix[i,8], dimmatrix[i,9], dimmatrix[i,10]];
maxpos[counter]=maximum(real(data[:,:,:,:,dimmatrix[i,1], dimmatrix[i,2], dimmatrix[i,3], dimmatrix[i,4], dimmatrix[i,5], dimmatrix[i,6], dimmatrix[i,7], dimmatrix[i,8], dimmatrix[i,9], dimmatrix[i,10]]));
maxneg[counter]=minimum(real(data[:,:,:,:,dimmatrix[i,1], dimmatrix[i,2], dimmatrix[i,3], dimmatrix[i,4], dimmatrix[i,5], dimmatrix[i,6], dimmatrix[i,7], dimmatrix[i,8], dimmatrix[i,9], dimmatrix[i,10]]));
maxpos[counter+frameCount]=maximum(imag(data[:,:,:,:,dimmatrix[i,1], dimmatrix[i,2], dimmatrix[i,3], dimmatrix[i,4], dimmatrix[i,5], dimmatrix[i,6], dimmatrix[i,7], dimmatrix[i,8], dimmatrix[i,9], dimmatrix[i,10]]));
maxneg[counter+frameCount]=minimum(imag(data[:,:,:,:,dimmatrix[i,1], dimmatrix[i,2], dimmatrix[i,3], dimmatrix[i,4], dimmatrix[i,5], dimmatrix[i,6], dimmatrix[i,7], dimmatrix[i,8], dimmatrix[i,9], dimmatrix[i,10]]));
end
end

## Claculate slope and off
# later in write2dseq: discdata=(data-offset)/slope

if calcOffsetSlope
if prod(VisuCoreDataSlope[:])==1 && sum(abs.(VisuCoreDataOffs[:]))==0
VisuCoreDataOffs=zeros(length(maxpos));
VisuCoreDataSlope=zeros(length(maxpos));
for i=1:length(maxpos)
if keepimagezero
slope_pos=maxpos[i]/allowed_max;
slope_neg=maxneg[i]/allowed_min;
VisuCoreDataSlope[i]=maximum([slope_pos, slope_neg]);
# VisuCoreDataOffs=0; (still done)
else
VisuCoreDataSlope[i]=(maxpos[i]-maxneg[i])/(allowed_max-allowed_min);
VisuCoreDataOffs[i]=maxneg[i]-allowed_min*VisuCoreDataSlope[i];
end
end
end
else
VisuCoreDataOffs=zeros(length(maxpos),1);
VisuCoreDataSlope=ones(length(maxpos),1);
end

## Calculate VisuCoreDataMax and VisuCoreDataMin
VisuCoreDataMax=zeros(length(maxpos));
VisuCoreDataMin=zeros(length(maxpos));
for i=1:length(maxpos)
VisuCoreDataMax[i]=(maxpos[i]-VisuCoreDataOffs[i])/VisuCoreDataSlope[i];
VisuCoreDataMin[i]=(maxneg[i]-VisuCoreDataOffs[i])/VisuCoreDataSlope[i];
if VisuCoreDataMax[i] > allowed_max+1
@warn "Your dataslope and data of are cutting the values"
VisuCoreDataMax=allowed_max+1;
end
if VisuCoreDataMin[i] < allowed_min-1
@warn "Your dataslope and data of are cutting the values"
end
end

return VisuCoreDataSlope, VisuCoreDataOffs, VisuCoreDataMin, VisuCoreDataMax
end



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