Conda installation¶

Download the Python 2.7 version of miniconda corresponding to your plateform from http://conda.pydata.org/miniconda.html

Execute the downloaded file: this will install the Conda package manager.

Add the dfroger binstar channel to your config:

conda config --add channels https://conda.binstar.org/dfroger

Heimdali installation¶

Install the heimdali package in a environment called heim or whather name you want:

conda create -n heim heimdali

Activate the environment:

source activate heim

Your are ready to use Heimdali.

Test Heimdali installation¶

Download some input data to test:

git clone https://github.com/dfroger/heimdali-data

Execute the par command:

par heimdali-data/imtest_z5_y4_x3_c2.h5

Heimdali update¶

You can update Heimdali when a new version is released:

conda update heimdali

You may also want to keep the currently installed Heimdali version, and install a new version in another Conda environment:

conda create -n heim0.1 heimdali==0.1.0

You can now switch between the two version of Heimdali:

source activate heim

or

source activate heim0.1

Synopsis¶

h5toinr  [--] [--version] [-h] <inputFilename> <outputFilename>

Synopsis¶

inrtoh5  [--] [--version] [-h] <inputFilename> <outputFilename>

Synopsis¶

par  [--wr <output.txt>] [--x0] [--y0] [--z0] [-o] [-x] [-y] [-z] [--]
     [--version] [-h] <INPUT> ...

Description¶

par print on stdout in the file outout.txt, the format parameters of iamges given as arguments.

The –wr options can be given the special file names stdout and stderr. If the file name output.txt starts with >>, result are written at the end of the file.

If one or more options –x0 –y0 –z0 -x -y -z is given, par print the corresponding parameters, in the Format options. This allow to use par in command subsitution, as for example:

create image-copy.h5 `par -x -y image.h5` -r

If no options are given, all format parameters are printed for all images on argument.

Synopsis¶

tpr  [-x <NX>] [-y <NY>] [-z <NZ>] [-i <IX>] [-j <IY>] [-k <IZ>] [--]
        [--version] [-h] <IMAGE> ...

Description¶

tpr prints on standard output pixel values of IMAGE given in argument.

Synopsis¶

ad image0-in image1-in [image-out]
so image0-in image1-in [image-out]
mu image0-in image1-in [image-out]
di image0-in image1-in [image-out]
min image0-in image1-in [image-out]
max image0-in image1-in [image-out]

Description¶

All of these commands perform an operation between image0-in and image1-in and write result to image-out. If argument image0-in or image1-in is equal to -, the command reads on standard input. If argument image-out is absent, the command writes to standard output.

All operation are performed on pixels element by element.

See also¶

See also Local arithmetic operations.

Synopsis¶

bi -n value [image-in] [image-out]
sc -n coeff [image-in] [image-out]
sd -n coeff [image-in] [image-out]
lo value [image-in] [image-out]
exp [image-in] [image-out]
ra [image-in] [image-out]
sba -n threshold [image-in] [image-out]
sha -n threshold [image-in] [image-out]
mb -n threshold [image-in] [image-out]
mh -n threshold [image-in] [image-out]
mo [image-in] [image-out]
car [image-in] [image-out]
vb -n threshold value [image-in] [image-out]
vh -n threshold value [image-in] [image-out]

Description¶

All of these commands perform an operation on image-in (which can be of any type), and write result in image-out.

image-in and image-out must have the same dimension.

If argument image-in is absent or egal to -, the command reads on standard input.

If argument image-out is absent, the command writes on standard output.

Values passed with -n are float.

Synopsis¶

cco  [--] [--version] [-h] <inputFilename> <outputFilename>

Description¶

cco convert IMAGE-IN into IMAGE-OUT.

Synopsis¶

extg  [-x <NX>] [-y <NY>] [-z <NZ>] [-i <IX>] [-j <IY>] [-k <IZ>] [--]
         [--version] [-h] <FILE-IN> <FILE-OUT>

Description¶

extg extract a subregion in FILE-IN and write it in FILE-OUT.

Synopsis¶

raz  [-x <NX>] [-y <NY>] [-z <NZ>] [-i <IX>] [-j <IY>] [-k <IZ>] [--]
        [--version] [-h] <IMAGE> ...

Description¶

raz fill the image IMAGE given in arguments with zero values.

Synopsis¶

melg  [--idv <IDV>] [--idx <IDX>] [--idy <IDY>] [--idz <IDZ>] [--ivo
      <IXO>] [--ixo <IXO>] [--iyo <IYO>] [--izo <IZO>] [--ivi <IXI>]
      [--ixi <IXI>] [--iyi <IYI>] [--izi <IZI>] [--] [--version] [-h]
      <IMAGE-IN> <IMAGE-OUT

Description¶

melg replace pixels of a subregion IMAGE-OUT with pixels of IMAGE-IN.

Synopsis¶

fzoom  [--sc <X>] [--] [--version] [-h] <IMAGE-IN> <IMAGE-OUT>

Description¶

fzoom increse or reduce the size of an image by lineary interpolation.

Image definition¶

The file heimdali/itkhelper.hxx defines the type of an image.

typedef float PixelFloat

const unsigned int ImageDimension

All images are 3-dimensional.

typedef itk::VectorImage< PixelFloat, ImageDimension > ImageFloat

Images are 3-dimensionial, of size (nz, ny, nx).

Images contains nx * ny * nx pixels, and each pixel is a vector of nv value of type float.

Internally, the image is stored in a continous block of memory, ie is a float*.

Building¶

Proving command line interface¶

Creating image¶

ImageFloat::Pointer CreateImage(unsigned int nx, unsigned int ny, unsigned int nz = 1, unsigned int nv = 1)

itkhelper.hxx defines the CreateImage function to create an image in the temporary program memory. It does not do any persistant operation on the disk.

For example:

Heimdali::ImageFloat::Pointer image = Heimdali::CreateImage(5,5,5,2);

create a image of 3-dimensional image with 5 planes, 5 rows and 5 columns, where is value is a vector of 2 floats.

The following code:

Heimdali::ImageFloat::Pointer image = Heimdali::CreateImage(5,5);

create a image of 3-dimensional image with 1 planes, 5 rows and 5 columns, where is value is a vector of 1 float.

See the file createInputImage.cxx for a running example.

Read and writting image¶

Modifiyting image¶

Install dependencies¶

Create a conda enviromnent named heimdali-dev containing all dependencies:

conda config --add channels http://conda.binstar.org/dfroger
conda create -n heimdali-dev h5unixpipe itk-heimdali libinrimage tclap cmake pip

For the rest of the section, we need to activate the conda environment, and set the CONDA_ENV_PATH environment variable:

source activate heimdali-dev
hash -r
CONDA_ENV_PATH=$(conda info -e | grep '*' | tr -s ' ' | cut -d" " -f3)

Install lettuce:

pip install lettuce

Build Heimdali¶

Build heidmali, asking CMake to search dependances in the Conda environment:

On Mac OS X your will need to install /Developer/SDKs/MacOSX10.5, and use it:

export MACOSX_DEPLOYMENT_TARGET=10.5

cd heimdali
mkdir build; cd build
cmake -DCMAKE_PREFIX_PATH=$CONDA_ENV_PATH ..
make

Configure examples¶

As before, the Conda environment is used. Moreover, because Heimdali has been built in heimdali/build and is not installed (development mode), we need to specified all paths to CMake.

cd heimdali
HEIMDALI_ROOT=$PWD
[ `uname` == 'Darwin' ] && EXT=dylib || EXT=so
cd example
mkdir build; cd build
cmake \
    -DCMAKE_PREFIX_PATH=$CONDA_ENV_PATH \
    -DHEIMDALI_INCLUDE=$HEIMDALI_ROOT/libheimdali \
    -DITKINRIMAGEIO_INCLUDE=$HEIMDALI_ROOT/itkINRimageIO/include \
    -DHEIMDALI_LIBRARY=$HEIMDALI_ROOT/build/libheimdali/libheimdali.$EXT \
    -DITKINRIMAGEIO_LIBRARY=$HEIMDALI_ROOT/build/itkINRimageIO/libitkINRImageIO.$EXT \
    ..

Run functional tests¶

Get Heimdali data files, and set HEIMDALI_DATA_DIR:

git clone https://github.com/dfroger/heimdali-data
export HEIMDALI_DATA_DIR=/path/to/heimdali-data

Add path to the built executables:

cd heimdali
export PATH=$PWD/build/cmd:$PATH

Run the functional tests:

cd tests
lettuce