Heimdali’s overview¶
Heimdali is a set of commmand line tools to perform Image processing tools, based on ITK and HDF5
User guide¶
Installation¶
The recommanded way to install Heimdali is using the Conda package manager.
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
Format options¶
These are options describing the image format. There are used each time an image is created.
| option | description |
|---|---|
| -z N | Number of planes |
| -y N | Number of lines |
| -x N | Number of pixel per line |
| -v N | Number of value per pixel |
| -r | Floating point values |
h5toinr¶
h5toinr convert an HDF5 image into INRimage image.
Synopsis¶
h5toinr [--] [--version] [-h] <inputFilename> <outputFilename>
inrtoh5¶
inrtoh5 convert an INRimage image into HDF5 image.
Synopsis¶
inrtoh5 [--] [--version] [-h] <inputFilename> <outputFilename>
par¶
par prints format parameters of images.
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.
tpr¶
tpr prints the pixel values of a image subregion
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.
| option | description |
|---|---|
| -ix, -iy, -iz | Index (counted from 0) of the subregion |
| -x, -y, -z | Size (counted from 0) of the subregion |
Artithmetic operations¶
Arithmetic operations between two images element by element.
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.
| command | description |
|---|---|
| ad | Add two images |
| so | Subtract two images |
| mu | Multiply two images |
| div | Divide two images |
| min | Compute minimum of two images |
| max | Compute maximum of two images |
All operation are performed on pixels element by element.
See also¶
See also Local arithmetic operations.
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.
| command | description |
|---|---|
| bi | Add value to each pixel. |
| sc | Multiply each pixel by coeff. |
| sd | Divied each pixel by coeff. |
| lo | Compute logarithm of each pixel. |
| exp | Compute exponential of each pixel. |
| ra | Compute square root of each pixel. |
| sba | Every pixel inferior or egual to threshold is replaced by threshold. |
| sha | Every pixel greater or egual to threshold is replaced by threshold. |
| mb | Every pixel inferior or egual to threshold is replaced by 1 and others by 0. |
| mh | Every pixel greater or egual to threshold is replaced by 1 and others by 0. |
| mo | Compute each pixel modulo |
| car | Compute each pixel square |
| vb | Every pixel inferior or egual to threshold is replaced by value. |
| vh | Every pixel greater or egual to threshold is replaced by value. |
cco¶
cco change pixel type of image
Synopsis¶
cco [--] [--version] [-h] <inputFilename> <outputFilename>
Description¶
cco convert IMAGE-IN into IMAGE-OUT.
extg¶
extg extract a image subregion
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.
| option | description |
|---|---|
| -ix, -iy, -iz | Index (counted from 0) of the subregion |
| -x, -y, -z | Size (counted from 0) of the subregion |
raz¶
raz Fill an image with zero values
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.
| option | description |
|---|---|
| -x, -y, -z | Size (counted from 0) of the subregion |
melg¶
melg mix two images, testing on pixel 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.
| option | description |
|---|---|
| -ixi, -iyi, -izi | Index (counted from 0) of IMAGE-IN subregion |
| -ixo, -iyo, -izo | Index (counted from 0) of IMAGE-OUT subregion |
| -idx, -idy, -idz | Size of subregion |
Heimdali API¶
Community¶
Developer guide¶
Build Heimdali in development mode¶
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 tclap cmake pip
Install lettuce:
source activate heimdali-dev
hash -r
pip install lettuce
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
Build heidmali:
| variable | meaning |
|---|---|
| CONDA_ENV_PATH | For example, ~/miniconda/envs/heimdali |
| CMAKE_PREFIX_PATH | Where CMake will search for dependent libraries |
| .. | Path to Heimdali main CMakeLists.txt |
mkdir build
cd build
source activate heimdali-dev
CONDA_ENV_PATH=$(conda info -e | grep '*' | tr -s ' ' | cut -d" " -f3)
cmake -DCMAKE_PREFIX_PATH=$CONDA_ENV_PATH ..
make
Add path to the built executables:
cd build
export PATH=$PWD/cmd:$PATH
Execute the functional tests:
cd tests
lettuce