# Multi Paganin¶

For sample like flesh with bones it is possible to trigger automatically the removal of the bone signal from the data. The filtered data are then (always automatically) reconstructed with the appropriate Paganin parameters for the flesh. A tutorial based on the provided nonregressions tests is givene here Multi Paganin Tutorial. The final image is a collage where the bones are sticked above from another reconstruction with bones appropriate parameters.

The basic usage is the following. Supposing the the par file already contains the parameters appropriate for Paganin reconstruction of flesh, you have to add at the bottom

MULTI_PAGANIN_PARS={}
MULTI_PAGANIN_PARS["BONE_Lmicron"]= 1023.083771
MULTI_PAGANIN_PARS["THRESHOLD"] = 0.32
MULTI_PAGANIN_PARS["DILATE"] = 2
MULTI_PAGANIN_PARS["MEDIANR"] = 4


The above steps are all what is required for the basic usage. An optional keyword

MULTI_PAGANIN_PARS["REPLACEMENT"]


is by default zero. If it is zero the bone correction will be taken with respect to an intrapolated background that diffused from the boundaries of the masked regions: a sort of average of the values found at the border. If it is instead different from zero ( if it is set in the input file) then no diffusion is done but the value is fixed by the given parameter.

The reconstruction passes through several intermediated steps, with temporary files in /tmp , with automatic random names, which are afterwords canceled.

You can redirect the intermediate data on files of your choice for inspection. To do this you can set a selection or the whole of the following options (or just add nothing if you are not interested in the intermediate steps)

MULTI_PAGANIN_PARS["PAGBONE_FILE"]= "pagbone.vol"
MULTI_PAGANIN_PARS["ABSBONE_FILE"]= "absbone.vol"
MULTI_PAGANIN_PARS["CORRBONE_FILE"]= "corrbone.vol"
MULTI_PAGANIN_PARS["CORRPROJSPATTERN"] =  "/tmp/tmppnohHx.vol/proj_%05d.edf"
MULTI_PAGANIN_PARS["CORRECTEDVOL_FILE"] = "corrected.vol"

These files, when they are set by the user and not named automatically in absence of the option,

will not be canceled after usage.

The intermediate files are generated/used in the following steps:

• STEP 1 : generates pagbone.vol with the Paganin for bones

• STEP 2 : generates maskbone.vol from pagbone.vol according to the threshold, the radius for the median filter window and the dilatation

• STEP 3 : generates the absorption reconstruction in absbone.vol

• STEP 4 : generates corrbone.vol from maskbone.vol and absbone.vol. It contains the mask times (absbone.vol -average_around)

• STEP 5 : generates a set of projections in CORRPROJSPATTERN like files from corrbone.vol

• STEP 6 : generates corrected.vol from the original data, but the synthetised projections are used to correct the radiographies before applying Paganin.

• STEP 7 : Produces the final result merging together corrected.vol and pagbone.vol where maskbone.vol is 1.

You can perform selected steps giving the option

*  MULTI_PAGANIN_PARS["STEPS"]= [1,1,1,1,1,1,1]


whose value is a list with seven integers which can be 0 or 1. If a step is activated and previous ones are not, the required files for the selected steps must be already there from a previous run.

Your can select the temporary directory. Its default is /tmp

MULTI_PAGANIN_PARS["TMPDIR"]= "/scratch"