Example project.xml for Diffraction Processing

<?xml version="1.0" encoding="UTF-8" standalone="no" ?>
<EMDataInfo xmlns:iplt="http://iplt.org">
<DiffProcessing>
  <!-- The mask for the directory names - mandatory -->
  <ImageMask value="XYZ"/>

  <!-- the mask for the file name (default is %%.tif) - the %% pattern will be replace by the current dataset name, as assembled from the ImageMask entry -->
  <ImageFileMask value="%%.tif" type="string"/>

  
  <!-- Parameters for the diff_mask step. NOTE: the beamstop mask itself is defined further below -->
  <FindMask>
    <!-- if set to true, reduce size by factor of 2 to speed up calculation and reduce the noise-->
    <PreShrink value="1" type="bool"/>
    <!-- If set to true, use only center 50%, reducing image by (another) factor of 2. Using only the center makes the mask finding algorithm more robust as the very dark regions at the edge of the image are removed.-->
    <PreCut value="1" type="bool"/>
    <!-- if present, clips the image to this minimum value prior to running the algorithms -->    
    <MinCutoff value="0.0" type="float"/>
    <!-- 
      Beamstop Mask Detection Algorithm:
      Mode 0 (default) uses a histogram analysis to determine a min max clipping window, which 
      is then used in the cross-correlation with the artificial beamstop image (useful in most cases)
      Mode 1 applies a simply gaussian filter prior to running the CC
      Mode 2 uses local sigma thresholding to extract the beamstop shape (required when strong falloff
      of pixel values across beamstop)
    -->
    <Mode value="0" type="int"/>
    <!-- tweak factor for mode 0, default is 1.2 -->
    <HistoMultiplier value="1.2" type="float"/>
    <!-- tweak factor for mode 2, default is 4 -->
    <LocalSigmaSize value="4" type="int"/>
    <!-- tweak factor for mode 2, default is 8.0 -->
    <LocalSigmaLevel value="8.0" type="float"/>
  </FindMask>

  <!-- Parameters for the 'iplt_diff search' step -->
  <LatticeSearch>
    <!-- apply a gaussian filter to the diff pattern prior to peak search - set to 0.0 to turn this feature off -->
    <GaussFilterStrength value="1.0" type="float"/>
    <!-- minimal and maximal lattice vectors (in pixel) to consider, especially the min value is sometimes needed -->
    <MinimalLatticeLength value="30.0" type="float"/>
    <MaximalLatticeLength value="1.0e4" type="float"/>
    <PeakSearchParams>
      <!-- see the PeakSearch ctor for a description of these parameters -->
      <OuterWindowSize value="10" type="int"/>
      <OuterWindowSensitivity value="0.2" type="float"/>
      <InnerWindowSize value="4" type="int"/>
      <InnerWindowSensitivity value="0.0" type="float"/>
    </PeakSearchParams>
  </LatticeSearch>

  <!-- Parameters for the extraction and integration of intensity profiles, i.e. 'iplt_diff extract' and 'iplt_diff integrate' -->
  <LatticeExtract>
    <!-- half-box size, i.e. total integration box will be 2n+1 pixels large -->
    <BoxSize value="7" type="int"/>
    <!-- if this is greater than zero, a box grow algorithm will be employed to find the optimal box size per peak integration -->
    <BoxGrowAmount value="0" type="int"/>
    <!-- size of the background rim, values of 1 or 2 are best -->
    <BackgroundRimSize value="2" type="int"/>
    <!-- flag to turn on the local background correction based on the gaussian fit - recommended -->
    <BackgroundSubtract value="1" type="bool"/>
    <!-- flag to turn on the fit of the spiral and barrel distortion during lattice refinement - not recommended for good datasets-->
    <RefineLatticeDistortions value="0" type="bool"/>
  </LatticeExtract>

  <!-- strong filter for the reflections that are used in the lattice refinement -->
  <StrongFilter>
    <MinimumQuality value="2" type="float"/>
    <MaximumOffset value="2" type="float"/>
    <MaximumHalfWidth value="7.0" type="float"/>
    <MaximumElipticalRatio value="2" type="float"/>
  </StrongFilter>

  <!-- weak filter for the reflections that are subjected to integration -->
  <WeakFilter>
    <MinimumQuality value="1.2" type="float"/>
    <MaximumOffset value="5" type="float"/>
  </WeakFilter>

  <!-- Parameters for 'iplt_diff sym' -->
  <Symmetrize>
    <!-- 0 = do not merge Friedel mates; 1 = merge Friedel mates, keep singular reflections; 2 = merge Friedel mates, throw out singular ones; 3 = MRC style Friedel merging -->
    <FriedelMode value="0" type="int"/>
  </Symmetrize>

  <!-- unit cell parameters and symmetry -->
  <OrigUnitCell>
   <unitcell type="spatial">
    <a value="65.0" type="float"/>
    <b value="65.0" type="float"/>
    <gamma value="90" type="float"/>
    <thickness value="140" type="float"/>
    <symmetry value="P 4 21 2"/>
   </unitcell>
  </OrigUnitCell>

  <!-- pixel sampling of the images in reciprocal angstrom - not really needed -->
  <Sampling value="4.24e-4" type="float"/>

  <!-- global resolution limit of the processing, for individual iplt_diff steps as well as iplt_diff_merge -->
  <ResLim>
   <rlow value="100" type="float"/>
   <rhigh value="2" type="float"/>
  </ResLim>

  <!-- Parameters for the scaling -->
  <Scale>
    <!-- resolution limits -->
    <Resolution>
      <low value="40" type="float"/>
      <high value="2.5" type="float"/>
    </Resolution>
    <!-- number of bins for the weighted bin scaling -->
    <BinCount value="16" type="int"/>
    <!-- cutoffs for the filtering step after scaling, based on the weighted bins -->
    <WBinISigICutoff value="0.1" type="float"/>
    <WBinSigmaCutoff value="10.0" type="float"/>
    <!-- minimum tilt angle (in degree) for which to invoke an anisotropic pre-scaling-->
    <AnisoMinTilt value="90" type="float"/>
  </Scale>

  <!-- Parameters for the lattice line fitting -->
  <LLFit>
    <!-- experimental weighting algorithms, use mode 1 and cutoff 0.0 for all practical purposes -->
    <Weighting>
      <T1 value="10.0" type="float"/>
      <T2 value="40.0" type="float"/>
      <Mode value="1" type="int"/>
      <Cutoff value="0.0" type="float"/>
    </Weighting>
    <!-- iteration limit for the internal non-linear fitting routine -->
    <MaxIterations value="1000" type="int"/>
    <!-- iteration precision for the internal non-linear fitting routine -->
    <IterationPrecision value="1e-2" type="float"/>
    <!-- bootstrapping mode for improved sigma generation, recommended -->
    <BootstrapFlag value="1" type="bool"/>
    <BootstrapIterations value="20" type="int"/>
    <!-- initial guess mode prior to fitting; 0=from weighted bins, 1=random phase, unit amplitude, 2=totally random-->
    <GuessMode value="0" type="int"/>
    <!-- multiple iterations with different starting values, not as powerful as bootstrapping, best kept at 1 -->
    <Iterations value="1" type="int"/>
    <!-- phantom mode includes two additional values at +- sigma z* -->
    <PhantomMode value="0" type="bool"/>
  </LLFit>

  <!-- Parameters for the post llfit refinement -->
  <Refine>
    <!-- lattice line curve fitting mode 0 (based on Imax and z*max) or 1 (bases on sigmaI and sigmaz*) -->
    <CurveFitMode value="0" type="int"/>
    <!-- zstar fudge factor, experimental -->
    <ZWeight value="8.0" type="float"/>
    <!-- flag to turn intensity scale refinement on or off -->
    <RefineScale value="1" type="bool"/>
    <!-- flag to turn tilt geometry refinement on or off -->
    <RefineTilt value="1" type="bool"/>
    <!-- resolution limits to determine new tilt geometry -->
    <RefineTiltRLow value="10" type="float"/>
    <RefineTiltRHigh value="4" type="float"/>     
  </Refine>


  <!-- This will be created automatically by the 'giplt_diff edit_mask' command. Remove the tag if not needed -->
  <BeamStopMask>
  </BeamStopMask>

  </DiffProcessing>
</EMDataInfo>

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