TODO

Remove all references to perl PERL
Get output images only produced in BINARY_DIR.

-- (DONE) Have python code line extractor throw warning when lines are too long to print. 
-- Reduce line length in ITK proper
-- Figure out which pictures need "flipping" and how to do that with imagemagik.
-- Order all tex files in SoftwareGuide/Latex/*.tex to be ordered when listed with a ##-${filename} prefix.
-- Re-order chapters
-- Add "Remote Module documentation"
-- Remove "CenteredTransforms" from all examples in book.
-- Remove redundant information.
-- Describe Modularization as part of a ITKv3->ITKv4 transition appendix
-- Update Acknowledgments
-- Test clean builds
-- Support "USE_SYSTEM_ITK"

==========================================================
This is a list of potential topics to be added to the Software Guide.

Chapter 1

Add more on the "Data" section: expand it in order to mention

  - IBSR repository: add a paragraph, how to get their data,
      how to read it with ITK. And add a \ref{} to ImageIO 
      chapter and MetaImages.

  - BrainWeb repository: add a paragraph, how the get their data.
      how to read it  using MetaImage.

  - MIRC (RSNA).  www.rsna.org/mirc  add a paragraph about it.

 Mention that the reader has to go to the ImageIO chapter in order 
 to learn about all the fileformats in ITK.


Chapter 2

- Update list of compilers
     
      Intel (Linux, Windows),  7.1, 8.0
      Sun native CC 5.6 
      SGI 7.4 (??) check with Bill Lorensen
      Mac GCC 3.3
      Free VC++
      Visual Studio  6.0 ,  7.0,   7.1
      Borland 5.5
      MinGW  gcc
      Cygwin gcc 

 - Configuration:

     Add CMake screen shots for the Mac (from Jon).

Chapter 3

    Check with Will...

Chapter 4    Data Representation

(1) Luis
   - 4.1.4 Update it to mention OriginType and SpacingType instead of
     arrays of doubles and/or floats.


(1) Luis
  - 4.1.7  Import Data to image

     Take from the tutorial and build up this section

     https://www.itk.org/CourseWare/Training/GettingStarted-V.pdf


     Explain how to put an ITK pipeline inside a C function and
     prevent the output image from being destroyed.

     Add... source code examples to the CVS Examples directory.

  Mesh  (Karthik)
     
(1) 
     - Double check that the AutomaticMesh example works as advertised... 
        [Status: done. 
          It works
        ]

(1)
    -  Double check that all the examples are still working... 
      [Status: done 
        Checked.. work
      ]

(3)
    - Check with Will about the AutoPointer...  maybe remove the 
      notation of TakeOwnership,... check with vtkAbstracCell.


(2)
   - Add example on how to use the Neighborhood links 

     
           BuildCellLinks()

      [Status: Pending
        Approporiate Example ?
      ]

(1)
   - Add section on the Simplex 
     (check Leila Baghdadi, and Thomas Boettger).

(5)
   - Graph cuts (liver segmentation).
     check mailing list archives, check the Voronoi.





Chapter 5  Spatial Objects
(Julien+Stephen outsourcing) + a few pages in 1 month.


    Coordinate with Julien Jomier at UNC. 
    They plan to update this section.

    e.g. add the ImageMaskSpatialObject.

    PolygonSpatialObject ??



    

      
    

Chapter 6 Filtering



(1) Karthik
   - in Thresholding add examples:

       OtsuThresholdImageCalculator (using it alone)    [Status: Done]
       OtsuThresholdImageFilter (already there, but needs refinement).  [Status: Done]

       OtsuMultipleThreshold Calculator (using it alone).          
       OtsuMultipeleThreshodl Filter (add example + filter).       
        
        [Status: Done]
        [ToDo: Maybe update Otsu Multiple Threshold filter example to the new itkOtsuThresholdFilter]
        added by Padfiled. The earlier one used the ThresholdCalculator class
          cvs add Art/OtsuThresholdImageFilterOutput.png
          cvs commit Insight/Examples/Filtering/OtsuMultipeleThresholdImageFilter.cxx
        ]




(5) 
 - 6.2.1 Casting filters (low priority)

     splitting CastImageFilter into 4 separate .cxx
     
     and check if we have other casting filters...


 (1)     
 - Double check equation pdf-page 147. Equations were correctd.




(2) [Add 1 and ask Jim what to choose]
 - Mathematical morphology, 

     add Examples for the new filters that Jim Miller (GE)
     added recently


         GrayScaleFillHoleImageFilter
         GrayScaleGrindPeakImageFilter
         GrayScaleConnecteOpeningImageFilter
         GrayScaleConnecteCloseningImageFilter
         GrayScaleGeodesicDilateImageFilter
         GrayScaleGeodesicErodeImageFilter


(1) Karthik
- FFT examples. (Fourier)

        Maybe add a couple more examples...
        
        at least comment the existing ones
        and generate output example images.
        [Status: Postponed. Necessary ??
          One example exists and works. Maybe add some figures. 
          Rescale FFT outputs to log and display, Change example, add logMappingFuctor ?]


(1) Luis
- RecursiveGaussianImage filter DC component bug, keep track
  of it during the example. check BUG in the bug tracker.





- Voting filters

(2) Luis 
    Add examples for Voting filters
    HoleFilling


(2) Luis
- Add example for BinaryMedianImageFilter, take a noisy
  segmentation (e.g. plain thresholding) and then post-
  process it with this filter.
    [Status: done.]
    [ToDo: Add Examples/Filtering/BinaryMedianImageFilter.cxx to CVS]
    [Add BinaryMedianImageFilterOutput.jpg to SoftwareGuide/Art/]
    [Add BinaryThresholdImageFilterOutput.jpg to SoftwareGuide/Art/]



(3)
- Discrete Gaussian needs to fix the graphic according
  to the original. Check with Jim Miller, to get the
  paper.



  

- Check with Andy : capture the command line used for running
  the regression testing and paste it on Latex.


(1) Karthik
- Edge preserving filtering: move the Median filter here,
  and show the effect of running many iterations of a median.
  Explain its relationship to Voting filters.
  
  [Ask Luis about Recursive Filter discrepancy ?? What's going on ?]
  
  [Status Done: 
    cvs commit SoftwareGuide/Latex/Filtering.tex]



(3) Luis
- MinMaxCurvatureFlowImage check this example,
  Ask Lydia what was wrong with the example.



(1) Karthik 
- Signed distance based on running Danielsson twice,

  Mention that the same can be done with ReinitializeLevelSetImageFilter
  ...maybe add an example...
  https://www.itk.org/Insight/Doxygen/html/classitk_1_1ReinitializeLevelSetImageFilter.html

  Check with Lydia (Brain Allen Institute) and/or Josh Cates (Utah)

  [Status: Done]
  [Added Insight/Code/BasicFilters/itkSignedDanielssonDistanceMapImageFilter.hxx, 
         Insight/Code/BasicFilters/itkSignedDanielssonDistanceMapImageFilter.h
         Testing/BasicFilters/SignedDanielssonDistanceMapImageFilterTest.cxx
          to repository]
  [ToDo: Commit 
      cvs add Insight/Examples/Filtering/SignedDanielssonDistanceMapImageFilter.cxx 
      cvs add SoftwareGuide/Art/SignedDanielssonDistanceMapImageFilterOutput.png
      cvs add SoftwareGuide/Art/Circle.png
      cvs commit /InsightDocuments/SoftwareGuide/Examples/CMakeLists.txt
  ]


(1) Luis
- Geometric Transform Filters

  Double check that the changes in CenteredTransforms are not breaking
  any code, and that the comments are appropriate.


(2) Will
- MRI Bias correction from InsightApplications (Martin Styner).



Chapter 7 IO


(1) Karthik
- Update Figure 7.3 to add all the known fileformats

- Add a table with all  the fileformat from the FAQ in Wiki.

    [Status: Done]
    [ToDo: Update figure InsightDocuments/Art/SoftwareGuideImageIOFactoriesClassDiagram.fig in CVS]


- Add the examples for Series Read Write:

  The .cxx are there, they need to:

    1. Revision of their comments
    2. Make sure they have regression testing.
    3. Make sure they are input in Latex
    
    
  - ImageReadImageSeriesWrite.cxx
  - ImageSeriesReadWrite.cxx      [unnecessary if there is a series write and a series read anyway ?]
  - RGBImageSeriesReadWrite.cxx
  
  [Status: Done]


(1) Mathieu
- Add a section on DICOM

  - Maybe introduction by Mathieu 
    - short history, web site, standards.
      JPEG compression... etc.

  - How to read single DICOM slice
  - How to write single DICOM slice
  - How to read a DICOM series 
  - How to write a DICOM series 
  - How to printout an entire DICOM header
  - How to get specific entries.

    DicomSeriesReadImageWrite.cxx
    DicomSeriesReadImageWrite2.cxx
    DicomSeriesReadPrintTags.cxx
    DicomSeriesReadSeriesWrite.cxx

  [Status: Added little bit, Ask Mathieu to finish the rest]
  [Added SWGuide comments to file /Insight/Examples/IO/DicomSeriesReadImageWrite2.cxx]
  [Changed IO.tex to include GDCMDicom instead of older DICOM]
  [ToDo: cvs Update files: 
          /Insight/Examples/IO/DicomSeriesReadImageWrite2.cxx
          /InsightDocuments/SoftwareGuide/IO/IO.tex
          /InsightDocuments/Latex/Insight.bib  
          /InsightDocuments/SoftwareGuide/Examples/CMakeLists.txt
  ]




- Chapter 8  Registration

 (1) Luis 
  - Add a diagram from the PPT tutorial
    regarding pixel spacing.

(3) 
  - Add time performance for the examples & 
    describe Zion. (check about multithreading).

(1) Karthik (add them to the list, not making new examples).
  - Section 8.4  Add the other MI metrics


    - Kullback Leibler MI
    - Normalized Mutual Information Histogram

    Add other Metrics: (find a section for them...)
    
    - MatchCardinality metric
    - GradientDifferenceImageMetric      
    - KappaStatistics
    - MeanReciprocalSquares

  [Status: Done]
  [ToDo: Update
      /SoftwareGuide/Latex/ImageMetrics.tex
      /InsightDocuments/Latex/Insight.bib
  ]


(1) Luis
  - ImageRegistration8 --> 3D example
    

(2) Luis
  - Add ImageRegistration7 & the Similarity transform.


(1) Luis
  - In Multi-Resolution add comment regarding the approach
    of fine-tunning the parameters for each level.

(3) Luis
  -  ImageRegistration11.cxx  use of the OnePlusOne optimizer + MI metric.
    
  
(2) Luis
   - Move Section 8.11 Multires pyramid filter to the Section on 
     Multiresolution and link it with the .cxx example on the 
     use of this filter.
     Commit the example for StarsEnd on MultiresolutionPyramidFilter.cxx
     polish the comments and add the Latex section.


(5) Leave it alone !
  -  What to do with METRIC & Parameters Plots ?
     they are probably not valid anymore
     but it will take a long time to regenerate them.
  


(1) Luis --> coordinate with Lydia and Stephen
  - Transforms Section:

      Full revision: discuss with Stephen & Lydia, regarding
      parameters & center of rotation.


(1) Karthik
  - Metrics:

      Add new metrics

       - Kullbak Leibler
       - MutualInformationHistogramBased 
       - MatchCardinality metric
       - GradientDifferenceImageMetric      
       - KappaStatistics
       - MeanReciprocalSquares
       - MeanSquaresHistogram
       - CorrelationCoefficientHistogramMetric
       - CompareHistogramImageToImageMetric
    [Status: Done. 
      2 of the above metrics not added
      Not sure if it is necessary to add "CorrelationCoefficientHistogramMetric".. 
      Pretty much the same as NormalizedCorrelationMetric... 
      "CompareHistogramImageToImageMetric" will be used by KullbackLiebler
    ]
      
  


(1) Luis
  - Add Section on PointSet-To-Image registration
    describe the method of the Narrowband to Image
    registration.



(2) Karthik
  - Warping Image 
  
     1) A way of creating ground truth for
        evaluating deformable registration. 
        like morphing.

        [Status: ToDo
          Maybe ask Luis for some fMRI datasets...
        ]  
      

     2) A mechanism for initializing displacement
          fields for deformable registration methods
          like Demons.

      - BSplineWarping
      - LandmarWarping
        [Status: Done
          ToDo: cvs add ThinPlateSplineWarp.cxx
        ]

      [Status: Clarify with Luis
        Not sure what's necessary. The deformation field may be computed with
        BSplineWarping etc and Demons can be initialized via SetInitialDeformationField.
                
       Illustrate how to use Paraview for visualizing
       the deformation field

      [Status: Done
        Added section on viewing 2D deformation fields
        Adding section on viewing 3D deformation fields

      ToDo:
        cvs add /InsightDocuments/SoftwareGuide/Latex/VisualizingDeformationFieldsUsingParaview.tex
        cvs add /InsightDocuments/SoftwareGuide/Art/ParaviewScreenshot1.jpg
        cvs add /InsightDocuments/SoftwareGuide/Art/ParaviewScreenshot2.jpg
        cvs add /InsightDocuments/SoftwareGuide/Art/ParaviewScreenshot3.jpg
        cvs add /InsightDocuments/SoftwareGuide/Art/ParaviewScreenshot1.eps
        cvs add /InsightDocuments/SoftwareGuide/Art/ParaviewScreenshot2.eps
        cvs add /InsightDocuments/SoftwareGuide/Art/ParaviewScreenshot3.eps
        cvs add /InsightDocuments/SoftwareGuide/Art/ParaviewScreenshot4.eps
        cvs commit /InsightDocuments/SoftwareGuide/Latex/Registration.tex
      ]

     - Show an example on the deformation of the grid.
        [Status: ToDo]



     


(1) Will 
    Luis-->Checking FEM PPT from RPI course.

     - Add two examples more for FEM
       using the exact same code but changing the parameter
       file.

(2) Luis help for examples:
       Illustrate how to select the "Elasticity" and "Roc"

       Illustrate the use of Landmarks in the FEM framework.
       FiniteElementRegistrationLandmarks.txt

     - Add a 3D example.... do rendering with Volview ? Paraview ?
    

(3) Luis
       Specially show the modifications needed in the input
       parameter file in order to do 3D.

       

(1) Karthik
   - DEMONS

      - Add example for Symmetric forces demons, explain
        why... from Thirion's paper.
        DeformableRegistration3.cxx example...

        [Status: Done
          Was already there..
        Other changes:
          Removed DeformableRegistration2.cxx and DeformableRegistration3.cxx 
          from Latex/DeformableRegistration.tex, cause its present in 
          Latex/DemonsRegistration.tex
        
        ToDo: 
          cvs commit InsightDocuments/SoftwareGuide/Latex/DemonsRegistration.tex
                     InsightDocuments/SoftwareGuide/Latex/DeformableRegistration.tex
        ]

(2) Karthik
      - Add a 3D example ( on the same image of the 3D FEM)  
    
      - Results visualized in ParaView...
        [Status: Doing]

(1) Karthik (Luis help)
      - FIX equations in section 8.13 for the K factor for
        pixel spacing, and mention the lack of unit-balance
        on Thirion's paper.

      - Run this for the extra examples to be added for FEM.

    [Status: Pending
    ]


(1) Luis
   -  Add example on LevelSet MotionRegistration (Jim filter)
      DeformableRegistration5.cxx:


(2) Karthik
   -  Examples on BSplines 
      2D & 3D and both optimizers LBFGS LBSFGSB.
      DeformableRegistration7 & 8
      (give credit to filter contributor).

    [Status: Working on it
      Will add that to vis using Paraview section
    ]


(2) (Luis) Delegate to Stephen & Julien
   - Model to Image registration (Check with Stephen & Julien)

       - Show the image of the real SpatialObject (e.g. draw
         the Ellipsoid using VTK.

       - Add example of 3D vasculature tree & CT, or Ultrasound.


    

   
Chapter 9 Segmentation


(3) Karthik
    - For all the Region Growing examples add a 3D example,
      and surface render the result with VolView or Paraview.
      run the Plugins in VolView.
      [Status: Done
        Added a 3D example for ConfidenceConnected filter
        Some images and segmented white matter with Volview.
      ToDo:
        cvs add 3DregionGrowingScreenshot1.eps
        cvs add SlicesBrainWebConfidenceConnected.eps
        cvs add ConfidenceConnectedOnBrainWeb.tex        
      ]
      

(1) Karthik
    - Clarify that many seed points can be provided.
      e.g. illustrate the use on the figure 9.1 page 319.
      [Status: Done
        The previous 3D segmentation used 5 seed points. Hopefully that
        clarifies the point.
      ]

(1) Karthik
    - 9.1.4 Add example showing that the seed can be both in
            bright or dark places. 

      [ ?? Not sure if needed ?? The book has segmentations of gray matter!]
    

(2) (Luis) Outsource to Sayan            
    - Add example for KLMRegionGrowing (Check with Sayan).
      & fix Doxygen documentation.
      From the Doxygen page on Groups, remove the helper
      classes used in the KLM filter (e.g. border & region).
      


(2) (Luis) Outsource to Josh 
    - Watersheds :   Add screenshot of the Segmentation Editor ?
                     and a 3D example ?
                    

        -Add example for the new filter
        IsolatedWatershed.


(1) Karthik
    - Level Sets:  Verify that all of them run & eventually
      fine tune the  parameters from the Regression testing.
    [Status: Working on it
    ]
    

(2) Luis
      - Add 3D examples from VolView ?

          - FastMarching
          - ShapeDetection
        X - GeodesicActiveContours
          - Threshold Segmentation


(3) 
    - LevelSet in MultiResolution (Jim Miller GE example).


(1) Will
    - Talk about iso-surface extraction in order to visualize
      the level set.

        - Plug it to VTK
        - monitor the iterations >>> ADD example ITK+VTK ***
          (Look at SNAP) 

(3) 
    - CURVES LevelSet for tubular objects
      Add a .cxx example


(1) Karthik
    - Active Shape Models (Leventon paper by Lydia).
      GeodesicActiveContourShapePriorLevelSetImageFilter.cxx
      [ ?? ]
    


(2) Will (preprocessing for visualization)
    - Use of LevelSets for AntiAliasing & Fourth Order level set.



(2) Luis
    - Voting Filters 
         - General voting filter
         - Majority filter
         - HoleFilling
       X - HoleFillingIterative


(4)
   - Cellular segmentation
        - 2D example
        - Run 3D example



(1) Karthik
   - Hybrid Methods

       Remove Fuzzy : It is patented

       Deformable model : fix an example in 3D and show the output

(3) (Luis) Delegate to Leila & Thomas
       Deformable model Simplex Mesh: InsightApplications (put screenshot).
 
  
(1) Karthik - (eg. Run in microscopy)
  - Relabel Filter & Connected components. (put it in Filtering ???).


(1) Delegate - Stephen
  -  KMeans segmentation (or in Statistics chapter).
  -  MarkovRandomFields (or in Statistics chapter).
       

(1) Outsource - Julien
  - Feature extraction: (check with Julien)

         eventually add figures  ???

  

(2) Will
New Chapter : Visualization


   - Paraview 

       display vector fields
       scalar image


   - VolView 

       a bit of volume rendering
       a bit about ITK Plugins


   - Slicer

       mention ITK filters 


   - Analyze

       mention ITK filters
       
       
   - ImageViewer in InsightApplications


   - ImageMagick


   - MRICro

   - MRIConvert (DICOM)

   - Valmet (segmentation validation)

   - SNAP (Insight Applications).


   
   connecting ITK with VTK

   Take from the Tutorial



   https://www.itk.org/CourseWare/Training/GettingStarted-II.pdf


   Show the example in InsightApplications


   itkReadITKImageShowVTK.cxx
   itkReadITKImageSegmentShowVTK.cxx
   itkReadITKImage3DSegmentShowVTK.cxx


Automation process:

- Added tags to most examples in Filtering/, Segmentation/, Iterators/
- Option to Build Figures
- Option to Flip specified list of input figures (and their output figure dependencies)


Other fixes: (Karthik)
-Fixed Examples Registration/ImageRegistration10.cxx and added outputs
-Fixed Examples Registration/ImageRegistration11.cxx and added outputs
-Fixed Examples Registration/ImageRegistration13.cxx and added outputs





%%% More topics to consider in future releases
%%% \chapter{Application}
%%% 
%%% Pointers and a brief description of the available ITK applications.
%%% 
%%% \chapter{Infrastructure}
%%% \label{chapter:Infrastructure}
%%% 
%%% Smart pointers, exceptions, events, object factories.
%%% \chapter{GUI}
%%% 
%%% Interface to GUI's such as FLTK, Qt, and wxWindows.
%%% \chapter{Wrapping}
%%% 
%%% Using wrappers and generating wrappers.
%%%
%%%\chapter{Numerics}
%%%
%%%Making use of the numerics libraries; interface classes to the numerics classes