1. Slicer and ITK generic image reader module
Alex Yarmarkovich

2. Goal Use extensive ITK IO library in Slicer.
Supported image file formats:
Meta
PNG
 VTK
Gipl
Analyze
Stimulate
JPEG
TIFF
Nrrd
BMP
DICOM2

3. ITK -> VTK -> Slicer
Architecture:
Generic Reader Module TCL / TK
Slicer
vtkITKArchetypeImageSeriesReader
VTK
itk::ImageSeriesReader
itk::ImageFileReader
ITK

4. ITK image readers Itk::ImageFileReader Itk::ImageSeriesReader
uses itk::ImageIOFactory to create specific file format reader
Itk::ImageSeriesReader
internally uses itk::ImageFileReader for reading single images
given one file name generates names for the series

5. vtkITK ArchetypeImageSeriesReader
Encapsulates ITK pipeline
Outputs VTK image: vtkImageData
Extends vtkImageSource
Sets filename template: vtkSetStringMacro(Archetype);
vtkGetStringMacro(Archetype);
Sets image data type (float, char, etc.)
Uses itk::ImageSeriesReader or
itk::ImageFileReader

6. vtkITK ArchetypeImageSeriesReader
ExecuteInformation() methods reads one image and outputs image metadata: origin, spacing, etc.
ExecuteData(vtkDataObject *output) method reads in image data

7. vtkITK ArchetypeImageSeriesReader
if (this->FileNames.size() == 1) {
switch (this->OutputScalarType)
vtkITKExecuteDataFromFile(VTK_DOUBLE, double);
vtkITKExecuteDataFromFile(VTK_FLOAT, float);
vtkITKExecuteDataFromFile(VTK_LONG, long);
vtkITKExecuteDataFromFile(VTK_UNSIGNED_LONG, unsigned long);
vtkITKExecuteDataFromFile(VTK_INT, int);
vtkITKExecuteDataFromFile(VTK_UNSIGNED_INT, unsigned int);
vtkITKExecuteDataFromFile(VTK_SHORT, short);
vtkITKExecuteDataFromFile(VTK_UNSIGNED_SHORT, unsigned short);
vtkITKExecuteDataFromFile(VTK_CHAR, char);
vtkITKExecuteDataFromFile(VTK_UNSIGNED_CHAR, unsigned char);
default:
vtkErrorMacro(<< "UpdateFromFile: Unknown data type"); }

8. vtkITK ArchetypeImageSeriesReader
#define vtkITKExecuteDataFromFile(typeN, type) \
case typeN: \ {\
typedef itk::Image<type,3> image2##typeN;\
itk::ImageFileReader<image2##typeN>::Pointer reader2##typeN = \
itk::ImageFileReader<image2##typeN>::New(); \
reader2##typeN->SetFileName(this->FileNames[0].c_str()); \
reader2##typeN->UpdateLargestPossibleRegion();\
itk::ImportImageContainer<unsigned long, type>::Pointer PixelContainer2##typeN;\
PixelContainer2##typeN = reader2##typeN->GetOutput()->GetPixelContainer();\
void *ptr = static_cast<void *> (PixelContainer2##typeN->GetBufferPointer());\
(dynamic_cast<vtkImageData *>( output))->GetPointData()->GetScalars()->SetVoidArray(ptr, PixelContainer2##typeN->Size(), 0);\
PixelContainer2##typeN->ContainerManageMemoryOff();\ }\
break

9. vtkITK ArchetypeImageSeriesReader
Expended and beatified macro :
case VTK_INT: {
typedef itk::Image<int,3> imageType;
itk::ImageFileReader<imageType>::Pointer reader =
itk::ImageFileReader< imageType>::New();
reader->SetFileName(this->FileNames[0].c_str());
reader->UpdateLargestPossibleRegion();
itk::ImportImageContainer<unsigned long, int>::Pointer pixelContainer;
pixelContainer = reader->GetOutput()->GetPixelContainer();
void *ptr = static_cast<void *> (pixelContainer->GetBufferPointer());
(dynamic_cast<vtkImageData *>( output))->GetPointData()-> GetScalars()->SetVoidArray(ptr, pixelContainer->Size(), 0);\
pixelContainer->ContainerManageMemoryOff();\ }
break

10. Generic Reader Module Tcl procedures:
VolGenericInit – sets callbacks and defaults in Volume(readerModules, volGeneric, xxx)
VolGenericBuildGUI – creates UI menus
VolGenericApply – populates Volume MRML node with metadata: Volume(1,node)
VolGenericReaderProc – populates Volume with data: Volume(1,vol). Called both from the reader and the Scene Loader.

11. Generic Reader Module UI

12. VolGenericInit proc VolGenericInit {} {
global Gui VolGeneric Volume Slice Module
if {$Module(verbose) == 1} {puts "VolGenericInit starting"}
set e VolGeneric
set Volume(readerModules,$e,name) "Generic Readers"
set Volume(readerModules,$e,tooltip) "This tab lets you read in Generic volumes"
set Volume(readerModules,$e,procGUI) ${e}BuildGUI ;#called in MainBoot
set Volume(readerModules,$e,procEnter) ${e}Enter ;# called when module UI is exposed
set Volume(readerModules,$e,procExit) ${e}Exit ;# called when module UI is hidden
set Volume(VolGeneric,idList) ""
# for closing out a scene
set Module($e,procMainFileCloseUpdateEntered) VolGenericMainFileCloseUpdate
# register the procedures in this file that will read in volumes
set Module(Volumes,readerProc,Generic) VolGenericReaderProc }

13. VolGenericBuildGUI proc VolGenericBuildGUI {parentFrame} {
global Gui Volume Module
set f $parentFrame.fVolume
DevAddFileBrowse $f Volume firstFile "First Image File:" "VolumesSetFirst" "" "\$Volume(DefaultDir)" "Open" "Browse for the first Image file" "Browse to the first file in the volume" "Absolute"
frame $f.fLabelMap -bg $Gui(activeWorkspace)
frame $f.fDesc -bg $Gui(activeWorkspace)
frame $f.fName -bg $Gui(activeWorkspace)
frame $f.fscalarType -bg $Gui(activeWorkspace)
pack $f.fLabelMap -side top -padx $Gui(pad) -pady $Gui(pad) -fill x
pack $f.fDesc -side top -padx $Gui(pad) -pady $Gui(pad) -fill x
pack $f.fName -side top -padx $Gui(pad) -pady $Gui(pad) -fill x
pack $f.fscalarType -side top -padx $Gui(pad) -pady $Gui(pad) -fill x

14. VolGenericBuildGUI # Name row set f $parentFrame.fVolume.fName
eval {label $f.lName -text "Name:"} $Gui(WLA)
eval {entry $f.eName -textvariable Volume(name) -width 13} $Gui(WEA)
pack $f.lName -side left -padx $Gui(pad)
pack $f.eName -side left -padx $Gui(pad) -expand 1 -fill x
pack $f.lName -side left -padx $Gui(pad)

15. VolGenericBuildGUI #-------------------------------------------
# Apply frame
set f $parentFrame.fApply
DevAddButton $f.bApply "Apply" "set Volume(fileType) Generic; VolGenericApply; VolumesSetPropertyType VolHeader" 8
DevAddButton $f.bCancel "Cancel" "VolumesPropsCancel" 8
grid $f.bApply $f.bCancel -padx $Gui(pad)

16. VolGenericApply # add a mrml node set n [MainMrmlAddNode Volume]
set i [$n GetID]
# read image metadata
vtkITKArchetypeImageSeriesReader genreader
genreader SetArchetype $Volume(VolGeneric,FileName)
genreader SetOutputScalarTypeTo$Volume(scalarType)
# flip the image data going from ITK to VTK
vtkImageFlip Volume($i,vol,rw)
Volume($i,vol,rw) SetFilteredAxis 1
Volume($i,vol,rw) SetInput [genreader GetOutput]

17. VolGenericReaderProc
proc VolGenericReaderProc {v} {
global Volume
catch "genreader Delete"
vtkITKArchetypeImageSeriesReader genreader
genreader SetArchetype [Volume($v,node) GetFullPrefix]
genreader SetOutputScalarType [Volume($v,node) GetScalarType]
catch "flip Delete"
vtkImageFlip flip
flip SetFilteredAxis 1
flip SetInput [genreader GetOutput]
flip Update
Volume($v,vol) SetImageData [flip GetOutput]
flip Delete
genreader Delete }