9.81. Read Images [3D Stack] (ITK)
This filter directly wraps an ITK filter of the same name.
Group (Subgroup)
ITKImageProcessing (ITKImageProcessing)
Description
Read in a stack of 2D images and stack the images into a 3D Volume using the ITK library. Supports most common scalar pixel types and the many file formats supported by ITK. The filter will create a new Image Geometry. The user can specify a value for the origin and the spacing if the defaults are not appropriate. The default value for the origin will be at (0, 0, 0) and the default spacing value will be (1.0, 1.0, 1.0). If the user needs to have the create Image Geometry located in a different location in the global reference frame, the user can change the default origin value. The “origin” of the image is at a normal Cartesian style origin. The user can decide to scale the images as they are being read in by turning on the Scale Images option, and setting a scale value. A scale value of 10.0 resamples the images in the stack to one-tenth the number of pixels, a scale value of 200.0 resamples the images in the stack to double the number of pixels. The default scale value is 100.0.
Image Operations
The user can select to flip the images about the X or Y Axis during import. The result of these operations can be seen in Figures 1, 2 and 3
Input Parameter(s)
Parameter Name |
Parameter Type |
Parameter Notes |
Description |
|---|---|---|---|
Origin |
Vector of Float32 Values |
Order=X,y,Z |
The origin of the 3D volume |
Spacing |
Vector of Float32 Values |
Order=X,y,Z |
The spacing of the 3D volume |
Optional Slice Operations |
Choices |
Operation that is performed on each slice. 0=None, 1=Flip about X, 2=Flip about Y |
|
Convert To GrayScale |
Bool |
The filter will show an error if the images are already in grayscale format |
|
Color Weighting |
Vector of Float32 Values |
Order=Red,Green,Blue |
RGB weights for the grayscale conversion using the luminosity algorithm. |
Resample Images |
Choices |
Mode can be [0] Do Not Rescale, [1] Scaling as Percent, [2] Exact X/Y Dimensions For Resampling Along Z Axis |
|
Scaling |
Scalar Value |
Float32 |
The scaling of the 3D volume, in percentages. Percentage must be greater than or equal to 1.0f. Larger percentages will cause more voxels, smaller percentages will cause less voxels. For example, 10.0 is one-tenth the original number of pixels. 200.0 is double the number of pixels. |
Exact 2D Dimensions |
Vector of UInt64 Values |
Order=X,Y |
The supplied dimensions will be used to determine the resampled output geometry size. See associated Filter documentation for further detail. |
Set Image Data Type |
Bool |
Set the final created image data type. |
|
Output Data Type |
Choices |
Numeric Type of data to create |
Input File List
Parameter Name |
Parameter Type |
Parameter Notes |
Description |
|---|---|---|---|
Input File List |
GeneratedFileList |
The list of 2D image files to be read in to a 3D volume |
Output Data
Parameter Name |
Parameter Type |
Parameter Notes |
Description |
|---|---|---|---|
Created Image Geometry |
DataGroupCreation |
The path to the created Image Geometry |
|
Cell Data Name |
DataObjectName |
The name of the created cell attribute matrix |
|
Created Image Data |
DataObjectName |
The path to the created image data array |
Note on Resampling
The optional resampling parameter has two options that affect the output image and size of the resulting geometry.
Scaling Factor (1) - This is the scaling option that previously existed with the filter. It functions by providing a float value that becomes a XYZ scaling factor vector that is applied to each image before it is inserted into the final geometry. This means that the number of pixels in the resulting output image will be resampled to
{X * (ScalingFactor / 100.0), Y * (ScalingFactor / 100.0), Number of Images In Stack} (XYZ). This means that a value of 100 (Like 100%) will NOT perform any resampling. A value of 50 will produce a final output image that has half as many pixels along the X and Y Axis. A value of 200 will have twice as many voxels along the X and Y Axis.Exact XY Dimensions (2) - This is provided to allow for precision resampling along the Z Axis. The number of pixels in the resulting output image will be resampled to
{User Supplied X, User Supplied Y, Number of Images In Stack} (XYZ).
Both options are different ways to parameterize the resampling functionality. The main difference should be that Scaling Factor (1) is implicity uniform in its resampling across the X and Y dimensions, but the same is not true for Exact XY Dimensions (2).
Example Pipelines
(08) Image Initial Visualization
(09) Image Segmentation
License & Copyright
Please see the description file distributed with this plugin.
DREAM3D-NX Help
If you need help, need to file a bug report or want to request a new feature, please head over to the DREAM3DNX-Issues GitHub site where the community of DREAM3D-NX users can help answer your questions.