itkImageFileReader¶
- MLModule¶
genre ITKTools author Wolf Spindler package FMEwork/ReleaseMeVis dll MLITKManualBinding definition MLITKManualBinding.def see also ImageLoad, ImageSave, itkImageFileWriter, MLImageFormatSave, MLImageFormatFileCache, MLImageFormatLoad keywords load, image, read, file, import, nifti, nrrd, bmp, nii, pic, mha, mhd, tiff, vtk, spr, lsm, jpg, jpeg, gipl, img,, hdr,, imggz, mask
Purpose¶
The itkImageFileReader module modules permits access to the file formats supported in itk.
Usage¶
Set Dimension field with the dimension of the file to be loaded, the voxel type for the output image to be created in Voxel Type field and then then use the Browse button to select the file to be loaded.
Tips¶
- Use itkImageFileReader for itk example data.
- Use ImageLoad for MeVisLab example data.
- File loading maps the entire image in memory. For large images this can lead to out of memory problems.
- Color images can only be read correctly if color channels are stored in separate image planes (r,r,r,....g,g,g,...b,b,b). If color channels are stored interleaved (r,g,b,....r,g,b,...r,g,b)the images can be read into 3d vector voxels and then converted to a color image with the module TypeToScalars using Output Dimension C.
- The itkImageFileReader reads tiff file written with MeVisLab only as 2d and in 8 bit without paging which leads to limited data quality and dimension when loading MeVisLab example data which are stored in that format. Use the ImageLoad module for full 3D paged tiff files of any data type.
Output Fields¶
The loaded file is available at output 0. On load failures the output normally will be deactivated. Check the status message in the Info field or in the image output tool tip for additional information.
Parameter Fields¶
Field Index¶
| Close: Trigger | Num Dimensions: Integer |
| Component Type: String | Open: Trigger |
| Correct Sub Voxel Shift: Bool | Pixel Type: String |
| Dimension: Enum | True File Name: String |
| File Name: String | Voxel Type: Enum |
| File Type: String | |
| Info: String | |
| Loader Type: String |
The following parameters are available in the module panel:
Visible Fields¶
True File Name¶
- name: fileName, type: String, persistent: no¶
This read-only field shows the real file name used to save the file. It a a resolved version of the File Name field which might contains variables.
Default is "".
Voxel Type¶
- name: fileDataType, type: Enum, default: int16¶
This is the voxel type to be used for the loaded file. Note that files could be stored in another voxel type - then the voxel type is automatically cast to the selected one. If a file cannot be loaded because the the voxel components cannot be converted then try other voxel types which may fit better to the stored voxel type.
Values:
| Title | Name |
|---|---|
| int8 | int8 |
| unsigned int8 | unsigned int8 |
| int16 | int16 |
| unsigned int16 | unsigned int16 |
| int32 | int32 |
| unsigned int32 | unsigned int32 |
| float | float |
| double | double |
| int64 | int64 |
| unsigned int64 | unsigned int64 |
| complexf | complexf |
| complexd | complexd |
| quaternionf | quaternionf |
| quaterniond | quaterniond |
| vecf2 | vecf2 |
| vec2 | vec2 |
| vecf3 | vecf3 |
| vec3 | vec3 |
| vecf4 | vecf4 |
| vec4 | vec4 |
| vecf5 | vecf5 |
| vec5 | vec5 |
| vecf6 | vecf6 |
| vec6 | vec6 |
| vecf7 | vecf7 |
| vec7 | vec7 |
| vecf8 | vecf8 |
| vec8 | vec8 |
| vecf9 | vecf9 |
| vec9 | vec9 |
| vecf10 | vecf10 |
| vec10 | vec10 |
| vecf16 | vecf16 |
| vec16 | vec16 |
| vecf32 | vecf32 |
| vec32 | vec32 |
| vecf64 | vecf64 |
| vec64 | vec64 |
| matf2 | matf2 |
| mat2 | mat2 |
| matf3 | matf3 |
| mat3 | mat3 |
| matf4 | matf4 |
| mat4 | mat4 |
| matf5 | matf5 |
| mat5 | mat5 |
| matf6 | matf6 |
| mat6 | mat6 |
| Vector2i8 | Vector2i8 |
| Vector2i16 | Vector2i16 |
| Vector2i32 | Vector2i32 |
| Vector2i64 | Vector2i64 |
| Vector3i8 | Vector3i8 |
| Vector3i16 | Vector3i16 |
| Vector3i32 | Vector3i32 |
| Vector3i64 | Vector3i64 |
| Vector4i8 | Vector4i8 |
| Vector4i16 | Vector4i16 |
| Vector4i32 | Vector4i32 |
| Vector4i64 | Vector4i64 |
| Vector5i8 | Vector5i8 |
| Vector5i16 | Vector5i16 |
| Vector5i32 | Vector5i32 |
| Vector5i64 | Vector5i64 |
| Vector6i8 | Vector6i8 |
| Vector6i16 | Vector6i16 |
| Vector6i32 | Vector6i32 |
| Vector6i64 | Vector6i64 |
| Vector7i8 | Vector7i8 |
| Vector7i16 | Vector7i16 |
| Vector7i32 | Vector7i32 |
| Vector7i64 | Vector7i64 |
| Vector8i8 | Vector8i8 |
| Vector8i16 | Vector8i16 |
| Vector8i32 | Vector8i32 |
| Vector8i64 | Vector8i64 |
| Vector9i8 | Vector9i8 |
| Vector9i16 | Vector9i16 |
| Vector9i32 | Vector9i32 |
| Vector9i64 | Vector9i64 |
| Vector10i8 | Vector10i8 |
| Vector10i16 | Vector10i16 |
| Vector10i32 | Vector10i32 |
| Vector10i64 | Vector10i64 |
| Vector16i8 | Vector16i8 |
| Vector16i16 | Vector16i16 |
| Vector16i32 | Vector16i32 |
| Vector16i64 | Vector16i64 |
| Vector32i8 | Vector32i8 |
| Vector32i16 | Vector32i16 |
| Vector32i32 | Vector32i32 |
| Vector32i64 | Vector32i64 |
| Vector64i8 | Vector64i8 |
| Vector64i16 | Vector64i16 |
| Vector64i32 | Vector64i32 |
| Vector64i64 | Vector64i64 |
Correct Sub Voxel Shift¶
- name: correctSubVoxelShift, type: Bool, default: FALSE¶
ITK and ML use different origins for voxel coordinates (at center or atorigin of the pixel). This is usually corrected on transfers of image data between itk and ML algorithms, however, when loading images this is sometimes not expected, because e.g. an image origin at (0,0,0) is desired. Therefore this correction is disabled by default when loading images. If the correction is wanted then this flag shall can be activated.
Dimension¶
- name: fileDimension, type: Enum, default: 3¶
When loading data the created output file will have this dimension. If the stored file has a higher dimension, only an image of the specified dimension will be generated. If a file cannot be loaded because the image dimension cannot be converted then try other dimensions.
Values:
| Title | Name |
|---|---|
| 2 | 2 |
| 3 | 3 |
| 4 | 4 |
| 6 | 6 |
Info¶
- name: info, type: String, default: Invalid path¶
This is a read-only status field showing information and error information, normally about the recent load operation.
Close¶
- name: close, type: Trigger¶
Closes a file if it is open. This can be useful to remove file locks, when a file is overwritten by another file.
Open¶
- name: open, type: Trigger¶
This opens or reopens a file. Normally this is done automatically when specifying any load parameter, however, changes of the file on disk do not lead to a file reopen. This can be done manually using this button.
Num Dimensions¶
- name: numDims, type: Integer, default: 0¶
Dimensionality as it was found in the file by itk::ImageIOBase.
File Type¶
- name: fileType, type: String, default: TypeNotApplicable¶
File type as it was found in the file by itk::ImageIOBase (normally ASCII or Binary).
Component Type¶
- name: componentType, type: String¶
Scalar component type as it was found in the file by itk::ImageIOBase.
Pixel Type¶
- name: pixelType, type: String, default: UNKNOWNPIXELTYPE¶
The way pixels are composed as it was found in the file by the itk::ImageIOBase.
File Name¶
- name: unresolvedFileName, type: String, deprecated name: path¶
This is the file name parameter which normally should contain the full absolute path to the file to be loaded. Note that also variables can be used such as $(NETWORK), $(HOME), and $(DemoDataPath)to specify paths into the current network directory, the user's homedirecory and to the installed example data directory of MeVisLab.
Default is "".