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ENH: Various ReadPeregrineHDF5File Improvements #1016

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Jul 12, 2024
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ENH: Various ReadPeregrineHDF5File Improvements #1016

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e58498d
Peregrine HDF5 reader now allows enabling/disabling all datasets.
joeykleingers Jul 11, 2024
0fce237
Peregrine HDF5 reader: Specify camera data location and datasets.
joeykleingers Jul 11, 2024
88287d2
Update the Peregrine HDF5 reader documentation.
joeykleingers Jul 11, 2024
3f55edb
Default all dataset import boolean parameters to False.
joeykleingers Jul 11, 2024
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38 changes: 22 additions & 16 deletions wrapping/python/plugins/NXDataAnalysisToolkit/docs/ReadPeregrineHDF5FileFilter.md
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Expand Up @@ -10,40 +10,46 @@ The `ReadPeregrineHDF5File` filter is designed to read an HDF5 file that is in a

### Input Parameters
- **`Input Peregrine HDF5 File`** (string): Specifies the complete file path to the target HDF5 file.

## Slice Data Parameters
- **`Slice Data Geometry`**: Path to the Slice Data image geometry to be created.
- **`Slice Data Cell Attribute Matrix Name`**: Name of the Slice Data cell attribute matrix to be created.
- **`Read Segmentation Results`** (boolean): Toggles the reading of segmentation results stored in the HDF5 file.
- **`Segmentation Results`** (string): Comma-delimited string that specifies which segmentation results datasets should be read.
- **`Read Camera Data`** (boolean): Toggles the reading of camera data stored in the HDF5 file.
- **`Camera Data HDF5 Parent Path`**: The path to the parent group of the camera datasets in the HDF5 file.
- **`Camera Data Datasets`**: Comma-delimited string that specifies which camera data datasets should be read.
- **`Read Part Ids`** (boolean): Determines whether part ids data should be read.
- **`Part Ids Array Name`**: Name of the part ids array to be created.
- **`Read Sample Ids`** (boolean): Determines whether sample ids data should be read.
- **`Read Anomaly Detection`** (boolean): Determines whether anomaly detection data should be read.
- **`Read X-Ray CT`** (boolean): Determines whether X-ray computed tomography data should be read.
- **`Read Slices Subvolume`** (boolean): Enables or disables the reading of a specific subvolume of slices data within the HDF5 file. If set to True, additional parameters for specifying the subvolume bounds (`Slices Subvolume X Bounds`, `Slices Subvolume Y Bounds`, `Slices Subvolume Z Bounds`) are required.
- **`Sample Ids Array Name`**: Name of the sample ids array to be created.
- **`Enable Slices Subvolume`** (boolean): Enables or disables the reading of a specific subvolume of slices data within the HDF5 file. If set to True, additional parameters for specifying the subvolume bounds (`Slices Subvolume X Bounds`, `Slices Subvolume Y Bounds`, `Slices Subvolume Z Bounds`) are required.
- **`Slices Subvolume X Bounds`** (tuple of integers): Defines the minimum and maximum x-coordinates of the slices subvolume to be read.
- **`Slices Subvolume Y Bounds`** (tuple of integers): Defines the minimum and maximum y-coordinates of the slices subvolume to be read.
- **`Slices Subvolume Z Bounds`** (tuple of integers): Defines the minimum and maximum z-coordinates of the slices subvolume to be read.
- **`Read Registered Data Subvolume`** (boolean): Enables or disables the reading of a specific subvolume of registered data within the HDF5 file. If set to True, additional parameters for specifying the subvolume bounds (`Registered Data Subvolume X Bounds`, `Registered Data Subvolume Y Bounds`, `Registered Data Subvolume Z Bounds`) are required.
- **`Registered Data Subvolume X Bounds`** (tuple of integers): Defines the minimum and maximum x-coordinates of the registered data subvolume to be read.
- **`Registered Data Subvolume Y Bounds`** (tuple of integers): Defines the minimum and maximum y-coordinates of the registered data subvolume to be read.
- **`Registered Data Subvolume Z Bounds`** (tuple of integers): Defines the minimum and maximum z-coordinates of the registered data subvolume to be read.
- **`Read Scan Data Subvolume`** (boolean): Enables or disables the reading of specific slices of scan data within the HDF5 file. If set to True, an additional parameter for specifying the slice bounds (`Scan Data Slice Bounds`) is required.
- **`Scan Data Slice Bounds`** (tuple of integers): Defines the minimum and maximum slices of the scan data to be read.

### Created Data Objects
- **`Slice Data Geometry`**: Path to the Slice Data image geometry to be created.
- **`Slice Data Cell Attribute Matrix Name`**: Name of the Slice Data cell attribute matrix to be created.
- **`Camera Data 0 Array Name`**: Name of the first camera data array to be created.
- **`Camera Data 1 Array Name`**: Name of the second camera data array to be created.
- **`Part Ids Array Name`**: Name of the part ids array to be created.
- **`Sample Ids Array Name`**: Name of the sample ids array to be created.
## Registered Data Parameters
- **`Registered Data Geometry`**: Path to the Registered Data image geometry to be created.
- **`Registered Data Cell Attribute Matrix Name`**: Name of the Registered Data cell attribute matrix to be created.
- **`Read Anomaly Detection`** (boolean): Determines whether anomaly detection data should be read.
- **`Anomaly Detection Array Name`**: Name of the Anomaly Detection array to be created.
- **`Read X-Ray CT`** (boolean): Determines whether X-ray computed tomography data should be read.
- **`X-Ray CT Array Name`**: Name of the X-Ray CT array to be created.
- **`Enable Registered Data Subvolume`** (boolean): Enables or disables the reading of a specific subvolume of registered data within the HDF5 file. If set to True, additional parameters for specifying the subvolume bounds (`Registered Data Subvolume X Bounds`, `Registered Data Subvolume Y Bounds`, `Registered Data Subvolume Z Bounds`) are required.
- **`Registered Data Subvolume X Bounds`** (tuple of integers): Defines the minimum and maximum x-coordinates of the registered data subvolume to be read.
- **`Registered Data Subvolume Y Bounds`** (tuple of integers): Defines the minimum and maximum y-coordinates of the registered data subvolume to be read.
- **`Registered Data Subvolume Z Bounds`** (tuple of integers): Defines the minimum and maximum z-coordinates of the registered data subvolume to be read.

### Scan Data Parameters
- **`Read Scan Datasets`** (boolean): Toggles the reading of the scan datasets stored in the HDF5 file.
- **`Scan Data Geometry`**: Path to the Scan Data edge geometry to be created.
- **`Scan Data Edge Attribute Matrix Name`**: Name of the Scan Data edge attribute matrix to be created.
- **`Scan Data Vertex Attribute Matrix Name`**: Name of the Scan Data vertex attribute matrix to be created.
- **`Scan Data Vertex List Array Name`**: Name of the Scan Data vertex list array to be created.
- **`Scan Data Edge List Array Name`**: Name of the Scan Data edge list array to be created.
- **`Scan Data Time of Travel Array Name`**: Name of the Scan Data Time of Travel array to be created.
- **`Enable Scan Data Subvolume`** (boolean): Enables or disables the reading of specific slices of scan data within the HDF5 file. If set to True, an additional parameter for specifying the slice bounds (`Scan Data Slice Bounds`) is required.
- **`Scan Data Slice Bounds`** (tuple of integers): Defines the minimum and maximum slices of the scan data to be read.

## Example Pipelines

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