Generate heatmap transforms #8579
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Adds a `GenerateHeatmap` transform to create gaussian response maps from landmark coordinates. This transform is implemented for both array and dictionary-based workflows. It enables the generation of heatmaps from landmark data, facilitating tasks like landmark localization and visualization. The transform supports 2D and 3D coordinates and offers options for controlling the gaussian standard deviation, spatial shape, truncation, normalization, and data type.
Introduces a new interactive notebook demonstrating landmark to heatmap conversion using MONAI transforms. This includes: - A notebook with array and dictionary transform modes. - A test suite for the `GenerateHeatmap` transform. This enhancement enables users to visualize and interact with heatmap generation, facilitating a better understanding and application of the MONAI transforms.
Extends the `GenerateHeatmap` transform to support batched inputs, allowing for more efficient processing of multiple landmark sets. This change modifies the transform to handle inputs with a batch dimension (B, N, spatial_dims) in addition to single-point inputs (N, spatial_dims). It also includes a demonstration of 3D heatmap generation using PyVista for visualization.
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Streamlines the GenerateHeatmap and GenerateHeatmapd transforms for better usability and code clarity. Specifically: - Improves the input landmark array validation to provide a more descriptive error message. - Removes example notebooks. DCO Remediation Commit for sewon.jeon <[email protected]> I, sewon.jeon <[email protected]>, hereby add my Signed-off-by to this commit: 8ef905b I, sewon.jeon <[email protected]>, hereby add my Signed-off-by to this commit: 226bf90 I, sewon.jeon <[email protected]>, hereby add my Signed-off-by to this commit: 3097baf I, sewon.jeon <[email protected]>, hereby add my Signed-off-by to this commit: 0072cb0 Signed-off-by: sewon.jeon <[email protected]>
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Signed-off-by: sewon.jeon <[email protected]>
Signed-off-by: sewon.jeon <[email protected]>
Signed-off-by: sewon.jeon <[email protected]>
Signed-off-by: sewon.jeon <[email protected]>
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Fixes #3328 .
Description
A few sentences describing the changes proposed in this pull request.
This pull request introduces
GenerateHeatmapandGenerateHeatmapdtransforms for creating Gaussian heatmaps from landmark coordinates.The input points are currently expected in ZYX order, but this can be changed to support XYZ if preferred.
The transforms support both batched (B, N, D) and non-batched (N, D) inputs.
Example notebooks are included for demonstration and will be removed before the PR is merged.
Types of changes
./runtests.sh -f -u --net --coverage../runtests.sh --quick --unittests --disttests.make htmlcommand in thedocs/folder.