Merge pull request #19 from yajivunev/master

components logic redux

Author: sheridana

lsd/train/gp/add_local_shape_descriptor.py

@@ -43,6 +43,24 @@ class AddLocalShapeDescriptor(BatchFilter):
             to compute a weighed average of statistics inside an object.
             ``sphere`` accumulates values in a sphere.
 
+        components (string, optional): The components of the local shape descriptors to
+            compute and return. Should be a string of integers chosen from 0 through 9 (if 3D)
+            or 6 (if 2D), in order. Example: "0129" or "345". Defaults to all components.
+
+            Component string lookup, where example component : "3D axes", "2D axes"
+
+                mean offset (mean) : "012", "01"
+                orthogonal covariance (ortho) : "345", "23"
+                diagonal covariance (diag) : "678", "4"
+                size : "9", "5"
+
+            Example combinations:
+
+                diag + size : "6789", "45"
+                mean + diag + size : "0126789", "0145"
+                mean + ortho + diag : "012345678", "01234"
+                ortho + diag : "345678", "234"
+
         downsample (int, optional): Downsample the segmentation mask to extract
             the statistics with the given factore. Default is 1 (no
             downsampling).
@@ -57,6 +75,7 @@ def __init__(
         unlabelled=None,
         sigma=5.0,
         mode="gaussian",
+        components=None,
         downsample=1,
     ):
 
@@ -65,6 +84,7 @@ def __init__(
         self.lsds_mask = lsds_mask
         self.labels_mask = labels_mask
         self.unlabelled = unlabelled
+        self.components = components
 
         try:
             self.sigma = tuple(sigma)
@@ -149,6 +169,7 @@ def process(self, batch, request):
 
         descriptor = self.extractor.get_descriptors(
             segmentation=segmentation_array.data,
+            components=self.components,
             voxel_size=self.voxel_size,
             roi=voxel_roi_in_seg,
         )