Adding Minnie streamline

CAVEconnectome · Apr 15, 2023 · 838c330 · 838c330
1 parent 06d1a4f
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diff --git a/README.md b/README.md
@@ -116,9 +116,6 @@ v1dd_ds.streamline_nm.radial_distance(xyz0, xyz1)
 
 A particular resolution can be used by passing it as an argument to `dataset.transform_res(voxel_resolution)` or `dataset.streamline_res(voxel_resolution)`.
 
-Note: Currently a data-driven streamline is only available for v1dd.
-Minnie65 is using a placeholder "identity streamline" that is just a straight line in the y direction.
-
 ### Minnie65
 
 * `minnie_transform_nm` : Transform from nanometer units in the original Minnie65 space to microns in a space where the pial surface is flat in x and z along y=0.

diff --git a/standard_transform/data/minnie_um_streamline.json b/standard_transform/data/minnie_um_streamline.json
@@ -0,0 +1 @@
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diff --git a/standard_transform/datasets.py b/standard_transform/datasets.py
@@ -4,11 +4,12 @@
 import os
 import warnings
 
-V1DD_STREAMLINE_POINT_FILE = os.path.join(
-    os.path.dirname(__file__),
-    'data',
-    'v1dd_um_streamline.json',
-)
+def _get_data_path(filename):
+    return os.path.join(os.path.dirname(__file__), 'data', filename)
+
+V1DD_STREAMLINE_POINT_FILE = _get_data_path('v1dd_um_streamline.json')
+MINNIE_STREAMLINE_POINT_FILE = _get_data_path('minnie_um_streamline.json')
+
 MINNIE_VOXEL_RESOLUTION = np.array([4, 4, 40])
 V1DD_VOXEL_RESOLUTION = np.array([9, 9, 45])
 
@@ -87,15 +88,15 @@ def v1dd_streamline_vx(voxel_resolution=V1DD_VOXEL_RESOLUTION):
 def minnie_streamline_nm():
     "Streamline for minnie65 dataset for nm coordinates"
     return Streamline(
-        np.array([[0, 0, 0], [0, 1, 0]]),
+        MINNIE_STREAMLINE_POINT_FILE,
         tform=minnie_transform_nm(),
         transform_points=False,
     )
 
 def minnie_streamline_vx(voxel_resolution=MINNIE_VOXEL_RESOLUTION):
     "Streamline for minnie65 dataset for voxel coordinates"
     return Streamline(
-        np.array([[0, 0, 0], [0, 1000, 0]]),
+        MINNIE_STREAMLINE_POINT_FILE,
         tform=minnie_transform_vx(voxel_resolution),
         transform_points=False,
     )
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
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