Add test_dataset

tests/test_data/linear_allen_mouse/alignment_linear.json

+{"name":"PyNutil_testdataset","target":"ABA_Mouse_CCFv3_2017_25um.cutlas","target-resolution":[456.0, 528.0, 320.0],"slices":[
+{"filename":"test_s001.png","nr":1,"width":1500,"height":1000,"anchoring":[-5.145275115966797, 361.8014440433213, 331.1490739071843, 456.0, 0.0, 0.0, 0.0, 0.0, -320.0]}, 
+{"filename":"test_s002.png","nr":2,"width":1500,"height":1000,"anchoring":[-3.8589563369750977, 318.7157039711191, 340.24552914037605, 456.0, 0.0, 0.0, 0.0, 0.0, -320.0]}, 
+{"filename":"test_s003.png","nr":3,"width":1500,"height":1000,"anchoring":[-2.8942172527313232, 275.6299638989171, 350.0189942541106, 456.0, 0.0, 0.0, 0.0, 0.0, -320.0]}, 
+{"filename":"test_s004.png","nr":4,"width":1500,"height":1000,"anchoring":[-3.0282087922096252, 232.54422382671487, 364.1366059225139, 456.0, 0.0, 0.0, 0.0, 0.0, -320.0]}, 
+{"filename":"test_s005.png","nr":5,"width":1500,"height":1000,"anchoring":[-0.6163610816001892, 189.45848375451277, 374.2485759765199, 456.0, 0.0, 0.0, 0.0, 0.0, -320.0]}]}
\ No newline at end of file

workflows/basic_example_custom_atlas.py

@@ -14,12 +14,12 @@ from PyNutil import PyNutil
 ###The object_cutoff is a cut-off for min object size
 
 pnt = PyNutil(
-    segmentation_folder="../tests/test_data/nonlinear_allen_mouse/",
-    alignment_json="../tests/test_data/nonlinear_allen_mouse/alignment.json",
+    segmentation_folder="../tests/test_data/linear_allen_mouse/",
+    alignment_json="../tests/test_data/linear_allen_mouse/alignment_linear.json",
     colour=[0, 0, 0],
     atlas_path="../tests/test_data/allen_mouse_2017_atlas/annotation_25_reoriented_2017.nrrd",
     label_path="../tests/test_data/allen_mouse_2017_atlas//allen2017_colours.csv",
 )
 pnt.get_coordinates(object_cutoff=0)
 pnt.quantify_coordinates()
-pnt.save_analysis("../demo_data/test_nonlinear_allen_mouse")
+pnt.save_analysis("../test_result/test_linear_allen_mouse")