diff --git a/test/test8_PyNutil_bigcaudoputamen.json b/test/test8_PyNutil_bigcaudoputamen.json new file mode 100644 index 0000000000000000000000000000000000000000..f790fdf0ef0b187d7e7c4237f99890f6fd6ec72c --- /dev/null +++ b/test/test8_PyNutil_bigcaudoputamen.json @@ -0,0 +1,9 @@ +{ + "volume_path": "allen2017", + "label_path": "PyNutil/annotation_volumes/allen2017_colours.csv", + "segmentation_folder": "PyNutil/test_data/PyTest_seg", + "alignment_json": "PyNutil/test_data/PyNutil_testdataset_Nonlin_SY_fixed_bigcaudoputamen.json", + "nonlinear": true, + "colour": [0, 0, 0], + "points_json_path": "PyNutil/outputs/test8_PyNutil.json" +} diff --git a/test/test8_PyNutil_fixed.json b/test/test8_PyNutil_fixed.json deleted file mode 100644 index 4b2d6a18bf250644986f1a5c8d5e1cbccd7ad080..0000000000000000000000000000000000000000 --- a/test/test8_PyNutil_fixed.json +++ /dev/null @@ -1,8 +0,0 @@ -{ "volume_path": "allen2017", - "label_path": "PyNutil/annotation_volumes/allen2017_colours.csv", - "segmentation_folder": "PyNutil/test_data/PyTest_seg", - "alignment_json": "PyNutil/test_data/PyNutil_testdataset_Nonlin_SY_fixed_bigcaudoputamen.json", - "nonlinear": true, - "colour": [0, 0, 0], - "points_json_path": "PyNutil/outputs/test8_PyNutil_use_flat.json" -} \ No newline at end of file diff --git a/testOOP.py b/testOOP.py index ab1365d4d7ce2d3a5cf274d8be9b2ffd120833a4..4b752b1efafe6d6c4d30329a6659d37fe32c4046 100644 --- a/testOOP.py +++ b/testOOP.py @@ -1,13 +1,13 @@ from PyNutil import PyNutil -pnt = PyNutil(settings_file=r"PyNutil/test/test8_PyNutil_fixed.json") +pnt = PyNutil(settings_file=r"PyNutil/test/test8_PyNutil_bigcaudoputamen.json") ##Use flat can be set to True if you want to use the flat file # instead of the visualign json (this is only useful for testing and will be removed) -pnt.get_coordinates(object_cutoff=0, use_flat=True) +pnt.get_coordinates(object_cutoff=0, use_flat=False) pnt.quantify_coordinates() -pnt.save_analysis("PyNutil/outputs/test8_PyNutil_bigcaudoputamen_newatlasmaps") +pnt.save_analysis("PyNutil/outputs/test8_PyNutil_bigcaudoputamen_noflat") # remove name, r, g, b, from pixel_ # add to region_areas df