diff --git a/extensions/chaeo/batch_jobs/proj0004-exp0038-fixed.py b/extensions/chaeo/batch_jobs/proj0004-exp0038-fixed.py index 9ad9208e1d9b8f8d31e475872db982c864c9fcc0..93a9cf6f868543d6bafa56b7ed6daa7dc0681550 100644 --- a/extensions/chaeo/batch_jobs/proj0004-exp0038-fixed.py +++ b/extensions/chaeo/batch_jobs/proj0004-exp0038-fixed.py @@ -11,7 +11,7 @@ if __name__ == '__main__': 'batch-output' ) - px_ilp = Path.home() / 'model-server' / 'ilastik' / 'AF405-bodies_boundaries.ilp' + px_ilp = Path.home() / 'model_server' / 'ilastik' / 'AF405-bodies_boundaries.ilp' params = { 'pxmap_threshold': 0.25, diff --git a/extensions/chaeo/conf/testing.py b/extensions/chaeo/conf/testing.py index 4ca906805e02919cd55dce69c0fea5d9e2b7abc2..00389e08d8adbe01a3bd14c19f76342a9c00ccea 100644 --- a/extensions/chaeo/conf/testing.py +++ b/extensions/chaeo/conf/testing.py @@ -1,6 +1,6 @@ from pathlib import Path -root = Path.home() / 'model-server' +root = Path.home() / 'model_server' multichannel_zstack = { 'path': root / 'testing' / 'zmask-test-stack-chlorophyl.tif', @@ -11,12 +11,12 @@ multichannel_zstack = { } pixel_classifier = { - 'path': root / 'ilastik' / 'AF405-bodies_boundaries.ilp' + 'path': root / 'testing' / 'zmask' / 'AF405-bodies_boundaries.ilp' } pipeline_params = { 'threshold': 0.6, } -output_path = root / 'testing_output' / 'chaeo' +output_path = root / 'testing' / 'output' / 'chaeo' output_path.mkdir(parents=True, exist_ok=True) \ No newline at end of file diff --git a/extensions/chaeo/examples/batch_obj_cla.py b/extensions/chaeo/examples/batch_obj_cla.py index 105f8e46fcaf08eb83975986d0ed363c107bf073..ec230d79587c70d748ac5777de21b1501ce51fd3 100644 --- a/extensions/chaeo/examples/batch_obj_cla.py +++ b/extensions/chaeo/examples/batch_obj_cla.py @@ -15,8 +15,8 @@ if __name__ == '__main__': 'zmask_to_automic', ) - px_ilp = Path.home() / 'model-server' / 'testing' / 'zmask' / 'AF405-bodies_boundaries.ilp' - ob_ilp = Path.home() / 'model-server' / 'testing' / 'zmask' / 'auto_obj_after.ilp' + px_ilp = Path.home() / 'model_server' / 'testing' / 'zmask' / 'AF405-bodies_boundaries.ilp' + ob_ilp = Path.home() / 'model_server' / 'testing' / 'zmask' / 'auto_obj_after.ilp' params = { 'pxmap_threshold': 0.25, diff --git a/extensions/chaeo/examples/export_patch_focus_metrics.py b/extensions/chaeo/examples/export_patch_focus_metrics.py index 93a9fb458a8d582f68fdd78bd9028b3f85b2d113..31258117785c6d26ea0bc48f2110432d43467c62 100644 --- a/extensions/chaeo/examples/export_patch_focus_metrics.py +++ b/extensions/chaeo/examples/export_patch_focus_metrics.py @@ -112,7 +112,7 @@ if __name__ == '__main__': ) csv_args = {'mode': 'w', 'header': True} # when creating file - px_ilp = Path.home() / 'model-server' / 'ilastik' / 'AF405-bodies_boundaries.ilp' + px_ilp = Path.home() / 'model_server' / 'ilastik' / 'AF405-bodies_boundaries.ilp' for ff in where_czi.iterdir(): if ff.stem != 'Selection--W0000--P0009-T0001':