biomedisa 24.8.11__py3-none-any.whl → 25.6.1__py3-none-any.whl

biomedisa/features/random_walk/rw_large.py

@@ -1,6 +1,6 @@
 ##########################################################################
 ##                                                                      ##
-##  Copyright (c) 2019-2024 Philipp Lösel. All rights reserved.         ##
+##  Copyright (c) 2019-2025 Philipp Lösel. All rights reserved.         ##
 ##                                                                      ##
 ##  This file is part of the open source project biomedisa.             ##
 ##                                                                      ##
@@ -176,7 +176,11 @@ def _diffusion_child(comm, bm=None):
             mask = bm.labelData>0
             dice = Dice_score(bm.labelData, final*mask)
             if dice < 0.3:
-                print('Warning: Bad result! Use "--allaxis" if you labeled axes other than the xy-plane.')
+                if bm.slicer:
+                    message = 'Bad result! If you label outside the red (axial) window, enable "All axes" and ensure that at least one slice is empty between pre-segmented slices in each view.'
+                    _error_(bm, message, level=0)
+                else:
+                    print('Warning: Bad result! Use "--allaxis" if you labeled axes other than the xy-plane.')
 
             # regular result
             final_result = np.zeros((bm.zsh, bm.ysh, bm.xsh), dtype=np.uint8)

biomedisa/features/random_walk/rw_small.py

@@ -1,6 +1,6 @@
 ##########################################################################
 ##                                                                      ##
-##  Copyright (c) 2019-2024 Philipp Lösel. All rights reserved.         ##
+##  Copyright (c) 2019-2025 Philipp Lösel. All rights reserved.         ##
 ##                                                                      ##
 ##  This file is part of the open source project biomedisa.             ##
 ##                                                                      ##
@@ -29,7 +29,7 @@
 from biomedisa.features.remove_outlier import clean, fill
 from biomedisa.features.active_contour import activeContour
 from biomedisa.features.biomedisa_helper import (_get_device, save_data, unique_file_path,
-    sendToChild, _split_indices, get_labels, Dice_score)
+    sendToChild, _split_indices, get_labels, Dice_score, _error_)
 from mpi4py import MPI
 import numpy as np
 import time
@@ -179,7 +179,11 @@ def _diffusion_child(comm, bm=None):
         mask = bm.labelData>0
         dice = Dice_score(bm.labelData, final_zero*mask)
         if dice < 0.3:
-            print('Warning: Bad result! Use "--allaxis" if you labeled axes other than the xy-plane.')
+            if bm.slicer:
+                message = 'Bad result! If you label outside the red (axial) window, enable "All axes" and ensure that at least one slice is empty between pre-segmented slices in each view.'
+                _error_(bm, message, level=0)
+            else:
+                print('Warning: Bad result! Use "--allaxis" if you labeled axes other than the xy-plane.')
 
         # regular result
         final_result = np.zeros((bm.zsh, bm.ysh, bm.xsh), dtype=np.uint8)

biomedisa/interpolation.py

@@ -43,7 +43,7 @@ class Biomedisa(object):
 def smart_interpolation(data, labelData, nbrw=10, sorw=4000, acwe=False, acwe_alpha=1.0, acwe_smooth=1, acwe_steps=3,
     path_to_data=None, path_to_labels=None, denoise=False, uncertainty=False, platform=None,
     allaxis=False, ignore='none', only='all', smooth=0, compression=True, return_hits=False,
-    img_id=None, label_id=None, remote=False, queue=0, clean=None, fill=None):
+    img_id=None, label_id=None, remote=False, queue=0, clean=None, fill=None, slicer=False):
 
     freeze_support()
 
@@ -351,6 +351,8 @@ if __name__ == '__main__':
                         help='The interpolation is carried out on a remote server. Must be set up in config.py')
     parser.add_argument('-q','--queue', type=int, default=0,
                         help='Processing queue when using a remote server')
+    parser.add_argument('--slicer', action='store_true', default=False,
+                        help='Required for starting Biomedisa from 3D Slicer')
     kwargs = vars(parser.parse_args())
 
     # run interpolation

{biomedisa-24.8.11.dist-info → biomedisa-25.6.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: biomedisa
-Version: 24.8.11
+Version: 25.6.1
 Summary: Segmentation of 3D volumetric image data
 Author: Philipp Lösel
 Author-email: philipp.loesel@anu.edu.au
@@ -13,6 +13,7 @@ Classifier: Operating System :: OS Independent
 Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
+Dynamic: license-file
 
 [![biomedisa](https://raw.githubusercontent.com/biomedisa/biomedisa/master/biomedisa_app/static/biomedisa_logo.svg)](https://biomedisa.info)
 -----------

{biomedisa-24.8.11.dist-info → biomedisa-25.6.1.dist-info}/RECORD

@@ -1,21 +1,21 @@
 biomedisa/__init__.py,sha256=hw4mzEjGFXm-vxus2DBfKFW0nKoG0ibL5SH6ShfchrY,1526
 biomedisa/__main__.py,sha256=a1--8vhtztWEloHVtbM43FZLCfrFo4BELgdsgtWE8ls,536
-biomedisa/deeplearning.py,sha256=J7i3Sz0mJOSbImQ16QsflF6O-CZEr_Qf0HIcCvWZNa0,29138
-biomedisa/interpolation.py,sha256=MR9rrnF_cRXF8kltUFgVoeu89Zd8hGoGcFprkoUcURg,17074
+biomedisa/deeplearning.py,sha256=7psQOP-pdRplxCGDFyfRFrRpz50VDYBhRvqVhHVGJO4,30126
+biomedisa/interpolation.py,sha256=wiauUPPsklAi3aJpsXI6RjKzy00Iezvfba-ixtPfJAo,17239
 biomedisa/mesh.py,sha256=ArBsKtf2m-KlWNUFMFRJgoiMcKJnHuUMtHI5NvQd4kQ,16067
-biomedisa/features/DataGenerator.py,sha256=pAq_xGky49Y1_VYVLcNcTJ4JmJAn4orIDxGBlQmYTKs,19627
+biomedisa/features/DataGenerator.py,sha256=xgejeY7CpPbSHbxTBwyTFmTvSey1mb_mWhmhim-YVQ0,17734
 biomedisa/features/DataGeneratorCrop.py,sha256=KtGqNadghOd59wIU9hATM_5YgSks95rS1kJ2lsSSX7w,6612
-biomedisa/features/PredictDataGenerator.py,sha256=JH8SPGQm-Y7_Drec2fw3jBUupvpIkQ1FvkDXP7mUjDY,4074
+biomedisa/features/PredictDataGenerator.py,sha256=r-iWdw4LP9Oqc2h8imvNVQkdu1vRTfKLhT2QbR5FSuM,4170
 biomedisa/features/PredictDataGeneratorCrop.py,sha256=HF5tJbGtlJMHr7lMT9IiIdLG2CTjXstbKoOjlZJ93Is,3431
 biomedisa/features/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biomedisa/features/active_contour.py,sha256=FnPuvYck_KL4xYRFqwzm4Grdm288EdlcLFt88E0OtqA,17938
 biomedisa/features/assd.py,sha256=q9NUQXEoA4Pi3d8b5fmys615CWu06Sm0N9-OGwJOFnw,6537
-biomedisa/features/biomedisa_helper.py,sha256=pryGkMxAFdSDFpVF46DssUynmoyr1uLgKat9U_lFizw,33313
+biomedisa/features/biomedisa_helper.py,sha256=4Tvg1XXOc-xuAYRFcVrXSnA19OJTcjO0hQRVXet_Avo,34204
 biomedisa/features/create_slices.py,sha256=uSDH1OcEYc5BFPZHSy3UpS4P2DuoVnxOZ-l7wmyT_Po,13108
-biomedisa/features/crop_helper.py,sha256=ng0zc7csK23n1rr07adzxCS5OHvchqn20OI0EeRLzs8,24343
+biomedisa/features/crop_helper.py,sha256=6OmLSK8rH-lT8OaU3zTndnp0rpciWd1r37jKhEgyD_I,24255
 biomedisa/features/curvop_numba.py,sha256=AjKQJcUBoURTB8pq1HmugQYpBwBELthhcEu51_r_xPI,7049
 biomedisa/features/django_env.py,sha256=LNrZ6rBHZ5I0FaWa5xN8K-ASPgq0r5dGDEUI56HzJxE,8615
-biomedisa/features/keras_helper.py,sha256=zykmixj1EktjQ-yFzRhO9Zhz49462mWec6P5731o-ZM,69496
+biomedisa/features/keras_helper.py,sha256=pAcjsV5q9G1aUaNmtOaKXgcU8VZzsQ9KKsRhwEWTsh0,74619
 biomedisa/features/nc_reader.py,sha256=RoRMwu3ELSNfoV3qZtaT2OWACnXb2EhNFu_DAF1T93o,7406
 biomedisa/features/pid.py,sha256=Jmn1VIp0fBlgBrqZ-yUIQVVb5-NAxNBdibXALVr2PPI,2545
 biomedisa/features/process_image.py,sha256=VtS3fGDvglqJiiJLPK1toe76J58j914NJ8XQKg3CRwo,11091
@@ -35,10 +35,10 @@ biomedisa/features/random_walk/pycuda_small.py,sha256=rSwjq2DdtGyNGH1_EfiRQGSgEs
 biomedisa/features/random_walk/pycuda_small_allx.py,sha256=z4koEQNWqy3EYOhHbMkO8sP6mpl6R7i8mM6OEQQ4kUQ,18225
 biomedisa/features/random_walk/pyopencl_large.py,sha256=q79AxG3p3qFjxfiAZfUK9I5BAYT2prq48yEEmpP1Yjk,31015
 biomedisa/features/random_walk/pyopencl_small.py,sha256=opNlS-qzOa9qWafBNJdvf6r1aRAFf7_JXf6ISDnkdXE,17068
-biomedisa/features/random_walk/rw_large.py,sha256=ZnITvk00Y11ZZlGuBRaJO1EwU0wYBdEwdpj9vvXCqF4,19805
-biomedisa/features/random_walk/rw_small.py,sha256=RPzZe24YrEwYelJukDjvqaoD_SyhgdriEi7uV3kZGXI,14881
-biomedisa-24.8.11.dist-info/LICENSE,sha256=sehayP6UhydNnmstfL4yFR3genMRdpuUh6uZVWJN1H0,14152
-biomedisa-24.8.11.dist-info/METADATA,sha256=4t6agbFHiT5W4BbEUh2X7OKSZhwVMQP4VoC2VLihje4,9933
-biomedisa-24.8.11.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
-biomedisa-24.8.11.dist-info/top_level.txt,sha256=opsf1Eb4vCguPSxev4HHSeiUKCccT_C_RcUCdAYbHWQ,10
-biomedisa-24.8.11.dist-info/RECORD,,
+biomedisa/features/random_walk/rw_large.py,sha256=LtBffUEmNBU6OmcjkKUbISf2ZPTTnzXzbDlinspSm8g,20105
+biomedisa/features/random_walk/rw_small.py,sha256=BudR1LVCcEPOYK45N-2400CK__MX3aVbunDwhEVvseY,15174
+biomedisa-25.6.1.dist-info/licenses/LICENSE,sha256=sehayP6UhydNnmstfL4yFR3genMRdpuUh6uZVWJN1H0,14152
+biomedisa-25.6.1.dist-info/METADATA,sha256=pXSLmSKc-LMVaPxdz_x2GjYj2nRxFIEUrljenX6nuFQ,9954
+biomedisa-25.6.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+biomedisa-25.6.1.dist-info/top_level.txt,sha256=opsf1Eb4vCguPSxev4HHSeiUKCccT_C_RcUCdAYbHWQ,10
+biomedisa-25.6.1.dist-info/RECORD,,

{biomedisa-24.8.11.dist-info → biomedisa-25.6.1.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.8.0)
+Generator: setuptools (80.9.0)
 Root-Is-Purelib: true
 Tag: py3-none-any