biomedisa 24.8.11__py3-none-any.whl → 25.7.1__py3-none-any.whl

biomedisa/features/random_walk/pyopencl_large.py

@@ -259,7 +259,7 @@ def walk(comm, raw, slices, indices, nbrw, sorw, blockmin, blockmax,
     # allocate device memory or use subdomains
     memory_error = False
     subdomains = False
-    if zsh * ysh * xsh > 42e8 or platform.split('_')[-1] == 'GPU':
+    if zsh * ysh * xsh > 42e8:# or platform.split('_')[-1] == 'GPU':
         if zsh * ysh * xsh > 42e8:
             print('Warning: Volume indexes exceed unsigned long int range. The volume is splitted into subdomains.')
         else:

biomedisa/features/random_walk/pyopencl_small.py

@@ -98,9 +98,9 @@ def _walk_on_current_gpu(raw, slices, allLabels, indices, nbrw, sorw, name, ctx,
     segment_cl = cl.Buffer(ctx, mf.READ_ONLY | mf.COPY_HOST_PTR, hostbuf=np.int32(0))
 
     # block and grid size
-    #block = (1, 32, 32)
-    #x_grid = ((xsh // 32) + 1)*32
-    #y_grid = ((ysh // 32) + 1)*32
+    #block = (1, 16, 16)
+    #x_grid = ((xsh // 16) + 1)*16
+    #y_grid = ((ysh // 16) + 1)*16
     #grid = (slshape, y_grid, x_grid)
 
     block = None

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-25.7.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: biomedisa
-Version: 24.8.11
+Version: 25.7.1
 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)
 -----------
@@ -36,13 +37,14 @@ License-File: LICENSE
 Biomedisa (https://biomedisa.info) is a free and easy-to-use open-source application for segmenting large 3D volumetric images such as CT and MRI scans, developed at [The Australian National University CTLab](https://ctlab.anu.edu.au/). Biomedisa's smart interpolation of sparsely pre-segmented slices enables accurate semi-automated segmentation by considering the complete underlying image data. Additionally, Biomedisa enables deep learning for fully automated segmentation across similar samples and structures. It is compatible with segmentation tools like Amira/Avizo, ImageJ/Fiji, and 3D Slicer. If you are using Biomedisa or the data for your research please cite: Lösel, P.D. et al. [Introducing Biomedisa as an open-source online platform for biomedical image segmentation.](https://www.nature.com/articles/s41467-020-19303-w) *Nat. Commun.* **11**, 5577 (2020).
 
 ## Hardware Requirements
-+ One or more NVIDIA GPUs
++ One or more NVIDIA, AMD, or Intel GPUs
 
 ## Installation (command-line based)
 + [Ubuntu 22/24 + Smart Interpolation](https://github.com/biomedisa/biomedisa/blob/master/README/ubuntu_interpolation_cli.md)
 + [Ubuntu 22/24 + Deep Learning](https://github.com/biomedisa/biomedisa/blob/master/README/ubuntu_deeplearning_cli.md)
 + [Ubuntu 22/24 + Smart Interpolation + Deep Learning](https://github.com/biomedisa/biomedisa/blob/master/README/ubuntu_cli.md)
-+ [Windows 10/11 + Smart Interpolation + Deep Learning](https://github.com/biomedisa/biomedisa/blob/master/README/windows_wsl.md)
++ [Windows (WSL) + Smart Interpolation + Deep Learning ("advanced")](https://github.com/biomedisa/biomedisa/blob/master/README/windows_wsl.md)
++ [Windows 10/11 + Smart Interpolation (NVIDIA, AMD, Intel) ("simple")](https://github.com/biomedisa/biomedisa/blob/master/README/windows_interpolation.md)
 
 ## Installation (3D Slicer extension)
 + [Ubuntu 22/24](https://github.com/biomedisa/biomedisa/blob/master/README/ubuntu_slicer.md)

{biomedisa-24.8.11.dist-info → biomedisa-25.7.1.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=6VP45eaI0q2t6rmU4mF6tsvZVB0VU0lZfs96j7GZQSQ,35184
 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=1-UXcIECeBpPOQZneqlH9q5w75q5BANQCe01yITk7ls,74651
 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
@@ -33,12 +33,12 @@ biomedisa/features/random_walk/pycuda_large.py,sha256=Vfvd0uFRB-qLReDFKIyAAhdWDL
 biomedisa/features/random_walk/pycuda_large_allx.py,sha256=zjy1Ai8D-foXjaT-6G33vGMANS1i00BBbLCTAMUfP5c,30677
 biomedisa/features/random_walk/pycuda_small.py,sha256=rSwjq2DdtGyNGH1_EfiRQGSgEsCZqvVUrh1UN64AEc8,15786
 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/pyopencl_large.py,sha256=fBUellvpE2rOuT_ksZWwrqq_KFlqHx2o3mMLnUzGYp8,31017
+biomedisa/features/random_walk/pyopencl_small.py,sha256=V4afT0kJRNQmfD7FEf8oBQ8warn0OaDIngkpmJhpfK0,17068
+biomedisa/features/random_walk/rw_large.py,sha256=LtBffUEmNBU6OmcjkKUbISf2ZPTTnzXzbDlinspSm8g,20105
+biomedisa/features/random_walk/rw_small.py,sha256=BudR1LVCcEPOYK45N-2400CK__MX3aVbunDwhEVvseY,15174
+biomedisa-25.7.1.dist-info/licenses/LICENSE,sha256=sehayP6UhydNnmstfL4yFR3genMRdpuUh6uZVWJN1H0,14152
+biomedisa-25.7.1.dist-info/METADATA,sha256=zRhrraJQzojxLxELMMUAH7InMOs0REkrv9r9Xbkioic,10138
+biomedisa-25.7.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+biomedisa-25.7.1.dist-info/top_level.txt,sha256=opsf1Eb4vCguPSxev4HHSeiUKCccT_C_RcUCdAYbHWQ,10
+biomedisa-25.7.1.dist-info/RECORD,,

{biomedisa-24.8.11.dist-info → biomedisa-25.7.1.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