biomedisa 24.8.10__py3-none-any.whl → 25.6.1__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (17) hide show
  1. biomedisa/deeplearning.py +35 -9
  2. biomedisa/features/DataGenerator.py +192 -123
  3. biomedisa/features/PredictDataGenerator.py +7 -5
  4. biomedisa/features/biomedisa_helper.py +59 -14
  5. biomedisa/features/crop_helper.py +7 -7
  6. biomedisa/features/keras_helper.py +281 -157
  7. biomedisa/features/random_walk/rw_large.py +6 -2
  8. biomedisa/features/random_walk/rw_small.py +7 -3
  9. biomedisa/features/remove_outlier.py +3 -3
  10. biomedisa/features/split_volume.py +12 -11
  11. biomedisa/interpolation.py +6 -9
  12. biomedisa/mesh.py +2 -2
  13. {biomedisa-24.8.10.dist-info → biomedisa-25.6.1.dist-info}/METADATA +3 -2
  14. {biomedisa-24.8.10.dist-info → biomedisa-25.6.1.dist-info}/RECORD +17 -17
  15. {biomedisa-24.8.10.dist-info → biomedisa-25.6.1.dist-info}/WHEEL +1 -1
  16. {biomedisa-24.8.10.dist-info → biomedisa-25.6.1.dist-info/licenses}/LICENSE +0 -0
  17. {biomedisa-24.8.10.dist-info → biomedisa-25.6.1.dist-info}/top_level.txt +0 -0
biomedisa/features/random_walk/rw_large.py CHANGED
@@ -1,6 +1,6 @@
1
1
  ##########################################################################
2
2
  ## ##
3
- ## Copyright (c) 2019-2024 Philipp Lösel. All rights reserved. ##
3
+ ## Copyright (c) 2019-2025 Philipp Lösel. All rights reserved. ##
4
4
  ## ##
5
5
  ## This file is part of the open source project biomedisa. ##
6
6
  ## ##
@@ -176,7 +176,11 @@ def _diffusion_child(comm, bm=None):
176
176
  mask = bm.labelData>0
177
177
  dice = Dice_score(bm.labelData, final*mask)
178
178
  if dice < 0.3:
179
- print('Warning: Bad result! Use "--allaxis" if you labeled axes other than the xy-plane.')
179
+ if bm.slicer:
180
+ 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.'
181
+ _error_(bm, message, level=0)
182
+ else:
183
+ print('Warning: Bad result! Use "--allaxis" if you labeled axes other than the xy-plane.')
180
184
 
181
185
  # regular result
182
186
  final_result = np.zeros((bm.zsh, bm.ysh, bm.xsh), dtype=np.uint8)
biomedisa/features/random_walk/rw_small.py CHANGED
@@ -1,6 +1,6 @@
1
1
  ##########################################################################
2
2
  ## ##
3
- ## Copyright (c) 2019-2024 Philipp Lösel. All rights reserved. ##
3
+ ## Copyright (c) 2019-2025 Philipp Lösel. All rights reserved. ##
4
4
  ## ##
5
5
  ## This file is part of the open source project biomedisa. ##
6
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  ## ##
@@ -29,7 +29,7 @@
29
29
  from biomedisa.features.remove_outlier import clean, fill
30
30
  from biomedisa.features.active_contour import activeContour
31
31
  from biomedisa.features.biomedisa_helper import (_get_device, save_data, unique_file_path,
32
- sendToChild, _split_indices, get_labels, Dice_score)
32
+ sendToChild, _split_indices, get_labels, Dice_score, _error_)
33
33
  from mpi4py import MPI
34
34
  import numpy as np
35
35
  import time
@@ -179,7 +179,11 @@ def _diffusion_child(comm, bm=None):
179
179
  mask = bm.labelData>0
180
180
  dice = Dice_score(bm.labelData, final_zero*mask)
181
181
  if dice < 0.3:
182
- print('Warning: Bad result! Use "--allaxis" if you labeled axes other than the xy-plane.')
182
+ if bm.slicer:
183
+ 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.'
184
+ _error_(bm, message, level=0)
185
+ else:
186
+ print('Warning: Bad result! Use "--allaxis" if you labeled axes other than the xy-plane.')
183
187
 
184
188
  # regular result
185
189
  final_result = np.zeros((bm.zsh, bm.ysh, bm.xsh), dtype=np.uint8)
biomedisa/features/remove_outlier.py CHANGED
@@ -30,7 +30,7 @@
30
30
  import os
31
31
  import biomedisa
32
32
  from biomedisa.features.biomedisa_helper import (load_data, save_data,
33
- unique_file_path, silent_remove)
33
+ unique_file_path, silent_remove, unique)
34
34
  import numpy as np
35
35
  from scipy import ndimage
36
36
  import argparse
@@ -60,7 +60,7 @@ def reduce_blocksize(data):
60
60
 
61
61
  def clean(image, threshold=0.1):
62
62
  image_i = np.copy(image, order='C')
63
- allLabels = np.unique(image_i)
63
+ allLabels = unique(image_i)
64
64
  mask = np.empty_like(image_i)
65
65
  s = [[[0,0,0], [0,1,0], [0,0,0]], [[0,1,0], [1,1,1], [0,1,0]], [[0,0,0], [0,1,0], [0,0,0]]]
66
66
  for k in allLabels[1:]:
@@ -99,7 +99,7 @@ def clean(image, threshold=0.1):
99
99
 
100
100
  def fill(image, threshold=0.9):
101
101
  image_i = np.copy(image, order='C')
102
- allLabels = np.unique(image_i)
102
+ allLabels = unique(image_i)
103
103
  mask = np.empty_like(image_i)
104
104
  s = [[[0,0,0], [0,1,0], [0,0,0]], [[0,1,0], [1,1,1], [0,1,0]], [[0,0,0], [0,1,0], [0,0,0]]]
105
105
  for k in allLabels[1:]:
biomedisa/features/split_volume.py CHANGED
@@ -132,17 +132,18 @@ if __name__ == '__main__':
132
132
  labelData = labelData[datamin_z:datamax_z,datamin_y:datamax_y,datamin_x:datamax_x].copy()
133
133
 
134
134
  # interpolation
135
- results = smart_interpolation(data, labelData, uncertainty=args.uncertainty, allaxis=args.allaxis, smooth=args.smooth)
136
-
137
- # append results
138
- final[blockmin_z:blockmax_z,blockmin_y:blockmax_y,blockmin_x:blockmax_x] \
139
- = results['regular'][blockmin_z-datamin_z:blockmax_z-datamin_z,blockmin_y-datamin_y:blockmax_y-datamin_y,blockmin_x-datamin_x:blockmax_x-datamin_x]
140
- if 'smooth' in results and results['smooth'] is not None:
141
- final_smooth[blockmin_z:blockmax_z,blockmin_y:blockmax_y,blockmin_x:blockmax_x] \
142
- = results['smooth'][blockmin_z-datamin_z:blockmax_z-datamin_z,blockmin_y-datamin_y:blockmax_y-datamin_y,blockmin_x-datamin_x:blockmax_x-datamin_x]
143
- if 'uncertainty' in results and results['uncertainty'] is not None:
144
- final_uncertainty[blockmin_z:blockmax_z,blockmin_y:blockmax_y,blockmin_x:blockmax_x] \
145
- = results['uncertainty'][blockmin_z-datamin_z:blockmax_z-datamin_z,blockmin_y-datamin_y:blockmax_y-datamin_y,blockmin_x-datamin_x:blockmax_x-datamin_x]
135
+ if np.any(labelData):
136
+ results = smart_interpolation(data, labelData, uncertainty=args.uncertainty, allaxis=args.allaxis, smooth=args.smooth)
137
+
138
+ # append results
139
+ final[blockmin_z:blockmax_z,blockmin_y:blockmax_y,blockmin_x:blockmax_x] \
140
+ = results['regular'][blockmin_z-datamin_z:blockmax_z-datamin_z,blockmin_y-datamin_y:blockmax_y-datamin_y,blockmin_x-datamin_x:blockmax_x-datamin_x]
141
+ if 'smooth' in results and results['smooth'] is not None:
142
+ final_smooth[blockmin_z:blockmax_z,blockmin_y:blockmax_y,blockmin_x:blockmax_x] \
143
+ = results['smooth'][blockmin_z-datamin_z:blockmax_z-datamin_z,blockmin_y-datamin_y:blockmax_y-datamin_y,blockmin_x-datamin_x:blockmax_x-datamin_x]
144
+ if 'uncertainty' in results and results['uncertainty'] is not None:
145
+ final_uncertainty[blockmin_z:blockmax_z,blockmin_y:blockmax_y,blockmin_x:blockmax_x] \
146
+ = results['uncertainty'][blockmin_z-datamin_z:blockmax_z-datamin_z,blockmin_y-datamin_y:blockmax_y-datamin_y,blockmin_x-datamin_x:blockmax_x-datamin_x]
146
147
 
147
148
  # path to regular result
148
149
  filename, extension = os.path.splitext(os.path.basename(args.path_to_data))
biomedisa/interpolation.py CHANGED
@@ -1,7 +1,7 @@
1
1
  #!/usr/bin/python3
2
2
  ##########################################################################
3
3
  ## ##
4
- ## Copyright (c) 2019-2024 Philipp Lösel. All rights reserved. ##
4
+ ## Copyright (c) 2019-2025 Philipp Lösel. All rights reserved. ##
5
5
  ## ##
6
6
  ## This file is part of the open source project biomedisa. ##
7
7
  ## ##
@@ -43,7 +43,7 @@ class Biomedisa(object):
43
43
  def smart_interpolation(data, labelData, nbrw=10, sorw=4000, acwe=False, acwe_alpha=1.0, acwe_smooth=1, acwe_steps=3,
44
44
  path_to_data=None, path_to_labels=None, denoise=False, uncertainty=False, platform=None,
45
45
  allaxis=False, ignore='none', only='all', smooth=0, compression=True, return_hits=False,
46
- img_id=None, label_id=None, remote=False, queue=0, clean=None, fill=None):
46
+ img_id=None, label_id=None, remote=False, queue=0, clean=None, fill=None, slicer=False):
47
47
 
48
48
  freeze_support()
49
49
 
@@ -165,13 +165,8 @@ def smart_interpolation(data, labelData, nbrw=10, sorw=4000, acwe=False, acwe_al
165
165
  bm.imageSize = int(bm.data.nbytes * 10e-7)
166
166
 
167
167
  # add boundaries
168
- zsh, ysh, xsh = bm.data.shape
169
- tmp = np.zeros((1+zsh+1, 1+ysh+1, 1+xsh+1), dtype=bm.labelData.dtype)
170
- tmp[1:-1, 1:-1, 1:-1] = bm.labelData
171
- bm.labelData = tmp.copy(order='C')
172
- tmp = np.zeros((1+zsh+1, 1+ysh+1, 1+xsh+1), dtype=bm.data.dtype)
173
- tmp[1:-1, 1:-1, 1:-1] = bm.data
174
- bm.data = tmp.copy(order='C')
168
+ bm.data = np.pad(bm.data, pad_width=1, mode='constant', constant_values=0)
169
+ bm.labelData = np.pad(bm.labelData, pad_width=1, mode='constant', constant_values=0)
175
170
  bm.zsh, bm.ysh, bm.xsh = bm.data.shape
176
171
 
177
172
  # check if labeled slices are adjacent
@@ -356,6 +351,8 @@ if __name__ == '__main__':
356
351
  help='The interpolation is carried out on a remote server. Must be set up in config.py')
357
352
  parser.add_argument('-q','--queue', type=int, default=0,
358
353
  help='Processing queue when using a remote server')
354
+ parser.add_argument('--slicer', action='store_true', default=False,
355
+ help='Required for starting Biomedisa from 3D Slicer')
359
356
  kwargs = vars(parser.parse_args())
360
357
 
361
358
  # run interpolation
biomedisa/mesh.py CHANGED
@@ -30,7 +30,7 @@
30
30
  import os
31
31
  import numpy as np
32
32
  import biomedisa
33
- from biomedisa.features.biomedisa_helper import load_data, unique_file_path
33
+ from biomedisa.features.biomedisa_helper import load_data, unique_file_path, unique
34
34
  from biomedisa.features.django_env import create_pid_object
35
35
  from vtk.util.numpy_support import vtk_to_numpy, numpy_to_vtk
36
36
  from stl import mesh
@@ -107,7 +107,7 @@ def save_mesh(path_to_result, labels, x_res=1, y_res=1, z_res=1,
107
107
 
108
108
  # get labels
109
109
  zsh, ysh, xsh = labels.shape
110
- allLabels = np.unique(labels)
110
+ allLabels = unique(labels)
111
111
  b = np.empty_like(labels)
112
112
  arr = np.empty((0,3,3))
113
113
  nTotalCells = [0]
{biomedisa-24.8.10.dist-info → biomedisa-25.6.1.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
1
- Metadata-Version: 2.2
1
+ Metadata-Version: 2.4
2
2
  Name: biomedisa
3
- Version: 24.8.10
3
+ Version: 25.6.1
4
4
  Summary: Segmentation of 3D volumetric image data
5
5
  Author: Philipp Lösel
6
6
  Author-email: philipp.loesel@anu.edu.au
@@ -13,6 +13,7 @@ Classifier: Operating System :: OS Independent
13
13
  Requires-Python: >=3.9
14
14
  Description-Content-Type: text/markdown
15
15
  License-File: LICENSE
16
+ Dynamic: license-file
16
17
 
17
18
  [![biomedisa](https://raw.githubusercontent.com/biomedisa/biomedisa/master/biomedisa_app/static/biomedisa_logo.svg)](https://biomedisa.info)
18
19
  -----------
{biomedisa-24.8.10.dist-info → biomedisa-25.6.1.dist-info}/RECORD RENAMED
@@ -1,27 +1,27 @@
1
1
  biomedisa/__init__.py,sha256=hw4mzEjGFXm-vxus2DBfKFW0nKoG0ibL5SH6ShfchrY,1526
2
2
  biomedisa/__main__.py,sha256=a1--8vhtztWEloHVtbM43FZLCfrFo4BELgdsgtWE8ls,536
3
- biomedisa/deeplearning.py,sha256=xLVe8buzjKRgzQL1cYK8bpv73iIwDwsR7_qKGfy4KDc,28600
4
- biomedisa/interpolation.py,sha256=i10aqwEl-wsVU_nQ-zyubhAs27NSKF4ial7LyhaBLv0,17273
5
- biomedisa/mesh.py,sha256=8-iuVsrfW5JovaMrAez7qSxv1LCU3eiqOdik0s0DV1w,16062
6
- biomedisa/features/DataGenerator.py,sha256=CEC-5VKdsuLjq-qMJWXn7wT6AJF-qWa4zEqLvi5GsVg,13130
3
+ biomedisa/deeplearning.py,sha256=7psQOP-pdRplxCGDFyfRFrRpz50VDYBhRvqVhHVGJO4,30126
4
+ biomedisa/interpolation.py,sha256=wiauUPPsklAi3aJpsXI6RjKzy00Iezvfba-ixtPfJAo,17239
5
+ biomedisa/mesh.py,sha256=ArBsKtf2m-KlWNUFMFRJgoiMcKJnHuUMtHI5NvQd4kQ,16067
6
+ biomedisa/features/DataGenerator.py,sha256=xgejeY7CpPbSHbxTBwyTFmTvSey1mb_mWhmhim-YVQ0,17734
7
7
  biomedisa/features/DataGeneratorCrop.py,sha256=KtGqNadghOd59wIU9hATM_5YgSks95rS1kJ2lsSSX7w,6612
8
- biomedisa/features/PredictDataGenerator.py,sha256=JH8SPGQm-Y7_Drec2fw3jBUupvpIkQ1FvkDXP7mUjDY,4074
8
+ biomedisa/features/PredictDataGenerator.py,sha256=r-iWdw4LP9Oqc2h8imvNVQkdu1vRTfKLhT2QbR5FSuM,4170
9
9
  biomedisa/features/PredictDataGeneratorCrop.py,sha256=HF5tJbGtlJMHr7lMT9IiIdLG2CTjXstbKoOjlZJ93Is,3431
10
10
  biomedisa/features/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
11
11
  biomedisa/features/active_contour.py,sha256=FnPuvYck_KL4xYRFqwzm4Grdm288EdlcLFt88E0OtqA,17938
12
12
  biomedisa/features/assd.py,sha256=q9NUQXEoA4Pi3d8b5fmys615CWu06Sm0N9-OGwJOFnw,6537
13
- biomedisa/features/biomedisa_helper.py,sha256=oIsOmIJ8xUQVwgbzMgw65dXcZmzwePpFQoIdbgLTnF8,32727
13
+ biomedisa/features/biomedisa_helper.py,sha256=4Tvg1XXOc-xuAYRFcVrXSnA19OJTcjO0hQRVXet_Avo,34204
14
14
  biomedisa/features/create_slices.py,sha256=uSDH1OcEYc5BFPZHSy3UpS4P2DuoVnxOZ-l7wmyT_Po,13108
15
- biomedisa/features/crop_helper.py,sha256=ng0zc7csK23n1rr07adzxCS5OHvchqn20OI0EeRLzs8,24343
15
+ biomedisa/features/crop_helper.py,sha256=6OmLSK8rH-lT8OaU3zTndnp0rpciWd1r37jKhEgyD_I,24255
16
16
  biomedisa/features/curvop_numba.py,sha256=AjKQJcUBoURTB8pq1HmugQYpBwBELthhcEu51_r_xPI,7049
17
17
  biomedisa/features/django_env.py,sha256=LNrZ6rBHZ5I0FaWa5xN8K-ASPgq0r5dGDEUI56HzJxE,8615
18
- biomedisa/features/keras_helper.py,sha256=kwMgi0djdsI2XRFQkvYAu2PQLQ5Bq2CZL3fcBJ8QfUI,69507
18
+ biomedisa/features/keras_helper.py,sha256=pAcjsV5q9G1aUaNmtOaKXgcU8VZzsQ9KKsRhwEWTsh0,74619
19
19
  biomedisa/features/nc_reader.py,sha256=RoRMwu3ELSNfoV3qZtaT2OWACnXb2EhNFu_DAF1T93o,7406
20
20
  biomedisa/features/pid.py,sha256=Jmn1VIp0fBlgBrqZ-yUIQVVb5-NAxNBdibXALVr2PPI,2545
21
21
  biomedisa/features/process_image.py,sha256=VtS3fGDvglqJiiJLPK1toe76J58j914NJ8XQKg3CRwo,11091
22
22
  biomedisa/features/pycuda_test.py,sha256=UGAGIz_dgcCJkzjyCqnMlflp-WJPzpCtFQmE9C5DwIo,3275
23
- biomedisa/features/remove_outlier.py,sha256=C2m-Wsw-n3q8Ft21SGNwEd3wDU_T1ghqQ5hldwU_rqI,16627
24
- biomedisa/features/split_volume.py,sha256=UgMpHhZPvH90xFo-mJ0Oc0tBXbrf8FQF0kzVySAlO8g,8917
23
+ biomedisa/features/remove_outlier.py,sha256=xa_a4hyEYv8dZRbBrbJyVTxzBGjgsIGZDU-XY1SSYNo,16629
24
+ biomedisa/features/split_volume.py,sha256=Selyt55ailT621XKpgcJ9IOahBETFhQZYWOUuD0P7gQ,8995
25
25
  biomedisa/features/amira_to_np/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
26
26
  biomedisa/features/amira_to_np/amira_data_stream.py,sha256=JrZTyKP01CKDFB5d9BlGtSFwBgoAo0AJeAmn3pADH88,32618
27
27
  biomedisa/features/amira_to_np/amira_grammar.py,sha256=z1yajLHmn-GDb-rzZ5iHlKmPZDDbO9fNqP2jXf8z3KE,14324
@@ -35,10 +35,10 @@ biomedisa/features/random_walk/pycuda_small.py,sha256=rSwjq2DdtGyNGH1_EfiRQGSgEs
35
35
  biomedisa/features/random_walk/pycuda_small_allx.py,sha256=z4koEQNWqy3EYOhHbMkO8sP6mpl6R7i8mM6OEQQ4kUQ,18225
36
36
  biomedisa/features/random_walk/pyopencl_large.py,sha256=q79AxG3p3qFjxfiAZfUK9I5BAYT2prq48yEEmpP1Yjk,31015
37
37
  biomedisa/features/random_walk/pyopencl_small.py,sha256=opNlS-qzOa9qWafBNJdvf6r1aRAFf7_JXf6ISDnkdXE,17068
38
- biomedisa/features/random_walk/rw_large.py,sha256=ZnITvk00Y11ZZlGuBRaJO1EwU0wYBdEwdpj9vvXCqF4,19805
39
- biomedisa/features/random_walk/rw_small.py,sha256=RPzZe24YrEwYelJukDjvqaoD_SyhgdriEi7uV3kZGXI,14881
40
- biomedisa-24.8.10.dist-info/LICENSE,sha256=sehayP6UhydNnmstfL4yFR3genMRdpuUh6uZVWJN1H0,14152
41
- biomedisa-24.8.10.dist-info/METADATA,sha256=LKbD530R9ff_NW-ym4m5RS2pCCE8q2ov5s4ygfWK-k4,9933
42
- biomedisa-24.8.10.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
43
- biomedisa-24.8.10.dist-info/top_level.txt,sha256=opsf1Eb4vCguPSxev4HHSeiUKCccT_C_RcUCdAYbHWQ,10
44
- biomedisa-24.8.10.dist-info/RECORD,,
38
+ biomedisa/features/random_walk/rw_large.py,sha256=LtBffUEmNBU6OmcjkKUbISf2ZPTTnzXzbDlinspSm8g,20105
39
+ biomedisa/features/random_walk/rw_small.py,sha256=BudR1LVCcEPOYK45N-2400CK__MX3aVbunDwhEVvseY,15174
40
+ biomedisa-25.6.1.dist-info/licenses/LICENSE,sha256=sehayP6UhydNnmstfL4yFR3genMRdpuUh6uZVWJN1H0,14152
41
+ biomedisa-25.6.1.dist-info/METADATA,sha256=pXSLmSKc-LMVaPxdz_x2GjYj2nRxFIEUrljenX6nuFQ,9954
42
+ biomedisa-25.6.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
43
+ biomedisa-25.6.1.dist-info/top_level.txt,sha256=opsf1Eb4vCguPSxev4HHSeiUKCccT_C_RcUCdAYbHWQ,10
44
+ biomedisa-25.6.1.dist-info/RECORD,,
{biomedisa-24.8.10.dist-info → biomedisa-25.6.1.dist-info}/WHEEL RENAMED
@@ -1,5 +1,5 @@
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  Wheel-Version: 1.0
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- Generator: setuptools (75.8.0)
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+ Generator: setuptools (80.9.0)
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  Root-Is-Purelib: true
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  Tag: py3-none-any
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