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Merged
davidmeunier79 merged 33 commits into from
Dec 10, 2025
Merged

Correct kmeans #77

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f2b847d
-skull option
davidmeunier79 May 28, 2025
555cbe2
NB
davidmeunier79 May 28, 2025
cf0f16e
``
davidmeunier79 May 28, 2025
e5f807c
|
davidmeunier79 May 28, 2025
8011cc0
Merge branch 'main' of github.com:davidmeunier79/skullTo3d
davidmeunier79 Jun 11, 2025
2b01a25
Merge branch 'main' of github.com:Macatools/skullTo3d
davidmeunier79 Jul 16, 2025
6608428
Merge branch 'main' of github.com:Macatools/skullTo3d
davidmeunier79 Aug 4, 2025
41435d7
Merge branch 'main' of github.com:Macatools/skullTo3d
davidmeunier79 Aug 6, 2025
257f376
Merge branch 'main' of github.com:Macatools/skullTo3d
davidmeunier79 Aug 26, 2025
c9e9d89
Merge branch 'main' of github.com:Macatools/skullTo3d
davidmeunier79 Aug 29, 2025
4dee626
Merge branch 'main' of github.com:Macatools/skullTo3d
davidmeunier79 Aug 29, 2025
ba1adb1
Merge branch 'main' of github.com:Macatools/skullTo3d
davidmeunier79 Dec 10, 2025
9524aa7
Tips and tricks
davidmeunier79 Dec 10, 2025
4ffd17a
Merge branch 'add_doc'
davidmeunier79 Dec 10, 2025
79b1a60
ref
davidmeunier79 Dec 10, 2025
83889f0
___
davidmeunier79 Dec 10, 2025
9823a9a
-skull option
davidmeunier79 Dec 10, 2025
9b9f1e1
Merge branch 'correct_rebase'
davidmeunier79 Dec 10, 2025
afa4597
Merge branch 'main' of github.com:davidmeunier79/skullTo3d
davidmeunier79 Dec 10, 2025
4856a05
indent NB
davidmeunier79 Dec 10, 2025
1fa041c
no indent
davidmeunier79 Dec 10, 2025
cb21cc0
indent
davidmeunier79 Dec 10, 2025
737998a
simplified indent
davidmeunier79 Dec 10, 2025
b86332c
all bold
davidmeunier79 Dec 10, 2025
0f56ac5
NB
davidmeunier79 Dec 10, 2025
59cb168
spaces
davidmeunier79 Dec 10, 2025
0674174
Merge branch 'main' of github.com:Macatools/skullTo3d
davidmeunier79 Dec 10, 2025
01fd3d7
rewritten kmeans function
davidmeunier79 Dec 10, 2025
f7fd547
kmeans
davidmeunier79 Dec 10, 2025
66340c2
only_kmeans
davidmeunier79 Dec 10, 2025
f2f80eb
default
davidmeunier79 Dec 10, 2025
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davidmeunier79 Dec 10, 2025
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davidmeunier79 Dec 10, 2025
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319 changes: 32 additions & 287 deletions skullTo3d/nodes/skull.py
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4 changes: 2 additions & 2 deletions skullTo3d/pipelines/skull_pipe.py
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Original file line number Diff line number Diff line change
Expand Up @@ -117,7 +117,7 @@ def _create_head_mask(name="headmask_pipe", params={}, prefix=""):
head_auto_mask = NodeParams(
interface=niu.Function(
input_names=["img_file", "operation",
"index", "sample_bins", "distance", "kmeans"],
"index"],
output_names=["mask_img_file"],
function=mask_auto_img),
params=parse_key(params, prefix + "head_auto_mask"),
Expand Down Expand Up @@ -658,7 +658,7 @@ def _create_skullmask_ct_pipe(name="skullmask_ct_pipe", params={}):
ct_skull_auto_mask = NodeParams(
interface=niu.Function(
input_names=["img_file", "operation",
"index", "sample_bins", "distance", "kmeans"],
"index"],
output_names=["mask_img_file"],
function=mask_auto_img),
params=parse_key(params, "ct_skull_auto_mask"),
Expand Down
11 changes: 1 addition & 10 deletions workflows/params_segment_macaque_0p5_ants_4animal_skull.json
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Expand Up @@ -89,11 +89,8 @@
{
"t1_head_auto_mask":
{
"kmeans": true,
"operation": "lower",
"index": 2,
"sample_bins": 30,
"distance": 10
"index": 2
},
"t1_head_dilate":
{
Expand Down Expand Up @@ -341,9 +338,6 @@
{
"ct_skull_auto_mask":
{
"kmeans": true,
"sample_bins": 30,
"distance": 10,
"operation": "lower",
"index": 2
},
Expand All @@ -367,9 +361,6 @@
{
"ct_skull_auto_mask":
{
"kmeans": true,
"sample_bins": 30,
"distance": 10,
"operation": "lower",
"index": 2
},
Expand Down
11 changes: 1 addition & 10 deletions workflows/params_segment_macaque_0p5_ants_4animal_skullnoisypetra.json
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Original file line number Diff line number Diff line change
Expand Up @@ -89,11 +89,8 @@
{
"t1_head_auto_mask":
{
"kmeans": true,
"operation": "lower",
"index": 2,
"sample_bins": 30,
"distance": 10
"index": 2
},
"t1_head_dilate":
{
Expand Down Expand Up @@ -356,9 +353,6 @@
{
"ct_skull_auto_mask":
{
"kmeans": true,
"sample_bins": 30,
"distance": 10,
"operation": "lower",
"index": 2
},
Expand All @@ -382,9 +376,6 @@
{
"ct_skull_auto_mask":
{
"kmeans": true,
"sample_bins": 30,
"distance": 10,
"operation": "lower",
"index": 2
},
Expand Down
11 changes: 1 addition & 10 deletions workflows/params_segment_macaque_0p5_ants_quick_skull.json
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Expand Up @@ -88,11 +88,8 @@
{
"t1_head_auto_mask":
{
"kmeans": true,
"operation": "lower",
"index": 2,
"sample_bins": 30,
"distance": 10
"index": 2
},
"t1_head_dilate":
{
Expand Down Expand Up @@ -340,9 +337,6 @@
{
"ct_skull_auto_mask":
{
"kmeans": true,
"sample_bins": 30,
"distance": 10,
"operation": "lower",
"index": 2
},
Expand All @@ -366,9 +360,6 @@
{
"ct_skull_auto_mask":
{
"kmeans": true,
"sample_bins": 30,
"distance": 10,
"operation": "lower",
"index": 2
},
Expand Down
11 changes: 1 addition & 10 deletions workflows/params_segment_macaque_0p5_ants_quick_skullnoisypetra.json
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Original file line number Diff line number Diff line change
Expand Up @@ -88,11 +88,8 @@
{
"t1_head_auto_mask":
{
"kmeans": true,
"operation": "lower",
"index": 2,
"sample_bins": 30,
"distance": 10
"index": 2
},
"t1_head_dilate":
{
Expand Down Expand Up @@ -355,9 +352,6 @@
{
"ct_skull_auto_mask":
{
"kmeans": true,
"sample_bins": 30,
"distance": 10,
"operation": "lower",
"index": 2
},
Expand All @@ -381,9 +375,6 @@
{
"ct_skull_auto_mask":
{
"kmeans": true,
"sample_bins": 30,
"distance": 10,
"operation": "lower",
"index": 2
},
Expand Down
11 changes: 1 addition & 10 deletions workflows/params_segment_macaque_0p5_ants_skull.json
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Original file line number Diff line number Diff line change
Expand Up @@ -94,11 +94,8 @@
{
"t1_head_auto_mask":
{
"kmeans": true,
"operation": "lower",
"index": 2,
"sample_bins": 30,
"distance": 10
"index": 2
},
"t1_head_dilate":
{
Expand Down Expand Up @@ -346,9 +343,6 @@
{
"ct_skull_auto_mask":
{
"kmeans": true,
"sample_bins": 30,
"distance": 10,
"operation": "lower",
"index": 2
},
Expand All @@ -372,9 +366,6 @@
{
"ct_skull_auto_mask":
{
"kmeans": true,
"sample_bins": 30,
"distance": 10,
"operation": "lower",
"index": 2
},
Expand Down
11 changes: 1 addition & 10 deletions workflows/params_segment_macaque_0p5_ants_skullnoisypetra.json
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Original file line number Diff line number Diff line change
Expand Up @@ -94,11 +94,8 @@
{
"t1_head_auto_mask":
{
"kmeans": true,
"operation": "lower",
"index": 2,
"sample_bins": 30,
"distance": 10
"index": 2
},
"t1_head_dilate":
{
Expand Down Expand Up @@ -361,9 +358,6 @@
{
"ct_skull_auto_mask":
{
"kmeans": true,
"sample_bins": 30,
"distance": 10,
"operation": "lower",
"index": 2
},
Expand All @@ -387,9 +381,6 @@
{
"ct_skull_auto_mask":
{
"kmeans": true,
"sample_bins": 30,
"distance": 10,
"operation": "lower",
"index": 2
},
Expand Down
3 changes: 0 additions & 3 deletions workflows/params_segment_macaque_ants_4animal_skull.json
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Original file line number Diff line number Diff line change
Expand Up @@ -347,9 +347,6 @@
{
"ct_skull_auto_mask":
{
"kmeans": true,
"sample_bins": 30,
"distance": 10,
"operation": "lower",
"index": 2
},
Expand Down
3 changes: 0 additions & 3 deletions workflows/params_segment_macaque_ants_4animal_skullnoisypetra.json
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Expand Up @@ -358,9 +358,6 @@
{
"ct_skull_auto_mask":
{
"kmeans": true,
"sample_bins": 30,
"distance": 10,
"operation": "lower",
"index": 2
},
Expand Down
3 changes: 0 additions & 3 deletions workflows/params_segment_macaque_ants_quick_skull.json
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Expand Up @@ -345,9 +345,6 @@
{
"ct_skull_auto_mask":
{
"kmeans": true,
"sample_bins": 30,
"distance": 10,
"operation": "lower",
"index": 2
},
Expand Down
3 changes: 0 additions & 3 deletions workflows/params_segment_macaque_ants_quick_skullnoisypetra.json
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Expand Up @@ -357,9 +357,6 @@
{
"ct_skull_auto_mask":
{
"kmeans": true,
"sample_bins": 30,
"distance": 10,
"operation": "lower",
"index": 2
},
Expand Down
3 changes: 0 additions & 3 deletions workflows/params_segment_macaque_ants_skull.json
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Expand Up @@ -351,9 +351,6 @@
{
"ct_skull_auto_mask":
{
"kmeans": true,
"sample_bins": 30,
"distance": 10,
"operation": "lower",
"index": 2
},
Expand Down
3 changes: 0 additions & 3 deletions workflows/params_segment_macaque_ants_skullnoisypetra.json
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Expand Up @@ -363,9 +363,6 @@
{
"ct_skull_auto_mask":
{
"kmeans": true,
"sample_bins": 30,
"distance": 10,
"operation": "lower",
"index": 2
},
Expand Down
3 changes: 0 additions & 3 deletions workflows/params_segment_macaque_skull.json
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Expand Up @@ -130,9 +130,6 @@
{
"ct_skull_auto_mask":
{
"kmeans": true,
"sample_bins": 30,
"distance": 10,
"operation": "lower",
"index": 2
},
Expand Down
3 changes: 0 additions & 3 deletions workflows/params_segment_macaque_spm_skull.json
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Expand Up @@ -206,9 +206,6 @@
{
"ct_skull_auto_mask":
{
"kmeans": true,
"sample_bins": 30,
"distance": 10,
"operation": "lower",
"index": 2
},
Expand Down
3 changes: 0 additions & 3 deletions workflows/params_segment_macaque_spm_skullnoisypetra.json
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Expand Up @@ -221,9 +221,6 @@
{
"ct_skull_auto_mask":
{
"kmeans": true,
"sample_bins": 30,
"distance": 10,
"operation": "lower",
"index": 2
},
Expand Down
3 changes: 0 additions & 3 deletions workflows/params_segment_marmo_ants_4animal_skull.json
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Expand Up @@ -308,9 +308,6 @@
{
"ct_skull_auto_mask":
{
"kmeans": true,
"sample_bins": 30,
"distance": 10,
"operation": "lower",
"index": 2
},
Expand Down
3 changes: 0 additions & 3 deletions workflows/params_segment_marmo_ants_quick_skull.json
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Expand Up @@ -306,9 +306,6 @@
{
"ct_skull_auto_mask":
{
"kmeans": true,
"sample_bins": 30,
"distance": 10,
"operation": "lower",
"index": 2
},
Expand Down
3 changes: 0 additions & 3 deletions workflows/params_segment_marmo_ants_skull.json
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Expand Up @@ -311,9 +311,6 @@
{
"ct_skull_auto_mask":
{
"kmeans": true,
"sample_bins": 30,
"distance": 10,
"operation": "lower",
"index": 2
},
Expand Down
3 changes: 0 additions & 3 deletions workflows/params_segment_marmo_ants_skullnoisypetra.json
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Expand Up @@ -361,9 +361,6 @@
{
"ct_skull_auto_mask":
{
"kmeans": true,
"sample_bins": 30,
"distance": 10,
"operation": "lower",
"index": 2
},
Expand Down
3 changes: 0 additions & 3 deletions workflows/params_segment_marmo_spm_skull.json
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Expand Up @@ -306,9 +306,6 @@
{
"ct_skull_auto_mask":
{
"kmeans": true,
"sample_bins": 30,
"distance": 10,
"operation": "lower",
"index": 2
},
Expand Down
3 changes: 0 additions & 3 deletions workflows/params_segment_marmot2_ants_4animal_skull.json
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Expand Up @@ -309,9 +309,6 @@
{
"ct_skull_auto_mask":
{
"kmeans": true,
"sample_bins": 30,
"distance": 10,
"operation": "lower",
"index": 2
},
Expand Down
3 changes: 0 additions & 3 deletions workflows/params_segment_marmot2_ants_skull.json
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Expand Up @@ -307,9 +307,6 @@
{
"ct_skull_auto_mask":
{
"kmeans": true,
"sample_bins": 30,
"distance": 10,
"operation": "lower",
"index": 2
},
Expand Down
3 changes: 0 additions & 3 deletions workflows/params_segment_marmot2_spm_skull.json
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Expand Up @@ -311,9 +311,6 @@
{
"ct_skull_auto_mask":
{
"kmeans": true,
"sample_bins": 30,
"distance": 10,
"operation": "lower",
"index": 2
},
Expand Down