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Hendrik-code merged 2 commits into from
Sep 2, 2026
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docs(tutorials): update notebooks and atlas example to current API #149

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876980c
update tutorials and atlas example to current API
robert-graf Sep 1, 2026
46f4c7f
Merge branch 'main' into tutorial
Hendrik-code Sep 2, 2026
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95 changes: 4 additions & 91 deletions examples/registration/atlas_poi_transfer_leg/example.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -59,14 +59,7 @@
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"from TPTBox.segmentation.TotalVibeSeg import run_totalvibeseg\n",
"\n",
"path_to_ct = \"...\"\n",
"out_seg = \"seg.nii.gz\"\n",
"ddevice = \"cpu\" #\"cuda\" / \"mps\"\n",
"run_totalvibeseg(path_to_ct,out_seg=out_seg,override=False,gpu=1,ddevice=ddevice,dataset_id=10,keep_size=True)"
]
"source": "from TPTBox.segmentation import run_vibeseg\n\npath_to_ct = \"...\"\nout_seg = \"seg.nii.gz\"\nddevice = \"cpu\" # \"cuda\" / \"mps\"\nrun_vibeseg(path_to_ct, out_seg=out_seg, override=False, gpu=1, ddevice=ddevice, dataset_id=10, keep_size=True)\n"
},
{
"cell_type": "markdown",
Expand Down Expand Up @@ -130,58 +123,7 @@
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"#Step 1\n",
"from pathlib import Path\n",
"\n",
"from atlas_poi_transfer import parse_coordinates_to_poi, prep_Atlas\n",
"\n",
"from TPTBox import POI, to_nii\n",
"from TPTBox.core.vert_constants import Full_Body_Instance, Lower_Body\n",
"\n",
"##########################################\n",
"#Settings\n",
"text_file_is_left_leg = True\n",
"file_text = \"010__left.txt\"\n",
"segmentation_path = \"/DATA/NAS/datasets_processed/CT_fullbody/dataset-watrinet/source/Dataset001_all/0001/bone.nii.gz\"\n",
"out_folder = Path(\"/DATA/NAS/datasets_processed/CT_fullbody/dataset-watrinet/atlas\")\n",
"atlas_id = 1\n",
"##########################################\n",
"# Load segmentation\n",
"seg = to_nii(segmentation_path,True)\n",
"\n",
"if not text_file_is_left_leg:\n",
" axis = seg.get_axis(\"R\")\n",
" if axis == 0:\n",
" target = seg.set_array(seg.get_array()[::-1]).copy()\n",
" elif axis == 1:\n",
" target = seg.set_array(seg.get_array()[:, ::-1]).copy()\n",
" elif axis == 2:\n",
" target = seg.set_array(seg.get_array()[:, :, ::-1]).copy()\n",
"assert text_file_is_left_leg, \"Not implement: Flip NII and POI\"\n",
"# Prep atlas\n",
"atlas_path = out_folder/f\"atlas{atlas_id:03}.nii.gz\"\n",
"atlas_cms_poi_path = out_folder/f\"atlas{atlas_id:03}_cms_poi.json\" # Center of mass\n",
"atlas_poi_path = out_folder/f\"atlas{atlas_id:03}_poi.json\"\n",
"prep_Atlas(target,atlas_path,atlas_cms_poi_path,text_file_is_left_leg)\n",
"\n",
"\n",
"poi = parse_coordinates_to_poi(file_text, True).to_other(seg) if \".txt\" in file_text else POI.load(file_text).resample_from_to(seg)\n",
"if not text_file_is_left_leg:\n",
" for k1, k2, (x, y, z) in poi.items():\n",
" axis = poi.get_axis(\"R\")\n",
" if axis == 0:\n",
" poi[k1, k2] = (poi.shape[0] - 1 - x, y, z)\n",
" elif axis == 1:\n",
" poi[k1, k2] = (x, poi.shape[1] - 1 - y, z)\n",
" elif axis == 2:\n",
" poi[k1, k2] = (x, y, poi.shape[2] - 1 - z)\n",
" else:\n",
" raise ValueError(axis)\n",
"poi.level_one_info=Full_Body_Instance\n",
"poi.level_two_info=Lower_Body\n",
"poi.to_global().save(atlas_poi_path)\n"
]
"source": "#Step 1\nfrom pathlib import Path\n\nfrom atlas_poi_transfer_leg_ct import parse_coordinates_to_poi, prep_Atlas\n\nfrom TPTBox import POI, to_nii\nfrom TPTBox.core.vert_constants import Full_Body_Instance, Lower_Body\n\n##########################################\n#Settings\ntext_file_is_left_leg = True\nfile_text = \"010__left.txt\"\nsegmentation_path = \"/DATA/NAS/datasets_processed/CT_fullbody/dataset-watrinet/source/Dataset001_all/0001/bone.nii.gz\"\nct_path = \"/DATA/NAS/datasets_processed/CT_fullbody/dataset-watrinet/source/Dataset001_all/0001/ct.nii.gz\"\nout_folder = Path(\"/DATA/NAS/datasets_processed/CT_fullbody/dataset-watrinet/atlas\")\natlas_id = 1\n##########################################\n# Load segmentation\nseg = to_nii(segmentation_path,True)\n\nif not text_file_is_left_leg:\n axis = seg.get_axis(\"R\")\n if axis == 0:\n target = seg.set_array(seg.get_array()[::-1]).copy()\n elif axis == 1:\n target = seg.set_array(seg.get_array()[:, ::-1]).copy()\n elif axis == 2:\n target = seg.set_array(seg.get_array()[:, :, ::-1]).copy()\nassert text_file_is_left_leg, \"Not implement: Flip NII and POI\"\n# Prep atlas\natlas_path = out_folder/f\"atlas{atlas_id:03}.nii.gz\"\nct_atlas_path = out_folder/f\"atlas{atlas_id:03}_ct.nii.gz\" # cropped CT saved next to the atlas\natlas_cms_poi_path = out_folder/f\"atlas{atlas_id:03}_cms_poi.json\" # Center of mass\natlas_poi_path = out_folder/f\"atlas{atlas_id:03}_poi.json\"\nprep_Atlas(seg, ct_path, atlas_path, ct_atlas_path, atlas_cms_poi_path, atlas_left=text_file_is_left_leg)\n\n\npoi = parse_coordinates_to_poi(file_text, True).to_other(seg) if \".txt\" in file_text else POI.load(file_text).resample_from_to(seg)\nif not text_file_is_left_leg:\n for k1, k2, (x, y, z) in poi.items():\n axis = poi.get_axis(\"R\")\n if axis == 0:\n poi[k1, k2] = (poi.shape[0] - 1 - x, y, z)\n elif axis == 1:\n poi[k1, k2] = (x, poi.shape[1] - 1 - y, z)\n elif axis == 2:\n poi[k1, k2] = (x, y, poi.shape[2] - 1 - z)\n else:\n raise ValueError(axis)\npoi.level_one_info=Full_Body_Instance\npoi.level_two_info=Lower_Body\npoi.to_global().save(atlas_poi_path)\n"
},
{
"cell_type": "markdown",
Expand Down Expand Up @@ -217,36 +159,7 @@
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"#Step 1\n",
"from pathlib import Path\n",
"\n",
"from atlas_poi_transfer import Register_Point_Atlas\n",
"\n",
"from TPTBox import POI, to_nii\n",
"\n",
"##########################################\n",
"#Settings\n",
"target_seg_path = \"/DATA/NAS/datasets_processed/CT_fullbody/dataset-watrinet/source/Dataset001_all/0003/bone.nii.gz\"#TODO Path to target seg\n",
"s = str(target_seg_path).split('.')[0]\n",
"split_leg_path = s + \"_seg-left-right-split_msk.nii.gz\"\n",
"out_new_pois = s + \"_desc-leg_poi.json\"\n",
"out_new_pois_nii = s + \"_desc-leg_poi.nii.gz\"\n",
"atlas_id = 1\n",
"ddevice = \"cuda\"\n",
"gpu = 0\n",
"##########################################\n",
"# Atlas\n",
"atlas_p = out_folder/f\"atlas{atlas_id:03}.nii.gz\"\n",
"atlas_centroids = out_folder/f\"atlas{atlas_id:03}_cms_poi.json\" # Center of mass\n",
"atlas_poi_path = out_folder/f\"atlas{atlas_id:03}_poi.json\"\n",
"# Load segmentation\n",
"target = to_nii(target_seg_path,True)\n",
"atlas = to_nii(atlas_p,True)\n",
"\n",
"#Creating this object will start the registration\n",
"registration_obj = Register_Point_Atlas(target,atlas,split_leg_path=split_leg_path,atlas_centroids=atlas_centroids,gpu=gpu,ddevice=ddevice, verbose=0)"
]
"source": "#Step 1\nfrom pathlib import Path\n\nfrom atlas_poi_transfer_leg_ct import Register_Point_Atlas\n\nfrom TPTBox import POI, to_nii\n\n##########################################\n#Settings\ntarget_seg_path = \"/DATA/NAS/datasets_processed/CT_fullbody/dataset-watrinet/source/Dataset001_all/0003/bone.nii.gz\"#TODO Path to target seg\ns = str(target_seg_path).split('.')[0]\nsplit_leg_path = s + \"_seg-left-right-split_msk.nii.gz\"\nout_new_pois = s + \"_desc-leg_poi.json\"\nout_new_pois_nii = s + \"_desc-leg_poi.nii.gz\"\natlas_id = 1\nddevice = \"cuda\"\ngpu = 0\n##########################################\n# Atlas\natlas_p = out_folder/f\"atlas{atlas_id:03}.nii.gz\"\natlas_centroids = out_folder/f\"atlas{atlas_id:03}_cms_poi.json\" # Center of mass\natlas_poi_path = out_folder/f\"atlas{atlas_id:03}_poi.json\"\n# Load segmentation\ntarget = to_nii(target_seg_path,True)\natlas = to_nii(atlas_p,True)\n\n#Creating this object will start the registration\nregistration_obj = Register_Point_Atlas(target,atlas,split_leg_path=split_leg_path,atlas_centroids=atlas_centroids,gpu=gpu,ddevice=ddevice, verbose=0)\n"
},
{
"cell_type": "code",
Expand Down Expand Up @@ -321,4 +234,4 @@
},
"nbformat": 4,
"nbformat_minor": 2
}
}
4 changes: 3 additions & 1 deletion examples/registration/atlas_poi_transfer_leg/example.py
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Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,7 @@
text_file_is_left_leg = True
file_text = "/DATA/NAS/tools/TPTBox/examples/atlas_poi_transfer_leg/010__left.txt"
segmentation_path = "/DATA/NAS/datasets_processed/CT_fullbody/dataset-watrinet/source/Dataset001_all/0001/bone.nii.gz"
ct_path = "/DATA/NAS/datasets_processed/CT_fullbody/dataset-watrinet/source/Dataset001_all/0001/ct.nii.gz"
out_folder = Path("/DATA/NAS/datasets_processed/CT_fullbody/dataset-watrinet/atlas2")
atlas_id = 1
##########################################
Expand All @@ -31,9 +32,10 @@
assert text_file_is_left_leg, "Not implement: Flip NII and POI"
# Prep atlas
atlas_path = out_folder / f"atlas{atlas_id:03}.nii.gz"
ct_atlas_path = out_folder / f"atlas{atlas_id:03}_ct.nii.gz" # cropped CT saved next to the atlas
atlas_cms_poi_path = out_folder / f"atlas{atlas_id:03}_cms_poi.json" # Center of mass
atlas_poi_path = out_folder / f"atlas{atlas_id:03}_poi.json"
prep_Atlas(seg, atlas_path, atlas_cms_poi_path, text_file_is_left_leg)
prep_Atlas(seg, ct_path, atlas_path, ct_atlas_path, atlas_cms_poi_path, atlas_left=text_file_is_left_leg)


poi = parse_coordinates_to_poi(file_text, True).to_other(seg) if ".txt" in file_text else POI.load(file_text).resample_from_to(seg)
Expand Down
103 changes: 4 additions & 99 deletions tutorials/tutorial_Dataset_processing.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -896,54 +896,14 @@
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"from pathlib import Path\n",
"\n",
"from TPTBox import NII, Location, Vertebra_Instance, calc_poi_from_subreg_vert, to_nii\n",
"from TPTBox.registration import Point_Registration, ridged_points_from_poi\n",
"\n",
"# Example registration two sagittal images, like for compensating movement between scans.\n",
"poi_fixed = calc_poi_from_subreg_vert(nii_instance1, nii_semantic1, subreg_id=[Location.Vertebra_Corpus, Location.Spinosus_Process]).round(\n",
" 2\n",
")\n",
"poi_moving = calc_poi_from_subreg_vert(nii_instance2, nii_semantic2, subreg_id=[Location.Vertebra_Corpus, Location.Spinosus_Process]).round(\n",
" 2\n",
")\n",
"\n",
"registration_object: Point_Registration = ridged_points_from_poi(poi_fixed, poi_moving, c_val=0)\n",
"\n",
"# Move image\n",
"moved_nii = registration_object.transform_nii(image2)\n",
"print(moved_nii, \"\\n\", image2, \"\\n\")\n",
"# Move poi\n",
"moved_poi = registration_object.transform_poi(poi_moving).round(1)\n",
"print(moved_poi, \"\\n\", poi_moving, \"\\n\")\n"
]
"source": "from pathlib import Path\n\nfrom TPTBox import NII, Location, Vertebra_Instance, calc_poi_from_subreg_vert, to_nii\nfrom TPTBox.registration import Point_Registration, ridged_points_from_poi\n\n# Example registration two sagittal images, like for compensating movement between scans.\npoi_fixed = calc_poi_from_subreg_vert(nii_instance1, nii_semantic1, subreg_id=[Location.Vertebra_Corpus, Location.Spinosus_Process]).round(\n 2\n)\npoi_moving = calc_poi_from_subreg_vert(nii_instance2, nii_semantic2, subreg_id=[Location.Vertebra_Corpus, Location.Spinosus_Process]).round(\n 2\n)\n\nregistration_object: Point_Registration = ridged_points_from_poi(poi_fixed, poi_moving)\n\n# Move image\nmoved_nii = registration_object.transform_nii(image2)\nprint(moved_nii, \"\\n\", image2, \"\\n\")\n# Move poi\nmoved_poi = registration_object.transform_poi(poi_moving).round(1)\nprint(moved_poi, \"\\n\", poi_moving, \"\\n\")\n"
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"from TPTBox import NII, Location, Vertebra_Instance, calc_poi_from_subreg_vert\n",
"from TPTBox.registration import Point_Registration, ridged_points_from_poi\n",
"\n",
"# Example registration two sagittal images, like for compensating movement between scans.\n",
"poi_fixed = calc_poi_from_subreg_vert(nii_instance1, nii_semantic1, subreg_id=[Location.Vertebra_Corpus, Location.Spinosus_Process]).round(\n",
" 2\n",
")\n",
"poi_moving = calc_poi_from_subreg_vert(nii_instance2, nii_semantic2, subreg_id=[Location.Vertebra_Corpus, Location.Spinosus_Process]).round(\n",
" 2\n",
")\n",
"registration_object: Point_Registration = ridged_points_from_poi(poi_fixed, poi_moving, c_val=0)\n",
"# Move image\n",
"moved_nii = registration_object.transform_nii(image2, output_space=fixed_image)\n",
"print(moved_nii, \"\\n\", image2, \"\\n\")\n",
"# Move poi\n",
"moved_poi = registration_object.transform_poi(poi_moving).round(1)\n",
"print(moved_poi, \"\\n\", poi_moving, \"\\n\")\n"
]
"source": "from TPTBox import NII, Location, Vertebra_Instance, calc_poi_from_subreg_vert\nfrom TPTBox.registration import Point_Registration, ridged_points_from_poi\n\n# Example registration two sagittal images, like for compensating movement between scans.\npoi_fixed = calc_poi_from_subreg_vert(nii_instance1, nii_semantic1, subreg_id=[Location.Vertebra_Corpus, Location.Spinosus_Process]).round(\n 2\n)\npoi_moving = calc_poi_from_subreg_vert(nii_instance2, nii_semantic2, subreg_id=[Location.Vertebra_Corpus, Location.Spinosus_Process]).round(\n 2\n)\nregistration_object: Point_Registration = ridged_points_from_poi(poi_fixed, poi_moving)\n# Move image\nmoved_nii = registration_object.transform_nii(image2, output_space=fixed_image)\nprint(moved_nii, \"\\n\", image2, \"\\n\")\n# Move poi\nmoved_poi = registration_object.transform_poi(poi_moving).round(1)\nprint(moved_poi, \"\\n\", poi_moving, \"\\n\")\n"
},
{
"cell_type": "code",
Expand Down Expand Up @@ -980,62 +940,7 @@
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"from TPTBox import NII, Location, Vertebra_Instance, calc_poi_from_subreg_vert\n",
"from TPTBox.registration import Point_Registration, ridged_points_from_poi\n",
"from TPTBox.segmentation.VibeSeg.vibeseg import extract_vertebra_bodies_from_VibeSeg\n",
"\n",
"# Example registration axial and sagittal with points.\n",
"# T2w axial points are computed from the vibe segment.\n",
"dataset = target_folder / \"dataset-tutorial-data-processing\"\n",
"\n",
"nii_instance_path2 = out_paths[\"out_vert\"]\n",
"nii_semantic_path2 = out_paths[\"out_spine\"]\n",
"# We recommend if you registrade spineps points too use at least two points.\n",
"poi_fixed = calc_poi_from_subreg_vert(nii_instance_path, nii_semantic_path, subreg_id=[Location.Vertebra_Corpus]).round(1)\n",
"fixed_image = BIDS_FILE(\n",
" f\"{dataset}/rawdata_stiched/sub-111168223/ses-20230128/T2w/sub-111168223_ses-20230128_sequ-401-stiched_acq-sag_part-inphase_T2w.nii.gz\",\n",
" dataset,\n",
")\n",
"\n",
"moving_file = BIDS_FILE(\n",
" f\"{dataset}/rawdata_stiched/sub-111168223/ses-20230128/dixon/sub-111168223_ses-20230128_sequ-501-stiched_acq-ax_part-water_dixon.nii.gz\",\n",
" dataset,\n",
")\n",
"out_file = moving_file.get_changed_path(\n",
" \"nii.gz\", \"msk\", parent=\"derivative\", info={\"seg\": \"VibeSegmentator\", \"mod\": moving_file.bids_format}\n",
")\n",
"moving_image = to_nii(moving_file)\n",
"out_file = to_nii(out_file, True)\n",
"\n",
"#### Let's move the image, so we see better that the registration is working.\n",
"moving_image.origin = (moving_image.origin[0], moving_image.origin[1], moving_image.origin[2] + 175)\n",
"out_file.origin = moving_image.origin\n",
"####\n",
"\n",
"# Ensure that we count the same as in the T2w sagittal\n",
"num_thoracic_verts = 12\n",
"if Vertebra_Instance.T13.value in poi_fixed.keys_region():\n",
" num_thoracic_verts = 13\n",
"if Vertebra_Instance.T12.value not in poi_fixed.keys_region():\n",
" num_thoracic_verts = 11\n",
"num_lumbar_verts = 5\n",
"if Vertebra_Instance.L6.value in poi_fixed.keys_region():\n",
" num_lumbar_verts = 6\n",
"if Vertebra_Instance.L5.value not in poi_fixed.keys_region():\n",
" num_lumbar_verts = 4\n",
"# Note: this function currently assumes that we see the sacrum in the image.\n",
"nii, poi_moving = extract_vertebra_bodies_from_VibeSeg(out_file, num_lumbar_verts=num_lumbar_verts, num_thoracic_verts=num_thoracic_verts)\n",
"\n",
"registration_object: Point_Registration = ridged_points_from_poi(poi_fixed, poi_moving, c_val=0)\n",
"\n",
"# Move image\n",
"moved_nii = registration_object.transform_nii(moving_image)\n",
"print(moved_nii, \"\\n\", moving_image, \"\\n\")\n",
"# Move poi\n",
"moved_poi = registration_object.transform_poi(poi_moving).round(1)\n",
"print(moved_poi, \"\\n\", poi_moving, \"\\n\")\n"
]
"source": "from TPTBox import NII, Location, Vertebra_Instance, calc_poi_from_subreg_vert\nfrom TPTBox.registration import Point_Registration, ridged_points_from_poi\nfrom TPTBox.segmentation.VibeSeg.vibeseg import extract_vertebra_bodies_from_VibeSeg\n\n# Example registration axial and sagittal with points.\n# T2w axial points are computed from the vibe segment.\ndataset = target_folder / \"dataset-tutorial-data-processing\"\n\nnii_instance_path2 = out_paths[\"out_vert\"]\nnii_semantic_path2 = out_paths[\"out_spine\"]\n# We recommend if you registrade spineps points too use at least two points.\npoi_fixed = calc_poi_from_subreg_vert(nii_instance_path, nii_semantic_path, subreg_id=[Location.Vertebra_Corpus]).round(1)\nfixed_image = BIDS_FILE(\n f\"{dataset}/rawdata_stiched/sub-111168223/ses-20230128/T2w/sub-111168223_ses-20230128_sequ-401-stiched_acq-sag_part-inphase_T2w.nii.gz\",\n dataset,\n)\n\nmoving_file = BIDS_FILE(\n f\"{dataset}/rawdata_stiched/sub-111168223/ses-20230128/dixon/sub-111168223_ses-20230128_sequ-501-stiched_acq-ax_part-water_dixon.nii.gz\",\n dataset,\n)\nout_file = moving_file.get_changed_path(\n \"nii.gz\", \"msk\", parent=\"derivative\", info={\"seg\": \"VibeSegmentator\", \"mod\": moving_file.bids_format}\n)\nmoving_image = to_nii(moving_file)\nout_file = to_nii(out_file, True)\n\n#### Let's move the image, so we see better that the registration is working.\nmoving_image.origin = (moving_image.origin[0], moving_image.origin[1], moving_image.origin[2] + 175)\nout_file.origin = moving_image.origin\n####\n\n# Ensure that we count the same as in the T2w sagittal\nnum_thoracic_verts = 12\nif Vertebra_Instance.T13.value in poi_fixed.keys_region():\n num_thoracic_verts = 13\nif Vertebra_Instance.T12.value not in poi_fixed.keys_region():\n num_thoracic_verts = 11\nnum_lumbar_verts = 5\nif Vertebra_Instance.L6.value in poi_fixed.keys_region():\n num_lumbar_verts = 6\nif Vertebra_Instance.L5.value not in poi_fixed.keys_region():\n num_lumbar_verts = 4\n# Note: this function currently assumes that we see the sacrum in the image.\nnii, poi_moving = extract_vertebra_bodies_from_VibeSeg(out_file, num_lumbar_verts=num_lumbar_verts, num_thoracic_verts=num_thoracic_verts)\n\nregistration_object: Point_Registration = ridged_points_from_poi(poi_fixed, poi_moving)\n\n# Move image\nmoved_nii = registration_object.transform_nii(moving_image)\nprint(moved_nii, \"\\n\", moving_image, \"\\n\")\n# Move poi\nmoved_poi = registration_object.transform_poi(poi_moving).round(1)\nprint(moved_poi, \"\\n\", poi_moving, \"\\n\")\n"
},
{
"cell_type": "code",
Expand Down Expand Up @@ -1192,4 +1097,4 @@
},
"nbformat": 4,
"nbformat_minor": 0
}
}
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