replaced BIDS with TPTBox

.github/workflows/python-publish.yml

@@ -17,15 +17,16 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v3
       with:
-        python-version: '3.x'
+        python-version: '3.11'
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
         pip install build
     - name: Build package
       run: python -m build
     - name: Publish package
-      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
+      uses: pypa/gh-action-pypi-publish@release/v1 #pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
       with:
-        user: Hendrik_Code
+        #user: Hendrik_Code
+        verbose: true
         password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/tests.yml

@@ -0,0 +1,40 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: tests
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10", "3.11", "3.12"]
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install flake8 pytest
+        pip install -e .
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test with pytest
+      run: |
+        pytest

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "poetry_dynamic_versioning.backend"
 
 [tool.poetry]
 name = "SPINEPS"
-version = "0.0.0"
+version = "1.0.0"
 description = "Framework for out-of-the box whole spine MRI segmentation."
 authors = ["Hendrik Möller <[email protected]>"]
 repository = "https://github.com/Hendrik-code/spineps"
@@ -29,6 +29,7 @@ torchmetrics = "^1.1.2"
 tqdm = "^4.66.1"
 einops= "^0.6.1"
 nnunetv2 = "2.2"
+tptbox = "*"
 
 
 [tool.poetry-dynamic-versioning]

spineps/entrypoint.py

@@ -5,7 +5,7 @@
 from pathlib import Path
 from time import perf_counter
 
-from BIDS import BIDS_FILE, Log_Type, No_Logger
+from TPTBox import BIDS_FILE, Log_Type, No_Logger
 
 from spineps.models import get_instance_model, get_segmentation_model, get_semantic_model, modelid2folder_instance, modelid2folder_semantic
 from spineps.seg_run import process_dataset, process_img_nii
@@ -214,7 +214,7 @@ def run_sample(opt: Namespace):
 
     start_time = perf_counter()
     if opt.run_cprofiler:
-        from BIDS.logger.log_file import format_time_short, get_time
+        from TPTBox.logger.log_file import format_time_short, get_time
 
         timestamp = format_time_short(get_time())
         cprofile_out = bids_sample.get_changed_path(
@@ -286,7 +286,7 @@ def run_dataset(opt: Namespace):
     }
 
     if opt.run_cprofiler:
-        from BIDS.logger.log_file import format_time_short, get_time
+        from TPTBox.logger.log_file import format_time_short, get_time
 
         start_time = get_time()
         start_time_short = format_time_short(start_time)

spineps/example/helper_parallel.py

@@ -5,7 +5,7 @@
 sys.path.append(str(file.parents[1]))
 sys.path.append(str(file.parents[2]))
 
-from BIDS import (
+from TPTBox import (
     BIDS_FILE,
 )
 from spineps.models import get_segmentation_model

spineps/example/template_roll_out.py

@@ -5,7 +5,7 @@
 sys.path.append(str(file.parents[1]))
 sys.path.append(str(file.parents[2]))
 
-from BIDS import (
+from TPTBox import (
     BIDS_Global_info,
     BIDS_FILE,
     No_Logger,
@@ -14,12 +14,12 @@
 )
 import time
 from spineps.seg_run import process_img_nii, ErrCode
-from spineps.models import MODELS
+from spineps.models import get_semantic_model, get_instance_model
 import numpy as np
 
 # INPUT
 in_ds = Path("DATASET_PATH")
-raw = "rawdata"
+raw = "rawdata"  # TODO
 der = "derivatives"  # TODO
 
 head_logger = No_Logger()  # (in_ds, log_filename="source-convert-to-unet-train", default_verbose=True)
@@ -29,8 +29,8 @@
 parent_raw = str(Path(raw).joinpath(str(block)))
 parent_der = str(Path(der).joinpath(str(block)))
 
-model_subreg = MODELS.T2w_NAKOSPIDER_HIGHRES_CUT().load()
-model_vert = MODELS.VERT_HIGHRES().load()
+model_semantic = get_semantic_model("Model_name")
+model_instance = get_instance_model("Model_name")
 
 bids_ds = BIDS_Global_info(datasets=[in_ds], parents=[parent_raw, parent_der], verbose=False)
 
@@ -70,8 +70,8 @@ def injection_function(seg_nii: NII):
         output_paths, errcode = process_img_nii(
             img_ref=ref,
             derivative_name=der,
-            model_semantic=model_subreg,
-            model_instance=model_vert,
+            model_semantic=model_semantic,
+            model_instance=model_instance,
             override_semantic=False,
             override_instance=False,
             lambda_semantic=injection_function,
@@ -89,9 +89,9 @@ def injection_function(seg_nii: NII):
 
         # Load Outputs
         img_nii = ref.open_nii()
-        seg_nii = NII.load(output_paths["out_spine"], seg=True)  # subregion mask
-        vert_nii = NII.load(output_paths["out_vert"], seg=True)  # subregion mask
-        ctd = POI.load(output_paths["out_ctd"])  # subregion mask
+        seg_nii = NII.load(output_paths["out_spine"], seg=True)  # semantic mask
+        vert_nii = NII.load(output_paths["out_vert"], seg=True)  # instance mask
+        ctd = POI.load(output_paths["out_ctd"])  # centroid file
 
         # TODO do something with outputs, potentially saving them again to the output paths
 

spineps/models.py

@@ -1,7 +1,7 @@
 import os
 from pathlib import Path
 
-from BIDS import Log_Type, No_Logger
+from TPTBox import Log_Type, No_Logger
 
 from spineps.seg_enums import Modality
 from spineps.seg_model import Segmentation_Model, modeltype2class

spineps/phase_instance.py

@@ -1,8 +1,7 @@
 # from utils.predictor import nnUNetPredictor
 import numpy as np
-from BIDS import NII, Location, Log_Type
-from BIDS.core.np_utils import np_approx_center_of_mass, np_calc_crop_around_centerpoint, np_dice
-from scipy.ndimage import center_of_mass
+from TPTBox import NII, Location, Log_Type
+from TPTBox.core.np_utils import np_calc_crop_around_centerpoint, np_dice
 from tqdm import tqdm
 
 from spineps.seg_enums import ErrCode, OutputType

spineps/phase_post.py

@@ -1,7 +1,7 @@
 # from utils.predictor import nnUNetPredictor
 import numpy as np
-from BIDS import NII, Location, Log_Type, v_idx2name, v_name2idx
-from BIDS.core.np_utils import np_bbox_nd, np_connected_components, np_dilate_msk, np_map_labels, np_approx_center_of_mass
+from TPTBox import NII, Location, Log_Type, v_idx2name, v_name2idx
+from TPTBox.core.np_utils import np_bbox_nd, np_connected_components, np_dilate_msk, np_map_labels, np_approx_center_of_mass
 from scipy.ndimage import center_of_mass
 
 from spineps.seg_pipeline import logger, vertebra_subreg_labels

spineps/phase_semantic.py

@@ -1,5 +1,5 @@
 # from utils.predictor import nnUNetPredictor
-from BIDS import NII, Location, Log_Type
+from TPTBox import NII, Location, Log_Type
 import numpy as np
 from spineps.utils.proc_functions import clean_cc_artifacts, n4_bias
 from spineps.seg_model import Segmentation_Model

spineps/seg_model.py

@@ -1,7 +1,7 @@
 from pathlib import Path
 import os
 
-from BIDS import Image_Reference, NII, to_nii, Logger, No_Logger, Zooms, Log_Type
+from TPTBox import Image_Reference, NII, to_nii, Logger, No_Logger, Zooms, Log_Type
 from spineps.utils.filepaths import search_path
 import torch
 from torch import from_numpy

spineps/seg_modelconfig.py

@@ -1,6 +1,6 @@
 from pathlib import Path
 
-from BIDS import Zooms, Location, v_name2idx, Ax_Codes, Logger_Interface, Log_Type
+from TPTBox import Zooms, Location, v_name2idx, Ax_Codes, Logger_Interface, Log_Type
 import json
 from spineps.seg_enums import Modality, Acquisition, ModelType, InputType
 

spineps/seg_pipeline.py

@@ -1,7 +1,7 @@
 # from utils.predictor import nnUNetPredictor
-from BIDS import NII, Location, No_Logger, Zooms
-from BIDS.core import poi
-from BIDS.logger.log_file import get_time, format_time_short
+from TPTBox import NII, Location, No_Logger, Zooms
+from TPTBox.core import poi
+from TPTBox.logger.log_file import get_time, format_time_short
 from spineps.seg_model import Segmentation_Model
 import subprocess
 

spineps/seg_run.py

@@ -6,8 +6,8 @@
 
 import nibabel as nib
 import numpy as np
-from BIDS import BIDS_FILE, NII, BIDS_Global_info, Centroids, Location, Log_Type, Logger
-from BIDS.snapshot2D.snapshot_templates import mri_snapshot
+from TPTBox import BIDS_FILE, NII, BIDS_Global_info, Centroids, Location, Log_Type, Logger
+from TPTBox.spine.snapshot2D.snapshot_templates import mri_snapshot
 
 from spineps.phase_instance import predict_instance_mask
 from spineps.phase_post import phase_postprocess_combined

spineps/seg_utils.py

@@ -1,5 +1,5 @@
 # from utils.predictor import nnUNetPredictor
-from BIDS import BIDS_FILE, Log_Type, Zooms
+from TPTBox import BIDS_FILE, Log_Type, Zooms
 from spineps.seg_model import Segmentation_Model
 from spineps.seg_pipeline import logger
 from spineps.seg_enums import Modality, Acquisition

spineps/utils/inference_api.py

@@ -2,8 +2,8 @@
 import os.path
 import torch
 from spineps.utils.predictor import nnUNetPredictor
-from BIDS import NII, No_Logger, Log_Type
-from BIDS.core import sitk_utils
+from TPTBox import NII, No_Logger, Log_Type
+from TPTBox.core import sitk_utils
 import nibabel as nib
 import numpy as np
 

spineps/utils/proc_functions.py

@@ -1,5 +1,5 @@
 from ants.utils.convert_nibabel import from_nibabel
-from BIDS import Logger_Interface, NII, np_utils
+from TPTBox import Logger_Interface, NII, np_utils
 import numpy as np
 from scipy.ndimage import center_of_mass
 from tqdm import tqdm