Merge branch 'master' of github.com:karanphil/scilpy into b1_correction

.github/workflows/freeze_requirements.yml

@@ -7,7 +7,7 @@ on:
 
 jobs:
   freeze_requirements:
-    runs-on: ubuntu-latest
+    runs-on: scilus-runners
     steps:
       - 
         name: Checkout scilpy

.github/workflows/test.yml

@@ -0,0 +1,70 @@
+name: Scilpy test suite
+
+on:
+  push:
+    branches:
+      - master
+  pull_request_target:
+    branches:
+      - master
+
+env:
+  MPLBACKEND: agg
+  OPENBLAS_NUM_THREADS: 1
+
+jobs:
+  test:
+    runs-on: scilus-runners
+    steps:
+      - name: Checkout repository
+        uses: actions/[email protected]
+
+      - name: Fetch python version from repository
+        id: python-selector
+        run: echo "python-version=$(cat .python-version)" >> $GITHUB_OUTPUT
+
+      - name: Set up Python for Scilpy
+        uses: actions/[email protected]
+        with:
+          python-version: ${{ steps.python-selector.outputs.python-version }}
+          cache: 'pip'
+
+      - name: Install non-python dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y \
+            build-essential \
+            curl \
+            git \
+            libblas-dev \
+            liblapack-dev \
+            libfreetype6-dev
+
+      - name: Install Scilpy
+        run: |
+          python -m pip install --upgrade pip setuptools wheel
+          python -m pip install -e .
+
+      - name: Run tests
+        run: |
+          export C_INCLUDE_PATH=$pythonLocation/include/python${{ steps.python-selector.outputs.python-version }}:$C_INCLUDE_PATH
+          pytest --cov-report term-missing:skip-covered
+
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v3
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+        with:
+          flags: unittests
+          name: scilpy-unittests-${{ github.run_id }}
+          verbose: true
+          directory: .test_reports/
+          fail_ci_if_error: true
+          root_dir: $GITHUB_WORKSPACE/scilpy/
+
+      - name: Upload test reports and coverage to artifacts
+        uses: actions/[email protected]
+        with:
+          name: test-reports
+          path: |
+            .test_reports/*

MANIFEST.in

@@ -3,6 +3,7 @@ include LICENSE
 include requirements.txt
 include .python-version
 
+recursive-include data/LUT *
 recursive-include scilpy *.c
 recursive-include scilpy *.cpp
 recursive-include scilpy *.pyx

codecov.yml

@@ -0,0 +1,34 @@
+codecov:
+  allow_coverage_offsets: True
+
+coverage:
+  status:
+    project:
+      default:
+        target: 75%
+        threshold: 2%
+        branches: 
+          - master
+        if_ci_failed: error
+        only_pulls: false
+    patch:
+      default:
+        target: 90%
+        branches: 
+          - master
+        if_ci_failed: error
+        only_pulls: false
+
+component_management:
+  individual_components:
+    - component_id: scilpy_scripts
+      name: Scripts
+      paths:
+        - scripts/
+    - component_id: scilpy_library
+      name: Library
+      paths:
+        - scilpy/
+
+comment:
+  layout: "condensed_header, diff, components"

requirements.txt

@@ -36,6 +36,7 @@ python-dateutil==2.8.*
 pytz==2022.6.*
 requests==2.28.*
 scikit-learn==1.2.*
+scikit-image==0.22.*
 scipy==1.9.*
 six==1.16.*
 spams==2.6.*

scilpy/image/tests/test_volume_math.py

@@ -19,6 +19,8 @@
                                       cut_up_cube,
                                       lower_threshold_eq, upper_threshold_eq,
                                       lower_threshold, upper_threshold,
+                                      lower_threshold_otsu,
+                                      upper_threshold_otsu,
                                       lower_clip, upper_clip,
                                       absolute_value,
                                       around, ceil, floor,
@@ -299,6 +301,36 @@ def test_upper_threshold():
     assert_array_equal(output_data, expected_output)
 
 
+def test_lower_threshold_otsu():
+    # Create a sample nib.Nifti1Image object
+    img_data = np.array([0, 1, 1, 50, 60, 60]).astype(float)
+    affine = np.eye(4)
+    img = nib.Nifti1Image(img_data, affine)
+
+    # Otsu is expected to separate foreground and background
+    expected_output = np.array([0, 0, 0, 1, 1, 1]).astype(float)
+
+    output_data = lower_threshold_otsu([img], img)
+
+    # compare output and expected arrays
+    assert_array_equal(output_data, expected_output)
+
+
+def test_upper_threshold_otsu():
+    # Create a sample nib.Nifti1Image object
+    img_data = np.array([0, 1, 1, 50, 60, 60]).astype(float)
+    affine = np.eye(4)
+    img = nib.Nifti1Image(img_data, affine)
+
+    # Otsu is expected to separate foreground and background
+    expected_output = np.array([1, 1, 1, 0, 0, 0]).astype(float)
+
+    output_data = upper_threshold_otsu([img], img)
+
+    # compare output and expected arrays
+    assert_array_equal(output_data, expected_output)
+
+
 def test_lower_clip():
     img_data = np.array([-1, 0, 1, 2, 3, 4]).astype(float)
     affine = np.eye(4)

scilpy/image/volume_math.py

@@ -17,6 +17,7 @@
 from scipy.ndimage import (binary_closing, binary_dilation,
                            binary_erosion, binary_opening,
                            gaussian_filter)
+from skimage.filters import threshold_otsu
 
 from scilpy.utils.util import is_float
 
@@ -31,6 +32,8 @@ def get_array_ops():
         ('upper_threshold', upper_threshold),
         ('lower_threshold_eq', lower_threshold_eq),
         ('upper_threshold_eq', upper_threshold_eq),
+        ('lower_threshold_otsu', lower_threshold_otsu),
+        ('upper_threshold_otsu', upper_threshold_otsu),
         ('lower_clip', lower_clip),
         ('upper_clip', upper_clip),
         ('absolute_value', absolute_value),
@@ -146,6 +149,45 @@ def cut_up_cube(data, blck):
     return data
 
 
+def lower_threshold_otsu(input_list, ref_img):
+    """
+    lower_threshold_otsu: IMG
+        All values below or equal to the Otsu threshold will be set to zero.
+        All values above the Otsu threshold will be set to one.
+    """
+    _validate_length(input_list, 1)
+    _validate_type(input_list[0], nib.Nifti1Image)
+
+    output_data = np.zeros(ref_img.header.get_data_shape(), dtype=np.float64)
+    data = input_list[0].get_fdata(dtype=np.float64)
+    threshold = threshold_otsu(data)
+
+    output_data[data <= threshold] = 0
+    output_data[data > threshold] = 1
+
+    return output_data
+
+
+def upper_threshold_otsu(input_list, ref_img):
+    """
+    upper_threshold_otsu: IMG
+        All values below the Otsu threshold will be set to one.
+        All values above or equal to the Otsu threshold will be set to zero.
+        Equivalent to lower_threshold_otsu followed by an inversion.
+    """
+    _validate_length(input_list, 1)
+    _validate_type(input_list[0], nib.Nifti1Image)
+
+    output_data = np.zeros(ref_img.header.get_data_shape(), dtype=np.float64)
+    data = input_list[0].get_fdata(dtype=np.float64)
+    threshold = threshold_otsu(data)
+
+    output_data[data < threshold] = 1
+    output_data[data >= threshold] = 0
+
+    return output_data
+
+
 def lower_threshold_eq(input_list, ref_img):
     """
     lower_threshold_eq: IMG THRESHOLD

scripts/scil_tractogram_assign_custom_color.py

@@ -200,7 +200,9 @@ def main():
                 data = np.clip(data, np.quantile(data, 0.05),
                                np.quantile(data, 0.95))
         elif args.use_dpp:
-            data = np.squeeze(sft.data_per_point[args.use_dpp]._data)
+            tmp = [np.squeeze(sft.data_per_point[args.use_dpp][s]) for s in
+                   range(len(sft))]
+            data = np.hstack(tmp)
         elif args.load_dps:
             data = np.squeeze(load_matrix_in_any_format(args.load_dps))
             if len(data) != len(sft):