Test refactor (#83)

* move tests on operators in folder.

* ci: split the test with the operators folder.

* test pynfft on local runner.

* local runner setup pynfft2

* use venv

* fix: skip 3D tests for slow transforms.

* fix import

* ci: remove pynfft from gpu

2D is done on CPU and is good enough.

.github/workflows/test-ci.yml

@@ -81,7 +81,7 @@ jobs:
         shell: bash
         run: |
           export COVERAGE_FILE=coverage_${{ matrix.backend }}
-          pytest --backend ${{ matrix.backend }} --ref ${{ env.ref_backend }} --cov --disable-pytest-warnings --cov-branch --cov-report=term
+          pytest -k='operators' --backend ${{ matrix.backend }} --ref ${{ env.ref_backend }} --cov --disable-pytest-warnings --cov-branch --cov-report=term
       - name: Upload coverage
         uses: actions/upload-artifact@v3
         with:
@@ -111,7 +111,9 @@ jobs:
           pip install torch --index-url https://download.pytorch.org/whl/cu118
           pip install finufft
 
+
       - name: Install backend
+        if: ${{ matrix.backend == 'gpunufft' || matrix.backend == 'cufinufft' }}
         shell: bash
         run: |
           source $RUNNER_WORKSPACE/venv/bin/activate
@@ -120,13 +122,20 @@ jobs:
           export LD_LIBRARY_PATH=/usr/local/cuda-11.8/lib/{LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}
           pip install ${{ matrix.backend }}
 
+      - name: Install pynfft
+        if: ${{ matrix.backend == 'pynfft' }}
+        shell: bash
+        run: |
+          source $RUNNER_WORKSPACE/venv/bin/activate
+          pip install pynfft2
+
       - name: Run Tests
         shell: bash
         run: |
           cd $RUNNER_WORKSPACE/mri-nufft
           source $RUNNER_WORKSPACE/venv/bin/activate
           export COVERAGE_FILE=coverage_${{ matrix.backend }}
-          python -m pytest --ref ${{ env.ref_backend }} --backend ${{ matrix.backend }} --disable-pytest-warnings --cov --cov-branch --cov-report=term
+          python -m pytest -k='operators' --ref ${{ env.ref_backend }} --backend ${{ matrix.backend }} --disable-pytest-warnings --cov --cov-branch --cov-report=term
 
       - name: Upload coverage
         if: success()
@@ -168,7 +177,7 @@ jobs:
         shell: bash
         run: |
           export COVERAGE_FILE=coverage_plots
-          pytest examples --cov --cov-branch --cov-report=term
+          pytest examples tests -k="not operators" --cov --cov-branch --cov-report=term
 
       - name: Upload coverage
         if: success()

tests/operators/test_gpunufft.py

@@ -0,0 +1,40 @@
+"""Specific test for gpunufft."""
+
+import numpy as np
+import numpy.testing as npt
+from pytest_cases import parametrize, parametrize_with_cases
+
+from case_trajectories import CasesTrajectories
+from helpers import assert_correlate
+from mrinufft.density import cell_count, voronoi, pipe
+from mrinufft.density.utils import normalize_weights
+from mrinufft._utils import proper_trajectory
+
+
+def radial_distance(traj, shape):
+    """Compute the radial distance of a trajectory."""
+    proper_traj = proper_trajectory(traj, normalize="unit")
+    weights = np.linalg.norm(proper_traj, axis=-1)
+    return weights
+
+
+@parametrize("osf", [1, 1.25, 2])
+@parametrize_with_cases(
+    "traj, shape",
+    cases=[
+        CasesTrajectories.case_nyquist_radial2D,
+        CasesTrajectories.case_nyquist_radial3D,
+    ],
+)
+@parametrize(backend=["gpunufft"])
+def test_pipe(backend, traj, shape, osf):
+    """Test the pipe method."""
+    distance = radial_distance(traj, shape)
+    result = pipe(traj, shape, osf=osf, num_iterations=10)
+    result = result / np.mean(result)
+    distance = distance / np.mean(distance)
+    if osf != 2:
+        # If OSF < 2, we dont perfectly estimate
+        assert_correlate(result, distance, slope=1, slope_err=None, r_value_err=0.2)
+    else:
+        assert_correlate(result, distance, slope=1, slope_err=0.1, r_value_err=0.1)

tests/test_interfaces.py → tests/operators/test_interfaces.py

@@ -1,6 +1,7 @@
 """Test the interfaces module."""
 
 import numpy as np
+import pytest
 from pytest_cases import parametrize_with_cases, parametrize, fixture
 from mrinufft import get_operator
 from case_trajectories import CasesTrajectories
@@ -43,6 +44,8 @@ def operator(
     n_coils=1,
 ):
     """Generate an operator."""
+    if backend in ["pynfft", "sigpy"] and kspace_locs.shape[-1] == 3:
+        pytest.skip("3D for slow cpu is not tested")
     return get_operator(backend)(kspace_locs, shape, n_coils=n_coils, smaps=None)
 
 

tests/test_density.py

@@ -61,25 +61,3 @@ def test_voronoi(traj, shape):
     result = result / np.mean(result)
     distance = distance / np.mean(distance)
     assert_correlate(result, distance, slope=1)
-
-
-@parametrize("osf", [1, 1.25, 2])
-@parametrize_with_cases(
-    "traj, shape",
-    cases=[
-        CasesTrajectories.case_nyquist_radial2D,
-        CasesTrajectories.case_nyquist_radial3D,
-    ],
-)
-@parametrize(backend=["gpunufft"])
-def test_pipe(backend, traj, shape, osf):
-    """Test the pipe method."""
-    distance = radial_distance(traj, shape)
-    result = pipe(traj, shape, osf=osf, num_iterations=10)
-    result = result / np.mean(result)
-    distance = distance / np.mean(distance)
-    if osf != 2:
-        # If OSF < 2, we dont perfectly estimate
-        assert_correlate(result, distance, slope=1, slope_err=None, r_value_err=0.2)
-    else:
-        assert_correlate(result, distance, slope=1, slope_err=0.1, r_value_err=0.1)