Add tests from httomolib-data

Author: namannimmo10

.github/workflows/httomolibgpu_tests_run_iris.yml

@@ -45,6 +45,10 @@ jobs:
           pip install .[dev]
           micromamba list
 
-      - name: Run tests
+      - name: Run unit tests on small data
         run: |
           pytest tests/
+
+      - name: Run Zenodo tests
+        run: |
+          pytest zenodo-tests/

zenodo-tests/conftest.py

@@ -0,0 +1,67 @@
+import os
+import cupy as cp
+import numpy as np
+import pytest
+
+CUR_DIR = os.path.abspath(os.path.dirname(__file__))
+
+
+@pytest.fixture(scope="session")
+def test_data_path():
+    return os.path.join(CUR_DIR, "large_data_archive")
+
+
+@pytest.fixture(scope="session")
+def data_i12LFOV_file(test_data_path):
+    in_file = os.path.join(test_data_path, "i12LFOV.npz")
+    return np.load(in_file)
+
+
+@pytest.fixture(scope="session")
+def data_i12_sandstone_file(test_data_path):
+    in_file = os.path.join(test_data_path, "i12_sandstone_50sinoslices.npz")
+    return np.load(in_file)
+
+
+@pytest.fixture(scope="session")
+def data_geant4sim_file(test_data_path):
+    in_file = os.path.join(test_data_path, "geant4_640_540_proj360.npz")
+    return np.load(in_file)
+
+@pytest.fixture
+def i12LFOV_data(data_i12LFOV_file):
+    return (
+        cp.asarray(data_i12LFOV_file["projdata"]),
+        data_i12LFOV_file["angles"],
+        cp.asarray(data_i12LFOV_file["flats"]),
+        cp.asarray(data_i12LFOV_file["darks"]),
+    )
+
+
+@pytest.fixture
+def i12sandstone_data(data_i12_sandstone_file):
+    return (
+        cp.asarray(data_i12_sandstone_file["projdata"]),
+        data_i12_sandstone_file["angles"],
+        cp.asarray(data_i12_sandstone_file["flats"]),
+        cp.asarray(data_i12_sandstone_file["darks"]),
+    )
+
+
+@pytest.fixture
+def geantsim_data(data_geant4sim_file):
+    return (
+        cp.asarray(data_geant4sim_file["projdata"]),
+        data_geant4sim_file["angles"],
+        cp.asarray(data_geant4sim_file["flats"]),
+        cp.asarray(data_geant4sim_file["darks"]),
+    )
+
+
+@pytest.fixture
+def ensure_clean_memory():
+    cp.get_default_memory_pool().free_all_blocks()
+    cp.get_default_pinned_memory_pool().free_all_blocks()
+    yield None
+    cp.get_default_memory_pool().free_all_blocks()
+    cp.get_default_pinned_memory_pool().free_all_blocks()

zenodo-tests/test_recon/__init__.py

@@ -0,0 +1,69 @@
+import cupy as cp
+import numpy as np
+import pytest
+
+from httomolibgpu.prep.normalize import normalize
+from httomolibgpu.recon.rotation import find_center_vo
+
+
+def test_center_vo_i12LFOV(i12LFOV_data, ensure_clean_memory):
+    projdata = i12LFOV_data[0]
+    flats = i12LFOV_data[2]
+    darks = i12LFOV_data[3]
+    del i12LFOV_data
+
+    data_normalised = normalize(projdata, flats, darks, minus_log=False)
+    del flats, darks, projdata
+
+    mid_slice = data_normalised.shape[1] // 2
+    cor = find_center_vo(data_normalised[:, mid_slice, :])
+
+    assert cor == 1197.75
+    assert cor.dtype == np.float32
+
+
+def test_center_vo_average_i12LFOV(i12LFOV_data, ensure_clean_memory):
+    projdata = i12LFOV_data[0]
+    flats = i12LFOV_data[2]
+    darks = i12LFOV_data[3]
+    del i12LFOV_data
+
+    data_normalised = normalize(projdata, flats, darks, minus_log=False)
+    del flats, darks, projdata
+
+    cor = find_center_vo(data_normalised[:, 10:25, :], average_radius=5)
+
+    assert cor == 1199.25
+    assert cor.dtype == np.float32
+
+
+def test_center_vo_i12_sandstone(i12sandstone_data, ensure_clean_memory):
+    projdata = i12sandstone_data[0]
+    flats = i12sandstone_data[2]
+    darks = i12sandstone_data[3]
+    del i12sandstone_data
+
+    data_normalised = normalize(projdata, flats, darks, minus_log=True)
+    del flats, darks, projdata
+
+    mid_slice = data_normalised.shape[1] // 2
+    cor = find_center_vo(data_normalised[:, mid_slice, :])
+
+    assert cor == 1253.75
+    assert cor.dtype == np.float32
+
+
+def test_center_vo_i12_geantsim(geantsim_data, ensure_clean_memory):
+    projdata = geantsim_data[0]
+    flats = geantsim_data[2]
+    darks = geantsim_data[3]
+    del geantsim_data
+
+    data_normalised = normalize(projdata, flats, darks, minus_log=True)
+    del flats, darks, projdata
+
+    mid_slice = data_normalised.shape[1] // 2
+    cor = find_center_vo(data_normalised[:, mid_slice, :])
+
+    assert cor == 319.5
+    assert cor.dtype == np.float32