adding new zenodo tests and fixing the rest of tests

Author: dkazanc

httomolibgpu/recon/rotation.py

@@ -474,7 +474,7 @@ def find_center_360(
     (overlap, side, overlap_position) = _find_overlap(
         sino_top, sino_bot, win_width, side, denoise, norm, use_overlap
     )
-    cor = ncol - overlap / 2.0 - 1.0
+    cor = ncol - overlap / 2
 
     return cor, overlap, side, overlap_position
 

tests/test_recon/test_rotation.py

@@ -96,9 +96,9 @@ def test_find_center_360_data(data):
     eps = 1e-5
     (cor, overlap, side, overlap_pos) = find_center_360(data, norm=True, denoise=False)
 
-    assert_allclose(cor, 132.45317, rtol=eps)
+    assert_allclose(cor, 133.453167, rtol=eps)
     assert_allclose(overlap, 53.093666, rtol=eps)
-    assert side == 'right'
+    assert side == "right"
     assert_allclose(overlap_pos, 111.906334, rtol=eps)
 
 

zenodo-tests/conftest.py

@@ -105,6 +105,22 @@ def i12_dataset4(i12_dataset4_file):
     )
 
 
+@pytest.fixture(scope="session")
+def i12_dataset5_file(test_data_path):
+    in_file = os.path.join(test_data_path, "i12_dataset5.npz")
+    return np.load(in_file)
+
+
+@pytest.fixture
+def i12_dataset5(i12_dataset5_file):
+    return (
+        cp.asarray(i12_dataset5_file["projdata"]),
+        i12_dataset5_file["angles"],
+        cp.asarray(i12_dataset5_file["flats"]),
+        cp.asarray(i12_dataset5_file["darks"]),
+    )
+
+
 @pytest.fixture(scope="session")
 def i13_dataset1_file(test_data_path):
     in_file = os.path.join(test_data_path, "i13_dataset1.npz")

zenodo-tests/test_misc/test_morph.py

@@ -49,3 +49,24 @@ def test_sino_360_to_180_i13_dataset3(i13_dataset3):
     assert stiched_data_180degrees.shape == (3000, 3, 4682)
     assert stiched_data_180degrees.dtype == np.float32
     assert stiched_data_180degrees.flags.c_contiguous
+
+
+def test_sino_360_to_180_i12_dataset5(i12_dataset5):
+    projdata = i12_dataset5[0]
+    flats = i12_dataset5[2]
+    darks = i12_dataset5[3]
+    del i12_dataset5
+
+    data_normalised = normalize(projdata, flats, darks, minus_log=True)
+    del flats, darks, projdata
+    force_clean_gpu_memory()
+
+    stiched_data_180degrees = sino_360_to_180(
+        data_normalised, overlap=186.66, side="left"
+    )
+    stiched_data_180degrees = stiched_data_180degrees.get()
+
+    assert_allclose(np.sum(stiched_data_180degrees), 145920580.0, rtol=1e-07, atol=1e-6)
+    assert stiched_data_180degrees.shape == (1800, 15, 4933)
+    assert stiched_data_180degrees.dtype == np.float32
+    assert stiched_data_180degrees.flags.c_contiguous

zenodo-tests/test_recon/test_algorithm.py

@@ -277,6 +277,37 @@ def test_reconstruct_FBP3d_tomobar_i13_dataset3(i13_dataset3):
 
     assert recon_data.flags.c_contiguous
     recon_data = recon_data.get()
-        
+
     assert recon_data.dtype == np.float32
     assert recon_data.shape == (4682, 3, 4682)
+
+
+def test_reconstruct_FBP3d_tomobar_i12_dataset5(i12_dataset5):
+    force_clean_gpu_memory()
+    projdata = i12_dataset5[0]
+    angles = i12_dataset5[1]
+    flats = i12_dataset5[2]
+    darks = i12_dataset5[3]
+    del i12_dataset5
+
+    data_normalised = normalize(projdata, flats, darks, minus_log=True)
+    del flats, darks, projdata
+    force_clean_gpu_memory()
+
+    stiched_data_180degrees = sino_360_to_180(
+        data_normalised, overlap=186.66, side="left"
+    )
+    force_clean_gpu_memory()
+
+    recon_data = FBP3d_tomobar(
+        stiched_data_180degrees,
+        np.deg2rad(angles[0:1800]),
+        center=2466,
+        filter_freq_cutoff=0.35,
+    )
+
+    assert recon_data.flags.c_contiguous
+    recon_data = recon_data.get()
+
+    assert recon_data.dtype == np.float32
+    assert recon_data.shape == (4933, 15, 4933)

zenodo-tests/test_recon/test_rotation.py

@@ -124,27 +124,6 @@ def test_center_pc_i12_dataset3(i12_dataset3, ensure_clean_memory):
     assert cor_pc.dtype == np.float32
 
 
-# ----------------------------------------------------------#
-# i13_dataset1 tests
-# 360 degrees dataset
-def test_center_360_i13_dataset1(i13_dataset1, ensure_clean_memory):
-    projdata = i13_dataset1[0]
-    flats = i13_dataset1[2]
-    darks = i13_dataset1[3]
-    del i13_dataset1
-
-    data_normalised = normalize(projdata, flats, darks, minus_log=False)
-    del flats, darks, projdata
-
-    ensure_clean_memory
-    cor, overlap, side, overlap_position = find_center_360(data_normalised)
-
-    assert int(cor) == 2322
-    assert side == "right"
-    assert int(overlap) == 473  # actual 473.822265625
-    assert cor.dtype == np.float64
-
-
 # ----------------------------------------------------------#
 # i13_dataset2 tests
 # 180 degrees dataset (2500 projections)
@@ -167,35 +146,6 @@ def test_center_vo_i13_dataset2(i13_dataset2, ensure_clean_memory):
     assert cor.dtype == np.float32
 
 
-# ----------------------------------------------------------#
-# i13_dataset3 tests
-# 360 degrees dataset
-def test_center_360_i13_dataset3(i13_dataset3, ensure_clean_memory):
-    projdata = i13_dataset3[0]
-    flats = i13_dataset3[2]
-    darks = i13_dataset3[3]
-    del i13_dataset3
-
-    data_normalised = normalize(projdata, flats, darks, minus_log=False)
-    del flats, darks, projdata
-
-    ensure_clean_memory
-    cor, overlap, side, overlap_position = find_center_360(
-        data_normalised,
-        ind=1,
-        win_width=50,
-        side=None,
-        denoise=True,
-        norm=True,
-        use_overlap=True,
-    )
-
-    assert int(cor) == 218  # actual 218.08 (not correct CoR actually, should be 2341)
-    assert side == "left"
-    assert int(overlap) == 438  # actual 438.173828
-    assert cor.dtype == np.float64
-
-
 # ----------------------------------------------------------#
 # geant4_dataset1 tests
 def test_center_vo_geant4_dataset1(geant4_dataset1, ensure_clean_memory):
@@ -234,3 +184,74 @@ def test_center_vo_k11_dataset1(k11_dataset1, ensure_clean_memory):
 
     assert cor == 1269.25
     assert cor.dtype == np.float32
+
+
+# ----------------------------------------------------------#
+# i12_dataset5 tests
+# 360 degrees dataset
+def test_center_360_i12_dataset5(i12_dataset5, ensure_clean_memory):
+    projdata = i12_dataset5[0]
+    flats = i12_dataset5[2]
+    darks = i12_dataset5[3]
+    del i12_dataset5
+
+    data_normalised = normalize(projdata, flats, darks, minus_log=True)
+    del flats, darks, projdata
+
+    ensure_clean_memory
+    cor, overlap, side, overlap_position = find_center_360(data_normalised)
+
+    assert int(cor) == 2466
+    assert side == "left"
+    assert int(overlap) == 186
+    assert cor.dtype == np.float64
+
+
+# ----------------------------------------------------------#
+# i13_dataset1 tests
+# 360 degrees dataset
+def test_center_360_i13_dataset1(i13_dataset1, ensure_clean_memory):
+    projdata = i13_dataset1[0]
+    flats = i13_dataset1[2]
+    darks = i13_dataset1[3]
+    del i13_dataset1
+
+    data_normalised = normalize(projdata, flats, darks, minus_log=True)
+    del flats, darks, projdata
+
+    ensure_clean_memory
+    cor, overlap, side, overlap_position = find_center_360(data_normalised)
+
+    assert int(cor) == 2323
+    assert side == "right"
+    assert int(overlap) == 473  # actual 473.822265625
+    assert cor.dtype == np.float64
+
+
+# ----------------------------------------------------------#
+# i13_dataset3 tests
+# 360 degrees dataset
+def test_center_360_i13_dataset3(i13_dataset3, ensure_clean_memory):
+    projdata = i13_dataset3[0]
+    flats = i13_dataset3[2]
+    darks = i13_dataset3[3]
+    del i13_dataset3
+
+    data_normalised = normalize(projdata, flats, darks, minus_log=True)
+    del flats, darks, projdata
+
+    ensure_clean_memory
+    cor, overlap, side, overlap_position = find_center_360(
+        data_normalised,
+        ind=1,
+        win_width=50,
+        side=None,
+        denoise=True,
+        norm=True,
+        use_overlap=True,
+    )
+
+    assert int(cor) == 2340
+    assert side == "left"
+    assert int(overlap) == 438  # actual 438.173828
+    assert cor.dtype == np.float64