finishing zenodo tests

Author: dkazanc

httomolibgpu/recon/algorithm.py

@@ -180,7 +180,8 @@ def FBP3d_tomobar(
         data, angles, center, detector_pad, recon_size, gpu_id
     )
 
-    reconstruction = RecToolsCP.FBP(data,
+    reconstruction = RecToolsCP.FBP(
+        data,
         cutoff_freq=filter_freq_cutoff,
         recon_mask_radius=recon_mask_radius,
         data_axes_labels_order=input_data_axis_labels,
@@ -242,7 +243,8 @@ def LPRec3d_tomobar(
         data, angles, center, detector_pad, recon_size, 0
     )
 
-    reconstruction = RecToolsCP.FOURIER_INV(data,
+    reconstruction = RecToolsCP.FOURIER_INV(
+        data,
         recon_mask_radius=recon_mask_radius,
         data_axes_labels_order=input_data_axis_labels,
         filter_type=filter_type,
@@ -620,6 +622,7 @@ def _instantiate_iterative_recon_class(
     )
     return RecToolsCP
 
+
 def __estimate_detectorHoriz_padding(detX_size) -> int:
     det_half = detX_size // 2
     padded_value_exact = int(np.sqrt(2 * (det_half**2))) - det_half

tests/test_prep/test_stripe.py

@@ -65,7 +65,7 @@ def test_stripe_raven_cupy(data, flats, darks):
     data_norm = minus_log(data_norm)
 
     data_after_raven_gpu = cp.asnumpy(raven_filter(data_norm))
-    
+
     data = None  #: free up GPU memory
     assert_allclose(np.mean(data_after_raven_gpu), 0.2892464, rtol=1e-06)
 
@@ -154,7 +154,6 @@ def test_remove_all_stripe_on_data(data, flats, darks):
     data_norm = dark_flat_field_correction(cp.copy(data), flats, darks, cutoff=10)
     data_norm = minus_log(data_norm)
 
-
     data_after_stripe_removal = cp.asnumpy(remove_all_stripe(data_norm))
 
     assert_allclose(np.mean(data_after_stripe_removal), 0.266914, rtol=1e-05)

tests/test_recon/test_algorithm.py

@@ -65,7 +65,8 @@ def test_reconstruct_FBP3d_tomobar_1(data, flats, darks, ensure_clean_memory):
     normalised_data = dark_flat_field_correction(data, flats, darks, cutoff=10)
     normalised_data = minus_log(normalised_data)
 
-    recon_data = FBP3d_tomobar(normalised_data,
+    recon_data = FBP3d_tomobar(
+        normalised_data,
         np.linspace(0.0 * np.pi / 180.0, 180.0 * np.pi / 180.0, data.shape[0]),
         79.5,
         filter_freq_cutoff=1.1,
@@ -80,11 +81,13 @@ def test_reconstruct_FBP3d_tomobar_1(data, flats, darks, ensure_clean_memory):
     assert recon_data.dtype == np.float32
     assert recon_data.shape == (160, 128, 160)
 
+
 def test_reconstruct_FBP3d_tomobar_2(data, flats, darks, ensure_clean_memory):
     normalised_data = dark_flat_field_correction(data, flats, darks, cutoff=10)
     normalised_data = minus_log(normalised_data)
 
-    recon_data = FBP3d_tomobar(normalised_data,
+    recon_data = FBP3d_tomobar(
+        normalised_data,
         np.linspace(5.0 * np.pi / 360.0, 180.0 * np.pi / 360.0, data.shape[0]),
         15.5,
         filter_freq_cutoff=1.1,
@@ -100,11 +103,14 @@ def test_reconstruct_FBP3d_tomobar_2(data, flats, darks, ensure_clean_memory):
     assert recon_data.dtype == np.float32
 
 
-def test_reconstruct_FBP3d_tomobar_3_detpad_true(data, flats, darks, ensure_clean_memory):
+def test_reconstruct_FBP3d_tomobar_3_detpad_true(
+    data, flats, darks, ensure_clean_memory
+):
     normalised_data = dark_flat_field_correction(data, flats, darks, cutoff=10)
     normalised_data = minus_log(normalised_data)
 
-    recon_data = FBP3d_tomobar(normalised_data,
+    recon_data = FBP3d_tomobar(
+        normalised_data,
         np.linspace(5.0 * np.pi / 360.0, 180.0 * np.pi / 360.0, data.shape[0]),
         79,  # center
         True,  # detector pad
@@ -126,7 +132,8 @@ def test_reconstruct_LPRec3d_tomobar_1(data, flats, darks, ensure_clean_memory):
     normalised_data = dark_flat_field_correction(data, flats, darks, cutoff=10)
     normalised_data = minus_log(normalised_data)
 
-    recon_data = LPRec3d_tomobar(normalised_data,
+    recon_data = LPRec3d_tomobar(
+        normalised_data,
         angles=np.linspace(0.0 * np.pi / 180.0, 180.0 * np.pi / 180.0, data.shape[0]),
         center=79.5,
         detector_pad=0,
@@ -144,7 +151,8 @@ def test_reconstruct_LPRec3d_tomobar_1_pad(data, flats, darks, ensure_clean_memo
     normalised_data = dark_flat_field_correction(data, flats, darks, cutoff=10)
     normalised_data = minus_log(normalised_data)
 
-    recon_data = LPRec3d_tomobar(normalised_data,
+    recon_data = LPRec3d_tomobar(
+        normalised_data,
         angles=np.linspace(0.0 * np.pi / 180.0, 180.0 * np.pi / 180.0, data.shape[0]),
         center=79.5,
         detector_pad=10,
@@ -163,7 +171,8 @@ def test_reconstruct_SIRT3d_tomobar(data, flats, darks, ensure_clean_memory):
     normalised_data = dark_flat_field_correction(data, flats, darks, cutoff=10)
     normalised_data = minus_log(normalised_data)
 
-    recon_data = SIRT3d_tomobar(normalised_data,
+    recon_data = SIRT3d_tomobar(
+        normalised_data,
         np.linspace(0.0 * np.pi / 180.0, 180.0 * np.pi / 180.0, data.shape[0]),
         79.5,
         recon_size=objrecon_size,
@@ -182,7 +191,8 @@ def test_reconstruct_CGLS3d_tomobar(data, flats, darks, ensure_clean_memory):
     normalised_data = dark_flat_field_correction(data, flats, darks, cutoff=10)
     normalised_data = minus_log(normalised_data)
 
-    recon_data = CGLS3d_tomobar(normalised_data,
+    recon_data = CGLS3d_tomobar(
+        normalised_data,
         np.linspace(0.0 * np.pi / 180.0, 180.0 * np.pi / 180.0, data.shape[0]),
         center=79.5,
         recon_size=objrecon_size,
@@ -203,7 +213,8 @@ def test_reconstruct_CGLS3d_tomobar_detpad_true(
     normalised_data = dark_flat_field_correction(data, flats, darks, cutoff=10)
     normalised_data = minus_log(normalised_data)
 
-    recon_data = CGLS3d_tomobar(normalised_data,
+    recon_data = CGLS3d_tomobar(
+        normalised_data,
         np.linspace(0.0 * np.pi / 180.0, 180.0 * np.pi / 180.0, data.shape[0]),
         center=79.5,
         detector_pad=True,
@@ -218,12 +229,13 @@ def test_reconstruct_CGLS3d_tomobar_detpad_true(
     assert recon_data.dtype == np.float32
 
 
-def test_reconstruct_FISTA3d_tomobar_pd_tv(data, flats, darks, ensure_clean_memory):    
+def test_reconstruct_FISTA3d_tomobar_pd_tv(data, flats, darks, ensure_clean_memory):
     objrecon_size = data.shape[2]
     normalised_data = dark_flat_field_correction(data, flats, darks, cutoff=10)
     normalised_data = minus_log(normalised_data)
 
-    recon_data = FISTA3d_tomobar(normalised_data,
+    recon_data = FISTA3d_tomobar(
+        normalised_data,
         np.linspace(0.0 * np.pi / 180.0, 180.0 * np.pi / 180.0, data.shape[0]),
         center=79.5,
         detector_pad=0,
@@ -250,7 +262,8 @@ def test_reconstruct_FISTA3d_tomobar_pd_tv_detpad_true(
     normalised_data = dark_flat_field_correction(data, flats, darks, cutoff=10)
     normalised_data = minus_log(normalised_data)
 
-    recon_data = FISTA3d_tomobar(normalised_data,
+    recon_data = FISTA3d_tomobar(
+        normalised_data,
         np.linspace(0.0 * np.pi / 180.0, 180.0 * np.pi / 180.0, data.shape[0]),
         center=79.5,
         detector_pad=True,
@@ -276,7 +289,8 @@ def test_reconstruct_FISTA3d_tomobar_rof_tv(data, flats, darks, ensure_clean_mem
     normalised_data = dark_flat_field_correction(data, flats, darks, cutoff=10)
     normalised_data = minus_log(normalised_data)
 
-    recon_data = FISTA3d_tomobar(normalised_data,
+    recon_data = FISTA3d_tomobar(
+        normalised_data,
         np.linspace(0.0 * np.pi / 180.0, 180.0 * np.pi / 180.0, data.shape[0]),
         79.5,
         recon_size=objrecon_size,

tests/test_recon/test_rotation.py

@@ -145,7 +145,7 @@ def test_find_center_360_performance(ensure_clean_memory):
     assert "performance in ms" == duration_ms
 
 
-def test_find_center_pc(data, flats, darks, ensure_clean_memory):    
+def test_find_center_pc(data, flats, darks, ensure_clean_memory):
     data_normalize = dark_flat_field_correction(cp.copy(data), flats, darks)
     proj1 = data_normalize[0, :, :]
     proj2 = data_normalize[179, :, :]

zenodo-tests/test_misc/test_morph.py

@@ -9,8 +9,8 @@ def test_sino_360_to_180_i13_dataset1(i13_dataset1):
     projdata = i13_dataset1[0]
     flats = i13_dataset1[2]
     darks = i13_dataset1[3]
-    del i13_dataset1    
-    
+    del i13_dataset1
+
     data_normalised = dark_flat_field_correction(projdata, flats, darks, cutoff=10)
 
     del flats, darks, projdata
@@ -63,4 +63,4 @@ def test_sino_360_to_180_i12_dataset5(i12_dataset5):
 
     assert stiched_data_180degrees.shape == (1800, 15, 4933)
     assert stiched_data_180degrees.dtype == np.float32
-    assert stiched_data_180degrees.flags.c_contiguous
+    assert stiched_data_180degrees.flags.c_contiguous

zenodo-tests/test_prep/test_phase.py

@@ -5,6 +5,7 @@
 from httomolibgpu.prep.phase import paganin_filter
 from conftest import force_clean_gpu_memory
 
+
 # ----------------------------------------------------------#
 # appplying paganin filter to i12_dataset3
 def test_paganin_filter_i12_dataset3(i12_dataset3, ensure_clean_memory):

zenodo-tests/test_prep/test_stripe.py

@@ -39,7 +39,9 @@ def test_remove_stripe_based_sorting_i12_dataset4(
     request, dataset_fixture, size_filt, norm_res_expected
 ):
     dataset = request.getfixturevalue(dataset_fixture)
-    data_normalised = dark_flat_field_correction(dataset[0], dataset[2], dataset[3], cutoff=10)
+    data_normalised = dark_flat_field_correction(
+        dataset[0], dataset[2], dataset[3], cutoff=10
+    )
     data_normalised = minus_log(data_normalised)
 
     del dataset
@@ -83,7 +85,9 @@ def test_remove_stripe_ti_i12_dataset4(
     request, dataset_fixture, beta_val, norm_res_expected
 ):
     dataset = request.getfixturevalue(dataset_fixture)
-    data_normalised = dark_flat_field_correction(dataset[0], dataset[2], dataset[3], cutoff=10)
+    data_normalised = dark_flat_field_correction(
+        dataset[0], dataset[2], dataset[3], cutoff=10
+    )
     data_normalised = minus_log(data_normalised)
 
     del dataset
@@ -114,7 +118,9 @@ def test_remove_all_stripe_i12_dataset4(
     request, dataset_fixture, snr_val, la_size_val, sm_size_val, norm_res_expected
 ):
     dataset = request.getfixturevalue(dataset_fixture)
-    data_normalised = dark_flat_field_correction(dataset[0], dataset[2], dataset[3], cutoff=10)
+    data_normalised = dark_flat_field_correction(
+        dataset[0], dataset[2], dataset[3], cutoff=10
+    )
     data_normalised = minus_log(data_normalised)
 
     del dataset
@@ -154,10 +160,10 @@ def test_raven_filter_i12_dataset4(
         dataset[0][:, 10:20, :],
         dataset[2][:, 10:20, :],
         dataset[3][:, 10:20, :],
-        cutoff=10)
+        cutoff=10,
+    )
     data_normalised = minus_log(data_normalised)
 
-
     del dataset
     force_clean_gpu_memory()
 

zenodo-tests/test_recon/test_algorithm.py

@@ -32,7 +32,7 @@ def test_reconstruct_FBP2d_astra_i12_dataset1(i12_dataset1: tuple):
 
     data_normalised = dark_flat_field_correction(projdata, flats, darks, cutoff=10)
     data_normalised = minus_log(data_normalised)
-    
+
     del flats, darks, projdata
     force_clean_gpu_memory()
 
@@ -294,7 +294,7 @@ def test_reconstruct_LPRec3d_tomobar_i13_dataset2(i13_dataset2: tuple):
 
     data_normalised = dark_flat_field_correction(projdata, flats, darks, cutoff=10)
     data_normalised = minus_log(data_normalised)
-    
+
     del flats, darks, projdata
     force_clean_gpu_memory()
 
@@ -403,7 +403,7 @@ def test_reconstruct_FBP3d_tomobar_i12_dataset5(i12_dataset5: tuple):
 
     data_normalised = dark_flat_field_correction(projdata, flats, darks, cutoff=10)
     data_normalised = minus_log(data_normalised)
-    
+
     del flats, darks, projdata
     force_clean_gpu_memory()
 

zenodo-tests/test_recon/test_rotation.py

@@ -9,6 +9,7 @@
 from httomolibgpu.recon.rotation import find_center_vo, find_center_pc, find_center_360
 from conftest import force_clean_gpu_memory
 
+
 # ----------------------------------------------------------#
 # i12_dataset1 tests
 def test_center_vo_i12_dataset1(i12_dataset1):
@@ -113,7 +114,7 @@ def test_center_pc_i12_dataset3(i12_dataset3, ensure_clean_memory):
     projdata = cp.empty((2, np.shape(proj1)[0], np.shape(proj1)[1]))
     projdata[0, :, :] = proj1
     projdata[1, :, :] = proj2
-    
+
     data_normalised = dark_flat_field_correction(projdata, flats, darks, cutoff=10)
     data_normalised = minus_log(data_normalised)
 
@@ -136,7 +137,7 @@ def test_center_vo_i13_dataset2(i13_dataset2, ensure_clean_memory):
     flats = i13_dataset2[2]
     darks = i13_dataset2[3]
     del i13_dataset2
-    
+
     data_normalised = dark_flat_field_correction(projdata, flats, darks, cutoff=10)
 
     del flats, darks, projdata