Merge pull request #131 from DiamondLightSource/vomem

Vo Centering memory estimator fixes

Author: dkazanc

docs/source/examples/Cor_largesino.ipynb

@@ -80,7 +80,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "httomo",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -98,5 +98,5 @@
   }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }

docs/source/examples/DistortionCorr.ipynb

@@ -14,7 +14,7 @@
     "#### This example shows how to use methods from the HTTomolibgpu library to do the following:\n",
     "\n",
     "* normalise the data \n",
-    "* calculate the centre of rotation \n",
+    "* calculate the centre of rotation using phase-cross correlation method\n",
     "* reconstruct using the iterative algorithm"
    ]
   },
@@ -159,7 +159,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "httomo",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -177,5 +177,5 @@
   }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }

docs/source/examples/pipeline1_FBP.ipynb

@@ -18,7 +18,8 @@
 
     examples/pipeline1_FBP
     examples/pipeline2_iterative
-    examples/DistortionCorr
+    examples/Cor_largesino
+    examples/DistortionCorr    
 
 .. _reference_content:
 

docs/source/examples/pipeline2_iterative.ipynb

@@ -238,6 +238,7 @@ def __remove_all_stripe(
         sino = data[:, m, :]
         sino = _rs_dead(sino, snr, la_size, matindex)
         sino = _rs_sort2(sino, sm_size, matindex, dim)
+        sino = cp.nan_to_num(sino)
         data[:, m, :] = sino
     return data
 

docs/source/index.rst

@@ -246,7 +246,7 @@ def _calculate_chunks(
         shift_size  # it needs only half (RFFT), but complex64, so it's the same
     )
     fft_plan_size = freq_domain_size
-    size_per_shift = fft_plan_size + freq_domain_size + shift_size
+    size_per_shift = 2 * (fft_plan_size + freq_domain_size + shift_size)
     nshift_max = available_memory // size_per_shift
     assert nshift_max > 0, "Not enough memory to process"
     num_chunks = int(np.ceil(nshifts / nshift_max))

httomolibgpu/prep/stripe.py

@@ -65,6 +65,17 @@ def ensure_clean_memory():
     cp.get_default_pinned_memory_pool().free_all_blocks()
 
 
+@pytest.fixture(scope="session")
+def sino3600_file(test_data_path):
+    in_file = os.path.join(test_data_path, "3600proj_sino.npz")
+    return np.load(in_file)
+
+
+@pytest.fixture
+def sino3600(sino3600_file):
+    return cp.asarray(sino3600_file["sinogram"])
+
+
 @pytest.fixture
 def host_data(data_file):
     return np.copy(data_file["data"])