Merge pull request #57 from DiamondLightSource/pipeupdates

dkazanc · web-flow · commit 6ea8f1e8c575 · 2025-05-12T11:39:46.000+01:00
reconstruction methods names updates
diff --git a/httomo_backends/methods_database/packages/backends/httomolibgpu/httomolibgpu.yaml b/httomo_backends/methods_database/packages/backends/httomolibgpu/httomolibgpu.yaml
@@ -145,7 +145,7 @@ prep:
         method: module
 recon:
   algorithm:
-    FBP:
+    FBP3d_tomobar:
       pattern: sinogram
       output_dims_change: True
       implementation: gpu_cupy
@@ -154,7 +154,7 @@ recon:
       memory_gpu:
         multiplier: None
         method: module
-    SIRT:
+    SIRT3d_tomobar:
       pattern: sinogram
       output_dims_change: True
       implementation: gpu_cupy
@@ -163,7 +163,7 @@ recon:
       memory_gpu:
         multiplier: None
         method: module
-    CGLS:
+    CGLS3d_tomobar:
       pattern: sinogram
       output_dims_change: True
       implementation: gpu_cupy
diff --git a/httomo_backends/methods_database/packages/backends/httomolibgpu/supporting_funcs/recon/algorithm.py b/httomo_backends/methods_database/packages/backends/httomolibgpu/supporting_funcs/recon/algorithm.py
@@ -26,12 +26,12 @@
 from httomo_backends.cufft import CufftType, cufft_estimate_1d
 
 __all__ = [
-    "_calc_memory_bytes_FBP",
-    "_calc_memory_bytes_SIRT",
-    "_calc_memory_bytes_CGLS",
-    "_calc_output_dim_FBP",
-    "_calc_output_dim_SIRT",
-    "_calc_output_dim_CGLS",
+    "_calc_memory_bytes_FBP3d_tomobar",
+    "_calc_memory_bytes_SIRT3d_tomobar",
+    "_calc_memory_bytes_CGLS3d_tomobar",
+    "_calc_output_dim_FBP3d_tomobar",
+    "_calc_output_dim_SIRT3d_tomobar",
+    "_calc_output_dim_CGLS3d_tomobar",
 ]
 
 
@@ -49,19 +49,19 @@ def __calc_output_dim_recon(non_slice_dims_shape, **kwargs):
     return output_dims
 
 
-def _calc_output_dim_FBP(non_slice_dims_shape, **kwargs):
+def _calc_output_dim_FBP3d_tomobar(non_slice_dims_shape, **kwargs):
     return __calc_output_dim_recon(non_slice_dims_shape, **kwargs)
 
 
-def _calc_output_dim_SIRT(non_slice_dims_shape, **kwargs):
+def _calc_output_dim_SIRT3d_tomobar(non_slice_dims_shape, **kwargs):
     return __calc_output_dim_recon(non_slice_dims_shape, **kwargs)
 
 
-def _calc_output_dim_CGLS(non_slice_dims_shape, **kwargs):
+def _calc_output_dim_CGLS3d_tomobar(non_slice_dims_shape, **kwargs):
     return __calc_output_dim_recon(non_slice_dims_shape, **kwargs)
 
 
-def _calc_memory_bytes_FBP(
+def _calc_memory_bytes_FBP3d_tomobar(
     non_slice_dims_shape: Tuple[int, int],
     dtype: np.dtype,
     **kwargs,
@@ -118,7 +118,7 @@ def _calc_memory_bytes_FBP(
 
     # 7. astra backprojection will generate an output array
     # https://github.com/dkazanc/ToMoBAR/blob/54137829b6326406e09f6ef9c95eb35c213838a7/tomobar/astra_wrappers/astra_base.py#L524
-    output_dims = _calc_output_dim_FBP(non_slice_dims_shape, **kwargs)
+    output_dims = _calc_output_dim_FBP3d_tomobar(non_slice_dims_shape, **kwargs)
     recon_output_size = np.prod(output_dims) * np.float32().itemsize
 
     # 7. astra backprojection makes a copy of the input
@@ -148,14 +148,14 @@ def _calc_memory_bytes_FBP(
     return (tot_memory_bytes, fixed_amount)
 
 
-def _calc_memory_bytes_SIRT(
+def _calc_memory_bytes_SIRT3d_tomobar(
     non_slice_dims_shape: Tuple[int, int],
     dtype: np.dtype,
     **kwargs,
 ) -> Tuple[int, int]:
     DetectorsLengthH = non_slice_dims_shape[1]
     # calculate the output shape
-    output_dims = _calc_output_dim_SIRT(non_slice_dims_shape, **kwargs)
+    output_dims = _calc_output_dim_SIRT3d_tomobar(non_slice_dims_shape, **kwargs)
 
     in_data_size = np.prod(non_slice_dims_shape) * dtype.itemsize
     out_data_size = np.prod(output_dims) * dtype.itemsize
@@ -166,14 +166,14 @@ def _calc_memory_bytes_SIRT(
     return (tot_memory_bytes, 0)
 
 
-def _calc_memory_bytes_CGLS(
+def _calc_memory_bytes_CGLS3d_tomobar(
     non_slice_dims_shape: Tuple[int, int],
     dtype: np.dtype,
     **kwargs,
 ) -> Tuple[int, int]:
     DetectorsLengthH = non_slice_dims_shape[1]
     # calculate the output shape
-    output_dims = _calc_output_dim_CGLS(non_slice_dims_shape, **kwargs)
+    output_dims = _calc_output_dim_CGLS3d_tomobar(non_slice_dims_shape, **kwargs)
 
     in_data_size = np.prod(non_slice_dims_shape) * dtype.itemsize
     out_data_size = np.prod(output_dims) * dtype.itemsize
diff --git a/httomo_backends/pipelines_full/gpu_360_distortion_FBP_directive.yaml b/httomo_backends/pipelines_full/gpu_360_distortion_FBP_directive.yaml
@@ -10,7 +10,7 @@
   module_path: httomolibgpu.misc.morph
 - method: remove_stripe_based_sorting
   module_path: httomolibgpu.prep.stripe
-- method: FBP
+- method: FBP3d_tomobar
   module_path: httomolibgpu.recon.algorithm
 - method: calculate_stats
   module_path: httomo.methods
diff --git a/httomo_backends/pipelines_full/gpu_360_paganin_FBP_directive.yaml b/httomo_backends/pipelines_full/gpu_360_paganin_FBP_directive.yaml
@@ -6,11 +6,11 @@
   module_path: httomolibgpu.recon.rotation
 - method: sino_360_to_180
   module_path: httomolibgpu.misc.morph
-- method: paganin_filter_tomopy
-  module_path: httomolibgpu.prep.phase
 - method: remove_stripe_based_sorting
   module_path: httomolibgpu.prep.stripe
-- method: FBP
+- method: paganin_filter_tomopy
+  module_path: httomolibgpu.prep.phase
+- method: FBP3d_tomobar
   module_path: httomolibgpu.recon.algorithm
 - method: calculate_stats
   module_path: httomo.methods
diff --git a/httomo_backends/pipelines_full/gpu_diad_FBP_directive.yaml b/httomo_backends/pipelines_full/gpu_diad_FBP_directive.yaml
@@ -8,7 +8,7 @@
   module_path: httomolibgpu.prep.normalize
 - method: remove_stripe_based_sorting
   module_path: httomolibgpu.prep.stripe
-- method: FBP
+- method: FBP3d_tomobar
   module_path: httomolibgpu.recon.algorithm
 - method: calculate_stats
   module_path: httomo.methods
diff --git a/httomo_backends/pipelines_full/gpu_diad_FBP_noimagesaving_directive.yaml b/httomo_backends/pipelines_full/gpu_diad_FBP_noimagesaving_directive.yaml
@@ -8,5 +8,5 @@
   module_path: httomolibgpu.prep.normalize
 - method: remove_stripe_based_sorting
   module_path: httomolibgpu.prep.stripe
-- method: FBP
+- method: FBP3d_tomobar
   module_path: httomolibgpu.recon.algorithm
diff --git a/httomo_backends/pipelines_full/gpu_pipelineFBP2d_astra_directive.yaml b/httomo_backends/pipelines_full/gpu_pipelineFBP2d_astra_directive.yaml
@@ -0,0 +1,9 @@
+- method: standard_tomo
+  module_path: httomo.data.hdf.loaders
+- method: find_center_vo
+  module_path: httomolibgpu.recon.rotation
+- method: normalize
+  module_path: httomolibgpu.prep.normalize
+- method: FBP2d_astra
+  module_path: httomolibgpu.recon.algorithm
+
diff --git a/httomo_backends/pipelines_full/gpu_pipelineFBP_denoising_directive.yaml b/httomo_backends/pipelines_full/gpu_pipelineFBP_denoising_directive.yaml
@@ -8,7 +8,7 @@
   module_path: httomolibgpu.prep.normalize
 - method: remove_all_stripe
   module_path: httomolibgpu.prep.stripe
-- method: FBP
+- method: FBP3d_tomobar
   module_path: httomolibgpu.recon.algorithm
 - method: total_variation_PD
   module_path: httomolibgpu.misc.denoise
diff --git a/httomo_backends/pipelines_full/gpu_pipelineFBP_directive.yaml b/httomo_backends/pipelines_full/gpu_pipelineFBP_directive.yaml
@@ -8,7 +8,7 @@
   module_path: httomolibgpu.prep.normalize
 - method: remove_all_stripe
   module_path: httomolibgpu.prep.stripe
-- method: FBP
+- method: FBP3d_tomobar
   module_path: httomolibgpu.recon.algorithm
 - method: calculate_stats
   module_path: httomo.methods
diff --git a/httomo_backends/pipelines_full/gpu_pipelineLPRec_directive.yaml b/httomo_backends/pipelines_full/gpu_pipelineLPRec_directive.yaml
@@ -0,0 +1,9 @@
+- method: standard_tomo
+  module_path: httomo.data.hdf.loaders
+- method: find_center_vo
+  module_path: httomolibgpu.recon.rotation
+- method: normalize
+  module_path: httomolibgpu.prep.normalize
+- method: LPRec3d_tomobar
+  module_path: httomolibgpu.recon.algorithm
+
diff --git a/httomo_backends/pipelines_full/gpu_pipeline_sweep_FBP_directive.yaml b/httomo_backends/pipelines_full/gpu_pipeline_sweep_FBP_directive.yaml
@@ -2,7 +2,7 @@
   module_path: httomo.data.hdf.loaders
 - method: normalize
   module_path: httomolibgpu.prep.normalize
-- method: FBP
+- method: FBP3d_tomobar
   module_path: httomolibgpu.recon.algorithm
   sweep_parameter: center
   sweep_start: 1100
diff --git a/tests/test_httomolibgpu.py b/tests/test_httomolibgpu.py
@@ -25,7 +25,7 @@
 )
 from httomolibgpu.misc.corr import remove_outlier
 from httomolibgpu.misc.denoise import total_variation_ROF, total_variation_PD
-from httomolibgpu.recon.algorithm import FBP, SIRT, CGLS
+from httomolibgpu.recon.algorithm import FBP3d_tomobar, SIRT3d_tomobar, CGLS3d_tomobar
 from httomolibgpu.misc.rescale import rescale_to_int
 
 from httomo_backends.methods_database.packages.backends.httomolibgpu.supporting_funcs.misc.morph import *
@@ -525,7 +525,7 @@ def test_data_sampler_memoryhook(slices, newshape, interpolation, ensure_clean_m
 @pytest.mark.parametrize("projections", [1801, 3601])
 @pytest.mark.parametrize("slices", [7, 11, 15])
 @pytest.mark.parametrize("detectorX", [1200, 2560])
-def test_recon_FBP_memoryhook(
+def test_recon_FBP3d_tomobar_memoryhook(
     slices, detectorX, projections, ensure_clean_memory, mocker: MockerFixture
 ):
     data = cp.random.random_sample((projections, slices, detectorX), dtype=np.float32)
@@ -544,7 +544,7 @@ def test_recon_FBP_memoryhook(
     )
 
     with hook:
-        recon_data = FBP(cp.copy(data), **kwargs)
+        recon_data = FBP3d_tomobar(cp.copy(data), **kwargs)
 
     p1.assert_called_once()
 
@@ -554,7 +554,7 @@ def test_recon_FBP_memoryhook(
     )  # the amount of memory in bytes needed for the method according to memoryhook
 
     # now we estimate how much of the total memory required for this data
-    (estimated_memory_bytes, subtract_bytes) = _calc_memory_bytes_FBP(
+    (estimated_memory_bytes, subtract_bytes) = _calc_memory_bytes_FBP3d_tomobar(
         (projections, detectorX), dtype=np.float32(), **kwargs
     )
     estimated_memory_mb = round(slices * estimated_memory_bytes / (1024**2), 2)
@@ -575,14 +575,14 @@ def test_recon_FBP_memoryhook(
 @pytest.mark.cupy
 @pytest.mark.parametrize("slices", [3, 5])
 @pytest.mark.parametrize("recon_size_it", [1200, 2000])
-def test_recon_SIRT_memoryhook(slices, recon_size_it, ensure_clean_memory):
+def test_recon_SIRT3d_tomobar_memoryhook(slices, recon_size_it, ensure_clean_memory):
     data = cp.random.random_sample((1801, slices, 2560), dtype=np.float32)
     kwargs = {}
     kwargs["recon_size"] = recon_size_it
 
     hook = MaxMemoryHook()
     with hook:
-        recon_data = SIRT(
+        recon_data = SIRT3d_tomobar(
             cp.copy(data),
             np.linspace(0.0 * np.pi / 180.0, 180.0 * np.pi / 180.0, data.shape[0]),
             1200,
@@ -597,7 +597,7 @@ def test_recon_SIRT_memoryhook(slices, recon_size_it, ensure_clean_memory):
     )  # the amount of memory in bytes needed for the method according to memoryhook
 
     # now we estimate how much of the total memory required for this data
-    (estimated_memory_bytes, subtract_bytes) = _calc_memory_bytes_SIRT(
+    (estimated_memory_bytes, subtract_bytes) = _calc_memory_bytes_SIRT3d_tomobar(
         (1801, 2560), dtype=np.float32(), **kwargs
     )
     estimated_memory_mb = round(slices * estimated_memory_bytes / (1024**2), 2)
@@ -616,14 +616,14 @@ def test_recon_SIRT_memoryhook(slices, recon_size_it, ensure_clean_memory):
 @pytest.mark.cupy
 @pytest.mark.parametrize("slices", [3, 5])
 @pytest.mark.parametrize("recon_size_it", [1200, 2000])
-def test_recon_CGLS_memoryhook(slices, recon_size_it, ensure_clean_memory):
+def test_recon_CGLS3d_tomobar_memoryhook(slices, recon_size_it, ensure_clean_memory):
     data = cp.random.random_sample((1801, slices, 2560), dtype=np.float32)
     kwargs = {}
     kwargs["recon_size"] = recon_size_it
 
     hook = MaxMemoryHook()
     with hook:
-        recon_data = CGLS(
+        recon_data = CGLS3d_tomobar(
             cp.copy(data),
             np.linspace(0.0 * np.pi / 180.0, 180.0 * np.pi / 180.0, data.shape[0]),
             1200,
@@ -638,7 +638,7 @@ def test_recon_CGLS_memoryhook(slices, recon_size_it, ensure_clean_memory):
     )  # the amount of memory in bytes needed for the method according to memoryhook
 
     # now we estimate how much of the total memory required for this data
-    (estimated_memory_bytes, subtract_bytes) = _calc_memory_bytes_CGLS(
+    (estimated_memory_bytes, subtract_bytes) = _calc_memory_bytes_CGLS3d_tomobar(
         (1801, 2560), dtype=np.float32(), **kwargs
     )
     estimated_memory_mb = round(slices * estimated_memory_bytes / (1024**2), 2)
diff --git a/tests/test_method_query.py b/tests/test_method_query.py
@@ -53,7 +53,7 @@ def test_httomolibgpu_default_save_result():
 
 
 def test_httomolibgpu_default_save_result_recon():
-    query = MethodsDatabaseQuery("httomolibgpu.recon.algorithm", "FBP")
+    query = MethodsDatabaseQuery("httomolibgpu.recon.algorithm", "FBP3d_tomobar")
 
     assert query.save_result_default() is True
 
