Frames averaging support files

httomo_backends/methods_database/packages/backends/httomolibgpu/httomolibgpu.yaml

@@ -66,6 +66,15 @@ misc:
       memory_gpu:
         multiplier: None
         method: module
+    average_projection_frames:
+      pattern: sinogram
+      output_dims_change: True
+      implementation: gpu_cupy
+      save_result_default: False
+      padding: False
+      memory_gpu:
+        multiplier: 2.1
+        method: direct
   rescale:
     rescale_to_int:
       pattern: all

httomo_backends/methods_database/packages/backends/httomolibgpu/supporting_funcs/misc/morph.py

@@ -25,20 +25,35 @@
 from typing import Tuple
 import numpy as np
 
-from httomolibgpu.misc.morph import data_resampler, sino_360_to_180
+from httomolibgpu.misc.morph import (
+    data_resampler,
+    sino_360_to_180,
+    average_projection_frames,
+)
 
 __all__ = [
     "_calc_memory_bytes_data_resampler",
     "_calc_output_dim_data_resampler",
     "_calc_memory_bytes_sino_360_to_180",
     "_calc_output_dim_sino_360_to_180",
+    "_calc_output_dim_average_projection_frames",
 ]
 
 
 def _calc_output_dim_data_resampler(non_slice_dims_shape, **kwargs):
     return kwargs["newshape"]
 
 
+def _calc_output_dim_average_projection_frames(non_slice_dims_shape, **kwargs):
+    k: float = kwargs["projection_averaging_factor"]
+
+    n_proj = non_slice_dims_shape[0]
+    n_full = n_proj // k
+    remainder = n_proj % k
+    n_out = n_full + (remainder > 0)
+    return n_out, non_slice_dims_shape[1]
+
+
 def _calc_memory_bytes_data_resampler(
     non_slice_dims_shape: Tuple[int, int],
     dtype: np.dtype,

httomo_backends/pipelines_full/angles_averaging_directive.yaml

@@ -0,0 +1,20 @@
+- method: standard_tomo
+  module_path: httomo.data.hdf.loaders
+- method: remove_outlier
+  module_path: httomolibgpu.misc.corr
+- method: dark_flat_field_correction
+  module_path: httomolibgpu.prep.normalize
+- method: find_center_vo
+  module_path: httomolibgpu.recon.rotation  
+- method: average_projection_frames
+  module_path: httomolibgpu.misc.morph
+- method: minus_log
+  module_path: httomolibgpu.prep.normalize
+- method: LPRec3d_tomobar
+  module_path: httomolibgpu.recon.algorithm
+- method: calculate_stats
+  module_path: httomo.methods
+- method: rescale_to_int
+  module_path: httomolib.misc.rescale
+- method: save_to_images
+  module_path: httomolib.misc.images

httomo_backends/scripts/yaml_pipelines_generator.py

@@ -221,6 +221,13 @@ def yaml_pipelines_generator(
                     key="path_to_stiched_params_file",
                     comment="Provide an absolute path to the text file with seam index and blending width.",
                 )
+            elif "average_projection_frames" in method_name:
+                pipeline_full.yaml_set_comment_before_after_key(
+                    i,
+                    "--- Apply averaging of projection data in the angular dimension. --- ",
+                    indent=0,
+                )
+                pipeline_full += yaml_template_method
             elif "data_resampler" in method_name:
                 pipeline_full.yaml_set_comment_before_after_key(
                     i,