Merge pull request #96 from DiamondLightSource/find_center

adding a fix for find_center template generator

Author: dkazanc

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

@@ -89,7 +89,7 @@ def _calc_memory_bytes_sino_360_to_180(
         kwargs["overlap"] = params["overlap"].default
     overlap: float = kwargs["overlap"]
 
-    original_sino_width = non_slice_dims_shape[1] # detX
+    original_sino_width = non_slice_dims_shape[1]  # detX
     stitched_sino_width = original_sino_width * 2 - math.ceil(overlap)
     stitched_sino_padded = original_sino_width * 2
 
@@ -123,4 +123,4 @@ def _calc_memory_bytes_sino_360_to_180(
         + 4 * summand_size
     )
 
-    return int(1.1*total_memory_bytes), 0
+    return int(1.1 * total_memory_bytes), 0

httomo_backends/scripts/yaml_pipelines_generator.py

@@ -220,7 +220,7 @@ def yaml_pipelines_generator(
                 pipeline_full[i]["parameters"].yaml_add_eol_comment(
                     key="path_to_stiched_params_file",
                     comment="Provide an absolute path to the text file with seam index and blending width.",
-                )                
+                )
             elif "data_resampler" in method_name:
                 pipeline_full.yaml_set_comment_before_after_key(
                     i,

httomo_backends/scripts/yaml_templates_generator.py

@@ -29,7 +29,6 @@
 import importlib
 import inspect
 import os
-import re
 from typing import Any, List, Dict
 
 import yaml
@@ -163,18 +162,18 @@ def _set_dict_special_cases(method_dict: Dict, method_name: str):
         method_dict: Dictionary of modules and parameters
         method_name: Name of method
     """
-    if method_name in ["find_center_vo", "find_center_pc"]:
+    if method_name in ["find_center", "find_center_vo", "find_center_pc"]:
         method_dict["id"] = "centering"
         method_dict["side_outputs"] = {"cor": "centre_of_rotation"}
-    if method_name in "find_center_360":
+    if method_name in ["find_center_360"]:
         method_dict["id"] = "centering"
         method_dict["side_outputs"] = {
             "cor": "centre_of_rotation",
             "overlap": "overlap",
             "side": "side",
             "overlap_position": "overlap_position",
         }
-    if method_name in "calculate_stats":
+    if method_name in ["calculate_stats"]:
         method_dict["id"] = "statistics"
         method_dict["side_outputs"] = {"glob_stats": "glob_stats"}