Merge pull request #64 from DiamondLightSource/rescaletointC

dkazanc · web-flow · commit ef8e487c8cbf · 2025-09-01T16:32:26.000+01:00
adding rescale to int to library and update full pipelines
diff --git a/httomo_backends/methods_database/packages/backends/httomolib/httomolib.yaml b/httomo_backends/methods_database/packages/backends/httomolib/httomolib.yaml
@@ -1,4 +1,12 @@
 misc:
+  rescale:
+    rescale_to_int:
+      pattern: all
+      output_dims_change: False
+      implementation: cpu
+      memory_gpu: None
+      save_result_default: False
+      padding: False
   morph:
     data_reducer:
       pattern: all
diff --git a/httomo_backends/methods_database/packages/backends/httomolib/httomolib_modules.yaml b/httomo_backends/methods_database/packages/backends/httomolib/httomolib_modules.yaml
@@ -1,3 +1,4 @@
+- httomolib.misc.rescale
 - httomolib.misc.morph
 - httomolib.misc.images
 - httomolib.misc.segm
diff --git a/httomo_backends/methods_database/packages/backends/tomopy/supporting_funcs/misc/corr.py b/httomo_backends/methods_database/packages/backends/tomopy/supporting_funcs/misc/corr.py
@@ -18,7 +18,7 @@
 # Created By  : Tomography Team at DLS <scientificsoftware@diamond.ac.uk>
 # Created Date: 18/July/2024
 # ---------------------------------------------------------------------------
-""" Modules for memory estimation, padding, data dims estimation """
+"""Modules for memory estimation, padding, data dims estimation"""
 
 from typing import Tuple
 
diff --git a/httomo_backends/methods_database/packages/backends/tomopy/supporting_funcs/prep/stripe.py b/httomo_backends/methods_database/packages/backends/tomopy/supporting_funcs/prep/stripe.py
@@ -18,7 +18,7 @@
 # Created By  : Tomography Team at DLS <scientificsoftware@diamond.ac.uk>
 # Created Date: 18/July/2024
 # ---------------------------------------------------------------------------
-""" Modules for memory estimation, padding, data dims estimation """
+"""Modules for memory estimation, padding, data dims estimation"""
 
 from typing import Tuple
 
diff --git a/httomo_backends/pipelines_full/FBP3d_tomobar_denoising_directive.yaml b/httomo_backends/pipelines_full/FBP3d_tomobar_denoising_directive.yaml
@@ -15,6 +15,6 @@
 - method: calculate_stats
   module_path: httomo.methods
 - method: rescale_to_int
-  module_path: httomolibgpu.misc.rescale
+  module_path: httomolib.misc.rescale
 - method: save_to_images
   module_path: httomolib.misc.images
diff --git a/httomo_backends/pipelines_full/FBP3d_tomobar_directive.yaml b/httomo_backends/pipelines_full/FBP3d_tomobar_directive.yaml
@@ -13,6 +13,6 @@
 - method: calculate_stats
   module_path: httomo.methods
 - method: rescale_to_int
-  module_path: httomolibgpu.misc.rescale
+  module_path: httomolib.misc.rescale
 - method: save_to_images
   module_path: httomolib.misc.images
diff --git a/httomo_backends/pipelines_full/LPRec3d_tomobar_directive.yaml b/httomo_backends/pipelines_full/LPRec3d_tomobar_directive.yaml
@@ -13,7 +13,7 @@
 - method: calculate_stats
   module_path: httomo.methods
 - method: rescale_to_int
-  module_path: httomolibgpu.misc.rescale
+  module_path: httomolib.misc.rescale
 - method: save_to_images
   module_path: httomolib.misc.images
 
diff --git a/httomo_backends/pipelines_full/deg360_distortion_FBP3d_tomobar_directive.yaml b/httomo_backends/pipelines_full/deg360_distortion_FBP3d_tomobar_directive.yaml
@@ -15,6 +15,6 @@
 - method: calculate_stats
   module_path: httomo.methods
 - method: rescale_to_int
-  module_path: httomolibgpu.misc.rescale
+  module_path: httomolib.misc.rescale
 - method: save_to_images
   module_path: httomolib.misc.images
diff --git a/httomo_backends/pipelines_full/deg360_paganin_FBP3d_tomobar_directive.yaml b/httomo_backends/pipelines_full/deg360_paganin_FBP3d_tomobar_directive.yaml
@@ -15,6 +15,6 @@
 - method: calculate_stats
   module_path: httomo.methods
 - method: rescale_to_int
-  module_path: httomolibgpu.misc.rescale
+  module_path: httomolib.misc.rescale
 - method: save_to_images
   module_path: httomolib.misc.images
diff --git a/httomo_backends/pipelines_full/tomopy_gridrec_directive.yaml b/httomo_backends/pipelines_full/tomopy_gridrec_directive.yaml
@@ -13,6 +13,6 @@
 - method: calculate_stats
   module_path: httomo.methods
 - method: rescale_to_int
-  module_path: httomolibgpu.misc.rescale
+  module_path: httomolib.misc.rescale
 - method: save_to_images
   module_path: httomolib.misc.images
diff --git a/httomo_backends/scripts/yaml_pipelines_generator.py b/httomo_backends/scripts/yaml_pipelines_generator.py
@@ -158,7 +158,7 @@ def yaml_pipelines_generator(
             elif "corr" in module_name and "remove_outlier" in method_name:
                 pipeline_full.yaml_set_comment_before_after_key(
                     i,
-                    "--- Removing dead pixels in the data, aka zingers. Use if sharp streaks are present in reconstruction. ---",
+                    "--- Removing dead pixels in the data, aka zingers. Use if sharp streaks are present in reconstruction. Please use before normalisation. ---",
                     indent=0,
                 )
                 pipeline_full += yaml_template_method

Original file line number	Diff line number	Diff line change
`@@ -1,3 +1,4 @@`
	`1`	`+- httomolib.misc.rescale`
`1`	`2`	`- httomolib.misc.morph`
`2`	`3`	`- httomolib.misc.images`
`3`	`4`	`- httomolib.misc.segm`