httomo-backends 0.7.2__tar.gz → 0.9.0__tar.gz

{httomo_backends-0.7.2 → httomo_backends-0.9.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: httomo-backends
-Version: 0.7.2
+Version: 0.9.0
 Summary: Supplementary files for HTTomo backends.
 Author: Garry ODonnell, Jacob Williamson
 Author-email: Daniil Kazantsev <daniil.kazantsev@diamond.ac.uk>, Yousef Moazzam <yousef.moazzam@diamond.ac.uk>, Jessica Verschoyle <jessica.verschoyle@diamond.ac.uk>, Naman Gera <naman.gera@diamond.ac.uk>, scientificsoftware@diamond.ac.uk

{httomo_backends-0.7.2 → httomo_backends-0.9.0}/httomo_backends/methods_database/packages/backends/httomolib/httomolib.yaml

@@ -1,4 +1,12 @@
 misc:
+  utils:
+    data_checker:
+      pattern: all
+      output_dims_change: False
+      implementation: cpu
+      memory_gpu: None
+      save_result_default: False
+      padding: False
   rescale:
     rescale_to_int:
       pattern: all

{httomo_backends-0.7.2 → httomo_backends-0.9.0}/httomo_backends/methods_database/packages/backends/httomolib/httomolib_modules.yaml

@@ -1,3 +1,4 @@
+- httomolib.misc.utils
 - httomolib.misc.rescale
 - httomolib.misc.morph
 - httomolib.misc.images

{httomo_backends-0.7.2 → httomo_backends-0.9.0}/httomo_backends/methods_database/packages/backends/httomolibgpu/httomolibgpu.yaml

@@ -1,4 +1,14 @@
 misc:
+  utils:
+    data_checker:
+      pattern: all
+      output_dims_change: False
+      implementation: gpu_cupy
+      save_result_default: False
+      padding: False
+      memory_gpu:
+        multiplier: 1.0
+        method: direct
   corr:
     median_filter:
       pattern: all
@@ -68,7 +78,7 @@ misc:
         method: module
 prep:
   normalize:
-    normalize:
+    dark_flat_field_correction:
       pattern: projection
       output_dims_change: False
       implementation: gpu_cupy
@@ -77,8 +87,17 @@ prep:
       memory_gpu:
         multiplier: None
         method: module
+    minus_log:
+      pattern: all
+      output_dims_change: False
+      implementation: gpu_cupy
+      save_result_default: False
+      padding: False
+      memory_gpu:
+        multiplier: 3.0
+        method: direct      
   phase:
-    paganin_filter_tomopy:
+    paganin_filter:
       pattern: projection
       output_dims_change: False
       implementation: gpu_cupy
@@ -87,6 +106,15 @@ prep:
       memory_gpu:
         multiplier: None
         method: module
+    paganin_filter_savu_legacy:
+      pattern: projection
+      output_dims_change: False
+      implementation: gpu_cupy
+      save_result_default: False
+      padding: False
+      memory_gpu:
+        multiplier: None
+        method: module       
   alignment:
     distortion_correction_proj_discorpy:
       pattern: projection

{httomo_backends-0.7.2 → httomo_backends-0.9.0}/httomo_backends/methods_database/packages/backends/httomolibgpu/httomolibgpu_modules.yaml

@@ -1,3 +1,4 @@
+- httomolibgpu.misc.utils
 - httomolibgpu.misc.corr
 - httomolibgpu.misc.denoise
 - httomolibgpu.misc.morph

{httomo_backends-0.7.2 → httomo_backends-0.9.0}/httomo_backends/methods_database/packages/backends/httomolibgpu/supporting_funcs/prep/normalize.py

@@ -3,11 +3,11 @@ import numpy as np
 
 
 __all__ = [
-    "_calc_memory_bytes_normalize",
+    "_calc_memory_bytes_dark_flat_field_correction",
 ]
 
 
-def _calc_memory_bytes_normalize(
+def _calc_memory_bytes_dark_flat_field_correction(
     non_slice_dims_shape: Tuple[int, int],
     dtype: np.dtype,
     **kwargs,

{httomo_backends-0.7.2 → httomo_backends-0.9.0}/httomo_backends/methods_database/packages/backends/httomolibgpu/supporting_funcs/prep/phase.py

@@ -20,23 +20,30 @@
 # ---------------------------------------------------------------------------
 """Modules for memory estimation for phase retrieval and phase-contrast enhancement"""
 
-import math
 from typing import Tuple
 import numpy as np
 
 from httomo_backends.cufft import CufftType, cufft_estimate_2d
 
 __all__ = [
-    "_calc_memory_bytes_paganin_filter_tomopy",
+    "_calc_memory_bytes_paganin_filter",
+    "_calc_memory_bytes_paganin_filter_savu_legacy",
 ]
 
 
-def _calc_memory_bytes_paganin_filter_tomopy(
+def _calc_memory_bytes_paganin_filter_savu_legacy(
+    non_slice_dims_shape: Tuple[int, int],
+    dtype: np.dtype,
+    **kwargs,
+) -> Tuple[int, int]:
+    return _calc_memory_bytes_paganin_filter(non_slice_dims_shape, dtype, **kwargs)
+
+
+def _calc_memory_bytes_paganin_filter(
     non_slice_dims_shape: Tuple[int, int],
     dtype: np.dtype,
     **kwargs,
 ) -> Tuple[int, int]:
-    from httomolibgpu.prep.phase import _shift_bit_length
 
     # Input (unpadded)
     unpadded_in_slice_size = np.prod(non_slice_dims_shape) * dtype.itemsize
@@ -44,7 +51,7 @@ def _calc_memory_bytes_paganin_filter_tomopy(
     # estimate padding size here based on non_slice dimensions
     pad_tup = []
     for dim_len in non_slice_dims_shape:
-        diff = _shift_bit_length(dim_len + 1) - dim_len
+        diff = __shift_bit_length(dim_len + 1) - dim_len
         if dim_len % 2 == 0:
             pad_width = diff // 2
             pad_width = (pad_width, pad_width)
@@ -107,3 +114,7 @@ def _calc_memory_bytes_paganin_filter_tomopy(
     subtract_bytes = int(filter_size + grid_size)
 
     return (tot_memory_bytes, subtract_bytes)
+
+
+def __shift_bit_length(x: int) -> int:
+    return 1 << (x - 1).bit_length()

{httomo_backends-0.7.2 → httomo_backends-0.9.0}/httomo_backends/methods_database/packages/backends/httomolibgpu/supporting_funcs/recon/algorithm.py

@@ -189,7 +189,7 @@ def _calc_memory_bytes_LPRec3d_tomobar(
     if detector_pad is True:
         detector_pad = __estimate_detectorHoriz_padding(non_slice_dims_shape[1])
     elif detector_pad is False:
-        detector_pad = 0        
+        detector_pad = 0
 
     min_mem_usage_filter = False
     if "min_mem_usage_filter" in kwargs:
@@ -208,9 +208,9 @@ def _calc_memory_bytes_LPRec3d_tomobar(
     _CENTER_SIZE_MIN = 192  # must be divisible by 8
 
     n = DetectorsLengthH
-    if(power_of_2_cropping):
+    if power_of_2_cropping:
         n_pow2 = 2 ** math.ceil(math.log2(n))
-        if( 0.9 < n / n_pow2 ):
+        if 0.9 < n / n_pow2:
             n = n_pow2
 
     odd_horiz = False
@@ -309,10 +309,7 @@ def _calc_memory_bytes_LPRec3d_tomobar(
         DetectorsLengthH_prepad * DetectorsLengthH_prepad * np.float32().itemsize
     )
     ifft2_plan_slice_size = (
-        cufft_estimate_2d(
-            nx=2 * n, ny=2 * n, fft_type=CufftType.CUFFT_C2C
-        )
-        / 2
+        cufft_estimate_2d(nx=2 * n, ny=2 * n, fft_type=CufftType.CUFFT_C2C) / 2
     )
     circular_mask_size = np.prod(output_dims) / 2 * np.int64().itemsize * 4
     after_recon_swapaxis_slice = recon_output_size
@@ -351,38 +348,74 @@ def _calc_memory_bytes_LPRec3d_tomobar(
     add_to_memory_counters(tmp_p_input_slice, True)
     if min_mem_usage_filter:
         add_to_memory_counters(rfft_plan_slice_size / 4 / projection_chunk_count, False)
-        add_to_memory_counters(irfft_plan_slice_size / 4 / projection_chunk_count, False)
+        add_to_memory_counters(
+            irfft_plan_slice_size / 4 / projection_chunk_count, False
+        )
         add_to_memory_counters(padded_tmp_p_input_slice / projection_chunk_count, False)
 
         add_to_memory_counters(rfft_result_size / projection_chunk_count, False)
-        add_to_memory_counters(filtered_rfft_result_size / projection_chunk_count, False)
+        add_to_memory_counters(
+            filtered_rfft_result_size / projection_chunk_count, False
+        )
         add_to_memory_counters(-rfft_result_size / projection_chunk_count, False)
-        add_to_memory_counters(-padded_tmp_p_input_slice / projection_chunk_count, False)
+        add_to_memory_counters(
+            -padded_tmp_p_input_slice / projection_chunk_count, False
+        )
 
-        add_to_memory_counters(irfft_scratch_memory_size / projection_chunk_count, False)
-        add_to_memory_counters(-irfft_scratch_memory_size / projection_chunk_count, False)
+        add_to_memory_counters(
+            irfft_scratch_memory_size / projection_chunk_count, False
+        )
+        add_to_memory_counters(
+            -irfft_scratch_memory_size / projection_chunk_count, False
+        )
         add_to_memory_counters(irfft_result_size / projection_chunk_count, False)
-        add_to_memory_counters(-filtered_rfft_result_size / projection_chunk_count, False)
+        add_to_memory_counters(
+            -filtered_rfft_result_size / projection_chunk_count, False
+        )
 
         add_to_memory_counters(-irfft_result_size / projection_chunk_count, False)
     else:
-        add_to_memory_counters(rfft_plan_slice_size / chunk_count / projection_chunk_count * 2, True)
-        add_to_memory_counters(irfft_plan_slice_size / chunk_count / projection_chunk_count * 2, True)
+        add_to_memory_counters(
+            rfft_plan_slice_size / chunk_count / projection_chunk_count * 2, True
+        )
+        add_to_memory_counters(
+            irfft_plan_slice_size / chunk_count / projection_chunk_count * 2, True
+        )
         # add_to_memory_counters(irfft_scratch_memory_size / chunk_count / projection_chunk_count, True)
         for _ in range(0, chunk_count):
-            add_to_memory_counters(padded_tmp_p_input_slice / chunk_count / projection_chunk_count, True)
-
-            add_to_memory_counters(rfft_result_size / chunk_count / projection_chunk_count, True)
-            add_to_memory_counters(filtered_rfft_result_size / chunk_count / projection_chunk_count, True)
-            add_to_memory_counters(-rfft_result_size / chunk_count / projection_chunk_count, True)
-            add_to_memory_counters(-padded_tmp_p_input_slice / chunk_count / projection_chunk_count, True)
-
-            add_to_memory_counters(irfft_scratch_memory_size / chunk_count / projection_chunk_count, True)
-            add_to_memory_counters(-irfft_scratch_memory_size / chunk_count / projection_chunk_count, True)
-            add_to_memory_counters(irfft_result_size / chunk_count / projection_chunk_count, True)
-            add_to_memory_counters(-filtered_rfft_result_size / chunk_count / projection_chunk_count, True)
-
-            add_to_memory_counters(-irfft_result_size / chunk_count / projection_chunk_count, True)
+            add_to_memory_counters(
+                padded_tmp_p_input_slice / chunk_count / projection_chunk_count, True
+            )
+
+            add_to_memory_counters(
+                rfft_result_size / chunk_count / projection_chunk_count, True
+            )
+            add_to_memory_counters(
+                filtered_rfft_result_size / chunk_count / projection_chunk_count, True
+            )
+            add_to_memory_counters(
+                -rfft_result_size / chunk_count / projection_chunk_count, True
+            )
+            add_to_memory_counters(
+                -padded_tmp_p_input_slice / chunk_count / projection_chunk_count, True
+            )
+
+            add_to_memory_counters(
+                irfft_scratch_memory_size / chunk_count / projection_chunk_count, True
+            )
+            add_to_memory_counters(
+                -irfft_scratch_memory_size / chunk_count / projection_chunk_count, True
+            )
+            add_to_memory_counters(
+                irfft_result_size / chunk_count / projection_chunk_count, True
+            )
+            add_to_memory_counters(
+                -filtered_rfft_result_size / chunk_count / projection_chunk_count, True
+            )
+
+            add_to_memory_counters(
+                -irfft_result_size / chunk_count / projection_chunk_count, True
+            )
 
     add_to_memory_counters(-padded_in_slice_size, True)
     add_to_memory_counters(-filter_size, False)
@@ -433,7 +466,7 @@ def _calc_memory_bytes_SIRT3d_tomobar(
     if detector_pad is True:
         detector_pad = __estimate_detectorHoriz_padding(non_slice_dims_shape[1])
     elif detector_pad is False:
-        detector_pad = 0        
+        detector_pad = 0
 
     anglesnum = non_slice_dims_shape[0]
     DetectorsLengthH_padded = non_slice_dims_shape[1] + 2 * detector_pad
@@ -456,7 +489,7 @@ def _calc_memory_bytes_SIRT3d_tomobar(
     Res_times_R = Res
     C_times_res = out_data_size
 
-    astra_projection = (in_data_size + out_data_size)
+    astra_projection = in_data_size + out_data_size
 
     tot_memory_bytes = int(
         recon_data_size_original
@@ -483,7 +516,7 @@ def _calc_memory_bytes_CGLS3d_tomobar(
     if detector_pad is True:
         detector_pad = __estimate_detectorHoriz_padding(non_slice_dims_shape[1])
     elif detector_pad is False:
-        detector_pad = 0        
+        detector_pad = 0
 
     anglesnum = non_slice_dims_shape[0]
     DetectorsLengthH_padded = non_slice_dims_shape[1] + 2 * detector_pad
@@ -535,7 +568,7 @@ def _calc_memory_bytes_FISTA3d_tomobar(
     if detector_pad is True:
         detector_pad = __estimate_detectorHoriz_padding(non_slice_dims_shape[1])
     elif detector_pad is False:
-        detector_pad = 0        
+        detector_pad = 0
 
     anglesnum = non_slice_dims_shape[0]
     DetectorsLengthH_padded = non_slice_dims_shape[1] + 2 * detector_pad
@@ -574,5 +607,5 @@ def _calc_memory_bytes_FISTA3d_tomobar(
 def __estimate_detectorHoriz_padding(detX_size) -> int:
     det_half = detX_size // 2
     padded_value_exact = int(np.sqrt(2 * (det_half**2))) - det_half
-    padded_add_margin = int(0.1 * padded_value_exact)
+    padded_add_margin = padded_value_exact // 2
     return padded_value_exact + padded_add_margin

{httomo_backends-0.7.2 → httomo_backends-0.9.0}/httomo_backends/pipelines_full/FBP2d_astra_directive.yaml

@@ -1,9 +1,11 @@
 - method: standard_tomo
   module_path: httomo.data.hdf.loaders
+- method: dark_flat_field_correction
+  module_path: httomolibgpu.prep.normalize
 - method: find_center_vo
   module_path: httomolibgpu.recon.rotation
-- method: normalize
-  module_path: httomolibgpu.prep.normalize
+- method: minus_log
+  module_path: httomolibgpu.prep.normalize   
 - method: FBP2d_astra
   module_path: httomolibgpu.recon.algorithm
 

{httomo_backends-0.7.2 → httomo_backends-0.9.0}/httomo_backends/pipelines_full/FBP3d_tomobar_denoising_directive.yaml

@@ -1,13 +1,15 @@
 - method: standard_tomo
   module_path: httomo.data.hdf.loaders
-- method: find_center_vo
-  module_path: httomolibgpu.recon.rotation
 - method: remove_outlier
   module_path: httomolibgpu.misc.corr
-- method: normalize
+- method: dark_flat_field_correction
   module_path: httomolibgpu.prep.normalize
+- method: find_center_vo
+  module_path: httomolibgpu.recon.rotation  
 - method: remove_all_stripe
   module_path: httomolibgpu.prep.stripe
+- method: minus_log
+  module_path: httomolibgpu.prep.normalize
 - method: FBP3d_tomobar
   module_path: httomolibgpu.recon.algorithm
 - method: total_variation_PD

{httomo_backends-0.7.2 → httomo_backends-0.9.0}/httomo_backends/pipelines_full/FBP3d_tomobar_directive.yaml

@@ -1,13 +1,15 @@
 - method: standard_tomo
   module_path: httomo.data.hdf.loaders
-- method: find_center_vo
-  module_path: httomolibgpu.recon.rotation
 - method: remove_outlier
   module_path: httomolibgpu.misc.corr
-- method: normalize
+- method: dark_flat_field_correction
   module_path: httomolibgpu.prep.normalize
+- method: find_center_vo
+  module_path: httomolibgpu.recon.rotation 
 - method: remove_all_stripe
   module_path: httomolibgpu.prep.stripe
+- method: minus_log
+  module_path: httomolibgpu.prep.normalize  
 - method: FBP3d_tomobar
   module_path: httomolibgpu.recon.algorithm
 - method: calculate_stats

{httomo_backends-0.7.2 → httomo_backends-0.9.0}/httomo_backends/pipelines_full/FBP3d_tomobar_noimagesaving_directive.yaml

@@ -1,12 +1,14 @@
 - method: standard_tomo
   module_path: httomo.data.hdf.loaders
-- method: find_center_vo
-  module_path: httomolibgpu.recon.rotation
 - method: remove_outlier
   module_path: httomolibgpu.misc.corr
-- method: normalize
+- method: dark_flat_field_correction
   module_path: httomolibgpu.prep.normalize
+- method: find_center_vo
+  module_path: httomolibgpu.recon.rotation
 - method: remove_stripe_based_sorting
   module_path: httomolibgpu.prep.stripe
+- method: minus_log
+  module_path: httomolibgpu.prep.normalize
 - method: FBP3d_tomobar
   module_path: httomolibgpu.recon.algorithm

{httomo_backends-0.7.2 → httomo_backends-0.9.0}/httomo_backends/pipelines_full/FISTA3d_tomobar_directive.yaml

@@ -1,9 +1,11 @@
 - method: standard_tomo
   module_path: httomo.data.hdf.loaders
+- method: dark_flat_field_correction
+  module_path: httomolibgpu.prep.normalize
 - method: find_center_vo
   module_path: httomolibgpu.recon.rotation
-- method: normalize
-  module_path: httomolibgpu.prep.normalize
+- method: minus_log
+  module_path: httomolibgpu.prep.normalize  
 - method: FISTA3d_tomobar
   module_path: httomolibgpu.recon.algorithm
 - method: calculate_stats

{httomo_backends-0.7.2 → httomo_backends-0.9.0}/httomo_backends/pipelines_full/LPRec3d_tomobar_directive.yaml

@@ -1,13 +1,15 @@
 - method: standard_tomo
   module_path: httomo.data.hdf.loaders
-- method: find_center_vo
-  module_path: httomolibgpu.recon.rotation
 - method: remove_outlier
   module_path: httomolibgpu.misc.corr
-- method: normalize
+- method: dark_flat_field_correction
   module_path: httomolibgpu.prep.normalize
+- method: find_center_vo
+  module_path: httomolibgpu.recon.rotation  
 - method: remove_all_stripe
   module_path: httomolibgpu.prep.stripe
+- method: minus_log
+  module_path: httomolibgpu.prep.normalize
 - method: LPRec3d_tomobar
   module_path: httomolibgpu.recon.algorithm
 - method: calculate_stats

{httomo_backends-0.7.2 → httomo_backends-0.9.0}/httomo_backends/pipelines_full/deg360_distortion_FBP3d_tomobar_directive.yaml

@@ -1,15 +1,17 @@
 - method: standard_tomo
   module_path: httomo.data.hdf.loaders
-- method: find_center_360
-  module_path: httomolibgpu.recon.rotation
-- method: normalize
+- method: dark_flat_field_correction
   module_path: httomolibgpu.prep.normalize
 - method: distortion_correction_proj_discorpy
   module_path: httomolibgpu.prep.alignment
+- method: find_center_360
+  module_path: httomolibgpu.recon.rotation  
 - method: sino_360_to_180
   module_path: httomolibgpu.misc.morph
 - method: remove_stripe_based_sorting
   module_path: httomolibgpu.prep.stripe
+- method: minus_log
+  module_path: httomolibgpu.prep.normalize
 - method: FBP3d_tomobar
   module_path: httomolibgpu.recon.algorithm
 - method: calculate_stats

{httomo_backends-0.7.2 → httomo_backends-0.9.0}/httomo_backends/pipelines_full/deg360_paganin_FBP3d_tomobar_directive.yaml

@@ -1,14 +1,14 @@
 - method: standard_tomo
   module_path: httomo.data.hdf.loaders
+- method: dark_flat_field_correction
+  module_path: httomolibgpu.prep.normalize
 - method: find_center_360
-  module_path: httomolibgpu.recon.rotation
-- method: normalize
-  module_path: httomolibgpu.prep.normalize  
+  module_path: httomolibgpu.recon.rotation  
 - method: sino_360_to_180
   module_path: httomolibgpu.misc.morph
 - method: remove_stripe_based_sorting
   module_path: httomolibgpu.prep.stripe
-- method: paganin_filter_tomopy
+- method: paganin_filter
   module_path: httomolibgpu.prep.phase
 - method: FBP3d_tomobar
   module_path: httomolibgpu.recon.algorithm

{httomo_backends-0.7.2 → httomo_backends-0.9.0}/httomo_backends/pipelines_full/sweep_center_FBP3d_tomobar_directive.yaml

@@ -1,7 +1,9 @@
 - method: standard_tomo
   module_path: httomo.data.hdf.loaders
-- method: normalize
+- method: dark_flat_field_correction
   module_path: httomolibgpu.prep.normalize
+- method: minus_log
+  module_path: httomolibgpu.prep.normalize  
 - method: FBP3d_tomobar
   module_path: httomolibgpu.recon.algorithm
   sweep_parameter: center

{httomo_backends-0.7.2 → httomo_backends-0.9.0}/httomo_backends/pipelines_full/sweep_paganin_FBP3d_tomobar_directive.yaml

@@ -1,12 +1,12 @@
 - method: standard_tomo
   module_path: httomo.data.hdf.loaders
+- method: dark_flat_field_correction
+  module_path: httomolibgpu.prep.normalize
 - method: find_center_vo
   module_path: httomolibgpu.recon.rotation  
-- method: normalize
-  module_path: httomolibgpu.prep.normalize
-- method: paganin_filter_tomopy
+- method: paganin_filter
   module_path: httomolibgpu.prep.phase
-  sweep_parameter: alpha
-  sweep_values: [0.01, 0.001, 0.0001]
+  sweep_parameter: ratio_delta_beta
+  sweep_values: [10, 150, 350]
 - method: FBP3d_tomobar
-  module_path: httomolibgpu.recon.algorithm
+  module_path: httomolibgpu.recon.algorithm

{httomo_backends-0.7.2 → httomo_backends-0.9.0}/httomo_backends/pipelines_full/titaren_center_pc_FBP3d_resample_directive.yaml

@@ -1,11 +1,13 @@
 - method: standard_tomo
   module_path: httomo.data.hdf.loaders
+- method: dark_flat_field_correction
+  module_path: httomolibgpu.prep.normalize
 - method: find_center_pc
   module_path: httomolibgpu.recon.rotation
-- method: normalize
-  module_path: httomolibgpu.prep.normalize
 - method: remove_stripe_ti
   module_path: httomolibgpu.prep.stripe
+- method: minus_log
+  module_path: httomolibgpu.prep.normalize
 - method: FBP3d_tomobar
   module_path: httomolibgpu.recon.algorithm
 - method: data_resampler

{httomo_backends-0.7.2 → httomo_backends-0.9.0}/httomo_backends/scripts/yaml_pipelines_generator.py

@@ -94,6 +94,7 @@ def yaml_pipelines_generator(
     with open(path_to_pipelines, "r") as file:
         try:
             pipeline_file_content = yaml.load(file)
+            # print(f"Loading pipeline: {file.name}") # useful for debugging
         except OSError as e:
             print("loading yaml file with methods failed", e)
 
@@ -138,7 +139,7 @@ def yaml_pipelines_generator(
 
             pipeline_full.yaml_set_start_comment(
                 "This pipeline should be supported by the latest developments of HTTomo. Use module load httomo/latest module at Diamond."
-            )            
+            )
 
             if "loaders" in module_name:
                 # should be the first method in the list
@@ -157,7 +158,7 @@ def yaml_pipelines_generator(
                 pipeline_full += yaml_template_method
                 pipeline_full[i]["parameters"].yaml_add_eol_comment(
                     key="ind",
-                    comment="A vertical slice (sinogram) index to calculate CoR, `mid` can be used for middle",
+                    comment="A vertical slice (sinogram) index to calculate CoR, 'mid' can be used for middle",
                 )
                 pipeline_full[i]["parameters"].yaml_add_eol_comment(
                     key="cor_initialisation_value",
@@ -169,7 +170,7 @@ def yaml_pipelines_generator(
                 )
                 pipeline_full[i]["parameters"].yaml_add_eol_comment(
                     key="side",
-                    comment="'None' corresponds to fully automated determination, '0' to the left side, '1' to the right side.",
+                    comment="'None' corresponds to fully automated determination, 'left' to the left side, 'right' to the right side.",
                 )
                 pipeline_full[i]["side_outputs"].yaml_add_eol_comment(
                     key="cor",
@@ -182,7 +183,7 @@ 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 unresponsive pixels in the data, aka zingers. Use if sharp streaks are present in the reconstruction. To be applied before normalisation. ---",
+                    "--- Removing unresponsive/dead pixels in the data, aka zingers. Use if sharp streaks are present in the reconstruction. To be applied before normalisation. ---",
                     indent=0,
                 )
                 pipeline_full += yaml_template_method
@@ -223,21 +224,24 @@ def yaml_pipelines_generator(
             elif "sino_360_to_180" in method_name:
                 pipeline_full.yaml_set_comment_before_after_key(
                     i,
-                    "--- Using the overlap provided, converting 360 degrees scan to 180 degrees scan. --- ",
+                    "--- Using the overlap and side provided, converting 360 degrees scan to 180 degrees scan. --- ",
                     indent=0,
                 )
                 pipeline_full += yaml_template_method
-            elif "normalize" in module_name:
+            elif "dark_flat_field_correction" in method_name:
                 pipeline_full.yaml_set_comment_before_after_key(
                     i,
-                    "--- Normalisation of projection data using collected flats/darks images. --- ",
+                    "--- Flat-field and dark-field projection correction. --- ",
                     indent=0,
                 )
                 pipeline_full += yaml_template_method
-                pipeline_full[i]["parameters"].yaml_add_eol_comment(
-                    key="minus_log",
-                    comment="If Paganin method is used bellow, set it to false.",
+            elif "minus_log" in method_name:
+                pipeline_full.yaml_set_comment_before_after_key(
+                    i,
+                    "--- Negative log is required for reconstruction to convert raw intensity measurements into the line integrals of attenuation. --- ",
+                    indent=0,
                 )
+                pipeline_full += yaml_template_method
             elif "phase" in module_name:
                 pipeline_full.yaml_set_comment_before_after_key(
                     i,
@@ -246,8 +250,20 @@ def yaml_pipelines_generator(
                 )
                 pipeline_full += yaml_template_method
                 pipeline_full[i]["parameters"].yaml_add_eol_comment(
-                    key="alpha",
-                    comment="Controls the balance between the strength of the filter and the amount of noise reduction. Smaller values lead to less noise and more blur.",
+                    key="ratio_delta_beta",
+                    comment="The ratio of delta/beta for filter strength control. Larger values lead to more smoothing.",
+                )
+                pipeline_full[i]["parameters"].yaml_add_eol_comment(
+                    key="pixel_size",
+                    comment="Detector pixel size (resolution) in MICRON units.",
+                )
+                pipeline_full[i]["parameters"].yaml_add_eol_comment(
+                    key="distance",
+                    comment="Propagation distance of the wavefront from sample to detector in METRE units.",
+                )
+                pipeline_full[i]["parameters"].yaml_add_eol_comment(
+                    key="energy",
+                    comment="Beam energy in keV.",
                 )
             elif "stripe" in module_name:
                 pipeline_full.yaml_set_comment_before_after_key(
@@ -269,11 +285,11 @@ def yaml_pipelines_generator(
                 )
                 pipeline_full[i]["parameters"].yaml_add_eol_comment(
                     key="detector_pad",
-                    comment="Horizontal detector padding to minimise circle/arc-type artifacts in the reconstruction. Set to true to enable automatic padding or an integer",
+                    comment="Horizontal detector padding to minimise circle/arc-type artifacts in the reconstruction. Set to 'true' to enable automatic padding or an integer",
                 )
                 pipeline_full[i]["parameters"].yaml_add_eol_comment(
                     key="recon_mask_radius",
-                    comment="Zero pixels outside the mask-circle radius.",
+                    comment="Zero pixels outside the mask-circle radius. Make radius equal to 2.0 to remove the mask effect.",
                 )
                 pipeline_full[i]["parameters"].yaml_add_eol_comment(
                     key="neglog",
@@ -284,7 +300,7 @@ def yaml_pipelines_generator(
                     pipeline_full[i]["parameters"]["algorithm"] = "gridrec"
                     pipeline_full[i]["parameters"].yaml_add_eol_comment(
                         key="algorithm",
-                        comment="Select the required algorithm, e.g. `gridrec`",
+                        comment="Select the required algorithm, e.g. 'gridrec'",
                     )
             elif "denoise" in module_name:
                 pipeline_full.yaml_set_comment_before_after_key(

{httomo_backends-0.7.2 → httomo_backends-0.9.0}/httomo_backends/scripts/yaml_templates_generator.py

@@ -221,6 +221,10 @@ def _get_discard_keys() -> List[str]:
         "step_xy",
         "jpeg_quality",
         "watermark_vals",
+        "power_of_2_oversampling",
+        "power_of_2_cropping",
+        "min_mem_usage_filter",
+        "min_mem_usage_ifft2",
     ]
     return discard_keys