PyPI - httomo-backends - Versions diffs - 0.7.2__py3-none-any.whl → 0.9.0__py3-none-any.whl - Mend

httomo-backends 0.7.2py3-none-any.whl → 0.9.0py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (39) hide show

httomo_backends/methods_database/packages/backends/httomolib/httomolib.yaml CHANGED Viewed

@@ -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/methods_database/packages/backends/httomolib/httomolib_modules.yaml CHANGED Viewed

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

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

@@ -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/methods_database/packages/backends/httomolibgpu/httomolibgpu_modules.yaml CHANGED Viewed

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

httomo_backends/methods_database/packages/backends/httomolibgpu/supporting_funcs/prep/normalize.py CHANGED Viewed

@@ -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/methods_database/packages/backends/httomolibgpu/supporting_funcs/prep/phase.py CHANGED Viewed

@@ -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/methods_database/packages/backends/httomolibgpu/supporting_funcs/recon/algorithm.py CHANGED Viewed

@@ -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/pipelines_full/FBP2d_astra_directive.yaml CHANGED Viewed

@@ -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/pipelines_full/FBP3d_tomobar_denoising_directive.yaml CHANGED Viewed

@@ -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/pipelines_full/FBP3d_tomobar_directive.yaml CHANGED Viewed

@@ -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/pipelines_full/FBP3d_tomobar_noimagesaving_directive.yaml CHANGED Viewed

@@ -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/pipelines_full/FISTA3d_tomobar_directive.yaml CHANGED Viewed

@@ -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/pipelines_full/LPRec3d_tomobar_directive.yaml CHANGED Viewed

@@ -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/pipelines_full/deg360_distortion_FBP3d_tomobar_directive.yaml CHANGED Viewed

@@ -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/pipelines_full/deg360_paganin_FBP3d_tomobar_directive.yaml CHANGED Viewed

@@ -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/pipelines_full/sweep_center_FBP3d_tomobar_directive.yaml CHANGED Viewed

@@ -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/pipelines_full/sweep_paganin_FBP3d_tomobar_directive.yaml CHANGED Viewed

@@ -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/pipelines_full/titaren_center_pc_FBP3d_resample_directive.yaml CHANGED Viewed

@@ -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/scripts/yaml_pipelines_generator.py CHANGED Viewed

@@ -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/scripts/yaml_templates_generator.py CHANGED Viewed

@@ -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

httomo_backends/yaml_templates/httomo/httomo.data.hdf.loaders/standard_tomo.yaml CHANGED Viewed

@@ -15,3 +15,4 @@
         stop: null
     darks: null
     flats: null
+    continuous_scan_subset: null

httomo_backends/yaml_templates/httomolib/httomolib.misc.utils/data_checker.yaml ADDED Viewed

@@ -0,0 +1,7 @@
+- method: data_checker
+  module_path: httomolib.misc.utils
+  parameters:
+    infsnans_correct: true
+    zeros_warning: false
+    data_to_method_name: null
+    verbosity: true

httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.misc.utils/data_checker.yaml ADDED Viewed

@@ -0,0 +1,7 @@
+- method: data_checker
+  module_path: httomolibgpu.misc.utils
+  parameters:
+    infsnans_correct: true
+    zeros_warning: false
+    data_to_method_name: null
+    verbosity: true

httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.normalize/{normalize.yaml → dark_flat_field_correction.yaml} RENAMED Viewed

@@ -1,9 +1,6 @@
-- method: normalize
+- method: dark_flat_field_correction
   module_path: httomolibgpu.prep.normalize
   parameters:
     flats_multiplier: 1.0
     darks_multiplier: 1.0
     cutoff: 10.0
-    minus_log: true
-    nonnegativity: false
-    remove_nans: false

httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.normalize/minus_log.yaml ADDED Viewed

@@ -0,0 +1,3 @@
+- method: minus_log
+  module_path: httomolibgpu.prep.normalize
+  parameters: {}

httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.phase/paganin_filter.yaml ADDED Viewed

@@ -0,0 +1,7 @@
+- method: paganin_filter
+  module_path: httomolibgpu.prep.phase
+  parameters:
+    pixel_size: 1.28
+    distance: 1.0
+    energy: 53.0
+    ratio_delta_beta: 250

httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.phase/paganin_filter_savu_legacy.yaml ADDED Viewed

@@ -0,0 +1,7 @@
+- method: paganin_filter_savu_legacy
+  module_path: httomolibgpu.prep.phase
+  parameters:
+    pixel_size: 1.28
+    distance: 1.0
+    energy: 53.0
+    ratio_delta_beta: 250

httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/CGLS3d_tomobar.yaml CHANGED Viewed

@@ -7,4 +7,3 @@
     recon_mask_radius: 0.95
     iterations: 20
     nonnegativity: true
-    neglog: false

httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/FBP2d_astra.yaml CHANGED Viewed

@@ -8,4 +8,3 @@
     filter_d: null
     recon_size: null
     recon_mask_radius: 0.95
-    neglog: false

httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/FBP3d_tomobar.yaml CHANGED Viewed

@@ -6,4 +6,3 @@
     filter_freq_cutoff: 0.35
     recon_size: null
     recon_mask_radius: 0.95
-    neglog: false

httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/FISTA3d_tomobar.yaml CHANGED Viewed

@@ -12,4 +12,3 @@
     regularisation_iterations: 50
     regularisation_half_precision: true
     nonnegativity: true
-    neglog: false

httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/LPRec3d_tomobar.yaml CHANGED Viewed

@@ -7,8 +7,3 @@
     filter_freq_cutoff: 1.0
     recon_size: null
     recon_mask_radius: 0.95
-    power_of_2_oversampling: true
-    power_of_2_cropping: true
-    min_mem_usage_filter: false
-    min_mem_usage_ifft2: false
-    neglog: false

httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/SIRT3d_tomobar.yaml CHANGED Viewed

@@ -7,4 +7,3 @@
     recon_mask_radius: 0.95
     iterations: 300
     nonnegativity: true
-    neglog: false

{httomo_backends-0.7.2.dist-info → httomo_backends-0.9.0.dist-info}/METADATA RENAMED Viewed

@@ -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.dist-info → httomo_backends-0.9.0.dist-info}/RECORD RENAMED Viewed

@@ -4,11 +4,11 @@ httomo_backends/methods_database/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRk
 httomo_backends/methods_database/query.py,sha256=8jZQTmE351Me0Todn3NzyIjfZhLkzoJmagFGWAegYDw,5890
 httomo_backends/methods_database/packages/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 httomo_backends/methods_database/packages/httomo.yaml,sha256=tI3D-7IJcdu4EbKwjsje5MVKihOr3oswHzOrxtpBYBQ,535
-httomo_backends/methods_database/packages/backends/httomolib/httomolib.yaml,sha256=8l2Z6GGlXIIe2vcX85GK4wis5zxhgmg7EmlwLMV_rtI,938
-httomo_backends/methods_database/packages/backends/httomolib/httomolib_modules.yaml,sha256=tbvivxcAc90Wu36v1yFnGN-WqBIA1NHGWrg_D28UXi8,117
+httomo_backends/methods_database/packages/backends/httomolib/httomolib.yaml,sha256=JMi2qB1HAYN9yjoS9M_qjcVERIGN6Ok7oVsERfY7syE,1119
+httomo_backends/methods_database/packages/backends/httomolib/httomolib_modules.yaml,sha256=LnjKM2EnAhmC7L_yXi_Mg5hhSWc35sGFhlH1PP1FI-8,140
 httomo_backends/methods_database/packages/backends/httomolibgpu/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-httomo_backends/methods_database/packages/backends/httomolibgpu/httomolibgpu.yaml,sha256=Y1a3J_OCeojiG4HhbRPkDdJ0KvdpGARkEk6k5OcIzHY,5347
-httomo_backends/methods_database/packages/backends/httomolibgpu/httomolibgpu_modules.yaml,sha256=HZWQ74Ygi25hjNg7wR9muPDdmN8STtOMY-LXWaTfspc,282
+httomo_backends/methods_database/packages/backends/httomolibgpu/httomolibgpu.yaml,sha256=8l7bCXVegTaRM1T6UZ69MWCuTpDD7EeEkHhND4ibW5E,6055
+httomo_backends/methods_database/packages/backends/httomolibgpu/httomolibgpu_modules.yaml,sha256=i58Fb01apGyJQxc3_xxDtvHuzcQAB7AdXkHPs_0q85E,308
 httomo_backends/methods_database/packages/backends/httomolibgpu/supporting_funcs/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 httomo_backends/methods_database/packages/backends/httomolibgpu/supporting_funcs/misc/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 httomo_backends/methods_database/packages/backends/httomolibgpu/supporting_funcs/misc/corr.py,sha256=rwO9JEyefb4_6cgqn3MkFtoiDloO9N2cYqTNgVTU_A0,417
@@ -16,11 +16,11 @@ httomo_backends/methods_database/packages/backends/httomolibgpu/supporting_funcs
 httomo_backends/methods_database/packages/backends/httomolibgpu/supporting_funcs/misc/morph.py,sha256=FVqYI5iCmHJyLfHmgltIh7PPWr-cMK3Tpcs4EnCrqjc,4323
 httomo_backends/methods_database/packages/backends/httomolibgpu/supporting_funcs/misc/rescale.py,sha256=iFE8X-GR9zjuFLbBE_glQL8wMoXOjkzcaleflm8VVzA,574
 httomo_backends/methods_database/packages/backends/httomolibgpu/supporting_funcs/prep/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-httomo_backends/methods_database/packages/backends/httomolibgpu/supporting_funcs/prep/normalize.py,sha256=Ekxyp3j5bpg2-4iZmXI49VEBFFYUV6rfYBEqGdaqV6M,645
-httomo_backends/methods_database/packages/backends/httomolibgpu/supporting_funcs/prep/phase.py,sha256=kYznizW0jMVJdGyuE10McVLsWWggUsP5bvJiHEVvSSM,4075
+httomo_backends/methods_database/packages/backends/httomolibgpu/supporting_funcs/prep/normalize.py,sha256=EdUrUZ1TWKUzKAFwoml_A7v6nchrRbAnElUGbA5xwHQ,679
+httomo_backends/methods_database/packages/backends/httomolibgpu/supporting_funcs/prep/phase.py,sha256=ph02VlQnvkO9GPetUGsh89RbAtgyElqgvjL5z8_ZUXo,4360
 httomo_backends/methods_database/packages/backends/httomolibgpu/supporting_funcs/prep/stripe.py,sha256=KnS8IpcXaLeiIWr4qAKwOrcK1vS9zrU6u5gOITZ159k,4623
 httomo_backends/methods_database/packages/backends/httomolibgpu/supporting_funcs/recon/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-httomo_backends/methods_database/packages/backends/httomolibgpu/supporting_funcs/recon/algorithm.py,sha256=Jq4gp0NDuixGcOD1oHGJg0Vjg58JPVwisaMIb5JYqX8,21529
+httomo_backends/methods_database/packages/backends/httomolibgpu/supporting_funcs/recon/algorithm.py,sha256=76Fl19BNMm2mo1gciAe_08QWSe5xmU5R2cpTFjelha0,21931
 httomo_backends/methods_database/packages/backends/httomolibgpu/supporting_funcs/recon/peak_memory_line_profile_hook.py,sha256=hb-CyqD5TKxDg6Rg5fvFeXIO2nvjbp_XMTeRdJZ8ONo,6347
 httomo_backends/methods_database/packages/backends/tomopy/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 httomo_backends/methods_database/packages/backends/tomopy/tomopy.yaml,sha256=URe18BAV1EbGLil53t88T42BuKSiUHz6r3uzs_wo8Ug,11215
@@ -32,26 +32,26 @@ httomo_backends/methods_database/packages/backends/tomopy/supporting_funcs/prep/
 httomo_backends/methods_database/packages/backends/tomopy/supporting_funcs/prep/stripe.py,sha256=SzQRDvKrWKMIyQtF4PHhtk0t6GCX3nltZSkepKQhvV8,1725
 httomo_backends/methods_database/packages/backends/tomopy/supporting_funcs/recon/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 httomo_backends/methods_database/packages/backends/tomopy/supporting_funcs/recon/algorithm.py,sha256=0v_zIq46Tm55Rm46s3GZhXZ-V07sf_YgbA-qv3AVT-c,1385
-httomo_backends/pipelines_full/FBP2d_astra_directive.yaml,sha256=BAT4wUa3nOacHRAStkeUgOfp1gMizsQnMaBISSMZlIo,261
-httomo_backends/pipelines_full/FBP3d_tomobar_denoising_directive.yaml,sha256=Ycu8X7mS2n872e0ji4btPLjSTYgEhcZVPeMEeI6MPAk,644
-httomo_backends/pipelines_full/FBP3d_tomobar_directive.yaml,sha256=QyqyAmWZjmcgV0PjhgmZtSjytHt8BeRLncH4hkJRmcs,574
-httomo_backends/pipelines_full/FBP3d_tomobar_noimagesaving_directive.yaml,sha256=uute7GdEEshbnmljjeyDi3Z5aqZftBTvo7Ti4wKgzhk,403
-httomo_backends/pipelines_full/FISTA3d_tomobar_directive.yaml,sha256=xuBtnN3vT2tfpKwmW0CH12CRXeV2evNN2hpdPul9L6c,445
-httomo_backends/pipelines_full/LPRec3d_tomobar_directive.yaml,sha256=c6c-cXCstUgLVqprfMFVdxzcTCeE8H-Dnhq7kmSIhYc,577
+httomo_backends/pipelines_full/FBP2d_astra_directive.yaml,sha256=jIsGyQiqBzNawY0pVVpfjNjdtHFAEiMoYW_UfjXfgBM,344
+httomo_backends/pipelines_full/FBP3d_tomobar_denoising_directive.yaml,sha256=Uh_2cZenybVwBqs7yTSAwse491buCrRnN7ch40ARSig,726
+httomo_backends/pipelines_full/FBP3d_tomobar_directive.yaml,sha256=avc7Sfy6rf3ejvJnTq5we2UDVG41xgOoto6r7iX2U50,657
+httomo_backends/pipelines_full/FBP3d_tomobar_noimagesaving_directive.yaml,sha256=Z2RqYrjAUJKCXkw0RaM_UwxawY0hnhMzQt9TgnIRCFo,483
+httomo_backends/pipelines_full/FISTA3d_tomobar_directive.yaml,sha256=zxQVf68XnP_QXelzdN2OneawZ4BpklqtDu3UDeaNeUI,527
+httomo_backends/pipelines_full/LPRec3d_tomobar_directive.yaml,sha256=f5uIcyufLcDDmLw6EC9VwsOpl0Dh2NARBUZ_4Fh7CiY,659
 httomo_backends/pipelines_full/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-httomo_backends/pipelines_full/deg360_distortion_FBP3d_tomobar_directive.yaml,sha256=3Ht3yAzi97VW29OfvDE9j_p3NYbZfHDlfZMuRivsdKo,676
-httomo_backends/pipelines_full/deg360_paganin_FBP3d_tomobar_directive.yaml,sha256=Qikcxqq_b3_9TpaOg5eSlYqfs1Vj9l30vx56cl5YoVI,660
-httomo_backends/pipelines_full/sweep_center_FBP3d_tomobar_directive.yaml,sha256=ERai5NvyAQz9-1EAdMUw3XkjlMvZhh6LCtXQpRh7mv4,277
-httomo_backends/pipelines_full/sweep_paganin_FBP3d_tomobar_directive.yaml,sha256=qoiY62uP5kHSL4qqSThJAaMwHq4PTN-dJSNRsBFxyQw,397
-httomo_backends/pipelines_full/titaren_center_pc_FBP3d_resample_directive.yaml,sha256=lhT-jE2karklr_-cgEyvPRYLVwNGJgpf8XBI1r1TMLc,574
+httomo_backends/pipelines_full/deg360_distortion_FBP3d_tomobar_directive.yaml,sha256=Hf-Gbemiv09CigWGqpezuKzcVa4e-TBc3GmpszCAxSw,758
+httomo_backends/pipelines_full/deg360_paganin_FBP3d_tomobar_directive.yaml,sha256=mI6LAgOmd5Vqcx8Dqtb0_NT2opBO-kIzBbUb7xvEFV0,670
+httomo_backends/pipelines_full/sweep_center_FBP3d_tomobar_directive.yaml,sha256=-RDXP6L_Z_6DYZITjeSPagJjhXuRXS0FeZrBrknSag8,359
+httomo_backends/pipelines_full/sweep_paganin_FBP3d_tomobar_directive.yaml,sha256=W071aoUsP7BGYzv2zq0f_ZouvoSSb4u0_Ky52NrEQgs,412
+httomo_backends/pipelines_full/titaren_center_pc_FBP3d_resample_directive.yaml,sha256=9tULNx9WIqaqlpYeA4z29F0r7Bbq-Sn4tiR92uepGbg,654
 httomo_backends/pipelines_full/tomopy_gridrec_directive.yaml,sha256=NlrX-mqyzjJvwGotTLwosBnC4d9pPRNB1JWFA7YXHuM,533
 httomo_backends/scripts/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 httomo_backends/scripts/json_pipelines_generator.py,sha256=iWTsYr1i0Ei77Imaml5HXWvZUUeX-tkU1WRIdxskV3M,8322
-httomo_backends/scripts/yaml_pipelines_generator.py,sha256=t_B3qJ0AGsjzd1_rSp76pC-9o4JbO7e28UIfWcN9olk,16393
-httomo_backends/scripts/yaml_templates_generator.py,sha256=NjE5q8YXxkXjA-9WTg4YB8ccawNA0veeJE1C8yyWqlI,8532
+httomo_backends/scripts/yaml_pipelines_generator.py,sha256=ZwJSOIgZksrEcQUD4lvvXG6LiWfsDp6qe9ew5AI1xI4,17285
+httomo_backends/scripts/yaml_templates_generator.py,sha256=I2RrpHeIO0SBh71aYYSeaZ_VrPhHMDxqn7sa6e1PeX8,8661
 httomo_backends/scripts/yaml_unsupported_tomopy_remove.py,sha256=R3ZAfFgpVsBWS7zBjLlU83-66nawo7EBegFsIAHBWmQ,3715
 httomo_backends/yaml_templates/httomo/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-httomo_backends/yaml_templates/httomo/httomo.data.hdf.loaders/standard_tomo.yaml,sha256=t81Y-sNTPwOu9UCwGUrTYjIHHSjjQVdtwpf5n7E6YHw,535
+httomo_backends/yaml_templates/httomo/httomo.data.hdf.loaders/standard_tomo.yaml,sha256=mFGaYZZrE_dft7FE9Ngm-vXsd3dTftgwwjmLUCUkEZM,568
 httomo_backends/yaml_templates/httomo/httomo.methods/calculate_stats.yaml,sha256=rG4e2yEJ2flK-tGRj1FbRWXnSHNWYrShzMaPznbObdw,133
 httomo_backends/yaml_templates/httomo/httomo.methods/save_intermediate_data.yaml,sha256=pEUY6KqGVKdUWIfRob1CP-qTmsl7pjCM_NtsA0mnjj4,219
 httomo_backends/yaml_templates/httomolib/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -59,6 +59,7 @@ httomo_backends/yaml_templates/httomolib/httomolib.misc.images/save_to_images.ya
 httomo_backends/yaml_templates/httomolib/httomolib.misc.morph/data_reducer.yaml,sha256=RYCat3aMz6fr57Y2zeHVVJwXQDrU-ihV2eqV9MyBOPk,105
 httomo_backends/yaml_templates/httomolib/httomolib.misc.rescale/rescale_to_int.yaml,sha256=UoMe5tiq531UyE0NOCTcu1MRLDq74sokHSHaK-r7Dog,195
 httomo_backends/yaml_templates/httomolib/httomolib.misc.segm/binary_thresholding.yaml,sha256=12oWhXFxBF0kAhnRdlsKB3ewI5GJ-qWKOKv3JTM8xxI,154
+httomo_backends/yaml_templates/httomolib/httomolib.misc.utils/data_checker.yaml,sha256=8UwM4K_u3KITvYtgKEXDC7h2LvZQJlRcmJqlgbf3p1g,175
 httomo_backends/yaml_templates/httomolib/httomolib.prep.phase/paganin_filter.yaml,sha256=Y02ifIbl9SS_qtqT_G7SA40MAmKeAYJ9fHSAP21_ECc,147
 httomo_backends/yaml_templates/httomolibgpu/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.misc.corr/median_filter.yaml,sha256=vKTeGhT0eLXWMDBvfglisIIZINlBKagOjwRo4JFQRpQ,108
@@ -68,19 +69,22 @@ httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.misc.denoise/total_vari
 httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.misc.morph/data_resampler.yaml,sha256=4fDcC2seGd_TFUyMG0DAs68NrJn5lmIsx7WQ_6bn-A4,142
 httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.misc.morph/sino_360_to_180.yaml,sha256=vikNDlp_Py6kye8-dySMpCxhYlJp_-AODQNGHTQCarQ,171
 httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.misc.rescale/rescale_to_int.yaml,sha256=WR_exoyowYnXgDOUH5JYGPQ17-MfUayuVkNwMQTHzac,198
+httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.misc.utils/data_checker.yaml,sha256=edpl5jnuYWKL11LkqkekfMbkBXeYdMJxeBgFYTRLfu0,178
 httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.alignment/distortion_correction_proj_discorpy.yaml,sha256=KxWTzuZOoHUymFt4OJZVT7jhPs6oAuUmSQskQJqKwZk,163
-httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.normalize/normalize.yaml,sha256=PIfA4jwCmnWtz7V5n0Zng8lPvD4h1YyIriBSL39CtVM,214
-httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.phase/paganin_filter_tomopy.yaml,sha256=sHWZibK7drnBufYVOND9LZATaBRMtHKkbbBoquCBcmE,157
+httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.normalize/dark_flat_field_correction.yaml,sha256=2ZVyqLaxVOJcyCZ3aCZP97g9iHOPZVeDs46VZFRpQpg,163
+httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.normalize/minus_log.yaml,sha256=qQKxL4hXjpqZDOEqFr-eru6_R9giQXTF3h2KsXVwBOg,80
+httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.phase/paganin_filter.yaml,sha256=7UVaKZD9JpVguIZONF3Q1wieqHAsE323tzCTEIW7WdA,160
+httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.phase/paganin_filter_savu_legacy.yaml,sha256=xj9kPKDJPQnMOHSLVfJQzu-DiphU9MtOIaWqZIOZLwk,172
 httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.stripe/raven_filter.yaml,sha256=SDqgP_RLq7jjnL9Fz7hfrKko4F7-yahCsabBIJ0XMC8,169
 httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.stripe/remove_all_stripe.yaml,sha256=MfoMeF_C2zRE7-W5cknhmG9-a5QYb5lpSdz9dwOndJQ,138
 httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.stripe/remove_stripe_based_sorting.yaml,sha256=xyv_XKqFhs801VcsMUfWPHiKvek0qh8RhkbnInWR5i8,116
 httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.stripe/remove_stripe_ti.yaml,sha256=5Ed2YbB0Kf-08_nNP5dzTukNDZopRTOo1I6ODJVRrlM,95
-httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/CGLS3d_tomobar.yaml,sha256=oWoW2vYNXyAeQ81NaV865A0K8XDi3QIbzV9WcRQqi_A,276
-httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/FBP2d_astra.yaml,sha256=MxUbW-dMxMrI4Exn5mgh2ovie4Ldv1Eb-zS68ETsNCU,301
-httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/FBP3d_tomobar.yaml,sha256=H9-PTd8qW2qXqgHYw-NfZGgy2yut7ReKsbsR3x0_OOA,261
-httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/FISTA3d_tomobar.yaml,sha256=i2K7Yc19VY6uZZR8bVjb85jpWIShlM_yCGD-Z5Eb-5E,442
-httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/LPRec3d_tomobar.yaml,sha256=mm3vUiZbLm-KtxjN1VL0LtMaWHdHHolpFFQc1OPkuZk,412
-httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/SIRT3d_tomobar.yaml,sha256=oom622LQ8xAZbZiHm4t0PSKKsMkX5G743vVBqRbMQek,277
+httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/CGLS3d_tomobar.yaml,sha256=Hv1hPa0Q_9Ck_gEDqhcOC06zygIunsvcRPQKy-z2Ia8,258
+httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/FBP2d_astra.yaml,sha256=QTtdZkiDpbPODWanCtVRMEwn_q7qJmbDS5Pis8OzlzE,283
+httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/FBP3d_tomobar.yaml,sha256=vMc5nKi5kCv4b0uEc8L-rX7vY78uG6aWBAxvaHnmrQs,243
+httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/FISTA3d_tomobar.yaml,sha256=ZudW6q9poUfsfWpWn_TPSVvPeBIXsshb5fuVfYXhgKg,424
+httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/LPRec3d_tomobar.yaml,sha256=cwARAcP_-YbNuDr6qtFU_uL0_00rcETyMNaPFa2CcLs,267
+httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/SIRT3d_tomobar.yaml,sha256=yuZVlfD-XrPjcMYqi4QDrbmPKSullbGNU8mulVSRW-4,259
 httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.rotation/find_center_360.yaml,sha256=nXjbgTBDQcIlBWvXwMd8FoNimtq-8QabgNWAI-fiFU8,322
 httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.rotation/find_center_pc.yaml,sha256=g3CNIaLhhBI6igluIMwytFqVXzrDlv8A1EU1C7ey4FE,208
 httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.rotation/find_center_vo.yaml,sha256=CmJ_0a73jX7MmOxQIvQrrKg_2HEtK0MXNVXLrfR3caU,296
@@ -144,8 +148,8 @@ httomo_backends/yaml_templates/tomopy/tomopy.sim.project/add_zingers.yaml,sha256
 httomo_backends/yaml_templates/tomopy/tomopy.sim.project/project.yaml,sha256=XBVhW5ZxT9C89tHcwDG7OOgcWNdNtQq97mqlBEoiMnU,202
 httomo_backends/yaml_templates/tomopy/tomopy.sim.project/project2.yaml,sha256=5raeQ-w9nS9mbAzn2ZqhPjdcyfLOkkJflKNStdEnYRA,238
 httomo_backends/yaml_templates/tomopy/tomopy.sim.project/project3.yaml,sha256=oyofKSMi-_dSpfjrKVMNDqoBhBCCSYbEVRz2Lsc8uTI,257
-httomo_backends-0.7.2.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-httomo_backends-0.7.2.dist-info/METADATA,sha256=F0PpEdrCwHMrpibOI1lUZczembzVccVwj_-j1mtbu4E,2272
-httomo_backends-0.7.2.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-httomo_backends-0.7.2.dist-info/top_level.txt,sha256=v4x8d4CeEyMwo8QoqIvL_p-WoXAVD1bVnASPIrLjSTg,16
-httomo_backends-0.7.2.dist-info/RECORD,,
+httomo_backends-0.9.0.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+httomo_backends-0.9.0.dist-info/METADATA,sha256=vDm2PjePbvsEYF3U0YGYaK8Yx7Y6ukqXQ8eQgcZ-3bM,2272
+httomo_backends-0.9.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+httomo_backends-0.9.0.dist-info/top_level.txt,sha256=v4x8d4CeEyMwo8QoqIvL_p-WoXAVD1bVnASPIrLjSTg,16
+httomo_backends-0.9.0.dist-info/RECORD,,

httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.phase/paganin_filter_tomopy.yaml DELETED Viewed

@@ -1,7 +0,0 @@
-- method: paganin_filter_tomopy
-  module_path: httomolibgpu.prep.phase
-  parameters:
-    pixel_size: 0.0001
-    dist: 50.0
-    energy: 53.0
-    alpha: 0.001

{httomo_backends-0.7.2.dist-info → httomo_backends-0.9.0.dist-info}/WHEEL RENAMED Viewed

File without changes

{httomo_backends-0.7.2.dist-info → httomo_backends-0.9.0.dist-info}/licenses/LICENSE RENAMED Viewed

File without changes

{httomo_backends-0.7.2.dist-info → httomo_backends-0.9.0.dist-info}/top_level.txt RENAMED Viewed

File without changes

httomo-backends 0.7.2__py3-none-any.whl → 0.9.0__py3-none-any.whl

httomo-backends 0.7.2py3-none-any.whl → 0.9.0py3-none-any.whl