httomo-backends 0.7.1__py3-none-any.whl → 0.8.0__py3-none-any.whl

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

@@ -78,7 +78,7 @@ prep:
         multiplier: None
         method: module
   phase:
-    paganin_filter_tomopy:
+    paganin_filter:
       pattern: projection
       output_dims_change: False
       implementation: gpu_cupy

httomo_backends/methods_database/packages/backends/httomolibgpu/supporting_funcs/prep/phase.py

@@ -20,23 +20,21 @@
 # ---------------------------------------------------------------------------
 """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",
 ]
 
 
-def _calc_memory_bytes_paganin_filter_tomopy(
+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 +42,7 @@ 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 +105,7 @@ 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

@@ -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:
@@ -197,6 +197,9 @@ def _calc_memory_bytes_LPRec3d_tomobar(
     min_mem_usage_ifft2 = False
     if "min_mem_usage_ifft2" in kwargs:
         min_mem_usage_ifft2 = kwargs["min_mem_usage_ifft2"]
+    power_of_2_cropping = False
+    if "power_of_2_cropping" in kwargs:
+        power_of_2_cropping = kwargs["power_of_2_cropping"]
 
     angles_tot = non_slice_dims_shape[0]
     DetectorsLengthH_prepad = non_slice_dims_shape[1]
@@ -205,6 +208,10 @@ def _calc_memory_bytes_LPRec3d_tomobar(
     _CENTER_SIZE_MIN = 192  # must be divisible by 8
 
     n = DetectorsLengthH
+    if power_of_2_cropping:
+        n_pow2 = 2 ** math.ceil(math.log2(n))
+        if 0.9 < n / n_pow2:
+            n = n_pow2
 
     odd_horiz = False
     if (n % 2) != 0:
@@ -302,10 +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
@@ -344,38 +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)
@@ -426,7 +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
@@ -449,7 +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
@@ -476,7 +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
@@ -528,7 +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
@@ -567,5 +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/deg360_paganin_FBP3d_tomobar_directive.yaml

@@ -8,7 +8,7 @@
   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_paganin_FBP3d_tomobar_directive.yaml

@@ -4,9 +4,9 @@
   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/scripts/yaml_pipelines_generator.py

@@ -138,7 +138,7 @@ 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 +157,7 @@ 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 +169,7 @@ 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 +182,7 @@ 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
@@ -223,7 +223,7 @@ 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
@@ -236,7 +236,7 @@ def yaml_pipelines_generator(
                 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.",
+                    comment="If Paganin method is used bellow, set it to 'false'.",
                 )
             elif "phase" in module_name:
                 pipeline_full.yaml_set_comment_before_after_key(
@@ -246,8 +246,20 @@ 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 +281,11 @@ 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 +296,7 @@ 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/yaml_templates/httomolibgpu/httomolibgpu.prep.phase/paganin_filter.yaml

@@ -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.recon.algorithm/LPRec3d_tomobar.yaml

@@ -8,6 +8,7 @@
     recon_size: null
     recon_mask_radius: 0.95
     power_of_2_oversampling: true
-    min_mem_usage_filter: false
-    min_mem_usage_ifft2: false
+    power_of_2_cropping: false
+    min_mem_usage_filter: true
+    min_mem_usage_ifft2: true
     neglog: false

{httomo_backends-0.7.1.dist-info → httomo_backends-0.8.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: httomo-backends
-Version: 0.7.1
+Version: 0.8.0
 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
@@ -22,7 +22,6 @@ Requires-Dist: h5py
 Requires-Dist: astra-toolbox
 Requires-Dist: tomobar
 Requires-Dist: scikit-image
-Requires-Dist: ccpi-regularisation-cupy
 Provides-Extra: dev
 Requires-Dist: pytest; extra == "dev"
 Requires-Dist: pytest-mock; extra == "dev"

{httomo_backends-0.7.1.dist-info → httomo_backends-0.8.0.dist-info}/RECORD

@@ -7,7 +7,7 @@ httomo_backends/methods_database/packages/httomo.yaml,sha256=tI3D-7IJcdu4EbKwjsj
 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/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.yaml,sha256=OCAjJSM5PlfkN3kkXKW9QWhr1WGWfFIToNUQFrj_dFQ,5340
 httomo_backends/methods_database/packages/backends/httomolibgpu/httomolibgpu_modules.yaml,sha256=HZWQ74Ygi25hjNg7wR9muPDdmN8STtOMY-LXWaTfspc,282
 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
@@ -17,10 +17,10 @@ httomo_backends/methods_database/packages/backends/httomolibgpu/supporting_funcs
 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/phase.py,sha256=gzrQJ-T2iBqhlWq3LmXKn_sLK5K__u1LtxoZYZjBDsQ,4070
 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=CuiMAxu7qG0I41XiucrvSf2kZHjid_dgD0gUXF9cE0k,21267
+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
@@ -40,14 +40,14 @@ httomo_backends/pipelines_full/FISTA3d_tomobar_directive.yaml,sha256=xuBtnN3vT2t
 httomo_backends/pipelines_full/LPRec3d_tomobar_directive.yaml,sha256=c6c-cXCstUgLVqprfMFVdxzcTCeE8H-Dnhq7kmSIhYc,577
 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/deg360_paganin_FBP3d_tomobar_directive.yaml,sha256=q15zplcnr4i5EFw4F0pi2-dhqxvOkhLyAjqnVQMnoi0,653
 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/sweep_paganin_FBP3d_tomobar_directive.yaml,sha256=Y1K7Dl_Bs_6nU_oBGEEchn3l8TL0VSKq023IDQU4ZPo,395
 httomo_backends/pipelines_full/titaren_center_pc_FBP3d_resample_directive.yaml,sha256=lhT-jE2karklr_-cgEyvPRYLVwNGJgpf8XBI1r1TMLc,574
 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_pipelines_generator.py,sha256=nY66CcAc2HK8ViUyOEk1ezQsEEVylD3HfhfWkaA6e3k,17030
 httomo_backends/scripts/yaml_templates_generator.py,sha256=NjE5q8YXxkXjA-9WTg4YB8ccawNA0veeJE1C8yyWqlI,8532
 httomo_backends/scripts/yaml_unsupported_tomopy_remove.py,sha256=R3ZAfFgpVsBWS7zBjLlU83-66nawo7EBegFsIAHBWmQ,3715
 httomo_backends/yaml_templates/httomo/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -70,7 +70,7 @@ httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.misc.morph/sino_360_to_
 httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.misc.rescale/rescale_to_int.yaml,sha256=WR_exoyowYnXgDOUH5JYGPQ17-MfUayuVkNwMQTHzac,198
 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.phase/paganin_filter.yaml,sha256=7UVaKZD9JpVguIZONF3Q1wieqHAsE323tzCTEIW7WdA,160
 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
@@ -79,7 +79,7 @@ httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/CGLS3d_
 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=X_qcuTOcFW_rXaXU-XhZYQUaPkOgKe5r7uX5stpf1mE,382
+httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/LPRec3d_tomobar.yaml,sha256=qqHNsYxW4D3QggXkJQGFSLKZ0mR4h_LIxR379g51HVc,411
 httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/SIRT3d_tomobar.yaml,sha256=oom622LQ8xAZbZiHm4t0PSKKsMkX5G743vVBqRbMQek,277
 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
@@ -144,8 +144,8 @@ 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-0.7.1.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-httomo_backends-0.7.1.dist-info/METADATA,sha256=fifr2fnWW5CvPDXWR1WA-9McdqN4LCbmtWW_QRf7BUI,2312
-httomo_backends-0.7.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-httomo_backends-0.7.1.dist-info/top_level.txt,sha256=v4x8d4CeEyMwo8QoqIvL_p-WoXAVD1bVnASPIrLjSTg,16
-httomo_backends-0.7.1.dist-info/RECORD,,
+httomo_backends-0.8.0.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+httomo_backends-0.8.0.dist-info/METADATA,sha256=G9IVCwxGSE39qlVAwr1LCubkFrjMeJHUXDuOuqnjqYU,2272
+httomo_backends-0.8.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+httomo_backends-0.8.0.dist-info/top_level.txt,sha256=v4x8d4CeEyMwo8QoqIvL_p-WoXAVD1bVnASPIrLjSTg,16
+httomo_backends-0.8.0.dist-info/RECORD,,

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

@@ -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