httomo-backends 0.9.1__py3-none-any.whl → 1.0.1__py3-none-any.whl

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

@@ -135,6 +135,15 @@ prep:
       memory_gpu:
         multiplier: 1.17
         method: direct
+    remove_stripe_fw:
+      pattern: sinogram
+      output_dims_change: False
+      implementation: gpu_cupy
+      save_result_default: False
+      padding: False
+      memory_gpu:
+        multiplier: None
+        method: iterative
     remove_stripe_ti:
       pattern: sinogram
       output_dims_change: False

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

@@ -25,9 +25,11 @@ from typing import Tuple
 import numpy as np
 
 from httomo_backends.cufft import CufftType, cufft_estimate_1d
+from httomolibgpu.prep.stripe import remove_stripe_fw
 
 
 __all__ = [
+    "_calc_memory_bytes_for_slices_remove_stripe_fw",
     "_calc_memory_bytes_remove_stripe_ti",
     "_calc_memory_bytes_remove_all_stripe",
     "_calc_memory_bytes_raven_filter",
@@ -53,6 +55,14 @@ def _calc_memory_bytes_remove_stripe_ti(
     return (tot_memory_bytes, gamma_mem)
 
 
+def _calc_memory_bytes_for_slices_remove_stripe_fw(
+    dims_shape: Tuple[int, int, int],
+    dtype: np.dtype,
+    **kwargs,
+) -> int:
+    return remove_stripe_fw(dims_shape, calc_peak_gpu_mem=True, **kwargs)
+
+
 def _calc_memory_bytes_remove_all_stripe(
     non_slice_dims_shape: Tuple[int, int],
     dtype: np.dtype,

httomo_backends/scripts/yaml_pipelines_generator.py

@@ -265,6 +265,14 @@ def yaml_pipelines_generator(
                     key="energy",
                     comment="Beam energy in keV.",
                 )
+                pipeline_full[i]["parameters"].yaml_add_eol_comment(
+                    key="calculate_padding_value_method",
+                    comment="Select type of padding from 'next_power_of_2', 'next_fast_length' and 'use_pad_x_y'.",
+                )
+                pipeline_full[i]["parameters"].yaml_add_eol_comment(
+                    key="pad_x_y",
+                    comment="Manual padding is enabled when 'calculate_padding_value_method' is set to 'use_pad_x_y'.",
+                )
             elif "stripe" in module_name:
                 pipeline_full.yaml_set_comment_before_after_key(
                     i,

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

@@ -5,3 +5,5 @@
     distance: 1.0
     energy: 53.0
     ratio_delta_beta: 250
+    calculate_padding_value_method: next_power_of_2
+    pad_x_y: null

httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.stripe/remove_stripe_fw.yaml

@@ -0,0 +1,6 @@
+- method: remove_stripe_fw
+  module_path: httomolibgpu.prep.stripe
+  parameters:
+    sigma: 2
+    wname: db5
+    level: null

{httomo_backends-0.9.1.dist-info → httomo_backends-1.0.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: httomo-backends
-Version: 0.9.1
+Version: 1.0.1
 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-0.9.1.dist-info → httomo_backends-1.0.1.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=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=aURnvUvHB7dfrUsUi9QJyHKhAbDnzFaIEbhsnLaDhzo,6061
+httomo_backends/methods_database/packages/backends/httomolibgpu/httomolibgpu.yaml,sha256=p090iNoIQQo9VEyVe4b8u3kTtd9e0DHIR6ekoH5aRAA,6293
 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
@@ -18,7 +18,7 @@ httomo_backends/methods_database/packages/backends/httomolibgpu/supporting_funcs
 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=EdUrUZ1TWKUzKAFwoml_A7v6nchrRbAnElUGbA5xwHQ,679
 httomo_backends/methods_database/packages/backends/httomolibgpu/supporting_funcs/prep/phase.py,sha256=LCj4iNuZjtrDwvL21ilfWGem4uXm2bUPEk30cZEyuN4,1759
-httomo_backends/methods_database/packages/backends/httomolibgpu/supporting_funcs/prep/stripe.py,sha256=KnS8IpcXaLeiIWr4qAKwOrcK1vS9zrU6u5gOITZ159k,4623
+httomo_backends/methods_database/packages/backends/httomolibgpu/supporting_funcs/prep/stripe.py,sha256=cVISJkAkC3eLteUS7AtRUot5mWWoeGIjCfcJXyZ3RI8,4942
 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=76Fl19BNMm2mo1gciAe_08QWSe5xmU5R2cpTFjelha0,21931
 httomo_backends/methods_database/packages/backends/httomolibgpu/supporting_funcs/recon/peak_memory_line_profile_hook.py,sha256=hb-CyqD5TKxDg6Rg5fvFeXIO2nvjbp_XMTeRdJZ8ONo,6347
@@ -47,7 +47,7 @@ httomo_backends/pipelines_full/titaren_center_pc_FBP3d_resample_directive.yaml,s
 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=ZwJSOIgZksrEcQUD4lvvXG6LiWfsDp6qe9ew5AI1xI4,17285
+httomo_backends/scripts/yaml_pipelines_generator.py,sha256=Tsmb_J5hSZGzveJsITECCzAOcmDtRLJTd_Bhr7OSJNc,17788
 httomo_backends/scripts/yaml_templates_generator.py,sha256=Bb6qOPYRGiSZujMk65A59zCzuLZqSPkbZL3B-ypxX4k,8690
 httomo_backends/scripts/yaml_unsupported_tomopy_remove.py,sha256=R3ZAfFgpVsBWS7zBjLlU83-66nawo7EBegFsIAHBWmQ,3715
 httomo_backends/yaml_templates/httomo/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -73,11 +73,12 @@ httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.misc.utils/data_checker
 httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.alignment/distortion_correction_proj_discorpy.yaml,sha256=KxWTzuZOoHUymFt4OJZVT7jhPs6oAuUmSQskQJqKwZk,163
 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.yaml,sha256=-B9aQIiTe_93wwyxWGUFz5h6q0R2ClCA2QDpY9W-zkI,230
 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_fw.yaml,sha256=9E0w7T2O0WQI_n-eGH5GIK8Hk6E42BmxfC3KI0Tqit8,125
 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=Hv1hPa0Q_9Ck_gEDqhcOC06zygIunsvcRPQKy-z2Ia8,258
 httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/FBP2d_astra.yaml,sha256=QTtdZkiDpbPODWanCtVRMEwn_q7qJmbDS5Pis8OzlzE,283
@@ -148,8 +149,8 @@ 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-0.9.1.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-httomo_backends-0.9.1.dist-info/METADATA,sha256=OlXNJspw7aBRdZ3L4yC_-_q4yFhuKpg0we2tjMiQAXo,2272
-httomo_backends-0.9.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-httomo_backends-0.9.1.dist-info/top_level.txt,sha256=v4x8d4CeEyMwo8QoqIvL_p-WoXAVD1bVnASPIrLjSTg,16
-httomo_backends-0.9.1.dist-info/RECORD,,
+httomo_backends-1.0.1.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+httomo_backends-1.0.1.dist-info/METADATA,sha256=Gnv8VDTY7cQJ8R_0d-GI_3ZqKw-XBE1cs-dnJBXkg8c,2272
+httomo_backends-1.0.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+httomo_backends-1.0.1.dist-info/top_level.txt,sha256=v4x8d4CeEyMwo8QoqIvL_p-WoXAVD1bVnASPIrLjSTg,16
+httomo_backends-1.0.1.dist-info/RECORD,,