httomo-backends 0.9.1__tar.gz → 1.0.1__tar.gz

{httomo_backends-0.9.1 → httomo_backends-1.0.1}/PKG-INFO

@@ -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 → httomo_backends-1.0.1}/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-0.9.1 → httomo_backends-1.0.1}/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-0.9.1 → httomo_backends-1.0.1}/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-0.9.1 → httomo_backends-1.0.1}/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-1.0.1/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 → httomo_backends-1.0.1}/httomo_backends.egg-info/PKG-INFO

@@ -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 → httomo_backends-1.0.1}/httomo_backends.egg-info/SOURCES.txt

@@ -86,6 +86,7 @@ httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.phase/paganin_filt
 httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.stripe/raven_filter.yaml
 httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.stripe/remove_all_stripe.yaml
 httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.stripe/remove_stripe_based_sorting.yaml
+httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.stripe/remove_stripe_fw.yaml
 httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.stripe/remove_stripe_ti.yaml
 httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/CGLS3d_tomobar.yaml
 httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/FBP2d_astra.yaml

{httomo_backends-0.9.1 → httomo_backends-1.0.1}/pyproject.toml

@@ -24,7 +24,7 @@ dev_template = "{tag}"
 
 [project]
 name = "httomo-backends"
-version = "0.9.1"
+version = "1.0.1"
 description = "Supplementary files for HTTomo backends."
 readme = "README.rst"
 license = {text = "BSD-3-Clause"}

{httomo_backends-0.9.1 → httomo_backends-1.0.1}/tests/test_httomolibgpu.py

@@ -19,6 +19,7 @@ from httomolibgpu.prep.phase import paganin_filter, paganin_filter_savu_legacy
 from httomolibgpu.prep.alignment import distortion_correction_proj_discorpy
 from httomolibgpu.prep.stripe import (
     remove_stripe_based_sorting,
+    remove_stripe_fw,
     remove_stripe_ti,
     remove_all_stripe,
     raven_filter,
@@ -445,6 +446,35 @@ def test_remove_stripe_ti_memoryhook(slices, ensure_clean_memory):
     assert percents_relative_maxmem <= 20
 
 
+@pytest.mark.cupy
+@pytest.mark.parametrize("slices", [64, 129])
+def test_remove_stripe_fw_memoryhook(slices, ensure_clean_memory):
+    dim_x = 156
+    dim_y = 216
+    data = cp.random.random_sample((slices, dim_x, dim_y), dtype=np.float32)
+    hook = MaxMemoryHook()
+    with hook:
+        remove_stripe_fw(cp.copy(data)).get()
+    max_mem = (
+        hook.max_mem
+    )  # the amount of memory in bytes needed for the method according to memoryhook
+
+    # now we estimate how much of the total memory required for this data
+    estimated_memory_bytes = _calc_memory_bytes_for_slices_remove_stripe_fw(
+        (slices, dim_x, dim_y), dtype=np.float32()
+    )
+    estimated_memory_mb = round(estimated_memory_bytes / (1024**2), 2)
+    max_mem_mb = round(max_mem / (1024**2), 2)
+
+    # now we compare both memory estimations
+    difference_mb = abs(estimated_memory_mb - max_mem_mb)
+    percents_relative_maxmem = round((difference_mb / max_mem_mb) * 100)
+    # the estimated_memory_mb should be LARGER or EQUAL to max_mem_mb
+    # the resulting percent value should not deviate from max_mem on more than 1%
+    assert estimated_memory_mb >= max_mem_mb
+    assert percents_relative_maxmem <= 20
+
+
 @pytest.mark.cupy
 @pytest.mark.parametrize("projections", [180, 360, 720, 1080, 1440])
 def test_raven_filter_memoryhook(projections, ensure_clean_memory):