httomo-backends 1.0__tar.gz → 1.1.0__tar.gz

{httomo_backends-1.0 → httomo_backends-1.1.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: httomo-backends
-Version: 1.0
+Version: 1.1.0
 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-1.0 → httomo_backends-1.1.0}/httomo_backends/cufft.py

@@ -2,7 +2,6 @@ import ctypes
 import sys
 from enum import Enum
 
-
 if "linux" not in sys.platform:
     raise RuntimeError("Linux is currently the only supported platform")
 

{httomo_backends-1.0 → httomo_backends-1.1.0}/httomo_backends/methods_database/packages/backends/httomolibgpu/httomolibgpu.yaml

@@ -227,6 +227,15 @@ recon:
       memory_gpu:
         multiplier: None
         method: module
+    ADMM3d_tomobar:
+      pattern: sinogram
+      output_dims_change: True
+      implementation: gpu_cupy
+      save_result_default: True
+      padding: True
+      memory_gpu:
+        multiplier: None
+        method: module
   rotation:
     find_center_vo:
       pattern: projection

{httomo_backends-1.0 → httomo_backends-1.1.0}/httomo_backends/methods_database/packages/backends/httomolibgpu/supporting_funcs/misc/corr.py

@@ -1,5 +1,7 @@
+import inspect
 from typing import Tuple
 
+from httomolibgpu.misc.corr import median_filter, remove_outlier
 
 __all__ = [
     "_calc_padding_remove_outlier",
@@ -8,10 +10,18 @@ __all__ = [
 
 
 def _calc_padding_remove_outlier(**kwargs) -> Tuple[int, int]:
+    if "kernel_size" not in kwargs:
+        params = inspect.signature(remove_outlier).parameters
+        kwargs["kernel_size"] = params["kernel_size"].default
+
     kernel_size = kwargs["kernel_size"]
     return (kernel_size // 2, kernel_size // 2)
 
 
 def _calc_padding_median_filter(**kwargs) -> Tuple[int, int]:
+    if "kernel_size" not in kwargs:
+        params = inspect.signature(median_filter).parameters
+        kwargs["kernel_size"] = params["kernel_size"].default
+
     kernel_size = kwargs["kernel_size"]
     return (kernel_size // 2, kernel_size // 2)

{httomo_backends-1.0 → httomo_backends-1.1.0}/httomo_backends/methods_database/packages/backends/httomolibgpu/supporting_funcs/misc/denoise.py

@@ -1,6 +1,5 @@
 from typing import Tuple
 
-
 __all__ = [
     "_calc_padding_total_variation_ROF",
     "_calc_padding_total_variation_PD",

{httomo_backends-1.0 → httomo_backends-1.1.0}/httomo_backends/methods_database/packages/backends/httomolibgpu/supporting_funcs/misc/morph.py

@@ -20,10 +20,13 @@
 # ---------------------------------------------------------------------------
 """Modules for memory estimation for morph functions"""
 
+import inspect
 import math
 from typing import Tuple
 import numpy as np
 
+from httomolibgpu.misc.morph import data_resampler, sino_360_to_180
+
 __all__ = [
     "_calc_memory_bytes_data_resampler",
     "_calc_output_dim_data_resampler",
@@ -42,6 +45,10 @@ def _calc_memory_bytes_data_resampler(
     **kwargs,
 ) -> Tuple[int, int]:
     newshape = kwargs["newshape"]
+
+    if "interpolation" not in kwargs:
+        params = inspect.signature(data_resampler).parameters
+        kwargs["interpolation"] = params["interpolation"].default
     interpolation = kwargs["interpolation"]
 
     input_size = np.prod(non_slice_dims_shape) * dtype.itemsize
@@ -62,7 +69,9 @@ def _calc_output_dim_sino_360_to_180(
     non_slice_dims_shape: Tuple[int, int],
     **kwargs,
 ) -> Tuple[int, int]:
-    assert "overlap" in kwargs, "Expected overlap in method parameters"
+    if "overlap" not in kwargs:
+        params = inspect.signature(sino_360_to_180).parameters
+        kwargs["overlap"] = params["overlap"].default
     overlap: float = kwargs["overlap"]
 
     original_sino_width = non_slice_dims_shape[1]
@@ -75,7 +84,9 @@ def _calc_memory_bytes_sino_360_to_180(
     dtype: np.dtype,
     **kwargs,
 ) -> Tuple[int, int]:
-    assert "overlap" in kwargs, "Expected overlap in method parameters"
+    if "overlap" not in kwargs:
+        params = inspect.signature(sino_360_to_180).parameters
+        kwargs["overlap"] = params["overlap"].default
     overlap: float = kwargs["overlap"]
 
     original_sino_width = non_slice_dims_shape[1]

{httomo_backends-1.0 → httomo_backends-1.1.0}/httomo_backends/methods_database/packages/backends/httomolibgpu/supporting_funcs/misc/rescale.py

@@ -1,6 +1,9 @@
+import inspect
 from typing import Tuple
 import numpy as np
 
+from httomolibgpu.misc.rescale import rescale_to_int
+
 __all__ = [
     "_calc_memory_bytes_rescale_to_int",
 ]
@@ -11,6 +14,9 @@ def _calc_memory_bytes_rescale_to_int(
     dtype: np.dtype,
     **kwargs,
 ) -> Tuple[int, int]:
+    if "bits" not in kwargs:
+        params = inspect.signature(rescale_to_int).parameters
+        kwargs["bits"] = params["bits"].default
     bits: int = kwargs["bits"]
     if bits == 8:
         itemsize = 1

{httomo_backends-1.0 → httomo_backends-1.1.0}/httomo_backends/methods_database/packages/backends/httomolibgpu/supporting_funcs/prep/normalize.py

@@ -1,7 +1,6 @@
 from typing import Tuple
 import numpy as np
 
-
 __all__ = [
     "_calc_memory_bytes_dark_flat_field_correction",
 ]

{httomo_backends-1.0 → httomo_backends-1.1.0}/httomo_backends/methods_database/packages/backends/httomolibgpu/supporting_funcs/prep/stripe.py

@@ -20,13 +20,13 @@
 # ---------------------------------------------------------------------------
 """Modules for memory estimation for stripe removal methods"""
 
+import inspect
 import math
 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
-
+from httomolibgpu.prep.stripe import raven_filter, remove_stripe_fw
 
 __all__ = [
     "_calc_memory_bytes_for_slices_remove_stripe_fw",
@@ -87,7 +87,14 @@ def _calc_memory_bytes_raven_filter(
     **kwargs,
 ) -> Tuple[int, int]:
 
+    if "pad_x" not in kwargs:
+        params = inspect.signature(raven_filter).parameters
+        kwargs["pad_x"] = params["pad_x"].default
     pad_x = kwargs["pad_x"]
+
+    if "pad_y" not in kwargs:
+        params = inspect.signature(raven_filter).parameters
+        kwargs["pad_y"] = params["pad_y"].default
     pad_y = kwargs["pad_y"]
 
     # Unpadded input

{httomo_backends-1.0 → httomo_backends-1.1.0}/httomo_backends/methods_database/packages/backends/httomolibgpu/supporting_funcs/recon/algorithm.py

@@ -24,6 +24,7 @@ import math
 from typing import Tuple
 import numpy as np
 from httomo_backends.cufft import CufftType, cufft_estimate_1d, cufft_estimate_2d
+from httomolibgpu.recon.algorithm import ADMM3d_tomobar
 
 __all__ = [
     "_calc_memory_bytes_FBP3d_tomobar",
@@ -31,13 +32,16 @@ __all__ = [
     "_calc_memory_bytes_SIRT3d_tomobar",
     "_calc_memory_bytes_CGLS3d_tomobar",
     "_calc_memory_bytes_FISTA3d_tomobar",
+    "_calc_memory_bytes_ADMM3d_tomobar",
     "_calc_output_dim_FBP2d_astra",
     "_calc_output_dim_FBP3d_tomobar",
     "_calc_output_dim_LPRec3d_tomobar",
     "_calc_output_dim_SIRT3d_tomobar",
     "_calc_output_dim_CGLS3d_tomobar",
     "_calc_output_dim_FISTA3d_tomobar",
+    "_calc_output_dim_ADMM3d_tomobar",
     "_calc_padding_FISTA3d_tomobar",
+    "_calc_padding_ADMM3d_tomobar",
 ]
 
 
@@ -45,6 +49,10 @@ def _calc_padding_FISTA3d_tomobar(**kwargs) -> Tuple[int, int]:
     return (5, 5)
 
 
+def _calc_padding_ADMM3d_tomobar(**kwargs) -> Tuple[int, int]:
+    return (5, 5)
+
+
 def __calc_output_dim_recon(non_slice_dims_shape, **kwargs):
     """Function to calculate output dimensions for all reconstructors.
     The change of the dimension depends either on the user-provided "recon_size"
@@ -52,7 +60,7 @@ def __calc_output_dim_recon(non_slice_dims_shape, **kwargs):
 
     """
     DetectorsLengthH = non_slice_dims_shape[1]
-    recon_size = kwargs["recon_size"]
+    recon_size = kwargs.get("recon_size", None)
     if recon_size is None:
         recon_size = DetectorsLengthH
     output_dims = (recon_size, recon_size)
@@ -83,6 +91,10 @@ def _calc_output_dim_FISTA3d_tomobar(non_slice_dims_shape, **kwargs):
     return __calc_output_dim_recon(non_slice_dims_shape, **kwargs)
 
 
+def _calc_output_dim_ADMM3d_tomobar(non_slice_dims_shape, **kwargs):
+    return __calc_output_dim_recon(non_slice_dims_shape, **kwargs)
+
+
 def _calc_memory_bytes_FBP3d_tomobar(
     non_slice_dims_shape: Tuple[int, int],
     dtype: np.dtype,
@@ -604,6 +616,58 @@ def _calc_memory_bytes_FISTA3d_tomobar(
     return (tot_memory_bytes, 0)
 
 
+def _calc_memory_bytes_ADMM3d_tomobar(
+    non_slice_dims_shape: Tuple[int, int],
+    dtype: np.dtype,
+    **kwargs,
+) -> Tuple[int, int]:
+    detector_pad = 0
+    if "detector_pad" in kwargs:
+        detector_pad = kwargs["detector_pad"]
+    if detector_pad is True:
+        detector_pad = __estimate_detectorHoriz_padding(non_slice_dims_shape[1])
+    elif detector_pad is False:
+        detector_pad = 0
+
+    anglesnum = non_slice_dims_shape[0]
+    DetectorsLengthH_padded = non_slice_dims_shape[1] + 2 * detector_pad
+
+    # calculate the output shape
+    output_dims = _calc_output_dim_FISTA3d_tomobar(non_slice_dims_shape, **kwargs)
+    recon_data_size_original = (
+        np.prod(output_dims) * dtype.itemsize
+    )  # recon user-defined size
+
+    in_data_siz_pad = (anglesnum * DetectorsLengthH_padded) * dtype.itemsize
+    output_dims_larger_grid = (DetectorsLengthH_padded, DetectorsLengthH_padded)
+
+    out_data_size = np.prod(output_dims_larger_grid) * dtype.itemsize
+    x0 = out_data_size
+    x = out_data_size
+    z = out_data_size
+    u = out_data_size
+    grad_data = out_data_size
+    grad_admm = out_data_size
+    arithmetic = 3 * out_data_size
+
+    admm_part = (
+        recon_data_size_original
+        + in_data_siz_pad
+        + x0
+        + x
+        + z
+        + u
+        + grad_data
+        + grad_admm
+        + out_data_size
+        + arithmetic
+    )
+    regul_part = 8 * np.prod(output_dims_larger_grid) * dtype.itemsize
+
+    tot_memory_bytes = int(admm_part + regul_part)
+    return (tot_memory_bytes, 0)
+
+
 def __estimate_detectorHoriz_padding(detX_size) -> int:
     det_half = detX_size // 2
     padded_value_exact = int(np.sqrt(2 * (det_half**2))) - det_half

{httomo_backends-1.0 → httomo_backends-1.1.0}/httomo_backends/methods_database/packages/backends/tomopy/supporting_funcs/recon/algorithm.py

@@ -23,7 +23,6 @@
 from typing import Tuple
 import numpy as np
 
-
 __all__ = [
     "_calc_output_dim_recon",
 ]

{httomo_backends-1.0 → httomo_backends-1.1.0}/httomo_backends/scripts/yaml_pipelines_generator.py

@@ -25,13 +25,13 @@
 Please run the generator as:
     python -m yaml_pipelines_generator -i /path/to/pipelines.yml -o /path/to/output/
 """
+
 import argparse
 import os
 import ruamel.yaml
 import httomo_backends
 import yaml
 
-
 CS = ruamel.yaml.comments.CommentedSeq  # defaults to block style
 
 
@@ -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-1.0 → httomo_backends-1.1.0}/httomo_backends/scripts/yaml_templates_generator.py

@@ -24,6 +24,7 @@
 Please run the generator as:
     python -m yaml_templates_generator -i /path/to/modules.yml -o /path/to/output/
 """
+
 import argparse
 import importlib
 import inspect

{httomo_backends-1.0 → httomo_backends-1.1.0}/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-1.1.0/httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/ADMM3d_tomobar.yaml

@@ -0,0 +1,17 @@
+- method: ADMM3d_tomobar
+  module_path: httomolibgpu.recon.algorithm
+  parameters:
+    center: ${{centering.side_outputs.centre_of_rotation}}
+    detector_pad: false
+    recon_size: null
+    recon_mask_radius: 0.95
+    iterations: 3
+    subsets_number: 24
+    initialisation: FBP
+    ADMM_rho_const: 1.0
+    ADMM_relax_par: 1.7
+    regularisation_type: PD_TV
+    regularisation_parameter: 0.0025
+    regularisation_iterations: 40
+    regularisation_half_precision: true
+    nonnegativity: false

{httomo_backends-1.0 → httomo_backends-1.1.0}/httomo_backends.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: httomo-backends
-Version: 1.0
+Version: 1.1.0
 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-1.0 → httomo_backends-1.1.0}/httomo_backends.egg-info/SOURCES.txt

@@ -88,6 +88,7 @@ httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.stripe/remove_all_
 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/ADMM3d_tomobar.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/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/FBP3d_tomobar.yaml

{httomo_backends-1.0 → httomo_backends-1.1.0}/pyproject.toml

@@ -24,7 +24,7 @@ dev_template = "{tag}"
 
 [project]
 name = "httomo-backends"
-version = "1.0"
+version = "1.1.0"
 description = "Supplementary files for HTTomo backends."
 readme = "README.rst"
 license = {text = "BSD-3-Clause"}