httomo-backends 0.5.3__tar.gz → 0.6.1__tar.gz

{httomo_backends-0.5.3 → httomo_backends-0.6.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: httomo-backends
-Version: 0.5.3
+Version: 0.6.1
 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-0.5.3 → httomo_backends-0.6.1}/httomo_backends/methods_database/packages/backends/httomolib/httomolib.yaml

@@ -1,4 +1,12 @@
 misc:
+  rescale:
+    rescale_to_int:
+      pattern: all
+      output_dims_change: False
+      implementation: cpu
+      memory_gpu: None
+      save_result_default: False
+      padding: False
   morph:
     data_reducer:
       pattern: all

{httomo_backends-0.5.3 → httomo_backends-0.6.1}/httomo_backends/methods_database/packages/backends/httomolib/httomolib_modules.yaml

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

{httomo_backends-0.5.3 → httomo_backends-0.6.1}/httomo_backends/methods_database/packages/backends/httomolibgpu/httomolibgpu.yaml

@@ -7,7 +7,7 @@ misc:
       save_result_default: False
       padding: True
       memory_gpu:
-        multiplier: 2.1
+        multiplier: 2.5
         method: direct
     remove_outlier:
       pattern: all
@@ -16,7 +16,7 @@ misc:
       save_result_default: False
       padding: True
       memory_gpu:
-        multiplier: 2.1
+        multiplier: 2.5
         method: direct
   denoise:
     total_variation_ROF:
@@ -87,15 +87,6 @@ prep:
       memory_gpu:
         multiplier: None
         method: module
-    paganin_filter_savu:
-      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
@@ -207,7 +198,7 @@ recon:
       save_result_default: False
       padding: False
       memory_gpu:
-        multiplier: 0
+        multiplier: 2
         method: direct
     find_center_pc:
       pattern: projection

{httomo_backends-0.5.3 → httomo_backends-0.6.1}/httomo_backends/methods_database/packages/backends/httomolibgpu/supporting_funcs/prep/phase.py

@@ -27,70 +27,10 @@ import numpy as np
 from httomo_backends.cufft import CufftType, cufft_estimate_2d
 
 __all__ = [
-    "_calc_memory_bytes_paganin_filter_savu",
     "_calc_memory_bytes_paganin_filter_tomopy",
 ]
 
 
-def _calc_memory_bytes_paganin_filter_savu(
-    non_slice_dims_shape: Tuple[int, int],
-    dtype: np.dtype,
-    **kwargs,
-) -> Tuple[int, int]:
-    pad_x = kwargs["pad_x"]
-    pad_y = kwargs["pad_y"]
-
-    # Input (unpadded)
-    unpadded_in_slice_size = np.prod(non_slice_dims_shape) * dtype.itemsize
-
-    # Padded input
-    padded_non_slice_dims_shape = (
-        non_slice_dims_shape[0] + 2 * pad_y,
-        non_slice_dims_shape[1] + 2 * pad_x,
-    )
-    padded_in_slice_size = (
-        padded_non_slice_dims_shape[0] * padded_non_slice_dims_shape[1] * dtype.itemsize
-    )
-
-    # Padded input cast to `complex64`
-    complex_slice = padded_in_slice_size / dtype.itemsize * np.complex64().nbytes
-
-    # Plan size for 2D FFT
-    fftplan_slice_size = cufft_estimate_2d(
-        nx=padded_non_slice_dims_shape[1],
-        ny=padded_non_slice_dims_shape[0],
-        fft_type=CufftType.CUFFT_C2C,
-    )
-
-    # Shape of 2D filter is the same as the padded `complex64` slice shape, so the size will be
-    # the same
-    filter_size = complex_slice
-
-    # Size of cropped/unpadded + cast to float32 result of 2D IFFT
-    cropped_float32_res_slice = np.prod(non_slice_dims_shape) * np.float32().nbytes
-
-    # If the FFT plan size is negligible for some reason, this changes where the peak GPU
-    # memory usage occurs. Hence, the if/else branching below for calculating the total bytes.
-    NEGLIGIBLE_FFT_PLAN_SIZE = 16
-    if fftplan_slice_size < NEGLIGIBLE_FFT_PLAN_SIZE:
-        tot_memory_bytes = int(
-            unpadded_in_slice_size + padded_in_slice_size + complex_slice
-        )
-    else:
-        tot_memory_bytes = int(
-            unpadded_in_slice_size
-            + padded_in_slice_size
-            + complex_slice
-            # The padded float32 array is deallocated when a copy is made when casting to complex64
-            # and the variable `padded_tomo` is reassigned to the complex64 version
-            - padded_in_slice_size
-            + fftplan_slice_size
-            + cropped_float32_res_slice
-        )
-
-    return (tot_memory_bytes, filter_size)
-
-
 def _calc_memory_bytes_paganin_filter_tomopy(
     non_slice_dims_shape: Tuple[int, int],
     dtype: np.dtype,

{httomo_backends-0.5.3 → httomo_backends-0.6.1}/httomo_backends/methods_database/packages/backends/httomolibgpu/supporting_funcs/recon/algorithm.py

@@ -77,12 +77,17 @@ def _calc_memory_bytes_FBP3d_tomobar(
     dtype: np.dtype,
     **kwargs,
 ) -> Tuple[int, int]:
-    det_height = non_slice_dims_shape[0]
-    det_width = non_slice_dims_shape[1]
+    if "detector_pad" in kwargs:
+        detector_pad = kwargs["detector_pad"]
+    else:
+        detector_pad = 0
+
+    angles_tot = non_slice_dims_shape[0]
+    det_width = non_slice_dims_shape[1] + 2 * detector_pad
     SLICES = 200  # dummy multiplier+divisor to pass large batch size threshold
 
     # 1. input
-    input_slice_size = np.prod(non_slice_dims_shape) * dtype.itemsize
+    input_slice_size = (angles_tot * det_width) * dtype.itemsize
 
     ########## FFT / filter / IFFT (filtersync_cupy)
 
@@ -91,13 +96,13 @@ def _calc_memory_bytes_FBP3d_tomobar(
         cufft_estimate_1d(
             nx=det_width,
             fft_type=CufftType.CUFFT_R2C,
-            batch=det_height * SLICES,
+            batch=angles_tot * SLICES,
         )
         / SLICES
     )
 
     # 3. RFFT output size (proj_f in code)
-    proj_f_slice = det_height * (det_width // 2 + 1) * np.complex64().itemsize
+    proj_f_slice = angles_tot * (det_width // 2 + 1) * np.complex64().itemsize
 
     # 4. Filter size (independent of number of slices)
     filter_size = (det_width // 2 + 1) * np.float32().itemsize
@@ -107,7 +112,7 @@ def _calc_memory_bytes_FBP3d_tomobar(
         cufft_estimate_1d(
             nx=det_width,
             fft_type=CufftType.CUFFT_C2R,
-            batch=det_height * SLICES,
+            batch=angles_tot * SLICES,
         )
         / SLICES
     )
@@ -123,9 +128,7 @@ def _calc_memory_bytes_FBP3d_tomobar(
 
     # 6. we swap the axes before passing data to Astra in ToMoBAR
     # https://github.com/dkazanc/ToMoBAR/blob/54137829b6326406e09f6ef9c95eb35c213838a7/tomobar/methodsDIR_CuPy.py#L135
-    pre_astra_input_swapaxis_slice = (
-        np.prod(non_slice_dims_shape) * np.float32().itemsize
-    )
+    pre_astra_input_swapaxis_slice = (angles_tot * det_width) * np.float32().itemsize
 
     # 7. astra backprojection will generate an output array
     # https://github.com/dkazanc/ToMoBAR/blob/54137829b6326406e09f6ef9c95eb35c213838a7/tomobar/astra_wrappers/astra_base.py#L524
@@ -151,7 +154,7 @@ def _calc_memory_bytes_FBP3d_tomobar(
     #      so it does not add to the memory overall
 
     # We assume for safety here that one FFT plan is not freed and one is freed
-    tot_memory_bytes = (
+    tot_memory_bytes = int(
         projection_mem_size + filtersync_size - ifftplan_slice_size + recon_output_size
     )
 
@@ -166,8 +169,14 @@ def _calc_memory_bytes_LPRec3d_tomobar(
 ) -> Tuple[int, int]:
     # Based on: https://github.com/dkazanc/ToMoBAR/pull/112/commits/4704ecdc6ded3dd5ec0583c2008aa104f30a8a39
 
+    if "detector_pad" in kwargs:
+        detector_pad = kwargs["detector_pad"]
+    else:
+        detector_pad = 0
+
     angles_tot = non_slice_dims_shape[0]
-    DetectorsLengthH = non_slice_dims_shape[1]
+    DetectorsLengthH_prepad = non_slice_dims_shape[1]
+    DetectorsLengthH = non_slice_dims_shape[1] + 2 * detector_pad
     SLICES = 200  # dummy multiplier+divisor to pass large batch size threshold
     _CENTER_SIZE_MIN = 192  # must be divisible by 8
 
@@ -210,7 +219,7 @@ def _calc_memory_bytes_LPRec3d_tomobar(
     if odd_horiz:
         output_dims = tuple(x + 1 for x in output_dims)
 
-    in_slice_size = np.prod(non_slice_dims_shape) * dtype.itemsize
+    in_slice_size = (angles_tot * DetectorsLengthH) * dtype.itemsize
     padded_in_slice_size = angles_tot * n * np.float32().itemsize
 
     theta_size = angles_tot * np.float32().itemsize
@@ -256,7 +265,9 @@ def _calc_memory_bytes_LPRec3d_tomobar(
         center_size * center_size * (1 + angle_range_pi_count * 2) * np.int16().itemsize
     )
 
-    recon_output_size = DetectorsLengthH * DetectorsLengthH * np.float32().itemsize
+    recon_output_size = (
+        DetectorsLengthH_prepad * DetectorsLengthH_prepad * np.float32().itemsize
+    )
     ifft2_plan_slice_size = (
         cufft_estimate_2d(
             nx=(2 * m + 2 * n), ny=(2 * m + 2 * n), fft_type=CufftType.CUFFT_C2C
@@ -342,7 +353,6 @@ def _calc_memory_bytes_LPRec3d_tomobar(
     add_to_memory_counters(after_recon_swapaxis_slice, True)
 
     return (tot_memory_bytes * 1.05, fixed_amount + 250 * 1024 * 1024)
-    # return (tot_memory_bytes, fixed_amount)
 
 
 def _calc_memory_bytes_SIRT3d_tomobar(
@@ -350,16 +360,22 @@ def _calc_memory_bytes_SIRT3d_tomobar(
     dtype: np.dtype,
     **kwargs,
 ) -> Tuple[int, int]:
-    DetectorsLengthH = non_slice_dims_shape[1]
+
+    if "detector_pad" in kwargs:
+        detector_pad = kwargs["detector_pad"]
+    else:
+        detector_pad = 0
+    anglesnum = non_slice_dims_shape[0]
+    DetectorsLengthH = non_slice_dims_shape[1] + 2 * detector_pad
     # calculate the output shape
     output_dims = _calc_output_dim_SIRT3d_tomobar(non_slice_dims_shape, **kwargs)
 
-    in_data_size = np.prod(non_slice_dims_shape) * dtype.itemsize
+    in_data_size = (anglesnum * DetectorsLengthH) * dtype.itemsize
     out_data_size = np.prod(output_dims) * dtype.itemsize
 
     astra_projection = 2.5 * (in_data_size + out_data_size)
 
-    tot_memory_bytes = 2 * in_data_size + 2 * out_data_size + astra_projection
+    tot_memory_bytes = int(2 * in_data_size + 2 * out_data_size + astra_projection)
     return (tot_memory_bytes, 0)
 
 
@@ -368,14 +384,20 @@ def _calc_memory_bytes_CGLS3d_tomobar(
     dtype: np.dtype,
     **kwargs,
 ) -> Tuple[int, int]:
-    DetectorsLengthH = non_slice_dims_shape[1]
+    if "detector_pad" in kwargs:
+        detector_pad = kwargs["detector_pad"]
+    else:
+        detector_pad = 0
+
+    anglesnum = non_slice_dims_shape[0]
+    DetectorsLengthH = non_slice_dims_shape[1] + 2 * detector_pad
     # calculate the output shape
     output_dims = _calc_output_dim_CGLS3d_tomobar(non_slice_dims_shape, **kwargs)
 
-    in_data_size = np.prod(non_slice_dims_shape) * dtype.itemsize
+    in_data_size = (anglesnum * DetectorsLengthH) * dtype.itemsize
     out_data_size = np.prod(output_dims) * dtype.itemsize
 
     astra_projection = 2.5 * (in_data_size + out_data_size)
 
-    tot_memory_bytes = 2 * in_data_size + 2 * out_data_size + astra_projection
+    tot_memory_bytes = int(2 * in_data_size + 2 * out_data_size + astra_projection)
     return (tot_memory_bytes, 0)

{httomo_backends-0.5.3 → httomo_backends-0.6.1}/httomo_backends/methods_database/packages/backends/tomopy/supporting_funcs/misc/corr.py

@@ -18,7 +18,7 @@
 # Created By  : Tomography Team at DLS <scientificsoftware@diamond.ac.uk>
 # Created Date: 18/July/2024
 # ---------------------------------------------------------------------------
-""" Modules for memory estimation, padding, data dims estimation """
+"""Modules for memory estimation, padding, data dims estimation"""
 
 from typing import Tuple
 

{httomo_backends-0.5.3 → httomo_backends-0.6.1}/httomo_backends/methods_database/packages/backends/tomopy/supporting_funcs/prep/stripe.py

@@ -18,7 +18,7 @@
 # Created By  : Tomography Team at DLS <scientificsoftware@diamond.ac.uk>
 # Created Date: 18/July/2024
 # ---------------------------------------------------------------------------
-""" Modules for memory estimation, padding, data dims estimation """
+"""Modules for memory estimation, padding, data dims estimation"""
 
 from typing import Tuple
 

{httomo_backends-0.5.3 → httomo_backends-0.6.1}/httomo_backends/pipelines_full/FBP3d_tomobar_denoising_directive.yaml

@@ -15,6 +15,6 @@
 - method: calculate_stats
   module_path: httomo.methods
 - method: rescale_to_int
-  module_path: httomolibgpu.misc.rescale
+  module_path: httomolib.misc.rescale
 - method: save_to_images
   module_path: httomolib.misc.images

{httomo_backends-0.5.3 → httomo_backends-0.6.1}/httomo_backends/pipelines_full/FBP3d_tomobar_directive.yaml

@@ -13,6 +13,6 @@
 - method: calculate_stats
   module_path: httomo.methods
 - method: rescale_to_int
-  module_path: httomolibgpu.misc.rescale
+  module_path: httomolib.misc.rescale
 - method: save_to_images
   module_path: httomolib.misc.images

{httomo_backends-0.5.3 → httomo_backends-0.6.1}/httomo_backends/pipelines_full/LPRec3d_tomobar_directive.yaml

@@ -13,7 +13,7 @@
 - method: calculate_stats
   module_path: httomo.methods
 - method: rescale_to_int
-  module_path: httomolibgpu.misc.rescale
+  module_path: httomolib.misc.rescale
 - method: save_to_images
   module_path: httomolib.misc.images
 

{httomo_backends-0.5.3 → httomo_backends-0.6.1}/httomo_backends/pipelines_full/deg360_distortion_FBP3d_tomobar_directive.yaml

@@ -1,11 +1,11 @@
 - method: standard_tomo
   module_path: httomo.data.hdf.loaders
+- method: find_center_360
+  module_path: httomolibgpu.recon.rotation
 - method: normalize
   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
@@ -15,6 +15,6 @@
 - method: calculate_stats
   module_path: httomo.methods
 - method: rescale_to_int
-  module_path: httomolibgpu.misc.rescale
+  module_path: httomolib.misc.rescale
 - method: save_to_images
   module_path: httomolib.misc.images

{httomo_backends-0.5.3 → httomo_backends-0.6.1}/httomo_backends/pipelines_full/deg360_paganin_FBP3d_tomobar_directive.yaml

@@ -1,9 +1,9 @@
 - method: standard_tomo
   module_path: httomo.data.hdf.loaders
-- method: normalize
-  module_path: httomolibgpu.prep.normalize  
 - method: find_center_360
   module_path: httomolibgpu.recon.rotation
+- method: normalize
+  module_path: httomolibgpu.prep.normalize  
 - method: sino_360_to_180
   module_path: httomolibgpu.misc.morph
 - method: remove_stripe_based_sorting
@@ -15,6 +15,6 @@
 - method: calculate_stats
   module_path: httomo.methods
 - method: rescale_to_int
-  module_path: httomolibgpu.misc.rescale
+  module_path: httomolib.misc.rescale
 - method: save_to_images
   module_path: httomolib.misc.images

httomo_backends-0.6.1/httomo_backends/pipelines_full/sweep_paganin_FBP3d_tomobar_directive.yaml

@@ -0,0 +1,12 @@
+- method: standard_tomo
+  module_path: httomo.data.hdf.loaders
+- method: find_center_vo
+  module_path: httomolibgpu.recon.rotation  
+- method: normalize
+  module_path: httomolibgpu.prep.normalize
+- method: paganin_filter_tomopy
+  module_path: httomolibgpu.prep.phase
+  sweep_parameter: alpha
+  sweep_values: [0.01, 0.001, 0.0001]
+- method: FBP3d_tomobar
+  module_path: httomolibgpu.recon.algorithm

{httomo_backends-0.5.3 → httomo_backends-0.6.1}/httomo_backends/pipelines_full/tomopy_gridrec_directive.yaml

@@ -13,6 +13,6 @@
 - method: calculate_stats
   module_path: httomo.methods
 - method: rescale_to_int
-  module_path: httomolibgpu.misc.rescale
+  module_path: httomolib.misc.rescale
 - method: save_to_images
   module_path: httomolib.misc.images

{httomo_backends-0.5.3 → httomo_backends-0.6.1}/httomo_backends/scripts/yaml_pipelines_generator.py

@@ -31,6 +31,8 @@ import ruamel.yaml
 import httomo_backends
 import yaml
 
+from httomo import __version__ as httomo_version
+
 CS = ruamel.yaml.comments.CommentedSeq  # defaults to block style
 
 
@@ -55,6 +57,20 @@ def __sweeprange_representer(
     )
 
 
+class SweepManual:
+    """SweepManual class."""
+
+    def __init__(self, lst):
+        self._lst = lst
+
+
+def __sweepmanual_representer(
+    dumper: yaml.SafeDumper, swp: SweepManual
+) -> yaml.nodes.SequenceNode:
+    """Represent a sweepmanual as a YAML sequence node."""
+    return dumper.represent_sequence("!Sweep", swp._lst)
+
+
 def __represent_none(self, data):
     return self.represent_scalar("tag:yaml.org,2002:null", "null")
 
@@ -86,17 +102,22 @@ def yaml_pipelines_generator(
         # a loop over methods in the high-level pipeline file (directive)
         methods_no = len(pipeline_file_content)
         pipeline_full = CS()
-        sweep_enabled = False
+        sweep_enabled_range = False
+        sweep_enabled_value = False
         for i in range(methods_no):
             method_content = pipeline_file_content[i]
             method_name = method_content["method"]
             module_name = method_content["module_path"]
             if "sweep_parameter" in method_content:
                 sweep_parameter = method_content["sweep_parameter"]
-                sweep_start = method_content["sweep_start"]
-                sweep_stop = method_content["sweep_stop"]
-                sweep_step = method_content["sweep_step"]
-                sweep_enabled = True
+                if "sweep_start" in method_content:
+                    sweep_start = method_content["sweep_start"]
+                    sweep_stop = method_content["sweep_stop"]
+                    sweep_step = method_content["sweep_step"]
+                    sweep_enabled_range = True
+                else:
+                    sweep_values = method_content["sweep_values"]
+                    sweep_enabled_value = True
 
             # get the corresponding yaml template from httomo-backends
             backend_name = module_name[0 : module_name.find(".")]
@@ -116,6 +137,13 @@ def yaml_pipelines_generator(
                 except OSError as e:
                     print("loading yaml template failed", e)
 
+            version_split = httomo_version.split(".")
+            major = version_split[0]
+            minor = version_split[1]
+            pipeline_full.yaml_set_start_comment(
+                f"This pipeline is supported by HTTomo ver. {major}.{minor}"
+            )            
+
             if "loaders" in module_name:
                 # should be the first method in the list
                 pipeline_full.yaml_set_comment_before_after_key(
@@ -149,7 +177,7 @@ def yaml_pipelines_generator(
                 )
                 pipeline_full[i]["side_outputs"].yaml_add_eol_comment(
                     key="cor",
-                    comment="A side output of the method, here a CoR scalar value",
+                    comment="An estimated CoR value provided as a side output",
                 )
                 pipeline_full[i]["side_outputs"].yaml_add_eol_comment(
                     key="overlap",
@@ -158,17 +186,22 @@ 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 dead pixels in the data, aka zingers. Use if sharp streaks are present in reconstruction. ---",
+                    "--- Removing unresponsive 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
                 if pipeline_full[i]["parameters"]["dif"] == "REQUIRED":
                     # fix for the absent parameter in TomoPy's algorithm
                     pipeline_full[i]["parameters"]["dif"] = 0.1
+                pipeline_full[i]["parameters"].yaml_add_eol_comment(
+                    key="kernel_size",
+                    comment="The size of the 3D neighbourhood surrounding the voxel. Odd integer.",
+                )
                 pipeline_full[i]["parameters"].yaml_add_eol_comment(
                     key="dif",
-                    comment="A difference between the outlier value and the median value of neighboring pixels.",
+                    comment="A difference between the outlier value and the median value of neighbouring pixels.",
                 )
+
             elif "distortion" in method_name:
                 pipeline_full.yaml_set_comment_before_after_key(
                     i,
@@ -225,7 +258,11 @@ def yaml_pipelines_generator(
                 pipeline_full += yaml_template_method
                 pipeline_full[i]["parameters"].yaml_add_eol_comment(
                     key="center",
-                    comment="Reference to center of rotation side output OR an integer.",
+                    comment="Reference to center of rotation side output above OR a float number.",
+                )
+                pipeline_full[i]["parameters"].yaml_add_eol_comment(
+                    key="detector_pad",
+                    comment="Horizontal detector padding to minimise circle/arc-type artifacts in the reconstruction",
                 )
                 pipeline_full[i]["parameters"].yaml_add_eol_comment(
                     key="recon_mask_radius",
@@ -282,13 +319,20 @@ def yaml_pipelines_generator(
                 )
                 pipeline_full += yaml_template_method
 
-            if sweep_enabled:
+            if sweep_enabled_range:
                 pipeline_full[i]["parameters"][sweep_parameter] = SweepRange(
                     start=sweep_start, stop=sweep_stop, step=sweep_step
                 )
+                yaml.representer.add_representer(SweepRange, __sweeprange_representer)
+                sweep_enabled_range = False
+            if sweep_enabled_value:
+                pipeline_full[i]["parameters"][sweep_parameter] = SweepManual(
+                    list(sweep_values)
+                )
+                yaml.representer.add_representer(SweepManual, __sweepmanual_representer)
+                sweep_enabled_value = False
 
         yaml.representer.add_representer(type(None), __represent_none)
-        yaml.representer.add_representer(SweepRange, __sweeprange_representer)
         yaml.dump(pipeline_full, f)
 
     return 0

httomo_backends-0.6.1/httomo_backends/yaml_templates/httomolib/httomolib.misc.rescale/rescale_to_int.yaml

@@ -0,0 +1,7 @@
+- method: rescale_to_int
+  module_path: httomolib.misc.rescale
+  parameters:
+    perc_range_min: 0.0
+    perc_range_max: 100.0
+    bits: 8
+    glob_stats: ${{statistics.side_outputs.glob_stats}}

{httomo_backends-0.5.3 → httomo_backends-0.6.1}/httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.misc.corr/remove_outlier.yaml

@@ -2,4 +2,4 @@
   module_path: httomolibgpu.misc.corr
   parameters:
     kernel_size: 3
-    dif: 0.1
+    dif: 1000

{httomo_backends-0.5.3 → httomo_backends-0.6.1}/httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/CGLS3d_tomobar.yaml

@@ -2,6 +2,7 @@
   module_path: httomolibgpu.recon.algorithm
   parameters:
     center: ${{centering.side_outputs.centre_of_rotation}}
+    detector_pad: 0
     recon_size: null
     iterations: 20
     nonnegativity: true

{httomo_backends-0.5.3 → httomo_backends-0.6.1}/httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/FBP2d_astra.yaml

@@ -2,6 +2,7 @@
   module_path: httomolibgpu.recon.algorithm
   parameters:
     center: ${{centering.side_outputs.centre_of_rotation}}
+    detector_pad: 0
     filter_type: ram-lak
     filter_parameter: null
     filter_d: null

{httomo_backends-0.5.3 → httomo_backends-0.6.1}/httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/FBP3d_tomobar.yaml

@@ -2,6 +2,7 @@
   module_path: httomolibgpu.recon.algorithm
   parameters:
     center: ${{centering.side_outputs.centre_of_rotation}}
+    detector_pad: 0
     filter_freq_cutoff: 0.35
     recon_size: null
     recon_mask_radius: 0.95

{httomo_backends-0.5.3 → httomo_backends-0.6.1}/httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/LPRec3d_tomobar.yaml

@@ -2,6 +2,7 @@
   module_path: httomolibgpu.recon.algorithm
   parameters:
     center: ${{centering.side_outputs.centre_of_rotation}}
+    detector_pad: 0
     filter_type: shepp
     filter_freq_cutoff: 1.0
     recon_size: null

{httomo_backends-0.5.3 → httomo_backends-0.6.1}/httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/SIRT3d_tomobar.yaml

@@ -2,6 +2,7 @@
   module_path: httomolibgpu.recon.algorithm
   parameters:
     center: ${{centering.side_outputs.centre_of_rotation}}
+    detector_pad: 0
     recon_size: null
     iterations: 300
     nonnegativity: true

{httomo_backends-0.5.3 → httomo_backends-0.6.1}/httomo_backends.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: httomo-backends
-Version: 0.5.3
+Version: 0.6.1
 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-0.5.3 → httomo_backends-0.6.1}/httomo_backends.egg-info/SOURCES.txt

@@ -49,6 +49,7 @@ httomo_backends/pipelines_full/__init__.py
 httomo_backends/pipelines_full/deg360_distortion_FBP3d_tomobar_directive.yaml
 httomo_backends/pipelines_full/deg360_paganin_FBP3d_tomobar_directive.yaml
 httomo_backends/pipelines_full/sweep_center_FBP3d_tomobar_directive.yaml
+httomo_backends/pipelines_full/sweep_paganin_FBP3d_tomobar_directive.yaml
 httomo_backends/pipelines_full/tomopy_gridrec_directive.yaml
 httomo_backends/scripts/__init__.py
 httomo_backends/scripts/json_pipelines_generator.py
@@ -62,6 +63,7 @@ httomo_backends/yaml_templates/httomo/httomo.methods/save_intermediate_data.yaml
 httomo_backends/yaml_templates/httomolib/__init__.py
 httomo_backends/yaml_templates/httomolib/httomolib.misc.images/save_to_images.yaml
 httomo_backends/yaml_templates/httomolib/httomolib.misc.morph/data_reducer.yaml
+httomo_backends/yaml_templates/httomolib/httomolib.misc.rescale/rescale_to_int.yaml
 httomo_backends/yaml_templates/httomolib/httomolib.misc.segm/binary_thresholding.yaml
 httomo_backends/yaml_templates/httomolib/httomolib.prep.phase/paganin_filter.yaml
 httomo_backends/yaml_templates/httomolibgpu/__init__.py

{httomo_backends-0.5.3 → httomo_backends-0.6.1}/pyproject.toml

@@ -24,7 +24,7 @@ dev_template = "{tag}"
 
 [project]
 name = "httomo-backends"
-version = "0.5.3"
+version = "0.6.1"
 description = "Supplementary files for HTTomo backends."
 readme = "README.rst"
 license = {text = "BSD-3-Clause"}