httomo-backends 0.6__py3-none-any.whl → 0.6.1__py3-none-any.whl

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/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/methods_database/packages/backends/httomolibgpu/supporting_funcs/recon/algorithm.py

@@ -354,6 +354,7 @@ def _calc_memory_bytes_LPRec3d_tomobar(
 
     return (tot_memory_bytes * 1.05, fixed_amount + 250 * 1024 * 1024)
 
+
 def _calc_memory_bytes_SIRT3d_tomobar(
     non_slice_dims_shape: Tuple[int, int],
     dtype: np.dtype,

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

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

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/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. Please use before normalisation. ---",
+                    "--- 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.dist-info → httomo_backends-0.6.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: httomo-backends
-Version: 0.6
+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-0.6.dist-info → httomo_backends-0.6.1.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=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=mrN9qyOK2GG1mZi7jr7GOJm-Q96b7eaeLYB8ah_har4,5352
+httomo_backends/methods_database/packages/backends/httomolibgpu/httomolibgpu.yaml,sha256=HXfQPfhYjlNbnfRaBdTf7zs71Chvfl8B93P0ZfJQN7U,5118
 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=k3PGyn8jn2DH2NN2tu3U1xE0JFsJk0E_b-Jf_lL6h6E,6195
+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/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=rMegPP3muruRe6ih3hNlcgSjxJ0FaNuccQHt4gtyBIo,14971
+httomo_backends/methods_database/packages/backends/httomolibgpu/supporting_funcs/recon/algorithm.py,sha256=PiCLqsGudum2fvVNWrU_lZq4lLJmcKpCS7wEorb6HsA,14972
 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
@@ -38,13 +38,14 @@ httomo_backends/pipelines_full/FBP3d_tomobar_directive.yaml,sha256=QyqyAmWZjmcgV
 httomo_backends/pipelines_full/FBP3d_tomobar_noimagesaving_directive.yaml,sha256=uute7GdEEshbnmljjeyDi3Z5aqZftBTvo7Ti4wKgzhk,403
 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=7tHclsalkymiUGXRrbXSeDjJgVmw_H-bWFj6LC34he0,676
-httomo_backends/pipelines_full/deg360_paganin_FBP3d_tomobar_directive.yaml,sha256=43ugLxzkqnRsL4UJSZWErjfgwvpEfLP2QSwtQQLh6RQ,660
+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/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/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=OjrE6zMhdnta87Odwp3vOiW6OcoUSkkYjxyHvz3h_V4,14170
+httomo_backends/scripts/yaml_pipelines_generator.py,sha256=TLiwfSeQY1y0TVnvwjZDJeBqZg91NbfpXLMdhbqpTTo,15940
 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
@@ -141,8 +142,8 @@ 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-0.6.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-httomo_backends-0.6.dist-info/METADATA,sha256=l2D7BiEs5l475GAEgXAsUYY6N3VVGUswQjqJ-BGQXAE,2310
-httomo_backends-0.6.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-httomo_backends-0.6.dist-info/top_level.txt,sha256=v4x8d4CeEyMwo8QoqIvL_p-WoXAVD1bVnASPIrLjSTg,16
-httomo_backends-0.6.dist-info/RECORD,,
+httomo_backends-0.6.1.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+httomo_backends-0.6.1.dist-info/METADATA,sha256=JdaS98Vkzffu2CJ590WfH5H1j5nkRK74JJmh65OuA1s,2312
+httomo_backends-0.6.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+httomo_backends-0.6.1.dist-info/top_level.txt,sha256=v4x8d4CeEyMwo8QoqIvL_p-WoXAVD1bVnASPIrLjSTg,16
+httomo_backends-0.6.1.dist-info/RECORD,,