httomo-backends 0.9.0__py3-none-any.whl → 0.9.1__py3-none-any.whl

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

@@ -105,7 +105,7 @@ prep:
       padding: False
       memory_gpu:
         multiplier: None
-        method: module
+        method: iterative
     paganin_filter_savu_legacy:
       pattern: projection
       output_dims_change: False
@@ -114,7 +114,7 @@ prep:
       padding: False
       memory_gpu:
         multiplier: None
-        method: module       
+        method: iterative       
   alignment:
     distortion_correction_proj_discorpy:
       pattern: projection

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

@@ -23,98 +23,25 @@
 from typing import Tuple
 import numpy as np
 
-from httomo_backends.cufft import CufftType, cufft_estimate_2d
+from httomolibgpu.prep.phase import paganin_filter, paganin_filter_savu_legacy
 
 __all__ = [
-    "_calc_memory_bytes_paganin_filter",
-    "_calc_memory_bytes_paganin_filter_savu_legacy",
+    "_calc_memory_bytes_for_slices_paganin_filter",
+    "_calc_memory_bytes_for_slices_paganin_filter_savu_legacy",
 ]
 
 
-def _calc_memory_bytes_paganin_filter_savu_legacy(
-    non_slice_dims_shape: Tuple[int, int],
+def _calc_memory_bytes_for_slices_paganin_filter(
+    dims_shape: Tuple[int, int, int],
     dtype: np.dtype,
     **kwargs,
-) -> Tuple[int, int]:
-    return _calc_memory_bytes_paganin_filter(non_slice_dims_shape, dtype, **kwargs)
+) -> int:
+    return paganin_filter(dims_shape, calc_peak_gpu_mem=True, **kwargs)
 
 
-def _calc_memory_bytes_paganin_filter(
-    non_slice_dims_shape: Tuple[int, int],
+def _calc_memory_bytes_for_slices_paganin_filter_savu_legacy(
+    dims_shape: Tuple[int, int, int],
     dtype: np.dtype,
     **kwargs,
-) -> Tuple[int, int]:
-
-    # Input (unpadded)
-    unpadded_in_slice_size = np.prod(non_slice_dims_shape) * dtype.itemsize
-
-    # estimate padding size here based on non_slice dimensions
-    pad_tup = []
-    for dim_len in non_slice_dims_shape:
-        diff = __shift_bit_length(dim_len + 1) - dim_len
-        if dim_len % 2 == 0:
-            pad_width = diff // 2
-            pad_width = (pad_width, pad_width)
-        else:
-            # need an uneven padding for odd-number lengths
-            left_pad = diff // 2
-            right_pad = diff - left_pad
-            pad_width = (left_pad, right_pad)
-        pad_tup.append(pad_width)
-
-    # Padded input
-    padded_in_slice_size = (
-        (non_slice_dims_shape[0] + pad_tup[0][0] + pad_tup[0][1])
-        * (non_slice_dims_shape[1] + pad_tup[1][0] + pad_tup[1][1])
-        * dtype.itemsize
-    )
-
-    # Padded input cast to `complex64`
-    complex_slice = padded_in_slice_size / dtype.itemsize * np.complex64().nbytes
-
-    # Plan size for 2D FFT
-    ny = non_slice_dims_shape[0] + pad_tup[0][0] + pad_tup[0][1]
-    nx = non_slice_dims_shape[1] + pad_tup[1][0] + pad_tup[1][1]
-    fftplan_slice_size = cufft_estimate_2d(
-        nx=nx,
-        ny=ny,
-        fft_type=CufftType.CUFFT_C2C,
-    )
-
-    # Size of "reciprocal grid" generated, based on padded projections shape
-    grid_size = np.prod((ny, nx)) * np.float32().nbytes
-    filter_size = grid_size
-
-    # Size of cropped/unpadded + cast to float32 result of 2D IFFT
-    cropped_float32_res_slice = np.prod(non_slice_dims_shape) * np.float32().nbytes
-
-    # Size of negative log of cropped float32 result of 2D IFFT
-    negative_log_slice = cropped_float32_res_slice
-
-    # 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
-            + negative_log_slice
-        )
-
-    subtract_bytes = int(filter_size + grid_size)
-
-    return (tot_memory_bytes, subtract_bytes)
-
-
-def __shift_bit_length(x: int) -> int:
-    return 1 << (x - 1).bit_length()
+) -> int:
+    return paganin_filter_savu_legacy(dims_shape, calc_peak_gpu_mem=True, **kwargs)

httomo_backends/methods_database/query.py

@@ -143,6 +143,16 @@ class MethodsDatabaseQuery:
         )
         return memory_bytes
 
+    def calculate_memory_bytes_for_slices(
+        self, dims_shape: Tuple[int, int, int], dtype: np.dtype, **kwargs
+    ) -> int:
+        smodule = self._import_supporting_funcs_module()
+        module_mem: Callable = getattr(
+            smodule, "_calc_memory_bytes_for_slices_" + self.method_name
+        )
+        memory_bytes: int = module_mem(dims_shape, dtype, **kwargs)
+        return memory_bytes
+
     def calculate_output_dims(
         self, non_slice_dims_shape: Tuple[int, int], **kwargs
     ) -> Tuple[int, int]:

httomo_backends/scripts/yaml_templates_generator.py

@@ -225,6 +225,7 @@ def _get_discard_keys() -> List[str]:
         "power_of_2_cropping",
         "min_mem_usage_filter",
         "min_mem_usage_ifft2",
+        "calc_peak_gpu_mem",
     ]
     return discard_keys
 

{httomo_backends-0.9.0.dist-info → httomo_backends-0.9.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: httomo-backends
-Version: 0.9.0
+Version: 0.9.1
 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-0.9.0.dist-info → httomo_backends-0.9.1.dist-info}/RECORD

@@ -1,13 +1,13 @@
 httomo_backends/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 httomo_backends/cufft.py,sha256=mhxI6NeaEdX6-bFEHdQ2RZmf9Iu7LzVQZsJP6OLCjwQ,3283
 httomo_backends/methods_database/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-httomo_backends/methods_database/query.py,sha256=8jZQTmE351Me0Todn3NzyIjfZhLkzoJmagFGWAegYDw,5890
+httomo_backends/methods_database/query.py,sha256=kjWuhkGhs7Sdqm4yUpHutVHxjWTq0abGVi-FEXesFzA,6298
 httomo_backends/methods_database/packages/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 httomo_backends/methods_database/packages/httomo.yaml,sha256=tI3D-7IJcdu4EbKwjsje5MVKihOr3oswHzOrxtpBYBQ,535
 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=8l7bCXVegTaRM1T6UZ69MWCuTpDD7EeEkHhND4ibW5E,6055
+httomo_backends/methods_database/packages/backends/httomolibgpu/httomolibgpu.yaml,sha256=aURnvUvHB7dfrUsUi9QJyHKhAbDnzFaIEbhsnLaDhzo,6061
 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
@@ -17,7 +17,7 @@ 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=EdUrUZ1TWKUzKAFwoml_A7v6nchrRbAnElUGbA5xwHQ,679
-httomo_backends/methods_database/packages/backends/httomolibgpu/supporting_funcs/prep/phase.py,sha256=ph02VlQnvkO9GPetUGsh89RbAtgyElqgvjL5z8_ZUXo,4360
+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/recon/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 httomo_backends/methods_database/packages/backends/httomolibgpu/supporting_funcs/recon/algorithm.py,sha256=76Fl19BNMm2mo1gciAe_08QWSe5xmU5R2cpTFjelha0,21931
@@ -48,7 +48,7 @@ httomo_backends/pipelines_full/tomopy_gridrec_directive.yaml,sha256=NlrX-mqyzjJv
 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_templates_generator.py,sha256=I2RrpHeIO0SBh71aYYSeaZ_VrPhHMDxqn7sa6e1PeX8,8661
+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
 httomo_backends/yaml_templates/httomo/httomo.data.hdf.loaders/standard_tomo.yaml,sha256=mFGaYZZrE_dft7FE9Ngm-vXsd3dTftgwwjmLUCUkEZM,568
@@ -148,8 +148,8 @@ 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-0.9.0.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-httomo_backends-0.9.0.dist-info/METADATA,sha256=vDm2PjePbvsEYF3U0YGYaK8Yx7Y6ukqXQ8eQgcZ-3bM,2272
-httomo_backends-0.9.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-httomo_backends-0.9.0.dist-info/top_level.txt,sha256=v4x8d4CeEyMwo8QoqIvL_p-WoXAVD1bVnASPIrLjSTg,16
-httomo_backends-0.9.0.dist-info/RECORD,,
+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,,