httomo-backends 0.6.3__py3-none-any.whl → 0.7.1__py3-none-any.whl

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

@@ -26,7 +26,7 @@ misc:
       save_result_default: False
       padding: True
       memory_gpu:
-        multiplier: 5
+        multiplier: 6.1
         method: direct
     total_variation_PD:
       pattern: all
@@ -35,7 +35,7 @@ misc:
       save_result_default: False
       padding: True
       memory_gpu:
-        multiplier: 7
+        multiplier: 9.1
         method: direct        
   morph:
     sino_360_to_180:
@@ -181,6 +181,15 @@ recon:
       memory_gpu:
         multiplier: None
         method: module
+    FISTA3d_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/methods_database/packages/backends/httomolibgpu/supporting_funcs/recon/algorithm.py

@@ -30,14 +30,21 @@ __all__ = [
     "_calc_memory_bytes_LPRec3d_tomobar",
     "_calc_memory_bytes_SIRT3d_tomobar",
     "_calc_memory_bytes_CGLS3d_tomobar",
+    "_calc_memory_bytes_FISTA3d_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_padding_FISTA3d_tomobar",
 ]
 
 
+def _calc_padding_FISTA3d_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"
@@ -72,14 +79,21 @@ def _calc_output_dim_CGLS3d_tomobar(non_slice_dims_shape, **kwargs):
     return __calc_output_dim_recon(non_slice_dims_shape, **kwargs)
 
 
+def _calc_output_dim_FISTA3d_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,
     **kwargs,
 ) -> Tuple[int, int]:
+    detector_pad = 0
     if "detector_pad" in kwargs:
         detector_pad = kwargs["detector_pad"]
-    else:
+    if detector_pad is True:
+        detector_pad = __estimate_detectorHoriz_padding(non_slice_dims_shape[1])
+    elif detector_pad is False:
         detector_pad = 0
 
     angles_tot = non_slice_dims_shape[0]
@@ -132,11 +146,11 @@ def _calc_memory_bytes_FBP3d_tomobar(
 
     # 7. astra backprojection will generate an output array
     # https://github.com/dkazanc/ToMoBAR/blob/54137829b6326406e09f6ef9c95eb35c213838a7/tomobar/astra_wrappers/astra_base.py#L524
-    output_dims = _calc_output_dim_FBP3d_tomobar(non_slice_dims_shape, **kwargs)
+    output_dims = _calc_output_dim_FBP3d_tomobar((angles_tot, det_width), **kwargs)
     recon_output_size = np.prod(output_dims) * np.float32().itemsize
 
     # 7. astra backprojection makes a copy of the input
-    astra_input_slice_size = np.prod(non_slice_dims_shape) * np.float32().itemsize
+    astra_input_slice_size = (angles_tot * det_width) * np.float32().itemsize
 
     ## now we calculate back projection memory (2 copies of the input + reconstruction output)
     projection_mem_size = (
@@ -169,10 +183,20 @@ def _calc_memory_bytes_LPRec3d_tomobar(
 ) -> Tuple[int, int]:
     # Based on: https://github.com/dkazanc/ToMoBAR/pull/112/commits/4704ecdc6ded3dd5ec0583c2008aa104f30a8a39
 
+    detector_pad = 0
     if "detector_pad" in kwargs:
         detector_pad = kwargs["detector_pad"]
-    else:
-        detector_pad = 0
+    if detector_pad is True:
+        detector_pad = __estimate_detectorHoriz_padding(non_slice_dims_shape[1])
+    elif detector_pad is False:
+        detector_pad = 0        
+
+    min_mem_usage_filter = False
+    if "min_mem_usage_filter" in kwargs:
+        min_mem_usage_filter = kwargs["min_mem_usage_filter"]
+    min_mem_usage_ifft2 = False
+    if "min_mem_usage_ifft2" in kwargs:
+        min_mem_usage_ifft2 = kwargs["min_mem_usage_ifft2"]
 
     angles_tot = non_slice_dims_shape[0]
     DetectorsLengthH_prepad = non_slice_dims_shape[1]
@@ -195,11 +219,22 @@ def _calc_memory_bytes_LPRec3d_tomobar(
         )
     )
 
-    center_size = 6144
-    center_size = min(center_size, n * 2 + m * 2)
+    center_size = 32768
+    center_size = min(center_size, n * 2)
+
+    chunk_count = 4
+    projection_chunk_count = 4
+    oversampling_level = 4  # at least 3 or larger required
+    power_of_2_oversampling = True
+
+    if power_of_2_oversampling:
+        ne = 2 ** math.ceil(math.log2(DetectorsLengthH_prepad * 3))
+        if n > ne:
+            ne = 2 ** math.ceil(math.log2(n))
+    else:
+        ne = int(oversampling_level * DetectorsLengthH_prepad)
+        ne = max(ne, n)
 
-    oversampling_level = 2  # at least 2 or larger required
-    ne = oversampling_level * n
     padding_m = ne // 2 - n // 2
 
     if "angles" in kwargs:
@@ -213,8 +248,6 @@ def _calc_memory_bytes_LPRec3d_tomobar(
             np.ceil(2)
         )  # assume a 2 * PI projection angle range
 
-    chunk_count = 4
-
     output_dims = __calc_output_dim_recon(non_slice_dims_shape, **kwargs)
     if odd_horiz:
         output_dims = tuple(x + 1 for x in output_dims)
@@ -252,7 +285,7 @@ def _calc_memory_bytes_LPRec3d_tomobar(
     irfft_result_size = angles_tot * (n + padding_m * 2) * np.float32().itemsize
 
     datac_size = angles_tot * n * np.complex64().itemsize / 2
-    fde_size = (2 * m + 2 * n) * (2 * m + 2 * n) * np.complex64().itemsize / 2
+    fde_size = 2 * n * 2 * n * np.complex64().itemsize / 2
     fft_plan_slice_size = (
         cufft_estimate_1d(nx=n, fft_type=CufftType.CUFFT_C2C, batch=angles_tot * SLICES)
         / SLICES
@@ -270,7 +303,7 @@ def _calc_memory_bytes_LPRec3d_tomobar(
     )
     ifft2_plan_slice_size = (
         cufft_estimate_2d(
-            nx=(2 * m + 2 * n), ny=(2 * m + 2 * n), fft_type=CufftType.CUFFT_C2C
+            nx=2 * n, ny=2 * n, fft_type=CufftType.CUFFT_C2C
         )
         / 2
     )
@@ -309,24 +342,40 @@ def _calc_memory_bytes_LPRec3d_tomobar(
     add_to_memory_counters(scaled_filter_size, False)
 
     add_to_memory_counters(tmp_p_input_slice, True)
+    if min_mem_usage_filter:
+        add_to_memory_counters(rfft_plan_slice_size / 4 / projection_chunk_count, False)
+        add_to_memory_counters(irfft_plan_slice_size / 4 / projection_chunk_count, False)
+        add_to_memory_counters(padded_tmp_p_input_slice / projection_chunk_count, False)
+
+        add_to_memory_counters(rfft_result_size / projection_chunk_count, False)
+        add_to_memory_counters(filtered_rfft_result_size / projection_chunk_count, False)
+        add_to_memory_counters(-rfft_result_size / projection_chunk_count, False)
+        add_to_memory_counters(-padded_tmp_p_input_slice / projection_chunk_count, False)
+
+        add_to_memory_counters(irfft_scratch_memory_size / projection_chunk_count, False)
+        add_to_memory_counters(-irfft_scratch_memory_size / projection_chunk_count, False)
+        add_to_memory_counters(irfft_result_size / projection_chunk_count, False)
+        add_to_memory_counters(-filtered_rfft_result_size / projection_chunk_count, False)
+
+        add_to_memory_counters(-irfft_result_size / projection_chunk_count, False)
+    else:
+        add_to_memory_counters(rfft_plan_slice_size / chunk_count / projection_chunk_count * 2, True)
+        add_to_memory_counters(irfft_plan_slice_size / chunk_count / projection_chunk_count * 2, True)
+        # add_to_memory_counters(irfft_scratch_memory_size / chunk_count / projection_chunk_count, True)
+        for _ in range(0, chunk_count):
+            add_to_memory_counters(padded_tmp_p_input_slice / chunk_count / projection_chunk_count, True)
 
-    add_to_memory_counters(rfft_plan_slice_size / chunk_count * 2, True)
-    add_to_memory_counters(irfft_plan_slice_size / chunk_count * 2, True)
-    # add_to_memory_counters(irfft_scratch_memory_size / chunk_count, True)
-    for _ in range(0, chunk_count):
-        add_to_memory_counters(padded_tmp_p_input_slice / chunk_count, True)
-
-        add_to_memory_counters(rfft_result_size / chunk_count, True)
-        add_to_memory_counters(filtered_rfft_result_size / chunk_count, True)
-        add_to_memory_counters(-rfft_result_size / chunk_count, True)
-        add_to_memory_counters(-padded_tmp_p_input_slice / chunk_count, True)
+            add_to_memory_counters(rfft_result_size / chunk_count / projection_chunk_count, True)
+            add_to_memory_counters(filtered_rfft_result_size / chunk_count / projection_chunk_count, True)
+            add_to_memory_counters(-rfft_result_size / chunk_count / projection_chunk_count, True)
+            add_to_memory_counters(-padded_tmp_p_input_slice / chunk_count / projection_chunk_count, True)
 
-        add_to_memory_counters(irfft_scratch_memory_size / chunk_count, True)
-        add_to_memory_counters(-irfft_scratch_memory_size / chunk_count, True)
-        add_to_memory_counters(irfft_result_size / chunk_count, True)
-        add_to_memory_counters(-filtered_rfft_result_size / chunk_count, True)
+            add_to_memory_counters(irfft_scratch_memory_size / chunk_count / projection_chunk_count, True)
+            add_to_memory_counters(-irfft_scratch_memory_size / chunk_count / projection_chunk_count, True)
+            add_to_memory_counters(irfft_result_size / chunk_count / projection_chunk_count, True)
+            add_to_memory_counters(-filtered_rfft_result_size / chunk_count / projection_chunk_count, True)
 
-        add_to_memory_counters(-irfft_result_size / chunk_count, True)
+            add_to_memory_counters(-irfft_result_size / chunk_count / projection_chunk_count, True)
 
     add_to_memory_counters(-padded_in_slice_size, True)
     add_to_memory_counters(-filter_size, False)
@@ -342,17 +391,27 @@ def _calc_memory_bytes_LPRec3d_tomobar(
 
     add_to_memory_counters(-fft_result_size, True)
 
-    add_to_memory_counters(ifft2_plan_slice_size / chunk_count * 2, True)
-    for _ in range(0, chunk_count):
-        add_to_memory_counters(fde_size / chunk_count, True)
-        add_to_memory_counters(-fde_size / chunk_count, True)
+    if min_mem_usage_ifft2:
+        add_to_memory_counters(ifft2_plan_slice_size, False)
+        add_to_memory_counters(fde_size * 2, False)
+        add_to_memory_counters(-fde_size * 2, False)
+    else:
+        add_to_memory_counters(ifft2_plan_slice_size / chunk_count * 2, True)
+        for _ in range(0, chunk_count):
+            add_to_memory_counters(fde_size / chunk_count, True)
+            add_to_memory_counters(-fde_size / chunk_count, True)
 
     add_to_memory_counters(recon_output_size, True)
     add_to_memory_counters(-fde_size, True)
     add_to_memory_counters(circular_mask_size, False)
     add_to_memory_counters(after_recon_swapaxis_slice, True)
 
-    return (tot_memory_bytes * 1.05, fixed_amount + 250 * 1024 * 1024)
+    if min_mem_usage_filter and min_mem_usage_ifft2:
+        return (tot_memory_bytes * 1.15, fixed_amount)
+    elif min_mem_usage_filter and not min_mem_usage_ifft2:
+        return (tot_memory_bytes + 60 * 1024 * 1024, fixed_amount)
+    else:
+        return (tot_memory_bytes * 1.1, fixed_amount)
 
 
 def _calc_memory_bytes_SIRT3d_tomobar(
@@ -361,21 +420,48 @@ def _calc_memory_bytes_SIRT3d_tomobar(
     **kwargs,
 ) -> Tuple[int, int]:
 
+    detector_pad = 0
     if "detector_pad" in kwargs:
         detector_pad = kwargs["detector_pad"]
-    else:
-        detector_pad = 0
+    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 = non_slice_dims_shape[1] + 2 * detector_pad
+    DetectorsLengthH_padded = non_slice_dims_shape[1] + 2 * detector_pad
     # calculate the output shape
     output_dims = _calc_output_dim_SIRT3d_tomobar(non_slice_dims_shape, **kwargs)
+    recon_data_size_original = (
+        np.prod(output_dims) * dtype.itemsize
+    )  # x_rec user-defined size
+
+    in_data_size = (anglesnum * DetectorsLengthH_padded) * dtype.itemsize
+
+    output_dims_larger_grid = (DetectorsLengthH_padded, DetectorsLengthH_padded)
 
-    in_data_size = (anglesnum * DetectorsLengthH) * dtype.itemsize
-    out_data_size = np.prod(output_dims) * dtype.itemsize
+    out_data_size = np.prod(output_dims_larger_grid) * dtype.itemsize
 
-    astra_projection = 2.5 * (in_data_size + out_data_size)
+    R = in_data_size
+    C = out_data_size
 
-    tot_memory_bytes = int(2 * in_data_size + 2 * out_data_size + astra_projection)
+    Res = in_data_size
+    Res_times_R = Res
+    C_times_res = out_data_size
+
+    astra_projection = (in_data_size + out_data_size)
+
+    tot_memory_bytes = int(
+        recon_data_size_original
+        + in_data_size
+        + out_data_size
+        + R
+        + C
+        + Res
+        + Res_times_R
+        + C_times_res
+        + astra_projection
+    )
     return (tot_memory_bytes, 0)
 
 
@@ -384,20 +470,102 @@ def _calc_memory_bytes_CGLS3d_tomobar(
     dtype: np.dtype,
     **kwargs,
 ) -> Tuple[int, int]:
+    detector_pad = 0
     if "detector_pad" in kwargs:
         detector_pad = kwargs["detector_pad"]
-    else:
-        detector_pad = 0
+    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 = non_slice_dims_shape[1] + 2 * detector_pad
+    DetectorsLengthH_padded = non_slice_dims_shape[1] + 2 * detector_pad
     # calculate the output shape
     output_dims = _calc_output_dim_CGLS3d_tomobar(non_slice_dims_shape, **kwargs)
+    recon_data_size_original = (
+        np.prod(output_dims) * dtype.itemsize
+    )  # x_rec user-defined size
+
+    in_data_size = (anglesnum * DetectorsLengthH_padded) * dtype.itemsize
+    output_dims_larger_grid = (DetectorsLengthH_padded, DetectorsLengthH_padded)
+    recon_data_size = (
+        np.prod(output_dims_larger_grid) * dtype.itemsize
+    )  # large volume in the algorithm
+    recon_data_size2 = recon_data_size  # x_rec linearised
+    d_recon = recon_data_size
+    d_recon2 = d_recon  # linearised, possibly a copy
+
+    data_r = in_data_size
+    Ad = recon_data_size
+    Ad2 = Ad
+    s = data_r
+    collection = (
+        in_data_size
+        + recon_data_size_original
+        + recon_data_size
+        + recon_data_size2
+        + d_recon
+        + d_recon2
+        + data_r
+        + Ad
+        + Ad2
+        + s
+    )
+    astra_contribution = in_data_size + recon_data_size
 
-    in_data_size = (anglesnum * DetectorsLengthH) * dtype.itemsize
-    out_data_size = np.prod(output_dims) * dtype.itemsize
+    tot_memory_bytes = int(collection + astra_contribution)
+    return (tot_memory_bytes, 0)
 
-    astra_projection = 2.5 * (in_data_size + out_data_size)
 
-    tot_memory_bytes = int(2 * in_data_size + 2 * out_data_size + astra_projection)
+def _calc_memory_bytes_FISTA3d_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)
+
+    residual_grad = in_data_siz_pad
+    out_data_size = np.prod(output_dims_larger_grid) * dtype.itemsize
+    X_t = out_data_size
+    X_old = out_data_size
+
+    grad_fidelity = out_data_size
+
+    fista_part = (
+        recon_data_size_original
+        + in_data_siz_pad
+        + residual_grad
+        + grad_fidelity
+        + X_t
+        + X_old
+        + out_data_size
+    )
+    regul_part = 8 * np.prod(output_dims_larger_grid) * dtype.itemsize
+
+    tot_memory_bytes = int(fista_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
+    padded_add_margin = int(0.1 * padded_value_exact)
+    return padded_value_exact + padded_add_margin

httomo_backends/pipelines_full/FISTA3d_tomobar_directive.yaml

@@ -0,0 +1,14 @@
+- 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: FISTA3d_tomobar
+  module_path: httomolibgpu.recon.algorithm
+- method: calculate_stats
+  module_path: httomo.methods
+- method: rescale_to_int
+  module_path: httomolib.misc.rescale
+- method: save_to_images
+  module_path: httomolib.misc.images

httomo_backends/scripts/yaml_pipelines_generator.py

@@ -31,14 +31,10 @@ import ruamel.yaml
 import httomo_backends
 import yaml
 
-try:
-    from httomo import __version__ as httomo_version
-except:
-    httomo_version = "2.6"  # temporary version fix for sphinx build
-    pass
 
 CS = ruamel.yaml.comments.CommentedSeq  # defaults to block style
 
+
 class SweepRange:
     """SweepRange class."""
 
@@ -140,11 +136,8 @@ 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}"
+                "This pipeline should be supported by the latest developments of HTTomo. Use module load httomo/latest module at Diamond."
             )            
 
             if "loaders" in module_name:
@@ -254,7 +247,7 @@ def yaml_pipelines_generator(
                 pipeline_full += yaml_template_method
                 pipeline_full[i]["parameters"].yaml_add_eol_comment(
                     key="alpha",
-                    comment="Controls the balance between the strength of the filter and the amount of noise reduction. Higher leads to less noise and more blur.",
+                    comment="Controls the balance between the strength of the filter and the amount of noise reduction. Smaller values lead to less noise and more blur.",
                 )
             elif "stripe" in module_name:
                 pipeline_full.yaml_set_comment_before_after_key(
@@ -276,7 +269,7 @@ def yaml_pipelines_generator(
                 )
                 pipeline_full[i]["parameters"].yaml_add_eol_comment(
                     key="detector_pad",
-                    comment="Horizontal detector padding to minimise circle/arc-type artifacts in the reconstruction",
+                    comment="Horizontal detector padding to minimise circle/arc-type artifacts in the reconstruction. Set to true to enable automatic padding or an integer",
                 )
                 pipeline_full[i]["parameters"].yaml_add_eol_comment(
                     key="recon_mask_radius",

httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.misc.denoise/total_variation_PD.yaml

@@ -6,3 +6,4 @@
     isotropic: true
     nonnegativity: false
     lipschitz_const: 8.0
+    half_precision: false

httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.misc.denoise/total_variation_ROF.yaml

@@ -4,3 +4,4 @@
     regularisation_parameter: 1.0e-05
     iterations: 3000
     time_marching_parameter: 0.001
+    half_precision: false

httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/CGLS3d_tomobar.yaml

@@ -2,8 +2,9 @@
   module_path: httomolibgpu.recon.algorithm
   parameters:
     center: ${{centering.side_outputs.centre_of_rotation}}
-    detector_pad: 0
+    detector_pad: false
     recon_size: null
+    recon_mask_radius: 0.95
     iterations: 20
     nonnegativity: true
     neglog: false

httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/FBP2d_astra.yaml

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

httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/FBP3d_tomobar.yaml

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

httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/FISTA3d_tomobar.yaml

@@ -0,0 +1,15 @@
+- method: FISTA3d_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: 20
+    subsets_number: 6
+    regularisation_type: PD_TV
+    regularisation_parameter: 1.0e-06
+    regularisation_iterations: 50
+    regularisation_half_precision: true
+    nonnegativity: true
+    neglog: false

httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/LPRec3d_tomobar.yaml

@@ -2,9 +2,12 @@
   module_path: httomolibgpu.recon.algorithm
   parameters:
     center: ${{centering.side_outputs.centre_of_rotation}}
-    detector_pad: 0
+    detector_pad: false
     filter_type: shepp
     filter_freq_cutoff: 1.0
     recon_size: null
     recon_mask_radius: 0.95
+    power_of_2_oversampling: true
+    min_mem_usage_filter: false
+    min_mem_usage_ifft2: false
     neglog: false

httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/SIRT3d_tomobar.yaml

@@ -2,8 +2,9 @@
   module_path: httomolibgpu.recon.algorithm
   parameters:
     center: ${{centering.side_outputs.centre_of_rotation}}
-    detector_pad: 0
+    detector_pad: false
     recon_size: null
+    recon_mask_radius: 0.95
     iterations: 300
     nonnegativity: true
     neglog: false

{httomo_backends-0.6.3.dist-info → httomo_backends-0.7.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: httomo-backends
-Version: 0.6.3
+Version: 0.7.1
 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-0.6.3.dist-info → httomo_backends-0.7.1.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=HXfQPfhYjlNbnfRaBdTf7zs71Chvfl8B93P0ZfJQN7U,5118
+httomo_backends/methods_database/packages/backends/httomolibgpu/httomolibgpu.yaml,sha256=Y1a3J_OCeojiG4HhbRPkDdJ0KvdpGARkEk6k5OcIzHY,5347
 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
@@ -20,7 +20,7 @@ httomo_backends/methods_database/packages/backends/httomolibgpu/supporting_funcs
 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=PiCLqsGudum2fvVNWrU_lZq4lLJmcKpCS7wEorb6HsA,14972
+httomo_backends/methods_database/packages/backends/httomolibgpu/supporting_funcs/recon/algorithm.py,sha256=CuiMAxu7qG0I41XiucrvSf2kZHjid_dgD0gUXF9cE0k,21267
 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
@@ -36,6 +36,7 @@ httomo_backends/pipelines_full/FBP2d_astra_directive.yaml,sha256=BAT4wUa3nOacHRA
 httomo_backends/pipelines_full/FBP3d_tomobar_denoising_directive.yaml,sha256=Ycu8X7mS2n872e0ji4btPLjSTYgEhcZVPeMEeI6MPAk,644
 httomo_backends/pipelines_full/FBP3d_tomobar_directive.yaml,sha256=QyqyAmWZjmcgV0PjhgmZtSjytHt8BeRLncH4hkJRmcs,574
 httomo_backends/pipelines_full/FBP3d_tomobar_noimagesaving_directive.yaml,sha256=uute7GdEEshbnmljjeyDi3Z5aqZftBTvo7Ti4wKgzhk,403
+httomo_backends/pipelines_full/FISTA3d_tomobar_directive.yaml,sha256=xuBtnN3vT2tfpKwmW0CH12CRXeV2evNN2hpdPul9L6c,445
 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=3Ht3yAzi97VW29OfvDE9j_p3NYbZfHDlfZMuRivsdKo,676
@@ -46,7 +47,7 @@ httomo_backends/pipelines_full/titaren_center_pc_FBP3d_resample_directive.yaml,s
 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=9OeC8lEYSvGUEv0ceZMvuyL4kxoQ63NeIBMfOrlC_HQ,16540
+httomo_backends/scripts/yaml_pipelines_generator.py,sha256=t_B3qJ0AGsjzd1_rSp76pC-9o4JbO7e28UIfWcN9olk,16393
 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
@@ -62,24 +63,24 @@ httomo_backends/yaml_templates/httomolib/httomolib.prep.phase/paganin_filter.yam
 httomo_backends/yaml_templates/httomolibgpu/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.misc.corr/median_filter.yaml,sha256=vKTeGhT0eLXWMDBvfglisIIZINlBKagOjwRo4JFQRpQ,108
 httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.misc.corr/remove_outlier.yaml,sha256=k3y2Iwuv401EHdQZWIUreGAyEFoWasu7-0i7ibxRrhQ,110
-httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.misc.denoise/total_variation_PD.yaml,sha256=U46wnCcmvLXXiMVU91CpEjfq2XsTLG81v6i6O5wZBMA,213
-httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.misc.denoise/total_variation_ROF.yaml,sha256=2l4-tfLFSGM-emRS8x695WIGhMCxmTzTqO5x1t-2RyA,179
+httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.misc.denoise/total_variation_PD.yaml,sha256=73fCwAO9IcPuuC36g5_XJaIB9ujWPli5UdbqrLhWyIk,239
+httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.misc.denoise/total_variation_ROF.yaml,sha256=eXaD6jtKZ1gSplMG663lAhdS6Q79xns4AgKSuMx9Sgc,205
 httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.misc.morph/data_resampler.yaml,sha256=4fDcC2seGd_TFUyMG0DAs68NrJn5lmIsx7WQ_6bn-A4,142
 httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.misc.morph/sino_360_to_180.yaml,sha256=vikNDlp_Py6kye8-dySMpCxhYlJp_-AODQNGHTQCarQ,171
 httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.misc.rescale/rescale_to_int.yaml,sha256=WR_exoyowYnXgDOUH5JYGPQ17-MfUayuVkNwMQTHzac,198
 httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.alignment/distortion_correction_proj_discorpy.yaml,sha256=KxWTzuZOoHUymFt4OJZVT7jhPs6oAuUmSQskQJqKwZk,163
 httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.normalize/normalize.yaml,sha256=PIfA4jwCmnWtz7V5n0Zng8lPvD4h1YyIriBSL39CtVM,214
-httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.phase/paganin_filter_savu.yaml,sha256=9Hwxgu1WG6lMXliXF7XWx2Z9O1D1yMSWkRjXNfdrn9o,226
 httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.phase/paganin_filter_tomopy.yaml,sha256=sHWZibK7drnBufYVOND9LZATaBRMtHKkbbBoquCBcmE,157
 httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.stripe/raven_filter.yaml,sha256=SDqgP_RLq7jjnL9Fz7hfrKko4F7-yahCsabBIJ0XMC8,169
 httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.stripe/remove_all_stripe.yaml,sha256=MfoMeF_C2zRE7-W5cknhmG9-a5QYb5lpSdz9dwOndJQ,138
 httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.stripe/remove_stripe_based_sorting.yaml,sha256=xyv_XKqFhs801VcsMUfWPHiKvek0qh8RhkbnInWR5i8,116
 httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.stripe/remove_stripe_ti.yaml,sha256=5Ed2YbB0Kf-08_nNP5dzTukNDZopRTOo1I6ODJVRrlM,95
-httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/CGLS3d_tomobar.yaml,sha256=q6qCBdZHAkzVTvilkjhWATV88neFjzjUu9Kvcs2VrkM,244
-httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/FBP2d_astra.yaml,sha256=Nf2Gh0XewTK4PRwctIPU7KtAdnbd3YWGWHgJMQLLhhs,297
-httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/FBP3d_tomobar.yaml,sha256=PuJf07CK3wdoACwwRoI769oD0BLXJSVXXbkW9ABMm58,257
-httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/LPRec3d_tomobar.yaml,sha256=CgJxNqpeTLWG6DvQXTgkqzmX2wZaJCCG9_aJ-o_AAIs,281
-httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/SIRT3d_tomobar.yaml,sha256=MI3XHxpgKz-dQ3n0Zjfr9ir0hgh-7Uruke3iovgvGuc,245
+httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/CGLS3d_tomobar.yaml,sha256=oWoW2vYNXyAeQ81NaV865A0K8XDi3QIbzV9WcRQqi_A,276
+httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/FBP2d_astra.yaml,sha256=MxUbW-dMxMrI4Exn5mgh2ovie4Ldv1Eb-zS68ETsNCU,301
+httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/FBP3d_tomobar.yaml,sha256=H9-PTd8qW2qXqgHYw-NfZGgy2yut7ReKsbsR3x0_OOA,261
+httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/FISTA3d_tomobar.yaml,sha256=i2K7Yc19VY6uZZR8bVjb85jpWIShlM_yCGD-Z5Eb-5E,442
+httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/LPRec3d_tomobar.yaml,sha256=X_qcuTOcFW_rXaXU-XhZYQUaPkOgKe5r7uX5stpf1mE,382
+httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/SIRT3d_tomobar.yaml,sha256=oom622LQ8xAZbZiHm4t0PSKKsMkX5G743vVBqRbMQek,277
 httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.rotation/find_center_360.yaml,sha256=nXjbgTBDQcIlBWvXwMd8FoNimtq-8QabgNWAI-fiFU8,322
 httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.rotation/find_center_pc.yaml,sha256=g3CNIaLhhBI6igluIMwytFqVXzrDlv8A1EU1C7ey4FE,208
 httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.rotation/find_center_vo.yaml,sha256=CmJ_0a73jX7MmOxQIvQrrKg_2HEtK0MXNVXLrfR3caU,296
@@ -143,8 +144,8 @@ 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-0.6.3.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-httomo_backends-0.6.3.dist-info/METADATA,sha256=NkXRxl2hgozpRzwHrzLrPCzRmlzweZBgF1EsdngfNj0,2312
-httomo_backends-0.6.3.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-httomo_backends-0.6.3.dist-info/top_level.txt,sha256=v4x8d4CeEyMwo8QoqIvL_p-WoXAVD1bVnASPIrLjSTg,16
-httomo_backends-0.6.3.dist-info/RECORD,,
+httomo_backends-0.7.1.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+httomo_backends-0.7.1.dist-info/METADATA,sha256=fifr2fnWW5CvPDXWR1WA-9McdqN4LCbmtWW_QRf7BUI,2312
+httomo_backends-0.7.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+httomo_backends-0.7.1.dist-info/top_level.txt,sha256=v4x8d4CeEyMwo8QoqIvL_p-WoXAVD1bVnASPIrLjSTg,16
+httomo_backends-0.7.1.dist-info/RECORD,,

httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.phase/paganin_filter_savu.yaml

@@ -1,11 +0,0 @@
-- method: paganin_filter_savu
-  module_path: httomolibgpu.prep.phase
-  parameters:
-    ratio: 250.0
-    energy: 53.0
-    distance: 1.0
-    resolution: 1.28
-    pad_y: 100
-    pad_x: 100
-    pad_method: edge
-    increment: 0.0