httomo-backends 0.8.0__tar.gz → 0.9.0__tar.gz

{httomo_backends-0.8.0 → httomo_backends-0.9.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: httomo-backends
-Version: 0.8.0
+Version: 0.9.0
 Summary: Supplementary files for HTTomo backends.
 Author: Garry ODonnell, Jacob Williamson
 Author-email: Daniil Kazantsev <daniil.kazantsev@diamond.ac.uk>, Yousef Moazzam <yousef.moazzam@diamond.ac.uk>, Jessica Verschoyle <jessica.verschoyle@diamond.ac.uk>, Naman Gera <naman.gera@diamond.ac.uk>, scientificsoftware@diamond.ac.uk

{httomo_backends-0.8.0 → httomo_backends-0.9.0}/httomo_backends/methods_database/packages/backends/httomolib/httomolib.yaml

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

{httomo_backends-0.8.0 → httomo_backends-0.9.0}/httomo_backends/methods_database/packages/backends/httomolib/httomolib_modules.yaml

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

{httomo_backends-0.8.0 → httomo_backends-0.9.0}/httomo_backends/methods_database/packages/backends/httomolibgpu/httomolibgpu.yaml

@@ -1,4 +1,14 @@
 misc:
+  utils:
+    data_checker:
+      pattern: all
+      output_dims_change: False
+      implementation: gpu_cupy
+      save_result_default: False
+      padding: False
+      memory_gpu:
+        multiplier: 1.0
+        method: direct
   corr:
     median_filter:
       pattern: all
@@ -68,7 +78,7 @@ misc:
         method: module
 prep:
   normalize:
-    normalize:
+    dark_flat_field_correction:
       pattern: projection
       output_dims_change: False
       implementation: gpu_cupy
@@ -77,6 +87,15 @@ prep:
       memory_gpu:
         multiplier: None
         method: module
+    minus_log:
+      pattern: all
+      output_dims_change: False
+      implementation: gpu_cupy
+      save_result_default: False
+      padding: False
+      memory_gpu:
+        multiplier: 3.0
+        method: direct      
   phase:
     paganin_filter:
       pattern: projection
@@ -87,6 +106,15 @@ prep:
       memory_gpu:
         multiplier: None
         method: module
+    paganin_filter_savu_legacy:
+      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

{httomo_backends-0.8.0 → httomo_backends-0.9.0}/httomo_backends/methods_database/packages/backends/httomolibgpu/httomolibgpu_modules.yaml

@@ -1,3 +1,4 @@
+- httomolibgpu.misc.utils
 - httomolibgpu.misc.corr
 - httomolibgpu.misc.denoise
 - httomolibgpu.misc.morph

{httomo_backends-0.8.0 → httomo_backends-0.9.0}/httomo_backends/methods_database/packages/backends/httomolibgpu/supporting_funcs/prep/normalize.py

@@ -3,11 +3,11 @@ import numpy as np
 
 
 __all__ = [
-    "_calc_memory_bytes_normalize",
+    "_calc_memory_bytes_dark_flat_field_correction",
 ]
 
 
-def _calc_memory_bytes_normalize(
+def _calc_memory_bytes_dark_flat_field_correction(
     non_slice_dims_shape: Tuple[int, int],
     dtype: np.dtype,
     **kwargs,

{httomo_backends-0.8.0 → httomo_backends-0.9.0}/httomo_backends/methods_database/packages/backends/httomolibgpu/supporting_funcs/prep/phase.py

@@ -27,9 +27,18 @@ from httomo_backends.cufft import CufftType, cufft_estimate_2d
 
 __all__ = [
     "_calc_memory_bytes_paganin_filter",
+    "_calc_memory_bytes_paganin_filter_savu_legacy",
 ]
 
 
+def _calc_memory_bytes_paganin_filter_savu_legacy(
+    non_slice_dims_shape: Tuple[int, int],
+    dtype: np.dtype,
+    **kwargs,
+) -> Tuple[int, int]:
+    return _calc_memory_bytes_paganin_filter(non_slice_dims_shape, dtype, **kwargs)
+
+
 def _calc_memory_bytes_paganin_filter(
     non_slice_dims_shape: Tuple[int, int],
     dtype: np.dtype,

{httomo_backends-0.8.0 → httomo_backends-0.9.0}/httomo_backends/pipelines_full/FBP2d_astra_directive.yaml

@@ -1,9 +1,11 @@
 - method: standard_tomo
   module_path: httomo.data.hdf.loaders
+- method: dark_flat_field_correction
+  module_path: httomolibgpu.prep.normalize
 - method: find_center_vo
   module_path: httomolibgpu.recon.rotation
-- method: normalize
-  module_path: httomolibgpu.prep.normalize
+- method: minus_log
+  module_path: httomolibgpu.prep.normalize   
 - method: FBP2d_astra
   module_path: httomolibgpu.recon.algorithm
 

{httomo_backends-0.8.0 → httomo_backends-0.9.0}/httomo_backends/pipelines_full/FBP3d_tomobar_denoising_directive.yaml

@@ -1,13 +1,15 @@
 - method: standard_tomo
   module_path: httomo.data.hdf.loaders
-- method: find_center_vo
-  module_path: httomolibgpu.recon.rotation
 - method: remove_outlier
   module_path: httomolibgpu.misc.corr
-- method: normalize
+- method: dark_flat_field_correction
   module_path: httomolibgpu.prep.normalize
+- method: find_center_vo
+  module_path: httomolibgpu.recon.rotation  
 - method: remove_all_stripe
   module_path: httomolibgpu.prep.stripe
+- method: minus_log
+  module_path: httomolibgpu.prep.normalize
 - method: FBP3d_tomobar
   module_path: httomolibgpu.recon.algorithm
 - method: total_variation_PD

{httomo_backends-0.8.0 → httomo_backends-0.9.0}/httomo_backends/pipelines_full/FBP3d_tomobar_directive.yaml

@@ -1,13 +1,15 @@
 - method: standard_tomo
   module_path: httomo.data.hdf.loaders
-- method: find_center_vo
-  module_path: httomolibgpu.recon.rotation
 - method: remove_outlier
   module_path: httomolibgpu.misc.corr
-- method: normalize
+- method: dark_flat_field_correction
   module_path: httomolibgpu.prep.normalize
+- method: find_center_vo
+  module_path: httomolibgpu.recon.rotation 
 - method: remove_all_stripe
   module_path: httomolibgpu.prep.stripe
+- method: minus_log
+  module_path: httomolibgpu.prep.normalize  
 - method: FBP3d_tomobar
   module_path: httomolibgpu.recon.algorithm
 - method: calculate_stats

{httomo_backends-0.8.0 → httomo_backends-0.9.0}/httomo_backends/pipelines_full/FBP3d_tomobar_noimagesaving_directive.yaml

@@ -1,12 +1,14 @@
 - method: standard_tomo
   module_path: httomo.data.hdf.loaders
-- method: find_center_vo
-  module_path: httomolibgpu.recon.rotation
 - method: remove_outlier
   module_path: httomolibgpu.misc.corr
-- method: normalize
+- method: dark_flat_field_correction
   module_path: httomolibgpu.prep.normalize
+- method: find_center_vo
+  module_path: httomolibgpu.recon.rotation
 - method: remove_stripe_based_sorting
   module_path: httomolibgpu.prep.stripe
+- method: minus_log
+  module_path: httomolibgpu.prep.normalize
 - method: FBP3d_tomobar
   module_path: httomolibgpu.recon.algorithm

{httomo_backends-0.8.0 → httomo_backends-0.9.0}/httomo_backends/pipelines_full/FISTA3d_tomobar_directive.yaml

@@ -1,9 +1,11 @@
 - method: standard_tomo
   module_path: httomo.data.hdf.loaders
+- method: dark_flat_field_correction
+  module_path: httomolibgpu.prep.normalize
 - method: find_center_vo
   module_path: httomolibgpu.recon.rotation
-- method: normalize
-  module_path: httomolibgpu.prep.normalize
+- method: minus_log
+  module_path: httomolibgpu.prep.normalize  
 - method: FISTA3d_tomobar
   module_path: httomolibgpu.recon.algorithm
 - method: calculate_stats

{httomo_backends-0.8.0 → httomo_backends-0.9.0}/httomo_backends/pipelines_full/LPRec3d_tomobar_directive.yaml

@@ -1,13 +1,15 @@
 - method: standard_tomo
   module_path: httomo.data.hdf.loaders
-- method: find_center_vo
-  module_path: httomolibgpu.recon.rotation
 - method: remove_outlier
   module_path: httomolibgpu.misc.corr
-- method: normalize
+- method: dark_flat_field_correction
   module_path: httomolibgpu.prep.normalize
+- method: find_center_vo
+  module_path: httomolibgpu.recon.rotation  
 - method: remove_all_stripe
   module_path: httomolibgpu.prep.stripe
+- method: minus_log
+  module_path: httomolibgpu.prep.normalize
 - method: LPRec3d_tomobar
   module_path: httomolibgpu.recon.algorithm
 - method: calculate_stats

{httomo_backends-0.8.0 → httomo_backends-0.9.0}/httomo_backends/pipelines_full/deg360_distortion_FBP3d_tomobar_directive.yaml

@@ -1,15 +1,17 @@
 - method: standard_tomo
   module_path: httomo.data.hdf.loaders
-- method: find_center_360
-  module_path: httomolibgpu.recon.rotation
-- method: normalize
+- method: dark_flat_field_correction
   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
   module_path: httomolibgpu.prep.stripe
+- method: minus_log
+  module_path: httomolibgpu.prep.normalize
 - method: FBP3d_tomobar
   module_path: httomolibgpu.recon.algorithm
 - method: calculate_stats

{httomo_backends-0.8.0 → httomo_backends-0.9.0}/httomo_backends/pipelines_full/deg360_paganin_FBP3d_tomobar_directive.yaml

@@ -1,9 +1,9 @@
 - method: standard_tomo
   module_path: httomo.data.hdf.loaders
+- method: dark_flat_field_correction
+  module_path: httomolibgpu.prep.normalize
 - method: find_center_360
-  module_path: httomolibgpu.recon.rotation
-- method: normalize
-  module_path: httomolibgpu.prep.normalize  
+  module_path: httomolibgpu.recon.rotation  
 - method: sino_360_to_180
   module_path: httomolibgpu.misc.morph
 - method: remove_stripe_based_sorting

{httomo_backends-0.8.0 → httomo_backends-0.9.0}/httomo_backends/pipelines_full/sweep_center_FBP3d_tomobar_directive.yaml

@@ -1,7 +1,9 @@
 - method: standard_tomo
   module_path: httomo.data.hdf.loaders
-- method: normalize
+- method: dark_flat_field_correction
   module_path: httomolibgpu.prep.normalize
+- method: minus_log
+  module_path: httomolibgpu.prep.normalize  
 - method: FBP3d_tomobar
   module_path: httomolibgpu.recon.algorithm
   sweep_parameter: center

{httomo_backends-0.8.0 → httomo_backends-0.9.0}/httomo_backends/pipelines_full/sweep_paganin_FBP3d_tomobar_directive.yaml

@@ -1,9 +1,9 @@
 - method: standard_tomo
   module_path: httomo.data.hdf.loaders
+- method: dark_flat_field_correction
+  module_path: httomolibgpu.prep.normalize
 - method: find_center_vo
   module_path: httomolibgpu.recon.rotation  
-- method: normalize
-  module_path: httomolibgpu.prep.normalize
 - method: paganin_filter
   module_path: httomolibgpu.prep.phase
   sweep_parameter: ratio_delta_beta

{httomo_backends-0.8.0 → httomo_backends-0.9.0}/httomo_backends/pipelines_full/titaren_center_pc_FBP3d_resample_directive.yaml

@@ -1,11 +1,13 @@
 - method: standard_tomo
   module_path: httomo.data.hdf.loaders
+- method: dark_flat_field_correction
+  module_path: httomolibgpu.prep.normalize
 - method: find_center_pc
   module_path: httomolibgpu.recon.rotation
-- method: normalize
-  module_path: httomolibgpu.prep.normalize
 - method: remove_stripe_ti
   module_path: httomolibgpu.prep.stripe
+- method: minus_log
+  module_path: httomolibgpu.prep.normalize
 - method: FBP3d_tomobar
   module_path: httomolibgpu.recon.algorithm
 - method: data_resampler

{httomo_backends-0.8.0 → httomo_backends-0.9.0}/httomo_backends/scripts/yaml_pipelines_generator.py

@@ -94,6 +94,7 @@ def yaml_pipelines_generator(
     with open(path_to_pipelines, "r") as file:
         try:
             pipeline_file_content = yaml.load(file)
+            # print(f"Loading pipeline: {file.name}") # useful for debugging
         except OSError as e:
             print("loading yaml file with methods failed", e)
 
@@ -227,17 +228,20 @@ def yaml_pipelines_generator(
                     indent=0,
                 )
                 pipeline_full += yaml_template_method
-            elif "normalize" in module_name:
+            elif "dark_flat_field_correction" in method_name:
                 pipeline_full.yaml_set_comment_before_after_key(
                     i,
-                    "--- Normalisation of projection data using collected flats/darks images. --- ",
+                    "--- Flat-field and dark-field projection correction. --- ",
                     indent=0,
                 )
                 pipeline_full += yaml_template_method
-                pipeline_full[i]["parameters"].yaml_add_eol_comment(
-                    key="minus_log",
-                    comment="If Paganin method is used bellow, set it to 'false'.",
+            elif "minus_log" in method_name:
+                pipeline_full.yaml_set_comment_before_after_key(
+                    i,
+                    "--- Negative log is required for reconstruction to convert raw intensity measurements into the line integrals of attenuation. --- ",
+                    indent=0,
                 )
+                pipeline_full += yaml_template_method
             elif "phase" in module_name:
                 pipeline_full.yaml_set_comment_before_after_key(
                     i,

{httomo_backends-0.8.0 → httomo_backends-0.9.0}/httomo_backends/scripts/yaml_templates_generator.py

@@ -221,6 +221,10 @@ def _get_discard_keys() -> List[str]:
         "step_xy",
         "jpeg_quality",
         "watermark_vals",
+        "power_of_2_oversampling",
+        "power_of_2_cropping",
+        "min_mem_usage_filter",
+        "min_mem_usage_ifft2",
     ]
     return discard_keys
 

{httomo_backends-0.8.0 → httomo_backends-0.9.0}/httomo_backends/yaml_templates/httomo/httomo.data.hdf.loaders/standard_tomo.yaml

@@ -15,3 +15,4 @@
         stop: null
     darks: null
     flats: null
+    continuous_scan_subset: null

httomo_backends-0.9.0/httomo_backends/yaml_templates/httomolib/httomolib.misc.utils/data_checker.yaml

@@ -0,0 +1,7 @@
+- method: data_checker
+  module_path: httomolib.misc.utils
+  parameters:
+    infsnans_correct: true
+    zeros_warning: false
+    data_to_method_name: null
+    verbosity: true

httomo_backends-0.9.0/httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.misc.utils/data_checker.yaml

@@ -0,0 +1,7 @@
+- method: data_checker
+  module_path: httomolibgpu.misc.utils
+  parameters:
+    infsnans_correct: true
+    zeros_warning: false
+    data_to_method_name: null
+    verbosity: true

httomo_backends-0.8.0/httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.normalize/normalize.yaml → httomo_backends-0.9.0/httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.normalize/dark_flat_field_correction.yaml

@@ -1,9 +1,6 @@
-- method: normalize
+- method: dark_flat_field_correction
   module_path: httomolibgpu.prep.normalize
   parameters:
     flats_multiplier: 1.0
     darks_multiplier: 1.0
     cutoff: 10.0
-    minus_log: true
-    nonnegativity: false
-    remove_nans: false

httomo_backends-0.9.0/httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.normalize/minus_log.yaml

@@ -0,0 +1,3 @@
+- method: minus_log
+  module_path: httomolibgpu.prep.normalize
+  parameters: {}

httomo_backends-0.9.0/httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.phase/paganin_filter_savu_legacy.yaml

@@ -0,0 +1,7 @@
+- method: paganin_filter_savu_legacy
+  module_path: httomolibgpu.prep.phase
+  parameters:
+    pixel_size: 1.28
+    distance: 1.0
+    energy: 53.0
+    ratio_delta_beta: 250

{httomo_backends-0.8.0 → httomo_backends-0.9.0}/httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/CGLS3d_tomobar.yaml

@@ -7,4 +7,3 @@
     recon_mask_radius: 0.95
     iterations: 20
     nonnegativity: true
-    neglog: false

{httomo_backends-0.8.0 → httomo_backends-0.9.0}/httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/FBP2d_astra.yaml

@@ -8,4 +8,3 @@
     filter_d: null
     recon_size: null
     recon_mask_radius: 0.95
-    neglog: false

{httomo_backends-0.8.0 → httomo_backends-0.9.0}/httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/FBP3d_tomobar.yaml

@@ -6,4 +6,3 @@
     filter_freq_cutoff: 0.35
     recon_size: null
     recon_mask_radius: 0.95
-    neglog: false

{httomo_backends-0.8.0 → httomo_backends-0.9.0}/httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/FISTA3d_tomobar.yaml

@@ -12,4 +12,3 @@
     regularisation_iterations: 50
     regularisation_half_precision: true
     nonnegativity: true
-    neglog: false

{httomo_backends-0.8.0 → httomo_backends-0.9.0}/httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/LPRec3d_tomobar.yaml

@@ -7,8 +7,3 @@
     filter_freq_cutoff: 1.0
     recon_size: null
     recon_mask_radius: 0.95
-    power_of_2_oversampling: true
-    power_of_2_cropping: false
-    min_mem_usage_filter: true
-    min_mem_usage_ifft2: true
-    neglog: false

{httomo_backends-0.8.0 → httomo_backends-0.9.0}/httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/SIRT3d_tomobar.yaml

@@ -7,4 +7,3 @@
     recon_mask_radius: 0.95
     iterations: 300
     nonnegativity: true
-    neglog: false

{httomo_backends-0.8.0 → httomo_backends-0.9.0}/httomo_backends.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: httomo-backends
-Version: 0.8.0
+Version: 0.9.0
 Summary: Supplementary files for HTTomo backends.
 Author: Garry ODonnell, Jacob Williamson
 Author-email: Daniil Kazantsev <daniil.kazantsev@diamond.ac.uk>, Yousef Moazzam <yousef.moazzam@diamond.ac.uk>, Jessica Verschoyle <jessica.verschoyle@diamond.ac.uk>, Naman Gera <naman.gera@diamond.ac.uk>, scientificsoftware@diamond.ac.uk

{httomo_backends-0.8.0 → httomo_backends-0.9.0}/httomo_backends.egg-info/SOURCES.txt

@@ -67,6 +67,7 @@ httomo_backends/yaml_templates/httomolib/httomolib.misc.images/save_to_images.ya
 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.misc.utils/data_checker.yaml
 httomo_backends/yaml_templates/httomolib/httomolib.prep.phase/paganin_filter.yaml
 httomo_backends/yaml_templates/httomolibgpu/__init__.py
 httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.misc.corr/median_filter.yaml
@@ -76,9 +77,12 @@ httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.misc.denoise/total_vari
 httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.misc.morph/data_resampler.yaml
 httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.misc.morph/sino_360_to_180.yaml
 httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.misc.rescale/rescale_to_int.yaml
+httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.misc.utils/data_checker.yaml
 httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.alignment/distortion_correction_proj_discorpy.yaml
-httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.normalize/normalize.yaml
+httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.normalize/dark_flat_field_correction.yaml
+httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.normalize/minus_log.yaml
 httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.phase/paganin_filter.yaml
+httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.phase/paganin_filter_savu_legacy.yaml
 httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.stripe/raven_filter.yaml
 httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.stripe/remove_all_stripe.yaml
 httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.stripe/remove_stripe_based_sorting.yaml

{httomo_backends-0.8.0 → httomo_backends-0.9.0}/pyproject.toml

@@ -24,7 +24,7 @@ dev_template = "{tag}"
 
 [project]
 name = "httomo-backends"
-version = "0.8.0"
+version = "0.9.0"
 description = "Supplementary files for HTTomo backends."
 readme = "README.rst"
 license = {text = "BSD-3-Clause"}

{httomo_backends-0.8.0 → httomo_backends-0.9.0}/tests/test_httomolibgpu.py

@@ -14,7 +14,7 @@ from httomo_backends.methods_database.query import MethodsDatabaseQuery
 
 
 from httomolibgpu.misc.morph import data_resampler, sino_360_to_180
-from httomolibgpu.prep.normalize import normalize
+from httomolibgpu.prep.normalize import dark_flat_field_correction, minus_log
 from httomolibgpu.prep.phase import paganin_filter
 from httomolibgpu.prep.alignment import distortion_correction_proj_discorpy
 from httomolibgpu.prep.stripe import (
@@ -78,7 +78,9 @@ class MaxMemoryHook(cp.cuda.MemoryHook):
 @pytest.mark.parametrize("dtype", ["uint16", "float32"])
 @pytest.mark.parametrize("slices", [50, 121])
 @pytest.mark.cupy
-def test_normalize_memoryhook(flats, darks, ensure_clean_memory, dtype, slices):
+def test_dark_flat_field_correction_memoryhook(
+    flats, darks, ensure_clean_memory, dtype, slices
+):
     hook = MaxMemoryHook()
     data = cp.random.random_sample(
         (slices, flats.shape[1], flats.shape[2]), dtype=np.float32
@@ -88,7 +90,7 @@ def test_normalize_memoryhook(flats, darks, ensure_clean_memory, dtype, slices):
         flats = flats.astype(np.uint16)
         data = data.astype(np.uint16)
     with hook:
-        normalize(cp.copy(data), flats, darks, minus_log=True).get()
+        dark_flat_field_correction(cp.copy(data), flats, darks).get()
 
     # make sure estimator function is within range (80% min, 100% max)
     max_mem = (
@@ -96,8 +98,8 @@ def test_normalize_memoryhook(flats, darks, ensure_clean_memory, dtype, slices):
     )  # the amount of memory in bytes needed for the method according to memoryhook
 
     # now we estimate how much of the total memory required for this data
-    (estimated_memory_bytes, subtract_bytes) = _calc_memory_bytes_normalize(
-        data.shape[1:], dtype=data.dtype
+    (estimated_memory_bytes, subtract_bytes) = (
+        _calc_memory_bytes_dark_flat_field_correction(data.shape[1:], dtype=data.dtype)
     )
 
     estimated_memory_mb = round(slices * estimated_memory_bytes / (1024**2), 2)
@@ -113,6 +115,41 @@ def test_normalize_memoryhook(flats, darks, ensure_clean_memory, dtype, slices):
     assert percents_relative_maxmem <= 20
 
 
+@pytest.mark.parametrize("slices", [3, 10, 20])
+@pytest.mark.cupy
+def test_minus_log_memoryhook(ensure_clean_memory, slices):
+    hook = MaxMemoryHook()
+    data = cp.random.random_sample((slices, 2560, 2560), dtype=np.float32)
+
+    with hook:
+        minus_log(cp.copy(data))
+
+    # make sure estimator function is within range (80% min, 100% max)
+    max_mem = (
+        hook.max_mem
+    )  # the amount of memory in bytes needed for the method according to memoryhook
+
+    # now we estimate how much of the total memory required for this data
+    method_query = MethodsDatabaseQuery("httomolibgpu.prep.normalize", "minus_log")
+    memory_requirements = method_query.get_memory_gpu_params()
+    assert memory_requirements is not None
+    assert memory_requirements.multiplier is not None
+    estimated_memory_bytes = (
+        memory_requirements.multiplier * np.prod(cp.shape(data)) * float32().nbytes
+    )
+
+    estimated_memory_mb = round(estimated_memory_bytes / (1024**2), 2)
+
+    max_mem_mb = round(max_mem / (1024**2), 2)
+    # now compare both memory estimations
+    difference_mb = abs(estimated_memory_mb - max_mem_mb)
+    percents_relative_maxmem = round((difference_mb / max_mem_mb) * 100)
+    # the estimated_memory_mb should be LARGER or EQUAL to max_mem_mb
+    # the resulting percent value should not deviate from max_mem on more than 20%
+    assert estimated_memory_mb >= max_mem_mb
+    assert percents_relative_maxmem <= 20
+
+
 @pytest.mark.parametrize("dtype", ["uint16"])
 @pytest.mark.parametrize("slices", [10, 20])
 @pytest.mark.cupy

{httomo_backends-0.8.0 → httomo_backends-0.9.0}/tests/test_method_query.py

@@ -32,12 +32,16 @@ def test_get_invalid_method():
 
 
 def test_httomolibgpu_pattern():
-    query = MethodsDatabaseQuery("httomolibgpu.prep.normalize", "normalize")
+    query = MethodsDatabaseQuery(
+        "httomolibgpu.prep.normalize", "dark_flat_field_correction"
+    )
     assert query.get_pattern() == Pattern.projection
 
 
 def test_httomolibgpu_implementation():
-    query = MethodsDatabaseQuery("httomolibgpu.prep.normalize", "normalize")
+    query = MethodsDatabaseQuery(
+        "httomolibgpu.prep.normalize", "dark_flat_field_correction"
+    )
     assert query.get_implementation() == "gpu_cupy"
 
 
@@ -47,12 +51,16 @@ def test_httomolibgpu_implementation2():
 
 
 def test_httomolibgpu_output_dims_change():
-    query = MethodsDatabaseQuery("httomolibgpu.prep.normalize", "normalize")
+    query = MethodsDatabaseQuery(
+        "httomolibgpu.prep.normalize", "dark_flat_field_correction"
+    )
     assert query.get_output_dims_change() is False
 
 
 def test_httomolibgpu_default_save_result():
-    query = MethodsDatabaseQuery("httomolibgpu.prep.normalize", "normalize")
+    query = MethodsDatabaseQuery(
+        "httomolibgpu.prep.normalize", "dark_flat_field_correction"
+    )
 
     assert query.save_result_default() is False
 
@@ -64,7 +72,9 @@ def test_httomolibgpu_default_save_result_recon():
 
 
 def test_httomolibgpu_padding_false():
-    query = MethodsDatabaseQuery("httomolibgpu.prep.normalize", "normalize")
+    query = MethodsDatabaseQuery(
+        "httomolibgpu.prep.normalize", "dark_flat_field_correction"
+    )
     assert query.padding() is False
 
 
@@ -90,7 +100,9 @@ def test_all_methods_have_padding_parameter():
 
 
 def test_get_gpu_memory_params():
-    query = MethodsDatabaseQuery("httomolibgpu.prep.normalize", "normalize")
+    query = MethodsDatabaseQuery(
+        "httomolibgpu.prep.normalize", "dark_flat_field_correction"
+    )
     mempars = query.get_memory_gpu_params()
     assert mempars is not None
     assert mempars.method == "module"