initial commit (#135)

royerlab · Apr 7, 2022 · 7dd1a39 · 7dd1a39
1 parent 1a0a1f1
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Showing 14 changed files with 75 additions and 71 deletions.
diff --git a/aydin/it/classic_denoisers/_defaults.py b/aydin/it/classic_denoisers/_defaults.py
@@ -1,12 +1,16 @@
-default_optimiser = 'smart'
-default_enable_extended_blind_spot = False
-default_jinv_interpolation_mode = 'gaussian'
-default_crop_size_normal = 96000
-default_crop_size_large = 128000
-default_crop_size_verylarge = 256000
-default_max_evals_hyperlow = 16
-default_max_evals_ultralow = 32
-default_max_evals_verylow = 64
-default_max_evals_low = 128
-default_max_evals_normal = 256
-default_max_evals_high = 512
+from collections import namedtuple
+
+DefaultValue = namedtuple(typename="DefaultValue", field_names=["value"])
+
+default_optimiser = DefaultValue('smart')
+default_enable_extended_blind_spot = DefaultValue(False)
+default_jinv_interpolation_mode = DefaultValue('gaussian')
+default_crop_size_normal = DefaultValue(96000)
+default_crop_size_large = DefaultValue(128000)
+default_crop_size_verylarge = DefaultValue(256000)
+default_max_evals_hyperlow = DefaultValue(16)
+default_max_evals_ultralow = DefaultValue(32)
+default_max_evals_verylow = DefaultValue(64)
+default_max_evals_low = DefaultValue(128)
+default_max_evals_normal = DefaultValue(256)
+default_max_evals_high = DefaultValue(512)
diff --git a/aydin/it/classic_denoisers/bilateral.py b/aydin/it/classic_denoisers/bilateral.py
@@ -14,11 +14,11 @@
 def calibrate_denoise_bilateral(
     image: ArrayLike,
     bins: int = 10000,
-    crop_size_in_voxels: Optional[int] = _defaults.default_crop_size_normal,
-    optimiser: str = _defaults.default_optimiser,
-    max_num_evaluations: int = _defaults.default_max_evals_normal,
-    enable_extended_blind_spot: bool = _defaults.default_enable_extended_blind_spot,
-    jinv_interpolation_mode: str = _defaults.default_jinv_interpolation_mode,
+    crop_size_in_voxels: Optional[int] = _defaults.default_crop_size_normal.value,
+    optimiser: str = _defaults.default_optimiser.value,
+    max_num_evaluations: int = _defaults.default_max_evals_normal.value,
+    enable_extended_blind_spot: bool = _defaults.default_enable_extended_blind_spot.value,
+    jinv_interpolation_mode: str = _defaults.default_jinv_interpolation_mode.value,
     display_images: bool = False,
     display_crop: bool = False,
     **other_fixed_parameters,

diff --git a/aydin/it/classic_denoisers/butterworth.py b/aydin/it/classic_denoisers/butterworth.py
@@ -27,11 +27,11 @@ def calibrate_denoise_butterworth(
     max_freq: float = 1.0,
     min_order: float = 1.0,
     max_order: float = 8.0,
-    crop_size_in_voxels: Optional[int] = _defaults.default_crop_size_large,
-    optimiser: str = _defaults.default_optimiser,
-    max_num_evaluations: int = _defaults.default_max_evals_normal,
-    enable_extended_blind_spot: bool = _defaults.default_enable_extended_blind_spot,
-    jinv_interpolation_mode: str = _defaults.default_jinv_interpolation_mode,
+    crop_size_in_voxels: Optional[int] = _defaults.default_crop_size_large.value,
+    optimiser: str = _defaults.default_optimiser.value,
+    max_num_evaluations: int = _defaults.default_max_evals_normal.value,
+    enable_extended_blind_spot: bool = _defaults.default_enable_extended_blind_spot.value,
+    jinv_interpolation_mode: str = _defaults.default_jinv_interpolation_mode.value,
     multi_core: bool = True,
     display_images: bool = False,
     display_crop: bool = False,

diff --git a/aydin/it/classic_denoisers/dictionary_fixed.py b/aydin/it/classic_denoisers/dictionary_fixed.py
@@ -27,11 +27,11 @@ def calibrate_denoise_dictionary_fixed(
     try_threshold: bool = False,
     num_sparsity_values_to_try: int = 6,
     dictionaries: str = 'dct',
-    crop_size_in_voxels: Optional[int] = _defaults.default_crop_size_normal,
-    optimiser: str = _defaults.default_optimiser,
-    max_num_evaluations: int = _defaults.default_max_evals_low,
-    enable_extended_blind_spot: bool = _defaults.default_enable_extended_blind_spot,
-    jinv_interpolation_mode: str = _defaults.default_jinv_interpolation_mode,
+    crop_size_in_voxels: Optional[int] = _defaults.default_crop_size_normal.value,
+    optimiser: str = _defaults.default_optimiser.value,
+    max_num_evaluations: int = _defaults.default_max_evals_low.value,
+    enable_extended_blind_spot: bool = _defaults.default_enable_extended_blind_spot.value,
+    jinv_interpolation_mode: str = _defaults.default_jinv_interpolation_mode.value,
     display_dictionary: bool = False,
     display_images: bool = False,
     display_crop: bool = False,

diff --git a/aydin/it/classic_denoisers/dictionary_learned.py b/aydin/it/classic_denoisers/dictionary_learned.py
@@ -29,16 +29,16 @@ def calibrate_denoise_dictionary_learned(
     try_ica: bool = False,
     try_sdl: bool = False,
     num_sparsity_values_to_try: int = 6,
-    optimiser: str = _defaults.default_optimiser,
+    optimiser: str = _defaults.default_optimiser.value,
     num_iterations: int = 1024,
     batch_size: int = 3,
     alpha: int = 1,
     do_cleanup_dictionary: bool = True,
     do_denoise_dictionary: bool = False,
-    crop_size_in_voxels: Optional[int] = _defaults.default_crop_size_normal,
-    max_num_evaluations: int = _defaults.default_max_evals_low,
-    enable_extended_blind_spot: bool = _defaults.default_enable_extended_blind_spot,
-    jinv_interpolation_mode: str = _defaults.default_jinv_interpolation_mode,
+    crop_size_in_voxels: Optional[int] = _defaults.default_crop_size_normal.value,
+    max_num_evaluations: int = _defaults.default_max_evals_low.value,
+    enable_extended_blind_spot: bool = _defaults.default_enable_extended_blind_spot.value,
+    jinv_interpolation_mode: str = _defaults.default_jinv_interpolation_mode.value,
     display_dictionary: bool = False,
     display_images: bool = False,
     display_crop: bool = False,

diff --git a/aydin/it/classic_denoisers/gaussian.py b/aydin/it/classic_denoisers/gaussian.py
@@ -16,11 +16,11 @@ def calibrate_denoise_gaussian(
     min_sigma: float = 0.0,
     max_sigma: float = 2.0,
     max_num_truncate: int = 4,
-    crop_size_in_voxels: Optional[int] = _defaults.default_crop_size_large,
+    crop_size_in_voxels: Optional[int] = _defaults.default_crop_size_large.value,
     optimiser: str = 'smart',
-    max_num_evaluations: int = _defaults.default_max_evals_high,
-    enable_extended_blind_spot: bool = _defaults.default_enable_extended_blind_spot,
-    jinv_interpolation_mode: str = _defaults.default_jinv_interpolation_mode,
+    max_num_evaluations: int = _defaults.default_max_evals_high.value,
+    enable_extended_blind_spot: bool = _defaults.default_enable_extended_blind_spot.value,
+    jinv_interpolation_mode: str = _defaults.default_jinv_interpolation_mode.value,
     display_images: bool = False,
     display_crop: bool = False,
     **other_fixed_parameters,

diff --git a/aydin/it/classic_denoisers/gm.py b/aydin/it/classic_denoisers/gm.py
@@ -13,11 +13,11 @@
 def calibrate_denoise_gm(
     image: ArrayLike,
     max_filter_size: int = 3,
-    crop_size_in_voxels: Optional[int] = _defaults.default_crop_size_normal,
-    optimiser: str = _defaults.default_optimiser,
-    max_num_evaluations: int = _defaults.default_max_evals_normal,
-    enable_extended_blind_spot: bool = _defaults.default_enable_extended_blind_spot,
-    jinv_interpolation_mode: str = _defaults.default_jinv_interpolation_mode,
+    crop_size_in_voxels: Optional[int] = _defaults.default_crop_size_normal.value,
+    optimiser: str = _defaults.default_optimiser.value,
+    max_num_evaluations: int = _defaults.default_max_evals_normal.value,
+    enable_extended_blind_spot: bool = _defaults.default_enable_extended_blind_spot.value,
+    jinv_interpolation_mode: str = _defaults.default_jinv_interpolation_mode.value,
     display_images: bool = False,
     display_crop: bool = False,
     **other_fixed_parameters,

diff --git a/aydin/it/classic_denoisers/harmonic.py b/aydin/it/classic_denoisers/harmonic.py
@@ -23,11 +23,11 @@
 def calibrate_denoise_harmonic(
     image: ArrayLike,
     rank: bool = False,
-    crop_size_in_voxels: Optional[int] = _defaults.default_crop_size_normal,
-    optimiser: str = _defaults.default_optimiser,
-    max_num_evaluations: int = _defaults.default_max_evals_hyperlow,
-    enable_extended_blind_spot: bool = _defaults.default_enable_extended_blind_spot,
-    jinv_interpolation_mode: str = _defaults.default_jinv_interpolation_mode,
+    crop_size_in_voxels: Optional[int] = _defaults.default_crop_size_normal.value,
+    optimiser: str = _defaults.default_optimiser.value,
+    max_num_evaluations: int = _defaults.default_max_evals_hyperlow.value,
+    enable_extended_blind_spot: bool = _defaults.default_enable_extended_blind_spot.value,
+    jinv_interpolation_mode: str = _defaults.default_jinv_interpolation_mode.value,
     display_images: bool = False,
     display_crop: bool = False,
     **other_fixed_parameters,

diff --git a/aydin/it/classic_denoisers/lipschitz.py b/aydin/it/classic_denoisers/lipschitz.py
@@ -14,7 +14,7 @@ def calibrate_denoise_lipschitz(
     lipschitz: float = 0.1,
     percentile: float = 0.001,
     alpha: float = 0.1,
-    max_num_iterations: int = _defaults.default_max_evals_normal,
+    max_num_iterations: int = _defaults.default_max_evals_normal.value,
     **other_fixed_parameters,
 ):
     """

diff --git a/aydin/it/classic_denoisers/nlm.py b/aydin/it/classic_denoisers/nlm.py
@@ -16,11 +16,11 @@ def calibrate_denoise_nlm(
     image: ArrayLike,
     patch_size: int = 7,
     patch_distance: int = 11,
-    crop_size_in_voxels: Optional[int] = _defaults.default_crop_size_normal,
-    optimiser: str = _defaults.default_optimiser,
-    max_num_evaluations: int = _defaults.default_max_evals_normal,
-    enable_extended_blind_spot: bool = _defaults.default_enable_extended_blind_spot,
-    jinv_interpolation_mode: str = _defaults.default_jinv_interpolation_mode,
+    crop_size_in_voxels: Optional[int] = _defaults.default_crop_size_normal.value,
+    optimiser: str = _defaults.default_optimiser.value,
+    max_num_evaluations: int = _defaults.default_max_evals_normal.value,
+    enable_extended_blind_spot: bool = _defaults.default_enable_extended_blind_spot.value,
+    jinv_interpolation_mode: str = _defaults.default_jinv_interpolation_mode.value,
     display_images: bool = False,
     display_crop: bool = False,
     **other_fixed_parameters,

diff --git a/aydin/it/classic_denoisers/pca.py b/aydin/it/classic_denoisers/pca.py
@@ -20,11 +20,11 @@
 def calibrate_denoise_pca(
     image: ArrayLike,
     patch_size: Optional[Union[int, Tuple[int], str]] = None,
-    crop_size_in_voxels: Optional[int] = _defaults.default_crop_size_normal,
-    optimiser: str = _defaults.default_optimiser,
-    max_num_evaluations: int = _defaults.default_max_evals_hyperlow,
-    enable_extended_blind_spot: bool = _defaults.default_enable_extended_blind_spot,
-    jinv_interpolation_mode: str = _defaults.default_jinv_interpolation_mode,
+    crop_size_in_voxels: Optional[int] = _defaults.default_crop_size_normal.value,
+    optimiser: str = _defaults.default_optimiser.value,
+    max_num_evaluations: int = _defaults.default_max_evals_hyperlow.value,
+    enable_extended_blind_spot: bool = _defaults.default_enable_extended_blind_spot.value,
+    jinv_interpolation_mode: str = _defaults.default_jinv_interpolation_mode.value,
     multi_core: bool = True,
     display_images: bool = False,
     display_crop: bool = False,

diff --git a/aydin/it/classic_denoisers/spectral.py b/aydin/it/classic_denoisers/spectral.py
@@ -27,11 +27,11 @@ def calibrate_denoise_spectral(
     try_fft: bool = True,
     try_dst: bool = False,
     max_order: float = 6.0,
-    crop_size_in_voxels: Optional[int] = _defaults.default_crop_size_normal,
-    optimiser: str = _defaults.default_optimiser,
-    max_num_evaluations: int = _defaults.default_max_evals_low,
-    enable_extended_blind_spot: bool = _defaults.default_enable_extended_blind_spot,
-    jinv_interpolation_mode: str = _defaults.default_jinv_interpolation_mode,
+    crop_size_in_voxels: Optional[int] = _defaults.default_crop_size_normal.value,
+    optimiser: str = _defaults.default_optimiser.value,
+    max_num_evaluations: int = _defaults.default_max_evals_low.value,
+    enable_extended_blind_spot: bool = _defaults.default_enable_extended_blind_spot.value,
+    jinv_interpolation_mode: str = _defaults.default_jinv_interpolation_mode.value,
     multi_core: bool = True,
     display_images: bool = False,
     display_crop: bool = False,

diff --git a/aydin/it/classic_denoisers/tv.py b/aydin/it/classic_denoisers/tv.py
@@ -16,11 +16,11 @@
 def calibrate_denoise_tv(
     image: ArrayLike,
     enable_mixing: bool = True,
-    crop_size_in_voxels: Optional[int] = _defaults.default_crop_size_normal,
-    optimiser: str = _defaults.default_optimiser,
-    max_num_evaluations: int = _defaults.default_max_evals_high,
-    enable_extended_blind_spot: bool = _defaults.default_enable_extended_blind_spot,
-    jinv_interpolation_mode: str = _defaults.default_jinv_interpolation_mode,
+    crop_size_in_voxels: Optional[int] = _defaults.default_crop_size_normal.value,
+    optimiser: str = _defaults.default_optimiser.value,
+    max_num_evaluations: int = _defaults.default_max_evals_high.value,
+    enable_extended_blind_spot: bool = _defaults.default_enable_extended_blind_spot.value,
+    jinv_interpolation_mode: str = _defaults.default_jinv_interpolation_mode.value,
     display_images: bool = False,
     display_crop: bool = False,
     **other_fixed_parameters,

diff --git a/aydin/it/classic_denoisers/wavelet.py b/aydin/it/classic_denoisers/wavelet.py
@@ -15,11 +15,11 @@ def calibrate_denoise_wavelet(
     image: ArrayLike,
     all_wavelets: bool = False,
     wavelet_name_filter: str = '',
-    crop_size_in_voxels: Optional[int] = _defaults.default_crop_size_normal,
+    crop_size_in_voxels: Optional[int] = _defaults.default_crop_size_normal.value,
     optimiser: str = 'smart',  # using smart optimiser is important here!
-    max_num_evaluations: int = _defaults.default_max_evals_normal,
-    enable_extended_blind_spot: bool = _defaults.default_enable_extended_blind_spot,
-    jinv_interpolation_mode: str = _defaults.default_jinv_interpolation_mode,
+    max_num_evaluations: int = _defaults.default_max_evals_normal.value,
+    enable_extended_blind_spot: bool = _defaults.default_enable_extended_blind_spot.value,
+    jinv_interpolation_mode: str = _defaults.default_jinv_interpolation_mode.value,
     display_images: bool = False,
     display_crop: bool = False,
     **other_fixed_parameters,