Merge pull request #90 from DiamondLightSource/estimators-fetch-default-param-values

Fetch default value for parameters required in estimator functions

Author: yousefmoazzam

httomo_backends/methods_database/packages/backends/httomolibgpu/supporting_funcs/misc/corr.py

@@ -1,5 +1,7 @@
+import inspect
 from typing import Tuple
 
+from httomolibgpu.misc.corr import median_filter, remove_outlier
 
 __all__ = [
     "_calc_padding_remove_outlier",
@@ -8,10 +10,18 @@
 
 
 def _calc_padding_remove_outlier(**kwargs) -> Tuple[int, int]:
+    if "kernel_size" not in kwargs:
+        params = inspect.signature(remove_outlier).parameters
+        kwargs["kernel_size"] = params["kernel_size"].default
+
     kernel_size = kwargs["kernel_size"]
     return (kernel_size // 2, kernel_size // 2)
 
 
 def _calc_padding_median_filter(**kwargs) -> Tuple[int, int]:
+    if "kernel_size" not in kwargs:
+        params = inspect.signature(median_filter).parameters
+        kwargs["kernel_size"] = params["kernel_size"].default
+
     kernel_size = kwargs["kernel_size"]
     return (kernel_size // 2, kernel_size // 2)

httomo_backends/methods_database/packages/backends/httomolibgpu/supporting_funcs/misc/morph.py

@@ -20,10 +20,13 @@
 # ---------------------------------------------------------------------------
 """Modules for memory estimation for morph functions"""
 
+import inspect
 import math
 from typing import Tuple
 import numpy as np
 
+from httomolibgpu.misc.morph import data_resampler, sino_360_to_180
+
 __all__ = [
     "_calc_memory_bytes_data_resampler",
     "_calc_output_dim_data_resampler",
@@ -42,6 +45,10 @@ def _calc_memory_bytes_data_resampler(
     **kwargs,
 ) -> Tuple[int, int]:
     newshape = kwargs["newshape"]
+
+    if "interpolation" not in kwargs:
+        params = inspect.signature(data_resampler).parameters
+        kwargs["interpolation"] = params["interpolation"].default
     interpolation = kwargs["interpolation"]
 
     input_size = np.prod(non_slice_dims_shape) * dtype.itemsize
@@ -62,7 +69,9 @@ def _calc_output_dim_sino_360_to_180(
     non_slice_dims_shape: Tuple[int, int],
     **kwargs,
 ) -> Tuple[int, int]:
-    assert "overlap" in kwargs, "Expected overlap in method parameters"
+    if "overlap" not in kwargs:
+        params = inspect.signature(sino_360_to_180).parameters
+        kwargs["overlap"] = params["overlap"].default
     overlap: float = kwargs["overlap"]
 
     original_sino_width = non_slice_dims_shape[1]
@@ -75,7 +84,9 @@ def _calc_memory_bytes_sino_360_to_180(
     dtype: np.dtype,
     **kwargs,
 ) -> Tuple[int, int]:
-    assert "overlap" in kwargs, "Expected overlap in method parameters"
+    if "overlap" not in kwargs:
+        params = inspect.signature(sino_360_to_180).parameters
+        kwargs["overlap"] = params["overlap"].default
     overlap: float = kwargs["overlap"]
 
     original_sino_width = non_slice_dims_shape[1]

httomo_backends/methods_database/packages/backends/httomolibgpu/supporting_funcs/misc/rescale.py

@@ -1,6 +1,9 @@
+import inspect
 from typing import Tuple
 import numpy as np
 
+from httomolibgpu.misc.rescale import rescale_to_int
+
 __all__ = [
     "_calc_memory_bytes_rescale_to_int",
 ]
@@ -11,6 +14,9 @@ def _calc_memory_bytes_rescale_to_int(
     dtype: np.dtype,
     **kwargs,
 ) -> Tuple[int, int]:
+    if "bits" not in kwargs:
+        params = inspect.signature(rescale_to_int).parameters
+        kwargs["bits"] = params["bits"].default
     bits: int = kwargs["bits"]
     if bits == 8:
         itemsize = 1

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

@@ -20,12 +20,13 @@
 # ---------------------------------------------------------------------------
 """Modules for memory estimation for stripe removal methods"""
 
+import inspect
 import math
 from typing import Tuple
 import numpy as np
 
 from httomo_backends.cufft import CufftType, cufft_estimate_1d
-from httomolibgpu.prep.stripe import remove_stripe_fw
+from httomolibgpu.prep.stripe import raven_filter, remove_stripe_fw
 
 
 __all__ = [
@@ -87,7 +88,14 @@ def _calc_memory_bytes_raven_filter(
     **kwargs,
 ) -> Tuple[int, int]:
 
+    if "pad_x" not in kwargs:
+        params = inspect.signature(raven_filter).parameters
+        kwargs["pad_x"] = params["pad_x"].default
     pad_x = kwargs["pad_x"]
+
+    if "pad_y" not in kwargs:
+        params = inspect.signature(raven_filter).parameters
+        kwargs["pad_y"] = params["pad_y"].default
     pad_y = kwargs["pad_y"]
 
     # Unpadded input

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

@@ -52,7 +52,7 @@ def __calc_output_dim_recon(non_slice_dims_shape, **kwargs):
 
     """
     DetectorsLengthH = non_slice_dims_shape[1]
-    recon_size = kwargs["recon_size"]
+    recon_size = kwargs.get("recon_size", None)
     if recon_size is None:
         recon_size = DetectorsLengthH
     output_dims = (recon_size, recon_size)

tests/test_httomolibgpu.py

@@ -35,6 +35,7 @@
 )
 from httomolibgpu.misc.rescale import rescale_to_int
 
+from httomo_backends.methods_database.packages.backends.httomolibgpu.supporting_funcs.misc.corr import *
 from httomo_backends.methods_database.packages.backends.httomolibgpu.supporting_funcs.misc.morph import *
 from httomo_backends.methods_database.packages.backends.httomolibgpu.supporting_funcs.prep.phase import *
 from httomo_backends.methods_database.packages.backends.httomolibgpu.supporting_funcs.prep.stripe import *
@@ -1166,3 +1167,94 @@ def test_FBP2d_astra_output_dim():
         recon_size=recon_size,
     )
     assert output_dims == (recon_size, recon_size)
+
+
+def test_remove_outlier_padding_calculator_fetches_default_param_value():
+    try:
+        _calc_padding_remove_outlier(**{})
+    except KeyError as e:
+        pytest.fail(f"Failed to get default value for {e} parameter")
+
+
+def test_median_filter_padding_calculator_fetches_default_param_value():
+    try:
+        _calc_padding_median_filter(**{})
+    except KeyError as e:
+        pytest.fail(f"Failed to get default value for {e} parameter")
+
+
+def test_data_resampler_memory_estimator_fetches_default_param_value():
+    try:
+        _calc_memory_bytes_data_resampler((2, 2), np.float32(), **{"newshape": (1, 1)})
+    except KeyError as e:
+        pytest.fail(f"Failed to get default value for {e} parameter")
+
+
+def test_sino_360_to_180_output_dims_calculator_fetches_default_param_value():
+    try:
+        _calc_output_dim_sino_360_to_180((1, 1), **{})
+    except KeyError as e:
+        pytest.fail(f"Failed to get default value for {e} parameter")
+
+
+def test_sino_360_to_180_memory_estimator_fetches_default_param_value():
+    try:
+        _calc_memory_bytes_sino_360_to_180((1, 1), np.float32(), **{})
+    except KeyError as e:
+        pytest.fail(f"Failed to get default value for {e} parameter")
+
+
+def test_rescale_to_int_memory_estimator_fetches_default_param_value():
+    try:
+        _calc_memory_bytes_rescale_to_int((1, 1), np.float32(), **{})
+    except KeyError as e:
+        pytest.fail(f"Failed to get default value for {e} parameter")
+
+
+def test_raven_filter_memory_estimator_fetches_default_param_value():
+    try:
+        _calc_memory_bytes_raven_filter((1, 1), np.float32(), **{})
+    except KeyError as e:
+        pytest.fail(f"Failed to get default value for {e} parameter")
+
+
+def test_FBP2d_astra_output_dims_calculator_fetches_default_param_value():
+    try:
+        _calc_output_dim_FBP2d_astra((1, 1), **{})
+    except KeyError as e:
+        pytest.fail(f"Failed to get default value for {e} parameter")
+
+
+def test_FBP3d_tomobar_output_dims_calculator_fetches_default_param_value():
+    try:
+        _calc_output_dim_FBP3d_tomobar((1, 1), **{})
+    except KeyError as e:
+        pytest.fail(f"Failed to get default value for {e} parameter")
+
+
+def test_LPRec3d_tomobar_output_dims_calculator_fetches_default_param_value():
+    try:
+        _calc_output_dim_LPRec3d_tomobar((1, 1), **{})
+    except KeyError as e:
+        pytest.fail(f"Failed to get default value for {e} parameter")
+
+
+def test_SIRT3d_tomobar_output_dims_calculator_fetches_default_param_value():
+    try:
+        _calc_output_dim_SIRT3d_tomobar((1, 1), **{})
+    except KeyError as e:
+        pytest.fail(f"Failed to get default value for {e} parameter")
+
+
+def test_CGLS3d_tomobar_output_dims_calculator_fetches_default_param_value():
+    try:
+        _calc_output_dim_CGLS3d_tomobar((1, 1), **{})
+    except KeyError as e:
+        pytest.fail(f"Failed to get default value for {e} parameter")
+
+
+def test_FISTA3d_tomobar_output_dims_calculator_fetches_default_param_value():
+    try:
+        _calc_output_dim_FISTA3d_tomobar((1, 1), **{})
+    except KeyError as e:
+        pytest.fail(f"Failed to get default value for {e} parameter")