diff --git a/docs/source/api/httomolibgpu.cuda_kernels.rst b/docs/source/api/httomolibgpu.cuda_kernels.rst deleted file mode 100644 index 7ef07975..00000000 --- a/docs/source/api/httomolibgpu.cuda_kernels.rst +++ /dev/null @@ -1,10 +0,0 @@ -httomolibgpu.cuda\_kernels package -================================== - -Module contents ---------------- - -.. automodule:: httomolibgpu.cuda_kernels - :members: - :show-inheritance: - :undoc-members: diff --git a/docs/source/api/httomolibgpu.cupywrapper.rst b/docs/source/api/httomolibgpu.cupywrapper.rst deleted file mode 100644 index 91fd8ed1..00000000 --- a/docs/source/api/httomolibgpu.cupywrapper.rst +++ /dev/null @@ -1,6 +0,0 @@ -:mod:`httomolibgpu.cupywrapper` -============================================ -.. automodule:: httomolibgpu.cupywrapper - :members: - :show-inheritance: - :undoc-members: \ No newline at end of file diff --git a/docs/source/api/httomolibgpu.misc.corr.rst b/docs/source/api/httomolibgpu.misc.corr.rst deleted file mode 100644 index ee9c349c..00000000 --- a/docs/source/api/httomolibgpu.misc.corr.rst +++ /dev/null @@ -1,6 +0,0 @@ -:mod:`httomolibgpu.misc.corr` -============================================ -.. automodule:: httomolibgpu.misc.corr - :members: - :show-inheritance: - :undoc-members: \ No newline at end of file diff --git a/docs/source/api/httomolibgpu.misc.denoise.rst b/docs/source/api/httomolibgpu.misc.denoise.rst deleted file mode 100644 index f0581acc..00000000 --- a/docs/source/api/httomolibgpu.misc.denoise.rst +++ /dev/null @@ -1,6 +0,0 @@ -:mod:`httomolibgpu.misc.denoise` -============================================ -.. automodule:: httomolibgpu.misc.denoise - :members: - :show-inheritance: - :undoc-members: \ No newline at end of file diff --git a/docs/source/api/httomolibgpu.misc.morph.rst b/docs/source/api/httomolibgpu.misc.morph.rst deleted file mode 100644 index 37b14602..00000000 --- a/docs/source/api/httomolibgpu.misc.morph.rst +++ /dev/null @@ -1,6 +0,0 @@ -:mod:`httomolibgpu.misc.morph` -============================================ -.. automodule:: httomolibgpu.misc.morph - :members: - :show-inheritance: - :undoc-members: \ No newline at end of file diff --git a/docs/source/api/httomolibgpu.misc.rescale.rst b/docs/source/api/httomolibgpu.misc.rescale.rst deleted file mode 100644 index d1c42a3f..00000000 --- a/docs/source/api/httomolibgpu.misc.rescale.rst +++ /dev/null @@ -1,6 +0,0 @@ -:mod:`httomolibgpu.misc.rescale` -============================================ -.. automodule:: httomolibgpu.misc.rescale - :members: - :show-inheritance: - :undoc-members: \ No newline at end of file diff --git a/docs/source/api/httomolibgpu.misc.rst b/docs/source/api/httomolibgpu.misc.rst deleted file mode 100644 index 2dc48965..00000000 --- a/docs/source/api/httomolibgpu.misc.rst +++ /dev/null @@ -1,22 +0,0 @@ -httomolibgpu.misc package -========================= - -Submodules ----------- - -.. toctree:: - :maxdepth: 4 - - httomolibgpu.misc.corr - httomolibgpu.misc.denoise - httomolibgpu.misc.morph - httomolibgpu.misc.rescale - httomolibgpu.misc.supp_func - -Module contents ---------------- - -.. automodule:: httomolibgpu.misc - :members: - :show-inheritance: - :undoc-members: diff --git a/docs/source/api/httomolibgpu.prep.alignment.rst b/docs/source/api/httomolibgpu.prep.alignment.rst deleted file mode 100644 index e0f04ada..00000000 --- a/docs/source/api/httomolibgpu.prep.alignment.rst +++ /dev/null @@ -1,6 +0,0 @@ -:mod:`httomolibgpu.prep.alignment` -============================================ -.. automodule:: httomolibgpu.prep.alignment - :members: - :show-inheritance: - :undoc-members: \ No newline at end of file diff --git a/docs/source/api/httomolibgpu.prep.normalize.rst b/docs/source/api/httomolibgpu.prep.normalize.rst deleted file mode 100644 index 9ebb6370..00000000 --- a/docs/source/api/httomolibgpu.prep.normalize.rst +++ /dev/null @@ -1,6 +0,0 @@ -:mod:`httomolibgpu.prep.normalize` -============================================ -.. automodule:: httomolibgpu.prep.normalize - :members: - :show-inheritance: - :undoc-members: \ No newline at end of file diff --git a/docs/source/api/httomolibgpu.prep.phase.rst b/docs/source/api/httomolibgpu.prep.phase.rst deleted file mode 100644 index 83cbe74b..00000000 --- a/docs/source/api/httomolibgpu.prep.phase.rst +++ /dev/null @@ -1,6 +0,0 @@ -:mod:`httomolibgpu.prep.phase` -============================================ -.. automodule:: httomolibgpu.prep.phase - :members: - :show-inheritance: - :undoc-members: \ No newline at end of file diff --git a/docs/source/api/httomolibgpu.prep.rst b/docs/source/api/httomolibgpu.prep.rst deleted file mode 100644 index 3b05deaf..00000000 --- a/docs/source/api/httomolibgpu.prep.rst +++ /dev/null @@ -1,21 +0,0 @@ -httomolibgpu.prep package -========================= - -Submodules ----------- - -.. toctree:: - :maxdepth: 4 - - httomolibgpu.prep.alignment - httomolibgpu.prep.normalize - httomolibgpu.prep.phase - httomolibgpu.prep.stripe - -Module contents ---------------- - -.. automodule:: httomolibgpu.prep - :members: - :show-inheritance: - :undoc-members: diff --git a/docs/source/api/httomolibgpu.prep.stripe.rst b/docs/source/api/httomolibgpu.prep.stripe.rst deleted file mode 100644 index 12123a20..00000000 --- a/docs/source/api/httomolibgpu.prep.stripe.rst +++ /dev/null @@ -1,6 +0,0 @@ -:mod:`httomolibgpu.prep.stripe` -============================================ -.. automodule:: httomolibgpu.prep.stripe - :members: - :show-inheritance: - :undoc-members: \ No newline at end of file diff --git a/docs/source/api/httomolibgpu.recon.algorithm.rst b/docs/source/api/httomolibgpu.recon.algorithm.rst deleted file mode 100644 index bec9bea2..00000000 --- a/docs/source/api/httomolibgpu.recon.algorithm.rst +++ /dev/null @@ -1,6 +0,0 @@ -:mod:`httomolibgpu.recon.algorithm` -============================================ -.. automodule:: httomolibgpu.recon.algorithm - :members: - :show-inheritance: - :undoc-members: \ No newline at end of file diff --git a/docs/source/api/httomolibgpu.recon.rotation.rst b/docs/source/api/httomolibgpu.recon.rotation.rst deleted file mode 100644 index 515c70ee..00000000 --- a/docs/source/api/httomolibgpu.recon.rotation.rst +++ /dev/null @@ -1,6 +0,0 @@ -:mod:`httomolibgpu.recon.rotation` -============================================ -.. automodule:: httomolibgpu.recon.rotation - :members: - :show-inheritance: - :undoc-members: \ No newline at end of file diff --git a/docs/source/api/httomolibgpu.recon.rst b/docs/source/api/httomolibgpu.recon.rst deleted file mode 100644 index 105ad389..00000000 --- a/docs/source/api/httomolibgpu.recon.rst +++ /dev/null @@ -1,19 +0,0 @@ -httomolibgpu.recon package -========================== - -Submodules ----------- - -.. toctree:: - :maxdepth: 4 - - httomolibgpu.recon.algorithm - httomolibgpu.recon.rotation - -Module contents ---------------- - -.. automodule:: httomolibgpu.recon - :members: - :show-inheritance: - :undoc-members: diff --git a/docs/source/api/httomolibgpu.rst b/docs/source/api/httomolibgpu.rst deleted file mode 100644 index 9de44c43..00000000 --- a/docs/source/api/httomolibgpu.rst +++ /dev/null @@ -1,29 +0,0 @@ -httomolibgpu package -==================== - -Subpackages ------------ - -.. toctree:: - :maxdepth: 4 - - httomolibgpu.cuda_kernels - httomolibgpu.misc - httomolibgpu.prep - httomolibgpu.recon - -Submodules ----------- - -.. toctree:: - :maxdepth: 4 - - httomolibgpu.cupywrapper - -Module contents ---------------- - -.. automodule:: httomolibgpu - :members: - :show-inheritance: - :undoc-members: diff --git a/docs/source/scripts/methods_to_generate_images.py b/docs/source/scripts/methods_to_generate_images.py index fed021ff..ca99a81b 100644 --- a/docs/source/scripts/methods_to_generate_images.py +++ b/docs/source/scripts/methods_to_generate_images.py @@ -21,7 +21,6 @@ import argparse from typing import Union import numpy as np -import cupy import cupy as cp from PIL import Image @@ -106,11 +105,13 @@ def run_methods(path_to_data: str, output_folder: str) -> int: ## %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% methods_name = "normalisation" print("___{}___".format(methods_name)) - from httomolibgpu.prep.normalize import normalize + from httomolibgpu.prep.normalize import dark_flat_field_correction, minus_log - data_normalized = normalize( - cp.asarray(proj_raw), cp.asarray(flats), cp.asarray(darks), minus_log=True + data_normalized = dark_flat_field_correction( + cp.asarray(proj_raw), cp.asarray(flats), cp.asarray(darks) ) + + data_normalized = minus_log(data_normalized) data_normalized_np = data_normalized.get() max_scale_data_normalized = np.max(data_normalized_np) diff --git a/httomolibgpu/prep/normalize.py b/httomolibgpu/prep/normalize.py index c7b76ae9..92df401e 100644 --- a/httomolibgpu/prep/normalize.py +++ b/httomolibgpu/prep/normalize.py @@ -47,7 +47,7 @@ def dark_flat_field_correction( cutoff: float = 10.0, ) -> cp.ndarray: """ - Normalize raw projection data using the flat and dark field projections. + Perform dark/flat field correction of raw projection data. Parameters ---------- @@ -67,7 +67,7 @@ def dark_flat_field_correction( Returns ------- cp.ndarray - Normalised by dark/flat fields 3D tomographic data as a CuPy array. + dark/flat field corrected 3D tomographic data as a CuPy array. """ _check_valid_input_normalise(data, flats, darks)