httomolibgpu 2.7__tar.gz → 3.0__tar.gz

{httomolibgpu-2.7/httomolibgpu.egg-info → httomolibgpu-3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: httomolibgpu
-Version: 2.7
+Version: 3.0
 Summary: Commonly used tomography data processing methods at DLS.
 Author-email: Daniil Kazantsev <daniil.kazantsev@diamond.ac.uk>, Yousef Moazzam <yousef.moazzam@diamond.ac.uk>, Naman Gera <naman.gera@diamond.ac.uk>
 License: BSD-3-Clause
@@ -71,7 +71,7 @@ Conda environment
 
    $ conda create --name httomolibgpu # create a fresh conda environment
    $ conda activate httomolibgpu # activate the environment
-   $ conda install -c conda-forge cupy==12.3.0 # for linux users
+   $ conda install conda-forge::cupy==12.3.0
    $ pip install httomolibgpu
 
 Setup the development environment:

{httomolibgpu-2.7 → httomolibgpu-3.0}/README.rst

@@ -34,7 +34,7 @@ Conda environment
 
    $ conda create --name httomolibgpu # create a fresh conda environment
    $ conda activate httomolibgpu # activate the environment
-   $ conda install -c conda-forge cupy==12.3.0 # for linux users
+   $ conda install conda-forge::cupy==12.3.0
    $ pip install httomolibgpu
 
 Setup the development environment:

{httomolibgpu-2.7 → httomolibgpu-3.0}/httomolibgpu/misc/corr.py

@@ -114,7 +114,7 @@ def median_filter(
 
 
 def remove_outlier(
-    data: cp.ndarray, kernel_size: int = 3, dif: float = 0.1
+    data: cp.ndarray, kernel_size: int = 3, dif: float = 1000
 ) -> cp.ndarray:
     """Selectively applies 3D median filter to a 3D CuPy array to remove outliers. Also called a dezinger.
     For more detailed information, see :ref:`method_outlier_removal`.
@@ -126,8 +126,8 @@ def remove_outlier(
     kernel_size : int, optional
         The size of the filter's kernel (a diameter).
     dif : float, optional
-        Expected difference value between outlier value and the
-        median value of the array.
+        Expected difference value between the outlier value (central voxel) and the
+        median value of the neighbourhood. Lower values lead to median filtering.
 
     Returns
     -------

{httomolibgpu-2.7 → httomolibgpu-3.0}/httomolibgpu/misc/rescale.py

@@ -24,32 +24,32 @@ import numpy as np
 from httomolibgpu import cupywrapper
 
 cp = cupywrapper.cp
-cupy_run = cupywrapper.cupy_run
 
 from typing import Literal, Optional, Tuple, Union
 
 from httomolibgpu.misc.supp_func import data_checker
 
+
 __all__ = [
     "rescale_to_int",
 ]
 
 
 def rescale_to_int(
-    data: Union[np.ndarray, cp.ndarray],
+    data: cp.ndarray,
     perc_range_min: float = 0.0,
     perc_range_max: float = 100.0,
     bits: Literal[8, 16, 32] = 8,
     glob_stats: Optional[Tuple[float, float, float, int]] = None,
-) -> Union[np.ndarray, cp.ndarray]:
+) -> cp.ndarray:
     """
     Rescales the data given as float32 type and converts it into the range of an unsigned integer type
     with the given number of bits. For more detailed information and examples, see :ref:`method_rescale_to_int`.
 
     Parameters
     ----------
-    data : Union[np.ndarray, cp.ndarray]
-        Input data as a numpy or cupy array (the function is cpu-gpu agnostic)
+    data : cp.ndarray
+        Input data as a cupy array
     perc_range_min: float, optional
         The lower cutoff point in the input data, in percent of the data range (defaults to 0).
         The lower bound is computed as min + perc_range_min/100*(max-min)
@@ -69,7 +69,7 @@ def rescale_to_int(
 
     Returns
     -------
-    Union[np.ndarray, cp.ndarray]
+    cp.ndarray
         The original data, clipped to the range specified with the perc_range_min and
         perc_range_max, and scaled to the full range of the output integer type
     """
@@ -82,18 +82,13 @@ def rescale_to_int(
 
     data = data_checker(data, verbosity=True, method_name="rescale_to_int")
 
-    if cupy_run:
-        xp = cp.get_array_module(data)
-    else:
-        import numpy as xp
-
     # get the min and max integer values of the output type
-    output_min = xp.iinfo(output_dtype).min
-    output_max = xp.iinfo(output_dtype).max
+    output_min = cp.iinfo(output_dtype).min
+    output_max = cp.iinfo(output_dtype).max
 
     if not isinstance(glob_stats, tuple):
-        min_value = float(xp.min(data))
-        max_value = float(xp.max(data))
+        min_value = float(cp.min(data))
+        max_value = float(cp.max(data))
     else:
         min_value = glob_stats[0]
         max_value = glob_stats[1]
@@ -102,32 +97,21 @@ def rescale_to_int(
     input_min = (perc_range_min * (range_intensity) / 100) + min_value
     input_max = (perc_range_max * (range_intensity) / 100) + min_value
 
+    factor = cp.float32(1.0)
     if (input_max - input_min) != 0.0:
-        factor = xp.float32((output_max - output_min) / (input_max - input_min))
-    else:
-        factor = 1.0
-
-    res = xp.empty(data.shape, dtype=output_dtype)
-    if xp.__name__ == "numpy":
-        if input_max == pow(2, 32):
-            input_max -= 1
-        res = np.copy(data.astype(float))
-        res[data.astype(float) < input_min] = int(input_min)
-        res[data.astype(float) > input_max] = int(input_max)
-        res -= input_min
-        res *= factor
-        res = output_dtype(res)
-    else:
-        rescale_kernel = cp.ElementwiseKernel(
-            "T x, raw T input_min, raw T input_max, raw T factor",
-            "O out",
-            """
-            T x_clean = isnan(x) || isinf(x) ? T(0) : x;
-            T x_clipped = x_clean < input_min ? input_min : (x_clean > input_max ? input_max : x_clean);
-            T x_rebased = x_clipped - input_min;
-            out = O(x_rebased * factor);
-            """,
-            "rescale_to_int",
-        )
-        rescale_kernel(data, input_min, input_max, factor, res)
+        factor = cp.float32((output_max - output_min) / (input_max - input_min))
+
+    res = cp.empty(data.shape, dtype=output_dtype)
+    rescale_kernel = cp.ElementwiseKernel(
+        "T x, raw T input_min, raw T input_max, raw T factor",
+        "O out",
+        """
+        T x_clean = isnan(x) || isinf(x) ? T(0) : x;
+        T x_clipped = x_clean < input_min ? input_min : (x_clean > input_max ? input_max : x_clean);
+        T x_rebased = x_clipped - input_min;
+        out = O(x_rebased * factor);
+        """,
+        "rescale_to_int",
+    )
+    rescale_kernel(data, input_min, input_max, factor, res)
     return res

{httomolibgpu-2.7 → httomolibgpu-3.0}/httomolibgpu/misc/supp_func.py

@@ -162,7 +162,7 @@ def data_checker(
 ) -> bool:
     """
     Function that performs the variety of checks on input data, in some cases also correct the data and prints warnings.
-    Currently it checks for: the presence of infs and nans in data; the number of zero elements.
+    Currently it checks for: the presence of infs and nans in data.
 
     Parameters
     ----------
@@ -181,11 +181,12 @@ def data_checker(
 
     data = _naninfs_check(data, verbosity=verbosity, method_name=method_name)
 
-    _zeros_check(
-        data,
-        verbosity=verbosity,
-        percentage_threshold=50,
-        method_name=method_name,
-    )
+    # ! The number of zero elements check is currently switched off as it requires sorting or AtomicAdd, which makes it inefficient on GPUs. !
+    # _zeros_check(
+    #     data,
+    #     verbosity=verbosity,
+    #     percentage_threshold=50,
+    #     method_name=method_name,
+    # )
 
     return data

{httomolibgpu-2.7 → httomolibgpu-3.0}/httomolibgpu/recon/algorithm.py

@@ -18,7 +18,7 @@
 # Created By  : Tomography Team at DLS <scientificsoftware@diamond.ac.uk>
 # Changes relative to ToMoBAR 2024.01 version
 # ---------------------------------------------------------------------------
-"""Module for tomographic reconstruction"""
+"""Module for tomographic reconstruction. For more detailed information see :ref:`image_reconstruction_module`"""
 
 import numpy as np
 from httomolibgpu import cupywrapper
@@ -59,6 +59,7 @@ def FBP2d_astra(
     data: np.ndarray,
     angles: np.ndarray,
     center: Optional[float] = None,
+    detector_pad: int = 0,
     filter_type: str = "ram-lak",
     filter_parameter: Optional[float] = None,
     filter_d: Optional[float] = None,
@@ -70,10 +71,9 @@ def FBP2d_astra(
     """
     Perform Filtered Backprojection (FBP) reconstruction slice-by-slice (2d) using ASTRA toolbox :cite:`van2016fast` and
     ToMoBAR :cite:`kazantsev2020tomographic` wrappers.
-    This is a 2D recon using ASTRA's API for the FBP method, see for more parameters ASTRA's documentation here:
-    https://astra-toolbox.com/docs/algs/FBP_CUDA.html.
+    This is a 2D recon using ASTRA's API for the FBP_CUDA method, see more in :ref:`method_FBP2d_astra`.
 
-    Parameters`
+    Parameters
     ----------
     data : np.ndarray
         Projection data as a 3d numpy array.
@@ -81,6 +81,8 @@ def FBP2d_astra(
         An array of angles given in radians.
     center : float, optional
         The center of rotation (CoR).
+    detector_pad : int
+        Detector width padding with edge values to remove circle/arc type artifacts in the reconstruction.
     filter_type: str
         Type of projection filter, see ASTRA's API for all available options for filters.
     filter_parameter: float, optional
@@ -112,7 +114,7 @@ def FBP2d_astra(
         recon_size = data_shape[2]
 
     RecTools = _instantiate_direct_recon2d_class(
-        data, angles, center, recon_size, gpu_id
+        data, angles, center, detector_pad, recon_size, gpu_id
     )
 
     detY_size = data_shape[1]
@@ -140,6 +142,7 @@ def FBP3d_tomobar(
     data: cp.ndarray,
     angles: np.ndarray,
     center: Optional[float] = None,
+    detector_pad: int = 0,
     filter_freq_cutoff: float = 0.35,
     recon_size: Optional[int] = None,
     recon_mask_radius: Optional[float] = 0.95,
@@ -149,7 +152,8 @@ def FBP3d_tomobar(
     """
     Perform Filtered Backprojection (FBP) reconstruction using ASTRA toolbox :cite:`van2016fast` and
     ToMoBAR :cite:`kazantsev2020tomographic` wrappers.
-    This is a 3D recon from the CuPy array directly and using a custom built SINC filter for filtration in Fourier space.
+    This is a 3D recon from the CuPy array directly and using a custom built SINC filter for filtration in Fourier space, 
+    see more in :ref:`method_FBP3d_tomobar`.
 
     Parameters
     ----------
@@ -159,8 +163,10 @@ def FBP3d_tomobar(
         An array of angles given in radians.
     center : float, optional
         The center of rotation (CoR).
+    detector_pad : int
+        Detector width padding with edge values to remove circle/arc type artifacts in the reconstruction.
     filter_freq_cutoff : float
-        Cutoff frequency parameter for the SINC filter, the lower values produce better contrast but noisy reconstruction.
+        Cutoff frequency parameter for the SINC filter, the lower values may produce better contrast but noisy reconstruction. The filter change will also affect the dynamic range of the reconstructed image. 
     recon_size : int, optional
         The [recon_size, recon_size] shape of the reconstructed slice in pixels.
         By default (None), the reconstructed size will be the dimension of the horizontal detector.
@@ -182,7 +188,7 @@ def FBP3d_tomobar(
     data = data_checker(data, verbosity=True, method_name="FBP3d_tomobar")
 
     RecToolsCP = _instantiate_direct_recon_class(
-        data, angles, center, recon_size, gpu_id
+        data, angles, center, detector_pad, recon_size, gpu_id
     )
 
     reconstruction = RecToolsCP.FBP(
@@ -200,6 +206,7 @@ def LPRec3d_tomobar(
     data: cp.ndarray,
     angles: np.ndarray,
     center: Optional[float] = None,
+    detector_pad: int = 0,
     filter_type: str = "shepp",
     filter_freq_cutoff: float = 1.0,
     recon_size: Optional[int] = None,
@@ -209,7 +216,7 @@ def LPRec3d_tomobar(
     """
     Fourier direct inversion in 3D on unequally spaced (also called as Log-Polar) grids using
     CuPy array as an input. This implementation follows V. Nikitin's CUDA-C implementation and TomoCuPy package.
-    :cite:`andersson2016fast`.
+    :cite:`andersson2016fast`, see more in :ref:`method_LPRec3d_tomobar`.
 
     Parameters
     ----------
@@ -219,10 +226,12 @@ def LPRec3d_tomobar(
         An array of angles given in radians.
     center : float, optional
         The center of rotation (CoR).
+    detector_pad : int
+        Detector width padding with edge values to remove circle/arc type artifacts in the reconstruction.
     filter_type : str
         Filter type, the accepted strings are: none, ramp, shepp, cosine, cosine2, hamming, hann, parzen.
     filter_freq_cutoff : float
-        Cutoff frequency parameter for a filter. The higher values increase the resolution but also amplify the noise.
+        Cutoff frequency parameter for a filter.
     recon_size : int, optional
         The [recon_size, recon_size] shape of the reconstructed slice in pixels.
         By default (None), the reconstructed size will be the dimension of the horizontal detector.
@@ -242,7 +251,9 @@ def LPRec3d_tomobar(
 
     data = data_checker(data, verbosity=True, method_name="LPRec3d_tomobar")
 
-    RecToolsCP = _instantiate_direct_recon_class(data, angles, center, recon_size, 0)
+    RecToolsCP = _instantiate_direct_recon_class(
+        data, angles, center, detector_pad, recon_size, 0
+    )
 
     reconstruction = RecToolsCP.FOURIER_INV(
         _take_neg_log(data) if neglog else data,
@@ -260,6 +271,7 @@ def SIRT3d_tomobar(
     data: cp.ndarray,
     angles: np.ndarray,
     center: Optional[float] = None,
+    detector_pad: int = 0,
     recon_size: Optional[int] = None,
     iterations: Optional[int] = 300,
     nonnegativity: Optional[bool] = True,
@@ -280,6 +292,8 @@ def SIRT3d_tomobar(
         An array of angles given in radians.
     center : float, optional
         The center of rotation (CoR).
+    detector_pad : int
+        Detector width padding with edge values to remove circle/arc type artifacts in the reconstruction.
     recon_size : int, optional
         The [recon_size, recon_size] shape of the reconstructed slice in pixels.
         By default (None), the reconstructed size will be the dimension of the horizontal detector.
@@ -304,6 +318,7 @@ def SIRT3d_tomobar(
         data,
         angles,
         center,
+        detector_pad,
         recon_size,
         gpu_id,
         datafidelity="LS",
@@ -327,6 +342,7 @@ def CGLS3d_tomobar(
     data: cp.ndarray,
     angles: np.ndarray,
     center: Optional[float] = None,
+    detector_pad: int = 0,
     recon_size: Optional[int] = None,
     iterations: Optional[int] = 20,
     nonnegativity: Optional[bool] = True,
@@ -347,6 +363,8 @@ def CGLS3d_tomobar(
         An array of angles given in radians.
     center : float, optional
         The center of rotation (CoR).
+    detector_pad : int
+        Detector width padding with edge values to remove circle/arc type artifacts in the reconstruction.
     recon_size : int, optional
         The [recon_size, recon_size] shape of the reconstructed slice in pixels.
         By default (None), the reconstructed size will be the dimension of the horizontal detector.
@@ -368,7 +386,7 @@ def CGLS3d_tomobar(
     data = data_checker(data, verbosity=True, method_name="CGLS3d_tomobar")
 
     RecToolsCP = _instantiate_iterative_recon_class(
-        data, angles, center, recon_size, gpu_id, datafidelity="LS"
+        data, angles, center, detector_pad, recon_size, gpu_id, datafidelity="LS"
     )
 
     _data_ = {
@@ -386,6 +404,7 @@ def _instantiate_direct_recon_class(
     data: cp.ndarray,
     angles: np.ndarray,
     center: Optional[float] = None,
+    detector_pad: int = 0,
     recon_size: Optional[int] = None,
     gpu_id: int = 0,
 ) -> Type:
@@ -395,6 +414,7 @@ def _instantiate_direct_recon_class(
         data (cp.ndarray): data array
         angles (np.ndarray): angles
         center (Optional[float], optional): center of recon. Defaults to None.
+        detector_pad (int): Detector width padding. Defaults to 0.
         recon_size (Optional[int], optional): recon_size. Defaults to None.
         gpu_id (int, optional): gpu ID. Defaults to 0.
 
@@ -407,6 +427,7 @@ def _instantiate_direct_recon_class(
         recon_size = data.shape[2]
     RecToolsCP = RecToolsDIRCuPy(
         DetectorsDimH=data.shape[2],  # Horizontal detector dimension
+        DetectorsDimH_pad=detector_pad,  # padding for horizontal detector
         DetectorsDimV=data.shape[1],  # Vertical detector dimension (3D case)
         CenterRotOffset=data.shape[2] / 2
         - center
@@ -423,6 +444,7 @@ def _instantiate_direct_recon2d_class(
     data: np.ndarray,
     angles: np.ndarray,
     center: Optional[float] = None,
+    detector_pad: int = 0,
     recon_size: Optional[int] = None,
     gpu_id: int = 0,
 ) -> Type:
@@ -432,6 +454,7 @@ def _instantiate_direct_recon2d_class(
         data (cp.ndarray): data array
         angles (np.ndarray): angles
         center (Optional[float], optional): center of recon. Defaults to None.
+        detector_pad (int): Detector width padding. Defaults to 0.
         recon_size (Optional[int], optional): recon_size. Defaults to None.
         gpu_id (int, optional): gpu ID. Defaults to 0.
 
@@ -444,6 +467,7 @@ def _instantiate_direct_recon2d_class(
         recon_size = data.shape[2]
     RecTools = RecToolsDIR(
         DetectorsDimH=data.shape[2],  # Horizontal detector dimension
+        DetectorsDimH_pad=detector_pad,  # padding for horizontal detector
         DetectorsDimV=None,  # 2d case
         CenterRotOffset=data.shape[2] / 2
         - center
@@ -459,6 +483,7 @@ def _instantiate_iterative_recon_class(
     data: cp.ndarray,
     angles: np.ndarray,
     center: Optional[float] = None,
+    detector_pad: int = 0,
     recon_size: Optional[int] = None,
     gpu_id: int = 0,
     datafidelity: str = "LS",
@@ -469,6 +494,7 @@ def _instantiate_iterative_recon_class(
         data (cp.ndarray): data array
         angles (np.ndarray): angles
         center (Optional[float], optional): center of recon. Defaults to None.
+        detector_pad (int): Detector width padding. Defaults to 0.
         recon_size (Optional[int], optional): recon_size. Defaults to None.
         datafidelity (str, optional): Data fidelity
         gpu_id (int, optional): gpu ID. Defaults to 0.
@@ -482,6 +508,7 @@ def _instantiate_iterative_recon_class(
         recon_size = data.shape[2]
     RecToolsCP = RecToolsIRCuPy(
         DetectorsDimH=data.shape[2],  # Horizontal detector dimension
+        DetectorsDimH_pad=detector_pad,  # padding for horizontal detector
         DetectorsDimV=data.shape[1],  # Vertical detector dimension (3D case)
         CenterRotOffset=data.shape[2] / 2
         - center

{httomolibgpu-2.7 → httomolibgpu-3.0}/httomolibgpu/recon/rotation.py

@@ -425,7 +425,7 @@ def find_center_360(
     Find the center-of-rotation (COR) in a 360-degree scan and also an offset
     to perform data transformation from 360 to 180 degrees scan. See :cite:`vo2021data`.
 
-    Parameters Tuple[np.float32, np.float32, Literal["left", "right"], np.float32]:
+    Parameters
     ----------
     data : cp.ndarray
         3D tomographic data as a Cupy array.

{httomolibgpu-2.7 → httomolibgpu-3.0/httomolibgpu.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: httomolibgpu
-Version: 2.7
+Version: 3.0
 Summary: Commonly used tomography data processing methods at DLS.
 Author-email: Daniil Kazantsev <daniil.kazantsev@diamond.ac.uk>, Yousef Moazzam <yousef.moazzam@diamond.ac.uk>, Naman Gera <naman.gera@diamond.ac.uk>
 License: BSD-3-Clause
@@ -71,7 +71,7 @@ Conda environment
 
    $ conda create --name httomolibgpu # create a fresh conda environment
    $ conda activate httomolibgpu # activate the environment
-   $ conda install -c conda-forge cupy==12.3.0 # for linux users
+   $ conda install conda-forge::cupy==12.3.0
    $ pip install httomolibgpu
 
 Setup the development environment: