httomolibgpu 3.1.1__py3-none-any.whl → 5.0__py3-none-any.whl

httomolibgpu/recon/rotation.py

@@ -32,7 +32,7 @@ from unittest.mock import Mock
 if cupy_run:
     from httomolibgpu.cuda_kernels import load_cuda_module
     from cupyx.scipy.ndimage import shift, gaussian_filter
-    from skimage.registration import phase_cross_correlation
+    from ._phase_cross_correlation import phase_cross_correlation
     from cupyx.scipy.fftpack import get_fft_plan
     from cupyx.scipy.fft import fft2, fftshift
 else:
@@ -49,7 +49,7 @@ else:
 import math
 from typing import List, Literal, Optional, Tuple, Union
 
-from httomolibgpu.misc.supp_func import data_checker
+from httomolibgpu.misc.utils import data_checker
 
 __all__ = [
     "find_center_vo",
@@ -110,7 +110,12 @@ def find_center_vo(
         data = cp.expand_dims(data, 1)
         ind = 0
 
-    data = data_checker(data, verbosity=True, method_name="find_center_vo")
+    data = data_checker(
+        data,
+        infsnans_correct=True,
+        zeros_warning=False,
+        data_to_method_name="find_center_vo",
+    )
 
     angles_tot, detY_size, detX_size = data.shape
 
@@ -459,7 +464,12 @@ def find_center_360(
     if data.ndim != 3:
         raise ValueError("A 3D array must be provided")
 
-    data = data_checker(data, verbosity=True, method_name="find_center_360")
+    data = data_checker(
+        data,
+        infsnans_correct=True,
+        zeros_warning=False,
+        data_to_method_name="find_center_360",
+    )
 
     # this method works with a 360-degree sinogram.
     if ind is None:
@@ -741,9 +751,6 @@ def _calculate_curvature(list_metric):
     return curvature, np.float32(min_pos)
 
 
-# %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-
 ## %%%%%%%%%%%%%%%%%%%%%%find_center_pc%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 def find_center_pc(
     proj1: cp.ndarray,
@@ -775,9 +782,18 @@ def find_center_pc(
     np.float32
         Rotation axis location.
     """
-
-    proj1 = data_checker(proj1, verbosity=True, method_name="find_center_pc")
-    proj2 = data_checker(proj2, verbosity=True, method_name="find_center_pc")
+    proj1 = data_checker(
+        proj1,
+        infsnans_correct=True,
+        zeros_warning=False,
+        data_to_method_name="find_center_pc",
+    )
+    proj2 = data_checker(
+        proj2,
+        infsnans_correct=True,
+        zeros_warning=False,
+        data_to_method_name="find_center_pc",
+    )
 
     imgshift = 0.0 if rotc_guess is None else rotc_guess - (proj1.shape[1] - 1.0) / 2.0
 
@@ -789,7 +805,7 @@ def find_center_pc(
 
     # do phase cross correlation between two images
     shiftr = phase_cross_correlation(
-        reference_image=proj1.get(), moving_image=proj2.get(), upsample_factor=1.0 / tol
+        reference_image=proj1, moving_image=proj2, upsample_factor=1.0 / tol
     )
 
     # Compute center of rotation as the center of first image and the

{httomolibgpu-3.1.1.dist-info → httomolibgpu-5.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: httomolibgpu
-Version: 3.1.1
+Version: 5.0
 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

httomolibgpu-5.0.dist-info/RECORD

@@ -0,0 +1,29 @@
+httomolibgpu/__init__.py,sha256=Fdj5ipIGgeKqSCYRb5bBVMAZ04ZvZJzuBoGOAqc0zgk,937
+httomolibgpu/cupywrapper.py,sha256=6ITGJ2Jw5I5kVmKEL5LlsnLRniEqqBLsHiAjvLtk0Xk,493
+httomolibgpu/cuda_kernels/__init__.py,sha256=VQNMaGcVDwiE-C64FfLtubHpLriLG0Y3_QnjHBSHrN0,884
+httomolibgpu/cuda_kernels/calc_metrics.cu,sha256=oV7ZPcwjWafmZjbNsUkBYPvOViJ_nX3zBoOAuPCmIrA,11335
+httomolibgpu/cuda_kernels/center_360_shifts.cu,sha256=Ya_8hxjXGtPBsPY3qfGJaugwnYrTFjFFretRcLiUfFQ,1631
+httomolibgpu/cuda_kernels/generate_mask.cu,sha256=3il3r1J2cnTCd3UXO4GWGfBgGxj4pvrZnXviW_SXpO0,2650
+httomolibgpu/cuda_kernels/median_kernel.cu,sha256=EECLUCoJkT9GQ9Db_FF6fYOG6cDSiAePTRZNxE4VZ68,1692
+httomolibgpu/cuda_kernels/raven_filter.cu,sha256=KX2TM_9tMpvoGCHezDNWYABCnv2cT9mlMo4IhxRUac0,1437
+httomolibgpu/cuda_kernels/remove_nan_inf.cu,sha256=gv0ihkf6A_D_po9x7pmgFsQFhwZ1dB_HYc_0Tu-bpUU,630
+httomolibgpu/misc/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+httomolibgpu/misc/corr.py,sha256=e1eUsWLSM9SB5xzWTDW0o9pAD_lbrr4DL-QQmyM8v4c,4503
+httomolibgpu/misc/denoise.py,sha256=-D9UPbZyUAcCptBHUUXsmj1NFzd6HrrRjJJh4T5gmhQ,4787
+httomolibgpu/misc/morph.py,sha256=T_JxZE6xulB3FwvFH0iqF26pJmBJoln_sGuvOoRGAHQ,7266
+httomolibgpu/misc/rescale.py,sha256=8MwTd68tF8HTMk4qbCYgcaBsRV7wOxlrbFPAjUcx0zs,4285
+httomolibgpu/misc/utils.py,sha256=rHRuQUO47SlTanvKDBgiC0im4tXlGLCw5B_zvlLzzbc,4736
+httomolibgpu/prep/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+httomolibgpu/prep/alignment.py,sha256=GVxnyioipmqsHb4s3mPQ8tKGoPIQMPftDrQxUO-HBuE,5491
+httomolibgpu/prep/normalize.py,sha256=hee0H4mE7FrSZgcF1fjLsKT06xjTJymkyAxpe2itQe4,4202
+httomolibgpu/prep/phase.py,sha256=eDi4Y2dZ0ZDgblCku1XhHiSuK6rHnmsDFuZdDvlnHMU,8505
+httomolibgpu/prep/stripe.py,sha256=8_DV0ON6AWARuziqkmhom56gWTardtqC_z3xG8geg0o,14774
+httomolibgpu/recon/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+httomolibgpu/recon/_phase_cross_correlation.py,sha256=h5r1g5lMmS9p32k2SuC8pjji6McpwBZiN95zQd2xvBo,16616
+httomolibgpu/recon/algorithm.py,sha256=ds-_io7kGzo5FiJq8k4--PYtIWak3y9H7yuyg1lymyQ,25121
+httomolibgpu/recon/rotation.py,sha256=GaSwNrlDnlP_iIrTfKUQLiXsShJ5aSDvdKPwofggtwQ,27948
+httomolibgpu-5.0.dist-info/licenses/LICENSE,sha256=bXeLsgelPUUXw8HCIYiVC97Dpjhm2nB54m7TACdH8ng,48032
+httomolibgpu-5.0.dist-info/METADATA,sha256=0_lrMXVwbSoLpLzIx_i24kCU7VWAMkXFaBaT6rQ0O-c,3339
+httomolibgpu-5.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+httomolibgpu-5.0.dist-info/top_level.txt,sha256=nV0Ty_YvSPVd1O6MNWuIplD0w1nwk5hT76YgBZ-bzUw,13
+httomolibgpu-5.0.dist-info/RECORD,,

httomolibgpu/misc/supp_func.py

@@ -1,192 +0,0 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-# ---------------------------------------------------------------------------
-# Copyright 2022 Diamond Light Source Ltd.
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-#     http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-# ---------------------------------------------------------------------------
-# Created By  : Tomography Team at DLS <scientificsoftware@diamond.ac.uk>
-# Created Date: 02/June/2025
-# ---------------------------------------------------------------------------
-"""This is a collection of supplementary functions (utils) to perform various data checks"""
-
-from httomolibgpu import cupywrapper
-from typing import Optional
-
-cp = cupywrapper.cp
-cupy_run = cupywrapper.cupy_run
-
-import numpy as np
-
-from unittest.mock import Mock
-
-if cupy_run:
-    from httomolibgpu.cuda_kernels import load_cuda_module
-else:
-    load_cuda_module = Mock()
-
-
-def _naninfs_check(
-    data: cp.ndarray,
-    verbosity: bool = True,
-    method_name: Optional[str] = None,
-) -> cp.ndarray:
-    """
-    This function finds NaN's, +-Inf's in the input data and then prints the warnings and correct the data if correction is enabled.
-
-    Parameters
-    ----------
-    data : cp.ndarray
-        Input CuPy or Numpy array either float32 or uint16 data type.
-    verbosity : bool
-        If enabled, then the printing of the warning happens when data contains infs or nans
-    method_name : str, optional.
-        Method's name for which input data is tested.
-
-    Returns
-    -------
-    ndarray
-        Uncorrected or corrected (nans and infs converted to zeros) input array.
-    """
-    present_nans_infs_b = False
-
-    if cupy_run:
-        xp = cp.get_array_module(data)
-    else:
-        import numpy as xp
-
-    if xp.__name__ == "cupy":
-        input_type = data.dtype
-        if len(data.shape) == 2:
-            dy, dx = data.shape
-            dz = 1
-        else:
-            dz, dy, dx = data.shape
-
-        present_nans_infs = cp.zeros(shape=(1)).astype(cp.uint8)
-
-        block_x = 128
-        # setting grid/block parameters
-        block_dims = (block_x, 1, 1)
-        grid_x = (dx + block_x - 1) // block_x
-        grid_y = dy
-        grid_z = dz
-        grid_dims = (grid_x, grid_y, grid_z)
-        params = (data, dz, dy, dx, present_nans_infs)
-
-        kernel_args = "remove_nan_inf<{0}>".format(
-            "float" if input_type == "float32" else "unsigned short"
-        )
-
-        module = load_cuda_module("remove_nan_inf", name_expressions=[kernel_args])
-        remove_nan_inf_kernel = module.get_function(kernel_args)
-        remove_nan_inf_kernel(grid_dims, block_dims, params)
-
-        if present_nans_infs[0].get() == 1:
-            present_nans_infs_b = True
-    else:
-        if not np.all(np.isfinite(data)):
-            present_nans_infs_b = True
-            np.nan_to_num(data, copy=False, nan=0.0, posinf=0.0, neginf=0.0)
-
-    if present_nans_infs_b:
-        if verbosity:
-            print(
-                f"Warning!!! Input data to method: {method_name} contains Inf's or/and NaN's. This will be corrected but it is recommended to check the validity of input to the method."
-            )
-
-    return data
-
-
-def _zeros_check(
-    data: cp.ndarray,
-    verbosity: bool = True,
-    percentage_threshold: float = 50,
-    method_name: Optional[str] = None,
-) -> bool:
-    """
-    This function finds all zeros present in the data. If the amount of zeros is larger than percentage_threshold it prints the warning.
-
-    Parameters
-    ----------
-    data : cp.ndarray
-        Input CuPy or Numpy array.
-    verbosity : bool
-        If enabled, then the printing of the warning happens when data contains infs or nans.
-    percentage_threshold: float:
-        If the number of zeros in input data is more than the percentage of all data points, then print the data warning
-    method_name : str, optional.
-        Method's name for which input data is tested.
-
-    Returns
-    -------
-    bool
-        True if the data contains too many zeros
-    """
-    if cupy_run:
-        xp = cp.get_array_module(data)
-    else:
-        import numpy as xp
-
-    nonzero_elements_total = 1
-    for tot_elements_mult in data.shape:
-        nonzero_elements_total *= tot_elements_mult
-
-    warning_zeros = False
-    zero_elements_total = nonzero_elements_total - int(xp.count_nonzero(data))
-
-    if (zero_elements_total / nonzero_elements_total) * 100 >= percentage_threshold:
-        warning_zeros = True
-        if verbosity:
-            print(
-                f"Warning!!! Input data to method: {method_name} contains more than {percentage_threshold} percent of zeros."
-            )
-
-    return warning_zeros
-
-
-def data_checker(
-    data: cp.ndarray,
-    verbosity: bool = True,
-    method_name: Optional[str] = None,
-) -> cp.ndarray:
-    """
-    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.
-
-    Parameters
-    ----------
-    data : xp.ndarray
-        Input CuPy or Numpy array either float32 or uint16 data type.
-    verbosity : bool
-        If enabled, then the printing of the warning happens when data contains infs or nans.
-    method_name : str, optional.
-        Method's name for which input data is tested.
-
-    Returns
-    -------
-    cp.ndarray
-        Returns corrected or not data array.
-    """
-
-    data = _naninfs_check(data, verbosity=verbosity, 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-3.1.1.dist-info/RECORD

@@ -1,28 +0,0 @@
-httomolibgpu/__init__.py,sha256=sz3ia5rSjC4lj6Xw4VZekh3OxmeVB2E2747bzyHqQdY,838
-httomolibgpu/cupywrapper.py,sha256=6ITGJ2Jw5I5kVmKEL5LlsnLRniEqqBLsHiAjvLtk0Xk,493
-httomolibgpu/cuda_kernels/__init__.py,sha256=VQNMaGcVDwiE-C64FfLtubHpLriLG0Y3_QnjHBSHrN0,884
-httomolibgpu/cuda_kernels/calc_metrics.cu,sha256=oV7ZPcwjWafmZjbNsUkBYPvOViJ_nX3zBoOAuPCmIrA,11335
-httomolibgpu/cuda_kernels/center_360_shifts.cu,sha256=Ya_8hxjXGtPBsPY3qfGJaugwnYrTFjFFretRcLiUfFQ,1631
-httomolibgpu/cuda_kernels/generate_mask.cu,sha256=3il3r1J2cnTCd3UXO4GWGfBgGxj4pvrZnXviW_SXpO0,2650
-httomolibgpu/cuda_kernels/median_kernel.cu,sha256=EECLUCoJkT9GQ9Db_FF6fYOG6cDSiAePTRZNxE4VZ68,1692
-httomolibgpu/cuda_kernels/raven_filter.cu,sha256=KX2TM_9tMpvoGCHezDNWYABCnv2cT9mlMo4IhxRUac0,1437
-httomolibgpu/cuda_kernels/remove_nan_inf.cu,sha256=gv0ihkf6A_D_po9x7pmgFsQFhwZ1dB_HYc_0Tu-bpUU,630
-httomolibgpu/misc/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-httomolibgpu/misc/corr.py,sha256=1tUjwMku-MAPiLaH9IFe3zmF0p6rJFLruoObXSZelXY,4665
-httomolibgpu/misc/denoise.py,sha256=l5FVdpur1I6YQcJJBfYTKjEsiDNyRYtpdOQZ7ZHicJw,4997
-httomolibgpu/misc/morph.py,sha256=AlLk_kGFHF6vNrdICMpsXmTUDnCc7ey97-_DqwZb3Wc,7475
-httomolibgpu/misc/rescale.py,sha256=K4VQ1AdxOAhe8tTSVb9VXVZsjBap5VlOtxHVdf9MU08,4416
-httomolibgpu/misc/supp_func.py,sha256=yDzNmRlIlIikQ4sKd2y9trQ9yQtblECmQ2JM5vmIY5I,6233
-httomolibgpu/prep/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-httomolibgpu/prep/alignment.py,sha256=BuFTfLZD5_THQAKP_ikQ3fRE8JpN-JItGllZgrHRU5s,5657
-httomolibgpu/prep/normalize.py,sha256=ozVUAs4UY2DY7MQtJKllUgahp_4wRFKPuc_3iQl6bCE,4879
-httomolibgpu/prep/phase.py,sha256=zIuAVqlnHVqcDUBtj40NRBoHaO7O2KqGZ5CCUABRXBQ,7282
-httomolibgpu/prep/stripe.py,sha256=YgOVb7Z5H7NFM3d2Y1jfNNwwj7ZMDv9nMZMMCvdBnVM,15150
-httomolibgpu/recon/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-httomolibgpu/recon/algorithm.py,sha256=pCByNRby-6SUdH8QfC1z1BXVazTGcErLAyRgOPlm37o,28075
-httomolibgpu/recon/rotation.py,sha256=k_E0lBRprJz6AGclagIkrzk_9dipADxPtL5BxrggSwM,27729
-httomolibgpu-3.1.1.dist-info/licenses/LICENSE,sha256=bXeLsgelPUUXw8HCIYiVC97Dpjhm2nB54m7TACdH8ng,48032
-httomolibgpu-3.1.1.dist-info/METADATA,sha256=W0UoO0iumuI9Hs5WmIa3Q0Pxyf0v69yF4LLRq_D_g34,3341
-httomolibgpu-3.1.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-httomolibgpu-3.1.1.dist-info/top_level.txt,sha256=nV0Ty_YvSPVd1O6MNWuIplD0w1nwk5hT76YgBZ-bzUw,13
-httomolibgpu-3.1.1.dist-info/RECORD,,