httomolibgpu 5.1__py3-none-any.whl → 5.3__py3-none-any.whl

httomolibgpu/__init__.py

@@ -9,6 +9,7 @@ from httomolibgpu.prep.normalize import dark_flat_field_correction, minus_log
 from httomolibgpu.prep.phase import paganin_filter, paganin_filter_savu_legacy
 from httomolibgpu.prep.stripe import (
     remove_stripe_based_sorting,
+    remove_stripe_fw,
     remove_stripe_ti,
     remove_all_stripe,
     raven_filter,

httomolibgpu/cuda_kernels/remove_stripe_fw.cu

@@ -0,0 +1,155 @@
+template<int WSize>
+__global__ void grouped_convolution_x(
+    int dim_x,
+    int dim_y,
+    int dim_z,
+    const float* in,
+    int in_stride_x,
+    int in_stride_y,
+    int in_stride_z,
+    float* out,
+    int out_stride_z,
+    int out_stride_group,
+    const float* w
+)
+{
+    const int g_thd_x = blockDim.x * blockIdx.x + threadIdx.x;
+    const int g_thd_y = blockDim.y * blockIdx.y + threadIdx.y;
+    const int g_thd_z = blockDim.z * blockIdx.z + threadIdx.z;
+    if (g_thd_x >= dim_x || g_thd_y >= dim_y || g_thd_z >= dim_z)
+    {
+        return;
+    }
+
+    constexpr int out_groups = 2;
+    for (int i = 0; i < out_groups; ++i)
+    {
+        float acc = 0.F;
+        for (int j = 0; j < WSize; ++j)
+        {
+            const int w_idx = i * WSize + j;
+            const int in_idx = (g_thd_x * in_stride_x + j) + g_thd_y * in_stride_y + g_thd_z * in_stride_z;
+            acc += w[w_idx] * in[in_idx];
+        }
+        const int out_idx = g_thd_x + g_thd_y * dim_x + g_thd_z * out_stride_z + i * out_stride_group;
+        out[out_idx] = acc;
+    }
+}
+
+template<int WSize>
+__global__ void grouped_convolution_y(
+    int dim_x,
+    int dim_y,
+    int dim_z,
+    const float* in,
+    int in_stride_x,
+    int in_stride_y,
+    int in_stride_z,
+    int in_stride_group,
+    float* out,
+    int out_stride_z,
+    int out_stride_group,
+    const float* w
+)
+{
+    const int g_thd_x = blockDim.x * blockIdx.x + threadIdx.x;
+    const int g_thd_y = blockDim.y * blockIdx.y + threadIdx.y;
+    const int g_thd_z = blockDim.z * blockIdx.z + threadIdx.z;
+    if (g_thd_x >= dim_x || g_thd_y >= dim_y || g_thd_z >= dim_z)
+    {
+        return;
+    }
+
+    constexpr int in_groups = 2;
+    constexpr int out_groups = 2;
+    constexpr int item_stride_y = 2;
+    for (int group = 0; group < in_groups; ++group)
+    {
+        for (int i = 0; i < out_groups; ++i)
+        {
+            float acc = 0.F;
+            for (int j = 0; j < WSize; ++j)
+            {
+                const int w_idx = (out_groups * group + i) * WSize + j;
+                const int in_idx = g_thd_x * in_stride_x + (item_stride_y * g_thd_y + j) * in_stride_y + group * in_stride_group + g_thd_z * in_stride_z;
+                acc += w[w_idx] * in[in_idx];
+            }
+            const int out_idx = g_thd_x + g_thd_y * dim_x + g_thd_z * out_stride_z + (out_groups * group + i) * out_stride_group;
+            out[out_idx] = acc;
+        }
+    }
+}
+
+template<int WSize>
+__global__ void transposed_convolution_x(
+    int dim_x,
+    int dim_y,
+    int dim_z,
+    const float* in,
+    int in_dim_x,
+    int in_stride_y,
+    int in_stride_z,
+    const float* w,
+    float* out
+)
+{
+    const int g_thd_x = blockDim.x * blockIdx.x + threadIdx.x;
+    const int g_thd_y = blockDim.y * blockIdx.y + threadIdx.y;
+    const int g_thd_z = blockDim.z * blockIdx.z + threadIdx.z;
+    if (g_thd_x >= dim_x || g_thd_y >= dim_y || g_thd_z >= dim_z)
+    {
+        return;
+    }
+
+    constexpr int item_out_stride = 2;
+    float acc = 0.F;
+    for (int i = 0; i < WSize; ++i)
+    {
+        const int in_x = (g_thd_x - i) / item_out_stride;
+        const int in_x_mod = (g_thd_x - i) % item_out_stride;
+        if (in_x_mod == 0 && in_x >= 0 && in_x < in_dim_x)
+        {
+            const int in_idx = in_x + g_thd_y * in_stride_y + g_thd_z * in_stride_z;
+            acc += in[in_idx] * w[i];
+        }
+    }
+    const int out_idx = g_thd_x + dim_x * g_thd_y + dim_x * dim_y * g_thd_z;
+    out[out_idx] = acc;
+}
+
+template<int WSize>
+__global__ void transposed_convolution_y(
+    int dim_x,
+    int dim_y,
+    int dim_z,
+    const float* in,
+    int in_dim_y,
+    int in_stride_y,
+    int in_stride_z,
+    const float* w,
+    float* out
+)
+{
+    const int g_thd_x = blockDim.x * blockIdx.x + threadIdx.x;
+    const int g_thd_y = blockDim.y * blockIdx.y + threadIdx.y;
+    const int g_thd_z = blockDim.z * blockIdx.z + threadIdx.z;
+    if (g_thd_x >= dim_x || g_thd_y >= dim_y || g_thd_z >= dim_z)
+    {
+        return;
+    }
+
+    constexpr int item_out_stride = 2;
+    float acc = 0.F;
+    for (int i = 0; i < WSize; ++i)
+    {
+        const int in_y = (g_thd_y - i) / item_out_stride;
+        const int in_y_mod = (g_thd_y - i) % item_out_stride;
+        if (in_y_mod == 0 && in_y >= 0 && in_y < in_dim_y)
+        {
+            const int in_idx = g_thd_x + in_y * in_stride_y + g_thd_z * in_stride_z;
+            acc += in[in_idx] * w[i];
+        }
+    }
+    const int out_idx = g_thd_x + dim_x * g_thd_y + dim_x * dim_y * g_thd_z;
+    out[out_idx] = acc;
+}

httomolibgpu/cupywrapper.py

@@ -2,6 +2,7 @@ cupy_run = False
 try:
     import cupy as cp
     import nvtx
+    from cupyx.scipy.fft import next_fast_len
 
     try:
         cp.cuda.Device(0).compute_capability
@@ -15,5 +16,6 @@ except ImportError as e:
     )
     from unittest.mock import Mock
     import numpy as cp
+    from scipy.fft import next_fast_len
 
     nvtx = Mock()

httomolibgpu/prep/phase.py

@@ -26,6 +26,7 @@ from httomolibgpu.memory_estimator_helpers import _DeviceMemStack
 
 cp = cupywrapper.cp
 cupy_run = cupywrapper.cupy_run
+next_fast_len = cupywrapper.next_fast_len
 
 from unittest.mock import Mock
 
@@ -38,7 +39,7 @@ else:
     fftshift = Mock()
 
 from numpy import float32
-from typing import Optional, Tuple
+from typing import Literal, Optional, Tuple
 import math
 
 __all__ = [
@@ -56,6 +57,10 @@ def paganin_filter(
     distance: float = 1.0,
     energy: float = 53.0,
     ratio_delta_beta: float = 250,
+    calculate_padding_value_method: Literal[
+        "next_power_of_2", "next_fast_length", "use_pad_x_y"
+    ] = "next_power_of_2",
+    pad_x_y: Optional[list] = None,
     calc_peak_gpu_mem: bool = False,
 ) -> cp.ndarray:
     """
@@ -74,6 +79,10 @@ def paganin_filter(
         Beam energy in keV.
     ratio_delta_beta : float
         The ratio of delta/beta, where delta is the phase shift and real part of the complex material refractive index and beta is the absorption.
+    calculate_padding_value_method: str
+        Method to calculate the padded size of the input data. Accepted values are 'next_power_of_2', 'next_fast_length' and 'use_pad_x_y`.
+    pad_x_y list | None:
+        Padding values in pixels horizontally and vertically. Must be None, unless `calculate_padding_value_method` is 'use_pad_x_y'.
     calc_peak_gpu_mem: bool
         Parameter to support memory estimation in HTTomo. Irrelevant to the method itself and can be ignored by user.
 
@@ -93,9 +102,9 @@ def paganin_filter(
         mem_stack.malloc(np.prod(tomo) * np.float32().itemsize)
     dz_orig, dy_orig, dx_orig = tomo.shape if not mem_stack else tomo
 
-    # Perform padding to the power of 2 as FFT is O(n*log(n)) complexity
-    # TODO: adding other options of padding?
-    padded_tomo, pad_tup = _pad_projections_to_second_power(tomo, mem_stack)
+    padded_tomo, pad_tup = _pad_projections(
+        tomo, calculate_padding_value_method, pad_x_y, mem_stack
+    )
 
     dz, dy, dx = padded_tomo.shape if not mem_stack else padded_tomo
 
@@ -219,21 +228,59 @@ def _shift_bit_length(x: int) -> int:
     return 1 << (x - 1).bit_length()
 
 
-def _calculate_pad_size(datashape: tuple) -> list:
+def _calculate_pad_size(
+    datashape: tuple,
+    calculate_padding_value_method: Literal[
+        "next_power_of_2", "next_fast_length", "use_pad_x_y"
+    ],
+    pad_x_y: Optional[list],
+) -> list:
     """Calculating the padding size
 
     Args:
-        datashape (tuple): the shape of the 3D data
+        datashape (tuple):
+            the shape of the 3D data
+        calculate_padding_value_method: str
+            Method to calculate the padded size of the input data. Accepted values are 'next_power_of_2', 'next_fast_length' and 'use_pad_x_y`.
+        pad_x_y (int, int) | None:
+            Padding values in pixels horizontally and vertically. Must be None, unless `calculate_padding_value_method` is 'use_pad_x_y'.
 
     Returns:
         list: the padded dimensions
     """
+    if pad_x_y is not None and calculate_padding_value_method != "use_pad_x_y":
+        raise ValueError(
+            'calculate_padding_value_method must be "use_pad_x_y" when pad_x_y is specified'
+        )
+    elif calculate_padding_value_method == "use_pad_x_y":
+        if pad_x_y is None:
+            raise ValueError(
+                'pad_x_y must be provided when calculate_padding_value_method is "use_pad_x_y"'
+            )
+        elif (
+            not isinstance(pad_x_y, list)
+            or len(pad_x_y) != 2
+            or not isinstance(pad_x_y[0], int)
+            or not isinstance(pad_x_y[1], int)
+        ):
+            raise ValueError("pad_x_y must be a list of two integers")
+
+    if calculate_padding_value_method == "next_power_of_2":
+        calculate_padded_dim = lambda _, size: _shift_bit_length(size + 1)
+    elif calculate_padding_value_method == "next_fast_length":
+        calculate_padded_dim = lambda _, size: next_fast_len(size)
+    elif calculate_padding_value_method == "use_pad_x_y":
+        calculate_padded_dim = lambda dim, size: size + 2 * pad_x_y[2 - dim]
+    else:
+        raise ValueError(
+            f'Unexpected calculate_padding_value_method: "{calculate_padding_value_method}"'
+        )
     pad_list = []
     for index, element in enumerate(datashape):
         if index == 0:
             pad_width = (0, 0)  # do not pad the slicing dim
         else:
-            diff = _shift_bit_length(element + 1) - element
+            diff = calculate_padded_dim(index, element) - element
             if element % 2 == 0:
                 pad_width_scalar = diff // 2
                 pad_width = (pad_width_scalar, pad_width_scalar)
@@ -248,17 +295,27 @@ def _calculate_pad_size(datashape: tuple) -> list:
     return pad_list
 
 
-def _pad_projections_to_second_power(
-    tomo: cp.ndarray, mem_stack: Optional[_DeviceMemStack]
+def _pad_projections(
+    tomo: cp.ndarray,
+    calculate_padding_value_method: Literal[
+        "next_power_of_2", "next_fast_length", "use_pad_x_y"
+    ],
+    pad_x_y: Optional[list],
+    mem_stack: Optional[_DeviceMemStack],
 ) -> Tuple[cp.ndarray, Tuple[int, int]]:
     """
-    Performs padding of each projection to the next power of 2.
+    Performs padding of each projection to a size optimal for FFT.
     If the shape is not even we also care of that before padding.
 
     Parameters
     ----------
     tomo : cp.ndarray
         3d projection data
+    calculate_padding_value_method: str
+        Method to calculate the padded size of the input data. Accepted values are 'next_power_of_2', 'next_fast_length' and 'use_pad_x_y`.
+    pad_x_y: list | None:
+        Padding values in pixels horizontally and vertically. Must be None, unless `calculate_padding_value_method` is 'use_pad_x_y'.
+
 
     Returns
     -------
@@ -268,7 +325,9 @@ def _pad_projections_to_second_power(
     """
     full_shape_tomo = cp.shape(tomo) if not mem_stack else tomo
 
-    pad_list = _calculate_pad_size(full_shape_tomo)
+    pad_list = _calculate_pad_size(
+        full_shape_tomo, calculate_padding_value_method, pad_x_y
+    )
 
     if mem_stack:
         padded_tomo = [

httomolibgpu/prep/stripe.py

@@ -21,6 +21,7 @@
 """Module for stripes removal"""
 
 import numpy as np
+import pywt
 from httomolibgpu import cupywrapper
 
 cp = cupywrapper.cp
@@ -31,6 +32,7 @@ from unittest.mock import Mock
 if cupy_run:
     from cupyx.scipy.ndimage import median_filter, binary_dilation, uniform_filter1d
     from cupyx.scipy.fft import fft2, ifft2, fftshift
+    from cupyx.scipy.fftpack import get_fft_plan
     from httomolibgpu.cuda_kernels import load_cuda_module
 else:
     median_filter = Mock()
@@ -41,10 +43,11 @@ else:
     fftshift = Mock()
 
 
-from typing import Union
+from typing import Optional, Tuple, Union
 
 __all__ = [
     "remove_stripe_based_sorting",
+    "remove_stripe_fw",
     "remove_stripe_ti",
     "remove_all_stripe",
     "raven_filter",
@@ -156,6 +159,604 @@ def remove_stripe_ti(
         return data
 
 
+###### Ring removal with wavelet filtering (adapted for cupy from pytroch_wavelet package https://pytorch-wavelets.readthedocs.io/)##########
+# These functions are taken from TomoCuPy package
+# *************************************************************************** #
+#                  Copyright © 2022, UChicago Argonne, LLC                    #
+#                           All Rights Reserved                               #
+#                         Software Name: Tomocupy                             #
+#                     By: Argonne National Laboratory                         #
+#                                                                             #
+#                           OPEN SOURCE LICENSE                               #
+#                                                                             #
+# Redistribution and use in source and binary forms, with or without          #
+# modification, are permitted provided that the following conditions are met: #
+#                                                                             #
+# 1. Redistributions of source code must retain the above copyright notice,   #
+#    this list of conditions and the following disclaimer.                    #
+# 2. Redistributions in binary form must reproduce the above copyright        #
+#    notice, this list of conditions and the following disclaimer in the      #
+#    documentation and/or other materials provided with the distribution.     #
+# 3. Neither the name of the copyright holder nor the names of its            #
+#    contributors may be used to endorse or promote products derived          #
+#    from this software without specific prior written permission.            #
+#                                                                             #
+#                                                                             #
+# *************************************************************************** #
+
+
+def _reflect(x: np.ndarray, minx: float, maxx: float) -> np.ndarray:
+    """Reflect the values in matrix *x* about the scalar values *minx* and
+    *maxx*.  Hence a vector *x* containing a long linearly increasing series is
+    converted into a waveform which ramps linearly up and down between *minx*
+    and *maxx*.  If *x* contains integers and *minx* and *maxx* are (integers +
+    0.5), the ramps will have repeated max and min samples.
+
+    .. codeauthor:: Rich Wareham <rjw57@cantab.net>, Aug 2013
+    .. codeauthor:: Nick Kingsbury, Cambridge University, January 1999.
+
+    """
+    rng = maxx - minx
+    rng_by_2 = 2 * rng
+    mod = np.fmod(x - minx, rng_by_2)
+    normed_mod = np.where(mod < 0, mod + rng_by_2, mod)
+    out = np.where(normed_mod >= rng, rng_by_2 - normed_mod, normed_mod) + minx
+    return np.array(out, dtype=x.dtype)
+
+
+class _DeviceMemStack:
+    def __init__(self) -> None:
+        self.allocations = []
+        self.current = 0
+        self.highwater = 0
+
+    def malloc(self, bytes):
+        self.allocations.append(bytes)
+        allocated = self._round_up(bytes)
+        self.current += allocated
+        self.highwater = max(self.current, self.highwater)
+
+    def free(self, bytes):
+        assert bytes in self.allocations
+        self.allocations.remove(bytes)
+        self.current -= self._round_up(bytes)
+        assert self.current >= 0
+
+    def _round_up(self, size):
+        ALLOCATION_UNIT_SIZE = 512
+        size = (size + ALLOCATION_UNIT_SIZE - 1) // ALLOCATION_UNIT_SIZE
+        return size * ALLOCATION_UNIT_SIZE
+
+
+def _mypad(
+    x: cp.ndarray, pad: Tuple[int, int, int, int], mem_stack: Optional[_DeviceMemStack]
+) -> cp.ndarray:
+    """Function to do numpy like padding on Arrays. Only works for 2-D
+    padding.
+
+    Inputs:
+        x (array): Array to pad
+        pad (tuple): tuple of (left, right, top, bottom) pad sizes
+    """
+    # Vertical only
+    if pad[0] == 0 and pad[1] == 0:
+        m1, m2 = pad[2], pad[3]
+        l = x.shape[-2] if not mem_stack else x[-2]
+        xe = _reflect(np.arange(-m1, l + m2, dtype="int32"), -0.5, l - 0.5)
+        if mem_stack:
+            ret_shape = [x[0], x[1], xe.size, x[3]]
+            mem_stack.malloc(np.prod(ret_shape) * np.float32().itemsize)
+            return ret_shape
+        return x[:, :, xe, :]
+    # horizontal only
+    elif pad[2] == 0 and pad[3] == 0:
+        m1, m2 = pad[0], pad[1]
+        l = x.shape[-1] if not mem_stack else x[-1]
+        xe = _reflect(np.arange(-m1, l + m2, dtype="int32"), -0.5, l - 0.5)
+        if mem_stack:
+            ret_shape = [x[0], x[1], x[2], xe.size]
+            mem_stack.malloc(np.prod(ret_shape) * np.float32().itemsize)
+            return ret_shape
+        return x[:, :, :, xe]
+
+
+def _next_power_of_two(x: int, max_val: int = 128) -> int:
+    n = 1
+    while n < x and n < max_val:
+        n *= 2
+    return n
+
+
+def _conv2d(
+    x: cp.ndarray,
+    w: np.ndarray,
+    stride: Tuple[int, int],
+    groups: int,
+    mem_stack: Optional[_DeviceMemStack],
+) -> cp.ndarray:
+    """Convolution (equivalent pytorch.conv2d)"""
+    b, ci, hi, wi = x.shape if not mem_stack else x
+    co, _, hk, wk = w.shape
+    ho = int(np.floor(1 + (hi - hk) / stride[0]))
+    wo = int(np.floor(1 + (wi - wk) / stride[1]))
+    out_shape = [b, co, ho, wo]
+    if mem_stack:
+        mem_stack.malloc(np.prod(out_shape) * np.float32().itemsize)
+        return out_shape
+
+    out = cp.zeros(out_shape, dtype="float32")
+    w = cp.asarray(w)
+    x = cp.expand_dims(x, axis=1)
+    w = np.expand_dims(w, axis=0)
+    symbol_names = [f"grouped_convolution_x<{wk}>", f"grouped_convolution_y<{hk}>"]
+    module = load_cuda_module("remove_stripe_fw", name_expressions=symbol_names)
+    dim_x = out.shape[-1]
+    dim_y = out.shape[-2]
+    dim_z = out.shape[0]
+    in_stride_x = stride[1]
+    in_stride_y = x.strides[-2] // x.dtype.itemsize
+    in_stride_z = x.strides[0] // x.dtype.itemsize
+    out_stride_z = out.strides[0] // x.dtype.itemsize
+    out_stride_group = out.strides[1] // x.dtype.itemsize
+
+    block_x = _next_power_of_two(dim_x)
+    block_dim = (block_x, 1, 1)
+    grid_x = (dim_x + block_x - 1) // block_x
+    grid_dim = (grid_x, dim_y, dim_z)
+
+    if groups == 1:
+        grouped_convolution_kernel_x = module.get_function(symbol_names[0])
+        grouped_convolution_kernel_x(
+            grid_dim,
+            block_dim,
+            (
+                dim_x,
+                dim_y,
+                dim_z,
+                x,
+                in_stride_x,
+                in_stride_y,
+                in_stride_z,
+                out,
+                out_stride_z,
+                out_stride_group,
+                w,
+            ),
+        )
+        return out
+
+    grouped_convolution_kernel_y = module.get_function(symbol_names[1])
+    in_stride_group = x.strides[2] // x.dtype.itemsize
+    grouped_convolution_kernel_y(
+        grid_dim,
+        block_dim,
+        (
+            dim_x,
+            dim_y,
+            dim_z,
+            x,
+            in_stride_x,
+            in_stride_y,
+            in_stride_z,
+            in_stride_group,
+            out,
+            out_stride_z,
+            out_stride_group,
+            w,
+        ),
+    )
+    del w
+    return out
+
+
+def _conv_transpose2d(
+    x: cp.ndarray,
+    w: np.ndarray,
+    stride: Tuple[int, int],
+    pad: Tuple[int, int],
+    groups: int,
+    mem_stack: Optional[_DeviceMemStack],
+) -> cp.ndarray:
+    """Transposed convolution (equivalent pytorch.conv_transpose2d)"""
+    b, co, ho, wo = x.shape if not mem_stack else x
+    co, ci, hk, wk = w.shape
+
+    hi = (ho - 1) * stride[0] + hk
+    wi = (wo - 1) * stride[1] + wk
+    out_shape = [b, ci, hi, wi]
+    if mem_stack:
+        mem_stack.malloc(np.prod(out_shape) * np.float32().itemsize)
+        mem_stack.malloc(w.size * np.float32().itemsize)
+        if pad != 0:
+            new_out_shape = [
+                out_shape[0],
+                out_shape[1],
+                out_shape[2] - 2 * pad[0],
+                out_shape[3] - 2 * pad[1],
+            ]
+            mem_stack.malloc(np.prod(new_out_shape) * np.float32().itemsize)
+            mem_stack.free(np.prod(out_shape) * np.float32().itemsize)
+            out_shape = new_out_shape
+        mem_stack.free(w.size * np.float32().itemsize)
+        return out_shape
+
+    out = cp.zeros(out_shape, dtype="float32")
+    w = cp.asarray(w)
+
+    symbol_names = [
+        f"transposed_convolution_x<{wk}>",
+        f"transposed_convolution_y<{hk}>",
+    ]
+    module = load_cuda_module("remove_stripe_fw", name_expressions=symbol_names)
+    dim_x = out.shape[-1]
+    dim_y = out.shape[-2]
+    dim_z = out.shape[0]
+    in_dim_x = x.shape[-1]
+    in_dim_y = x.shape[-2]
+    in_stride_y = x.strides[-2] // x.dtype.itemsize
+    in_stride_z = x.strides[0] // x.dtype.itemsize
+
+    block_x = _next_power_of_two(dim_x)
+    block_dim = (block_x, 1, 1)
+    grid_x = (dim_x + block_x - 1) // block_x
+    grid_dim = (grid_x, dim_y, dim_z)
+
+    if wk > 1:
+        transposed_convolution_kernel_x = module.get_function(symbol_names[0])
+        transposed_convolution_kernel_x(
+            grid_dim,
+            block_dim,
+            (dim_x, dim_y, dim_z, x, in_dim_x, in_stride_y, in_stride_z, w, out),
+        )
+    elif hk > 1:
+        transposed_convolution_kernel_y = module.get_function(symbol_names[1])
+        transposed_convolution_kernel_y(
+            grid_dim,
+            block_dim,
+            (dim_x, dim_y, dim_z, x, in_dim_y, in_stride_y, in_stride_z, w, out),
+        )
+    else:
+        assert False
+
+    if pad != 0:
+        out = out[:, :, pad[0] : out.shape[2] - pad[0], pad[1] : out.shape[3] - pad[1]]
+    return cp.ascontiguousarray(out)
+
+
+def _afb1d(
+    x: cp.ndarray,
+    h0: np.ndarray,
+    h1: np.ndarray,
+    dim: int,
+    mem_stack: Optional[_DeviceMemStack],
+) -> cp.ndarray:
+    """1D analysis filter bank (along one dimension only) of an image
+
+    Parameters
+    ----------
+    x (array): 4D input with the last two dimensions the spatial input
+    h0 (array): 4D input for the lowpass filter. Should have shape (1, 1,
+        h, 1) or (1, 1, 1, w)
+    h1 (array): 4D input for the highpass filter. Should have shape (1, 1,
+        h, 1) or (1, 1, 1, w)
+    dim (int) - dimension of filtering. d=2 is for a vertical filter (called
+        column filtering but filters across the rows). d=3 is for a
+        horizontal filter, (called row filtering but filters across the
+        columns).
+
+    Returns
+    -------
+    lohi: lowpass and highpass subbands concatenated along the channel
+        dimension
+    """
+    C = x.shape[1] if not mem_stack else x[1]
+    # Convert the dim to positive
+    d = dim % 4
+    s = (2, 1) if d == 2 else (1, 2)
+    N = x.shape[d] if not mem_stack else x[d]
+    L = h0.size
+    shape = [1, 1, 1, 1]
+    shape[d] = L
+    h = np.concatenate([h0.reshape(*shape), h1.reshape(*shape)] * C, axis=0)
+    # Calculate the pad size
+    outsize = pywt.dwt_coeff_len(N, L, mode="symmetric")
+    p = 2 * (outsize - 1) - N + L
+    pad = (0, 0, p // 2, (p + 1) // 2) if d == 2 else (p // 2, (p + 1) // 2, 0, 0)
+    padded_x = _mypad(x, pad=pad, mem_stack=mem_stack)
+    lohi = _conv2d(padded_x, h, stride=s, groups=C, mem_stack=mem_stack)
+    if mem_stack:
+        mem_stack.free(np.prod(padded_x) * np.float32().itemsize)
+    del padded_x
+    return lohi
+
+
+def _sfb1d(
+    lo: cp.ndarray,
+    hi: cp.ndarray,
+    g0: np.ndarray,
+    g1: np.ndarray,
+    dim: int,
+    mem_stack: Optional[_DeviceMemStack],
+) -> cp.ndarray:
+    """1D synthesis filter bank of an image Array"""
+
+    C = lo.shape[1] if not mem_stack else lo[1]
+    d = dim % 4
+    L = g0.size
+    shape = [1, 1, 1, 1]
+    shape[d] = L
+    s = (2, 1) if d == 2 else (1, 2)
+    g0 = np.concatenate([g0.reshape(*shape)] * C, axis=0)
+    g1 = np.concatenate([g1.reshape(*shape)] * C, axis=0)
+    pad = (L - 2, 0) if d == 2 else (0, L - 2)
+    y_lo = _conv_transpose2d(lo, g0, stride=s, pad=pad, groups=C, mem_stack=mem_stack)
+    y_hi = _conv_transpose2d(hi, g1, stride=s, pad=pad, groups=C, mem_stack=mem_stack)
+    if mem_stack:
+        # Allocation of the sum
+        mem_stack.malloc(np.prod(y_hi) * np.float32().itemsize)
+        mem_stack.free(np.prod(y_lo) * np.float32().itemsize)
+        mem_stack.free(np.prod(y_hi) * np.float32().itemsize)
+        return y_lo
+    return y_lo + y_hi
+
+
+class _DWTForward:
+    """Performs a 2d DWT Forward decomposition of an image
+
+    Args:
+        wave (str): Which wavelet to use.
+    """
+
+    def __init__(self, wave: str):
+        super().__init__()
+
+        wave = pywt.Wavelet(wave)
+        h0_col, h1_col = wave.dec_lo, wave.dec_hi
+        h0_row, h1_row = h0_col, h1_col
+
+        self.h0_col = np.array(h0_col).astype("float32")[::-1].reshape((1, 1, -1, 1))
+        self.h1_col = np.array(h1_col).astype("float32")[::-1].reshape((1, 1, -1, 1))
+        self.h0_row = np.array(h0_row).astype("float32")[::-1].reshape((1, 1, 1, -1))
+        self.h1_row = np.array(h1_row).astype("float32")[::-1].reshape((1, 1, 1, -1))
+
+    def apply(
+        self, x: cp.ndarray, mem_stack: Optional[_DeviceMemStack] = None
+    ) -> Tuple[cp.ndarray, cp.ndarray]:
+        """Forward pass of the DWT.
+
+        Args:
+            x (array): Input of shape :math:`(N, C_{in}, H_{in}, W_{in})`
+
+        Returns:
+            (yl, yh)
+                tuple of lowpass (yl) and bandpass (yh) coefficients.
+                yh is a list of scale coefficients. yl has shape
+                :math:`(N, C_{in}, H_{in}', W_{in}')` and yh has shape
+                :math:`list(N, C_{in}, 3, H_{in}'', W_{in}'')`. The new
+                dimension in yh iterates over the LH, HL and HH coefficients.
+
+        Note:
+            :math:`H_{in}', W_{in}', H_{in}'', W_{in}''` denote the correctly
+            downsampled shapes of the DWT pyramid.
+        """
+        # Do a multilevel transform
+        # Do 1 level of the transform
+        lohi = _afb1d(x, self.h0_row, self.h1_row, dim=3, mem_stack=mem_stack)
+        y = _afb1d(lohi, self.h0_col, self.h1_col, dim=2, mem_stack=mem_stack)
+        if mem_stack:
+            y_shape = [y[0], np.prod(y) // y[0] // 4 // y[-2] // y[-1], 4, y[-2], y[-1]]
+            x_shape = [y_shape[0], y_shape[1], y_shape[3], y_shape[4]]
+            yh_shape = [y_shape[0], y_shape[1], y_shape[2] - 1, y_shape[3], y_shape[4]]
+
+            mem_stack.free(np.prod(lohi) * np.float32().itemsize)
+            mem_stack.malloc(np.prod(x_shape) * np.float32().itemsize)
+            mem_stack.malloc(np.prod(yh_shape) * np.float32().itemsize)
+            mem_stack.free(np.prod(y) * np.float32().itemsize)
+            return x_shape, yh_shape
+        del lohi
+        s = y.shape
+        y = y.reshape(s[0], -1, 4, s[-2], s[-1])
+        x = cp.ascontiguousarray(y[:, :, 0])
+        yh = cp.ascontiguousarray(y[:, :, 1:])
+        return (x, yh)
+
+
+class _DWTInverse:
+    """Performs a 2d DWT Inverse reconstruction of an image
+
+    Args:
+        wave (str): Which wavelet to use.
+    """
+
+    def __init__(self, wave: str):
+        super().__init__()
+        wave = pywt.Wavelet(wave)
+        g0_col, g1_col = wave.rec_lo, wave.rec_hi
+        g0_row, g1_row = g0_col, g1_col
+        # Prepare the filters
+        self.g0_col = np.array(g0_col).astype("float32").reshape((1, 1, -1, 1))
+        self.g1_col = np.array(g1_col).astype("float32").reshape((1, 1, -1, 1))
+        self.g0_row = np.array(g0_row).astype("float32").reshape((1, 1, 1, -1))
+        self.g1_row = np.array(g1_row).astype("float32").reshape((1, 1, 1, -1))
+
+    def apply(
+        self,
+        coeffs: Tuple[cp.ndarray, cp.ndarray],
+        mem_stack: Optional[_DeviceMemStack] = None,
+    ) -> cp.ndarray:
+        """
+        Args:
+            coeffs (yl, yh): tuple of lowpass and bandpass coefficients, where:
+              yl is a lowpass array of shape :math:`(N, C_{in}, H_{in}',
+              W_{in}')` and yh is a list of bandpass arrays of shape
+              :math:`list(N, C_{in}, 3, H_{in}'', W_{in}'')`. I.e. should match
+              the format returned by DWTForward
+
+        Returns:
+            Reconstructed input of shape :math:`(N, C_{in}, H_{in}, W_{in})`
+
+        Note:
+            :math:`H_{in}', W_{in}', H_{in}'', W_{in}''` denote the correctly
+            downsampled shapes of the DWT pyramid.
+
+        """
+        yl, yh = coeffs
+        lh = yh[:, :, 0, :, :] if not mem_stack else [yh[0], yh[1], yh[3], yh[4]]
+        hl = yh[:, :, 1, :, :] if not mem_stack else [yh[0], yh[1], yh[3], yh[4]]
+        hh = yh[:, :, 2, :, :] if not mem_stack else [yh[0], yh[1], yh[3], yh[4]]
+        lo = _sfb1d(yl, lh, self.g0_col, self.g1_col, dim=2, mem_stack=mem_stack)
+        hi = _sfb1d(hl, hh, self.g0_col, self.g1_col, dim=2, mem_stack=mem_stack)
+        yl = _sfb1d(lo, hi, self.g0_row, self.g1_row, dim=3, mem_stack=mem_stack)
+        if mem_stack:
+            mem_stack.free(np.prod(lo) * np.float32().itemsize)
+            mem_stack.free(np.prod(hi) * np.float32().itemsize)
+        del lo
+        del hi
+        return yl
+
+
+def _repair_memory_fragmentation_if_needed(fragmentation_threshold: float = 0.2):
+    pool = cp.get_default_memory_pool()
+    total = pool.total_bytes()
+    if (total / pool.used_bytes()) - 1 > fragmentation_threshold:
+        pool.free_all_blocks()
+
+
+def remove_stripe_fw(
+    data: cp.ndarray,
+    sigma: float = 2,
+    wname: str = "db5",
+    level: Optional[int] = None,
+    calc_peak_gpu_mem: bool = False,
+) -> cp.ndarray:
+    """
+    Remove horizontal stripes from sinogram using the Fourier-Wavelet (FW) based method :cite:`munch2009stripe`. The original source code
+    taken from TomoCupy and NABU packages.
+
+    Parameters
+    ----------
+    data : ndarray
+        3D tomographic data as a CuPy array.
+    sigma : float
+        Damping parameter in Fourier space.
+    wname : str
+        Type of the wavelet filter: select from 'db5', 'db7', 'haar', 'sym5', 'sym16' 'bior4.4'.
+    level : int, optional
+        Number of discrete wavelet transform levels.
+    calc_peak_gpu_mem: str:
+        Parameter to support memory estimation in HTTomo. Irrelevant to the method itself and can be ignored by user.
+
+    Returns
+    -------
+    ndarray
+        Stripe-corrected 3D tomographic data as a CuPy array.
+    """
+
+    if level is None:
+        if calc_peak_gpu_mem:
+            size = np.max(data)  # data is a tuple in this case
+        else:
+            size = np.max(data.shape)
+        level = int(np.ceil(np.log2(size)))
+
+    [nproj, nz, ni] = data.shape if not calc_peak_gpu_mem else data
+
+    nproj_pad = nproj + nproj // 8
+
+    # Accepts all wave types available to PyWavelets
+    xfm = _DWTForward(wave=wname)
+    ifm = _DWTInverse(wave=wname)
+
+    # Wavelet decomposition.
+    cc = []
+    sli_shape = [nz, 1, nproj_pad, ni]
+
+    if calc_peak_gpu_mem:
+        mem_stack = _DeviceMemStack()
+        # A data copy is assumed when invoking the function
+        mem_stack.malloc(np.prod(data) * np.float32().itemsize)
+        mem_stack.malloc(np.prod(sli_shape) * np.float32().itemsize)
+        cc = []
+        fcV_bytes = None
+        for k in range(level):
+            new_sli_shape, c = xfm.apply(sli_shape, mem_stack)
+            mem_stack.free(np.prod(sli_shape) * np.float32().itemsize)
+            sli_shape = new_sli_shape
+            cc.append(c)
+
+            if fcV_bytes:
+                mem_stack.free(fcV_bytes)
+            fcV_shape = [c[0], c[3], c[4]]
+            fcV_bytes = np.prod(fcV_shape) * np.complex64().itemsize
+            mem_stack.malloc(fcV_bytes)
+
+            # For the FFT
+            mem_stack.malloc(2 * np.prod(fcV_shape) * np.float32().itemsize)
+            mem_stack.malloc(2 * fcV_bytes)
+
+            fft_dummy = cp.empty(fcV_shape, dtype="float32")
+            fft_plan = get_fft_plan(fft_dummy)
+            fft_plan_size = fft_plan.work_area.mem.size
+            del fft_dummy
+            del fft_plan
+            mem_stack.malloc(fft_plan_size)
+            mem_stack.free(2 * np.prod(fcV_shape) * np.float32().itemsize)
+            mem_stack.free(fft_plan_size)
+            mem_stack.free(2 * fcV_bytes)
+
+            # The rest of the iteration doesn't contribute to the peak
+        # NOTE: The last iteration of fcV is "leaked"
+
+        for k in range(level)[::-1]:
+            new_sli_shape = [sli_shape[0], sli_shape[1], cc[k][-2], cc[k][-1]]
+            new_sli_shape = ifm.apply((new_sli_shape, cc[k]), mem_stack)
+            mem_stack.free(np.prod(sli_shape) * np.float32().itemsize)
+            sli_shape = new_sli_shape
+
+        mem_stack.malloc(np.prod(data) * np.float32().itemsize)
+        for c in cc:
+            mem_stack.free(np.prod(c) * np.float32().itemsize)
+        mem_stack.free(np.prod(sli_shape) * np.float32().itemsize)
+        return int(mem_stack.highwater * 1.1)
+
+    sli = cp.zeros(sli_shape, dtype="float32")
+    sli[:, 0, (nproj_pad - nproj) // 2 : (nproj_pad + nproj) // 2] = data.swapaxes(0, 1)
+    for k in range(level):
+        sli, c = xfm.apply(sli)
+        cc.append(c)
+        # FFT
+        fft_in = cp.ascontiguousarray(cc[k][:, 0, 1])
+        fft_plan = get_fft_plan(fft_in, axes=1)
+        with fft_plan:
+            fcV = cp.fft.fft(fft_in, axis=1)
+        del fft_plan
+        del fft_in
+        _, my, mx = fcV.shape
+        # Damping of ring artifact information.
+        y_hat = np.fft.ifftshift((np.arange(-my, my, 2) + 1) / 2)
+        damp = -np.expm1(-(y_hat**2) / (2 * sigma**2))
+        fcV *= cp.tile(damp, (mx, 1)).swapaxes(0, 1)
+        # Inverse FFT.
+        ifft_in = cp.ascontiguousarray(fcV)
+        ifft_plan = get_fft_plan(ifft_in, axes=1)
+        with ifft_plan:
+            cc[k][:, 0, 1] = cp.fft.ifft(ifft_in, my, axis=1).real
+        del ifft_plan
+        del ifft_in
+        _repair_memory_fragmentation_if_needed()
+
+    # Wavelet reconstruction.
+    for k in range(level)[::-1]:
+        shape0 = cc[k][0, 0, 1].shape
+        sli = sli[:, :, : shape0[0], : shape0[1]]
+        sli = ifm.apply((sli, cc[k]))
+        _repair_memory_fragmentation_if_needed()
+
+    data = sli[:, 0, (nproj_pad - nproj) // 2 : (nproj_pad + nproj) // 2, :ni]
+    data = data.swapaxes(0, 1)
+    return cp.ascontiguousarray(data)
+
+
 ######## Optimized version for Vo-all ring removal in tomopy########
 # This function is taken from TomoCuPy package
 # *************************************************************************** #

{httomolibgpu-5.1.dist-info → httomolibgpu-5.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: httomolibgpu
-Version: 5.1
+Version: 5.3
 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
@@ -19,6 +19,7 @@ Requires-Dist: scipy
 Requires-Dist: pillow
 Requires-Dist: scikit-image
 Requires-Dist: tomobar
+Requires-Dist: PyWavelets
 Provides-Extra: dev
 Requires-Dist: pytest; extra == "dev"
 Requires-Dist: pytest-cov; extra == "dev"

{httomolibgpu-5.1.dist-info → httomolibgpu-5.3.dist-info}/RECORD

@@ -1,5 +1,5 @@
-httomolibgpu/__init__.py,sha256=Fdj5ipIGgeKqSCYRb5bBVMAZ04ZvZJzuBoGOAqc0zgk,937
-httomolibgpu/cupywrapper.py,sha256=6ITGJ2Jw5I5kVmKEL5LlsnLRniEqqBLsHiAjvLtk0Xk,493
+httomolibgpu/__init__.py,sha256=Dt_TYhjJGPVathlceTYQhoRSyH8n7FGQJlRMUlFZNdc,959
+httomolibgpu/cupywrapper.py,sha256=vHuBN4Wo3YxPnQP0OAJypLfZA6AXyXFgVmaZw_67pvo,579
 httomolibgpu/memory_estimator_helpers.py,sha256=QaJady-z8y9Emw7W-lB608vBTNvVYv3obboQKVj6E9M,705
 httomolibgpu/cuda_kernels/__init__.py,sha256=VQNMaGcVDwiE-C64FfLtubHpLriLG0Y3_QnjHBSHrN0,884
 httomolibgpu/cuda_kernels/calc_metrics.cu,sha256=oV7ZPcwjWafmZjbNsUkBYPvOViJ_nX3zBoOAuPCmIrA,11335
@@ -8,6 +8,7 @@ httomolibgpu/cuda_kernels/generate_mask.cu,sha256=3il3r1J2cnTCd3UXO4GWGfBgGxj4pv
 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/cuda_kernels/remove_stripe_fw.cu,sha256=J_vy0RUYYKT-mOzERsn3kjgt4hbE7vHPFRuJYNzs6sM,4504
 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
@@ -17,14 +18,14 @@ httomolibgpu/misc/utils.py,sha256=rHRuQUO47SlTanvKDBgiC0im4tXlGLCw5B_zvlLzzbc,47
 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=yKJe9gmWuFaUSIuoctV5X1Pb7yEgOmkQ6jxvZkSSwpQ,12128
-httomolibgpu/prep/stripe.py,sha256=8_DV0ON6AWARuziqkmhom56gWTardtqC_z3xG8geg0o,14774
+httomolibgpu/prep/phase.py,sha256=N3Ep_Krn4rqbGOnNhApSbIYM7gVstBtequXTklBDQLk,14907
+httomolibgpu/prep/stripe.py,sha256=OZPimFxe9TOSaEcErORFxd6HCcFcR62-q5XYBvC10FM,36918
 httomolibgpu/recon/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 httomolibgpu/recon/_phase_cross_correlation.py,sha256=Ru2oLAPv8XOSSuZer5yNQrxD_8lMAwBSvtkVAVs5TCc,16469
 httomolibgpu/recon/algorithm.py,sha256=ds-_io7kGzo5FiJq8k4--PYtIWak3y9H7yuyg1lymyQ,25121
 httomolibgpu/recon/rotation.py,sha256=GaSwNrlDnlP_iIrTfKUQLiXsShJ5aSDvdKPwofggtwQ,27948
-httomolibgpu-5.1.dist-info/licenses/LICENSE,sha256=bXeLsgelPUUXw8HCIYiVC97Dpjhm2nB54m7TACdH8ng,48032
-httomolibgpu-5.1.dist-info/METADATA,sha256=zSD4pi1w0lyFkgkZrB38m1DuhmGj5ad4uWJENNX_J44,3339
-httomolibgpu-5.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-httomolibgpu-5.1.dist-info/top_level.txt,sha256=nV0Ty_YvSPVd1O6MNWuIplD0w1nwk5hT76YgBZ-bzUw,13
-httomolibgpu-5.1.dist-info/RECORD,,
+httomolibgpu-5.3.dist-info/licenses/LICENSE,sha256=bXeLsgelPUUXw8HCIYiVC97Dpjhm2nB54m7TACdH8ng,48032
+httomolibgpu-5.3.dist-info/METADATA,sha256=prUDINLOyJMUnUz3YQCkfhuDJtPyQCoELYedj2ktUD0,3365
+httomolibgpu-5.3.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+httomolibgpu-5.3.dist-info/top_level.txt,sha256=nV0Ty_YvSPVd1O6MNWuIplD0w1nwk5hT76YgBZ-bzUw,13
+httomolibgpu-5.3.dist-info/RECORD,,