nabu 2024.1.1__py3-none-any.whl → 2024.1.3__py3-none-any.whl

build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/dataset_validator.py

@@ -1,19 +0,0 @@
-from ..fullfield.dataset_validator import *
-from ...utils import copy_dict_items
-
-
-class HelicalDatasetValidator(FullFieldDatasetValidator):
-    """Allows more freedom in the choice of the slice indices"""
-
-    # this in the fullfield base  class is instead True
-    _check_also_z = False
-
-    def _check_slice_indices(self):
-        """Slice indices can be far beyond what fullfield pipeline accepts, no check here, but
-        Nabu expects that rec_region is initialised here"""
-
-        what = ["start_x", "end_x", "start_y", "end_y", "start_z", "end_z"]
-
-        self.rec_region = copy_dict_items(self.rec_params, what)
-
-        return

build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/fbp.py

@@ -1,147 +0,0 @@
-from ...reconstruction.fbp import *
-from .filtering import HelicalSinoFilter
-from ...utils import convert_index
-
-
-class BackprojectorHelical(Backprojector):
-    """This is the Backprojector derived class for helical reconstruction.
-    The modifications are detailed here :
-
-         * the backprojection is decoupled from the filtering. This allows, in the pipeline,
-           for doing first a filtering using backprojector_object.sino_filter subobject,
-           then calling backprojector_object.backprojection only after reweigthing the result of
-           the filter_sino method of sino_filter subobject.
-         * the angles can be resetted on the fly, and the class can work with a variable number of projection.
-           As a matter of fact, with the helical_chunked_regridded.py pipeline, the reconstruction is done
-           each time with the same set of angles, this because of the regridding mechanism. The feature
-           might return useful in the future if alternative approachs are developed again.
-         *
-    """
-
-    def __init__(self, *args, **kwargs):
-        """This became needed after the _d_sino allocation was removed from the base class"""
-        super().__init__(*args, **kwargs)
-        self._d_sino = self._processing.allocate_array("d_sino", self.sino_shape, "f")
-
-    def set_custom_angles_and_axis_corrections(self, angles_rad, x_per_proj):
-        """To arbitrarily change angles
-        Parameters
-        ==========
-
-        angles_rad: array of floats
-           one angle per each projection in radians
-
-        x_per_proj: array of floats
-           each entry is the axis shift for a projection, in pixels.
-
-        """
-        self.n_provided_angles = len(angles_rad)
-        self._axis_correction = np.zeros((1, self.n_angles), dtype=np.float32)
-
-        self._axis_correction[0, : self.n_provided_angles] = -x_per_proj
-
-        self.angles[: self.n_provided_angles] = angles_rad
-
-        self._compute_angles_again()
-
-        self.kern_proj_args[1] = self.n_provided_angles
-        self.kern_proj_args[6] = self.offsets["x"]
-        self.kern_proj_args[7] = self.offsets["y"]
-
-    def _compute_angles_again(self):
-        """to update angles dependent auxiliary arrays"""
-        self.h_cos[0] = np.cos(self.angles).astype("f")
-        self.h_msin[0] = (-np.sin(self.angles)).astype("f")
-        self._d_msin[:] = self.h_msin[0]
-        self._d_cos[:] = self.h_cos[0]
-        if self._axis_correction is not None:
-            self._d_axcorr[:] = self._axis_correction
-
-    def _init_filter(self, filter_name):
-        """To use the HelicalSinoFilter which is derived from SinoFilter
-        with a slightly different padding scheme
-        """
-        self.filter_name = filter_name
-        self.sino_filter = HelicalSinoFilter(
-            self.sino_shape,
-            filter_name=self.filter_name,
-            padding_mode=self.padding_mode,
-            cuda_options={"ctx": self.cuda_processing.ctx},
-        )
-
-    def backprojection(self, sino, output=None):
-        """Redefined here to do backprojection only, compare to the base class method."""
-        self._d_sino[:] = sino
-        res = self.backproj(self._d_sino, output=output)
-        return res
-
-    def _init_geometry(self, sino_shape, slice_shape, angles, rot_center, slice_roi):
-        """this is identical to _init_geometry of the base class with the
-        exception that self.extra_options["centered_axis"] is not considered
-        and as a consequence  self.offsets is not set here and the one of  _set_slice_roi
-        is kept.
-        """
-        if slice_shape is not None and slice_roi is not None:
-            raise ValueError("slice_shape and slice_roi cannot be used together")
-        self.sino_shape = sino_shape
-        if len(sino_shape) == 2:
-            n_angles, dwidth = sino_shape
-        else:
-            raise ValueError("Expected 2D sinogram")
-        self.dwidth = dwidth
-        self.rot_center = rot_center or (self.dwidth - 1) / 2.0
-        self._set_slice_shape(
-            slice_shape,
-        )
-        self.axis_pos = self.rot_center
-        self._set_angles(angles, n_angles)
-        self._set_slice_roi(slice_roi)
-        self._set_axis_corr()
-
-    def _set_slice_shape(self, slice_shape):
-        """this is identical to the _set_slice_shape ofthe base class
-        with the exception that n_y,n_x default to the largest possible reconstructible slice
-        """
-
-        n_y = self.dwidth + abs(self.dwidth - 1 - self.rot_center * 2)
-        n_x = self.dwidth + abs(self.dwidth - 1 - self.rot_center * 2)
-
-        if slice_shape is not None:
-            if np.isscalar(slice_shape):
-                slice_shape = (slice_shape, slice_shape)
-            n_y, n_x = slice_shape
-
-        self.n_x = n_x
-        self.n_y = n_y
-        self.slice_shape = (n_y, n_x)
-
-    def _set_slice_roi(self, slice_roi):
-        """Automatically tune the offset to in all cases."""
-        self.slice_roi = slice_roi
-        if slice_roi is None:
-            off = -(self.dwidth - 1 - self.rot_center * 2)
-            if off < 0:
-                self.offsets = {"x": off, "y": off}
-            else:
-                self.offsets = {"x": 0, "y": 0}
-        else:
-            start_x, end_x, start_y, end_y = slice_roi
-            # convert negative indices
-            slice_width, _ = self.slice_shape
-
-            off = min(0, -(self.dwidth - 1 - self.rot_center * 2))
-
-            if end_x < start_x:
-                start_x = off
-                end_x = off + slice_width
-
-            if end_y < start_y:
-                start_y = off
-                end_y = off + slice_width
-
-            self.slice_shape = (end_y - start_y, end_x - start_x)
-
-            self.n_x = self.slice_shape[-1]
-            self.n_y = self.slice_shape[-2]
-
-            self.offsets = {"x": start_x, "y": start_y}

build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/filtering.py

@@ -1,246 +0,0 @@
-# pylint: disable=too-many-arguments
-import numpy as np
-from ...utils import get_cuda_srcfile, updiv
-from ...reconstruction.filtering import get_next_power
-from ...reconstruction.filtering_cuda import CudaSinoFilter
-
-# pylint: disable=too-many-arguments,too-many-instance-attributes,too-many-function-args
-
-
-class HelicalSinoFilter(CudaSinoFilter):
-    def __init__(
-        self,
-        sino_shape,
-        filter_name=None,
-        padding_mode="zeros",
-        extra_options=None,
-        cuda_options=None,
-    ):
-        """Derived from nabu.reconstruction.filtering.SinoFilter
-        It is used by helical_chunked_regridded pipeline.
-        The shape of the processed sino, as a matter of fact which is due to the helical_chunked_regridded.py module
-        which is using the here present class, is always, but not necessarily [nangles, nslices, nhorizontal]
-        with nslices = 1. This  because  helical_chunked_regridded.py after a first preprocessing phase,
-        always processes slices one by one.
-        In helical_chunked_regridded .py, the call to the filter_sino method here contained  is
-        followed by  the weight redistribution ( done by another module), which solves the HA problem,
-        and the backprojection. The latter is performed by fbp.py or hbp.py
-
-        The reason for having this class, derived from nabu.reconstruction.filtering.SinoFilter,
-        is that the padding mechanism here implemented incorporates the padding with the available
-        theta+180 projection on the half-tomo side.
-
-        """
-        super().__init__(
-            sino_shape,
-            filter_name=filter_name,
-            padding_mode=padding_mode,
-            extra_options=extra_options,
-            cuda_options=cuda_options,
-        )
-
-        self._init_pad_kernel()
-
-    def _check_array(self, arr):
-        """
-        This class may work with an arbitrary number of projections. This is a consequence
-        of the first implementation of the helical pipeline. In the first implementation
-        the slices were reconstructed by backprojecting several turns, and the number of useful projections
-        was different from the beginning or end, to the center of the scan.
-        Now in helical_chunked_regridded.py the number of projections is fixed. The only relic left
-        is that the present class may work with an arbitrary number of projections.
-        """
-        if arr.dtype != np.float32:
-            raise ValueError("Expected data type = numpy.float32")
-        if arr.shape[1:] != self.sino_shape[1:]:
-            raise ValueError("Expected sinogram shape %s, got %s" % (self.sino_shape, arr.shape))
-
-    def _init_pad_kernel(self):
-        """The four possible padding kernels.
-        The first two, compared to nabu.reconstruction.filtering.SinoFilter
-        can work with an arbitrary number of projection.
-        The latter two implement the padding with the available information from theta+180.
-        """
-
-        self.kern_args = (self.d_sino_f, self.d_filter_f)
-        self.kern_args += self.d_sino_f.shape[::-1]
-        self._pad_mirror_edges_kernel = self.cuda.kernel(
-            "padding",
-            filename=get_cuda_srcfile("helical_padding.cu"),
-            signature="PPfiiiii",
-            options=[str("-DMIRROR_EDGES")],
-        )
-        self._pad_mirror_constant_kernel = self.cuda.kernel(
-            "padding",
-            filename=get_cuda_srcfile("helical_padding.cu"),
-            signature="PPfiiiiiff",
-            options=[str("-DMIRROR_CONSTANT")],
-        )
-
-        self._pad_mirror_edges_variable_rot_pos_kernel = self.cuda.kernel(
-            "padding",
-            filename=get_cuda_srcfile("helical_padding.cu"),
-            signature="PPPiiiii",
-            options=[str("-DMIRROR_EDGES_VARIABLE_ROT_POS")],
-        )
-        self._pad_mirror_constant_variable_rot_pos_kernel = self.cuda.kernel(
-            "padding",
-            filename=get_cuda_srcfile("helical_padding.cu"),
-            signature="PPPiiiiiff",
-            options=[str("-DMIRROR_CONSTANT_VARIABLE_ROT_POS")],
-        )
-
-        self.d_mirror_indexes = self.cuda.allocate_array(
-            "d_mirror_indexes", (self.sino_padded_shape[-2],), dtype=np.int32
-        )
-        self.d_variable_rot_pos = self.cuda.allocate_array(
-            "d_variable_rot_pos", (self.sino_padded_shape[-2],), dtype=np.float32
-        )
-        self._pad_edges_kernel = self.cuda.kernel(
-            "padding_edge", filename=get_cuda_srcfile("padding.cu"), signature="Piiiiiiii"
-        )
-        self._pad_block = (32, 32, 1)
-        self._pad_grid = tuple([updiv(n, p) for n, p in zip(self.sino_padded_shape[::-1], self._pad_block)])
-
-    def _pad_sino(self, sino, mirror_indexes=None, rot_center=None):
-        """redefined here to adapt the memory copy to the lenght of the sino argument
-        which, in the general helical case may be varying
-        """
-        if mirror_indexes is None:
-            self._pad_sino_simple(sino)
-
-        self.d_mirror_indexes[:] = np.zeros([len(self.d_mirror_indexes)], np.int32)
-        self.d_mirror_indexes[: len(mirror_indexes)] = mirror_indexes.astype(np.int32)
-
-        if np.isscalar(rot_center):
-            argument_rot_center = rot_center
-            tmp_pad_mirror_edges_kernel = self._pad_mirror_edges_kernel
-            tmp_pad_mirror_constant_kernel = self._pad_mirror_constant_kernel
-        else:
-            self.d_variable_rot_pos[: len(rot_center)] = rot_center
-            argument_rot_center = self.d_variable_rot_pos
-            tmp_pad_mirror_edges_kernel = self._pad_mirror_edges_variable_rot_pos_kernel
-            tmp_pad_mirror_constant_kernel = self._pad_mirror_constant_variable_rot_pos_kernel
-
-        self.d_sino_padded[: len(sino), : self.dwidth] = sino[:]
-        if self.padding_mode == "edges":
-            tmp_pad_mirror_edges_kernel(
-                self.d_sino_padded,
-                self.d_mirror_indexes,
-                argument_rot_center,
-                self.dwidth,
-                self.n_angles,
-                self.dwidth_padded,
-                self.pad_left,
-                self.pad_right,
-                grid=self._pad_grid,
-                block=self._pad_block,
-            )
-        else:
-            tmp_pad_mirror_constant_kernel(
-                self.d_sino_padded,
-                self.d_mirror_indexes,
-                argument_rot_center,
-                self.dwidth,
-                self.n_angles,
-                self.dwidth_padded,
-                self.pad_left,
-                self.pad_right,
-                0.0,
-                0.0,
-                grid=self._pad_grid,
-                block=self._pad_block,
-            )
-
-    def _pad_sino_simple(self, sino):
-        if self.padding_mode == "edges":
-            self.d_sino_padded[: len(sino), : self.dwidth] = sino[:]
-            self._pad_edges_kernel(
-                self.d_sino_padded,
-                self.dwidth,
-                self.n_angles,
-                self.dwidth_padded,
-                self.n_angles,
-                self.pad_left,
-                self.pad_right,
-                0,
-                0,
-                grid=self._pad_grid,
-                block=self._pad_block,
-            )
-        else:  # zeros
-            self.d_sino_padded.fill(0)
-            if self.ndim == 2:
-                self.d_sino_padded[: len(sino), : self.dwidth] = sino[:]
-            else:
-                self.d_sino_padded[: len(sino), :, : self.dwidth] = sino[:]
-
-    def filter_sino(self, sino, mirror_indexes=None, rot_center=None, output=None, no_output=False):
-        """
-        Perform the sinogram siltering.
-        redefined here to use also mirror data
-        Parameters
-        ----------
-        sino: numpy.ndarray or pycuda.gpuarray.GPUArray
-            Input sinogram (2D or 3D)
-        output: numpy.ndarray or pycuda.gpuarray.GPUArray, optional
-            Output array.
-        no_output: bool, optional
-            If set to True, no copy is be done. The resulting data lies
-            in self.d_sino_padded.
-        """
-        self._check_array(sino)
-        # copy2d/copy3d
-        self._pad_sino(sino, mirror_indexes=mirror_indexes, rot_center=rot_center)
-        # FFT
-        self.fft.fft(self.d_sino_padded, output=self.d_sino_f)
-
-        # multiply padded sinogram with filter in the Fourier domain
-        self.mult_kernel(*self.kern_args)  # TODO tune block size ?
-
-        # iFFT
-        self.fft.ifft(self.d_sino_f, output=self.d_sino_padded)
-
-        # return
-        if no_output:
-            return self.d_sino_padded
-        if output is None:
-            res = np.zeros(self.sino_shape, dtype=np.float32)
-            # can't do memcpy2d D->H ? (self.d_sino_padded[:, w]) I have to get()
-            sino_ref = self.d_sino_padded.get()
-        else:
-            res = output
-            sino_ref = self.d_sino_padded
-        if self.ndim == 2:
-            res[:] = sino_ref[:, : self.dwidth]
-        else:
-            res[:] = sino_ref[:, :, : self.dwidth]
-        return res
-
-    def _calculate_shapes(self, sino_shape):
-        self.ndim = len(sino_shape)
-        if self.ndim == 2:
-            n_angles, dwidth = sino_shape
-            n_sinos = 1
-        elif self.ndim == 3:
-            n_sinos, n_angles, dwidth = sino_shape
-        else:
-            raise ValueError("Invalid sinogram number of dimensions")
-        self.sino_shape = sino_shape
-        self.n_angles = n_angles
-        self.dwidth = dwidth
-        # int() is crucial here ! Otherwise some pycuda arguments (ex. memcpy2D)
-        # will not work with numpy.int64 (as for 2018.X)
-
-        ### the original get_next_power used in  nabu gives a lower ram footprint
-        self.dwidth_padded = 2 * int(get_next_power(self.dwidth))
-
-        self.sino_padded_shape = (n_angles, self.dwidth_padded)
-        if self.ndim == 3:
-            self.sino_padded_shape = (n_sinos,) + self.sino_padded_shape
-        sino_f_shape = list(self.sino_padded_shape)
-        sino_f_shape[-1] = sino_f_shape[-1] // 2 + 1
-        self.sino_f_shape = tuple(sino_f_shape)
-        #
-        self.pad_left = (self.dwidth_padded - self.dwidth) // 2
-        self.pad_right = self.dwidth_padded - self.dwidth - self.pad_left