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

build/lib/build/lib/build/lib/nabu/stitching/z_stitching.py

@@ -1,2279 +0,0 @@
-# coding: utf-8
-# /*##########################################################################
-#
-# Copyright (c) 2016-2017 European Synchrotron Radiation Facility
-#
-# Permission is hereby granted, free of charge, to any person obtaining a copy
-# of this software and associated documentation files (the "Software"), to deal
-# in the Software without restriction, including without limitation the rights
-# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-# copies of the Software, and to permit persons to whom the Software is
-# furnished to do so, subject to the following conditions:
-#
-# The above copyright notice and this permission notice shall be included in
-# all copies or substantial portions of the Software.
-#
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-# THE SOFTWARE.
-#
-# ###########################################################################*/
-
-__authors__ = ["H. Payno"]
-__license__ = "MIT"
-__date__ = "10/05/2022"
-
-
-import os
-from copy import copy
-from datetime import datetime
-from typing import Optional, Union, Iterable
-import numpy
-from math import ceil
-from contextlib import AbstractContextManager
-import h5py
-import logging
-from scipy.ndimage import shift as shift_scipy
-from functools import lru_cache as cache
-
-from silx.io.utils import get_data
-from silx.io.url import DataUrl
-from silx.io.dictdump import dicttonx
-
-from nxtomo.nxobject.nxdetector import ImageKey
-from nxtomo.nxobject.nxtransformations import NXtransformations
-from nxtomo.paths.nxtomo import get_paths as _get_nexus_paths
-from nxtomo.utils.transformation import build_matrix, LRDetTransformation, UDDetTransformation
-
-from tomoscan.io import HDF5File
-from tomoscan.esrf.scan.utils import cwd_context
-from tomoscan.identifier import BaseIdentifier
-from tomoscan.esrf import NXtomoScan, EDFTomoScan
-from tomoscan.volumebase import VolumeBase
-from tomoscan.esrf.volume import HDF5Volume
-from tomoscan.serie import Serie
-from tomoscan.factory import Factory as TomoscanFactory
-from tomoscan.utils.volume import concatenate as concatenate_volumes
-from tomoscan.esrf.scan.utils import (
-    get_compacted_dataslices,
-)  # this version has a 'return_url_set' needed here. At one point they should be merged together
-from pyunitsystem.metricsystem import MetricSystem
-
-from nxtomo.application.nxtomo import NXtomo
-from silx.io.dictdump import dicttonx
-
-from nabu.io.utils import DatasetReader
-from nabu.stitching.frame_composition import ZFrameComposition
-from nabu.stitching.utils import find_projections_relative_shifts, find_volumes_relative_shifts, ShiftAlgorithm
-from nabu.stitching.config import (
-    CROSS_CORRELATION_SLICE_FIELD,
-    PreProcessedZStitchingConfiguration,
-    PostProcessedZStitchingConfiguration,
-    ZStitchingConfiguration,
-    KEY_IMG_REG_METHOD,
-    KEY_RESCALE_MIN_PERCENTILES,
-    KEY_RESCALE_MAX_PERCENTILES,
-    KEY_THRESHOLD_FREQUENCY,
-)
-from nabu.stitching.alignment import align_horizontally, AlignmentAxis1
-from nabu.utils import Progress
-from nabu import version as nabu_version
-from nabu.io.writer import get_datetime
-from .overlap import (
-    ZStichOverlapKernel,
-    check_overlaps,
-)
-from .. import version as nabu_version
-from nabu.io.writer import get_datetime
-from nabu.misc.utils import rescale_data
-from nabu.stitching.alignment import PaddedRawData
-from nabu.stitching.sample_normalization import normalize_frame as normalize_frame_by_sample
-
-_logger = logging.getLogger(__name__)
-
-
-def z_stitching(configuration: ZStitchingConfiguration, progress=None) -> BaseIdentifier:
-    """
-    Apply stitching from provided configuration.
-    Return a DataUrl with the created NXtomo or Volume
-    """
-    if isinstance(configuration, PreProcessedZStitchingConfiguration):
-        stitcher = PreProcessZStitcher(configuration=configuration, progress=progress)
-    elif isinstance(configuration, PostProcessedZStitchingConfiguration):
-        stitcher = PostProcessZStitcher(configuration=configuration, progress=progress)
-    else:
-        raise TypeError(
-            f"configuration is expected to be in {(PreProcessedZStitchingConfiguration, PostProcessedZStitchingConfiguration)}. {type(configuration)} provided"
-        )
-    return stitcher.stitch()
-
-
-class ZStitcher:
-    @staticmethod
-    def param_is_auto(param):
-        return param in ("auto", ("auto",))
-
-    def __init__(self, configuration, progress: Progress = None) -> None:
-        if not isinstance(configuration, ZStitchingConfiguration):
-            raise TypeError
-
-        # flag to check if the serie has been ordered yet or not
-        self._configuration = copy(configuration)
-        # copy configuration because we will edit it
-        self._frame_composition = None
-        self._progress = progress
-        self._overlap_kernels = []
-        # kernels to create the stitching on overlaps.
-
-        self._axis_0_rel_shifts = []
-        self._axis_2_rel_shifts = []
-        # shift between upper and lower frames
-
-        self._stitching_width = None
-        # stitching width: larger volume width. Other volume will be pad
-
-        # z serie must be defined from daughter class
-        assert hasattr(self, "_z_serie")
-
-        def shifts_is_scalar(shifts):
-            return isinstance(shifts, ShiftAlgorithm) or numpy.isscalar(shifts)
-
-        # 'expend' shift algorithm
-        if shifts_is_scalar(self.configuration.axis_0_pos_px):
-            self.configuration.axis_0_pos_px = [
-                self.configuration.axis_0_pos_px,
-            ] * (len(self.z_serie) - 1)
-        if shifts_is_scalar(self.configuration.axis_1_pos_px):
-            self.configuration.axis_1_pos_px = [
-                self.configuration.axis_1_pos_px,
-            ] * (len(self.z_serie) - 1)
-        if shifts_is_scalar(self.configuration.axis_2_pos_px):
-            self.configuration.axis_2_pos_px = [
-                self.configuration.axis_2_pos_px,
-            ] * (len(self.z_serie) - 1)
-        if numpy.isscalar(self.configuration.axis_0_params):
-            self.configuration.axis_0_params = [
-                self.configuration.axis_0_params,
-            ] * (len(self.z_serie) - 1)
-        if numpy.isscalar(self.configuration.axis_1_params):
-            self.configuration.axis_1_params = [
-                self.configuration.axis_1_params,
-            ] * (len(self.z_serie) - 1)
-        if numpy.isscalar(self.configuration.axis_2_params):
-            self.configuration.axis_2_params = [
-                self.configuration.axis_2_params,
-            ] * (len(self.z_serie) - 1)
-
-    @property
-    def frame_composition(self):
-        return self._frame_composition
-
-    def get_final_axis_positions_in_px(self) -> dict:
-        """
-        :return: dict with tomo object identifier (str) as key and a tuple of position in pixel (axis_0_pos, axis_1_pos, axis_2_pos)
-        :rtype: dict
-        """
-        final_shifts_axis_0 = [
-            0,
-        ]
-        final_shifts_axis_0.extend(self._axis_0_rel_shifts)
-        final_shifts_axis_0 = numpy.array(final_shifts_axis_0)
-
-        final_shifts_axis_2 = [
-            0,
-        ]
-        final_shifts_axis_2.extend(self._axis_2_rel_shifts)
-        final_shifts_axis_2 = numpy.array(final_shifts_axis_2)
-
-        estimated_shifts_axis_0 = self._axis_0_estimated_shifts.copy()
-        estimated_shifts_axis_0.insert(0, 0)
-
-        final_pos = {}
-        previous_shift = 0
-        for tomo_obj, pos_axis_0, pos_axis_2, final_shift_axis_0, estimated_shift_axis_0, final_shift_axis_2 in zip(
-            self.z_serie,
-            self.configuration.axis_0_pos_px,
-            self.configuration.axis_2_pos_px,
-            estimated_shifts_axis_0,
-            final_shifts_axis_0,
-            final_shifts_axis_2,
-        ):
-            # warning estimated_shift is the estimatation from the overlap. So playes no role here
-            final_pos[tomo_obj.get_identifier().to_str()] = (
-                pos_axis_0 - (final_shift_axis_0 - estimated_shift_axis_0) + previous_shift,
-                None,  # axis 1 is not handled for now
-                pos_axis_2 + final_shift_axis_2,
-            )
-            previous_shift += final_shift_axis_0 - estimated_shift_axis_0
-        return final_pos
-
-    def from_abs_pos_to_rel_pos(self, abs_position: tuple):
-        """
-        return relative position from on object to the other but in relative this time
-        :param tuple abs_position: tuple containing the absolute positions
-        :return: len(abs_position) - 1 relative position
-        :rtype: tuple
-        """
-        return tuple([pos_obj_b - pos_obj_a for (pos_obj_a, pos_obj_b) in zip(abs_position[:-1], abs_position[1:])])
-
-    def from_rel_pos_to_abs_pos(self, rel_positions: tuple, init_pos: int):
-        """
-        return absolute positions from a tuple of relative position and an initial position
-        :param tuple rel_positions: tuple containing the absolute positions
-        :return: len(rel_positions) + 1 relative position
-        :rtype: tuple
-        """
-        abs_pos = [
-            init_pos,
-        ]
-        for rel_pos in rel_positions:
-            abs_pos.append(abs_pos[-1] + rel_pos)
-        return abs_pos
-
-    def stitch(self, store_composition: bool = True) -> BaseIdentifier:
-        """
-        Apply expected stitch from configuration and return the DataUrl of the object created
-
-        :param bool store_composition: if True then store the composition used for stitching in frame_composition.
-                                       So it can be reused by third part (like tomwer) to display composition made
-        """
-        raise NotImplementedError("base class")
-
-    def settle_flips(self):
-        """
-        User can provide some information on existing flips at frame level.
-        The goal of this step is to get one flip_lr and on flip_ud value per scan or volume
-        """
-        if numpy.isscalar(self.configuration.flip_lr):
-            self.configuration.flip_lr = tuple([self.configuration.flip_lr] * len(self.z_serie))
-        else:
-            if not len(self.configuration.flip_lr) == len(self.z_serie):
-                raise ValueError("flip_lr expects a scalar value or one value per element to stitch")
-            self.configuration.flip_lr = tuple(self.configuration.flip_lr)
-            for elmt in self.configuration.flip_lr:
-                if not isinstance(elmt, bool):
-                    raise TypeError
-
-        if numpy.isscalar(self.configuration.flip_ud):
-            self.configuration.flip_ud = tuple([self.configuration.flip_ud] * len(self.z_serie))
-        else:
-            if not len(self.configuration.flip_ud) == len(self.z_serie):
-                raise ValueError("flip_ud expects a scalar value or one value per element to stitch")
-            self.configuration.flip_ud = tuple(self.configuration.flip_ud)
-            for elmt in self.configuration.flip_ud:
-                if not isinstance(elmt, bool):
-                    raise TypeError
-
-    def _compute_shifts(self):
-        """
-        after this stage the final shifts must be determine
-        """
-        raise NotImplementedError("base class")
-
-    def _createOverlapKernels(self):
-        """
-        after this stage the overlap kernels must be created and with the final overlap size
-        """
-        if self._axis_0_rel_shifts is None or len(self._axis_0_rel_shifts) == 0:
-            raise RuntimeError(
-                "axis 0 shifts have not been defined yet. Please define them before calling this function"
-            )
-
-        overlap_size = self.configuration.axis_0_params.get("overlap_size", None)
-        if overlap_size in (None, "None", ""):
-            overlap_size = -1
-        else:
-            overlap_size = int(overlap_size)
-
-        self._stitching_width = max([get_obj_width(obj) for obj in self.z_serie])
-
-        for axis_0_shift in self._axis_0_rel_shifts:
-            if overlap_size == -1:
-                height = abs(axis_0_shift)
-            else:
-                height = overlap_size
-
-            self._overlap_kernels.append(
-                ZStichOverlapKernel(
-                    frame_width=self._stitching_width,
-                    stitching_strategy=self.configuration.stitching_strategy,
-                    overlap_size=height,
-                    extra_params=self.configuration.stitching_kernels_extra_params,
-                )
-            )
-
-    @property
-    def z_serie(self) -> Serie:
-        return self._z_serie
-
-    @property
-    def configuration(self) -> ZStitchingConfiguration:
-        return self._configuration
-
-    @property
-    def progress(self) -> Optional[Progress]:
-        return self._progress
-
-    @staticmethod
-    def get_overlap_areas(
-        upper_frame: numpy.ndarray,
-        lower_frame: numpy.ndarray,
-        upper_frame_key_line: int,
-        lower_frame_key_line: int,
-        overlap_size: int,
-        stitching_axis: int,
-    ):
-        """
-        return the requested area from lower_frame and upper_frame.
-
-        Lower_frame contains at the end of it the 'real overlap' with the upper_frame.
-        Upper_frame contains the 'real overlap' at the end of it.
-
-        For some reason the user can ask the stitching height to be smaller than the `real overlap`.
-
-        Here are some drawing to have a better of view of those regions:
-
-        .. image:: images/stitching/z_stitch_real_overlap.png
-            :width: 600
-
-        .. image:: z_stitch_stitch_height.png
-            :width: 600
-        """
-        assert stitching_axis in (0, 1, 2)
-        for pf, pn in zip((lower_frame_key_line, upper_frame_key_line), ("lower_frame", "upper_frame")):
-            if not isinstance(pf, (int, numpy.number)):
-                raise TypeError(f"{pn} is expected to be a number. {type(pf)} provided")
-        assert overlap_size >= 0
-
-        lf_start = ceil(lower_frame_key_line - overlap_size / 2)
-        lf_end = ceil(lower_frame_key_line + overlap_size / 2)
-        uf_start = ceil(upper_frame_key_line - overlap_size / 2)
-        uf_end = ceil(upper_frame_key_line + overlap_size / 2)
-
-        lf_start, lf_end = min(lf_start, lf_end), max(lf_start, lf_end)
-        uf_start, uf_end = min(uf_start, uf_end), max(uf_start, uf_end)
-        if lf_start < 0 or uf_start < 0:
-            raise ValueError(
-                f"requested overlap ({overlap_size}) is incoherent with key line positions ({lower_frame_key_line}, {upper_frame_key_line}) - expected to be smaller."
-            )
-        overlap_upper = upper_frame[uf_start:uf_end]
-        overlap_lower = lower_frame[lf_start:lf_end]
-        if not overlap_upper.shape == overlap_lower.shape:
-            # maybe in the future: try to reduce one according to the other ????
-            raise RuntimeError(
-                f"lower and upper frame have different overlap size ({overlap_upper.shape} vs {overlap_lower.shape})"
-            )
-        return overlap_upper, overlap_lower
-
-    @staticmethod
-    def _data_bunch_iterator(slices, bunch_size):
-        """util to get indices by bunch until we reach n_frames"""
-        if isinstance(slices, slice):
-            # note: slice step is handled at a different level
-            start = end = slices.start
-
-            while True:
-                start, end = end, min((end + bunch_size), slices.stop)
-                yield (start, end)
-                if end >= slices.stop:
-                    break
-        # in the case of non-contiguous frames
-        elif isinstance(slices, Iterable):
-            for s in slices:
-                yield (s, s + 1)
-        else:
-            raise TypeError(f"slices is provided as {type(slices)}. When Iterable or slice is expected")
-
-    def rescale_frames(self, frames: tuple):
-        """
-        rescale_frames if requested by the configuration
-        """
-        _logger.info("apply rescale frames")
-
-        def cast_percentile(percentile) -> int:
-            if isinstance(percentile, str):
-                percentile.replace(" ", "").rstrip("%")
-            return int(percentile)
-
-        rescale_min_percentile = cast_percentile(self.configuration.rescale_params.get(KEY_RESCALE_MIN_PERCENTILES, 0))
-        rescale_max_percentile = cast_percentile(
-            self.configuration.rescale_params.get(KEY_RESCALE_MAX_PERCENTILES, 100)
-        )
-
-        new_min = numpy.percentile(frames[0], rescale_min_percentile)
-        new_max = numpy.percentile(frames[0], rescale_max_percentile)
-
-        def rescale(data):
-            # FIXME: takes time because browse several time the dataset, twice for percentiles and twices to get min and max when calling rescale_data...
-            data_min = numpy.percentile(data, rescale_min_percentile)
-            data_max = numpy.percentile(data, rescale_max_percentile)
-            return rescale_data(data, new_min=new_min, new_max=new_max, data_min=data_min, data_max=data_max)
-
-        return tuple([rescale(data) for data in frames])
-
-    def normalize_frame_by_sample(self, frames: tuple):
-        """
-        normalize frame from a sample picked on the left or the right
-        """
-        _logger.info("apply normalization by a sample")
-        return tuple(
-            [
-                normalize_frame_by_sample(
-                    frame=frame,
-                    side=self.configuration.normalization_by_sample.side,
-                    method=self.configuration.normalization_by_sample.method,
-                    margin_before_sample=self.configuration.normalization_by_sample.margin,
-                    sample_width=self.configuration.normalization_by_sample.width,
-                )
-                for frame in frames
-            ]
-        )
-
-    @staticmethod
-    def stitch_frames(
-        frames: Union[tuple, numpy.ndarray],
-        x_relative_shifts: tuple,
-        y_relative_shifts: tuple,
-        output_dtype: numpy.ndarray,
-        stitching_axis: int,
-        overlap_kernels: tuple,
-        output_dataset: Optional[Union[h5py.Dataset, numpy.ndarray]] = None,
-        dump_frame_fct=None,
-        check_inputs=True,
-        shift_mode="nearest",
-        i_frame=None,
-        return_composition_cls=False,
-        alignment="center",
-        pad_mode="constant",
-        new_width: Optional[int] = None,
-    ) -> numpy.ndarray:
-        """
-        shift frames according to provided `shifts` (as y, x tuples) then stitch all the shifted frames together and
-        save them to output_dataset.
-
-        :param tuple frames: element must be a DataUrl or a 2D numpy array
-        """
-        if check_inputs:
-            if len(frames) < 2:
-                raise ValueError(f"Not enought frames provided for stitching ({len(frames)} provided)")
-            if len(frames) != len(x_relative_shifts) + 1:
-                raise ValueError(
-                    f"Incoherent number of shift provided ({len(x_relative_shifts)}) compare to number of frame ({len(frames)}). len(frames) - 1 expected"
-                )
-            if len(x_relative_shifts) != len(overlap_kernels):
-                raise ValueError(
-                    f"expect to have the same number of x_relative_shifts ({len(x_relative_shifts)}) and y_overlap ({len(overlap_kernels)})"
-                )
-            if len(y_relative_shifts) != len(overlap_kernels):
-                raise ValueError(
-                    f"expect to have the same number of y_relative_shifts ({len(y_relative_shifts)}) and y_overlap ({len(overlap_kernels)})"
-                )
-
-            relative_positions = [(0, 0)]
-            for y_rel_pos, x_rel_pos in zip(y_relative_shifts, x_relative_shifts):
-                relative_positions.append(
-                    (
-                        y_rel_pos + relative_positions[-1][0],
-                        x_rel_pos + relative_positions[-1][1],
-                    )
-                )
-            check_overlaps(
-                frames=tuple(frames),
-                positions=tuple(relative_positions),
-                axis=0,
-                raise_error=False,
-            )
-
-        def check_frame_is_2d(frame):
-            if frame.ndim != 2:
-                raise ValueError(f"2D frame expected when {frame.ndim}D provided")
-
-        # step_0 load data if from url
-        data = []
-        for frame in frames:
-            if isinstance(frame, DataUrl):
-                data_frame = get_data(frame)
-                if check_inputs:
-                    check_frame_is_2d(data_frame)
-                data.append(data_frame)
-            elif isinstance(frame, numpy.ndarray):
-                if check_inputs:
-                    check_frame_is_2d(frame)
-                data.append(frame)
-            else:
-                raise TypeError(f"frames are expected to be DataUrl or 2D numpy array. Not {type(frame)}")
-
-        # step 1: shift each frames (except the first one)
-        x_shifted_data = [data[0]]
-        for frame, x_relative_shift in zip(data[1:], x_relative_shifts):
-            # note: for now we only shift data in x. the y shift is handled in the FrameComposition
-            x_relative_shift = numpy.asarray(x_relative_shift).astype(numpy.int8)
-            if x_relative_shift == 0:
-                shifted_frame = frame
-            else:
-                # TO speed up: should use the Fourier transform
-                shifted_frame = shift_scipy(
-                    frame,
-                    mode=shift_mode,
-                    shift=[0, -x_relative_shift],
-                    order=1,
-                )
-            x_shifted_data.append(shifted_frame)
-
-        # step 2: create stitched frame
-        res = stitch_vertically_raw_frames(
-            frames=x_shifted_data,
-            key_lines=(
-                [
-                    (int(frame.shape[stitching_axis] - abs(y_relative_shift / 2)), int(abs(y_relative_shift / 2)))
-                    for y_relative_shift, frame in zip(y_relative_shifts, frames)
-                ]
-            ),
-            overlap_kernels=overlap_kernels,
-            check_inputs=check_inputs,
-            output_dtype=output_dtype,
-            return_composition_cls=return_composition_cls,
-            alignment=alignment,
-            pad_mode=pad_mode,
-            new_width=new_width,
-        )
-        if return_composition_cls:
-            stitched_frame, _ = res
-        else:
-            stitched_frame = res
-
-        # step 3: dump stitched frame
-        if output_dataset is not None and i_frame is not None:
-            dump_frame_fct(
-                output_dataset=output_dataset,
-                index=i_frame,
-                stitched_frame=stitched_frame,
-            )
-        return res
-
-    @staticmethod
-    @cache(maxsize=None)
-    def _get_UD_flip_matrix():
-        return UDDetTransformation().as_matrix()
-
-    @staticmethod
-    @cache(maxsize=None)
-    def _get_LR_flip_matrix():
-        return LRDetTransformation().as_matrix()
-
-    @staticmethod
-    @cache(maxsize=None)
-    def _get_UD_AND_LR_flip_matrix():
-        return numpy.matmul(
-            ZStitcher._get_UD_flip_matrix(),
-            ZStitcher._get_LR_flip_matrix(),
-        )
-
-
-class PreProcessZStitcher(ZStitcher):
-    def __init__(self, configuration, progress=None) -> None:
-        # z serie must be defined first
-        self._z_serie = Serie("z-serie", iterable=configuration.input_scans, use_identifiers=False)
-        self._reading_orders = []
-        self._x_flips = []
-        self._y_flips = []
-        # some scan can have been taken in the opposite order (so must be read on the opposite order one from the other)
-        self._axis_0_estimated_shifts = None
-        super().__init__(configuration, progress)
-
-        # 'expend' auto shift request if only set once for all
-        if numpy.isscalar(self.configuration.axis_0_pos_px):
-            self.configuration.axis_0_pos_px = [
-                self.configuration.axis_0_pos_px,
-            ] * (len(self.z_serie) - 1)
-        if numpy.isscalar(self.configuration.axis_1_pos_px):
-            self.configuration.axis_1_pos_px = [
-                self.configuration.axis_1_pos_px,
-            ] * (len(self.z_serie) - 1)
-        if numpy.isscalar(self.configuration.axis_2_pos_px):
-            self.configuration.axis_2_pos_px = [
-                self.configuration.axis_2_pos_px,
-            ] * (len(self.z_serie) - 1)
-
-        if self.configuration.axis_0_params is None:
-            self.configuration.axis_0_params = {}
-        if self.configuration.axis_1_params is None:
-            self.configuration.axis_1_params = {}
-        if self.configuration.axis_2_params is None:
-            self.configuration.axis_2_params = {}
-
-    @staticmethod
-    def _dump_frame(output_dataset: h5py.Dataset, index: int, stitched_frame: numpy.ndarray):
-        output_dataset[index] = stitched_frame
-
-    @property
-    def reading_orders(self):
-        """
-        as scan can be take on one direction or the order (rotation goes from X to Y then from Y to X)
-        we might need to read data from one direction or another
-        """
-        return self._reading_orders
-
-    @property
-    def x_flips(self) -> list:
-        return self._x_flips
-
-    @property
-    def y_flips(self) -> list:
-        return self._y_flips
-
-    def stitch(self, store_composition=True) -> BaseIdentifier:
-        """
-        :param bool return_composition: if True then return the frame composition (used by the GUI for example to display a background with the same class)
-        """
-        if self.progress is not None:
-            self.progress.set_name("order scans")
-        self._order_scans()
-        if self.progress is not None:
-            self.progress.set_name("check inputs")
-        self._check_inputs()
-        self.settle_flips()
-        self._compute_positions_as_px()
-        self._compute_axis_0_estimated_shifts()
-        if self.progress is not None:
-            self.progress.set_name("compute flat field")
-        self._compute_reduced_flats_and_darks()
-        if self.progress is not None:
-            self.progress.set_name("compute shifts")
-        self._compute_shifts()
-        self._createOverlapKernels()
-        if self.progress is not None:
-            self.progress.set_name("stitch projections, save them and create NXtomo")
-        self._create_nx_tomo(store_composition=store_composition)
-        if self.progress is not None:
-            self.progress.set_name("dump configuration")
-        self._dump_stitching_configuration()
-        stitched_scan = self.configuration.get_output_object()
-        return stitched_scan.get_identifier()
-
-    def _order_scans(self):
-        """
-        ensure scans are in z decreasing order
-        """
-
-        def get_min_z(scan):
-            return scan.get_bounding_box(axis=0).min
-
-        # order scans from higher z to lower z
-        # if axis 0 position is provided then use directly it
-        if self.configuration.axis_0_pos_px is not None and len(self.configuration.axis_0_pos_px) > 0:
-            order = numpy.argsort(self.configuration.axis_0_pos_px)[::-1]
-            sorted_z_serie = Serie(
-                self.z_serie.name,
-                numpy.take_along_axis(numpy.array(self.z_serie[:]), order, axis=0),
-                use_identifiers=False,
-            )
-        else:
-            # else use bounding box
-            sorted_z_serie = Serie(
-                self.z_serie.name,
-                sorted(self.z_serie[:], key=get_min_z, reverse=True),
-                use_identifiers=False,
-            )
-        if sorted_z_serie != self.z_serie:
-            if sorted_z_serie[:] != self.z_serie[::-1]:
-                raise ValueError("Unable to get comprehensive input. Z (decreasing) ordering is not respected.")
-            else:
-                _logger.warning(
-                    f"z decreasing order haven't been respected. Need to reorder z serie ({[str(scan) for scan in sorted_z_serie[:]]}). Will also reorder overlap height, stitching height and invert shifts"
-                )
-                if self.configuration.axis_0_pos_mm is not None:
-                    self.configuration.axis_0_pos_mm = self.configuration.axis_0_pos_mm[::-1]
-                if self.configuration.axis_0_pos_px is not None:
-                    self.configuration.axis_0_pos_px = self.configuration.axis_0_pos_px[::-1]
-                if self.configuration.axis_1_pos_mm is not None:
-                    self.configuration.axis_1_pos_mm = self.configuration.axis_1_pos_mm[::-1]
-                if self.configuration.axis_1_pos_px is not None:
-                    self.configuration.axis_1_pos_px = self.configuration.axis_1_pos_px[::-1]
-                if self.configuration.axis_2_pos_mm is not None:
-                    self.configuration.axis_2_pos_mm = self.configuration.axis_2_pos_mm[::-1]
-                if self.configuration.axis_2_pos_px is not None:
-                    self.configuration.axis_2_pos_px = self.configuration.axis_2_pos_px[::-1]
-                if not numpy.isscalar(self._configuration.flip_ud):
-                    self._configuration.flip_ud = self._configuration.flip_ud[::-1]
-                if not numpy.isscalar(self._configuration.flip_lr):
-                    self._configuration.flip_ud = self._configuration.flip_lr[::-1]
-
-        self._z_serie = sorted_z_serie
-
-    def _check_inputs(self):
-        """
-        insure input data is coherent
-        """
-        n_scans = len(self.z_serie)
-        if n_scans == 0:
-            raise ValueError("no scan to stich together")
-
-        for scan in self.z_serie:
-            from tomoscan.scanbase import TomoScanBase
-
-            if not isinstance(scan, TomoScanBase):
-                raise TypeError(f"z-preproc stitching expects instances of {TomoScanBase}. {type(scan)} provided.")
-
-        # check output file path and data path are provided
-        if self.configuration.output_file_path in (None, ""):
-            raise ValueError("outptu_file_path should be provided to the configuration")
-        if self.configuration.output_data_path in (None, ""):
-            raise ValueError("output_data_path should be provided to the configuration")
-
-        # check number of shift provided
-        for axis_pos_px, axis_name in zip(
-            (
-                self.configuration.axis_0_pos_px,
-                self.configuration.axis_1_pos_px,
-                self.configuration.axis_2_pos_px,
-                self.configuration.axis_0_pos_mm,
-                self.configuration.axis_1_pos_mm,
-                self.configuration.axis_2_pos_mm,
-            ),
-            (
-                "axis_0_pos_px",
-                "axis_1_pos_px",
-                "axis_2_pos_px",
-                "axis_0_pos_mm",
-                "axis_1_pos_mm",
-                "axis_2_pos_mm",
-            ),
-        ):
-            if isinstance(axis_pos_px, Iterable) and len(axis_pos_px) != (n_scans):
-                raise ValueError(f"{axis_name} expect {n_scans} shift defined. Get {len(axis_pos_px)}")
-
-        self._reading_orders = []
-        # the first scan will define the expected reading orderd, and expected flip.
-        # if all scan are flipped then we will keep it this way
-        self._reading_orders.append(1)
-
-        # check scans are coherent (nb projections, rotation angle, energy...)
-        for scan_0, scan_1 in zip(self.z_serie[0:-1], self.z_serie[1:]):
-            if len(scan_0.projections) != len(scan_1.projections):
-                raise ValueError(f"{scan_0} and {scan_1} have a different number of projections")
-            if isinstance(scan_0, NXtomoScan) and isinstance(scan_1, NXtomoScan):
-                # check rotation (only of is an NXtomoScan)
-                scan_0_angles = numpy.asarray(scan_0.rotation_angle)
-                scan_0_projections_angles = scan_0_angles[
-                    numpy.asarray(scan_0.image_key_control) == ImageKey.PROJECTION.value
-                ]
-                scan_1_angles = numpy.asarray(scan_1.rotation_angle)
-                scan_1_projections_angles = scan_1_angles[
-                    numpy.asarray(scan_1.image_key_control) == ImageKey.PROJECTION.value
-                ]
-                if not numpy.allclose(scan_0_projections_angles, scan_1_projections_angles, atol=10e-1):
-                    if numpy.allclose(
-                        scan_0_projections_angles,
-                        scan_1_projections_angles[::-1],
-                        atol=10e-1,
-                    ):
-                        reading_order = -1 * self._reading_orders[-1]
-                    else:
-                        raise ValueError(f"Angles from {scan_0} and {scan_1} are different")
-                else:
-                    reading_order = 1 * self._reading_orders[-1]
-                self._reading_orders.append(reading_order)
-            # check energy
-            if scan_0.energy is None:
-                _logger.warning(f"no energy found for {scan_0}")
-            elif not numpy.isclose(scan_0.energy, scan_1.energy, rtol=1e-03):
-                _logger.warning(
-                    f"different energy found between {scan_0} ({scan_0.energy}) and {scan_1} ({scan_1.energy})"
-                )
-            # check FOV
-            if not scan_0.field_of_view == scan_1.field_of_view:
-                raise ValueError(f"{scan_0} and {scan_1} have different field of view")
-            # check distance
-            if scan_0.distance is None:
-                _logger.warning(f"no distance found for {scan_0}")
-            elif not numpy.isclose(scan_0.distance, scan_1.distance, rtol=10e-3):
-                raise ValueError(f"{scan_0} and {scan_1} have different sample / detector distance")
-            # check pixel size
-            if not numpy.isclose(scan_0.x_pixel_size, scan_1.x_pixel_size):
-                raise ValueError(
-                    f"{scan_0} and {scan_1} have different x pixel size. {scan_0.x_pixel_size} vs {scan_1.x_pixel_size}"
-                )
-            if not numpy.isclose(scan_0.y_pixel_size, scan_1.y_pixel_size):
-                raise ValueError(
-                    f"{scan_0} and {scan_1} have different y pixel size. {scan_0.y_pixel_size} vs {scan_1.y_pixel_size}"
-                )
-            if scan_0.dim_1 != scan_1.dim_1:
-                raise ValueError(
-                    f"projections width are expected to be the same. Not the canse for {scan_0} ({scan_0.dim_1} and {scan_1} ({scan_1.dim_1}))"
-                )
-
-        for scan in self.z_serie:
-            # check x, y and z translation are constant (only if is an NXtomoScan)
-            if isinstance(scan, NXtomoScan):
-                if scan.x_translation is not None and not numpy.isclose(
-                    min(scan.x_translation), max(scan.x_translation)
-                ):
-                    _logger.warning(
-                        "x translations appears to be evolving over time. Might end up with wrong stitching"
-                    )
-                if scan.y_translation is not None and not numpy.isclose(
-                    min(scan.y_translation), max(scan.y_translation)
-                ):
-                    _logger.warning(
-                        "y translations appears to be evolving over time. Might end up with wrong stitching"
-                    )
-                if scan.z_translation is not None and not numpy.isclose(
-                    min(scan.z_translation), max(scan.z_translation)
-                ):
-                    _logger.warning(
-                        "z translations appears to be evolving over time. Might end up with wrong stitching"
-                    )
-
-    def _compute_positions_as_px(self):
-        """insure we have or we can deduce an estimated position as pixel"""
-
-        def get_position_as_px_on_axis(axis, pos_as_px, pos_as_mm):
-            if pos_as_px is not None:
-                if pos_as_mm is not None:
-                    raise ValueError(
-                        f"position of axis {axis} is provided twice: as mm and as px. Please provide one only ({pos_as_mm} vs {pos_as_px})"
-                    )
-                else:
-                    return pos_as_px
-
-            elif pos_as_mm is not None:
-                # deduce from position given in configuration and pixel size
-                axis_N_pos_px = []
-                for scan, pos_in_mm in zip(self.z_serie, pos_as_mm):
-                    pixel_size_m = self.configuration.pixel_size or scan.pixel_size
-                    axis_N_pos_px.append((pos_in_mm / MetricSystem.MILLIMETER.value) / pixel_size_m)
-                return axis_N_pos_px
-            else:
-                # deduce from motor position and pixel size
-                axis_N_pos_px = []
-                base_position_m = self.z_serie[0].get_bounding_box(axis=axis).min
-                for scan in self.z_serie:
-                    pixel_size_m = self.configuration.pixel_size or scan.pixel_size
-                    scan_axis_bb = scan.get_bounding_box(axis=axis)
-                    axis_N_mean_pos_m = (scan_axis_bb.max - scan_axis_bb.min) / 2 + scan_axis_bb.min
-                    axis_N_mean_rel_pos_m = axis_N_mean_pos_m - base_position_m
-                    axis_N_pos_px.append(int(axis_N_mean_rel_pos_m / pixel_size_m))
-                return axis_N_pos_px
-
-        self.configuration.axis_0_pos_px = get_position_as_px_on_axis(
-            axis=0,
-            pos_as_px=self.configuration.axis_0_pos_px,
-            pos_as_mm=self.configuration.axis_0_pos_mm,
-        )
-        self.configuration.axis_0_pos_mm = None
-
-        self.configuration.axis_2_pos_px = get_position_as_px_on_axis(
-            axis=2,
-            pos_as_px=self.configuration.axis_2_pos_px,
-            pos_as_mm=self.configuration.axis_2_pos_mm,
-        )
-        self.configuration.axis_2_pos_mm = None
-
-        # add some log
-        if self.configuration.axis_1_pos_mm is not None or self.configuration.axis_1_pos_px is not None:
-            _logger.warning("axis 1 position is not handled by the z-stitcher. Will be ignored")
-        axis_0_pos = ", ".join([f"{pos}px" for pos in self.configuration.axis_0_pos_px])
-        axis_2_pos = ", ".join([f"{pos}px" for pos in self.configuration.axis_2_pos_px])
-        _logger.info(f"axis 0 position to be used: " + axis_0_pos)
-        _logger.info(f"axis 2 position to be used: " + axis_2_pos)
-
-    def _compute_reduced_flats_and_darks(self):
-        """
-        make sure reduced dark and flats are existing otherwise compute them
-        """
-        for scan in self.z_serie:
-            try:
-                reduced_darks, darks_infos = scan.load_reduced_darks(return_info=True)
-            except:
-                _logger.info("no reduced dark found. Try to compute them.")
-            if reduced_darks in (None, {}):
-                reduced_darks, darks_infos = scan.compute_reduced_darks(return_info=True)
-                try:
-                    # if we don't have write in the folder containing the .nx for example
-                    scan.save_reduced_darks(reduced_darks, darks_infos=darks_infos)
-                except Exception as e:
-                    pass
-            scan.set_reduced_darks(reduced_darks, darks_infos=darks_infos)
-
-            try:
-                reduced_flats, flats_infos = scan.load_reduced_flats(return_info=True)
-            except:
-                _logger.info("no reduced flats found. Try to compute them.")
-            if reduced_flats in (None, {}):
-                reduced_flats, flats_infos = scan.compute_reduced_flats(return_info=True)
-                try:
-                    # if we don't have write in the folder containing the .nx for example
-                    scan.save_reduced_flats(reduced_flats, flats_infos=flats_infos)
-                except Exception as e:
-                    pass
-            scan.set_reduced_flats(reduced_flats, flats_infos=flats_infos)
-
-    def _compute_shifts(self):
-        """
-        compute all shift requested (set to 'auto' in the configuration)
-        """
-        n_scans = len(self.configuration.input_scans)
-        if n_scans == 0:
-            raise ValueError("no scan to stich provided")
-
-        projection_for_shift = self.configuration.slice_for_cross_correlation or "middle"
-        y_rel_shifts = self._axis_0_estimated_shifts
-        x_rel_shifts = self.from_abs_pos_to_rel_pos(self.configuration.axis_2_pos_px)
-
-        final_rel_shifts = []
-        for (
-            scan_0,
-            scan_1,
-            order_s0,
-            order_s1,
-            x_rel_shift,
-            y_rel_shift,
-        ) in zip(
-            self.z_serie[:-1],
-            self.z_serie[1:],
-            self.reading_orders[:-1],
-            self.reading_orders[1:],
-            x_rel_shifts,
-            y_rel_shifts,
-        ):
-            x_cross_algo = self.configuration.axis_2_params.get(KEY_IMG_REG_METHOD, None)
-            y_cross_algo = self.configuration.axis_0_params.get(KEY_IMG_REG_METHOD, None)
-
-            # compute relative shift
-            found_shift_y, found_shift_x = find_projections_relative_shifts(
-                upper_scan=scan_0,
-                lower_scan=scan_1,
-                projection_for_shift=projection_for_shift,
-                x_cross_correlation_function=x_cross_algo,
-                y_cross_correlation_function=y_cross_algo,
-                x_shifts_params=self.configuration.axis_2_params,
-                y_shifts_params=self.configuration.axis_0_params,
-                invert_order=order_s1 != order_s0,
-                estimated_shifts=(y_rel_shift, x_rel_shift),
-            )
-            final_rel_shifts.append(
-                (found_shift_y, found_shift_x),
-            )
-
-        # set back values. Now position should start at 0
-        self._axis_0_rel_shifts = [final_shift[0] for final_shift in final_rel_shifts]
-        self._axis_2_rel_shifts = [final_shift[1] for final_shift in final_rel_shifts]
-        _logger.info(f"axis 2 relative shifts (x in radio ref) to be used will be {self._axis_0_rel_shifts}")
-        print(f"axis 2 relative shifts (x in radio ref) to be used will be {self._axis_0_rel_shifts}")
-        _logger.info(f"axis 0 relative shifts (y in radio ref) y to be used will be {self._axis_2_rel_shifts}")
-        print(f"axis 0 relative shifts (y in radio ref) y to be used will be {self._axis_2_rel_shifts}")
-
-    @staticmethod
-    def _get_bunch_of_data(
-        bunch_start: int,
-        bunch_end: int,
-        step: int,
-        scans: tuple,
-        scans_projections_indexes: tuple,
-        reading_orders: tuple,
-        flip_lr_arr: tuple,
-        flip_ud_arr: tuple,
-    ):
-        """
-        goal is to load contiguous projections as much as possible...
-
-        :param int bunch_start: begining of the bunch
-        :param int bunch_end: end of the bunch
-        :param int scans: ordered scan for which we want to get data
-        :param scans_projections_indexes: tuple with scans and scan projection indexes to be loaded
-        :param tuple flip_lr_arr: extra information from the user to left-right flip frames
-        :param tuple flip_ud_arr: extra information from the user to up-down flip frames
-        :return: list of list. For each frame we want to stitch contains the (flat fielded) frames to stich together
-        """
-        assert len(scans) == len(scans_projections_indexes)
-        assert isinstance(flip_lr_arr, tuple)
-        assert isinstance(flip_ud_arr, tuple)
-        assert isinstance(step, int)
-        scans_proj_urls = []
-        # for each scan store the real indices and the data url
-
-        for scan, scan_projection_indexes in zip(scans, scans_projections_indexes):
-            scan_proj_urls = {}
-            # for each scan get the list of url to be loaded
-            for i_proj in range(bunch_start, bunch_end):
-                if i_proj % step != 0:
-                    continue
-                proj_index_in_full_scan = scan_projection_indexes[i_proj]
-                scan_proj_urls[proj_index_in_full_scan] = scan.projections[proj_index_in_full_scan]
-            scans_proj_urls.append(scan_proj_urls)
-
-        # then load data
-        all_scan_final_data = numpy.empty((bunch_end - bunch_start, len(scans)), dtype=object)
-        from nabu.preproc.flatfield import FlatFieldArrays
-
-        for i_scan, (scan_urls, scan_flip_lr, scan_flip_ud, reading_order) in enumerate(
-            zip(scans_proj_urls, flip_lr_arr, flip_ud_arr, reading_orders)
-        ):
-            i_frame = 0
-            _, set_of_compacted_slices = get_compacted_dataslices(scan_urls, return_url_set=True)
-            for _, url in set_of_compacted_slices.items():
-                scan = scans[i_scan]
-                url = DataUrl(
-                    file_path=url.file_path(),
-                    data_path=url.data_path(),
-                    scheme="silx",
-                    data_slice=url.data_slice(),
-                )
-                raw_radios = get_data(url)[::reading_order]
-                radio_indices = url.data_slice()
-                if isinstance(radio_indices, slice):
-                    step = radio_indices.step if radio_indices is not None else 1
-                    radio_indices = numpy.arange(
-                        start=radio_indices.start,
-                        stop=radio_indices.stop,
-                        step=step,
-                        dtype=numpy.int16,
-                    )
-
-                missing = []
-                if len(scan.reduced_flats) == 0:
-                    missing = "flats"
-                if len(scan.reduced_darks) == 0:
-                    missing = "darks"
-
-                if len(missing) > 0:
-                    _logger.warning(f"missing {'and'.join(missing)}. Unable to do flat field correction")
-                    ff_arrays = None
-                    data = raw_radios
-                else:
-                    has_reduced_metadata = (
-                        scan.reduced_flats_infos is not None
-                        and len(scan.reduced_flats_infos.machine_electric_current) > 0
-                        and scan.reduced_darks_infos is not None
-                        and len(scan.reduced_darks_infos.machine_electric_current) > 0
-                    )
-                    if not has_reduced_metadata:
-                        _logger.warning("no metadata about current found. Won't normalize according to machine current")
-
-                    ff_arrays = FlatFieldArrays(
-                        radios_shape=(len(radio_indices), scan.dim_2, scan.dim_1),
-                        flats=scan.reduced_flats,
-                        darks=scan.reduced_darks,
-                        radios_indices=radio_indices,
-                        radios_srcurrent=scan.electric_current[radio_indices] if has_reduced_metadata else None,
-                        flats_srcurrent=(
-                            scan.reduced_flats_infos.machine_electric_current if has_reduced_metadata else None
-                        ),
-                    )
-                    # note: we need to cast radios to float 32. Darks and flats are cast to anyway
-                    data = ff_arrays.normalize_radios(raw_radios.astype(numpy.float32))
-
-                transformations = list(scans[i_scan].get_detector_transformations(tuple()))
-                if scan_flip_lr:
-                    transformations.append(LRDetTransformation())
-                if scan_flip_ud:
-                    transformations.append(UDDetTransformation())
-
-                transformation_matrix_det_space = build_matrix(transformations)
-                if transformation_matrix_det_space is None or numpy.allclose(
-                    transformation_matrix_det_space, numpy.identity(3)
-                ):
-                    flip_ud = False
-                    flip_lr = False
-                elif numpy.array_equal(transformation_matrix_det_space, ZStitcher._get_UD_flip_matrix()):
-                    flip_ud = True
-                    flip_lr = False
-                elif numpy.allclose(transformation_matrix_det_space, ZStitcher._get_LR_flip_matrix()):
-                    flip_ud = False
-                    flip_lr = True
-                elif numpy.allclose(transformation_matrix_det_space, ZStitcher._get_UD_AND_LR_flip_matrix()):
-                    flip_ud = True
-                    flip_lr = True
-                else:
-                    raise ValueError("case not handled... For now only handle up-down flip as left-right flip")
-
-                for frame in data:
-                    if flip_ud:
-                        frame = numpy.flipud(frame)
-                    if flip_lr:
-                        frame = numpy.fliplr(frame)
-                    all_scan_final_data[i_frame, i_scan] = frame
-                    i_frame += 1
-
-        return all_scan_final_data
-
-    def _compute_axis_0_estimated_shifts(self):
-        axis_0_pos_px = self.configuration.axis_0_pos_px
-        self._axis_0_estimated_shifts = []
-        # compute overlap along axis 0
-        for upper_scan, lower_scan, upper_scan_axis_0_pos, lower_scan_axis_0_pos in zip(
-            self.z_serie[:-1], self.z_serie[1:], axis_0_pos_px[:-1], axis_0_pos_px[1:]
-        ):
-            upper_scan_pos = upper_scan_axis_0_pos - upper_scan.dim_2 / 2
-            lower_scan_high_pos = lower_scan_axis_0_pos + lower_scan.dim_2 / 2
-            # simple test of overlap. More complete test are runned by check_overlaps later
-            if lower_scan_high_pos <= upper_scan_pos:
-                raise ValueError(f"no overlap found between {upper_scan} and {lower_scan}")
-            self._axis_0_estimated_shifts.append(
-                int(lower_scan_high_pos - upper_scan_pos)  # overlap are expected to be int for now
-            )
-
-    def _create_nx_tomo(self, store_composition: bool = False):
-        """
-        create final NXtomo with stitched frames.
-        Policy: save all projections flat fielded. So this NXtomo will only contain projections (no dark and no flat).
-        But nabu will be able to reconstruct it with field `flatfield` set to False
-        """
-        nx_tomo = NXtomo()
-
-        nx_tomo.energy = self.z_serie[0].energy
-        start_times = list(filter(None, [scan.start_time for scan in self.z_serie]))
-        end_times = list(filter(None, [scan.end_time for scan in self.z_serie]))
-
-        if len(start_times) > 0:
-            nx_tomo.start_time = (
-                numpy.asarray([numpy.datetime64(start_time) for start_time in start_times]).min().astype(datetime)
-            )
-        else:
-            _logger.warning("Unable to find any start_time from input")
-        if len(end_times) > 0:
-            nx_tomo.end_time = (
-                numpy.asarray([numpy.datetime64(end_time) for end_time in end_times]).max().astype(datetime)
-            )
-        else:
-            _logger.warning("Unable to find any end_time from input")
-
-        title = ";".join([scan.sequence_name or "" for scan in self.z_serie])
-        nx_tomo.title = f"stitch done from {title}"
-
-        self._slices_to_stitch, n_proj = self.configuration.settle_slices()
-
-        # handle detector (without frames)
-        nx_tomo.instrument.detector.field_of_view = self.z_serie[0].field_of_view
-        nx_tomo.instrument.detector.distance = self.z_serie[0].distance
-        nx_tomo.instrument.detector.x_pixel_size = self.z_serie[0].x_pixel_size
-        nx_tomo.instrument.detector.y_pixel_size = self.z_serie[0].y_pixel_size
-        nx_tomo.instrument.detector.image_key_control = [ImageKey.PROJECTION] * n_proj
-        nx_tomo.instrument.detector.tomo_n = n_proj
-        # note: stitching process insure unflipping of frames. So make sure transformations is defined as an empty set
-        nx_tomo.instrument.detector.transformations = NXtransformations()
-
-        if isinstance(self.z_serie[0], NXtomoScan):
-            # note: first scan is always the reference as order to read data (so no rotation_angle inversion here)
-            rotation_angle = numpy.asarray(self.z_serie[0].rotation_angle)
-            nx_tomo.sample.rotation_angle = rotation_angle[
-                numpy.asarray(self.z_serie[0].image_key_control) == ImageKey.PROJECTION.value
-            ]
-        elif isinstance(self.z_serie[0], EDFTomoScan):
-            nx_tomo.sample.rotation_angle = numpy.linspace(
-                start=0, stop=self.z_serie[0].scan_range, num=self.z_serie[0].tomo_n
-            )
-        else:
-            raise NotImplementedError(
-                f"scan type ({type(self.z_serie[0])} is not handled)",
-                NXtomoScan,
-                isinstance(self.z_serie[0], NXtomoScan),
-            )
-
-        # do a sub selection of the rotation angle if a we are only computing a part of the slices
-        def apply_slices_selection(array, slices):
-            if isinstance(slices, slice):
-                return array[slices.start : slices.stop : 1]
-            elif isinstance(slices, Iterable):
-                return list([array[index] for index in slices])
-            else:
-                raise RuntimeError("slices must be instance of a slice or of an iterable")
-
-        nx_tomo.sample.rotation_angle = apply_slices_selection(
-            array=nx_tomo.sample.rotation_angle, slices=self._slices_to_stitch
-        )
-
-        # handle sample
-        n_frames = n_proj
-        if False not in [isinstance(scan, NXtomoScan) for scan in self.z_serie]:
-            # we consider the new x, y and z position to be at the center of the one created
-            x_translation = [scan.x_translation for scan in self.z_serie if scan.x_translation is not None]
-            nx_tomo.sample.x_translation = [numpy.asarray(x_translation).mean()] * n_frames
-            y_translation = [scan.y_translation for scan in self.z_serie if scan.y_translation is not None]
-            nx_tomo.sample.y_translation = [numpy.asarray(y_translation).mean()] * n_frames
-            z_translation = [scan.z_translation for scan in self.z_serie if scan.z_translation is not None]
-            nx_tomo.sample.z_translation = [numpy.asarray(z_translation).mean()] * n_frames
-
-            nx_tomo.sample.name = self.z_serie[0].sample_name
-
-        # compute stiched frame shape
-        stitched_frame_shape = (
-            n_proj,
-            (
-                numpy.asarray([scan.dim_2 for scan in self.z_serie]).sum()
-                - numpy.asarray([abs(overlap) for overlap in self._axis_0_rel_shifts]).sum()
-            ),
-            self._stitching_width,
-        )
-
-        # get expected output dataset first (just in case output and input files are the same)
-        first_proj_idx = sorted(self.z_serie[0].projections.keys())[0]
-        first_proj_url = self.z_serie[0].projections[first_proj_idx]
-        if h5py.is_hdf5(first_proj_url.file_path()):
-            first_proj_url = DataUrl(
-                file_path=first_proj_url.file_path(),
-                data_path=first_proj_url.data_path(),
-                scheme="h5py",
-            )
-
-        # first save the NXtomo entry without the frame
-        # dicttonx will fail if the folder does not exists
-        dir_name = os.path.dirname(self.configuration.output_file_path)
-        if dir_name not in (None, ""):
-            os.makedirs(dir_name, exist_ok=True)
-        nx_tomo.save(
-            file_path=self.configuration.output_file_path,
-            data_path=self.configuration.output_data_path,
-            nexus_path_version=self.configuration.output_nexus_version,
-            overwrite=self.configuration.overwrite_results,
-        )
-
-        transformation_matrices = {
-            scan.get_identifier()
-            .to_str()
-            .center(80, "-"): numpy.array2string(build_matrix(scan.get_detector_transformations(tuple())))
-            for scan in self.z_serie
-        }
-        _logger.info(
-            "scan detector transformation matrices are:\n"
-            "\n".join(["/n".join(item) for item in transformation_matrices.items()])
-        )
-
-        _logger.info(
-            f"reading order is {self.reading_orders}",
-        )
-
-        def get_output_data_type():
-            return numpy.float32  # because we will apply flat field correction on it and they are not raw data
-            # scan = self.z_serie[0]
-            # radio_url = tuple(scan.projections.values())[0]
-            # assert isinstance(radio_url, DataUrl)
-            # data = get_data(radio_url)
-            # return data.dtype
-
-        output_dtype = get_output_data_type()
-        # append frames ("instrument/detactor/data" dataset)
-        with HDF5File(filename=self.configuration.output_file_path, mode="a") as h5f:
-            # note: nx_tomo.save already handles the possible overwrite conflict by removing
-            # self.configuration.output_file_path or raising an error
-
-            stitched_frame_path = "/".join(
-                [
-                    self.configuration.output_data_path,
-                    _get_nexus_paths(self.configuration.output_nexus_version).PROJ_PATH,
-                ]
-            )
-            projection_dataset = h5f.create_dataset(
-                name=stitched_frame_path,
-                shape=stitched_frame_shape,
-                dtype=output_dtype,
-            )
-            # TODO: we could also create in several time and create a virtual dataset from it.
-            scans_projections_indexes = []
-            for scan, reverse in zip(self.z_serie, self.reading_orders):
-                scans_projections_indexes.append(sorted(scan.projections.keys(), reverse=(reverse == -1)))
-            if self.progress:
-                self.progress.set_max_advancement(len(scan.projections.keys()))
-
-            if isinstance(self._slices_to_stitch, slice):
-                step = self._slices_to_stitch.step or 1
-            else:
-                step = 1
-            i_proj = 0
-            for bunch_start, bunch_end in PreProcessZStitcher._data_bunch_iterator(
-                slices=self._slices_to_stitch, bunch_size=50
-            ):
-                for data_frames in PreProcessZStitcher._get_bunch_of_data(
-                    bunch_start,
-                    bunch_end,
-                    step=step,
-                    scans=self.z_serie,
-                    scans_projections_indexes=scans_projections_indexes,
-                    flip_ud_arr=self.configuration.flip_ud,
-                    flip_lr_arr=self.configuration.flip_lr,
-                    reading_orders=self.reading_orders,
-                ):
-                    if self.configuration.rescale_frames:
-                        data_frames = self.rescale_frames(data_frames)
-                    if self.configuration.normalization_by_sample.is_active():
-                        data_frames = self.normalize_frame_by_sample(data_frames)
-
-                    sf = ZStitcher.stitch_frames(
-                        frames=data_frames,
-                        x_relative_shifts=self._axis_2_rel_shifts,
-                        y_relative_shifts=self._axis_0_rel_shifts,
-                        output_dataset=projection_dataset,
-                        overlap_kernels=self._overlap_kernels,
-                        i_frame=i_proj,
-                        output_dtype=output_dtype,
-                        dump_frame_fct=self._dump_frame,
-                        return_composition_cls=store_composition if i_proj == 0 else False,
-                        stitching_axis=0,
-                        pad_mode=self.configuration.pad_mode,
-                        alignment=self.configuration.alignment_axis_2,
-                        new_width=self._stitching_width,
-                        check_inputs=i_proj == 0,  # on process check on the first iteration
-                    )
-                    if i_proj == 0 and store_composition:
-                        _, self._frame_composition = sf
-                    if self.progress is not None:
-                        self.progress.increase_advancement()
-
-                    i_proj += 1
-
-            # create link to this dataset that can be missing
-            # "data/data" link
-            if "data" in h5f[self.configuration.output_data_path]:
-                data_group = h5f[self.configuration.output_data_path]["data"]
-                if not stitched_frame_path.startswith("/"):
-                    stitched_frame_path = "/" + stitched_frame_path
-                data_group["data"] = h5py.SoftLink(stitched_frame_path)
-                if "default" not in h5f[self.configuration.output_data_path].attrs:
-                    h5f[self.configuration.output_data_path].attrs["default"] = "data"
-                for attr_name, attr_value in zip(
-                    ("NX_class", "SILX_style/axis_scale_types", "signal"),
-                    ("NXdata", ["linear", "linear"], "data"),
-                ):
-                    if attr_name not in data_group.attrs:
-                        data_group.attrs[attr_name] = attr_value
-
-        return nx_tomo
-
-    def _dump_stitching_configuration(self):
-        """dump configuration used for stitching at the NXtomo entry"""
-        process_name = "stitching_configuration"
-        config_dict = self.configuration.to_dict()
-        # adding nabu specific information
-        nabu_process_info = {
-            "@NX_class": "NXentry",
-            f"{process_name}@NX_class": "NXprocess",
-            f"{process_name}/program": "nabu-stitching",
-            f"{process_name}/version": nabu_version,
-            f"{process_name}/date": get_datetime(),
-            f"{process_name}/configuration": config_dict,
-        }
-
-        dicttonx(
-            nabu_process_info,
-            h5file=self.configuration.output_file_path,
-            h5path=self.configuration.output_data_path,
-            update_mode="replace",
-            mode="a",
-        )
-
-
-class PostProcessZStitcher(ZStitcher):
-    def __init__(self, configuration, progress: Progress = None) -> None:
-        self._input_volumes = configuration.input_volumes
-        self.__output_data_type = None
-
-        self._z_serie = Serie("z-serie", iterable=self._input_volumes, use_identifiers=False)
-        super().__init__(configuration, progress)
-
-    @staticmethod
-    def _dump_frame(output_dataset: h5py.Dataset, index: int, stitched_frame: numpy.ndarray):
-        # fix numpy array direction to be coherent with input data
-        # stitched_frame is received a `z-down` frame and we want to return in the same orientation (`z-up`)
-        output_dataset[:, index, :] = stitched_frame
-
-    def stitch(self, store_composition=True) -> BaseIdentifier:
-        """
-        Apply expected stitch from configuration and return the DataUrl of the object created
-        """
-        if self.progress is not None:
-            self.progress.set_name("order volumes")
-        self._order_volumes()
-        if self.progress is not None:
-            self.progress.set_name("check inputs")
-        self._check_inputs()
-        self.settle_flips()
-        if self.progress is not None:
-            self.progress.set_name("compute shifts")
-        self._compute_positions_as_px()
-        self._compute_axis_0_estimated_shifts()
-        self._compute_shifts()
-        self._createOverlapKernels()
-        if self.progress is not None:
-            self.progress.set_name("stitch volumes")
-        self._create_stitched_volume(store_composition=store_composition)
-        if self.progress is not None:
-            self.progress.set_name("dump configuration")
-        self._dump_stitching_configuration()
-        return self.configuration.output_volume.get_identifier()
-
-    def _order_volumes(self):
-        """
-        ensure scans are in z increasing order
-        """
-
-        def get_min_z(volume):
-            try:
-                bb = volume.get_bounding_box(axis="z")
-            except ValueError:  #  if missing information
-                bb = None
-            if bb is not None:
-                return bb.min
-            else:
-                # if can't find bounding box (missing metadata to the volume
-                # try to get it from the scan
-                metadata = volume.metadata or volume.load_metadata()
-                scan_location = metadata.get("nabu_config", {}).get("dataset", {}).get("location", None)
-                scan_entry = metadata.get("nabu_config", {}).get("dataset", {}).get("hdf5_entry", None)
-                if scan_location is not None:
-                    # this work around (until most volume have position metadata) works only for Hdf5volume
-                    with cwd_context(os.path.dirname(volume.file_path)):
-                        o_scan = NXtomoScan(scan_location, scan_entry)
-                        bb_acqui = o_scan.get_bounding_box(axis=None)
-                        # for next step volume position will be required.
-                        # if you can find it set it directly
-                        volume.position = (numpy.array(bb_acqui.max) - numpy.array(bb_acqui.min)) / 2.0 + numpy.array(
-                            bb_acqui.min
-                        )
-                        # for now translation are stored in pixel size ref instead of real_pixel_size
-                        volume.pixel_size = o_scan.x_real_pixel_size
-                        if bb_acqui is not None:
-                            return bb_acqui.min[0]
-                raise ValueError("Unable to find volume position. Unable to deduce z position")
-
-        try:
-            # order volumes from higher z to lower z
-            # if axis 0 position is provided then use directly it
-            if self.configuration.axis_0_pos_px is not None and len(self.configuration.axis_0_pos_px) > 0:
-                order = numpy.argsort(self.configuration.axis_0_pos_px)
-                sorted_z_serie = Serie(
-                    self.z_serie.name,
-                    numpy.take_along_axis(numpy.array(self.z_serie[:]), order, axis=0)[::-1],
-                    use_identifiers=False,
-                )
-            else:
-                # else use bounding box
-                sorted_z_serie = Serie(
-                    self.z_serie.name,
-                    sorted(self.z_serie[:], key=get_min_z, reverse=True),
-                    use_identifiers=False,
-                )
-        except ValueError:
-            _logger.warning(
-                "Unable to find volume positions in metadata. Expect the volume to be ordered already (decreasing along axis 0.)"
-            )
-        else:
-            if sorted_z_serie == self.z_serie:
-                pass
-            elif sorted_z_serie != self.z_serie:
-                if sorted_z_serie[:] != self.z_serie[::-1]:
-                    raise ValueError(
-                        "Unable to get comprehensive input. ordering along axis 0 is not respected (decreasing)."
-                    )
-                else:
-                    _logger.warning(
-                        f"z decreasing order haven't been respected. Need to reorder z serie ({[str(scan) for scan in sorted_z_serie[:]]}). Will also reorder positions"
-                    )
-                    if self.configuration.axis_0_pos_mm is not None:
-                        self.configuration.axis_0_pos_mm = self.configuration.axis_0_pos_mm[::-1]
-                    if self.configuration.axis_0_pos_px is not None:
-                        self.configuration.axis_0_pos_px = self.configuration.axis_0_pos_px[::-1]
-                    if self.configuration.axis_1_pos_mm is not None:
-                        self.configuration.axis_1_pos_mm = self.configuration.axis_1_pos_mm[::-1]
-                    if self.configuration.axis_1_pos_px is not None:
-                        self.configuration.axis_1_pos_px = self.configuration.axis_1_pos_px[::-1]
-                    if self.configuration.axis_2_pos_mm is not None:
-                        self.configuration.axis_2_pos_mm = self.configuration.axis_2_pos_mm[::-1]
-                    if self.configuration.axis_2_pos_px is not None:
-                        self.configuration.axis_2_pos_px = self.configuration.axis_2_pos_px[::-1]
-                    if not numpy.isscalar(self._configuration.flip_ud):
-                        self._configuration.flip_ud = self._configuration.flip_ud[::-1]
-                    if not numpy.isscalar(self._configuration.flip_lr):
-                        self._configuration.flip_ud = self._configuration.flip_lr[::-1]
-
-                    self._z_serie = sorted_z_serie
-
-    def _compute_positions_as_px(self):
-        """compute if necessary position other axis 0 from volume metadata"""
-
-        def get_position_as_px_on_axis(axis, pos_as_px, pos_as_mm):
-            if pos_as_px is not None:
-                if pos_as_mm is not None:
-                    raise ValueError(
-                        f"position of axis {axis} is provided twice: as mm and as px. Please provide one only ({pos_as_mm} vs {pos_as_px})"
-                    )
-                else:
-                    return pos_as_px
-
-            elif pos_as_mm is not None:
-                # deduce from position given in configuration and pixel size
-                axis_N_pos_px = []
-                for volume, pos_in_mm in zip(self.z_serie, pos_as_mm):
-                    voxel_size_m = self.configuration.voxel_size or volume.voxel_size
-                    axis_N_pos_px.append((pos_in_mm / MetricSystem.MILLIMETER.value) / voxel_size_m[0])
-                return axis_N_pos_px
-            else:
-                # deduce from motor position and pixel size
-                axis_N_pos_px = []
-                base_position_m = self.z_serie[0].get_bounding_box(axis=axis).min
-                for volume in self.z_serie:
-                    voxel_size_m = self.configuration.voxel_size or volume.voxel_size
-                    volume_axis_bb = volume.get_bounding_box(axis=axis)
-                    axis_N_mean_pos_m = (volume_axis_bb.max - volume_axis_bb.min) / 2 + volume_axis_bb.min
-                    axis_N_mean_rel_pos_m = axis_N_mean_pos_m - base_position_m
-                    axis_N_pos_px.append(int(axis_N_mean_rel_pos_m / voxel_size_m[0]))
-                return axis_N_pos_px
-
-        self.configuration.axis_0_pos_px = get_position_as_px_on_axis(
-            axis=0,
-            pos_as_px=self.configuration.axis_0_pos_px,
-            pos_as_mm=self.configuration.axis_0_pos_mm,
-        )
-        self.configuration.axis_0_pos_mm = None
-
-        self.configuration.axis_2_pos_px = get_position_as_px_on_axis(
-            axis=2,
-            pos_as_px=self.configuration.axis_2_pos_px,
-            pos_as_mm=self.configuration.axis_2_pos_mm,
-        )
-        self.configuration.axis_2_pos_mm = None
-
-    def _compute_axis_0_estimated_shifts(self):
-        axis_0_pos_px = self.configuration.axis_0_pos_px
-        self._axis_0_estimated_shifts = []
-        # compute overlap along axis 0
-        for upper_volume, lower_volume, upper_volume_axis_0_pos, lower_volume_axis_0_pos in zip(
-            self.z_serie[:-1], self.z_serie[1:], axis_0_pos_px[:-1], axis_0_pos_px[1:]
-        ):
-            upper_volume_low_pos = upper_volume_axis_0_pos - upper_volume.get_volume_shape()[0] / 2
-            lower_volume_high_pos = lower_volume_axis_0_pos + lower_volume.get_volume_shape()[0] / 2
-            self._axis_0_estimated_shifts.append(
-                int(lower_volume_high_pos - upper_volume_low_pos)  # overlap are expected to be int for now
-            )
-
-    def _compute_shifts(self):
-        n_volumes = len(self.configuration.input_volumes)
-        if n_volumes == 0:
-            raise ValueError("no scan to stich provided")
-
-        slice_for_shift = self.configuration.slice_for_cross_correlation or "middle"
-        y_rel_shifts = self._axis_0_estimated_shifts
-        x_rel_shifts = self.from_abs_pos_to_rel_pos(self.configuration.axis_2_pos_px)
-        dim_axis_1 = max([volume.get_volume_shape()[1] for volume in self.z_serie])
-
-        final_rel_shifts = []
-        for (
-            upper_volume,
-            lower_volume,
-            x_rel_shift,
-            y_rel_shift,
-            flip_ud_upper,
-            flip_ud_lower,
-        ) in zip(
-            self.z_serie[:-1],
-            self.z_serie[1:],
-            x_rel_shifts,
-            y_rel_shifts,
-            self.configuration.flip_ud[:-1],
-            self.configuration.flip_ud[1:],
-        ):
-            x_cross_algo = self.configuration.axis_2_params.get(KEY_IMG_REG_METHOD, None)
-            y_cross_algo = self.configuration.axis_0_params.get(KEY_IMG_REG_METHOD, None)
-
-            # compute relative shift
-            found_shift_y, found_shift_x = find_volumes_relative_shifts(
-                upper_volume=upper_volume,
-                lower_volume=lower_volume,
-                dtype=self.get_output_data_type(),
-                dim_axis_1=dim_axis_1,
-                slice_for_shift=slice_for_shift,
-                x_cross_correlation_function=x_cross_algo,
-                y_cross_correlation_function=y_cross_algo,
-                x_shifts_params=self.configuration.axis_2_params,
-                y_shifts_params=self.configuration.axis_0_params,
-                estimated_shifts=(y_rel_shift, x_rel_shift),
-                flip_ud_lower_frame=flip_ud_lower,
-                flip_ud_upper_frame=flip_ud_upper,
-                alignment_axis_1=self.configuration.alignment_axis_1,
-                alignment_axis_2=self.configuration.alignment_axis_2,
-            )
-            final_rel_shifts.append(
-                (found_shift_y, found_shift_x),
-            )
-
-        # set back values. Now position should start at 0
-        self._axis_0_rel_shifts = [final_shift[0] for final_shift in final_rel_shifts]
-        self._axis_2_rel_shifts = [final_shift[1] for final_shift in final_rel_shifts]
-        _logger.info(f"axis 2 relative shifts (x in radio ref) to be used will be {self._axis_2_rel_shifts}")
-        print(f"axis 2 relative shifts (x in radio ref) to be used will be {self._axis_2_rel_shifts}")
-        _logger.info(f"axis 0 relative shifts (y in radio ref) y to be used will be {self._axis_0_rel_shifts}")
-        print(f"axis 0 relative shifts (y in radio ref) y to be used will be {self._axis_0_rel_shifts}")
-
-    def _dump_stitching_configuration(self):
-        voxel_size = self._input_volumes[0].voxel_size
-
-        def get_position():
-            # the z-serie is z-ordered from higher to lower. We can reuse this with pixel size and shape to
-            # compute the position of the stitched volume
-            if voxel_size is None:
-                return None
-            return numpy.array(self._input_volumes[0].position) + voxel_size * (
-                numpy.array(self._input_volumes[0].get_volume_shape()) / 2.0
-                - numpy.array(self.configuration.output_volume.get_volume_shape()) / 2.0
-            )
-
-        self.configuration.output_volume.voxel_size = voxel_size or ""
-        try:
-            self.configuration.output_volume.position = get_position()
-        except Exception:
-            self.configuration.output_volume.position = numpy.array([0, 0, 0])
-
-        self.configuration.output_volume.metadata.update(
-            {
-                "program": "nabu-stitching",
-                "version": nabu_version,
-                "date": get_datetime(),
-                "configuration": self.configuration.to_dict(),
-            }
-        )
-        self.configuration.output_volume.save_metadata()
-
-    def _check_inputs(self):
-        """
-        insure input data is coherent
-        """
-        # check input volume
-        if self.configuration.output_volume is None:
-            raise ValueError("input volume should be provided")
-
-        n_volumes = len(self.z_serie)
-        if n_volumes == 0:
-            raise ValueError("no scan to stich together")
-
-        if not isinstance(self.configuration.output_volume, VolumeBase):
-            raise TypeError(f"make sure we return a volume identifier not {(type(self.configuration.output_volume))}")
-
-        # check axis 0 position
-        if isinstance(self.configuration.axis_0_pos_px, Iterable) and len(self.configuration.axis_0_pos_px) != (
-            n_volumes
-        ):
-            raise ValueError(f"expect {n_volumes} overlap defined. Get {len(self.configuration.axis_0_pos_px)}")
-        if isinstance(self.configuration.axis_0_pos_mm, Iterable) and len(self.configuration.axis_0_pos_mm) != (
-            n_volumes
-        ):
-            raise ValueError(f"expect {n_volumes} overlap defined. Get {len(self.configuration.axis_0_pos_mm)}")
-
-        # check axis 1 position
-        if isinstance(self.configuration.axis_1_pos_px, Iterable) and len(self.configuration.axis_1_pos_px) != (
-            n_volumes
-        ):
-            raise ValueError(f"expect {n_volumes} overlap defined. Get {len(self.configuration.axis_1_pos_px)}")
-        if isinstance(self.configuration.axis_1_pos_mm, Iterable) and len(self.configuration.axis_1_pos_mm) != (
-            n_volumes
-        ):
-            raise ValueError(f"expect {n_volumes} overlap defined. Get {len(self.configuration.axis_1_pos_mm)}")
-
-        # check axis 2 position
-        if isinstance(self.configuration.axis_2_pos_px, Iterable) and len(self.configuration.axis_2_pos_px) != (
-            n_volumes
-        ):
-            raise ValueError(f"expect {n_volumes} overlap defined. Get {len(self.configuration.axis_2_pos_px)}")
-        if isinstance(self.configuration.axis_2_pos_mm, Iterable) and len(self.configuration.axis_2_pos_mm) != (
-            n_volumes
-        ):
-            raise ValueError(f"expect {n_volumes} overlap defined. Get {len(self.configuration.axis_2_pos_mm)}")
-
-        self._reading_orders = []
-        # the first scan will define the expected reading orderd, and expected flip.
-        # if all scan are flipped then we will keep it this way
-        self._reading_orders.append(1)
-
-    def get_output_data_type(self):
-        if self.__output_data_type is None:
-
-            def find_output_data_type():
-                first_vol = self._input_volumes[0]
-                if first_vol.data is not None:
-                    return first_vol.data.dtype
-                elif isinstance(first_vol, HDF5Volume):
-                    with DatasetReader(first_vol.data_url) as vol_dataset:
-                        return vol_dataset.dtype
-                else:
-                    return first_vol.load_data(store=False).dtype
-
-            self.__output_data_type = find_output_data_type()
-        return self.__output_data_type
-
-    def _create_stitched_volume(self, store_composition: bool):
-        overlap_kernels = self._overlap_kernels
-        self._slices_to_stitch, n_slices = self.configuration.settle_slices()
-
-        # sync overwrite_results with volume overwrite parameter
-        self.configuration.output_volume.overwrite = self.configuration.overwrite_results
-
-        # init final volume
-        final_volume = self.configuration.output_volume
-        final_volume_shape = (
-            int(
-                numpy.asarray([volume.get_volume_shape()[0] for volume in self._input_volumes]).sum()
-                - numpy.asarray([abs(overlap) for overlap in self._axis_0_rel_shifts]).sum(),
-            ),
-            n_slices,
-            self._stitching_width,
-        )
-
-        data_type = self.get_output_data_type()
-
-        if self.progress:
-            self.progress.set_max_advancement(final_volume_shape[1])
-
-        y_index = 0
-        if isinstance(self._slices_to_stitch, slice):
-            step = self._slices_to_stitch.step or 1
-        else:
-            step = 1
-        with PostProcessZStitcher._FinalDatasetContext(
-            volume=final_volume, volume_shape=final_volume_shape, dtype=data_type
-        ) as output_dataset:
-            # note: output_dataset is a HDF5 dataset if final volume is an HDF5 volume else is a numpy array
-            with PostProcessZStitcher._RawDatasetsContext(
-                self._input_volumes,
-                alignment_axis_1=self.configuration.alignment_axis_1,
-            ) as raw_datasets:
-                # note: raw_datasets can be numpy arrays or HDF5 dataset (in the case of HDF5Volume)
-                # to speed up we read by bunch of dataset. For numpy array this doesn't change anything
-                # but for HDF5 dataset this can speed up a lot the processing (depending on HDF5 dataset chuncks)
-                # note: we read trhough axis 1
-                for bunch_start, bunch_end in PostProcessZStitcher._data_bunch_iterator(
-                    slices=self._slices_to_stitch, bunch_size=50
-                ):
-                    for data_frames in PostProcessZStitcher._get_bunch_of_data(
-                        bunch_start,
-                        bunch_end,
-                        step=step,
-                        volumes=raw_datasets,
-                        flip_lr_arr=self.configuration.flip_lr,
-                        flip_ud_arr=self.configuration.flip_ud,
-                    ):
-                        if self.configuration.rescale_frames:
-                            data_frames = self.rescale_frames(data_frames)
-                        if self.configuration.normalization_by_sample.is_active():
-                            data_frames = self.normalize_frame_by_sample(data_frames)
-
-                        sf = ZStitcher.stitch_frames(
-                            frames=data_frames,
-                            x_relative_shifts=self._axis_2_rel_shifts,
-                            y_relative_shifts=self._axis_0_rel_shifts,
-                            overlap_kernels=overlap_kernels,
-                            output_dataset=output_dataset,
-                            dump_frame_fct=self._dump_frame,
-                            i_frame=y_index,
-                            output_dtype=data_type,
-                            return_composition_cls=store_composition if y_index == 0 else False,
-                            stitching_axis=0,
-                            check_inputs=y_index == 0,  # on process check on the first iteration
-                        )
-                        if y_index == 0 and store_composition:
-                            _, self._frame_composition = sf
-
-                        if self.progress is not None:
-                            self.progress.increase_advancement()
-                        y_index += 1
-
-    @staticmethod
-    def _get_bunch_of_data(
-        bunch_start: int,
-        bunch_end: int,
-        step: int,
-        volumes: tuple,
-        flip_lr_arr: bool,
-        flip_ud_arr: bool,
-    ):
-        """
-        goal is to load contiguous frames as much as possible...
-        return for each volume the bunch of slice along axis 1
-        warning: they can have different shapes
-        """
-
-        def get_sub_volume(volume, flip_lr, flip_ud):
-            sub_volume = volume[:, bunch_start:bunch_end:step, :]
-            if flip_lr:
-                sub_volume = numpy.fliplr(sub_volume)
-            if flip_ud:
-                sub_volume = numpy.flipud(sub_volume)
-            return sub_volume
-
-        sub_volumes = [
-            get_sub_volume(volume, flip_lr, flip_ud)
-            for volume, flip_lr, flip_ud in zip(volumes, flip_lr_arr, flip_ud_arr)
-        ]
-        # generator on it self: we want to iterate over the y axis
-        n_slices_in_bunch = ceil((bunch_end - bunch_start) / step)
-        assert isinstance(n_slices_in_bunch, int)
-        for i in range(n_slices_in_bunch):
-            yield [sub_volume[:, i, :] for sub_volume in sub_volumes]
-
-    class _FinalDatasetContext(AbstractContextManager):
-        """Manager to create the data volume and save it (data only !). target: used for volume stitching
-        In the case of HDF5 we want to save this directly in the file to avoid
-        keeping the full volume in memory.
-        Insure also contain processing will be common between the different processing
-        """
-
-        def __init__(self, volume: VolumeBase, volume_shape: tuple, dtype: numpy.dtype) -> None:
-            super().__init__()
-            if not isinstance(volume, VolumeBase):
-                raise TypeError(
-                    f"Volume is expected to be an instance of {VolumeBase}. {type(volume)} provided instead"
-                )
-
-            self._volume = volume
-            self._volume_shape = volume_shape
-            self.__file_handler = None
-            self._dtype = dtype
-
-        def __enter__(self):
-            # handle the specific case of HDF5. Goal: avoid getting the full stitched volume in memory
-            if isinstance(self._volume, HDF5Volume):
-                self.__file_handler = HDF5File(filename=self._volume.data_url.file_path(), mode="a")
-                # if need to delete an existing dataset
-                if self._volume.overwrite and self._volume.data_path in self.__file_handler:
-                    try:
-                        del self.__file_handler[self._volume.data_path]
-                    except Exception as e:
-                        _logger.error(f"Fail to overwrite data. Reason is {e}")
-                        data = None
-                        self.__file_handler.close()
-                        return data
-
-                # create dataset
-                try:
-                    data = self.__file_handler.create_dataset(
-                        self._volume.data_url.data_path(),
-                        shape=self._volume_shape,
-                        dtype=self._dtype,
-                    )
-                except Exception as e2:
-                    _logger.error(f"Fail to create final dataset. Reason is {e2}")
-                    data = None
-                    self.__file_handler.close()
-            # for other file format: create the full dataset in memory
-            else:
-                data = numpy.empty(self._volume_shape, dtype=self._dtype)
-            return data
-
-        def __exit__(self, *exc):
-            if self.__file_handler is not None:
-                return self.__file_handler.close()
-            else:
-                self._volume.save_data()
-
-    class _RawDatasetsContext(AbstractContextManager):
-        """
-        return volume data for all input volume (target: used for volume stitching).
-        If the volume is an HDF5Volume then the HDF5 dataset will be used (on disk)
-        If the volume is of another type then it will be loaded in memory then used (more memory consuming)
-        """
-
-        def __init__(self, volumes: tuple, alignment_axis_1) -> None:
-            super().__init__()
-            for volume in volumes:
-                if not isinstance(volume, VolumeBase):
-                    raise TypeError(
-                        f"Volumes are expected to be an instance of {VolumeBase}. {type(volume)} provided instead"
-                    )
-
-            self._volumes = volumes
-            self.__file_handlers = []
-            self._alignment_axis_1 = alignment_axis_1
-
-        @property
-        def alignment_axis_1(self):
-            return self._alignment_axis_1
-
-        def __enter__(self):
-            # handle the specific case of HDF5. Goal: avoid getting the full stitched volume in memory
-            datasets = []
-            shapes = {volume.get_volume_shape()[1] for volume in self._volumes}
-            axis_1_dim = max(shapes)
-            axis_1_need_padding = len(shapes) > 1
-
-            try:
-                for volume in self._volumes:
-                    if volume.data is not None:
-                        data = volume.data
-                    elif isinstance(volume, HDF5Volume):
-                        file_handler = HDF5File(filename=volume.data_url.file_path(), mode="r")
-                        dataset = file_handler[volume.data_url.data_path()]
-                        data = dataset
-                        self.__file_handlers.append(file_handler)
-                    # for other file format: load the full dataset in memory
-                    else:
-                        data = volume.load_data(store=False)
-                        if data is None:
-                            raise ValueError(f"No data found for volume {volume.get_identifier()}")
-                    if axis_1_need_padding:
-                        data = self.add_padding(data=data, axis_1_dim=axis_1_dim, alignment=self.alignment_axis_1)
-                    datasets.append(data)
-            except Exception as e:
-                # if some errors happen during loading HDF5
-                for file_handled in self.__file_handlers:
-                    file_handled.close()
-                raise e
-
-            return datasets
-
-        def __exit__(self, *exc):
-            success = True
-            for file_handler in self.__file_handlers:
-                success = success and file_handler.close()
-            return success
-
-        def add_padding(self, data: Union[h5py.Dataset, numpy.ndarray], axis_1_dim, alignment: AlignmentAxis1):
-            alignment = AlignmentAxis1.from_value(alignment)
-            if alignment is AlignmentAxis1.BACK:
-                axis_1_pad_width = (axis_1_dim - data.shape[1], 0)
-            elif alignment is AlignmentAxis1.CENTER:
-                half_width = int((axis_1_dim - data.shape[1]) / 2)
-                axis_1_pad_width = (half_width, axis_1_dim - data.shape[1] - half_width)
-            elif alignment is AlignmentAxis1.FRONT:
-                axis_1_pad_width = (0, axis_1_dim - data.shape[1])
-            else:
-                raise ValueError(f"alignment {alignment} is not handled")
-
-            return PaddedRawData(
-                data=data,
-                axis_1_pad_width=axis_1_pad_width,
-            )
-
-
-def stitch_vertically_raw_frames(
-    frames: tuple,
-    key_lines: tuple,
-    overlap_kernels: Union[ZStichOverlapKernel, tuple],
-    output_dtype: numpy.dtype = numpy.float32,
-    check_inputs=True,
-    raw_frames_compositions: Optional[ZFrameComposition] = None,
-    overlap_frames_compositions: Optional[ZFrameComposition] = None,
-    return_composition_cls=False,
-    alignment="center",
-    pad_mode="constant",
-    new_width: Optional[int] = None,
-) -> numpy.ndarray:
-    """
-    stitches raw frames (already shifted and flat fielded !!!) together using
-    raw stitching (no pixel interpolation, y_overlap_in_px is expected to be a int).
-    Sttiching is done vertically (along the y axis of the frame ref)
-
-      |    --------------
-      |    |            |
-      |    |  Frame 1   |                        --------------
-      |    |            |                        |  Frame 1    |
-      |    --------------                        |             |
-    Y |                         --> stitching    |~ stitching ~|
-      |    --------------                        |             |
-      |    |            |                        |  Frame 2    |
-      |    |  Frame 2   |                         --------------
-      |    |            |
-      |    --------------
-      \/
-
-    returns stitched_projection, raw_img_1, raw_img_2, computed_overlap
-    proj_0 and pro_1 are already expected to be in a row. Having stitching_height_in_px in common. At top of proj_0
-    and at bottom of proj_1
-
-    :param tuple frames: tuple of 2D numpy array. Expected to be Z up oriented at this stage
-    :param tuple key_lines: for each jonction define the two lines to overlaid (from the upper and the lower frames). In the reference where 0 is the bottom line of the image.
-    :param overlap_kernels: ZStichOverlapKernel overlap kernel to be used or a list of kernel (one per overlap). Define startegy and overlap heights
-    :param numpy.dtype output_dtype: dataset dtype. For now must be provided because flat field corrcetion change data type (numpy.float32 for now)
-    :param bool check_inputs: if True will do more test on inputs parameters like checking frame shapes, coherence of the request.. As it can be time consuming it is optional
-    :param raw_frames_compositions: pre computed raw frame composition. If not provided will compute them. allow providing it to speed up calculation
-    :param overlap_frames_compositions: pre computed stitched frame composition. If not provided will compute them. allow providing it to speed up calculation
-    :param bool return_frame_compositions: if False return simply the stitched frames. Else return a tuple with stitching frame and the dictionnary with the composition frames...
-    """
-    assert overlap_kernels is not None, "overlap kernels must be provided"
-
-    if check_inputs:
-
-        def check_frame(proj):
-            if not isinstance(proj, numpy.ndarray) and proj.ndim == 2:
-                raise ValueError(f"frames are expected to be 2D numpy array")
-
-        [check_frame(frame) for frame in frames]
-        for frame_0, frame_1 in zip(frames[:-1], frames[1:]):
-            if not (frame_0.ndim == frame_1.ndim == 2):
-                raise ValueError("Frames are expected to be 2D")
-
-        for frame_0, frame_1, kernel in zip(frames[:-1], frames[1:], overlap_kernels):
-            if frame_0.shape[0] < kernel.overlap_size:
-                raise ValueError(
-                    f"frame_0 height ({frame_0.shape[0]}) is less than kernel overlap ({kernel.overlap_size})"
-                )
-            if frame_1.shape[0] < kernel.overlap_size:
-                raise ValueError(
-                    f"frame_1 height ({frame_1.shape[0]}) is less than kernel overlap ({kernel.overlap_size})"
-                )
-        if not len(key_lines) == len(overlap_kernels):
-            raise ValueError("we expect to have the same number of key_lines then the number of kernel")
-        else:
-            for key_line in key_lines:
-                for value in key_line:
-                    if not isinstance(value, (int, numpy.integer)):
-                        raise TypeError(f"key_line is expected to be an integer. {type(key_line)} provided")
-                    elif value < 0:
-                        raise ValueError(f"key lines are expected to be positive values. Get {value} as key line value")
-
-    if new_width is None:
-        new_width = max([frame.shape[-1] for frame in frames])
-    frames = tuple(
-        [
-            align_horizontally(
-                data=frame,
-                alignment=alignment,
-                new_width=new_width,
-                pad_mode=pad_mode,
-            )
-            for frame in frames
-        ]
-    )
-
-    # step 1: create numpy array that will contain stitching
-    # if raw composition doesn't exists create it
-    if raw_frames_compositions is None:
-        raw_frames_compositions = ZFrameComposition.compute_raw_frame_compositions(
-            frames=frames,
-            overlap_kernels=overlap_kernels,
-            key_lines=key_lines,
-            stitching_axis=0,
-        )
-    new_frame_height = raw_frames_compositions.global_end_y[-1] - raw_frames_compositions.global_start_y[0]
-    stitched_projection_shape = (
-        # here we only handle frames because shift are already done
-        int(new_frame_height),
-        new_width,
-    )
-    stitch_array = numpy.empty(stitched_projection_shape, dtype=output_dtype)
-
-    # step 2: set raw data
-    # fill stitch array with raw data raw data
-    raw_frames_compositions.compose(
-        output_frame=stitch_array,
-        input_frames=frames,
-    )
-
-    # step 3 set stitched data
-
-    # 3.1 create stitched overlaps
-    stitched_overlap = []
-    for frame_0, frame_1, kernel, key_line in zip(frames[:-1], frames[1:], overlap_kernels, key_lines):
-        assert kernel.overlap_size >= 0
-        frame_0_overlap, frame_1_overlap = ZStitcher.get_overlap_areas(
-            upper_frame=frame_0,
-            lower_frame=frame_1,
-            upper_frame_key_line=key_line[0],
-            lower_frame_key_line=key_line[1],
-            overlap_size=kernel.overlap_size,
-            stitching_axis=0,
-        )
-
-        assert (
-            frame_0_overlap.shape[0] == frame_1_overlap.shape[0] == kernel.overlap_size
-        ), f"{frame_0_overlap.shape[0]} == {frame_1_overlap.shape[0]} == {kernel.overlap_size}"
-
-        stitched_overlap.append(
-            kernel.stitch(
-                frame_0_overlap,
-                frame_1_overlap,
-            )[0]
-        )
-    # 3.2 fill stitched overlap on output array
-    if overlap_frames_compositions is None:
-        overlap_frames_compositions = ZFrameComposition.compute_stitch_frame_composition(
-            frames=frames,
-            overlap_kernels=overlap_kernels,
-            key_lines=key_lines,
-            stitching_axis=0,
-        )
-    overlap_frames_compositions.compose(
-        output_frame=stitch_array,
-        input_frames=stitched_overlap,
-    )
-    if return_composition_cls:
-        return (
-            stitch_array,
-            {
-                "raw_compositon": raw_frames_compositions,
-                "overlap_compositon": overlap_frames_compositions,
-            },
-        )
-
-    return stitch_array
-
-
-class StitchingPostProcAggregation:
-    """
-    for remote stitching each process will stitch a part of the volume or projections.
-    Then once all are finished we want to aggregate them all to a final volume or NXtomo.
-
-    This is the goal of this class.
-    Please be careful with API. This is already inheriting from a tomwer class
-
-    :param ZStitchingConfiguration stitching_config: configuration of the stitching configuration
-    :param Optional[tuple] futures: futures that just runned
-    :param Optional[tuple] existing_objs: futures that just runned
-    :param
-    """
-
-    def __init__(
-        self,
-        stitching_config: ZStitchingConfiguration,
-        futures: Optional[tuple] = None,
-        existing_objs_ids: Optional[tuple] = None,
-    ) -> None:
-        if not isinstance(stitching_config, (ZStitchingConfiguration)):
-            raise TypeError(f"stitching_config should be an instance of {ZStitchingConfiguration}")
-        if not ((existing_objs_ids is None) ^ (futures is None)):
-            raise ValueError("Either existing_objs or futures should be provided (can't provide both)")
-        self._futures = futures
-        self._stitching_config = stitching_config
-        self._existing_objs_ids = existing_objs_ids
-
-    @property
-    def futures(self):
-        # TODO: deprecate it ?
-        return self._futures
-
-    def retrieve_tomo_objects(self) -> tuple():
-        """
-        Return tomo objects to be stitched together. Either from future or from existing_objs
-        """
-        if self._existing_objs_ids is not None:
-            scan_ids = self._existing_objs_ids
-        else:
-            results = {}
-            _logger.info(f"wait for slurm job to be completed")
-            for obj_id, future in self.futures.items():
-                results[obj_id] = future.result()
-
-            failed = tuple(
-                filter(
-                    lambda x: x.exception() is not None,
-                    self.futures.values(),
-                )
-            )
-            if len(failed) > 0:
-                # if some job failed: unseless to do the concatenation
-                exceptions = " ; ".join([f"{job} : {job.exception()}" for job in failed])
-                raise RuntimeError(f"some job failed. Won't do the concatenation. Exceptiosn are {exceptions}")
-
-            canceled = tuple(
-                filter(
-                    lambda x: x.cancelled(),
-                    self.futures.values(),
-                )
-            )
-            if len(canceled) > 0:
-                # if some job canceled: unseless to do the concatenation
-                raise RuntimeError(f"some job failed. Won't do the concatenation. Jobs are {' ; '.join(canceled)}")
-            scan_ids = results.keys()
-        return [TomoscanFactory.create_tomo_object_from_identifier(scan_id) for scan_id in scan_ids]
-
-    def dump_stiching_config_as_nx_process(self, file_path: str, data_path: str, overwrite: bool, process_name: str):
-        dict_to_dump = {
-            process_name: {
-                "config": self._stitching_config.to_dict(),
-                "program": "nabu-stitching",
-                "version": nabu_version,
-                "date": get_datetime(),
-            },
-            f"{process_name}@NX_class": "NXprocess",
-        }
-
-        dicttonx(
-            dict_to_dump,
-            h5file=file_path,
-            h5path=data_path,
-            update_mode="replace" if overwrite else "add",
-            mode="a",
-        )
-
-    @property
-    def stitching_config(self) -> ZStitchingConfiguration:
-        return self._stitching_config
-
-    def process(self) -> None:
-        """
-        main function
-        """
-
-        # concatenate result
-        _logger.info("all job succeeded. Concatenate results")
-        if isinstance(self._stitching_config, PreProcessedZStitchingConfiguration):
-            # 1: case of a pre-processing stitching
-            scans = self.retrieve_tomo_objects()
-            nx_tomos = []
-            for scan in scans:
-                nx_tomos.append(
-                    NXtomo().load(
-                        file_path=scan.master_file,
-                        data_path=scan.entry,
-                    )
-                )
-            final_nx_tomo = NXtomo.concatenate(nx_tomos)
-            final_nx_tomo.save(
-                file_path=self.stitching_config.output_file_path,
-                data_path=self.stitching_config.output_data_path,
-                overwrite=self.stitching_config.overwrite_results,
-            )
-
-            # dump NXprocess if possible
-            parts = self.stitching_config.output_data_path.split("/")
-            process_name = parts[-1] + "_stitching"
-            if len(parts) < 2:
-                data_path = "/"
-            else:
-                data_path = "/".join(parts[:-1])
-
-            self.dump_stiching_config_as_nx_process(
-                file_path=self.stitching_config.output_file_path,
-                data_path=data_path,
-                process_name=process_name,
-                overwrite=self.stitching_config.overwrite_results,
-            )
-
-        elif isinstance(self.stitching_config, PostProcessedZStitchingConfiguration):
-            # 2: case of a post-processing stitching
-            outputs_sub_volumes = self.retrieve_tomo_objects()
-            concatenate_volumes(
-                output_volume=self.stitching_config.output_volume,
-                volumes=tuple(outputs_sub_volumes),
-                axis=1,
-            )
-
-            if isinstance(self.stitching_config.output_volume, HDF5Volume):
-                parts = self.stitching_config.output_volume.metadata_url.data_path().split("/")
-                process_name = parts[-1] + "_stitching"
-                if len(parts) < 2:
-                    data_path = "/"
-                else:
-                    data_path = "/".join(parts[:-1])
-
-                self.dump_stiching_config_as_nx_process(
-                    file_path=self.stitching_config.output_volume.metadata_url.file_path(),
-                    data_path=data_path,
-                    process_name=process_name,
-                    overwrite=self.stitching_config.overwrite_results,
-                )
-        else:
-            raise TypeError(f"stitching_config type ({type(self.stitching_config)}) not handled")
-
-
-def get_obj_width(obj: Union[NXtomoScan, VolumeBase]) -> int:
-    """
-    return tomo object width
-    """
-    if isinstance(obj, NXtomoScan):
-        return obj.dim_1
-    elif isinstance(obj, VolumeBase):
-        return obj.get_volume_shape()[-1]
-    else:
-        raise TypeError(f"obj type ({type(obj)}) is not handled")