nabu 2022.3.0a1__py3-none-any.whl → 2023.1.0a2__py3-none-any.whl

nabu/pipeline/fullfield/chunked_black.py

@@ -0,0 +1,881 @@
+from os import path
+from time import time
+import numpy as np
+from silx.io.url import DataUrl
+from ...resources.logger import LoggerOrPrint
+from ...resources.utils import is_hdf5_extension, extract_parameters
+from ...io.reader import ChunkReader, HDF5Loader, get_hdf5_dataset_shape
+from ...preproc.ccd import Log, CCDFilter
+from ...preproc.flatfield import FlatFieldDataUrls
+from ...preproc.distortion import DistortionCorrection
+from ...preproc.shift import VerticalShift
+from ...preproc.double_flatfield import DoubleFlatField
+from ...preproc.phase import PaganinPhaseRetrieval
+from ...reconstruction.sinogram import SinoBuilder, SinoNormalization
+from ...misc.rotation import Rotation
+from ...preproc.rings import MunchDeringer
+from ...misc.unsharp import UnsharpMask
+from ...misc.histogram import PartialHistogram, hist_as_2Darray
+from ..utils import use_options, pipeline_step, WriterConfigurator
+
+# For now we don't have a plain python/numpy backend for reconstruction
+try:
+    from ...reconstruction.fbp_opencl import Backprojector
+except:
+    Backprojector = None
+
+
+class ChunkedPipeline:
+    """
+    Pipeline for "regular" full-field tomography.
+    Data is processed by chunks. A chunk consists in K contiguous lines of all the radios.
+    In parallel geometry, a chunk of K radios lines gives K sinograms,
+    and equivalently K reconstructed slices.
+    """
+
+    backend = "numpy"
+    FlatFieldClass = FlatFieldDataUrls
+    DoubleFlatFieldClass = DoubleFlatField
+    CCDCorrectionClass = CCDFilter
+    PaganinPhaseRetrievalClass = PaganinPhaseRetrieval
+    UnsharpMaskClass = UnsharpMask
+    ImageRotationClass = Rotation
+    VerticalShiftClass = VerticalShift
+    SinoBuilderClass = SinoBuilder
+    SinoDeringerClass = MunchDeringer
+    MLogClass = Log
+    SinoNormalizationClass = SinoNormalization
+    FBPClass = Backprojector
+    HistogramClass = PartialHistogram
+
+    def __init__(self, process_config, sub_region, logger=None, extra_options=None, phase_margin=None):
+        """
+        Initialize a "Chunked" pipeline.
+
+        Parameters
+        ----------
+        processing_config: `ProcessConfig`
+            Process configuration.
+        sub_region: tuple
+            Sub-region to process in the volume for this worker, in the format
+            `(start_x, end_x, start_z, end_z)`.
+        logger: `nabu.app.logger.Logger`, optional
+            Logger class
+        extra_options: dict, optional
+            Advanced extra options.
+        phase_margin: tuple, optional
+            Margin to use when performing phase retrieval, in the form ((up, down), (left, right)).
+            See also the documentation of PaganinPhaseRetrieval.
+            If not provided, no margin is applied.
+
+
+        Notes
+        ------
+        Using a `phase_margin` results in a lesser number of reconstructed slices.
+        More specifically, if `phase_margin = (V, H)`, then there will be `delta_z - 2*V`
+        reconstructed slices (if the sub-region is in the middle of the volume)
+        or `delta_z - V` reconstructed slices (if the sub-region is on top or bottom
+        of the volume).
+        """
+        self.logger = LoggerOrPrint(logger)
+        self._set_params(process_config, sub_region, extra_options, phase_margin)
+        self.set_subregion(sub_region)
+        self._init_pipeline()
+
+    def _set_params(self, process_config, sub_region, extra_options, phase_margin):
+        self.process_config = process_config
+        self.dataset_info = self.process_config.dataset_info
+        self.dataset_infos = self.process_config.dataset_info  # shorthand - deprecated
+        self.processing_steps = self.process_config.processing_steps.copy()
+        self.processing_options = self.process_config.processing_options
+        self.sub_region = self._check_subregion(sub_region)
+        self.delta_z = sub_region[-1] - sub_region[-2]
+        self.chunk_size = self.delta_z
+        self._set_phase_margin(phase_margin)
+        self._set_extra_options(extra_options)
+        self._callbacks = {}
+        self._steps_name2component = {}
+        self._steps_component2name = {}
+        self._data_dump = {}
+        self._resume_from_step = None
+
+    @staticmethod
+    def _check_subregion(sub_region):
+        if len(sub_region) < 4:
+            assert len(sub_region) == 2
+            sub_region = (None, None) + sub_region
+        if None in sub_region[-2:]:
+            raise ValueError("Cannot set z_min or z_max to None")
+        return sub_region
+
+    def _set_extra_options(self, extra_options):
+        if extra_options is None:
+            extra_options = {}
+        advanced_options = {}
+        advanced_options.update(extra_options)
+        self.extra_options = advanced_options
+
+    def _set_phase_margin(self, phase_margin):
+        if phase_margin is None:
+            phase_margin = ((0, 0), (0, 0))
+        self._phase_margin_up = phase_margin[0][0]
+        self._phase_margin_down = phase_margin[0][1]
+        self._phase_margin_left = phase_margin[1][0]
+        self._phase_margin_right = phase_margin[1][1]
+
+    def set_subregion(self, sub_region):
+        """
+        Set a sub-region to process.
+
+        Parameters
+        ----------
+        sub_region: tuple
+            Sub-region to process in the volume, in the format
+            `(start_x, end_x, start_z, end_z)` or `(start_z, end_z)`.
+        """
+        sub_region = self._check_subregion(sub_region)
+        dz = sub_region[-1] - sub_region[-2]
+        if dz != self.delta_z:
+            raise ValueError(
+                "Class was initialized for delta_z = %d but provided sub_region has delta_z = %d" % (self.delta_z, dz)
+            )
+        self.sub_region = sub_region
+        self.z_min = sub_region[-2]
+        self.z_max = sub_region[-1]
+
+    def _compute_phase_kernel_margin(self):
+        """
+        Get the "margin" to pass to classes like PaganinPhaseRetrieval.
+        In order to have a good accuracy for filter-based phase retrieval methods,
+        we need to load extra data around the edges of each image. Otherwise,
+        a default padding type is applied.
+        """
+        if not (self.use_radio_processing_margin):
+            self._phase_margin = None
+            return
+        up_margin = self._phase_margin_up
+        down_margin = self._phase_margin_down
+        # Horizontal margin is not implemented
+        left_margin, right_margin = (0, 0)
+        self._phase_margin = ((up_margin, down_margin), (left_margin, right_margin))
+
+    @property
+    def use_radio_processing_margin(self):
+        return ("phase" in self.processing_steps) or ("unsharp_mask" in self.processing_steps)
+
+    def _get_phase_margin(self):
+        if not (self.use_radio_processing_margin):
+            return ((0, 0), (0, 0))
+        return self._phase_margin
+
+    def _get_cropped_radios(self):
+        ((up_margin, down_margin), (left_margin, right_margin)) = self._phase_margin
+        zslice = slice(up_margin or None, -down_margin or None)
+        xslice = slice(left_margin or None, -right_margin or None)
+        self._radios_cropped = self.radios[:, zslice, xslice]
+        return self._radios_cropped
+
+    @property
+    def phase_margin(self):
+        """
+        Return the margin for phase retrieval in the form ((up, down), (left, right))
+        """
+        return self._get_phase_margin()
+
+    @property
+    def n_recs(self):
+        """
+        Return the final number of reconstructed slices.
+        """
+        n_recs = self.delta_z
+        n_recs -= sum(self._get_phase_margin()[0])
+        return n_recs
+
+    def _get_process_name(self, kind="reconstruction"):
+        # In the future, might be something like "reconstruction-<ID>"
+        if kind == "reconstruction":
+            return "reconstruction"
+        elif kind == "histogram":
+            return "histogram"
+        return kind
+
+    def _configure_dump(self, step_name):
+        if step_name not in self.processing_steps:
+            if step_name == "sinogram" and self.process_config._dump_sinogram:
+                fname_full = self.process_config._dump_sinogram_file
+            else:
+                return
+        else:
+            if not self.processing_options[step_name].get("save", False):
+                return
+            fname_full = self.processing_options[step_name]["save_steps_file"]
+
+        fname, ext = path.splitext(fname_full)
+        dirname, file_prefix = path.split(fname)
+        output_dir = path.join(dirname, file_prefix)
+        file_prefix += str("_%04d" % self._get_image_start_index())
+
+        self._data_dump[step_name] = WriterConfigurator(
+            output_dir,
+            file_prefix,
+            file_format="hdf5",
+            overwrite=True,
+            logger=self.logger,
+            nx_info={
+                "process_name": step_name,
+                "processing_index": 0,  # TODO
+                "config": {
+                    "processing_options": self.processing_options,
+                    "nabu_config": self.process_config.nabu_config,
+                },
+                "entry": getattr(self.dataset_info.dataset_scanner, "entry", None),
+            },
+        )
+
+    def _configure_data_dumps(self):
+        for step_name in self.processing_steps:
+            self._configure_dump(step_name)
+        # sinogram is a special keyword: not in processing_steps, but guaranteed to be before sinogram generation
+        if self.process_config._dump_sinogram:
+            self._configure_dump("sinogram")
+
+    #
+    # Callbacks
+    #
+
+    def register_callback(self, step_name, callback):
+        """
+        Register a callback for a pipeline processing step.
+
+        Parameters
+        ----------
+        step_name: str
+            processing step name
+        callback: callable
+            A function. It will be executed once the processing step `step_name`
+            is finished. The function takes only one argument: the class instance.
+        """
+        if step_name not in self.processing_steps:
+            raise ValueError("'%s' is not in processing steps %s" % (step_name, self.processing_steps))
+        if step_name in self._callbacks:
+            self._callbacks[step_name].append(callback)
+        else:
+            self._callbacks[step_name] = [callback]
+
+    def _reshape_radios_after_phase(self):
+        """
+        Callback executed after phase retrieval, if margin != (0, 0).
+        It modifies self.radios so that further processing will be done
+        on the "inner part".
+        """
+        if sum(self._get_phase_margin()[0]) <= 0:
+            return
+        self._orig_radios = self.radios
+        self.logger.debug("Reshaping radios from %s to %s" % (str(self.radios.shape), str(self._radios_cropped.shape)))
+        self.radios = self._radios_cropped
+
+    #
+    # Overwritten in inheriting classes
+    #
+
+    def _get_shape(self, step_name):
+        """
+        Get the shape to provide to the class corresponding to step_name.
+        """
+        if step_name == "flatfield":
+            shape = self.radios.shape
+        elif step_name == "double_flatfield":
+            shape = self.radios.shape
+        elif step_name == "rotate_projections":
+            shape = self.radios.shape[1:]
+        elif step_name == "phase":
+            shape = self.radios.shape[1:]
+        elif step_name == "ccd_correction":
+            shape = self.radios.shape[1:]
+        elif step_name == "unsharp_mask":
+            shape = self.radios.shape[1:]
+        elif step_name == "take_log":
+            shape = self._radios_cropped_shape
+        elif step_name == "radios_movements":
+            shape = self._radios_cropped_shape
+        elif step_name == "sino_normalization":
+            shape = self._radios_cropped_shape
+        elif step_name == "build_sino":
+            shape = self._radios_cropped_shape
+        elif step_name == "sino_rings_correction":
+            shape = self.sino_builder.output_shape
+        elif step_name == "reconstruction":
+            shape = self.sino_builder.output_shape[1:]
+        else:
+            raise ValueError("Unknown processing step %s" % step_name)
+        self.logger.debug("Data shape for %s is %s" % (step_name, str(shape)))
+        return shape
+
+    def _get_phase_output_shape(self):
+        if not (self.use_radio_processing_margin):
+            self._radios_cropped_shape = self.radios.shape
+            return
+        ((up_margin, down_margin), (left_margin, right_margin)) = self._phase_margin
+        self._radios_cropped_shape = (
+            self.radios.shape[0],
+            self.radios.shape[1] - (up_margin + down_margin),
+            self.radios.shape[2] - (left_margin + right_margin),
+        )
+
+    def _allocate_array(self, shape, dtype, name=None):
+        return np.zeros(shape, dtype=dtype)
+
+    def _allocate_sinobuilder_output(self):
+        return self._allocate_array(self.sino_builder.output_shape, "f", name="sinos")
+
+    def _allocate_recs(self, ny, nx):
+        self.n_slices = self.radios.shape[1]  # TODO modify with vertical shifts
+        if self.use_radio_processing_margin:
+            self.n_slices -= sum(self.phase_margin[0])
+        self.recs = self._allocate_array((self.n_slices, ny, nx), "f", name="recs")
+
+    def _reset_memory(self):
+        pass
+
+    def _get_read_dump_subregion(self):
+        read_opts = self.processing_options["read_chunk"]
+        if read_opts.get("process_file", None) is None:
+            return None
+        dump_start_z, dump_end_z = read_opts["dump_start_z"], read_opts["dump_end_z"]
+        relative_start_z = self.z_min - dump_start_z
+        relative_end_z = relative_start_z + self.delta_z
+        # (n_angles, n_z, n_x)
+        subregion = (None, None, relative_start_z, relative_end_z, None, None)
+        return subregion
+
+    def _check_resume_from_step(self):
+        if self._resume_from_step is None:
+            return
+        read_opts = self.processing_options["read_chunk"]
+        expected_radios_shape = get_hdf5_dataset_shape(
+            read_opts["process_file"],
+            read_opts["process_h5_path"],
+            sub_region=self._get_read_dump_subregion(),
+        )
+        # TODO check
+
+    def _init_reader_finalize(self):
+        """
+        Method called after _init_reader
+        """
+        self._check_resume_from_step()
+        self.radios = self.chunk_reader.data
+        self._compute_phase_kernel_margin()
+        self._get_phase_output_shape()
+
+    def _process_finalize(self):
+        """
+        Method called once the pipeline has been executed
+        """
+        if sum(self._get_phase_margin()[0]) > 0:
+            self.radios = self._orig_radios
+
+    def _get_slice_start_index(self):
+        return self.z_min + self._phase_margin_up
+
+    _get_image_start_index = _get_slice_start_index
+
+    #
+    # Pipeline initialization
+    #
+
+    def _init_pipeline(self):
+        self._init_reader()
+        self._init_flatfield()
+        self._init_double_flatfield()
+        self._init_ccd_corrections()
+        self._init_radios_rotation()
+        self._init_phase()
+        self._init_unsharp()
+        self._init_radios_movements()
+        self._init_mlog()
+        self._init_sino_normalization()
+        self._init_sino_builder()
+        self._init_sino_rings_correction()
+        self._prepare_reconstruction()
+        self._init_reconstruction()
+        self._init_histogram()
+        self._init_writer()
+        self._configure_data_dumps()
+
+    @use_options("read_chunk", "chunk_reader")
+    def _init_reader(self):
+        if "read_chunk" not in self.processing_steps:
+            raise ValueError("Cannot proceed without reading data")
+        options = self.processing_options["read_chunk"]
+        process_file = options.get("process_file", None)
+        if process_file is None:
+            # Standard case - start pipeline from raw data
+            # ChunkReader always take a non-subsampled dictionary "files"
+            self.chunk_reader = ChunkReader(
+                options["files"],
+                sub_region=self.sub_region,
+                convert_float=True,
+                binning=options["binning"],
+                dataset_subsampling=options["dataset_subsampling"],
+            )
+        else:
+            # Resume pipeline from dumped intermediate step
+            self.chunk_reader = HDF5Loader(
+                process_file, options["process_h5_path"], sub_region=self._get_read_dump_subregion()
+            )
+            self._resume_from_step = options["step_name"]
+            self.logger.debug(
+                "Load subregion %s from file %s" % (str(self.chunk_reader.sub_region), self.chunk_reader.fname)
+            )
+        self._init_reader_finalize()
+
+    @use_options("flatfield", "flatfield")
+    def _init_flatfield(self, shape=None):
+        if shape is None:
+            shape = self._get_shape("flatfield")
+        options = self.processing_options["flatfield"]
+
+        distortion_correction = None
+        if options["do_flat_distortion"]:
+            self.logger.info("Flats distortion correction will be applied")
+            estimation_kwargs = {}
+            estimation_kwargs.update(options["flat_distortion_params"])
+            estimation_kwargs["logger"] = self.logger
+            distortion_correction = DistortionCorrection(
+                estimation_method="fft-correlation", estimation_kwargs=estimation_kwargs, correction_method="interpn"
+            )
+
+        # FlatField parameter "radios_indices" must account for subsampling
+        self.flatfield = self.FlatFieldClass(
+            shape,
+            flats=self.dataset_info.flats,
+            darks=self.dataset_info.darks,
+            radios_indices=options["projs_indices"],
+            interpolation="linear",
+            distortion_correction=distortion_correction,
+            sub_region=self.sub_region,
+            binning=options["binning"],
+            convert_float=True,
+        )
+
+    @use_options("double_flatfield", "double_flatfield")
+    def _init_double_flatfield(self):
+        options = self.processing_options["double_flatfield"]
+        avg_is_on_log = options["sigma"] is not None
+        result_url = None
+        if options["processes_file"] not in (None, ""):
+            result_url = DataUrl(
+                file_path=options["processes_file"],
+                data_path=(self.dataset_info.hdf5_entry or "entry") + "/double_flatfield/results/data",
+            )
+            self.logger.info("Loading double flatfield from %s" % result_url.file_path())
+        self.double_flatfield = self.DoubleFlatFieldClass(
+            self._get_shape("double_flatfield"),
+            result_url=result_url,
+            sub_region=self.sub_region,
+            input_is_mlog=False,
+            output_is_mlog=False,
+            average_is_on_log=avg_is_on_log,
+            sigma_filter=options["sigma"],
+        )
+
+    @use_options("ccd_correction", "ccd_correction")
+    def _init_ccd_corrections(self):
+        options = self.processing_options["ccd_correction"]
+        self.ccd_correction = self.CCDCorrectionClass(
+            self._get_shape("ccd_correction"), median_clip_thresh=options["median_clip_thresh"]
+        )
+
+    @use_options("phase", "phase_retrieval")
+    def _init_phase(self):
+        options = self.processing_options["phase"]
+        # If unsharp mask follows phase retrieval, then it should be done
+        # before cropping to the "inner part".
+        # Otherwise, crop the data just after phase retrieval.
+        if "unsharp_mask" in self.processing_steps:
+            margin = None
+        else:
+            margin = self._phase_margin
+        self.phase_retrieval = self.PaganinPhaseRetrievalClass(
+            self._get_shape("phase"),
+            distance=options["distance_m"],
+            energy=options["energy_kev"],
+            delta_beta=options["delta_beta"],
+            pixel_size=options["pixel_size_m"],
+            padding=options["padding_type"],
+            margin=margin,
+            fftw_num_threads=0,  # TODO tune in advanced params of nabu config file
+        )
+        if self.phase_retrieval.use_fftw:
+            self.logger.debug(
+                "PaganinPhaseRetrieval using FFTW with %d threads" % self.phase_retrieval.fftw.num_threads
+            )
+        if "unsharp_mask" not in self.processing_steps:
+            self.register_callback("phase", ChunkedPipeline._reshape_radios_after_phase)
+
+    @use_options("unsharp_mask", "unsharp_mask")
+    def _init_unsharp(self):
+        options = self.processing_options["unsharp_mask"]
+        self.unsharp_mask = self.UnsharpMaskClass(
+            self._get_shape("unsharp_mask"),
+            options["unsharp_sigma"],
+            options["unsharp_coeff"],
+            mode="reflect",
+            method=options["unsharp_method"],
+        )
+        self.register_callback("unsharp_mask", ChunkedPipeline._reshape_radios_after_phase)
+
+    @use_options("take_log", "mlog")
+    def _init_mlog(self):
+        options = self.processing_options["take_log"]
+        self.mlog = self.MLogClass(
+            self._get_shape("take_log"), clip_min=options["log_min_clip"], clip_max=options["log_max_clip"]
+        )
+
+    @use_options("rotate_projections", "projs_rot")
+    def _init_radios_rotation(self):
+        options = self.processing_options["rotate_projections"]
+        center = options["center"]
+        if center is None:
+            nx, ny = self.dataset_info.radio_dims
+            center = (nx / 2 - 0.5, ny / 2 - 0.5)
+        center = (center[0], center[1] - self.z_min)
+        self.projs_rot = self.ImageRotationClass(
+            self._get_shape("rotate_projections"), options["angle"], center=center, mode="edge", reshape=False
+        )
+        self._tmp_rotated_radio = self._allocate_array(
+            self._get_shape("rotate_projections"), "f", name="tmp_rotated_radio"
+        )
+
+    @use_options("radios_movements", "radios_movements")
+    def _init_radios_movements(self):
+        options = self.processing_options["radios_movements"]
+        self._vertical_shifts = options["translation_movements"][:, 1]
+        self.radios_movements = self.VerticalShiftClass(self._get_shape("radios_movements"), self._vertical_shifts)
+
+    @use_options("sino_normalization", "sino_normalization")
+    def _init_sino_normalization(self):
+        options = self.processing_options["sino_normalization"]
+        self.sino_normalization = self.SinoNormalizationClass(
+            kind=options["method"],
+            radios_shape=self._get_shape("sino_normalization"),
+            normalization_array=options["normalization_array"],
+        )
+
+    @use_options("build_sino", "sino_builder")
+    def _init_sino_builder(self):
+        options = self.processing_options["build_sino"]
+        self.sino_builder = self.SinoBuilderClass(
+            radios_shape=self._get_shape("build_sino"),
+            rot_center=options["rotation_axis_position"],
+            halftomo=options["enable_halftomo"],
+        )
+        if not (options["enable_halftomo"]):
+            self._sinobuilder_copy = False
+            self._sinobuilder_output = None
+            self.sinos = None
+        else:
+            self._sinobuilder_copy = True
+            self.sinos = self._allocate_sinobuilder_output()
+            self._sinobuilder_output = self.sinos
+
+    @use_options("sino_rings_correction", "sino_deringer")
+    def _init_sino_rings_correction(self):
+        options = self.processing_options["sino_rings_correction"]
+        fw_params = extract_parameters(options["user_options"])
+        fw_sigma = fw_params.pop("sigma", 1.0)
+        self.sino_deringer = self.SinoDeringerClass(
+            fw_sigma, sinos_shape=self._get_shape("sino_rings_correction"), **fw_params
+        )
+
+    # this should be renamed, as it could be confused with _init_reconstruction. What about _get_reconstruction_array ?
+    @use_options("reconstruction", "reconstruction")
+    def _prepare_reconstruction(self):
+        options = self.processing_options["reconstruction"]
+        x_s, x_e = options["start_x"], options["end_x"]
+        y_s, y_e = options["start_y"], options["end_y"]
+        self._rec_roi = (x_s, x_e + 1, y_s, y_e + 1)
+        self._allocate_recs(y_e - y_s + 1, x_e - x_s + 1)
+
+    @use_options("reconstruction", "reconstruction")
+    def _init_reconstruction(self):
+        options = self.processing_options["reconstruction"]
+        if self.sino_builder is None:
+            raise ValueError("Reconstruction cannot be done without build_sino")
+        if self.FBPClass is None:
+            raise ValueError("No usable FBP module was found")
+
+        if options["enable_halftomo"]:
+            rot_center = options["rotation_axis_position_halftomo"]
+        else:
+            rot_center = options["rotation_axis_position"]
+        if self.sino_builder._halftomo_flip:
+            rot_center = self.sino_builder.rot_center
+
+        self.reconstruction = self.FBPClass(
+            self._get_shape("reconstruction"),
+            angles=options["angles"],
+            rot_center=rot_center,
+            filter_name=options["fbp_filter_type"],
+            slice_roi=self._rec_roi,
+            padding_mode=options["padding_type"],
+            extra_options={
+                "scale_factor": 1.0 / options["pixel_size_cm"],
+                "axis_correction": options["axis_correction"],
+                "centered_axis": options["centered_axis"],
+                "clip_outer_circle": options["clip_outer_circle"],
+                "filter_cutoff": options["fbp_filter_cutoff"],
+            },
+        )
+        if options["fbp_filter_type"] is None:
+            self.reconstruction.fbp = self.reconstruction.backproj
+
+    @use_options("histogram", "histogram")
+    def _init_histogram(self):
+        options = self.processing_options["histogram"]
+        self.histogram = self.HistogramClass(method="fixed_bins_number", num_bins=options["histogram_bins"])
+
+    @use_options("save", "writer")
+    def _init_writer(self):
+        # TODO: henri: have a look to simplify
+        options = self.processing_options["save"]
+        file_prefix = options["file_prefix"]
+        output_dir = path.join(options["location"], file_prefix)
+        nx_info = None
+        self._hdf5_output = is_hdf5_extension(options["file_format"], errors=False)
+        if self._hdf5_output:
+            fname_start_index = None
+            file_prefix += str("_%04d" % self._get_slice_start_index())
+            entry = getattr(self.dataset_info.dataset_scanner, "entry", None)
+            nx_info = {
+                "process_name": self._get_process_name(),
+                "processing_index": 0,
+                "config": {
+                    # "processing_options": self.processing_options, # Takes too much time to write, not useful for partial files
+                    "nabu_config": self.process_config.nabu_config,
+                },
+                "entry": entry,
+            }
+            self._histogram_processing_index = nx_info["processing_index"] + 1
+        else:
+            fname_start_index = self._get_slice_start_index()
+            self._histogram_processing_index = 1
+        writer_options = {}
+        if options["tiff_single_file"]:
+            writer_options = {
+                "tiff_single_file": options["tiff_single_file"],
+                "single_tiff_initialized": getattr(self.process_config, "single_tiff_initialized", False),
+            }
+            self.process_config.single_tiff_initialized = True
+        self._writer_configurator = WriterConfigurator(
+            output_dir,
+            file_prefix,
+            file_format=options["file_format"],
+            overwrite=options["overwrite"],
+            start_index=fname_start_index,
+            logger=self.logger,
+            nx_info=nx_info,
+            write_histogram=("histogram" in self.processing_steps),
+            histogram_entry=getattr(self.dataset_info.dataset_scanner, "entry", "entry"),
+            writer_options=writer_options,
+            extra_options={
+                "jpeg2000_compression_ratio": options["jpeg2000_compression_ratio"],
+                "float_clip_values": options["float_clip_values"],
+            },
+        )
+        self.writer = self._writer_configurator.writer
+        self._writer_exec_args = self._writer_configurator._writer_exec_args
+        self._writer_exec_kwargs = self._writer_configurator._writer_exec_kwargs
+        self.histogram_writer = self._writer_configurator.get_histogram_writer()
+
+    #
+    # Pipeline re-initialization
+    #
+
+    def _reset_sub_region(self, sub_region):
+        self.set_subregion(sub_region)
+        self._reset_reader_subregion()
+        self._reset_flatfield()
+
+    def _reset_flatfield(self):
+        self._init_flatfield()
+
+    #
+    # Pipeline execution
+    #
+
+    @pipeline_step("chunk_reader", "Reading data")
+    def _read_data(self):
+        self.logger.debug("Region = %s" % str(self.sub_region))
+        t0 = time()
+        self.chunk_reader.load_data()
+        el = time() - t0
+
+        shp = self.chunk_reader.data.shape
+        itemsize = self.chunk_reader.dtype.itemsize if hasattr(self.chunk_reader, "dtype") else 4
+        GB = np.prod(shp) * itemsize / 1e9
+        self.logger.info("Read subvolume %s in %.2f s" % (str(shp), el))
+
+    def _reset_reader_subregion(self):
+        if self._resume_from_step is None:
+            self.chunk_reader._set_subregion(self.sub_region)
+            self.chunk_reader._init_reader()
+            self.chunk_reader._loaded = False
+        else:
+            self.chunk_reader._set_subregion(self._get_read_dump_subregion())
+            self.chunk_reader._loaded = False
+
+    @pipeline_step("flatfield", "Applying flat-field")
+    def _flatfield(self):
+        self.flatfield.normalize_radios(self.radios)
+
+    @pipeline_step("double_flatfield", "Applying double flat-field")
+    def _double_flatfield(self, radios=None):
+        if radios is None:
+            radios = self.radios
+        self.double_flatfield.apply_double_flatfield(radios)
+
+    @pipeline_step("ccd_correction", "Applying CCD corrections")
+    def _ccd_corrections(self, radios=None):
+        if radios is None:
+            radios = self.radios
+        _tmp_radio = self._allocate_array(radios.shape[1:], "f", name="tmp_ccdcorr_radio")
+        for i in range(radios.shape[0]):
+            self.ccd_correction.median_clip_correction(radios[i], output=_tmp_radio)
+            radios[i][:] = _tmp_radio[:]
+
+    @pipeline_step("projs_rot", "Rotating projections")
+    def _rotate_projections(self, radios=None):
+        if radios is None:
+            radios = self.radios
+        tmp_radio = self._tmp_rotated_radio
+        for i in range(radios.shape[0]):
+            self.projs_rot.rotate(radios[i], output=tmp_radio)
+            radios[i][:] = tmp_radio[:]
+
+    @pipeline_step("phase_retrieval", "Performing phase retrieval")
+    def _retrieve_phase(self):
+        if "unsharp_mask" in self.processing_steps:
+            output = self.radios
+        else:
+            self._get_cropped_radios()
+            output = self._radios_cropped
+        for i in range(self.radios.shape[0]):
+            self.phase_retrieval.apply_filter(self.radios[i], output=output[i])
+
+    @pipeline_step("unsharp_mask", "Performing unsharp mask")
+    def _apply_unsharp(self):
+        for i in range(self.radios.shape[0]):
+            self.radios[i] = self.unsharp_mask.unsharp(self.radios[i])
+        self._get_cropped_radios()
+
+    @pipeline_step("mlog", "Taking logarithm")
+    def _take_log(self):
+        self.mlog.take_logarithm(self.radios)
+
+    @pipeline_step("radios_movements", "Applying radios movements")
+    def _radios_movements(self, radios=None):
+        if radios is None:
+            radios = self.radios
+        self.radios_movements.apply_vertical_shifts(radios, list(range(radios.shape[0])))
+
+    @pipeline_step("sino_normalization", "Normalizing sinograms")
+    def _normalize_sinos(self, radios=None):
+        if radios is None:
+            radios = self.radios
+        sinos = radios.transpose((1, 0, 2))
+        self.sino_normalization.normalize(sinos)
+
+    def _dump_sinogram(self, radios=None):
+        if radios is None:
+            radios = self.radios
+        self._dump_data_to_file("sinogram", data=radios)
+
+    @pipeline_step("sino_builder", "Building sinograms")
+    def _build_sino(self, radios=None):
+        if radios is None:
+            radios = self.radios
+        # Either a new array (previously allocated in "_sinobuilder_output"),
+        # or a view of "radios"
+        self.sinos = self.sino_builder.radios_to_sinos(
+            radios, output=self._sinobuilder_output, copy=self._sinobuilder_copy
+        )
+
+    @pipeline_step("sino_deringer", "Removing rings on sinograms")
+    def _destripe_sinos(self, sinos=None):
+        if sinos is None:
+            sinos = self.sinos
+        self.sino_deringer.remove_rings(sinos)
+
+    @pipeline_step("reconstruction", "Reconstruction")
+    def _reconstruct(self, sinos=None):
+        if sinos is None:
+            sinos = self.sinos
+        for i in range(sinos.shape[0]):
+            self.reconstruction.fbp(sinos[i], output=self.recs[i])
+
+    @pipeline_step("histogram", "Computing histogram")
+    def _compute_histogram(self, data=None):
+        if data is None:
+            data = self.recs
+        self.recs_histogram = self.histogram.compute_histogram(data)
+
+    @pipeline_step("writer", "Saving data")
+    def _write_data(self, data=None):
+        if data is None:
+            data = self.recs
+        self.writer.write(data, *self._writer_exec_args, **self._writer_exec_kwargs)
+        self.logger.info("Wrote %s" % self.writer.get_filename())
+        self._write_histogram()
+
+    def _write_histogram(self):
+        if "histogram" not in self.processing_steps:
+            return
+        self.logger.info("Saving histogram")
+        self.histogram_writer.write(
+            hist_as_2Darray(self.recs_histogram),
+            self._get_process_name(kind="histogram"),
+            processing_index=self._histogram_processing_index,
+            config={
+                "file": path.basename(self.writer.get_filename()),
+                "bins": self.processing_options["histogram"]["histogram_bins"],
+            },
+        )
+
+    def _dump_data_to_file(self, step_name, data=None):
+        if step_name not in self._data_dump:
+            return
+        if data is None:
+            data = self.radios
+        writer = self._data_dump[step_name]
+        self.logger.info("Dumping data to %s" % writer.fname)
+        writer.write_data(data)
+
+    def _process_chunk(self):
+        self._flatfield()
+        self._double_flatfield()
+        self._ccd_corrections()
+        self._rotate_projections()
+        self._retrieve_phase()
+        self._apply_unsharp()
+        self._take_log()
+        self._radios_movements()
+        self._normalize_sinos()
+        self._dump_sinogram()
+        self._build_sino()
+        self._destripe_sinos()
+        self._reconstruct()
+        self._compute_histogram()
+        self._write_data()
+        self._process_finalize()
+
+    def process_chunk(self, sub_region=None):
+        if sub_region is not None:
+            self._reset_sub_region(sub_region)
+            self._reset_memory()
+            self._init_writer()
+            self._init_double_flatfield()
+            self._configure_data_dumps()
+        self._read_data()
+        self._process_chunk()