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

build/lib/build/lib/nabu/pipeline/fullfield/processconfig.py

@@ -1,825 +0,0 @@
-import os
-import posixpath
-import numpy as np
-from silx.io import get_data
-from silx.io.url import DataUrl
-from ...utils import copy_dict_items, compare_dicts
-from ...io.utils import hdf5_entry_exists, get_h5_value
-from ...io.reader import import_h5_to_dict
-from ...resources.utils import extract_parameters, get_values_from_file
-from ...resources.nxflatfield import update_dataset_info_flats_darks
-from ...resources.utils import get_quantities_and_units
-from ..estimators import estimate_cor
-from ..processconfig import ProcessConfigBase
-from .nabu_config import nabu_config, renamed_keys
-from .dataset_validator import FullFieldDatasetValidator
-from nxtomo.nxobject.nxdetector import ImageKey
-
-
-class ProcessConfig(ProcessConfigBase):
-
-    """
-    A ProcessConfig object has these main fields:
-      - dataset_info: information about the current dataset
-      - nabu_config: configuration from the user side
-      - processing_steps/processing_options: configuration "ready-to use" for underlying classes
-
-    It is built from the following steps.
-
-    (1a) parse config: (conf_fname or conf_dict) --> "nabu_config"
-
-    (1b) browse dataset: (nabu_config or existing dataset_info)  --> dataset_info
-
-
-    (2) update_dataset_info_with_user_config
-      - Update flats/darks
-      - CoR  (value or estimation method) # no estimation yet
-      - rotation angles
-      - translations files
-      - user sino normalization (eg. subtraction etc)
-
-    (3) estimations
-      - tilt
-      - CoR
-
-    (4) coupled validation
-
-    (5) build processing steps
-
-    (6) configure checkpoints (save/resume)
-    """
-
-    default_nabu_config = nabu_config
-    config_renamed_keys = renamed_keys
-    _use_horizontal_translations = True
-    _all_processing_steps = [
-        "read_chunk",
-        "flatfield",
-        "ccd_correction",
-        "double_flatfield",
-        "rotate_projections",
-        "phase",
-        "unsharp_mask",
-        "take_log",
-        "radios_movements",  # radios are cropped after this step, if needed
-        "sino_normalization",
-        "sino_rings_correction",
-        "reconstruction",
-        "histogram",
-        "save",
-    ]
-
-    def _update_dataset_info_with_user_config(self):
-        """
-        Update the 'dataset_info' (DatasetAnalyzer class instance) data structure with options from user configuration.
-        """
-        self.logger.debug("Updating dataset information with user configuration")
-        if self.dataset_info.kind == "hdf5":
-            update_dataset_info_flats_darks(
-                self.dataset_info,
-                self.nabu_config["preproc"]["flatfield"],
-                output_dir=self.nabu_config["output"]["location"],
-                darks_flats_dir=self.nabu_config["dataset"]["darks_flats_dir"],
-            )
-        self.rec_params = self.nabu_config["reconstruction"]
-
-        self._update_dataset_with_user_overwrites()
-        self._get_rotation_axis_position()
-        self._update_rotation_angles()
-        self._get_translation_file("reconstruction", "translation_movements_file", "translations")
-        self._get_user_sino_normalization()
-
-    def _update_dataset_with_user_overwrites(self):
-        user_overwrites = self.nabu_config["dataset"]["overwrite_metadata"].strip()
-        if user_overwrites in ("", None):
-            return
-        possible_overwrites = {"pixel_size": 1e6, "distance": 1.0, "energy": 1.0}
-        try:
-            overwrites = get_quantities_and_units(user_overwrites)
-        except ValueError:
-            msg = (
-                "Something wrong in config file in 'overwrite_metadata': could not get quantities/units from '%s'. Please check that separators are ';' and that units are provided (separated by a space)"
-                % user_overwrites
-            )
-            self.logger.fatal(msg)
-            raise ValueError(msg)
-        for quantity, conversion_factor in possible_overwrites.items():
-            user_value = overwrites.pop(quantity, None)
-            if user_value is not None:
-                self.logger.info("Overwriting %s = %s" % (quantity, user_value))
-                user_value *= conversion_factor
-                setattr(self.dataset_info, quantity, user_value)
-
-    def _get_translation_file(self, config_section, config_key, dataset_info_attr, last_dim=2):
-        transl_file = self.nabu_config[config_section][config_key]
-        if transl_file in (None, ""):
-            return
-        translations = None
-        if transl_file is not None and "://" not in transl_file:
-            try:
-                translations = get_values_from_file(
-                    transl_file, shape=(self.dataset_info.n_angles, last_dim), any_size=True
-                ).astype(np.float32)
-            except ValueError:
-                print("Something wrong with translation_movements_file %s" % transl_file)
-                raise
-        else:
-            try:
-                translations = get_data(transl_file)
-            except:
-                print("Something wrong with translation_movements_file %s" % transl_file)
-                raise
-        setattr(self.dataset_info, dataset_info_attr, translations)
-        if self._use_horizontal_translations and translations is not None:
-            # Horizontal translations are handled by "axis_correction" in backprojector
-            horizontal_translations = translations[:, 0]
-            if np.max(np.abs(horizontal_translations)) > 1e-3:
-                self.dataset_info.axis_correction = horizontal_translations
-
-    def _get_rotation_axis_position(self):
-        super()._get_rotation_axis_position()
-        rec_params = self.nabu_config["reconstruction"]
-        axis_correction_file = rec_params["axis_correction_file"]
-        axis_correction = None
-        if axis_correction_file is not None:
-            try:
-                axis_correction = get_values_from_file(
-                    axis_correction_file,
-                    n_values=self.dataset_info.n_angles,
-                    any_size=True,
-                ).astype(np.float32)
-            except ValueError:
-                print("Something wrong with axis correction file %s" % axis_correction_file)
-                raise
-        self.dataset_info.axis_correction = axis_correction
-
-    def _update_rotation_angles(self):
-        rec_params = self.nabu_config["reconstruction"]
-        n_angles = self.dataset_info.n_angles
-        angles_file = rec_params["angles_file"]
-        if angles_file is not None:
-            try:
-                angles = get_values_from_file(angles_file, n_values=n_angles, any_size=True)
-                angles = np.deg2rad(angles)
-            except ValueError:
-                self.logger.fatal("Something wrong with angle file %s" % angles_file)
-                raise
-            self.dataset_info.rotation_angles = angles
-        elif self.dataset_info.rotation_angles is None:
-            angles_range_txt = "[0, 180[ degrees"
-            if rec_params["enable_halftomo"]:
-                angles_range_txt = "[0, 360] degrees"
-                angles = np.linspace(0, 2 * np.pi, n_angles, True)
-            else:
-                angles = np.linspace(0, np.pi, n_angles, False)
-            self.logger.warning(
-                "No information was found on rotation angles. Using default %s (half tomo is %s)"
-                % (angles_range_txt, {0: "OFF", 1: "ON"}[int(self.do_halftomo)])
-            )
-            self.dataset_info.rotation_angles = angles
-
-    def _get_cor(self):
-        cor = self.nabu_config["reconstruction"]["rotation_axis_position"]
-        if isinstance(cor, str):  # auto-CoR
-            cor = estimate_cor(
-                cor,
-                self.dataset_info,
-                do_flatfield=(self.nabu_config["preproc"]["flatfield"] is not False),
-                cor_options=self.nabu_config["reconstruction"]["cor_options"],
-                logger=self.logger,
-            )
-            self.logger.info("Estimated center of rotation: %.3f" % cor)
-        self.dataset_info.axis_position = cor
-
-    def _get_user_sino_normalization(self):
-        self._sino_normalization_arr = None
-        norm = self.nabu_config["preproc"]["sino_normalization"]
-        if norm not in ["subtraction", "division"]:
-            return
-        norm_path = "silx://" + self.nabu_config["preproc"]["sino_normalization_file"].strip()
-        url = DataUrl(norm_path)
-        try:
-            norm_array = get_data(url)
-            self._sino_normalization_arr = norm_array.astype("f")
-        except (ValueError, OSError) as exc:
-            error_msg = "Could not load sino_normalization_file %s. The error was: %s" % (norm_path, str(exc))
-            self.logger.error(error_msg)
-            raise ValueError(error_msg)
-
-    @property
-    def do_halftomo(self):
-        """
-        Return True if the current dataset is to be reconstructed using 'half-acquisition' setting.
-        """
-        enable_halftomo = self.nabu_config["reconstruction"]["enable_halftomo"]
-        is_halftomo_dataset = self.dataset_info.is_halftomo
-        if enable_halftomo == "auto":
-            if is_halftomo_dataset is None:
-                raise ValueError(
-                    "enable_halftomo was set to 'auto', but information on field of view was not found. Please set either 0 or 1 for enable_halftomo"
-                )
-            return is_halftomo_dataset
-        return enable_halftomo
-
-    def _coupled_validation(self):
-        self.logger.debug("Doing coupled validation")
-        self._dataset_validator = FullFieldDatasetValidator(self.nabu_config, self.dataset_info)
-        # Not so ideal to propagate fields like this
-        for what in ["rec_params", "rec_region", "binning", "subsampling_factor"]:
-            setattr(self, what, getattr(self._dataset_validator, what))
-
-    #
-    # Attributes that combine dataset information and user overwrites (eg. binning).
-    # Must be accessed after __init__() is done
-    #
-
-    @property
-    def binning_x(self):
-        return getattr(self, "binning", (1, 1))[0]
-
-    @property
-    def binning_z(self):
-        return getattr(self, "binning", (1, 1))[1]
-
-    @property
-    def subsampling(self):
-        return getattr(self, "subsampling_factor", None)
-
-    def radio_shape(self, binning=False):
-        n_x, n_z = self.dataset_info.radio_dims
-        if binning:
-            n_z //= self.binning_z
-            n_x //= self.binning_x
-        return (n_z, n_x)
-
-    def n_angles(self, subsampling=False):
-        rot_angles = self.dataset_info.rotation_angles
-        if subsampling:
-            rot_angles = rot_angles[:: (self.subsampling or 1)]
-        return len(rot_angles)
-
-    def radios_shape(self, binning=False, subsampling=False):
-        n_z, n_x = self.radio_shape(binning=binning)
-        n_a = self.n_angles(subsampling=subsampling)
-        return (n_a, n_z, n_x)
-
-    def rotation_axis_position(self, binning=False):
-        cor = self.dataset_info.axis_position  # might be None (default to the middle of detector)
-        if cor is None and self.do_halftomo:
-            raise ValueError("No information on center of rotation, cannot use half-tomography reconstruction")
-        if cor is not None and binning:
-            # Backprojector uses middle of pixel for coordinate indices.
-            # This means that the leftmost edge of the leftmost pixel has coordinate -0.5.
-            # When using binning with a factor 'b', the CoR has to adapted as
-            #   cor_binned  =  (cor + 0.5)/b - 0.5
-            cor = (cor + 0.5) / self.binning_x - 0.5
-        return cor
-
-    def sino_shape(self, binning=False, subsampling=False):
-        """
-        Return the shape of a sinogram image.
-
-        Parameter
-        ---------
-        binning: bool
-            Whether to account for image binning
-        subsampling: bool
-            Whether to account for projections subsampling
-        """
-        n_a, _, n_x = self.radios_shape(binning=binning, subsampling=subsampling)
-        return (n_a, n_x)
-
-    def sinos_shape(self, binning=False, subsampling=False):
-        n_z, _ = self.radio_shape(binning=binning)
-        return (n_z,) + self.sino_shape(binning=binning, subsampling=subsampling)
-
-    def projs_indices(self, subsampling=False):
-        step = 1
-        if subsampling:
-            step = self.subsampling or 1
-        return sorted(self.dataset_info.projections.keys())[::step]
-
-    def rotation_angles(self, subsampling=False):
-        step = 1
-        if subsampling:
-            step = self.subsampling or 1
-        return self.dataset_info.rotation_angles[::step]
-
-    @property
-    def rec_roi(self):
-        """
-        Returns the reconstruction region of interest (ROI), accounting for binning in both dimensions.
-        """
-        rec_params = self.rec_params  # accounts for binning
-        x_s, x_e = rec_params["start_x"], rec_params["end_x"]
-        y_s, y_e = rec_params["start_y"], rec_params["end_y"]
-        # Upper bound (end_xy) is INCLUDED in nabu config, hence the +1 here
-        return (x_s, x_e + 1, y_s, y_e + 1)
-
-    @property
-    def rec_shape(self):
-        # Accounts for binning!
-        return tuple(np.diff(self.rec_roi)[::-2])
-
-    @property
-    def rec_delta_z(self):
-        # Accounts for binning!
-        z_s, z_e = self.rec_params["start_z"], self.rec_params["end_z"]
-        # Upper bound (end_xy) is INCLUDED in nabu config, hence the +1 here
-        return z_e + 1 - z_s
-
-    def is_before_radios_cropping(self, step):
-        """
-        Return true if a given processing step happens before radios cropping
-        """
-        if step == "sinogram":
-            return False
-        if step not in self._all_processing_steps:
-            raise ValueError("Unknown step: '%s'. Available are: %s" % (step, self._all_processing_steps))
-        # sino_normalization
-        return self._all_processing_steps.index(step) <= self._all_processing_steps.index("radios_movements")
-
-    #
-    # Build processing steps
-    #
-
-    # TODO update behavior and remove this function once GroupedPipeline cuda backend is implemented
-    def get_radios_rotation_mode(self):
-        """
-        Determine whether projections are to be rotated, and if so, when they are to be rotated.
-
-        Returns
-        -------
-        method: str or None
-            Rotation method: one of the values of `nabu.resources.params.radios_rotation_mode`
-        """
-        user_rotate_projections = self.nabu_config["preproc"]["rotate_projections"]
-        tilt = self.dataset_info.detector_tilt
-        phase_method = self.nabu_config["phase"]["method"]
-        do_ctf = phase_method == "CTF"
-        do_pag = phase_method == "paganin"
-        do_unsharp = (
-            self.nabu_config["phase"]["unsharp_method"] is not None and self.nabu_config["phase"]["unsharp_coeff"] > 0
-        )
-        if user_rotate_projections is None and tilt is None:
-            return None
-        if do_ctf:
-            return "full"
-        # TODO "chunked" rotation is done only when using a "processing margin"
-        # For now the processing margin is enabled only if phase or unsharp is enabled.
-        # We can either
-        #   - Enable processing margin if rotating projections is needed (more complicated to implement)
-        #   - Always do "full" rotation (simpler to implement, at the expense of performances)
-        if do_pag or do_unsharp:
-            return "chunk"
-        else:
-            return "full"
-
-    def _build_processing_steps(self):
-        nabu_config = self.nabu_config
-        dataset_info = self.dataset_info
-        binning = (nabu_config["dataset"]["binning"], nabu_config["dataset"]["binning_z"])
-        tasks = []
-        options = {}
-
-        #
-        # Dataset / Get data
-        #
-        # First thing to do is to get the data (radios or sinograms)
-        # For now data is assumed to be on disk (see issue #66).
-        tasks.append("read_chunk")
-        options["read_chunk"] = {
-            "files": dataset_info.projections,
-            "sub_region": None,
-            "binning": binning,
-            "dataset_subsampling": nabu_config["dataset"]["projections_subsampling"],
-        }
-        #
-        # Flat-field
-        #
-        if nabu_config["preproc"]["flatfield"]:
-            tasks.append("flatfield")
-            options["flatfield"] = {
-                #  ChunkReader handles binning/subsampling by itself,
-                # but FlatField needs "real" indices (after binning/subsampling)
-                "projs_indices": self.projs_indices(subsampling=False),
-                "binning": binning,
-                "do_flat_distortion": nabu_config["preproc"]["flat_distortion_correction_enabled"],
-                "flat_distortion_params": extract_parameters(nabu_config["preproc"]["flat_distortion_params"]),
-            }
-            normalize_srcurrent = nabu_config["preproc"]["normalize_srcurrent"]
-            radios_srcurrent = None
-            flats_srcurrent = None
-            if normalize_srcurrent:
-                if (
-                    dataset_info.projections_srcurrent is None
-                    or dataset_info.flats_srcurrent is None
-                    or len(dataset_info.flats_srcurrent) == 0
-                ):
-                    self.logger.error("Cannot do SRCurrent normalization: missing flats and/or projections SRCurrent")
-                    normalize_srcurrent = False
-                else:
-                    radios_srcurrent = dataset_info.projections_srcurrent
-                    flats_srcurrent = dataset_info.flats_srcurrent
-            options["flatfield"].update(
-                {
-                    "normalize_srcurrent": normalize_srcurrent,
-                    "radios_srcurrent": radios_srcurrent,
-                    "flats_srcurrent": flats_srcurrent,
-                }
-            )
-        #
-        # Spikes filter
-        #
-        if nabu_config["preproc"]["ccd_filter_enabled"]:
-            tasks.append("ccd_correction")
-            options["ccd_correction"] = {
-                "type": "median_clip",  # only one available for now
-                "median_clip_thresh": nabu_config["preproc"]["ccd_filter_threshold"],
-            }
-        #
-        # Double flat field
-        #
-        if nabu_config["preproc"]["double_flatfield_enabled"]:
-            tasks.append("double_flatfield")
-            options["double_flatfield"] = {
-                "sigma": nabu_config["preproc"]["dff_sigma"],
-                "processes_file": nabu_config["preproc"]["processes_file"],
-                "log_min_clip": nabu_config["preproc"]["log_min_clip"],
-                "log_max_clip": nabu_config["preproc"]["log_max_clip"],
-            }
-        #
-        # Radios rotation (do it here if possible)
-        #
-        if self.get_radios_rotation_mode() == "chunk":
-            tasks.append("rotate_projections")
-            options["rotate_projections"] = {
-                "angle": nabu_config["preproc"]["rotate_projections"] or dataset_info.detector_tilt,
-                "center": nabu_config["preproc"]["rotate_projections_center"],
-                "mode": "chunk",
-            }
-        #
-        #
-        # Phase retrieval
-        #
-        if nabu_config["phase"]["method"] is not None:
-            tasks.append("phase")
-            options["phase"] = copy_dict_items(nabu_config["phase"], ["method", "delta_beta", "padding_type"])
-            options["phase"].update(
-                {
-                    "energy_kev": dataset_info.energy,
-                    "distance_cm": dataset_info.distance * 1e2,
-                    "distance_m": dataset_info.distance,
-                    "pixel_size_microns": dataset_info.pixel_size,
-                    "pixel_size_m": dataset_info.pixel_size * 1e-6,
-                }
-            )
-            if binning != (1, 1):
-                options["phase"]["delta_beta"] /= binning[0] * binning[1]
-            if options["phase"]["method"] == "CTF":
-                self._get_ctf_parameters(options["phase"])
-        #
-        # Unsharp
-        #
-        if (
-            nabu_config["phase"]["unsharp_method"] is not None
-            and nabu_config["phase"]["unsharp_coeff"] > 0
-            and nabu_config["phase"]["unsharp_sigma"] > 0
-        ):
-            tasks.append("unsharp_mask")
-            options["unsharp_mask"] = copy_dict_items(
-                nabu_config["phase"], ["unsharp_coeff", "unsharp_sigma", "unsharp_method"]
-            )
-        #
-        # -logarithm
-        #
-        if nabu_config["preproc"]["take_logarithm"]:
-            tasks.append("take_log")
-            options["take_log"] = copy_dict_items(nabu_config["preproc"], ["log_min_clip", "log_max_clip"])
-        #
-        # Radios rotation (do it here if mode=="full")
-        #
-        if self.get_radios_rotation_mode() == "full":
-            tasks.append("rotate_projections")
-            options["rotate_projections"] = {
-                "angle": nabu_config["preproc"]["rotate_projections"] or dataset_info.detector_tilt,
-                "center": nabu_config["preproc"]["rotate_projections_center"],
-                "mode": "full",
-            }
-        #
-        # Translation movements
-        #
-        translations = dataset_info.translations
-        if translations is not None:
-            tasks.append("radios_movements")
-            options["radios_movements"] = {"translation_movements": dataset_info.translations[:: self.binning_z]}
-        #
-        # Sinogram normalization (before half-tomo)
-        #
-        if nabu_config["preproc"]["sino_normalization"] is not None:
-            tasks.append("sino_normalization")
-            options["sino_normalization"] = {
-                "method": nabu_config["preproc"]["sino_normalization"],
-                "normalization_array": self._sino_normalization_arr,
-            }
-
-        #
-        # Sinogram-based rings artefacts removal
-        #
-        if nabu_config["preproc"]["sino_rings_correction"]:
-            tasks.append("sino_rings_correction")
-            options["sino_rings_correction"] = {
-                "method": nabu_config["preproc"]["sino_rings_correction"],
-                "user_options": nabu_config["preproc"]["sino_rings_options"],
-            }
-        #
-        # Reconstruction
-        #
-        if nabu_config["reconstruction"]["method"] is not None:
-            tasks.append("reconstruction")
-            # Iterative is not supported through configuration file for now.
-            options["reconstruction"] = copy_dict_items(
-                self.rec_params,
-                [
-                    "method",
-                    "fbp_filter_type",
-                    "fbp_filter_cutoff",
-                    "padding_type",
-                    "start_x",
-                    "end_x",
-                    "start_y",
-                    "end_y",
-                    "start_z",
-                    "end_z",
-                    "centered_axis",
-                    "clip_outer_circle",
-                    "source_sample_dist",
-                    "sample_detector_dist",
-                ],
-            )
-            rec_options = options["reconstruction"]
-            rec_options["rotation_axis_position"] = self.rotation_axis_position(binning=True)
-            rec_options["enable_halftomo"] = self.do_halftomo
-            rec_options["axis_correction"] = dataset_info.axis_correction
-            if dataset_info.axis_correction is not None:
-                rec_options["axis_correction"] = rec_options["axis_correction"][:: self.subsampling_factor]
-            rec_options["angles"] = np.array(self.rotation_angles(subsampling=True))
-            rec_options["angles"] += np.deg2rad(nabu_config["reconstruction"]["angle_offset"])
-            voxel_size = dataset_info.pixel_size * 1e-4
-            rec_options["voxel_size_cm"] = (
-                voxel_size,
-                voxel_size,
-                voxel_size,
-            )  # pix size is in microns in dataset_info
-
-            # x/y/z position information
-            def get_mean_pos(position_array):
-                if position_array is None:
-                    return None
-                else:
-                    position_array = np.array(position_array)
-                    # filter only projections. Avoid getting noise
-                    position_array = position_array[
-                        np.asarray(dataset_info.dataset_scanner.image_key_control) == ImageKey.PROJECTION.value
-                    ]
-                    return float(np.mean(position_array))
-
-            mean_positions_xyz = (
-                get_mean_pos(dataset_info.dataset_scanner.z_translation),
-                get_mean_pos(dataset_info.dataset_scanner.y_translation),
-                get_mean_pos(dataset_info.dataset_scanner.x_translation),
-            )
-            if all([m is not None for m in mean_positions_xyz]):
-                rec_options["position"] = mean_positions_xyz
-            if rec_options["sample_detector_dist"] is None:
-                rec_options["sample_detector_dist"] = self.dataset_info.distance  # was checked to be not None earlier
-
-            # New key
-            rec_options["cor_estimated_auto"] = isinstance(nabu_config["reconstruction"]["rotation_axis_position"], str)
-        #
-        # Histogram
-        #
-        if nabu_config["postproc"]["output_histogram"]:
-            tasks.append("histogram")
-            options["histogram"] = copy_dict_items(nabu_config["postproc"], ["histogram_bins"])
-        #
-        # Save
-        #
-        if nabu_config["output"]["location"] is not None:
-            tasks.append("save")
-            options["save"] = copy_dict_items(nabu_config["output"], list(nabu_config["output"].keys()))
-            options["save"]["overwrite"] = nabu_config["output"]["overwrite_results"]
-
-        self.processing_steps = tasks
-        self.processing_options = options
-        if set(self.processing_steps) != set(self.processing_options.keys()):
-            raise ValueError("Something wrong with process_config: options do not correspond to steps")
-        # Add check
-        if set(self.processing_steps) != set(self.processing_options.keys()):
-            raise ValueError("Something wrong when building processing steps")
-
-    def _get_ctf_parameters(self, phase_options):
-        dataset_info = self.dataset_info
-        user_phase_options = self.nabu_config["phase"]
-
-        ctf_geom = extract_parameters(user_phase_options["ctf_geometry"])
-        ctf_advanced_params = extract_parameters(user_phase_options["ctf_advanced_params"])
-
-        # z1_vh
-        z1_v = ctf_geom["z1_v"]
-        z1_h = ctf_geom["z1_h"]
-        z1_vh = None
-        if z1_h is None and z1_v is None:
-            # parallel beam
-            z1_vh = None
-        elif (z1_v is None) ^ (z1_h is None):
-            # only one is provided: source-sample distance
-            z1_vh = z1_v or z1_h
-        if z1_h is not None and z1_v is not None:
-            # distance of the vertically focused source (horizontal line) and the horizontaly focused source (vertical line)
-            # for KB mirrors
-            z1_vh = (z1_v, z1_h)
-        # pix_size_det
-        pix_size_det = ctf_geom["detec_pixel_size"] or dataset_info.pixel_size * 1e-6
-        # wavelength
-        wavelength = 1.23984199e-9 / dataset_info.energy
-
-        phase_options["ctf_geo_pars"] = {
-            "z1_vh": z1_vh,
-            "z2": phase_options["distance_m"],
-            "pix_size_det": pix_size_det,
-            "wavelength": wavelength,
-            "magnification": bool(ctf_geom["magnification"]),
-            "length_scale": ctf_advanced_params["length_scale"],
-        }
-        phase_options["ctf_lim1"] = ctf_advanced_params["lim1"]
-        phase_options["ctf_lim2"] = ctf_advanced_params["lim2"]
-        phase_options["ctf_normalize_by_mean"] = ctf_advanced_params["normalize_by_mean"]
-
-    def _configure_save_steps(self, steps_to_save=None):
-        self.steps_to_save = []
-        self.dump_sinogram = False
-        if steps_to_save is None:
-            steps_to_save = self.nabu_config["pipeline"]["save_steps"]
-            if steps_to_save in (None, ""):
-                return
-            steps_to_save = [s.strip() for s in steps_to_save.split(",")]
-        for step in self.processing_steps:
-            step = step.strip()
-            if step in steps_to_save:
-                self.processing_options[step]["save"] = True
-                self.processing_options[step]["save_steps_file"] = self.get_save_steps_file(step_name=step)
-        # "sinogram" is a special keyword, not explicitly in the processing steps
-        if "sinogram" in steps_to_save:
-            self.dump_sinogram = True
-            self.dump_sinogram_file = self.get_save_steps_file(step_name="sinogram")
-        self.steps_to_save = steps_to_save
-
-    def _get_dump_file_and_h5_path(self):
-        resume_from = self.resume_from_step
-        process_file = self.get_save_steps_file(step_name=resume_from)
-        if not os.path.isfile(process_file):
-            self.logger.error("Cannot resume processing from step '%s': no such file %s" % (resume_from, process_file))
-            return None, None
-        h5_entry = self.dataset_info.hdf5_entry or "entry"
-        process_h5_path = posixpath.join(h5_entry, resume_from, "results/data")
-        if not hdf5_entry_exists(process_file, process_h5_path):
-            self.logger.error("Could not find data in %s in file %s" % (process_h5_path, process_file))
-            process_h5_path = None
-        return process_file, process_h5_path
-
-    def _configure_resume(self, resume_from=None):
-        self.resume_from_step = None
-        if resume_from is None:
-            resume_from = self.nabu_config["pipeline"]["resume_from_step"]
-            if resume_from in (None, ""):
-                return
-            resume_from = resume_from.strip(" ,;")
-        self.resume_from_step = resume_from
-
-        processing_steps = self.processing_steps
-        # special case: resume from sinogram
-        if resume_from == "sinogram":
-            # disable up to 'reconstruction', not included
-            if "sino_rings_correction" in processing_steps:
-                # Sinogram destriping is done before building the half tomo sino.
-                # Not sure if this is needed (i.e can we do before building the extended sino ?)
-                # TODO find a more elegant way
-                idx = processing_steps.index("sino_rings_correction")
-            else:
-                idx = processing_steps.index("reconstruction")
-        #
-        elif resume_from in processing_steps:
-            idx = processing_steps.index(resume_from) + 1  # disable up to resume_from, included
-        else:
-            msg = "Cannot resume processing from step '%s': no such step in the current configuration" % resume_from
-            self.logger.error(msg)
-            self.resume_from_step = None
-            return
-
-        # Get corresponding file and h5 path
-        process_file, process_h5_path = self._get_dump_file_and_h5_path()
-        if process_file is None or process_h5_path is None:
-            self.resume_from_step = None
-            return
-        dump_info = self._check_dump_file(process_file, raise_on_error=False)
-        if dump_info is None:
-            self.logger.error("Cannot resume from step %s: cannot use file %s" % (resume_from, process_file))
-            self.resume_from_step = None
-            return
-        dump_start_z, dump_end_z = dump_info
-
-        # Disable steps
-        steps_to_disable = processing_steps[1:idx]
-        self.logger.debug("Disabling steps %s" % str(steps_to_disable))
-        for step_name in steps_to_disable:
-            processing_steps.remove(step_name)
-            self.processing_options.pop(step_name)
-
-        # Update configuration
-        self.logger.info("Processing will be resumed from step '%s' using file %s" % (resume_from, process_file))
-        self._old_read_chunk = self.processing_options["read_chunk"]
-        self.processing_options["read_chunk"] = {
-            "process_file": process_file,
-            "process_h5_path": process_h5_path,
-            "step_name": resume_from,
-            "dump_start_z": dump_start_z,
-            "dump_end_z": dump_end_z,
-        }
-        # Dont dump a step if we resume from this step
-        if resume_from in self.steps_to_save:
-            self.logger.warning(
-                "Processing is resumed from step '%s'. This step won't be dumped to a file" % resume_from
-            )
-            self.steps_to_save.remove(resume_from)
-            if resume_from == "sinogram":
-                self.dump_sinogram = False
-            else:
-                if resume_from in self.processing_options:  # should not happen
-                    self.processing_options[resume_from].pop("save")
-
-    def _check_dump_file(self, process_file, raise_on_error=False):
-        """
-        Return (start_z, end_z) on success
-        Return None on failure
-        """
-        # Ensure data in the file correspond to what is currently asked
-        if self.resume_from_step is None:
-            return None
-
-        # Check dataset shape/start_z/end_z
-        rec_cfg_h5_path = posixpath.join(
-            self.dataset_info.hdf5_entry or "entry",
-            self.resume_from_step,
-            "configuration/processing_options/reconstruction",
-        )
-        dump_start_z = get_h5_value(process_file, posixpath.join(rec_cfg_h5_path, "start_z"))
-        dump_end_z = get_h5_value(process_file, posixpath.join(rec_cfg_h5_path, "end_z"))
-        if dump_end_z < 0:
-            dump_end_z += self.radio_shape(binning=False)[0]
-        start_z, end_z = (
-            self.processing_options["reconstruction"]["start_z"],
-            self.processing_options["reconstruction"]["end_z"],
-        )
-        if not (dump_start_z <= start_z and end_z <= dump_end_z):
-            msg = (
-                "File %s was built with start_z=%d, end_z=%d but current configuration asks for start_z=%d, end_z=%d"
-                % (process_file, dump_start_z, dump_end_z, start_z, end_z)
-            )
-            if not raise_on_error:
-                self.logger.error(msg)
-                return None
-            self.logger.fatal(msg)
-            raise ValueError(msg)
-
-        # Check parameters other than reconstruction
-        filedump_nabu_config = import_h5_to_dict(
-            process_file,
-            posixpath.join(self.dataset_info.hdf5_entry or "entry", self.resume_from_step, "configuration/nabu_config"),
-        )
-        sections_to_ignore = ["reconstruction", "output", "pipeline"]
-        for section in sections_to_ignore:
-            filedump_nabu_config[section] = self.nabu_config[section]
-        # special case of the "save_steps process"
-        # filedump_nabu_config["pipeline"]["save_steps"] = self.nabu_config["pipeline"]["save_steps"]
-
-        diff = compare_dicts(filedump_nabu_config, self.nabu_config)
-        if diff is not None:
-            msg = "Nabu configuration in file %s differ from the current one: %s" % (process_file, diff)
-            if not raise_on_error:
-                self.logger.error(msg)
-                return None
-            self.logger.fatal(msg)
-            raise ValueError(msg)
-        #
-
-        return (dump_start_z, dump_end_z)
-
-    def get_save_steps_file(self, step_name=None):
-        if self.nabu_config["pipeline"]["steps_file"] not in (None, ""):
-            return self.nabu_config["pipeline"]["steps_file"]
-        nabu_save_options = self.nabu_config["output"]
-        output_dir = nabu_save_options["location"]
-        file_prefix = step_name + "_" + nabu_save_options["file_prefix"]
-        fname = os.path.join(output_dir, file_prefix) + ".hdf5"
-        return fname