edfscan.py

# coding: utf-8
# /*##########################################################################
# Copyright (C) 2016-2020 European Synchrotron Radiation Facility
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# 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
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"""contains EDFTomoScan, class to be used with EDF acquisition"""


__authors__ = ["H.Payno"]
__license__ = "MIT"
__date__ = "10/10/2019"


import os
import re
import fabio
import copy
from lxml import etree
import json
import io
from typing import Union, Iterable
from ..scanbase import TomoScanBase
from .utils import get_parameters_frm_par_or_info, extract_urls_from_edf
from ..unitsystem.metricsystem import MetricSystem
from ..utils import docstring
import logging

_logger = logging.getLogger(__name__)


class EDFTomoScan(TomoScanBase):
    """
    TomoScanBase instanciation for scan defined from .edf files

    :param scan: path to the root folder containing the scan.
    :type scan: Union[str,None]
    :param n_frames: Number of frames in each EDF file.
        If not provided, it will be inferred by reading the files.
        In this case, the frame number is guessed from the file name.
    :type n_frames: Union[int, None]=None
    """

    _TYPE = "edf"

    INFO_EXT = ".info"

    ABORT_FILE = ".abo"

    _REFHST_PREFIX = "refHST"

    _DARKHST_PREFIX = "dark.edf"

    _SCHEME = "fabio"

    def __init__(
        self,
        scan: Union[str, None],
        n_frames: Union[int, None] = None,
        ignore_projections: Union[None, Iterable] = None,
    ):
        TomoScanBase.__init__(
            self, scan=scan, type_=self._TYPE, ignore_projections=ignore_projections
        )

        # data caches
        self._darks = None
        self._flats = None
        self.__tomo_n = None
        self.__ref_n = None
        self.__dark_n = None
        self.__dim1 = None
        self.__dim2 = None
        self.__pixel_size = None
        self.__ref_on = None
        self.__scan_range = None
        self._edf_n_frames = n_frames
        self.__distance = None
        self.__energy = None
        self.__estimated_cor_frm_motor = None
        self.update()

    @docstring(TomoScanBase.clear_caches)
    def clear_caches(self):
        super().clear_caches()
        self._darks = None
        self._flats = None
        self._projections = None
        self.__tomo_n = None
        self.__ref_n = None
        self.__dark_n = None
        self.__dim1 = None
        self.__dim2 = None
        self.__pixel_size = None
        self.__ref_on = None
        self.__scan_range = None

    @docstring(TomoScanBase.tomo_n)
    @property
    def tomo_n(self) -> Union[None, int]:
        if self.__tomo_n is None:
            self.__tomo_n = EDFTomoScan.get_tomo_n(scan=self.path)
        return self.__tomo_n

    @property
    @docstring(TomoScanBase.dark_n)
    def dark_n(self) -> Union[None, int]:
        if self.__dark_n is None:
            self.__dark_n = EDFTomoScan.get_dark_n(scan=self.path)
        return self.__dark_n

    @property
    @docstring(TomoScanBase.ref_n)
    def ref_n(self) -> Union[None, int]:
        if self.__ref_n is None:
            self.__ref_n = EDFTomoScan.get_ref_n(scan=self.path)
        return self.__ref_n

    @property
    @docstring(TomoScanBase.pixel_size)
    def pixel_size(self) -> Union[None, int]:
        """

        :return: pixel size
        :rtype: float
        """
        if self.__pixel_size is None:
            self.__pixel_size = EDFTomoScan._get_pixel_size(scan=self.path)
        return self.__pixel_size

    @property
    @docstring(TomoScanBase.dim_1)
    def dim_1(self) -> Union[None, int]:
        """

        :return: image dim1
        :rtype: int
        """
        if self.__dim1 is None and self.path is not None:
            self.__dim1, self.__dim2 = EDFTomoScan.get_dim1_dim2(scan=self.path)
        return self.__dim1

    @property
    @docstring(TomoScanBase.dim_2)
    def dim_2(self) -> Union[None, int]:
        """

        :return: image dim2
        :rtype: int
        """
        if self.__dim2 is None and self.path is not None:
            self.__dim1, self.__dim2 = EDFTomoScan.get_dim1_dim2(scan=self.path)
        return self.__dim2

    @property
    @docstring(TomoScanBase.x_translation)
    def x_translation(self) -> Union[None, tuple]:
        raise NotImplementedError("Not supported for EDF")

    @property
    @docstring(TomoScanBase.y_translation)
    def y_translation(self) -> Union[None, tuple]:
        raise NotImplementedError("Not supported for EDF")

    @property
    @docstring(TomoScanBase.z_translation)
    def z_translation(self) -> Union[None, tuple]:
        raise NotImplementedError("Not supported for EDF")

    @property
    @docstring(TomoScanBase.ff_interval)
    def ff_interval(self) -> Union[None, int]:
        if self.__ref_on is None and self.path is not None:
            self.__ref_on = EDFTomoScan.get_ff_interval(scan=self.path)
        return self.__ref_on

    @property
    @docstring(TomoScanBase.scan_range)
    def scan_range(self) -> Union[None, int]:
        if self.__scan_range is None and self.path is not None:
            self.__scan_range = EDFTomoScan.get_scan_range(scan=self.path)
        return self.__scan_range

    @property
    @docstring(TomoScanBase.flats)
    def flats(self) -> Union[None, dict]:
        """
        flats are given as a dictionary with index as key and DataUrl as
        value"""
        if self._flats is None and self.path is not None:
            self._flats = self.get_refs_url(scan_path=self.path)
        return self._flats

    @docstring(TomoScanBase.is_tomoscan_dir)
    @staticmethod
    def is_tomoscan_dir(directory: str, **kwargs) -> bool:
        return os.path.isfile(
            EDFTomoScan.get_info_file(directory=directory, kwargs=kwargs)
        )

    @staticmethod
    def get_info_file(directory: str, **kwargs) -> str:
        basename = os.path.basename(directory)
        assert basename != ""
        info_file = os.path.join(directory, basename + EDFTomoScan.INFO_EXT)

        if "src_pattern" in kwargs and kwargs["srx_pattern"] is not None:
            assert "dest_pattern" in kwargs
            info_file = info_file.replace(
                kwargs["src_pattern"], kwargs["dest_pattern"], 1
            )
        return info_file

    @docstring(TomoScanBase.is_abort)
    def is_abort(self, **kwargs) -> bool:
        abort_file = os.path.basename(self.path) + self.ABORT_FILE
        abort_file = os.path.join(self.path, abort_file)
        if "src_pattern" in kwargs and kwargs["src_pattern"] is not None:
            assert "dest_pattern" in kwargs
            abort_file = abort_file.replace(
                kwargs["src_pattern"], kwargs["dest_pattern"]
            )
        return os.path.isfile(abort_file)

    @property
    @docstring(TomoScanBase.darks)
    def darks(self) -> dict:
        if self._darks is None and self.path is not None:
            self._darks = self.get_darks_url(scan_path=self.path)
        return self._darks

    @docstring(TomoScanBase.get_proj_angle_url)
    def get_proj_angle_url(self) -> dict:
        # TODO: we might use fabio.open_serie instead
        if self.path is None:
            _logger.warning(
                "no path specified for scan, unable to retrieve" " the projections"
            )
            return {}
        n_projection = self.tomo_n
        data_urls = EDFTomoScan.get_proj_urls(self.path)
        return TomoScanBase.map_urls_on_scan_range(
            urls=data_urls, n_projection=n_projection, scan_range=self.scan_range
        )

    @docstring(TomoScanBase.update)
    def update(self):
        if self.path is not None:
            all_projections = EDFTomoScan.get_proj_urls(
                self.path, n_frames=self._edf_n_frames
            )

            def select_proj(ddict, from_, to_):
                indexes = sorted(set(ddict.keys()))
                sel_indexes = indexes[from_:to_]
                res = {}
                for index in sel_indexes:
                    res[index] = ddict[index]
                return res

            if self.tomo_n is not None and len(all_projections) > self.tomo_n:
                self._projections = select_proj(all_projections, 0, self.tomo_n)
                self._alignment_projections = select_proj(
                    all_projections, self.tomo_n, None
                )
            else:
                self._projections = all_projections
                self._alignment_projections = {}
            if self.ignore_projections is not None:
                for idx in self.ignore_projections:
                    self._projections.pop(idx, None)

            self._darks = EDFTomoScan.get_darks_url(self.path)
            self._flats = EDFTomoScan.get_refs_url(self.path)

    @docstring(TomoScanBase.load_from_dict)
    def load_from_dict(self, desc: Union[dict, io.TextIOWrapper]):
        if isinstance(desc, io.TextIOWrapper):
            data = json.load(desc)
        else:
            data = desc
        if not (self.DICT_TYPE_KEY in data and data[self.DICT_TYPE_KEY] == self._TYPE):
            raise ValueError("Description is not an EDFScan json description")

        assert self.DICT_PATH_KEY in data
        self.path = data[self.DICT_PATH_KEY]
        return self

    @staticmethod
    def get_proj_urls(scan: str, n_frames: Union[int, None] = None) -> dict:
        """
        Return the dict of radios / projection for the given scan.
        Keys of the dictionary is the slice number
        Return all the file on the root of scan starting by the name of scan and
        ending by .edf

        :param scan: is the path to the folder of acquisition
        :type scan: str
        :param n_frames: Number of frames in each EDF file.
            If not provided, it is inferred by reading each file.
        :type n_frames: int
        :return: dict of radios files with radio index as key and file as value
        :rtype: dict
        """
        urls = dict({})
        if (scan is None) or not (os.path.isdir(scan)):
            return urls

        if os.path.isdir(scan):
            for f in os.listdir(scan):
                if EDFTomoScan.is_a_proj_path(fileName=f, scanID=scan):
                    gfile = os.path.join(scan, f)
                    index = EDFTomoScan.guess_index_frm_file_name(
                        gfile, basename=os.path.basename(scan)
                    )
                    urls.update(
                        extract_urls_from_edf(
                            start_index=index, file_=gfile, n_frames=n_frames
                        )
                    )

        return urls

    @staticmethod
    def is_a_proj_path(fileName: str, scanID: str) -> bool:
        """Return True if the given fileName can fit to a Radio name"""
        fileBasename = os.path.basename(fileName)
        folderBasename = os.path.basename(scanID)

        if fileBasename.endswith(".edf") and fileBasename.startswith(folderBasename):
            localstring = fileName.rstrip(".edf")
            # remove the scan
            localstring = re.sub(folderBasename, "", localstring)
            if "slice_" in localstring:
                # case of a reconstructed file
                return False
            if "refHST" in localstring:
                return False
            s = localstring.split("_")
            if s[-1].isdigit():
                # check that the next value is a digit
                return True

        return False

    @staticmethod
    def guess_index_frm_file_name(_file: str, basename: str) -> Union[None, int]:
        """
        Guess the index of the file. Index is most of the an integer but can be
        a float for 'ref' for example if several are taken.

        :param _file:
        :param basename:
        """

        def extract_index(my_str, type_):
            res = []
            modified_str = copy.copy(my_str)
            while modified_str != "" and modified_str[-1].isdigit():
                res.append(modified_str[-1])
                modified_str = modified_str[:-1]
            if len(res) == 0:
                return None, modified_str
            else:
                orignalOrder = res[::-1]
                if type_ is int:
                    return int("".join(orignalOrder)), modified_str
                else:
                    return float(".".join(("0", "".join(orignalOrder)))), modified_str

        _file = os.path.basename(_file)
        if _file.endswith(".edf"):
            name = _file.replace(basename, "", 1)
            name = name.rstrip(".edf")

            part_1, name = extract_index(name, type_=int)
            if name.endswith("_"):
                name = name.rstrip("_")
                part_2, name = extract_index(name, type_=float)
            else:
                part_2 = None

            if part_1 is None:
                return None
            if part_2 is None:
                if part_1 is None:
                    return None
                else:
                    return int(part_1)
            else:
                return float(part_1) + part_2
        else:
            raise ValueError("only edf files are managed")

    @staticmethod
    def get_tomo_n(scan: str) -> Union[None, int]:
        return EDFTomoScan.retrieve_information(
            scan=os.path.abspath(scan),
            ref_file=None,
            key="TOMO_N",
            type_=int,
            key_aliases=["tomo_N", "Tomo_N"],
        )

    @staticmethod
    def get_dark_n(scan: str) -> Union[None, int]:
        return EDFTomoScan.retrieve_information(
            scan=os.path.abspath(scan),
            ref_file=None,
            key="DARK_N",
            type_=int,
            key_aliases=[
                "dark_N",
            ],
        )

    @staticmethod
    def get_ref_n(scan: str) -> Union[None, int]:
        return EDFTomoScan.retrieve_information(
            scan=os.path.abspath(scan),
            ref_file=None,
            key="REF_N",
            type_=int,
            key_aliases=[
                "ref_N",
            ],
        )

    @staticmethod
    def get_ff_interval(scan: str) -> Union[None, int]:
        return EDFTomoScan.retrieve_information(
            scan=os.path.abspath(scan),
            ref_file=None,
            key="REF_ON",
            type_=int,
            key_aliases=[
                "ref_On",
            ],
        )

    @staticmethod
    def get_scan_range(scan: str) -> Union[None, int]:
        return EDFTomoScan.retrieve_information(
            scan=os.path.abspath(scan),
            ref_file=None,
            key="ScanRange",
            type_=int,
            key_aliases=[
                "scanRange",
            ],
        )

    @staticmethod
    def get_dim1_dim2(scan: str) -> Union[None, tuple]:
        _info_file = os.path.join(scan, os.path.basename(scan) + ".info")
        d1 = EDFTomoScan.retrieve_information(
            scan=os.path.abspath(scan),
            ref_file=None,
            key="Dim_1",
            key_aliases=["projectionSize/DIM_1"],
            type_=int,
        )
        d2 = EDFTomoScan.retrieve_information(
            scan=os.path.abspath(scan),
            ref_file=None,
            key="Dim_2",
            key_aliases=["projectionSize/DIM_2"],
            type_=int,
        )

        return d1, d2

    @property
    @docstring(TomoScanBase.distance)
    def distance(self) -> Union[None, float]:
        if self.__distance is None:
            self.__distance = EDFTomoScan.retrieve_information(
                self.path, None, "Distance", type_=float, key_aliases=("distance",)
            )
        if self.__distance is None:
            return None
        else:
            return self.__distance * MetricSystem.MILLIMETER.value

    @property
    @docstring(TomoScanBase.field_of_view)
    def field_of_view(self):
        # not managed for EDF files
        return None

    @property
    @docstring(TomoScanBase.estimated_cor_frm_motor)
    def estimated_cor_frm_motor(self):
        # not managed for EDF files
        return None

    @property
    @docstring(TomoScanBase.energy)
    def energy(self):
        if self.__energy is None:
            self.__energy = EDFTomoScan.retrieve_information(
                self.path, None, "Energy", type_=float, key_aliases=("energy",)
            )
        return self.__energy

    @staticmethod
    def _get_pixel_size(scan: str) -> Union[None, float]:
        if os.path.isdir(scan) is False:
            return None
        value = EDFTomoScan.retrieve_information(
            scan=scan,
            ref_file=None,
            key="PixelSize",
            type_=float,
            key_aliases=[
                "pixelSize",
            ],
        )
        if value is None:
            parFile = os.path.join(scan, os.path.basename(scan) + ".par")
            if os.path.exists(parFile):
                try:
                    ddict = get_parameters_frm_par_or_info(parFile)
                except ValueError as e:
                    _logger.error(e)
                if "IMAGE_PIXEL_SIZE_1".lower() in ddict:
                    value = float(ddict["IMAGE_PIXEL_SIZE_1".lower()])
        # for now pixel size are stored in microns.
        # We want to return them in meter
        if value is not None:
            return value * MetricSystem.MICROMETER.value
        else:
            return None

    @staticmethod
    def get_darks_url(
        scan_path: str, prefix: str = "dark", file_ext: str = ".edf"
    ) -> dict:
        """

        :param scan_path:
        :type scan_path: str
        :param prefix: ref / flat field file prefix
        :type prefix: str
        :param file_ext: ref / flat field file extension
        :type file_ext: str
        :return: list of refs as silx's `DataUrl`
        """
        res = {}
        if os.path.isdir(scan_path) is False:
            _logger.error(
                scan_path + " is not a directory. Cannot extract " "DarkHST files"
            )
            return res
        for file_ in os.listdir(scan_path):
            _prefix = prefix
            if prefix.endswith(file_ext):
                _prefix = prefix.rstrip(file_ext)
            if file_.startswith(_prefix) and file_.endswith(file_ext):
                # usuelly the dark file name should be dark.edf, but some
                # darkHSTXXXX remains...
                file_fp = file_.lstrip(_prefix).rstrip(file_ext).lstrip("HST")
                if file_fp == "" or file_fp.isnumeric() is True:
                    index = EDFTomoScan.guess_index_frm_file_name(
                        _file=file_, basename=os.path.basename(scan_path)
                    )
                    urls = extract_urls_from_edf(
                        os.path.join(scan_path, file_), start_index=index
                    )
                    res.update(urls)
        return res

    @staticmethod
    def get_refs_url(
        scan_path: str, prefix: str = "refHST", file_ext: str = ".edf", ignore=None
    ) -> dict:
        """

        :param scan_path:
        :type scan_path: str
        :param prefix: ref / flat field file prefix
        :type prefix: str
        :param file_ext: ref / flat field file extension
        :type file_ext: str
        :return: list of refs as silx's `DataUrl`
        """
        res = {}
        if os.path.isdir(scan_path) is False:
            _logger.error(
                scan_path + " is not a directory. Cannot extract " "RefHST files"
            )
            return res

        def get_next_free_index(key, keys):
            """return next free key from keys by converting it to a string
            with `key_value (n)` after it
            """
            new_key = key
            index = 2
            while new_key in keys:
                new_key = "%s (%s)" % (key, index)
                index += 1
            return new_key

        def ignore_file(file_name, to_ignore):
            if to_ignore is None:
                return False
            for pattern in to_ignore:
                if pattern in file_name:
                    return True
            return False

        for file_ in os.listdir(scan_path):
            if (
                file_.startswith(prefix)
                and file_.endswith(file_ext)
                and not ignore_file(file_, ignore)
            ):
                index = EDFTomoScan.guess_index_frm_file_name(
                    _file=file_, basename=os.path.basename(scan_path)
                )
                file_fp = os.path.join(scan_path, file_)
                urls = extract_urls_from_edf(start_index=index, file_=file_fp)
                for key in urls:
                    if key in res:
                        key_ = get_next_free_index(key, res.keys())
                    else:
                        key_ = key
                    res[key_] = urls[key]
        return res

    @staticmethod
    def retrieve_information(
        scan: str,
        ref_file: Union[str, None],
        key: str,
        type_: type,
        key_aliases: Union[list, tuple, None] = None,
    ):
        """
        Try to retrieve information a .info file, an .xml or a flat field file.

        file.
        Look for the key 'key' or one of it aliases.

        :param scan: root folder of an acquisition. Must be an absolute path
        :param ref_file: the refXXXX_YYYY which should contain information
                         about the scan.
        :param key: the key (information) we are looking for
        :type key: str
        :param type_: requestde out type if the information is found
        :type type_: return type if the information is found.
        :param key_aliases: aliases of the key in the different file
        :type key_aliases: list
        :return: the requested information or None if not found
        """
        info_aliases = [key]
        if key_aliases is not None:
            assert type(key_aliases) in (tuple, list)
            [info_aliases.append(alias) for alias in key_aliases]

        if not os.path.isdir(scan):
            return None

        # 1st look for ref file if any given
        def parseRefFile(filePath):
            header = fabio.open(filePath).header
            for k in key_aliases:
                if k in header:
                    return type_(header[k])
            return None

        if ref_file is not None and os.path.isfile(ref_file):
            try:
                info = parseRefFile(ref_file)
            except IOError as e:
                _logger.warning(e)
            else:
                if info is not None:
                    return info

        # 2nd look for .info file
        def parseInfoFile(filePath):
            def extractInformation(text, alias):
                text = text.replace(alias, "")
                text = text.replace("\n", "")
                text = text.replace(" ", "")
                text = text.replace("=", "")
                return type_(text)

            info = None
            f = open(filePath, "r")
            line = f.readline()
            while line:
                for alias in info_aliases:
                    if alias in line:
                        info = extractInformation(line, alias)
                        break
                line = f.readline()
            f.close()
            return info

        baseName = os.path.basename(scan)
        infoFiles = [os.path.join(scan, baseName + ".info")]
        infoOnDataVisitor = infoFiles[0].replace("lbsram", "")
        # hack to check in lbsram, would need to be removed to add some consistency
        if os.path.isfile(infoOnDataVisitor):
            infoFiles.append(infoOnDataVisitor)
        for infoFile in infoFiles:
            if os.path.isfile(infoFile) is True:
                info = parseInfoFile(infoFile)
                if info is not None:
                    return info

        # 3td look for xml files
        def parseXMLFile(filePath):
            try:
                for alias in info_aliases:
                    tree = etree.parse(filePath)
                    elmt = tree.find("acquisition/" + alias)
                    if elmt is None:
                        continue
                    else:
                        info = type_(elmt.text)
                        if info == -1:
                            return None
                        else:
                            return info
            except etree.XMLSyntaxError as e:
                _logger.warning(e)
                return None

        xmlFiles = [os.path.join(scan, baseName + ".xml")]
        xmlOnDataVisitor = xmlFiles[0].replace("lbsram", "")
        # hack to check in lbsram, would need to be removed to add some consistency
        if os.path.isfile(xmlOnDataVisitor):
            xmlFiles.append(xmlOnDataVisitor)
        for xmlFile in xmlFiles:
            if os.path.isfile(xmlFile) is True:
                info = parseXMLFile(xmlFile)
                if info is not None:
                    return info

        return None

    def get_range(self):
        if self.path is not None:
            return self.get_scan_range(self.path)
        else:
            return None