Source code for silx.io.specfilewrapper

# coding: utf-8
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"""This module provides a backward compatibility layer with the legacy
specfile wrapper.

If you are starting a new project, please consider using :mod:`silx.io.specfile`
instead of this module.

If you want to use this module for an existing project that used the old
wrapper through PyMca, you can try replacing::

    from PyMca5.PyMcaIO import specfilewrapper

with::

    from silx.io import specfilewrapper

There might still be differences between this module and the old
wrapper, due to differences in the underlying implementation.
Any of these differences that break your code should be reported on
https://github.com/silx-kit/silx/issues

The documentation mentions only the methods and attributes that are different
from the ones in :class:`silx.io.specfile.SpecFile` and
:class:`silx.io.specfile.Scan`. You should refer to the documentation of these
base classes for more information.
"""
from silx.io.specfile import SpecFile, Scan

__authors__ = ["P. Knobel"]
__license__ = "MIT"
__date__ = "15/09/2016"


def _format_number_list(number_list):
    """Return string representation of a list of integers,
    using ``,`` as a separator and ``:`` as a range separator.
    """
    ret = ""
    first_in_range = number_list[0]
    last_in_range = number_list[0]
    previous = number_list[0]
    for number in number_list[1:]:
        if number - previous != 1:
            # reached end of range
            if last_in_range > first_in_range:
                ret += "%d:%d," % (first_in_range, last_in_range)
            # passed isolated number
            else:
                ret += "%d," % previous
            # reinitialize range
            first_in_range = number
            last_in_range = number
        else:
            # still inside a continuous range
            last_in_range = number

        previous = number

    # last number
    if last_in_range > first_in_range:
        ret += "%d:%d" % (first_in_range, last_in_range)
    else:
        ret += "%d" % previous

    return ret


[docs]class Specfile(SpecFile): """ This class is a subclass of :class:`silx.io.specfile.SpecFile`. It redefines following methods: - :meth:`__getitem__`: returns a :class:`scandata` object instead of a :class:`silx.io.specfile.Scan` object - :meth:`list`: returns a string representation of a list instead of a list of integers Following methods are added: - :meth:`select` - :meth:`scanno` - :meth:`allmotors` - :meth:`epoch` - :meth:`title` """ def __init__(self, filename): SpecFile.__init__(self, filename)
[docs] def __getitem__(self, key): """Get scan by 0-based index :param key: 0-based scan index :type key: int :return: Scan :rtype: :class:`scandata` """ if not isinstance(key, int): raise TypeError("Scan index must be an integer") scan_index = key # allow negative index, like lists if scan_index < 0: scan_index += len(self) if not 0 <= scan_index < len(self): msg = "Scan index must be in range 0-%d" % (len(self) - 1) raise IndexError(msg) return scandata(self, scan_index)
[docs] def list(self): """Return a string representation of a list of scan numbers. The scans numbers are listed in the order in which they appear in the file. Continuous ranges of scan numbers are represented as ``first:last``. For instance, let's assume our specfile contains following scans: *1, 2, 3, 4, 5, 684, 685, 687, 688, 689, 700, 688, 688*. This method will then return:: "1:5,684:685,687:689,700,688,688" """ number_list = SpecFile.list(self) return _format_number_list(number_list)
[docs] def select(self, key): """Get scan by ``n.m`` key :param key: ``"s.o"`` (scan number, scan order) :type key: str :return: Scan :rtype: :class:`scandata` """ msg = "Key must be a string 'N.M' with N being the scan" msg += " number and M the order (eg '2.3')." if not hasattr(key, "lower") or "." not in key: raise TypeError(msg) try: (number, order) = map(int, key.split(".")) scan_index = self.index(number, order) except (ValueError, IndexError): # self.index can raise an index error # int() can raise a value error raise KeyError(msg + "\nValid keys: '" + "', '".join(self.keys()) + "'") except AttributeError: # e.g. "AttrErr: 'float' object has no attribute 'split'" raise TypeError(msg) if not 0 <= scan_index < len(self): msg = "Scan index must be in range 0-%d" % (len(self) - 1) raise IndexError(msg) return scandata(self, scan_index)
[docs] def scanno(self): """Return the number of scans in the SpecFile This is an alias for :meth:`__len__`, for compatibility with the old specfile wrapper API. """ return len(self)
[docs] def allmotors(self, scan_index=0): """ This is an alias for :meth:`motor_names`, for compatibility with the old specfile wrapper API. """ return self.motor_names(scan_index)
[docs] def epoch(self): """:return: Epoch, from last word on file header line *#E* :rtype: int :raise: ValueError if *#E* line not found in header or last word on *#E* cannot be converted to type *int*""" fh = self.file_header() for line in fh: if line.startswith("#E "): return int(line.split()[-1]) raise ValueError("No #E header found in specfile")
[docs] def title(self): """:return: Title, from second field on *#C* header line (field are strings separated by two spaces) :rtype: str :raise: ValueError if *#C* line not found in header or line is empty""" fh = self.file_header() for line in fh: if line.startswith("#C "): line1 = line.lstrip("#C ") return line1.split(" ")[0] raise ValueError("No #C header found in specfile")
# # these functions exist in the old API but don't seem to be # # used, and are not easy to implement # def show(self): # raise NotImplementedError # # def user(self): # raise NotImplementedError # # def update(self): # raise NotImplementedError # PEP8 violation in class name is to respect old API
[docs]class scandata(Scan): # noqa """ This class is a subclass of :class:`silx.io.specfile.Scan`. It redefines following methods/attributes: - :meth:`data` becomes a method returning an array, instead of just an array - :meth:`mca`: becomes a method returning an array, instead of a :class:`silx.io.specfile.MCA` object - :meth:`header`: becomes a method returning a list of **scan** header lines (or a list of a single header line, if a key is specified), instead of just a list of all header lines Following methods are added: - :meth:`allmotors` - :meth:`allmotorpos` - :meth:`alllabels` - :meth:`cols` - :meth:`lines` - :meth:`command` - :meth:`date` - :meth:`datacol` - :meth:`dataline` - :meth:`fileheader` - :meth:`nbmca` """ def __init__(self, specfile, scan_index): Scan.__init__(self, specfile, scan_index)
[docs] def allmotors(self): """Return a list of all motor names (identical to :attr:`motor_names`). """ return self.motor_names
[docs] def allmotorpos(self): """Return a list of all motor positions (identical to :attr:`motor_positions`). """ return self.motor_positions
[docs] def alllabels(self): """ Return a list of all labels (:attr:`labels`). """ return self.labels
[docs] def cols(self): """Return the number of data columns (number of detectors)""" return super(scandata, self).data.shape[1]
[docs] def command(self): """Return the command called for this scan (``#S`` header line)""" return self._specfile.command(self._index)
[docs] def data(self): """Return the data in this scan as a 2D numpy array. The first index corresponds to the columns/detectors in the original file, and the second index is the row index from the original file. Indices are 0-based. For instance, this is how you access the 18th data sample for the 3rd detector (assuming ``sc`` is your scan object): >>> scdata = sc.data() >>> data_sample = scdata[2, 17]""" return super(scandata, self).data
[docs] def datacol(self, col): """Return a data column (all data for one detector) :param col: column number (1-based index)""" return super(scandata, self).data[col - 1, :]
[docs] def dataline(self, line): """Return a data line (one sample for all detectors) :param line: line number (1-based index)""" return super(scandata, self).data[:, line - 1]
[docs] def date(self): """Return the date from the scan header line ``#D``""" return self._specfile.date(self._index)
[docs] def fileheader(self, key=''): # noqa """Return a list of file header lines""" # key is there for compatibility return self.file_header
[docs] def header(self, key=""): """Return a list of scan header lines if no key is specified. If a valid key is specified, return a list of a single header line. :param key: Header key (e.g. ``S, N, L, @CALIB``…) If ``key`` is an empty string, return complete list of scan header lines. If ``key`` does not match any header line, return empty list. :return: List of scan header lines :rtype: List[str] """ if key.strip() == "": return self.scan_header if self.record_exists_in_hdr(key): prefix = "#" + key + " " # there is no leading @ in self.mca_header_dict keys key_mca_dict = key.lstrip("@") if key.startswith("@") else None if key_mca_dict in self.mca_header_dict: return [prefix + self.mca_header_dict[key_mca_dict]] elif key in self.scan_header_dict: return [prefix + self.scan_header_dict[key]] elif key in self.file_header_dict: return [prefix + self.file_header_dict[key]] elif self.record_exists_in_hdr("@" + key): # in case key is a mca header key without the @ if key in self.mca_header_dict: prefix = "#@" + key + " " return [prefix + self.mca_header_dict[key]] return []
[docs] def lines(self): """Return the number of data lines (number of data points per detector)""" return super(scandata, self).data.shape[0]
[docs] def mca(self, number): """Return one MCA spectrum :param number: MCA number (1-based index) :rtype: 1D numpy array""" # in the base class, mca is an object that can be indexed (but 0-based) return super(scandata, self).mca[number - 1]
[docs] def nbmca(self): """Return number of MCAs in this scan""" return len(super(scandata, self).mca)