diffpy.srfit 3.1.0__py3-none-any.whl

diffpy/srfit/fitbase/profileparser.py

@@ -0,0 +1,179 @@
+#!/usr/bin/env python
+##############################################################################
+#
+# diffpy.srfit      by DANSE Diffraction group
+#                   Simon J. L. Billinge
+#                   (c) 2008 The Trustees of Columbia University
+#                   in the City of New York.  All rights reserved.
+#
+# File coded by:    Chris Farrow
+#
+# See AUTHORS.txt for a list of people who contributed.
+# See LICENSE_DANSE.txt for license information.
+#
+##############################################################################
+"""This module contains classes for parsing profiles from files.
+
+ProfileParser is a base class for parsing data. It can interact with a
+Profile object to automatically set the Profile's data and metadata.
+Each specific file format must be encapsulated in a ProfileParser
+subclass.
+
+See the class documentation for more information.
+"""
+
+
+from diffpy.srfit.exceptions import ParseError
+
+
+class ProfileParser(object):
+    """Class for parsing data from a or string.
+
+    Attributes
+
+    _format     --  Name of the data format that this parses (string, default
+                    ""). The format string is a unique identifier for the data
+                    format handled by the parser.
+    _banks      --  The data from each bank. Each bank contains a (x, y, dx,
+                    dy)
+                    tuple:
+                    x       --  A numpy array containing the independent
+                                variable read from the file.
+                    y       --  A numpy array containing the profile
+                                from the file.
+                    dx      --  A numpy array containing the uncertainty in x
+                                read from the file. This is None if the
+                                uncertainty cannot be read.
+                    dy      --  A numpy array containing the uncertainty read
+                                from the file. This is None if the uncertainty
+                                cannot be read.
+    _x          --  Independent variable from the chosen bank
+    _y          --  Profile from the chosen bank
+    _dx         --  Uncertainty in independent variable from the chosen bank
+    _dy         --  Uncertainty in profile from the chosen bank
+    _meta       --  A dictionary containing metadata read from the file.
+
+    General Metadata
+
+    filename    --  The name of the file from which data was parsed. This key
+                    will not exist if data was not read from file.
+    nbanks      --  The number of banks parsed.
+    bank        --  The chosen bank number.
+    """
+
+    _format = ""
+
+    def __init__(self):
+        """Initialize the attributes."""
+        self._banks = []
+        self._meta = {}
+        self._x = None
+        self._y = None
+        self._dx = None
+        self._dy = None
+        return
+
+    def getFormat(self):
+        """Get the format string."""
+        return self._format
+
+    def parseString(self, patstring):
+        """Parse a string and set the _x, _y, _dx, _dy and _meta variables.
+
+        When _dx or _dy cannot be obtained in the data format it is set to
+        None.
+
+        This wipes out the currently loaded data and selected bank number.
+
+        Arguments
+        patstring   --  A string containing the pattern
+
+        Raises ParseError if the string cannot be parsed
+        """
+        raise NotImplementedError()
+
+    def parseFile(self, filename):
+        """Parse a file and set the _x, _y, _dx, _dy and _meta variables.
+
+        This wipes out the currently loaded data and selected bank number.
+
+        Arguments
+        filename    --  The name of the file to parse
+
+        Raises IOError if the file cannot be read
+        Raises ParseError if the file cannot be parsed
+        """
+        infile = open(filename, "r")
+        self._banks = []
+        self._meta = {}
+        filestring = infile.read()
+        self.parseString(filestring)
+        infile.close()
+        self._meta["filename"] = filename
+
+        if len(self._banks) < 1:
+            raise ParseError("There are no data in the banks")
+
+        self.selectBank(0)
+        return
+
+    def getNumBanks(self):
+        """Get the number of banks read by the parser."""
+        return len(self._banks)
+
+    def selectBank(self, index):
+        """Select which bank to use.
+
+        This method should only be called after the data has been parsed.  The
+        chosen bank number is not persistent, and so must be re-selected if the
+        parser is used to parse more data. This uses python list notation, so
+        index -n returns the nth bank from the end.
+
+        Arguments:
+        index  --  index of bank (integer, starting at 0).
+
+        Raises IndexError if requesting a bank that does not exist
+        """
+        if index is None:
+            index = self._meta.get("bank", 0)
+
+        numbanks = self.getNumBanks()
+        if index > numbanks:
+            raise IndexError("Bank index out of range")
+
+        if index < 0:
+            index += numbanks
+
+        if index < 0:
+            raise IndexError("Bank index out of range")
+
+        self._meta["bank"] = index
+        self._meta["nbanks"] = numbanks
+        self._x, self._y, self._dx, self._dy = self._banks[index]
+        return
+
+    def getData(self, index=None):
+        """Get the data.
+
+        This method should only be called after the data has been parsed.  The
+        chosen bank number is not persistent, and so must be re-selected if the
+        parser is used to parse more data. This uses python list notation, so
+        index -n returns the nth bank from the end.
+
+        Arguments:
+        index  --   index of bank (integer, starting at 0, default None). If
+                    index is None then the currently selected bank is used.
+
+        This returns (x, y, dx, dy) tuple for the bank. dx is 0 if it cannot
+        be determined from the data format.
+        """
+        self.selectBank(index)
+
+        return self._x, self._y, self._dx, self._dy
+
+    def getMetaData(self):
+        """Get the parsed metadata."""
+        return self._meta
+
+
+# End of ProfileParser