# Copyright (c) 2019 Fabien Georget <fabien.georget@epfl.ch>, EPFL
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# 1. Redistributions of source code must retain the above copyright notice,
# this list of conditions and the following disclaimer.
#
# 2. Redistributions in binary form must reproduce the above copyright notice,
# this list of conditions and the following disclaimer in the documentation
# and/or other materials provided with the distribution.
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# 3. Neither the name of the copyright holder nor the names of its contributors
# may be used to endorse or promote products derived from this software without
# specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
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# POSSIBILITY OF SUCH DAMAGE.
"""
This module provides raw loading and saving helper functions.
It defines how the maps are read before any transformation from the algorithm.
Example: Read txt format from bruker Esprit software::
bse_map_asarray = load_txt_map("map234_BSE.txt", esprit_ascii_map_format)
"""
import csv
import numpy as np
__all__ = ["TextMapFormat",
"esprit_ascii_map_format", "esprit_ascii_bse_format",
"aztec_ascii_map_format", "aztec_ascii_bse_format",
"imagej_ascii_bse_format",
"load_txt_map", "save_txt_map",
"load_pickle_map", "save_pickle_map"
]
[docs]class TextMapFormat:
"""A struct-like class to contain formatting information about raw
EDS maps.
"""
def __init__(self, delimiter, min_value, max_value, saveformat="%.4f"):
"""
:param delimiter: delimiter between cells
:param max_value: maximum value possible
:param min_value: minimum value possible
:param saveformat: format used when saving a map
"""
self._delimiter = delimiter
self._max_value = max_value
self._min_value = min_value
self._saveformat = saveformat
def __str__(self):
return "TextMapFormat('{0}',{1},{2})".format(
self.escaped_delimiter, self.min_value, self.max_value)
def __repr__(self):
return "TextMapFormat('{0}',{1},{2})".format(
self.escaped_delimiter, self.min_value, self.max_value)
@property
def delimiter(self):
"""Return the column delimiter"""
return self._delimiter
@delimiter.setter
def delimiter(self, value):
"""Set the column delimiter"""
self._delimiter = value
@property
def escaped_delimiter(self):
"""Return an escaped version of the delimiter"""
if self._delimiter == "\t":
return "\\t"
else:
return self._delimiter
@escaped_delimiter.setter
def escaped_delimiter(self, value):
if value == "\\t":
self._delimiter = "\t"
else:
self._delimiter = value
@property
def max_value(self):
"""Return the maximum value allowed in the map"""
return self._max_value
@max_value.setter
def max_value(self, value):
"""Set the maximum value allowed in the map"""
self._max_value = value
@property
def min_value(self):
"""Return the minimum value allowed in the map"""
return self._min_value
@min_value.setter
def min_value(self, value):
"""Set the minimum value allowed in the map"""
self._min_value = value
@property
def saveformat(self):
"""Set the save format"""
return self._saveformat
@saveformat.setter
def saveformat(self, astring):
"""Set the save format"""
self._saveformat = astring
[docs] def copy(self):
"""Copy the format
:returns: a copy of the text map format
"""
return TextMapFormat(self.delimiter, self.min_value, self.max_value, self.saveformat)
#: Default EDS map format for the Bruker Esprit software
esprit_ascii_map_format = TextMapFormat(delimiter=";", min_value=0, max_value=100)
#: Default BSE map format for the Bruker Esprit software
esprit_ascii_bse_format = TextMapFormat(delimiter=";", min_value=0, max_value=-1)
#: Default EDS map format for the Oxford Aztec software
aztec_ascii_map_format = TextMapFormat(delimiter=",", min_value=0, max_value=100)
#: Default BSE map format for the Oxford Aztec software
aztec_ascii_bse_format = TextMapFormat(delimiter=",", min_value=0, max_value=-1)
#: Format for a text image produced by ImageJ
imagej_ascii_bse_format = TextMapFormat(delimiter="\t", min_value=0, max_value=-1)
def guess_delimiter(filename):
"""Guess the delimiter used by a CSV-type format.
Use python CSV sniffer."""
with open(filename, newline='') as csvfile:
dialect = csv.Sniffer().sniff(csvfile.read(1024))
return dialect.delimiter
def guess_format(filename, min_value=None, max_value=None):
"""Guess the TextMapFormat for a file"""
delim = guess_delimiter(filename)
if min_value is None:
min_value = 0
if max_value is None:
max_value = -1
return TextMapFormat(delimiter=delim, min_value=min_value, max_value=max_value)
[docs]def load_txt_map(filename, txtformat, resize=1):
"""Load a 2D map
:param filename: filepath to the text map
:param txtformat: the format of the text map
:param resize: Stretch the map in each axis)
:returns: a 2D numpy array normalized between [0,1]
:raises: whatever numpy.loadtxt can raise
"""
data = np.genfromtxt(filename, delimiter=txtformat.delimiter, dtype=np.float)
data = data[:,~np.all(np.isnan(data), axis=0)] # remove nan columns
# normalize to [0,1]
if txtformat.max_value==-1:
data = (data-txtformat.min_value)/(data.max()-txtformat.min_value)
else:
data = (data-txtformat.min_value)/(txtformat.max_value-txtformat.min_value)
data = np.clip(data, 0.0, 1.0)
if resize > 1:
data = np.kron(data,np.ones((resize,resize)))
return data
[docs]def save_txt_map(filename, amap, txtformat):
"""Save a 2D map
Perform a copy first to normalize the data according the format.
:param filename: filepath to the file
:param amap: a 2D map
:format txtformat: the format of the ascii saved map
"""
data = amap.copy()
data = data*(txtformat.max_value-txtformat.min_value)+txtformat.min_value
np.savetxt(filename, data, delimiter=txtformat.delimiter, fmt=txtformat.saveformat)
[docs]def load_pickle_map(filepath):
"""Load a map that was previously saved as a pickle dump"""
return np.load(filepath)
[docs]def save_pickle_map(filepath, data):
"""Dump a map in a binary format"""
np.save(filepath, data)
