# Copyright (c) 2019 Fabien Georget <fabien.georget@epfl.ch>, EPFL
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"""
This module contains the utilities to describe an experiment.
The main class is :class:`edxia.core.experiment.MappingExperiment`.
"""
from ..utils import path
from ..io import raw_io
[docs]class MappingExperiment:
"""This class contains the main information describing an experiment, such
as the filepaths, the map formats, the list of components... This class is
shared between many other classes.
Example:
exp = MappingExperiment("mymap_{components}.csv", label="OPC 28d")
:param str pattern: the pattern of the file paths
:param label: short, unique label for this set of map
:type label: str or None
:param str description: optional, longer description
:type description: str or None
:param map_format: the file format of the raw EDS maps.
:type map_format: edxia.io.raw_io.TextMapFormat
:param bse_format: the file format of the raw EDS maps.
:type bse_format: edxia.io.raw_io.TextMapFormat
:param list[str] components: list of available components for this experiment
"""
_exp_number=0 # variable for automatic labelling of experiments
def __init__(self, pattern,
label=None,
description=None,
map_format=None, bse_format=None,
map_scale_factor=1,
components=None):
self._pattern = pattern
if description is None:
description = ""
if label is None:
label = str(MappingExperiment._exp_number)
MappingExperiment._exp_number += 1
if map_format is None:
map_format=raw_io.esprit_ascii_map_format
if bse_format is None:
bse_format=raw_io.esprit_ascii_bse_format
self._label = label
self._description = description
self._map_format = map_format
self._bse_format = bse_format
self._map_scale_factor = map_scale_factor
if components is None:
components = path.find_components(pattern)
self._list_components = components
if len(self._list_components) == 0:
raise RuntimeError("No components found for pattern '{0}'".format(pattern))
@property
def pattern(self):
"""
:return: the pattern of filepaths to the maps
:rtype: str
"""
return self._pattern
@property
def label(self):
"""
:return: an identifying label for this experiment
:rtype: str
"""
return self._label
@property
def list_components(self):
"""
:return: a list of available components
:rtype: list[str]
"""
return self._list_components
@property
def map_format(self):
"""
:return: the format of the EDS maps
:rtype: edxia.io.raw_io.TextMapFormat
"""
return self._map_format
@property
def bse_format(self):
"""
:return: the format of the raw BSE map
:rtype: edxia.io.raw_io.TextMapFormat
"""
return self._bse_format
[docs] def get_path_map(self, component):
"""
:return: the filepath to the raw map of 'component'
:rtype: str
:raises RuntimeError: if the component is not valid
"""
if component not in self._list_components:
raise RuntimeError("'{0}' is not a valid component.".format(component))
return path.find_component_path(self._pattern, component)
[docs] def load_raw_map(self, component):
"""Load the map for a component.
This is a low-level function, a loader (:mod:`edxia.io.loader`) should be used in normal operations
:return: a map
:rtype: a numpy array
"""
if component == "BSE":
return raw_io.load_txt_map(self.get_path_map(component), self.bse_format)
else:
return raw_io.load_txt_map(self.get_path_map(component),
self.map_format,
resize=self._map_scale_factor
)
[docs] def is_valid(self):
"""Check if the experiment describes a valid set of maps.
:return: True if the experiment is valid, and the exception otherwise
:rtype: tuple(bool, Exception or None)
"""
if len(self._list_components) == 0:
return (False, RuntimeError("No components found"))
try:
amap = self.load_raw_map("BSE")
except Exception as e:
return (False, e)
return (True, None)
[docs]class PointsExperiment:
"""
An experiment describing a EDS point experiment
"""
def __init__(self,
components,
label=None,
description=None):
pass
[docs] def is_valid(self):
"""Check if the experiment describes a valid set of maps.
:return: True if the experiment is valid, and the exception otherwise
:rtype: tuple(bool, Exception or None)
"""
return (True, None)
@property
def label(self):
"""
:return: an identifying label for this experiment
:rtype: str
"""
return self._label
@property
def list_components(self):
"""
:return: a list of available components
:rtype: list[str]
"""
return self._list_components
[docs]class PartOfExperiment:
"""
Base class for a subset of an experiment.
Classes that should have access to the information provided by
:class:`edxia.core.experiment.Experiment` should inherit from this class.
"""
def __init__(self, parent=None):
self._parent = parent
@property
def parent(self):
"""
:returns: the experiment from which this effect was created
:rtype: edxia.core.experiment.Experiment
"""
return self._parent
