# coding: utf-8
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"""
Widget to handle regions of interest (:class:`ROI`) on curves displayed in a
:class:`PlotWindow`.
This widget is meant to work with :class:`PlotWindow`.
"""
__authors__ = ["V.A. Sole", "T. Vincent", "H. Payno"]
__license__ = "MIT"
__date__ = "13/03/2018"
from collections import OrderedDict
import logging
import os
import sys
import functools
import numpy
from silx.io import dictdump
from silx.utils import deprecation
from silx.utils.weakref import WeakMethodProxy
from silx.utils.proxy import docstring
from .. import icons, qt
from silx.math.combo import min_max
import weakref
from silx.gui.widgets.TableWidget import TableWidget
from . import items
from .items.roi import _RegionOfInterestBase
_logger = logging.getLogger(__name__)
class _FloatItem(qt.QTableWidgetItem):
"""
Simple QTableWidgetItem overloading the < operator to deal with ordering
"""
def __init__(self):
qt.QTableWidgetItem.__init__(self, type=qt.QTableWidgetItem.Type)
def __lt__(self, other):
if self.text() in ('', ROITable.INFO_NOT_FOUND):
return False
if other.text() in ('', ROITable.INFO_NOT_FOUND):
return True
return float(self.text()) < float(other.text())
[docs]class ROITable(TableWidget):
"""Table widget displaying ROI information.
See :class:`QTableWidget` for constructor arguments.
Behavior: listen at the active curve changed only when the widget is
visible. Otherwise won't compute the row and net counts...
"""
activeROIChanged = qt.Signal()
"""Signal emitted when the active roi changed or when the value of the
active roi are changing"""
COLUMNS_INDEX = OrderedDict([
('ID', 0),
('ROI', 1),
('Type', 2),
('From', 3),
('To', 4),
('Raw Counts', 5),
('Net Counts', 6),
('Raw Area', 7),
('Net Area', 8),
])
COLUMNS = list(COLUMNS_INDEX.keys())
INFO_NOT_FOUND = '????????'
def __init__(self, parent=None, plot=None, rois=None):
super(ROITable, self).__init__(parent)
self._showAllMarkers = False
self._userIsEditingRoi = False
"""bool used to avoid conflict when editing the ROI object"""
self._isConnected = False
self._roiToItems = {}
self._roiDict = {}
"""dict of ROI object. Key is ROi id, value is the ROI object"""
self._markersHandler = _RoiMarkerManager()
"""
Associate for each marker legend used when the `_showAllMarkers` option
is active a roi.
"""
self.setColumnCount(len(self.COLUMNS))
self.setPlot(plot)
self.__setTooltip()
self.setSortingEnabled(True)
self.itemChanged.connect(self._itemChanged)
@property
def roidict(self):
return self._getRoiDict()
@property
def activeRoi(self):
return self._markersHandler._activeRoi
def _getRoiDict(self):
ddict = {}
for id in self._roiDict:
ddict[self._roiDict[id].getName()] = self._roiDict[id]
return ddict
[docs] def clear(self):
"""
.. note:: clear the interface only. keep the roidict...
"""
self._markersHandler.clear()
self._roiToItems = {}
self._roiDict = {}
qt.QTableWidget.clear(self)
self.setRowCount(0)
self.setHorizontalHeaderLabels(self.COLUMNS)
header = self.horizontalHeader()
if hasattr(header, 'setSectionResizeMode'): # Qt5
header.setSectionResizeMode(qt.QHeaderView.ResizeToContents)
else: # Qt4
header.setResizeMode(qt.QHeaderView.ResizeToContents)
self.sortByColumn(0, qt.Qt.AscendingOrder)
self.hideColumn(self.COLUMNS_INDEX['ID'])
def setPlot(self, plot):
self.clear()
self.plot = plot
def __setTooltip(self):
self.horizontalHeaderItem(self.COLUMNS_INDEX['ROI']).setToolTip(
'Region of interest identifier')
self.horizontalHeaderItem(self.COLUMNS_INDEX['Type']).setToolTip(
'Type of the ROI')
self.horizontalHeaderItem(self.COLUMNS_INDEX['From']).setToolTip(
'X-value of the min point')
self.horizontalHeaderItem(self.COLUMNS_INDEX['To']).setToolTip(
'X-value of the max point')
self.horizontalHeaderItem(self.COLUMNS_INDEX['Raw Counts']).setToolTip(
'Estimation of the integral between y=0 and the selected curve')
self.horizontalHeaderItem(self.COLUMNS_INDEX['Net Counts']).setToolTip(
'Estimation of the integral between the segment [maxPt, minPt] '
'and the selected curve')
[docs] def setRois(self, rois, order=None):
"""Set the ROIs by providing a dictionary of ROI information.
The dictionary keys are the ROI names.
Each value is a sub-dictionary of ROI info with the following fields:
- ``"from"``: x coordinate of the left limit, as a float
- ``"to"``: x coordinate of the right limit, as a float
- ``"type"``: type of ROI, as a string (e.g "channels", "energy")
:param roidict: Dictionary of ROIs
:param str order: Field used for ordering the ROIs.
One of "from", "to", "type".
None (default) for no ordering, or same order as specified
in parameter ``roidict`` if provided as an OrderedDict.
"""
assert order in [None, "from", "to", "type"]
self.clear()
# backward compatibility since 0.10.0
if isinstance(rois, dict):
for roiName, roi in rois.items():
if isinstance(roi, ROI):
_roi = roi
else:
roi['name'] = roiName
_roi = ROI._fromDict(roi)
self.addRoi(_roi)
else:
for roi in rois:
assert isinstance(roi, ROI)
self.addRoi(roi)
self._updateMarkers()
[docs] def addRoi(self, roi):
"""
:param :class:`ROI` roi: roi to add to the table
"""
assert isinstance(roi, ROI)
self._getItem(name='ID', row=None, roi=roi)
self._roiDict[roi.getID()] = roi
self._markersHandler.add(roi, _RoiMarkerHandler(roi, self.plot))
self._updateRoiInfo(roi.getID())
callback = functools.partial(WeakMethodProxy(self._updateRoiInfo),
roi.getID())
roi.sigChanged.connect(callback)
# set it as the active one
self.setActiveRoi(roi)
def _getItem(self, name, row, roi):
if row:
item = self.item(row, self.COLUMNS_INDEX[name])
else:
item = None
if item:
return item
else:
if name == 'ID':
assert roi
if roi.getID() in self._roiToItems:
return self._roiToItems[roi.getID()]
else:
# create a new row
row = self.rowCount()
self.setRowCount(self.rowCount() + 1)
item = qt.QTableWidgetItem(str(roi.getID()),
type=qt.QTableWidgetItem.Type)
self._roiToItems[roi.getID()] = item
elif name == 'ROI':
item = qt.QTableWidgetItem(roi.getName() if roi else '',
type=qt.QTableWidgetItem.Type)
if roi.getName().upper() in ('ICR', 'DEFAULT'):
item.setFlags(qt.Qt.ItemIsSelectable | qt.Qt.ItemIsEnabled)
else:
item.setFlags(qt.Qt.ItemIsSelectable |
qt.Qt.ItemIsEnabled |
qt.Qt.ItemIsEditable)
elif name == 'Type':
item = qt.QTableWidgetItem(type=qt.QTableWidgetItem.Type)
item.setFlags((qt.Qt.ItemIsSelectable | qt.Qt.ItemIsEnabled))
elif name in ('To', 'From'):
item = _FloatItem()
if roi.getName().upper() in ('ICR', 'DEFAULT'):
item.setFlags(qt.Qt.ItemIsSelectable | qt.Qt.ItemIsEnabled)
else:
item.setFlags(qt.Qt.ItemIsSelectable |
qt.Qt.ItemIsEnabled |
qt.Qt.ItemIsEditable)
elif name in ('Raw Counts', 'Net Counts', 'Raw Area', 'Net Area'):
item = _FloatItem()
item.setFlags((qt.Qt.ItemIsSelectable | qt.Qt.ItemIsEnabled))
else:
raise ValueError('item type not recognized')
self.setItem(row, self.COLUMNS_INDEX[name], item)
return item
def _itemChanged(self, item):
def getRoi():
IDItem = self.item(item.row(), self.COLUMNS_INDEX['ID'])
assert IDItem
id = int(IDItem.text())
assert id in self._roiDict
roi = self._roiDict[id]
return roi
def signalChanged(roi):
if self.activeRoi and roi.getID() == self.activeRoi.getID():
self.activeROIChanged.emit()
self._userIsEditingRoi = True
if item.column() in (self.COLUMNS_INDEX['To'], self.COLUMNS_INDEX['From']):
roi = getRoi()
if item.text() not in ('', self.INFO_NOT_FOUND):
try:
value = float(item.text())
except ValueError:
value = 0
changed = False
if item.column() == self.COLUMNS_INDEX['To']:
if value != roi.getTo():
roi.setTo(value)
changed = True
else:
assert(item.column() == self.COLUMNS_INDEX['From'])
if value != roi.getFrom():
roi.setFrom(value)
changed = True
if changed:
self._updateMarker(roi.getName())
signalChanged(roi)
if item.column() is self.COLUMNS_INDEX['ROI']:
roi = getRoi()
if roi.getName() != item.text():
roi.setName(item.text())
self._markersHandler.getMarkerHandler(roi.getID()).updateTexts()
signalChanged(roi)
self._userIsEditingRoi = False
[docs] def deleteActiveRoi(self):
"""
remove the current active roi
"""
activeItems = self.selectedItems()
if len(activeItems) == 0:
return
old = self.blockSignals(True) # avoid several emission of sigROISignal
roiToRm = set()
for item in activeItems:
row = item.row()
itemID = self.item(row, self.COLUMNS_INDEX['ID'])
roiToRm.add(self._roiDict[int(itemID.text())])
[self.removeROI(roi) for roi in roiToRm]
self.blockSignals(old)
self.setActiveRoi(None)
[docs] def removeROI(self, roi):
"""
remove the requested roi
:param str name: the name of the roi to remove from the table
"""
if roi and roi.getID() in self._roiToItems:
item = self._roiToItems[roi.getID()]
self.removeRow(item.row())
del self._roiToItems[roi.getID()]
assert roi.getID() in self._roiDict
del self._roiDict[roi.getID()]
self._markersHandler.remove(roi)
callback = functools.partial(WeakMethodProxy(self._updateRoiInfo),
roi.getID())
roi.sigChanged.connect(callback)
[docs] def setActiveRoi(self, roi):
"""
Define the given roi as the active one.
.. warning:: this roi should already be registred / added to the table
:param :class:`ROI` roi: the roi to defined as active
"""
if roi is None:
self.clearSelection()
self._markersHandler.setActiveRoi(None)
self.activeROIChanged.emit()
else:
assert isinstance(roi, ROI)
if roi and roi.getID() in self._roiToItems.keys():
# avoid several call back to setActiveROI
old = self.blockSignals(True)
self.selectRow(self._roiToItems[roi.getID()].row())
self.blockSignals(old)
self._markersHandler.setActiveRoi(roi)
self.activeROIChanged.emit()
def _updateRoiInfo(self, roiID):
if self._userIsEditingRoi is True:
return
if roiID not in self._roiDict:
return
roi = self._roiDict[roiID]
if roi.isICR():
activeCurve = self.plot.getActiveCurve()
if activeCurve:
xData = activeCurve.getXData()
if len(xData) > 0:
min, max = min_max(xData)
roi.blockSignals(True)
roi.setFrom(min)
roi.setTo(max)
roi.blockSignals(False)
itemID = self._getItem(name='ID', roi=roi, row=None)
itemName = self._getItem(name='ROI', row=itemID.row(), roi=roi)
itemName.setText(roi.getName())
itemType = self._getItem(name='Type', row=itemID.row(), roi=roi)
itemType.setText(roi.getType() or self.INFO_NOT_FOUND)
itemFrom = self._getItem(name='From', row=itemID.row(), roi=roi)
fromdata = str(roi.getFrom()) if roi.getFrom() is not None else self.INFO_NOT_FOUND
itemFrom.setText(fromdata)
itemTo = self._getItem(name='To', row=itemID.row(), roi=roi)
todata = str(roi.getTo()) if roi.getTo() is not None else self.INFO_NOT_FOUND
itemTo.setText(todata)
rawCounts, netCounts = roi.computeRawAndNetCounts(
curve=self.plot.getActiveCurve(just_legend=False))
itemRawCounts = self._getItem(name='Raw Counts', row=itemID.row(),
roi=roi)
rawCounts = str(rawCounts) if rawCounts is not None else self.INFO_NOT_FOUND
itemRawCounts.setText(rawCounts)
itemNetCounts = self._getItem(name='Net Counts', row=itemID.row(),
roi=roi)
netCounts = str(netCounts) if netCounts is not None else self.INFO_NOT_FOUND
itemNetCounts.setText(netCounts)
rawArea, netArea = roi.computeRawAndNetArea(
curve=self.plot.getActiveCurve(just_legend=False))
itemRawArea = self._getItem(name='Raw Area', row=itemID.row(),
roi=roi)
rawArea = str(rawArea) if rawArea is not None else self.INFO_NOT_FOUND
itemRawArea.setText(rawArea)
itemNetArea = self._getItem(name='Net Area', row=itemID.row(),
roi=roi)
netArea = str(netArea) if netArea is not None else self.INFO_NOT_FOUND
itemNetArea.setText(netArea)
if self.activeRoi and roi.getID() == self.activeRoi.getID():
self.activeROIChanged.emit()
[docs] def currentChanged(self, current, previous):
if previous and current.row() != previous.row() and current.row() >= 0:
roiItem = self.item(current.row(),
self.COLUMNS_INDEX['ID'])
assert roiItem
self.setActiveRoi(self._roiDict[int(roiItem.text())])
self._markersHandler.updateAllMarkers()
qt.QTableWidget.currentChanged(self, current, previous)
[docs] @deprecation.deprecated(reason="Removed",
replacement="roidict and roidict.values()",
since_version="0.10.0")
def getROIListAndDict(self):
"""
:return: the list of roi objects and the dictionary of roi name to roi
object.
"""
roidict = self._roiDict
return list(roidict.values()), roidict
[docs] def calculateRois(self, roiList=None, roiDict=None):
"""
Update values of all registred rois (raw and net counts in particular)
:param roiList: deprecated parameter
:param roiDict: deprecated parameter
"""
if roiDict:
deprecation.deprecated_warning(name='roiDict', type_='Parameter',
reason='Unused parameter',
since_version="0.10.0")
if roiList:
deprecation.deprecated_warning(name='roiList', type_='Parameter',
reason='Unused parameter',
since_version="0.10.0")
for roiID in self._roiDict:
self._updateRoiInfo(roiID)
def _updateMarker(self, roiID):
"""Make sure the marker of the given roi name is updated"""
if self._showAllMarkers or (self.activeRoi
and self.activeRoi.getName() == roiID):
self._updateMarkers()
def _updateMarkers(self):
if self._showAllMarkers is True:
self._markersHandler.updateMarkers()
else:
if not self.activeRoi or not self.plot:
return
assert isinstance(self.activeRoi, ROI)
markerHandler = self._markersHandler.getMarkerHandler(self.activeRoi.getID())
if markerHandler is not None:
markerHandler.updateMarkers()
[docs] def getRois(self, order):
"""
Return the currently defined ROIs, as an ordered dict.
The dictionary keys are the ROI names.
Each value is a :class:`ROI` object..
:param order: Field used for ordering the ROIs.
One of "from", "to", "type", "netcounts", "rawcounts".
None (default) to get the same order as displayed in the widget.
:return: Ordered dictionary of ROI information
"""
if order is None or order.lower() == "none":
ordered_roilist = list(self._roiDict.values())
res = OrderedDict([(roi.getName(), self._roiDict[roi.getID()]) for roi in ordered_roilist])
else:
assert order in ["from", "to", "type", "netcounts", "rawcounts"]
ordered_roilist = sorted(self._roiDict.keys(),
key=lambda roi_id: self._roiDict[roi_id].get(order))
res = OrderedDict([(roi.getName(), self._roiDict[id]) for id in ordered_roilist])
return res
[docs] def save(self, filename):
"""
Save current ROIs of the widget as a dict of ROI to a file.
:param str filename: The file to which to save the ROIs
"""
roilist = []
roidict = {}
for roiID, roi in self._roiDict.items():
roilist.append(roi.toDict())
roidict[roi.getName()] = roi.toDict()
datadict = {'ROI': {'roilist': roilist, 'roidict': roidict}}
dictdump.dump(datadict, filename)
[docs] def load(self, filename):
"""
Load ROI widget information from a file storing a dict of ROI.
:param str filename: The file from which to load ROI
"""
roisDict = dictdump.load(filename)
rois = []
# Remove rawcounts and netcounts from ROIs
for roiDict in roisDict['ROI']['roidict'].values():
roiDict.pop('rawcounts', None)
roiDict.pop('netcounts', None)
rois.append(ROI._fromDict(roiDict))
self.setRois(rois)
[docs] def showAllMarkers(self, _show=True):
"""
:param bool _show: if true show all the markers of all the ROIs
boundaries otherwise will only show the one of
the active ROI.
"""
self._markersHandler.setShowAllMarkers(_show)
[docs] def setMiddleROIMarkerFlag(self, flag=True):
"""
Activate or deactivate middle marker.
This allows shifting both min and max limits at once, by dragging
a marker located in the middle.
:param bool flag: True to activate middle ROI marker
"""
self._markersHandler._middleROIMarkerFlag = flag
def _handleROIMarkerEvent(self, ddict):
"""Handle plot signals related to marker events."""
if ddict['event'] == 'markerMoved':
label = ddict['label']
roiID = self._markersHandler.getRoiID(markerID=label)
if roiID is not None:
# avoid several emission of sigROISignal
old = self.blockSignals(True)
self._markersHandler.changePosition(markerID=label,
x=ddict['x'])
self.blockSignals(old)
self._updateRoiInfo(roiID)
[docs] def showEvent(self, event):
self._visibilityChangedHandler(visible=True)
qt.QWidget.showEvent(self, event)
[docs] def hideEvent(self, event):
self._visibilityChangedHandler(visible=False)
qt.QWidget.hideEvent(self, event)
def _visibilityChangedHandler(self, visible):
"""Handle widget's visibility updates.
It is connected to plot signals only when visible.
"""
if visible:
assert self.plot
if self._isConnected is False:
self.plot.sigPlotSignal.connect(self._handleROIMarkerEvent)
self.plot.sigActiveCurveChanged.connect(self._activeCurveChanged)
self._isConnected = True
self.calculateRois()
else:
if self._isConnected:
self.plot.sigPlotSignal.disconnect(self._handleROIMarkerEvent)
self.plot.sigActiveCurveChanged.disconnect(self._activeCurveChanged)
self._isConnected = False
def _activeCurveChanged(self, curve):
self.calculateRois()
[docs] def setCountsVisible(self, visible):
"""
Display the columns relative to areas or not
:param bool visible: True if the columns 'Raw Area' and 'Net Area'
should be visible.
"""
if visible is True:
self.showColumn(self.COLUMNS_INDEX['Raw Counts'])
self.showColumn(self.COLUMNS_INDEX['Net Counts'])
else:
self.hideColumn(self.COLUMNS_INDEX['Raw Counts'])
self.hideColumn(self.COLUMNS_INDEX['Net Counts'])
[docs] def setAreaVisible(self, visible):
"""
Display the columns relative to areas or not
:param bool visible: True if the columns 'Raw Area' and 'Net Area'
should be visible.
"""
if visible is True:
self.showColumn(self.COLUMNS_INDEX['Raw Area'])
self.showColumn(self.COLUMNS_INDEX['Net Area'])
else:
self.hideColumn(self.COLUMNS_INDEX['Raw Area'])
self.hideColumn(self.COLUMNS_INDEX['Net Area'])
[docs] def fillFromROIDict(self, roilist=(), roidict=None, currentroi=None):
"""
This function API is kept for compatibility.
But `setRois` should be preferred.
Set the ROIs by providing a list of ROI names and a dictionary
of ROI information for each ROI.
The ROI names must match an existing dictionary key.
The name list is used to provide an order for the ROIs.
The dictionary's values are sub-dictionaries containing 3
mandatory fields:
- ``"from"``: x coordinate of the left limit, as a float
- ``"to"``: x coordinate of the right limit, as a float
- ``"type"``: type of ROI, as a string (e.g "channels", "energy")
:param roilist: List of ROI names (keys of roidict)
:type roilist: List
:param dict roidict: Dict of ROI information
:param currentroi: Name of the selected ROI or None (no selection)
"""
if roidict is not None:
self.setRois(roidict)
else:
self.setRois(roilist)
if currentroi:
self.setActiveRoi(currentroi)
_indexNextROI = 0
[docs]class ROI(_RegionOfInterestBase):
"""The Region Of Interest is defined by:
- A name
- A type. The type is the label of the x axis. This can be used to apply or
not some ROI to a curve and do some post processing.
- The x coordinate of the left limit (fromdata)
- The x coordinate of the right limit (todata)
:param str: name of the ROI
:param fromdata: left limit of the roi
:param todata: right limit of the roi
:param type: type of the ROI
"""
sigChanged = qt.Signal()
"""Signal emitted when the ROI is edited"""
def __init__(self, name, fromdata=None, todata=None, type_=None):
_RegionOfInterestBase.__init__(self)
self.setName(name)
global _indexNextROI
self._id = _indexNextROI
_indexNextROI += 1
self._fromdata = fromdata
self._todata = todata
self._type = type_ or 'Default'
self.sigItemChanged.connect(self.__itemChanged)
def __itemChanged(self, event):
"""Handle name change"""
if event == items.ItemChangedType.NAME:
self.sigChanged.emit()
[docs] def getID(self):
"""
:return int: the unique ID of the ROI
"""
return self._id
[docs] def setType(self, type_):
"""
:param str type_:
"""
if self._type != type_:
self._type = type_
self.sigChanged.emit()
[docs] def getType(self):
"""
:return str: the type of the ROI.
"""
return self._type
[docs] def setFrom(self, frm):
"""
:param frm: set x coordinate of the left limit
"""
if self._fromdata != frm:
self._fromdata = frm
self.sigChanged.emit()
[docs] def getFrom(self):
"""
:return: x coordinate of the left limit
"""
return self._fromdata
[docs] def setTo(self, to):
"""
:param to: x coordinate of the right limit
"""
if self._todata != to:
self._todata = to
self.sigChanged.emit()
[docs] def getTo(self):
"""
:return: x coordinate of the right limit
"""
return self._todata
[docs] def getMiddle(self):
"""
:return: middle position between 'from' and 'to' values
"""
return 0.5 * (self.getFrom() + self.getTo())
[docs] def toDict(self):
"""
:return: dict containing the roi parameters
"""
ddict = {
'type': self._type,
'name': self.getName(),
'from': self._fromdata,
'to': self._todata,
}
if hasattr(self, '_extraInfo'):
ddict.update(self._extraInfo)
return ddict
@staticmethod
def _fromDict(dic):
assert 'name' in dic
roi = ROI(name=dic['name'])
roi._extraInfo = {}
for key in dic:
if key == 'from':
roi.setFrom(dic['from'])
elif key == 'to':
roi.setTo(dic['to'])
elif key == 'type':
roi.setType(dic['type'])
else:
roi._extraInfo[key] = dic[key]
return roi
[docs] def isICR(self):
"""
:return: True if the ROI is the `ICR`
"""
return self.getName() == 'ICR'
[docs] def computeRawAndNetCounts(self, curve):
"""Compute the Raw and net counts in the ROI for the given curve.
- Raw count: Points values sum of the curve in the defined Region Of
Interest.
.. image:: img/rawCounts.png
- Net count: Raw counts minus background
.. image:: img/netCounts.png
:param CurveItem curve:
:return tuple: rawCount, netCount
"""
assert isinstance(curve, items.Curve) or curve is None
if curve is None:
return None, None
x = curve.getXData(copy=False)
y = curve.getYData(copy=False)
idx = numpy.nonzero((self._fromdata <= x) &
(x <= self._todata))[0]
if len(idx):
xw = x[idx]
yw = y[idx]
rawCounts = yw.sum(dtype=numpy.float)
deltaX = xw[-1] - xw[0]
deltaY = yw[-1] - yw[0]
if deltaX > 0.0:
slope = (deltaY / deltaX)
background = yw[0] + slope * (xw - xw[0])
netCounts = (rawCounts -
background.sum(dtype=numpy.float))
else:
netCounts = 0.0
else:
rawCounts = 0.0
netCounts = 0.0
return rawCounts, netCounts
[docs] def computeRawAndNetArea(self, curve):
"""Compute the Raw and net counts in the ROI for the given curve.
- Raw area: integral of the curve between the min ROI point and the
max ROI point to the y = 0 line.
.. image:: img/rawArea.png
- Net area: Raw counts minus background
.. image:: img/netArea.png
:param CurveItem curve:
:return tuple: rawArea, netArea
"""
assert isinstance(curve, items.Curve) or curve is None
if curve is None:
return None, None
x = curve.getXData(copy=False)
y = curve.getYData(copy=False)
y = y[(x >= self._fromdata) & (x <= self._todata)]
x = x[(x >= self._fromdata) & (x <= self._todata)]
if x.size == 0:
return 0.0, 0.0
rawArea = numpy.trapz(y, x=x)
# to speed up and avoid an intersection calculation we are taking the
# closest index to the ROI
closestXLeftIndex = (numpy.abs(x - self.getFrom())).argmin()
closestXRightIndex = (numpy.abs(x - self.getTo())).argmin()
yBackground = y[closestXLeftIndex], y[closestXRightIndex]
background = numpy.trapz(yBackground, x=x)
netArea = rawArea - background
return rawArea, netArea
[docs] @docstring(_RegionOfInterestBase)
def contains(self, position):
return self._fromdata <= position[0] <= self._todata
class _RoiMarkerManager(object):
"""
Deal with all the ROI markers
"""
def __init__(self):
self._roiMarkerHandlers = {}
self._middleROIMarkerFlag = False
self._showAllMarkers = False
self._activeRoi = None
def setActiveRoi(self, roi):
self._activeRoi = roi
self.updateAllMarkers()
def setShowAllMarkers(self, show):
if show != self._showAllMarkers:
self._showAllMarkers = show
self.updateAllMarkers()
def add(self, roi, markersHandler):
assert isinstance(roi, ROI)
assert isinstance(markersHandler, _RoiMarkerHandler)
if roi.getID() in self._roiMarkerHandlers:
raise ValueError('roi with the same ID already existing')
else:
self._roiMarkerHandlers[roi.getID()] = markersHandler
def getMarkerHandler(self, roiID):
if roiID in self._roiMarkerHandlers:
return self._roiMarkerHandlers[roiID]
else:
return None
def clear(self):
roisHandler = list(self._roiMarkerHandlers.values())
for roiHandler in roisHandler:
self.remove(roiHandler.roi)
def remove(self, roi):
if roi is None:
return
assert isinstance(roi, ROI)
if roi.getID() in self._roiMarkerHandlers:
self._roiMarkerHandlers[roi.getID()].clear()
del self._roiMarkerHandlers[roi.getID()]
def hasMarker(self, markerID):
assert type(markerID) is str
return self.getMarker(markerID) is not None
def changePosition(self, markerID, x):
markerHandler = self.getMarker(markerID)
if markerHandler is None:
raise ValueError('Marker %s not register' % markerID)
markerHandler.changePosition(markerID=markerID, x=x)
def updateMarker(self, markerID):
markerHandler = self.getMarker(markerID)
if markerHandler is None:
raise ValueError('Marker %s not register' % markerID)
roiID = self.getRoiID(markerID)
visible = (self._activeRoi and self._activeRoi.getID() == roiID) or self._showAllMarkers is True
markerHandler.setVisible(visible)
markerHandler.updateAllMarkers()
def updateRoiMarkers(self, roiID):
if roiID in self._roiMarkerHandlers:
visible = ((self._activeRoi and self._activeRoi.getID() == roiID)
or self._showAllMarkers is True)
_roi = self._roiMarkerHandlers[roiID]._roi()
if _roi and not _roi.isICR():
self._roiMarkerHandlers[roiID].showMiddleMarker(self._middleROIMarkerFlag)
self._roiMarkerHandlers[roiID].setVisible(visible)
self._roiMarkerHandlers[roiID].updateMarkers()
def getMarker(self, markerID):
assert type(markerID) is str
for marker in list(self._roiMarkerHandlers.values()):
if marker.hasMarker(markerID):
return marker
def updateMarkers(self):
for markerHandler in list(self._roiMarkerHandlers.values()):
markerHandler.updateMarkers()
def getRoiID(self, markerID):
for roiID, markerHandler in self._roiMarkerHandlers.items():
if markerHandler.hasMarker(markerID):
return roiID
return None
def setShowMiddleMarkers(self, show):
self._middleROIMarkerFlag = show
self._roiMarkerHandlers.updateAllMarkers()
def updateAllMarkers(self):
for roiID in self._roiMarkerHandlers:
self.updateRoiMarkers(roiID)
def getVisibleRois(self):
res = {}
for roiID, roiHandler in self._roiMarkerHandlers.items():
markers = (roiHandler.getMarker('min'), roiHandler.getMarker('max'),
roiHandler.getMarker('middle'))
for marker in markers:
if marker.isVisible():
if roiID not in res:
res[roiID] = []
res[roiID].append(marker)
return res
class _RoiMarkerHandler(object):
"""Used to deal with ROI markers used in ROITable"""
def __init__(self, roi, plot):
assert roi and isinstance(roi, ROI)
assert plot
self._roi = weakref.ref(roi)
self._plot = weakref.ref(plot)
self._draggable = False if roi.isICR() else True
self._color = 'black' if roi.isICR() else 'blue'
self._displayMidMarker = False
self._visible = True
@property
def draggable(self):
return self._draggable
@property
def plot(self):
return self._plot()
def clear(self):
if self.plot and self.roi:
self.plot.removeMarker(self._markerID('min'))
self.plot.removeMarker(self._markerID('max'))
self.plot.removeMarker(self._markerID('middle'))
@property
def roi(self):
return self._roi()
def setVisible(self, visible):
if visible != self._visible:
self._visible = visible
self.updateMarkers()
def showMiddleMarker(self, visible):
if self.draggable is False and visible is True:
_logger.warning("ROI is not draggable. Won't display middle marker")
return
self._displayMidMarker = visible
self.getMarker('middle').setVisible(self._displayMidMarker)
def updateMarkers(self):
if self.roi is None:
return
self._updateMinMarkerPos()
self._updateMaxMarkerPos()
self._updateMiddleMarkerPos()
def _updateMinMarkerPos(self):
self.getMarker('min').setPosition(x=self.roi.getFrom(), y=None)
self.getMarker('min').setVisible(self._visible)
def _updateMaxMarkerPos(self):
self.getMarker('max').setPosition(x=self.roi.getTo(), y=None)
self.getMarker('max').setVisible(self._visible)
def _updateMiddleMarkerPos(self):
self.getMarker('middle').setPosition(x=self.roi.getMiddle(), y=None)
self.getMarker('middle').setVisible(self._displayMidMarker and self._visible)
def getMarker(self, markerType):
if self.plot is None:
return None
assert markerType in ('min', 'max', 'middle')
if self.plot._getMarker(self._markerID(markerType)) is None:
assert self.roi
if markerType == 'min':
val = self.roi.getFrom()
elif markerType == 'max':
val = self.roi.getTo()
else:
val = self.roi.getMiddle()
_color = self._color
if markerType == 'middle':
_color = 'yellow'
self.plot.addXMarker(val,
legend=self._markerID(markerType),
text=self.getMarkerName(markerType),
color=_color,
draggable=self.draggable)
return self.plot._getMarker(self._markerID(markerType))
def _markerID(self, markerType):
assert markerType in ('min', 'max', 'middle')
assert self.roi
return '_'.join((str(self.roi.getID()), markerType))
def getMarkerName(self, markerType):
assert markerType in ('min', 'max', 'middle')
assert self.roi
return ' '.join((self.roi.getName(), markerType))
def updateTexts(self):
self.getMarker('min').setText(self.getMarkerName('min'))
self.getMarker('max').setText(self.getMarkerName('max'))
self.getMarker('middle').setText(self.getMarkerName('middle'))
def changePosition(self, markerID, x):
assert self.hasMarker(markerID)
markerType = self._getMarkerType(markerID)
assert markerType is not None
if self.roi is None:
return
if markerType == 'min':
self.roi.setFrom(x)
self._updateMiddleMarkerPos()
elif markerType == 'max':
self.roi.setTo(x)
self._updateMiddleMarkerPos()
else:
delta = x - 0.5 * (self.roi.getFrom() + self.roi.getTo())
self.roi.setFrom(self.roi.getFrom() + delta)
self.roi.setTo(self.roi.getTo() + delta)
self._updateMinMarkerPos()
self._updateMaxMarkerPos()
def hasMarker(self, marker):
return marker in (self._markerID('min'),
self._markerID('max'),
self._markerID('middle'))
def _getMarkerType(self, markerID):
if markerID.endswith('_min'):
return 'min'
elif markerID.endswith('_max'):
return 'max'
elif markerID.endswith('_middle'):
return 'middle'
else:
return None
