def __init__(self, parent=None, backend=None, logger=None, title="Plot2D"):
super(Plot2D, self).__init__(parent=parent, backend=backend)
self._logger = logger or getLogger("Plot2D")
self._index = None
self._title = title
self.setWindowTitle(self._title)
self._image = None
self._mask = None
self._origin = (0, 0)
self._scale = (1, 1)
self._xlabel = 'X'
self._ylabel = 'Y'
self.setKeepDataAspectRatio(True)
self.getDefaultColormap().setName('viridis')
Utilities to work with 2D grids and interpolation
=================================================
"""
from __future__ import division, print_function
import warnings
import numpy as np
# suppress warnings
try:
import numexpr
except ImportError:
pass
from larch.utils.logging import getLogger
_logger = getLogger('gridxyz')
### GLOBAL VARIABLES ###
MODNAME = '_math'
def gridxyz(xcol, ycol, zcol, xystep=None, lib='scipy', method='cubic'):
"""Grid (X, Y, Z) 1D data on a 2D regular mesh
Parameters
----------
xcol, ycol, zcol : 1D arrays repesenting the map (z is the intensity)
xystep : the step size of the XY grid
lib : library used for griddata
[scipy]
matplotlib
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
RIXS GUI APPLICATION
====================
"""
import sys
import argparse
import signal
from larch.utils.logging import getLogger
_logger = getLogger('lach.qtrixs.application')
def createParser():
"""Application parser"""
parser = argparse.ArgumentParser(description="Larch-RIXS GUI parser")
return parser
def mainQtApp(options):
"""Part of the main application depending on Qt"""
try:
# it should be loaded before h5py
import hdf5plugin # noqa
except ImportError:
_logger.debug("Backtrace", exc_info=True)
import h5py
import silx
#!/usr/bin/env python
"""
Convert an Athena Project file to HDF5
"""
import os
import h5py
from silx.io.dictdump import dicttoh5
from larch.io.athena_project import AthenaProject
from larch.utils.logging import getLogger
_logger = getLogger("athena_to_hdf5", level="INFO")
def athena_to_hdf5(
filename,
fileout=None,
overwrite=False,
match=None,
do_preedge=True,
do_bkg=True,
do_fft=True,
use_hashkey=False,
_larch=None,
):
"""Read Athena project file (.prj) and write to HDF5 (.h5)
Arguments:
filename (string): name of Athena Project file
fileout (None or string): name of the output file [None -> filename_root.h5]
overwrite (boolean): force overwrite if fileout exists [False]
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""This module provides base classes to implement models for
spectroscopy data.
"""
from __future__ import absolute_import, division
import os
from silx.gui import qt
import silx.io
from .items import (ExperimentItem, GroupItem, FileItem, ScanItem)
from larch.utils.logging import getLogger
_logger = getLogger('larch.qtlib.view')
class HorizontalHeaderView(qt.QHeaderView):
def __init__(self, parent=None):
super(HorizontalHeaderView, self).__init__(qt.Qt.Horizontal, parent)
# Some properties
self.setStretchLastSection(True)
# self.setSectionsMovable(True)
# Context menu
self.setContextMenuPolicy(qt.Qt.CustomContextMenu)
self.customContextMenuRequested.connect(self.showContextMenu)
def showContextMenu(self, position):
menu = qt.QMenu('Horizontal Header View Menu', self)
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
RIXS data object
================
"""
import numpy as np
from scipy.interpolate import griddata
from silx.io.dictdump import (dicttoh5, h5todict)
from larch.math.gridxyz import gridxyz
from larch.utils.logging import getLogger
_logger = getLogger('rixsdata') #: module logger
def _tostr(arr):
"""Numpy array to string"""
return arr.tostring().decode()
class RixsData(object):
"""RIXS plane object"""
#: loaded from dictionary/HDF5 -> self.load_from_h5()
sample_name = 'Unknown'
counter_all, counter_signal, counter_norm = None, None, None
_x, _y, _z = None, None, None
ene_in, ene_out, rixs_map = None, None, None
ene_et, rixs_et_map = None, None
ene_grid, ene_unit = None, None
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
This module provides classes to implement model items for spectroscopy data.
"""
from __future__ import absolute_import, division
import weakref
from silx.gui import qt
from silx.utils.weakref import WeakList
from larch.utils.logging import getLogger
_logger = getLogger('larch.qtlib.items')
__authors__ = ['Marius Retegan', 'Mauro Rovezzi']
class Signal(object):
"""Base class for signal objects."""
def __init__(self):
self._slots = WeakList()
def connect(self, slot):
"""Register a slot.
Adding an already registered slot has no effect.
:param callable slot: The function or method to register.
"""
if slot not in self._slots:
"""
from silx.gui import qt
from silx.gui.plot.actions import PlotAction
from silx.gui.plot.tools.roi import RegionOfInterestManager
from silx.gui.plot.tools.roi import RegionOfInterestTableWidget
# from silx.gui.plot.items.roi import RectangleROI
from silx.gui.plot.items import LineMixIn, SymbolMixIn
from larch.utils.logging import getLogger
from larch.qtlib.plotarea import PlotArea, MdiSubWindow
from larch.qtlib.plot1D import Plot1D
from larch.qtlib.plot2D import Plot2D
from .profiletoolbar import (_DEFAULT_OVERLAY_COLORS, RixsProfileToolBar)
from .view import RixsListView
from .model import RixsListModel
_logger = getLogger("larch.qtrixs.plotrixs")
class RixsROIManager(RegionOfInterestManager):
def __init__(self, plot, color='pink'):
super(RixsROIManager, self).__init__(plot)
self.setColor(color)
self.sigRoiAdded.connect(self.updateAddedRegionOfInterest)
def updateAddedRegionOfInterest(self, roi):
"""Called for each added region of interest: set the name"""
if roi.getLabel() == '':
roi.setLabel('%d' % len(self.getRois()))
if isinstance(roi, LineMixIn):
roi.setLineWidth(2)
roi.setLineStyle('--')
===========================================
.. note: RIXS stands for Resonant Inelastic X-ray Scattering
.. note: 13-ID-E is GSECARS-CAT
"""
import os
import time
import glob
import numpy as np
from silx.io.dictdump import dicttoh5
from larch.utils.logging import getLogger
_logger = getLogger('io_rixs_gsecars')
def _parse_header(fname):
"""Get parsed header
Return
------
header : dict
{
'columns': list of strings,
'Analyzer.Energy': float,
}
"""
with open(fname) as f:
lines = f.read().splitlines()
def __init__(self, parent=None, with_ipykernel=True, logger=None):
"""Constructor"""
self._logger = logger or getLogger('RixsAppWindow')
super(RixsAppWindow, self).__init__(parent=parent)
if parent is not None:
#: behave as a widget
self.setWindowFlags(qt.Qt.Widget)
else:
#: main window
self.setWindowTitle('RIXS_VIEW')
# TODO: Add icon to the application
#ico = qt.QIcon(os.path.join(_resourcesPath, "logo",
# "xraysloth_logo_04.svg"))
#self.setWindowIcon(ico)
#: IPython kernel status
self._with_ipykernel = with_ipykernel
#: Model/view
self._model = RixsModel()
self._view = RixsView(parent=self)
self._view.setModel(self._model)
# Add additional sections to the header.
values = [
HeaderSection(name='Plot',
roles={qt.Qt.DisplayRole: 'currentPlotWindowIndex',
qt.Qt.EditRole: 'plotWindowsIndexes'
},
delegate=ComboBoxDelegate),
]
for value in values:
section = len(self._model.header)
orientation = qt.Qt.Horizontal
self._model.setHeaderData(section, orientation, value)
# Add (empty) menu bar -> contents added later
self._menuBar = qt.QMenuBar()
self.setMenuBar(self._menuBar)
self._initAppMenu()
#: Plot Area
self._plotArea = RixsPlotArea(self)
self.setCentralWidget(self._plotArea)
#: TreeView dock widget
self._dockDataWidget = qt.QDockWidget(parent=self)
self._dockDataWidget.setObjectName('Data View')
self._dockDataWidget.setWidget(self._view)
self.addDockWidget(qt.Qt.LeftDockWidgetArea, self._dockDataWidget)
#: Plots update
self._model.dataChanged.connect(self.updatePlot)
self._plotArea.changed.connect(self.updateModel)
#: Console
if self._with_ipykernel:
# Initialize internal ipykernel
self._ipykernel = InternalIPyKernel()
self._ipykernel.init_kernel(backend='qt')
self._ipykernel.add_to_namespace('view', self._view)
self._ipykernel.add_to_namespace('model', self._model)
self._ipykernel.add_to_namespace('plot', self._plotArea)
# Add IPython console at menu
self._initConsoleMenu()
else:
self._ipykernel = None