forked from id03/binoculars
/
fitaid.py
1238 lines (1008 loc) · 47.8 KB
/
fitaid.py
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import h5py
import sys
import numpy
import os.path
from PyQt4 import QtGui, QtCore, Qt
import BINoculars.main, BINoculars.space, BINoculars.plot, BINoculars.fit, BINoculars.util
from scipy.interpolate import griddata
from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg, NavigationToolbar2QTAgg
import matplotlib.figure, matplotlib.image
from matplotlib.pyplot import Rectangle
import itertools
from scipy.spatial import qhull
class Window(QtGui.QMainWindow):
def __init__(self, parent=None):
super(Window, self).__init__(parent)
newproject = QtGui.QAction("New project", self)
newproject.triggered.connect(self.newproject)
loadproject = QtGui.QAction("Open project", self)
loadproject.triggered.connect(self.loadproject)
addspace = QtGui.QAction("Import space", self)
addspace.triggered.connect(self.add_to_project)
menu_bar = QtGui.QMenuBar()
file = menu_bar.addMenu("&File")
file.addAction(newproject)
file.addAction(loadproject)
file.addAction(addspace)
self.setMenuBar(menu_bar)
self.statusbar = QtGui.QStatusBar()
self.tab_widget = QtGui.QTabWidget(self)
self.tab_widget.setTabsClosable(True)
QtCore.QObject.connect(self.tab_widget, QtCore.SIGNAL("tabCloseRequested(int)"), self.tab_widget.removeTab)
self.setCentralWidget(self.tab_widget)
self.setMenuBar(menu_bar)
self.setStatusBar(self.statusbar)
def newproject(self):
dialog = QtGui.QFileDialog(self, "project filename");
dialog.setFilter('BINoculars fit file (*.fit)');
dialog.setDefaultSuffix('fit');
dialog.setFileMode(QtGui.QFileDialog.AnyFile);
dialog.setAcceptMode(QtGui.QFileDialog.AcceptSave);
if not dialog.exec_():
return
fname = dialog.selectedFiles()[0]
if not fname:
return
try:
widget = TopWidget(str(fname), parent=self)
self.tab_widget.addTab(widget, short_filename(str(fname)))
self.tab_widget.setCurrentWidget(widget)
except Exception as e:
QtGui.QMessageBox.critical(self, 'New project', 'Unable to save project to {}: {}'.format(fname, e))
def loadproject(self, filename = None):
if not filename:
dialog = QtGui.QFileDialog(self, "Load project");
dialog.setFilter('BINoculars fit file (*.fit)');
dialog.setFileMode(QtGui.QFileDialog.ExistingFiles);
dialog.setAcceptMode(QtGui.QFileDialog.AcceptOpen);
if not dialog.exec_():
return
fname = dialog.selectedFiles()[0]
if not fname:
return
try:
widget = TopWidget(str(fname), parent=self)
self.tab_widget.addTab(widget, short_filename(str(fname)))
self.tab_widget.setCurrentWidget(widget)
except Exception as e:
QtGui.QMessageBox.critical(self, 'Load project', 'Unable to load project from {}: {}'.format(fname, e))
else:
widget = TopWidget(str(fname), parent=self)
self.tab_widget.addTab(widget, 'fname')
self.tab_widget.setCurrentWidget(widget)
def add_to_project(self, filename = None):
if self.tab_widget.count() == 0:
QtGui.QMessageBox.warning(self, 'Warning', 'First select a file to store data')
self.newproject()
if not filename:
dialog = QtGui.QFileDialog(self, "Import spaces");
dialog.setFilter('BINoculars space file (*.hdf5)');
dialog.setFileMode(QtGui.QFileDialog.ExistingFiles);
dialog.setAcceptMode(QtGui.QFileDialog.AcceptOpen);
if not dialog.exec_():
return
fname = dialog.selectedFiles()
if not fname:
return
for name in fname:
try:
widget = self.tab_widget.currentWidget()
widget.addspace(str(name))
except Exception as e:
QtGui.QMessageBox.critical(self, 'Import spaces', 'Unable to import space {}: {}'.format(fname, e))
else:
widget = self.tab_widget.currentWidget()
widget.addspace(filename)
class TopWidget(QtGui.QWidget):
def __init__(self, filename , parent=None):
super(TopWidget, self).__init__(parent)
hbox = QtGui.QHBoxLayout()
vbox = QtGui.QVBoxLayout()
minihbox = QtGui.QHBoxLayout()
minihbox2 = QtGui.QHBoxLayout()
self.database = FitData(filename)
self.table = TableWidget(self.database)
self.nav = ButtonedSlider()
self.nav.connect(self.nav, QtCore.SIGNAL('slice_index'), self.index_change)
self.table.trigger.connect(self.active_change)
self.table.check_changed.connect(self.refresh_plot)
self.tab_widget = QtGui.QTabWidget()
self.fitwidget = FitWidget(self.database)
self.integratewidget = IntegrateWidget(self.database)
self.plotwidget = OverviewWidget(self.database)
self.tab_widget.addTab(self.fitwidget, 'Fit')
self.tab_widget.addTab(self.integratewidget, 'Integrate')
self.tab_widget.addTab(self.plotwidget, 'plot')
self.emptywidget = QtGui.QWidget()
self.emptywidget.setLayout(vbox)
vbox.addWidget(self.table)
vbox.addWidget(self.nav)
self.functions = list()
self.function_box = QtGui.QComboBox()
for function in dir(BINoculars.fit):
cls = getattr(BINoculars.fit, function)
if isinstance(cls, type) and issubclass(cls, BINoculars.fit.PeakFitBase):
self.functions.append(cls)
self.function_box.addItem(function)
self.function_box.setCurrentIndex(self.function_box.findText('PolarLorentzian2D'))
vbox.addWidget(self.function_box)
vbox.addLayout(minihbox)
vbox.addLayout(minihbox2)
self.all_button = QtGui.QPushButton('fit all')
self.rod_button = QtGui.QPushButton('fit rod')
self.slice_button = QtGui.QPushButton('fit slice')
self.all_button.clicked.connect(self.fit_all)
self.rod_button.clicked.connect(self.fit_rod)
self.slice_button.clicked.connect(self.fit_slice)
minihbox.addWidget(self.all_button)
minihbox.addWidget(self.rod_button)
minihbox.addWidget(self.slice_button)
self.allint_button = QtGui.QPushButton('int all')
self.rodint_button = QtGui.QPushButton('int rod')
self.sliceint_button = QtGui.QPushButton('int slice')
self.allint_button.clicked.connect(self.int_all)
self.rodint_button.clicked.connect(self.int_rod)
self.sliceint_button.clicked.connect(self.int_slice)
minihbox2.addWidget(self.allint_button)
minihbox2.addWidget(self.rodint_button)
minihbox2.addWidget(self.sliceint_button)
splitter = QtGui.QSplitter(QtCore.Qt.Horizontal)
splitter.addWidget(self.emptywidget)
splitter.addWidget(self.tab_widget)
self.tab_widget.currentChanged.connect(self.tab_change)
hbox.addWidget(splitter)
self.setLayout(hbox)
def tab_change(self, index):
if index == 2:
self.refresh_plot()
def addspace(self,filename = None):
if filename == None:
filename = str(QtGui.QFileDialog.getOpenFileName(self, 'Open Project', '.', '*.hdf5'))
self.table.addspace(filename)
def active_change(self):
rodkey, axis, resolution = self.table.currentkey()
newdatabase = RodData(self.database.filename, rodkey, axis, resolution)
self.integratewidget.database = newdatabase
self.integratewidget.set_axis()
self.fitwidget.database = newdatabase
self.nav.set_length(newdatabase.rodlength())
index = newdatabase.load('index')
if index == None:
index = 0
self.nav.set_index(index)
self.index_change(index)
def index_change(self, index):
if index == None:
index = 0
self.fitwidget.database.save('index', self.nav.index())
self.fitwidget.plot(index)
self.integratewidget.plot(index)
def refresh_plot(self):
self.plotwidget.refresh(list(RodData(self.database.filename, rodkey, axis, resolution) for rodkey, axis, resolution in self.table.checked()))
@property
def fitclass(self):
return self.functions[self.function_box.currentIndex()]
def fit_slice(self):
index = self.nav.index()
space = self.fitwidget.database.space_from_index(index)
self.fitwidget.fit(index, space, self.fitclass)
self.fit_loc(self.fitwidget.database)
self.fitwidget.plot(index)
def fit_rod(self):
def function(index, space):
self.fitwidget.fit(index, space, self.fitclass)
self.progressbox(self.fitwidget.database.rodkey, function, enumerate(self.fitwidget.database), self.fitwidget.database.rodlength())
self.fit_loc(self.fitwidget.database)
self.fitwidget.plot()
def fit_all(self):
def function(index, space):
self.fitwidget.fit(index, space, self.fitclass)
for rodkey, axis, resolution in self.table.checked():
self.fitwidget.database = RodData(self.database.filename, rodkey, axis, resolution)
self.progressbox(self.fitwidget.database.rodkey, function, enumerate(self.fitwidget.database), self.fitwidget.database.rodlength())
self.fit_loc(self.fitwidget.database)
self.fitwidget.plot()
def int_slice(self):
index = self.nav.index()
space = self.fitwidget.database.space_from_index(index)
self.integratewidget.integrate(index, space)
self.integratewidget.plot(index)
def int_rod(self):
self.progressbox(self.integratewidget.database.rodkey,self.integratewidget.integrate, enumerate(self.integratewidget.database), self.integratewidget.database.rodlength())
self.integratewidget.plot()
def int_all(self):
for rodkey, axis, resolution in self.table.checked():
self.integratewidget.database = RodData(self.database.filename, rodkey, axis, resolution)
self.progressbox(self.integratewidget.database.rodkey,self.integratewidget.integrate, enumerate(self.integratewidget.database), self.integratewidget.database.rodlength())
self.integratewidget.plot()
def fit_loc(self, database):
deg = 2
for param in database.all_attrkeys():
if param.startswith('loc'):
x, y = database.all_from_key(param)
x, yvar = database.all_from_key('var_{0}'.format(param))
cx = x[numpy.invert(y.mask)]
y = y.compressed()
yvar = yvar.compressed()
w = numpy.log(1 / yvar)
w[w == numpy.inf] = 0
w = numpy.nan_to_num(w)
w[w < 0] = 0
w[w < numpy.median(w)] = 0
if len(x) > 0:
c = numpy.polynomial.polynomial.polyfit(cx, y, deg, w = w)
newy = numpy.polynomial.polynomial.polyval(x, c)
for index, newval in enumerate(newy):
database.save_sliceattr(index, 'guessloc{0}'.format(param.lstrip('loc')) , newval)
def progressbox(self, rodkey , function, iterator, length):
pd = QtGui.QProgressDialog('Processing {0}'.format(rodkey), 'Cancel', 0, length)
pd.setWindowModality(QtCore.Qt.WindowModal)
pd.show()
def progress(index, item):
pd.setValue(index)
if pd.wasCanceled():
raise KeyboardInterrupt
QtGui.QApplication.processEvents()
function(*item)
for index, item in enumerate(iterator):
progress(index, item)
pd.close()
class TableWidget(QtGui.QWidget):
trigger = QtCore.pyqtSignal()
check_changed = QtCore.pyqtSignal()
def __init__(self, database, parent=None):
super(TableWidget, self).__init__(parent)
hbox = QtGui.QHBoxLayout()
self.database = database
self.activeindex = 0
self.table = QtGui.QTableWidget(0, 5)
self.table.setHorizontalHeaderLabels(['','rod', 'axis', 'res', 'remove'])
self.table.cellClicked.connect(self.setlength)
for index, width in enumerate([25,150,40,50,70]):
self.table.setColumnWidth(index, width)
for filename, rodkey in zip(database.filelist, database.rods()):
self.addspace(filename, rodkey)
hbox.addWidget(self.table)
self.setLayout(hbox)
def addspace(self, filename, rodkey = None):
def remove_callback(rodkey):
return lambda: self.remove(rodkey)
def activechange_callback(index):
return lambda: self.setlength(index, 1)
if rodkey == None:
rodkey = short_filename(filename)
if rodkey in self.database.rods():
newkey = find_unused_rodkey(rodkey, self.database.rods())
self.database.copy(rodkey, newkey)
rodkey = newkey
old_axis, old_resolution = self.database.load(rodkey, 'axis'), self.database.load(rodkey, 'resolution')
self.database.create_rod(rodkey, filename)
index = self.table.rowCount()
self.table.insertRow(index)
axes = BINoculars.space.Axes.fromfile(filename)
checkboxwidget = QtGui.QCheckBox()
checkboxwidget.rodkey = rodkey
checkboxwidget.setChecked(0)
self.table.setCellWidget(index,0, checkboxwidget)
checkboxwidget.clicked.connect(self.check_changed)
item = QtGui.QTableWidgetItem(rodkey)
self.table.setItem(index, 1, item)
axis = QtGui.QComboBox()
for ax in axes:
axis.addItem(ax.label)
self.table.setCellWidget(index, 2, axis)
if not old_axis == None:
self.table.cellWidget(index, 2).setCurrentIndex(axes.index(old_axis))
elif index > 0:
self.table.cellWidget(0, 2).setCurrentIndex(self.table.cellWidget(0,2).currentIndex())
resolution = QtGui.QLineEdit()
if not old_resolution == None:
resolution.setText(str(old_resolution))
elif index > 0:
resolution.setText(self.table.cellWidget(0,3).text())
else:
resolution.setText(str(axes[axes.index(str(axis.currentText()))].res))
resolution.editingFinished.connect(activechange_callback(index))
self.table.setCellWidget(index, 3, resolution)
buttonwidget = QtGui.QPushButton('remove')
buttonwidget.clicked.connect(remove_callback(rodkey))
self.table.setCellWidget(index,4, buttonwidget)
def remove(self, rodkey):
table_rodkeys = list(self.table.cellWidget(index, 0).rodkey for index in range(self.table.rowCount()))
for index, label in enumerate(table_rodkeys):
if rodkey == label:
self.table.removeRow(index)
self.database.delete_rod(rodkey)
print 'removed: {0}'.format(rodkey)
def setlength(self, y, x = 1):
if x == 1:
self.activeindex = y
rodkey, axis, resolution = self.currentkey()
self.database.save(rodkey, 'axis', axis)
self.database.save(rodkey, 'resolution', resolution)
self.trigger.emit()
def currentkey(self):
rodkey = self.table.cellWidget(self.activeindex, 0).rodkey
axis = str(self.table.cellWidget(self.activeindex,2).currentText())
resolution = float(self.table.cellWidget(self.activeindex,3).text())
return rodkey, axis, resolution
def checked(self):
selection = []
for index in range(self.table.rowCount()):
checkbox = self.table.cellWidget(index, 0)
if checkbox.checkState():
rodkey = self.table.cellWidget(index, 0).rodkey
axis = str(self.table.cellWidget(index,2).currentText())
resolution = float(self.table.cellWidget(index,3).text())
selection.append((rodkey, axis, resolution))
return selection
class FitData(object):
def __init__(self, filename):
self.filename = filename
self.axdict = dict()
with h5py.File(self.filename,'a') as db:
for rodkey in self.rods():
spacename = db[rodkey].attrs['filename']
if not os.path.exists(spacename):
warningbox = QtGui.QMessageBox(2, 'Warning', 'Cannot find space {0} at file {1}; locate proper space'.format(rodkey, spacename), buttons = QtGui.QMessageBox.Open)
warningbox.exec_()
spacename = str(QtGui.QFileDialog.getOpenFileName(caption = 'Open space {0}'.format(rodkey), directory = '.', filter = '*.hdf5'))
if not spacename:
raise IOError('Select proper input')
db[rodkey].attrs['filename'] = spacename
self.axdict[rodkey] = BINoculars.space.Axes.fromfile(spacename)
def create_rod(self, rodkey, spacename):
with h5py.File(self.filename,'a') as db:
if rodkey not in db.keys():
db.create_group(rodkey)
db[rodkey].attrs['filename'] = spacename
self.axdict[rodkey] = BINoculars.space.Axes.fromfile(spacename)
def delete_rod(self, rodkey):
with h5py.File(self.filename,'a') as db:
del db[rodkey]
def rods(self):
with h5py.File(self.filename,'a') as db:
rods = db.keys()
return rods
def copy(self, oldkey, newkey):
with h5py.File(self.filename,'a') as db:
if oldkey in db.keys():
db.copy(db[oldkey], db, name = newkey)
@property
def filelist(self):
filelist = []
with h5py.File(self.filename,'a') as db:
for key in db.iterkeys():
filelist.append(db[key].attrs['filename'])
return filelist
def save(self, rodkey, key, value):
with h5py.File(self.filename,'a') as db:
db[rodkey].attrs[str(key)] = value
def load(self, rodkey, key):
with h5py.File(self.filename,'a') as db:
if rodkey in db:
if key in db[rodkey].attrs:
return db[rodkey].attrs[str(key)]
else:
return None
class RodData(FitData):
def __init__(self, filename, rodkey, axis, resolution):
super(RodData, self).__init__(filename)
self.rodkey = rodkey
self.slicekey = '{0}_{1}'.format(axis, resolution)
self.axis = axis
self.resolution = resolution
with h5py.File(self.filename,'a') as db:
if rodkey in db:
if self.slicekey not in db[rodkey]:
db[rodkey].create_group(self.slicekey)
db[rodkey][self.slicekey].create_group('attrs')
def save(self, key, value):
super(RodData, self).save(self.rodkey, key, value)
def load(self, key):
return super(RodData, self).load(self.rodkey, key)
def paxes(self):
axes = self.axdict[self.rodkey]
projected = list(axes)
axindex = axes.index(self.axis)
projected.pop(axindex)
return projected
def get_bins(self):
axes = self.axdict[self.rodkey]
axindex = axes.index(self.axis)
ax = axes[axindex]
bins = BINoculars.space.get_bins(ax, self.resolution)
return bins, ax, axindex
def rodlength(self):
bins, ax, axindex = self.get_bins()
return numpy.alen(bins) - 1
def get_index_value(self, index):
return BINoculars.space.get_axis_values(self.axdict[self.rodkey], self.axis, self.resolution)[index]
def get_key(self, index):
axes = self.axdict[self.rodkey]
bins, ax, axindex = self.get_bins()
start, stop = bins[index], bins[index + 1]
k = [slice(None) for i in axes]
k[axindex] = slice(start, stop)
return k
def space_from_index(self, index):
with h5py.File(self.filename,'a') as db:
filename = db[self.rodkey].attrs['filename']
return BINoculars.space.Space.fromfile(filename, self.get_key(index)).project(self.axis)
def save_data(self, index, key, data):
with h5py.File(self.filename,'a') as db:
id = '{0}_{1}_data'.format(int(index), key)
mid = '{0}_{1}_mask'.format(int(index), key)
try:
db[self.rodkey][self.slicekey].create_dataset(id, data.shape, dtype=data.dtype, compression='gzip').write_direct(data)
db[self.rodkey][self.slicekey].create_dataset(mid, data.shape, dtype=data.mask.dtype, compression='gzip').write_direct(data.mask)
except RuntimeError:
del db[self.rodkey][self.slicekey][id]
del db[self.rodkey][self.slicekey][mid]
db[self.rodkey][self.slicekey].create_dataset(id, data.shape, dtype=data.dtype, compression='gzip').write_direct(data)
db[self.rodkey][self.slicekey].create_dataset(mid, data.shape, dtype=data.mask.dtype, compression='gzip').write_direct(data.mask)
def load_data(self, index, key):
with h5py.File(self.filename,'a') as db:
id = '{0}_{1}_data'.format(int(index), key)
mid = '{0}_{1}_mask'.format(int(index), key)
try:
return numpy.ma.array(db[self.rodkey][self.slicekey][id][...], mask = db[self.rodkey][self.slicekey][mid][...])
except KeyError:
return None
def save_sliceattr(self, index, key, value):
mkey = 'mask{0}'.format(key)
with h5py.File(self.filename,'a') as db:
try:
group = db[self.rodkey][self.slicekey]['attrs']## else it breaks with the old fitaid
except KeyError:
db[rodkey][slicekey].create_group('attrs')
group = db[self.rodkey][self.slicekey]['attrs']
if not key in group:
group.create_dataset(key, (self.rodlength(),))
group.create_dataset(mkey, (self.rodlength(),), dtype = numpy.bool).write_direct(numpy.ones(self.rodlength(), dtype = numpy.bool))
group[key][index] = value
group[mkey][index] = 0
def load_sliceattr(self, index, key):
mkey = 'mask{0}'.format(key)
with h5py.File(self.filename,'a') as db:
try:
group = db[self.rodkey][self.slicekey]['attrs']
except KeyError:
db[self.rodkey][self.slicekey].create_group('attrs')
group = db[self.rodkey][self.slicekey]['attrs']
if key in group.keys():
return numpy.ma.array(group[key][index], mask = group[mkey][index])
else:
return None
def all_attrkeys(self):
with h5py.File(self.filename,'a') as db:
group = db[self.rodkey][self.slicekey]['attrs']
return group.keys()
def all_from_key(self, key):
mkey = 'mask{0}'.format(key)
axes = self.axdict[self.rodkey]
with h5py.File(self.filename,'a') as db:
group = db[self.rodkey][self.slicekey]['attrs']
if key in group.keys():
return BINoculars.space.get_axis_values(axes, self.axis, self.resolution), numpy.ma.array(group[key], mask = numpy.array(group[mkey]))
def load_loc(self, index):
loc = list()
with h5py.File(self.filename,'a') as db:
count = itertools.count()
key = 'guessloc{0}'.format(count.next())
while self.load_sliceattr(index, key) != None:
loc.append(self.load_sliceattr(index, key))
key = 'guessloc{0}'.format(count.next())
if len(loc) > 0:
return loc
else:
count = itertools.count()
key = 'loc{0}'.format(count.next())
while self.load_sliceattr(index, key) != None:
loc.append(self.load_sliceattr(index, key))
key = 'loc{0}'.format(count.next())
if len(loc) > 0:
return loc
else:
return None
def save_loc(self, index, loc):
for i, value in enumerate(loc):
self.save_sliceattr(index, 'guessloc{0}'.format(i), value)
def __iter__(self):
for index in range(self.rodlength()):
yield self.space_from_index(index)
def short_filename(filename):
return filename.split('/')[-1].split('.')[0]
class HiddenToolbar(NavigationToolbar2QTAgg):
def __init__(self, corner_callback, canvas):
NavigationToolbar2QTAgg.__init__(self, canvas, None)
self._corner_callback = corner_callback
self.zoom()
def press(self, event):
self._corner_preclick = self._views()
def release(self, event):
if self._corner_preclick == self._views():
self._corner_callback(event.xdata, event.ydata)
self._corner_preclick = None
class FitWidget(QtGui.QWidget):
def __init__(self, database ,parent=None):
super(FitWidget, self).__init__(parent)
self.database = database
vbox = QtGui.QHBoxLayout()
self.figure = matplotlib.figure.Figure()
self.canvas = FigureCanvasQTAgg(self.figure)
self.toolbar = HiddenToolbar(self.loc_callback, self.canvas)
vbox.addWidget(self.canvas)
self.setLayout(vbox)
def loc_callback(self, x, y):
if self.ax:
self.database.save_loc(self.currentindex(), numpy.array([x, y]))
def plot(self, index = None):
if index == None:
index = self.currentindex()
space = self.database.space_from_index(index)
fitdata = self.database.load_data(index, 'fit')
self.figure.clear()
self.figure.space_axes = space.axes
info = self.database.get_index_value(index)
label = self.database.axis
if fitdata is not None:
if space.dimension == 1:
self.ax = self.figure.add_subplot(111)
BINoculars.plot.plot(space, self.figure, self.ax, fit = fitdata)
elif space.dimension == 2:
self.ax = self.figure.add_subplot(121)
BINoculars.plot.plot(space, self.figure, self.ax, fit = None)
self.ax = self.figure.add_subplot(122)
BINoculars.plot.plot(space, self.figure, self.ax, fit = fitdata)
else:
self.ax = self.figure.add_subplot(111)
BINoculars.plot.plot(space, self.figure, self.ax)
self.figure.suptitle('{0}, res = {1}, {2} = {3}'.format(self.database.rodkey, self.database.resolution, label, info))
self.canvas.draw()
def fit(self, index, space, function):
print index
if not len(space.get_masked().compressed()) == 0:
loc = self.database.load_loc(index)
if loc:
if loc == list(float(0) for i in loc):
loc = None
fit = function(space, loc = loc)
fit.fitdata.mask = space.get_masked().mask
self.database.save_data(index, 'fit', fit.fitdata)
params = list(line.split(':')[0] for line in fit.summary.split('\n'))
print fit.result, fit.variance
for key, value in zip(params, fit.result):
self.database.save_sliceattr(index, key, value)
for key, value in zip(params, fit.variance):
self.database.save_sliceattr(index, 'var_{0}'.format(key), value)
def currentindex(self):
index = self.database.load('index')
if index == None:
return 0
else:
return index
class IntegrateWidget(QtGui.QWidget):
def __init__(self, database, parent = None):
super(IntegrateWidget, self).__init__(parent)
self.database = database
self.figure = matplotlib.figure.Figure()
self.canvas = FigureCanvasQTAgg(self.figure)
self.toolbar = HiddenToolbar(self.loc_callback, self.canvas)
hbox = QtGui.QHBoxLayout()
splitter = QtGui.QSplitter(QtCore.Qt.Vertical)
self.make_controlwidget()
splitter.addWidget(self.canvas)
splitter.addWidget(self.control_widget)
hbox.addWidget(splitter)
self.setLayout(hbox)
def make_controlwidget(self):
self.control_widget = QtGui.QWidget()
integratebox = QtGui.QVBoxLayout()
intensitybox = QtGui.QHBoxLayout()
backgroundbox = QtGui.QHBoxLayout()
self.tracker = QtGui.QCheckBox('peak tracker')
self.tracker.setChecked(1)
self.locx = QtGui.QDoubleSpinBox()
self.locy = QtGui.QDoubleSpinBox()
self.locx.setDisabled(True)
self.locy.setDisabled(True)
self.tracker.clicked.connect(self.refresh_tracker)
self.aroundroi = QtGui.QCheckBox('background around roi')
self.aroundroi.setChecked(1)
self.aroundroi.clicked.connect(self.refresh_aroundroi)
self.hsize = QtGui.QDoubleSpinBox()
self.vsize = QtGui.QDoubleSpinBox()
intensitybox.addWidget(QtGui.QLabel('roi size:'))
intensitybox.addWidget(self.hsize)
intensitybox.addWidget(self.vsize)
self.left = QtGui.QDoubleSpinBox()
self.right = QtGui.QDoubleSpinBox()
self.top = QtGui.QDoubleSpinBox()
self.bottom = QtGui.QDoubleSpinBox()
QtCore.QObject.connect(self.hsize, QtCore.SIGNAL("valueChanged(double)"), self.send)
QtCore.QObject.connect(self.vsize, QtCore.SIGNAL("valueChanged(double)"), self.send)
QtCore.QObject.connect(self.left, QtCore.SIGNAL("valueChanged(double)"), self.send)
QtCore.QObject.connect(self.right, QtCore.SIGNAL("valueChanged(double)"), self.send)
QtCore.QObject.connect(self.top, QtCore.SIGNAL("valueChanged(double)"), self.send)
QtCore.QObject.connect(self.bottom, QtCore.SIGNAL("valueChanged(double)"), self.send)
backgroundbox.addWidget(self.aroundroi)
backgroundbox.addWidget(self.left)
backgroundbox.addWidget(self.right)
backgroundbox.addWidget(self.top)
backgroundbox.addWidget(self.bottom)
integratebox.addLayout(intensitybox)
integratebox.addLayout(backgroundbox)
minibox = QtGui.QHBoxLayout()
minibox.addWidget(self.tracker)
minibox.addWidget(self.locx)
minibox.addWidget(self.locy)
integratebox.addLayout(minibox)
self.control_widget.setLayout(integratebox)
def refresh_aroundroi(self):
self.database.save('aroundroi', self.aroundroi.checkState())
axes = self.database.paxes()
if not self.aroundroi.checkState():
self.left.setMinimum(axes[0].min)
self.left.setMaximum(axes[0].max)
self.right.setMinimum(axes[0].min)
self.right.setMaximum(axes[0].max)
self.top.setMinimum(axes[1].min)
self.top.setMaximum(axes[1].max)
self.bottom.setMinimum(axes[1].min)
self.bottom.setMaximum(axes[1].max)
else:
self.left.setMinimum(0)
self.left.setMaximum(axes[0].max - axes[0].min)
self.right.setMinimum(0)
self.right.setMaximum(axes[0].max - axes[0].min)
self.top.setMinimum(0)
self.top.setMaximum(axes[1].max - axes[1].min)
self.bottom.setMinimum(0)
self.bottom.setMaximum(axes[1].max - axes[1].min)
def refresh_tracker(self):
self.database.save('tracker', self.tracker.checkState())
if self.tracker.checkState():
self.locx.setDisabled(True)
self.locy.setDisabled(True)
else:
self.locx.setDisabled(False)
self.locy.setDisabled(False)
self.plot_box()
def set_axis(self):
roi = self.database.load('roi')
aroundroi = self.database.load('aroundroi')
if aroundroi != None:
self.aroundroi.setChecked(aroundroi)
else:
self.aroundroi.setChecked(True)
self.refresh_aroundroi()
axes = self.database.paxes()
self.hsize.setSingleStep(axes[1].res)
self.hsize.setDecimals(len(str(axes[1].res)) - 2)
self.vsize.setSingleStep(axes[0].res)
self.vsize.setDecimals(len(str(axes[0].res)) - 2)
self.left.setSingleStep(axes[1].res)
self.left.setDecimals(len(str(axes[1].res)) - 2)
self.right.setSingleStep(axes[1].res)
self.right.setDecimals(len(str(axes[1].res)) - 2)
self.top.setSingleStep(axes[0].res)
self.top.setDecimals(len(str(axes[0].res)) - 2)
self.bottom.setSingleStep(axes[0].res)
self.bottom.setDecimals(len(str(axes[0].res)) - 2)
self.locx.setSingleStep(axes[0].res)
self.locx.setDecimals(len(str(axes[0].res)) - 2)
self.locx.setMinimum(axes[0].min)
self.locx.setMaximum(axes[0].max)
self.locy.setSingleStep(axes[1].res)
self.locy.setDecimals(len(str(axes[1].res)) - 2)
self.locy.setMinimum(axes[1].min)
self.locy.setMaximum(axes[1].max)
tracker = self.database.load('tracker')
if tracker != None:
self.tracker.setChecked(tracker)
else:
self.tracker.setChecked(True)
if roi is not None:
for box, value in zip([self.hsize, self.vsize, self.left, self.right, self.top, self.bottom], roi):
box.setValue(value)
if self.fixed_loc() != None:
x,y = self.fixed_loc()
self.locx.setValue(x)
self.locy.setValue(y)
def send(self):
roi = [self.hsize.value(), self.vsize.value(), self.left.value() ,self.right.value() ,self.top.value(), self.bottom.value()]
self.database.save('roi', roi)
self.plot_box()
def integrate(self, index, space):
if self.tracker.checkState():
loc = self.database.load_loc(index)
else:
loc = self.fixed_loc()
if loc != None:
axes = space.axes
key = space.get_key(self.intkey(loc, axes))
fitdata = self.database.load_data(index, 'fit')
if fitdata != None:
fitintensity = fitdata[key].data.flatten()
fitbkg = numpy.hstack(fitdata[space.get_key(bkgkey)].data.flatten() for bkgkey in self.bkgkeys(loc, axes))
if numpy.alen(fitbkg) == 0:
fitstructurefactor = fitintensity.sum()
elif numpy.alen(fitintensity) == 0:
fitstructurefactor = numpy.nan
else:
fitstructurefactor = numpy.sqrt(fitintensity.sum() - numpy.alen(fitintensity) * 1.0 / numpy.alen(fitbkg) * fitbkg.sum())
self.database.save_sliceattr(index, 'fitsf', fitstructurefactor)
niintensity = space[self.intkey(loc, axes)].get_masked().compressed()
try:
intensity = interpolate(space[self.intkey(loc, axes)]).flatten()
bkg = numpy.hstack(space[bkgkey].get_masked().compressed() for bkgkey in self.bkgkeys(loc, axes))
interdata = space.get_masked()
interdata[key] = intensity.reshape(interdata[key].shape)
interdata[key].mask = numpy.zeros_like(interdata[key])
self.database.save_data(index, 'inter', interdata)
except Exception as e:
print 'Warning error interpolating slice {0}: {1}'.format(index, e.message)
intensity = numpy.array([])
bkg = numpy.array([])
if numpy.alen(intensity) == 0:
structurefactor = numpy.nan
nistructurefactor = numpy.nan
elif numpy.alen(bkg) == 0:
structurefactor = numpy.sqrt(intensity.sum())
nistructurefactor = numpy.sqrt(niintensity.sum())
else:
structurefactor = numpy.sqrt(intensity.sum() - numpy.alen(intensity) * 1.0 / numpy.alen(bkg) * bkg.sum())
nistructurefactor = numpy.sqrt(niintensity.sum() - numpy.alen(niintensity) * 1.0 / numpy.alen(bkg) * bkg.sum())
self.database.save_sliceattr(index, 'sf', structurefactor)
self.database.save_sliceattr(index, 'nisf', nistructurefactor)
print 'Structurefactor {0}: {1}'.format(index, structurefactor)
def intkey(self, coords, axes):
vsize = self.vsize.value() / 2
hsize = self.hsize.value() / 2
return tuple(ax.restrict(slice(coord - size, coord + size)) for ax, coord, size in zip(axes, coords, [vsize, hsize]))
def bkgkeys(self, coords, axes):
aroundroi = self.database.load('aroundroi')
if aroundroi:
key = self.intkey(coords, axes)
vsize = self.vsize.value() / 2
hsize = self.hsize.value() / 2
leftkey = (key[0], axes[1].restrict(slice(coords[1] - hsize - self.left.value(), coords[1] - hsize)))
rightkey = (key[0], axes[1].restrict(slice(coords[1] + hsize, coords[1] + hsize + self.right.value())))
topkey = (axes[0].restrict(slice(coords[0] - vsize - self.top.value(), coords[0] - vsize)), key[1])
bottomkey = (axes[0].restrict(slice(coords[0] + vsize, coords[0] + vsize + self.bottom.value())), key[1])
return leftkey, rightkey, topkey, bottomkey
else:
return [(axes[0].restrict(slice(self.left.value(), self.right.value())), axes[1].restrict(slice(self.top.value(), self.bottom.value())))]
def fixed_loc(self):
x = self.database.load('fixed_locx')
y = self.database.load('fixed_locy')
if x != None and y != None:
return numpy.array([x, y])
else:
return None
def loc_callback(self, x, y):
if self.ax:
self.database.save_loc(self.currentindex(), numpy.array([x, y]))
if not self.tracker.checkState():
self.database.save('fixed_locx', x)
self.database.save('fixed_locy', y)
self.locx.setValue(x)
self.locy.setValue(y)
self.plot_box()
def plot(self, index = None):
if index == None:
index = self.currentindex()
space = self.database.space_from_index(index)
interdata = self.database.load_data(index, 'inter')
info = self.database.get_index_value(index)
label = self.database.axis
self.figure.clear()
self.figure.space_axes = space.axes
if interdata is not None:
if space.dimension == 1:
self.ax = self.figure.add_subplot(111)
BINoculars.plot.plot(space, self.figure, self.ax, fit = interdata)
elif space.dimension == 2:
self.ax = self.figure.add_subplot(121)
BINoculars.plot.plot(space, self.figure, self.ax, fit = None)
self.ax = self.figure.add_subplot(122)
BINoculars.plot.plot(space, self.figure, self.ax, fit = interdata)
else:
self.ax = self.figure.add_subplot(111)
BINoculars.plot.plot(space, self.figure, self.ax)
self.figure.suptitle('{0}, res = {1}, {2} = {3}'.format(self.database.rodkey, self.database.resolution, label, info))
self.plot_box()
self.canvas.draw()
def plot_box(self):
if not self.tracker.checkState():
loc = self.fixed_loc()
else:
loc = self.database.load_loc(self.currentindex())
if len(self.figure.get_axes()) != 0 and loc != None:
ax = self.figure.get_axes()[0]
axes = self.figure.space_axes
key = self.intkey(loc, axes)
bkgkey = self.bkgkeys(loc, axes)
ax.patches = []