def __init__(self, parent=None):
super(PrintGeometryWidget, self).__init__(parent)
self.mainLayout = qt.QGridLayout(self)
self.mainLayout.setContentsMargins(0, 0, 0, 0)
self.mainLayout.setSpacing(2)
hbox = qt.QWidget(self)
hboxLayout = qt.QHBoxLayout(hbox)
hboxLayout.setContentsMargins(0, 0, 0, 0)
hboxLayout.setSpacing(2)
label = qt.QLabel(self)
label.setText("Units")
label.setAlignment(qt.Qt.AlignCenter)
self._pageButton = qt.QRadioButton()
self._pageButton.setText("Page")
self._inchButton = qt.QRadioButton()
self._inchButton.setText("Inches")
self._cmButton = qt.QRadioButton()
self._cmButton.setText("Centimeters")
self._buttonGroup = qt.QButtonGroup(self)
self._buttonGroup.addButton(self._pageButton)
self._buttonGroup.addButton(self._inchButton)
self._buttonGroup.addButton(self._cmButton)
self._buttonGroup.setExclusive(True)
# units
self.mainLayout.addWidget(label, 0, 0, 1, 4)
hboxLayout.addWidget(self._pageButton)
hboxLayout.addWidget(self._inchButton)
hboxLayout.addWidget(self._cmButton)
self.mainLayout.addWidget(hbox, 1, 0, 1, 4)
self._pageButton.setChecked(True)
# xOffset
label = qt.QLabel(self)
label.setText("X Offset:")
self.mainLayout.addWidget(label, 2, 0)
self._xOffset = FloatEdit(self, 0.1)
self.mainLayout.addWidget(self._xOffset, 2, 1)
# yOffset
label = qt.QLabel(self)
label.setText("Y Offset:")
self.mainLayout.addWidget(label, 2, 2)
self._yOffset = FloatEdit(self, 0.1)
self.mainLayout.addWidget(self._yOffset, 2, 3)
# width
label = qt.QLabel(self)
label.setText("Width:")
self.mainLayout.addWidget(label, 3, 0)
self._width = FloatEdit(self, 0.9)
self.mainLayout.addWidget(self._width, 3, 1)
# height
label = qt.QLabel(self)
label.setText("Height:")
self.mainLayout.addWidget(label, 3, 2)
self._height = FloatEdit(self, 0.9)
self.mainLayout.addWidget(self._height, 3, 3)
# aspect ratio
self._aspect = qt.QCheckBox(self)
self._aspect.setText("Keep screen aspect ratio")
self._aspect.setChecked(True)
self.mainLayout.addWidget(self._aspect, 4, 1, 1, 2)
def createCenteredLabel(self, text, parent=None):
label = qt.QLabel(parent)
label.setAlignment(qt.Qt.AlignCenter)
label.setText(text)
return label
def __init__(self,
parent=None,
title="Subtract strip background prior to estimation"):
super(BackgroundPage, self).__init__(parent)
self.setTitle(title)
self.setCheckable(True)
self.setToolTip(
"The strip algorithm strips away peaks to compute the " +
"background signal.\nAt each iteration, a sample is compared " +
"to the average of the two samples at a given distance in both" +
" directions,\n and if its value is higher than the average,"
"it is replaced by the average.")
layout = qt.QGridLayout(self)
self.setLayout(layout)
for i, label_text in enumerate([
"Strip width (in samples)", "Number of iterations",
"Strip threshold factor"
]):
label = qt.QLabel(label_text)
layout.addWidget(label, i, 0)
self.stripWidthSpin = qt.QSpinBox(self)
self.stripWidthSpin.setToolTip(
"Width, in number of samples, of the strip operator")
self.stripWidthSpin.setRange(1, 999999)
layout.addWidget(self.stripWidthSpin, 0, 1)
self.numIterationsSpin = qt.QSpinBox(self)
self.numIterationsSpin.setToolTip(
"Number of iterations of the strip algorithm")
self.numIterationsSpin.setRange(1, 999999)
layout.addWidget(self.numIterationsSpin, 1, 1)
self.thresholdFactorEntry = qt.QLineEdit(self)
self.thresholdFactorEntry.setToolTip(
"Factor used by the strip algorithm to decide whether a sample" +
"value should be stripped.\nThe value must be higher than the " +
"average of the 2 samples at +- w times this factor.\n")
self.thresholdFactorEntry.setValidator(qt.QDoubleValidator())
layout.addWidget(self.thresholdFactorEntry, 2, 1)
self.smoothStripGB = qt.QGroupBox("Apply smoothing prior to strip",
self)
self.smoothStripGB.setCheckable(True)
self.smoothStripGB.setToolTip(
"Apply a smoothing before subtracting strip background" +
" in fit and estimate processes")
smoothlayout = qt.QHBoxLayout(self.smoothStripGB)
label = qt.QLabel("Smoothing width (Savitsky-Golay)")
smoothlayout.addWidget(label)
self.smoothingWidthSpin = qt.QSpinBox(self)
self.smoothingWidthSpin.setToolTip(
"Width parameter for Savitsky-Golay smoothing (number of samples, must be odd)"
)
self.smoothingWidthSpin.setRange(3, 101)
self.smoothingWidthSpin.setSingleStep(2)
smoothlayout.addWidget(self.smoothingWidthSpin)
layout.addWidget(self.smoothStripGB, 3, 0, 1, 2)
layout.setRowStretch(4, 1)
self.setDefault()
def __init__(self, parent=None):
qt.QWidget.__init__(self, parent)
self.mainLayout = qt.QGridLayout(self)
self.mainLayout.setColumnStretch(1, 1)
# Algorithm choice ---------------------------------------------------
self.algorithmComboLabel = qt.QLabel(self)
self.algorithmComboLabel.setText("Background algorithm")
self.algorithmCombo = qt.QComboBox(self)
self.algorithmCombo.addItem("Strip")
self.algorithmCombo.addItem("Snip")
self.algorithmCombo.activated[int].connect(
self._algorithmComboActivated)
# Strip parameters ---------------------------------------------------
self.stripWidthLabel = qt.QLabel(self)
self.stripWidthLabel.setText("Strip Width")
self.stripWidthSpin = qt.QSpinBox(self)
self.stripWidthSpin.setMaximum(100)
self.stripWidthSpin.setMinimum(1)
self.stripWidthSpin.valueChanged[int].connect(self._emitSignal)
self.stripIterLabel = qt.QLabel(self)
self.stripIterLabel.setText("Strip Iterations")
self.stripIterValue = qt.QLineEdit(self)
validator = qt.QIntValidator(self.stripIterValue)
self.stripIterValue._v = validator
self.stripIterValue.setText("0")
self.stripIterValue.editingFinished[()].connect(self._emitSignal)
self.stripIterValue.setToolTip(
"Number of iterations for strip algorithm.\n" +
"If greater than 999, an 2nd pass of strip filter is " +
"applied to remove artifacts created by first pass.")
# Snip parameters ----------------------------------------------------
self.snipWidthLabel = qt.QLabel(self)
self.snipWidthLabel.setText("Snip Width")
self.snipWidthSpin = qt.QSpinBox(self)
self.snipWidthSpin.setMaximum(300)
self.snipWidthSpin.setMinimum(0)
self.snipWidthSpin.valueChanged[int].connect(self._emitSignal)
# Smoothing parameters -----------------------------------------------
self.smoothingFlagCheck = qt.QCheckBox(self)
self.smoothingFlagCheck.setText("Smoothing Width (Savitsky-Golay)")
self.smoothingFlagCheck.toggled.connect(self._smoothingToggled)
self.smoothingSpin = qt.QSpinBox(self)
self.smoothingSpin.setMinimum(3)
#self.smoothingSpin.setMaximum(40)
self.smoothingSpin.setSingleStep(2)
self.smoothingSpin.valueChanged[int].connect(self._emitSignal)
# Anchors ------------------------------------------------------------
self.anchorsGroup = qt.QWidget(self)
anchorsLayout = qt.QHBoxLayout(self.anchorsGroup)
anchorsLayout.setSpacing(2)
anchorsLayout.setContentsMargins(0, 0, 0, 0)
self.anchorsFlagCheck = qt.QCheckBox(self.anchorsGroup)
self.anchorsFlagCheck.setText("Use anchors")
self.anchorsFlagCheck.setToolTip(
"Define X coordinates of points that must remain fixed")
self.anchorsFlagCheck.stateChanged[int].connect(self._anchorsToggled)
anchorsLayout.addWidget(self.anchorsFlagCheck)
maxnchannel = 16384 * 4 # Fixme ?
self.anchorsList = []
num_anchors = 4
for i in range(num_anchors):
anchorSpin = qt.QSpinBox(self.anchorsGroup)
anchorSpin.setMinimum(0)
anchorSpin.setMaximum(maxnchannel)
anchorSpin.valueChanged[int].connect(self._emitSignal)
anchorsLayout.addWidget(anchorSpin)
self.anchorsList.append(anchorSpin)
# Layout ------------------------------------------------------------
self.mainLayout.addWidget(self.algorithmComboLabel, 0, 0)
self.mainLayout.addWidget(self.algorithmCombo, 0, 2)
self.mainLayout.addWidget(self.stripWidthLabel, 1, 0)
self.mainLayout.addWidget(self.stripWidthSpin, 1, 2)
self.mainLayout.addWidget(self.stripIterLabel, 2, 0)
self.mainLayout.addWidget(self.stripIterValue, 2, 2)
self.mainLayout.addWidget(self.snipWidthLabel, 3, 0)
self.mainLayout.addWidget(self.snipWidthSpin, 3, 2)
self.mainLayout.addWidget(self.smoothingFlagCheck, 4, 0)
self.mainLayout.addWidget(self.smoothingSpin, 4, 2)
self.mainLayout.addWidget(self.anchorsGroup, 5, 0, 1, 4)
# Initialize interface -----------------------------------------------
self._setAlgorithm("strip")
self.smoothingFlagCheck.setChecked(False)
self._smoothingToggled(is_checked=False)
self.anchorsFlagCheck.setChecked(False)
self._anchorsToggled(is_checked=False)
def __createConfigurationPanel(self, parent):
panel = qt.QWidget(parent=parent)
layout = qt.QVBoxLayout()
panel.setLayout(layout)
self.__kind = qt.QButtonGroup(self)
self.__kind.setExclusive(True)
group = qt.QGroupBox(self)
group.setTitle("Image")
layout.addWidget(group)
groupLayout = qt.QVBoxLayout(group)
button = qt.QRadioButton(parent=panel)
button.setText("Island")
button.clicked.connect(self.generateIsland)
button.setCheckable(True)
button.setChecked(True)
groupLayout.addWidget(button)
self.__kind.addButton(button)
button = qt.QRadioButton(parent=panel)
button.setText("Gravity")
button.clicked.connect(self.generateGravityField)
button.setCheckable(True)
groupLayout.addWidget(button)
self.__kind.addButton(button)
button = qt.QRadioButton(parent=panel)
button.setText("Magnetic")
button.clicked.connect(self.generateMagneticField)
button.setCheckable(True)
groupLayout.addWidget(button)
self.__kind.addButton(button)
button = qt.QRadioButton(parent=panel)
button.setText("Spiral")
button.clicked.connect(self.generateSpiral)
button.setCheckable(True)
groupLayout.addWidget(button)
self.__kind.addButton(button)
button = qt.QRadioButton(parent=panel)
button.setText("Gradient")
button.clicked.connect(self.generateGradient)
button.setCheckable(True)
groupLayout.addWidget(button)
self.__kind.addButton(button)
button = qt.QRadioButton(parent=panel)
button.setText("Composite gradient")
button.clicked.connect(self.generateCompositeGradient)
button.setCheckable(True)
groupLayout.addWidget(button)
self.__kind.addButton(button)
button = qt.QPushButton(parent=panel)
button.setText("Generate a new image")
button.clicked.connect(self.generate)
groupLayout.addWidget(button)
# Contours
group = qt.QGroupBox(self)
group.setTitle("Contours")
layout.addWidget(group)
groupLayout = qt.QVBoxLayout(group)
button = qt.QCheckBox(parent=panel)
button.setText("Use the plot's mask")
button.setCheckable(True)
button.setChecked(True)
button.clicked.connect(self.updateContours)
groupLayout.addWidget(button)
self.__useMaskButton = button
button = qt.QPushButton(parent=panel)
button.setText("Update contours")
button.clicked.connect(self.updateContours)
groupLayout.addWidget(button)
# Implementations
group = qt.QGroupBox(self)
group.setTitle("Implementation")
layout.addWidget(group)
groupLayout = qt.QVBoxLayout(group)
self.__impl = qt.QButtonGroup(self)
self.__impl.setExclusive(True)
button = qt.QRadioButton(parent=panel)
button.setText("silx")
button.clicked.connect(self.updateContours)
button.setCheckable(True)
button.setChecked(True)
groupLayout.addWidget(button)
self.__implMerge = button
self.__impl.addButton(button)
button = qt.QRadioButton(parent=panel)
button.setText("silx with cache")
button.clicked.connect(self.updateContours)
button.setCheckable(True)
groupLayout.addWidget(button)
self.__implMergeCache = button
self.__impl.addButton(button)
button = qt.QRadioButton(parent=panel)
button.setText("skimage")
button.clicked.connect(self.updateContours)
button.setCheckable(True)
groupLayout.addWidget(button)
self.__implSkimage = button
self.__impl.addButton(button)
if MarchingSquaresSciKitImage is None:
button.setEnabled(False)
button.setToolTip("skimage is not installed or not compatible")
# Processing
group = qt.QGroupBox(self)
group.setTitle("Processing")
layout.addWidget(group)
group.setLayout(self.__createInfoLayout(group))
# Processing
group = qt.QGroupBox(self)
group.setTitle("Custom level")
layout.addWidget(group)
groupLayout = qt.QVBoxLayout(group)
label = qt.QLabel(parent=panel)
self.__value = qt.QSlider(panel)
self.__value.setOrientation(qt.Qt.Horizontal)
self.__value.sliderMoved.connect(self.__updateCustomContours)
self.__value.valueChanged.connect(self.__updateCustomContours)
groupLayout.addWidget(self.__value)
return panel
def createCenteredLabel(self, text):
label = qt.QLabel(self)
label.setAlignment(qt.Qt.AlignCenter)
label.setText(text)
return label
def __init__(self, plot, curve, **kwargs):
super(XsocsPlot2DColorDialog, self).__init__(plot, **kwargs)
colormap = plot.getPlotColormap(curve)
self.__plot = weakref.ref(plot)
self.__curve = curve
self.__histogram = histo = plot.getHistogram(curve, colormap.nColors)
if colormap is None:
minVal = histo.edges[0][0]
maxVal = histo.edges[0][-1]
cmap = cm.jet
nColors = _defaultNColors
else:
minVal = colormap.minVal
maxVal = colormap.maxVal
cmap = colormap.colormap
if cmap not in self.colormaps:
self.colormaps[cmap.name] = cmap
nColors = colormap.nColors
if minVal is None:
minVal = histo.edges[0][0]
if maxVal is None:
maxVal = histo.edges[0][-1]
index = self.colormaps.keys().index(cmap.name)
self.__colormap = XsocsPlot2DColormap(colormap=cmap,
minVal=minVal,
maxVal=maxVal,
nColors=nColors)
layout = Qt.QGridLayout(self)
grpBox = GroupBox('Colormap')
grpBoxLayout = Qt.QGridLayout(grpBox)
self.__cmapCBox = cmapCBox = Qt.QComboBox()
for key, value in self.colormaps.items():
cmapCBox.addItem(key, userData=value)
cmapCBox.setCurrentIndex(index)
grpBoxLayout.addWidget(cmapCBox, 0, 0, Qt.Qt.AlignCenter)
cmapCBox.currentIndexChanged.connect(self.__cmapCBoxChanged)
self.__colorLabel = colorLabel = Qt.QLabel()
colorLabel.setFrameStyle(Qt.QFrame.Panel | Qt.QFrame.Sunken)
colorLabel.setLineWidth(2)
colorLabel.setMidLineWidth(2)
grpBoxLayout.addWidget(colorLabel, 1, 0)
grpBox.setSizePolicy(Qt.QSizePolicy.Fixed, Qt.QSizePolicy.Fixed)
layout.addWidget(grpBox, 0, 0)
grpBox = GroupBox('Range')
grpBoxLayout = Qt.QGridLayout(grpBox)
self.__rngSlider = rngSlider = RangeSlider()
grpBoxLayout.addWidget(rngSlider, 0, 0, 1, 2)
self.__filledProfile = filledProfile = ColorFilledProfile()
filledProfile.setFixedHeight(100)
grpBoxLayout.addWidget(filledProfile, 1, 0, 1, 2)
self.__minEdit = minEdit = StyledLineEdit(nChar=6)
self.__maxEdit = maxEdit = StyledLineEdit(nChar=6)
minEdit.setValidator(Qt.QDoubleValidator())
maxEdit.setValidator(Qt.QDoubleValidator())
minEdit.editingFinished.connect(self.__lineEditFinished)
maxEdit.editingFinished.connect(self.__lineEditFinished)
grpBoxLayout.addWidget(minEdit, 2, 0)
grpBoxLayout.addWidget(maxEdit, 2, 1)
grpBox.setSizePolicy(Qt.QSizePolicy.Fixed, Qt.QSizePolicy.Fixed)
layout.addWidget(grpBox, 1, 0, Qt.Qt.AlignCenter)
bnBox = Qt.QDialogButtonBox(Qt.QDialogButtonBox.Close)
bnBox.button(Qt.QDialogButtonBox.Close).clicked.connect(self.accept)
layout.addWidget(bnBox, 2, 0)
self.__setupWidgets()
rngSlider.sigSliderMoved.connect(self.__rngSliderMoved)
def __init__(self,
read_only=False,
**kwargs):
super(AcqParamsWidget, self).__init__(**kwargs)
layout = Qt.QGridLayout(self)
layout.setContentsMargins(0, 0, 0, 0)
self.__read_only = read_only
self.__beam_energy = None
self.__dir_beam_h = None
self.__dir_beam_v = None
self.__chpdeg_h = None
self.__chpdeg_v = None
class DblValidator(Qt.QDoubleValidator):
def validate(self, text, pos):
if len(text) == 0:
return Qt.QValidator.Acceptable, text, pos
return super(DblValidator, self).validate(text, pos)
def dblLineEditWidget(width):
wid = StyledLineEdit(nChar=width,
readOnly=read_only)
wid.setValidator(DblValidator())
return wid
# ===========
# beam energy
# ===========
row = 0
h_layout = Qt.QHBoxLayout()
beam_nrg_edit = dblLineEditWidget(8)
h_layout.addWidget(beam_nrg_edit)
h_layout.addWidget(Qt.QLabel('<b>eV</b>'))
layout.addWidget(Qt.QLabel('Beam energy :'), row, 0)
layout.addLayout(h_layout, row, 1,
alignment=Qt.Qt.AlignLeft | Qt.Qt.AlignTop)
# ===
row += 1
h_line = Qt.QFrame()
h_line.setFrameShape(Qt.QFrame.HLine)
h_line.setFrameShadow(Qt.QFrame.Sunken)
layout.addWidget(h_line, row, 0, 1, 2)
# ===========
# direct beam
# ===========
row += 1
h_layout = Qt.QHBoxLayout()
layout.addLayout(h_layout, row, 1,
alignment=Qt.Qt.AlignLeft | Qt.Qt.AlignTop)
dir_beam_h_edit = dblLineEditWidget(6)
h_layout.addWidget(Qt.QLabel('v='))
h_layout.addWidget(dir_beam_h_edit)
dir_beam_v_edit = dblLineEditWidget(6)
h_layout.addWidget(Qt.QLabel(' h='))
h_layout.addWidget(dir_beam_v_edit)
h_layout.addWidget(Qt.QLabel('<b>px</b>'))
layout.addWidget(Qt.QLabel('Direct beam :'), row, 0)
# ===
row += 1
h_line = Qt.QFrame()
h_line.setFrameShape(Qt.QFrame.HLine)
h_line.setFrameShadow(Qt.QFrame.Sunken)
layout.addWidget(h_line, row, 0, 1, 3)
# ===========
# chan per degree
# ===========
row += 1
h_layout = Qt.QHBoxLayout()
layout.addLayout(h_layout, row, 1,
alignment=Qt.Qt.AlignLeft | Qt.Qt.AlignTop)
chpdeg_h_edit = dblLineEditWidget(6)
h_layout.addWidget(Qt.QLabel('v='))
h_layout.addWidget(chpdeg_h_edit)
chpdeg_v_edit = dblLineEditWidget(6)
h_layout.addWidget(Qt.QLabel(' h='))
h_layout.addWidget(chpdeg_v_edit)
h_layout.addWidget(Qt.QLabel('<b>px</b>'))
layout.addWidget(Qt.QLabel('Chan. per deg. :'), row, 0)
# ===
row += 1
h_line = Qt.QFrame()
h_line.setFrameShape(Qt.QFrame.HLine)
h_line.setFrameShadow(Qt.QFrame.Sunken)
layout.addWidget(h_line, row, 0, 1, 3)
# ===========
# size constraints
# ===========
self.setSizePolicy(Qt.QSizePolicy(Qt.QSizePolicy.Fixed,
Qt.QSizePolicy.Fixed))
# named tuple with references to all the important widgets
self.__beam_nrg_edit = beam_nrg_edit
self.__dir_beam_h_edit = dir_beam_h_edit
self.__dir_beam_v_edit = dir_beam_v_edit
self.__chpdeg_h_edit = chpdeg_h_edit
self.__chpdeg_v_edit = chpdeg_v_edit
def main(argv=None):
"""Display an image from a file in an :class:`ImageView` widget.
:param argv: list of command line arguments or None (the default)
to use sys.argv.
:type argv: list of str
:return: Exit status code
:rtype: int
:raises IOError: if no image can be loaded from the file
"""
import argparse
import os.path
from silx.third_party.EdfFile import EdfFile
# Command-line arguments
parser = argparse.ArgumentParser(
description='Browse the images of an EDF file.')
parser.add_argument('-o',
'--origin',
nargs=2,
type=float,
default=(0., 0.),
help="""Coordinates of the origin of the image: (x, y).
Default: 0., 0.""")
parser.add_argument('-s',
'--scale',
nargs=2,
type=float,
default=(1., 1.),
help="""Scale factors applied to the image: (sx, sy).
Default: 1., 1.""")
parser.add_argument(
'-l',
'--log',
action="store_true",
help="Use logarithm normalization for colormap, default: Linear.")
parser.add_argument('filename',
nargs='?',
help='EDF filename of the image to open')
args = parser.parse_args(args=argv)
# Open the input file
if not args.filename:
logger.warning('No image file provided, displaying dummy data')
edfFile = None
size = 512
xx, yy = numpy.ogrid[-size:size, -size:size]
data = numpy.cos(xx / (size // 5)) + numpy.cos(yy / (size // 5))
data = numpy.random.poisson(numpy.abs(data))
nbFrames = 1
else:
if not os.path.isfile(args.filename):
raise IOError('No input file: %s' % args.filename)
else:
edfFile = EdfFile(args.filename)
data = edfFile.GetData(0)
nbFrames = edfFile.GetNumImages()
if nbFrames == 0:
raise IOError('Cannot read image(s) from file: %s' %
args.filename)
global app # QApplication must be global to avoid seg fault on quit
app = qt.QApplication([])
sys.excepthook = qt.exceptionHandler
mainWindow = ImageViewMainWindow()
mainWindow.setAttribute(qt.Qt.WA_DeleteOnClose)
if args.log: # Use log normalization by default
colormap = mainWindow.getDefaultColormap()
colormap.setNormalization(colormap.LOGARITHM)
mainWindow.setImage(data, origin=args.origin, scale=args.scale)
if edfFile is not None and nbFrames > 1:
# Add a toolbar for multi-frame EDF support
multiFrameToolbar = qt.QToolBar('Multi-frame')
multiFrameToolbar.addWidget(qt.QLabel('Frame [0-%d]:' %
(nbFrames - 1)))
spinBox = qt.QSpinBox()
spinBox.setRange(0, nbFrames - 1)
def updateImage(index):
mainWindow.setImage(edfFile.GetData(index),
origin=args.origin,
scale=args.scale,
reset=False)
spinBox.valueChanged[int].connect(updateImage)
multiFrameToolbar.addWidget(spinBox)
mainWindow.addToolBar(multiFrameToolbar)
mainWindow.show()
mainWindow.setFocus(qt.Qt.OtherFocusReason)
return app.exec_()
def createWidget(self, parent):
widget = qt.QLabel(parent)
widget.setWordWrap(True)
widget.setStyleSheet("QLabel { color : red; }")
return widget
def __init__(self,
spec_file=None,
img_dir=None,
spec_version=1,
output_dir=None,
tmp_dir=None,
**kwargs):
super(MergeWidget, self).__init__(**kwargs)
Qt.QGridLayout(self)
# ################
# input QGroupBox
# ################
if spec_file is not None:
specFile = spec_file
else:
specFile = ''
if img_dir is not None:
imgDir = img_dir
else:
imgDir = ''
if spec_version is not None:
specVersion = spec_version
else:
specVersion = self._defaultVersion
if output_dir is not None:
outputDir = output_dir
else:
outputDir = ''
# parameters
self.__input = {
'specfile': specFile,
'imgdir': imgDir,
'version': specVersion,
'padding': None,
'offset': None
}
self.__output = {'outdir': outputDir, 'prefix': ''}
inputGbx = GroupBox("Input")
layout = Qt.QGridLayout(inputGbx)
self.layout().addWidget(inputGbx, 0, 0, Qt.Qt.AlignTop)
first_col = 0
file_bn_col = 4
last_col = file_bn_col + 1
spec_row = 0
img_path_row = 1
version_row = 2
apply_bn_row = 3
# spec file input
specFileChooser = FileChooser(fileMode=Qt.QFileDialog.ExistingFile,
noLabel=True)
specFileChooser.lineEdit.setText(specFile)
specFileChooser.sigSelectionChanged.connect(self.__slotSpecFileChanged)
layout.addWidget(Qt.QLabel('Spec file :'), spec_row, 0)
layout.addWidget(specFileChooser, spec_row, 1)
# image folder input
imgDirChooser = FileChooser(fileMode=Qt.QFileDialog.Directory,
noLabel=True)
imgDirChooser.lineEdit.setText(imgDir)
imgDirChooser.sigSelectionChanged.connect(self.__slotImgDirChanged)
layout.addWidget(Qt.QLabel('Img dir. :'), img_path_row, 0)
layout.addWidget(imgDirChooser, img_path_row, 1)
# version selection
optionLayout = Qt.QHBoxLayout()
optionLayout.addStretch(1)
lab = Qt.QLabel('Version :')
self.__versionCBx = versionCBx = Qt.QComboBox()
for version in range(len(self._versions)):
versionCBx.addItem(str(version))
versionCBx.addItem('')
optionLayout.addWidget(lab, Qt.Qt.AlignLeft)
optionLayout.addWidget(versionCBx, Qt.Qt.AlignLeft)
# filename padding for the nextNr counter
self.__padSpinBox = padSpinBox = Qt.QSpinBox()
optionLayout.addWidget(_vLine())
optionLayout.addWidget(Qt.QLabel('nextNr padding:'))
optionLayout.addWidget(padSpinBox, Qt.Qt.AlignLeft)
padSpinBox.valueChanged[int].connect(self.__slotPaddingValueChanged)
# filename offset for the nextNr counter
self.__nextNrSpinBox = nextNrSpinBox = Qt.QSpinBox()
nextNrSpinBox.setMinimum(-100)
nextNrSpinBox.setMaximum(100)
optionLayout.addWidget(_vLine())
optionLayout.addWidget(Qt.QLabel('nextNr offset:'))
optionLayout.addWidget(nextNrSpinBox, Qt.Qt.AlignLeft)
nextNrSpinBox.valueChanged[int].connect(self.__slotNextNrValueChanged)
optionLayout.addStretch(100)
layout.addLayout(optionLayout, version_row, 0, 1, layout.columnCount(),
Qt.Qt.AlignLeft)
# last row : apply button
self.__parseBn = parseBn = FixedSizePushButon('Parse file')
parseBn.clicked.connect(self.__slotParseBnClicked,
Qt.Qt.QueuedConnection)
layout.addWidget(parseBn, apply_bn_row, 0, 1, last_col - first_col,
Qt.Qt.AlignHCenter)
# ################
# scans + edf QGroupBox
# ################
self.__scansGbx = scansGbx = GroupBox("Spec + EDF")
grpLayout = Qt.QHBoxLayout(scansGbx)
self.layout().addWidget(scansGbx, 1, 0,
Qt.Qt.AlignLeft | Qt.Qt.AlignTop)
# ===========
# valid scans
# ===========
scanLayout = Qt.QGridLayout()
grpLayout.addLayout(scanLayout)
hLayout = Qt.QHBoxLayout()
label = Qt.QLabel('<span style=" font-weight:600; color:#00916a;">'
'Matched scans</span>')
label.setTextFormat(Qt.Qt.RichText)
editScansBn = FixedSizePushButon('Edit')
editScansBn.clicked.connect(self.__slotEditScansClicked)
hLayout.addWidget(label)
hLayout.addWidget(editScansBn)
scanLayout.addLayout(hLayout, 0, 0, 1, 2)
label = Qt.QLabel('Total :')
self.__totalScansEdit = totalScansEdit = Qt.QLineEdit('0')
totalScansEdit.setReadOnly(True)
fm = totalScansEdit.fontMetrics()
width = (fm.boundingRect('0123456').width() +
fm.boundingRect('00').width())
totalScansEdit.setMaximumWidth(width)
totalScansEdit.setAlignment(Qt.Qt.AlignRight)
scanLayout.addWidget(label, 1, 0, Qt.Qt.AlignLeft)
scanLayout.addWidget(totalScansEdit, 1, 1, Qt.Qt.AlignLeft)
# ====
label = Qt.QLabel('Selected :')
self.__selectedScansEdit = selectedScansEdit = Qt.QLineEdit('0')
selectedScansEdit.setReadOnly(True)
fm = selectedScansEdit.fontMetrics()
width = (fm.boundingRect('0123456').width() +
fm.boundingRect('00').width())
selectedScansEdit.setMaximumWidth(width)
selectedScansEdit.setAlignment(Qt.Qt.AlignRight)
scanLayout.addWidget(label, 2, 0, Qt.Qt.AlignLeft)
scanLayout.addWidget(selectedScansEdit, 2, 1, Qt.Qt.AlignLeft)
# ===
grpLayout.addWidget(_vLine())
# ===========
# "other" scans
# ===========
scanLayout = Qt.QGridLayout()
grpLayout.addLayout(scanLayout)
hLayout = Qt.QHBoxLayout()
label = Qt.QLabel('<span style=" font-weight:600; color:#ff6600;">'
'Other scans</span>')
otherScansBn = FixedSizePushButon('View')
otherScansBn.clicked.connect(self.__slotOtherScansClicked)
hLayout.addWidget(label)
hLayout.addWidget(otherScansBn)
scanLayout.addLayout(hLayout, 0, 0, 1, 2)
label = Qt.QLabel('No match :')
self.__noMatchScansEdit = noMatchScansEdit = Qt.QLineEdit('0')
noMatchScansEdit.setReadOnly(True)
fm = noMatchScansEdit.fontMetrics()
width = (fm.boundingRect('0123456').width() +
fm.boundingRect('00').width())
noMatchScansEdit.setMaximumWidth(width)
noMatchScansEdit.setAlignment(Qt.Qt.AlignRight)
scanLayout.addWidget(label, 1, 0, Qt.Qt.AlignLeft)
scanLayout.addWidget(noMatchScansEdit, 1, 1, Qt.Qt.AlignLeft)
# ====
label = Qt.QLabel('No img info :')
self.__noImgInfoEdit = noImgInfoEdit = Qt.QLineEdit('0')
noImgInfoEdit.setReadOnly(True)
fm = noImgInfoEdit.fontMetrics()
width = (fm.boundingRect('0123456').width() +
fm.boundingRect('00').width())
noImgInfoEdit.setMaximumWidth(width)
noImgInfoEdit.setAlignment(Qt.Qt.AlignRight)
scanLayout.addWidget(label, 2, 0, Qt.Qt.AlignLeft)
scanLayout.addWidget(noImgInfoEdit, 2, 1, Qt.Qt.AlignLeft)
# ===
grpLayout.addWidget(_vLine())
# ################
# parameters
# ################
self.__acqParamsGbx = acqParamsGbx = GroupBox("Acq. Parameters")
grpLayout = Qt.QVBoxLayout(acqParamsGbx)
self.__acqParamWid = acqParamWid = AcqParamsWidget()
self.layout().addWidget(acqParamsGbx, 2, 0,
Qt.Qt.AlignLeft | Qt.Qt.AlignTop)
grpLayout.addWidget(acqParamWid)
# ################
# output options
# ################
self.__outputGbx = outputGbx = GroupBox("Output")
layout = Qt.QGridLayout(outputGbx)
self.layout().addWidget(outputGbx, 3, 0, Qt.Qt.AlignTop)
# ===========
# master
# ===========
lab = Qt.QLabel('Prefix :')
self.__prefixEdit = prefixEdit = StyledLineEdit(nChar=20)
prefixEdit.textChanged.connect(self.__slotPrefixChanged)
hLayout = Qt.QHBoxLayout()
layout.addLayout(hLayout, 0, 1, Qt.Qt.AlignLeft)
resetPrefixBn = Qt.QToolButton()
icon = Qt.qApp.style().standardIcon(Qt.QStyle.SP_BrowserReload)
resetPrefixBn.setIcon(icon)
resetPrefixBn.clicked.connect(self.__slotResetPrefixClicked)
layout.addWidget(lab, 0, 0, Qt.Qt.AlignLeft)
sp = prefixEdit.sizePolicy()
sp.setHorizontalPolicy(Qt.QSizePolicy.Maximum)
prefixEdit.setSizePolicy(sp)
hLayout.addWidget(prefixEdit, Qt.Qt.AlignLeft)
hLayout.addWidget(resetPrefixBn, Qt.Qt.AlignLeft)
# ===========
# output folder
# ===========
outDirChooser = FileChooser(fileMode=Qt.QFileDialog.Directory,
noLabel=True)
outDirChooser.lineEdit.setText(outputDir)
outDirChooser.sigSelectionChanged.connect(self.__slotOutDirChanged)
layout.addWidget(Qt.QLabel('Output directory :'), 1, 0)
layout.addWidget(outDirChooser, 1, 1)
# ################
# merge button
# ################
self.__mergeBn = mergeBn = Qt.QPushButton('Merge')
cancelBn = Qt.QPushButton('Cancel')
hLayout = Qt.QHBoxLayout()
self.layout().addLayout(hLayout, 4, 0, 1, 1,
Qt.Qt.AlignHCenter | Qt.Qt.AlignTop)
hLayout.addWidget(mergeBn)
hLayout.addWidget(cancelBn)
mergeBn.clicked.connect(self.__slotMergeBnClicked)
cancelBn.clicked.connect(self.reject)
# #################
# setting initial state
# #################
# scansGbx.setEnabled(False)
# acqParamsGbx.setEnabled(False)
# outputGbx.setEnabled(False)
# mergeBn.setEnabled(False)
parseBn.setEnabled(False)
self.__merger = None
self.__parser = None
self.info_wid = None
if tmp_dir is None:
tmp_dir, delete_tmp, q_tmp_dir = _create_tmp_dir()
else:
delete_tmp = False
q_tmp_dir = None
self.__tmp_root = tmp_dir
self.__delete_tmp_root = delete_tmp
self.__q_tmp_dir = q_tmp_dir
tmp_dir = os.path.join(self.__tmp_root, 'xsocs_merge')
if not os.path.exists(tmp_dir):
os.makedirs(tmp_dir)
self.__tmp_dir_merge = tmp_dir
print('Using temporary folder : {0}.'.format(tmp_dir))
self.__widgetIsSetup = False
self.__xsocs_h5 = None
versionCBx.setCurrentIndex(spec_version)
self.__slotVersionChanged(spec_version)
versionCBx.currentIndexChanged[int].connect(self.__slotVersionChanged)
self.__resetState()
self.__sigParsed.connect(self.__slotParsed, Qt.Qt.QueuedConnection)
def _initThresholdGroupBox(self):
"""Init thresholding widgets"""
self.belowThresholdAction = qt.QAction(
icons.getQIcon('plot-roi-below'), 'Mask below threshold', self)
self.belowThresholdAction.setToolTip(
'Mask image where values are below given threshold')
self.belowThresholdAction.setCheckable(True)
self.belowThresholdAction.setChecked(True)
self.betweenThresholdAction = qt.QAction(
icons.getQIcon('plot-roi-between'), 'Mask within range', self)
self.betweenThresholdAction.setToolTip(
'Mask image where values are within given range')
self.betweenThresholdAction.setCheckable(True)
self.aboveThresholdAction = qt.QAction(
icons.getQIcon('plot-roi-above'), 'Mask above threshold', self)
self.aboveThresholdAction.setToolTip(
'Mask image where values are above given threshold')
self.aboveThresholdAction.setCheckable(True)
self.thresholdActionGroup = qt.QActionGroup(self)
self.thresholdActionGroup.setExclusive(True)
self.thresholdActionGroup.addAction(self.belowThresholdAction)
self.thresholdActionGroup.addAction(self.betweenThresholdAction)
self.thresholdActionGroup.addAction(self.aboveThresholdAction)
self.thresholdActionGroup.triggered.connect(
self._thresholdActionGroupTriggered)
self.loadColormapRangeAction = qt.QAction(
icons.getQIcon('view-refresh'), 'Set min-max from colormap', self)
self.loadColormapRangeAction.setToolTip(
'Set min and max values from current colormap range')
self.loadColormapRangeAction.setCheckable(False)
self.loadColormapRangeAction.triggered.connect(
self._loadRangeFromColormapTriggered)
widgets = []
for action in self.thresholdActionGroup.actions():
btn = qt.QToolButton()
btn.setDefaultAction(action)
widgets.append(btn)
spacer = qt.QWidget(parent=self)
spacer.setSizePolicy(qt.QSizePolicy.Expanding,
qt.QSizePolicy.Preferred)
widgets.append(spacer)
loadColormapRangeBtn = qt.QToolButton()
loadColormapRangeBtn.setDefaultAction(self.loadColormapRangeAction)
widgets.append(loadColormapRangeBtn)
toolBar = self._hboxWidget(*widgets, stretch=False)
config = qt.QGridLayout()
config.setContentsMargins(0, 0, 0, 0)
self.minLineLabel = qt.QLabel("Min:", self)
self.minLineEdit = FloatEdit(self, value=0)
config.addWidget(self.minLineLabel, 0, 0)
config.addWidget(self.minLineEdit, 0, 1)
self.maxLineLabel = qt.QLabel("Max:", self)
self.maxLineEdit = FloatEdit(self, value=0)
config.addWidget(self.maxLineLabel, 1, 0)
config.addWidget(self.maxLineEdit, 1, 1)
self.applyMaskBtn = qt.QPushButton('Apply mask')
self.applyMaskBtn.clicked.connect(self._maskBtnClicked)
layout = qt.QVBoxLayout()
layout.addWidget(toolBar)
layout.addLayout(config)
layout.addWidget(self.applyMaskBtn)
layout.addStretch(1)
self.thresholdGroup = qt.QGroupBox('Threshold')
self.thresholdGroup.setLayout(layout)
# Init widget state
self._thresholdActionGroupTriggered(self.belowThresholdAction)
return self.thresholdGroup
def _initMaskGroupBox(self):
"""Init general mask operation widgets"""
# Mask level
self.levelSpinBox = qt.QSpinBox()
self.levelSpinBox.setRange(1, self._maxLevelNumber)
self.levelSpinBox.setToolTip(
'Choose which mask level is edited.\n'
'A mask can have up to 255 non-overlapping levels.')
self.levelSpinBox.valueChanged[int].connect(self._updateColors)
self._levelWidget = self._hboxWidget(qt.QLabel('Mask level:'),
self.levelSpinBox)
# Transparency
self._transparencyWidget = self._initTransparencyWidget()
style = qt.QApplication.style()
def getIcon(*identifiyers):
for i in identifiyers:
if isinstance(i, str):
if qt.QIcon.hasThemeIcon(i):
return qt.QIcon.fromTheme(i)
elif isinstance(i, qt.QIcon):
return i
else:
return style.standardIcon(i)
return qt.QIcon()
undoAction = qt.QAction(self)
undoAction.setText('Undo')
icon = getIcon("edit-undo", qt.QStyle.SP_ArrowBack)
undoAction.setIcon(icon)
undoAction.setShortcut(qt.QKeySequence.Undo)
undoAction.setToolTip('Undo last mask change <b>%s</b>' %
undoAction.shortcut().toString())
self._mask.sigUndoable.connect(undoAction.setEnabled)
undoAction.triggered.connect(self._mask.undo)
redoAction = qt.QAction(self)
redoAction.setText('Redo')
icon = getIcon("edit-redo", qt.QStyle.SP_ArrowForward)
redoAction.setIcon(icon)
redoAction.setShortcut(qt.QKeySequence.Redo)
redoAction.setToolTip('Redo last undone mask change <b>%s</b>' %
redoAction.shortcut().toString())
self._mask.sigRedoable.connect(redoAction.setEnabled)
redoAction.triggered.connect(self._mask.redo)
loadAction = qt.QAction(self)
loadAction.setText('Load...')
icon = icons.getQIcon("document-open")
loadAction.setIcon(icon)
loadAction.setToolTip('Load mask from file')
loadAction.triggered.connect(self._loadMask)
saveAction = qt.QAction(self)
saveAction.setText('Save...')
icon = icons.getQIcon("document-save")
saveAction.setIcon(icon)
saveAction.setToolTip('Save mask to file')
saveAction.triggered.connect(self._saveMask)
invertAction = qt.QAction(self)
invertAction.setText('Invert')
icon = icons.getQIcon("mask-invert")
invertAction.setIcon(icon)
invertAction.setShortcut(qt.Qt.CTRL + qt.Qt.Key_I)
invertAction.setToolTip('Invert current mask <b>%s</b>' %
invertAction.shortcut().toString())
invertAction.triggered.connect(self._handleInvertMask)
clearAction = qt.QAction(self)
clearAction.setText('Clear')
icon = icons.getQIcon("mask-clear")
clearAction.setIcon(icon)
clearAction.setShortcut(qt.QKeySequence.Delete)
clearAction.setToolTip('Clear current mask level <b>%s</b>' %
clearAction.shortcut().toString())
clearAction.triggered.connect(self._handleClearMask)
clearAllAction = qt.QAction(self)
clearAllAction.setText('Clear all')
icon = icons.getQIcon("mask-clear-all")
clearAllAction.setIcon(icon)
clearAllAction.setToolTip('Clear all mask levels')
clearAllAction.triggered.connect(self.resetSelectionMask)
# Buttons group
margin1 = qt.QWidget(self)
margin1.setMinimumWidth(6)
margin2 = qt.QWidget(self)
margin2.setMinimumWidth(6)
actions = (loadAction, saveAction, margin1, undoAction, redoAction,
margin2, invertAction, clearAction, clearAllAction)
widgets = []
for action in actions:
if isinstance(action, qt.QWidget):
widgets.append(action)
continue
btn = qt.QToolButton()
btn.setDefaultAction(action)
widgets.append(btn)
if action is clearAllAction:
self._clearAllBtn = btn
container = self._hboxWidget(*widgets)
container.layout().setSpacing(1)
layout = qt.QVBoxLayout()
layout.addWidget(container)
layout.addWidget(self._levelWidget)
layout.addWidget(self._transparencyWidget)
layout.addStretch(1)
maskGroup = qt.QGroupBox('Mask')
maskGroup.setLayout(layout)
return maskGroup
def __init__(self, qspaceFile, **kwargs):
super(FitWidget, self).__init__(**kwargs)
self.__qspaceH5 = qspaceH5 = QSpaceH5(qspaceFile)
self.__progTimer = None
self.__outputFile = None
self.__nPeaks = 1
layout = Qt.QGridLayout(self)
self.__roiWidget = roiWidget = Roi3DSelectorWidget()
layout.addWidget(roiWidget)
fileLayout = Qt.QHBoxLayout()
self.__fileEdit = fileEdit = StyledLineEdit(nChar=20, readOnly=True)
fileLayout.addWidget(Qt.QLabel('File :'))
fileLayout.addWidget(fileEdit)
layout.addLayout(fileLayout, 1, 0)
fitLayout = Qt.QHBoxLayout()
self.__fitTypeCb = fitTypeCb = Qt.QComboBox()
fitTypeCb.addItems(list(FitWidget.FitTypes.keys()))
fitTypeCb.setCurrentIndex(0)
fitLayout.addWidget(Qt.QLabel('Fit :'))
fitLayout.addWidget(fitTypeCb)
fitTypeCb.currentIndexChanged[str].connect(
self.__slotCurrentTextChanged)
layout.addLayout(fitLayout, 2, 0, alignment=Qt.Qt.AlignLeft)
self.__nPeaksSpinBox = spinbox = Qt.QSpinBox()
# spinbox.setMinimum(1)
# spinbox.setMaximum(20)
# spinbox.setValue(self.__nPeaks)
# spinbox.setToolTip('Max. number of expected peaks.')
# spinbox.valueChanged.connect(self.__slotValueChanged)
# fitLayout.addWidget(spinbox)
# fitLayout.addWidget(Qt.QLabel('peak(s)'))
runLayout = Qt.QHBoxLayout()
self.__runButton = runButton = Qt.QPushButton('Run')
runButton.setEnabled(False)
runButton.clicked.connect(self.__slotRunClicked)
runLayout.addWidget(runButton)
self.__progBar = progBar = Qt.QProgressBar()
runLayout.addWidget(progBar)
layout.addLayout(runLayout, 3, 0, alignment=Qt.Qt.AlignCenter)
self.__statusLabel = statusLabel = Qt.QLabel('Ready')
statusLabel.setFrameStyle(Qt.QFrame.Panel | Qt.QFrame.Sunken)
layout.addWidget(statusLabel, 4, 0)
with qspaceH5:
qx = qspaceH5.qx
qy = qspaceH5.qy
qz = qspaceH5.qz
roiWidget.xSlider().setRange([qx[0], qx[-1]])
roiWidget.ySlider().setRange([qy[0], qy[-1]])
roiWidget.zSlider().setRange([qz[0], qz[-1]])
self.__sigFitDone.connect(self.__slotFitDone)
layout.setRowStretch(layout.rowCount(), 1)
layout.setColumnStretch(layout.columnCount(), 1)
def setArrayData(self, data, labels=None, copy=True, editable=False):
"""Set the data array. Update frame browsers and labels.
:param data: Numpy array or similar object (e.g. nested sequence,
h5py dataset...)
:param labels: list of labels for each dimension of the array, or
boolean ``True`` to use default labels ("dimension 0",
"dimension 1", ...). `None` to disable labels (default).
:param bool copy: If *True*, store a copy of *data* in the model. If
*False*, store a reference to *data* if possible (only possible if
*data* is a proper numpy array or an object that implements the
same methods).
:param bool editable: Flag to enable editing data. Default is *False*
"""
self._data_shape = _get_shape(data)
n_widgets = len(self._browserWidgets)
n_dimensions = len(self._data_shape)
# Reset text of labels
self._dimensionLabelsText = []
for i in range(n_dimensions):
if labels in [True, 1]:
label_text = "Dimension %d" % i
elif labels is None or i >= len(labels):
label_text = ""
else:
label_text = labels[i]
self._dimensionLabelsText.append(label_text)
# not enough widgets, create new ones (we need n_dim - 2)
for i in range(n_widgets, n_dimensions - 2):
browser = HorizontalSliderWithBrowser(self.browserContainer)
self.browserLayout.addWidget(browser, i, 1)
self._browserWidgets.append(browser)
browser.valueChanged.connect(self._browserSlot)
browser.setEnabled(False)
browser.hide()
label = qt.QLabel(self.browserContainer)
self._browserLabels.append(label)
self.browserLayout.addWidget(label, i, 0)
label.hide()
n_widgets = len(self._browserWidgets)
for i in range(n_widgets):
label = self._browserLabels[i]
browser = self._browserWidgets[i]
if (i + 2) < n_dimensions:
label.setText(self._dimensionLabelsText[i])
browser.setRange(0, self._data_shape[i] - 1)
browser.setEnabled(True)
browser.show()
if labels is not None:
label.show()
else:
label.hide()
else:
browser.setEnabled(False)
browser.hide()
label.hide()
# set model
self.model.setArrayData(data, copy=copy, editable=editable)
# some linux distributions need this call
self.view.setModel(self.model)
if editable:
self.view.enableCut()
self.view.enablePaste()
# initialize & connect axesSelector
self.axesSelector.setNDimensions(n_dimensions)
self.axesSelector.sigDimensionsChanged.connect(self.setFrameAxes)
def _initMaskGroupBox(self):
"""Init general mask operation widgets"""
# Mask level
self.levelSpinBox = qt.QSpinBox()
self.levelSpinBox.setRange(1, self._maxLevelNumber)
self.levelSpinBox.setToolTip(
'Choose which mask level is edited.\n'
'A mask can have up to 255 non-overlapping levels.')
self.levelSpinBox.valueChanged[int].connect(self._updateColors)
self.levelWidget = self._hboxWidget(qt.QLabel('Mask level:'),
self.levelSpinBox)
# Transparency
self.transparencyWidget = self._initTransparencyWidget()
# Buttons group
invertBtn = qt.QPushButton('Invert')
invertBtn.setShortcut(qt.Qt.CTRL + qt.Qt.Key_I)
invertBtn.setToolTip('Invert current mask <b>%s</b>' %
invertBtn.shortcut().toString())
invertBtn.clicked.connect(self._handleInvertMask)
clearBtn = qt.QPushButton('Clear')
clearBtn.setShortcut(qt.QKeySequence.Delete)
clearBtn.setToolTip('Clear current mask level <b>%s</b>' %
clearBtn.shortcut().toString())
clearBtn.clicked.connect(self._handleClearMask)
invertClearWidget = self._hboxWidget(invertBtn,
clearBtn,
stretch=False)
undoBtn = qt.QPushButton('Undo')
undoBtn.setShortcut(qt.QKeySequence.Undo)
undoBtn.setToolTip('Undo last mask change <b>%s</b>' %
undoBtn.shortcut().toString())
self._mask.sigUndoable.connect(undoBtn.setEnabled)
undoBtn.clicked.connect(self._mask.undo)
redoBtn = qt.QPushButton('Redo')
redoBtn.setShortcut(qt.QKeySequence.Redo)
redoBtn.setToolTip('Redo last undone mask change <b>%s</b>' %
redoBtn.shortcut().toString())
self._mask.sigRedoable.connect(redoBtn.setEnabled)
redoBtn.clicked.connect(self._mask.redo)
undoRedoWidget = self._hboxWidget(undoBtn, redoBtn, stretch=False)
self.clearAllBtn = qt.QPushButton('Clear all')
self.clearAllBtn.setToolTip('Clear all mask levels')
self.clearAllBtn.clicked.connect(self.resetSelectionMask)
loadBtn = qt.QPushButton('Load...')
loadBtn.clicked.connect(self._loadMask)
saveBtn = qt.QPushButton('Save...')
saveBtn.clicked.connect(self._saveMask)
self.loadSaveWidget = self._hboxWidget(loadBtn, saveBtn, stretch=False)
layout = qt.QVBoxLayout()
layout.addWidget(self.levelWidget)
layout.addWidget(self.transparencyWidget)
layout.addWidget(invertClearWidget)
layout.addWidget(undoRedoWidget)
layout.addWidget(self.clearAllBtn)
layout.addWidget(self.loadSaveWidget)
layout.addStretch(1)
maskGroup = qt.QGroupBox('Mask')
maskGroup.setLayout(layout)
return maskGroup
def __init__(self,
parent=None,
resetzoom=True,
backend=None,
autoScale=False,
logScale=False,
grid=False,
colormap=True,
aspectRatio=True,
yinverted=True,
copy=True,
save=True,
print_=True,
control=False,
position=None,
mask=True):
qt.QMainWindow.__init__(self, parent)
if parent is not None:
# behave as a widget
self.setWindowFlags(qt.Qt.Widget)
else:
self.setWindowTitle('StackView')
self._stack = None
"""Loaded stack, as a 3D array, a 3D dataset or a list of 2D arrays."""
self.__transposed_view = None
"""View on :attr:`_stack` with the axes sorted, to have
the orthogonal dimension first"""
self._perspective = 0
"""Orthogonal dimension (depth) in :attr:`_stack`"""
self._stackItem = ImageStack()
"""Hold the item displaying the stack"""
imageLegend = '__StackView__image' + str(id(self))
self._stackItem.setName(imageLegend)
self.__autoscaleCmap = False
"""Flag to disable/enable colormap auto-scaling
based on the min/max values of the entire 3D volume"""
self.__dimensionsLabels = ["Dimension 0", "Dimension 1", "Dimension 2"]
"""These labels are displayed on the X and Y axes.
:meth:`setLabels` updates this attribute."""
self._first_stack_dimension = 0
"""Used for dimension labels and combobox"""
self._titleCallback = self._defaultTitleCallback
"""Function returning the plot title based on the frame index.
It can be set to a custom function using :meth:`setTitleCallback`"""
self.calibrations3D = (calibration.NoCalibration(),
calibration.NoCalibration(),
calibration.NoCalibration())
central_widget = qt.QWidget(self)
self._plot = PlotWindow(parent=central_widget,
backend=backend,
resetzoom=resetzoom,
autoScale=autoScale,
logScale=logScale,
grid=grid,
curveStyle=False,
colormap=colormap,
aspectRatio=aspectRatio,
yInverted=yinverted,
copy=copy,
save=save,
print_=print_,
control=control,
position=position,
roi=False,
mask=mask)
self._plot.addItem(self._stackItem)
self._plot.getIntensityHistogramAction().setVisible(True)
self.sigInteractiveModeChanged = self._plot.sigInteractiveModeChanged
self.sigActiveImageChanged = self._plot.sigActiveImageChanged
self.sigPlotSignal = self._plot.sigPlotSignal
if silx.config.DEFAULT_PLOT_IMAGE_Y_AXIS_ORIENTATION == 'downward':
self._plot.getYAxis().setInverted(True)
self._addColorBarAction()
self._profileToolBar = Profile3DToolBar(parent=self._plot,
stackview=self)
self._plot.addToolBar(self._profileToolBar)
self._plot.getXAxis().setLabel('Columns')
self._plot.getYAxis().setLabel('Rows')
self._plot.sigPlotSignal.connect(self._plotCallback)
self._plot.getSaveAction().setFileFilter(
'image',
self.IMAGE_STACK_FILTER_NXDATA,
func=self._saveImageStack,
appendToFile=True)
self.__planeSelection = PlanesWidget(self._plot)
self.__planeSelection.sigPlaneSelectionChanged.connect(
self.setPerspective)
self._browser_label = qt.QLabel("Image index (Dim0):")
self._browser = HorizontalSliderWithBrowser(central_widget)
self._browser.setRange(0, 0)
self._browser.valueChanged[int].connect(self.__updateFrameNumber)
self._browser.setEnabled(False)
layout = qt.QGridLayout()
layout.setContentsMargins(0, 0, 0, 0)
layout.addWidget(self._plot, 0, 0, 1, 3)
layout.addWidget(self.__planeSelection, 1, 0)
layout.addWidget(self._browser_label, 1, 1)
layout.addWidget(self._browser, 1, 2)
central_widget.setLayout(layout)
self.setCentralWidget(central_widget)
# clear profile lines when the perspective changes (plane browsed changed)
self.__planeSelection.sigPlaneSelectionChanged.connect(
self._profileToolBar.clearProfile)
def gui(self, log=False, maximize=False, pick=True):
"""
:param log: show z in log scale
"""
if self.fig is None:
self.fig = pyplot.figure()
self.fig.subplots_adjust(right=0.75)
# add 3 subplots at the same position for debye-sherrer image, contour-plot and massif contour
self.ax = self.fig.add_subplot(111)
self.ct = self.fig.add_subplot(111)
self.msp = self.fig.add_subplot(111)
toolbar = self.fig.canvas.toolbar
toolbar.addSeparator()
a = toolbar.addAction('Opts', self.on_option_clicked)
a.setToolTip('open options window')
if pick:
label = qt.QLabel("Ring #", toolbar)
toolbar.addWidget(label)
self.spinbox = qt.QSpinBox(toolbar)
self.spinbox.setMinimum(0)
self.sb_action = toolbar.addWidget(self.spinbox)
a = toolbar.addAction('Refine', self.on_refine_clicked)
a.setToolTip('switch to refinement mode')
self.ref_action = a
self.mpl_connectId = self.fig.canvas.mpl_connect(
'button_press_event', self.onclick)
if log:
data_disp = numpy.log1p(self.data - self.data.min())
txt = 'Log colour scale (skipping lowest/highest per mille)'
else:
data_disp = self.data
txt = 'Linear colour scale (skipping lowest/highest per mille)'
# skip lowest and highest per mille of image values via vmin/vmax
sorted_list = data_disp.flatten() # explicit copy
sorted_list.sort()
show_min = sorted_list[int(round(1e-3 * (sorted_list.size - 1)))]
show_max = sorted_list[int(round(0.999 * (sorted_list.size - 1)))]
im = self.ax.imshow(
data_disp,
vmin=show_min,
vmax=show_max,
origin="lower",
interpolation="nearest",
)
self.ax.set_ylabel('y in pixels')
self.ax.set_xlabel('x in pixels')
if self.detector:
s1, s2 = self.data.shape
s1 -= 1
s2 -= 1
self.ax.set_xlim(0, s2)
self.ax.set_ylim(0, s1)
d1 = numpy.array([0, s1, s1, 0])
d2 = numpy.array([0, 0, s2, s2])
p1, p2, _ = self.detector.calc_cartesian_positions(d1=d1, d2=d2)
ax = self.fig.add_subplot(1,
1,
1,
xbound=False,
ybound=False,
xlabel=r'dim2 ($\approx m$)',
ylabel=r'dim1 ($\approx m$)',
xlim=(p2.min(), p2.max()),
ylim=(p1.min(), p1.max()),
aspect='equal',
zorder=-1)
ax.xaxis.set_label_position('top')
ax.yaxis.set_label_position('right')
ax.yaxis.label.set_color('blue')
ax.xaxis.label.set_color('blue')
ax.tick_params(colors="blue",
labelbottom='off',
labeltop='on',
labelleft='off',
labelright='on')
# ax.autoscale_view(False, False, False)
else:
_cbar = self.fig.colorbar(im, label=txt)
# self.ax.autoscale_view(False, False, False)
update_fig(self.fig)
if maximize:
maximize_fig(self.fig)
if not gui_utils.main_loop:
self.fig.show()
def __init__(self, parent=None):
super(SearchPage, self).__init__(parent)
layout = qt.QVBoxLayout(self)
self.manualFwhmGB = qt.QGroupBox("Define FWHM manually", self)
self.manualFwhmGB.setCheckable(True)
self.manualFwhmGB.setToolTip(
"If disabled, the FWHM parameter used for peak search is " +
"estimated based on the highest peak in the data")
layout.addWidget(self.manualFwhmGB)
# ------------ GroupBox fwhm--------------------------
layout2 = qt.QHBoxLayout(self.manualFwhmGB)
self.manualFwhmGB.setLayout(layout2)
label = qt.QLabel("Fwhm Points", self.manualFwhmGB)
layout2.addWidget(label)
self.fwhmPointsSpin = qt.QSpinBox(self.manualFwhmGB)
self.fwhmPointsSpin.setRange(0, 999999)
self.fwhmPointsSpin.setToolTip(
"Typical peak fwhm (number of data points)")
layout2.addWidget(self.fwhmPointsSpin)
# ----------------------------------------------------
self.manualScalingGB = qt.QGroupBox("Define scaling manually", self)
self.manualScalingGB.setCheckable(True)
self.manualScalingGB.setToolTip(
"If disabled, the Y scaling used for peak search is " +
"estimated automatically")
layout.addWidget(self.manualScalingGB)
# ------------ GroupBox scaling-----------------------
layout3 = qt.QHBoxLayout(self.manualScalingGB)
self.manualScalingGB.setLayout(layout3)
label = qt.QLabel("Y Scaling", self.manualScalingGB)
layout3.addWidget(label)
self.yScalingEntry = qt.QLineEdit(self.manualScalingGB)
self.yScalingEntry.setToolTip(
"Data values will be multiplied by this value prior to peak" +
" search")
self.yScalingEntry.setValidator(qt.QDoubleValidator())
layout3.addWidget(self.yScalingEntry)
# ----------------------------------------------------
# ------------------- grid layout --------------------
containerWidget = qt.QWidget(self)
layout4 = qt.QHBoxLayout(containerWidget)
containerWidget.setLayout(layout4)
label = qt.QLabel("Sensitivity", containerWidget)
layout4.addWidget(label)
self.sensitivityEntry = qt.QLineEdit(containerWidget)
self.sensitivityEntry.setToolTip(
"Peak search sensitivity threshold, expressed as a multiple " +
"of the standard deviation of the noise.\nMinimum value is 1 " +
"(to be detected, peak must be higher than the estimated noise)")
sensivalidator = qt.QDoubleValidator()
sensivalidator.setBottom(1.0)
self.sensitivityEntry.setValidator(sensivalidator)
layout4.addWidget(self.sensitivityEntry)
# ----------------------------------------------------
layout.addWidget(containerWidget)
self.forcePeakPresenceCB = qt.QCheckBox("Force peak presence", self)
self.forcePeakPresenceCB.setToolTip(
"If peak search algorithm is unsuccessful, place one peak " +
"at the maximum of the curve")
layout.addWidget(self.forcePeakPresenceCB)
layout.addStretch()
self.setDefault()
def createWidget(self, parent):
return qt.QLabel(parent)
def __init__(self,
parent=None,
resetzoom=True,
backend=None,
autoScale=False,
logScale=False,
grid=False,
colormap=True,
aspectRatio=True,
yinverted=True,
copy=True,
save=True,
print_=True,
control=False,
position=None,
mask=True):
qt.QMainWindow.__init__(self, parent)
if parent is not None:
# behave as a widget
self.setWindowFlags(qt.Qt.Widget)
else:
self.setWindowTitle('StackView')
self._stack = None
"""Loaded stack, as a 3D array, a 3D dataset or a list of 2D arrays."""
self.__transposed_view = None
"""View on :attr:`_stack` with the axes sorted, to have
the orthogonal dimension first"""
self._perspective = 0
"""Orthogonal dimension (depth) in :attr:`_stack`"""
self.__imageLegend = '__StackView__image' + str(id(self))
self.__autoscaleCmap = False
"""Flag to disable/enable colormap auto-scaling
based on the min/max values of the entire 3D volume"""
self.__dimensionsLabels = ["Dimension 0", "Dimension 1", "Dimension 2"]
"""These labels are displayed on the X and Y axes.
:meth:`setLabels` updates this attribute."""
self._first_stack_dimension = 0
"""Used for dimension labels and combobox"""
central_widget = qt.QWidget(self)
self._plot = PlotWindow(parent=central_widget,
backend=backend,
resetzoom=resetzoom,
autoScale=autoScale,
logScale=logScale,
grid=grid,
curveStyle=False,
colormap=colormap,
aspectRatio=aspectRatio,
yInverted=yinverted,
copy=copy,
save=save,
print_=print_,
control=control,
position=position,
roi=False,
mask=mask)
self.sigInteractiveModeChanged = self._plot.sigInteractiveModeChanged
self.sigActiveImageChanged = self._plot.sigActiveImageChanged
self.sigPlotSignal = self._plot.sigPlotSignal
self._plot.profile = Profile3DToolBar(parent=self._plot, plot=self)
self._plot.addToolBar(self._plot.profile)
self._plot.setGraphXLabel('Columns')
self._plot.setGraphYLabel('Rows')
self._plot.sigPlotSignal.connect(self._plotCallback)
self.__planeSelection = PlanesWidget(self._plot)
self.__planeSelection.sigPlaneSelectionChanged.connect(
self.__setPerspective)
self._browser_label = qt.QLabel("Image index (Dim0):")
self._browser = HorizontalSliderWithBrowser(central_widget)
self._browser.valueChanged[int].connect(self.__updateFrameNumber)
self._browser.setEnabled(False)
layout = qt.QGridLayout()
layout.setContentsMargins(0, 0, 0, 0)
layout.addWidget(self._plot, 0, 0, 1, 3)
layout.addWidget(self.__planeSelection, 1, 0)
layout.addWidget(self._browser_label, 1, 1)
layout.addWidget(self._browser, 1, 2)
central_widget.setLayout(layout)
self.setCentralWidget(central_widget)
# clear profile lines when the perspective changes (plane browsed changed)
self.__planeSelection.sigPlaneSelectionChanged.connect(
self._plot.profile.getProfilePlot().clear)
self.__planeSelection.sigPlaneSelectionChanged.connect(
self._plot.profile.clearProfile)