def __init__(self, parent):
qt.QTreeView.__init__(self, parent)
#
# Model is qt.QFileSystemModel()
#
fsModel = qt.QFileSystemModel()
self.setModel(fsModel)
#
# Set up monitor for the file system
#
self.watcher = qt.QFileSystemWatcher()
self.watcher.directoryChanged.connect(
self.handleDirectoryChangedSignal)
#
# Context menu
#
self.setContextMenuPolicy(qt.Qt.DefaultContextMenu)
if hasattr(parent, 'handleContextMenuAction'):
self.callback = parent.handleContextMenuAction
else:
self.callback = None
#
# List to keep track of files and avoid unnecessary
#
self.fileList = []
def add_overlay(self,
flag,
image,
alpha,
colorTableAlpha,
minValue=-1,
maxValue=1):
if flag:
self.flagAlpha = True
self.dataVolumeAlpha = image
self.alpha = alpha
self.colortableAlpha = []
if (minValue == -1) and (maxValue == -1):
self.maxAlpha = self.dataVolumeAlpha.max()
self.minAlpha = self.dataVolumeAlpha.min()
else:
self.maxAlpha = maxValue
self.minAlpha = minValue
R = colorTableAlpha[1]
G = colorTableAlpha[2]
B = colorTableAlpha[3]
for i in range(256):
if int(alpha * 255) > i:
self.colortableAlpha.append(qt.qRgba(R[i], G[i], B[i], i))
else:
self.colortableAlpha.append(
qt.qRgba(R[i], G[i], B[i], int(alpha * 255)))
else:
self.flagAlpha = False
def mouseMoved(self, ddict):
if (ddict['event'] == 'MouseMoved'):
x = int(ddict['x'])
y = int(ddict['y'])
ddict = {}
ddict['event'] = "MouseMoved"
if (self.currentPlaneSection == 0):
z = self.sliceSlider.value()
ddict['PlaneSection'] = 0
ddict['x'] = x
ddict['y'] = y
ddict['z'] = z
self.emit(qt.SIGNAL("movedOnVizualizer"), ddict)
if (self.currentPlaneSection == 1):
z = self.sliceSlider.value()
ddict['PlaneSection'] = 1
ddict['x'] = x
ddict['y'] = z
ddict['z'] = y
self.emit(qt.SIGNAL("movedOnVizualizer"), ddict)
if (self.currentPlaneSection == 2):
z = self.sliceSlider.value()
ddict['PlaneSection'] = 2
ddict['x'] = z
ddict['y'] = x
ddict['z'] = y
self.emit(qt.SIGNAL("movedOnVizualizer"), ddict)
def __init__(
self,
scan_list,
parent=None,
):
qt.QWidget.__init__(self, parent)
self.mainLayout = qt.QGridLayout()
self.scan_list = scan_list
self.widgetList = []
for scan in self.scan_list:
w = qt.QCheckBox(scan)
self.widgetList.append(w)
self.startImporting = qt.QPushButton("OK")
index = 0
for w in self.widgetList:
w.setChecked(True)
self.mainLayout.addWidget(w, index % 15, int(index / 15))
index += 1
self.mainLayout.addWidget(self.startImporting)
self.setLayout(self.mainLayout)
def check_parameters_files(self):
source_file_color = open('./VTK_parameters/history', "r")
files_para = source_file_color.readlines()
if len(files_para) != 3:
msgBox = qt.QMessageBox(self)
msgBox.setText('Missing parameters files in the history')
msgBox.exec_()
else:
matching = [s for s in files_para if ".col" in s]
if len(str(matching)) != 2:
self.color_file = str(matching[0]).rstrip('\n')
else:
self.color_file = 'empty'
msgBox = qt.QMessageBox(self)
msgBox.setText('Missing color file')
msgBox.exec_()
matching = [s for s in files_para if ".alp" in s]
if len(str(matching)) != 2:
self.alpha_file = str(matching[0]).rstrip('\n')
else:
self.alpha_file = 'empty'
msgBox = qt.QMessageBox(self)
msgBox.setText('Missing alpha file')
msgBox.exec_()
matching = [s for s in files_para if ".pr" in s]
if len(str(matching)) != 2:
self.para_file = str(matching[0]).rstrip('\n')
else:
self.para_file = 'empty'
msgBox = qt.QMessageBox(self)
msgBox.setText('Missing parameters file')
msgBox.exec_()
def fill_alphaTable(self):
if self.alpha_file != 'empty':
try:
source_file_alpha = open('./VTK_parameters/' + self.alpha_file,
"r")
except IOError:
msgBox = qt.QMessageBox(self)
msgBox.setText('The alpha file ' + self.alpha_file +
' does not exist')
msgBox.exec_()
all_lines = source_file_alpha.readlines()
j = 0
for line in all_lines:
line = line.rstrip('\n')
line = line.split(' ')
try:
line.remove('')
except:
pass
if len(line) == 2:
for i in range(2):
Item = qt.QTableWidgetItem()
Item.setText(str(line[i]))
self.AlphaCoef.setItem(j, i, Item)
elif len(line) == 4:
for i in range(4):
Item = qt.QTableWidgetItem()
Item.setText(str(line[i]))
self.AlphaCoef.setItem(j, i, Item)
j += 1
def display_image(self):
self.flagFirstCircle = True
self.image = qt.QImage(self.data, self.data.shape[1],
self.data.shape[0], self.data.shape[1],
qt.QImage.Format_Indexed8)
self.image.setColorTable(self.colortable)
pixMap = qt.QPixmap.fromImage(self.image)
pixItem = qt.QGraphicsPixmapItem(pixMap)
pixItem.setZValue(-1)
self.scene.addItem(pixItem)
self.scene.setSceneRect(0, 0, self.image.width(), self.image.height())
if self.flagAlpha:
imageAlpha = qt.QImage(self.dataAlpha, self.dataAlpha.shape[1],
self.dataAlpha.shape[0],
self.dataAlpha.shape[1],
qt.QImage.Format_Indexed8)
imageAlpha.setColorTable(self.colortableAlpha)
#
pixMapAlpha = qt.QPixmap.fromImage(imageAlpha)
pixMapAlpha.hasAlpha()
pixItemAlpha = qt.QGraphicsPixmapItem(pixMapAlpha)
#
self.scene.addItem(pixItemAlpha)
self.scene.setSceneRect(0, 0, self.image.width(),
self.image.height())
self.scene.update
def drawEllipse(self, x, y, r):
self.Item = qt.QGraphicsEllipseItem(x - r / 2, y - r / 2, r, r)
self.Item.setFlag(qt.QGraphicsItem.ItemIsMovable)
pen = qt.QPen(qt.Qt.blue)
pen.setWidth(3)
brush = qt.QBrush(qt.QColor(0xFF, 0, 0, 0x00))
self.Item.setBrush(brush)
self.Item.setPen(pen)
self.scene.addItem(self.Item)
def __init__(self, parent=None):
uiPath = UiPaths.bandPassFilterID32UiPath()
super(BandPassID32Window, self).__init__(uiPath=uiPath, parent=parent)
self.setUI()
self.setWindowTitle('Band Pass Filter ID32')
self._values = {
'energy': self.photonEdit,
'binning': self.binningEdit,
'preset': self.exposureEdit
}
self.setValues({
'energy': str(932.0),
'binning': str(4),
'preset': str(300)
})
#
# Set validators for the line edits
#
photonValidator = qt.QDoubleValidator()
photonValidator.setBottom(0.0)
photonValidator.setTop(10000.0)
photonValidator.setDecimals(4)
binningValidator = qt.QIntValidator()
binningValidator.setBottom(0)
binningValidator.setTop(512)
exposureValidator = qt.QIntValidator()
exposureValidator.setBottom(0)
exposureValidator.setTop(100000)
self.photonEdit.setValidator(photonValidator)
self.binningEdit.setValidator(binningValidator)
self.exposureEdit.setValidator(exposureValidator)
#
# Connects
#
self.photonEdit.textEdited.connect(self.emitValuesChangedSignal)
self.binningEdit.textEdited.connect(self.emitValuesChangedSignal)
self.exposureEdit.textEdited.connect(self.emitValuesChangedSignal)
self.photonEdit.returnPressed.connect(self.emitValuesChangedSignal)
self.binningEdit.returnPressed.connect(self.emitValuesChangedSignal)
self.exposureEdit.returnPressed.connect(self.emitValuesChangedSignal)
#
# Process
#
self.process = Filter.bandPassFilterID32
def __init__(self,parent=None, Orientation=1) :
qt.QWidget.__init__(self, parent)
self.slider=qt.QSlider(1)
self.slider.setMinimum(1)
self.slider.setMaximum(100)
self.Label=qt.QLabel("0")
self.Label.setFixedSize(45,45)
self.layout=qt.QHBoxLayout()
self.layout.addWidget(self.slider)
self.layout.addWidget(self.Label)
self._changeLabel()
self.connect(self.slider,qt.SIGNAL("valueChanged(int)"),self._changeLabel)
self.setLayout(self.layout)
def unitTest_FileSystemBrowser():
app = qt.QApplication([])
browser = FileSystemBrowser()
browser.addSignal.connect(DummyNotifier.signalReceived)
browser.show()
app.exec_()
def changeColorMap(self, R, G, B):
if len(R) != 256 or len(G) != 256 or len(B) != 256:
print "Wrong Color Array shape"
else:
self.colortable = []
for i in range(256):
self.colortable.append(qt.qRgba(R[i], G[i], B[i], 255))
def mousePressEvent(self, event):
if (event.button() == qt.Qt.LeftButton):
dx = event.pos().x()
dy = event.pos().y()
clickPosition = self.mapToScene(dx, dy)
ddict = {}
ddict['event'] = "MousePressed"
ddict['x'] = clickPosition.x()
ddict['y'] = clickPosition.y()
if (event.button() == qt.Qt.RightButton):
dx = event.pos().x()
dy = event.pos().y()
clickPosition = self.mapToScene(dx, dy)
ddict = {}
ddict['event'] = "RMousePressed"
ddict['x'] = clickPosition.x()
ddict['y'] = clickPosition.y()
self.emit(qt.SIGNAL("CustomGraphicsViewEvent"), ddict)
return qt.QGraphicsView.mousePressEvent(self, event)
def run(self):
self.FileReference = str(self.inputFiles[0])
self.inputDir = os.path.dirname(self.FileReference)
image = ImageReader(self.FileReference, 'rb')
data = image.getData()
self.shapeReference = data.shape
typeImage = data.dtype
self.inputData = np.zeros((len(
self.inputFiles), self.shapeReference[0], self.shapeReference[1]),
dtype=typeImage)
i = 0
for filename in self.inputFiles:
filename = str(filename)
image = ImageReader(filename, 'rb')
data = image.getData()
if (data.ndim == 2):
self.inputData[i, :, :] = data
else:
self.inputData[i, :, :] = data[:, :, 0]
i += 1
self.emit(qt.SIGNAL("Progress"), i)
def fill_para(self):
if self.para_file != 'empty':
try:
source_file_para = open('./VTK_parameters/' + self.para_file,
"r")
except IOError:
msgBox = qt.QMessageBox(self)
msgBox.setText('The parameters fil : ' + self.para_file +
' does not exist')
msgBox.exec_()
line = source_file_para.readlines()[0]
parameters = line.split(' ')
if int(parameters[0]) == 2:
self.checkBox.setChecked(2)
else:
self.checkBox.setChecked(0)
self.sliderAmb._defaultValue(float(parameters[1]))
self.sliderDif._defaultValue(float(parameters[2]))
self.sliderSpe._defaultValue(float(parameters[3]))
self.sliderSpeP._defaultValue(float(parameters[4]))
self.sliderOpa._defaultValue(float(parameters[5]))
else:
self.sliderAmb._defaultValue(1)
self.sliderDif._defaultValue(1)
self.sliderSpe._defaultValue(1)
self.sliderSpeP._defaultValue(1)
self.sliderOpa._defaultValue(1)
def _buttonAlphaSavePushed(self):
source_file_color = open('./VTK_parameters/history', "r")
files_para = source_file_color.readlines()
matching = [s for s in files_para if ".alp" in s]
if len(str(matching)) != 2:
alpha_file = str(matching[0]).rstrip('\n')
if alpha_file == 'alpha_rendering_default.alp':
msgBox = qt.QMessageBox(self)
msgBox.setText(
'Overwrite the default file is not allowed. Create a new file to save your table'
)
msgBox.exec_()
else:
alphaFileToWrite = open('./VTK_parameters/' + alpha_file, "w")
for i in range(10):
for j in range(4):
try:
alphaFileToWrite.writelines(
self.AlphaCoef.item(i, j).text() + ' ')
except:
if j == 4:
alphaFileToWrite.writelines('0.5 ')
else:
alphaFileToWrite.writelines('0 ')
alphaFileToWrite.writelines('\n')
self.check_parameters_files()
def _buttonParaSavePushed(self):
source_file_color = open('./VTK_parameters/history', "r")
files_para = source_file_color.readlines()
matching = [s for s in files_para if ".pr" in s]
if len(str(matching)) != 2:
para_file = str(matching[0]).rstrip('\n')
if para_file == 'para_rendering_default.pr':
msgBox = qt.QMessageBox(self)
msgBox.setText(
'Overwrite the default file is not allowed. Create a new file to save your table'
)
msgBox.exec_()
else:
paraFileToWrite = open('./VTK_parameters/' + para_file, "w")
paraFileToWrite.writelines(
str(self.checkBox.checkState()) + ' ')
paraFileToWrite.writelines(str(self.sliderAmb.value()) + ' ')
paraFileToWrite.writelines(str(self.sliderDif.value()) + ' ')
paraFileToWrite.writelines(str(self.sliderSpe.value()) + ' ')
paraFileToWrite.writelines(str(self.sliderSpe.value()) + ' ')
paraFileToWrite.writelines(str(self.sliderSpeP.value()) + ' ')
paraFileToWrite.writelines(str(self.sliderOpa.value()))
self.check_parameters_files()
def test():
from PyMca5.PyMca import SpecfitFunctions
a = SpecfitFunctions.SpecfitFunctions()
x = numpy.arange(1000).astype(numpy.float64)
p1 = numpy.array([1500, 100., 50.0])
p2 = numpy.array([1500, 700., 50.0])
y = a.gauss(p1, x) + 1
y = y + a.gauss(p2, x)
fit = SimpleFit()
fit.importFunctions(SpecfitFunctions)
fit.setFitFunction('Gaussians')
#fit.setBackgroundFunction('Gaussians')
#fit.setBackgroundFunction('Constant')
fit.setData(x, y)
fit.fit()
print("Expected parameters 1500,100.,50.0, 1500,700.,50.0")
print("Found: ", fit.paramlist)
from PyMca5.PyMca import PyMcaQt as qt
from PyMca5.PyMca import Parameters
a = qt.QApplication(sys.argv)
a.lastWindowClosed.connect(a.quit)
w = Parameters.Parameters()
w.fillfromfit(fit.paramlist)
w.show()
a.exec_()
def unitTest_BandPassFilter():
dummy = DummyNotifier()
app = qt.QApplication([])
filterWindow = ImageAlignmenWindow()
# filterWindow.exportSelectedSignal.connect(dummy.signalReceived)
# filterWindow.exportCurrentSignal.connect(dummy.signalReceived)
filterWindow.show()
app.exec_()
def _build(self) :
self.layout=qt.QHBoxLayout()
self.label =None
self.lineEdit =None
self.button =None
if(self.boolLabel) :
self.label=qt.QLabel(self.textLabel,self)
self.layout.addWidget(self.label)
if(self.booltextEdit) :
self.lineEdit= qt.QLineEdit(self.textEdit,self)
self.layout.addWidget(self.lineEdit)
if(self.boolButton) :
self.button=qt.QPushButton(self.textButton,self)
self.layout.addWidget(self.button)
self.connect(self.button,qt.SIGNAL("clicked()"),self.buttonPushed)
self.setLayout(self.layout)
def _axialViewClicked(self, ddict):
x = int(ddict['x'])
y = int(ddict['y'])
ddict = {}
z = self.axialWidget.sliceSlider.value()
ddict['event'] = "MousePressed"
ddict['x'] = x
ddict['y'] = y
ddict['z'] = z
self.emit(qt.SIGNAL("CustomGraphicsViewEvent"), ddict)
def test():
from PyMca5 import StackBase
testFileName = "TiffTest.tif"
nrows = 2000
ncols = 2000
#create a dummy stack with 100 images
nImages = 100
imagestack = True
a = numpy.ones((nrows, ncols), numpy.float32)
if not os.path.exists(testFileName):
print("Creating test filename %s" % testFileName)
tif = TiffIO.TiffIO(testFileName, mode='wb+')
for i in range(nImages):
data = (a * i).astype(numpy.float32)
if i == 1:
tif = TiffIO.TiffIO(testFileName, mode='rb+')
tif.writeImage(data,
info={'Title': 'Image %d of %d' % (i + 1, nImages)})
tif = None
stackData = TiffStack(imagestack=imagestack)
stackData.loadFileList([testFileName], dynamic=True)
if 0:
stack = StackBase.StackBase()
stack.setStack(stackData)
print("This should be 0 = %f" %
stack.calculateROIImages(0, 0)['ROI'].sum())
print("This should be %f = %f" %\
(a.sum(),stack.calculateROIImages(1, 2)['ROI'].sum()))
if imagestack:
print("%f should be = %f" %\
(stackData.data[0:10,:,:].sum(),
stack.calculateROIImages(0, 10)['ROI'].sum()))
print("Test small ROI 10 should be = %f" %\
stackData.data[10:11,[10],11].sum())
print("Test small ROI 40 should be = %f" %\
stackData.data[10:11,[10,12,14,16],11].sum())
else:
print("%f should be = %f" %\
(stackData.data[:,:, 0:10].sum(),
stack.calculateROIImages(0, 10)['ROI'].sum()))
print("Test small ROI %f" %\
stackData.data[10:11,[29],:].sum())
else:
from PyMca5.PyMca import PyMcaQt as qt
from PyMca5.PyMca import QStackWidget
app = qt.QApplication([])
w = QStackWidget.QStackWidget()
print("Setting stack")
w.setStack(stackData)
w.show()
app.exec_()
def __init__(self, planeSection, parent=None):
qt.QWidget.__init__(self, parent)
self.currentPlaneSection = planeSection
self.scene = qt.QGraphicsScene()
self.view = CustomGraphicsView(self.scene, self)
self.sliceSlider = SliderAndLabel(self)
self.sliceSlider._setRange(0, 0)
self.flagFirstCircle = True
self.connect(self.view, qt.SIGNAL("CustomGraphicsViewEvent"),
self.clickedOnView)
self.connect(self.view, qt.SIGNAL("CustomGraphicsViewEvent"),
self.mouseMoved)
self.connect(self.sliceSlider.slider, qt.SIGNAL("valueChanged(int)"),
self._changeSlice)
self.flagAlpha = False
self.Items = {}
self.colortable = []
self.posPolyPoints = []
for i in range(256):
self.colortable.append(qt.qRgba(i, i, i, 255))
layout = qt.QVBoxLayout()
layout.addWidget(self.view)
layout.addWidget(self.sliceSlider)
self.setLayout(layout)
def __init__(
self,
scan_list,
parent=None,
):
qt.QWidget.__init__(self, parent)
self.mainLayout = qt.QGridLayout()
self.scan_list = scan_list
self.widgetList = []
for scan in self.scan_list:
w = qt.QCheckBox(scan)
self.widgetList.append(w)
self.startImporting = qt.QPushButton("OK")
for w in self.widgetList:
self.mainLayout.addWidget(w)
self.mainLayout.addWidget(self.startImporting)
self.setLayout(self.mainLayout)
def mouseMoveEvent(self, event):
if (event.button() == qt.Qt.NoButton):
dx = event.pos().x()
dy = event.pos().y()
clickPosition = self.mapToScene(dx, dy)
ddict = {}
ddict['event'] = "MouseMoved"
ddict['x'] = clickPosition.x()
ddict['y'] = clickPosition.y()
self.emit(qt.SIGNAL("CustomGraphicsViewEvent"), ddict)
return qt.QGraphicsView.mouseMoveEvent(self, event) # <-- added this line.
def run(self):
if self.extension == '.mat':
filename = self.outputFiles + self.extension
writter = ImageWritter(filename, self.dataToSave)
writter.writeData()
else:
for i in range(0, self.dataToSave.shape[0] - 1):
image = self.dataToSave[i, :, :]
filename = self.outputFiles + '%4.4d' % i + self.extension
writter = ImageWritter(filename, image)
writter.writeData()
self.emit(qt.SIGNAL("Progress"), i)
class SumImageTool(AbstractToolWindow):
__doc__ = """GUI to transform image to spectrum by summation along lines/columns"""
exportSelectedSignal = qt.pyqtSignal()
exportCurrentSignal = qt.pyqtSignal()
def __init__(self, parent=None):
uiPath = UiPaths.sumToolUiPath()
super(SumImageTool, self).__init__(uiPath=uiPath, parent=parent)
self.setUI()
self.setWindowTitle('Integration')
self._values = {'axis': self.axisComboBox}
self.axisComboBox.addItems(['columns', 'rows'])
self.setValues({'axis': 'columns'})
#
# Connect the buttons
#
self.selectedButton.clicked.connect(self.exportSelectedSignal.emit)
self.currentButton.clicked.connect(self.exportCurrentSignal.emit)
#
# Process
#
self.process = self.sumImage
def sumImage(self, image, param=None):
params = self.getValues()
if str(params['axis']) == 'columns':
axis = 1
else:
axis = 0
return Integration.axisSum(image, {'axis': axis})
class EnergyScaleTool(AbstractToolWindow):
__doc__ = """GUI to set an energy scale to the project"""
energyScaleSignal = qt.pyqtSignal()
def __init__(self, parent=None):
uiPath = UiPaths.energyAlignmentUiPath()
super(EnergyScaleTool, self).__init__(uiPath=uiPath, parent=parent)
self.setUI()
self.setWindowTitle('Energy alignment')
self._values = {'slope': self.slopeSpinBox, 'zero': self.zeroSpinBox}
self.setValues({'slope': 1.0, 'zero': 0.})
#
# Connect the spin boxes
#
self.slopeSpinBox.valueChanged.connect(self.energyScaleSignal)
#
# Process
#
self.process = self.energyScale
def energyScale(self):
#
# Create function item
#
scale = FunctionItem('Energy scale', '')
#
# Set expression
#
scale.setExpression(lambda x, a, b: a * x + b)
#
# Set parameters
#
parameters = self.getValues()
scale.setParameters({
'a': parameters['slope'],
'b': parameters['zero']
})
if DEBUG >= 1:
print('EnergyScaleTool.energyScale -- called')
return scale
def closeDir(self, safeClose=True):
"""
:param bool safeClose: Prompts user to confirm closing of working directory. Default: True
Removes the working directory currently selected in the drop down menu.
"""
#
# Prompt warning
#
if safeClose:
msg = qt.QMessageBox()
msg.setIcon(qt.QMessageBox.Warning)
msg.setWindowTitle('Close directory')
msg.setText(
'Are you shure you want to close the current working directory?'
)
msg.setStandardButtons(qt.QMessageBox.Ok | qt.QMessageBox.Cancel)
if msg.exec_() == qt.QMessageBox.Cancel:
if DEBUG >= 1:
print('FileSystemBrowser.closeDir -- Abort')
return
#
# Inteact with QDirListModel
#
currentIdx = self.workingDirCB.currentIndex()
model = self.workingDirCB.model()
if model.rowCount() > 0:
model.removeDirs(row=currentIdx, count=1)
if model.rowCount() <= 0:
self.closeDirButton.setEnabled(False)
self.workingDirCB.setCurrentIndex(-1)
else:
self.workingDirCB.setCurrentIndex(0)
#
# Reset the DirTree to the users home directory
#
homeDir = qt.QDir.home()
self.fsView.setRootDirectory(homeDir)
def handleFilesChanged(self, fileList):
"""
:param list fileList: Contains file paths to modified files
Emits addSignal with the a :py:class:`qt.QFileInfoList` as parameter
"""
#
# Check if files shall be automatically added to the project
#
if self.autoAddCheckBox.checkState() == qt.Qt.Unchecked:
if DEBUG >= 1:
print('FileSystemBrowser.handleFilesChanged -- AutoAdd off')
return
#
# Create a file info list
#
if DEBUG >= 1:
print('FileSystemBrowser.handleFilesChanged -- \n\tfileList: %s' %
str(fileList))
fileInfoList = [qt.QFileInfo(path) for path in fileList]
self.addSignal.emit(fileInfoList)