def mhd_getRatios(fname):
"""
Get relative axis ratios from MHD file defined by fname
"""
if not os.path.exists(fname):
print "imageStackLoader.mhd_getRatios can not find %s" % fname
return
try:
#Attempt to use the vtk module to read the element spacing
imp.find_module('vtk')
import vtk
imr = vtk.vtkMetaImageReader()
imr.SetFileName(fname)
imr.Update()
im = imr.GetOutput()
spacing = im.GetSpacing()
except ImportError:
#If the vtk module fails, we try to read the spacing using the built-in reader
info = mhd_read_header_file(fname)
if info.has_key('elementspacing'):
spacing = info['elementspacing']
else:
print "Failed to find spacing info in MHA file. Using default axis length values"
return lasHelp.readPreference('defaultAxisRatios') #defaults
if len(spacing)==0:
print "Failed to find spacing valid spacing info in MHA file. Using default axis length values"
return lasHelp.readPreference('defaultAxisRatios') #defaults
return spacingToRatio(spacing)
def __init__(self, parent=None, data=None, fnameAbsPath="", enable=True, objectName=""):
super(lines, self).__init__(parent, data, fnameAbsPath, enable, objectName, pgObject="PlotCurveItem")
# Choose symbols from preferences file.
# TODO: read symbols from GUI
self.symbol = lasHelp.readPreference("symbolOrder")[0]
self.symbolSize = int(self.parent.markerSize_spinBox.value())
self.alpha = int(self.parent.markerAlpha_spinBox.value())
self.lineWidth = int(self.parent.lineWidth_spinBox.value())
# Add to the imageStackLayers_model which is associated with the points QTreeView
name = QtGui.QStandardItem(objectName)
name.setEditable(False)
# Add checkbox
thing = QtGui.QStandardItem()
thing.setFlags(QtCore.Qt.ItemIsEnabled | QtCore.Qt.ItemIsEditable | QtCore.Qt.ItemIsUserCheckable)
thing.setCheckState(QtCore.Qt.Checked)
# self.modelItems=(name,thing) #Remove this for now because I have NO CLUE how to get access to the checkbox state
self.modelItems = name
self.model = self.parent.points_Model
self.addToList()
# Set the colour of the object based on how many items are already present
number_of_colors = 6
thisNumber = (self.parent.points_Model.rowCount() - 1) % number_of_colors
cm_subsection = linspace(0, 1, number_of_colors)
colors = [cm.jet(x) for x in cm_subsection]
color = colors[thisNumber]
self.color = [color[0] * 255, color[1] * 255, color[2] * 255]
def showLoadDialog(self):
"""
This slot brings up the load dialog and retrieves the file name.
If the file name is valid, it loads the base stack using the load method.
"""
fname = self.lasagna.showFileLoadDialog(fileFilter="LSM (*.lsm)")
if fname is None:
return
colorOrder = lasHelp.readPreference('colorOrder')
if os.path.isfile(fname):
im=tifffile.imread(str(fname))
print("Found LSM stack with dimensions:")
print(im.shape)
for ii in range(im.shape[2]):
stack=im[0,:,ii,:,:]
objName="layer_%d" % (ii+1)
self.lasagna.addIngredient(objectName=objName,
kind='imagestack',
data=stack,
fname=fname
)
self.lasagna.returnIngredientByName(objName).addToPlots() #Add item to all three 2D plots
print("Adding '%s' layer" % colorOrder[ii])
self.lasagna.returnIngredientByName(objName).lut=colorOrder[ii]
self.lasagna.initialiseAxes()
else:
self.lasagna.statusBar.showMessage("Unable to find " + str(fname))
def __init__(self, parent=None, data=None, fnameAbsPath='', enable=True, objectName=''):
super(sparsepoints,self).__init__(parent, data, fnameAbsPath, enable, objectName,
pgObject='ScatterPlotItem'
)
#Choose symbols from preferences file. TODO: in future could increment through so successive ingredients have different symbols and colors
self.symbol = lasHelp.readPreference('symbolOrder')[0]
self.symbolSize = int(self.parent.markerSize_spinBox.value())
self.alpha = int(self.parent.markerAlpha_spinBox.value())
self.lineWidth = None #Not used right now
#Add to the imageStackLayers_model which is associated with the points QTreeView
name = QtGui.QStandardItem(objectName)
name.setEditable(False)
#Add checkbox
thing = QtGui.QStandardItem()
thing.setFlags(QtCore.Qt.ItemIsEnabled | QtCore.Qt.ItemIsEditable | QtCore.Qt.ItemIsUserCheckable)
thing.setCheckState(QtCore.Qt.Checked)
#self.modelItems=(name,thing) #Remove this for now because I have NO CLUE how to get the checkbox state bacl
self.modelItems=name
self.model = self.parent.points_Model
self.addToList()
#Set the colour of the object based on how many items are already present
number_of_colors = 6
thisNumber = (self.parent.points_Model.rowCount()-1)%number_of_colors
cm_subsection = linspace(0, 1, number_of_colors)
colors = [ cm.jet(x) for x in cm_subsection ]
color = colors[thisNumber]
self.color = [color[0]*255, color[1]*255, color[2]*255]
def showLoadDialog(self):
"""
This slot brings up the load dialog and retrieves the file name.
If the file name is valid, it loads the base stack using the load method.
"""
fname = self.lasagna.showFileLoadDialog(fileFilter="LSM (*.lsm)")
if fname is None:
return
colorOrder = lasHelp.readPreference('colorOrder')
if os.path.isfile(fname):
im=tifffile.imread(str(fname))
print "Found LSM stack with dimensions:"
print im.shape
for ii in range(im.shape[2]):
stack=im[0,:,ii,:,:]
objName="layer_%d" % (ii+1)
self.lasagna.addIngredient(objectName=objName,
kind='imagestack',
data=stack,
fname=fname
)
self.lasagna.returnIngredientByName(objName).addToPlots() #Add item to all three 2D plots
print "Adding '%s' layer" % colorOrder[ii]
self.lasagna.returnIngredientByName(objName).lut=colorOrder[ii]
self.lasagna.initialiseAxes()
else:
self.lasagna.statusBar.showMessage("Unable to find " + str(fname))
def __init__(self,
thisPlotWidget,
lasagna,
axisName='',
minMax=(0, 1500),
axisRatio=1,
axisToPlot=0):
"""
thisPlotWidget - the PlotWidget to which we will add the axes
minMax - the minimum and maximum values of the plotted image.
axisRatio - the voxel size ratio along the x and y axes. 1 means square voxels.
axisToPlot - the dimension along which we are slicing the data.
"""
#Create properties
self.axisToPlot = axisToPlot #the axis in 3D space that this view correponds to
self.axisName = axisName
#We can link this projection to two others
self.linkedXprojection = None
self.linkedYprojection = None
print("Creating axis at " + str(thisPlotWidget.objectName()))
self.view = thisPlotWidget #This should target the axes to a particular plot widget
if lasHelp.readPreference('hideZoomResetButtonOnImageAxes') == True:
self.view.hideButtons()
if lasHelp.readPreference('hideAxes') == True:
self.view.hideAxis('left')
self.view.hideAxis('bottom')
self.view.setAspectLocked(True, axisRatio)
#Loop through the ingredients list and add them to the ViewBox
self.lasagna = lasagna
self.items = [
] #a list of added plot items TODO: check if we really need this
self.addItemsToPlotWidget(self.lasagna.ingredientList)
#The currently plotted slice
self.currentSlice = None
#Link the progressLayer signal to a slot that will move through image layers as the wheel is turned
self.view.getViewBox().progressLayer.connect(self.wheel_layer_slot)
def getVoxelSpacing(fname,fallBackMode=False):
"""
Attempts to get the voxel spacing in all three dimensions. This allows us to set the axis
ratios automatically. TODO: Currently this will only work for MHD files, but we may be able
to swing something for TIFFs (e.g. by creating Icy-like metadata files)
"""
if fname.lower().endswith('.mhd'):
return mhd_getRatios(fname)
if fname.lower().endswith('.nrrd') or fname.lower().endswith('.nrd'):
return nrrd_getRatios(fname)
else:
return lasHelp.readPreference('defaultAxisRatios') #defaults
def __init__(self, thisPlotWidget, lasagna, axisName='', minMax=(0,1500), axisRatio=1, axisToPlot=0):
"""
thisPlotWidget - the PlotWidget to which we will add the axes
minMax - the minimum and maximum values of the plotted image.
axisRatio - the voxel size ratio along the x and y axes. 1 means square voxels.
axisToPlot - the dimension along which we are slicing the data.
"""
#Create properties
self.axisToPlot = axisToPlot #the axis in 3D space that this view correponds to
self.axisName = axisName
#We can link this projection to two others
self.linkedXprojection=None
self.linkedYprojection=None
print "Creating axis at " + str(thisPlotWidget.objectName())
self.view = thisPlotWidget #This should target the axes to a particular plot widget
if lasHelp.readPreference('hideZoomResetButtonOnImageAxes')==True:
self.view.hideButtons()
if lasHelp.readPreference('hideAxes')==True:
self.view.hideAxis('left')
self.view.hideAxis('bottom')
self.view.setAspectLocked(True,axisRatio)
#Loop through the ingredients list and add them to the ViewBox
self.lasagna = lasagna
self.items=[] #a list of added plot items TODO: check if we really need this
self.addItemsToPlotWidget(self.lasagna.ingredientList)
#The currently plotted slice
self.currentSlice=None
#Link the progressLayer signal to a slot that will move through image layers as the wheel is turned
self.view.getViewBox().progressLayer.connect(self.wheel_layer_slot)
def loadOther_pushButton_slot(self,fnameToLoad=False):
"""
Load a user-selected atlas file but use the labels from the ARA in the drop-down box.
Can optionally load a specific file name (used for de-bugging)
"""
if fnameToLoad==False:
fileFilter="Images (*.mhd *.mha *.tiff *.tif *.nrrd)"
fnameToLoad = QtGui.QFileDialog.getOpenFileName(self, 'Open file', lasHelp.readPreference('lastLoadDir'), fileFilter)
fnameToLoad = str(fnameToLoad)
#re-load labels
selectedName = str(self.araName_comboBox.itemText(self.araName_comboBox.currentIndex()))
paths = self.paths[selectedName]
self.data['labels'] = self.loadLabels(paths['labels'])
#load the selected atlas (without displaying it)
self.data['atlas'] = imageStackLoader.loadStack(fnameToLoad)
self.data['currentlyLoadedAtlasName'] = fnameToLoad.split(os.path.sep)[-1]
def chooseStack_slot(self, fnameToChoose=False):
"""
Choose the stack to transform
can optionally load a specific file name (used for de-bugging)
"""
if fnameToChoose==False:
fileFilter="Images (*.mhd *.mha)"
fnameToChoose = QtGui.QFileDialog.getOpenFileName(self, 'Choose stack', lasHelp.readPreference('lastLoadDir'), fileFilter)
fnameToChoose = str(fnameToChoose)
if os.path.exists(fnameToChoose):
self.inputImagePath = fnameToChoose
else:
self.inputImagePath = ''
#TODO: make an alert box for this case
print "that file does not exits"
self.checkIfReadyToRun()
lasHelp.preferenceWriter('lastLoadDir', lasHelp.stripTrailingFileFromPath(fnameToChoose))
self.stackName_label.setText(fnameToChoose.split(os.path.sep)[-1])
def chooseTransform_slot(self, fnameToChoose=False):
"""
Choose the transform file to use
can optionally load a specific file name (used for de-bugging)
"""
if fnameToChoose == False:
fileFilter = "Images (*.txt)"
fnameToChoose = QtGui.QFileDialog.getOpenFileName(
self, 'Choose transform',
lasHelp.readPreference('lastLoadDir'), fileFilter)
fnameToChoose = str(fnameToChoose)
if os.path.exists(fnameToChoose):
self.transformPath = fnameToChoose
else:
self.transformPath = ''
#TODO: make an alert box for this case
print("that file does not exits")
self.checkIfReadyToRun()
lasHelp.preferenceWriter(
'lastLoadDir', lasHelp.stripTrailingFileFromPath(fnameToChoose))
self.transformName_label.setText(fnameToChoose.split(os.path.sep)[-1])
def loadOther_pushButton_slot(self, fnameToLoad=False):
"""
Load a user-selected atlas file but use the labels from the ARA in the drop-down box.
Can optionally load a specific file name (used for de-bugging)
"""
if fnameToLoad == False:
fileFilter = "Images (*.mhd *.mha *.tiff *.tif *.nrrd)"
fnameToLoad = QtGui.QFileDialog.getOpenFileName(
self, 'Open file', lasHelp.readPreference('lastLoadDir'),
fileFilter)
fnameToLoad = str(fnameToLoad)
#re-load labels
selectedName = str(
self.araName_comboBox.itemText(
self.araName_comboBox.currentIndex()))
paths = self.paths[selectedName]
self.data['labels'] = self.loadLabels(paths['labels'])
#load the selected atlas (without displaying it)
self.data['atlas'] = imageStackLoader.loadStack(fnameToLoad)
self.data['currentlyLoadedAtlasName'] = fnameToLoad.split(
os.path.sep)[-1]