def warnAndQuit(self,msg):
"""
Display alert and (maybe) quit the plugin
"""
self.lasagna.alert = alert(self.lasagna,alertText=msg)
self.lasagna.stopPlugin(self.__module__) #This will call self.closePlugin
self.lasagna.pluginActions[self.__module__].setChecked(False) #Uncheck the menu item associated with this plugin's name
def __init__(self, lasagna_serving, parent=None):
super(plugin, self).__init__(
lasagna_serving
) # This calls the LasagnaPlugin constructor which in turn calls subsequent constructors
# Is the Elastix binary in the system path?
if which('elastix') is None:
# TODO: does not stop properly. Have to uncheck and recheck the plugin menu item to get it to run a second time.
from lasagna.alert import alert
self.alert = alert(
lasagna_serving,
'The elastix binary does not appear to be in your path.<br>Not starting plugin.'
)
self.lasagna.pluginActions[self.__module__].setChecked(
False
) # Uncheck the menu item associated with this plugin's name
self.deleteLater()
return
else:
print("Using elastix binary at " + which('elastix'))
# re-define some default properties that were originally defined in LasagnaPlugin
self.pluginShortName = 'Elastix' # Appears on the menu
self.pluginLongName = 'registration of images' # Can be used for other purposes (e.g. tool-tip)
self.pluginAuthor = 'Rob Campbell'
# This is the file name we monitor during running
self.elastixLogName = 'elastix.log'
# Create widgets defined in the designer file
self.setupUi(self)
self.show()
# The dictionary which will store the command components
# the param files and output are separate as they are stored in the list view and ouput path text edit box
self.elastix_cmd = {
'f': '', # fixed image
'm': '' # moving image
}
# A dictionary for storing location of temporary parameter files
# Temporary parameter files are created as the user edits them and are
# removed when the registration starts
self.tmpParamFiles = {}
# Create some properties which we will need
self.fixedStackPath = '' # absolute path to reference image
self.movingStackPath = '' # absolute path to sample image
# Set up the list view on Tab 2
self.paramItemModel = QtGui.QStandardItemModel(self.paramListView)
self.paramListView.setModel(self.paramItemModel)
# Link signals to slots
# Tab 1 - Loading data
self.loadFixed.released.connect(self.loadFixed_slot)
self.loadMoving.released.connect(self.loadMoving_slot)
self.originalMovingImage = None # The original moving image is stored here
self.originalMovingFname = None
# Flip axis
self.flipAxis1.released.connect(lambda: self.flipAxis_Slot(0))
self.flipAxis2.released.connect(lambda: self.flipAxis_Slot(1))
self.flipAxis3.released.connect(lambda: self.flipAxis_Slot(2))
# Rotate axis
self.rotAxis1.released.connect(lambda: self.rotAxis_Slot(0))
self.rotAxis2.released.connect(lambda: self.rotAxis_Slot(1))
self.rotAxis3.released.connect(lambda: self.rotAxis_Slot(2))
# Swap axes
self.swapAxis1_2.released.connect(lambda: self.swapAxis_Slot(0, 1))
self.swapAxis2_3.released.connect(lambda: self.swapAxis_Slot(1, 2))
self.swapAxis3_1.released.connect(lambda: self.swapAxis_Slot(2, 0))
self.saveModifiedMovingStack.released.connect(
self.saveModifiedMovingStack_slot)
# Tab 2 - Building the registration command
self.outputDirSelect_button.released.connect(self.selectOutputDir_slot)
self.removeParameter.released.connect(self.removeParameter_slot)
self.loadParamFile.released.connect(self.loadParamFile_slot)
self.moveParamUp_button.released.connect(self.moveParamUp_button_slot)
self.moveParamDown_button.released.connect(
self.moveParamDown_button_slot)
# Tab 3 - parameter file
self.plainTextEditParam.textChanged.connect(
self.plainTextEditParam_slot)
self.comboBoxParam.activated.connect(
self.comboBoxParamLoadOnSelect_slot)
# Tab 4: running
self.runElastix_button.released.connect(self.runElastix_button_slot)
self.runElastix_button.setEnabled(False)
# Start a QTimer to poll for finished analyses
self.finishedMonitorTimer = QtCore.QTimer()
self.finishedMonitorTimer.timeout.connect(self.analysisFinished_slot)
self.finishedMonitorTimer.start(
2500) # Number of milliseconds between poll events
self.listofDirectoriesWithRunningAnalyses = []
# Set up list view on the running tab
self.runningAnalysesItemModel = QtGui.QStandardItemModel(
self.runningRegistrations_ListView)
self.runningRegistrations_ListView.setModel(
self.runningAnalysesItemModel)
# Tab 5: results
self.resultsItemModel = QtGui.QStandardItemModel(
self.registrationResults_ListView)
self.registrationResults_ListView.setModel(self.resultsItemModel)
self.registrationResults_ListView.clicked.connect(
self.resultImageClicked_Slot)
self.resultImages_Dict = {
} # the keys are result image file names and the values are the result images
self.showHighlightedResult_radioButton.toggled.connect(
self.overlayRadioButtons_Slot)
self.showOriginalMovingImage_radioButton.toggled.connect(
self.overlayRadioButtons_Slot)
# Clear all image stacks
self.lasagna.removeIngredientByType('imagestack')
# -------------------------------------------------------------------------------------
# The following will either be hugely changed or deleted when the plugin is no longer
# under heavy development
debug = False # runs certain things quickly to help development
if debug and os.path.expanduser(
"~"
) == '/home/rob': #Ensure only I can trigger this. Ensures that it doesn't activate if I accidently push with debug enabled
self.fixedStackPath = '/mnt/data/TissueCyte/registrationTests/regPipelinePrototype/YH84_150507_target.mhd'
self.movingStackPath = '/mnt/data/TissueCyte/registrationTests/regPipelinePrototype/YH84_150507_moving.mhd'
do_real_load = True
if do_real_load:
self.loadFixed_slot(self.fixedStackPath)
self.loadMoving_slot(self.movingStackPath)
self.lasagna.initialiseAxes()
do_param_file = True
if do_param_file:
# load param file list
param_files = [
'/mnt/data/TissueCyte/registrationTests/regPipelinePrototype/Par0000affine.txt',
'/mnt/data/TissueCyte/registrationTests/regPipelinePrototype/Par0000bspline.txt'
]
param_files = [
'/mnt/data/TissueCyte/registrationTests/regPipelinePrototype/Par0000affine_quick.txt'
]
self.loadParamFile_slot(param_files)
self.outputDir_label.setText(
self.absToRelPath(
'/mnt/data/TissueCyte/registrationTests/regPipelinePrototype/reg2'
))
self.updateWidgets_slot()
self.tabWidget.setCurrentIndex(3)
def __init__(self, lasagna_serving, parent=None):
super(plugin, self).__init__(lasagna_serving) # This calls the LasagnaPlugin constructor which in turn calls subsequent constructors
# Is the Transformix (or Elastix) binary in the system path?
# We search for both in case we in the future add the ability to calculate inverse transforms and other good stuff
if which('transformix') is None or which('elastix') is None:
#TODO: does it stop properly? Will we have to uncheck and recheck the plugin menu item to get it to run a second time?
from lasagna.alert import alert
self.alert = alert(lasagna_serving,
'The elastix or transformix binaries do not appear'
' to be in your path.<br>Not starting plugin.')
self.lasagna.pluginActions[self.__module__].setChecked(False) # Uncheck the menu item associated with this plugin's name
self.deleteLater()
return
else:
print("Using transformix binary at " + which('transformix'))
print("Using elastix binary at " + which('elastix'))
# re-define some default properties that were originally defined in LasagnaPlugin
self.pluginShortName = 'Transformix' # Appears on the menu
self.pluginLongName = 'registration of images' # Can be used for other purposes (e.g. tool-tip)
self.pluginAuthor = 'Rob Campbell'
# This is the file name we monitor during running
self.elastixLogName = 'elastix.log'
self.transformixLogName = 'transformix.log'
self.transformixCommand = '' # the command we will run
# Create widgets defined in the designer file
self.setupUi(self)
self.show()
# A dictionary for storing location of temporary parameter files
# Temporary parameter files are created as the user edits them and are
# removed when the registration starts
self.tmpParamFiles = {}
# Create some properties which we will need
self.inputImagePath = '' # absolute path to the image we will transform
self.transformPath = '' # absolute path to the tranform file we will use
self.outputDirPath = ''
self.transformixCommand = ''
# Link signals to slots
self.chooseStack_pushButton.released.connect(self.chooseStack_slot)
self.chooseTransform_pushButton.released.connect(self.chooseTransform_slot)
self.outputDirSelect_pushButton.released.connect(self.selectOutputDir_slot)
self.run_pushButton.released.connect(self.run_slot)
self.loadResult_pushButton.released.connect(self.loadResult_slot)
# Disable UI elements that won't be available until the user has completed all actions
self.run_pushButton.setEnabled(False)
self.loadResult_pushButton.setEnabled(False)
# -------------------------------------------------------------------------------------
# The following will either be hugely changed or deleted when the plugin is no longer
# under heavy development
debug = False # runs certain things quickly to help development
if debug and os.path.expanduser("~") == '/home/rob': # Ensure only I can trigger this. Ensures that it doesn't activate if I accidently push with debug enabled
self.inputImagePath = '' # absolute path to the image we will transform
self.transformPath = '' # absolute path to the tranform file we will use
def warnAndQuit(self, msg):
"""
Display alert and (maybe) quit the plugin
"""
self.lasagna.alert = alert(self.lasagna, alertText=msg)
self.deregister_from_lasagna()