def __init__(self,debug=False,projectID=None):
'''
constructor
'''
## construct and set main variables
QtGui.QMainWindow.__init__(self)
## variables
self.buff = 2.0
self.controller = Controller(debug=debug)
self.mainWidget = QtGui.QWidget(self)
self.reset_view_workspace()
self.stateList = ['Initial','Data Processing','Quality Assurance','Model Run','Model Results',
'Analysis','Analysis Results','Reports']
self.resultsModeList = ['modes','components']
## enable the transition class
self.transitions = Transitions(self)
self.transitions.move_to_initial()
## settings
self.showMaximized()
self.setWindowTitle(self.controller.appName)
screen = QtGui.QDesktopWidget().screenGeometry()
self.screenWidth = screen.width()
self.screenHeight = screen.height()
self.eSize = 0.04 * self.screenWidth
self.printer = None
self.sizeLabel = QtGui.QLabel()
self.sizeLabel.setFrameStyle(QtGui.QFrame.StyledPanel|QtGui.QFrame.Sunken)
self.create_statusbar()
create_menubar_toolbar(self)
## error check and use shortcut to open existing project if specified form cmd line
if projectID != None:
if os.path.isdir(projectID) == False:
homeDir = os.path.join(self.controller.baseDir,"projects",projectID)
else:
homeDir = projectID
if os.path.isdir(homeDir) == False:
print "Controller: ERROR: home dir specified not found: fatal error"
print "\t", homeDir
sys.exit()
if os.path.exists(os.path.join(homeDir,os.path.split(homeDir)[-1]+".log")) == False:
print "Controller: ERROR: home dir specified not a valid cytostream dir: fatal error"
print "\t", homeDir
sys.exit()
self.open_existing_project_handler(homeDir)
def initialize(self):
self.controller = Controller()
self.controller.initialize_project(self.projectID)
firstFile = True
goFlag = True
for fileName in self.allFiles:
if os.path.isfile(fileName) == False:
print 'ERROR: Bad file name skipping', fileName
continue
print 'adding...', fileName
fileName = str(fileName)
if firstFile == True:
self.controller.create_new_project(fileName)
firstFile = False
else:
goFlag = self.controller.load_additional_fcs_files(fileName)
if self.controller.homeDir == None:
print "ERROR: project failed to initialize"
return
else:
print "project created."
# subsampling
print "handling subsampling"
self.controller.log.log['subsample'] = self.subsample
self.controller.handle_subsampling()
self.controller.save()
# qa image creation
if self.makeQaFigs == True:
print 'making qa images'
self.controller.process_images('qa')
class MainWindow(QtGui.QMainWindow):
def __init__(self,debug=False,projectID=None):
'''
constructor
'''
## construct and set main variables
QtGui.QMainWindow.__init__(self)
## variables
self.buff = 2.0
self.controller = Controller(debug=debug)
self.mainWidget = QtGui.QWidget(self)
self.reset_view_workspace()
self.stateList = ['Initial','Data Processing','Quality Assurance','Model Run','Model Results',
'Analysis','Analysis Results','Reports']
self.resultsModeList = ['modes','components']
## enable the transition class
self.transitions = Transitions(self)
self.transitions.move_to_initial()
## settings
self.showMaximized()
self.setWindowTitle(self.controller.appName)
screen = QtGui.QDesktopWidget().screenGeometry()
self.screenWidth = screen.width()
self.screenHeight = screen.height()
self.eSize = 0.04 * self.screenWidth
self.printer = None
self.sizeLabel = QtGui.QLabel()
self.sizeLabel.setFrameStyle(QtGui.QFrame.StyledPanel|QtGui.QFrame.Sunken)
self.create_statusbar()
create_menubar_toolbar(self)
## error check and use shortcut to open existing project if specified form cmd line
if projectID != None:
if os.path.isdir(projectID) == False:
homeDir = os.path.join(self.controller.baseDir,"projects",projectID)
else:
homeDir = projectID
if os.path.isdir(homeDir) == False:
print "Controller: ERROR: home dir specified not found: fatal error"
print "\t", homeDir
sys.exit()
if os.path.exists(os.path.join(homeDir,os.path.split(homeDir)[-1]+".log")) == False:
print "Controller: ERROR: home dir specified not a valid cytostream dir: fatal error"
print "\t", homeDir
sys.exit()
self.open_existing_project_handler(homeDir)
def reset_view_workspace(self):
self.log = self.controller.log
self.model = self.controller.model
self.image = QtGui.QImage()
self.dirty = False
self.filename = None
self.dockWidget = None
self.fileSelector = None
self.plotSelector = None
self.plotTickControls = None
self.channelSelector = None
self.vizModeSelector = None
self.subsampleSelector = None
self.clusterSelector = None
self.gateSelector = None
self.saveImgsBtn = None
self.dpc = None
self.pDock = None
self.dock = None
self.tv = None
self.nwv = None
self.allFilePaths = []
self.controller.masterChannelList = None
self.reset_layout()
def reset_layout(self):
'''
reset the main widget layouts
'''
self.vbl = QtGui.QVBoxLayout()
self.vboxTop = QtGui.QVBoxLayout()
self.vboxTop.setAlignment(QtCore.Qt.AlignTop)
self.vboxCenter = QtGui.QVBoxLayout()
self.vboxCenter.setAlignment(QtCore.Qt.AlignCenter)
self.vboxBottom = QtGui.QVBoxLayout()
self.vboxBottom.setAlignment(QtCore.Qt.AlignBottom)
self.vbl.addLayout(self.vboxTop)
self.vbl.addLayout(self.vboxBottom)
self.vbl.addLayout(self.vboxCenter)
def create_statusbar(self):
self.status = self.statusBar()
self.status.setSizeGripEnabled(False)
self.status.addPermanentWidget(self.sizeLabel)
self.status.showMessage("Ready", 5000)
def restore_docks(self,override=False):
'''
a dummy function to restore the application docks
'''
restore_docks(self,override=override)
def add_pipeline_dock(self,noBtns=False):
## prepare widget
self.pipelineDock = QtGui.QDockWidget(self)
self.pipelineDock.setObjectName("PipelineDockWidget")
self.pipelineDock.setAllowedAreas(QtCore.Qt.TopDockWidgetArea|QtCore.Qt.BottomDockWidgetArea)
try:
appColor = self.controller.log.log['app_color']
except:
appColor = '#999999'
self.pipelineDockWidget = QtGui.QWidget(self)
self.pDock = PipelineDock(self.controller.log, self.stateList,parent=self.pipelineDockWidget,eSize=0.07*self.screenWidth,mainWindow=self,
appColor=appColor,noBtns=noBtns)
palette = self.pipelineDockWidget.palette()
role = self.pipelineDockWidget.backgroundRole()
palette.setColor(role, QtGui.QColor('black'))
self.pipelineDockWidget.setPalette(palette)
self.pipelineDockWidget.setAutoFillBackground(True)
hbl1 = QtGui.QHBoxLayout()
hbl1.setAlignment(QtCore.Qt.AlignCenter)
hbl1.addWidget(self.pipelineDock)
vbl = QtGui.QVBoxLayout(self.pipelineDockWidget)
vbl.addLayout(hbl1)
vbl.setAlignment(QtCore.Qt.AlignCenter)
self.pipelineDock.setWidget(self.pDock)
self.addDockWidget(QtCore.Qt.RightDockWidgetArea, self.pipelineDock)
self.pipelineDock.setMinimumWidth(0.08 * self.screenWidth)
self.pipelineDock.setMaximumWidth(0.08 * self.screenWidth)
def remove_project(self):
projectID,projectInd = self.existingProjectOpener.get_selected_project()
reply = QtGui.QMessageBox.question(self, self.controller.appName,
"Are you sure you want to completely remove '%s'?"%projectID, QtGui.QMessageBox.Yes, QtGui.QMessageBox.No)
if reply == QtGui.QMessageBox.Yes:
homeDir = os.path.join(self.controller.baseDir,"projects",projectID)
self.controller.remove_project(homeDir)
self.transitions.move_to_open()
else:
pass
def create_new_project(self):
## ask for project name
projectID, ok = QtGui.QInputDialog.getText(self, 'Name designation', 'Enter the name of your new project:')
projectID = re.sub("\s+","_",str(projectID))
idValid = True
if projectID == '':
self.status.showMessage("New project creation aborted", 5000)
return None
defaultDir = self.controller.defaultDir
projectDir = QtGui.QFileDialog.getExistingDirectory(self, 'Select a location to save your project',
options=QtGui.QFileDialog.ShowDirsOnly, directory=defaultDir)
projectID = re.sub("\s+","_",str(projectID))
if projectDir == '':
self.status.showMessage("New project creation aborted", 5000)
return None
projectDir = str(projectDir)
if os.path.isdir(projectDir) == False:
print "ERROR: MainWindow - specified project directory does not exist"
self.status.showMessage("New project creation aborted", 5000)
return None
## ensure project name is valid and not alreaedy used
homeDir = os.path.join(projectDir,projectID)
if os.path.isdir(homeDir) == True:
idValid = False
while idValid == False:
reply = QtGui.QMessageBox.question(self, 'Message', "A project named\n'%s'\nalready exists. Do you want to overwrite it?"%homeDir,
QtGui.QMessageBox.Yes, QtGui.QMessageBox.No)
if reply == QtGui.QMessageBox.Yes:
idValid = True
if self.controller.verbose == True:
print 'INFO: overwriting old project'
else:
self.status.showMessage("New project creation aborted", 5000)
return None
## check to see if project creation was canceled
if projectID == '':
self.status.showMessage("New project creation aborted", 5000)
return None
if self.controller.verbose == True:
print 'INFO: creating new project', projectID
## initialize and load project
goFlag = self.controller.create_new_project(homeDir)
if goFlag == True:
self.transitions.move_to_data_processing()
self.status.showMessage("New project successfully created", 5000)
else:
print "ERROR: create new project did not succeed"
def open_existing_project(self):
'''
a reference function to move to the open screen
'''
if self.controller.verbose == True:
print 'INFO: open existing project'
self.transitions.move_to_open()
self.status.showMessage("Existing project successfully loaded", 5000)
def open_existing_project_handler(self,homeDir):
'''
from the open projects page open a selected project
'''
## error check
if homeDir == None:
print "ERROR: mainWindow.open_existing_projects_handler - homeDir is None"
return
if os.path.isdir(homeDir) == False:
print "ERROR: mainWindow.open_existing_projects_handler - homeDir does not exist"
return
projectID = os.path.split(homeDir)[-1]
projectLog = os.path.join(homeDir,projectID+".log")
if os.path.exists(projectLog) == False:
print "ERROR: mainWindow.open_existing_projects_handler - homeDir not a cytostream project"
self.display_warning("Specified project dir is not a valid cytostream project")
return
## prepare variables and move
print 'open existing project handler'
move_transition(self)
print '...move transition made'
self.reset_view_workspace()
print '...reset workspace'
self.controller.initialize_project(homeDir,loadExisting=True)
print '...initializing controller'
self.controller.masterChannelList = self.model.get_master_channel_list()
print '...getting master channel list'
self.refresh_state()
def load_files_with_progressbar(self,progressBar):
'''
callback for loading files from data processing
'''
## error check
if type(self.allFilePaths) != type([]):
print "ERROR: MainWindow -- load_files_with_progressbar -- bad input type"
if len(self.allFilePaths) < 1:
print "WARNING: MainWindow -- load_files_with_progressbar -- allFilePaths is empty"
if len(self.dpc.fileUploader.loadedFilePaths) > 0:
compensationFilePath = self.dpc.fileUploader.loadedFilePaths[0]
self.controller.compensationFilePath = compensationFilePath
self.controller.load_files_handler(self.allFilePaths,progressBar=progressBar,view=self)
self.allFilePaths = []
move_transition(self)
self.refresh_state()
def fileSave(self):
'''
saves current state of software
'''
if self.controller.homeDir != None:
self.controller.save()
else:
self.display_warning("Must open project first before saving")
return None
self.display_info("Progress saved")
def fileSaveAs(self):
self.display_info("This function is not yet implemented")
def filePrint(self):
self.display_info("This function is not yet implemented")
#if self.image.isNull():
# return
#if self.printer is None:
# self.printer = QtGui.QPrinter(QtGui.QPrinter.HighResolution)
# self.printer.setPageSize(QtGui.QPrinter.Letter)
#form = QtGui.QPrintDialog(self.printer, self)
#if form.exec_():
# painter = QtGui.QPainter(self.printer)
# rect = painter.viewport()
# size = self.image.size()
# size.scale(rect.size(), QtCore.Qt.KeepAspectRatio)
# painter.setViewport(rect.x(), rect.y(), size.width(),
# size.height())
# painter.drawImage(0, 0, self.image)
def helpAbout(self):
QtGui.QMessageBox.about(self, "About %s"%self.controller.appName,
"""<b>%s</b> v %s
<p>Copyright © 2010 Duke University.
All rights reserved.
<p>This application can be used to perform
model based analysis of flow cytometry data.
<p>Python %s - Qt %s - PyQt %s on %s""" % (self.controller.appName,
__version__, platform.python_version(),
QT_VERSION_STR, PYQT_VERSION_STR, platform.system()))
def show_model_log_info(self):
self.set_selected_model()
selectedModel, selectedModelIndex = self.fileSelector.get_selected_model()
fullModelName = re.sub("\.fcs|\.pickle","",self.log.log['selected_file']) + "_" + selectedModel
QtGui.QMessageBox.about(self, "%s - Model Information"%self.controller.appName,
"""<br><b>Project ID</b> - %s
<br><b>Model name</b> - %s
<br><b>Date time</b> - %s
<br><b>Full name</b> - %s
<br><b>File name</b> - %s
<br><b>Components</b> - %s
<br><b>Modes</b> - %s
<br><b>Run time</b> - %s"""%(modelLogFile['project id'],selectedModel,modelLogFile['timestamp'],
modelLogFile['full model name'],modelLogFile['file name'],
modelLogFile['number components'], modelLogFile['number modes'],modelLogFile['model runtime'])
)
def show_more_info(self):
currentState = self.log.log['current_state']
if moreInfoDict.has_key(currentState):
msg = moreInfoDict[currentState]
else:
msg = """<br>Helpful information not yet present... %s"""%currentState
QtGui.QMessageBox.about(self, "%s - Information"%self.controller.appName,msg)
def helpHelp(self):
self.display_info("The help is not yet implimented")
#form = helpform.HelpForm("index.html", self)
#form.show()
################################################################################################3
def generic_callback(self):
print "this button/widget does not do anything yet"
def set_num_components(self,value):
diff = value % 16
if diff == 0:
newValue = value
elif (value - diff) % 16 == 0:
newValue = value - diff
elif (value + diff) % 16 == 0:
newValue = value + diff
self.log.log['selected_k'] = newValue
def handle_model_to_run_callback(self,item=None):
'''
handles the selection of model to run
'''
if item in ['dpmm']:
self.log.log['model_to_run'] == item
else:
self.display_info("Selected model is not yet available")
self.modelToRunSelector.set_checked('dpmm')
def handle_model_mode_callback(self,item=None):
'''
handles the selection of model to run
normal, onefit, pooled, target
'''
if item in ['normal']:
self.log.log['model_mode'] == item
self.log.log('file_in_focus','all')
else:
self.display_info("Selected model mode is not yet available")
self.modelModeSelector.set_checked('normal')
def handle_model_edit_return(self):
'''
handles the model edit return
'''
self.move_to_model_run(self,modelMode='progressbar')
def handle_save_images_callback(self):
if self.log.log['current_state'] == 'Quality Assurance':
figMode = 'qa'
else:
figMode = 'analysis'
validViews = ['plot']
currentPlotView = str(self.controller.currentPlotView)
if currentPlotView in validViews:
defaultDir = os.path.join(self.controller.homeDir,'documents')
fileFilter = "*.png;;*.jpg;;*.pdf"
imgFileName, extension = QtGui.QFileDialog.getSaveFileNameAndFilter(self, 'Save As', directory=defaultDir, filter=fileFilter)
imgFileName = str(imgFileName)
extension = str(extension)[1:]
figName = re.sub(extension,"",imgFileName) + extension
numSubplots = int(re.sub('plot-','',currentPlotView))
figTitle = None
ss = SaveSubplots(self.controller.homeDir,figName,numSubplots,figMode=figMode,figTitle=figTitle,forceScale=True)
print 'plot saved as ', figName
else:
print "WARNING: MainWindow.handle_save_images_callback - call to save from invalid mode",
def update_highest_state(self):
'''
keep track of the highest state achieved in software
'''
## keep track of the highest state
if self.stateList.__contains__(self.controller.log.log['current_state']):
if self.stateList.index(self.controller.log.log['current_state']) > int(self.controller.log.log['highest_state']):
self.controller.log.log['highest_state'] = self.stateList.index(self.controller.log.log['current_state'])
self.controller.save()
def run_file_aligner(self):
'''
handles the running of the file aligner
'''
print 'this is where we run the file aligner'
def run_progress_bar(self):
mode = self.log.log['current_state']
## handle subsampling
if self.log.log['current_state'] == 'Quality Assurance':
subsample = self.log.log['subsample_qa']
else:
subsample = self.log.log['subsample_analysis']
self.controller.handle_subsampling(subsample)
fileList = get_fcs_file_names(self.controller.homeDir)
if mode == 'Quality Assurance':
self.qac.progressBar.button.setText('Please wait...')
self.qac.progressBar.button.setEnabled(False)
self.fileSelector.setEnabled(False)
self.subsampleSelector.setEnabled(False)
self.channelSelector.setEnabled(False)
self.moreInfoBtn.setEnabled(False)
QtCore.QCoreApplication.processEvents()
self.controller.process_images('qa',progressBar=self.qac.progressBar,view=self)
self.display_thumbnails()
elif mode == 'Model Run':
self.mc.set_disable()
QtCore.QCoreApplication.processEvents()
if self.controller.log.log['model_to_run'] in ['dpmm-mcmc']:
self.controller.run_selected_model_cpu(progressBar=self.mc.progressBar,view=self)
else:
self.controller.run_selected_model_cpu(progressBar=self.mc.progressBar,view=self)
else:
print "ERROR: got unexpected mode for MainWindow.run_progress_bar",mode
def on_model_run_finish(self):
'''
after completion of model run automatically creatue figures
'''
self.transitions.move_to_model_run()
self.mc.set_disable()
QtCore.QCoreApplication.processEvents()
self.mc.widgetSubtitle.setText("Creating figures...")
self.mc.progressBar.progressLabel.setText("Creating figures...")
subsample = self.controller.log.log['subsample_analysis']
modelRunID = 'run' + str(self.log.log['models_run_count'])
self.controller.handle_subsampling(subsample)
self.controller.process_images('analysis',modelRunID=modelRunID,progressBar=self.mc.progressBar,view=self)
self.transitions.move_to_model_results(mode='menu')
def recreate_figures(self):
'''
call back from state transtions to enable thumbnail figure recreation
'''
if self.log.log['current_state'] == 'Quality Assurance':
self.transitions.move_to_quality_assurance(mode='progressbar')
elif self.log.log['current_state'] == 'Model Results':
self.transitions.move_to_model_results()
#self.on_model_run_finish()
def plots_enable_disable(self,mode='thumbnails'):
'''
enables and disables widgets for thumbnail and plot view modes
'''
## docks check
if self.dockWidget == None:
add_left_dock(self)
if self.pDock == None:
self.add_pipeline_dock()
if mode == 'thumbnails':
if self.fileSelector:
self.fileSelector.setEnabled(True)
if self.plotSelector:
self.plotSelector.setEnabled(False)
if self.channelSelector:
self.channelSelector.setEnabled(False)
if self.plotTickControls:
self.plotTickControls.setEnabled(False)
if self.vizModeSelector:
self.vizModeSelector.setEnabled(True)
self.vizModeSelector.set_checked(mode)
if self.subsampleSelector:
self.subsampleSelector.setEnabled(False)
if self.clusterSelector:
self.clusterSelector.setEnabled(False)
if self.gateSelector:
self.gsScrollArea.setEnabled(False)
self.gateSelector.setEnabled(False)
elif mode == 'plot':
if self.log.log['current_state'] == 'Quality Assurance':
self.pDock.enable_continue_btn(self.transitions.move_to_model_run)
self.plotTickControls.labelsCB.setEnabled(False)
else:
self.plotTickControls.labelsCB.setEnabled(True)
if self.fileSelector:
self.fileSelector.setEnabled(True)
if self.plotSelector:
self.plotSelector.setEnabled(True)
if self.channelSelector:
self.channelSelector.setEnabled(True)
if self.plotTickControls:
self.plotTickControls.setEnabled(True)
if self.vizModeSelector:
self.vizModeSelector.setEnabled(True)
self.vizModeSelector.set_checked(mode)
if self.subsampleSelector:
self.subsampleSelector.setEnabled(True)
if self.clusterSelector:
self.clusterSelector.setEnabled(True)
if self.gateSelector:
self.gsScrollArea.setEnabled(True)
self.gateSelector.setEnabled(True)
if self.saveImgsBtn and self.controller.log.log['num_subplots'] != '1':
self.saveImgsBtn.setEnabled(True)
self.pDock.contBtn.setEnabled(True)
self.pDock.enable_disable_states()
def display_thumbnails(self,runNew=False,forceMode=None):
'''
displays thumbnail images for quality assurance or results navigation states
'''
## enable/disable
if forceMode != None:
mode = forceMode
else:
mode = self.log.log['current_state']
## setup layout
self.reset_layout()
hbl = QtGui.QHBoxLayout()
hbl.setAlignment(QtCore.Qt.AlignCenter)
## adjust the selected file
fileList = get_fcs_file_names(self.controller.homeDir)
if type(self.log.log['excluded_files']) == type([]) and len(self.log.log['excluded_files']) > 0:
for f in self.log.log['excluded_files']:
fileList.remove(f)
self.log.log['selected_file'] == re.sub("\.txt|\.fcs","",fileList[0])
if mode == 'Quality Assurance':
excludedChannels = self.log.log['excluded_channels_qa']
self.mainWidget = QtGui.QWidget(self)
imgDir = os.path.join(self.controller.homeDir,"figs")
fileChannels = self.log.log['alternate_channel_labels']
channelsToView = np.array(fileChannels)[list(set(range(len(fileChannels))).difference(set(excludedChannels)))].tolist()
thumbDir = os.path.join(imgDir,'qa',self.log.log['selected_file']+"_thumbs")
self.tv = ThumbnailViewer(self.mainWidget,thumbDir,fileChannels,self.controller.channelDict,mainWindow=self)
elif mode == 'Model Results':
excludedChannels = self.log.log['excluded_channels_analysis']
self.mainWidget = QtGui.QWidget(self)
fileChannels = self.log.log['alternate_channel_labels']
imgDir = os.path.join(self.controller.homeDir,'figs',self.log.log['selected_model'])
if os.path.isdir(imgDir) == False:
print "ERROR: MainWindow.display_thumbnails -- a bad imgDir has been specified", imgDir
thumbDir = os.path.join(imgDir,self.log.log['selected_file']+"_thumbs")
channelsToView = np.array(fileChannels)[list(set(range(len(fileChannels))).difference(set(excludedChannels)))].tolist()
self.tv = ThumbnailViewer(self.mainWidget,thumbDir,channelsToView,self.controller.channelDict,mainWindow=self)
else:
print "ERROR: bad mode specified in display thumbnails", mode
return
## for either mode
self.plots_enable_disable(mode='thumbnails')
self.tvScrollarea = QtGui.QScrollArea()
self.tvScrollarea.setWidget(self.tv)
self.tvScrollarea.setAlignment(QtCore.Qt.AlignCenter)
#hbl.addWidget(self.tv)
hbl.addWidget(self.tvScrollarea)
self.vboxCenter.addLayout(hbl)
self.mainWidget.setLayout(self.vbl)
self.refresh_main_widget()
## disable buttons
if self.dock != None:
self.dock.disable_all()
QtCore.QCoreApplication.processEvents()
return True
def models_run_btn_callback(self):
'''
Left dock button callback to return to Results Nav. menu
'''
self.transitions.move_to_model_results()
def set_selected_file(self):
'''
set the selected file
'''
selectedFile = self.fileSelector.get_selected_file()
self.log.log['selected_file'] = re.sub("\.txt|\.fcs","",selectedFile)
self.controller.save()
def get_master_channel_list(self):
'''
returns the master channels list
'''
if self.controller.masterChannelList == None or len(self.controller.masterChannelList) == 0:
self.controller.masterChannelList = self.model.get_master_channel_list()
return self.controller.masterChannelList
def refresh_state(self,withProgressBar=False,qaMode='thumbnails'):
'''
given the current state return to normal widget view
'''
if self.controller.log.log['current_state'] == "Data Processing":
self.transitions.move_to_data_processing(withProgressBar=withProgressBar)
elif self.controller.log.log['current_state'] == "Quality Assurance":
self.transitions.move_to_quality_assurance(mode=qaMode)
elif self.controller.log.log['current_state'] == "Model Run":
self.transitions.move_to_model_run()
elif self.controller.log.log['current_state'] == "Model Results":
self.transitions.move_to_model_results()
elif self.controller.log.log['current_state'] == "Analysis":
self.transitions.move_to_analysis(self)
elif self.controller.log.log['current_state'] == "Sample Aligner":
self.transitions.move_to_sample_aligner(self)
elif self.controller.log.log['current_state'] == "Basic Subsets":
self.transitions.move_to_basic_subsets(self)
elif self.controller.log.log['current_state'] == "Positivity":
self.transitions.move_to_positivity(self)
elif self.controller.log.log['current_state'] == "Analysis Results":
self.transitions.move_to_analysis_results(self)
elif self.controller.log.log['current_state'] == "Reports":
self.transitions.move_to_reports(self)
elif self.controller.log.log['current_state'] == "Initial":
self.transitions.move_to_initial(self)
else:
print "ERROR: MainWindow.refresh_state was given invalid state", self.log.log['current_state']
QtCore.QCoreApplication.processEvents()
def handle_show_plot(self,img=None,gating=False):
'''
main handle to show a plot
'''
self.transitions.begin_wait()
mode = self.log.log['current_state']
self.set_selected_file()
## handle transition from thumbnails to plot view
if img != None:
self.log.log['num_subplots'] = 1
self.vizModeSelector.update_num_subplots(1)
chanInds = re.findall("\d+\_\d+\_thumb",img)
i,j,k = chanInds[0].split("_")
i,j = int(i),int(j)
self.controller.log.log['plots_to_view_channels'][0] = (i,j)
self.controller.log.log['plots_to_view_files'][0] = self.controller.fileNameList.index(self.log.log['selected_file'])
self.controller.save()
## initialize transition
fileChannels = self.log.log['alternate_channel_labels']
self.reset_layout()
self.mainWidget = QtGui.QWidget(self)
## set the model runs to view to be currently selected model
self.log.log['plots_to_view_runs'] = [self.log.log['selected_model'] for i in self.log.log['plots_to_view_runs']]
self.controller.save()
## mode specific variables for NWayViewer
if self.log.log['current_state'] == "Quality Assurance":
figMode = 'qa'
elif self.log.log['current_state'] == "Model Results":
figMode = 'model results'
else:
print "ERROR: MainWindow --- unspecified state"
self.nwv = NWayViewer(self.controller,self.log.log['plots_to_view_channels'],self.log.log['plots_to_view_files'],
self.log.log['plots_to_view_runs'],self.log.log['plots_to_view_highlights'],
self.log.log['num_subplots'],figMode=figMode,background=True,modelType='components',
useScaled=self.log.log['use_scaled_plots'],parent=self,mainWindow=self,gating=gating)
hbl = QtGui.QHBoxLayout()
hbl.setAlignment(QtCore.Qt.AlignCenter)
hbl.addWidget(self.nwv)
## enable/disable
self.plots_enable_disable(mode='plot')
## finalize layout
self.vboxCenter.addLayout(hbl)
self.mainWidget.setLayout(self.vbl)
self.refresh_main_widget()
QtCore.QCoreApplication.processEvents()
self.transitions.end_wait()
def display_info(self,msg):
'''
display info
generic function to display info to user
'''
reply = QtGui.QMessageBox.information(self,'Information',msg)
def display_warning(self,msg):
'''
display warning
generic function to display a warning to user
'''
reply = QtGui.QMessageBox.warning(self, "Warning", msg)
def refresh_main_widget(self):
'''
main function to reset main widget
'''
self.setCentralWidget(self.mainWidget)
self.mainWidget.activateWindow()
self.mainWidget.update()
self.show()
for o, a in optlist:
if o == '-h':
homeDir = a
if o == '-f':
figName = a
if o == '-c':
chanInd = int(a)
if o == '-s':
subsample = a
if subsample != 'original':
subsample = int(float(subsample))
## initialze project and fetch data
fileList = get_fcs_file_names(homeDir)
controller = Controller(debug=False)
controller.initialize_project(homeDir,loadExisting=True)
plotsToViewFiles = controller.log.log['plots_to_view_files']
fileName = fileList[int(plotsToViewFiles[0])]
data = controller.get_events(fileName,subsample='1e05')
data = data[:,chanInd]
## prepare figure and plot
fig = plt.figure(figsize=(3,3))
ax = fig.add_subplot(111)
n, bins, patches = plt.hist(data,bins=15,normed=1,facecolor='#333333',alpha=0.75)
## axes and save
ax.set_yticks([])
ax.set_xticks([])
ax.set_title('')
class NoGuiAnalysis():
def __init__(self,projectID,allFiles,subsample='1e4',makeQaFigs=True,makeResultsFigs=True, numComponents=16):
## error checking
if type(allFiles) != type([]):
print "ERROR:allFiles input must be of type list"
return None
self.projectID = projectID
self.allFiles = allFiles
self.subsample = subsample
self.makeQaFigs = makeQaFigs
self.makeResultsFigs = makeResultsFigs
self.numComponents = numComponents
self.initialize()
for fileName in self.allFiles:
self.controller.log.log['selectedFile'] = os.path.split(fileName)[-1]
print 'running model on', self.controller.log.log['selectedFile']
self.run_selected_model()
## create figures
if self.makeResultsFigs == True:
print 'creating results figures'
self.controller.process_images('results')
def initialize(self):
self.controller = Controller()
self.controller.initialize_project(self.projectID)
firstFile = True
goFlag = True
for fileName in self.allFiles:
if os.path.isfile(fileName) == False:
print 'ERROR: Bad file name skipping', fileName
continue
print 'adding...', fileName
fileName = str(fileName)
if firstFile == True:
self.controller.create_new_project(fileName)
firstFile = False
else:
goFlag = self.controller.load_additional_fcs_files(fileName)
if self.controller.homeDir == None:
print "ERROR: project failed to initialize"
return
else:
print "project created."
# subsampling
print "handling subsampling"
self.controller.log.log['subsample'] = self.subsample
self.controller.handle_subsampling()
self.controller.save()
# qa image creation
if self.makeQaFigs == True:
print 'making qa images'
self.controller.process_images('qa')
def run_selected_model(self):
self.controller.log.log['numComponents'] = self.numComponents
self.controller.log.log['modelToRun'] = 'dpmm'
self.controller.run_selected_model()
selectedFile = self.controller.log.log['selectedFile']
modelName = "%s_sub%s_dpmm"%(re.sub("\.fcs|\.pickle","",selectedFile),int(float(self.subsample)))
statModelModes, statModelClasses = self.controller.model.load_model_results_pickle(modelName,'modes')