class ControllerTest(unittest.TestCase):
def setUp(self):
cwd = os.getcwd()
if os.path.split(cwd)[1] == 'tests':
BASEDIR = os.path.split(cwd)[0]
elif os.path.split(cwd)[1] == 'gdi':
BASEDIR = cwd
else:
print "ERROR: Model test cannot find home dir -- cwd", cwd
self.controller = Controller()
self.controller.initialize_project("utest")
self.testFilePathName = os.path.join(BASEDIR,"tests","example_data", "simple_mmu_list.csv")
self.fileName ="simple_mmu_list.csv"
def testLog(self):
self.controller.create_new_project(view=None,projectID='utest')
self.controller.save()
self.assertTrue(os.path.isfile(os.path.join(self.controller.homeDir,"%s.log"%self.controller.projectID)))
def testCreateNewProject(self):
self.controller.create_new_project(view=None,projectID='utest')
self.assertTrue(os.path.isdir(os.path.join(self.controller.homeDir,"data")))
self.assertTrue(os.path.isdir(os.path.join(self.controller.homeDir,"figs")))
self.assertTrue(os.path.isdir(os.path.join(self.controller.homeDir,"models")))
def testGeneListFetching(self):
self.controller.model.load_files([self.testFilePathName])
self.failIf(len(os.listdir(os.path.join(self.controller.homeDir,"data"))) != 1)
fName = re.sub('\s+','_',os.path.split(self.fileName)[-1])
fName = re.sub('\.csv|\.txt','',fName)
geneList = self.controller.model.get_genes(fName)
self.assertEqual(len(geneList),7)
def __init__(self):
## construct and set main variables
QtGui.QMainWindow.__init__(self)
## variables
self.buff = 2.0
self.controller = Controller()
self.mainWidget = QtGui.QWidget(self)
self.reset_view_workspace()
self.stateList = ['Data Processing','Subset Finder','Results Navigation']
##self.possibleModels = ['dpmm']
##self.resultsModeList = ['modes','components']
self.sizeLabel = QtGui.QLabel()
self.sizeLabel.setFrameStyle(QtGui.QFrame.StyledPanel|QtGui.QFrame.Sunken)
self.create_statusbar()
create_menubar_toolbar(self)
## 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
print 'moving to initial...'
move_to_initial(self)
def setUp(self):
cwd = os.getcwd()
if os.path.split(cwd)[1] == 'tests':
BASEDIR = os.path.split(cwd)[0]
elif os.path.split(cwd)[1] == 'gdi':
BASEDIR = cwd
else:
print "ERROR: Model test cannot find home dir -- cwd", cwd
self.controller = Controller()
self.controller.initialize_project("utest")
self.testFilePathName = os.path.join(BASEDIR,"tests","example_data", "simple_mmu_list.csv")
self.fileName ="simple_mmu_list.csv"
class MainWindow(QtGui.QMainWindow):
def __init__(self):
## construct and set main variables
QtGui.QMainWindow.__init__(self)
## variables
self.buff = 2.0
self.controller = Controller()
self.mainWidget = QtGui.QWidget(self)
self.reset_view_workspace()
self.stateList = ['Data Processing','Subset Finder','Results Navigation']
##self.possibleModels = ['dpmm']
##self.resultsModeList = ['modes','components']
self.sizeLabel = QtGui.QLabel()
self.sizeLabel.setFrameStyle(QtGui.QFrame.StyledPanel|QtGui.QFrame.Sunken)
self.create_statusbar()
create_menubar_toolbar(self)
## 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
print 'moving to initial...'
move_to_initial(self)
#################################################
#
# variables and states
#
#################################################
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.mainWidget = None
self.dockWidget = None
self.fileSelector = None
self.pDock = None
self.dock = None
self.tv = None
self.lastChanI = None
self.lastChanJ = None
#################################################
#
# forwarded functions
#
#################################################
def add_left_dock(self):
add_left_dock(self)
def remove_left_dock(self):
remove_left_dock(self)
def move_to_initial(self,dummy=None):
move_to_initial(self)
def move_to_data_processing(self,dummy=None):
move_to_data_processing(self)
def move_to_subset_finder(self,dummy=None):
move_to_subset_finder(self)
def move_to_results_navigation(self,dummy=None):
move_to_results_navigation(self)
#################################################
#
# Statusbar
#
#################################################
def create_statusbar(self):
status = self.statusBar()
status.setSizeGripEnabled(False)
status.addPermanentWidget(self.sizeLabel)
status.showMessage("Ready", 5000)
#################################################
#
# menubar and toolbar
#
#################################################
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.open_existing_project()
else:
pass
def create_new_project(self):
self.controller.create_new_project(self)
if self.controller.homeDir != None:
self.pDock.set_btn_highlight('data processing')
move_to_data_processing(self)
def add_files_to_project(self):
allFiles = QtGui.QFileDialog.getOpenFileNames(self, 'Open file(s)')
allFilesList = [str(fileName) for fileName in allFiles]
self.controller.model.load_files(allFilesList)
move_to_data_processing(self)
def open_existing_project(self):
if self.controller.projectID != None:
reply = QtGui.QMessageBox.question(self, self.controller.appName,
"Are you sure you want to close the current project - '%s'?"%self.controller.projectID,
QtGui.QMessageBox.Yes, QtGui.QMessageBox.No)
if reply == QtGui.QMessageBox.No:
return
self.controller.reset_workspace()
if self.dockWidget != None:
remove_left_dock(self)
closeBtnFn = lambda a=self: move_to_initial(a)
self.mainWidget = QtGui.QWidget(self)
projectList = get_project_names(self.controller.baseDir)
self.existingProjectOpener = OpenExistingProject(projectList,parent=self.mainWidget,openBtnFn=self.open_existing_project_handler,
closeBtnFn=closeBtnFn,rmBtnFn=self.remove_project)
hbl = QtGui.QHBoxLayout(self.mainWidget)
hbl.setAlignment(QtCore.Qt.AlignTop)
hbl.addWidget(self.existingProjectOpener)
self.refresh_main_widget()
def open_existing_project_handler(self):
projectID,projectInd = self.existingProjectOpener.get_selected_project()
self.controller.initialize_project(projectID,loadExisting=True)
self.reset_view_workspace()
self.refresh_state()
#self.refresh_state() # done twice to force correct visualation in pipeline
def fileSave(self):
if self.controller.homeDir != None:
self.controller.save()
else:
self.display_warning("Must open project first before saving")
def fileSaveAs(self):
self.display_info("This function is not yet implimented")
def filePrint(self):
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 show_image(self, percent=None):
if self.image.isNull():
return
image = self.image
self.pngViewer.setPixmap(QtGui.QPixmap.fromImage(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['selectedFile']) + "_" + selectedModel
modelLogFile = self.log.read_model_log('%s_sub%s_%s'%(re.sub("\.fcs|\.pickle","",self.log.log['selectedFile']),
int(float(self.log.log['subsample'])),self.log.log['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 helpHelp(self):
self.display_info("The help is not yet implimented")
#form = helpform.HelpForm("index.html", self)
#form.show()
################################################################################################3
def move_transition(self):
bp = BlankPage(parent=self.mainWidget)
vbl = QtGui.QVBoxLayout()
vbl.setAlignment(QtCore.Qt.AlignCenter)
hbl = QtGui.QHBoxLayout()
hbl.setAlignment(QtCore.Qt.AlignCenter)
hbl.addWidget(bp)
vbl.addLayout(hbl)
self.mainWidget.setLayout(vbl)
self.refresh_main_widget()
QtCore.QCoreApplication.processEvents()
def generic_callback(self):
print "this button/widget does not do anything yet"
#################################################
#
# Setters and handlers
#
#################################################
def set_checks_array(self):
if self.log.log['currentState'] == "Data Processing":
checksArray = self.dpc.get_selected_channels()
if type(checksArray) != type(np.array([])):
print "ERROR in set_checks_array"
return False
self.log.log['checksArray'] = checksArray
if self.log.log['checksArray'].sum() == 0:
return True
self.set_excluded_files_channels()
return True
#def set_excluded_files_channels(self):
# if type(self.log.log['checksArray']) != type(np.array([])):
# print "ERROR cannot set excluded files or channels bad checksArray"
#
# excludedFiles = []
# excludedChannels = []
# masterChannelList = self.model.get_master_channel_list()
# fileList = get_fcs_file_names(self.controller.homeDir)
# sumCols = self.log.log['checksArray'].sum(axis=0)
# sumRows = self.log.log['checksArray'].sum(axis=1)
# excludedChannels = np.array(masterChannelList)[[int(i) for i in np.where(sumCols == 0)[0]]]
# excludedFiles = np.array(fileList)[[int(i) for i in np.where(sumRows == 0)[0]]]
#
# self.log.log['excludedChannels'] = excludedChannels.tolist()
# self.log.log['excludedFiles'] = excludedFiles.tolist()
#
# if self.controller.verbose == True:
# print 'setting excluding channels', excludedChannels
# print 'setting excluding files', excludedFiles
#
# ## adjust the selected file
# fileList = get_fcs_file_names(self.controller.homeDir)
# if type(self.log.log['excludedFiles']) == type([]) and len(self.log.log['excludedFiles']) > 0:
# for f in self.log.log['excludedFiles']:
# fileList.remove(f)
# self.log.log['selectedFile'] == fileList[0]
#def set_num_components(self,value):
# diff = value % 8
# #print value, diff
# if diff == 0:
# newValue = value
# elif (value - diff) % 8 == 0:
# newValue = value - diff
# elif (value + diff) % 8 == 0:
# newValue = value + diff
#
# self.log.log['numComponents'] = newValue
def set_model_to_run(self):
sm, smInd = self.dock.get_model_to_run()
if sm == 'DPMM':
self.log.log['modelToRun'] = 'dpmm'
elif sm == 'K-means':
self.log.log['modelToRun'] = 'kmeans'
else:
print "ERROR: invalid selection for modelToRun"
def track_highest_state(self):
## keep track of the highest state
if self.stateList.__contains__(self.log.log['currentState']):
if self.stateList.index(self.log.log['currentState']) > self.log.log['highestState']:
self.log.log['highestState'] = self.stateList.index(self.log.log['currentState'])
def run_progress_bar(self):
mode = self.log.log['currentState']
self.set_widgets_enabled(False)
if self.controller.subsampleIndices == None:
self.controller.handle_subsampling()
fileList = get_fcs_file_names(self.controller.homeDir)
if mode == 'Quality Assurance':
self.controller.process_images('qa',progressBar=self.progressBar,view=self)
self.display_thumbnails()
if mode == 'Model':
self.set_model_to_run()
self.controller.run_selected_model(progressBar=self.mc.progressBar,view=self)
remove_left_dock(self)
self.mainWidget = QtGui.QWidget(self)
self.progressBar = ProgressBar(parent=self.mainWidget,buttonLabel="Create the figures")
self.progressBar.set_callback(self.create_results_thumbs)
hbl = QtGui.QHBoxLayout(self.mainWidget)
hbl.addWidget(self.progressBar)
hbl.setAlignment(QtCore.Qt.AlignCenter)
self.refresh_main_widget()
self.add_left_dock()
self.set_widgets_enabled(True)
def create_results_thumbs(self):
self.controller.process_images('results',progressBar=self.progressBar,view=self)
move_to_results_navigation(self,runNew=True)
def display_thumbnails(self,runNew=False):
mode = self.log.log['currentState']
hbl = QtGui.QHBoxLayout()
vbl = QtGui.QVBoxLayout()
vbl.setAlignment(QtCore.Qt.AlignCenter)
hbl.setAlignment(QtCore.Qt.AlignCenter)
## adjust the selected file
fileList = get_fcs_file_names(self.controller.homeDir)
if type(self.log.log['excludedFiles']) == type([]) and len(self.log.log['excludedFiles']) > 0:
for f in self.log.log['excludedFiles']:
fileList.remove(f)
self.log.log['selectedFile'] == fileList[0]
if mode == 'Quality Assurance':
self.mainWidget = QtGui.QWidget(self)
imgDir = os.path.join(self.controller.homeDir,"figs")
fileChannels = self.model.get_file_channel_list(self.log.log['selectedFile'])
thumbDir = os.path.join(imgDir,self.log.log['selectedFile'][:-4]+"_thumbs")
self.tv = ThumbnailViewer(self.mainWidget,thumbDir,fileChannels,viewScatterFn=self.handle_show_scatter)
elif mode == 'Results Navigation':
## error checking
modelsRun = get_models_run(self.controller.homeDir,self.possibleModels)
if len(modelsRun) == 0:
self.display_info("No models have been run yet -- so results cannot be viewed")
return False
self.log.log['selectedModel'] = modelsRun[0]
if self.log.log['selectedModel'] not in modelsRun:
print "ERROR selected model not in models run"
## thumbs viewer
self.mainWidget = QtGui.QWidget(self)
fileChannels = self.model.get_file_channel_list(self.log.log['selectedFile'])
if self.log.log['subsample'] == 'original':
imgDir = os.path.join(self.controller.homeDir,'figs',self.log.log['selectedModel'])
else:
subset = str(int(float(self.log.log['subsample'])))
imgDir = os.path.join(self.controller.homeDir,'figs',"sub%s_%s"%(subset,self.log.log['selectedModel']))
if os.path.isdir(imgDir) == False:
print "ERROR: a bad imgDir has been specified", imgDir
thumbDir = os.path.join(imgDir,self.log.log['selectedFile'][:-4]+"_thumbs")
self.tv = ThumbnailViewer(self.mainWidget,thumbDir,fileChannels,viewScatterFn=self.handle_show_scatter)
else:
print "ERROR: bad mode specified in display thumbnails"
## for either mode
hbl.addWidget(self.tv)
vbl.addLayout(hbl)
self.mainWidget.setLayout(vbl)
self.refresh_main_widget()
if self.dock != None:
## disable buttons
self.dock.disable_all()
QtCore.QCoreApplication.processEvents()
return True
def handle_data_processing_mode_callback(self,item=None):
if item != None:
self.log.log['dataProcessingAction'] = item
if item not in ['channel select']:
self.display_info("This stage is in beta testing and is not yet suggested for general use")
move_to_data_processing(self)
def set_selected_results_mode(self):
#selectedMode, selectedModeInd = self.dock.get_selected_results_mode()
selectedMode = self.dock.get_results_mode()
self.log.log['resultsMode'] = selectedMode
self.handle_show_scatter(img=None)
def set_selected_file(self):
selectedFile, selectedFileInd = self.fileSelector.get_selected_file()
self.log.log['selectedFile'] = selectedFile
def set_selected_model(self):
selectedModel, selectedModleInd = self.fileSelector.get_selected_model()
self.log.log['selectedModel'] = selectedModel
def refresh_state(self):
if self.log.log['currentState'] == "Data Processing":
move_to_data_processing(self)
elif self.log.log['currentState'] == "Quality Assurance":
move_to_quality_assurance(self)
elif self.log.log['currentState'] == "Model":
move_to_model(self)
elif self.log.log['currentState'] == "Results Navigation":
move_to_results_navigation(self)
elif self.log.log['currentState'] == "Results Summary":
move_to_results_summary(self)
QtCore.QCoreApplication.processEvents()
def handle_show_scatter(self,img=None):
mode = self.log.log['currentState']
self.set_selected_file()
## layout and widget setup
self.mainWidget = QtGui.QWidget(self)
bp = BlankPage(parent=self.mainWidget)
vbl = QtGui.QVBoxLayout()
vbl.setAlignment(QtCore.Qt.AlignCenter)
hbl = QtGui.QHBoxLayout()
hbl.setAlignment(QtCore.Qt.AlignCenter)
hbl.addWidget(bp)
vbl.addLayout(hbl)
self.mainWidget.setLayout(vbl)
self.refresh_main_widget()
QtCore.QCoreApplication.processEvents()
if img != None:
channels = re.sub("%s\_|\_thumb.png"%re.sub("\.fcs","",self.log.log['selectedFile']),"",img)
channels = re.split("\_",channels)
chanI = channels[-2]
chanJ = channels[-1]
self.lastChanI = chanI
self.lastChanJ = chanJ
if self.lastChanI == None or self.lastChanJ == None:
print "ERROR: lastChanI or lastChanJ not defined"
return False
if mode == "Quality Assurance":
self.mainWidget = QtGui.QWidget(self)
vbl = QtGui.QVBoxLayout(self.mainWidget)
sp = ScatterPlotter(self.controller.homeDir,self.log.log['selectedFile'],self.lastChanI,self.lastChanJ,
parent=self.mainWidget,subset=self.log.log['subsample'])
ntb = NavigationToolbar(sp, self.mainWidget)
vbl.addWidget(sp)
vbl.addWidget(ntb)
elif mode == "Results Navigation":
self.set_selected_model()
self.mainWidget = QtGui.QWidget(self)
vbl = QtGui.QVBoxLayout(self.mainWidget)
if self.log.log['subsample'] == 'original':
modelName = re.sub("\.pickle|\.fcs","",self.log.log['selectedFile']) + "_" + self.log.log['selectedModel']
else:
subset = str(int(float(self.log.log['subsample'])))
modelName = re.sub("\.pickle|\.fcs","",self.log.log['selectedFile']) + "_" + "sub%s_%s"%(subset,self.log.log['selectedModel'])
sp = ScatterPlotter(self.controller.homeDir,self.log.log['selectedFile'],self.lastChanI,self.lastChanJ,subset=self.log.log['subsample'],
modelName=modelName,modelType=self.log.log['resultsMode'],parent=self.mainWidget)
ntb = NavigationToolbar(sp, self.mainWidget)
vbl.addWidget(sp)
vbl.addWidget(ntb)
## enable buttons
self.dock.enable_all()
self.refresh_main_widget()
QtCore.QCoreApplication.processEvents()
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):
self.setCentralWidget(self.mainWidget)
self.mainWidget.activateWindow()
self.mainWidget.update()
self.show()
#QtCore.QCoreApplication.processEvents()
def set_widgets_enabled(self,flag):
if flag not in [True, False]:
print "ERROR: invalid flag sent to widgets_enable_all"
return None
if self.log.log['currentState'] == 'Data Processing':
self.dock1.setEnabled(flag)
self.dock2.setEnabled(flag)
self.fileSelector.setEnabled(flag)
self.pDock.setEnabled(flag)
elif self.log.log['currentState'] == 'Quality Assurance':
self.dock.setEnabled(flag)
self.fileSelector.setEnabled(flag)
self.pDock.setEnabled(flag)