def __init__(self, lasagna):
super(plugin, self).__init__(lasagna)
self.lasagna = lasagna
self.pluginShortName = "ARA explorer"
self.pluginLongName = "Allen Reference Atlas explorer"
self.pluginAuthor = "Rob Campbell"
#Read file locations from preferences file (creating a default file if none exists)
self.pref_file = lasHelp.getLasagna_prefDir() + 'ARA_plugin_prefs.yml'
self.prefs = lasHelp.loadAllPreferences(
prefFName=self.pref_file, defaultPref=self.defaultPrefs())
#The last value the mouse hovered over. When this changes, we re-calculate the contour
self.lastValue = -1
#default names of the three files that we need:
self.atlasFileName = 'atlas'
self.templateFileName = 'template'
self.labelsFileName = 'labels'
#The root node index of the ARA
self.rootNode = 8
#Warn and quit if there are no paths
if len(self.prefs['ara_paths']) == 0:
self.warnAndQuit(
'Please fill in preferences file at<br>%s<br><a href="http://raacampbell.github.io/lasagna/ara_explorer_plugin.html">http://raacampbell.github.io/lasagna/ara_explorer_plugin.html</a>'
% self.pref_file)
return
#Set up the UI
self.setupUi(self)
self.show()
self.statusBarName_checkBox.setChecked(
self.prefs['enableNameInStatusBar'])
self.highlightArea_checkBox.setChecked(self.prefs['enableOverlay'])
self.brainArea_itemModel = QtGui.QStandardItemModel(
self.brainArea_treeView)
self.brainArea_treeView.setModel(self.brainArea_itemModel)
#Link the selections in the tree view to a slot in order to allow highlighting of the selected area
self.brainArea_treeView.selectionModel().selectionChanged[
QtCore.QItemSelection,
QtCore.QItemSelection].connect(self.highlightSelectedAreaFromList)
#Link signals to slots
self.araName_comboBox.activated.connect(self.araName_comboBox_slot)
self.load_pushButton.released.connect(self.load_pushButton_slot)
self.overlayTemplate_checkBox.stateChanged.connect(
self.overlayTemplate_checkBox_slot)
self.statusBarName_checkBox.stateChanged.connect(
self.statusBarName_checkBox_slot)
self.highlightArea_checkBox.stateChanged.connect(
self.highlightArea_checkBox_slot)
#Loop through all paths and add to combobox.
self.paths = dict()
n = 1
for path in self.prefs['ara_paths']:
if not os.path.exists(path):
print("%s does not exist. skipping" % path)
continue
filesInPath = os.listdir(path)
if len(filesInPath) == 0:
print("No files in %s . skipping" % path)
continue
pths = dict(atlas='', labels='', template='')
print("\n %d. Looking for files in directory %s" % (n, path))
n += 1
files = os.listdir(path)
#get the file names
for thisFile in files:
if thisFile.startswith(self.atlasFileName):
if thisFile.endswith('raw'):
continue
pths['atlas'] = os.path.join(path, thisFile)
print("Adding atlas file %s" % thisFile)
break
for thisFile in files:
if thisFile.startswith(self.labelsFileName):
pths['labels'] = os.path.join(path, thisFile)
print("Adding labels file %s" % thisFile)
break
for thisFile in files:
if thisFile.startswith(self.templateFileName):
if thisFile.endswith('raw'):
continue
pths['template'] = os.path.join(path, thisFile)
print("Adding template file %s" % thisFile)
break
if len(pths['atlas']) == 0 | len(pths['labels']) == 0:
print('Skipping empty empty paths entry')
continue
#If we're here, this entry should at least have a valid atlas file and a valid labels file
#We will index the self.paths dictionary by the name of the atlas file as this is also
#what will be put into the combobox.
atlasDirName = path.split(os.path.sep)[-1]
#skip if a file with this name already exists
if atlasDirName in self.paths:
print(
"Skipping as a directory called %s is already in the list"
% atlasDirName)
continue
#Add this ARA to the paths dictionary and to the combobox
self.paths[atlasDirName] = pths
self.araName_comboBox.addItem(atlasDirName)
#blank line
print("")
#If we have no paths to ARAs by the end of this, issue an error alertbox and quit
if len(self.paths) == 0:
self.warnAndQuit(
'Found no valid paths in preferences file at<br>%s.<br>SEE <a href="http://raacampbell.github.io/lasagna/ara_explorer_plugin.html">http://raacampbell.github.io/lasagna/ara_explorer_plugin.html</a>'
% self.pref_file)
return
self.lasagna.removeIngredientByType(
'imagestack') #remove all image stacks
#If the user has asked for this, load the first ARA entry automatically
self.data = dict(currentlyLoadedAtlasName='',
currentlyLoadedOverlay='')
currentlySelectedARA = str(
self.araName_comboBox.itemText(
self.araName_comboBox.currentIndex()))
if self.prefs['loadFirstAtlasOnStartup']:
print("Auto-Loading " + currentlySelectedARA)
self.loadARA(currentlySelectedARA)
self.load_pushButton.setEnabled(
False
) #disable because the current selection has now been loaded
#Make a lines ingredient that will house the contours for the currently selected area.
self.contourName = 'aracontour'
self.lasagna.addIngredient(objectName=self.contourName,
kind='lines',
data=[])
self.lasagna.returnIngredientByName(
self.contourName).addToPlots() #Add item to all three 2D plots
def __init__(self,lasagna):
super(plugin,self).__init__(lasagna)
self.lasagna=lasagna
self.pluginShortName="ARA explorer"
self.pluginLongName="Allen Reference Atlas explorer"
self.pluginAuthor="Rob Campbell"
#Read file locations from preferences file (creating a default file if none exists)
self.pref_file = lasHelp.getLasagna_prefDir() + 'ARA_plugin_prefs.yml'
self.prefs = lasHelp.loadAllPreferences(prefFName=self.pref_file,defaultPref=self.defaultPrefs())
#The last value the mouse hovered over. When this changes, we re-calculate the contour
self.lastValue=-1
#default names of the three files that we need:
self.atlasFileName = 'atlas'
self.templateFileName = 'template'
self.labelsFileName = 'labels'
#The root node index of the ARA
self.rootNode=8
#Warn and quit if there are no paths
if len(self.prefs['ara_paths'])==0:
self.warnAndQuit('Please fill in preferences file at<br>%s<br><a href="http://raacampbell13.github.io/lasagna/ara_explorer_plugin.html">http://raacampbell13.github.io/lasagna/ara_explorer_plugin.html</a>' % self.pref_file)
return
#Set up the UI
self.setupUi(self)
self.show()
self.statusBarName_checkBox.setChecked(self.prefs['enableNameInStatusBar'])
self.highlightArea_checkBox.setChecked(self.prefs['enableOverlay'])
self.brainArea_itemModel = QtGui.QStandardItemModel(self.brainArea_treeView)
self.brainArea_treeView.setModel(self.brainArea_itemModel)
#Link the selections in the tree view to a slot in order to allow highlighting of the selected area
QtCore.QObject.connect(self.brainArea_treeView.selectionModel(), QtCore.SIGNAL("selectionChanged(QItemSelection, QItemSelection)"), self.highlightSelectedAreaFromList)
#Link signals to slots
self.araName_comboBox.activated.connect(self.araName_comboBox_slot)
self.load_pushButton.released.connect(self.load_pushButton_slot)
self.overlayTemplate_checkBox.stateChanged.connect(self.overlayTemplate_checkBox_slot)
self.statusBarName_checkBox.stateChanged.connect(self.statusBarName_checkBox_slot)
self.highlightArea_checkBox.stateChanged.connect(self.highlightArea_checkBox_slot)
#Loop through all paths and add to combobox.
self.paths = dict()
n=1
for path in self.prefs['ara_paths']:
if not os.path.exists(path):
print "%s does not exist. skipping" % path
continue
filesInPath = os.listdir(path)
if len(filesInPath)==0:
print "No files in %s . skipping" % path
continue
pths = dict(atlas='', labels='', template='')
print "\n %d. Looking for files in directory %s" % (n,path)
n += 1
files = os.listdir(path)
#get the file names
for thisFile in files:
if thisFile.startswith(self.atlasFileName):
if thisFile.endswith('raw'):
continue
pths['atlas'] = os.path.join(path,thisFile)
print "Adding atlas file %s" % thisFile
break
for thisFile in files:
if thisFile.startswith(self.labelsFileName):
pths['labels'] = os.path.join(path,thisFile)
print "Adding labels file %s" % thisFile
break
for thisFile in files:
if thisFile.startswith(self.templateFileName):
if thisFile.endswith('raw'):
continue
pths['template'] = os.path.join(path,thisFile)
print "Adding template file %s" % thisFile
break
if len(pths['atlas'])==0 | len(pths['labels'])==0 :
print 'Skipping empty empty paths entry'
continue
#If we're here, this entry should at least have a valid atlas file and a valid labels file
#We will index the self.paths dictionary by the name of the atlas file as this is also
#what will be put into the combobox.
atlasDirName = path.split(os.path.sep)[-1]
#skip if a file with this name already exists
if self.paths.has_key(atlasDirName):
print "Skipping as a directory called %s is already in the list" % atlasDirName
continue
#Add this ARA to the paths dictionary and to the combobox
self.paths[atlasDirName] = pths
self.araName_comboBox.addItem(atlasDirName)
#blank line
print ""
#If we have no paths to ARAs by the end of this, issue an error alertbox and quit
if len(self.paths)==0:
self.warnAndQuit('Found no valid paths is preferences file at<br>%s.<br>SEE <a href="http://raacampbell13.github.io/lasagna/ara_explorer_plugin.html">http://raacampbell13.github.io/lasagna/ara_explorer_plugin.html</a>' % self.pref_file)
return
self.lasagna.removeIngredientByType('imagestack') #remove all image stacks
#If the user has asked for this, load the first ARA entry automatically
self.data = dict(currentlyLoadedAtlasName='', currentlyLoadedOverlay='')
currentlySelectedARA = str(self.araName_comboBox.itemText(self.araName_comboBox.currentIndex()))
if self.prefs['loadFirstAtlasOnStartup']:
print "Auto-Loading " + currentlySelectedARA
self.loadARA(currentlySelectedARA)
self.load_pushButton.setEnabled(False) #disable because the current selection has now been loaded
#Make a lines ingredient that will house the contours for the currently selected area.
self.contourName = 'aracontour'
self.lasagna.addIngredient(objectName=self.contourName,
kind='lines',
data=[])
self.lasagna.returnIngredientByName(self.contourName).addToPlots() #Add item to all three 2D plots
def __init__(self,lasagna):
super(plugin,self).__init__(lasagna)
self.lasagna=lasagna
self.pluginShortName="area namer"
self.pluginLongName="brain area namer"
self.pluginAuthor="Rob Campbell"
#Read file locations from preferences file (creating a default file if none exists)
self.pref_file = lasHelp.getLasagna_prefDir() + 'ARA_plugin_prefs.yml'
self.prefs = lasHelp.loadAllPreferences(prefFName=self.pref_file,defaultPref=self.defaultPrefs())
#The last value the mouse hovered over. When this changes, we re-calcualte the contour
self.lastValue=-1
#default names of the three files that we need:
self.atlasFileName = 'atlas'
self.labelsFileName = 'labels'
#The root node index of the ARA
self.rootNode=8
#Warn and quit if there are no paths
if len(self.prefs['ara_paths'])==0:
self.warnAndQuit('Please fill in preferences file at<br>%s<br><a href="http://raacampbell13.github.io/lasagna/ara_explorer_plugin.html">http://raacampbell13.github.io/lasagna/ara_explorer_plugin.html</a>' % self.pref_file)
return
#Set up the UI
self.setupUi(self)
self.show()
self.statusBarName_checkBox.setChecked(self.prefs['enableNameInStatusBar'])
self.highlightArea_checkBox.setChecked(self.prefs['enableOverlay'])
#Link signals to slots
self.araName_comboBox.activated.connect(self.araName_comboBox_slot)
self.loadOrig_pushButton.released.connect(self.loadOrig_pushButton_slot)
self.loadOther_pushButton.released.connect(self.loadOther_pushButton_slot)
self.statusBarName_checkBox.stateChanged.connect(self.statusBarName_checkBox_slot)
self.highlightArea_checkBox.stateChanged.connect(self.highlightArea_checkBox_slot)
#Loop through all paths and add to combobox.
self.paths = dict()
n=1
for path in self.prefs['ara_paths']:
if not os.path.exists(path):
print "%s does not exist. skipping" % path
continue
filesInPath = os.listdir(path)
if len(filesInPath)==0:
print "No files in %s . skipping" % path
continue
pths = dict(atlas='', labels='')
print "\n %d. Looking for files in directory %s" % (n,path)
n += 1
files = os.listdir(path)
#get the file names
for thisFile in files:
if thisFile.startswith(self.atlasFileName):
if thisFile.endswith('raw'):
continue
pths['atlas'] = os.path.join(path,thisFile)
print "Adding atlas file %s" % thisFile
break
for thisFile in files:
if thisFile.startswith(self.labelsFileName):
pths['labels'] = os.path.join(path,thisFile)
print "Adding labels file %s" % thisFile
break
if len(pths['atlas'])==0 | len(pths['labels'])==0 :
print 'Skipping empty empty paths entry'
continue
#If we're here, this entry should at least have a valid atlas file and a valid labels file
#We will index the self.paths dictionary by the name of the atlas file as this is also
#what will be put into the combobox.
atlasDirName = path.split(os.path.sep)[-1]
#skip if a file with this name already exists
if self.paths.has_key(atlasDirName):
print "Skipping as a directory called %s is already in the list" % atlasDirName
continue
#Add this ARA to the paths dictionary and to the combobox
self.paths[atlasDirName] = pths
self.araName_comboBox.addItem(atlasDirName)
#blank line
print ""
#If we have no paths to ARAs by the end of this, issue an error alertbox and quit
if len(self.paths)==0:
self.warnAndQuit('Found no valid paths is preferences file at<br>%s.<br>SEE <a href="http://raacampbell13.github.io/lasagna/ara_explorer_plugin.html">http://raacampbell13.github.io/lasagna/ara_explorer_plugin.html</a>' % self.pref_file)
return
#If the user has asked for this, load the first ARA entry automatically
self.data = dict(currentlyLoadedAtlasName='', currentlyLoadedOverlay='', atlas=np.ndarray([]))
#Make a lines ingredient that will house the contours for the currently selected area.
self.addAreaContour() #from ARA_plotter
def __init__(self, lasagna):
super(plugin, self).__init__(lasagna)
self.lasagna = lasagna
self.pluginShortName = "area namer"
self.pluginLongName = "brain area namer"
self.pluginAuthor = "Rob Campbell"
#Read file locations from preferences file (creating a default file if none exists)
self.pref_file = lasHelp.getLasagna_prefDir() + 'ARA_plugin_prefs.yml'
self.prefs = lasHelp.loadAllPreferences(
prefFName=self.pref_file, defaultPref=self.defaultPrefs())
#The last value the mouse hovered over. When this changes, we re-calcualte the contour
self.lastValue = -1
#default names of the three files that we need:
self.atlasFileName = 'atlas'
self.labelsFileName = 'labels'
#The root node index of the ARA
self.rootNode = 8
#Warn and quit if there are no paths
if len(self.prefs['ara_paths']) == 0:
self.warnAndQuit(
'Please fill in preferences file at<br>%s<br><a href="http://raacampbell13.github.io/lasagna/ara_explorer_plugin.html">http://raacampbell13.github.io/lasagna/ara_explorer_plugin.html</a>'
% self.pref_file)
return
#Set up the UI
self.setupUi(self)
self.show()
self.statusBarName_checkBox.setChecked(
self.prefs['enableNameInStatusBar'])
self.highlightArea_checkBox.setChecked(self.prefs['enableOverlay'])
#Link signals to slots
self.araName_comboBox.activated.connect(self.araName_comboBox_slot)
self.loadOrig_pushButton.released.connect(
self.loadOrig_pushButton_slot)
self.loadOther_pushButton.released.connect(
self.loadOther_pushButton_slot)
self.statusBarName_checkBox.stateChanged.connect(
self.statusBarName_checkBox_slot)
self.highlightArea_checkBox.stateChanged.connect(
self.highlightArea_checkBox_slot)
#Loop through all paths and add to combobox.
self.paths = dict()
n = 1
for path in self.prefs['ara_paths']:
if not os.path.exists(path):
print "%s does not exist. skipping" % path
continue
filesInPath = os.listdir(path)
if len(filesInPath) == 0:
print "No files in %s . skipping" % path
continue
pths = dict(atlas='', labels='')
print "\n %d. Looking for files in directory %s" % (n, path)
n += 1
files = os.listdir(path)
#get the file names
for thisFile in files:
if thisFile.startswith(self.atlasFileName):
if thisFile.endswith('raw'):
continue
pths['atlas'] = os.path.join(path, thisFile)
print "Adding atlas file %s" % thisFile
break
for thisFile in files:
if thisFile.startswith(self.labelsFileName):
pths['labels'] = os.path.join(path, thisFile)
print "Adding labels file %s" % thisFile
break
if len(pths['atlas']) == 0 | len(pths['labels']) == 0:
print 'Skipping empty empty paths entry'
continue
#If we're here, this entry should at least have a valid atlas file and a valid labels file
#We will index the self.paths dictionary by the name of the atlas file as this is also
#what will be put into the combobox.
atlasDirName = path.split(os.path.sep)[-1]
#skip if a file with this name already exists
if self.paths.has_key(atlasDirName):
print "Skipping as a directory called %s is already in the list" % atlasDirName
continue
#Add this ARA to the paths dictionary and to the combobox
self.paths[atlasDirName] = pths
self.araName_comboBox.addItem(atlasDirName)
#blank line
print ""
#If we have no paths to ARAs by the end of this, issue an error alertbox and quit
if len(self.paths) == 0:
self.warnAndQuit(
'Found no valid paths is preferences file at<br>%s.<br>SEE <a href="http://raacampbell13.github.io/lasagna/ara_explorer_plugin.html">http://raacampbell13.github.io/lasagna/ara_explorer_plugin.html</a>'
% self.pref_file)
return
#If the user has asked for this, load the first ARA entry automatically
self.data = dict(currentlyLoadedAtlasName='',
currentlyLoadedOverlay='',
atlas=np.ndarray([]))
#Make a lines ingredient that will house the contours for the currently selected area.
self.addAreaContour() #from ARA_plotter
