class PlateReader(object):
""" Main controller for the PlateReader software.
This serves as the interface between PlateImage and GUI
"""
#The PlateImage
_plateImage = None
#The GUI. This will also display the GUI
_gui = None
def __init__(self):
#The PlateImage
self._plateImage = PlateImage()
#Properties
@property
def fileName(self):
""" The current file name.
This is also retriavable via getObjectsForReporting, but that
is rather computationally demanding
"""
return self._plateImage.fileName
def getImagesForReporting(self):
""" Get images used for generating reports.
This is used when exporting to RTF in the GUI
"""
#This should return the processed image with markup. Therefore save the current setting
#and recalculate if needed
usingMarkup = self._plateImage.getParameter('showMarkup')
self._plateImage.setParameter('showMarkup', True)
image = self._plateImage.image
self._plateImage.setParameter('showMarkup', usingMarkup)
return (self._plateImage.rawImage, image, self._plateImage.histogram)
def getStatistics(self):
""" Get a dictionary with the statistics."""
return self._plateImage.statistics
def showGUI(self):
""" Load and show the GUI."""
self._gui = GUI(self)
#If anything has been loaded in the plateImage object then update the
#GUI accordingly
rImage = self._plateImage.rawImage
if not rImage is None:
self._gui.setOriginalImage(rImage)
#Start with controls enabled if there is an image loaded
self._gui.changeEnabled(True, [])
wImage = self._plateImage.image
if not wImage is None:
self._gui.setWorkingImage(wImage)
if not self._plateImage.histogram is None:
self._gui.setHistogram(self._plateImage.histogram)
if not self._plateImage.statistics is None:
self._gui.printStatistics(self._plateImage.statistics)
#Show GUI and give control over to the main GUI loop
self._gui.show()
def setColColor(self, points):
""" Set the colony color and update the feature detection."""
#Note that this doesn't round the values. Use np.rint if required
#Note the shift in x/y
color = self._plateImage.rawImage[[
points.astype(int)[:, 1],
points.astype(int)[:, 0]
]]
self._plateImage.colColor = color.mean(0)
self._plateImage.detectBlobs()
self._plateImage.detectColonies()
#Update the view
if not self._gui is None:
self._gui.setWorkingImage(self._plateImage.image)
self._gui.setHistogram(self._plateImage.histogram)
self._gui.printStatistics(self._plateImage.statistics)
def setMaskUnmask(self, setToMask):
""" Set whether to mask or unmask areas when using the manual drawing tools."""
self._plateImage.maskWhenDrawing = setToMask
def maskUnmaskArea(self, points, geometry):
""" Mask or unmask an area.
geometry: 'line', 'rect' or 'circle'
"""
self._plateImage.maskUnmaskArea(points, geometry)
#This repeats all calculations. This is wasteful, but I keep it for now
self._plateImage.detectBlobs()
self._plateImage.detectColonies()
#Display the new image
if not self._gui is None:
self._gui.setWorkingImage(self._plateImage.image)
self._gui.setHistogram(self._plateImage.histogram)
self._gui.printStatistics(self._plateImage.statistics)
def setBgColor(self, points):
""" Set the background color and update the feature detection."""
#Note that this doesn't round the values. Use np.rint if required
#Note the shift in w/y
color = self._plateImage.rawImage[[
points.astype(int)[:, 1],
points.astype(int)[:, 0]
]]
self._plateImage.bgColor = color.mean(0)
self._plateImage.detectBlobs()
self._plateImage.detectColonies()
#Update the view
if not self._gui is None:
self._gui.setWorkingImage(self._plateImage.image)
self._gui.setHistogram(self._plateImage.histogram)
self._gui.printStatistics(self._plateImage.statistics)
def setParameter(self, name, value):
""" Set a parameter."""
self._plateImage.setParameter(name, value)
if not name is 'showMarkup':
self._plateImage.detectBlobs()
self._plateImage.detectColonies()
#Display the new image
if not self._gui is None:
self._gui.setWorkingImage(self._plateImage.image)
self._gui.setHistogram(self._plateImage.histogram)
self._gui.printStatistics(self._plateImage.statistics)
def getParameter(self, name):
""" Get a parameter."""
return self._plateImage.getParameter(name)
def getAllParameterNames(self):
""" Get all parameter names."""
return self._plateImage.getAllParameterNames()
def fitPlateGeometry(self, points):
""" Fit plate geometry in the PlateImage object and update the GUI accordingly."""
self._plateImage.fitPlateGeometry(points)
#This is to prevent having to select new colors if loading a new image after
#they have been selected
self._plateImage.detectBlobs()
self._plateImage.detectColonies()
#Display the new image
if not self._gui is None:
self._gui.setWorkingImage(self._plateImage.image)
self._gui.setOriginalImage(self._plateImage.rawImage)
self._gui.setHistogram(self._plateImage.histogram)
self._gui.printStatistics(self._plateImage.statistics)
def loadImage(self, fileName=None):
""" Load an image file.
Sets both the working and original images
"""
try:
if not fileName is None:
self._plateImage.loadImage(fileName)
else:
#This reloads the current image
self._plateImage.loadImage()
except:
if not self._gui is None:
if not fileName is None:
self._gui.setStatusMessage('Could not load ' + fileName)
else:
self._gui.setStatusMessage('Could not reload image')
return
if not self._gui is None:
self._gui.setWorkingImage(self._plateImage.rawImage)
self._gui.setOriginalImage(self._plateImage.rawImage)
self._gui.setHistogram(self._plateImage.histogram)
self._gui.printStatistics(self._plateImage.statistics)
if not fileName is None:
self._gui.setStatusMessage('Successfully loaded ' + fileName)
else:
self._gui.setStatusMessage('Successfully reloaded image')
class PlateReader(object):
""" Main controller for the PlateReader software.
This serves as the interface between PlateImage and GUI
"""
#The PlateImage
_plateImage=None
#The GUI. This will also display the GUI
_gui=None
def __init__(self):
#The PlateImage
self._plateImage=PlateImage()
#Properties
@property
def fileName(self):
""" The current file name.
This is also retriavable via getObjectsForReporting, but that
is rather computationally demanding
"""
return self._plateImage.fileName
def getImagesForReporting(self):
""" Get images used for generating reports.
This is used when exporting to RTF in the GUI
"""
#This should return the processed image with markup. Therefore save the current setting
#and recalculate if needed
usingMarkup=self._plateImage.getParameter('showMarkup')
self._plateImage.setParameter('showMarkup',True)
image=self._plateImage.image
self._plateImage.setParameter('showMarkup',usingMarkup)
return (self._plateImage.rawImage,image,self._plateImage.histogram)
def getStatistics(self):
""" Get a dictionary with the statistics."""
return self._plateImage.statistics
def showGUI(self):
""" Load and show the GUI."""
self._gui=GUI(self)
#If anything has been loaded in the plateImage object then update the
#GUI accordingly
rImage=self._plateImage.rawImage
if not rImage is None:
self._gui.setOriginalImage(rImage)
#Start with controls enabled if there is an image loaded
self._gui.changeEnabled(True,[])
wImage=self._plateImage.image
if not wImage is None:
self._gui.setWorkingImage(wImage)
if not self._plateImage.histogram is None:
self._gui.setHistogram(self._plateImage.histogram)
if not self._plateImage.statistics is None:
self._gui.printStatistics(self._plateImage.statistics)
#Show GUI and give control over to the main GUI loop
self._gui.show()
def setColColor(self,points):
""" Set the colony color and update the feature detection."""
#Note that this doesn't round the values. Use np.rint if required
#Note the shift in x/y
color=self._plateImage.rawImage[[points.astype(int)[:,1],points.astype(int)[:,0]]]
self._plateImage.colColor=color.mean(0)
self._plateImage.detectBlobs()
self._plateImage.detectColonies()
#Update the view
if not self._gui is None:
self._gui.setWorkingImage(self._plateImage.image)
self._gui.setHistogram(self._plateImage.histogram)
self._gui.printStatistics(self._plateImage.statistics)
def setMaskUnmask(self,setToMask):
""" Set whether to mask or unmask areas when using the manual drawing tools."""
self._plateImage.maskWhenDrawing=setToMask
def maskUnmaskArea(self,points,geometry):
""" Mask or unmask an area.
geometry: 'line', 'rect' or 'circle'
"""
self._plateImage.maskUnmaskArea(points,geometry)
#This repeats all calculations. This is wasteful, but I keep it for now
self._plateImage.detectBlobs()
self._plateImage.detectColonies()
#Display the new image
if not self._gui is None:
self._gui.setWorkingImage(self._plateImage.image)
self._gui.setHistogram(self._plateImage.histogram)
self._gui.printStatistics(self._plateImage.statistics)
def setBgColor(self,points):
""" Set the background color and update the feature detection."""
#Note that this doesn't round the values. Use np.rint if required
#Note the shift in w/y
color=self._plateImage.rawImage[[points.astype(int)[:,1],points.astype(int)[:,0]]]
self._plateImage.bgColor=color.mean(0)
self._plateImage.detectBlobs()
self._plateImage.detectColonies()
#Update the view
if not self._gui is None:
self._gui.setWorkingImage(self._plateImage.image)
self._gui.setHistogram(self._plateImage.histogram)
self._gui.printStatistics(self._plateImage.statistics)
def setParameter(self,name,value):
""" Set a parameter."""
self._plateImage.setParameter(name,value)
if not name is 'showMarkup':
self._plateImage.detectBlobs()
self._plateImage.detectColonies()
#Display the new image
if not self._gui is None:
self._gui.setWorkingImage(self._plateImage.image)
self._gui.setHistogram(self._plateImage.histogram)
self._gui.printStatistics(self._plateImage.statistics)
def getParameter(self,name):
""" Get a parameter."""
return self._plateImage.getParameter(name)
def getAllParameterNames(self):
""" Get all parameter names."""
return self._plateImage.getAllParameterNames()
def fitPlateGeometry(self,points):
""" Fit plate geometry in the PlateImage object and update the GUI accordingly."""
self._plateImage.fitPlateGeometry(points)
#This is to prevent having to select new colors if loading a new image after
#they have been selected
self._plateImage.detectBlobs()
self._plateImage.detectColonies()
#Display the new image
if not self._gui is None:
self._gui.setWorkingImage(self._plateImage.image)
self._gui.setOriginalImage(self._plateImage.rawImage)
self._gui.setHistogram(self._plateImage.histogram)
self._gui.printStatistics(self._plateImage.statistics)
def loadImage(self,fileName=None):
""" Load an image file.
Sets both the working and original images
"""
try:
if not fileName is None:
self._plateImage.loadImage(fileName)
else:
#This reloads the current image
self._plateImage.loadImage()
except:
if not self._gui is None:
if not fileName is None:
self._gui.setStatusMessage('Could not load ' + fileName)
else:
self._gui.setStatusMessage('Could not reload image')
return
if not self._gui is None:
self._gui.setWorkingImage(self._plateImage.rawImage)
self._gui.setOriginalImage(self._plateImage.rawImage)
self._gui.setHistogram(self._plateImage.histogram)
self._gui.printStatistics(self._plateImage.statistics)
if not fileName is None:
self._gui.setStatusMessage('Successfully loaded ' + fileName)
else:
self._gui.setStatusMessage('Successfully reloaded image')
def __init__(self):
#The PlateImage
self._plateImage = PlateImage()
def __init__(self):
#The PlateImage
self._plateImage=PlateImage()
