class SetManager(object):
def __init__(self):
self.parameters = ParametersManager()
self.image_manager = ImageManager()
self.segments_manager = SegmentsManager()
self.cells_manager = None
self.fret_manager = FRETManager()
self.reports_manager = ReportsManager(self.parameters)
self.control_params = None
self.working_dir = None
def load_phase_image(self, filename=None):
if filename is None:
filename = tkFileDialog.askopenfilename(initialdir=self.working_dir)
self.working_dir = "/".join(filename.split("/")[:len(filename.split("/"))-1])
self.image_manager.load_phase_image(filename,
self.parameters.imageloaderparams.border)
print "Phase Image Loaded"
def compute_mask(self):
"""Calls the compute_mask method from image_manager."""
self.image_manager.compute_mask(self.parameters.imageloaderparams)
print "Mask Computation Finished"
def load_fluor_image(self, channel, filename=None):
"""Calls the load_fluor_image method from the ImageManager
Can be called without a filename or by passing one as an arg
(filename=...)"""
if filename is None:
filename = tkFileDialog.askopenfilename(initialdir=self.working_dir)
self.image_manager.load_fluor_image(channel,
self.parameters.imageloaderparams,
filename)
print "Fluor Image Loaded"
def compute_segments(self):
"""Calls the compute_segments method from Segments.
Requires the prior loading of both the phase and fluor images and
the computation of the mask"""
self.segments_manager = SegmentsManager()
self.segments_manager.compute_segments(self.parameters.
imageprocessingparams,
self.image_manager)
print "Segments Computation Finished"
def compute_cells(self):
"""Creates an instance of the CellManager class and uses the
compute_cells_method to create a list of cells based on the labels
computed by the SegmentsManager instance."""
self.cells_manager = CellsManager(self.parameters)
self.cells_manager.compute_cells(self.parameters.cellprocessingparams,
self.image_manager,
self.segments_manager)
print "Cells Computation Finished"
def merge_cells(self, label_c1, label_c2):
"""Merges two cells using the merge_cells method from the cell_manager
instance and the compute_merged_cells to create a new list of cells,
containing a cell corresponding to the merge of the previous two."""
self.cells_manager.merge_cells(label_c1, label_c2,
self.parameters.cellprocessingparams,
self.segments_manager,
self.image_manager)
self.cells_manager.overlay_cells(self.image_manager)
print "Merge Finished"
def split_cells(self, label_c1):
"""Splits a previously merged cell, requires the label of cell to be
splitted.
Calls the split_cells method from the cell_manager instance"""
self.cells_manager.split_cells(int(label_c1),
self.parameters.cellprocessingparams,
self.segments_manager,
self.image_manager)
self.cells_manager.overlay_cells(self.image_manager)
print "Split Finished"
def define_as_noise(self, label_c1, noise):
"""Method used to change the state of a cell to noise or to undo it"""
self.cells_manager.mark_cell_as_noise(label_c1, self.image_manager,
noise)
def process_cells(self):
self.cells_manager.process_cells(self.parameters.cellprocessingparams, self.image_manager)
print "Cells Processing Finished"
def pick_channel(self):
self.fret_manager.start_channel_picker(self.image_manager, self.cells_manager)
def compute_autofluorescence(self):
self.fret_manager.compute_autofluorescence(self.image_manager, self.cells_manager)
def compute_correction_factors(self):
self.fret_manager.compute_correction_factors(self.image_manager, self.cells_manager)
def compute_g(self):
self.fret_manager.compute_g(self.image_manager, self.cells_manager)
def compute_fret_efficiency(self):
self.fret_manager.compute_fret_efficiency(self.image_manager, self.cells_manager)
def generate_report(self):
self.reports_manager.generate_report(self.image_manager, self.cells_manager, self.fret_manager)
