def generate_reports(self, filename=None, label=None):
"""Generates the report files by calling the generate_report method
from Reports"""
if filename is None:
filename = tkFileDialog.askdirectory()
if label is None:
label = self.fluor_path.split("/")
label = label[len(label) - 1].split(".")
if len(label) > 2:
label = label[len(label) - 3] + "." + label[len(label) - 2]
else:
label = label[len(label) - 2]
if len(self.linescan_manager.lines.keys()) > 0:
self.linescan_manager.measure_fluorescence(
self.image_manager.fluor_image)
self.report_manager = ReportManager(self.parameters)
self.report_manager.generate_report(filename, label, self.cell_manager,
self.linescan_manager,
self.parameters)
if self.get_cell_images:
self.report_manager.get_cell_images(filename, label,
self.image_manager,
self.cell_manager,
self.parameters)
print "Reports Generated"
def run(self, args):
# First try to authenticate
if self.passboltServer.api.authenticate(
self.keyringManager.keyring,
self.configManager.user()['fingerprint'],
self.configManager.server()['fingerprint']):
resources = self.__fetchResources(args)
reportManager = ReportManager(self.configManager, args)
# Initialize a map that will contain the statistics of the renewal
renewalStats = {
'foundItems': 0,
'renewableItems': 0,
'items': {
'success': [], # Successfully renewed, no problem
'failures': [], # The service did not accept the renewal
'rollback':
[], # The password was renewed but not committed to passbolt, so it has been rollbacked
'errors': [
] # Everything failed, including the rollback of the password
}
}
# In the case where we are renewing resources that belong to a group, we will need
# to filter which resources are shared with edit rights, and which resources are not shared with
# this right
if not args.personal:
self.logger.info('Found [{}] resources available'.format(
len(resources)))
renewalStats['foundItems'] = len(resources)
resources = self.passboltServer.filterUpdatableResources(
resources)
self.logger.info('Found [{}] resources that can be renewed'.format(
len(resources)))
if args.limit != 0 and len(resources) >= args.limit:
self.logger.info(
'Limiting renewal to the first [{}] resources'.format(
args.limit))
resources = resources[:len(resources) - args.limit]
renewalStats['renewableItems'] = len(resources)
try:
for resource in resources:
self.__renewResource(resource, args, renewalStats)
except KeyboardInterrupt:
self.logger.info('Interrupted, sending report and exiting ...')
# At the end of the process, show and / or send a report
reportManager.sendReports(renewalStats)
else:
self.logger.error('Failed to authenticate to the Passbolt server.')
def generate_reports(self, filename=None, label=None):
"""Generates the report files by calling the generate_report method
from Reports"""
if filename is None:
filename = tkFileDialog.askdirectory()
if label is None:
label = self.fluor_path.split("/")
label = label[len(label) - 1].split(".")[0]
if len(self.linescan_manager.lines.keys()) > 0:
self.linescan_manager.measure_fluorescence(
self.image_manager.fluor_image)
self.report_manager = ReportManager(self.parameters)
self.report_manager.generate_report(filename, label,
self.cell_manager,
self.linescan_manager,
self.parameters)
if self.get_cell_images:
self.report_manager.get_cell_images(filename, label,
self.image_manager,
self.cell_manager,
self.parameters)
print "Reports Generated"
class EHooke(object):
"""Main class of the software.
Starts with an instance of the Parameters and Image class.
Contains the methods needed to perform the analysis"""
def __init__(self, cell_data=False):
self.parameters = ParametersManager()
self.image_manager = ImageManager()
self.segments_manager = None
self.cell_manager = None
self.linescan_manager = None
self.report_manager = None
self.base_path = None
self.fluor_path = None
self.get_cell_images = cell_data
def load_base_image(self, filename=None):
"""Calls the load_base_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()
self.base_path = filename
self.image_manager.load_base_image(filename,
self.parameters.imageloaderparams)
print "Base 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, 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()
self.fluor_path = filename
self.image_manager.load_fluor_image(self.fluor_path,
self.parameters.imageloaderparams)
print "Fluor Image Loaded"
def load_option_image(self, filename=None):
"""Calls the load_optional_image method from the ImageManager
Can be called without a filename or by passing on as an arg"""
if filename is None:
filename = tkFileDialog.askopenfilename()
self.image_manager.load_option_image(filename)
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.cell_manager = CellManager(self.parameters)
self.cell_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.cell_manager.merge_cells(label_c1, label_c2,
self.parameters.cellprocessingparams,
self.segments_manager,
self.image_manager)
self.cell_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.cell_manager.split_cells(int(label_c1),
self.parameters.cellprocessingparams,
self.segments_manager,
self.image_manager)
self.cell_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.cell_manager.mark_cell_as_noise(label_c1, self.image_manager,
noise)
def process_cells(self):
"""Process the list of computed cells to identify the different regions
of each cell and computes the stats related to the fluorescence"""
self.cell_manager.process_cells(self.parameters.cellprocessingparams,
self.image_manager)
self.linescan_manager = LineScanManager()
print "Processing Cells Finished"
def add_line_linescan(self, point_1, point_2, point_3):
self.linescan_manager.add_line(point_1, point_2, point_3)
def remove_line_linescan(self, line_id):
self.linescan_manager.remove_line(line_id)
def select_all_cells(self):
"""Method used to mark all the cells as selected"""
for k in self.cell_manager.cells.keys():
if self.cell_manager.cells[k].selection_state != 0:
self.cell_manager.cells[k].selection_state = 1
self.cell_manager.overlay_cells(self.image_manager)
def reject_all_cells(self):
"""Method used to mark all the cells as rejected"""
for k in self.cell_manager.cells.keys():
if self.cell_manager.cells[k].selection_state != 0:
self.cell_manager.cells[k].selection_state = -1
self.cell_manager.overlay_cells(self.image_manager)
def select_from_file(self, filename=None):
if filename is None:
filename = tkFileDialog.askopenfilename()
o_file = open(filename)
data = o_file.readlines()
o_file.close()
data = data[0].split(";")[:len(data[0].split(";")) - 1]
for key in data:
self.cell_manager.cells[key].selection_state = 1
self.cell_manager.overlay_cells(self.image_manager)
def filter_cells(self):
"""Filters the cell based on the filters defined in the
params.cellprocessingparams. Calls the filter_cells method from the
cell_manager instance"""
self.cell_manager.filter_cells(self.parameters.cellprocessingparams,
self.image_manager)
print "Finished Filtering Cells"
def generate_reports(self, filename=None, label=None):
"""Generates the report files by calling the generate_report method
from Reports"""
if filename is None:
filename = tkFileDialog.askdirectory()
if label is None:
label = self.fluor_path.split("/")
label = label[len(label) - 1].split(".")[0]
if len(self.linescan_manager.lines.keys()) > 0:
self.linescan_manager.measure_fluorescence(
self.image_manager.fluor_image)
self.report_manager = ReportManager(self.parameters)
self.report_manager.generate_report(filename, label,
self.cell_manager,
self.linescan_manager,
self.parameters)
if self.get_cell_images:
self.report_manager.get_cell_images(filename, label,
self.image_manager,
self.cell_manager,
self.parameters)
print "Reports Generated"
class EHooke(object):
"""Main class of the software.
Starts with an instance of the Parameters and Image class.
Contains the methods needed to perform the analysis"""
def __init__(self, cell_data=False):
self.parameters = ParametersManager()
self.image_manager = ImageManager()
self.segments_manager = None
self.cell_manager = None
self.linescan_manager = None
self.report_manager = None
self.working_dir = None
self.base_path = None
self.fluor_path = None
self.get_cell_images = cell_data
def load_base_image(self, filename=None):
"""Calls the load_base_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.working_dir = "/".join(
filename.split("/")[:len(filename.split("/")) - 1])
self.base_path = filename
self.image_manager.load_base_image(filename,
self.parameters.imageloaderparams)
print "Base Image Loaded"
def compute_mask(self):
"""Calls the compute_mask method from image_manager."""
self.image_manager.compute_mask(self.parameters.imageloaderparams)
if self.image_manager.fluor_image is not None:
self.load_fluor_image(self.fluor_path)
print "Mask Computation Finished"
def load_fluor_image(self, 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.fluor_path = filename
self.image_manager.load_fluor_image(self.fluor_path,
self.parameters.imageloaderparams)
print "Fluor Image Loaded"
def load_option_image(self, filename=None):
"""Calls the load_optional_image method from the ImageManager
Can be called without a filename or by passing on as an arg"""
if filename is None:
filename = tkFileDialog.askopenfilename()
self.image_manager.load_option_image(filename)
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.cell_manager = CellManager(self.parameters)
self.cell_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.cell_manager.merge_cells(label_c1, label_c2,
self.parameters.cellprocessingparams,
self.segments_manager,
self.image_manager)
self.cell_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.cell_manager.split_cells(int(label_c1),
self.parameters.cellprocessingparams,
self.segments_manager,
self.image_manager)
self.cell_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.cell_manager.mark_cell_as_noise(label_c1, self.image_manager,
noise)
def process_cells(self):
"""Process the list of computed cells to identify the different regions
of each cell and computes the stats related to the fluorescence"""
self.cell_manager.process_cells(self.parameters.cellprocessingparams,
self.image_manager)
self.linescan_manager = LineScanManager()
print "Processing Cells Finished"
def add_line_linescan(self, point_1, point_2, point_3):
self.linescan_manager.add_line(point_1, point_2, point_3)
def remove_line_linescan(self, line_id):
self.linescan_manager.remove_line(line_id)
def select_all_cells(self):
"""Method used to mark all the cells as selected"""
for k in self.cell_manager.cells.keys():
if self.cell_manager.cells[k].selection_state != 0:
self.cell_manager.cells[k].selection_state = 1
self.cell_manager.overlay_cells(self.image_manager)
def reject_all_cells(self):
"""Method used to mark all the cells as rejected"""
for k in self.cell_manager.cells.keys():
if self.cell_manager.cells[k].selection_state != 0:
self.cell_manager.cells[k].selection_state = -1
self.cell_manager.overlay_cells(self.image_manager)
def select_from_file(self, filename=None):
if filename is None:
filename = tkFileDialog.askopenfilename()
o_file = open(filename)
data = o_file.readlines()
o_file.close()
data = data[0].split(";")[:len(data[0].split(";")) - 1]
for key in data:
self.cell_manager.cells[key].selection_state = 1
self.cell_manager.overlay_cells(self.image_manager)
def filter_cells(self):
"""Filters the cell based on the filters defined in the
params.cellprocessingparams. Calls the filter_cells method from the
cell_manager instance"""
self.cell_manager.filter_cells(self.parameters.cellprocessingparams,
self.image_manager)
print "Finished Filtering Cells"
def generate_reports(self, filename=None, label=None):
"""Generates the report files by calling the generate_report method
from Reports"""
if filename is None:
filename = tkFileDialog.askdirectory()
if label is None:
label = self.fluor_path.split("/")
label = label[len(label) - 1].split(".")
if len(label) > 2:
label = label[len(label) - 3] + "." + label[len(label) - 2]
else:
label = label[len(label) - 2]
if len(self.linescan_manager.lines.keys()) > 0:
self.linescan_manager.measure_fluorescence(
self.image_manager.fluor_image)
self.report_manager = ReportManager(self.parameters)
self.report_manager.generate_report(filename, label, self.cell_manager,
self.linescan_manager,
self.parameters)
if self.get_cell_images:
self.report_manager.get_cell_images(filename, label,
self.image_manager,
self.cell_manager,
self.parameters)
print "Reports Generated"
class EHooke(object):
"""Main class of the software.
Starts with an instance of the Parameters and Image class.
Contains the methods needed to perform the analysis
"""
def __init__(self, cell_data=True):
self.parameters = ParametersManager()
self.image_manager = ImageManager()
self.cellcycleclassifier = CellCycleClassifier()
self.segments_manager = None
self.cell_manager = None
self.linescan_manager = None
self.coloc_manager = None
self.report_manager = None
self.working_dir = None
self.base_path = None
self.fluor_path = None
self.get_cell_images = cell_data
def load_base_image(self, filename=None):
"""Calls the load_base_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.working_dir = "/".join(
filename.split("/")[:len(filename.split("/")) - 1])
self.base_path = filename
self.image_manager.load_base_image(filename,
self.parameters.imageloaderparams)
print("Base Image Loaded")
def compute_mask(self):
"""Calls the compute_mask method from image_manager."""
self.image_manager.compute_mask(self.parameters.imageloaderparams)
if self.image_manager.fluor_image is not None:
self.load_fluor_image(self.fluor_path)
print("Mask Computation Finished")
def load_fluor_image(self, 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.fluor_path = filename
self.image_manager.load_fluor_image(filename,
self.parameters.imageloaderparams)
print("Fluor Image Loaded")
def load_option_image(self, filename=None):
"""Calls the load_optional_image method from the ImageManager
Can be called without a filename or by passing on as an arg
"""
if filename is None:
filename = tkFileDialog.askopenfilename(
initialdir=self.working_dir)
self.image_manager.load_option_image(filename,
self.parameters.imageloaderparams)
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.cell_manager = CellManager(self.parameters)
self.cell_manager.compute_cells(self.parameters, 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.cell_manager.merge_cells(label_c1, label_c2, self.parameters,
self.segments_manager,
self.image_manager)
self.cell_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.cell_manager.split_cells(int(label_c1), self.parameters,
self.segments_manager,
self.image_manager)
self.cell_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.cell_manager.mark_cell_as_noise(label_c1, self.image_manager,
noise)
def process_cells(self):
"""Process the list of computed cells to identify the different regions
of each cell and computes the stats related to the fluorescence
"""
self.cell_manager.process_cells(self.parameters.cellprocessingparams,
self.image_manager)
self.linescan_manager = LineScanManager()
if self.parameters.cellprocessingparams.classify_cells:
self.compute_cellcyclephases()
else:
for k in self.cell_manager.cells.keys():
self.cell_manager.cells[k].stats["Cell Cycle Phase"] = 0
print("Processing Cells Finished")
def select_cells_phase(self, phase):
"""Helper function for GUI. For each cell in a specific (user defined) cell phase,
sets the selection flag to a boolean True (1)
"""
for k in self.cell_manager.cells.keys():
if self.cell_manager.cells[k].stats["Cell Cycle Phase"] == phase:
self.cell_manager.cells[k].selection_state = 1
self.cell_manager.overlay_cells(self.image_manager)
def add_line_linescan(self, point_1, point_2, point_3):
""" Helper function for GUI. Adds a line given three user defined points."""
self.linescan_manager.add_line(point_1, point_2, point_3)
def remove_line_linescan(self, line_id):
""" Helper function for GUI. Removes a user specified line."""
self.linescan_manager.remove_line(line_id)
def select_all_cells(self):
"""Method used to mark all the cells as selected"""
for k in self.cell_manager.cells.keys():
if self.cell_manager.cells[k].selection_state != 0:
self.cell_manager.cells[k].selection_state = 1
self.cell_manager.overlay_cells(self.image_manager)
def reject_all_cells(self):
"""Method used to mark all the cells as rejected"""
for k in self.cell_manager.cells.keys():
if self.cell_manager.cells[k].selection_state != 0:
self.cell_manager.cells[k].selection_state = -1
self.cell_manager.overlay_cells(self.image_manager)
def invert_selection(self):
for k in self.cell_manager.cells.keys():
self.cell_manager.cells[k].selection_state *= -1
self.cell_manager.overlay_cells(self.image_manager)
def select_from_file(self, filename=None):
"""Selects cells based upon a user fed txt file. Assumes correct formatting of said file"""
if filename is None:
filename = tkFileDialog.askopenfilename()
o_file = open(filename)
data = o_file.readlines()
o_file.close()
data = data[0].split(";")[:len(data[0].split(";")) - 1]
for key in data:
self.cell_manager.cells[key].selection_state = 1
self.cell_manager.overlay_cells(self.image_manager)
def filter_cells(self):
"""Filters the cell based on the filters defined in the
params.cellprocessingparams. Calls the filter_cells method from the
cell_manager instance
"""
self.cell_manager.filter_cells(self.parameters.cellprocessingparams,
self.image_manager)
print("Finished Filtering Cells")
def compute_coloc(self, label=None):
"""Calls the necessary method to calculate colocalization (through PCC) of two proteins.
REQUIRES an additional optional fluorescent image
"""
if label is None:
label = self.fluor_path.split("/")
label = label[len(label) - 1].split(".")
if len(label) > 2:
label = label[len(label) - 3] + "." + label[len(label) - 2]
else:
label = label[len(label) - 2]
# TODO facilitate user experience by separating the different optional images (PCC, DNA, etc)
if self.image_manager.optional_image is not None:
self.coloc_manager = ColocManager()
self.coloc_manager.compute_pcc(self.cell_manager,
self.image_manager, self.parameters,
label)
else:
print("Optional Image not loaded")
def compute_cellcyclephases(self):
self.cellcycleclassifier.classify_cells(
self.image_manager, self.cell_manager,
self.parameters.cellprocessingparams.microscope)
def select_cells_optional(self, signal_ratio):
if self.image_manager.optional_image is not None:
self.cell_manager.select_cells_optional(signal_ratio,
self.image_manager)
self.cell_manager.overlay_cells(self.image_manager)
else:
print("No optional image loaded")
def assign_cell_cycle_phase(self, key, phase):
self.cell_manager.cells[key].stats["Cell Cycle Phase"] = int(phase)
def generate_reports(self, filename=None, label=None):
"""Generates the report files by calling the generate_report method
from Reports
"""
if filename is None:
filename = tkFileDialog.askdirectory(initialdir=self.working_dir)
if label is None:
label = self.fluor_path.split("/")
label = label[len(label) - 1].split(".")
if len(label) > 2:
label = label[len(label) - 3] + "." + label[len(label) - 2]
else:
label = label[len(label) - 2]
if len(self.linescan_manager.lines.keys()) > 0:
self.linescan_manager.measure_fluorescence(
self.image_manager.fluor_image)
self.report_manager = ReportManager(self.parameters)
self.report_manager.generate_report(filename, label, self.cell_manager,
self.linescan_manager,
self.parameters)
if self.get_cell_images:
self.report_manager.get_cell_images(filename, label,
self.image_manager,
self.cell_manager,
self.parameters)
print("Reports Generated")
def save_mask(self):
self.image_manager.save_mask()
def save_labels(self):
self.segments_manager.save_labels()
