class EHooke:
"""Encapsulates all the code for processing a fluorescence frame"""
def __init__(self,params_obj=None,param_file=None):
"""Creates FluorFrame object, sets up parameters and loads images
It makes no sense to create a EHooke object without data or parameters.
So one must either supply params, a Parameters object, or param_file, in
which case EHooke loads the parameters file.
"""
self.params = None
"""Parameters: this can be a reference to an external object to be
changed for recomputing any step.
"""
if params_obj is None:
self.params = Parameters()
self.params.load_parameters(param_file)
else:
self.params = params_obj
self.fluor_frame = FluorFrame()
"""FluorFrame: manager for the fluor and phase images, plus masks"""
def load_images(self):
"""checks which images to load and loads them into the fluor_frame
"""
ffparams = self.params.fluor_frame_params
self.fluor_frame.load_fluor(ffparams)
if ffparams.phase_file is not None:
self.fluor_frame.load_phase(ffparams)
def create_masks(self):
"""creates masks using the current parameters"""
mparams = self.params.mask_params
self.fluor_frame.create_masks(mparams)
def align_fluor_to_phase(self):
"""aligns the fluorescence image to the phase mask, if a phase file exists"""
if ffparams.phase_file is not None:
self.fluor_frame.align_fluor(self.params.fluor_frame_params)
def save_mask_overlay(self, fname, back=(0,0,1), fore=(1,1,0), mask='phase',image='phase'):
"""saves the mask overlay image to a file"""
img = self.fluor_frame.mask_overlay(back, fore, mask,image)
imsave(fname,img)
def save_mask_contour(self, fname, mask='phase',image='phase', color=(1,1,0)):
"""saves the mask contour image to a file"""
img = self.fluor_frame.contour_overlay(mask,image,color)
imsave(fname,img)
class Session:
"""eHooke session
This class manages the folder with data and report files (in the server path)
and a EHooke instance for running the computations
"""
def __init__(self):
self.id=str(uuid.uuid4())
"""str: Unique identifier for this session"""
self.folder = SESSION_FOLDER+'/'+self.id
"""str: main session folder with all generated files"""
self.data_folder = self.folder+'/Data'
"""str: subfolder for session data (phase, fluor and params file)"""
self.params = Parameters()
"""Parameters: parameters object to share with ehooke instance"""
self.params_file = None
"""str: parameters file name"""
self.fluor_file = None
"""str: fluor file name, to override parameters so that params can be imported from other sessions"""
self.phase_file = None
"""str: phase file name, to override parameters so that params can be imported from other sessions"""
self.name = 'Session'
"""str: session name, user defined"""
self.description = ''
"""str: session description, user defined"""
self.mask_image = None
"""str: filename for the current mask image, none if no mask is computed"""
self.ehooke = None
"""EHooke: to be initialized upon starting the session (only with images and parameters"""
#TODO change this to work with multiprocessing
#<LK 2015-06-30>
def setup(self):
"""creates session folder (add other setup stuff here)"""
if not os.path.exists(self.folder):
os.mkdir(self.folder)
if not os.path.exists(self.data_folder):
os.mkdir(self.data_folder)
def set_phase(self,file_name):
"""sets the phase file without computing anything
Overrides the file name in the parameters file. This is necessary
in order to allow importing parameter files to the session
"""
self.phase_file = file_name
self.params.fluor_frame_params.phase_file = file_name
def set_fluor(self,file_name):
"""sets the fluorescence file without computing anything
Overrides the file name in the parameters file. This is necessary
in order to allow importing parameter files to the session
"""
self.fluor_file = file_name
self.params.fluor_frame_params.fluor_file = file_name
def set_parameters_file(self, file_name):
"""sets and reloads parameters
(but overrides fluor_file and phase_file in order to allow parameter
updates after uploading the image files
"""
self.params_file = file_name
self.params.load_parameters(file_name)
if self.fluor_file != self.params.fluor_frame_params.fluor_file or \
self.phase_file != self.params.fluor_frame_params.phase_file:
self.params.fluor_frame_params.fluor_file = self.fluor_file
self.params.fluor_frame_params.phase_file = self.phase_file
self.params.save_parameters(file_name)
def start_ehooke(self):
"""Initiates the ehooke process and loads images
if there is no fluorescence image specified, returns false and error message
otherwise returns true,''
if ehooke is not none does nothing and returns ok
"""
if self.ehooke is not None:
return (True,'')
if self.fluor_file is None:
return (False,'Cannot start eHooke without a fluorescence image')
self.ehooke = EHooke(self.params)
self.ehooke.load_images()
return (True,'')
def save_overlay(self, back=(1,1,1), fore=(0,1,1), mask='phase',image='phase'):
"""saves the overlay image to overlay.png"""
self.ehooke.save_mask_overlay(self.folder+'/overlay.png',back, fore, mask,image)
self.mask_image = self.folder+'/overlay.png'
def recompute_mask(self):
res,msg = self.start_ehooke()
if res:
self.ehooke.create_masks()
self.save_overlay()
return (res,msg)
class Session:
"""eHooke session
This class manages the folder with data and report files (in the server path)
and a EHooke instance for running the computations
"""
def __init__(self):
self.id = str(uuid.uuid4())
"""str: Unique identifier for this session"""
self.folder = SESSION_FOLDER + '/' + self.id
"""str: main session folder with all generated files"""
self.data_folder = self.folder + '/Data'
"""str: subfolder for session data (phase, fluor and params file)"""
self.params = Parameters()
"""Parameters: parameters object to share with ehooke instance"""
self.params_file = None
"""str: parameters file name"""
self.fluor_file = None
"""str: fluor file name, to override parameters so that params can be imported from other sessions"""
self.phase_file = None
"""str: phase file name, to override parameters so that params can be imported from other sessions"""
self.name = 'Session'
"""str: session name, user defined"""
self.description = ''
"""str: session description, user defined"""
self.mask_image = None
"""str: filename for the current mask image, none if no mask is computed"""
self.ehooke = None
"""EHooke: to be initialized upon starting the session (only with images and parameters"""
#TODO change this to work with multiprocessing
#<LK 2015-06-30>
def setup(self):
"""creates session folder (add other setup stuff here)"""
if not os.path.exists(self.folder):
os.mkdir(self.folder)
if not os.path.exists(self.data_folder):
os.mkdir(self.data_folder)
def set_phase(self, file_name):
"""sets the phase file without computing anything
Overrides the file name in the parameters file. This is necessary
in order to allow importing parameter files to the session
"""
self.phase_file = file_name
self.params.fluor_frame_params.phase_file = file_name
def set_fluor(self, file_name):
"""sets the fluorescence file without computing anything
Overrides the file name in the parameters file. This is necessary
in order to allow importing parameter files to the session
"""
self.fluor_file = file_name
self.params.fluor_frame_params.fluor_file = file_name
def set_parameters_file(self, file_name):
"""sets and reloads parameters
(but overrides fluor_file and phase_file in order to allow parameter
updates after uploading the image files
"""
self.params_file = file_name
self.params.load_parameters(file_name)
if self.fluor_file != self.params.fluor_frame_params.fluor_file or \
self.phase_file != self.params.fluor_frame_params.phase_file:
self.params.fluor_frame_params.fluor_file = self.fluor_file
self.params.fluor_frame_params.phase_file = self.phase_file
self.params.save_parameters(file_name)
def start_ehooke(self):
"""Initiates the ehooke process and loads images
if there is no fluorescence image specified, returns false and error message
otherwise returns true,''
if ehooke is not none does nothing and returns ok
"""
if self.ehooke is not None:
return (True, '')
if self.fluor_file is None:
return (False, 'Cannot start eHooke without a fluorescence image')
self.ehooke = EHooke(self.params)
self.ehooke.load_images()
return (True, '')
def save_overlay(self,
back=(1, 1, 1),
fore=(0, 1, 1),
mask='phase',
image='phase'):
"""saves the overlay image to overlay.png"""
self.ehooke.save_mask_overlay(self.folder + '/overlay.png', back, fore,
mask, image)
self.mask_image = self.folder + '/overlay.png'
def recompute_mask(self):
res, msg = self.start_ehooke()
if res:
self.ehooke.create_masks()
self.save_overlay()
return (res, msg)
class EHooke:
"""Encapsulates all the code for processing a fluorescence frame"""
def __init__(self, params_obj=None, param_file=None):
"""Creates FluorFrame object, sets up parameters and loads images
It makes no sense to create a EHooke object without data or parameters.
So one must either supply params, a Parameters object, or param_file, in
which case EHooke loads the parameters file.
"""
self.params = None
"""Parameters: this can be a reference to an external object to be
changed for recomputing any step.
"""
if params_obj is None:
self.params = Parameters()
self.params.load_parameters(param_file)
else:
self.params = params_obj
self.fluor_frame = FluorFrame()
"""FluorFrame: manager for the fluor and phase images, plus masks"""
def load_images(self):
"""checks which images to load and loads them into the fluor_frame
"""
ffparams = self.params.fluor_frame_params
self.fluor_frame.load_fluor(ffparams)
if ffparams.phase_file is not None:
self.fluor_frame.load_phase(ffparams)
def create_masks(self):
"""creates masks using the current parameters"""
mparams = self.params.mask_params
self.fluor_frame.create_masks(mparams)
def align_fluor_to_phase(self):
"""aligns the fluorescence image to the phase mask, if a phase file exists"""
if ffparams.phase_file is not None:
self.fluor_frame.align_fluor(self.params.fluor_frame_params)
def save_mask_overlay(self,
fname,
back=(0, 0, 1),
fore=(1, 1, 0),
mask='phase',
image='phase'):
"""saves the mask overlay image to a file"""
img = self.fluor_frame.mask_overlay(back, fore, mask, image)
imsave(fname, img)
def save_mask_contour(self,
fname,
mask='phase',
image='phase',
color=(1, 1, 0)):
"""saves the mask contour image to a file"""
img = self.fluor_frame.contour_overlay(mask, image, color)
imsave(fname, img)
