def import_files(self, file_list):
file_import.import_files(self.chest, file_list)
self.image_controller = MappableImageController(
parent=self, treasure_chest=self.chest)
self.cell_controller = CellController(parent=self,
treasure_chest=self.chest)
self.log_action(action="import", files=file_list)
def open_treasure_chest(self, filename):
if self.chest is not None:
self.chest.close()
chest = file_import.open_treasure_chest(filename)
self.chest = chest
self.image_controller = MappableImageController(parent=self,
treasure_chest=chest)
self.cell_controller = CellController(parent=self,
treasure_chest=chest)
self.mda_controller = MDAViewController(parent=self,
treasure_chest=chest)
self.title = " - %s" % os.path.split(filename)[1]
self.has_chest = True
def import_files(self, file_list):
file_import.import_files(self.chest, file_list)
self.image_controller = MappableImageController(parent=self,
treasure_chest=self.chest)
self.cell_controller = CellController(parent=self,
treasure_chest=self.chest)
self.log_action(action="import", files=file_list)
def new_treasure_chest(self, filename):
if self.chest is not None:
self.chest.close()
# first, clear any existing controllers
self.image_controller = MappableImageController(parent=self)
self.cell_controller = CellController(parent=self)
self.mda_controller = MDAViewController(parent=self)
# open a new chest
prefix, ext = os.path.splitext(filename)
if "chest" in ext:
filename = prefix
chest = file_import.new_treasure_chest(filename)
self.chest = chest
self.image_controller = MappableImageController(parent=self,
treasure_chest=chest)
self.cell_controller = CellController(parent=self,
treasure_chest=chest)
self.title = " - %s" % os.path.split(filename)[1]
self.has_chest=True
def new_treasure_chest(self, filename):
if self.chest is not None:
self.chest.close()
# first, clear any existing controllers
self.image_controller = MappableImageController(parent=self)
self.cell_controller = CellController(parent=self)
self.mda_controller = MDAViewController(parent=self)
# open a new chest
prefix, ext = os.path.splitext(filename)
if "chest" in ext:
filename = prefix
chest = file_import.new_treasure_chest(filename)
self.chest = chest
self.image_controller = MappableImageController(parent=self,
treasure_chest=chest)
self.cell_controller = CellController(parent=self,
treasure_chest=chest)
self.title = " - %s" % os.path.split(filename)[1]
self.has_chest = True
def open_treasure_chest(self, filename):
if self.chest is not None:
self.chest.close()
chest = file_import.open_treasure_chest(filename)
self.chest = chest
self.image_controller = MappableImageController(parent=self,
treasure_chest=chest)
self.cell_controller = CellController(parent=self,
treasure_chest=chest)
self.mda_controller = MDAViewController(parent=self, treasure_chest=chest)
self.title = " - %s" % os.path.split(filename)[1]
self.has_chest=True
def update_cell_data(self):
self.cell_controller = CellController(parent=self,
treasure_chest=self.chest)
def __init__(self, *args, **kw):
super(HighSeasAdventure, self).__init__(*args, **kw)
self.image_controller = MappableImageController(parent=self)
self.cell_controller = CellController(parent=self)
self.mda_controller = MDAViewController(parent=self)
self.chest = None
class HighSeasAdventure(Atom):
has_chest = Bool(False)
show_image_view = Bool(False)
show_cell_view = Bool(False)
show_score_view = Bool(False)
show_factor_view = Bool(False)
title = Unicode("")
image_controller = Instance(MappableImageController)
cell_controller = Instance(CellController)
mda_controller = Instance(MDAViewController)
chest = Instance(tb.File)
def __init__(self, *args, **kw):
super(HighSeasAdventure, self).__init__(*args, **kw)
self.image_controller = MappableImageController(parent=self)
self.cell_controller = CellController(parent=self)
self.mda_controller = MDAViewController(parent=self)
self.chest = None
def update_cell_data(self):
self.cell_controller = CellController(parent=self,
treasure_chest=self.chest)
def add_cell_data(self, data, name):
self.cell_controller.add_cell_data(data,name)
def update_mda_data(self):
self.mda_controller = MDAViewController(parent=self,
treasure_chest=self.chest)
self.show_factor_view = True
self.show_score_view = True
def update_image_data(self):
self.image_controller.data_updated()
self.crop_controller.data_updated()
def new_treasure_chest(self, filename):
if self.chest is not None:
self.chest.close()
# first, clear any existing controllers
self.image_controller = MappableImageController(parent=self)
self.cell_controller = CellController(parent=self)
self.mda_controller = MDAViewController(parent=self)
# open a new chest
prefix, ext = os.path.splitext(filename)
if "chest" in ext:
filename = prefix
chest = file_import.new_treasure_chest(filename)
self.chest = chest
self.image_controller = MappableImageController(parent=self,
treasure_chest=chest)
self.cell_controller = CellController(parent=self,
treasure_chest=chest)
self.title = " - %s" % os.path.split(filename)[1]
self.has_chest=True
def open_treasure_chest(self, filename):
if self.chest is not None:
self.chest.close()
chest = file_import.open_treasure_chest(filename)
self.chest = chest
self.image_controller = MappableImageController(parent=self,
treasure_chest=chest)
self.cell_controller = CellController(parent=self,
treasure_chest=chest)
self.mda_controller = MDAViewController(parent=self, treasure_chest=chest)
self.title = " - %s" % os.path.split(filename)[1]
self.has_chest=True
def import_files(self, file_list):
file_import.import_files(self.chest, file_list)
self.image_controller = MappableImageController(parent=self,
treasure_chest=self.chest)
self.cell_controller = CellController(parent=self,
treasure_chest=self.chest)
self.log_action(action="import", files=file_list)
def load_test_data(self):
# create the test pattern
tp = get_test_pattern((256,256))
# save it as a file, for user's reference, and because we have
# to load files into chests (TODO: fix this to be more generic?)
imsave('tp.png', tp)
# create a new project
self.new_treasure_chest('test_pattern')
# import the newly saved test pattern file
self.import_files(['tp.png'])
# delete the file for cleanliness?
def characterize_peaks(self):
has_cells = self.cell_controller._can_change_idx
# TODO: need to make peak width a user-specified value, or some
# auto-detect algorithm...
self.image_controller.characterize_peaks()
#if has_cells:
# TODO: cell_controller accesses the database for
# the image controller here. Need to clean up.
#self.cell_controller.map_peaks_to_cells()
def open_crop_UI(self):
crop_controller = CellCropController(parent=self,
treasure_chest=self.chest)
cell_cropper = simple_session('cropper', 'Cell cropper', CellCropperInterface,
controller=crop_controller)
Application.instance().add_factories([cell_cropper])
session_id = Application.instance().start_session('cropper')
crop_controller._session_id = session_id
def open_MDA_UI(self):
mda_controller = MDAExecutionController(parent=self,
treasure_chest=self.chest)
mda_dialog = simple_session('mda', 'MDA dialog', MDAInterface,
controller=mda_controller)
Application.instance().add_factories([mda_dialog])
session_id = Application.instance().start_session('mda')
mda_controller._session_id = session_id
def log_action(self, action, **parameters):
"""
action - a short string describing the action itself (e.g. crop cells)
parameters - pass any number of named parameters. These will be recorded as
a string that can then be recovered as a dictionary at some later date.
version - the version of analyzarr used to perform that action
"""
row = self.chest.root.log.row
row['date']=time()
row['action']=action
# record parameter dictionary as string. Can be brought back with:
# dict2 = eval(string_from_table)
# http://stackoverflow.com/questions/4547274/convert-a-python-dict-to-a-string-and-back
row['parameters'] = parameters
row['version'] = version
row.append()
self.chest.root.log.flush()
class HighSeasAdventure(HasTraits):
has_chest = Bool(False)
show_image_view = Bool(False)
show_cell_view = Bool(False)
show_score_view = Bool(False)
show_factor_view = Bool(False)
title = String("")
image_controller = Instance(MappableImageController)
cell_controller = Instance(CellController)
mda_controller = Instance(MDAViewController)
def __init__(self, *args, **kw):
super(HighSeasAdventure, self).__init__(*args, **kw)
self.image_controller = MappableImageController(parent=self)
self.cell_controller = CellController(parent=self)
self.mda_controller = MDAViewController(parent=self)
self.chest = None
def update_cell_data(self):
self.cell_controller = CellController(parent=self,
treasure_chest=self.chest)
def add_image_data(self, data, name):
self.image_controller.add_data(data,name)
def add_cell_data(self, data, name):
self.cell_controller.add_data(data,name)
def update_mda_data(self):
self.mda_controller = MDAViewController(parent=self,
treasure_chest=self.chest)
self.show_factor_view = True
self.show_score_view = True
def update_image_data(self):
self.image_controller.data_updated()
self.crop_controller.data_updated()
def new_treasure_chest(self, filename):
if self.chest is not None:
self.chest.close()
# first, clear any existing controllers
self.image_controller = MappableImageController(parent=self)
self.cell_controller = CellController(parent=self)
self.mda_controller = MDAViewController(parent=self)
# open a new chest
prefix, ext = os.path.splitext(filename)
if "chest" in ext:
filename = prefix
chest = file_import.new_treasure_chest(filename)
self.chest = chest
self.image_controller = MappableImageController(parent=self,
treasure_chest=chest)
self.cell_controller = CellController(parent=self,
treasure_chest=chest)
self.title = " - %s" % os.path.split(filename)[1]
self.has_chest=True
def open_treasure_chest(self, filename):
if self.chest is not None:
self.chest.close()
chest = file_import.open_treasure_chest(filename)
self.chest = chest
self.image_controller = MappableImageController(parent=self,
treasure_chest=chest)
self.cell_controller = CellController(parent=self,
treasure_chest=chest)
self.mda_controller = MDAViewController(parent=self, treasure_chest=chest)
self.title = " - %s" % os.path.split(filename)[1]
self.has_chest=True
def import_files(self, file_list):
file_import.import_files(self.chest, file_list)
self.image_controller = MappableImageController(parent=self,
treasure_chest=self.chest)
self.cell_controller = CellController(parent=self,
treasure_chest=self.chest)
self.log_action(action="import", files=file_list)
def load_test_data(self):
# create the test pattern
tp = get_test_pattern((256,256))
# save it as a file, for user's reference, and because we have
# to load files into chests (TODO: fix this to be more generic?)
imsave('tp.png', tp)
# create a new project
self.new_treasure_chest('test_pattern')
# import the newly saved test pattern file
self.import_files(['tp.png'])
# delete the file for cleanliness?
def characterize_peaks(self):
has_cells = self.cell_controller.get_num_files()>0
# TODO: need to make peak width a user-specified value, or some
# auto-detect algorithm...
self.image_controller.characterize_peaks()
if has_cells:
# TODO: cell_controller accesses the database for
# the image controller here. Need to clean up.
self.map_global_peaks_to_cells()
def open_crop_UI(self):
crop_controller = CellCropController(parent=self,
treasure_chest=self.chest)
cell_cropper = simple_session('cropper', 'Cell cropper', CellCropperInterface,
controller=crop_controller)
Application.instance().add_factories([cell_cropper])
session_id = Application.instance().start_session('cropper')
crop_controller._session_id = session_id
def open_MDA_UI(self):
mda_controller = MDAExecutionController(parent=self,
treasure_chest=self.chest)
mda_dialog = simple_session('mda', 'MDA dialog', MDAInterface,
controller=mda_controller)
Application.instance().add_factories([mda_dialog])
session_id = Application.instance().start_session('mda')
mda_controller._session_id = session_id
def log_action(self, action, **parameters):
"""
action - a short string describing the action itself (e.g. crop cells)
parameters - pass any number of named parameters. These will be recorded as
a string that can then be recovered as a dictionary at some later date.
version - the version of analyzarr used to perform that action
"""
row = self.chest.root.log.row
row['date']=time()
row['action']=action
# record parameter dictionary as string. Can be brought back with:
# dict2 = eval(string_from_table)
# http://stackoverflow.com/questions/4547274/convert-a-python-dict-to-a-string-and-back
row['parameters'] = parameters
row['version'] = version
row.append()
self.chest.root.log.flush()
def get_peak_data(self, node_name):
indices = self.chest.get_node('/image_peaks').get_where_list(
'(filename=="%s")'%node_name)
return self.chest.root.image_peaks[indices]
def find_best_matching_global_peaks(self, target_locations_x_y, node_name):
coords_x=self.image_controller.get_expression_data("x", "/image_peaks", node_name)
coords_y=self.image_controller.get_expression_data("y", "/image_peaks", node_name)
coords = np.vstack((coords_x, coords_y)).T
indices=[pc.best_match(coords, target) for target in target_locations_x_y]
return self.get_peak_data(node_name=node_name)[indices]
def map_global_peaks_to_cells(self):
try:
# wipe out old results
self.chest.remove_node('/cell_peaks')
except:
# any errors will be because the table doesn't exist. That's OK.
pass
# get the average cell image and find peaks on it
peaks=pc.two_dim_findpeaks(self.cell_controller.get_average_cell(),
xc_filter=False, kill_edges=False)
# generate a list of column names
names = [('x%i, y%i, dx%i, dy%i, h%i, o%i, e%i, sx%i, sy%i' % ((x,)*9)).split(', ')
for x in xrange(peaks.shape[0])]
# flatten that from a list of lists to a simple list
names = [item for sublist in names for item in sublist]
# make tuples of each column name and 'f8' for the data type
dtypes = zip(names, ['f8', ] * peaks.shape[0]*9)
# prepend the filename and index columns
dtypes = [('filename', '|S250'), ('file_idx', 'i4'), ('omit', 'bool')] + dtypes
# create an empty recarray with our data type
desc = np.recarray((0,), dtype=dtypes)
# create the table using the empty description recarray
self.chest.create_table(self.chest.root,
'cell_peaks', description=desc)
self.chest.set_node_attr('/cell_peaks','number_of_peaks', peaks.shape[0])
self.chest.flush()
# loop over each peak, finding the peak that best matches this cell's position
# plus the offset for the peak.
for node in self.image_controller.get_node_iterator():
cell_data = self.cell_controller.get_cell_set(node.name)
data = np.zeros((cell_data.shape[0]),dtype=dtypes)
data["filename"] = node.name
data['file_idx'] = np.arange(cell_data.shape[0])
for idx, peak in enumerate(peaks):
#TODO: need to rework this whole get_expression_data concept. It is
# a column accessor.
target_x = self.image_controller.get_expression_data("x_coordinate",
table_loc="/cell_description",
filename=node.name)+peak[0]
target_y = self.image_controller.get_expression_data("y_coordinate",
table_loc="/cell_description",
filename=node.name)+peak[1]
if target_x.shape[0]>0:
chars = self.find_best_matching_global_peaks(np.array([target_x,target_y]).T,
node.name)
# add the peak ids (or data) to table representing cell peak characteristics
data["x%i"%idx] = chars["x"]-target_x+peak[0]
data["y%i"%idx] = chars["y"]-target_y+peak[1]
data["dx%i"%idx] = chars["x"]-target_x
data["dy%i"%idx] = chars["y"]-target_y
data["h%i"%idx] = chars["h"]
data["o%i"%idx] = chars["o"]
data["e%i"%idx] = chars["e"]
data["sx%i"%idx] = chars["sx"]
data["sy%i"%idx] = chars["sy"]
# commit the data to the table
self.chest.root.cell_peaks.append(data)
self.chest.root.cell_peaks.flush()
self.chest.flush()
self.cell_controller._can_show_peak_ids=True
def update_cell_data(self):
self.cell_controller = CellController(parent=self,
treasure_chest=self.chest)
def __init__(self, *args, **kw):
super(HighSeasAdventure, self).__init__(*args, **kw)
self.image_controller = MappableImageController(parent=self)
self.cell_controller = CellController(parent=self)
self.mda_controller = MDAViewController(parent=self)
self.chest = None
class HighSeasAdventure(HasTraits):
has_chest = Bool(False)
show_image_view = Bool(False)
show_cell_view = Bool(False)
show_score_view = Bool(False)
show_factor_view = Bool(False)
title = String("")
image_controller = Instance(MappableImageController)
cell_controller = Instance(CellController)
mda_controller = Instance(MDAViewController)
def __init__(self, *args, **kw):
super(HighSeasAdventure, self).__init__(*args, **kw)
self.image_controller = MappableImageController(parent=self)
self.cell_controller = CellController(parent=self)
self.mda_controller = MDAViewController(parent=self)
self.chest = None
def update_cell_data(self):
self.cell_controller = CellController(parent=self,
treasure_chest=self.chest)
def add_image_data(self, data, name):
self.image_controller.add_data(data, name)
def add_cell_data(self, data, name):
self.cell_controller.add_data(data, name)
def update_mda_data(self):
self.mda_controller = MDAViewController(parent=self,
treasure_chest=self.chest)
self.show_factor_view = True
self.show_score_view = True
def update_image_data(self):
self.image_controller.data_updated()
self.crop_controller.data_updated()
def new_treasure_chest(self, filename):
if self.chest is not None:
self.chest.close()
# first, clear any existing controllers
self.image_controller = MappableImageController(parent=self)
self.cell_controller = CellController(parent=self)
self.mda_controller = MDAViewController(parent=self)
# open a new chest
prefix, ext = os.path.splitext(filename)
if "chest" in ext:
filename = prefix
chest = file_import.new_treasure_chest(filename)
self.chest = chest
self.image_controller = MappableImageController(parent=self,
treasure_chest=chest)
self.cell_controller = CellController(parent=self,
treasure_chest=chest)
self.title = " - %s" % os.path.split(filename)[1]
self.has_chest = True
def open_treasure_chest(self, filename):
if self.chest is not None:
self.chest.close()
chest = file_import.open_treasure_chest(filename)
self.chest = chest
self.image_controller = MappableImageController(parent=self,
treasure_chest=chest)
self.cell_controller = CellController(parent=self,
treasure_chest=chest)
self.mda_controller = MDAViewController(parent=self,
treasure_chest=chest)
self.title = " - %s" % os.path.split(filename)[1]
self.has_chest = True
def import_files(self, file_list):
file_import.import_files(self.chest, file_list)
self.image_controller = MappableImageController(
parent=self, treasure_chest=self.chest)
self.cell_controller = CellController(parent=self,
treasure_chest=self.chest)
self.log_action(action="import", files=file_list)
def load_test_data(self):
# create the test pattern
tp = get_test_pattern((256, 256))
# save it as a file, for user's reference, and because we have
# to load files into chests (TODO: fix this to be more generic?)
imsave('tp.png', tp)
# create a new project
self.new_treasure_chest('test_pattern')
# import the newly saved test pattern file
self.import_files(['tp.png'])
# delete the file for cleanliness?
def characterize_peaks(self):
has_cells = self.cell_controller.get_num_files() > 0
# TODO: need to make peak width a user-specified value, or some
# auto-detect algorithm...
self.image_controller.characterize_peaks()
if has_cells:
# TODO: cell_controller accesses the database for
# the image controller here. Need to clean up.
self.map_global_peaks_to_cells()
def open_crop_UI(self):
crop_controller = CellCropController(parent=self,
treasure_chest=self.chest)
cell_cropper = simple_session('cropper',
'Cell cropper',
CellCropperInterface,
controller=crop_controller)
Application.instance().add_factories([cell_cropper])
session_id = Application.instance().start_session('cropper')
crop_controller._session_id = session_id
def open_MDA_UI(self):
mda_controller = MDAExecutionController(parent=self,
treasure_chest=self.chest)
mda_dialog = simple_session('mda',
'MDA dialog',
MDAInterface,
controller=mda_controller)
Application.instance().add_factories([mda_dialog])
session_id = Application.instance().start_session('mda')
mda_controller._session_id = session_id
def log_action(self, action, **parameters):
"""
action - a short string describing the action itself (e.g. crop cells)
parameters - pass any number of named parameters. These will be recorded as
a string that can then be recovered as a dictionary at some later date.
version - the version of analyzarr used to perform that action
"""
row = self.chest.root.log.row
row['date'] = time()
row['action'] = action
# record parameter dictionary as string. Can be brought back with:
# dict2 = eval(string_from_table)
# http://stackoverflow.com/questions/4547274/convert-a-python-dict-to-a-string-and-back
row['parameters'] = parameters
row['version'] = version
row.append()
self.chest.root.log.flush()
def get_peak_data(self, node_name):
indices = self.chest.get_node('/image_peaks').get_where_list(
'(filename=="%s")' % node_name)
return self.chest.root.image_peaks[indices]
def find_best_matching_global_peaks(self, target_locations_x_y, node_name):
coords_x = self.image_controller.get_expression_data(
"x", "/image_peaks", node_name)
coords_y = self.image_controller.get_expression_data(
"y", "/image_peaks", node_name)
coords = np.vstack((coords_x, coords_y)).T
indices = [
pc.best_match(coords, target) for target in target_locations_x_y
]
return self.get_peak_data(node_name=node_name)[indices]
def map_global_peaks_to_cells(self):
try:
# wipe out old results
self.chest.remove_node('/cell_peaks')
except:
# any errors will be because the table doesn't exist. That's OK.
pass
# get the average cell image and find peaks on it
peaks = pc.two_dim_findpeaks(self.cell_controller.get_average_cell(),
xc_filter=False,
kill_edges=False)
# generate a list of column names
names = [('x%i, y%i, dx%i, dy%i, h%i, o%i, e%i, sx%i, sy%i' %
((x, ) * 9)).split(', ') for x in xrange(peaks.shape[0])]
# flatten that from a list of lists to a simple list
names = [item for sublist in names for item in sublist]
# make tuples of each column name and 'f8' for the data type
dtypes = zip(names, [
'f8',
] * peaks.shape[0] * 9)
# prepend the filename and index columns
dtypes = [('filename', '|S250'), ('file_idx', 'i4'),
('omit', 'bool')] + dtypes
# create an empty recarray with our data type
desc = np.recarray((0, ), dtype=dtypes)
# create the table using the empty description recarray
self.chest.create_table(self.chest.root,
'cell_peaks',
description=desc)
self.chest.set_node_attr('/cell_peaks', 'number_of_peaks',
peaks.shape[0])
self.chest.flush()
# loop over each peak, finding the peak that best matches this cell's position
# plus the offset for the peak.
for node in self.image_controller.get_node_iterator():
cell_data = self.cell_controller.get_cell_set(node.name)
data = np.zeros((cell_data.shape[0]), dtype=dtypes)
data["filename"] = node.name
data['file_idx'] = np.arange(cell_data.shape[0])
for idx, peak in enumerate(peaks):
#TODO: need to rework this whole get_expression_data concept. It is
# a column accessor.
target_x = self.image_controller.get_expression_data(
"x_coordinate",
table_loc="/cell_description",
filename=node.name) + peak[0]
target_y = self.image_controller.get_expression_data(
"y_coordinate",
table_loc="/cell_description",
filename=node.name) + peak[1]
if target_x.shape[0] > 0:
chars = self.find_best_matching_global_peaks(
np.array([target_x, target_y]).T, node.name)
# add the peak ids (or data) to table representing cell peak characteristics
data["x%i" % idx] = chars["x"] - target_x + peak[0]
data["y%i" % idx] = chars["y"] - target_y + peak[1]
data["dx%i" % idx] = chars["x"] - target_x
data["dy%i" % idx] = chars["y"] - target_y
data["h%i" % idx] = chars["h"]
data["o%i" % idx] = chars["o"]
data["e%i" % idx] = chars["e"]
data["sx%i" % idx] = chars["sx"]
data["sy%i" % idx] = chars["sy"]
# commit the data to the table
self.chest.root.cell_peaks.append(data)
self.chest.root.cell_peaks.flush()
self.chest.flush()
self.cell_controller._can_show_peak_ids = True