repository_name stringlengths 5 67 | func_path_in_repository stringlengths 4 234 | func_name stringlengths 0 314 | whole_func_string stringlengths 52 3.87M | language stringclasses 6
values | func_code_string stringlengths 52 3.87M | func_documentation_string stringlengths 1 47.2k | func_code_url stringlengths 85 339 |
|---|---|---|---|---|---|---|---|
signetlabdei/sem | sem/manager.py | CampaignManager.check_repo_ok | def check_repo_ok(self):
"""
Make sure that the ns-3 repository's HEAD commit is the same as the one
saved in the campaign database, and that the ns-3 repository is clean
(i.e., no untracked or modified files exist).
"""
from git import Repo, exc
# Check that git ... | python | def check_repo_ok(self):
"""
Make sure that the ns-3 repository's HEAD commit is the same as the one
saved in the campaign database, and that the ns-3 repository is clean
(i.e., no untracked or modified files exist).
"""
from git import Repo, exc
# Check that git ... | Make sure that the ns-3 repository's HEAD commit is the same as the one
saved in the campaign database, and that the ns-3 repository is clean
(i.e., no untracked or modified files exist). | https://github.com/signetlabdei/sem/blob/5077dd7a6d15644a18790bb6fde320e905f0fef0/sem/manager.py#L616-L642 |
signetlabdei/sem | sem/cli.py | run | def run(ns_3_path, results_dir, script, no_optimization, parameters,
max_processes):
"""
Run multiple simulations.
"""
sem.parallelrunner.MAX_PARALLEL_PROCESSES = max_processes
# Create a campaign
campaign = sem.CampaignManager.new(ns_3_path,
scri... | python | def run(ns_3_path, results_dir, script, no_optimization, parameters,
max_processes):
"""
Run multiple simulations.
"""
sem.parallelrunner.MAX_PARALLEL_PROCESSES = max_processes
# Create a campaign
campaign = sem.CampaignManager.new(ns_3_path,
scri... | Run multiple simulations. | https://github.com/signetlabdei/sem/blob/5077dd7a6d15644a18790bb6fde320e905f0fef0/sem/cli.py#L55-L94 |
signetlabdei/sem | sem/cli.py | view | def view(results_dir, result_id, hide_simulation_output, parameters, no_pager):
"""
View results of simulations.
"""
campaign = sem.CampaignManager.load(results_dir)
# Pick the most appropriate function based on the level of detail we want
if hide_simulation_output:
get_results_functio... | python | def view(results_dir, result_id, hide_simulation_output, parameters, no_pager):
"""
View results of simulations.
"""
campaign = sem.CampaignManager.load(results_dir)
# Pick the most appropriate function based on the level of detail we want
if hide_simulation_output:
get_results_functio... | View results of simulations. | https://github.com/signetlabdei/sem/blob/5077dd7a6d15644a18790bb6fde320e905f0fef0/sem/cli.py#L128-L168 |
signetlabdei/sem | sem/cli.py | command | def command(results_dir, result_id):
"""
Print the command that needs to be used to reproduce a result.
"""
campaign = sem.CampaignManager.load(results_dir)
result = campaign.db.get_results(result_id=result_id)[0]
click.echo("Simulation command:")
click.echo(sem.utils.get_command_from_resu... | python | def command(results_dir, result_id):
"""
Print the command that needs to be used to reproduce a result.
"""
campaign = sem.CampaignManager.load(results_dir)
result = campaign.db.get_results(result_id=result_id)[0]
click.echo("Simulation command:")
click.echo(sem.utils.get_command_from_resu... | Print the command that needs to be used to reproduce a result. | https://github.com/signetlabdei/sem/blob/5077dd7a6d15644a18790bb6fde320e905f0fef0/sem/cli.py#L181-L195 |
signetlabdei/sem | sem/cli.py | export | def export(results_dir, filename, do_not_try_parsing, parameters):
"""
Export results to file.
An extension in filename is required to deduce the file type. If no
extension is specified, a directory tree export will be used. Note that
this command automatically tries to parse the simulation output.... | python | def export(results_dir, filename, do_not_try_parsing, parameters):
"""
Export results to file.
An extension in filename is required to deduce the file type. If no
extension is specified, a directory tree export will be used. Note that
this command automatically tries to parse the simulation output.... | Export results to file.
An extension in filename is required to deduce the file type. If no
extension is specified, a directory tree export will be used. Note that
this command automatically tries to parse the simulation output.
Supported extensions:
.mat (Matlab file),
.npy (Numpy file),
... | https://github.com/signetlabdei/sem/blob/5077dd7a6d15644a18790bb6fde320e905f0fef0/sem/cli.py#L220-L268 |
signetlabdei/sem | sem/cli.py | merge | def merge(move, output_dir, sources):
"""
Merge multiple results folder into one, by copying the results over to a new folder.
For a faster operation (which on the other hand destroys the campaign data
if interrupted), the move option can be used to directly move results to
the new folder.
"""
... | python | def merge(move, output_dir, sources):
"""
Merge multiple results folder into one, by copying the results over to a new folder.
For a faster operation (which on the other hand destroys the campaign data
if interrupted), the move option can be used to directly move results to
the new folder.
"""
... | Merge multiple results folder into one, by copying the results over to a new folder.
For a faster operation (which on the other hand destroys the campaign data
if interrupted), the move option can be used to directly move results to
the new folder. | https://github.com/signetlabdei/sem/blob/5077dd7a6d15644a18790bb6fde320e905f0fef0/sem/cli.py#L286-L335 |
signetlabdei/sem | sem/cli.py | get_params_and_defaults | def get_params_and_defaults(param_list, db):
"""
Deduce [parameter, default] pairs from simulations available in the db.
Args:
param_list (list): List of parameters to query for.
db (DatabaseManager): Database where to query for defaults.
"""
return [[p, d] for p, d in db.get_all_values... | python | def get_params_and_defaults(param_list, db):
"""
Deduce [parameter, default] pairs from simulations available in the db.
Args:
param_list (list): List of parameters to query for.
db (DatabaseManager): Database where to query for defaults.
"""
return [[p, d] for p, d in db.get_all_values... | Deduce [parameter, default] pairs from simulations available in the db.
Args:
param_list (list): List of parameters to query for.
db (DatabaseManager): Database where to query for defaults. | https://github.com/signetlabdei/sem/blob/5077dd7a6d15644a18790bb6fde320e905f0fef0/sem/cli.py#L338-L346 |
signetlabdei/sem | sem/cli.py | query_parameters | def query_parameters(param_list, defaults=None):
"""
Asks the user for parameters. If available, proposes some defaults.
Args:
param_list (list): List of parameters to ask the user for values.
defaults (list): A list of proposed defaults. It must be a list of the
same length as ... | python | def query_parameters(param_list, defaults=None):
"""
Asks the user for parameters. If available, proposes some defaults.
Args:
param_list (list): List of parameters to ask the user for values.
defaults (list): A list of proposed defaults. It must be a list of the
same length as ... | Asks the user for parameters. If available, proposes some defaults.
Args:
param_list (list): List of parameters to ask the user for values.
defaults (list): A list of proposed defaults. It must be a list of the
same length as param_list. A value of None in one element of the
... | https://github.com/signetlabdei/sem/blob/5077dd7a6d15644a18790bb6fde320e905f0fef0/sem/cli.py#L349-L367 |
signetlabdei/sem | sem/cli.py | import_parameters_from_file | def import_parameters_from_file(parameters_file):
"""
Try importing a parameter dictionary from file.
We expect values in parameters_file to be defined as follows:
param1: value1
param2: [value2, value3]
"""
params = {}
with open(parameters_file, 'r') as f:
matches = re... | python | def import_parameters_from_file(parameters_file):
"""
Try importing a parameter dictionary from file.
We expect values in parameters_file to be defined as follows:
param1: value1
param2: [value2, value3]
"""
params = {}
with open(parameters_file, 'r') as f:
matches = re... | Try importing a parameter dictionary from file.
We expect values in parameters_file to be defined as follows:
param1: value1
param2: [value2, value3] | https://github.com/signetlabdei/sem/blob/5077dd7a6d15644a18790bb6fde320e905f0fef0/sem/cli.py#L370-L386 |
signetlabdei/sem | sem/parallelrunner.py | ParallelRunner.run_simulations | def run_simulations(self, parameter_list, data_folder):
"""
This function runs multiple simulations in parallel.
Args:
parameter_list (list): list of parameter combinations to simulate.
data_folder (str): folder in which to create output folders.
"""
self... | python | def run_simulations(self, parameter_list, data_folder):
"""
This function runs multiple simulations in parallel.
Args:
parameter_list (list): list of parameter combinations to simulate.
data_folder (str): folder in which to create output folders.
"""
self... | This function runs multiple simulations in parallel.
Args:
parameter_list (list): list of parameter combinations to simulate.
data_folder (str): folder in which to create output folders. | https://github.com/signetlabdei/sem/blob/5077dd7a6d15644a18790bb6fde320e905f0fef0/sem/parallelrunner.py#L12-L24 |
signetlabdei/sem | sem/parallelrunner.py | ParallelRunner.launch_simulation | def launch_simulation(self, parameter):
"""
Launch a single simulation, using SimulationRunner's facilities.
This function is used by ParallelRunner's run_simulations to map
simulation running over the parameter list.
Args:
parameter (dict): the parameter combinatio... | python | def launch_simulation(self, parameter):
"""
Launch a single simulation, using SimulationRunner's facilities.
This function is used by ParallelRunner's run_simulations to map
simulation running over the parameter list.
Args:
parameter (dict): the parameter combinatio... | Launch a single simulation, using SimulationRunner's facilities.
This function is used by ParallelRunner's run_simulations to map
simulation running over the parameter list.
Args:
parameter (dict): the parameter combination to simulate. | https://github.com/signetlabdei/sem/blob/5077dd7a6d15644a18790bb6fde320e905f0fef0/sem/parallelrunner.py#L26-L37 |
why2pac/dp-tornado | dp_tornado/helper/serialization/json.py | JsonHelper.stringify | def stringify(self, obj, beautify=False, raise_exception=False):
"""Alias of helper.string.serialization.json.stringify"""
return self.helper.string.serialization.json.stringify(
obj=obj,
beautify=beautify,
raise_exception=raise_exception) | python | def stringify(self, obj, beautify=False, raise_exception=False):
"""Alias of helper.string.serialization.json.stringify"""
return self.helper.string.serialization.json.stringify(
obj=obj,
beautify=beautify,
raise_exception=raise_exception) | Alias of helper.string.serialization.json.stringify | https://github.com/why2pac/dp-tornado/blob/a5948f5693f6ee2d9bab31f611fedc074e1caa96/dp_tornado/helper/serialization/json.py#L9-L15 |
why2pac/dp-tornado | dp_tornado/helper/serialization/json.py | JsonHelper.parse | def parse(self, text, encoding='utf8', raise_exception=False):
"""Alias of helper.string.serialization.json.parse"""
return self.helper.string.serialization.json.parse(
text=text,
encoding=encoding,
raise_exception=raise_exception) | python | def parse(self, text, encoding='utf8', raise_exception=False):
"""Alias of helper.string.serialization.json.parse"""
return self.helper.string.serialization.json.parse(
text=text,
encoding=encoding,
raise_exception=raise_exception) | Alias of helper.string.serialization.json.parse | https://github.com/why2pac/dp-tornado/blob/a5948f5693f6ee2d9bab31f611fedc074e1caa96/dp_tornado/helper/serialization/json.py#L17-L23 |
signetlabdei/sem | sem/database.py | DatabaseManager.new | def new(cls, script, commit, params, campaign_dir, overwrite=False):
"""
Initialize a new class instance with a set configuration and filename.
The created database has the same name of the campaign directory.
Args:
script (str): the ns-3 name of the script that will be use... | python | def new(cls, script, commit, params, campaign_dir, overwrite=False):
"""
Initialize a new class instance with a set configuration and filename.
The created database has the same name of the campaign directory.
Args:
script (str): the ns-3 name of the script that will be use... | Initialize a new class instance with a set configuration and filename.
The created database has the same name of the campaign directory.
Args:
script (str): the ns-3 name of the script that will be used in this
campaign;
commit (str): the commit of the ns-3 inst... | https://github.com/signetlabdei/sem/blob/5077dd7a6d15644a18790bb6fde320e905f0fef0/sem/database.py#L39-L95 |
signetlabdei/sem | sem/database.py | DatabaseManager.load | def load(cls, campaign_dir):
"""
Initialize from an existing database.
It is assumed that the database json file has the same name as its
containing folder.
Args:
campaign_dir (str): The path to the campaign directory.
"""
# We only accept absolute ... | python | def load(cls, campaign_dir):
"""
Initialize from an existing database.
It is assumed that the database json file has the same name as its
containing folder.
Args:
campaign_dir (str): The path to the campaign directory.
"""
# We only accept absolute ... | Initialize from an existing database.
It is assumed that the database json file has the same name as its
containing folder.
Args:
campaign_dir (str): The path to the campaign directory. | https://github.com/signetlabdei/sem/blob/5077dd7a6d15644a18790bb6fde320e905f0fef0/sem/database.py#L98-L135 |
signetlabdei/sem | sem/database.py | DatabaseManager.get_next_rngruns | def get_next_rngruns(self):
"""
Yield the next RngRun values that can be used in this campaign.
"""
available_runs = [result['params']['RngRun'] for result in
self.get_results()]
yield from DatabaseManager.get_next_values(available_runs) | python | def get_next_rngruns(self):
"""
Yield the next RngRun values that can be used in this campaign.
"""
available_runs = [result['params']['RngRun'] for result in
self.get_results()]
yield from DatabaseManager.get_next_values(available_runs) | Yield the next RngRun values that can be used in this campaign. | https://github.com/signetlabdei/sem/blob/5077dd7a6d15644a18790bb6fde320e905f0fef0/sem/database.py#L180-L186 |
signetlabdei/sem | sem/database.py | DatabaseManager.insert_result | def insert_result(self, result):
"""
Insert a new result in the database.
This function also verifies that the result dictionaries saved in the
database have the following structure (with {'a': 1} representing a
dictionary, 'a' a key and 1 its value)::
{
... | python | def insert_result(self, result):
"""
Insert a new result in the database.
This function also verifies that the result dictionaries saved in the
database have the following structure (with {'a': 1} representing a
dictionary, 'a' a key and 1 its value)::
{
... | Insert a new result in the database.
This function also verifies that the result dictionaries saved in the
database have the following structure (with {'a': 1} representing a
dictionary, 'a' a key and 1 its value)::
{
'params': {
'param1'... | https://github.com/signetlabdei/sem/blob/5077dd7a6d15644a18790bb6fde320e905f0fef0/sem/database.py#L188-L231 |
signetlabdei/sem | sem/database.py | DatabaseManager.get_results | def get_results(self, params=None, result_id=None):
"""
Return all the results available from the database that fulfill some
parameter combinations.
If params is None (or not specified), return all results.
If params is specified, it must be a dictionary specifying the result
... | python | def get_results(self, params=None, result_id=None):
"""
Return all the results available from the database that fulfill some
parameter combinations.
If params is None (or not specified), return all results.
If params is specified, it must be a dictionary specifying the result
... | Return all the results available from the database that fulfill some
parameter combinations.
If params is None (or not specified), return all results.
If params is specified, it must be a dictionary specifying the result
values we are interested in, with multiple values specified as li... | https://github.com/signetlabdei/sem/blob/5077dd7a6d15644a18790bb6fde320e905f0fef0/sem/database.py#L233-L304 |
signetlabdei/sem | sem/database.py | DatabaseManager.get_result_files | def get_result_files(self, result):
"""
Return a dictionary containing filename: filepath values for each
output file associated with an id.
Result can be either a result dictionary (e.g., obtained with the
get_results() method) or a result id.
"""
if isinstance(... | python | def get_result_files(self, result):
"""
Return a dictionary containing filename: filepath values for each
output file associated with an id.
Result can be either a result dictionary (e.g., obtained with the
get_results() method) or a result id.
"""
if isinstance(... | Return a dictionary containing filename: filepath values for each
output file associated with an id.
Result can be either a result dictionary (e.g., obtained with the
get_results() method) or a result id. | https://github.com/signetlabdei/sem/blob/5077dd7a6d15644a18790bb6fde320e905f0fef0/sem/database.py#L306-L327 |
signetlabdei/sem | sem/database.py | DatabaseManager.get_complete_results | def get_complete_results(self, params=None, result_id=None):
"""
Return available results, analogously to what get_results does, but
also read the corresponding output files for each result, and
incorporate them in the result dictionary under the output key, as a
dictionary of fi... | python | def get_complete_results(self, params=None, result_id=None):
"""
Return available results, analogously to what get_results does, but
also read the corresponding output files for each result, and
incorporate them in the result dictionary under the output key, as a
dictionary of fi... | Return available results, analogously to what get_results does, but
also read the corresponding output files for each result, and
incorporate them in the result dictionary under the output key, as a
dictionary of filename: file_contents.
Args:
params (dict): parameter specific... | https://github.com/signetlabdei/sem/blob/5077dd7a6d15644a18790bb6fde320e905f0fef0/sem/database.py#L329-L377 |
signetlabdei/sem | sem/database.py | DatabaseManager.wipe_results | def wipe_results(self):
"""
Remove all results from the database.
This also removes all output files, and cannot be undone.
"""
# Clean results table
self.db.purge_table('results')
# Get rid of contents of data dir
map(shutil.rmtree, glob.glob(os.path.jo... | python | def wipe_results(self):
"""
Remove all results from the database.
This also removes all output files, and cannot be undone.
"""
# Clean results table
self.db.purge_table('results')
# Get rid of contents of data dir
map(shutil.rmtree, glob.glob(os.path.jo... | Remove all results from the database.
This also removes all output files, and cannot be undone. | https://github.com/signetlabdei/sem/blob/5077dd7a6d15644a18790bb6fde320e905f0fef0/sem/database.py#L379-L389 |
signetlabdei/sem | sem/database.py | DatabaseManager.have_same_structure | def have_same_structure(d1, d2):
"""
Given two dictionaries (possibly with other nested dictionaries as
values), this function checks whether they have the same key structure.
>>> from sem import DatabaseManager
>>> d1 = {'a': 1, 'b': 2}
>>> d2 = {'a': [], 'b': 3}
... | python | def have_same_structure(d1, d2):
"""
Given two dictionaries (possibly with other nested dictionaries as
values), this function checks whether they have the same key structure.
>>> from sem import DatabaseManager
>>> d1 = {'a': 1, 'b': 2}
>>> d2 = {'a': [], 'b': 3}
... | Given two dictionaries (possibly with other nested dictionaries as
values), this function checks whether they have the same key structure.
>>> from sem import DatabaseManager
>>> d1 = {'a': 1, 'b': 2}
>>> d2 = {'a': [], 'b': 3}
>>> d3 = {'a': 4, 'c': 5}
>>> DatabaseManag... | https://github.com/signetlabdei/sem/blob/5077dd7a6d15644a18790bb6fde320e905f0fef0/sem/database.py#L417-L455 |
signetlabdei/sem | sem/database.py | DatabaseManager.get_all_values_of_all_params | def get_all_values_of_all_params(self):
"""
Return a dictionary containing all values that are taken by all
available parameters.
Always returns the parameter list in alphabetical order.
"""
values = collections.OrderedDict([[p, []] for p in
... | python | def get_all_values_of_all_params(self):
"""
Return a dictionary containing all values that are taken by all
available parameters.
Always returns the parameter list in alphabetical order.
"""
values = collections.OrderedDict([[p, []] for p in
... | Return a dictionary containing all values that are taken by all
available parameters.
Always returns the parameter list in alphabetical order. | https://github.com/signetlabdei/sem/blob/5077dd7a6d15644a18790bb6fde320e905f0fef0/sem/database.py#L457-L480 |
why2pac/dp-tornado | dp_tornado/helper/serialization/__init__.py | SerializationHelper.serialize | def serialize(self, obj, method='json', beautify=False, raise_exception=False):
"""Alias of helper.string.serialization.serialize"""
return self.helper.string.serialization.serialize(
obj=obj, method=method, beautify=beautify, raise_exception=raise_exception) | python | def serialize(self, obj, method='json', beautify=False, raise_exception=False):
"""Alias of helper.string.serialization.serialize"""
return self.helper.string.serialization.serialize(
obj=obj, method=method, beautify=beautify, raise_exception=raise_exception) | Alias of helper.string.serialization.serialize | https://github.com/why2pac/dp-tornado/blob/a5948f5693f6ee2d9bab31f611fedc074e1caa96/dp_tornado/helper/serialization/__init__.py#L9-L13 |
why2pac/dp-tornado | dp_tornado/helper/serialization/__init__.py | SerializationHelper.deserialize | def deserialize(self, text, method='json', encoding='utf8', raise_exception=False):
"""Alias of helper.string.serialization.deserialize"""
return self.helper.string.serialization.deserialize(
text, method=method, encoding=encoding, raise_exception=raise_exception) | python | def deserialize(self, text, method='json', encoding='utf8', raise_exception=False):
"""Alias of helper.string.serialization.deserialize"""
return self.helper.string.serialization.deserialize(
text, method=method, encoding=encoding, raise_exception=raise_exception) | Alias of helper.string.serialization.deserialize | https://github.com/why2pac/dp-tornado/blob/a5948f5693f6ee2d9bab31f611fedc074e1caa96/dp_tornado/helper/serialization/__init__.py#L15-L19 |
signetlabdei/sem | sem/gridrunner.py | GridRunner.run_simulations | def run_simulations(self, parameter_list, data_folder):
"""
This function runs multiple simulations in parallel.
"""
# Open up a session
s = drmaa.Session()
s.initialize()
# Create a job template for each parameter combination
jobs = {}
for param... | python | def run_simulations(self, parameter_list, data_folder):
"""
This function runs multiple simulations in parallel.
"""
# Open up a session
s = drmaa.Session()
s.initialize()
# Create a job template for each parameter combination
jobs = {}
for param... | This function runs multiple simulations in parallel. | https://github.com/signetlabdei/sem/blob/5077dd7a6d15644a18790bb6fde320e905f0fef0/sem/gridrunner.py#L24-L118 |
signetlabdei/sem | sem/gridrunner.py | GridRunner.get_available_parameters | def get_available_parameters(self):
"""
Return a list of the parameters made available by the script.
"""
# At the moment, we rely on regex to extract the list of available
# parameters. A tighter integration with waf would allow for a more
# natural extraction of the in... | python | def get_available_parameters(self):
"""
Return a list of the parameters made available by the script.
"""
# At the moment, we rely on regex to extract the list of available
# parameters. A tighter integration with waf would allow for a more
# natural extraction of the in... | Return a list of the parameters made available by the script. | https://github.com/signetlabdei/sem/blob/5077dd7a6d15644a18790bb6fde320e905f0fef0/sem/gridrunner.py#L141-L163 |
signetlabdei/sem | sem/gridrunner.py | GridRunner.run_program | def run_program(self, command, working_directory=os.getcwd(),
environment=None, cleanup_files=True,
native_spec="-l cputype=intel"):
"""
Run a program through the grid, capturing the standard output.
"""
try:
s = drmaa.Session()
... | python | def run_program(self, command, working_directory=os.getcwd(),
environment=None, cleanup_files=True,
native_spec="-l cputype=intel"):
"""
Run a program through the grid, capturing the standard output.
"""
try:
s = drmaa.Session()
... | Run a program through the grid, capturing the standard output. | https://github.com/signetlabdei/sem/blob/5077dd7a6d15644a18790bb6fde320e905f0fef0/sem/gridrunner.py#L165-L208 |
CellProfiler/centrosome | centrosome/cpmorphology.py | fill_labeled_holes | def fill_labeled_holes(labels, mask=None, size_fn = None):
'''Fill all background pixels that are holes inside the foreground
A pixel is a hole inside a foreground object if
* there is no path from the pixel to the edge AND
* there is no path from the pixel to any other non-hole
pixel ... | python | def fill_labeled_holes(labels, mask=None, size_fn = None):
'''Fill all background pixels that are holes inside the foreground
A pixel is a hole inside a foreground object if
* there is no path from the pixel to the edge AND
* there is no path from the pixel to any other non-hole
pixel ... | Fill all background pixels that are holes inside the foreground
A pixel is a hole inside a foreground object if
* there is no path from the pixel to the edge AND
* there is no path from the pixel to any other non-hole
pixel AND
* there is no path from the pixel to two similarly-... | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L33-L149 |
CellProfiler/centrosome | centrosome/cpmorphology.py | adjacent | def adjacent(labels):
'''Return a binary mask of all pixels which are adjacent to a pixel of
a different label.
'''
high = labels.max()+1
if high > np.iinfo(labels.dtype).max:
labels = labels.astype(np.int)
image_with_high_background = labels.copy()
image_with_high_backgr... | python | def adjacent(labels):
'''Return a binary mask of all pixels which are adjacent to a pixel of
a different label.
'''
high = labels.max()+1
if high > np.iinfo(labels.dtype).max:
labels = labels.astype(np.int)
image_with_high_background = labels.copy()
image_with_high_backgr... | Return a binary mask of all pixels which are adjacent to a pixel of
a different label. | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L151-L169 |
CellProfiler/centrosome | centrosome/cpmorphology.py | binary_thin | def binary_thin(image, strel1, strel2):
"""Morphologically thin an image
strel1 - the required values of the pixels in order to survive
strel2 - at each pixel, the complement of strel1 if we care about the value
"""
hit_or_miss = scind.binary_hit_or_miss(image, strel1, strel2)
return np.logical_... | python | def binary_thin(image, strel1, strel2):
"""Morphologically thin an image
strel1 - the required values of the pixels in order to survive
strel2 - at each pixel, the complement of strel1 if we care about the value
"""
hit_or_miss = scind.binary_hit_or_miss(image, strel1, strel2)
return np.logical_... | Morphologically thin an image
strel1 - the required values of the pixels in order to survive
strel2 - at each pixel, the complement of strel1 if we care about the value | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L171-L177 |
CellProfiler/centrosome | centrosome/cpmorphology.py | binary_shrink_old | def binary_shrink_old(image, iterations=-1):
"""Shrink an image by repeatedly removing pixels which have partners
above, to the left, to the right and below until the image doesn't change
image - binary image to be manipulated
iterations - # of times to shrink, -1 to shrink until idempo... | python | def binary_shrink_old(image, iterations=-1):
"""Shrink an image by repeatedly removing pixels which have partners
above, to the left, to the right and below until the image doesn't change
image - binary image to be manipulated
iterations - # of times to shrink, -1 to shrink until idempo... | Shrink an image by repeatedly removing pixels which have partners
above, to the left, to the right and below until the image doesn't change
image - binary image to be manipulated
iterations - # of times to shrink, -1 to shrink until idempotent
There are horizontal/vertical th... | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L181-L317 |
CellProfiler/centrosome | centrosome/cpmorphology.py | binary_shrink | def binary_shrink(image, iterations=-1):
"""Shrink an image by repeatedly removing pixels which have partners
above, to the left, to the right and below until the image doesn't change
image - binary image to be manipulated
iterations - # of times to shrink, -1 to shrink until idempotent... | python | def binary_shrink(image, iterations=-1):
"""Shrink an image by repeatedly removing pixels which have partners
above, to the left, to the right and below until the image doesn't change
image - binary image to be manipulated
iterations - # of times to shrink, -1 to shrink until idempotent... | Shrink an image by repeatedly removing pixels which have partners
above, to the left, to the right and below until the image doesn't change
image - binary image to be manipulated
iterations - # of times to shrink, -1 to shrink until idempotent
There are horizontal/vertical th... | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L324-L430 |
CellProfiler/centrosome | centrosome/cpmorphology.py | strel_disk | def strel_disk(radius):
"""Create a disk structuring element for morphological operations
radius - radius of the disk
"""
iradius = int(radius)
x,y = np.mgrid[-iradius:iradius+1,-iradius:iradius+1]
radius2 = radius * radius
strel = np.zeros(x.shape)
strel[x*x+y*y <= radius2] =... | python | def strel_disk(radius):
"""Create a disk structuring element for morphological operations
radius - radius of the disk
"""
iradius = int(radius)
x,y = np.mgrid[-iradius:iradius+1,-iradius:iradius+1]
radius2 = radius * radius
strel = np.zeros(x.shape)
strel[x*x+y*y <= radius2] =... | Create a disk structuring element for morphological operations
radius - radius of the disk | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L432-L442 |
CellProfiler/centrosome | centrosome/cpmorphology.py | strel_diamond | def strel_diamond(radius):
"""Create a diamond structuring element for morphological operations
radius - the offset of the corners of the diamond from the origin
rounded down (e.g. r=2: (0, 2), (2, 0), (0, -2), (-2, 0))
returns a two-dimensional binary array
"""
iradi... | python | def strel_diamond(radius):
"""Create a diamond structuring element for morphological operations
radius - the offset of the corners of the diamond from the origin
rounded down (e.g. r=2: (0, 2), (2, 0), (0, -2), (-2, 0))
returns a two-dimensional binary array
"""
iradi... | Create a diamond structuring element for morphological operations
radius - the offset of the corners of the diamond from the origin
rounded down (e.g. r=2: (0, 2), (2, 0), (0, -2), (-2, 0))
returns a two-dimensional binary array | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L444-L457 |
CellProfiler/centrosome | centrosome/cpmorphology.py | strel_line | def strel_line(length, angle):
"""Create a line structuring element for morphological operations
length - distance between first and last pixels of the line, rounded down
angle - angle from the horizontal, counter-clockwise in degrees.
Note: uses draw_line's Bresenham algorithm to select ... | python | def strel_line(length, angle):
"""Create a line structuring element for morphological operations
length - distance between first and last pixels of the line, rounded down
angle - angle from the horizontal, counter-clockwise in degrees.
Note: uses draw_line's Bresenham algorithm to select ... | Create a line structuring element for morphological operations
length - distance between first and last pixels of the line, rounded down
angle - angle from the horizontal, counter-clockwise in degrees.
Note: uses draw_line's Bresenham algorithm to select points. | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L459-L483 |
CellProfiler/centrosome | centrosome/cpmorphology.py | strel_octagon | def strel_octagon(radius):
"""Create an octagonal structuring element for morphological operations
radius - the distance from the origin to each edge of the octagon
"""
#
# Inscribe a diamond in a square to get an octagon.
#
iradius = int(radius)
i, j = np.mgrid[-iradius:(iradius + ... | python | def strel_octagon(radius):
"""Create an octagonal structuring element for morphological operations
radius - the distance from the origin to each edge of the octagon
"""
#
# Inscribe a diamond in a square to get an octagon.
#
iradius = int(radius)
i, j = np.mgrid[-iradius:(iradius + ... | Create an octagonal structuring element for morphological operations
radius - the distance from the origin to each edge of the octagon | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L485-L506 |
CellProfiler/centrosome | centrosome/cpmorphology.py | strel_pair | def strel_pair(x, y):
"""Create a structing element composed of the origin and another pixel
x, y - x and y offsets of the other pixel
returns a structuring element
"""
x_center = int(np.abs(x))
y_center = int(np.abs(y))
result = np.zeros((y_center * 2 + 1, x_center * 2 + 1), bool... | python | def strel_pair(x, y):
"""Create a structing element composed of the origin and another pixel
x, y - x and y offsets of the other pixel
returns a structuring element
"""
x_center = int(np.abs(x))
y_center = int(np.abs(y))
result = np.zeros((y_center * 2 + 1, x_center * 2 + 1), bool... | Create a structing element composed of the origin and another pixel
x, y - x and y offsets of the other pixel
returns a structuring element | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L508-L521 |
CellProfiler/centrosome | centrosome/cpmorphology.py | strel_periodicline | def strel_periodicline(xoff, yoff, n):
"""Create a structuring element composed of a line of evenly-spaced points
xoff, yoff - the line goes through the origin and this point
n - the line is composed of the origin and n points on either side of the
origin for a total of 2*n + 1 points
... | python | def strel_periodicline(xoff, yoff, n):
"""Create a structuring element composed of a line of evenly-spaced points
xoff, yoff - the line goes through the origin and this point
n - the line is composed of the origin and n points on either side of the
origin for a total of 2*n + 1 points
... | Create a structuring element composed of a line of evenly-spaced points
xoff, yoff - the line goes through the origin and this point
n - the line is composed of the origin and n points on either side of the
origin for a total of 2*n + 1 points
The structuring element is composed of... | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L523-L540 |
CellProfiler/centrosome | centrosome/cpmorphology.py | strel_rectangle | def strel_rectangle(width, height):
"""Create a rectangular structuring element
width - the width of the structuring element (in the j direction). The
width will be rounded down to the nearest multiple of 2*n+1
height = the height of the structuring element (in the i direction)... | python | def strel_rectangle(width, height):
"""Create a rectangular structuring element
width - the width of the structuring element (in the j direction). The
width will be rounded down to the nearest multiple of 2*n+1
height = the height of the structuring element (in the i direction)... | Create a rectangular structuring element
width - the width of the structuring element (in the j direction). The
width will be rounded down to the nearest multiple of 2*n+1
height = the height of the structuring element (in the i direction). The
height will be rounded do... | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L542-L551 |
CellProfiler/centrosome | centrosome/cpmorphology.py | cpmaximum | def cpmaximum(image, structure=np.ones((3,3),dtype=bool),offset=None):
"""Find the local maximum at each point in the image, using the given structuring element
image - a 2-d array of doubles
structure - a boolean structuring element indicating which
local elements should be sampled
... | python | def cpmaximum(image, structure=np.ones((3,3),dtype=bool),offset=None):
"""Find the local maximum at each point in the image, using the given structuring element
image - a 2-d array of doubles
structure - a boolean structuring element indicating which
local elements should be sampled
... | Find the local maximum at each point in the image, using the given structuring element
image - a 2-d array of doubles
structure - a boolean structuring element indicating which
local elements should be sampled
offset - the offset to the center of the structuring element | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L561-L574 |
CellProfiler/centrosome | centrosome/cpmorphology.py | relabel | def relabel(image):
"""Given a labeled image, relabel each of the objects consecutively
image - a labeled 2-d integer array
returns - (labeled image, object count)
"""
#
# Build a label table that converts an old label # into
# labels using the new numbering scheme
#
unique_lab... | python | def relabel(image):
"""Given a labeled image, relabel each of the objects consecutively
image - a labeled 2-d integer array
returns - (labeled image, object count)
"""
#
# Build a label table that converts an old label # into
# labels using the new numbering scheme
#
unique_lab... | Given a labeled image, relabel each of the objects consecutively
image - a labeled 2-d integer array
returns - (labeled image, object count) | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L576-L596 |
CellProfiler/centrosome | centrosome/cpmorphology.py | convex_hull_image | def convex_hull_image(image):
'''Given a binary image, return an image of the convex hull'''
labels = image.astype(int)
points, counts = convex_hull(labels, np.array([1]))
output = np.zeros(image.shape, int)
for i in range(counts[0]):
inext = (i+1) % counts[0]
draw_line(output, point... | python | def convex_hull_image(image):
'''Given a binary image, return an image of the convex hull'''
labels = image.astype(int)
points, counts = convex_hull(labels, np.array([1]))
output = np.zeros(image.shape, int)
for i in range(counts[0]):
inext = (i+1) % counts[0]
draw_line(output, point... | Given a binary image, return an image of the convex hull | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L598-L607 |
CellProfiler/centrosome | centrosome/cpmorphology.py | convex_hull | def convex_hull(labels, indexes=None, fast=True):
"""Given a labeled image, return a list of points per object ordered by
angle from an interior point, representing the convex hull.s
labels - the label matrix
indexes - an array of label #s to be processed, defaults to all non-zero
lab... | python | def convex_hull(labels, indexes=None, fast=True):
"""Given a labeled image, return a list of points per object ordered by
angle from an interior point, representing the convex hull.s
labels - the label matrix
indexes - an array of label #s to be processed, defaults to all non-zero
lab... | Given a labeled image, return a list of points per object ordered by
angle from an interior point, representing the convex hull.s
labels - the label matrix
indexes - an array of label #s to be processed, defaults to all non-zero
labels
Returns a matrix and a vector. The matrix co... | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L609-L646 |
CellProfiler/centrosome | centrosome/cpmorphology.py | convex_hull_ijv | def convex_hull_ijv(pixel_labels, indexes, fast=True):
'''Return the convex hull for each label using an ijv labeling
pixel_labels: the labeling of the pixels in i,j,v form where
i & j are the coordinates of a pixel and v is
the pixel's label number
indexes: the inde... | python | def convex_hull_ijv(pixel_labels, indexes, fast=True):
'''Return the convex hull for each label using an ijv labeling
pixel_labels: the labeling of the pixels in i,j,v form where
i & j are the coordinates of a pixel and v is
the pixel's label number
indexes: the inde... | Return the convex hull for each label using an ijv labeling
pixel_labels: the labeling of the pixels in i,j,v form where
i & j are the coordinates of a pixel and v is
the pixel's label number
indexes: the indexes at which to measure the convex hull
Returns a matrix ... | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L648-L887 |
CellProfiler/centrosome | centrosome/cpmorphology.py | triangle_areas | def triangle_areas(p1,p2,p3):
"""Compute an array of triangle areas given three arrays of triangle pts
p1,p2,p3 - three Nx2 arrays of points
"""
v1 = (p2 - p1).astype(np.float)
v2 = (p3 - p1).astype(np.float)
# Original:
# cross1 = v1[:,1] * v2[:,0]
# cross2 = v2[:,1] * v1[:,0]
... | python | def triangle_areas(p1,p2,p3):
"""Compute an array of triangle areas given three arrays of triangle pts
p1,p2,p3 - three Nx2 arrays of points
"""
v1 = (p2 - p1).astype(np.float)
v2 = (p3 - p1).astype(np.float)
# Original:
# cross1 = v1[:,1] * v2[:,0]
# cross2 = v2[:,1] * v1[:,0]
... | Compute an array of triangle areas given three arrays of triangle pts
p1,p2,p3 - three Nx2 arrays of points | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L889-L915 |
CellProfiler/centrosome | centrosome/cpmorphology.py | fill_convex_hulls | def fill_convex_hulls(ch_pts, ch_counts):
'''Return the points within the convex hulls of objects
ch_pts - a Nx3 array of columns of label #, i and j as output by convex_hull
ch_counts - the number of points per object
returns the points in ijv format.
'''
if len(ch_pts) == 0:
... | python | def fill_convex_hulls(ch_pts, ch_counts):
'''Return the points within the convex hulls of objects
ch_pts - a Nx3 array of columns of label #, i and j as output by convex_hull
ch_counts - the number of points per object
returns the points in ijv format.
'''
if len(ch_pts) == 0:
... | Return the points within the convex hulls of objects
ch_pts - a Nx3 array of columns of label #, i and j as output by convex_hull
ch_counts - the number of points per object
returns the points in ijv format. | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L917-L997 |
CellProfiler/centrosome | centrosome/cpmorphology.py | draw_line | def draw_line(labels,pt0,pt1,value=1):
"""Draw a line between two points
pt0, pt1 are in i,j format which is the reverse of x,y format
Uses the Bresenham algorithm
Some code transcribed from http://www.cs.unc.edu/~mcmillan/comp136/Lecture6/Lines.html
"""
y0,x0 = pt0
y1,x1 = pt1
diff... | python | def draw_line(labels,pt0,pt1,value=1):
"""Draw a line between two points
pt0, pt1 are in i,j format which is the reverse of x,y format
Uses the Bresenham algorithm
Some code transcribed from http://www.cs.unc.edu/~mcmillan/comp136/Lecture6/Lines.html
"""
y0,x0 = pt0
y1,x1 = pt1
diff... | Draw a line between two points
pt0, pt1 are in i,j format which is the reverse of x,y format
Uses the Bresenham algorithm
Some code transcribed from http://www.cs.unc.edu/~mcmillan/comp136/Lecture6/Lines.html | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L999-L1033 |
CellProfiler/centrosome | centrosome/cpmorphology.py | get_line_pts | def get_line_pts(pt0i, pt0j, pt1i, pt1j):
'''Retrieve the coordinates of the points along lines
pt0i, pt0j - the starting coordinates of the lines (1-d nparray)
pt1i, pt1j - the ending coordinates of the lines (1-d nparray)
use the Bresenham algorithm to find the coordinates along the lines
... | python | def get_line_pts(pt0i, pt0j, pt1i, pt1j):
'''Retrieve the coordinates of the points along lines
pt0i, pt0j - the starting coordinates of the lines (1-d nparray)
pt1i, pt1j - the ending coordinates of the lines (1-d nparray)
use the Bresenham algorithm to find the coordinates along the lines
... | Retrieve the coordinates of the points along lines
pt0i, pt0j - the starting coordinates of the lines (1-d nparray)
pt1i, pt1j - the ending coordinates of the lines (1-d nparray)
use the Bresenham algorithm to find the coordinates along the lines
connectiong pt0 and pt1. pt01, pt0j, pt1i and p... | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L1035-L1181 |
CellProfiler/centrosome | centrosome/cpmorphology.py | polygon_lines_to_mask | def polygon_lines_to_mask(pt0i, pt0j, pt1i, pt1j, shape):
'''Convert a series of polygon lines to a background / foreground mask
pt0i, pt0j, pt1i, pt1j - start / end points of lines. Points are rounded
to the nearest integer coordinate if float.
shape - shape of the ma... | python | def polygon_lines_to_mask(pt0i, pt0j, pt1i, pt1j, shape):
'''Convert a series of polygon lines to a background / foreground mask
pt0i, pt0j, pt1i, pt1j - start / end points of lines. Points are rounded
to the nearest integer coordinate if float.
shape - shape of the ma... | Convert a series of polygon lines to a background / foreground mask
pt0i, pt0j, pt1i, pt1j - start / end points of lines. Points are rounded
to the nearest integer coordinate if float.
shape - shape of the mask array
This algorithm assumes that the lines form clos... | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L1183-L1282 |
CellProfiler/centrosome | centrosome/cpmorphology.py | fixup_scipy_ndimage_result | def fixup_scipy_ndimage_result(whatever_it_returned):
"""Convert a result from scipy.ndimage to a numpy array
scipy.ndimage has the annoying habit of returning a single, bare
value instead of an array if the indexes passed in are of length 1.
For instance:
scind.maximum(image, labels, [1]) retu... | python | def fixup_scipy_ndimage_result(whatever_it_returned):
"""Convert a result from scipy.ndimage to a numpy array
scipy.ndimage has the annoying habit of returning a single, bare
value instead of an array if the indexes passed in are of length 1.
For instance:
scind.maximum(image, labels, [1]) retu... | Convert a result from scipy.ndimage to a numpy array
scipy.ndimage has the annoying habit of returning a single, bare
value instead of an array if the indexes passed in are of length 1.
For instance:
scind.maximum(image, labels, [1]) returns a float
but
scind.maximum(image, labels, [1,2]) r... | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L1284-L1297 |
CellProfiler/centrosome | centrosome/cpmorphology.py | centers_of_labels | def centers_of_labels(labels):
'''Return the i,j coordinates of the centers of a labels matrix
The result returned is an 2 x n numpy array where n is the number
of the label minus one, result[0,x] is the i coordinate of the center
and result[x,1] is the j coordinate of the center.
You can unpac... | python | def centers_of_labels(labels):
'''Return the i,j coordinates of the centers of a labels matrix
The result returned is an 2 x n numpy array where n is the number
of the label minus one, result[0,x] is the i coordinate of the center
and result[x,1] is the j coordinate of the center.
You can unpac... | Return the i,j coordinates of the centers of a labels matrix
The result returned is an 2 x n numpy array where n is the number
of the label minus one, result[0,x] is the i coordinate of the center
and result[x,1] is the j coordinate of the center.
You can unpack the result as "i,j = centers_of_labe... | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L1299-L1318 |
CellProfiler/centrosome | centrosome/cpmorphology.py | maximum_position_of_labels | def maximum_position_of_labels(image, labels, indices):
'''Return the i,j coordinates of the maximum value within each object
image - measure the maximum within this image
labels - use the objects within this labels matrix
indices - label #s to measure
The result returned is an 2 x n numpy... | python | def maximum_position_of_labels(image, labels, indices):
'''Return the i,j coordinates of the maximum value within each object
image - measure the maximum within this image
labels - use the objects within this labels matrix
indices - label #s to measure
The result returned is an 2 x n numpy... | Return the i,j coordinates of the maximum value within each object
image - measure the maximum within this image
labels - use the objects within this labels matrix
indices - label #s to measure
The result returned is an 2 x n numpy array where n is the number
of the label minus one, result... | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L1320-L1340 |
CellProfiler/centrosome | centrosome/cpmorphology.py | minimum_enclosing_circle | def minimum_enclosing_circle(labels, indexes = None,
hull_and_point_count = None):
"""Find the location of the minimum enclosing circle and its radius
labels - a labels matrix
indexes - an array giving the label indexes to be processed
hull_and_point_count - convex_hul... | python | def minimum_enclosing_circle(labels, indexes = None,
hull_and_point_count = None):
"""Find the location of the minimum enclosing circle and its radius
labels - a labels matrix
indexes - an array giving the label indexes to be processed
hull_and_point_count - convex_hul... | Find the location of the minimum enclosing circle and its radius
labels - a labels matrix
indexes - an array giving the label indexes to be processed
hull_and_point_count - convex_hull output if already done. None = calculate
returns an Nx3 array organized as i,j of the center and radius
A... | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L1381-L1706 |
CellProfiler/centrosome | centrosome/cpmorphology.py | associate_by_distance | def associate_by_distance(labels_a, labels_b, distance):
'''Find the objects that are within a given distance of each other
Given two labels matrices and a distance, find pairs of objects that
are within the given distance of each other where the distance is
the minimum distance between any point i... | python | def associate_by_distance(labels_a, labels_b, distance):
'''Find the objects that are within a given distance of each other
Given two labels matrices and a distance, find pairs of objects that
are within the given distance of each other where the distance is
the minimum distance between any point i... | Find the objects that are within a given distance of each other
Given two labels matrices and a distance, find pairs of objects that
are within the given distance of each other where the distance is
the minimum distance between any point in the convex hull of the
two objects.
labels_a - fi... | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L1708-L1843 |
CellProfiler/centrosome | centrosome/cpmorphology.py | minimum_distance2 | def minimum_distance2(hull_a, center_a, hull_b, center_b):
'''Return the minimum distance or 0 if overlap between 2 convex hulls
hull_a - list of points in clockwise direction
center_a - a point within the hull
hull_b - list of points in clockwise direction
center_b - a point within the hull
... | python | def minimum_distance2(hull_a, center_a, hull_b, center_b):
'''Return the minimum distance or 0 if overlap between 2 convex hulls
hull_a - list of points in clockwise direction
center_a - a point within the hull
hull_b - list of points in clockwise direction
center_b - a point within the hull
... | Return the minimum distance or 0 if overlap between 2 convex hulls
hull_a - list of points in clockwise direction
center_a - a point within the hull
hull_b - list of points in clockwise direction
center_b - a point within the hull | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L1845-L1856 |
CellProfiler/centrosome | centrosome/cpmorphology.py | slow_minimum_distance2 | def slow_minimum_distance2(hull_a, hull_b):
'''Do the minimum distance by exhaustive examination of all points'''
d2_min = np.iinfo(int).max
for a in hull_a:
if within_hull(a, hull_b):
return 0
for b in hull_b:
if within_hull(b, hull_a):
return 0
for pt_a in h... | python | def slow_minimum_distance2(hull_a, hull_b):
'''Do the minimum distance by exhaustive examination of all points'''
d2_min = np.iinfo(int).max
for a in hull_a:
if within_hull(a, hull_b):
return 0
for b in hull_b:
if within_hull(b, hull_a):
return 0
for pt_a in h... | Do the minimum distance by exhaustive examination of all points | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L1858-L1882 |
CellProfiler/centrosome | centrosome/cpmorphology.py | faster_minimum_distance2 | def faster_minimum_distance2(hull_a, center_a, hull_b, center_b):
'''Do the minimum distance using the bimodal property of hull ordering
'''
#
# Find the farthest vertex in b from some point within A. Find the
# vertices within A visible from this point in B. If the point in A
# is within B... | python | def faster_minimum_distance2(hull_a, center_a, hull_b, center_b):
'''Do the minimum distance using the bimodal property of hull ordering
'''
#
# Find the farthest vertex in b from some point within A. Find the
# vertices within A visible from this point in B. If the point in A
# is within B... | Do the minimum distance using the bimodal property of hull ordering | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L1884-L1970 |
CellProfiler/centrosome | centrosome/cpmorphology.py | lines_intersect | def lines_intersect(pt1_p, pt2_p, pt1_q, pt2_q):
'''Return true if two line segments intersect
pt1_p, pt2_p - endpoints of first line segment
pt1_q, pt2_q - endpoints of second line segment
'''
#
# The idea here is to do the cross-product of the vector from
# point 1 to point 2 of one segmen... | python | def lines_intersect(pt1_p, pt2_p, pt1_q, pt2_q):
'''Return true if two line segments intersect
pt1_p, pt2_p - endpoints of first line segment
pt1_q, pt2_q - endpoints of second line segment
'''
#
# The idea here is to do the cross-product of the vector from
# point 1 to point 2 of one segmen... | Return true if two line segments intersect
pt1_p, pt2_p - endpoints of first line segment
pt1_q, pt2_q - endpoints of second line segment | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L1972-L1996 |
CellProfiler/centrosome | centrosome/cpmorphology.py | find_farthest | def find_farthest(point, hull):
'''Find the vertex in hull farthest away from a point'''
d_start = np.sum((point-hull[0,:])**2)
d_end = np.sum((point-hull[-1,:])**2)
if d_start > d_end:
# Go in the forward direction
i = 1
inc = 1
term = hull.shape[0]
d2_max = d_st... | python | def find_farthest(point, hull):
'''Find the vertex in hull farthest away from a point'''
d_start = np.sum((point-hull[0,:])**2)
d_end = np.sum((point-hull[-1,:])**2)
if d_start > d_end:
# Go in the forward direction
i = 1
inc = 1
term = hull.shape[0]
d2_max = d_st... | Find the vertex in hull farthest away from a point | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L2003-L2025 |
CellProfiler/centrosome | centrosome/cpmorphology.py | find_visible | def find_visible(hull, observer, background):
'''Given an observer location, find the first and last visible
points in the hull
The observer at "observer" is looking at the hull whose most distant
vertex from the observer is "background. Find the vertices that are
the furthest di... | python | def find_visible(hull, observer, background):
'''Given an observer location, find the first and last visible
points in the hull
The observer at "observer" is looking at the hull whose most distant
vertex from the observer is "background. Find the vertices that are
the furthest di... | Given an observer location, find the first and last visible
points in the hull
The observer at "observer" is looking at the hull whose most distant
vertex from the observer is "background. Find the vertices that are
the furthest distance from the line between observer and background.... | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L2027-L2061 |
CellProfiler/centrosome | centrosome/cpmorphology.py | distance2_to_line | def distance2_to_line(pt, l0, l1):
'''The perpendicular distance squared from a point to a line
pt - point in question
l0 - one point on the line
l1 - another point on the line
'''
pt = np.atleast_1d(pt)
l0 = np.atleast_1d(l0)
l1 = np.atleast_1d(l1)
reshape = pt.ndim == 1
if... | python | def distance2_to_line(pt, l0, l1):
'''The perpendicular distance squared from a point to a line
pt - point in question
l0 - one point on the line
l1 - another point on the line
'''
pt = np.atleast_1d(pt)
l0 = np.atleast_1d(l0)
l1 = np.atleast_1d(l1)
reshape = pt.ndim == 1
if... | The perpendicular distance squared from a point to a line
pt - point in question
l0 - one point on the line
l1 - another point on the line | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L2063-L2081 |
CellProfiler/centrosome | centrosome/cpmorphology.py | within_hull | def within_hull(point, hull):
'''Return true if the point is within the convex hull'''
h_prev_pt = hull[-1,:]
for h_pt in hull:
if np.cross(h_pt-h_prev_pt, point - h_pt) >= 0:
return False
h_prev_pt = h_pt
return True | python | def within_hull(point, hull):
'''Return true if the point is within the convex hull'''
h_prev_pt = hull[-1,:]
for h_pt in hull:
if np.cross(h_pt-h_prev_pt, point - h_pt) >= 0:
return False
h_prev_pt = h_pt
return True | Return true if the point is within the convex hull | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L2084-L2091 |
CellProfiler/centrosome | centrosome/cpmorphology.py | all_true | def all_true(a, indexes):
'''Find which vectors have all-true elements
Given an array, "a" and indexes into the first elements of vectors
within that array, return an array where each element is true if
all elements of the corresponding vector are true.
Example: a = [ 1,1,0,1,1,1,1], index... | python | def all_true(a, indexes):
'''Find which vectors have all-true elements
Given an array, "a" and indexes into the first elements of vectors
within that array, return an array where each element is true if
all elements of the corresponding vector are true.
Example: a = [ 1,1,0,1,1,1,1], index... | Find which vectors have all-true elements
Given an array, "a" and indexes into the first elements of vectors
within that array, return an array where each element is true if
all elements of the corresponding vector are true.
Example: a = [ 1,1,0,1,1,1,1], indexes=[0,3]
vectors = [... | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L2093-L2115 |
CellProfiler/centrosome | centrosome/cpmorphology.py | ellipse_from_second_moments | def ellipse_from_second_moments(image, labels, indexes, wants_compactness = False):
"""Calculate measurements of ellipses equivalent to the second moments of labels
image - the intensity at each point
labels - for each labeled object, derive an ellipse
indexes - sequence of indexes to process
... | python | def ellipse_from_second_moments(image, labels, indexes, wants_compactness = False):
"""Calculate measurements of ellipses equivalent to the second moments of labels
image - the intensity at each point
labels - for each labeled object, derive an ellipse
indexes - sequence of indexes to process
... | Calculate measurements of ellipses equivalent to the second moments of labels
image - the intensity at each point
labels - for each labeled object, derive an ellipse
indexes - sequence of indexes to process
returns the following arrays:
coordinates of the center of the ellipse
e... | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L2117-L2149 |
CellProfiler/centrosome | centrosome/cpmorphology.py | ellipse_from_second_moments_ijv | def ellipse_from_second_moments_ijv(i,j, image, labels, indexes, wants_compactness = False):
"""Calculate measurements of ellipses equivalent to the second moments of labels
i,j - coordinates of each point
image - the intensity at each point
labels - for each labeled object, derive an ellipse
... | python | def ellipse_from_second_moments_ijv(i,j, image, labels, indexes, wants_compactness = False):
"""Calculate measurements of ellipses equivalent to the second moments of labels
i,j - coordinates of each point
image - the intensity at each point
labels - for each labeled object, derive an ellipse
... | Calculate measurements of ellipses equivalent to the second moments of labels
i,j - coordinates of each point
image - the intensity at each point
labels - for each labeled object, derive an ellipse
indexes - sequence of indexes to process
returns the following arrays:
coordinates o... | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L2151-L2233 |
CellProfiler/centrosome | centrosome/cpmorphology.py | calculate_extents | def calculate_extents(labels, indexes):
"""Return the area of each object divided by the area of its bounding box"""
fix = fixup_scipy_ndimage_result
areas = fix(scind.sum(np.ones(labels.shape),labels,np.array(indexes, dtype=np.int32)))
y,x = np.mgrid[0:labels.shape[0],0:labels.shape[1]]
xmin = fix(... | python | def calculate_extents(labels, indexes):
"""Return the area of each object divided by the area of its bounding box"""
fix = fixup_scipy_ndimage_result
areas = fix(scind.sum(np.ones(labels.shape),labels,np.array(indexes, dtype=np.int32)))
y,x = np.mgrid[0:labels.shape[0],0:labels.shape[1]]
xmin = fix(... | Return the area of each object divided by the area of its bounding box | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L2235-L2245 |
CellProfiler/centrosome | centrosome/cpmorphology.py | __calculate_perimeter_scoring | def __calculate_perimeter_scoring():
"""Return a 512 element vector which gives the perimeter given surrounding pts
"""
#
# This is the array from the paper - a 256 - element array leaving out
# the center point. The first value is the index, the second, the perimeter
#
prashker = np.ar... | python | def __calculate_perimeter_scoring():
"""Return a 512 element vector which gives the perimeter given surrounding pts
"""
#
# This is the array from the paper - a 256 - element array leaving out
# the center point. The first value is the index, the second, the perimeter
#
prashker = np.ar... | Return a 512 element vector which gives the perimeter given surrounding pts | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L2260-L2309 |
CellProfiler/centrosome | centrosome/cpmorphology.py | calculate_perimeters | def calculate_perimeters(labels, indexes):
"""Count the distances between adjacent pixels in the perimeters of the labels"""
#
# Create arrays that tell whether a pixel is like its neighbors.
# index = 0 is the pixel -1,-1 from the pixel of interest, 1 is -1,0, etc.
#
m = table_idx_from_labels(l... | python | def calculate_perimeters(labels, indexes):
"""Count the distances between adjacent pixels in the perimeters of the labels"""
#
# Create arrays that tell whether a pixel is like its neighbors.
# index = 0 is the pixel -1,-1 from the pixel of interest, 1 is -1,0, etc.
#
m = table_idx_from_labels(l... | Count the distances between adjacent pixels in the perimeters of the labels | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L2313-L2321 |
CellProfiler/centrosome | centrosome/cpmorphology.py | table_idx_from_labels | def table_idx_from_labels(labels):
'''Return an array of indexes into a morphology lookup table
labels - a labels matrix
returns a matrix of values between 0 and 511 of indices appropriate
for table_lookup where a pixel's index is determined based on whether
or not the pixel has the same label ... | python | def table_idx_from_labels(labels):
'''Return an array of indexes into a morphology lookup table
labels - a labels matrix
returns a matrix of values between 0 and 511 of indices appropriate
for table_lookup where a pixel's index is determined based on whether
or not the pixel has the same label ... | Return an array of indexes into a morphology lookup table
labels - a labels matrix
returns a matrix of values between 0 and 511 of indices appropriate
for table_lookup where a pixel's index is determined based on whether
or not the pixel has the same label as its neighbors (and is labeled) | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L2323-L2348 |
CellProfiler/centrosome | centrosome/cpmorphology.py | calculate_convex_hull_areas | def calculate_convex_hull_areas(labels,indexes=None):
"""Calulculate the area of the convex hull of each labeled object
labels - a label matrix
indexes - None: calculate convex hull area over entire image
number: calculate convex hull for a single label
sequence: calculate c... | python | def calculate_convex_hull_areas(labels,indexes=None):
"""Calulculate the area of the convex hull of each labeled object
labels - a label matrix
indexes - None: calculate convex hull area over entire image
number: calculate convex hull for a single label
sequence: calculate c... | Calulculate the area of the convex hull of each labeled object
labels - a label matrix
indexes - None: calculate convex hull area over entire image
number: calculate convex hull for a single label
sequence: calculate convex hull for labels matching a sequence
... | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L2350-L2464 |
CellProfiler/centrosome | centrosome/cpmorphology.py | calculate_solidity | def calculate_solidity(labels,indexes=None):
"""Calculate the area of each label divided by the area of its convex hull
labels - a label matrix
indexes - the indexes of the labels to measure
"""
if indexes is not None:
""" Convert to compat 32bit integer """
indexes = np.array(i... | python | def calculate_solidity(labels,indexes=None):
"""Calculate the area of each label divided by the area of its convex hull
labels - a label matrix
indexes - the indexes of the labels to measure
"""
if indexes is not None:
""" Convert to compat 32bit integer """
indexes = np.array(i... | Calculate the area of each label divided by the area of its convex hull
labels - a label matrix
indexes - the indexes of the labels to measure | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L2466-L2477 |
CellProfiler/centrosome | centrosome/cpmorphology.py | euler_number | def euler_number(labels, indexes=None):
"""Calculate the Euler number of each label
labels - a label matrix
indexes - the indexes of the labels to measure or None to
treat the labels matrix as a binary matrix
"""
if indexes is None:
labels = labels != 0
indexes = n... | python | def euler_number(labels, indexes=None):
"""Calculate the Euler number of each label
labels - a label matrix
indexes - the indexes of the labels to measure or None to
treat the labels matrix as a binary matrix
"""
if indexes is None:
labels = labels != 0
indexes = n... | Calculate the Euler number of each label
labels - a label matrix
indexes - the indexes of the labels to measure or None to
treat the labels matrix as a binary matrix | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L2479-L2592 |
CellProfiler/centrosome | centrosome/cpmorphology.py | block | def block(shape, block_shape):
"""Create a labels image that divides the image into blocks
shape - the shape of the image to be blocked
block_shape - the shape of one block
returns a labels matrix and the indexes of all labels generated
The idea here is to block-process an image by us... | python | def block(shape, block_shape):
"""Create a labels image that divides the image into blocks
shape - the shape of the image to be blocked
block_shape - the shape of one block
returns a labels matrix and the indexes of all labels generated
The idea here is to block-process an image by us... | Create a labels image that divides the image into blocks
shape - the shape of the image to be blocked
block_shape - the shape of one block
returns a labels matrix and the indexes of all labels generated
The idea here is to block-process an image by using SciPy label
routines. This rou... | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L2594-L2622 |
CellProfiler/centrosome | centrosome/cpmorphology.py | white_tophat | def white_tophat(image, radius=None, mask=None, footprint=None):
'''White tophat filter an image using a circular structuring element
image - image in question
radius - radius of the circular structuring element. If no radius, use
an 8-connected structuring element.
mask - mask of sig... | python | def white_tophat(image, radius=None, mask=None, footprint=None):
'''White tophat filter an image using a circular structuring element
image - image in question
radius - radius of the circular structuring element. If no radius, use
an 8-connected structuring element.
mask - mask of sig... | White tophat filter an image using a circular structuring element
image - image in question
radius - radius of the circular structuring element. If no radius, use
an 8-connected structuring element.
mask - mask of significant pixels in the image. Points outside of
the mask wil... | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L2624-L2643 |
CellProfiler/centrosome | centrosome/cpmorphology.py | black_tophat | def black_tophat(image, radius=None, mask=None, footprint=None):
'''Black tophat filter an image using a circular structuring element
image - image in question
radius - radius of the circular structuring element. If no radius, use
an 8-connected structuring element.
mask - mask of sig... | python | def black_tophat(image, radius=None, mask=None, footprint=None):
'''Black tophat filter an image using a circular structuring element
image - image in question
radius - radius of the circular structuring element. If no radius, use
an 8-connected structuring element.
mask - mask of sig... | Black tophat filter an image using a circular structuring element
image - image in question
radius - radius of the circular structuring element. If no radius, use
an 8-connected structuring element.
mask - mask of significant pixels in the image. Points outside of
the mask wil... | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L2645-L2664 |
CellProfiler/centrosome | centrosome/cpmorphology.py | grey_erosion | def grey_erosion(image, radius=None, mask=None, footprint=None):
'''Perform a grey erosion with masking'''
if footprint is None:
if radius is None:
footprint = np.ones((3,3),bool)
radius = 1
else:
footprint = strel_disk(radius)==1
else:
radius = ma... | python | def grey_erosion(image, radius=None, mask=None, footprint=None):
'''Perform a grey erosion with masking'''
if footprint is None:
if radius is None:
footprint = np.ones((3,3),bool)
radius = 1
else:
footprint = strel_disk(radius)==1
else:
radius = ma... | Perform a grey erosion with masking | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L2666-L2689 |
CellProfiler/centrosome | centrosome/cpmorphology.py | grey_reconstruction | def grey_reconstruction(image, mask, footprint=None, offset=None):
'''Perform a morphological reconstruction of the image
grey_dilate the image, constraining each pixel to have a value that is
at most that of the mask.
image - the seed image
mask - the mask, giving the maximum allowed value at ... | python | def grey_reconstruction(image, mask, footprint=None, offset=None):
'''Perform a morphological reconstruction of the image
grey_dilate the image, constraining each pixel to have a value that is
at most that of the mask.
image - the seed image
mask - the mask, giving the maximum allowed value at ... | Perform a morphological reconstruction of the image
grey_dilate the image, constraining each pixel to have a value that is
at most that of the mask.
image - the seed image
mask - the mask, giving the maximum allowed value at each point
footprint - a boolean array giving the neighborhood pixels ... | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L2719-L2836 |
CellProfiler/centrosome | centrosome/cpmorphology.py | opening | def opening(image, radius=None, mask=None, footprint=None):
'''Do a morphological opening
image - pixel image to operate on
radius - use a structuring element with the given radius. If no radius,
use an 8-connected structuring element.
mask - if present, only use unmasked pixels for op... | python | def opening(image, radius=None, mask=None, footprint=None):
'''Do a morphological opening
image - pixel image to operate on
radius - use a structuring element with the given radius. If no radius,
use an 8-connected structuring element.
mask - if present, only use unmasked pixels for op... | Do a morphological opening
image - pixel image to operate on
radius - use a structuring element with the given radius. If no radius,
use an 8-connected structuring element.
mask - if present, only use unmasked pixels for operations | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L2838-L2847 |
CellProfiler/centrosome | centrosome/cpmorphology.py | closing | def closing(image, radius=None, mask=None, footprint = None):
'''Do a morphological closing
image - pixel image to operate on
radius - use a structuring element with the given radius. If no structuring
element, use an 8-connected structuring element.
mask - if present, only use unmaske... | python | def closing(image, radius=None, mask=None, footprint = None):
'''Do a morphological closing
image - pixel image to operate on
radius - use a structuring element with the given radius. If no structuring
element, use an 8-connected structuring element.
mask - if present, only use unmaske... | Do a morphological closing
image - pixel image to operate on
radius - use a structuring element with the given radius. If no structuring
element, use an 8-connected structuring element.
mask - if present, only use unmasked pixels for operations | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L2849-L2858 |
CellProfiler/centrosome | centrosome/cpmorphology.py | openlines | def openlines(image, linelength=10, dAngle=10, mask=None):
"""
Do a morphological opening along lines of different angles.
Return difference between max and min response to different angles for each pixel.
This effectively removes dots and only keeps lines.
image - pixel image to operate on
le... | python | def openlines(image, linelength=10, dAngle=10, mask=None):
"""
Do a morphological opening along lines of different angles.
Return difference between max and min response to different angles for each pixel.
This effectively removes dots and only keeps lines.
image - pixel image to operate on
le... | Do a morphological opening along lines of different angles.
Return difference between max and min response to different angles for each pixel.
This effectively removes dots and only keeps lines.
image - pixel image to operate on
length - length of the structural element
angluar_resolution - angle ... | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L2860-L2881 |
CellProfiler/centrosome | centrosome/cpmorphology.py | table_lookup | def table_lookup(image, table, border_value, iterations = None):
'''Perform a morphological transform on an image, directed by its neighbors
image - a binary image
table - a 512-element table giving the transform of each pixel given
the values of that pixel and its 8-connected neighbors.
... | python | def table_lookup(image, table, border_value, iterations = None):
'''Perform a morphological transform on an image, directed by its neighbors
image - a binary image
table - a 512-element table giving the transform of each pixel given
the values of that pixel and its 8-connected neighbors.
... | Perform a morphological transform on an image, directed by its neighbors
image - a binary image
table - a 512-element table giving the transform of each pixel given
the values of that pixel and its 8-connected neighbors.
border_value - the value of pixels beyond the border of the image.
... | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L2883-L2960 |
CellProfiler/centrosome | centrosome/cpmorphology.py | pattern_of | def pattern_of(index):
'''Return the pattern represented by an index value'''
return np.array([[index & 2**0,index & 2**1,index & 2**2],
[index & 2**3,index & 2**4,index & 2**5],
[index & 2**6,index & 2**7,index & 2**8]], bool) | python | def pattern_of(index):
'''Return the pattern represented by an index value'''
return np.array([[index & 2**0,index & 2**1,index & 2**2],
[index & 2**3,index & 2**4,index & 2**5],
[index & 2**6,index & 2**7,index & 2**8]], bool) | Return the pattern represented by an index value | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L2962-L2966 |
CellProfiler/centrosome | centrosome/cpmorphology.py | index_of | def index_of(pattern):
'''Return the index of a given pattern'''
return (pattern[0,0] * 2**0 + pattern[0,1] * 2**1 + pattern[0,2] * 2**2 +
pattern[1,0] * 2**3 + pattern[1,1] * 2**4 + pattern[1,2] * 2**5 +
pattern[2,0] * 2**6 + pattern[2,1] * 2**7 + pattern[2,2] * 2**8) | python | def index_of(pattern):
'''Return the index of a given pattern'''
return (pattern[0,0] * 2**0 + pattern[0,1] * 2**1 + pattern[0,2] * 2**2 +
pattern[1,0] * 2**3 + pattern[1,1] * 2**4 + pattern[1,2] * 2**5 +
pattern[2,0] * 2**6 + pattern[2,1] * 2**7 + pattern[2,2] * 2**8) | Return the index of a given pattern | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L2968-L2972 |
CellProfiler/centrosome | centrosome/cpmorphology.py | make_table | def make_table(value, pattern, care=np.ones((3,3),bool)):
'''Return a table suitable for table_lookup
value - set all table entries matching "pattern" to "value", all others
to not "value"
pattern - a 3x3 boolean array with the pattern to match
care - a 3x3 boolean array where each v... | python | def make_table(value, pattern, care=np.ones((3,3),bool)):
'''Return a table suitable for table_lookup
value - set all table entries matching "pattern" to "value", all others
to not "value"
pattern - a 3x3 boolean array with the pattern to match
care - a 3x3 boolean array where each v... | Return a table suitable for table_lookup
value - set all table entries matching "pattern" to "value", all others
to not "value"
pattern - a 3x3 boolean array with the pattern to match
care - a 3x3 boolean array where each value is true if the pattern
must match at that posi... | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L2974-L2992 |
CellProfiler/centrosome | centrosome/cpmorphology.py | branchpoints | def branchpoints(image, mask=None):
'''Remove all pixels from an image except for branchpoints
image - a skeletonized image
mask - a mask of pixels excluded from consideration
1 0 1 ? 0 ?
0 1 0 -> 0 1 0
0 1 0 0 ? 0
'''
global branchpoints_table
if mask is None:
... | python | def branchpoints(image, mask=None):
'''Remove all pixels from an image except for branchpoints
image - a skeletonized image
mask - a mask of pixels excluded from consideration
1 0 1 ? 0 ?
0 1 0 -> 0 1 0
0 1 0 0 ? 0
'''
global branchpoints_table
if mask is None:
... | Remove all pixels from an image except for branchpoints
image - a skeletonized image
mask - a mask of pixels excluded from consideration
1 0 1 ? 0 ?
0 1 0 -> 0 1 0
0 1 0 0 ? 0 | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L3006-L3025 |
CellProfiler/centrosome | centrosome/cpmorphology.py | branchings | def branchings(image, mask=None):
'''Count the number of branches eminating from each pixel
image - a binary image
mask - optional mask of pixels not to consider
This is the count of the number of branches that
eminate from a pixel. A pixel with neighbors fore
and aft has branches fore and... | python | def branchings(image, mask=None):
'''Count the number of branches eminating from each pixel
image - a binary image
mask - optional mask of pixels not to consider
This is the count of the number of branches that
eminate from a pixel. A pixel with neighbors fore
and aft has branches fore and... | Count the number of branches eminating from each pixel
image - a binary image
mask - optional mask of pixels not to consider
This is the count of the number of branches that
eminate from a pixel. A pixel with neighbors fore
and aft has branches fore and aft = 2. An endpoint
has one branch.... | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L3043-L3074 |
CellProfiler/centrosome | centrosome/cpmorphology.py | bridge | def bridge(image, mask=None, iterations = 1):
'''Fill in pixels that bridge gaps.
1 0 0 1 0 0
0 0 0 -> 0 1 0
0 0 1 0 0 1
'''
global bridge_table
if mask is None:
masked_image = image
else:
masked_image = image.astype(bool).copy()
masked_image[~mask] = F... | python | def bridge(image, mask=None, iterations = 1):
'''Fill in pixels that bridge gaps.
1 0 0 1 0 0
0 0 0 -> 0 1 0
0 0 1 0 0 1
'''
global bridge_table
if mask is None:
masked_image = image
else:
masked_image = image.astype(bool).copy()
masked_image[~mask] = F... | Fill in pixels that bridge gaps.
1 0 0 1 0 0
0 0 0 -> 0 1 0
0 0 1 0 0 1 | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L3086-L3102 |
CellProfiler/centrosome | centrosome/cpmorphology.py | clean | def clean(image, mask=None, iterations = 1):
'''Remove isolated pixels
0 0 0 0 0 0
0 1 0 -> 0 0 0
0 0 0 0 0 0
Border pixels and pixels adjoining masks are removed unless one valid
neighbor is true.
'''
global clean_table
if mask is None:
masked_image = imag... | python | def clean(image, mask=None, iterations = 1):
'''Remove isolated pixels
0 0 0 0 0 0
0 1 0 -> 0 0 0
0 0 0 0 0 0
Border pixels and pixels adjoining masks are removed unless one valid
neighbor is true.
'''
global clean_table
if mask is None:
masked_image = imag... | Remove isolated pixels
0 0 0 0 0 0
0 1 0 -> 0 0 0
0 0 0 0 0 0
Border pixels and pixels adjoining masks are removed unless one valid
neighbor is true. | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L3109-L3128 |
CellProfiler/centrosome | centrosome/cpmorphology.py | diag | def diag(image, mask=None, iterations=1):
'''4-connect pixels that are 8-connected
0 0 0 0 0 ?
0 0 1 -> 0 1 1
0 1 0 ? 1 ?
'''
global diag_table
if mask is None:
masked_image = image
else:
masked_image = image.astype(bool).copy()
masked_image[~ma... | python | def diag(image, mask=None, iterations=1):
'''4-connect pixels that are 8-connected
0 0 0 0 0 ?
0 0 1 -> 0 1 1
0 1 0 ? 1 ?
'''
global diag_table
if mask is None:
masked_image = image
else:
masked_image = image.astype(bool).copy()
masked_image[~ma... | 4-connect pixels that are 8-connected
0 0 0 0 0 ?
0 0 1 -> 0 1 1
0 1 0 ? 1 ? | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L3159-L3176 |
CellProfiler/centrosome | centrosome/cpmorphology.py | endpoints | def endpoints(image, mask=None):
'''Remove all pixels from an image except for endpoints
image - a skeletonized image
mask - a mask of pixels excluded from consideration
1 0 0 ? 0 0
0 1 0 -> 0 1 0
0 0 0 0 0 0
'''
global endpoints_table
if mask is None:
masked... | python | def endpoints(image, mask=None):
'''Remove all pixels from an image except for endpoints
image - a skeletonized image
mask - a mask of pixels excluded from consideration
1 0 0 ? 0 0
0 1 0 -> 0 1 0
0 0 0 0 0 0
'''
global endpoints_table
if mask is None:
masked... | Remove all pixels from an image except for endpoints
image - a skeletonized image
mask - a mask of pixels excluded from consideration
1 0 0 ? 0 0
0 1 0 -> 0 1 0
0 0 0 0 0 0 | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L3185-L3204 |
CellProfiler/centrosome | centrosome/cpmorphology.py | fill | def fill(image, mask=None, iterations=1):
'''Fill isolated black pixels
1 1 1 1 1 1
1 0 1 -> 1 1 1
1 1 1 1 1 1
'''
global fill_table
if mask is None:
masked_image = image
else:
masked_image = image.astype(bool).copy()
masked_image[~mask] = True
r... | python | def fill(image, mask=None, iterations=1):
'''Fill isolated black pixels
1 1 1 1 1 1
1 0 1 -> 1 1 1
1 1 1 1 1 1
'''
global fill_table
if mask is None:
masked_image = image
else:
masked_image = image.astype(bool).copy()
masked_image[~mask] = True
r... | Fill isolated black pixels
1 1 1 1 1 1
1 0 1 -> 1 1 1
1 1 1 1 1 1 | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L3211-L3227 |
CellProfiler/centrosome | centrosome/cpmorphology.py | fill4 | def fill4(image, mask=None, iterations=1):
'''Fill 4-connected black pixels
x 1 x x 1 x
1 0 1 -> 1 1 1
x 1 x x 1 x
'''
global fill4_table
if mask is None:
masked_image = image
else:
masked_image = image.astype(bool).copy()
masked_image[~mask] = True
... | python | def fill4(image, mask=None, iterations=1):
'''Fill 4-connected black pixels
x 1 x x 1 x
1 0 1 -> 1 1 1
x 1 x x 1 x
'''
global fill4_table
if mask is None:
masked_image = image
else:
masked_image = image.astype(bool).copy()
masked_image[~mask] = True
... | Fill 4-connected black pixels
x 1 x x 1 x
1 0 1 -> 1 1 1
x 1 x x 1 x | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L3236-L3252 |
CellProfiler/centrosome | centrosome/cpmorphology.py | hbreak | def hbreak(image, mask=None, iterations=1):
'''Remove horizontal breaks
1 1 1 1 1 1
0 1 0 -> 0 0 0 (this case only)
1 1 1 1 1 1
'''
global hbreak_table
if mask is None:
masked_image = image
else:
masked_image = image.astype(bool).copy()
masked_image[... | python | def hbreak(image, mask=None, iterations=1):
'''Remove horizontal breaks
1 1 1 1 1 1
0 1 0 -> 0 0 0 (this case only)
1 1 1 1 1 1
'''
global hbreak_table
if mask is None:
masked_image = image
else:
masked_image = image.astype(bool).copy()
masked_image[... | Remove horizontal breaks
1 1 1 1 1 1
0 1 0 -> 0 0 0 (this case only)
1 1 1 1 1 1 | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L3260-L3276 |
CellProfiler/centrosome | centrosome/cpmorphology.py | vbreak | def vbreak(image, mask=None, iterations=1):
'''Remove horizontal breaks
1 1 1 1 1 1
0 1 0 -> 0 0 0 (this case only)
1 1 1 1 1 1
'''
global vbreak_table
if mask is None:
masked_image = image
else:
masked_image = image.astype(bool).copy()
masked_image[... | python | def vbreak(image, mask=None, iterations=1):
'''Remove horizontal breaks
1 1 1 1 1 1
0 1 0 -> 0 0 0 (this case only)
1 1 1 1 1 1
'''
global vbreak_table
if mask is None:
masked_image = image
else:
masked_image = image.astype(bool).copy()
masked_image[... | Remove horizontal breaks
1 1 1 1 1 1
0 1 0 -> 0 0 0 (this case only)
1 1 1 1 1 1 | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L3284-L3300 |
CellProfiler/centrosome | centrosome/cpmorphology.py | majority | def majority(image, mask=None, iterations=1):
'''A pixel takes the value of the majority of its neighbors
'''
global majority_table
if mask is None:
masked_image = image
else:
masked_image = image.astype(bool).copy()
masked_image[~mask] = False
result = table_lookup(... | python | def majority(image, mask=None, iterations=1):
'''A pixel takes the value of the majority of its neighbors
'''
global majority_table
if mask is None:
masked_image = image
else:
masked_image = image.astype(bool).copy()
masked_image[~mask] = False
result = table_lookup(... | A pixel takes the value of the majority of its neighbors | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L3312-L3325 |
CellProfiler/centrosome | centrosome/cpmorphology.py | remove | def remove(image, mask=None, iterations=1):
'''Turn 1 pixels to 0 if their 4-connected neighbors are all 0
? 1 ? ? 1 ?
1 1 1 -> 1 0 1
? 1 ? ? 1 ?
'''
global remove_table
if mask is None:
masked_image = image
else:
masked_image = image.astype(bool).copy()
... | python | def remove(image, mask=None, iterations=1):
'''Turn 1 pixels to 0 if their 4-connected neighbors are all 0
? 1 ? ? 1 ?
1 1 1 -> 1 0 1
? 1 ? ? 1 ?
'''
global remove_table
if mask is None:
masked_image = image
else:
masked_image = image.astype(bool).copy()
... | Turn 1 pixels to 0 if their 4-connected neighbors are all 0
? 1 ? ? 1 ?
1 1 1 -> 1 0 1
? 1 ? ? 1 ? | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L3340-L3356 |
CellProfiler/centrosome | centrosome/cpmorphology.py | spur | def spur(image, mask=None, iterations=1):
'''Remove spur pixels from an image
0 0 0 0 0 0
0 1 0 -> 0 0 0
0 0 1 0 0 ?
'''
global spur_table_1,spur_table_2
if mask is None:
masked_image = image
else:
masked_image = image.astype(bool).copy()
masked_image[~... | python | def spur(image, mask=None, iterations=1):
'''Remove spur pixels from an image
0 0 0 0 0 0
0 1 0 -> 0 0 0
0 0 1 0 0 ?
'''
global spur_table_1,spur_table_2
if mask is None:
masked_image = image
else:
masked_image = image.astype(bool).copy()
masked_image[~... | Remove spur pixels from an image
0 0 0 0 0 0
0 1 0 -> 0 0 0
0 0 1 0 0 ? | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L3378-L3402 |
CellProfiler/centrosome | centrosome/cpmorphology.py | thicken | def thicken(image, mask=None, iterations=1):
'''Thicken the objects in an image where doing so does not connect them
0 0 0 ? ? ?
0 0 0 -> ? 1 ?
0 0 1 ? ? ?
1 0 0 ? ? ?
0 0 0 -> ? 0 ?
0 0 1 ? ? ?
'''
global thicken_table
if mask is None:
masked_image ... | python | def thicken(image, mask=None, iterations=1):
'''Thicken the objects in an image where doing so does not connect them
0 0 0 ? ? ?
0 0 0 -> ? 1 ?
0 0 1 ? ? ?
1 0 0 ? ? ?
0 0 0 -> ? 0 ?
0 0 1 ? ? ?
'''
global thicken_table
if mask is None:
masked_image ... | Thicken the objects in an image where doing so does not connect them
0 0 0 ? ? ?
0 0 0 -> ? 1 ?
0 0 1 ? ? ?
1 0 0 ? ? ?
0 0 0 -> ? 0 ?
0 0 1 ? ? ? | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L3412-L3432 |
CellProfiler/centrosome | centrosome/cpmorphology.py | thin | def thin(image, mask=None, iterations=1):
'''Thin an image to lines, preserving Euler number
Implements thinning as described in algorithm # 1 from
Guo, "Parallel Thinning with Two Subiteration Algorithms",
Communications of the ACM, Vol 32 #3 page 359.
'''
global thin_table, eight_connect
... | python | def thin(image, mask=None, iterations=1):
'''Thin an image to lines, preserving Euler number
Implements thinning as described in algorithm # 1 from
Guo, "Parallel Thinning with Two Subiteration Algorithms",
Communications of the ACM, Vol 32 #3 page 359.
'''
global thin_table, eight_connect
... | Thin an image to lines, preserving Euler number
Implements thinning as described in algorithm # 1 from
Guo, "Parallel Thinning with Two Subiteration Algorithms",
Communications of the ACM, Vol 32 #3 page 359. | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/cpmorphology.py#L3456-L3505 |
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