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 |
|---|---|---|---|---|---|---|---|
sunt05/SuPy | src/supy/supy_save.py | save_df_state | def save_df_state(
df_state: pd.DataFrame,
site: str = '',
path_dir_save: Path = Path('.'),)->Path:
'''save `df_state` to a csv file
Parameters
----------
df_state : pd.DataFrame
a dataframe of model states produced by a supy run
site : str, optional
site ide... | python | def save_df_state(
df_state: pd.DataFrame,
site: str = '',
path_dir_save: Path = Path('.'),)->Path:
'''save `df_state` to a csv file
Parameters
----------
df_state : pd.DataFrame
a dataframe of model states produced by a supy run
site : str, optional
site ide... | save `df_state` to a csv file
Parameters
----------
df_state : pd.DataFrame
a dataframe of model states produced by a supy run
site : str, optional
site identifier (the default is '', which indicates an empty site code)
path_dir_save : Path, optional
path to directory to sav... | https://github.com/sunt05/SuPy/blob/47178bd5aee50a059414e3e504940662fbfae0dc/src/supy/supy_save.py#L194-L221 |
sunt05/SuPy | src/supy/supy_save.py | get_save_info | def get_save_info(path_runcontrol: str)->Tuple[int, Path, str]:
'''get necessary information for saving supy results, which are (freq_s, dir_save, site)
Parameters
----------
path_runcontrol : Path
Path to SUEWS :ref:`RunControl.nml <suews:RunControl.nml>`
Returns
-------
tuple
... | python | def get_save_info(path_runcontrol: str)->Tuple[int, Path, str]:
'''get necessary information for saving supy results, which are (freq_s, dir_save, site)
Parameters
----------
path_runcontrol : Path
Path to SUEWS :ref:`RunControl.nml <suews:RunControl.nml>`
Returns
-------
tuple
... | get necessary information for saving supy results, which are (freq_s, dir_save, site)
Parameters
----------
path_runcontrol : Path
Path to SUEWS :ref:`RunControl.nml <suews:RunControl.nml>`
Returns
-------
tuple
A tuple including (freq_s, dir_save, site):
freq_s: output... | https://github.com/sunt05/SuPy/blob/47178bd5aee50a059414e3e504940662fbfae0dc/src/supy/supy_save.py#L226-L260 |
sunt05/SuPy | src/supy/supy_util.py | gen_FS_DF | def gen_FS_DF(df_output):
"""generate DataFrame of scores.
Parameters
----------
df_WS_data : type
Description of parameter `df_WS_data`.
Returns
-------
type
Description of returned object.
"""
df_day = pd.pivot_table(
df_output,
values=['T2', 'U10... | python | def gen_FS_DF(df_output):
"""generate DataFrame of scores.
Parameters
----------
df_WS_data : type
Description of parameter `df_WS_data`.
Returns
-------
type
Description of returned object.
"""
df_day = pd.pivot_table(
df_output,
values=['T2', 'U10... | generate DataFrame of scores.
Parameters
----------
df_WS_data : type
Description of parameter `df_WS_data`.
Returns
-------
type
Description of returned object. | https://github.com/sunt05/SuPy/blob/47178bd5aee50a059414e3e504940662fbfae0dc/src/supy/supy_util.py#L140-L174 |
sunt05/SuPy | src/supy/supy_util.py | gen_WS_DF | def gen_WS_DF(df_WS_data):
"""generate DataFrame of weighted sums.
Parameters
----------
df_WS_data : type
Description of parameter `df_WS_data`.
Returns
-------
type
Description of returned object.
"""
df_fs = gen_FS_DF(df_WS_data)
list_index = [('mean', 'T2'... | python | def gen_WS_DF(df_WS_data):
"""generate DataFrame of weighted sums.
Parameters
----------
df_WS_data : type
Description of parameter `df_WS_data`.
Returns
-------
type
Description of returned object.
"""
df_fs = gen_FS_DF(df_WS_data)
list_index = [('mean', 'T2'... | generate DataFrame of weighted sums.
Parameters
----------
df_WS_data : type
Description of parameter `df_WS_data`.
Returns
-------
type
Description of returned object. | https://github.com/sunt05/SuPy/blob/47178bd5aee50a059414e3e504940662fbfae0dc/src/supy/supy_util.py#L177-L208 |
sunt05/SuPy | src/supy/supy_util.py | gen_TMY | def gen_TMY(df_output):
'''generate TMY (typical meteorological year) from SuPy output.
Parameters
----------
df_output : pandas.DataFrame
Output from `run_supy`: longterm (e.g., >10 years) simulation results, otherwise not very useful.
'''
# calculate weighted score
ws = gen_WS_D... | python | def gen_TMY(df_output):
'''generate TMY (typical meteorological year) from SuPy output.
Parameters
----------
df_output : pandas.DataFrame
Output from `run_supy`: longterm (e.g., >10 years) simulation results, otherwise not very useful.
'''
# calculate weighted score
ws = gen_WS_D... | generate TMY (typical meteorological year) from SuPy output.
Parameters
----------
df_output : pandas.DataFrame
Output from `run_supy`: longterm (e.g., >10 years) simulation results, otherwise not very useful. | https://github.com/sunt05/SuPy/blob/47178bd5aee50a059414e3e504940662fbfae0dc/src/supy/supy_util.py#L327-L354 |
sunt05/SuPy | src/supy/supy_util.py | _geoid_radius | def _geoid_radius(latitude: float) -> float:
"""Calculates the GEOID radius at a given latitude
Parameters
----------
latitude : float
Latitude (degrees)
Returns
-------
R : float
GEOID Radius (meters)
"""
lat = deg2rad(latitude)
return sqrt(1/(cos(lat) ** 2 / R... | python | def _geoid_radius(latitude: float) -> float:
"""Calculates the GEOID radius at a given latitude
Parameters
----------
latitude : float
Latitude (degrees)
Returns
-------
R : float
GEOID Radius (meters)
"""
lat = deg2rad(latitude)
return sqrt(1/(cos(lat) ** 2 / R... | Calculates the GEOID radius at a given latitude
Parameters
----------
latitude : float
Latitude (degrees)
Returns
-------
R : float
GEOID Radius (meters) | https://github.com/sunt05/SuPy/blob/47178bd5aee50a059414e3e504940662fbfae0dc/src/supy/supy_util.py#L518-L532 |
sunt05/SuPy | src/supy/supy_util.py | geometric2geopotential | def geometric2geopotential(z: float, latitude: float) -> float:
"""Converts geometric height to geopoential height
Parameters
----------
z : float
Geometric height (meters)
latitude : float
Latitude (degrees)
Returns
-------
h : float
Geopotential Height (meters... | python | def geometric2geopotential(z: float, latitude: float) -> float:
"""Converts geometric height to geopoential height
Parameters
----------
z : float
Geometric height (meters)
latitude : float
Latitude (degrees)
Returns
-------
h : float
Geopotential Height (meters... | Converts geometric height to geopoential height
Parameters
----------
z : float
Geometric height (meters)
latitude : float
Latitude (degrees)
Returns
-------
h : float
Geopotential Height (meters) above the reference ellipsoid | https://github.com/sunt05/SuPy/blob/47178bd5aee50a059414e3e504940662fbfae0dc/src/supy/supy_util.py#L535-L553 |
sunt05/SuPy | src/supy/supy_util.py | geopotential2geometric | def geopotential2geometric(h: float, latitude: float) -> float:
"""Converts geopoential height to geometric height
Parameters
----------
h : float
Geopotential height (meters)
latitude : float
Latitude (degrees)
Returns
-------
z : float
Geometric Height (meters... | python | def geopotential2geometric(h: float, latitude: float) -> float:
"""Converts geopoential height to geometric height
Parameters
----------
h : float
Geopotential height (meters)
latitude : float
Latitude (degrees)
Returns
-------
z : float
Geometric Height (meters... | Converts geopoential height to geometric height
Parameters
----------
h : float
Geopotential height (meters)
latitude : float
Latitude (degrees)
Returns
-------
z : float
Geometric Height (meters) above the reference ellipsoid | https://github.com/sunt05/SuPy/blob/47178bd5aee50a059414e3e504940662fbfae0dc/src/supy/supy_util.py#L556-L574 |
sunt05/SuPy | src/supy/supy_util.py | get_ser_val_alt | def get_ser_val_alt(lat: float, lon: float,
da_alt_x: xr.DataArray,
da_alt: xr.DataArray, da_val: xr.DataArray)->pd.Series:
'''interpolate atmospheric variable to a specified altitude
Parameters
----------
lat : float
latitude of specified site
lon : ... | python | def get_ser_val_alt(lat: float, lon: float,
da_alt_x: xr.DataArray,
da_alt: xr.DataArray, da_val: xr.DataArray)->pd.Series:
'''interpolate atmospheric variable to a specified altitude
Parameters
----------
lat : float
latitude of specified site
lon : ... | interpolate atmospheric variable to a specified altitude
Parameters
----------
lat : float
latitude of specified site
lon : float
longitude of specified site
da_alt_x : xr.DataArray
desired altitude to interpolate variable at
da_alt : xr.DataArray
altitude associ... | https://github.com/sunt05/SuPy/blob/47178bd5aee50a059414e3e504940662fbfae0dc/src/supy/supy_util.py#L578-L617 |
sunt05/SuPy | src/supy/supy_util.py | get_df_val_alt | def get_df_val_alt(lat: float, lon: float, da_alt_meas: xr.DataArray, ds_val: xr.Dataset):
'''interpolate atmospheric variables to a specified altitude
Parameters
----------
lat : float
latitude of specified site
lon : float
longitude of specified site
da_alt_x : xr.DataArray
... | python | def get_df_val_alt(lat: float, lon: float, da_alt_meas: xr.DataArray, ds_val: xr.Dataset):
'''interpolate atmospheric variables to a specified altitude
Parameters
----------
lat : float
latitude of specified site
lon : float
longitude of specified site
da_alt_x : xr.DataArray
... | interpolate atmospheric variables to a specified altitude
Parameters
----------
lat : float
latitude of specified site
lon : float
longitude of specified site
da_alt_x : xr.DataArray
desired altitude to interpolate variable at
da_alt : xr.DataArray
altitude assoc... | https://github.com/sunt05/SuPy/blob/47178bd5aee50a059414e3e504940662fbfae0dc/src/supy/supy_util.py#L620-L661 |
sunt05/SuPy | src/supy/supy_util.py | gen_req_sfc | def gen_req_sfc(lat_x, lon_x, start, end, grid=[0.125, 0.125], scale=0):
'''generate a dict of reqs kwargs for (lat_x,lon_x) spanning [start, end]
Parameters
----------
lat_x : [type]
[description]
lon_x : [type]
[description]
start : [type]
[description]
end : [type... | python | def gen_req_sfc(lat_x, lon_x, start, end, grid=[0.125, 0.125], scale=0):
'''generate a dict of reqs kwargs for (lat_x,lon_x) spanning [start, end]
Parameters
----------
lat_x : [type]
[description]
lon_x : [type]
[description]
start : [type]
[description]
end : [type... | generate a dict of reqs kwargs for (lat_x,lon_x) spanning [start, end]
Parameters
----------
lat_x : [type]
[description]
lon_x : [type]
[description]
start : [type]
[description]
end : [type]
[description]
grid : list, optional
[description] (the def... | https://github.com/sunt05/SuPy/blob/47178bd5aee50a059414e3e504940662fbfae0dc/src/supy/supy_util.py#L756-L808 |
sunt05/SuPy | src/supy/supy_util.py | sel_list_pres | def sel_list_pres(ds_sfc_x):
'''
select proper levels for model level data download
'''
p_min, p_max = ds_sfc_x.sp.min().values, ds_sfc_x.sp.max().values
list_pres_level = [
'1', '2', '3',
'5', '7', '10',
'20', '30', '50',
'70', '100', '125',
'150', '175', '20... | python | def sel_list_pres(ds_sfc_x):
'''
select proper levels for model level data download
'''
p_min, p_max = ds_sfc_x.sp.min().values, ds_sfc_x.sp.max().values
list_pres_level = [
'1', '2', '3',
'5', '7', '10',
'20', '30', '50',
'70', '100', '125',
'150', '175', '20... | select proper levels for model level data download | https://github.com/sunt05/SuPy/blob/47178bd5aee50a059414e3e504940662fbfae0dc/src/supy/supy_util.py#L811-L838 |
ecell/ecell4 | ecell4/util/simulation.py | load_world | def load_world(filename):
"""
Load a world from the given HDF5 filename.
The return type is determined by ``ecell4_base.core.load_version_information``.
Parameters
----------
filename : str
A HDF5 filename.
Returns
-------
w : World
Return one from ``BDWorld``, ``EG... | python | def load_world(filename):
"""
Load a world from the given HDF5 filename.
The return type is determined by ``ecell4_base.core.load_version_information``.
Parameters
----------
filename : str
A HDF5 filename.
Returns
-------
w : World
Return one from ``BDWorld``, ``EG... | Load a world from the given HDF5 filename.
The return type is determined by ``ecell4_base.core.load_version_information``.
Parameters
----------
filename : str
A HDF5 filename.
Returns
-------
w : World
Return one from ``BDWorld``, ``EGFRDWorld``, ``MesoscopicWorld``,
... | https://github.com/ecell/ecell4/blob/a4a1229661c39b2059adbbacae9090e5ba664e01/ecell4/util/simulation.py#L10-L44 |
ecell/ecell4 | ecell4/util/simulation.py | run_simulation | def run_simulation(
t, y0=None, volume=1.0, model=None, solver='ode',
is_netfree=False, species_list=None, without_reset=False,
return_type='matplotlib', opt_args=(), opt_kwargs=None,
structures=None, observers=(), progressbar=0, rndseed=None,
factory=None, ## deprecated
... | python | def run_simulation(
t, y0=None, volume=1.0, model=None, solver='ode',
is_netfree=False, species_list=None, without_reset=False,
return_type='matplotlib', opt_args=(), opt_kwargs=None,
structures=None, observers=(), progressbar=0, rndseed=None,
factory=None, ## deprecated
... | Run a simulation with the given model and plot the result on IPython
notebook with matplotlib.
Parameters
----------
t : array or Real
A sequence of time points for which to solve for 'm'.
y0 : dict
Initial condition.
volume : Real or Real3, optional
A size of the simula... | https://github.com/ecell/ecell4/blob/a4a1229661c39b2059adbbacae9090e5ba664e01/ecell4/util/simulation.py#L96-L318 |
ecell/ecell4 | ecell4/util/simulation.py | number_observer | def number_observer(t=None, targets=None):
"""
Return a number observer. If t is None, return NumberObserver. If t is a number,
return FixedIntervalNumberObserver. If t is an iterable (a list of numbers), return
TimingNumberObserver.
Parameters
----------
t : float, list or tuple, optional.... | python | def number_observer(t=None, targets=None):
"""
Return a number observer. If t is None, return NumberObserver. If t is a number,
return FixedIntervalNumberObserver. If t is an iterable (a list of numbers), return
TimingNumberObserver.
Parameters
----------
t : float, list or tuple, optional.... | Return a number observer. If t is None, return NumberObserver. If t is a number,
return FixedIntervalNumberObserver. If t is an iterable (a list of numbers), return
TimingNumberObserver.
Parameters
----------
t : float, list or tuple, optional. default None
A timing of the observation. See ... | https://github.com/ecell/ecell4/blob/a4a1229661c39b2059adbbacae9090e5ba664e01/ecell4/util/simulation.py#L320-L349 |
ecell/ecell4 | ecell4/util/show.py | show | def show(target, *args, **kwargs):
"""
An utility function to display the given target object in the proper way.
Paramters
---------
target : NumberObserver, TrajectoryObserver, World, str
When a NumberObserver object is given, show it with viz.plot_number_observer.
When a Trajector... | python | def show(target, *args, **kwargs):
"""
An utility function to display the given target object in the proper way.
Paramters
---------
target : NumberObserver, TrajectoryObserver, World, str
When a NumberObserver object is given, show it with viz.plot_number_observer.
When a Trajector... | An utility function to display the given target object in the proper way.
Paramters
---------
target : NumberObserver, TrajectoryObserver, World, str
When a NumberObserver object is given, show it with viz.plot_number_observer.
When a TrajectoryObserver object is given, show it with viz.plo... | https://github.com/ecell/ecell4/blob/a4a1229661c39b2059adbbacae9090e5ba664e01/ecell4/util/show.py#L15-L43 |
ecell/ecell4 | ecell4/util/progressbar.py | ProgressBarSimulatorWrapper.run | def run(self, duration, obs):
"""Run the simulation.
Parameters
----------
duration : Real
a duration for running a simulation.
A simulation is expected to be stopped at t() + duration.
observers : list of Obeservers, optional
observers
... | python | def run(self, duration, obs):
"""Run the simulation.
Parameters
----------
duration : Real
a duration for running a simulation.
A simulation is expected to be stopped at t() + duration.
observers : list of Obeservers, optional
observers
... | Run the simulation.
Parameters
----------
duration : Real
a duration for running a simulation.
A simulation is expected to be stopped at t() + duration.
observers : list of Obeservers, optional
observers | https://github.com/ecell/ecell4/blob/a4a1229661c39b2059adbbacae9090e5ba664e01/ecell4/util/progressbar.py#L140-L169 |
ecell/ecell4 | ecell4/util/progressbar.py | ProgressBarNotebook.run | def run(self, duration, obs=None):
"""Run the simulation.
Parameters
----------
duration : Real
a duration for running a simulation.
A simulation is expected to be stopped at t() + duration.
obs : list of Obeservers, optional
observers
... | python | def run(self, duration, obs=None):
"""Run the simulation.
Parameters
----------
duration : Real
a duration for running a simulation.
A simulation is expected to be stopped at t() + duration.
obs : list of Obeservers, optional
observers
... | Run the simulation.
Parameters
----------
duration : Real
a duration for running a simulation.
A simulation is expected to be stopped at t() + duration.
obs : list of Obeservers, optional
observers | https://github.com/ecell/ecell4/blob/a4a1229661c39b2059adbbacae9090e5ba664e01/ecell4/util/progressbar.py#L236-L276 |
ecell/ecell4 | ecell4/extra/azure_batch.py | print_batch_exception | def print_batch_exception(batch_exception):
"""Prints the contents of the specified Batch exception.
:param batch_exception:
"""
_log.error('-------------------------------------------')
_log.error('Exception encountered:')
if batch_exception.error and \
batch_exception.error.messag... | python | def print_batch_exception(batch_exception):
"""Prints the contents of the specified Batch exception.
:param batch_exception:
"""
_log.error('-------------------------------------------')
_log.error('Exception encountered:')
if batch_exception.error and \
batch_exception.error.messag... | Prints the contents of the specified Batch exception.
:param batch_exception: | https://github.com/ecell/ecell4/blob/a4a1229661c39b2059adbbacae9090e5ba664e01/ecell4/extra/azure_batch.py#L45-L60 |
ecell/ecell4 | ecell4/extra/azure_batch.py | upload_file_to_container | def upload_file_to_container(block_blob_client, container_name, file_path):
"""Uploads a local file to an Azure Blob storage container.
:param block_blob_client: A blob service client.
:type block_blob_client: `azure.storage.blob.BlockBlobService`
:param str container_name: The name of the Azure Blob s... | python | def upload_file_to_container(block_blob_client, container_name, file_path):
"""Uploads a local file to an Azure Blob storage container.
:param block_blob_client: A blob service client.
:type block_blob_client: `azure.storage.blob.BlockBlobService`
:param str container_name: The name of the Azure Blob s... | Uploads a local file to an Azure Blob storage container.
:param block_blob_client: A blob service client.
:type block_blob_client: `azure.storage.blob.BlockBlobService`
:param str container_name: The name of the Azure Blob storage container.
:param str file_path: The local path to the file.
:rtype:... | https://github.com/ecell/ecell4/blob/a4a1229661c39b2059adbbacae9090e5ba664e01/ecell4/extra/azure_batch.py#L62-L91 |
ecell/ecell4 | ecell4/extra/azure_batch.py | get_container_sas_token | def get_container_sas_token(block_blob_client,
container_name, blob_permissions):
"""Obtains a shared access signature granting the specified permissions to the
container.
:param block_blob_client: A blob service client.
:type block_blob_client: `azure.storage.blob.BlockBlob... | python | def get_container_sas_token(block_blob_client,
container_name, blob_permissions):
"""Obtains a shared access signature granting the specified permissions to the
container.
:param block_blob_client: A blob service client.
:type block_blob_client: `azure.storage.blob.BlockBlob... | Obtains a shared access signature granting the specified permissions to the
container.
:param block_blob_client: A blob service client.
:type block_blob_client: `azure.storage.blob.BlockBlobService`
:param str container_name: The name of the Azure Blob storage container.
:param BlobPermissions blob... | https://github.com/ecell/ecell4/blob/a4a1229661c39b2059adbbacae9090e5ba664e01/ecell4/extra/azure_batch.py#L93-L114 |
ecell/ecell4 | ecell4/extra/azure_batch.py | wrap_commands_in_shell | def wrap_commands_in_shell(ostype, commands):
"""Wrap commands in a shell
Originally in azure-batch-samples.Python.Batch.common.helpers
:param list commands: list of commands to wrap
:param str ostype: OS type, linux or windows
:rtype: str
:return: a shell wrapping commands
"""
if ostyp... | python | def wrap_commands_in_shell(ostype, commands):
"""Wrap commands in a shell
Originally in azure-batch-samples.Python.Batch.common.helpers
:param list commands: list of commands to wrap
:param str ostype: OS type, linux or windows
:rtype: str
:return: a shell wrapping commands
"""
if ostyp... | Wrap commands in a shell
Originally in azure-batch-samples.Python.Batch.common.helpers
:param list commands: list of commands to wrap
:param str ostype: OS type, linux or windows
:rtype: str
:return: a shell wrapping commands | https://github.com/ecell/ecell4/blob/a4a1229661c39b2059adbbacae9090e5ba664e01/ecell4/extra/azure_batch.py#L144-L159 |
ecell/ecell4 | ecell4/extra/azure_batch.py | create_pool | def create_pool(batch_service_client, pool_id,
resource_files, publisher, offer, sku,
task_file, vm_size, node_count):
"""Creates a pool of compute nodes with the specified OS settings.
:param batch_service_client: A Batch service client.
:type batch_service_client: `azure.b... | python | def create_pool(batch_service_client, pool_id,
resource_files, publisher, offer, sku,
task_file, vm_size, node_count):
"""Creates a pool of compute nodes with the specified OS settings.
:param batch_service_client: A Batch service client.
:type batch_service_client: `azure.b... | Creates a pool of compute nodes with the specified OS settings.
:param batch_service_client: A Batch service client.
:type batch_service_client: `azure.batch.BatchServiceClient`
:param str pool_id: An ID for the new pool.
:param list resource_files: A collection of resource files for the pool's
sta... | https://github.com/ecell/ecell4/blob/a4a1229661c39b2059adbbacae9090e5ba664e01/ecell4/extra/azure_batch.py#L161-L232 |
ecell/ecell4 | ecell4/extra/azure_batch.py | create_job | def create_job(batch_service_client, job_id, pool_id):
"""Creates a job with the specified ID, associated with the specified pool.
:param batch_service_client: A Batch service client.
:type batch_service_client: `azure.batch.BatchServiceClient`
:param str job_id: The ID for the job.
:param str pool... | python | def create_job(batch_service_client, job_id, pool_id):
"""Creates a job with the specified ID, associated with the specified pool.
:param batch_service_client: A Batch service client.
:type batch_service_client: `azure.batch.BatchServiceClient`
:param str job_id: The ID for the job.
:param str pool... | Creates a job with the specified ID, associated with the specified pool.
:param batch_service_client: A Batch service client.
:type batch_service_client: `azure.batch.BatchServiceClient`
:param str job_id: The ID for the job.
:param str pool_id: The ID for the pool. | https://github.com/ecell/ecell4/blob/a4a1229661c39b2059adbbacae9090e5ba664e01/ecell4/extra/azure_batch.py#L234-L252 |
ecell/ecell4 | ecell4/extra/azure_batch.py | add_tasks | def add_tasks(batch_service_client, job_id, loads,
output_container_name, output_container_sas_token,
task_file, acount_name):
"""Adds a task for each input file in the collection to the specified job.
:param batch_service_client: A Batch service client.
:type batch_service_clie... | python | def add_tasks(batch_service_client, job_id, loads,
output_container_name, output_container_sas_token,
task_file, acount_name):
"""Adds a task for each input file in the collection to the specified job.
:param batch_service_client: A Batch service client.
:type batch_service_clie... | Adds a task for each input file in the collection to the specified job.
:param batch_service_client: A Batch service client.
:type batch_service_client: `azure.batch.BatchServiceClient`
:param str job_id: The ID of the job to which to add the tasks.
:param list input_files: A collection of input files.... | https://github.com/ecell/ecell4/blob/a4a1229661c39b2059adbbacae9090e5ba664e01/ecell4/extra/azure_batch.py#L254-L302 |
ecell/ecell4 | ecell4/extra/azure_batch.py | wait_for_tasks_to_complete | def wait_for_tasks_to_complete(batch_service_client, job_ids, timeout):
"""Returns when all tasks in the specified job reach the Completed state.
:param batch_service_client: A Batch service client.
:type batch_service_client: `azure.batch.BatchServiceClient`
:param str job_id: The id of the job whose ... | python | def wait_for_tasks_to_complete(batch_service_client, job_ids, timeout):
"""Returns when all tasks in the specified job reach the Completed state.
:param batch_service_client: A Batch service client.
:type batch_service_client: `azure.batch.BatchServiceClient`
:param str job_id: The id of the job whose ... | Returns when all tasks in the specified job reach the Completed state.
:param batch_service_client: A Batch service client.
:type batch_service_client: `azure.batch.BatchServiceClient`
:param str job_id: The id of the job whose tasks should be to monitored.
:param timedelta timeout: The duration to wai... | https://github.com/ecell/ecell4/blob/a4a1229661c39b2059adbbacae9090e5ba664e01/ecell4/extra/azure_batch.py#L304-L337 |
ecell/ecell4 | ecell4/extra/azure_batch.py | download_blobs_from_container | def download_blobs_from_container(block_blob_client,
container_name, directory_path,
prefix=None):
"""Downloads all blobs from the specified Azure Blob storage container.
:param block_blob_client: A blob service client.
:type block_blob_cl... | python | def download_blobs_from_container(block_blob_client,
container_name, directory_path,
prefix=None):
"""Downloads all blobs from the specified Azure Blob storage container.
:param block_blob_client: A blob service client.
:type block_blob_cl... | Downloads all blobs from the specified Azure Blob storage container.
:param block_blob_client: A blob service client.
:type block_blob_client: `azure.storage.blob.BlockBlobService`
:param container_name: The Azure Blob storage container from which to
download files.
:param directory_path: The loca... | https://github.com/ecell/ecell4/blob/a4a1229661c39b2059adbbacae9090e5ba664e01/ecell4/extra/azure_batch.py#L339-L368 |
ecell/ecell4 | ecell4/extra/azure_batch.py | _read_stream_as_string | def _read_stream_as_string(stream, encoding):
"""Read stream as string
Originally in azure-batch-samples.Python.Batch.common.helpers
:param stream: input stream generator
:param str encoding: The encoding of the file. The default is utf-8.
:return: The file content.
:rtype: str
"""
outp... | python | def _read_stream_as_string(stream, encoding):
"""Read stream as string
Originally in azure-batch-samples.Python.Batch.common.helpers
:param stream: input stream generator
:param str encoding: The encoding of the file. The default is utf-8.
:return: The file content.
:rtype: str
"""
outp... | Read stream as string
Originally in azure-batch-samples.Python.Batch.common.helpers
:param stream: input stream generator
:param str encoding: The encoding of the file. The default is utf-8.
:return: The file content.
:rtype: str | https://github.com/ecell/ecell4/blob/a4a1229661c39b2059adbbacae9090e5ba664e01/ecell4/extra/azure_batch.py#L370-L388 |
ecell/ecell4 | ecell4/extra/azure_batch.py | read_task_file_as_string | def read_task_file_as_string(
batch_client, job_id, task_id, file_name, encoding=None):
"""Reads the specified file as a string.
Originally in azure-batch-samples.Python.Batch.common.helpers
:param batch_client: The batch client to use.
:type batch_client: `batchserviceclient.BatchServiceClient... | python | def read_task_file_as_string(
batch_client, job_id, task_id, file_name, encoding=None):
"""Reads the specified file as a string.
Originally in azure-batch-samples.Python.Batch.common.helpers
:param batch_client: The batch client to use.
:type batch_client: `batchserviceclient.BatchServiceClient... | Reads the specified file as a string.
Originally in azure-batch-samples.Python.Batch.common.helpers
:param batch_client: The batch client to use.
:type batch_client: `batchserviceclient.BatchServiceClient`
:param str job_id: The id of the job.
:param str task_id: The id of the task.
:param str ... | https://github.com/ecell/ecell4/blob/a4a1229661c39b2059adbbacae9090e5ba664e01/ecell4/extra/azure_batch.py#L390-L405 |
ecell/ecell4 | ecell4/extra/azure_batch.py | print_task_output | def print_task_output(batch_client, job_id, task_ids, encoding=None):
"""Prints the stdout and stderr for each task specified.
Originally in azure-batch-samples.Python.Batch.common.helpers
:param batch_client: The batch client to use.
:type batch_client: `batchserviceclient.BatchServiceClient`
:par... | python | def print_task_output(batch_client, job_id, task_ids, encoding=None):
"""Prints the stdout and stderr for each task specified.
Originally in azure-batch-samples.Python.Batch.common.helpers
:param batch_client: The batch client to use.
:type batch_client: `batchserviceclient.BatchServiceClient`
:par... | Prints the stdout and stderr for each task specified.
Originally in azure-batch-samples.Python.Batch.common.helpers
:param batch_client: The batch client to use.
:type batch_client: `batchserviceclient.BatchServiceClient`
:param str job_id: The id of the job to monitor.
:param task_ids: The collect... | https://github.com/ecell/ecell4/blob/a4a1229661c39b2059adbbacae9090e5ba664e01/ecell4/extra/azure_batch.py#L407-L439 |
ecell/ecell4 | ecell4/extra/azure_batch.py | run_azure | def run_azure(target, jobs, n=1, path='.', delete=True, config=None):
"""Execute a function for multiple sets of arguments on Microsoft Azure,
and return the results as a list.
:param function target: A target function.
:param list jobs: A list of sets of arguments given to the target.
:param int n... | python | def run_azure(target, jobs, n=1, path='.', delete=True, config=None):
"""Execute a function for multiple sets of arguments on Microsoft Azure,
and return the results as a list.
:param function target: A target function.
:param list jobs: A list of sets of arguments given to the target.
:param int n... | Execute a function for multiple sets of arguments on Microsoft Azure,
and return the results as a list.
:param function target: A target function.
:param list jobs: A list of sets of arguments given to the target.
:param int n: The number of repeats running the target. 1 as default.
:param str path... | https://github.com/ecell/ecell4/blob/a4a1229661c39b2059adbbacae9090e5ba664e01/ecell4/extra/azure_batch.py#L441-L755 |
ecell/ecell4 | ecell4/extra/azure_batch.py | singlerun | def singlerun(job, task_id=0, job_id=0):
"""This task is for an example."""
import ecell4_base
import ecell4
import ecell4.util.simulation
import ecell4.util.decorator
print('ecell4_base.__version__ = {:s}'.format(ecell4_base.__version__))
print('ecell4.__version__ = {:s}'.format(ecell4.__v... | python | def singlerun(job, task_id=0, job_id=0):
"""This task is for an example."""
import ecell4_base
import ecell4
import ecell4.util.simulation
import ecell4.util.decorator
print('ecell4_base.__version__ = {:s}'.format(ecell4_base.__version__))
print('ecell4.__version__ = {:s}'.format(ecell4.__v... | This task is for an example. | https://github.com/ecell/ecell4/blob/a4a1229661c39b2059adbbacae9090e5ba664e01/ecell4/extra/azure_batch.py#L757-L779 |
ecell/ecell4 | ecell4/util/viz.py | plot_number_observer | def plot_number_observer(*args, **kwargs):
"""
Generate a plot from NumberObservers and show it.
See plot_number_observer_with_matplotlib and _with_nya for details.
Parameters
----------
obs : NumberObserver (e.g. FixedIntervalNumberObserver)
interactive : bool, default False
Choose... | python | def plot_number_observer(*args, **kwargs):
"""
Generate a plot from NumberObservers and show it.
See plot_number_observer_with_matplotlib and _with_nya for details.
Parameters
----------
obs : NumberObserver (e.g. FixedIntervalNumberObserver)
interactive : bool, default False
Choose... | Generate a plot from NumberObservers and show it.
See plot_number_observer_with_matplotlib and _with_nya for details.
Parameters
----------
obs : NumberObserver (e.g. FixedIntervalNumberObserver)
interactive : bool, default False
Choose a visualizer. If False, show the plot with matplotlib.... | https://github.com/ecell/ecell4/blob/a4a1229661c39b2059adbbacae9090e5ba664e01/ecell4/util/viz.py#L28-L58 |
ecell/ecell4 | ecell4/util/viz.py | plot_world | def plot_world(*args, **kwargs):
"""
Generate a plot from received instance of World and show it.
See also plot_world_with_elegans and plot_world_with_matplotlib.
Parameters
----------
world : World or str
World or a HDF5 filename to render.
interactive : bool, default True
... | python | def plot_world(*args, **kwargs):
"""
Generate a plot from received instance of World and show it.
See also plot_world_with_elegans and plot_world_with_matplotlib.
Parameters
----------
world : World or str
World or a HDF5 filename to render.
interactive : bool, default True
... | Generate a plot from received instance of World and show it.
See also plot_world_with_elegans and plot_world_with_matplotlib.
Parameters
----------
world : World or str
World or a HDF5 filename to render.
interactive : bool, default True
Choose a visualizer. If False, show the plot ... | https://github.com/ecell/ecell4/blob/a4a1229661c39b2059adbbacae9090e5ba664e01/ecell4/util/viz.py#L60-L83 |
ecell/ecell4 | ecell4/util/viz.py | plot_movie | def plot_movie(*args, **kwargs):
"""
Generate a movie from received instances of World and show them.
See also plot_movie_with_elegans and plot_movie_with_matplotlib.
Parameters
----------
worlds : list of World
Worlds to render.
interactive : bool, default True
Choose a vis... | python | def plot_movie(*args, **kwargs):
"""
Generate a movie from received instances of World and show them.
See also plot_movie_with_elegans and plot_movie_with_matplotlib.
Parameters
----------
worlds : list of World
Worlds to render.
interactive : bool, default True
Choose a vis... | Generate a movie from received instances of World and show them.
See also plot_movie_with_elegans and plot_movie_with_matplotlib.
Parameters
----------
worlds : list of World
Worlds to render.
interactive : bool, default True
Choose a visualizer. If False, show the plot with matplot... | https://github.com/ecell/ecell4/blob/a4a1229661c39b2059adbbacae9090e5ba664e01/ecell4/util/viz.py#L85-L103 |
ecell/ecell4 | ecell4/util/viz.py | plot_trajectory | def plot_trajectory(*args, **kwargs):
"""
Generate a plot from received instance of TrajectoryObserver and show it
See also plot_trajectory_with_elegans and plot_trajectory_with_matplotlib.
Parameters
----------
obs : TrajectoryObserver
TrajectoryObserver to render.
interactive : bo... | python | def plot_trajectory(*args, **kwargs):
"""
Generate a plot from received instance of TrajectoryObserver and show it
See also plot_trajectory_with_elegans and plot_trajectory_with_matplotlib.
Parameters
----------
obs : TrajectoryObserver
TrajectoryObserver to render.
interactive : bo... | Generate a plot from received instance of TrajectoryObserver and show it
See also plot_trajectory_with_elegans and plot_trajectory_with_matplotlib.
Parameters
----------
obs : TrajectoryObserver
TrajectoryObserver to render.
interactive : bool, default True
Choose a visualizer. If F... | https://github.com/ecell/ecell4/blob/a4a1229661c39b2059adbbacae9090e5ba664e01/ecell4/util/viz.py#L105-L128 |
ecell/ecell4 | ecell4/util/viz.py | plot_number_observer_with_matplotlib | def plot_number_observer_with_matplotlib(*args, **kwargs):
"""
Generate a plot from NumberObservers and show it on IPython notebook
with matplotlib.
Parameters
----------
obs : NumberObserver (e.g. FixedIntervalNumberObserver)
fmt : str, optional
opt : dict, optional
matplotlib ... | python | def plot_number_observer_with_matplotlib(*args, **kwargs):
"""
Generate a plot from NumberObservers and show it on IPython notebook
with matplotlib.
Parameters
----------
obs : NumberObserver (e.g. FixedIntervalNumberObserver)
fmt : str, optional
opt : dict, optional
matplotlib ... | Generate a plot from NumberObservers and show it on IPython notebook
with matplotlib.
Parameters
----------
obs : NumberObserver (e.g. FixedIntervalNumberObserver)
fmt : str, optional
opt : dict, optional
matplotlib plot options.
Examples
--------
>>> plot_number_observer(o... | https://github.com/ecell/ecell4/blob/a4a1229661c39b2059adbbacae9090e5ba664e01/ecell4/util/viz.py#L130-L274 |
ecell/ecell4 | ecell4/util/viz.py | plot_number_observer_with_nya | def plot_number_observer_with_nya(obs, config=None, width=600, height=400, x=None, y=None, to_png=False):
"""
Generate a plot from NumberObservers and show it on IPython notebook
with nyaplot.
Parameters
----------
obs : NumberObserver (e.g. FixedIntervalNumberObserver)
config : dict, optio... | python | def plot_number_observer_with_nya(obs, config=None, width=600, height=400, x=None, y=None, to_png=False):
"""
Generate a plot from NumberObservers and show it on IPython notebook
with nyaplot.
Parameters
----------
obs : NumberObserver (e.g. FixedIntervalNumberObserver)
config : dict, optio... | Generate a plot from NumberObservers and show it on IPython notebook
with nyaplot.
Parameters
----------
obs : NumberObserver (e.g. FixedIntervalNumberObserver)
config : dict, optional
A config data for coloring. The dictionary will be updated during this plot.
width : int, optional
... | https://github.com/ecell/ecell4/blob/a4a1229661c39b2059adbbacae9090e5ba664e01/ecell4/util/viz.py#L276-L350 |
ecell/ecell4 | ecell4/util/viz.py | __parse_world | def __parse_world(
world, radius=None, species_list=None, max_count=None,
predicator=None):
"""
Private function to parse world. Return infomation about particles
(name, coordinates and particle size) for each species.
"""
from ecell4_base.core import Species
if species_list is... | python | def __parse_world(
world, radius=None, species_list=None, max_count=None,
predicator=None):
"""
Private function to parse world. Return infomation about particles
(name, coordinates and particle size) for each species.
"""
from ecell4_base.core import Species
if species_list is... | Private function to parse world. Return infomation about particles
(name, coordinates and particle size) for each species. | https://github.com/ecell/ecell4/blob/a4a1229661c39b2059adbbacae9090e5ba664e01/ecell4/util/viz.py#L352-L403 |
ecell/ecell4 | ecell4/util/viz.py | plot_movie_with_elegans | def plot_movie_with_elegans(
worlds, radius=None, width=500, height=500, config=None, grid=False,
species_list=None):
"""
Generate a movie from received instances of World and show them
on IPython notebook.
Parameters
----------
worlds : list of World
Worlds to render.
... | python | def plot_movie_with_elegans(
worlds, radius=None, width=500, height=500, config=None, grid=False,
species_list=None):
"""
Generate a movie from received instances of World and show them
on IPython notebook.
Parameters
----------
worlds : list of World
Worlds to render.
... | Generate a movie from received instances of World and show them
on IPython notebook.
Parameters
----------
worlds : list of World
Worlds to render.
radius : float, default None
If this value is set, all particles in the world will be rendered
as if their radius are the same.... | https://github.com/ecell/ecell4/blob/a4a1229661c39b2059adbbacae9090e5ba664e01/ecell4/util/viz.py#L476-L539 |
ecell/ecell4 | ecell4/util/viz.py | plot_world_with_elegans | def plot_world_with_elegans(
world, radius=None, width=350, height=350, config=None, grid=True,
wireframe=False, species_list=None, debug=None, max_count=1000,
camera_position=(-22, 23, 32), camera_rotation=(-0.6, 0.5, 0.6),
return_id=False, predicator=None):
"""
Generate a plot ... | python | def plot_world_with_elegans(
world, radius=None, width=350, height=350, config=None, grid=True,
wireframe=False, species_list=None, debug=None, max_count=1000,
camera_position=(-22, 23, 32), camera_rotation=(-0.6, 0.5, 0.6),
return_id=False, predicator=None):
"""
Generate a plot ... | Generate a plot from received instance of World and show it on IPython notebook.
This method returns the instance of dict that indicates color setting
for each speices. You can use the dict as the parameter of plot_world,
in order to use the same colors in another plot.
Parameters
----------
wo... | https://github.com/ecell/ecell4/blob/a4a1229661c39b2059adbbacae9090e5ba664e01/ecell4/util/viz.py#L541-L648 |
ecell/ecell4 | ecell4/util/viz.py | plot_dense_array | def plot_dense_array(
arr, length=256, ranges=None, colors=("#a6cee3", "#fb9a99"), grid=False, camera_position=(-22, 23, 32), camera_rotation=(-0.6, 0.5, 0.6)):
"""
Volume renderer
Parameters
----------
arr : list of numpy.array
i.e. [array([[1,2,3], [2,3,4]]), array([[1,2,3]])]
... | python | def plot_dense_array(
arr, length=256, ranges=None, colors=("#a6cee3", "#fb9a99"), grid=False, camera_position=(-22, 23, 32), camera_rotation=(-0.6, 0.5, 0.6)):
"""
Volume renderer
Parameters
----------
arr : list of numpy.array
i.e. [array([[1,2,3], [2,3,4]]), array([[1,2,3]])]
... | Volume renderer
Parameters
----------
arr : list of numpy.array
i.e. [array([[1,2,3], [2,3,4]]), array([[1,2,3]])]
ranges : list of tuple
ranges for x, y, and z axis
i.e. [(-100, 100), (-100, 100), (-100, 100)]
colors : list of string
colors for species
length : ... | https://github.com/ecell/ecell4/blob/a4a1229661c39b2059adbbacae9090e5ba664e01/ecell4/util/viz.py#L705-L800 |
ecell/ecell4 | ecell4/util/viz.py | generate_html | def generate_html(keywords, tmpl_path, package_name='ecell4.util'):
"""
Generate static html file from JSON model and its own id.
Parameters
----------
model : dict
JSON model from which ecell4.viz generates a plot.
model_id : string
Unique id for the plot.
Returns
----... | python | def generate_html(keywords, tmpl_path, package_name='ecell4.util'):
"""
Generate static html file from JSON model and its own id.
Parameters
----------
model : dict
JSON model from which ecell4.viz generates a plot.
model_id : string
Unique id for the plot.
Returns
----... | Generate static html file from JSON model and its own id.
Parameters
----------
model : dict
JSON model from which ecell4.viz generates a plot.
model_id : string
Unique id for the plot.
Returns
-------
html :
A HTML object | https://github.com/ecell/ecell4/blob/a4a1229661c39b2059adbbacae9090e5ba664e01/ecell4/util/viz.py#L802-L825 |
ecell/ecell4 | ecell4/util/viz.py | plot_trajectory_with_elegans | def plot_trajectory_with_elegans(
obs, width=350, height=350, config=None, grid=True, wireframe=False,
max_count=10, camera_position=(-22, 23, 32), camera_rotation=(-0.6, 0.5, 0.6),
plot_range=None):
"""
Generate a plot from received instance of TrajectoryObserver and show it
on IPyt... | python | def plot_trajectory_with_elegans(
obs, width=350, height=350, config=None, grid=True, wireframe=False,
max_count=10, camera_position=(-22, 23, 32), camera_rotation=(-0.6, 0.5, 0.6),
plot_range=None):
"""
Generate a plot from received instance of TrajectoryObserver and show it
on IPyt... | Generate a plot from received instance of TrajectoryObserver and show it
on IPython notebook.
Parameters
----------
obs : TrajectoryObserver
TrajectoryObserver to render.
width : float, default 350
Width of the plotting area.
height : float, default 350
Height of the plo... | https://github.com/ecell/ecell4/blob/a4a1229661c39b2059adbbacae9090e5ba664e01/ecell4/util/viz.py#L828-L932 |
ecell/ecell4 | ecell4/util/viz.py | plot_world_with_matplotlib | def plot_world_with_matplotlib(
world, marker_size=3, figsize=6, grid=True,
wireframe=False, species_list=None, max_count=1000, angle=None,
legend=True, noaxis=False, **kwargs):
"""
Generate a plot from received instance of World and show it on IPython notebook.
Parameters
-----... | python | def plot_world_with_matplotlib(
world, marker_size=3, figsize=6, grid=True,
wireframe=False, species_list=None, max_count=1000, angle=None,
legend=True, noaxis=False, **kwargs):
"""
Generate a plot from received instance of World and show it on IPython notebook.
Parameters
-----... | Generate a plot from received instance of World and show it on IPython notebook.
Parameters
----------
world : World or str
World to render. A HDF5 filename is also acceptable.
marker_size : float, default 3
Marker size for all species. Size is passed to scatter function
as argu... | https://github.com/ecell/ecell4/blob/a4a1229661c39b2059adbbacae9090e5ba664e01/ecell4/util/viz.py#L1106-L1153 |
ecell/ecell4 | ecell4/util/viz.py | plot_trajectory_with_matplotlib | def plot_trajectory_with_matplotlib(
obs, max_count=10, figsize=6, legend=True, angle=None,
wireframe=False, grid=True, noaxis=False, plot_range=None, **kwargs):
"""
Generate a plot from received instance of TrajectoryObserver and show it
on IPython notebook.
Parameters
----------
... | python | def plot_trajectory_with_matplotlib(
obs, max_count=10, figsize=6, legend=True, angle=None,
wireframe=False, grid=True, noaxis=False, plot_range=None, **kwargs):
"""
Generate a plot from received instance of TrajectoryObserver and show it
on IPython notebook.
Parameters
----------
... | Generate a plot from received instance of TrajectoryObserver and show it
on IPython notebook.
Parameters
----------
obs : TrajectoryObserver
TrajectoryObserver to render.
max_count : Integer, default 10
The maximum number of particles to show. If None, show all.
figsize : float,... | https://github.com/ecell/ecell4/blob/a4a1229661c39b2059adbbacae9090e5ba664e01/ecell4/util/viz.py#L1155-L1208 |
ecell/ecell4 | ecell4/util/viz.py | plot_trajectory2d_with_matplotlib | def plot_trajectory2d_with_matplotlib(
obs, plane='xy', max_count=10, figsize=6, legend=True,
wireframe=False, grid=True, noaxis=False, plot_range=None, **kwargs):
"""
Make a 2D plot from received instance of TrajectoryObserver and show it
on IPython notebook.
Parameters
----------
... | python | def plot_trajectory2d_with_matplotlib(
obs, plane='xy', max_count=10, figsize=6, legend=True,
wireframe=False, grid=True, noaxis=False, plot_range=None, **kwargs):
"""
Make a 2D plot from received instance of TrajectoryObserver and show it
on IPython notebook.
Parameters
----------
... | Make a 2D plot from received instance of TrajectoryObserver and show it
on IPython notebook.
Parameters
----------
obs : TrajectoryObserver
TrajectoryObserver to render.
plane : str, default 'xy'
'xy', 'yz', 'zx'.
max_count : Integer, default 10
The maximum number of par... | https://github.com/ecell/ecell4/blob/a4a1229661c39b2059adbbacae9090e5ba664e01/ecell4/util/viz.py#L1243-L1304 |
ecell/ecell4 | ecell4/util/viz.py | plot_movie_of_trajectory2d_with_matplotlib | def plot_movie_of_trajectory2d_with_matplotlib(
obs, plane='xy', figsize=6, grid=True,
wireframe=False, max_count=None, angle=None, noaxis=False,
interval=0.16, repeat_delay=3000, stride=1, rotate=None,
legend=True, output=None, crf=10, bitrate='1M', plot_range=None, **kwargs):
"""
... | python | def plot_movie_of_trajectory2d_with_matplotlib(
obs, plane='xy', figsize=6, grid=True,
wireframe=False, max_count=None, angle=None, noaxis=False,
interval=0.16, repeat_delay=3000, stride=1, rotate=None,
legend=True, output=None, crf=10, bitrate='1M', plot_range=None, **kwargs):
"""
... | Generate a move from the received list of instances of World,
and show it on IPython notebook. This function may require ffmpeg.
Parameters
----------
worlds : list or FixedIntervalHDF5Observer
A list of Worlds to render.
plane : str, default 'xy'
'xy', 'yz', 'zx'.
figsize : flo... | https://github.com/ecell/ecell4/blob/a4a1229661c39b2059adbbacae9090e5ba664e01/ecell4/util/viz.py#L1306-L1410 |
ecell/ecell4 | ecell4/util/viz.py | plot_movie_of_trajectory_with_matplotlib | def plot_movie_of_trajectory_with_matplotlib(
obs, figsize=6, grid=True,
wireframe=False, max_count=None, angle=None, noaxis=False,
interval=0.16, repeat_delay=3000, stride=1, rotate=None,
legend=True, output=None, crf=10, bitrate='1M', plot_range=None, **kwargs):
"""
Generate a ... | python | def plot_movie_of_trajectory_with_matplotlib(
obs, figsize=6, grid=True,
wireframe=False, max_count=None, angle=None, noaxis=False,
interval=0.16, repeat_delay=3000, stride=1, rotate=None,
legend=True, output=None, crf=10, bitrate='1M', plot_range=None, **kwargs):
"""
Generate a ... | Generate a move from the received list of instances of World,
and show it on IPython notebook. This function may require ffmpeg.
Parameters
----------
worlds : list or FixedIntervalHDF5Observer
A list of Worlds to render.
marker_size : float, default 3
Marker size for all species. S... | https://github.com/ecell/ecell4/blob/a4a1229661c39b2059adbbacae9090e5ba664e01/ecell4/util/viz.py#L1534-L1639 |
ecell/ecell4 | ecell4/util/viz.py | plot_world_with_attractive_mpl | def plot_world_with_attractive_mpl(
world, marker_size=6, figsize=6, grid=True,
wireframe=False, species_list=None, max_count=1000, angle=None,
legend=True, noaxis=False, whratio=1.33, scale=1.0, **kwargs):
"""
Generate a plot from received instance of World and show it on IPython notebo... | python | def plot_world_with_attractive_mpl(
world, marker_size=6, figsize=6, grid=True,
wireframe=False, species_list=None, max_count=1000, angle=None,
legend=True, noaxis=False, whratio=1.33, scale=1.0, **kwargs):
"""
Generate a plot from received instance of World and show it on IPython notebo... | Generate a plot from received instance of World and show it on IPython notebook.
Parameters
----------
world : World or str
World to render. A HDF5 filename is also acceptable.
marker_size : float, default 3
Marker size for all species. Size is passed to scatter function
as argu... | https://github.com/ecell/ecell4/blob/a4a1229661c39b2059adbbacae9090e5ba664e01/ecell4/util/viz.py#L1643-L1699 |
ecell/ecell4 | ecell4/util/viz.py | plot_movie_with_attractive_mpl | def plot_movie_with_attractive_mpl(
worlds, marker_size=6, figsize=6, grid=True,
wireframe=False, species_list=None, max_count=None, angle=None, noaxis=False,
interval=0.16, repeat_delay=3000, stride=1, rotate=None,
legend=True, whratio=1.33, scale=1, output=None, crf=10, bitrate='1M', *... | python | def plot_movie_with_attractive_mpl(
worlds, marker_size=6, figsize=6, grid=True,
wireframe=False, species_list=None, max_count=None, angle=None, noaxis=False,
interval=0.16, repeat_delay=3000, stride=1, rotate=None,
legend=True, whratio=1.33, scale=1, output=None, crf=10, bitrate='1M', *... | Generate a move from the received list of instances of World,
and show it on IPython notebook. This function may require ffmpeg.
Parameters
----------
worlds : list or FixedIntervalHDF5Observer
A list of Worlds to render.
marker_size : float, default 3
Marker size for all species. S... | https://github.com/ecell/ecell4/blob/a4a1229661c39b2059adbbacae9090e5ba664e01/ecell4/util/viz.py#L1774-L1906 |
ecell/ecell4 | ecell4/util/viz.py | plot_world2d_with_matplotlib | def plot_world2d_with_matplotlib(
world, plane='xy', marker_size=3, figsize=6, grid=True,
wireframe=False, species_list=None, max_count=1000, angle=None,
legend=True, noaxis=False, scale=1.0, **kwargs):
"""
Make a 2D plot from received instance of World and show it on IPython notebook.
... | python | def plot_world2d_with_matplotlib(
world, plane='xy', marker_size=3, figsize=6, grid=True,
wireframe=False, species_list=None, max_count=1000, angle=None,
legend=True, noaxis=False, scale=1.0, **kwargs):
"""
Make a 2D plot from received instance of World and show it on IPython notebook.
... | Make a 2D plot from received instance of World and show it on IPython notebook.
Parameters
----------
world : World or str
World to render. A HDF5 filename is also acceptable.
plane : str, default 'xy'
'xy', 'yz', 'zx'.
marker_size : float, default 3
Marker size for all spec... | https://github.com/ecell/ecell4/blob/a4a1229661c39b2059adbbacae9090e5ba664e01/ecell4/util/viz.py#L1908-L1974 |
ecell/ecell4 | ecell4/util/viz.py | plot_movie2d_with_matplotlib | def plot_movie2d_with_matplotlib(
worlds, plane='xy', marker_size=3, figsize=6, grid=True,
wireframe=False, species_list=None, max_count=None, angle=None, noaxis=False,
interval=0.16, repeat_delay=3000, stride=1, rotate=None,
legend=True, scale=1, output=None, crf=10, bitrate='1M', **kwa... | python | def plot_movie2d_with_matplotlib(
worlds, plane='xy', marker_size=3, figsize=6, grid=True,
wireframe=False, species_list=None, max_count=None, angle=None, noaxis=False,
interval=0.16, repeat_delay=3000, stride=1, rotate=None,
legend=True, scale=1, output=None, crf=10, bitrate='1M', **kwa... | Generate a movie projected on the given plane from the received list
of instances of World, and show it on IPython notebook.
This function may require ffmpeg.
Parameters
----------
worlds : list or FixedIntervalHDF5Observer
A list of Worlds to render.
plane : str, default 'xy'
'... | https://github.com/ecell/ecell4/blob/a4a1229661c39b2059adbbacae9090e5ba664e01/ecell4/util/viz.py#L1999-L2134 |
ecell/ecell4 | ecell4/util/viz.py | plot_world_with_plotly | def plot_world_with_plotly(world, species_list=None, max_count=1000):
"""
Plot a World on IPython Notebook
"""
if isinstance(world, str):
from .simulation import load_world
world = load_world(world)
if species_list is None:
species_list = [sp.serial() for sp in world.list_sp... | python | def plot_world_with_plotly(world, species_list=None, max_count=1000):
"""
Plot a World on IPython Notebook
"""
if isinstance(world, str):
from .simulation import load_world
world = load_world(world)
if species_list is None:
species_list = [sp.serial() for sp in world.list_sp... | Plot a World on IPython Notebook | https://github.com/ecell/ecell4/blob/a4a1229661c39b2059adbbacae9090e5ba664e01/ecell4/util/viz.py#L2136-L2182 |
ecell/ecell4 | ecell4/extra/_unit.py | getUnitRegistry | def getUnitRegistry(length="meter", time="second", substance="item", volume=None, other=()):
"""Return a pint.UnitRegistry made compatible with ecell4.
Parameters
----------
length : str, optional
A default unit for '[length]'. 'meter' is its default.
time : str, optional
A default ... | python | def getUnitRegistry(length="meter", time="second", substance="item", volume=None, other=()):
"""Return a pint.UnitRegistry made compatible with ecell4.
Parameters
----------
length : str, optional
A default unit for '[length]'. 'meter' is its default.
time : str, optional
A default ... | Return a pint.UnitRegistry made compatible with ecell4.
Parameters
----------
length : str, optional
A default unit for '[length]'. 'meter' is its default.
time : str, optional
A default unit for '[time]'. 'second' is its default.
substance : str, optional
A default unit for... | https://github.com/ecell/ecell4/blob/a4a1229661c39b2059adbbacae9090e5ba664e01/ecell4/extra/_unit.py#L32-L74 |
ecell/ecell4 | ecell4/datasource/biogrid.py | biogridDataSource.interactor | def interactor(self, geneList=None, org=None):
"""
Supposing geneList returns an unique item.
"""
geneList = geneList or []
organisms = organisms or []
querydata = self.interactions(geneList, org)
returnData = {}
for i in querydata:
if not ret... | python | def interactor(self, geneList=None, org=None):
"""
Supposing geneList returns an unique item.
"""
geneList = geneList or []
organisms = organisms or []
querydata = self.interactions(geneList, org)
returnData = {}
for i in querydata:
if not ret... | Supposing geneList returns an unique item. | https://github.com/ecell/ecell4/blob/a4a1229661c39b2059adbbacae9090e5ba664e01/ecell4/datasource/biogrid.py#L96-L109 |
ecell/ecell4 | ecell4/datasource/psicquic.py | parse_psimitab | def parse_psimitab(content, fmt='tab27'):
"""https://code.google.com/archive/p/psimi/wikis/PsimiTab27Format.wiki
"""
columns = [
'Unique identifier for interactor A',
'Unique identifier for interactor B',
'Alternative identifier for interactor A',
'Alternative identifier for ... | python | def parse_psimitab(content, fmt='tab27'):
"""https://code.google.com/archive/p/psimi/wikis/PsimiTab27Format.wiki
"""
columns = [
'Unique identifier for interactor A',
'Unique identifier for interactor B',
'Alternative identifier for interactor A',
'Alternative identifier for ... | https://code.google.com/archive/p/psimi/wikis/PsimiTab27Format.wiki | https://github.com/ecell/ecell4/blob/a4a1229661c39b2059adbbacae9090e5ba664e01/ecell4/datasource/psicquic.py#L176-L236 |
ecell/ecell4 | ecell4/util/ports.py | export_sbml | def export_sbml(model, y0=None, volume=1.0, is_valid=True):
"""
Export a model as a SBMLDocument.
Parameters
----------
model : NetworkModel
y0 : dict
Initial condition.
volume : Real or Real3, optional
A size of the simulation volume. 1 as a default.
is_valid : bool, op... | python | def export_sbml(model, y0=None, volume=1.0, is_valid=True):
"""
Export a model as a SBMLDocument.
Parameters
----------
model : NetworkModel
y0 : dict
Initial condition.
volume : Real or Real3, optional
A size of the simulation volume. 1 as a default.
is_valid : bool, op... | Export a model as a SBMLDocument.
Parameters
----------
model : NetworkModel
y0 : dict
Initial condition.
volume : Real or Real3, optional
A size of the simulation volume. 1 as a default.
is_valid : bool, optional
Check if the generated model is valid. True as a default. | https://github.com/ecell/ecell4/blob/a4a1229661c39b2059adbbacae9090e5ba664e01/ecell4/util/ports.py#L31-L218 |
ecell/ecell4 | ecell4/util/ports.py | save_sbml | def save_sbml(filename, model, y0=None, volume=1.0, is_valid=True):
"""
Save a model in the SBML format.
Parameters
----------
model : NetworkModel
y0 : dict
Initial condition.
volume : Real or Real3, optional
A size of the simulation volume.
is_valid : bool, optional
... | python | def save_sbml(filename, model, y0=None, volume=1.0, is_valid=True):
"""
Save a model in the SBML format.
Parameters
----------
model : NetworkModel
y0 : dict
Initial condition.
volume : Real or Real3, optional
A size of the simulation volume.
is_valid : bool, optional
... | Save a model in the SBML format.
Parameters
----------
model : NetworkModel
y0 : dict
Initial condition.
volume : Real or Real3, optional
A size of the simulation volume.
is_valid : bool, optional
Check if the generated model is valid. True as a default. | https://github.com/ecell/ecell4/blob/a4a1229661c39b2059adbbacae9090e5ba664e01/ecell4/util/ports.py#L220-L245 |
ecell/ecell4 | ecell4/util/ports.py | import_sbml | def import_sbml(document):
"""
Import a model from a SBMLDocument.
Parameters
----------
document : SBMLDocument
Returns
-------
model : NetworkModel
y0 : dict
Initial condition.
volume : Real or Real3, optional
A size of the simulation volume.
"""
from... | python | def import_sbml(document):
"""
Import a model from a SBMLDocument.
Parameters
----------
document : SBMLDocument
Returns
-------
model : NetworkModel
y0 : dict
Initial condition.
volume : Real or Real3, optional
A size of the simulation volume.
"""
from... | Import a model from a SBMLDocument.
Parameters
----------
document : SBMLDocument
Returns
-------
model : NetworkModel
y0 : dict
Initial condition.
volume : Real or Real3, optional
A size of the simulation volume. | https://github.com/ecell/ecell4/blob/a4a1229661c39b2059adbbacae9090e5ba664e01/ecell4/util/ports.py#L252-L375 |
ecell/ecell4 | ecell4/util/ports.py | load_sbml | def load_sbml(filename):
"""
Load a model from a SBML file.
Parameters
----------
filename : str
The input SBML filename.
Returns
-------
model : NetworkModel
y0 : dict
Initial condition.
volume : Real or Real3, optional
A size of the simulation volume.
... | python | def load_sbml(filename):
"""
Load a model from a SBML file.
Parameters
----------
filename : str
The input SBML filename.
Returns
-------
model : NetworkModel
y0 : dict
Initial condition.
volume : Real or Real3, optional
A size of the simulation volume.
... | Load a model from a SBML file.
Parameters
----------
filename : str
The input SBML filename.
Returns
-------
model : NetworkModel
y0 : dict
Initial condition.
volume : Real or Real3, optional
A size of the simulation volume. | https://github.com/ecell/ecell4/blob/a4a1229661c39b2059adbbacae9090e5ba664e01/ecell4/util/ports.py#L377-L411 |
ecell/ecell4 | ecell4/util/decorator.py | get_model | def get_model(is_netfree=False, without_reset=False, seeds=None, effective=False):
"""
Generate a model with parameters in the global scope, ``SPECIES_ATTRIBUTES``
and ``REACTIONRULES``.
Parameters
----------
is_netfree : bool, optional
Return ``NetfreeModel`` if True, and ``NetworkMode... | python | def get_model(is_netfree=False, without_reset=False, seeds=None, effective=False):
"""
Generate a model with parameters in the global scope, ``SPECIES_ATTRIBUTES``
and ``REACTIONRULES``.
Parameters
----------
is_netfree : bool, optional
Return ``NetfreeModel`` if True, and ``NetworkMode... | Generate a model with parameters in the global scope, ``SPECIES_ATTRIBUTES``
and ``REACTIONRULES``.
Parameters
----------
is_netfree : bool, optional
Return ``NetfreeModel`` if True, and ``NetworkModel`` if else.
Default is False.
without_reset : bool, optional
Do not reset ... | https://github.com/ecell/ecell4/blob/a4a1229661c39b2059adbbacae9090e5ba664e01/ecell4/util/decorator.py#L143-L194 |
ecell/ecell4 | ecell4/extra/ensemble.py | run_serial | def run_serial(target, jobs, n=1, **kwargs):
"""
Evaluate the given function with each set of arguments, and return a list of results.
This function does in series.
Parameters
----------
target : function
A function to be evaluated. The function must accepts three arguments,
whi... | python | def run_serial(target, jobs, n=1, **kwargs):
"""
Evaluate the given function with each set of arguments, and return a list of results.
This function does in series.
Parameters
----------
target : function
A function to be evaluated. The function must accepts three arguments,
whi... | Evaluate the given function with each set of arguments, and return a list of results.
This function does in series.
Parameters
----------
target : function
A function to be evaluated. The function must accepts three arguments,
which are a list of arguments given as `jobs`, a job and tas... | https://github.com/ecell/ecell4/blob/a4a1229661c39b2059adbbacae9090e5ba664e01/ecell4/extra/ensemble.py#L22-L71 |
ecell/ecell4 | ecell4/extra/ensemble.py | run_multiprocessing | def run_multiprocessing(target, jobs, n=1, nproc=None, **kwargs):
"""
Evaluate the given function with each set of arguments, and return a list of results.
This function does in parallel by using `multiprocessing`.
Parameters
----------
target : function
A function to be evaluated. The ... | python | def run_multiprocessing(target, jobs, n=1, nproc=None, **kwargs):
"""
Evaluate the given function with each set of arguments, and return a list of results.
This function does in parallel by using `multiprocessing`.
Parameters
----------
target : function
A function to be evaluated. The ... | Evaluate the given function with each set of arguments, and return a list of results.
This function does in parallel by using `multiprocessing`.
Parameters
----------
target : function
A function to be evaluated. The function must accepts three arguments,
which are a list of arguments g... | https://github.com/ecell/ecell4/blob/a4a1229661c39b2059adbbacae9090e5ba664e01/ecell4/extra/ensemble.py#L73-L147 |
ecell/ecell4 | ecell4/extra/ensemble.py | run_sge | def run_sge(target, jobs, n=1, nproc=None, path='.', delete=True, wait=True, environ=None, modules=(), **kwargs):
"""
Evaluate the given function with each set of arguments, and return a list of results.
This function does in parallel on the Sun Grid Engine einvironment.
Parameters
----------
t... | python | def run_sge(target, jobs, n=1, nproc=None, path='.', delete=True, wait=True, environ=None, modules=(), **kwargs):
"""
Evaluate the given function with each set of arguments, and return a list of results.
This function does in parallel on the Sun Grid Engine einvironment.
Parameters
----------
t... | Evaluate the given function with each set of arguments, and return a list of results.
This function does in parallel on the Sun Grid Engine einvironment.
Parameters
----------
target : function
A function to be evaluated. The function must accepts three arguments,
which are a list of ar... | https://github.com/ecell/ecell4/blob/a4a1229661c39b2059adbbacae9090e5ba664e01/ecell4/extra/ensemble.py#L149-L323 |
ecell/ecell4 | ecell4/extra/ensemble.py | run_azure | def run_azure(target, jobs, n=1, nproc=None, path='.', delete=True, config=None, **kwargs):
"""
Evaluate the given function with each set of arguments, and return a list of results.
This function does in parallel with Microsoft Azure Batch.
This function is the work in progress.
The argument `nproc... | python | def run_azure(target, jobs, n=1, nproc=None, path='.', delete=True, config=None, **kwargs):
"""
Evaluate the given function with each set of arguments, and return a list of results.
This function does in parallel with Microsoft Azure Batch.
This function is the work in progress.
The argument `nproc... | Evaluate the given function with each set of arguments, and return a list of results.
This function does in parallel with Microsoft Azure Batch.
This function is the work in progress.
The argument `nproc` doesn't work yet.
See `ecell4.extra.azure_batch.run_azure` for details.
See Also
--------... | https://github.com/ecell/ecell4/blob/a4a1229661c39b2059adbbacae9090e5ba664e01/ecell4/extra/ensemble.py#L503-L523 |
ecell/ecell4 | ecell4/extra/ensemble.py | getseed | def getseed(myseed, i):
"""
Return a single seed from a long seed given by `genseeds`.
Parameters
----------
myseed : bytes
A long seed given by `genseeds(n)`.
i : int
An index less than n.
Returns
-------
rndseed : int
A seed (less than (2 ** 31))
"""
... | python | def getseed(myseed, i):
"""
Return a single seed from a long seed given by `genseeds`.
Parameters
----------
myseed : bytes
A long seed given by `genseeds(n)`.
i : int
An index less than n.
Returns
-------
rndseed : int
A seed (less than (2 ** 31))
"""
... | Return a single seed from a long seed given by `genseeds`.
Parameters
----------
myseed : bytes
A long seed given by `genseeds(n)`.
i : int
An index less than n.
Returns
-------
rndseed : int
A seed (less than (2 ** 31)) | https://github.com/ecell/ecell4/blob/a4a1229661c39b2059adbbacae9090e5ba664e01/ecell4/extra/ensemble.py#L543-L562 |
ecell/ecell4 | ecell4/extra/ensemble.py | list_species | def list_species(model, seeds=None):
"""This function is deprecated."""
seeds = None or []
from ecell4_base.core import Species
if not isinstance(seeds, list):
seeds = list(seeds)
expanded = model.expand([Species(serial) for serial in seeds])
species_list = [sp.serial() for sp in expa... | python | def list_species(model, seeds=None):
"""This function is deprecated."""
seeds = None or []
from ecell4_base.core import Species
if not isinstance(seeds, list):
seeds = list(seeds)
expanded = model.expand([Species(serial) for serial in seeds])
species_list = [sp.serial() for sp in expa... | This function is deprecated. | https://github.com/ecell/ecell4/blob/a4a1229661c39b2059adbbacae9090e5ba664e01/ecell4/extra/ensemble.py#L582-L594 |
ecell/ecell4 | ecell4/extra/ensemble.py | ensemble_simulations | def ensemble_simulations(
t, y0=None, volume=1.0, model=None, solver='ode',
is_netfree=False, species_list=None, without_reset=False,
return_type='matplotlib', opt_args=(), opt_kwargs=None,
structures=None, rndseed=None,
n=1, nproc=None, method=None, errorbar=True,
**kwargs):
"""
Run sim... | python | def ensemble_simulations(
t, y0=None, volume=1.0, model=None, solver='ode',
is_netfree=False, species_list=None, without_reset=False,
return_type='matplotlib', opt_args=(), opt_kwargs=None,
structures=None, rndseed=None,
n=1, nproc=None, method=None, errorbar=True,
**kwargs):
"""
Run sim... | Run simulations multiple times and return its ensemble.
Arguments are almost same with ``ecell4.util.simulation.run_simulation``.
`observers` and `progressbar` is not available here.
Parameters
----------
n : int, optional
A number of runs. Default is 1.
nproc : int, optional
A ... | https://github.com/ecell/ecell4/blob/a4a1229661c39b2059adbbacae9090e5ba664e01/ecell4/extra/ensemble.py#L597-L775 |
ecell/ecell4 | ecell4/extra/bdml.py | save_bd5 | def save_bd5(
space, filename,
group_index=0, object_name="molecule", spatial_unit="meter", time_unit="second",
trunc=False, with_radius=False):
"""Save a space in the BDML-BD5 format (https://github.com/openssbd/BDML-BD5).
Open file for read/write, if it already exists, and create a ne... | python | def save_bd5(
space, filename,
group_index=0, object_name="molecule", spatial_unit="meter", time_unit="second",
trunc=False, with_radius=False):
"""Save a space in the BDML-BD5 format (https://github.com/openssbd/BDML-BD5).
Open file for read/write, if it already exists, and create a ne... | Save a space in the BDML-BD5 format (https://github.com/openssbd/BDML-BD5).
Open file for read/write, if it already exists, and create a new file, otherwise.
If trunc is True, always create a new file.
A new group named `group_name` is created. If the group already exists, returns
an exception.
Pa... | https://github.com/ecell/ecell4/blob/a4a1229661c39b2059adbbacae9090e5ba664e01/ecell4/extra/bdml.py#L6-L53 |
dlon/html2markdown | html2markdown.py | _escapeCharacters | def _escapeCharacters(tag):
"""non-recursively escape underlines and asterisks
in the tag"""
for i,c in enumerate(tag.contents):
if type(c) != bs4.element.NavigableString:
continue
c.replace_with(_escapeCharSub(r'\\\1', c)) | python | def _escapeCharacters(tag):
"""non-recursively escape underlines and asterisks
in the tag"""
for i,c in enumerate(tag.contents):
if type(c) != bs4.element.NavigableString:
continue
c.replace_with(_escapeCharSub(r'\\\1', c)) | non-recursively escape underlines and asterisks
in the tag | https://github.com/dlon/html2markdown/blob/5946da7136e69a67b3dd37fd0e896be4d6a5b482/html2markdown.py#L148-L154 |
dlon/html2markdown | html2markdown.py | _breakRemNewlines | def _breakRemNewlines(tag):
"""non-recursively break spaces and remove newlines in the tag"""
for i,c in enumerate(tag.contents):
if type(c) != bs4.element.NavigableString:
continue
c.replace_with(re.sub(r' {2,}', ' ', c).replace('\n','')) | python | def _breakRemNewlines(tag):
"""non-recursively break spaces and remove newlines in the tag"""
for i,c in enumerate(tag.contents):
if type(c) != bs4.element.NavigableString:
continue
c.replace_with(re.sub(r' {2,}', ' ', c).replace('\n','')) | non-recursively break spaces and remove newlines in the tag | https://github.com/dlon/html2markdown/blob/5946da7136e69a67b3dd37fd0e896be4d6a5b482/html2markdown.py#L156-L161 |
dlon/html2markdown | html2markdown.py | _markdownify | def _markdownify(tag, _listType=None, _blockQuote=False, _listIndex=1):
"""recursively converts a tag into markdown"""
children = tag.find_all(recursive=False)
if tag.name == '[document]':
for child in children:
_markdownify(child)
return
if tag.name not in _supportedTags or not _supportedAttrs(tag):
if ... | python | def _markdownify(tag, _listType=None, _blockQuote=False, _listIndex=1):
"""recursively converts a tag into markdown"""
children = tag.find_all(recursive=False)
if tag.name == '[document]':
for child in children:
_markdownify(child)
return
if tag.name not in _supportedTags or not _supportedAttrs(tag):
if ... | recursively converts a tag into markdown | https://github.com/dlon/html2markdown/blob/5946da7136e69a67b3dd37fd0e896be4d6a5b482/html2markdown.py#L163-L330 |
dlon/html2markdown | html2markdown.py | convert | def convert(html):
"""converts an html string to markdown while preserving unsupported markup."""
bs = BeautifulSoup(html, 'html.parser')
_markdownify(bs)
ret = unicode(bs).replace(u'\xa0', ' ')
ret = re.sub(r'\n{3,}', r'\n\n', ret)
# ! FIXME: hack
ret = re.sub(r'<<<FLOATING LINK: (.+)>>>'... | python | def convert(html):
"""converts an html string to markdown while preserving unsupported markup."""
bs = BeautifulSoup(html, 'html.parser')
_markdownify(bs)
ret = unicode(bs).replace(u'\xa0', ' ')
ret = re.sub(r'\n{3,}', r'\n\n', ret)
# ! FIXME: hack
ret = re.sub(r'<<<FLOATING LINK: (.+)>>>'... | converts an html string to markdown while preserving unsupported markup. | https://github.com/dlon/html2markdown/blob/5946da7136e69a67b3dd37fd0e896be4d6a5b482/html2markdown.py#L332-L347 |
timknip/pyswf | swf/filters.py | SWFFilterFactory.create | def create(cls, type):
""" Return the specified Filter """
if type == 0: return FilterDropShadow(id)
elif type == 1: return FilterBlur(id)
elif type == 2: return FilterGlow(id)
elif type == 3: return FilterBevel(id)
elif type == 4: return FilterGradientGlow(id)
el... | python | def create(cls, type):
""" Return the specified Filter """
if type == 0: return FilterDropShadow(id)
elif type == 1: return FilterBlur(id)
elif type == 2: return FilterGlow(id)
elif type == 3: return FilterBevel(id)
elif type == 4: return FilterGradientGlow(id)
el... | Return the specified Filter | https://github.com/timknip/pyswf/blob/3740cc80d7650156831e728ea0d408819e5671eb/swf/filters.py#L220-L231 |
timknip/pyswf | swf/data.py | SWFRectangle.dimensions | def dimensions(self):
"""
Returns dimensions as (x, y) tuple.
"""
return (self.xmax - self.xmin, self.ymax - self.ymin) | python | def dimensions(self):
"""
Returns dimensions as (x, y) tuple.
"""
return (self.xmax - self.xmin, self.ymax - self.ymin) | Returns dimensions as (x, y) tuple. | https://github.com/timknip/pyswf/blob/3740cc80d7650156831e728ea0d408819e5671eb/swf/data.py#L1000-L1004 |
timknip/pyswf | swf/movie.py | SWF.export | def export(self, exporter=None, force_stroke=False):
"""
Export this SWF using the specified exporter.
When no exporter is passed in the default exporter used
is swf.export.SVGExporter.
Exporters should extend the swf.export.BaseExporter class.
@param ... | python | def export(self, exporter=None, force_stroke=False):
"""
Export this SWF using the specified exporter.
When no exporter is passed in the default exporter used
is swf.export.SVGExporter.
Exporters should extend the swf.export.BaseExporter class.
@param ... | Export this SWF using the specified exporter.
When no exporter is passed in the default exporter used
is swf.export.SVGExporter.
Exporters should extend the swf.export.BaseExporter class.
@param exporter : the exporter to use
@param force_stroke : set to true ... | https://github.com/timknip/pyswf/blob/3740cc80d7650156831e728ea0d408819e5671eb/swf/movie.py#L114-L131 |
timknip/pyswf | swf/movie.py | SWF.parse | def parse(self, data):
"""
Parses the SWF.
The @data parameter can be a file object or a SWFStream
"""
self._data = data = data if isinstance(data, SWFStream) else SWFStream(data)
self._header = SWFHeader(self._data)
if self._header.compressed:
... | python | def parse(self, data):
"""
Parses the SWF.
The @data parameter can be a file object or a SWFStream
"""
self._data = data = data if isinstance(data, SWFStream) else SWFStream(data)
self._header = SWFHeader(self._data)
if self._header.compressed:
... | Parses the SWF.
The @data parameter can be a file object or a SWFStream | https://github.com/timknip/pyswf/blob/3740cc80d7650156831e728ea0d408819e5671eb/swf/movie.py#L137-L162 |
timknip/pyswf | swf/stream.py | int32 | def int32(x):
""" Return a signed or unsigned int """
if x>0xFFFFFFFF:
raise OverflowError
if x>0x7FFFFFFF:
x=int(0x100000000-x)
if x<2147483648:
return -x
else:
return -2147483648
return x | python | def int32(x):
""" Return a signed or unsigned int """
if x>0xFFFFFFFF:
raise OverflowError
if x>0x7FFFFFFF:
x=int(0x100000000-x)
if x<2147483648:
return -x
else:
return -2147483648
return x | Return a signed or unsigned int | https://github.com/timknip/pyswf/blob/3740cc80d7650156831e728ea0d408819e5671eb/swf/stream.py#L490-L500 |
timknip/pyswf | swf/stream.py | SWFStream.bin | def bin(self, s):
""" Return a value as a binary string """
return str(s) if s<=1 else bin(s>>1) + str(s&1) | python | def bin(self, s):
""" Return a value as a binary string """
return str(s) if s<=1 else bin(s>>1) + str(s&1) | Return a value as a binary string | https://github.com/timknip/pyswf/blob/3740cc80d7650156831e728ea0d408819e5671eb/swf/stream.py#L22-L24 |
timknip/pyswf | swf/stream.py | SWFStream.calc_max_bits | def calc_max_bits(self, signed, values):
""" Calculates the maximim needed bits to represent a value """
b = 0
vmax = -10000000
for val in values:
if signed:
b = b | val if val >= 0 else b | ~val << 1
vmax = val if vmax < val else vmax... | python | def calc_max_bits(self, signed, values):
""" Calculates the maximim needed bits to represent a value """
b = 0
vmax = -10000000
for val in values:
if signed:
b = b | val if val >= 0 else b | ~val << 1
vmax = val if vmax < val else vmax... | Calculates the maximim needed bits to represent a value | https://github.com/timknip/pyswf/blob/3740cc80d7650156831e728ea0d408819e5671eb/swf/stream.py#L26-L42 |
timknip/pyswf | swf/stream.py | SWFStream.readbits | def readbits(self, bits):
"""
Read the specified number of bits from the stream.
Returns 0 for bits == 0.
"""
if bits == 0:
return 0
# fast byte-aligned path
if bits % 8 == 0 and self._bits_pending == 0:
return self._read_... | python | def readbits(self, bits):
"""
Read the specified number of bits from the stream.
Returns 0 for bits == 0.
"""
if bits == 0:
return 0
# fast byte-aligned path
if bits % 8 == 0 and self._bits_pending == 0:
return self._read_... | Read the specified number of bits from the stream.
Returns 0 for bits == 0. | https://github.com/timknip/pyswf/blob/3740cc80d7650156831e728ea0d408819e5671eb/swf/stream.py#L56-L105 |
timknip/pyswf | swf/stream.py | SWFStream.readSB | def readSB(self, bits):
""" Read a signed int using the specified number of bits """
shift = 32 - bits
return int32(self.readbits(bits) << shift) >> shift | python | def readSB(self, bits):
""" Read a signed int using the specified number of bits """
shift = 32 - bits
return int32(self.readbits(bits) << shift) >> shift | Read a signed int using the specified number of bits | https://github.com/timknip/pyswf/blob/3740cc80d7650156831e728ea0d408819e5671eb/swf/stream.py#L111-L114 |
timknip/pyswf | swf/stream.py | SWFStream.readEncodedU32 | def readEncodedU32(self):
""" Read a encoded unsigned int """
self.reset_bits_pending();
result = self.readUI8();
if result & 0x80 != 0:
result = (result & 0x7f) | (self.readUI8() << 7)
if result & 0x4000 != 0:
result = (result & 0x3fff) | (self.re... | python | def readEncodedU32(self):
""" Read a encoded unsigned int """
self.reset_bits_pending();
result = self.readUI8();
if result & 0x80 != 0:
result = (result & 0x7f) | (self.readUI8() << 7)
if result & 0x4000 != 0:
result = (result & 0x3fff) | (self.re... | Read a encoded unsigned int | https://github.com/timknip/pyswf/blob/3740cc80d7650156831e728ea0d408819e5671eb/swf/stream.py#L155-L167 |
timknip/pyswf | swf/stream.py | SWFStream.readFLOAT16 | def readFLOAT16(self):
""" Read a 2 byte float """
self.reset_bits_pending()
word = self.readUI16()
sign = -1 if ((word & 0x8000) != 0) else 1
exponent = (word >> 10) & 0x1f
significand = word & 0x3ff
if exponent == 0:
if significand == 0:
... | python | def readFLOAT16(self):
""" Read a 2 byte float """
self.reset_bits_pending()
word = self.readUI16()
sign = -1 if ((word & 0x8000) != 0) else 1
exponent = (word >> 10) & 0x1f
significand = word & 0x3ff
if exponent == 0:
if significand == 0:
... | Read a 2 byte float | https://github.com/timknip/pyswf/blob/3740cc80d7650156831e728ea0d408819e5671eb/swf/stream.py#L174-L192 |
timknip/pyswf | swf/stream.py | SWFStream.readSTYLECHANGERECORD | def readSTYLECHANGERECORD(self, states, fill_bits, line_bits, level = 1):
""" Read a SWFShapeRecordStyleChange """
return SWFShapeRecordStyleChange(self, states, fill_bits, line_bits, level) | python | def readSTYLECHANGERECORD(self, states, fill_bits, line_bits, level = 1):
""" Read a SWFShapeRecordStyleChange """
return SWFShapeRecordStyleChange(self, states, fill_bits, line_bits, level) | Read a SWFShapeRecordStyleChange | https://github.com/timknip/pyswf/blob/3740cc80d7650156831e728ea0d408819e5671eb/swf/stream.py#L263-L265 |
timknip/pyswf | swf/stream.py | SWFStream.readTEXTRECORD | def readTEXTRECORD(self, glyphBits, advanceBits, previousRecord=None, level=1):
""" Read a SWFTextRecord """
if self.readUI8() == 0:
return None
else:
self.seek(self.tell() - 1)
return SWFTextRecord(self, glyphBits, advanceBits, previousRecord, level) | python | def readTEXTRECORD(self, glyphBits, advanceBits, previousRecord=None, level=1):
""" Read a SWFTextRecord """
if self.readUI8() == 0:
return None
else:
self.seek(self.tell() - 1)
return SWFTextRecord(self, glyphBits, advanceBits, previousRecord, level) | Read a SWFTextRecord | https://github.com/timknip/pyswf/blob/3740cc80d7650156831e728ea0d408819e5671eb/swf/stream.py#L271-L277 |
timknip/pyswf | swf/stream.py | SWFStream.readACTIONRECORD | def readACTIONRECORD(self):
""" Read a SWFActionRecord """
action = None
actionCode = self.readUI8()
if actionCode != 0:
actionLength = self.readUI16() if actionCode >= 0x80 else 0
#print "0x%x"%actionCode, actionLength
action = SWFActionFactory.create... | python | def readACTIONRECORD(self):
""" Read a SWFActionRecord """
action = None
actionCode = self.readUI8()
if actionCode != 0:
actionLength = self.readUI16() if actionCode >= 0x80 else 0
#print "0x%x"%actionCode, actionLength
action = SWFActionFactory.create... | Read a SWFActionRecord | https://github.com/timknip/pyswf/blob/3740cc80d7650156831e728ea0d408819e5671eb/swf/stream.py#L307-L316 |
timknip/pyswf | swf/stream.py | SWFStream.readACTIONRECORDs | def readACTIONRECORDs(self):
""" Read zero or more button records (zero-terminated) """
out = []
while 1:
action = self.readACTIONRECORD()
if action:
out.append(action)
else:
break
return out | python | def readACTIONRECORDs(self):
""" Read zero or more button records (zero-terminated) """
out = []
while 1:
action = self.readACTIONRECORD()
if action:
out.append(action)
else:
break
return out | Read zero or more button records (zero-terminated) | https://github.com/timknip/pyswf/blob/3740cc80d7650156831e728ea0d408819e5671eb/swf/stream.py#L318-L327 |
timknip/pyswf | swf/stream.py | SWFStream.readCLIPACTIONRECORD | def readCLIPACTIONRECORD(self, version):
""" Read a SWFClipActionRecord """
pos = self.tell()
flags = self.readUI32() if version >= 6 else self.readUI16()
if flags == 0:
return None
else:
self.seek(pos)
return SWFClipActionRecord(self, version) | python | def readCLIPACTIONRECORD(self, version):
""" Read a SWFClipActionRecord """
pos = self.tell()
flags = self.readUI32() if version >= 6 else self.readUI16()
if flags == 0:
return None
else:
self.seek(pos)
return SWFClipActionRecord(self, version) | Read a SWFClipActionRecord | https://github.com/timknip/pyswf/blob/3740cc80d7650156831e728ea0d408819e5671eb/swf/stream.py#L333-L341 |
timknip/pyswf | swf/stream.py | SWFStream.readRGB | def readRGB(self):
""" Read a RGB color """
self.reset_bits_pending();
r = self.readUI8()
g = self.readUI8()
b = self.readUI8()
return (0xff << 24) | (r << 16) | (g << 8) | b | python | def readRGB(self):
""" Read a RGB color """
self.reset_bits_pending();
r = self.readUI8()
g = self.readUI8()
b = self.readUI8()
return (0xff << 24) | (r << 16) | (g << 8) | b | Read a RGB color | https://github.com/timknip/pyswf/blob/3740cc80d7650156831e728ea0d408819e5671eb/swf/stream.py#L347-L353 |
timknip/pyswf | swf/stream.py | SWFStream.readRGBA | def readRGBA(self):
""" Read a RGBA color """
self.reset_bits_pending();
r = self.readUI8()
g = self.readUI8()
b = self.readUI8()
a = self.readUI8()
return (a << 24) | (r << 16) | (g << 8) | b | python | def readRGBA(self):
""" Read a RGBA color """
self.reset_bits_pending();
r = self.readUI8()
g = self.readUI8()
b = self.readUI8()
a = self.readUI8()
return (a << 24) | (r << 16) | (g << 8) | b | Read a RGBA color | https://github.com/timknip/pyswf/blob/3740cc80d7650156831e728ea0d408819e5671eb/swf/stream.py#L355-L362 |
timknip/pyswf | swf/stream.py | SWFStream.readString | def readString(self):
""" Read a string """
s = self.f.read(1)
string = b""
while ord(s) > 0:
string += s
s = self.f.read(1)
return string.decode() | python | def readString(self):
""" Read a string """
s = self.f.read(1)
string = b""
while ord(s) > 0:
string += s
s = self.f.read(1)
return string.decode() | Read a string | https://github.com/timknip/pyswf/blob/3740cc80d7650156831e728ea0d408819e5671eb/swf/stream.py#L368-L375 |
timknip/pyswf | swf/stream.py | SWFStream.readFILTER | def readFILTER(self):
""" Read a SWFFilter """
filterId = self.readUI8()
filter = SWFFilterFactory.create(filterId)
filter.parse(self)
return filter | python | def readFILTER(self):
""" Read a SWFFilter """
filterId = self.readUI8()
filter = SWFFilterFactory.create(filterId)
filter.parse(self)
return filter | Read a SWFFilter | https://github.com/timknip/pyswf/blob/3740cc80d7650156831e728ea0d408819e5671eb/swf/stream.py#L377-L382 |
timknip/pyswf | swf/stream.py | SWFStream.readFILTERLIST | def readFILTERLIST(self):
""" Read a length-prefixed list of FILTERs """
number = self.readUI8()
return [self.readFILTER() for _ in range(number)] | python | def readFILTERLIST(self):
""" Read a length-prefixed list of FILTERs """
number = self.readUI8()
return [self.readFILTER() for _ in range(number)] | Read a length-prefixed list of FILTERs | https://github.com/timknip/pyswf/blob/3740cc80d7650156831e728ea0d408819e5671eb/swf/stream.py#L384-L387 |
timknip/pyswf | swf/stream.py | SWFStream.readBUTTONRECORDs | def readBUTTONRECORDs(self, version):
""" Read zero or more button records (zero-terminated) """
out = []
while 1:
button = self.readBUTTONRECORD(version)
if button:
out.append(button)
else:
break
return out | python | def readBUTTONRECORDs(self, version):
""" Read zero or more button records (zero-terminated) """
out = []
while 1:
button = self.readBUTTONRECORD(version)
if button:
out.append(button)
else:
break
return out | Read zero or more button records (zero-terminated) | https://github.com/timknip/pyswf/blob/3740cc80d7650156831e728ea0d408819e5671eb/swf/stream.py#L409-L418 |
timknip/pyswf | swf/stream.py | SWFStream.readBUTTONCONDACTIONSs | def readBUTTONCONDACTIONSs(self):
""" Read zero or more button-condition actions """
out = []
while 1:
action = self.readBUTTONCONDACTION()
if action:
out.append(action)
else:
break
return out | python | def readBUTTONCONDACTIONSs(self):
""" Read zero or more button-condition actions """
out = []
while 1:
action = self.readBUTTONCONDACTION()
if action:
out.append(action)
else:
break
return out | Read zero or more button-condition actions | https://github.com/timknip/pyswf/blob/3740cc80d7650156831e728ea0d408819e5671eb/swf/stream.py#L427-L436 |
timknip/pyswf | swf/stream.py | SWFStream.readtag_header | def readtag_header(self):
""" Read a tag header """
pos = self.tell()
tag_type_and_length = self.readUI16()
tag_length = tag_type_and_length & 0x003f
if tag_length == 0x3f:
# The SWF10 spec sez that this is a signed int.
# Shouldn't it be an unsigned int?
... | python | def readtag_header(self):
""" Read a tag header """
pos = self.tell()
tag_type_and_length = self.readUI16()
tag_length = tag_type_and_length & 0x003f
if tag_length == 0x3f:
# The SWF10 spec sez that this is a signed int.
# Shouldn't it be an unsigned int?
... | Read a tag header | https://github.com/timknip/pyswf/blob/3740cc80d7650156831e728ea0d408819e5671eb/swf/stream.py#L459-L468 |
timknip/pyswf | swf/stream.py | SWFStream.read | def read(self, count=0):
""" Read """
return self.f.read(count) if count > 0 else self.f.read() | python | def read(self, count=0):
""" Read """
return self.f.read(count) if count > 0 else self.f.read() | Read | https://github.com/timknip/pyswf/blob/3740cc80d7650156831e728ea0d408819e5671eb/swf/stream.py#L478-L480 |
timknip/pyswf | swf/tag.py | TagFactory.create | def create(cls, type):
""" Return the created tag by specifying an integer """
if type == 0: return TagEnd()
elif type == 1: return TagShowFrame()
elif type == 2: return TagDefineShape()
elif type == 4: return TagPlaceObject()
elif type == 5: return TagRemoveObject()
... | python | def create(cls, type):
""" Return the created tag by specifying an integer """
if type == 0: return TagEnd()
elif type == 1: return TagShowFrame()
elif type == 2: return TagDefineShape()
elif type == 4: return TagPlaceObject()
elif type == 5: return TagRemoveObject()
... | Return the created tag by specifying an integer | https://github.com/timknip/pyswf/blob/3740cc80d7650156831e728ea0d408819e5671eb/swf/tag.py#L18-L79 |
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