Tutorial for GenMultiDecay class¶
This tutorial shows how phasespace.fromdecay.GenMultiDecay can be used.
In order to use this functionality, you need to install the extra dependencies, for example through
pip install phasespace[fromdecay].
This submodule makes it possible for phasespace and DecayLanguage to work together.
More generally, GenMultiDecay can also be used as a high-level interface for simulating particles that can decay in multiple different ways.
# Import libraries
from pprint import pprint
import zfit
from particle import Particle
from decaylanguage import DecFileParser, DecayChainViewer, DecayChain, DecayMode
import tensorflow as tf
from phasespace.fromdecay import GenMultiDecay
/home/docs/checkouts/readthedocs.org/user_builds/phasespace/envs/latest/lib/python3.11/site-packages/zfit/__init__.py:63: UserWarning: TensorFlow warnings are by default suppressed by zfit. In order to show them, set the environment variable ZFIT_DISABLE_TF_WARNINGS=0. In order to suppress the TensorFlow warnings AND this warning, set ZFIT_DISABLE_TF_WARNINGS=1.
warnings.warn(
2024-04-01 23:19:16.324910: E external/local_xla/xla/stream_executor/cuda/cuda_dnn.cc:9261] Unable to register cuDNN factory: Attempting to register factory for plugin cuDNN when one has already been registered
2024-04-01 23:19:16.324967: E external/local_xla/xla/stream_executor/cuda/cuda_fft.cc:607] Unable to register cuFFT factory: Attempting to register factory for plugin cuFFT when one has already been registered
2024-04-01 23:19:16.326167: E external/local_xla/xla/stream_executor/cuda/cuda_blas.cc:1515] Unable to register cuBLAS factory: Attempting to register factory for plugin cuBLAS when one has already been registered
No module named 'nlopt'
Quick Intro to DecayLanguage¶
DecayLanguage can be used to parse and view .dec files. These files contain information about how a particle decays and with which probability. For more information about DecayLanguage and .dec files, see the DecayLanguage documentation.
We will begin by parsing a .dec file using DecayLanguage:
parser = DecFileParser('../tests/fromdecay/example_decays.dec')
parser.parse()
From the parser variable, one can access a certain decay for a particle using parser.build_decay_chains. This will be a dict that contains all information about how the mother particle, daughter particles etc. decay.
pi0_chain = parser.build_decay_chains("pi0")
pprint(pi0_chain)
{
'pi0'
:
[
{
'bf'
:
0.988228297
,
'fs'
:
['gamma', 'gamma']
,
'model'
:
'PHSP'
,
'model_params'
:
''
}
,
{
'bf'
:
0.011738247
,
'fs'
:
['e+', 'e-', 'gamma']
,
'model'
:
'PI0_DALITZ'
,
'model_params'
:
''
}
,
{
'bf'
:
3.3392e-05
,
'fs'
:
['e+', 'e+', 'e-', 'e-']
,
'model'
:
'PHSP'
,
'model_params'
:
''
}
,
{
'bf'
:
6.5e-08
,
'fs'
:
['e+', 'e-']
,
'model'
:
'PHSP'
,
'model_params'
:
''
}
]
}
This dict can also be displayed in a more human-readable way using DecayChainViewer:
DecayChainViewer(pi0_chain)
---------------------------------------------------------------------------
FileNotFoundError Traceback (most recent call last)
File ~/checkouts/readthedocs.org/user_builds/phasespace/envs/latest/lib/python3.11/site-packages/graphviz/backend/execute.py:76, in run_check(cmd, input_lines, encoding, quiet, **kwargs)
75 kwargs['stdout'] = kwargs['stderr'] = subprocess.PIPE
---> 76 proc = _run_input_lines(cmd, input_lines, kwargs=kwargs)
77 else:
File ~/checkouts/readthedocs.org/user_builds/phasespace/envs/latest/lib/python3.11/site-packages/graphviz/backend/execute.py:96, in _run_input_lines(cmd, input_lines, kwargs)
95 def _run_input_lines(cmd, input_lines, *, kwargs):
---> 96 popen = subprocess.Popen(cmd, stdin=subprocess.PIPE, **kwargs)
98 stdin_write = popen.stdin.write
File ~/.asdf/installs/python/3.11.6/lib/python3.11/subprocess.py:1026, in Popen.__init__(self, args, bufsize, executable, stdin, stdout, stderr, preexec_fn, close_fds, shell, cwd, env, universal_newlines, startupinfo, creationflags, restore_signals, start_new_session, pass_fds, user, group, extra_groups, encoding, errors, text, umask, pipesize, process_group)
1023 self.stderr = io.TextIOWrapper(self.stderr,
1024 encoding=encoding, errors=errors)
-> 1026 self._execute_child(args, executable, preexec_fn, close_fds,
1027 pass_fds, cwd, env,
1028 startupinfo, creationflags, shell,
1029 p2cread, p2cwrite,
1030 c2pread, c2pwrite,
1031 errread, errwrite,
1032 restore_signals,
1033 gid, gids, uid, umask,
1034 start_new_session, process_group)
1035 except:
1036 # Cleanup if the child failed starting.
File ~/.asdf/installs/python/3.11.6/lib/python3.11/subprocess.py:1950, in Popen._execute_child(self, args, executable, preexec_fn, close_fds, pass_fds, cwd, env, startupinfo, creationflags, shell, p2cread, p2cwrite, c2pread, c2pwrite, errread, errwrite, restore_signals, gid, gids, uid, umask, start_new_session, process_group)
1949 err_msg = os.strerror(errno_num)
-> 1950 raise child_exception_type(errno_num, err_msg, err_filename)
1951 raise child_exception_type(err_msg)
FileNotFoundError: [Errno 2] No such file or directory: PosixPath('dot')
The above exception was the direct cause of the following exception:
ExecutableNotFound Traceback (most recent call last)
File ~/checkouts/readthedocs.org/user_builds/phasespace/envs/latest/lib/python3.11/site-packages/IPython/core/formatters.py:977, in MimeBundleFormatter.__call__(self, obj, include, exclude)
974 method = get_real_method(obj, self.print_method)
976 if method is not None:
--> 977 return method(include=include, exclude=exclude)
978 return None
979 else:
File ~/checkouts/readthedocs.org/user_builds/phasespace/envs/latest/lib/python3.11/site-packages/decaylanguage/decay/viewer.py:259, in DecayChainViewer._repr_mimebundle_(self, include, exclude, **kwargs)
255 """
256 IPython display helper.
257 """
258 try:
--> 259 return self._graph._repr_mimebundle_(
260 include=include, exclude=exclude, **kwargs
261 )
262 except AttributeError:
263 return {"image/svg+xml": self._graph._repr_svg_()}
File ~/checkouts/readthedocs.org/user_builds/phasespace/envs/latest/lib/python3.11/site-packages/graphviz/jupyter_integration.py:98, in JupyterIntegration._repr_mimebundle_(self, include, exclude, **_)
96 include = set(include) if include is not None else {self._jupyter_mimetype}
97 include -= set(exclude or [])
---> 98 return {mimetype: getattr(self, method_name)()
99 for mimetype, method_name in MIME_TYPES.items()
100 if mimetype in include}
File ~/checkouts/readthedocs.org/user_builds/phasespace/envs/latest/lib/python3.11/site-packages/graphviz/jupyter_integration.py:98, in <dictcomp>(.0)
96 include = set(include) if include is not None else {self._jupyter_mimetype}
97 include -= set(exclude or [])
---> 98 return {mimetype: getattr(self, method_name)()
99 for mimetype, method_name in MIME_TYPES.items()
100 if mimetype in include}
File ~/checkouts/readthedocs.org/user_builds/phasespace/envs/latest/lib/python3.11/site-packages/graphviz/jupyter_integration.py:112, in JupyterIntegration._repr_image_svg_xml(self)
110 def _repr_image_svg_xml(self) -> str:
111 """Return the rendered graph as SVG string."""
--> 112 return self.pipe(format='svg', encoding=SVG_ENCODING)
File ~/checkouts/readthedocs.org/user_builds/phasespace/envs/latest/lib/python3.11/site-packages/graphviz/piping.py:104, in Pipe.pipe(self, format, renderer, formatter, neato_no_op, quiet, engine, encoding)
55 def pipe(self,
56 format: typing.Optional[str] = None,
57 renderer: typing.Optional[str] = None,
(...)
61 engine: typing.Optional[str] = None,
62 encoding: typing.Optional[str] = None) -> typing.Union[bytes, str]:
63 """Return the source piped through the Graphviz layout command.
64
65 Args:
(...)
102 '<?xml version='
103 """
--> 104 return self._pipe_legacy(format,
105 renderer=renderer,
106 formatter=formatter,
107 neato_no_op=neato_no_op,
108 quiet=quiet,
109 engine=engine,
110 encoding=encoding)
File ~/checkouts/readthedocs.org/user_builds/phasespace/envs/latest/lib/python3.11/site-packages/graphviz/_tools.py:171, in deprecate_positional_args.<locals>.decorator.<locals>.wrapper(*args, **kwargs)
162 wanted = ', '.join(f'{name}={value!r}'
163 for name, value in deprecated.items())
164 warnings.warn(f'The signature of {func.__name__} will be reduced'
165 f' to {supported_number} positional args'
166 f' {list(supported)}: pass {wanted}'
167 ' as keyword arg(s)',
168 stacklevel=stacklevel,
169 category=category)
--> 171 return func(*args, **kwargs)
File ~/checkouts/readthedocs.org/user_builds/phasespace/envs/latest/lib/python3.11/site-packages/graphviz/piping.py:121, in Pipe._pipe_legacy(self, format, renderer, formatter, neato_no_op, quiet, engine, encoding)
112 @_tools.deprecate_positional_args(supported_number=2)
113 def _pipe_legacy(self,
114 format: typing.Optional[str] = None,
(...)
119 engine: typing.Optional[str] = None,
120 encoding: typing.Optional[str] = None) -> typing.Union[bytes, str]:
--> 121 return self._pipe_future(format,
122 renderer=renderer,
123 formatter=formatter,
124 neato_no_op=neato_no_op,
125 quiet=quiet,
126 engine=engine,
127 encoding=encoding)
File ~/checkouts/readthedocs.org/user_builds/phasespace/envs/latest/lib/python3.11/site-packages/graphviz/piping.py:149, in Pipe._pipe_future(self, format, renderer, formatter, neato_no_op, quiet, engine, encoding)
146 if encoding is not None:
147 if codecs.lookup(encoding) is codecs.lookup(self.encoding):
148 # common case: both stdin and stdout need the same encoding
--> 149 return self._pipe_lines_string(*args, encoding=encoding, **kwargs)
150 try:
151 raw = self._pipe_lines(*args, input_encoding=self.encoding, **kwargs)
File ~/checkouts/readthedocs.org/user_builds/phasespace/envs/latest/lib/python3.11/site-packages/graphviz/backend/piping.py:212, in pipe_lines_string(engine, format, input_lines, encoding, renderer, formatter, neato_no_op, quiet)
206 cmd = dot_command.command(engine, format,
207 renderer=renderer,
208 formatter=formatter,
209 neato_no_op=neato_no_op)
210 kwargs = {'input_lines': input_lines, 'encoding': encoding}
--> 212 proc = execute.run_check(cmd, capture_output=True, quiet=quiet, **kwargs)
213 return proc.stdout
File ~/checkouts/readthedocs.org/user_builds/phasespace/envs/latest/lib/python3.11/site-packages/graphviz/backend/execute.py:81, in run_check(cmd, input_lines, encoding, quiet, **kwargs)
79 except OSError as e:
80 if e.errno == errno.ENOENT:
---> 81 raise ExecutableNotFound(cmd) from e
82 raise
84 if not quiet and proc.stderr:
ExecutableNotFound: failed to execute PosixPath('dot'), make sure the Graphviz executables are on your systems' PATH
<decaylanguage.decay.viewer.DecayChainViewer at 0x7f1c45ee7000>
You can also create a decay using the DecayChain and DecayMode classes. However, a DecayChain can only contain one chain, i.e., a particle cannot decay in multiple ways.
dplus_decay = DecayMode(1, "K- pi+ pi+ pi0", model="PHSP")
pi0_decay = DecayMode(1, "gamma gamma")
dplus_single = DecayChain("D+", {"D+": dplus_decay, "pi0": pi0_decay})
DecayChainViewer(dplus_single.to_dict())
---------------------------------------------------------------------------
FileNotFoundError Traceback (most recent call last)
File ~/checkouts/readthedocs.org/user_builds/phasespace/envs/latest/lib/python3.11/site-packages/graphviz/backend/execute.py:76, in run_check(cmd, input_lines, encoding, quiet, **kwargs)
75 kwargs['stdout'] = kwargs['stderr'] = subprocess.PIPE
---> 76 proc = _run_input_lines(cmd, input_lines, kwargs=kwargs)
77 else:
File ~/checkouts/readthedocs.org/user_builds/phasespace/envs/latest/lib/python3.11/site-packages/graphviz/backend/execute.py:96, in _run_input_lines(cmd, input_lines, kwargs)
95 def _run_input_lines(cmd, input_lines, *, kwargs):
---> 96 popen = subprocess.Popen(cmd, stdin=subprocess.PIPE, **kwargs)
98 stdin_write = popen.stdin.write
File ~/.asdf/installs/python/3.11.6/lib/python3.11/subprocess.py:1026, in Popen.__init__(self, args, bufsize, executable, stdin, stdout, stderr, preexec_fn, close_fds, shell, cwd, env, universal_newlines, startupinfo, creationflags, restore_signals, start_new_session, pass_fds, user, group, extra_groups, encoding, errors, text, umask, pipesize, process_group)
1023 self.stderr = io.TextIOWrapper(self.stderr,
1024 encoding=encoding, errors=errors)
-> 1026 self._execute_child(args, executable, preexec_fn, close_fds,
1027 pass_fds, cwd, env,
1028 startupinfo, creationflags, shell,
1029 p2cread, p2cwrite,
1030 c2pread, c2pwrite,
1031 errread, errwrite,
1032 restore_signals,
1033 gid, gids, uid, umask,
1034 start_new_session, process_group)
1035 except:
1036 # Cleanup if the child failed starting.
File ~/.asdf/installs/python/3.11.6/lib/python3.11/subprocess.py:1950, in Popen._execute_child(self, args, executable, preexec_fn, close_fds, pass_fds, cwd, env, startupinfo, creationflags, shell, p2cread, p2cwrite, c2pread, c2pwrite, errread, errwrite, restore_signals, gid, gids, uid, umask, start_new_session, process_group)
1949 err_msg = os.strerror(errno_num)
-> 1950 raise child_exception_type(errno_num, err_msg, err_filename)
1951 raise child_exception_type(err_msg)
FileNotFoundError: [Errno 2] No such file or directory: PosixPath('dot')
The above exception was the direct cause of the following exception:
ExecutableNotFound Traceback (most recent call last)
File ~/checkouts/readthedocs.org/user_builds/phasespace/envs/latest/lib/python3.11/site-packages/IPython/core/formatters.py:977, in MimeBundleFormatter.__call__(self, obj, include, exclude)
974 method = get_real_method(obj, self.print_method)
976 if method is not None:
--> 977 return method(include=include, exclude=exclude)
978 return None
979 else:
File ~/checkouts/readthedocs.org/user_builds/phasespace/envs/latest/lib/python3.11/site-packages/decaylanguage/decay/viewer.py:259, in DecayChainViewer._repr_mimebundle_(self, include, exclude, **kwargs)
255 """
256 IPython display helper.
257 """
258 try:
--> 259 return self._graph._repr_mimebundle_(
260 include=include, exclude=exclude, **kwargs
261 )
262 except AttributeError:
263 return {"image/svg+xml": self._graph._repr_svg_()}
File ~/checkouts/readthedocs.org/user_builds/phasespace/envs/latest/lib/python3.11/site-packages/graphviz/jupyter_integration.py:98, in JupyterIntegration._repr_mimebundle_(self, include, exclude, **_)
96 include = set(include) if include is not None else {self._jupyter_mimetype}
97 include -= set(exclude or [])
---> 98 return {mimetype: getattr(self, method_name)()
99 for mimetype, method_name in MIME_TYPES.items()
100 if mimetype in include}
File ~/checkouts/readthedocs.org/user_builds/phasespace/envs/latest/lib/python3.11/site-packages/graphviz/jupyter_integration.py:98, in <dictcomp>(.0)
96 include = set(include) if include is not None else {self._jupyter_mimetype}
97 include -= set(exclude or [])
---> 98 return {mimetype: getattr(self, method_name)()
99 for mimetype, method_name in MIME_TYPES.items()
100 if mimetype in include}
File ~/checkouts/readthedocs.org/user_builds/phasespace/envs/latest/lib/python3.11/site-packages/graphviz/jupyter_integration.py:112, in JupyterIntegration._repr_image_svg_xml(self)
110 def _repr_image_svg_xml(self) -> str:
111 """Return the rendered graph as SVG string."""
--> 112 return self.pipe(format='svg', encoding=SVG_ENCODING)
File ~/checkouts/readthedocs.org/user_builds/phasespace/envs/latest/lib/python3.11/site-packages/graphviz/piping.py:104, in Pipe.pipe(self, format, renderer, formatter, neato_no_op, quiet, engine, encoding)
55 def pipe(self,
56 format: typing.Optional[str] = None,
57 renderer: typing.Optional[str] = None,
(...)
61 engine: typing.Optional[str] = None,
62 encoding: typing.Optional[str] = None) -> typing.Union[bytes, str]:
63 """Return the source piped through the Graphviz layout command.
64
65 Args:
(...)
102 '<?xml version='
103 """
--> 104 return self._pipe_legacy(format,
105 renderer=renderer,
106 formatter=formatter,
107 neato_no_op=neato_no_op,
108 quiet=quiet,
109 engine=engine,
110 encoding=encoding)
File ~/checkouts/readthedocs.org/user_builds/phasespace/envs/latest/lib/python3.11/site-packages/graphviz/_tools.py:171, in deprecate_positional_args.<locals>.decorator.<locals>.wrapper(*args, **kwargs)
162 wanted = ', '.join(f'{name}={value!r}'
163 for name, value in deprecated.items())
164 warnings.warn(f'The signature of {func.__name__} will be reduced'
165 f' to {supported_number} positional args'
166 f' {list(supported)}: pass {wanted}'
167 ' as keyword arg(s)',
168 stacklevel=stacklevel,
169 category=category)
--> 171 return func(*args, **kwargs)
File ~/checkouts/readthedocs.org/user_builds/phasespace/envs/latest/lib/python3.11/site-packages/graphviz/piping.py:121, in Pipe._pipe_legacy(self, format, renderer, formatter, neato_no_op, quiet, engine, encoding)
112 @_tools.deprecate_positional_args(supported_number=2)
113 def _pipe_legacy(self,
114 format: typing.Optional[str] = None,
(...)
119 engine: typing.Optional[str] = None,
120 encoding: typing.Optional[str] = None) -> typing.Union[bytes, str]:
--> 121 return self._pipe_future(format,
122 renderer=renderer,
123 formatter=formatter,
124 neato_no_op=neato_no_op,
125 quiet=quiet,
126 engine=engine,
127 encoding=encoding)
File ~/checkouts/readthedocs.org/user_builds/phasespace/envs/latest/lib/python3.11/site-packages/graphviz/piping.py:149, in Pipe._pipe_future(self, format, renderer, formatter, neato_no_op, quiet, engine, encoding)
146 if encoding is not None:
147 if codecs.lookup(encoding) is codecs.lookup(self.encoding):
148 # common case: both stdin and stdout need the same encoding
--> 149 return self._pipe_lines_string(*args, encoding=encoding, **kwargs)
150 try:
151 raw = self._pipe_lines(*args, input_encoding=self.encoding, **kwargs)
File ~/checkouts/readthedocs.org/user_builds/phasespace/envs/latest/lib/python3.11/site-packages/graphviz/backend/piping.py:212, in pipe_lines_string(engine, format, input_lines, encoding, renderer, formatter, neato_no_op, quiet)
206 cmd = dot_command.command(engine, format,
207 renderer=renderer,
208 formatter=formatter,
209 neato_no_op=neato_no_op)
210 kwargs = {'input_lines': input_lines, 'encoding': encoding}
--> 212 proc = execute.run_check(cmd, capture_output=True, quiet=quiet, **kwargs)
213 return proc.stdout
File ~/checkouts/readthedocs.org/user_builds/phasespace/envs/latest/lib/python3.11/site-packages/graphviz/backend/execute.py:81, in run_check(cmd, input_lines, encoding, quiet, **kwargs)
79 except OSError as e:
80 if e.errno == errno.ENOENT:
---> 81 raise ExecutableNotFound(cmd) from e
82 raise
84 if not quiet and proc.stderr:
ExecutableNotFound: failed to execute PosixPath('dot'), make sure the Graphviz executables are on your systems' PATH
<decaylanguage.decay.viewer.DecayChainViewer at 0x7f1c45af55c0>
Creating a GenMultiDecay object¶
A regular phasespace.GenParticle instance would not be able to simulate this decay, since the \(\pi^0\) particle can decay in four different ways. However, a GenMultiDecay object can be created directly from a DecayLanguage dict:
pi0_decay = GenMultiDecay.from_dict(pi0_chain)
When creating a GenMultiDecay object, the DecayLanguage dict is “unpacked” into separate GenParticle instances, where each GenParticle instance corresponds to one way that the particle can decay.
These GenParticle instances and the probabilities of that decay mode can be accessed via GenMultiDecay.gen_particles. This is a list of tuples, where the first element in the tuple is the probability and the second element is the GenParticle.
for probability, particle in pi0_decay.gen_particles:
print(f"There is a probability of {probability} "
f"that pi0 decays into {', '.join(child.name for child in particle.children)}")
There is a probability of 0.988228297 that pi0 decays into gamma, gamma [0]
There is a probability of 0.011738247 that pi0 decays into e+, e-, gamma [1]
There is a probability of 3.3392e-05 that pi0 decays into e+ [0], e+ [1], e- [0], e- [1]
There is a probability of 6.5e-08 that pi0 decays into e+ [2], e- [2]
One can simulate this decay using the .generate method, which works the same as the GenParticle.generate method.
When calling the GenMultiDecay.generate method, it internally calls the generate method on the of the GenParticle instances in GenMultiDecay.gen_particles. The outputs are placed in a list, which is returned.
weights, events = pi0_decay.generate(n_events=10_000)
print("Number of events for each decay mode:", ", ".join(str(len(w)) for w in weights))
WARNING: All log messages before absl::InitializeLog() is called are written to STDERR
I0000 00:00:1712013561.849163 745 device_compiler.h:186] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.
2024-04-01 23:19:21.850196: E external/local_xla/xla/stream_executor/stream_executor_internal.h:177] SetPriority unimplemented for this stream.
2024-04-01 23:19:21.900163: E external/local_xla/xla/stream_executor/stream_executor_internal.h:177] SetPriority unimplemented for this stream.
Number of events for each decay mode:
9890, 110
We can confirm that the counts above are close to the expected counts based on the probabilities.
Changing mass settings¶
Since DecayLanguage dicts do not contain any information about the mass of a particle, the fromdecay submodule uses the particle package to find the mass of a particle based on its name.
The mass can either be a constant value or a function (besides the top particle, which is always a constant).
These settings can be modified by passing in additional parameters to GenMultiDecay.from_dict.
There are two optional parameters that can be passed to GenMultiDecay.from_dict: tolerance and mass_converter.
Constant vs variable mass¶
If a particle has a width less than tolerance, its mass is set to a constant value.
This will be demonsttrated with the decay below:
dsplus_chain = parser.build_decay_chains("D*+", stable_particles=["D+"])
DecayChainViewer(dsplus_chain)
---------------------------------------------------------------------------
FileNotFoundError Traceback (most recent call last)
File ~/checkouts/readthedocs.org/user_builds/phasespace/envs/latest/lib/python3.11/site-packages/graphviz/backend/execute.py:76, in run_check(cmd, input_lines, encoding, quiet, **kwargs)
75 kwargs['stdout'] = kwargs['stderr'] = subprocess.PIPE
---> 76 proc = _run_input_lines(cmd, input_lines, kwargs=kwargs)
77 else:
File ~/checkouts/readthedocs.org/user_builds/phasespace/envs/latest/lib/python3.11/site-packages/graphviz/backend/execute.py:96, in _run_input_lines(cmd, input_lines, kwargs)
95 def _run_input_lines(cmd, input_lines, *, kwargs):
---> 96 popen = subprocess.Popen(cmd, stdin=subprocess.PIPE, **kwargs)
98 stdin_write = popen.stdin.write
File ~/.asdf/installs/python/3.11.6/lib/python3.11/subprocess.py:1026, in Popen.__init__(self, args, bufsize, executable, stdin, stdout, stderr, preexec_fn, close_fds, shell, cwd, env, universal_newlines, startupinfo, creationflags, restore_signals, start_new_session, pass_fds, user, group, extra_groups, encoding, errors, text, umask, pipesize, process_group)
1023 self.stderr = io.TextIOWrapper(self.stderr,
1024 encoding=encoding, errors=errors)
-> 1026 self._execute_child(args, executable, preexec_fn, close_fds,
1027 pass_fds, cwd, env,
1028 startupinfo, creationflags, shell,
1029 p2cread, p2cwrite,
1030 c2pread, c2pwrite,
1031 errread, errwrite,
1032 restore_signals,
1033 gid, gids, uid, umask,
1034 start_new_session, process_group)
1035 except:
1036 # Cleanup if the child failed starting.
File ~/.asdf/installs/python/3.11.6/lib/python3.11/subprocess.py:1950, in Popen._execute_child(self, args, executable, preexec_fn, close_fds, pass_fds, cwd, env, startupinfo, creationflags, shell, p2cread, p2cwrite, c2pread, c2pwrite, errread, errwrite, restore_signals, gid, gids, uid, umask, start_new_session, process_group)
1949 err_msg = os.strerror(errno_num)
-> 1950 raise child_exception_type(errno_num, err_msg, err_filename)
1951 raise child_exception_type(err_msg)
FileNotFoundError: [Errno 2] No such file or directory: PosixPath('dot')
The above exception was the direct cause of the following exception:
ExecutableNotFound Traceback (most recent call last)
File ~/checkouts/readthedocs.org/user_builds/phasespace/envs/latest/lib/python3.11/site-packages/IPython/core/formatters.py:977, in MimeBundleFormatter.__call__(self, obj, include, exclude)
974 method = get_real_method(obj, self.print_method)
976 if method is not None:
--> 977 return method(include=include, exclude=exclude)
978 return None
979 else:
File ~/checkouts/readthedocs.org/user_builds/phasespace/envs/latest/lib/python3.11/site-packages/decaylanguage/decay/viewer.py:259, in DecayChainViewer._repr_mimebundle_(self, include, exclude, **kwargs)
255 """
256 IPython display helper.
257 """
258 try:
--> 259 return self._graph._repr_mimebundle_(
260 include=include, exclude=exclude, **kwargs
261 )
262 except AttributeError:
263 return {"image/svg+xml": self._graph._repr_svg_()}
File ~/checkouts/readthedocs.org/user_builds/phasespace/envs/latest/lib/python3.11/site-packages/graphviz/jupyter_integration.py:98, in JupyterIntegration._repr_mimebundle_(self, include, exclude, **_)
96 include = set(include) if include is not None else {self._jupyter_mimetype}
97 include -= set(exclude or [])
---> 98 return {mimetype: getattr(self, method_name)()
99 for mimetype, method_name in MIME_TYPES.items()
100 if mimetype in include}
File ~/checkouts/readthedocs.org/user_builds/phasespace/envs/latest/lib/python3.11/site-packages/graphviz/jupyter_integration.py:98, in <dictcomp>(.0)
96 include = set(include) if include is not None else {self._jupyter_mimetype}
97 include -= set(exclude or [])
---> 98 return {mimetype: getattr(self, method_name)()
99 for mimetype, method_name in MIME_TYPES.items()
100 if mimetype in include}
File ~/checkouts/readthedocs.org/user_builds/phasespace/envs/latest/lib/python3.11/site-packages/graphviz/jupyter_integration.py:112, in JupyterIntegration._repr_image_svg_xml(self)
110 def _repr_image_svg_xml(self) -> str:
111 """Return the rendered graph as SVG string."""
--> 112 return self.pipe(format='svg', encoding=SVG_ENCODING)
File ~/checkouts/readthedocs.org/user_builds/phasespace/envs/latest/lib/python3.11/site-packages/graphviz/piping.py:104, in Pipe.pipe(self, format, renderer, formatter, neato_no_op, quiet, engine, encoding)
55 def pipe(self,
56 format: typing.Optional[str] = None,
57 renderer: typing.Optional[str] = None,
(...)
61 engine: typing.Optional[str] = None,
62 encoding: typing.Optional[str] = None) -> typing.Union[bytes, str]:
63 """Return the source piped through the Graphviz layout command.
64
65 Args:
(...)
102 '<?xml version='
103 """
--> 104 return self._pipe_legacy(format,
105 renderer=renderer,
106 formatter=formatter,
107 neato_no_op=neato_no_op,
108 quiet=quiet,
109 engine=engine,
110 encoding=encoding)
File ~/checkouts/readthedocs.org/user_builds/phasespace/envs/latest/lib/python3.11/site-packages/graphviz/_tools.py:171, in deprecate_positional_args.<locals>.decorator.<locals>.wrapper(*args, **kwargs)
162 wanted = ', '.join(f'{name}={value!r}'
163 for name, value in deprecated.items())
164 warnings.warn(f'The signature of {func.__name__} will be reduced'
165 f' to {supported_number} positional args'
166 f' {list(supported)}: pass {wanted}'
167 ' as keyword arg(s)',
168 stacklevel=stacklevel,
169 category=category)
--> 171 return func(*args, **kwargs)
File ~/checkouts/readthedocs.org/user_builds/phasespace/envs/latest/lib/python3.11/site-packages/graphviz/piping.py:121, in Pipe._pipe_legacy(self, format, renderer, formatter, neato_no_op, quiet, engine, encoding)
112 @_tools.deprecate_positional_args(supported_number=2)
113 def _pipe_legacy(self,
114 format: typing.Optional[str] = None,
(...)
119 engine: typing.Optional[str] = None,
120 encoding: typing.Optional[str] = None) -> typing.Union[bytes, str]:
--> 121 return self._pipe_future(format,
122 renderer=renderer,
123 formatter=formatter,
124 neato_no_op=neato_no_op,
125 quiet=quiet,
126 engine=engine,
127 encoding=encoding)
File ~/checkouts/readthedocs.org/user_builds/phasespace/envs/latest/lib/python3.11/site-packages/graphviz/piping.py:149, in Pipe._pipe_future(self, format, renderer, formatter, neato_no_op, quiet, engine, encoding)
146 if encoding is not None:
147 if codecs.lookup(encoding) is codecs.lookup(self.encoding):
148 # common case: both stdin and stdout need the same encoding
--> 149 return self._pipe_lines_string(*args, encoding=encoding, **kwargs)
150 try:
151 raw = self._pipe_lines(*args, input_encoding=self.encoding, **kwargs)
File ~/checkouts/readthedocs.org/user_builds/phasespace/envs/latest/lib/python3.11/site-packages/graphviz/backend/piping.py:212, in pipe_lines_string(engine, format, input_lines, encoding, renderer, formatter, neato_no_op, quiet)
206 cmd = dot_command.command(engine, format,
207 renderer=renderer,
208 formatter=formatter,
209 neato_no_op=neato_no_op)
210 kwargs = {'input_lines': input_lines, 'encoding': encoding}
--> 212 proc = execute.run_check(cmd, capture_output=True, quiet=quiet, **kwargs)
213 return proc.stdout
File ~/checkouts/readthedocs.org/user_builds/phasespace/envs/latest/lib/python3.11/site-packages/graphviz/backend/execute.py:81, in run_check(cmd, input_lines, encoding, quiet, **kwargs)
79 except OSError as e:
80 if e.errno == errno.ENOENT:
---> 81 raise ExecutableNotFound(cmd) from e
82 raise
84 if not quiet and proc.stderr:
ExecutableNotFound: failed to execute PosixPath('dot'), make sure the Graphviz executables are on your systems' PATH
<decaylanguage.decay.viewer.DecayChainViewer at 0x7f1c45d14cc0>
print(f"pi0 width = {Particle.from_evtgen_name('pi0').width}\n"
f"D0 width = {Particle.from_evtgen_name('D0').width}")
pi0 width = 7.81e-06
D0 width = 1.604e-09
\(\pi^0\) has a greater width than \(D^0\). If the tolerance is set to a value between their widths, the \(D^0\) particle will have a constant mass while \(\pi^0\) will not.
dstar_decay = GenMultiDecay.from_dict(dsplus_chain, tolerance=1e-8)
# Loop over D0 and pi+ particles, see graph above
for particle in dstar_decay.gen_particles[0][1].children:
# If a particle width is less than tolerance or if it does not have any children, its mass will be fixed.
assert particle.has_fixed_mass
# Loop over D+ and pi0. See above.
for particle in dstar_decay.gen_particles[1][1].children:
if particle.name == "pi0":
assert not particle.has_fixed_mass
Configuring mass functions¶
By default, the mass function used for variable mass is the relativistic Breit-Wigner distribution. This can however be changed. If you want the mother particle to have a specific mass function for a specific decay, you can add a zfit parameter to the DecayLanguage dict. Consider for example the previous \(D^{*+}\) example:
dsplus_custom_mass_func = dsplus_chain.copy()
dsplus_chain_subset = dsplus_custom_mass_func["D*+"][1]["fs"][1]
print("Before:")
pprint(dsplus_chain_subset)
# Set the mass function of pi0 to a gaussian distribution when it decays into two photons (gamma)
dsplus_chain_subset["pi0"][0]["zfit"] = "gauss"
print("After:")
pprint(dsplus_chain_subset)
Before:
{
'pi0'
:
[
{
'bf'
:
0.988228297
,
'fs'
:
['gamma', 'gamma']
,
'model'
:
'PHSP'
,
'model_params'
:
''
}
,
{
'bf'
:
0.011738247
,
'fs'
:
['e+', 'e-', 'gamma']
,
'model'
:
'PI0_DALITZ'
,
'model_params'
:
''
}
,
{
'bf'
:
3.3392e-05
,
'fs'
:
['e+', 'e+', 'e-', 'e-']
,
'model'
:
'PHSP'
,
'model_params'
:
''
}
,
{
'bf'
:
6.5e-08
,
'fs'
:
['e+', 'e-']
,
'model'
:
'PHSP'
,
'model_params'
:
''
}
]
}
After:
{
'pi0'
:
[
{
'bf'
:
0.988228297
,
'fs'
:
['gamma', 'gamma']
,
'model'
:
'PHSP'
,
'model_params'
:
''
,
'zfit'
:
'gauss'
}
,
{
'bf'
:
0.011738247
,
'fs'
:
['e+', 'e-', 'gamma']
,
'model'
:
'PI0_DALITZ'
,
'model_params'
:
''
}
,
{
'bf'
:
3.3392e-05
,
'fs'
:
['e+', 'e+', 'e-', 'e-']
,
'model'
:
'PHSP'
,
'model_params'
:
''
}
,
{
'bf'
:
6.5e-08
,
'fs'
:
['e+', 'e-']
,
'model'
:
'PHSP'
,
'model_params'
:
''
}
]
}
Notice the added zfit field to the first decay mode of the \(\pi^0\) particle. This dict can then be passed to GenMultiDecay.from_dict, like before.
GenMultiDecay.from_dict(dsplus_custom_mass_func)
<phasespace.fromdecay.genmultidecay.GenMultiDecay at 0x7f1c4415fd10>
If you want all \(\pi^0\) particles to decay with the same mass function, you do not need to specify the zfit parameter for each decay in the dict. Instead, one can pass the particle_model_map parameter to the constructor:
GenMultiDecay.from_dict(dsplus_chain, particle_model_map={'pi0': 'gauss'}) # pi0 always decays with a gaussian mass distribution.
<phasespace.fromdecay.genmultidecay.GenMultiDecay at 0x7f1c4549c350>
When using DecayChains, the syntax for specifying the mass function becomes cleaner:
dplus_decay = DecayMode(1, "K- pi+ pi+ pi0", model="PHSP") # The model parameter will be ignored by GenMultiDecay
pi0_decay = DecayMode(1, "gamma gamma", zfit="gauss") # Make pi0 have a gaussian mass distribution
dplus_single = DecayChain("D+", {"D+": dplus_decay, "pi0": pi0_decay})
GenMultiDecay.from_dict(dplus_single.to_dict())
<phasespace.fromdecay.genmultidecay.GenMultiDecay at 0x7f1c454ade90>
Custom mass functions¶
The built-in supported mass function names are gauss, bw, and relbw, with gauss being the gaussian distribution, bw being the Breit-Wigner distribution, and relbw being the relativistic Breit-Wigner distribution.
If a non-supported value for the zfit parameter is not specified, it will automatically use the relativistic Breit-Wigner distribution. This behavior can be changed by changing the value of GenMultiDecay.DEFAULT_MASS_FUNC to a different string, e.g., "gauss". If an invalid value for the zfit parameter is used, a KeyError is raised.
It is also possible to add your own mass functions besides the built-in ones. You should then create a function that takes the mass and width of a particle and returns a mass function which with the format that is used for all phasespace mass functions. Below is an example of a custom gaussian distribution (implemented in the same way as the built-in gaussian distribution), which uses zfit PDFs:
def custom_gauss(mass, width):
particle_mass = tf.cast(mass, tf.float64)
particle_width = tf.cast(width, tf.float64)
# This is the actual mass function that will be returned
def mass_func(min_mass, max_mass, n_events):
min_mass = tf.cast(min_mass, tf.float64)
max_mass = tf.cast(max_mass, tf.float64)
# Use a zfit PDF
pdf = zfit.pdf.Gauss(mu=particle_mass, sigma=particle_width, obs="")
iterator = tf.stack([min_mass, max_mass], axis=-1)
return tf.vectorized_map(
lambda lim: pdf.sample(1, limits=(lim[0], lim[1])), iterator
)
return mass_func
This function can then be passed to GenMultiDecay.from_dict as a dict, where the key specifies the zfit parameter name. In the example below, it is set to "custom_gauss". However, this name can be chosen arbitrarily and does not need to be the same as the function name.
dsplus_chain_subset = dsplus_custom_mass_func["D*+"][1]["fs"][1]
print("Before:")
pprint(dsplus_chain_subset)
# Set the mass function of pi0 to the custom gaussian distribution
# when it decays into an electron-positron pair and a photon (gamma)
dsplus_chain_subset["pi0"][1]["zfit"] = "custom_gauss"
print("After:")
pprint(dsplus_chain_subset)
Before:
{
'pi0'
:
[
{
'bf'
:
0.988228297
,
'fs'
:
['gamma', 'gamma']
,
'model'
:
'PHSP'
,
'model_params'
:
''
,
'zfit'
:
'gauss'
}
,
{
'bf'
:
0.011738247
,
'fs'
:
['e+', 'e-', 'gamma']
,
'model'
:
'PI0_DALITZ'
,
'model_params'
:
''
}
,
{
'bf'
:
3.3392e-05
,
'fs'
:
['e+', 'e+', 'e-', 'e-']
,
'model'
:
'PHSP'
,
'model_params'
:
''
}
,
{
'bf'
:
6.5e-08
,
'fs'
:
['e+', 'e-']
,
'model'
:
'PHSP'
,
'model_params'
:
''
}
]
}
After:
{
'pi0'
:
[
{
'bf'
:
0.988228297
,
'fs'
:
['gamma', 'gamma']
,
'model'
:
'PHSP'
,
'model_params'
:
''
,
'zfit'
:
'gauss'
}
,
{
'bf'
:
0.011738247
,
'fs'
:
['e+', 'e-', 'gamma']
,
'model'
:
'PI0_DALITZ'
,
'model_params'
:
''
,
'zfit'
:
'custom_gauss'
}
,
{
'bf'
:
3.3392e-05
,
'fs'
:
['e+', 'e+', 'e-', 'e-']
,
'model'
:
'PHSP'
,
'model_params'
:
''
}
,
{
'bf'
:
6.5e-08
,
'fs'
:
['e+', 'e-']
,
'model'
:
'PHSP'
,
'model_params'
:
''
}
]
}
GenMultiDecay.from_dict(dsplus_custom_mass_func, {"custom_gauss": custom_gauss})
<phasespace.fromdecay.genmultidecay.GenMultiDecay at 0x7f1c4549ccd0>