Download envs/kitoverlay/skimage/_shared/utils.py from AVSim/simulation-package: direct link, hf CLI and curl.
- Browser
- Download file 36.6 kB
-
https://huggingface.co/datasets/AVSim/simulation-package/resolve/main/envs/kitoverlay/skimage/_shared/utils.py
- Command line
-
hf download hf://datasets/AVSim/simulation-package/envs/kitoverlay/skimage/_shared/utils.py
-
curl -L -o utils.py https://huggingface.co/datasets/AVSim/simulation-package/resolve/main/envs/kitoverlay/skimage/_shared/utils.py
36.6 kB
| import functools | |
| import inspect | |
| import sys | |
| import warnings | |
| from contextlib import contextmanager | |
| import numpy as np | |
| from ._warnings import all_warnings, warn | |
| __all__ = [ | |
| 'deprecate_func', | |
| 'get_bound_method_class', | |
| 'all_warnings', | |
| 'safe_as_int', | |
| 'check_shape_equality', | |
| 'check_nD', | |
| 'warn', | |
| 'reshape_nd', | |
| 'identity', | |
| 'slice_at_axis', | |
| "deprecate_parameter", | |
| "DEPRECATED", | |
| ] | |
| def count_inner_wrappers(func): | |
| """Count the number of inner wrappers by unpacking ``__wrapped__``. | |
| If a wrapped function wraps another wrapped function, then we refer to the | |
| wrapping of the second function as an *inner wrapper*. | |
| For example, consider this code fragment: | |
| .. code-block:: python | |
| @wrap_outer | |
| @wrap_inner | |
| def foo(): | |
| pass | |
| Here ``@wrap_inner`` applies a wrapper to ``foo``, and ``@wrap_outer`` | |
| applies a wrapper to the result. | |
| Parameters | |
| ---------- | |
| func : callable | |
| The callable of which to determine the number of inner wrappers. | |
| Returns | |
| ------- | |
| count : int | |
| The number of times `func` has been wrapped. | |
| See Also | |
| -------- | |
| count_global_wrappers | |
| """ | |
| unwrapped = func | |
| count = 0 | |
| while hasattr(unwrapped, "__wrapped__"): | |
| unwrapped = unwrapped.__wrapped__ | |
| count += 1 | |
| return count | |
| def _warning_stacklevel(func): | |
| """Find stacklevel of `func` relative to its global representation. | |
| Determine automatically with which stacklevel a warning should be raised. | |
| Parameters | |
| ---------- | |
| func : Callable | |
| Tries to find the global version of `func` and counts the number of | |
| additional wrappers around `func`. | |
| Returns | |
| ------- | |
| stacklevel : int | |
| The stacklevel. Minimum of 2. | |
| """ | |
| # Count number of wrappers around `func` | |
| inner_wrapped_count = count_inner_wrappers(func) | |
| global_wrapped_count = count_global_wrappers(func) | |
| stacklevel = global_wrapped_count - inner_wrapped_count + 1 | |
| return max(stacklevel, 2) | |
| def count_global_wrappers(func): | |
| """Count the total number of times a function as been wrapped globally. | |
| Similar to :func:`count_inner_wrappers`, this counts the number of times | |
| `func` has been wrapped. However, this function doesn't start counting | |
| from `func` but instead tries to access the "global representation" of | |
| `func`. This means that you could use this function from inside a wrapper | |
| that was applied first, and still count wrappers that were applied on | |
| top of it afterwards. | |
| E.g., `func` might be wrapped by multiple decorators that emit | |
| warnings. In that case, calling this function in the inner-most decorator | |
| will still return the total count of wrappers. | |
| Parameters | |
| ---------- | |
| func : callable | |
| The callable of which to determine the number of wrappers. Can be a | |
| function or method of a class. | |
| Returns | |
| ------- | |
| count : int | |
| The number of times `func` has been wrapped. | |
| See Also | |
| -------- | |
| count_inner_wrappers | |
| """ | |
| if "<locals>" in func.__qualname__: | |
| msg = ( | |
| "Cannot determine stacklevel of a function defined in another " | |
| "function's local namespace. Set the stacklevel manually." | |
| ) | |
| raise ValueError(msg) | |
| first_name, *other = func.__qualname__.split(".") | |
| global_func = func.__globals__.get(first_name, func) | |
| # Account for `func` being a method, in which case it's an attribute of | |
| # what we got from `func.__globals__` | |
| for part in other: | |
| global_func = getattr(global_func, part, global_func) | |
| count = count_inner_wrappers(global_func) | |
| assert count >= 0 | |
| return count | |
| class change_default_value: | |
| """Decorator for changing the default value of an argument. | |
| Parameters | |
| ---------- | |
| arg_name : str | |
| The name of the argument to be updated. | |
| new_value : any | |
| The argument new value. | |
| changed_version : str | |
| The package version in which the change will be introduced. | |
| warning_msg : str | |
| Optional warning message. If None, a generic warning message | |
| is used. | |
| stacklevel : {None, int}, optional | |
| If None, the decorator attempts to detect the appropriate stacklevel for the | |
| deprecation warning automatically. This can fail, e.g., due to | |
| decorating a closure, in which case you can set the stacklevel manually | |
| here. The outermost decorator should have stacklevel 2, the next inner | |
| one stacklevel 3, etc. | |
| """ | |
| def __init__( | |
| self, arg_name, *, new_value, changed_version, warning_msg=None, stacklevel=None | |
| ): | |
| self.arg_name = arg_name | |
| self.new_value = new_value | |
| self.warning_msg = warning_msg | |
| self.changed_version = changed_version | |
| self.stacklevel = stacklevel | |
| def __call__(self, func): | |
| parameters = inspect.signature(func).parameters | |
| arg_idx = list(parameters.keys()).index(self.arg_name) | |
| old_value = parameters[self.arg_name].default | |
| if self.warning_msg is None: | |
| self.warning_msg = ( | |
| f'The new recommended value for {self.arg_name} is ' | |
| f'{self.new_value}. Until version {self.changed_version}, ' | |
| f'the default {self.arg_name} value is {old_value}. ' | |
| f'From version {self.changed_version}, the {self.arg_name} ' | |
| f'default value will be {self.new_value}. To avoid ' | |
| f'this warning, please explicitly set {self.arg_name} value.' | |
| ) | |
| def fixed_func(*args, **kwargs): | |
| if len(args) < arg_idx + 1 and self.arg_name not in kwargs.keys(): | |
| stacklevel = ( | |
| self.stacklevel | |
| if self.stacklevel is not None | |
| else _warning_stacklevel(func) | |
| ) | |
| # warn that arg_name default value changed: | |
| warnings.warn(self.warning_msg, FutureWarning, stacklevel=stacklevel) | |
| return func(*args, **kwargs) | |
| return fixed_func | |
| class PatchClassRepr(type): | |
| """Control class representations in rendered signatures.""" | |
| def __repr__(cls): | |
| return f"<{cls.__name__}>" | |
| class DEPRECATED(metaclass=PatchClassRepr): | |
| """Signal value to help with deprecating parameters that use None. | |
| This is a proxy object, used to signal that a parameter has not been set. | |
| This is useful if ``None`` is already used for a different purpose or just | |
| to highlight a deprecated parameter in the signature. | |
| """ | |
| class deprecate_parameter: | |
| """Deprecate a parameter of a function. | |
| Parameters | |
| ---------- | |
| deprecated_name : str | |
| The name of the deprecated parameter. | |
| start_version : str | |
| The package version in which the warning was introduced. | |
| stop_version : str | |
| The package version in which the warning will be replaced by | |
| an error / the deprecation is completed. | |
| template : str, optional | |
| If given, this message template is used instead of the default one. | |
| new_name : str, optional | |
| If given, the default message will recommend the new parameter name and an | |
| error will be raised if the user uses both old and new names for the | |
| same parameter. | |
| modify_docstring : bool, optional | |
| If the wrapped function has a docstring, add the deprecated parameters | |
| to the "Other Parameters" section. | |
| stacklevel : {None, int}, optional | |
| If None, the decorator attempts to detect the appropriate stacklevel for the | |
| deprecation warning automatically. This can fail, e.g., due to | |
| decorating a closure, in which case you can set the stacklevel manually | |
| here. The outermost decorator should have stacklevel 2, the next inner | |
| one stacklevel 3, etc. | |
| Notes | |
| ----- | |
| Assign `DEPRECATED` as the new default value for the deprecated parameter. | |
| This marks the status of the parameter also in the signature and rendered | |
| HTML docs. | |
| This decorator can be stacked to deprecate more than one parameter. | |
| Examples | |
| -------- | |
| >>> from skimage._shared.utils import deprecate_parameter, DEPRECATED | |
| >>> @deprecate_parameter( | |
| ... "b", new_name="c", start_version="0.1", stop_version="0.3" | |
| ... ) | |
| ... def foo(a, b=DEPRECATED, *, c=None): | |
| ... return a, c | |
| Calling ``foo(1, b=2)`` will warn with:: | |
| FutureWarning: Parameter `b` is deprecated since version 0.1 and will | |
| be removed in 0.3 (or later). To avoid this warning, please use the | |
| parameter `c` instead. For more details, see the documentation of | |
| `foo`. | |
| """ | |
| DEPRECATED = DEPRECATED # Make signal value accessible for convenience | |
| remove_parameter_template = ( | |
| "Parameter `{deprecated_name}` is deprecated since version " | |
| "{deprecated_version} and will be removed in {changed_version} (or " | |
| "later). To avoid this warning, please do not use the parameter " | |
| "`{deprecated_name}`. For more details, see the documentation of " | |
| "`{func_name}`." | |
| ) | |
| replace_parameter_template = ( | |
| "Parameter `{deprecated_name}` is deprecated since version " | |
| "{deprecated_version} and will be removed in {changed_version} (or " | |
| "later). To avoid this warning, please use the parameter `{new_name}` " | |
| "instead. For more details, see the documentation of `{func_name}`." | |
| ) | |
| def __init__( | |
| self, | |
| deprecated_name, | |
| *, | |
| start_version, | |
| stop_version, | |
| template=None, | |
| new_name=None, | |
| modify_docstring=True, | |
| stacklevel=None, | |
| ): | |
| self.deprecated_name = deprecated_name | |
| self.new_name = new_name | |
| self.template = template | |
| self.start_version = start_version | |
| self.stop_version = stop_version | |
| self.modify_docstring = modify_docstring | |
| self.stacklevel = stacklevel | |
| def __call__(self, func): | |
| parameters = inspect.signature(func).parameters | |
| try: | |
| deprecated_idx = list(parameters.keys()).index(self.deprecated_name) | |
| except ValueError as e: | |
| raise ValueError(f"{self.deprecated_name!r} not in parameters") from e | |
| new_idx = False | |
| if self.new_name: | |
| try: | |
| new_idx = list(parameters.keys()).index(self.new_name) | |
| except ValueError as e: | |
| raise ValueError(f"{self.new_name!r} not in parameters") from e | |
| if parameters[self.deprecated_name].default is not DEPRECATED: | |
| raise RuntimeError( | |
| f"Expected `{self.deprecated_name}` to have the value {DEPRECATED!r} " | |
| f"to indicate its status in the rendered signature." | |
| ) | |
| if self.template is not None: | |
| template = self.template | |
| elif self.new_name is not None: | |
| template = self.replace_parameter_template | |
| else: | |
| template = self.remove_parameter_template | |
| warning_message = template.format( | |
| deprecated_name=self.deprecated_name, | |
| deprecated_version=self.start_version, | |
| changed_version=self.stop_version, | |
| func_name=func.__qualname__, | |
| new_name=self.new_name, | |
| ) | |
| def fixed_func(*args, **kwargs): | |
| deprecated_value = DEPRECATED | |
| new_value = DEPRECATED | |
| # Extract value of deprecated parameter | |
| if len(args) > deprecated_idx: | |
| deprecated_value = args[deprecated_idx] | |
| # Overwrite old with DEPRECATED if replacement exists | |
| if self.new_name is not None: | |
| args = ( | |
| args[:deprecated_idx] | |
| + (DEPRECATED,) | |
| + args[deprecated_idx + 1 :] | |
| ) | |
| if self.deprecated_name in kwargs.keys(): | |
| deprecated_value = kwargs[self.deprecated_name] | |
| # Overwrite old with DEPRECATED if replacement exists | |
| if self.new_name is not None: | |
| kwargs[self.deprecated_name] = DEPRECATED | |
| # Extract value of new parameter (if present) | |
| if new_idx is not False and len(args) > new_idx: | |
| new_value = args[new_idx] | |
| if self.new_name and self.new_name in kwargs.keys(): | |
| new_value = kwargs[self.new_name] | |
| if deprecated_value is not DEPRECATED: | |
| stacklevel = ( | |
| self.stacklevel | |
| if self.stacklevel is not None | |
| else _warning_stacklevel(func) | |
| ) | |
| warnings.warn( | |
| warning_message, category=FutureWarning, stacklevel=stacklevel | |
| ) | |
| if new_value is not DEPRECATED: | |
| raise ValueError( | |
| f"Both deprecated parameter `{self.deprecated_name}` " | |
| f"and new parameter `{self.new_name}` are used. Use " | |
| f"only the latter to avoid conflicting values." | |
| ) | |
| elif self.new_name is not None: | |
| # Assign old value to new one | |
| kwargs[self.new_name] = deprecated_value | |
| return func(*args, **kwargs) | |
| if self.modify_docstring and func.__doc__ is not None: | |
| newdoc = _docstring_add_deprecated( | |
| func, {self.deprecated_name: self.new_name}, self.start_version | |
| ) | |
| fixed_func.__doc__ = newdoc | |
| return fixed_func | |
| def _docstring_add_deprecated(func, kwarg_mapping, deprecated_version): | |
| """Add deprecated kwarg(s) to the "Other Params" section of a docstring. | |
| Parameters | |
| ---------- | |
| func : function | |
| The function whose docstring we wish to update. | |
| kwarg_mapping : dict | |
| A dict containing {old_arg: new_arg} key/value pairs, see | |
| `deprecate_parameter`. | |
| deprecated_version : str | |
| A major.minor version string specifying when old_arg was | |
| deprecated. | |
| Returns | |
| ------- | |
| new_doc : str | |
| The updated docstring. Returns the original docstring if numpydoc is | |
| not available. | |
| """ | |
| if func.__doc__ is None: | |
| return None | |
| try: | |
| from numpydoc.docscrape import FunctionDoc, Parameter | |
| except ImportError: | |
| # Return an unmodified docstring if numpydoc is not available. | |
| return func.__doc__ | |
| Doc = FunctionDoc(func) | |
| for old_arg, new_arg in kwarg_mapping.items(): | |
| desc = [] | |
| if new_arg is None: | |
| desc.append(f'`{old_arg}` is deprecated.') | |
| else: | |
| desc.append(f'Deprecated in favor of `{new_arg}`.') | |
| desc += ['', f'.. deprecated:: {deprecated_version}'] | |
| Doc['Other Parameters'].append( | |
| Parameter(name=old_arg, type='DEPRECATED', desc=desc) | |
| ) | |
| new_docstring = str(Doc) | |
| # new_docstring will have a header starting with: | |
| # | |
| # .. function:: func.__name__ | |
| # | |
| # and some additional blank lines. We strip these off below. | |
| split = new_docstring.split('\n') | |
| no_header = split[1:] | |
| while not no_header[0].strip(): | |
| no_header.pop(0) | |
| # Store the initial description before any of the Parameters fields. | |
| # Usually this is a single line, but the while loop covers any case | |
| # where it is not. | |
| descr = no_header.pop(0) | |
| while no_header[0].strip(): | |
| descr += '\n ' + no_header.pop(0) | |
| descr += '\n\n' | |
| # '\n ' rather than '\n' here to restore the original indentation. | |
| final_docstring = descr + '\n '.join(no_header) | |
| # strip any extra spaces from ends of lines | |
| final_docstring = '\n'.join([line.rstrip() for line in final_docstring.split('\n')]) | |
| return final_docstring | |
| class FailedEstimationAccessError(AttributeError): | |
| """Error from use of failed estimation instance | |
| This error arises from attempts to use an instance of | |
| :class:`FailedEstimation`. | |
| """ | |
| class FailedEstimation: | |
| """Class to indicate a failed transform estimation. | |
| The ``from_estimate`` class method of each transform type may return an | |
| instance of this class to indicate some failure in the estimation process. | |
| Parameters | |
| ---------- | |
| message : str | |
| Message indicating reason for failed estimation. | |
| Attributes | |
| ---------- | |
| message : str | |
| Message above. | |
| Raises | |
| ------ | |
| FailedEstimationAccessError | |
| Exception raised for missing attributes or if the instance is used as a | |
| callable. | |
| """ | |
| error_cls = FailedEstimationAccessError | |
| hint = ( | |
| "You can check for a failed estimation by truth testing the returned " | |
| "object. For failed estimations, `bool(estimation_result)` will be `False`. " | |
| "E.g.\n\n" | |
| " if not estimation_result:\n" | |
| " raise RuntimeError(f'Failed estimation: {estimation_result}')" | |
| ) | |
| def __init__(self, message): | |
| self.message = message | |
| def __bool__(self): | |
| return False | |
| def __repr__(self): | |
| return f"{type(self).__name__}({self.message!r})" | |
| def __str__(self): | |
| return self.message | |
| def __call__(self, *args, **kwargs): | |
| msg = ( | |
| f'{type(self).__name__} is not callable. {self.message}\n\n' | |
| f'Hint: {self.hint}' | |
| ) | |
| raise self.error_cls(msg) | |
| def __getattr__(self, name): | |
| msg = ( | |
| f'{type(self).__name__} has no attribute {name!r}. {self.message}\n\n' | |
| f'Hint: {self.hint}' | |
| ) | |
| raise self.error_cls(msg) | |
| def _ignore_deprecated_estimate_warning(): | |
| """Filter warnings about the deprecated `estimate` method. | |
| Use either as decorator or context manager. | |
| """ | |
| with warnings.catch_warnings(): | |
| warnings.filterwarnings( | |
| action="ignore", | |
| category=FutureWarning, | |
| message="`estimate` is deprecated", | |
| module="skimage", | |
| ) | |
| yield | |
| class channel_as_last_axis: | |
| """Decorator for automatically making channels axis last for all arrays. | |
| This decorator reorders axes for compatibility with functions that only | |
| support channels along the last axis. After the function call is complete | |
| the channels axis is restored back to its original position. | |
| Parameters | |
| ---------- | |
| channel_arg_positions : tuple of int, optional | |
| Positional arguments at the positions specified in this tuple are | |
| assumed to be multichannel arrays. The default is to assume only the | |
| first argument to the function is a multichannel array. | |
| channel_kwarg_names : tuple of str, optional | |
| A tuple containing the names of any keyword arguments corresponding to | |
| multichannel arrays. | |
| multichannel_output : bool, optional | |
| A boolean that should be True if the output of the function is not a | |
| multichannel array and False otherwise. This decorator does not | |
| currently support the general case of functions with multiple outputs | |
| where some or all are multichannel. | |
| """ | |
| def __init__( | |
| self, | |
| channel_arg_positions=(0,), | |
| channel_kwarg_names=(), | |
| multichannel_output=True, | |
| ): | |
| self.arg_positions = set(channel_arg_positions) | |
| self.kwarg_names = set(channel_kwarg_names) | |
| self.multichannel_output = multichannel_output | |
| def __call__(self, func): | |
| def fixed_func(*args, **kwargs): | |
| channel_axis = kwargs.get('channel_axis', None) | |
| if channel_axis is None: | |
| return func(*args, **kwargs) | |
| # TODO: convert scalars to a tuple in anticipation of eventually | |
| # supporting a tuple of channel axes. Right now, only an | |
| # integer or a single-element tuple is supported, though. | |
| if np.isscalar(channel_axis): | |
| channel_axis = (channel_axis,) | |
| if len(channel_axis) > 1: | |
| raise ValueError("only a single channel axis is currently supported") | |
| if channel_axis == (-1,) or channel_axis == -1: | |
| return func(*args, **kwargs) | |
| if self.arg_positions: | |
| new_args = [] | |
| for pos, arg in enumerate(args): | |
| if pos in self.arg_positions: | |
| new_args.append(np.moveaxis(arg, channel_axis[0], -1)) | |
| else: | |
| new_args.append(arg) | |
| new_args = tuple(new_args) | |
| else: | |
| new_args = args | |
| for name in self.kwarg_names: | |
| kwargs[name] = np.moveaxis(kwargs[name], channel_axis[0], -1) | |
| # now that we have moved the channels axis to the last position, | |
| # change the channel_axis argument to -1 | |
| kwargs["channel_axis"] = -1 | |
| # Call the function with the fixed arguments | |
| out = func(*new_args, **kwargs) | |
| if self.multichannel_output: | |
| out = np.moveaxis(out, -1, channel_axis[0]) | |
| return out | |
| return fixed_func | |
| class deprecate_func: | |
| """Decorate a deprecated function and warn when it is called. | |
| Adapted from <http://wiki.python.org/moin/PythonDecoratorLibrary>. | |
| Parameters | |
| ---------- | |
| deprecated_version : str | |
| The package version when the deprecation was introduced. | |
| removed_version : str | |
| The package version in which the deprecated function will be removed. | |
| hint : str, optional | |
| A hint on how to address this deprecation, | |
| e.g., "Use `skimage.submodule.alternative_func` instead." | |
| stacklevel : {None, int}, optional | |
| If None, the decorator attempts to detect the appropriate stacklevel for the | |
| deprecation warning automatically. This can fail, e.g., due to | |
| decorating a closure, in which case you can set the stacklevel manually | |
| here. The outermost decorator should have stacklevel 2, the next inner | |
| one stacklevel 3, etc. | |
| Examples | |
| -------- | |
| >>> @deprecate_func( | |
| ... deprecated_version="1.0.0", | |
| ... removed_version="1.2.0", | |
| ... hint="Use `bar` instead." | |
| ... ) | |
| ... def foo(): | |
| ... pass | |
| Calling ``foo`` will warn with:: | |
| FutureWarning: `foo` is deprecated since version 1.0.0 | |
| and will be removed in version 1.2.0. Use `bar` instead. | |
| """ | |
| def __init__( | |
| self, *, deprecated_version, removed_version=None, hint=None, stacklevel=None | |
| ): | |
| self.deprecated_version = deprecated_version | |
| self.removed_version = removed_version | |
| self.hint = hint | |
| self.stacklevel = stacklevel | |
| def __call__(self, func): | |
| message = ( | |
| f"`{func.__name__}` is deprecated since version {self.deprecated_version}" | |
| ) | |
| if self.removed_version: | |
| message += f" and will be removed in version {self.removed_version}." | |
| if self.hint: | |
| # Prepend space and make sure it closes with "." | |
| message += f" {self.hint.rstrip('.')}." | |
| def wrapped(*args, **kwargs): | |
| stacklevel = ( | |
| self.stacklevel | |
| if self.stacklevel is not None | |
| else _warning_stacklevel(func) | |
| ) | |
| warnings.warn(message, category=FutureWarning, stacklevel=stacklevel) | |
| return func(*args, **kwargs) | |
| # modify docstring to display deprecation warning | |
| doc = f'**Deprecated:** {message}' | |
| if wrapped.__doc__ is None: | |
| wrapped.__doc__ = doc | |
| else: | |
| wrapped.__doc__ = doc + '\n\n ' + wrapped.__doc__ | |
| return wrapped | |
| def _deprecate_estimate(func, class_name=None): | |
| """Deprecate ``estimate`` method.""" | |
| class_name = func.__qualname__.split('.')[0] if class_name is None else class_name | |
| return deprecate_func( | |
| deprecated_version="0.26", | |
| removed_version="2.2", | |
| hint=f"Please use `{class_name}.from_estimate` class constructor instead.", | |
| stacklevel=2, | |
| )(func) | |
| def _deprecate_inherited_estimate(cls): | |
| """Deprecate inherited ``estimate`` instance method. | |
| This needs a class decorator so we can correctly specify the class of the | |
| `from_estimate` class method in the deprecation message. | |
| """ | |
| def estimate(self, *args, **kwargs): | |
| return self._estimate(*args, **kwargs) is None | |
| # The inherited method will always be wrapped by deprecator. | |
| inherited_meth = getattr(cls, 'estimate').__wrapped__ | |
| estimate.__doc__ = inherited_meth.__doc__ | |
| estimate.__signature__ = inspect.signature(inherited_meth) | |
| cls.estimate = _deprecate_estimate(estimate, cls.__name__) | |
| return cls | |
| def _update_from_estimate_docstring(cls): | |
| """Fix docstring for inherited ``from_estimate`` class method. | |
| Even for classes that inherit the `from_estimate` method, and do not | |
| override it, we nevertheless need to change the *docstring* of the | |
| `from_estimate` method to point the user to the current (inheriting) class, | |
| rather than the class in which the method is defined (the inherited class). | |
| This needs a class decorator so we can modify the docstring of the new | |
| class method. CPython currently does not allow us to modify class method | |
| docstrings by updating ``__doc__``. | |
| """ | |
| inherited_cmeth = getattr(cls, 'from_estimate') | |
| def from_estimate(cls, *args, **kwargs): | |
| return inherited_cmeth(*args, **kwargs) | |
| inherited_class_name = inherited_cmeth.__qualname__.split('.')[-2] | |
| from_estimate.__doc__ = inherited_cmeth.__doc__.replace( | |
| inherited_class_name, cls.__name__ | |
| ) | |
| from_estimate.__signature__ = inspect.signature(inherited_cmeth) | |
| cls.from_estimate = classmethod(from_estimate) | |
| return cls | |
| def get_bound_method_class(m): | |
| """Return the class for a bound method.""" | |
| return m.im_class if sys.version < '3' else m.__self__.__class__ | |
| def safe_as_int(val, atol=1e-3): | |
| """ | |
| Attempt to safely cast values to integer format. | |
| Parameters | |
| ---------- | |
| val : scalar or iterable of scalars | |
| Number or container of numbers which are intended to be interpreted as | |
| integers, e.g., for indexing purposes, but which may not carry integer | |
| type. | |
| atol : float | |
| Absolute tolerance away from nearest integer to consider values in | |
| ``val`` functionally integers. | |
| Returns | |
| ------- | |
| val_int : NumPy scalar or ndarray of dtype `np.int64` | |
| Returns the input value(s) coerced to dtype `np.int64` assuming all | |
| were within ``atol`` of the nearest integer. | |
| Notes | |
| ----- | |
| This operation calculates ``val`` modulo 1, which returns the mantissa of | |
| all values. Then all mantissas greater than 0.5 are subtracted from one. | |
| Finally, the absolute tolerance from zero is calculated. If it is less | |
| than ``atol`` for all value(s) in ``val``, they are rounded and returned | |
| in an integer array. Or, if ``val`` was a scalar, a NumPy scalar type is | |
| returned. | |
| If any value(s) are outside the specified tolerance, an informative error | |
| is raised. | |
| Examples | |
| -------- | |
| >>> safe_as_int(7.0) | |
| 7 | |
| >>> safe_as_int([9, 4, 2.9999999999]) | |
| array([9, 4, 3]) | |
| >>> safe_as_int(53.1) | |
| Traceback (most recent call last): | |
| ... | |
| ValueError: Integer argument required but received 53.1, check inputs. | |
| >>> safe_as_int(53.01, atol=0.01) | |
| 53 | |
| """ | |
| mod = np.asarray(val) % 1 # Extract mantissa | |
| # Check for and subtract any mod values > 0.5 from 1 | |
| if mod.ndim == 0: # Scalar input, cannot be indexed | |
| if mod > 0.5: | |
| mod = 1 - mod | |
| else: # Iterable input, now ndarray | |
| mod[mod > 0.5] = 1 - mod[mod > 0.5] # Test on each side of nearest int | |
| if not np.allclose(mod, 0, atol=atol): | |
| raise ValueError(f'Integer argument required but received {val}, check inputs.') | |
| return np.round(val).astype(np.int64) | |
| def check_shape_equality(*images): | |
| """Check that all images have the same shape""" | |
| image0 = images[0] | |
| if not all(image0.shape == image.shape for image in images[1:]): | |
| raise ValueError('Input images must have the same dimensions.') | |
| return | |
| def slice_at_axis(sl, axis): | |
| """ | |
| Construct tuple of slices to slice an array in the given dimension. | |
| Parameters | |
| ---------- | |
| sl : slice | |
| The slice for the given dimension. | |
| axis : int | |
| The axis to which `sl` is applied. All other dimensions are left | |
| "unsliced". | |
| Returns | |
| ------- | |
| sl : tuple of slices | |
| A tuple with slices matching `shape` in length. | |
| Examples | |
| -------- | |
| >>> slice_at_axis(slice(None, 3, -1), 1) | |
| (slice(None, None, None), slice(None, 3, -1), Ellipsis) | |
| """ | |
| return (slice(None),) * axis + (sl,) + (...,) | |
| def reshape_nd(arr, ndim, dim): | |
| """Reshape a 1D array to have n dimensions, all singletons but one. | |
| Parameters | |
| ---------- | |
| arr : array, shape (N,) | |
| Input array | |
| ndim : int | |
| Number of desired dimensions of reshaped array. | |
| dim : int | |
| Which dimension/axis will not be singleton-sized. | |
| Returns | |
| ------- | |
| arr_reshaped : array, shape ([1, ...], N, [1,...]) | |
| View of `arr` reshaped to the desired shape. | |
| Examples | |
| -------- | |
| >>> rng = np.random.default_rng() | |
| >>> arr = rng.random(7) | |
| >>> reshape_nd(arr, 2, 0).shape | |
| (7, 1) | |
| >>> reshape_nd(arr, 3, 1).shape | |
| (1, 7, 1) | |
| >>> reshape_nd(arr, 4, -1).shape | |
| (1, 1, 1, 7) | |
| """ | |
| if arr.ndim != 1: | |
| raise ValueError("arr must be a 1D array") | |
| new_shape = [1] * ndim | |
| new_shape[dim] = -1 | |
| return np.reshape(arr, new_shape) | |
| def check_nD(array, ndim, arg_name='image'): | |
| """ | |
| Verify an array meets the desired ndims and array isn't empty. | |
| Parameters | |
| ---------- | |
| array : array-like | |
| Input array to be validated | |
| ndim : int or iterable of ints | |
| Allowable ndim or ndims for the array. | |
| arg_name : str, optional | |
| The name of the array in the original function. | |
| """ | |
| array = np.asanyarray(array) | |
| msg_incorrect_dim = "The parameter `%s` must be a %s-dimensional array" | |
| msg_empty_array = "The parameter `%s` cannot be an empty array" | |
| if isinstance(ndim, int): | |
| ndim = [ndim] | |
| if array.size == 0: | |
| raise ValueError(msg_empty_array % (arg_name)) | |
| if array.ndim not in ndim: | |
| raise ValueError( | |
| msg_incorrect_dim % (arg_name, '-or-'.join([str(n) for n in ndim])) | |
| ) | |
| def convert_to_float(image, preserve_range): | |
| """Convert input image to float image with the appropriate range. | |
| Parameters | |
| ---------- | |
| image : ndarray | |
| Input image. | |
| preserve_range : bool | |
| Determines if the range of the image should be kept or transformed | |
| using img_as_float. Also see | |
| https://scikit-image.org/docs/dev/user_guide/data_types.html | |
| Notes | |
| ----- | |
| * Input images with `float32` data type are not upcast. | |
| Returns | |
| ------- | |
| image : ndarray | |
| Transformed version of the input. | |
| """ | |
| if image.dtype == np.float16: | |
| return image.astype(np.float32) | |
| if preserve_range: | |
| # Convert image to double only if it is not single or double | |
| # precision float | |
| if image.dtype.char not in 'df': | |
| image = image.astype(float) | |
| else: | |
| from ..util.dtype import img_as_float | |
| image = img_as_float(image) | |
| return image | |
| def _validate_interpolation_order(image_dtype, order): | |
| """Validate and return spline interpolation's order. | |
| Parameters | |
| ---------- | |
| image_dtype : dtype | |
| Image dtype. | |
| order : {None, int}, optional | |
| The order of the spline interpolation. The order has to be in the range | |
| 0-5. If ``None`` assume order 0 for Boolean images, otherwise 1. See | |
| `skimage.transform.warp` for detail. | |
| Returns | |
| ------- | |
| order : int | |
| if input order is None, returns 0 if image_dtype is bool and 1 | |
| otherwise. Otherwise, image_dtype is checked and input order | |
| is validated accordingly (order > 0 is not supported for bool | |
| image dtype) | |
| """ | |
| if order is None: | |
| return 0 if image_dtype == bool else 1 | |
| if order < 0 or order > 5: | |
| raise ValueError("Spline interpolation order has to be in the range 0-5.") | |
| if image_dtype == bool and order != 0: | |
| raise ValueError( | |
| "Input image dtype is bool. Interpolation is not defined " | |
| "with bool data type. Please set order to 0 or explicitly " | |
| "cast input image to another data type." | |
| ) | |
| return order | |
| def _to_np_mode(mode): | |
| """Convert padding modes from `ndi.correlate` to `np.pad`.""" | |
| mode_translation_dict = dict(nearest='edge', reflect='symmetric', mirror='reflect') | |
| if mode in mode_translation_dict: | |
| mode = mode_translation_dict[mode] | |
| return mode | |
| def _to_ndimage_mode(mode): | |
| """Convert from `numpy.pad` mode name to the corresponding ndimage mode.""" | |
| mode_translation_dict = dict( | |
| constant='constant', | |
| edge='nearest', | |
| symmetric='reflect', | |
| reflect='mirror', | |
| wrap='wrap', | |
| ) | |
| if mode not in mode_translation_dict: | |
| raise ValueError( | |
| f"Unknown mode: '{mode}', or cannot translate mode. The " | |
| f"mode should be one of 'constant', 'edge', 'symmetric', " | |
| f"'reflect', or 'wrap'. See the documentation of numpy.pad for " | |
| f"more info." | |
| ) | |
| return _fix_ndimage_mode(mode_translation_dict[mode]) | |
| def _fix_ndimage_mode(mode): | |
| # SciPy 1.6.0 introduced grid variants of constant and wrap which | |
| # have less surprising behavior for images. Use these when available | |
| grid_modes = {'constant': 'grid-constant', 'wrap': 'grid-wrap'} | |
| return grid_modes.get(mode, mode) | |
| new_float_type = { | |
| # preserved types | |
| np.float32().dtype.char: np.float32, | |
| np.float64().dtype.char: np.float64, | |
| np.complex64().dtype.char: np.complex64, | |
| np.complex128().dtype.char: np.complex128, | |
| # altered types | |
| np.float16().dtype.char: np.float32, | |
| 'g': np.float64, # np.float128 ; doesn't exist on windows | |
| 'G': np.complex128, # np.complex256 ; doesn't exist on windows | |
| } | |
| def _supported_float_type(input_dtype, allow_complex=False): | |
| """Return an appropriate floating-point dtype for a given dtype. | |
| float32, float64, complex64, complex128 are preserved. | |
| float16 is promoted to float32. | |
| complex256 is demoted to complex128. | |
| Other types are cast to float64. | |
| Parameters | |
| ---------- | |
| input_dtype : np.dtype or tuple of np.dtype | |
| The input dtype. If a tuple of multiple dtypes is provided, each | |
| dtype is first converted to a supported floating point type and the | |
| final dtype is then determined by applying `np.result_type` on the | |
| sequence of supported floating point types. | |
| allow_complex : bool, optional | |
| If False, raise a ValueError on complex-valued inputs. | |
| Returns | |
| ------- | |
| float_type : dtype | |
| Floating-point dtype for the image. | |
| """ | |
| if isinstance(input_dtype, tuple): | |
| return np.result_type(*(_supported_float_type(d) for d in input_dtype)) | |
| input_dtype = np.dtype(input_dtype) | |
| if not allow_complex and input_dtype.kind == 'c': | |
| raise ValueError("complex valued input is not supported") | |
| return new_float_type.get(input_dtype.char, np.float64) | |
| def identity(image, *args, **kwargs): | |
| """Returns the first argument unmodified.""" | |
| return image | |
| def as_binary_ndarray(array, *, variable_name): | |
| """Return `array` as a numpy.ndarray of dtype bool. | |
| Raises | |
| ------ | |
| ValueError: | |
| An error including the given `variable_name` if `array` can not be | |
| safely cast to a boolean array. | |
| """ | |
| array = np.asarray(array) | |
| if array.dtype != bool: | |
| if np.any((array != 1) & (array != 0)): | |
| raise ValueError( | |
| f"{variable_name} array is not of dtype boolean or " | |
| f"contains values other than 0 and 1 so cannot be " | |
| f"safely cast to boolean array." | |
| ) | |
| return np.asarray(array, dtype=bool) | |