| 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. |
| """ |
| |
| 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) |
|
|
| |
| |
| 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.' |
| ) |
|
|
| @functools.wraps(func) |
| 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) |
| ) |
| |
| 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 |
|
|
| 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, |
| ) |
|
|
| @functools.wraps(func) |
| def fixed_func(*args, **kwargs): |
| deprecated_value = DEPRECATED |
| new_value = DEPRECATED |
|
|
| |
| if len(args) > deprecated_idx: |
| deprecated_value = args[deprecated_idx] |
| |
| 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] |
| |
| if self.new_name is not None: |
| kwargs[self.deprecated_name] = DEPRECATED |
|
|
| |
| 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: |
| |
| 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 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) |
|
|
| |
| |
| |
| |
| |
| split = new_docstring.split('\n') |
| no_header = split[1:] |
| while not no_header[0].strip(): |
| no_header.pop(0) |
|
|
| |
| |
| |
| descr = no_header.pop(0) |
| while no_header[0].strip(): |
| descr += '\n ' + no_header.pop(0) |
| descr += '\n\n' |
| |
| final_docstring = descr + '\n '.join(no_header) |
| |
| 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) |
|
|
|
|
| @contextmanager |
| 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): |
| @functools.wraps(func) |
| def fixed_func(*args, **kwargs): |
| channel_axis = kwargs.get('channel_axis', None) |
|
|
| if channel_axis is None: |
| return func(*args, **kwargs) |
|
|
| |
| |
| |
| 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) |
|
|
| |
| |
| kwargs["channel_axis"] = -1 |
|
|
| |
| 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: |
| |
| message += f" {self.hint.rstrip('.')}." |
|
|
| @functools.wraps(func) |
| 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) |
|
|
| |
| 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 |
|
|
| |
| 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 |
|
|
| |
| if mod.ndim == 0: |
| if mod > 0.5: |
| mod = 1 - mod |
| else: |
| mod[mod > 0.5] = 1 - mod[mod > 0.5] |
|
|
| 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: |
| |
| |
| 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): |
| |
| |
| grid_modes = {'constant': 'grid-constant', 'wrap': 'grid-wrap'} |
| return grid_modes.get(mode, mode) |
|
|
|
|
| new_float_type = { |
| |
| np.float32().dtype.char: np.float32, |
| np.float64().dtype.char: np.float64, |
| np.complex64().dtype.char: np.complex64, |
| np.complex128().dtype.char: np.complex128, |
| |
| np.float16().dtype.char: np.float32, |
| 'g': np.float64, |
| 'G': np.complex128, |
| } |
|
|
|
|
| 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) |
|
|