def _write_multiple_layers_with_plugins(
path: str,
layers: List[Layer],
*,
plugin_name: Optional[str] = None,
plugin_manager=napari_plugin_manager,
) -> List[str]:
"""Write data from multiple layers data with a plugin.
If a ``plugin_name`` is not provided we loop through plugins to find the
first one that knows how to handle the combination of layers and is able to
write the file. If no plugins offer ``napari_get_writer`` for that
combination of layers then the default ``napari_get_writer`` will create a
folder and call ``napari_write_<layer>`` for each layer using the
``layer.name`` variable to modify the path such that the layers are written
to unique files in the folder.
If a ``plugin_name`` is provided, then call ``napari_get_writer`` for that
plugin. If it doesn’t return a ``WriterFunction`` we error, otherwise we
call it and if that fails if it we error.
Exceptions will be caught and stored as PluginErrors
(in plugins.exceptions.PLUGIN_ERRORS)
Parameters
----------
path : str
The path (file, directory, url) to write.
layers : List of napari.layers.Layer
List of napari layers to write.
plugin_name : str, optional
If provided, force the plugin manager to use the ``napari_get_writer``
from the requested ``plugin_name``. If none is available, or if it is
incapable of handling the layers, this function will fail.
plugin_manager : plugins.PluginManager, optional
Instance of a PluginManager. by default the main napari
plugin_manager will be used.
Returns
-------
list of str
A list of filenames, if any, that were written.
"""
layer_data = [layer.as_layer_data_tuple() for layer in layers]
layer_types = [ld[2] for ld in layer_data]
hook_caller = plugin_manager.hook.napari_get_writer
path = abspath_or_url(path)
if plugin_name:
# if plugin has been specified we just directly call napari_get_writer
# with that plugin_name.
if plugin_name not in plugin_manager.plugins:
names = {i.plugin_name for i in hook_caller.get_hookimpls()}
raise ValueError(
f"There is no registered plugin named '{plugin_name}'.\n"
f"Names of plugins offering writers are: {names}"
)
implementation = hook_caller.get_plugin_implementation(plugin_name)
writer_function = hook_caller(
_plugin=plugin_name, path=path, layer_types=layer_types
)
else:
result = hook_caller.call_with_result_obj(
path=path, layer_types=layer_types, _return_impl=True
)
writer_function = result.result
implementation = result.implementation
if not callable(writer_function):
if plugin_name:
msg = f'Requested plugin "{plugin_name}" is not capable'
else:
msg = 'Unable to find plugin capable'
msg += f' of writing this combination of layer types: {layer_types}'
raise ValueError(msg)
try:
return writer_function(abspath_or_url(path), layer_data)
except Exception as exc:
raise PluginCallError(implementation, cause=exc)
def read_data_with_plugins(
path: Union[str, Sequence[str]],
plugin: Optional[str] = None,
plugin_manager: PluginManager = napari_plugin_manager,
) -> List[LayerData]:
"""Iterate reader hooks and return first non-None LayerData or None.
This function returns as soon as the path has been read successfully,
while catching any plugin exceptions, storing them for later retrievial,
providing useful error messages, and relooping until either layer data is
returned, or no valid readers are found.
Exceptions will be caught and stored as PluginErrors
(in plugins.exceptions.PLUGIN_ERRORS)
Parameters
----------
path : str
The path (file, directory, url) to open
plugin : str, optional
Name of a plugin to use. If provided, will force ``path`` to be read
with the specified ``plugin``. If the requested plugin cannot read
``path``, a PluginCallError will be raised.
plugin_manager : plugins.PluginManager, optional
Instance of a napari PluginManager. by default the main napari
plugin_manager will be used.
Returns
-------
LayerData : list of tuples, or None
LayerData that can be passed to :func:`Viewer._add_layer_from_data()
<napari.components.viewer_model.ViewerModel._add_layer_from_data>`.
``LayerData`` is a list tuples, where each tuple is one of
``(data,)``, ``(data, meta)``, or ``(data, meta, layer_type)`` .
If no reader plugins are (or they all error), returns ``None``
Raises
------
PluginCallError
If ``plugin`` is specified but raises an Exception while reading.
"""
hook_caller = plugin_manager.hook.napari_get_reader
if plugin:
if plugin not in plugin_manager.plugins:
names = {i.plugin_name for i in hook_caller.get_hookimpls()}
raise ValueError(
f"There is no registered plugin named '{plugin}'.\n"
f"Names of plugins offering readers are: {names}"
)
reader = hook_caller._call_plugin(plugin, path=path)
if not callable(reader):
raise ValueError(f'Plugin {plugin!r} does not support file {path}')
return reader(path) or []
errors: List[PluginCallError] = []
path = abspath_or_url(path)
skip_impls: List[HookImplementation] = []
layer_data = None
while True:
result = hook_caller.call_with_result_obj(
path=path, _skip_impls=skip_impls
)
reader = result.result # will raise exceptions if any occurred
if not reader:
# we're all out of reader plugins
break
try:
layer_data = reader(path) # try to read data
if layer_data:
break
except Exception as exc:
# collect the error and log it, but don't raise it.
err = PluginCallError(result.implementation, cause=exc)
err.log(logger=logger)
errors.append(err)
# don't try this impl again
skip_impls.append(result.implementation)
if not layer_data:
# if layer_data is empty, it means no plugin could read path
# we just want to provide some useful feedback, which includes
# whether or not paths were passed to plugins as a list.
if isinstance(path, (tuple, list)):
path_repr = f"[{path[0]}, ...] as stack"
else:
path_repr = repr(path)
# TODO: change to a warning notification in a later PR
raise ValueError(f'No plugin found capable of reading {path_repr}.')
if errors:
names = set([repr(e.plugin_name) for e in errors])
err_msg = f"({len(errors)}) error{'s' if len(errors) > 1 else ''} "
err_msg += f"occurred in plugins: {', '.join(names)}. "
err_msg += 'See full error logs in "Plugins → Plugin Errors..."'
logger.error(err_msg)
return layer_data or []
def _write_multiple_layers_with_plugins(
path: str,
layers: List[Layer],
*,
plugin_name: Optional[str] = None,
_writer: Optional[WriterContribution] = None,
) -> List[str]:
"""Write data from multiple layers data with a plugin.
If a ``plugin_name`` is not provided we loop through plugins to find the
first one that knows how to handle the combination of layers and is able to
write the file. If no plugins offer ``napari_get_writer`` for that
combination of layers then the default ``napari_get_writer`` will create a
folder and call ``napari_write_<layer>`` for each layer using the
``layer.name`` variable to modify the path such that the layers are written
to unique files in the folder.
If a ``plugin_name`` is provided, then call ``napari_get_writer`` for that
plugin. If it doesn’t return a ``WriterFunction`` we error, otherwise we
call it and if that fails if it we error.
Exceptions will be caught and stored as PluginErrors
(in plugins.exceptions.PLUGIN_ERRORS)
Parameters
----------
path : str
The path (file, directory, url) to write.
layers : List of napari.layers.Layer
List of napari layers to write.
plugin_name : str, optional
If provided, force the plugin manager to use the ``napari_get_writer``
from the requested ``plugin_name``. If none is available, or if it is
incapable of handling the layers, this function will fail.
Returns
-------
list of str
A list of filenames, if any, that were written.
"""
# Try to use NPE2 first
written_paths = _npe2.write_layers(path, layers, plugin_name, _writer)
if written_paths:
return written_paths
logger.debug("Falling back to original plugin engine.")
layer_data = [layer.as_layer_data_tuple() for layer in layers]
layer_types = [ld[2] for ld in layer_data]
if not plugin_name and isinstance(path, (str, pathlib.Path)):
extension = os.path.splitext(path)[-1]
plugin_name = plugin_manager.get_writer_for_extension(extension)
hook_caller = plugin_manager.hook.napari_get_writer
path = abspath_or_url(path)
logger.debug(f"Writing to {path}. Hook caller: {hook_caller}")
if plugin_name:
# if plugin has been specified we just directly call napari_get_writer
# with that plugin_name.
if plugin_name not in plugin_manager.plugins:
names = {i.plugin_name for i in hook_caller.get_hookimpls()}
raise ValueError(
trans._(
"There is no registered plugin named '{plugin_name}'.\nNames of plugins offering writers are: {names}",
deferred=True,
plugin_name=plugin_name,
names=names,
))
implementation = hook_caller.get_plugin_implementation(plugin_name)
writer_function = hook_caller(_plugin=plugin_name,
path=path,
layer_types=layer_types)
else:
result = hook_caller.call_with_result_obj(path=path,
layer_types=layer_types,
_return_impl=True)
writer_function = result.result
implementation = result.implementation
if not callable(writer_function):
if plugin_name:
msg = trans._(
'Requested plugin "{plugin_name}" is not capable of writing this combination of layer types: {layer_types}',
deferred=True,
plugin_name=plugin_name,
layer_types=layer_types,
)
else:
msg = trans._(
'Unable to find plugin capable of writing this combination of layer types: {layer_types}',
deferred=True,
layer_types=layer_types,
)
raise ValueError(msg)
try:
return writer_function(abspath_or_url(path), layer_data)
except Exception as exc:
raise PluginCallError(implementation, cause=exc)
def read_data_with_plugins(
paths: Sequence[str],
plugin: Optional[str] = None,
stack: bool = False,
) -> Tuple[Optional[List[LayerData]], Optional[HookImplementation]]:
"""Iterate reader hooks and return first non-None LayerData or None.
This function returns as soon as the path has been read successfully,
while catching any plugin exceptions, storing them for later retrieval,
providing useful error messages, and re-looping until either a read
operation was successful, or no valid readers were found.
Exceptions will be caught and stored as PluginErrors
(in plugins.exceptions.PLUGIN_ERRORS)
Parameters
----------
paths : str, or list of string
The of path (file, directory, url) to open
plugin : str, optional
Name of a plugin to use. If provided, will force ``path`` to be read
with the specified ``plugin``. If the requested plugin cannot read
``path``, a PluginCallError will be raised.
stack : bool
See `Viewer.open`
Returns
-------
LayerData : list of tuples, or None
LayerData that can be passed to :func:`Viewer._add_layer_from_data()
<napari.components.viewer_model.ViewerModel._add_layer_from_data>`.
``LayerData`` is a list tuples, where each tuple is one of
``(data,)``, ``(data, meta)``, or ``(data, meta, layer_type)`` .
If no reader plugins were found (or they all failed), returns ``None``
Raises
------
PluginCallError
If ``plugin`` is specified but raises an Exception while reading.
"""
if plugin == 'builtins':
warnings.warn(
'The "builtins" plugin name is deprecated and will not work in a future '
'version. Please use "napari" instead.', )
plugin = 'napari'
assert isinstance(paths, list)
if not stack:
assert len(paths) == 1
hookimpl: Optional[HookImplementation]
res = _npe2.read(paths, plugin, stack=stack)
if res is not None:
_ld, hookimpl = res
return [] if _is_null_layer_sentinel(
_ld) else _ld, hookimpl # type: ignore [return-value]
hook_caller = plugin_manager.hook.napari_get_reader
paths = [abspath_or_url(p, must_exist=True) for p in paths]
if not plugin and not stack:
extension = os.path.splitext(paths[0])[-1]
plugin = plugin_manager.get_reader_for_extension(extension)
# npe1 compact whether we are reading as stack or not is carried in the type
# of paths
npe1_path = paths if stack else paths[0]
hookimpl = None
if plugin:
if plugin == 'napari':
# napari is npe2 only
message = trans._(
'No plugin found capable of reading {repr_path!r}.',
deferred=True,
repr_path=npe1_path,
)
raise ValueError(message)
if plugin not in plugin_manager.plugins:
names = {i.plugin_name for i in hook_caller.get_hookimpls()}
raise ValueError(
trans._(
"There is no registered plugin named '{plugin}'.\nNames of plugins offering readers are: {names}",
deferred=True,
plugin=plugin,
names=names,
))
reader = hook_caller._call_plugin(plugin, path=npe1_path)
if not callable(reader):
raise ValueError(
trans._(
'Plugin {plugin!r} does not support file(s) {paths}',
deferred=True,
plugin=plugin,
paths=paths,
))
hookimpl = hook_caller.get_plugin_implementation(plugin)
layer_data = reader(npe1_path)
# if the reader returns a "null layer" sentinel indicating an empty
# file, return an empty list, otherwise return the result or None
if _is_null_layer_sentinel(layer_data):
return [], hookimpl
return layer_data or None, hookimpl
layer_data = None
result = hook_caller.call_with_result_obj(path=npe1_path)
if reader := result.result: # will raise exceptions if any occurred
try:
layer_data = reader(npe1_path) # try to read data
hookimpl = result.implementation
except Exception as exc:
raise PluginCallError(result.implementation, cause=exc) from exc
def read_data_with_plugins(
path: Union[str, Sequence[str]],
plugin: Optional[str] = None,
) -> Tuple[Optional[List[LayerData]], Optional[HookImplementation]]:
"""Iterate reader hooks and return first non-None LayerData or None.
This function returns as soon as the path has been read successfully,
while catching any plugin exceptions, storing them for later retrieval,
providing useful error messages, and re-looping until either a read
operation was successful, or no valid readers were found.
Exceptions will be caught and stored as PluginErrors
(in plugins.exceptions.PLUGIN_ERRORS)
Parameters
----------
path : str
The path (file, directory, url) to open
plugin : str, optional
Name of a plugin to use. If provided, will force ``path`` to be read
with the specified ``plugin``. If the requested plugin cannot read
``path``, a PluginCallError will be raised.
Returns
-------
LayerData : list of tuples, or None
LayerData that can be passed to :func:`Viewer._add_layer_from_data()
<napari.components.viewer_model.ViewerModel._add_layer_from_data>`.
``LayerData`` is a list tuples, where each tuple is one of
``(data,)``, ``(data, meta)``, or ``(data, meta, layer_type)`` .
If no reader plugins were found (or they all failed), returns ``None``
Raises
------
PluginCallError
If ``plugin`` is specified but raises an Exception while reading.
"""
hookimpl: Optional[HookImplementation]
res = _npe2.read(path, plugin)
if res is not None:
_ld, hookimpl = res
return [] if _is_null_layer_sentinel(_ld) else _ld, hookimpl
hook_caller = plugin_manager.hook.napari_get_reader
path = abspath_or_url(path)
if not plugin and isinstance(path, (str, pathlib.Path)):
extension = os.path.splitext(path)[-1]
plugin = plugin_manager.get_reader_for_extension(extension)
hookimpl = None
if plugin:
if plugin not in plugin_manager.plugins:
names = {i.plugin_name for i in hook_caller.get_hookimpls()}
raise ValueError(
trans._(
"There is no registered plugin named '{plugin}'.\nNames of plugins offering readers are: {names}",
deferred=True,
plugin=plugin,
names=names,
))
reader = hook_caller._call_plugin(plugin, path=path)
if not callable(reader):
raise ValueError(
trans._(
'Plugin {plugin!r} does not support file {path}',
deferred=True,
plugin=plugin,
path=path,
))
hookimpl = hook_caller.get_plugin_implementation(plugin)
layer_data = reader(path)
# if the reader returns a "null layer" sentinel indicating an empty
# file, return an empty list, otherwise return the result or None
if _is_null_layer_sentinel(layer_data):
return [], hookimpl
return layer_data or None, hookimpl
errors: List[PluginCallError] = []
skip_impls: List[HookImplementation] = []
layer_data = None
while True:
result = hook_caller.call_with_result_obj(path=path,
_skip_impls=skip_impls)
reader = result.result # will raise exceptions if any occurred
if not reader:
# we're all out of reader plugins
break
try:
layer_data = reader(path) # try to read data
if layer_data:
hookimpl = result.implementation
break
except Exception as exc:
# collect the error and log it, but don't raise it.
err = PluginCallError(result.implementation, cause=exc)
err.log(logger=logger)
errors.append(err)
# don't try this impl again
skip_impls.append(result.implementation)
if not layer_data:
# if layer_data is empty, it means no plugin could read path
# we just want to provide some useful feedback, which includes
# whether or not paths were passed to plugins as a list.
if isinstance(path, (tuple, list)):
message = trans._(
'No plugin found capable of reading [{repr_path}, ...] as stack.',
deferred=True,
repr_path=path[0],
)
else:
message = trans._(
'No plugin found capable of reading {repr_path}.',
deferred=True,
repr_path=repr(path),
)
# TODO: change to a warning notification in a later PR
raise ValueError(message)
if errors:
names = {repr(e.plugin_name) for e in errors}
err_msg = f"({len(errors)}) error{'s' if len(errors) > 1 else ''} "
err_msg += f"occurred in plugins: {', '.join(names)}. "
err_msg += 'See full error logs in "Plugins → Plugin Errors..."'
logger.error(err_msg)
# if the reader returns a "null layer" sentinel indicating an empty file,
# return an empty list, otherwise return the result or None
_data = [] if _is_null_layer_sentinel(layer_data) else layer_data or None
return _data, hookimpl
def read_data_with_plugins(
path: Union[str, Sequence[str]],
plugin: Optional[str] = None,
plugin_manager=napari_plugin_manager,
) -> Optional[LayerData]:
"""Iterate reader hooks and return first non-None LayerData or None.
This function returns as soon as the path has been read successfully,
while catching any plugin exceptions, storing them for later retrievial,
providing useful error messages, and relooping until either layer data is
returned, or no valid readers are found.
Exceptions will be caught and stored as PluginErrors
(in plugins.exceptions.PLUGIN_ERRORS)
Parameters
----------
path : str
The path (file, directory, url) to open
plugin : str, optional
Name of a plugin to use. If provided, will force ``path`` to be read
with the specified ``plugin``. If the requested plugin cannot read
``path``, a PluginCallError will be raised.
plugin_manager : plugins.PluginManager, optional
Instance of a napari PluginManager. by default the main napari
plugin_manager will be used.
Returns
-------
LayerData : list of tuples, or None
LayerData that can be passed to :func:`Viewer._add_layer_from_data()
<napari.components.add_layers_mixin.AddLayersMixin._add_layer_from_data>`.
``LayerData`` is a list tuples, where each tuple is one of
``(data,)``, ``(data, meta)``, or ``(data, meta, layer_type)`` .
If no reader plugins are (or they all error), returns ``None``
Raises
------
PluginCallError
If ``plugin`` is specified but raises an Exception while reading.
"""
hook_caller = plugin_manager.hook.napari_get_reader
if plugin:
reader = hook_caller._call_plugin(plugin, path=path)
return reader(path)
path = abspath_or_url(path)
skip_impls: List[HookImplementation] = []
while True:
result = hook_caller.call_with_result_obj(path=path,
_skip_impls=skip_impls)
reader = result.result # will raise exceptions if any occured
if not reader:
# we're all out of reader plugins
return None
try:
return reader(path) # try to read data
except Exception as exc:
err = PluginCallError(result.implementation, cause=exc)
# don't try this impl again
skip_impls.append(result.implementation)
if result.implementation != 'builtins':
# If builtins doesn't work, they will get a "no reader" found
# error anyway, so it looks a bit weird to show them that the
# "builtin plugin" didn't work.
err.log(logger=logger)
