can't save RGB image

[dani-ham]

error in extrema_image function.
note : I used napari built-in sample image(astronaut)

ValueError                                Traceback (most recent call last)
File ~\anaconda3\Lib\site-packages\app_model\backends\qt\_qaction.py:59, in QCommandAction._on_triggered(self=QMenuItemAction(MenuItem(when=None, group='4_sav...tle=None, toggled=None), alt=None), app='napari'), checked=False)
     55 def _on_triggered(self, checked: bool) -> None:
     56     # execute_command returns a Future, for the sake of eventually being
     57     # asynchronous without breaking the API.  For now, we call result()
     58     # to raise any exceptions.
---> 59     self._app.commands.execute_command(self._command_id).result()
        self._command_id = 'napari.window.file.save_layers_dialog'
        self = QMenuItemAction(MenuItem(when=None, group='4_save', order=None, command=CommandRule(id='napari.window.file.save_layers_dialog', title='Save All Layers...', category=None, tooltip=None, status_tip=None, icon=None, icon_visible_in_menu=True, enablement=Expr.parse('num_layers > 0'), short_title=None, toggled=None), alt=None), app='napari')
        self._app = Application('napari')

File ~\anaconda3\Lib\site-packages\app_model\registries\_commands_reg.py:247, in CommandsRegistry.execute_command(self=<CommandsRegistry at 0x2972a013790 (144 commands)>, id='napari.window.file.save_layers_dialog', execute_asynchronously=False, *args=(), **kwargs={})
    243 except Exception as e:
    244     if self._raise_synchronous_exceptions:
    245         # note, the caller of this function can also achieve this by
    246         # calling `future.result()` on the returned future object.
--> 247         raise e
    248     future.set_exception(e)
    250 return future

File ~\anaconda3\Lib\site-packages\app_model\registries\_commands_reg.py:242, in CommandsRegistry.execute_command(self=<CommandsRegistry at 0x2972a013790 (144 commands)>, id='napari.window.file.save_layers_dialog', execute_asynchronously=False, *args=(), **kwargs={})
    240 future: Future = Future()
    241 try:
--> 242     future.set_result(cmd(*args, **kwargs))
        future = <Future at 0x2972f52e3d0 state=pending>
        cmd = <function QtViewer._save_layers_dialog at 0x000002972D416660>
        args = ()
        kwargs = {}
    243 except Exception as e:
    244     if self._raise_synchronous_exceptions:
    245         # note, the caller of this function can also achieve this by
    246         # calling `future.result()` on the returned future object.

File ~\anaconda3\Lib\site-packages\in_n_out\_store.py:934, in Store.inject_processors.<locals>._deco.<locals>._exec(*args=(), **kwargs={})
    932 @wraps(func)
    933 def _exec(*args: P.args, **kwargs: P.kwargs) -> R:
--> 934     result = func(*args, **kwargs)
        func = <function QtViewer._save_layers_dialog at 0x000002972D414680>
        args = ()
        kwargs = {}
    935     if result is not None:
    936         self.process(
    937             result,
    938             type_hint=type_hint,
   (...)
    941             _funcname=getattr(func, "__qualname__", str(func)),
    942         )

File ~\anaconda3\Lib\site-packages\in_n_out\_store.py:804, in Store.inject.<locals>._inner.<locals>._exec(*args=(), **kwargs={})
    797 logger.debug(
    798     "  Calling %s with %r (injected %r)",
    799     _fname,
    800     bound.arguments,
    801     _injected_names,
    802 )
    803 try:
--> 804     result = func(**bound.arguments)
        bound = <BoundArguments (selected=False, self=<napari._qt.qt_viewer.QtViewer object at 0x0000029729FBA0E0>)>
        func = <function QtViewer._save_layers_dialog at 0x0000029729FF8720>
        bound.arguments = {'selected': False, 'self': <napari._qt.qt_viewer.QtViewer object at 0x0000029729FBA0E0>}
    805 except TypeError as e:
    806     if "missing" not in e.args[0]:

File ~\anaconda3\Lib\site-packages\napari\_qt\qt_viewer.py:804, in QtViewer._save_layers_dialog(self=<napari._qt.qt_viewer.QtViewer object>, selected=False)
    800 writer = _npe2_decode_selected_filter(
    801     ext_str, selected_filter, writers
    802 )
    803 with warnings.catch_warnings(record=True) as wa:
--> 804     saved = self.viewer.layers.save(
        self = <napari._qt.qt_viewer.QtViewer object at 0x0000029729FBA0E0>
        self.viewer.layers = [<Image layer 'astronaut' at 0x29737646490>]
        self.viewer = Viewer(camera=Camera(center=(0.0, 255.5, 255.5), zoom=1.3818603515625, angles=(0.0, 0.0, 90.0), perspective=0.0, mouse_pan=True, mouse_zoom=True), cursor=Cursor(position=(-129.4882576906172, -5.380194161691563), scaled=True, style=<CursorStyle.STANDARD: 'standard'>, size=1.0), dims=Dims(ndim=2, ndisplay=2, order=(0, 1), axis_labels=('0', '1'), rollable=(True, True), range=(RangeTuple(start=0.0, stop=511.0, step=1.0), RangeTuple(start=0.0, stop=511.0, step=1.0)), margin_left=(0.0, 0.0), margin_right=(0.0, 0.0), point=(255.0, 255.0), last_used=0), grid=GridCanvas(stride=1, shape=(-1, -1), enabled=False), layers=[<Image layer 'astronaut' at 0x29737646490>], help='use <2> for transform', status='', tooltip=Tooltip(visible=False, text=''), theme='dark', title='napari', mouse_over_canvas=False, mouse_move_callbacks=[], mouse_drag_callbacks=[], mouse_double_click_callbacks=[<function double_click_to_zoom at 0x0000029729930D60>], mouse_wheel_callbacks=[<function dims_scroll at 0x0000029729930CC0>], _persisted_mouse_event={}, _mouse_drag_gen={}, _mouse_wheel_gen={}, _keymap={})
        filename = 'C:/Users/kei/export/astronaut.svg'
        selected = False
        writer = WriterContribution(command='napari-svg.svg_writer', layer_types=['image*', 'labels*', 'points*', 'shapes*', 'vectors*'], filename_extensions=['.svg'], display_name='')
    805         filename, selected=selected, _writer=writer
    806     )
    807     logging.debug('Saved %s', saved)
    808     error_messages = '\n'.join(str(x.message.args[0]) for x in wa)

File ~\anaconda3\Lib\site-packages\napari\components\layerlist.py:486, in LayerList.save(self=[<Image layer 'astronaut' at 0x29737646490>], path='C:/Users/kei/export/astronaut.svg', selected=False, plugin=None, _writer=WriterContribution(command='napari-svg.svg_write...], filename_extensions=['.svg'], display_name=''))
    483     warnings.warn(msg)
    484     return []
--> 486 return save_layers(path, layers, plugin=plugin, _writer=_writer)
        layers = [<Image layer 'astronaut' at 0x29737646490>]
        path = 'C:/Users/kei/export/astronaut.svg'
        plugin = None
        _writer = WriterContribution(command='napari-svg.svg_writer', layer_types=['image*', 'labels*', 'points*', 'shapes*', 'vectors*'], filename_extensions=['.svg'], display_name='')

File ~\anaconda3\Lib\site-packages\napari\plugins\io.py:244, in save_layers(path='C:/Users/kei/export/astronaut.svg', layers=[<Image layer 'astronaut'>], plugin=None, _writer=WriterContribution(command='napari-svg.svg_write...], filename_extensions=['.svg'], display_name=''))
    240     written, writer_name = _write_multiple_layers_with_plugins(
    241         path, layers, plugin_name=plugin, _writer=_writer
    242     )
    243 elif len(layers) == 1:
--> 244     _written, writer_name = _write_single_layer_with_plugins(
        writer_name = ''
        layers = [<Image layer 'astronaut' at 0x29737646490>]
        path = 'C:/Users/kei/export/astronaut.svg'
        plugin = None
        _writer = WriterContribution(command='napari-svg.svg_writer', layer_types=['image*', 'labels*', 'points*', 'shapes*', 'vectors*'], filename_extensions=['.svg'], display_name='')
        layers[0] = <Image layer 'astronaut' at 0x29737646490>
    245         path, layers[0], plugin_name=plugin, _writer=_writer
    246     )
    247     written = [_written] if _written else []
    248 else:

File ~\anaconda3\Lib\site-packages\napari\plugins\io.py:457, in _write_single_layer_with_plugins(path='C:/Users/kei/export/astronaut.svg', layer=<Image layer 'astronaut'>, plugin_name=None, _writer=WriterContribution(command='napari-svg.svg_write...], filename_extensions=['.svg'], display_name=''))
    420 """Write single layer data with a plugin.
    421
    422 If ``plugin_name`` is not provided then we just directly call
   (...)
    453     Name of the plugin selected to write the data.
    454 """
    456 # Try to use NPE2 first
--> 457 written_paths, writer_name = _npe2.write_layers(
        _npe2 = <module 'napari.plugins._npe2' from 'C:\\Users\\kei\\anaconda3\\Lib\\site-packages\\napari\\plugins\\_npe2.py'>
        path = 'C:/Users/kei/export/astronaut.svg'
        [layer] = [<Image layer 'astronaut' at 0x29737646490>]
        plugin_name = None
        _writer = WriterContribution(command='napari-svg.svg_writer', layer_types=['image*', 'labels*', 'points*', 'shapes*', 'vectors*'], filename_extensions=['.svg'], display_name='')
        layer = <Image layer 'astronaut' at 0x29737646490>
    458     path, [layer], plugin_name, _writer
    459 )
    460 if writer_name:
    461     return (written_paths[0], writer_name)

File ~\anaconda3\Lib\site-packages\napari\plugins\_npe2.py:115, in write_layers(path='C:/Users/kei/export/astronaut.svg', layers=[<Image layer 'astronaut'>], plugin_name=None, writer=WriterContribution(command='napari-svg.svg_write...], filename_extensions=['.svg'], display_name=''))
    113 n = sum(ltc.max() for ltc in writer.layer_type_constraints())
    114 args = (path, *layer_data[0][:2]) if n <= 1 else (path, layer_data)
--> 115 res = writer.exec(args=args)
        args = ('C:/Users/kei/export/astronaut.svg', [(array([[[154, 147, 151],
        [109, 103, 124],
        ...,
        [120, 117, 106],
        [125, 119, 110]],

       [[177, 171, 171],
        [144, 141, 143],
        ...,
        [124, 115, 108],
        [121, 116, 105]],

       ...,

       [[183, 169, 170],
        [182, 167, 171],
        ...,
        [  1,   1,   1],
        [  0,   0,   0]],

       [[184, 167, 172],
        [183, 165, 169],
        ...,
        [  1,   1,   1],
        [  0,   0,   0]]], dtype=uint8), {'affine': array([[1., 0., 0.],
       [0., 1., 0.],
       [0., 0., 1.]]), 'axis_labels': ('axis -2', 'axis -1'), 'blending': 'translucent_no_depth', 'experimental_clipping_planes': [], 'metadata': {}, 'name': 'astronaut', 'opacity': 1.0, 'projection_mode': <ImageProjectionMode.NONE: 'none'>, 'rotate': [[1.0, 0.0], [0.0, 1.0]], 'scale': [1.0, 1.0], 'shear': [0.0], 'translate': [0.0, 0.0], 'units': (<Unit('pixel')>, <Unit('pixel')>), 'visible': True, 'rgb': True, 'multiscale': False, 'colormap': {'colors': ColorArray([[0.     , 0.     , 0.     , 1.     ],
            [0.00392, 0.00392, 0.00392, 1.     ],
            ...,
            [0.99608, 0.99608, 0.99608, 1.     ],
            [1.     , 1.     , 1.     , 1.     ]], dtype=float32), 'name': 'gray', 'interpolation': <ColormapInterpolationMode.LINEAR: 'linear'>, 'controls': array([0.     , 0.00392, ..., 0.99608, 1.     ], dtype=float32)}, 'contrast_limits': [0, 255], 'interpolation2d': 'nearest', 'interpolation3d': 'linear', 'rendering': 'mip', 'depiction': 'volume', 'plane': {'normal': (1.0, 0.0, 0.0), 'position': (0.0, 0.0, 0.0), 'thickness': 1.0}, 'iso_threshold': 127.5, 'attenuation': 0.05, 'gamma': 1.0, 'custom_interpolation_kernel_2d': array([[1.]], dtype=float32)}, 'image')])
        writer = WriterContribution(command='napari-svg.svg_writer', layer_types=['image*', 'labels*', 'points*', 'shapes*', 'vectors*'], filename_extensions=['.svg'], display_name='')
    116 if isinstance(
    117     res, str
    118 ):  # pragma: no cover # it shouldn't be... bad plugin.
    119     return [res], writer.plugin_name

File ~\anaconda3\Lib\site-packages\npe2\manifest\utils.py:61, in Executable.exec(self=WriterContribution(command='napari-svg.svg_write...], filename_extensions=['.svg'], display_name=''), args=('C:/Users/kei/export/astronaut.svg', [(array([[[154, 147, 151],
        [109, 103, 124]... 1,   1],
        [  0,   0,   0]]], dtype=uint8), {'affine': array([[1., 0., 0.],
       [0., 1., ...olation_kernel_2d': array([[1.]], dtype=float32)}, 'image')]), kwargs={}, _registry=None)
     59     kwargs = {}
     60 reg = _registry or kwargs.pop("_registry", None)
---> 61 return self.get_callable(reg)(*args, **kwargs)
        reg = None
        kwargs = {}
        args = ('C:/Users/kei/export/astronaut.svg', [(array([[[154, 147, 151],
        [109, 103, 124],
        ...,
        [120, 117, 106],
        [125, 119, 110]],

       [[177, 171, 171],
        [144, 141, 143],
        ...,
        [124, 115, 108],
        [121, 116, 105]],

       ...,

       [[183, 169, 170],
        [182, 167, 171],
        ...,
        [  1,   1,   1],
        [  0,   0,   0]],

       [[184, 167, 172],
        [183, 165, 169],
        ...,
        [  1,   1,   1],
        [  0,   0,   0]]], dtype=uint8), {'affine': array([[1., 0., 0.],
       [0., 1., 0.],
       [0., 0., 1.]]), 'axis_labels': ('axis -2', 'axis -1'), 'blending': 'translucent_no_depth', 'experimental_clipping_planes': [], 'metadata': {}, 'name': 'astronaut', 'opacity': 1.0, 'projection_mode': <ImageProjectionMode.NONE: 'none'>, 'rotate': [[1.0, 0.0], [0.0, 1.0]], 'scale': [1.0, 1.0], 'shear': [0.0], 'translate': [0.0, 0.0], 'units': (<Unit('pixel')>, <Unit('pixel')>), 'visible': True, 'rgb': True, 'multiscale': False, 'colormap': {'colors': ColorArray([[0.     , 0.     , 0.     , 1.     ],
            [0.00392, 0.00392, 0.00392, 1.     ],
            ...,
            [0.99608, 0.99608, 0.99608, 1.     ],
            [1.     , 1.     , 1.     , 1.     ]], dtype=float32), 'name': 'gray', 'interpolation': <ColormapInterpolationMode.LINEAR: 'linear'>, 'controls': array([0.     , 0.00392, ..., 0.99608, 1.     ], dtype=float32)}, 'contrast_limits': [0, 255], 'interpolation2d': 'nearest', 'interpolation3d': 'linear', 'rendering': 'mip', 'depiction': 'volume', 'plane': {'normal': (1.0, 0.0, 0.0), 'position': (0.0, 0.0, 0.0), 'thickness': 1.0}, 'iso_threshold': 127.5, 'attenuation': 0.05, 'gamma': 1.0, 'custom_interpolation_kernel_2d': array([[1.]], dtype=float32)}, 'image')])
        self = WriterContribution(command='napari-svg.svg_writer', layer_types=['image*', 'labels*', 'points*', 'shapes*', 'vectors*'], filename_extensions=['.svg'], display_name='')

File ~\anaconda3\Lib\site-packages\napari_svg\hook_implementations.py:83, in writer(path='C:/Users/kei/export/astronaut.svg', layer_data=[(array([[[154, 147, 151],
        [109, 103, 124]... 1,   1],
        [  0,   0,   0]]], dtype=uint8), {'affine': array([[1., 0., 0.],
       [0., 1., ...olation_kernel_2d': array([[1.]], dtype=float32)}, 'image')])
     81 for ld in layer_data:
     82     function_string = ld[2] + '_to_xml(ld[0], ld[1])'
---> 83     layer_xml, extrema = eval(function_string)
        function_string = 'image_to_xml(ld[0], ld[1])'
     84     full_xml_list.append(layer_xml)
     85     if full_extrema is None:

File <string>:1

File ~\anaconda3\Lib\site-packages\napari_svg\layer_to_xml.py:182, in image_to_xml(data=array([[[154, 147, 151],
        [109, 103, 124]... 1,   1],
        [  0,   0,   0]]], dtype=uint8), meta={'affine': array([[1., 0., 0.],
       [0., 1., ...olation_kernel_2d': array([[1.]], dtype=float32)})
    179     image = data
    181 # Find extrema of data
--> 182 extrema = extrema_image(image, meta)
        meta = {'affine': array([[1., 0., 0.],
       [0., 1., 0.],
       [0., 0., 1.]]), 'axis_labels': ('axis -2', 'axis -1'), 'blending': 'translucent_no_depth', 'experimental_clipping_planes': [], 'metadata': {}, 'name': 'astronaut', 'opacity': 1.0, 'projection_mode': <ImageProjectionMode.NONE: 'none'>, 'rotate': [[1.0, 0.0], [0.0, 1.0]], 'scale': [1.0, 1.0], 'shear': [0.0], 'translate': [0.0, 0.0], 'units': (<Unit('pixel')>, <Unit('pixel')>), 'visible': True, 'rgb': True, 'multiscale': False, 'colormap': {'colors': ColorArray([[0.     , 0.     , 0.     , 1.     ],
            [0.00392, 0.00392, 0.00392, 1.     ],
            ...,
            [0.99608, 0.99608, 0.99608, 1.     ],
            [1.     , 1.     , 1.     , 1.     ]], dtype=float32), 'name': 'gray', 'interpolation': <ColormapInterpolationMode.LINEAR: 'linear'>, 'controls': array([0.     , 0.00392, ..., 0.99608, 1.     ], dtype=float32)}, 'contrast_limits': [0, 255], 'interpolation2d': 'nearest', 'interpolation3d': 'linear', 'rendering': 'mip', 'depiction': 'volume', 'plane': {'normal': (1.0, 0.0, 0.0), 'position': (0.0, 0.0, 0.0), 'thickness': 1.0}, 'iso_threshold': 127.5, 'attenuation': 0.05, 'gamma': 1.0, 'custom_interpolation_kernel_2d': array([[1.]], dtype=float32)}
        image = array([[[154, 147, 151],
        [109, 103, 124],
        ...,
        [120, 117, 106],
        [125, 119, 110]],

       [[177, 171, 171],
        [144, 141, 143],
        ...,
        [124, 115, 108],
        [121, 116, 105]],

       ...,

       [[183, 169, 170],
        [182, 167, 171],
        ...,
        [  1,   1,   1],
        [  0,   0,   0]],

       [[184, 167, 172],
        [183, 165, 169],
        ...,
        [  1,   1,   1],
        [  0,   0,   0]]], dtype=uint8)
    184 if rgb:
    185     mapped_image = image

File ~\anaconda3\Lib\site-packages\napari_svg\layer_to_xml.py:116, in extrema_image(image=array([[[154, 147, 151],
        [109, 103, 124]... 1,   1],
        [  0,   0,   0]]], dtype=uint8), meta={'affine': array([[1., 0., 0.],
       [0., 1., ...olation_kernel_2d': array([[1.]], dtype=float32)})
    114 def extrema_image(image, meta):
    115     """Compute the extrema of an image layer, accounting for transforms."""
--> 116     coords = np.array([[0, 0], list(image.shape)])
        np = <module 'numpy' from 'C:\\Users\\kei\\anaconda3\\Lib\\site-packages\\numpy\\__init__.py'>
        image = array([[[154, 147, 151],
        [109, 103, 124],
        ...,
        [120, 117, 106],
        [125, 119, 110]],

       [[177, 171, 171],
        [144, 141, 143],
        ...,
        [124, 115, 108],
        [121, 116, 105]],

       ...,

       [[183, 169, 170],
        [182, 167, 171],
        ...,
        [  1,   1,   1],
        [  0,   0,   0]],

       [[184, 167, 172],
        [183, 165, 169],
        ...,
        [  1,   1,   1],
        [  0,   0,   0]]], dtype=uint8)
    117     return extrema_coords(coords, meta)

ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 1 dimensions. The detected shape was (2,) + inhomogeneous part.

np.array received rgb image shape.([512, 512, 3])
this shape not match 1st arg [0, 0].

for example can use this fix.

coords = np.array([[0, 0],  list(image.shape)])

to

coords = np.array([[0, 0], list(image.shape[:2])])

thx.

log

[jni]

Thanks for the report @dani-ham! This is the same as #50, which is good cos I'd missed this issue. 😂 The fix is detailed in this comment. We'd welcome a contribution to address this! 🙏