image series annotator not exiting on last image in series #754
Description
when trying to click "next image" while on the last image nothing happens besides following error pops up:
---------------------------------------------------------------------------
IndexError Traceback (most recent call last)
File ~/miniforge3/envs/samtest/lib/python3.11/site-packages/psygnal/_signal.py:1196, in SignalInstance._run_emit_loop(self=<SignalInstance 'changed' on PushButton(value=False, annotation=None, name='call_button')>, args=(False,))
1195 with Signal._emitting(self):
-> 1196 self._run_emit_loop_inner()
self = <SignalInstance 'changed' on PushButton(value=False, annotation=None, name='call_button')>
self._run_emit_loop_inner = <bound method SignalInstance._run_emit_loop_immediate of <SignalInstance 'changed' on PushButton(value=False, annotation=None, name='call_button')>>
1197 except RecursionError as e:
File ~/miniforge3/envs/samtest/lib/python3.11/site-packages/psygnal/_signal.py:1225, in SignalInstance._run_emit_loop_immediate(self=<SignalInstance 'changed' on PushButton(value=False, annotation=None, name='call_button')>)
1224 for caller in self._slots:
-> 1225 caller.cb(args)
args = (False,)
caller = <StrongFunction on magicgui.widgets._function_gui.FunctionGui.__init__.<locals>._disable_button_and_call>
File ~/miniforge3/envs/samtest/lib/python3.11/site-packages/psygnal/_weak_callback.py:357, in StrongFunction.cb(self=<StrongFunction on magicgui.widgets._function_gu...onGui.__init__.<locals>._disable_button_and_call>, args=())
356 args = args[: self._max_args]
--> 357 self._f(*self._args, *args, **self._kwargs)
args = ()
self._f = <function FunctionGui.__init__.<locals>._disable_button_and_call at 0x721eb63da980>
self = <StrongFunction on magicgui.widgets._function_gui.FunctionGui.__init__.<locals>._disable_button_and_call>
self._args = ()
self._kwargs = {}
File ~/miniforge3/envs/samtest/lib/python3.11/site-packages/magicgui/widgets/_function_gui.py:228, in FunctionGui.__init__.<locals>._disable_button_and_call()
227 try:
--> 228 self.__call__()
self = <FunctionGui next_image(*args)>
229 finally:
File ~/miniforge3/envs/samtest/lib/python3.11/site-packages/magicgui/widgets/_function_gui.py:346, in FunctionGui.__call__(self=<FunctionGui next_image(*args)>, *args=(), **kwargs={})
345 with _function_name_pointing_to_widget(self):
--> 346 value = self._function(*bound.args, **bound.kwargs)
self = <FunctionGui next_image(*args)>
bound = <BoundArguments (args=())>
self._function = <function image_series_annotator.<locals>.next_image at 0x721ec7f05440>
348 self._call_count += 1
File ~/Documents/git-repositories/micro-sam/micro_sam/sam_annotator/image_series_annotator.py:233, in image_series_annotator.<locals>.next_image(*args=())
232 # Save the current segmentation.
--> 233 _save_segmentation(images[next_image_id], next_image_id, segmentation)
segmentation = array([[0, 0, ..., 0, 0],
[0, 0, ..., 0, 0],
...,
[0, 0, ..., 0, 0],
[0, 0, ..., 0, 0]], dtype=uint32)
next_image_id = 15
images = ['data/cells/images/001_img.png', 'data/cells/images/008_img.png', 'data/cells/images/009_img.png', 'data/cells/images/011_img.png', 'data/cells/images/018_img.png', 'data/cells/images/019_img.png', 'data/cells/images/028_img.png', 'data/cells/images/034_img.png', 'data/cells/images/040_img.png', 'data/cells/images/042_img.png', 'data/cells/images/043_img.png', 'data/cells/images/045_img.png', 'data/cells/images/046_img.png', 'data/cells/images/048_img.png', 'data/cells/images/050_img.png']
235 # Clear the segmentation already to avoid lagging removal.
IndexError: list index out of range
The above exception was the direct cause of the following exception:
EmitLoopError Traceback (most recent call last)
File ~/miniforge3/envs/samtest/lib/python3.11/site-packages/magicgui/widgets/bases/_value_widget.py:71, in ValueWidget._on_value_change(self=PushButton(value=False, annotation=None, name='call_button'), value=False)
69 if value is self.null_value and not self._nullable:
70 return
---> 71 self.changed.emit(value)
value = False
self.changed = <SignalInstance 'changed' on PushButton(value=False, annotation=None, name='call_button')>
self = PushButton(value=False, annotation=None, name='call_button')
File ~/miniforge3/envs/samtest/lib/python3.11/site-packages/psygnal/_signal.py:1176, in SignalInstance.emit(self=<SignalInstance 'changed' on PushButton(value=False, annotation=None, name='call_button')>, check_nargs=False, check_types=False, *args=(False,))
1172 from ._group import EmissionInfo
1174 SignalInstance._debug_hook(EmissionInfo(self, args))
-> 1176 self._run_emit_loop(args)
self = <SignalInstance 'changed' on PushButton(value=False, annotation=None, name='call_button')>
args = (False,)
File ~/miniforge3/envs/samtest/lib/python3.11/site-packages/psygnal/_signal.py:1213, in SignalInstance._run_emit_loop(self=<SignalInstance 'changed' on PushButton(value=False, annotation=None, name='call_button')>, args=(False,))
1205 loop_err = EmitLoopError(
1206 exc=cb_err,
1207 signal=self,
(...)
1210 emit_queue=self._emit_queue,
1211 ).with_traceback(cb_err.__traceback__)
1212 # this comment will show up in the traceback
-> 1213 raise loop_err from cb_err # emit() call ABOVE || callback error BELOW
loop_err = EmitLoopError("\n\nWhile emitting signal 'magicgui.widgets.PushButton.changed', a IndexError occurred in a callback:\n\n Signal emitted at: /home/freckmann15/miniforge3/envs/samtest/lib/python3.11/site-packages/magicgui/widgets/bases/_value_widget.py:71, in _on_value_change\n > self.changed.emit(value)\n\n Callback error at: /home/freckmann15/Documents/git-repositories/micro-sam/micro_sam/sam_annotator/image_series_annotator.py:233, in next_image\n > _save_segmentation(images[next_image_id], next_image_id, segmentation)\n\n Local variables:\n args = ()\n segmentation = array([[0, 0, 0, ..., 0, 0, 0],\n [0, 0, 0, ..., 0, 0, ...\n abort = False\n _get_save_path = <function image_series_annotator.<locals>._get_save_path at ...\n _save_segmentation = <function image_series_annotator.<locals>._save_segmentation...\n annotator = <micro_sam.sam_annotator.annotator_2d.Annotator2d object at ...\n decoder = DecoderAdapter(\n (base): ConvBlock2d(\n (block): Sequenti...\n device = None\n embedding_paths = ['embeddings/cells/vit_b_lm/001_img.zarr', 'embeddings/cells...\n end_msg = 'You have annotated the last image. Do you wish to close nap...\n halo = None\n have_inputs_as_arrays = False\n images = ['data/cells/images/001_img.png', 'data/cells/images/008_img...\n is_volumetric = False\n model_type = 'vit_b_lm'\n next_image_id = 15\n precompute_amg_state = False\n predictor = <mobile_sam.predictor.SamPredictor object at 0x721ef0bb8190>\n skip_segmented = True\n state = AnnotatorState(image_embeddings={'features': array([[[[-0.01...\n tile_shape = None\n viewer = Viewer(camera=Camera(center=(0.0, 215.8179510554866, 260.959...\n\nSee IndexError above for original traceback.")
1214 finally:
1215 self._recursion_depth -= 1
File ~/miniforge3/envs/samtest/lib/python3.11/site-packages/psygnal/_signal.py:1196, in SignalInstance._run_emit_loop(self=<SignalInstance 'changed' on PushButton(value=False, annotation=None, name='call_button')>, args=(False,))
1192 self._max_recursion_depth = max(
1193 self._max_recursion_depth, self._recursion_depth
1194 )
1195 with Signal._emitting(self):
-> 1196 self._run_emit_loop_inner()
self = <SignalInstance 'changed' on PushButton(value=False, annotation=None, name='call_button')>
self._run_emit_loop_inner = <bound method SignalInstance._run_emit_loop_immediate of <SignalInstance 'changed' on PushButton(value=False, annotation=None, name='call_button')>>
1197 except RecursionError as e:
1198 raise RecursionError(
1199 f"RecursionError when "
1200 f"emitting signal {self.name!r} with args {args}"
1201 ) from e
File ~/miniforge3/envs/samtest/lib/python3.11/site-packages/psygnal/_signal.py:1225, in SignalInstance._run_emit_loop_immediate(self=<SignalInstance 'changed' on PushButton(value=False, annotation=None, name='call_button')>)
1223 args = self._emit_queue.popleft()
1224 for caller in self._slots:
-> 1225 caller.cb(args)
args = (False,)
caller = <StrongFunction on magicgui.widgets._function_gui.FunctionGui.__init__.<locals>._disable_button_and_call>
File ~/miniforge3/envs/samtest/lib/python3.11/site-packages/psygnal/_weak_callback.py:357, in StrongFunction.cb(self=<StrongFunction on magicgui.widgets._function_gu...onGui.__init__.<locals>._disable_button_and_call>, args=())
355 if self._max_args is not None:
356 args = args[: self._max_args]
--> 357 self._f(*self._args, *args, **self._kwargs)
args = ()
self._f = <function FunctionGui.__init__.<locals>._disable_button_and_call at 0x721eb63da980>
self = <StrongFunction on magicgui.widgets._function_gui.FunctionGui.__init__.<locals>._disable_button_and_call>
self._args = ()
self._kwargs = {}
File ~/miniforge3/envs/samtest/lib/python3.11/site-packages/magicgui/widgets/_function_gui.py:228, in FunctionGui.__init__.<locals>._disable_button_and_call()
226 self._call_button.enabled = False
227 try:
--> 228 self.__call__()
self = <FunctionGui next_image(*args)>
229 finally:
230 self._call_button.enabled = True
File ~/miniforge3/envs/samtest/lib/python3.11/site-packages/magicgui/widgets/_function_gui.py:346, in FunctionGui.__call__(self=<FunctionGui next_image(*args)>, *args=(), **kwargs={})
344 self._tqdm_depth = 0 # reset the tqdm stack count
345 with _function_name_pointing_to_widget(self):
--> 346 value = self._function(*bound.args, **bound.kwargs)
self = <FunctionGui next_image(*args)>
bound = <BoundArguments (args=())>
self._function = <function image_series_annotator.<locals>.next_image at 0x721ec7f05440>
348 self._call_count += 1
349 if self._result_widget is not None:
File ~/Documents/git-repositories/micro-sam/micro_sam/sam_annotator/image_series_annotator.py:233, in image_series_annotator.<locals>.next_image(*args=())
230 return
232 # Save the current segmentation.
--> 233 _save_segmentation(images[next_image_id], next_image_id, segmentation)
segmentation = array([[0, 0, ..., 0, 0],
[0, 0, ..., 0, 0],
...,
[0, 0, ..., 0, 0],
[0, 0, ..., 0, 0]], dtype=uint32)
next_image_id = 15
images = ['data/cells/images/001_img.png', 'data/cells/images/008_img.png', 'data/cells/images/009_img.png', 'data/cells/images/011_img.png', 'data/cells/images/018_img.png', 'data/cells/images/019_img.png', 'data/cells/images/028_img.png', 'data/cells/images/034_img.png', 'data/cells/images/040_img.png', 'data/cells/images/042_img.png', 'data/cells/images/043_img.png', 'data/cells/images/045_img.png', 'data/cells/images/046_img.png', 'data/cells/images/048_img.png', 'data/cells/images/050_img.png']
235 # Clear the segmentation already to avoid lagging removal.
236 viewer.layers["committed_objects"].data = np.zeros_like(viewer.layers["committed_objects"].data)
EmitLoopError:
While emitting signal 'magicgui.widgets.PushButton.changed', a IndexError occurred in a callback:
Signal emitted at: /home/freckmann15/miniforge3/envs/samtest/lib/python3.11/site-packages/magicgui/widgets/bases/_value_widget.py:71, in _on_value_change
> self.changed.emit(value)
Callback error at: /home/freckmann15/Documents/git-repositories/micro-sam/micro_sam/sam_annotator/image_series_annotator.py:233, in next_image
> _save_segmentation(images[next_image_id], next_image_id, segmentation)
Local variables:
args = ()
segmentation = array([[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, ...
abort = False
_get_save_path = <function image_series_annotator.<locals>._get_save_path at ...
_save_segmentation = <function image_series_annotator.<locals>._save_segmentation...
annotator = <micro_sam.sam_annotator.annotator_2d.Annotator2d object at ...
decoder = DecoderAdapter(
(base): ConvBlock2d(
(block): Sequenti...
device = None
embedding_paths = ['embeddings/cells/vit_b_lm/001_img.zarr', 'embeddings/cells...
end_msg = 'You have annotated the last image. Do you wish to close nap...
halo = None
have_inputs_as_arrays = False
images = ['data/cells/images/001_img.png', 'data/cells/images/008_img...
is_volumetric = False
model_type = 'vit_b_lm'
next_image_id = 15
precompute_amg_state = False
predictor = <mobile_sam.predictor.SamPredictor object at 0x721ef0bb8190>
skip_segmented = True
state = AnnotatorState(image_embeddings={'features': array([[[[-0.01...
tile_shape = None
viewer = Viewer(camera=Camera(center=(0.0, 215.8179510554866, 260.959...
See IndexError above for original traceback.