IndexError:

[josenimo]

When selecting columns quantile75_Ecadherin to quantile75_DAPI_5 this happens

15:33:29.94 | DEBUG | Gates dataframe from  loaded and checked.
INFO: Gates dataframe loaded from:
INFO: Removed 4 out of list of 24.
---------------------------------------------------------------------------
IndexError                                Traceback (most recent call last)
File ~/Jose_BI/napari-cell-gater/src/cell_gater/widgets/sample_widget.py:271, in SampleWidget._validate(self=<cell_gater.widgets.sample_widget.SampleWidget object>)
    267             del self.model.markers[marker]
    269 napari_notification(f"Removed {n_markers - len(self.model.markers)} out of list of {n_markers}.")
--> 271 self._scatter_widget = ScatterInputWidget(self.model, self.viewer)
        self._scatter_widget = <cell_gater.widgets.scatter_widget.ScatterInputWidget object at 0x28c368670>
        self = <cell_gater.widgets.sample_widget.SampleWidget object at 0x16982f490>
        ScatterInputWidget = <class 'cell_gater.widgets.scatter_widget.ScatterInputWidget'>
    272 self.viewer.window.add_dock_widget(
    273     self._scatter_widget, name="cell_gater", area="right", menu=self._viewer.window.window_menu, tabify=True
    274 )
    276 self.model.validated = True

File ~/Jose_BI/napari-cell-gater/src/cell_gater/widgets/scatter_widget.py:120, in ScatterInputWidget.__init__(self=<cell_gater.widgets.scatter_widget.ScatterInputWidget object>, model=DataModel(events=<napari.utils.events.event.Emit...  0.0

[100 rows x 3 columns], _current_gate=0.0), viewer=Viewer(camera=Camera(center=(0.0, 4159.0, 4159.0...ouse_drag_gen={}, _mouse_wheel_gen={}, keymap={}))
    118 self._read_mask_image()
    119 self._load_labels()
--> 120 self._load_image()
        self = <cell_gater.widgets.scatter_widget.ScatterInputWidget object at 0x12b475f30>
    121 self.load_ref_channel()
    123 # scatter plot

File ~/Jose_BI/napari-cell-gater/src/cell_gater/widgets/scatter_widget.py:388, in ScatterInputWidget._load_image(self=<cell_gater.widgets.scatter_widget.ScatterInputWidget object>)
    386 """Load the image into the napari viewer."""
    387 marker_index = self.model.markers_image_indices[self.model.active_marker]
--> 388 self.viewer.add_image(self._image[marker_index], name=self.model.active_marker + "_" + self.model.active_sample, blending="additive", colormap="green")
        marker_index = 65
        self._image = dask.array<_map_read_frame, shape=(30, 8319, 8319), dtype=uint16, chunksize=(1, 8319, 8319), chunktype=numpy.ndarray>
        self = <cell_gater.widgets.scatter_widget.ScatterInputWidget object at 0x12b475f30>

File /opt/homebrew/Caskroom/mambaforge/base/envs/napari/lib/python3.10/site-packages/dask/array/core.py:1979, in Array.__getitem__(self=dask.array<_map_read_frame, shape=(30, 8319, 831...unksize=(1, 8319, 8319), chunktype=numpy.ndarray>, index=(65,))
   1971     index = (index,)
   1973 from dask.array.slicing import (
   1974     normalize_index,
   1975     slice_with_bool_dask_array,
   1976     slice_with_int_dask_array,
   1977 )
-> 1979 index2 = normalize_index(index, self.shape)
        index = (65,)
        self = dask.array<_map_read_frame, shape=(30, 8319, 8319), dtype=uint16, chunksize=(1, 8319, 8319), chunktype=numpy.ndarray>
   1980 dependencies = {self.name}
   1981 for i in index2:

File /opt/homebrew/Caskroom/mambaforge/base/envs/napari/lib/python3.10/site-packages/dask/array/slicing.py:922, in normalize_index(idx=(65, slice(None, None, None), slice(None, None, None)), shape=(30, 8319, 8319))
    920 for axis, (i, d) in enumerate(zip(idx, none_shape)):
    921     if d is not None:
--> 922         check_index(axis, i, d)
        i = 65
        axis = 0
        d = 30
    923 idx = tuple(map(sanitize_index, idx))
    924 idx = tuple(map(normalize_slice, idx, none_shape))

File /opt/homebrew/Caskroom/mambaforge/base/envs/napari/lib/python3.10/site-packages/dask/array/slicing.py:994, in check_index(axis=0, ind=65, dimension=30)
    991     return
    993 elif ind >= dimension or ind < -dimension:
--> 994     raise IndexError(
        ind = 65
        dimension = 30
        axis = 0
    995         f"Index {ind} is out of bounds for axis {axis} with size {dimension}"
    996     )

IndexError: Index 65 is out of bounds for axis 0 with size 30
INFO: Removed 4 out of list of 24.
---------------------------------------------------------------------------
IndexError                                Traceback (most recent call last)
File ~/Jose_BI/napari-cell-gater/src/cell_gater/widgets/sample_widget.py:271, in SampleWidget._validate(self=<cell_gater.widgets.sample_widget.SampleWidget object>)
    267             del self.model.markers[marker]
    269 napari_notification(f"Removed {n_markers - len(self.model.markers)} out of list of {n_markers}.")
--> 271 self._scatter_widget = ScatterInputWidget(self.model, self.viewer)
        self._scatter_widget = <cell_gater.widgets.scatter_widget.ScatterInputWidget object at 0x28c368670>
        self = <cell_gater.widgets.sample_widget.SampleWidget object at 0x16982f490>
        ScatterInputWidget = <class 'cell_gater.widgets.scatter_widget.ScatterInputWidget'>
    272 self.viewer.window.add_dock_widget(
    273     self._scatter_widget, name="cell_gater", area="right", menu=self._viewer.window.window_menu, tabify=True
    274 )
    276 self.model.validated = True

File ~/Jose_BI/napari-cell-gater/src/cell_gater/widgets/scatter_widget.py:120, in ScatterInputWidget.__init__(self=<cell_gater.widgets.scatter_widget.ScatterInputWidget object>, model=DataModel(events=<napari.utils.events.event.Emit...  0.0

[100 rows x 3 columns], _current_gate=0.0), viewer=Viewer(camera=Camera(center=(0.0, 4159.0, 4159.0...ouse_drag_gen={}, _mouse_wheel_gen={}, keymap={}))
    118 self._read_mask_image()
    119 self._load_labels()
--> 120 self._load_image()
        self = <cell_gater.widgets.scatter_widget.ScatterInputWidget object at 0x12bd500d0>
    121 self.load_ref_channel()
    123 # scatter plot

File ~/Jose_BI/napari-cell-gater/src/cell_gater/widgets/scatter_widget.py:388, in ScatterInputWidget._load_image(self=<cell_gater.widgets.scatter_widget.ScatterInputWidget object>)
    386 """Load the image into the napari viewer."""
    387 marker_index = self.model.markers_image_indices[self.model.active_marker]
--> 388 self.viewer.add_image(self._image[marker_index], name=self.model.active_marker + "_" + self.model.active_sample, blending="additive", colormap="green")
        marker_index = 65
        self._image = dask.array<_map_read_frame, shape=(30, 8319, 8319), dtype=uint16, chunksize=(1, 8319, 8319), chunktype=numpy.ndarray>
        self = <cell_gater.widgets.scatter_widget.ScatterInputWidget object at 0x12bd500d0>

File /opt/homebrew/Caskroom/mambaforge/base/envs/napari/lib/python3.10/site-packages/dask/array/core.py:1979, in Array.__getitem__(self=dask.array<_map_read_frame, shape=(30, 8319, 831...unksize=(1, 8319, 8319), chunktype=numpy.ndarray>, index=(65,))
   1971     index = (index,)
   1973 from dask.array.slicing import (
   1974     normalize_index,
   1975     slice_with_bool_dask_array,
   1976     slice_with_int_dask_array,
   1977 )
-> 1979 index2 = normalize_index(index, self.shape)
        index = (65,)
        self = dask.array<_map_read_frame, shape=(30, 8319, 8319), dtype=uint16, chunksize=(1, 8319, 8319), chunktype=numpy.ndarray>
   1980 dependencies = {self.name}
   1981 for i in index2:

File /opt/homebrew/Caskroom/mambaforge/base/envs/napari/lib/python3.10/site-packages/dask/array/slicing.py:922, in normalize_index(idx=(65, slice(None, None, None), slice(None, None, None)), shape=(30, 8319, 8319))
    920 for axis, (i, d) in enumerate(zip(idx, none_shape)):
    921     if d is not None:
--> 922         check_index(axis, i, d)
        i = 65
        axis = 0
        d = 30
    923 idx = tuple(map(sanitize_index, idx))
    924 idx = tuple(map(normalize_slice, idx, none_shape))

File /opt/homebrew/Caskroom/mambaforge/base/envs/napari/lib/python3.10/site-packages/dask/array/slicing.py:994, in check_index(axis=0, ind=65, dimension=30)
    991     return
    993 elif ind >= dimension or ind < -dimension:
--> 994     raise IndexError(
        ind = 65
        dimension = 30
        axis = 0
    995         f"Index {ind} is out of bounds for axis {axis} with size {dimension}"
    996     )

IndexError: Index 65 is out of bounds for axis 0 with size 30
WARNING: Populating font family aliases took 139 ms. Replace uses of missing font family "Monospace" with one that exists to avoid this cost.
15:36:06 WARNING Populating font family aliases took 139 ms. Replace uses of missing font family "Monospace" with one that exists to avoid this cost.
❯ napari
INFO: Loaded 5 regionprops csvs.
INFO: 5 paths of images loaded.
INFO: 5 paths of masks loaded.
INFO: Removed 5 out of list of 25.
---------------------------------------------------------------------------
IndexError                                Traceback (most recent call last)
File ~/Jose_BI/napari-cell-gater/src/cell_gater/widgets/sample_widget.py:271, in SampleWidget._validate(self=<cell_gater.widgets.sample_widget.SampleWidget object>)
    267             del self.model.markers[marker]
    269 napari_notification(f"Removed {n_markers - len(self.model.markers)} out of list of {n_markers}.")
--> 271 self._scatter_widget = ScatterInputWidget(self.model, self.viewer)
        self._scatter_widget = None
        self = <cell_gater.widgets.sample_widget.SampleWidget object at 0x15f82f490>
        ScatterInputWidget = <class 'cell_gater.widgets.scatter_widget.ScatterInputWidget'>
    272 self.viewer.window.add_dock_widget(
    273     self._scatter_widget, name="cell_gater", area="right", menu=self._viewer.window.window_menu, tabify=True
    274 )
    276 self.model.validated = True

File ~/Jose_BI/napari-cell-gater/src/cell_gater/widgets/scatter_widget.py:120, in ScatterInputWidget.__init__(self=<cell_gater.widgets.scatter_widget.ScatterInputWidget object>, model=DataModel(events=<napari.utils.events.event.Emit...taFrame
Columns: []
Index: [], _current_gate=0.0), viewer=Viewer(camera=Camera(center=(0.0, 4159.0, 4159.0...ouse_drag_gen={}, _mouse_wheel_gen={}, keymap={}))
    118 self._read_mask_image()
    119 self._load_labels()
--> 120 self._load_image()
        self = <cell_gater.widgets.scatter_widget.ScatterInputWidget object at 0x292a88670>
    121 self.load_ref_channel()
    123 # scatter plot

File ~/Jose_BI/napari-cell-gater/src/cell_gater/widgets/scatter_widget.py:388, in ScatterInputWidget._load_image(self=<cell_gater.widgets.scatter_widget.ScatterInputWidget object>)
    386 """Load the image into the napari viewer."""
    387 marker_index = self.model.markers_image_indices[self.model.active_marker]
--> 388 self.viewer.add_image(self._image[marker_index], name=self.model.active_marker + "_" + self.model.active_sample, blending="additive", colormap="green")
        marker_index = 65
        self._image = dask.array<_map_read_frame, shape=(30, 8319, 8319), dtype=uint16, chunksize=(1, 8319, 8319), chunktype=numpy.ndarray>
        self = <cell_gater.widgets.scatter_widget.ScatterInputWidget object at 0x292a88670>

File /opt/homebrew/Caskroom/mambaforge/base/envs/napari/lib/python3.10/site-packages/dask/array/core.py:1979, in Array.__getitem__(self=dask.array<_map_read_frame, shape=(30, 8319, 831...unksize=(1, 8319, 8319), chunktype=numpy.ndarray>, index=(65,))
   1971     index = (index,)
   1973 from dask.array.slicing import (
   1974     normalize_index,
   1975     slice_with_bool_dask_array,
   1976     slice_with_int_dask_array,
   1977 )
-> 1979 index2 = normalize_index(index, self.shape)
        index = (65,)
        self = dask.array<_map_read_frame, shape=(30, 8319, 8319), dtype=uint16, chunksize=(1, 8319, 8319), chunktype=numpy.ndarray>
   1980 dependencies = {self.name}
   1981 for i in index2:

File /opt/homebrew/Caskroom/mambaforge/base/envs/napari/lib/python3.10/site-packages/dask/array/slicing.py:922, in normalize_index(idx=(65, slice(None, None, None), slice(None, None, None)), shape=(30, 8319, 8319))
    920 for axis, (i, d) in enumerate(zip(idx, none_shape)):
    921     if d is not None:
--> 922         check_index(axis, i, d)
        i = 65
        axis = 0
        d = 30
    923 idx = tuple(map(sanitize_index, idx))
    924 idx = tuple(map(normalize_slice, idx, none_shape))

File /opt/homebrew/Caskroom/mambaforge/base/envs/napari/lib/python3.10/site-packages/dask/array/slicing.py:994, in check_index(axis=0, ind=65, dimension=30)
    991     return
    993 elif ind >= dimension or ind < -dimension:
--> 994     raise IndexError(
        ind = 65
        dimension = 30
        axis = 0
    995         f"Index {ind} is out of bounds for axis {axis} with size {dimension}"
    996     )

IndexError: Index 65 is out of bounds for axis 0 with size 30

[josenimo]

ok, so if you have more than 1 metric per channel, choosing any of those extra metrics will cause the indexing to fail. (picking column 34 on your matrix, will not allow you to pick channel 34 because there are only 30 channels on your image).