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[builtins writer] using .png or .jpg extension when saving single-channel image layer results in a traceback #6670

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psobolewskiPhD opened this issue Feb 19, 2024 · 2 comments 路 May be fixed by #6884
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[builtins writer] using .png or .jpg extension when saving single-channel image layer results in a traceback #6670

psobolewskiPhD opened this issue Feb 19, 2024 · 2 comments 路 May be fixed by #6884
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@psobolewskiPhD
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psobolewskiPhD commented Feb 19, 2024 •
edited

馃悰 Bug Report

First reported here: #3080 (comment)
If you have a simple image layer like:
np.zeros or np.ones -- anything single channel -- and use Save Selected Layers... and use .png or .jpg extension to save as png, you get a traceback:
OSError: cannot write mode F as PNG


Traceback (most recent call last):
  File "/Users/piotrsobolewski/Dev/miniforge3/envs/napari-dev/lib/python3.11/site-packages/PIL/PngImagePlugin.py", line 1279, in _save
    rawmode, mode = _OUTMODES[mode]
                    ~~~~~~~~~^^^^^^
KeyError: 'F'

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/Users/piotrsobolewski/Dev/miniforge3/envs/napari-dev/lib/python3.11/site-packages/app_model/backends/qt/_qaction.py", line 53, in _on_triggered
    self._app.commands.execute_command(self._command_id).result()
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/piotrsobolewski/Dev/miniforge3/envs/napari-dev/lib/python3.11/site-packages/app_model/registries/_commands_reg.py", line 197, in execute_command
    raise e
  File "/Users/piotrsobolewski/Dev/miniforge3/envs/napari-dev/lib/python3.11/site-packages/app_model/registries/_commands_reg.py", line 192, in execute_command
    future.set_result(cmd(*args, **kwargs))
                      ^^^^^^^^^^^^^^^^^^^^
  File "/Users/piotrsobolewski/Dev/miniforge3/envs/napari-dev/lib/python3.11/site-packages/in_n_out/_store.py", line 936, in _exec
    result = func(*args, **kwargs)
             ^^^^^^^^^^^^^^^^^^^^^
  File "/Users/piotrsobolewski/Dev/miniforge3/envs/napari-dev/lib/python3.11/site-packages/in_n_out/_store.py", line 804, in _exec
    result = func(**bound.arguments)
             ^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/piotrsobolewski/Dev/napari/napari/_qt/_qapp_model/qactions/_file.py", line 30, in _save_selected_layers
    qt_viewer._save_layers_dialog(selected=True)
  File "/Users/piotrsobolewski/Dev/napari/napari/_qt/qt_viewer.py", line 745, in _save_layers_dialog
    saved = self.viewer.layers.save(
            ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/piotrsobolewski/Dev/napari/napari/components/layerlist.py", line 491, in save
    return save_layers(path, layers, plugin=plugin, _writer=_writer)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/piotrsobolewski/Dev/napari/napari/plugins/io.py", line 243, in save_layers
    _written, writer_name = _write_single_layer_with_plugins(
                            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/piotrsobolewski/Dev/napari/napari/plugins/io.py", line 456, in _write_single_layer_with_plugins
    written_paths, writer_name = _npe2.write_layers(
                                 ^^^^^^^^^^^^^^^^^^^
  File "/Users/piotrsobolewski/Dev/napari/napari/plugins/_npe2.py", line 125, in write_layers
    res = writer.exec(args=args)
          ^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/piotrsobolewski/Dev/miniforge3/envs/napari-dev/lib/python3.11/site-packages/npe2/manifest/utils.py", line 61, in exec
    return self.get_callable(reg)(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/piotrsobolewski/Dev/napari/napari_builtins/io/_write.py", line 124, in napari_write_image
    imsave(path, data)
  File "/Users/piotrsobolewski/Dev/napari/napari/utils/io.py", line 28, in imsave
    imsave_png(filename, data)
  File "/Users/piotrsobolewski/Dev/napari/napari/utils/io.py", line 58, in imsave_png
    iio.imwrite(
  File "/Users/piotrsobolewski/Dev/miniforge3/envs/napari-dev/lib/python3.11/site-packages/imageio/v3.py", line 139, in imwrite
    with imopen(
  File "/Users/piotrsobolewski/Dev/miniforge3/envs/napari-dev/lib/python3.11/site-packages/imageio/core/v3_plugin_api.py", line 367, in __exit__
    self.close()
  File "/Users/piotrsobolewski/Dev/miniforge3/envs/napari-dev/lib/python3.11/site-packages/imageio/plugins/pillow.py", line 144, in close
    self._flush_writer()
  File "/Users/piotrsobolewski/Dev/miniforge3/envs/napari-dev/lib/python3.11/site-packages/imageio/plugins/pillow.py", line 485, in _flush_writer
    primary_image.save(self._request.get_file(), **self.save_args)
  File "/Users/piotrsobolewski/Dev/miniforge3/envs/napari-dev/lib/python3.11/site-packages/PIL/Image.py", line 2439, in save
    save_handler(self, fp, filename)
  File "/Users/piotrsobolewski/Dev/miniforge3/envs/napari-dev/lib/python3.11/site-packages/PIL/PngImagePlugin.py", line 1282, in _save
    raise OSError(msg) from e
OSError: cannot write mode F as PNG

Worse yet, a file is created, but it's empty so it's misleading.

Seems related to the layer/file type, because RGB layers are fine.

Edit: OK, it's because these simple np layers are dtype('float64')

馃挕 Steps to Reproduce

Use:

import numpy as np
import napari

w = napari.Viewer()
w.add_image(np.ones((10,10)))

(or you can use zeros)
Then try Meta/Command-S (Save selected layers) and use .png as extension

馃挕 Expected Behavior

The data should be saved properly.

馃寧 Environment

napari: 0.5.0a2.dev543+gad78ee21a
Platform: macOS-13.3.1-arm64-arm-64bit
System: MacOS 13.3.1
Python: 3.11.7 | packaged by conda-forge | (main, Dec 23 2023, 14:38:07) [Clang 16.0.6 ]
Qt: 6.6.1
PyQt6:
NumPy: 1.26.3
SciPy: 1.12.0
Dask: 2024.1.1
VisPy: 0.14.1
magicgui: 0.8.1
superqt: 0.6.1
in-n-out: 0.1.9
app-model: 0.2.4
npe2: 0.7.4

OpenGL:

  • GL version: 2.1 Metal - 83.1
  • MAX_TEXTURE_SIZE: 16384
  • GL_MAX_3D_TEXTURE_SIZE: 2048

Screens:

  • screen 1: resolution 1680x1050, scale 2.0

Settings path:

  • /Users/piotrsobolewski/Library/Application Support/napari/napari-dev_a1eb8b76ba95fa16ad06e26097b46b8455dfbf0b/settings.yaml

馃挕 Additional Context

No response
@psobolewskiPhD psobolewskiPhD added the bug Something isn't working label Feb 19, 2024
@psobolewskiPhD
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psobolewskiPhD commented Feb 19, 2024 •
edited

I think converting from float could be tricky, so best solution is to warn the user?
Alas, for image layers convert type isn't implemented, so little recourse in the GUI.

@Czaki
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Czaki commented Feb 19, 2024

I think that we could use here code from #6537

@psobolewskiPhD psobolewskiPhD linked a pull request May 2, 2024 that will close this issue
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[bugfix] Warn if float image data being saved to non-tiff psobolewskiPhD/napari
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@Czaki @psobolewskiPhD