StarDist2D path issue: models are not stored in the user defined location

[CellKai]

Describe the bug

• The trained model is not saved in the user defined location
• notebook version v1.20

To Reproduce

Steps to reproduce the behavior:
Run ZeroCostDL4Mic StarDist 2D on Google Colab with the sample data provided in the notebook and the default settings.

When running StarDist 2D locally on a Windows machine using Zereocolstdl4MicEverywhere, a similar path problem exists. The model is saved to a location different from what is defined in the notebook.

Expected behavior
On Google Colab: model should be saved in content/data/results/test, but is instead saved to /data/results/test

Screenshots

[esgomezm]

Hi @CellKai
We are not able to reproduce this issue. The models are saved in the folder specified in the notebook. Could you please show us the paths you are writing in the notebook to save the model?

[CellKai]

Hi @esgomezm , thank you for the reply!
I just wanted to reproduce the issue again, but it failed elsewhere.

Steps to reproduce:

• Start ZeroCostDL4Mic StarDist 2D on Google Colab
• execute Step 1.1 (Install key dependencies) --> runs fine
• execute step 1.3 () --> fails with below error

2.18.0
Tensorflow enabled.


A module that was compiled using NumPy 1.x cannot be run in
NumPy 2.0.2 as it may crash. To support both 1.x and 2.x
versions of NumPy, modules must be compiled with NumPy 2.0.
Some module may need to rebuild instead e.g. with 'pybind11>=2.12'.

If you are a user of the module, the easiest solution will be to
downgrade to 'numpy<2' or try to upgrade the affected module.
We expect that some modules will need time to support NumPy 2.

Traceback (most recent call last):  File "<frozen runpy>", line 198, in _run_module_as_main
  File "<frozen runpy>", line 88, in _run_code
  File "/usr/local/lib/python3.11/dist-packages/colab_kernel_launcher.py", line 37, in <module>
    ColabKernelApp.launch_instance()
  File "/usr/local/lib/python3.11/dist-packages/traitlets/config/application.py", line 992, in launch_instance
    app.start()
  File "/usr/local/lib/python3.11/dist-packages/ipykernel/kernelapp.py", line 712, in start
    self.io_loop.start()
  File "/usr/local/lib/python3.11/dist-packages/tornado/platform/asyncio.py", line 205, in start
    self.asyncio_loop.run_forever()
  File "/usr/lib/python3.11/asyncio/base_events.py", line 608, in run_forever
    self._run_once()
  File "/usr/lib/python3.11/asyncio/base_events.py", line 1936, in _run_once
    handle._run()
  File "/usr/lib/python3.11/asyncio/events.py", line 84, in _run
    self._context.run(self._callback, *self._args)
  File "/usr/local/lib/python3.11/dist-packages/ipykernel/kernelbase.py", line 510, in dispatch_queue
    await self.process_one()
  File "/usr/local/lib/python3.11/dist-packages/ipykernel/kernelbase.py", line 499, in process_one
    await dispatch(*args)
  File "/usr/local/lib/python3.11/dist-packages/ipykernel/kernelbase.py", line 406, in dispatch_shell
    await result
  File "/usr/local/lib/python3.11/dist-packages/ipykernel/kernelbase.py", line 730, in execute_request
    reply_content = await reply_content
  File "/usr/local/lib/python3.11/dist-packages/ipykernel/ipkernel.py", line 383, in do_execute
    res = shell.run_cell(
  File "/usr/local/lib/python3.11/dist-packages/ipykernel/zmqshell.py", line 528, in run_cell
    return super().run_cell(*args, **kwargs)
  File "/usr/local/lib/python3.11/dist-packages/IPython/core/interactiveshell.py", line 2975, in run_cell
    result = self._run_cell(
  File "/usr/local/lib/python3.11/dist-packages/IPython/core/interactiveshell.py", line 3030, in _run_cell
    return runner(coro)
  File "/usr/local/lib/python3.11/dist-packages/IPython/core/async_helpers.py", line 78, in _pseudo_sync_runner
    coro.send(None)
  File "/usr/local/lib/python3.11/dist-packages/IPython/core/interactiveshell.py", line 3257, in run_cell_async
    has_raised = await self.run_ast_nodes(code_ast.body, cell_name,
  File "/usr/local/lib/python3.11/dist-packages/IPython/core/interactiveshell.py", line 3473, in run_ast_nodes
    if (await self.run_code(code, result,  async_=asy)):
  File "/usr/local/lib/python3.11/dist-packages/IPython/core/interactiveshell.py", line 3553, in run_code
    exec(code_obj, self.user_global_ns, self.user_ns)
  File "<ipython-input-2-cf3586e39615>", line 58, in <cell line: 0>
    from stardist import fill_label_holes, random_label_cmap, calculate_extents, gputools_available, relabel_image_stardist, random_label_cmap,  relabel_image_stardist, _draw_polygons, export_imagej_rois
  File "/usr/local/lib/python3.11/dist-packages/stardist/__init__.py", line 15, in <module>
    from .geometry import star_dist,   polygons_to_label,   relabel_image_stardist, ray_angles, dist_to_coord
  File "/usr/local/lib/python3.11/dist-packages/stardist/geometry/__init__.py", line 5, in <module>
    from .geom2d import star_dist, relabel_image_stardist, ray_angles, dist_to_coord, polygons_to_label, polygons_to_label_coord
  File "/usr/local/lib/python3.11/dist-packages/stardist/geometry/geom2d.py", line 11, in <module>
    from ..lib.stardist2d import c_star_dist

---------------------------------------------------------------------------

AttributeError                            Traceback (most recent call last)

AttributeError: _ARRAY_API not found

---------------------------------------------------------------------------

ImportError                               Traceback (most recent call last)

[<ipython-input-2-cf3586e39615>](https://localhost:8080/#) in <cell line: 0>()
     56 
     57 # ------- Variable specific to Stardist -------
---> 58 from stardist import fill_label_holes, random_label_cmap, calculate_extents, gputools_available, relabel_image_stardist, random_label_cmap,  relabel_image_stardist, _draw_polygons, export_imagej_rois
     59 from stardist.models import Config2D, StarDist2D, StarDistData2D # import objects
     60 from stardist.matching import matching_dataset

2 frames

[/usr/local/lib/python3.11/dist-packages/stardist/geometry/geom2d.py](https://localhost:8080/#) in <module>
      9 from ..utils import path_absolute, _is_power_of_2, _normalize_grid
     10 from ..matching import _check_label_array
---> 11 from ..lib.stardist2d import c_star_dist
     12 
     13 

ImportError: numpy.core.multiarray failed to import


---------------------------------------------------------------------------
NOTE: If your import is failing due to a missing package, you can
manually install dependencies using either !pip or !apt.

To view examples of installing some common dependencies, click the
"Open Examples" button below.
---------------------------------------------------------------------------