WIP: transition from pyclesperanto_prototype to pyclesperanto #73

haesleinhuepf · 2024-09-05T09:00:00Z

Hey @StRigaud ,

just FYI: I'm just making this transition on this branch.

In order to complete, these functions are yet missing in pyclesperanto:

I presume some are on the way, and some others (e.g. merge...) are not planned?

Best,
Robert

closes #72

StRigaud · 2024-09-05T11:46:45Z

Some are soon to be available, see clEsperanto/CLIc#335

For the other function, best is to decide which one we do and do not

StRigaud · 2024-09-15T09:05:02Z

@haesleinhuepf

I have merge the PR clEsperanto/pyclesperanto#232 for the categories.

Can you tell me which, in the list of missing operation, we want to actually have in pyclesperanto side? I will try to implement asap to make the transition possible.

haesleinhuepf · 2024-09-16T09:43:15Z

Can you tell me which, in the list of missing operation, we want to actually have in pyclesperanto side?

How about all? Lowest priority should have the merge_ methods because they require the graph stuff. But the others are all practically useful.

StRigaud · 2024-09-28T16:34:03Z

haesleinhuepf · 2024-09-29T06:28:56Z

Hey @StRigaud

pixel_count_map seems not available in 0.13.1 ...

haesleinhuepf · 2024-09-29T06:30:32Z

Also exclude_labels_with_map_values_within_range is missing yet.

haesleinhuepf · 2024-09-29T06:31:16Z

Also exclude_labels_with_map_values_out_of_range is missing

StRigaud · 2024-09-29T07:46:22Z

exclude_labels_with_map_values_out_of_range & exclude_labels_with_map_values_within_range

I forgot the _map_ in the name -> exclude_labels_with_values_out_of_range

pixel_count_map

is label_pixel_count_map no? I did not find a reference to just pixel_count_map at first but after looking It appreas to be an alias in the prototype:

from ._label_pixel_count_map import label_pixel_count_map
from ._label_pixel_count_map import label_pixel_count_map as pixel_count_map

Which name do we keep then?

I will fix these in a 0.13.2 version

haesleinhuepf · 2024-09-29T07:47:57Z

Which name do we keep then?

No matter which, we need aliases for backwards compatibility. I'm hitting the same roadblock in multiple places. If the old names would be still accessible, everything would be easier to update.

StRigaud · 2024-09-29T07:54:53Z

No matter which, we need aliases for backwards compatibility. I'm hitting the same roadblock in multiple places. If the old names would be still accessible, everything would be easier to update.

Got this, but there 2 ways to do this: an alias in the python only code or an alias in the C++ code which should then also impact the java part.

I will make it in the C++ for now, but it is getting difficult to adapt to all name changes and aliases. Same, I am loosing tracks on the different categories. Error like that will continue to build up 😞

I will make the changes today, all this should be fix before monday noon.

StRigaud · 2024-09-29T15:53:07Z

Okay, it will be with the 0.13.3. This should be available on pypip anytime soon, and on conda later in the day or tomorrow.

Hopefully this time is the good one :)

StRigaud · 2024-10-02T15:52:55Z

ready to be tested with 0.13.3 😄

haesleinhuepf · 2024-10-10T13:32:41Z

It works! Now, only the "merge*" functions are missing. I guess this will stay like this for a while.

haesleinhuepf · 2024-10-10T13:36:19Z

Btw. also the code generation works now with pyclespernanto. I'm going to merge this, release some new versions and then everything should be ready for I2K. Great work @StRigaud !

haesleinhuepf · 2024-10-10T14:01:55Z

Ah ok, tests are failing. I would wait for a comment / fix on clEsperanto/pyclesperanto#255 before merging.

StRigaud · 2024-10-15T12:02:11Z

Should be fixed with the incoming 0.13.4, just waiting for the conda bot to push the new release

StRigaud · 2024-10-16T14:23:03Z

Need to fix clEsperanto/CLIc#372

haesleinhuepf · 2024-10-18T09:17:49Z

Tests pass locally on Windows, so I'm going to merge this. Shall the CI go to hell.

(dne2) C:\structure\code\napari_pyclesperanto_assistant>pytest
================================================= test session starts =================================================
platform win32 -- Python 3.12.7, pytest-8.3.3, pluggy-1.5.0
PyQt5 5.15.9 -- Qt runtime 5.15.8 -- Qt compiled 5.15.8
rootdir: C:\structure\code\napari_pyclesperanto_assistant
plugins: anyio-3.7.1, napari-0.5.0, napari-plugin-engine-0.2.0, npe2-0.7.7, qt-4.4.0
collected 7 items

napari_pyclesperanto_assistant\_tests\test_functions.py ......                                                   [ 85%]
napari_pyclesperanto_assistant\_tests\test_neighborhood_statistics.py .                                          [100%]

================================================== warnings summary ===================================================
..\..\..\Users\rober\miniforge3\envs\dne2\Lib\copy.py:151
  C:\Users\rober\miniforge3\envs\dne2\Lib\copy.py:151: DeprecationWarning: Pickle, copy, and deepcopy support will be removed from itertools in Python 3.14.
    rv = reductor(4)

..\..\..\Users\rober\miniforge3\envs\dne2\Lib\copy.py:261
  C:\Users\rober\miniforge3\envs\dne2\Lib\copy.py:261: DeprecationWarning: Pickle, copy, and deepcopy support will be removed from itertools in Python 3.14.
    y.__setstate__(state)

..\..\..\Users\rober\miniforge3\envs\dne2\Lib\site-packages\jupyter_client\connect.py:27
  C:\Users\rober\miniforge3\envs\dne2\Lib\site-packages\jupyter_client\connect.py:27: DeprecationWarning: Jupyter is migrating its paths to use standard platformdirs
  given by the platformdirs library.  To remove this warning and
  see the appropriate new directories, set the environment variable
  `JUPYTER_PLATFORM_DIRS=1` and then run `jupyter --paths`.
  The use of platformdirs will be the default in `jupyter_core` v6
    from jupyter_core.paths import jupyter_data_dir

napari_pyclesperanto_assistant/_tests/test_functions.py::test_labeling_and_statistics
napari_pyclesperanto_assistant/_tests/test_functions.py::test_numpy_functions
  C:\structure\code\napari_pyclesperanto_assistant\napari_pyclesperanto_assistant\_statistics_of_labeled_pixels.py:80: UserWarning: 'Statistics of labeled pixels' is deprecated. Use 'Label statistics' instead.
    warnings.warn("'Statistics of labeled pixels' is deprecated. Use 'Label statistics' instead.")

napari_pyclesperanto_assistant/_tests/test_functions.py::test_numpy_functions
napari_pyclesperanto_assistant/_tests/test_functions.py::test_numpy_functions
napari_pyclesperanto_assistant/_tests/test_functions.py::test_cle_functions
napari_pyclesperanto_assistant/_tests/test_functions.py::test_advanced_statistics
napari_pyclesperanto_assistant/_tests/test_functions.py::test_example_data
napari_pyclesperanto_assistant/_tests/test_neighborhood_statistics.py::test_neighborhood_statistics
  C:\Users\rober\miniforge3\envs\dne2\Lib\site-packages\pyopencl\cache.py:495: CompilerWarning: Non-empty compiler output encountered. Set the environment variable PYOPENCL_COMPILER_OUTPUT=1 to see more.
    _create_built_program_from_source_cached(

napari_pyclesperanto_assistant/_tests/test_functions.py::test_cle_functions
  C:\Users\rober\miniforge3\envs\dne2\Lib\site-packages\pyclesperanto_prototype\_tier3\_generate_touch_mean_intensity_matrix.py:30: UserWarning: generate_touch_mean_intensity_matrix is supposed to work with images of integer type only.
  Loss of information is possible when passing non-integer images.
    warnings.warn("generate_touch_mean_intensity_matrix is supposed to work with images of integer type only.\n" +

napari_pyclesperanto_assistant/_tests/test_functions.py::test_cle_functions
  C:\Users\rober\miniforge3\envs\dne2\Lib\site-packages\pyclesperanto_prototype\_tier0\_opencl_execute.py:281: RuntimeWarning: overflow encountered in cast
    arguments.append(np.array([value], np.float32))

napari_pyclesperanto_assistant/_tests/test_functions.py::test_advanced_statistics
  C:\structure\code\napari_pyclesperanto_assistant\napari_pyclesperanto_assistant\_advanced_statistics.py:18: UserWarning: 'Statistics of labeled pixels including neighborhood statistics' is deprecated. Use 'Label statistics' instead.
    warnings.warn("'Statistics of labeled pixels including neighborhood statistics' is deprecated. Use 'Label statistics' instead.")

napari_pyclesperanto_assistant/_tests/test_neighborhood_statistics.py::test_neighborhood_statistics
  C:\Users\rober\miniforge3\envs\dne2\Lib\site-packages\pyclesperanto_prototype\_tier2\_touch_matrix_to_adjacency_matrix.py:34: DeprecationWarning: touch_matrix_to_adjacency_matrix is deprecated, use symmetric_maximum_matrix or symmetric_minimum_matrix or symmetric_mean_matrix instead.
    warnings.warn("touch_matrix_to_adjacency_matrix is deprecated, use symmetric_maximum_matrix or symmetric_minimum_matrix or symmetric_mean_matrix instead.", DeprecationWarning)

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
=========================================== 7 passed, 15 warnings in 8.20s ============================================

WIP: transition from pyclesperanto_prototype to pyclesperanto

3afc3d2

StRigaud mentioned this pull request Sep 18, 2024

Add new filters and operations clEsperanto/CLIc#343

Merged

haesleinhuepf mentioned this pull request Sep 29, 2024

pyclesperanto compatibility haesleinhuepf/devbio-napari#51

Open

make functions use pyclesperanto without prototype

1893529

StRigaud mentioned this pull request Sep 29, 2024

Patch-0.13.2 clEsperanto/CLIc#349

Merged

haesleinhuepf marked this pull request as ready for review October 10, 2024 13:36

haesleinhuepf added 3 commits October 10, 2024 15:37

make compatible with pyclesperanto 0.13.3

472e387

update dependency versions

1462fb3

bump version

120a7a9

Update requirements.txt

a872eb0

haesleinhuepf added 3 commits October 18, 2024 10:39

upgrade required/tested python to 3.9 - 3.11

8ec4e37

test CI with pyclesperanto 0.13.3

7b36564

use 2 functions from prototype, install right version

8542157

haesleinhuepf merged commit ecc2152 into master Oct 18, 2024
0 of 3 checks passed

haesleinhuepf deleted the pyclesperanto-without-prototype branch October 18, 2024 09:18

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WIP: transition from pyclesperanto_prototype to pyclesperanto #73

WIP: transition from pyclesperanto_prototype to pyclesperanto #73

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WIP: transition from pyclesperanto_prototype to pyclesperanto #73

WIP: transition from pyclesperanto_prototype to pyclesperanto #73

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