WIP: transition from pyclesperanto_prototype to pyclesperanto

[haesleinhuepf]

Hey @StRigaud ,

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

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

• exclude_small_labels
• exclude_large_labels
• exclude_labels_with_map_values_out_of_range
• exclude_labels_with_map_values_within_range
• reduce_labels_to_centroids
• extension_ratio_map
• pixel_count_map
• merge_labels_with_border_intensity_within_range
• merge_touching_labels
• sub_stack
• reduce_stack
• merge_annotated_touching_labels

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

Best,
Robert

closes #72

[StRigaud]

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]

@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]

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]

Hi @haesleinhuepf

The following function should now be available with the 0.13.1
I skip the merge_* as they implied the mesh functions. I hope this can help toward the transition.

• exclude_small_labels
• exclude_large_labels
• exclude_labels_with_map_values_out_of_range
• exclude_labels_with_map_values_within_range
• reduce_labels_to_centroids
• extension_ratio_map
• pixel_count_map
• merge_labels_with_border_intensity_within_range
• merge_touching_labels
• sub_stack
• reduce_stack
• merge_annotated_touching_labels

[haesleinhuepf]

Hey @StRigaud

pixel_count_map seems not available in 0.13.1 ...

[haesleinhuepf]

Also exclude_labels_with_map_values_within_range is missing yet.

[haesleinhuepf]

Also exclude_labels_with_map_values_out_of_range is missing

[StRigaud]

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]

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]

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]

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]

ready to be tested with 0.13.3 😄