[WIP] feature/python_module : Adding libpointmatcher's Python bindings (#222) #397

aguenette · 2020-08-06T21:06:46Z

Here are the python's bindings for libpointmatcher as requested in the issue #222.

Things to do before merging :

Make sure that the module get installed in the sites-packages of the current Python environment (maybe using pip install?).
Provide a tutorial on how to compile and install the module.
Provide a tutorial on how to use it.
Finish to transpose the C++ examples into Python.
Merging PR Replaced the remaining raw pointers with shared pointers in Registrar.h #395
Make sure that the bindings compile on macOS?

Testing :

If you want to test the Python module on your side, clone my libpointmatcher's fork. Then, follow the compilation and installation instructions from this tutorial.

I've tested it with g++ 7.5.0 ~~and clang++ 10.0.0~~ on Ubuntu 18.04.

Edit: The bindings no longer compiles on clang++ 10.0, and on clang++ 6.0 either, since the adding of the IO module.

Feedback on the bindings themselves and the tutorials will be really appreciated, thanks! 🙂

Last edited : 20 august 2020

The python module now only link with pointmatcher instead of building it. The python module can now be installed.

Also fixed a typo in the IO.cpp file

Removed the bindings for ParametersDoc and Parameters in parametrizable.cpp

In order to get more consistent tests results with the Python version examples.

Added the suffix _const at the end of the method signature

YoshuaNava

Hi @AlexandreG87,
This PR looks really cool. Just left a few minor comments.

pointmatcher/IO.cpp

python/pointmatcher/io.cpp

CMakeLists.txt

doc/CompilationPython.md

examples/align_sequence.cpp

python/CMakeLists.txt

python/datapointsfilters/covariancesampling.cpp

YoshuaNava · 2020-08-18T21:37:07Z

python/pypointmatcher_helper.h

@@ -0,0 +1,72 @@
+#ifndef PYTHON_PYPOINTMATCHER_HELPER_H
+#define PYTHON_PYPOINTMATCHER_HELPER_H
+


The name of this file is not very clear. To me it is more like a centralized typedefs-header.

I agree that it ended up being that way, but in the main purpose of this file was to regroup all the necessary include in one place and also the PYBIND11_MAKE_OPAQUE macro declaration as mentioned in pybind11 documentation. I thought about whether I put these aliases just before their use, like the io.cpp source file, or in a common header file like it is right now. Some of them are used across some other files, so I did this to avoid re-declaring them every time I needed it. But, if you suggest that it would be better to declare it only where it is needed (saying that make me realize that it makes much more sense to do so 😅), I have no problem to fix this.

Hey. For now I think it's ok to keep the file. But I would rename it to pypointmatcher_typedefs or pypointmatcher_types. It would be easier to understand its content.

Alright, I'll see what I can do about that.

aguenette · 2020-08-19T19:32:37Z

@YoshuaNava Thank you for the feedback and I hope you will be satisfied with my answers. 😄

Now giving the possibility to choose between system installed pybind11 and a git sub-module by setting USE_SYSTEM_PYBIND11 variable.

Also, making PLYProperties and PLYDescPropMap typedefs opaque in order to avoid unwanted behavior.

Based on PR norlab-ulaval#397 feedback

A copy was made every time it was called because no return value policy was specified.

YoshuaNava · 2020-08-22T11:40:46Z

@YoshuaNava Thank you for the feedback and I hope you will be satisfied with my answers.

I am, thank you for addressing all of them. Really cool work ⚡

I left just a few minor comments. Most of the items are resolved in my opinion.

Before approving I have some final questions:

On which platforms have you tested the bindings?
Which versions of Python are you supporting? Is there any performance variation or change needed to run with Python 2/3?
Have you tested both building/running, but also installing the bindings? If so, where do they get installed?
Does the uninstall target also remove the bindings?

Prevent pybind11 to convert them into Python's list and dict.

* Added some documentation * Switched to opaque container Parameters

YoshuaNava · 2020-09-10T08:32:02Z

@AlexandreG87 What is the status of this PR?

I can give this a try under Windows. Do you also plan to test the bindings generation when compiling with ROS?

aguenette · 2020-09-13T16:02:12Z

@AlexandreG87 What is the status of this PR?

Hi @YoshuaNava, I would say that it's not quite finished yet. I'll start to address your comments first, then we'll see what needs to be done to make it better.

I can give this a try under Windows.

Thanks, it's very appreciated. Maybe, I'll give it a try too.

Do you also plan to test the bindings generation when compiling with ROS?

It was not in my plans, I'll need to check with @pomerlef what can be done about that.

aguenette · 2020-09-13T16:15:36Z

Before approving I have some final questions:

1. On which platforms have you tested the bindings?

2. Which versions of Python are you supporting? Is there any performance variation or change needed to run with Python 2/3?

3. Have you tested both building/running, but also installing the bindings? If so, where do they get installed?

4. Does the uninstall target also remove the bindings?

So far, I've only been testing on Ubuntu 18.04 with Python 3.6.9 and pybind11 2.5.0.
We will support Python 3 only, since Python 2 is deprecated.
Yes, I've tested building and running, but also installing. You can find these answers in the compilation tutorial.
Yes, it does.

YoshuaNava · 2020-09-14T17:37:43Z

@AlexandreG87 Regarding your answers:

Thanks, it's very appreciated. Maybe, I'll give it a try too.

Oki.

It was not in my plans, I'll need to check with @pomerlef what can be done about that.

I would say that for minimum support we should make sure that the ROS build still runs. In a separate PR I plan to submit a new CMake setup, that allows you to have ROS CI/CD, running tests, and at the same time build without catkin, in case wanted. I'll open an issue to propose it.

So far, I've only been testing on Ubuntu 18.04 with Python 3.6.9 and pybind11 2.5.0.

We will support Python 3 only, since Python 2 is deprecated.

That's good 👍

Yes, I've tested building and running, but also installing. You can find these answers in the compilation tutorial.

Yes, it does.

Very good. No more comments from my side apart from the open ones.

Based on PR norlab-ulaval#397 feedback

… feature/python_module

pomerlef · 2020-10-27T01:51:06Z

I would go on an merge this PR and open issues if something go wrong. For now, I don't have time to test it on MacOs.

Examples use float instead of double

aguenette · 2020-10-30T01:31:02Z

I would go on an merge this PR and open issues if something go wrong. For now, I don't have time to test it on MacOs.

@pomerlef There were some more things that I wanted to do before you merge this PR and I will do them as soon as possible.

aguenette · 2020-11-02T01:22:48Z

@pomerlef You can proceed to the merge when you're ready.

aguenette requested a review from pomerlef August 6, 2020 21:06

aguenette added the Enhancement label Aug 6, 2020

aguenette force-pushed the feature/python_module branch from 717c92e to 84c322f Compare August 6, 2020 21:18

aguenette changed the title ~~[WIP] feature/python_module : Adding libpointmatcher's Python bindings~~ [WIP] feature/python_module : Adding libpointmatcher's Python bindings (#222) Aug 7, 2020

aguenette force-pushed the feature/python_module branch from 84c322f to c8fd787 Compare August 7, 2020 13:47

aguenette added 2 commits August 12, 2020 10:12

Adding libpointmatcher's Python bindings

3e6227b

Merge branch 'master' into feature/python_module

b80b5ac

aguenette force-pushed the feature/python_module branch from 315d98c to b80b5ac Compare August 12, 2020 14:14

aguenette added 2 commits August 14, 2020 13:21

Improved CMakeLists.txt

c519c15

The python module now only link with pointmatcher instead of building it. The python module can now be installed.

Adding the compilation tutorial to the documentation.

9f4d0c9

aguenette force-pushed the feature/python_module branch from 840b003 to 9f4d0c9 Compare August 15, 2020 00:29

simonpierredeschenes force-pushed the feature/python_module branch from 9476203 to f8273ca Compare August 15, 2020 20:13

Fixed error in CMakeLists.txt.

6b909ea

simonpierredeschenes force-pushed the feature/python_module branch from f8273ca to 6b909ea Compare August 15, 2020 20:15

aguenette added 5 commits August 18, 2020 13:25

Added the IO module

8170e5d

Also fixed a typo in the IO.cpp file

Fixed icp_advance_api.py and icp_customized.py examples

35926a8

Removed the bindings for ParametersDoc and Parameters in parametrizable.cpp

Change C++ examples base type from float to double

ee50bb4

In order to get more consistent tests results with the Python version examples.

Change the way that vectors are bonded

6ccdc71

Fixed overloaded methods ambiguities based on constness

5c3a25c

Added the suffix _const at the end of the method signature

YoshuaNava reviewed Aug 18, 2020

View reviewed changes

aguenette added 6 commits August 21, 2020 15:32

Improved the CMakeLists.txt

1c0bcaa

Now giving the possibility to choose between system installed pybind11 and a git sub-module by setting USE_SYSTEM_PYBIND11 variable.

Forgot to name the members of PLYElement.

5c011a9

Also, making PLYProperties and PLYDescPropMap typedefs opaque in order to avoid unwanted behavior.

Improved compilation's tutorial

2969fa6

Based on PR norlab-ulaval#397 feedback

Added 3 new examples

a03e81a

Removed a pure virtual method that didn't have to be mapped

d550d13

Fixed PointMatcher get() method

61517b3

A copy was made every time it was called because no return value policy was specified.

aguenette added 2 commits August 25, 2020 10:18

Replaced double type declaration to ScalarType type declaration

073f2a4

Moved header's #include directive to source

ed2a295

aguenette and others added 9 commits August 25, 2020 10:40

Renamed #include directive

c724bd2

Removed unnecessary namespace aliases

4ba0b15

Moved header's aliases declaration to source

dbf15ed

Named members and parameters that were forgotten

da515b9

Renamed files to conform to the Python naming convention

c900da2

Made std::vector and std::map opaque

d463b11

Prevent pybind11 to convert them into Python's list and dict.

Improved the Python examples

9936878

* Added some documentation * Switched to opaque container Parameters

Added the usage tutorial

dcde397

Minor corrections in Python documentation.

3fa79e3

simonpierredeschenes pushed a commit to simonpierredeschenes/libpointmatcher that referenced this pull request Oct 17, 2020

Improved compilation's tutorial

270a965

Based on PR norlab-ulaval#397 feedback

aguenette and others added 2 commits October 20, 2020 10:05

Merge branch 'master' of github.com:AlexandreG87/libpointmatcher into…

d662059

… feature/python_module

Merge branch 'master' into feature/python_module

d937274

Revert change C++ examples base type from float to double.

e9dc721

Examples use float instead of double

aguenette added 2 commits November 1, 2020 18:56

Reorganization of the namespace structure

956aadb

Merge branch 'master' into feature/python_module

0c1c68f

pomerlef merged commit 99d2937 into norlab-ulaval:master Nov 2, 2020

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

[WIP] feature/python_module : Adding libpointmatcher's Python bindings (#222) #397

[WIP] feature/python_module : Adding libpointmatcher's Python bindings (#222) #397

aguenette commented Aug 6, 2020 •

edited

YoshuaNava left a comment

YoshuaNava Aug 18, 2020

aguenette Aug 19, 2020

YoshuaNava Aug 22, 2020

aguenette Sep 13, 2020

aguenette commented Aug 19, 2020

YoshuaNava commented Aug 22, 2020 •

edited

YoshuaNava commented Sep 10, 2020

aguenette commented Sep 13, 2020 •

edited

aguenette commented Sep 13, 2020

YoshuaNava commented Sep 14, 2020

pomerlef commented Oct 27, 2020

aguenette commented Oct 30, 2020

aguenette commented Nov 2, 2020

		@@ -0,0 +1,72 @@
		#ifndef PYTHON_PYPOINTMATCHER_HELPER_H
		#define PYTHON_PYPOINTMATCHER_HELPER_H

[WIP] feature/python_module : Adding libpointmatcher's Python bindings (#222) #397

[WIP] feature/python_module : Adding libpointmatcher's Python bindings (#222) #397

Conversation

aguenette commented Aug 6, 2020 • edited

Things to do before merging :

Testing :

YoshuaNava left a comment

Choose a reason for hiding this comment

YoshuaNava Aug 18, 2020

Choose a reason for hiding this comment

aguenette Aug 19, 2020

Choose a reason for hiding this comment

YoshuaNava Aug 22, 2020

Choose a reason for hiding this comment

aguenette Sep 13, 2020

Choose a reason for hiding this comment

aguenette commented Aug 19, 2020

YoshuaNava commented Aug 22, 2020 • edited

YoshuaNava commented Sep 10, 2020

aguenette commented Sep 13, 2020 • edited

aguenette commented Sep 13, 2020

YoshuaNava commented Sep 14, 2020

pomerlef commented Oct 27, 2020

aguenette commented Oct 30, 2020

aguenette commented Nov 2, 2020

aguenette commented Aug 6, 2020 •

edited

YoshuaNava commented Aug 22, 2020 •

edited

aguenette commented Sep 13, 2020 •

edited