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Pyoints: A Python package for point cloud, voxel and raster processing.

License: Other

TeX 1.00% Python 81.98% Shell 1.08% Makefile 0.12% Batchfile 0.18% Jupyter Notebook 15.63%

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pyoints's Issues

[JOSS-REVIEW] Installation instructions

In relation to openjournals/joss-reviews#990

The installation instructions are only written for Ubuntu, although in the text it is somewhat hinted that Windows is also supported.

A clear description of which systems this package is intended for would be nice. Since this is a Python package it (theoretically) should work on at least Linux, OS X and Windows.

I recommend adding a conda environment file and basing the installation instructions on that instead. This will improve the chances of a successful installation immensely.

As a side note, I happen to work on a Mac and am having issues getting started with the installation. This package is not at fault, a mix of homebrew several GDAL and Python installations are complicating things a bit here. This could be avoided with a conda setup.

JOSS review - conda installation error

Related to #2 and openjournals/joss-reviews#990, I was also unsuccessful in trying to install from conda (on my local machine: osx and on binder - e.g. try jupyter, which runs linux 64bit). Here is the error log I got:

Solving environment: failed

CondaHTTPError: HTTP 404 NOT FOUND for url <https://conda.anaconda.org/leampy/noarch/repodata.json>
Elapsed: 00:00.148486
CF-RAY: 4968e3cded3fc56a-ORD

The remote server could not find the noarch directory for the
requested channel with url: https://conda.anaconda.org/leampy

As of conda 4.3, a valid channel must contain a `noarch/repodata.json` and
associated `noarch/repodata.json.bz2` file, even if `noarch/repodata.json` is
empty. please request that the channel administrator create
`noarch/repodata.json` and associated `noarch/repodata.json.bz2` files.
$ mkdir noarch
$ echo '{}' > noarch/repodata.json
$ bzip2 -k noarch/repodata.json

You will need to adjust your conda configuration to proceed.
Use `conda config --show channels` to view your configuration's current state.
Further configuration help can be found at <https://conda.io/docs/config.html>.

For the JOSS submission, you do not necessarily have to have this resolved, but I would suggest that in the README, you

describe the machine specs for which the conda install should work
provide alternate installation instructions for installing from source (as @kbevers described in #2):
- git clone https://github.com/laempy/pyoints.git
- pip install gdal # is there a reason this is not listed in your requirements.txt?
- conda install gdal, pyproj, rtree
- pip install -e .

about [python] Test

First and foremost, great development work.
I was just wondering if failing 2 tests from test_pyoints.py still needed me to take further action to make the pyoints module work well. I am running Ubuntu 20.04 LTS and Python 3.8.3 (default, Jul 2 2020, 16:21:59)

...............Run doctests for Pyoints 0.2.0
...................../home/andrew/pyoints/pyoints/georecords.py:216: UserWarning: 'proj' not set, so I assume '+proj=latlong +datum=WGS84 +to +proj=latlong +datum=WGS84 +units=m +no_defs'
  warnings.warn("'proj' not set, so I assume '%s'" % proj.proj4)
.........................................../home/andrew/anaconda3/lib/python3.8/site-packages/numpy/core/numeric.py:207: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  a = empty(shape, dtype, order)
...FF............................................................
======================================================================
FAIL: GeoTransform (pyoints.projection)
Doctest: pyoints.projection.GeoTransform
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/andrew/anaconda3/lib/python3.8/doctest.py", line 2204, in runTest
    raise self.failureException(self.format_failure(new.getvalue()))
AssertionError: Failed doctest test for pyoints.projection.GeoTransform
  File "/home/andrew/pyoints/pyoints/projection.py", line 161, in GeoTransform

----------------------------------------------------------------------
File "/home/andrew/pyoints/pyoints/projection.py", line 187, in pyoints.projection.GeoTransform
Failed example:
    print_rounded(tCoords, 3)
Expected:
    [[ 2560446.801  5537522.386]
     [ 2560808.009  5537303.984]
     [ 2564724.211  5539797.116]
     [ 2566007.32   5552049.646]]
Got:
    [[ 2560396.394  5537394.098]
     [ 2560757.556  5537175.718]
     [ 2564673.297  5539668.53 ]
     [ 2565956.354  5551919.643]]


======================================================================
FAIL: Proj (pyoints.projection)
Doctest: pyoints.projection.Proj
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/andrew/anaconda3/lib/python3.8/doctest.py", line 2204, in runTest
    raise self.failureException(self.format_failure(new.getvalue()))
AssertionError: Failed doctest test for pyoints.projection.Proj
  File "/home/andrew/pyoints/pyoints/projection.py", line 38, in Proj

----------------------------------------------------------------------
File "/home/andrew/pyoints/pyoints/projection.py", line 63, in pyoints.projection.Proj
Failed example:
    print('AUTHORITY["EPSG","4326"]' in proj.wkt)
Expected:
    True
Got:
    False
----------------------------------------------------------------------
File "/home/andrew/pyoints/pyoints/projection.py", line 73, in pyoints.projection.Proj
Failed example:
    print('AUTHORITY["EPSG","4326"]' in proj.wkt)
Expected:
    True
Got:
    False


----------------------------------------------------------------------
Ran 144 tests in 3.743s

FAILED (failures=2)

Once again, great work on this module. I hope to use it on my research and will gladly cite you if so.
Regards,
Andrew

Syntax error

pyoints/pyoints/storage/RasterHandler.py

Line 147 in be574c9

if wkt is not '':

This should be stated as if wkt != '': instead of if wkt is not '':

[JOSS-REVIEW] Missing DOI in reference list

In relation to openjournals/joss-reviews#990

The following reference is missing DOI's:

Rusu, R. B., & Cousins, S. (2011). 3D is here: Point Cloud Library (PCL). In IEEE
International Conference on Robotics and Automation (ICRA). Shanghai, China.

[JOSS-REVIEW] Community guidelines missing

In relation to openjournals/joss-reviews#990

The community guidelines currently consists of these few words under the section "Contact":

In case of questions, suggestions for improvement or software issues, please use 	
the issue board or contact Sebastian Lamprecht, [email protected]. 	
Contribution to the software is always welcome.

While this touches the bare minimum I would appreciate a separate section called "Community" or "Contributing", describing in a bit more words how to contribute to the project either with code or bug reports. GitHub has a nice feature for this in contributing.md files.

add GeoTIFF LAS support

The GeoTIFF spatial reference definition of LAS is currently handled with the optional dependency liblas. So, a way to convert GeoTIFF tags to WKT and vice versa would be nice.

[JOSS-REVIEW] Citations in paper.md

In relation to openjournals/joss-reviews#990

In text citation for various software packages are done in an incorrect manner. Instead of

Libraries, like (Rusu & Cousins, 2011), (Zhou, Park, & Koltun, 2018) and (PDAL contributors, 2018) focus on 3D point cloud processing.

write

Libraries, like PCL (Rusu & Cousins, 2011), Open3D (Zhou, Park, & Koltun, 2018) and PDAL (PDAL contributors, 2018) focus on 3D point cloud processing.

See here for more examples of correct use of in-text citations.

JOSS review - paper citations

Just a couple minor items with respect to the paper:

for the Bradski citation, it there a url that could be included to point to the source
is the consortium, P citation correct? I imagine it is intended to be cited as the "Pantheon Consortium" or similar?
in the GitHub citation - I would recommend either
- (preferred): set up zenodo with this repository so that the code is archived with a doi and cite that (you will need to create a doi to finalize the JOSS submission anyways)
- or if you would like to use the github url, then I would suggest that rather than citing the main github url that you cite the link to your repository.
For the Rusu & Cousins citation: is there a doi for the paper that could be included?

pygdal version

Pip installation fails because pygdal doesn't recognise the installed GDAL Version.

As an workaround pip install pygdal==$(gdal-config --version).* is used.

JOSS Review - examples / getting started

It would be really helpful in the documentation to include a first example to get new users up and running and doing something with pyoints. The documentation is really focussed on the API. Having a Getting Started,User Guide, or Examples section with a simple example that produces a plot can help motivate users to explore what they can do with the package. For inspiration, here are a few docs that were recently accepted into JOSS and are well-done:

For the JOSS submission (openjournals/joss-reviews#990), I think clear pointers to a single example from the README or the docs would suffice.

Tolerances too narrow in some tests

While running the test-suite I found that three tests failed. The test results are correct but the test fail since the output in the unittest is not reproduced 100% as seen in the output below. We are talking about minor numerical instabilities here. Usually this sort of problem is dealt with by specifying a tolerance for which the requested value is to lie within. Here it can be done by only printing a set amount of decimals for the test output which should truncate the floating point errors seen below.

$ python tests/test_pyoints.py
Run doctests for Pyoints
..................................../Users/kevers/dev/pyoints/pyoints/georecords.py:200: UserWarning: 'proj' not set, so I assume '+proj=latlong +datum=WGS84 +to +proj=latlong +datum=WGS84 +units=m +no_defs'
  warnings.warn("'proj' not set, so I assume '%s'" % proj.proj4)
......F................F................................................F.............................Warning 1: Setting nodata to nan on band 2, but band 1 has nodata at nan. The TIFFTAG_GDAL_NODATA only support one value per dataset. This value of nan will be used for all bands on re-opening
Warning 1: Setting nodata to nan on band 3, but band 1 has nodata at nan. The TIFFTAG_GDAL_NODATA only support one value per dataset. This value of nan will be used for all bands on re-opening
..Warning 1: Setting nodata to nan on band 2, but band 1 has nodata at nan. The TIFFTAG_GDAL_NODATA only support one value per dataset. This value of nan will be used for all bands on re-opening
Warning 1: Setting nodata to nan on band 3, but band 1 has nodata at nan. The TIFFTAG_GDAL_NODATA only support one value per dataset. This value of nan will be used for all bands on re-opening
..
======================================================================
FAIL: from_corners (pyoints.grid.grid.Grid)
Doctest: pyoints.grid.grid.Grid.from_corners
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/miniconda3/envs/pyoints/lib/python3.7/doctest.py", line 2198, in runTest
    raise self.failureException(self.format_failure(new.getvalue()))
AssertionError: Failed doctest test for pyoints.grid.grid.Grid.from_corners
  File "/Users/kevers/dev/pyoints/pyoints/grid/grid.py", line 188, in from_corners

----------------------------------------------------------------------
File "/Users/kevers/dev/pyoints/pyoints/grid/grid.py", line 210, in pyoints.grid.grid.Grid.from_corners
Failed example:
    print(raster.shape)
Expected:
    (2, 4)
Got:
    (2, 3)


======================================================================
FAIL: PolynomInterpolator (pyoints.interpolate)
Doctest: pyoints.interpolate.PolynomInterpolator
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/miniconda3/envs/pyoints/lib/python3.7/doctest.py", line 2198, in runTest
    raise self.failureException(self.format_failure(new.getvalue()))
AssertionError: Failed doctest test for pyoints.interpolate.PolynomInterpolator
  File "/Users/kevers/dev/pyoints/pyoints/interpolate.py", line 296, in PolynomInterpolator

----------------------------------------------------------------------
File "/Users/kevers/dev/pyoints/pyoints/interpolate.py", line 327, in pyoints.interpolate.PolynomInterpolator
Failed example:
    print(interpolator([0, 1]))
Expected:
    1.5
Got:
    1.4999999999999998


======================================================================
FAIL: Plane (pyoints.vector)
Doctest: pyoints.vector.Plane
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/miniconda3/envs/pyoints/lib/python3.7/doctest.py", line 2198, in runTest
    raise self.failureException(self.format_failure(new.getvalue()))
AssertionError: Failed doctest test for pyoints.vector.Plane
  File "/Users/kevers/dev/pyoints/pyoints/vector.py", line 909, in Plane

----------------------------------------------------------------------
File "/Users/kevers/dev/pyoints/pyoints/vector.py", line 1033, in pyoints.vector.Plane
Failed example:
    print(plane.t.to_global(local_coords))
Expected:
    [[ 1.  2.]
     [ 4.  6.]
     [ 0.  1.]
     [ 7. 10.]]
Got:
    [[ 1.00000000e+00  2.00000000e+00]
     [ 4.00000000e+00  6.00000000e+00]
     [-2.77555756e-17  1.00000000e+00]
     [ 7.00000000e+00  1.00000000e+01]]


----------------------------------------------------------------------
Ran 142 tests in 2.893s

FAILED (failures=3)

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