[PRE REVIEW]: DetecTree: Tree detection from aerial imagery in Python #2143

whedon · 2020-03-04T10:34:47Z

Submitting author: @martibosch (Martí Bosch)
Repository: https://github.com/martibosch/detectree
Version: v0.3.0
Editor: @kthyng
Reviewers: @JeffWalton-PSC , @rmsare
Managing EiC: Kevin M. Moerman

Author instructions

Thanks for submitting your paper to JOSS @martibosch. Currently, there isn't an JOSS editor assigned to your paper.

@martibosch if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

Editor instructions

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The text was updated successfully, but these errors were encountered:

whedon · 2020-03-04T10:34:51Z

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

whedon · 2020-03-04T10:35:04Z

Software report (experimental):

github.com/AlDanial/cloc v 1.84  T=0.22 s (139.4 files/s, 13978.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          13            380            754           1449
TeX                              2             10              0            111
Markdown                         4             56              0             96
YAML                             2              7              4             43
reStructuredText                 7             19             31             21
make                             1              4              6             10
Lisp                             1              1              0              6
-------------------------------------------------------------------------------
SUM:                            30            477            795           1736
-------------------------------------------------------------------------------


Statistical information for the repository '2143' was gathered on 2020/03/04.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Martí Bosch                     11          2659             76          100.00

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Martí Bosch                2583           97.1          0.2               14.32

whedon · 2020-03-04T10:35:10Z

PDF failed to compile for issue #2143 with the following error:

/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-45a043c4bfc2/lib/whedon.rb:200:in block in parse_authors': Author (Martí Bosch) is missing affiliation (RuntimeError) from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-45a043c4bfc2/lib/whedon.rb:198:in each'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-45a043c4bfc2/lib/whedon.rb:198:in parse_authors' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-45a043c4bfc2/lib/whedon.rb:91:in initialize'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-45a043c4bfc2/lib/whedon/processor.rb:36:in new' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-45a043c4bfc2/lib/whedon/processor.rb:36:in set_paper'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-45a043c4bfc2/bin/whedon:55:in prepare' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:in run'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:in dispatch'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-45a043c4bfc2/bin/whedon:116:in <top (required)>'
from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in load' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in

'

whedon · 2020-03-04T10:35:12Z

Reference check summary:

OK DOIs

- None

MISSING DOIs

- None

INVALID DOIs

- https://doi.org/10.1007/3-540-59119-2_166 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1023/A:1011139631724 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1109/TPAMI.2004.60 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1145/1653771.1653792 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.5555/1953048.2078195 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1109/MCSE.2011.37 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.7717/peerj.453 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.25080/Majora-7b98e3ed-013 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.25080/Majora-4af1f417-011 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1038/s41592-019-0686-2 is INVALID because of 'https://doi.org/' prefix

Kevin-Mattheus-Moerman · 2020-03-04T10:43:03Z

@openjournals/dev can you help compile this paper?

martibosch · 2020-03-04T10:53:40Z

@whedon generate pdf

whedon · 2020-03-04T10:53:53Z

PDF failed to compile for issue #2143 with the following error:

/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-45a043c4bfc2/lib/whedon.rb:200:in block in parse_authors': Author (Martí Bosch) is missing affiliation (RuntimeError) from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-45a043c4bfc2/lib/whedon.rb:198:in each'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-45a043c4bfc2/lib/whedon.rb:198:in parse_authors' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-45a043c4bfc2/lib/whedon.rb:91:in initialize'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-45a043c4bfc2/lib/whedon/processor.rb:36:in new' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-45a043c4bfc2/lib/whedon/processor.rb:36:in set_paper'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-45a043c4bfc2/bin/whedon:55:in prepare' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:in run'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:in dispatch'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-45a043c4bfc2/bin/whedon:116:in <top (required)>'
from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in load' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in

'

Kevin-Mattheus-Moerman · 2020-03-04T10:54:11Z

@terrytangyuan @arokem @kthyng could one of you edit this submission?

Some potential reviewer overlap may exist with:
#2056
#1825

martibosch · 2020-03-04T10:55:40Z

the affiliation is copied from my other JOSS paper source, in which I am also the sole author. I do not know what might be wrong.

arfon · 2020-03-04T11:14:59Z

the affiliation is copied from my other JOSS paper source, in which I am also the sole author. I do not know what might be wrong.

Yes, but this isn't compliant with our updated format. Please follow the example in our docs and break the affiliations into their own YAML key.

martibosch · 2020-03-04T13:58:39Z

@whedon generate pdf

whedon · 2020-03-04T13:59:15Z

👉 Check article proof 📄 👈

martibosch · 2020-03-04T14:01:09Z

Hello @arfon I am sorry about that and I thank you for your help. I have amended the paper md source and the PDF is compiled correcly now 😄

martibosch · 2020-03-06T15:48:13Z

Hello @Kevin-Mattheus-Moerman , should I tag more potential editors, or should we wait for the tagged ones to answer?

kthyng · 2020-03-06T16:45:19Z

Hi! I can take this one.

kthyng · 2020-03-06T16:45:26Z

@whedon assign @kthyng as editor

whedon · 2020-03-06T16:45:31Z

OK, the editor is @kthyng

kthyng · 2020-03-06T16:46:27Z

@martibosch It looks like your documentation could be improved. I went to your readthedocs but it doesn't include the more useful documentation from your readme or from the example repo you mention.

kthyng · 2020-03-06T16:48:59Z

@martibosch Could you look through the reviewer list (https://bit.ly/joss-reviewers) and give suggestions of who might be relevant reviewers for your software? Please don't use "@" to mention them so that they do not get emailed about this, just list their github username. You can also provide information for reviewers who are not on the list if you have other suggestions.

martibosch · 2020-03-06T17:27:15Z

First of all thank you for editing my submission 😄

@martibosch It looks like your documentation could be improved. I went to your readthedocs but it doesn't include the more useful documentation from your readme or from the example repo you mention.

I understand that you mean that I should include the documentation for the technical methods described in the background.ipynb notebook of the example repository (e.g., the classes and methods to build the features and image descriptors)? The reason that I had not included them in the readthedocs site is because end users are not supposed to use this methods directly but through the arguments of the TrainingSelector, Classifier and ClassifierTrainer classes and their methods - which are documented. However it is indeed a good idea to document the other background methods as well, e.g., to help potential contributors. I will get to it tomorrow 👍

kthyng · 2020-03-06T17:27:54Z

/ooo March 7, 2020 to March 15, 2020

ooo · 2020-03-06T17:27:55Z

👍 Marked @kthyng as OOO from Saturday, March 7th 2020 to Sunday, March 15th 2020. 📆

martibosch · 2020-03-06T17:46:43Z

some well suited potential reviewers that I could find are: rmsare scivision stsievert thomakra juliohm JeffWalton-PSC

ooo · 2020-03-11T15:44:30Z

👋 Hey @martibosch...

Letting you know, @kthyng is currently OOO until Sunday, March 15th 2020. ❤️

arfon · 2020-03-14T00:22:06Z

Dear authors and reviewers

We wanted to notify you that in light of the current COVID-19 pandemic, JOSS has decided to suspend submission of new manuscripts and to handle existing manuscripts (such as this one) on a "best efforts basis". We understand that you may need to attend to more pressing issues than completing a review or updating a repository in response to a review. If this is the case, a quick note indicating that you need to put a "pause" on your involvement with a review would be appreciated but is not required.

Thanks in advance for your understanding.

Arfon Smith, Editor in Chief, on behalf of the JOSS editorial team.

kthyng · 2020-03-19T19:03:09Z

I understand that you mean that I should include the documentation for the technical methods described in the background.ipynb notebook of the example repository (e.g., the classes and methods to build the features and image descriptors)? The reason that I had not included them in the readthedocs site is because end users are not supposed to use this methods directly but through the arguments of the TrainingSelector, Classifier and ClassifierTrainer classes and their methods - which are documented. However it is indeed a good idea to document the other background methods as well, e.g., to help potential contributors. I will get to it tomorrow 👍

I mean — I am trying to learn about the package you wrote, like I have been as an editor, and I want to go somewhere to learn about it more. Normally readthedocs functions this way, but yours (previously) was strictly description of the functions. Where do you imagine a new user starting with your code? The readme seems like a good start, but also seems too short.

Anyway, this will surely come up in review too, but I figured you could start working on it :)

kthyng · 2020-03-19T19:05:52Z

@JeffWalton-PSC and @thomakra Are you interested and willing to review this JOSS submission? Normally I would ask for the reviews within about 3 weeks, but many things are unusual right now, so timing is flexible too. Let me know what you think. Thanks.

kthyng · 2020-03-19T19:06:25Z

here is more information about reviewing: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html

JeffWalton-PSC · 2020-03-19T19:31:15Z

Kristen, Yes, I’m interested. I will look through the documentation link you sent. Thanks, Jeff From: Kristen Thyng [mailto:[email protected]] Sent: Thursday, 19 March, 2020 15:06 To: openjournals/joss-reviews <[email protected]> Cc: Jeff Walton <[email protected]>; Mention <[email protected]> Subject: Re: [openjournals/joss-reviews] [PRE REVIEW]: DetecTree: Tree detection from aerial imagery in Python (#2143) @JeffWalton-PSC<https://github.com/JeffWalton-PSC> and @thomakra<https://github.com/thomakra> Are you interested and willing to review this JOSS submission? Normally I would ask for the reviews within about 3 weeks, but many things are unusual right now, so timing is flexible too. Let me know what you think. Thanks. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub<#2143 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AI5VWG3MHUPQKPCXUGNRYCDRIJUKBANCNFSM4LBCHJ2Q>.

thomakra · 2020-03-23T08:58:10Z

Hi Kristen, Unfortunately I do not have the capacity at this time, although the project seems interesting.

…

-Thomas-

On Thu, 19 Mar 2020 at 20:06, Kristen Thyng ***@***.***> wrote: @JeffWalton-PSC <https://github.com/JeffWalton-PSC> and @thomakra <https://github.com/thomakra> Are you interested and willing to review this JOSS submission? Normally I would ask for the reviews within about 3 weeks, but many things are unusual right now, so timing is flexible too. Let me know what you think. Thanks. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#2143 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABOAW3YCZBHV3LQRB3FWKSDRIJUKBANCNFSM4LBCHJ2Q> .

kthyng · 2020-04-07T13:21:53Z

Thanks @JeffWalton-PSC! I'll add you as a reviewer and continue to search for a second reviewer.

kthyng · 2020-04-07T13:22:26Z

@whedon assign @JeffWalton-PSC as reviewer

whedon · 2020-04-07T13:22:32Z

OK, @JeffWalton-PSC is now a reviewer

kthyng · 2020-04-07T13:26:15Z

@juliohm Do you have the availability and interest to review this JOSS submission? We understand people are quite busy in these unusual times and reviews may take extra time right now, that is ok. Thanks for your consideration.

juliohm · 2020-04-07T15:12:31Z

Thank you @kthyng for pinging. I wish I could review the paper, but I am very busy at the moment with some deadlines. Hope you can find another reviewer.

kthyng · 2020-04-07T18:21:37Z

@rmsare Might you be able to review this submission to JOSS? Thanks for your consideration.

rmsare · 2020-04-07T19:01:54Z

@kthyng, thanks for the request - this submission looks really interesting. I expect I could complete a review by 3 May (unfortunately I have a late April deadline). Would this be timely enough for this review?

kthyng · 2020-04-07T19:27:16Z

@rmsare Yes, that would be great. We are grateful for any time people can dedicate to JOSS right now in these unusual times. I will add you as the second reviewer and we can move ahead to start the review.

kthyng · 2020-04-07T19:27:27Z

@whedon add @rmsare as reviewer

whedon · 2020-04-07T19:27:32Z

OK, @rmsare is now a reviewer

kthyng · 2020-04-07T19:28:53Z

@whedon start review

whedon · 2020-04-07T19:28:58Z

OK, I've started the review over in #2172.

kthyng · 2020-04-07T19:31:16Z

@JeffWalton-PSC and @rmsare please head over to #2172 for the actual review.

whedon added the pre-review label Mar 4, 2020

whedon added Python TeX labels Mar 4, 2020

whedon assigned kthyng Mar 6, 2020

This was referenced Mar 9, 2020

[REVIEW]: infotheory: A C++/Python package for multivariate information theoretic analysis #1609

Closed

[REVIEW]: Using drones to quantify the length of marine animals #2097

Closed

[PRE REVIEW]: A Framework to Quality Control Oceanographic Data #1985

Closed

ooo bot mentioned this issue Mar 13, 2020

[REVIEW]: A Framework to Quality Control Oceanographic Data #2063

Closed

38 tasks

whedon assigned JeffWalton-PSC and kthyng and unassigned kthyng Apr 7, 2020

whedon assigned JeffWalton-PSC, kthyng and rmsare and unassigned kthyng and JeffWalton-PSC Apr 7, 2020

whedon closed this as completed Apr 7, 2020

[PRE REVIEW]: DetecTree: Tree detection from aerial imagery in Python #2143

[PRE REVIEW]: DetecTree: Tree detection from aerial imagery in Python #2143

Comments

whedon commented Mar 4, 2020 • edited Loading

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JeffWalton-PSC commented Mar 19, 2020 via email

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whedon commented Mar 4, 2020 •

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