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[REVIEW]: InsarViz: An open source Python package for the interactive visualization of satellite SAR interferometry data #6440

Closed editorialbot closed 1 month ago

editorialbot commented 7 months ago

Submitting author: !--author-handle-->@margauxmouchene<!--end-author-handle-- (Margaux Mouchene) Repository: https://gricad-gitlab.univ-grenoble-alpes.fr/deformvis/insarviz Branch with paper.md (empty if default branch): develop Version: Version 1.1 Editor: !--editor-->@pdebuyl<!--end-editor-- Reviewers: @JessicaS11, @kvenkman Archive: 10.5281/zenodo.13477439

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Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@JessicaS11 & @jiangyuinsar, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:

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The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @pdebuyl know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @JessicaS11

📝 Checklist for @kvenkman

editorialbot commented 7 months ago

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editorialbot commented 7 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.05 s (882.9 files/s, 167196.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          26           1256           1876           4235
reStructuredText                13            232             86            293
Cython                           1            104            179            173
Markdown                         1             35              0            124
HTML                             1            112              1            101
TeX                              1             23              4             74
YAML                             2              3              2             58
SVG                              1              1              1             51
TOML                             1              8              0             42
CSS                              1              3              0             13
-------------------------------------------------------------------------------
SUM:                            48           1777           2149           5164
-------------------------------------------------------------------------------

Commit count by author:

   206  MargauxMouchene
   162  mouchenm
   141  Franck Thollard
    39  Margaux Mouchene
    38  Romain
    14  blanch
     1  Renaud Blanch
     1  margauxmouchene
editorialbot commented 7 months ago

Paper file info:

📄 Wordcount for paper.md is 1144

✅ The paper includes a Statement of need section

editorialbot commented 7 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.5281/zenodo.5884351 is OK
- 10.1029/2004EO050004 is OK
- 10.3390/rs12030424 is OK
- 10.3390/rs13183734 is OK

MISSING DOIs

- None

INVALID DOIs

- None
editorialbot commented 7 months ago

License info:

🟡 License found: GNU General Public License v3.0 (Check here for OSI approval)

editorialbot commented 7 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

pdebuyl commented 7 months ago

@JessicaS11 @jiangyuinsar please check the information text at the top of this page.

As the review takes place into this discussion page, feel free to provide a partial review at some point, to ask clarifications to the author here, or to ask me about the review process.

Some reviewers also open issues at the repository under review. This is fine for bug reports or requests about the documentation, for instance. In that case, please report the resulting bugfix or other result from the discussion here so that I can get proper notification.

margauxmouchene commented 7 months ago

@JessicaS11 @jiangyuinsar Thank you for accepting to review this paper! I can provide several datasets on which you can test the package if you want/need, just let me know!

JessicaS11 commented 7 months ago

Review checklist for @JessicaS11

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

JessicaS11 commented 6 months ago

@JessicaS11 @jiangyuinsar Thank you for accepting to review this paper! I can provide several datasets on which you can test the package if you want/need, just let me know!

@margauxmouchene Thanks for this offer - I'd like to use one of the example datasets you have for testing. Could you please share the best way for me to access?

margauxmouchene commented 6 months ago

@JessicaS11 @jiangyuinsar Thank you for accepting to review this paper! I can provide several datasets on which you can test the package if you want/need, just let me know!

@margauxmouchene Thanks for this offer - I'd like to use one of the example datasets you have for testing. Could you please share the best way for me to access?

Hello, I sent you both an invite through github to a private github repo where I uploaded a small dataset. Let me know if this works for you or if you need anything else!

pdebuyl commented 6 months ago

Hello, thanks @JessicaS11 for starting the review :-)

pdebuyl commented 6 months ago

@jiangyuinsar can you start to review the paper as well? While we are not very strict on timing, it is reasonable to keep the process to a few weeks to the first overal review.

pdebuyl commented 6 months ago

@margauxmouchene would it be possible to share the data publicly? In other cases, the author requested the source agency for the authorization to publish sample data. See for instance the JOSS article https://joss.theoj.org/papers/10.21105/joss.05074 (the dataset is at https://zenodo.org/records/7886737 )

margauxmouchene commented 6 months ago

@pdebuyl @JessicaS11 @jiangyuinsar Yes! The dataset I shared with the reviewers is a subset of a dataset that is produced and made publicly available through the french data and services hub Form@ter.

You can access the complete dataset here (including all products from the processing chain). The datacube you want to download and open with InsarViz is GDM_DTs_geo_4rlks.tiff (in ground geometry) or GDM_DTs_radar_4rlks.tiff (in radar geometry), and their associated metadata files GDM_DTs_geo_4rlks.meta and GDM_DTs_radar_4rlks.meta, respectively.

Please let me know if this works for you and if you need anything!

JessicaS11 commented 6 months ago

Hello @margauxmouchene! Below please find my review comments. @pdebuyl I have provided them here rather than as issues in the source repo because I did not want to create a new GitLab account via the hosting organization.

General Checks

Contribution and authorship

There is a "former contributor" who is not included in the author list, and an author listed whose contributions are unclear. Could you share the authors' GitLab handles and the authorship criteria used?

Functionality

Installation: Does installation proceed as outlined in the documentation?

Mostly yes, with the caveat that the instructions require users have an organizational GitLab account (presumably a public one will not work). An open issue notes the need to clarify this and otherwise suggest an https clone command. I agree with this recommendation to include the https clone command, likely as the primary installation method for those unlikely to become contributors. With this minor exception, the installation instructions are stellar - I especially appreciated the "if you encounter this issue, try..." portions.

functionality

I was able to use the software as expected with the data provided by the authors (thank you!). However, I was unable to visualize any other data (I tried a netcdf and flat geotiff).

Documentation

Statement of need Example usage Functionality documentation Community guidelines

These items are (in whole or in part) missing from the documentation. Many of them are included in the Software Paper, but not available in the documentation itself.

Automated tests

The (2) tests run as expected. Many portions of the codebase are challenging to test given the interactive nature of the software. To improve verifiability, the authors might consider adding tests for utility functions and/or providing the user with more information in the UI (such as the reference value computed and used in plotting) to provide confidence in the computations/plotting (as well as improve reproducibility).

Software paper

The software paper is well written for a technical (but non-specialist) audience.

To my understanding, InsarViz is a powerful visualization tool to be used in conjunction with some of these other tools, rather than instead of. Thus, additional context (and citations for all packages listed) would be helpful for demonstrating the state of the field. Articulating the role of this package relative to other data cube visualization packages would also be insightful; it is not immediately apparent to me how this tool is handling "radar geometry, wrapped phase, relative measurement in space and in time, multiple types of products needed for interpretation" (lines 47-48) differently than a less-specialized data cube visualization library, given that the data must be pre-processed into a data cube for ingest. Handling these characteristics of InSAR data would thus be part of this pre-processing.

jiangyuinsar commented 6 months ago

I tried multiple times last week for the installation but failed. Therefore I could not provide further comments on the software performance.

I would prefer to have a more smooth installation experience than this.

On Fri, 29 Mar 2024 at 22:05, Jessica Scheick @.***> wrote:

Hello @margauxmouchene https://github.com/margauxmouchene! Below please find my review comments. @pdebuyl https://github.com/pdebuyl I have provided them here rather than as issues in the source repo because I did not want to create a new GitLab account via the hosting organization. General Checks

Contribution and authorship

There is a "former contributor" who is not included in the author list, and an author listed whose contributions are unclear. Could you share the authors' GitLab handles and the authorship criteria used? Functionality

Installation: Does installation proceed as outlined in the documentation?

Mostly yes, with the caveat that the instructions require users have an organizational GitLab account (presumably a public one will not work). An open issue https://gricad-gitlab.univ-grenoble-alpes.fr/deformvis/insarviz/-/issues/101 notes the need to clarify this and otherwise suggest an https clone command. I agree with this recommendation to include the https clone command, likely as the primary installation method for those unlikely to become contributors. With this minor exception, the installation instructions are stellar - I especially appreciated the "if you encounter this issue, try..." portions.

functionality

I was able to use the software as expected with the data provided by the authors (thank you!). However, I was unable to visualize any other data (I tried a netcdf and flat geotiff). Documentation

Statement of need Example usage Functionality documentation Community guidelines

These items are (in whole or in part) missing from the documentation. Many of them are included in the Software Paper, but not available in the documentation itself.

  • The API documentation does not include "parameters" or "returns" type headings, and several modules are missing descriptions - is this intended behavior?
  • It would be helpful to expand the Supported data formats section to be more specific. In using the software, it appears that ONLY data cubes are accepted. I was unable to visualize a flat geotiff, and many other "GDAL types" (e.g. hdf5, netcdf) similarly open but do not display any data.
  • The color palettes section of the documentation is great! It's super clear and I appreciate the availability and promotion of accessible and non-distorting color maps.

Automated tests

The (2) tests run as expected. Many portions of the codebase are challenging to test given the interactive nature of the software. To improve verifiability, the authors might consider adding tests for utility functions and/or providing the user with more information in the UI (such as the reference value computed and used in plotting) to provide confidence in the computations/plotting (as well as improve reproducibility). Software paper

The software paper is well written for a technical (but non-specialist) audience.

To my understanding, InsarViz is a powerful visualization tool to be used in conjunction with some of these other tools, rather than instead of. Thus, additional context (and citations for all packages listed) would be helpful for demonstrating the state of the field. Articulating the role of this package relative to other data cube visualization packages would also be insightful; it is not immediately apparent to me how this tool is handling "radar geometry, wrapped phase, relative measurement in space and in time, multiple types of products needed for interpretation" (lines 47-48) differently than a less-specialized data cube visualization library, given that the data must be pre-processed into a data cube for ingest. Handling these characteristics of InSAR data would thus be part of this pre-processing.

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/6440#issuecomment-2027292860, or unsubscribe https://github.com/notifications/unsubscribe-auth/AE2225GD5TSLYU7A5NFDL6DY2VYJFAVCNFSM6AAAAABEFHH5KSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMRXGI4TEOBWGA . You are receiving this because you were mentioned.Message ID: @.***>

margauxmouchene commented 6 months ago

@JessicaS11 Thank you very much for your review! I will be working on including your suggestions in the next few days to improve the documentation and the paper.

margauxmouchene commented 6 months ago

@jiangyuinsar Can we work together to see where the install fails? Can you please share your config (your os, whether you are using a virtual/conda environment or not, the install procedure you tried) and the error message you get?

pdebuyl commented 6 months ago

Thanks @JessicaS11 for the review !

pdebuyl commented 6 months ago

Regarding installation, @jiangyuinsar can you explain the issues you had? (on my side, I tried with a venv and pip install -r requirements then pip install . and had no problem).

jiangyuinsar commented 6 months ago

Here are more details about the installation. I aim to install it under Linux and macOS with Anaconda.

In short, the installation under Linux is successful, but some commands are not functional; the installation under macOS is not successful.

For Linux, I successfully installed the package after running pip install . I could run test_ts_io.py but I cannot call ts_viz.

ts_viz --help Traceback (most recent call last):

Cell In[2], line 1 ts_viz --help

NameError: name 'ts_viz' is not defined

ts_viz Traceback (most recent call last):

Cell In[3], line 1 ts_viz

NameError: name 'ts_viz' is not defined

For macOS (Apple M1), something is wrong.

In [1]: ls AUTHORS.rst insarviz/ LICENCE.txt pyproject.toml LICENSE.txt releases/ README.rst* requirements.txt doc/ setup.py environment.yaml temp_insarviz_dataset-main/ icons/ testing/

In [2]: conda env update -n insarviz-env --file environment.yaml Collecting package metadata (repodata.json): done Solving environment: done

==> WARNING: A newer version of conda exists. <== current version: 22.9.0 latest version: 24.3.0

Please update conda by running

$ conda update -n base -c defaults conda

Preparing transaction: done Verifying transaction: done Executing transaction: done #

To activate this environment, use

#

$ conda activate insarviz-env

#

To deactivate an active environment, use

#

$ conda deactivate

Retrieving notices: ...working... done

Note: you may need to restart the kernel to use updated packages.

In [3]: conda activate insarviz-env

CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'. To initialize your shell, run

$ conda init <SHELL_NAME>

Currently supported shells are:

See 'conda init --help' for more information and options.

IMPORTANT: You may need to close and restart your shell after running 'conda init'.

Note: you may need to restart the kernel to use updated packages.

On Wed, 3 Apr 2024 at 20:03, Pierre de Buyl @.***> wrote:

Regarding installation, @jiangyuinsar https://github.com/jiangyuinsar can you explain the issues you had? (on my side, I tried with a venv and pip install -r requirements then pip install . and had no problem).

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/6440#issuecomment-2034394622, or unsubscribe https://github.com/notifications/unsubscribe-auth/AE2225DJ3W5G6M4YRWIDMTTY3PVZZAVCNFSM6AAAAABEFHH5KSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMZUGM4TINRSGI . You are receiving this because you were mentioned.Message ID: @.***>

margauxmouchene commented 6 months ago

@jiangyuinsar thank you for the feedback!

1) for the Linux install: did you install it in a virtual (or conda) environnement or not? If yes, check that the environment is activated before trying to run ts_viz. If not, then I will need more info: did you get the 'Insarviz successfully installed' message (may not be the exact wording, but something similar)? Are you trying to launch ts_viz right after that? What happens then? Is there an error message?

2) for the Mac install: it looks like you are trying to activate the environment from within a Python or ipython shell (I am guessing this from the In[1]: format in your log), hence the CommandNotFoundError.

jiangyuinsar commented 6 months ago
  1. for the Linux install: I install a conda environment, insarviz-env. I do activate it, conda activate insasrviz-env. I could run test_ts_io.py which means insarviz is installed successfully. But I still cannot run ts_viz successfully, as I mentioned earlier: NameError: name 'ts_viz' is not defined
  2. I prefer not to try Mac install anymore. This just takes me too much time.

In short, I prefer that you could fix the problem under Linux, so that I could provide my comments for you.

On Fri, 5 Apr 2024 at 17:02, margauxmouchene @.***> wrote:

@jiangyuinsar https://github.com/jiangyuinsar thank you for the feedback!

1.

for the Linux install: did you install it in a virtual (or conda) environnement or not? If yes, check that the environment is activated before trying to run ts_viz. If not, then I will need more info: did you get the 'Insarviz successfully installed' message (may not be the exact wording, but something similar)? Are you trying to launch ts_viz right after that? What happens then? Is there an error message? 2.

for the Mac install: it looks like you are trying to activate the environment from within a Python or ipython shell (I am guessing this from the In[1]: format in your log), hence the CommandNotFoundError.

-

Try running the conda activate insarviz-env command directly from a Terminal. Then ts_viz from there.

If you still get the CommandNotFoundError relating to conda activate, then there may be an issue with your Anaconda install (which I'm happy to help you work out, but we'll move this discussion to private emails as this is not linked to the paper).

I am very sorry this is not running smoothly for you, this may be due to unclear instructions on our part. Depending on what we find, I will make sure to improve the documentation. Thank you for your patience.

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/6440#issuecomment-2039272858, or unsubscribe https://github.com/notifications/unsubscribe-auth/AE2225CSZU3TFIZ2SIGDNM3Y3ZSATAVCNFSM6AAAAABEFHH5KSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMZZGI3TEOBVHA . You are receiving this because you were mentioned.Message ID: @.***>

margauxmouchene commented 6 months ago

@jiangyuinsar I am sorry this is not working and I don't really know why since I am not able to reproduce this error. Can you try to run ts_viz.py directly (the command ts_viz is like a shortcut for that)? This means:

This should launch the app so at least you can test it.

jiangyuinsar commented 6 months ago

ts_viz.py works for me.

I can see the interface and load the file ''GDM_DTs_geo_4rlks.tiff", but I can no fringes.

On Mon, 8 Apr 2024 at 15:00, margauxmouchene @.***> wrote:

@jiangyuinsar https://github.com/jiangyuinsar I am sorry this is not working and I don't really know why since I am not able to reproduce this error. Can you try to run ts_viz.py directly (the command ts_viz is like a shortcut for that)? This means:

  • move to the directory insarviz/insarviz (where `ts_viz.py is located)
  • run : python ts_viz.py or python3 ts_viz.py

This should launch the app so at least you can test it.

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/6440#issuecomment-2041998807, or unsubscribe https://github.com/notifications/unsubscribe-auth/AE2225EPIZJPLQH5TTTOCHLY4I57ZAVCNFSM6AAAAABEFHH5KSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANBRHE4TQOBQG4 . You are receiving this because you were mentioned.Message ID: @.***>

margauxmouchene commented 6 months ago

Hello @jiangyuinsar! Great news!

The file I provided is a datacube containing deformation maps (not interferograms). This is the final product of the processing chain. The values you are seeing are amounts of deformation in the direction of the line of sight of the satellite.

You can change the color palette and dynamic range as shown in the documentation here but there are no fringes as this is an unwrapped, processed product. Does this make sense?

You can test the plotting tools as shown in the documentation here.

Let me know if you need any other information.

margauxmouchene commented 5 months ago

Answering @JessicaS11 's review:

General Checks

Contribution and authorship

There is a "former contributor" who is not included in the author list, and an author listed whose contributions are unclear. Could you share the authors' GitLab handles and the authorship criteria used?

Functionality

Installation: Does installation proceed as outlined in the documentation?

Mostly yes, with the caveat that the instructions require users have an organizational GitLab account (presumably a public one will not work). An open issue notes the need to clarify this and otherwise suggest an https clone command. I agree with this recommendation to include the https clone command, likely as the primary installation method for those unlikely to become contributors. With this minor exception, the installation instructions are stellar - I especially appreciated the "if you encounter this issue, try..." portions.

Good point! Install instructions updated to include the https clone command.

functionality

I was able to use the software as expected with the data provided by the authors (thank you!). However, I was unable to visualize any other data (I tried a netcdf and flat geotiff).

Geotiffs should work, but yes, the tool is intended for datacubes. I updated the documentation to make this clearer.

Documentation

Statement of need Example usage Functionality documentation Community guidelines

These items are (in whole or in part) missing from the documentation. Many of them are included in the Software Paper, but not available in the documentation itself.

The statement of need from the paper is now added (slightly modified for clarity) to the documentation.

Example usage is in the Tutorial section of the documentation.

  • The API documentation does not include "parameters" or "returns" type headings, and several modules are missing descriptions - is this intended behavior?

Yes, it looks like we missed that! This is fixed now, all modules, methods, properties are automatically documented.

  • It would be helpful to expand the Supported data formats section to be more specific. In using the software, it appears that ONLY data cubes are accepted. I was unable to visualize a flat geotiff, and many other "GDAL types" (e.g. hdf5, netcdf) similarly open but do not display any data.

Done in the documentation.

  • The color palettes section of the documentation is great! It's super clear and I appreciate the availability and promotion of accessible and non-distorting color maps.

Thanks! We feel strongly about color palettes and we thought it was worth explaining why.

Automated tests

The (2) tests run as expected. Many portions of the codebase are challenging to test given the interactive nature of the software. To improve verifiability, the authors might consider adding tests for utility functions and/or providing the user with more information in the UI (such as the reference value computed and used in plotting) to provide confidence in the computations/plotting (as well as improve reproducibility).

We plan on improving the tests in future versions by implementing pytest-qt tests, which allows to test interactive features (simulate button clicks, hovering, etc.).

Software paper

The software paper is well written for a technical (but non-specialist) audience.

To my understanding, InsarViz is a powerful visualization tool to be used in conjunction with some of these other tools, rather than instead of. Thus, additional context (and citations for all packages listed) would be helpful for demonstrating the state of the field. Articulating the role of this package relative to other data cube visualization packages would also be insightful; it is not immediately apparent to me how this tool is handling "radar geometry, wrapped phase, relative measurement in space and in time, multiple types of products needed for interpretation" (lines 47-48) differently than a less-specialized data cube visualization library, given that the data must be pre-processed into a data cube for ingest. Handling these characteristics of InSAR data would thus be part of this pre-processing.

@JessicaS11 We would like to thank you very much for taking the time to test the package and thoroughly review the paper, your insightful comments helped us improve the paper, the code documentation and the overall experience for the future users of the package. :+1:

pdebuyl commented 5 months ago

@jiangyuinsar were you able to proceed with your tests ?

jiangyuinsar commented 5 months ago

Sorry. I just came back from EGU. I will review this tonight.

On Tue, 23 Apr 2024 at 17:40, Pierre de Buyl @.***> wrote:

@jiangyuinsar https://github.com/jiangyuinsar were you able to proceed with your tests ?

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/6440#issuecomment-2071862855, or unsubscribe https://github.com/notifications/unsubscribe-auth/AE2225HUZCNSIVXD55ADYJLY6YUAFAVCNFSM6AAAAABEFHH5KSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANZRHA3DEOBVGU . You are receiving this because you were mentioned.Message ID: @.***>

jiangyuinsar commented 5 months ago

I still cannot see fringes when I open the file ''GDM_DTs_geo_4rlks.tiff".

By the way, could you send the review checklist to me?

On Tue, 23 Apr 2024 at 17:40, Pierre de Buyl @.***> wrote:

@jiangyuinsar https://github.com/jiangyuinsar were you able to proceed with your tests ?

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/6440#issuecomment-2071862855, or unsubscribe https://github.com/notifications/unsubscribe-auth/AE2225HUZCNSIVXD55ADYJLY6YUAFAVCNFSM6AAAAABEFHH5KSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANZRHA3DEOBVGU . You are receiving this because you were mentioned.Message ID: @.***>

margauxmouchene commented 5 months ago

Hello @jiangyuinsar ,

What "fringes" did you expect to see?

The file I provided is a datacube containing deformation maps (not interferograms). This is the final product of the processing chain. The values you are seeing are amounts of deformation in the direction of the line of sight of the satellite.

You can change the color palette and dynamic range as shown in the documentation here but there are no fringes as this is an unwrapped, processed product. Does this make sense?

You can test the plotting tools as shown in the documentation here.

jiangyuinsar commented 5 months ago

Sorry. I mean the deformation map (not fringes). What I saw was plain grey.

On Tue, 23 Apr 2024 at 21:08, margauxmouchene @.***> wrote:

Hello @jiangyuinsar https://github.com/jiangyuinsar ,

What "fringes" did you expect to see?

The file I provided is a datacube containing deformation maps (not interferograms). This is the final product of the processing chain. The values you are seeing are amounts of deformation in the direction of the line of sight of the satellite.

You can change the color palette and dynamic range as shown in the documentation here https://deformvis.gricad-pages.univ-grenoble-alpes.fr/insarviz/tutorial.html#color-rendering but there are no fringes as this is an unwrapped, processed product. Does this make sense?

You can test the plotting tools as shown in the documentation here https://deformvis.gricad-pages.univ-grenoble-alpes.fr/insarviz/tutorial.html#exploring-the-data .

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/6440#issuecomment-2072263542, or unsubscribe https://github.com/notifications/unsubscribe-auth/AE2225GW3AHA6M4L3ARJ2UTY6ZMOLAVCNFSM6AAAAABEFHH5KSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANZSGI3DGNJUGI . You are receiving this because you were mentioned.Message ID: @.***>

margauxmouchene commented 5 months ago

So you launch ts_viz doing python ts_viz.pyin a Terminal, then File > Open > select the file I sent (GDM_DTs_geo_4rlks.tiff) and nothing happens?

There should be at least a message in the Terminal, what does it say? Is the filename listed in the left-hand side panel? Can you switch between dates with the band switch at the top of the window? Can you adjust the colormap in the right-hand side panel?

jiangyuinsar commented 5 months ago

This is my first time reviewing an open-access software-based manuscript. I am not completely sure how the review process is going.

I think I should comment on this manuscript from a reviewer's point. My current impression is that, I spend hours on the installation, and hours viewing the deformation map which shows plain grey.

Therefore, I am afraid I am not suitable to review this manuscript. Sorry for this.

The following is the message in the Terminal that you requested: "Attribute Qt::AA_ShareOpenGLContexts must be set before QCoreApplication is created. 2024-04-24 14:18:12,386 - main - INFO - loading None 2024-04-24 14:18:21,424 - main - INFO - GUI: loading /250insarviz/testing/data/GDM_DTs_geo_4rlks.tiff opened <open DatasetReader name='/250insarviz/testing/data/GDM_DTs_geo_4rlks.tiff' mode='r'> driver GTiff dtype float32 nodata 0.0 width 5870 height 4359 count 15 crs EPSG:4326 transform | 0.00, 0.00,-119.52| | 0.00,-0.00, 37.14| | 0.00, 0.00, 1.00| blockysize 1 tiled False interleave pixel no metadata file found

of dates = 15

loaded band 7 in 0.8203151226043701 s Traceback (most recent call last):

File ~/.conda/envs/insarviz-env/lib/python3.12/site-packages/insarviz/map/MapModel.py:118 in show_band ) = self.textures[i]

KeyError: 7

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File ~/Program/250insarviz/insarviz/ts_viz.py:404 in display_date self.map_model.show_band(i=date_number)

File ~/.conda/envs/insarviz-env/lib/python3.12/site-packages/insarviz/map/MapModel.py:150 in show_band glTexImage2D(

File ~/.conda/envs/insarviz-env/lib/python3.12/site-packages/OpenGL/latebind.py:43 in call return self._finalCall( *args, **named )

File ~/.conda/envs/insarviz-env/lib/python3.12/site-packages/OpenGL/wrapper.py:889 in wrapperCall raise err

File ~/.conda/envs/insarviz-env/lib/python3.12/site-packages/OpenGL/wrapper.py:882 in wrapperCall result = wrappedOperation( *cArguments )

File ~/.conda/envs/insarviz-env/lib/python3.12/site-packages/OpenGL/error.py:230 in glCheckError raise self._errorClass(

GLError: GLError( err = 1281, description = b'invalid value', baseOperation = glTexImage2D, pyArgs = ( GL_TEXTURE_2D, 0, GL_RG32F, 5870, 4359, 0, GL_RG, GL_FLOAT, array([[[0., 0.], [0., 0.], [0., 0.], ..., [0., 0.], [0., 0.], [0., 0..., ), cArgs = ( GL_TEXTURE_2D, 0, GL_RG32F, 5870, 4359, 0, GL_RG, GL_FLOAT, array([[[0., 0.], [0., 0.], [0., 0.], ..., [0., 0.], [0., 0.], [0., 0..., ), cArguments = ( GL_TEXTURE_2D, 0, GL_RG32F, 5870, 4359, 0, GL_RG, GL_FLOAT, array([[[0., 0.], [0., 0.], [0., 0.], ..., [0., 0.], [0., 0.], [0., 0..., ) )"

On Tue, 23 Apr 2024 at 22:07, margauxmouchene @.***> wrote:

So you launch ts_viz doing python ts_viz.pyin a Terminal, then File > Open > select the file I sent (GDM_DTs_geo_4rlks.tiff) and nothing happens?

There should be at least a message in the Terminal, what does it say? Is the filename listed in the left-hand side panel? Can you switch between dates with the band switch at the top of the window? Can you adjust the colormap in the right-hand side panel?

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/6440#issuecomment-2072413111, or unsubscribe https://github.com/notifications/unsubscribe-auth/AE2225BHJB7CDRUI3FPYBHTY6ZTKRAVCNFSM6AAAAABEFHH5KSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANZSGQYTGMJRGE . You are receiving this because you were mentioned.Message ID: @.***>

margauxmouchene commented 5 months ago

@jiangyuinsar I understand the frustration and I apologize for the inconvenience, there seems to be a problem with your install and I don't know how to resolve this further. Thank you for your time!

margauxmouchene commented 5 months ago

@pdebuyl what should we do? should we try to find another reviewer?

pdebuyl commented 5 months ago

Hello @jiangyuinsar @margauxmouchene I will look for another reviewer.

Thank you for your time @jiangyuinsar , sorry that you cannot proceed.

pdebuyl commented 5 months ago

@editorialbot remove @jiangyuinsar from reviewers

editorialbot commented 5 months ago

@jiangyuinsar removed from the reviewers list!

JessicaS11 commented 5 months ago

Thanks for addressing my comments, @margauxmouchene - is there a test build of the docs from the development branch? After checking out the commits, I'm excited to see all the updates you made to continue filling out the review checklist.

JessicaS11 commented 5 months ago

@editorialbot generate pdf

editorialbot commented 5 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

simonrp84 commented 5 months ago

Hello all. @pdebuyl pinged me about this article / software. I'm not qualified enough to review it (haven't used SAR data) but after seeing the comment chain above I thought I'd test installation. I followed the conda installation instructions (incl. creating a new environment) from the readme and all went smoothly, but when I run ts_viz I get an error:

2024-04-25 08:11:01,169 - insarviz.ts_viz - INFO - loading None
Traceback (most recent call last):
  File "<frozen runpy>", line 198, in _run_module_as_main
  File "<frozen runpy>", line 88, in _run_code
  File "C:\Users\simon.proud\Anaconda3\envs\main\envs\insarviz-env\Scripts\ts_viz.exe\__main__.py", line 7, in <module>
  File "C:\Users\simon.proud\Anaconda3\envs\main\envs\insarviz-env\Lib\site-packages\insarviz\ts_viz.py", line 724, in main
    ex = MainWindow(filename=args.i,
         ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\simon.proud\Anaconda3\envs\main\envs\insarviz-env\Lib\site-packages\insarviz\ts_viz.py", line 54, in __init__
    self.initUI(filename)
  File "C:\Users\simon.proud\Anaconda3\envs\main\envs\insarviz-env\Lib\site-packages\insarviz\ts_viz.py", line 96, in initUI
    self.palette_widget = Palette(self.map_widget, self.minimap_widget)
                          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\simon.proud\Anaconda3\envs\main\envs\insarviz-env\Lib\site-packages\insarviz\PaletteView.py", line 25, in __init__
    self._add_custom_gradients()
  File "C:\Users\simon.proud\Anaconda3\envs\main\envs\insarviz-env\Lib\site-packages\insarviz\PaletteView.py", line 143, in _add_custom_gradients
    act.triggered.connect(self.gradient.contextMenuClicked)
                          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'GradientEditorItem' object has no attribute 'contextMenuClicked'. Did you mean: 'colorMapMenuClicked'?

Tracing the error back, it seems that contextMenuClicked was replaced by colorMapMenuClicked in version 0.13.5 of pyqtgraph. When I downgrade pyqtgraph to version 0.13.4 then the InsarViz interface loads. So you will either have to update your code for the new function name or you'll have to pin that library to an older version in the requirements.

margauxmouchene commented 5 months ago

@simonrp84 Thank you for this bug report AND debugging! For now, I pinned the version of pyqtgraph, but the code will be updated in future versions.

margauxmouchene commented 5 months ago

@JessicaS11 you can build the documentation locally with: sphinx-build -a -b html doc doc-html (from the insarviz root directory)

The corresponding html files will be stored in the doc-html directory.

simonrp84 commented 5 months ago

@margauxmouchene No problem, happy to help!

pdebuyl commented 4 months ago

Hello @margauxmouchene sorry for the delays, I still haven't found an extra reviewer but keep looking.

margauxmouchene commented 4 months ago

Hello @pdebuyl, thank you for keeping me updated!

pdebuyl commented 4 months ago

@editorialbot add @kvenkman as reviewer