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added masking for NGC objects #575

Merged
merged 24 commits into from
Sep 16, 2022
Merged

added masking for NGC objects #575

merged 24 commits into from
Sep 16, 2022

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martinkilbinger
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@martinkilbinger martinkilbinger commented Jun 29, 2022 •
edited by sfarrens
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Summary

Enhancements to the mask runner module:

  • A catalogue with NGC object information is read.
  • NGC and Messier objects have the same format, now FITS instead of npy.
  • Both are treated by the same methods (as Deep Space Objects)

Minor changes to get_image runner module

  • added log file output for checking existing files before download

Closes #564

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@martinkilbinger martinkilbinger added the enhancement New feature or request label Jun 29, 2022
@martinkilbinger martinkilbinger added this to the Summer 2022 patch milestone Jun 29, 2022
@martinkilbinger martinkilbinger self-assigned this Jun 29, 2022
sfarrens
sfarrens reviewed Jun 29, 2022
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I did tests, seems to work well. I think review points are all fixed, @sfarrens you can have a look again, please.

sfarrens
sfarrens requested changes Jul 5, 2022
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martinkilbinger and others added 15 commits September 12, 2022 14:32
@martinkilbinger @sfarrens
Update shapepipe/modules/mask_package/mask.py
812e841 
Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>
@martinkilbinger @sfarrens
Update shapepipe/modules/mask_package/mask.py
98b8c25 
Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>
@martinkilbinger @sfarrens
Update shapepipe/modules/mask_package/mask.py
a24e2dc 
Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>
@martinkilbinger @sfarrens
Update shapepipe/modules/mask_package/mask.py
6283f6a 
Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>
@martinkilbinger
added symlink
5d97cce
@martinkilbinger @sfarrens
Update shapepipe/pipeline/file_io.py
5d44417 
Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>
@martinkilbinger @sfarrens
Update shapepipe/modules/mask_package/mask.py
635fbe4 
Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>
@martinkilbinger @sfarrens
Update shapepipe/pipeline/file_io.py
6bddb1f 
Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>
@martinkilbinger @sfarrens
Update shapepipe/pipeline/file_io.py
d51f81e 
Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>
@martinkilbinger @sfarrens
Update shapepipe/pipeline/file_io.py
b3949fa 
Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>
@martinkilbinger @sfarrens
Update shapepipe/pipeline/file_io.py
eff9b6c 
Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>
@martinkilbinger
Merge remote-tracking branch 'upstream/develop' into ngc
9d67abd
@martinkilbinger @sfarrens
Update shapepipe/modules/mask_package/mask.py
a27e19c 
Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>
@martinkilbinger @sfarrens
Update shapepipe/modules/mask_package/mask.py
5b24439 
Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>
@martinkilbinger @sfarrens
Update shapepipe/modules/mask_package/mask.py
d0c6f2a 
Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>
martinkilbinger and others added 3 commits September 14, 2022 10:34
@martinkilbinger @sfarrens
Update shapepipe/pipeline/file_io.py
baf372f 
Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>
@martinkilbinger
PR suggestions
84f991a
@martinkilbinger
Fixed html link
74a8ca1
@sfarrens sfarrens merged commit aa602a1 into develop Sep 16, 2022
@sfarrens sfarrens deleted the ngc branch September 16, 2022 11:06
@sfarrens sfarrens mentioned this pull request Sep 16, 2022
Merged
sfarrens added a commit that referenced this pull request Sep 17, 2022
@sfarrens @martinkilbinger @tobias-liaudat
Summer 2022 Patch Release v1.0.1 (#581)
ee5f566 
* added CD GitHub action

* fixed bug in RunLog class (#548)

* 800deg2 (#544)

* added config files for matching 800deg2 survey

* Added Xavier as contributor; match external catalogue fix

* match 800

* match_ext: output distance

* match_ext output_dist def value

* Tutorial documentation (#543)

* updating job script and tutorial

* tutorial; fix config file

* tutorial finished

* no change

* psfex update (minor bug)

* psfex running

* updated MCCD config files

* comment in config file

* config file fix for MCCD

* config file fix for MCCD

* removed unused option in usage str

* Update docs/source/pipeline_tutorial.md

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* improved tutorial according to PR review

* Update docs/source/pipeline_tutorial.md

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* tutorial clean-up

* post_proc cleaned up; tutorial added output dir names

* changes to tutorial, post-proc and mccd plot doc

* get_images error msg testing

* Update docs/source/pipeline_tutorial.md

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update docs/source/pipeline_tutorial.md

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update docs/source/pipeline_tutorial.md

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update docs/source/pipeline_tutorial.md

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* removed prompt from bash example

* Update docs/source/post_processing.md

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* PR review changes to doc

* PR review changes to doc

* Update docs/source/post_processing.md

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* added contribution guidelines (#550)

* added contribution guidelines

* Update CODE_OF_CONDUCT.md

* tutorial bugfixes (#552)

Co-authored-by: Lucie Baumont <lucie.baumont@cea.fr>

* removed pep8 error exceptions (#554)

* Understanding the API docs (#553)

* added md for understanding the api docs

* updates following reviwer comments

* Update package versions (#539)

* updated doc-tests

* updated package versions

* pin documentation packages

* updated ShapePipe version and cleaned up

* Config file clean up (#556)

* Removed unused config files in example/cfis

* Removed obsolete config dirs tutorial and ps3pi_cfis

* removed old unions config files

* Update docs/source/configuration.md

Co-authored-by: Martin Kilbinger <martin.kilbinger@cea.fr>

* final clean up

* removed obsolete distance-based overlap region flagging

* removed errornous mccd_interp_runner call

* Added Tobias' MCCD plot config file to validate joint cat

* Added Tobias' MCCD plot config file to validate joint cat

* removed duplicate config file

* Random catalogue improvements (#570)

* merge_final script: added option for additional tile ID path to select tiles; clean-up

* typo in doc string

* Updated docs and references (#579)

* updated docs and references

* Update docs/source/module_develop.md

Co-authored-by: Martin Kilbinger <martin.kilbinger@cea.fr>

Co-authored-by: Martin Kilbinger <martin.kilbinger@cea.fr>

* Random runner updates (#573)

* merge_final script: added option for additional tile ID path to select tiles; clean-up

* typo in doc string

* started to implement healpix mask output

* healpix options for random/mask

* Update shapepipe/modules/random_cat_package/random_cat.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update shapepipe/modules/random_cat_package/random_cat.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update shapepipe/modules/random_cat_package/random_cat.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update shapepipe/modules/random_cat_package/random_cat.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Modifications for PR review

* comments from PR review

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* added masking for NGC objects (#575)

* added masking for NGC objects

* debugging ngc np binary file

* Fixed bugs in new mask handling (input FITS files)

* debug info to log file for checking existing images

* mask: combined dso masks into dictionary

* PR edits

* Update shapepipe/modules/mask_package/mask.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update shapepipe/modules/mask_package/mask.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update shapepipe/modules/mask_package/mask.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update shapepipe/modules/mask_package/mask.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* added symlink

* Update shapepipe/pipeline/file_io.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update shapepipe/modules/mask_package/mask.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update shapepipe/pipeline/file_io.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update shapepipe/pipeline/file_io.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update shapepipe/pipeline/file_io.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update shapepipe/pipeline/file_io.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update shapepipe/modules/mask_package/mask.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update shapepipe/modules/mask_package/mask.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update shapepipe/modules/mask_package/mask.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update shapepipe/pipeline/file_io.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* PR suggestions

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* update patch version

Co-authored-by: Martin Kilbinger <martin.kilbinger@cea.fr>
Co-authored-by: Lucie Baumont <lucie.baumont@stonybrook.edu>
Co-authored-by: Lucie Baumont <lucie.baumont@cea.fr>
Co-authored-by: Tobias Liaudat <tobiasliaudat@gmail.com>
sfarrens added a commit that referenced this pull request Oct 12, 2022
@martinkilbinger @sfarrens @tobias-liaudat
Bug fix(es) for v1.0.1 (#586)
1254ce3 
* Summer 2022 Patch Release v1.0.1 (#581)

* added CD GitHub action

* fixed bug in RunLog class (#548)

* 800deg2 (#544)

* added config files for matching 800deg2 survey

* Added Xavier as contributor; match external catalogue fix

* match 800

* match_ext: output distance

* match_ext output_dist def value

* Tutorial documentation (#543)

* updating job script and tutorial

* tutorial; fix config file

* tutorial finished

* no change

* psfex update (minor bug)

* psfex running

* updated MCCD config files

* comment in config file

* config file fix for MCCD

* config file fix for MCCD

* removed unused option in usage str

* Update docs/source/pipeline_tutorial.md

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* improved tutorial according to PR review

* Update docs/source/pipeline_tutorial.md

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* tutorial clean-up

* post_proc cleaned up; tutorial added output dir names

* changes to tutorial, post-proc and mccd plot doc

* get_images error msg testing

* Update docs/source/pipeline_tutorial.md

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update docs/source/pipeline_tutorial.md

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update docs/source/pipeline_tutorial.md

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update docs/source/pipeline_tutorial.md

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* removed prompt from bash example

* Update docs/source/post_processing.md

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* PR review changes to doc

* PR review changes to doc

* Update docs/source/post_processing.md

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* added contribution guidelines (#550)

* added contribution guidelines

* Update CODE_OF_CONDUCT.md

* tutorial bugfixes (#552)

Co-authored-by: Lucie Baumont <lucie.baumont@cea.fr>

* removed pep8 error exceptions (#554)

* Understanding the API docs (#553)

* added md for understanding the api docs

* updates following reviwer comments

* Update package versions (#539)

* updated doc-tests

* updated package versions

* pin documentation packages

* updated ShapePipe version and cleaned up

* Config file clean up (#556)

* Removed unused config files in example/cfis

* Removed obsolete config dirs tutorial and ps3pi_cfis

* removed old unions config files

* Update docs/source/configuration.md

Co-authored-by: Martin Kilbinger <martin.kilbinger@cea.fr>

* final clean up

* removed obsolete distance-based overlap region flagging

* removed errornous mccd_interp_runner call

* Added Tobias' MCCD plot config file to validate joint cat

* Added Tobias' MCCD plot config file to validate joint cat

* removed duplicate config file

* Random catalogue improvements (#570)

* merge_final script: added option for additional tile ID path to select tiles; clean-up

* typo in doc string

* Updated docs and references (#579)

* updated docs and references

* Update docs/source/module_develop.md

Co-authored-by: Martin Kilbinger <martin.kilbinger@cea.fr>

Co-authored-by: Martin Kilbinger <martin.kilbinger@cea.fr>

* Random runner updates (#573)

* merge_final script: added option for additional tile ID path to select tiles; clean-up

* typo in doc string

* started to implement healpix mask output

* healpix options for random/mask

* Update shapepipe/modules/random_cat_package/random_cat.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update shapepipe/modules/random_cat_package/random_cat.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update shapepipe/modules/random_cat_package/random_cat.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update shapepipe/modules/random_cat_package/random_cat.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Modifications for PR review

* comments from PR review

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* added masking for NGC objects (#575)

* added masking for NGC objects

* debugging ngc np binary file

* Fixed bugs in new mask handling (input FITS files)

* debug info to log file for checking existing images

* mask: combined dso masks into dictionary

* PR edits

* Update shapepipe/modules/mask_package/mask.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update shapepipe/modules/mask_package/mask.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update shapepipe/modules/mask_package/mask.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update shapepipe/modules/mask_package/mask.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* added symlink

* Update shapepipe/pipeline/file_io.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update shapepipe/modules/mask_package/mask.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update shapepipe/pipeline/file_io.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update shapepipe/pipeline/file_io.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update shapepipe/pipeline/file_io.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update shapepipe/pipeline/file_io.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update shapepipe/modules/mask_package/mask.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update shapepipe/modules/mask_package/mask.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update shapepipe/modules/mask_package/mask.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update shapepipe/pipeline/file_io.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* PR suggestions

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* update patch version

Co-authored-by: Martin Kilbinger <martin.kilbinger@cea.fr>
Co-authored-by: Lucie Baumont <lucie.baumont@stonybrook.edu>
Co-authored-by: Lucie Baumont <lucie.baumont@cea.fr>
Co-authored-by: Tobias Liaudat <tobiasliaudat@gmail.com>

* fixed typo in variable name

* config file vignet runner output fixed

* typo in make_cat config ini file fixed

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>
Co-authored-by: Lucie Baumont <lucie.baumont@stonybrook.edu>
Co-authored-by: Lucie Baumont <lucie.baumont@cea.fr>
Co-authored-by: Tobias Liaudat <tobiasliaudat@gmail.com>
sfarrens added a commit that referenced this pull request Oct 12, 2022
@sfarrens @martinkilbinger @tobias-liaudat
Patch fixes for v1.0.1 (#589)
32fe713 
* added CD GitHub action

* fixed bug in RunLog class (#548)

* 800deg2 (#544)

* added config files for matching 800deg2 survey

* Added Xavier as contributor; match external catalogue fix

* match 800

* match_ext: output distance

* match_ext output_dist def value

* Tutorial documentation (#543)

* updating job script and tutorial

* tutorial; fix config file

* tutorial finished

* no change

* psfex update (minor bug)

* psfex running

* updated MCCD config files

* comment in config file

* config file fix for MCCD

* config file fix for MCCD

* removed unused option in usage str

* Update docs/source/pipeline_tutorial.md

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* improved tutorial according to PR review

* Update docs/source/pipeline_tutorial.md

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* tutorial clean-up

* post_proc cleaned up; tutorial added output dir names

* changes to tutorial, post-proc and mccd plot doc

* get_images error msg testing

* Update docs/source/pipeline_tutorial.md

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update docs/source/pipeline_tutorial.md

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update docs/source/pipeline_tutorial.md

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update docs/source/pipeline_tutorial.md

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* removed prompt from bash example

* Update docs/source/post_processing.md

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* PR review changes to doc

* PR review changes to doc

* Update docs/source/post_processing.md

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* added contribution guidelines (#550)

* added contribution guidelines

* Update CODE_OF_CONDUCT.md

* tutorial bugfixes (#552)

Co-authored-by: Lucie Baumont <lucie.baumont@cea.fr>

* removed pep8 error exceptions (#554)

* Understanding the API docs (#553)

* added md for understanding the api docs

* updates following reviwer comments

* Update package versions (#539)

* updated doc-tests

* updated package versions

* pin documentation packages

* updated ShapePipe version and cleaned up

* Config file clean up (#556)

* Removed unused config files in example/cfis

* Removed obsolete config dirs tutorial and ps3pi_cfis

* removed old unions config files

* Update docs/source/configuration.md

Co-authored-by: Martin Kilbinger <martin.kilbinger@cea.fr>

* final clean up

* removed obsolete distance-based overlap region flagging

* removed errornous mccd_interp_runner call

* Added Tobias' MCCD plot config file to validate joint cat

* Added Tobias' MCCD plot config file to validate joint cat

* removed duplicate config file

* Random catalogue improvements (#570)

* merge_final script: added option for additional tile ID path to select tiles; clean-up

* typo in doc string

* Updated docs and references (#579)

* updated docs and references

* Update docs/source/module_develop.md

Co-authored-by: Martin Kilbinger <martin.kilbinger@cea.fr>

Co-authored-by: Martin Kilbinger <martin.kilbinger@cea.fr>

* Random runner updates (#573)

* merge_final script: added option for additional tile ID path to select tiles; clean-up

* typo in doc string

* started to implement healpix mask output

* healpix options for random/mask

* Update shapepipe/modules/random_cat_package/random_cat.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update shapepipe/modules/random_cat_package/random_cat.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update shapepipe/modules/random_cat_package/random_cat.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update shapepipe/modules/random_cat_package/random_cat.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Modifications for PR review

* comments from PR review

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* added masking for NGC objects (#575)

* added masking for NGC objects

* debugging ngc np binary file

* Fixed bugs in new mask handling (input FITS files)

* debug info to log file for checking existing images

* mask: combined dso masks into dictionary

* PR edits

* Update shapepipe/modules/mask_package/mask.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update shapepipe/modules/mask_package/mask.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update shapepipe/modules/mask_package/mask.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update shapepipe/modules/mask_package/mask.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* added symlink

* Update shapepipe/pipeline/file_io.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update shapepipe/modules/mask_package/mask.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update shapepipe/pipeline/file_io.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update shapepipe/pipeline/file_io.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update shapepipe/pipeline/file_io.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update shapepipe/pipeline/file_io.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update shapepipe/modules/mask_package/mask.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update shapepipe/modules/mask_package/mask.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update shapepipe/modules/mask_package/mask.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update shapepipe/pipeline/file_io.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* PR suggestions

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* update patch version

* random runner: hp masks working; doc updated (#580)

* random runner: hp masks working; doc updated

* random runner config file updated

* Update shapepipe/modules/random_cat_package/random_cat.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* passing tests

* Update shapepipe/modules/random_cat_package/__init__.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update shapepipe/modules/random_cat_package/__init__.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Bug fix(es) for v1.0.1 (#586)

* Summer 2022 Patch Release v1.0.1 (#581)

* added CD GitHub action

* fixed bug in RunLog class (#548)

* 800deg2 (#544)

* added config files for matching 800deg2 survey

* Added Xavier as contributor; match external catalogue fix

* match 800

* match_ext: output distance

* match_ext output_dist def value

* Tutorial documentation (#543)

* updating job script and tutorial

* tutorial; fix config file

* tutorial finished

* no change

* psfex update (minor bug)

* psfex running

* updated MCCD config files

* comment in config file

* config file fix for MCCD

* config file fix for MCCD

* removed unused option in usage str

* Update docs/source/pipeline_tutorial.md

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* improved tutorial according to PR review

* Update docs/source/pipeline_tutorial.md

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* tutorial clean-up

* post_proc cleaned up; tutorial added output dir names

* changes to tutorial, post-proc and mccd plot doc

* get_images error msg testing

* Update docs/source/pipeline_tutorial.md

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update docs/source/pipeline_tutorial.md

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update docs/source/pipeline_tutorial.md

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update docs/source/pipeline_tutorial.md

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* removed prompt from bash example

* Update docs/source/post_processing.md

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* PR review changes to doc

* PR review changes to doc

* Update docs/source/post_processing.md

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* added contribution guidelines (#550)

* added contribution guidelines

* Update CODE_OF_CONDUCT.md

* tutorial bugfixes (#552)

Co-authored-by: Lucie Baumont <lucie.baumont@cea.fr>

* removed pep8 error exceptions (#554)

* Understanding the API docs (#553)

* added md for understanding the api docs

* updates following reviwer comments

* Update package versions (#539)

* updated doc-tests

* updated package versions

* pin documentation packages

* updated ShapePipe version and cleaned up

* Config file clean up (#556)

* Removed unused config files in example/cfis

* Removed obsolete config dirs tutorial and ps3pi_cfis

* removed old unions config files

* Update docs/source/configuration.md

Co-authored-by: Martin Kilbinger <martin.kilbinger@cea.fr>

* final clean up

* removed obsolete distance-based overlap region flagging

* removed errornous mccd_interp_runner call

* Added Tobias' MCCD plot config file to validate joint cat

* Added Tobias' MCCD plot config file to validate joint cat

* removed duplicate config file

* Random catalogue improvements (#570)

* merge_final script: added option for additional tile ID path to select tiles; clean-up

* typo in doc string

* Updated docs and references (#579)

* updated docs and references

* Update docs/source/module_develop.md

Co-authored-by: Martin Kilbinger <martin.kilbinger@cea.fr>

Co-authored-by: Martin Kilbinger <martin.kilbinger@cea.fr>

* Random runner updates (#573)

* merge_final script: added option for additional tile ID path to select tiles; clean-up

* typo in doc string

* started to implement healpix mask output

* healpix options for random/mask

* Update shapepipe/modules/random_cat_package/random_cat.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update shapepipe/modules/random_cat_package/random_cat.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update shapepipe/modules/random_cat_package/random_cat.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update shapepipe/modules/random_cat_package/random_cat.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Modifications for PR review

* comments from PR review

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* added masking for NGC objects (#575)

* added masking for NGC objects

* debugging ngc np binary file

* Fixed bugs in new mask handling (input FITS files)

* debug info to log file for checking existing images

* mask: combined dso masks into dictionary

* PR edits

* Update shapepipe/modules/mask_package/mask.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update shapepipe/modules/mask_package/mask.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update shapepipe/modules/mask_package/mask.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update shapepipe/modules/mask_package/mask.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* added symlink

* Update shapepipe/pipeline/file_io.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update shapepipe/modules/mask_package/mask.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update shapepipe/pipeline/file_io.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update shapepipe/pipeline/file_io.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update shapepipe/pipeline/file_io.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update shapepipe/pipeline/file_io.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update shapepipe/modules/mask_package/mask.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update shapepipe/modules/mask_package/mask.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update shapepipe/modules/mask_package/mask.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* Update shapepipe/pipeline/file_io.py

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* PR suggestions

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>

* update patch version

Co-authored-by: Martin Kilbinger <martin.kilbinger@cea.fr>
Co-authored-by: Lucie Baumont <lucie.baumont@stonybrook.edu>
Co-authored-by: Lucie Baumont <lucie.baumont@cea.fr>
Co-authored-by: Tobias Liaudat <tobiasliaudat@gmail.com>

* fixed typo in variable name

* config file vignet runner output fixed

* typo in make_cat config ini file fixed

Co-authored-by: Samuel Farrens <samuel.farrens@gmail.com>
Co-authored-by: Lucie Baumont <lucie.baumont@stonybrook.edu>
Co-authored-by: Lucie Baumont <lucie.baumont@cea.fr>
Co-authored-by: Tobias Liaudat <tobiasliaudat@gmail.com>

* fixed blank lines

Co-authored-by: Martin Kilbinger <martin.kilbinger@cea.fr>
Co-authored-by: Lucie Baumont <lucie.baumont@stonybrook.edu>
Co-authored-by: Lucie Baumont <lucie.baumont@cea.fr>
Co-authored-by: Tobias Liaudat <tobiasliaudat@gmail.com>
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@sfarrens sfarrens sfarrens requested changes

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@martinkilbinger martinkilbinger

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Summer 2022 patch
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[NEW FEATURE] NGC masks
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@martinkilbinger @sfarrens