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Automatic tests + paper update + PEP8 formatting + minor changes to completeness curves/maps #537

Merged
merged 100 commits into from
May 9, 2022
Merged

Automatic tests + paper update + PEP8 formatting + minor changes to completeness curves/maps #537

merged 100 commits into from
May 9, 2022

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VChristiaens
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  • New automatic tests for NEGFC (3D and 4D cases) and bad pixel correction
  • Docs & code formatting using autopep8
  • Paper update as per co-author feedback
    -metrics: completeness curves and maps algorithms moved to a separate file, and based on a call to a 3sigma contrast curve when ini_contrast is not provided.

@VChristiaens
Updated docs to reflect inclusion of a new IFS data processing tutorial
9541377
@VChristiaens
Added new automatic test for NEGFC-MCMC (3D ADI cube case)
57e1bef
@VChristiaens
Added new automatic test for NEGFC-MCMC (4D IFS+ADI cube case)
7bbdce2
@VChristiaens
Removed unnecessary 'plsc' argument from NEGFC routines + update of a…
5c6b415 
…ll documentation
@VChristiaens
Re-arranged order of 'plsc' argument in cube injection routine
8aaea38
@VChristiaens
Re-arranged order of 'plsc' argument in cube injection routine + typo…
b198e07 
… fixes
@VChristiaens
Re-arranged order of 'plsc' argument in cube injection routine used f…
bfc497b 
…or contrast curve
@VChristiaens
Added new collapse method: mean of absolute residuals
50beed8
@VChristiaens
Unified merge by removing 'HEAD' comments in code
ff9f174
@VChristiaens
Unified bug fixes from negfc_simplex and pca_fullfr files
9153d5e
@VChristiaens
Replaced VORTEX team by PSILab in README
382f115
@VChristiaens
Made input planet parameters format to cube_planet_free more flexible
6ada48c
@VChristiaens
Merge branch 'master' into better_injection
1bb37b4
@VChristiaens
Made input format of planet parameters more flexible for cube_planet_…
e2be71c 
…free
@VChristiaens
Added latest paper pdf version
18d2c53
@VChristiaens
minor bug fixes in rarely used negfc options
4590ab9
@VChristiaens
Merge branch 'master' into better_injection
117730e
@VChristiaens
Adapted test parameters for 3D NEGFC to reduce length of test, and re…
bdbada8 
…duced IFS+ADI 4D cube size passed to NEGFC for faster test
@VChristiaens
Adapted test parameters for 3D NEGFC to reduce length of test, and re…
32fd123 
…duced IFS+ADI 4D cube size passed to NEGFC for faster test
@VChristiaens
typo fix in NEGFC test
2680160
@VChristiaens
typo fix in NEGFC test
18fa060
@VChristiaens
Added acknowledgement
5bdabe5
@VChristiaens
defined algo_options for all algorithms
a00ea47
@VChristiaens
improved algo parameters for 4D negfc
b8fac2c
@VChristiaens
Merge branch 'master' into better_injection
6a811c9
@VChristiaens
Added outlier removal option in residual speckle noise estimator to p…
7657e75 
…revent the risk of all but one deviations to fit in a single bin of the histogram
@VChristiaens
changed test approval condition to estimated value to be within 2 sig…
c0f2a28 
…ma of ground truth
@VChristiaens
Updated NEGFC test approval condition + small bug fix in confidence f…
594879e 
…or the force_rPA=True case
@VChristiaens
Merge branch 'master' into better_injection
757b603
@VChristiaens
Fixed bug in expected result in NEGFC test in the case of force_rPA
b897efc
VChristiaens added 28 commits May 5, 2022 15:53
@VChristiaens
Added make command for auto pep8 formatting of all .py files
3e74ea7
@VChristiaens
Added autotpep8 requirement for developers
d4c5973
@VChristiaens
Fixes multiprocessing bug
0c91bc0
@VChristiaens
PEP8 formatting
76ba991
@VChristiaens
PEP8 formatting
d054860
@VChristiaens
minor bug fixes in tests + speed improvements
64c1fda
@VChristiaens
Updated description + added timing in routines of invprob module
6cddffa
@VChristiaens
Updated tutorials
e1e47be
@VChristiaens
fixed deprecation warnings
141c035
@VChristiaens
Fixed format of routine documentation
db2c110
@VChristiaens
Updated completeness curves/maps description
8ab8ad3
@VChristiaens
Updated Tuto 4 with completeness curves/maps example
6304f3d
@VChristiaens
paper: updated pdf
35ca9f1
@VChristiaens
adapted automatic tests for contrast curves and bad pixel correction …
b0b97c2 
…for IFS
@VChristiaens
Tutorials: Updated derotation angles for example dataset - to match N…
046ad04 
…orth up, East left
@VChristiaens
typo fixes in description of fmmf and paco
d888f90
@VChristiaens
more efficient test implementation and division in smaller tests for …
8ccd3d2 
…timing
@VChristiaens
Optimized tests for minimal running time
35e7014
@VChristiaens
Paper: updated author order
84fd8f3
@VChristiaens
paper: updated author order
b995bae
@VChristiaens
Optimized tests
5734340
@VChristiaens
Made tests more efficient
64b9385
@VChristiaens
Fixed importation error in test
e246adf
@VChristiaens
Updated bad pixel clump detection test
9fb1d28
@VChristiaens
Updated bad pixel clump detection test values
1b93d6f
@VChristiaens
Updated bad pixel clump detection test values
13e9375
@VChristiaens
Adapted non-jit version of clip_array for better detection of bad pixels
08b50fb
@VChristiaens
Minor bug fix in clip array (bad pixel identification)
4da14f1
@VChristiaens VChristiaens merged commit b6cefde into vortex-exoplanet:master May 9, 2022
@VChristiaens VChristiaens deleted the better_injection branch May 9, 2022 12:29
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@VChristiaens