Machine uses perturbation class by jorgemarpa · Pull Request #60 · SSDataLab/psfmachine

jorgemarpa · 2022-04-06T03:09:23Z

This PR adapts machine to use the new perturbation classes introduced in #59.

It modifies the following methods:

self.build_time_model()
self.plot_time_model()
self.fit_models()
new self._get_perturbed_model(), computes the perturbed matrix for a given time.

It adds a new attribute self.P3 which is a PerturbationMatrix3D object that manages the perturbation matrix.

TODO:

EDIT:
The original mac.time_corrector = "pos_corr", "centroid" options can be mimic by including the following arguments to PerturbationMatrix3D at initialization: other_vectors = [poscorr1, poscorr2, poscorr1 * poscorr2], poly_order=0. In this way the perturbation matrix will use only the centroids/poscorr as components with no time.

Co-authored-by: Jorge Martínez-Palomera <jorgemarpa@users.noreply.github.com>

…on API

Co-authored-by: Jorge Martínez-Palomera <jorgemarpa@users.noreply.github.com>

… into machine-perturbation

…o machine-perturbation

Co-authored-by: Christina Hedges <14965634+christinahedges@users.noreply.github.com>

jorgemarpa

@christinahedges I reviewed this PR again, added some minor docstrings, and removed duplicated functions in utils.py.

It looks Ok to me. Please review again before merging

christinahedges

I think this looks good, just two very minor docstring changes and then I will merge

christinahedges · 2022-06-21T19:40:20Z

 def pca(self, y, ncomponents=5, smooth_time_scale=0):
 """Adds the principal components of `y` to the design matrix

+ Will add two time scales of principal components, definied by `long_time_scale`


This isn't true anymore can we fix this docstring here?

christinahedges · 2022-06-21T19:51:32Z

 pixels_in_tpf = np.ones_like(self.row, dtype=bool)

+ # enheance pixel mask
+ time_corr = np.nanpercentile(bkg_flux, 20, axis=1)[:, None]


Why is this 20%? Is this why stuff goes negative so often? Can you add a short docstring explainer about what's going on here?

That part is only used to create a naive model of the background as a function of time to then find and mask out variable pixels. So it does not play into building the bkg model.
Changing the percentile will only change which pixels to look at in the distribution each time.

jorgemarpa · 2022-04-06T03:09:23Z

This PR adapts machine to use the new perturbation classes introduced in #59.

It modifies the following methods:

self.build_time_model()
self.plot_time_model()
self.fit_models()
new self._get_perturbed_model(), computes the perturbed matrix for a given time.

It adds a new attribute self.P3 which is a PerturbationMatrix3D object that manages the perturbation matrix.

TODO:

EDIT:
The original mac.time_corrector = "pos_corr", "centroid" options can be mimic by including the following arguments to PerturbationMatrix3D at initialization: other_vectors = [poscorr1, poscorr2, poscorr1 * poscorr2], poly_order=0. In this way the perturbation matrix will use only the centroids/poscorr as components with no time.

Co-authored-by: Jorge Martínez-Palomera <jorgemarpa@users.noreply.github.com>

…on API

Co-authored-by: Jorge Martínez-Palomera <jorgemarpa@users.noreply.github.com>

… into machine-perturbation

…o machine-perturbation

Co-authored-by: Christina Hedges <14965634+christinahedges@users.noreply.github.com>

jorgemarpa

@christinahedges I reviewed this PR again, added some minor docstrings, and removed duplicated functions in utils.py.

It looks Ok to me. Please review again before merging

christinahedges

I think this looks good, just two very minor docstring changes and then I will merge

christinahedges · 2022-06-21T19:40:20Z

 def pca(self, y, ncomponents=5, smooth_time_scale=0):
 """Adds the principal components of `y` to the design matrix

+ Will add two time scales of principal components, definied by `long_time_scale`


This isn't true anymore can we fix this docstring here?

christinahedges · 2022-06-21T19:51:32Z

 pixels_in_tpf = np.ones_like(self.row, dtype=bool)

+ # enheance pixel mask
+ time_corr = np.nanpercentile(bkg_flux, 20, axis=1)[:, None]


Why is this 20%? Is this why stuff goes negative so often? Can you add a short docstring explainer about what's going on here?

That part is only used to create a naive model of the background as a function of time to then find and mask out variable pixels. So it does not play into building the bkg model.
Changing the percentile will only change which pixels to look at in the distribution each time.

jorgemarpa · 2022-04-06T03:09:23Z

This PR adapts machine to use the new perturbation classes introduced in #59.

It modifies the following methods:

self.build_time_model()
self.plot_time_model()
self.fit_models()
new self._get_perturbed_model(), computes the perturbed matrix for a given time.

It adds a new attribute self.P3 which is a PerturbationMatrix3D object that manages the perturbation matrix.

TODO:

EDIT:
The original mac.time_corrector = "pos_corr", "centroid" options can be mimic by including the following arguments to PerturbationMatrix3D at initialization: other_vectors = [poscorr1, poscorr2, poscorr1 * poscorr2], poly_order=0. In this way the perturbation matrix will use only the centroids/poscorr as components with no time.

Co-authored-by: Jorge Martínez-Palomera <jorgemarpa@users.noreply.github.com>

…on API

Co-authored-by: Jorge Martínez-Palomera <jorgemarpa@users.noreply.github.com>

… into machine-perturbation

…o machine-perturbation

Co-authored-by: Christina Hedges <14965634+christinahedges@users.noreply.github.com>

jorgemarpa

@christinahedges I reviewed this PR again, added some minor docstrings, and removed duplicated functions in utils.py.

It looks Ok to me. Please review again before merging

christinahedges

I think this looks good, just two very minor docstring changes and then I will merge

christinahedges · 2022-06-21T19:40:20Z

 def pca(self, y, ncomponents=5, smooth_time_scale=0):
 """Adds the principal components of `y` to the design matrix

+ Will add two time scales of principal components, definied by `long_time_scale`


This isn't true anymore can we fix this docstring here?

christinahedges · 2022-06-21T19:51:32Z

 pixels_in_tpf = np.ones_like(self.row, dtype=bool)

+ # enheance pixel mask
+ time_corr = np.nanpercentile(bkg_flux, 20, axis=1)[:, None]


Why is this 20%? Is this why stuff goes negative so often? Can you add a short docstring explainer about what's going on here?

That part is only used to create a naive model of the background as a function of time to then find and mask out variable pixels. So it does not play into building the bkg model.
Changing the percentile will only change which pixels to look at in the distribution each time.

jorgemarpa · 2022-04-06T03:09:23Z

This PR adapts machine to use the new perturbation classes introduced in #59.

It modifies the following methods:

self.build_time_model()
self.plot_time_model()
self.fit_models()
new self._get_perturbed_model(), computes the perturbed matrix for a given time.

It adds a new attribute self.P3 which is a PerturbationMatrix3D object that manages the perturbation matrix.

TODO:

EDIT:
The original mac.time_corrector = "pos_corr", "centroid" options can be mimic by including the following arguments to PerturbationMatrix3D at initialization: other_vectors = [poscorr1, poscorr2, poscorr1 * poscorr2], poly_order=0. In this way the perturbation matrix will use only the centroids/poscorr as components with no time.

Co-authored-by: Jorge Martínez-Palomera <jorgemarpa@users.noreply.github.com>

…on API

Co-authored-by: Jorge Martínez-Palomera <jorgemarpa@users.noreply.github.com>

… into machine-perturbation

…o machine-perturbation

Co-authored-by: Christina Hedges <14965634+christinahedges@users.noreply.github.com>

jorgemarpa

@christinahedges I reviewed this PR again, added some minor docstrings, and removed duplicated functions in utils.py.

It looks Ok to me. Please review again before merging

christinahedges

I think this looks good, just two very minor docstring changes and then I will merge

christinahedges · 2022-06-21T19:40:20Z

 def pca(self, y, ncomponents=5, smooth_time_scale=0):
 """Adds the principal components of `y` to the design matrix

+ Will add two time scales of principal components, definied by `long_time_scale`


This isn't true anymore can we fix this docstring here?

christinahedges · 2022-06-21T19:51:32Z

 pixels_in_tpf = np.ones_like(self.row, dtype=bool)

+ # enheance pixel mask
+ time_corr = np.nanpercentile(bkg_flux, 20, axis=1)[:, None]


Why is this 20%? Is this why stuff goes negative so often? Can you add a short docstring explainer about what's going on here?

That part is only used to create a naive model of the background as a function of time to then find and mask out variable pixels. So it does not play into building the bkg model.
Changing the percentile will only change which pixels to look at in the distribution each time.

jorgemarpa · 2022-04-06T03:09:23Z

This PR adapts machine to use the new perturbation classes introduced in #59.

It modifies the following methods:

self.build_time_model()
self.plot_time_model()
self.fit_models()
new self._get_perturbed_model(), computes the perturbed matrix for a given time.

It adds a new attribute self.P3 which is a PerturbationMatrix3D object that manages the perturbation matrix.

TODO:

EDIT:
The original mac.time_corrector = "pos_corr", "centroid" options can be mimic by including the following arguments to PerturbationMatrix3D at initialization: other_vectors = [poscorr1, poscorr2, poscorr1 * poscorr2], poly_order=0. In this way the perturbation matrix will use only the centroids/poscorr as components with no time.

Co-authored-by: Jorge Martínez-Palomera <jorgemarpa@users.noreply.github.com>

…on API

Co-authored-by: Jorge Martínez-Palomera <jorgemarpa@users.noreply.github.com>

… into machine-perturbation

…o machine-perturbation

Co-authored-by: Christina Hedges <14965634+christinahedges@users.noreply.github.com>

jorgemarpa

@christinahedges I reviewed this PR again, added some minor docstrings, and removed duplicated functions in utils.py.

It looks Ok to me. Please review again before merging

christinahedges

I think this looks good, just two very minor docstring changes and then I will merge

christinahedges · 2022-06-21T19:40:20Z

 def pca(self, y, ncomponents=5, smooth_time_scale=0):
 """Adds the principal components of `y` to the design matrix

+ Will add two time scales of principal components, definied by `long_time_scale`


This isn't true anymore can we fix this docstring here?

christinahedges · 2022-06-21T19:51:32Z

 pixels_in_tpf = np.ones_like(self.row, dtype=bool)

+ # enheance pixel mask
+ time_corr = np.nanpercentile(bkg_flux, 20, axis=1)[:, None]


Why is this 20%? Is this why stuff goes negative so often? Can you add a short docstring explainer about what's going on here?

That part is only used to create a naive model of the background as a function of time to then find and mask out variable pixels. So it does not play into building the bkg model.
Changing the percentile will only change which pixels to look at in the distribution each time.

jorgemarpa · 2022-04-06T03:09:23Z

This PR adapts machine to use the new perturbation classes introduced in #59.

It modifies the following methods:

self.build_time_model()
self.plot_time_model()
self.fit_models()
new self._get_perturbed_model(), computes the perturbed matrix for a given time.

It adds a new attribute self.P3 which is a PerturbationMatrix3D object that manages the perturbation matrix.

TODO:

EDIT:
The original mac.time_corrector = "pos_corr", "centroid" options can be mimic by including the following arguments to PerturbationMatrix3D at initialization: other_vectors = [poscorr1, poscorr2, poscorr1 * poscorr2], poly_order=0. In this way the perturbation matrix will use only the centroids/poscorr as components with no time.

Co-authored-by: Jorge Martínez-Palomera <jorgemarpa@users.noreply.github.com>

…on API

Co-authored-by: Jorge Martínez-Palomera <jorgemarpa@users.noreply.github.com>

… into machine-perturbation

…o machine-perturbation

Co-authored-by: Christina Hedges <14965634+christinahedges@users.noreply.github.com>

jorgemarpa

@christinahedges I reviewed this PR again, added some minor docstrings, and removed duplicated functions in utils.py.

It looks Ok to me. Please review again before merging

christinahedges

I think this looks good, just two very minor docstring changes and then I will merge

christinahedges · 2022-06-21T19:40:20Z

 def pca(self, y, ncomponents=5, smooth_time_scale=0):
 """Adds the principal components of `y` to the design matrix

+ Will add two time scales of principal components, definied by `long_time_scale`


This isn't true anymore can we fix this docstring here?

christinahedges · 2022-06-21T19:51:32Z

 pixels_in_tpf = np.ones_like(self.row, dtype=bool)

+ # enheance pixel mask
+ time_corr = np.nanpercentile(bkg_flux, 20, axis=1)[:, None]


Why is this 20%? Is this why stuff goes negative so often? Can you add a short docstring explainer about what's going on here?

That part is only used to create a naive model of the background as a function of time to then find and mask out variable pixels. So it does not play into building the bkg model.
Changing the percentile will only change which pixels to look at in the distribution each time.

jorgemarpa · 2022-04-06T03:09:23Z

This PR adapts machine to use the new perturbation classes introduced in #59.

It modifies the following methods:

self.build_time_model()
self.plot_time_model()
self.fit_models()
new self._get_perturbed_model(), computes the perturbed matrix for a given time.

It adds a new attribute self.P3 which is a PerturbationMatrix3D object that manages the perturbation matrix.

TODO:

EDIT:
The original mac.time_corrector = "pos_corr", "centroid" options can be mimic by including the following arguments to PerturbationMatrix3D at initialization: other_vectors = [poscorr1, poscorr2, poscorr1 * poscorr2], poly_order=0. In this way the perturbation matrix will use only the centroids/poscorr as components with no time.

Co-authored-by: Jorge Martínez-Palomera <jorgemarpa@users.noreply.github.com>

…on API

Co-authored-by: Jorge Martínez-Palomera <jorgemarpa@users.noreply.github.com>

… into machine-perturbation

…o machine-perturbation

Co-authored-by: Christina Hedges <14965634+christinahedges@users.noreply.github.com>

jorgemarpa

@christinahedges I reviewed this PR again, added some minor docstrings, and removed duplicated functions in utils.py.

It looks Ok to me. Please review again before merging

christinahedges

I think this looks good, just two very minor docstring changes and then I will merge

christinahedges · 2022-06-21T19:40:20Z

 def pca(self, y, ncomponents=5, smooth_time_scale=0):
 """Adds the principal components of `y` to the design matrix

+ Will add two time scales of principal components, definied by `long_time_scale`


This isn't true anymore can we fix this docstring here?

christinahedges · 2022-06-21T19:51:32Z

 pixels_in_tpf = np.ones_like(self.row, dtype=bool)

+ # enheance pixel mask
+ time_corr = np.nanpercentile(bkg_flux, 20, axis=1)[:, None]


Why is this 20%? Is this why stuff goes negative so often? Can you add a short docstring explainer about what's going on here?

That part is only used to create a naive model of the background as a function of time to then find and mask out variable pixels. So it does not play into building the bkg model.
Changing the percentile will only change which pixels to look at in the distribution each time.

jorgemarpa · 2022-04-06T03:09:23Z

This PR adapts machine to use the new perturbation classes introduced in #59.

It modifies the following methods:

self.build_time_model()
self.plot_time_model()
self.fit_models()
new self._get_perturbed_model(), computes the perturbed matrix for a given time.

It adds a new attribute self.P3 which is a PerturbationMatrix3D object that manages the perturbation matrix.

TODO:

EDIT:
The original mac.time_corrector = "pos_corr", "centroid" options can be mimic by including the following arguments to PerturbationMatrix3D at initialization: other_vectors = [poscorr1, poscorr2, poscorr1 * poscorr2], poly_order=0. In this way the perturbation matrix will use only the centroids/poscorr as components with no time.

Co-authored-by: Jorge Martínez-Palomera <jorgemarpa@users.noreply.github.com>

…on API

Co-authored-by: Jorge Martínez-Palomera <jorgemarpa@users.noreply.github.com>

… into machine-perturbation

…o machine-perturbation

Co-authored-by: Christina Hedges <14965634+christinahedges@users.noreply.github.com>

jorgemarpa

@christinahedges I reviewed this PR again, added some minor docstrings, and removed duplicated functions in utils.py.

It looks Ok to me. Please review again before merging

christinahedges

I think this looks good, just two very minor docstring changes and then I will merge

christinahedges · 2022-06-21T19:40:20Z

 def pca(self, y, ncomponents=5, smooth_time_scale=0):
 """Adds the principal components of `y` to the design matrix

+ Will add two time scales of principal components, definied by `long_time_scale`


This isn't true anymore can we fix this docstring here?

christinahedges · 2022-06-21T19:51:32Z

 pixels_in_tpf = np.ones_like(self.row, dtype=bool)

+ # enheance pixel mask
+ time_corr = np.nanpercentile(bkg_flux, 20, axis=1)[:, None]


Why is this 20%? Is this why stuff goes negative so often? Can you add a short docstring explainer about what's going on here?

That part is only used to create a naive model of the background as a function of time to then find and mask out variable pixels. So it does not play into building the bkg model.
Changing the percentile will only change which pixels to look at in the distribution each time.

christinahedgesand others added 15 commits March 29, 2022 21:21

✨ Developing PerturbationMatrix class
05f4e26

✅ fixing flake8
172fbda

✨ added a 3D matrix
fb31d8b

🎨 fairly good sketch
d37a540

Update src/psfmachine/perturbation.py
884f24d
Co-authored-by: Jorge Martínez-Palomera <jorgemarpa@users.noreply.github.com>

Update src/psfmachine/perturbation.py
18cca59

fixing identation and _clean_vectors when segments=True
3df9bea

⚡ faster!
b64b9cc

🎨 adding pixel masking
2d55aa1

📝 added docstrings
7310ed3

smooth vector fx
34d943c

improved plots and docstrings
7648325

machine uses PerturbationMatrix3D
b330ee6

demoving _time_bin method
cc99962

normalize poscorr/centr and fixing pytest to work with new perturbati…
5e2de68
…on API

jorgemarpa force-pushed the machine-perturbation branch from 95d05bc to 5e2de68Compare April 6, 2022 19:56

christinahedges reviewed Apr 8, 2022
View reviewed changes

jorgemarpaand others added 13 commits April 11, 2022 10:58

smooth_vector API improved
cceeb2b

gaussian smooth -> spline smooth
c3cdfb1

matching arguments between perturbation and machine
e5f3f8e

✨ Added PCA method
84a064c

🎨 added fbpca explicitly as dependency
3da1557

📝 docs
1520001

merging from refactor-time
612d3fd

🐛 fixing pca
78633dc

🐛 fix@jorgemarpabug
14babe3

📝 update docstrings
9d4a80f

merging from refactor-time
88c7493

Update src/psfmachine/perturbation.py
556317d
Co-authored-by: Jorge Martínez-Palomera <jorgemarpa@users.noreply.github.com>

adding perturbation-pca into machine
648211e

christinahedgesand others added 19 commits April 12, 2022 16:25

🎨 flake8
18fdc55

perturbed model
de15bfc

🎨 no comment block
eb9ce3c

📝 docstrings
2efb963

Merge branch 'refactor-time' ofhttps://github.com/SSDataLab/psfmachine…
f7650e5
… into machine-perturbation

time_resolution attr
70af6ac

matrix transpose hotfix
514f72b

agressive bkg pixel mask
c6ebac8

🎨 updating sane defaults, adding smooth PCA components
eaa807f

🎨 sane defaults
e1bc28e

Merge branch 'refactor-time' ofhttps://github.com/SSDataLab/psfmachine…
65ef6db
… into machine-perturbation

pca smooth time scale arg visible
9d336fb

time_resolution kwarg
ea876cc

using time_knots kwarg
12cd2a2

new time model diag plot and components API
dc1a8e6

Merge branch 'master' ofhttps://github.com/jorgemarpa/psfmachineint…
5aff7e9
…o machine-perturbation

updated lock
7ac7b71

pytest fixed
1e6b8a4

better pixel mask in build_time_model
90385d9

christinahedges reviewed Apr 29, 2022
View reviewed changes

Comment threadpyproject.toml Outdated

jorgemarpaand others added 2 commits April 29, 2022 12:37

Update pyproject.toml
5b18a7e
Co-authored-by: Christina Hedges <14965634+christinahedges@users.noreply.github.com>

bump up mac version to 1.1.2, missing docstr and removed dup fx in utils
88ca62c

jorgemarpa commented Jun 3, 2022
View reviewed changes

jorgemarpa requested a review from christinahedges June 7, 2022 18:21

christinahedges changed the title ~~[WIP] Machine uses perturbation class~~Machine uses perturbation classJun 21, 2022

christinahedges reviewed Jun 21, 2022
View reviewed changes

docstrings fixed
a6612f6

jorgemarpa mentioned this pull request Jun 22, 2022
Option to use CBVs and better priors #63
Merged
1 task

christinahedges merged commit 3784cba into SSDataLab:masterJun 28, 2022

jorgemarpa mentioned this pull request Dec 13, 2022
PSFMachine perturbation matrix needs a refactor #55
Closed

christinahedgesand others added 15 commits March 29, 2022 21:21

✨ Developing PerturbationMatrix class
05f4e26

✅ fixing flake8
172fbda

✨ added a 3D matrix
fb31d8b

🎨 fairly good sketch
d37a540

Update src/psfmachine/perturbation.py
884f24d
Co-authored-by: Jorge Martínez-Palomera <jorgemarpa@users.noreply.github.com>

Update src/psfmachine/perturbation.py
18cca59

fixing identation and _clean_vectors when segments=True
3df9bea

⚡ faster!
b64b9cc

🎨 adding pixel masking
2d55aa1

📝 added docstrings
7310ed3

smooth vector fx
34d943c

improved plots and docstrings
7648325

machine uses PerturbationMatrix3D
b330ee6

demoving _time_bin method
cc99962

normalize poscorr/centr and fixing pytest to work with new perturbati…
5e2de68
…on API

jorgemarpa force-pushed the machine-perturbation branch from 95d05bc to 5e2de68Compare April 6, 2022 19:56

christinahedges reviewed Apr 8, 2022
View reviewed changes

jorgemarpaand others added 13 commits April 11, 2022 10:58

smooth_vector API improved
cceeb2b

gaussian smooth -> spline smooth
c3cdfb1

matching arguments between perturbation and machine
e5f3f8e

✨ Added PCA method
84a064c

🎨 added fbpca explicitly as dependency
3da1557

📝 docs
1520001

merging from refactor-time
612d3fd

🐛 fixing pca
78633dc

🐛 fix@jorgemarpabug
14babe3

📝 update docstrings
9d4a80f

merging from refactor-time
88c7493

Update src/psfmachine/perturbation.py
556317d
Co-authored-by: Jorge Martínez-Palomera <jorgemarpa@users.noreply.github.com>

adding perturbation-pca into machine
648211e

christinahedgesand others added 19 commits April 12, 2022 16:25

🎨 flake8
18fdc55

perturbed model
de15bfc

🎨 no comment block
eb9ce3c

📝 docstrings
2efb963

Merge branch 'refactor-time' ofhttps://github.com/SSDataLab/psfmachine…
f7650e5
… into machine-perturbation

time_resolution attr
70af6ac

matrix transpose hotfix
514f72b

agressive bkg pixel mask
c6ebac8

🎨 updating sane defaults, adding smooth PCA components
eaa807f

🎨 sane defaults
e1bc28e

Merge branch 'refactor-time' ofhttps://github.com/SSDataLab/psfmachine…
65ef6db
… into machine-perturbation

pca smooth time scale arg visible
9d336fb

time_resolution kwarg
ea876cc

using time_knots kwarg
12cd2a2

new time model diag plot and components API
dc1a8e6

Merge branch 'master' ofhttps://github.com/jorgemarpa/psfmachineint…
5aff7e9
…o machine-perturbation

updated lock
7ac7b71

pytest fixed
1e6b8a4

better pixel mask in build_time_model
90385d9

christinahedges reviewed Apr 29, 2022
View reviewed changes

Comment threadpyproject.toml Outdated

jorgemarpaand others added 2 commits April 29, 2022 12:37

Update pyproject.toml
5b18a7e
Co-authored-by: Christina Hedges <14965634+christinahedges@users.noreply.github.com>

bump up mac version to 1.1.2, missing docstr and removed dup fx in utils
88ca62c

jorgemarpa commented Jun 3, 2022
View reviewed changes

jorgemarpa requested a review from christinahedges June 7, 2022 18:21

christinahedges changed the title ~~[WIP] Machine uses perturbation class~~Machine uses perturbation classJun 21, 2022

christinahedges reviewed Jun 21, 2022
View reviewed changes

docstrings fixed
a6612f6

jorgemarpa mentioned this pull request Jun 22, 2022
Option to use CBVs and better priors #63
Merged
1 task

christinahedges merged commit 3784cba into SSDataLab:masterJun 28, 2022

jorgemarpa mentioned this pull request Dec 13, 2022
PSFMachine perturbation matrix needs a refactor #55
Closed

christinahedgesand others added 15 commits March 29, 2022 21:21

✨ Developing PerturbationMatrix class
05f4e26

✅ fixing flake8
172fbda

✨ added a 3D matrix
fb31d8b

🎨 fairly good sketch
d37a540

Update src/psfmachine/perturbation.py
884f24d
Co-authored-by: Jorge Martínez-Palomera <jorgemarpa@users.noreply.github.com>

Update src/psfmachine/perturbation.py
18cca59

fixing identation and _clean_vectors when segments=True
3df9bea

⚡ faster!
b64b9cc

🎨 adding pixel masking
2d55aa1

📝 added docstrings
7310ed3

smooth vector fx
34d943c

improved plots and docstrings
7648325

machine uses PerturbationMatrix3D
b330ee6

demoving _time_bin method
cc99962

normalize poscorr/centr and fixing pytest to work with new perturbati…
5e2de68
…on API

jorgemarpa force-pushed the machine-perturbation branch from 95d05bc to 5e2de68Compare April 6, 2022 19:56

christinahedges reviewed Apr 8, 2022
View reviewed changes

jorgemarpaand others added 13 commits April 11, 2022 10:58

smooth_vector API improved
cceeb2b

gaussian smooth -> spline smooth
c3cdfb1

matching arguments between perturbation and machine
e5f3f8e

✨ Added PCA method
84a064c

🎨 added fbpca explicitly as dependency
3da1557

📝 docs
1520001

merging from refactor-time
612d3fd

🐛 fixing pca
78633dc

🐛 fix@jorgemarpabug
14babe3

📝 update docstrings
9d4a80f

merging from refactor-time
88c7493

Update src/psfmachine/perturbation.py
556317d
Co-authored-by: Jorge Martínez-Palomera <jorgemarpa@users.noreply.github.com>

adding perturbation-pca into machine
648211e

christinahedgesand others added 19 commits April 12, 2022 16:25

🎨 flake8
18fdc55

perturbed model
de15bfc

🎨 no comment block
eb9ce3c

📝 docstrings
2efb963

Merge branch 'refactor-time' ofhttps://github.com/SSDataLab/psfmachine…
f7650e5
… into machine-perturbation

time_resolution attr
70af6ac

matrix transpose hotfix
514f72b

agressive bkg pixel mask
c6ebac8

🎨 updating sane defaults, adding smooth PCA components
eaa807f

🎨 sane defaults
e1bc28e

Merge branch 'refactor-time' ofhttps://github.com/SSDataLab/psfmachine…
65ef6db
… into machine-perturbation

pca smooth time scale arg visible
9d336fb

time_resolution kwarg
ea876cc

using time_knots kwarg
12cd2a2

new time model diag plot and components API
dc1a8e6

Merge branch 'master' ofhttps://github.com/jorgemarpa/psfmachineint…
5aff7e9
…o machine-perturbation

updated lock
7ac7b71

pytest fixed
1e6b8a4

better pixel mask in build_time_model
90385d9

christinahedges reviewed Apr 29, 2022
View reviewed changes

Comment threadpyproject.toml Outdated

jorgemarpaand others added 2 commits April 29, 2022 12:37

Update pyproject.toml
5b18a7e
Co-authored-by: Christina Hedges <14965634+christinahedges@users.noreply.github.com>

bump up mac version to 1.1.2, missing docstr and removed dup fx in utils
88ca62c

jorgemarpa commented Jun 3, 2022
View reviewed changes

jorgemarpa requested a review from christinahedges June 7, 2022 18:21

christinahedges changed the title ~~[WIP] Machine uses perturbation class~~Machine uses perturbation classJun 21, 2022

christinahedges reviewed Jun 21, 2022
View reviewed changes

docstrings fixed
a6612f6

jorgemarpa mentioned this pull request Jun 22, 2022
Option to use CBVs and better priors #63
Merged
1 task

christinahedges merged commit 3784cba into SSDataLab:masterJun 28, 2022

jorgemarpa mentioned this pull request Dec 13, 2022
PSFMachine perturbation matrix needs a refactor #55
Closed

christinahedgesand others added 15 commits March 29, 2022 21:21

✨ Developing PerturbationMatrix class
05f4e26

✅ fixing flake8
172fbda

✨ added a 3D matrix
fb31d8b

🎨 fairly good sketch
d37a540

Update src/psfmachine/perturbation.py
884f24d
Co-authored-by: Jorge Martínez-Palomera <jorgemarpa@users.noreply.github.com>

Update src/psfmachine/perturbation.py
18cca59

fixing identation and _clean_vectors when segments=True
3df9bea

⚡ faster!
b64b9cc

🎨 adding pixel masking
2d55aa1

📝 added docstrings
7310ed3

smooth vector fx
34d943c

improved plots and docstrings
7648325

machine uses PerturbationMatrix3D
b330ee6

demoving _time_bin method
cc99962

normalize poscorr/centr and fixing pytest to work with new perturbati…
5e2de68
…on API

jorgemarpa force-pushed the machine-perturbation branch from 95d05bc to 5e2de68Compare April 6, 2022 19:56

christinahedges reviewed Apr 8, 2022
View reviewed changes

jorgemarpaand others added 13 commits April 11, 2022 10:58

smooth_vector API improved
cceeb2b

gaussian smooth -> spline smooth
c3cdfb1

matching arguments between perturbation and machine
e5f3f8e

✨ Added PCA method
84a064c

🎨 added fbpca explicitly as dependency
3da1557

📝 docs
1520001

merging from refactor-time
612d3fd

🐛 fixing pca
78633dc

🐛 fix@jorgemarpabug
14babe3

📝 update docstrings
9d4a80f

merging from refactor-time
88c7493

Update src/psfmachine/perturbation.py
556317d
Co-authored-by: Jorge Martínez-Palomera <jorgemarpa@users.noreply.github.com>

adding perturbation-pca into machine
648211e

christinahedgesand others added 19 commits April 12, 2022 16:25

🎨 flake8
18fdc55

perturbed model
de15bfc

🎨 no comment block
eb9ce3c

📝 docstrings
2efb963

Merge branch 'refactor-time' ofhttps://github.com/SSDataLab/psfmachine…
f7650e5
… into machine-perturbation

time_resolution attr
70af6ac

matrix transpose hotfix
514f72b

agressive bkg pixel mask
c6ebac8

🎨 updating sane defaults, adding smooth PCA components
eaa807f

🎨 sane defaults
e1bc28e

Merge branch 'refactor-time' ofhttps://github.com/SSDataLab/psfmachine…
65ef6db
… into machine-perturbation

pca smooth time scale arg visible
9d336fb

time_resolution kwarg
ea876cc

using time_knots kwarg
12cd2a2

new time model diag plot and components API
dc1a8e6

Merge branch 'master' ofhttps://github.com/jorgemarpa/psfmachineint…
5aff7e9
…o machine-perturbation

updated lock
7ac7b71

pytest fixed
1e6b8a4

better pixel mask in build_time_model
90385d9

christinahedges reviewed Apr 29, 2022
View reviewed changes

Comment threadpyproject.toml Outdated

jorgemarpaand others added 2 commits April 29, 2022 12:37

Update pyproject.toml
5b18a7e
Co-authored-by: Christina Hedges <14965634+christinahedges@users.noreply.github.com>

bump up mac version to 1.1.2, missing docstr and removed dup fx in utils
88ca62c

jorgemarpa commented Jun 3, 2022
View reviewed changes

jorgemarpa requested a review from christinahedges June 7, 2022 18:21

christinahedges changed the title ~~[WIP] Machine uses perturbation class~~Machine uses perturbation classJun 21, 2022

christinahedges reviewed Jun 21, 2022
View reviewed changes

docstrings fixed
a6612f6

jorgemarpa mentioned this pull request Jun 22, 2022
Option to use CBVs and better priors #63
Merged
1 task

christinahedges merged commit 3784cba into SSDataLab:masterJun 28, 2022

jorgemarpa mentioned this pull request Dec 13, 2022
PSFMachine perturbation matrix needs a refactor #55
Closed

christinahedgesand others added 15 commits March 29, 2022 21:21

✨ Developing PerturbationMatrix class
05f4e26

✅ fixing flake8
172fbda

✨ added a 3D matrix
fb31d8b

🎨 fairly good sketch
d37a540

Update src/psfmachine/perturbation.py
884f24d
Co-authored-by: Jorge Martínez-Palomera <jorgemarpa@users.noreply.github.com>

Update src/psfmachine/perturbation.py
18cca59

fixing identation and _clean_vectors when segments=True
3df9bea

⚡ faster!
b64b9cc

🎨 adding pixel masking
2d55aa1

📝 added docstrings
7310ed3

smooth vector fx
34d943c

improved plots and docstrings
7648325

machine uses PerturbationMatrix3D
b330ee6

demoving _time_bin method
cc99962

normalize poscorr/centr and fixing pytest to work with new perturbati…
5e2de68
…on API

jorgemarpa force-pushed the machine-perturbation branch from 95d05bc to 5e2de68Compare April 6, 2022 19:56

christinahedges reviewed Apr 8, 2022
View reviewed changes

jorgemarpaand others added 13 commits April 11, 2022 10:58

smooth_vector API improved
cceeb2b

gaussian smooth -> spline smooth
c3cdfb1

matching arguments between perturbation and machine
e5f3f8e

✨ Added PCA method
84a064c

🎨 added fbpca explicitly as dependency
3da1557

📝 docs
1520001

merging from refactor-time
612d3fd

🐛 fixing pca
78633dc

🐛 fix@jorgemarpabug
14babe3

📝 update docstrings
9d4a80f

merging from refactor-time
88c7493

Update src/psfmachine/perturbation.py
556317d
Co-authored-by: Jorge Martínez-Palomera <jorgemarpa@users.noreply.github.com>

adding perturbation-pca into machine
648211e

christinahedgesand others added 19 commits April 12, 2022 16:25

🎨 flake8
18fdc55

perturbed model
de15bfc

🎨 no comment block
eb9ce3c

📝 docstrings
2efb963

Merge branch 'refactor-time' ofhttps://github.com/SSDataLab/psfmachine…
f7650e5
… into machine-perturbation

time_resolution attr
70af6ac

matrix transpose hotfix
514f72b

agressive bkg pixel mask
c6ebac8

🎨 updating sane defaults, adding smooth PCA components
eaa807f

🎨 sane defaults
e1bc28e

Merge branch 'refactor-time' ofhttps://github.com/SSDataLab/psfmachine…
65ef6db
… into machine-perturbation

pca smooth time scale arg visible
9d336fb

time_resolution kwarg
ea876cc

using time_knots kwarg
12cd2a2

new time model diag plot and components API
dc1a8e6

Merge branch 'master' ofhttps://github.com/jorgemarpa/psfmachineint…
5aff7e9
…o machine-perturbation

updated lock
7ac7b71

pytest fixed
1e6b8a4

better pixel mask in build_time_model
90385d9

christinahedges reviewed Apr 29, 2022
View reviewed changes

Comment threadpyproject.toml Outdated

jorgemarpaand others added 2 commits April 29, 2022 12:37

Update pyproject.toml
5b18a7e
Co-authored-by: Christina Hedges <14965634+christinahedges@users.noreply.github.com>

bump up mac version to 1.1.2, missing docstr and removed dup fx in utils
88ca62c

jorgemarpa commented Jun 3, 2022
View reviewed changes

jorgemarpa requested a review from christinahedges June 7, 2022 18:21

christinahedges changed the title ~~[WIP] Machine uses perturbation class~~Machine uses perturbation classJun 21, 2022

christinahedges reviewed Jun 21, 2022
View reviewed changes

docstrings fixed
a6612f6

jorgemarpa mentioned this pull request Jun 22, 2022
Option to use CBVs and better priors #63
Merged
1 task

christinahedges merged commit 3784cba into SSDataLab:masterJun 28, 2022

jorgemarpa mentioned this pull request Dec 13, 2022
PSFMachine perturbation matrix needs a refactor #55
Closed

christinahedgesand others added 15 commits March 29, 2022 21:21

✨ Developing PerturbationMatrix class
05f4e26

✅ fixing flake8
172fbda

✨ added a 3D matrix
fb31d8b

🎨 fairly good sketch
d37a540

Update src/psfmachine/perturbation.py
884f24d
Co-authored-by: Jorge Martínez-Palomera <jorgemarpa@users.noreply.github.com>

Update src/psfmachine/perturbation.py
18cca59

fixing identation and _clean_vectors when segments=True
3df9bea

⚡ faster!
b64b9cc

🎨 adding pixel masking
2d55aa1

📝 added docstrings
7310ed3

smooth vector fx
34d943c

improved plots and docstrings
7648325

machine uses PerturbationMatrix3D
b330ee6

demoving _time_bin method
cc99962

normalize poscorr/centr and fixing pytest to work with new perturbati…
5e2de68
…on API

jorgemarpa force-pushed the machine-perturbation branch from 95d05bc to 5e2de68Compare April 6, 2022 19:56

christinahedges reviewed Apr 8, 2022
View reviewed changes

jorgemarpaand others added 13 commits April 11, 2022 10:58

smooth_vector API improved
cceeb2b

gaussian smooth -> spline smooth
c3cdfb1

matching arguments between perturbation and machine
e5f3f8e

✨ Added PCA method
84a064c

🎨 added fbpca explicitly as dependency
3da1557

📝 docs
1520001

merging from refactor-time
612d3fd

🐛 fixing pca
78633dc

🐛 fix@jorgemarpabug
14babe3

📝 update docstrings
9d4a80f

merging from refactor-time
88c7493

Update src/psfmachine/perturbation.py
556317d
Co-authored-by: Jorge Martínez-Palomera <jorgemarpa@users.noreply.github.com>

adding perturbation-pca into machine
648211e

christinahedgesand others added 19 commits April 12, 2022 16:25

🎨 flake8
18fdc55

perturbed model
de15bfc

🎨 no comment block
eb9ce3c

📝 docstrings
2efb963

Merge branch 'refactor-time' ofhttps://github.com/SSDataLab/psfmachine…
f7650e5
… into machine-perturbation

time_resolution attr
70af6ac

matrix transpose hotfix
514f72b

agressive bkg pixel mask
c6ebac8

🎨 updating sane defaults, adding smooth PCA components
eaa807f

🎨 sane defaults
e1bc28e

Merge branch 'refactor-time' ofhttps://github.com/SSDataLab/psfmachine…
65ef6db
… into machine-perturbation

pca smooth time scale arg visible
9d336fb

time_resolution kwarg
ea876cc

using time_knots kwarg
12cd2a2

new time model diag plot and components API
dc1a8e6

Merge branch 'master' ofhttps://github.com/jorgemarpa/psfmachineint…
5aff7e9
…o machine-perturbation

updated lock
7ac7b71

pytest fixed
1e6b8a4

better pixel mask in build_time_model
90385d9

christinahedges reviewed Apr 29, 2022
View reviewed changes

Comment threadpyproject.toml Outdated

jorgemarpaand others added 2 commits April 29, 2022 12:37

Update pyproject.toml
5b18a7e
Co-authored-by: Christina Hedges <14965634+christinahedges@users.noreply.github.com>

bump up mac version to 1.1.2, missing docstr and removed dup fx in utils
88ca62c

jorgemarpa commented Jun 3, 2022
View reviewed changes

jorgemarpa requested a review from christinahedges June 7, 2022 18:21

christinahedges changed the title ~~[WIP] Machine uses perturbation class~~Machine uses perturbation classJun 21, 2022

christinahedges reviewed Jun 21, 2022
View reviewed changes

docstrings fixed
a6612f6

jorgemarpa mentioned this pull request Jun 22, 2022
Option to use CBVs and better priors #63
Merged
1 task

christinahedges merged commit 3784cba into SSDataLab:masterJun 28, 2022

jorgemarpa mentioned this pull request Dec 13, 2022
PSFMachine perturbation matrix needs a refactor #55
Closed

christinahedgesand others added 15 commits March 29, 2022 21:21

✨ Developing PerturbationMatrix class
05f4e26

✅ fixing flake8
172fbda

✨ added a 3D matrix
fb31d8b

🎨 fairly good sketch
d37a540

Update src/psfmachine/perturbation.py
884f24d
Co-authored-by: Jorge Martínez-Palomera <jorgemarpa@users.noreply.github.com>

Update src/psfmachine/perturbation.py
18cca59

fixing identation and _clean_vectors when segments=True
3df9bea

⚡ faster!
b64b9cc

🎨 adding pixel masking
2d55aa1

📝 added docstrings
7310ed3

smooth vector fx
34d943c

improved plots and docstrings
7648325

machine uses PerturbationMatrix3D
b330ee6

demoving _time_bin method
cc99962

normalize poscorr/centr and fixing pytest to work with new perturbati…
5e2de68
…on API

jorgemarpa force-pushed the machine-perturbation branch from 95d05bc to 5e2de68Compare April 6, 2022 19:56

christinahedges reviewed Apr 8, 2022
View reviewed changes

jorgemarpaand others added 13 commits April 11, 2022 10:58

smooth_vector API improved
cceeb2b

gaussian smooth -> spline smooth
c3cdfb1

matching arguments between perturbation and machine
e5f3f8e

✨ Added PCA method
84a064c

🎨 added fbpca explicitly as dependency
3da1557

📝 docs
1520001

merging from refactor-time
612d3fd

🐛 fixing pca
78633dc

🐛 fix@jorgemarpabug
14babe3

📝 update docstrings
9d4a80f

merging from refactor-time
88c7493

Update src/psfmachine/perturbation.py
556317d
Co-authored-by: Jorge Martínez-Palomera <jorgemarpa@users.noreply.github.com>

adding perturbation-pca into machine
648211e

christinahedgesand others added 19 commits April 12, 2022 16:25

🎨 flake8
18fdc55

perturbed model
de15bfc

🎨 no comment block
eb9ce3c

📝 docstrings
2efb963

Merge branch 'refactor-time' ofhttps://github.com/SSDataLab/psfmachine…
f7650e5
… into machine-perturbation

time_resolution attr
70af6ac

matrix transpose hotfix
514f72b

agressive bkg pixel mask
c6ebac8

🎨 updating sane defaults, adding smooth PCA components
eaa807f

🎨 sane defaults
e1bc28e

Merge branch 'refactor-time' ofhttps://github.com/SSDataLab/psfmachine…
65ef6db
… into machine-perturbation

pca smooth time scale arg visible
9d336fb

time_resolution kwarg
ea876cc

using time_knots kwarg
12cd2a2

new time model diag plot and components API
dc1a8e6

Merge branch 'master' ofhttps://github.com/jorgemarpa/psfmachineint…
5aff7e9
…o machine-perturbation

updated lock
7ac7b71

pytest fixed
1e6b8a4

better pixel mask in build_time_model
90385d9

christinahedges reviewed Apr 29, 2022
View reviewed changes

Comment threadpyproject.toml Outdated

jorgemarpaand others added 2 commits April 29, 2022 12:37

Update pyproject.toml
5b18a7e
Co-authored-by: Christina Hedges <14965634+christinahedges@users.noreply.github.com>

bump up mac version to 1.1.2, missing docstr and removed dup fx in utils
88ca62c

jorgemarpa commented Jun 3, 2022
View reviewed changes

jorgemarpa requested a review from christinahedges June 7, 2022 18:21

christinahedges changed the title ~~[WIP] Machine uses perturbation class~~Machine uses perturbation classJun 21, 2022

christinahedges reviewed Jun 21, 2022
View reviewed changes

docstrings fixed
a6612f6

jorgemarpa mentioned this pull request Jun 22, 2022
Option to use CBVs and better priors #63
Merged
1 task

christinahedges merged commit 3784cba into SSDataLab:masterJun 28, 2022

jorgemarpa mentioned this pull request Dec 13, 2022
PSFMachine perturbation matrix needs a refactor #55
Closed

christinahedgesand others added 15 commits March 29, 2022 21:21

✨ Developing PerturbationMatrix class
05f4e26

✅ fixing flake8
172fbda

✨ added a 3D matrix
fb31d8b

🎨 fairly good sketch
d37a540

Update src/psfmachine/perturbation.py
884f24d
Co-authored-by: Jorge Martínez-Palomera <jorgemarpa@users.noreply.github.com>

Update src/psfmachine/perturbation.py
18cca59

fixing identation and _clean_vectors when segments=True
3df9bea

⚡ faster!
b64b9cc

🎨 adding pixel masking
2d55aa1

📝 added docstrings
7310ed3

smooth vector fx
34d943c

improved plots and docstrings
7648325

machine uses PerturbationMatrix3D
b330ee6

demoving _time_bin method
cc99962

normalize poscorr/centr and fixing pytest to work with new perturbati…
5e2de68
…on API

jorgemarpa force-pushed the machine-perturbation branch from 95d05bc to 5e2de68Compare April 6, 2022 19:56

christinahedges reviewed Apr 8, 2022
View reviewed changes

jorgemarpaand others added 13 commits April 11, 2022 10:58

smooth_vector API improved
cceeb2b

gaussian smooth -> spline smooth
c3cdfb1

matching arguments between perturbation and machine
e5f3f8e

✨ Added PCA method
84a064c

🎨 added fbpca explicitly as dependency
3da1557

📝 docs
1520001

merging from refactor-time
612d3fd

🐛 fixing pca
78633dc

🐛 fix@jorgemarpabug
14babe3

📝 update docstrings
9d4a80f

merging from refactor-time
88c7493

Update src/psfmachine/perturbation.py
556317d
Co-authored-by: Jorge Martínez-Palomera <jorgemarpa@users.noreply.github.com>

adding perturbation-pca into machine
648211e

christinahedgesand others added 19 commits April 12, 2022 16:25

🎨 flake8
18fdc55

perturbed model
de15bfc

🎨 no comment block
eb9ce3c

📝 docstrings
2efb963

Merge branch 'refactor-time' ofhttps://github.com/SSDataLab/psfmachine…
f7650e5
… into machine-perturbation

time_resolution attr
70af6ac

matrix transpose hotfix
514f72b

agressive bkg pixel mask
c6ebac8

🎨 updating sane defaults, adding smooth PCA components
eaa807f

🎨 sane defaults
e1bc28e

Merge branch 'refactor-time' ofhttps://github.com/SSDataLab/psfmachine…
65ef6db
… into machine-perturbation

pca smooth time scale arg visible
9d336fb

time_resolution kwarg
ea876cc

using time_knots kwarg
12cd2a2

new time model diag plot and components API
dc1a8e6

Merge branch 'master' ofhttps://github.com/jorgemarpa/psfmachineint…
5aff7e9
…o machine-perturbation

updated lock
7ac7b71

pytest fixed
1e6b8a4

better pixel mask in build_time_model
90385d9

christinahedges reviewed Apr 29, 2022
View reviewed changes

Comment threadpyproject.toml Outdated

jorgemarpaand others added 2 commits April 29, 2022 12:37

Update pyproject.toml
5b18a7e
Co-authored-by: Christina Hedges <14965634+christinahedges@users.noreply.github.com>

bump up mac version to 1.1.2, missing docstr and removed dup fx in utils
88ca62c

jorgemarpa commented Jun 3, 2022
View reviewed changes

jorgemarpa requested a review from christinahedges June 7, 2022 18:21

christinahedges changed the title ~~[WIP] Machine uses perturbation class~~Machine uses perturbation classJun 21, 2022

christinahedges reviewed Jun 21, 2022
View reviewed changes

docstrings fixed
a6612f6

jorgemarpa mentioned this pull request Jun 22, 2022
Option to use CBVs and better priors #63
Merged
1 task

christinahedges merged commit 3784cba into SSDataLab:masterJun 28, 2022

jorgemarpa mentioned this pull request Dec 13, 2022
PSFMachine perturbation matrix needs a refactor #55
Closed

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jorgemarpa commented Apr 6, 2022• edited Loading Uh oh! There was an error while loading. Please reload this page.

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jorgemarpa commented Apr 6, 2022•
edited
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jorgemarpa commented Apr 6, 2022•
edited
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jorgemarpa commented Apr 6, 2022•
edited
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jorgemarpa commented Apr 6, 2022•
edited
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