Fitting time model for intra-quarter segments - #52

Merged
christinahedges merged 6 commits into
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jorgemarpa:segment-time-model
Mar 28, 2022
Merged

Fitting time model for intra-quarter segments #52
christinahedges merged 6 commits into
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jorgemarpa:segment-time-model

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@jorgemarpajorgemarpa commented Mar 15, 2022•
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This PR allows fitting different time models to light curve segments inside a quarter by using a common shape model and pixel lightcurve normalization.
It finds how many segments are in the quarter by finding discontinuities in the time data. Then iterates over these segments to build and fit time models accordingly.

The build_time_model() takes the split_models argument (boolean) to split or not by segments.
The plot_time_model() method takes the segment argument to select which segment to plot.

I fixed the downsampling in _time_bin() to capture the start/end of each segment. This fix makes the one pytest fail. Need to see what's going on there.

TODO:

  • Maybe split_models argument could also accept an array of indexes for user-custom splits
  • Fix pytest fail for _time_bin()

@jorgemarpajorgemarpa added the enhancement New feature or request label Mar 15, 2022
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We're going to have to think about how to test this functionality...!

Comment threadsrc/psfmachine/machine.py Outdated
Comment threadsrc/psfmachine/machine.py
Comment threadsrc/psfmachine/machine.py Outdated
Comment threadsrc/psfmachine/machine.py Outdated
Comment threadsrc/psfmachine/machine.py Outdated
Comment threadsrc/psfmachine/machine.py Outdated
Comment threadsrc/psfmachine/machine.py Outdated
Comment threadsrc/psfmachine/machine.py Outdated
Comment threadsrc/psfmachine/machine.py
Comment threadsrc/psfmachine/machine.py
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I fixed the pytest to take into account the normalization of the centroids/poscorrs.

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This is really great functionality. I think this is done neatly, within the API we have. I do believe we could do with a refactor here in future. A, A_cp, A2, and A3` are getting confusing, and we have no way to build the perturbed model for a given time easily. (see #55)

However, I think that's really for future work. I think this is what we need to get the functionality we need, and we'll look into a refactor in future.

Comment threadsrc/psfmachine/machine.py Outdated
.astype(int)
)
# use breaks as downsample points
dwns_idx = breaks

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Seems not necessary?

Comment threadsrc/psfmachine/machine.py Outdated
Comment threadsrc/psfmachine/machine.py Outdated
Comment threadsrc/psfmachine/machine.py Outdated

# No saturated pixels
k = (
(flux_binned_raw < 1.4e5).all(axis=0)[None, :]

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Hard coded value here...might be fine?

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We can "inflate" this mask by ~2 pixel in the row dimension in order to ensure that we are not getting any ends of bleed columns. I think that would really help us in future. However, that might not belong in this PR!

Comment threadsrc/psfmachine/machine.py Outdated
jorgemarpaand others added 3 commits March 24, 2022 12:33
@christinahedges
christinahedges merged commit 0e05097 into SSDataLab:masterMar 28, 2022
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jorgemarpa deleted the segment-time-model branch April 29, 2022 23:56
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, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
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}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

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Fitting time model for intra-quarter segments  - #52
Merged
christinahedges merged 6 commits into
SSDataLab:masterfrom 
jorgemarpa:segment-time-model
Mar 28, 2022
Merged
Fitting time model for intra-quarter segments #52
christinahedges merged 6 commits into
SSDataLab:masterfrom 
jorgemarpa:segment-time-model
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@jorgemarpa
@jorgemarpajorgemarpa
commented
Mar 15, 2022•

edited

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This PR allows fitting different time models to light curve segments inside a quarter by using a common shape model and pixel lightcurve normalization.

It finds how many segments are in the quarter by finding discontinuities in the time data. Then iterates over these segments to build and fit time models accordingly.
The build_time_model() takes the split_models argument (boolean) to split or not by segments.

The plot_time_model() method takes the segment argument to select which segment to plot.
I fixed the downsampling in _time_bin() to capture the start/end of each segment. This fix makes the one pytest fail. Need to see what's going on there.
TODO:
  •  Maybe split_models argument could also accept an array of indexes for user-custom splits
  •  Fix pytest fail for _time_bin()
@jorgemarpajorgemarpa
added
the 
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We're going to have to think about how to test this functionality...!
Comment threadsrc/psfmachine/machine.py
Outdated

Comment threadsrc/psfmachine/machine.py
Comment threadsrc/psfmachine/machine.py
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Comment threadsrc/psfmachine/machine.py
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Comment threadsrc/psfmachine/machine.py
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Comment threadsrc/psfmachine/machine.py
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Comment threadsrc/psfmachine/machine.py
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Comment threadsrc/psfmachine/machine.py
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Comment threadsrc/psfmachine/machine.py
Comment threadsrc/psfmachine/machine.py
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I fixed the pytest to take into account the normalization of the centroids/poscorrs.
christinahedges
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This is really great functionality. I think this is done neatly, within the API we have. I do believe we could do with a refactor here in future. A, A_cp, A2, and A3` are getting confusing, and we have no way to build the perturbed model for a given time easily. (see #55)
However, I think that's really for future work. I think this is what we need to get the functionality we need, and we'll look into a refactor in future.
Comment threadsrc/psfmachine/machine.py
Outdated

 .astype(int)
 )
 # use breaks as downsample points
 dwns_idx = breaks
@christinahedgeschristinahedgesMar 24, 2022

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Seems not necessary?
Comment threadsrc/psfmachine/machine.py
Outdated

Comment threadsrc/psfmachine/machine.py
Outdated

Comment threadsrc/psfmachine/machine.py
Outdated


 # No saturated pixels
 k = (
 (flux_binned_raw < 1.4e5).all(axis=0)[None, :]
@christinahedgeschristinahedgesMar 24, 2022

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Hard coded value here...might be fine?
@christinahedgeschristinahedgesMar 24, 2022

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We can "inflate" this mask by ~2 pixel in the row dimension in order to ensure that we are not getting any ends of bleed columns. I think that would really help us in future. However, that might not belong in this PR!
Comment threadsrc/psfmachine/machine.py
Outdated

jorgemarpaand others
added 3 commits
March 24, 2022 12:33
@christinahedges
christinahedges
merged commit 0e05097
into
SSDataLab:masterMar 28, 2022
@jorgemarpa
jorgemarpa
deleted the

segment-time-model

branch
April 29, 2022 23:56
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if (__m === '*' || __re.test(location.href)) {
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})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Fitting time model for intra-quarter segments  - #52
Merged
christinahedges merged 6 commits into
SSDataLab:masterfrom 
jorgemarpa:segment-time-model
Mar 28, 2022
Merged
Fitting time model for intra-quarter segments #52
christinahedges merged 6 commits into
SSDataLab:masterfrom 
jorgemarpa:segment-time-model
Conversation
@jorgemarpa
@jorgemarpajorgemarpa
commented
Mar 15, 2022•

edited

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This PR allows fitting different time models to light curve segments inside a quarter by using a common shape model and pixel lightcurve normalization.

It finds how many segments are in the quarter by finding discontinuities in the time data. Then iterates over these segments to build and fit time models accordingly.
The build_time_model() takes the split_models argument (boolean) to split or not by segments.

The plot_time_model() method takes the segment argument to select which segment to plot.
I fixed the downsampling in _time_bin() to capture the start/end of each segment. This fix makes the one pytest fail. Need to see what's going on there.
TODO:
  •  Maybe split_models argument could also accept an array of indexes for user-custom splits
  •  Fix pytest fail for _time_bin()
@jorgemarpajorgemarpa
added
the 
enhancement
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christinahedges
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reviewed
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We're going to have to think about how to test this functionality...!
Comment threadsrc/psfmachine/machine.py
Outdated

Comment threadsrc/psfmachine/machine.py
Comment threadsrc/psfmachine/machine.py
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Comment threadsrc/psfmachine/machine.py
Outdated

Comment threadsrc/psfmachine/machine.py
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Comment threadsrc/psfmachine/machine.py
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Comment threadsrc/psfmachine/machine.py
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Comment threadsrc/psfmachine/machine.py
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Comment threadsrc/psfmachine/machine.py
Comment threadsrc/psfmachine/machine.py
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@jorgemarpa
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commented
Mar 22, 2022

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I fixed the pytest to take into account the normalization of the centroids/poscorrs.
christinahedges
christinahedges
reviewed
Mar 24, 2022
View reviewed changes
@christinahedgeschristinahedges
left a comment
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edited

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This is really great functionality. I think this is done neatly, within the API we have. I do believe we could do with a refactor here in future. A, A_cp, A2, and A3` are getting confusing, and we have no way to build the perturbed model for a given time easily. (see #55)
However, I think that's really for future work. I think this is what we need to get the functionality we need, and we'll look into a refactor in future.
Comment threadsrc/psfmachine/machine.py
Outdated

 .astype(int)
 )
 # use breaks as downsample points
 dwns_idx = breaks
@christinahedgeschristinahedgesMar 24, 2022

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Seems not necessary?
Comment threadsrc/psfmachine/machine.py
Outdated

Comment threadsrc/psfmachine/machine.py
Outdated

Comment threadsrc/psfmachine/machine.py
Outdated


 # No saturated pixels
 k = (
 (flux_binned_raw < 1.4e5).all(axis=0)[None, :]
@christinahedgeschristinahedgesMar 24, 2022

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Hard coded value here...might be fine?
@christinahedgeschristinahedgesMar 24, 2022

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We can "inflate" this mask by ~2 pixel in the row dimension in order to ensure that we are not getting any ends of bleed columns. I think that would really help us in future. However, that might not belong in this PR!
Comment threadsrc/psfmachine/machine.py
Outdated

jorgemarpaand others
added 3 commits
March 24, 2022 12:33
@christinahedges
christinahedges
merged commit 0e05097
into
SSDataLab:masterMar 28, 2022
@jorgemarpa
jorgemarpa
deleted the

segment-time-model

branch
April 29, 2022 23:56
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms");
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})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Fitting time model for intra-quarter segments  - #52
Merged
christinahedges merged 6 commits into
SSDataLab:masterfrom 
jorgemarpa:segment-time-model
Mar 28, 2022
Merged
Fitting time model for intra-quarter segments #52
christinahedges merged 6 commits into
SSDataLab:masterfrom 
jorgemarpa:segment-time-model
Conversation
@jorgemarpa
@jorgemarpajorgemarpa
commented
Mar 15, 2022•

edited

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This PR allows fitting different time models to light curve segments inside a quarter by using a common shape model and pixel lightcurve normalization.

It finds how many segments are in the quarter by finding discontinuities in the time data. Then iterates over these segments to build and fit time models accordingly.
The build_time_model() takes the split_models argument (boolean) to split or not by segments.

The plot_time_model() method takes the segment argument to select which segment to plot.
I fixed the downsampling in _time_bin() to capture the start/end of each segment. This fix makes the one pytest fail. Need to see what's going on there.
TODO:
  •  Maybe split_models argument could also accept an array of indexes for user-custom splits
  •  Fix pytest fail for _time_bin()
@jorgemarpajorgemarpa
added
the 
enhancement
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christinahedges
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We're going to have to think about how to test this functionality...!
Comment threadsrc/psfmachine/machine.py
Outdated

Comment threadsrc/psfmachine/machine.py
Comment threadsrc/psfmachine/machine.py
Outdated

Comment threadsrc/psfmachine/machine.py
Outdated

Comment threadsrc/psfmachine/machine.py
Outdated

Comment threadsrc/psfmachine/machine.py
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Comment threadsrc/psfmachine/machine.py
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Comment threadsrc/psfmachine/machine.py
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Comment threadsrc/psfmachine/machine.py
Comment threadsrc/psfmachine/machine.py
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I fixed the pytest to take into account the normalization of the centroids/poscorrs.
christinahedges
christinahedges
reviewed
Mar 24, 2022
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This is really great functionality. I think this is done neatly, within the API we have. I do believe we could do with a refactor here in future. A, A_cp, A2, and A3` are getting confusing, and we have no way to build the perturbed model for a given time easily. (see #55)
However, I think that's really for future work. I think this is what we need to get the functionality we need, and we'll look into a refactor in future.
Comment threadsrc/psfmachine/machine.py
Outdated

 .astype(int)
 )
 # use breaks as downsample points
 dwns_idx = breaks
@christinahedgeschristinahedgesMar 24, 2022

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Seems not necessary?
Comment threadsrc/psfmachine/machine.py
Outdated

Comment threadsrc/psfmachine/machine.py
Outdated

Comment threadsrc/psfmachine/machine.py
Outdated


 # No saturated pixels
 k = (
 (flux_binned_raw < 1.4e5).all(axis=0)[None, :]
@christinahedgeschristinahedgesMar 24, 2022

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Hard coded value here...might be fine?
@christinahedgeschristinahedgesMar 24, 2022

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We can "inflate" this mask by ~2 pixel in the row dimension in order to ensure that we are not getting any ends of bleed columns. I think that would really help us in future. However, that might not belong in this PR!
Comment threadsrc/psfmachine/machine.py
Outdated

jorgemarpaand others
added 3 commits
March 24, 2022 12:33
@christinahedges
christinahedges
merged commit 0e05097
into
SSDataLab:masterMar 28, 2022
@jorgemarpa
jorgemarpa
deleted the

segment-time-model

branch
April 29, 2022 23:56
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, 'i');
if (__m === '*' || __re.test(location.href)) {
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(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

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Fitting time model for intra-quarter segments  - #52
Merged
christinahedges merged 6 commits into
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jorgemarpa:segment-time-model
Mar 28, 2022
Merged
Fitting time model for intra-quarter segments #52
christinahedges merged 6 commits into
SSDataLab:masterfrom 
jorgemarpa:segment-time-model
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Mar 15, 2022•

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This PR allows fitting different time models to light curve segments inside a quarter by using a common shape model and pixel lightcurve normalization.

It finds how many segments are in the quarter by finding discontinuities in the time data. Then iterates over these segments to build and fit time models accordingly.
The build_time_model() takes the split_models argument (boolean) to split or not by segments.

The plot_time_model() method takes the segment argument to select which segment to plot.
I fixed the downsampling in _time_bin() to capture the start/end of each segment. This fix makes the one pytest fail. Need to see what's going on there.
TODO:
  •  Maybe split_models argument could also accept an array of indexes for user-custom splits
  •  Fix pytest fail for _time_bin()
@jorgemarpajorgemarpa
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We're going to have to think about how to test this functionality...!
Comment threadsrc/psfmachine/machine.py
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Comment threadsrc/psfmachine/machine.py
Comment threadsrc/psfmachine/machine.py
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Comment threadsrc/psfmachine/machine.py
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Comment threadsrc/psfmachine/machine.py
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Comment threadsrc/psfmachine/machine.py
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Comment threadsrc/psfmachine/machine.py
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Comment threadsrc/psfmachine/machine.py
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Comment threadsrc/psfmachine/machine.py
Comment threadsrc/psfmachine/machine.py
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I fixed the pytest to take into account the normalization of the centroids/poscorrs.
christinahedges
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This is really great functionality. I think this is done neatly, within the API we have. I do believe we could do with a refactor here in future. A, A_cp, A2, and A3` are getting confusing, and we have no way to build the perturbed model for a given time easily. (see #55)
However, I think that's really for future work. I think this is what we need to get the functionality we need, and we'll look into a refactor in future.
Comment threadsrc/psfmachine/machine.py
Outdated

 .astype(int)
 )
 # use breaks as downsample points
 dwns_idx = breaks
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Seems not necessary?
Comment threadsrc/psfmachine/machine.py
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Comment threadsrc/psfmachine/machine.py
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Comment threadsrc/psfmachine/machine.py
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 # No saturated pixels
 k = (
 (flux_binned_raw < 1.4e5).all(axis=0)[None, :]
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Hard coded value here...might be fine?
@christinahedgeschristinahedgesMar 24, 2022

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We can "inflate" this mask by ~2 pixel in the row dimension in order to ensure that we are not getting any ends of bleed columns. I think that would really help us in future. However, that might not belong in this PR!
Comment threadsrc/psfmachine/machine.py
Outdated

jorgemarpaand others
added 3 commits
March 24, 2022 12:33
@christinahedges
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merged commit 0e05097
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@jorgemarpa
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deleted the

segment-time-model

branch
April 29, 2022 23:56
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Fitting time model for intra-quarter segments  - #52
Merged
christinahedges merged 6 commits into
SSDataLab:masterfrom 
jorgemarpa:segment-time-model
Mar 28, 2022
Merged
Fitting time model for intra-quarter segments #52
christinahedges merged 6 commits into
SSDataLab:masterfrom 
jorgemarpa:segment-time-model
Conversation
@jorgemarpa
@jorgemarpajorgemarpa
commented
Mar 15, 2022•

edited

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This PR allows fitting different time models to light curve segments inside a quarter by using a common shape model and pixel lightcurve normalization.

It finds how many segments are in the quarter by finding discontinuities in the time data. Then iterates over these segments to build and fit time models accordingly.
The build_time_model() takes the split_models argument (boolean) to split or not by segments.

The plot_time_model() method takes the segment argument to select which segment to plot.
I fixed the downsampling in _time_bin() to capture the start/end of each segment. This fix makes the one pytest fail. Need to see what's going on there.
TODO:
  •  Maybe split_models argument could also accept an array of indexes for user-custom splits
  •  Fix pytest fail for _time_bin()
@jorgemarpajorgemarpa
added
the 
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We're going to have to think about how to test this functionality...!
Comment threadsrc/psfmachine/machine.py
Outdated

Comment threadsrc/psfmachine/machine.py
Comment threadsrc/psfmachine/machine.py
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Comment threadsrc/psfmachine/machine.py
Outdated

Comment threadsrc/psfmachine/machine.py
Outdated

Comment threadsrc/psfmachine/machine.py
Outdated

Comment threadsrc/psfmachine/machine.py
Outdated

Comment threadsrc/psfmachine/machine.py
Outdated

Comment threadsrc/psfmachine/machine.py
Comment threadsrc/psfmachine/machine.py
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I fixed the pytest to take into account the normalization of the centroids/poscorrs.
christinahedges
christinahedges
reviewed
Mar 24, 2022
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This is really great functionality. I think this is done neatly, within the API we have. I do believe we could do with a refactor here in future. A, A_cp, A2, and A3` are getting confusing, and we have no way to build the perturbed model for a given time easily. (see #55)
However, I think that's really for future work. I think this is what we need to get the functionality we need, and we'll look into a refactor in future.
Comment threadsrc/psfmachine/machine.py
Outdated

 .astype(int)
 )
 # use breaks as downsample points
 dwns_idx = breaks
@christinahedgeschristinahedgesMar 24, 2022

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Seems not necessary?
Comment threadsrc/psfmachine/machine.py
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Comment threadsrc/psfmachine/machine.py
Outdated

Comment threadsrc/psfmachine/machine.py
Outdated


 # No saturated pixels
 k = (
 (flux_binned_raw < 1.4e5).all(axis=0)[None, :]
@christinahedgeschristinahedgesMar 24, 2022

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Hard coded value here...might be fine?
@christinahedgeschristinahedgesMar 24, 2022

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We can "inflate" this mask by ~2 pixel in the row dimension in order to ensure that we are not getting any ends of bleed columns. I think that would really help us in future. However, that might not belong in this PR!
Comment threadsrc/psfmachine/machine.py
Outdated

jorgemarpaand others
added 3 commits
March 24, 2022 12:33
@christinahedges
christinahedges
merged commit 0e05097
into
SSDataLab:masterMar 28, 2022
@jorgemarpa
jorgemarpa
deleted the

segment-time-model

branch
April 29, 2022 23:56
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers");
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Fitting time model for intra-quarter segments  - #52
Merged
christinahedges merged 6 commits into
SSDataLab:masterfrom 
jorgemarpa:segment-time-model
Mar 28, 2022
Merged
Fitting time model for intra-quarter segments #52
christinahedges merged 6 commits into
SSDataLab:masterfrom 
jorgemarpa:segment-time-model
Conversation
@jorgemarpa
@jorgemarpajorgemarpa
commented
Mar 15, 2022•

edited

Loading

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Contributor
This PR allows fitting different time models to light curve segments inside a quarter by using a common shape model and pixel lightcurve normalization.

It finds how many segments are in the quarter by finding discontinuities in the time data. Then iterates over these segments to build and fit time models accordingly.
The build_time_model() takes the split_models argument (boolean) to split or not by segments.

The plot_time_model() method takes the segment argument to select which segment to plot.
I fixed the downsampling in _time_bin() to capture the start/end of each segment. This fix makes the one pytest fail. Need to see what's going on there.
TODO:
  •  Maybe split_models argument could also accept an array of indexes for user-custom splits
  •  Fix pytest fail for _time_bin()
@jorgemarpajorgemarpa
added
the 
enhancement
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label
Mar 15, 2022
christinahedges
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reviewed
Mar 15, 2022
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We're going to have to think about how to test this functionality...!
Comment threadsrc/psfmachine/machine.py
Outdated

Comment threadsrc/psfmachine/machine.py
Comment threadsrc/psfmachine/machine.py
Outdated

Comment threadsrc/psfmachine/machine.py
Outdated

Comment threadsrc/psfmachine/machine.py
Outdated

Comment threadsrc/psfmachine/machine.py
Outdated

Comment threadsrc/psfmachine/machine.py
Outdated

Comment threadsrc/psfmachine/machine.py
Outdated

Comment threadsrc/psfmachine/machine.py
Comment threadsrc/psfmachine/machine.py
@jorgemarpajorgemarpa
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Mar 16, 2022
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Mar 22, 2022

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I fixed the pytest to take into account the normalization of the centroids/poscorrs.
christinahedges
christinahedges
reviewed
Mar 24, 2022
View reviewed changes
@christinahedgeschristinahedges
left a comment
•

edited

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This is really great functionality. I think this is done neatly, within the API we have. I do believe we could do with a refactor here in future. A, A_cp, A2, and A3` are getting confusing, and we have no way to build the perturbed model for a given time easily. (see #55)
However, I think that's really for future work. I think this is what we need to get the functionality we need, and we'll look into a refactor in future.
Comment threadsrc/psfmachine/machine.py
Outdated

 .astype(int)
 )
 # use breaks as downsample points
 dwns_idx = breaks
@christinahedgeschristinahedgesMar 24, 2022

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Seems not necessary?
Comment threadsrc/psfmachine/machine.py
Outdated

Comment threadsrc/psfmachine/machine.py
Outdated

Comment threadsrc/psfmachine/machine.py
Outdated


 # No saturated pixels
 k = (
 (flux_binned_raw < 1.4e5).all(axis=0)[None, :]
@christinahedgeschristinahedgesMar 24, 2022

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Hard coded value here...might be fine?
@christinahedgeschristinahedgesMar 24, 2022

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We can "inflate" this mask by ~2 pixel in the row dimension in order to ensure that we are not getting any ends of bleed columns. I think that would really help us in future. However, that might not belong in this PR!
Comment threadsrc/psfmachine/machine.py
Outdated

jorgemarpaand others
added 3 commits
March 24, 2022 12:33
@christinahedges
christinahedges
merged commit 0e05097
into
SSDataLab:masterMar 28, 2022
@jorgemarpa
jorgemarpa
deleted the

segment-time-model

branch
April 29, 2022 23:56
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode");
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();

Skip to content
Fitting time model for intra-quarter segments  - #52
Merged
christinahedges merged 6 commits into
SSDataLab:masterfrom 
jorgemarpa:segment-time-model
Mar 28, 2022
Merged
Fitting time model for intra-quarter segments #52
christinahedges merged 6 commits into
SSDataLab:masterfrom 
jorgemarpa:segment-time-model
Conversation
@jorgemarpa
@jorgemarpajorgemarpa
commented
Mar 15, 2022•

edited

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This PR allows fitting different time models to light curve segments inside a quarter by using a common shape model and pixel lightcurve normalization.

It finds how many segments are in the quarter by finding discontinuities in the time data. Then iterates over these segments to build and fit time models accordingly.
The build_time_model() takes the split_models argument (boolean) to split or not by segments.

The plot_time_model() method takes the segment argument to select which segment to plot.
I fixed the downsampling in _time_bin() to capture the start/end of each segment. This fix makes the one pytest fail. Need to see what's going on there.
TODO:
  •  Maybe split_models argument could also accept an array of indexes for user-custom splits
  •  Fix pytest fail for _time_bin()
@jorgemarpajorgemarpa
added
the 
enhancement
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christinahedges
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reviewed
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We're going to have to think about how to test this functionality...!
Comment threadsrc/psfmachine/machine.py
Outdated

Comment threadsrc/psfmachine/machine.py
Comment threadsrc/psfmachine/machine.py
Outdated

Comment threadsrc/psfmachine/machine.py
Outdated

Comment threadsrc/psfmachine/machine.py
Outdated

Comment threadsrc/psfmachine/machine.py
Outdated

Comment threadsrc/psfmachine/machine.py
Outdated

Comment threadsrc/psfmachine/machine.py
Outdated

Comment threadsrc/psfmachine/machine.py
Comment threadsrc/psfmachine/machine.py
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Mar 22, 2022

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I fixed the pytest to take into account the normalization of the centroids/poscorrs.
christinahedges
christinahedges
reviewed
Mar 24, 2022
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This is really great functionality. I think this is done neatly, within the API we have. I do believe we could do with a refactor here in future. A, A_cp, A2, and A3` are getting confusing, and we have no way to build the perturbed model for a given time easily. (see #55)
However, I think that's really for future work. I think this is what we need to get the functionality we need, and we'll look into a refactor in future.
Comment threadsrc/psfmachine/machine.py
Outdated

 .astype(int)
 )
 # use breaks as downsample points
 dwns_idx = breaks
@christinahedgeschristinahedgesMar 24, 2022

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Seems not necessary?
Comment threadsrc/psfmachine/machine.py
Outdated

Comment threadsrc/psfmachine/machine.py
Outdated

Comment threadsrc/psfmachine/machine.py
Outdated


 # No saturated pixels
 k = (
 (flux_binned_raw < 1.4e5).all(axis=0)[None, :]
@christinahedgeschristinahedgesMar 24, 2022

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Hard coded value here...might be fine?
@christinahedgeschristinahedgesMar 24, 2022

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We can "inflate" this mask by ~2 pixel in the row dimension in order to ensure that we are not getting any ends of bleed columns. I think that would really help us in future. However, that might not belong in this PR!
Comment threadsrc/psfmachine/machine.py
Outdated

jorgemarpaand others
added 3 commits
March 24, 2022 12:33
@christinahedges
christinahedges
merged commit 0e05097
into
SSDataLab:masterMar 28, 2022
@jorgemarpa
jorgemarpa
deleted the

segment-time-model

branch
April 29, 2022 23:56
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