legacy code to port - #48

Closed
LucaMarconato wants to merge 48 commits into
mainfrom
feature/transform_and_coord_spaces
Closed

legacy code to port#48
LucaMarconato wants to merge 48 commits into
mainfrom
feature/transform_and_coord_spaces

Conversation

@LucaMarconato

@LucaMarconatoLucaMarconato commented Nov 2, 2022•
edited
Loading

Copy link
Copy Markdown
Member

Merge postponed.
Before merging (an updated version of) this pr, the following will be isolated in a separate pr, improved, and merged.

  • coordinate systems
  • coordinate transformations
  • io branch from @giovp

About this pr.

This pull request implements a first working version of coordinate systems, transformations, as long as all what spatialdata needs to perform basic io operatations with its elements. Spatialdata-sandbox and napari_spatialdata support this branch. They will also need to be adapted to the new improved code described in the incremental prs listed above.

giovpand others added 30 commits August 17, 2022 09:05
@giovp
add io test
cb4ddf6
@LucaMarconato
io for transforms, fixed bugs when testing on the merfish dataset
0981821
@LucaMarconato
merged with main
707f047
@LucaMarconato
bugfix
b7cb647
@LucaMarconato
fixed tests
561d252
@LucaMarconato
Merge branch 'tests/io' into feature/transform
b10419c
@giovp@pre-commit-ci
add io test (#21)
31525d0
* add io test
* [pre-commit.ci] pre-commit autoupdate (#13)
updates:
- [github.com/asottile/yesqa: v1.3.0 → v1.4.0](asottile/yesqa@v1.3.0...v1.4.0)
- [github.com/PyCQA/flake8: 5.0.1 → 5.0.4](PyCQA/flake8@5.0.1...5.0.4)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@LucaMarconato
workaround against bug with backed dask arrays
140198f
@LucaMarconato
Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
5764882
…ldata into feature/transform
@LucaMarconato
woring on a bug with io; fixed repr for points
7ece121
@LucaMarconato
quick code changes for to_zarr bug report
ce23cb7
@LucaMarconato
patched tests after discussion on the to_zarr bug
67c1d7a
see discussion here ome/ome-zarr-py#219
@LucaMarconato
more io tests, fixed related bugs
6221fa2
@LucaMarconato
first io support for polygons
f36ed27
@giovp
fix precommits
087600d
@giovp
fix flake8
14c4cd0
@LucaMarconato
wip implementation of the ngff transform
98cd743
@LucaMarconato
Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
f8517d7
…ldata into feature/transform
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
ba85569
for more information, see https://pre-commit.ci
@LucaMarconato
wip transformations, tests pass but io not compatible
3db58b7
@LucaMarconato
Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
b694423
…ldata into feature/transform
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
db61de8
for more information, see https://pre-commit.ci
@LucaMarconato
wip write for new transforms specs
3a83b21
@LucaMarconato
Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
569abdd
…ldata into feature/transform
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
018f290
for more information, see https://pre-commit.ci
@LucaMarconato
fstring in format.py
833bb5c
@LucaMarconato
Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
ccfe5e9
…ldata into feature/transform
@LucaMarconato
fix in format.py
8460500
@LucaMarconato
io working for the new transform specs (no coord spaces yet)
f00f7fd
@LucaMarconato
fix in affine
983b638
LucaMarconatoand others added 18 commits October 3, 2022 21:13
@LucaMarconato
new constructor accepting base elements
670b104
@LucaMarconato
Merge branch 'feature/coordspaces' into feature/transform_and_coord_s…
aaeea79
…paces
@LucaMarconato
wip support for coordinate systems and multiple transformations
1bcff01
@LucaMarconato
wip coordinate spaces
0271f19
@LucaMarconato
io with multiple trans and coord systems working for points and polygons
22f249e
@LucaMarconato
io with multiple trans and coord systems for images
d321be4
@LucaMarconato
io with multiple trans and coord sys fully working
d0a91cb
@LucaMarconato
napari viz working
1ee47fe
@LucaMarconato
filtering by coordinate spaces
bb9a862
@LucaMarconato
bidirectional communication with napari
054c5cd
@LucaMarconato
bugfixes; bug in axes order still present
4f2bb0c
@LucaMarconato
run some precommits
80ec3a7
@LucaMarconato
fixed axes bug, simplified constructor
2756e4a
@LucaMarconato
moved geojson parser in spatialdata-io
176f909
@LucaMarconato
added cli for peeking .zarr files
e78a168
@LucaMarconato
support for multiscale images and labels
22c6e9a
@LucaMarconato
fix with multiscales
4e80b0e
@LucaMarconato
fix bug polygon; workaround dask .chunks
1990172
@LucaMarconatoLucaMarconato changed the title enough features for the first applicationsenough features for the first applications (wip)Nov 2, 2022
@LucaMarconatoLucaMarconato mentioned this pull request Nov 30, 2022
Closed
@kevinyamauchi

kevinyamauchi commented Dec 13, 2022•
edited
Loading

Copy link
Copy Markdown
Collaborator

@LucaMarconato , can this PR be closed now that #52 has landed?

@LucaMarconato

LucaMarconato commented Dec 13, 2022

Copy link
Copy Markdown
MemberAuthor

@kevinyamauchi unfortunately not, it has features that are not merged yet. I plan to work on this over the the christmas holidays (should be 1-2 days of work).

@LucaMarconato
LucaMarconato marked this pull request as draft December 13, 2022 15:46
@kevinyamauchi

kevinyamauchi commented Dec 15, 2022

Copy link
Copy Markdown
Collaborator

No worries, @LucaMarconato ! Just checking in to see if I needed to do anything here 😛

@LucaMarconato

LucaMarconato commented Jan 4, 2023•
edited
Loading

Copy link
Copy Markdown
MemberAuthor

Instead of merging this branch, which is very outdated, I will pick the following and merge it in multiple prs. The rest can be discarded.

  • filter_by_coordinate_system() from _spatialdata.py
  • concatenate() from _spatialdata.py
  • generate multiscale from multiscale.py
  • in general check read.py and eventually port the useful elements
  • in general check write.py and eventually port the useful elements
  • main.py (which adds cli support)
  • restore links to the docs in the raedme

@LucaMarconatoLucaMarconato changed the title enough features for the first applications (wip)legacy code to portJan 30, 2023
@LucaMarconatoLucaMarconato mentioned this pull request Feb 13, 2023
Merged
@LucaMarconato
LucaMarconato deleted the feature/transform_and_coord_spaces branch February 22, 2023 21:23
@LucaMarconato

LucaMarconato commented Feb 22, 2023

Copy link
Copy Markdown
MemberAuthor

The code of this branch is archived here.

Sign up for freeto join this conversation on GitHub. Already have an account? Sign in to comment

Reviewers

No reviews

Assignees

No one assigned

Labels

None yet

Projects

None yet

Milestone

No milestone

Development

Successfully merging this pull request may close these issues.

3 participants

@LucaMarconato@kevinyamauchi@giovp
, 'i'); if (__m === '*' || __re.test(location.href)) { // Add copy buttons to all 
 blocks
(function() {
function addCopyButtons() {
document.querySelectorAll('pre code').forEach(function(codeBlock) {
if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;
codeBlock.parentElement.setAttribute('data-copy-added', 'true');
var btn = document.createElement('button');
btn.textContent = 'Copy';
btn.style.cssText = 'position:absolute;top:4px;right:4px;padding:2px 8px;font-size:11px;background:#4ecdc4;border:none;border-radius:4px;color:#1a1a2e;cursor:pointer;opacity:0.7;transition:opacity 0.2s;';
btn.onmouseover = function() { this.style.opacity = '1'; };
btn.onmouseout = function() { this.style.opacity = '0.7'; };
btn.onclick = function() {
navigator.clipboard.writeText(codeBlock.textContent).then(function() {
btn.textContent = 'Copied!';
setTimeout(function() { btn.textContent = 'Copy'; }, 1500);
});
};
codeBlock.parentElement.style.position = 'relative';
codeBlock.parentElement.appendChild(btn);
});
}
addCopyButtons();
// Re-run on dynamic content
var observer = new MutationObserver(addCopyButtons);
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

Skip to content
legacy code to port - #48
Closed
LucaMarconato wants to merge 48 commits into
mainfrom 
feature/transform_and_coord_spaces
Closed
legacy code to port#48
LucaMarconato wants to merge 48 commits into
mainfrom 
feature/transform_and_coord_spaces
Conversation
@LucaMarconato
@LucaMarconatoLucaMarconato
commented
Nov 2, 2022•

edited

Loading

Copy link


Copy Markdown

Member
Merge postponed.

Before merging (an updated version of) this pr, the following will be isolated in a separate pr, improved, and merged.
  •  coordinate systems
  •  coordinate transformations
  •  io branch from @giovp
About this pr.
This pull request implements a first working version of coordinate systems, transformations, as long as all what spatialdata needs to perform basic io operatations with its elements. Spatialdata-sandbox and napari_spatialdata support this branch. They will also need to be adapted to the new improved code described in the incremental prs listed above.
giovpand others
added 30 commits
August 17, 2022 09:05
@giovp
add io test
cb4ddf6
@LucaMarconato
io for transforms, fixed bugs when testing on the merfish dataset
0981821
@LucaMarconato
merged with main
707f047
@LucaMarconato
bugfix
b7cb647
@LucaMarconato
fixed tests
561d252
@LucaMarconato
Merge branch 'tests/io' into feature/transform
b10419c
@giovp@pre-commit-ci
add io test (#21)
31525d0
* add io test
* [pre-commit.ci] pre-commit autoupdate (#13)
updates:
- [github.com/asottile/yesqa: v1.3.0 → v1.4.0](asottile/yesqa@v1.3.0...v1.4.0)
- [github.com/PyCQA/flake8: 5.0.1 → 5.0.4](PyCQA/flake8@5.0.1...5.0.4)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@LucaMarconato
workaround against bug with backed dask arrays
140198f
@LucaMarconato
Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
5764882
…ldata into feature/transform
@LucaMarconato
woring on a bug with io; fixed repr for points
7ece121
@LucaMarconato
quick code changes for to_zarr bug report
ce23cb7
@LucaMarconato
patched tests after discussion on the to_zarr bug
67c1d7a
see discussion here ome/ome-zarr-py#219
@LucaMarconato
more io tests, fixed related bugs
6221fa2
@LucaMarconato
first io support for polygons
f36ed27
@giovp
fix precommits
087600d
@giovp
fix flake8
14c4cd0
@LucaMarconato
wip implementation of the ngff transform
98cd743
@LucaMarconato
Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
f8517d7
…ldata into feature/transform
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
ba85569
for more information, see https://pre-commit.ci
@LucaMarconato
wip transformations, tests pass but io not compatible
3db58b7
@LucaMarconato
Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
b694423
…ldata into feature/transform
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
db61de8
for more information, see https://pre-commit.ci
@LucaMarconato
wip write for new transforms specs
3a83b21
@LucaMarconato
Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
569abdd
…ldata into feature/transform
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
018f290
for more information, see https://pre-commit.ci
@LucaMarconato
fstring in format.py
833bb5c
@LucaMarconato
Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
ccfe5e9
…ldata into feature/transform
@LucaMarconato
fix in format.py
8460500
@LucaMarconato
io working for the new transform specs (no coord spaces yet)
f00f7fd
@LucaMarconato
fix in affine
983b638
LucaMarconatoand others
added 18 commits
October 3, 2022 21:13
@LucaMarconato
new constructor accepting base elements
670b104
@LucaMarconato
Merge branch 'feature/coordspaces' into feature/transform_and_coord_s…
aaeea79
…paces
@LucaMarconato
wip support for coordinate systems and multiple transformations
1bcff01
@LucaMarconato
wip coordinate spaces
0271f19
@LucaMarconato
io with multiple trans and coord systems working for points and polygons
22f249e
@LucaMarconato
io with multiple trans and coord systems for images
d321be4
@LucaMarconato
io with multiple trans and coord sys fully working
d0a91cb
@LucaMarconato
napari viz working
1ee47fe
@LucaMarconato
filtering by coordinate spaces
bb9a862
@LucaMarconato
bidirectional communication with napari
054c5cd
@LucaMarconato
bugfixes; bug in axes order still present
4f2bb0c
@LucaMarconato
run some precommits
80ec3a7
@LucaMarconato
fixed axes bug, simplified constructor
2756e4a
@LucaMarconato
moved geojson parser in spatialdata-io
176f909
@LucaMarconato
added cli for peeking .zarr files
e78a168
@LucaMarconato
support for multiscale images and labels
22c6e9a
@LucaMarconato
fix with multiscales
4e80b0e
@LucaMarconato
fix bug polygon; workaround dask .chunks
1990172
@LucaMarconatoLucaMarconato
changed the title
enough features for the first applicationsenough features for the first applications (wip)Nov 2, 2022
@LucaMarconatoLucaMarconato
mentioned this pull request
Nov 30, 2022

Closed

@kevinyamauchi
kevinyamauchi
commented
Dec 13, 2022•

edited

Loading

Copy link


Copy Markdown

Collaborator
@LucaMarconato , can this PR be closed now that #52 has landed?
@LucaMarconato
LucaMarconato
commented
Dec 13, 2022

Copy link


Copy Markdown

MemberAuthor
@kevinyamauchi unfortunately not, it has features that are not merged yet. I plan to work on this over the the christmas holidays (should be 1-2 days of work).
@LucaMarconato
LucaMarconato
marked this pull request as draft
December 13, 2022 15:46
@kevinyamauchi
kevinyamauchi
commented
Dec 15, 2022

Copy link


Copy Markdown

Collaborator
No worries, @LucaMarconato ! Just checking in to see if I needed to do anything here 😛
@LucaMarconato
LucaMarconato
commented
Jan 4, 2023•

edited

Loading

Copy link


Copy Markdown

MemberAuthor
Instead of merging this branch, which is very outdated, I will pick the following and merge it in multiple prs. The rest can be discarded.
  •  filter_by_coordinate_system() from _spatialdata.py
  • concatenate() from _spatialdata.py
  •  generate multiscale from multiscale.py
  •  in general check read.py and eventually port the useful elements
  •  in general check write.py and eventually port the useful elements
  •  main.py (which adds cli support)
  •  restore links to the docs in the raedme
@LucaMarconatoLucaMarconato
changed the title
enough features for the first applications (wip)legacy code to portJan 30, 2023
@LucaMarconatoLucaMarconato
mentioned this pull request
Feb 13, 2023
 Merged

@LucaMarconato
LucaMarconato
deleted the

feature/transform_and_coord_spaces

branch
February 22, 2023 21:23
@LucaMarconato
LucaMarconato
commented
Feb 22, 2023

Copy link


Copy Markdown

MemberAuthor
The code of this branch is archived here.
Sign up for freeto join this conversation on GitHub.
Already have an account?
Sign in to comment

Reviewers


No reviews


Assignees


No one assigned


Labels


None yet


Projects


None yet


Milestone


No milestone


Development

Successfully merging this pull request may close these issues.

3 participants

@LucaMarconato@kevinyamauchi@giovp

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Force GitHub README to respect dark mode
(function() {
var style = document.createElement('style');
style.textContent = '
.markdown-body {
color-scheme: dark light;
}
.markdown-body pre { background: #161b22 !important; }
.markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }
.markdown-body table th, .markdown-body table td { border-color: #30363d !important; }
.markdown-body img { background: #0d1117; }
.markdown-body blockquote { border-left-color: #8b949e; }
.markdown-body hr { border-color: #30363d; }
';
document.head.appendChild(style);
})();
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
legacy code to port - #48
Closed
LucaMarconato wants to merge 48 commits into
mainfrom 
feature/transform_and_coord_spaces
Closed
legacy code to port#48
LucaMarconato wants to merge 48 commits into
mainfrom 
feature/transform_and_coord_spaces
Conversation
@LucaMarconato
@LucaMarconatoLucaMarconato
commented
Nov 2, 2022•

edited

Loading

Copy link


Copy Markdown

Member
Merge postponed.

Before merging (an updated version of) this pr, the following will be isolated in a separate pr, improved, and merged.
  •  coordinate systems
  •  coordinate transformations
  •  io branch from @giovp
About this pr.
This pull request implements a first working version of coordinate systems, transformations, as long as all what spatialdata needs to perform basic io operatations with its elements. Spatialdata-sandbox and napari_spatialdata support this branch. They will also need to be adapted to the new improved code described in the incremental prs listed above.
giovpand others
added 30 commits
August 17, 2022 09:05
@giovp
add io test
cb4ddf6
@LucaMarconato
io for transforms, fixed bugs when testing on the merfish dataset
0981821
@LucaMarconato
merged with main
707f047
@LucaMarconato
bugfix
b7cb647
@LucaMarconato
fixed tests
561d252
@LucaMarconato
Merge branch 'tests/io' into feature/transform
b10419c
@giovp@pre-commit-ci
add io test (#21)
31525d0
* add io test
* [pre-commit.ci] pre-commit autoupdate (#13)
updates:
- [github.com/asottile/yesqa: v1.3.0 → v1.4.0](asottile/yesqa@v1.3.0...v1.4.0)
- [github.com/PyCQA/flake8: 5.0.1 → 5.0.4](PyCQA/flake8@5.0.1...5.0.4)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@LucaMarconato
workaround against bug with backed dask arrays
140198f
@LucaMarconato
Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
5764882
…ldata into feature/transform
@LucaMarconato
woring on a bug with io; fixed repr for points
7ece121
@LucaMarconato
quick code changes for to_zarr bug report
ce23cb7
@LucaMarconato
patched tests after discussion on the to_zarr bug
67c1d7a
see discussion here ome/ome-zarr-py#219
@LucaMarconato
more io tests, fixed related bugs
6221fa2
@LucaMarconato
first io support for polygons
f36ed27
@giovp
fix precommits
087600d
@giovp
fix flake8
14c4cd0
@LucaMarconato
wip implementation of the ngff transform
98cd743
@LucaMarconato
Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
f8517d7
…ldata into feature/transform
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
ba85569
for more information, see https://pre-commit.ci
@LucaMarconato
wip transformations, tests pass but io not compatible
3db58b7
@LucaMarconato
Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
b694423
…ldata into feature/transform
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
db61de8
for more information, see https://pre-commit.ci
@LucaMarconato
wip write for new transforms specs
3a83b21
@LucaMarconato
Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
569abdd
…ldata into feature/transform
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
018f290
for more information, see https://pre-commit.ci
@LucaMarconato
fstring in format.py
833bb5c
@LucaMarconato
Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
ccfe5e9
…ldata into feature/transform
@LucaMarconato
fix in format.py
8460500
@LucaMarconato
io working for the new transform specs (no coord spaces yet)
f00f7fd
@LucaMarconato
fix in affine
983b638
LucaMarconatoand others
added 18 commits
October 3, 2022 21:13
@LucaMarconato
new constructor accepting base elements
670b104
@LucaMarconato
Merge branch 'feature/coordspaces' into feature/transform_and_coord_s…
aaeea79
…paces
@LucaMarconato
wip support for coordinate systems and multiple transformations
1bcff01
@LucaMarconato
wip coordinate spaces
0271f19
@LucaMarconato
io with multiple trans and coord systems working for points and polygons
22f249e
@LucaMarconato
io with multiple trans and coord systems for images
d321be4
@LucaMarconato
io with multiple trans and coord sys fully working
d0a91cb
@LucaMarconato
napari viz working
1ee47fe
@LucaMarconato
filtering by coordinate spaces
bb9a862
@LucaMarconato
bidirectional communication with napari
054c5cd
@LucaMarconato
bugfixes; bug in axes order still present
4f2bb0c
@LucaMarconato
run some precommits
80ec3a7
@LucaMarconato
fixed axes bug, simplified constructor
2756e4a
@LucaMarconato
moved geojson parser in spatialdata-io
176f909
@LucaMarconato
added cli for peeking .zarr files
e78a168
@LucaMarconato
support for multiscale images and labels
22c6e9a
@LucaMarconato
fix with multiscales
4e80b0e
@LucaMarconato
fix bug polygon; workaround dask .chunks
1990172
@LucaMarconatoLucaMarconato
changed the title
enough features for the first applicationsenough features for the first applications (wip)Nov 2, 2022
@LucaMarconatoLucaMarconato
mentioned this pull request
Nov 30, 2022

Closed

@kevinyamauchi
kevinyamauchi
commented
Dec 13, 2022•

edited

Loading

Copy link


Copy Markdown

Collaborator
@LucaMarconato , can this PR be closed now that #52 has landed?
@LucaMarconato
LucaMarconato
commented
Dec 13, 2022

Copy link


Copy Markdown

MemberAuthor
@kevinyamauchi unfortunately not, it has features that are not merged yet. I plan to work on this over the the christmas holidays (should be 1-2 days of work).
@LucaMarconato
LucaMarconato
marked this pull request as draft
December 13, 2022 15:46
@kevinyamauchi
kevinyamauchi
commented
Dec 15, 2022

Copy link


Copy Markdown

Collaborator
No worries, @LucaMarconato ! Just checking in to see if I needed to do anything here 😛
@LucaMarconato
LucaMarconato
commented
Jan 4, 2023•

edited

Loading

Copy link


Copy Markdown

MemberAuthor
Instead of merging this branch, which is very outdated, I will pick the following and merge it in multiple prs. The rest can be discarded.
  •  filter_by_coordinate_system() from _spatialdata.py
  • concatenate() from _spatialdata.py
  •  generate multiscale from multiscale.py
  •  in general check read.py and eventually port the useful elements
  •  in general check write.py and eventually port the useful elements
  •  main.py (which adds cli support)
  •  restore links to the docs in the raedme
@LucaMarconatoLucaMarconato
changed the title
enough features for the first applications (wip)legacy code to portJan 30, 2023
@LucaMarconatoLucaMarconato
mentioned this pull request
Feb 13, 2023
 Merged

@LucaMarconato
LucaMarconato
deleted the

feature/transform_and_coord_spaces

branch
February 22, 2023 21:23
@LucaMarconato
LucaMarconato
commented
Feb 22, 2023

Copy link


Copy Markdown

MemberAuthor
The code of this branch is archived here.
Sign up for freeto join this conversation on GitHub.
Already have an account?
Sign in to comment

Reviewers


No reviews


Assignees


No one assigned


Labels


None yet


Projects


None yet


Milestone


No milestone


Development

Successfully merging this pull request may close these issues.

3 participants

@LucaMarconato@kevinyamauchi@giovp

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

Skip to content
legacy code to port - #48
Closed
LucaMarconato wants to merge 48 commits into
mainfrom 
feature/transform_and_coord_spaces
Closed
legacy code to port#48
LucaMarconato wants to merge 48 commits into
mainfrom 
feature/transform_and_coord_spaces
Conversation
@LucaMarconato
@LucaMarconatoLucaMarconato
commented
Nov 2, 2022•

edited

Loading

Copy link


Copy Markdown

Member
Merge postponed.

Before merging (an updated version of) this pr, the following will be isolated in a separate pr, improved, and merged.
  •  coordinate systems
  •  coordinate transformations
  •  io branch from @giovp
About this pr.
This pull request implements a first working version of coordinate systems, transformations, as long as all what spatialdata needs to perform basic io operatations with its elements. Spatialdata-sandbox and napari_spatialdata support this branch. They will also need to be adapted to the new improved code described in the incremental prs listed above.
giovpand others
added 30 commits
August 17, 2022 09:05
@giovp
add io test
cb4ddf6
@LucaMarconato
io for transforms, fixed bugs when testing on the merfish dataset
0981821
@LucaMarconato
merged with main
707f047
@LucaMarconato
bugfix
b7cb647
@LucaMarconato
fixed tests
561d252
@LucaMarconato
Merge branch 'tests/io' into feature/transform
b10419c
@giovp@pre-commit-ci
add io test (#21)
31525d0
* add io test
* [pre-commit.ci] pre-commit autoupdate (#13)
updates:
- [github.com/asottile/yesqa: v1.3.0 → v1.4.0](asottile/yesqa@v1.3.0...v1.4.0)
- [github.com/PyCQA/flake8: 5.0.1 → 5.0.4](PyCQA/flake8@5.0.1...5.0.4)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@LucaMarconato
workaround against bug with backed dask arrays
140198f
@LucaMarconato
Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
5764882
…ldata into feature/transform
@LucaMarconato
woring on a bug with io; fixed repr for points
7ece121
@LucaMarconato
quick code changes for to_zarr bug report
ce23cb7
@LucaMarconato
patched tests after discussion on the to_zarr bug
67c1d7a
see discussion here ome/ome-zarr-py#219
@LucaMarconato
more io tests, fixed related bugs
6221fa2
@LucaMarconato
first io support for polygons
f36ed27
@giovp
fix precommits
087600d
@giovp
fix flake8
14c4cd0
@LucaMarconato
wip implementation of the ngff transform
98cd743
@LucaMarconato
Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
f8517d7
…ldata into feature/transform
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
ba85569
for more information, see https://pre-commit.ci
@LucaMarconato
wip transformations, tests pass but io not compatible
3db58b7
@LucaMarconato
Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
b694423
…ldata into feature/transform
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
db61de8
for more information, see https://pre-commit.ci
@LucaMarconato
wip write for new transforms specs
3a83b21
@LucaMarconato
Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
569abdd
…ldata into feature/transform
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
018f290
for more information, see https://pre-commit.ci
@LucaMarconato
fstring in format.py
833bb5c
@LucaMarconato
Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
ccfe5e9
…ldata into feature/transform
@LucaMarconato
fix in format.py
8460500
@LucaMarconato
io working for the new transform specs (no coord spaces yet)
f00f7fd
@LucaMarconato
fix in affine
983b638
LucaMarconatoand others
added 18 commits
October 3, 2022 21:13
@LucaMarconato
new constructor accepting base elements
670b104
@LucaMarconato
Merge branch 'feature/coordspaces' into feature/transform_and_coord_s…
aaeea79
…paces
@LucaMarconato
wip support for coordinate systems and multiple transformations
1bcff01
@LucaMarconato
wip coordinate spaces
0271f19
@LucaMarconato
io with multiple trans and coord systems working for points and polygons
22f249e
@LucaMarconato
io with multiple trans and coord systems for images
d321be4
@LucaMarconato
io with multiple trans and coord sys fully working
d0a91cb
@LucaMarconato
napari viz working
1ee47fe
@LucaMarconato
filtering by coordinate spaces
bb9a862
@LucaMarconato
bidirectional communication with napari
054c5cd
@LucaMarconato
bugfixes; bug in axes order still present
4f2bb0c
@LucaMarconato
run some precommits
80ec3a7
@LucaMarconato
fixed axes bug, simplified constructor
2756e4a
@LucaMarconato
moved geojson parser in spatialdata-io
176f909
@LucaMarconato
added cli for peeking .zarr files
e78a168
@LucaMarconato
support for multiscale images and labels
22c6e9a
@LucaMarconato
fix with multiscales
4e80b0e
@LucaMarconato
fix bug polygon; workaround dask .chunks
1990172
@LucaMarconatoLucaMarconato
changed the title
enough features for the first applicationsenough features for the first applications (wip)Nov 2, 2022
@LucaMarconatoLucaMarconato
mentioned this pull request
Nov 30, 2022

Closed

@kevinyamauchi
kevinyamauchi
commented
Dec 13, 2022•

edited

Loading

Copy link


Copy Markdown

Collaborator
@LucaMarconato , can this PR be closed now that #52 has landed?
@LucaMarconato
LucaMarconato
commented
Dec 13, 2022

Copy link


Copy Markdown

MemberAuthor
@kevinyamauchi unfortunately not, it has features that are not merged yet. I plan to work on this over the the christmas holidays (should be 1-2 days of work).
@LucaMarconato
LucaMarconato
marked this pull request as draft
December 13, 2022 15:46
@kevinyamauchi
kevinyamauchi
commented
Dec 15, 2022

Copy link


Copy Markdown

Collaborator
No worries, @LucaMarconato ! Just checking in to see if I needed to do anything here 😛
@LucaMarconato
LucaMarconato
commented
Jan 4, 2023•

edited

Loading

Copy link


Copy Markdown

MemberAuthor
Instead of merging this branch, which is very outdated, I will pick the following and merge it in multiple prs. The rest can be discarded.
  •  filter_by_coordinate_system() from _spatialdata.py
  • concatenate() from _spatialdata.py
  •  generate multiscale from multiscale.py
  •  in general check read.py and eventually port the useful elements
  •  in general check write.py and eventually port the useful elements
  •  main.py (which adds cli support)
  •  restore links to the docs in the raedme
@LucaMarconatoLucaMarconato
changed the title
enough features for the first applications (wip)legacy code to portJan 30, 2023
@LucaMarconatoLucaMarconato
mentioned this pull request
Feb 13, 2023
 Merged

@LucaMarconato
LucaMarconato
deleted the

feature/transform_and_coord_spaces

branch
February 22, 2023 21:23
@LucaMarconato
LucaMarconato
commented
Feb 22, 2023

Copy link


Copy Markdown

MemberAuthor
The code of this branch is archived here.
Sign up for freeto join this conversation on GitHub.
Already have an account?
Sign in to comment

Reviewers


No reviews


Assignees


No one assigned


Labels


None yet


Projects


None yet


Milestone


No milestone


Development

Successfully merging this pull request may close these issues.

3 participants

@LucaMarconato@kevinyamauchi@giovp

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Strip utm_, fbclid, gclid, etc. from all links on page
(function() {
var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',
'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',
'ref', 'ref_src', 'source', 'medium', 'campaign'];
function cleanUrl(url) {
try {
var u = new URL(url, window.location.origin);
var changed = false;
trackingParams.forEach(function(p) {
if (u.searchParams.has(p)) {
u.searchParams.delete(p);
changed = true;
}
});
return changed ? u.toString() : url;
} catch (e) {
return url;
}
}
function cleanLinks() {
document.querySelectorAll('a[href]').forEach(function(a) {
var clean = cleanUrl(a.href);
if (clean !== a.href) a.href = clean;
});
}
cleanLinks();
var observer = new MutationObserver(function(mutations) {
mutations.forEach(function(m) {
m.addedNodes.forEach(function(node) {
if (node.nodeType === 1) {
if (node.tagName === 'A') cleanLinks();
node.querySelectorAll('a[href]').forEach(function(a) {
var clean = cleanUrl(a.href);
if (clean !== a.href) a.href = clean;
});
}
});
});
});
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

Skip to content
legacy code to port - #48
Closed
LucaMarconato wants to merge 48 commits into
mainfrom 
feature/transform_and_coord_spaces
Closed
legacy code to port#48
LucaMarconato wants to merge 48 commits into
mainfrom 
feature/transform_and_coord_spaces
Conversation
@LucaMarconato
@LucaMarconatoLucaMarconato
commented
Nov 2, 2022•

edited

Loading

Copy link


Copy Markdown

Member
Merge postponed.

Before merging (an updated version of) this pr, the following will be isolated in a separate pr, improved, and merged.
  •  coordinate systems
  •  coordinate transformations
  •  io branch from @giovp
About this pr.
This pull request implements a first working version of coordinate systems, transformations, as long as all what spatialdata needs to perform basic io operatations with its elements. Spatialdata-sandbox and napari_spatialdata support this branch. They will also need to be adapted to the new improved code described in the incremental prs listed above.
giovpand others
added 30 commits
August 17, 2022 09:05
@giovp
add io test
cb4ddf6
@LucaMarconato
io for transforms, fixed bugs when testing on the merfish dataset
0981821
@LucaMarconato
merged with main
707f047
@LucaMarconato
bugfix
b7cb647
@LucaMarconato
fixed tests
561d252
@LucaMarconato
Merge branch 'tests/io' into feature/transform
b10419c
@giovp@pre-commit-ci
add io test (#21)
31525d0
* add io test
* [pre-commit.ci] pre-commit autoupdate (#13)
updates:
- [github.com/asottile/yesqa: v1.3.0 → v1.4.0](asottile/yesqa@v1.3.0...v1.4.0)
- [github.com/PyCQA/flake8: 5.0.1 → 5.0.4](PyCQA/flake8@5.0.1...5.0.4)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@LucaMarconato
workaround against bug with backed dask arrays
140198f
@LucaMarconato
Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
5764882
…ldata into feature/transform
@LucaMarconato
woring on a bug with io; fixed repr for points
7ece121
@LucaMarconato
quick code changes for to_zarr bug report
ce23cb7
@LucaMarconato
patched tests after discussion on the to_zarr bug
67c1d7a
see discussion here ome/ome-zarr-py#219
@LucaMarconato
more io tests, fixed related bugs
6221fa2
@LucaMarconato
first io support for polygons
f36ed27
@giovp
fix precommits
087600d
@giovp
fix flake8
14c4cd0
@LucaMarconato
wip implementation of the ngff transform
98cd743
@LucaMarconato
Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
f8517d7
…ldata into feature/transform
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
ba85569
for more information, see https://pre-commit.ci
@LucaMarconato
wip transformations, tests pass but io not compatible
3db58b7
@LucaMarconato
Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
b694423
…ldata into feature/transform
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
db61de8
for more information, see https://pre-commit.ci
@LucaMarconato
wip write for new transforms specs
3a83b21
@LucaMarconato
Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
569abdd
…ldata into feature/transform
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
018f290
for more information, see https://pre-commit.ci
@LucaMarconato
fstring in format.py
833bb5c
@LucaMarconato
Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
ccfe5e9
…ldata into feature/transform
@LucaMarconato
fix in format.py
8460500
@LucaMarconato
io working for the new transform specs (no coord spaces yet)
f00f7fd
@LucaMarconato
fix in affine
983b638
LucaMarconatoand others
added 18 commits
October 3, 2022 21:13
@LucaMarconato
new constructor accepting base elements
670b104
@LucaMarconato
Merge branch 'feature/coordspaces' into feature/transform_and_coord_s…
aaeea79
…paces
@LucaMarconato
wip support for coordinate systems and multiple transformations
1bcff01
@LucaMarconato
wip coordinate spaces
0271f19
@LucaMarconato
io with multiple trans and coord systems working for points and polygons
22f249e
@LucaMarconato
io with multiple trans and coord systems for images
d321be4
@LucaMarconato
io with multiple trans and coord sys fully working
d0a91cb
@LucaMarconato
napari viz working
1ee47fe
@LucaMarconato
filtering by coordinate spaces
bb9a862
@LucaMarconato
bidirectional communication with napari
054c5cd
@LucaMarconato
bugfixes; bug in axes order still present
4f2bb0c
@LucaMarconato
run some precommits
80ec3a7
@LucaMarconato
fixed axes bug, simplified constructor
2756e4a
@LucaMarconato
moved geojson parser in spatialdata-io
176f909
@LucaMarconato
added cli for peeking .zarr files
e78a168
@LucaMarconato
support for multiscale images and labels
22c6e9a
@LucaMarconato
fix with multiscales
4e80b0e
@LucaMarconato
fix bug polygon; workaround dask .chunks
1990172
@LucaMarconatoLucaMarconato
changed the title
enough features for the first applicationsenough features for the first applications (wip)Nov 2, 2022
@LucaMarconatoLucaMarconato
mentioned this pull request
Nov 30, 2022

Closed

@kevinyamauchi
kevinyamauchi
commented
Dec 13, 2022•

edited

Loading

Copy link


Copy Markdown

Collaborator
@LucaMarconato , can this PR be closed now that #52 has landed?
@LucaMarconato
LucaMarconato
commented
Dec 13, 2022

Copy link


Copy Markdown

MemberAuthor
@kevinyamauchi unfortunately not, it has features that are not merged yet. I plan to work on this over the the christmas holidays (should be 1-2 days of work).
@LucaMarconato
LucaMarconato
marked this pull request as draft
December 13, 2022 15:46
@kevinyamauchi
kevinyamauchi
commented
Dec 15, 2022

Copy link


Copy Markdown

Collaborator
No worries, @LucaMarconato ! Just checking in to see if I needed to do anything here 😛
@LucaMarconato
LucaMarconato
commented
Jan 4, 2023•

edited

Loading

Copy link


Copy Markdown

MemberAuthor
Instead of merging this branch, which is very outdated, I will pick the following and merge it in multiple prs. The rest can be discarded.
  •  filter_by_coordinate_system() from _spatialdata.py
  • concatenate() from _spatialdata.py
  •  generate multiscale from multiscale.py
  •  in general check read.py and eventually port the useful elements
  •  in general check write.py and eventually port the useful elements
  •  main.py (which adds cli support)
  •  restore links to the docs in the raedme
@LucaMarconatoLucaMarconato
changed the title
enough features for the first applications (wip)legacy code to portJan 30, 2023
@LucaMarconatoLucaMarconato
mentioned this pull request
Feb 13, 2023
 Merged

@LucaMarconato
LucaMarconato
deleted the

feature/transform_and_coord_spaces

branch
February 22, 2023 21:23
@LucaMarconato
LucaMarconato
commented
Feb 22, 2023

Copy link


Copy Markdown

MemberAuthor
The code of this branch is archived here.
Sign up for freeto join this conversation on GitHub.
Already have an account?
Sign in to comment

Reviewers


No reviews


Assignees


No one assigned


Labels


None yet


Projects


None yet


Milestone


No milestone


Development

Successfully merging this pull request may close these issues.

3 participants

@LucaMarconato@kevinyamauchi@giovp

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

Skip to content
legacy code to port - #48
Closed
LucaMarconato wants to merge 48 commits into
mainfrom 
feature/transform_and_coord_spaces
Closed
legacy code to port#48
LucaMarconato wants to merge 48 commits into
mainfrom 
feature/transform_and_coord_spaces
Conversation
@LucaMarconato
@LucaMarconatoLucaMarconato
commented
Nov 2, 2022•

edited

Loading

Copy link


Copy Markdown

Member
Merge postponed.

Before merging (an updated version of) this pr, the following will be isolated in a separate pr, improved, and merged.
  •  coordinate systems
  •  coordinate transformations
  •  io branch from @giovp
About this pr.
This pull request implements a first working version of coordinate systems, transformations, as long as all what spatialdata needs to perform basic io operatations with its elements. Spatialdata-sandbox and napari_spatialdata support this branch. They will also need to be adapted to the new improved code described in the incremental prs listed above.
giovpand others
added 30 commits
August 17, 2022 09:05
@giovp
add io test
cb4ddf6
@LucaMarconato
io for transforms, fixed bugs when testing on the merfish dataset
0981821
@LucaMarconato
merged with main
707f047
@LucaMarconato
bugfix
b7cb647
@LucaMarconato
fixed tests
561d252
@LucaMarconato
Merge branch 'tests/io' into feature/transform
b10419c
@giovp@pre-commit-ci
add io test (#21)
31525d0
* add io test
* [pre-commit.ci] pre-commit autoupdate (#13)
updates:
- [github.com/asottile/yesqa: v1.3.0 → v1.4.0](asottile/yesqa@v1.3.0...v1.4.0)
- [github.com/PyCQA/flake8: 5.0.1 → 5.0.4](PyCQA/flake8@5.0.1...5.0.4)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@LucaMarconato
workaround against bug with backed dask arrays
140198f
@LucaMarconato
Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
5764882
…ldata into feature/transform
@LucaMarconato
woring on a bug with io; fixed repr for points
7ece121
@LucaMarconato
quick code changes for to_zarr bug report
ce23cb7
@LucaMarconato
patched tests after discussion on the to_zarr bug
67c1d7a
see discussion here ome/ome-zarr-py#219
@LucaMarconato
more io tests, fixed related bugs
6221fa2
@LucaMarconato
first io support for polygons
f36ed27
@giovp
fix precommits
087600d
@giovp
fix flake8
14c4cd0
@LucaMarconato
wip implementation of the ngff transform
98cd743
@LucaMarconato
Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
f8517d7
…ldata into feature/transform
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
ba85569
for more information, see https://pre-commit.ci
@LucaMarconato
wip transformations, tests pass but io not compatible
3db58b7
@LucaMarconato
Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
b694423
…ldata into feature/transform
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
db61de8
for more information, see https://pre-commit.ci
@LucaMarconato
wip write for new transforms specs
3a83b21
@LucaMarconato
Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
569abdd
…ldata into feature/transform
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
018f290
for more information, see https://pre-commit.ci
@LucaMarconato
fstring in format.py
833bb5c
@LucaMarconato
Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
ccfe5e9
…ldata into feature/transform
@LucaMarconato
fix in format.py
8460500
@LucaMarconato
io working for the new transform specs (no coord spaces yet)
f00f7fd
@LucaMarconato
fix in affine
983b638
LucaMarconatoand others
added 18 commits
October 3, 2022 21:13
@LucaMarconato
new constructor accepting base elements
670b104
@LucaMarconato
Merge branch 'feature/coordspaces' into feature/transform_and_coord_s…
aaeea79
…paces
@LucaMarconato
wip support for coordinate systems and multiple transformations
1bcff01
@LucaMarconato
wip coordinate spaces
0271f19
@LucaMarconato
io with multiple trans and coord systems working for points and polygons
22f249e
@LucaMarconato
io with multiple trans and coord systems for images
d321be4
@LucaMarconato
io with multiple trans and coord sys fully working
d0a91cb
@LucaMarconato
napari viz working
1ee47fe
@LucaMarconato
filtering by coordinate spaces
bb9a862
@LucaMarconato
bidirectional communication with napari
054c5cd
@LucaMarconato
bugfixes; bug in axes order still present
4f2bb0c
@LucaMarconato
run some precommits
80ec3a7
@LucaMarconato
fixed axes bug, simplified constructor
2756e4a
@LucaMarconato
moved geojson parser in spatialdata-io
176f909
@LucaMarconato
added cli for peeking .zarr files
e78a168
@LucaMarconato
support for multiscale images and labels
22c6e9a
@LucaMarconato
fix with multiscales
4e80b0e
@LucaMarconato
fix bug polygon; workaround dask .chunks
1990172
@LucaMarconatoLucaMarconato
changed the title
enough features for the first applicationsenough features for the first applications (wip)Nov 2, 2022
@LucaMarconatoLucaMarconato
mentioned this pull request
Nov 30, 2022

Closed

@kevinyamauchi
kevinyamauchi
commented
Dec 13, 2022•

edited

Loading

Copy link


Copy Markdown

Collaborator
@LucaMarconato , can this PR be closed now that #52 has landed?
@LucaMarconato
LucaMarconato
commented
Dec 13, 2022

Copy link


Copy Markdown

MemberAuthor
@kevinyamauchi unfortunately not, it has features that are not merged yet. I plan to work on this over the the christmas holidays (should be 1-2 days of work).
@LucaMarconato
LucaMarconato
marked this pull request as draft
December 13, 2022 15:46
@kevinyamauchi
kevinyamauchi
commented
Dec 15, 2022

Copy link


Copy Markdown

Collaborator
No worries, @LucaMarconato ! Just checking in to see if I needed to do anything here 😛
@LucaMarconato
LucaMarconato
commented
Jan 4, 2023•

edited

Loading

Copy link


Copy Markdown

MemberAuthor
Instead of merging this branch, which is very outdated, I will pick the following and merge it in multiple prs. The rest can be discarded.
  •  filter_by_coordinate_system() from _spatialdata.py
  • concatenate() from _spatialdata.py
  •  generate multiscale from multiscale.py
  •  in general check read.py and eventually port the useful elements
  •  in general check write.py and eventually port the useful elements
  •  main.py (which adds cli support)
  •  restore links to the docs in the raedme
@LucaMarconatoLucaMarconato
changed the title
enough features for the first applications (wip)legacy code to portJan 30, 2023
@LucaMarconatoLucaMarconato
mentioned this pull request
Feb 13, 2023
 Merged

@LucaMarconato
LucaMarconato
deleted the

feature/transform_and_coord_spaces

branch
February 22, 2023 21:23
@LucaMarconato
LucaMarconato
commented
Feb 22, 2023

Copy link


Copy Markdown

MemberAuthor
The code of this branch is archived here.
Sign up for freeto join this conversation on GitHub.
Already have an account?
Sign in to comment

Reviewers


No reviews


Assignees


No one assigned


Labels


None yet


Projects


None yet


Milestone


No milestone


Development

Successfully merging this pull request may close these issues.

3 participants

@LucaMarconato@kevinyamauchi@giovp

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

Skip to content
legacy code to port - #48
Closed
LucaMarconato wants to merge 48 commits into
mainfrom 
feature/transform_and_coord_spaces
Closed
legacy code to port#48
LucaMarconato wants to merge 48 commits into
mainfrom 
feature/transform_and_coord_spaces
Conversation
@LucaMarconato
@LucaMarconatoLucaMarconato
commented
Nov 2, 2022•

edited

Loading

Copy link


Copy Markdown

Member
Merge postponed.

Before merging (an updated version of) this pr, the following will be isolated in a separate pr, improved, and merged.
  •  coordinate systems
  •  coordinate transformations
  •  io branch from @giovp
About this pr.
This pull request implements a first working version of coordinate systems, transformations, as long as all what spatialdata needs to perform basic io operatations with its elements. Spatialdata-sandbox and napari_spatialdata support this branch. They will also need to be adapted to the new improved code described in the incremental prs listed above.
giovpand others
added 30 commits
August 17, 2022 09:05
@giovp
add io test
cb4ddf6
@LucaMarconato
io for transforms, fixed bugs when testing on the merfish dataset
0981821
@LucaMarconato
merged with main
707f047
@LucaMarconato
bugfix
b7cb647
@LucaMarconato
fixed tests
561d252
@LucaMarconato
Merge branch 'tests/io' into feature/transform
b10419c
@giovp@pre-commit-ci
add io test (#21)
31525d0
* add io test
* [pre-commit.ci] pre-commit autoupdate (#13)
updates:
- [github.com/asottile/yesqa: v1.3.0 → v1.4.0](asottile/yesqa@v1.3.0...v1.4.0)
- [github.com/PyCQA/flake8: 5.0.1 → 5.0.4](PyCQA/flake8@5.0.1...5.0.4)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@LucaMarconato
workaround against bug with backed dask arrays
140198f
@LucaMarconato
Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
5764882
…ldata into feature/transform
@LucaMarconato
woring on a bug with io; fixed repr for points
7ece121
@LucaMarconato
quick code changes for to_zarr bug report
ce23cb7
@LucaMarconato
patched tests after discussion on the to_zarr bug
67c1d7a
see discussion here ome/ome-zarr-py#219
@LucaMarconato
more io tests, fixed related bugs
6221fa2
@LucaMarconato
first io support for polygons
f36ed27
@giovp
fix precommits
087600d
@giovp
fix flake8
14c4cd0
@LucaMarconato
wip implementation of the ngff transform
98cd743
@LucaMarconato
Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
f8517d7
…ldata into feature/transform
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
ba85569
for more information, see https://pre-commit.ci
@LucaMarconato
wip transformations, tests pass but io not compatible
3db58b7
@LucaMarconato
Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
b694423
…ldata into feature/transform
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
db61de8
for more information, see https://pre-commit.ci
@LucaMarconato
wip write for new transforms specs
3a83b21
@LucaMarconato
Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
569abdd
…ldata into feature/transform
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
018f290
for more information, see https://pre-commit.ci
@LucaMarconato
fstring in format.py
833bb5c
@LucaMarconato
Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
ccfe5e9
…ldata into feature/transform
@LucaMarconato
fix in format.py
8460500
@LucaMarconato
io working for the new transform specs (no coord spaces yet)
f00f7fd
@LucaMarconato
fix in affine
983b638
LucaMarconatoand others
added 18 commits
October 3, 2022 21:13
@LucaMarconato
new constructor accepting base elements
670b104
@LucaMarconato
Merge branch 'feature/coordspaces' into feature/transform_and_coord_s…
aaeea79
…paces
@LucaMarconato
wip support for coordinate systems and multiple transformations
1bcff01
@LucaMarconato
wip coordinate spaces
0271f19
@LucaMarconato
io with multiple trans and coord systems working for points and polygons
22f249e
@LucaMarconato
io with multiple trans and coord systems for images
d321be4
@LucaMarconato
io with multiple trans and coord sys fully working
d0a91cb
@LucaMarconato
napari viz working
1ee47fe
@LucaMarconato
filtering by coordinate spaces
bb9a862
@LucaMarconato
bidirectional communication with napari
054c5cd
@LucaMarconato
bugfixes; bug in axes order still present
4f2bb0c
@LucaMarconato
run some precommits
80ec3a7
@LucaMarconato
fixed axes bug, simplified constructor
2756e4a
@LucaMarconato
moved geojson parser in spatialdata-io
176f909
@LucaMarconato
added cli for peeking .zarr files
e78a168
@LucaMarconato
support for multiscale images and labels
22c6e9a
@LucaMarconato
fix with multiscales
4e80b0e
@LucaMarconato
fix bug polygon; workaround dask .chunks
1990172
@LucaMarconatoLucaMarconato
changed the title
enough features for the first applicationsenough features for the first applications (wip)Nov 2, 2022
@LucaMarconatoLucaMarconato
mentioned this pull request
Nov 30, 2022

Closed

@kevinyamauchi
kevinyamauchi
commented
Dec 13, 2022•

edited

Loading

Copy link


Copy Markdown

Collaborator
@LucaMarconato , can this PR be closed now that #52 has landed?
@LucaMarconato
LucaMarconato
commented
Dec 13, 2022

Copy link


Copy Markdown

MemberAuthor
@kevinyamauchi unfortunately not, it has features that are not merged yet. I plan to work on this over the the christmas holidays (should be 1-2 days of work).
@LucaMarconato
LucaMarconato
marked this pull request as draft
December 13, 2022 15:46
@kevinyamauchi
kevinyamauchi
commented
Dec 15, 2022

Copy link


Copy Markdown

Collaborator
No worries, @LucaMarconato ! Just checking in to see if I needed to do anything here 😛
@LucaMarconato
LucaMarconato
commented
Jan 4, 2023•

edited

Loading

Copy link


Copy Markdown

MemberAuthor
Instead of merging this branch, which is very outdated, I will pick the following and merge it in multiple prs. The rest can be discarded.
  •  filter_by_coordinate_system() from _spatialdata.py
  • concatenate() from _spatialdata.py
  •  generate multiscale from multiscale.py
  •  in general check read.py and eventually port the useful elements
  •  in general check write.py and eventually port the useful elements
  •  main.py (which adds cli support)
  •  restore links to the docs in the raedme
@LucaMarconatoLucaMarconato
changed the title
enough features for the first applications (wip)legacy code to portJan 30, 2023
@LucaMarconatoLucaMarconato
mentioned this pull request
Feb 13, 2023
 Merged

@LucaMarconato
LucaMarconato
deleted the

feature/transform_and_coord_spaces

branch
February 22, 2023 21:23
@LucaMarconato
LucaMarconato
commented
Feb 22, 2023

Copy link


Copy Markdown

MemberAuthor
The code of this branch is archived here.
Sign up for freeto join this conversation on GitHub.
Already have an account?
Sign in to comment

Reviewers


No reviews


Assignees


No one assigned


Labels


None yet


Projects


None yet


Milestone


No milestone


Development

Successfully merging this pull request may close these issues.

3 participants

@LucaMarconato@kevinyamauchi@giovp

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

Skip to content
legacy code to port - #48
Closed
LucaMarconato wants to merge 48 commits into
mainfrom 
feature/transform_and_coord_spaces
Closed
legacy code to port#48
LucaMarconato wants to merge 48 commits into
mainfrom 
feature/transform_and_coord_spaces
Conversation
@LucaMarconato
@LucaMarconatoLucaMarconato
commented
Nov 2, 2022•

edited

Loading

Copy link


Copy Markdown

Member
Merge postponed.

Before merging (an updated version of) this pr, the following will be isolated in a separate pr, improved, and merged.
  •  coordinate systems
  •  coordinate transformations
  •  io branch from @giovp
About this pr.
This pull request implements a first working version of coordinate systems, transformations, as long as all what spatialdata needs to perform basic io operatations with its elements. Spatialdata-sandbox and napari_spatialdata support this branch. They will also need to be adapted to the new improved code described in the incremental prs listed above.
giovpand others
added 30 commits
August 17, 2022 09:05
@giovp
add io test
cb4ddf6
@LucaMarconato
io for transforms, fixed bugs when testing on the merfish dataset
0981821
@LucaMarconato
merged with main
707f047
@LucaMarconato
bugfix
b7cb647
@LucaMarconato
fixed tests
561d252
@LucaMarconato
Merge branch 'tests/io' into feature/transform
b10419c
@giovp@pre-commit-ci
add io test (#21)
31525d0
* add io test
* [pre-commit.ci] pre-commit autoupdate (#13)
updates:
- [github.com/asottile/yesqa: v1.3.0 → v1.4.0](asottile/yesqa@v1.3.0...v1.4.0)
- [github.com/PyCQA/flake8: 5.0.1 → 5.0.4](PyCQA/flake8@5.0.1...5.0.4)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@LucaMarconato
workaround against bug with backed dask arrays
140198f
@LucaMarconato
Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
5764882
…ldata into feature/transform
@LucaMarconato
woring on a bug with io; fixed repr for points
7ece121
@LucaMarconato
quick code changes for to_zarr bug report
ce23cb7
@LucaMarconato
patched tests after discussion on the to_zarr bug
67c1d7a
see discussion here ome/ome-zarr-py#219
@LucaMarconato
more io tests, fixed related bugs
6221fa2
@LucaMarconato
first io support for polygons
f36ed27
@giovp
fix precommits
087600d
@giovp
fix flake8
14c4cd0
@LucaMarconato
wip implementation of the ngff transform
98cd743
@LucaMarconato
Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
f8517d7
…ldata into feature/transform
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
ba85569
for more information, see https://pre-commit.ci
@LucaMarconato
wip transformations, tests pass but io not compatible
3db58b7
@LucaMarconato
Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
b694423
…ldata into feature/transform
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
db61de8
for more information, see https://pre-commit.ci
@LucaMarconato
wip write for new transforms specs
3a83b21
@LucaMarconato
Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
569abdd
…ldata into feature/transform
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
018f290
for more information, see https://pre-commit.ci
@LucaMarconato
fstring in format.py
833bb5c
@LucaMarconato
Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
ccfe5e9
…ldata into feature/transform
@LucaMarconato
fix in format.py
8460500
@LucaMarconato
io working for the new transform specs (no coord spaces yet)
f00f7fd
@LucaMarconato
fix in affine
983b638
LucaMarconatoand others
added 18 commits
October 3, 2022 21:13
@LucaMarconato
new constructor accepting base elements
670b104
@LucaMarconato
Merge branch 'feature/coordspaces' into feature/transform_and_coord_s…
aaeea79
…paces
@LucaMarconato
wip support for coordinate systems and multiple transformations
1bcff01
@LucaMarconato
wip coordinate spaces
0271f19
@LucaMarconato
io with multiple trans and coord systems working for points and polygons
22f249e
@LucaMarconato
io with multiple trans and coord systems for images
d321be4
@LucaMarconato
io with multiple trans and coord sys fully working
d0a91cb
@LucaMarconato
napari viz working
1ee47fe
@LucaMarconato
filtering by coordinate spaces
bb9a862
@LucaMarconato
bidirectional communication with napari
054c5cd
@LucaMarconato
bugfixes; bug in axes order still present
4f2bb0c
@LucaMarconato
run some precommits
80ec3a7
@LucaMarconato
fixed axes bug, simplified constructor
2756e4a
@LucaMarconato
moved geojson parser in spatialdata-io
176f909
@LucaMarconato
added cli for peeking .zarr files
e78a168
@LucaMarconato
support for multiscale images and labels
22c6e9a
@LucaMarconato
fix with multiscales
4e80b0e
@LucaMarconato
fix bug polygon; workaround dask .chunks
1990172
@LucaMarconatoLucaMarconato
changed the title
enough features for the first applicationsenough features for the first applications (wip)Nov 2, 2022
@LucaMarconatoLucaMarconato
mentioned this pull request
Nov 30, 2022

Closed

@kevinyamauchi
kevinyamauchi
commented
Dec 13, 2022•

edited

Loading

Copy link


Copy Markdown

Collaborator
@LucaMarconato , can this PR be closed now that #52 has landed?
@LucaMarconato
LucaMarconato
commented
Dec 13, 2022

Copy link


Copy Markdown

MemberAuthor
@kevinyamauchi unfortunately not, it has features that are not merged yet. I plan to work on this over the the christmas holidays (should be 1-2 days of work).
@LucaMarconato
LucaMarconato
marked this pull request as draft
December 13, 2022 15:46
@kevinyamauchi
kevinyamauchi
commented
Dec 15, 2022

Copy link


Copy Markdown

Collaborator
No worries, @LucaMarconato ! Just checking in to see if I needed to do anything here 😛
@LucaMarconato
LucaMarconato
commented
Jan 4, 2023•

edited

Loading

Copy link


Copy Markdown

MemberAuthor
Instead of merging this branch, which is very outdated, I will pick the following and merge it in multiple prs. The rest can be discarded.
  •  filter_by_coordinate_system() from _spatialdata.py
  • concatenate() from _spatialdata.py
  •  generate multiscale from multiscale.py
  •  in general check read.py and eventually port the useful elements
  •  in general check write.py and eventually port the useful elements
  •  main.py (which adds cli support)
  •  restore links to the docs in the raedme
@LucaMarconatoLucaMarconato
changed the title
enough features for the first applications (wip)legacy code to portJan 30, 2023
@LucaMarconatoLucaMarconato
mentioned this pull request
Feb 13, 2023
 Merged

@LucaMarconato
LucaMarconato
deleted the

feature/transform_and_coord_spaces

branch
February 22, 2023 21:23
@LucaMarconato
LucaMarconato
commented
Feb 22, 2023

Copy link


Copy Markdown

MemberAuthor
The code of this branch is archived here.
Sign up for freeto join this conversation on GitHub.
Already have an account?
Sign in to comment

Reviewers


No reviews


Assignees


No one assigned


Labels


None yet


Projects


None yet


Milestone


No milestone


Development

Successfully merging this pull request may close these issues.

3 participants

@LucaMarconato@kevinyamauchi@giovp