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save metadata of aws result files to firebase #201

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711bd8e
Working variable count distributions
mogres Aug 16, 2023
8a00bbd
* add radius to molecules array
mogres Sep 8, 2023
c5aa16b
Test recipe and config for variable size
mogres Sep 8, 2023
de95dfe
add radius to ingredient array dict
mogres Sep 12, 2023
9bcd67f
turn off resolving inheritance while uploading
rugeli Sep 12, 2023
5c14f8a
able to upload recipes having "inherit" key
rugeli Sep 12, 2023
dde4a72
get download and pack to work, refactors needed
rugeli Sep 15, 2023
316fee7
add test variable size recipe
meganrm Sep 15, 2023
945eccb
create packed objects class
meganrm Sep 15, 2023
283015e
Merge branch 'feature/variable_size' of https://github.com/mesoscope/…
meganrm Sep 15, 2023
7db8bec
removing .molecules
meganrm Sep 15, 2023
8eb3190
pack variable size ingredient successfully
meganrm Sep 20, 2023
a23bdde
Merge branch 'main' of https://github.com/mesoscope/cellpack into fea…
meganrm Sep 20, 2023
fb3dcb9
pack sphere_tree ingredient
meganrm Sep 20, 2023
4c47c8c
DRY code
meganrm Sep 20, 2023
3b97426
store ingredient in packed object
meganrm Sep 21, 2023
b665e77
change to compartment_id
meganrm Sep 21, 2023
7836419
cleanup
meganrm Sep 21, 2023
5541d22
add second example
meganrm Sep 21, 2023
49446bc
Merge branch 'main' of https://github.com/mesoscope/cellpack into fea…
rugeli Sep 25, 2023
00628e9
refactors
rugeli Sep 26, 2023
c8bcccf
Merge branch 'main' of https://github.com/mesoscope/cellpack into fea…
rugeli Sep 27, 2023
d161baa
Merge branch 'feature/run-recipes-from-firebase' into feature/run-inh…
rugeli Sep 27, 2023
3d82959
Merge branch 'feature/run-inherited-objects' of https://github.com/me…
rugeli Oct 3, 2023
00601e3
initial draft
rugeli Oct 4, 2023
5318f33
reorder methods in firebase handler
rugeli Oct 5, 2023
eac5704
avoid initializing app twice
rugeli Oct 5, 2023
1539654
modularize firebase handler
rugeli Oct 5, 2023
e58dbe5
modularize AWSHandler & refactors
rugeli Oct 6, 2023
d5207c5
* fixed broken image export
mogres Oct 6, 2023
aae4e49
fix flake8 linting errors
mogres Oct 9, 2023
d4084c4
Update cellpack/autopack/ingredient/Ingredient.py
meganrm Oct 9, 2023
ca1464d
Update cellpack/autopack/ingredient/Ingredient.py
meganrm Oct 9, 2023
41a300e
Update cellpack/tests/packing-configs/test_variable_count_config.json
meganrm Oct 9, 2023
9d3e0cd
Update cellpack/autopack/ingredient/Ingredient.py
meganrm Oct 9, 2023
75c870c
Update cellpack/autopack/ingredient/Ingredient.py
meganrm Oct 9, 2023
eadb2e6
Update cellpack/autopack/utils.py
meganrm Oct 9, 2023
862d2e5
get ingredient directly
meganrm Oct 9, 2023
c0741ba
revert change to static method
meganrm Oct 9, 2023
67b59e3
Merge branch 'feature/results-in-memory' of https://github.com/mesosc…
meganrm Oct 9, 2023
ec51ab4
fix test
meganrm Oct 9, 2023
d480893
* use kwargs to overload voxelization function
mogres Oct 10, 2023
9065f17
fix tests
mogres Oct 10, 2023
e9dc5b6
removed afvi from `get_partners` which was erroring out
mogres Oct 10, 2023
4be3fed
remove `afvi` argument causing partner packing to break
mogres Oct 11, 2023
ee214e3
add get methods for packed objects
meganrm Oct 11, 2023
6430603
Merge branch 'feature/results-in-memory' of https://github.com/mesosc…
meganrm Oct 11, 2023
1605221
move when we store compartments in packed_objects
meganrm Oct 11, 2023
4a887de
change radius
meganrm Oct 11, 2023
25d9839
use ingredient stored for compartment
meganrm Oct 11, 2023
fe89fb7
fix linting
mogres Oct 12, 2023
c975872
pack sphere trees successfully and plot in 2D
meganrm Oct 12, 2023
5d9ecae
Merge branch 'feature/results-in-memory' of https://github.com/mesosc…
meganrm Oct 12, 2023
9105668
fix/S3 uploads and new browser tabs handling (#203)
rugeli Oct 12, 2023
d35738d
format fixed
meganrm Oct 12, 2023
5da57e0
Fix gradient inversion (#196)
mogres Oct 13, 2023
aae7ed1
Merge pull request #193 from mesoscope/feature/results-in-memory
meganrm Oct 13, 2023
7e2c633
Merge branch 'main' of https://github.com/mesoscope/cellpack into fea…
rugeli Oct 17, 2023
0d577fe
Merge branch 'feature/run-recipes-from-firebase' of https://github.co…
rugeli Oct 17, 2023
44c3cb2
formatting
rugeli Oct 17, 2023
7c0aae3
testing and refactor
rugeli Oct 23, 2023
e6777dd
initial draft
rugeli Oct 4, 2023
c14dfbc
reorder methods in firebase handler
rugeli Oct 5, 2023
ad7c7c4
avoid initializing app twice
rugeli Oct 5, 2023
7f7f0f7
modularize firebase handler
rugeli Oct 5, 2023
1c8ac68
modularize AWSHandler & refactors
rugeli Oct 6, 2023
82f7f7f
Merge branch 'feature/save-metadata' of https://github.com/mesoscope/…
rugeli Oct 23, 2023
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add test variable size recipe
meganrm committed Sep 15, 2023
commit 316fee77f0ffe0bcfa02eeaf9a139f5a31ec528b
Original file line number Diff line number Diff line change
@@ -6,7 +6,7 @@
"ordered_packing": false,
"out": "cellpack/tests/outputs/",
"overwrite_place_method": true,
"number_of_packings": 10,
"number_of_packings": 2,
"place_method": "spheresSST",
"save_analyze_result": true,
"show_grid_plot": false,
87 changes: 87 additions & 0 deletions cellpack/tests/recipes/v2/test_variable_size.json
Original file line number Diff line number Diff line change
@@ -0,0 +1,87 @@
{
"version": "1.0.0",
"format_version": "2.0",
"name": "test_variable_size",
"bounding_box": [
[
0,
0,
0
],
[
100,
100,
1
]
],
"objects": {
"base": {
"jitter_attempts": 10,
"orient_bias_range": [
-3.1415927,
3.1415927
],
"rotation_range": 6.2831,
"cutoff_boundary": 0,
"max_jitter": [
1,
1,
0
],
"perturb_axis_amplitude": 0.1,
"packing_mode": "random",
"principal_vector": [
0,
0,
1
],
"rejection_threshold": 50,
"place_method": "spheresSST",
"cutoff_surface": 42,
"rotation_axis": [
0,
0,
1
],
"available_regions": {
"interior": {},
"surface": {},
"outer_leaflet": {},
"inner_leaflet": {}
}
},
"sphere_25": {
"type": "single_sphere",
"inherit": "base",
"color": [
0.5,
0.5,
0.5
],
"radius": 25,
"max_jitter": [
1,
1,
0
]
}
},
"composition": {
"space": {
"regions": {
"interior": [
"A"
]
}
},
"A": {
"object": "sphere_25",
"count": 10,
"size_options": {
"distribution": "uniform",
"min": 5,
"max": 30
}
}
}
}