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Constructing spatial neighborhood with custom parameters #126

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Dec 15, 2023
Merged

Constructing spatial neighborhood with custom parameters #126

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7d98cd2
Constructing spatial neighborhood with custom parameters
Dec 13, 2023
bdac0af
Separate each function into individual file
Qirongmao97 Dec 14, 2023
3f68c32
Delete preprocessing/neighbors/neighborhood_construction.py
Qirongmao97 Dec 14, 2023
3890170
Delete preprocessing/neighbors/neighborhood_construction.yml
Qirongmao97 Dec 14, 2023
4130adf
Update delaunay_triangulation.py
Qirongmao97 Dec 14, 2023
36367e9
Update coord_type.py
Qirongmao97 Dec 14, 2023
6e77564
Update n_neighs.py
Qirongmao97 Dec 14, 2023
d30d4ac
Update n_rings.py
Qirongmao97 Dec 14, 2023
ee5533f
Update radius.py
Qirongmao97 Dec 14, 2023
235a298
Update and rename n_neighs.py to n_neighbourhood.py
Qirongmao97 Dec 14, 2023
ea486da
Update delaunay_triangulation.py
Qirongmao97 Dec 14, 2023
0625fdb
Delete preprocessing/neighbors/coord_type.py
Qirongmao97 Dec 14, 2023
d87dcf7
Delete preprocessing/neighbors/coord_type.yml
Qirongmao97 Dec 14, 2023
e76411a
Update n_neighbourhood.py
Qirongmao97 Dec 14, 2023
f8e317b
Update delaunay_triangulation.py
Qirongmao97 Dec 14, 2023
db8597d
Update n_rings.py
Qirongmao97 Dec 14, 2023
fb659d7
Update radius.py
Qirongmao97 Dec 14, 2023
6c551de
Committing changes based on the comments
Dec 14, 2023
94528f3
Putting each function to subdirectory
Dec 15, 2023
97c6bd2
Removing config file of Delaunay Traingulation
Dec 15, 2023
dc59a5b
remove config reading
niklasmueboe Dec 15, 2023
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6 changes: 0 additions & 6 deletions preprocessing/neighbors/config.json
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3 changes: 3 additions & 0 deletions preprocessing/neighbors/delaunay_traingulation/config/config_1.json
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@niklasmueboe niklasmueboe Dec 15, 2023 •
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Why delaunay: false. I think for this one we won't need a config at all. And delaunay should always be true

Original file line number Diff line number Diff line change
@@ -0,0 +1,3 @@
{
"delaunay":false
}
0 ...sing/neighbors/delaunay_traingulation.yml → ..._traingulation/delaunay_traingulation.yml
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5 changes: 4 additions & 1 deletion ...ssing/neighbors/delaunay_triangulation.py → ...y_traingulation/delaunay_triangulation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -37,6 +37,8 @@
out_dir = Path(args.out_dir)

spatial_connectivities_file = out_dir / "spatial_connectivities.mtx"
##spatial_distances_file = out_dir / "spatial_distances.mtx"


# Use these filepaths and inputs ...
coord_file = args.coordinates
Expand Down Expand Up @@ -89,11 +91,12 @@ def get_anndata(args):
sq.gr.spatial_neighbors(adata, delaunay=delaunay, coord_type="generic")

neighbors = adata.obsp["spatial_connectivities"].astype(int)
##distance = adata.obsp["spatial_distances"].astype(float)

## Write output
import scipy as sp

out_dir.mkdir(parents=True, exist_ok=True)

sp.io.mmwrite(spatial_connectivities_file, neighbors)
##sp.io.mmwrite(spatial_distances_file, distance)
3 changes: 3 additions & 0 deletions preprocessing/neighbors/n_neighbourhood/config/config_1.json
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Original file line number Diff line number Diff line change
@@ -0,0 +1,3 @@
{
"n_neighs":6
}
4 changes: 3 additions & 1 deletion preprocessing/neighbors/n_neighbourhood.py → ...ghbors/n_neighbourhood/n_neighbourhood.py
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Original file line number Diff line number Diff line change
Expand Up @@ -42,6 +42,7 @@
out_dir = Path(args.out_dir)

spatial_connectivities_file = out_dir / "spatial_connectivities.mtx"
##spatial_distances_file = out_dir / "spatial_distances.mtx"

# Use these filepaths and inputs ...
coord_file = args.coordinates
Expand Down Expand Up @@ -94,11 +95,12 @@ def get_anndata(args):
sq.gr.spatial_neighbors(adata, n_neighs=n_neighs, coord_type="generic")

neighbors = adata.obsp["spatial_connectivities"].astype(int)
##distance = adata.obsp["spatial_distances"].astype(float)

## Write output
import scipy as sp

out_dir.mkdir(parents=True, exist_ok=True)

sp.io.mmwrite(spatial_connectivities_file, neighbors)

##sp.io.mmwrite(spatial_distances_file, distance)
0 preprocessing/neighbors/n_neighbourhood.yml → ...hbors/n_neighbourhood/n_neighbourhood.yml
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3 changes: 3 additions & 0 deletions preprocessing/neighbors/n_rings/config/config_1.json
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Original file line number Diff line number Diff line change
@@ -0,0 +1,3 @@
{
"n_rings":1
}
4 changes: 3 additions & 1 deletion preprocessing/neighbors/n_rings.py → preprocessing/neighbors/n_rings/n_rings.py
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Original file line number Diff line number Diff line change
Expand Up @@ -43,6 +43,7 @@
out_dir = Path(args.out_dir)

spatial_connectivities_file = out_dir / "spatial_connectivities.mtx"
##spatial_distances_file = out_dir / "spatial_distances.mtx"

# Use these filepaths and inputs ...
coord_file = args.coordinates
Expand Down Expand Up @@ -96,11 +97,12 @@ def get_anndata(args):
sq.gr.spatial_neighbors(adata,n_rings=n_rings, coord_type="grid")

neighbors = adata.obsp["spatial_connectivities"].astype(int)
##distance = adata.obsp["spatial_distances"].astype(float)

## Write output
import scipy as sp

out_dir.mkdir(parents=True, exist_ok=True)

sp.io.mmwrite(spatial_connectivities_file, neighbors)

##sp.io.mmwrite(spatial_distances_file, distance)
0 preprocessing/neighbors/n_rings.yml → preprocessing/neighbors/n_rings/n_rings.yml
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3 changes: 3 additions & 0 deletions preprocessing/neighbors/radius/config/config_1.json
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Original file line number Diff line number Diff line change
@@ -0,0 +1,3 @@
{
"radius":1
}
4 changes: 3 additions & 1 deletion preprocessing/neighbors/radius.py → preprocessing/neighbors/radius/radius.py
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Original file line number Diff line number Diff line change
Expand Up @@ -42,6 +42,7 @@
out_dir = Path(args.out_dir)

spatial_connectivities_file = out_dir / "spatial_connectivities.mtx"
##spatial_distances_file = out_dir / "spatial_distances.mtx"

# Use these filepaths and inputs ...
coord_file = args.coordinates
Expand Down Expand Up @@ -94,11 +95,12 @@ def get_anndata(args):
sq.gr.spatial_neighbors(adata, radius=radius, coord_type='generic')

neighbors = adata.obsp["spatial_connectivities"].astype(int)
##distance = adata.obsp["spatial_distances"].astype(float)

## Write output
import scipy as sp

out_dir.mkdir(parents=True, exist_ok=True)

sp.io.mmwrite(spatial_connectivities_file, neighbors)

##sp.io.mmwrite(spatial_distances_file, distance)
0 preprocessing/neighbors/radius.yml → preprocessing/neighbors/radius/radius.yml
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File renamed without changes.