Adjust visium spot positions

pyproject.toml

@@ -31,6 +31,7 @@ torchvision = "^0.6.0"
 tqdm = "^4.41.0"
 umap-learn = "^0.3.10"
 opencv-python = "^4.2.0"
+pycpd = "^2.0.0"
 
 [tool.poetry.dev-dependencies]
 mypy = "^0.761"

tests/data/files/visium/barcode_list.tsv

@@ -0,0 +1,64 @@
+AAA	1	1
+AAT	1	3
+AAG	1	5
+AAC	1	7
+ATA	1	9
+ATT	1	11
+ATG	1	13
+ATC	1	15
+AGA	2	1
+AGT	2	3
+AGG	2	5
+AGC	2	7
+ACA	2	9
+ACT	2	11
+ACG	2	13
+ACC	2	15
+TAA	3	1
+TAT	3	3
+TAG	3	5
+TAC	3	7
+TTA	3	9
+TTT	3	11
+TTG	3	13
+TTC	3	15
+TGA	4	1
+TGT	4	3
+TGG	4	5
+TGC	4	7
+TCA	4	9
+TCT	4	11
+TCG	4	13
+TCC	4	15
+GAA	5	1
+GAT	5	3
+GAG	5	5
+GAC	5	7
+GTA	5	9
+GTT	5	11
+GTG	5	13
+GTC	5	15
+GGA	6	1
+GGT	6	3
+GGG	6	5
+GGC	6	7
+GCA	6	9
+GCT	6	11
+GCG	6	13
+GCC	6	15
+CAA	7	1
+CAT	7	3
+CAG	7	5
+CAC	7	7
+CTA	7	9
+CTT	7	11
+CTG	7	13
+CTC	7	15
+CGA	8	1
+CGT	8	3
+CGG	8	5
+CGC	8	7
+CCA	8	9
+CCT	8	11
+CCG	8	13
+CCC	8	15

tests/data/files/visium/genepix_data.gpr

@@ -0,0 +1,70 @@
+ATF	1
+7	9
+"Type=GenePix Results 3"
+"BlockMapFiducials= A1:1"
+"BlockMapOligos= A1:2"
+Block	Column	Row	Name	X	Y	Dia.	Flags
+1	0	0	FRAME	10	10	8.0	0
+1	0	1	FRAME	10	21	8.0	1
+1	0	2	FRAME	10	33	8.0	0
+1	0	3	FRAME	10	44	8.0	0
+1	0	4	FRAME	10	56	8.0	0
+1	0	5	FRAME	10	67	8.0	0
+1	0	6	FRAME	10	79	8.0	0
+1	0	7	FRAME	10	90	8.0	0
+1	1	0	FRAME	21	10	8.0	1
+2	1	1	spot-1	21	21	5.0	0
+2	1	2	spot-2	21	33	5.0	0
+2	1	3	spot-3	21	44	5.0	0
+2	1	4	spot-4	21	56	5.0	0
+2	1	5	spot-5	21	67	5.0	0
+2	1	6	spot-6	21	79	5.0	0
+1	1	7	FRAME	21	90	8.0	0
+1	2	0	FRAME	33	10	8.0	1
+2	2	1	spot-7	33	21	5.0	1
+2	2	2	spot-8	33	33	5.0	0
+2	2	3	spot-9	33	44	5.0	0
+2	2	4	spot-10	33	56	5.0	0
+2	2	5	spot-11	33	67	5.0	0
+2	2	6	spot-12	33	79	5.0	0
+1	2	7	FRAME	33	90	8.0	0
+1	3	0	FRAME	44	10	8.0	0
+2	3	1	spot-13	44	21	5.0	1
+2	3	2	spot-14	44	33	5.0	0
+2	3	3	spot-15	44	44	5.0	0
+2	3	4	spot-16	44	56	5.0	0
+2	3	5	spot-17	44	67	5.0	1
+2	3	6	spot-18	44	79	5.0	0
+1	3	7	FRAME	44	90	8.0	0
+1	4	0	FRAME	56	10	8.0	0
+2	4	1	spot-19	56	21	5.0	0
+2	4	2	spot-20	56	33	5.0	0
+2	4	3	spot-21	56	44	5.0	0
+2	4	4	spot-22	56	56	5.0	0
+2	4	5	spot-23	56	67	5.0	0
+2	4	6	spot-24	56	79	5.0	0
+1	4	7	FRAME	56	90	8.0	0
+1	5	0	FRAME	67	10	8.0	0
+2	5	1	spot-25	67	21	5.0	0
+2	5	2	spot-26	67	33	5.0	1
+2	5	3	spot-27	67	44	5.0	0
+2	5	4	spot-28	67	56	5.0	0
+2	5	5	spot-29	67	67	5.0	0
+2	5	6	spot-30	67	79	5.0	0
+1	5	7	FRAME	67	90	8.0	0
+1	6	0	FRAME	79	10	8.0	0
+2	6	1	spot-31	79	21	5.0	0
+2	6	2	spot-32	79	33	5.0	0
+2	6	3	spot-33	79	44	5.0	0
+2	6	4	spot-34	79	56	5.0	0
+2	6	5	spot-35	79	67	5.0	0
+2	6	6	spot-36	79	79	5.0	1
+1	6	7	FRAME	79	90	8.0	0
+1	7	0	FRAME	90	10	8.0	0
+1	7	1	FRAME	90	21	8.0	0
+1	7	2	FRAME	90	33	8.0	1
+1	7	3	FRAME	90	44	8.0	0
+1	7	4	FRAME	90	56	8.0	0
+1	7	5	FRAME	90	67	8.0	0
+1	7	6	FRAME	90	79	8.0	0
+1	7	7	FRAME	90	90	8.0	0