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Fix test snapshots for mesmer-derived csvs
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This changes all of these to summarizeCsv.
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@jmuhlich
jmuhlich committed Aug 19, 2024
1 parent d4b27a8 commit 344dfd6
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Showing 2 changed files with 183 additions and 22 deletions.
16 changes: 8 additions & 8 deletions tests/main.nf.test
View file
Original file line number Diff line number Diff line change
Expand Up @@ -40,7 +40,7 @@ nextflow_workflow {
assert snapshot (
path("$outputDir/registration/ashlar/TEST1.ome.tif"),
path("$outputDir/segmentation/deepcell_mesmer/mask_TEST1.tif"),
CsvUtils.roundAndHashCsv("$outputDir/quantification/mcquant/mesmer/TEST1_mask_TEST1.csv"),
CsvUtils.summarizeCsv("$outputDir/quantification/mcquant/mesmer/TEST1_mask_TEST1.csv"),
).match()
},
{ assert workflow.success }
Expand Down Expand Up @@ -129,7 +129,7 @@ nextflow_workflow {
assert snapshot (
path("$outputDir/registration/ashlar/TEST1.ome.tif"),
path("$outputDir/segmentation/deepcell_mesmer/mask_TEST1.tif"),
CsvUtils.roundAndHashCsv("$outputDir/quantification/mcquant/mesmer/TEST1_mask_TEST1.csv")
CsvUtils.summarizeCsv("$outputDir/quantification/mcquant/mesmer/TEST1_mask_TEST1.csv")
).match()
},
{ assert workflow.success }
Expand Down Expand Up @@ -191,7 +191,7 @@ nextflow_workflow {
assert snapshot (
path("$outputDir/registration/ashlar/cycif-tonsil.ome.tif"),
path("$outputDir/segmentation/deepcell_mesmer/mask_cycif-tonsil.tif"),
CsvUtils.roundAndHashCsv("$outputDir/quantification/mcquant/mesmer/cycif-tonsil_mask_cycif-tonsil.csv")
CsvUtils.summarizeCsv("$outputDir/quantification/mcquant/mesmer/cycif-tonsil_mask_cycif-tonsil.csv")
).match()
},
{ assert workflow.success }
Expand Down Expand Up @@ -257,8 +257,8 @@ nextflow_workflow {
path("$outputDir/registration/ashlar/cycif-tonsil2.ome.tif"),
path("$outputDir/segmentation/deepcell_mesmer/mask_cycif-tonsil.tif"),
path("$outputDir/segmentation/deepcell_mesmer/mask_cycif-tonsil2.tif"),
CsvUtils.roundAndHashCsv("$outputDir/quantification/mcquant/mesmer/cycif-tonsil_mask_cycif-tonsil.csv"),
CsvUtils.roundAndHashCsv("$outputDir/quantification/mcquant/mesmer/cycif-tonsil2_mask_cycif-tonsil2.csv"),
CsvUtils.summarizeCsv("$outputDir/quantification/mcquant/mesmer/cycif-tonsil_mask_cycif-tonsil.csv"),
CsvUtils.summarizeCsv("$outputDir/quantification/mcquant/mesmer/cycif-tonsil2_mask_cycif-tonsil2.csv"),
).match()
},
{ assert workflow.success }
Expand Down Expand Up @@ -326,8 +326,8 @@ nextflow_workflow {
path("$outputDir/segmentation/deepcell_mesmer/mask_cycif-tonsil2.tif"),
path("$outputDir/segmentation/cellpose/cycif-tonsil.ome_cp_masks.tif"),
path("$outputDir/segmentation/cellpose/cycif-tonsil2.ome_cp_masks.tif"),
CsvUtils.roundAndHashCsv("$outputDir/quantification/mcquant/mesmer/cycif-tonsil_mask_cycif-tonsil.csv"),
CsvUtils.roundAndHashCsv("$outputDir/quantification/mcquant/mesmer/cycif-tonsil2_mask_cycif-tonsil2.csv"),
CsvUtils.summarizeCsv("$outputDir/quantification/mcquant/mesmer/cycif-tonsil_mask_cycif-tonsil.csv"),
CsvUtils.summarizeCsv("$outputDir/quantification/mcquant/mesmer/cycif-tonsil2_mask_cycif-tonsil2.csv"),
CsvUtils.roundAndHashCsv("$outputDir/quantification/mcquant/cellpose/cycif-tonsil_cycif-tonsil.csv"),
CsvUtils.roundAndHashCsv("$outputDir/quantification/mcquant/cellpose/cycif-tonsil2_cycif-tonsil2.csv"),
).match()
Expand Down Expand Up @@ -464,7 +464,7 @@ nextflow_workflow {
ImageUtils.getImageMetadata("$outputDir/registration/ashlar/cycif-tonsil.ome.tif"),
ImageUtils.getImageMetadata("$outputDir/registration/ashlar/cycif-tonsil2.ome.tif"),
ImageUtils.getImageMetadata("$outputDir/segmentation/deepcell_mesmer/mask_cycif-tonsil.tif"),
path("$outputDir/segmentation/deepcell_mesmer/mask_cycif-tonsil2.tif"),
ImageUtils.getImageMetadata("$outputDir/segmentation/deepcell_mesmer/mask_cycif-tonsil2.tif"),
CsvUtils.summarizeCsv("$outputDir/quantification/mcquant/mesmer/cycif-tonsil_mask_cycif-tonsil.csv"),
CsvUtils.summarizeCsv("$outputDir/quantification/mcquant/mesmer/cycif-tonsil2_mask_cycif-tonsil2.csv"),
ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/cycif-tonsil-cycle1.ome-dfp.tiff"),
Expand Down
189 changes: 175 additions & 14 deletions tests/main.nf.test.snap
View file
Original file line number Diff line number Diff line change
Expand Up @@ -3,13 +3,39 @@
"content": [
"cycif-tonsil.ome.tif:md5,5f4165203545b7efe04ed5f4a6d5ac9d",
"mask_cycif-tonsil.tif:md5,3103759bd55b9deeb8c8a0dade798d9a",
"cycif-tonsil_mask_cycif-tonsil.csv:rounded:md5,1a5d00850b8194d4d6b3ee41000ed0c0"
{
"headers": [
"CellID",
"DNA_6",
"ELANE",
"CD57",
"CD45",
"DNA_7",
"ELANE7",
"CD577",
"CD457",
"DNA_8",
"ELANE8",
"CD578",
"CD458",
"X_centroid",
"Y_centroid",
"Area",
"MajorAxisLength",
"MinorAxisLength",
"Eccentricity",
"Solidity",
"Extent",
"Orientation"
],
"rowCount": 2111
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.4"
},
"timestamp": "2024-08-14T13:22:51.207081332"
"timestamp": "2024-08-19T09:56:59.706545924"
},
"cycle: basicpy illumination correction": {
"content": [
Expand Down Expand Up @@ -95,16 +121,60 @@
"mask_cycif-tonsil2.tif:md5,cfd4ef0f19766bcc8156a0f0ab117777",
"cycif-tonsil.ome_cp_masks.tif:md5,88690c63ef3b695f44e5bad40b8175a3",
"cycif-tonsil2.ome_cp_masks.tif:md5,c4590940d460cfe34168661573cfd87d",
"cycif-tonsil_mask_cycif-tonsil.csv:rounded:md5,31a563b928c6c2ad3558f0a696383add",
"cycif-tonsil2_mask_cycif-tonsil2.csv:rounded:md5,b55ab8e8a1394dc316ed95f2c3beb144",
{
"headers": [
"CellID",
"DNA_6",
"ELANE",
"CD57",
"CD45",
"DNA_7",
"ELANE7",
"CD577",
"CD457",
"X_centroid",
"Y_centroid",
"Area",
"MajorAxisLength",
"MinorAxisLength",
"Eccentricity",
"Solidity",
"Extent",
"Orientation"
],
"rowCount": 2111
},
{
"headers": [
"CellID",
"DNA_6",
"ELANE",
"CD57",
"CD45",
"DNA_7",
"ELANE7",
"CD577",
"CD457",
"X_centroid",
"Y_centroid",
"Area",
"MajorAxisLength",
"MinorAxisLength",
"Eccentricity",
"Solidity",
"Extent",
"Orientation"
],
"rowCount": 2082
},
"cycif-tonsil_cycif-tonsil.csv:rounded:md5,96c0754e24b8474d4c191bdff4351701",
"cycif-tonsil2_cycif-tonsil2.csv:rounded:md5,a53cf1c3df3ff3edfa93e1d266185701"
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.4"
},
"timestamp": "2024-08-14T13:30:38.624374798"
"timestamp": "2024-08-19T09:59:20.121769085"
},
"cycle: no illumination correction, cellpose segmentation": {
"content": [
Expand All @@ -122,13 +192,31 @@
"content": [
"TEST1.ome.tif:md5,ae98ac74e3c818bb26c99ba4b9c2dd51",
"mask_TEST1.tif:md5,3103759bd55b9deeb8c8a0dade798d9a",
"TEST1_mask_TEST1.csv:rounded:md5,5f05c32de9104a23cc8d98583f781d1b"
{
"headers": [
"CellID",
"DNA_6",
"ELANE",
"CD57",
"CD45",
"X_centroid",
"Y_centroid",
"Area",
"MajorAxisLength",
"MinorAxisLength",
"Eccentricity",
"Solidity",
"Extent",
"Orientation"
],
"rowCount": 2111
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.4"
},
"timestamp": "2024-08-14T13:21:06.616299154"
"timestamp": "2024-08-19T09:54:49.029179502"
},
"cycle: multiple file ashlar input with basicpy correction": {
"content": [
Expand Down Expand Up @@ -300,7 +388,18 @@
"physicalSizeY": 1.0,
"physicalSizeZ": null
},
"mask_cycif-tonsil2.tif:md5,e88138acfedf06c4ac83634a96c4df3d",
{
"format": "Tagged Image File Format",
"type": "int32",
"sizeX": 591,
"sizeY": 468,
"sizeZ": 1,
"sizeC": 1,
"sizeT": 1,
"physicalSizeX": 1.0,
"physicalSizeY": 1.0,
"physicalSizeZ": null
},
{
"headers": [
"CellID",
Expand Down Expand Up @@ -424,34 +523,96 @@
"nf-test": "0.8.4",
"nextflow": "24.04.4"
},
"timestamp": "2024-08-14T13:32:13.483473681"
"timestamp": "2024-08-19T10:01:39.136409344"
},
"cycle: manual illumination correction": {
"content": [
"TEST1.ome.tif:md5,ae98ac74e3c818bb26c99ba4b9c2dd51",
"mask_TEST1.tif:md5,3103759bd55b9deeb8c8a0dade798d9a",
"TEST1_mask_TEST1.csv:rounded:md5,5f05c32de9104a23cc8d98583f781d1b"
{
"headers": [
"CellID",
"DNA_6",
"ELANE",
"CD57",
"CD45",
"X_centroid",
"Y_centroid",
"Area",
"MajorAxisLength",
"MinorAxisLength",
"Eccentricity",
"Solidity",
"Extent",
"Orientation"
],
"rowCount": 2111
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.4"
},
"timestamp": "2024-08-14T13:22:19.054423541"
"timestamp": "2024-08-19T09:56:17.141863983"
},
"cycle: multiple file ashlar input with multiple samples no correction": {
"content": [
"cycif-tonsil.ome.tif:md5,9d4fca1d7ec97be3f6343eb712af9dea",
"cycif-tonsil2.ome.tif:md5,ea772fef41d398ffd76cbb6354266678",
"mask_cycif-tonsil.tif:md5,3103759bd55b9deeb8c8a0dade798d9a",
"mask_cycif-tonsil2.tif:md5,cfd4ef0f19766bcc8156a0f0ab117777",
"cycif-tonsil_mask_cycif-tonsil.csv:rounded:md5,31a563b928c6c2ad3558f0a696383add",
"cycif-tonsil2_mask_cycif-tonsil2.csv:rounded:md5,b55ab8e8a1394dc316ed95f2c3beb144"
{
"headers": [
"CellID",
"DNA_6",
"ELANE",
"CD57",
"CD45",
"DNA_7",
"ELANE7",
"CD577",
"CD457",
"X_centroid",
"Y_centroid",
"Area",
"MajorAxisLength",
"MinorAxisLength",
"Eccentricity",
"Solidity",
"Extent",
"Orientation"
],
"rowCount": 2111
},
{
"headers": [
"CellID",
"DNA_6",
"ELANE",
"CD57",
"CD45",
"DNA_7",
"ELANE7",
"CD577",
"CD457",
"X_centroid",
"Y_centroid",
"Area",
"MajorAxisLength",
"MinorAxisLength",
"Eccentricity",
"Solidity",
"Extent",
"Orientation"
],
"rowCount": 2082
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.4"
},
"timestamp": "2024-04-22T15:59:42.197064018"
"timestamp": "2024-08-19T09:57:45.598919397"
},
"cycle: no illumination correction, coreograph": {
"content": [
Expand Down

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