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run fastseg on lightweight test data
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@AlexVCaron
AlexVCaron committed Sep 4, 2024
1 parent aa7c870 commit faccae7
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Showing 3 changed files with 47 additions and 245 deletions.
28 changes: 22 additions & 6 deletions modules/nf-scil/segmentation/fastseg/tests/main.nf.test
View file
Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@ nextflow_process {
script "../../../../../subworkflows/nf-scil/load_test_data/main.nf"
process {
"""
input[0] = Channel.from( [ "heavy.zip" ] )
input[0] = Channel.from( [ "T1w.zip" ] )
input[1] = "test.load-test-data"
"""
}
Expand All @@ -34,7 +34,7 @@ nextflow_process {
input[0] = LOAD_DATA.out.test_data_directory.map{
test_data_directory -> [
[ id:'test', single_end:false ], // meta map
file("\${test_data_directory}/anat/anat_image.nii.gz", checkIfExists: true,),
file("\${test_data_directory}/T1w.nii.gz", checkIfExists: true,),
[]
]
}
Expand All @@ -45,7 +45,15 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
{ assert snapshot(
niftiMD5SUM(process.out.wm_mask.get(0).get(1)),
niftiMD5SUM(process.out.gm_mask.get(0).get(1)),
niftiMD5SUM(process.out.csf_mask.get(0).get(1)),
niftiMD5SUM(process.out.wm_map.get(0).get(1)),
niftiMD5SUM(process.out.gm_map.get(0).get(1)),
niftiMD5SUM(process.out.csf_map.get(0).get(1)),
process.out.versions
).match() }
)
}
}
Expand All @@ -56,8 +64,8 @@ nextflow_process {
input[0] = LOAD_DATA.out.test_data_directory.map{
test_data_directory -> [
[ id:'test', single_end:false ], // meta map
file("\${test_data_directory}/anat/anat_image.nii.gz", checkIfExists: true,),
file("\${test_data_directory}/anat/anat_mask.nii.gz", checkIfExists: true)
file("\${test_data_directory}/T1w.nii.gz", checkIfExists: true,),
file("\${test_data_directory}/T1w_mask.nii.gz", checkIfExists: true)
]
}
"""
Expand All @@ -67,7 +75,15 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
{ assert snapshot(
niftiMD5SUM(process.out.wm_mask.get(0).get(1)),
niftiMD5SUM(process.out.gm_mask.get(0).get(1)),
niftiMD5SUM(process.out.csf_mask.get(0).get(1)),
niftiMD5SUM(process.out.wm_map.get(0).get(1)),
niftiMD5SUM(process.out.gm_map.get(0).get(1)),
niftiMD5SUM(process.out.csf_map.get(0).get(1)),
process.out.versions
).match() }
)
}
}
Expand Down
262 changes: 24 additions & 238 deletions modules/nf-scil/segmentation/fastseg/tests/main.nf.test.snap
View file
Original file line number Diff line number Diff line change
@@ -1,252 +1,38 @@
{
"segmentation - fastseg - lesion": {
"content": [
{
"0": [
[
{
"id": "test",
"single_end": false
},
"test__mask_wm.nii.gz:md5,2b2ced42fcf870d68ff44bf90d2701d4"
]
],
"1": [
[
{
"id": "test",
"single_end": false
},
"test__mask_gm.nii.gz:md5,39396421c6d1d32ea7943a5ec7a49dce"
]
],
"2": [
[
{
"id": "test",
"single_end": false
},
"test__mask_csf.nii.gz:md5,d0fbc088059f17faff38fbcd33257d27"
]
],
"3": [
[
{
"id": "test",
"single_end": false
},
"test__map_wm.nii.gz:md5,1d5a9655d4e3c832b14c83e9424b00fc"
]
],
"4": [
[
{
"id": "test",
"single_end": false
},
"test__map_gm.nii.gz:md5,f7e51eb14af645c687db5d2c6a4f5bf4"
]
],
"5": [
[
{
"id": "test",
"single_end": false
},
"test__map_csf.nii.gz:md5,9c14d8f70e69d641d9c214d0d52b3663"
]
],
"6": [
"versions.yml:md5,d42da2620c5aa82292375b0f9d8d7092"
],
"csf_map": [
[
{
"id": "test",
"single_end": false
},
"test__map_csf.nii.gz:md5,9c14d8f70e69d641d9c214d0d52b3663"
]
],
"csf_mask": [
[
{
"id": "test",
"single_end": false
},
"test__mask_csf.nii.gz:md5,d0fbc088059f17faff38fbcd33257d27"
]
],
"gm_map": [
[
{
"id": "test",
"single_end": false
},
"test__map_gm.nii.gz:md5,f7e51eb14af645c687db5d2c6a4f5bf4"
]
],
"gm_mask": [
[
{
"id": "test",
"single_end": false
},
"test__mask_gm.nii.gz:md5,39396421c6d1d32ea7943a5ec7a49dce"
]
],
"versions": [
"versions.yml:md5,d42da2620c5aa82292375b0f9d8d7092"
],
"wm_map": [
[
{
"id": "test",
"single_end": false
},
"test__map_wm.nii.gz:md5,1d5a9655d4e3c832b14c83e9424b00fc"
]
],
"wm_mask": [
[
{
"id": "test",
"single_end": false
},
"test__mask_wm.nii.gz:md5,2b2ced42fcf870d68ff44bf90d2701d4"
]
]
}
"test__mask_wm.nii.gz:md5:header,18e02970ee42367e0ee9f81b36cde160,data,e4d00ba5559d32119050e6afe77b627c",
"test__mask_gm.nii.gz:md5:header,cb2d88714675fc7d8c450de4db5227c6,data,d713974dbe87760182112e10f96a7f82",
"test__mask_csf.nii.gz:md5:header,cb2d88714675fc7d8c450de4db5227c6,data,29599fab55e3ee75318cef36563684a4",
"test__map_wm.nii.gz:md5:header,58dc3623694060dace951ba8073d5e01,data,62a268dbc74814d62ed9f9596b5a72e5",
"test__map_gm.nii.gz:md5:header,58dc3623694060dace951ba8073d5e01,data,420e7664f81a5899f7007f71c08f28d8",
"test__map_csf.nii.gz:md5:header,58dc3623694060dace951ba8073d5e01,data,2bde307c6dae36a5fc00eba7a2ca7933",
[
"versions.yml:md5,d42da2620c5aa82292375b0f9d8d7092"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nf-test": "0.9.0-rc1",
"nextflow": "24.04.4"
},
"timestamp": "2024-06-17T13:59:58.264241"
"timestamp": "2024-09-04T20:12:08.928978"
},
"segmentation - fastseg": {
"content": [
{
"0": [
[
{
"id": "test",
"single_end": false
},
"test__mask_wm.nii.gz:md5,f849e268007a747714e342162f13f631"
]
],
"1": [
[
{
"id": "test",
"single_end": false
},
"test__mask_gm.nii.gz:md5,39396421c6d1d32ea7943a5ec7a49dce"
]
],
"2": [
[
{
"id": "test",
"single_end": false
},
"test__mask_csf.nii.gz:md5,d0fbc088059f17faff38fbcd33257d27"
]
],
"3": [
[
{
"id": "test",
"single_end": false
},
"test__map_wm.nii.gz:md5,1d5a9655d4e3c832b14c83e9424b00fc"
]
],
"4": [
[
{
"id": "test",
"single_end": false
},
"test__map_gm.nii.gz:md5,f7e51eb14af645c687db5d2c6a4f5bf4"
]
],
"5": [
[
{
"id": "test",
"single_end": false
},
"test__map_csf.nii.gz:md5,9c14d8f70e69d641d9c214d0d52b3663"
]
],
"6": [
"versions.yml:md5,d42da2620c5aa82292375b0f9d8d7092"
],
"csf_map": [
[
{
"id": "test",
"single_end": false
},
"test__map_csf.nii.gz:md5,9c14d8f70e69d641d9c214d0d52b3663"
]
],
"csf_mask": [
[
{
"id": "test",
"single_end": false
},
"test__mask_csf.nii.gz:md5,d0fbc088059f17faff38fbcd33257d27"
]
],
"gm_map": [
[
{
"id": "test",
"single_end": false
},
"test__map_gm.nii.gz:md5,f7e51eb14af645c687db5d2c6a4f5bf4"
]
],
"gm_mask": [
[
{
"id": "test",
"single_end": false
},
"test__mask_gm.nii.gz:md5,39396421c6d1d32ea7943a5ec7a49dce"
]
],
"versions": [
"versions.yml:md5,d42da2620c5aa82292375b0f9d8d7092"
],
"wm_map": [
[
{
"id": "test",
"single_end": false
},
"test__map_wm.nii.gz:md5,1d5a9655d4e3c832b14c83e9424b00fc"
]
],
"wm_mask": [
[
{
"id": "test",
"single_end": false
},
"test__mask_wm.nii.gz:md5,f849e268007a747714e342162f13f631"
]
]
}
"test__mask_wm.nii.gz:md5:header,cb2d88714675fc7d8c450de4db5227c6,data,08b5c8665f0a07c182eb63f045d01855",
"test__mask_gm.nii.gz:md5:header,cb2d88714675fc7d8c450de4db5227c6,data,d713974dbe87760182112e10f96a7f82",
"test__mask_csf.nii.gz:md5:header,cb2d88714675fc7d8c450de4db5227c6,data,29599fab55e3ee75318cef36563684a4",
"test__map_wm.nii.gz:md5:header,58dc3623694060dace951ba8073d5e01,data,62a268dbc74814d62ed9f9596b5a72e5",
"test__map_gm.nii.gz:md5:header,58dc3623694060dace951ba8073d5e01,data,420e7664f81a5899f7007f71c08f28d8",
"test__map_csf.nii.gz:md5:header,58dc3623694060dace951ba8073d5e01,data,2bde307c6dae36a5fc00eba7a2ca7933",
[
"versions.yml:md5,d42da2620c5aa82292375b0f9d8d7092"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nf-test": "0.9.0-rc1",
"nextflow": "24.04.4"
},
"timestamp": "2024-06-13T19:52:04.291343"
"timestamp": "2024-09-04T20:03:24.730234"
}
}
2 changes: 1 addition & 1 deletion tests/config/test_data.json
View file
Original file line number Diff line number Diff line change
Expand Up @@ -48,7 +48,7 @@
"DWIss300-dir8.zip": "ef1335775c9fbf11452c71e01b097282",
"DWIss1000-dir32.zip": "c72fd590a3f400278299a068eeffd1d0",
"DWIss2000-dir60.zip": "9ad7ccb4e30b39c47f374018db2e6424",
"T1w.zip": "10e27bb2ddd4d01be968a93b2166096c",
"T1w.zip": "8e9cf2beec4595d407732152a19589f5",
"dti.zip": "ba866c59fc4d984f626691a6b941fc32",
"responses.zip": "1a5b862b91c72740bcce0431a1f9254a",
"segmentation.zip": "ab51be6d142ad1a8e30ffb964447d010"
Expand Down

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