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#45 - Change category cropvolume module (move to image) [WIP] #78

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#45 - Change category cropvolume module (move to image) [WIP] #78

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c91f038
copy cropvolume
Manonedde Dec 12, 2024
e251ddb
copy cropvolume
Manonedde Dec 12, 2024
7927191
update betcrop to image in all scripts
Manonedde Dec 12, 2024
3e2e971
add test.snap module
Manonedde Dec 12, 2024
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2 changes: 0 additions & 2 deletions modules/nf-neuro/betcrop/cropvolume/tests/tags.yml
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This file was deleted.

2 changes: 1 addition & 1 deletion ...-neuro/betcrop/cropvolume/environment.yml → ...nf-neuro/image/cropvolume/environment.yml
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@@ -1,3 +1,3 @@
channels: []
dependencies: []
name: betcrop_cropvolume
name: image_cropvolume
2 changes: 1 addition & 1 deletion modules/nf-neuro/betcrop/cropvolume/main.nf → modules/nf-neuro/image/cropvolume/main.nf
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@@ -1,5 +1,5 @@

process BETCROP_CROPVOLUME {
process IMAGE_CROPVOLUME {
tag "$meta.id"
label 'process_single'

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2 changes: 1 addition & 1 deletion modules/nf-neuro/betcrop/cropvolume/meta.yml → modules/nf-neuro/image/cropvolume/meta.yml
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@@ -1,6 +1,6 @@
---
# yaml-language-server: $schema=https://raw.githubusercontent.com/scilus/nf-neuro/main/modules/meta-schema.json
name: "betcrop_cropvolume"
name: "image_cropvolume"
description: Crop empty planes around the data in a volume
keywords:
- nifti
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12 changes: 6 additions & 6 deletions ...uro/betcrop/cropvolume/tests/main.nf.test → ...neuro/image/cropvolume/tests/main.nf.test
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@@ -1,14 +1,14 @@
nextflow_process {

name "Test Process BETCROP_CROPVOLUME"
name "Test Process IMAGE_CROPVOLUME"
script "../main.nf"
process "BETCROP_CROPVOLUME"
process "IMAGE_CROPVOLUME"
config "./nextflow.config"

tag "modules"
tag "modules_nfcore"
tag "betcrop"
tag "betcrop/cropvolume"
tag "image"
tag "image/cropvolume"

tag "subworkflows"
tag "subworkflows/load_test_data"
Expand All @@ -25,7 +25,7 @@ nextflow_process {
}
}

test("betcrop - cropvolume") {
test("image - cropvolume") {

when {
process {
Expand All @@ -50,7 +50,7 @@ nextflow_process {

}

test("betcrop - cropvolume - outputbbox") {
test("image - cropvolume - outputbbox") {

config "./nextflow_bbox.config"

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52 changes: 26 additions & 26 deletions ...etcrop/cropvolume/tests/main.nf.test.snap → .../image/cropvolume/tests/main.nf.test.snap
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@@ -1,5 +1,5 @@
{
"betcrop - cropvolume - outputbbox": {
"image - cropvolume": {
"content": [
{
"0": [
Expand All @@ -12,25 +12,13 @@
]
],
"1": [
[
{
"id": "test",
"single_end": false
},
"test_cropped_bbox.pkl:md5,d6a03b61669b07683e8c4b21a613f16c"
]

],
"2": [
"versions.yml:md5,3b089d55a1116feffa69d739ced1d99f"
"versions.yml:md5,c9f9039fc9103e716e831016a61807f9"
],
"bounding_box": [
[
{
"id": "test",
"single_end": false
},
"test_cropped_bbox.pkl:md5,d6a03b61669b07683e8c4b21a613f16c"
]

],
"image": [
[
Expand All @@ -42,17 +30,17 @@
]
],
"versions": [
"versions.yml:md5,3b089d55a1116feffa69d739ced1d99f"
"versions.yml:md5,c9f9039fc9103e716e831016a61807f9"
]
}
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
"nextflow": "24.10.0"
},
"timestamp": "2024-10-28T19:30:09.320626173"
"timestamp": "2024-12-12T18:59:41.317523464"
},
"betcrop - cropvolume": {
"image - cropvolume - outputbbox": {
"content": [
{
"0": [
Expand All @@ -65,13 +53,25 @@
]
],
"1": [

[
{
"id": "test",
"single_end": false
},
"test_cropped_bbox.pkl:md5,d6a03b61669b07683e8c4b21a613f16c"
]
],
"2": [
"versions.yml:md5,3b089d55a1116feffa69d739ced1d99f"
"versions.yml:md5,c9f9039fc9103e716e831016a61807f9"
],
"bounding_box": [

[
{
"id": "test",
"single_end": false
},
"test_cropped_bbox.pkl:md5,d6a03b61669b07683e8c4b21a613f16c"
]
],
"image": [
[
Expand All @@ -83,14 +83,14 @@
]
],
"versions": [
"versions.yml:md5,3b089d55a1116feffa69d739ced1d99f"
"versions.yml:md5,c9f9039fc9103e716e831016a61807f9"
]
}
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
"nextflow": "24.10.0"
},
"timestamp": "2024-10-28T19:30:00.033087617"
"timestamp": "2024-12-12T18:59:50.080977383"
}
}
2 changes: 1 addition & 1 deletion .../betcrop/cropvolume/tests/nextflow.config → ...ro/image/cropvolume/tests/nextflow.config
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@@ -1,5 +1,5 @@
process {
withName: "BETCROP_CROPVOLUME" {
withName: "IMAGE_CROPVOLUME" {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
}
}
2 changes: 1 addition & 1 deletion ...rop/cropvolume/tests/nextflow_bbox.config → ...age/cropvolume/tests/nextflow_bbox.config
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@@ -1,5 +1,5 @@
process {
withName: "BETCROP_CROPVOLUME" {
withName: "IMAGE_CROPVOLUME" {
ext.output_bbox = true
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
}
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2 changes: 2 additions & 0 deletions modules/nf-neuro/image/cropvolume/tests/tags.yml
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@@ -0,0 +1,2 @@
image/cropvolume:
- "modules/nf-neuro/image/cropvolume/**"
8 changes: 4 additions & 4 deletions subworkflows/nf-neuro/preproc_dwi/main.nf
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@@ -1,7 +1,7 @@
include { DENOISING_MPPCA as DENOISE_DWI } from '../../../modules/nf-neuro/denoising/mppca/main'
include { DENOISING_MPPCA as DENOISE_REVDWI } from '../../../modules/nf-neuro/denoising/mppca/main'
include { BETCROP_FSLBETCROP } from '../../../modules/nf-neuro/betcrop/fslbetcrop/main'
include { BETCROP_CROPVOLUME } from '../../../modules/nf-neuro/betcrop/cropvolume/main'
include { IMAGE_CROPVOLUME } from '../../../modules/nf-neuro/image/cropvolume/main'
include { PREPROC_N4 as N4_DWI } from '../../../modules/nf-neuro/preproc/n4/main'
include { PREPROC_NORMALIZE as NORMALIZE_DWI } from '../../../modules/nf-neuro/preproc/normalize/main'
include { IMAGE_RESAMPLE as RESAMPLE_DWI } from '../../../modules/nf-neuro/image/resample/main'
Expand Down Expand Up @@ -78,12 +78,12 @@ workflow PREPROC_DWI {
ch_crop_b0 = TOPUP_EDDY.out.b0
.join(BETCROP_FSLBETCROP.out.bbox)

BETCROP_CROPVOLUME ( ch_crop_b0 )
ch_versions = ch_versions.mix(BETCROP_CROPVOLUME.out.versions.first())
IMAGE_CROPVOLUME ( ch_crop_b0 )
ch_versions = ch_versions.mix(IMAGE_CROPVOLUME.out.versions.first())

// ** N4 DWI ** //
ch_N4 = BETCROP_FSLBETCROP.out.image
.join(BETCROP_CROPVOLUME.out.image)
.join(IMAGE_CROPVOLUME.out.image)
.join(BETCROP_FSLBETCROP.out.mask)

N4_DWI ( ch_N4 )
Expand Down
2 changes: 1 addition & 1 deletion subworkflows/nf-neuro/preproc_dwi/meta.yml
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Expand Up @@ -45,7 +45,7 @@ keywords:
- Normalization
- Resampling
components:
- betcrop/cropvolume
- image/cropvolume
- betcrop/fslbetcrop
- denoising/mppca
- image/resample
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2 changes: 1 addition & 1 deletion subworkflows/nf-neuro/preproc_dwi/tests/main.nf.test
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Expand Up @@ -9,7 +9,7 @@ nextflow_workflow {
tag "subworkflows_nfcore"
tag "subworkflows/preproc_dwi"
tag "subworkflows/topup_eddy"
tag "betcrop/cropvolume"
tag "image/cropvolume"
tag "betcrop/fslbetcrop"
tag "denoising/mppca"
tag "image/resample"
Expand Down
2 changes: 1 addition & 1 deletion subworkflows/nf-neuro/preproc_dwi/tests/nextflow.config
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Expand Up @@ -41,7 +41,7 @@ process {
ext.voxel_size = 1
ext.interp = "lin"
}
withName: "BETCROP_CROPVOLUME" {
withName: "IMAGE_CROPVOLUME" {
ext.output_bbox = false
}

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20 changes: 10 additions & 10 deletions subworkflows/nf-neuro/preproc_t1/main.nf
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Expand Up @@ -4,8 +4,8 @@ include { PREPROC_N4 } from '../../../modules/nf-neuro/preproc/n4/main'
include { IMAGE_RESAMPLE } from '../../../modules/nf-neuro/image/resample/main'
include { BETCROP_ANTSBET } from '../../../modules/nf-neuro/betcrop/antsbet/main'
include { BETCROP_SYNTHBET} from '../../../modules/nf-neuro/betcrop/synthbet/main'
include { BETCROP_CROPVOLUME as BETCROP_CROPVOLUME_T1 } from '../../../modules/nf-neuro/betcrop/cropvolume/main'
include { BETCROP_CROPVOLUME as BETCROP_CROPVOLUME_MASK } from '../../../modules/nf-neuro/betcrop/cropvolume/main'
include { IMAGE_CROPVOLUME as IMAGE_CROPVOLUME_T1 } from '../../../modules/nf-neuro/image/cropvolume/main'
include { IMAGE_CROPVOLUME as IMAGE_CROPVOLUME_MASK } from '../../../modules/nf-neuro/image/cropvolume/main'

params.run_synthbet = false

Expand Down Expand Up @@ -104,24 +104,24 @@ workflow PREPROC_T1 {
ch_crop = image_bet
.map{ it + [[]] }

BETCROP_CROPVOLUME_T1 ( ch_crop )
ch_versions = ch_versions.mix(BETCROP_CROPVOLUME_T1.out.versions.first())
IMAGE_CROPVOLUME_T1 ( ch_crop )
ch_versions = ch_versions.mix(IMAGE_CROPVOLUME_T1.out.versions.first())

// ** Crop mask ** //
ch_crop_mask = mask_bet
.join(BETCROP_CROPVOLUME_T1.out.bounding_box)
.join(IMAGE_CROPVOLUME_T1.out.bounding_box)

BETCROP_CROPVOLUME_MASK ( ch_crop_mask )
ch_versions = ch_versions.mix(BETCROP_CROPVOLUME_MASK.out.versions.first())
IMAGE_CROPVOLUME_MASK ( ch_crop_mask )
ch_versions = ch_versions.mix(IMAGE_CROPVOLUME_MASK.out.versions.first())

emit:
t1_final = BETCROP_CROPVOLUME_T1.out.image // channel: [ val(meta), t1-preprocessed ]
mask_final = BETCROP_CROPVOLUME_MASK.out.image // channel: [ val(meta), t1-mask ]
t1_final = IMAGE_CROPVOLUME_T1.out.image // channel: [ val(meta), t1-preprocessed ]
mask_final = IMAGE_CROPVOLUME_MASK.out.image // channel: [ val(meta), t1-mask ]
image_nlmeans = DENOISING_NLMEANS.out.image // channel: [ val(meta), t1-after-denoise ]
image_N4 = PREPROC_N4.out.image // channel: [ val(meta), t1-after-unbias ]
image_resample = IMAGE_RESAMPLE.out.image // channel: [ val(meta), t1-after-resample ]
image_bet = image_bet // channel: [ val(meta), t1-after-bet ]
mask_bet = mask_bet // channel: [ val(meta), intermediary-mask ]
crop_box = BETCROP_CROPVOLUME_T1.out.bounding_box // channel: [ val(meta), bounding-box ]
crop_box = IMAGE_CROPVOLUME_T1.out.bounding_box // channel: [ val(meta), bounding-box ]
versions = ch_versions // channel: [ versions.yml ]
}
2 changes: 1 addition & 1 deletion subworkflows/nf-neuro/preproc_t1/meta.yml
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Expand Up @@ -45,7 +45,7 @@ components:
- image/resample
- betcrop/antsbet
- betcrop/synthbet
- betcrop/cropvolume
- image/cropvolume

input:
- ch_image:
Expand Down
2 changes: 1 addition & 1 deletion subworkflows/nf-neuro/preproc_t1/tests/main.nf.test
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Expand Up @@ -13,7 +13,7 @@ nextflow_workflow {
tag "image/resample"
tag "betcrop/antsbet"
tag "betcrop/synthbet"
tag "betcrop/cropvolume"
tag "image/cropvolume"

tag "load_test_data"

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2 changes: 1 addition & 1 deletion subworkflows/nf-neuro/preproc_t1/tests/nextflow.config
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Expand Up @@ -4,7 +4,7 @@ process {
ext.voxel_size = 1
ext.interp = "lin"
}
withName: "BETCROP_CROPVOLUME_T1" {
withName: "IMAGE_CROPVOLUME_T1" {
ext.output_bbox = true
ext.first_suffix = "t1"
}
Expand Down
2 changes: 1 addition & 1 deletion subworkflows/nf-neuro/preproc_t1/tests/nextflow_synthbet.config
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Expand Up @@ -4,7 +4,7 @@ process {
ext.voxel_size = 1
ext.interp = "lin"
}
withName: "BETCROP_CROPVOLUME_T1" {
withName: "IMAGE_CROPVOLUME_T1" {
ext.output_bbox = true
ext.first_suffix = "t1"
}
Expand Down
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