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Tests for 4d, 3d cmr and 3d breast imaging.
1 parent f5e5a3c commit ea0a4bc

7 files changed

+196
-94
lines changed

Diff for: ‎tests/config.json

-12
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@@ -25,18 +25,6 @@
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"allow_multiple": true,
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"name": "images"
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},
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{
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"value": "unique_file_id_5e14abe0a37012.29503907",
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"required": true,
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"allow_multiple": true,
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"name": "images"
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},
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{
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"value": "unique_file_id_5e14abe0a37012.29503908",
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"required": true,
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"allow_multiple": true,
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"name": "masks"
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},
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{
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"value": "unique_file_id_5e14abe0a37012.29503909",
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"required": true,

Diff for: ‎tests/config_3d_breast.json

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{
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"output_files": [
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{
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"name": "radiomics_results",
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"required": true,
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"allow_multiple": false,
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"file": {
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"file_type": "CSV",
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"data_type": "machine_learning_features",
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"file_path": "/home/user/vre_radiomics_tool/tests/run000/radiomics_results.csv",
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"sources": ""
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}
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}
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],
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"input_files": [
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{
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"value": "unique_file_id_5e14abe0a37012.29503907",
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"required": true,
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"allow_multiple": true,
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"name": "images"
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},
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{
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"value": "unique_file_id_5e14abe0a37012.29503911",
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"required": true,
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"allow_multiple": true,
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"name": "masks"
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}
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],
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"arguments": [
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{
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"value": "/home/user/vre_radiomics_tool/tests/run000",
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"name": "execution"
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},
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{
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"value": "my_project_id",
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"name": "project"
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},
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{
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"value": "30",
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"name": "bin_width"
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}
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]
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}

Diff for: ‎tests/config_3d_cmr.json

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{
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"output_files": [
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{
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"name": "radiomics_results",
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"required": true,
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"allow_multiple": false,
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"file": {
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"file_type": "CSV",
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"data_type": "machine_learning_features",
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"file_path": "/home/user/vre_radiomics_tool/tests/run000/radiomics_results.csv",
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"sources": ""
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}
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}
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],
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"input_files": [
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{
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"value": "unique_file_id_5e14abe0a37012.29503908",
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"required": true,
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"allow_multiple": true,
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"name": "images"
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},
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{
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"value": "unique_file_id_5e14abe0a37012.29503912",
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"required": true,
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"allow_multiple": true,
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"name": "masks"
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}
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],
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"arguments": [
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{
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"value": "/home/user/vre_radiomics_tool/tests/run000",
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"name": "execution"
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},
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{
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"value": "my_project_id",
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"name": "project"
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},
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{
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"value": "30",
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"name": "bin_width"
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}
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]
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}

Diff for: ‎tests/in_metadata.json

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@@ -54,34 +54,7 @@
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"sources": []
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},
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{
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"_id": "unique_file_id_5e14abe0a37012.29503907",
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"file_path": "/home/user/vre_radiomics_tool/data/mic/training2/img/patient003_4d.nii.gz",
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"file_type": "NIFTI",
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"data_type": "bioimage",
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"compressed": "GZ",
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"user_id": "user_id",
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"creation_time": {
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"sec": 1578413024,
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"usec": 0
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},
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"meta_data": {
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"type": "file",
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"size": 0,
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"project": "my_project_id",
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"atime": {
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"sec": 1578413024,
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"usec": 0
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},
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"parentDir": "unique_file_id_5e14abe0a37742.64003100",
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"lastAccess": {
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"sec": 1578413024,
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"usec": 0
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}
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},
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"sources": []
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},
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{
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"_id": "unique_file_id_5e14abe0a37012.29503908",
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"_id": "unique_file_id_5e14abe0a37012.29503909",
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"file_path": "/home/user/vre_radiomics_tool/data/mic/training2/msk/patient001_4d_label.nii.gz",
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"file_type": "NIFTI",
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"data_type": "image_mask",
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"sources": []
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},
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{
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"_id": "unique_file_id_5e14abe0a37012.29503909",
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"_id": "unique_file_id_5e14abe0a37012.29503910",
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"file_path": "/home/user/vre_radiomics_tool/data/mic/training2/msk/patient002_4d_label.nii.gz",
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"file_type": "NIFTI",
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"data_type": "image_mask",
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}
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},
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"sources": []
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},
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{
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"_id": "unique_file_id_5e14abe0a37012.29503910",
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"file_path": "/home/user/vre_radiomics_tool/data/mic/training2/msk/patient003_4d_label.nii.gz",
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"file_type": "NIFTI",
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"data_type": "image_mask",
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"compressed": "GZ",
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"user_id": "user_id",
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"creation_time": {
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"sec": 1578413024,
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"usec": 0
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},
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"meta_data": {
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"labels": {
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"lv": 1,
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"myo": 2,
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"rv": 3
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},
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"ED": "",
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"ES": "",
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"parentDir": "unique_file_id_5e14abe0a37742.64003100",
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"lastAccess": {
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"sec": 1578413024,
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"usec": 0
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}
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},
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"sources": []
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},
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{
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"_id": "unique_file_id_5e14abe0a37012.29503911",
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"file_path": "/home/user/vre_radiomics_tool/data/mic/training2/metadata.csv",
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"file_type": "CSV",
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"data_type": "parameter_file",
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"user_id": "user_id",
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"creation_time": {
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"sec": 1578413024,
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"usec": 0
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},
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"meta_data": {
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"type": "file",
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"size": 0,
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"project": "my_project_id",
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"atime": {
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"sec": 1578413024,
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"usec": 0
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},
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"parentDir": "unique_file_id_5e14abe0a37742.64003100",
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"lastAccess": {
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"sec": 1578413024,
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"usec": 0
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}
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},
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"sources": []
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}
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]

Diff for: ‎tests/in_metadata_3d_breast.json

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[
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{
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"_id": "unique_file_id_5e14abe0a37012.29503907",
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"file_path": "/home/user/vre_radiomics_tool/data/mic/breast/breast_image.nii",
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"file_type": "NIFTI",
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"data_type": "bioimage",
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"compressed": "GZ",
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"user_id": "user_id",
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"creation_time": {
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"sec": 1578413024,
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"usec": 0
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},
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"meta_data": {
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"type": "file",
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"size": 0,
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"project": "my_project_id",
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"atime": {
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"sec": 1578413024,
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"usec": 0
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},
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"parentDir": "unique_file_id_5e14abe0a37742.64003100",
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"lastAccess": {
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"sec": 1578413024,
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"usec": 0
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}
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},
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"sources": []
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},
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{
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"_id": "unique_file_id_5e14abe0a37012.29503911",
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"file_path": "/home/user/vre_radiomics_tool/data/mic/breast/breast_image_s.nii.gz",
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"file_type": "NIFTI",
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"data_type": "image_mask",
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"compressed": "GZ",
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"user_id": "user_id",
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"creation_time": {
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"sec": 1578413024,
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"usec": 0
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},
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"meta_data": {
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"labels": {
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"lesion": 1
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},
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"parentDir": "unique_file_id_5e14abe0a37742.64003100",
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"lastAccess": {
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"sec": 1578413024,
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"usec": 0
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}
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},
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"sources": []
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}
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]

Diff for: ‎tests/in_metadata_3d_cmr.json

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[
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{
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"_id": "unique_file_id_5e14abe0a37012.29503908",
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"file_path": "/home/user/vre_radiomics_tool/data/mic/training/img/patient001/patient001_frame01.nii.gz",
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"file_type": "NIFTI",
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"data_type": "bioimage",
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"compressed": "GZ",
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"user_id": "user_id",
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"creation_time": {
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"sec": 1578413024,
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"usec": 0
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},
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"meta_data": {
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"type": "file",
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"size": 0,
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"project": "my_project_id",
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"atime": {
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"sec": 1578413024,
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"usec": 0
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},
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"parentDir": "unique_file_id_5e14abe0a37742.64003100",
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"lastAccess": {
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"sec": 1578413024,
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"usec": 0
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}
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},
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"sources": []
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},
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{
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"_id": "unique_file_id_5e14abe0a37012.29503912",
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"file_path": "/home/user/vre_radiomics_tool/data/mic/training/msk/patient001/patient001_frame01_label.nii.gz",
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"file_type": "NIFTI",
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"data_type": "image_mask",
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"compressed": "GZ",
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"user_id": "user_id",
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"creation_time": {
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"sec": 1578413024,
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"usec": 0
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},
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"meta_data": {
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"labels": {
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"lv": 1, "myo": 2, "rv": 3
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},
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"parentDir": "unique_file_id_5e14abe0a37742.64003100",
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"lastAccess": {
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"sec": 1578413024,
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"usec": 0
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}
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},
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"sources": []
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}
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]

Diff for: ‎tests/vre_execution.sh

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@@ -25,3 +25,7 @@ echo "--- Test execution: $WORKING_DIR"
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echo "--- Start time: `date`"
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time $TOOL_EXECUTABLE --config $TEST_DATA_DIR/config.json --in_metadata $TEST_DATA_DIR/in_metadata.json --out_metadata $WORKING_DIR/out_metadata.json # > $WORKING_DIR/tool.log
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time $TOOL_EXECUTABLE --config $TEST_DATA_DIR/config_3d_cmr.json --in_metadata $TEST_DATA_DIR/in_metadata_3d_cmr.json --out_metadata $WORKING_DIR/out_metadata_3d_cmr.json # > $WORKING_DIR/tool.log
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time $TOOL_EXECUTABLE --config $TEST_DATA_DIR/config_3d_breast.json --in_metadata $TEST_DATA_DIR/in_metadata_3d_breast.json --out_metadata $WORKING_DIR/out_metadata_3d_breast.json # > $WORKING_DIR/tool.log

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