Ft pipelines

PipelineData.jsx

@@ -0,0 +1,201 @@
+ PipelineData = {
+        name: "fastsurfer_dev",
+        authors: "[email protected]",
+        description: "test",
+        category: "mri",
+        locked: false,
+        plugin_tree: JSON.stringify([
+            {
+                plugin_name: "pl-simpledsapp",
+                plugin_version: "2.0.2",
+                previous_index: null,
+            },
+            {
+                plugin_name: "pl-pfdicom_tagextract",
+                plugin_version: "3.1.2",
+                previous_index: 0,
+                plugin_parameter_defaults: [
+                    {
+                        name: "outputFileType",
+                        default: "txt,scv,json,html",
+                    },
+                    {
+                        name: "outputFileStem",
+                        default: "Post-Sub",
+                    },
+                    {
+                        name: "imageFile",
+                        default: "'m:%_nospc|-_ProtocolName.jpg'",
+                    },
+                    {
+                        name: "imageScale",
+                        default: "3:none",
+                    },
+                ],
+            },
+            {
+                plugin_name: "pl-pfdicom_tagsub",
+                plugin_version: "3.2.3",
+                previous_index: 0,
+                plugin_parameter_defaults: [
+                    {
+                        name: "extension",
+                        default: ".dcm",
+                    },
+                    {
+                        name: "splitToken",
+                        default: "++",
+                    },
+                    {
+                        name: "splitKeyValue",
+                        default: ",",
+                    },
+                    {
+                        name: "tagInfo",
+                        default:
+                            "'PatientName,%_name|patientID_PatientName ++ PatientID,%_md5|7_PatientID ++ AccessionNumber,%_md5|8_AccessionNumber ++ PatientBirthDate,%_strmsk|******01_PatientBirthDate ++ re:.*hysician,%_md5|4_#tag ++ re:.*stitution,#tag ++ re:.*ddress,#tag'",
+                    },
+                ],
+            },
+            {
+                plugin_name: "pl-pfdicom_tagextract",
+                plugin_version: "3.1.2",
+                previous_index: 2,
+                plugin_parameter_default: [
+                    {
+                        name: "outputFileType",
+                        default: "txt,scv,json,html",
+                    },
+                    {
+                        name: "outputFileStem",
+                        default: "Post-Sub",
+                    },
+                    {
+                        name: "imageFile",
+                        default: "'m:%_nospc|-_ProtocolName.jpg'",
+                    },
+                    {
+                        name: "imageScale",
+                        default: "3:none",
+                    },
+                    {
+                        name: "extension",
+                        default: ".dcm",
+                    },
+                ],
+            },
+            {
+                plugin_name: "pl-fshack",
+                plugin_version: "1.2.0",
+                previous_index: 2,
+                plugin_parameter_default: [
+                    {
+                        name: "exec",
+                        default: "recon-all",
+                    },
+                    {
+                        name: "args",
+                        default: "'ARGS:-autorecon1'",
+                    },
+                    {
+                        name: "outputFile",
+                        default: "recon-of-SAG-anon-dcm",
+                    },
+                    {
+                        name: "inputFile",
+                        default: ".dcm",
+                    },
+                ],
+            },
+            {
+                plugin_name: "pl-fastsurfer_inference",
+                plugin_version: "1.0.15",
+                previous_index: 4,
+                plugin_parameter_default: [
+                    {
+                        name: "subjectDir",
+                        default: "recon-of-SAG-anon-dcm",
+                    },
+                    {
+                        name: "subject",
+                        default: "mri",
+                    },
+                    {
+                        name: "copyInputFiles",
+                        default: "mgz",
+                    },
+                    {
+                        name: "iname",
+                        default: "brainmask.mgz",
+                    },
+                ],
+            },
+            {
+                plugin_name: "pl-multipass",
+                plugin_version: "1.2.12",
+                previous_index: 5,
+                plugin_parameter_default: [
+                    {
+                        name: "splitExpr",
+                        default: "++",
+                    },
+                    {
+                        name: "commonArgs",
+                        default:
+                            "'--printElapsedTime --verbosity 5 --saveImages --skipAllLabels --outputFileStem sample --outputFileType png'",
+                    },
+                    {
+                        name: "specificArgs",
+                        default:
+                            "'--inputFile mri/brainmask.mgz --wholeVolume brainVolume ++ --inputFile mri/aparc.DKTatlas+aseg.deep.mgz --wholeVolume segVolume --lookupTable __fs__'",
+                    },
+                    {
+                        name: "exec",
+                        default: "pfdo_mgz2image",
+                    },
+                ],
+            },
+            {
+                plugin_name: "pl-pfdorun",
+                plugin_version: "2.2.6",
+                previous_index: 6,
+                plugin_parameter_default: [
+                    {
+                        name: "dirFilter",
+                        default: "label-brainVolume",
+                    },
+                    {
+                        name: "fileFilter",
+                        default: "png",
+                    },
+                    {
+                        name: "exec",
+                        default:
+                            "'composite -dissolve 90 -gravity Center %inputWorkingDir/%inputWorkingFile %inputWorkingDir/../../aparc.DKTatlas+aseg.deep.mgz/label-segVolume/%inputWorkingFile -alpha Set %outputWorkingDir/%inputWorkingFile'",
+                    },
+                    {
+                        name: "verbose",
+                        default: "5",
+                    },
+                ],
+            },
+            {
+                plugin_name: "pl-mgz2lut_report",
+                plugin_version: "1.3.1",
+                previous_index: 5,
+                plugin_parameter_default: [
+                    {
+                        name: "file_name",
+                        default: "mri/aparc.DKTatlas+aseg.deep.mgz",
+                    },
+                    {
+                        name: "report_types",
+                        default: "txt,csv,json,html,pdf",
+                    },
+                ],
+            },
+        ]),
+    };
+
+    return data;
+};

package.json

@@ -27,6 +27,10 @@
     "@patternfly/react-core": "^4.75.2",
     "@patternfly/react-icons": "^4.7.16",
     "@patternfly/react-table": "^4.27.7",
+    "@types/jest": "^27.4.0",
+    "@types/node": "^17.0.8",
+    "@types/react": "^17.0.38",
+    "@types/react-dom": "^17.0.11",
     "classnames": "^2.2.6",
     "core-js": "^2.5.7",
     "cross-env": "^5.2.0",
@@ -42,7 +46,9 @@
     "prop-types": "^15.6.2",
     "react": "^17.0.2",
     "react-bootstrap": "^0.32.1",
+    "react-d3-tree": "^3.2.1",
     "react-dom": "^17.0.2",
+    "react-icons": "^4.3.1",
     "react-router-dom": "^5.2.0",
     "react-scripts": "3.4.3",
     "react-test-renderer": "^16.4.1",