Schema updates

i14/notebooks/xanes_autoprocessing0.ipynb

@@ -417,7 +417,7 @@
     "                                               reference=\"current\",\n",
     "                                               bin_rule=\"sturges\",\n",
     "                                               max_fractional_shift=max_fractional_shift,\n",
-    "                                               brute=False\n",
+    "                                               brute=brute\n",
     "                                              )\n",
     "    s_element_align.align2D(shifts=shifts)\n",
     "elif method == \"fourier\":\n",

i14/schema/xanesPointSchema.json

@@ -13,7 +13,6 @@
     "edgeElement": {
       "type": "string",
       "enum": [
-        "",
         "H",
         "He",
         "Li",
@@ -136,7 +135,7 @@
     },
     "edgeTransition": {
       "type": "string",
-      "enum": ["", "Ka", "Kb", "La", "Lb", "M"]
+      "enum": ["Ka", "Kb", "La", "Lb", "M"]
     },
     "normalise": {
       "type": "boolean",

i14/schema/xanesSchema.json

@@ -19,21 +19,35 @@
     },
     "edgeTransition": {
       "type": "string",
-      "enum": ["", "Ka", "Kb", "La", "Lb", "M"]
+      "enum": ["Ka", "Kb", "La", "Lb", "M"]
     },
     "elementToAlign": {
       "$ref": "#/$defs/elements"
     },
     "transitionToAlign": {
       "type": "string",
-      "enum": ["", "Ka", "Kb", "La", "Lb", "M"]
+      "enum": ["Ka", "Kb", "La", "Lb", "M"]
     },
     "method": {
       "type": "string",
       "enum": ["mutual", "fourier"],
       "title": "Method",
       "description": "The method to use for alignment. `mutual` (mutual information) or `fourier` (Fourier correlation)."
     },
+    "max_fractional_shift": {
+      "type": "number",
+      "title": "Max Fractional Shift",
+      "default": 0.2,
+      "maximum": 1,
+      "minimum": 0,
+      "description": "This number is used to define the maximum shift that could be applied to an axis, as a fraction of the size of the axis. Setting it to a higher number results in longer duration of alignment."
+    },
+    "brute": {
+      "type": "boolean",
+      "title": "Brute",
+      "default": false,
+      "description": "To use a brute force method or mutual information."
+    },
     "normalise": {
       "type": "boolean",
       "title": "Normalise",
@@ -46,7 +60,6 @@
     "elements": {
       "type": "string",
       "enum": [
-        "",
         "H",
         "He",
         "Li",

i14/schema/xanesSparseSchema.json

@@ -22,7 +22,6 @@
     "edgeElement": {
       "type": "string",
       "enum": [
-        "",
         "H",
         "He",
         "Li",
@@ -145,7 +144,7 @@
     },
     "edgeTransition": {
       "type": "string",
-      "enum": ["", "Ka", "Kb", "La", "Lb", "M"]
+      "enum": ["Ka", "Kb", "La", "Lb", "M"]
     }
   },
   "required": ["outputFolder", "multiScan", "edgeElement", "edgeTransition"]

i14/schema/xanesUISchema.json

@@ -1,5 +1,8 @@
 {
   "type": "VerticalLayout",
+  "options": {
+    "formWidth": "80%"
+  },
   "elements": [
     {
       "type": "Control",
@@ -29,7 +32,29 @@
         },
         {
           "type": "Control",
-          "scope": "#/properties/normalise"
+          "scope": "#/properties/brute",
+          "rule": {
+            "effect": "SHOW",
+            "condition": {
+              "scope": "#/properties/method",
+              "schema": {
+                "const": "mutual"
+              }
+            }
+          }
+        },
+        {
+          "type": "Control",
+          "scope": "#/properties/max_fractional_shift",
+          "rule": {
+            "effect": "SHOW",
+            "condition": {
+              "scope": "#/properties/brute",
+              "schema": {
+                "const": true
+              }
+            }
+          }
         }
       ]
     },
@@ -59,6 +84,10 @@
         }
       ]
     },
+    {
+      "type": "Control",
+      "scope": "#/properties/normalise"
+    },
     {
       "type": "Control",
       "scope": "#/properties/outputFolder"

i14/schema/xrfTomoSchema.json

@@ -26,7 +26,7 @@
                 },
                 "edgeTransition": {
                     "type": "string",
-                    "enum": ["", "Ka", "Kb", "La", "Lb", "M"]
+                    "enum": ["Ka", "Kb", "La", "Lb", "M"]
                 }
             }
         }
@@ -36,7 +36,7 @@
     },
     "transitionToAlign": {
       "type": "string",
-      "enum": ["", "Ka", "Kb", "La", "Lb", "M"]
+      "enum": ["Ka", "Kb", "La", "Lb", "M"]
     },
     "alignmentSection": {
       "type": "string",
@@ -95,7 +95,6 @@
     "elements": {
       "type": "string",
       "enum": [
-        "",
         "H",
         "He",
         "Li",

i14/templates/xanes-auto-template.yaml

@@ -39,6 +39,10 @@ spec:
       value: None
     - name: transitionToAlign
       value: None
+    - name: max_fractional_shift
+      value: 0.2
+    - name: brute
+      value: false
     - name: normalise
       value: true
   volumeClaimTemplates:
@@ -89,6 +93,10 @@ spec:
             value: "{{`{{ workflow.parameters.edgeElement }}`}}-{{`{{ workflow.parameters.edgeTransition }}`}}"
           - name: elementToAlign
             value: "{{`{{ steps.gen-element-to-align.outputs.result }}`}}"
+          - name: max_fractional_shift
+            value: "{{`{{ workflow.parameters.max_fractional_shift }}`}}"
+          - name: brute
+            value: "{{`{{ workflow.parameters.brute }}`}}"
           - name: method
             value: "{{`{{ workflow.parameters.method }}`}}"
           - name: normalise
@@ -117,6 +125,8 @@ spec:
       - name: outputFolder
       - name: edgeElement
       - name: elementToAlign
+      - name: max_fractional_shift
+      - name: brute
       - name: method
       - name: normalise
     script:
@@ -147,7 +157,8 @@ spec:
           -p window_width 40 \
           -p sztol 0.9 \
           -p ref_index None \
-          -p max_fractional_shift 0.2 \
+          -p max_fractional_shift "{{`{{ inputs.parameters.max_fractional_shift }}`}}" \
+          -p brute "{{`{{ inputs.parameters.brute }}`}}" \
           -p auto_processing False \
           > $OUTPUT/papermill.log 2>&1
 

nxstacker/schema/nxstackerSchema.json

@@ -128,7 +128,6 @@
         "element": {
           "type": "string",
           "enum": [
-            "",
             "H",
             "He",
             "Li",
@@ -251,7 +250,7 @@
         },
         "transition": {
           "type": "string",
-          "enum": ["", "Ka", "Kb", "La", "Lb", "M"]
+          "enum": ["Ka", "Kb", "La", "Lb", "M"]
         }
       }
     },