Update for I14 templates, relating to boolean values

i14/notebooks/ptycho-tomo-phase.ipynb

@@ -88,6 +88,24 @@
    "cell_type": "markdown",
    "id": "2f61bb2f",
    "metadata": {},
+   "source": [
+    "## Set normalise boolean"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "e3300162-404a-4660-b4ac-136bbd517727",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "normalise = True if normalise.lower() == \"true\" else False"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "5d23b863-a0da-40f4-aa72-c5b5cc911c00",
+   "metadata": {},
    "source": [
     "## Initialise np array"
    ]

i14/notebooks/xanes_autoprocessing0.ipynb

@@ -169,6 +169,22 @@
     "print(f\"The PNG file will be saved as {png_outpath}\")"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Set normalised boolean\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "normalised = True if normalised.lower() == \"true\" else False"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},

i14/notebooks/xanes_point_autoprocessing0.ipynb

@@ -84,6 +84,22 @@
     "    raise FileNotFoundError(msg)"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Set normalise boolean"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "normalise = True if normalise.lower() == \"true\" else False"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},

i14/notebooks/xanes_sparse_stack_autoprocessing0.ipynb

@@ -119,6 +119,22 @@
     "print(f\"HyperSpy version: {version('hyperspy')}\")"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Set normalised"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "normalised = True if normalised.lower() == \"true\" else False"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},

i14/schema/xanesPointSchema.json

@@ -141,6 +141,7 @@
     "normalise": {
       "type": "boolean",
       "title": "Normalise",
+      "default": true,
       "description": "Whether to normalise the windowed intensity by 'adc_ionCh1a'"
     }
   },

i14/schema/xanesSchema.json

@@ -37,6 +37,7 @@
     "normalise": {
       "type": "boolean",
       "title": "Normalise",
+      "default": true,
       "description": "Whether to normalise the stack by I0"
     }
   },

i14/schema/xanesSparseSchema.json

@@ -16,7 +16,8 @@
     },
     "normalise": {
       "type": "boolean",
-      "title": "Normalise"
+      "title": "Normalise",
+      "default": true
     },
     "edgeElement": {
       "type": "string",

i14/schema/xrfTomoSchema.json

@@ -52,6 +52,7 @@
     "normalise": {
       "type": "boolean",
       "title": "Normalise",
+      "default": true,
       "description": "Whether to normalise the stack using the total mass of each projection."
     },
     "cor": {

i14/templates/phase-template.yaml

@@ -27,7 +27,7 @@ spec:
     - name: maskpath
       value: ""
     - name: normalise
-      value: False
+      value: false
     - name: outpath
       value: ""
   volumeClaimTemplates:

i14/templates/xanes-auto-template.yaml

@@ -40,7 +40,7 @@ spec:
     - name: transitionToAlign
       value: None
     - name: normalise
-      value: "True"
+      value: true
   volumeClaimTemplates:
   - metadata:
       name: tmp

i14/templates/xanes-point-template.yaml

@@ -33,7 +33,7 @@ spec:
     - name: edgeTransition
       value: "Ka"
     - name: normalise
-      value: "True"
+      value: true
   volumeClaimTemplates:
   - metadata:
       name: tmp

i14/templates/xanes-sparse-template.yaml

@@ -34,7 +34,7 @@ spec:
     - name: edgeTransition
       value: "Ka"
     - name: normalise
-      value: "True"
+      value: true
   volumeClaimTemplates:
   - metadata:
       name: tmp

nxstacker/schema/nxstackerSchema.json

@@ -14,11 +14,13 @@
     "quiet": {
       "type": "boolean",
       "title": "Quiet",
+      "default": false,
       "description": "Suppress log messages"
     },
     "dryRun": {
       "type": "boolean",
-      "title": "Perform a dry run"
+      "title": "Perform a dry run",
+      "default": false
     },
     "projDir": {
       "type": "string",
@@ -93,21 +95,25 @@
     "sortByAngle": {
       "type": "boolean",
       "title": "Sort by angle",
+      "default": false,
       "description": "Sort the projections by their rotation angles"
     },
     "padToMax": {
       "type": "boolean",
       "title": "Pad to max",
+      "default": false,
       "description": "Pad projection to the maximum size of the stack"
     },
     "compress": {
       "type": "boolean",
       "title": "Compress",
+      "default": false,
       "description": "Compress the NXtomo file"
     },
     "skipCheck": {
       "type": "boolean",
       "title": "Skip check",
+      "default": false,
       "description": "Skip the validation of the projection file"
     },
     "retrievalMethod": {
@@ -251,36 +257,44 @@
     },
     "saveComplex": {
       "type": "boolean",
-      "title": "Save complex"
+      "title": "Save complex",
+      "default": false
     },
     "saveModulus": {
       "type": "boolean",
-      "title": "Save modulus"
+      "title": "Save modulus",
+      "default": false
     },
     "savePhase": {
       "type": "boolean",
-      "title": "Save phase"
+      "title": "Save phase",
+      "default": false
     },
     "removeRamp": {
       "type": "boolean",
-      "title": "Remove ramp"
+      "title": "Remove ramp",
+      "default": false
     },
     "medianNorm": {
       "type": "boolean",
       "title": "Median norm",
-      "description": "Normalise the phase by shifting its median"
+      "description": "Normalise the phase by shifting its median",
+      "default": false
     },
     "unwrapPhase": {
       "type": "boolean",
-      "title": "Unwrap phase"
+      "title": "Unwrap phase",
+      "default": false
     },
     "rescale": {
       "type": "boolean",
-      "title": "Rescale"
+      "title": "Rescale",
+      "default": false
     },
     "ignoreRaw": {
       "type": "boolean",
-      "title": "Ignore Raw"
+      "title": "Ignore Raw",
+      "default": false
     }
   },
   "required": ["experimentType"]