diff --git a/i14/notebooks/ptycho-tomo-phase.ipynb b/i14/notebooks/ptycho-tomo-phase.ipynb index ec0d64d..48a0c6a 100644 --- a/i14/notebooks/ptycho-tomo-phase.ipynb +++ b/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" ] diff --git a/i14/notebooks/xanes_autoprocessing0.ipynb b/i14/notebooks/xanes_autoprocessing0.ipynb index ed3f052..53ba234 100644 --- a/i14/notebooks/xanes_autoprocessing0.ipynb +++ b/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": {}, diff --git a/i14/notebooks/xanes_point_autoprocessing0.ipynb b/i14/notebooks/xanes_point_autoprocessing0.ipynb index 8d7918f..9e70baa 100644 --- a/i14/notebooks/xanes_point_autoprocessing0.ipynb +++ b/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": {}, diff --git a/i14/notebooks/xanes_sparse_stack_autoprocessing0.ipynb b/i14/notebooks/xanes_sparse_stack_autoprocessing0.ipynb index 26b7137..0d62c66 100644 --- a/i14/notebooks/xanes_sparse_stack_autoprocessing0.ipynb +++ b/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": {}, diff --git a/i14/schema/xanesPointSchema.json b/i14/schema/xanesPointSchema.json index 0dae244..7fc80ae 100644 --- a/i14/schema/xanesPointSchema.json +++ b/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'" } }, diff --git a/i14/schema/xanesSchema.json b/i14/schema/xanesSchema.json index 29758e5..9929b37 100644 --- a/i14/schema/xanesSchema.json +++ b/i14/schema/xanesSchema.json @@ -37,6 +37,7 @@ "normalise": { "type": "boolean", "title": "Normalise", + "default": true, "description": "Whether to normalise the stack by I0" } }, diff --git a/i14/schema/xanesSparseSchema.json b/i14/schema/xanesSparseSchema.json index 310151d..c98083c 100644 --- a/i14/schema/xanesSparseSchema.json +++ b/i14/schema/xanesSparseSchema.json @@ -16,7 +16,8 @@ }, "normalise": { "type": "boolean", - "title": "Normalise" + "title": "Normalise", + "default": true }, "edgeElement": { "type": "string", diff --git a/i14/schema/xrfTomoSchema.json b/i14/schema/xrfTomoSchema.json index 2441a12..d7417ec 100644 --- a/i14/schema/xrfTomoSchema.json +++ b/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": { diff --git a/i14/templates/phase-template.yaml b/i14/templates/phase-template.yaml index 46b0ad2..2e56716 100644 --- a/i14/templates/phase-template.yaml +++ b/i14/templates/phase-template.yaml @@ -27,7 +27,7 @@ spec: - name: maskpath value: "" - name: normalise - value: False + value: false - name: outpath value: "" volumeClaimTemplates: diff --git a/i14/templates/xanes-auto-template.yaml b/i14/templates/xanes-auto-template.yaml index baa9eb2..8c89469 100644 --- a/i14/templates/xanes-auto-template.yaml +++ b/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 diff --git a/i14/templates/xanes-point-template.yaml b/i14/templates/xanes-point-template.yaml index 57dfd21..7a0b81a 100644 --- a/i14/templates/xanes-point-template.yaml +++ b/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 diff --git a/i14/templates/xanes-sparse-template.yaml b/i14/templates/xanes-sparse-template.yaml index e6975d0..8f6c74f 100644 --- a/i14/templates/xanes-sparse-template.yaml +++ b/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 diff --git a/nxstacker/schema/nxstackerSchema.json b/nxstacker/schema/nxstackerSchema.json index b65fd15..c9c3351 100644 --- a/nxstacker/schema/nxstackerSchema.json +++ b/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"]