Adding OLEM config

Author: daurer

i14/configs/httomo_config_olem.yaml

@@ -0,0 +1,74 @@
+# --- Standard tomography loader for NeXus files. ---
+- method: standard_tomo
+  module_path: httomo.data.hdf.loaders
+  parameters:
+    data_path: auto
+    image_key_path: auto
+    rotation_angles: auto
+    preview:
+      detector_x:   # horizontal data previewing/cropping.
+        # when null, the full data dimension is used, i.e., no previewing
+        start: null
+        stop: null
+      detector_y:   # vertical data previewing/cropping.
+        # when null, the full data dimension is used, i.e., no previewing
+        start: null
+        stop: null
+    darks: null
+    flats: null
+- method: remove_outlier
+  module_path: httomolibgpu.misc.corr
+  parameters:
+    kernel_size: 3  # The size of the 3D neighbourhood surrounding the voxel. Odd integer.
+    dif: 1000 # A difference between the outlier value and the median value of neighbouring pixels.
+  save_result: true
+- method: find_center
+  module_path: tomopy.recon.rotation
+  parameters:
+    ind: null
+    init: 48
+    tol: 0.5
+    mask: true
+    ratio: 1.0
+    sinogram_order: false
+  id: centering
+  side_outputs:
+    cor: centre_of_rotation
+# --- Reconstruction method. ---
+- method: OSEM3d_tomobar
+  module_path: httomolibgpu.recon.algorithm
+  parameters:
+    center: ${{centering.side_outputs.centre_of_rotation}}
+    detector_pad: false
+    recon_size: null
+    recon_mask_radius: 0.95
+    iterations: 20
+    subsets_number: 12
+    regularisation_type: PD_TV
+    regularisation_parameter: 0.01
+    regularisation_iterations: 30
+    regularisation_half_precision: true
+    nonnegativity: true
+# --- Calculate global statistics on the reconstructed volume, required for data rescaling. ---
+- method: calculate_stats
+  module_path: httomo.methods
+  parameters: {}
+  id: statistics
+  side_outputs:
+    glob_stats: glob_stats
+# --- Rescaling the data using min/max obtained from `calculate_stats`. ---
+- method: rescale_to_int
+  module_path: httomolibgpu.misc.rescale
+  parameters:
+    perc_range_min: 0.0
+    perc_range_max: 100.0
+    bits: 32
+    glob_stats: ${{statistics.side_outputs.glob_stats}}
+# --- Saving data into images. ---
+- method: save_to_images
+  module_path: httomolib.misc.images
+  parameters:
+    subfolder_name: images
+    axis: auto
+    file_format: tif  # `tif` or `jpeg` can be used.
+    asynchronous: true

i14/templates/xrf-tomo-template.yaml

@@ -25,11 +25,11 @@ spec:
     - name: outputFolder
       value: "testing"
     - name: multiScan
-      value: '[{"multiScan":{"start":423844,"end":423947,"excluded":[423908,423909,423911,423916,423917,423935,423936,423937,423940,423942,423943,423944,423945]}}]'
+      value: '[{"multiScan":{"start":436147,"end":436230,"excluded":[]}}]'
     - name: multiEdge
-      value: '[{"edgeElement":"Pb","edgeTransition":"La"},{"edgeElement":"Br","edgeTransition":"Ka"}]'
+      value: '[{"edgeElement":"Tl","edgeTransition":"La"},{"edgeElement":"Ga","edgeTransition":"Ka"}]'
     - name: elementToAlign
-      value: "Pb"
+      value: "Tl"
     - name: transitionToAlign
       value: "La"
     - name: alignmentSection
@@ -57,16 +57,14 @@ spec:
       volumeMounts:
       - name: session
         mountPath: "{{`{{ workflow.parameters.visitdir }}`}}"
-      - name: tmp
-        mountPath: /tmp
       command: [bash]
       source: |
         OUTPUT="{{`{{ workflow.parameters.visitdir }}`}}"/processing/workflows/"{{`{{ workflow.parameters.outputFolder }}`}}"
         mkdir -p $OUTPUT
         echo '{{ .Files.Get "notebooks/xrf_tomo_align_initial.ipynb" | b64enc }}' | base64 -d > $OUTPUT/align_initial.ipynb
         echo '{{ .Files.Get "notebooks/xrf_tomo_align_and_normalise.ipynb" | b64enc }}' | base64 -d > $OUTPUT/align_and_normalise.ipynb
         echo '{{ .Files.Get "notebooks/xrf_tomo_plotting.ipynb" | b64enc }}' | base64 -d > $OUTPUT/plotting.ipynb
-        echo '{{ .Files.Get "configs/httomo_config_fbp.yaml" | b64enc }}' | base64 -d > $OUTPUT/httomo.yaml
+        echo '{{ .Files.Get "configs/httomo_config_olem.yaml" | b64enc }}' | base64 -d > $OUTPUT/httomo.yaml
     volumes:
     - name: session
       hostPath:
@@ -266,7 +264,7 @@ spec:
       parameters:
         - name: edge
     script:
-      image: ghcr.io/diamondlightsource/httomo:2.5
+      image: ghcr.io/diamondlightsource/httomo:3.2.1
       env:
       - name: CUPY_CACHE_DIR
         value: /tmp/.cupy/kernel_cache