1arcsec imaging fixes

steps/average_intermediate_resolution.cwl

@@ -19,6 +19,14 @@ inputs:
       itemSeparator: ','
       valueFrom: "[$(self.map(function(d) { return d.path || d.location; }).join(','))]"
 
+  - id: ncpu
+    type: int?
+    default: 24
+    inputBinding:
+      position: 1
+      shellQuote: false
+      prefix: 'numthreads='
+
 outputs:
   - id: ms_avg
     doc: |
@@ -44,6 +52,7 @@ arguments:
   - msout=concat_1asec.ms
   - bdaaverager.timebase=70e3
   - bdaaverager.maxinterval=32
+  - numthreads=$(inputs.ncpu)
 
 requirements:
   - class: ShellCommandRequirement
@@ -56,7 +65,7 @@ hints:
     listing:
       - entry: $(inputs.msin)
   - class: ResourceRequirement
-    coresMin: 12
+    coresMin: $(inputs.ncpu)
 
 stdout: dp3_intermediate_avg.log
 stderr: dp3_intermediate_avg_err.log

steps/wsclean.cwl

@@ -5,7 +5,7 @@ label: WSClean
 doc: Runs WSClean on the input data to produce an image.
 
 baseCommand: wsclean
-arguments: [-verbose, -log-time, -no-update-model-required]
+arguments: [-verbose, -log-time, -no-update-model-required, -reorder]
 
 inputs:
   - id: msin
@@ -16,15 +16,15 @@ inputs:
       position: 2
       shellQuote: false
       itemSeparator: ' '
-  - id: tempdir
-    type: string
+  - id: tmpdir
+    type: string?
     default: '.'
     inputBinding:
       position: 1
       shellQuote: false
       itemSeparator: ' '
       prefix: '-temp-dir'
-  - id: cores
+  - id: ncpu
     type: int?
     default: 24
     inputBinding:
@@ -58,6 +58,13 @@ inputs:
       position: 1
       shellQuote: false
       prefix: '-weight'
+  - id: weighting-rank-filter
+    type: int?
+    default: 3
+    inputBinding:
+      position: 1
+      shellQuote: false
+      prefix: '-weighting-rank-filter'
   - id: parallel-reordering
     type: int?
     default: 6
@@ -67,7 +74,7 @@ inputs:
       prefix: '-parallel-reordering'
   - id: mgain
     type: float?
-    default: 0.7
+    default: 0.75
     inputBinding:
       position: 1
       shellQuote: false
@@ -81,7 +88,7 @@ inputs:
       prefix: '-data-column'
   - id: auto-mask
     type: float?
-    default: 3.0
+    default: 2.5
     inputBinding:
       position: 1
       shellQuote: false
@@ -130,7 +137,7 @@ inputs:
       prefix: '-niter'
   - id: multiscale-scale-bias
     type: float?
-    default: 0.6
+    default: 0.7
     inputBinding:
       position: 1
       shellQuote: false
@@ -144,7 +151,7 @@ inputs:
       prefix: '-parallel-deconvolution'
   - id: parallel-gridding
     type: int?
-    default: 4
+    default: 6
     inputBinding:
       position: 1
       shellQuote: false
@@ -172,7 +179,7 @@ inputs:
       prefix: '-nmiter'
   - id: channels-out
     type: int?
-    default: 6
+    default: 12
     inputBinding:
       position: 1
       shellQuote: false
@@ -186,18 +193,31 @@ inputs:
       prefix: '-join-channels'
   - id: fit-spectral-pol
     type: int?
-    default: 3
+    default: 9
     inputBinding:
       position: 1
       shellQuote: false
       prefix: '-fit-spectral-pol'
   - id: deconvolution-channels
     type: int?
-    default: 3
     inputBinding:
       position: 1
       shellQuote: false
       prefix: '-deconvolution-channels'
+  - id: local-rms-window
+    type: int?
+    default: 50
+    inputBinding:
+      position: 1
+      shellQuote: false
+      prefix: '-local-rms-window'
+  - id: local-rms
+    type: boolean?
+    default: true
+    inputBinding:
+      position: 1
+      shellQuote: false
+      prefix: '-local-rms'
   - id: gridder
     type: string?
     default: wgridder
@@ -207,11 +227,39 @@ inputs:
       prefix: '-gridder'
   - id: apply-primary-beam
     type: boolean?
-    default: true
+    default: false
     inputBinding:
       position: 1
       shellQuote: false
       prefix: '-apply-primary-beam'
+  - id: apply-facet-beam
+    type: boolean?
+    default: true
+    inputBinding:
+      position: 1
+      shellQuote: false
+      prefix: '-apply-facet-beam'
+  - id: facet-beam-update
+    type: int?
+    default: 600
+    inputBinding:
+      position: 1
+      shellQuote: false
+      prefix: '-facet-beam-update'
+  - id: dd-psf-grid
+    type: int[]?
+    default: [3, 3]
+    inputBinding:
+      position: 1
+      shellQuote: false
+      prefix: '-dd-psf-grid'
+  - id: scalar-visibilities
+    type: boolean?
+    default: true
+    inputBinding:
+      position: 1
+      shellQuote: false
+      prefix: '-scalar-visibilities'
   - id: use-differential-lofar-beam
     type: boolean?
     default: true
@@ -301,7 +349,7 @@ requirements:
     listing:
       - entry: $(inputs.msin)
   - class: ResourceRequirement
-    coresMin: $(inputs.cores)
+    coresMin: $(inputs.ncpu)
 
 stdout: wsclean.log
 stderr: wsclean_err.log

workflows/image_intermediate_resolution.cwl

@@ -15,9 +15,9 @@ inputs:
       type: Directory[]
       doc: MeasurementSets that will be imaged.
 
-    - id: number_cores
+    - id: ncpu
       type: int?
-      default: 12
+      default: 24
       doc: The minimum number of cores that should be available for steps that require high I/O.
 
     - id: dd_solutions
@@ -38,12 +38,19 @@ inputs:
       type: File?
       doc: Optional user-provided facet layout file
 
+    - id: tmpdir_wsclean
+      type: string?
+      default: '.'
+      doc: Temporary directory for wsclean reordering
+
 steps:
     - id: average_data
       label: average
       in:
         - id: msin
           source: msin
+        - id: ncpu
+          source: ncpu
       out:
         - id: ms_avg
       run: ../steps/average_intermediate_resolution.cwl
@@ -52,7 +59,8 @@ steps:
       label: facet_layout
       in:
         - id: msin
-          source: average_data/ms_avg
+          source: msin
+          valueFrom: $(self[0])
         - id: h5parm
           source: dd_solutions
         - id: imsize
@@ -73,9 +81,11 @@ steps:
       label: intermediate_resolution_image
       in:
         - id: msin
-          source: msin
-        - id: cores
-          source: number_cores
+          source: average_data/ms_avg
+        - id: ncpu
+          source: ncpu
+        - id: tmpdir
+          source: tmpdir_wsclean
         - id: size
           source: image_size
         - id: scale
@@ -106,7 +116,6 @@ steps:
         - id: MFS_model
         - id: MFS_psf
         - id: channel_model_images
-
       run: ../steps/wsclean.cwl
 
     - id: validate_image
@@ -116,10 +125,8 @@ steps:
           source: make_intermediate_resolution_image/MFS_image_pb
       out:
         - id: validation_csv
-
       run: ../steps/validate_1arcsec_image.cwl
 
-
 outputs:
     - id: facet_region
       type: File?
@@ -136,7 +143,7 @@ outputs:
       doc: |
         Final primary-beam corrected MFS FITS image at intermediate resolution.
     - id: MFS_image
-      outputSource: make_intermediate_resolution_image/MFS_image_pb
+      outputSource: make_intermediate_resolution_image/MFS_image
       type: File
       doc: |
         Final apparent corrected MFS FITS image at intermediate resolution.
@@ -147,7 +154,7 @@ outputs:
       doc: |
         Final primary-beam corrected MFS FITS image at intermediate resolution.
     - id: MFS_residual
-      outputSource: make_intermediate_resolution_image/MFS_residual_pb
+      outputSource: make_intermediate_resolution_image/MFS_residual
       type: File
       doc: |
         Final apparent corrected MFS FITS image at intermediate resolution.
@@ -158,7 +165,7 @@ outputs:
       doc: |
         Final primary-beam corrected MFS FITS image at intermediate resolution.
     - id: MFS_model
-      outputSource: make_intermediate_resolution_image/MFS_model_pb
+      outputSource: make_intermediate_resolution_image/MFS_model
       type: File
       doc: |
         Final apparent corrected MFS FITS image at intermediate resolution.