diff --git a/scripts/TargetListToCoords.py b/scripts/TargetListToCoords.py
index 115e566a4e83acce5397404364fe68c5c08abe99..0f3a2da718fc5b3c19d81b393831e06065e4b86a 100644
--- a/scripts/TargetListToCoords.py
+++ b/scripts/TargetListToCoords.py
@@ -32,7 +32,7 @@ def plugin_main(**kwargs):
DEC_val = [DEC_val[0]]
Source_id = Source_id[0]
if isinstance(Source_id, str):
- pass
+ Source_id = [Source_id]
else:
Source_id = ['S' + str(Source_id)]
@@ -45,6 +45,6 @@ def plugin_main(**kwargs):
else:
raise ValueError("Argument mode must be one of"
+ " \"delay_calibration\", \"split_directions\""
- + f" but was {mode}.")
+ + f" but was \"{mode}\".")
return {'name' : ",".join(Source_id), 'coords' : ss}
diff --git a/steps/Ateamclipper.cwl b/steps/Ateamclipper.cwl
deleted file mode 100755
index 1cac6b1cfecefc738e771d25ebdc3995aaaf2df8..0000000000000000000000000000000000000000
--- a/steps/Ateamclipper.cwl
+++ /dev/null
@@ -1,71 +0,0 @@
-class: CommandLineTool
-cwlVersion: v1.2
-id: Ateamclipper
-label: A-team clipper
-doc: |
- Clipping of the A-team sources
- using LINC`s Ateamclipper script.
-
-baseCommand:
- - python3
- - Ateamclipper.py
-
-inputs:
- - id: msin
- type:
- - Directory
- - type: array
- items: Directory
- inputBinding:
- position: 0
- doc: Input measurementSet.
-
- - id: number_cores
- type: int?
- default: 12
- doc: |
- Number of cores to use per job for tasks with
- high I/O or memory.
-
- - id: linc_libraries
- type: File[]
- doc: |
- Scripts and reference files from the
- LOFAR INitial calibration pipeline.
- Must contain `Ateamclipper.py`.
-
-outputs:
- - id: msout
- doc: Output MeasurementSet.
- type: Directory
- outputBinding:
- glob: $(inputs.msin.basename)
-
- - id: logfile
- type: File[]
- outputBinding:
- glob: Ateamclipper.log
- doc: The files containing the stdout from the step.
-
- - id: output
- type: File
- outputBinding:
- glob: Ateamclipper.txt
- doc: A text file containing flagging fraction statistics.
-
-hints:
- - class: InitialWorkDirRequirement
- listing:
- - entry: $(inputs.msin)
- writable: true
- - entry: $(inputs.linc_libraries)
- - class: InplaceUpdateRequirement
- inplaceUpdate: true
- - class: DockerRequirement
- dockerPull: vlbi-cwl
- - class: InlineJavascriptRequirement
- - class: ResourceRequirement
- coresMin: $(inputs.number_cores)
-
-stdout: Ateamclipper.log
-stderr: Ateamclipper_err.log
diff --git a/steps/predict.cwl b/steps/clipper.cwl
similarity index 61%
rename from steps/predict.cwl
rename to steps/clipper.cwl
index b10cd1ff0956e7462a530e2798661a434cbf51e2..237b05a29707a78f9b8616fdeb1a40015e362768 100644
--- a/steps/predict.cwl
+++ b/steps/clipper.cwl
@@ -1,25 +1,26 @@
class: CommandLineTool
cwlVersion: v1.2
-id: predict_ateam
-label: DP3 predict A-team
+id: Ateamclipper
+label: clip A-team
doc: |
- Simulates data for the A-team sources
- based off a skymodel. Writes the simulated
- data to the MSOUT datacolumn of the given
- MeasurementSet.
+ Simulates data for the A-team sources based off a skymodel,
+ and flags the visibilities of the input MeasuremenSet where
+ the model data exceeds the threshold for LBA (50 janskys)
+ or HBA (5 janksys).
baseCommand: DP3
arguments:
- - steps=[filter,predict]
- - predict.sourcedb=Ateam_LBA_CC.skymodel
- - predict.usechannelfreq=False
- - predict.operation=replace
- - predict.beamproximitylimit=2000
+ - steps=[filter,clipper,counter]
+ - clipper.sourcedb=Ateam_LBA_CC.skymodel
+ - clipper.usechannelfreq=False
+ - clipper.operation=replace
+ - clipper.beamproximitylimit=2000
- filter.baseline=[CR]S*&
- filter.remove=False
+ - counter.savetojson=True
+ - counter.jsonfilename=Ateamclipper.json
- msout=.
-
inputs:
- id: msin
type: Directory
@@ -42,18 +43,6 @@ inputs:
Data column of the MeasurementSet
from which input data is read.
- - id: msout_datacolumn
- type: string?
- default: MODEL_DATA
- inputBinding:
- position: 0
- prefix: msout.datacolumn=
- separate: false
- shellQuote: false
- doc: |
- Data column of the MeasurementSet
- into which output data is written.
-
- id: linc_libraries
type: File[]
doc: |
@@ -70,7 +59,7 @@ inputs:
- "TauAGG"
inputBinding:
position: 0
- prefix: predict.sources=
+ prefix: clipper.sources=
separate: false
itemSeparator: ','
valueFrom: '"$(self)"'
@@ -84,34 +73,11 @@ inputs:
default: true
inputBinding:
position: 0
- prefix: predict.usebeammodel=True
+ prefix: clipper.usebeammodel=True
shellQuote: false
doc: |
Determines whether to use the beam model.
- - id: storagemanager
- type: string?
- default: "dysco"
- inputBinding:
- prefix: msout.storagemanager=
- separate: false
- shellQuote: false
- doc: |
- String that specifies what storage manager
- to use. By default uses `dysco` compression.
-
- - id: databitrate
- type: int?
- default: 0
- inputBinding:
- prefix: msout.storagemanager.databitrate=
- separate: false
- shellQuote: false
- doc: |
- Number of bits per float used for columns
- containing visibilities. Default compresses
- weights only.
-
- id: max_dp3_threads
type: int?
default: 5
@@ -121,6 +87,13 @@ inputs:
shellQuote: false
doc: The number of threads per DP3 process.
+ - id: number_cores
+ type: int?
+ default: 12
+ doc: |
+ Number of cores to use per job for tasks with
+ high I/O or memory.
+
requirements:
- class: InitialWorkDirRequirement
listing:
@@ -140,16 +113,22 @@ outputs:
- id: logfile
type: File[]
outputBinding:
- glob: predict_ateam*.log
+ glob: clipper*.log
doc: |
The files containing the stdout
and stderr from the step.
+ - id: output
+ type: File
+ outputBinding:
+ glob: Ateamclipper.json
+ doc: A text file containing flagging fraction statistics.
+
hints:
- class: ResourceRequirement
- coresMin: 6
+ coresMin: $(inputs.number_cores)
- class: DockerRequirement
dockerPull: vlbi-cwl
-stdout: predict_ateam.log
-stderr: predict_ateam_err.log
+stdout: clipper.log
+stderr: clipper_err.log
diff --git a/workflows/subworkflows/clip_A-team.cwl b/workflows/subworkflows/clip_A-team.cwl
index 288100c11319746f2957340f216227f54bf9c690..57504a05cebd7bf4542e5f5c830c0f5007c11e65 100644
--- a/workflows/subworkflows/clip_A-team.cwl
+++ b/workflows/subworkflows/clip_A-team.cwl
@@ -62,7 +62,7 @@ steps:
- id: flag_statistics_before
- id: flag_statistics_after
run: ../../steps/dp3_prep_target.cwl
- - id: predict
+ - id: Ateamclipper
in:
- id: msin
source: dp3_prep_target/msout
@@ -70,25 +70,13 @@ steps:
source: max_dp3_threads
- id: linc_libraries
source: linc_libraries
- out:
- - id: msout
- - id: logfile
- run: ../../steps/predict.cwl
- label: predict
- - id: Ateamcliptar
- in:
- - id: msin
- source: predict/msout
- id: number_cores
source: number_cores
- - id: linc_libraries
- source: linc_libraries
out:
- id: msout
- id: logfile
- - id: output
- run: ../../steps/Ateamclipper.cwl
- label: Ateamcliptar
+ - id: output
+ run: ../../steps/clipper.cwl
- id: concat_logfiles_prep_targ
label: concat_logfiles_prep_target
in:
@@ -101,24 +89,13 @@ steps:
out:
- id: output
run: ../../steps/concatenate_files.cwl
- - id: concat_logfiles_predict
- in:
- - id: file_list
- linkMerge: merge_flattened
- source: predict/logfile
- - id: file_prefix
- default: predict
- out:
- - id: output
- run: ../../steps/concatenate_files.cwl
- label: concat_logfiles_predict
- id: concat_logfiles_cliptar
in:
- id: file_list
linkMerge: merge_flattened
- source: Ateamcliptar/logfile
+ source: Ateamclipper/logfile
- id: file_prefix
- default: Ateamcliptar
+ default: Ateamclipper
out:
- id: output
run: ../../steps/concatenate_files.cwl
@@ -129,7 +106,6 @@ steps:
linkMerge: merge_flattened
source:
- concat_logfiles_prep_targ/output
- - concat_logfiles_predict/output
- concat_logfiles_cliptar/output
- id: file_prefix
default: Ateamcliptar
@@ -149,7 +125,7 @@ outputs:
- id: msout
outputSource:
- - Ateamcliptar/msout
+ - Ateamclipper/msout
type: Directory
doc: |
The input data in MeasurementSet format after