diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000000000000000000000000000000000000..d4731a6ccdc8b3b80c226a0cba8229f3ef55ab77
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,5 @@
+# Virtual env
+.venv
+
+# Measurement Sets
+*.MS
\ No newline at end of file
diff --git a/LICENSE b/LICENSE
new file mode 100644
index 0000000000000000000000000000000000000000..261eeb9e9f8b2b4b0d119366dda99c6fd7d35c64
--- /dev/null
+++ b/LICENSE
@@ -0,0 +1,201 @@
+ Apache License
+ Version 2.0, January 2004
+ http://www.apache.org/licenses/
+
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diff --git a/README.md b/README.md
new file mode 100644
index 0000000000000000000000000000000000000000..20f3e857d530fa0dad8f9701cd55d855884581dc
--- /dev/null
+++ b/README.md
@@ -0,0 +1,41 @@
+# Lofar imaging compression pipeline
+
+This is a CWL workflow used to compress Lofar imaging data.
+
+## Workflow steps
+
+
+
+- identify known issues and apply them if necessary. It uses in place updates to prevent copying the measurement set
+ - in place update does not work well with CWL conditional steps, so a small bash script is used which either calls the fixing script or does nothing depending if the specific issue for the step was found
+- Compress the measurement set with Dysco
+- Produces inspection plots and collects metrics to quantify the amount of missing/flagged data
+
+
+## Requirements
+
+- CWL v1.2 compatible runner (e.g. cwltool/toil)
+- Docker
+
+## Docker images
+
+- astronsdc/lofar-legacy
+- astronsdc/lofar-ms-software
+
+## Running the workflow
+In the repositories there are two workflows.
+One is capable to process the data as described in section [workflow steps](#workflow-steps) and can be executed as following
+```bash
+# Run the workflow
+cwltool compress_pipeline.cwl [--flag_autocorrelation] --msin MEASUREMENT_SET
+```
+
+Another workflow, that is meant to be executed by the LDV infrastructure, takes as an input instead of a measurement set a SURL link of the data. Such a workflow can be execute with the command
+```bash
+# Run the workflow
+cwltool download_and_compress_pipeline.cwl [--flag_autocorrelation] --surls [list of surl to process]
+```
+
+## License
+
+See `LICENSE`
diff --git a/compress_pipeline.cwl b/compress_pipeline.cwl
index f83ba79ec6e8ae9946ae3b31a8fa3dab36817975..fcd6f49a0c1b30ef7d3b660e0db115bb8ef600f8 100644
--- a/compress_pipeline.cwl
+++ b/compress_pipeline.cwl
@@ -1,5 +1,5 @@
class: Workflow
-cwlVersion: v1.1
+cwlVersion: v1.2
id: compress_pipeline_cwl
label: compress_pipeline.cwl
inputs:
@@ -33,6 +33,57 @@ outputs:
outputSource:
- inspect_flagging_dataloss/flags_output
steps:
+ - id: identify_issues
+ run: steps/identify_issues.cwl
+ in:
+ - id: msin
+ source: msin
+ out:
+ - issue_list
+ - msout
+ - id: fix_ai_2013
+ run: steps/fix_antenna_information_2013.cwl
+ in:
+ - id: msin
+ source: identify_issues/msout
+ - id: apply
+ source: identify_issues/issue_list
+ valueFrom: $(self.includes("FIX_ANTENNA_TABLE"))
+ out:
+ - id: msout
+ - id: fix_weight_issue
+ run: steps/fix_weightissue_flagging.cwl
+ in:
+ - id: msin
+ source:
+ - fix_ai_2013/msout
+ - id: apply
+ source: identify_issues/issue_list
+ valueFrom: $(self.includes("FIX_WEIGHT_SPECTRUM"))
+ out:
+ - id: msout
+ - id: fix_ai_2015
+ run: steps/fix_antenna_information_2015.cwl
+ in:
+ - id: msin
+ source:
+ - fix_weight_issue/msout
+ - id: apply
+ source: identify_issues/issue_list
+ valueFrom: $(self.includes("FIX_BROKEN_TILES"))
+ out:
+ - id: msout
+ - id: fix_baselines
+ run: steps/fix_long_baselines.cwl
+ in:
+ - id: msin
+ source:
+ - fix_ai_2015/msout
+ - id: apply
+ source: identify_issues/issue_list
+ valueFrom: $(self.includes("FIX_STATION_ADDER"))
+ out:
+ - id: msout
- id: extract_sip_meta
in:
- id: msin
@@ -47,9 +98,10 @@ steps:
- id: parset
source: define_parset/output
- id: msin
- source: msin
+ source:
+ - fix_baselines/msout
- id: msout_name
- source: msin
+ source: fix_baselines/msout
valueFrom: '$("COMPRESSED_" + self.basename)'
- id: writefullresflag
default: true
@@ -81,7 +133,8 @@ steps:
- id: inspect_flagging_dataloss
in:
- id: input
- source: msin
+ source:
+ - fix_baselines/msout
out:
- id: output
- id: flags_output
@@ -105,3 +158,4 @@ steps:
requirements:
- class: StepInputExpressionRequirement
- class: InlineJavascriptRequirement
+ - class: MultipleInputFeatureRequirement
diff --git a/docker/Dockerfile.identify_issues b/docker/Dockerfile.identify_issues
new file mode 100644
index 0000000000000000000000000000000000000000..bfcecb91344193be2962d6ca6bc4205954dfa49e
--- /dev/null
+++ b/docker/Dockerfile.identify_issues
@@ -0,0 +1,6 @@
+FROM python:3.9-slim
+
+WORKDIR /scripts
+COPY requirements.txt /scripts/
+RUN pip install -r requirements.txt
+COPY fix_common_ms_issues.py /scripts/
\ No newline at end of file
diff --git a/pipeline.png b/pipeline.png
new file mode 100644
index 0000000000000000000000000000000000000000..0001d7f2ad03f79e6f2987f4c69b7d60024f0a2a
Binary files /dev/null and b/pipeline.png differ
diff --git a/steps/fix_antenna_information_2013.cwl b/steps/fix_antenna_information_2013.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..aaf5e8b94e41461ce911f44f7b5bf7ec7f2d7c58
--- /dev/null
+++ b/steps/fix_antenna_information_2013.cwl
@@ -0,0 +1,40 @@
+id: fix_antenna_information_2013
+label: Fix Antenna Information 2013
+cwlVersion: v1.2
+class: CommandLineTool
+baseCommand:
+ - bash
+ - script.sh
+inputs:
+ - id: msin
+ type: Directory
+ - id: apply
+ type: boolean
+outputs:
+ - id: msout
+ type: Directory
+ outputBinding:
+ glob: $(inputs.msin.basename)
+
+requirements:
+ - class: InitialWorkDirRequirement
+ listing:
+ - entry: $(inputs.msin)
+ writable: true
+ entryname: $(inputs.msin.basename)
+ - entryname: script.sh
+ entry: |
+ #!/bin/bash
+
+ execute=$(inputs.apply)
+ if [ $execute = 'true' ] ; then
+ echo "Appling fix antenna information 2013"
+ fixinfo $(inputs.msin.basename) /opt/fixinfo
+ fi
+ echo "Skipping apply fix antenna information 2013"
+
+ - class: InplaceUpdateRequirement
+ inplaceUpdate: true
+hints:
+ - class: DockerRequirement
+ dockerPull: "astronsdc/lofar-legacy:latest"
diff --git a/steps/fix_antenna_information_2015.cwl b/steps/fix_antenna_information_2015.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..27acaa1777f7451169a0e3c0442ec5747104f294
--- /dev/null
+++ b/steps/fix_antenna_information_2015.cwl
@@ -0,0 +1,43 @@
+id: fix_antenna_information_2015
+label: Fix Antenna Information_2015
+cwlVersion: v1.2
+class: CommandLineTool
+baseCommand:
+ - bash
+ - script.sh
+
+inputs:
+ - id: msin
+ type: Directory
+ - id: apply
+ type: boolean
+
+outputs:
+ - id: msout
+ type: Directory
+ outputBinding:
+ glob: $(inputs.msin.basename)
+
+
+requirements:
+ - class: InitialWorkDirRequirement
+ listing:
+ - entry: $(inputs.msin)
+ writable: true
+ entryname: $(inputs.msin.basename)
+ - entryname: script.sh
+ entry: |
+ #!/bin/bash
+
+ execute=$(inputs.apply)
+ if [ $execute = 'true' ] ; then
+ echo "Appling fix antenna information 2015"
+ fixbeaminfo $(inputs.msin.basename) /opt/fixbeaminfo
+ fi
+ echo "Skipping apply fix antenna information 2015"
+
+ - class: InplaceUpdateRequirement
+ inplaceUpdate: true
+hints:
+ - class: DockerRequirement
+ dockerPull: "astronsdc/lofar-legacy:latest"
diff --git a/steps/fix_long_baselines.cwl b/steps/fix_long_baselines.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..ce51c9de3f3251b378793c7cbee343577d5102dd
--- /dev/null
+++ b/steps/fix_long_baselines.cwl
@@ -0,0 +1,45 @@
+id: fix_long_baseline
+label: Fix weighted sum for long baseline pipeline
+cwlVersion: v1.2
+class: CommandLineTool
+baseCommand:
+ - bash
+ - script.sh
+
+requirements:
+ - class: InitialWorkDirRequirement
+ listing:
+ - entry: $(inputs.msin)
+ writable: true
+ entryname: $(inputs.msin.basename)
+ - entryname: script.sh
+ entry: |
+ #!/bin/bash
+
+ execute=$(inputs.apply)
+ if [ $execute = 'true' ] ; then
+ echo "Appling fix weighted sum UVW"
+ fix_weightedsum_uvw -f $(inputs.msin.basename) -n $(inputs.new_station)
+ fi
+ echo "Skipping apply fix weighted sum UVW"
+
+ - class: InplaceUpdateRequirement
+ inplaceUpdate: true
+inputs:
+ - id: msin
+ type: Directory
+ - id: new_station
+ doc: new station name (default ST001)
+ type: string?
+ default: ST001
+ - id: apply
+ type: boolean
+outputs:
+ - id: msout
+ type: Directory
+ outputBinding:
+ glob: $(inputs.msin.basename)
+
+hints:
+ - class: DockerRequirement
+ dockerPull: "astronsdc/lofar-legacy:latest"
diff --git a/steps/fix_weightissue_flagging.cwl b/steps/fix_weightissue_flagging.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..641e179768cf7539e5056a654886b6b50ebd65b2
--- /dev/null
+++ b/steps/fix_weightissue_flagging.cwl
@@ -0,0 +1,38 @@
+id: fix_weight_issue_flagging
+label: Fix Weight Issue Flagging
+cwlVersion: v1.2
+class: CommandLineTool
+baseCommand:
+ - bash
+ - script.sh
+requirements:
+ - class: InitialWorkDirRequirement
+ listing:
+ - entry: $(inputs.msin)
+ writable: true
+ entryname: $(inputs.msin.basename)
+ - entryname: script.sh
+ entry: |
+ #!/bin/bash
+
+ execute=$(inputs.apply)
+ if [ $execute = 'true' ] ; then
+ echo "Appling fix weight issue flagging"
+ fix_weightspectrum $(inputs.msin.basename)
+ fi
+ echo "Skipping apply fix weight issue flagging"
+ - class: InplaceUpdateRequirement
+ inplaceUpdate: true
+inputs:
+ - id: msin
+ type: Directory
+ - id: apply
+ type: boolean
+outputs:
+ - id: msout
+ type: Directory
+ outputBinding:
+ glob: $(inputs.msin.basename)
+hints:
+ - class: DockerRequirement
+ dockerPull: "astronsdc/lofar-legacy:latest"
diff --git a/steps/identify_issues.cwl b/steps/identify_issues.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..e0023870bd01935ea94528efd46d8c81b194fe00
--- /dev/null
+++ b/steps/identify_issues.cwl
@@ -0,0 +1,39 @@
+id: identify_issues
+label: Identify Known issues
+class: CommandLineTool
+cwlVersion: v1.0
+hints:
+ DockerRequirement:
+ dockerPull: astronsdc/lofar-legacy:latest
+
+inputs:
+ - id: msin
+ type: Directory
+ inputBinding:
+ position: 1
+
+outputs:
+ - id: issue_list
+ type: string[]
+ outputBinding:
+ glob: output.txt
+ loadContents: true
+ outputEval: $(JSON.parse(self[0].contents))
+
+ - id: msout
+ type: Directory
+ outputBinding:
+ glob: $(inputs.msin.basename)
+stdout: output.txt
+
+baseCommand:
+ - python3
+ - /usr/local/bin/fix_common_ms_issues
+
+requirements:
+ - class: InlineJavascriptRequirement
+ - class: InitialWorkDirRequirement
+ listing:
+ - entry: $(inputs.msin)
+ writable: true
+ entryname: $(inputs.msin.basename)
diff --git a/steps/plot_uvw_coverage.cwl b/steps/plot_uvw_coverage.cwl
index f188063f70104a5060d8a6ef909c390ee6b7a59d..7dc064d77d1f71e656f15a7ad52b1fad579d590f 100644
--- a/steps/plot_uvw_coverage.cwl
+++ b/steps/plot_uvw_coverage.cwl
@@ -18,6 +18,9 @@ outputs:
type: File
outputBinding:
glob: $(inputs.output_name)
+hints:
+ - class: DockerRequirement
+ dockerPull: astronsdc/lofar-ms-software
requirements:
- class: InlineJavascriptRequirement
- class: InitialWorkDirRequirement