From 0f5bf10bb459452570f58b7bb5f843b0bae2b629 Mon Sep 17 00:00:00 2001
From: mancini <mancini@astron.nl>
Date: Thu, 26 Sep 2019 14:02:16 +0200
Subject: [PATCH] Fix CWL and python for parsetgenerator
---
steps/AveragingStepGenerator.cwl | 27 ++++---
steps/DP3_flag_averaging.cwl | 123 +++++++++++++++++++++++++++++++
steps/echo.cwl | 12 +++
utils/parset_concat.py | 2 +-
4 files changed, 151 insertions(+), 13 deletions(-)
create mode 100644 steps/DP3_flag_averaging.cwl
create mode 100644 steps/echo.cwl
diff --git a/steps/AveragingStepGenerator.cwl b/steps/AveragingStepGenerator.cwl
index 1abe69cf..0be4cc15 100755
--- a/steps/AveragingStepGenerator.cwl
+++ b/steps/AveragingStepGenerator.cwl
@@ -15,53 +15,56 @@ inputs:
- id: parset
type: File
inputBinding:
- prefix: --input_parset=
- position: 1
-
+ position: -1
+ prefix: --input_parset
- id: step_name
type: string
default: average
doc: unique name for the step
inputBinding:
- position: 2
+ position: -1
- id: timestep
type: int
default: 1
doc: Number of time slots to average. It is truncated if exceeding the actual number of times.
inputBinding:
- prefix: timestep=
-
+ prefix: timestep=
+ separate: false
- id: freqstep
type: int
default: 1
doc: Number of channels to average. It is truncated if exceeding the actual number of channels.
inputBinding:
- prefix: freqstep=
-
+ prefix: freqstep=
+ separate: false
- id: minpoints
type: int
doc: If number of averaged unflagged input points < minpoints, the averaged point is flagged.
default: 0
inputBinding:
- prefix: minpoints=
+ prefix: minpoints=
+ separate: false
- id: minperc
type: float
doc: Like minpoints, but expressed as a percentage of timestep*freqstep.
default: 0
inputBinding:
- prefix: minperc=
+ prefix: minperc=
+ separate: false
- id: timeresolution
type: float
doc: Target time resolution, in seconds. If this is given, and bigger than zero, it overrides <step>.timestep
default: 0
inputBinding:
- prefix: timeresolution
+ prefix: timeresolution=
+ separate: false
- id: freqresolution
type: float
doc: Target frequency resolution, in Hz (or append “MHz” or “kHz” to specify it in those units). If this is given, and bigger than zero, it overrides <step>.freqstep
default: 0
inputBinding:
- prefix: freqresolution=
+ prefix: freqresolution=
+ separate: false
outputs:
diff --git a/steps/DP3_flag_averaging.cwl b/steps/DP3_flag_averaging.cwl
new file mode 100644
index 00000000..7556cc69
--- /dev/null
+++ b/steps/DP3_flag_averaging.cwl
@@ -0,0 +1,123 @@
+cwlVersion: 1.1
+class: CommandLineTool
+baseCommand: [DPPP]
+
+label: "Flagging and Averaging"
+
+hints:
+ DockerRequirements:
+ dockerPull: lofaruser/imaging-pipeline
+
+inputs:
+ msin:
+ type: Directory
+
+ msin_data_column:
+ type: string
+ default: "DATA"
+
+ msin_writefullresflag:
+ type: boolean
+ default: False
+
+ msin_baselines:
+ type: string
+ default: ""
+
+ msin_autoweight:
+ type: boolean
+ default: False
+
+ msout_data_column:
+ type: string
+ default: "DATA"
+
+ msout_writefullresflag:
+ type: boolean
+ default: False
+
+ msout_overwrite:
+ type: boolean
+ default: True
+
+ msout_storagemanager:
+ type: string
+ default: "Dysco"
+
+ msout_storagemanager_databitrate:
+ type: int
+ default: 0
+
+ flagger_memory_used:
+ type: int
+ default: 0
+
+ flagger_keep_statistics:
+ type: boolean
+ default: False
+
+ flag_baseline:
+ type: string
+ default: ""
+
+ flag_elevation:
+ type: string
+ default: "0deg..20deg"
+
+ flag_amplitude:
+ type: double
+ default: 1.e-30
+
+ interpolate_windowsize:
+ type: int
+
+
+ avg_timeresolution:
+ type: int
+ avg_frequenciesresolution:
+ type: int
+
+ demixer_baseline:
+ type: string
+ default: ""
+
+ demixer_frequency_steps:
+ type: int
+ default: 4
+
+ demixer_time_steps:
+ type: int
+ default: 4
+
+ demixer_ignore_target:
+ type: boolean
+ default: False
+
+ demixer_target_source:
+ type: string
+
+ demixer_subtract_sources:
+ type: string
+
+
+
+outputs:
+
+
+
+
+ndppp_prep_cal.control.type = dppp
+ndppp_prep_cal.control.max_per_node = {{ num_proc_per_node_limit }}
+ndppp_prep_cal.control.error_tolerance = {{ error_tolerance }}
+ndppp_prep_cal.argument.numthreads = {{ max_dppp_threads }}
+
+ndppp_prep_cal.argument.steps = [{{ initial_flagging }},{{ demix_step }}interp,avg]
+ndppp_prep_cal.argument.flagedge.type = preflagger
+ndppp_prep_cal.argument.flagedge.chan = [0..nchan/32-1,31*nchan/32..nchan-1] # we are running on a single subband
+
+ndppp_prep_cal.argument.flagbaseline.type = preflagger
+ndppp_prep_cal.argument.flagamp.type = preflagger
+ndppp_prep_cal.argument.interp.type = interpolate
+ndppp_prep_cal.argument.avg.type = average
+ndppp_prep_cal.argument.flagamp.type = preflagger
+ndppp_prep_cal.argument.demix.type = demixer
diff --git a/steps/echo.cwl b/steps/echo.cwl
new file mode 100644
index 00000000..8e273f66
--- /dev/null
+++ b/steps/echo.cwl
@@ -0,0 +1,12 @@
+class: CommandLineTool
+cwlVersion: v1.0
+id: echo
+baseCommand:
+ - cat
+inputs:
+ file:
+ type: File
+ inputBinding:
+ position: 1
+
+outputs: []
\ No newline at end of file
diff --git a/utils/parset_concat.py b/utils/parset_concat.py
index 5d488417..c4c05062 100755
--- a/utils/parset_concat.py
+++ b/utils/parset_concat.py
@@ -9,8 +9,8 @@ from argparse import ArgumentParser
def parse_arguments(args):
parser = ArgumentParser(description='Concatenate step defined to the input parset')
- parser.add_argument('step_type', help='type of the step')
parser.add_argument('step_name', help='name of the step')
+ parser.add_argument('step_type', help='type of the step')
parser.add_argument('--input_parset', default=None, help='input parset')
parser.add_argument('step_arguments', help='step arguments', nargs='+')
--
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