diff --git a/pyproject.toml b/pyproject.toml
index 62d261f8b80a0f03f7eca4a8ad0f8d64fd642b2b..55c1d7bae7c458b03b789373c3528f9fef05f397 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -50,7 +50,6 @@ dynamic = ["version"]
[tool.setuptools]
packages = []
script-files = [
- "scripts/Ateamclipper.py",
"scripts/BLsmooth.py",
"scripts/add_missing_stations.py",
"scripts/blank_image_reg.py",
diff --git a/scripts/Ateamclipper.py b/scripts/Ateamclipper.py
deleted file mode 100755
index fcd8a0ad3dc316b2151a123a3c8d168a1db256b9..0000000000000000000000000000000000000000
--- a/scripts/Ateamclipper.py
+++ /dev/null
@@ -1,65 +0,0 @@
-#!/usr/bin/env python
-
-## changelog
-# W.Williams 2014/11/03 add - to give input/output statistics per channel
-# W.Williams 2014/11/03 fix - statistics per correlation
-# A.Drabent 2019/07/24 write fraction of flagged data into output file (for prefactor/LINC)
-
-import numpy
-import pyrap.tables as pt
-import os
-import sys
-
-msname = str(sys.argv[1])
-
-cliplevelhba = 5.0
-cliplevellba = 50.0
-
-t = pt.table(msname, readonly=False)
-data = t.getcol('MODEL_DATA')
-flag = t.getcol('FLAG')
-freq_tab= pt.table(msname + '::SPECTRAL_WINDOW')
-freq = freq_tab.getcol('REF_FREQUENCY')
-
-if freq[0] > 100e6:
- cliplevel = cliplevelhba
-if freq[0] < 100e6:
- cliplevel = cliplevellba
-
-
-print('------------------------------')
-print('SB Frequency [MHz]', freq[0]/1e6)
-for chan in range(0,numpy.size(data[0,:,0])):
- print('chan %i : %.5f%% input XX flagged' %( chan, 100.*numpy.sum(flag[:,chan,0] == True)/numpy.size(flag[:,chan,0]) ))
- print('chan %i : %.5f%% input YY flagged' %( chan, 100.*numpy.sum(flag[:,chan,3] == True)/numpy.size(flag[:,chan,3]) ))
-input_flags_xx = 100. * numpy.sum(flag[:,:,0] == True)/numpy.size(flag[:,:,0])
-input_flags_yy = 100. * numpy.sum(flag[:,:,3] == True)/numpy.size(flag[:,:,3])
-print('Total : %.5f%% input XX flagged' %( input_flags_xx ))
-print('Total : %.5f%% input YY flagged' %( input_flags_yy ))
-print('')
-print('Cliplevel used [Jy]', cliplevel)
-print('\n\n')
-
-for pol in range(0,numpy.size(data[0,0,:])):
- for chan in range(0,numpy.size(data[0,:,0])):
- print('Doing polarization,chan', pol, chan)
- idx = numpy.where(abs(data[:,chan,pol]) > cliplevel)
- flag[idx,chan,0] = True
- flag[idx,chan,1] = True
- flag[idx,chan,2] = True
- flag[idx,chan,3] = True
-
-print('')
-for chan in range(0,numpy.size(data[0,:,0])):
- print('chan %i : %.5f%% output XX flagged' %( chan, 100.*numpy.sum(flag[:,chan,0] == True)/numpy.size(flag[:,chan,0]) ))
- print('chan %i : %.5f%% output YY flagged' %( chan, 100.*numpy.sum(flag[:,chan,3] == True)/numpy.size(flag[:,chan,3]) ))
-output_flags_xx = 100. * numpy.sum(flag[:,:,0] == True)/numpy.size(flag[:,:,0])
-output_flags_yy = 100. * numpy.sum(flag[:,:,3] == True)/numpy.size(flag[:,:,3])
-print('Total : %.5f%% output XX flagged' %( output_flags_xx ))
-print('Total : %.5f%% output YY flagged' %( output_flags_yy ))
-print('')
-t.putcol('FLAG', flag)
-t.close()
-freq_tab.close()
-
-os.system('echo ' + str(freq[0]) + ' ' + str(output_flags_xx - input_flags_xx) + ' ' + str(output_flags_yy - input_flags_yy) + ' >> Ateamclipper.txt')
diff --git a/scripts/plot_Ateamclipper.py b/scripts/plot_Ateamclipper.py
index 1e084d9709e458bad920b6c6bec5f3929b3d72d5..e1f54c3ffcc1c42518314445623fdfd009ad2291 100755
--- a/scripts/plot_Ateamclipper.py
+++ b/scripts/plot_Ateamclipper.py
@@ -2,48 +2,92 @@
# -* coding: utf-8 -*-
"""
-Adds phases (=0) and amplitudes (=1) to any missing station if they appear in an h5parm, but not in a particular soltab.
-
-Created on Tue Jul 24 2019
+Created on Wed Mar 12, 2025
@author: Alexander Drabent
"""
-import argparse
+import numpy
+import multiprocessing
import matplotlib as mpl
-mpl.use('Agg')
-import matplotlib
+
+mpl.use("Agg")
import matplotlib.pyplot as plt
-import numpy
+import casacore.tables as ctab
+
+
+def process_table(table):
+ tt = ctab.table(table, readonly=True)
+ freqs = tt.getcol("Frequency")
+ flag_perc = tt.getcol("Percentage")
+ flags_per_freq = {}
+ for i, freq in enumerate(freqs):
+ flags_per_freq[freq] = flag_perc[i]
+ tt.close()
+ return flags_per_freq
+
+
+def main(flagfreq_before, flagfreq_after, outfile="Ateamclipper.png"):
+
+ ## reading in all flagging percentages
+ pool = multiprocessing.Pool(processes=int(multiprocessing.cpu_count() / 2))
+ flag_perc_before = {
+ freq: flag_perc
+ for entry in pool.map(process_table, flagfreq_before)
+ for freq, flag_perc in entry.items()
+ }
+ flag_perc_after = {
+ freq: flag_perc
+ for entry in pool.map(process_table, flagfreq_after)
+ for freq, flag_perc in entry.items()
+ }
+
+ freq_list = list(flag_perc_before.keys() | flag_perc_after.keys())
+ flag_perc_diff = {
+ freq: flag_perc_after[freq] - flag_perc_before[freq] for freq in freq_list
+ }
+
+ perc_list = [flag_perc_diff[freq] for freq in freq_list]
-def main(txtfile = 'Ateamclipper.txt', outfile = 'Ateamclipper.png'):
-
- frac_list_xx = []
- frac_list_yy = []
- freq_list = []
- with open(txtfile, 'r') as infile:
- for line in infile:
- freq_list.append(float(line.split()[0]))
- frac_list_xx.append(float(line.split()[1]))
- frac_list_yy.append(float(line.split()[2]))
-
# Plot the amount of clipped data vs. frequency potentially contaminated by the A-team
- plt.scatter(numpy.array(freq_list) / 1e6, numpy.array(frac_list_xx), marker = '.', s = 10)
- plt.xlabel('frequency [MHz]')
- plt.ylabel('A-team clipping fraction [%]')
+ plt.scatter(numpy.array(freq_list) / 1e6, numpy.array(perc_list), marker=".", s=10)
+ plt.xlabel("frequency [MHz]")
+ plt.ylabel("A-Team clipping fraction [%]")
plt.savefig(outfile)
- return(0)
+ return 0
+
if __name__ == "__main__":
- parser = argparse.ArgumentParser(description='Adds phases and amplitudes to any missing station if they appear in an h5parm, but not in a particular soltab.')
+ import argparse
- parser.add_argument('txtfile', type=str,
- help='Input text file containing frequency and flag fraction of the XX and YY polarization.')
- parser.add_argument('outfile', type=str,
- help='Output image file containing frequency and flag fraction of the XX and YY polarization.')
+ parser = argparse.ArgumentParser(
+ description="Compare the flagging percentage of two given sets/lists of flagfreq tables provided by the DP3 count step"
+ )
+ parser.add_argument(
+ "--flagfreq_before",
+ type=str,
+ nargs="+",
+ help="One or more flagfreq tables before running flagging",
+ )
+ parser.add_argument(
+ "--flagfreq_after",
+ type=str,
+ nargs="+",
+ help="One or more flagfreq tables after running flagging",
+ )
+ parser.add_argument(
+ "--outfile",
+ type=str,
+ nargs="?",
+ help="Output file name for the plot",
+ default="Ateamclipper.png",
+ )
args = parser.parse_args()
- main(txtfile = args.txtfile, outfile = args.outfile)
-
+ main(
+ flagfreq_before=args.flagfreq_before,
+ flagfreq_after=args.flagfreq_after,
+ outfile=args.outfile,
+ )
diff --git a/steps/Ateamclipper.cwl b/steps/Ateamclipper.cwl
deleted file mode 100755
index 7ed4fea9758fe710113d3def1cc70d4ce0eb8a7a..0000000000000000000000000000000000000000
--- a/steps/Ateamclipper.cwl
+++ /dev/null
@@ -1,42 +0,0 @@
-class: CommandLineTool
-cwlVersion: v1.2
-id: check_ateam_separation
-baseCommand:
- - Ateamclipper.py
-inputs:
- - id: msin
- type:
- - Directory
- - type: array
- items: Directory
- inputBinding:
- position: 0
- doc: Input measurement set
-outputs:
- - id: msout
- doc: Output MS
- type: Directory
- outputBinding:
- glob: $(inputs.msin.basename)
- - id: logfile
- type: File[]
- outputBinding:
- glob: Ateamclipper.log
- - id: output
- type: File
- outputBinding:
- glob: Ateamclipper.txt
-label: Ateamclipper
-hints:
- - class: InitialWorkDirRequirement
- listing:
- - entry: $(inputs.msin)
- writable: true
- - class: InplaceUpdateRequirement
- inplaceUpdate: true
- - class: DockerRequirement
- dockerPull: astronrd/linc
- - class: InlineJavascriptRequirement
- - class: ResourceRequirement
- coresMin: 8
-stdout: Ateamclipper.log
diff --git a/steps/H5ParmCollector.cwl b/steps/H5ParmCollector.cwl
old mode 100755
new mode 100644
diff --git a/steps/LoSoTo.Polalign.cwl b/steps/LoSoTo.Polalign.cwl
old mode 100755
new mode 100644
diff --git a/steps/clipper.cwl b/steps/clipper.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..1d53dcf7a4de5408010c489b8a41614ee942419a
--- /dev/null
+++ b/steps/clipper.cwl
@@ -0,0 +1,171 @@
+class: CommandLineTool
+cwlVersion: v1.2
+id: Ateamclipper
+label: clip A-team
+doc: |
+ 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,count1,clipper,count2]
+ - msout=.
+ - count1.save=true
+ - count2.save=true
+
+inputs:
+ - id: msin
+ type: Directory
+ inputBinding:
+ position: 0
+ prefix: msin=
+ separate: false
+ shellQuote: false
+ doc: Input data in MeasurementSet format.
+ - id: msin_datacolumn
+ type: string?
+ default: DATA
+ inputBinding:
+ position: 0
+ prefix: msin.datacolumn=
+ separate: false
+ shellQuote: false
+ doc: |
+ Data column of the MeasurementSet
+ from which input data is read.
+
+ - id: storagemanager
+ type: string?
+ default: ""
+ inputBinding:
+ prefix: msout.storagemanager=
+ separate: false
+ - id: databitrate
+ type: int?
+ default: 0
+ inputBinding:
+ prefix: msout.storagemanager.databitrate=
+ separate: false
+
+ - id: operation
+ type:
+ type: enum
+ symbols:
+ - replace
+ doc: |
+ Type of operation to be performed on clipped data.
+ inputBinding:
+ prefix: clipper.operation=
+ separate: false
+
+ - id: sourcedb
+ type:
+ - File
+ - Directory
+ inputBinding:
+ position: 0
+ prefix: clipper.sourcedb=
+ separate: false
+ - default: null
+ id: sources
+ type: string[]?
+ inputBinding:
+ position: 0
+ prefix: clipper.sources=
+ separate: false
+ itemSeparator: ','
+ valueFrom: "[$(self.join(','))]"
+ doc: |
+ Labels of the skymodel patches to
+ use to simulate visibilities.
+ - id: usechannelfreq
+ default: false
+ type: boolean?
+ inputBinding:
+ valueFrom: $(!self)
+ position: 0
+ prefix: clipper.usechannelfreq=False
+ separate: false
+ - id: usebeammodel
+ type: boolean?
+ default: true
+ inputBinding:
+ position: 0
+ prefix: clipper.usebeammodel=True
+ shellQuote: false
+ doc: |
+ Determines whether to use the beam model.
+ - id: beamproximitylimit
+ doc: |
+ Specified in arcseconds, and if non-zero, sources that are near each other are clustered
+ and the beam is only calculated for each cluster.
+ type: int?
+ default: 2000
+ inputBinding:
+ position: 0
+ prefix: clipper.beamproximitylimit=
+ separate: false
+
+ - id: filter_baselines
+ type: string?
+ inputBinding:
+ position: 0
+ prefix: filter.baseline=
+ separate: false
+ valueFrom: $(self)
+ - id: filter_remove
+ default: false
+ type: boolean?
+ inputBinding:
+ position: 0
+ prefix: filter.remove=True
+
+ - id: max_dp3_threads
+ type: int?
+ inputBinding:
+ prefix: numthreads=
+ separate: false
+ doc: The number of threads per DP3 process.
+
+outputs:
+ - id: msout
+ doc: Output data in MeasurementSet format.
+ type: Directory
+ outputBinding:
+ glob: $(inputs.msin.basename)
+ - id: logfile
+ type: File[]
+ outputBinding:
+ glob: clipper*.log
+ doc: |
+ The files containing the stdout
+ and stderr from the step.
+ - id: flagfreq_before
+ type: Directory
+ outputBinding:
+ glob: '$(inputs.msin.nameroot.split(".")[0])_count1.flagfreq'
+ doc: A MS file containing flagging fraction statistics before clipping.
+ - id: flagfreq_after
+ type: Directory
+ outputBinding:
+ glob: '$(inputs.msin.nameroot.split(".")[0])_count2.flagfreq'
+ doc: A MS file containing flagging fraction statistics after clipping.
+
+requirements:
+ - class: InplaceUpdateRequirement
+ inplaceUpdate: true
+ - class: InitialWorkDirRequirement
+ listing:
+ - entry: $(inputs.msin)
+ writable: true
+ - class: InlineJavascriptRequirement
+ - class: ResourceRequirement
+ coresMin: $(inputs.max_dp3_threads)
+hints:
+ - class: DockerRequirement
+ dockerPull: astronrd/linc
+
+stdout: clipper.log
+stderr: clipper_err.log
diff --git a/steps/dp3_make_parset_cal.cwl b/steps/dp3_make_parset_cal.cwl
old mode 100755
new mode 100644
diff --git a/steps/dp3_make_parset_target.cwl b/steps/dp3_make_parset_target.cwl
old mode 100755
new mode 100644
diff --git a/steps/dp3_prep_cal.cwl b/steps/dp3_prep_cal.cwl
old mode 100755
new mode 100644
diff --git a/steps/dp3_prep_target.cwl b/steps/dp3_prep_target.cwl
old mode 100755
new mode 100644
diff --git a/steps/filter_predict.cwl b/steps/filter_predict.cwl
deleted file mode 100644
index ea730f9de07c3d5237c72ffc07c373c1673038f4..0000000000000000000000000000000000000000
--- a/steps/filter_predict.cwl
+++ /dev/null
@@ -1,140 +0,0 @@
-class: CommandLineTool
-cwlVersion: v1.2
-id: predict
-baseCommand:
- - DP3
-inputs:
- - id: max_dp3_threads
- type: int?
- inputBinding:
- position: 0
- prefix: numthreads=
- separate: false
- - id: msin
- type: Directory
- inputBinding:
- position: 0
- prefix: msin=
- separate: false
- doc: Input Measurement Set
- - default: DATA
- id: msin_datacolumn
- type: string?
- inputBinding:
- position: 0
- prefix: msin.datacolumn=
- separate: false
- doc: Input data Column
- - default: MODEL_DATA
- id: msout_datacolumn
- type: string?
- inputBinding:
- position: 0
- prefix: msout.datacolumn=
- separate: false
- - id: sources_db
- type:
- - File
- - Directory
- inputBinding:
- position: 0
- prefix: predict.sourcedb=
- separate: false
- - default: null
- id: sources
- type: string[]?
- inputBinding:
- position: 0
- prefix: predict.sources=
- separate: false
- itemSeparator: ','
- valueFrom: "[$(self.join(','))]"
- - default: false
- id: usebeammodel
- type: boolean?
- inputBinding:
- position: 0
- prefix: predict.usebeammodel=True
- - id: usechannelfreq
- default: true
- type: boolean?
- inputBinding:
- valueFrom: $(!self)
- position: 0
- prefix: predict.usechannelfreq=False
- - default: false
- id: onebeamperpatch
- type: boolean?
- inputBinding:
- position: 0
- prefix: predict.onebeamperpatch=True
- - default: null
- id: filter_baselines
- type: string?
- inputBinding:
- position: 0
- prefix: filter.baseline=
- separate: false
- valueFrom: $(self)
- - default: false
- id: filter_remove
- type: boolean?
- inputBinding:
- position: 0
- prefix: filter.remove=True
- - id: writefullresflag
- type: boolean?
- default: false
- inputBinding:
- prefix: msout.writefullresflag=True
- - default: default
- id: beammode
- type: string?
- inputBinding:
- position: 0
- prefix: predict.beammode=
- separate: false
- - id: overwrite
- type: boolean?
- default: false
- inputBinding:
- prefix: msout.overwrite=True
- - id: storagemanager
- type: string?
- default: ""
- inputBinding:
- prefix: msout.storagemanager=
- separate: false
- - id: databitrate
- type: int?
- inputBinding:
- prefix: msout.storagemanager.databitrate=
- separate: false
-outputs:
- - id: msout
- doc: Output Measurement Set
- type: Directory
- outputBinding:
- glob: $(inputs.msin.basename)
- - id: logfile
- type: File[]
- outputBinding:
- glob: 'filter_predict*.log'
-arguments:
- - steps=[filter,predict,count]
- - msout=.
-requirements:
- - class: InitialWorkDirRequirement
- listing:
- - entry: $(inputs.msin)
- writable: true
- - class: InplaceUpdateRequirement
- inplaceUpdate: true
- - class: InlineJavascriptRequirement
- - class: ResourceRequirement
- coresMin: $(inputs.max_dp3_threads)
-hints:
- - class: DockerRequirement
- dockerPull: astronrd/linc
-stdout: filter_predict.log
-stderr: filter_predict_err.log
diff --git a/steps/merge_skymodels.cwl b/steps/merge_skymodels.cwl
old mode 100755
new mode 100644
diff --git a/steps/plot_Ateamclipper.cwl b/steps/plot_Ateamclipper.cwl
index 1ccf53a01f3365de7758f2daf184ccce78940fc3..19f3983e34a9eaa85540f2c64bb41208ed8def44 100644
--- a/steps/plot_Ateamclipper.cwl
+++ b/steps/plot_Ateamclipper.cwl
@@ -4,15 +4,22 @@ id: plot_Ateamclipper
baseCommand:
- plot_Ateamclipper.py
inputs:
- - id: clipper_output
- type: File?
+ - id: flagfreq_before
+ type: Directory[]
inputBinding:
position: 1
+ prefix: '--flagfreq_before'
+ - id: flagfreq_after
+ type: Directory[]
+ inputBinding:
+ position: 1
+ prefix: '--flagfreq_after'
- id: outputimage
type: string?
default: Ateamclipper.png
inputBinding:
position: 2
+ prefix: '--outfile'
outputs:
- id: output_imag
doc: Output image
@@ -22,4 +29,4 @@ outputs:
label: plot_Ateamclipper
hints:
- class: DockerRequirement
- dockerPull: astronrd/linc
+ dockerPull: astronrd/linc
\ No newline at end of file
diff --git a/workflows/linc_target/dp3_prep_targ.cwl b/workflows/linc_target/dp3_prep_targ.cwl
index 8a61bba6afe587c407c0dc4465423e5f0577e64e..eb258439da71dbed036fa6f6ed2c4c90f6fd560e 100644
--- a/workflows/linc_target/dp3_prep_targ.cwl
+++ b/workflows/linc_target/dp3_prep_targ.cwl
@@ -105,11 +105,6 @@ outputs:
outputSource:
- concat_logfiles_dp3/output
type: File
- - id: predict_logfile
- outputSource:
- - concat_logfiles_predict/output
- type: File
- pickValue: all_non_null
- id: clipper_logfile
outputSource:
- concat_logfiles_clipper/output
@@ -117,14 +112,19 @@ outputs:
pickValue: all_non_null
- id: msout
outputSource:
- - Ateamclipper/msout
+ - clipper/msout
- dp3_execute/msout
type: Directory
pickValue: first_non_null
- - id: clipper_output
+ - id: clipper_flags_before
outputSource:
- - Ateamclipper/output
- type: File
+ - clipper/flagfreq_before
+ type: Directory
+ pickValue: all_non_null
+ - id: clipper_flags_after
+ outputSource:
+ - clipper/flagfreq_after
+ type: Directory
pickValue: all_non_null
- id: instrument_tables
outputSource:
@@ -198,26 +198,11 @@ steps:
- id: output
run: ../../steps/concatenate_files.cwl
label: concat_logfiles_dp3
- - id: concat_logfiles_predict
- in:
- - id: file_list
- source:
- - predict/logfile
- pickValue: all_non_null
- - id: file_prefix
- default: predict_targ
- - id: execute
- source: clipAteam
- out:
- - id: output
- run: ../../steps/concatenate_files.cwl
- when: $(inputs.execute)
- label: concat_logfiles_predict
- id: concat_logfiles_clipper
in:
- id: file_list
source:
- - Ateamclipper/logfile
+ - clipper/logfile
pickValue: all_non_null
- id: file_prefix
default: Ateamclipper
@@ -263,53 +248,45 @@ steps:
- id: logfile
run: ../../steps/dp3_prep_target.cwl
label: DP3.Execute
- - id: predict
+ - id: clipper
in:
- - id: max_dp3_threads
- source: max_dp3_threads
- id: msin
source: dp3_execute/msout
- id: msin_datacolumn
default: DATA
- - id: msout_datacolumn
- default: MODEL_DATA
- - id: sources_db
+ - id: storagemanager
+ default: Dysco
+ - id: databitrate
+ default: 0
+ - id: operation
+ default: replace
+ - id: sourcedb
source: skymodel
- id: sources
source:
- clip_sources
- id: usebeammodel
default: true
- - id: storagemanager
- default: Dysco
- - id: databitrate
- default: 0
+ - id: usechannelfreq
+ default: false
+ - id: beamproximitylimit
+ default: 2000
- id: filter_baselines
source: process_baselines_target
- - id: usechannelfreq
+ - id: filter_remove
default: false
+ - id: max_dp3_threads
+ source: max_dp3_threads
- id: execute
source: clipAteam
out:
- id: msout
- id: logfile
- run: ../../steps/filter_predict.cwl
- when: $(inputs.execute)
- - id: Ateamclipper
- in:
- - id: msin
- source:
- - predict/msout
- pickValue: all_non_null
- - id: execute
- source: clipAteam
- out:
- - id: msout
- - id: logfile
- - id: output
- run: ../../steps/Ateamclipper.cwl
+ - id: flagfreq_before
+ - id: flagfreq_after
+ run: ../../steps/clipper.cwl
when: $(inputs.execute)
- label: Ateamclipper
+
requirements:
- class: InlineJavascriptRequirement
- class: StepInputExpressionRequirement
diff --git a/workflows/linc_target/prep.cwl b/workflows/linc_target/prep.cwl
index abcd945c67ba61b3f738eb6eb05b268b5e0036d9..63e33829a7747b5d8a64c6c8c37d81ade5cc0795 100644
--- a/workflows/linc_target/prep.cwl
+++ b/workflows/linc_target/prep.cwl
@@ -167,7 +167,6 @@ outputs:
- concat_logfiles_stationlist/output
- concat_logfiles_RMextract/output
- concat_logfiles_prep_targ/output
- - concat_logfiles_predict_targ/output
- concat_logfiles_clipper_targ/output
- concat_logfiles_plot_demix/output
type: File[]
@@ -476,10 +475,10 @@ steps:
- id: prep_flags_out
- id: initial_flags_out
- id: prep_logfile
- - id: predict_logfile
- id: clipper_logfile
- id: msout
- - id: clipper_output
+ - id: clipper_flags_before
+ - id: clipper_flags_after
- id: instrument_tables
run: ./dp3_prep_targ.cwl
label: dp3_prep_target
@@ -487,15 +486,17 @@ steps:
- msin
- id: plot_Ateamclipper
in:
- - id: clipper_output
- source: concat_logfiles_clipper_output/output
+ - id: flagfreq_before
+ source: dp3_prep_target/clipper_flags_before
+ - id: flagfreq_after
+ source: dp3_prep_target/clipper_flags_after
- id: execute
source: clipAteam
out:
- id: output_imag
run: ../../steps/plot_Ateamclipper.cwl
when: $(inputs.execute)
- label: concat_logfiles_clipper_output
+ label: plot_Ateamclipper
- id: plot_demix
in:
- id: instrument_tables
@@ -508,23 +509,6 @@ steps:
run: ../../steps/plot_demix.cwl
label: plot_demix_solutions
when: $(inputs.demix)
- - id: concat_logfiles_clipper_output
- in:
- - id: file_list
- linkMerge: merge_flattened
- source:
- - dp3_prep_target/clipper_output
- - id: file_prefix
- default: Ateamclipper
- - id: file_suffix
- default: txt
- - id: execute
- source: clipAteam
- out:
- - id: output
- run: ../../steps/concatenate_files.cwl
- when: $(inputs.execute)
- label: concat_logfiles_clipper_output
- id: concat_logfiles_prep_targ
in:
- id: file_list
@@ -537,21 +521,6 @@ steps:
- id: output
run: ../../steps/concatenate_files.cwl
label: concat_logfiles_prep_target
- - id: concat_logfiles_predict_targ
- in:
- - id: file_list
- linkMerge: merge_flattened
- source:
- - dp3_prep_target/predict_logfile
- - id: file_prefix
- default: predict_targ
- - id: execute
- source: clipAteam
- out:
- - id: output
- run: ../../steps/concatenate_files.cwl
- when: $(inputs.execute)
- label: concat_logfiles_predict_targ
- id: concat_logfiles_clipper_targ
in:
- id: file_list