diff --git a/steps/AveragingStepGenerator.cwl b/steps/AveragingStepGenerator.cwl index 1abe69cf3f372e2249e97c6c57431ec2365274df..0be4cc15232de2e1d7a4347a1a51c72a7d05881f 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 0000000000000000000000000000000000000000..7556cc69a995b7120324014393d8f75fdc7c7cb3 --- /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 0000000000000000000000000000000000000000..8e273f668bb0e83e240422e5524ab7aa03294408 --- /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 5d488417df344e72dfa6990c6515bc6e97aa6c3c..c4c0506208e3d20c13db9cd650ebd24163ccc054 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='+')