diff --git a/docs/source/operations.rst b/docs/source/operations.rst
index a89dfc57cff9aefbe1594a9ac37b00caf1c31c07..26b45fe3ab0c86d087cb8e9554988e89f669a2cf 100644
--- a/docs/source/operations.rst
+++ b/docs/source/operations.rst
@@ -13,13 +13,17 @@ Calibrate
This operation calibrates the data using the current sky model. The exact steps done during calibration depend on the strategy, but essentially there are two main parts: a phase-only (scalar) solve on short timescales (the "fast-phase" solve, which corrects for ionospheric errors) and a phase and amplitude (diagonal) solve on long time scales (the "slow-gain" solve, which corrects for beam errors). The slow-gain solve is divided into two parts: an optional amplitude-only solve that constrains all stations to have the same solutions and a phase plus amplitude solve (without the station constraint and usually with a longer solution interval). This calibration strategy is based on the LBA strategy of the `LiLF pipeline <https://linc.readthedocs.io/>`_, with the idea that the same strategy can be used for both HBA and LBA (similar to the way the calibrator pipeline works in LINC). Lastly, processing of the resulting solutions is done, including smoothing, renormalization, and the generation of a-term images (if 2-D screens are used).
-For calibration, Rapthor searches for bright, compact sources (or groups of sources) throughout the field to use as calibrator sources. A target (apparent) flux density is used to ensure that the calibrators are sufficiently bright (set by :term:`target_flux` in the processing strategy). Rapthor then tessellates the full sky model, using the calibrators as the facet centers. This method ensures that each facet has a bright calibrator source in it. Despite this designation of calibrators for the tesselation, all sources are used in the calibration (not just the bright sources).
+For calibration, Rapthor searches for bright, compact sources (or groups of sources) throughout the field to use as calibrator sources. A target (apparent) flux density is used to ensure that the calibrators are sufficiently bright (set by :term:`target_flux` in the processing strategy). Rapthor then tessellates the full sky model, using the calibrators as the facet centers. This method ensures that each calibration patch (or facet) has a bright calibrator source in it. Despite this designation of calibrators for the tesselation, all sources are used in the calibration (not just the bright sources).
When multiple nodes are available, this task is distributed.
Primary products:
- * ``field-solutions.h5``, stored in ``solutions/calibrate_X``, where ``X`` is the cycle number - the calibration solution table containing both fast-phase and slow-gain solutions.
- * ``*.png`` files, stored in ``plots/calibrate_X``, where ``X`` is the cycle number - plots of the calibration solutions.
+ * In ``skymodels/calibrate_X``, where ``X`` is the cycle number:
+ * ``calibration_skymodel.txt`` - the sky model used for calibration, grouped into calibration patches (one per facet/direction). If a sky model was supplied by the user, this model will be identical (but potentially with a different grouping of the sources). If the sky model results from the previous cycle of self calibration, this model will be the sum of models from the imaging sectors (see :ref:`image` for details).
+ * In ``solutions/calibrate_X``, where ``X`` is the cycle number:
+ * ``field-solutions.h5`` - the calibration solution table containing both fast-phase and slow-gain solutions.
+ * In ``plots/calibrate_X``, where ``X`` is the cycle number:
+ * ``*.png`` files - plots of the calibration solutions. Plots are typically made with one file per direction (calibration patch), per solution type (amplitude, phase, or scalar phase). For example, the file ``scalarphase_dir[Patch_127].png`` contains the scalar phase solutions (from the "fast-phase" solve) for patch 127. If the "slow-gain" solve was done, additional files should be present with the names ``phase_dir[Patch_127]_polXX.png`` and ``amplitude_dir[Patch_127]_polXX.png`` (and similarly for the YY polarization). If the optional amplitude-only slow-gain solve was done, the solutions are combined with the phase plus amplitude solve before plotting.
.. _predict:
@@ -30,9 +34,13 @@ This operation predicts visibilities for subtraction. Sources that lie outside o
When multiple nodes are available, this task is distributed.
-Primary products (in ``pipelines/predict_X``, where ``X`` is the cycle number):
- * Temporary measurement sets used for the subsequent image operation.
-
+Primary products:
+ * In ``skymodels/predict_X``, where ``X`` is the cycle number:
+ * ``outlier_*_predict_skymodel.txt`` - sky models used for outlier subtraction
+ * ``bright_source_*_predict_skymodel.txt`` - sky models used for bright-source subtraction
+ * ``sector_*_predict_skymodel.txt`` - sky models used when multiple imaging sectors are used
+ * In ``pipelines/predict_X``, where ``X`` is the cycle number:
+ * Temporary measurement sets used for subsequent operations.
.. _image:
@@ -45,17 +53,25 @@ Diagnostics for each image are written to the log. They include the following:
* The minimum and theoretical RMS noise. The minimum noise is derived from 2-D RMS maps generated by PyBDSF. The theoretical noise is calculated following `SKA Memo 113 <http://www.skatelescope.org/uploaded/59513_113_Memo_Nijboer.pdf>`_ and the `LOFAR Image Noise Calculator <https://support.astron.nl/ImageNoiseCalculator/sens.php>`_. The calculation takes into account the amount of flagged data but does not include the effects of elevation.
* The median RMS noise. The median noise is derived from 2-D RMS maps generated by PyBDSF. This median noise, along with the dynamic range (see below) is used to determine whether selfcal has converged (using the :term:`convergence_ratio` and :term:`divergence_ratio` defined by the processing strategy).
- * The dynamic range, calculated as the maximum value in the image divided by the minimum RMS noise. This quantity gives an estimate of how well focused the brightest source in the image is and is used, along with the median noise (see above) to determine whether selfcal has converged (see ).
+ * The dynamic range, calculated as the maximum value in the image divided by the minimum RMS noise. This quantity gives an estimate of how well focused the brightest source in the image is and is used, along with the median noise (see above) to determine whether selfcal has converged.
* The number of sources found by PyBDSF.
* The reference (central) frequency of the image.
* The restoring beam size and position angle.
* The fraction of unflagged data.
- * An estimate of the LOFAR-to-TGSS flux ratio. This ratio gives an indication of the accuracy of the overall flux scale of the image.
- * Estimates of the LOFAR-to-TGSS RA and Dec offsets. These offsets give an indication of the accuracy of the astrometry.
+ * An estimate of the LOFAR-to-TGSS flux ratio (calculated as the mean of the measured LOFAR flux densities divided by the TGSS flux densities, after sigma clipping). This ratio gives an indication of the accuracy of the overall flux scale of the image.
+ * Estimates of the LOFAR-to-TGSS RA and Dec offsets (calculated as the mean of the LOFAR values minus the TGSS values, after sigma clipping). These offsets give an indication of the accuracy of the astrometry.
When multiple nodes are available, it is possible to distribute the imaging over multiple nodes. This is done by running wsclean-mp instead of wsclean. Currently, Toil does not fully support openmpi. To remedy this, a wrapping script around wsclean-mp is used on the 'master' node. Because of this, imaging can only use the worker nodes, and the master node is idle.
Subtracted sources are restored in the image pipeline (near the end, in a step named wsclean_restore).
-Primary products (in ``images/image_X``, where ``X`` is the cycle number):
- * ``field-MFS-I-image.fits`` - the Stokes I image
+Primary products:
+ * In ``images/image_X``, where ``X`` is the cycle number:
+ * ``field-MFS-image.fits`` - the Stokes I image, uncorrected for the primary beam attenuation (i.e., the apparent-sky, "flat-noise" image)
+ * ``field-MFS-image-pb.fits`` - the Stokes I image, corrected for the primary beam attenuation (i.e., the true-sky image)
+ * ``field-MFS-residual.fits`` - the Stokes I residual image
+ * ``field-MFS-model.fits`` - the Stokes I model image
+ * In ``skymodels/image_X``, where ``X`` is the cycle number:
+ * ``bright_source_skymodel.txt`` - sky model used to restore bright sources after imaging (present only if bright sources were subtracted in the preceding predict operation).
+ * ``sector_Y.true_sky.txt``, where ``Y`` is the image sector number - the sky model (generated by WSClean) for the sector, with true-sky flux densities.
+ * ``sector_Y.apparent_sky.txt``, where ``Y`` is the image sector number - the sky model for the sector, with apparent-sky flux densities, generated from the true-sky one by attenuating it with the LOFAR primary beam.
diff --git a/docs/source/products.rst b/docs/source/products.rst
index 2fe40a0901a00275624adcc6d974d30d367b0383..b3a2adbb72ce64a372851af69d6d2a0351998884 100644
--- a/docs/source/products.rst
+++ b/docs/source/products.rst
@@ -6,22 +6,22 @@ Output
Rapthor produces the following output inside the working directory:
``logs/``
- Directory containing the log files.
+ Directory containing the log files. The main log file for the run is called ``rapthor.log``. The detailed logs of each step of the processing can be found in the subdirectories.
``images/``
- Directory containing the FITS images.
+ Directory containing the FITS images. See :ref:`image` for a detailed description of the images.
``pipelines/``
- Directory containing intermediate files of each operation's pipeline.
+ Directory containing intermediate files of each operation's pipeline. Once a run has finished successfully, this directory can be removed.
``regions/``
- Directory containing ds9 region files.
+ Directory containing ds9 region files. These regions define the imaged areas and the facet layout (if used).
``skymodels/``
- Directory containing sky model files.
+ Directory containing sky model files. See :ref:`calibrate` and :ref:`image` for a detailed description of the sky models.
``solutions/``
- Directory containing the calibration solution h5parm files.
+ Directory containing the calibration solution h5parm files. See :ref:`calibrate` for a detailed description of the solution files.
``plots/``
- Directory containing the PNG plots of the calibration solutions and images.
+ Directory containing the PNG plots of the calibration solutions and images. See :ref:`calibrate` for a detailed description of the plots.
diff --git a/rapthor/operations/image.py b/rapthor/operations/image.py
index c712da783a579d29bdd50b7a52456ae19a26f58e..60340f0e54d80cd384a443939d20dbafc833b0d7 100644
--- a/rapthor/operations/image.py
+++ b/rapthor/operations/image.py
@@ -208,7 +208,8 @@ class Image(Operation):
image_root = os.path.join(self.pipeline_working_dir, sector.name)
sector.I_image_file_true_sky = image_root + '-MFS-image-pb.fits'
sector.I_image_file_apparent_sky = image_root + '-MFS-image.fits'
- sector.I_model_file_true_sky = image_root + '-MFS-model-pb.fits'
+ sector.I_model_file_true_sky = image_root + '-MFS-model.fits'
+ sector.I_residual_file_apparent_sky = image_root + '-MFS-residual.fits'
# Check to see if a clean mask image was made (only made when at least one
# island is found in the Stokes I image). The filename is defined
@@ -227,6 +228,13 @@ class Image(Operation):
# in the rapthor/scripts/filter_skymodel.py file)
sector.image_skymodel_file_true_sky = image_root + '.true_sky.txt'
sector.image_skymodel_file_apparent_sky = image_root + '.apparent_sky.txt'
+ dst_dir = os.path.join(self.parset['dir_working'], 'skymodels', 'image_{}'.format(self.index))
+ misc.create_directory(dst_dir)
+ for src_filename in [sector.image_skymodel_file_true_sky, sector.image_skymodel_file_apparent_sky]:
+ dst_filename = os.path.join(dst_dir, os.path.basename(src_filename))
+ if os.path.exists(dst_filename):
+ os.remove(dst_filename)
+ shutil.copy(src_filename, dst_filename)
# The ds9 region file, if made
if self.field.dde_method == 'facets':
diff --git a/rapthor/operations/mosaic.py b/rapthor/operations/mosaic.py
index aa11f3d1cb069cc3b5678e2587dc888bd1bcd271..399231a04c87691ef929172ec29f0010e580808b 100644
--- a/rapthor/operations/mosaic.py
+++ b/rapthor/operations/mosaic.py
@@ -17,6 +17,11 @@ class Mosaic(Operation):
"""
def __init__(self, field, index):
super(Mosaic, self).__init__(field, name='mosaic', index=index)
+
+ # For each image type we use a subworkflow, so we set the template filename
+ # for that here
+ self.subpipeline_parset_template = '{0}_type_pipeline.cwl'.format(self.rootname)
+
# Determine whether processing is needed
self.skip_processing = len(self.field.imaging_sectors) < 2
@@ -31,6 +36,7 @@ class Mosaic(Operation):
else:
max_cores = self.field.parset['cluster_specific']['max_cores']
self.parset_parms = {'rapthor_pipeline_dir': self.rapthor_pipeline_dir,
+ 'pipeline_working_dir': self.pipeline_working_dir,
'max_cores': max_cores,
'skip_processing': self.skip_processing,
'do_slowgain_solve': self.field.do_slowgain_solve}
@@ -43,20 +49,34 @@ class Mosaic(Operation):
sector_image_filename = []
sector_vertices_filename = []
regridded_image_filename = []
- for sector in self.field.imaging_sectors:
- sector_image_filename.append(CWLFile(sector.I_image_file_true_sky).to_json())
- sector_vertices_filename.append(CWLFile(sector.vertices_file).to_json())
- regridded_image_filename.append(os.path.basename(sector.I_image_file_true_sky) + '.regridded')
- template_image_filename = self.name + '_template.fits'
+ template_image_filename = []
+ self.image_names = ['I_image_file_true_sky', 'I_image_file_apparent_sky',
+ 'I_model_file_true_sky', 'I_residual_file_apparent_sky']
+ for image_name in self.image_names:
+ image_list = []
+ vertices_list = []
+ regridded_list = []
+ for sector in self.field.imaging_sectors:
+ image_list.append(getattr(sector, image_name))
+ vertices_list.append(sector.vertices_file)
+ regridded_list.append(os.path.basename(getattr(sector, image_name)) + '.regridded')
+ sector_image_filename.append(CWLFile(image_list).to_json())
+ sector_vertices_filename.append(CWLFile(vertices_list).to_json())
+ regridded_image_filename.append(regridded_list)
+ template_image_filename.append(self.name + '_template.fits')
+ self.mosaic_filename = []
if self.skip_processing:
if len(self.field.imaging_sectors) > 0:
- # Use unprocessed file as mosaic file
- self.mosaic_filename = self.field.imaging_sectors[0].I_image_file_true_sky
+ # Use unprocessed files as mosaic files
+ for image_name in self.image_names:
+ self.mosaic_filename.append(getattr(self.field.imaging_sectors[0], image_name))
else:
- self.mosaic_filename = None
+ self.mosaic_filename.append(None)
else:
- self.mosaic_filename = self.name + '-MFS-I-image.fits'
+ for image_name in self.image_names:
+ suffix = getattr(self.field.imaging_sectors[0], image_name).split('MFS')[-1]
+ self.mosaic_filename.append('{0}-MFS{1}'.format(self.name, suffix))
self.input_parms = {'skip_processing': self.skip_processing,
'sector_image_filename': sector_image_filename,
@@ -69,22 +89,23 @@ class Mosaic(Operation):
"""
Finalize this operation
"""
- if self.mosaic_filename is None:
- return
-
- # Save the FITS image and model
- dst_dir = os.path.join(self.field.parset['dir_working'], 'images',
- 'image_{}'.format(self.index))
- misc.create_directory(dst_dir)
- self.field.field_image_filename_prev = self.field.field_image_filename
- self.field.field_image_filename = os.path.join(dst_dir, 'field-MFS-I-image.fits')
- shutil.copy(os.path.join(self.pipeline_working_dir, self.mosaic_filename),
- self.field.field_image_filename)
-
- # TODO: make mosaic of model + QUV?
-# self.field_model_filename = os.path.join(dst_dir, 'field-MFS-I-model.fits')
+ for i, image_name in enumerate(self.image_names):
+ if self.mosaic_filename[i] is None:
+ continue
- # TODO: clean up template+regridded images
+ # Copy the image to the images directory
+ dst_dir = os.path.join(self.field.parset['dir_working'], 'images',
+ 'image_{}'.format(self.index))
+ misc.create_directory(dst_dir)
+ suffix = getattr(self.field.imaging_sectors[0], image_name).split('MFS')[-1]
+ field_image_filename = os.path.join(dst_dir, 'field-MFS{}'.format(suffix))
+ if image_name == 'I_image_file_true_sky':
+ # Save the Stokes I true-sky image filename as an attribute of the field
+ # object for later use
+ self.field.field_image_filename_prev = self.field.field_image_filename
+ self.field.field_image_filename = field_image_filename
+ shutil.copy(os.path.join(self.pipeline_working_dir, self.mosaic_filename[i]),
+ field_image_filename)
# Finally call finalize() in the parent class
- super().finalize()
\ No newline at end of file
+ super().finalize()
diff --git a/rapthor/pipeline/parsets/image_sector_pipeline.cwl b/rapthor/pipeline/parsets/image_sector_pipeline.cwl
index 2bff70745ea1a9e36219855040af82980d4642a0..9b8f8366eb58b0790b89166c5a31818d95335476 100644
--- a/rapthor/pipeline/parsets/image_sector_pipeline.cwl
+++ b/rapthor/pipeline/parsets/image_sector_pipeline.cwl
@@ -336,6 +336,8 @@ outputs:
- image/image_nonpb_name
- image/image_pb_name
{% endif %}
+ - image/residual_name
+ - image/model_name
- image/skymodel_nonpb
- image/skymodel_pb
type: File[]
@@ -548,6 +550,8 @@ steps:
out:
- id: image_nonpb_name
- id: image_pb_name
+ - id: residual_name
+ - id: model_name
- id: skymodel_nonpb
- id: skymodel_pb
diff --git a/rapthor/pipeline/parsets/mosaic_pipeline.cwl b/rapthor/pipeline/parsets/mosaic_pipeline.cwl
index 208c4593abe58736890a2875f22df5452394333c..fe38d45825d32ffd1eb866d5d7b40591ae68d5e2 100644
--- a/rapthor/pipeline/parsets/mosaic_pipeline.cwl
+++ b/rapthor/pipeline/parsets/mosaic_pipeline.cwl
@@ -9,8 +9,10 @@ doc: |
# start not skip_processing
requirements:
+ MultipleInputFeatureRequirement: {}
ScatterFeatureRequirement: {}
StepInputExpressionRequirement: {}
+ SubworkflowFeatureRequirement: {}
{% if max_cores is not none %}
hints:
@@ -23,32 +25,44 @@ inputs:
- id: sector_image_filename
label: Filenames of images
doc: |
- The filenames of the sector FITS images (length = n_sectors).
- type: File[]
+ The filenames of the sector FITS images (length = n_sectors * n_img_types).
+ type:
+ type: array
+ items:
+ type: array
+ items: File
- id: sector_vertices_filename
label: Filenames of vertices files
doc: |
- The filenames of the sector vertices files (length = n_sectors).
- type: File[]
+ The filenames of the sector vertices files (length = n_sectors * n_img_types).
+ type:
+ type: array
+ items:
+ type: array
+ items: File
- id: template_image_filename
label: Filename of template image
doc: |
- The filename of the temporary mosaic template image (length = 1).
- type: string
+ The filename of the temporary mosaic template image (length = n_img_types).
+ type: string[]
- id: regridded_image_filename
label: Filenames of images
doc: |
- The filenames of the regridded sector images (length = n_sectors).
- type: string[]
+ The filenames of the regridded sector images (length = n_sectors * n_img_types).
+ type:
+ type: array
+ items:
+ type: array
+ items: string
- id: mosaic_filename
label: Filename of mosiac image
doc: |
- The filename of the final mosaic image (length = 1).
- type: string
+ The filename of the final mosaic image (length = n_img_types).
+ type: string[]
- id: skip_processing
label: Flag to skip processing
@@ -59,65 +73,32 @@ inputs:
outputs:
- id: mosaic_image
outputSource:
- - make_mosaic/mosaic_image
- type: File
+ - mosaic_by_type/mosaic_image
+ type: File[]
steps:
- - id: make_mosaic_template
- label: Make mosaic template
- doc: |
- This step makes a temporary template FITS image that is used
- in the regrid_image and make_mosaic steps.
- run: {{ rapthor_pipeline_dir }}/steps/make_mosaic_template.cwl
- in:
- - id: input_image_list
- source: sector_image_filename
- - id: vertices_file_list
- source: sector_vertices_filename
- - id: output_image
- source: template_image_filename
- - id: skip
- source: skip_processing
- out:
- - id: template_image
-
- - id: regrid_image
- label: Regrid image
+ - id: mosaic_by_type
+ label: Mosiac an image type
doc: |
- This step regrids FITS images to the grid of the template FITS
- image made in the make_mosaic_template step.
- run: {{ rapthor_pipeline_dir }}/steps/regrid_image.cwl
+ This step is a subpipeline that performs the processing for each image
+ type.
+ run: {{ pipeline_working_dir }}/subpipeline_parset.cwl
in:
- - id: input_image
- source: sector_image_filename
- - id: template_image
- source: make_mosaic_template/template_image
- - id: vertices_file
- source: sector_vertices_filename
- - id: output_image
- source: regridded_image_filename
- - id: skip
- source: skip_processing
- scatter: [input_image, vertices_file, output_image]
+ - id: sector_image_filename
+ source: sector_image_filename
+ - id: sector_vertices_filename
+ source: sector_vertices_filename
+ - id: template_image_filename
+ source: template_image_filename
+ - id: regridded_image_filename
+ source: regridded_image_filename
+ - id: mosaic_filename
+ source: mosaic_filename
+ - id: skip_processing
+ source: skip_processing
+ scatter: [sector_image_filename, sector_vertices_filename, template_image_filename,
+ regridded_image_filename, mosaic_filename]
scatterMethod: dotproduct
- out:
- - id: regridded_image
-
- - id: make_mosaic
- label: Make mosaic
- doc: |
- This step makes the final mosaic FITS image from the regridded
- sector images.
- run: {{ rapthor_pipeline_dir }}/steps/make_mosaic.cwl
- in:
- - id: input_image_list
- source: regrid_image/regridded_image
- - id: template_image
- source: make_mosaic_template/template_image
- - id: output_image
- source: mosaic_filename
- - id: skip
- source: skip_processing
out:
- id: mosaic_image
diff --git a/rapthor/pipeline/parsets/mosaic_type_pipeline.cwl b/rapthor/pipeline/parsets/mosaic_type_pipeline.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..629f21a4ebc9c6c34b4e77364e1e71f3fc9319aa
--- /dev/null
+++ b/rapthor/pipeline/parsets/mosaic_type_pipeline.cwl
@@ -0,0 +1,119 @@
+cwlVersion: v1.2
+class: Workflow
+label: Rapthor mosaicking subpipeline
+doc: |
+ This subworkflow performs the mosaicking of a single type of image made with the
+ imaging pipeline. If only a single image was made, processing is (mostly) skipped.
+
+requirements:
+ ScatterFeatureRequirement: {}
+ StepInputExpressionRequirement: {}
+
+{% if max_cores is not none %}
+hints:
+ ResourceRequirement:
+ coresMin: {{ max_cores }}
+ coresMax: {{ max_cores }}
+{% endif %}
+
+inputs:
+ - id: sector_image_filename
+ label: Filenames of images
+ doc: |
+ The filenames of the sector FITS images (length = n_sectors).
+ type: File[]
+
+ - id: sector_vertices_filename
+ label: Filenames of vertices files
+ doc: |
+ The filenames of the sector vertices files (length = n_sectors).
+ type: File[]
+
+ - id: template_image_filename
+ label: Filename of template image
+ doc: |
+ The filename of the temporary mosaic template image (length = 1).
+ type: string
+
+ - id: regridded_image_filename
+ label: Filenames of images
+ doc: |
+ The filenames of the regridded sector images (length = n_sectors).
+ type: string[]
+
+ - id: mosaic_filename
+ label: Filename of mosiac image
+ doc: |
+ The filename of the final mosaic image (length = 1).
+ type: string
+
+ - id: skip_processing
+ label: Flag to skip processing
+ doc: |
+ The flag that sets whether processing is skipped or not (length = 1).
+ type: boolean
+
+outputs:
+ - id: mosaic_image
+ outputSource:
+ - make_mosaic/mosaic_image
+ type: File
+
+steps:
+ - id: make_mosaic_template
+ label: Make mosaic template
+ doc: |
+ This step makes a temporary template FITS image that is used
+ in the regrid_image and make_mosaic steps.
+ run: {{ rapthor_pipeline_dir }}/steps/make_mosaic_template.cwl
+ in:
+ - id: input_image_list
+ source: sector_image_filename
+ - id: vertices_file_list
+ source: sector_vertices_filename
+ - id: output_image
+ source: template_image_filename
+ - id: skip
+ source: skip_processing
+ out:
+ - id: template_image
+
+ - id: regrid_image
+ label: Regrid image
+ doc: |
+ This step regrids FITS images to the grid of the template FITS
+ image made in the make_mosaic_template step.
+ run: {{ rapthor_pipeline_dir }}/steps/regrid_image.cwl
+ in:
+ - id: input_image
+ source: sector_image_filename
+ - id: template_image
+ source: make_mosaic_template/template_image
+ - id: vertices_file
+ source: sector_vertices_filename
+ - id: output_image
+ source: regridded_image_filename
+ - id: skip
+ source: skip_processing
+ scatter: [input_image, vertices_file, output_image]
+ scatterMethod: dotproduct
+ out:
+ - id: regridded_image
+
+ - id: make_mosaic
+ label: Make mosaic
+ doc: |
+ This step makes the final mosaic FITS image from the regridded
+ sector images.
+ run: {{ rapthor_pipeline_dir }}/steps/make_mosaic.cwl
+ in:
+ - id: input_image_list
+ source: regrid_image/regridded_image
+ - id: template_image
+ source: make_mosaic_template/template_image
+ - id: output_image
+ source: mosaic_filename
+ - id: skip
+ source: skip_processing
+ out:
+ - id: mosaic_image
diff --git a/rapthor/pipeline/steps/wsclean_image_facets.cwl b/rapthor/pipeline/steps/wsclean_image_facets.cwl
index be767b47255c26922e3832e65f27de42e6aabbde..6bec5ee8cee08113799ee6389330662a738c7ba6 100644
--- a/rapthor/pipeline/steps/wsclean_image_facets.cwl
+++ b/rapthor/pipeline/steps/wsclean_image_facets.cwl
@@ -162,6 +162,14 @@ outputs:
type: File
outputBinding:
glob: $(inputs.name)-MFS-image-pb.fits
+ - id: residual_name
+ type: File
+ outputBinding:
+ glob: $(inputs.name)-MFS-residual.fits
+ - id: model_name
+ type: File
+ outputBinding:
+ glob: $(inputs.name)-MFS-model.fits
- id: skymodel_nonpb
type: File
outputBinding:
diff --git a/rapthor/pipeline/steps/wsclean_image_no_dde.cwl b/rapthor/pipeline/steps/wsclean_image_no_dde.cwl
index ec3f9acc4301a04b2599e20cc7ef887326807fe0..e76d4a361140971eae547fbd1071e05e652c4d51 100644
--- a/rapthor/pipeline/steps/wsclean_image_no_dde.cwl
+++ b/rapthor/pipeline/steps/wsclean_image_no_dde.cwl
@@ -127,6 +127,14 @@ outputs:
type: File
outputBinding:
glob: $(inputs.name)-MFS-image-pb.fits
+ - id: residual_name
+ type: File
+ outputBinding:
+ glob: $(inputs.name)-MFS-residual.fits
+ - id: model_name
+ type: File
+ outputBinding:
+ glob: $(inputs.name)-MFS-model.fits
- id: skymodel_nonpb
type: File
outputBinding:
diff --git a/rapthor/pipeline/steps/wsclean_image_screens.cwl b/rapthor/pipeline/steps/wsclean_image_screens.cwl
index 2eb0d24c94ff3e95db9ed086a321c6e02ce31f27..7f81c5e99e21f6dd22ed438896d64a1ac2f362e4 100644
--- a/rapthor/pipeline/steps/wsclean_image_screens.cwl
+++ b/rapthor/pipeline/steps/wsclean_image_screens.cwl
@@ -219,6 +219,22 @@ outputs:
type: File
outputBinding:
glob: $(inputs.name)-MFS-image-pb.fits
+ - id: residual_name
+ label: Output residual image
+ doc: |
+ The filename of the output residual image. The value is constructed from
+ the input parameter "name"
+ type: File
+ outputBinding:
+ glob: $(inputs.name)-MFS-residual.fits
+ - id: model_name
+ label: Output model image
+ doc: |
+ The filename of the output model image. The value is constructed from the
+ input parameter "name"
+ type: File
+ outputBinding:
+ glob: $(inputs.name)-MFS-model.fits
- id: skymodel_nonpb
label: Output non-PB-corrected sky model
doc: |
diff --git a/rapthor/pipeline/steps/wsclean_mpi_image_screens.cwl b/rapthor/pipeline/steps/wsclean_mpi_image_screens.cwl
index 0dc9a006cbabc3455ac8c76e968722a12fc25860..66de71af15289801fcfdc47eaeb98e7e799a23d0 100644
--- a/rapthor/pipeline/steps/wsclean_mpi_image_screens.cwl
+++ b/rapthor/pipeline/steps/wsclean_mpi_image_screens.cwl
@@ -169,6 +169,14 @@ outputs:
type: File
outputBinding:
glob: $(inputs.name)-MFS-image-pb.fits
+ - id: residual_name
+ type: File
+ outputBinding:
+ glob: $(inputs.name)-MFS-residual.fits
+ - id: model_name
+ type: File
+ outputBinding:
+ glob: $(inputs.name)-MFS-model.fits
- id: skymodel_nonpb
type: File
outputBinding: