Merge branch 'main' into docs

Author: PaulHancock

.gitignore

@@ -26,3 +26,6 @@ profiling.md
 /docs/build
 /docs/doctrees
 example_data/
+build/
+scripts/epochs.txt
+scripts/mean.txt

README.md

@@ -107,7 +107,14 @@ once this is complete, run the viewer in the main Nextflow directory via:
 This will run the viewer using the images within the default ``results`` directory. If your directory is different to the default, you can add either the relative or absolute path as an optional argument:
 
 ```
-./run_robbie_viewer.sh path_to_dir
+./run_robbie_viewer.sh -p path_to_dir
+```
+
+When plotting large images, it is recommended to also specify an RA and DEC position, as well as a size in coordinate units, to cutout a portion of the image for plotting.
+For example, if we want to plot an image with centre position of RA 335°, DEC -15° and size of 5°:
+
+```
+./run_robbie_viewer.sh path_to_dir 335 -15 5
 ```
 
 ## Credit

docker/Dockerfile

@@ -20,4 +20,5 @@ RUN pip install -r requirements.txt && \
     python setup.py install && \
     rm -rf /tmp/build
 
+#  set env
 ENV HOME=/tmp

docker/build_docker_arm.sh

@@ -3,6 +3,6 @@ cd ..
 version=$(robbie_version.sh)
 
 # build the container and update tag
-docker buildx build . --platform linux/amd64 -f docker/Dockerfile -t "paulhancock/robbie-next:${version}" && \
+docker buildx build . --platform linux/amd64 --no-cache -f docker/Dockerfile -t "paulhancock/robbie-next:${version}" && \
 docker tag paulhancock/robbie-next:${version} paulhancock/robbie-next:latest
 cd -

docs/source/visualisation.md

@@ -1,6 +1,7 @@
 (visualisation)=
 ## Visualisation
 
+### Running locally with Docker
 To start the Docker container containing the Bokeh server, run the following script in the main Nextflow directory:
 
 ``` bash
@@ -10,9 +11,32 @@ To start the Docker container containing the Bokeh server, run the following scr
 This will run the viewer using the images output from Robbie within the default ``results`` directory. If your output directory is different to the default, you can add either the relative or absolute path as an optional argument:
 
 ``` bash
-./run_robbie_viewer.sh path_to_dir
+./run_robbie_viewer.sh -p path_to_dir
 ```
 
+When plotting large images, it is recommended to also specify an RA and DEC position, as well as a size in coordinate units, to cutout a portion of the image for plotting. For example, if we want to plot an image with centre position of RA 335°, DEC -15° and size of 5°:
+
+``` bash
+./run_robbie_viewer.sh -p path_to_dir -c 335,-15,5
+```
+
+### Running on a cluster with Singularity
+
+The Robbie Viewer is available on Pawsey as a part of the SHPC (Singularity Recipe HPC). To install it, we will load the SHPC module, install the viewer as a module and then load it:
+
+``` bash
+module load shpc/0.0.53
+shpc install cjproud/robbie_viewer
+module load cjproud/robbie_viewer/latest/module
+```
+
+Now, the viewer will be available on our path and we can run it as normal:
+
+``` bash
+./run_robbie_viewer.sh -p path_to_dir -c RA,DEC,PAD
+```
+
+
 ### Visualising transients 
 
 Visualising different transient candidates can be done in multiple ways. For example, the transient candidate can be selected using the table, sky plot or variables plot as shown below:

nextflow.config

@@ -42,6 +42,8 @@ timeline.enabled = true
 report.enabled = true
 dag.enabled = true
 
+// get hostname
+host = "$HOSTNAME".split('-')[0]
 
 profiles {
     local {
@@ -102,12 +104,14 @@ profiles {
       }
     }
 }
-if ( "\$HOSTNAME".startsWith("garrawarla") ) {
+
+if ( host == "garrawarla") ) {
   // Set up container
   process.module = 'singularity/3.7.4'
   singularity {
     enabled = true
     envWhitelist = 'SINGULARITY_BINDPATH, SINGULARITYENV_LD_LIBRARY_PATH'
+    runOptions = '--bind $HOME:/$HOME'
   }
   params.containerDir = '/pawsey/mwa/singularity'
 

robbie.nf

@@ -177,7 +177,7 @@ process download_gleam_catalogue {
     try:
       cat.write(data_load.REF_CAT, format='fits')
       os.symlink(data_load.REF_CAT, "GLEAM_ref_cat.fits")
-    except PermissionError:
+    except OSError:
       # No permission so dump it here
       cat.write("GLEAM_ref_cat.fits", format='fits')
   """
@@ -553,7 +553,7 @@ process reproject_images {
   """
   echo ${task.process} on \${HOSTNAME}
   mkdir reprojected_images
-  ls *Epoch* > temp_epochs.txt
+  ls *.fits | grep -v "mean_image" > temp_epochs.txt
   ls *mean_image.* > temp_mean.txt
   reprojection.py --epochs temp_epochs.txt --mean temp_mean.txt --reproj_dir reprojected_images
   """
@@ -588,6 +588,7 @@ workflow {
     image_ch = fits_warp.out
     image_bkg_rms = fits_warp.out.concat(bane_raw.out.map{ it -> [it[0], [it[1..2]]]}).groupTuple().map{ it -> [ it[0], it[1][0], it[1][1][0][1]]}
   }
+
   make_mean_image( image_ch.map{ it -> it[1] }.collect() )
   make_sky_coverage( image_ch.map{ it -> it[1] }.collect() )
   bane_mean_image( make_mean_image.out[0] )

robbie_viewer_server/Dockerfile

@@ -15,5 +15,3 @@ RUN pip install -r requirements.txt
 
 # EXPOSE PORTS
 EXPOSE 5006
-
-CMD bokeh serve . --args /data 

robbie_viewer_server/build_docker.sh

@@ -1,4 +1,4 @@
 #! /usr/bin/env bash
 
 # build the container and add a target
-docker build . -f ./Dockerfile -t "paulhancock/robbie-viewer:latest"
+docker build . -f ./Dockerfile -t "paulhancock/robbie-viewer:latest"

robbie_viewer_server/build_docker_arm.sh

@@ -1,4 +1,4 @@
 #! /usr/bin/env bash
 
 # build the container and add a target
-docker buildx build . --platform linux/amd64 -f ./Dockerfile -t "paulhancock/robbie-viewer:latest"
+docker buildx build . --platform linux/amd64 -f ./Dockerfile -t "paulhancock/robbie-viewer:latest"