Initial commit

links

+https://vo.astron.nl/getproduct/APERTIF_DR1/200425057_AP_B015/image_mf_02.fits
+https://vo.astron.nl/getproduct/APERTIF_DR1/200425057_AP_B022/image_mf_02.fits
+https://vo.astron.nl/getproduct/APERTIF_DR1/200425057_AP_B008/image_mf_04.fits
+https://vo.astron.nl/getproduct/APERTIF_DR1/191026001_AP_B014/image_mf_01.fits

prepare_env.sh

+#!/bin/bash
+
+export PATH=$PATH:$PWD/resources/scripts/

resources/scripts/imageplotter.py

+#!/usr/bin/env python3
+from astropy.io import fits
+import sys
+from argparse import ArgumentParser
+import matplotlib.pyplot as plt
+import numpy as np
+
+
+def parse_args():
+    parser = ArgumentParser(description='Reduce noise in a fits image')
+    parser.add_argument('images', nargs='+')
+    parser.add_argument('output_file')
+    parser.add_argument('--cut_size', type=int, default=200)
+    parser.add_argument('--max_intensity', type=float, default=1.e3)
+    parser.add_argument('--max_columns', type=int, default=2)
+    
+    return parser.parse_args()
+    
+
+def open_image(image):
+    hdus = fits.open(image)
+    return hdus[0]
+
+def plot_images(images_list, output_file, cut_size=200, v_max= 1.e3, max_columns=2):
+    n_images = len(images_list)
+    max_rows = n_images // max_columns + 1
+    figure = plt.figure()
+    for i in range(n_images):
+        ax = figure.add_subplot(max_columns, max_rows, i + 1)
+        hdu = open_image(images_list[i])
+        size = hdu.data.shape[2]
+        data_sub_domain = hdu.data[0, 0, (size//2 - 400): (size//2 + 401), (size//2 - 400):(size//2 + 401)]
+        ax.imshow(data_sub_domain, vmax=1.e-3)
+    plt.tight_layout()
+    figure.savefig(output_file)
+    return hdu
+    
+if __name__ == '__main__':
+    args = parse_args()
+    plot_images(args.images, args.output_file,
+                args.cut_size, args.max_intensity, args.max_columns)

resources/scripts/noiseremover.py

+#!/usr/bin/env python3
+from astropy.io import fits
+import sys
+from argparse import ArgumentParser
+import numpy as np
+
+
+def parse_args():
+    parser = ArgumentParser(description='Reduce noise in a fits image')
+    parser.add_argument('input_fits')
+    parser.add_argument('output_fits')
+    return parser.parse_args()
+    
+def open_image(image):
+    hdus = fits.open(image)
+    return hdus[0]
+
+def clean_image(input_image, output_image):
+    hdu = open_image(input_image)
+    
+    noise = np.std(hdu.data)
+    hdu.data = hdu.data - 3 * noise
+    hdu.data[hdu.data < 0] = 0
+    hdu.data += np.random.normal(0, noise, hdu.data.shape)
+    
+    fits.writeto(output_image, hdu.data, hdu.header)
+    return hdu
+    
+if __name__ == '__main__':
+    args = parse_args()
+    clean_image(args.input_fits, args.output_fits)

resources/steps/download_images.cwl

+class: CommandLineTool
+cwlVersion: v1.0
+$namespaces:
+  sbg: 'https://www.sevenbridges.com/'
+id: download_images
+baseCommand:
+  - wget
+inputs:
+  - id: url_list
+    type: File
+    inputBinding:
+      position: 0
+      prefix: '-i'
+outputs:
+  - id: output
+    type: 'File[]'
+    outputBinding:
+      glob: '*.fits'
+label: download_images

resources/steps/imageplotter.cwl

+class: CommandLineTool
+cwlVersion: v1.0
+id: imageplotter
+baseCommand:
+  - imageplotter.py
+inputs:
+  - id: input_fits
+    type: 'File[]'
+    inputBinding:
+      position: 0
+  - id: output_image
+    type: string
+    inputBinding:
+      position: 1
+outputs:
+  - id: output
+    type: File
+    outputBinding:
+      glob: $(inputs.output_image)
+label: imageplotter
+requirements:
+  - class: InlineJavascriptRequirement

resources/steps/noiseremover.cwl

+class: CommandLineTool
+cwlVersion: v1.0
+id: noiseremover
+baseCommand:
+  - noiseremover.py
+inputs:
+  - id: input
+    type: File
+    inputBinding:
+      position: 0
+  - id: output_file_name
+    type: string
+    inputBinding:
+      position: 1
+outputs:
+  - id: output
+    type: File
+    outputBinding:
+      glob: $(inputs.output_file_name)
+label: noiseremover
+requirements:
+  - class: InlineJavascriptRequirement

resources/workflows/process_images.cwl

+class: Workflow
+cwlVersion: v1.0
+id: process_images
+label: process_images
+inputs:
+  - id: url_list
+    type: File
+outputs:
+  - id: before_noise_remover
+    outputSource:
+      - imageplotter/output
+    type: File
+  - id: after_noise_remover_plot
+    outputSource:
+      - after_plot_inspect/output
+    type: File
+steps:
+  - id: imageplotter
+    in:
+      - id: input_fits
+        source:
+          - download_images/output
+      - id: output_image
+        default: before_noise_remover.png
+    out:
+      - id: output
+    run: ./imageplotter.cwl
+    label: imageplotter
+  - id: noiseremover
+    in:
+      - id: input
+        source: download_images/output
+      - id: output_file_name
+        valueFrom: $('no_noise' + inputs.input.basename)
+    out:
+      - id: output
+    run: ./noiseremover.cwl
+    label: noiseremover
+    scatter:
+      - input
+  - id: download_images
+    in:
+      - id: url_list
+        source: url_list
+    out:
+      - id: output
+    run: ./download_images.cwl
+    label: download_images
+  - id: after_plot_inspect
+    in:
+      - id: input_fits
+        source:
+          - noiseremover/output
+      - id: output_image
+        default: after_noise_remover.png
+    out:
+      - id: output
+    run: ./imageplotter.cwl
+    label: imageplotter
+requirements:
+  - class: ScatterFeatureRequirement
+  - class: StepInputExpressionRequirement
+  - class: InlineJavascriptRequirement