Update tool HESS to 0.0.2+galaxy0

.github/workflows/live-preview.yaml

@@ -7,6 +7,8 @@ on:
       - opened
       - labeled
       - synchronize
+      - unlabeled
+      - closed
     paths-ignore:
       - '.github/**'
       - 'deprecated/**'
@@ -18,7 +20,7 @@ env:
 
 jobs:
   setup:
-    if: contains( github.event.pull_request.labels.*.name, 'test-live')
+    if: contains( github.event.pull_request.labels.*.name, 'test-live') && github.event.action != 'closed'
     name: Determine changed repositories
     runs-on: ubuntu-latest
     outputs:
@@ -73,3 +75,24 @@ jobs:
 
           ansible-playbook deploy.yml
         done
+
+  uninstall:
+    name: Uninstall
+    if: contains( github.event.pull_request.labels.*.name, 'test-live') == false || github.event.action == 'closed'
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Install requirenments
+        run: sudo apt-get install -y ansible
+      - name: Install SSH key
+        uses: shimataro/ssh-key-action@v2
+        with:
+          key: ${{ secrets.SSH_PRIVATE_KEY }}
+          known_hosts: ${{ secrets.KNOWN_HOSTS }}
+      - name: Uninstall tools
+        env: 
+          pr_num: ${{ github.event.pull_request.number }}
+        run: |
+          cd deploy-preview
+          ansible-playbook remove.yml

deploy-preview/deploy.yml

@@ -44,7 +44,6 @@
         path: "{{ dest_tools_conf }}"
         regexp: '^\s*<tool\s+file="{{ tool_dir }}_pr{{ pr_num }}/'
         state: absent
-      loop: "{{ tools_list }}"
 
     - name: Enable tools
       lineinfile:

deploy-preview/remove.yml

@@ -0,0 +1,26 @@
+---
+- hosts: all
+  become: true
+  become_user: root
+  vars:
+    dest_tools_dir: /srv/galaxy/staging_tools
+    dest_tools_conf: /srv/galaxy/server/config/staging_tool_conf.xml
+    pr_num: "{{ lookup('env', 'pr_num') }}"
+
+
+  tasks:
+    - name: Clean reference
+      lineinfile:
+        path: "{{ dest_tools_conf }}"
+        regexp: '^\s*<tool\s+file=".*_pr{{ pr_num }}/'
+        state: absent
+
+    - name: Restart Galaxy
+      command: galaxyctl restart
+      changed_when: true
+
+    - name: Remove tool dir
+      ansible.builtin.file:
+        path: "{{ dest_tools_dir }}/.*_pr{{ pr_num }}"
+        state: absent
+        mode: 0755

tools/hess/Image.py

@@ -14,9 +14,13 @@
 from astropy.io import fits
 from astropy.time import Time
 from numpy import cos, pi
+from oda_api.api import ProgressReporter
 from oda_api.data_products import ImageDataProduct, PictureProduct
 from oda_api.json import CustomJSONEncoder
 
+pr = ProgressReporter()
+pr.report_progress(stage="Progress", progress=5.0)
+
 if os.path.exists("hess_dl3_dr1.tar.gz") == False:
     get_ipython().system(   # noqa: F821
         "wget https://zenodo.org/record/1421099/files/hess_dl3_dr1.tar.gz"
@@ -28,12 +32,12 @@
 DEC = 22.014700  # http://odahub.io/ontology#PointOfInterestDEC
 T1 = "2000-10-09T13:16:00.0"  # http://odahub.io/ontology#StartTime
 T2 = "2022-10-10T13:16:00.0"  # http://odahub.io/ontology#EndTime
-Radius = 2.5  # http://odahub.io/ontology#AngleDegrees
+Radius = 1.0  # http://odahub.io/ontology#AngleDegrees
 pixsize = (
-    0.1  # http://odahub.io/ontology#AngleDegrees ; oda:label "Pixel size"
+    0.05  # http://odahub.io/ontology#AngleDegrees ; oda:label "Pixel size"
 )
-Emin = 100.0  # http://odahub.io/ontology#Energy_GeV
-Emax = 10000.0  # http://odahub.io/ontology#Energy_GeV
+Emin = 1  # http://odahub.io/ontology#Energy_TeV
+Emax = 100.0  # http://odahub.io/ontology#Energy_TeV
 
 _galaxy_wd = os.getcwd()
 
@@ -95,9 +99,14 @@
 message
 
 cdec = cos(DEC * pi / 180.0)
-Npix = int(4 * Radius / pixsize) + 1
-RA_bins = np.linspace(RA - Radius / cdec, RA + Radius / cdec, Npix + 1)
-DEC_bins = np.linspace(DEC - Radius, DEC + Radius, Npix + 1)
+Npix = int(2 * Radius / pixsize) + 1
+RA_bins = np.linspace(
+    RA - Npix * pixsize / cdec / 2, RA + Npix * pixsize / cdec / 2, Npix + 1
+)
+DEC_bins = np.linspace(
+    DEC - Npix * pixsize / 2, DEC + Npix * pixsize / 2, Npix + 1
+)
+
 image = np.zeros((Npix, Npix))
 for f in OBSlist:
     hdul = fits.open("data/" + f)
@@ -106,62 +115,76 @@
     ev_dec = ev["DEC"]
     ev_en = ev["ENERGY"]
     ev_time = ev["TIME"]
-    h = np.histogram2d(ev_ra, ev_dec, bins=[RA_bins, DEC_bins])
+    mask = (ev_en > Emin) & (ev_en < Emax)
+    h = np.histogram2d(ev_ra[mask], ev_dec[mask], bins=[RA_bins, DEC_bins])
     image += h[0]
     hdul.close()
 
+image = np.transpose(image)
+
 plt.imshow(
-    np.flip(image, axis=1),
-    extent=(RA_bins[-1], RA_bins[0], DEC_bins[0], DEC_bins[-1]),
+    image,
+    extent=(RA_bins[0], RA_bins[-1], DEC_bins[0], DEC_bins[-1]),
     origin="lower",
 )
 plt.colorbar()
 
+plt.xlim(*plt.xlim()[::-1])
+
 plt.xlabel("RA, degrees")
 plt.ylabel("DEC,degrees")
-plt.savefig("Image.png", format="png")
 
 # Create a new WCS object.  The number of axes must be set
 # from the start
 w = wcs.WCS(naxis=2)
 
-# Set up an "Airy's zenithal" projection
-# Vector properties may be set with Python lists, or Numpy arrays
-w.wcs.crpix = [Npix / 2.0, Npix / 2.0]
-w.wcs.cdelt = np.array([pixsize / cdec, pixsize])
-w.wcs.crval = [RA, DEC]
-w.wcs.ctype = ["RA---AIR", "DEC--AIR"]
-w.wcs.set_pv([(2, 1, 45.0)])
+w.wcs.ctype = ["RA---CAR", "DEC--CAR"]
+# we need a Plate carrée (CAR) projection since histogram is binned by ra-dec
+# the peculiarity here is that CAR projection produces rectilinear grid only if CRVAL2==0
+# also, we will follow convention of RA increasing from right to left (CDELT1<0, need to flip an input image)
+# otherwise, aladin-lite doesn't show it
+w.wcs.crval = [RA, 0]
+w.wcs.crpix = [Npix / 2.0 + 0.5, 0.5 - DEC_bins[0] / pixsize]
+w.wcs.cdelt = np.array([-pixsize / cdec, pixsize])
 
-# Now, write out the WCS object as a FITS header
 header = w.to_header()
 
-# header is an astropy.io.fits.Header object.  We can use it to create a new
-# PrimaryHDU and write it to a file.
-hdu = fits.PrimaryHDU(image, header=header)
+hdu = fits.PrimaryHDU(np.flip(image, axis=1), header=header)
 hdu.writeto("Image.fits", overwrite=True)
 hdu = fits.open("Image.fits")
 im = hdu[0].data
-from astropy.wcs import WCS
-
-wcs = WCS(hdu[0].header)
-plt.subplot(projection=wcs)
+wcs1 = wcs.WCS(hdu[0].header)
+ax = plt.subplot(projection=wcs1)
 plt.imshow(im, origin="lower")
+plt.colorbar(label="Counts per pixel")
+plt.scatter(
+    [RA], [DEC], marker="x", color="white", transform=ax.get_transform("world")
+)
+plt.text(
+    RA,
+    DEC + 0.5 * pixsize,
+    src_name,
+    color="white",
+    transform=ax.get_transform("world"),
+)
+
 plt.grid(color="white", ls="solid")
 plt.xlabel("RA")
 plt.ylabel("Dec")
+pr.report_progress(stage="Progress", progress=100.0)
+plt.savefig("Image.png", format="png")
 
 bin_image = PictureProduct.from_file("Image.png")
 fits_image = ImageDataProduct.from_fits_file("Image.fits")
 
-picture = bin_image  # http://odahub.io/ontology#ODAPictureProduct
-image = fits_image  # http://odahub.io/ontology#Image
+png = bin_image  # http://odahub.io/ontology#ODAPictureProduct
+fits = fits_image  # http://odahub.io/ontology#Image
 
 # output gathering
 _galaxy_meta_data = {}
 _oda_outs = []
-_oda_outs.append(("out_Image_picture", "picture_galaxy.output", picture))
-_oda_outs.append(("out_Image_image", "image_galaxy.output", image))
+_oda_outs.append(("out_Image_png", "png_galaxy.output", png))
+_oda_outs.append(("out_Image_fits", "fits_galaxy.output", fits))
 
 for _outn, _outfn, _outv in _oda_outs:
     _galaxy_outfile_name = os.path.join(_galaxy_wd, _outfn)

tools/hess/Lightcurve.py

@@ -21,17 +21,21 @@
         "wget https://zenodo.org/record/1421099/files/hess_dl3_dr1.tar.gz"
     )
     get_ipython().system("tar -zxvf hess_dl3_dr1.tar.gz")   # noqa: F821
+from oda_api.api import ProgressReporter
+
+pr = ProgressReporter()
+pr.report_progress(stage="Progress", progress=5.0)
 
 src_name = "Crab"  # http://odahub.io/ontology#AstrophysicalObject
 RA = 83.628700  # http://odahub.io/ontology#PointOfInterestRA
 DEC = 22.014700  # http://odahub.io/ontology#PointOfInterestDEC
-T1 = "2003-10-09T13:16:00.0"  # http://odahub.io/ontology#StartTime
-T2 = "2005-10-10T13:16:00.0"  # http://odahub.io/ontology#EndTime
+T1 = "2004-11-20T13:16:00.0"  # http://odahub.io/ontology#StartTime
+T2 = "2004-12-20T13:16:00.0"  # http://odahub.io/ontology#EndTime
 Radius = 2.5  # http://odahub.io/ontology#AngleDegrees
 R_s = 0.2  # http://odahub.io/ontology#AngleDegrees
-Emin = 100.0  # http://odahub.io/ontology#Energy_GeV
-Emax = 10000.0  # http://odahub.io/ontology#Energy_GeV
-NTbins = 10  # http://odahub.io/ontology#Integer
+Emin = 1  # http://odahub.io/ontology#Energy_TeV
+Emax = 100.0  # http://odahub.io/ontology#Energy_TeV
+NTbins = 30  # http://odahub.io/ontology#Integer
 
 _galaxy_wd = os.getcwd()
 
@@ -105,7 +109,12 @@
 flux_b = np.zeros(NTbins)
 flux_b_err = np.zeros(NTbins)
 Expos = np.zeros(NTbins)
+src_cts = np.zeros(NTbins)
+bkg_cts = np.zeros(NTbins)
 for count, f in enumerate(OBSlist):
+    pr.report_progress(
+        stage="Progress", progress=5.0 + 95 * count / len(OBSlist)
+    )
     hdul = fits.open("data/" + f)
     RA_pnt = hdul[1].header["RA_PNT"]
     DEC_pnt = hdul[1].header["DEC_PNT"]
@@ -124,6 +133,7 @@
     ev_dec = ev["DEC"]
     ev_en = ev["ENERGY"]
     ev_time = (ev["TIME"] - Trun_start) / 86400.0 + Tbegs[count]
+    Nevents = len(ev)
     print(ev_time[0])
     ev_coords = SkyCoord(ev_ra, ev_dec, unit="degree")
     sep_s = ev_coords.separation(Coords_s).deg
@@ -138,18 +148,31 @@
     Thmin = hdu["THETA_LO"][0]
     Thmax = hdu["THETA_HI"][0]
     ind = np.argmin((Thmin - dist) ** 2)
-    AA = AA[ind] * Texp * 1e4
-    mask = np.where((sep_s < R_s))
-    cts1 = np.histogram2d(ev_time[mask], ev_en[mask], bins=[Tbins, EEbins])[0]
-    mask = sep_b < R_s
-    cts2 = np.histogram2d(ev_time[mask], ev_en[mask], bins=[Tbins, EEbins])[0]
-    src = cts1 - cts2
-    src_err = sqrt(cts1 + cts2)
-    flux += np.sum(src / AA, axis=1)
-    flux_err += np.sum(src_err / AA, axis=1)
-    flux_b += np.sum(cts2 / AA, axis=1)
-    flux_b_err += np.sum(sqrt(cts2) / AA, axis=1)
+    mask = EE < Emin
+    ind_en = len(EE[mask])
+    Expos += np.histogram(
+        ev_time,
+        weights=AA[ind, ind_en] * Texp * 1e4 * np.ones(Nevents) / Nevents,
+        bins=Tbins,
+    )[0]
+    mask = np.where((sep_s < R_s) & (ev_en > Emin) & (ev_en < Emax))
+    src_cts += np.histogram(ev_time[mask], bins=Tbins)[0]
+    mask = np.where((sep_b < R_s) & (ev_en > Emin) & (ev_en < Emax))
+    bkg_cts += np.histogram(ev_time[mask], bins=Tbins)[0]
     hdul.close()
+print(src_cts)
+print(bkg_cts)
+print(Expos)
+src = src_cts - bkg_cts
+src_err = sqrt(src_cts + bkg_cts)
+flux = src / (Expos + 1)
+flux_err = src_err / (Expos + 1)
+flux_b = bkg_cts / (Expos + 1)
+flux_b_err = sqrt(bkg_cts) / (Expos + 1)
+# flux_err+=np.sum(src_err/AA,axis=1)
+# flux_b+=np.sum(cts2/AA,axis=1)
+# flux_b_err+=np.sum(sqrt(cts2)/AA,axis=1)
+print(flux)
 
 if message == "":
     plt.errorbar(
@@ -193,20 +216,14 @@
     )
     lc = ODAAstropyTable(Table(data, names=names))
 
-picture = bin_image  # http://odahub.io/ontology#ODAPictureProduct
-lightcurve_astropy_table = lc  # http://odahub.io/ontology#ODAAstropyTable
+png = bin_image  # http://odahub.io/ontology#ODAPictureProduct
+table = lc  # http://odahub.io/ontology#ODAAstropyTable
 
 # output gathering
 _galaxy_meta_data = {}
 _oda_outs = []
-_oda_outs.append(("out_Lightcurve_picture", "picture_galaxy.output", picture))
-_oda_outs.append(
-    (
-        "out_Lightcurve_lightcurve_astropy_table",
-        "lightcurve_astropy_table_galaxy.output",
-        lightcurve_astropy_table,
-    )
-)
+_oda_outs.append(("out_Lightcurve_png", "png_galaxy.output", png))
+_oda_outs.append(("out_Lightcurve_table", "table_galaxy.output", table))
 
 for _outn, _outfn, _outv in _oda_outs:
     _galaxy_outfile_name = os.path.join(_galaxy_wd, _outfn)