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Import spectra from Fritz #2

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Sep 2, 2023
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Import spectra from Fritz #2

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4 changes: 4 additions & 0 deletions readme.md
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Original file line number Diff line number Diff line change
Expand Up @@ -79,6 +79,10 @@ Create `secrets.json` with confidential/secret data:
"token": null // set to your token
}
},
"fritz": {
"url": "https://fritz.science",
"token": null // set to your token, optional
}
}
}
```
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131 changes: 131 additions & 0 deletions ztf-variable-marshal/server.py
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Expand Up @@ -11,6 +11,7 @@

import aiofiles
import aiohttp
from astropy.time import Time
import aiohttp_jinja2
import jinja2
import jwt
Expand Down Expand Up @@ -183,6 +184,30 @@ async def add_master_program(_mongo):
print(_err)


# query fritz
def api(endpoint, method="GET", data=None):
import requests

try:
base_url = config["fritz"]["url"]
token = config["fritz"]["token"]
response = requests.request(
method,
f"{base_url}/api/{endpoint}",
headers={"Authorization": f"token {token}"}, # noqa
json=data,
)
if response.status_code != 200:
raise Exception(response.text)
else:
q = response.json()["data"]
return q
except Exception:
return None


fritz_instruments = api("instrument")

routes = web.RouteTableDef()


Expand Down Expand Up @@ -2142,6 +2167,14 @@ async def source_get_handler(request):
.to_list(length=None)
)

data = api(
f"sources?ra={source['ra']}&dec={source['dec']}&radius={3/3600}&hasSpectrum=true"
)
if data is not None and len(data.get("sources", [])) > 0:
source["fritz_sources"] = [d["id"] for d in data["sources"]]
else:
source["fritz_sources"] = []

context = {
"logo": config["server"]["logo"],
"user": session["user_id"],
Expand Down Expand Up @@ -3625,6 +3658,104 @@ async def source_post_handler(request):

return web.json_response({"message": "success"}, status=200)

elif _r["action"] == "import_fritz_spectra":
# fetch spectra from Fritz for the source in _r.get('source_id', None)
# and ingest them into the source

fritz_source_id = _r.get("source_id", None)
data = api(f"sources/{fritz_source_id}/spectra", method="GET")
if data is not None and len(data.get("spectra", [])) > 0:
new = False
for fritz_spectrum in data["spectra"]:
try:
telescope = [
fritz_instrument["telescope"]
for fritz_instrument in fritz_instruments
if fritz_instrument["name"]
== fritz_spectrum["instrument_name"]
][0]["nickname"]
except Exception:
telescope = "Unknown"

flux_unit = fritz_spectrum["units"]
if flux_unit in [None, "None", ""]:
flux_unit = fritz_spectrum.get("altdata", {}).get(
"BUNIT", "Unknown"
)

spectrum = {
"instrument": fritz_spectrum["instrument_name"],
"telescope": telescope,
"filter": "Unknown",
"wavelength_unit": "A",
"flux_unit": flux_unit,
"data": {
"wavelength": fritz_spectrum["wavelengths"],
"flux": fritz_spectrum["fluxes"],
"fluxerr": fritz_spectrum["errors"],
},
"mjd": Time(
fritz_spectrum["observed_at"], format="isot"
).mjd,
}

# check that there isn't a spectrum with the same mjd, instrument, telescope, filter already
# in the source
existing_spectra = source["spec"]
exists = False
for existing_spectrum in existing_spectra:
if (
existing_spectrum["mjd"] == spectrum["mjd"]
and existing_spectrum["instrument"]
== spectrum["instrument"]
and existing_spectrum["telescope"]
== spectrum["telescope"]
and existing_spectrum["filter"] == spectrum["filter"]
):
exists = True
break

if exists:
continue

# generate unique _id:
spectrum["_id"] = random_alphanumeric_str(length=24)

# make history
time_tag = utc_now()
h = {
"note_type": "spec",
"time_tag": time_tag,
"user": user,
"note": f'{spectrum["telescope"]} {spectrum["instrument"]} {spectrum["filter"]}',
}

await request.app["mongo"].sources.update_one(
{"_id": _id},
{
"$push": {"spec": spectrum, "history": h},
"$set": {"last_modified": utc_now()},
},
)
new = True

if not new:
return web.json_response(
{
"message": f"All spectra from fritz source {fritz_source_id} already imported"
},
status=200,
)

return web.json_response({"message": "success"}, status=200)
else:
return web.json_response(
{
"message": f"failure: no spectra found in fritz for {fritz_source_id}"
},
status=200,
)

else:
return web.json_response(
{"message": "failure: unknown action requested"}, status=200
Expand Down
1 change: 0 additions & 1 deletion ztf-variable-marshal/templates/template-search.html
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Expand Up @@ -332,7 +332,6 @@ <h5 class="modal-title" id="modal-query-id"></h5>
// display details
function detailFormatter(index, row, element) {
var html = [];
console.log(row)

{#let jdd = new JulianDate();#}
{#let date_utc = moment(jdd.julian(parseFloat(row['jd'])).getDate()).utc().format('YYYYMMDD');#}
Expand Down
72 changes: 67 additions & 5 deletions ztf-variable-marshal/templates/template-source.html
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Original file line number Diff line number Diff line change
Expand Up @@ -262,9 +262,6 @@ <h4>
{% else %}
{% set dec_string = source['dec'] | string %}
{% endif %}
<a href="javascript:document.getElementById('kowalski_form').submit();"
role="button" class="btn btn-secondary btn-sm"
id="survey_ztf_alerts">ZTF Alerts</a>
<a href="https://ps1images.stsci.edu/cgi-bin/ps1cutouts?pos={{ source['ra'] }}{{ dec_string }}&filter=color&filter=g&filter=r&filter=i&filter=z&filter=y&filetypes=stack&auxiliary=data&size=240&output_size=0&verbose=0&autoscale=99.500000&catlist="
target="_blank" role="button" class="btn btn-secondary btn-sm"
id="survey_panstarrs">PanSTARRS-1</a>
Expand Down Expand Up @@ -327,10 +324,31 @@ <h4>
...
]
}</code></pre>
"wavelen_unit" can be "A", "nm", or "m".
"wavelength_unit" can be "A", "nm", or "m".
You can use either mjd or hjd for the time stamp.
Other fields above are mandatory, however you can add any custom fields.
</p>
<!-- if the source has 'has_fritz_spectra' True, show a test like: "Nearby sources with spectra found in Fritz" -->
<div class="mt-2">
<b>Fritz sources (with spectra, within 3 arcsec):</b>
{% if source['fritz_sources'] | length > 0 %}
{% for fritz_source in source['fritz_sources'] %}
<div class="mt-1" style="display: flex; flex-direction: row; align-items: center;">
<p>
<a href="http://fritz.science/source/{{ fritz_source }}" target="_blank" role="button" class="btn btn-secondary btn-sm">
{{ fritz_source }}
</a>
<!-- add a button to import spectra -->
<button type="button" class="btn btn-dark btn-sm"
id="import_fritz_spectra" onclick="import_fritz_spectra('{{ fritz_source }}')">Import</button>
</p>
</div>
{% endfor %}
{% else %}
<p><em>No sources found.</em></p>
{% endif %}
</div>

</div>

<div class="tab-pane fade mt-2" id="nav-auxiliary"
Expand Down Expand Up @@ -541,7 +559,7 @@ <h5 class="modal-title" id="modal-query-id"></h5>
error_y: {type: 'data',
array: {{ lc['data'][key]['magerr'] }},
width: 2,
thickness: 0.8,
thickness: 0.4,
color: "{{ lc['color'] }}",
opacity: 0.5,
visible: true},
Expand Down Expand Up @@ -1269,6 +1287,50 @@ <h5 class="modal-title" id="modal-query-id"></h5>
{% endfor %}
});
{% endif %}

{# import spectra from a fritz source, takes the source id as input #}
function import_fritz_spectra(source_id) {
bootbox.confirm({
message: "Do you want to import spectra from a fritz source?",
buttons: {
cancel: {
label: '<i class="fas fa-times"></i> No'
},
confirm: {
label: '<i class="fas fa-check"></i> Yes'
}
},
callback: function (result) {
// confirmed?
if (result) {
$.ajax({url: '{{-script_root-}}/sources/{{-source["_id"]-}}',
method: 'POST',
data: JSON.stringify({'action': 'import_fritz_spectra', 'source_id': source_id}),
processData: false,
contentType: 'application/json',
success: function(data) {
if (data['message'] === 'success') {
showFlashingMessage('Info:', 'Successfully imported spectra: ' + data['message'], 'success');
setTimeout(window.location.href = '{{-script_root-}}/sources/{{ source["_id"] }}', 1000);
}
else if (data['message'] === `All spectra from fritz source ${source_id} already imported`) {
showFlashingMessage('Info:', `All spectra from fritz source ${source_id} already imported`, 'info');
}
else {
showFlashingMessage('Info:', 'Failed to import spectra: ' + data['message'], 'danger');
}
},
error: function(data) {
showFlashingMessage('Info:', 'Failed to import spectra', 'danger');
}
});
}
}
});
}

{# import light curves from a fritz source, takes the source id as input #}

</script>

{% endblock %}
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