def get_samp_client() -> SAMPIntegratedClient:
"""
creates a new SAMP client and tries to connect to the hub
:return: the new samp client
"""
while True:
try:
client = SAMPIntegratedClient("PhotometryTool")
client.connect()
except SAMPHubError:
time.sleep(0.5)
else:
return client
def send_map_layers_to_samp(maps, defer_cleanup_s=5):
client = SAMPIntegratedClient()
client.connect()
params = {}
message = {"samp.mtype": "jhv.load.image", "samp.params": params}
tmp_files = []
for energy_band in maps:
params["url"] = []
for i in range(len(maps[energy_band])):
f = NamedTemporaryFile(delete=False, suffix=".fits")
f.close()
maps[energy_band][i].save(f.name)
tmp_files.append(f.name)
# use file:/// workaround for windows as JHV currently can't handle windows paths
params["url"].append(("file:///" + f.name.replace("\\", "/")
) if f.name.find("\\") >= 0 else f.name)
client.notify_all(
message
) # message holds a reference to params which is updated in the loop
client.disconnect()
time.sleep(
defer_cleanup_s
) # wait to make sure JHV could read the files before they're removed
for filename in tmp_files:
del_file(filename) # cleanup
def __init__(self, callback, check_connection_period=1):
self.callback = callback
self.dirname = os.path.dirname(os.path.abspath(__file__))
self.timer = None
self.samp_hub = None
self.samp_client = None
self.metadata = {
'samp.name': 'iSpec',
'samp.description.text': 'iSpec',
'samp.icon.url': 'file://' + self.dirname + '/images/iSpec.png',
}
self.samp_client = SAMPIntegratedClient(metadata=self.metadata,
addr='localhost')
self.check_connection_period = check_connection_period # seconds
self.__check_connection()
signal.signal(signal.SIGINT, self.__signal_handler)
def __check_connection(self):
status = "Status: "
if not self.is_connected():
if self.samp_client is not None and self.samp_client.is_connected(
):
# Destroy old client to completely reset the connection status
del self.samp_client
self.samp_client = SAMPIntegratedClient(metadata=self.metadata,
addr='localhost')
logging.info("SAMP Connection lost")
status += "Disconnected"
self.__connect()
else:
status += "Connected"
pass
logging.debug(status)
self.timer = threading.Timer(self.check_connection_period,
self.__check_connection)
self.timer.start()
class SAMP4JHVClient:
def __init__(self):
self.client = SAMPIntegratedClient()
self.tmp_files = []
def send_image_maps(self, maps):
""" Takes a list of SunPy Map objects, saves them to disk one by one and sends the file-locations to JHV """
params = {}
params["url"] = []
for m in maps:
f = NamedTemporaryFile(delete=False, suffix=".fits")
f.close()
m.save(f.name)
self.tmp_files.append(f.name)
# use file:/// workaround for windows as JHV currently can't handle windows paths
params["url"].append(("file:///" + f.name.replace("\\", "/")
) if f.name.find("\\") >= 0 else f.name)
self.client.connect()
self.client.notify_all({
"samp.mtype": "jhv.load.image",
"samp.params": params
})
self.client.disconnect()
def remove_tmp_files(self):
""" Removes temporary files that were created for JHV to be read.
Mind that after calling this function, the images might not be available in JHV anymore
due to JHVs internal memory management, that might require to re-read the files at some point.
"""
for f in self.tmp_files:
del_file(f) # cleanup
class TestWebProfile(BaseTestStandardProfile):
def setup_method(self, method):
self.dialog = AlwaysApproveWebProfileDialog()
t = threading.Thread(target=self.dialog.poll)
t.start()
self.tmpdir = tempfile.mkdtemp()
lockfile = os.path.join(self.tmpdir, '.samp')
self.hub = SAMPHubServer(web_profile_dialog=self.dialog,
lockfile=lockfile,
web_port=0, pool_size=1)
self.hub.start()
self.client1 = SAMPIntegratedClient()
self.client1.connect(hub=self.hub, pool_size=1)
self.client1_id = self.client1.get_public_id()
self.client1_key = self.client1.get_private_key()
self.client2 = SAMPIntegratedWebClient()
self.client2.connect(web_port=self.hub._web_port, pool_size=2)
self.client2_id = self.client2.get_public_id()
self.client2_key = self.client2.get_private_key()
def teardown_method(self, method):
if self.client1.is_connected:
self.client1.disconnect()
if self.client2.is_connected:
self.client2.disconnect()
self.hub.stop()
self.dialog.stop()
# The full communication tests are run since TestWebProfile inherits
# test_main from TestStandardProfile
def test_web_profile(self):
# Check some additional queries to the server
with get_readable_fileobj('http://localhost:{0}/crossdomain.xml'.format(self.hub._web_port)) as f:
assert f.read() == CROSS_DOMAIN
with get_readable_fileobj('http://localhost:{0}/clientaccesspolicy.xml'.format(self.hub._web_port)) as f:
assert f.read() == CLIENT_ACCESS_POLICY
# Check headers
req = Request('http://localhost:{0}/crossdomain.xml'.format(self.hub._web_port))
req.add_header('Origin', 'test_web_profile')
resp = urlopen(req)
assert resp.getheader('Access-Control-Allow-Origin') == 'test_web_profile'
assert resp.getheader('Access-Control-Allow-Headers') == 'Content-Type'
assert resp.getheader('Access-Control-Allow-Credentials') == 'true'
def setup_method(self, method):
self.dialog = AlwaysApproveWebProfileDialog()
t = threading.Thread(target=self.dialog.poll)
t.start()
self.tmpdir = tempfile.mkdtemp()
lockfile = os.path.join(self.tmpdir, '.samp')
self.hub = SAMPHubServer(web_profile_dialog=self.dialog,
lockfile=lockfile,
web_port=0, pool_size=1)
self.hub.start()
self.client1 = SAMPIntegratedClient()
self.client1.connect(hub=self.hub, pool_size=1)
self.client1_id = self.client1.get_public_id()
self.client1_key = self.client1.get_private_key()
self.client2 = SAMPIntegratedWebClient()
self.client2.connect(web_port=self.hub._web_port, pool_size=2)
self.client2_id = self.client2.get_public_id()
self.client2_key = self.client2.get_private_key()
def SAMP_conn():
"""a context manager to give the controlled block a SAMP connection.
The program will disconnect as the controlled block is exited.
"""
client = SAMPIntegratedClient(name="serialquery",
description="A serial SCS querier.")
client.connect()
try:
yield client
finally:
client.disconnect()
def connection(
client_name="pyvo client", description="A generic PyVO client", **kwargs
):
"""
a context manager to give the controlled block a SAMP connection.
The program will disconnect as the controlled block is exited.
"""
client = SAMPIntegratedClient(
name=client_name, description=description, **kwargs)
client.connect()
try:
yield client
finally:
client.disconnect()
def capCommand(self, *args, **kwargs):
MSG=self.MSG
self.cli = SAMPIntegratedClient()
self.cli.connect()
self.r = Receiver(self.cli)
MSG( 'Binding methods' )
#=> case MTYPE: qgis.message
def qMessage():
MSG( 'Message: ' + self.r.params['script'])
#=> case MTYPE: qgis.load.vectorlayer
def qLoadVectorlayer(): # case MTYPE: qgis.load.vectorlayer
self.LoadVectorLayer(self.r.params['url'], self.r.params['name'])
#=> case MTYPE: table.load.votable
def addVLayerToCanvas(self,vlayer):
self.iface.mapCanvas().freeze()
#QgsMapLayerRegistry.instance().addMapLayer(vlayer) # order is importaint here
QgsProject.instance().addMapLayer(vlayer)
# self.root.addLayer(vlayer)
self.root.insertLayer(0,vlayer)
#QgsMapLayerRegistry.instance().reloadAllLayers()
QgsProject.instance().reloadAllLayers()
self.iface.mapCanvas().freeze(False)
def qLoadVotable():
loadWMS = lambda vot: VOTableLoaderHelper.loadWMS(vot, self.iface, self.root)
makeComplFeat = VOTableLoaderHelper.makeComplFeat
MSG('Loading VOtable\n from url: \n'+self.r.params['url']);say('SAMP Params are: ' + str(self.r.params))
ttime.sleep(2)
vot = Table.read(download_file(self.r.params['url'],timeout=200)) #fixes timeout bug
if 'access_format' in vot.colnames:
say(str(vot.columns['access_format'][0])) #<+===
if b'application/x-wms'in vot.columns['access_format'][0]:
try:
loadWMS(vot)
except Exception:
self.MSG('OOPS something went wrong while loading WMS')
tb=traceback.format_exc()
say(tb)
finally:
return
mURL = tempfile.mkdtemp()
MSG("converting to GeoJSON");say('Number of features to write: '+ str(len(vot)) )
featList=[]
for i in range(len(vot)):
self.MSG('writing number' + str(i))
featList.append(makeComplFeat(vot, i))
with open(mURL + '/vot.geojson', 'w') as f: f.write(geojson.dumps({"type":"FeatureCollection","features":featList}))
self.MSG('finished download, converting to SpatiaLite')
try:
self.MSG("vlayer")
ttime.sleep(2)
vlayer = QgsVectorLayer(mURL + '/vot.geojson',"mygeojson","ogr")
except Exception:
self.MSG("ops creating geojson")
ttime.sleep(2)
self.MSG('OOPS something went wrong while creating a vector layer from geojson')
return
say("writing to SpatiaLite")
try:
self.MSG("Writing...")
#ttime.sleep(2)
options = QgsVectorFileWriter.SaveVectorOptions()
#options.actionOnExistingFile = QgsVectorFileWriter.CreateOrOverwriteLayer
#options.EditionCapability = QgsVectorFileWriter.CanAddNewLayer
#options.fileEncoding="utf-8"
options.driverName="SQLite"
options.layerName = vlayer.name()
QgsVectorFileWriter.writeAsVectorFormat(vlayer, mURL +r"/vot.sqlite", options)
except Exception as e:
# #logf = open(r"/home/gnodj/test/download.log", "w")
# self.MSG("201")
# fname = r'/home/vhyradus/test/'
# logging.basicConfig(filename=fname + 'log.log', level=logging.DEBUG,format='%(asctime)s %(levelname)s %(name)s %(message)s')
# logger=logging.getLogger(__name__)
# logger.error(e)
# ttime.sleep(2)
self.MSG('OOPS something went wrong while writing SQLite')
#ttime.sleep(2)
return
say("loading SpatiaLite")
try:
self.MSG("Loading...")
vlayer = QgsVectorLayer(mURL+r"/vot.sqlite",str(self.r.params['name']),"ogr")
except Exception as e:
# self.MSG("215")
# ttime.sleep(2)
# self.MSG('OOPS something went wrong while creating a vector Layer')
# fname = r'/home/vhyradus/test/'
# logging.basicConfig(filename=fname + 'log.log', level=logging.DEBUG,format='%(asctime)s %(levelname)s %(name)s %(message)s')
# logger=logging.getLogger(__name__)
# logger.error(e)
# ttime.sleep(2)
self.MSG('OOPS something went wrong while writing SQLite')
# ttime.sleep(2)
return
# say(vot.meta['description']) #description is not available with complex queries
# vlayer = QgsVectorLayer( mURL+r"/vot.sqlite",str(vot.meta['description']),"ogr")
say("adding layer to canvas")
try:
self.MSG("Adding...")
ttime.sleep(2)
self.addVLayerToCanvas(vlayer)
except Exception as e:
# self.MSG("234")
# fname = r'/home/vhyradus/test/'
# logging.basicConfig(filename=fname + 'log.log', level=logging.DEBUG,format='%(asctime)s %(levelname)s %(name)s %(message)s')
# logger=logging.getLogger(__name__)
# logger.error(e)
# ttime.sleep(2)
# ttime.sleep(2)
self.MSG('OOPS something went wrong while trying to add layer to canvas')
return
say("done")
mTypeDict={'qgis.message':qMessage,'qgis.load.vectorlayer':qLoadVectorlayer,'table.load.votable':qLoadVotable}
list(map(self.bindSamp, list(mTypeDict.keys())))
MSG("Disconnected")
while self.connectionState:
MSG("starting")
self.r.received = False
while not self.r.received and self.connectionState:
MSG("waiting"); ttime.sleep(2)
if self.connectionState:
mTypeDict[self.r.mtype]()
ttime.sleep(2)
class SAMPState(State):
status = CallbackProperty('Not connected to SAMP Hub')
connected = CallbackProperty(False)
clients = CallbackProperty([])
highlight_is_selection = CallbackProperty(False)
def __init__(self):
super(SAMPState, self).__init__()
self.hub = SAMPHubServer()
self.client = SAMPIntegratedClient()
self.add_callback('connected', self.on_connected)
def start_samp(self):
if not self.client.is_connected:
try:
self.client.connect()
except SAMPHubError:
try:
self.hub.start()
self.client.connect()
except Exception:
self.connected = False
self.status = 'Could not connect to Hub'
else:
self.connected = True
self.status = 'Connected to (glue) SAMP Hub'
except:
self.connected = False
self.status = 'Could not connect to Hub'
else:
self.connected = True
self.status = 'Connected to SAMP Hub'
def stop_samp(self):
if self.client.is_connected:
self.client.disconnect()
if self.hub.is_running:
self.hub.stop()
self.connected = False
self.status = 'Not connected to SAMP Hub'
def on_connected(self, *args):
if self.connected:
metadata = {
'author.email': '*****@*****.**',
'author.name': 'Thomas Robitaille',
'home.page': 'http://www.glueviz.org',
'samp.description.text':
'Multi-dimensional linked data exploration',
'samp.documentation.url': 'http://www.glueviz.org',
'samp.icon.url': 'file://' + ICON_PATH,
'samp.name': 'glueviz',
'glue.version': glue_version
}
self.client.declare_metadata(metadata)
self.on_client_change()
def on_client_change(self):
clients = []
for client in self.client.get_registered_clients():
metadata = self.client.get_metadata(client)
clients.append((client, metadata.get('samp.name', client)))
self.clients = clients
def send_data(self, layer=None, client=None):
filename = tempfile.mktemp()
message = {}
message["samp.params"] = {}
if isinstance(layer, Data):
if layer.ndim == 1:
table = data_to_astropy_table(layer)
table.write(filename, format='votable')
message["samp.mtype"] = "table.load.votable"
if 'samp-table-id' not in layer.meta:
layer.meta['samp-table-id'] = layer.label
message["samp.params"]['table-id'] = layer.meta[
'samp-table-id']
elif layer.ndim == 2:
fits_writer(filename, layer)
message["samp.mtype"] = "image.load.fits"
if 'samp-image-id' not in layer.meta:
layer.meta['samp-image-id'] = layer.label
message["samp.params"]['image-id'] = layer.meta[
'samp-image-id']
else:
return
message["samp.params"]['name'] = layer.label
message["samp.params"]['url'] = 'file://' + os.path.abspath(
filename)
else:
message['samp.mtype'] = 'table.select.rowList'
if layer.ndim == 1:
message["samp.params"]['table-id'] = layer.data.meta[
'samp-table-id']
message["samp.params"]['row-list'] = np.nonzero(
layer.to_mask())[0].astype(str).tolist()
else:
return
if client is None:
self.client.notify_all(message)
else:
# Make sure client is subscribed otherwise an exception is raised
subscriptions = self.client.get_subscriptions(client)
for mtype in subscriptions:
if fnmatch(message['samp.mtype'], mtype):
self.client.notify(client, message)
return
else:
return
class SAMPManager(object):
def __init__(self, callback, check_connection_period=1):
self.callback = callback
self.dirname = os.path.dirname(os.path.abspath(__file__))
self.timer = None
self.samp_hub = None
self.samp_client = None
self.metadata = {
'samp.name': 'iSpec',
'samp.description.text': 'iSpec',
'samp.icon.url': 'file://' + self.dirname + '/images/iSpec.png',
}
self.samp_client = SAMPIntegratedClient(metadata=self.metadata,
addr='localhost')
self.check_connection_period = check_connection_period # seconds
self.__check_connection()
signal.signal(signal.SIGINT, self.__signal_handler)
def is_connected(self):
working_connection = False
if self.samp_client is not None and self.samp_client.is_connected():
try:
self.samp_client.ping()
working_connection = True
except:
working_connection = False
return working_connection
def __check_connection(self):
status = "Status: "
if not self.is_connected():
if self.samp_client is not None and self.samp_client.is_connected(
):
# Destroy old client to completely reset the connection status
del self.samp_client
self.samp_client = SAMPIntegratedClient(metadata=self.metadata,
addr='localhost')
logging.info("SAMP Connection lost")
status += "Disconnected"
self.__connect()
else:
status += "Connected"
pass
logging.debug(status)
self.timer = threading.Timer(self.check_connection_period,
self.__check_connection)
self.timer.start()
def __connect(self):
# Before we start, let's kill off any zombies
try:
self.shutdown()
except:
pass
# sampy seems to fall over sometimes if 'localhost' isn't specified, even though it shouldn't
#self.samp_hub = sampy.SAMPHubServer(addr='localhost')
#self.samp_hub.start()
try:
self.samp_client.connect()
logging.info("SAMP Connection established")
except Exception:
pass
else:
#samp_client.bindReceiveNotification("*", self.__samp_receive_notification)
#samp_client.bindReceiveCall("*", self.__samp_receive_call)
self.samp_client.bind_receive_notification(
"samp.hub.event.register", self.__samp_receive_notification)
self.samp_client.bind_receive_notification(
"samp.hub.event.metadata", self.__samp_receive_notification)
self.samp_client.bind_receive_notification(
"samp.hub.event.subscriptions",
self.__samp_receive_notification)
self.samp_client.bind_receive_notification(
"samp.hub.event.unregister", self.__samp_receive_notification)
self.samp_client.bind_receive_notification(
"table.load.votable", self.__samp_receive_notification)
self.samp_client.bind_receive_notification(
"spectrum.load.ssa-generic", self.__samp_receive_notification)
self.samp_client.bind_receive_call("table.load.votable",
self.__samp_receive_call)
self.samp_client.bind_receive_call("spectrum.load.ssa-generic",
self.__samp_receive_call)
def __samp_receive_notification(self, private_key, sender_id, mtype,
params, extra):
#print "Notification:", private_key, sender_id, mtype, params, extra
if mtype == 'samp.hub.event.register':
#print "Registered:", params['id']
pass
elif mtype == 'samp.hub.event.metadata':
#print "Metadata:", params['id'], "=", params['metadata']['samp.name']
pass
elif mtype == 'samp.hub.event.subscriptions':
if 'spectrum.load.ssa-generic' in list(
params['subscriptions'].keys()):
#print params['id'], "supports spectrum"
pass
if 'table.load.votable' in list(params['subscriptions'].keys()):
#print params['id'], "supports votable"
pass
#print params
elif mtype == 'samp.hub.event.unregister':
#print params['id'], "unregistered"
pass
else:
# For instance, VOSpec sends load votable/spectrum in form of notification
# so we should try to process them also
msg_id = None
spectrum = self.__samp_receive_and_transform_spectrum(
mtype, params)
logging.info("Spectrum received via SAMP")
self.callback(spectrum, "Received_spectrum")
# Function called when a call is received
def __samp_receive_call(self, private_key, sender_id, msg_id, mtype,
params, extra):
#print "Call:", private_key, sender_id, msg_id, mtype, params, extra
spectrum = self.__samp_receive_and_transform_spectrum(mtype, params)
self.samp_client.ereply(msg_id,
sampy.SAMP_STATUS_OK,
result={"txt": "printed"})
logging.info("Spectrum received via SAMP")
self.callback(spectrum, "Received_spectrum")
def __samp_receive_and_transform_spectrum(self, mtype, params):
if mtype == 'table.load.votable':
#print "Received votable", params['url']
votable = self.__read_votable(params['url'])
spectrum = self.__votable_to_spectrum(votable)
#print "Spectrum success"
elif mtype == 'spectrum.load.ssa-generic':
#print "Received spectrum", params['url'], "in format", params['meta']['Access.Format']
if params['meta']['Access.Format'] == 'application/votable':
#print "- Votable"
votable = self.__read_votable(params['url'])
spectrum = self.__votable_to_spectrum(votable)
#print "Spectrum success"
elif params['meta']['Access.Format'] == 'application/fits':
#print "- FITS"
spectrum = self.__read_vofits(params['url'])
#print "Spectrum success"
else:
raise Exception("Unknown format")
else:
raise Exception("Unknown action")
return spectrum
def __signal_handler(self, signal, frame):
print('SIGTERM received (ctrl+c)')
self.shutdown()
def shutdown(self):
if self.timer is not None: self.timer.cancel()
if self.samp_client.is_connected():
try:
self.samp_client.disconnect()
except Exception:
pass
if self.samp_hub is not None and self.samp_hub._is_running:
self.samp_hub.stop()
sys.exit(0)
def __get_target_client(self, target_client_name):
neighbours = samp_client.get_registered_clients()
for neighbour in neighbours:
metadata = self.samp_client.get_metadata(neighbour)
try:
if (metadata['samp.name'] == target_client_name):
return neighbour
except KeyError:
continue
return None
########### [start] File operations
def __votable_to_spectrum(self, votable):
spectrum = None
# Search for what it is required
has_waveobs = False
has_flux = False
target_table = None
waveobs_units = None
for resource in votable.resources:
for table in resource.tables:
if len(table.array) > 0 and len(table.fields) >= 2:
for field in table.fields:
if field.name in ["wave", "waveobs"]:
has_waveobs = True
waveobs_units = field.unit
elif field.name == "flux":
has_flux = True
if has_waveobs and has_flux:
break
if has_waveobs and has_flux:
target_table = table
break
if has_waveobs and has_flux:
break
if target_table is not None:
spectrum = np.recarray((len(target_table.array), ),
dtype=[('waveobs', float), ('flux', float),
('err', float)])
if 'waveobs' in list(target_table.array.dtype.fields.keys()):
spectrum['waveobs'] = target_table.array['waveobs']
elif 'wave' in list(target_table.array.dtype.fields.keys()):
spectrum['waveobs'] = target_table.array['wave']
else:
# the first column
spectrum['waveobs'] = target_table.array[
target_table.array.dtype.names[0]]
if 'flux' in list(target_table.array.dtype.fields.keys()):
spectrum['flux'] = target_table.array['flux']
else:
# the second column
spectrum['flux'] = target_table.array[
target_table.array.dtype.names[1]]
if 'err' in list(target_table.array.dtype.fields.keys()):
spectrum['err'] = target_table.array['err']
elif 'error' in list(target_table.array.dtype.fields.keys()):
spectrum['err'] = target_table.array['error']
elif 'errors' in list(target_table.array.dtype.fields.keys()):
spectrum['err'] = target_table.array['errors']
if 'sigma' in list(target_table.array.dtype.fields.keys()):
spectrum['err'] = target_table.array['sigma']
elif len(table.fields) >= 3:
# the third column if exists
spectrum['err'] = target_table.array[
target_table.array.dtype.names[2]]
else:
spectrum['err'] = 0.0
if target_table is None or spectrum is None:
raise Exception("Table not compatible")
return spectrum
def __read_votable(self, url):
votable = None
if url.startswith('http://'):
u = urllib.request.urlopen(url)
tmp = tempfile.NamedTemporaryFile(mode="wt",
suffix=".xml",
delete=False,
encoding='utf-8')
tmp.write(u.read())
tmp.close()
#print tmp.name
votable = parse(tmp.name, pedantic=False)
os.remove(tmp.name)
elif url.startswith('file://localhost/'):
filename = url[17:]
if filename[0] != "/":
filename = "/" + filename
votable = parse(filename, pedantic=False)
else:
raise Exception("Unkown URL")
return votable
def __read_vofits(self, url):
spectrum = None
#print url
if url.startswith('http://localhost/'):
u = urllib.request.urlopen(url)
tmp = tempfile.NamedTemporaryFile(mode="wt",
suffix=".xml",
delete=False,
encoding='utf-8')
tmp.write(u.read())
tmp.close()
#print tmp.name
hdulist = pyfits.open(tmp.name)
os.remove(tmp)
elif url.startswith('file://localhost/'):
filename = url[17:]
if filename[0] != "/":
filename = "/" + filename
hdulist = pyfits.open(filename)
else:
raise Exception("Unkown URL")
# Find hdu containing data
target_hdu = None
for hdu in hdulist:
if hdu.data is not None and len(hdu.data) > 0 and len(
list(hdu.data.dtype.fields.keys())) >= 2:
target_hdu = hdu
spectrum = np.recarray((len(target_hdu.data), ),
dtype=[('waveobs', float), ('flux', float),
('err', float)])
# the first column
spectrum['waveobs'] = target_hdu.data[target_hdu.data.dtype.names[0]]
# the second column
spectrum['flux'] = target_hdu.data[target_hdu.data.dtype.names[1]]
if len(list(hdu.data.dtype.fields.keys())) >= 3:
# the third column if exists
spectrum['err'] = target_hdu.data[target_hdu.data.dtype.names[2]]
else:
spectrum['err'] = 0.0
if target_hdu is None or spectrum is None:
raise Exception("FITS not compatible")
return spectrum
def __spectrum_to_vofits(self, spectrum):
t = pyfits.new_table(spectrum)
t.header['TTYPE1'] = "WAVELENGTH"
t.header['TTYPE2'] = "FLUX"
t.header['TTYPE3'] = "SIGMA"
fits = pyfits.HDUList(pyfits.PrimaryHDU())
fits.append(t)
return fits
def __spectrum_to_votable(self, spectrum):
# Create a new VOTable file...
votable = VOTableFile()
# ...with one resource...
resource = Resource()
votable.resources.append(resource)
# ... with one table
table = Table(votable)
resource.tables.append(table)
# Define some fields
waveobs = Field(votable,
name="waveobs",
datatype="double",
unit="nm",
ucd="em.wl")
flux = Field(votable,
name="flux",
datatype="double",
unit="Jy",
ucd="phot.flux")
err = Field(votable,
name="err",
datatype="double",
ucd="stat.error;phot.flux")
table.fields.extend([waveobs, flux, err])
table.groups.extend([Group([flux, err])])
#import ipdb
#ipdb.set_trace()
# Now, use those field definitions to create the numpy record arrays, with
# the given number of rows
table.create_arrays(len(spectrum))
# Now table.array can be filled with data
table.array['waveobs'] = spectrum['waveobs']
table.array['flux'] = spectrum['flux']
table.array['err'] = spectrum['err']
#votable.set_all_tables_format('binary') # VOSpec does not understand binary format
return votable
########### [end] File operations
def get_subscribers(self):
ids = []
names = []
as_tables = []
try:
if self.samp_client.is_connected():
subscribers1 = self.samp_client.get_subscribed_clients(
"table.load.votable")
subscribers2 = self.samp_client.get_subscribed_clients(
"spectrum.load.ssa-generic")
subscribers = dict(
list(subscribers1.items()) + list(subscribers2.items()))
for subscriber in list(subscribers.keys()):
metadata = self.samp_client.get_metadata(subscriber)
name = ""
if 'samp.name' in metadata:
name = metadata['samp.name']
ids.append(subscriber)
names.append(name)
# Prefered form: "spectrum.load.ssa-generic"
if subscriber in list(subscribers2.keys()):
as_tables.append(False)
else:
as_tables.append(True)
# If there are repeated names, add the identifier as a prefix
uniq_names, uniq_names_index = np.unique(names,
return_index=True)
if len(names) != len(uniq_names):
for i in np.arange(len(names)):
# Only add a preffix to the repeated application names
if i not in uniq_names_index:
names[i] += " [" + ids[i] + "]"
except Exception:
pass
return (ids, names, as_tables)
# Broadcast a table file to TOPCAT
def broadcast_spectrum(self,
spectrum,
spectrum_name,
target_client,
target_client_is_name=False,
as_table=True,
as_fits=False):
if as_fits:
suffix = ".fits"
else:
suffix = ".xml"
tmp = tempfile.NamedTemporaryFile(mode="wt",
suffix=suffix,
delete=False,
encoding='utf-8')
tmp.close()
if not as_fits:
votable = self.__spectrum_to_votable(spectrum)
votable.to_xml(tmp.name)
else:
fits = self.__spectrum_to_vofits(spectrum)
fits.writeto(tmp.name, clobber=True)
if as_table:
mtype = 'table.load.votable'
else:
mtype = 'spectrum.load.ssa-generic'
metadata = {
'samp.mtype': mtype,
'samp.params': {
'name': spectrum_name,
'table-id': spectrum_name,
'url': 'file://localhost/' + tmp.name
}
}
if target_client_is_name:
target_client_name = target_client
target_client = self.__get_target_client(target_client_name)
response = False
if target_client is not None:
try:
response = self.samp_client.notify(target_client, metadata)
logging.info("Spectrum sent via SAMP")
except Exception:
pass
# Do not delete or the target client will not have time to read it
#os.remove(tmp.name)
return response
def __init__(self):
self.sampClient = SAMPIntegratedClient(
"A2P2 samp relay"
) # TODO get title from main program class instead of HardCoded value
class A2p2SampClient():
# TODO watch hub disconnection
def __init__(self):
self.sampClient = SAMPIntegratedClient(
"A2P2 samp relay"
) # TODO get title from main program class instead of HardCoded value
def __del__(self):
self.disconnect()
def connect(self):
self.sampClient.connect()
# an error is thrown here if no hub is present
# TODO get samp client name and display it in the UI
# Instantiate the receiver
self.r = Receiver(self.sampClient)
# Listen for any instructions to load a table
self.sampClient.bind_receive_call("ob.load.data", self.r.receive_call)
self.sampClient.bind_receive_notification("ob.load.data",
self.r.receive_notification)
def disconnect(self):
self.sampClient.disconnect()
def is_connected(self):
# Workarround the 'non' reliable is_connected attribute
# this helps to reconnect after hub connection lost
try:
return self.sampClient.is_connected and (
self.sampClient.ping() or self.sampClient.is_connected)
except:
# consider connection refused exception as not connected state
return False
def get_status(self):
if self.is_connected():
return "connected [%s]" % (self.sampClient.get_public_id())
else:
return "not connected"
def get_public_id(self):
return self.sampClient.get_public_id()
def has_message(self):
return self.is_connected() and self.r.received
def clear_message(self):
return self.r.clear()
def get_ob_url(self):
url = self.r.params['url']
if url.startswith("file:///"):
return url[7:]
elif url.startswith("file:/"): # work arround bugged file urls
return url[5:]
return url
def __init__(self):
self._client = SAMPIntegratedClient()
class AladinViaSAMP(object):
def __init__(self):
self._client = SAMPIntegratedClient()
def send_file(self, infile=str()):
"""Sending a file (image or table) to Aladin Sky Atlas using the SAMPIntegratedClient class.
http://docs.astropy.org/en/stable/vo/samp/example_table_image.html
"""
self._client.connect()
params = {}
if sys.version > '3':
params["url"] = urllib.parse.urljoin('file:', os.path.abspath(infile))
else:
params["url"] = urlparse.urljoin('file:', os.path.abspath(infile))
message = {}
message[ "samp.mtype" ] = "image.load.fits"
message[ "samp.params" ] = params
self._client.notify_all(message)
self._client.disconnect()
def move(self, script=str()):
"""Sending a script to Aladin Sky Atlas using the SAMPIntegratedClient class.
http://docs.astropy.org/en/stable/vo/samp/example_table_image.html
"""
self._client.connect()
params = {}
message = {}
message[ "samp.mtype" ] = "coord.pointAt.sky"
message[ "samp.params" ] = { "script" : script }
self._client.notify_all(message)
self._client.disconnect()
def send_script_command(self, script=str()):
"""Sending a script to Aladin Sky Atlas using the SAMPIntegratedClient class.
http://docs.astropy.org/en/stable/vo/samp/example_table_image.html
"""
self._client.connect()
params = {}
message = {}
message[ "samp.mtype" ] = "script.aladin.send"
message[ "samp.params" ] = { "script" : script }
self._client.notify_all(message)
self._client.disconnect()
import os
parser = argparse.ArgumentParser()
parser.add_argument("-i",
"--input",
required=True,
metavar="file",
help="input JHV request file")
parser.add_argument("-value",
help="Send request as message value",
action="store_true")
args = parser.parse_args()
input_file = os.path.abspath(args.input)
client = SAMPIntegratedClient()
client.connect()
params = {}
if args.value:
with open(input_file, "r") as f:
params["value"] = f.read()
else:
params["url"] = input_file
message = {}
message["samp.mtype"] = "jhv.load.request"
message["samp.params"] = params
client.notify_all(message)
class ClientRunner(object):
#class ClientRunner(QThread):
def __init__(self, iface, pinstance):
self.iface = iface
# self.dlg = VOScriptReceiverDialog()
self.dlg = ClientRunnerDialog()
self.MSG = self.dlg.label.setText
self.ProjInstance = pinstance
self.root = self.ProjInstance.layerTreeRoot()
self.connectionState = False
self.dlg.connectBtn.clicked.connect(self.switchCState)
def capCommand(self, *args, **kwargs):
MSG = self.MSG
self.cli = SAMPIntegratedClient()
self.cli.connect()
self.r = Receiver(self.cli)
MSG('Binding methods')
#=> case MTYPE: qgis.message
def qMessage():
MSG('Message: ' + self.r.params['script'])
#=> case MTYPE: qgis.load.vectorlayer
def qLoadVectorlayer(): # case MTYPE: qgis.load.vectorlayer
self.LoadVectorLayer(self.r.params['url'], self.r.params['name'])
#=> case MTYPE: table.load.votable
def qLoadVotable():
loadWMS = lambda vot: VOTableLoaderHelper.loadWMS(
vot, self.iface, self.root)
makeComplFeat = VOTableLoaderHelper.makeComplFeat
MSG('Loading VOtable\n from url: \n' + self.r.params['url'])
say('SAMP Params are: ' + str(self.r.params))
vot = Table.read(download_file(self.r.params['url'],
timeout=200)) #fixes timeout bug
if 'access_format' in vot.colnames:
say(str(vot.columns['access_format'][0])) #<+===
if b'application/x-wms' in vot.columns['access_format'][0]:
try:
loadWMS(vot)
except Exception:
self.MSG('OOPS something went wrong while loading WMS')
tb = traceback.format_exc()
say(tb)
finally:
return
mURL = tempfile.mkdtemp()
MSG("converting to GeoJSON")
say('Number of features to write: ' + str(len(vot)))
featList = []
for i in range(len(vot)):
self.MSG('writing number' + str(i))
featList.append(makeComplFeat(vot, i))
with open(mURL + '/vot.geojson', 'w') as f:
f.write(
geojson.dumps({
"type": "FeatureCollection",
"features": featList
}))
self.MSG('finished download, converting to SpatiaLite')
try:
vlayer = QgsVectorLayer(mURL + '/vot.geojson', "mygeojson",
"ogr")
except Exception:
self.MSG(
'OOPS something went wrong while creating a vector layer from geojson'
)
return
say("writing to SpatiaLite")
try:
QgsVectorFileWriter.writeAsVectorFormat(
vlayer, mURL + r"/vot.sqlite", "utf-8", None, "SpatiaLite")
except Exception:
self.MSG('OOPS something went wrong while writing SQLite')
return
say("loading SpatiaLite")
try:
vlayer = QgsVectorLayer(mURL + r"/vot.sqlite",
str(self.r.params['name']), "ogr")
except Exception:
self.MSG(
'OOPS something went wrong while creating a vector Layer')
return
# say(vot.meta['description']) #description is not available with complex queries
# vlayer = QgsVectorLayer( mURL+r"/vot.sqlite",str(vot.meta['description']),"ogr")
say("adding layer to canvas")
try:
self.addVLayerToCanvas(vlayer)
except Exception:
self.MSG(
'OOPS something went wrong while trying to add layer to canvas'
)
return
say("done")
mTypeDict = {
'qgis.message': qMessage,
'qgis.load.vectorlayer': qLoadVectorlayer,
'table.load.votable': qLoadVotable
}
map(self.bindSamp, mTypeDict.keys())
MSG("Disconnected")
while self.connectionState:
MSG("starting")
self.r.received = False
while not self.r.received and self.connectionState:
MSG("waiting")
ttime.sleep(2)
if self.connectionState:
mTypeDict[self.r.mtype]()
ttime.sleep(2)
def switchCState(self, *args, **kwargs):
sys.stdout.write('switching state')
say("Switching connection state")
self.connectionState = not self.connectionState
say("New state is " + str(self.connectionState))
if self.connectionState:
self.tc = threading.Thread(name="client",
target=self.capCommand,
args=(self, ))
self.tc.start()
else:
self.cli.disconnect()
self.MSG('Disconnected')
def bindSamp(self, MType):
self.cli.bind_receive_call(MType, self.r.receive_call)
self.cli.bind_receive_notification(MType, self.r.receive_notification)
def addVLayerToCanvas(self, vlayer):
self.iface.mapCanvas().freeze()
QgsMapLayerRegistry.instance().addMapLayer(
vlayer) # order is importaint here
# self.root.addLayer(vlayer)
self.root.insertLayer(0, vlayer)
QgsMapLayerRegistry.instance().reloadAllLayers()
self.iface.mapCanvas().freeze(False)
def run(self):
self.dlg.show()
# self.MSG("hello")
self.MSG("Disconnected")
result = self.dlg.exec_()
if self.connectionState:
self.cli.disconnect(
) # if user closes window - call disconnect to make sure
def capCommand(self, *args, **kwargs):
MSG = self.MSG
self.cli = SAMPIntegratedClient()
self.cli.connect()
self.r = Receiver(self.cli)
MSG('Binding methods')
#=> case MTYPE: qgis.message
def qMessage():
MSG('Message: ' + self.r.params['script'])
#=> case MTYPE: qgis.load.vectorlayer
def qLoadVectorlayer(): # case MTYPE: qgis.load.vectorlayer
self.LoadVectorLayer(self.r.params['url'], self.r.params['name'])
#=> case MTYPE: table.load.votable
def qLoadVotable():
loadWMS = lambda vot: VOTableLoaderHelper.loadWMS(
vot, self.iface, self.root)
makeComplFeat = VOTableLoaderHelper.makeComplFeat
MSG('Loading VOtable\n from url: \n' + self.r.params['url'])
say('SAMP Params are: ' + str(self.r.params))
vot = Table.read(download_file(self.r.params['url'],
timeout=200)) #fixes timeout bug
if 'access_format' in vot.colnames:
say(str(vot.columns['access_format'][0])) #<+===
if b'application/x-wms' in vot.columns['access_format'][0]:
try:
loadWMS(vot)
except Exception:
self.MSG('OOPS something went wrong while loading WMS')
tb = traceback.format_exc()
say(tb)
finally:
return
mURL = tempfile.mkdtemp()
MSG("converting to GeoJSON")
say('Number of features to write: ' + str(len(vot)))
featList = []
for i in range(len(vot)):
self.MSG('writing number' + str(i))
featList.append(makeComplFeat(vot, i))
with open(mURL + '/vot.geojson', 'w') as f:
f.write(
geojson.dumps({
"type": "FeatureCollection",
"features": featList
}))
self.MSG('finished download, converting to SpatiaLite')
try:
vlayer = QgsVectorLayer(mURL + '/vot.geojson', "mygeojson",
"ogr")
except Exception:
self.MSG(
'OOPS something went wrong while creating a vector layer from geojson'
)
return
say("writing to SpatiaLite")
try:
QgsVectorFileWriter.writeAsVectorFormat(
vlayer, mURL + r"/vot.sqlite", "utf-8", None, "SpatiaLite")
except Exception:
self.MSG('OOPS something went wrong while writing SQLite')
return
say("loading SpatiaLite")
try:
vlayer = QgsVectorLayer(mURL + r"/vot.sqlite",
str(self.r.params['name']), "ogr")
except Exception:
self.MSG(
'OOPS something went wrong while creating a vector Layer')
return
# say(vot.meta['description']) #description is not available with complex queries
# vlayer = QgsVectorLayer( mURL+r"/vot.sqlite",str(vot.meta['description']),"ogr")
say("adding layer to canvas")
try:
self.addVLayerToCanvas(vlayer)
except Exception:
self.MSG(
'OOPS something went wrong while trying to add layer to canvas'
)
return
say("done")
mTypeDict = {
'qgis.message': qMessage,
'qgis.load.vectorlayer': qLoadVectorlayer,
'table.load.votable': qLoadVotable
}
map(self.bindSamp, mTypeDict.keys())
MSG("Disconnected")
while self.connectionState:
MSG("starting")
self.r.received = False
while not self.r.received and self.connectionState:
MSG("waiting")
ttime.sleep(2)
if self.connectionState:
mTypeDict[self.r.mtype]()
ttime.sleep(2)
def __init__(self):
self.client = SAMPIntegratedClient()
self.tmp_files = []
def connect(self):
self.__client = SAMPIntegratedClient(name=self.__server_name,
metadata=self.sampMetadata())
self.__client.connect()
self.bind_to_server()
class SAMPManager():
__client = None
__received = False
__params = {}
__hub = None
__server_name = "frastro server"
__server_description = "frastro Web client"
__server_description_html = "<h1>frastro Web client</h1>"
__author = "Camilo E. Jimenez-Angel"
__instritution = "IAC"
__email_contact = "*****@*****.**"
__url_icon = "http://localhost:8000/static/img/frastro_icon.jpg"
def __init__(self, server_name=""):
# Instantiate the client and connect to the hub
self.__server_name = server_name if server_name != "" else self.__server_name
self.connect()
def starHubServer(self, web_profile=True):
if self.__hub is None:
self.__hub = SAMPHubServer(web_profile=web_profile,
label=self.__server_name)
self.__hub.start()
def receive_call(self, private_key, sender_id, msg_id, mtype, params,
extra):
self.__params = params
self.__received = True
self.__client.reply(msg_id, {
"samp.status": "samp.ok",
"samp.result": {}
})
def receive_notification(self, private_key, sender_id, mtype, params,
extra):
self.__params = params
self.__received = True
def bind_to_server(self):
# Listen for any instructions to load a table
self.__client.bind_receive_call("table.load.votable",
self.receive_call)
self.__client.bind_receive_notification("table.load.votable",
self.receive_notification)
def sampMetadata(self):
meta = {
"samp.name": self.__server_name,
"samp.description.text": self.__server_description,
"samp.description.html": self.__server_description_html,
"samp.icon.url": self.__url_icon,
"author.affiliation": self.__instritution,
"author.name": self.__author,
"author.email": self.__email_contact
}
return meta
def getRegisteredClients(self):
clients = self.__client.get_registered_clients()
run_clients = {}
for client in clients:
client_data = self.getMetadata(client)
run_clients[client] = client_data
return run_clients
def getMetadata(self, client_id):
return self.__client.get_metadata(client_id)
def sendTable(self, message, recipient="all"):
if recipient == "all":
self.__client.notify_all(message)
else:
self.__client.notify(recipient, message)
def connect(self):
self.__client = SAMPIntegratedClient(name=self.__server_name,
metadata=self.sampMetadata())
self.__client.connect()
self.bind_to_server()
def sendImage(self, params, id=""):
message = {}
message["samp.mtype"] = "image.load.fits"
message["samp.params"] = params
if id == "" or id == "all":
self.__client.notify_all(message)
else:
self.__client.notify(recipient_id=id, message=message)
def sendMessage(self, params, id=""):
message = {}
message["samp.mtype"] = "table.load.votable"
message["samp.params"] = params
if id == "" or id == "all":
self.__client.notify_all(message)
else:
self.__client.notify(recipient_id=id, message=message)
def disconnect(self):
self.__client.disconnect()
def __del__(self):
self.disconnect()
def __init__(self):
super(SAMPState, self).__init__()
self.hub = SAMPHubServer()
self.client = SAMPIntegratedClient()
self.add_callback('connected', self.on_connected)