AstroToolkit 1.0.0__py3-none-any.whl

AstroToolkit/Surveys/SkyMapper.py

@@ -0,0 +1,215 @@
+import pandas as pd
+from astropy.table import Table
+from astropy.io import fits
+from astropy.visualization import PercentileInterval, AsinhStretch
+from io import BytesIO
+import PIL
+from PIL import Image
+import requests
+import numpy as np
+from astropy.wcs import WCS
+import warnings
+from astropy.utils.exceptions import AstropyWarning
+import math
+import astropy
+import re
+from bokeh.plotting import figure
+from bokeh.models import Range1d
+
+#Ignore warning about deprecated header
+warnings.simplefilter('ignore', category=AstropyWarning)
+
+def get_image(ra,dec,size=30,band='g'):
+	service='https://api.skymapper.nci.org.au/public/siap/dr2/query'
+	url=f'{service}?POS={ra},{dec}&SIZE={size},{size}&BAND={band}&FORMAT=image/fits&VERB=3&INTERSECT=covers&RESPONSEFORMAT=CSV'
+
+	try:
+		table=pd.read_csv(url)
+		table=Table.from_pandas(table)
+	except:
+		print('[SkyMapper: get_image_data] Error: experiencing issues with SkyMapper.')
+		return None, None, None
+	
+	if len(table)>0:
+		urlMain=table['get_image'][0]
+	else:
+		print('[SkyMapper: get_image_data] Error: no SkyMapper images found using given fields.')
+		return None, None, None
+	
+	# Need to add filter check functionality
+	'''
+	shortnames=[]
+	for i in range(0,len(table)):
+		shortnames.append(table['shortname'][i])
+	
+	missing_filters=[]
+	if len(table)!=len(band):
+		for i in range(0,len(band)):
+			filterCheck='.'+band[i]+'.'
+			if any(filterCheck in shortname for shortname in shortnames):
+				pass
+			else:
+				print('[PanSTARRS: get_image_data] Note:  no PanSTARRS data in '+band[i]+' band')
+				missing_filters.append(band[i])
+				
+	for i in range(0,len(missing_filters)):
+		band=band.replace(missing_filters[i],'')
+	'''
+		
+	try:
+		r=requests.get(urlMain,timeout=15)
+		if r.status_code!=200:
+			print('[SkyMapper: get_image_data] Error: experiencing issues with SkyMapper.')
+			return None, None, None
+	except:
+		print('[SkyMapper: get_image_data] Error: experiencing issues with SkyMapper.')
+		return None, None, None
+	
+	try:
+		fh=fits.open(BytesIO(r.content))
+		fitsImage=fh[0].data
+		image_header=fh[0].header
+		fitsImage[np.isnan(fitsImage)]=0.0
+		transform=AsinhStretch()+PercentileInterval(95)
+		image=transform(fitsImage)
+			
+		if not isinstance(image,np.ndarray):
+			print('[SkyMapper: get_image_data] Error: no SkyMapper images found using given fields.')
+			return None, None, None
+			
+		return image, image_header, band
+	
+	except:
+		print('[SkyMapper: get_image_data] Error: no SkyMapper images found using given fields.')
+		return None, None, None
+
+def get_info(ra,dec,size=30,band='g'):
+	ra,dec,size,sizeAS,band=input_management(ra=ra,dec=dec,size=size,band=band)
+
+	image_data=get_image(ra=ra,dec=dec,size=size,band=band)[1]
+	
+	if not isinstance(image_data,astropy.io.fits.header.Header):
+		return None, None
+	
+	wcs=WCS(image_data)
+	
+	mjd=image_data['MJD-OBS']
+	
+	return wcs, mjd
+
+def input_management(ra,dec,size=30,band='g'):
+	if len(band)!=len(set(band)):
+		raise Exception('duplicate detected in filter selection')
+
+	if not isinstance(ra,float):
+		try:
+			ra=float(ra)
+		except:
+			raise Exception('object RA must be a float or an integer')
+	if not isinstance(dec,float):
+		try:
+			dec=float(dec)
+		except:
+			raise Exception('object DEC must be a float or an integer')
+	
+	band=band.lower()
+	
+	if isinstance(size,int):
+		pass
+	else:
+		raise Exception('size must take an integer value')
+
+	if size>600:
+		raise Exception('SkyMapper image takes a maximum size of 10 arcmin')
+		
+	sizeAS=size
+	size=size/3600
+	
+	if re.match('^[grizuv]+$', band):
+			pass
+	else:
+		raise Exception('bands must be in list: [g,r,i,z,u,v]')
+	
+	band=list(band)
+	temp_string=''
+	for i in range(0,len(band)):
+		temp_string+=(band[i]+',')
+	band=temp_string[:-1]
+
+	return ra,dec,size,sizeAS,band
+
+def get_plot(ra,dec,size=30,band='g'):
+	ra,dec,size,sizeAS,band=input_management(ra,dec,size=size,band=band)
+
+	# Create axes and plot image
+	plot=figure(width=400,height=400,title=f'SkyMapper Image ({sizeAS}")')
+	# Fixes scaling issue
+	plot.min_border=75
+
+	plot.xgrid.grid_line_color=None
+	plot.ygrid.grid_line_color=None	
+
+	image,image_data,_=get_image(ra=ra,dec=dec,size=size,band=band)
+	
+	if not isinstance(image,np.ndarray) or not isinstance(image_data,astropy.io.fits.header.Header):
+		return None
+
+	# Get x and y limit (in pixels) from image header
+	xlim=image_data['NAXIS1']
+	ylim=image_data['NAXIS2']
+	
+	# Get points on axes in world coordinates (deg)
+	points=[]
+	wcs=WCS(image_data)
+
+	# Get array of pixels in x and y
+	x_points=np.arange(start=0,stop=xlim+1,step=1)
+	y_points=np.arange(start=0,stop=ylim+1,step=1)
+
+	# Apply transformation to coordinates
+	coords=wcs.all_pix2world(x_points,y_points,1)
+	x_points,y_points=coords[0],coords[1]
+	
+	# Get image size in degrees
+	x_range=max(x_points)-min(x_points)
+	y_range=max(y_points)-min(y_points)
+
+	plot.x_range=Range1d(max(x_points),min(x_points))
+	plot.y_range=Range1d(min(y_points),max(y_points))
+
+	plot.image(image=[image],x=x_points[0],y=y_points[0],dw=x_range,dh=y_range,palette='Greys256',level="image",origin='bottom_right',anchor='bottom_right')
+
+	return plot
+
+def SkyMapperQueryCoords(ObjRa,ObjDec,radius=3):
+	radius=radius/3600
+
+	#Had to use JSON format to get this to work, the CSV format used is not easily formattable by pandas
+	url=f'https://skymapper.anu.edu.au/sm-cone/public/query?RA={ObjRa}&DEC={ObjDec}&SR={radius}&RESPONSEFORMAT=CSV'
+	try:
+		r=requests.get(url)
+	except:
+		print('[SkyMapper: SkyMapperQueryCoords] Error: experiencing issues with SkyMapper.')
+		return None
+	
+	if r.status_code!=200:
+		print('[SkyMapper: SkyMapperQueryCoords] Error: experiencing issues with SkyMapper.')
+		return None
+
+	data=BytesIO(r.content)
+	try:
+		data=pd.read_csv(data)
+	except:
+		print('[SkyMapper: SkyMapperQueryCoords] Note: No data found using given coordinates')
+	
+	return data
+	
+def SkyMapperGetPhotometryCoords(ObjRa,ObjDec,radius=3):
+	data=SkyMapperQueryCoords(ObjRa,ObjDec,radius=radius)
+	
+	if not isinstance(data,pd.DataFrame) or data.empty:
+		print('[SkyMapper: SkyMapperGetPhotometryCoords] Note: No SkyMapper data at given coordinates.')
+		return None
+	
+	photometry=data[['raj2000','dej2000','object_id','g_psf','e_g_psf','r_psf','e_r_psf','i_psf','e_i_psf','z_psf','e_z_psf','u_psf','e_u_psf','v_psf','e_v_psf']].copy()
+	return photometry

AstroToolkit/Surveys/TWOMASS.py

@@ -0,0 +1,45 @@
+from astroquery.vizier import Vizier
+import astropy.coordinates as coord
+import pandas as pd
+from astropy import units as u
+
+catalogue_name='II/246/out'
+
+Vizier.ROW_LIMIT = -1
+
+def get_data(ra,dec,radius=3):
+	data=[]
+	
+	if not isinstance(radius,int) and not isinstance(radius,float):
+		raise Exception('search radius must be a float or an integer')
+	
+	if not isinstance(ra,float):
+		try:
+			ra=float(ra)
+		except:
+			raise Exception('object RA must be a float or an integer')
+	if not isinstance(dec,float):
+		try:
+			dec=float(dec)
+		except:
+			raise Exception('object DEC must be a float or an integer')
+	
+	v=Vizier(columns=['**'])
+
+	#Sends Vizier query, can return multiple objects in given search radius
+	data.append(v.query_region(coord.SkyCoord(ra=ra,dec=dec,unit=(u.deg,u.deg),frame='icrs'),width=radius*u.arcsec,catalog=catalogue_name))
+	if len(data[0])==0:
+		print('[TWOMASS: get_data] Error: no 2MASS data found at given coordinates')
+		return None
+	data=data[0][0].to_pandas()
+	data=data.reset_index(drop=True)
+	return data
+	
+def get_photometry(ra,dec,radius=3):
+	TWOMASSdata=get_data(ra,dec,radius=radius)
+	if not isinstance(TWOMASSdata,pd.DataFrame) or TWOMASSdata.empty:
+		return None
+	
+	photometry=TWOMASSdata[['RAJ2000','DEJ2000','_2MASS','Jmag','e_Jmag','Hmag','e_Hmag','Kmag','e_Kmag']].copy()
+
+	return photometry

AstroToolkit/Surveys/WISE.py

@@ -0,0 +1,45 @@
+from astroquery.vizier import Vizier
+import astropy.coordinates as coord
+import pandas as pd
+from astropy import units as u
+
+catalogue_name='II/311/wise'
+
+Vizier.ROW_LIMIT = -1
+
+def get_data(ra,dec,radius=3):
+	data=[]
+	
+	if not isinstance(radius,int) and not isinstance(radius,float):
+		raise Exception('search radius must be a float or an integer')
+	
+	if not isinstance(ra,float):
+		try:
+			ra=float(ra)
+		except:
+			raise Exception('object RA must be a float or an integer')
+	if not isinstance(dec,float):
+		try:
+			dec=float(dec)
+		except:
+			raise Exception('object DEC must be a float or an integer')
+	
+	v=Vizier(columns=['**'])
+
+	#Sends Vizier query, can return multiple objects in given search radius
+	data.append(v.query_region(coord.SkyCoord(ra=ra,dec=dec,unit=(u.deg,u.deg),frame='icrs'),width=radius*u.arcsec,catalog=catalogue_name))
+	if len(data[0])==0:
+		print('[WISE: get_data] Error: no WISE data found at given coordinates')
+		return None
+	data=data[0][0].to_pandas()
+	data=data.reset_index(drop=True)
+	return data
+	
+def get_photometry(ra,dec,radius=3):
+	WISEdata=get_data(ra,dec,radius=radius)
+	if not isinstance(WISEdata,pd.DataFrame) or WISEdata.empty:
+		return None
+	
+	photometry=WISEdata[['RAJ2000','DEJ2000','WISE','W1mag','e_W1mag','W2mag','e_W2mag','W3mag','e_W3mag','W4mag','e_W4mag']].copy()
+
+	return photometry

AstroToolkit/Surveys/ZTF.py

@@ -0,0 +1,206 @@
+import requests
+import pandas as pd
+from io import BytesIO
+import re
+import numpy as np
+from requests.adapters import HTTPAdapter, Retry
+import matplotlib
+from bokeh.plotting import figure, show
+from bokeh.models import Whisker, ColumnDataSource
+from bokeh.transform import linear_cmap
+from bokeh.layouts import gridplot
+
+def getData(ra,dec,radius=3):
+	#Filters inputs
+	if not isinstance(ra,float):
+		try:
+			ra=float(ra)
+		except:
+			raise Exception('object RA must be a float or an integer')
+	if not isinstance(radius,float):
+		try:
+			radius=float(radius)
+		except:
+			raise Exception('search radius must be a float or an integer')
+	if not isinstance(dec,float):
+		try:
+			dec=float(dec)
+		except:
+			raise Exception('object DEC must be a float or an integer') 
+	
+	#Convert radius into degrees
+	radius=radius/3600
+	
+	#Perform query
+	service='https://irsa.ipac.caltech.edu/cgi-bin/ZTF/nph_light_curves'
+	url=f'{service}?POS=CIRCLE {ra} {dec} {radius}&BANDNAME=g,r,i&FORMAT=CSV'
+	
+	s=requests.Session()
+	retries=Retry(total=5,backoff_factor=0.1,status_forcelist=[500,502,503,504])
+	s.mount('http://',HTTPAdapter(max_retries=retries))
+	try:
+		r=s.get(url,timeout=15)
+	except:
+		print('[ZTF: getData] Error: experiencing issues with ZTF.')
+		return [None, None, None]
+	
+	if r.status_code!=200:
+		print('[ZTF: getData] Error: experiencing issues with ZTF.')
+		return [None, None, None]
+
+	#Convert to pandas array (containing all bands)
+	data=pd.read_csv(BytesIO(r.content))
+	if len(data)==0:
+		print('[ZTF: getData] Error:  no ZTF data found using given fields')
+		return [None, None, None]
+	
+	#Split into separate bands
+	gData=data.loc[data['filtercode']=='zg']
+	rData=data.loc[data['filtercode']=='zr']
+	iData=data.loc[data['filtercode']=='zi']
+	
+	gData,rData,iData=gData.reset_index(drop=True),rData.reset_index(drop=True),iData.reset_index(drop=True)
+	
+	if gData.empty:
+		gData=None
+	if rData.empty:
+		rData=None
+	if iData.empty:
+		iData=None
+
+	Data=[gData,rData,iData]
+	
+	return Data
+	
+def getLightCurve(ra,dec,radius=3,return_raw=False):
+	Data=getData(ra=ra,dec=dec,radius=radius)
+	
+	try:
+		if Data==None:
+			if return_raw==False:
+				return None
+			else:
+				return None, None, None
+	except:
+		pass
+	
+	#Check if there is any returned data
+	if not isinstance(Data[0],pd.DataFrame) and not isinstance(Data[1],pd.DataFrame) and not isinstance(Data[2],pd.DataFrame):
+		if return_raw==False:
+			return None
+		else:
+			return None, None, None
+
+	gBand,rBand,iBand=False,False,False
+	
+	g_colourmap=matplotlib.colors.LinearSegmentedColormap.from_list('',['greenyellow','forestgreen','greenyellow'])
+	g_palette=[matplotlib.colors.rgb2hex(c) for c in g_colourmap(np.linspace(0,1,255))]	
+
+	r_colourmap=matplotlib.colors.LinearSegmentedColormap.from_list('',['yellow','red','yellow'])
+	r_palette=[matplotlib.colors.rgb2hex(c) for c in r_colourmap(np.linspace(0,1,255))]	
+
+	i_colourmap=matplotlib.colors.LinearSegmentedColormap.from_list('',['aqua','royalblue','aqua'])
+	i_palette=[matplotlib.colors.rgb2hex(c) for c in i_colourmap(np.linspace(0,1,255))]	
+
+	#Separate data into different bands, find number of subplots needed and which bands have data
+	if isinstance(Data[0],pd.DataFrame):
+		gData=Data[0]
+		g_hjd=gData.loc[:,'hjd'].tolist()
+		g_hjd_min=min(g_hjd)
+		g_hjd=[x-g_hjd_min for x in g_hjd]
+		g_mag=gData.loc[:,'mag'].tolist()
+		g_mag=np.array(g_mag)
+		g_mag_err=gData.loc[:,'magerr'].tolist()
+		gBand=True
+	if isinstance(Data[1],pd.DataFrame):
+		rData=Data[1]
+		r_hjd=rData.loc[:,'hjd'].tolist()
+		r_hjd_min=min(r_hjd)
+		r_hjd=[x-r_hjd_min for x in r_hjd]
+		r_mag=rData.loc[:,'mag'].tolist()
+		r_mag=np.array(r_mag)
+		r_mag_err=rData.loc[:,'magerr'].tolist()
+		rBand=True
+	if isinstance(Data[2],pd.DataFrame):
+		iData=Data[2]
+		i_hjd=iData.loc[:,'hjd'].tolist()
+		i_hjd_min=min(i_hjd)
+		i_hjd=[x-i_hjd_min for x in i_hjd]
+		i_mag=iData.loc[:,'mag'].tolist()
+		i_mag=np.array(i_mag)
+		i_mag_err=iData.loc[:,'magerr'].tolist()
+		iBand=True
+	
+	#Plot data
+	if gBand:
+		gPlot=figure(width=400,height=400,title='ZTF g Lightcurve',x_axis_label=r'\[\text{Observation Date [days]}\]',y_axis_label=r'\[\text{g}\]')
+		
+		gPlot.y_range.flipped=True
+
+		upper=[x+e for x,e in zip(g_mag,g_mag_err)]
+		lower=[x-e for x,e in zip(g_mag,g_mag_err)]
+		source=ColumnDataSource(data=dict(hjd=g_hjd,mag=g_mag,upper=upper,lower=lower))
+
+		g_mapper=linear_cmap(field_name='mag',palette=g_palette,low=min(g_mag),high=max(g_mag))
+
+		gPlot.circle(x='hjd',y='mag',source=source,color=g_mapper)
+		errors=Whisker(source=source,base='hjd',upper='upper',lower='lower',line_width=0.5,line_color='forestgreen')
+		errors.upper_head.line_width,errors.lower_head.line_width=0.5,0.5
+		errors.upper_head.size,errors.lower_head.size=3,3
+		errors.upper_head.line_color,errors.lower_head.line_color='forestgreen','forestgreen'		
+
+		gPlot.add_layout(errors)
+	else:
+		gPlot=None
+
+	if rBand:
+		rPlot=figure(width=400,height=400,title='ZTF r Lightcurve',x_axis_label=r'\[\text{Observation Date [days]}\]',y_axis_label=r'\[\text{r}\]')
+		
+		rPlot.y_range.flipped=True
+
+		upper=[x+e for x,e in zip(r_mag,r_mag_err)]
+		lower=[x-e for x,e in zip(r_mag,r_mag_err)]
+		source=ColumnDataSource(data=dict(hjd=r_hjd,mag=r_mag,upper=upper,lower=lower))
+
+		r_mapper=linear_cmap(field_name='mag',palette=r_palette,low=min(r_mag),high=max(r_mag))
+
+		rPlot.circle(x='hjd',y='mag',source=source,color=r_mapper)
+		errors=Whisker(source=source,base='hjd',upper='upper',lower='lower',line_width=0.5,line_color='red')
+		errors.upper_head.line_width,errors.lower_head.line_width=0.5,0.5
+		errors.upper_head.size,errors.lower_head.size=3,3
+		errors.upper_head.line_color,errors.lower_head.line_color='red','red'		
+
+		rPlot.add_layout(errors)
+	else:
+		rPlot=None
+		
+	if iBand:
+		iPlot=figure(width=400,height=400,title='ZTF i Lightcurve',x_axis_label=r'\[\text{Observation Date [days]}\]',y_axis_label=r'\[\text{i}\]')
+		
+		iPlot.y_range.flipped=True
+
+		upper=[x+e for x,e in zip(i_mag,i_mag_err)]
+		lower=[x-e for x,e in zip(i_mag,i_mag_err)]
+		source=ColumnDataSource(data=dict(hjd=i_hjd,mag=i_mag,upper=upper,lower=lower))
+
+		i_mapper=linear_cmap(field_name='mag',palette=i_palette,low=min(i_mag),high=max(i_mag))
+
+		iPlot.circle(x='hjd',y='mag',source=source,color=i_mapper)
+		errors=Whisker(source=source,base='hjd',upper='upper',lower='lower',line_width=0.5,line_color='royalblue')
+		errors.upper_head.line_width,errors.lower_head.line_width=0.5,0.5
+		errors.upper_head.size,errors.lower_head.size=3,3
+		errors.upper_head.line_color,errors.lower_head.line_color='royalblue','royalblue'
+		
+		iPlot.add_layout(errors)
+	else:
+		iPlot=None
+
+	if return_raw==True:
+		return gPlot,rPlot,iPlot
+	else:
+		grid=gridplot([[gPlot,rPlot,iPlot]],width=400,height=400)
+		return grid
+
+if __name__=='__main__':
+	plot=getLightCurve(245.4470133276900,-22.8862182469700)
+	show(plot)