def example():
"""
This is just an example. Cut and paste that on the python prompt.
It can also be run as specplot.example().
"""
import numpy as np
import matplotlib.pyplot as plt
from astropy import wcs
from astrodata import AstroData
ad = AstroData('JHK.fits')
x_values = np.arange(ad.get_key_value('NAXIS1'))
wcs_ad = wcs.WCS(ad.header.tostring())
wlen = wcs_ad.wcs_pix2world(zip(x_values), 0)
plt.plot(wlen, ad.data)
plt.xlabel('Wavelength [Angstrom]')
plt.ylabel('Counts')
plt.axis('tight')
plt.ylim(-100, 800)
plt.show()
ad.close()
#plt.axis[[-100,1000,ymin,ymax]]
def mktable_helper(tablename, auto=True, rawdir="./"):
"""
Create or append to an observation summary table.
This function is interactive and requires input from the users.
:param tablename: Filename for the table. If it exists it will
be extended.
:type tablename: str
:param auto: If True, get some of the information directly from
the FITS headers. [Default: True]
:type auto: boolean
:param rawdir: Path to raw data. Required for auto=True.
[Default: "./"]
:type rawdir: str
"""
import obstable
import os.path
if auto:
from astrodata import AstroData
# Create an ObsTable. If the file already exists on disk,
# then read it. Otherwise, leave it empty.
# Error handling: If the file exists but there's an read error,
# raise, otherwise assume that you are creating a new file.
table = obstable.ObsTable()
table.filename = tablename
try:
table.read_table()
except IOError:
if os.path.exists(tablename):
print "Error reading table %s\n" % tablename
raise
else:
print "New table will be created."
# Start the prompting the user and the data for the information
# that needs to go in the table.
user_not_done = True
while user_not_done:
user_inputs = {}
if auto:
filename_not_known = True
# Get list of prompts for user or data supplied information.
req_input_list = get_req_input_list()
# Loop through record elements
for input_request in req_input_list:
if (not input_request['in_hdr'] or not auto):
# if auto and this is a Science entry, get the targetname from
# the header. If not Science, then you need to prompt user.
if auto and input_request['id'] == 'targetname' and \
user_inputs.has_key('datatype') and \
user_inputs['datatype'] == 'Science':
input_value = query_header(ad, input_request['id'])
else:
# prompt the user
input_value = raw_input(input_request['prompt'])
user_inputs[input_request['id']] = input_value
# Assume that the user has a brain.
# Probe only the first file in 'filerange' since all the
# files in 'filerange' should be similar.
#
# Once we know the name of the first MEF file, open it
# and keep it open until we're done requesting inputs
# (instead of opening and closing it every time).
if auto and filename_not_known:
if user_inputs.has_key('rootname') and \
user_inputs.has_key('filerange'):
# parse filerange, build filename (with rawdir path)
filenumbers = parse_filerange(user_inputs['filerange'])
filename = "%sS%04d.fits" % \
(user_inputs['rootname'], filenumbers[0])
filename = os.path.join(rawdir, filename)
# open ad
ad = AstroData(filename)
filename_not_known = False
else:
# get value from header
input_value = query_header(ad, input_request['id'])
user_inputs[input_request['id']] = input_value
if auto:
ad.close()
# Create record
new_record = create_record(user_inputs)
# Append to table
table.add_records_to_table(new_record)
# Prompt user: add another entry?
answer = raw_input('Add another entry (y/n): ')
user_not_done = ((answer=='y') or False)
# All the info is now in the ObsTable.
# Write the ObsTable to disk and close everything, we're done.
table.write_table()
table.pretty_table()
return
def test_method_close_3():
ad = AstroData(TESTFILE)
ad.close()
with pytest.raises(TypeError):
ad[0]
def test_method_close_2():
ad = AstroData(TESTFILE)
ad.close()
with pytest.raises(AstroDataError):
ad.append(moredata=hdu1)
def test_method_close_1():
ad = AstroData(TESTFILE)
ad.close()
assert not ad.hdulist
mem.memtrack("testmemprofile", lineno()); line += 1
ad = AstroData("data/N20131223S0243.fits")
mem.memtrack("testmemprofile", lineno()); line += 1
if True:
datas = []
for ext in ad:
mem.memtrack("data pull in %s,%d" % (ext.extname(), ext.extver()), line); line += 1
#print np.median(ext.data)
#malloc = np.ones((2000,2000), dtype = np.float32)
datas.append(ext.data)
mem.memtrack("before ad.write(..)", lineno());
ad.write("tmp.fits", clobber = True)
mem.memtrack("before ad.close()", lineno());
ad.close()
mem.memtrack("before del(ad)", lineno());
del(ad)
mem.memtrack("sleep .25 seconds", lineno());
time.sleep(.25)
mem.memtrack("end sleep .25 seconds", lineno());
def mktable_helper(tablename, auto=True, rawdir="./"):
"""
Create or append to an observation summary table.
This function is interactive and requires input from the users.
:param tablename: Filename for the table. If it exists it will
be extended.
:type tablename: str
:param auto: If True, get some of the information directly from
the FITS headers. [Default: True]
:type auto: boolean
:param rawdir: Path to raw data. Required for auto=True.
[Default: "./"]
:type rawdir: str
"""
from klpyastro.utils import obstable
import os.path
# TODO: change to new astrodata when ready
if auto:
from astrodata import AstroData
# Create an ObsTable. If the file already exists on disk,
# then read it. Otherwise, leave it empty.
# Error handling: If the file exists but there's an read error,
# raise, otherwise assume that you are creating a new file.
table = obstable.ObsTable()
table.filename = tablename
try:
table.read_table()
except IOError:
if os.path.exists(tablename):
print("Error reading table %s\n" % tablename)
raise
else:
print("New table will be created.")
# Start the prompting the user and the data for the information
# that needs to go in the table.
user_not_done = True
while user_not_done:
user_inputs = {}
if auto:
filename_not_known = True
# Get list of prompts for user or data supplied information.
req_input_list = get_req_input_list()
# Loop through record elements
for input_request in req_input_list:
if not input_request['in_hdr'] or not auto:
# if auto and this is a Science entry, get the targetname from
# the header. If not Science, then you need to prompt user.
if auto and input_request['id'] == 'targetname' and \
'datatype' in user_inputs and \
user_inputs['datatype'] == 'Science':
input_value = query_header(ad, input_request['id'])
else:
# prompt the user
try:
input = raw_input
except NameError:
pass
input_value = input(input_request['prompt'])
user_inputs[input_request['id']] = input_value
# Assume that the user has a brain.
# Probe only the first file in 'filerange' since all the
# files in 'filerange' should be similar.
#
# Once we know the name of the first MEF file, open it
# and keep it open until we're done requesting inputs
# (instead of opening and closing it every time).
if auto and filename_not_known:
if 'rootname' in user_inputs and 'filerange' in user_inputs:
# parse filerange, build filename (with rawdir path)
filenumbers = parse_filerange(user_inputs['filerange'])
filename = "%sS%04d.fits" % \
(user_inputs['rootname'], filenumbers[0])
filename = os.path.join(rawdir, filename)
# open ad
ad = AstroData(filename)
filename_not_known = False
else:
# get value from header
input_value = query_header(ad, input_request['id'])
user_inputs[input_request['id']] = input_value
if auto:
ad.close()
# Create record
new_record = create_record(user_inputs)
# Append to table
table.add_records_to_table(new_record)
# Prompt user: add another entry?
try:
input = raw_input
except NameError:
pass
answer = input('Add another entry (y/n): ')
user_not_done = ((answer == 'y') or False)
# All the info is now in the ObsTable.
# Write the ObsTable to disk and close everything, we're done.
table.write_table()
table.pretty_table()
return
def test_method_close_3():
ad = AstroData(TESTFILE)
ad.close()
with pytest.raises(TypeError):
ad[0]
def test_method_close_2():
ad = AstroData(TESTFILE)
ad.close()
with pytest.raises(AstroDataError):
ad.append(moredata=hdu1)
def test_method_close_1():
ad = AstroData(TESTFILE)
ad.close()
assert not ad.hdulist
