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io.py
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io.py
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# -*- coding: utf-8 -*-
import glob
import numpy as np
import pandas as pd
import paramiko
import os
import sqlite3
import folium
from geopy.point import Point
from fastkml.kml import KML
from .astronomy import FitsOps
from .astronomy import AstCalc
from datetime import datetime
from astropy.table import Table
import datetime as dt
from termcolor import colored
import smtplib
from email.mime.multipart import MIMEMultipart
from email.mime.text import MIMEText
from email.header import Header
import requests, json
import geopandas as gpd
class FileOps:
def make_date(self, datestr, datefrmt='%Y-%m-%d'):
return datetime.strptime(datestr.decode('ascii'), datefrmt)
def read_file_as_array(self, file_name):
"""
Reads text file into numpy array.
@param file_name: Text file name and path
@type file_name: str
@return: array
"""
try:
return (np.genfromtxt(file_name,
comments='#',
delimiter=' | ',
dtype="U"))
except Exception as e:
print(e)
def read_table_as_array(self, file_name, delimiter=None):
"""
Reads A-Track result file into numpy array.
@param file_name: Text file name and path
@type file_name: str
@return: array
"""
data = np.genfromtxt(file_name,
delimiter=delimiter,
dtype="|U30")
return data
def read_sch_file(self, file_name):
"""
Reads text file into numpy array.
@param file_name: Text file name and path
@type file_name: str
@return: array
"""
try:
with open(file_name) as fin:
sch_dict = {}
for line in fin:
keyword_value = line.replace("\n", "")
if "=" in keyword_value:
keyword, value = keyword_value.split("=")
else:
continue
if "TITLE" in keyword:
sch_dict["TITLE"] = value.strip()
elif "OBSERVER" in keyword:
sch_dict["OBSERVER"] = value.strip()
elif "BLOCK" in keyword:
sch_dict["BLOCK"] = value.strip()
elif "SOURCE" in keyword:
sch_dict["SOURCE"] = value.strip()
elif " RA" in keyword:
sch_dict["RA"] = value.strip()
elif "DEC" in keyword:
sch_dict["DEC"] = value.strip()
elif "EPOCH" in keyword:
sch_dict["EPOCH"] = value.strip()
elif "FILTER" in keyword:
subsets = value.strip()
sch_dict["FILTER"] = subsets.replace(
"'", "").strip().split(",")
elif "DURATION" in keyword:
duration = value.strip()
sch_dict["DURATION"] = duration.replace(
"'", "").strip().split(",")
elif "BINNING" in keyword:
sch_dict["BINNING"] = value.strip()
elif "SUBIMAGE" in keyword:
sch_dict["SUBIMAGE"] = value.strip()
elif "LSTDELTA" in keyword:
sch_dict["LSTDELTA"] = value.strip()
elif "PRIORITY" in keyword:
sch_dict["PRIORITY"] = value.strip()
elif "COMPRESS" in keyword:
sch_dict["COMPRESS"] = value.strip()
elif "IMAGEDIR" in keyword:
sch_dict["IMAGEDIR"] = value.strip()
elif " REPEAT" in keyword:
sch_dict["REPEAT"] = value.strip()
elif "BLOCKREPEAT" in keyword:
sch_dict["BLOCKREPEAT"] = value.strip()
return sch_dict
except Exception as e:
print(e)
return False
def print_sch_file(self, schs_path, dT=60, dF=4, dS=6, email_format=True,
pi_name=None, pi_surname=None, email_to=None, project_term=None):
"""
Reads text file into numpy array.
@param file_name: Text file name and path
@type file_name: str
@param dT: Time consumed for a single pointing
@type float
@param dF: Time consumed in changing the filters
@type float
@param dS: Time consumed in downloading the frame from CCD
@type float
@param email_format: Print e-mail format
@type str
@param pi_name: PI name
@type float
@param pi_surname: PI surname
@type str
@param email_to: Email to content
@type string
@param project_term: Project term
@type string
@return: array
"""
sch_files = sorted(glob.glob("{0}/*.sch".format(schs_path)))
project_proper = []
total_exposure_time = []
total_observation_time = []
exposures = []
filters = []
filter_dict = {"U": "U",
"B": "B",
"V": "V",
"R": "R",
"I": "I",
"C": "C",
"1": "u'",
"2": "g'",
"3": "r'",
"4": "i'",
"5": "z'",
"H": "H-alpha",}
sch_dict = {}
for file_name in sch_files:
sch_dict = self.read_sch_file(file_name)
filter_and_durations = []
durations = 0
for i, filter in enumerate(sch_dict['FILTER']):
try:
filter = filter_dict[filter]
except:
filter = "Filtre girilmedi!"
filter_and_durations.append(
"{0}({1})".format(filter, sch_dict['DURATION'][i]))
try:
durations += float(sch_dict['DURATION'][i])
except ValueError:
durations += 0
try:
exposures.append(float(sch_dict['DURATION'][i]))
except ValueError:
exposures.append(0)
filters.append(sch_dict['FILTER'][i])
total_exposure_time.append(durations * float(sch_dict['REPEAT']))
total_observation_time.append(
dT + (float(sch_dict['REPEAT']) * len(sch_dict['FILTER']) * (dF + dS)) +
(float(sch_dict['REPEAT']) * durations))
project_proper.append([sch_dict['SOURCE'], sch_dict['RA'], sch_dict['DEC'], " ".join(filter_and_durations),
sch_dict['REPEAT']])
pid = str(sch_dict['SOURCE']).split("_")[0]
project_proper_np = np.asarray(project_proper)
project_proper_tbl = Table(project_proper_np, names=('Nesne',
'RA',
'Dec',
'Filtre',
'Tekrar'))
project_proper_tbl['Nesne'].unit = ''
project_proper_tbl['RA'].unit = 'HH:MM:SS'
project_proper_tbl['Dec'].unit = 'DD:MM:SS'
project_proper_tbl['Filtre'].unit = 's'
project_proper_tbl['Tekrar'].unit = 'cnt'
project_proper_tbl = "".join(project_proper_tbl.pformat(html=True, max_lines=32, max_width=-1, align="<")).replace("table",
'table cellspacing="0" cellpadding="6" border="1"')
used_filters = sorted(set(filters))
# used_filters = ''
if '' in used_filters:
note = "Not: Filtre/Poz süreleri belirtilmemiş nesneleriniz bulunmaktadır. " \
"Lütfen en kısa sürede talep ettiğiniz filtre/poz sürelerini iletiniz."
note += "<br>"
else:
note = ""
if email_format is True:
if project_term is not None:
if "A" in project_term:
project_term = project_term + " (Şubat - Mayıs)"
elif "B" in project_term:
project_term = project_term + " (Haziran - Eylül)"
elif "C" in project_term:
project_term = project_term + " (Ekim - Ocak)"
message = "<strong>{pid}</strong> nolu projeniz kapsamında, <strong>{project_term}</strong> ".format(
pid=pid,
project_term=project_term)
message += "döneminde gözlenecek olan nesneleriniz TUG PTS sisteminde aşağıdaki gibi kayıtlıdır. " \
"Herhangi bir düzeltme talebinizin olmaması durumunda " \
"gözlemleriniz bu şekilde gerçekleştirilecektir."
else:
message = "Talep ettiğiniz değişiklik sisteme aşağıdaki gibi uygulanmıştır."
html = """\
<html>
<body>
<div style="margin-left: 1em">
<p>
Sayın <strong>{pi_name} {pi_surname}</strong>,<br><br>
{message}
<p style="color:red">
<br>
Sistemde bir uyumsuzluk olduğunu düşünüyorsanız lütfen bildiriniz.
</p>
</p>
Toplam nesne sayısı: <strong>{total_object_count}</strong>.
<br>
Toplam poz süresi: <strong>{total_exposure_time}</strong> saniye.
<br>
Toplam gözlem zamanı: <strong>{total_observation_time}</strong> saniye.
<br><br>
<div class="row">
<div class="col-md-5">
{project_table}
</div>
</div>
<p style="color:red">
{note}
</p>
<p>
Bilgilerinize sunar,
<br>
İyi çalışmalar dileriz.
<br><br>
</p>
TÜBİTAK Ulusal Gözlemevi (TUG) - Robotik T60 Gözlem Kontrol Sistemi (v2.0-beta) - © {year}
<br>
</div>
</body>
</html>
""".format(
pi_name=pi_name,
pi_surname=pi_surname,
message=message,
total_exposure_time=sum(total_exposure_time),
total_observation_time=sum(total_observation_time),
total_object_count=len(project_proper_np),
project_table=project_proper_tbl,
note=note,
year=datetime.today().year)
if email_to is not None:
self.send_email(receivers=[email_to],
subject="TUG Robotik T60 Teleskobu {0} Dönemi Nesne Kontrol Talebi - {1}".format(
project_term,
pid),
content=html)
return html
def list_all_exposures(self, schs_path):
"""
Reads text file into numpy array.
@param schs_path: SCH files path
@type schs_path: str
@return: list
"""
sch_files = sorted(glob.glob("{0}/*.sch".format(schs_path)))
project_proper = []
total_exposure_time = []
total_observation_time = []
exposures = []
filters = []
filter_dict = {"U": "U",
"B": "B",
"V": "V",
"R": "R",
"I": "I",
"C": "C",
"1": "u'",
"2": "g'",
"3": "r'",
"4": "i'",
"5": "z'",
"H": "H-alpha", }
for file_name in sch_files:
sch_dict = self.read_sch_file(file_name)
filter_and_durations = []
durations = 0
for i, filter in enumerate(sch_dict['FILTER']):
filter = filter_dict[filter]
filter_and_durations.append(
"{0}({1})".format(filter, sch_dict['DURATION'][i]))
try:
durations += float(sch_dict['DURATION'][i])
except ValueError:
durations += 0
try:
exposures.append(float(sch_dict['DURATION'][i]))
except ValueError:
exposures.append(0)
filters.append(sch_dict['FILTER'][i])
return sorted(set(filters)), sorted(set(exposures))
def list_pts_objects(self, project_term=None, telescope="t60",
key=None,
out_file_path="./"):
"""
Returns all objects from TUG PTS by project term.
Parameters
----------
project_term: str
Robotic T60 Telescope project term.
key: str
API key.
out_file_path: str
Out file path.
Returns
-------
'Talon sch files'
Example:
-------
"""
api_uri = "http://api.pts.trgozlemevleri.gov.tr/v1/{telescope}/projects/terms/{project_term}".format(
project_term=project_term, telescope=telescope)
headers = {
'Content-Type': 'application/json',
'PTS-API-KEY': str(key)
}
try:
data = requests.get(api_uri, headers=headers, timeout=1)
if (data.status_code != 200):
pass
except requests.exceptions.RequestException:
pass
except requests.exceptions.HTTPError as e:
return e
except requests.exceptions.ConnectionError as e:
return e
except requests.exceptions.Timeout as e:
return e
projects = data.json()['content']
# print(projects)
pts_ak_score_dict = {}
for project in projects:
# print(project['parent_id'], float(project['ak_score']))
if project['parent_id'] == 0:
pid = project['id']
else:
pid = project['parent_id']
print(project['objects'])
return True
def pts_to_sch_files(self, project_term=None,
key=None,
out_file_path="./"):
"""
Returns all objects from TUG PTS by project term.
Parameters
----------
project_term: str
Robotic T60 Telescope project term.
key: str
API key.
out_file_path: str
Out file path.
Returns
-------
'Talon sch files'
Example:
-------
"""
api_uri = "http://api.pts.trgozlemevleri.gov.tr/v1/t60/projects/terms/{project_term}".format(
project_term=project_term)
headers = {
'Content-Type': 'application/json',
'PTS-API-KEY': str(key)
}
try:
data = requests.get(api_uri, headers=headers, timeout=1)
if (data.status_code != 200):
pass
except requests.exceptions.RequestException:
pass
except requests.exceptions.HTTPError as e:
return e
except requests.exceptions.ConnectionError as e:
return e
except requests.exceptions.Timeout as e:
return e
projects = data.json()['content']
# print(projects)
pts_ak_score_dict = {}
for project in projects:
# print(project['parent_id'], float(project['ak_score']))
if project['parent_id'] == 0:
pid = project['id']
else:
pid = project['parent_id']
pts_ak_score_dict[pid] = float(project['ak_score'])
pts_ak_score_dict = {k: v for k, v in sorted(pts_ak_score_dict.items(), key=lambda item: item[1], reverse=True)}
priority_dict = {}
counter = 0
ak_score_check = None
for pid, ak_score in pts_ak_score_dict.items():
if ak_score_check != ak_score:
counter += 1
priority_dict[pid] = counter
ak_score_check = ak_score
print (pts_ak_score_dict)
print(priority_dict)
for project in projects:
if project['parent_id'] == 0:
pid = project['id']
else:
pid = project['parent_id']
objects = project['objects']
for object in objects:
target_name = object['name'].replace(".", "_")
target_name = target_name.replace("+", "_")
target_name = target_name.replace("-", "_")
target_name = target_name.replace("V*", "")
ra = object['ra']
dec = object['dec']
if "-" not in dec[0]:
if "+" not in dec[0]:
dec = "+" + object['dec']
subsets = []
durations = []
filter_names = object['filter_names']
pts_durations = object['durations']
for fw in filter_names:
fw_index = filter_names.index(fw)
if float(pts_durations[fw_index]) > 0:
duration = pts_durations[fw_index]
if "u" in fw:
fw = "1"
elif "g" in fw:
fw = "2"
elif "r" in fw:
fw = "3"
elif "i" in fw:
fw = "4"
elif "H-alpha" in fw:
fw = "H"
elif "z" in fw:
fw = "5"
subsets.append(fw)
durations.append(str(duration))
priority = priority_dict[pid]
repeat = object['repeat']
print(pid, target_name, ra, dec, ",".join(
subsets), ",".join(durations), str(priority), str(repeat))
self.create_sch_file(out_file_path=out_file_path,
pid=pid,
target_name=target_name,
ra=ra,
dec=dec,
subsets=",".join(subsets),
durations=",".join(durations),
priority=str(priority),
repeat=str(repeat))
return True
def csv_to_sch_files(self, csv_file, out_file_path="./", delimiter=",",
priority=[]):
"""
Reads object list and creates sch_files.
@param csv_file: Text file name and path
@type csv_file: str
@return: file
"""
objects = self.read_table_as_array(csv_file, delimiter=delimiter)
filters_in_wheel = ["C", "U", "B", "V", "R", "I",
"u", "g", "r", "i", "z", "H-alpha", "H-beta"]
for object in objects:
aco = AstCalc()
pid = object[0]
target_name = object[1].replace(".", "_")
target_name = target_name.replace("+", "_")
target_name = target_name.replace("-", "_")
ra = aco.deg2hmsdms(object[2], object[3]).split(" ")[0][:-3]
dec = aco.deg2hmsdms(object[2], object[3]).split(" ")[1][:-3]
subsets = []
durations = []
for fw in filters_in_wheel:
if fw in object[4]:
filters = object[4].split(";")
for filter_and_duration in filters:
if fw in filter_and_duration:
filter, duration = filter_and_duration.split("=")
filter = filter.replace("{", "")
duration = duration.replace("}", "")
subsets.append(filter)
durations.append(duration)
if len(priority) > 0:
prior = priority.index(int(pid)) + 1
else:
prior = 1
repeat = object[5]
print(pid, target_name, ra, dec, ",".join(
subsets), ",".join(durations), prior, repeat)
self.create_sch_file(out_file_path=out_file_path,
pid=pid,
target_name=target_name,
ra=ra,
dec=dec,
subsets=",".join(subsets),
durations=",".join(durations),
priority=prior,
repeat=repeat)
return True
def get_unique_filter_duration(self, csv_file, delimiter=","):
"""
Reads object list and returns filters and durations.
@param csv_file: Text file name and path
@type csv_file: str
@return: file
"""
objects = self.read_table_as_array(csv_file, delimiter=delimiter)
filters_in_wheel = ["C", "U", "B", "V", "R", "I",
"u", "g", "r", "i", "z", "H-alpha", "H-beta"]
subsets = []
durations = []
for object in objects:
aco = AstCalc()
for fw in filters_in_wheel:
if fw in object[4]:
filters = object[4].split(";")
for filter_and_duration in filters:
if fw in filter_and_duration:
filter, duration = filter_and_duration.split("=")
filter = filter.replace("{", "")
duration = duration.replace("}", "")
if filter not in subsets:
subsets.append(filter)
if float(duration) not in durations:
durations.append(float(duration))
return {'filters': subsets, 'durations': sorted(durations)}
def create_sch_file(self, out_file_path="./", pid="3141", target_name="tug", ra=None,
dec=None,
subsets="U,B,V,R,I",
durations="60,60,60,60,60",
priority=1,
repeat=1):
"""
Reads A-Track result file into numpy array.
@param file_name: Text file name and path
@type file_name: str
@return: array
"""
try:
sch_template = """! Generated by TUG/astrolib
TITLE = {0}_{1}
OBSERVER = 'TUG'
BLOCK = '1'
SOURCE = {0}_{1}
RA = {2}
DEC = {3}
EPOCH = 2000
FILTER = '{4}'
DURATION = '{5}'
BINNING = '1,1'
SUBIMAGE = '0,0,2048,2048'
LSTDELTA = '3'
PRIORITY = {6}
COMPRESS = 0
IMAGEDIR = '/usr/local/telescope/user/images'
REPEAT = {7}
/
BLOCKREPEAT = 1
""".format(pid,
target_name,
ra,
dec,
subsets,
durations,
priority,
repeat)
with open("{0}/{1}_{2}.sch".format(out_file_path,
pid, target_name), "w") as file:
file.write(sch_template)
file.close()
print(">>> {0}_{1}.sch file created in {2}".format(
pid, target_name, out_file_path))
return True
except Exception as e:
print(e)
return False
def sch_to_database(self, sch_file,
sqlite_file="db.sqlite3",
table_name="portal_schedule",
keywords=None):
print(">>> SCH2DB: {0}".format(sch_file))
if keywords is None:
keywords = ['source_name',
'ra',
'dec',
'epoch',
'filterU',
'filterB',
'filterV',
'filterR',
'filterI',
'filterC',
'priority',
'repeat',
'is_ongoing_project',
'project_id']
sch_dict = self.read_sch_file(sch_file)
filters = sch_dict['FILTER']
try:
u_filter = sch_dict['DURATION'][filters.index("U")]
except ValueError:
u_filter = 0
try:
b_filter = sch_dict['DURATION'][filters.index("B")]
except ValueError:
b_filter = 0
try:
v_filter = sch_dict['DURATION'][filters.index("V")]
except ValueError:
v_filter = 0
try:
r_filter = sch_dict['DURATION'][filters.index("R")]
except ValueError:
r_filter = 0
try:
i_filter = sch_dict['DURATION'][filters.index("I")]
except ValueError:
i_filter = 0
try:
c_filter = sch_dict['DURATION'][filters.index("C")]
except ValueError:
c_filter = 0
pid = sch_dict['SOURCE'].split("_")[0]
print(["_".join(sch_dict['SOURCE'].split("_")[1:]),
sch_dict['RA'],
sch_dict['DEC'],
sch_dict['EPOCH'],
u_filter,
b_filter,
v_filter,
r_filter,
i_filter,
c_filter,
sch_dict['PRIORITY'],
sch_dict['REPEAT'],
1,
pid])
# Connecting to the database file
conn = sqlite3.connect(sqlite_file)
c = conn.cursor()
c.execute("INSERT OR IGNORE INTO {tn} {cn} VALUES {vls}".format(
tn=table_name,
cn=tuple(keywords),
vls=tuple(["_".join(sch_dict['SOURCE'].split("_")[1:]),
sch_dict['RA'],
sch_dict['DEC'],
sch_dict['EPOCH'],
u_filter,
b_filter,
v_filter,
r_filter,
i_filter,
c_filter,
sch_dict['PRIORITY'],
sch_dict['REPEAT'],
1,
pid])))
conn.commit()
conn.close()
return (True)
def read_res(self, file_name):
"""
Reads A-Track result file into numpy array.
@param file_name: Text file name and path
@type file_name: str
@return: array
"""
try:
data = np.genfromtxt(file_name,
comments='#',
skip_header=2,
invalid_raise=False,
delimiter=None,
usecols=(0, 1, 3, 4, 5))
return (data[~np.isnan(data).any(axis=1)])
except Exception as e:
print(e)
def read_sextractor_file(self, file_name):
"""
Reads A-Track result file into numpy array.
@param file_name: Text file name and path
@type file_name: str
@return: array
"""
try:
with open(file_name) as fp:
columns = []
units = []
for cnt, line in enumerate(fp):
if "#" in line:
line = line.replace("\n", "")
line = line.split()
columns.append(line[2])
if "[" in line[-1]:
unit = line[-1].replace("[", "")
unit = unit.replace("]", "")
units.append(unit)
else:
units.append("")
# print("Line {}: {}".format(cnt, line.split()))
else:
break
data = np.genfromtxt(file_name,
comments='#',
invalid_raise=False,
delimiter=None)
np_result = (data[~np.isnan(data).any(axis=1)])
tbl_result = Table(np_result,
names=tuple(columns))
for k, column in enumerate(columns):
tbl_result[column].unit = units[k]
return tbl_result
except Exception as e:
print(e)
def get_file_list(self, dir_name):
"""
List FITS images in a folder into a numpy array.
@param dir_name: Directory of FITS images
@type dir_name: str
@return: array
"""
images = sorted(glob.glob(dir_name + '/*.fit*'))
return (images)
def get_fits_from_server(self,
hostname,
username,
password,
dirname="/mnt/data/images",
fits_ext=".fts",
header2sqlite=False,
sqlite_file="gozlemler.sqlite"):
ssh = paramiko.SSHClient()
ssh.set_missing_host_key_policy(paramiko.AutoAddPolicy())
try:
ssh.connect(hostname=hostname,
username=username,
password=password)
except paramiko.SSHException:
print("Connection Failed")
quit()
sftp = ssh.open_sftp()
try:
sftp.chdir(dirname)
except FileNotFoundError:
print("Folder not found!")
ret = False
for fileattr in sftp.listdir_attr():
if not os.path.exists(fileattr.filename) and \
fits_ext in fileattr.filename:
sftp.get(fileattr.filename, fileattr.filename)
if header2sqlite is True:
f2db = self.fitshead_to_database(
fileattr.filename, sqlite_file=sqlite_file)
if f2db is False:
print(">>> Something wrong with the FITS file: {0}".format(
fileattr.filename))
continue
ret = True
print("{0} => {1}".format(fileattr.filename,
fileattr.filename))
print("Done")
ssh.close()
if ret is False:
print("No file(s) found!")
return(ret)
def get_latest_fits_from_server(self,
hostname,
username,
password,
dirname="/mnt/data/images",
fits_ext=".fts",
header2sqlite=False,
sqlite_file="observation.db"):
ssh = paramiko.SSHClient()
ssh.set_missing_host_key_policy(paramiko.AutoAddPolicy())
try:
ssh.connect(hostname=hostname,
username=username,
password=password)
except paramiko.SSHException:
print("Connection Failed")
quit()
sftp = ssh.open_sftp()
try:
sftp.chdir(dirname)
except FileNotFoundError:
print("No such folder!")
ssh.close()
raise SystemExit
ret = False
latest = 0
latestfile = None
for fileattr in sftp.listdir_attr():
if fits_ext in fileattr.filename and fileattr.st_mtime > latest:
latest = fileattr.st_mtime
latestfile = fileattr.filename
if latestfile is not None and \
os.path.exists(fileattr.filename) is False:
sftp.get(latestfile, latestfile)
print("{0} => {1}".format(latestfile,
latestfile))
ret = True
if header2sqlite is True:
self.fitshead_to_database(latestfile, sqlite_file=sqlite_file)
print("Done")
ssh.close()
if ret is False:
print("No file(s) found!")
return (latestfile)
def fitshead_to_database(self, fits_file,
sqlite_file="observations.db",
table_name="T60",
keywords=None):
print(">>> FITS2DB: {0}".format(fits_file))
if keywords is None:
keywords = ['xfactor',
'yfactor',
'exptime',
'object',
'priority',
'instrume',
'jd',
'date-obs',
'time-obs',
'lst',
'latitude',
'elevatio',
'azimuth',
'ha',
'ra',
'dec',
'objra',
'objdec',
'epoch',
'equinox',
'filter',
'camtemp',
'focuspos',
'wxtemp',
'wxpres',
'wxwndspd',
'wxwnddir',
'wxhumid',