Skip to content
Snippets Groups Projects
Commit c00b338f authored by Marcel Loose's avatar Marcel Loose :sunglasses:
Browse files

Task #3130: Added CEP/GSM to the build. Removed obsolete GSM/LSM scripts in CEP/pyparmdb

parent 1653deea
No related branches found
No related tags found
No related merge requests found
Expand all Hide whitespace changes
Inline Side-by-side
.gitattributes
+ 0
− 2
View file @ c00b338f
...@@ -954,8 +954,6 @@ CEP/Pipeline/test/test_framework/fixture/pyrap/__init__.py -text ...@@ -954,8 +954,6 @@ CEP/Pipeline/test/test_framework/fixture/pyrap/__init__.py -text
CEP/Pipeline/test/test_framework/fixture/pyrap/tables.py -text CEP/Pipeline/test/test_framework/fixture/pyrap/tables.py -text
CEP/Pipeline/test/test_framework/fixture/read.me -text CEP/Pipeline/test/test_framework/fixture/read.me -text
CEP/Pipeline/test/test_framework/unittest_runner.py -text CEP/Pipeline/test/test_framework/unittest_runner.py -text
CEP/pyparmdb/src/gsmutils.py -text
CEP/pyparmdb/src/lsm.py -text
CMake/FindAskapSoft.cmake -text CMake/FindAskapSoft.cmake -text
CMake/FindCasarest.cmake -text CMake/FindCasarest.cmake -text
CMake/FindJNI.cmake -text CMake/FindJNI.cmake -text
......
CEP/CMakeLists.txt
+ 1
− 0
View file @ c00b338f
...@@ -2,6 +2,7 @@ ...@@ -2,6 +2,7 @@
lofar_add_package(Calibration) lofar_add_package(Calibration)
lofar_add_package(DP3) lofar_add_package(DP3)
lofar_add_package(GSM)
lofar_add_package(Imager) lofar_add_package(Imager)
lofar_add_package(LMWCommon) lofar_add_package(LMWCommon)
lofar_add_package(MS) lofar_add_package(MS)
......
CEP/GSM/CMakeLists.txt 0 → 100644
+ 9
− 0
View file @ c00b338f
# $Id$
lofar_package(GSM 1.0)
include(LofarFindPackage)
lofar_find_package(Python REQUIRED)
add_subdirectory(src)
#add_subdirectory(db)
CEP/GSM/src/CMakeLists.txt 0 → 100644
+ 6
− 0
View file @ c00b338f
# $Id$
include(PythonInstall)
# Install Python modules
python_install(gsmutils.py DESTINATION lofar/gsm)
CEP/pyparmdb/src/CMakeLists.txt
+ 0
− 4
View file @ c00b338f
...@@ -26,8 +26,4 @@ lofar_add_bin_program(versionpyparmdb versionpyparmdb.cc) ...@@ -26,8 +26,4 @@ lofar_add_bin_program(versionpyparmdb versionpyparmdb.cc)
# Install Python modules # Install Python modules
python_install(__init__.py DESTINATION lofar/parmdb) python_install(__init__.py DESTINATION lofar/parmdb)
python_install(gsmutils.py DESTINATION lofar)
install(PROGRAMS
gsm.py
DESTINATION bin)
CEP/pyparmdb/src/gsm.py deleted 100755 → 0
+ 0
− 287
View file @ 1653deea
#!/usr/bin/env python
# Select a subset from the GSM and write into a makesourcdb input file.
# ra and dec both in degrees
# integrated flux [in Jy] above which the sources will be selected
# You should know that:
# cat_id = 3 => NVSS
# cat_id = 4 => VLSS
# cat_id = 5 => WENSS
def doSelect (outfile, dirSelect, fluxi_mins, cat_ids):
import os
import monetdb.sql as db
from monetdb.sql import Error as Error
db_type = "MonetDB"
db_host = "ldb001"
db_port = 50000
db_dbase = "gsm"
db_user = "gsm"
db_passwd = "msss"
#db_lang = "sql"
# If a single catalog, use =
if len(cat_ids) == 1:
catSelect = 'c1.cat_id = %d AND c1.i_int_avg >= %f' % (cat_ids[0], fluxi_mins[0])
else:
# Multiple catalogs.
# If a single minimum flux, use it for all catalogs.
# Note that the IN clause needs (), not [].
if len(fluxi_mins) == 1:
catSelect = 'c1.cat_id IN (%s) AND c1.i_int_avg >= %f' % (str(cat_ids)[1:-1], fluxi_mins[0])
else:
# There is a minimum flux per catalog.
catSelect = ''
for i in range(len(cat_ids)):
if i > 0:
catSelect += ' OR '
catSelect += '(c1.cat_id = %d AND c1.i_int_avg >= %f)' % (cat_ids[i], fluxi_mins[i])
# Form the entire where clause.
where = 'WHERE (%s) AND (%s)' % (catSelect, dirSelect)
conn = db.connect(hostname=db_host \
,port=db_port \
,database=db_dbase \
,username=db_user \
,password=db_passwd \
)
# Remove output file if already existing.
if os.path.isfile(outfile):
os.remove(outfile)
try:
cursor = conn.cursor()
# This query concatenates the requested columns per row in a single string in the correct BBS format.
cursor.execute(#"COPY " + \
"SELECT t.line " + \
" FROM (SELECT CAST(CONCAT(t0.catsrcname, CONCAT(',', " + \
" CONCAT(t0.src_type, CONCAT(',', " + \
" CONCAT(ra2bbshms(t0.ra), CONCAT(',', " + \
" CONCAT(decl2bbsdms(t0.decl), CONCAT(',', " + \
" CONCAT(t0.i, CONCAT(',', " + \
" CONCAT(t0.q, CONCAT(',', " + \
" CONCAT(t0.u, CONCAT(',', " + \
" CONCAT(t0.v, CONCAT(',', " + \
" CONCAT(t0.MajorAxis, CONCAT(',', " + \
" CONCAT(t0.MinorAxis, CONCAT(',', " + \
" CONCAT(t0.Orientation, CONCAT(',', " + \
" CONCAT(t0.ReferenceFrequency, CONCAT(',', " + \
" CASE WHEN t0.SpectralIndexDegree = 0" + \
" THEN '[]'" + \
" ELSE CASE WHEN t0.SpectralIndexDegree = 1" + \
" THEN CONCAT('[', CONCAT(t0.SpectralIndex_0, ']'))" + \
" ELSE CONCAT('[', CONCAT(t0.SpectralIndex_0, CONCAT(',', CONCAT(t0.SPECTRALINDEX_1, ']'))))" + \
" END" + \
" END" + \
")))))))))))))))))))))))" + \
" ) AS VARCHAR(300)) AS line " + \
" FROM (SELECT CAST(TRIM(c1.catsrcname) AS VARCHAR(23)) AS catsrcname " + \
" ,CASE WHEN c1.pa IS NULL " + \
" THEN CAST('POINT' AS VARCHAR(23)) " + \
" ELSE CAST('GAUSSIAN' AS VARCHAR(23)) " + \
" END AS src_type " + \
" ,CAST(c1.ra AS VARCHAR(23)) AS ra " + \
" ,CAST(c1.decl AS VARCHAR(23)) AS decl " + \
" ,CAST(c1.i_int_avg AS VARCHAR(23)) AS i " + \
" ,CAST(0 AS VARCHAR(23)) AS q " + \
" ,CAST(0 AS VARCHAR(23)) AS u " + \
" ,CAST(0 AS VARCHAR(23)) AS v " + \
" ,CASE WHEN c1.pa IS NULL " + \
" THEN CAST('' AS VARCHAR(23)) " + \
" ELSE CASE WHEN c1.major IS NULL " + \
" THEN CAST('' AS VARCHAR(23)) " + \
" ELSE CAST(c1.major AS varchar(23)) " + \
" END " + \
" END AS MajorAxis " + \
" ,CASE WHEN c1.pa IS NULL " + \
" THEN CAST('' AS VARCHAR(23)) " + \
" ELSE CASE WHEN c1.minor IS NULL " + \
" THEN CAST('' AS VARCHAR(23)) " + \
" ELSE CAST(c1.minor AS varchar(23)) " + \
" END " + \
" END AS MinorAxis " + \
" ,CASE WHEN c1.pa IS NULL " + \
" THEN CAST('' AS VARCHAR(23)) " + \
" ELSE CAST(c1.pa AS varchar(23)) " + \
" END AS Orientation " + \
" ,CAST(c1.freq_eff AS VARCHAR(23)) AS ReferenceFrequency " + \
" ,CASE WHEN si.spindx_degree IS NULL " + \
" THEN 0 " + \
" ELSE si.spindx_degree " + \
" END AS SpectralIndexDegree " + \
" ,CASE WHEN si.c0 IS NULL " + \
" THEN 0 " + \
" ELSE si.c0 " + \
" END AS SpectralIndex_0 " + \
" ,CASE WHEN si.c1 IS NULL " + \
" THEN 0 " + \
" ELSE si.c1 " + \
" END AS SpectralIndex_1 " + \
" FROM catalogedsources c1 " + \
" LEFT OUTER JOIN spectralindices si ON c1.catsrcid = si.catsrc_id " + \
where +
" ) t0 " + \
" ) t " , ())
y = cursor.fetchall()
cursor.close()
#print "y:", y
except db.Error, e:
import logging
logging.warn("gsmSelect to file %s failed " % (outfile))
logging.warn("Failed on query for reason: %s " % (e))
logging.debug("Failed select query: %s" % (e))
return -1
file = open(outfile,'w')
file.write ("format = Name, Type, Ra, Dec, I, Q, U, V, MajorAxis, MinorAxis, Orientation, ReferenceFrequency='60e6', SpectralIndex='[]'\n")
for i in range(len(y)):
file.write(y[i][0] + '\n')
file.close()
return len(y)
def gsmSelectCone (outfile, ra, dec, radius, fluxi_mins, cat_ids):
if ra < 0 or ra > 360:
print 'RA', ra, 'is invalid: <0 or >360 degrees'
return -1
if dec < -90 or dec > 90:
print 'DEC', dec, 'is invalid: <-90 or >90 degrees'
return -1
if radius < 0 or radius > 90:
print 'radius', radius, 'is invalid: <0 or >90 degrees'
return -1
# Determine DEC boundaries (for hopefully faster query).
# Convert degrees to radians.
import math
mindec = dec - radius
maxdec = dec + radius
d2r = math.pi / 180.
ra *= d2r
dec *= d2r
radius *= d2r
# Source (srcRA,srcDEC) is inside the cone if:
# sin(dec)*sin(srcDEC) + cos(dec)*cos(srcDEC)*cos(ra-srcRA) >= cos(radius)
select = '(c1.decl BETWEEN %17.12f AND %17.12f) AND (%17.14f*sin(c1.decl*%17.14f) + %17.14f*cos(c1.decl*%17.14f)*cos(%17.14f-c1.ra*%17.14f) > %17.14f)' % (mindec, maxdec, math.sin(dec), d2r, math.cos(dec), d2r, ra, d2r, math.cos(radius))
return doSelect (outfile, select, fluxi_mins, cat_ids)
def gsmSelectBox (outfile, ra_st, ra_end, dec_st, dec_end, fluxi_mins, cat_ids):
for ra in [ra_st,ra_end]:
if ra < 0 or ra > 360:
print 'RA', ra, 'is invalid: <0 or >360 degrees'
return -1
for dec in [dec_st,dec_end]:
if dec < -90 or dec > 90:
print 'DEC', dec, 'is invalid: <-90 or >90 degrees'
return -1
if dec_st > dec_end:
print 'invalid DEC: start', dec_st, '> end', dec_end
return -1
# Form the selection for the RA,DEC.
# If RA crosses 360 degrees, split in two parts.
if ra_st <= ra_end:
select = '(c1.ra BETWEEN %17.12f AND %17.12f)' % (ra_st, ra_end)
else:
select = '(c1.ra BETWEEN %17.12f AND 360 OR c1.ra BETWEEN 0 AND %17.12f)' % (ra_st, ra_end)
select += ' AND (c1.decl BETWEEN %17.12f AND %17.12f)' % (dec_st, dec_end)
return doSelect (outfile, select, fluxi_mins, cat_ids)
# Interpret the arguments and do the selection.
def gsmMain (name, argv):
useBox = False
starg = 0
optarg = 4
if len(argv) > 0 and argv[0] == '-b':
# select using a box
useBox = True
starg = 1
optarg = 6
if len(argv) < optarg:
print ''
print 'Insufficient arguments given; run as:'
print ''
print ' %s outfile RA DEC radius [minFluxI [catalogs]]' % name
print 'to select using a cone'
print ''
print ' %s -b outfile stRA endRA stDEC endDEC [minFluxI [catalogs]]' % name
print 'to select using a box'
print ''
print ' outfile path-name of the output file'
print ' It will be overwritten if already existing'
print ' RA cone center Right Ascension (J2000, degrees)'
print ' DEC cone center Declination (J2000, degrees)'
print ' radius cone radius (degrees)'
print ' stRA box start Right Ascension (J2000, degrees)'
print ' endRA box end Right Ascension (J2000, degrees)'
print ' stRA can be > endRA indicating crossing 360 deg'
print ' minDEC box start Declination (J2000, degrees)'
print ' maxDEC box end Declination (J2000, degrees)'
print ' minFluxI minimum flux (integrated Stokes I flux in Jy)'
print ' If a single value is given, it is used for all catalogs.'
print ' If multiple values given (separated by commas), each applies'
print ' to the corresponding catalog.'
print ' Default is 0.5'
print ' catalogs names of catalogs to search (case-insensitive)'
print ' (NVSS, VLSS, and/or WENSS)'
print ' If multiple, separate by commas'
print ' Default is WENSS'
print ''
return False
# Get the arguments.
outfile = argv[starg]
a1 = float(argv[starg+1])
a2 = float(argv[starg+2])
a3 = float(argv[starg+3])
if useBox:
a4 = float(argv[starg+4])
minFlux = [0.5]
if len(argv) > optarg and len(argv[optarg]) > 0:
minFlux = [float(x) for x in argv[optarg].split(',')]
# cat_id = 3 => NVSS
# cat_id = 4 => VLSS
# cat_id = 5 => WENSS
cats = ['WENSS']
if len(argv) > optarg+1 and len(argv[optarg+1]) > 0:
cats = argv[optarg+1].split (',')
cat_ids = []
for cat in cats:
cat = cat.upper()
if cat == 'NVSS':
cat_ids.append (3)
elif cat == 'VLSS':
cat_ids.append (4)
elif cat == 'WENSS':
cat_ids.append (5)
else:
print cat, 'is an invalid catalog name'
return False
if len(minFlux) != 1 and len(minFlux) != len(cat_ids):
print 'Nr of minFlux values (%s) must be 1 or match nr of catalogs' % argv[5]
return False;
# Do the selection and create the makesourcedb file.
if useBox:
nr = gsmSelectBox (outfile, a1, a2, a3, a4, minFlux, cat_ids)
else:
nr = gsmSelectCone (outfile, a1, a2, a3, minFlux, cat_ids)
if nr < 0:
return False
elif nr == 0:
print 'Warning: no matching sources found in GSM for'
if useBox:
print ' stRA=%f endRA=%f stDEC=%f endDEC=%f' % (a1,a2,a3,a4)
else:
print ' RA=%f DEC=%f radius=%f' % (a1,a2,a3)
print ' minFluxI=%s catalogs=%s' % (str(minFlux), cats)
else:
print '%d sources written into %s' % (nr, outfile)
return True
# This is the main entry.
if __name__ == "__main__":
import sys
if gsmMain (sys.argv[0], sys.argv[1:]):
sys.exit(0)
sys.exit(1)
CEP/pyparmdb/src/gsmutils.py deleted 100644 → 0
+ 0
− 537
View file @ 1653deea
This diff is collapsed.
CEP/pyparmdb/src/lsm.py deleted 100644 → 0
+ 0
− 43
View file @ 1653deea
#!/usr/bin/python
#
# Script used for testing the bbs skymodel files
#
import sys, os, time
import monetdb
import monetdb.sql as db
import gsmutils as gsm
db_host = "ldb001"
db_dbase = "gsm"
db_user = "gsm"
db_passwd = "msss"
db_port = 50000
try:
conn = monetdb.sql.connect(hostname=db_host, database=db_dbase, username=db_user, password=db_passwd, port=db_port)
except db.Error, e:
raise
#ra_c = 289.89258333333333
#decl_c = 0.0017444444444444445
ra_c = 287.80216666666666
decl_c = 9.096861111111112
#ra_c = 362
#decl_c = 10
#ra_c = 286.87425
#decl_c = 7.1466111111111115
#ra_c = 70.0
#decl_c = 33.0
fov_radius = 5.0
assoc_theta = 0.025
gsm.expected_fluxes_in_fov(conn, ra_c, decl_c, fov_radius, assoc_theta, 'bbs.skymodel.test', storespectraplots=False)
conn.close()
CMake/LofarPackageList.cmake
+ 1
− 0
View file @ c00b338f
...@@ -16,6 +16,7 @@ if(NOT DEFINED LOFAR_PACKAGE_LIST_INCLUDED) ...@@ -16,6 +16,7 @@ if(NOT DEFINED LOFAR_PACKAGE_LIST_INCLUDED)
set(LOFAR_PACKAGE_LIST_INCLUDED TRUE) set(LOFAR_PACKAGE_LIST_INCLUDED TRUE)
set(Calibration_SOURCE_DIR ${CMAKE_SOURCE_DIR}/CEP/Calibration) set(Calibration_SOURCE_DIR ${CMAKE_SOURCE_DIR}/CEP/Calibration)
set(DP3_SOURCE_DIR ${CMAKE_SOURCE_DIR}/CEP/DP3) set(DP3_SOURCE_DIR ${CMAKE_SOURCE_DIR}/CEP/DP3)
set(GSM_SOURCE_DIR ${CMAKE_SOURCE_DIR}/CEP/GSM)
set(Imager_SOURCE_DIR ${CMAKE_SOURCE_DIR}/CEP/Imager) set(Imager_SOURCE_DIR ${CMAKE_SOURCE_DIR}/CEP/Imager)
set(LMWCommon_SOURCE_DIR ${CMAKE_SOURCE_DIR}/CEP/LMWCommon) set(LMWCommon_SOURCE_DIR ${CMAKE_SOURCE_DIR}/CEP/LMWCommon)
set(MS_SOURCE_DIR ${CMAKE_SOURCE_DIR}/CEP/MS) set(MS_SOURCE_DIR ${CMAKE_SOURCE_DIR}/CEP/MS)
......
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment