#xp = XParam()
#xp.SPOT_RANGE = [2, 12],[44, 54]
#print xp.SPOT_RANGE
#xp.SPOT_RANGE = "2 12", "44 54"
#xp.DATA_RANGE = 8, 8
#xp.INCLUDE_RESOLUTION_RANGE= 70.0, 2.0
#xp.NBX = 3
#xp.NBY = 3
if "-a" in sys.argv:
sys.argv.remove('-a')
xp.update(getProfilRefPar())
xp["JOB"] = "DEFPIX", "INTEGRATE", "CORRECT"
xp["REFINE_INTEGRATE"] = "ORIENTATION", "BEAM", "CELL" #"DISTANCE",
shutil.copyfile("GXPARM.XDS","XPARM.XDS")
if "-i" in sys.argv:
optid = sys.argv.index("-i")
_xds_input = sys.argv[optid+1]
xp.update(xdsInp2Param(inp_str=_xds_input))
sys.argv.remove('-i')
sys.argv.remove(_xds_input)
if "-norun" in sys.argv:
saveLastVersion(LP_names)
sys.exit()
else:
ARGV = sys.argv[1:]
while ARGV:
ARG = ARGV.pop()
xp.update(xdsInp2Param(inp_str=ARG))
run_xds(xp, inp_f="XDS.INP")
saveLastVersion(LP_names)
_mkdir(head)
if tail:
os.mkdir(newdir)
def make_xds_input(image_name):
try:
image_name_real = os.path.realpath(image_name)
datacoll = XIO.Collect(image_name_real)
datacoll.interpretImage()
datacoll.lookup_imageRanges()
except XIO.XIOError:
print "\nError while trying to acceess %s.\nSorry." % filename
sys.exit()
newPar = datacoll.export("xds")
newPar.pop("SPECIFIC_KEYWORDS")
newPar["JOB"] = "XYCORR", "INIT"
newPar["BACKGROUND_RANGE"] = newPar["DATA_RANGE"]
TMPL = datacoll.get_export_template("xds")
newDir = DIRNAME_PREFIX + datacoll.prefix
return TMPL, newPar, newDir
if __name__ == '__main__':
tmpl, par, new_dir = make_xds_input(sys.argv[1])
mkdir(new_dir)
os.chdir(new_dir)
opWriteCl("XDS.INP", tmpl[:-25] % par)
run_xds(par, inp_f="XDS.INP")
saveLastVersion(LP_names)
if "-i" in sys.argv:
optid = sys.argv.index("-i")
_xds_input = sys.argv[optid + 1]
xp.update(xdsInp2Param(inp_str=""))
sys.argv.remove('-i')
sys.argv.remove(_xds_input)
#if "-norun" in sys.argv:
# saveLastVersion(LP_names)
# sys.exit()
ARGV = sys.argv[1:]
while ARGV:
ARG = ARGV.pop()
xp.update(xdsInp2Param(inp_str=ARG))
open("gnuplot.inp").write(
"gnuplot_template" %
(len(STRONG_PIXEL_LIST_1), len(MIN_SPOT_SIZE_LIST_1)))
xp["JOB"] = "COLSPOT", "IDXREF"
for spot_size in MIN_SPOT_SIZE_LIST_1:
for strong_pixel in STRONG_PIXEL_LIST_1:
xp["MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT"] = spot_size
xp["STRONG_PIXEL"] = strong_pixel
run_xds(xp, inp_f="XDS.INP", out_f="xds_indexer.log")
saveLastVersion(LP_names)
res = XDSLogParser("IDXREF.LP", verbose=False).results
log("%4d %5.1f" % (spot_size, strong_pixel))
log("%(indexed_percentage)6.1f %(indexed_spots)9d %(total_spots)9d"
% res)
log("%(xy_spot_position_ESD)6.2f %(z_spot_position_ESD)6.2f" % res)
log(" %(refined_cell_str)s\n" % res)
sys.argv.remove('-a')
xp.update(getProfilRefPar())
xp["JOB"] = "DEFPIX", "INTEGRATE", "CORRECT"
xp["NUMBER_OF_PROFILE_GRID_POINTS_ALONG_ALPHA_BETA"] = 15
xp["NUMBER_OF_PROFILE_GRID_POINTS_ALONG_GAMMA"] = 15
xp["REFINE_INTEGRATE"] = "ORIENTATION", "BEAM", "CELL" #"DISTANCE",
shutil.copyfile("GXPARM.XDS", "XPARM.XDS")
if "-p" in sys.argv:
sys.argv.remove('-p')
xp.update(getProfilRefPar())
xp["JOB"] = "DEFPIX", "INTEGRATE", "CORRECT"
xp["NUMBER_OF_PROFILE_GRID_POINTS_ALONG_ALPHA_BETA"] = 15
xp["NUMBER_OF_PROFILE_GRID_POINTS_ALONG_GAMMA"] = 15
xp["REFINE_INTEGRATE"] = "ORIENTATION", "BEAM", "CELL" #"DISTANCE",
if "-i" in sys.argv:
optid = sys.argv.index("-i")
_xds_input = sys.argv[optid + 1]
xp.update(xdsInp2Param(inp_str=_xds_input))
sys.argv.remove('-i')
sys.argv.remove(_xds_input)
if "-norun" in sys.argv:
saveLastVersion(LP_names)
sys.exit()
else:
ARGV = sys.argv[1:]
while ARGV:
ARG = ARGV.pop()
xp.update(xdsInp2Param(inp_str=ARG))
run_xds(xp, inp_f="XDS.INP")
saveLastVersion(LP_names)
# xp["REFINE_INTEGRATE"] = "ORIENTATION", "BEAM", "CELL" #"DISTANCE",
# shutil.copyfile("GXPARM.XDS","XPARM.XDS")
if "-i" in sys.argv:
optid = sys.argv.index("-i")
_xds_input = sys.argv[optid+1]
xp.update(xdsInp2Param(inp_str=""))
sys.argv.remove('-i')
sys.argv.remove(_xds_input)
#if "-norun" in sys.argv:
# saveLastVersion(LP_names)
# sys.exit()
ARGV = sys.argv[1:]
while ARGV:
ARG = ARGV.pop()
xp.update(xdsInp2Param(inp_str=ARG))
open("gnuplot.inp").write("gnuplot_template" % (len(STRONG_PIXEL_LIST_1), len(MIN_SPOT_SIZE_LIST_1)))
xp["JOB"] = "COLSPOT", "IDXREF"
for spot_size in MIN_SPOT_SIZE_LIST_1:
for strong_pixel in STRONG_PIXEL_LIST_1:
xp["MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT"] = spot_size
xp["STRONG_PIXEL"] = strong_pixel
run_xds(xp, inp_f="XDS.INP", out_f="xds_indexer.log")
saveLastVersion(LP_names)
res = XDSLogParser("IDXREF.LP", verbose=False).results
log( "%4d %5.1f" % (spot_size, strong_pixel))
log( "%(indexed_percentage)6.1f %(indexed_spots)9d %(total_spots)9d" % res)
log( "%(xy_spot_position_ESD)6.2f %(z_spot_position_ESD)6.2f" % res)
log( " %(refined_cell_str)s\n" % res)