class DistlOrganizer(object):
def __init__(self,verbose = 0,**kwargs):
self.rundir = os.getcwd()
self.verbose = verbose
self.phil_params = kwargs["phil_params"]
if self.phil_params.distl.dxtbx:
self.set_dxtbx_input()
return
if kwargs.has_key('argument_module'):
# new interface
self.setCommandInput(kwargs['argument_module'])
def set_dxtbx_input(self):
pass
def setCommandInput(self,argument_module):
from spotfinder.diffraction.imagefiles import spotfinder_image_files as ImageFiles
self.Files = ImageFiles(argument_module,self.phil_params)
self.frames = self.Files.frames()
def update_spotfinder(self):
# used by distl.image_viewer
S = spotfinder_factory(self.rundir,self.Files,self.phil_params)
self.S = S
for frame in self.frames:
if self.verbose:
pretty_image_stats(S,frame)
notes(S,self.frames[0])
def printSpots(self):
'''spotfinder and pickle implicitly assumes ADSC format'''
if self.phil_params.distl.dxtbx:
self.S = S = dxtbx_spotfinder_factory(self.phil_params)
else:
self.S = S = spotfinder_factory(self.rundir,self.Files,self.phil_params)
for frame in self.frames:
if self.verbose:
pretty_image_stats(S,frame)
notes(S,self.frames[0])
def do_POST(self):
T = Timer("do_POST")
parsed = urlparse(self.path)
qs = parse_qs(parsed.query)
expect = self.headers.getheaders("Expect")
if len(expect) >= 1:
if True in [item.find("200") >= 0 for item in expect]:
self.send_response(
200) # untested; has no apparent affect on libcurl
return
# Get arguments by reading body of request.
# We read this in chunks to avoid straining
# socket.read(); around the 10 or 15Mb mark, some platforms
# begin to have problems (bug #792570).
max_chunk_size = 10 * 1024 * 1024
size_remaining = int(self.headers["content-length"])
L = []
while size_remaining:
chunk_size = min(size_remaining, max_chunk_size)
L.append(self.rfile.read(chunk_size))
size_remaining -= len(L[-1])
data = ''.join(L)
post_data = StringIO(data)
# Parse the multipart/form-data
contentTypeHeader = self.headers.getheaders('content-type').pop()
# Extract the boundary parameter in the content-type header
headerParameters = contentTypeHeader.split(";")
boundary = headerParameters[1].split("=")
boundary = boundary[1].strip()
parts = cgi.parse_multipart(
post_data, {
"boundary":
boundary,
"content-disposition":
self.headers.getheaders('content-disposition')
})
print "*****************************"
for item in parts.keys():
if len(parts[item][0]) < 1000:
print item, parts[item]
print "*****************************"
if parts["filename"][0].find("EXIT") >= 0:
self.shutdown()
return
from spotfinder.diffraction.imagefiles import spotfinder_image_files as ImageFiles
from spotfinder.diffraction.imagefiles import Spotspickle_argument_module
response_params = copy.deepcopy(common_parameters_singleton).extract()
Files = ImageFiles(Spotspickle_argument_module(parts["filename"][0]),
response_params)
print "Final image object:"
Files.images[0].show_header()
print "beam_center_convention", Files.images[0].beam_center_convention
print "beam_center_reference_frame", Files.images[
0].beam_center_reference_frame
logfile = StringIO()
if response_params.distl.bins.verbose: sys.stdout = logfile
from spotfinder.applications.wrappers import spotfinder_factory
S = spotfinder_factory(None, Files, response_params)
print
sys.stdout = sys.__stdout__
frames = Files.frames()
sys.stdout = logfile
print "Image: %s" % parts["filename"][0]
from spotfinder.applications.stats_distl import pretty_image_stats, notes
for frame in frames:
#pretty_image_stats(S,frame)
#notes(S,frames[0])
module_image_stats(S, frame)
sys.stdout = sys.__stdout__
log = logfile.getvalue()
print log
ctype = 'text/plain'
self.send_response(200)
self.send_header("Content-type", ctype)
self.send_header("Content-length", len(log))
self.end_headers()
self.wfile.write(log)
self.opt_logging()
def do_POST(self):
T = Timer("do_POST")
parsed = urlparse(self.path)
qs = parse_qs(parsed.query)
expect = self.headers.getheaders("Expect")
if len(expect)>=1:
if True in [item.find("200")>=0 for item in expect]:
self.send_response(200) # untested; has no apparent affect on libcurl
return
# Get arguments by reading body of request.
# We read this in chunks to avoid straining
# socket.read(); around the 10 or 15Mb mark, some platforms
# begin to have problems (bug #792570).
max_chunk_size = 10*1024*1024
size_remaining = int(self.headers["content-length"])
L = []
while size_remaining:
chunk_size = min(size_remaining, max_chunk_size)
L.append(self.rfile.read(chunk_size))
size_remaining -= len(L[-1])
data = ''.join(L)
post_data = StringIO.StringIO(data)
# Parse the multipart/form-data
contentTypeHeader = self.headers.getheaders('content-type').pop()
# Extract the boundary parameter in the content-type header
headerParameters = contentTypeHeader.split(";")
boundary = headerParameters[1].split("=")
boundary = boundary[1].strip()
parts = cgi.parse_multipart(post_data,
{"boundary":boundary,
"content-disposition":self.headers.getheaders('content-disposition')
})
print "*****************************"
for item in parts.keys():
if len(parts[item][0])< 1000:
print item, parts[item]
print "*****************************"
if parts["filename"][0].find("EXIT")>=0:
self.shutdown()
return
from spotfinder.diffraction.imagefiles import spotfinder_image_files as ImageFiles
from spotfinder.diffraction.imagefiles import Spotspickle_argument_module
response_params = copy.deepcopy(common_parameters_singleton).extract()
Files = ImageFiles(Spotspickle_argument_module(parts["filename"][0]),response_params)
print "Final image object:"
Files.images[0].show_header()
print "beam_center_convention",Files.images[0].beam_center_convention
print "beam_center_reference_frame",Files.images[0].beam_center_reference_frame
logfile = StringIO.StringIO()
if response_params.distl.bins.verbose: sys.stdout = logfile
from spotfinder.applications.wrappers import spotfinder_factory
S = spotfinder_factory(None, Files, response_params)
print
sys.stdout = sys.__stdout__
frames = Files.frames()
sys.stdout = logfile
print "Image: %s"%parts["filename"][0]
from spotfinder.applications.stats_distl import pretty_image_stats,notes
for frame in frames:
#pretty_image_stats(S,frame)
#notes(S,frames[0])
module_image_stats(S,frame)
sys.stdout = sys.__stdout__
log = logfile.getvalue()
print log
ctype = 'text/plain'
self.send_response(200)
self.send_header("Content-type", ctype)
self.send_header("Content-length",len(log))
self.end_headers()
self.wfile.write(log)
self.opt_logging()
def setCommandInput(self,argument_module): from spotfinder.diffraction.imagefiles import spotfinder_image_files as ImageFiles self.Files = ImageFiles(argument_module,self.phil_params) self.frames = self.Files.frames()
