def pixmap(Isize1,Isize2,this_frame_phi_deg,pixel_size,size1,size2,spot_convention,procid):
# returms a list of data points in a chunk of each image with info to calculate the h,k,l
from spotfinder.applications.xfel import cxi_phil
from iotbx.detectors.context.spot_xy_convention import spot_xy_convention
SXYC = spot_xy_convention(pixel_size*size1,pixel_size*size2)
from spotfinder.math_support import pixels_to_mmPos
# for parallel running; calculate the range that will be worked on by this process
chunksize = int(Isize2/nproc)
if (Isize2 % nproc != 0):
chunksize += 1
y1 = procid*chunksize
y2 = y1 + chunksize
if (y2>Isize2):
y2=Isize2
# now walk through the pixels and create the list of data points
raw_spot_input = flex.vec3_double()
for y in xrange(y1,y2): # slow dimension
for x in xrange(Isize1): # fast dimension
mmPos = pixels_to_mmPos(x,y,pixel_size)
rawspot = (mmPos[0],mmPos[1],this_frame_phi_deg)
transpot = SXYC.select(rawspot,spot_convention)
raw_spot_input.append(transpot)
return raw_spot_input
def pixmap(Isize1,Isize2,this_frame_phi_deg,pixel_size,size1,size2,spot_convention,procid):
# returms a list of data points in a chunk of each image with info to calculate the h,k,l
from spotfinder.applications.xfel import cxi_phil
from iotbx.detectors.context.spot_xy_convention import spot_xy_convention
SXYC = spot_xy_convention(pixel_size*size1,pixel_size*size2)
from spotfinder.math_support import pixels_to_mmPos
# for parallel running; calculate the range that will be worked on by this process
chunksize = int(Isize1/nproc)
if (Isize1 % nproc != 0):
chunksize += 1
x1 = procid*chunksize
x2 = x1 + chunksize
if (x2>Isize1):
x2=Isize1
# now walk through the pixels and create the list of data points
raw_spot_input = flex.vec3_double()
for x in xrange(x1,x2): # slow dimension
for y in xrange(Isize2): # fast dimension
mmPos = pixels_to_mmPos(x,y,pixel_size)
rawspot = (mmPos[0],mmPos[1],this_frame_phi_deg)
transpot = SXYC.select(rawspot,spot_convention)
raw_spot_input.append(transpot)
return raw_spot_input
# parse the input file line into a diffuse image file name and scale factor
words = line.split()
imgname = os.path.join(procpath + "/" + words[1])
scale = float(words[2])
print "processing file %s with scale factor %f" % (imgname, scale)
I = QuickImage(imgname)
I.read()
DATA = I.linearintdata
print "transform pixel numbers to mm positions and rotational degrees"
from iotbx.detectors.context.spot_xy_convention import spot_xy_convention
SF = results.spotfinder_results
SXYC = spot_xy_convention(SF.pixel_size * SF.size1,
SF.pixel_size * SF.size2)
from spotfinder.math_support import pixels_to_mmPos
this_frame_phi_deg = I.deltaphi / 2.0 + I.osc_start
print "Creating pixel map in parallel..."
t0 = clock()
raw_spot_input_all = flex.vec3_double()
Isize1 = I.size1
Isize2 = I.size2
pixel_size = SF.pixel_size
# prepare the list of arguments to run pixmap in parallel
pixmap_tasks = [
(Isize1, Isize2, this_frame_phi_deg, SF.pixel_size, SF.size1,
SF.size2, results.horizons_phil.spot_convention, procid)
for procid in range(nproc)
]
# parse the input file line into a diffuse image file name and scale factor
words = line.split()
imgname = words[1]
scale = float(words[2])
print "processing file %s with scale factor %f"%(imgname,scale)
I = QuickImage(imgname)
I.read()
DATA = I.linearintdata
print "transform pixel numbers to mm positions and rotational degrees"
from iotbx.detectors.context.spot_xy_convention import spot_xy_convention
SF = results.spotfinder_results
SXYC = spot_xy_convention(SF.pixel_size*SF.size1,SF.pixel_size*SF.size2)
from spotfinder.math_support import pixels_to_mmPos
this_frame_phi_deg = I.deltaphi/2.0+I.osc_start
print "Creating pixel map in parallel..."
t0 = clock()
raw_spot_input_all = flex.vec3_double()
Isize1 = I.size1
Isize2 = I.size2
pixel_size = SF.pixel_size
# prepare the list of arguments to run pixmap in parallel
pixmap_tasks = [(Isize1,Isize2,this_frame_phi_deg,SF.pixel_size,SF.size1,SF.size2,results.horizons_phil.spot_convention,procid) for procid in range(nproc)]
# run pixmap in parallel and collect results
raw_spot_input_it = pool.map(pixmapstar,pixmap_tasks)
# gather pixmap results into a single collection of data points
for raw_spot_input_this in raw_spot_input_it: