def pilatus_slice_from_file_url(url):
from six.moves import urllib
parsed = urllib.parse.urlparse(url)
assert parsed.scheme == "file"
file = parsed.path.split("?")[0]
if file == parsed.path:
return PilatusImage(file)
qs = urllib.parse.parse_qs(parsed.path.split("?")[1])
sliceindex = int(qs["slice"][0])
object = PilatusImage(file)
object.readHeader()
return pilatus_slice_from_object_and_slicenumber(object, sliceindex)
def detectorbase_start(self):
self.detectorbase = PilatusImage(self._image_file)
self.detectorbase.readHeader()
self.detectorbase.parameters["SIZE1"] = 2167
self.detectorbase.parameters["SIZE2"] = 2070
def test_all(dirpath, timer=False):
for file in generate_paths(dirpath):
from iotbx.detectors.pilatus_minicbf import PilatusImage
if timer: print(os.path.basename(file))
P = PilatusImage(file)
if timer: G = Profiler("cbflib no-opt read")
P.read(algorithm="cbflib")
read1 = P.linearintdata
if timer: G = Profiler("cbflib optimized read")
P.linearintdata = None #won't read again without resetting first
P.read(algorithm="cbflib_optimized")
read2 = P.linearintdata
if timer: G = Profiler("buffer-based read")
P.linearintdata = None #won't read again without resetting first
P.read(algorithm="buffer_based")
read3 = P.linearintdata
if timer: del G
expected_image_size = {
"Pilatus-6M": (2527, 2463),
"Pilatus-2M": (1679, 1475),
"Pilatus-300K": (619, 487)
}[P.vendortype]
assert read1.accessor().focus() == read2.accessor().focus(
) == expected_image_size
from cbflib_adaptbx import assert_equal
#print "Equality of arrays from two decompress methods", assert_equal(read1,read2), "\n"
assert assert_equal(read1, read2)
assert assert_equal(read1, read3)
def pilatus_slice_from_file_url(url):
#backward compatibility with Python 2.5
try: from urlparse import parse_qs
except Exception: from cgi import parse_qs
from urlparse import urlparse
parsed = urlparse(url)
assert parsed.scheme == "file"
file = parsed.path.split("?")[0]
if file == parsed.path:
return PilatusImage(file)
qs = parse_qs(parsed.path.split("?")[1])
sliceindex = int(qs["slice"][0])
object = PilatusImage(file)
object.readHeader()
return pilatus_slice_from_object_and_slicenumber(object,sliceindex)
def detectorbase_start(self):
from iotbx.detectors.pilatus_minicbf import PilatusImage
self.detectorbase = PilatusImage(self._image_file)
self.detectorbase.readHeader()
self.detectorbase.parameters['SIZE1'] = 2167
self.detectorbase.parameters['SIZE2'] = 2070
def detectorbase_start(self):
from iotbx.detectors.pilatus_minicbf import PilatusImage
self.detectorbase = PilatusImage(self._image_file)
self.detectorbase.readHeader() # necessary for LABELIT
linearintdata = flex.int(
self.object.linearintdata[start_index:stop_index])
linearintdata.reshape(flex.grid((195, 2463)))
del self.object #once the data are copied, no need to keep the original
return linearintdata
def read(self):
if self.already_read_data: return
self.bin_safe_set_data(self.slice_callback())
self.already_read_data = True
if __name__ == '__main__':
import sys
full_path_to_file = sys.argv[1]
a = PilatusImage(testing_file)
a.read()
print a
print a.parameters
print a.rawdata, len(a.rawdata), a.size1 * a.size2
for dataitem in [
'bin', 'filename', 'header', 'headerlines', 'linearintdata',
'parameters', 'vendortype'
]:
print dataitem,
exec("print a.%s" % dataitem)
print pilatus_slice_from_object_and_slicenumber(a, 5)
P = pilatus_slice_from_file_url(url="file://%s?slice=5" %
full_path_to_file)
def detectorbase_start(self):
self.detectorbase = PilatusImage(self._image_file)
self.detectorbase.readHeader() # necessary for LABELIT
