def __init__(self, filename, index=0):
DetectorImageBase.__init__(self, filename)
self.vendortype = "EigerX"
self.supports_multiple_images = True
self.img_number = index # 0-indexed to clients, internally 1-indexed
if self.img_number == None: self.img_number = 0
self.vendor_specific_null_value = -1
def __init__(self, filename):
DetectorImageBase.__init__(self, filename)
try:
from cbflib_adaptbx import CBFAdaptor # optional package
self.adaptor = CBFAdaptor(filename)
# for testing only:
'''
self.adaptor.read_header()
print " size1:", self.adaptor.size1()
print " size2:", self.adaptor.size2()
print " overload:", self.adaptor.overload()
print "wavelength:", self.adaptor.wavelength()
print " distance:", self.adaptor.distance()
print "pixel size:", self.adaptor.pixel_size()
print " beamx:", self.adaptor.beam_index_slow*self.adaptor.pixel_size()
print " beamy:", self.adaptor.beam_index_fast*self.adaptor.pixel_size()
print " osc_start:", self.adaptor.osc_start()
print " osc_range:", self.adaptor.osc_range()
print self.adaptor.raster_description()
flags = self.adaptor.transform_flags()
print flags.transpose, flags.reverse_slow, flags.reverse_fast
'''
except Exception:
from iotbx.detectors.marIP import NullAdaptor
self.adaptor = NullAdaptor()
self.vendortype = "CBF"
self.readHeader()
try:
self.vendor_specific_null_value = int(
self.adaptor.undefined_value())
except RuntimeError as e:
self.vendor_specific_null_value = 0
def __init__(self,filename):
DetectorImageBase.__init__(self,filename)
try:
from cbflib_adaptbx import CBFAdaptor # optional package
self.adaptor = CBFAdaptor(filename)
# for testing only:
'''
self.adaptor.read_header()
print " size1:", self.adaptor.size1()
print " size2:", self.adaptor.size2()
print " overload:", self.adaptor.overload()
print "wavelength:", self.adaptor.wavelength()
print " distance:", self.adaptor.distance()
print "pixel size:", self.adaptor.pixel_size()
print " beamx:", self.adaptor.beam_index_slow*self.adaptor.pixel_size()
print " beamy:", self.adaptor.beam_index_fast*self.adaptor.pixel_size()
print " osc_start:", self.adaptor.osc_start()
print " osc_range:", self.adaptor.osc_range()
print self.adaptor.raster_description()
flags = self.adaptor.transform_flags()
print flags.transpose, flags.reverse_slow, flags.reverse_fast
'''
except Exception:
from iotbx.detectors.marIP import NullAdaptor
self.adaptor = NullAdaptor()
self.vendortype = "CBF"
self.readHeader()
self.vendor_specific_null_value = int(self.adaptor.undefined_value())
def debug_write(self, fileout, mod_data=None):
try:
if mod_data == None:
mod_data = self.get_raw_data().iround()
except AttributeError:
pass
DetectorImageBase.debug_write(self, fileout, mod_data)
def __init__(self,filename):
DetectorImageBase.__init__(self,filename)
try:
from cbflib_adaptbx import Mar345Adaptor # optional package
self.adaptor = Mar345Adaptor(filename)
except Exception:
self.adaptor = NullAdaptor()
self.vendortype = "MARIP"
def debug_write(self,fileout,mod_data=None):
try:
if mod_data == None:
mod_data = self.get_raw_data().iround()
except AttributeError:
pass
DetectorImageBase.debug_write(self,fileout,mod_data)
def __init__(self, filename):
DetectorImageBase.__init__(self, filename)
try:
from cbflib_adaptbx import Mar345Adaptor # optional package
self.adaptor = Mar345Adaptor(filename)
except Exception:
self.adaptor = NullAdaptor()
self.vendortype = "MARIP"
def __init__(self,filename):
DetectorImageBase.__init__(self,filename)
self.vendortype = "MARCCD"
byte_order = str(open(self.filename,"rb").read(2))
if byte_order == 'II':
self.endian = 0
else:
self.endian = 1
assert not self.isCompressed()
def __init__(self, filename):
DetectorImageBase.__init__(self, filename)
self.vendortype = "MARCCD"
with open(self.filename, "rb") as fh:
byte_order = fh.read(2)
if byte_order == b"II":
self.endian = 0
else:
self.endian = 1
assert not self.isCompressed()
def __init__(self, file_name):
DetectorImageBase.__init__(self, file_name)
raw = open(file_name, "rb").read()
self.binary_sections = get_binary_sections(raw)
self.header_sections = get_header_sections(raw, self.binary_sections)
assert len(self.binary_sections)==1
cif = iotbx.cif.fast_reader(input_string=self.header_sections)
self.cif_model = cif.model()
im1 = self.cif_model["image_1"]
self.vendortype = "CBF"
self.readHeader()
def __init__(self, file_name):
DetectorImageBase.__init__(self, file_name)
raw = open(file_name, "rb").read()
self.binary_sections = get_binary_sections(raw)
self.header_sections = get_header_sections(raw, self.binary_sections)
assert len(self.binary_sections) == 1
cif = iotbx.cif.fast_reader(input_string=self.header_sections)
self.cif_model = cif.model()
im1 = self.cif_model["image_1"]
self.vendortype = "CBF"
self.readHeader()
def exercise_debug_write():
#---------Write out a test file
D = DetectorImageBase('no_file')
D.parameters = {'SIZE1':filesize,
'SIZE2':filesize,
'PIXEL_SIZE':0.1,
'DISTANCE':100.0,
'TWOTHETA':0.0,
'OSC_START':0.0,
'OSC_RANGE':1.0,
'WAVELENGTH':1.0,
'BEAM_CENTER_X':12.5,
'BEAM_CENTER_Y':12.5,
}
def getEndian():
return 0
D.getEndian = getEndian
sindata = flex.int()
for x in xrange(filesize):
sindata.append(min(255,abs(int(256*sinfunc(x)))))
moddata = flex.int()
accum = 0
for x in xrange(filesize):
for y in xrange(filesize):
value = sindata[x]*sindata[y]
moddata.append(value)
accum+=value
D.debug_write(filename,mod_data=moddata)
#---------Read back the test file
a = adsc.ADSCImage(filename)
a.read()
assert a.size1 == filesize
assert a.size2 == filesize
assert a.npixels == filesize*filesize
assert approx_equal(a.pixel_size, 0.1)
assert approx_equal(a.osc_start, 0)
checkaccum = 0
for x in xrange(a.npixels):
if moddata[x]!=a.linearintdata[x]:
print x,moddata[x],a.linearintdata[x]
checkaccum+=a.linearintdata[x]
assert accum == checkaccum
os.remove(filename)
def __init__(self, filename):
"""Initialize the instance"""
# Make sure the image name is a string for iotbx
try:
image_str = unicodedata.normalize("NFKD", filename).encode("ascii", "ignore")
except TypeError:
image_str = filename
DetectorImageBase.__init__(self, image_str)
# self.vendortype = "MARCCD"
byte_order = str(open(self.filename, "rb").read(2))
if byte_order == "II":
self.endian = 0
else:
self.endian = 1
assert not self.isCompressed()
def exercise_debug_write():
#---------Write out a test file
D = DetectorImageBase('no_file')
D.parameters = {
'SIZE1': filesize,
'SIZE2': filesize,
'PIXEL_SIZE': 0.1,
'DISTANCE': 100.0,
'TWOTHETA': 0.0,
'OSC_START': 0.0,
'OSC_RANGE': 1.0,
'WAVELENGTH': 1.0,
'BEAM_CENTER_X': 12.5,
'BEAM_CENTER_Y': 12.5,
}
def getEndian():
return 0
D.getEndian = getEndian
sindata = flex.int()
for x in range(filesize):
sindata.append(min(255, abs(int(256 * sinfunc(x)))))
moddata = flex.int()
accum = 0
for x in range(filesize):
for y in range(filesize):
value = sindata[x] * sindata[y]
moddata.append(value)
accum += value
D.debug_write(filename, mod_data=moddata)
#---------Read back the test file
a = adsc.ADSCImage(filename)
a.read()
assert a.size1 == filesize
assert a.size2 == filesize
assert a.npixels == filesize * filesize
assert approx_equal(a.pixel_size, 0.1)
assert approx_equal(a.osc_start, 0)
checkaccum = 0
for x in range(a.npixels):
if moddata[x] != a.linearintdata[x]:
print(x, moddata[x], a.linearintdata[x])
checkaccum += a.linearintdata[x]
assert accum == checkaccum
os.remove(filename)
def __init__(self,filename): DetectorImageBase.__init__(self,filename) self.vendortype = "Eiger" self.vendor_specific_null_value = -1
def __init__(self, filename, source_data=None):
DetectorImageBase.__init__(self, filename)
self.vendortype = "npy_raw"
self.source_data = source_data
def __init__(self,filename): DetectorImageBase.__init__(self,filename) self.vendortype = "ADSC"
def __init__(self,filename): DetectorImageBase.__init__(self,filename) Raxis.__init__(self,filename) self.vendortype = "RAXIS"
def __init__(self, filename):
DetectorImageBase.__init__(self, filename)
self.vendortype = "Pilatus"
self.vendor_specific_null_value = -1
def __init__(self,filename): DetectorImageBase.__init__(self,filename) self.vendortype = "ADSC" self.open_file = open # default: open files with built-in, unless otherwise instructed by dxtbx format
def __init__(self, filename, source_data=None):
DetectorImageBase.__init__(self, filename)
self.vendortype = "npy_raw"
self.source_data = image_dict_to_unicode(source_data)
def __init__(self,filename): DetectorImageBase.__init__(self,filename) self.vendortype = "EIGER" self.supports_multiple_images = True self.img_number = 0 # 0-indexed to clients, internally 1-indexed
def __init__(self,filename): DetectorImageBase.__init__(self,filename) self.vendortype = "RigakuSaturn"
def __init__(self,filename): DetectorImageBase.__init__(self,filename) self.vendortype = "SMV(Generic)"
def __init__(self,filename): DetectorImageBase.__init__(self,filename) self.filename = filename self.vendortype = "MacScience" self.getImageSize()
def __init__(self,filename): DetectorImageBase.__init__(self,filename) self.filename = filename self.vendortype = "MacScience" self.getImageSize()
def __init__(self,first,last):
adopt_init_args(self, locals())
def size(self): return self.last-self.first+1
class test_divider:
def tile_slow_interval(self,idx):
if idx in [0,1,2]: return test_tile(4,2043)
if idx in [3,4,5]: return test_tile(2052,4091)
if idx in [6,7,8]: return test_tile(4100,6139)
def tile_fast_interval(self,idx):
if idx in [0,3,6]: return test_tile(4,2043)
if idx in [1,4,7]: return test_tile(2052,4091)
if idx in [2,5,8]: return test_tile(4100,6139)
input_parameters = {'BEAM_CENTER_X':154.9,'BEAM_CENTER_Y':148.7,
'SIZE1':6144,'SIZE2':6144,'PIXEL_SIZE':0.051294}
from iotbx.detectors.detectorbase import DetectorImageBase
input_object = DetectorImageBase("no file")
input_object.parameters = input_parameters
ID = test_divider()
S = StringIO.StringIO()
for convention in xrange(8):
for moduleidx in xrange(9):
B = convert_beam_instrument_to_module(input_object,ID,moduleidx,convention)
print >>S,"(%.1f,%.1f)"%(B[0],B[1]),
print >>S
assert not show_diff(S.getvalue(),
"""(154.7,148.5) (154.7,43.4) (154.7,-61.6) (49.6,148.5) (49.6,43.4) (49.6,-61.6) (-55.4,148.5) (-55.4,43.4) (-55.4,-61.6)
(148.5,154.7) (148.5,49.6) (148.5,-55.4) (43.4,154.7) (43.4,49.6) (43.4,-55.4) (-61.6,154.7) (-61.6,49.6) (-61.6,-55.4)
(154.7,166.2) (154.7,61.2) (154.7,-43.9) (49.6,166.2) (49.6,61.2) (49.6,-43.9) (-55.4,166.2) (-55.4,61.2) (-55.4,-43.9)
(148.5,160.0) (148.5,55.0) (148.5,-50.1) (43.4,160.0) (43.4,55.0) (43.4,-50.1) (-61.6,160.0) (-61.6,55.0) (-61.6,-50.1)
(160.0,148.5) (160.0,43.4) (160.0,-61.6) (55.0,148.5) (55.0,43.4) (55.0,-61.6) (-50.1,148.5) (-50.1,43.4) (-50.1,-61.6)
(166.2,154.7) (166.2,49.6) (166.2,-55.4) (61.2,154.7) (61.2,49.6) (61.2,-55.4) (-43.9,154.7) (-43.9,49.6) (-43.9,-55.4)
def __init__(self, filename):
DetectorImageBase.__init__(self, filename)
self.vendortype = "SMV(Generic)"
if idx in [6, 7, 8]: return test_tile(4100, 6139)
def tile_fast_interval(self, idx):
if idx in [0, 3, 6]: return test_tile(4, 2043)
if idx in [1, 4, 7]: return test_tile(2052, 4091)
if idx in [2, 5, 8]: return test_tile(4100, 6139)
input_parameters = {
'BEAM_CENTER_X': 154.9,
'BEAM_CENTER_Y': 148.7,
'SIZE1': 6144,
'SIZE2': 6144,
'PIXEL_SIZE': 0.051294
}
from iotbx.detectors.detectorbase import DetectorImageBase
input_object = DetectorImageBase("no file")
input_object.parameters = input_parameters
ID = test_divider()
S = StringIO.StringIO()
for convention in range(8):
for moduleidx in range(9):
B = convert_beam_instrument_to_module(input_object, ID, moduleidx,
convention)
print >> S, "(%.1f,%.1f)" % (B[0], B[1]),
print >> S
assert not show_diff(
S.getvalue(),
"""(154.7,148.5) (154.7,43.4) (154.7,-61.6) (49.6,148.5) (49.6,43.4) (49.6,-61.6) (-55.4,148.5) (-55.4,43.4) (-55.4,-61.6)
(148.5,154.7) (148.5,49.6) (148.5,-55.4) (43.4,154.7) (43.4,49.6) (43.4,-55.4) (-61.6,154.7) (-61.6,49.6) (-61.6,-55.4)
(154.7,166.2) (154.7,61.2) (154.7,-43.9) (49.6,166.2) (49.6,61.2) (49.6,-43.9) (-55.4,166.2) (-55.4,61.2) (-55.4,-43.9)
(148.5,160.0) (148.5,55.0) (148.5,-50.1) (43.4,160.0) (43.4,55.0) (43.4,-50.1) (-61.6,160.0) (-61.6,55.0) (-61.6,-50.1)
def __init__(self, filename):
DetectorImageBase.__init__(self, filename)
self.vendortype = "Hamamatsu"
def __init__(self,filename): DetectorImageBase.__init__(self,filename) self.vendortype = "RigakuSaturn"
def __init__(self, filename):
DetectorImageBase.__init__(self, filename)
Raxis.__init__(self, filename)
self.vendortype = "RAXIS"
def __init__(self, filename, source_data = None): DetectorImageBase.__init__(self, filename) self.vendortype = "npy_raw" self.source_data = source_data
