def EndStation_from_ImageObject(imageobject,phil_params):
endstation = EndStation()
endstation.set_camera_convention(1)
endstation.set_rotation_axis("ROTATION HORIZ ANTI")
import six
if isinstance(imageobject.parameters["DETECTOR_SN"],six.string_types) and \
"S/N E-32-0105" in imageobject.parameters["DETECTOR_SN"]:
# vertical goniometer axis at Max-IV
endstation.set_rotation_axis("ROTATION VERT ANTI")
print "MAX-IV Eiger 16M"
endstation.mos['mosflm_detector'] = """
# Specific implementation for Max IV BioMAX
DETECTOR EIGE OMEGA 270
"""
if imageobject.vendortype == "Bruker Proteus CCD":
endstation.set_rotation_axis("ROTATION VERT ANTI")
print "BRUKER rotation", endstation.rot_axi
if imageobject.vendortype == "RAXIS":
endstation.set_rotation_axis("ROTATION VERT CLOCK")
#clockwise horizontal phi at most CHESS beamlines
#also at Australian Synchrotron
if imageobject.vendortype == "ADSC" and \
imageobject.serial_number in [406,414,441,448,457,471,924,928]:
endstation.set_rotation_axis("ROTATION HORIZ CLOCK")
if imageobject.vendortype == "ADSC" and imageobject.serial_number == 910:
if ADSC910_at_BioCARS(imageobject):
endstation.set_rotation_axis("ROTATION HORIZ CLOCK")
else:
endstation.set_rotation_axis("ROTATION VERT ANTI") # just a hypothesis
#vertical phi at APS 19ID
if imageobject.vendortype == "ADSC" and \
imageobject.serial_number in [914]:
endstation.set_rotation_axis("ROTATION HORIZ CLOCK")
if imageobject.vendortype == "RigakuSaturn":
endstation.set_rotation_axis("ROTATION VERT ANTI")
#change in phi axis rotation at CHESS A1
if imageobject.vendortype == "ADSC" and \
imageobject.serial_number in [441]:
record_date = imageobject.parameters["DATE"]
record_tse = time.mktime(time.strptime(record_date))
cutoff_441 = time.mktime(time.strptime("Fri Oct 01 00:00:00 2004"))
if record_tse < cutoff_441:
endstation.set_rotation_axis("ROTATION HORIZ ANTI")
# Special cases: Pringle-Shen goniometer at CHESS F3
if imageobject.vendortype == "ADSC" and \
imageobject.serial_number in [414] and \
phil_params.goniometer_rotation.lower().find(
'pringle-shen')>=0 and \
'AXIS' in imageobject.parameters and \
imageobject.parameters['AXIS']=='phi':
endstation.set_rotation_axis("ROTATION VERT ANTI")
if 'OMEGA' in imageobject.parameters and \
imageobject.parameters['OMEGA'] != 0.0 :
omega = imageobject.parameters['OMEGA']
from iotbx.detectors import rotate_vector_around
endstation.set_rotation_axis(
rotate_vector_around(endstation.rotation_axis(),
(0,1,0),-omega*math.pi/180.)
)
'''
#tested for CHESS F1 s/n 406:
SCANNER ROTATION HORIZ CLOCK FAST horizontal ORIGIN UR RECT TYPE ADSC
LIMITS RMIN 5 RMAX 137.2 XMAX 96.5 YMAX 97.5 XSCAN 94.0 YSCAN 94.0
BACKSTOP RADIUS 7.00 CENTRE 90.100 91.500
ADCOFFSET 20
NULLPIX 0
GAIN 0.300
#tested for CHESS F3 Pringle-Shen
SCANNER ROTATION VERT ANTI FAST horizontal ORIGIN UR RECT TYPE ADSC
LIMITS RMIN 5 RMAX 143.3 XMAX 106.8 YMAX 95.7 XSCAN 94.0 YSCAN 94.0
BACKSTOP RADIUS 4.00 CENTRE 106.600 94.200
GAIN 0.500
BIAS 5
'''
if imageobject.vendortype == "MacScience":
if imageobject.size1==3000:
endstation.mos['mosflm_detector'] = """DETECTOR DIP2030\n"""
endstation.set_rotation_axis("ROTATION HORIZ CLOCK")
if imageobject.vendortype == "MARCCD":
if imageobject.size1*imageobject.bin>=4096:
parameters = {'sz' : imageobject.size1*imageobject.bin,
'pix': imageobject.pixel_size / imageobject.bin}
parameters['scan']=parameters['pix']*parameters['sz']/2
endstation.mos['mosflm_detector'] = """#MARCCD detector
LIMITS XMIN 0 XMAX xmax_tag YMIN 0 YMAX ymax_tag xscan %(scan)d yscan %(scan)d
SIZE %(sz)d %(sz)d HEADER 1 byte 4096
PIXEL %(pix)f
NULLPIX 0
#4Kx4K MarCCD format is unknown to MOSFLM, which apparently defaults
#the nullpix to 10. This is a problem for weak-background images.
"""%parameters
'''the correct xmax_tag and ymax_tag are added later in the interface module'''
#identification of specific beamlines at Spring8 with Reversephi:
# BL41XU Mar MX225HE--Serial number 40
# BL32XU Mar MX225HE--Serial number 31
# rely on detector serial number, uncertain how to decode geometric description
# of rotation axis within the header.
if imageobject.parameters["DETECTOR_SN"] in [7]:
endstation.set_rotation_axis("ROTATION HORIZ CLOCK")
endstation.mos['mosflm_detector'] = """
# Specific implementation for APS SER-CAT BM22, chi=180 setting
DETECTOR MARCCD
DETECTOR REVERSEPHI
SIZE 4096 4096
PIXEL 0.07324 0.07324
"""
endstation.mos['mosflm_beamline'] = """GAIN 0.37
POLARISATION 0.99
DIVE 0.0001 0.00001
DISPER 0.0001
"""
if imageobject.parameters["DETECTOR_SN"] in [31,40]:
endstation.set_rotation_axis("ROTATION HORIZ CLOCK")
endstation.mos['mosflm_detector'] = """
# Specific implementation for Spring8 BL41XU Mar MX225HE
DETECTOR MARCCD
DETECTOR REVERSEPHI
SIZE 3072 3072
PIXEL 0.07324 0.07324
LIMITS RMIN 2 RMAX 159.1 XMAX 159.1 YMAX 112.5 XSCAN 159.1 YSCAN 159.1
"""
endstation.mos['mosflm_beamline'] = """GAIN 0.37
POLARISATION 0.99
DIVE 0.0001 0.00001
DISPER 0.0001
!offset 0.0 0.0
"""
if imageobject.vendortype == "ADSC" and \
endstation.rot_axi_string!="ROTATION HORIZ ANTI":
# Rough idea of the MOSFLM LIMITS
mmsize = imageobject.size1 * imageobject.pixel_size
maxx = max( abs(imageobject.beamx-mmsize), abs(imageobject.beamx) )
maxy = max( abs(imageobject.beamy-mmsize), abs(imageobject.beamy) )
parameters = {'rotation': endstation.rot_axi_string,
'rmax': math.sqrt(maxx*maxx + maxy*maxy),
'xmax': maxx,
'ymax': maxy,
'xscan': mmsize/2.,
'yscan': mmsize/2.}
if imageobject.serial_number in [457,928]: parameters['gain']=0.32
else: parameters['gain']=0.30
endstation.mos['mosflm_detector'] = """#detector
SCANNER %(rotation)s FAST horizontal ORIGIN UR RECT TYPE ADSC
LIMITS RMIN 5 RMAX %(rmax).1f XMAX %(xmax).1f YMAX %(ymax).1f XSCAN %(xscan).1f YSCAN %(yscan).1f
GAIN %(gain).3f
"""%parameters
if imageobject.serial_number in [457,928]:
endstation.mos['mosflm_beamline'] = beamlines['Australian']
else:
endstation.mos['mosflm_beamline'] = beamlines['CHESS']
if imageobject.vendortype == "ADSC" and imageobject.serial_number == 910:
if ADSC910_at_BioCARS(imageobject):
endstation.mos['mosflm_detector']=endstation.mos['mosflm_detector']+\
"#BIOCARS 14-BM-C S/N=910"
if imageobject.vendortype in [ "RAXIS" ]:
endstation.mos['mosflm_detector'] = """#detector
ADCOFFSet 5
"""
if imageobject.serial_number.lower().find('dr. r-axis iv')==0:
endstation.mos['mosflm_detector']=endstation.mos['mosflm_detector']+\
'DETECTOR RAXISIV'
#At least for MOSFLM 6.2.4, this seems to be important because it
# allows the program to accept large standard deviations for spots
# (above 32767). Otherwise MOSFLM can crash with SERIOUS ERROR message.
# Both DTrek and Raxis formats have "RAXIS" vendortype but only Raxis has "head" attribute
if "head" in imageobject.__dict__ and \
imageobject.head['Device'].lower().find('r-axis2')==0:
endstation.mos['mosflm_detector']=endstation.mos['mosflm_detector']+\
'detector raxis'
endstation.mos['mosflm_beamline'] = beamlines['RAXIS']
if imageobject.vendortype in [ "CBF" ]:
endstation.mos['mosflm_detector'] = """#detector cbf"""
if imageobject.vendortype in [ "Pilatus-6M" ]:
endstation.mos['mosflm_detector'] = """#detector Pilatus-6M"""
#flags mosflm interface to include the start & angle fix, mosflm 7.0.3 & below
if imageobject.vendortype in [ "MARIP" ]:
endstation.mos['mosflm_detector'] = """#detector
ADCOFFSet 5
"""#Just a guess: image plates require an offset to insure stability
# over long integration sweeps. Example: TM0064/11_20_01/1c3p3
#additional information for universally specifying image size
endstation.mos['mosflm_detector'] = endstation.mos['mosflm_detector'] + \
"\n#UIS_PIXEL %(pix)f\n#UIS_SIZE %(sz)d"%{
'sz' : imageobject.size1*imageobject.bin,
'pix': imageobject.pixel_size / imageobject.bin}
return endstation
def EndStation_from_ImageObject(imageobject,phil_params):
endstation = EndStation()
endstation.set_camera_convention(1)
endstation.set_rotation_axis("ROTATION HORIZ ANTI")
if imageobject.vendortype == "Bruker Proteus CCD":
endstation.set_rotation_axis("ROTATION VERT ANTI")
print "BRUKER rotation", endstation.rot_axi
if imageobject.vendortype == "RAXIS":
endstation.set_rotation_axis("ROTATION VERT CLOCK")
#clockwise horizontal phi at most CHESS beamlines
#also at Australian Synchrotron
if imageobject.vendortype == "ADSC" and \
imageobject.serial_number in [406,414,441,448,457,471,924,928]:
endstation.set_rotation_axis("ROTATION HORIZ CLOCK")
if imageobject.vendortype == "ADSC" and imageobject.serial_number == 910:
if ADSC910_at_BioCARS(imageobject):
endstation.set_rotation_axis("ROTATION HORIZ CLOCK")
else:
endstation.set_rotation_axis("ROTATION VERT ANTI") # just a hypothesis
#vertical phi at APS 19ID
if imageobject.vendortype == "ADSC" and \
imageobject.serial_number in [914]:
endstation.set_rotation_axis("ROTATION HORIZ CLOCK")
if imageobject.vendortype == "RigakuSaturn":
endstation.set_rotation_axis("ROTATION VERT ANTI")
#change in phi axis rotation at CHESS A1
if imageobject.vendortype == "ADSC" and \
imageobject.serial_number in [441]:
record_date = imageobject.parameters["DATE"]
record_tse = time.mktime(time.strptime(record_date))
cutoff_441 = time.mktime(time.strptime("Fri Oct 01 00:00:00 2004"))
if record_tse < cutoff_441:
endstation.set_rotation_axis("ROTATION HORIZ ANTI")
# Special cases: Pringle-Shen goniometer at CHESS F3
if imageobject.vendortype == "ADSC" and \
imageobject.serial_number in [414] and \
phil_params.goniometer_rotation.lower().find(
'pringle-shen')>=0 and \
imageobject.parameters.has_key('AXIS') and \
imageobject.parameters['AXIS']=='phi':
endstation.set_rotation_axis("ROTATION VERT ANTI")
if imageobject.parameters.has_key('OMEGA') and \
imageobject.parameters['OMEGA'] != 0.0 :
omega = imageobject.parameters['OMEGA']
from iotbx.detectors import rotate_vector_around
endstation.set_rotation_axis(
rotate_vector_around(endstation.rotation_axis(),
(0,1,0),-omega*math.pi/180.)
)
'''
#tested for CHESS F1 s/n 406:
SCANNER ROTATION HORIZ CLOCK FAST horizontal ORIGIN UR RECT TYPE ADSC
LIMITS RMIN 5 RMAX 137.2 XMAX 96.5 YMAX 97.5 XSCAN 94.0 YSCAN 94.0
BACKSTOP RADIUS 7.00 CENTRE 90.100 91.500
ADCOFFSET 20
NULLPIX 0
GAIN 0.300
#tested for CHESS F3 Pringle-Shen
SCANNER ROTATION VERT ANTI FAST horizontal ORIGIN UR RECT TYPE ADSC
LIMITS RMIN 5 RMAX 143.3 XMAX 106.8 YMAX 95.7 XSCAN 94.0 YSCAN 94.0
BACKSTOP RADIUS 4.00 CENTRE 106.600 94.200
GAIN 0.500
BIAS 5
'''
if imageobject.vendortype == "MacScience":
if imageobject.size1==3000:
endstation.mos['mosflm_detector'] = """DETECTOR DIP2030\n"""
endstation.set_rotation_axis("ROTATION HORIZ CLOCK")
if imageobject.vendortype == "MARCCD":
if imageobject.size1*imageobject.bin>=4096:
parameters = {'sz' : imageobject.size1*imageobject.bin,
'pix': imageobject.pixel_size / imageobject.bin}
parameters['scan']=parameters['pix']*parameters['sz']/2
endstation.mos['mosflm_detector'] = """#MARCCD detector
LIMITS XMIN 0 XMAX xmax_tag YMIN 0 YMAX ymax_tag xscan %(scan)d yscan %(scan)d
SIZE %(sz)d %(sz)d HEADER 1 byte 4096
PIXEL %(pix)f
NULLPIX 0
#4Kx4K MarCCD format is unknown to MOSFLM, which apparently defaults
#the nullpix to 10. This is a problem for weak-background images.
"""%parameters
'''the correct xmax_tag and ymax_tag are added later in the interface module'''
#identification of specific beamlines at Spring8 with Reversephi:
# BL41XU Mar MX225HE--Serial number 40
# BL32XU Mar MX225HE--Serial number 31
# rely on detector serial number, uncertain how to decode geometric description
# of rotation axis within the header.
if imageobject.parameters["DETECTOR_SN"] in [31,40]:
endstation.set_rotation_axis("ROTATION HORIZ CLOCK")
endstation.mos['mosflm_detector'] = """
# Specific implementation for Spring8 BL41XU Mar MX225HE
DETECTOR MARCCD
DETECTOR REVERSEPHI
SIZE 3072 3072
PIXEL 0.07324 0.07324
LIMITS RMIN 2 RMAX 159.1 XMAX 159.1 YMAX 112.5 XSCAN 159.1 YSCAN 159.1
"""
endstation.mos['mosflm_beamline'] = """GAIN 0.37
POLARISATION 0.99
DIVE 0.0001 0.00001
DISPER 0.0001
!offset 0.0 0.0
"""
if imageobject.vendortype == "ADSC" and \
endstation.rot_axi_string!="ROTATION HORIZ ANTI":
# Rough idea of the MOSFLM LIMITS
mmsize = imageobject.size1 * imageobject.pixel_size
maxx = max( abs(imageobject.beamx-mmsize), abs(imageobject.beamx) )
maxy = max( abs(imageobject.beamy-mmsize), abs(imageobject.beamy) )
parameters = {'rotation': endstation.rot_axi_string,
'rmax': math.sqrt(maxx*maxx + maxy*maxy),
'xmax': maxx,
'ymax': maxy,
'xscan': mmsize/2.,
'yscan': mmsize/2.}
if imageobject.serial_number in [457,928]: parameters['gain']=0.32
else: parameters['gain']=0.30
endstation.mos['mosflm_detector'] = """#detector
SCANNER %(rotation)s FAST horizontal ORIGIN UR RECT TYPE ADSC
LIMITS RMIN 5 RMAX %(rmax).1f XMAX %(xmax).1f YMAX %(ymax).1f XSCAN %(xscan).1f YSCAN %(yscan).1f
GAIN %(gain).3f
"""%parameters
if imageobject.serial_number in [457,928]:
endstation.mos['mosflm_beamline'] = beamlines['Australian']
else:
endstation.mos['mosflm_beamline'] = beamlines['CHESS']
if imageobject.vendortype == "ADSC" and imageobject.serial_number == 910:
if ADSC910_at_BioCARS(imageobject):
endstation.mos['mosflm_detector']=endstation.mos['mosflm_detector']+\
"#BIOCARS 14-BM-C S/N=910"
if imageobject.vendortype in [ "RAXIS" ]:
endstation.mos['mosflm_detector'] = """#detector
ADCOFFSet 5
"""
if imageobject.serial_number.lower().find('dr. r-axis iv')==0:
endstation.mos['mosflm_detector']=endstation.mos['mosflm_detector']+\
'DETECTOR RAXISIV'
#At least for MOSFLM 6.2.4, this seems to be important because it
# allows the program to accept large standard deviations for spots
# (above 32767). Otherwise MOSFLM can crash with SERIOUS ERROR message.
# Both DTrek and Raxis formats have "RAXIS" vendortype but only Raxis has "head" attribute
if imageobject.__dict__.has_key("head") and \
imageobject.head['Device'].lower().find('r-axis2')==0:
endstation.mos['mosflm_detector']=endstation.mos['mosflm_detector']+\
'detector raxis'
endstation.mos['mosflm_beamline'] = beamlines['RAXIS']
if imageobject.vendortype in [ "CBF" ]:
endstation.mos['mosflm_detector'] = """#detector cbf"""
if imageobject.vendortype in [ "Pilatus-6M" ]:
endstation.mos['mosflm_detector'] = """#detector Pilatus-6M"""
#flags mosflm interface to include the start & angle fix, mosflm 7.0.3 & below
if imageobject.vendortype in [ "MARIP" ]:
endstation.mos['mosflm_detector'] = """#detector
ADCOFFSet 5
"""#Just a guess: image plates require an offset to insure stability
# over long integration sweeps. Example: TM0064/11_20_01/1c3p3
#additional information for universally specifying image size
endstation.mos['mosflm_detector'] = endstation.mos['mosflm_detector'] + \
"\n#UIS_PIXEL %(pix)f\n#UIS_SIZE %(sz)d"%{
'sz' : imageobject.size1*imageobject.bin,
'pix': imageobject.pixel_size / imageobject.bin}
return endstation