def condense_array(field_dict, field_base):
field_keys = field_dict.keys()
arrays_dict = odict()
n = 0
max_idx = len(field_keys)
# advance to first array entry
while (n < max_idx and field_keys[n].find(field_base) < 0):
n += 1
if n == max_idx:
return arrays_dict
# initialize all the arrays present.. do this by creating lists
# for every new field where the index is 0
idx = 0
while (True):
field = field_keys[n]
if (field.find(field_base) < 0):
break
# field is like this: 'sSliceArray.asSlice[0].sPosition.dTra'
# it gets decomposed into tail: '0].sPosition.dTra'
tail = field.split('[')[-1]
# then decomposed into the number and name: ['0', '.sPosition.dTra']
idx_str, a_name = tail.split(']')
idx = int(idx_str)
if idx == 0:
arrays_dict[a_name[1:]] = [field_dict[field]]
else:
arrays_dict[a_name[1:]].append(field_dict[field])
n += 1
for a_name, a in arrays_dict.items():
arrays_dict[a_name] = np.array(a)
return arrays_dict
def strip_ascconv(hdr_str):
# scan forward to the 2nd 'ASCCONV BEGIN' string
pos = hdr_str.find('ASCCONV BEGIN')
## hdr_str = hdr_str[pos+100:] # make sure to clear the 'ASCCONV' stuff
## pos = hdr_str.find('ASCCONV BEGIN')
hdr_str = hdr_str[pos:]
# get to the first line of the ASCCONV section
pos = hdr_str.find('\n')
hdr_str = hdr_str[pos + 1:]
f = cStringIO.StringIO(hdr_str)
field_dict = odict()
for line in f.readlines():
if line.find('ASCCONV END') >= 0:
break
line = line.strip('\n')
field, val = line.split('=')
field = field.strip()
val = val.strip()
val = val.split(' #')[0] # there may be comments like on this line??
if (val.find('"') >= 0):
field_dict[field] = val.strip('"')
elif (val.find('0x') >= 0):
field_dict[field] = int(val, 16)
else:
field_dict[field] = float(val)
return field_dict
def condense_array(field_dict, field_base):
field_keys = field_dict.keys()
arrays_dict = odict()
n = 0
max_idx = len(field_keys)
# advance to first array entry
while(n < max_idx and field_keys[n].find(field_base) < 0):
n += 1
if n==max_idx:
return arrays_dict
# initialize all the arrays present.. do this by creating lists
# for every new field where the index is 0
idx = 0
while(True):
field = field_keys[n]
if(field.find(field_base) < 0):
break
# field is like this: 'sSliceArray.asSlice[0].sPosition.dTra'
# it gets decomposed into tail: '0].sPosition.dTra'
tail = field.split('[')[-1]
# then decomposed into the number and name: ['0', '.sPosition.dTra']
idx_str, a_name = tail.split(']')
idx = int(idx_str)
if idx==0:
arrays_dict[a_name[1:]] = [field_dict[field]]
else:
arrays_dict[a_name[1:]].append(field_dict[field])
n += 1
for a_name, a in arrays_dict.items():
arrays_dict[a_name] = np.array(a)
return arrays_dict
def strip_ascconv(hdr_str):
# scan forward to the 2nd 'ASCCONV BEGIN' string
pos = hdr_str.find('ASCCONV BEGIN')
## hdr_str = hdr_str[pos+100:] # make sure to clear the 'ASCCONV' stuff
## pos = hdr_str.find('ASCCONV BEGIN')
hdr_str = hdr_str[pos:]
# get to the first line of the ASCCONV section
pos = hdr_str.find('\n')
hdr_str = hdr_str[pos+1:]
f = cStringIO.StringIO(hdr_str)
field_dict = odict()
for line in f.readlines():
if line.find('ASCCONV END') >= 0:
break
line = line.strip('\n')
field, val = line.split('=')
field = field.strip()
val = val.strip()
val = val.split(' #')[0] # there may be comments like on this line??
if(val.find('"') >= 0):
field_dict[field] = val.strip('"')
elif(val.find('0x') >= 0):
field_dict[field] = int(val, 16)
else:
field_dict[field] = float(val)
return field_dict
from ConfigParser import SafeConfigParser
from optparse import OptionParser
from recon.odict import odict
from recon import import_from
tool_map = odict(
(("dumpheader", "DumpHeader"), ("fdf2img", "Fdf2Img"),
("getparam", "GetParam"), ("recon-doc", "ImagingDoc"), ("recon", "Recon"),
("recon_gui", "ReconGUI"), ("viewimage", "ViewImageTool")))
tool_names = tool_map.keys()
default_logfile = "recon.log"
#-----------------------------------------------------------------------------
def getToolByName(toolname):
if not tool_map.has_key(toolname):
raise ValueError("No tool called '%s'." % toolname)
classname = tool_map[toolname]
modulename = "recon.tools.%s" % classname
try:
return import_from(modulename, classname)
except ImportError:
raise RuntimeError("Tool class %s.%s not found." %
(modulename, classname))
def parseVolRangeOption(vol_range, parser):
"""
Separates out the command-line option volume range into distinct numbers
@param vol_range: volume range as x:y
import numpy as np
from os import path
from recon.odict import odict
from recon import import_from
from recon.inplane_xforms import compose_xform
from recon.util import Quaternion, integer_ranges, scale_data
# module-private dict specifying available image readers
_readers = odict((
("analyze", ("recon.analyze","readImage")),
("nifti", ("recon.nifti","readImage")),
("fid", ("recon.scanners.varian","FidImage")),
("fdf", ("recon.scanners.varian","FDFImage")),
("siemens", ("recon.scanners.siemens", "SiemensImage"))))
available_readers = _readers.keys()
# module-private dict specifying available image writers
_writers = odict((
("analyze", ("recon.analyze","writeImage")),
("nifti-single", ("recon.nifti","writeImage")),
("nifti-dual", ("recon.nifti","writeDualImage")),
))
available_writers = _writers.keys()
recon_output2dtype = odict((
('magnitude', np.dtype(np.float32)),
('complex', np.dtype(np.complex64)),
('double', np.dtype(np.float64)),
('byte', np.dtype(np.int8)),
('ubyte', np.dtype(np.uint8)),
</menu>
</menubar>
</ui>'''
cmap_lookup = odict((
(0, P.cm.Blues),
(1, P.cm.Greens),
(2, P.cm.Greys),
(3, P.cm.Oranges),
(4, P.cm.Purples),
(5, P.cm.Reds),
(6, P.cm.Spectral),
(7, P.cm.autumn),
(8, P.cm.bone),
(9, P.cm.cool),
(10, P.cm.copper),
(11, P.cm.gist_earth),
(12, P.cm.gist_gray),
(13, P.cm.gist_heat),
(14, P.cm.gist_rainbow),
(15, P.cm.gray),
(16, P.cm.hot),
(17, P.cm.hsv),
(18, P.cm.jet),
(19, P.cm.spring),
(20, P.cm.summer),
(21, P.cm.winter),
))
interp_types = ['nearest', 'bilinear', 'sinc']
interp_lookup = odict([(num, name) for num, name in enumerate(interp_types)])
import numpy as np
from os import path
from recon.odict import odict
from recon import import_from
from recon.inplane_xforms import compose_xform
from recon.util import Quaternion, integer_ranges, scale_data
# module-private dict specifying available image readers
_readers = odict(
(("analyze", ("recon.analyze", "readImage")), ("nifti", ("recon.nifti",
"readImage")),
("fid", ("recon.scanners.varian",
"FidImage")), ("fdf", ("recon.scanners.varian", "FDFImage")),
("siemens", ("recon.scanners.siemens", "SiemensImage"))))
available_readers = _readers.keys()
# module-private dict specifying available image writers
_writers = odict((
("analyze", ("recon.analyze", "writeImage")),
("nifti-single", ("recon.nifti", "writeImage")),
("nifti-dual", ("recon.nifti", "writeDualImage")),
))
available_writers = _writers.keys()
recon_output2dtype = odict((
('magnitude', np.dtype(np.float32)),
('complex', np.dtype(np.complex64)),
('double', np.dtype(np.float64)),
('byte', np.dtype(np.int8)),
('ubyte', np.dtype(np.uint8)),
</menu>
</menubar>
</ui>'''
cmap_lookup = odict((
(0, P.cm.Blues),
(1, P.cm.Greens),
(2, P.cm.Greys),
(3, P.cm.Oranges),
(4, P.cm.Purples),
(5, P.cm.Reds),
(6, P.cm.Spectral),
(7, P.cm.autumn),
(8, P.cm.bone),
(9, P.cm.cool),
(10, P.cm.copper),
(11, P.cm.gist_earth),
(12, P.cm.gist_gray),
(13, P.cm.gist_heat),
(14, P.cm.gist_rainbow),
(15, P.cm.gray),
(16, P.cm.hot),
(17, P.cm.hsv),
(18, P.cm.jet),
(19, P.cm.spring),
(20, P.cm.summer),
(21, P.cm.winter),
))
interp_types = ['nearest', 'bilinear', 'sinc']
interp_lookup = odict([(num,name) for num,name in enumerate(interp_types)])
byteorders = {
sys.byteorder: sys.byteorder == 'little' and LITTLE_ENDIAN or BIG_ENDIAN,
'swapped': sys.byteorder == 'little' and BIG_ENDIAN or LITTLE_ENDIAN
}
HEADER_SIZE = 348
struct_fields = odict(
(('sizeof_hdr', 'i'), ('data_type', '10s'), ('db_name', '18s'),
('extents', 'i'), ('session_error', 'h'), ('regular', 'c'), ('hkey_un0',
'c'),
('ndim', 'h'), ('idim', 'h'), ('jdim', 'h'), ('kdim', 'h'), ('tdim', 'h'),
('dim5', 'h'), ('dim6', 'h'), ('dim7', 'h'), ('vox_units', '4s'),
('cal_units', '8s'), ('unused1', 'h'), ('datatype', 'h'), ('bitpix', 'h'),
('dim_un0', 'h'), ('pixdim0', 'f'), ('isize', 'f'), ('jsize', 'f'),
('ksize', 'f'), ('tsize', 'f'), ('pixdim5', 'f'), ('pixdim6', 'f'),
('pixdim7', 'f'), ('vox_offset', 'f'), ('scale_factor', 'f'),
('funused2', 'f'), ('funused3', 'f'), ('cal_max', 'f'), ('cal_min', 'f'),
('compressed', 'i'), ('verified', 'i'), ('glmax', 'i'), ('glmin', 'i'),
('descrip', '80s'), ('aux_file', '24s'), ('orient', 'B'), ('x0', 'h'),
('y0', 'h'), ('z0', 'h'), ('sunused', '4s'), ('generated', '10s'),
('scannum', '10s'), ('patient_id', '10s'), ('exp_date',
'10s'), ('exp_time', '10s'),
('hist_un0', '3s'), ('views', 'i'), ('vols_added', 'i'), ('start_field',
'i'),
('field_skip', 'i'), ('omax', 'i'), ('omin', 'i'), ('smax', 'i'), ('smin',
'i')))
field_formats = struct_fields.values()
##############################################################################
class AnalyzeReader:
struct_fields = odict((
('sizeof_hdr','i'),
('data_type','10s'),
('db_name','18s'),
('extents','i'),
('session_error','h'),
('regular','c'),
('dim_info','B'),
# these are short dim[8]
('ndim','h'),
('idim','h'),
('jdim','h'),
('kdim','h'),
('tdim','h'),
('dim5','h'),
('dim6','h'),
('dim7','h'),
('intent_p1','f'),
('intent_p2','f'),
('intent_p3','f'),
('intent_code','h'),
('datatype', 'h'),
('bitpix','h'),
('slice_start', 'h'),
# these 8 float are float pixdim[8] (pixdim[0] encodes qfac)
('qfac','f'),
('isize','f'),
('jsize','f'),
('ksize','f'),
('tsize','f'),
('pixdim5','f'),
('pixdim6','f'),
('pixdim7','f'),
('vox_offset','f'),
('scl_slope','f'),
('scl_inter','f'),
('slice_end','h'),
('slice_code','B'),
('xyzt_units','B'),
('cal_max','f'),
('cal_min','f'),
('slice_duration','f'),
('toffset','f'),
('glmax','i'),
('glmin','i'),
('descrip','80s'),
('aux_file','24s'),
('qform_code','h'),
('sform_code','h'),
('quatern_b','f'),
('quatern_c','f'),
('quatern_d','f'),
('qoffset_x','f'),
('qoffset_y','f'),
('qoffset_z','f'),
('srow_x0','f'),
('srow_x1','f'),
('srow_x2','f'),
('srow_x3','f'),
('srow_y0','f'),
('srow_y1','f'),
('srow_y2','f'),
('srow_y3','f'),
('srow_z0','f'),
('srow_z1','f'),
('srow_z2','f'),
('srow_z3','f'),
('intent_name','16s'),
('magic','4s'),
))
struct_fields = odict(
(
("sizeof_hdr", "i"),
("data_type", "10s"),
("db_name", "18s"),
("extents", "i"),
("session_error", "h"),
("regular", "c"),
("hkey_un0", "c"),
("ndim", "h"),
("idim", "h"),
("jdim", "h"),
("kdim", "h"),
("tdim", "h"),
("dim5", "h"),
("dim6", "h"),
("dim7", "h"),
("vox_units", "4s"),
("cal_units", "8s"),
("unused1", "h"),
("datatype", "h"),
("bitpix", "h"),
("dim_un0", "h"),
("pixdim0", "f"),
("isize", "f"),
("jsize", "f"),
("ksize", "f"),
("tsize", "f"),
("pixdim5", "f"),
("pixdim6", "f"),
("pixdim7", "f"),
("vox_offset", "f"),
("scale_factor", "f"),
("funused2", "f"),
("funused3", "f"),
("cal_max", "f"),
("cal_min", "f"),
("compressed", "i"),
("verified", "i"),
("glmax", "i"),
("glmin", "i"),
("descrip", "80s"),
("aux_file", "24s"),
("orient", "B"),
("x0", "h"),
("y0", "h"),
("z0", "h"),
("sunused", "4s"),
("generated", "10s"),
("scannum", "10s"),
("patient_id", "10s"),
("exp_date", "10s"),
("exp_time", "10s"),
("hist_un0", "3s"),
("views", "i"),
("vols_added", "i"),
("start_field", "i"),
("field_skip", "i"),
("omax", "i"),
("omin", "i"),
("smax", "i"),
("smin", "i"),
)
)
from ConfigParser import SafeConfigParser
from optparse import OptionParser
from recon.odict import odict
from recon import import_from
tool_map = odict(
(
("dumpheader", "DumpHeader"),
("fdf2img", "Fdf2Img"),
("getparam", "GetParam"),
("recon-doc", "ImagingDoc"),
("recon", "Recon"),
("recon_gui", "ReconGUI"),
("viewimage", "ViewImageTool"),
)
)
tool_names = tool_map.keys()
default_logfile = "recon.log"
# -----------------------------------------------------------------------------
def getToolByName(toolname):
if not tool_map.has_key(toolname):
raise ValueError("No tool called '%s'." % toolname)
classname = tool_map[toolname]
modulename = "recon.tools.%s" % classname
try:
return import_from(modulename, classname)
except ImportError:
raise RuntimeError("Tool class %s.%s not found." % (modulename, classname))