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NIMS 1.1 #106

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Jan 5, 2015
Merged

NIMS 1.1 #106

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537e841
adapt nims1 to use nimsdata2
kevlarkevin Sep 24, 2014
efe5f3a
adapt sorter and processors for tgz datasets
kevlarkevin Nov 6, 2014
a1421c7
add upload route
Sep 30, 2014
7e171b5
adds update guide, tmux startup scripts and config
kevlarkevin Dec 10, 2014
a87c567
processor updates some Epoch metadata after recon
kevlarkevin Dec 16, 2014
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adapt sorter and processors for tgz datasets 
- pfiles.tgz are unpacked for parsing, and sorting
- updates db models to include num_mux_cal_cycles to allow processor
to identify candidate muxepi aux files from db
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@kevlarkevin
kevlarkevin committed Jan 5, 2015
commit efe5f3a0751505ad87d3c7f92fe34f0b13825b24
2 changes: 1 addition & 1 deletion nimsdata
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Submodule nimsdata updated from 687554 to e7536f
8 changes: 5 additions & 3 deletions nimsgears/model/nims.py
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Original file line number Diff line number Diff line change
Expand Up @@ -509,7 +509,7 @@ def __unicode__(self):

@classmethod
def from_mrfile(cls, mrfile):
subj_code, group_name, exp_name = nimsutil.parse_patient_id__(mrfile.subj_code, mrfile.group_name, mrfile.project_name, ResearchGroup.all_ids())
subj_code, group_name, exp_name = nimsutil.parse_patient_id(mrfile.patient_id, ResearchGroup.all_ids())
query = cls.query.join(Experiment, cls.experiment).filter(Experiment.name == exp_name)
query = query.join(ResearchGroup, Experiment.owner).filter(ResearchGroup.gid == group_name)
if subj_code:
Expand Down Expand Up @@ -605,7 +605,7 @@ def from_mrfile(cls, mrfile):
# central authority and/or querying the schedule database. But for now,
# just let the operator be None if the user isn't already in the system.
operator = User.by_uid(unicode(mrfile.operator), create=False)
session = Session(uid=uid, exam=mrfile.exam_no if isinstance(mrfile.exam_no, int) else 0, subject=subject, operator=operator)
session = Session(uid=uid, exam=int(mrfile.exam_no) if isinstance(mrfile.exam_no, (unicode, int)) else 0, subject=subject, operator=operator)
return session

@classmethod
Expand Down Expand Up @@ -696,6 +696,7 @@ class Epoch(DataContainer):
phase_encode_undersample = Field(Float)
slice_encode_undersample = Field(Float)
acquisition_matrix = Field(Unicode(255))
num_mux_cal_cycle = Field(Integer)

session = ManyToOne('Session')

Expand Down Expand Up @@ -727,7 +728,7 @@ def from_mrfile(cls, mrfile):
flip_angle = mrfile.flip_angle,
pixel_bandwidth = mrfile.pixel_bandwidth,
num_slices = mrfile.num_slices,
num_timepoints = mrfile.num_timepoints,
num_timepoints = mrfile.num_timepoints or 1,
num_averages = mrfile.num_averages,
num_echos = mrfile.num_echos,
receive_coil_name = unicode(mrfile.receive_coil_name),
Expand All @@ -744,6 +745,7 @@ def from_mrfile(cls, mrfile):
phase_encode_undersample = mrfile.phase_encode_undersample,
slice_encode_undersample = mrfile.slice_encode_undersample,
acquisition_matrix = unicode(str(mrfile.acquisition_matrix)),
num_mux_cal_cycle = mrfile.num_mux_cal_cycle if mrfile.filetype == u'pfile' else None, # hack for pfile
qa_status = u'pending',
# to unpack fov, mm_per_vox, and acquisition_matrix: np.fromstring(str(mm)[1:-1],sep=',')
)
Expand Down
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