def main(argv):
root = argv[1]
an_mod = __import__(argv[2])
an = an_mod.Analysis()
fieldnos = set('1234')
def wanted(bn, path, isdir):
return isdir and bn in fieldnos
count = 0
skipset = set()
done = set()
def error_in(path, tbck, skip=False):
if (path, tbck) in done:
return
done.add((path, tbck))
if skip:
assert not path in skipset, path
skipset.add(path)
import sys
print >> sys.stderr, 'ERROR in %s:\n%s' % (path, tbck)
for pass_ in an.passes:
for hdf in gimme(root, wanted):
cell_line, plate, rc, sdcdir = (hdf.split('/'))[-5:-1]
fieldno = sdcdir[0]
index = '%s_%s_%s_%s' % (cell_line, plate, rc, fieldno)
# plate, rc = (hdf.split('/'))[-4:-2]
r, c = rc[0], rc[1:]
try:
with h5py.File(hdf, 'r') as h5:
wells = list(sdc_extract.iterwells(h5))
w = None
try:
w = wells[0][1]
assert len(wells) == 1
except:
wisnone = w is None
error_in(hdf, tb.format_exc(), skip=wisnone)
if wisnone:
continue
try:
assert (plate, r, c) == sdc_extract.well_coords(w)
except:
error_in(hdf, tb.format_exc())
try:
means, stddevs = sdc_extract.well_stats(w)
assert (len(means), len(stddevs)) == (26, 26), \
repr((len(means), len(stddevs)))
except:
error_in(hdf, tb.format_exc())
flds = list(sdc_extract.iterfields(w))
f = None
try:
f = flds[0]
assert len(flds) == 1, repr((hdf, len(flds)))
except:
fisnone = f is None
error_in(hdf, tb.format_exc(), skip=fisnone)
if fisnone:
continue
an.process_rows(sdc_extract.field_feature_values(f), index, pass_)
except SystemExit:
raise
except:
error_in(hdf, tb.format_exc())
finally:
try:
h5.close()
except:
pass
#print >> sys.stderr, 'oops: %s' % tb.format_exc()
# count += 1
# if count >= 5:
# break
an.finish(pass_)
an.finish()
an.report()
def main(argv=sys.argv):
global READOUTS
READOUTS = dict()
global HEADERS
HEADERS = dict()
global COUNT
COUNT = 0
global OUTH
OUTH = sys.stdout
root = argv[1]
platemap = _get_exp_design(argv[2])
try:
outpath = argv[3]
except IndexError:
outpath = None
try:
terminator = '\r\n' if argv[4].lower() == 'windows' else '\n'
except IndexError:
terminator = None
payload = namedtuple('_payload',
'cell_line treatment info data')
wl2wl={'530': '488', '685': '647'}
wanted_wavelengths = sorted(wl2wl.keys())
wanted_features = tuple(['Whole_w%s (Mean)' % s
for s in wanted_wavelengths])
last_cell_line = None
print_headers = True
cell_line_data = headers = None
done = False
def wanted(bn, path, isdir):
return isdir and is_valid_rc(bn)
well_paths = gimme(root, wanted)
while True:
try:
well_path = well_paths.next()
except StopIteration:
well_path = None
if well_path:
cell_line, plate, rc = (well_path.split('/'))[-3:]
treatment, info = platemap[plate][rc]
coords = info.coords
r, c = rc[0], rc[1:]
else:
done = True
if done or cell_line != last_cell_line:
_print_as_datapflex(cell_line_data,
print_headers,
wl2wl, wanted_wavelengths,
wanted_features,
outpath=outpath,
terminator=terminator)
if done:
break
last_cell_line = cell_line
print_headers = False
cell_line_data = defaultdict(lambda:
defaultdict(lambda:
defaultdict(lambda:
defaultdict(list))))
fields_used = []
data = []
for sdc in sorted(os.listdir(well_path)):
if not sdc.endswith('.sdc'):
continue
hdf = op.join(well_path, sdc, 'Data.h5')
try:
with h5py.File(hdf, 'r') as h5:
wells = list(sdc_extract.iterwells(h5))
if not len(wells):
# TODO: log warning
continue
flds = list(sdc_extract.iterfields(wells[0][1]))
assert len(flds) == 1, str((hdf, len(flds)))
data.append(sdc_extract.field_feature_values(flds[0],
wanted_features))
fieldno = sdc[-5]
fields_used.append(unicode(fieldno))
except IOError:
tb.print_exc()
finally:
try:
h5.close()
except:
pass
info = info._replace(coords=tuple([coords + (fn,)
for fn in fields_used]))
zone = info.zone
ligand = treatment.ligand_name
conc = treatment.ligand_concentration
time_ = treatment.time
cell_line_data[zone][ligand][conc][time_].append(payload(unicode(cell_line),
treatment, info, data))
return 0