def write_screen(data_dir, plate, outf):
d, ch_names = group_files(data_dir)
extra_kv = {"AxisTypes": "CT", "ChannelNames": ",".join(ch_names)}
n_fields = len(d)
writer = ScreenWriter(plate, ROWS, COLUMNS, n_fields)
assert ROWS == COLUMNS == 1
field_values = []
for field_idx in sorted(d):
field_values.append(os.path.join(data_dir, d[field_idx]))
writer.add_well(field_values, extra_kv=extra_kv)
writer.write(outf)
def consistency_check(d):
if len(d) != ROWS * COLUMNS:
writer = ScreenWriter("foo", ROWS, COLUMNS, FIELDS)
missing = []
for idx in xrange(ROWS * COLUMNS):
k = writer.index2d(idx)
if k not in d:
missing.append(k)
print "ERROR: missing well(s):", missing
for v in d.itervalues():
assert set(v) == set(EXPECTED_FIELDS)
def consistency_check(d):
if len(d) != ROWS * COLUMNS:
writer = ScreenWriter("foo", ROWS, COLUMNS, FIELDS)
missing = []
for idx in range(ROWS * COLUMNS):
k = writer.index2d(idx)
if k not in d:
missing.append(k)
print("ERROR: missing well(s):", missing)
for v in d.itervalues():
assert set(v) == set(EXPECTED_FIELDS)
def setUp(self, screen_name=None):
super(TestScreenWriter, self).setUp(screen_name=screen_name)
fout = StringIO()
self.all_field_values = []
self.extra_kv = {"Dimensions": "ZCT"}
kwargs = {"screen_name": screen_name} if screen_name else {}
writer = ScreenWriter(
self.name, self.rows, self.columns, self.fields, **kwargs
)
for i in xrange(self.size):
writer.add_well(self._field_values(i), extra_kv=self.extra_kv)
writer.write(fout)
fout.seek(0)
self.cp = ConfigParser.ConfigParser()
self.cp.readfp(fout)
def write_screen(data_dir, plate, outf, screen=None):
kwargs = {"screen_name": screen} if screen else {}
writer = ScreenWriter(plate, ROWS, COLUMNS, FIELDS, **kwargs)
for i in xrange(ROWS):
for j in xrange(COLUMNS):
x, y = j, i
subdir = os.path.join(data_dir, "field--X%02d--Y%02d" % (x, y))
field_values = []
if not os.path.isdir(subdir):
sys.stderr.write("WARNING: no subdir for X=%d, Y=%d (%s)\n" % (x, y, subdir))
else:
pattern = find_pattern(subdir)
if pattern is not None:
field_values.append(os.path.join(subdir, pattern))
else:
sys.stderr.write("WARNING: no images in subdir for X=%d, Y=%d (%s)\n" % (x, y, subdir))
writer.add_well(field_values)
writer.write(outf)
def write_screen(data_dir, plate, outf, screen=None):
kwargs = {"screen_name": screen} if screen else {}
patterns = get_patterns(data_dir)
writer = ScreenWriter(plate, ROWS, COLUMNS, FIELDS, **kwargs)
for idx in range(ROWS * COLUMNS):
well_tag = "%s%02d" % writer.coordinates(idx)
try:
field_map = patterns[well_tag]
except KeyError:
writer.add_well([])
continue
field_values = []
for i in range(1, FIELDS + 1):
field_values.append(os.path.join(data_dir, field_map[i]))
writer.add_well(field_values, extra_kv=EXTRA_KV)
writer.write(outf)
def write_screen(data_dir, plate, outf, screen=None):
kwargs = {"screen_name": screen} if screen else {}
patterns = get_patterns(data_dir)
writer = ScreenWriter(plate, ROWS, COLUMNS, FIELDS, **kwargs)
for idx in xrange(ROWS * COLUMNS):
well_tag = "%s%02d" % writer.coordinates(idx)
try:
field_map = patterns[well_tag]
except KeyError:
writer.add_well([])
continue
field_values = []
for i in xrange(1, FIELDS + 1):
field_values.append(os.path.join(data_dir, field_map[i]))
writer.add_well(field_values, extra_kv=EXTRA_KV)
writer.write(outf)
def write_screen(data_dir, plate, outf, rev_well_tag=False):
writer = ScreenWriter(plate, ROWS, COLUMNS, FIELDS)
for idx in range(ROWS * COLUMNS):
r, c = writer.coordinates(idx)
well_tag = "%d%s" % (c, r) if rev_well_tag else "%s%d" % (r, c)
fn = first_existing(data_dir, [well_tag.lower(), well_tag])
if fn is None:
sys.stderr.write("missing: %s\n" %
os.path.join(data_dir, well_tag.lower()))
field_values = None
else:
field_values = [fn]
writer.add_well(field_values)
writer.write(outf)
def write_screen(data_dir, plate, outf):
d, ch_names = group_files(data_dir)
extra_kv = {"AxisTypes": "CT", "ChannelNames": ",".join(ch_names)}
n_fields = len(d)
writer = ScreenWriter(plate, ROWS, COLUMNS, n_fields)
assert ROWS == COLUMNS == 1
field_values = []
for field_idx in sorted(d):
field_values.append(os.path.join(data_dir, d[field_idx]))
writer.add_well(field_values, extra_kv=extra_kv)
writer.write(outf)
def write_screen(data_dir, plate, outf):
writer = ScreenWriter(plate, ROWS, COLUMNS, FIELDS)
for idx in range(ROWS * COLUMNS):
r, c = writer.coordinates(idx)
well_tag = "Well %s%03d" % (r, c)
subdir = os.path.join(data_dir, well_tag)
field_values = []
if not os.path.isdir(subdir):
sys.stderr.write("missing: %s\n" % subdir)
elif not has_images(subdir):
sys.stderr.write("no images: %s\n" % subdir)
else:
field_values.append(os.path.join(subdir, PATTERN))
writer.add_well(field_values, extra_kv=EXTRA_KV)
writer.write(outf)
def write_screen(data_dir, plate, outf, rev_well_tag=False):
writer = ScreenWriter(plate, ROWS, COLUMNS, FIELDS)
for idx in xrange(ROWS * COLUMNS):
r, c = writer.coordinates(idx)
well_tag = "%d%s" % (c, r) if rev_well_tag else "%s%d" % (r, c)
fn = first_existing(data_dir, [well_tag.lower(), well_tag])
if fn is None:
sys.stderr.write("missing: %s\n" % os.path.join(data_dir, well_tag.lower()))
field_values = None
else:
field_values = [fn]
writer.add_well(field_values)
writer.write(outf)
def write_screen(data_dir, plate, outf):
d = group_files(data_dir)
consistency_check(d)
writer = ScreenWriter(plate, ROWS, COLUMNS, FIELDS,
exclude_readers=EXCLUDE_READERS)
for idx in range(ROWS * COLUMNS):
well_coords = writer.index2d(idx)
field_values = []
try:
by_field = d[well_coords]
except KeyError:
sys.stderr.write("missing well: %r\n" % (well_coords,))
else:
for i, field_coords in enumerate(EXPECTED_FIELDS):
field_values.append(build_pattern(by_field[field_coords]))
writer.add_well(field_values)
writer.write(outf)
def write_screen(data_dir, plate, outf):
writer = ScreenWriter(plate, ROWS, COLUMNS, FIELDS)
for idx in xrange(ROWS * COLUMNS):
r, c = writer.coordinates(idx)
well_tag = "%s%s%03d" % (os.path.basename(data_dir), r, c)
subdir = os.path.join(data_dir, well_tag)
field_values = []
if not os.path.isdir(subdir):
sys.stderr.write("missing: %s\n" % subdir)
else:
patterns = get_patterns(subdir)
if not patterns:
sys.stderr.write("missing images: %s\n" % subdir)
for p in patterns:
field_values.append(os.path.join(subdir, p))
writer.add_well(field_values, extra_kv=EXTRA_KV)
writer.write(outf)
def write_screen(data_dir, plate, outf):
writer = ScreenWriter(plate, ROWS, COLUMNS, FIELDS)
for idx in xrange(ROWS * COLUMNS):
r, c = writer.coordinates(idx)
well_tag = "Well %s%03d" % (r, c)
subdir = os.path.join(data_dir, well_tag)
field_values = []
if not os.path.isdir(subdir):
sys.stderr.write("missing: %s\n" % subdir)
else:
pattern = "<FITC,Hoechst,Tritc>_Flo - n000000.tif"
field_values.append(os.path.join(subdir, pattern))
writer.add_well(field_values, extra_kv=EXTRA_KV)
writer.write(outf)
def write_screen(data_dir, plate, outf):
writer = ScreenWriter(plate, ROWS, COLUMNS, FIELDS)
for idx in xrange(ROWS * COLUMNS):
r, c = writer.coordinates(idx)
well_tag = "%s%s%03d" % (os.path.basename(data_dir), r, c)
subdir = os.path.join(data_dir, well_tag)
field_values = []
if not os.path.isdir(subdir):
sys.stderr.write("missing: %s\n" % subdir)
else:
for run in xrange(FIELDS):
pattern = "%s_<A,H,T>%d.tif" % (well_tag, run + 1)
field_values.append(os.path.join(subdir, pattern))
writer.add_well(field_values, extra_kv=EXTRA_KV)
writer.write(outf)
def write_screen(data_dir, plate, outf):
writer = ScreenWriter(plate, ROWS, COLUMNS, FIELDS)
for idx in xrange(ROWS * COLUMNS):
r, c = writer.coordinates(idx)
well_tag = "Well %s%03d" % (r, c)
subdir = os.path.join(data_dir, well_tag)
field_values = []
if not os.path.isdir(subdir):
sys.stderr.write("missing: %s\n" % subdir)
elif not has_images(subdir):
sys.stderr.write("no images: %s\n" % subdir)
else:
field_values.append(os.path.join(subdir, PATTERN))
writer.add_well(field_values, extra_kv=EXTRA_KV)
writer.write(outf)
def write_screen(data_dir, plate, outf):
d = group_files(data_dir)
consistency_check(d)
writer = ScreenWriter(plate, ROWS, COLUMNS, FIELDS)
for idx in xrange(ROWS * COLUMNS):
r, c = writer.coordinates(idx)
well = "%s%02d" % (r.lower(), c)
field_values = []
by_field = d[well]
for i in xrange(FIELDS):
field = "%d" % (i + 1)
seq = by_field[field]
assert len(set(_[1] for _ in seq)) == 1
head = seq[0][1]
c_block = "<%s>" % ",".join(_[0] for _ in sorted(seq))
pattern = "%s_%s_s%s_w%s.tif" % (head, well, field, c_block)
field_values.append(os.path.join(data_dir, pattern))
writer.add_well(field_values, extra_kv=EXTRA_KV)
writer.write(outf)
def write_screen(data_dir, plate, outf):
# For the second screen, remove "-(\d\d)", "-repeated", etc.
well_tag = os.path.basename(data_dir)
p1 = well_tag.find("(")
p2 = well_tag.find(")")
if p1 > 0 and p2 > 0:
well_tag = well_tag[0:p1 - 1]
well_tag += well_tag[p2:]
well_tag = well_tag.replace("-repeated", "")
well_tag = well_tag.replace("-used pics", "")
# Special case these!
well_tag = well_tag.replace("Plate1-Blue-A", "P1-Bl-A")
well_tag = well_tag.replace("Plate2-Red-B", "P2-Red-B")
well_tag = well_tag.replace("Plate2-Blue-A", "Plate2-Red-B")
count = 0
writer = ScreenWriter(plate, ROWS, COLUMNS, FIELDS)
for idx in range(ROWS * COLUMNS):
r, c = writer.coordinates(idx)
field_values = []
pattern = "*[_-]%s%s[_-]*.[cz][zv]i" % (r, c)
glob_str = os.path.join(data_dir, pattern)
found = sorted(glob.glob(glob_str))
assert str(found), len(found) >= 1 and len(found) <= FIELDS
for idx in range(FIELDS):
if found:
field_values.append(os.path.join(data_dir, found.pop(0)))
else:
field_values.append("")
if not any(field_values):
print("missing well: %s (%s%s)" % (well_tag, r, c),
file=sys.stderr)
field_values = []
else:
count += 1
writer.add_well(field_values)
if not count:
raise Exception("no wells: %s" % plate)
writer.write(outf)
def write_screen(data_dir, plate, outf):
d = group_files(data_dir)
consistency_check(d)
writer = ScreenWriter(plate, ROWS, COLUMNS, FIELDS,
exclude_readers=EXCLUDE_READERS)
for idx in xrange(ROWS * COLUMNS):
well_coords = writer.index2d(idx)
field_values = []
try:
by_field = d[well_coords]
except KeyError:
sys.stderr.write("missing well: %r\n" % (well_coords,))
else:
for i, field_coords in enumerate(EXPECTED_FIELDS):
field_values.append(build_pattern(by_field[field_coords]))
writer.add_well(field_values)
writer.write(outf)
def write_screen(data_dir, plate, outf):
writer = ScreenWriter(plate, ROWS, COLUMNS, FIELDS)
for idx in xrange(ROWS * COLUMNS):
r, c = writer.coordinates(idx)
well_tag = "%s%s%03d" % (os.path.basename(data_dir), r, c)
subdir = os.path.join(data_dir, well_tag)
field_values = []
if not os.path.isdir(subdir):
sys.stderr.write("missing: %s\n" % subdir)
else:
patterns = get_patterns(subdir)
if not patterns:
sys.stderr.write("missing images: %s\n" % subdir)
for p in patterns:
field_values.append(os.path.join(subdir, p))
writer.add_well(field_values, extra_kv=EXTRA_KV)
writer.write(outf)
def setUp(self, screen_name=None):
super(TestScreenWriter, self).setUp(screen_name=screen_name)
fout = StringIO()
self.all_field_values = []
self.exclude_readers = ["z.x.FooReader", "z.x.BarReader"]
self.extra_kv = {"Dimensions": "ZCT"}
kwargs = {"exclude_readers": self.exclude_readers}
if screen_name:
kwargs["screen_name"] = screen_name
writer = ScreenWriter(
self.name, self.rows, self.columns, self.fields, **kwargs
)
for i in xrange(self.size):
writer.add_well(self._field_values(i), extra_kv=self.extra_kv)
writer.write(fout)
fout.seek(0)
self.cp = ConfigParser.ConfigParser()
self.cp.readfp(fout)
def write_screen(data_dir, plate, outf):
# For the second screen, remove "-(\d\d)", "-repeated", etc.
well_tag = os.path.basename(data_dir)
p1 = well_tag.find("(")
p2 = well_tag.find(")")
if p1 > 0 and p2 > 0:
well_tag = well_tag[0:p1-1]
well_tag += well_tag[p2:]
well_tag = well_tag.replace("-repeated", "")
well_tag = well_tag.replace("-used pics", "")
# Special case these!
well_tag = well_tag.replace("Plate1-Blue-A", "P1-Bl-A")
well_tag = well_tag.replace("Plate2-Red-B", "P2-Red-B")
well_tag = well_tag.replace("Plate2-Blue-A", "Plate2-Red-B")
count = 0
writer = ScreenWriter(plate, ROWS, COLUMNS, FIELDS)
for idx in xrange(ROWS * COLUMNS):
r, c = writer.coordinates(idx)
field_values = []
pattern = "*[_-]%s%s[_-]*.[cz][zv]i" % (r, c)
glob_str = os.path.join(data_dir, pattern)
found = sorted(glob.glob(glob_str))
assert str(found), len(found) >= 1 and len(found) <= FIELDS
for idx in range(FIELDS):
if found:
field_values.append(os.path.join(data_dir, found.pop(0)))
else:
field_values.append("")
if not any(field_values):
print >>sys.stderr, "missing well: %s (%s%s)" % (well_tag, r, c)
field_values = []
else:
count += 1
writer.add_well(field_values)
if not count:
raise Exception("no wells: %s" % plate)
writer.write(outf)
def write_screen(data_dir, plate, outf, screen=None):
kwargs = {"screen_name": screen} if screen else {}
writer = ScreenWriter(plate, ROWS, COLUMNS, FIELDS, **kwargs)
for i in range(ROWS):
for j in range(COLUMNS):
x, y = j, i
subdir = os.path.join(data_dir, "field--X%02d--Y%02d" % (x, y))
field_values = []
if not os.path.isdir(subdir):
sys.stderr.write("WARNING: no subdir for X=%d, Y=%d (%s)\n" %
(x, y, subdir))
else:
pattern = find_pattern(subdir)
if pattern is not None:
field_values.append(os.path.join(subdir, pattern))
else:
sys.stderr.write(
"WARNING: no images in subdir for X=%d, Y=%d (%s)\n" %
(x, y, subdir))
writer.add_well(field_values)
writer.write(outf)
def write_screen(data_dir, plate, outf, screen=None):
kwargs = {"screen_name": screen} if screen else {}
channel_map = get_channel_map(data_dir)
try:
channel_tags = channel_map[plate]
except KeyError:
raise ValueError("Plate %r not found" % (plate,))
file_maps = {}
n_fields = []
for c in channel_tags:
subd = os.path.join(data_dir, "%s-%s" % (plate, c))
file_maps[c], nf = get_file_map(subd)
n_fields.append(nf)
n_fields = max(n_fields)
base_path = os.path.join(data_dir, "%s-" % plate)
writer = ScreenWriter(plate, ROWS, COLUMNS, n_fields, **kwargs)
for idx in xrange(ROWS * COLUMNS):
well_tag = "%s%02d" % writer.coordinates(idx)
if not any(well_tag in file_maps[_] for _ in channel_tags):
sys.stderr.write(
"WARNING: plate %s: missing well: %s\n" % (plate, well_tag)
)
writer.add_well([])
continue
field_values = []
for i in xrange(n_fields):
try:
fnames = [file_maps[_][well_tag][i] for _ in channel_tags]
except IndexError:
sys.stderr.write(
"WARNING: plate %s: missing field for well %s: %d\n" %
(plate, well_tag, i)
)
else:
split_fnames = [os.path.splitext(_) for _ in fnames]
assert len(set(_[1] for _ in split_fnames)) == 1
ext = split_fnames[0][1]
elems = [os.path.join(c, t[0])
for (c, t) in zip(channel_tags, split_fnames)]
field_values.append(
"%s<%s>%s" % (base_path, ",".join(elems), ext)
)
if len(field_values) == n_fields:
extra_kv = EXTRA_KV.copy()
extra_kv['ChannelNames'] = ",".join(channel_tags)
writer.add_well(field_values, extra_kv=extra_kv)
else:
# treat wells with less than n_fields as missing
writer.add_well([])
writer.write(outf)
