def main(argv=sys.argv[1:]):
assert len(argv) == 1
su.mkdirp(OUTPUTDIR)
for target, spec in readinput(argv[0]):
output = outpath(target)
write_signature(output, rows, marker_labels, lims=None)
def main(argv=sys.argv[1:]):
assert len(argv) == 1
su.mkdirp(OUTPUTDIR)
for target, spec in readinput(argv[0]):
output = outpath(target)
write_signature(output, rows, marker_labels, lims=None)
def main(argv):
_parseargs(argv)
def want_h5(b, d, i):
return b == 'Data.h5'
subdir = '.DATA'
extent, path, antibody = [getattr(PARAM, a) for a in
'extent path antibody'
.split()]
# if extent == 'plate':
# ncrmode = bool(int(argv[3])) if nargs > 3 else False
# else:
# ncrmode = _scrape_ncrmode(path, antibody)
param = PARAM
if extent == 'plate':
def mode(path, wells, antibody):
modes = map(partial(_scrape_ncrmode, antibody=antibody),
[op.join(path, w) for w in wells])
if all(modes):
return True
else:
assert all(map(notop, modes))
return False
q = [(sum([list(find(op.join(path, w), want_h5))
for w in c], []),
_dimspec(mode(path, z, antibody), **param.__dict__),
op.join(path, subdir, antibody, ','.join(c)))
for c, z in getcontrols(path)]
else:
ncrmode = _scrape_ncrmode(path, antibody)
assert extent == 'well'
q = [(find(path, want_h5),
_dimspec(ncrmode, **param.__dict__),
op.join(path, subdir, antibody))]
for paths, param, basedir in q:
data, warnings = extractdata(paths, param)
processed, rawheaders = process(data, param)
preamble = makepreamble(rawheaders, warnings)
dir_ = op.join(basedir, param.readout)
mkdirp(dir_)
dump(dir_, transpose_map(dict(data=processed, preamble=preamble)))
return 0
def main(argv=sys.argv[1:]):
assert len(argv) == 1
su.mkdirp(OUTPUTDIR)
rows = readinput(argv[0])
specs, data, lims = process(rows)
spd = sp.ScatterplotData
for pair in it.product(data, data):
ax, vs = zip(*pair)
if ax[0] == ax[1]: continue
output = outpath(ax)
spd = tuple(spd(*(k + (x, y))) for k, x, y in zip(specs, *vs))
axis_labels = tuple(', '.join(l) for l in ax)
write_scatterplot(output, spd, axis_labels, lims)
def main(argv=sys.argv[1:]):
assert len(argv) == 1
su.mkdirp(OUTPUTDIR)
rows = readinput(argv[0])
specs, data, lims = process(rows)
spd = sp.ScatterplotData
for pair in it.product(data, data):
ax, vs = zip(*pair)
if ax[0] == ax[1]: continue
output = outpath(ax)
spd = tuple(spd(*(k + (x, y))) for k, x, y in zip(specs, *vs))
axis_labels = tuple(', '.join(l) for l in ax)
write_scatterplot(output, spd, axis_labels, lims)
def main(argv=sys.argv[1:]):
assert len(argv) == 1
su.mkdirp(OUTPUTDIR)
rows = readinput(argv[0])
cl_metadata, responses = parse(rows)
_to_do = co.namedtuple('_to_do', 'args imgid')
_args = co.namedtuple('_args', 'xy_data xy_metadata output')
to_do = []
for xr, yr in it.product(responses, responses):
(xmd, ymd), (xs, ys) = zip(xr, yr)
if xmd >= ymd or xmd.time != ymd.time: continue
base_id = _base_id((xmd, ymd))
output = outpath(base_id)
if not CLOBBEROK and op.exists(output):
raise Exception("won't clobber %s" % output)
img_id = IDPREFIX + base_id
to_do.append(_to_do(_args((xs, ys), (xmd, ymd), output), img_id))
pixel_maps = do_scatterplots(cl_metadata, responses, to_do, WITHLIMITS)
print_pixel_annotations(pixel_maps)
def main(argv=sys.argv[1:]):
assert len(argv) == 1
su.mkdirp(OUTPUTDIR)
rows = readinput(argv[0])
cl_metadata, responses = parse(rows)
_to_do = co.namedtuple('_to_do', 'args imgid')
_args = co.namedtuple('_args', 'xy_data xy_metadata output')
to_do = []
for xr, yr in it.product(responses, responses):
(xmd, ymd), (xs, ys) = zip(xr, yr)
if xmd >= ymd or xmd.time != ymd.time: continue
base_id = _base_id((xmd, ymd))
output = outpath(base_id)
if not CLOBBEROK and op.exists(output):
raise Exception("won't clobber %s" % output)
img_id = IDPREFIX + base_id
to_do.append(_to_do(_args((xs, ys), (xmd, ymd), output), img_id))
pixel_maps = do_scatterplots(cl_metadata, responses, to_do, WITHLIMITS)
print_pixel_annotations(pixel_maps)
def main(argv):
argparser = argparse.ArgumentParser(
description='Build sampattavanich_2014 app resources.')
argparser.add_argument('-n', '--no-media', action='store_true',
default=False,
help="Don't copy media files)")
args = argparser.parse_args()
cur_dir = op.abspath(op.dirname(__file__))
html_dir = op.abspath(op.join(
cur_dir, '..', 'temp', 'docroot', 'explore', 'sampattavanich-2014'))
html_filename = op.join(html_dir, 'index.html')
cell_img_out_dir = op.join(html_dir, 'img', 'cell')
popup_img_out_dir = op.join(html_dir, 'img', 'popup')
platemap = build_platemap(PLATEMAP_FILENAME)
ligand_concs = [c for c in sorted(platemap.ligand_conc.unique()) if c > 0]
table = []
for row, ligand_conc in enumerate(ligand_concs):
intensity = (CONCENTRATION_COLOR_BEGIN +
(CONCENTRATION_COLOR_END - CONCENTRATION_COLOR_BEGIN) /
len(ligand_concs) * row)
color = '#' + ('%02x' % intensity * 3)
table_row = {'ligand_conc': ligand_conc,
'color': color,
'cells': []}
for col, ligand in enumerate(LIGAND_ORDER):
location = ((platemap.ligand_conc == ligand_conc) &
(platemap.ligand == ligand) &
(platemap.inhibitor == ''))
table_row['cells'].append(platemap[location].iloc[0])
table.append(table_row)
# FIXME We should really just build a pivoted dataframe in the right way so
# that we can just iterate over it cleanly. This duplication is not good.
table_inhibitors = []
for row, inhibitor in enumerate(INHIBITOR_ORDER):
color = '#' + ('%02x' % CONCENTRATION_COLOR_END * 3)
table_row = {'ligand_conc': ligand_concs[-1],
'color': color,
'inhibitors': inhibitor.split(' + '),
'cells': []}
for col, ligand in enumerate(LIGAND_ORDER):
location = ((platemap.inhibitor == inhibitor) &
(platemap.ligand == ligand))
table_row['cells'].append(platemap[location].iloc[0])
table_inhibitors.append(table_row)
data = {'ligands': LIGAND_ORDER,
'table': table,
'table_inhibitors': table_inhibitors,
'num_ligand_concs': len(ligand_concs),
'num_inhibitors': len(INHIBITOR_ORDER),
'STATIC_URL': django.conf.settings.STATIC_URL,
}
content = render_to_string('sampattavanich_2014/index.html', data)
with codecs.open(html_filename, 'w', 'utf-8') as out_file:
out_file.write(content)
if not args.no_media:
su.mkdirp(cell_img_out_dir)
for src_filename in os.listdir(CELL_IMAGE_PATH):
if not src_filename.endswith('.png'):
continue
src_path = op.join(CELL_IMAGE_PATH, src_filename)
dest_filename = src_filename.partition(CELL_IMAGE_PREFIX)[2]
dest_path = op.join(cell_img_out_dir, dest_filename)
shutil.copy(src_path, dest_path)
os.chmod(dest_path, 0644)
su.mkdirp(popup_img_out_dir)
for src_filename in os.listdir(POPUP_IMAGE_PATH):
if not src_filename.endswith('.png'):
continue
src_path = op.join(POPUP_IMAGE_PATH, src_filename)
dest_filename = src_filename
dest_path = op.join(popup_img_out_dir, dest_filename)
shutil.copy(src_path, dest_path)
os.chmod(dest_path, 0644)
return 0
def create_output_path(*elements):
"Create and canonicalize a path relative to the output directory."
path = op.join(DOCROOT, *elements)
su.mkdirp(path)
return path
def stash_put(name, obj):
"Stash an object by name (to disk) for later retrieval."
path = _stash_path(name)
su.mkdirp(op.dirname(path))
pickle_file = open(path, 'w');
pickle.dump(obj, pickle_file)
def main(argv):
argparser = argparse.ArgumentParser(
description='Build single_cell_dynamics app resources.')
argparser.add_argument('-d', '--no-data', action='store_true',
default=False,
help="Don't copy data files")
argparser.add_argument('-m', '--no-media', action='store_true',
default=False,
help="Don't copy media files")
args = argparser.parse_args()
cur_dir = op.abspath(op.dirname(__file__))
data_out_dir = op.join(DOCROOT, 'data')
cell_img_out_dir = op.join(DOCROOT, 'img', 'cell')
popup_img_out_dir = op.join(DOCROOT, 'img', 'popup')
movie_out_dir = op.join(DOCROOT, 'movies')
platemap = build_platemap(PLATEMAP_FILENAME)
platemap = platemap[platemap.egf_conc == 100]
inhibitor_concs = [c for c in sorted(platemap.inhibitor_conc.unique())
if c > 0]
inhibitors = platemap.inhibitor.unique()
batimastat_concs = [c for c in sorted(platemap.batimastat_conc.unique())]
table = []
for row, inhibitor_conc in enumerate(inhibitor_concs):
intensity = (CONCENTRATION_COLOR_BEGIN +
(CONCENTRATION_COLOR_END - CONCENTRATION_COLOR_BEGIN) /
len(inhibitor_concs) * row)
color = '#' + ('%02x' % intensity * 3)
table_row = {'inhibitor_conc': inhibitor_conc,
'color': color,
'cells': []}
for batimastat_conc in batimastat_concs:
for inhibitor in inhibitors:
location = ((platemap.inhibitor == inhibitor) &
(platemap.inhibitor_conc == inhibitor_conc) &
(platemap.batimastat_conc == batimastat_conc))
table_row['cells'].append(platemap[location].iloc[0])
table.append(table_row)
data = {'inhibitors': inhibitors,
'table': table,
'num_inhibitor_concs': len(inhibitor_concs),
'num_inhibitors': len(inhibitors),
'batimastat_concs': batimastat_concs,
'STATIC_URL': django.conf.settings.STATIC_URL,
'BASE_URL': BASE_URL,
}
su.mkdirp(DOCROOT)
render_template('single_cell_dynamics/index.html', data,
DOCROOT, 'index.html')
if not args.no_data:
su.mkdirp(data_out_dir)
for src_filename in os.listdir(DATA_PATH):
match = re.match(r'H5OUT_(r\d+)_(c\d+)\.h5', src_filename)
if not match:
continue
src_path = op.join(DATA_PATH, src_filename)
dest_filename = 'ekar_single_cell_data_%s%s.csv' % match.groups()
dest_path = op.join(data_out_dir, dest_filename)
data = extract_well_data(src_path)
with open(dest_path, 'w') as f:
data.to_csv(f, index=False)
if not args.no_media:
su.mkdirp(cell_img_out_dir)
for src_filename in os.listdir(VIDEO_PATH):
if not (src_filename.startswith(CELL_IMAGE_PREFIX) and
src_filename.endswith('.png')):
continue
src_path = op.join(VIDEO_PATH, src_filename)
dest_filename = src_filename[len(CELL_IMAGE_PREFIX):]
dest_path = op.join(cell_img_out_dir, dest_filename)
shutil.copy(src_path, dest_path)
os.chmod(dest_path, 0644)
su.mkdirp(popup_img_out_dir)
for src_filename in os.listdir(VIDEO_PATH):
if not re.match(r'r\d+c\d+\.png', src_filename):
continue
src_path = op.join(VIDEO_PATH, src_filename)
dest_filename = src_filename
dest_path = op.join(popup_img_out_dir, dest_filename)
shutil.copy(src_path, dest_path)
os.chmod(dest_path, 0644)
su.mkdirp(movie_out_dir)
for src_filename in os.listdir(VIDEO_PATH):
if not src_filename.endswith('.mp4'):
continue
src_path = op.join(VIDEO_PATH, src_filename)
dest_filename = re.sub(r'myMov_(\w+)f1ratio', r'\1', src_filename)
dest_path = op.join(movie_out_dir, dest_filename)
shutil.copy(src_path, dest_path)
os.chmod(dest_path, 0644)
return 0
def stash_put(name, obj):
"Stash an object by name (to disk) for later retrieval."
path = _stash_path(name)
su.mkdirp(op.dirname(path))
pickle_file = open(path, 'w')
pickle.dump(obj, pickle_file)
def main(argv):
argparser = argparse.ArgumentParser(
description='Build sampattavanich_2014 app resources.')
argparser.add_argument('-n',
'--no-media',
action='store_true',
default=False,
help="Don't copy media files)")
args = argparser.parse_args()
cur_dir = op.abspath(op.dirname(__file__))
html_dir = op.abspath(
op.join(cur_dir, '..', 'temp', 'docroot', 'explore',
'sampattavanich-2014'))
html_filename = op.join(html_dir, 'index.html')
cell_img_out_dir = op.join(html_dir, 'img', 'cell')
popup_img_out_dir = op.join(html_dir, 'img', 'popup')
platemap = build_platemap(PLATEMAP_FILENAME)
ligand_concs = [c for c in sorted(platemap.ligand_conc.unique()) if c > 0]
table = []
for row, ligand_conc in enumerate(ligand_concs):
intensity = (CONCENTRATION_COLOR_BEGIN +
(CONCENTRATION_COLOR_END - CONCENTRATION_COLOR_BEGIN) /
len(ligand_concs) * row)
color = '#' + ('%02x' % intensity * 3)
table_row = {'ligand_conc': ligand_conc, 'color': color, 'cells': []}
for col, ligand in enumerate(LIGAND_ORDER):
location = ((platemap.ligand_conc == ligand_conc) &
(platemap.ligand == ligand) &
(platemap.inhibitor == ''))
table_row['cells'].append(platemap[location].iloc[0])
table.append(table_row)
# FIXME We should really just build a pivoted dataframe in the right way so
# that we can just iterate over it cleanly. This duplication is not good.
table_inhibitors = []
for row, inhibitor in enumerate(INHIBITOR_ORDER):
color = '#' + ('%02x' % CONCENTRATION_COLOR_END * 3)
table_row = {
'ligand_conc': ligand_concs[-1],
'color': color,
'inhibitors': inhibitor.split(' + '),
'cells': []
}
for col, ligand in enumerate(LIGAND_ORDER):
location = ((platemap.inhibitor == inhibitor) &
(platemap.ligand == ligand))
table_row['cells'].append(platemap[location].iloc[0])
table_inhibitors.append(table_row)
data = {
'ligands': LIGAND_ORDER,
'table': table,
'table_inhibitors': table_inhibitors,
'num_ligand_concs': len(ligand_concs),
'num_inhibitors': len(INHIBITOR_ORDER),
'STATIC_URL': django.conf.settings.STATIC_URL,
}
content = render_to_string('sampattavanich_2014/index.html', data)
with codecs.open(html_filename, 'w', 'utf-8') as out_file:
out_file.write(content)
if not args.no_media:
su.mkdirp(cell_img_out_dir)
for src_filename in os.listdir(CELL_IMAGE_PATH):
if not src_filename.endswith('.png'):
continue
src_path = op.join(CELL_IMAGE_PATH, src_filename)
dest_filename = src_filename.partition(CELL_IMAGE_PREFIX)[2]
dest_path = op.join(cell_img_out_dir, dest_filename)
shutil.copy(src_path, dest_path)
os.chmod(dest_path, 0644)
su.mkdirp(popup_img_out_dir)
for src_filename in os.listdir(POPUP_IMAGE_PATH):
if not src_filename.endswith('.png'):
continue
src_path = op.join(POPUP_IMAGE_PATH, src_filename)
dest_filename = src_filename
dest_path = op.join(popup_img_out_dir, dest_filename)
shutil.copy(src_path, dest_path)
os.chmod(dest_path, 0644)
return 0
