def convert_folder2imcfolder(fol, out_folder, dozip=True):
"""
Convert a folder containing IMC acquisitions
(mcd and tiff)
to a zipfolder containing standardized names files.
"""
if fol.endswith(ZIP_FILENDING):
tmpdir = temporarydirectory.TemporaryDirectory()
with zipfile.ZipFile(fol) as zipf:
zipf.extractall(tmpdir.name)
in_fol = tmpdir.name
istmp = True
else:
in_fol = fol
istmp = False
try:
files = [
os.path.join(root, fn) for root, dirs, files in os.walk(in_fol)
for fn in files
]
mcd_files = [f for f in files if f.endswith(MCD_FILENDING)]
assert (len(mcd_files) == 1)
schema_files = [f for f in files if f.endswith(SCHEMA_FILENDING)]
if len(schema_files) > 0:
schema_file = schema_files[0]
else:
schema_file = None
mcd = McdParser(mcd_files[0], metafilename=schema_file)
txt_acids = {
_txtfn_to_ac(f): f
for f in files if f.endswith(TXT_FILENDING)
}
mcd_acs = mcd.get_all_imcacquistions()
mcd_acids = set(m.image_ID for m in mcd_acs)
txtonly_acs = set(txt_acids.keys()).difference(mcd_acids)
for txta in txtonly_acs:
print('Using TXT file for acquisition: ' + txta)
try:
mcd_acs.append(
TxtParser(txt_acids[txta]).get_imc_acquisition())
except:
print('TXT file was also corrupted.')
imc_fol = ImcFolderWriter(out_folder,
mcddata=mcd,
imcacquisitions=mcd_acs)
imc_fol.write_imc_folder(zipfolder=dozip)
if istmp:
tmpdir.cleanup()
finally:
if istmp:
tmpdir.cleanup()
def _txtfn_to_ac(fn):
return TxtParser._txtfn_to_ac(fn)