def all_files_with_ext(topdir, ext, cs=False):
"""Iterates over files with extension ``ext`` recursively from ``topdir``
"""
if not isinstance(topdir, str):
msg = PARAM_TYPE_ERR.format(param="topdir",
func="all_files_with_ext", type="str")
LOG.error(msg)
raise ValueError(msg)
if not isinstance(ext, str):
msg = PARAM_TYPE_ERR.format(param="ext",
func="all_files_with_ext", type="str")
LOG.error(msg)
raise ValueError(msg)
if not isinstance(cs, bool):
msg = PARAM_TYPE_ERR.format(param="cs",
func="all_files_with_ext", type="bool")
LOG.error(msg)
raise ValueError(msg)
# Trim any leading spaces from the extension we've been given
if ext.startswith("."):
ext = ext[1:]
# For speed, we pre-convert the ext to lowercase here if we're being case
# insensitive
if not cs:
ext = ext.lower()
# OK, walk the dir. we only care about files, hence why dirs never gets
# touched
for root, folders, files in os.walk(topdir):
# These *must* be in place, not f = sorted(f)
folders.sort()
files.sort()
for folder in folders:
if folder.startswith("_"):
folders.remove(folder)
for fpath in files:
# split out ext, and do any case-conversion we need
fname, fext = path.splitext(fpath)
if not cs:
fext = fext.lower()
# remove the dot at the start, as splitext returns ("fn", ".ext")
fext = fext[1:]
if fext == ext:
# we give the whole path to the file
yield path.join(root, fpath)
def ts_format_date(dt):
if isinstance(dt, str):
return dt
elif isinstance(dt, datetime):
return dt.strftime(TS_DATE_FORMAT)
else:
msg = PARAM_TYPE_ERR.format(param="dt", func="ts_format_date",
type="datetime.datetime")
LOG.error(msg)
raise TypeError(msg)
def all_files_with_exts(topdir, exts, cs=False):
"""Creates a dictionary of {"ext": [files]} for each ext in exts
"""
if not isinstance(exts, list):
msg = PARAM_TYPE_ERR.format(param="exts",
func="all_files_with_exts", type="list")
LOG.error(msg)
raise ValueError(msg)
ext_dict = {}
for ext in exts:
ext_dict[ext] = sorted(list(all_files_with_ext(topdir, ext, cs)))
return ext_dict
def ts_get_image(ts_path, date, n=0, write_manifest=False):
"""Get the image path of the image in ``ts_path`` at ``date``
"""
if isinstance(date, datetime):
date = ts_format_date(date)
if not isinstance(date, str):
msg = PARAM_TYPE_ERR.format(param="date",
func="ts_get_image",
type="datetime.datetime or str")
LOG.error(msg)
raise ValueError(msg)
if not isinstance(ts_path, str):
msg = PARAM_TYPE_ERR.format(param="ts_path",
func="all_files_with_ext", type="str")
LOG.error(msg)
raise ValueError(msg)
# Get ts_info from manifest
ts_info = ts_get_manifest(ts_path)
# Bail early if we know it's missing
if date in ts_info["missing"]:
return None
# Format the path below the ts root (ts_path)
relpath = _ts_date_to_path(ts_info["name"], ts_info["extension"],
ts_parse_date(date), n)
# Join to make "absolute" path, i.e. path including ts_path
abspath = path.join(ts_path, relpath)
# not-so-silently fail if we can't find the image
if path.exists(abspath):
LOG.debug("Image at {} in {} is {}.".format(date, ts_path, abspath))
return abspath
else:
LOG.warn("Expected image {} at {} in {} did not exist.".format(
abspath, date, ts_path))
if write_manifest:
ts_info["missing"].append(date)
ts_update_manifest(ts_path, ts_info)
ts_info = ts_get_manifest(ts_path)
return None
def traypos_to_chamber_index(traypos, tray_cap=20, col_cap=5):
if not isinstance(traypos, str):
msg = PARAM_TYPE_ERR.format(func='traypos_to_chamber_index',
param='traypos', type='str')
LOG.error(msg)
raise TypeError(msg)
extractor = re.compile(r'^(\d{1,2})([a-zA-Z])([1-9])$')
match = extractor.match(traypos)
if match is None:
msg = "Tray Pos '{}' is invalid".format(traypos)
LOG.error(msg)
raise ValueError(msg)
tray, col, row = match.groups()
tray = int(tray)
col = ord(col.upper()) - 65 # Numericise the col num, 0-based
row = int(row)
index = (tray - 1) * tray_cap + col * col_cap + row
return index
