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Support regex wildcards #12

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Support regex wildcards #12

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136aeac
Support regex wildcards
hannah-martinez May 5, 2026
fd08c3f
Fix condition where there are more than 3 regex fields in the template
hannah-martinez May 6, 2026
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56 changes: 29 additions & 27 deletions vsvi2precomputed/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -85,8 +85,8 @@ def convert_precomputed_tiles(vsvi_root_path, vsvi_data, output_path):
'''
input_bucket, base_prefix = vsvi_root_path.replace("s3://", "").split("/", 1)

source_prefix = vsvi_data.get("SourceFileNameTemplate").split("/")[:-2]
prefix = os.path.join(base_prefix, "/".join(source_prefix))
source_prefix = vsvi_data.get("SourceFileNameTemplate").split("/")[1]
prefix = os.path.join(base_prefix, source_prefix)

# Prepend "file://" if path is local and does not already have it
if output_path[:5] != "s3://" and output_path[:7] != "file://":
Expand Down Expand Up @@ -130,13 +130,13 @@ def _convert_tile(vol, filepath, vsvi_data, input_bucket=None):
# y_stop = min(y_start + dy, vsvi_data["TargetDataSizeY"])
z_stop = z_start + 1

if input_bucket:
image_data = Image.open(io.BytesIO(_get_object_data(input_bucket, filepath)))
else:
image_data = Image.open(filepath)
w, h = image_data.size

try:
if input_bucket:
image_data = Image.open(io.BytesIO(_get_object_data(input_bucket, filepath)))
else:
image_data = Image.open(filepath)
w, h = image_data.size

image = np.asarray(image_data)
image = image.swapaxes(0, 1)
image = np.expand_dims(image, 2)
Expand Down Expand Up @@ -189,30 +189,32 @@ def _list_objects_local(dir):
yield file


def _parse_filename(filename, template):
def _parse_filename(path, template):
'''
Get section (z), row (y), and column (x) numbers for a tile from tile filename. Format showing positions of z, y, x within string is given in template param.
Inputs: filename to parse (str or pathlib object) example: section_001_tr10-tc16.png
"SourceFileNameTemplate" field from vsvi file (str) example: section_%05d_tr%d-tc%d.png
Outputs: z, y, x
'''
filename = pathlib.Path(filename)

# Template for where z, y, x are in the string is given in vsvi file, but
# may not have same path type as filesystem code is running on
template_string = pathlib.PurePath(template)
if template_string.name == template:
if os.name == "nt":
template_string = pathlib.PurePosixPath(template)
elif os.name == "posix":
template_string = pathlib.PureWindowsPath(template)

# Replace %d in template with regex indicator for digits
regex_template = re.sub('%[0-9]*d', '([0-9]+)', template_string.name)
# Parse digits out of input string
integer_matches = re.search(regex_template, filename.name)
z = int(integer_matches.group(1))
y = int(integer_matches.group(2))
x = int(integer_matches.group(3))
# 1. normalize
path = str(path).replace("\\", "/")
template = str(template).replace("\\", "/").lstrip("./")

# 2. escape everything
regex = re.escape(template)

# 3. restore semantics
regex = re.sub(r'%0?(\d*)d',
lambda m: rf'(\d{{{m.group(1)}}})' if m.group(1) else r'(\d+)',
regex)
regex = regex.replace(r'\*', r'[^/]*')

# 4. match
m = re.search(regex + r'$', path)
if not m:
raise ValueError(f"No match:\n{path}\n{template}")

z = int(m.groups()[-3])
y = int(m.groups()[-2])
x = int(m.groups()[-1])
return z, y, x
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