batch2p 0.1.0__py3-none-any.whl

batch2p/multi.py

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+#!/usr/bin/env python3
+"""batch2p-multi — generate one data.json per directory from a template.
+
+Usage:
+    batch2p-multi <template_data.json> <dir_list.txt> --params-file <params.json> [--output-dir <dir>]
+
+The template data.json may contain {{ job_id }} and {{ root_dir }} placeholders,
+which are substituted per-directory at generation time.  The dir_list file must
+contain one directory path per line (blank lines and lines starting with # are
+ignored).
+
+For each directory the script:
+  - collects all .tif/.tiff files and .b64 files (lexicographically sorted),
+  - substitutes {{ job_id }} and {{ root_dir }} in all string fields,
+  - writes <output_dir>/<job_id>_<n>_data.json  (1-based index, zero-padded).
+"""
+import argparse
+import json
+import re
+import sys
+from pathlib import Path
+
+
+def _apply_template_vars(obj, variables: dict):
+    """Recursively replace {{ var }} placeholders in string values.
+
+    Placeholders whose variable is absent or empty are left verbatim.
+    """
+    if isinstance(obj, str):
+        def _replace(m):
+            val = variables.get(m.group(1).strip())
+            return val if val else m.group(0)
+        return re.sub(r'\{\{\s*(\w+)\s*\}\}', _replace, obj)
+    if isinstance(obj, dict):
+        return {k: _apply_template_vars(v, variables) for k, v in obj.items()}
+    if isinstance(obj, list):
+        return [_apply_template_vars(x, variables) for x in obj]
+    return obj
+
+
+def _replace_literal(obj, old: str, new: str):
+    """Recursively replace all occurrences of `old` with `new` in string values."""
+    if isinstance(obj, str):
+        return obj.replace(old, new)
+    if isinstance(obj, dict):
+        return {k: _replace_literal(v, old, new) for k, v in obj.items()}
+    if isinstance(obj, list):
+        return [_replace_literal(x, old, new) for x in obj]
+    return obj
+
+
+def _collect_files(directory: Path, pattern: str) -> list[str]:
+    return sorted(str(p) for p in directory.glob(pattern))
+
+
+def main():
+    parser = argparse.ArgumentParser(
+        description="Generate one data.json per directory from a template."
+    )
+    parser.add_argument("template",       help="Template data.json with {{ }} placeholders.")
+    parser.add_argument("dir_list",       help="Text file with one directory per line.")
+    parser.add_argument("--params-file",  required=True,
+                        help="Path to the params.json file (same for all outputs).")
+    parser.add_argument("--output-dir",   default=".",
+                        help="Directory where generated data.json files are written (default: cwd).")
+    parser.add_argument("--tif-regexp",   default=None,
+                        help="Only include .tif/.tiff files whose filename matches this regexp.")
+    parser.add_argument("--force-sync",   action="store_true",
+                        help="Require .b64 files to be present and match the number of tif files; "
+                             "skip directories where this condition is not met.")
+    args = parser.parse_args()
+
+    template_path = Path(args.template)
+    dir_list_path = Path(args.dir_list)
+    params_file   = str(Path(args.params_file).resolve())
+    out_dir       = Path(args.output_dir)
+
+    tif_regexp = re.compile(args.tif_regexp) if args.tif_regexp else None
+
+    # Load template
+    if not template_path.exists():
+        sys.exit(f"Template not found: {template_path}")
+    with open(template_path) as f:
+        template = json.load(f)
+
+    # Load directory list
+    if not dir_list_path.exists():
+        sys.exit(f"Directory list not found: {dir_list_path}")
+    directories = []
+    with open(dir_list_path) as f:
+        for raw in f:
+            line = raw.strip()
+            if not line or line.startswith("#"):
+                continue
+            p = Path(line)
+            if not p.is_dir():
+                print(f"Warning: not a directory, skipping: {line}", file=sys.stderr)
+                continue
+            directories.append(p)
+
+    if not directories:
+        sys.exit("No valid directories found in the list.")
+
+    out_dir.mkdir(parents=True, exist_ok=True)
+
+    # Derive base job_id from the template (may itself contain a placeholder)
+    base_job_id = template.get("job_id", "run")
+    digits = len(str(len(directories)))
+
+    # If the template has a literal root_path, treat it as the prototype root: every
+    # occurrence of that path in any string field will be replaced with the current
+    # directory.  This lets real data.json files (with no {{ }} placeholders) be used
+    # directly as templates without manual editing.
+    proto_root = template.get("root_path", "").rstrip("/")
+
+    generated = []
+    for idx, directory in enumerate(directories, start=1):
+        root_dir = str(directory.absolute())
+
+        # Collect files
+        tif_files = sorted(set(
+            _collect_files(directory, "*.tif") +
+            _collect_files(directory, "*.tiff")
+        ))
+        if tif_regexp is not None:
+            tif_files = [p for p in tif_files if tif_regexp.search(Path(p).name)]
+        if not tif_files:
+            print(f"Warning: no tif files found, skipping: {directory}", file=sys.stderr)
+            continue
+        b64_files = _collect_files(directory, "*.b64")
+        if args.force_sync:
+            if not b64_files:
+                print(f"Warning: --force-sync: no b64 files found, skipping: {directory}", file=sys.stderr)
+                continue
+            if len(b64_files) != len(tif_files):
+                print(f"Warning: --force-sync: {len(b64_files)} b64 vs {len(tif_files)} tif, skipping: {directory}", file=sys.stderr)
+                continue
+
+        # Substitute variables in the template (produces the per-dir job_id).
+        # Step 1: replace the prototype root_path literally in all string fields so
+        #   that templates with real paths (no {{ }} placeholders) work correctly.
+        # Step 2: apply {{ }} placeholder substitution for explicit placeholders.
+        suffix = f"_{idx:0{digits}d}"
+        working = _replace_literal(template, proto_root, root_dir) if proto_root else template
+        resolved_base_job_id = _apply_template_vars(
+            _replace_literal(base_job_id, proto_root, root_dir) if proto_root else base_job_id,
+            {"root_dir": root_dir},
+        )
+        variables = {"job_id": resolved_base_job_id, "root_dir": root_dir}
+        data_dict = _apply_template_vars(working, variables)
+
+        # Resolve the job_id after substitution, then append numeric suffix
+        resolved_job_id = data_dict.get("job_id", resolved_base_job_id)
+        final_job_id = f"{resolved_job_id}{suffix}"
+
+        data_dict["job_id"]      = final_job_id
+        data_dict["params_file"] = params_file
+        data_dict["root_path"]   = root_dir
+        data_dict["data"]        = tif_files
+        if b64_files:
+            data_dict["behavior_data"] = b64_files
+        elif "behavior_data" in data_dict:
+            del data_dict["behavior_data"]
+
+        out_path = out_dir / f"{final_job_id}_data.json"
+        with open(out_path, "w") as f:
+            json.dump(data_dict, f, indent=2)
+
+        generated.append(out_path)
+        print(f"  [{idx:>{digits}}/{len(directories)}] {out_path.name}  ({len(tif_files)} tif, {len(b64_files)} b64)  {root_dir}")
+
+    print(f"\nGenerated {len(generated)} data.json file(s) in: {out_dir.resolve()}")
+
+
+if __name__ == "__main__":
+    main()

batch2p-0.1.0.dist-info/METADATA

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+Metadata-Version: 2.4
+Name: batch2p
+Version: 0.1.0
+Author: Francesco P. Battaglia
+License-Expression: GPL-3.0-or-later
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Requires-Python: >=3.11
+Requires-Dist: numpy
+Requires-Dist: pynapple
+Requires-Dist: suite2p
+Requires-Dist: tifffile
+Requires-Dist: tifftrim
+Requires-Dist: totalsync-2p
+Requires-Dist: totalsync-utils
+Provides-Extra: gui
+Requires-Dist: pyqt5; extra == 'gui'

batch2p-0.1.0.dist-info/RECORD

@@ -0,0 +1,13 @@
+batch2p/__init__.py,sha256=L3g3zkH1gR1Igqp0olvgeWwpSxEXqC4qbTx8ldPQATg,56
+batch2p/cli.py,sha256=PsHrTxl8fjyFmWapu4bMkH527jpVCxDLnmAV4uzFFjA,17731
+batch2p/compute_F_sub.py,sha256=QEPU4rPtEwLBVyET-urM3Pqc1uEHiZcPWjq3wWaAcVE,5249
+batch2p/gui.py,sha256=WRgFrDio47fHDrxj3nzBqPE_XGC3HWto_iHs2k-cH70,74149
+batch2p/multi.py,sha256=KPfcDELcroNEJZ-b7cI8w6648Jr-_YmgdQ4H1gRpnTg,7387
+batch2p/extractors/__init__.py,sha256=bYtbjPhfst7z6sodVsJ2T3XRPrsWfOmNVUyM216odZs,470
+batch2p/extractors/base.py,sha256=l23PUW71DHv2k7vFc3rShE13lOuFxXtKN9e2Fal602c,1089
+batch2p/extractors/suite2p.py,sha256=eVYmkicuTmSYLHFIgNpkmlAfG3R90TSdDTMOJ7KWE1c,13267
+batch2p/extractors/suite3d.py,sha256=wsuRteMgYH3Yi-blEHtnTe8ny4oV7l1fKBINFYSKykc,5609
+batch2p-0.1.0.dist-info/METADATA,sha256=FtmtoM9qBN3A6jhOAs56KYhHIMwf2mc9NmAvRY6VmWk,470
+batch2p-0.1.0.dist-info/WHEEL,sha256=mffPy8wBnZQn2VnJUU5jE99KsxaSfiyMHV9Yt0aLVxs,87
+batch2p-0.1.0.dist-info/entry_points.txt,sha256=lFNxgFg89kcBWBqakObR0uPdz80N3Z5VnJMcdpkEL8Y,161
+batch2p-0.1.0.dist-info/RECORD,,

batch2p-0.1.0.dist-info/WHEEL

@@ -0,0 +1,4 @@
+Wheel-Version: 1.0
+Generator: hatchling 1.30.1
+Root-Is-Purelib: true
+Tag: py3-none-any

batch2p-0.1.0.dist-info/entry_points.txt

@@ -0,0 +1,5 @@
+[console_scripts]
+batch2p = batch2p.cli:main
+batch2p-compute-fsub = batch2p.compute_F_sub:main
+batch2p-gui = batch2p.gui:main
+batch2p-multi = batch2p.multi:main