Add feature to make studies from embedded images

makestudy

@@ -26,6 +26,7 @@ fi
 
 if [ "$#" -eq 1 ]; then
     studydir="$(basename "${graphml%.*}")"
+    studydir="${studydir%.graphml}"
 else
     studydir="$2"
 fi

makestudy.bat

@@ -12,11 +12,23 @@ set "ext1=%~x1"
 set "file1=!file1:\=\\!"
 set "dir1=!dir1:\=\\!"
 
+:: when the input file is 'something.graphml.jpg'
+if /I "!name1:~-8!"==".graphml" set "name1=!name1:~0,-8!"
+
 :: If the second argument (file2) is not provided
 if not defined file2 (
     if /I "%ext1%"==".graphml" (
         echo python mkconcore.py "!file1!" "!dir1!" "!name1!" windows
         python mkconcore.py "!file1!" "!dir1!" "!name1!" windows
+    ) else if /I "%ext1%"==".png" (
+        echo python mkconcore.py "!file1!" "!dir1!" "!name1!" windows
+        python mkconcore.py "!file1!" "!dir1!" "!name1!" windows
+    ) else if /I "%ext1%"==".jpg" (
+        echo python mkconcore.py "!file1!" "!dir1!" "!name1!" windows
+        python mkconcore.py "!file1!" "!dir1!" "!name1!" windows
+    ) else if /I "%ext1%"==".jpeg" (
+        echo python mkconcore.py "!file1!" "!dir1!" "!name1!" windows
+        python mkconcore.py "!file1!" "!dir1!" "!name1!" windows
     ) else (
         echo python mkconcore.py "!dir1!!name1!.graphml" "!dir1!" "!name1!" windows
         python mkconcore.py "!dir1!!name1!.graphml" "!dir1!" "!name1!" windows
@@ -25,6 +37,15 @@ if not defined file2 (
     if /I "%ext1%"==".graphml" (
         echo python mkconcore.py "!file1!" "!dir1!" "!file2!" windows
         python mkconcore.py "!file1!" "!dir1!" "!file2!" windows
+    ) else if /I "%ext1%"==".png" (
+        echo python mkconcore.py "!file1!" "!dir1!" "!file2!" windows
+        python mkconcore.py "!file1!" "!dir1!" "!file2!" windows
+    ) else if /I "%ext1%"==".jpg" (
+        echo python mkconcore.py "!file1!" "!dir1!" "!file2!" windows
+        python mkconcore.py "!file1!" "!dir1!" "!file2!" windows
+    ) else if /I "%ext1%"==".jpeg" (
+        echo python mkconcore.py "!file1!" "!dir1!" "!file2!" windows
+        python mkconcore.py "!file1!" "!dir1!" "!file2!" windows
     ) else (
         echo python mkconcore.py "!dir1!!name1!.graphml" "!dir1!" "!file2!" windows
         python mkconcore.py "!dir1!!name1!.graphml" "!dir1!" "!file2!" windows

mkconcore.py

@@ -69,7 +69,8 @@
 import sys
 import os
 import shutil
-import stat
+import stat
+import tempfile
 import copy_with_port_portname
 import numpy as np
 import shlex  # Added for POSIX shell escaping
@@ -144,6 +145,35 @@ def _resolve_concore_path():
 
 ORIGINAL_CWD = os.getcwd()
 GRAPHML_FILE = os.path.abspath(sys.argv[1])
+
+# --- Image input support: extract embedded GraphML from PNG/JPG ---
+_IMAGE_EXTS = {".png", ".jpg", ".jpeg"}
+_tmp_graphml_file = None  # keep reference so the temp file isn't deleted early
+if os.path.splitext(GRAPHML_FILE)[1].lower() in _IMAGE_EXTS:
+    try:
+        import importlib.util
+        _tool_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), "tools", "extract_graphml.py")
+        _spec = importlib.util.spec_from_file_location("extract_graphml", _tool_path)
+        _extract_graphml_module = importlib.util.module_from_spec(_spec)
+        _spec.loader.exec_module(_extract_graphml_module)
+        _extract_graphml = _extract_graphml_module.extract_graphml
+        _graphml_str = _extract_graphml(GRAPHML_FILE)
+        if _graphml_str is None:
+            print(f"No embedded GraphML found in '{GRAPHML_FILE}'.")
+            sys.exit(1)
+        _tmp_graphml_file = tempfile.NamedTemporaryFile(
+            mode="w", suffix=".graphml", delete=False, encoding="utf-8"
+        )
+        _tmp_graphml_file.write(_graphml_str)
+        _tmp_graphml_file.close()
+        GRAPHML_FILE = _tmp_graphml_file.name
+        import atexit as _atexit
+        _atexit.register(os.unlink, GRAPHML_FILE)
+    except Exception as _e:
+        print(f"Failed to extract GraphML from image: {_e}")
+        sys.exit(1)
+# ------------------------------------------------------------------
+
 TRIMMED_LOGS = True
 CONCOREPATH = _resolve_concore_path()
 CPPWIN    = os.environ.get("CONCORE_CPPWIN", "g++")          #Windows C++  6/22/21

tools/extract_graphml.py

@@ -0,0 +1,189 @@
+from typing import Optional
+import struct
+import zlib
+import sys
+import os
+
+
+# ---------------------------------------------------------------------------
+# PNG extraction
+# ---------------------------------------------------------------------------
+
+_PNG_SIGNATURE = b"\x89PNG\r\n\x1a\n"
+
+
+def _extract_from_png(data: bytes) -> Optional[str]:
+    #Return the GraphML string embedded in a PNG file, or None
+    if data[:8] != _PNG_SIGNATURE:
+        return None
+
+    pos = 8
+    while pos + 12 <= len(data):
+        length = struct.unpack(">I", data[pos : pos + 4])[0]
+        chunk_type = data[pos + 4 : pos + 8]
+        chunk_data = data[pos + 8 : pos + 8 + length]
+
+        if chunk_type == b"tEXt":
+            try:
+                null_pos = chunk_data.index(b"\x00")
+            except ValueError:
+                pos += 12 + length
+                continue
+            keyword = chunk_data[:null_pos].decode("latin-1")
+            if keyword.lower() == "graphml":
+                text = chunk_data[null_pos + 1 :].decode("latin-1")
+                return text
+
+        elif chunk_type == b"zTXt":
+            try:
+                null_pos = chunk_data.index(b"\x00")
+            except ValueError:
+                pos += 12 + length
+                continue
+            keyword = chunk_data[:null_pos].decode("latin-1")
+            if keyword.lower() == "graphml":
+                # compression method byte follows null, then deflate data
+                compressed = chunk_data[null_pos + 2 :]
+                try:
+                    text = zlib.decompress(compressed).decode("utf-8")
+                    return text
+                except Exception:
+                    pass
+
+        elif chunk_type == b"iTXt":
+            # Keyword, null, compression flag, compression method, lang,
+            # translated keyword, null, text (may be compressed)
+            try:
+                null_pos = chunk_data.index(b"\x00")
+                keyword = chunk_data[:null_pos].decode("latin-1")
+                if keyword.lower() == "graphml":
+                    rest = chunk_data[null_pos + 1 :]
+                    comp_flag = rest[0]
+                    comp_method = rest[1]
+                    rest = rest[2:]
+                    # skip language tag
+                    second_null = rest.index(b"\x00")
+                    rest = rest[second_null + 1 :]
+                    # skip translated keyword
+                    third_null = rest.index(b"\x00")
+                    text_bytes = rest[third_null + 1 :]
+                    if comp_flag == 1:
+                        text_bytes = zlib.decompress(text_bytes)
+                    return text_bytes.decode("utf-8")
+            except Exception:
+                pass
+
+        elif chunk_type == b"IEND":
+            break
+
+        pos += 12 + length
+
+    return None
+
+
+# ---------------------------------------------------------------------------
+# JPEG extraction
+# ---------------------------------------------------------------------------
+
+_JPEG_SOI = b"\xff\xd8"
+
+
+def _extract_from_jpeg(data: bytes) -> Optional[str]:
+    #Return the GraphML string embedded in a JPEG file, or None.
+    if data[:2] != _JPEG_SOI:
+        return None
+
+    # Strategy 1: look for raw <?xml ... </graphml> span anywhere in the file.
+    xml_start = data.find(b"<?xml")
+    if xml_start == -1:
+        # Also try without XML declaration
+        xml_start = data.find(b"<graphml")
+        if xml_start == -1:
+            return None
+
+    graphml_end = data.find(b"</graphml>", xml_start)
+    if graphml_end == -1:
+        return None
+
+    xml_bytes = data[xml_start : graphml_end + len(b"</graphml>")]
+    try:
+        return xml_bytes.decode("utf-8")
+    except UnicodeDecodeError:
+        try:
+            return xml_bytes.decode("latin-1")
+        except Exception:
+            return None
+
+
+# ---------------------------------------------------------------------------
+# Public API
+# ---------------------------------------------------------------------------
+
+
+def extract_graphml(image_path: str) -> Optional[str]:
+    try:
+        with open(image_path, "rb") as fh:
+            data = fh.read()
+    except OSError as exc:
+        print(f"[extract_graphml] Cannot open '{image_path}': {exc}", file=sys.stderr)
+        return None
+
+    # Detect by magic bytes
+    if data[:8] == _PNG_SIGNATURE:
+        return _extract_from_png(data)
+
+    if data[:2] == _JPEG_SOI:
+        return _extract_from_jpeg(data)
+
+    print(
+        f"[extract_graphml] '{image_path}' is neither PNG nor JPEG.",
+        file=sys.stderr,
+    )
+    return None
+
+
+def extract_graphml_to_file(image_path: str, output_path: Optional[str] = None) -> Optional[str]:
+    graphml = extract_graphml(image_path)
+    if graphml is None:
+        print(
+            f"[extract_graphml] No embedded GraphML found in '{image_path}'.",
+            file=sys.stderr,
+        )
+        return None
+
+    if output_path is None:
+        base, _ = os.path.splitext(image_path)
+        # Handle double-extension names like "foo.graphml.png" -> "foo.graphml"
+        if base.endswith(".graphml"):
+            output_path = base
+        else:
+            output_path = base + ".graphml"
+
+    try:
+        with open(output_path, "w", encoding="utf-8") as fh:
+            fh.write(graphml)
+        print(f"[extract_graphml] Extracted GraphML written to '{output_path}'.")
+        return output_path
+    except OSError as exc:
+        print(
+            f"[extract_graphml] Cannot write to '{output_path}': {exc}",
+            file=sys.stderr,
+        )
+        return None
+
+
+# ---------------------------------------------------------------------------
+# CLI entry point
+# ---------------------------------------------------------------------------
+
+if __name__ == "__main__":
+    if len(sys.argv) < 2:
+        print("Usage: python extract_graphml.py <image.png|jpg|jpeg> [output.graphml]")
+        sys.exit(1)
+
+    in_path = sys.argv[1]
+    out_path = sys.argv[2] if len(sys.argv) >= 3 else None
+
+    result = extract_graphml_to_file(in_path, out_path)
+    if result is None:
+        sys.exit(1)