scitex 2.7.0__py3-none-any.whl → 2.7.3__py3-none-any.whl

scitex/io/_save_modules/_canvas.py

@@ -3,7 +3,7 @@
 # Timestamp: 2025-12-08
 # File: /home/ywatanabe/proj/scitex-code/src/scitex/io/_save_modules/_canvas.py
 """
-Save canvas directory (.canvas) for scitex.vis.
+Save canvas directory (.canvas) for scitex.fig.
 
 Canvas directories are portable figure bundles containing:
     - canvas.json: Layout, panels, composition settings
@@ -113,7 +113,7 @@ def _export_canvas_figures(
         formats = ["png", "pdf", "svg"]
 
     try:
-        from scitex.vis.io.export import _compose_and_export
+        from scitex.fig.io.export import _compose_and_export
         import json
 
         # Load canvas.json
@@ -136,7 +136,7 @@ def _export_canvas_figures(
                 transparent=False,
             )
     except ImportError:
-        # scitex.vis not available
+        # scitex.fig not available
         pass
     except Exception as e:
         # Log but don't fail save if export fails

scitex/io/_save_modules/_image.py

@@ -8,11 +8,12 @@ import os
 __FILE__ = __file__
 
 import io as _io
-import logging
 
 import plotly
 from PIL import Image
 
+from scitex import logging
+
 logger = logging.getLogger(__name__)
 
 
@@ -66,9 +67,7 @@ def save_image(
                     fig = obj if hasattr(obj, "savefig") else obj.figure
                     obj = add_qr_to_figure(fig, metadata, position=qr_position)
             except Exception as e:
-                import warnings
-
-                warnings.warn(f"Failed to add QR code: {e}")
+                logger.warning(f"Failed to add QR code: {e}")
 
     # png
     if fmt == 'png':
@@ -216,9 +215,7 @@ def save_image(
             if verbose:
                 logger.debug(f"  • Embedded metadata: {metadata}")
         except Exception as e:
-            import warnings
-
-            warnings.warn(f"Failed to embed metadata: {e}")
+            logger.warning(f"Failed to embed metadata: {e}")
 
 def _save_stats_from_figure(obj, spath, verbose=False):
     """
@@ -297,8 +294,7 @@ def _save_stats_from_figure(obj, spath, verbose=False):
             logger.info(f"  • Auto-saved stats to: {stats_path}")
 
     except Exception as e:
-        import warnings
-        warnings.warn(f"Failed to auto-save stats: {e}")
+        logger.warning(f"Failed to auto-save stats: {e}")
 
 
 # EOF

scitex/io/_save_modules/_tex.py

@@ -20,7 +20,10 @@ Supports multiple input types:
 """
 
 from typing import Union, Optional, Any
-import warnings
+
+from scitex import logging
+
+logger = logging.getLogger(__name__)
 
 
 def save_tex(
@@ -121,21 +124,21 @@ def save_tex(
                 tex_content = _wrap_with_table_env(tex_content, caption, label)
 
         except ImportError:
-            warnings.warn(
+            logger.warning(
                 "Cannot convert dict/list to LaTeX: "
                 "scitex.stats.utils.convert_results not available. "
                 "Converting to string instead."
             )
             tex_content = str(obj)
         except Exception as e:
-            warnings.warn(
+            logger.warning(
                 f"Failed to convert object to LaTeX: {e}. Converting to string instead."
             )
             tex_content = str(obj)
 
     else:
         # Fallback: convert to string
-        warnings.warn(
+        logger.warning(
             f"Unsupported type {type(obj)} for LaTeX export. Converting to string."
         )
         tex_content = str(obj)

scitex/io/utils/h5_to_zarr.py

@@ -33,9 +33,9 @@ import numpy as np
 import os
 from pathlib import Path
 from typing import Optional, Union, Dict, Any, List, Tuple
-import warnings
 from tqdm import tqdm
 
+from scitex import logging
 from scitex.errors import (
     IOError as SciTeXIOError,
     FileFormatError,
@@ -46,6 +46,8 @@ from scitex.errors import (
     warn_performance,
 )
 
+logger = logging.getLogger(__name__)
+
 
 def _get_zarr_compressor(
     compressor: Optional[Union[str, Any]] = "zstd",
@@ -114,7 +116,7 @@ def _copy_h5_attributes(
 
             zarr_obj.attrs[key] = value
         except Exception as e:
-            warnings.warn(f"Could not copy attribute '{key}': {e}")
+            logger.warning(f"Could not copy attribute '{key}': {e}")
 
 
 def _migrate_dataset(
@@ -132,7 +134,7 @@ def _migrate_dataset(
         if hasattr(h5_dataset, "dtype"):
             test_dtype = h5_dataset.dtype
     except Exception as e:
-        warnings.warn(f"Skipping corrupted dataset '{name}': {e}")
+        logger.warning(f"Skipping corrupted dataset '{name}': {e}")
         return None
 
     # Get dataset info
@@ -241,7 +243,7 @@ def _migrate_dataset(
             else:  # Scalar
                 zarr_array[()] = h5_dataset[()]
         except Exception as e:
-            warnings.warn(
+            logger.warning(
                 f"Error copying data for dataset '{name}': {e}. Leaving empty."
             )
             # The array structure is created but data might be zeros/empty
@@ -268,14 +270,14 @@ def _migrate_group(
     try:
         keys = list(h5_group.keys())
     except Exception as e:
-        warnings.warn(f"Cannot access group keys: {e}")
+        logger.warning(f"Cannot access group keys: {e}")
         return
 
     for key in keys:
         try:
             item = h5_group[key]
         except Exception as e:
-            warnings.warn(f"Cannot access item '{key}': {e}")
+            logger.warning(f"Cannot access item '{key}': {e}")
             continue
 
         if isinstance(item, h5py.Dataset):
@@ -297,7 +299,7 @@ def _migrate_group(
             )
 
         else:
-            warnings.warn(f"Unknown HDF5 object type for '{key}': {type(item)}")
+            logger.warning(f"Unknown HDF5 object type for '{key}': {type(item)}")
 
 
 def migrate_h5_to_zarr(
@@ -418,7 +420,7 @@ def migrate_h5_to_zarr(
     except OSError as e:
         if "Unable to open file" in str(e) or "bad symbol table" in str(e):
             # File is corrupted
-            warnings.warn(f"HDF5 file appears to be corrupted: {h5_path}")
+            logger.warning(f"HDF5 file appears to be corrupted: {h5_path}")
             raise FileFormatError(
                 str(h5_path), expected_format="HDF5", actual_format="corrupted HDF5"
             )
@@ -452,7 +454,7 @@ def _validate_migration(
             # Compare dtypes (approximately)
             if h5_item.dtype.kind != "O" and zarr_item.dtype.kind != "O":
                 if h5_item.dtype != zarr_item.dtype:
-                    warnings.warn(
+                    logger.warning(
                         f"Dtype mismatch at {path}: "
                         f"HDF5={h5_item.dtype}, Zarr={zarr_item.dtype}"
                     )

scitex/msword/__init__.py

@@ -0,0 +1,255 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+# Timestamp: 2025-12-11 15:15:00
+# File: /home/ywatanabe/proj/scitex-code/src/scitex/msword/__init__.py
+
+"""
+MS Word (DOCX) import/export utilities for SciTeX.
+
+This module provides high-level functions to convert between
+MS Word .docx files and SciTeX's internal writer document model.
+
+Strategy:
+---------
+- Word users write text only (paragraphs, minimal formatting)
+- SciTeX handles: figures, tables, references, LaTeX generation
+- SciTeX JSON is the "source of truth", Word is just a view/edit layer
+
+Typical usage:
+--------------
+    from scitex.msword import load_docx, save_docx, list_profiles
+
+    # Import from Word
+    doc = load_docx("input.docx", profile="generic")
+
+    # Manipulate via scitex.writer...
+    # doc.normalize()
+
+    # Export to Word (different journal template)
+    save_docx(doc, "output.docx", profile="mdpi-ijerph")
+
+Available profiles:
+-------------------
+- generic: Standard Word with Heading 1/2/3
+- mdpi-ijerph: MDPI IJERPH journal template
+- resna-2025: RESNA 2025 scientific paper template
+- iop-double-anonymous: IOP double-anonymous template
+"""
+
+from __future__ import annotations
+
+from pathlib import Path
+from typing import Any, Optional
+
+from .profiles import (
+    BaseWordProfile,
+    get_profile,
+    list_profiles,
+    register_profile,
+)
+from .reader import WordReader
+from .writer import WordWriter
+from .utils import (
+    link_captions_to_images,
+    link_captions_to_images_by_proximity,
+    normalize_section_headings,
+    validate_document,
+    create_post_import_hook,
+)
+
+
+def load_docx(
+    path: str | Path,
+    profile: str | None = None,
+    extract_images: bool = True,
+) -> dict[str, Any]:
+    """
+    Load a DOCX file and convert it into a SciTeX writer document.
+
+    Parameters
+    ----------
+    path : str | Path
+        Path to the .docx file.
+    profile : str | None
+        Optional profile name that specifies how to interpret Word styles
+        (e.g., "mdpi-ijerph", "resna-2025"). If None, "generic" is used.
+    extract_images : bool
+        If True, extract embedded images and store references.
+
+    Returns
+    -------
+    dict
+        A SciTeX writer document structure containing:
+        - blocks: List of document blocks (headings, paragraphs, captions, etc.)
+        - metadata: Profile and source file information
+        - images: Extracted image references (if extract_images=True)
+        - references: Parsed reference entries
+
+    Examples
+    --------
+    >>> from scitex.msword import load_docx
+    >>> doc = load_docx("manuscript.docx", profile="mdpi-ijerph")
+    >>> print(doc["metadata"]["profile"])
+    'mdpi-ijerph'
+    """
+    path = Path(path)
+    profile_obj: BaseWordProfile = get_profile(profile)
+    reader = WordReader(profile=profile_obj, extract_images=extract_images)
+    return reader.read(path)
+
+
+def save_docx(
+    writer_doc: dict[str, Any] | Any,
+    path: str | Path,
+    profile: str | None = None,
+    overwrite: bool = True,
+    template_path: str | Path | None = None,
+) -> Path:
+    """
+    Save a SciTeX writer document as a DOCX file.
+
+    Parameters
+    ----------
+    writer_doc : dict | Any
+        SciTeX writer document instance to export.
+    path : str | Path
+        Output path for the .docx file.
+    profile : str | None
+        Optional profile name that controls how sections, headings,
+        figures, tables and references are mapped to Word styles.
+        If None, "generic" is used.
+    overwrite : bool
+        If False and the file already exists, raises FileExistsError.
+    template_path : str | Path | None
+        Optional path to a Word template (.dotx/.docx) to use as base.
+        This allows using journal-specific formatting.
+
+    Returns
+    -------
+    Path
+        The path to the written .docx file.
+
+    Examples
+    --------
+    >>> from scitex.msword import save_docx
+    >>> save_docx(doc, "submission_resna_2025.docx", profile="resna-2025")
+    PosixPath('submission_resna_2025.docx')
+    """
+    output_path = Path(path)
+    if output_path.exists() and not overwrite:
+        raise FileExistsError(f"File already exists: {output_path}")
+
+    profile_obj: BaseWordProfile = get_profile(profile)
+    writer = WordWriter(profile=profile_obj, template_path=template_path)
+    writer.write(writer_doc, output_path)
+    return output_path
+
+
+def convert_docx_to_tex(
+    input_path: str | Path,
+    output_path: str | Path,
+    profile: str | None = None,
+    *,
+    image_dir: str | Path | None = None,
+    link_images: bool = True,
+    link_mode: str = "by-number",
+    normalize_headings: bool = True,
+    validate: bool = True,
+) -> Path:
+    """
+    Convert a DOCX file directly to LaTeX.
+
+    This is a convenience function that:
+    1. Loads the DOCX file into SciTeX intermediate format
+    2. (Optionally) normalizes headings
+    3. (Optionally) links figure captions to images
+    4. (Optionally) validates the document and adds warnings
+    5. Exports to LaTeX (including figures via image_dir)
+
+    Parameters
+    ----------
+    input_path : str | Path
+        Path to the input .docx file.
+    output_path : str | Path
+        Path for the output .tex file.
+    profile : str | None
+        Word profile for interpreting styles
+        (e.g., "resna-2025", "iop-double-anonymous").
+    image_dir : str | Path | None, optional
+        Directory where extracted figure image files will be saved.
+        If None, the LaTeX exporter will create "<tex_stem>_figures"
+        next to `output_path`.
+    link_images : bool, default True
+        Whether to link figure captions to extracted images so that
+        LaTeX can generate \\includegraphics inside figure environments.
+    link_mode : {"by-number", "by-proximity"}, default "by-number"
+        Strategy for linking captions to images:
+        - "by-number": Figure 1 -> first image, Figure 2 -> second image...
+        - "by-proximity": assign images in document order, useful when
+          figure numbers and image order don't match.
+    normalize_headings : bool, default True
+        If True, apply common heading normalizations
+        (e.g., "intro" -> "Introduction").
+    validate : bool, default True
+        If True, run basic structural checks and populate
+        doc["warnings"] with any issues.
+
+    Returns
+    -------
+    Path
+        The path to the written .tex file.
+
+    Examples
+    --------
+    >>> from scitex.msword import convert_docx_to_tex
+    >>> convert_docx_to_tex(
+    ...     "RESNA 2025 Scientific Paper Template.docx",
+    ...     "manuscript.tex",
+    ...     profile="resna-2025",
+    ...     image_dir="figures",
+    ... )
+    PosixPath('manuscript.tex')
+    """
+    # Import here to avoid circular imports
+    from scitex.tex import export_tex
+
+    # 1. DOCX -> SciTeX intermediate format
+    doc = load_docx(input_path, profile=profile, extract_images=True)
+
+    # 2. Normalize headings (optional)
+    if normalize_headings:
+        doc = normalize_section_headings(doc)
+
+    # 3. Link captions to images (optional)
+    if link_images and doc.get("images"):
+        if link_mode == "by-proximity":
+            doc = link_captions_to_images_by_proximity(doc)
+        else:
+            # Default: link by figure number
+            doc = link_captions_to_images(doc)
+
+    # 4. Validate document structure (optional)
+    if validate:
+        doc = validate_document(doc)
+
+    # 5. SciTeX -> LaTeX (with figures)
+    return export_tex(doc, output_path, image_dir=image_dir)
+
+
+__all__ = [
+    "load_docx",
+    "save_docx",
+    "convert_docx_to_tex",
+    "list_profiles",
+    "get_profile",
+    "register_profile",
+    "BaseWordProfile",
+    "WordReader",
+    "WordWriter",
+    # Utility functions for post-processing
+    "link_captions_to_images",
+    "link_captions_to_images_by_proximity",
+    "normalize_section_headings",
+    "validate_document",
+    "create_post_import_hook",
+]