scitex 2.10.3__py3-none-any.whl → 2.13.0__py3-none-any.whl

scitex/io/_load_modules/_canvas.py

@@ -3,7 +3,7 @@
 # Timestamp: 2025-12-08
 # File: /home/ywatanabe/proj/scitex-code/src/scitex/io/_load_modules/_canvas.py
 """
-Load canvas directory (.canvas) for scitex.fig.
+Load canvas directory (.canvas) for scitex.canvas.
 
 Canvas directories are portable figure bundles containing:
     - canvas.json: Layout, panels, composition settings
@@ -100,7 +100,7 @@ def _load_canvas(
     # Return Canvas object by default
     if not as_dict:
         try:
-            from scitex.fig.canvas import Canvas
+            from scitex.canvas.canvas import Canvas
 
             canvas_obj = Canvas.from_dict(canvas_dict)
             # Store reference to original directory for copying

scitex/io/_load_modules/_con.py

@@ -1,20 +1,31 @@
 #!/usr/bin/env python3
-# -*- coding: utf-8 -*-
 # Time-stamp: "2024-11-14 07:51:45 (ywatanabe)"
 # File: ./scitex_repo/src/scitex/io/_load_modules/_con.py
 
 from typing import Any
 
-import mne
+try:
+    import mne
+
+    MNE_AVAILABLE = True
+except ImportError:
+    MNE_AVAILABLE = False
+    mne = None
 
 
 def _load_con(lpath: str, **kwargs) -> Any:
+    if not MNE_AVAILABLE:
+        raise ImportError(
+            "MNE-Python is not installed. Please install with: pip install mne"
+        )
+
     if not lpath.endswith(".con"):
         raise ValueError("File must have .con extension")
-    obj = mne.io.read_raw_fif(lpath, preload=True, **kwargs)
-    obj = obj.to_data_frame()
-    obj["samp_rate"] = obj.info["sfreq"]
-    return obj
+    raw = mne.io.read_raw_fif(lpath, preload=True, **kwargs)
+    sfreq = raw.info["sfreq"]
+    df = raw.to_data_frame()
+    df["samp_rate"] = sfreq
+    return df
 
 
 # EOF

scitex/io/_load_modules/_eeg.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python3
-# -*- coding: utf-8 -*-
 # Time-stamp: "2024-11-14 07:56:27 (ywatanabe)"
 # File: ./scitex_repo/src/scitex/io/_load_modules/_eeg.py
 
@@ -7,10 +6,16 @@ import os
 import warnings
 from typing import Any
 
-import mne
+try:
+    import mne
 
+    MNE_AVAILABLE = True
+except ImportError:
+    MNE_AVAILABLE = False
+    mne = None
 
-def _load_eeg_data(path: str, **kwargs) -> Any:
+
+def _load_eeg_data(lpath: str, **kwargs) -> Any:
     """
     Load EEG data based on file extension and associated files using MNE-Python.
 
@@ -39,19 +44,24 @@ def _load_eeg_data(path: str, **kwargs) -> Any:
     This function uses MNE-Python to load the EEG data. It automatically detects the file format
     based on the file extension and uses the appropriate MNE function to load the data.
     """
+    if not MNE_AVAILABLE:
+        raise ImportError(
+            "MNE-Python is not installed. Please install with: pip install mne"
+        )
+
     # Get the file extension
     extension = lpath.split(".")[-1]
 
     allowed_extensions = [
-        ".vhdr",
-        ".vmrk",
-        ".edf",
-        ".bdf",
-        ".gdf",
-        ".cnt",
-        ".egi",
-        ".eeg",
-        ".set",
+        "vhdr",
+        "vmrk",
+        "edf",
+        "bdf",
+        "gdf",
+        "cnt",
+        "egi",
+        "eeg",
+        "set",
     ]
 
     if extension not in allowed_extensions:
@@ -59,6 +69,9 @@ def _load_eeg_data(path: str, **kwargs) -> Any:
             f"File must have one of these extensions: {', '.join(allowed_extensions)}"
         )
 
+    # Remove preload from kwargs if present - we always use preload=True
+    kwargs.pop("preload", None)
+
     with warnings.catch_warnings():
         warnings.simplefilter("ignore", RuntimeWarning)
 
@@ -98,9 +111,11 @@ def _load_eeg_data(path: str, **kwargs) -> Any:
                 lpath_v = lpath.replace(".eeg", ".vhdr")
                 raw = mne.io.read_raw_brainvision(lpath_v, preload=True, **kwargs)
             # Nihon Koden
-            if is_NihonKoden:
+            elif is_NihonKoden:
                 # raw = mne.io.read_raw_nihon(lpath, preload=True, **kwargs)
                 raw = mne.io.read_raw(lpath, preload=True, **kwargs)
+            else:
+                raise ValueError("No associated files found for .eeg file")
         else:
             raise ValueError(f"Unsupported file extension: {extension}")
 

scitex/io/_load_modules/_optuna.py

@@ -1,10 +1,17 @@
 #!/usr/bin/env python3
-# -*- coding: utf-8 -*-
 # Time-stamp: "2024-11-14 07:55:45 (ywatanabe)"
 # File: ./scitex_repo/src/scitex/io/_load_modules/_optuna.py
 
 from ._yaml import _load_yaml
 
+try:
+    import optuna
+
+    OPTUNA_AVAILABLE = True
+except ImportError:
+    OPTUNA_AVAILABLE = False
+    optuna = None
+
 
 def load_yaml_as_an_optuna_dict(fpath_yaml, trial):
     """
@@ -31,7 +38,14 @@ def load_yaml_as_an_optuna_dict(fpath_yaml, trial):
         If the specified YAML file does not exist.
     ValueError
         If the YAML file contains invalid configuration for Optuna.
+    ImportError
+        If Optuna is not installed.
     """
+    if not OPTUNA_AVAILABLE:
+        raise ImportError(
+            "Optuna is not installed. Please install with: pip install optuna"
+        )
+
     _d = _load_yaml(fpath_yaml)
 
     for k, v in _d.items():
@@ -74,6 +88,8 @@ def load_study_rdb(study_name, rdb_raw_bytes_url):
     -------
     optuna.exceptions.StorageInvalidUsageError
         If there's an error loading the study from the storage.
+    ImportError
+        If Optuna is not installed.
 
     Example:
     --------
@@ -82,7 +98,10 @@ def load_study_rdb(study_name, rdb_raw_bytes_url):
     ...     rdb_raw_bytes_url="sqlite:///path/to/your/study.db"
     ... )
     """
-    import optuna
+    if not OPTUNA_AVAILABLE:
+        raise ImportError(
+            "Optuna is not installed. Please install with: pip install optuna"
+        )
 
     storage = optuna.storages.RDBStorage(url=rdb_raw_bytes_url)
     study = optuna.load_study(study_name=study_name, storage=storage)
@@ -90,65 +109,4 @@ def load_study_rdb(study_name, rdb_raw_bytes_url):
     return study
 
 
-def load_yaml_as_an_optuna_dict(fpath_yaml, trial):
-    """
-    Load a YAML file and convert it to an Optuna-compatible dictionary.
-
-    Parameters:
-    -----------
-    fpath_yaml : str
-        The path to the YAML file.
-    trial : optuna.trial.Trial
-        The Optuna trial object.
-
-    Returns:
-    --------
-    dict
-        A dictionary with Optuna-compatible parameter suggestions.
-    """
-    _d = _load_yaml(fpath_yaml)
-
-    for k, v in _d.items():
-        dist = v["distribution"]
-
-        if dist == "categorical":
-            _d[k] = trial.suggest_categorical(k, v["values"])
-
-        elif dist == "uniform":
-            _d[k] = trial.suggest_int(k, float(v["min"]), float(v["max"]))
-
-        elif dist == "loguniform":
-            _d[k] = trial.suggest_loguniform(k, float(v["min"]), float(v["max"]))
-
-        elif dist == "intloguniform":
-            _d[k] = trial.suggest_int(k, float(v["min"]), float(v["max"]), log=True)
-
-    return _d
-
-
-def load_study_rdb(study_name, rdb_raw_bytes_url):
-    """
-    Load an Optuna study from a RDB storage.
-
-    Parameters:
-    -----------
-    study_name : str
-        The name of the Optuna study.
-    rdb_raw_bytes_url : str
-        The URL of the RDB storage.
-
-    Returns:
-    --------
-    optuna.study.Study
-        The loaded Optuna study object.
-    """
-    import optuna
-
-    # rdb_raw_bytes_url = "sqlite:////tmp/fake/ywatanabe/_MicroNN_WindowSize-1.0-sec_MaxEpochs_100_2021-1216-1844/optuna_study_test_file#0.db"
-    storage = optuna.storages.RDBStorage(url=rdb_raw_bytes_url)
-    study = optuna.load_study(study_name=study_name, storage=storage)
-    print(f"\nLoaded: {rdb_raw_bytes_url}\n")
-    return study
-
-
 # EOF

scitex/io/_load_modules/_torch.py

@@ -1,13 +1,21 @@
 #!/usr/bin/env python3
-# -*- coding: utf-8 -*-
 # Time-stamp: "2024-11-14 07:41:34 (ywatanabe)"
 # File: ./scitex_repo/src/scitex/io/_load_modules/_torch.py
 
+try:
+    import torch
+
+    TORCH_AVAILABLE = True
+except ImportError:
+    TORCH_AVAILABLE = False
+
 
 def _load_torch(lpath, **kwargs):
     """Load PyTorch model/checkpoint file."""
-    # Lazy import to avoid circular import issues
-    import torch
+    if not TORCH_AVAILABLE:
+        raise ImportError(
+            "PyTorch is not installed. Please install with: pip install torch"
+        )
 
     if not lpath.endswith((".pth", ".pt")):
         raise ValueError("File must have .pth or .pt extension")

scitex/io/_save.py

@@ -6,7 +6,7 @@
 Save utilities for various data types to different file formats.
 
 Supported formats include CSV, NPY, PKL, JOBLIB, PNG, HTML, TIFF, MP4, YAML,
-JSON, HDF5, PTH, MAT, CBM, and FTS bundles (.zip or directory).
+JSON, HDF5, PTH, MAT, CBM, and SciTeX bundles (.zip or directory).
 """
 
 import inspect
@@ -40,8 +40,6 @@ from ._save_modules import (
     save_npz,
     save_pickle,
     save_pickle_compressed,
-    save_pltz_bundle,
-    save_stx_bundle,
     save_tex,
     save_text,
     save_torch,
@@ -53,12 +51,9 @@ from ._save_modules import (
 
 logger = logging.getLogger()
 
-# Re-export for backward compatibility
 _get_figure_with_data = get_figure_with_data
 _symlink = symlink
 _symlink_to = symlink_to
-_save_stx_bundle = save_stx_bundle
-_save_pltz_bundle = save_pltz_bundle
 _handle_image_with_csv = handle_image_with_csv
 
 
@@ -278,17 +273,17 @@ def _save(
     """Core dispatcher for saving objects to various formats."""
     ext = _os.path.splitext(spath)[1].lower()
 
-    # Check if this is a matplotlib figure being saved to FTS bundle format
-    # FTS bundles use .zip (archive) or no extension (directory)
+    # Check if this is a matplotlib figure being saved to SciTeX bundle format
+    # SciTeX bundles use .zip (archive) or no extension (directory)
     if _is_matplotlib_figure(obj):
-        # Save as FTS bundle if:
+        # Save as SciTeX bundle if:
         # 1. Path ends with .zip (create ZIP bundle)
         # 2. Path has no extension and doesn't match other formats (create directory bundle)
         if ext == ".zip" or (ext == "" and not spath.endswith("/")):
-            # Check if explicitly requesting FTS bundle or just .zip
+            # Check if explicitly requesting SciTeX bundle or just .zip
             # Pop as_zip from kwargs to avoid duplicate parameter error
             as_zip = kwargs.pop("as_zip", ext == ".zip")
-            _save_fts_bundle(
+            _save_scitex_bundle(
                 obj, spath, as_zip, verbose, symlink_from_cwd, symlink_to, **kwargs
             )
             return
@@ -348,12 +343,12 @@ def _is_matplotlib_figure(obj):
         return False
 
 
-def _save_fts_bundle(
+def _save_scitex_bundle(
     obj, spath, as_zip, verbose, symlink_from_cwd, symlink_to_path, **kwargs
 ):
-    """Save matplotlib figure as FTS bundle (.zip or directory).
+    """Save matplotlib figure as SciTeX bundle (.zip or directory).
 
-    Delegates to scitex.fts.from_matplotlib as the single source of truth
+    Delegates to scitex.io.bundle.from_matplotlib as the single source of truth
     for bundle structure (canonical/artifacts/payload/children).
 
     When figrecipe is available and enabled on the figure, also saves
@@ -362,7 +357,7 @@ def _save_fts_bundle(
     # Get the actual matplotlib figure
     import matplotlib.figure
 
-    from scitex.fts import from_matplotlib
+    from scitex.io.bundle import from_matplotlib
 
     from ._save_modules._figure_utils import get_figure_with_data
 
@@ -390,7 +385,7 @@ def _save_fts_bundle(
             except Exception:
                 pass
 
-    # Delegate to FTS (single source of truth)
+    # Delegate to Bundle (single source of truth)
     # Encoding is built from CSV columns directly for consistency
     from_matplotlib(fig, spath, name=name, csv_df=csv_df, dpi=dpi)
 

scitex/io/_save_modules/__init__.py

@@ -55,14 +55,10 @@ from ._mp4 import _mk_mp4 as save_mp4
 from ._numpy import _save_npy as save_npy
 from ._numpy import _save_npz as save_npz
 from ._optuna_study_as_csv_and_pngs import save_optuna_study_as_csv_and_pngs
-from ._pickle import (
-    _save_pickle as save_pickle,
-)
-from ._pickle import (
-    _save_pickle_gz as save_pickle_compressed,
-)
-from ._pltz_bundle import save_pltz_bundle
-from ._pltz_stx import save_pltz_as_stx
+from ._pickle import _save_pickle as save_pickle
+from ._pickle import _save_pickle_gz as save_pickle_compressed
+from ._plot_bundle import save_plot_bundle
+from ._plot_scitex import save_plot_as_scitex
 from ._stx_bundle import save_stx_bundle
 from ._symlink import symlink, symlink_to
 from ._tex import _save_tex as save_tex
@@ -121,8 +117,8 @@ __all__ = [
     "save_optuna_study_as_csv_and_pngs",
     # Bundle save functions
     "save_stx_bundle",
-    "save_pltz_bundle",
-    "save_pltz_as_stx",
+    "save_plot_bundle",
+    "save_plot_as_scitex",
     "save_separate_legends",
     "handle_image_with_csv",
     # Utilities

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.fig.
+Save canvas directory (.canvas) for scitex.canvas.
 
 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.fig.io.export import _compose_and_export
+        from scitex.canvas.io.export import _compose_and_export
         import json
 
         # Load canvas.json
@@ -136,7 +136,7 @@ def _export_canvas_figures(
                 transparent=False,
             )
     except ImportError:
-        # scitex.fig not available
+        # scitex.canvas not available
         pass
     except Exception as e:
         # Log but don't fail save if export fails

scitex/io/_save_modules/_optuna_study_as_csv_and_pngs.py

@@ -1,11 +1,22 @@
 #!/usr/bin/env python3
-# -*- coding: utf-8 -*-
 # Time-stamp: "2024-11-02 17:01:15 (ywatanabe)"
 # File: ./scitex_repo/src/scitex/io/_save_optuna_study_as_csv_and_pngs.py
 
+try:
+    import optuna
+
+    OPTUNA_AVAILABLE = True
+except ImportError:
+    OPTUNA_AVAILABLE = False
+    optuna = None
+
 
 def save_optuna_study_as_csv_and_pngs(study, sdir):
-    import optuna
+    if not OPTUNA_AVAILABLE:
+        raise ImportError(
+            "Optuna is not installed. Please install with: pip install optuna"
+        )
+
     from .._save import save
 
     ## Trials DataFrame

scitex/io/_save_modules/_plot_bundle.py

@@ -0,0 +1,112 @@
+#!/usr/bin/env python3
+# Timestamp: 2025-12-19
+# File: /home/ywatanabe/proj/scitex-code/src/scitex/io/_save_modules/_plot_bundle.py
+
+"""Save matplotlib figures as .plot bundles."""
+
+import tempfile
+from pathlib import Path
+
+from scitex import logging
+
+from ._figure_utils import get_figure_with_data
+
+logger = logging.getLogger()
+
+
+def save_plot_bundle(obj, spath, as_zip=False, data=None, layered=True, **kwargs):
+    """Save a matplotlib figure as a .plot bundle.
+
+    Bundle structure v2.0 (layered - default):
+        plot.plot/
+            spec.json           # Semantic: WHAT to plot (canonical)
+            style.json          # Appearance: HOW it looks (canonical)
+            data.csv            # Raw data (immutable)
+            exports/            # PNG, SVG, hitmap
+            cache/              # geometry_px.json, render_manifest.json
+
+    Parameters
+    ----------
+    obj : matplotlib.figure.Figure
+        The figure to save.
+    spath : str or Path
+        Output path (e.g., "plot.plot" or "plot.plot.zip").
+    as_zip : bool
+        If True, save as ZIP archive.
+    data : pandas.DataFrame, optional
+        Data to embed in the bundle as plot.csv.
+    layered : bool
+        If True (default), use new layered format (spec/style/geometry).
+    **kwargs
+        Additional arguments passed to savefig.
+    """
+    import shutil
+
+    import matplotlib.figure
+
+    p = Path(spath)
+
+    # Extract basename from path
+    basename = p.stem
+    if basename.endswith(".plot"):
+        basename = basename[:-5]
+    elif basename.endswith(".zip"):
+        basename = Path(basename).stem
+        if basename.endswith(".plot"):
+            basename = basename[:-5]
+
+    # Extract figure from various matplotlib object types
+    fig = obj
+    if hasattr(obj, "figure"):
+        fig = obj.figure
+    elif hasattr(obj, "fig"):
+        fig = obj.fig
+
+    if not isinstance(fig, matplotlib.figure.Figure):
+        raise TypeError(f"Expected matplotlib Figure, got {type(obj).__name__}")
+
+    dpi = kwargs.pop("dpi", 300)
+
+    # === Always use layered format ===
+    # Determine bundle directory path
+    if as_zip:
+        temp_dir = Path(tempfile.mkdtemp())
+        bundle_dir = temp_dir / f"{basename}.plot"
+        zip_path = p if not str(p).endswith(".zip") else p
+    else:
+        bundle_dir = p if str(p).endswith(".plot") else Path(str(p) + ".plot")
+        temp_dir = None
+
+    # Get CSV data from figure if not provided
+    csv_df = data
+    if csv_df is None:
+        csv_source = get_figure_with_data(obj)
+        if csv_source is not None and hasattr(csv_source, "export_as_csv"):
+            try:
+                csv_df = csv_source.export_as_csv()
+            except Exception:
+                pass
+
+    from scitex.plt.io import save_layered_plot_bundle
+
+    save_layered_plot_bundle(
+        fig=fig,
+        bundle_dir=bundle_dir,
+        basename=basename,
+        dpi=dpi,
+        csv_df=csv_df,
+    )
+
+    # Compress to ZIP if requested
+    if as_zip:
+        import zipfile
+
+        with zipfile.ZipFile(zip_path, "w", zipfile.ZIP_DEFLATED) as zf:
+            for file_path in bundle_dir.rglob("*"):
+                if file_path.is_file():
+                    arcname = file_path.relative_to(bundle_dir.parent)
+                    zf.write(file_path, arcname)
+        shutil.rmtree(temp_dir)
+
+
+# EOF

scitex/io/_save_modules/{_pltz_stx.py → _plot_scitex.py}

@@ -1,8 +1,8 @@
 #!/usr/bin/env python3
 # Timestamp: 2025-12-19
-# File: /home/ywatanabe/proj/scitex-code/src/scitex/io/_save_modules/_pltz_stx.py
+# File: /home/ywatanabe/proj/scitex-code/src/scitex/io/_save_modules/_plot_scitex.py
 
-"""Save matplotlib figures as FTS bundles (ZIP or directory) with plot content type."""
+"""Save matplotlib figures as SciTeX bundles (ZIP or directory) with plot content type."""
 
 import json
 import tempfile
@@ -199,8 +199,8 @@ def _build_theme_from_figure(fig):
     }
 
 
-def save_pltz_as_stx(obj, spath, as_zip=True, basename=None, **kwargs):
-    """Save a matplotlib figure as an FTS bundle (ZIP or directory).
+def save_plot_as_scitex(obj, spath, as_zip=True, basename=None, **kwargs):
+    """Save a matplotlib figure as a SciTeX bundle (ZIP or directory).
 
     Bundle structure:
         plot_name/              # or plot_name.zip (with plot_name/ inside)
@@ -463,7 +463,7 @@ def _generate_readme(bundle_dir, basename, spec, csv_df):
     from datetime import datetime
 
     readme_lines = [
-        f"# {basename} FTS Bundle",
+        f"# {basename} SciTeX Bundle",
         "",
         "## Overview",
         "",
@@ -517,9 +517,9 @@ def _generate_readme(bundle_dir, basename, spec, csv_df):
             "## Usage",
             "",
             "```python",
-            "from scitex.fts import FTS",
+            "from scitex.io.bundle import Bundle",
             "",
-            f'bundle = FTS("{basename}.zip")  # or "{basename}/" directory',
+            f'bundle = Bundle("{basename}.zip")  # or "{basename}/" directory',
             "bundle.show()  # Display",
             'bundle.export("output.png")  # Export',
             "```",