scitex 2.5.0__py3-none-any.whl → 2.7.3__py3-none-any.whl

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__)
 
 
@@ -23,8 +24,24 @@ def save_image(
     add_qr=False,
     qr_position="bottom-right",
     verbose=False,
+    save_stats=True,
     **kwargs,
 ):
+    # Determine if spath is a file-like object (e.g., BytesIO)
+    is_file_like = not isinstance(spath, str)
+
+    # Get format from file extension or kwargs
+    if is_file_like:
+        fmt = kwargs.get('format', '').lower()
+    else:
+        # Get extension without the leading dot
+        fmt = spath.lower().rsplit('.', 1)[-1] if '.' in spath else ''
+
+    # Auto-save stats BEFORE saving (obj may be deleted during save)
+    # Only for file paths, not file-like objects
+    if save_stats and not is_file_like:
+        _save_stats_from_figure(obj, spath, verbose=verbose)
+
     # Add URL to metadata if not present
     if metadata is not None:
         if verbose:
@@ -50,12 +67,10 @@ 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 spath.endswith(".png"):
+    if fmt == 'png':
         # plotly
         if isinstance(obj, plotly.graph_objs.Figure):
             obj.write_image(file=spath, format="png")
@@ -71,7 +86,7 @@ def save_image(
         del obj
 
     # tiff
-    elif spath.endswith(".tiff") or spath.endswith(".tif"):
+    elif fmt in ('tiff', 'tif'):
         # PIL image
         if isinstance(obj, Image.Image):
             obj.save(spath)
@@ -88,7 +103,7 @@ def save_image(
         del obj
 
     # jpeg
-    elif spath.endswith(".jpeg") or spath.endswith(".jpg"):
+    elif fmt in ('jpeg', 'jpg'):
         buf = _io.BytesIO()
 
         # plotly
@@ -125,7 +140,7 @@ def save_image(
         del obj
 
     # GIF
-    elif spath.endswith(".gif"):
+    elif fmt == 'gif':
         # PIL image
         if isinstance(obj, Image.Image):
             obj.save(spath, save_all=True)
@@ -153,7 +168,7 @@ def save_image(
         del obj
 
     # SVG
-    elif spath.endswith(".svg"):
+    elif fmt == 'svg':
         # Plotly
         if isinstance(obj, plotly.graph_objs.Figure):
             obj.write_image(file=spath, format="svg")
@@ -168,7 +183,7 @@ def save_image(
         del obj
 
     # PDF
-    elif spath.endswith(".pdf"):
+    elif fmt == 'pdf':
         # Plotly
         if isinstance(obj, plotly.graph_objs.Figure):
             obj.write_image(file=spath, format="pdf")
@@ -191,8 +206,8 @@ def save_image(
                 obj.figure.savefig(spath, **save_kwargs)
         del obj
 
-    # Embed metadata if provided
-    if metadata is not None:
+    # Embed metadata if provided (only for file paths, not file-like objects)
+    if metadata is not None and not is_file_like:
         from .._metadata import embed_metadata
 
         try:
@@ -200,8 +215,86 @@ def save_image(
             if verbose:
                 logger.debug(f"  • Embedded metadata: {metadata}")
         except Exception as e:
-            import warnings
+            logger.warning(f"Failed to embed metadata: {e}")
+
+def _save_stats_from_figure(obj, spath, verbose=False):
+    """
+    Extract and save statistical annotations from a figure.
+
+    Saves to {basename}_stats.csv if stats are found.
+    """
+    try:
+        from scitex.bridge import extract_stats_from_axes
+    except ImportError:
+        return  # Bridge not available
+
+    # Get the matplotlib figure
+    fig = None
+    if hasattr(obj, "savefig"):
+        fig = obj
+    elif hasattr(obj, "figure") and hasattr(obj.figure, "savefig"):
+        fig = obj.figure
+    elif hasattr(obj, "_fig_mpl"):
+        fig = obj._fig_mpl
+
+    if fig is None:
+        return
+
+    # Extract stats from all axes
+    all_stats = []
+    try:
+        for ax in fig.axes:
+            stats = extract_stats_from_axes(ax)
+            all_stats.extend(stats)
+    except Exception:
+        return  # Silently fail if extraction fails
+
+    if not all_stats:
+        return  # No stats to save
+
+    # Build stats dataframe
+    try:
+        import pandas as pd
+
+        stats_data = []
+        for stat in all_stats:
+            row = {
+                "test_type": stat.test_type,
+                "statistic_name": stat.statistic.get("name", ""),
+                "statistic_value": stat.statistic.get("value", ""),
+                "p_value": stat.p_value,
+                "stars": stat.stars,
+            }
+            # Add effect size if available
+            if stat.effect_size:
+                row["effect_size_name"] = stat.effect_size.get("name", "")
+                row["effect_size_value"] = stat.effect_size.get("value", "")
+            # Add CI if available
+            if stat.ci_95:
+                row["ci_95_lower"] = stat.ci_95[0]
+                row["ci_95_upper"] = stat.ci_95[1]
+            # Add sample/group info if available (for consistent naming with plot CSV)
+            if stat.samples:
+                for group_name, group_info in stat.samples.items():
+                    if isinstance(group_info, dict):
+                        row[f"n_{group_name}"] = group_info.get("n")
+                        row[f"mean_{group_name}"] = group_info.get("mean")
+                        row[f"std_{group_name}"] = group_info.get("std")
+            stats_data.append(row)
+
+        stats_df = pd.DataFrame(stats_data)
+
+        # Save to {basename}_stats.csv
+        import os
+        base, ext = os.path.splitext(spath)
+        stats_path = f"{base}_stats.csv"
+        stats_df.to_csv(stats_path, index=False)
+
+        if verbose:
+            logger.info(f"  • Auto-saved stats to: {stats_path}")
+
+    except Exception as e:
+        logger.warning(f"Failed to auto-save stats: {e}")
 
-            warnings.warn(f"Failed to embed metadata: {e}")
 
 # EOF

scitex/io/_save_modules/_joblib.py

@@ -9,14 +9,14 @@ import joblib
 def _save_joblib(obj, spath):
     """
     Save an object using joblib serialization.
-    
+
     Parameters
     ----------
     obj : Any
         Object to serialize.
     spath : str
         Path where the joblib file will be saved.
-        
+
     Returns
     -------
     None

scitex/io/_save_modules/_json.py

@@ -4,29 +4,69 @@
 # File: /data/gpfs/projects/punim2354/ywatanabe/scitex_repo/src/scitex/io/_save_modules/_json.py
 
 import json
+import re
 from typing import Any
 
 
+class PrecisionEncoder(json.JSONEncoder):
+    """
+    Custom JSON encoder that formats FixedFloat objects with fixed decimal places.
+
+    This encoder produces output like:
+        "position": [0.250, 0.294, 0.500, 0.412]
+
+    instead of:
+        "position": [0.25, 0.294, 0.5, 0.412]
+    """
+    def default(self, obj):
+        # Handle FixedFloat from _collect_figure_metadata
+        if hasattr(obj, 'value') and hasattr(obj, 'precision'):
+            # Return a special marker that we'll post-process
+            return f"__FIXED_{obj.precision}_{obj.value}__"
+        return super().default(obj)
+
+
+def _format_fixed_floats(json_str: str) -> str:
+    """
+    Post-process JSON string to format FixedFloat markers with proper precision.
+
+    Converts: "__FIXED_3_0.25__" -> 0.250
+    """
+    pattern = r'"__FIXED_(\d+)_([-\d.]+)__"'
+
+    def replacer(match):
+        precision = int(match.group(1))
+        value = float(match.group(2))
+        return f"{value:.{precision}f}"
+
+    return re.sub(pattern, replacer, json_str)
+
+
 def _convert_to_serializable(obj: Any) -> Any:
     """
     Convert non-JSON-serializable objects to serializable format.
 
     Handles:
+    - FixedFloat -> marker string for post-processing
     - DotDict -> dict
     - DataFrame -> dict of lists
     - numpy arrays -> lists
     - etc.
     """
+    # Handle FixedFloat (from _collect_figure_metadata)
+    if hasattr(obj, 'value') and hasattr(obj, 'precision') and hasattr(obj, '__class__') and obj.__class__.__name__ == 'FixedFloat':
+        return f"__FIXED_{obj.precision}_{obj.value}__"
+
     # Handle DotDict
-    if hasattr(obj, '__class__') and obj.__class__.__name__ == 'DotDict':
+    if hasattr(obj, "__class__") and obj.__class__.__name__ == "DotDict":
         return _convert_to_serializable(dict(obj))
 
     # Handle pandas DataFrame
-    if hasattr(obj, '__class__') and obj.__class__.__name__ == 'DataFrame':
-        return obj.to_dict('list')
+    if hasattr(obj, "__class__") and obj.__class__.__name__ == "DataFrame":
+        return obj.to_dict("list")
 
     # Handle numpy arrays
-    if hasattr(obj, 'tolist'):
+    if hasattr(obj, "tolist"):
         return obj.tolist()
 
     # Handle dict recursively
@@ -50,7 +90,8 @@ def _save_json(obj, spath):
     Save a Python object as a JSON file.
 
     Automatically converts DotDict objects and pandas DataFrames
-    to JSON-serializable formats.
+    to JSON-serializable formats. Supports FixedFloat objects for
+    consistent decimal place formatting.
 
     Parameters
     ----------
@@ -66,5 +107,9 @@ def _save_json(obj, spath):
     # Convert to serializable format
     serializable_obj = _convert_to_serializable(obj)
 
+    # Use custom encoder and post-process for fixed-precision floats
+    json_str = json.dumps(serializable_obj, indent=4, cls=PrecisionEncoder)
+    json_str = _format_fixed_floats(json_str)
+
     with open(spath, "w") as f:
-        json.dump(serializable_obj, f, indent=4)
+        f.write(json_str)

scitex/io/_save_modules/_listed_dfs_as_csv.py

@@ -4,6 +4,7 @@
 # File: /ssh:sp:/home/ywatanabe/proj/scitex_repo/src/scitex/io/_save_modules/_save_listed_dfs_as_csv.py
 # ----------------------------------------
 import os
+
 __FILE__ = __file__
 __DIR__ = os.path.dirname(__FILE__)
 # ----------------------------------------
@@ -16,7 +17,6 @@ import numpy as np
 from .._mv_to_tmp import _mv_to_tmp
 
 
-
 def _save_listed_dfs_as_csv(
     listed_dfs,
     spath_csv,
@@ -52,4 +52,5 @@ def _save_listed_dfs_as_csv(
     if verbose:
         print("Saved to: {}".format(spath_csv))
 
+
 # EOF

scitex/io/_save_modules/_listed_scalars_as_csv.py

@@ -4,6 +4,7 @@
 # File: /ssh:sp:/home/ywatanabe/proj/scitex_repo/src/scitex/io/_save_modules/_save_listed_scalars_as_csv.py
 # ----------------------------------------
 import os
+
 __FILE__ = __file__
 __DIR__ = os.path.dirname(__FILE__)
 # ----------------------------------------
@@ -14,7 +15,6 @@ import numpy as np
 from .._mv_to_tmp import _mv_to_tmp
 
 
-
 def _save_listed_scalars_as_csv(
     listed_scalars,
     spath_csv,
@@ -38,4 +38,5 @@ def _save_listed_scalars_as_csv(
     if verbose:
         print("\nSaved to: {}\n".format(spath_csv))
 
+
 # EOF

scitex/io/_save_modules/_matlab.py

@@ -9,14 +9,14 @@ import scipy.io
 def _save_matlab(obj, spath):
     """
     Save a Python dictionary to a MATLAB .mat file.
-    
+
     Parameters
     ----------
     obj : dict
         Dictionary of arrays to save in MATLAB format.
     spath : str
         Path where the MATLAB file will be saved.
-        
+
     Returns
     -------
     None

scitex/io/_save_modules/_numpy.py

@@ -9,14 +9,14 @@ import numpy as np
 def _save_npy(obj, spath):
     """
     Save a numpy array to .npy format.
-    
+
     Parameters
     ----------
     obj : numpy.ndarray
         The numpy array to save.
     spath : str
         Path where the .npy file will be saved.
-        
+
     Returns
     -------
     None
@@ -27,18 +27,18 @@ def _save_npy(obj, spath):
 def _save_npz(obj, spath):
     """
     Save numpy arrays to .npz format.
-    
+
     Parameters
     ----------
     obj : dict or list/tuple of numpy.ndarray
         Either a dictionary of arrays or a list/tuple of arrays.
     spath : str
         Path where the .npz file will be saved.
-        
+
     Returns
     -------
     None
-    
+
     Raises
     ------
     ValueError
@@ -46,9 +46,7 @@ def _save_npz(obj, spath):
     """
     if isinstance(obj, dict):
         np.savez_compressed(spath, **obj)
-    elif isinstance(obj, (list, tuple)) and all(
-        isinstance(x, np.ndarray) for x in obj
-    ):
+    elif isinstance(obj, (list, tuple)) and all(isinstance(x, np.ndarray) for x in obj):
         obj = {str(ii): obj[ii] for ii in range(len(obj))}
         np.savez_compressed(spath, **obj)
     else:

scitex/io/_save_modules/_pickle.py

@@ -10,14 +10,14 @@ import gzip
 def _save_pickle(obj, spath):
     """
     Save an object using Python's pickle serialization.
-    
+
     Parameters
     ----------
     obj : Any
         Object to serialize.
     spath : str
         Path where the pickle file will be saved.
-        
+
     Returns
     -------
     None
@@ -29,14 +29,14 @@ def _save_pickle(obj, spath):
 def _save_pickle_gz(obj, spath):
     """
     Save an object using Python's pickle serialization with gzip compression.
-    
+
     Parameters
     ----------
     obj : Any
         Object to serialize.
     spath : str
         Path where the compressed pickle file will be saved.
-        
+
     Returns
     -------
     None

scitex/io/_save_modules/_plotly.py

@@ -9,14 +9,14 @@ import plotly
 def _save_plotly_html(obj, spath):
     """
     Save a Plotly figure as an HTML file.
-    
+
     Parameters
     ----------
     obj : plotly.graph_objs.Figure
         The Plotly figure to save.
     spath : str
         Path where the HTML file will be saved.
-        
+
     Returns
     -------
     None
@@ -24,4 +24,4 @@ def _save_plotly_html(obj, spath):
     if isinstance(obj, plotly.graph_objs.Figure):
         obj.write_html(file=spath)
     else:
-        raise TypeError("Object must be a plotly.graph_objs.Figure")
+        raise TypeError("Object must be a plotly.graph_objs.Figure")

scitex/io/_save_modules/_tex.py

@@ -4,6 +4,7 @@
 # File: /home/ywatanabe/proj/scitex_repo/src/scitex/io/_save_modules/_tex.py
 # ----------------------------------------
 import os
+
 __FILE__ = __file__
 __DIR__ = os.path.dirname(__FILE__)
 # ----------------------------------------
@@ -19,7 +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(
@@ -30,7 +34,7 @@ def save_tex(
     document: bool = False,
     longtable: bool = False,
     escape: bool = True,
-    **kwargs
+    **kwargs,
 ) -> None:
     """
     Save object as LaTeX/TeX format.
@@ -105,38 +109,37 @@ def save_tex(
             label=label,
             longtable=longtable,
             escape=escape,
-            **kwargs
+            **kwargs,
         )
 
     elif isinstance(obj, (dict, list)):
         # Try to convert using stats module's convert_results
         try:
             from scitex.stats.utils._normalizers import convert_results
-            tex_content = convert_results(obj, return_as='latex', **kwargs)
+
+            tex_content = convert_results(obj, return_as="latex", **kwargs)
 
             # Add caption and label if provided
             if caption or label:
                 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(
-                f"Failed to convert object to LaTeX: {e}. "
-                f"Converting to string instead."
+            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(
-            f"Unsupported type {type(obj)} for LaTeX export. "
-            f"Converting to string."
+        logger.warning(
+            f"Unsupported type {type(obj)} for LaTeX export. Converting to string."
         )
         tex_content = str(obj)
 
@@ -145,17 +148,17 @@ def save_tex(
         tex_content = _wrap_in_document(tex_content)
 
     # Write to file
-    with open(spath, 'w') as f:
+    with open(spath, "w") as f:
         f.write(tex_content)
 
 
 def _dataframe_to_latex(
-    df: 'pd.DataFrame',
+    df: "pd.DataFrame",
     caption: Optional[str] = None,
     label: Optional[str] = None,
     longtable: bool = False,
     escape: bool = True,
-    **kwargs
+    **kwargs,
 ) -> str:
     """
     Convert pandas DataFrame to LaTeX table.
@@ -184,18 +187,18 @@ def _dataframe_to_latex(
 
     # Build to_latex arguments
     latex_kwargs = {
-        'index': False,
-        'escape': escape,
+        "index": False,
+        "escape": escape,
     }
 
     if longtable:
-        latex_kwargs['longtable'] = True
+        latex_kwargs["longtable"] = True
 
     if caption:
-        latex_kwargs['caption'] = caption
+        latex_kwargs["caption"] = caption
 
     if label:
-        latex_kwargs['label'] = label
+        latex_kwargs["label"] = label
 
     # Merge with user kwargs
     latex_kwargs.update(kwargs)
@@ -205,9 +208,7 @@ def _dataframe_to_latex(
 
 
 def _wrap_with_table_env(
-    content: str,
-    caption: Optional[str] = None,
-    label: Optional[str] = None
+    content: str, caption: Optional[str] = None, label: Optional[str] = None
 ) -> str:
     """
     Wrap LaTeX content in table environment with caption and label.
@@ -226,18 +227,18 @@ def _wrap_with_table_env(
     str
         Wrapped LaTeX content
     """
-    lines = ['\\begin{table}[htbp]', '\\centering']
+    lines = ["\\begin{table}[htbp]", "\\centering"]
 
     if caption:
-        lines.append(f'\\caption{{{caption}}}')
+        lines.append(f"\\caption{{{caption}}}")
 
     if label:
-        lines.append(f'\\label{{{label}}}')
+        lines.append(f"\\label{{{label}}}")
 
     lines.append(content)
-    lines.append('\\end{table}')
+    lines.append("\\end{table}")
 
-    return '\n'.join(lines)
+    return "\n".join(lines)
 
 
 def _wrap_in_document(content: str) -> str:
@@ -254,7 +255,7 @@ def _wrap_in_document(content: str) -> str:
     str
         Complete LaTeX document
     """
-    document_template = r'''\documentclass{article}
+    document_template = r"""\documentclass{article}
 \usepackage{booktabs}
 \usepackage{longtable}
 \usepackage{array}
@@ -267,7 +268,7 @@ def _wrap_in_document(content: str) -> str:
 %s
 
 \end{document}
-'''
+"""
     return document_template % content
 
 

scitex/io/_save_modules/_text.py

@@ -7,14 +7,14 @@
 def _save_text(obj, spath):
     """
     Save text content to a file.
-    
+
     Parameters
     ----------
     obj : str
         The text content to save.
     spath : str
         Path where the text file will be saved.
-        
+
     Returns
     -------
     None