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

scitex/plt/ax/_style/_set_log_scale.py

@@ -22,7 +22,7 @@ from typing import Union, Optional, List
 
 def set_log_scale(
     ax,
-    axis: str = 'both',
+    axis: str = "both",
     base: Union[int, float] = 10,
     show_minor_ticks: bool = True,
     minor_tick_length: float = 2.0,
@@ -34,11 +34,11 @@ def set_log_scale(
     grid_alpha: float = 0.3,
     minor_grid_alpha: float = 0.15,
     format_minor_labels: bool = False,
-    scientific_notation: bool = True
+    scientific_notation: bool = True,
 ) -> object:
     """
     Set logarithmic scale with comprehensive minor tick support.
-    
+
     Parameters
     ----------
     ax : matplotlib.axes.Axes
@@ -69,112 +69,143 @@ def set_log_scale(
         Whether to show labels on minor ticks, by default False
     scientific_notation : bool, optional
         Whether to use scientific notation for labels, by default True
-        
+
     Returns
     -------
     matplotlib.axes.Axes
         The modified axes object
-        
+
     Examples
     --------
     >>> fig, ax = plt.subplots()
     >>> ax.semilogy([1, 10, 100, 1000], [1, 2, 3, 4])
     >>> set_log_scale(ax, axis='y', show_minor_ticks=True, grid=True)
     """
-    
-    if axis in ['x', 'both']:
-        _configure_log_axis(ax, 'x', base, show_minor_ticks, 
-                           minor_tick_length, major_tick_length,
-                           minor_tick_width, major_tick_width,
-                           grid, minor_grid, grid_alpha, minor_grid_alpha,
-                           format_minor_labels, scientific_notation)
-    
-    if axis in ['y', 'both']:
-        _configure_log_axis(ax, 'y', base, show_minor_ticks,
-                           minor_tick_length, major_tick_length, 
-                           minor_tick_width, major_tick_width,
-                           grid, minor_grid, grid_alpha, minor_grid_alpha,
-                           format_minor_labels, scientific_notation)
-    
+
+    if axis in ["x", "both"]:
+        _configure_log_axis(
+            ax,
+            "x",
+            base,
+            show_minor_ticks,
+            minor_tick_length,
+            major_tick_length,
+            minor_tick_width,
+            major_tick_width,
+            grid,
+            minor_grid,
+            grid_alpha,
+            minor_grid_alpha,
+            format_minor_labels,
+            scientific_notation,
+        )
+
+    if axis in ["y", "both"]:
+        _configure_log_axis(
+            ax,
+            "y",
+            base,
+            show_minor_ticks,
+            minor_tick_length,
+            major_tick_length,
+            minor_tick_width,
+            major_tick_width,
+            grid,
+            minor_grid,
+            grid_alpha,
+            minor_grid_alpha,
+            format_minor_labels,
+            scientific_notation,
+        )
+
     return ax
 
 
 def _configure_log_axis(
-    ax, axis_name: str, base: Union[int, float], show_minor_ticks: bool,
-    minor_tick_length: float, major_tick_length: float,
-    minor_tick_width: float, major_tick_width: float,
-    grid: bool, minor_grid: bool, grid_alpha: float, minor_grid_alpha: float,
-    format_minor_labels: bool, scientific_notation: bool
+    ax,
+    axis_name: str,
+    base: Union[int, float],
+    show_minor_ticks: bool,
+    minor_tick_length: float,
+    major_tick_length: float,
+    minor_tick_width: float,
+    major_tick_width: float,
+    grid: bool,
+    minor_grid: bool,
+    grid_alpha: float,
+    minor_grid_alpha: float,
+    format_minor_labels: bool,
+    scientific_notation: bool,
 ) -> None:
     """Configure a single axis for logarithmic scale."""
-    
+
     # Set the logarithmic scale
-    if axis_name == 'x':
-        ax.set_xscale('log', base=base)
+    if axis_name == "x":
+        ax.set_xscale("log", base=base)
         axis_obj = ax.xaxis
-        tick_params_kwargs = {'axis': 'x'}
+        tick_params_kwargs = {"axis": "x"}
     else:  # y-axis
-        ax.set_yscale('log', base=base)
+        ax.set_yscale("log", base=base)
         axis_obj = ax.yaxis
-        tick_params_kwargs = {'axis': 'y'}
-    
+        tick_params_kwargs = {"axis": "y"}
+
     # Configure major ticks
     major_locator = LogLocator(base=base, numticks=12)
     axis_obj.set_major_locator(major_locator)
-    
+
     # Configure major tick formatting
     if scientific_notation:
         major_formatter = LogFormatter(base=base, labelOnlyBase=False)
     else:
         major_formatter = LogFormatter(base=base, labelOnlyBase=True)
     axis_obj.set_major_formatter(major_formatter)
-    
+
     # Configure minor ticks
     if show_minor_ticks:
         # Create minor tick positions
-        minor_locator = LogLocator(base=base, subs='all', numticks=100)
+        minor_locator = LogLocator(base=base, subs="all", numticks=100)
         axis_obj.set_minor_locator(minor_locator)
-        
+
         # Format minor tick labels
         if format_minor_labels:
             minor_formatter = LogFormatter(base=base, labelOnlyBase=False)
         else:
             minor_formatter = NullFormatter()  # No labels on minor ticks
         axis_obj.set_minor_formatter(minor_formatter)
-        
+
         # Set minor tick appearance
         ax.tick_params(
-            which='minor',
+            which="minor",
             length=minor_tick_length,
             width=minor_tick_width,
-            **tick_params_kwargs
+            **tick_params_kwargs,
         )
-    
+
     # Set major tick appearance
     ax.tick_params(
-        which='major',
+        which="major",
         length=major_tick_length,
         width=major_tick_width,
-        **tick_params_kwargs
+        **tick_params_kwargs,
     )
-    
+
     # Configure grid
     if grid or minor_grid:
-        ax.grid(True, which='major', alpha=grid_alpha if grid else 0)
+        ax.grid(True, which="major", alpha=grid_alpha if grid else 0)
         if minor_grid and show_minor_ticks:
-            ax.grid(True, which='minor', alpha=minor_grid_alpha)
+            ax.grid(True, which="minor", alpha=minor_grid_alpha)
 
 
 def smart_log_limits(
     data: Union[List, np.ndarray],
-    axis: str = 'y',
+    axis: str = "y",
     base: Union[int, float] = 10,
     padding_factor: float = 0.1,
-    min_decades: int = 1
+    min_decades: int = 1,
 ) -> tuple:
     """
     Calculate smart logarithmic axis limits based on data.
-    
+
     Parameters
     ----------
     data : Union[List, np.ndarray]
@@ -187,12 +218,12 @@ def smart_log_limits(
         Padding as fraction of data range, by default 0.1
     min_decades : int, optional
         Minimum number of decades to show, by default 1
-        
+
     Returns
     -------
     tuple
         (lower_limit, upper_limit)
-        
+
     Examples
     --------
     >>> smart_log_limits([1, 10, 100, 1000])
@@ -200,49 +231,49 @@ def smart_log_limits(
     """
     data_array = np.array(data)
     positive_data = data_array[data_array > 0]
-    
+
     if len(positive_data) == 0:
         return 1, base**min_decades
-    
+
     data_min = np.min(positive_data)
     data_max = np.max(positive_data)
-    
+
     # Calculate log range
     log_min = np.log(data_min) / np.log(base)
     log_max = np.log(data_max) / np.log(base)
     log_range = log_max - log_min
-    
+
     # Ensure minimum range
     if log_range < min_decades:
         log_center = (log_min + log_max) / 2
         log_min = log_center - min_decades / 2
         log_max = log_center + min_decades / 2
         log_range = min_decades
-    
+
     # Add padding
     padding = log_range * padding_factor
     log_min_padded = log_min - padding
     log_max_padded = log_max + padding
-    
+
     # Convert back to linear scale
-    lower_limit = base ** log_min_padded
-    upper_limit = base ** log_max_padded
-    
+    lower_limit = base**log_min_padded
+    upper_limit = base**log_max_padded
+
     return lower_limit, upper_limit
 
 
 def add_log_scale_indicator(
     ax,
-    axis: str = 'y',
+    axis: str = "y",
     base: Union[int, float] = 10,
-    position: str = 'auto',
-    fontsize: Union[str, int] = 'small',
-    color: str = 'gray',
-    alpha: float = 0.7
+    position: str = "auto",
+    fontsize: Union[str, int] = "small",
+    color: str = "gray",
+    alpha: float = 0.7,
 ) -> None:
     """
     Add a log scale indicator to the plot.
-    
+
     Parameters
     ----------
     ax : matplotlib.axes.Axes
@@ -259,41 +290,45 @@ def add_log_scale_indicator(
         Color of indicator text, by default 'gray'
     alpha : float, optional
         Alpha transparency, by default 0.7
-        
+
     Examples
     --------
     >>> add_log_scale_indicator(ax, axis='y', base=10)
     """
     # Determine position
-    if position == 'auto':
-        if axis == 'y':
-            position = 'top-left'
+    if position == "auto":
+        if axis == "y":
+            position = "top-left"
         else:
-            position = 'bottom-right'
-    
+            position = "bottom-right"
+
     # Position mapping
     positions = {
-        'top-left': (0.05, 0.95),
-        'top-right': (0.95, 0.95),
-        'bottom-left': (0.05, 0.05),
-        'bottom-right': (0.95, 0.05)
+        "top-left": (0.05, 0.95),
+        "top-right": (0.95, 0.95),
+        "bottom-left": (0.05, 0.05),
+        "bottom-right": (0.95, 0.05),
     }
-    
+
     x_pos, y_pos = positions.get(position, (0.05, 0.95))
-    
+
     # Create indicator text
     if base == 10:
         indicator_text = f"Log₁₀ scale ({axis}-axis)"
     else:
         indicator_text = f"Log_{{{base}}} scale ({axis}-axis)"
-    
+
     # Add text
-    ax.text(x_pos, y_pos, indicator_text,
-           transform=ax.transAxes,
-           fontsize=fontsize,
-           color=color,
-           alpha=alpha,
-           bbox=dict(boxstyle="round,pad=0.3", facecolor='white', alpha=0.8))
+    ax.text(
+        x_pos,
+        y_pos,
+        indicator_text,
+        transform=ax.transAxes,
+        fontsize=fontsize,
+        color=color,
+        alpha=alpha,
+        bbox=dict(boxstyle="round,pad=0.3", facecolor="white", alpha=0.8),
+    )
 
 
-# EOF
+# EOF

scitex/plt/ax/_style/_set_meta.py

@@ -13,11 +13,19 @@ from typing import Optional, List, Dict, Any
 
 
 # Functions
-def set_meta(ax, caption=None, methods=None, stats=None, keywords=None, 
-             experimental_details=None, journal_style=None, 
-             significance=None, **kwargs):
+def set_meta(
+    ax,
+    caption=None,
+    methods=None,
+    stats=None,
+    keywords=None,
+    experimental_details=None,
+    journal_style=None,
+    significance=None,
+    **kwargs,
+):
     """Set comprehensive scientific metadata for figures with YAML export
-    
+
     Parameters
     ----------
     ax : matplotlib.axes.Axes or scitex AxisWrapper
@@ -38,12 +46,12 @@ def set_meta(ax, caption=None, methods=None, stats=None, keywords=None,
         Significance statement or implications
     **kwargs : additional metadata
         Any additional metadata fields
-        
+
     Returns
     -------
     ax : matplotlib.axes.Axes or scitex AxisWrapper
         The modified axes
-        
+
     Examples
     --------
     >>> fig, ax = scitex.plt.subplots()
@@ -65,67 +73,78 @@ def set_meta(ax, caption=None, methods=None, stats=None, keywords=None,
     ... )
     >>> scitex.io.save(fig, 'neural_recording.png')  # YAML metadata auto-saved
     """
-    
+
     # Build comprehensive metadata dictionary
     metadata = {}
-    
+
     if caption is not None:
-        metadata['caption'] = caption
+        metadata["caption"] = caption
     if methods is not None:
-        metadata['methods'] = methods
+        metadata["methods"] = methods
     if stats is not None:
-        metadata['statistical_analysis'] = stats
+        metadata["statistical_analysis"] = stats
     if keywords is not None:
-        metadata['keywords'] = keywords if isinstance(keywords, list) else [keywords]
+        metadata["keywords"] = keywords if isinstance(keywords, list) else [keywords]
     if experimental_details is not None:
-        metadata['experimental_details'] = experimental_details
+        metadata["experimental_details"] = experimental_details
     if journal_style is not None:
-        metadata['journal_style'] = journal_style
+        metadata["journal_style"] = journal_style
     if significance is not None:
-        metadata['significance'] = significance
-    
+        metadata["significance"] = significance
+
     # Add any additional metadata
     for key, value in kwargs.items():
         if value is not None:
             metadata[key] = value
-    
+
     # Add automatic metadata
     import datetime
-    metadata['created_timestamp'] = datetime.datetime.now().isoformat()
-    
+
+    metadata["created_timestamp"] = datetime.datetime.now().isoformat()
+
     # Get version dynamically
     try:
         import scitex
-        metadata['scitex_version'] = getattr(scitex, '__version__', 'unknown')
+
+        metadata["scitex_version"] = getattr(scitex, "__version__", "unknown")
     except ImportError:
-        metadata['scitex_version'] = 'unknown'
-    
+        metadata["scitex_version"] = "unknown"
+
     # Store metadata in figure for automatic saving
     fig = ax.get_figure()
-    if not hasattr(fig, '_scitex_metadata'):
+    if not hasattr(fig, "_scitex_metadata"):
         fig._scitex_metadata = {}
-    
+
     # Use axis as key for panel-specific metadata
     fig._scitex_metadata[ax] = metadata
-    
+
     # Also store as YAML-ready structure
-    if not hasattr(fig, '_scitex_yaml_metadata'):
+    if not hasattr(fig, "_scitex_yaml_metadata"):
         fig._scitex_yaml_metadata = {}
     fig._scitex_yaml_metadata[ax] = metadata
-    
+
     # Backward compatibility - store simple caption
     if caption is not None:
-        if not hasattr(fig, '_scitex_captions'):
+        if not hasattr(fig, "_scitex_captions"):
             fig._scitex_captions = {}
         fig._scitex_captions[ax] = caption
-    
+
     return ax
 
 
-def set_figure_meta(ax, caption=None, methods=None, stats=None, significance=None,
-                   funding=None, conflicts=None, data_availability=None, **kwargs):
+def set_figure_meta(
+    ax,
+    caption=None,
+    methods=None,
+    stats=None,
+    significance=None,
+    funding=None,
+    conflicts=None,
+    data_availability=None,
+    **kwargs,
+):
     """Set figure-level metadata for multi-panel figures
-    
+
     Parameters
     ----------
     ax : matplotlib.axes.Axes or scitex AxisWrapper
@@ -146,19 +165,19 @@ def set_figure_meta(ax, caption=None, methods=None, stats=None, significance=Non
         Data availability statement
     **kwargs : additional metadata
         Any additional figure-level metadata
-        
+
     Returns
     -------
     ax : matplotlib.axes.Axes or scitex AxisWrapper
         The modified axes
-        
+
     Examples
     --------
     >>> fig, ((ax1, ax2), (ax3, ax4)) = scitex.plt.subplots(2, 2)
     >>> # Set individual panel metadata...
     >>> ax1.set_meta(caption='Panel A analysis...')
     >>> ax2.set_meta(caption='Panel B comparison...')
-    >>> 
+    >>>
     >>> # Set figure-level metadata
     >>> ax1.set_figure_meta(
     ...     caption='Comprehensive analysis of neural dynamics...',
@@ -167,48 +186,49 @@ def set_figure_meta(ax, caption=None, methods=None, stats=None, significance=Non
     ...     data_availability='Data available at doi:10.5061/dryad.example'
     ... )
     """
-    
+
     # Build figure-level metadata
     figure_metadata = {}
-    
+
     if caption is not None:
-        figure_metadata['main_caption'] = caption
+        figure_metadata["main_caption"] = caption
     if methods is not None:
-        figure_metadata['overall_methods'] = methods
+        figure_metadata["overall_methods"] = methods
     if stats is not None:
-        figure_metadata['overall_statistics'] = stats
+        figure_metadata["overall_statistics"] = stats
     if significance is not None:
-        figure_metadata['significance'] = significance
+        figure_metadata["significance"] = significance
     if funding is not None:
-        figure_metadata['funding'] = funding
+        figure_metadata["funding"] = funding
     if conflicts is not None:
-        figure_metadata['conflicts_of_interest'] = conflicts
+        figure_metadata["conflicts_of_interest"] = conflicts
     if data_availability is not None:
-        figure_metadata['data_availability'] = data_availability
-    
+        figure_metadata["data_availability"] = data_availability
+
     # Add any additional metadata
     for key, value in kwargs.items():
         if value is not None:
             figure_metadata[key] = value
-    
+
     # Add automatic metadata
     import datetime
-    figure_metadata['created_timestamp'] = datetime.datetime.now().isoformat()
-    
+
+    figure_metadata["created_timestamp"] = datetime.datetime.now().isoformat()
+
     # Store in figure
     fig = ax.get_figure()
     fig._scitex_figure_metadata = figure_metadata
-    
+
     # Backward compatibility
     if caption is not None:
         fig._scitex_main_caption = caption
-    
+
     return ax
 
 
 def export_metadata_yaml(fig, filepath):
     """Export all figure metadata to YAML file
-    
+
     Parameters
     ----------
     fig : matplotlib.figure.Figure
@@ -217,29 +237,29 @@ def export_metadata_yaml(fig, filepath):
         Output YAML file path
     """
     import datetime
-    
+
     # Collect all metadata
     export_data = {
-        'figure_metadata': {},
-        'panel_metadata': {},
-        'export_info': {
-            'timestamp': datetime.datetime.now().isoformat(),
-            'scitex_version': '1.11.0'
-        }
+        "figure_metadata": {},
+        "panel_metadata": {},
+        "export_info": {
+            "timestamp": datetime.datetime.now().isoformat(),
+            "scitex_version": "1.11.0",
+        },
     }
-    
+
     # Figure-level metadata
-    if hasattr(fig, '_scitex_figure_metadata'):
-        export_data['figure_metadata'] = fig._scitex_figure_metadata
-    
+    if hasattr(fig, "_scitex_figure_metadata"):
+        export_data["figure_metadata"] = fig._scitex_figure_metadata
+
     # Panel-level metadata
-    if hasattr(fig, '_scitex_yaml_metadata'):
+    if hasattr(fig, "_scitex_yaml_metadata"):
         for i, (ax, metadata) in enumerate(fig._scitex_yaml_metadata.items()):
-            panel_key = f'panel_{i+1}'
-            export_data['panel_metadata'][panel_key] = metadata
-    
+            panel_key = f"panel_{i + 1}"
+            export_data["panel_metadata"][panel_key] = metadata
+
     # Write YAML file
-    with open(filepath, 'w') as f:
+    with open(filepath, "w") as f:
         yaml.dump(export_data, f, default_flow_style=False, sort_keys=False, indent=2)
 
 
@@ -248,21 +268,24 @@ if __name__ == "__main__":
     import sys
     import matplotlib.pyplot as plt
     import scitex
+
     CONFIG, sys.stdout, sys.stderr, plt, CC = scitex.session.start(sys, plt)
 
     # Example usage
     fig, ax = plt.subplots()
     ax.plot([1, 2, 3], [1, 4, 2])
-    
-    set_meta(ax, 
-             caption='Example figure showing data trends.',
-             methods='Synthetic data generated for demonstration.',
-             keywords=['example', 'demo', 'synthetic'],
-             experimental_details={'n_samples': 3, 'data_type': 'synthetic'})
-    
-    export_metadata_yaml(fig, 'example_metadata.yaml')
+
+    set_meta(
+        ax,
+        caption="Example figure showing data trends.",
+        methods="Synthetic data generated for demonstration.",
+        keywords=["example", "demo", "synthetic"],
+        experimental_details={"n_samples": 3, "data_type": "synthetic"},
+    )
+
+    export_metadata_yaml(fig, "example_metadata.yaml")
 
     # Close
     scitex.session.close(CONFIG)
 
-# EOF
+# EOF