scitex 2.5.0__py3-none-any.whl → 2.7.0__py3-none-any.whl

scitex/plt/_subplots/_export_as_csv_formatters/_format_violinplot.py

@@ -1,75 +1,82 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
-# Timestamp: "2025-05-18 18:14:26 (ywatanabe)"
-# File: /data/gpfs/projects/punim2354/ywatanabe/scitex_repo/src/scitex/plt/_subplots/_export_as_csv_formatters/_format_violinplot.py
-# ----------------------------------------
-import os
-__FILE__ = __file__
-__DIR__ = os.path.dirname(__FILE__)
-# ----------------------------------------
+# Timestamp: "2025-12-09 12:00:00 (ywatanabe)"
+# File: /home/ywatanabe/proj/scitex-code/src/scitex/plt/_subplots/_export_as_csv_formatters/_format_violinplot.py
 
 import numpy as np
 import pandas as pd
 
+from scitex.plt.utils._csv_column_naming import get_csv_column_name
+from ._format_plot import _parse_tracking_id
+
+
 def _format_violinplot(id, tracked_dict, kwargs):
     """Format data from a violinplot call.
-    
+
     Formats data in a long-format for better compatibility.
-    
+
     Args:
         id (str): Identifier for the plot
         tracked_dict (dict): Dictionary containing tracked data
         kwargs (dict): Keyword arguments passed to violinplot
-        
+
     Returns:
         pd.DataFrame: Formatted violinplot data in long format
     """
-    # Check if tracked_dict is empty or not a dictionary
     if not tracked_dict or not isinstance(tracked_dict, dict):
         return pd.DataFrame()
-    
-    # Get the args from tracked_dict
-    args = tracked_dict.get('args', [])
-    
-    # Similar to violin plot
+
+    # Parse tracking ID to get axes position and trace ID
+    ax_row, ax_col, trace_id = _parse_tracking_id(id)
+
+    args = tracked_dict.get("args", [])
+
     if len(args) >= 1:
         data = args[0]
-        
+
         # Handle case when data is a simple array or list
-        if isinstance(data, (list, np.ndarray)) and not isinstance(data[0], (list, np.ndarray, dict)):
-            # Convert to long format with group and value columns
-            rows = [{'group': '0', 'value': val} for val in data]
+        if isinstance(data, (list, np.ndarray)) and not isinstance(
+            data[0], (list, np.ndarray, dict)
+        ):
+            rows = [{"group": "0", "value": val} for val in data]
             df = pd.DataFrame(rows)
-            # Prefix columns with id
-            df.columns = [f"{id}_violinplot_{col}" for col in df.columns]
+            # Use structured column naming
+            col_group = get_csv_column_name("group", ax_row, ax_col, trace_id=trace_id)
+            col_value = get_csv_column_name("value", ax_row, ax_col, trace_id=trace_id)
+            df.columns = [col_group, col_value]
             return df
-            
+
         # Handle case when data is a dictionary
         elif isinstance(data, dict):
-            # Convert to long format with group and value columns
             rows = []
             for group, values in data.items():
                 for val in values:
-                    rows.append({'group': str(group), 'value': val})
-            
+                    rows.append({"group": str(group), "value": val})
+
             if rows:
                 df = pd.DataFrame(rows)
-                # Prefix columns with id
-                df.columns = [f"{id}_violinplot_{col}" for col in df.columns]
+                col_group = get_csv_column_name("group", ax_row, ax_col, trace_id=trace_id)
+                col_value = get_csv_column_name("value", ax_row, ax_col, trace_id=trace_id)
+                df.columns = [col_group, col_value]
                 return df
-            
+
         # Handle case when data is a list of arrays
-        elif isinstance(data, (list, tuple)) and all(isinstance(x, (list, np.ndarray)) for x in data):
+        elif isinstance(data, (list, tuple)) and all(
+            isinstance(x, (list, np.ndarray)) for x in data
+        ):
             rows = []
             for i, values in enumerate(data):
                 for val in values:
-                    rows.append({'group': str(i), 'value': val})
-            
+                    rows.append({"group": str(i), "value": val})
+
             if rows:
                 df = pd.DataFrame(rows)
-                # Prefix columns with id
-                df.columns = [f"{id}_violinplot_{col}" for col in df.columns]
+                col_group = get_csv_column_name("group", ax_row, ax_col, trace_id=trace_id)
+                col_value = get_csv_column_name("value", ax_row, ax_col, trace_id=trace_id)
+                df.columns = [col_group, col_value]
                 return df
-    
-    # If we get here, either no data or unsupported format
-    return pd.DataFrame()
+
+    return pd.DataFrame()
+
+
+# EOF

scitex/plt/_subplots/_export_as_csv_formatters/verify_formatters.py

@@ -8,19 +8,21 @@ import sys
 import numpy as np
 import pandas as pd
 import matplotlib
-matplotlib.use('Agg')  # Non-interactive backend
+
+matplotlib.use("Agg")  # Non-interactive backend
 
 # Add src to path if needed
-src_path = os.path.abspath(os.path.join(os.path.dirname(__file__), '../../../../../'))
+src_path = os.path.abspath(os.path.join(os.path.dirname(__file__), "../../../../../"))
 if src_path not in sys.path:
     sys.path.insert(0, src_path)
 
 import scitex
 
 # Create output directory
-OUTPUT_DIR = os.path.join(os.path.dirname(__file__), 'formatter_test_output')
+OUTPUT_DIR = os.path.join(os.path.dirname(__file__), "formatter_test_output")
 os.makedirs(OUTPUT_DIR, exist_ok=True)
 
+
 def test_all_formatters():
     """
     Test all formatters by creating actual plots and saving both image and CSV files.
@@ -36,153 +38,162 @@ def test_all_formatters():
     test_plot_ecdf()
     test_multiple_plots()
 
+
 def test_plot_kde():
     """Test KDE plotting and CSV export."""
     print("Testing stx_kde...")
-    
+
     # Create figure
     fig, ax = scitex.plt.subplots()
-    
+
     # Generate data
     np.random.seed(42)  # For reproducibility
     data = np.concatenate([np.random.normal(0, 1, 500), np.random.normal(5, 1, 300)])
-    
+
     # Plot with ID for tracking
     ax.stx_kde(data, label="Bimodal Distribution", id="kde_test")
-    
+
     # Style the plot
     ax.set_xyt("Value", "Density", "KDE Test")
     ax.legend()
-    
+
     # Save both image and data
     save_path = os.path.join(OUTPUT_DIR, "kde_test.png")
     scitex.io.save(fig, save_path)
-    
+
     # Verify CSV was created
     csv_path = save_path.replace(".png", ".csv")
     assert os.path.exists(csv_path), f"CSV file not created: {csv_path}"
-    
+
     # Read CSV and verify contents
     df = pd.read_csv(csv_path)
     assert "kde_test_kde_x" in df.columns, "Expected column 'kde_test_kde_x' not found"
-    assert "kde_test_kde_density" in df.columns, "Expected column 'kde_test_kde_density' not found"
-    
+    assert "kde_test_kde_density" in df.columns, (
+        "Expected column 'kde_test_kde_density' not found"
+    )
+
     # Close figure
     scitex.plt.close(fig)
     print("✓ stx_kde test successful")
 
+
 def test_plot_image():
     """Test image plotting and CSV export."""
     print("Testing stx_image...")
-    
+
     # Create figure
     fig, ax = scitex.plt.subplots()
-    
+
     # Generate data
     np.random.seed(42)  # For reproducibility
     data = np.random.rand(20, 20)
-    
+
     # Plot with ID for tracking
     ax.stx_image(data, cmap="viridis", id="image_test")
-    
+
     # Style the plot
     ax.set_xyt("X", "Y", "Image Test")
-    
+
     # Save both image and data
     save_path = os.path.join(OUTPUT_DIR, "image_test.png")
     scitex.io.save(fig, save_path)
-    
+
     # Verify CSV was created
     csv_path = save_path.replace(".png", ".csv")
     assert os.path.exists(csv_path), f"CSV file not created: {csv_path}"
-    
+
     # Read CSV and verify contents
     df = pd.read_csv(csv_path)
     # The formatter should have converted the 2D array to a DataFrame
     assert not df.empty, "CSV file is empty"
-    
+
     # Close figure
     scitex.plt.close(fig)
     print("✓ stx_image test successful")
 
+
 def test_plot_shaded_line():
     """Test shaded line plotting and CSV export."""
     print("Testing stx_shaded_line...")
-    
+
     # Create figure
     fig, ax = scitex.plt.subplots()
-    
+
     # Generate data
     np.random.seed(42)  # For reproducibility
     x = np.linspace(0, 10, 100)
     y_middle = np.sin(x)
     y_lower = y_middle - 0.2
     y_upper = y_middle + 0.2
-    
+
     # Plot with ID for tracking
-    ax.stx_shaded_line(x, y_lower, y_middle, y_upper, label="Sine with error", id="shaded_line_test")
-    
+    ax.stx_shaded_line(
+        x, y_lower, y_middle, y_upper, label="Sine with error", id="shaded_line_test"
+    )
+
     # Style the plot
     ax.set_xyt("X", "Y", "Shaded Line Test")
     ax.legend()
-    
+
     # Save both image and data
     save_path = os.path.join(OUTPUT_DIR, "shaded_line_test.png")
     scitex.io.save(fig, save_path)
-    
+
     # Verify CSV was created
     csv_path = save_path.replace(".png", ".csv")
     assert os.path.exists(csv_path), f"CSV file not created: {csv_path}"
-    
+
     # Read CSV and verify contents
     df = pd.read_csv(csv_path)
     assert not df.empty, "CSV file is empty"
-    
+
     # Close figure
     scitex.plt.close(fig)
     print("✓ stx_shaded_line test successful")
 
+
 def test_plot_scatter_hist():
     """Test scatter histogram plotting and CSV export."""
     print("Testing stx_scatter_hist...")
-    
+
     # Create figure
     fig, ax = scitex.plt.subplots(figsize=(8, 8))
-    
+
     # Generate data
     np.random.seed(42)  # For reproducibility
     x = np.random.normal(0, 1, 500)
     y = x + np.random.normal(0, 0.5, 500)
-    
+
     # Plot with ID for tracking
     ax.stx_scatter_hist(x, y, hist_bins=30, scatter_alpha=0.7, id="scatter_hist_test")
-    
+
     # Style the plot
     ax.set_xyt("X Values", "Y Values", "Scatter Histogram Test")
-    
+
     # Save both image and data
     save_path = os.path.join(OUTPUT_DIR, "scatter_hist_test.png")
     scitex.io.save(fig, save_path)
-    
+
     # Verify CSV was created
     csv_path = save_path.replace(".png", ".csv")
     assert os.path.exists(csv_path), f"CSV file not created: {csv_path}"
-    
+
     # Read CSV and verify contents
     df = pd.read_csv(csv_path)
     assert not df.empty, "CSV file is empty"
-    
+
     # Close figure
     scitex.plt.close(fig)
     print("✓ stx_scatter_hist test successful")
 
+
 def test_plot_violin():
     """Test violin plotting and CSV export."""
     print("Testing stx_violin...")
-    
+
     # Create figure
     fig, ax = scitex.plt.subplots()
-    
+
     # Generate data
     np.random.seed(42)  # For reproducibility
     data = [
@@ -191,42 +202,45 @@ def test_plot_violin():
         np.random.normal(5, 0.8, 100),
     ]
     labels = ["Group A", "Group B", "Group C"]
-    
+
     # Plot with ID for tracking
-    ax.stx_violin(data, labels=labels, colors=["red", "blue", "green"], id="violin_test")
-    
+    ax.stx_violin(
+        data, labels=labels, colors=["red", "blue", "green"], id="violin_test"
+    )
+
     # Style the plot
     ax.set_xyt("Groups", "Values", "Violin Plot Test")
-    
+
     # Save both image and data
     save_path = os.path.join(OUTPUT_DIR, "violin_test.png")
     scitex.io.save(fig, save_path)
-    
+
     # Verify CSV was created
     csv_path = save_path.replace(".png", ".csv")
     assert os.path.exists(csv_path), f"CSV file not created: {csv_path}"
-    
+
     # Read CSV and verify contents
     df = pd.read_csv(csv_path)
     assert not df.empty, "CSV file is empty"
-    
+
     # Close figure
     scitex.plt.close(fig)
     print("✓ stx_violin test successful")
 
+
 def test_plot_heatmap():
     """Test heatmap plotting and CSV export."""
     print("Testing stx_heatmap...")
-    
+
     # Create figure
     fig, ax = scitex.plt.subplots()
-    
+
     # Generate data
     np.random.seed(42)  # For reproducibility
     data = np.random.rand(5, 10)
-    x_labels = [f"X{ii+1}" for ii in range(5)]
-    y_labels = [f"Y{ii+1}" for ii in range(10)]
-    
+    x_labels = [f"X{ii + 1}" for ii in range(5)]
+    y_labels = [f"Y{ii + 1}" for ii in range(10)]
+
     # Plot with ID for tracking
     ax.stx_heatmap(
         data,
@@ -238,105 +252,108 @@ def test_plot_heatmap():
         cmap="viridis",
         id="heatmap_test",
     )
-    
+
     # Style the plot
     ax.set_title("Heatmap Test")
-    
+
     # Save both image and data
     save_path = os.path.join(OUTPUT_DIR, "heatmap_test.png")
     scitex.io.save(fig, save_path)
-    
+
     # Verify CSV was created
     csv_path = save_path.replace(".png", ".csv")
     assert os.path.exists(csv_path), f"CSV file not created: {csv_path}"
-    
+
     # Read CSV and verify contents
     df = pd.read_csv(csv_path)
     assert not df.empty, "CSV file is empty"
-    
+
     # Close figure
     scitex.plt.close(fig)
     print("✓ stx_heatmap test successful")
 
+
 def test_plot_ecdf():
     """Test ECDF plotting and CSV export."""
     print("Testing stx_ecdf...")
-    
+
     # Create figure
     fig, ax = scitex.plt.subplots()
-    
+
     # Generate data
     np.random.seed(42)  # For reproducibility
     data = np.random.normal(0, 1, 1000)
-    
+
     # Plot with ID for tracking
     ax.stx_ecdf(data, label="Normal Distribution", id="ecdf_test")
-    
+
     # Style the plot
     ax.set_xyt("Value", "Cumulative Probability", "ECDF Test")
     ax.legend()
-    
+
     # Save both image and data
     save_path = os.path.join(OUTPUT_DIR, "ecdf_test.png")
     scitex.io.save(fig, save_path)
-    
+
     # Verify CSV was created
     csv_path = save_path.replace(".png", ".csv")
     assert os.path.exists(csv_path), f"CSV file not created: {csv_path}"
-    
+
     # Read CSV and verify contents
     df = pd.read_csv(csv_path)
     assert not df.empty, "CSV file is empty"
-    
+
     # Close figure
     scitex.plt.close(fig)
     print("✓ stx_ecdf test successful")
 
+
 def test_multiple_plots():
     """Test multiple plots on the same axis."""
     print("Testing multiple plots on the same axis...")
-    
+
     # Create figure
     fig, ax = scitex.plt.subplots()
-    
+
     # Generate data
     np.random.seed(42)  # For reproducibility
     x = np.linspace(0, 10, 100)
     y1 = np.sin(x)
     y2 = np.cos(x)
-    
+
     # Create multiple plots with different IDs
     ax.stx_line(y1, label="Sine", id="multi_test_sine")
     ax.stx_line(y2, label="Cosine", id="multi_test_cosine")
-    
+
     # Style the plot
     ax.set_xyt("X", "Y", "Multiple Plots Test")
     ax.legend()
-    
+
     # Save both image and data
     save_path = os.path.join(OUTPUT_DIR, "multiple_plots_test.png")
     scitex.io.save(fig, save_path)
-    
+
     # Verify CSV was created
     csv_path = save_path.replace(".png", ".csv")
     assert os.path.exists(csv_path), f"CSV file not created: {csv_path}"
-    
+
     # Read CSV and verify contents
     df = pd.read_csv(csv_path)
     assert not df.empty, "CSV file is empty"
-    
+
     # Check that both plots are in the CSV
     sine_cols = [col for col in df.columns if col.startswith("multi_test_sine")]
     cosine_cols = [col for col in df.columns if col.startswith("multi_test_cosine")]
     assert len(sine_cols) > 0, "Sine plot data not found in CSV"
     assert len(cosine_cols) > 0, "Cosine plot data not found in CSV"
-    
+
     # Close figure
     scitex.plt.close(fig)
     print("✓ Multiple plots test successful")
 
+
 if __name__ == "__main__":
     print("Starting formatter verification tests...")
     test_all_formatters()
     print("\nAll formatter tests completed successfully!")
-    print(f"Output files are in: {OUTPUT_DIR}")
+    print(f"Output files are in: {OUTPUT_DIR}")

scitex/plt/_tpl.py

@@ -11,17 +11,18 @@ def termplot(*args):
     Plots given y values against x using termplotlib, or plots a single y array against its indices if x is not provided.
 
     Parameters:
-    - *args: Accepts either one argument (y values) or two arguments (x and y values).
+    - *args: Accepts either one argument (y values) or two+ arguments (x and y values, extras ignored).
 
     Returns:
     None. Displays the plot in the terminal.
     """
     if len(args) == 1:
-        y = args[0]  # [REVISED]
+        y = args[0]
         x = np.arange(len(y))
-
-    if len(args) == 2:
-        x, y = args
+    elif len(args) >= 2:
+        x, y = args[0], args[1]
+    else:
+        raise ValueError("termplot requires at least one argument (y values)")
 
     fig = tpl.figure()
     fig.plot(x, y)

scitex/plt/ax/_plot/__init__.py

@@ -29,6 +29,25 @@ from ._plot_statistical_shaded_line import (
 )
 from ._add_fitted_line import add_fitted_line
 
+from scitex.decorators import deprecated
+
+# Backward-compatible aliases for renamed functions with deprecation warnings
+@deprecated(reason="Use stx_line instead", forward_to="scitex.plt.ax._plot.stx_line")
+def plot_line(*args, **kwargs):
+    pass
+
+@deprecated(reason="Use stx_mean_std instead", forward_to="scitex.plt.ax._plot.stx_mean_std")
+def plot_mean_std(*args, **kwargs):
+    pass
+
+@deprecated(reason="Use stx_mean_ci instead", forward_to="scitex.plt.ax._plot.stx_mean_ci")
+def plot_mean_ci(*args, **kwargs):
+    pass
+
+@deprecated(reason="Use stx_median_iqr instead", forward_to="scitex.plt.ax._plot.stx_median_iqr")
+def plot_median_iqr(*args, **kwargs):
+    pass
+
 __all__ = [
     "stx_scatter_hist",
     "stx_heatmap",
@@ -50,6 +69,11 @@ __all__ = [
     "stx_mean_ci",
     "stx_median_iqr",
     "add_fitted_line",
+    # Backward-compatible aliases
+    "plot_line",
+    "plot_mean_std",
+    "plot_mean_ci",
+    "plot_median_iqr",
 ]
 
 # EOF

scitex/plt/ax/_plot/_add_fitted_line.py

@@ -15,8 +15,8 @@ def add_fitted_line(
     ax,
     x,
     y,
-    color: str = 'black',
-    linestyle: str = '--',
+    color: str = "black",
+    linestyle: str = "--",
     linewidth_mm: float = 0.2,
     label: Optional[str] = None,
     degree: int = 1,
@@ -120,30 +120,31 @@ def add_fitted_line(
         y_pos = poly_fn(x_pos)
 
         # Format statistics text with R² and significance stars
-        r_squared = stats_result.effect_size['value']  # r_squared from effect_size
+        r_squared = stats_result.effect_size["value"]  # r_squared from effect_size
         stars = stats_result.stars
 
-        if stars and stars != 'ns':  # Only show if significant
+        if stars and stars != "ns":  # Only show if significant
             stats_text = f"$R^2$ = {r_squared:.3f}{stars}"
         else:  # Not significant
             stats_text = f"$R^2$ = {r_squared:.3f} (ns)"
 
         # Add text annotation near the line
         ax.text(
-            x_pos, y_pos,
+            x_pos,
+            y_pos,
             stats_text,
-            verticalalignment='bottom',
-            fontsize=stats_fontsize
+            verticalalignment="bottom",
+            fontsize=stats_fontsize,
         )
 
         # Store stats in axes metadata for embedding in saved figures
-        if not hasattr(ax, '_scitex_metadata'):
+        if not hasattr(ax, "_scitex_metadata"):
             ax._scitex_metadata = {}
-        if 'stats' not in ax._scitex_metadata:
-            ax._scitex_metadata['stats'] = []
+        if "stats" not in ax._scitex_metadata:
+            ax._scitex_metadata["stats"] = []
 
         # Add this StatResult to the stats list
-        ax._scitex_metadata['stats'].append(stats_result.to_dict())
+        ax._scitex_metadata["stats"].append(stats_result.to_dict())
 
     return line, coeffs, stats_result
 

scitex/plt/ax/_plot/_plot_circular_hist.py

@@ -66,7 +66,9 @@ def plot_circular_hist(
         Container of individual artists used to create the histogram
         or list of such containers if there are multiple input datasets.
     """
-    assert_valid_axis(axis, "First argument must be a matplotlib axis or scitex axis wrapper")
+    assert_valid_axis(
+        axis, "First argument must be a matplotlib axis or scitex axis wrapper"
+    )
 
     # Wrap angles to [-pi, pi)
     radians = (radians + np.pi) % (2 * np.pi) - np.pi