research-copilot 0.1.0

package/app/out/skills/research-pilot-default-project-skills/matplotlib/references/common_issues.md

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+# Matplotlib Common Issues and Solutions
+
+Troubleshooting guide for frequently encountered matplotlib problems.
+
+## Display and Backend Issues
+
+### Issue: Plots Not Showing
+
+**Problem:** `plt.show()` doesn't display anything
+
+**Solutions:**
+```python
+# 1. Check if backend is properly set (for interactive use)
+import matplotlib
+print(matplotlib.get_backend())
+
+# 2. Try different backends
+matplotlib.use('TkAgg')  # or 'Qt5Agg', 'MacOSX'
+import matplotlib.pyplot as plt
+
+# 3. In Jupyter notebooks, use magic command
+%matplotlib inline  # Static images
+# or
+%matplotlib widget  # Interactive plots
+
+# 4. Ensure plt.show() is called
+plt.plot([1, 2, 3])
+plt.show()
+```
+
+### Issue: "RuntimeError: main thread is not in main loop"
+
+**Problem:** Interactive mode issues with threading
+
+**Solution:**
+```python
+# Switch to non-interactive backend
+import matplotlib
+matplotlib.use('Agg')
+import matplotlib.pyplot as plt
+
+# Or turn off interactive mode
+plt.ioff()
+```
+
+### Issue: Figures Not Updating Interactively
+
+**Problem:** Changes not reflected in interactive windows
+
+**Solution:**
+```python
+# Enable interactive mode
+plt.ion()
+
+# Draw after each change
+plt.plot(x, y)
+plt.draw()
+plt.pause(0.001)  # Brief pause to update display
+```
+
+## Layout and Spacing Issues
+
+### Issue: Overlapping Labels and Titles
+
+**Problem:** Labels, titles, or tick labels overlap or get cut off
+
+**Solutions:**
+```python
+# Solution 1: Constrained layout (RECOMMENDED)
+fig, ax = plt.subplots(constrained_layout=True)
+
+# Solution 2: Tight layout
+fig, ax = plt.subplots()
+plt.tight_layout()
+
+# Solution 3: Adjust margins manually
+plt.subplots_adjust(left=0.15, right=0.95, top=0.95, bottom=0.15)
+
+# Solution 4: Save with bbox_inches='tight'
+plt.savefig('figure.png', bbox_inches='tight')
+
+# Solution 5: Rotate long tick labels
+ax.set_xticklabels(labels, rotation=45, ha='right')
+```
+
+### Issue: Colorbar Affects Subplot Size
+
+**Problem:** Adding colorbar shrinks the plot
+
+**Solution:**
+```python
+# Solution 1: Use constrained layout
+fig, ax = plt.subplots(constrained_layout=True)
+im = ax.imshow(data)
+plt.colorbar(im, ax=ax)
+
+# Solution 2: Manually specify colorbar dimensions
+from mpl_toolkits.axes_grid1 import make_axes_locatable
+divider = make_axes_locatable(ax)
+cax = divider.append_axes("right", size="5%", pad=0.05)
+plt.colorbar(im, cax=cax)
+
+# Solution 3: For multiple subplots, share colorbar
+fig, axes = plt.subplots(1, 3, figsize=(15, 4))
+for ax in axes:
+    im = ax.imshow(data)
+fig.colorbar(im, ax=axes.ravel().tolist(), shrink=0.95)
+```
+
+### Issue: Subplots Too Close Together
+
+**Problem:** Multiple subplots overlapping
+
+**Solution:**
+```python
+# Solution 1: Use constrained_layout
+fig, axes = plt.subplots(2, 2, constrained_layout=True)
+
+# Solution 2: Adjust spacing with subplots_adjust
+fig, axes = plt.subplots(2, 2)
+plt.subplots_adjust(hspace=0.4, wspace=0.4)
+
+# Solution 3: Specify spacing in tight_layout
+plt.tight_layout(h_pad=2.0, w_pad=2.0)
+```
+
+## Memory and Performance Issues
+
+### Issue: Memory Leak with Multiple Figures
+
+**Problem:** Memory usage grows when creating many figures
+
+**Solution:**
+```python
+# Close figures explicitly
+fig, ax = plt.subplots()
+ax.plot(x, y)
+plt.savefig('plot.png')
+plt.close(fig)  # or plt.close('all')
+
+# Clear current figure without closing
+plt.clf()
+
+# Clear current axes
+plt.cla()
+```
+
+### Issue: Large File Sizes
+
+**Problem:** Saved figures are too large
+
+**Solutions:**
+```python
+# Solution 1: Reduce DPI
+plt.savefig('figure.png', dpi=150)  # Instead of 300
+
+# Solution 2: Use rasterization for complex plots
+ax.plot(x, y, rasterized=True)
+
+# Solution 3: Use vector format for simple plots
+plt.savefig('figure.pdf')  # or .svg
+
+# Solution 4: Compress PNG
+plt.savefig('figure.png', dpi=300, optimize=True)
+```
+
+### Issue: Slow Plotting with Large Datasets
+
+**Problem:** Plotting takes too long with many points
+
+**Solutions:**
+```python
+# Solution 1: Downsample data
+from scipy.signal import decimate
+y_downsampled = decimate(y, 10)  # Keep every 10th point
+
+# Solution 2: Use rasterization
+ax.plot(x, y, rasterized=True)
+
+# Solution 3: Use line simplification
+ax.plot(x, y)
+for line in ax.get_lines():
+    line.set_rasterized(True)
+
+# Solution 4: For scatter plots, consider hexbin or 2d histogram
+ax.hexbin(x, y, gridsize=50, cmap='viridis')
+```
+
+## Font and Text Issues
+
+### Issue: Font Warnings
+
+**Problem:** "findfont: Font family [...] not found"
+
+**Solutions:**
+```python
+# Solution 1: Use available fonts
+from matplotlib.font_manager import findfont, FontProperties
+print(findfont(FontProperties(family='sans-serif')))
+
+# Solution 2: Rebuild font cache
+import matplotlib.font_manager
+matplotlib.font_manager._rebuild()
+
+# Solution 3: Suppress warnings
+import warnings
+warnings.filterwarnings("ignore", category=UserWarning)
+
+# Solution 4: Specify fallback fonts
+plt.rcParams['font.sans-serif'] = ['Arial', 'DejaVu Sans', 'sans-serif']
+```
+
+### Issue: LaTeX Rendering Errors
+
+**Problem:** Math text not rendering correctly
+
+**Solutions:**
+```python
+# Solution 1: Use raw strings with r prefix
+ax.set_xlabel(r'$\alpha$')  # Not '\alpha'
+
+# Solution 2: Escape backslashes in regular strings
+ax.set_xlabel('$\\alpha$')
+
+# Solution 3: Disable LaTeX if not installed
+plt.rcParams['text.usetex'] = False
+
+# Solution 4: Use mathtext instead of full LaTeX
+# Mathtext is always available, no LaTeX installation needed
+ax.text(x, y, r'$\int_0^\infty e^{-x} dx$')
+```
+
+### Issue: Text Cut Off or Outside Figure
+
+**Problem:** Labels or annotations appear outside figure bounds
+
+**Solutions:**
+```python
+# Solution 1: Use bbox_inches='tight'
+plt.savefig('figure.png', bbox_inches='tight')
+
+# Solution 2: Adjust figure bounds
+plt.subplots_adjust(left=0.15, right=0.85, top=0.85, bottom=0.15)
+
+# Solution 3: Clip text to axes
+ax.text(x, y, 'text', clip_on=True)
+
+# Solution 4: Use constrained_layout
+fig, ax = plt.subplots(constrained_layout=True)
+```
+
+## Color and Colormap Issues
+
+### Issue: Colorbar Not Matching Plot
+
+**Problem:** Colorbar shows different range than data
+
+**Solution:**
+```python
+# Explicitly set vmin and vmax
+im = ax.imshow(data, vmin=0, vmax=1, cmap='viridis')
+plt.colorbar(im, ax=ax)
+
+# Or use the same norm for multiple plots
+import matplotlib.colors as mcolors
+norm = mcolors.Normalize(vmin=data.min(), vmax=data.max())
+im1 = ax1.imshow(data1, norm=norm, cmap='viridis')
+im2 = ax2.imshow(data2, norm=norm, cmap='viridis')
+```
+
+### Issue: Colors Look Wrong
+
+**Problem:** Unexpected colors in plots
+
+**Solutions:**
+```python
+# Solution 1: Check color specification format
+ax.plot(x, y, color='blue')  # Correct
+ax.plot(x, y, color=(0, 0, 1))  # Correct RGB
+ax.plot(x, y, color='#0000FF')  # Correct hex
+
+# Solution 2: Verify colormap exists
+print(plt.colormaps())  # List available colormaps
+
+# Solution 3: For scatter plots, ensure c shape matches
+ax.scatter(x, y, c=colors)  # colors should have same length as x, y
+
+# Solution 4: Check if alpha is set correctly
+ax.plot(x, y, alpha=1.0)  # 0=transparent, 1=opaque
+```
+
+### Issue: Reversed Colormap
+
+**Problem:** Colormap direction is backwards
+
+**Solution:**
+```python
+# Add _r suffix to reverse any colormap
+ax.imshow(data, cmap='viridis_r')
+```
+
+## Axis and Scale Issues
+
+### Issue: Axis Limits Not Working
+
+**Problem:** `set_xlim` or `set_ylim` not taking effect
+
+**Solutions:**
+```python
+# Solution 1: Set after plotting
+ax.plot(x, y)
+ax.set_xlim(0, 10)
+ax.set_ylim(-1, 1)
+
+# Solution 2: Disable autoscaling
+ax.autoscale(False)
+ax.set_xlim(0, 10)
+
+# Solution 3: Use axis method
+ax.axis([xmin, xmax, ymin, ymax])
+```
+
+### Issue: Log Scale with Zero or Negative Values
+
+**Problem:** ValueError when using log scale with data ≤ 0
+
+**Solutions:**
+```python
+# Solution 1: Filter out non-positive values
+mask = (data > 0)
+ax.plot(x[mask], data[mask])
+ax.set_yscale('log')
+
+# Solution 2: Use symlog for data with positive and negative values
+ax.set_yscale('symlog')
+
+# Solution 3: Add small offset
+ax.plot(x, data + 1e-10)
+ax.set_yscale('log')
+```
+
+### Issue: Dates Not Displaying Correctly
+
+**Problem:** Date axis shows numbers instead of dates
+
+**Solution:**
+```python
+import matplotlib.dates as mdates
+import pandas as pd
+
+# Convert to datetime if needed
+dates = pd.to_datetime(date_strings)
+
+ax.plot(dates, values)
+
+# Format date axis
+ax.xaxis.set_major_formatter(mdates.DateFormatter('%Y-%m-%d'))
+ax.xaxis.set_major_locator(mdates.DayLocator(interval=7))
+plt.xticks(rotation=45)
+```
+
+## Legend Issues
+
+### Issue: Legend Covers Data
+
+**Problem:** Legend obscures important parts of plot
+
+**Solutions:**
+```python
+# Solution 1: Use 'best' location
+ax.legend(loc='best')
+
+# Solution 2: Place outside plot area
+ax.legend(bbox_to_anchor=(1.05, 1), loc='upper left')
+
+# Solution 3: Make legend semi-transparent
+ax.legend(framealpha=0.7)
+
+# Solution 4: Put legend below plot
+ax.legend(bbox_to_anchor=(0.5, -0.15), loc='upper center', ncol=3)
+```
+
+### Issue: Too Many Items in Legend
+
+**Problem:** Legend is cluttered with many entries
+
+**Solutions:**
+```python
+# Solution 1: Only label selected items
+for i, (x, y) in enumerate(data):
+    label = f'Data {i}' if i % 5 == 0 else None
+    ax.plot(x, y, label=label)
+
+# Solution 2: Use multiple columns
+ax.legend(ncol=3)
+
+# Solution 3: Create custom legend with fewer entries
+from matplotlib.lines import Line2D
+custom_lines = [Line2D([0], [0], color='r'),
+                Line2D([0], [0], color='b')]
+ax.legend(custom_lines, ['Category A', 'Category B'])
+
+# Solution 4: Use separate legend figure
+fig_leg = plt.figure(figsize=(3, 2))
+ax_leg = fig_leg.add_subplot(111)
+ax_leg.legend(*ax.get_legend_handles_labels(), loc='center')
+ax_leg.axis('off')
+```
+
+## 3D Plot Issues
+
+### Issue: 3D Plots Look Flat
+
+**Problem:** Difficult to perceive depth in 3D plots
+
+**Solutions:**
+```python
+# Solution 1: Adjust viewing angle
+ax.view_init(elev=30, azim=45)
+
+# Solution 2: Add gridlines
+ax.grid(True)
+
+# Solution 3: Use color for depth
+scatter = ax.scatter(x, y, z, c=z, cmap='viridis')
+
+# Solution 4: Rotate interactively (if using interactive backend)
+# User can click and drag to rotate
+```
+
+### Issue: 3D Axis Labels Cut Off
+
+**Problem:** 3D axis labels appear outside figure
+
+**Solution:**
+```python
+from mpl_toolkits.mplot3d import Axes3D
+
+fig = plt.figure(figsize=(10, 8))
+ax = fig.add_subplot(111, projection='3d')
+ax.plot_surface(X, Y, Z)
+
+# Add padding
+fig.tight_layout(pad=3.0)
+
+# Or save with tight bounding box
+plt.savefig('3d_plot.png', bbox_inches='tight', pad_inches=0.5)
+```
+
+## Image and Colorbar Issues
+
+### Issue: Images Appear Flipped
+
+**Problem:** Image orientation is wrong
+
+**Solution:**
+```python
+# Set origin parameter
+ax.imshow(img, origin='lower')  # or 'upper' (default)
+
+# Or flip array
+ax.imshow(np.flipud(img))
+```
+
+### Issue: Images Look Pixelated
+
+**Problem:** Image appears blocky when zoomed
+
+**Solutions:**
+```python
+# Solution 1: Use interpolation
+ax.imshow(img, interpolation='bilinear')
+# Options: 'nearest', 'bilinear', 'bicubic', 'spline16', 'spline36', etc.
+
+# Solution 2: Increase DPI when saving
+plt.savefig('figure.png', dpi=300)
+
+# Solution 3: Use vector format if appropriate
+plt.savefig('figure.pdf')
+```
+
+## Common Errors and Fixes
+
+### "TypeError: 'AxesSubplot' object is not subscriptable"
+
+**Problem:** Trying to index single axes
+```python
+# Wrong
+fig, ax = plt.subplots()
+ax[0].plot(x, y)  # Error!
+
+# Correct
+fig, ax = plt.subplots()
+ax.plot(x, y)
+```
+
+### "ValueError: x and y must have same first dimension"
+
+**Problem:** Data arrays have mismatched lengths
+```python
+# Check shapes
+print(f"x shape: {x.shape}, y shape: {y.shape}")
+
+# Ensure they match
+assert len(x) == len(y), "x and y must have same length"
+```
+
+### "AttributeError: 'numpy.ndarray' object has no attribute 'plot'"
+
+**Problem:** Calling plot on array instead of axes
+```python
+# Wrong
+data.plot(x, y)
+
+# Correct
+ax.plot(x, y)
+# or for pandas
+data.plot(ax=ax)
+```
+
+## Best Practices to Avoid Issues
+
+1. **Always use the OO interface** - Avoid pyplot state machine
+   ```python
+   fig, ax = plt.subplots()  # Good
+   ax.plot(x, y)
+   ```
+
+2. **Use constrained_layout** - Prevents overlap issues
+   ```python
+   fig, ax = plt.subplots(constrained_layout=True)
+   ```
+
+3. **Close figures explicitly** - Prevents memory leaks
+   ```python
+   plt.close(fig)
+   ```
+
+4. **Set figure size at creation** - Better than resizing later
+   ```python
+   fig, ax = plt.subplots(figsize=(10, 6))
+   ```
+
+5. **Use raw strings for math text** - Avoids escape issues
+   ```python
+   ax.set_xlabel(r'$\alpha$')
+   ```
+
+6. **Check data shapes before plotting** - Catch size mismatches early
+   ```python
+   assert len(x) == len(y)
+   ```
+
+7. **Use appropriate DPI** - 300 for print, 150 for web
+   ```python
+   plt.savefig('figure.png', dpi=300)
+   ```
+
+8. **Test with different backends** - If display issues occur
+   ```python
+   import matplotlib
+   matplotlib.use('TkAgg')
+   ```