batplot 1.7.20__tar.gz → 1.7.22__tar.gz

{batplot-1.7.20/batplot.egg-info → batplot-1.7.22}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: batplot
-Version: 1.7.20
+Version: 1.7.22
 Summary: Interactive plotting tool for material science (1D plot) and electrochemistry (GC, CV, dQ/dV, CPC, operando) with batch processing
 Author-email: Tian Dai <tianda@uio.no>
 License-Expression: MIT

{batplot-1.7.20 → batplot-1.7.22}/batplot/__init__.py

@@ -1,5 +1,5 @@
 """batplot: Interactive plotting for battery data visualization."""
 
-__version__ = "1.7.20"
+__version__ = "1.7.22"
 
 __all__ = ["__version__"]

{batplot-1.7.20 → batplot-1.7.22}/batplot/args.py

@@ -9,7 +9,7 @@ the command-line interface, including:
 
 HOW COMMAND-LINE ARGUMENTS WORK:
 --------------------------------
-When you run 'batplot file.xy --interactive', Python's argparse library:
+When you run (for example) 'batplot --xaxis 2theta file.xy --i', Python's argparse library:
 1. Parses the command line into structured arguments
 2. Validates that required arguments are present
 3. Converts string arguments to appropriate types (int, float, bool, etc.)
@@ -26,7 +26,7 @@ import sys
 import re
 
 # ====================================================================
-# COLORED HELP OUTPUT (OPTIONAL ENHANCEMENT)
+# COLORED HELP OUTPUT
 # ====================================================================
 # The 'rich' library provides colored terminal output. If available,
 # we use it to make help text more readable by highlighting:
@@ -64,8 +64,8 @@ def _colorize_help(text: str) -> str:
     - Bullet points: • → bold
     
     Example:
-        Input:  "batplot file.xy --interactive"
-        Output: "[green]batplot[/green] [yellow]file.xy[/yellow] [cyan]--interactive[/cyan]"
+        Input:  "batplot file.qye --i"
+        Output: "[green]batplot[/green] [yellow]file.qye[/yellow] [cyan]--i[/cyan]"
     
     Args:
         text: Plain help text (uncolored)
@@ -133,78 +133,79 @@ def _print_general_help() -> None:
     msg = (
         version_str +
         "What it does:\n"
-        "  • XY: XRD/PDF/XAS/... curves\n"
-        "  • EC: GC/CPC/dQdV/CV (from .csv or .mpt)\n"
-        "  • Operando: contour maps from a folder of XY and .mpt files\n"
-        "  • Batch: export SVG plots for all files in a directory\n\n"
-        "  • Interactive mode: --i / --interactive flag opens a menu for styling, ranges, fonts, export, sessions\n\n"
-    "How to run (basics):\n"
-    "  [XY curves]\n"
-    "    batplot file1.xy file2.qye [option1] [option2]             # XY curves\n"
-    "    batplot allfiles                       # Plot all XY files in current directory on same figure\n"
-    "    batplot allfiles /path/to/dir          # Plot all XY files in specified directory\n"
-    "    batplot allfiles --interactive         # Plot all files with interactive menu\n"
-    "    batplot allxyfiles                     # Plot only .xy files (natural sorted)\n"
-    "    batplot /path/to/data allnorfiles --i  # Plot only .nor files from a directory\n"
-    "    batplot --all                          # Batch mode: all XY files → Figures/ as .svg\n"
-    "    batplot --all --format png             # Batch mode: export as .png files\n"
-    "    batplot --all --xaxis 2theta --xrange 10 80  # Batch mode with custom axis and range\n"
-    "    batplot --all style.bps                # Batch with style: apply style.bps to all XY files\n"
-    "    batplot --all ./Style/style.bps        # Batch with style: use relative path to style file\n"
-    "    batplot --all config.bpsg              # Batch with style+geom: apply to all XY files\n"
-    "    batplot file1.xy file2.xye style.bps  # Apply style to multiple files and export\n"
-    "    batplot file1.xy file2.xye ./Style/style.bps  # Apply style from relative path\n\n"
-    "  [Electrochemistry]\n"
-    "    batplot --gc FILE.mpt --mass 7.0       # EC GC from .mpt (requires --mass mg)\n"
-    "    batplot --gc FILE.csv                  # EC GC from supported .csv (no mass required)\n"
-    "    batplot --gc --all --mass 7.0          # Batch: all .mpt/.csv → Figures/ as .svg\n"
-    "    batplot --gc --all --mass 7 --format pdf  # Batch: export as .pdf files\n"
-    "    batplot --all --gc style.bps --mass 7  # Batch with style: apply style.bps to all GC files\n"
-    "    batplot --all --gc ./Style/style.bps --mass 7  # Batch with style: use relative path\n"
-    "    batplot --all --cv config.bpsg         # Batch with style+geom: apply to all CV files\n"
-    "    batplot --all --cv ./Style/config.bpsg  # Batch with style+geom: use relative path\n"
-    "    batplot --dqdv FILE.csv                # EC dQ/dV from supported .csv\n"
-    "    batplot --dqdv --all                   # Batch: all .csv in directory (dQdV mode)\n"
-    "    batplot --cv FILE.mpt                  # EC CV (cyclic voltammetry) from .mpt\n"
-    "    batplot --cv FILE.txt                  # EC CV (cyclic voltammetry) from .txt\n"
-    "    batplot --cv --all                     # Batch: all .mpt/.txt in directory (CV mode)\n\n"
-    "  [Operando]\n"
-    "    batplot --operando [FOLDER]            # Operando contour (with or without .mpt file)\n\n"
-        "Features:\n"
-    "  • Quick plotting with sensible defaults, no config files needed\n"
-    "  • Supports many common file formats (see -h xy/ec/op)\n"
-    "  • Interactive menus (--interactive): styling, ranges, fonts, export, sessions\n"
-    "  • Batch processing: use 'allfiles' / 'all<ext>files' to plot together, or --all for separate files\n"
-    "  • Batch exports saved to Figures/ subdirectory (default: .svg format)\n"
-    "  • Batch styling: apply .bps/.bpsg files to all exports (use --all flag)\n"
-    "  • Format option: use --format png/pdf/jpg/etc to change export format\n\n"
-    
-    "More help:\n"
-    "  batplot -h xy   # XY file plotting guide\n"
-    "  batplot -h ec   # Electrochemistry (GC/dQdV/CV/CPC) guide\n"
-    "  batplot -h op   # Operando guide\n"
-    "  batplot -m      # Open the illustrated txt manual with highlights\n"
+        "  • XY: XRD/PDF/XAS/User defined curves\n"
+        "  • EC: Galvanostatic cycling(GC)/Capacity per cycle(CPC)/Diffrential capacity(dQdV)/Cyclic Voltammetry(CV) from Neware (.csv) or Biologic (.mpt)\n"
+        "  • Operando: contour maps from a folder of .xy/.xye/.dat/.txt and optional file as side panel\n"
+        "  • Batch: export vector plots for all files in a directory\n\n"
+        "  • Interactive mode: --i / --interactive flag opens a menu for styling, ranges, export, and save\n\n"
+        "How to run (basics):\n"
+        "  [1D(XY) curves]\n"
+        "    batplot file1.xy file2.qye [option1] [option2]             # 1D curves, read the first two columns as X and Y axis by default\n"
+        "    batplot allfiles                       # Plot all files in current directory on same figure\n"
+        "    batplot allfiles /path/to/dir          # Plot all files in specified directory\n"
+        "    batplot allfiles --i                   # Plot all files with interactive menu\n"
+        "    batplot allxyfiles                     # Plot only .xy files (natural sorted)\n"
+        "    batplot /path/to/data allnorfiles --i  # Plot only .nor files from a directory\n"
+        "    batplot --all                          # Batch mode: all XY files → Figures/ as .svg\n"
+        "    batplot --all --format png             # Batch mode: export as .png files\n"
+        "    batplot --all --xaxis 2theta --xrange 10 80  # Batch mode with custom axis and range\n"
+        "    batplot --all style.bps                # Batch with style: apply style.bps to all files\n"
+        "    batplot --all ./Style/style.bps        # Batch with style: use relative path to style file\n"
+        "    batplot --all config.bpsg              # Batch with style+geom: apply to all XY files\n"
+        "    batplot file1.qye file2.qye style.bps  # Apply style to multiple files and export\n"
+        "    batplot file1.xy file2.xye ./Style/style.bps  # Apply style from relative path\n\n"
+        "  [Electrochemistry]\n"
+        "    batplot --gc file.mpt --mass 7.0       # EC GC from .mpt (requires --mass mg)\n"
+        "    batplot --gc file.csv --i              # EC GC from supported .csv (no mass required) with interactive menu\n"
+        "    batplot --gc --all --mass 7.0          # Batch: all .mpt/.csv → Figures/ as .svg\n"
+        "    batplot --gc --all --mass 7 --format png  # Batch: export as .png files\n"
+        "    batplot --all --dqdv style.bps --mass 7  # Batch with style: apply style.bps to all GC files\n"
+        "    batplot --all --gc ./Style/style.bps --mass 7  # Batch with style: use relative path\n"
+        "    batplot --all --cpc config.bpsg         # Batch with style+geom: apply to all CV files\n"
+        "    batplot --all --cv ./Style/config.bpsg  # Batch with style+geom: use relative path\n"
+        "    batplot --dqdv FILE.csv                # EC dQ/dV from supported .csv\n"
+        "    batplot --dqdv --all                   # Batch: all .csv in directory (dQdV mode)\n"
+        "    batplot --cv FILE.mpt                  # EC CV (cyclic voltammetry) from .mpt\n"
+        "    batplot --cv FILE.txt                  # EC CV (cyclic voltammetry) from .txt\n"
+        "    batplot --cv --all                     # Batch: all .mpt/.txt in directory (CV mode)\n\n"
+        "  [Operando]\n"
+        "    batplot --operando --i [FOLDER]        # Operando contour (with or without .mpt file) with interactive menu\n\n"
+            "Features:\n"
+        "  • Quick plotting with sensible defaults, no config files needed\n"
+        "  • Supports many common file formats (see -h xy/ec/op)\n"
+        "  • Interactive menus (--interactive): styling, ranges, fonts, export, sessions\n"
+        "  • Batch processing: use 'allfiles' / 'all<ext>files' to plot together, or --all for separate files\n"
+        "  • Batch exports saved to Figures/ subdirectory (default: .svg format)\n"
+        "  • Batch styling: apply .bps/.bpsg files to all exports (use --all flag)\n"
+        "  • Format option: use --format png/pdf/jpg/etc to change export format\n\n"
+        
+        "More help:\n"
+        "  batplot -h xy   # XY file plotting guide\n"
+        "  batplot -h ec   # Electrochemistry (GC/dQdV/CV/CPC) guide\n"
+        "  batplot -h op   # Operando guide\n"
+        "  batplot -m      # Open the illustrated txt manual with highlights\n"
 
-    "Contact & Updates:\n"
-    "  Subscribe to batplot-lab@kjemi.uio.no for updates\n"
-    "  (If you are not from UiO, send an email to sympa@kjemi.uio.no with the subject line \"subscribe batplot-lab@kjemi.uio.no your-name\")\n"
-    "  Kindly cite the pypi package page (https://pypi.org/project/batplot/) if the plot is used for publication\n"
-    "  Email: tianda@uio.no\n"
-    )
+        "Contact & Updates:\n\n"
+        "  Subscribe to batplot-lab@kjemi.uio.no for updates\n"
+        "  (If you are not from UiO, send an email to sympa@kjemi.uio.no with the subject line \"subscribe batplot-lab@kjemi.uio.no your-name\")\n"
+        "  Kindly cite the pypi package page (https://pypi.org/project/batplot/) if the plot is used for publication\n"
+        "  Email: tianda@uio.no\n"
+        )
     _print_help(msg)
 
 
 def _print_xy_help() -> None:
     msg = (
-        "XY plots (diffraction/PDF/XAS)\n\n"
-        "Supported files: .xye .xy .qye .dat .csv .gr .nor .chik .chir .txt (2-col). CIF overlays supported.\n\n"
-        "Axis detection: .qye→Q, .gr→r, .nor→energy, .chik→k, .chir→r, else use --xaxis (Q, 2theta, r, k, energy, rft, time).\n"
-        "If mixing 2θ data in Q, give wavelength per-file (file.xye:1.5406) or global --wl.\n"
+        "XY plots (XRD/PDF/XAS and many more)\n\n"
+        "Supported files: .xye .xy .qye .dat .csv .gr .nor .chik .chir .txt and other user specified formats. CIF overlays supported.\n\n"
+        "Axis detection: .qye→Q, .gr→r, .nor→energy, .chik→k, .chir→r, else use --xaxis (Q, 2theta, r, k, energy, time or user defined).\n"
+        "If mixing 2θ data in Q, give wavelength per-file (file.xye:1.5406) or global flag --wl.\n"
+        "A wavelength can be converted into a different wave length by file.xye:1.54:0.709.\n"
         "For electrochemistry CSV/MPT time-voltage plots, use --xaxis time.\n\n"
         "Examples:\n"
-        "  batplot a.xye:1.5406 b.qye --stack --interactive\n"
-        "  batplot a.dat b.xy --wl 1.54 --out fig.svg\n"
-        "  batplot pattern.qye ticks.cif --interactive\n\n"
+        "  batplot a.xye:1.5406 b.qye --stack --i\n"
+        "  batplot a.dat b.xy --wl 1.54 --i\n"
+        "  batplot pattern.qye ticks.cif:1.54 --i\n\n"
         "Plot all files together:\n"
         "  batplot allfiles                       # Plot all XY files on same figure\n"
         "  batplot allfiles /path/to/dir          # Plot all XY files in specified directory\n"

{batplot-1.7.20 → batplot-1.7.22}/batplot/batplot.py

@@ -1,6 +1,5 @@
-"""batplot - Interactive plotting for XRD, PDF, XAS and electrochemistry data.
-
-This module can be imported as a library (safe, no side effects) or run as CLI (via batplot_main()).
+"""batplot - Interactive plotting for 1D, electrochemistry and operando contour plots.
+   It is designed for researchers working on materials science and electrochemistry, aiming to speed up the plotting process.
 """
 
 from __future__ import annotations

{batplot-1.7.20 → batplot-1.7.22}/batplot/cpc_interactive.py

@@ -428,6 +428,8 @@ def _style_snapshot(fig, ax, ax2, sc_charge, sc_discharge, sc_eff, file_data=Non
                        'visible': ax2.spines.get('right').get_visible() if ax2.spines.get('right') else None,
                        'color': ax2.spines.get('right').get_edgecolor() if ax2.spines.get('right') else None},
         },
+        'spine_colors_auto': getattr(fig, '_cpc_spine_auto', False),
+        'spine_colors': dict(getattr(fig, '_cpc_spine_colors', {})),
         'labelpads': {
             'x': getattr(ax.xaxis, 'labelpad', None),
             'ly': getattr(ax.yaxis, 'labelpad', None),  # left y-axis (capacity)
@@ -806,6 +808,24 @@ def _apply_style(fig, ax, ax2, sc_charge, sc_discharge, sc_eff, cfg: Dict, file_
                         pass
                 if spec.get('color') is not None:
                     _set_spine_color('right', spec['color'])
+        # Restore spine colors from stored dict
+        spine_colors = cfg.get('spine_colors', {})
+        if spine_colors:
+            for spine_name, color in spine_colors.items():
+                _set_spine_color(spine_name, color)
+        # Restore auto setting
+        spine_auto = cfg.get('spine_colors_auto', False)
+        if spine_auto is not None:
+            fig._cpc_spine_auto = bool(spine_auto)
+            # If auto is enabled, apply colors immediately
+            if fig._cpc_spine_auto and not (file_data and len(file_data) > 1):
+                try:
+                    charge_col = _color_of(sc_charge)
+                    eff_col = _color_of(sc_eff)
+                    _set_spine_color('left', charge_col)
+                    _set_spine_color('right', eff_col)
+                except Exception:
+                    pass
     except Exception:
         pass
     # Restore labelpads (preserve current if not in config)
@@ -1428,6 +1448,9 @@ def cpc_interactive_menu(fig, ax, ax2, sc_charge, sc_discharge, sc_eff, file_dat
                             try:
                                 sc_charge.set_color(charge_col)
                                 sc_discharge.set_color(discharge_col)
+                                # Apply auto colors if enabled
+                                if not is_multi_file and getattr(fig, '_cpc_spine_auto', False):
+                                    _set_spine_color('left', charge_col)
                             except Exception:
                                 pass
                         try:
@@ -1555,6 +1578,9 @@ def cpc_interactive_menu(fig, ax, ax2, sc_charge, sc_discharge, sc_eff, file_dat
                                 col = val
                             try:
                                 sc_eff.set_color(col)
+                                # Apply auto colors if enabled
+                                if not is_multi_file and getattr(fig, '_cpc_spine_auto', False):
+                                    _set_spine_color('right', col)
                             except Exception:
                                 pass
                         try:
@@ -1573,12 +1599,42 @@ def cpc_interactive_menu(fig, ax, ax2, sc_charge, sc_discharge, sc_eff, file_dat
         elif key == 'k':
             # Spine colors (w=top, a=left, s=bottom, d=right)
             try:
-                print("Set spine colors (with matching tick and label colors):")
-                print(_colorize_inline_commands("  w : top spine    | a : left spine"))
-                print(_colorize_inline_commands("  s : bottom spine | d : right spine"))
-                print(_colorize_inline_commands("Example: w:red a:#4561F7 s:blue d:green"))
-                line = input("Enter mappings (e.g., w:red a:#4561F7) or q: ").strip()
-                if line and line.lower() != 'q':
+                while True:
+                    print("\nSet spine colors (with matching tick and label colors):")
+                    print(_colorize_inline_commands("  w : top spine    | a : left spine"))
+                    print(_colorize_inline_commands("  s : bottom spine | d : right spine"))
+                    print(_colorize_inline_commands("Example: w:red a:#4561F7 s:blue d:green"))
+                    # Add auto function when only one file is loaded
+                    if not is_multi_file:
+                        auto_enabled = getattr(fig, '_cpc_spine_auto', False)
+                        auto_status = "ON" if auto_enabled else "OFF"
+                        print(_colorize_inline_commands(f"  a : auto (apply capacity curve color to left y-axis, efficiency to right y-axis) [{auto_status}]"))
+                    print("q: back to main menu")
+                    line = input("Enter mappings (e.g., w:red a:#4561F7) or q: ").strip()
+                    if not line or line.lower() == 'q':
+                        break
+                    # Handle auto toggle when only one file is loaded
+                    if not is_multi_file and line.lower() == 'a':
+                        auto_enabled = getattr(fig, '_cpc_spine_auto', False)
+                        fig._cpc_spine_auto = not auto_enabled
+                        new_status = "ON" if fig._cpc_spine_auto else "OFF"
+                        print(f"Auto mode: {new_status}")
+                        if fig._cpc_spine_auto:
+                            # Apply auto colors immediately
+                            push_state("color-spine-auto")
+                            try:
+                                # Get capacity curve color (charge color)
+                                charge_col = _color_of(sc_charge)
+                                # Get efficiency curve color
+                                eff_col = _color_of(sc_eff)
+                                # Apply to left and right spines
+                                _set_spine_color('left', charge_col)
+                                _set_spine_color('right', eff_col)
+                                print(f"Applied: left y-axis = {charge_col}, right y-axis = {eff_col}")
+                                fig.canvas.draw()
+                            except Exception as e:
+                                print(f"Error applying auto colors: {e}")
+                        continue
                     push_state("color-spine")
                     # Map wasd to spine names
                     key_to_spine = {'w': 'top', 'a': 'left', 's': 'bottom', 'd': 'right'}
@@ -1597,8 +1653,6 @@ def cpc_interactive_menu(fig, ax, ax2, sc_charge, sc_discharge, sc_eff, file_dat
                         _set_spine_color(spine_name, resolved)
                         print(f"Set {spine_name} spine to {resolved}")
                     fig.canvas.draw()
-                else:
-                    print("Canceled.")
             except Exception as e:
                 print(f"Error in spine color menu: {e}")
             _print_menu()
@@ -1775,6 +1829,15 @@ def cpc_interactive_menu(fig, ax, ax2, sc_charge, sc_discharge, sc_eff, file_dat
                             vis = props.get('visible', False)
                             col = props.get('color')
                             print(f"  {name:<6} lw={lw} visible={vis} color={col}")
+                    # Spine colors (k command)
+                    spine_colors = snap.get('spine_colors', {})
+                    if spine_colors:
+                        print("Spine colors:")
+                        for name, color in spine_colors.items():
+                            print(f"  {name}: {color}")
+                    spine_auto = snap.get('spine_colors_auto', False)
+                    if spine_auto:
+                        print(f"Spine colors auto: ON (capacity → left y-axis, efficiency → right y-axis)")
                     
                     ticks = snap.get('ticks', {})
                     print(f"Tick widths: x_major={ticks.get('x_major_width')}, x_minor={ticks.get('x_minor_width')}")

{batplot-1.7.20 → batplot-1.7.22}/batplot/electrochem_interactive.py

@@ -227,6 +227,120 @@ def _savgol_smooth(y: np.ndarray, window: int = 9, poly: int = 3) -> np.ndarray:
     return smoothed
 
 
+def _apply_stored_smooth_settings(cycle_lines: Dict[int, Dict[str, Optional[object]]], fig) -> None:
+    """Apply stored smooth settings to newly visible cycles that haven't been smoothed yet."""
+    if not hasattr(fig, '_dqdv_smooth_settings'):
+        return
+    settings = fig._dqdv_smooth_settings
+    if not settings:
+        return
+    
+    method = settings.get('method')
+    if method == 'diffcap':
+        min_step = settings.get('min_step', 0.001)
+        window = settings.get('window', 9)
+        poly = settings.get('poly', 3)
+        for cyc, parts in cycle_lines.items():
+            iter_parts = [(None, parts)] if not isinstance(parts, dict) else parts.items()
+            for role, ln in iter_parts:
+                if ln is None or not ln.get_visible():
+                    continue
+                # Only apply if this cycle hasn't been smoothed yet
+                if hasattr(ln, '_smooth_applied') and ln._smooth_applied:
+                    continue
+                xdata = np.asarray(ln.get_xdata(), float)
+                ydata = np.asarray(ln.get_ydata(), float)
+                if xdata.size < 3:
+                    continue
+                # Get original data if available, otherwise use current data
+                if hasattr(ln, '_original_xdata'):
+                    xdata = np.asarray(ln._original_xdata, float)
+                    ydata = np.asarray(ln._original_ydata, float)
+                else:
+                    ln._original_xdata = np.array(xdata, copy=True)
+                    ln._original_ydata = np.array(ydata, copy=True)
+                x_clean, y_clean, removed = _diffcap_clean_series(xdata, ydata, min_step)
+                if x_clean.size < poly + 2:
+                    continue
+                y_smooth = _savgol_smooth(y_clean, window, poly)
+                ln.set_xdata(x_clean)
+                ln.set_ydata(y_smooth)
+                ln._smooth_applied = True
+    elif method == 'voltage_step':
+        threshold_v = settings.get('threshold_v', 0.0005)
+        for cyc, parts in cycle_lines.items():
+            for role in ("charge", "discharge"):
+                ln = parts.get(role) if isinstance(parts, dict) else parts
+                if ln is None or not ln.get_visible():
+                    continue
+                # Only apply if this cycle hasn't been smoothed yet
+                if hasattr(ln, '_smooth_applied') and ln._smooth_applied:
+                    continue
+                xdata = np.asarray(ln.get_xdata(), float)
+                ydata = np.asarray(ln.get_ydata(), float)
+                if xdata.size < 3:
+                    continue
+                # Get original data if available, otherwise use current data
+                if hasattr(ln, '_original_xdata'):
+                    xdata = np.asarray(ln._original_xdata, float)
+                    ydata = np.asarray(ln._original_ydata, float)
+                else:
+                    ln._original_xdata = np.array(xdata, copy=True)
+                    ln._original_ydata = np.array(ydata, copy=True)
+                dv = np.abs(np.diff(xdata))
+                mask = np.ones_like(xdata, dtype=bool)
+                mask[1:] &= dv >= threshold_v
+                mask[:-1] &= dv >= threshold_v
+                filtered_x = xdata[mask]
+                filtered_y = ydata[mask]
+                if len(filtered_x) < len(xdata):
+                    ln.set_xdata(filtered_x)
+                    ln.set_ydata(filtered_y)
+                    ln._smooth_applied = True
+    elif method == 'outlier':
+        outlier_method = settings.get('outlier_method', '1')
+        threshold = settings.get('threshold', 5.0)
+        for cyc, parts in cycle_lines.items():
+            for role in ("charge", "discharge"):
+                ln = parts.get(role) if isinstance(parts, dict) else parts
+                if ln is None or not ln.get_visible():
+                    continue
+                # Only apply if this cycle hasn't been smoothed yet
+                if hasattr(ln, '_smooth_applied') and ln._smooth_applied:
+                    continue
+                xdata = np.asarray(ln.get_xdata(), float)
+                ydata = np.asarray(ln.get_ydata(), float)
+                if xdata.size < 5:
+                    continue
+                # Get original data if available, otherwise use current data
+                if hasattr(ln, '_original_xdata'):
+                    xdata = np.asarray(ln._original_xdata, float)
+                    ydata = np.asarray(ln._original_ydata, float)
+                else:
+                    ln._original_xdata = np.array(xdata, copy=True)
+                    ln._original_ydata = np.array(ydata, copy=True)
+                if outlier_method == '1':
+                    mean_y = np.nanmean(ydata)
+                    std_y = np.nanstd(ydata)
+                    if not np.isfinite(std_y) or std_y == 0:
+                        continue
+                    zscores = np.abs((ydata - mean_y) / std_y)
+                    mask = zscores <= threshold
+                else:
+                    median_y = np.nanmedian(ydata)
+                    mad = np.nanmedian(np.abs(ydata - median_y))
+                    if not np.isfinite(mad) or mad == 0:
+                        continue
+                    deviations = np.abs(ydata - median_y) / mad
+                    mask = deviations <= threshold
+                filtered_x = xdata[mask]
+                filtered_y = ydata[mask]
+                if len(filtered_x) < len(xdata):
+                    ln.set_xdata(filtered_x)
+                    ln.set_ydata(filtered_y)
+                    ln._smooth_applied = True
+
+
 def _print_menu(n_cycles: int, is_dqdv: bool = False):
     # Three-column menu similar to operando: Styles | Geometries | Options
     # Use dynamic column widths for clean alignment.
@@ -1202,6 +1316,7 @@ def electrochem_interactive_menu(fig, ax, cycle_lines: Dict[int, Dict[str, Optio
             try:
                 ax.set_xlim(*snap.get('xlim', ax.get_xlim()))
                 ax.set_ylim(*snap.get('ylim', ax.get_ylim()))
+                _apply_nice_ticks()
             except Exception:
                 pass
             try:
@@ -1287,6 +1402,7 @@ def electrochem_interactive_menu(fig, ax, cycle_lines: Dict[int, Dict[str, Optio
                 if font_size is not None:
                     mpl.rcParams['font.size'] = font_size
                     _apply_font_size(ax, font_size)
+                    _rebuild_legend(ax)
             except Exception:
                 pass
             try:
@@ -1304,6 +1420,7 @@ def electrochem_interactive_menu(fig, ax, cycle_lines: Dict[int, Dict[str, Optio
                             _apply_font_family(ax, font_sans_serif[0])
                         elif font_family:
                             _apply_font_family(ax, font_family)
+                    _rebuild_legend(ax)
             except Exception:
                 pass
             # Title offsets - all four titles
@@ -2360,22 +2477,24 @@ def electrochem_interactive_menu(fig, ax, cycle_lines: Dict[int, Dict[str, Optio
         elif key == 'k':
             # Spine colors (w=top, a=left, s=bottom, d=right)
             try:
-                print("Set spine colors (with matching tick and label colors):")
-                print(_colorize_inline_commands("  w : top spine    | a : left spine"))
-                print(_colorize_inline_commands("  s : bottom spine | d : right spine"))
-                print(_colorize_inline_commands("Example: w:red a:#4561F7 s:blue d:green"))
-                user_colors = get_user_color_list(fig)
-                if user_colors:
-                    print("\nSaved colors (enter number or u# to reuse):")
-                    for idx, color in enumerate(user_colors, 1):
-                        print(f"  {idx}: {color_block(color)} {color}")
-                    print("Type 'u' to edit saved colors.")
-                line = input("Enter mappings (e.g., w:red a:#4561F7) or q: ").strip()
-                if line.lower() == 'u':
-                    manage_user_colors(fig)
-                    _print_menu(len(all_cycles), is_dqdv)
-                    continue
-                if line and line.lower() != 'q':
+                while True:
+                    print("\nSet spine colors (with matching tick and label colors):")
+                    print(_colorize_inline_commands("  w : top spine    | a : left spine"))
+                    print(_colorize_inline_commands("  s : bottom spine | d : right spine"))
+                    print(_colorize_inline_commands("Example: w:red a:#4561F7 s:blue d:green"))
+                    user_colors = get_user_color_list(fig)
+                    if user_colors:
+                        print("\nSaved colors (enter number or u# to reuse):")
+                        for idx, color in enumerate(user_colors, 1):
+                            print(f"  {idx}: {color_block(color)} {color}")
+                        print("Type 'u' to edit saved colors.")
+                    print("q: back to main menu")
+                    line = input("Enter mappings (e.g., w:red a:#4561F7) or q: ").strip()
+                    if not line or line.lower() == 'q':
+                        break
+                    if line.lower() == 'u':
+                        manage_user_colors(fig)
+                        continue
                     push_state("color-spine")
                     key_to_spine = {'w': 'top', 'a': 'left', 's': 'bottom', 'd': 'right'}
                     tokens = line.split()
@@ -2409,8 +2528,6 @@ def electrochem_interactive_menu(fig, ax, cycle_lines: Dict[int, Dict[str, Optio
                         except Exception as e:
                             print(f"Error setting {spine_name} color: {e}")
                     fig.canvas.draw()
-                else:
-                    print("Canceled.")
             except Exception as e:
                 print(f"Error in spine color menu: {e}")
             _print_menu(len(all_cycles), is_dqdv)
@@ -2874,6 +2991,10 @@ def electrochem_interactive_menu(fig, ax, cycle_lines: Dict[int, Dict[str, Optio
             # Reapply curve linewidth (in case it was set)
             _apply_curve_linewidth(fig, cycle_lines)
             
+            # Apply stored smooth settings to newly visible cycles (only in dQdV mode)
+            if is_dqdv and hasattr(fig, '_dqdv_smooth_settings'):
+                _apply_stored_smooth_settings(cycle_lines, fig)
+            
             # Rebuild legend and redraw
             _rebuild_legend(ax)
             _apply_nice_ticks()
@@ -3331,9 +3452,15 @@ def electrochem_interactive_menu(fig, ax, cycle_lines: Dict[int, Dict[str, Optio
                                 if hasattr(ln, '_original_xdata'):
                                     ln.set_xdata(ln._original_xdata)
                                     ln.set_ydata(ln._original_ydata)
+                                    # Clear smooth flag so smooth can be reapplied if needed
+                                    if hasattr(ln, '_smooth_applied'):
+                                        delattr(ln, '_smooth_applied')
                                     restored_count += 1
                         if restored_count:
                             print(f"Reset {restored_count} curve(s) to original data.")
+                            # Clear stored smooth settings
+                            if hasattr(fig, '_dqdv_smooth_settings'):
+                                fig._dqdv_smooth_settings = {}
                             fig.canvas.draw_idle()
                         else:
                             print("No filtered data to reset.")
@@ -3365,6 +3492,13 @@ def electrochem_interactive_menu(fig, ax, cycle_lines: Dict[int, Dict[str, Optio
                             print("Threshold must be positive.")
                             continue
                         push_state("smooth-apply")
+                        # Store smooth settings for future cycle changes
+                        if not hasattr(fig, '_dqdv_smooth_settings'):
+                            fig._dqdv_smooth_settings = {}
+                        fig._dqdv_smooth_settings.update({
+                            'method': 'voltage_step',
+                            'threshold_v': threshold_v
+                        })
                         filtered = 0
                         total_before = 0
                         total_after = 0
@@ -3391,6 +3525,7 @@ def electrochem_interactive_menu(fig, ax, cycle_lines: Dict[int, Dict[str, Optio
                                 if after < before:
                                     ln.set_xdata(filtered_x)
                                     ln.set_ydata(filtered_y)
+                                    ln._smooth_applied = True
                                     filtered += 1
                                     total_before += before
                                     total_after += after
@@ -3428,7 +3563,8 @@ def electrochem_interactive_menu(fig, ax, cycle_lines: Dict[int, Dict[str, Optio
                                 print("ΔV threshold must be positive.")
                                 continue
                             break
-                        if not delta_input or delta_input.lower() == 'q':  # User quit at previous step
+                        # Only skip if user explicitly quit with 'q', not if they pressed Enter (empty = use default)
+                        if delta_input and delta_input.lower() == 'q':  # User quit at previous step
                             continue
                         while True:
                             window_input = input("Savitzky–Golay window (odd, default 9, 'q'=quit, 'e'=explain): ").strip()
@@ -3446,7 +3582,8 @@ def electrochem_interactive_menu(fig, ax, cycle_lines: Dict[int, Dict[str, Optio
                                 continue
                             window = 9 if not window_input else int(window_input)
                             break
-                        if not window_input or window_input.lower() == 'q':  # User quit at previous step
+                        # Only skip if user explicitly quit with 'q', not if they pressed Enter (empty = use default)
+                        if window_input and window_input.lower() == 'q':  # User quit at previous step
                             continue
                         while True:
                             poly_input = input("Polynomial order (default 3, 'q'=quit, 'e'=explain): ").strip()
@@ -3465,7 +3602,8 @@ def electrochem_interactive_menu(fig, ax, cycle_lines: Dict[int, Dict[str, Optio
                                 continue
                             poly = 3 if not poly_input else int(poly_input)
                             break
-                        if not poly_input or poly_input.lower() == 'q':  # User quit at previous step
+                        # Only skip if user explicitly quit with 'q', not if they pressed Enter (empty = use default)
+                        if poly_input and poly_input.lower() == 'q':  # User quit at previous step
                             continue
                     except ValueError:
                         print("Invalid number.")
@@ -3477,6 +3615,15 @@ def electrochem_interactive_menu(fig, ax, cycle_lines: Dict[int, Dict[str, Optio
                     if poly < 1:
                         poly = 1
                     push_state("smooth-diffcap")
+                    # Store smooth settings for future cycle changes
+                    if not hasattr(fig, '_dqdv_smooth_settings'):
+                        fig._dqdv_smooth_settings = {}
+                    fig._dqdv_smooth_settings.update({
+                        'method': 'diffcap',
+                        'min_step': min_step,
+                        'window': window,
+                        'poly': poly
+                    })
                     cleaned_curves = 0
                     total_removed = 0
                     for cyc, parts in cycle_lines.items():
@@ -3497,6 +3644,7 @@ def electrochem_interactive_menu(fig, ax, cycle_lines: Dict[int, Dict[str, Optio
                             y_smooth = _savgol_smooth(y_clean, window, poly)
                             ln.set_xdata(x_clean)
                             ln.set_ydata(y_smooth)
+                            ln._smooth_applied = True
                             cleaned_curves += 1
                             total_removed += removed
                     if cleaned_curves:
@@ -3570,9 +3718,19 @@ def electrochem_interactive_menu(fig, ax, cycle_lines: Dict[int, Dict[str, Optio
                                     print("Threshold must be positive.")
                                     continue
                             break
-                        if not thresh_input or thresh_input.lower() == 'q':  # User quit
+                        # Only skip if user explicitly quit with 'q', not if they pressed Enter (empty = use default)
+                        if thresh_input and thresh_input.lower() == 'q':  # User quit
                             continue
                         push_state("smooth-outlier")
+                        # Store smooth settings for future cycle changes
+                        if not hasattr(fig, '_dqdv_smooth_settings'):
+                            fig._dqdv_smooth_settings = {}
+                        thresh_val = z_threshold if method == '1' else mad_threshold
+                        fig._dqdv_smooth_settings.update({
+                            'method': 'outlier',
+                            'outlier_method': method,
+                            'threshold': thresh_val
+                        })
                         filtered = 0
                         total_before = 0
                         total_after = 0
@@ -3609,6 +3767,7 @@ def electrochem_interactive_menu(fig, ax, cycle_lines: Dict[int, Dict[str, Optio
                                 if after < before:
                                     ln.set_xdata(filtered_x)
                                     ln.set_ydata(filtered_y)
+                                    ln._smooth_applied = True
                                     filtered += 1
                                     total_before += before
                                     total_after += after
@@ -3616,7 +3775,6 @@ def electrochem_interactive_menu(fig, ax, cycle_lines: Dict[int, Dict[str, Optio
                             removed = total_before - total_after
                             pct = 100 * removed / total_before if total_before else 0
                             method_name = "Z-score" if method == '1' else "MAD"
-                            thresh_val = z_threshold if method == '1' else mad_threshold
                             print(f"Removed outliers from {filtered} curve(s) using {method_name} (threshold={thresh_val}).")
                             print(f"Removed {removed} of {total_before} points ({pct:.1f}%).")
                             print("Tip: Adjust threshold to control sensitivity (always applied to raw data).")

{batplot-1.7.20 → batplot-1.7.22}/batplot/operando.py

@@ -11,11 +11,6 @@ An operando plot is a 2D visualization where:
 - Y-axis: Time/scan number (which file/measurement in sequence)
 - Color/Z-axis: Intensity (how bright the diffraction signal is)
 
-Think of it like a "heat map" where:
-- Each row is one diffraction pattern (one file)
-- Each column is one angle/Q value
-- Color intensity shows how strong the diffraction signal is
-
 Example use cases:
 - Watching a material transform during heating (phase transitions)
 - Monitoring battery electrode changes during cycling
@@ -24,12 +19,12 @@ Example use cases:
 
 HOW IT WORKS:
 ------------
-1. Scan folder for diffraction data files (.xy, .xye, .qye, .dat)
+1. Scan folder for XRD/PDF/XAS or other data files
 2. Load each file as one "scan" (one row in the contour)
 3. Create a common X-axis grid (interpolate all scans to same grid)
 4. Stack all scans vertically to form a 2D array
 5. Display as intensity contour (color map)
-6. Optionally add electrochemistry data as side panel (if .mpt file present)
+6. Optionally add electrochemistry/temperature/other data as side panel (if .mpt file present)
 
 AXIS MODE DETECTION:
 -------------------
@@ -37,14 +32,7 @@ The X-axis type is determined automatically:
 - If --xaxis Q specified → Use Q-space
 - If files are .qye → Use Q-space (already in Q)
 - If --wl specified → Convert 2θ to Q using wavelength
-- Otherwise → Use 2θ (degrees)
-
-NO NORMALIZATION:
----------------
-Unlike some other modes, operando plots don't normalize intensity.
-The color scale spans from minimum to maximum intensity across ALL scans.
-This preserves the absolute intensity information, which is important for
-comparing different time points.
+- Other operando data (such as PDF/XAS or others) → Plot the first two columns as X and Y
 """
 from __future__ import annotations
 

{batplot-1.7.20 → batplot-1.7.22}/batplot/operando_ec_interactive.py

@@ -2000,19 +2000,20 @@ def operando_ec_interactive_menu(fig, ax, im, cbar, ec_ax, file_paths=None):
                 ax.set_ylim(y1, y0)
             except Exception as e:
                 print(f"Operando reverse failed: {e}")
-            try:
-                ey0, ey1 = ec_ax.get_ylim()
-                ec_ax.set_ylim(ey1, ey0)
-                # If we have a stored time ylim for restoration later, invert it too
-                if hasattr(ec_ax, '_saved_time_ylim') and isinstance(ec_ax._saved_time_ylim, (tuple, list)) and len(ec_ax._saved_time_ylim)==2:
-                    lo, hi = ec_ax._saved_time_ylim
-                    try:
-                        ec_ax._saved_time_ylim = (hi, lo)
-                    except Exception:
-                        pass
-                fig.canvas.draw_idle()
-            except Exception as e:
-                print(f"EC reverse failed: {e}")
+            if ec_ax is not None:
+                try:
+                    ey0, ey1 = ec_ax.get_ylim()
+                    ec_ax.set_ylim(ey1, ey0)
+                    # If we have a stored time ylim for restoration later, invert it too
+                    if hasattr(ec_ax, '_saved_time_ylim') and isinstance(ec_ax._saved_time_ylim, (tuple, list)) and len(ec_ax._saved_time_ylim)==2:
+                        lo, hi = ec_ax._saved_time_ylim
+                        try:
+                            ec_ax._saved_time_ylim = (hi, lo)
+                        except Exception:
+                            pass
+                    fig.canvas.draw_idle()
+                except Exception as e:
+                    print(f"EC reverse failed: {e}")
             print_menu()
         elif cmd == 'f':
             # Font submenu with numbered options
@@ -2104,11 +2105,12 @@ def operando_ec_interactive_menu(fig, ax, im, cbar, ec_ax, file_paths=None):
                 ax.tick_params(axis='both', which='major', width=tick_w)
                 ax.tick_params(axis='both', which='minor', width=tick_w)
                 
-                # Apply to EC pane (ec_ax)
-                for spine in ec_ax.spines.values():
-                    spine.set_linewidth(frame_w)
-                ec_ax.tick_params(axis='both', which='major', width=tick_w)
-                ec_ax.tick_params(axis='both', which='minor', width=tick_w)
+                # Apply to EC pane (ec_ax) if present
+                if ec_ax is not None:
+                    for spine in ec_ax.spines.values():
+                        spine.set_linewidth(frame_w)
+                    ec_ax.tick_params(axis='both', which='major', width=tick_w)
+                    ec_ax.tick_params(axis='both', which='minor', width=tick_w)
                 
                 # Also apply to colorbar if present
                 if cbar is not None:
@@ -2125,7 +2127,10 @@ def operando_ec_interactive_menu(fig, ax, im, cbar, ec_ax, file_paths=None):
                 except Exception:
                     fig.canvas.draw_idle()
                 
-                print(f"Applied: frame={frame_w:.2f}, ticks={tick_w:.2f} to operando, EC, and colorbar")
+                if ec_ax is not None:
+                    print(f"Applied: frame={frame_w:.2f}, ticks={tick_w:.2f} to operando, EC, and colorbar")
+                else:
+                    print(f"Applied: frame={frame_w:.2f}, ticks={tick_w:.2f} to operando and colorbar")
             except ValueError:
                 print("Invalid number format.")
             except Exception as e:
@@ -4027,28 +4032,29 @@ def operando_ec_interactive_menu(fig, ax, im, cbar, ec_ax, file_paths=None):
                     except Exception as e:
                         print(f"Warning: Could not apply operando reverse: {e}")
                     
-                    try:
-                        # EC Y-axis reverse
-                        ec_cfg = cfg.get('ec', {})
-                        ec_y_reversed = ec_cfg.get('y_reversed', False)
-                        if ec_y_reversed:
-                            ey0, ey1 = ec_ax.get_ylim()
-                            if ey0 < ey1:  # Only reverse if not already reversed
-                                ec_ax.set_ylim(ey1, ey0)
-                                # Also update stored time ylim if present
-                                if hasattr(ec_ax, '_saved_time_ylim') and isinstance(ec_ax._saved_time_ylim, (tuple, list)) and len(ec_ax._saved_time_ylim)==2:
-                                    lo, hi = ec_ax._saved_time_ylim
-                                    ec_ax._saved_time_ylim = (hi, lo)
-                        else:
-                            ey0, ey1 = ec_ax.get_ylim()
-                            if ey0 > ey1:  # Un-reverse if currently reversed
-                                ec_ax.set_ylim(ey1, ey0)
-                                # Also update stored time ylim if present
-                                if hasattr(ec_ax, '_saved_time_ylim') and isinstance(ec_ax._saved_time_ylim, (tuple, list)) and len(ec_ax._saved_time_ylim)==2:
-                                    lo, hi = ec_ax._saved_time_ylim
-                                    ec_ax._saved_time_ylim = (hi, lo)
-                    except Exception as e:
-                        print(f"Warning: Could not apply EC reverse: {e}")
+                    if ec_ax is not None:
+                        try:
+                            # EC Y-axis reverse
+                            ec_cfg = cfg.get('ec', {})
+                            ec_y_reversed = ec_cfg.get('y_reversed', False)
+                            if ec_y_reversed:
+                                ey0, ey1 = ec_ax.get_ylim()
+                                if ey0 < ey1:  # Only reverse if not already reversed
+                                    ec_ax.set_ylim(ey1, ey0)
+                                    # Also update stored time ylim if present
+                                    if hasattr(ec_ax, '_saved_time_ylim') and isinstance(ec_ax._saved_time_ylim, (tuple, list)) and len(ec_ax._saved_time_ylim)==2:
+                                        lo, hi = ec_ax._saved_time_ylim
+                                        ec_ax._saved_time_ylim = (hi, lo)
+                            else:
+                                ey0, ey1 = ec_ax.get_ylim()
+                                if ey0 > ey1:  # Un-reverse if currently reversed
+                                    ec_ax.set_ylim(ey1, ey0)
+                                    # Also update stored time ylim if present
+                                    if hasattr(ec_ax, '_saved_time_ylim') and isinstance(ec_ax._saved_time_ylim, (tuple, list)) and len(ec_ax._saved_time_ylim)==2:
+                                        lo, hi = ec_ax._saved_time_ylim
+                                        ec_ax._saved_time_ylim = (hi, lo)
+                        except Exception as e:
+                            print(f"Warning: Could not apply EC reverse: {e}")
                     
                     # Apply intensity range (oz command)
                     try:

{batplot-1.7.20 → batplot-1.7.22/batplot.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: batplot
-Version: 1.7.20
+Version: 1.7.22
 Summary: Interactive plotting tool for material science (1D plot) and electrochemistry (GC, CV, dQ/dV, CPC, operando) with batch processing
 Author-email: Tian Dai <tianda@uio.no>
 License-Expression: MIT

{batplot-1.7.20 → batplot-1.7.22}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "batplot"
-version = "1.7.20"
+version = "1.7.22"
 description = "Interactive plotting tool for material science (1D plot) and electrochemistry (GC, CV, dQ/dV, CPC, operando) with batch processing"
 authors = [
     { name = "Tian Dai", email = "tianda@uio.no" }