batplot 1.8.3__py3-none-any.whl → 1.8.5__py3-none-any.whl

batplot/__init__.py

@@ -1,5 +1,5 @@
 """batplot: Interactive plotting for battery data visualization."""
 
-__version__ = "1.8.3"
+__version__ = "1.8.5"
 
 __all__ = ["__version__"]

batplot/args.py

@@ -141,6 +141,7 @@ def _print_general_help() -> None:
         "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 file1.xy file2.xy --1d --stack --i                  # Plot 1st derivatives with interactive menu\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"
@@ -208,7 +209,8 @@ def _print_xy_help() -> None:
         "Examples:\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"
+        "  batplot pattern.qye ticks.cif:1.54 --i\n"
+        "  batplot file1.xy file2.xy --1d --stack --i  # Plot 1st derivatives with interactive menu\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"
@@ -241,6 +243,8 @@ def _print_xy_help() -> None:
         "  --kchik                   : multiply y by x for EXAFS kχ(k) plots (sets labels to k (Å⁻¹) vs kχ(k) (Å⁻¹))\n"
         "  --k2chik                  : multiply y by x² for EXAFS k²χ(k) plots (sets labels to k (Å⁻¹) vs k²χ(k) (Å⁻²))\n"
         "  --k3chik                  : multiply y by x³ for EXAFS k³χ(k) plots (sets labels to k (Å⁻¹) vs k³χ(k) (Å⁻³))\n"
+        "  --1d                      : plot the first derivative (dy/dx) of the datasets\n"
+        "  --2d                      : plot the first derivative (dy/dx) of the datasets (alias for --1d)\n"
         "  --xrange/-r <min> <max>   : set x-axis range, e.g. --xrange 0 10\n"
         "  --out/-o <filename>       : save figure to file, e.g. --out file.svg\n"
         "  --xaxis <type>            : set x-axis type (Q, 2theta, r, k, energy, rft, time, or user defined)\n"
@@ -248,6 +252,14 @@ def _print_xy_help() -> None:
         "  --ro                      : swap x and y axes (exchange x and y values before plotting)\n"
         "                              e.g. --xaxis time --ro plots time as y-axis and voltage as x-axis\n"
         "  --wl <float>              : set wavelength for Q conversion for all files, e.g. --wl 1.5406\n"
+        "  --convert/-c <from> <to>  : convert XRD data and export to 'converted' subfolder:\n"
+        "                              - <wl1> <wl2>  : convert 2θ from wavelength1 to wavelength2\n"
+        "                              - <wl> q       : convert 2θ (with wavelength) to Q space\n"
+        "                              - q <wl>      : convert Q space to 2θ (with wavelength)\n"
+        "                              Examples:\n"
+        "                                batplot file.xye --convert 1.54 0.25\n"
+        "                                batplot file.xye --convert 1.54 q\n"
+        "                                batplot file.qye --convert q 1.54\n"
         "  File wavelength syntax   : specify wavelength(s) per file using colon syntax:\n"
         "                              - file:wl          : single wavelength (for Q conversion or CIF 2theta calculation)\n"
         "                              - file:wl1:wl2     : dual wavelength (convert 2theta→Q using wl1, then Q→2theta using wl2)\n"
@@ -332,12 +344,15 @@ def _print_op_help() -> None:
         "Operando contour plots\n\n"
         "Example usage:\n"
         "  batplot --operando --interactive --wl 0.25995  # Interactive mode with Q conversion\n"
-        "  batplot --operando --xaxis 2theta              # Using 2theta axis\n\n"
+        "  batplot --operando --xaxis 2theta              # Using 2theta axis\n"
+        "  batplot --operando --1d --interactive           # Plot derivatives as contour with interactive menu\n"
+        "  batplot --operando --2d --interactive          # Plot derivatives (alias for --1d)\n\n"
         "  • Folder should contain XY files (.xy/.xye/.qye/.dat).\n"
         "  • Intensity scale is auto-adjusted between min/max values.\n"
         "  • If no .qye present, provide --xaxis 2theta or set --wl for Q conversion.\n"
         "  • If a .mpt file is present, an EC side panel is added for dual-panel mode.\n"
-        "  • Without a .mpt file, operando-only mode shows the contour plot alone.\n\n"
+        "  • Without a .mpt file, operando-only mode shows the contour plot alone.\n"
+        "  • --1d / --2d: plot the first derivative (dy/dx) of each scan as a contour plot.\n\n"
         "Interactive (--interactive): resize axes/canvas, change colormap, set intensity range (oz),\n"
         "EC y-axis options (time ↔ ions), geometry tweaks, toggle spines/ticks/labels,\n"
         "print/export/import style, save session.\n"
@@ -416,7 +431,8 @@ def build_parser() -> argparse.ArgumentParser:
     parser.add_argument("--out", "-o", type=str, help=argparse.SUPPRESS)
     parser.add_argument("--errors", action="store_true", help=argparse.SUPPRESS)
     parser.add_argument("--xaxis", type=str, help=argparse.SUPPRESS)
-    parser.add_argument("--convert", "-c", nargs="+", help=argparse.SUPPRESS)
+    parser.add_argument("--convert", "-c", nargs=2, metavar=("FROM", "TO"), 
+                        help="Convert XRD data: wavelength-to-wavelength (e.g., 1.54 0.25), wavelength-to-Q (e.g., 1.54 q), or Q-to-wavelength (e.g., q 1.54). Exports to 'converted' subfolder.")
     parser.add_argument("--wl", type=float, help=argparse.SUPPRESS)
     parser.add_argument("--fullprof", nargs="+", type=float, help=argparse.SUPPRESS)
     parser.add_argument("--norm", action="store_true", help=argparse.SUPPRESS)
@@ -453,6 +469,8 @@ def build_parser() -> argparse.ArgumentParser:
                        help=argparse.SUPPRESS)
     parser.add_argument("--readcolcsv", nargs=2, type=int, metavar=('X_COL', 'Y_COL'),
                        help=argparse.SUPPRESS)
+    parser.add_argument("--1d", action="store_true", dest="derivative_1d", help=argparse.SUPPRESS)
+    parser.add_argument("--2d", action="store_true", dest="derivative_2d", help=argparse.SUPPRESS)
     return parser
 
 

batplot/batch.py

@@ -646,6 +646,18 @@ def batch_process(directory: str, args):
             else:
                 x_plot = x
 
+            # Calculate first derivative if requested (after axis conversion)
+            if getattr(args, 'derivative_1d', False) or getattr(args, 'derivative_2d', False):
+                # Calculate dy/dx using numpy gradient
+                # numpy.gradient handles non-uniform spacing automatically
+                if len(y) > 1:
+                    dy_dx = np.gradient(y, x_plot)
+                    y = dy_dx
+                else:
+                    # Single point or empty - cannot calculate derivative
+                    print(f"Warning: Cannot calculate derivative for {fname}: insufficient data points")
+                    continue
+
             # Normalize if --norm flag is set
             if getattr(args, 'norm', False):
                 if y.size:

batplot/batplot.py

@@ -9,7 +9,7 @@ from .electrochem_interactive import electrochem_interactive_menu
 from .args import parse_args as _bp_parse_args
 from .interactive import interactive_menu
 from .batch import batch_process, batch_process_ec
-from .converters import convert_to_qye
+from .converters import convert_xrd_data
 from .session import (
     dump_session as _bp_dump_session,
     load_ec_session,
@@ -1793,37 +1793,38 @@ def batplot_main() -> int:
         except ModuleNotFoundError as e:
             # Handle numpy._core and other module import errors
             if '_core' in str(e) or 'numpy' in str(e).lower():
+                # Try to extract version info before the error
+                from .session import _try_extract_version_from_pickle, _get_current_numpy_version
+                saved_versions = _try_extract_version_from_pickle(sess_path)
+                current_numpy = _get_current_numpy_version()
+                
+                saved_numpy = saved_versions.get('numpy', 'unknown')
+                
                 print(f"\nERROR: NumPy version mismatch detected when loading: {sess_path}")
                 print("This session was saved with a different NumPy version.")
+                print()
+                print(f"Session was saved with:  NumPy {saved_numpy}")
+                print(f"Currently installed:     NumPy {current_numpy}")
+                print()
                 print("The error 'No module named numpy._core' indicates:")
                 print("  - Session saved with NumPy 2.0+ but loading with NumPy <2.0, OR")
                 print("  - Session saved with NumPy <2.0 but loading with NumPy 2.0+")
-                print("\nSolutions:")
-                print("  1. Check NumPy version: python3 -c 'import numpy; print(numpy.__version__)'")
-                print("  2. Install matching version:")
-                print("     - If session was saved with NumPy 2.0+: pip install 'numpy>=2.0'")
-                print("     - If session was saved with NumPy <2.0: pip install 'numpy<2.0'")
-                print("  3. Recreate the session from original data files")
+                print()
+                print("Solutions:")
+                if saved_numpy != 'unknown':
+                    print(f"  1. Install matching version: pip install 'numpy=={saved_numpy}'")
+                else:
+                    print("  1. Try installing NumPy <2.0: pip install 'numpy<2.0'")
+                    print("     OR try installing NumPy 2.0+: pip install 'numpy>=2.0'")
+                print("  2. Recreate the session from original data files")
             else:
                 print(f"\nERROR: Module import error when loading: {sess_path}")
                 print(f"Error: {e}")
                 print("This usually indicates a package version mismatch.")
-                print("Try installing matching package versions or recreate the session.")
             exit(1)
         except Exception as e:
             print(f"Failed to load session: {e}")
             exit(1)
-        
-        # Check package version compatibility (if version info is available)
-        try:
-            from .session import _get_package_versions, _check_package_compatibility
-            saved_versions = sess.get('package_versions', {})
-            current_versions = _get_package_versions()
-            if saved_versions and not _check_package_compatibility(saved_versions, current_versions, sess_path):
-                exit(1)
-        except Exception:
-            # If compatibility checking fails, continue anyway (backward compatibility)
-            pass
         # If it's an EC GC session, load and open EC interactive menu directly
         if isinstance(sess, dict) and sess.get('kind') == 'ec_gc':
             try:
@@ -1963,16 +1964,58 @@ def batplot_main() -> int:
         y_loaded = sess.get('y_data', [])  # stored plotted (baseline+offset) values
         orig_loaded = sess.get('orig_y', [])  # stored baseline (normalized/raw w/out offsets)
         offsets_saved = sess.get('offsets', [])
+        # Restore processed data (for smooth/reduce operations)
+        original_x_data_list = sess.get('original_x_data_list')
+        original_y_data_list = sess.get('original_y_data_list')
+        smooth_settings = sess.get('smooth_settings')
+        if original_x_data_list is not None:
+            fig._original_x_data_list = [np.array(a) for a in original_x_data_list]
+        if original_y_data_list is not None:
+            fig._original_y_data_list = [np.array(a) for a in original_y_data_list]
+        full_processed_x_data_list = sess.get('full_processed_x_data_list')
+        full_processed_y_data_list = sess.get('full_processed_y_data_list')
+        if full_processed_x_data_list is not None:
+            fig._full_processed_x_data_list = [np.array(a) for a in full_processed_x_data_list]
+        if full_processed_y_data_list is not None:
+            fig._full_processed_y_data_list = [np.array(a) for a in full_processed_y_data_list]
+        if smooth_settings is not None:
+            fig._smooth_settings = dict(smooth_settings)
+        last_smooth_settings = sess.get('last_smooth_settings')
+        if last_smooth_settings is not None:
+            fig._last_smooth_settings = dict(last_smooth_settings)
+        # Restore derivative data (for derivative operations)
+        pre_derivative_x_data_list = sess.get('pre_derivative_x_data_list')
+        pre_derivative_y_data_list = sess.get('pre_derivative_y_data_list')
+        pre_derivative_ylabel = sess.get('pre_derivative_ylabel')
+        derivative_order = sess.get('derivative_order')
+        if pre_derivative_x_data_list is not None:
+            fig._pre_derivative_x_data_list = [np.array(a) for a in pre_derivative_x_data_list]
+        if pre_derivative_y_data_list is not None:
+            fig._pre_derivative_y_data_list = [np.array(a) for a in pre_derivative_y_data_list]
+        if pre_derivative_ylabel is not None:
+            fig._pre_derivative_ylabel = str(pre_derivative_ylabel)
+        if derivative_order is not None:
+            fig._derivative_order = int(derivative_order)
+        derivative_reversed = sess.get('derivative_reversed')
+        if derivative_reversed is not None:
+            fig._derivative_reversed = bool(derivative_reversed)
         n_curves = len(x_loaded)
         for i in range(n_curves):
-            x_arr = np.array(x_loaded[i])
+            # Ensure arrays are 1D and have matching shapes
+            x_arr = np.asarray(x_loaded[i], dtype=float).flatten()
             off = offsets_saved[i] if i < len(offsets_saved) else 0.0
             if orig_loaded and i < len(orig_loaded):
-                base = np.array(orig_loaded[i])
+                base = np.asarray(orig_loaded[i], dtype=float).flatten()
             else:
                 # Fallback: derive baseline by subtracting offset from stored y (handles legacy sessions)
-                y_arr_full = np.array(y_loaded[i]) if i < len(y_loaded) else np.array([])
+                y_arr_full = np.asarray(y_loaded[i], dtype=float).flatten() if i < len(y_loaded) else np.array([], dtype=float)
                 base = y_arr_full - off
+            # Ensure x and y have matching lengths
+            if x_arr.size != base.size:
+                print(f"Warning: Curve {i+1} has mismatched x/y lengths ({x_arr.size} vs {base.size}). Trimming to match.")
+                min_len = min(x_arr.size, base.size)
+                x_arr = x_arr[:min_len]
+                base = base[:min_len]
             y_plot = base + off
             x_data_list.append(x_arr)
             orig_y.append(base)
@@ -2276,8 +2319,24 @@ def batplot_main() -> int:
         cif_hkl_label_map = {k: dict(v) for k,v in sess.get('cif_hkl_label_map', {}).items()}
         cif_numbering_enabled = True
         cif_extend_suspended = False
-        show_cif_hkl = sess.get('show_cif_hkl', False)
-        show_cif_titles = sess.get('show_cif_titles', True)
+        # Restore CIF visibility flags - default to False for hkl (labels hidden by default)
+        # and True for titles (shown by default)
+        show_cif_hkl = bool(sess.get('show_cif_hkl', False))
+        show_cif_titles = bool(sess.get('show_cif_titles', True))
+        
+        # Store CIF state in __main__ module for interactive menu to access
+        # This ensures CIF commands (z, hkl, j) are available in the menu
+        try:
+            _bp_module = sys.modules.get('__main__')
+            if _bp_module is not None and cif_tick_series:
+                setattr(_bp_module, 'cif_tick_series', list(cif_tick_series))
+                setattr(_bp_module, 'cif_hkl_map', cif_hkl_map)
+                setattr(_bp_module, 'cif_hkl_label_map', cif_hkl_label_map)
+                setattr(_bp_module, 'show_cif_hkl', bool(show_cif_hkl))
+                setattr(_bp_module, 'show_cif_titles', bool(show_cif_titles))
+                setattr(_bp_module, 'cif_extend_suspended', False)
+        except Exception:
+            pass
         # Provide minimal stubs to satisfy interactive menu dependencies
         # Axis mode restoration informs downstream toggles (e.g., CIF conversions, crosshair availability)
         axis_mode_restored = sess.get('axis_mode', 'unknown')
@@ -2336,13 +2395,20 @@ def batplot_main() -> int:
                 if not cif_tick_series:
                     return
                 try:
-                    # Preserve both x and y-axis limits to prevent movement when toggling
+                    # Preserve current limits before drawing - use actual current limits
+                    # to prevent any movement when toggling
                     prev_xlim = ax.get_xlim()
                     prev_ylim = ax.get_ylim()
-                    # Use preserved y-axis limits for calculations to prevent incremental movement
-                    orig_ylim = prev_ylim
-                    orig_yr = orig_ylim[1] - orig_ylim[0]
-                    if orig_yr <= 0: orig_yr = 1.0
+                    
+                    # Use current ylim as fixed reference to prevent incremental movement
+                    # This ensures that repeated 'z' commands don't cause drift
+                    # Store it only once on first call, then reuse
+                    if not hasattr(ax, '_cif_initial_ylim'):
+                        ax._cif_initial_ylim = tuple(prev_ylim)
+                    fixed_ylim = ax._cif_initial_ylim
+                    fixed_yr = fixed_ylim[1] - fixed_ylim[0]
+                    if fixed_yr <= 0: fixed_yr = 1.0
+                    
                     # Check visibility flag first
                     show_titles_local = bool(show_cif_titles)  # Use closure variable from outer scope
                     # Also check figure attribute and module attribute as fallback
@@ -2356,38 +2422,53 @@ def batplot_main() -> int:
                             show_titles_local = bool(getattr(_bp_module, 'show_cif_titles', show_titles_local))
                     except Exception:
                         pass
-                    # Calculate base and spacing based on original y-axis limits
+                    
+                    # Check hkl visibility - check __main__ module first (where interactive menu stores it)
+                    # then fall back to closure variable
+                    show_hkl_local = False
+                    try:
+                        _bp_module = sys.modules.get('__main__')
+                        if _bp_module is not None and hasattr(_bp_module, 'show_cif_hkl'):
+                            show_hkl_local = bool(getattr(_bp_module, 'show_cif_hkl', False))
+                    except Exception:
+                        pass
+                    # Fall back to closure variable if not found in module
+                    if not show_hkl_local:
+                        try:
+                            show_hkl_local = bool(show_cif_hkl)
+                        except Exception:
+                            pass
+                    
+                    # Calculate base and spacing based on FIXED y-axis limits (not current)
+                    # This prevents incremental movement when toggling
                     if saved_stack or len(y_data_list) > 1:
-                        global_min = min(float(a.min()) for a in y_data_list if len(a)) if y_data_list else orig_ylim[0]
-                        base = global_min - 0.08*orig_yr; spacing = 0.05*orig_yr
+                        global_min = min(float(a.min()) for a in y_data_list if len(a)) if y_data_list else fixed_ylim[0]
+                        base = global_min - 0.08*fixed_yr; spacing = 0.05*fixed_yr
                     else:
                         global_min = min(float(a.min()) for a in y_data_list if len(a)) if y_data_list else 0.0
-                        base = global_min - 0.06*orig_yr; spacing = 0.04*orig_yr
+                        base = global_min - 0.06*fixed_yr; spacing = 0.04*fixed_yr
+                    
                     # Only adjust y-axis limits if titles are visible
-                    needed_min = base - (len(cif_tick_series)-1)*spacing - 0.04*orig_yr
+                    needed_min = base - (len(cif_tick_series)-1)*spacing - 0.04*fixed_yr
+                    if show_titles_local and needed_min < fixed_ylim[0]:
+                        # Expand y-axis only if needed, using fixed limits as reference
+                        ax.set_ylim(needed_min, fixed_ylim[1])
+                    else:
+                        # Restore to fixed limits if no expansion needed
+                        ax.set_ylim(fixed_ylim)
+                    
+                    # Get current limits for drawing (after potential expansion)
                     cur_ylim = ax.get_ylim()
                     yr = cur_ylim[1] - cur_ylim[0]
                     if yr <= 0: yr = 1.0
-                    if show_titles_local and needed_min < orig_ylim[0]:
-                        # Expand y-axis only if needed, using original limits as reference
-                        ax.set_ylim(needed_min, orig_ylim[1])
-                        cur_ylim = ax.get_ylim()
-                        yr = cur_ylim[1] - cur_ylim[0]
-                        if yr <= 0: yr = 1.0
-                        # Recalculate base with new limits if we expanded
-                        if saved_stack or len(y_data_list) > 1:
-                            global_min = min(float(a.min()) for a in y_data_list if len(a)) if y_data_list else cur_ylim[0]
-                            base = global_min - 0.08*yr; spacing = 0.05*yr
-                        else:
-                            global_min = min(float(a.min()) for a in y_data_list if len(a)) if y_data_list else 0.0
-                            base = global_min - 0.06*yr; spacing = 0.04*yr
+                    
                     # Clear previous artifacts
                     for art in getattr(ax, '_cif_tick_art', []):
                         try: art.remove()
                         except Exception: pass
                     new_art = []
-                    show_hkl_local = bool(show_cif_hkl)
                     wl_any = _session_ensure_wavelength()
+                    
                     # Draw each series
                     for i,(lab,fname,peaksQ,wl,qmax_sim,color) in enumerate(cif_tick_series):
                         y_line = base - i*spacing
@@ -2401,12 +2482,18 @@ def batplot_main() -> int:
                         xlow,xhigh = ax.get_xlim()
                         domain_peaks = [p for p in domain_peaks if xlow <= p <= xhigh]
                         # Build hkl label map (keys are Q values, not 2θ)
-                        label_map = cif_hkl_label_map.get(fname, {}) if show_hkl_local else {}
+                        # Only use label_map if hkl labels are enabled
+                        label_map = {}
+                        if show_hkl_local:
+                            label_map = cif_hkl_label_map.get(fname, {})
                         if show_hkl_local and len(domain_peaks) > 4000:
                             show_hkl_local = False  # safety
+                            label_map = {}  # Clear label map if too many peaks
                         for p in domain_peaks:
+                            # Use color from tuple (preserved from session)
                             ln, = ax.plot([p,p],[y_line, y_line+0.02*yr], color=color, lw=1.0, alpha=0.9, zorder=3)
                             new_art.append(ln)
+                            # Only show hkl labels if explicitly enabled
                             if show_hkl_local:
                                 # When axis is 2θ convert back to Q to look up hkl label
                                 if use_2th and (wl or wl_any):
@@ -2414,28 +2501,35 @@ def batplot_main() -> int:
                                     Qp = 4*np.pi*np.sin(theta)/(wl if wl is not None else wl_any)
                                 else:
                                     Qp = p
-                                lbl = label_map.get(round(Qp,6))
+                                Qp_rounded = round(Qp, 6)
+                                lbl = label_map.get(Qp_rounded)
                                 if lbl:
+                                    # Use same color as tick line
                                     t_hkl = ax.text(p, y_line+0.022*yr, lbl, ha='center', va='bottom', fontsize=7, rotation=90, color=color)
                                     new_art.append(t_hkl)
-                        # Removed numbering prefix; keep one leading space for padding from axis
                         # Only add title label if show_cif_titles is True
                         if show_titles_local:
                             label_text = f" {lab}"
+                            # Use color from tuple (preserved from session)
                             txt = ax.text(prev_xlim[0], y_line+0.005*yr, label_text,
                                           ha='left', va='bottom', fontsize=max(8,int(0.55*plt.rcParams.get('font.size',16))), color=color)
                             new_art.append(txt)
                     ax._cif_tick_art = new_art
-                    # Restore both x and y-axis limits to prevent movement
+                    # Restore x-axis limits
                     ax.set_xlim(prev_xlim)
                     # Restore y-axis: if titles are hidden, always restore; if titles are shown, only restore if we didn't need to expand
+                    # Use prev_ylim (current limits before drawing) to prevent any movement
                     if not show_titles_local:
                         # Titles hidden: always restore original limits
                         ax.set_ylim(prev_ylim)
                     elif needed_min >= prev_ylim[0]:
                         # Titles shown but no expansion needed: restore original limits
                         ax.set_ylim(prev_ylim)
-                    # Otherwise, keep the expanded limits (already set above)
+                    else:
+                        # Expansion needed: use the minimum of needed_min and prev_ylim[0] to prevent incremental growth
+                        # This ensures that repeated toggles don't cause drift
+                        new_ymin = min(needed_min, prev_ylim[0])
+                        ax.set_ylim(new_ymin, prev_ylim[1])
                     fig.canvas.draw_idle()
                 except Exception:
                     pass
@@ -2547,20 +2641,34 @@ def batplot_main() -> int:
             except Exception:
                 pass
     
+        # Prepare CIF globals for interactive menu (ensures CIF commands are available)
+        cif_globals_dict = None
+        if cif_tick_series:
+            cif_globals_dict = {
+                'cif_tick_series': list(cif_tick_series),
+                'cif_hkl_map': cif_hkl_map,
+                'cif_hkl_label_map': cif_hkl_label_map,
+                'show_cif_hkl': bool(show_cif_hkl),
+                'show_cif_titles': bool(show_cif_titles),
+                'cif_extend_suspended': False,
+                'keep_canvas_fixed': True,
+            }
+        
         interactive_menu(fig, ax, y_data_list, x_data_list, labels_list,
                          orig_y, label_text_objects, delta, x_label, args,
                          x_full_list, raw_y_full_list, offsets_list,
-                         use_Q, use_r, use_E, use_k, use_rft)
+                         use_Q, use_r, use_E, use_k, use_rft,
+                         cif_globals=cif_globals_dict)
         plt.show()
         exit()
 
     # ---------------- Handle conversion ----------------
     if args.convert:
-        if args.wl is None:
-            print("Error: --wl is required for --convert")
-       
+        if not args.files:
+            print("Error: --convert requires file(s) to convert")
             exit(1)
-        convert_to_qye(args.convert, args.wl)
+        from_param, to_param = args.convert
+        convert_xrd_data(args.files, from_param, to_param)
         exit()
 
     # ---------------- Plotting ----------------
@@ -2947,6 +3055,19 @@ def batplot_main() -> int:
         # ---- Store full (converted) arrays BEFORE cropping ----
         x_full = x_plot.copy()
         y_full_raw = y.copy()
+        
+        # ---- Calculate first derivative if requested ----
+        if getattr(args, 'derivative_1d', False) or getattr(args, 'derivative_2d', False):
+            # Calculate dy/dx using numpy gradient
+            # numpy.gradient handles non-uniform spacing automatically
+            if len(y_full_raw) > 1:
+                dy_dx = np.gradient(y_full_raw, x_full)
+                y_full_raw = dy_dx
+            else:
+                # Single point or empty - cannot calculate derivative
+                print(f"Warning: Cannot calculate derivative for {fname}: insufficient data points")
+                continue
+        
         raw_y_full_list.append(y_full_raw)
         x_full_list.append(x_full)
 
@@ -3180,13 +3301,20 @@ def batplot_main() -> int:
     def draw_cif_ticks():
         if not cif_tick_series:
             return
-        # Preserve both x and y-axis limits to prevent movement when toggling
+        # Preserve current limits before drawing - use actual current limits
+        # to prevent any movement when toggling
         prev_xlim = ax.get_xlim()
         prev_ylim = ax.get_ylim()
-        # Use preserved y-axis limits for calculations to prevent incremental movement
-        orig_ylim = prev_ylim
-        orig_yr = orig_ylim[1] - orig_ylim[0]
-        if orig_yr <= 0: orig_yr = 1.0
+        
+        # Store initial limits as fixed reference point to prevent incremental movement
+        # This ensures that repeated 'z' commands don't cause drift
+        # Only set once on first call, then reuse to prevent drift
+        if not hasattr(ax, '_cif_initial_ylim'):
+            ax._cif_initial_ylim = tuple(prev_ylim)
+        fixed_ylim = ax._cif_initial_ylim
+        fixed_yr = fixed_ylim[1] - fixed_ylim[0]
+        if fixed_yr <= 0: fixed_yr = 1.0
+        
         # Check visibility flag first to decide if we need to adjust y-axis
         show_titles = show_cif_titles  # Use closure variable
         try:
@@ -3199,38 +3327,50 @@ def batplot_main() -> int:
                 show_titles = bool(getattr(fig, '_bp_show_cif_titles', True))
         except Exception:
             pass
-        # Calculate base and spacing based on original y-axis limits
+        
+        # Calculate base and spacing based on FIXED y-axis limits (not current)
+        # This prevents incremental movement when toggling
         if args.stack or len(y_data_list) > 1:
-            global_min = min(float(a.min()) for a in y_data_list if len(a)) if y_data_list else orig_ylim[0]
-            base = global_min - 0.08*orig_yr; spacing = 0.05*orig_yr
+            global_min = min(float(a.min()) for a in y_data_list if len(a)) if y_data_list else fixed_ylim[0]
+            base = global_min - 0.08*fixed_yr; spacing = 0.05*fixed_yr
         else:
             global_min = min(float(a.min()) for a in y_data_list if len(a)) if y_data_list else 0.0
-            base = global_min - 0.06*orig_yr; spacing = 0.04*orig_yr
+            base = global_min - 0.06*fixed_yr; spacing = 0.04*fixed_yr
+        
         # Only adjust y-axis limits if titles are visible
-        needed_min = base - (len(cif_tick_series)-1)*spacing - 0.04*orig_yr
+        needed_min = base - (len(cif_tick_series)-1)*spacing - 0.04*fixed_yr
+        if show_titles and needed_min < fixed_ylim[0]:
+            # Expand y-axis only if needed, using fixed limits as reference
+            ax.set_ylim(needed_min, fixed_ylim[1])
+        else:
+            # Restore to fixed limits if no expansion needed
+            ax.set_ylim(fixed_ylim)
+        
+        # Get current limits for drawing (after potential expansion)
         cur_ylim = ax.get_ylim()
         yr = cur_ylim[1] - cur_ylim[0]
         if yr <= 0: yr = 1.0
-        if show_titles and needed_min < orig_ylim[0]:
-            # Expand y-axis only if needed, using original limits as reference
-            ax.set_ylim(needed_min, orig_ylim[1])
-            cur_ylim = ax.get_ylim()
-            yr = cur_ylim[1] - cur_ylim[0]
-            if yr <= 0: yr = 1.0
-            # Recalculate base with new limits if we expanded
-            if args.stack or len(y_data_list) > 1:
-                global_min = min(float(a.min()) for a in y_data_list if len(a)) if y_data_list else cur_ylim[0]
-                base = global_min - 0.08*yr; spacing = 0.05*yr
-            else:
-                global_min = min(float(a.min()) for a in y_data_list if len(a)) if y_data_list else 0.0
-                base = global_min - 0.06*yr; spacing = 0.04*yr
         # Clear previous
         for art in getattr(ax, '_cif_tick_art', []):
             try: art.remove()
             except Exception: pass
         new_art = []
         mixed_mode = (not cif_only)  # cif_only variable defined earlier in script context
-        show_hkl = globals().get('show_cif_hkl', False)
+        # Check hkl visibility - check __main__ module first (where interactive menu stores it)
+        # then fall back to closure variable
+        show_hkl = False
+        try:
+            _bp_module = sys.modules.get('__main__')
+            if _bp_module is not None and hasattr(_bp_module, 'show_cif_hkl'):
+                show_hkl = bool(getattr(_bp_module, 'show_cif_hkl', False))
+        except Exception:
+            pass
+        # Fall back to closure variable if not found in module
+        if not show_hkl:
+            try:
+                show_hkl = bool(globals().get('show_cif_hkl', False))
+            except Exception:
+                pass
         for i,(lab, fname, peaksQ, wl, qmax_sim, color) in enumerate(cif_tick_series):
             y_line = base - i*spacing
             if use_2th:
@@ -3252,14 +3392,12 @@ def batplot_main() -> int:
                                   ha='left', va='bottom', fontsize=max(8,int(0.55*plt.rcParams.get('font.size',12))), color=color)
                     new_art.append(txt)
                 continue
-            # Build map for quick hkl lookup by Q
-            hkl_entries = cif_hkl_map.get(fname, [])
-            # dictionary keyed by Q value
-            hkl_by_q = {}
-            for qval,h,k,l in hkl_entries:
-                hkl_by_q.setdefault(qval, []).append((h,k,l))
-            label_map = cif_hkl_label_map.get(fname, {})
+            # Build map for quick hkl lookup by Q (only if hkl labels are enabled)
+            label_map = {}
+            if show_hkl:
+                label_map = cif_hkl_label_map.get(fname, {})
             # --- Optimized tick & hkl label drawing ---
+            # Check if we should show hkl labels: need show_hkl, peaks, AND a non-empty label_map
             if show_hkl and peaksQ and label_map:
                 # Guard against pathological large peak lists (can freeze UI)
                 if len(peaksQ) > 4000 or len(domain_peaks) > 4000:
@@ -3282,7 +3420,8 @@ def batplot_main() -> int:
                         Qp = 4*np.pi*np.sin(theta)/wl
                     else:
                         Qp = p
-                    lbl = label_map.get(round(Qp,6))
+                    Qp_rounded = round(Qp, 6)
+                    lbl = label_map.get(Qp_rounded)
                     if lbl:
                         t_hkl = ax.text(p, y_line+0.022*yr, lbl, ha='center', va='bottom', fontsize=7, rotation=90, color=color)
                         new_art.append(t_hkl)
@@ -3308,7 +3447,11 @@ def batplot_main() -> int:
         elif needed_min >= prev_ylim[0]:
             # Titles shown but no expansion needed: restore original limits
             ax.set_ylim(prev_ylim)
-        # Otherwise, keep the expanded limits (already set above)
+        else:
+            # Expansion needed: use the minimum of needed_min and prev_ylim[0] to prevent incremental growth
+            # This ensures that repeated toggles don't cause drift
+            new_ymin = min(needed_min, prev_ylim[0])
+            ax.set_ylim(new_ymin, prev_ylim[1])
         # Store simplified metadata for hover: list of dicts with 'x','y','label'
         hover_meta = []
         show_hkl = globals().get('show_cif_hkl', False)

batplot/cli.py

@@ -59,6 +59,20 @@ def main(argv: Optional[list] = None) -> int:
 		>>> main()
 		0
 	"""
+	# ====================================================================
+	# STEP 0: PYTHON VERSION CHECK
+	# ====================================================================
+	# Check if Python version is 3.13 (required for batplot)
+	# ====================================================================
+	if sys.version_info.major != 3 or sys.version_info.minor != 13:
+		current_version = f"{sys.version_info.major}.{sys.version_info.minor}.{sys.version_info.micro}"
+		print(f"\n⚠️  WARNING: Python version mismatch detected!")
+		print(f"   batplot requires Python 3.13")
+		print(f"   Currently running: Python {current_version}")
+		print(f"\n   This may cause compatibility issues.")
+		print(f"   Please install Python 3.13 and use it to run batplot.")
+		print(f"   Continuing anyway, but expect potential issues...\n")
+	
 	# ====================================================================
 	# STEP 1: VERSION CHECK (NON-BLOCKING)
 	# ====================================================================