batplot 1.8.5__tar.gz → 1.8.8__tar.gz

{batplot-1.8.5/batplot.egg-info → batplot-1.8.8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: batplot
-Version: 1.8.5
+Version: 1.8.8
 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: MIT License

{batplot-1.8.5 → batplot-1.8.8}/batplot/__init__.py

@@ -1,5 +1,5 @@
 """batplot: Interactive plotting for battery data visualization."""
 
-__version__ = "1.8.5"
+__version__ = "1.8.8"
 
 __all__ = ["__version__"]

{batplot-1.8.5 → batplot-1.8.8}/batplot/batplot.py

@@ -422,7 +422,10 @@ def batplot_main() -> int:
                 # Ensure font and canvas settings match GC/dQdV
                 _plt.rcParams.update({
                     'font.family': 'sans-serif',
-                    'font.sans-serif': ['Arial', 'DejaVu Sans', 'Helvetica', 'STIXGeneral', 'Liberation Sans', 'Arial Unicode MS'],
+                    # Prefer DejaVu Sans first because it has good Unicode
+                    # coverage (including subscript/superscript digits), then
+                    # fall back to other common sans-serif fonts.
+                    'font.sans-serif': ['DejaVu Sans', 'Arial', 'Helvetica', 'STIXGeneral', 'Liberation Sans', 'Arial Unicode MS'],
                     'mathtext.fontset': 'dejavusans',
                     'font.size': 16
                 })
@@ -616,8 +619,10 @@ def batplot_main() -> int:
     # Set global default font
     plt.rcParams.update({
         'font.family': 'sans-serif',
-        'font.sans-serif': ['Arial', 'DejaVu Sans', 'Helvetica', 'STIXGeneral', 'Liberation Sans', 'Arial Unicode MS'],
-        'mathtext.fontset': 'dejavusans',   # keeps math consistent with Arial-like sans
+        # Use DejaVu Sans first to ensure good Unicode coverage (subscripts,
+        # superscripts, Greek, etc.), then fall back to other common fonts.
+        'font.sans-serif': ['DejaVu Sans', 'Arial', 'Helvetica', 'STIXGeneral', 'Liberation Sans', 'Arial Unicode MS'],
+        'mathtext.fontset': 'dejavusans',   # keeps math consistent with sans-serif
         'font.size': 16
     })
 
@@ -1165,11 +1170,9 @@ def batplot_main() -> int:
                     print(f"Skipped {file_basename}: unsupported format (must be .csv, .xlsx, or .mpt)")
                     continue
                 
-                # Assign colors: distinct hue for each file
+                # Assign colors: distinct hue per file
                 capacity_color = capacity_colors[file_idx % len(capacity_colors)]
                 efficiency_color = efficiency_colors[file_idx % len(efficiency_colors)]
-                # Generate discharge color using the same function as interactive menu
-                discharge_color = _generate_similar_color(capacity_color)
                 
                 file_data.append({
                     'filename': file_basename,
@@ -1179,7 +1182,6 @@ def batplot_main() -> int:
                     'cap_discharge': cap_discharge,
                     'eff': eff,
                     'color': capacity_color,
-                    'discharge_color': discharge_color,
                     'eff_color': efficiency_color,
                     'visible': True
                 })
@@ -1207,7 +1209,7 @@ def batplot_main() -> int:
             cap_charge = file_info['cap_charge']
             cap_discharge = file_info['cap_discharge']
             eff = file_info['eff']
-            color = file_info['color']  # Warm color for capacity
+            color = file_info['color']  # Base color for capacity (both charge/discharge)
             eff_color = file_info['eff_color']  # Cold color for efficiency
             label = file_info['filename']
             
@@ -1221,16 +1223,30 @@ def batplot_main() -> int:
                 label_dch = f'{label} (Dch)'
                 label_eff = f'{label} (Eff)'
             
-            # Use stored discharge color if available, otherwise generate it
-            if 'discharge_color' in file_info and file_info['discharge_color'] is not None:
-                discharge_color = file_info['discharge_color']
-            else:
-                discharge_color = _generate_similar_color(color)
-            
-            sc_charge = ax.scatter(cyc_nums, cap_charge, color=color, label=label_chg, 
-                                  s=32, zorder=3, alpha=0.8, marker='o')
-            sc_discharge = ax.scatter(cyc_nums, cap_discharge, color=discharge_color, label=label_dch, 
-                                     s=32, zorder=3, alpha=0.8, marker='s')
+            # Capacity curves: same color, different fill style
+            # - Charge: filled square
+            # - Discharge: hollow square (edge only)
+            sc_charge = ax.scatter(
+                cyc_nums,
+                cap_charge,
+                label=label_chg,
+                s=32,
+                zorder=3,
+                alpha=0.8,
+                marker='s',
+                color=color,
+            )
+            sc_discharge = ax.scatter(
+                cyc_nums,
+                cap_discharge,
+                label=label_dch,
+                s=32,
+                zorder=3,
+                alpha=0.8,
+                marker='s',
+                facecolor='none',
+                edgecolor=color,
+            )
             sc_eff = ax2.scatter(cyc_nums, eff, color=eff_color, marker='^', label=label_eff, 
                                s=40, alpha=0.7, zorder=3)
             
@@ -1247,27 +1263,25 @@ def batplot_main() -> int:
             h1, l1 = ax.get_legend_handles_labels()
             h2, l2 = ax2.get_legend_handles_labels()
             combined_handles = h1 + h2
-            leg = ax.legend(
-                combined_handles, l1 + l2,
-                loc='best',
-                frameon=False,
-                handlelength=1.0,
-                handletextpad=0.35,
-                labelspacing=0.25,
-                borderaxespad=0.5,
-                borderpad=0.3,
-                columnspacing=0.6,
-                labelcolor='linecolor',
-            )
-            if leg is not None:
-                try:
-                    leg.set_frame_on(False)
-                    leg.set_edgecolor('none')
-                    leg.set_facecolor('none')
-                except Exception:
-                    pass
-        except Exception:
-            pass
+            combined_labels = l1 + l2
+            if combined_handles:
+                # Don't use labelcolor='linecolor' for scatter plots with hollow markers
+                # as it causes issues with color extraction
+                leg = ax.legend(
+                    combined_handles, combined_labels,
+                    loc='best',
+                    frameon=False,
+                    handlelength=1.0,
+                    handletextpad=0.35,
+                    labelspacing=0.25,
+                    borderaxespad=0.5,
+                    borderpad=0.3,
+                    columnspacing=0.6,
+                )
+        except Exception as e:
+            print(f"Warning: Could not create CPC legend: {e}")
+            import traceback
+            traceback.print_exc()
 
         # Adjust layout to ensure top and bottom labels/titles are visible
         fig.subplots_adjust(left=0.12, right=0.88, top=0.88, bottom=0.15)
@@ -1842,6 +1856,11 @@ def batplot_main() -> int:
                     _plt.show(block=False)
                 except Exception:
                     pass
+                # Seed last-session path so 'os' overwrite command is available immediately
+                try:
+                    fig._last_session_save_path = os.path.abspath(sess_path)
+                except Exception:
+                    pass
                 try:
                     source_list = list(getattr(fig, '_bp_source_paths', []) or [])
                     sess_abs = os.path.abspath(sess_path)
@@ -1877,6 +1896,11 @@ def batplot_main() -> int:
                     _plt.show(block=False)
                 except Exception:
                     pass
+                # Seed last-session path so 'os' overwrite command is available immediately
+                try:
+                    fig2._last_session_save_path = os.path.abspath(sess_path)
+                except Exception:
+                    pass
                 try:
                     if operando_ec_interactive_menu is not None:
                         operando_ec_interactive_menu(fig2, ax2, im2, cbar2, ec_ax2)
@@ -1905,6 +1929,11 @@ def batplot_main() -> int:
                     _plt.show(block=False)
                 except Exception:
                     pass
+                # Seed last-session path so 'os' overwrite command is available immediately
+                try:
+                    fig_c._last_session_save_path = os.path.abspath(sess_path)
+                except Exception:
+                    pass
                 try:
                     if cpc_interactive_menu is not None:
                         cpc_interactive_menu(fig_c, ax_c, ax2_c, sc_c, sc_d, sc_e, file_data=file_data)
@@ -2207,6 +2236,14 @@ def batplot_main() -> int:
                 fig._tick_lengths['minor'] = minor_len
         except Exception:
             pass
+        # Tick direction restore (t submenu)
+        try:
+            tick_direction = sess.get('tick_direction', 'out')
+            if tick_direction:
+                setattr(fig, '_tick_direction', tick_direction)
+                ax.tick_params(axis='both', which='both', direction=tick_direction)
+        except Exception:
+            pass
         
         # Restore WASD state (spine, ticks, labels, title visibility for all 4 sides)
         try:
@@ -2675,8 +2712,24 @@ def batplot_main() -> int:
     offset = 0.0
     direction = -1 if args.stack else 1  # stack downward
     if args.interactive:
+        # Interactive: keep a reasonably compact default size so the window
+        # fits well on most screens; margins are handled by the menu logic.
         plt.ion()
-    fig, ax = plt.subplots(figsize=(8, 6))
+        figsize = (8, 6)
+    else:
+        # Non-interactive (no --i): use a slightly larger canvas so that labels,
+        # titles, legends, and CIF ticks are not clipped even with long filenames.
+        # The size (9, 6.4) keeps a similar aspect ratio but with a bit more room
+        # than the interactive default while still fitting comfortably on screen.
+        figsize = (9.5, 6.4)
+    fig, ax = plt.subplots(figsize=figsize)
+    
+    # Set consistent margins for all modes.
+    # This prevents labels/titles from being cut off at the edges.
+    try:
+        fig.subplots_adjust(left=0.125, right=0.9, top=0.88, bottom=0.11)
+    except Exception:
+        pass
 
     y_data_list = []
     x_data_list = []
@@ -2710,7 +2763,17 @@ def batplot_main() -> int:
         any_cif = any(f.lower().endswith(".cif") for f in args.files)
         non_cif_count = sum(0 if f.lower().endswith('.cif') else 1 for f in args.files)
         cif_only = any_cif and non_cif_count == 0
-        any_lambda = any(":" in f for f in args.files) or args.wl is not None
+        # Check for wavelength parameters (file:wl), but exclude Windows drive letters (C:\...)
+        def has_wavelength_param(f):
+            if ":" not in f:
+                return False
+            # Check if it's a Windows path (single letter followed by :\ or :/)
+            if len(f) >= 2 and f[1] == ':' and len(f[0]) == 1 and f[0].isalpha():
+                # This is a Windows drive letter, check after the drive path
+                # Look for additional colons beyond the drive letter
+                return ":" in f[2:]
+            return True
+        any_lambda = any(has_wavelength_param(f) for f in args.files) or args.wl is not None
 
         # Incompatibilities (no mixing of fundamentally different axis domains)
         if sum(bool(x) for x in (any_gr, any_nor, any_chik, any_chir, (any_qye or any_lambda or any_cif))) > 1:
@@ -2730,7 +2793,8 @@ def batplot_main() -> int:
         elif any_txt:
             # .txt is generic, require --xaxis
             if args.xaxis:
-                axis_mode = args.xaxis
+                # Normalize case: 'q' or 'Q' → 'Q' (uppercase), everything else lowercase
+                axis_mode = "Q" if args.xaxis.upper() == "Q" else args.xaxis.lower()
             else:
                 raise ValueError("Unknown file type. Use: batplot file.txt --xaxis [Q|2theta|r|k|energy|rft] or batplot -h for help.")
         elif any_lambda or any_cif:
@@ -2741,7 +2805,8 @@ def batplot_main() -> int:
                 # CIF files are in Q space
                 axis_mode = "Q"
         elif args.xaxis:
-            axis_mode = args.xaxis
+            # Normalize case: 'q' or 'Q' → 'Q' (uppercase), everything else lowercase
+            axis_mode = "Q" if args.xaxis.upper() == "Q" else args.xaxis.lower()
         else:
             raise ValueError("Unknown file type. Use: batplot file.csv --xaxis [Q|2theta|r|k|energy|rft] or batplot -h for help.")
 
@@ -2841,8 +2906,16 @@ def batplot_main() -> int:
     
     # Use data_files instead of args.files for processing
     for idx_file, file_entry in enumerate(data_files):
+        # Handle Windows paths (C:\...) vs wavelength parameters (file:wl)
+        # On Windows, check if first part is a single letter (drive letter)
         parts = file_entry.split(":")
-        fname = parts[0]
+        if len(parts) > 1 and len(parts[0]) == 1 and parts[0].isalpha():
+            # Windows drive letter detected (e.g., "C" from "C:\path")
+            # Rejoin the first two parts as the filename
+            fname = parts[0] + ":" + parts[1]
+            parts = [fname] + parts[2:]  # Reconstruct parts with full Windows path
+        else:
+            fname = parts[0]
         # Parse wavelength parameters: file:wl1 or file:wl1:wl2 or file.cif:wl
         wavelength_file = None
         original_wavelength = None  # First wavelength (for Q conversion)
@@ -3532,19 +3605,36 @@ def batplot_main() -> int:
             ax._cif_hover_cid = cid
 
     if cif_tick_series:
-        # Auto-assign distinct colors if all are default 'k'
+        # Auto-assign distinct colors for CIF tick series.
+        # For multiple CIF series:
+        #   - If <= 10 files, use 'tab10' but in a re-ordered sequence to
+        #     maximize visual separation between adjacent colors.
+        #   - If > 10 files, use 'viridis' with evenly spaced samples.
+        #
+        # This overrides any previous per-series color so that the requested
+        # colormap behavior is always enforced.
         if len(cif_tick_series) > 1:
-            if all(c[-1] == 'k' for c in cif_tick_series):
-                try:
-                    cmap_name = 'tab10' if len(cif_tick_series) <= 10 else 'hsv'
-                    cmap = plt.get_cmap(cmap_name)
+            try:
+                n_cif = len(cif_tick_series)
+                if n_cif <= 10:
+                    tab10 = plt.get_cmap('tab10').colors
+                    # Reorder indices for more distinct neighboring colors
+                    order = [0, 3, 6, 1, 4, 7, 2, 5, 8, 9]
                     new_series = []
-                    for i,(lab,fname,peaksQ,wl,qmax_sim,col) in enumerate(cif_tick_series):
-                        color = cmap(i / max(1,(len(cif_tick_series)-1)))
-                        new_series.append((lab,fname,peaksQ,wl,qmax_sim,color))
-                    cif_tick_series[:] = new_series
-                except Exception:
-                    pass
+                    for i, (lab, fname, peaksQ, wl, qmax_sim, col) in enumerate(cif_tick_series):
+                        idx = order[i] if i < len(order) else i % len(tab10)
+                        color = tab10[idx]
+                        new_series.append((lab, fname, peaksQ, wl, qmax_sim, color))
+                else:
+                    cmap = plt.get_cmap('viridis')
+                    positions = np.linspace(0.0, 1.0, n_cif)
+                    new_series = []
+                    for (pos, (lab, fname, peaksQ, wl, qmax_sim, col)) in zip(positions, cif_tick_series):
+                        color = cmap(pos)
+                        new_series.append((lab, fname, peaksQ, wl, qmax_sim, color))
+                cif_tick_series[:] = new_series
+            except Exception:
+                pass
         if use_2th:
             _ensure_wavelength_for_2theta()
         draw_cif_ticks()