batplot 1.1.8__tar.gz → 1.3.0__tar.gz

{batplot-1.1.8 → batplot-1.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: batplot
-Version: 1.1.8
+Version: 1.3.0
 Summary: Interactive plotting for XRD, PDF, and XAS data (.xye, .xy, .qye, .dat, .csv, .gr, .nor, .chik, .chir)
 Author-email: Tian Dai <tianda@uio.no>
 License: MIT License
@@ -107,6 +107,12 @@ batplot --gc all         # All .mpt/.csv files (.mpt needs --mass, .csv doesn't)
 batplot --cv all                    # All .mpt files (CV mode)
 batplot --dqdv all                  # All .csv files (dQdV mode)
 batplot --cpc all --mass 6.2        # All .mpt/.csv files (.mpt needs --mass, .csv doesn't)
+
+# Batch processing with style/geometry: apply consistent formatting to all files
+batplot --all mystyle.bps --gc --mass 7.0   # Apply .bps style to all GC files
+batplot --all config.bpsg --cv              # Apply .bpsg style+geometry to all CV files
+batplot --all style.bps --dqdv              # Apply style to all dQdV files
+batplot --all geom.bpsg --cpc --mass 5.4    # Apply style+geometry to all CPC files
 ```
 
 ### Operando Analysis

{batplot-1.1.8 → batplot-1.3.0}/README.md

@@ -58,6 +58,12 @@ batplot --gc all         # All .mpt/.csv files (.mpt needs --mass, .csv doesn't)
 batplot --cv all                    # All .mpt files (CV mode)
 batplot --dqdv all                  # All .csv files (dQdV mode)
 batplot --cpc all --mass 6.2        # All .mpt/.csv files (.mpt needs --mass, .csv doesn't)
+
+# Batch processing with style/geometry: apply consistent formatting to all files
+batplot --all mystyle.bps --gc --mass 7.0   # Apply .bps style to all GC files
+batplot --all config.bpsg --cv              # Apply .bpsg style+geometry to all CV files
+batplot --all style.bps --dqdv              # Apply style to all dQdV files
+batplot --all geom.bpsg --cpc --mass 5.4    # Apply style+geometry to all CPC files
 ```
 
 ### Operando Analysis

{batplot-1.1.8 → batplot-1.3.0}/batplot/__init__.py

@@ -1,6 +1,6 @@
 """batplot package."""
 
 # Skip version check to avoid OneDrive timeout issues
-__version__ = "1.0.18"
+__version__ = "1.3.0"
 
 __all__ = ["__version__"]

{batplot-1.1.8 → batplot-1.3.0}/batplot/args.py

@@ -23,6 +23,8 @@ def _print_general_help() -> None:
     "    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 in directory (.mpt needs --mass)\n"
+    "    batplot --all --gc style.bps --mass 7  # Batch with style: apply style.bps to all GC files\n"
+    "    batplot --all --cv config.bpsg         # Batch with style+geom: apply to all CV files\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"
@@ -34,7 +36,8 @@ def _print_general_help() -> None:
         "  • 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 'all' or directory path with any mode\n\n"
+        "  • Batch processing: use 'all' or directory path with any mode\n"
+        "  • Batch styling: apply .bps/.bpsg files to all exports (use --all flag)\n\n"
     
         "More help:\n"
         "  batplot -h xy   # XY file plotting guide\n"
@@ -93,6 +96,11 @@ def _print_ec_help() -> None:
         "  batplot --dqdv all                     # All .csv files (dQdV mode)\n"
         "  batplot --cpc all --mass 5.4           # All .mpt/.csv files (.mpt requires --mass)\n"
         "  batplot --gc /path/to/folder --mass 6  # Process specific directory\n\n"
+        "Batch mode with style/geometry: Apply .bps/.bpsg files to all batch exports.\n"
+        "  batplot --all --gc style.bps --mass 7  # Apply style to all GC plots\n"
+        "  batplot --all --cv config.bpsg         # Apply style+geometry to all CV plots\n"
+        "  batplot --all --dqdv my.bps            # Apply style to all dQdV plots\n"
+        "  batplot --all --cpc geom.bpsg --mass 6 # Apply style+geom to all CPC plots\n\n"
         "Interactive (--interactive): choose cycles, colors/palettes, line widths, axis scales (linear/log/symlog),\n"
         "rename axes, toggle ticks/titles/spines, print/export/import style (.bpcfg), save session (.pkl).\n"
         "Note: Batch mode exports SVG files automatically; --interactive is for single-file plotting only.\n"
@@ -139,6 +147,7 @@ def build_parser() -> argparse.ArgumentParser:
     parser.add_argument("--dqdv", action="store_true", help=argparse.SUPPRESS)
     parser.add_argument("--cv", action="store_true", help=argparse.SUPPRESS)
     parser.add_argument("--cpc", action="store_true", help=argparse.SUPPRESS)
+    parser.add_argument("--all", type=str, nargs='?', const='all', help=argparse.SUPPRESS)
     return parser
 
 

{batplot-1.1.8 → batplot-1.3.0}/batplot/batch.py

@@ -3,6 +3,7 @@
 from __future__ import annotations
 
 import os
+import json
 import numpy as np
 import matplotlib.pyplot as plt
 
@@ -16,6 +17,152 @@ from .readers import (
 from .utils import _confirm_overwrite
 
 
+def _load_style_file(style_path: str) -> dict | None:
+    """Load a .bps, .bpsg, or .bpcfg style file.
+    
+    Args:
+        style_path: Path to style configuration file
+        
+    Returns:
+        Style configuration dict or None if loading fails
+    """
+    try:
+        with open(style_path, 'r', encoding='utf-8') as f:
+            cfg = json.load(f)
+        return cfg
+    except Exception as e:
+        print(f"Warning: Could not load style file {style_path}: {e}")
+        return None
+
+
+def _apply_ec_style(fig, ax, cfg: dict):
+    """Apply style configuration to an EC batch plot.
+    
+    Applies formatting from .bps/.bpsg files including fonts, colors,
+    tick parameters, and geometry (if present in .bpsg files).
+    
+    Args:
+        fig: Matplotlib figure object
+        ax: Matplotlib axes object
+        cfg: Style configuration dictionary
+    """
+    try:
+        # Apply fonts
+        font_cfg = cfg.get('font', {})
+        if font_cfg:
+            family = font_cfg.get('family')
+            size = font_cfg.get('size')
+            if family:
+                plt.rcParams['font.sans-serif'] = [family] if isinstance(family, str) else family
+            if size is not None:
+                plt.rcParams['font.size'] = size
+        
+        # Apply figure size if present
+        fig_cfg = cfg.get('figure', {})
+        if fig_cfg:
+            canvas_size = fig_cfg.get('canvas_size')
+            if canvas_size and isinstance(canvas_size, (list, tuple)) and len(canvas_size) == 2:
+                try:
+                    fig.set_size_inches(canvas_size[0], canvas_size[1])
+                except Exception:
+                    pass
+        
+        # Apply tick parameters
+        ticks_cfg = cfg.get('ticks', {})
+        if ticks_cfg:
+            # Tick widths
+            widths = ticks_cfg.get('widths', {})
+            if widths.get('x_major') is not None:
+                ax.tick_params(axis='x', which='major', width=widths['x_major'])
+            if widths.get('x_minor') is not None:
+                ax.tick_params(axis='x', which='minor', width=widths['x_minor'])
+            if widths.get('y_major') is not None or widths.get('ly_major') is not None:
+                w = widths.get('y_major') or widths.get('ly_major')
+                ax.tick_params(axis='y', which='major', width=w)
+            if widths.get('y_minor') is not None or widths.get('ly_minor') is not None:
+                w = widths.get('y_minor') or widths.get('ly_minor')
+                ax.tick_params(axis='y', which='minor', width=w)
+            
+            # Tick lengths
+            lengths = ticks_cfg.get('lengths', {})
+            if lengths.get('major') is not None:
+                ax.tick_params(axis='both', which='major', length=lengths['major'])
+            if lengths.get('minor') is not None:
+                ax.tick_params(axis='both', which='minor', length=lengths['minor'])
+            
+            # Tick direction
+            direction = ticks_cfg.get('direction')
+            if direction:
+                ax.tick_params(axis='both', which='both', direction=direction)
+        
+        # Apply geometry if present (for .bpsg files)
+        kind = cfg.get('kind', '')
+        if 'geom' in kind.lower() and 'geometry' in cfg:
+            geom = cfg.get('geometry', {})
+            if geom.get('xlabel'):
+                ax.set_xlabel(geom['xlabel'])
+            if geom.get('ylabel'):
+                ax.set_ylabel(geom['ylabel'])
+            if 'xlim' in geom and isinstance(geom['xlim'], (list, tuple)) and len(geom['xlim']) == 2:
+                try:
+                    ax.set_xlim(geom['xlim'][0], geom['xlim'][1])
+                except Exception:
+                    pass
+            if 'ylim' in geom and isinstance(geom['ylim'], (list, tuple)) and len(geom['ylim']) == 2:
+                try:
+                    ax.set_ylim(geom['ylim'][0], geom['ylim'][1])
+                except Exception:
+                    pass
+        
+        # Apply line colors if available (for GC/CV/dQdV modes)
+        lines_cfg = cfg.get('lines', [])
+        if lines_cfg and len(ax.lines) > 0:
+            for entry in lines_cfg:
+                idx = entry.get('index')
+                if idx is not None and 0 <= idx < len(ax.lines):
+                    ln = ax.lines[idx]
+                    if 'color' in entry:
+                        try:
+                            ln.set_color(entry['color'])
+                        except Exception:
+                            pass
+                    if 'linewidth' in entry:
+                        try:
+                            ln.set_linewidth(entry['linewidth'])
+                        except Exception:
+                            pass
+                    if 'linestyle' in entry:
+                        try:
+                            ln.set_linestyle(entry['linestyle'])
+                        except Exception:
+                            pass
+        
+        # Apply spine configuration
+        spines_cfg = cfg.get('spines', {})
+        for spine_name, spine_props in spines_cfg.items():
+            if spine_name in ax.spines:
+                sp = ax.spines[spine_name]
+                if 'lw' in spine_props or 'linewidth' in spine_props:
+                    try:
+                        lw = spine_props.get('lw') or spine_props.get('linewidth')
+                        sp.set_linewidth(lw)
+                    except Exception:
+                        pass
+                if 'color' in spine_props:
+                    try:
+                        sp.set_edgecolor(spine_props['color'])
+                    except Exception:
+                        pass
+                if 'visible' in spine_props:
+                    try:
+                        sp.set_visible(spine_props['visible'])
+                    except Exception:
+                        pass
+        
+    except Exception as e:
+        print(f"Warning: Error applying style: {e}")
+
+
 def batch_process(directory: str, args):
     print(f"Batch mode: scanning {directory}")
     supported_ext = {'.xye', '.xy', '.qye', '.dat', '.csv', '.gr', '.nor', '.chik', '.chir', '.txt'}
@@ -168,15 +315,44 @@ def batch_process_ec(directory: str, args):
     Supports GC (.mpt/.csv), CV (.mpt), dQdV (.csv), and CPC (.mpt/.csv) modes.
     Exports SVG plots to batplot_svg subdirectory.
     
+    Can apply style/geometry from .bps/.bpsg files using --all flag:
+        batplot --all --gc style.bps       # Apply style.bps to all .mpt/.csv GC files
+        batplot --all --cv style.bpsg      # Apply style+geom to all CV files
+        batplot --all --dqdv mystyle.bps   # Apply style to all dQdV files
+        batplot --all --cpc config.bpsg    # Apply to all CPC files
+    
     Note: For GC and CPC modes with .csv files, --mass is not required as the
     capacity data is already in the file. For .mpt files, --mass is required.
     
     Args:
         directory: Directory containing EC files
-        args: Argument namespace with mode flags (gc, cv, dqdv, cpc) and mass
+        args: Argument namespace with mode flags (gc, cv, dqdv, cpc), mass, and all
     """
     print(f"EC Batch mode: scanning {directory}")
     
+    # Check if --all flag was used with a style file
+    style_cfg = None
+    style_file_arg = getattr(args, 'all', None)
+    if style_file_arg and style_file_arg != 'all':
+        # User provided a style file path
+        style_path = style_file_arg if os.path.isabs(style_file_arg) else os.path.join(directory, style_file_arg)
+        if os.path.exists(style_path) and style_path.lower().endswith(('.bps', '.bpsg', '.bpcfg')):
+            style_cfg = _load_style_file(style_path)
+            if style_cfg:
+                print(f"Using style file: {os.path.basename(style_path)}")
+        else:
+            # Try to find the file in current directory
+            for ext in ['.bps', '.bpsg', '.bpcfg']:
+                test_path = style_file_arg if style_file_arg.endswith(ext) else style_file_arg + ext
+                test_full = os.path.join(directory, test_path)
+                if os.path.exists(test_full):
+                    style_cfg = _load_style_file(test_full)
+                    if style_cfg:
+                        print(f"Using style file: {os.path.basename(test_full)}")
+                    break
+            if not style_cfg:
+                print(f"Warning: Could not find style file '{style_file_arg}'")
+    
     # Determine which EC mode is active
     mode = None
     if getattr(args, 'gc', False):
@@ -490,6 +666,13 @@ def batch_process_ec(directory: str, args):
                 ax_b.legend()
                 ax_b.set_title(f"{fname}")
             
+            # Apply style/geometry if provided via --all flag
+            if style_cfg:
+                try:
+                    _apply_ec_style(fig_b, ax_b, style_cfg)
+                except Exception as e:
+                    print(f"  Warning: Could not apply style to {fname}: {e}")
+            
             # Adjust layout and save
             fig_b.subplots_adjust(left=0.18, right=0.97, bottom=0.16, top=0.90)
             out_name = os.path.splitext(fname)[0] + f"_{mode}.svg"

{batplot-1.1.8 → batplot-1.3.0}/batplot/batplot.py

@@ -98,6 +98,11 @@ def batplot_main() -> int:
         getattr(args, 'cpc', False)
     ])
     
+    # Check for --all flag (with or without style file)
+    if ec_mode_active and getattr(args, 'all', None) is not None:
+        batch_process_ec(os.getcwd(), args)
+        exit()
+    
     if ec_mode_active and len(args.files) == 1:
         sole = args.files[0]
         if sole.lower() == 'all':
@@ -1362,6 +1367,23 @@ def batplot_main() -> int:
                 ax.tick_params(axis='y', which='minor', width=tw['y_minor'])
         except Exception:
             pass
+        # Tick lengths restore
+        try:
+            tl = sess.get('tick_lengths', {})
+            if tl.get('x_major') is not None or tl.get('y_major') is not None:
+                major_len = tl.get('x_major') or tl.get('y_major')
+                ax.tick_params(axis='both', which='major', length=major_len)
+                if not hasattr(fig, '_tick_lengths'):
+                    fig._tick_lengths = {}
+                fig._tick_lengths['major'] = major_len
+            if tl.get('x_minor') is not None or tl.get('y_minor') is not None:
+                minor_len = tl.get('x_minor') or tl.get('y_minor')
+                ax.tick_params(axis='both', which='minor', length=minor_len)
+                if not hasattr(fig, '_tick_lengths'):
+                    fig._tick_lengths = {}
+                fig._tick_lengths['minor'] = minor_len
+        except Exception:
+            pass
         # Rebuild label texts
         for i, lab in enumerate(labels_list):
             txt = ax.text(1.0, 1.0, f"{i+1}: {lab}", ha='right', va='top', transform=ax.transAxes,
@@ -1374,6 +1396,7 @@ def batplot_main() -> int:
         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)
         # 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')
@@ -1652,6 +1675,8 @@ def batplot_main() -> int:
         if args.xaxis and args.xaxis.lower() in ("2theta","two_theta","tth"):
             axis_mode = "2theta"
         else:
+            # If wavelength is provided, user wants to convert to Q
+            # CIF files are in Q space
             axis_mode = "Q"
     elif args.xaxis:
         axis_mode = args.xaxis
@@ -1665,6 +1690,16 @@ def batplot_main() -> int:
     use_k   = axis_mode == "k"      # NEW
     use_rft = axis_mode == "rft"    # NEW
 
+    # Validate: if using 2theta mode with CIF files, wavelength is required
+    if use_2th and any_cif and not wavelength_file:
+        raise ValueError(
+            "Cannot display CIF files in 2θ mode without wavelength.\n"
+            "Please provide wavelength using:\n"
+            "  --wl <wavelength_in_angstrom>\n"
+            "  or include wavelength in filename (e.g., data_wl1.5406.xy)\n"
+            "  or use Q mode (remove --xaxis 2theta)"
+        )
+
     # ---------------- Read and plot files ----------------
     # Helper to extract discrete peak positions from a simulated CIF pattern by local maxima picking
     def _extract_peak_positions(Q_array, I_array, min_rel_height=0.05):
@@ -1702,6 +1737,7 @@ def batplot_main() -> int:
     # Cached wavelength for CIF tick conversion (prevents interactive blocking prompts)
     cif_cached_wavelength = None
     show_cif_hkl = False
+    show_cif_titles = True  # show CIF filename labels by default
 
     for idx_file, file_entry in enumerate(args.files):
         parts = file_entry.split(":")
@@ -2058,10 +2094,12 @@ def batplot_main() -> int:
                     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)
             # Removed numbering; keep space padding (placed per CIF row)
-            label_text = f" {lab}"
-            txt = ax.text(ax.get_xlim()[0], y_line + 0.005*yr, label_text,
-                          ha='left', va='bottom', fontsize=max(8,int(0.55*plt.rcParams.get('font.size',12))), color=color)
-            new_art.append(txt)
+            # Only add title label if show_cif_titles is True
+            if globals().get('show_cif_titles', True):
+                label_text = f" {lab}"
+                txt = ax.text(ax.get_xlim()[0], y_line + 0.005*yr, label_text,
+                              ha='left', va='bottom', fontsize=max(8,int(0.55*plt.rcParams.get('font.size',12))), color=color)
+                new_art.append(txt)
         ax._cif_tick_art = new_art
         # Store simplified metadata for hover: list of dicts with 'x','y','label'
         hover_meta = []
@@ -2264,6 +2302,7 @@ def batplot_main() -> int:
             'cif_hkl_map': cif_hkl_map,
             'cif_hkl_label_map': cif_hkl_label_map,
             'show_cif_hkl': show_cif_hkl,
+            'show_cif_titles': show_cif_titles,
             'cif_extend_suspended': cif_extend_suspended,
             'keep_canvas_fixed': keep_canvas_fixed,
         }