batplot 1.8.39__tar.gz → 1.8.40__tar.gz

{batplot-1.8.39/batplot.egg-info → batplot-1.8.40}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: batplot
-Version: 1.8.39
+Version: 1.8.40
 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-1.8.39 → batplot-1.8.40}/batplot/__init__.py

@@ -1,5 +1,5 @@
 """batplot: Interactive plotting for battery data visualization."""
 
-__version__ = "1.8.39"
+__version__ = "1.8.40"
 
 __all__ = ["__version__"]

{batplot-1.8.39 → batplot-1.8.40}/batplot/args.py

@@ -37,6 +37,8 @@ import re
 #
 # If rich is not installed, we fall back to plain text (still works fine).
 # ====================================================================
+from .utils import parse_mass_mg_from_cli
+
 try:
     from rich.console import Console  # type: ignore[import]
     from rich.markup import escape  # type: ignore[import]
@@ -278,8 +280,9 @@ def _print_ec_help() -> None:
         "  • Neware: Customized report — check all boxes\n"
         "  • Biologic: Export all info to .mpt file\n\n"
         "Use --i for styling, colors, line widths, axis scales, etc.\n"
-        "GC from .mpt: requires active mass in mg to compute mAh g⁻¹.\n"
-        "  batplot --gc file.mpt --mass 6.5 --i\n\n"
+        "GC from .mpt or .npt: requires active mass to compute mAh g⁻¹ (default unit: mg; use a ``g`` suffix for grams, e.g. --mass 0.0065g).\n"
+        "  batplot --gc file.mpt --mass 6.5 --i\n"
+        "  batplot --gc file.npt --mass 10g --i\n\n"
         "GC from supported .csv: specific capacity read directly when available; use --mass for\n"
         "  Neware absolute-capacity files (Cycle Index / Step Index / DataPoint format).\n"
         "  batplot --gc file.csv\n"
@@ -289,9 +292,11 @@ def _print_ec_help() -> None:
         "  batplot f1.csv --mass 3.52 f2.mpt --mass 5.0 --cpc\n"
         "  # Files without --mass between them use the global --mass value (or none)\n"
         "  # Single --mass applies to all files: batplot f1.mpt f2.mpt --gc --mass 7.0\n\n"
-        "dQ/dV from supported .csv (pre-calculated column or computed from GC data):\n"
+        "dQ/dV from supported .csv (pre-calculated column or computed from GC data), or from Biologic .mpt/.npt (numerical dQ/dV from GC; requires --mass):\n"
         "  batplot --dqdv file.csv\n"
-        "  batplot --dqdv file.csv --mass 3.52     # Neware absolute-capacity CSV\n\n"
+        "  batplot --dqdv file.csv --mass 3.52     # Neware absolute-capacity CSV\n"
+        "  batplot --dqdv file.mpt --mass 6.5\n"
+        "  batplot --dqdv file.npt --mass 0.01g\n\n"
         "Cyclic voltammetry (CV) from .mpt or .txt: plots potential vs current for each cycle.\n"
         "  batplot --cv file.mpt\n"
         "  batplot --cv file.txt\n\n"
@@ -300,7 +305,7 @@ def _print_ec_help() -> None:
         "  batplot --cpc file.csv                 # Neware CSV (specific capacity)\n"
         "  batplot --cpc file.csv --mass 3.52     # Neware absolute-capacity CSV\n"
         "  batplot --cpc file.xlsx                # Landt/Lanhe Excel (Chinese tester)\n"
-        "  batplot --cpc file.mpt --mass 1.2              # Biologic MPT\n"
+        "  batplot --cpc file.mpt --mass 1.2              # Biologic .mpt / .npt\n"
         "  batplot file1.csv --mass 3.52 file2.mpt --mass 1.2 --cpc   # Per-file mass\n"
         "  batplot --cpc file1.csv file2.xlsx file3.mpt --mass 1.2 --i\n\n"
         "Excel support: Landt/Lanhe (蓝电/蓝河) .xlsx files with Chinese headers:\n"
@@ -342,6 +347,8 @@ def _print_op_help() -> None:
         "  batplot --operando --xaxis 2theta              # Using 2theta axis\n"
         "  batplot --operando --1d --i           # Plot derivatives as contour with interactive menu\n"
         "  batplot --operando --2d --i          # Plot derivatives (alias for --1d)\n\n"
+        "  batplot --operando --average 2 --i   # Average every 2 scans before contouring\n\n"
+        "  batplot --operando --sum 2 --i       # Sum every 2 scans to boost intensity\n\n"
         "Bruker operando (.brml):\n"
         "  • Place .brml files (e.g. XX_cyc1.brml, XX_cyc2.brml) in the folder.\n"
         "  • Each .brml is expanded into per-scan rows; files sorted by cyc1/cyc2/cyc3.\n"
@@ -355,6 +362,8 @@ def _print_op_help() -> None:
         "  • If a .mpt file is present, a side panel is added for dual-panel mode (time/potential/temp/etc.).\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"
+        "  • --average N: average every N consecutive scans to improve S/N (e.g., N=2 averages scans 1+2, 3+4, ...).\n\n"
+        "  • --sum N: sum every N consecutive scans (same binning as --average, but without division by N).\n\n"
         "Column selection (operando-specific):\n"
         "  --readcolc <x> <y>  : columns for contour plot (x,y in .xy/.xye/.qye/.dat files)\n"
         "  --readcols <x> <y>  : columns for side panel (x,y in .mpt file)\n"
@@ -384,7 +393,7 @@ def build_parser() -> argparse.ArgumentParser:
     --------------
     - Positional arguments: 'files' - list of file paths (can be 0 or more)
     - Flags (boolean): '--i' - True if present, False if absent
-    - Options with values: '--mass 7.0' - requires a value (float in this case)
+    - Options with values: '--mass 7.0' or '--mass 0.01g' - mass in mg, or grams with a ``g`` suffix
     - Optional arguments: '--help xy' - can have optional value
     
     WHY add_help=False?
@@ -461,9 +470,11 @@ def build_parser() -> argparse.ArgumentParser:
     parser.add_argument("--ry", action="store_true", help=argparse.SUPPRESS)
     parser.add_argument("--txaxis", action="store_true", help=argparse.SUPPRESS)
     parser.add_argument("--operando", "--contour", action="store_true", dest="operando", help=argparse.SUPPRESS)
+    parser.add_argument("--average", type=int, help=argparse.SUPPRESS)
+    parser.add_argument("--sum", dest="scan_sum", type=int, help=argparse.SUPPRESS)
     parser.add_argument("--debug", action="store_true", help=argparse.SUPPRESS)
     parser.add_argument("--gc", action="store_true", help=argparse.SUPPRESS)
-    parser.add_argument("--mass", type=float, action='append', help=argparse.SUPPRESS)
+    parser.add_argument("--mass", type=parse_mass_mg_from_cli, action='append', help=argparse.SUPPRESS)
     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)

{batplot-1.8.39 → batplot-1.8.40}/batplot/batch.py

@@ -28,6 +28,13 @@ from .readers import (
     read_biologic_txt_file,
 )
 
+# BioLogic EC-Lab ASCII exports use ``.mpt``; ``.npt`` is accepted as the same format.
+_MPT_LIKE_EXTS = frozenset({'.mpt', '.npt'})
+
+
+def _is_mpt_like_ext(ext: str) -> bool:
+    return (ext or '').lower() in _MPT_LIKE_EXTS
+
 
 def _resolve_mass(mass_arg, file_idx: int = 0):
     """Return mass (mg) for file at file_idx from a --mass list or single value."""
@@ -488,7 +495,7 @@ def batch_process(directory: str, args):
     known_ext = {'.xye', '.xy', '.qye', '.dat', '.csv', '.gr', '.nor', '.chik', '.chir', '.txt', '.brml', '.raw', '.xrdml', '.rasx'}
     
     # Extensions to exclude (not data files, or require special handling)
-    excluded_ext = {'.cif', '.pkl', '.py', '.md', '.json', '.yml', '.yaml', '.sh', '.bat', '.mpt'}
+    excluded_ext = {'.cif', '.pkl', '.py', '.md', '.json', '.yml', '.yaml', '.sh', '.bat', '.mpt', '.npt'}
     
     # Create output directory for saved plots
     out_dir = ensure_subdirectory('Figures', directory)
@@ -842,7 +849,7 @@ def batch_process(directory: str, args):
 def batch_process_ec(directory: str, args):
     """Batch process electrochemistry files in a directory.
     
-    Supports GC (.mpt/.csv), CV (.mpt), dQdV (.csv), and CPC (.mpt/.csv) modes.
+    Supports GC (.mpt/.npt/.csv), CV (.mpt/.npt/.txt), dQ/dV (.mpt/.npt/.csv), and CPC (.mpt/.npt/.csv) modes.
     Exports SVG plots to batplot_svg subdirectory.
     
     Can apply style/geometry from .bps/.bpsg files using --all flag:
@@ -852,7 +859,7 @@ def batch_process_ec(directory: str, args):
         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.
+    capacity data is already in the file. For .mpt/.npt files, --mass is required (mg by default; use a ``g`` suffix for grams, e.g. ``--mass 0.01g``).
     
     Args:
         directory: Directory containing EC files
@@ -906,19 +913,19 @@ def batch_process_ec(directory: str, args):
     mode = None
     if getattr(args, 'gc', False):
         mode = 'gc'
-        supported_ext = {'.mpt', '.csv'}
+        supported_ext = {'.mpt', '.npt', '.csv'}
     elif getattr(args, 'cv', False):
         mode = 'cv'
-        supported_ext = {'.mpt', '.txt'}
+        supported_ext = {'.mpt', '.npt', '.txt'}
     elif getattr(args, 'dqdv', False):
         mode = 'dqdv'
-        supported_ext = {'.csv'}
+        supported_ext = {'.mpt', '.npt', '.csv'}
     elif getattr(args, 'cpc', False):
         mode = 'cpc'
-        supported_ext = {'.mpt', '.csv'}
+        supported_ext = {'.mpt', '.npt', '.csv'}
     elif getattr(args, 'epc', False):
         mode = 'epc'
-        supported_ext = {'.mpt', '.csv'}
+        supported_ext = {'.mpt', '.npt', '.csv'}
     else:
         print("EC batch mode requires one of: --gc, --cv, --dqdv, or --cpc")
         return
@@ -1007,9 +1014,9 @@ def batch_process_ec(directory: str, args):
             
             # ---- GC Mode ----
             if mode == 'gc':
-                if ext == '.mpt':
+                if _is_mpt_like_ext(ext):
                     if mass_mg is None:
-                        print(f"  Skipped {fname}: GC mode (.mpt) requires --mass parameter")
+                        print(f"  Skipped {fname}: GC mode (.mpt/.npt) requires --mass parameter")
                         plt.close(fig_b)
                         continue
                     specific_capacity, voltage, cycle_numbers, charge_mask, discharge_mask = cast(
@@ -1089,13 +1096,13 @@ def batch_process_ec(directory: str, args):
             elif mode == 'cv':
                 if ext == '.txt':
                     voltage, current, cycles = read_biologic_txt_file(fpath, mode='cv')
-                elif ext == '.mpt':
+                elif _is_mpt_like_ext(ext):
                     voltage, current, cycles = cast(
                         Tuple[np.ndarray, np.ndarray, np.ndarray],
                         read_mpt_file(fpath, mode='cv'),
                     )
                 else:
-                    raise ValueError("CV mode requires .mpt or .txt file")
+                    raise ValueError("CV mode requires .mpt, .npt, or .txt file")
                 
                 cyc_int_raw = np.array(np.rint(cycles), dtype=int)
                 if cyc_int_raw.size:
@@ -1125,13 +1132,27 @@ def batch_process_ec(directory: str, args):
             
             # ---- dQdV Mode ----
             elif mode == 'dqdv':
-                if ext != '.csv':
-                    raise ValueError("dQdV mode requires .csv file")
-
                 # Try to load pre-calculated dQ/dV columns; fall back to numerical computation
                 _b_dqdv_header = None
                 _b_loaded = False
-                if is_biologic_datalogger_csv(fpath):
+                if _is_mpt_like_ext(ext):
+                    if mass_mg is None or mass_mg <= 0:
+                        print(f"  Skipped {fname}: dQ/dV (.mpt/.npt) requires --mass parameter")
+                        plt.close(fig_b)
+                        continue
+                    _b_gc_cap, _b_gc_volt, _b_gc_cyc, _b_gc_chgm, _b_gc_dchm = cast(
+                        Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray, np.ndarray],
+                        read_mpt_file(fpath, mode='gc', mass_mg=mass_mg),
+                    )
+                    voltage, dqdv, cycles, charge_mask, discharge_mask, y_label = \
+                        compute_dqdv_numerical(
+                            _b_gc_cap, _b_gc_volt, _b_gc_cyc, _b_gc_chgm, _b_gc_dchm,
+                        )
+                    _b_loaded = True
+                    print(f"dQ/dV batch: computing numerically from GC data for {fname!r}.")
+                elif ext != '.csv':
+                    raise ValueError(f"dQ/dV mode requires .csv or Biologic .mpt/.npt file, got {ext}")
+                elif is_biologic_datalogger_csv(fpath):
                     if mass_mg is None or mass_mg <= 0:
                         print(f"  Skipped {fname}: dQ/dV (Biologic DataLogger CSV) requires --mass parameter")
                         plt.close(fig_b)
@@ -1164,7 +1185,7 @@ def batch_process_ec(directory: str, args):
                             if _b_mass and _b_mass > 0:
                                 _b_gc_cap = _b_gc_cap * (1000.0 / float(_b_mass))
                             else:
-                                print(f"dQ/dV batch: {fname!r} — pass --mass <mg> for specific dQ/dV.")
+                                print(f"dQ/dV batch: {fname!r} — pass --mass (mg, or e.g. 0.01g) for specific dQ/dV.")
                     voltage, dqdv, cycles, charge_mask, discharge_mask, y_label = \
                         compute_dqdv_numerical(_b_gc_cap, _b_gc_volt, _b_gc_cyc, _b_gc_chgm, _b_gc_dchm)
                     print(f"dQ/dV batch: computing numerically from GC data for {fname!r}.")
@@ -1219,9 +1240,9 @@ def batch_process_ec(directory: str, args):
             
             # ---- CPC / EPC Mode ----
             elif mode in ('cpc', 'epc'):
-                if ext == '.mpt':
+                if _is_mpt_like_ext(ext):
                     if mass_mg is None:
-                        print(f"  Skipped {fname}: {mode.upper()} mode (.mpt) requires --mass parameter")
+                        print(f"  Skipped {fname}: {mode.upper()} mode (.mpt/.npt) requires --mass parameter")
                         plt.close(fig_b)
                         continue
                     if mode == 'cpc':

{batplot-1.8.39 → batplot-1.8.40}/batplot/batplot.py

@@ -106,6 +106,39 @@ try:
 except ImportError:
     operando_ec_interactive_menu = None
 
+
+def _run_saved_dqdv_2d_companion(fig, sess_path: str) -> None:
+    """If load_ec_session attached a saved dQ/dV 2D bundle, run its operando menu after the EC menu."""
+    b = getattr(fig, "_dqdv_2d_companion_bundle", None)
+    if not b or len(b) < 4:
+        return
+    cfig, cax, im, cbar = b[0], b[1], b[2], b[3]
+    if operando_ec_interactive_menu is None:
+        print("Operando interactive not available; skipping saved dQ/dV 2D map.")
+        return
+    paths = list(getattr(fig, "_bp_source_paths", []) or [])
+    if not paths:
+        paths = [sess_path]
+    print("\nSession includes a saved dQ/dV 2D map — opening contour interactive menu (q exits to finish).")
+    try:
+        plt.show(block=False)
+    except Exception:
+        pass
+    try:
+        operando_ec_interactive_menu(cfig, cax, im, cbar, None, file_paths=paths, canvas_mode=False)
+    except Exception as e:
+        print(f"Saved dQ/dV 2D map menu failed: {e}")
+    finally:
+        try:
+            plt.close(cfig)
+        except Exception:
+            pass
+        try:
+            delattr(fig, "_dqdv_2d_companion_bundle")
+        except Exception:
+            pass
+
+
 try:
     from .cpc_interactive import cpc_interactive_menu, _generate_similar_color, _build_compact_cpc_legend
 except ImportError:
@@ -2790,6 +2823,10 @@ def batplot_main() -> int:  # type: ignore
                         electrochem_interactive_menu(fig, ax, cycle_lines, file_path=sess_path)
                     except Exception as _ie:
                         print(f"Interactive menu failed: {_ie}")
+                try:
+                    _run_saved_dqdv_2d_companion(fig, sess_path)
+                except Exception as _c2d:
+                    print(f"Saved dQ/dV 2D companion: {_c2d}")
                 plt.show()
                 exit()
             except Exception as e:

{batplot-1.8.39 → batplot-1.8.40}/batplot/color_utils.py

@@ -104,6 +104,37 @@ def ensure_colormap(name: Optional[str]) -> bool:
     """
     if not name:
         return False
+
+    def _register_cmap_safe(cmap_name: str, cmap_obj) -> bool:
+        """Register cmap across matplotlib API variants."""
+        # matplotlib >= 3.5 style registry API
+        try:
+            reg = getattr(plt, "colormaps", None)
+            if reg is not None and hasattr(reg, "register"):
+                try:
+                    reg.register(cmap_obj, name=cmap_name, force=True)
+                except TypeError:
+                    # Older signature may not support force kwarg
+                    reg.register(cmap_obj, name=cmap_name)
+                return True
+        except Exception:
+            pass
+        # Older pyplot API fallback
+        try:
+            if hasattr(plt, "register_cmap"):
+                plt.register_cmap(name=cmap_name, cmap=cmap_obj)
+                return True
+        except ValueError:
+            # Already registered
+            return True
+        except Exception:
+            pass
+        # As a last resort, accept cmap object usability even if registration fails.
+        try:
+            _ = cmap_obj(0.5)
+            return True
+        except Exception:
+            return False
     
     # Handle reversed colormaps (remove '_r' suffix to get base name)
     # Example: 'viridis_r' → base = 'viridis', we'll reverse it later if needed
@@ -120,13 +151,7 @@ def ensure_colormap(name: Optional[str]) -> bool:
         import cmcrameri.cm as cmc
         if hasattr(cmc, base_lower):
             cmap_obj = getattr(cmc, base_lower)
-            try:
-                # Register it with matplotlib so it can be used like built-in colormaps
-                plt.register_cmap(name=base_lower, cmap=cmap_obj)
-            except ValueError:
-                # Already registered, that's fine
-                pass
-            return True
+            return _register_cmap_safe(base_lower, cmap_obj)
     except Exception:
         # cmcrameri not installed or colormap not found, continue to next step
         pass
@@ -139,13 +164,7 @@ def ensure_colormap(name: Optional[str]) -> bool:
             # N=256 means create 256 intermediate colors by interpolating between the given colors
             # This creates a smooth gradient
             cmap_obj = LinearSegmentedColormap.from_list(base_lower, custom, N=256)
-            try:
-                # Register with matplotlib
-                plt.register_cmap(name=base_lower, cmap=cmap_obj)
-            except ValueError:
-                # Already registered, that's fine
-                pass
-            return True
+            return _register_cmap_safe(base_lower, cmap_obj)
         except Exception:
             return False
     

{batplot-1.8.39 → batplot-1.8.40}/batplot/config.py

@@ -18,6 +18,10 @@ Example config.json structure:
         "#0000FF",
         "red",
         "blue"
+      ],
+      "recent_axis_names": [
+        "Potential (V)",
+        "dQ/dV (mAh V$^{-1}$)"
       ]
     }
 
@@ -192,7 +196,47 @@ def save_user_colors(colors: List[str]) -> None:
     save_config(config)  # Save entire config back to file
 
 
+_RECENT_AXIS_NAMES_KEY = 'recent_axis_names'
+RECENT_AXIS_NAMES_MAX = 20
+
+
+def get_recent_axis_names() -> List[str]:
+    """Return up to :data:`RECENT_AXIS_NAMES_MAX` recently typed axis labels (newest first)."""
+    raw = load_config().get(_RECENT_AXIS_NAMES_KEY, [])
+    if not isinstance(raw, list):
+        return []
+    out: List[str] = []
+    for item in raw:
+        s = str(item).strip()
+        if s and s not in out:
+            out.append(s)
+        if len(out) >= RECENT_AXIS_NAMES_MAX:
+            break
+    return out
+
+
+def record_recent_axis_name(name: str) -> None:
+    """Add an axis label to the shared recent list (dedupe, newest first, max 20)."""
+    s = str(name or '').strip()
+    if not s:
+        return
+    config = load_config()
+    raw = config.get(_RECENT_AXIS_NAMES_KEY, [])
+    names: List[str] = []
+    if isinstance(raw, list):
+        for item in raw:
+            t = str(item).strip()
+            if t and t != s:
+                names.append(t)
+    names.insert(0, s)
+    config[_RECENT_AXIS_NAMES_KEY] = names[:RECENT_AXIS_NAMES_MAX]
+    save_config(config)
+
+
 __all__ = [
     'get_user_colors',
     'save_user_colors',
+    'get_recent_axis_names',
+    'record_recent_axis_name',
+    'RECENT_AXIS_NAMES_MAX',
 ]