batplot 1.8.30__tar.gz → 1.8.33__tar.gz

batplot-1.8.33/MANIFEST.in

@@ -0,0 +1,2 @@
+include README.md LICENSE USER_MANUAL.md
+recursive-include batplot/data *.md

{batplot-1.8.30/batplot.egg-info → batplot-1.8.33}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: batplot
-Version: 1.8.30
+Version: 1.8.33
 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
@@ -57,13 +57,15 @@ Dynamic: license-file
 
 ## Features
 
-- **Electrochemistry Modes**: Galvanostatic cycling (GC), cyclic voltammetry (CV), differential capacity (dQdV), capacity per cycle (CPC) with multi-file support
-- **Normal xy plot**: Designed for XRD, PDF, XAS (XANES/EXAFS) but also support other types
-- **Operando Analysis**: Correlate in-situ characterizations (XRD/PDF/XAS) with electrochemical data
+With a single line of command to easily plot publication-ready plots with customized, intuitive interactive editing features such as:
+- **Electrochemistry Plot**: Galvanostatic cycling (GC), cyclic voltammetry (CV), differential capacity (dQdV), capacity per cycle (CPC) with multi-file support
+- **1D XY plot**: Designed for XRD, PDF, XAS (XANES/EXAFS) but also support other types
+- **Operando Contour plot**: Correlate in-situ characterizations (XRD/PDF/XAS) with electrochemical data
 - **Interactive plotting**: Real-time editing customized for each type of plottings
 - **Session Persistence**: Save and reload complete plot states with `.pkl` files
 - **Style Management**: Import/export plot styles as `.bps`/`.bpsg` files
 - **Batch Processing**: Export each file separately with `--all`
+- **Column preview**: `--showcol` prints numbered columns, header names when found, and the first 10 values per column (CSV, Excel, text, .mpt, .brml, Bruker .raw, etc.)
 
 ## Installation
 
@@ -249,6 +251,23 @@ batplot custom.mpt --gc --pw 0.01 3 --cd 0.2 --i
 
 ## Operando Mode
 
+Contour plots from a folder of diffraction data, optionally with an electrochemistry side panel.
+
+### Bruker operando (.brml)
+
+For Bruker operando XRD (multi-scan .brml files named cyc1, cyc2, cyc3, etc.):
+
+```bash
+# Place .brml files (e.g. RA_O5_cyc1.brml, RA_O5_cyc2.brml) in the folder
+# Use --wl for Q conversion (e.g. synchrotron λ=0.709 Å)
+batplot RA_O5 --operando --wl 0.709 --i
+
+# EC side panel: .mpt or Biologic DataLogger CSV (*--DataLogger.csv), sorted by cyc
+# Time vs potential is concatenated across files (continuous time axis)
+```
+
+### Standard XY files
+
 ```bash
 # Contour from folder of .xy/.xye/.qye/.dat
 batplot --operando --wl 1.54 --i
@@ -313,8 +332,9 @@ batplot --all --readcol 2 3 style.bps --xaxis 2theta
 
 | Type | Formats |
 |------|---------|
-| **Electrochemistry** | `.csv` (Neware), `.mpt` (Biologic), `.xlsx` (Landt/Lanhe CPC) |
+| **Electrochemistry** | `.csv` (Neware, Biologic DataLogger), `.mpt` (Biologic), `.xlsx` (Landt/Lanhe CPC) |
 | **XRD / PDF** | `.xye`, `.xy`, `.qye`, `.dat`, `.csv`, `.txt`; Bruker `.brml`, `.raw` |
+| **Operando** | `.xy`, `.xye`, `.qye`, `.dat`; Bruker `.brml` (cyc1/cyc2/cyc3); EC: `.mpt` or DataLogger `.csv` |
 | **XAS** | `.nor`, `.chik`, `.chir` |
 | **Generic** | Use `--readcol` and `--xaxis` for custom formats |
 
@@ -324,9 +344,11 @@ batplot --all --readcol 2 3 style.bps --xaxis 2theta
 
 With `--interactive`:
 - **Cycle/Scan Control**: Toggle visibility, change colors
+- **Multi-file palette (EC/CV/dQdV)**: Press `c`, then type `fall viridis` (all files), `f1-5 viridis` (files 1–5), or `f1 f3 f5 4` (each file gets one color)
+- **CPC file palette**: In `ly`/`ry` color submenu, apply palette to file range: `1-5 viridis`, `1 3 5 4`
 - **Styling**: Line widths, markers, fonts
 - **Axes**: Labels, limits, ticks, spine styles
-- **Export**: Sessions (`.pkl`), styles (`.bps`/`.bpsg`), high-res images
+- **Export**: Sessions (`.pkl`), styles (`.bps`/`.bpsg`), high-res images. Colors persist via `p` (print style), `i` (import), `s` (save session), `b` (undo)
 - **Live Preview**: All changes update in real-time
 
 ---

{batplot-1.8.30 → batplot-1.8.33}/README.md

@@ -6,13 +6,15 @@
 
 ## Features
 
-- **Electrochemistry Modes**: Galvanostatic cycling (GC), cyclic voltammetry (CV), differential capacity (dQdV), capacity per cycle (CPC) with multi-file support
-- **Normal xy plot**: Designed for XRD, PDF, XAS (XANES/EXAFS) but also support other types
-- **Operando Analysis**: Correlate in-situ characterizations (XRD/PDF/XAS) with electrochemical data
+With a single line of command to easily plot publication-ready plots with customized, intuitive interactive editing features such as:
+- **Electrochemistry Plot**: Galvanostatic cycling (GC), cyclic voltammetry (CV), differential capacity (dQdV), capacity per cycle (CPC) with multi-file support
+- **1D XY plot**: Designed for XRD, PDF, XAS (XANES/EXAFS) but also support other types
+- **Operando Contour plot**: Correlate in-situ characterizations (XRD/PDF/XAS) with electrochemical data
 - **Interactive plotting**: Real-time editing customized for each type of plottings
 - **Session Persistence**: Save and reload complete plot states with `.pkl` files
 - **Style Management**: Import/export plot styles as `.bps`/`.bpsg` files
 - **Batch Processing**: Export each file separately with `--all`
+- **Column preview**: `--showcol` prints numbered columns, header names when found, and the first 10 values per column (CSV, Excel, text, .mpt, .brml, Bruker .raw, etc.)
 
 ## Installation
 
@@ -198,6 +200,23 @@ batplot custom.mpt --gc --pw 0.01 3 --cd 0.2 --i
 
 ## Operando Mode
 
+Contour plots from a folder of diffraction data, optionally with an electrochemistry side panel.
+
+### Bruker operando (.brml)
+
+For Bruker operando XRD (multi-scan .brml files named cyc1, cyc2, cyc3, etc.):
+
+```bash
+# Place .brml files (e.g. RA_O5_cyc1.brml, RA_O5_cyc2.brml) in the folder
+# Use --wl for Q conversion (e.g. synchrotron λ=0.709 Å)
+batplot RA_O5 --operando --wl 0.709 --i
+
+# EC side panel: .mpt or Biologic DataLogger CSV (*--DataLogger.csv), sorted by cyc
+# Time vs potential is concatenated across files (continuous time axis)
+```
+
+### Standard XY files
+
 ```bash
 # Contour from folder of .xy/.xye/.qye/.dat
 batplot --operando --wl 1.54 --i
@@ -262,8 +281,9 @@ batplot --all --readcol 2 3 style.bps --xaxis 2theta
 
 | Type | Formats |
 |------|---------|
-| **Electrochemistry** | `.csv` (Neware), `.mpt` (Biologic), `.xlsx` (Landt/Lanhe CPC) |
+| **Electrochemistry** | `.csv` (Neware, Biologic DataLogger), `.mpt` (Biologic), `.xlsx` (Landt/Lanhe CPC) |
 | **XRD / PDF** | `.xye`, `.xy`, `.qye`, `.dat`, `.csv`, `.txt`; Bruker `.brml`, `.raw` |
+| **Operando** | `.xy`, `.xye`, `.qye`, `.dat`; Bruker `.brml` (cyc1/cyc2/cyc3); EC: `.mpt` or DataLogger `.csv` |
 | **XAS** | `.nor`, `.chik`, `.chir` |
 | **Generic** | Use `--readcol` and `--xaxis` for custom formats |
 
@@ -273,9 +293,11 @@ batplot --all --readcol 2 3 style.bps --xaxis 2theta
 
 With `--interactive`:
 - **Cycle/Scan Control**: Toggle visibility, change colors
+- **Multi-file palette (EC/CV/dQdV)**: Press `c`, then type `fall viridis` (all files), `f1-5 viridis` (files 1–5), or `f1 f3 f5 4` (each file gets one color)
+- **CPC file palette**: In `ly`/`ry` color submenu, apply palette to file range: `1-5 viridis`, `1 3 5 4`
 - **Styling**: Line widths, markers, fonts
 - **Axes**: Labels, limits, ticks, spine styles
-- **Export**: Sessions (`.pkl`), styles (`.bps`/`.bpsg`), high-res images
+- **Export**: Sessions (`.pkl`), styles (`.bps`/`.bpsg`), high-res images. Colors persist via `p` (print style), `i` (import), `s` (save session), `b` (undo)
 - **Live Preview**: All changes update in real-time
 
 ---

{batplot-1.8.30 → batplot-1.8.33}/batplot/__init__.py

@@ -1,5 +1,5 @@
 """batplot: Interactive plotting for battery data visualization."""
 
-__version__ = "1.8.30"
+__version__ = "1.8.33"
 
 __all__ = ["__version__"]

{batplot-1.8.30 → batplot-1.8.33}/batplot/args.py

@@ -135,7 +135,7 @@ def _print_general_help() -> None:
         "What it does:\n"
         "  • XY: XRD/PDF/XAS/User defined curves\n"
         "  • EC: Galvanostatic cycling(GC)/Capacity per cycle(CPC)/Diffrential capacity(dQdV)/Cyclic Voltammetry(CV) from Neware (.csv) or Biologic (.mpt)\n"
-        "  • Operando: contour maps from a folder of .xy/.xye/.dat/.txt and optional .mpt file as side panel\n"
+        "  • Operando: contour from .xy/.xye/.dat/.brml; Bruker .brml (cyc1/cyc2/cyc3) with optional .mpt or DataLogger CSV side panel\n"
         "  • Batch: export vector plots for all files in a directory\n"
         "  • Interactive mode: --i flag opens a menu for styling, ranges, export, and save\n\n"
         "How to run (basics):\n"
@@ -156,7 +156,8 @@ def _print_general_help() -> None:
         "    batplot --cv file.mpt --i                 # Cyclic voltammetry\n"
         "    batplot --cpc file.csv --mass 3.52 --i     # Capacity per cycle\n\n"
         "  [Operando]\n"
-        "    batplot --operando --i [FOLDER]  # Contour from folder\n\n"
+        "    batplot --operando --i [FOLDER]  # Contour from folder\n"
+        "    batplot Path/to/file --operando --wl 0.709 --i  # Bruker .brml, Q conversion\n\n"
         "Features:\n"
         "  • Interactive (--i): styling, ranges, fonts, export, sessions\n"
         "  • XRD wavelength: --wl 1.54 or file.xye:1.5406 for Q conversion\n"
@@ -167,6 +168,7 @@ def _print_general_help() -> None:
         
         "More help:\n"
         "  batplot --version       # Version and release info (with option to show full release notes)\n"
+        "  batplot --showcol FILE [FILE...]   # Preview column names + first 10 values per column\n"
         "  batplot --help          # This help\n"
         "  batplot --help xy       # XY file plotting guide\n"
         "  batplot --help ec       # Electrochemistry (GC/dQdV/CV/CPC) guide\n"
@@ -230,6 +232,8 @@ def _print_xy_help() -> None:
         "                              Works with --readcol for custom column layout (per-file, per-ext, or global):\n"
         "                                batplot data.csv --readcol 3 4 --convert 1.54 q\n"
         "                                batplot f1.txt --readcol 2 3 f2.txt --readcol 5 6 --convert 1.54 q\n"
+        "                              Directory: pass a folder to convert all .xy/.xye/.qye/.dat/.csv/.txt files:\n"
+        "                                batplot /path/to/folder --convert 0.25448 1.54\n"
         "                              Examples:\n"
         "                                batplot file.xye --convert 1.54 0.25\n"
         "                                batplot file.xye --convert 1.54 q\n"
@@ -313,8 +317,11 @@ def _print_ec_help() -> None:
         "  batplot file1.csv file2.csv ./Style/style.bps --dqdv                  # Style from relative path\n"
         "  batplot file1.csv file2.mpt style.bpsg --cpc --mass 6                 # CPC mode\n"
         "  batplot file1.csv file2.mpt ./Style/style.bpsg --cpc --mass 6         # Style+geom from relative path\n\n"
+        "Multi-file (EC/CV/dQdV): Press c, then type fall viridis (all files), f1-5 viridis (files 1–5), or f1 f3 f5 4.\n"
+        "CPC (ly/ry): Type 1-5 viridis or 1 3 5 4 for file range. Exported via p, restored via i/s/b.\n\n"
         "Interactive (--i): choose cycles, colors/palettes, line widths, axis scales (linear/log/symlog),\n"
         "rename axes, toggle ticks/titles/spines, print/export/import style (.bps/.bpsg), save session (.pkl).\n"
+        "Multi-file: In c (cycles/colors), type fall viridis (all files), f1-5 viridis (files 1–5), or f1 f3 f5 4 (files 1,3,5).\n"
         "Note: Batch mode (--all) exports SVG files automatically; --i is for single-file plotting only.\n\n"
         "Axis swapping:\n"
         "  --ro                      : swap x and y axes (exchange x and y values before plotting)\n"
@@ -333,7 +340,14 @@ 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"
-        "  • Folder should contain XY files (.xy/.xye/.qye/.dat).\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"
+        "  • Use --wl for Q conversion: batplot RA_O5 --operando --wl 0.709 --i\n"
+        "  • EC side panel: .mpt or Biologic DataLogger CSV (*--DataLogger.csv), sorted by cyc.\n"
+        "  • Time vs potential is concatenated across files (continuous time axis).\n\n"
+        "Standard XY files:\n"
+        "  • Folder should contain .xy/.xye/.qye/.dat files.\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, a side panel is added for dual-panel mode (time/potential/temp/etc.).\n"
@@ -404,6 +418,11 @@ def build_parser() -> argparse.ArgumentParser:
                         help=argparse.SUPPRESS)  # SUPPRESS hides from auto-generated help
     parser.add_argument("--version", action="store_true", dest="version",
                         help="Show version and current release info, then exit.")
+    parser.add_argument(
+        "--showcol",
+        action="store_true",
+        help=argparse.SUPPRESS,
+    )
     parser.add_argument("--manual", action="store_true", help=argparse.SUPPRESS)
     
     # ====================================================================
@@ -425,6 +444,8 @@ def build_parser() -> argparse.ArgumentParser:
     parser.add_argument("--xaxis", type=str, help=argparse.SUPPRESS)
     parser.add_argument("--convert", 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("--extract-brml-scans", nargs="?", const="", metavar="OUT_DIR",
+                        help="Extract each XRD scan from .brml file to separate .xy files. Optional OUT_DIR (default: <brml_stem>_scans).")
     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)
@@ -478,6 +499,8 @@ def build_parser() -> argparse.ArgumentParser:
                        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)
+    parser.add_argument("--canvas", action="store_true", dest="canvas",
+                        help="Canvas mode: combine multiple .pkl sessions into one layout. Use numbers to edit each panel.")
     return parser
 
 
@@ -530,9 +553,11 @@ def parse_args(argv=None):
     if argv is None:
         argv = sys.argv[1:]
     
-    # Normalize single-dash short forms to double-dash long forms (backward compatibility)
+    # Normalize short forms to long forms (both -x and --x for common flags)
     _SHORT_TO_LONG = {
-        '-h': '--help', '-v': '--version', '-V': '--version', '-m': '--manual',
+        '-h': '--help', '--h': '--help',
+        '-v': '--version', '-V': '--version', '--v': '--version',
+        '-m': '--manual', '--m': '--manual',
         '-i': '--i', '-d': '--delta', '-r': '--xrange', '-o': '--out', '-c': '--convert',
         '-b': '--b',
     }
@@ -674,13 +699,13 @@ def parse_args(argv=None):
     ns, _unknown = parser.parse_known_args(argv)
     if getattr(ns, "manual", False):
         try:
-            from .manual import show_manual  # Lazy import avoids matplotlib startup unless needed
-            pdf_path = show_manual(open_viewer=True)
+            from .manual import open_manual_url  # Lazy import avoids matplotlib startup unless needed
+            open_manual_url()
             if _HAS_RICH and _console:
-                _console.print(f"\n[green]Opened manual:[/green] {pdf_path}")
+                _console.print("\n[green]Opened manual in browser[/green]")
             else:
-                print(f"\nOpened manual: {pdf_path}")
-        except Exception as exc:  # pragma: no cover - rendering is best effort
+                print("\nOpened manual in browser")
+        except Exception as exc:  # pragma: no cover - best effort
             if _HAS_RICH and _console:
                 _console.print(f"\n[red]Failed to open manual:[/red] {exc}")
             else:

{batplot-1.8.30 → batplot-1.8.33}/batplot/batch.py

@@ -21,6 +21,9 @@ from .readers import (
     read_ec_csv_dqdv_file,
     compute_dqdv_numerical,
     is_cs_b_format,
+    is_biologic_datalogger_csv,
+    read_biologic_datalogger_csv,
+    read_biologic_datalogger_dqdv_file,
     _load_csv_header_and_rows,
     read_biologic_txt_file,
 )
@@ -1013,8 +1016,16 @@ def batch_process_ec(directory: str, args):
                     cap_x = specific_capacity
                     x_label = r'Specific Capacity (mAh g$^{-1}$)'
                 elif ext == '.csv':
-                    cap_x, voltage, cycle_numbers, charge_mask, discharge_mask = \
-                        read_ec_csv_file(fpath, prefer_specific=True)
+                    if is_biologic_datalogger_csv(fpath):
+                        if mass_mg is None:
+                            print(f"  Skipped {fname}: GC mode (Biologic DataLogger CSV) requires --mass parameter")
+                            plt.close(fig_b)
+                            continue
+                        cap_x, voltage, cycle_numbers, charge_mask, discharge_mask = \
+                            read_biologic_datalogger_csv(fpath, mass_mg=mass_mg)
+                    else:
+                        cap_x, voltage, cycle_numbers, charge_mask, discharge_mask = \
+                            read_ec_csv_file(fpath, prefer_specific=True)
                     x_label = r'Specific Capacity (mAh g$^{-1}$)'
                 else:
                     raise ValueError(f"Unsupported file type for GC: {ext}")
@@ -1116,13 +1127,21 @@ def batch_process_ec(directory: str, args):
 
                 # Try to load pre-calculated dQ/dV columns; fall back to numerical computation
                 _b_dqdv_header = None
-                try:
-                    _b_dqdv_header, _, _ = _load_csv_header_and_rows(fpath)
-                except Exception:
-                    pass
-
                 _b_loaded = False
-                if not _b_loaded:
+                if 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)
+                        continue
+                    voltage, dqdv, cycles, charge_mask, discharge_mask, y_label = \
+                        read_biologic_datalogger_dqdv_file(fpath, mass_mg=mass_mg, prefer_specific=True)
+                    _b_loaded = True
+                else:
+                    try:
+                        _b_dqdv_header, _, _ = _load_csv_header_and_rows(fpath)
+                    except Exception:
+                        pass
+
                     try:
                         voltage, dqdv, cycles, charge_mask, discharge_mask, y_label = \
                             read_ec_csv_dqdv_file(fpath, prefer_specific=True)