batplot 1.3.3__tar.gz → 1.3.5__tar.gz

{batplot-1.3.3 → batplot-1.3.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: batplot
-Version: 1.3.3
+Version: 1.3.5
 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
@@ -91,8 +91,11 @@ batplot --all
 # Batch mode with options: custom axis and range
 batplot --all --xaxis 2theta --xrange 10 80
 
-# Batch mode: convert 2theta to Q and use raw intensity
-batplot --all --wl 1.5406 --raw
+# Normalize data (--stack mode auto-normalizes by default)
+batplot allfiles --norm
+
+# Batch mode: convert 2theta to Q
+batplot --all --wl 1.5406
 ```
 
 ### Electrochemistry
@@ -132,6 +135,10 @@ batplot --all geom.bpsg --cpc --mass 5.4    # Apply style+geometry to all CPC fi
 # Correlate in-situ XRD with electrochemistry
 # (Place both .xye and .mpt files in same directory)
 batplot --operando --interactive
+
+# Operando mode without electrochemistry data
+# (Only .xye files, no .mpt file)
+batplot --operando --interactive
 ```
 
 ## Supported File Formats

{batplot-1.3.3 → batplot-1.3.5}/README.md

@@ -42,8 +42,11 @@ batplot --all
 # Batch mode with options: custom axis and range
 batplot --all --xaxis 2theta --xrange 10 80
 
-# Batch mode: convert 2theta to Q and use raw intensity
-batplot --all --wl 1.5406 --raw
+# Normalize data (--stack mode auto-normalizes by default)
+batplot allfiles --norm
+
+# Batch mode: convert 2theta to Q
+batplot --all --wl 1.5406
 ```
 
 ### Electrochemistry
@@ -83,6 +86,10 @@ batplot --all geom.bpsg --cpc --mass 5.4    # Apply style+geometry to all CPC fi
 # Correlate in-situ XRD with electrochemistry
 # (Place both .xye and .mpt files in same directory)
 batplot --operando --interactive
+
+# Operando mode without electrochemistry data
+# (Only .xye files, no .mpt file)
+batplot --operando --interactive
 ```
 
 ## Supported File Formats

{batplot-1.3.3 → batplot-1.3.5}/batplot/args.py

@@ -12,7 +12,7 @@ def _print_general_help() -> None:
         "What it does:\n"
         "  • XY: XRD/PDF/XAS/... curves\n"
         "  • EC: GC/CPC/dQdV/CV (from .csv or .mpt)\n"
-        "  • Operando: contour maps from a folder of XY and .mpt files (use --raw for raw intensity)\n"
+        "  • Operando: contour maps from a folder of XY and .mpt files\n"
         "  • Batch: export SVG plots for all files in a directory\n\n"
         "  • Interactive mode: --interactive flag opens a menu for styling, ranges, fonts, export, sessions\n\n"
     "How to run (basics):\n"
@@ -34,8 +34,7 @@ def _print_general_help() -> None:
     "    batplot --cv FILE.txt                  # EC CV (cyclic voltammetry) from .txt\n"
     "    batplot --cv --all                     # Batch: all .mpt/.txt in directory (CV mode)\n\n"
     "  [Operando]\n"
-    "    batplot --operando [FOLDER]            # Operando contour from folder (normalized by default)\n"
-    "    batplot --operando --raw               # Operando contour with raw intensity (no normalization)\n\n"
+    "    batplot --operando [FOLDER]            # Operando contour (with or without .mpt file)\n\n"
         "Features:\n"
         "  • Quick plotting with sensible defaults, no config files needed\n"
         "  • Supports many common file formats (see -h xy/ec/op)\n"
@@ -58,8 +57,9 @@ def _print_xy_help() -> None:
     msg = (
         "XY plots (diffraction/PDF/XAS)\n\n"
         "Supported files: .xye .xy .qye .dat .csv .gr .nor .chik .chir .txt (2-col). CIF overlays supported.\n\n"
-        "Axis detection: .qye→Q, .gr→r, .nor→energy, .chik→k, .chir→r, else use --xaxis (Q, 2theta, r, k, energy, rft).\n"
-        "If mixing 2θ data in Q, give wavelength per-file (file.xye:1.5406) or global --wl.\n\n"
+        "Axis detection: .qye→Q, .gr→r, .nor→energy, .chik→k, .chir→r, else use --xaxis (Q, 2theta, r, k, energy, rft, time).\n"
+        "If mixing 2θ data in Q, give wavelength per-file (file.xye:1.5406) or global --wl.\n"
+        "For electrochemistry CSV/MPT time-voltage plots, use --xaxis time.\n\n"
         "Examples:\n"
         "  batplot a.xye:1.5406 b.qye --stack --interactive\n"
         "  batplot a.dat b.xy --wl 1.54 --out fig.svg\n"
@@ -73,18 +73,19 @@ def _print_xy_help() -> None:
         "  batplot --all                          # Export all XY files to SVG\n"
         "  batplot --all --xaxis 2theta           # Batch mode with custom axis type\n"
         "  batplot --all --xrange 10 80           # Batch mode with X-axis range\n"
-        "  batplot --all --wl 1.5406 --raw        # Batch mode with wavelength and raw intensity\n\n"
+        "  batplot --all --wl 1.5406              # Batch mode with wavelength conversion\n\n"
         "Tips and options:\n"
         "[XY plot]\n"
     "  --interactive             : open interactive menu for styling, ranges, fonts, export, sessions\n"
     "  --delta/-d <float>        : spacing between curves, e.g. --delta 0.1\n"
-    "  --raw                     : plot raw intensity (normalized by default)\n"
+    "  --norm                    : normalize intensity to 0-1 range. Stack mode (--stack) auto-normalizes\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, or user defined), e.g. --xaxis 2theta\n"
+    "  --xaxis <type>            : set x-axis type (Q, 2theta, r, k, energy, rft, time, or user defined)\n"
+    "                              e.g. --xaxis 2theta, or --xaxis time for electrochemistry CSV/MPT time-voltage plots\n"
     "  --wl <float>              : set wavelength for Q conversion for all files, e.g. --wl 1.5406\n"
     "  --fullprof <args>         : FullProf overlay options\n"
-    "  --stack                   : stack curves vertically\n"
+    "  --stack                   : stack curves vertically (auto-enables normalization)\n"
     )
     print(msg)
 
@@ -130,14 +131,15 @@ 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 --raw --interactive         # Raw intensity (no normalization)\n"
         "  batplot --operando --xaxis 2theta              # Using 2theta axis\n\n"
         "  • Folder should contain XY files (.xy/.xye/.qye/.dat).\n"
-        "  • By default, data is normalized (0-1). Use --raw to plot raw intensity.\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 BioLogic .mpt is present, an EC side panel will be added automatically.\n\n"
-        "Interactive (--interactive): resize axes/canvas, change colormap, set intensity range (oi),\n"
-        "EC y-axis options (time ↔ ions), geometry tweaks, print/export/import style, save session.\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"
+        "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"
     )
     print(msg)
 
@@ -158,7 +160,7 @@ def build_parser() -> argparse.ArgumentParser:
     parser.add_argument("--convert", "-c", nargs="+", help=argparse.SUPPRESS)
     parser.add_argument("--wl", type=float, help=argparse.SUPPRESS)
     parser.add_argument("--fullprof", nargs="+", type=float, help=argparse.SUPPRESS)
-    parser.add_argument("--raw", action="store_true", help=argparse.SUPPRESS)
+    parser.add_argument("--norm", action="store_true", help=argparse.SUPPRESS)
     parser.add_argument("--interactive", action="store_true", help=argparse.SUPPRESS)
     parser.add_argument("--savefig", type=str, help=argparse.SUPPRESS)
     parser.add_argument("--stack", action="store_true", help=argparse.SUPPRESS)

{batplot-1.3.3 → batplot-1.3.5}/batplot/batch.py

@@ -278,16 +278,16 @@ def batch_process(directory: str, args):
             else:
                 x_plot = x
 
-            # Normalize or raw
-            if args.raw:
-                y_plot = y.copy()
-            else:
+            # Normalize if --norm flag is set
+            if getattr(args, 'norm', False):
                 if y.size:
                     ymin = float(y.min()); ymax = float(y.max())
                     span = ymax - ymin
                     y_plot = (y - ymin)/span if span > 0 else np.zeros_like(y)
                 else:
                     y_plot = y
+            else:
+                y_plot = y.copy()
 
             # Plot and save
             fig_b, ax_b = plt.subplots(figsize=(6,4))
@@ -309,7 +309,7 @@ def batch_process(directory: str, args):
                 ax_b.set_xlabel("Radial distance (Å)")
             else:
                 ax_b.set_xlabel(r"$2\theta\ (\mathrm{deg})$")
-            ax_b.set_ylabel("Intensity" if args.raw else "Normalized intensity (a.u.)")
+            ax_b.set_ylabel("Normalized intensity (a.u.)" if getattr(args, 'norm', False) else "Intensity")
             ax_b.set_title(fname)
             fig_b.subplots_adjust(left=0.18, right=0.97, bottom=0.16, top=0.90)
             out_name = os.path.splitext(fname)[0] + ".svg"

{batplot-1.3.3 → batplot-1.3.5}/batplot/batplot.py

@@ -28,6 +28,8 @@ from .readers import (
     read_mpt_file,
     read_ec_csv_file,
     read_ec_csv_dqdv_file,
+    read_csv_time_voltage,
+    read_mpt_time_voltage,
 )
 from .cif import (
     simulate_cif_pattern_Q,
@@ -1090,11 +1092,12 @@ def batplot_main() -> int:
                     except Exception:
                         pass
                     try:
-                        if has_ec and (operando_ec_interactive_menu is not None) and (ec_ax is not None):
+                        # Call interactive menu regardless of EC presence
+                        # When ec_ax is None, EC-related commands will be disabled
+                        if operando_ec_interactive_menu is not None:
                             operando_ec_interactive_menu(fig, ax, im, cbar, ec_ax)
                         else:
-                            # Operando-only interactive menu has been removed; fall back to non-interactive view
-                            print("Operando-only interactive menu is no longer available; showing figure without interactive controls.\nTip: include EC data to use the combined operando+EC interactive menu.")
+                            print("Interactive menu not available.")
                     except Exception as _ie:
                         print(f"Interactive menu failed: {_ie}")
                     _plt.show()
@@ -1236,7 +1239,7 @@ def batplot_main() -> int:
                 except Exception:
                     pass
                 try:
-                    if operando_ec_interactive_menu is not None and ec_ax2 is not None:
+                    if operando_ec_interactive_menu is not None:
                         operando_ec_interactive_menu(fig2, ax2, im2, cbar2, ec_ax2)
                 except Exception as _ie:
                     print(f"Interactive menu failed: {_ie}")
@@ -1641,8 +1644,8 @@ def batplot_main() -> int:
             args_subset = sess.get('args_subset', {})
             if 'autoscale' in args_subset:
                 args.autoscale = bool(args_subset['autoscale'])
-            if 'raw' in args_subset:
-                args.raw = bool(args_subset['raw'])
+            if 'norm' in args_subset:
+                args.norm = bool(args_subset['norm'])
         except Exception:
             pass
         try:
@@ -1701,49 +1704,59 @@ def batplot_main() -> int:
     # ---------------- Determine X-axis type ----------------
     def _ext_token(path):
         return os.path.splitext(path)[1].lower()  # includes leading dot
-    any_qye = any(f.lower().endswith(".qye") for f in args.files)
-    any_gr  = any(f.lower().endswith(".gr")  for f in args.files)
-    any_nor = any(f.lower().endswith(".nor") for f in args.files)
-    any_chik = any("chik" in _ext_token(f) for f in args.files)
-    any_chir = any("chir" in _ext_token(f) for f in args.files)
-    any_txt = any(f.lower().endswith(".txt") for f in args.files)
-    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
-
-    # 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:
-        raise ValueError("Cannot mix .gr (r), .nor (energy), .chik (k), .chir (FT-EXAFS R), and Q/2θ/CIF data together. Split runs.")
-
-    # Automatic axis selection based on file extensions
-    if any_qye:
-        axis_mode = "Q"
-    elif any_gr:
-        axis_mode = "r"
-    elif any_nor:
-        axis_mode = "energy"
-    elif any_chik:
-        axis_mode = "k"
-    elif any_chir:
-        axis_mode = "rft"
-    elif any_txt:
-        # .txt is generic, require --xaxis
-        if args.xaxis:
+    
+    # Check for CSV/MPT files with --xaxis time
+    any_csv = any(f.lower().endswith((".csv", ".mpt")) for f in args.files)
+    use_time_mode = any_csv and args.xaxis and args.xaxis.lower() == "time"
+    
+    if use_time_mode:
+        # Special mode: plot time (h) vs voltage (V) for electrochemistry CSV/MPT files
+        axis_mode = "time"
+    else:
+        # Regular XRD/PDF/XAS mode - proceed with normal detection
+        any_qye = any(f.lower().endswith(".qye") for f in args.files)
+        any_gr  = any(f.lower().endswith(".gr")  for f in args.files)
+        any_nor = any(f.lower().endswith(".nor") for f in args.files)
+        any_chik = any("chik" in _ext_token(f) for f in args.files)
+        any_chir = any("chir" in _ext_token(f) for f in args.files)
+        any_txt = any(f.lower().endswith(".txt") for f in args.files)
+        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
+
+        # 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:
+            raise ValueError("Cannot mix .gr (r), .nor (energy), .chik (k), .chir (FT-EXAFS R), and Q/2θ/CIF data together. Split runs.")
+
+        # Automatic axis selection based on file extensions
+        if any_qye:
+            axis_mode = "Q"
+        elif any_gr:
+            axis_mode = "r"
+        elif any_nor:
+            axis_mode = "energy"
+        elif any_chik:
+            axis_mode = "k"
+        elif any_chir:
+            axis_mode = "rft"
+        elif any_txt:
+            # .txt is generic, require --xaxis
+            if args.xaxis:
+                axis_mode = args.xaxis
+            else:
+                raise ValueError("Cannot determine X-axis type for .txt files. Please specify --xaxis (Q, 2theta, r, k, energy, rft, or 'user defined').")
+        elif any_lambda or any_cif:
+            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
         else:
-            raise ValueError("Cannot determine X-axis type for .txt files. Please specify --xaxis (Q, 2theta, r, k, energy, rft, or 'user defined').")
-    elif any_lambda or any_cif:
-        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
-    else:
-        raise ValueError("Cannot determine X-axis type (need .qye / .gr / .nor / .chik / .chir / .cif / wavelength / --xaxis). For .txt or unknown file types, use --xaxis Q, 2theta, r, k, energy, rft, or 'user defined'.")
+            raise ValueError("Cannot determine X-axis type (need .qye / .gr / .nor / .chik / .chir / .cif / wavelength / --xaxis). For .txt or unknown file types, use --xaxis Q, 2theta, r, k, energy, rft, or 'user defined'.")
 
     use_Q   = axis_mode == "Q"
     use_2th = axis_mode == "2theta"
@@ -1751,6 +1764,7 @@ def batplot_main() -> int:
     use_E   = axis_mode == "energy"
     use_k   = axis_mode == "k"      # NEW
     use_rft = axis_mode == "rft"    # NEW
+    use_time = axis_mode == "time"  # NEW: electrochemistry time mode
 
     # Validate: if using 2theta mode with CIF files, wavelength is required
     if use_2th and any_cif and not wavelength_file:
@@ -1816,8 +1830,19 @@ def batplot_main() -> int:
         if wavelength_file and not use_r and not use_E and file_ext not in (".gr", ".nor", ".cif"):
             label += f" (λ={wavelength_file:.5f} Å)"
 
-        # ---- Read data (added .nor branch) ----
-        if is_cif:
+        # ---- Read data (time mode for CSV/MPT or regular mode) ----
+        if use_time and file_ext in ('.csv', '.mpt'):
+            # Time mode: read time (h) vs voltage (V) for electrochemistry files
+            try:
+                if file_ext == '.csv':
+                    x, y = read_csv_time_voltage(fname)
+                elif file_ext == '.mpt':
+                    x, y = read_mpt_time_voltage(fname)
+                e = None
+            except Exception as e_read:
+                print(f"Error reading {fname} in time mode: {e_read}")
+                continue
+        elif is_cif:
             try:
                 # Simulate pattern directly in Q space regardless of current axis_mode
                 Q_sim, I_sim = simulate_cif_pattern_Q(fname)
@@ -1889,15 +1914,18 @@ def batplot_main() -> int:
                 args._warned_extensions.add(file_ext)
                 print(f"Note: Reading '{file_ext}' file as 2-column (x, y) data. Use --xaxis to specify x-axis type if needed.")
 
-        # ---- X-axis conversion logic updated (no conversion for energy) ----
-        if use_Q and file_ext not in (".qye", ".gr", ".nor"):
+        # ---- X-axis conversion logic updated (no conversion for energy or time) ----
+        if use_time:
+            # Time mode: data already in hours, no conversion needed
+            x_plot = x
+        elif use_Q and file_ext not in (".qye", ".gr", ".nor"):
             if wavelength_file:
                 theta_rad = np.radians(x/2)
                 x_plot = 4*np.pi*np.sin(theta_rad)/wavelength_file
             else:
                 x_plot = x
         else:
-            # r, energy, or already Q: direct
+            # r, energy, k, rft, or already Q: direct
             x_plot = x
 
         # ---- Store full (converted) arrays BEFORE cropping ----
@@ -1920,7 +1948,9 @@ def batplot_main() -> int:
             x_plot = x_full
 
         # ---- Normalize (display subset) ----
-        if not args.raw:
+        # Auto-normalize for --stack mode, or explicit --norm flag
+        should_normalize = args.stack or getattr(args, 'norm', False)
+        if should_normalize:
             # Min–max normalization to 0..1 within the currently displayed (cropped) segment
             if y_plot.size:
                 y_min = float(y_plot.min())
@@ -2295,15 +2325,20 @@ def batplot_main() -> int:
     elif use_rft: x_label = "Radial distance (Å)"
     elif use_Q: x_label = r"Q ($\mathrm{\AA}^{-1}$)"
     elif use_2th: x_label = r"$2\theta$ (deg)"
+    elif use_time: x_label = "Time (h)"
     elif args.xaxis:
         x_label = str(args.xaxis)
     else:
         x_label = "X"
     ax.set_xlabel(x_label, fontsize=16)
-    if args.raw:
-        ax.set_ylabel("Intensity", fontsize=16)
-    else:
+    # Y-axis label: normalized if --stack or --norm, or voltage for time mode
+    should_normalize = args.stack or getattr(args, 'norm', False)
+    if use_time:
+        ax.set_ylabel("Voltage (V)", fontsize=16)
+    elif should_normalize:
         ax.set_ylabel("Normalized intensity (a.u.)", fontsize=16)
+    else:
+        ax.set_ylabel("Intensity", fontsize=16)
 
     # Store originals for axis-title toggle restoration (t menu bn/ln)
     try:

{batplot-1.3.3 → batplot-1.3.5}/batplot/cpc_interactive.py

@@ -59,6 +59,7 @@ def _print_menu():
         " l: line",
         " m: marker sizes",
         " c: colors",
+        " k: spine colors",
         "ry: show/hide efficiency",
         " t: toggle axes",
         " h: legend",
@@ -1133,6 +1134,57 @@ def cpc_interactive_menu(fig, ax, ax2, sc_charge, sc_discharge, sc_eff, file_dat
             if is_multi_file:
                 _print_file_list(file_data, current_file_idx)
             continue
+        elif key == 'k':
+            # Spine colors (w=top, a=left, s=bottom, d=right)
+            try:
+                print("Set spine colors (with matching tick and label colors):")
+                print("  w : top spine    | a : left spine")
+                print("  s : bottom spine | d : right spine")
+                print("Example: w:red a:#4561F7 s:blue d:green")
+                line = input("Enter mappings (e.g., w:red a:#4561F7) or q: ").strip()
+                if line and line.lower() != 'q':
+                    push_state("color-spine")
+                    # Map wasd to spine names
+                    key_to_spine = {'w': 'top', 'a': 'left', 's': 'bottom', 'd': 'right'}
+                    tokens = line.split()
+                    for token in tokens:
+                        if ':' not in token:
+                            print(f"Skip malformed token: {token}")
+                            continue
+                        key_part, color = token.split(':', 1)
+                        key_part = key_part.lower()
+                        if key_part not in key_to_spine:
+                            print(f"Unknown key: {key_part} (use w/a/s/d)")
+                            continue
+                        spine_name = key_to_spine[key_part]
+                        # Set for both axes
+                        for curr_ax in [ax, ax2]:
+                            if curr_ax is None:
+                                continue
+                            if spine_name not in curr_ax.spines:
+                                continue
+                            try:
+                                # Set spine color
+                                curr_ax.spines[spine_name].set_edgecolor(color)
+                                # Set tick colors and axis label color for this axis
+                                if spine_name in ('top', 'bottom'):
+                                    curr_ax.tick_params(axis='x', which='both', colors=color)
+                                    curr_ax.xaxis.label.set_color(color)
+                                else:  # left or right
+                                    curr_ax.tick_params(axis='y', which='both', colors=color)
+                                    curr_ax.yaxis.label.set_color(color)
+                            except Exception as e:
+                                print(f"Error setting {spine_name} color: {e}")
+                        print(f"Set {spine_name} spine to {color}")
+                    fig.canvas.draw()
+                else:
+                    print("Canceled.")
+            except Exception as e:
+                print(f"Error in spine color menu: {e}")
+            _print_menu()
+            if is_multi_file:
+                _print_file_list(file_data, current_file_idx)
+            continue
         elif key == 'e':
             try:
                 fname = input("Export filename (default .svg if no extension, q=cancel): ").strip()