batplot 1.0.6__tar.gz → 1.0.7__tar.gz

{batplot-1.0.6 → batplot-1.0.7}/PKG-INFO

@@ -1,8 +1,8 @@
 Metadata-Version: 2.4
 Name: batplot
-Version: 1.0.6
+Version: 1.0.7
 Summary: Interactive plotting for XRD, PDF, and XAS data (.xye, .xy, .qye, .dat, .csv, .gr, .nor, .chik, .chir)
-Author-email: Your Name <your@email.com>
+Author-email: Tian Dai <tianda@uio.no>
 Requires-Python: >=3.7
 Description-Content-Type: text/markdown
 Requires-Dist: numpy

{batplot-1.0.6 → batplot-1.0.7}/batplot/batplot.py

@@ -649,19 +649,19 @@ def interactive_menu(fig, ax, y_data_list, x_data_list, labels, orig_y,
     # REPLACED print_main_menu with column layout (now hides 'd' and 'y' in --stack)
     is_diffraction = use_Q or (not use_r and not use_E and not use_k and not use_rft)  # 2θ or Q
     def print_main_menu():
-        col1 = ["c: colors", "f: font", "l: line", "t: ticks"]
+        has_cif = False
         try:
-            if any(f.lower().endswith('.cif') for f in args.files):
-                col1.append("z: hkl")
+            has_cif = any(f.lower().endswith('.cif') for f in args.files)
         except Exception:
             pass
+        col1 = ["c: colors", "f: font", "l: line", "t: ticks"]
+        if has_cif:
+            col1.append("z: hkl")
         col2 = ["a: rearrange", "d: offset", "r: rename", "g: size","x: change X", "y: change Y"]
-        # Added s: save (session). 'o: open' removed; load .pkl by invoking batplot file.pkl
         col3 = ["v: find peaks", "p: print style", "i: import style", "n: crosshair", "e: export", "s: save", "b: undo", "q: quit"]
         if args.stack:
             col2 = [item for item in col2 if not item.startswith("d:") and not item.startswith("y:")]
         if not is_diffraction:
-            # Remove crosshair option in non-diffraction modes
             col3 = [item for item in col3 if not item.startswith("n:")]
         rows = max(len(col1), len(col2), len(col3))
         print("\nInteractive menu:")
@@ -671,6 +671,17 @@ def interactive_menu(fig, ax, y_data_list, x_data_list, labels, orig_y,
             p2 = col2[i] if i < len(col2) else ""
             p3 = col3[i] if i < len(col3) else ""
             print(f"  {p1:<16} {p2:<16} {p3:<16}")
+
+    # --- Helper for spine visibility ---
+    def set_spine_visible(which, visible):
+        if which in ax.spines:
+            ax.spines[which].set_visible(visible)
+            fig.canvas.draw_idle()
+
+    def get_spine_visible(which):
+        if which in ax.spines:
+            return ax.spines[which].get_visible()
+        return False
     # Initial menu display REMOVED to avoid double print
     # print_main_menu()
     ax.set_aspect('auto', adjustable='datalim')
@@ -727,6 +738,20 @@ def interactive_menu(fig, ax, y_data_list, x_data_list, labels, orig_y,
             if new_family:
                 axis_label.set_fontfamily(new_family)
 
+        # Top duplicate label
+        if hasattr(ax, '_top_xlabel_artist') and ax._top_xlabel_artist is not None:
+            if new_size is not None:
+                ax._top_xlabel_artist.set_fontsize(new_size)
+            if new_family:
+                ax._top_xlabel_artist.set_fontfamily(new_family)
+
+        # Right duplicate manual label
+        if hasattr(ax, '_right_ylabel_artist') and ax._right_ylabel_artist is not None:
+            if new_size is not None:
+                ax._right_ylabel_artist.set_fontsize(new_size)
+            if new_family:
+                ax._right_ylabel_artist.set_fontfamily(new_family)
+
         # Tick labels
         for lbl in ax.get_xticklabels() + ax.get_yticklabels():
             if new_size is not None:
@@ -852,32 +877,6 @@ def interactive_menu(fig, ax, y_data_list, x_data_list, labels, orig_y,
                     if x == BIRD_X and y == bird_y:
                         ch = "@"
                     # obstacle
-                    else:
-                        for o in obstacles:
-                            if o.x == x:
-                                if not (o.gap_start <= y < o.gap_start + GAP_SIZE):
-                                    ch = "#"
-                                break
-                    row_chars.append(ch)
-                print("|" + "".join(row_chars) + "|")
-            print(top_border)
-            print(f"Tick: {tick}  Score: {score}  (j=jump, Enter=fall, q=quit)")
-
-        def collision():
-            # ground / ceiling
-            if bird_y < 0 or bird_y >= HEIGHT:
-                return True
-            for o in obstacles:
-                if o.x == BIRD_X:
-                    if not (o.gap_start <= bird_y < o.gap_start + GAP_SIZE):
-                        return True
-            return False
-
-        print("\n=== Jumping Bird ===")
-        print("Looks like you entered a wrong command!")
-        print("Goal: pass pillars (#). Controls each turn:")
-        print("  j + Enter -> jump")
-        print("  Enter     -> fall")
         print("  q         -> quit game")
         print("Bird = @  | Score increments when you pass a pillar.\n")
 
@@ -1402,6 +1401,8 @@ def interactive_menu(fig, ax, y_data_list, x_data_list, labels, orig_y,
                     if line.get_visible():
                         return line.get_linewidth()
                 return None
+            # Save spine visibility
+            spine_vis = {name: sp.get_visible() for name, sp in ax.spines.items()}
 
             bbox = ax.get_position()
             frame_w_in = bbox.width * fw
@@ -1439,7 +1440,8 @@ def interactive_menu(fig, ax, y_data_list, x_data_list, labels, orig_y,
                 "spines": {
                     name: {
                         "linewidth": sp.get_linewidth(),
-                        "color": sp.get_edgecolor()
+                        "color": sp.get_edgecolor(),
+                        "visible": spine_vis.get(name, True)
                     } for name, sp in ax.spines.items()
                 },
                 "lines": [
@@ -1621,6 +1623,8 @@ def interactive_menu(fig, ax, y_data_list, x_data_list, labels, orig_y,
                             ax.spines[name].set_edgecolor(sp_dict["color"])
                         except Exception:
                             pass
+                    if "visible" in sp_dict:
+                        ax.spines[name].set_visible(sp_dict["visible"])
 
             # ---- Lines (full style) ----
             for entry in cfg.get("lines", []):
@@ -1840,6 +1844,8 @@ def interactive_menu(fig, ax, y_data_list, x_data_list, labels, orig_y,
             fw, fh = fig.get_size_inches()
             frame_w_in = bbox.width * fw
             frame_h_in = bbox.height * fh
+            # Save spine visibility
+            spine_vis = {name: sp.get_visible() for name, sp in ax.spines.items()}
             sess = {
                 'version': SESSION_VERSION,
                 'x_data': [np.array(a) for a in x_data_list],
@@ -1877,7 +1883,8 @@ def interactive_menu(fig, ax, y_data_list, x_data_list, labels, orig_y,
                         'bottom': float(bbox.y0),
                         'right': float(bbox.x0 + bbox.width),
                         'top': float(bbox.y0 + bbox.height)
-                    }
+                    },
+                    'spine_vis': spine_vis
                 },
                 'tick_state': tick_state.copy(),
                 'font': {
@@ -1990,6 +1997,11 @@ def interactive_menu(fig, ax, y_data_list, x_data_list, labels, orig_y,
                 pass
             # Restore figure size & dpi if present
             fig_cfg = sess.get('figure', {})
+            # Restore spine visibility if present
+            spine_vis = fig_cfg.get('spine_vis', {})
+            for name, vis in spine_vis.items():
+                if name in ax.spines:
+                    ax.spines[name].set_visible(vis)
             try:
                 if fig_cfg.get('size') and isinstance(fig_cfg['size'], (list, tuple)) and len(fig_cfg['size']) == 2:
                     fw, fh = fig_cfg['size']
@@ -2357,11 +2369,16 @@ def interactive_menu(fig, ax, y_data_list, x_data_list, labels, orig_y,
             play_jump_game(); continue
         elif key == 'c':
             try:
+                has_cif = False
+                try:
+                    has_cif = any(f.lower().endswith('.cif') for f in args.files)
+                except Exception:
+                    pass
                 while True:
                     print("Color menu:")
                     print("  m : manual color mapping  (e.g., 1:red 2:#00B006)")
                     print("  p : apply colormap palette to a range (e.g., 1-3 viridis)")
-                    if cif_tick_series:
+                    if has_cif and cif_tick_series:
                         print("  t : change CIF tick set color (e.g., 1:red 2:#888888)")
                     print("  q : return to main menu")
                     sub = input("Choose (m/p/t/q): ").strip().lower()
@@ -2393,7 +2410,7 @@ def interactive_menu(fig, ax, y_data_list, x_data_list, labels, orig_y,
                                 except ValueError:
                                     print(f"Bad index: {idx_str}")
                         fig.canvas.draw()
-                    elif sub == 't' and cif_tick_series:
+                    elif sub == 't' and has_cif and cif_tick_series:
                         print("Current CIF tick sets:")
                         for i,(lab,_,_,_,_,color) in enumerate(cif_tick_series):
                             print(f"  {i+1}: {lab} (color {color})")
@@ -2514,8 +2531,17 @@ def interactive_menu(fig, ax, y_data_list, x_data_list, labels, orig_y,
                 print(f"Error in color menu: {e}")
         elif key == 'r':
             try:
+                has_cif = False
+                try:
+                    has_cif = any(f.lower().endswith('.cif') for f in args.files)
+                except Exception:
+                    pass
                 while True:
-                    mode = input("Rename (c=curve, t=cif tick label, x=x-axis, y=y-axis, q=return): ").strip().lower()
+                    rename_opts = "c=curve"
+                    if has_cif:
+                        rename_opts += ", t=cif tick label"
+                    rename_opts += ", x=x-axis, y=y-axis, q=return"
+                    mode = input(f"Rename ({rename_opts}): ").strip().lower()
                     if mode == 'q':
                         break
                     if mode == '':
@@ -3012,6 +3038,10 @@ def interactive_menu(fig, ax, y_data_list, x_data_list, labels, orig_y,
                     print("  tt  top    X axis title")
                     print("  lt  left   Y axis title")
                     print("  rt  right  Y axis title")
+                    print("  bl  bottom plot frame line (spine)")
+                    print("  tl  top    plot frame line (spine)")
+                    print("  ll  left   plot frame line (spine)")
+                    print("  rl  right  plot frame line (spine)")
                     print("  list show state   q return")
                     cmd = input("Enter code(s): ").strip().lower()
                     if not cmd:
@@ -3021,11 +3051,15 @@ def interactive_menu(fig, ax, y_data_list, x_data_list, labels, orig_y,
                     parts = cmd.split()
                     if parts == ['list']:
                         print_tick_state()
+                        # Print spine (frame) visibility
+                        print("Spine (frame) visibility:")
+                        for spine in ['bottom','top','left','right']:
+                            vis = get_spine_visible(spine)
+                            print(f"  {spine:<6}: {'ON ' if vis else 'off'}")
                         continue
                     push_state("tick-toggle")
-                    # Helper to sync font sizes after structural changes
-                    # (Use shared sync_fonts helper)
                     for p in parts:
+                        # Axis title toggles
                         if p in ('bt','tt','lt','rt'):
                             if p == 'bt':
                                 cur = ax.get_xlabel()
@@ -3038,7 +3072,6 @@ def interactive_menu(fig, ax, y_data_list, x_data_list, labels, orig_y,
                             elif p == 'tt':
                                 vis = getattr(ax, '_top_xlabel_on', False)
                                 if not vis:
-                                    # Create duplicate artist if not existing
                                     lbl_text = ax.get_xlabel()
                                     if not lbl_text:
                                         print("No bottom X label to duplicate.")
@@ -3066,12 +3099,10 @@ def interactive_menu(fig, ax, y_data_list, x_data_list, labels, orig_y,
                             elif p == 'rt':
                                 vis = getattr(ax, '_right_ylabel_on', False)
                                 if not vis:
-                                    # Create manual duplicate text artist
                                     base = ax.get_ylabel()
                                     if not base:
                                         print("No left Y label to duplicate.")
                                     else:
-                                        # Remove any previous artist
                                         if hasattr(ax,'_right_ylabel_artist') and ax._right_ylabel_artist is not None:
                                             try: ax._right_ylabel_artist.remove()
                                             except Exception: pass
@@ -3089,6 +3120,15 @@ def interactive_menu(fig, ax, y_data_list, x_data_list, labels, orig_y,
                                     ax._right_ylabel_on = False
                                     print("Hid right Y axis title")
                             continue
+                        # Plot frame (spine) toggles
+                        if p in ('bl','tl','ll','rl'):
+                            spine_map = {'bl':'bottom','tl':'top','ll':'left','rl':'right'}
+                            spine = spine_map[p]
+                            vis = get_spine_visible(spine)
+                            set_spine_visible(spine, not vis)
+                            print(f"Toggled {spine} spine -> {'ON' if not vis else 'off'}")
+                            continue
+                        # Tick toggles
                         if p in tick_state:
                             tick_state[p] = not tick_state[p]
                             print(f"Toggled {p} -> {'ON' if tick_state[p] else 'off'}")
@@ -3262,17 +3302,24 @@ def interactive_menu(fig, ax, y_data_list, x_data_list, labels, orig_y,
 #
 # ---------------- Argument Parsing ----------------
 parser = argparse.ArgumentParser(
-    description="batplot: Plot diffraction / PDF / XAS data (.xye, .xy, .qye, .dat, .csv, .gr, .nor, .chik, .chir)\n"
+    description="batplot: Plot diffraction / PDF / XAS data (.xye, .xy, .qye, .dat, .csv, .gr, .nor, .chik, .chir, .txt)\n"
                 "  --delta or -d : vertical offset between curves (default 0.0 if --stack)\n"
                 "  --xrange min max : X-axis range (2θ or Q), Example: --xrange 2 10\n"
                 "  --out or -o : output image filename (default SVG), Example: --out figure.svg\n"
-                "  --xaxis : X-axis type override if the file extension is neither .xye nor .qye (2theta, Q, or r for PDF)\n"
+                "  --xaxis : X-axis type override if the file extension is not recognized (choose from: 2theta, Q, r, k, energy, rft, or 'user defined')\n"
                 "  --wl : global wavelength (Å) for Q conversion, Example: --wl 1.5406\n"
                 "  --fullprof : FullProf matrix: xstart xend xstep [wavelength], Example: --fullprof 2 10 0.02 1.5406\n"
                 "  --raw : plot raw intensity values instead of normalized\n"
                 "  --stack : stack curves from top to bottom\n"
-                "test"
                 "  --interactive : keep figure open for interactive editing\n\n"
+                "File type and X-axis selection:\n"
+                "  - .qye: X axis is Q\n"
+                "  - .gr: X axis is r\n"
+                "  - .nor: X axis is Energy (eV)\n"
+                "  - .chik: X axis is k\n"
+                "  - .chir: X axis is r\n"
+                "  - .txt: Treated as generic 2-column data.\n"
+                "  If none of the files have a recognized extension, you must specify --xaxis (Q, 2theta, r, k, energy, rft, or 'user defined').\n"
                 "Example usages:\n"
                 "  batplot file1.xye:1.5406 file2.qye --stack --interactive\n"
                 "  batplot file1.dat file2.dat --xaxis Q --wl 1.5406 --delta 1.0 --out figure.svg\n"
@@ -3289,7 +3336,7 @@ parser.add_argument("--autoscale", action="store_true")
 parser.add_argument("--xrange", "-r", nargs=2, type=float)
 parser.add_argument("--out", "-o", type=str)
 parser.add_argument("--errors", action="store_true")
-parser.add_argument("--xaxis", choices=["2theta", "Q", "r"])
+parser.add_argument("--xaxis", type=str)
 parser.add_argument("--convert", "-c", nargs="+")
 parser.add_argument("--wl", type=float)
 parser.add_argument("--fullprof", nargs="+", type=float)
@@ -3326,7 +3373,7 @@ args = parser.parse_args()
 # ---------------- Batch Processing (directory or 'all') ----------------
 def batch_process(directory: str, args):
     print(f"Batch mode: scanning {directory}")
-    supported_ext = {'.xye', '.xy', '.qye', '.dat', '.csv', '.gr', '.nor', '.chik', '.chir'}  # added .xy
+    supported_ext = {'.xye', '.xy', '.qye', '.dat', '.csv', '.gr', '.nor', '.chik', '.chir', '.txt'}  # added .xy, .txt
     out_dir = os.path.join(directory, "batplot_svg")
     os.makedirs(out_dir, exist_ok=True)
     files = [f for f in sorted(os.listdir(directory))
@@ -3364,20 +3411,27 @@ def batch_process(directory: str, args):
                 x, y = data[:,0], data[:,1]; e = data[:,2] if data.shape[1] >= 3 else None
                 axis_mode = 'rft'
             else:
+                # Support .txt as generic 2-column data
                 data = np.loadtxt(fpath, comments="#")
                 if data.ndim == 1: data = data.reshape(1, -1)
                 if data.shape[1] < 2: raise ValueError("Invalid 2-column data")
                 x, y = data[:,0], data[:,1]
                 e = data[:,2] if data.shape[1] >= 3 else None
-                # Decide axis: priority: user --xaxis, .qye -> Q, else if wavelength provided -> Q, else 2theta
+                # Decide axis: priority: user --xaxis, .qye -> Q, .gr -> r, .nor -> energy, .chik -> k, .chir -> rft, else prompt for --xaxis
                 if ext == '.qye':
                     axis_mode = 'Q'
-                elif args.xaxis in ('Q','2theta'):
+                elif ext == '.gr':
+                    axis_mode = 'r'
+                elif ext == '.nor':
+                    axis_mode = 'energy'
+                elif 'chik' in ext:
+                    axis_mode = 'k'
+                elif 'chir' in ext:
+                    axis_mode = 'rft'
+                elif args.xaxis:
                     axis_mode = args.xaxis
-                elif args.wl is not None:
-                    axis_mode = 'Q'
                 else:
-                    axis_mode = '2theta'
+                    raise ValueError("Cannot determine X-axis type for file {} (need .qye / .gr / .nor / .chik / .chir or specify --xaxis).".format(fname))
             # ---- Convert to Q if needed ----
             if axis_mode == 'Q' and ext not in ('.qye', '.gr', '.nor'):
                 if args.wl is None:
@@ -3686,28 +3740,27 @@ raw_y_full_list = []
 offsets_list = []
 
 # ---------------- 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)  # <-- NEW
+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
-def _ext_token(path):
-    return os.path.splitext(path)[1].lower()  # includes leading dot
-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_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_qye or any_lambda or any_cif))) > 1 or \
-    (any_gr and args.xaxis in ("Q", "2theta", "r")) or \
-    (any_nor and args.xaxis in ("Q", "2theta", "r")):
-     raise ValueError("Cannot mix .gr (r), .nor (energy), and Q/2θ/CIF data. Plot them in separate runs.")
-
 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.")
+    raise ValueError("Cannot mix .gr (r), .nor (energy), .chik (k), .chir (FT-EXAFS R), and Q/2θ/CIF data together. Split runs.")
 
-if any_gr:
+# 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"
@@ -3715,6 +3768,12 @@ 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_qye or any_lambda or any_cif:
     if args.xaxis and args.xaxis.lower() in ("2theta","two_theta","tth"):
         axis_mode = "2theta"
@@ -3723,7 +3782,7 @@ elif any_qye or any_lambda or any_cif:
 elif args.xaxis:
     axis_mode = args.xaxis
 else:
-    raise ValueError("Cannot determine X-axis type (need .qye / .gr / .nor / .chik / .chir / .cif / wavelength / --xaxis).")
+    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"
@@ -4254,7 +4313,10 @@ elif use_k: x_label = r"k ($\mathrm{\AA}^{-1}$)"
 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)"
-else: x_label = "X"
+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)

{batplot-1.0.6 → batplot-1.0.7}/batplot.egg-info/PKG-INFO

@@ -1,8 +1,8 @@
 Metadata-Version: 2.4
 Name: batplot
-Version: 1.0.6
+Version: 1.0.7
 Summary: Interactive plotting for XRD, PDF, and XAS data (.xye, .xy, .qye, .dat, .csv, .gr, .nor, .chik, .chir)
-Author-email: Your Name <your@email.com>
+Author-email: Tian Dai <tianda@uio.no>
 Requires-Python: >=3.7
 Description-Content-Type: text/markdown
 Requires-Dist: numpy

{batplot-1.0.6 → batplot-1.0.7}/pyproject.toml

@@ -4,10 +4,10 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "batplot"
-version = "1.0.6"
+version = "1.0.7"
 description = "Interactive plotting for XRD, PDF, and XAS data (.xye, .xy, .qye, .dat, .csv, .gr, .nor, .chik, .chir)"
 authors = [
-    { name = "Your Name", email = "your@email.com" }
+    { name = "Tian Dai", email = "tianda@uio.no" }
 ]
 readme = "README.md"
 requires-python = ">=3.7"