batplot 1.3.6__tar.gz → 1.3.8__tar.gz

{batplot-1.3.6 → batplot-1.3.8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: batplot
-Version: 1.3.6
+Version: 1.3.8
 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

{batplot-1.3.6 → batplot-1.3.8}/batplot/__init__.py

@@ -1,5 +1,5 @@
 """batplot: Interactive plotting for battery data visualization."""
 
-__version__ = "1.3.6"
+__version__ = "1.3.8"
 
 __all__ = ["__version__"]

{batplot-1.3.6 → batplot-1.3.8}/batplot/batplot.py

@@ -79,6 +79,22 @@ except ImportError:
 keep_canvas_fixed = False
 
 
+def _natural_sort_key(filename: str) -> list:
+    """Generate a natural sorting key for filenames with numbers.
+    
+    Converts 'file_10.xy' to ['file_', 10, '.xy'] so numerical parts are sorted numerically.
+    This ensures file_2.xy comes before file_10.xy (natural order).
+    """
+    parts = []
+    for match in re.finditer(r'(\d+|\D+)', filename):
+        text = match.group(0)
+        if text.isdigit():
+            parts.append(int(text))
+        else:
+            parts.append(text.lower())
+    return parts
+
+
 def batplot_main() -> int:
     """Main entry point for batplot CLI.
     
@@ -1131,7 +1147,7 @@ def batplot_main() -> int:
             all_xy_files = []
             unknown_ext_files = []
             
-            for f in sorted(os.listdir(os.getcwd())):
+            for f in sorted(os.listdir(os.getcwd()), key=_natural_sort_key):
                 if not os.path.isfile(os.path.join(os.getcwd(), f)):
                     continue
                 ext = os.path.splitext(f)[1].lower()

{batplot-1.3.6 → batplot-1.3.8}/batplot/operando.py

@@ -32,6 +32,21 @@ KNOWN_DIFFRACTION_EXT = {".xy", ".xye", ".qye", ".dat"}
 _two_theta_re = re.compile(r"2[tT]heta|2th", re.IGNORECASE)
 _q_re = re.compile(r"^q$", re.IGNORECASE)
 
+def _natural_sort_key(path: Path) -> list:
+    """Generate a natural sorting key for filenames with numbers.
+    
+    Converts 'file_10.xy' to ['file_', 10, '.xy'] so numerical parts are sorted numerically.
+    This ensures file_2.xy comes before file_10.xy (natural order).
+    """
+    parts = []
+    for match in re.finditer(r'(\d+|\D+)', path.name):
+        text = match.group(0)
+        if text.isdigit():
+            parts.append(int(text))
+        else:
+            parts.append(text.lower())
+    return parts
+
 def _infer_axis_mode(args, any_qye: bool, has_unknown_ext: bool):
     # Priority: explicit --xaxis, else .qye presence (Q), else wavelength (Q), else default 2theta with warning
     # If unknown extensions are present, use "user defined" mode
@@ -83,12 +98,12 @@ def plot_operando_folder(folder: str, args) -> Tuple[plt.Figure, plt.Axes, Dict[
     p = Path(folder)
     if not p.is_dir():
         raise FileNotFoundError(f"Not a directory: {folder}")
-    # First try to find known diffraction files
-    files = sorted([f for f in p.iterdir() if f.suffix.lower() in KNOWN_DIFFRACTION_EXT])
+    # First try to find known diffraction files (filter out macOS resource fork files starting with ._)
+    files = sorted([f for f in p.iterdir() if f.suffix.lower() in KNOWN_DIFFRACTION_EXT and not f.name.startswith("._")], key=_natural_sort_key)
     has_unknown_ext = False
     # If no known files found, accept any file extension (except .mpt which is for electrochemistry)
     if not files:
-        files = sorted([f for f in p.iterdir() if f.is_file() and f.suffix.lower() != ".mpt"])
+        files = sorted([f for f in p.iterdir() if f.is_file() and f.suffix.lower() != ".mpt" and not f.name.startswith("._")], key=_natural_sort_key)
         has_unknown_ext = True
         if not files:
             raise FileNotFoundError("No data files found in folder (excluding .mpt files)")
@@ -137,7 +152,8 @@ def plot_operando_folder(folder: str, args) -> Tuple[plt.Figure, plt.Axes, Dict[
     Z = np.vstack(stack)  # shape (n_scans, n_x)
 
     # Detect an electrochemistry .mpt file in the same folder (if any)
-    mpt_files = sorted([f for f in p.iterdir() if f.suffix.lower() == ".mpt"])  # pick first if present
+    # Filter out macOS resource fork files (starting with ._)
+    mpt_files = sorted([f for f in p.iterdir() if f.suffix.lower() == ".mpt" and not f.name.startswith("._")], key=_natural_sort_key)  # pick first if present
     has_ec = len(mpt_files) > 0
     ec_ax = None
 
@@ -151,8 +167,8 @@ def plot_operando_folder(folder: str, args) -> Tuple[plt.Figure, plt.Axes, Dict[
     # Use imshow for speed; mask nans
     Zm = np.ma.masked_invalid(Z)
     extent = (grid_x.min(), grid_x.max(), 0, Zm.shape[0]-1)
-    # Top-to-down visual order (scan 0 at top) -> origin='upper'
-    im = ax.imshow(Zm, aspect='auto', origin='upper', extent=extent, cmap='viridis', interpolation='nearest')
+    # Bottom-to-top visual order (scan 0 at bottom) to match EC time progression -> origin='lower'
+    im = ax.imshow(Zm, aspect='auto', origin='lower', extent=extent, cmap='viridis', interpolation='nearest')
     # Place colorbar on the left
     cbar = fig.colorbar(im, ax=ax, location='left', pad=0.15)
     cbar.ax.yaxis.set_ticks_position('left')

{batplot-1.3.6 → batplot-1.3.8}/batplot/readers.py

@@ -95,12 +95,50 @@ def read_mpt_file(fname: str, mode: str = 'gc', mass_mg: float = None):
     """
     import re
     
+    # Check if this is a full EC-Lab format or a simple 2-column export
+    is_eclab_format = False
+    with open(fname, 'r', encoding='utf-8', errors='ignore') as f:
+        first_line = f.readline().strip()
+        if first_line.startswith('EC-Lab ASCII FILE'):
+            is_eclab_format = True
+    
+    # Handle simple 2-column time/voltage export format (for operando time mode)
+    if not is_eclab_format and mode == 'time':
+        try:
+            # Read with tab delimiter and handle European comma decimal separator
+            with open(fname, 'r', encoding='utf-8', errors='ignore') as f:
+                # Skip header line
+                f.readline()
+                time_vals = []
+                voltage_vals = []
+                for line in f:
+                    line = line.strip()
+                    if not line:
+                        continue
+                    parts = line.split('\t')
+                    if len(parts) >= 2:
+                        # Replace comma with period for European locale
+                        time_vals.append(float(parts[0].replace(',', '.')))
+                        voltage_vals.append(float(parts[1].replace(',', '.')))
+                
+                if not time_vals:
+                    raise ValueError("No data found in file")
+                
+                time_s = np.array(time_vals)
+                voltage_v = np.array(voltage_vals)
+                current_mA = np.zeros_like(time_s)  # No current data in simple format
+                return time_s, voltage_v, current_mA
+        except Exception as e:
+            raise ValueError(f"Failed to read simple .mpt format: {e}")
+    
+    # For non-time modes or EC-Lab format, require full EC-Lab format
+    if not is_eclab_format:
+        raise ValueError(f"Not a valid EC-Lab .mpt file: {fname}")
+    
     # Read header to find number of header lines
     header_lines = 0
     with open(fname, 'r', encoding='utf-8', errors='ignore') as f:
         first_line = f.readline().strip()
-        if not first_line.startswith('EC-Lab ASCII FILE'):
-            raise ValueError(f"Not a valid EC-Lab .mpt file: {fname}")
         
         # Find header lines count
         for line in f:

{batplot-1.3.6 → batplot-1.3.8}/batplot/session.py

@@ -135,12 +135,24 @@ def dump_session(
         for side in ('top', 'bottom', 'left', 'right'):
             sp_obj = axis.spines.get(side)
             prefix = {'top': 't', 'bottom': 'b', 'left': 'l', 'right': 'r'}[side]
+            # Consistent tick/title state logic for all sides
+            if side == 'left':
+                ylabel_text = axis.get_ylabel()
+                title_state = bool(ylabel_text)
+            elif side == 'bottom':
+                title_state = bool(axis.get_xlabel())
+            elif side == 'top':
+                title_state = bool(getattr(axis, '_top_xlabel_on', False))
+            elif side == 'right':
+                title_state = bool(getattr(axis, '_right_ylabel_on', False))
+            else:
+                title_state = False
             wasd[side] = {
                 'spine': bool(sp_obj.get_visible() if sp_obj else False),
                 'ticks': bool(ts.get(f'{prefix}_ticks', ts.get({'top':'tx','bottom':'bx','left':'ly','right':'ry'}[side], side=='bottom' or side=='left'))),
                 'minor': bool(ts.get(f'm{prefix}x' if side in ('top','bottom') else f'm{prefix}y', False)),
                 'labels': bool(ts.get(f'{prefix}_labels', ts.get({'top':'tx','bottom':'bx','left':'ly','right':'ry'}[side], side=='bottom' or side=='left'))),
-                'title': bool(getattr(axis, '_top_xlabel_on' if side=='top' else '_right_ylabel_on' if side=='right' else '', False)) if side in ('top','right') else bool(axis.get_xlabel() if side=='bottom' else axis.get_ylabel() if side=='left' else False),
+                'title': title_state,
             }
         return wasd
     
@@ -321,12 +333,26 @@ def dump_operando_session(
             for side in ('top', 'bottom', 'left', 'right'):
                 sp = axis.spines.get(side)
                 prefix = {'top': 't', 'bottom': 'b', 'left': 'l', 'right': 'r'}[side]
+                # For 'left' side ylabel: check if it's currently visible (has text)
+                # If hidden but has stored text, the title state should be False (hidden)
+                if side == 'left':
+                    ylabel_text = axis.get_ylabel()
+                    title_state = bool(ylabel_text)  # True only if currently visible with text
+                elif side == 'bottom':
+                    title_state = bool(axis.get_xlabel())
+                elif side == 'top':
+                    title_state = bool(getattr(axis, '_top_xlabel_on', False))
+                elif side == 'right':
+                    title_state = bool(getattr(axis, '_right_ylabel_on', False))
+                else:
+                    title_state = False
+                
                 wasd[side] = {
                     'spine': bool(sp.get_visible() if sp else False),
                     'ticks': bool(ts.get(f'{prefix}_ticks', ts.get({'top':'tx','bottom':'bx','left':'ly','right':'ry'}[side], side=='bottom' or side=='left'))),
                     'minor': bool(ts.get(f'm{prefix}x' if side in ('top','bottom') else f'm{prefix}y', False)),
                     'labels': bool(ts.get(f'{prefix}_labels', ts.get({'top':'tx','bottom':'bx','left':'ly','right':'ry'}[side], side=='bottom' or side=='left'))),
-                    'title': bool(getattr(axis, '_top_xlabel_on' if side=='top' else '_right_ylabel_on' if side=='right' else '', False)) if side in ('top','right') else bool(axis.get_xlabel() if side=='bottom' else axis.get_ylabel() if side=='left' else False),
+                    'title': title_state,
                 }
             return wasd
         
@@ -414,6 +440,7 @@ def dump_operando_session(
                 'wasd_state': ec_wasd_state,
                 'spines': ec_spines,
                 'ticks': {'widths': ec_ticks},
+                'stored_ylabel': getattr(ec_ax, '_stored_ylabel', None),  # Save hidden ylabel text
             }
 
         sess = {
@@ -440,6 +467,7 @@ def dump_operando_session(
                 'wasd_state': op_wasd_state,
                 'spines': op_spines,
                 'ticks': {'widths': op_ticks},
+                'stored_ylabel': getattr(ax, '_stored_ylabel', None),  # Save hidden ylabel text
             },
             'colorbar': {
                 'label': cb_label,
@@ -549,6 +577,11 @@ def load_operando_session(filename: str):
     # Persist custom labels
     setattr(ax, '_custom_labels', dict(op.get('custom_labels', {'x': None, 'y': None})))
     
+    # Restore stored ylabel if present (for cases where ylabel was hidden with a5)
+    stored_ylabel = op.get('stored_ylabel')
+    if stored_ylabel is not None:
+        setattr(ax, '_stored_ylabel', stored_ylabel)
+    
     # Apply operando WASD state if version 2+
     version = sess.get('version', 1)
     if version >= 2:
@@ -750,6 +783,11 @@ def load_operando_session(filename: str):
             except Exception:
                 pass
         
+        # Restore stored ylabel if present (for cases where ylabel was hidden)
+        stored_ylabel = ec.get('stored_ylabel')
+        if stored_ylabel is not None:
+            setattr(ec_ax, '_stored_ylabel', stored_ylabel)
+        
         # Apply EC WASD state if version 2+
         if version >= 2:
             ec_wasd = ec.get('wasd_state')

{batplot-1.3.6 → batplot-1.3.8}/batplot.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: batplot
-Version: 1.3.6
+Version: 1.3.8
 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

{batplot-1.3.6 → batplot-1.3.8}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "batplot"
-version = "1.3.6"
+version = "1.3.8"
 description = "Interactive plotting for XRD, PDF, and XAS data (.xye, .xy, .qye, .dat, .csv, .gr, .nor, .chik, .chir)"
 authors = [
     { name = "Tian Dai", email = "tianda@uio.no" }