batplot 1.8.4__tar.gz → 1.8.6__tar.gz

{batplot-1.8.4/batplot.egg-info → batplot-1.8.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: batplot
-Version: 1.8.4
+Version: 1.8.6
 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-1.8.4 → batplot-1.8.6}/USER_MANUAL.md

@@ -131,8 +131,29 @@ batplot file1.xy file2.xye style.bps --out output.svg
 
 batplot file1.xy file2.xye ./Style/style.bps --out output.svg
 # Normal mode: apply style from relative path to multiple files
+
+batplot file1.xy file2.xy --1d --stack --i
+# Plot the first derivative (dy/dx) of file1 and file2 with interactive menu
+```
+
+### Derivative Plotting
+
+The `--1d` and `--2d` flags (both equivalent) allow you to plot the first derivative (dy/dx) of your datasets. This is useful for identifying peaks, inflection points, and analyzing the rate of change in your data.
+
+**Examples:**
+```bash
+batplot file1.xy file2.xy --1d --stack --i
+# Plot 1st derivatives of file1 and file2, stacked with interactive menu
+
+batplot allfiles --1d --interactive
+# Plot 1st derivatives of all XY files with interactive menu
+
+batplot file1.xy --1d --xrange 10 80
+# Plot 1st derivative with custom X-axis range
 ```
 
+**Note:** The derivative is calculated using numpy's gradient function, which automatically handles non-uniform spacing in your X-axis data. The derivative calculation is applied after data loading and axis conversion, but before any transformations (EXAFS k-weighting, normalization, etc.).
+
 ### Wavelength Specification
 
 Batplot supports flexible wavelength specification for XRD data conversion and CIF tick calculation. You can specify wavelengths globally using `--wl` or per-file using colon syntax.

{batplot-1.8.4 → batplot-1.8.6}/batplot/__init__.py

@@ -1,5 +1,5 @@
 """batplot: Interactive plotting for battery data visualization."""
 
-__version__ = "1.8.4"
+__version__ = "1.8.6"
 
 __all__ = ["__version__"]

{batplot-1.8.4/batplot_backup_20251221_101150 → batplot-1.8.6/batplot}/args.py

@@ -141,6 +141,7 @@ def _print_general_help() -> None:
         "How to run (basics):\n"
         "  [1D(XY) curves]\n"
         "    batplot file1.xy file2.qye [option1] [option2]             # 1D curves, read the first two columns as X and Y axis by default\n"
+        "    batplot file1.xy file2.xy --1d --stack --i                  # Plot 1st derivatives with interactive menu\n"
         "    batplot allfiles                       # Plot all files in current directory on same figure\n"
         "    batplot allfiles /path/to/dir          # Plot all files in specified directory\n"
         "    batplot allfiles --i                   # Plot all files with interactive menu\n"
@@ -208,7 +209,8 @@ def _print_xy_help() -> None:
         "Examples:\n"
         "  batplot a.xye:1.5406 b.qye --stack --i\n"
         "  batplot a.dat b.xy --wl 1.54 --i\n"
-        "  batplot pattern.qye ticks.cif:1.54 --i\n\n"
+        "  batplot pattern.qye ticks.cif:1.54 --i\n"
+        "  batplot file1.xy file2.xy --1d --stack --i  # Plot 1st derivatives with interactive menu\n\n"
         "Plot all files together:\n"
         "  batplot allfiles                       # Plot all XY files on same figure\n"
         "  batplot allfiles /path/to/dir          # Plot all XY files in specified directory\n"
@@ -241,6 +243,8 @@ def _print_xy_help() -> None:
         "  --kchik                   : multiply y by x for EXAFS kχ(k) plots (sets labels to k (Å⁻¹) vs kχ(k) (Å⁻¹))\n"
         "  --k2chik                  : multiply y by x² for EXAFS k²χ(k) plots (sets labels to k (Å⁻¹) vs k²χ(k) (Å⁻²))\n"
         "  --k3chik                  : multiply y by x³ for EXAFS k³χ(k) plots (sets labels to k (Å⁻¹) vs k³χ(k) (Å⁻³))\n"
+        "  --1d                      : plot the first derivative (dy/dx) of the datasets\n"
+        "  --2d                      : plot the first derivative (dy/dx) of the datasets (alias for --1d)\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, time, or user defined)\n"
@@ -248,6 +252,14 @@ def _print_xy_help() -> None:
         "  --ro                      : swap x and y axes (exchange x and y values before plotting)\n"
         "                              e.g. --xaxis time --ro plots time as y-axis and voltage as x-axis\n"
         "  --wl <float>              : set wavelength for Q conversion for all files, e.g. --wl 1.5406\n"
+        "  --convert/-c <from> <to>  : convert XRD data and export to 'converted' subfolder:\n"
+        "                              - <wl1> <wl2>  : convert 2θ from wavelength1 to wavelength2\n"
+        "                              - <wl> q       : convert 2θ (with wavelength) to Q space\n"
+        "                              - q <wl>      : convert Q space to 2θ (with wavelength)\n"
+        "                              Examples:\n"
+        "                                batplot file.xye --convert 1.54 0.25\n"
+        "                                batplot file.xye --convert 1.54 q\n"
+        "                                batplot file.qye --convert q 1.54\n"
         "  File wavelength syntax   : specify wavelength(s) per file using colon syntax:\n"
         "                              - file:wl          : single wavelength (for Q conversion or CIF 2theta calculation)\n"
         "                              - file:wl1:wl2     : dual wavelength (convert 2theta→Q using wl1, then Q→2theta using wl2)\n"
@@ -332,12 +344,15 @@ 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 --xaxis 2theta              # Using 2theta axis\n\n"
+        "  batplot --operando --xaxis 2theta              # Using 2theta axis\n"
+        "  batplot --operando --1d --interactive           # Plot derivatives as contour with interactive menu\n"
+        "  batplot --operando --2d --interactive          # Plot derivatives (alias for --1d)\n\n"
         "  • Folder should contain XY files (.xy/.xye/.qye/.dat).\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, 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"
+        "  • 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"
         "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"
@@ -416,7 +431,8 @@ def build_parser() -> argparse.ArgumentParser:
     parser.add_argument("--out", "-o", type=str, help=argparse.SUPPRESS)
     parser.add_argument("--errors", action="store_true", help=argparse.SUPPRESS)
     parser.add_argument("--xaxis", type=str, help=argparse.SUPPRESS)
-    parser.add_argument("--convert", "-c", nargs="+", help=argparse.SUPPRESS)
+    parser.add_argument("--convert", "-c", 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("--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)
@@ -453,6 +469,8 @@ def build_parser() -> argparse.ArgumentParser:
                        help=argparse.SUPPRESS)
     parser.add_argument("--readcolcsv", nargs=2, type=int, metavar=('X_COL', 'Y_COL'),
                        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)
     return parser
 
 

{batplot-1.8.4 → batplot-1.8.6}/batplot/batch.py

@@ -646,6 +646,18 @@ def batch_process(directory: str, args):
             else:
                 x_plot = x
 
+            # Calculate first derivative if requested (after axis conversion)
+            if getattr(args, 'derivative_1d', False) or getattr(args, 'derivative_2d', False):
+                # Calculate dy/dx using numpy gradient
+                # numpy.gradient handles non-uniform spacing automatically
+                if len(y) > 1:
+                    dy_dx = np.gradient(y, x_plot)
+                    y = dy_dx
+                else:
+                    # Single point or empty - cannot calculate derivative
+                    print(f"Warning: Cannot calculate derivative for {fname}: insufficient data points")
+                    continue
+
             # Normalize if --norm flag is set
             if getattr(args, 'norm', False):
                 if y.size: