Add demo script for running riCOM in CLI with python

Author: ThFriedrich

ricom_demo.py

@@ -0,0 +1,109 @@
+#!/usr/bin/env python3
+"""
+Demo script for running riCOM from command line interface through python.
+This script demonstrates how to execute the riCOM executable with various arguments.
+"""
+
+import subprocess
+import os
+import matplotlib.pyplot as plt
+import numpy as np
+
+# Path to the riCOM executable (adjust as needed)
+RICOM_EXECUTABLE = "./build/RICOM"
+
+def demo_timepix_camera():
+    """
+    Demo: Process data from Timepix camera with dwell time setting.
+    Available arguments are:
+
+    Input/Connection:
+      -filename <path>        : Read from .mib or .t3p file
+    
+    Dimensions:
+      -nx <number>           : Width of scan image
+      -ny <number>           : Height of scan image
+      -cam_nx <number>       : Width of camera sensor
+      -cam_ny <number>       : Height of camera sensor
+    
+    Processing:
+      -skipr <number>        : Skip rows (skip n frames at the end of each line for flyback correction)
+      -skipi <number>        : Skip images (skip n frames at the end of each image for flyback correction)
+      -k <number>            : Kernel size for riCOM
+      -r <float>             : CBED rotation angle in degrees
+      -offset <x> <y>        : CBED center offset (two values)
+      -update_offset <0|1>   : Auto-update offset during processing
+      -radius <inner> <outer>: Virtual STEM detector radii (enables vSTEM)
+      -f <low> <high>        : Kernel filter frequency range
+      -threads <number>      : Number of processing threads
+      -queue_size <number>   : Size of processing queue
+      -rep <number>          : Number of repetitions
+    
+    Camera-specific:
+      -depth <number>        : Bit depth per pixel (Merlin camera)
+      -dwell_time <float>    : Dwell time in seconds (Timepix camera)
+    
+    Output:
+      -save_img_path <path>  : Save reconstruction as image file
+      -save_data_path <path> : Save reconstruction as numpy array (.npy)
+    
+    Visualization:
+      -redraw_interval <ms>  : Redraw interval in milliseconds (enables SDL display)
+      -plot_e_field <0|1>    : Plot electric field magnitude
+    """
+
+    args = [
+        RICOM_EXECUTABLE,
+        # "-filename", "/home/thomas/Documents/Git/4D-STEM-Data/data/cryst_1   mono_120_CL 115  Mag_2.55Mx  defocus_-198.67 CA_21.47 Tue_Jul_16_11_50_09_2024_STEM_300kV_2048x2048_4_us_1_scans.t3p",
+        "-filename", "/home/thomas/Documents/Git/4D-STEM-Data/data/cryst_5.5   mono_140_CL 115  Mag_2.55Mx  defocus_0 CA_24.70 Tue_Oct__1_17_48_58_2024_STEM_300kV_2048x2048_4_us_1_scans.t3p",
+        
+        # Timepix-specific setting
+        "-dwell_time", "4000",  # Dwell time in nanoseconds (Timepix camera)
+        
+        # Scan dimensions
+        "-nx", "2049",
+        "-ny", "2048",
+        
+        # Camera dimensions
+        "-cam_nx", "256",
+        "-cam_ny", "256",
+        
+        # Kernel
+        "-k", "12",   # Kernel half-size for riCOM
+        "-r", "260",  # CBED rotation angle in degrees
+        "-offset", "135.12", "116.694",  # CBED center (x, y)
+
+        # Processing
+        "-threads", "1",
+        "-redraw_interval", "200",  # Redraw every 200 ms
+        
+        # Output
+        "-save_data_path", "timepix_output.npy",
+    ]
+    
+    print("Running riCOM with Timepix camera data...")
+    print(" ".join(args))
+    subprocess.run(args, capture_output=False, text=True)
+
+
+if __name__ == "__main__":
+    
+    # Check if executable exists
+    if not os.path.exists(RICOM_EXECUTABLE):
+        print(f"Warning: Executable not found at {RICOM_EXECUTABLE}")
+        print("Please adjust RICOM_EXECUTABLE path in this script.")
+        print()
+
+    # Run reconstruction, and get COM_AVG from the output, which can be used for correction in the second run if needed
+    demo_timepix_camera()
+
+    # When given a data path, the script will save the reconstruction as a numpy array. We can load and visualize it here.
+    img_data = np.load("timepix_output.npy")
+    fig, ax = plt.subplots(1, 1, figsize=(8, 8))
+    im = ax.imshow(img_data, cmap='viridis')
+
+    ax.axis('off')
+    plt.colorbar(im, ax=ax, shrink=0.8)
+    plt.tight_layout()
+    plt.show()
+    

src/RunCLI.cpp

@@ -263,6 +263,7 @@ int run_cli(int argc, char *argv[], Ricom *ricom, CAMERA::Default_configurations
     {
         RICOM::run_ricom(ricom, ricom->mode);
     }
+    std::cout << "COM_AVG " << ricom->com_public[0] << " " << ricom->com_public[1] << std::endl;
     if (save_dat != "")
     {
         save_numpy(&save_dat, ricom->nx, ricom->ny, &ricom->ricom_data);