first pass

iadpython/iadcommand.py

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+# pylint: disable=line-too-long
+
+import sys
+from enum import Enum
+import argparse
+import iadpython
+
+class SlidePosition(Enum):
+    """All the combinations of glass and sample."""
+    NO_SLIDES = 0
+    ONE_SLIDE_ON_TOP = 1
+    TWO_IDENTICAL_SLIDES = 2
+    ONE_SLIDE_ON_BOTTOM = 3
+    ONE_SLIDE_NEAR_SPHERE = 4
+    ONE_SLIDE_NOT_NEAR_SPHERE = 5
+
+class LightCondition(Enum):
+    """Options for interpreting illumination."""
+    MR_IS_ONLY_RD = 1
+    MT_IS_ONLY_TD = 2
+    NO_UNSCATTERED_LIGHT = 3
+
+# Argument specifications
+arg_specs = [
+    {"flags": ["-1"], "dest": "r_sphere", "nargs": 5, "type": float, "help": "Five numbers separated by spaces"},
+    {"flags": ["-2"], "dest": "t_sphere", "nargs": 5, "type": float, "help": "Five numbers separated by spaces"},
+    {"flags": ["-a"], "type": float, "help": "Use this albedo"},
+    {"flags": ["-A"], "type": float, "help": "Use this absorption coefficient"},
+    {"flags": ["-b"], "type": float, "help": "Use this optical thickness"},
+    {"flags": ["-B"], "type": float, "help": "Beam diameter"},
+    {"flags": ["-c"], "type": float, "help": "Fraction of unscattered refl in MR"},
+    {"flags": ["-C"], "type": float, "help": "Fraction of unscattered trans in MT"},
+    {"flags": ["-d"], "type": float, "help": "Thickness of sample"},
+    {"flags": ["-D"], "type": float, "help": "Thickness of slide"},
+    {"flags": ["-e"], "type": float, "default": 0.0001, "help": "Error tolerance (default 0.0001)"},
+    {"flags": ["-E"], "type": float, "help": "Optical depth (=mua*D) for slides"},
+    {"flags": ["-f"], "type": float, "help": "Fraction 0.0-1.0 of light to hit sphere wall first"},
+    {"flags": ["-F"], "type": str, "help": "Use this scattering coefficient or formula"},
+    {"flags": ["-g"], "type": float, "default": 0, "help": "Scattering anisotropy (default 0)"},
+    {"flags": ["-G"], "type": str, "choices": ['0', '2', 't', 'b', 'n', 'f'], "help": "Type of boundary "},
+    {"flags": ["-i"], "type": float, "help": "Light incident at this angle in degrees"},
+    {"flags": ["-M"], "type": int, "help": "Number of Monte Carlo iterations"},
+    {"flags": ["-n"], "type": float, "help": "Index of refraction of slab"},
+    {"flags": ["-N"], "type": float, "help": "Index of refraction of slides"},
+    {"flags": ["-o"], "type": str, "help": "Filename for output"},
+    {"flags": ["-p"], "type": int, "help": "# of Monte Carlo photons (default 100000)"},
+    {"flags": ["-q"], "type": int, "default": 8, "help": "Number of quadrature points (default=8)"},
+    {"flags": ["-r"], "type": float, "help": "Total reflection measurement"},
+    {"flags": ["-R"], "type": float, "help": "Actual reflectance for 100% measurement"},
+    {"flags": ["-S"], "type": int, "choices": [0, 1, 2], "help": "Number of spheres used"},
+    {"flags": ["-t"], "type": float, "help": "Total transmission measurement"},
+    {"flags": ["-T"], "type": float, "help": "Actual transmission for 100% measurement"},
+    {"flags": ["-u"], "type": float, "help": "Unscattered transmission measurement"},
+    {"flags": ["-v"], "action": "store_true", "help": "Version information"},
+    {"flags": ["-V"], "type": int, "choices": [0, 1, 2], "help": "Verbosity level"},
+    {"flags": ["-x"], "type": int, "help": "Set debugging level"},
+    {"flags": ["-X"], "action": "store_true", "help": "Dual beam configuration"},
+    {"flags": ["-z"], "action": "store_true", "help": "Do forward calculation"},
+    {"flags": ["input"], "nargs": "?", "help": "Input file"}
+]
+
+# Initialize the parser and add options
+parser = argparse.ArgumentParser(description='iad command line program',
+                                 formatter_class=argparse.RawTextHelpFormatter)
+for spec in arg_specs:
+    parser.add_argument(*spec.pop("flags"), **spec)
+
+# Parse the arguments
+args = parser.parse_args()
+
+def print_version():
+    """Print the version information and quit."""
+    print("iadpython version:", iadpython.__version__)
+    print("Author:", iadpython.__author__, "-", iadpython.__email__)
+    print("Copyright:", iadpython.__copyright__)
+    print("License:", iadpython.__license__)
+    print("URL:", iadpython.__url__)
+    print("\nForward and inverse adding-doubling radiative transport calculations.")
+    print("Extensive documentation is at <https://iadpython.readthedocs.io>\n")
+    sys.exit(0)
+
+def print_usage():
+    """Print usage information and quit."""
+    usage_text = parser.format_help()
+    print(usage_text)
+    print("Examples:")
+    print("  iad file.rxt              Results will be put in file.txt")
+    print("  iad file                  Same as above")
+    print("  iad -c 0.9 file.rxt       Assume M_R includes 90%% of unscattered reflectance")
+    print("  iad -C 0.8 file.rxt       Assume M_T includes 80%% of unscattered transmittance")
+    print("  iad -e 0.0001 file.rxt    Better convergence to R & T values")
+    print("  iad -f 1.0 file.rxt       All light hits reflectance sphere wall first")
+    print("  iad -o out file.rxt       Calculated values in out")
+    print("  iad -r 0.3                R_total=0.")
+    sys.exit(0)
+
+
+# Main logic
+def main():
+    # Parse and use the arguments
+    albedo = args.a
+    # ... other arguments
+
+    # Perform calculations
+    # This would involve using functions from iadpython and additional logic
+    # For example:
+    # result = calculate_mr_mt(albedo, other_params)
+
+    # Output the results
+    # print(result)
+
+if __name__ == "__main__":
+    main()