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view build_file.py @ 0:c70012022f0f draft
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
author | muon-spectroscopy-computational-project |
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date | Thu, 25 Aug 2022 16:16:47 +0000 |
parents | |
children | 331d0776abb4 |
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import json import re import sys from muspinsim import MuSpinInput def write_file(file_name, content): """ Write muspinsim file :param file_name: name of file :param content: list of strings containing blocks to write """ with open(file_name, "w") as f: f.write( """ ####################################################### #Muspinsim Input File #Generated using Muon Galaxy Tool Muspinsim_Input #######################################################\n\n""" ) f.write("".join(content)) def build_block(title, vals): """ Build keyword block :param title: string - Keyword :param vals: list of strings - lines containing values for keyword :return: A string containing formatted keyword block """ return "{0}\n {1}\n".format(title, "\n ".join(vals)) def format_entry(entry): """ Helper function to remove whitespace between function parameters and remove ',' or ';' inbetween parameters :param entry: string - user entry :return: string containing only valid parameters """ stck = [] new_str = "" for i, char in enumerate(entry): if char == "(": stck.append(i) elif char == ")": if len(stck) == 0: raise ValueError( "Could not parse entry {0}" "brackets mismatch - unexpected ')' " "found on char {1}".format(entry, i) ) stck.pop() elif char == " " and len(stck) > 0: continue # remove ',' between functions elif char in [",", ";"] and len(stck) == 0: new_str += " " continue new_str += char if len(stck) != 0: raise ValueError( "Could not parse entry {0}" "brackets mismatch - unclosed '(' found on char(s): {1}".format( entry, stck ) ) return new_str def split_into_args(entry, nargs=1): """ Helper function to split input into a list of args :param entry: a string containing a user inputted line :param nargs: number of expected arguments :return: a list of arguments found :exception: ValueError - if number of arguments found does not match expected (nargs) """ # remove square brackets and extra whitespace/newline content = " ".join(entry.replace("[", "").replace("]", "").split()) # remove whitespace in between expressions/functions # remove commas/semicolons in between expressions/functions # split on whitespace to separate args content = re.split(r"\s", format_entry(content)) chars = [elem.strip() for elem in content if elem != ""] if len(chars) != nargs: raise ValueError( "Could not parse entry {0}" " incorrect number of args" " found {1}:\n({2})\nBut expected {3}".format( entry, len(chars), chars, nargs ) ) return chars def parse_matrix(entry_string, size): """ Helper function to parse and format matrix/vector to be readable by Muspinsim :param entry_string: a user input string for a matrix/vector :param size: (x, y) integer tuple: dimensions of matrix :return: a list of strings of length y, each string containing x elements (space separated) """ content = split_into_args(entry_string, nargs=size[0] * size[1]) return [ " ".join(content[x: x + size[0]]) for x in range(0, len(content), size[0]) ] def parse_interactions(interaction): """ Helper function to build keyword blocks for all interaction parameters entered (hyperfine, zeeman, dipolar, quadrupolar and dissipation) :param interaction: a dictionary containing all interaction parameters :return: a string containing several formatted blocks """ options = interaction["interaction_options"] interaction_type = options["interaction"] try: return { "zeeman": lambda options: build_block( "zeeman {0}".format(options["zeeman_index"]), parse_matrix(options["zeeman_vector"], (3, 1)), ), "hyperfine": lambda options: build_block( "hyperfine {0} {1}".format( options["hfine_index"], options["hfine_e_index"] if options["hfine_e_index"] else "", ).strip(), parse_matrix(options["hfine_matrix"], (3, 3)), ), "dipolar": lambda options: build_block( "dipolar {0} {1}".format( options["di_index"], options["di_index_2"] ), parse_matrix(options["di_vector"], (3, 1)), ), "quadrupolar": lambda options: build_block( "quadrupolar {0}".format(options["quad_index"]), parse_matrix(options["quad_matrix"], (3, 3)), ), "dissipation": lambda options: build_block( "dissipation {0}".format(options["dis_index"]), [options["dis_val"]], ), }.get(interaction_type)(options) except ValueError as e: raise ValueError("Error occurred when parsing {0}".format(e)) def parse_orientation(orientation): """ Helper function to parse orientation keyword arguments :param orientation: a dictionary containing one set of orientation arguments :return: a formatted string """ options = orientation["orientation_options"] preset = options["orientation_preset"] return { "zcw": lambda options: "zcw({0})".format( " ".join(split_into_args(options["zcw_n"], 1)) ), "eulrange": lambda options: "eulrange({0})".format( " ".join(split_into_args(options["eul_n"], 1)) ), "2_polar": lambda options: "{0} {1}".format( " ".join(split_into_args(options["theta"], 1)), " ".join(split_into_args(options["phi"], 1)), ), "3_euler": lambda options: "{0} {1} {2}".format( " ".join(split_into_args(options["eul_1"], 1)), " ".join(split_into_args(options["eul_2"], 1)), " ".join(split_into_args(options["eul_3"], 1)), ), "4_euler": lambda options: "{0} {1} {2} {3}".format( " ".join(split_into_args(options["eul_1"], 1)), " ".join(split_into_args(options["eul_2"], 1)), " ".join(split_into_args(options["eul_3"], 1)), options["weight"], ), }.get(preset)(options) def parse_polarization(polarization): """ Helper function to parse polarization keyword arguments :param polarization: a dictionary containing one set of polarization arguments :return: a formatted string """ options = polarization["polarization_options"] preset = options["polarization_preset"] if preset != "custom": return preset else: try: return " ".join(split_into_args(options["polarization"], 1)) except ValueError: return " ".join(split_into_args(options["polarization"], 3)) def parse_field(field): """ Helper function to parse field keyword arguments :param field: a dictionary containing one set of field arguments :return: a formatted string """ try: return " ".join(split_into_args(field["field"], 1)) except ValueError: return " ".join(split_into_args(field["field"], 3)) def parse_fitting_variables(fitting_variables): """ Helper function to parse field keyword fitting_variables :param fitting_variables: a dictionary containing one set of arguments :return: a formatted string """ return "{0} {1} {2} {3}".format( fitting_variables["var_name"].strip().replace(" ", "_"), " ".join(split_into_args(fitting_variables["start_val"], 1)) if fitting_variables["start_val"].strip() != "" else "", " ".join(split_into_args(fitting_variables["min_bound"], 1)) if fitting_variables["min_bound"].strip() != "" else "", " ".join(split_into_args(fitting_variables["max_bound"], 1)) if fitting_variables["max_bound"].strip() != "" else "", ).strip() def parse_spin(spin): if spin["spin_preset"] != "custom": return spin["spin_preset"] else: elem_name = spin["spin"].strip() if elem_name not in ['e', 'mu']: elem_name = elem_name.capitalize() return "{0}{1}".format( int(spin["atomic_mass"]) if spin["atomic_mass"] else "", elem_name ).strip() parse_func_dict = { "spins": lambda values: build_block( "spins", [ " ".join( [ parse_spin(entry["spin_options"]) for entry in values ] ) ], ), # either 1x3 vector or scalar or function "fields": lambda values: build_block( "field", [parse_field(entry) for entry in values] ), # either scalar or single function "times": lambda values: build_block( "time", [ " ".join(split_into_args(entry["time"], 1)) for entry in values ], ), # either scalar or single function "temperatures": lambda values: build_block( "temperature", [ " ".join(split_into_args(entry["temperature"], 1)) for entry in values ], ), "x_axis": lambda value: build_block("x_axis", [value]), "y_axis": lambda value: build_block("y_axis", [value]), "average_axes": lambda values: build_block( "average_axes", values ), "experiment_preset": lambda value: build_block( "experiment", [value] ), "orientations": lambda values: build_block( "orientation {0}".format(euler_convention), [parse_orientation(entry) for entry in values], ), "interactions": lambda values: "".join( [parse_interactions(entry) for entry in values] ), "polarizations": lambda values: build_block( "polarization", [parse_polarization(entry) for entry in values], ), "fitting": lambda value: build_block( "fitting_data", ['load("fitting_data.dat")'] ), "fitting_method": lambda value: build_block( "fitting_method", [value] ), "fitting_variables": lambda values: build_block( "fitting_variables", [parse_fitting_variables(entry) for entry in values], ), "fitting_tolerance": lambda value: build_block( "fitting_tolerance", [str(value)], ), } euler_convention = 'ZYZ' def main(): input_json_path = sys.argv[1] mu_params = json.load(open(input_json_path, "r")) out_file_name = mu_params["out_file_prefix"].strip().replace(" ", "_") # combine all sections mu_params = { **mu_params["spins"], **mu_params["interaction_params"], **mu_params["experiment_params"], **mu_params["fitting_params"]["fitting_options"], } # get experiment parameters experiment = mu_params["experiment"] mu_params = {**mu_params, **experiment} if experiment["experiment_preset"] == "custom": del mu_params["experiment_preset"] del mu_params["experiment"] global euler_convention euler_convention = mu_params["euler_convention"] err_found = False file_contents = [ build_block("name", [out_file_name.strip().replace(" ", "_")]) ] for keyword, val in mu_params.items(): if val and val not in ["None"]: try: keyword_func = parse_func_dict.get(keyword) if keyword_func: file_contents.append(keyword_func(val)) except ValueError as e: sys.stderr.write( "Error occurred when parsing {0}\n{1}".format( keyword, str(e) ) ) err_found = True if err_found: sys.exit(1) write_file("outfile.in", file_contents) try: MuSpinInput(open("outfile.in")) except Exception as e: sys.stdout.write( "Warning, This created file may not work properly. " "Error(s) encountered when trying to parse the file : {0}".format( str(e) ) ) sys.exit(1) if __name__ == "__main__": main()