626 idea generate mc summary table

pymchelper/estimator.py

@@ -62,6 +62,11 @@ def __init__(self):
         self.z = self.x
 
         self.number_of_primaries = 0  # number of histories simulated
+        self.run_time = 0  # runtime in seconds
+        self.run_time_sim = 0  # run time in seconds excluding initialization header
+        self.total_number_of_primaries = 0  # number of histories simulated
+        self.total_run_time = 0  # runtime in seconds
+        self.total_run_time_sim = 0  # run time in seconds excluding initialization header
         self.file_counter = 0  # number of files read
         self.file_corename = ""  # common core for paths of contributing files
         self.file_format = ""  # binary file format of the input files
@@ -131,9 +136,17 @@ def average_with_nan(estimator_list, error_estimate=ErrorEstimate.stderr):
     # TODO add compatibility check
     if not estimator_list:
         return None
+
     result = copy.deepcopy(estimator_list[0])
+
+    for n, estimator in enumerate(estimator_list, start=2):
+        result.total_number_of_primaries += estimator.number_of_primaries
+        result.total_run_time += estimator.run_time
+        result.total_run_time_sim += estimator.run_time_sim
+
     for page_no, page in enumerate(result.pages):
         page.data_raw = np.nanmean([estimator.pages[page_no].data_raw for estimator in estimator_list], axis=0)
+
     result.file_counter = len(estimator_list)
     if result.file_counter > 1 and error_estimate != ErrorEstimate.none:
         # s = stddev = sqrt(1/(n-1)sum(x-<x>)**2)

pymchelper/input_output.py

@@ -92,6 +92,9 @@ def fromfilelist(input_file_list, error=ErrorEstimate.stderr, nan: bool = True):
         # loop over all files with n running from 2
         for n, filename in enumerate(input_file_list[1:], start=2):
             current_estimator = fromfile(filename)  # x
+            result.total_number_of_primaries += current_estimator.number_of_primaries
+            result.total_run_time += current_estimator.run_time
+            result.total_run_time_sim += current_estimator.run_time_sim
 
             # Running variance algorithm based on algorithm by B. P. Welford,
             # presented in Donald Knuth's Art of Computer Programming, Vol 2, page 232, 3rd edition.

pymchelper/readers/shieldhit/binary_spec.py

@@ -208,6 +208,8 @@ class SHBDOTagID(IntEnum):
     SHBDOTagID.user: 'user',
     SHBDOTagID.host: 'host',
     SHBDOTagID.rt_nstat: 'number_of_primaries',
+    SHBDOTagID.rt_time: 'run_time',
+    SHBDOTagID.rt_timesim: 'run_time_sim',
     SHBDOTagID.number_of_pages: 'page_count',
     SHBDOTagID.geo_unit_ids: 'geo_unit_ids',
     SHBDOTagID.geo_units: 'geo_units',

pymchelper/readers/shieldhit/reader_bdo2019.py

@@ -176,6 +176,9 @@ def read_data(self, estimator, nscale=1):
                     page.error_raw /= np.float64(estimator.number_of_primaries)
 
         estimator.file_format = 'bdo2019'
+        estimator.total_number_of_primaries = estimator.number_of_primaries
+        estimator.total_run_time = estimator.run_time
+        estimator.total_run_time_sim = estimator.run_time_sim
 
         logger.debug("Done reading bdo file.")
         return True

pymchelper/run.py

@@ -81,6 +81,10 @@ def main(args=None):
 
     parser_inspect = subparsers.add_parser(Converters.inspect.name, help='prints metadata')
     add_default_options(parser_inspect)
+
+    parser_mcsum = subparsers.add_parser(Converters.mcsum.name, help='MC summary table after Sechopoulos et al (2018)')
+    add_default_options(parser_mcsum)
+
     parser_inspect.add_argument('-d', '--details',
                                 help='print detailed information about data attribute',
                                 action="store_true")

pymchelper/writers/common.py

@@ -9,6 +9,7 @@
 from pymchelper.writers.trip98ddd import TRiP98DDDWriter
 from pymchelper.writers.hdf import HdfWriter
 from pymchelper.writers.json import JsonWriter
+from pymchelper.writers.mcsum import MCSumWriter
 
 
 class Converters(IntEnum):
@@ -25,6 +26,7 @@ class Converters(IntEnum):
     inspect = 8
     hdf = 9
     json = 10
+    mcsum = 11
 
     @classmethod
     def _converter_mapping(cls, item):
@@ -38,7 +40,8 @@ def _converter_mapping(cls, item):
             cls.sparse: SparseWriter,
             cls.inspect: Inspector,
             cls.hdf: HdfWriter,
-            cls.json: JsonWriter
+            cls.json: JsonWriter,
+            cls.mcsum: MCSumWriter
         }.get(item)
 
     @classmethod

pymchelper/writers/mcsum.py

@@ -0,0 +1,42 @@
+import logging
+import time
+import urllib.parse
+
+logger = logging.getLogger(__name__)
+
+
+class MCSumWriter:
+    def __init__(self, filename, options):
+        logger.debug("Initialising Inspector writer")
+        self.options = options
+
+    def write(self, estimator):
+        """Print all keys and values from estimator structure
+
+        they include also a metadata read from binary output file
+        """
+
+        s = estimator.total_run_time
+        if s < 60:
+            ts = time.strftime('%S seconds', time.gmtime(s))
+        elif s < 3600:
+            ts = time.strftime('%M minutes', time.gmtime(s))
+        else:
+            ts = time.strftime('%H hours %M minutes', time.gmtime(s))
+
+        print('Item name |  Description | References')
+        print('|---|---|---|')
+        print(f'| Code Version | {estimator.mc_code_version} | |')
+        print('| Validation | |')
+        print(f'| Timing | {estimator.file_counter} jobs, {ts} total runtime |')
+        print('| Geometry | |')
+        print('| Source | |')
+        print('| Physics | |')
+        print('| Scoring | |')
+        print(f'|\\# histories | {estimator.total_number_of_primaries} | |')
+
+        url = urllib.parse.quote("https://doi.org/10.1002/mp.12702", safe="")
+        url = "https://doi.org/10.1002/mp.12702"
+        print('Table caption: Summary of Monte Carlo simulations parameters in AAPM TG268 format.')
+        print(f'[See Sechopoulos et al. (2018), {url}.]')
+        return 0