suggestion for MC-summary table, output in markdown format.

pymchelper/input_output.py

@@ -92,7 +92,6 @@ 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
-            print("filename", filename, n)
             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

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