Fix TOPAS reader

pymchelper/input_output.py

@@ -25,13 +25,25 @@ def guess_reader(filename):
     :return: Instantiated reader object
     """
     reader = None
+    logging.debug("Guessing reader for file %s", filename)
+    logging.debug("Checking FlukaReader")
     fluka_reader = FlukaReaderFactory(filename).get_reader()
+    logging.debug("Got: %s", fluka_reader)
     if fluka_reader:
+        logging.debug("Got FlukaReader")
         reader = fluka_reader(filename)
     else:
+        logging.debug("Checking SHReader")
         sh_reader = SHReaderFactory(filename).get_reader()
+        logging.debug("Got: %s", sh_reader)
         if sh_reader:
-            reader = sh_reader(filename)
+            try:
+                reader = sh_reader(filename)
+                reader.read_header(Estimator())
+            except ValueError as e:
+                topas_reader = TopasReaderFactory(filename).get_reader()
+                if topas_reader:
+                    reader = topas_reader(filename)
         else:
             topas_reader = TopasReaderFactory(filename).get_reader()
             if topas_reader:
@@ -55,7 +67,9 @@ def guess_corename(filename):
 def fromfile(filename: str) -> Optional[Estimator]:
     """Read estimator data from a binary file ```filename```"""
 
+    logger.debug("Reading file %s, guessing reader", filename)
     reader = guess_reader(filename)
+    logger.debug("Reader: %s", reader)
     if reader is None:
         raise Exception("File format not compatible", filename)
     estimator = Estimator()
@@ -140,8 +154,9 @@ def fromfilelist(input_file_list, error: ErrorEstimate = ErrorEstimate.stderr, n
 
     result.file_counter = len(input_file_list)
     core_names_dict = group_input_files(input_file_list)
-    if len(core_names_dict) == 1:
+    if len(core_names_dict) == 1 and getattr(result, 'file_corename', None) is None:
         result.file_corename = list(core_names_dict)[0]
+        print("here result.file_corename", result.file_corename)
 
     return result
 

pymchelper/readers/shieldhit/general.py

@@ -137,7 +137,7 @@ def get_reader(self):
             # format tag specifying binary standard was introduced in SH12A v0.7.4-dev on  07.06.2019 (commit 6eddf98)
             file_format = read_token(self.filename, SHBDOTagID.format)
             if file_format:
-                logger.debug("File format: {} {:s}".format(file_format, SHFileFormatId(file_format).name))
+                logger.debug("File format: %s %s", file_format, SHFileFormatId(file_format).name)
                 if file_format == SHFileFormatId.bdo2019:
                     reader = SHReaderBDO2019
                 elif file_format == SHFileFormatId.bdo2016:

pymchelper/readers/shieldhit/reader_base.py

@@ -4,6 +4,7 @@
 import numpy as np
 
 from pymchelper.axis import MeshAxis
+from pymchelper.estimator import Estimator
 from pymchelper.readers.common import Reader
 from pymchelper.shieldhit.detector.detector_type import SHDetType
 from pymchelper.shieldhit.detector.estimator_type import SHGeoType
@@ -16,7 +17,11 @@ class SHReader(Reader):
     Reads binary output files generated by SHIELD-HIT12A code.
     """
 
-    def read_data(self, estimator, nscale=1):
+    def read_header(self, _) -> str:
+        """Reads header of the file and returns True if header is valid."""
+        return True
+
+    def read_data(self, estimator: Estimator, nscale: int = 1) -> bool:
         """
         TODO
         :param estimator:
@@ -27,12 +32,12 @@ def read_data(self, estimator, nscale=1):
         return True
 
     @property
-    def corename(self):
+    def corename(self) -> str:
         """
         TODO
         :return:
         """
-        core_name = None
+        core_name = ''
 
         if self.filename.endswith(('.bdo', '.bdox')):  # TODO add more sophisticated check for file being SH12A output
             basename = os.path.basename(self.filename)
@@ -64,8 +69,9 @@ def mesh_unit_and_name(estimator, axis):
 
     unit = _geotyp_units.get(estimator.geotyp, _default_units)[axis]
 
-    if estimator.geotyp in {SHGeoType.msh, SHGeoType.dmsh, SHGeoType.voxscore, SHGeoType.geomap,
-                            SHGeoType.plane, SHGeoType.dplane}:
+    if estimator.geotyp in {
+            SHGeoType.msh, SHGeoType.dmsh, SHGeoType.voxscore, SHGeoType.geomap, SHGeoType.plane, SHGeoType.dplane
+    }:
         name = ("Position (X)", "Position (Y)", "Position (Z)")[axis]
     elif estimator.geotyp in {SHGeoType.cyl, SHGeoType.dcyl}:
         name = ("Radius (R)", "Angle (PHI)", "Position (Z)")[axis]
@@ -86,7 +92,7 @@ def mesh_unit_and_name(estimator, axis):
     return unit, name
 
 
-def _bintyp(n):
+def _bintyp(n: int):
     """
     Calculates type of binning based on number of bins.
 
@@ -161,9 +167,7 @@ def read_next_token(f):
     f is an open and readable file pointer.
     returns None if no token was found / EOF
     """
-    tag = np.dtype([('pl_id', '<u8'),
-                    ('pl_type', 'S8'),
-                    ('pl_len', '<u8')])
+    tag = np.dtype([('pl_id', '<u8'), ('pl_type', 'S8'), ('pl_len', '<u8')])
 
     x1 = np.fromfile(f, dtype=tag, count=1)  # read the data into numpy
 
@@ -174,9 +178,7 @@ def read_next_token(f):
         pl_type = x1['pl_type'][0]
         pl_len = x1['pl_len'][0]
         try:
-            pl = np.fromfile(f,
-                             dtype=pl_type,
-                             count=pl_len)  # read the data into numpy
+            pl = np.fromfile(f, dtype=pl_type, count=pl_len)  # read the data into numpy
             return pl_id, pl_type, pl_len, pl
         except TypeError:
             return None