Merge pull request #1 from nexusformat/master

updating fork

src/nxfeature.py

@@ -59,28 +59,57 @@ def entries(self):
         ent = []
         for entry in self.file.keys():
             try:
-                features = [int(feat, 16) for feat in os.listdir(RECIPIE_DIR)]
+                features = []
+                for feat in os.listdir(RECIPIE_DIR):
+                    try:
+                        features.append(int(feat, 16))
+                    except:
+                        print("Could not parse feature with name %s" % (feat))
                 ent.append(InsaneEntryWithFeatures(self.file, entry, features))
             except:
                 print "no recipes in " + RECIPIE_DIR
                 pass
         return ent
 
+class SingleFeatureDiscoverer:
+    def __init__(self, nxsfile, feature):
+        self.file = h5py.File(nxsfile, 'r')
+        self.feature = feature
 
-if __name__ == '__main__':
-    import optparse
-
-    usage = "%prog [options] nxs_file"
-    parser = optparse.OptionParser(usage=usage)
-    parser.add_option("-t", "--test", dest="test", help="Test file against all recipes", action="store_true",
-                      default=False)
+    def entries(self):
+        ent = []
+        for entry in self.file.keys():
+            try:
+                ent.append(InsaneEntryWithFeatures(self.file, entry, [self.feature]))
+            except:
+                print("Issues with parsing feature %i"% self.feature)
+                pass
+        return ent
 
-    (options, args) = parser.parse_args()
 
-    if options.test:
-        disco = AllFeatureDiscoverer(args[0])
+if __name__ == '__main__':
+    import argparse
+
+    parser = argparse.ArgumentParser()
+    parser.add_argument("-t", "--test", dest="test", help="Test file against all recipes", action="store_true",
+                        default=False)
+    parser.add_argument("-f", "--feature", dest="feature", help="Test file against a defined feature",
+                      default=None)
+    parser.add_argument("nexusfile", help="Nexus file to test")
+
+    args = parser.parse_args()
+
+    if args.feature:
+        try:
+            disco = SingleFeatureDiscoverer(args.nexusfile, int(args.feature, 16))
+        except:
+            print("The feature '%s' has not parsed correctly, exiting" %(args.feature))
+            sys.exit()
     else:
-        disco = InsaneFeatureDiscoverer(args[0])
+      if args.test:
+          disco = AllFeatureDiscoverer(args.nexusfile)
+      else:
+          disco = InsaneFeatureDiscoverer(args.nexusfile)
 
     for entry in disco.entries():
         fail_list = []
@@ -102,11 +131,12 @@ def entries(self):
                 try:
                     print("\t%s (%d) is invalid with the following errors:" % (entry.feature_title(feat), feat))
                     print("\t\t" + message.replace('\n', '\n\t\t'))
-                except:
-                    error_list.append(feat)
+                except :
+                    e = sys.exc_info()[0]
+                    error_list.append((feat, str(e)))
 
         if len(error_list) > 0:
             print("\nThe following features had unexpected errors (Are you running windows?):")
-            for feat in error_list:
-                print("  (%d)" % (feat))
+            for error in error_list:
+                print("  (%d)  %s" % error)
         print("\n")

src/recipes/000000005A403F80/recipe.py

@@ -0,0 +1,62 @@
+
+
+def find_class(nx_file, nx_class):
+    """
+    Find a given NXclass
+
+    """
+    hits = []
+    if not isinstance(nx_class, list):
+        nx_class = [nx_class]
+    def visitor(name, obj):
+        if "NX_class" in obj.attrs.keys():
+            if obj.attrs["NX_class"] in nx_class:
+                hits.append((name, obj))
+
+    nx_file.visititems(visitor)
+    return hits
+
+REQUIRED_FIELDS = ['photoelectrons_energy', 'detector_sensitivity', 'energy_direction', 'energy_dispersion']
+
+def check_detector(d):
+    hit = []
+    for f in REQUIRED_FIELDS:
+        if f in d.keys():
+            hit.append(f)
+    return hit
+
+class recipe(object):
+    """
+    Recipe to validate files with the NXrixs feature
+
+    WIP: just detector parameters at the moment
+
+    """
+
+    def __init__(self, filedesc, entrypath):
+        self.file = filedesc
+        self.entry = entrypath
+        self.title = "NXrixs"
+
+    def process(self):
+        hits = dict()
+        for en, e in find_class(self.file, 'NXentry'):
+            for dn, d in find_class(e, 'NXdetector'):
+                h = check_detector(d)
+                if h:
+                    hits[en + '/' + dn] = h
+
+        if len(hits) == 0:
+            raise Exception('No detectors found with any required fields')        
+        nh = len(REQUIRED_FIELDS)
+        msg = ''
+        for d in hits:
+            h = hits[d]
+            if len(h) != nh:
+                msg += 'Detector %s missing fields: only %s\n' % d, h 
+        if msg:
+            raise Exception(msg)
+
+        return hits
+
+

src/recipes/3930676423686820/recipe.py

@@ -0,0 +1,27 @@
+class recipe:
+    """
+    Has title.
+
+    Proposed by: [email protected]
+    """
+
+    def __init__(self, filedesc, entrypath):
+        """
+        :param filedesc: h5py file object of the NeXus/HDF5 file
+        :param entrypath: path of the entry containing this feature
+        """
+        self.file = filedesc
+        self.entry = entrypath
+        self.title = "Has title"
+
+    def process(self):
+        """
+        Finds the title.
+
+        :return: the title
+        :raises: AssertionError if field not found
+        """
+        try:
+            return self.file[self.entry]['title'][0]
+        except:
+            raise AssertionError("This file does not contain a title field")

src/recipes/8801154206180708/recipe.py

@@ -0,0 +1,27 @@
+class recipe:
+    """
+    Has experiment_identifier.
+
+    Proposed by: [email protected]
+    """
+
+    def __init__(self, filedesc, entrypath):
+        """
+        :param filedesc: h5py file object of the NeXus/HDF5 file
+        :param entrypath: path of the entry containing this feature
+        """
+        self.file = filedesc
+        self.entry = entrypath
+        self.title = "Has experiment_identifier"
+
+    def process(self):
+        """
+        Finds the experiment identifier.
+
+        :return: the experiment identifier
+        :raises: AssertionError if field not found
+        """
+        try:
+            return self.file[self.entry]['experiment_identifier'][0]
+        except:
+            raise AssertionError("This file does not contain an experiment_identfier field")