Merge pull request #5 from ashirsch/metadata

Fix Metadata Reading

spe2py.py

@@ -57,7 +57,7 @@ def __init__(self, filepath=None):
 
             self.xcoord, self.ycoord = self._get_coords()
 
-            self.data = self._read_data(file)
+            self.data, self.metadata, self.metanames = self._read_data(file)
         file.close()
 
     @staticmethod
@@ -103,6 +103,34 @@ def _get_dtype(file):
 
         return dtype
 
+    def _get_meta_dtype(self):
+        meta_types = []
+        meta_names = []
+        prev_item = None
+        for item in dir(self.footer.SpeFormat.MetaFormat.MetaBlock):
+            if item == 'TimeStamp' and prev_item != 'TimeStamp':  # Specify ExposureStarted vs. ExposureEnded
+                for element in self.footer.SpeFormat.MetaFormat.MetaBlock.TimeStamp:
+                    meta_names.append(element['event'])
+                    meta_types.append(element['type'])
+                prev_item = 'TimeStamp'
+            elif item == 'GateTracking' and prev_item != 'GateTracking':  # Specify Delay vs. Width
+                for element in self.footer.SpeFormat.MetaFormat.MetaBlock.GateTracking:
+                    meta_names.append(element['component'])
+                    meta_types.append(element['type'])
+                prev_item = 'GateTracking'
+            elif prev_item != item:  # All other metablock names only have one possible value
+                meta_names.append(item)
+                meta_types.append(getattr(self.footer.SpeFormat.MetaFormat.MetaBlock, item)['type'])
+                prev_item = item
+
+        for index, type_str in enumerate(meta_types):
+            if type_str == 'Int64':
+                meta_types[index] = np.int64
+            else:
+                meta_types[index] = np.float64
+
+        return meta_types, meta_names
+
     def _get_roi_info(self):
         """
         Returns region of interest attributes and numbers of regions of interest
@@ -147,7 +175,7 @@ def _get_dims(self):
         xdim = [int(block["width"]) for block in self.footer.SpeFormat.DataFormat.DataBlock.DataBlock]
         ydim = [int(block["height"]) for block in self.footer.SpeFormat.DataFormat.DataBlock.DataBlock]
 
-        return (xdim, ydim)
+        return xdim, ydim
 
     def _get_coords(self):
         """
@@ -179,6 +207,16 @@ def _read_data(self, file):
         """
         file.seek(4100)
 
+        frame_stride = int(self.footer.SpeFormat.DataFormat.DataBlock['stride'])
+        frame_size = int(self.footer.SpeFormat.DataFormat.DataBlock['size'])
+        metadata_size = frame_stride - frame_size
+        if metadata_size != 0:
+            metadata_dtypes, metadata_names = self._get_meta_dtype()
+            metadata = np.zeros((self.nframes, len(metadata_dtypes)))
+        else:
+            metadata_dtypes, metadata_names = None, None
+            metadata = None
+
         data = [[0 for _ in range(self.nroi)] for _ in range(self.nframes)]
         for frame in range(0, self.nframes):
             for region in range(0, self.nroi):
@@ -189,7 +227,11 @@ def _read_data(self, file):
                     data_xdim = np.asarray(self.xdim[region], np.uint32)
                     data_ydim = np.asarray(self.ydim[region], np.uint32)
                 data[frame][region] = np.fromfile(file, self.dtype, data_xdim * data_ydim).reshape(data_ydim, data_xdim)
-        return data
+            if metadata_dtypes is not None:
+                for meta_block in range(len(metadata_dtypes)):
+                    metadata[frame, meta_block] = np.fromfile(file, dtype=metadata_dtypes[meta_block], count=1)
+
+        return data, metadata, metadata_names
 
     def image(self, frame=0, roi=0):
         """