subtract dark data

Hi @dgeissbuhler,

I added some stuff to subtract the dark frame if needed. This is most probably not the best way to do it, but it works for now. I'll let you have a look and modify it to better fit in your whole framework ...

Note that this is not urgent ;)

Thanks Guillaume

bob/io/stream/stream.py

@@ -89,6 +89,10 @@ class Stream():
     def get_available_filters(self):
         return Stream.filters
 
+    # get parent
+    def get_parent(self):
+        return self.parent
+
 ################################################################################
 # filter decorator
 def stream_filter(name):
@@ -392,6 +396,42 @@ class StreamReproject(StreamFilter):
                                         self.camera_matrix, 
                                         self.dist_coeffs)
 
+
+
+### subtract dark frame ###
+@stream_filter('subtract_dark')
+class StreamSubtractDark(StreamFilter):
+
+    def __init__(self, name, parent):
+        super().__init__(name=name, parent=parent)
+
+    def process_frame(self, data, index):
+        
+        # tried to reproduce the hack in bob.db.batl2.loader.py:284
+        # not sure if it's ok though ...
+        if 'swir' in self.name:
+          index = 0
+
+        data = data[0]
+        dtype = data.dtype
+        data = data.astype(np.float)
+
+        # this should probably be handled in a better way
+        parent = self.parent
+        name = self.name
+        while(not isinstance(parent, StreamFile)):
+            if isinstance(parent, Stream):
+                name = parent.name
+            parent = parent.get_parent()
+        
+        dark_data = parent.load_dark_data(name, index)
+        dark_data = dark_data[0,0].astype(np.float)
+
+        data = data - dark_data
+        data[data < 0.] = 0.
+        data = np.stack([data]).astype(dtype)
+        return data
+
 class StreamCrop(StreamFilter):
     pass 
 
@@ -460,6 +500,7 @@ class StreamFile():
 
         indices = []
 
+
         # TODO load only relevant data if cropped
         if isinstance(index, tuple):
             index = index[0]
@@ -481,6 +522,32 @@ class StreamFile():
             raise Exception('index can only be int, slice, tuple or list')
             return None
         
+    def load_dark_data(self, stream_name, index):
+       
+        data_config = self.get_stream_config(stream_name)
+        data_path = data_config['path_dark']
+
+        if isinstance(index, tuple):
+            index = index[0]
+            print('WARNING: cropping not yet implemented')
+
+        if isinstance(index, int):
+            data = self.hdf5_file.lread(data_path, index)
+            data = np.stack([data])
+            return data
+        elif isinstance(index, slice):
+            if index.step == None:
+                indices = list(range(index.start, index.stop))
+            else:
+                indices = list(range(index.start, index.stop, index.step))
+            data = np.stack([self.hdf5_file.lread(data_path, i) for i in indices])
+            return data
+        elif isinstance(index, list):
+            return np.stack([self.hdf5_file.lread(data_path, i) for i in index])
+        else:
+            raise Exception('index can only be int, slice, tuple or list')
+            return None
+
 
     def stream(self, name):
         return Stream(name, self)