added roi, noise and gain (#143)

- Moved definitions of Cluster_2x2 and Cluster_3x3 to it's own file
- Added optional members for ROI, noise_map and gain_map in ClusterFile

**API:**

After creating the ClusterFile the user can set one or all of: roi,
noise_map, gain_map

```python
f = ClusterFile(fname)
f.set_roi(roi) #aare.ROI
f.set_noise_map(noise_map) #numpy array
f.set_gain_map(gain_map) #numpy array
```

**When reading clusters they are evaluated in the order:**

1. If ROI is enabled check that the cluster is within the ROI
1. If noise_map is enabled check that the cluster meets one of the
conditions
    - Center pixel above noise
    - Highest 2x2 sum above 2x noise
    - 3x3 sum above 3x noise
1. If gain_map is set apply the gain map before returning the clusters
(not used for noise cut)

**Open questions:**
1. Check for out of bounds access in noise and gain map?

closes #139 
closes #135 
closes #90

python/src/cluster_file.hpp

@@ -31,26 +31,22 @@ void define_cluster_file_io_bindings(py::module &m) {
                 auto v = new ClusterVector<int32_t>(self.read_clusters(n_clusters));
                 return v;
              },py::return_value_policy::take_ownership)
-        .def("read_clusters",
-                [](ClusterFile &self, size_t n_clusters, ROI roi) {
-                   auto v = new ClusterVector<int32_t>(self.read_clusters(n_clusters, roi));
-                   return v;
-                },py::return_value_policy::take_ownership)
         .def("read_frame",
              [](ClusterFile &self) {
                 auto v = new ClusterVector<int32_t>(self.read_frame());
                 return v;
              })
+        .def("set_roi", &ClusterFile::set_roi)
+        .def("set_noise_map", [](ClusterFile &self, py::array_t<int32_t> noise_map) {
+            auto view = make_view_2d(noise_map);
+            self.set_noise_map(view);
+        })
+        .def("set_gain_map", [](ClusterFile &self, py::array_t<double> gain_map) {
+            auto view = make_view_2d(gain_map);
+            self.set_gain_map(view);
+        })
+        .def("close", &ClusterFile::close)
         .def("write_frame", &ClusterFile::write_frame)
-        // .def("read_cluster_with_cut",
-        //      [](ClusterFile &self, size_t n_clusters,
-        //         py::array_t<double> noise_map, int nx, int ny) {
-        //          auto view = make_view_2d(noise_map);
-        //          auto *vec =
-        //              new std::vector<Cluster3x3>(self.read_cluster_with_cut(
-        //                  n_clusters, view.data(), nx, ny));
-        //          return return_vector(vec);
-        //      })
         .def("__enter__", [](ClusterFile &self) { return &self; })
         .def("__exit__",
              [](ClusterFile &self,