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

CMakeLists.txt

@@ -81,15 +81,29 @@ set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
 
 if(AARE_FETCH_LMFIT)
     #TODO! Should we fetch lmfit from the web or inlcude a tar.gz in the repo?
-    set(lmfit_patch git apply ${CMAKE_CURRENT_SOURCE_DIR}/patches/lmfit.patch)
-    FetchContent_Declare(
-        lmfit
-        GIT_REPOSITORY https://jugit.fz-juelich.de/mlz/lmfit.git
-        GIT_TAG        main
-        PATCH_COMMAND ${lmfit_patch}
-        UPDATE_DISCONNECTED 1
-        EXCLUDE_FROM_ALL 1
-    )
+    set(LMFIT_PATCH_COMMAND git apply ${CMAKE_CURRENT_SOURCE_DIR}/patches/lmfit.patch)
+
+    # For cmake < 3.28 we can't supply EXCLUDE_FROM_ALL to FetchContent_Declare
+    # so we need this workaround
+    if (${CMAKE_VERSION} VERSION_LESS "3.28")
+        FetchContent_Declare(
+            lmfit
+            GIT_REPOSITORY https://jugit.fz-juelich.de/mlz/lmfit.git
+            GIT_TAG        main
+            PATCH_COMMAND ${LMFIT_PATCH_COMMAND}
+            UPDATE_DISCONNECTED 1
+        )
+    else()
+        FetchContent_Declare(
+            lmfit
+            GIT_REPOSITORY https://jugit.fz-juelich.de/mlz/lmfit.git
+            GIT_TAG        main
+            PATCH_COMMAND ${LMFIT_PATCH_COMMAND}
+            UPDATE_DISCONNECTED 1
+            EXCLUDE_FROM_ALL 1
+        )
+    endif()
+    
     #Disable what we don't need from lmfit
     set(BUILD_TESTING OFF CACHE BOOL "")
     set(LMFIT_CPPTEST OFF CACHE BOOL "")
@@ -97,8 +111,15 @@ if(AARE_FETCH_LMFIT)
     set(LMFIT_CPPTEST OFF CACHE BOOL "")
     set(BUILD_SHARED_LIBS OFF CACHE BOOL "")
 
+    if (${CMAKE_VERSION} VERSION_LESS "3.28")
+        if(NOT lmfit_POPULATED)
+            FetchContent_Populate(lmfit)
+            add_subdirectory(${lmfit_SOURCE_DIR} ${lmfit_BINARY_DIR} EXCLUDE_FROM_ALL)
+        endif()
+    else()
+        FetchContent_MakeAvailable(lmfit)
+    endif()
     
-    FetchContent_MakeAvailable(lmfit)
     set_property(TARGET lmfit PROPERTY POSITION_INDEPENDENT_CODE ON)
 else()
     find_package(lmfit REQUIRED)
@@ -111,10 +132,13 @@ if(AARE_FETCH_ZMQ)
     if (${CMAKE_VERSION} VERSION_GREATER_EQUAL "3.30")
         cmake_policy(SET CMP0169 OLD)
     endif()
+    set(ZMQ_PATCH_COMMAND git apply ${CMAKE_CURRENT_SOURCE_DIR}/patches/libzmq_cmake_version.patch)
     FetchContent_Declare(
         libzmq
         GIT_REPOSITORY https://github.com/zeromq/libzmq.git
         GIT_TAG        v4.3.4
+        PATCH_COMMAND ${ZMQ_PATCH_COMMAND}
+        UPDATE_DISCONNECTED 1
     )
     # Disable unwanted options from libzmq
     set(BUILD_TESTS OFF CACHE BOOL "Switch off libzmq test build")
@@ -396,6 +420,7 @@ if(AARE_TESTS)
             ${CMAKE_CURRENT_SOURCE_DIR}/src/NDView.test.cpp
             ${CMAKE_CURRENT_SOURCE_DIR}/src/ClusterFinder.test.cpp
             ${CMAKE_CURRENT_SOURCE_DIR}/src/ClusterVector.test.cpp
+            ${CMAKE_CURRENT_SOURCE_DIR}/src/ClusterFile.test.cpp
             ${CMAKE_CURRENT_SOURCE_DIR}/src/Pedestal.test.cpp
             ${CMAKE_CURRENT_SOURCE_DIR}/src/NumpyFile.test.cpp
             ${CMAKE_CURRENT_SOURCE_DIR}/src/NumpyHelpers.test.cpp