WIP: Update pctpairprotons to support more uproot versions

applications/pctpairprotons/pctpairprotons.py

@@ -95,7 +95,15 @@ def load_tree_as_df(root_file, tree_name):
         tree = uproot.open(root_file)[tree_name]
         branches = tree.arrays(library="np")
 
-        dtype = [(name, branch.dtype) for name, branch in branches.items()]
+        # Some versions of uproot return a dictionnary, and some others a numpy.ndarray
+        # We handle both cases here to generate the dtype
+        if isinstance(branches, dict):
+            dtype = [(name, branch.dtype) for name, branch in branches.items()]
+        elif isinstance(branches, np.ndarray):
+            dtype = branches.dtype
+        else:
+            raise NotImplementedError
+
         ps = np.rec.recarray((len(branches["RunID"]),), dtype=dtype)
         for branch_name, _ in dtype:
             ps[branch_name] = branches[branch_name]

documentation/docs/installation.md

@@ -89,3 +89,10 @@ in the user's `.bashrc` file. This allows to run PCT applications from anywhere
 pip install opengate
 ```
 An example of proton CT GATE simulation can be found in [`gate/protonct.py`](https://github.com/RTKConsortium/PCT/blob/main/gate/protonct.py).
+
+### Uproot
+
+[Uproot](https://uproot.readthedocs.io/) is a library for reading and writing ROOT files in pure Python and NumPy. Some applications of PCT require Uproot, such as `pctpairprotons` and `pctweplfit`. The simplest way to install Uproot is by running
+```bash
+pip install uproot
+```

test/Baseline/pairs0000.mhd.sha512

@@ -0,0 +1 @@
+56279220dd768a08402ebe3b72ea943f3ed8d26c4ed0f79cc37f21a459ca23bea15a5284df4586c12bcac2ab263543cdda8b07fb66864d78bf70c8b6d1071df7

test/Baseline/pairs0000.raw.sha512

@@ -0,0 +1 @@
+586bad7576b71c55c8eb53176cf37b0e08d6ddff7d5194a40e3ec8fa69ad033c55eaf2a250283c870c11e5f357edf37093db93e37bce803b1835bbf6b3b3611a

test/CMakeLists.txt

@@ -32,4 +32,12 @@ if(PCT_BUILD_APPLICATIONS)
     ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/pctbinning
       -i DATA{Input/pairs0000.mhd,pairs0000.raw} -o ${ITK_TEST_OUTPUT_DIR}/projections.mhd --source 1000 --size=400,20,220
   )
+  itk_add_test(NAME pctapppairprotonstest
+    COMMAND itkTestDriver
+      --compare
+      DATA{Baseline/pairs0000.mhd,pairs0000.raw}
+      ${ITK_TEST_OUTPUT_DIR}/pairs.mhd
+    ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/pctpairprotons
+      -i DATA{Input/PhaseSpaceIn.root} -j DATA{Input/PhaseSpaceOut.root} -o ${ITK_TEST_OUTPUT_DIR}/pairs.mhd --plane-in -110 --plane-out 110 -v --psin PhaseSpaceIn --psout PhaseSpaceOut
+  )
 endif()

test/Input/PhaseSpaceIn.root.sha512

@@ -0,0 +1 @@
+b59642aa82c4160815295e5fb142536c842589dce20e17cdc399245bc928a4cde1c860ba1c023de165e1ddb7a7ac1cfbd906796b80e12f024cf2ebb6f23bf862

test/Input/PhaseSpaceOut.root.sha512

@@ -0,0 +1 @@
+9fb1aafd39da55c1b8e9280a2040772f80c73f6490bcadb8a90c7670aaf3db730cfe0704f386d22c03848c3855ce74915969855d6725551be39dc10ecfd5536b