Added fitting, fixed roi etc (#129)

Co-authored-by: Patrick <[email protected]>
Co-authored-by: JulianHeymes <[email protected]>

.github/workflows/deploy.yml → .github/workflows/build_and_deploy_conda.yml

@@ -4,7 +4,6 @@ on:
   push:
     branches:
      - main
-     - developer
 
 jobs:
   build:
@@ -34,7 +33,6 @@ jobs:
         run: conda install conda-build=24.9 conda-verify pytest anaconda-client
 
       - name: Enable upload
-        if: github.ref == 'refs/heads/main'
         run: conda config --set anaconda_upload yes
 
       - name: Build

.github/workflows/build_conda.yml

@@ -0,0 +1,40 @@
+name: Build pkgs and deploy if on main
+
+on:
+  push:
+    branches:
+     - developer
+
+jobs:
+  build:
+    strategy:
+      fail-fast: false
+      matrix:
+        platform: [ubuntu-latest, ] # macos-12, windows-2019]
+        python-version: ["3.12",]
+
+    runs-on: ${{ matrix.platform }}
+
+    # The setup-miniconda action needs this to activate miniconda
+    defaults:
+      run:
+        shell: "bash -l {0}"
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Get conda
+        uses: conda-incubator/[email protected]
+        with:
+          python-version: ${{ matrix.python-version }}
+          channels: conda-forge
+
+      - name: Prepare
+        run: conda install conda-build=24.9 conda-verify pytest anaconda-client
+
+      - name: Disable upload
+        run: conda config --set anaconda_upload no
+
+      - name: Build
+        run: conda build conda-recipe 
+

CMakeLists.txt

@@ -48,6 +48,7 @@ option(AARE_FETCH_PYBIND11 "Use FetchContent to download pybind11" ON)
 option(AARE_FETCH_CATCH "Use FetchContent to download catch2" ON)
 option(AARE_FETCH_JSON "Use FetchContent to download nlohmann::json" ON)
 option(AARE_FETCH_ZMQ "Use FetchContent to download libzmq" ON)
+option(AARE_FETCH_LMFIT "Use FetchContent to download lmfit" ON)
 
 
 #Convenience option to use system libraries only (no FetchContent)
@@ -76,6 +77,34 @@ endif()
 
 set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
 
+if(AARE_FETCH_LMFIT)
+    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 ${lmfit_patch}
+        UPDATE_DISCONNECTED 1
+        EXCLUDE_FROM_ALL
+    )
+    #Disable what we don't need from lmfit
+    set(BUILD_TESTING OFF CACHE BOOL "")
+    set(LMFIT_CPPTEST OFF CACHE BOOL "")
+    set(LIB_MAN OFF CACHE BOOL "")
+    set(LMFIT_CPPTEST OFF CACHE BOOL "")
+    set(BUILD_SHARED_LIBS OFF CACHE BOOL "")
+
+
+    FetchContent_MakeAvailable(lmfit)
+    set_property(TARGET lmfit PROPERTY POSITION_INDEPENDENT_CODE ON)
+
+    target_include_directories (lmfit PUBLIC "${libzmq_SOURCE_DIR}/lib")
+    message(STATUS "lmfit include dir: ${lmfit_SOURCE_DIR}/lib")
+else()
+    find_package(lmfit REQUIRED)
+endif()
+
+
 if(AARE_FETCH_ZMQ)
     # Fetchcontent_Declare is deprecated need to find a way to update this
     # for now setting the policy to old is enough
@@ -127,8 +156,8 @@ if (AARE_FETCH_FMT)
         LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
         ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
         RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
-        INCLUDES DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}
-)
+        INCLUDES DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}   
+    )  
 else()
       find_package(fmt 6 REQUIRED)
 endif()
@@ -146,7 +175,6 @@ if (AARE_FETCH_JSON)
     install(
         TARGETS nlohmann_json
         EXPORT "${TARGETS_EXPORT_NAME}"
-
     )
     message(STATUS "target: ${NLOHMANN_JSON_TARGET_NAME}")
 else()
@@ -283,11 +311,14 @@ set(PUBLICHEADERS
     include/aare/ClusterFile.hpp
     include/aare/CtbRawFile.hpp
     include/aare/ClusterVector.hpp
+    include/aare/decode.hpp
     include/aare/defs.hpp
     include/aare/Dtype.hpp
     include/aare/File.hpp
+    include/aare/Fit.hpp
     include/aare/FileInterface.hpp
     include/aare/Frame.hpp
+    include/aare/geo_helpers.hpp
     include/aare/NDArray.hpp
     include/aare/NDView.hpp
     include/aare/NumpyFile.hpp
@@ -298,6 +329,7 @@ set(PUBLICHEADERS
     include/aare/RawMasterFile.hpp
     include/aare/RawSubFile.hpp
     include/aare/VarClusterFinder.hpp
+    include/aare/utils/task.hpp
 
 )
 
@@ -307,14 +339,18 @@ set(SourceFiles
     ${CMAKE_CURRENT_SOURCE_DIR}/src/ClusterFile.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/src/defs.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/src/Dtype.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/decode.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/src/Frame.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/src/File.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/Fit.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/geo_helpers.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/src/NumpyFile.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/src/NumpyHelpers.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/src/PixelMap.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/src/RawFile.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/src/RawSubFile.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/src/RawMasterFile.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/utils/task.cpp
 )
 
 
@@ -334,6 +370,7 @@ target_link_libraries(
     ${STD_FS_LIB} # from helpers.cmake
     PRIVATE 
     aare_compiler_flags 
+    lmfit
 )
 
 set_target_properties(aare_core PROPERTIES
@@ -350,6 +387,7 @@ if(AARE_TESTS)
             ${CMAKE_CURRENT_SOURCE_DIR}/src/defs.test.cpp
             ${CMAKE_CURRENT_SOURCE_DIR}/src/Dtype.test.cpp
             ${CMAKE_CURRENT_SOURCE_DIR}/src/Frame.test.cpp
+            ${CMAKE_CURRENT_SOURCE_DIR}/src/geo_helpers.test.cpp
             ${CMAKE_CURRENT_SOURCE_DIR}/src/RawMasterFile.test.cpp
             ${CMAKE_CURRENT_SOURCE_DIR}/src/NDArray.test.cpp
             ${CMAKE_CURRENT_SOURCE_DIR}/src/NDView.test.cpp
@@ -359,6 +397,7 @@ if(AARE_TESTS)
             ${CMAKE_CURRENT_SOURCE_DIR}/src/NumpyFile.test.cpp
             ${CMAKE_CURRENT_SOURCE_DIR}/src/NumpyHelpers.test.cpp
             ${CMAKE_CURRENT_SOURCE_DIR}/src/RawFile.test.cpp
+            ${CMAKE_CURRENT_SOURCE_DIR}/src/utils/task.test.cpp
 
         )
     target_sources(tests PRIVATE ${TestSources} )
@@ -436,4 +475,4 @@ if(AARE_MASTER_PROJECT)
     set(CMAKE_INSTALL_DIR "share/cmake/${PROJECT_NAME}")
     set(PROJECT_LIBRARIES aare-core aare-compiler-flags )
     include(cmake/package_config.cmake)
-endif()
+endif()

conda-recipe/meta.yaml

@@ -1,6 +1,6 @@
 package:
   name: aare
-  version: 2024.12.16.dev0 #TODO! how to not duplicate this?
+  version: 2025.2.12 #TODO! how to not duplicate this?
 
 
 source:

docs/CMakeLists.txt

@@ -12,28 +12,7 @@ set(SPHINX_BUILD ${CMAKE_CURRENT_BINARY_DIR})
 
 
 file(GLOB SPHINX_SOURCE_FILES CONFIGURE_DEPENDS "src/*.rst")
-# set(SPHINX_SOURCE_FILES
-#   src/index.rst
-#   src/Installation.rst
-#   src/Requirements.rst
-#   src/NDArray.rst
-#   src/NDView.rst
-#   src/File.rst
-#   src/Frame.rst
-#   src/Dtype.rst
-#   src/ClusterFinder.rst
-#   src/ClusterFile.rst
-#   src/Pedestal.rst
-#   src/RawFile.rst
-#   src/RawSubFile.rst
-#   src/RawMasterFile.rst
-#   src/VarClusterFinder.rst
-#   src/pyVarClusterFinder.rst
-#   src/pyFile.rst
-#   src/pyCtbRawFile.rst
-#   src/pyRawFile.rst
-#   src/pyRawMasterFile.rst
-# )
+
 
 
 foreach(filename ${SPHINX_SOURCE_FILES})

docs/src/ClusterFinderMT.rst

@@ -0,0 +1,7 @@
+ClusterFinderMT
+==================
+
+
+.. doxygenclass:: aare::ClusterFinderMT
+   :members:
+   :undoc-members:

docs/src/index.rst

@@ -30,10 +30,13 @@ AARE
     pyFile
     pyCtbRawFile
     pyClusterFile
+    pyClusterVector
     pyRawFile
     pyRawMasterFile
     pyVarClusterFinder
 
+    pyFit
+
 
 .. toctree::
     :caption: C++ API
@@ -45,6 +48,7 @@ AARE
     File
     Dtype
     ClusterFinder
+    ClusterFinderMT
     ClusterFile
     ClusterVector
     Pedestal

docs/src/pyClusterVector.rst

@@ -0,0 +1,33 @@
+ClusterVector
+================
+
+The ClusterVector, holds clusters from the ClusterFinder. Since it is templated
+in C++  we use a suffix indicating the data type in python. The suffix is
+``_i`` for integer, ``_f`` for float, and ``_d`` for double.
+
+At the moment the functionality from python is limited and it is not supported
+to push_back clusters to the vector. The intended use case is to pass it to 
+C++ functions that support the ClusterVector or to view it as a numpy array.
+
+**View ClusterVector as numpy array**
+
+.. code:: python
+
+    from aare import ClusterFile
+    with ClusterFile("path/to/file") as f:
+        cluster_vector = f.read_frame()
+
+    # Create a copy of the cluster data in a numpy array
+    clusters = np.array(cluster_vector)
+
+    # Avoid copying the data by passing copy=False
+    clusters = np.array(cluster_vector, copy = False)
+
+
+.. py:currentmodule:: aare
+
+.. autoclass:: ClusterVector_i
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :inherited-members:

docs/src/pyFit.rst

@@ -0,0 +1,19 @@
+
+Fit
+========
+
+.. py:currentmodule:: aare
+
+
+**Functions**
+
+.. autofunction:: gaus
+
+.. autofunction:: pol1
+
+
+**Fitting**
+
+.. autofunction:: fit_gaus
+
+.. autofunction:: fit_pol1