python39Packages.opensfm: init at 0.5.2 (#152957)

Co-authored-by: Sandro <sandro.jaeckel@gmail.com>

5 files changed, 472 insertions, 0 deletions

diff --git a/pkgs/development/python-modules/opensfm/0002-cmake-find-system-distributed-gtest.patch b/pkgs/development/python-modules/opensfm/0002-cmake-find-system-distributed-gtest.patch
new file mode 100644
index 00000000000..27b87c0b2d0
--- /dev/null
+++ b/pkgs/development/python-modules/opensfm/0002-cmake-find-system-distributed-gtest.patch
@@ -0,0 +1,57 @@
+From 79577371be21df40f1f6d4a4fe3453be6df9e93c Mon Sep 17 00:00:00 2001
+From: Someone Serge <sergei.kozlukov@aalto.fi>
+Date: Fri, 31 Dec 2021 10:03:25 +0200
+Subject: [PATCH 2/4] cmake: find system-distributed gtest
+
+---
+ opensfm/src/CMakeLists.txt | 19 +++++++------------
+ 1 file changed, 7 insertions(+), 12 deletions(-)
+
+diff --git a/opensfm/src/CMakeLists.txt b/opensfm/src/CMakeLists.txt
+index c85aa6fb..640d47a6 100644
+--- a/opensfm/src/CMakeLists.txt
++++ b/opensfm/src/CMakeLists.txt
+@@ -52,12 +52,14 @@ if (OPENMP_FOUND)
+   set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
+ endif()
+ 
++find_package(gflags REQUIRED)
++
+ find_package(LAPACK)
+ find_package(SuiteSparse)
+ find_package(Eigen3 REQUIRED)
+ find_package(Ceres)
+-find_package(Gflags REQUIRED)
+-find_package(Glog REQUIRED)
++find_package(glog REQUIRED)
++find_package(GTest REQUIRED)
+ 
+ # Ceres2 exposes Ceres::ceres target.
+ # Ceres1 exposes just ceres.
+@@ -100,20 +102,13 @@ option(OPENSFM_BUILD_TESTS "Build OpenSfM unit tests." on)
+ 
+ if (OPENSFM_BUILD_TESTS)
+   enable_testing()
+-  include_directories(third_party/gtest)
+-  add_definitions(-DCERES_GFLAGS_NAMESPACE=${GFLAGS_NAMESPACE})
+-
+-  add_library(gtest
+-              third_party/gtest/gmock_gtest_all.cc
+-              third_party/gtest/gmock_main.cc)
+-  target_include_directories(gtest PRIVATE ${GFLAGS_INCLUDE_DIR})
+ 
+   set(TEST_MAIN test_main)
+   add_library(${TEST_MAIN} testing_main.cc)
+   target_link_libraries(${TEST_MAIN}
+-                        ${GFLAGS_LIBRARY}
+-                        ${GLOG_LIBRARY}
+-                        gtest)
++      gflags
++      glog::glog
++      GTest::gtest)
+ endif()
+ 
+ ####### OpenSfM libraries #######
+-- 
+2.33.1
+
diff --git a/pkgs/development/python-modules/opensfm/0003-cmake-use-system-pybind11.patch b/pkgs/development/python-modules/opensfm/0003-cmake-use-system-pybind11.patch
new file mode 100644
index 00000000000..2815886e7e1
--- /dev/null
+++ b/pkgs/development/python-modules/opensfm/0003-cmake-use-system-pybind11.patch
@@ -0,0 +1,161 @@
+From 36820fbab1abeeebd99f14e368093e0e3f934ca7 Mon Sep 17 00:00:00 2001
+From: Someone Serge <sergei.kozlukov@aalto.fi>
+Date: Sat, 19 Feb 2022 02:37:54 +0200
+Subject: [PATCH 3/4] cmake: use system pybind11
+
+---
+ opensfm/src/CMakeLists.txt            | 3 ++-
+ opensfm/src/bundle/CMakeLists.txt     | 2 +-
+ opensfm/src/dense/CMakeLists.txt      | 2 +-
+ opensfm/src/features/CMakeLists.txt   | 1 -
+ opensfm/src/foundation/CMakeLists.txt | 1 -
+ opensfm/src/geo/CMakeLists.txt        | 1 -
+ opensfm/src/geometry/CMakeLists.txt   | 1 -
+ opensfm/src/map/CMakeLists.txt        | 3 +--
+ opensfm/src/robust/CMakeLists.txt     | 1 -
+ opensfm/src/sfm/CMakeLists.txt        | 1 -
+ 10 files changed, 5 insertions(+), 11 deletions(-)
+
+diff --git a/opensfm/src/CMakeLists.txt b/opensfm/src/CMakeLists.txt
+index 640d47a6..6e391ffa 100644
+--- a/opensfm/src/CMakeLists.txt
++++ b/opensfm/src/CMakeLists.txt
+@@ -54,6 +54,8 @@ endif()
+ 
+ find_package(gflags REQUIRED)
+ 
++find_package(pybind11 REQUIRED)
++
+ find_package(LAPACK)
+ find_package(SuiteSparse)
+ find_package(Eigen3 REQUIRED)
+@@ -82,7 +84,6 @@ else()
+ endif()
+ 
+ ####### Third party libraries #######
+-add_subdirectory(third_party/pybind11)
+ add_subdirectory(third_party/akaze)
+ add_subdirectory(third_party/vlfeat)
+ 
+diff --git a/opensfm/src/bundle/CMakeLists.txt b/opensfm/src/bundle/CMakeLists.txt
+index 7cd9cf74..307e963a 100644
+--- a/opensfm/src/bundle/CMakeLists.txt
++++ b/opensfm/src/bundle/CMakeLists.txt
+@@ -52,7 +52,7 @@ target_link_libraries(pybundle PRIVATE
+   bundle
+   geometry
+   foundation
+-  pybind11)
++)
+ set_target_properties(pybundle PROPERTIES
+     LIBRARY_OUTPUT_DIRECTORY "${opensfm_SOURCE_DIR}/.."
+ )
+diff --git a/opensfm/src/dense/CMakeLists.txt b/opensfm/src/dense/CMakeLists.txt
+index cbebb5ea..2728749d 100644
+--- a/opensfm/src/dense/CMakeLists.txt
++++ b/opensfm/src/dense/CMakeLists.txt
+@@ -23,7 +23,7 @@ endif()
+ 
+ pybind11_add_module(pydense python/pybind.cc)
+ target_include_directories(pydense PRIVATE ${GLOG_INCLUDE_DIR})
+-target_link_libraries(pydense PRIVATE dense foundation pybind11)
++target_link_libraries(pydense PRIVATE dense foundation)
+ set_target_properties(pydense PROPERTIES
+     LIBRARY_OUTPUT_DIRECTORY "${opensfm_SOURCE_DIR}/.."
+ )
+diff --git a/opensfm/src/features/CMakeLists.txt b/opensfm/src/features/CMakeLists.txt
+index b131d30a..6db5b3f1 100644
+--- a/opensfm/src/features/CMakeLists.txt
++++ b/opensfm/src/features/CMakeLists.txt
+@@ -22,7 +22,6 @@ target_link_libraries(pyfeatures
+   PRIVATE
+     features
+     foundation
+-    pybind11
+     akaze
+ )
+ set_target_properties(pyfeatures PROPERTIES
+diff --git a/opensfm/src/foundation/CMakeLists.txt b/opensfm/src/foundation/CMakeLists.txt
+index 40185227..9e0e45e7 100644
+--- a/opensfm/src/foundation/CMakeLists.txt
++++ b/opensfm/src/foundation/CMakeLists.txt
+@@ -12,7 +12,6 @@ set(FOUNDATION_FILES
+ add_library(foundation ${FOUNDATION_FILES})
+ target_link_libraries(foundation
+   PUBLIC
+-    pybind11
+     ${OpenCV_LIBS}
+     ${OpenMP_libomp_LIBRARY}
+     Eigen3::Eigen
+diff --git a/opensfm/src/geo/CMakeLists.txt b/opensfm/src/geo/CMakeLists.txt
+index a9cbae02..75620d06 100644
+--- a/opensfm/src/geo/CMakeLists.txt
++++ b/opensfm/src/geo/CMakeLists.txt
+@@ -29,7 +29,6 @@ target_link_libraries(pygeo
+   PRIVATE
+     geo
+     foundation
+-    pybind11
+ )
+ set_target_properties(pygeo PROPERTIES
+     LIBRARY_OUTPUT_DIRECTORY "${opensfm_SOURCE_DIR}/.."
+diff --git a/opensfm/src/geometry/CMakeLists.txt b/opensfm/src/geometry/CMakeLists.txt
+index e6dda2c2..51bfd6c5 100644
+--- a/opensfm/src/geometry/CMakeLists.txt
++++ b/opensfm/src/geometry/CMakeLists.txt
+@@ -48,7 +48,6 @@ target_link_libraries(pygeometry
+   PRIVATE
+     geometry
+     foundation
+-    pybind11
+ )
+ set_target_properties(pygeometry PROPERTIES
+     LIBRARY_OUTPUT_DIRECTORY "${opensfm_SOURCE_DIR}/.."
+diff --git a/opensfm/src/map/CMakeLists.txt b/opensfm/src/map/CMakeLists.txt
+index b6f67bcd..f869aa4c 100644
+--- a/opensfm/src/map/CMakeLists.txt
++++ b/opensfm/src/map/CMakeLists.txt
+@@ -20,7 +20,7 @@ set(MAP_FILES
+ add_library(map ${MAP_FILES})
+ target_link_libraries(map
+   PUBLIC
+-    pybind11
++    pybind11::module
+     Eigen3::Eigen
+   PRIVATE
+     geo
+@@ -39,7 +39,6 @@ target_link_libraries(pymap
+     map
+     geometry
+     bundle
+-    pybind11
+ )
+ 
+ if (OPENSFM_BUILD_TESTS)
+diff --git a/opensfm/src/robust/CMakeLists.txt b/opensfm/src/robust/CMakeLists.txt
+index ce70749f..40bdf7a4 100644
+--- a/opensfm/src/robust/CMakeLists.txt
++++ b/opensfm/src/robust/CMakeLists.txt
+@@ -29,7 +29,6 @@ target_link_libraries(pyrobust
+   PRIVATE
+     robust
+     foundation
+-    pybind11
+ )
+ set_target_properties(pyrobust PROPERTIES
+     LIBRARY_OUTPUT_DIRECTORY "${opensfm_SOURCE_DIR}/.."
+diff --git a/opensfm/src/sfm/CMakeLists.txt b/opensfm/src/sfm/CMakeLists.txt
+index 98c28f41..7f56b791 100644
+--- a/opensfm/src/sfm/CMakeLists.txt
++++ b/opensfm/src/sfm/CMakeLists.txt
+@@ -35,7 +35,6 @@ target_include_directories(pysfm PRIVATE ${GLOG_INCLUDE_DIR})
+ target_link_libraries(pysfm
+   PRIVATE
+     foundation
+-    pybind11
+     sfm
+ )
+ set_target_properties(pysfm PROPERTIES
+-- 
+2.33.1
+
diff --git a/pkgs/development/python-modules/opensfm/0004-pybind_utils.h-conflicts-with-nixpkgs-pybind.patch b/pkgs/development/python-modules/opensfm/0004-pybind_utils.h-conflicts-with-nixpkgs-pybind.patch
new file mode 100644
index 00000000000..f3cb2db00ec
--- /dev/null
+++ b/pkgs/development/python-modules/opensfm/0004-pybind_utils.h-conflicts-with-nixpkgs-pybind.patch
@@ -0,0 +1,86 @@
+From c35b110a83286e7413d7309eb218eb43b52f7d48 Mon Sep 17 00:00:00 2001
+From: Someone Serge <sergei.kozlukov@aalto.fi>
+Date: Sat, 19 Feb 2022 14:36:12 +0200
+Subject: [PATCH 4/4] pybind_utils.h: conflicts with nixpkgs' pybind
+
+---
+ opensfm/src/map/pybind_utils.h | 45 +++-------------------------------
+ 1 file changed, 3 insertions(+), 42 deletions(-)
+
+diff --git a/opensfm/src/map/pybind_utils.h b/opensfm/src/map/pybind_utils.h
+index 817d1a16..3f98a2ab 100644
+--- a/opensfm/src/map/pybind_utils.h
++++ b/opensfm/src/map/pybind_utils.h
+@@ -52,38 +52,6 @@ struct sfm_iterator_state {
+ };
+ PYBIND11_NAMESPACE_END_(detail)
+ 
+-/// Makes an python iterator over the keys (`.first`) of a iterator over pairs
+-/// from a first and past-the-end InputIterator.
+-template <return_value_policy Policy = return_value_policy::reference_internal,
+-          typename Iterator, typename Sentinel,
+-          typename KeyType = decltype((*std::declval<Iterator>()).second),
+-          typename... Extra>
+-iterator make_value_iterator(Iterator first, Sentinel last, Extra &&... extra) {
+-  typedef detail::sfm_iterator_state<Iterator, Sentinel, detail::RefIterator,
+-                                     Policy>
+-      state;
+-
+-  if (!detail::get_type_info(typeid(state), false)) {
+-    class_<state>(handle(), "iterator", pybind11::module_local())
+-        .def("__iter__", [](state &s) -> state & { return s; })
+-        .def("__next__",
+-             [](state &s) -> KeyType {
+-               if (!s.first_or_done)
+-                 ++s.it;
+-               else
+-                 s.first_or_done = false;
+-               if (s.it == s.end) {
+-                 s.first_or_done = true;
+-                 throw stop_iteration();
+-               }
+-               return (*s.it).second;
+-             },
+-             std::forward<Extra>(extra)..., Policy);
+-  }
+-
+-  return cast(state{first, last, true});
+-}
+-
+ template <return_value_policy Policy = return_value_policy::reference_internal,
+           typename Iterator, typename Sentinel,
+           typename KeyType = decltype(&((*std::declval<Iterator>()).second)),
+@@ -148,12 +116,13 @@ iterator make_ref_iterator(Iterator first, Sentinel last, Extra &&... extra) {
+ }
+ 
+ /// Makes a python iterator from a first and past-the-end C++ InputIterator.
+-template <return_value_policy Policy = return_value_policy::reference_internal,
++template <typename Access,
++          return_value_policy Policy = return_value_policy::reference_internal,
+           typename Iterator, typename Sentinel,
+           typename ValueType = decltype(std::declval<Iterator>()),
+           typename... Extra>
+ iterator make_ptr_iterator(Iterator first, Sentinel last, Extra &&... extra) {
+-  typedef detail::iterator_state<Iterator, Sentinel, false, Policy> state;
++  typedef detail::iterator_state<Access, Policy, Iterator, Sentinel, ValueType, Extra...> state;
+ 
+   if (!detail::get_type_info(typeid(state), false)) {
+     class_<state>(handle(), "iterator", pybind11::module_local())
+@@ -176,14 +145,6 @@ iterator make_ptr_iterator(Iterator first, Sentinel last, Extra &&... extra) {
+   return cast(state{first, last, true});
+ }
+ 
+-/// Makes an iterator over the keys (`.first`) of a stl map-like container
+-/// supporting `std::begin()`/`std::end()`
+-template <return_value_policy Policy = return_value_policy::reference_internal,
+-          typename Type, typename... Extra>
+-iterator make_value_iterator(Type &value, Extra &&... extra) {
+-  return make_value_iterator<Policy>(std::begin(value), std::end(value),
+-                                     extra...);
+-}
+ template <return_value_policy Policy = return_value_policy::reference_internal,
+           typename Type, typename... Extra>
+ iterator make_unique_ptr_value_iterator(Type &value, Extra &&... extra) {
+-- 
+2.33.1
+
diff --git a/pkgs/development/python-modules/opensfm/default.nix b/pkgs/development/python-modules/opensfm/default.nix
new file mode 100644
index 00000000000..dec998f451c
--- /dev/null
+++ b/pkgs/development/python-modules/opensfm/default.nix
@@ -0,0 +1,127 @@
+{ lib
+, stdenv
+, buildPythonPackage
+, fetchFromGitHub
+, fetchpatch
+, cmake
+, opencv4
+, ceres-solver
+, suitesparse
+, metis
+, eigen
+, pkg-config
+, pybind11
+, numpy
+, pyyaml
+, lapack
+, gtest
+, gflags
+, glog
+, pytestCheckHook
+, networkx
+, pillow
+, exifread
+, gpxpy
+, pyproj
+, python-dateutil
+, joblib
+, repoze_lru
+, xmltodict
+, cloudpickle
+, scipy
+, sphinx
+, matplotlib
+, fpdf
+,
+}:
+
+let
+  ceresSplit = (builtins.length ceres-solver.outputs) > 1;
+  ceres' =
+    if ceresSplit
+    then ceres-solver.dev
+    else ceres-solver;
+in
+buildPythonPackage rec {
+  pname = "OpenSfM";
+  version = "0.5.2";
+
+  src = fetchFromGitHub {
+    owner = "mapillary";
+    repo = pname;
+    rev = "79aa4bdd8bd08dc0cd9e3086d170cedb29ac9760";
+    sha256 = "sha256-dHBrkYwLA1OUxUSoe7DysyeEm9Yy70tIJvAsXivdjrM=";
+  };
+  patches = [
+    (fetchpatch {
+      url = "https://github.com/mapillary/OpenSfM/pull/872/commits/a76671db11038f3f4dfe5b8f17582fb447ad7dd5.patch";
+      sha256 = "sha256-4nizQiZIjucdydOLrETvs1xdV3qiYqAQ7x1HECKvlHs=";
+    })
+    ./0002-cmake-find-system-distributed-gtest.patch
+    ./0003-cmake-use-system-pybind11.patch
+    ./0004-pybind_utils.h-conflicts-with-nixpkgs-pybind.patch
+    ./fix-scripts.patch
+  ];
+  postPatch = ''
+    rm opensfm/src/cmake/FindGlog.cmake
+    rm opensfm/src/cmake/FindGflags.cmake
+
+    # HAHOG is the default descriptor.
+    # We'll test both HAHOG and SIFT because this is
+    # where segfaults might be introduced in future
+    echo 'feature_type: SIFT' >> data/berlin/config.yaml
+    echo 'feature_type: HAHOG' >> data/lund/config.yaml
+  '';
+
+  nativeBuildInputs = [ cmake pkg-config sphinx ];
+  buildInputs = [
+    ceres'
+    suitesparse
+    metis
+    eigen
+    lapack
+    gflags
+    gtest
+    glog
+    pybind11
+  ];
+  propagatedBuildInputs = [
+    numpy
+    scipy
+    pyyaml
+    opencv4
+    networkx
+    pillow
+    matplotlib
+    fpdf
+    exifread
+    gpxpy
+    pyproj
+    python-dateutil
+    joblib
+    repoze_lru
+    xmltodict
+    cloudpickle
+  ];
+  checkInputs = [ pytestCheckHook ];
+
+  dontUseCmakeBuildDir = true;
+  cmakeFlags = [
+    "-Bcmake_build"
+    "-Sopensfm/src"
+  ];
+
+  disabledTests = lib.optionals stdenv.isDarwin [
+    "test_reconstruction_incremental"
+    "test_reconstruction_triangulation"
+  ];
+
+  pythonImportsCheck = [ "opensfm" ];
+
+  meta = {
+    maintainers = [ lib.maintainers.SomeoneSerge ];
+    license = lib.licenses.bsd2;
+    description = "Open source Structure-from-Motion pipeline from Mapillary";
+    homepage = "https://opensfm.org/";
+  };
+}
diff --git a/pkgs/development/python-modules/opensfm/fix-scripts.patch b/pkgs/development/python-modules/opensfm/fix-scripts.patch
new file mode 100644
index 00000000000..634820a3275
--- /dev/null
+++ b/pkgs/development/python-modules/opensfm/fix-scripts.patch
@@ -0,0 +1,41 @@
+diff --git a/bin/opensfm b/bin/opensfm
+index b5ee4b15..f05c0d1c 100755
+--- a/bin/opensfm
++++ b/bin/opensfm
+@@ -1,12 +1,6 @@
+-#!/bin/bash
++#!/usr/bin/env bash
+ set -e
+ 
+ DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
+ 
+-if [ -x "$(command -v python3)" ]; then
+-    PYTHON=python3
+-else
+-    PYTHON=python
+-fi
+-
+-"$PYTHON" "$DIR"/opensfm_main.py "$@"
++exec "$DIR"/opensfm_main.py "$@"
+diff --git a/bin/opensfm_main.py b/bin/opensfm_main.py
+index 31249e12..cc71560c 100755
+--- a/bin/opensfm_main.py
++++ b/bin/opensfm_main.py
+@@ -1,3 +1,5 @@
++#!/usr/bin/env python
++
+ import sys
+ from os.path import abspath, join, dirname
+ 
+diff --git a/setup.py b/setup.py
+index 1120717f..438a16db 100644
+--- a/setup.py
++++ b/setup.py
+@@ -71,6 +71,7 @@ setuptools.setup(
+     scripts=[
+         "bin/opensfm_run_all",
+         "bin/opensfm",
++        "bin/opensfm_main.py",
+     ],
+     package_data={
+         "opensfm": [