commit 95a230e3bb7f543f1fcc2cfe6d9241bf047c3f4c · pyrox.dev/nixpkgs

+239

pkgs/development/python-modules/opensfm/0005-fix-numpy-2-test-failures.patch

···

       1
       +
       diff --git a/opensfm/exif.py b/opensfm/exif.py

     

       2
       +
       --- a/opensfm/exif.py

     

       3
       +
       +++ b/opensfm/exif.py

     

       4
       +
       @@ -509,7 +509,7 @@ class EXIF:

     

       5
       +
                            )

     

       6
       +
                        )

     

       7
       +
        

     

       8
       +
       -            if np.all(ypr) is not None:

     

       9
       +
       +            if np.all(ypr != None):

     

       10
       +
                        ypr = np.radians(ypr)

     

       11
       +
        

     

       12
       +
                        # Convert YPR --> OPK

     

       13
       +
       diff --git a/opensfm/transformations.py b/opensfm/transformations.py

     

       14
       +
       --- a/opensfm/transformations.py

     

       15
       +
       +++ b/opensfm/transformations.py

     

       16
       +
       @@ -232,7 +232,7 @@ def translation_from_matrix(matrix: numpy.ndarray) -> numpy.ndarray:

     

       17
       +
            True

     

       18
       +
        

     

       19
       +
            """

     

       20
       +
       -    return numpy.array(matrix, copy=False)[:3, 3].copy()

     

       21
       +
       +    return numpy.asarray(matrix)[:3, 3].copy()

     

       22
       +
        

     

       23
       +
        

     

       24
       +
        def reflection_matrix(point: numpy.ndarray, normal: numpy.ndarray) -> numpy.ndarray:

     

       25
       +
       @@ -275,7 +275,7 @@ def reflection_from_matrix(

     

       26
       +
            True

     

       27
       +
        

     

       28
       +
            """

     

       29
       +
       -    M = numpy.array(matrix, dtype=numpy.float64, copy=False)

     

       30
       +
       +    M = numpy.asarray(matrix, dtype=numpy.float64)

     

       31
       +
            # normal: unit eigenvector corresponding to eigenvalue -1

     

       32
       +
            w, V = numpy.linalg.eig(M[:3, :3])

     

       33
       +
            i = numpy.where(abs(numpy.real(w) + 1.0) < 1e-8)[0]

     

       34
       +
       @@ -339,7 +339,7 @@ def rotation_matrix(

     

       35
       +
            M[:3, :3] = R

     

       36
       +
            if point is not None:

     

       37
       +
                # rotation not around origin

     

       38
       +
       -        point = numpy.array(point[:3], dtype=numpy.float64, copy=False)

     

       39
       +
       +        point = numpy.asarray(point[:3], dtype=numpy.float64)

     

       40
       +
                M[:3, 3] = point - numpy.dot(R, point)

     

       41
       +
            return M

     

       42
       +
        

     

       43
       +
       @@ -359,7 +359,7 @@ def rotation_from_matrix(

     

       44
       +
            True

     

       45
       +
        

     

       46
       +
            """

     

       47
       +
       -    R = numpy.array(matrix, dtype=numpy.float64, copy=False)

     

       48
       +
       +    R = numpy.asarray(matrix, dtype=numpy.float64)

     

       49
       +
            R33 = R[:3, :3]

     

       50
       +
            # direction: unit eigenvector of R33 corresponding to eigenvalue of 1

     

       51
       +
            w, W = numpy.linalg.eig(R33.T)

     

       52
       +
       @@ -444,7 +444,7 @@ def scale_from_matrix(

     

       53
       +
            True

     

       54
       +
        

     

       55
       +
            """

     

       56
       +
       -    M = numpy.array(matrix, dtype=numpy.float64, copy=False)

     

       57
       +
       +    M = numpy.asarray(matrix, dtype=numpy.float64)

     

       58
       +
            M33 = M[:3, :3]

     

       59
       +
            factor = numpy.trace(M33) - 2.0

     

       60
       +
            try:

     

       61
       +
       @@ -505,11 +505,11 @@ def projection_matrix(

     

       62
       +
        

     

       63
       +
            """

     

       64
       +
            M = numpy.identity(4)

     

       65
       +
       -    point = numpy.array(point[:3], dtype=numpy.float64, copy=False)

     

       66
       +
       +    point = numpy.asarray(point[:3], dtype=numpy.float64)

     

       67
       +
            normal = unit_vector(normal[:3])

     

       68
       +
            if perspective is not None:

     

       69
       +
                # perspective projection

     

       70
       +
       -        perspective = numpy.array(perspective[:3], dtype=numpy.float64, copy=False)

     

       71
       +
       +        perspective = numpy.asarray(perspective[:3], dtype=numpy.float64)

     

       72
       +
                M[0, 0] = M[1, 1] = M[2, 2] = numpy.dot(perspective - point, normal)

     

       73
       +
                M[:3, :3] -= numpy.outer(perspective, normal)

     

       74
       +
                if pseudo:

     

       75
       +
       @@ -522,7 +522,7 @@ def projection_matrix(

     

       76
       +
                M[3, 3] = numpy.dot(perspective, normal)

     

       77
       +
            elif direction is not None:

     

       78
       +
                # parallel projection

     

       79
       +
       -        direction = numpy.array(direction[:3], dtype=numpy.float64, copy=False)

     

       80
       +
       +        direction = numpy.asarray(direction[:3], dtype=numpy.float64)

     

       81
       +
                scale = numpy.dot(direction, normal)

     

       82
       +
                M[:3, :3] -= numpy.outer(direction, normal) / scale

     

       83
       +
                M[:3, 3] = direction * (numpy.dot(point, normal) / scale)

     

       84
       +
       @@ -569,7 +569,7 @@ def projection_from_matrix(

     

       85
       +
            True

     

       86
       +
        

     

       87
       +
            """

     

       88
       +
       -    M = numpy.array(matrix, dtype=numpy.float64, copy=False)

     

       89
       +
       +    M = numpy.asarray(matrix, dtype=numpy.float64)

     

       90
       +
            M33 = M[:3, :3]

     

       91
       +
            w, V = numpy.linalg.eig(M)

     

       92
       +
            i = numpy.where(abs(numpy.real(w) - 1.0) < 1e-8)[0]

     

       93
       +
       @@ -726,7 +726,7 @@ def shear_from_matrix(

     

       94
       +
            True

     

       95
       +
        

     

       96
       +
            """

     

       97
       +
       -    M = numpy.array(matrix, dtype=numpy.float64, copy=False)

     

       98
       +
       +    M = numpy.asarray(matrix, dtype=numpy.float64)

     

       99
       +
            M33 = M[:3, :3]

     

       100
       +
            # normal: cross independent eigenvectors corresponding to the eigenvalue 1

     

       101
       +
            w, V = numpy.linalg.eig(M33)

     

       102
       +
       @@ -790,7 +790,7 @@ def decompose_matrix(

     

       103
       +
            True

     

       104
       +
        

     

       105
       +
            """

     

       106
       +
       -    M = numpy.array(matrix, dtype=numpy.float64, copy=True).T

     

       107
       +
       +    M = numpy.asarray(matrix, dtype=numpy.float64, copy=True).T

     

       108
       +
            if abs(M[3, 3]) < _EPS:

     

       109
       +
                raise ValueError("M[3, 3] is zero")

     

       110
       +
            M /= M[3, 3]

     

       111
       +
       @@ -982,8 +982,8 @@ def affine_matrix_from_points(

     

       112
       +
            More examples in superimposition_matrix()

     

       113
       +
        

     

       114
       +
            """

     

       115
       +
       -    v0 = numpy.array(v0, dtype=numpy.float64, copy=True)

     

       116
       +
       -    v1 = numpy.array(v1, dtype=numpy.float64, copy=True)

     

       117
       +
       +    v0 = numpy.asarray(v0, dtype=numpy.float64, copy=True)

     

       118
       +
       +    v1 = numpy.asarray(v1, dtype=numpy.float64, copy=True)

     

       119
       +
        

     

       120
       +
            ndims = v0.shape[0]

     

       121
       +
            if ndims < 2 or v0.shape[1] < ndims or v0.shape != v1.shape:

     

       122
       +
       @@ -1099,8 +1099,8 @@ def superimposition_matrix(

     

       123
       +
            True

     

       124
       +
        

     

       125
       +
            """

     

       126
       +
       -    v0 = numpy.array(v0, dtype=numpy.float64, copy=False)[:3]

     

       127
       +
       -    v1 = numpy.array(v1, dtype=numpy.float64, copy=False)[:3]

     

       128
       +
       +    v0 = numpy.asarray(v0, dtype=numpy.float64)[:3]

     

       129
       +
       +    v1 = numpy.asarray(v1, dtype=numpy.float64)[:3]

     

       130
       +
            return affine_matrix_from_points(v0, v1, shear=False, scale=scale, usesvd=usesvd)

     

       131
       +
        

     

       132
       +
        

     

       133
       +
       @@ -1198,7 +1198,7 @@ def euler_from_matrix(

     

       134
       +
            j = _NEXT_AXIS[i + parity]

     

       135
       +
            k = _NEXT_AXIS[i - parity + 1]

     

       136
       +
        

     

       137
       +
       -    M = numpy.array(matrix, dtype=numpy.float64, copy=False)[:3, :3]

     

       138
       +
       +    M = numpy.asarray(matrix, dtype=numpy.float64)[:3, :3]

     

       139
       +
            if repetition:

     

       140
       +
                sy = math.sqrt(M[i, j] * M[i, j] + M[i, k] * M[i, k])

     

       141
       +
                if sy > _EPS:

     

       142
       +
       @@ -1329,7 +1329,7 @@ def quaternion_matrix(quaternion: numpy.ndarray) -> numpy.ndarray:

     

       143
       +
            True

     

       144
       +
        

     

       145
       +
            """

     

       146
       +
       -    q = numpy.array(quaternion, dtype=numpy.float64, copy=True)

     

       147
       +
       +    q = numpy.asarray(quaternion, dtype=numpy.float64, copy=True)

     

       148
       +
            n = numpy.dot(q, q)

     

       149
       +
            if n < _EPS:

     

       150
       +
                return numpy.identity(4)

     

       151
       +
       @@ -1379,7 +1379,7 @@ def quaternion_from_matrix(

     

       152
       +
            True

     

       153
       +
        

     

       154
       +
            """

     

       155
       +
       -    M = numpy.array(matrix, dtype=numpy.float64, copy=False)[:4, :4]

     

       156
       +
       +    M = numpy.asarray(matrix, dtype=numpy.float64)[:4, :4]

     

       157
       +
            if isprecise:

     

       158
       +
                q = numpy.empty((4,))

     

       159
       +
                t = numpy.trace(M)

     

       160
       +
       @@ -1460,7 +1460,7 @@ def quaternion_conjugate(quaternion: numpy.ndarray) -> numpy.ndarray:

     

       161
       +
            True

     

       162
       +
        

     

       163
       +
            """

     

       164
       +
       -    q = numpy.array(quaternion, dtype=numpy.float64, copy=True)

     

       165
       +
       +    q = numpy.asarray(quaternion, dtype=numpy.float64, copy=True)

     

       166
       +
            numpy.negative(q[1:], q[1:])

     

       167
       +
            return q

     

       168
       +
        

     

       169
       +
       @@ -1474,7 +1474,7 @@ def quaternion_inverse(quaternion: numpy.ndarray) -> numpy.ndarray:

     

       170
       +
            True

     

       171
       +
        

     

       172
       +
            """

     

       173
       +
       -    q = numpy.array(quaternion, dtype=numpy.float64, copy=True)

     

       174
       +
       +    q = numpy.asarray(quaternion, dtype=numpy.float64, copy=True)

     

       175
       +
            numpy.negative(q[1:], q[1:])

     

       176
       +
            return q / numpy.dot(q, q)

     

       177
       +
        

     

       178
       +
       @@ -1496,7 +1496,7 @@ def quaternion_imag(quaternion: numpy.ndarray) -> numpy.ndarray:

     

       179
       +
            array([ 0.,  1.,  2.])

     

       180
       +
        

     

       181
       +
            """

     

       182
       +
       -    return numpy.array(quaternion[1:4], dtype=numpy.float64, copy=True)

     

       183
       +
       +    return numpy.asarray(quaternion[1:4], dtype=numpy.float64, copy=True)

     

       184
       +
        

     

       185
       +
        

     

       186
       +
        def quaternion_slerp(

     

       187
       +
       @@ -1654,7 +1654,7 @@ def vector_norm(

     

       188
       +
            1.0

     

       189
       +
        

     

       190
       +
            """

     

       191
       +
       -    data = numpy.array(data, dtype=numpy.float64, copy=True)

     

       192
       +
       +    data = numpy.asarray(data, dtype=numpy.float64, copy=True)

     

       193
       +
            if out is None:

     

       194
       +
                if data.ndim == 1:

     

       195
       +
                    return math.sqrt(numpy.dot(data, data))

     

       196
       +
       @@ -1697,13 +1697,13 @@ def unit_vector(

     

       197
       +
        

     

       198
       +
            """

     

       199
       +
            if out is None:

     

       200
       +
       -        data = numpy.array(data, dtype=numpy.float64, copy=True)

     

       201
       +
       +        data = numpy.asarray(data, dtype=numpy.float64, copy=True)

     

       202
       +
                if data.ndim == 1:

     

       203
       +
                    data /= math.sqrt(numpy.dot(data, data))

     

       204
       +
                    return data

     

       205
       +
            else:

     

       206
       +
                if out is not data:

     

       207
       +
       -            out[:] = numpy.array(data, copy=False)

     

       208
       +
       +            out[:] = numpy.asarray(data)

     

       209
       +
                data = out

     

       210
       +
            length = numpy.atleast_1d(numpy.sum(data * data, axis))

     

       211
       +
            numpy.sqrt(length, length)

     

       212
       +
       @@ -1777,8 +1777,8 @@ def angle_between_vectors(

     

       213
       +
            True

     

       214
       +
        

     

       215
       +
            """

     

       216
       +
       -    v0 = numpy.array(v0, dtype=numpy.float64, copy=False)

     

       217
       +
       -    v1 = numpy.array(v1, dtype=numpy.float64, copy=False)

     

       218
       +
       +    v0 = numpy.asarray(v0, dtype=numpy.float64)

     

       219
       +
       +    v1 = numpy.asarray(v1, dtype=numpy.float64)

     

       220
       +
            dot = numpy.sum(v0 * v1, axis=axis)

     

       221
       +
            dot /= vector_norm(v0, axis=axis) * vector_norm(v1, axis=axis)

     

       222
       +
            dot = numpy.clip(dot, -1.0, 1.0)

     

       223
       +
       @@ -1826,9 +1826,9 @@ def is_same_transform(matrix0: numpy.ndarray, matrix1: numpy.ndarray) -> numpy.n

     

       224
       +
            False

     

       225
       +
        

     

       226
       +
            """

     

       227
       +
       -    matrix0 = numpy.array(matrix0, dtype=numpy.float64, copy=True)

     

       228
       +
       +    matrix0 = numpy.asarray(matrix0, dtype=numpy.float64, copy=True)

     

       229
       +
            matrix0 /= matrix0[3, 3]

     

       230
       +
       -    matrix1 = numpy.array(matrix1, dtype=numpy.float64, copy=True)

     

       231
       +
       +    matrix1 = numpy.asarray(matrix1, dtype=numpy.float64, copy=True)

     

       232
       +
            matrix1 /= matrix1[3, 3]

     

       233
       +
            return numpy.allclose(matrix0, matrix1)

     

       234
       +
        

     

       235
       +
       @@ -1874,3 +1874,4 @@ if __name__ == "__main__":

     

       236
       +
        

     

       237
       +
            numpy.set_printoptions(suppress=True, precision=5)

     

       238
       +
            doctest.testmod()

     

       239
       +
       +

+24 -8

pkgs/development/python-modules/opensfm/default.nix

···

       9
        
         suitesparse,

     

       10
        
         metis,

     

       11
        
         eigen,

     

       0
        
       
     

       12
        
         pkg-config,

     

       13
        
         pybind11,

     

       14
        
         numpy,

     
···

       27
        
         joblib,

     

       28
        
         repoze-lru,

     

       29
        
         xmltodict,

     

       0
        
       
     

       30
        
         cloudpickle,

     

       31
        
         scipy,

     

       32
        
         sphinx,

     
···

       34
        
         fpdf,

     

       35
        
       }:

     

       36
        
       

     

       37
       -
       let

     

       38
       -
         ceresSplit = (builtins.length ceres-solver.outputs) > 1;

     

       39
       -
         ceres' = if ceresSplit then ceres-solver.dev else ceres-solver;

     

       40
       -
       in

     

       41
        
       buildPythonPackage rec {

     

       42
        
         pname = "opensfm";

     

       43
        
         version = "unstable-2023-12-09";

     

       0
        
       
     

       44
        
       

     

       45
        
         src = fetchFromGitHub {

     

       46
        
           owner = "mapillary";

     
···

       48
        
           rev = "7f170d0dc352340295ff480378e3ac37d0179f8e";

     

       49
        
           sha256 = "sha256-l/HTVenC+L+GpMNnDgnSGZ7+Qd2j8b8cuTs3SmORqrg=";

     

       50
        
         };

     

       0
        
       
     

       51
        
         patches = [

     

       52
        
           ./0002-cmake-find-system-distributed-gtest.patch

     

       53
        
           ./0003-cmake-use-system-pybind11.patch

     

       54
        
           ./0004-pybind_utils.h-conflicts-with-nixpkgs-pybind.patch

     

       0
        
       
     

       55
        
           ./fix-scripts.patch

     

       56
        
         ];

     

       0
        
       
     

       57
        
         postPatch = ''

     

       58
        
           rm opensfm/src/cmake/FindGlog.cmake

     

       59
        
           rm opensfm/src/cmake/FindGflags.cmake

     
···

       64
        
           echo 'feature_type: SIFT' >> data/berlin/config.yaml

     

       65
        
           echo 'feature_type: HAHOG' >> data/lund/config.yaml

     

       66
        
       

     

       0
        
       
     

       0
        
       
     

       0
        
       
     

       67
        
           sed -i -e 's/^.*BuildDoc.*$//' setup.py

     

       68
        
         '';

     

       0
        
       
     

       0
        
       
     

       69
        
       

     

       70
        
         nativeBuildInputs = [

     

       71
        
           cmake

     

       72
        
           pkg-config

     

       73
        
           sphinx

     

       74
        
         ];

     

       0
        
       
     

       75
        
         buildInputs = [

     

       76
       -
           ceres'

     

       77
        
           suitesparse

     

       78
        
           metis

     

       79
        
           eigen

     
···

       83
        
           glog

     

       84
        
           pybind11

     

       85
        
         ];

     

       86
       -
         propagatedBuildInputs = [

     

       0
        
       
     

       87
        
           numpy

     

       88
        
           scipy

     

       89
        
           pyyaml

     
···

       101
        
           xmltodict

     

       102
        
           cloudpickle

     

       103
        
         ];

     

       104
       -
         nativeCheckInputs = [ pytestCheckHook ];

     

       0
        
       
     

       0
        
       
     

       0
        
       
     

       0
        
       
     

       105
        
       

     

       106
        
         dontUseCmakeBuildDir = true;

     

       107
        
         cmakeFlags = [

     
···

       122
        
       

     

       123
        
         meta = {

     

       124
        
           broken = stdenv.hostPlatform.isDarwin;

     

       125
       -
           maintainers = [ lib.maintainers.SomeoneSerge ];

     

       0
        
       
     

       0
        
       
     

       0
        
       
     

       126
        
           license = lib.licenses.bsd2;

     

       127
        
           changelog = "https://github.com/mapillary/OpenSfM/blob/${src.rev}/CHANGELOG.md";

     

       128
        
           description = "Open source Structure-from-Motion pipeline from Mapillary";

···

       9
        
         suitesparse,

     

       10
        
         metis,

     

       11
        
         eigen,

     

       12
       +
         setuptools,

     

       13
        
         pkg-config,

     

       14
        
         pybind11,

     

       15
        
         numpy,

     
···

       28
        
         joblib,

     

       29
        
         repoze-lru,

     

       30
        
         xmltodict,

     

       31
       +
         distutils,

     

       32
        
         cloudpickle,

     

       33
        
         scipy,

     

       34
        
         sphinx,

     
···

       36
        
         fpdf,

     

       37
        
       }:

     

       38
        
       

     

       0
        
       
     

       0
        
       
     

       0
        
       
     

       0
        
       
     

       39
        
       buildPythonPackage rec {

     

       40
        
         pname = "opensfm";

     

       41
        
         version = "unstable-2023-12-09";

     

       42
       +
         pyproject = true;

     

       43
        
       

     

       44
        
         src = fetchFromGitHub {

     

       45
        
           owner = "mapillary";

     
···

       47
        
           rev = "7f170d0dc352340295ff480378e3ac37d0179f8e";

     

       48
        
           sha256 = "sha256-l/HTVenC+L+GpMNnDgnSGZ7+Qd2j8b8cuTs3SmORqrg=";

     

       49
        
         };

     

       50
       +
       

     

       51
        
         patches = [

     

       52
        
           ./0002-cmake-find-system-distributed-gtest.patch

     

       53
        
           ./0003-cmake-use-system-pybind11.patch

     

       54
        
           ./0004-pybind_utils.h-conflicts-with-nixpkgs-pybind.patch

     

       55
       +
           ./0005-fix-numpy-2-test-failures.patch # not upstreamed due to cla, but you're free upstream it -@pbsds

     

       56
        
           ./fix-scripts.patch

     

       57
        
         ];

     

       58
       +
       

     

       59
        
         postPatch = ''

     

       60
        
           rm opensfm/src/cmake/FindGlog.cmake

     

       61
        
           rm opensfm/src/cmake/FindGflags.cmake

     
···

       66
        
           echo 'feature_type: SIFT' >> data/berlin/config.yaml

     

       67
        
           echo 'feature_type: HAHOG' >> data/lund/config.yaml

     

       68
        
       

     

       69
       +
           # make opensfm correctly import glog headers

     

       70
       +
           export CXXFLAGS=-DGLOG_USE_GLOG_EXPORT

     

       71
       +
       

     

       72
        
           sed -i -e 's/^.*BuildDoc.*$//' setup.py

     

       73
        
         '';

     

       74
       +
       

     

       75
       +
         build-system = [ setuptools ];

     

       76
        
       

     

       77
        
         nativeBuildInputs = [

     

       78
        
           cmake

     

       79
        
           pkg-config

     

       80
        
           sphinx

     

       81
        
         ];

     

       82
       +
       

     

       83
        
         buildInputs = [

     

       84
       +
           ceres-solver

     

       85
        
           suitesparse

     

       86
        
           metis

     

       87
        
           eigen

     
···

       91
        
           glog

     

       92
        
           pybind11

     

       93
        
         ];

     

       94
       +
       

     

       95
       +
         dependencies = [

     

       96
        
           numpy

     

       97
        
           scipy

     

       98
        
           pyyaml

     
···

       110
        
           xmltodict

     

       111
        
           cloudpickle

     

       112
        
         ];

     

       113
       +
       

     

       114
       +
         nativeCheckInputs = [

     

       115
       +
           pytestCheckHook

     

       116
       +
           distutils

     

       117
       +
         ];

     

       118
        
       

     

       119
        
         dontUseCmakeBuildDir = true;

     

       120
        
         cmakeFlags = [

     
···

       135
        
       

     

       136
        
         meta = {

     

       137
        
           broken = stdenv.hostPlatform.isDarwin;

     

       138
       +
           maintainers = [

     

       139
       +
             lib.maintainers.pbsds

     

       140
       +
             lib.maintainers.SomeoneSerge

     

       141
       +
           ];

     

       142
        
           license = lib.licenses.bsd2;

     

       143
        
           changelog = "https://github.com/mapillary/OpenSfM/blob/${src.rev}/CHANGELOG.md";

     

       144
        
           description = "Open source Structure-from-Motion pipeline from Mapillary";