pye57 0.4.4__tar.gz → 0.4.6__tar.gz

{pye57-0.4.4/src/pye57.egg-info → pye57-0.4.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pye57
-Version: 0.4.4
+Version: 0.4.6
 Summary: Python .e57 files reader/writer
 Home-page: https://www.github.com/davidcaron/pye57
 Author: David Caron
@@ -94,21 +94,21 @@ translation_x = scan_0["pose"]["translation"]["x"]
 
 ## Installation
 
-If you're on linux or Windows, a wheel should be available.
+On linux Windows or macos:
 
 `python -m pip install pye57`
 
-## Building from source
+## Building from source (for developers)
 
-### Cloning the repository and required submodules
+### Cloning the repository with required submodule
 
-Clone a new repository along with the required submodules
+Clone a new repository along with the libe57Format submodule
 
 `git clone https://github.com/davidcaron/pye57.git --recursive`
 
 If the repository has already been previously cloned, but without the --recursive flag
 
-```
+```Bash
 cd pye57 # go to the cloned repository
 git submodule init # this will initialise the submodules in the repository
 git submodule update # this will update the submodules in the repository
@@ -128,7 +128,7 @@ To get xerces-c, you can either build from source or if you're using conda:
 
 ### Run `pip install` from the repo source
 
-```
+```Bash
 cd pye57
 python -m pip install .
 ```
@@ -137,6 +137,6 @@ python -m pip install .
 
 Use pip again
 
-```
+```Bash
 python -m pip uninstall pye57
 ```

{pye57-0.4.4 → pye57-0.4.6}/README.md

@@ -68,21 +68,21 @@ translation_x = scan_0["pose"]["translation"]["x"]
 
 ## Installation
 
-If you're on linux or Windows, a wheel should be available.
+On linux Windows or macos:
 
 `python -m pip install pye57`
 
-## Building from source
+## Building from source (for developers)
 
-### Cloning the repository and required submodules
+### Cloning the repository with required submodule
 
-Clone a new repository along with the required submodules
+Clone a new repository along with the libe57Format submodule
 
 `git clone https://github.com/davidcaron/pye57.git --recursive`
 
 If the repository has already been previously cloned, but without the --recursive flag
 
-```
+```Bash
 cd pye57 # go to the cloned repository
 git submodule init # this will initialise the submodules in the repository
 git submodule update # this will update the submodules in the repository
@@ -102,7 +102,7 @@ To get xerces-c, you can either build from source or if you're using conda:
 
 ### Run `pip install` from the repo source
 
-```
+```Bash
 cd pye57
 python -m pip install .
 ```
@@ -111,6 +111,6 @@ python -m pip install .
 
 Use pip again
 
-```
+```Bash
 python -m pip uninstall pye57
 ```

{pye57-0.4.4 → pye57-0.4.6}/pyproject.toml

@@ -14,5 +14,5 @@ build-backend = "setuptools.build_meta"
 # before-all = "bash scripts/install_xerces_c.sh"
 # before-all = "powershell scripts/install_xerces_c.ps1"
 test-requires = "pytest"
-build = "cp*-manylinux_x86_64 cp*-win_amd64*"
+build = "cp*-manylinux_x86_64 cp*-win_amd64* cp*-macosx*"
 test-command = "python -m pytest {project}/tests"

{pye57-0.4.4 → pye57-0.4.6}/setup.py

@@ -43,7 +43,15 @@ if platform.system() == "Windows":
         # include xerces-c dll in the package
         shutil.copy2(xerces_dir / "bin" / "xerces-c_3_2.dll", HERE / "src" / "pye57")
         package_data.append("xerces-c_3_2.dll")
-
+elif platform.system() == "Darwin":
+    xerces_dir = Path("/usr/local/")
+    if xerces_dir.exists():
+        # include xerces-c dylib in the package
+        shutil.copy2(xerces_dir / "lib" / "libxerces-c-3.2.dylib", HERE / "src" / "pye57")
+        library_dirs.append(str(xerces_dir / "lib"))
+        include_dirs.append(str(xerces_dir / "include"))
+        package_data.append("libxerces-c.a")
+    libraries.append("xerces-c")
 else:
     libraries.append("xerces-c")
 
@@ -56,6 +64,9 @@ ext_modules = [
         libraries=libraries,
         library_dirs=library_dirs,
         language="c++",
+        extra_link_args=[
+            f"-Wl,-rpath,@loader_path",
+        ],
     ),
 ]
 

pye57-0.4.6/src/pye57/__version__.py

@@ -0,0 +1 @@
+__version__ = "0.4.6"

{pye57-0.4.4 → pye57-0.4.6}/src/pye57/libe57_wrapper.cpp

@@ -197,6 +197,9 @@ PYBIND11_MODULE(libe57, m) {
     cls_StructureNode.def("set", [](StructureNode &node, const std::string &pathName, StringNode &n){
         node.set(pathName, n);
     }, "pathName"_a, "n"_a);
+    cls_StructureNode.def("set", [](StructureNode &node, const std::string &pathName, BlobNode &n){
+        node.set(pathName, n);
+    }, "pathName"_a, "n"_a);
     cls_StructureNode.def(py::init<const e57::Node &>(), "n"_a);
     cls_StructureNode.def("isRoot", &StructureNode::isRoot);
     cls_StructureNode.def("parent", &StructureNode::parent);
@@ -268,6 +271,7 @@ PYBIND11_MODULE(libe57, m) {
                                             bool doScaling,
                                             size_t stride=0) {
         py::buffer_info info = np_array.request();
+        const std::string dtype = info.format;
 
         if (info.ndim != 1)
             throw std::runtime_error("Incompatible buffer dimension!");
@@ -276,24 +280,26 @@ PYBIND11_MODULE(libe57, m) {
             new (&s) SourceDestBuffer(imf, pathName, static_cast<int8_t *>(info.ptr), capacity, doConversion, doScaling, (stride == 0) ? sizeof(int8_t) : stride);
         else if (info.format == "B")
             new (&s) SourceDestBuffer(imf, pathName, static_cast<uint8_t *>(info.ptr), capacity, doConversion, doScaling, (stride == 0) ? sizeof(uint8_t) : stride);
-        else if (info.format == "h")
+        // Handle fixed or native byte order from https://docs.python.org/3/library/struct.html
+        // Note - these may be platform dependent. Could they cause strange bugs on some platforms ?
+        else if (dtype == "h" || dtype == "=h")
             new (&s) SourceDestBuffer(imf, pathName, static_cast<int16_t *>(info.ptr), capacity, doConversion, doScaling, (stride == 0) ? sizeof(int16_t) : stride);
-        else if (info.format == "H")
+        else if (dtype == "H" || dtype == "=H")
             new (&s) SourceDestBuffer(imf, pathName, static_cast<uint16_t *>(info.ptr), capacity, doConversion, doScaling, (stride == 0) ? sizeof(uint16_t) : stride);
-        else if (info.format == "l")
+        else if (dtype == "l" || dtype == "=l")
             new (&s) SourceDestBuffer(imf, pathName, static_cast<int32_t *>(info.ptr), capacity, doConversion, doScaling, (stride == 0) ? sizeof(int32_t) : stride);
-        else if (info.format == "L")
+        else if (dtype == "L" || dtype == "=L")
             new (&s) SourceDestBuffer(imf, pathName, static_cast<uint32_t *>(info.ptr), capacity, doConversion, doScaling, (stride == 0) ? sizeof(uint32_t) : stride);
-        else if (info.format == "q")
+        else if (dtype == "q" || dtype == "=q")
             new (&s) SourceDestBuffer(imf, pathName, static_cast<int64_t *>(info.ptr), capacity, doConversion, doScaling, (stride == 0) ? sizeof(int64_t) : stride);
-        else if (info.format == "?")
+        else if (dtype == "?")
             new (&s) SourceDestBuffer(imf, pathName, static_cast<bool *>(info.ptr), capacity, doConversion, doScaling, (stride == 0) ? sizeof(bool) : stride);
-        else if (info.format == "f")
+        else if (dtype == "f" || dtype == "=f")
             new (&s) SourceDestBuffer(imf, pathName, static_cast<float *>(info.ptr), capacity, doConversion, doScaling, (stride == 0) ? sizeof(float) : stride);
-        else if (info.format == "d")
+        else if (dtype == "d" || dtype == "=d")
             new (&s) SourceDestBuffer(imf, pathName, static_cast<double *>(info.ptr), capacity, doConversion, doScaling, (stride == 0) ? sizeof(double) : stride);
         else
-            throw py::value_error("Incompatible type (integers: bBhHlLq, bool: ?, floats: fd)");
+            throw py::value_error("Incompatible type (integers: bBhHlLq, bool: ?, floats: fd), got: " + dtype);
     },
     "destImageFile"_a, "pathName"_a, "b"_a, "capacity"_a, "doConversion"_a=false, "doScaling"_a=false, "stride"_a=0);
 //    cls_SourceDestBuffer.def(py::init<e57::ImageFile, const std::string, int8_t *, const size_t, bool, bool, size_t>(), "destImageFile"_a, "pathName"_a, "b"_a, "capacity"_a, "doConversion"_a=false, "doScaling"_a=false, "stride"_a=sizeof(int8_t));

pye57-0.4.6/src/pye57/utils.py

@@ -0,0 +1,117 @@
+from pye57 import libe57
+from pye57.libe57 import NodeType
+
+import numpy as np
+
+def get_fields(node):
+    return [node.get(id_).elementName() for id_ in range(node.childCount())]
+
+
+def get_node(node, name):
+    cast = {
+        NodeType.E57_BLOB: libe57.BlobNode,
+        NodeType.E57_COMPRESSED_VECTOR: libe57.CompressedVectorNode,
+        NodeType.E57_FLOAT: libe57.FloatNode,
+        NodeType.E57_INTEGER: libe57.IntegerNode,
+        NodeType.E57_SCALED_INTEGER: libe57.ScaledIntegerNode,
+        NodeType.E57_STRING: libe57.StringNode,
+        NodeType.E57_STRUCTURE: libe57.StructureNode,
+        NodeType.E57_VECTOR: libe57.VectorNode
+    }
+    n = node.get(name)
+    return cast[n.type()](n)
+
+def convert_spherical_to_cartesian(rae):
+    """
+    Converts spherical(rae) to cartesian(xyz), where rae = range, azimuth(theta), 
+    elevation(phi). Where range is in meters and angles are in radians.
+    
+    Reference for formula: http://www.libe57.org/bestCoordinates.html (Note: the 
+    formula is different from the one online, so please use formula at the above reference)
+    """
+    range_ = rae[:, :1]
+    theta = rae[:, 1:2]
+    phi =  rae[:, 2:3]
+    range_cos_phi = range_ * np.cos(phi)
+    return np.concatenate((
+        range_cos_phi * np.cos(theta),
+        range_cos_phi * np.sin(theta),
+        range_ * np.sin(phi)
+    ), axis=1)
+
+
+def copy_node(node, dest_image):
+    compressed_node_pairs = []
+    blob_node_pairs = []
+
+    out_node = None
+    # 'Element' Types
+    if (isinstance(node, libe57.FloatNode)):
+        out_node = libe57.FloatNode(
+            dest_image,
+            value=node.value(),
+            precision=node.precision(),
+            minimum=node.minimum(),
+            maximum=node.maximum())
+
+    elif (isinstance(node, libe57.IntegerNode)):
+        out_node = libe57.IntegerNode(
+            dest_image,
+            value=node.value(),
+            minimum=node.minimum(),
+            maximum=node.maximum())
+
+    elif (isinstance(node, libe57.ScaledIntegerNode)):
+        out_node = libe57.ScaledIntegerNode(
+            dest_image,
+            node.rawValue(),
+            minimum=node.minimum(),
+            maximum=node.maximum(),
+            scale=node.scale(),
+            offset=node.offset())
+
+    elif (isinstance(node, libe57.StringNode)):
+        out_node = libe57.StringNode(
+            dest_image,
+            node.value())
+
+    elif (isinstance(node, libe57.BlobNode)):
+        out_node = libe57.BlobNode(dest_image, node.byteCount())
+        blob_node_pairs.append({ 'in': node, 'out': out_node })
+
+    # 'Container' Types
+    elif (isinstance(node, libe57.CompressedVectorNode)):
+        in_prototype = libe57.StructureNode(node.prototype())
+        out_prototype, _, _  = copy_node(in_prototype, dest_image)
+        out_codecs, _, _ = copy_node(node.codecs(), dest_image)
+
+        out_node = libe57.CompressedVectorNode(dest_image, out_prototype, out_codecs)
+
+        compressed_node_pairs.append({
+            'in': node,
+            'out': out_node
+        })
+
+    elif isinstance(node, libe57.StructureNode):
+        out_node = libe57.StructureNode(dest_image)
+        for i in range(node.childCount()):
+            in_child = get_node(node, i)
+            in_child_name = in_child.elementName()
+            out_child, out_child_compressed_node_pairs, out_child_blob_node_pairs = copy_node(in_child, dest_image)
+
+            out_node.set(in_child_name, out_child)
+            compressed_node_pairs.extend(out_child_compressed_node_pairs)
+            blob_node_pairs.extend(out_child_blob_node_pairs)
+
+    elif isinstance(node, libe57.VectorNode):
+        out_node = libe57.VectorNode(dest_image, allowHeteroChildren=node.allowHeteroChildren())
+        for i in range(node.childCount()):
+            in_child = get_node(node, i)
+            in_child_name = f'{i}'
+            out_child, out_child_compressed_node_pairs, out_child_blob_node_pairs = copy_node(in_child, dest_image)
+
+            out_node.append(out_child)
+            compressed_node_pairs.extend(out_child_compressed_node_pairs)
+            blob_node_pairs.extend(out_child_blob_node_pairs)
+
+    return out_node, compressed_node_pairs, blob_node_pairs

{pye57-0.4.4 → pye57-0.4.6/src/pye57.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pye57
-Version: 0.4.4
+Version: 0.4.6
 Summary: Python .e57 files reader/writer
 Home-page: https://www.github.com/davidcaron/pye57
 Author: David Caron
@@ -94,21 +94,21 @@ translation_x = scan_0["pose"]["translation"]["x"]
 
 ## Installation
 
-If you're on linux or Windows, a wheel should be available.
+On linux Windows or macos:
 
 `python -m pip install pye57`
 
-## Building from source
+## Building from source (for developers)
 
-### Cloning the repository and required submodules
+### Cloning the repository with required submodule
 
-Clone a new repository along with the required submodules
+Clone a new repository along with the libe57Format submodule
 
 `git clone https://github.com/davidcaron/pye57.git --recursive`
 
 If the repository has already been previously cloned, but without the --recursive flag
 
-```
+```Bash
 cd pye57 # go to the cloned repository
 git submodule init # this will initialise the submodules in the repository
 git submodule update # this will update the submodules in the repository
@@ -128,7 +128,7 @@ To get xerces-c, you can either build from source or if you're using conda:
 
 ### Run `pip install` from the repo source
 
-```
+```Bash
 cd pye57
 python -m pip install .
 ```
@@ -137,6 +137,6 @@ python -m pip install .
 
 Use pip again
 
-```
+```Bash
 python -m pip uninstall pye57
 ```

{pye57-0.4.4 → pye57-0.4.6}/tests/test_main.py

@@ -6,6 +6,7 @@ import numpy as np
 
 import pye57
 from pye57 import libe57
+from pye57.utils import get_node, copy_node
 
 try:
     from exceptions import WindowsError
@@ -37,10 +38,18 @@ def delete_retry(path):
 def e57_path():
     return sample_data("test.e57")
 
+
 @pytest.fixture
 def e57_spherical_path():
     return sample_data("testSpherical.e57")
 
+
+@pytest.fixture
+def e57_with_data_and_images_path():
+    # From http://www.libe57.org/data.html
+    return sample_data("pumpAVisualReferenceImage.e57")
+
+
 @pytest.fixture
 def temp_e57_write(request):
     path = sample_data("test_write.e57")
@@ -302,3 +311,111 @@ def test_read_color_absent(e57_path):
 def test_scan_position(e57_path):
     e57 = pye57.E57(e57_path)
     assert np.allclose(e57.scan_position(3), np.array([[3.01323456e+05, 5.04260184e+06, 1.56040279e+01]]))
+
+
+BUFFER_TYPES = {
+    libe57.FloatNode: 'd',
+    libe57.IntegerNode: 'l',
+    libe57.ScaledIntegerNode: 'd'
+}
+
+
+def make_buffer(node: libe57.Node, capacity: int):
+    node_type = type(node)
+    if node_type not in BUFFER_TYPES:
+        raise ValueError("Unsupported field type!")
+
+    buffer_type = BUFFER_TYPES[node_type]
+
+    np_array = np.empty(capacity, buffer_type)
+    buffer = libe57.SourceDestBuffer(
+        node.destImageFile(), node.elementName(), np_array, capacity, True, True)
+    return np_array, buffer
+
+
+def make_buffers(node: libe57.StructureNode, capacity: int):
+    data = {}
+    buffers = libe57.VectorSourceDestBuffer()
+    for i in range(node.childCount()):
+        field = get_node(node, i)
+        d, b = make_buffer(field, capacity)
+        data[field.elementName()] = d
+        buffers.append(b)
+    return data, buffers
+
+
+def copy_compressed_vector_data(in_node: libe57.Node, out_node: libe57.Node):
+    chunk_size = 100000
+
+    in_prototype = libe57.StructureNode(in_node.prototype())
+    out_prototype = libe57.StructureNode(out_node.prototype())
+
+    in_data, in_buffers = make_buffers(in_prototype, chunk_size)
+    out_data, out_buffers = make_buffers(out_prototype, chunk_size)
+
+    in_reader = in_node.reader(in_buffers)
+    out_writer = out_node.writer(out_buffers)
+
+    n_points = in_node.childCount()
+    current_index = 0
+    while current_index != n_points:
+        current_chunk = min(n_points - current_index, chunk_size)
+
+        in_reader.read()
+        for field in in_data:
+            out_data[field][:current_chunk] = in_data[field][:current_chunk]
+
+        out_writer.write(current_chunk)
+
+        current_index += current_chunk
+
+    in_reader.close()
+    out_writer.close()
+
+
+def copy_blob_data(in_node, out_node):
+    chunk_size = 100000
+
+    byte_count = in_node.byteCount()
+    blob_buffer = np.empty(chunk_size, np.ubyte)
+    current_index = 0
+    while current_index != byte_count:
+        current_chunk = min(byte_count - current_index, chunk_size)
+
+        in_node.read(blob_buffer, current_index, current_chunk)
+        out_node.write(blob_buffer, current_index, current_chunk)
+
+        current_index += current_chunk
+
+
+def test_clone_e57(e57_with_data_and_images_path, temp_e57_write):
+
+    in_image = libe57.ImageFile(e57_with_data_and_images_path, "r")
+    out_image = libe57.ImageFile(temp_e57_write, "w")
+
+    for i in range(in_image.extensionsCount()):
+        out_image.extensionsAdd(
+            in_image.extensionsPrefix(i),
+            in_image.extensionsUri(i)
+        )
+    
+    in_root = in_image.root()
+    out_root = out_image.root()
+
+    compressed_node_pairs = []
+    for i in range(in_root.childCount()):
+        in_child = get_node(in_root, i)
+        in_child_name = in_child.elementName()
+        out_child, out_child_compressed_node_pairs, out_child_blob_node_pairs = copy_node(in_child, out_image)
+
+        out_root.set(in_child_name, out_child)
+        compressed_node_pairs.extend(out_child_compressed_node_pairs)
+    
+    for compressed_node_pair in compressed_node_pairs:
+        copy_compressed_vector_data(compressed_node_pair['in'], compressed_node_pair['out'])
+
+    for blob_node_pair in out_child_blob_node_pairs:
+        copy_blob_data(blob_node_pair['in'], blob_node_pair['out'])
+
+    in_image.close()
+    out_image.close()

pye57-0.4.4/src/pye57/__version__.py

@@ -1 +0,0 @@
-__version__ = "0.4.4"

pye57-0.4.4/src/pye57/utils.py

@@ -1,42 +0,0 @@
-from typing import Type
-
-from pye57 import libe57
-from pye57.libe57 import NodeType
-
-import numpy as np
-
-def get_fields(node):
-    return [node.get(id_).elementName() for id_ in range(node.childCount())]
-
-
-def get_node(node, name):
-    cast = {
-        NodeType.E57_BLOB: libe57.BlobNode,
-        NodeType.E57_COMPRESSED_VECTOR: libe57.CompressedVectorNode,
-        NodeType.E57_FLOAT: libe57.FloatNode,
-        NodeType.E57_INTEGER: libe57.IntegerNode,
-        NodeType.E57_SCALED_INTEGER: libe57.ScaledIntegerNode,
-        NodeType.E57_STRING: libe57.StringNode,
-        NodeType.E57_STRUCTURE: libe57.StructureNode,
-        NodeType.E57_VECTOR: libe57.VectorNode
-    }
-    n = node.get(name)
-    return cast[n.type()](n)
-
-def convert_spherical_to_cartesian(rae):
-    """
-    Converts spherical(rae) to cartesian(xyz), where rae = range, azimuth(theta), 
-    elevation(phi). Where range is in meters and angles are in radians.
-    
-    Reference for formula: http://www.libe57.org/bestCoordinates.html (Note: the 
-    formula is different from the one online, so please use formula at the above reference)
-    """
-    range_ = rae[:, :1]
-    theta = rae[:, 1:2]
-    phi =  rae[:, 2:3]
-    range_cos_phi = range_ * np.cos(phi)
-    return np.concatenate((
-        range_cos_phi * np.cos(theta),
-        range_cos_phi * np.sin(theta),
-        range_ * np.sin(phi)
-    ), axis=1)